title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2020-09 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: A strength-oriented exercise session required more recovery time than a power-oriented exercise session with equal work link: https://peerj.com/articles/10044 last-modified: 2020-09-30 description: The present randomized cross-over controlled study aimed to compare the rate of recovery from a strength-oriented exercise session vs. a power-oriented session with equal work. Sixteen strength-trained individuals conducted one strength-oriented session (five repetitions maximum (RM)) and one power-oriented session (50% of 5RM) in randomized order. Squat jump (SJ), countermovement jump (CMJ), 20-m sprint, and squat and bench press peak power and estimated 1RMs were combined with measures of rate of perceived exertion (RPE) and perceived recovery status (PRS), before, immediately after and 24 and 48 h after exercise. Both sessions induced trivial to moderate performance decrements in all variables. Small reductions in CMJ height were observed immediately after both the strength-oriented session (7 ± 6%) and power-oriented session (5 ± 5%). Between 24 and 48 h after both sessions CMJ and SJ heights and 20 m sprint were back to baseline. However, in contrast to the power-oriented session, recovery was not complete 48 h after the strength-oriented session, as indicated by greater impairments in CMJ eccentric and concentric peak forces, SJ rate of force development (RFD) and squat peak power. In agreement with the objective performance measurements, RPE and PRS ratings demonstrated that the strength-oriented session was experienced more strenuous than the power-oriented session. However, these subjective measurements agreed poorly with performance measurements at the individual level. In conclusion, we observed a larger degree of neuromuscular impairment and longer recovery times after a strength-oriented session than after a power-oriented session with equal total work, measured by both objective and subjective assessments. Nonetheless, most differences were small or trivial after either session. It appears necessary to combine several tests and within-test analyses (e.g., CMJ height, power and force) to reveal such differences. Objective and subjective assessments of fatigue and recovery cannot be used interchangeably; rather they should be combined to give a meaningful status for an individual in the days after a resistance exercise session. creator: Christian Helland creator: Magnus Midttun creator: Fredrik Saeland creator: Lars Haugvad creator: Daniela Schäfer Olstad creator: Paul Andre Solberg creator: Gøran Paulsen uri: https://doi.org/10.7717/peerj.10044 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Helland et al. title: Metabolomics analysis identifies metabolites associated with systemic acquired resistance in Arabidopsis link: https://peerj.com/articles/10047 last-modified: 2020-09-30 description: BackgroundSystemic acquired resistance (SAR) is a type of plant defense response that provides a long-lasting resistance to broad-spectrum pathogens in uninfected distal tissues following an initial localized infection. However, little information is available at present on the biological basis of SAR at the molecular level, especially in uninfected distal leaves.MethodsIn the present work, we used two SAR-inducing pathogens, avirulent Pseudomonas syringae pv. maculicola ES4326 harboring avrRpm1 (Psm avrRpm1) and virulent P. syringae pv. maculicola ES4326 (Psm ES4326), to induce SAR in Arabidopsis ecotype Col-0. A metabolomics approach based on ultra-high-performance liquid chromatography (UPLC) coupled with mass spectrometry (MS) was used to identify SAR-related metabolites in infected local leaves, and in uninfected distal leaves.ResultsDifferentially accumulated metabolites were distinguished by statistical analyses. The results showed that both the primary metabolism and the secondary metabolism were significantly altered in infected local leaves and in uninfected distal leaves, including phenolic compounds, amino acids, nucleotides, organic acids, and many other metabolites.ConclusionsThe content of amino acids and phenolic compounds increased in uninfected distal leaves, suggesting their contribution to the establishment of SAR. In addition, 2′-hydroxy-4, 4′, 6′-trimethoxychalcone, phenylalanine, and p-coumaric acid were identified as potential components which may play important roles both in basic resistance and in SAR. This work provides a reference for understanding of the metabolic mechanism associated with SAR in plants, which will be useful for further investigation of the molecular basis of the systemic immunity. creator: Hang Gao creator: Qian Zhou creator: Liu Yang creator: Kaili Zhang creator: Yeye Ma creator: Zi-Qin Xu uri: https://doi.org/10.7717/peerj.10047 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Gao et al. title: Forest structure dependency analysis of L-band SAR backscatter link: https://peerj.com/articles/10055 last-modified: 2020-09-30 description: Forest structure plays an important role in forest biomass inversion using synthetic aperture radar (SAR) backscatter. Synthetic aperture radar (SAR) sensors with long-wavelength have the potentiality to provide reliable and timely forest biomass inversion for their ability of deep penetration into the forest. L-band SAR backscatter shows useful for forest above-ground biomass (AGB) estimation. However, the way that forest structure mediating the biomass-backscatter affects the improvement of the related biomass estimation accuracy. In this paper, we have investigated L-band SAR backscatter sensitivity to forests with different mean canopy density, mean tree height and mean DBH (diameter at breast height) at the sub-compartment level. The forest species effects on their relationship were also considered in this study. The linear correlation coefficient R, non-linear correlation parameter, Maximal Information Coefficient (MIC), and the determination coefficient R2 from linear function, Logarithmic function and Quadratic function were used in this study to analyze forest structural properties effects on L-band SAR backscatter. The HV channel, which is more sensitive than HH to forest structure parameters, was chosen as the representative of SAR backscatter. 6037 sub-compartment were involved in the analysis. Canopy density showed a great influence on L-band backscatter than mean forest height and DBH. All of the R between canopy density and L-band backscatter were greater than 0.7 during the forest growth cycle. The sensitivity of L-band backscatter to mean forest height depends on forest canopy density. When canopy density was lower than 0.4, R values between mean forest height are smaller than 0.5. In contrast, the values of R were greater than 0.8 if canopy density was higher than 0.4. The sensitivity SAR backscatter to DBH fluctuated with canopy density, but it only showed obvious sensitivity when canopy density equals to 0.6, where both the linear and non-liner correlation values are higher than others. However, their effects on L-bang HV backscatter are affected by forest species, the effects on three forest structural parameters depend on tree species. creator: Yongjie Ji creator: Jimao Huang creator: Yilin Ju creator: Shipeng Guo creator: Cairong Yue uri: https://doi.org/10.7717/peerj.10055 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ji et al. title: Social influence on the effectiveness of virtual fencing in sheep link: https://peerj.com/articles/10066 last-modified: 2020-09-30 description: Early virtual fencing trials have effectively contained small groups of sheep within set areas of a paddock when all animals were wearing manual electronic collars. With sheep farming commonly involving large flocks, a potential cost-effective application of virtual fencing would involve applying equipment to only a proportion of the flock. In this study, we tested the ability of virtual fencing to control a small flock of sheep with differing proportions of the group exposed to the virtual fence (VF). Thirty-six Merino sheep were identified as leaders, middle or followers by moving them through a laneway. The sheep were then allocated to groups balanced for order of movement. The groups (n = 9 per group) included applying the VF to the following proportions of animals within each group: (1) 100% (n = 9 VF) (2) 66% (n = 6 VF; n = 3 no VF) (3) 33% (n = 3 VF; n = 6 no VF) (4) 0% (no VF; free to roam the paddock). The groups were given access to their own paddock (80 × 20 m) for two consecutive days, six hours per day, with the VF groups prevented from entering an exclusion zone that covered 50% of the north side of the paddock. During these hours, VF interactions, behavioural time budgets, and body temperature were recorded as measures of stress, and location was tracked with GPS. Group 100% VF and Control were tested on the first two days and groups 33% VF and 66% VF were tested on the following two days. During VF implementation the 100% VF and 66% VF group were successfully prevented from entering the exclusion zone. Having only 33% of the flock exposed to the virtual fence was not successful, with the sheep pushing forward through the VF to join flock mates in the exclusion zone. For learning to respond to the audio cue, sheep in the 33% group received more electrical stimuli with a 0.51 proportion for the ratio of electrical stimuli to audio cue, compared to 0.22 and 0.28 for the 100% and 66% groups, respectively. There were small differences in behavioural patterns of standing and lying on both days of testing, with the 100% VF and 66% VF groups spending more time lying. Although stress-induced hyperthermia did not occur in any of the VF groups, body temperature differed in the 33% VF group. There were no differences in temperature measures between the control and 100% VF animals. This study demonstrates that for a short period, controlling two-thirds of the flock was equally as effective as virtually fencing all animals, while controlling one-third of a flock with a virtual fence was not effective. For the short term, it appears that implementing the VF to a proportion of the flock can be an effective method of containment. Due to the limitations of this study, these results warrant further testing with larger flocks and for longer periods. creator: Danila Marini creator: Tellisa Kearton creator: Jackie Ouzman creator: Rick Llewellyn creator: Sue Belson creator: Caroline Lee uri: https://doi.org/10.7717/peerj.10066 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Marini et al. title: Identification of areas of very high biodiversity value to achieve the EU Biodiversity Strategy for 2030 key commitments link: https://peerj.com/articles/10067 last-modified: 2020-09-30 description: BackgroundThe European Union strives to increase protected areas of the EU terrestrial surface to 30% by year 2030, of which one third should be strictly protected. Designation of the Natura 2000 network, the backbone of nature protection in the EU, was mostly an expert-opinion process with little systematic conservation planning. The designation of the Natura 2000 network in Romania followed the same non-systematic approach, resulting in a suboptimal representation of invertebrates and plants. To help identify areas with very high biodiversity without repeating past planning missteps, we present a reproducible example of spatial prioritization using Romania’s current terrestrial Natura 2000 network and coarse-scale terrestrial species occurrence.MethodsWe used 371 terrestrial Natura 2000 Sites of Community Importance (Natura 2000 SCI), designated to protect 164 terrestrial species listed under Annex II of Habitats Directive in Romania in our spatial prioritization analyses (marine Natura 2000 sites and species were excluded). Species occurrences in terrestrial Natura 2000 sites were aggregated at a Universal Traverse Mercator spatial resolution of 1 km2. To identify priority terrestrial Natura 2000 sites for species conservation, and to explore if the Romanian Natura 2000 network sufficiently represents species included in Annex II of Habitats Directive, we used Zonation v4, a decision support software tool for spatial conservation planning. We carried out the analyses nationwide (all Natura 2000 sites) as well as separately for each biogeographic region (i.e., Alpine, Continental, Pannonian, Steppic and Black Sea).ResultsThe results of spatial prioritization of terrestrial Natura 2000 vary greatly by planning scenario. The performance of national-level planning of top priorities is minimal. On average, when 33% of the landscape of Natura 2000 sites is protected, only 20% of the distribution of species listed in Annex II of Habitats Directive are protected. As a consequence, the representation of species by priority terrestrial Natura 2000 sites is lessened when compared to the initial set of species. When planning by taxonomic group, the top-priority areas include only 10% of invertebrate distribution in Natura 2000. When selecting top-priority areas by biogeographical region, there are significantly fewer gap species than in the national level and by taxa scenarios; thusly, the scenario outperforms the national-level prioritization. The designation of strictly protected areas as required by the EU Biodiversity Strategy for 2030 should be followed by setting clear objectives, including a good representation of species and habitats at the biogeographical region level. creator: Iulia V. Miu creator: Laurentiu Rozylowicz creator: Viorel D. Popescu creator: Paulina Anastasiu uri: https://doi.org/10.7717/peerj.10067 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Miu et al. title: MULTI-DEEP: A novel CAD system for coronavirus (COVID-19) diagnosis from CT images using multiple convolution neural networks link: https://peerj.com/articles/10086 last-modified: 2020-09-30 description: Coronavirus (COVID-19) was first observed in Wuhan, China, and quickly propagated worldwide. It is considered the supreme crisis of the present era and one of the most crucial hazards threatening worldwide health. Therefore, the early detection of COVID-19 is essential. The common way to detect COVID-19 is the reverse transcription-polymerase chain reaction (RT-PCR) test, although it has several drawbacks. Computed tomography (CT) scans can enable the early detection of suspected patients, however, the overlap between patterns of COVID-19 and other types of pneumonia makes it difficult for radiologists to diagnose COVID-19 accurately. On the other hand, deep learning (DL) techniques and especially the convolutional neural network (CNN) can classify COVID-19 and non-COVID-19 cases. In addition, DL techniques that use CT images can deliver an accurate diagnosis faster than the RT-PCR test, which consequently saves time for disease control and provides an efficient computer-aided diagnosis (CAD) system. The shortage of publicly available datasets of CT images, makes the CAD system’s design a challenging task. The CAD systems in the literature are based on either individual CNN or two-fused CNNs; one used for segmentation and the other for classification and diagnosis. In this article, a novel CAD system is proposed for diagnosing COVID-19 based on the fusion of multiple CNNs. First, an end-to-end classification is performed. Afterward, the deep features are extracted from each network individually and classified using a support vector machine (SVM) classifier. Next, principal component analysis is applied to each deep feature set, extracted from each network. Such feature sets are then used to train an SVM classifier individually. Afterward, a selected number of principal components from each deep feature set are fused and compared with the fusion of the deep features extracted from each CNN. The results show that the proposed system is effective and capable of detecting COVID-19 and distinguishing it from non-COVID-19 cases with an accuracy of 94.7%, AUC of 0.98 (98%), sensitivity 95.6%, and specificity of 93.7%. Moreover, the results show that the system is efficient, as fusing a selected number of principal components has reduced the computational cost of the final model by almost 32%. creator: Omneya Attallah creator: Dina A. Ragab creator: Maha Sharkas uri: https://doi.org/10.7717/peerj.10086 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Attallah et al. title: The nine ADAMs family members serve as potential biomarkers for immune infiltration in pancreatic adenocarcinoma link: https://peerj.com/articles/9736 last-modified: 2020-09-30 description: BackgroundThe functional significance of ADAMs family members in the immune infiltration of pancreatic adenocarcinoma (PAAD) awaits elucidation.MethodsADAMs family members with significant expression were identified among differentially expressed genes of PAAD based on The Cancer Genome Atlas (TCGA) database followed by a verification based on the Oncomine database. The correlation of ADAMs in PAAD was estimated with the Spearman’s rho value. The pathway enrichment of ADAMs was performed by STRING and GSEALite, respectively. The protein–protein interaction and Gene Ontology analyses of ADAMs and their similar genes were exanimated in STRING and visualized by Cytoscape. Subsequently, the Box-Whisker plot was used to show a correlation between ADAMs and different tumor grade 1/2/3/4 with Student’s t-test. TIMER was applied to estimate a correlation of ADAMs expressions with immune infiltrates and immune checkpoint blockade (ICB) immunotherapy-related molecules. Furthermore, the effect of copy number variation (CNV) of ADAMs genes was assessed on the immune infiltration levels.ResultADAM8/9/10/12/15/19/28/TS2/TS12 were over-expressed in PAAD. Most of the nine ADAMs had a significant correlation. ADAM8/12/15/19 expression was remarkably increased in the comparison between grade 1 and grade 2/3 of PAAD. ADAM8/9/10/12/19/28/TS2/TS12 had a positive correlation with almost five immune infiltrates. ADAM12/19/TS2/TS12 dramatically related with ICB immunotherapy-related molecules. CNV of ADAMs genes potentially influenced the immune infiltration levels.ConclusionKnowledge of the expression level of the ADAMs family could provide a reasonable strategy for improved immunotherapies to PAAD. creator: Bing Qi creator: Han Liu creator: Ying Dong creator: Xueying Shi creator: Qi Zhou creator: Fen Zeng creator: Nabuqi Bao creator: Qian Li creator: Yuan Yuan creator: Lei Yao creator: Shilin Xia uri: https://doi.org/10.7717/peerj.9736 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Qi et al. title: Morphological and anatomical adaptations to dry, shady environments in Adiantum reniforme var. sinense (Pteridaceae) link: https://peerj.com/articles/9937 last-modified: 2020-09-30 description: The natural distribution of the rare perennial fern Adiantum reniforme var. sinense (Pteridaceae), which is endemic to shady cliff environments, is limited to small areas of Wanzhou County, Chongqing, China. In this study, we used brightfield and epifluorescence microscopy to investigate the anatomical structures and histochemical features that may allow this species to thrive in shady, dry cliff environments. The A. reniforme var. sinense sporophyte had a primary structure and a dictyostele. The plants of this species had an endodermis, sclerenchyma layers and hypodermal sterome, reflecting an adaption to dry cliff environments. Blades had a thin cuticle and isolateral mesophyll, suggesting a tolerance of shady environments. These characteristics are similar to many sciophyte ferns such as Lygodium japonicum and Pteris multifida. Thus, the morphological and anatomical characteristics of A. reniforme var. sinense identified in this study are consistent with adaptations to shady, dry cliff environments. creator: Di Wu creator: Linbao Li creator: Xiaobo Ma creator: Guiyun Huang creator: Chaodong Yang uri: https://doi.org/10.7717/peerj.9937 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Wu et al. title: Explicating anti-amyloidogenic role of curcumin and piperine via amyloid beta (Aβ) explicit pathway: recovery and reversal paradigm effects link: https://peerj.com/articles/10003 last-modified: 2020-09-30 description: Previously, we reported the synergistic effects of curcumin and piperine in cell cultures as potential anti-cholinesterase and anti-amyloidogenic agents. Due to limited findings on the enrolment of these compounds on epigenetic events in AD, we aimed at elucidating the expression profiles of Aβ42-induced SH-SY5Y cells using microarray profiling. In this study, an optimized concentration of 35 µM of curcumin and piperine in combination was used to treat Aβ42 fibril and high-throughput microarray profiling was performed on the extracted RNA. This was then compared to curcumin and piperine used singularly at 49.11 µM and 25 µM, respectively. Our results demonstrated that in the curcumin treated group, from the top 10 upregulated and top 10 downregulated significantly differentially expressed genes (p < 0.05; fold change ≥ 2 or ≤ −2), there were five upregulated and three downregulated genes involved in the amyloidogenic pathway. While from top 10 upregulated and top 10 downregulated significantly differentially expressed genes (p < 0.05; fold change ≥ 2 or ≤ − 2) in the piperine treated group, there were four upregulated and three downregulated genes involved in the same pathway, whereas there were five upregulated and two downregulated genes involved (p < 0.05; fold change ≥ 2 or ≤ − 2) in the curcumin-piperine combined group. Four genes namely GABARAPL1, CTSB, RAB5 and AK5 were expressed significantly in all groups. Other genes such as ITPR1, GSK3B, PPP3CC, ERN1, APH1A, CYCS and CALM2 were novel putative genes that are involved in the pathogenesis of AD. We revealed that curcumin and piperine have displayed their actions against Aβ via the modulation of various mechanistic pathways. Alterations in expression profiles of genes in the neuronal cell model may explain Aβ pathology post-treatment and provide new insights for remedial approaches of a combined treatment using curcumin and piperine. creator: Aimi Syamima Abdul Manap creator: Priya Madhavan creator: Shantini Vijayabalan creator: Adeline Chia creator: Koji Fukui uri: https://doi.org/10.7717/peerj.10003 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Abdul Manap et al. title: Identification of fertility-related genes for maize CMS-S via Bulked Segregant RNA-Seq link: https://peerj.com/articles/10015 last-modified: 2020-09-30 description: Cytoplasmic male sterility (CMS) is extensively used in maize hybrid production, and identification of genes related to fertility restoration for CMS is important for hybrid breeding. The fertility restoration of S type CMS is governed by several loci with major and minor effects, while the mechanism of fertility restoration for CMS-S is still unknown. In this study, BSR-Seq was conducted with two backcrossing populations with the fertility restoration genes, Rf3 and Rf10, respectively. Genetic mapping via BSR-Seq verified the positions of the two loci. A total of 353 and 176 differentially expressed genes (DEGs) between the male fertility and male sterile pools were identified in the populations with Rf3 and Rf10, respectively. In total, 265 DEGs were co-expressed in the two populations, which were up-regulated in the fertile plants, and they might be related to male fertility involving in anther or pollen development. Moreover, 35 and seven DEGs were specifically up-regulated in the fertile plants of the population with Rf3 and Rf10, respectively. Function analysis of these DEGs revealed that jasmonic acid (JA) signal pathway might be involved in the Rf3 mediated fertility restoration for CMS-S, while the small ubiquitin-related modifier system could play a role in the fertility restoration of Rf10. creator: Xiner Qin creator: Wenliang Zhang creator: Xue Dong creator: Shike Tian creator: Panpan Zhang creator: Yanxin Zhao creator: Yi Wang creator: Jianbing Yan creator: Bing Yue uri: https://doi.org/10.7717/peerj.10015 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Qin et al. title: Genetic identification and hybridization in the seagrass genus Halophila (Hydrocharitaceae) in Sri Lankan waters link: https://peerj.com/articles/10027 last-modified: 2020-09-30 description: Seagrasses, as marine angiosperms, play important roles in coastal ecosystems. With increasing anthropogenic impacts, they are facing dramatic declines on a global scale. Halophila is well-known as a complex taxonomic challenge mainly due to high morphological plasticity. By using only a morphological approach, the genus could be over-split or similar species could be erroneously lumped, thus masking its true biodiversity. In the present study, we incorporated genetic identification with morphological examination to reveal the identity of Halophila plants in southern and northwestern Sri Lankan waters. The nuclear ribosomal internal transcribed spacer (ITS) region and chloroplast ribulose-bisphosphate carboxylase gene (rbcL) were used to identify plants collected from the Gulf of Mannar, Puttalam Lagoon, and Matara, Sri Lanka. Based on genetic identification, H. major (Zoll.) Miquel is reported for the first time from Sri Lanka, which might have been misidentified as H. ovalis in previous literature based on morphology alone. We also observed a first hybridization case of Halophila cross between H. ovalis and H. major. Two potential cryptic species were found, herein designated Halophila sp. 1 (allied to H. minor) and Halophila sp. 2 (closely related to H. decipiens). In order to clarify taxonomic ambiguity caused by morphological plasticity and the low resolution of genetic markers, further comparative phylogenomic approaches might be needed to solve species boundary issues in this genus. creator: Shang Yin Vanson Liu creator: Terney Pradeep Kumara creator: Chi-Hsuan Hsu uri: https://doi.org/10.7717/peerj.10027 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Liu et al. title: Clinicopathological findings and imaging features of intraductal papillary neoplasms in bile ducts link: https://peerj.com/articles/10040 last-modified: 2020-09-30 description: BackgroundIntraductal papillary mucinous neoplasm of the bile duct (IPMN-B) is considered an uncommon tumor, and there is limited understanding of IPMN-B. This study aimed to investigate the prognosis and influential factors of the IPMN-B from 58 cases.MethodsThe clinical data of 58 patients with pathologically confirmed IPMN-B admitted to our hospital from January 1, 2012 to August 2017 were collected and analyzed. The patients were followed up by outpatient or telephone until January 1, 2019. SPSS 19.0 software was applied for data analysis. Survival analysis was performed using Kaplan-Meier method and parallel Log-rank test. Prognostic factors were analyzed by univariate analysis and multiple Cox regression model.ResultsAmong of all the patients, 26 cases were benign tumors and 32 cases were malignant tumors. The preoperative tumor markers CA242 and CEA of malignant IPNM-B patients were significantly higher than those in benign tumors (P < 0.05). Survival analysis showed that patients with malignant tumors had a worse prognosis. The median survival time of malignant IPMN-B patients was 40.6 ±  3.0 months, yet median survival time of benign IPMN-B patients was not reached (P = 0.19). The one-year survival rate and three-year survival rate of benign IPMN-B were 84% and 74% respectively. The one-year survival rate and three-year survival rate of malignant IPMN-B were 88% and 64% respectively. Univariate analysis showed that combined lymph node metastasis, surgical method, and differentiation degree could affect patients’ prognosis (P < 0.05). Multivariate analysis showed differentiation degree was an independent risk factor affecting prognosis (OR = 0.06, 95% confidence interval: 0.007∼0.486, P < 0.05).ConclusionThe levels of CEA and CA242 were helpful to identify benign and malignant of IPNM-B. Moreover, radical surgical resection could prolong patients’ survival. Finally, differentiation degree was an independent risk factor affecting malignant IPNM-B prognosis. creator: Honghui Zhang creator: Zhendong Zhong creator: Gaoyin Kong creator: Junaid Khan creator: Lianhong Zou creator: Yu Jiang creator: Xiehong Liu creator: Yixun Tang creator: Bo Jiang creator: Chuang Peng creator: Yinghui Song creator: Sulai Liu uri: https://doi.org/10.7717/peerj.10040 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhang et al. title: Hyaluronic acid ameliorates the proliferative ability of human amniotic epithelial cells through activation of TGF-β/BMP signaling link: https://peerj.com/articles/10104 last-modified: 2020-09-30 description: Human amniotic epithelial cells (hAECs) are a useful and noncontroversial source of stem cells for cell therapy and regenerative medicine, but their limited proliferative ability hinders the acquisition of adequate quantities of cells for clinical use due to not expressing telomerase in hAECs. Our previous study showed that hyaluronic acid (HA), an important component of the extracellular matrix, promoted the proliferation of human amniotic mesenchymal stem cells. Herein, we hypothesize that HA might improve the proliferative capability of hAECs. In the present study, the role of HA on the proliferation of human amniotic epithelial cells (hAECs) in vitro was investigated for the first time. HA at molecular weight of 300 kDa showed an obvious pro-proliferation effect on hAECs. Furthermore, HA not only kept phenotypic characteristics and differentiation capabilities of hAECs, but significantly promoted the secretion of the anti-inflammatory factors such as IL-10 and TGF-β1, and the expression of stem cell pluripotent factors such as Oct4 and Nanog. Analysis of PCR microarray data and RT-qPCR validation showed that TGF-β/BMP signaling was activated in the presence of HA. Further study showed that SB431542, an inhibitor of the TGF-β/BMP signaling, significantly suppressed the mRNA expression of TGFBR3, BMP4, BMP7, BMPR1B, SMAD3, SMAD4, and the pro-proliferative effect of HA on hAECs. These data suggest that HA is a safe and effective enhancer for in vitro expansion of hAECs, whose regulatory mechanism involves the TGF-β/BMP signaling. creator: Ya-Bing Tian creator: Nuo-Xin Wang creator: Yan Xu creator: Chang-Yin Yu creator: Ru-Ming Liu creator: Yi Luo creator: Jian-Hui Xiao uri: https://doi.org/10.7717/peerj.10104 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Tian et al. title: Global RNA editome landscape discovers reduced RNA editing in glioma: loss of editing of gamma-amino butyric acid receptor alpha subunit 3 (GABRA3) favors glioma migration and invasion link: https://peerj.com/articles/9755 last-modified: 2020-09-29 description: BackgroundGliomas are the most common and lethal type of intracranial tumors. With the current treatment regime, the median survival of patients with grade IV glioma (glioblastoma/GBM) remains at 14–16 months. RNA editing modifies the function and regulation of transcripts. The development of glial tumors may be caused by altered RNA editing events.MethodsIn this study, we uncover the global RNA editome landscape of glioma patients from RNA-seq data of control, lower grade glioma (LGG) and GBM samples (n = 1,083).ResultsA-to-I editing events were found to comprise 80% of the total editing events of which 96% were located in the Alu regions. The total RNA editing events were found to be reduced in glioma compared to control samples. More specifically, we found Gamma-aminobutyric acid type A receptor alpha3 (GABRA3) to be edited (c.1026 A-to-G; pI343M) in 73% (editing ratio 0.8) of control samples compared to LGG (28.96%; 0.47) and GBM (5.2%; 0.53) samples. GABRA3 transcript level was found to be downregulated in glioma compared to control in a grade-specific manner with GBMs having the lowest level of the transcript. Further, GABRA3 transcripts were observed to be higher in edited compared to unedited glioma samples. The transcript and protein levels of exogenously expressed gene were found to be higher for edited compared to unedited GABRA3 in glioma cells. Further, exogenously expressed edited GABRA3 inhibited migration and invasion of glioma cells efficiently but not the unedited GABRA3.ConclusionCollectively, our study discovered a reduction in RNA editing during glioma development. We further demonstrate that elevated RNA editing maintains a high level of GABRA3 RNA and protein in normal glial cells which provides a less migratory environment for the normal functioning of the brain. In contrast, the reduction in GABRA3 protein levels, due to lower stability of unedited RNA, results in the loss of function which confers an aggressive phenotype to GBM tumor. creator: Vikas Patil creator: Jagriti Pal creator: Kulandaivelu Mahalingam creator: Kumaravel Somasundaram uri: https://doi.org/10.7717/peerj.9755 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Patil et al. title: Interpreting character variation in turtles: Araripemys barretoi (Pleurodira: Pelomedusoides) from the Araripe Basin, Early Cretaceous of Northeastern Brazil link: https://peerj.com/articles/9840 last-modified: 2020-09-29 description: The Araripe Basin (Northeastern Brazil) has yielded a rich Cretaceous fossil fauna of both vertebrates and invertebrates found mainly in the Crato and Romualdo Formations, of Aptian and Albian ages respectively. Among the vertebrates, the turtles were found to be quite diverse, with several specimens retrieved and five valid species described to this date for the Romualdo Formation. There were also records of turtles from Ipubi and Crato Formations, mainly fragmentary material which precluded proper specific identification; however, Araripemys barretoi is supposed to occur on both Crato and Romualdo Formations. Here we describe thirteen specimens of A. barretoi-including the first description of an almost complete individual, bearing a skull, from the Crato Formation. We report a great amount of morphological variation, interpreted as being essentially of intraspecific nature, including individual, sexual and ontogenetic variation. creator: Saulo Limaverde creator: Rodrigo Vargas Pêgas creator: Rafael Damasceno creator: Chiara Villa creator: Gustavo R. Oliveira creator: Niels Bonde creator: Maria E.C. Leal uri: https://doi.org/10.7717/peerj.9840 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Limaverde et al. title: Computational perspectives revealed prospective vaccine candidates from five structural proteins of novel SARS corona virus 2019 (SARS-CoV-2) link: https://peerj.com/articles/9855 last-modified: 2020-09-29 description: BackgroundThe present pandemic COVID-19 is caused by SARS-CoV-2, a single-stranded positive-sense RNA virus from the Coronaviridae family. Due to a lack of antiviral drugs, vaccines against the virus are urgently required.MethodsIn this study, validated computational approaches were used to identify peptide-based epitopes from six structural proteins having antigenic properties. The Net-CTL 1.2 tool was used for the prediction of CD8+ T-cell epitopes, while the robust tools Bepi-Pred 2 and LBtope was employed for the identification of linear B-cell epitopes. Docking studies of the identified epitopes were performed using HADDOCK 2.4 and the structures were visualized by Discovery Studio and LigPlot+. Antigenicity, immunogenicity, conservancy, population coverage and allergenicity of the predicted epitopes were determined by the bioinformatics tools like VaxiJen v2.0 server, the Immune Epitope Database tools and AllerTOP v.2.0, AllergenFP 1.0 and ElliPro.ResultsThe predicted T cell and linear B-cell epitopes were considered as prime vaccine targets in case they passed the requisite parameters like antigenicity, immunogenicity, conservancy, non-allergenicity and broad range of population coverage. Among the predicted CD8+ T cell epitopes, potential vaccine targets from surface glycoprotein were; YQPYRVVVL, PYRVVVLSF, GVYFASTEK, QLTPTWRVY, and those from ORF3a protein were LKKRWQLAL, HVTFFIYNK. Similarly, RFLYIIKLI, LTWICLLQF from membrane protein and three epitopes viz; SPRWYFYYL, TWLTYTGAI, KTFPPTEPK from nucleocapsid phosphoprotein were the superior vaccine targets observed in our study. The negative values of HADDOCK and Z scores obtained for the best cluster indicated the potential of the epitopes as suitable vaccine candidates. Analysis of the 3D and 2D interaction diagrams of best cluster produced by HADDOCK 2.4 displayed the binding interaction of leading T cell epitopes within the MHC-1 peptide binding clefts. On the other hand, among linear B cell epitopes the majority of potential vaccine targets were from nucleocapsid protein, viz; 59−HGKEDLKFPRGQGVPINTNSSPDDQIGYYRRATRRIRGGDGKMKDLS−105, 227−LNQLE SKMSGKGQQQQGQTVTKKSAAEASKKPRQKRTATK−266, 3−DNGPQNQRNAPRITFGGP−20, 29−GERSGARSKQRRPQGL−45. Two other prime vaccine targets, 370−NSASFSTFKCYGVSPTKLNDLCFTNV−395 and 260−AGAAAYYVGYLQPRT−274 were identified in the spike protein. The potential B-cell conformational epitopes were predicted on the basis of a higher protrusion index indicating greater solvent accessibility. These conformational epitopes were of various lengths and belonged to spike, ORF3a, membrane and nucleocapsid proteins.ConclusionsTaken together, eleven T cell epitopes, seven B cell linear epitopes and ten B cell conformational epitopes were identified from five structural proteins of SARS-CoV-2 using advanced computational tools. These potential vaccine candidates may provide important timely directives for an effective vaccine against SARS-CoV-2. creator: Rajesh Anand creator: Subham Biswal creator: Renu Bhatt creator: Bhupendra N. Tiwary uri: https://doi.org/10.7717/peerj.9855 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Anand et al. title: Bigfin reef squid demonstrate capacity for conditional discrimination and projected future carbon dioxide levels have no effect on learning capabilities link: https://peerj.com/articles/9865 last-modified: 2020-09-29 description: Anthropogenic carbon dioxide (CO2) emissions are being absorbed by the oceans, a process known as ocean acidification, and risks adversely affecting a variety of behaviours in a range of marine species, including inhibited learning in some fishes. However, the effects of elevated CO2 on learning in advanced invertebrates such as cephalopods are unknown. Any impacts to the learning abilities of cephalopods could have far-reaching consequences for their populations and the communities they inhabit. Cephalopods have some of the most advanced cognitive abilities among invertebrates and are one of the few invertebrate taxa in which conditional discrimination has been demonstrated, though the trait has not been demonstrated in any species of squid. Here, we tested for the first time the capacity for conditional discrimination in a squid species (Sepioteuthis lessoniana). Furthermore, we investigated the effects of projected future CO2 levels (1,084 µatm) on conditional discrimination and learning more generally. A three-task experiment within a two-choice arena was used to test learning and conditional discrimination. Learning was measured by improvements in task completion in repeated trials over time and the number of trials required to pass each task. Squid exhibited significant learning capabilities, with an increase in correct choices over successive trials and a decrease in the number of trials needed to complete the successive tasks. Six of the 12 squid tested successfully passed all three tasks indicating a capacity for conditional discrimination in the species. Elevated CO2 had no effect on learning or on the capacity for conditional discrimination in squid. This study highlights the remarkable cognitive abilities of S. lessoniana, demonstrated by their capacity for conditional discrimination, and suggests that ocean acidification will not compromise learning abilities. However, other behavioural traits in the species have been shown to be altered at comparable elevated CO2 conditions. It is not clear why some ecologically important behaviours are altered by elevated CO2 whereas others are unaffected. Future research should focus on the physiological mechanism responsible for altered behaviours in squid at elevated CO2. creator: Blake L. Spady creator: Sue-Ann Watson uri: https://doi.org/10.7717/peerj.9865 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Spady and Watson title: The increasing prevalence of CPV-2c in domestic dogs in China link: https://peerj.com/articles/9869 last-modified: 2020-09-29 description: BackgroundCanine parvovirus type 2 (CPV-2), a serious pathogen, leads to high morbidity and mortality in dogs and several wild carnivore species. Although it is a DNA virus, it evolves particularly rapidly, with a genomic substitution rate of approximately 10−4 substitutions/site/year, close to that of some RNA viruses. Tracing the prevalence of CPV-2 in dogs is significant.MethodsIn this study, an aetiological survey was carried out from 2016 to 2019 in Guangdong Province, China, involving Guangzhou, Shenzhen and Dongguan. Furthermore, to systematically analyse the prevalence of CPV-2 in China, the VP2 gene sequences of all Chinese isolates were downloaded from the NCBI nucleotide database in December 2019, and changes in CPV-2 variants were examined.ResultsA total of 55.7% (34/61) of samples were CPV-2 positive by PCR detection and virus isolation. In addition to different variants circulating in dogs, coinfection with multiple variants was identified, as was coinfection with other canine enteric pathogens in some cases. Two previously reported amino acid sites, A5G and Q370R of CPV-2c mutants, reported in variants in China were assessed, and several CPV-2 isolates with P13S and K582N mutations were detected in this study. Finally, we speculate on the prevalence of different CPV-2 variants in China. According to the VP2 gene sequence obtained from the NCBI nucleotide database, the proportion of different variants in China has changed, and CPV-2c appears to be growing rapidly. In conclusion, this aetiology survey suggests that CPV-2 continues to be common in China and that the prevalence of CPV-2c is increasing. creator: Xiangqi Hao creator: Yuwei He creator: Chuhan Wang creator: Weiqi Xiao creator: Ruohan Liu creator: Xiangyu Xiao creator: Pei Zhou creator: Shoujun Li uri: https://doi.org/10.7717/peerj.9869 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Hao et al. title: The relationship between individual phenotype and the division of labour in naked mole-rats: it’s complicated link: https://peerj.com/articles/9891 last-modified: 2020-09-29 description: BackgroundThe naked mole-rat (Heterocephalus glaber) is among the most social mammals on the planet, living in eusocial groups of up to 300 individuals that contain a single reproductive female and up to three reproductive males. A critical aspect of their complex social system is the division of labour that allows non-breeders to form an effective workforce. Age- or weight-based polyethisms are widely cited as explanations for how labour is divided, but evidence in support of these hypotheses has been equivocal.MethodsTo assess the extent to which individual working behaviour is determined by sex, age, weight and social rank, we studied the behaviours of 103 animals from eight captive colonies. We performed focal sampling and ran mixed-effects models to assess which factors explained variation in working behaviour during six ten-minute observation periods per individual.ResultsContrary to widely-held beliefs, we found that working behaviour did not decrease linearly with weight, although polynomial regressions indicated younger and medium-sized individuals worked most frequently, while high-ranking individuals worked for the shortest periods of time. Working behaviour and its relationship with individual characteristics also varied between colonies.ConclusionsWhile age- or size-based polyethisms may have some influence on working behaviour, we argue that other characteristics of the individual and colony are also important. In particular, the interactions of individual, social and environmental factors must be considered in order to understand the emergence and effectiveness of the division of labour that is so critical to many social organisms. creator: James D. Gilbert creator: Stephen J. Rossiter creator: Chris G. Faulkes uri: https://doi.org/10.7717/peerj.9891 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Gilbert et al. title: Dynamical modeling predicts an inflammation-inducible CXCR7+ B cell precursor with potential implications in lymphoid blockage pathologies link: https://peerj.com/articles/9902 last-modified: 2020-09-29 description: BackgroundThe blockage at the early B lymphoid cell development pathway within the bone marrow is tightly associated with hematopoietic and immune diseases, where the disruption of basal regulatory networks prevents the continuous replenishment of functional B cells. Dynamic computational models may be instrumental for the comprehensive understanding of mechanisms underlying complex differentiation processes and provide novel prediction/intervention platforms to reinvigorate the system.MethodsBy reconstructing a three-module regulatory network including genetic transcription, intracellular transduction, and microenvironment communication, we have investigated the early B lineage cell fate decisions in normal and pathological settings. The early B cell differentiation network was simulated as a Boolean model and then transformed, using fuzzy logic, to a continuous model. We tested null and overexpression mutants to analyze the emergent behavior of the network. Due to its importance in inflammation, we investigated the effect of NFkB induction at different early B cell differentiation stages.ResultsWhile the exhaustive synchronous and asynchronous simulation of the early B cell regulatory network (eBCRN) reproduced the configurations of the hematopoietic progenitors and early B lymphoid precursors of the pathway, its simulation as a continuous model with fuzzy logics suggested a transient IL-7R+ ProB-to-Pre-B subset expressing pre-BCR and a series of dominant B-cell transcriptional factors. This conspicuous differentiating cell population up-regulated CXCR7 and reduced CXCR4 and FoxO1 expression levels. Strikingly, constant but intermediate NFkB signaling at specific B cell differentiation stages allowed stabilization of an aberrant CXCR7+ pre-B like phenotype with apparent affinity to proliferative signals, while under constitutive overactivation of NFkB, such cell phenotype was aberrantly exacerbated from the earliest stage of common lymphoid progenitors. Our mutant models revealed an abnormal delay in the BCR assembly upon NFkB activation, concomitant to sustained Flt3 signaling, down-regulation of Ebf1, Irf4 and Pax5 genes transcription, and reduced Ig recombination, pointing to a potential lineage commitment blockage.DiscussionFor the first time, an inducible CXCR7hi B cell precursor endowed with the potential capability of shifting central lymphoid niches, is inferred by computational modeling. Its phenotype is compatible with that of leukemia-initiating cells and might be the foundation that bridges inflammation with blockage-related malignancies and a wide range of immunological diseases. Besides the predicted differentiation impairment, inflammation-inducible phenotypes open the possibility of newly formed niches colonized by the reported precursor. Thus, emergent bone marrow ecosystems are predicted following a pro-inflammatory induction, that may lead to hematopoietic instability associated to blockage pathologies. creator: Jennifer Enciso creator: Luis Mendoza creator: Elena R. Álvarez-Buylla creator: Rosana Pelayo uri: https://doi.org/10.7717/peerj.9902 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Enciso et al. title: Study of marsh wetland landscape pattern evolution on the Zoigê Plateau due to natural/human dual-effects link: https://peerj.com/articles/9904 last-modified: 2020-09-29 description: Zoigê Plateau, China’s largest plateau marsh wetland, has experienced large-scale degradation of the marsh wetland and evolution of the wetland landscape pattern over the past 40 years due to climate warming and human activities. How exactly do the wetland landscape pattern characteristics change? How do climatic change and human activities affect the wetland evolution? These questions are yet to be systematically investigated. In order to investigate changes to the marsh wetland on the Zoigê Plateau, field investigations, spatial and statistical analysis were undertaken. Findings from our study indicate that from 1977–2016, the area of marsh wetland on the Plateau reduced by 56.54%, approximately 66,700 hm2 of marsh wetland has been lost. The centroids of both marsh and marshy meadow migrated and the landscape centroid migration behaviors were also correlated with the distribution and variation of the marsh wetland on different slopes. In addition, the number of marsh landscape patches initially increased before decreasing; the number of marshy meadow landscape patches also recorded an initial increase, followed by a decline before a final increase. As the effects of human activities weakened, the aggregation degrees of both marsh and marshy meadow increased. Overall, the fragmentation degree, diversity and fractal dimension of the marsh wetland all declined. An investigation into the driving factors affecting the Plateau area shows that the increase of annual average temperature was the natural factor while trenching and overgrazing were the main human factors resulting in wetland degradation. Results from this study provide basic data and theoretical foundation for the protection and restoration of marsh wetland in alpine regions. creator: Liqin Dong creator: Wen Yang creator: Kun Zhang creator: Shuo Zhen creator: Xiping Cheng creator: Lihua Wu uri: https://doi.org/10.7717/peerj.9904 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2020 Dong et al. title: A glycolysis-related gene pairs signature predicts prognosis in patients with hepatocellular carcinoma link: https://peerj.com/articles/9944 last-modified: 2020-09-29 description: BackgroundHepatocellular carcinoma (HCC) is one of the most universal malignant liver tumors worldwide. However, there were no systematic studies to establish glycolysis‑related gene pairs (GRGPs) signatures for the patients with HCC. Therefore, the study aimed to establish novel GRGPs signatures to better predict the prognosis of HCC.MethodsBased on the data from Gene Expression Omnibus, The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium databases, glycolysis-related mRNAs were used to construct GRGPs. Cox regression was applied to establish a seventeen GRGPs signature in TCGA dataset, which was verified in two validation (European and American, and Asian) datasets.ResultsSeventeen prognostic GRGPs (HMMR_PFKFB1, CHST1_GYS2, MERTK_GYS2, GPC1_GYS2, LDHA_GOT2, IDUA_GNPDA1, IDUA_ME2, IDUA_G6PD, IDUA_GPC1, MPI_GPC1, SDC2_LDHA, PRPS1_PLOD2, GALK1_IER3, MET_PLOD2, GUSB_IGFBP3, IL13RA1_IGFBP3 and CYB5A_IGFBP3) were identified to be significantly progressive factors for the patients with HCC in the TCGA dataset, which constituted a GRGPs signature. The patients with HCC were classified into low-risk group and high-risk group based on the GRGPs signature. The GRGPs signature was a significantly independent prognostic indicator for the patients with HCC in TCGA (log-rank P = 2.898e−14). Consistent with the TCGA dataset, the patients in low-risk group had a longer OS in two validation datasets (European and American: P = 1.143e−02, and Asian: P = 6.342e−08). Additionally, the GRGPs signature was also validated as a significantly independent prognostic indicator in two validation datasets.ConclusionThe seventeen GRGPs and their signature might be molecular biomarkers and therapeutic targets for the patients with HCC. creator: Weige Zhou creator: Shijing Zhang creator: Zheyou Cai creator: Fei Gao creator: Wenhui Deng creator: Yi Wen creator: Zhen-wen Qiu creator: Zheng-kun Hou creator: Xin-Lin Chen uri: https://doi.org/10.7717/peerj.9944 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Zhou et al. title: Identification of hub genes and small molecule therapeutic drugs related to breast cancer with comprehensive bioinformatics analysis link: https://peerj.com/articles/9946 last-modified: 2020-09-29 description: Breast cancer is one of the most common malignant tumors among women worldwide and has a high morbidity and mortality. This research aimed to identify hub genes and small molecule drugs for breast cancer by integrated bioinformatics analysis. After downloading multiple gene expression datasets from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database, 283 overlapping differentially expressed genes (DEGs) significantly enriched in different cancer-related functions and pathways were obtained using LIMMA, VennDiagram and ClusterProfiler packages of R. We then analyzed the topology of protein–protein interaction (PPI) network with overlapping DEGs and further obtained six hub genes (RRM2, CDC20, CCNB2, BUB1B, CDK1, and CCNA2) from the network via STRING and Cytoscape. Subsequently, we conducted genes expression verification, genetic alterations evaluation, immune infiltration prediction, clinicopathological parameters analysis, identification of transcriptional and post-transcriptional regulatory molecules, and survival analysis for these hub genes. Meanwhile, 29 possible drug candidates (e.g., Cladribine, Gallium nitrate, Alvocidib, 1β-hydroxyalantolactone, Berberine hydrochloride, Nitidine chloride) were identified from the DGIdb database and the GSE85871 dataset. In addition, some transcription factors and miRNAs (e.g., E2F1, PTTG1, TP53, ZBTB16, hsa-miR-130a-3p, hsa-miR-204-5p) targeting hub genes were identified as key regulators in the progression of breast cancer. In conclusion, our study identified six hub genes and 29 potential drug candidates for breast cancer. These findings may advance understanding regarding the diagnosis, prognosis and treatment of breast cancer. creator: Mingqian Hao creator: Wencong Liu creator: Chuanbo Ding creator: Xiaojuan Peng creator: Yue Zhang creator: Huiying Chen creator: Ling Dong creator: Xinglong Liu creator: Yingchun Zhao creator: Xueyan Chen creator: Sadia Khatoon creator: Yinan Zheng uri: https://doi.org/10.7717/peerj.9946 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Hao et al. title: Clostridioides difficile infection after cardiac surgery: Assessment of prevalence, risk factors and clinical outcomes—retrospective study link: https://peerj.com/articles/9972 last-modified: 2020-09-29 description: BackgroundClostridioides difficile infection (CDI) is the most common cause of hospital-acquired diarrhea. There is little available data regarding risk factors of CDI for patients who undergo cardiac surgery. The study evaluated the course of CDI in patients after cardiac surgery.MethodsOf 6,198 patients studied, 70 (1.1%) developed CDI. The control group consisted of 73 patients in whom CDI was excluded. Perioperative data and clinical outcomes were analyzed.ResultsPatients with CDI were significantly older in comparison to the control group (median age 73.0 vs 67.0, P = 0.005) and more frequently received proton pump inhibitors, statins, β-blockers and acetylsalicylic acid before surgery (P = 0.008, P = 0.012, P = 0.004, and P = 0.001, respectively). In addition, the presence of atherosclerosis, coronary disease and history of malignant neoplasms correlated positively with the development of CDI (P = 0.012, P = 0.036 and P = 0.05, respectively). There were no differences in the type or timing of surgery, aortic cross-clamp and cardiopulmonary bypass time, volume of postoperative drainage and administration of blood products between the studied groups. Relapse was more common among overweight patients with high postoperative plasma glucose or patients with higher C-reactive protein during the first episode of CDI, as well as those with a history of coronary disease or diabetes mellitus (P = 0.005, P = 0.030, P = 0.009, P = 0.049, and P = 0.025, respectively). Fifteen patients died (21.4%) from the CDI group and 7 (9.6%) from the control group (P = 0.050). Emergent procedures, prolonged stay in the intensive care unit, longer mechanical ventilation and high white blood cell count during the diarrhea were associated with higher mortality among patients with CDI (P = 0.05, P = 0.041, P = 0.004 and P = 0.007, respectively).ConclusionsThe study did not reveal any specific cardiac surgery-related risk factors for development of CDI. creator: Anna Rzucidło-Hymczak creator: Hubert Hymczak creator: Aldona Olechowska-Jarząb creator: Anna Gorczyca creator: Boguslaw Kapelak creator: Rafał Drwiła creator: Dariusz Plicner uri: https://doi.org/10.7717/peerj.9972 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Rzucidło-Hymczak et al. title: The predisposing factors of AKI for prophylactic strategies in burn care link: https://peerj.com/articles/9984 last-modified: 2020-09-29 description: BackgroundAcute kidney injury (AKI) is one of the most severe complications of burn injury. AKI with severe burn injury causes high mortality. This study aims to investigate the incidence of and predisposing factors for AKI in burn patients.MethodsThis is a single-center, retrospective, descriptive criterion standard study conducted from June 27, 2015, to March 8, 2016. We used Kidney Disease Improving Global Outcomes criteria to define and select patients with AKI. The study was conducted by recruiting in hospital patients who suffered from the flammable cornstarch-based powder explosion and were treated under primary care procedures. A total of 49 patients who suffered from flammable dust explosion-related burn injury were enrolled and admitted on June 27, 2015. The patients with more than 20% total body surface area of burn were transferred to the intensive care unit. Patients received fluid resuscitation in the first 24 hours based on the Parkland formula. The primary measurements were the incidence of and predisposing factors for AKI in these patients. Demographic characteristics, laboratory data, and inpatient outcomes were also evaluated. The incidence of AKI in this cohort was 61.2% (n = 30). The mortality rate was 2.0% (n = 1) during a 59-day follow-up period. The multivariate analysis revealed inhalation injury (adjusted OR = 22.0; 95% CI [1.4–358.2]) and meeting ≥3 American Burn Association (ABA) sepsis criteria (adjusted OR = 13.7; 95% CI [1.7–110.5]) as independent risk factors for early advanced AKI.ConclusionsThe incidence rate of AKI was higher in this cohort than in previous studies, possibly due to the flammable dust explosion-related burn injury. However, the mortality was lower than that expected. In clinical practice, indicators of inflammation, including ABA sepsis criteria may help in predicting the risk of AKI in patients with burn injury. creator: Shin-Yi Tsai creator: Chon-Fu Lio creator: Shou-Chuan Shih creator: Cheng-Jui Lin creator: Yu-Tien Chen creator: Chia-Meng Yu creator: Fang-ju Sun creator: Chien-Feng Kuo creator: Xiaofeng Jia uri: https://doi.org/10.7717/peerj.9984 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Tsai et al. title: Coral reefs as a source of climate-active aerosols link: https://peerj.com/articles/10023 last-modified: 2020-09-29 description: We review the evidence for bio-regulation by coral reefs of local climate through stress-induced emissions of aerosol precursors, such as dimethylsulfide. This is an issue that goes to the core of the coral ecosystem’s ability to maintain homeostasis in the face of increasing climate change impacts and other anthropogenic pressures. We examine this through an analysis of data on aerosol emissions by corals of the Great Barrier Reef, Australia. We focus on the relationship with local stressors, such as surface irradiance levels and sea surface temperature, both before and after notable coral bleaching events. We conclude that coral reefs may be able to regulate their exposure to environmental stressors through modification of the optical properties of the atmosphere, however this ability may be impaired as climate change intensifies. creator: Rebecca L. Jackson creator: Albert J. Gabric creator: Roger Cropp uri: https://doi.org/10.7717/peerj.10023 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Jackson et al. title: The mechanism of the plant roots’ soil-reinforcement based on generalized equivalent confining pressure link: https://peerj.com/articles/10064 last-modified: 2020-09-29 description: BackgroundTo quantitatively evaluate the contribution of plant roots to soil shear strength, the generalized equivalent confining pressure (GECP), which is the difference in confining pressure between the reinforced and un-reinforced soil specimens at the same shear strength, was proposed and considered in terms of the function of plant roots in soil reinforcement.MethodsIn this paper, silt loam soil was selected as the test soil, and the roots of Indigofera amblyantha were chosen as the reinforcing material. Different drainage conditions (consolidation drained (CD), consolidation undrained (CU), and unconsolidated undrained (UU)) were used to analyse the influences of different root distribution patterns (horizontal root (HR), vertical root (VR), and complex root (CR)) and root contents (0.25%, 0.50%, and 0.75%) on the shear strength of soil-root composites.ResultsThe cohesion (c) values of the soil-root composites varied under different drainage conditions and root contents, while the internal friction angle (φ ) values remain basically stable under different drainage conditions. Under the same root content and drainage conditions, the shear strength indexes ranked in order of lower to higher were HR, VR and CR. The GECP of the soil-root composites with a 0.75% root content was 1.5–2.0 times that with a 0.50% root content and more than 5 times that with a 0.25% root content under the CD and CU conditions. The GECP in reinforced soil followed the sequence of CD > CU > UU. The GECP of the plant roots increased as confining pressure increased under CD and CU conditions while showed a complex change to the confining pressure under the UU condition.ConclusionIt was concluded that the evaluation of plant root reinforcing soil based on GECP can be used to measure effectively the influences of roots on soil under different drainage conditions and root distribution patterns. creator: Ping Guo creator: Zhenyao Xia creator: Qi Liu creator: Hai Xiao creator: Feng Gao creator: Lun Zhang creator: Mingyi Li creator: Yueshu Yang creator: Wennian Xu uri: https://doi.org/10.7717/peerj.10064 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Guo et al. title: Hydrological and soil physiochemical variables determine the rhizospheric microbiota in subtropical lakeshore areas link: https://peerj.com/articles/10078 last-modified: 2020-09-29 description: BackgroundDue to intensive sluice construction and other human disturbances, lakeshore vegetation has been destroyed and ecosystems greatly changed. Rhizospheric microbiota constitute a key part of a functioning rhizosphere ecosystem. Maintaining rhizosphere microbial diversity is a central, critical issue for sustaining these rhizospheric microbiota functions and associated ecosystem services. However, the community composition and abiotic factors influencing rhizospheric microbiota in lakeshore remain largely understudied.MethodsThe spatiotemporal composition of lakeshore rhizospheric microbiota and the factors shaping them were seasonally investigated in three subtropical floodplain lakes (Lake Chaohu, Lake Wuchang, and Lake Dahuchi) along the Yangtze River in China through 16S rRNA amplicon high-throughput sequencing.ResultsOur results showed that four archaeal and 21 bacterial phyla (97.04 ± 0.25% of total sequences) dominated the rhizospheric microbiota communities of three lakeshore areas. Moreover, we uncovered significant differences among rhizospheric microbiota among the lakes, seasons, and average submerged depths. The Acidobacteria, Actinobacteria, Bacteroidetes, Bathyarchaeota, Gemmatimonadetes, and Proteobacteria differed significantly among the three lakes, with more than half of these dominant phyla showing significant changes in abundance between seasons, while the DHVEG-6, Ignavibacteriae, Nitrospirae, Spirochaetes, and Zixibacteria varied considerably across the average submerged depths (n = 58 sites in total). Canonical correspondence analyses revealed that the fluctuation range of water level and pH were the most important factors influencing the microbial communities and their dominant microbiota, followed by total nitrogen, moisture, and total phosphorus in soil. These results suggest a suite of hydrological and soil physiochemical variables together governed the differential structuring of rhizospheric microbiota composition among different lakes, seasons, and sampling sites. This work thus provides valuable ecological information to better manage rhizospheric microbiota and protect the vegetation of subtropical lakeshore areas. creator: Xiaoke Zhang creator: Huili Wang creator: Zhifei Li creator: Jun Xie creator: Jiajia Ni uri: https://doi.org/10.7717/peerj.10078 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhang et al. title: Loss of inner kinetochore genes is associated with the transition to an unconventional point centromere in budding yeast link: https://peerj.com/articles/10085 last-modified: 2020-09-29 description: BackgroundThe genomic sequences of centromeres, as well as the set of proteins that recognize and interact with centromeres, are known to quickly diverge between lineages potentially contributing to post-zygotic reproductive isolation. However, the actual sequence of events and processes involved in the divergence of the kinetochore machinery is not known. The patterns of gene loss that occur during evolution concomitant with phenotypic changes have been used to understand the timing and order of molecular changes.MethodsI screened the high-quality genomes of twenty budding yeast species for the presence of well-studied kinetochore genes. Based on the conserved gene order and complete genome assemblies, I identified gene loss events. Subsequently, I searched the intergenic regions to identify any un-annotated genes or gene remnants to obtain additional evidence of gene loss.ResultsMy analysis identified the loss of four genes (NKP1, NKP2, CENPL/IML3 and CENPN/CHL4) of the inner kinetochore constitutive centromere-associated network (CCAN/also known as CTF19 complex in yeast) in both the Naumovozyma species for which genome assemblies are available. Surprisingly, this collective loss of four genes of the CCAN/CTF19 complex coincides with the emergence of unconventional centromeres in N. castellii and N. dairenensis. My study suggests a tentative link between the emergence of unconventional point centromeres and the turnover of kinetochore genes in budding yeast. creator: Nagarjun Vijay uri: https://doi.org/10.7717/peerj.10085 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Vijay title: Expression of collagen type 1 alpha 1 indicates lymph node metastasis and poor outcomes in squamous cell carcinomas of the lung link: https://peerj.com/articles/10089 last-modified: 2020-09-29 description: BackgroundSquamous cell carcinomas of the lung are an extremely common and deadly form of non-small cell lung cancers. Clinical management of the disease is dependent on staging and metastatic status. Metastasis to the lymph node is especially crucial to diagnose as it occurs at an earlier stage. However, lymphadenectomies are invasive and tumor cells may be overlooked during evaluation.There are limited approved biomarkers for predicting lymph node metastasis with squamous cell carcinomas of the lung (LSCC).MethodsGenome data of 60 tumor-adjacent samples were downloaded from Genome Expression Omnibus. We identified over-expressed HUB genes using Cytoscape as key prognostic markers. The selected markers were further evaluated based on gene ontology and overall expression levels compared to normal tissue using The Cancer Genome Atlas. We further validated these results using clinical biopsy tissue taken from squamous cell carcinoma patients.ResultsAnalysis of the genome expression data resulted in 13 relevant hub genes that were differentially expressed in cancerous samples. All of these genes are associated with collagen biosynthesis within the tumor microenvironment. We chose Collagen Type 1 Alpha 1 (COL1A1) as the most relevant prognostic marker due to its high number of pathway connections and over expression in the tumor microenvironment compared to the other 12 genes. Additionally, based on analysis of The Cancer Genome Atlas, tumors with higher levels of COL1A1 expression are associated with poorer overall survival. Finally, evaluation of clinical biopsy samples suggests that overexpression of COL1A1 in the LSCC microenvironment highly correlates with lymph node metastasis. These results suggest COL1A1 is a clinically relevant marker that should be used to justify lymphadenectomies. creator: Siyuan Dong creator: Peiyao Zhu creator: Shuguang Zhang uri: https://doi.org/10.7717/peerj.10089 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Dong et al. title: The role of m6A-related genes in the prognosis and immune microenvironment of pancreatic adenocarcinoma link: https://peerj.com/articles/9602 last-modified: 2020-09-28 description: BackgroundPancreatic adenocarcinoma (PAAD) is among the most lethal diseases and has a dismal prognosis; however, efficient treatment is currently limited. Several studies have observed epigenetic variation during tumorigenesis, suggesting the potential role of RNA methylation, especially N6-methyladenosine (m6A) modification, as a novel epigenetic modification mediating PAAD prognosis.MethodsThe expression levels of m6A-related genes were downloaded from The Cancer Genome Atlas-Pancreatic Adenocarcinoma (TCGA) and Genotype-Tissue Expression (GTEx) projects, and the findings were validated in four Expression Omnibus (GEO) datasets. A predictive model was constructed using a lasso regression and evaluated by a survival analysis and receiver operating characteristic curve. Consensus clustering identified two distinct subgroups with different immune activity signatures based on the expression pattern of m6A-related genes. The relationship between the mutation state of m6A-related genes and infiltration of immune cells was established and visualized using Tumor Immune Estimation Resource (https://cistrome.shinyapps.io/timer/).ResultsFourteen of twenty-one m6A-related genes were differentially expressed between PAAD and normal tissues in TCGA-GTEx cohort. Among these genes, HNRNPC, IGF2BP2 and YTHDF1 were further validated in four GEO datasets. Moreover, an m6A-based model exhibited moderate accuracy in predicting overall survival in PAAD samples. Additionally, potential m6A modification targets were screened by selecting genes from a set of 23,391 genes that not only harbored the most m6A-modified sites but also showed a robust correlation with PAAD survival. Moreover, we correlated the expression level of m6A-related genes with the immune microenvironment of pancreatic cancer for the first time. Specifically, both arm-level gain and deletion of ALKBH5 decreased the infiltration of CD8+T cells (P < 0.05 and P < 0.01, respectively).ConclusionCollectively, our findings suggest a novel anticancer strategy for restoring balanced RNA methylation in tumor cells and guide clinical physicians in developing a new practical approach for considering the impact of related genes on prognosis. creator: Rong Tang creator: Yiyin Zhang creator: Chen Liang creator: Jin Xu creator: Qingcai Meng creator: Jie Hua creator: Jiang Liu creator: Bo Zhang creator: Xianjun Yu creator: Si Shi uri: https://doi.org/10.7717/peerj.9602 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Tang et al. title: No one-size-fits-all solution to clean GBIF link: https://peerj.com/articles/9916 last-modified: 2020-09-28 description: Species occurrence records provide the basis for many biodiversity studies. They derive from georeferenced specimens deposited in natural history collections and visual observations, such as those obtained through various mobile applications. Given the rapid increase in availability of such data, the control of quality and accuracy constitutes a particular concern. Automatic filtering is a scalable and reproducible means to identify potentially problematic records and tailor datasets from public databases such as the Global Biodiversity Information Facility (GBIF; http://www.gbif.org), for biodiversity analyses. However, it is unclear how much data may be lost by filtering, whether the same filters should be applied across all taxonomic groups, and what the effect of filtering is on common downstream analyses. Here, we evaluate the effect of 13 recently proposed filters on the inference of species richness patterns and automated conservation assessments for 18 Neotropical taxa, including terrestrial and marine animals, fungi, and plants downloaded from GBIF. We find that a total of 44.3% of the records are potentially problematic, with large variation across taxonomic groups (25–90%). A small fraction of records was identified as erroneous in the strict sense (4.2%), and a much larger proportion as unfit for most downstream analyses (41.7%). Filters of duplicated information, collection year, and basis of record, as well as coordinates in urban areas, or for terrestrial taxa in the sea or marine taxa on land, have the greatest effect. Automated filtering can help in identifying problematic records, but requires customization of which tests and thresholds should be applied to the taxonomic group and geographic area under focus. Our results stress the importance of thorough recording and exploration of the meta-data associated with species records for biodiversity research. creator: Alexander Zizka creator: Fernanda Antunes Carvalho creator: Alice Calvente creator: Mabel Rocio Baez-Lizarazo creator: Andressa Cabral creator: Jéssica Fernanda Ramos Coelho creator: Matheus Colli-Silva creator: Mariana Ramos Fantinati creator: Moabe F. Fernandes creator: Thais Ferreira-Araújo creator: Fernanda Gondim Lambert Moreira creator: Nathália Michellyda Cunha Santos creator: Tiago Andrade Borges Santos creator: Renata Clicia dos Santos-Costa creator: Filipe C. Serrano creator: Ana Paula Alves da Silva creator: Arthur de Souza Soares creator: Paolla Gabryelle Cavalcante de Souza creator: Eduardo Calisto Tomaz creator: Valéria Fonseca Vale creator: Tiago Luiz Vieira creator: Alexandre Antonelli uri: https://doi.org/10.7717/peerj.9916 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zizka et al. title: Identification of an 8-miRNA signature as a potential prognostic biomarker for glioma link: https://peerj.com/articles/9943 last-modified: 2020-09-28 description: BackgroundGlioma is the most common form of primary malignant intracranial tumor.MethodsIn the current study, miRNA matrix were obtained from the Chinese Glioma Genome Atlas (CGGA), and then univariate Cox regression analysis and Lasso regression analysis were utilized to select candidate miRNAs and multivariate Cox regression analysis was applied to establish a miRNA signature for predicting overall survival (OS) of glioma. The signature was assessed with the area under the curve (AUC) of the receiver operating characteristic curve (ROC) and validated by data from Gene Expression Omnibus (GEO).ResultsEight miRNAs (miR-1246, miR-148a, miR-150, miR-196a, miR-338-3p, miR-342-5p, miR-548h and miR-645) were included in the miRNA signature. The AUC of ROC analysis for 1- and 3-year OS in the CGGA dataset was 0.747 and 0.905, respectively. In the GEO dataset, The AUC for 1- and 3-year was 0.736 and 0.809, respectively. The AUC in both the CGGA and GEO datasets was similar to that based on WHO 2007 classification (0.736 and 0.799) and WHO 2016 classification (0.663 and 0.807). Additionally, Kaplan–Meier plot revealed that high-risk score patients had a poorer clinical outcome. Multivariate Cox regression analysis suggested that the miRNA signature was an independent prognosis-related factor [HR: 6.579, 95% CI [1.227−35.268], p = 0.028].ConclusionOn the whole, in the present study, based on eight miRNAs, a novel prognostic signature was developed for predicting the 1- and 3- year survival rate in glioma. The results may be conducive to predict the precise prognosis of glioma and to elucidate the underlying molecular mechanisms. However, further experimental researches of miRNAs are needed to validate the findings of this study. creator: Baowei Ji creator: Lihua Chen creator: Qiang Cai creator: Qiao Guo creator: Zhibiao Chen creator: Du He uri: https://doi.org/10.7717/peerj.9943 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ji et al. title: Isolation and characterization of a motility-defective mutant of Euglena gracilis link: https://peerj.com/articles/10002 last-modified: 2020-09-28 description: Euglena gracilis is a green photosynthetic microalga that swims using its flagellum. This species has been used as a model organism for over half a century to study its metabolism and the mechanisms of its behavior. The development of mass-cultivation technology has led to E. gracilis application as a feedstock in various products such as foods. Therefore, breeding of E. gracilis has been attempted to improve the productivity of this feedstock for potential industrial applications. For this purpose, a characteristic that preserves the microalgal energy e.g., reduces motility, should be added to the cultivars. The objective of this study was to verify our hypothesis that E. gracilis locomotion-defective mutants are suitable for industrial applications because they save the energy required for locomotion. To test this hypothesis, we screened for E. gracilis mutants from Fe-ion-irradiated cell suspensions and established a mutant strain, ${\mathrm{M}}_{3}^{-}$M3−ZFeL, which shows defects in flagellum formation and locomotion. The mutant strain exhibits a growth rate comparable to that of the wild type when cultured under autotrophic conditions, but had a slightly slower growth under heterotrophic conditions. It also stores 1.6 times the amount of paramylon, a crystal of β-1,3-glucan, under autotrophic culture conditions, and shows a faster sedimentation compared with that of the wild type, because of the deficiency in mobility and probably the high amount of paramylon accumulation. Such characteristics make E. gracilis mutant cells suitable for cost-effective mass cultivation and harvesting. creator: Shuki Muramatsu creator: Kohei Atsuji creator: Koji Yamada creator: Kazunari Ozasa creator: Hideyuki Suzuki creator: Takuto Takeuchi creator: Yuka Hashimoto-Marukawa creator: Yusuke Kazama creator: Tomoko Abe creator: Kengo Suzuki creator: Osamu Iwata uri: https://doi.org/10.7717/peerj.10002 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Muramatsu et al. title: Differing physiological and behavioral responses to anthropogenic factors between resident and non-resident African elephants at Mpala Ranch, Laikipia County, Kenya link: https://peerj.com/articles/10010 last-modified: 2020-09-28 description: BackgroundHeterogeneous landscapes like those of Laikipia County, Kenya consist of a mosaic of land-use types, which may exert differential physiological effects on elephants that occupy and traverse them. Understanding behavioral and physiological states of wild African elephants in response to the challenges of living in human-dominated landscapes is therefore important for conservation managers to evaluate risks imposed by elephants to humans and vice versa. Several conservation physiology tools have been developed to assess how animals respond to both natural and anthropogenic changes, and determine biological impacts. This study investigated how migratory and avoidance behavioral to vehicle presence, and vegetation quality affected fecal glucocorticoid (GC) metabolite (FGM) concentrations in African elephants at Mpala Ranch, Laikipia County, Kenya.MethodsThe study compared adrenal glucocorticoid activity of resident elephants that live within Mpala (n = 57) and non-resident elephants whose space use patterns overlap several ranches (n = 99) in Laikipia County, Kenya. Fecal samples were collected for a 4-month period between April and August for analysis of FGM concentrations. Behavioral reactions to research vehicles and body condition also were assessed. Satellite images from Terra Moderate Resolution Imaging (MODIS MOD13Q1) were downloaded and processed using Google Earth Engine to calculate a Normalized Difference Vegetation Index (NDVI) as a measure of vegetation quality.ResultsAs expected, there was a positive correlation between avoidance behavior to vehicle presence and FGM concentrations in both resident and non-resident elephants, whereas there was an inverse relationship between FGM concentrations and NDVI values. Our study also found a positive influence of age on the FGM concentrations, but there were no relationships between FGM and sex, social group type, herd size, and body condition. However, contrary to our expectations, resident elephants had higher FGM concentrations than non-residents.DiscussionFindings reveal elephants with stronger avoidance responses to research vehicles and resident elephants with relatively smaller home ranges exhibited higher FGM concentrations within the Mpala Ranch, Kenya and surrounding areas. Higher vegetative quality within the ranges occupied by non-resident elephants in Laikipia may be one reason for lower FGM, and an indication that the non-residents are tracking better forage quality to improve energy balance and reduce overall GC output. Additionally, our study found a positive influence of age, but no other demographic variables on FGM concentrations. Finally, adrenal glucocorticoid activity was inversely related to vegetative quality. Our findings can help conservation managers better understand how behavior and environment influences the physiological states of African elephants, and how management intervention might mitigate negative human–elephant interactions. creator: Sandy Oduor creator: Janine Brown creator: Geoffrey M. Macharia creator: Nicole Boisseau creator: Suzan Murray creator: Paul Obade uri: https://doi.org/10.7717/peerj.10010 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Oduor et al. title: Pyruvate is required for catecholamine-stimulated growth of different strains of Campylobacter jejuni link: https://peerj.com/articles/10011 last-modified: 2020-09-28 description: Humans and food-producing animals are constantly exposed to and affected by stress. As a consequence of stress, the release of stress-related catecholamines, such as norepinephrine (NE) and dopamine (DA), from nerve terminals in the gastrointestinal tract potentiates both the growth and the virulence of pathogenic bacteria. This may lead to the enhancement of gastrointestinal infections in humans or food-producing animals. Compared with foodborne bacterial pathogens such as Escherichia coli and Salmonella spp., less is known about the effect of stress catecholamines on Campylobacter jejuni subsp. jejuni. The present study focuses on the effect(s) of stress catecholamines DA and NE in iron-restricted media and how they affect the growth of different C. jejuni strains NCTC 11168, 81–176, and ML2126. Results demonstrated that DA- and NE-enhanced growth of C. jejuni in iron-restricted media may involve different mechanisms that cannot be explained by current understanding which relies on catecholamine-mediated iron delivery. Specifically, we found that DA-enhanced growth requires pyruvate, whereas NE-enhanced growth does not. We further report significant strain-specific dependence of C. jejuni growth on various catecholamines in the presence or absence of pyruvate. These data provide novel insights into the effect(s) of stress catecholamines on the in vitro growth of C. jejuni in iron-restricted environments, such as the intestinal tract. They suggest a mechanism by which stress-related catecholamines affect the growth of C. jejuni in the intestinal tract of food-producing animals, which in turn may influence colonization and transmission to humans. creator: Meicen Liu creator: Mark Lyte uri: https://doi.org/10.7717/peerj.10011 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Liu and Lyte title: The utility of MEWS for predicting the mortality in the elderly adults with COVID-19: a retrospective cohort study with comparison to other predictive clinical scores link: https://peerj.com/articles/10018 last-modified: 2020-09-28 description: BackgroundOlder adults have been reported to be a population with high-risk of death in the COVID-19 outbreak. Rapid detection of high-risk patients is crucial to reduce mortality in this population. The aim of this study was to evaluate the prognositc accuracy of the Modified Early Warning Score (MEWS) for in-hospital mortality in older adults with COVID-19.MethodsA retrospective cohort study was conducted in Wuhan Hankou Hospital in China from 1 January 2020 to 29 February 2020. Receiver operating characteristic (ROC) analysis was used to evaluate the predictive value of MEWS, Acute Physiology and Chronic Health Evaluation II (APACHE II), Sequential Organ Function Assessment (SOFA), quick Sequential Organ Function Assessment (qSOFA), Pneumonia Severity Index (PSI), Combination of Confusion, Urea, Respiratory Rate, Blood Pressure, and Age ≥65 (CURB-65), and the Systemic Inflammatory Response Syndrome Criteria (SIRS) for in-hospital mortality. Logistic regression models were performed to detect the high-risk older adults with COVID-19.ResultsAmong the 235 patients included in this study, 37 (15.74%) died and 131 (55.74%) were male, with an average age of 70.61 years (SD 8.02). ROC analysis suggested that the capacity of MEWS in predicting in-hospital mortality was as good as the APACHE II, SOFA, PSI and qSOFA (Difference in AUROC: MEWS vs. APACHE II, −0.025 (95% CI [−0.075 to 0.026]); MEWS vs. SOFA, −0.013 (95% CI [−0.049 to 0.024]); MEWS vs. PSI, −0.015 (95% CI [−0.065 to 0.035]); MEWS vs. qSOFA, 0.024 (95% CI [−0.029 to 0.076]), all P > 0.05), but was significantly higher than SIRS and CURB-65 (Difference in AUROC: MEWS vs. SIRS, 0.218 (95% CI [0.156–0.279]); MEWS vs. CURB-65, 0.064 (95% CI [0.002–0.125]), all P < 0.05). Logistic regression models implied that the male patients (≥75 years) had higher risk of death than the other older adults (estimated coefficients: 1.16, P = 0.044). Our analysis further suggests that the cut-off points of the MEWS score for the male patients (≥75 years) subpopulation and the other elderly patients should be 2.5 and 3.5, respectively.ConclusionsMEWS is an efficient tool for rapid assessment of elderly COVID-19 patients. MEWS has promising performance in predicting in-hospital mortality and identifying the high-risk group in elderly patients with COVID-19. creator: Lichun Wang creator: Qingquan Lv creator: Xiaofei Zhang creator: Binyan Jiang creator: Enhe Liu creator: Chaoxing Xiao creator: Xinyang Yu creator: Chunhua Yang creator: Lei Chen uri: https://doi.org/10.7717/peerj.10018 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Wang et al. title: Predicting CoVID-19 community mortality risk using machine learning and development of an online prognostic tool link: https://peerj.com/articles/10083 last-modified: 2020-09-28 description: BackgroundThe recent pandemic of CoVID-19 has emerged as a threat to global health security. There are very few prognostic models on CoVID-19 using machine learning.ObjectivesTo predict mortality among confirmed CoVID-19 patients in South Korea using machine learning and deploy the best performing algorithm as an open-source online prediction tool for decision-making.Materials and MethodsMortality for confirmed CoVID-19 patients (n = 3,524) between January 20, 2020 and May 30, 2020 was predicted using five machine learning algorithms (logistic regression, support vector machine, K nearest neighbor, random forest and gradient boosting). The performance of the algorithms was compared, and the best performing algorithm was deployed as an online prediction tool.ResultsThe logistic regression algorithm was the best performer in terms of discrimination (area under ROC curve = 0.830), calibration (Matthews Correlation Coefficient = 0.433; Brier Score = 0.036) and. The best performing algorithm (logistic regression) was deployed as the online CoVID-19 Community Mortality Risk Prediction tool named CoCoMoRP (https://ashis-das.shinyapps.io/CoCoMoRP/).ConclusionsWe describe the development and deployment of an open-source machine learning tool to predict mortality risk among CoVID-19 confirmed patients using publicly available surveillance data. This tool can be utilized by potential stakeholders such as health providers and policymakers to triage patients at the community level in addition to other approaches. creator: Ashis Kumar Das creator: Shiba Mishra creator: Saji Saraswathy Gopalan uri: https://doi.org/10.7717/peerj.10083 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Das et al. title: Suitability of native milkweed (Asclepias) species versus cultivars for supporting monarch butterflies and bees in urban gardens link: https://peerj.com/articles/9823 last-modified: 2020-09-25 description: Public interest in ecological landscaping and gardening is fueling a robust market for native plants. Most plants available to consumers through the horticulture trade are cultivated forms that have been selected for modified flowers or foliage, compactness, or other ornamental characteristics. Depending on their traits, some native plant cultivars seem to support pollinators, specialist insect folivores, and insect-based vertebrate food webs as effectively as native plant species, whereas others do not. There is particular need for information on whether native cultivars can be as effective as true or “wild-type” native species for supporting specialist native insects of conservation concern. Herein we compared the suitability of native milkweed species and their cultivars for attracting and supporting one such insect, the iconic monarch butterfly (Danaus plexippus L.), as well as native bees in urban pollinator gardens. Wild-type Asclepias incarnata L. (swamp milkweed) and Asclepias tuberosa L. (butterfly milkweed) and three additional cultivars of each that vary in stature, floral display, and foliage color were grown in a replicated common garden experiment at a public arboretum. We monitored the plants for colonization by wild monarchs, assessed their suitability for supporting monarch larvae in greenhouse trials, measured their defensive characteristics (leaf trichome density, latex, and cardenolide levels), and compared the proportionate abundance and diversity of bee families and genera visiting their blooms. Significantly more monarch eggs and larvae were found on A. incarnata than A. tuberosa in both years, but within each milkweed group, cultivars were colonized to the same extent as wild types. Despite some differences in defense allocation, all cultivars were as suitable as wild-type milkweeds in supporting monarch larval growth. Five bee families and 17 genera were represented amongst the 2,436 total bees sampled from blooms of wild-type milkweeds and their cultivars in the replicated gardens. Bee assemblages of A. incarnata were dominated by Apidae (Bombus, Xylocopa spp., and Apis mellifera), whereas A. tuberosa attracted relatively more Halictidae (especially Lasioglossum spp.) and Megachilidae. Proportionate abundance of bee families and genera was generally similar for cultivars and their respective wild types. This study suggests that, at least in small urban gardens, milkweed cultivars can be as suitable as their parental species for supporting monarch butterflies and native bees. creator: Adam M. Baker creator: Carl T. Redmond creator: Stephen B. Malcolm creator: Daniel A. Potter uri: https://doi.org/10.7717/peerj.9823 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Baker et al. title: Dung beetle species introductions: when an ecosystem service provider transforms into an invasive species link: https://peerj.com/articles/9872 last-modified: 2020-09-25 description: Dung beetle introduction programmes were designed to accelerate exotic livestock dung degradation and to control dung breeding pestiferous flies and livestock parasites. The introduction programmes provided exotic dung beetle species with an opportunity to cross natural barriers and spread beyond their native range. There are no reports that explain what probable adaptation mechanisms enable particular dung beetle species to be the most successful invader. Here we identify the morphological, biological, physiological, ecological and behavioural attributes of the four most widespread and successful dung beetle species in introduced areas on a global scale in relation to the assumption that these species are different from other exotic and native dung beetles. We have recognised Digitonthophagus gazella (Fabricius), Onthophagus taurus (Schreber), Euoniticellus intermedius (Reiche) and Aphodius fimetarius (Linnaeus) as the most successful invaders based on their spread, predominance, distribution range and the reports of invasion. Each of these four species has different natural history traits that increase their fitness making them successful invaders. D. gazella has high fecundity and spreading ability, can instantly locate and colonise fresh and nutritious dung, and has a broad thermal window. O. taurus has morphological plasticity, high fecundity, high brood survival rate due to bi-parenting, and is adapted to extreme thermal and moisture conditions. E. intermedius has remnant-dung feeding abilities, a wide thermal window, functioning best at upper-temperature levels, and successful breeding and survival abilities at extremely low soil moisture conditions. A. fimetarius is small-sized, has high breeding and dispersal abilities, and is adapted to lower thermal and upper moisture extremes and variable soil conditions. Discussed here are perspectives on adaptive attributes of dung beetle species that are important to consider during their selection for redistributions. We have elaborated on the fitness and success characteristics of the four species individually. Further, we recommend a prior-introduction baseline monitoring of native dung beetle assemblages so as to evaluate the future impact of exotic dung beetle introductions on the recipient ecosystem. creator: Min R. Pokhrel creator: Stuart C. Cairns creator: Nigel R. Andrew uri: https://doi.org/10.7717/peerj.9872 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Pokhrel et al. title: Exploring the role of individual learning in animal tool-use link: https://peerj.com/articles/9877 last-modified: 2020-09-25 description: The notion that tool-use is unique to humans has long been refuted by the growing number of observations of animals using tools across various contexts. Yet, the mechanisms behind the emergence and sustenance of these tool-use repertoires are still heavily debated. We argue that the current animal behaviour literature is biased towards a social learning approach, in which animal, and in particular primate, tool-use repertoires are thought to require social learning mechanisms (copying variants of social learning are most often invoked). However, concrete evidence for a widespread dependency on social learning is still lacking. On the other hand, a growing body of observational and experimental data demonstrates that various animal species are capable of acquiring the forms of their tool-use behaviours via individual learning, with (non-copying) social learning regulating the frequencies of the behavioural forms within (and, indirectly, between) groups. As a first outline of the extent of the role of individual learning in animal tool-use, a literature review of reports of the spontaneous acquisition of animal tool-use behaviours was carried out across observational and experimental studies. The results of this review suggest that perhaps due to the pervasive focus on social learning in the literature, accounts of the individual learning of tool-use forms by naïve animals may have been largely overlooked, and their importance under-examined. creator: Elisa Bandini creator: Claudio Tennie uri: https://doi.org/10.7717/peerj.9877 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Bandini and Tennie title: Genome-wide analysis of PRR gene family uncovers their roles in circadian rhythmic changes and response to drought stress in Gossypium hirsutum L. link: https://peerj.com/articles/9936 last-modified: 2020-09-25 description: BackgroundThe circadian clock not only participates in regulating various stages of plant growth, development and metabolism, but confers plant environmental adaptability to stress such as drought. Pseudo-Response Regulators (PRRs) are important component of the central oscillator (the core of circadian clock) and play a significant role in plant photoperiod pathway. However, no systematical study about this gene family has been performed in cotton.MethodsPRR genes were identified in diploid and tetraploid cotton using bioinformatics methods to investigate their homology, duplication and evolution relationship. Differential gene expression, KEGG enrichment analysis and qRT-PCR were conducted to analyze PRR gene expression patterns under diurnal changes and their response to drought stress.ResultsA total of 44 PRR family members were identified in four Gossypium species, with 16 in G. hirsutum, 10 in G. raimondii, and nine in G. barbadense as well as in G. arboreum. Phylogenetic analysis indicated that PRR proteins were divided into five subfamilies and whole genome duplication or segmental duplication contributed to the expansion of Gossypium PRR gene family. Gene structure analysis revealed that members in the same clade are similar, and multiple cis-elements related to light and drought stress response were enriched in the promoters of GhPRR genes. qRT-PCR results showed that GhPRR genes transcripts presented four expression peaks (6 h, 9 h, 12 h, 15 h) during 24 h and form obvious rhythmic expression trend. Transcriptome data with PEG treatment, along with qRT-PCR verification suggested that members of clade III (GhPRR5a, b, d) and clade V (GhPRR3a and GhPRR3c) may be involved in drought response. This study provides an insight into understanding the function of PRR genes in circadian rhythm and in response to drought stress in cotton. creator: Jingjing Wang creator: Zhaohai Du creator: Xuehan Huo creator: Juan Zhou creator: Yu Chen creator: Jingxia Zhang creator: Ao Pan creator: Xiaoyang Wang creator: Furong Wang creator: Jun Zhang uri: https://doi.org/10.7717/peerj.9936 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al. title: Analysis of the infant gut microbiome reveals metabolic functional roles associated with healthy infants and infants with atopic dermatitis using metaproteomics link: https://peerj.com/articles/9988 last-modified: 2020-09-25 description: The infant gut microbiome consists of a complex and diverse microbial community. Comprehensive taxonomic and metabolic functional knowledge about microbial communities supports medical and biological applications, such as fecal diagnostics. Among the omics approaches available for the investigation of microbial communities, metaproteomics-based analysis is a very powerful approach; under this method, the activity of microbial communities is explored by investigating protein expression within a sample. Through use of metaproteomics, this study aimed to investigate the microbial community composition of the infant gut to identify different key proteins playing metabolic functional roles in the microbiome of healthy infants and infants with atopic dermatitis in a Thai population-based birth cohort. Here, 18 fecal samples were analyzed by liquid chromatography-tandem mass spectrometry to conduct taxonomic, functional, and pathway-based protein annotation. Accordingly, 49,973 annotated proteins out of 68,232 total proteins were investigated in gut microbiome samples and compared between the healthy and atopic dermatitis groups. Through differentially expressed proteins (DEPs) analysis, 130 significant DEPs were identified between the healthy and atopic dermatitis groups. Among these DEPs, eight significant proteins were uniquely expressed in the atopic dermatitis group. For instance, triosephosphate isomerase (TPI) in Bifidobacteriaceae in the genus Alloscardovia and demethylmenaquinone methyltransferase (DMM) in Bacteroides were shown to potentially play metabolic functional roles related to disease. PPI network analysis revealed seven reporter proteins showing metabolic alterations between the healthy and disease groups associated with the biosynthesis of ubiquinone and other quinones as well as the energy supply. This study serves as a scaffold for microbial community-wide metabolic functional studies of the infant gut microbiome in relation to allergic disease. creator: Amornthep Kingkaw creator: Massalin Nakphaichit creator: Narissara Suratannon creator: Sunee Nitisinprasert creator: Chantha Wongoutong creator: Pantipa Chatchatee creator: Sucheewin Krobthong creator: Sawanya Charoenlappanit creator: Sittiruk Roytrakul creator: Wanwipa Vongsangnak uri: https://doi.org/10.7717/peerj.9988 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kingkaw et al. title: The mechanism and detection of alternative splicing events in circular RNAs link: https://peerj.com/articles/10032 last-modified: 2020-09-25 description: Circular RNAs (circRNAs) are considered as functional biomolecules with tissue/development-specific expression patterns. Generally, a single gene may generate multiple circRNA variants by alternative splicing, which contain different combinations of exons and/or introns. Due to the low abundance of circRNAs as well as overlapped with their linear counterparts, circRNA enrichment protocol is needed prior to sequencing. Compared with numerous algorithms, which use back-splicing reads for detection and functional characterization of circRNAs, original bioinformatic analyzing tools have been developed to large-scale determination of full-length circRNAs and accurate quantification. This review provides insights into the complexity of circRNA biogenesis and surveys the recent progresses in the experimental and bioinformatic methodologies that focus on accurately full-length circRNAs identification. creator: Xiaohan Li creator: Bing Zhang creator: Fuyu Li creator: Kequan Yu creator: Yunfei Bai uri: https://doi.org/10.7717/peerj.10032 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Li et al. title: Global gene expression analyses of the alkamide-producing plant Heliopsis longipes supports a polyketide synthase-mediated biosynthesis pathway link: https://peerj.com/articles/10074 last-modified: 2020-09-25 description: BackgroundAlkamides are plant-specific bioactive molecules. They are low molecular weight N-substituted α-unsaturated acyl amides that display biological explicit activities in different organisms from bacteria, fungi, insects to mammals and plants. The acyl chain has been proposed to be biosynthesized from a fatty acid; however, this has not been demonstrated yet. Heliopsis longipes (Asteraceae) accumulates in root a C10 alkamide called affinin in its roots, but not in leaves. The closely related species Heliopsis annua does not produce alkamides. To elucidate the biosynthetic pathway of the alkamides acyl chain, a comparative global gene expression analysis contrasting roots and leaves of both species was performed.MethodsTranscriptomics analysis allowed to identify genes highly expressed in H. longipes roots, but not in tissues and species that do not accumulate alkamides. The first domain searched was the Ketosynthase (KS) domain. The phylogenetic analysis using sequences of the KS domain of FAS and PKS from different organisms, revealed that KS domains of the differentially expressed transcripts in H. longipes roots and the KS domain found in transcripts of Echinacea purpurea, another alkamides producer species, were grouped together with a high bootstrap value of 100%, sharing great similarity. Among the annotated transcripts, we found some coding for the enzymatic domains KS, AT, ACP, DH, OR and TE, which presented higher expression in H. longipes roots than in leaves. The expression level of these genes was further evaluated by qRT-PCR. All unigenes tested showed higher expression in H. longipes roots than in any the other samples. Based on this and considering that the acyl chain of affinin presents unsaturated bonds at even C numbers, we propose a new putative biosynthesis pathway mediated by a four modules polyketide synthase (PKS).ResultsThe global gene expression analysis led to the selection of a set of candidate genes involved in the biosynthesis of the acyl chain of affinin, suggesting that it may be performed by a non-iterative, partially reductive, four module type I PKS complex (PKS alk) previously thought to be absent from the plant kingdom. creator: Génesis V. Buitimea-Cantúa creator: Nayelli Marsch-Martinez creator: Patricia Ríos-Chavez creator: Alfonso Méndez-Bravo creator: Jorge Molina-Torres uri: https://doi.org/10.7717/peerj.10074 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Buitimea-Cantúa et al. title: Life history and habitat do not mediate temporal changes in body size due to climate warming in rodents link: https://peerj.com/articles/9792 last-modified: 2020-09-24 description: Temporal changes in body size have been documented in a number of vertebrate species, with different contested drivers being suggested to explain these changes. Among these are climate warming, resource availability, competition, predation risk, human population density, island effects and others. Both life history traits (intrinsic factors such as lifespan and reproductive rate) and habitat (extrinsic factors such as vegetation type, latitude and elevation) are expected to mediate the existence of a significant temporal response of body size to climate warming but neither have been widely investigated. Using examples of rodents, we predicted that both life history traits and habitat might explain the probability of temporal response using two tests of this hypothesis. Firstly, taking advantage of new data from museum collections spanning the last 106 years, we investigated geographical and temporal variation in cranial size (a proxy for body size) in six African rodent species of two murid subfamilies (Murinae and Gerbillinae) of varying life history, degree of commensality, range size, and habitat. Two species, the commensal Mastomys natalensis, and the non-commensal Otomys unisulcatus showed significant temporal changes in body size, with the former increasing and the latter decreasing, in relation with climate warming. Commensalism could explain the increase in size with time due to steadily increasing food availability through increased agricultural production. Apart from this, we found no general life history or habitat predictors of a temporal response in African rodents. Secondly, in order to further test this hypothesis, we incorporated our data into a meta-analysis based on published literature on temporal responses in rodents, resulting in a combined dataset for 50 species from seven families worldwide; among these, 29 species showed no significant change, eight showed a significant increase in size, and 13 showed a decline in size. Using a binomial logistic regression model for these metadata, we found that none of our chosen life history or habitat predictors could significantly explain the probability of a temporal response to climate warming, reinforcing our conclusion based on the more detailed data from the six African species. creator: Aluwani Nengovhela creator: Christiane Denys creator: Peter J. Taylor uri: https://doi.org/10.7717/peerj.9792 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Nengovhela et al. title: Forest before the trees in the aquatic world: global and local processing in teleost fishes link: https://peerj.com/articles/9871 last-modified: 2020-09-24 description: BackgroundThe study of illusory phenomena is important to understanding the similarities and differences between mammals and birds’ perceptual systems. In recent years, the analysis has been enlarged to include cold-blooded vertebrates, such as fish. However, evidence collected in the literature have drawn a contradictory picture, with some fish species exhibiting a human-like perception of visual illusions and others showing either a reversed perception or no susceptibility to visual illusions. The possibility exists that these mixed results relate to interspecific variability in perceptual grouping mechanisms. Therefore, we studied whether fish of five species exhibit a spontaneous tendency to prioritize a global analysis of the visual scene—also known as global-to-local precedence—instead of focusing on local details.MethodsUsing Navon-like stimuli (i.e., larger recognisable shapes composed of copies of smaller different shapes), we trained redtail splitfin, zebrafish, angelfish, Siamese fighting fish and three spot gourami to discriminate between two figures characterized by congruency between global and local information (a circle made by small circles and a cross made by small crosses). In the test phase, we put global and local cues (e.g., a circle made by small crosses) into contrast to see whether fish spontaneously rely on global or local information.ResultsLike humans, fish seem to have an overall global-to-local precedence, with no significant differences among the species. However, looking at the species-specific level, only four out of five species showed a significant global-to-local precedence, and at different degrees. Because these species are distantly related and occupy a broad spectrum of ecological adaptations, we suggest that the tendency to prioritize a global analysis of visual inputs may be more similar in fish than expected by the mixed results of visual illusion studies. creator: Maria Santacà creator: Maria Elena Miletto Petrazzini creator: Marco Dadda creator: Christian Agrillo uri: https://doi.org/10.7717/peerj.9871 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Santacà et al. title: Distribution, habitat suitability, conservation state and natural history of endangered salamander Bolitoglossa pandi link: https://peerj.com/articles/9901 last-modified: 2020-09-24 description: BackgroundPandi’s mushroom-tongue salamander (Bolitoglossa pandi) is one of the threatened amphibians in South America, as well as a flagship species for the Colombian conservation agenda. This species is endemic to the Andean cloud forests of the western slope of the Cordillera Oriental of Colombia, occurring only in the department of Cundinamarca within a narrow elevational range. At night, B. pandi can be seen perching on the upper side of leaves at heights ranging from ground level to 2.5 m. During the day, it can be found under leaf litter or cover objects. Few studies have provided relevant information that can help the Colombian government to formulate lines of action for the conservation of this species; consequently, its threat assessments so far have been based on very limited information.MethodsWe conducted surveys for salamanders in four municipalities of Cundinamarca, Colombia, using two approaches: visual encounter surveys (Guaduas and Villeta) and the basic sampling protocol for single-species occupancy modeling (Supatá and Venecia). Multivariate analyses were employed to explore the correlation between habitat structure and natural history traits, abundance, and detection/non-detection of B. pandi. We evaluated the B. pandi activity pattern through kernel density curves for each sampling occasion and explored the variability of salamander abundance during their activity period by performing a nested ANOVA.ResultsWe report the discovery of two new populations of B. pandi, which represent the most northwestern records known. A significant correlation between body length, body mass, and habitat structure was observed. Multivariate analyses indicated that leaf litter depth, mean temperature, percent vegetation cover, and altitude were the habitat variables that together explained 60.3% of the B. pandi abundance variability, as well as the main determinants of its optimal habitat. Bolitoglossa pandi exhibits an activity pattern characterized by two main activity peaks, in which niche time-partitioning was observed. Across the surveyed area, we found a healthy, stable, highly dense population of B. pandi (>1,300 individuals), with seasonal variability between development stages.DiscussionGiven the high habitat specificity of B. pandi, the species is highly vulnerable to local changes. Thus, we recommend that B. pandi be retained as Endangered (EN) on the IUCN Red List, based on the IUCN Criterion B, given its restricted extent of occurrence (ca. 2,500 km2) and the ongoing threats from agriculture, cattle ranching, logging, and urban development, which continue to reduce its suitable habitat. creator: Teddy Angarita-Sierra creator: M. Argenis Bonilla-Gómez creator: David A. Sánchez creator: Andres R. Acosta-Galvis creator: Hefzi Medina-Ovalle creator: Anggi Solano-Moreno creator: Simon Ulloa-Rengifo creator: Daniela Guevara-Guevara creator: Juan J. Torres-Ramirez creator: Sebastián Curaca-Fierro creator: Diego M. Cabrera-Amaya creator: Jhon A. Infante-Betancour creator: Luisa F. Londoño-Montaño creator: Diana X. Albarán-Montoya creator: Lesly R. Peña-Baez uri: https://doi.org/10.7717/peerj.9901 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Angarita-Sierra et al. title: Description of the unusual digestive tract of Platax orbicularis and the potential impact of Tenacibaculum maritimum infection link: https://peerj.com/articles/9966 last-modified: 2020-09-24 description: BackgroundEphippidae fish are characterized by a discoid shape with a very small visceral cavity. Among them Platax orbicularis has a high economic potential due to its flesh quality and flesh to carcass ratio. Nonetheless, the development of its aquaculture is limited by high mortality rates, especially due to Tenacibaculum maritimum infection, occurring one to three weeks after the transfer of fishes from bio-secure land-based aquaculture system to the lagoon cages for growth. Among the lines of defense against this microbial infection, the gastrointestinal tract (GIT) is less studied. The knowledge about the morphofunctional anatomy of this organ in P. orbicularis is still scarce. Therefore, the aims of this study are to characterize the GIT in non-infected P. orbicularis juveniles to then investigate the impact of T. maritimum on this multifunctional organ.MethodsIn the first place, the morpho-anatomy of the GIT in non-infected individuals was characterized using various histological techniques. Then, infected individuals, experimentally challenged by T. maritimum were analysed and compared to the previously established GIT reference.ResultsThe overlapped shape of the GIT of P. orbicularis is probably due to its constrained compaction in a narrow visceral cavity. Firstly, the GIT was divided into 10 sections, from the esophagus to the rectum. For each section, the structure of the walls was characterized, with a focus on mucus secretions and the presence of the Na+/K+ ATPase pump. An identification key allowing the characterization of the GIT sections using in toto histology is given. Secondly, individuals challenged with T. maritimum exhibited differences in mucus type and proportion and, modifications in the mucosal and muscle layers. These changes could induce an imbalance in the trade-off between the GIT functions which may be in favour of protection and immunity to the disadvantage of nutrition capacities. creator: Maud Alix creator: Eric Gasset creator: Agnes Bardon-Albaret creator: Jean Noel creator: Nelly Pirot creator: Valérie Perez creator: Denis Coves creator: Denis Saulnier creator: Jehan-Hervé Lignot creator: Patricia N. Cucchi uri: https://doi.org/10.7717/peerj.9966 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Alix et al. title: Characterization of a high-resolution breath acetone meter for ketosis monitoring link: https://peerj.com/articles/9969 last-modified: 2020-09-24 description: BackgroundThe ketone bodies beta-hydroxybutyrate (BHB) and acetone are endogenous products of fatty acid metabolism. Although ketone levels can be monitored by measuring either blood BHB or breath acetone, determining the precise correlation between these two measurement methods has been challenging. The purpose of this study is to characterize the performance of a novel portable breath acetone meter (PBAM) developed by Readout, Inc., to compare single versus multiple daily ketone measurements, and to compare breath acetone (BrAce) and blood BHB measurements.MethodsWe conducted a 14-day prospective observational cohort study of 21 subjects attempting to follow either a low-carbohydrate/ketogenic or a standard diet. Subjects were asked to concurrently measure both blood BHB and BrAce five times per day and report the results using an online data entry system. We evaluated the utility of multiple daily measurements by calculating the coefficient of variation (CV) for each daily group of measurements. We calculated the correlation between coincident BrAce and blood BHB measurements using linear ordinary least squares regression analysis. We assessed the ability of the BrAce measurement to accurately predict blood BHB states using receiver operating characteristic (ROC) analysis. Finally, we calculated a daily ketone exposure (DKE) using the area under the curve (AUC) of a ketone concentration versus time graph and compared the DKE of BrAce and blood BHB using linear ordinary least squares regression.ResultsBrAce and blood BHB varied throughout the day by an average of 44% and 46%, respectively. The BrAce measurement accurately predicted whether blood BHB was greater than or less than the following thresholds: 0.3 mM (AUC = 0.898), 0.5 mM (AUC = 0.854), 1.0 mM (AUC = 0.887), and 1.5 mM (AUC = 0.935). Coincident BrAce and blood BHB measurements were moderately correlated with R2 = 0.57 (P < 0.0001), similar to literature reported values. However, daily ketone exposures, or areas under the curve, for BrAce and blood BHB were highly correlated with R2 = 0.80 (P < 0.0001).ConclusionsThe results validated the performance of the PBAM. The BrAce/BHB correlation was similar to literature values where BrAce was measured using highly accurate lab instruments. Additionally, BrAce measurements using the PBAM can be used to predict blood BHB states. The relatively high daily variability of ketone levels indicate that single blood or breath ketone measurements are often not sufficient to assess daily ketone exposure for most users. Finally, although single coincident blood and breath ketone measurements show only a moderate correlation, possibly due to the temporal lag between BrAce and blood BHB, daily ketone exposures for blood and breath are highly correlated. creator: Donald J. Suntrup III creator: Timothy V. Ratto creator: Matt Ratto creator: James P. McCarter uri: https://doi.org/10.7717/peerj.9969 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Suntrup III et al. title: A new species of Scapholeberis Schoedler, 1858 (Anomopoda: Daphniidae: Scapholeberinae) from the Colombian Amazon basin highlighted by DNA barcodes and morphology link: https://peerj.com/articles/9989 last-modified: 2020-09-24 description: BackgroundThe Amazon basin is recognized as one of the most complex and species-rich freshwater environments globally. The diversity of zooplankton here remains unknown, with many species undescribed.MethodsHere, we describe a new species of Scapholeberis Schoedler, 1858 (Cladocera: Anomopoda: Daphniidae: Scapholeberinae) from the Colombian Amazon Basin, collected with recently designed light traps. The description is based on detailed morphology (based on SEM and light microscopy) of parthenogenetic females, ephippial females, males, and molecular data based on the COI gene.ResultsScapholeberis yahuarcaquensis n. sp. has a combination of characters present in Scapholeberis kingi Sars, 1888 and Scapholeberis armata freyiDumont & Pensaert, 1983. These are a trilobate rostrum, with the middle lobe well developed with sides straight to relatively rounded, the presence of an elongated slit frontal head pore, a dorsal pore in the juncture of the cephalic shield and the valves, and a single denticulate membrane at the posterior rim of the valves, with stronger setae in the last third. The unique characters of the parthenogenetic females are ventral sucker with delicate triangles. Each has a filament-like projection in the lamellae’s inner side and an external section forming convex folds with denticle-like projections in the middle zone of the sucker-plate. There is a peculiar pitted sculpture in the ephippial females and a strong projection in the front of it. The male hook on the limb I with a blunt tip, a quirky lamella-like outgrow in the proximal side, and a paddle with well-developed spines scattered on its surface. The ventral sucker-lamellae in the male is much more developed than the female. The COI gene sequences showed an interspecific mean genetic divergence of 16.4% between S. yahuarcaquensis n. sp. and the closest species S. freyi from Mexico, supporting our results. A coalescence analysis and Barcode Index Number also support the new species based on the DNA sequences. New methods of collecting and integrative biology will give important support to recognize the fauna from the Amazon Basin, one of the most important sources of fresh water in the world that remains unknown in many respects. creator: Camilo Andrade-Sossa creator: Lorena Buitron-Caicedo creator: Manuel Elías-Gutiérrez uri: https://doi.org/10.7717/peerj.9989 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Andrade-Sossa et al. title: A model of twenty-three metabolic-related genes predicting overall survival for lung adenocarcinoma link: https://peerj.com/articles/10008 last-modified: 2020-09-24 description: BackgroundThe highest rate of cancer-related deaths worldwide is from lung adenocarcinoma (LUAD) annually. Metabolism was associated with tumorigenesis and cancer development. Metabolic-related genes may be important biomarkers and metabolic therapeutic targets for LUAD.Materials and MethodsIn this study, the gleaned cohort included LUAD RNA-SEQ data from the Cancer Genome Atlas (TCGA) and corresponding clinical data (n = 445). The training cohort was utilized to model construction, and data from the Gene Expression Omnibus (GEO, GSE30219 cohort, n = 83; GEO, GSE72094, n = 393) were regarded as a testing cohort and utilized for validation. First, we used a lasso-penalized Cox regression analysis to build a new metabolic-related signature for predicting the prognosis of LUAD patients. Next, we verified the metabolic gene model by survival analysis, C-index, receiver operating characteristic (ROC) analysis. Univariate and multivariate Cox regression analyses were utilized to verify the gene signature as an independent prognostic factor. Finally, we constructed a nomogram and performed gene set enrichment analysis to facilitate subsequent clinical applications and molecular mechanism analysis.ResultPatients with higher risk scores showed significantly associated with poorer survival. We also verified the signature can work as an independent prognostic factor for LUAD survival. The nomogram showed better clinical application performance for LUAD patient prognostic prediction. Finally, KEGG and GO pathways enrichment analyses suggested several especially enriched pathways, which may be helpful for us investigative the underlying mechanisms. creator: Zhenyu Zhao creator: Boxue He creator: Qidong Cai creator: Pengfei Zhang creator: Xiong Peng creator: Yuqian Zhang creator: Hui Xie creator: Xiang Wang uri: https://doi.org/10.7717/peerj.10008 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhao et al. title: The lemur baseline: how lemurs compare to monkeys and apes in the Primate Cognition Test Battery link: https://peerj.com/articles/10025 last-modified: 2020-09-24 description: Primates have relatively larger brains than other mammals even though brain tissue is energetically costly. Comparative studies of variation in cognitive skills allow testing of evolutionary hypotheses addressing socioecological factors driving the evolution of primate brain size. However, data on cognitive abilities for meaningful interspecific comparisons are only available for haplorhine primates (great apes, Old- and New World monkeys) although strepsirrhine primates (lemurs and lorises) serve as the best living models of ancestral primate cognitive skills, linking primates to other mammals. To begin filling this gap, we tested members of three lemur species (Microcebus murinus, Varecia variegata, Lemur catta) with the Primate Cognition Test Battery, a comprehensive set of experiments addressing physical and social cognitive skills that has previously been used in studies of haplorhines. We found no significant differences in cognitive performance among lemur species and, surprisingly, their average performance was not different from that of haplorhines in many aspects. Specifically, lemurs’ overall performance was inferior in the physical domain but matched that of haplorhines in the social domain. These results question a clear-cut link between brain size and cognitive skills, suggesting a more domain-specific distribution of cognitive abilities in primates, and indicate more continuity in cognitive abilities across primate lineages than previously thought. creator: Claudia Fichtel creator: Klara Dinter creator: Peter M. Kappeler uri: https://doi.org/10.7717/peerj.10025 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Fichtel et al. title: Identification and expression profiles of candidate chemosensory receptors in Histia rhodope (Lepidoptera: Zygaenidae) link: https://peerj.com/articles/10035 last-modified: 2020-09-24 description: Insect olfaction and vision play important roles in survival and reproduction. Diurnal butterflies mainly rely on visual cues whereas nocturnal moths rely on olfactory signals to locate external resources. Histia rhodope Cramer (Lepidoptera: Zygaenidae) is an important pest of the landscape tree Bischofia polycarpa in China and other Southeast Asian regions. As a diurnal moth, H. rhodope represents a suitable model for studying the evolutionary shift from olfactory to visual communication. However, only a few chemosensory soluble proteins have been characterized and information on H. rhodope chemoreceptor genes is currently lacking. In this study, we identified 45 odorant receptors (ORs), nine ionotropic receptors (IRs), eight gustatory receptors (GRs) and two sensory neuron membrane proteins (SNMPs) from our previously acquired H. rhodope antennal transcriptomic data. The number of chemoreceptors of H. rhodope was less compared with that found in many nocturnal moths. Some specific chemoreceptors such as OR co-receptor (ORco), ionotropic receptors co-receptor, CO2 receptors, sugar receptors and bitter receptors were predicted by phylogenetic analysis. Notably, two candidate pheromone receptors (PRs) were identified within a novel PR lineage. qRT-PCR results showed that almost all tested genes (22/24) were predominantly expressed in antennae, indicating that they may be important in olfactory function. Among these antennae-enriched genes, six ORs, five IRs and two GRs displayed female-biased expression, while two ORs displayed male-biased expression. Additionally, HrhoIR75q.2 and HrhoGR67 were more highly expressed in heads and legs. This study enriches the olfactory gene inventory of H. rhodope and provides the foundation for further research of the chemoreception mechanism in diurnal moths. creator: Haibo Yang creator: Junfeng Dong creator: Ya-Lan Sun creator: Zhenjie Hu creator: Qi-Hui Lyu creator: Dingxu Li uri: https://doi.org/10.7717/peerj.10035 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Yang et al. title: Saururus chinensis-controlled allergic pulmonary disease through NF-κB/COX-2 and PGE2 pathways link: https://peerj.com/articles/10043 last-modified: 2020-09-24 description: Saururus chinensis is a perennial herb found in the northeastern regions of Asia, including Korea, China, and Japan, and is used in traditional medicine. Studies have identified the four major constituents in Saururus chinensis water extract (LHF618®) as miquelianin (11.75 ± 0.092 mg/g), rutin (1.20 ± 0.008 mg/g), quercitrin (2.38 ± 0.389 mg/g), and quercetin (0.068 ± 0.017 mg/g). Saururus chinensis can improve the symptoms of ovalbumin- or fine dust-induced allergic pulmonary disease by suppressing the effects of WBCs and neutrophils in BALF and IgE in the serum. Saururus chinensis dose-dependently recovered morphological changes such as mucous hyper secretion (from 2.7 ± 0.46 to 0.6 ± 0.65), pulmonary epithelial cell hyperplasia (from 2.4 ± 0.55 to 0.7 ± 0.67), and inflammatory cell infiltration (from 2.3 ± 0.45 to 0.6 ± 0.43), and effectively controlled cDNA levels and protein levels of IL-13. It inhibited NF-κB translocation and COX-2 protein synthesis and suppressed the expression of PGE2. Our results show that Saururus chinensis controlled allergic pulmonary disease via the anti-inflammatory pathways, NF-κB/COX-2 and PGE2. Saururus chinensis may be a promising drug candidate against fine dust-induced allergic pulmonary disease. creator: MiKyung Song creator: Soon-Young Lee creator: Minhee Kim creator: Sangwoug Park creator: Juyeon Park creator: Yongbum Kwon creator: Dae-Hun Park uri: https://doi.org/10.7717/peerj.10043 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Song et al. title: Drought stress strengthens the link between chlorophyll fluorescence parameters and photosynthetic traits link: https://peerj.com/articles/10046 last-modified: 2020-09-24 description: Chlorophyll fluorescence (ChlF) has been used to understand photosynthesis and its response to climate change, particularly with satellite-based data. However, it remains unclear how the ChlF ratio and photosynthesis are linked at the leaf level under drought stress. Here, we examined the link between ChlF ratio and photosynthesis at the leaf level by measuring photosynthetic traits, such as net CO2 assimilation rate (An), the maximum carboxylation rate of Rubisco (Vcmax), the maximum rate of electron transport (Jmax), stomatal conductance (gs) and total chlorophyll content (Chlt). The ChlF ratio of the leaf level such as maximum quantum efficiency of PSII (Fv/Fm) is based on fluorescence kinetics. ChlF intensity ratio (LD685/LD740) based on spectrum analysis was obtained. We found that a combination of the stomatal limitation, non-stomatal limitation, and Chlt regulated leaf photosynthesis under drought stress, while Jmax and Chlt governed the ChlF ratio. A significant link between the ChlF ratio and An was found under drought stress while no significant correlation in the control, which indicated that drought stress strengthens the link between the ChlF ratio and photosynthetic traits. These results suggest that the ChlF ratio can be a powerful tool to track photosynthetic traits of terrestrial ecosystems under drought stress. creator: Jie Zhuang creator: Yonglin Wang creator: Yonggang Chi creator: Lei Zhou creator: Jijing Chen creator: Wen Zhou creator: Jun Song creator: Ning Zhao creator: Jianxi Ding uri: https://doi.org/10.7717/peerj.10046 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhuang et al. title: A comparison of common metrics used to quantify the effectiveness of conservation interventions link: https://peerj.com/articles/9873 last-modified: 2020-09-23 description: BackgroundEvidence-based conservation is urgently needed to identify, apply and promote effective interventions for mitigation of threats and recovery of the natural environment. Estimation of intervention effectiveness is subject to robust study design and statistical analysis, and much progress is documented in these fields. In contrast, little is understood about the accuracy and biases (underestimation and overestimation) of different effectiveness metrics and how they are affected by sample size.MethodsIn this study, a dataset (n = 500 cases) consisting of random, positive, integer numbers was simulated to produce frequency input data for the 2 × 2 contingency table. For each case, three metrics of the relative risk, odds ratio and the magnitude of change were calculated, their disparity was estimated and the characteristics of treatment (with intervention) and control (without intervention) samples significantly affecting this disparity were studied by means of linear regression. Further, four case studies from different conservation interventions are provided to support the results.ResultsThe study has shown that the relative risk and the magnitude of change produce identical estimates of intervention effectiveness only when treatment and control samples are equal, or when the number of target outcomes (e.g., number of livestock killed by predators) in treatment sample reaches zero. In other situations, the magnitude of change gives overestimates or underestimates, depending on relationships between treatment and control sample sizes. The table summarizing the conditions of equalities and biases between these two metrics is provided. These conditions are valid for both reduction-aimed interventions reducing negative target outcomes (e.g., livestock protection to reduce livestock losses to predators) and for addition-aimed interventions increasing positive target outcomes (e.g., establishment of protected areas to increase species presence). No significant effects on the odds ratio were found.ConclusionResearchers should set equal treatment and control sample sizes so that to produce identical estimates of intervention effectiveness by the relative risk and the magnitude of change. Otherwise, these estimates are biased if produced by the magnitude of change and the relative risk should be used instead. As setting equal treatment and control samples can be impractical, I encourage researchers and practitioners to use the relative risk in estimation of intervention effectiveness. This will not take additional efforts as both metrics are calculated from the same contingency table. Treatment and control sample sizes, along with their sub-samples affected and not by an intervention, should be explicitly reported by researchers to allow independent evaluation of intervention effectiveness. This approach can help obtain more accurate information on intervention effectiveness for making better decisions in conservation actions. creator: Igor Khorozyan uri: https://doi.org/10.7717/peerj.9873 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Khorozyan title: The health-related quality of life of Syrian refugee women in their reproductive age link: https://peerj.com/articles/9990 last-modified: 2020-09-23 description: BackgroundHealth-Related Quality of Life (HRQoL) for refugee women in reproductive age is highly affected by physical, political, psychosocial and environmental conditions in countries of asylum. HRQoL is enormously affected by the satisfaction of this vulnerable group with the physical, psychological, emotional and social care services provided in this critical time. Therefore, this study aimed toassess the HRQoL among Syrian refugee women of reproductive age living outside camps in Jordan.MethodsA cross-sectional correlational study was conducted with a convenience sample of 523 Syrian refugee women in the host communities in Jordan.Health-related quality of life (HRQOL) was measured using the short-form 36 (SF-36) questionnaire.ResultsSignificant negative correlations were found between SF-36 individual subscales score and the length of marriage, the number of children, parity and family income. The strongest correlations were between pain scale and length of marriage (r =  − .21), and between Energy/Fatigue and ‘number of children’ (r =  − .21). Conversely, antenatal care was positively correlated with physical, role emotional, pain, and general health. Physical functioning and general health were predicted significantly with less years of marriage, younger age at marriage, less violence and by higher family income.ConclusionThis study suggests low HRQoL scores for women of reproductive age across all domains. Several factors such as years of marriage, age at marriage, the number of children, violence, antenatal care and family income affected the women’s general health. The provision of appropriate and accessible reproductive and maternal healthcare services in antenatal visits is critical for ensuring the immediate and long-term health and wellbeing of refugee women and their families. creator: Manar Nabolsi creator: Reema Safadi creator: Carolyn Sun creator: Muayyad Ahmad creator: Du’a Al-Maharma creator: Suhaila Halasa creator: Mohammad Saleh creator: Jennifer Dohrn uri: https://doi.org/10.7717/peerj.9990 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Nabolsi et al. title: Measurements of the gingival papillae architecture using cone-beam computed tomography in young Chinese adults link: https://peerj.com/articles/10006 last-modified: 2020-09-23 description: BackgroundThe aim of this study was to measure the morphology of interdental papillae (IP) in maxillary anterior teeth using cone-beam computed tomography (CBCT).MethodsTwenty-seven periodontally healthy subjects with 135 IP were evaluated by means of periodontal examination and a CBCT scan with an elastomeric matrix containing radiopaque material in position. According to the status of tooth contact and presence of IP, subjects were categorized into three groups: open contact point, complete papillae, and deficient papillae group. The papillae height (PH), facial-lingual thickness (FLT), and interdental distance (IDD) were measured. Data was analyzed with the significance level at α = 0.05.ResultsThe mean PH values were 4.17 ± 0.51 mm, 3.99 ± 0.61 mm, and 3.99 ± 0.62 mm, for the open contact group, complete papilla, and deficient papilla group, respectively. The PH values of the recorded sites among central incisors, lateral incisors, and canine were 4.13 ± 0.56 mm, 3.87 ± 0. 63 mm, and 4.07 ± 0.58 mm, respectively. No statistically significant differences of the PH values were determined between the above three tested groups as well as between the different sites (p > 0.05). The IDD values obtained from the complete papilla group were significantly lower than the other tested groups (p < 0.05).ConclusionThe contact point condition of upper anterior sextants may not influence the presence and dimension of the IP in periodontally healthy subjects. creator: Gang Yang creator: Jie Cao creator: Wenjie Hu creator: Kwok-Hung Chung uri: https://doi.org/10.7717/peerj.10006 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Yang et al. title: Perception and practices during the COVID-19 pandemic in an urban community in Nigeria: a cross-sectional study link: https://peerj.com/articles/10038 last-modified: 2020-09-23 description: BackgroundVarious perceptions and practices have been associated with the COVID-19 pandemic. In this study, we assessed the perception and practices regarding COVID-19 among residents in selected urban communities of Ibadan, Oyo State, Nigeria.MethodsA descriptive cross-sectional study design using a multi-stage sampling technique was used to recruit 360 respondents (Mean age: 33.2 ± 10.6 years; 62.5% females) from households in Ibadan. Data were collected using an interviewer-administered questionnaire from 3rd to 6th June 2020. Those who demonstrated washing of the palm, back of the hand, spaces between the fingers, fingernails, wrist, and thumbs had six points and were categorized to have had a good practice of handwashing. Descriptive statistics were conducted. Bivariate analyses of sociodemographic characteristics and good handwashing practices were conducted using Chi-square test. Logistic regression was conducted to identify the determinants of good handwashing practices. P-values < 0.05 were statistically significant.ResultsGoing to the hospital (95%) and calling the COVID-19 help number (58.3%) were the frequently reported practices among respondents following the development of COVID-19 symptoms. Also, 89 (26%) knew they could contract COVID-19, while 41 (12%) perceived it as an exaggerated event. The effects most frequently reported by respondents were hunger/low income (48.8%) and academic delay (8.8%). Use of face masks by 64.5% and social distancing (48%) were the most frequently reported practices for prevention. Only 71 (20.8%) demonstrated good handwashing practices. The perception of the likelihood to contract COVID-19 and practices to prevent COVID-19 had a weak correlation of 0.239 (p < 0.001).ConclusionGaps exist in the practices that prevent COVID-19. There is a need to improve handwashing, use of face masks and other practices that prevent COVID-19. Implications across public health communication and policies were stated. creator: Olayinka Ilesanmi creator: Aanuoluwapo Afolabi uri: https://doi.org/10.7717/peerj.10038 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Ilesanmi and Afolabi title: Do Centres of Endemism provide a spatial context for predicting and preserving plant phylogeographic patterns in the Cape Floristic Region, South Africa? link: https://peerj.com/articles/10045 last-modified: 2020-09-23 description: AimThe evolutionary forces that gave rise to the exceptional plant species richness of the Cape Floristic Region (CFR) have also likely played a role at the intraspecific level (i.e. plant populations)—and thereby generating shared phylogeographic patterns among taxa. Here we test whether plant populations in the CFR exhibit phylogeographic breaks across the boundaries between Centres of Endemism (CoEs). The boundaries between CoEs (derived from the distribution ranges of endemic taxa and currently mapped at a coarse, Quarter Degree Square scale) represent a spatial proxy for the evolutionary diversifying drivers acting on plant taxa in the CFR.LocationThe CFR, located along the southern Cape of South Africa.MethodsPublished phylogeographic literature were compiled and spatial patterns of genetic divergence re-analysed to assess the frequency at which CFR plant taxa exhibit phylogeographic breaks either (1) across or (2) within CoE boundaries. Population pairs from each study were compared across and within CoEs and scored as either exhibiting a phylogeographic break or not.ResultsPhylogeographic breaks in Cape plants were found to occur across the boundaries of CoEs more often than not. Significantly more population pairs exhibited phylogeographic breaks across CoE boundaries (506 of the 540, χ2 = 886, p < 0.001) and fewer breaks within CoEs (94 of 619, χ2 = 300, p < 0.001) than would be expected if there was equal probability of a genetic break occurring across CoE boundaries.Main conclusionsThe evolutionary forces that have produced and maintained the exceptional plant diversity in the CFR appear to have operated at the population level, producing similar patterns of phylogeographic structuring of plant lineages regardless of life history or taxonomy. This tendency for Cape plants to exhibit shared patterns of spatially structured genetic diversity that match the distribution of endemic taxa may assist CFR phylogeographers to streamline sampling efforts and test novel hypotheses pertaining to the distribution of genetic diversity among CFR plant taxa. Additionally, the resolution at which CoEs are mapped should be refined, which may provide a valuable tool for future conservation planning and the development of precautionary guidelines for the translocation of genetic material during species reintroductions and commercial cultivation of Cape endemic crops. Thus, to answer the question ‘Do Centres of Endemism provide a spatial context for predicting and preserving plant phylogeographic patterns in the Cape Floristic Region, South Africa?’—yes, CoEs do appear to be an important tool for Cape phylogeographers. However, the data is limited and more plant phylogeography work is needed in the CFR. creator: Nicholas C. Galuszynski creator: Alastair J. Potts uri: https://doi.org/10.7717/peerj.10045 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Galuszynski and Potts title: Coral cover and rubble cryptofauna abundance and diversity at outplanted reefs in Okinawa, Japan link: https://peerj.com/articles/9185 last-modified: 2020-09-22 description: Global climate change is leading to damage and loss of coral reef ecosystems. On subtropical Okinawa Island in southwestern Japan, the prefectural government is working on coral reef restoration by outplanting coral colonies from family Acroporidae back to reefs after initially farming colonies inside protected nurseries. In order to establish a baseline for future comparisons, in this study we documented the current status of reefs undergoing outplanting at Okinawa Island, and nearby locations where no human manipulation has occurred. We examined three sites on the coast of Onna Village on the west coast of the island; each site included an outplanted and control location. We used (1) coral rubble sampling to measure and compare abundance and diversity of rubble cryptofauna; and (2) coral reef monitoring using Line Intercept Transects to track live coral coverage. Results showed that rubble shape had a positive correlation with the numbers of animals found within rubble themselves and may therefore constitute a reliable abundance predictor. Each outplanted location did not show differences with the corresponding control location in terms of rubble cryptofauna abundance, but outplanted locations had significantly lower coral coverage. Overall, differences between sites (Maeganeku1, Maeganeku2 and Manza, each including both outplanted and control locations) were significant, for both rubble cryptofauna and coral coverage. We recommend (1) to outplant colonies from more stress-resistant genera in place of Acropora, and (2) to conduct regular surveys to monitor the situation closely. With a lack of baseline data preceding impacts, rigorous monitoring over time can highlight trends towards increases or decreases in evaluated variables, allowing to obtain a clearer idea of the effects of transplants and on the trajectory of impacts due to climate change and local stressors . Finally, we also recommend (3) to establish conservation and sustainable practices that could aid the ongoing restoration efforts such as installing anchoring buoys to reduce impacts from anchoring, which could reduce coral mortality of both outplanted and native coral colonies. creator: Piera Biondi creator: Giovanni Diego Masucci creator: James Davis Reimer uri: https://doi.org/10.7717/peerj.9185 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Biondi et al. title: Predictive models for stage and risk classification in head and neck squamous cell carcinoma (HNSCC) link: https://peerj.com/articles/9656 last-modified: 2020-09-22 description: Machine learning techniques are increasingly used in the analysis of high throughput genome sequencing data to better understand the disease process and design of therapeutic modalities. In the current study, we have applied state of the art machine learning (ML) algorithms (Random Forest (RF), Support Vector Machine Radial Kernel (svmR), Adaptive Boost (AdaBoost), averaged Neural Network (avNNet), and Gradient Boosting Machine (GBM)) to stratify the HNSCC patients in early and late clinical stages (TNM) and to predict the risk using miRNAs expression profiles. A six miRNA signature was identified that can stratify patients in the early and late stages. The mean accuracy, sensitivity, specificity, and area under the curve (AUC) was found to be 0.84, 0.87, 0.78, and 0.82, respectively indicating the robust performance of the generated model. The prognostic signature of eight miRNAs was identified using LASSO (least absolute shrinkage and selection operator) penalized regression. These miRNAs were found to be significantly associated with overall survival of the patients. The pathway and functional enrichment analysis of the identified biomarkers revealed their involvement in important cancer pathways such as GP6 signalling, Wnt signalling, p53 signalling, granulocyte adhesion, and dipedesis. To the best of our knowledge, this is the first such study and we hope that these signature miRNAs will be useful for the risk stratification of patients and the design of therapeutic modalities. creator: Sugandh Kumar creator: Srinivas Patnaik creator: Anshuman Dixit uri: https://doi.org/10.7717/peerj.9656 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kumar et al. title: Fungal infection, decline and persistence in the only obligate troglodytic Neotropical salamander link: https://peerj.com/articles/9763 last-modified: 2020-09-22 description: The fungal pathogen Batrachochytrium dendrobatidis (Bd) is implicated in global mass die-offs and declines in amphibians. In Mesoamerica, the Bd epidemic wave hypothesis is supported by detection of Bd in historic museum specimens collected over the last century, yet the timing and impact of the early stages of the wave remain poorly understood. Chiropterotriton magnipes, the only obligate troglodytic Neotropical salamander, was abundant in its small range in the decade following its description in 1965, but subsequently disappeared from known localities and was not seen for 34 years. Its decline is roughly coincident with that of other populations of Neotropical salamanders associated with the invasion and spread of Bd. To determine the presence and infection intensity of Bd on C. magnipes and sympatric amphibian species (which are also Bd hosts), we used a noninvasive sampling technique and qPCR assay to detect Bd on museum specimens of C. magnipes collected from 1952 to 2012, and from extant populations of C. magnipes and sympatric species of amphibians. We also tested for the presence of the recently discovered Batrachochytrium salamandivorans (Bsal), another fungal chytridiomycete pathogen of salamanders, using a similar technique specific for Bsal. We did not detect Bd in populations of C. magnipes before 1969, while Bd was detected at low to moderate prevalence just prior to and during declines. This pattern is consistent with Bd-caused epizootics followed by host declines and extirpations described in other hosts. We did not detect Bsal in any extant population of C. magnipes. We obtained one of the earliest positive records of the fungus to date in Latin America, providing additional historical evidence consistent with the Bd epidemic wave hypothesis. Genotyping results show that at least one population is currently infected with the Global Panzootic Lineage of Bd, but our genotyping of the historical positive samples was unsuccessful. The lack of large samples from some years and the difficulty in genotyping historical Bd samples illustrate some of the difficulties inherent in assigning causality to historical amphibian declines. These data also provide an important historical baseline for actions to preserve the few known remaining populations of C. magnipes. creator: Mizraim Olivares-Miranda creator: Vance T. Vredenburg creator: Julio C. García-Sánchez creator: Allison Q. Byrne creator: Erica B. Rosenblum creator: Sean M. Rovito uri: https://doi.org/10.7717/peerj.9763 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Olivares-Miranda et al. title: Site selection by geese in a suburban landscape link: https://peerj.com/articles/9846 last-modified: 2020-09-22 description: BackgroundIn European and North American cities geese are among the most common and most visible large herbivores. As such, their presence and behaviour often conflict with the desires of the human residents. Fouling, noise, aggression and health concerns are all cited as reasons that there are “too many”. Lethal control is often used for population management; however, this raises questions about whether this is a sustainable strategy to resolve the conflict between humans and geese when, paradoxically, it is humans that are responsible for creating the habitat and often providing the food and protection of geese at other times. We hypothesise that the landscaping of suburban parks can be improved to decrease its attractiveness to geese and to reduce the opportunity for conflict between geese and humans.MethodsUsing observations collected over five years from a botanic garden situated in suburban Belgium and data from the whole of Flanders in Belgium, we examined landscape features that attract geese. These included the presence of islands in lakes, the distance from water, barriers to level flight and the size of exploited areas. The birds studied were the tadornine goose Alopochen aegyptiaca (L. 1766) (Egyptian goose) and the anserine geese, Branta canadensis (L. 1758) (Canada goose), Anser anser (L. 1758) (greylag goose) and Branta leucopsis (Bechstein, 1803) (barnacle goose). Landscape modification is a known method for altering goose behaviour, but there is little information on the power of such methods with which to inform managers and planners.ResultsOur results demonstrate that lakes with islands attract more than twice as many anserine geese than lakes without islands, but make little difference to Egyptian geese. Furthermore, flight barriers between grazing areas and lakes are an effective deterrent to geese using an area for feeding. Keeping grazing areas small and surrounded by trees reduces their attractiveness to geese.ConclusionThe results suggest that landscape design can be used successfully to reduce the number of geese and their conflict with humans. However, this approach has its limitations and would require humans to compromise on what they expect from their landscaped parks, such as open vistas, lakes, islands and closely cropped lawns. creator: Quentin J. Groom creator: Tim Adriaens creator: Claire Colsoulle creator: Pauline Delhez creator: Iris Van der Beeten uri: https://doi.org/10.7717/peerj.9846 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Groom et al. title: Dichocarpum hagiangense—a new species and an updated checklist of Ranunculaceae in Vietnam link: https://peerj.com/articles/9874 last-modified: 2020-09-22 description: Dichocarpum hagiangense from Ha Giang province, northern Vietnam is described and illustrated. Diagnostic features of the new species are a short rhizomatous stem, (2–)3-foliolate or simple leaves, and pink-purple flowers. The described species is distinct from closely allied D. trifoliolatum in having longer sepals, shape and obcordate apex of petal limbs, shorter flower stem, number and tooth shape of basal leaves; it differs from D. basilare and D. carinatum in having stem leaf, retuse apex and longer of central leaflet, number and (2–)3-foliated (or simple) of leaf. With the support of molecular data, the new species was clearly distinguished from other species in the Dichocarpum group by eight autapomorphic characters in nrITS sequence. A key to all species of Dichocarpum is provided. We suggest the IUCN conservation status of D. hagiangense to be “Critically Endangered”. A newest checklist of the family Ranunculaceae in Vietnam is updated. creator: Minh Ty Nguyen creator: Ngoc Bon Trinh creator: Thanh Thi Viet Tran creator: Tran Duc Thanh creator: Long Ke Phan creator: Van The Pham uri: https://doi.org/10.7717/peerj.9874 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Nguyen et al. title: Flavoured water consumption alters pharmacokinetic parameters and increases exposure of erlotinib and gefitinib in a preclinical study using Wistar rats link: https://peerj.com/articles/9881 last-modified: 2020-09-22 description: BackgroundErlotinib (ERL) and Gefitinib (GEF) are considered first line therapy for the management of non-small cell lung carcinoma (NSCLC). Like other tyrosine kinase inhibitors (TKIs), ERL and GEF are mainly metabolized by the cytochrome P450 (CYP450) CYP3A4 isoform and are substrates for transporter proteins with marked inter-/intra-individual pharmacokinetic (PK) variability. Therefore, ERL and GEF are candidates for drug-drug and food-drug interactions with a consequent effect on drug exposure and/or drug-related toxicities. In recent years, the consumption of flavoured water (FW) has gained in popularity. Among multiple ingredients, fruit extracts, which might constitute bioactive flavonoids, can possess an inhibitory effect on the CYP450 enzymes or transporter proteins. Therefore, in this study we investigated the effects of different types of FW on the PK parameters of ERL and GEF in Wistar rats.MethodsERL and GEF PK parameters in different groups of rats after four weeks consumption of different flavours of FW, namely berry, peach, lime, and pineapple, were determined from plasma drug concentrations using ultra-performance liquid chromatography–tandem mass spectrometry (UPLC-MS/MS).ResultsData indicated that tested FWs altered the PK parameters of both ERL and GEF differently. Lime water had the highest impact on most of ERL and GEF PK parameters, with a significant increase in Cmax (95% for ERL, 58% for GEF), AUC0–48 (111% for ERL, 203% for GEF), and AUC0–∞ (200% for ERL, 203% for GEF), along with a significant decrease in the apparent oral clearance of both drugs (65% for ERL, 67% for GEF). The order by which FW affected the PK parameters for ERL and GEF was as follows: lime > pineapple > berry > peach.ConclusionThe present study indicates that drinking FW could be of significance in rats receiving ERL or GEF. Our results indicate that the alteration in PKs was mostly recorded with lime, resulting in an enhanced bioavailability, and reduced apparent oral clearance of the drugs. Peach FW had a minimum effect on the PK parameters of ERL and no significant effect on GEF PKs. Accordingly, it might be of clinical importance to evaluate the PK parameters of ERL and GEF in human subjects who consume FW while receiving therapy. creator: Aliyah Almomen creator: Hadir M. Maher creator: Nourah Z. Alzoman creator: Shereen M. Shehata creator: Amal Alsubaie uri: https://doi.org/10.7717/peerj.9881 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Almomen et al. title: The reuse of public datasets in the life sciences: potential risks and rewards link: https://peerj.com/articles/9954 last-modified: 2020-09-22 description: The ‘big data’ revolution has enabled novel types of analyses in the life sciences, facilitated by public sharing and reuse of datasets. Here, we review the prodigious potential of reusing publicly available datasets and the associated challenges, limitations and risks. Possible solutions to issues and research integrity considerations are also discussed. Due to the prominence, abundance and wide distribution of sequencing data, we focus on the reuse of publicly available sequence datasets. We define ‘successful reuse’ as the use of previously published data to enable novel scientific findings. By using selected examples of successful reuse from different disciplines, we illustrate the enormous potential of the practice, while acknowledging the respective limitations and risks. A checklist to determine the reuse value and potential of a particular dataset is also provided. The open discussion of data reuse and the establishment of this practice as a norm has the potential to benefit all stakeholders in the life sciences. creator: Katharina Sielemann creator: Alenka Hafner creator: Boas Pucker uri: https://doi.org/10.7717/peerj.9954 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Sielemann et al. title: Analysis of dynamic and widespread lncRNA and miRNA expression in fetal sheep skeletal muscle link: https://peerj.com/articles/9957 last-modified: 2020-09-22 description: The sheep is an economically important animal, and there is currently a major focus on improving its meat quality through breeding. There are variations in the growth regulation mechanisms of different sheep breeds, making fundamental research on skeletal muscle growth essential in understanding the regulation of (thus far) unknown genes. Skeletal muscle development is a complex biological process regulated by numerous genes and non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). In this study, we used deep sequencing data from sheep longissimus dorsi (LD) muscles sampled at day 60, 90, and 120 of gestation, as well as at day 0 and 360 following birth, to identify and examine the lncRNA and miRNA temporal expression profiles that regulate sheep skeletal myogenesis. We stained LD muscles using histological sections to analyse the area and circumference of muscle fibers from the embryonic to postnatal development stages. Our results showed that embryonic skeletal muscle growth can be characterized by time. We obtained a total of 694 different lncRNAs and compared the differential expression between the E60 vs. E90, E90 vs. E120, E120 vs. D0, and D0 vs. D360 lncRNA and gene samples. Of the total 701 known sheep miRNAs we detected, the following showed a wide range of expression during the embryonic stage: miR-2387, miR-105, miR-767, miR-432, and miR-433. We propose that the detected lncRNA expression was time-specific during the gestational and postnatal stages. GO and KEGG analyses of the genes targeted by different miRNAs and lncRNAs revealed that these significantly enriched processes and pathways were consistent with skeletal muscle development over time across all sampled stages. We found four visual lncRNA–gene regulatory networks that can be used to explore the function of lncRNAs in sheep and may be valuable in helping improve muscle growth. This study also describes the function of several lncRNAs that interact with miRNAs to regulate myogenic differentiation. creator: Chao Yuan creator: Ke Zhang creator: Yaojing Yue creator: Tingting Guo creator: Jianbin Liu creator: Chune Niu creator: Xiaoping Sun creator: Ruilin Feng creator: Xiaolong Wang creator: Bohui Yang uri: https://doi.org/10.7717/peerj.9957 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Yuan et al. title: Species distribution modelling of Bryde’s whales, humpback whales, southern right whales, and sperm whales in the southern African region to inform their conservation in expanding economies link: https://peerj.com/articles/9997 last-modified: 2020-09-22 description: In southern African waters, information about species distribution and habitat preferences of many cetacean species is limited, despite the recent economic growth that may affect them. We determined the relative importance of eight environmental variables (bathymetry, distance to shore, slope, chlorophyll-a, salinity, eastwards sea water velocity, northwards sea water velocity and sea surface temperature) as drivers of seasonal habitat preferences of Bryde’s whales (Balaenoptera brydei), humpback whales (Megaptera novaeangliae), southern right whales (Eubalaena australis) and sperm whales (Physeter macrocephalus). Using presence only data from multiple sources, we constructed predictive species distribution models (SDMs) consisting of ensembles of seven algorithms for these species during both summer and winter. Predicted distribution for all cetaceans was high in southern Africa and, in particular, within the South African Exclusive Economic Zone (EEZ). Predictive models indicated a more pronounced seasonal variation for humpback, sperm and southern right whales than for Bryde’s whales. Southern right whales occurred closer to shore during winter, humpback whales were more likely to occur along the east coast in winter and the west coast in summer, and sperm whales were more concentrated off the shelf in winter. Our study shows that ensemble models using historical, incidental and scientific data, in conjunction with modern environmental variables, can provide baseline knowledge on important environmental drivers of cetacean distribution for conservation purposes. Results of this study can further be used to help develop marine spatial plans and identify important marine mammal areas. creator: Jean Purdon creator: Fannie W. Shabangu creator: Dawit Yemane creator: Marc Pienaar creator: Michael J. Somers creator: Ken Findlay uri: https://doi.org/10.7717/peerj.9997 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Purdon et al. title: Quinquelaophonte enormis sp. nov., a new interstitial copepod (Harpacticoida: Laophontidae) from Korea link: https://peerj.com/articles/10007 last-modified: 2020-09-22 description: We collected an undescribed laophontid copepod from a coarse sand habitat on the east coast of Korea and named it Quinquelaophonte enormissp. nov. We compared the detailed morphological characteristics of the new species with those of congeneric species. Among them, the new species shows a superficial resemblance to the Californian species Quinquelaophonte longifurcataLang, 1965. However, the two species are easily distinguishable by the setation of the syncoxa on the maxilliped and the fourth swimming leg. The new species has the variable setation on the second to fourth swimming legs. The variations appear among individuals or between the left and right rami of a pair of legs in a single specimen. Although complex chaetotaxical polymorphism occur in this new species, we used myCOI and Cytb to confirm that the new species is not a species complex. Also, partial sequences of 18S and 28S ribosomal RNA genes were used to analyze the position of the new species within the family Laophontidae. The new speciesis the fourteenth Quinquelaophonte species in the world and the second species in Korea. creator: Jaehyun Kim creator: Eunjung Nam creator: Wonchoel Lee uri: https://doi.org/10.7717/peerj.10007 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kim et al. title: Genome-wide identification and expression analysis of the ERF transcription factor family in pineapple (Ananas comosus (L.) Merr.) link: https://peerj.com/articles/10014 last-modified: 2020-09-22 description: Pineapple (Ananas comosus (L.) Merr.) is an important tropical fruit with high economic value. The quality and yield of pineapple will be affected by various environmental conditions. Under adverse conditions, plants can produce a complex reaction mechanism to enhance their resistance. It has been reported that the member of ethylene responsive transcription factors (ERFs) plays a crucial role in plant developmental process and stress response. However, the function of these proteins in pineapple remains limited. In this study, a total of 74 ERF genes (AcoERFs) were identified in pineapple genome, named from AcoERF1 to AcoERF74, and divided into 13 groups based on phylogenetic analysis. We also analyzed gene structure, conserved motif and chromosomal location of AcoERFs, and the AcoERFs within the same group possess similar gene structures and motif compositions. Three genes (AcoERF71, AcoERF73 and AcoERF74) were present on unanchored scaffolds, so they could not be conclusively mapped on chromosome. Synteny and cis-elements analysis of ERF genes provided deep insight into the evolution and function of pineapple ERF genes. Furthermore, we analyzed the expression profiling of AcoERF in different tissues and developmental stages, and 22 AcoERF genes were expressed in all examined tissues, in which five genes (AcoERF13, AcoERF16, AcoERF31, AcoERF42, and AcoERF65) had high expression levels. Additionally, nine AcoERF genes were selected for functional verification by qRT-PCR. These results provide useful information for further investigating the evolution and functions of ERF family in pineapple. creator: Youmei Huang creator: Yanhui Liu creator: Man Zhang creator: Mengnan Chai creator: Qing He creator: Bello Hassan Jakada creator: Fangqian Chen creator: Huihuang Chen creator: Xingyue Jin creator: Hanyang Cai creator: Yuan Qin uri: https://doi.org/10.7717/peerj.10014 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Huang et al. title: No Mow May lawns have higher pollinator richness and abundances: An engaged community provides floral resources for pollinators link: https://peerj.com/articles/10021 last-modified: 2020-09-22 description: No Mow May is a community science initiative popularized in recent years that encourages property owners to limit their lawn mowing practices during the month of May. The goal of No Mow May is to provide early season foraging resources for pollinators that emerge in the spring, especially in urban landscapes when few floral resources are available. We worked with the city council of Appleton, Wisconsin, USA. to allow No Mow May to take place in May 2020. Four hundred and thirty-five property owners registered for No Mow May in Appleton. We measured floral and bee richness and abundance in the yards of a subset of homes (N = 20) located near regularly mowed urban parks (N = 15) at the end of the month. We found that homes that participated in No Mow May had more diverse and abundant flora than regularly mowed green spaces throughout the city. No Mow May homes had three times higher bee richness and five times higher bee abundances than frequently mowed greenspaces. Using generalized linear models, we found that the best predictor of bee richness was the size of the designated unmowed area, and the best predictors of bee abundances were the size of the unmowed area as well as floral richness. While our findings cannot conclusively attribute increases in bee abundances and richness to the No Mow May efforts, our data does show that bee pollinators make use of no mow spaces as key floral resources during early spring in the upper midwestern United States. A post-No Mow May survey revealed that the participants were keen to increase native floral resources in their yards, increase native bee nesting habitat, reduce mowing intensities, and limit herbicide, pesticide, and fertilizer applications to their lawns. The No Mow May initiative educated an engaged community on best practices to improve the conservation of urban pollinators in future years. creator: Israel Del Toro creator: Relena R. Ribbons uri: https://doi.org/10.7717/peerj.10021 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Del Toro and Ribbons title: A comparison of sex, morphology, physiology and behavior of black-capped chickadees trapped using two common capture methods link: https://peerj.com/articles/10037 last-modified: 2020-09-22 description: Many biological studies require the capture of individuals for sampling, for example for measurement of morphological or physiological traits, or for marking individuals for later observations. Capture methods employed often vary both within and between studies, and these differing methods could be more or less effective in capture of different individuals based on their morphology or behavior. If individuals that are prone to capture by the selected method differ with respect to traits of interest, such sampling bias could generate misleading or simply inaccurate results. The selection of capture methods could introduce two different forms of sampling bias, with the individuals that are sampled differing from the population at large or with individuals sampled via one method differing from individuals that could be sampled using a different method. We investigated this latter form of sampling bias by comparing individual birds sampled using two common capture techniques. We caught free-ranging black-capped chickadees (Poecile atricapillus) using walk-in traps baited with seed and mist nets paired with playback of an audio stimulus (conspecific mobbing calls). We measured 18 traits that we expect might vary among birds that are trappable by these differing methods—one that targets birds that are food motivated and potentially less neophobic and another that targets birds that respond readily to a perceived predation risk. We found no differences in the sex, morphology, initial and stress-induced corticosterone concentrations, behavioral response to a novel object, or behavioral response to a predator between individuals captured by these two methods. Individual variation in the behavioral response to a novel object was greater among birds caught by mist nets, suggesting this method might provide a sample that better reflects population-level individual variation. We do not know if the birds caught by these two methods provide a representative sample of the population at large, but can conclude that selection of either of these two common capture methods can similarly sample mean trait values of a population of interest. To accurately assess individual variation, particularly in behavior, mist nets might be preferable. creator: Sara M. Burns creator: Frances Bonier uri: https://doi.org/10.7717/peerj.10037 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Burns and Bonier title: A laboratory comparison of the interactions between three plastic mulch types and 38 active substances found in pesticides link: https://peerj.com/articles/9876 last-modified: 2020-09-21 description: BackgroundIn semi-arid regions, the use of plastic mulch and pesticides in conventional agriculture is nearly ubiquitous. Although the sorption of pesticides on Low Density Polyethylene (LDPE) has been previously studied, no data are available for other plastics such as Pro-oxidant Additive Containing (PAC) plastics or “biodegradable” (Bio) plastics. The aim of this research was to measure the sorption pattern of active substances from pesticides on LDPE, PAC and Bio plastic mulches and to compare the decay of the active substances in the presence and absence of plastic debris.MethodsFor this purpose, 38 active substances from 17 insecticides, 15 fungicides and six herbicides commonly applied with plastic mulching in South-east Spain were incubated with a 3 × 3 cm2 piece of plastic mulch (LDPE, PAC and Bio). The incubation was done in a solution of 10% acetonitrile and 90% distilled water at 35 °C for 15 days in the dark. The Quick Easy Cheap Effective Rugged Safe approach was adapted to extract the pesticides.ResultsThe sorption behavior depended on both the pesticide and the plastic mulch type. On average, the sorption percentage was ~23% on LDPE and PAC and ~50% on Bio. The decay of active substances in the presence of plastic was ~30% lesser than the decay of active substances in solution alone. This study is the first attempt at assessing the behavior of a diversity of plastic mulches and pesticides to further define research needs. creator: Nicolas Beriot creator: Paul Zomer creator: Raul Zornoza creator: Violette Geissen uri: https://doi.org/10.7717/peerj.9876 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Beriot et al. title: Nest-site selection and breeding success of passerines in the world’s southernmost forests link: https://peerj.com/articles/9892 last-modified: 2020-09-21 description: BackgroundBirds can maximize their reproductive success through careful selection of nest-sites. The ‘total-foliage’ hypothesis predicts that nests concealed in vegetation should have higher survival. We propose an additional hypothesis, the ‘predator proximity’ hypothesis, which states that nests placed farther from predators would have higher survival. We examined these hypotheses in the world’s southernmost forests of Navarino Island, in the Cape Horn Biosphere reserve, Chile (55°S). This island has been free of mammalian ground predators until recently, and forest passerines have been subject to depredation only by diurnal and nocturnal raptors.MethodsDuring three breeding seasons (2014–2017), we monitored 104 nests for the five most abundant open-cup forest-dwelling passerines (Elaenia albiceps, Zonotrichia capensis, Phrygilus patagonicus, Turdus falcklandii, and Anairetes parulus). We identified nest predators using camera traps and assessed whether habitat characteristics affected nest-site selection and survival.ResultsNest predation was the main cause of nest failure (71% of failed nests). Milvago chimango was the most common predator, depredating 13 (87%) of the 15 nests where we could identify a predator. By contrast, the recently introduced mammal Neovison vison, the only ground predator, depredated one nest (7%). Species selected nest-sites with more understory cover and taller understory, which according to the total-foliage hypothesis would provide more concealment against both avian and mammal predators. However, these variables negatively influenced nest survival. The apparent disconnect between selecting nest-sites to avoid predation and the actual risk of predation could be due to recent changes in the predator assemblage driven by an increased abundance of native M. chimango associated with urban development, and/or the introduction of exotic mammalian ground predators to this island. These predator assemblage changes could have resulted in an ecological trap. Further research will be needed to assess hypotheses that could explain this mismatch between nest-site selection and nest survival. creator: Rocío Fernanda Jara creator: Ramiro Daniel Crego creator: Michael David Samuel creator: Ricardo Rozzi creator: Jaime Enrique Jiménez uri: https://doi.org/10.7717/peerj.9892 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Jara et al. title: Genetic diversity and structure of the critically endangered Artocarpus annulatus, a crop wild relative of jackfruit (A. heterophyllus) link: https://peerj.com/articles/9897 last-modified: 2020-09-21 description: Limestone karsts of Southeast Asia can harbor high levels of endemism, but are highly fragmented, increasingly threatened, and their biodiversity is often poorly studied. This is true of the Padawan Limestone Area of Sarawak, Malaysia, home to the endemic Artocarpus annulatus, the closest known wild relative of two important and underutilized fruit tree crops, jackfruit (A. heterophyllus) and cempedak (A. integer). Identifying and conserving crop wild relatives is critical for the conservation of crop genetic diversity and breeding. In 2016 and 2017, five A. annulatus populations were located, and leaf material, locality information, and demographic data were collected. Microsatellite markers were used to assess genetic diversity and structure among populations, and to compare levels of genetic diversity to closely related congeneric species. Results indicate no evidence of inbreeding in A. annulatus, and there is no genetic structure among the five populations. However, diversity measures trended lower in seedlings compared to mature trees, suggesting allelic diversity may be under threat in the youngest generation of plants. Also, genetic diversity is lower in A. annulatus compared to closely related congeners. The present study provides a baseline estimate of A. annulatus genetic diversity that can be used for comparison in future studies and to other species in the unique limestone karst ecosystems. Considerations for in situ and ex situ conservation approaches are discussed. creator: Leta Dickinson creator: Hilary Noble creator: Elliot Gardner creator: Aida Shafreena Ahmad Puad creator: Wan Nuur Fatiha Wan Zakaria creator: Nyree J.C. Zerega uri: https://doi.org/10.7717/peerj.9897 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Dickinson et al. title: Genome analysis and phylogenetic characterization of two deformed wing virus strains from Apis cerana in Vietnam link: https://peerj.com/articles/9911 last-modified: 2020-09-21 description: BackgroundDeformed wing virus (DWV) is a virulent virus that causes honeybee disease. DWV can exist as a latent infection in honeybees, outbreak into epidemics, and cause serious damage to beekeeping cross the world, including Vietnam.MethodsThe two DWV strains circulating in Vietnamese honeybee, Apis cerana, were first isolated from adult honeybees in North Vietnam (DWV-NVN) and South Vietnam (DWV-SVN). Their complete nucleotide sequences were determined, aligned, and compared with other DWV strains.ResultsThe two Vietnamese DWV strains comprised 10,113 bp and contained a large single open reading frame (ORF) of 2,893 amino acids, initiating at nucleotide 1,130 and terminating at nucleotide 9,812. Multiple nucleotide sequence alignment between these two DWV-VN strains and DWV strains in A. mellifera was performed. The DWV-VN strains showed a low genetic identity (from 91.4% to 92.0%) with almost of these strains, but lower identities (89.2% and 89.4%) with UK2 and (89.6%) with the China2 strain. Low identities (91.7% and 91.9%) were also observed between the China3 strain (in A. cerana) and the DWV-VN strains, respectively. The deduced amino acid sequence alignment showed high genetic similarities (97.0%–97.9%) when the USA1, Chile, Italy1, France, UK1, UK2, Japan, Korea2, China1, China2 and China3 strains were compared to the DWV-VN strains. This ratio was 96.7% and 96.8% when the Korea1 strain was compared to the DWV-SVN and DWV-NVN strains, respectively. Numerous amino acid substitutions were identified in the L, VP3, and RdRp sequences. Notably, we observed six substitutions positioned at amino acids 27 (E > I), 98 (S > T), 120 (A > V), 153 (M > T), 170 (D > F), and 174 (Y > F) in the L protein, two amino acid changes at positions 980 (S > A) and 1032 (E > T) in VP3, and one amino acid change at position 2627 (R > C) unique to the DWV-VN strains. Phylogenetic analysis based on complete genome sequences, RdRp sequences and Simplot analysis indicated that there was a significant difference between DWV-VN strains in A. cerana and DWV strains in A. mellifera. The results suggested that the genetic variations of the DWV-VN strains in A. cerana help them to adapt geographical conditions and may lead to change the viral pathogenicity of DWV-VN strains. creator: Ha T. Thu creator: Nguyen T.K. Lien creator: Pham T. Lanh creator: Bui T.T. Duong creator: Nguyen T. Hoa creator: Man H. Phuoc creator: Pham H. Thai creator: Dong Van Quyen uri: https://doi.org/10.7717/peerj.9911 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Thu et al. title: Identification of NUF2 and FAM83D as potential biomarkers in triple-negative breast cancer link: https://peerj.com/articles/9975 last-modified: 2020-09-21 description: BackgroundBreast cancer is a heterogeneous disease. Compared with other subtypes of breast cancer, triple-negative breast cancer (TNBC) is easy to metastasize and has a short survival time, less choice of treatment options. Here, we aimed to identify the potential biomarkers to TNBC diagnosis and prognosis.Material/MethodsThree independent data sets (GSE45827, GSE38959, GSE65194) were downloaded from the Gene Expression Omnibus (GEO). The R software packages were used to integrate the gene profiles and identify differentially expressed genes (DEGs). A variety of bioinformatics tools were used to explore the hub genes, including the DAVID database, STRING database and Cytoscape software. Reverse transcription quantitative PCR (RT-qPCR) was used to verify the hub genes in 14 pairs of TNBC paired tissues.ResultsIn this study, we screened out 161 DEGs between 222 non-TNBC and 126 TNBC samples, of which 105 genes were up-regulated and 56 were down-regulated. These DEGs were enriched for 27 GO terms and two pathways. GO analysis enriched mainly in “cell division”, “chromosome, centromeric region” and “microtubule motor activity”. KEGG pathway analysis enriched mostly in “Cell cycle” and “Oocyte meiosis”. PPI network was constructed and then 10 top hub genes were screened. According to the analysis results of the Kaplan-Meier survival curve, the expression levels of only NUF2, FAM83D and CENPH were associated with the recurrence-free survival in TNBC samples (P < 0.05). RT-qPCR confirmed that the expression levels of NUF2 and FAM83D in TNBC tissues were indeed up-regulated significantly.ConclusionsThe comprehensive analysis showed that NUF2 and FAM83D could be used as potential biomarkers for diagnosis and prognosis of TNBC. creator: Xiuming Zhai creator: Zhaowei Yang creator: Xiji Liu creator: Zihe Dong creator: Dandan Zhou uri: https://doi.org/10.7717/peerj.9975 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhai et al. title: Confidence intervals for the common coefficient of variation of rainfall in Thailand link: https://peerj.com/articles/10004 last-modified: 2020-09-21 description: The log-normal distribution is often used to analyze environmental data like daily rainfall amounts. The rainfall is of interest in Thailand because high variable climates can lead to periodic water stress and scarcity. The mean, standard deviation or coefficient of variation of the rainfall in the area is usually estimated. The climate moisture index is the ratio of plant water demand to precipitation. The climate moisture index should use the coefficient of variation instead of the standard deviation for comparison between areas with widely different means. The larger coefficient of variation indicates greater dispersion, whereas the lower coefficient of variation indicates the lower risk. The common coefficient of variation, is the weighted coefficients of variation based on k areas, presents the average daily rainfall. Therefore, the common coefficient of variation is used to describe overall water problems of k areas. In this paper, we propose four novel approaches for the confidence interval estimation of the common coefficient of variation of log-normal distributions based on the fiducial generalized confidence interval (FGCI), method of variance estimates recovery (MOVER), computational, and Bayesian approaches. A Monte Carlo simulation was used to evaluate the coverage probabilities and average lengths of the confidence intervals. In terms of coverage probability, the results show that the FGCI approach provided the best confidence interval estimates for most cases except for when the sample case was equal to six populations (k = 6) and the sample sizes were small (nI < 50), for which the MOVER confidence interval estimates were the best. The efficacies of the proposed approaches are illustrated with example using real-life daily rainfall datasets from regions of Thailand. creator: Warisa Thangjai creator: Sa-Aat Niwitpong creator: Suparat Niwitpong uri: https://doi.org/10.7717/peerj.10004 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Thangjai et al. title: Transcriptomic analysis reveals insights into the response to Hop stunt viroid (HSVd) in sweet cherry (Prunus avium L.) fruits link: https://peerj.com/articles/10005 last-modified: 2020-09-21 description: Hop stunt viroid (HSVd) is a member of the genus Hostuviroid of the family Pospiviroidae and has been found in a wide range of herbaceous and woody hosts. It causes serious dapple fruit symptoms on infected sweet cherry, notably inducing cherry tree decay. In order to better understand the molecular mechanisms of HSVd infection in sweet cherry fruit, transcriptome analysis of HSVd-infected and healthy sweet cherry fruits was carried out. A total of 1,572 differentially expressed genes (DEGs) were identified, involving 961 upregulated DEGs and 611 downregulated DEGs. Functional analysis indicated that the DEGs were mainly involved in plant hormone signal transduction, plant–pathogen interactions, secondary metabolism, and the MAPK signaling pathway. In addition, C2H2 zinc finger, MYB, bHLH, AP2/ERF, C2C2-dof, NAC and WRKY transcription factors can respond to HSVd infection. In order to confirm the high-throughput sequencing results, 16 DEGs were verified by RT-qPCR analysis. The results provided insight into the pathways and genes of sweet cherry fruit in response to HSVd infection. creator: Li Xu creator: Xiaojuan Zong creator: Jiawei Wang creator: Hairong Wei creator: Xin Chen creator: Qingzhong Liu uri: https://doi.org/10.7717/peerj.10005 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Xu et al. title: Θ-SEIHRD mathematical model of Covid19-stability analysis using fast-slow decomposition link: https://peerj.com/articles/10019 last-modified: 2020-09-21 description: In general, a mathematical model that contains many linear/nonlinear differential equations, describing a phenomenon, does not have an explicit hierarchy of system variables. That is, the identification of the fast variables and the slow variables of the system is not explicitly clear. The decomposition of a system into fast and slow subsystems is usually based on intuitive ideas and knowledge of the mathematical model being investigated. In this study, we apply the singular perturbed vector field (SPVF) method to the COVID-19 mathematical model of to expose the hierarchy of the model. This decomposition enables us to rewrite the model in new coordinates in the form of fast and slow subsystems and, hence, to investigate only the fast subsystem with different asymptotic methods. In addition, this decomposition enables us to investigate the stability analysis of the model, which is important in case of COVID-19. We found the stable equilibrium points of the mathematical model and compared the results of the model with those reported by the Chinese authorities and found a fit of approximately 96 percent. creator: OPhir Nave creator: Israel Hartuv creator: Uziel Shemesh uri: https://doi.org/10.7717/peerj.10019 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Nave et al. title: Microbiomes of fish, sediment and seagrass suggest connectivity of coral reef microbial populations link: https://peerj.com/articles/10026 last-modified: 2020-09-21 description: The benthic environments of coral reefs are heavily shaped by physiochemical factors, but also the ecological interactions of the animals and plants in the reef ecosystem. Microbial populations may be shared within the ecosystem of sediments, seagrasses and reef fish. In this study, we hypothesize that coral reef and seagrass environments share members of the microbial community that are rare in some habitats and enriched in others, and that animals may integrate this connectivity. We investigated the potential connectivity between the microbiomes of sediments, seagrass blades and roots (Syringodium isoetifolium), and a seagrass-specialist parrotfish (C. spinidens) guts in reef areas of Fiji. We contrasted these with sediment samples from the Florida Keys, gut samples from surgeonfish (A. nigricauda, Acanthurinae sp. unknown, C. striatus), and ocean water microbiomes from the Atlantic, Pacific and Indian Oceans to test the robustness of our characterizations of microbiome environments. In general, water, sediment and fish gut samples were all distinct microbiomes. Sediment microbiomes were mostly similar between Fiji and Florida, but also showed some regional similarities. In Fiji, we show connectivity of a shared microbiome between seagrass, fish and sediments. Additionally, we identified an environmental reservoir of a surgeonfish symbiont, Epulopiscium. The connection of these ecosystem components suggests that the total microbiome of these environments may vary as their animal inhabitants shift in a changing ocean. creator: Rosa León-Zayas creator: Molly McCargar creator: Joshua A. Drew creator: Jennifer F. Biddle uri: https://doi.org/10.7717/peerj.10026 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 León-Zayas et al. title: Development of a camera trap for perching dragonflies: a new tool for freshwater environmental assessment link: https://peerj.com/articles/9681 last-modified: 2020-09-18 description: Although dragonflies are excellent environmental indicators for monitoring terrestrial water ecosystems, automatic monitoring techniques using digital tools are limited. We designed a novel camera trapping system with an original dragonfly detector based on the hypothesis that perching dragonflies can be automatically detected using inexpensive and energy-saving photosensors built in a perch-like structure. A trial version of the camera trap was developed and evaluated in a case study targeting red dragonflies (Sympetrum spp.) in Japan. During an approximately 2-month period, the detector successfully detected Sympetrum dragonflies while using extremely low power consumption (less than 5 mW). Furthermore, a short-term field experiment using time-lapse cameras for validation at three locations indicated that the detection accuracy was sufficient for practical applications. The frequency of false positive detection ranged from 17 to 51 over an approximately 2-day period. The detection sensitivities were 0.67 and 1.0 at two locations, where a time-lapse camera confirmed that Sympetrum dragonflies perched on the trap more than once. However, the correspondence between the detection frequency by the camera trap and the abundance of Sympetrum dragonflies determined by field observations conducted in parallel was low when the dragonfly density was relatively high. Despite the potential for improvements in our camera trap and its application to the quantitative monitoring of dragonflies, the low cost and low power consumption of the detector make it a promising tool. creator: Akira Yoshioka creator: Akira Shimizu creator: Hiroyuki Oguma creator: Nao Kumada creator: Keita Fukasawa creator: Shoma Jingu creator: Taku Kadoya uri: https://doi.org/10.7717/peerj.9681 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Yoshioka et al. title: Assessing the responses of Sphagnum micro-eukaryotes to climate changes using high throughput sequencing link: https://peerj.com/articles/9821 last-modified: 2020-09-18 description: Current projections suggest that climate warming will be accompanied by more frequent and severe drought events. Peatlands store ca. one third of the world’s soil organic carbon. Warming and drought may cause peatlands to become carbon sources through stimulation of microbial activity increasing ecosystem respiration, with positive feedback effect on global warming. Micro-eukaryotes play a key role in the carbon cycle through food web interactions and therefore, alterations in their community structure and diversity may affect ecosystem functioning and could reflect these changes. We assessed the diversity and community composition of Sphagnum-associated eukaryotic microorganisms inhabiting peatlands and their response to experimental drought and warming using high throughput sequencing of environmental DNA. Under drier conditions, micro-eukaryotic diversity decreased, the relative abundance of autotrophs increased and that of osmotrophs (including Fungi and Peronosporomycetes) decreased. Furthermore, we identified climate change indicators that could be used as early indicators of change in peatland microbial communities and ecosystem functioning. The changes we observed indicate a shift towards a more “terrestrial” community in response to drought, in line with observed changes in the functioning of the ecosystem. creator: Monika K. Reczuga creator: Christophe Victor William Seppey creator: Matthieu Mulot creator: Vincent E.J. Jassey creator: Alexandre Buttler creator: Sandra Słowińska creator: Michał Słowiński creator: Enrique Lara creator: Mariusz Lamentowicz creator: Edward A.D. Mitchell uri: https://doi.org/10.7717/peerj.9821 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Reczuga et al. title: Differences in small noncoding RNAs profile between bull X and Y sperm link: https://peerj.com/articles/9822 last-modified: 2020-09-18 description: The differences in small noncoding RNAs (sncRNAs), including miRNAs, piRNAs, and tRNA-derived fragments (tsRNAs), between X and Y sperm of mammals remain unclear. Here, we employed high-throughput sequencing to systematically compare the sncRNA profiles of X and Y sperm from bulls (n = 3), which may have a wider implication for the whole mammalian class. For the comparison of miRNA profiles, we found that the abundance of bta-miR-652 and bta-miR-378 were significantly higher in X sperm, while nine miRNAs, including bta-miR-204 and bta-miR-3432a, had greater abundance in Y sperm (p < 0.05). qPCR was then used to further validate their abundances. Subsequent functional analysis revealed that their targeted genes in sperm were significantly involved in nucleosome binding and nucleosomal DNA binding. In contrast, their targeted genes in mature oocyte were significantly enriched in 11 catabolic processes, indicating that these differentially abundant miRNAs may trigger a series of catabolic processes for the catabolization of different X and Y sperm components during fertilization. Furthermore, we found that X and Y sperm showed differences in piRNA clusters distributed in the genome as well as piRNA and tsRNA abundance, two tsRNAs (tRNA-Ser-AGA and tRNA-Ser-TGA) had lower abundance in X sperm than Y sperm (p < 0.05). Overall, our work describes the different sncRNA profiles of X and Y sperm in cattle and enhances our understanding of their potential roles in the regulation of sex differences in sperm and early embryonic development. creator: Hao Zhou creator: Jiajia Liu creator: Wei Sun creator: Rui Ding creator: Xihe Li creator: Aishao Shangguan creator: Yang Zhou creator: Tesfaye Worku creator: Xingjie Hao creator: Faheem Ahmed Khan creator: Liguo Yang creator: Shujun Zhang uri: https://doi.org/10.7717/peerj.9822 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhou et al. title: A new tiny toad species of Amazophrynella (Anura: Bufonidae) from east of the Guiana Shield in Amazonia, Brazil link: https://peerj.com/articles/9887 last-modified: 2020-09-18 description: The combination of different approaches has successfully delimited new species within many Neotropical species complexes traditionally classified as a single nominal organism. Recent studies have shown that the Amazonian endemic genus Amazophrynella, currently composed of 12 small-sized species, could harbor several additional species. Based on morphology and molecular data, we describe a new species of Amazophrynella from east of the Guiana Shield, in Pará state, Brazil. The new species is characterized by having one of the biggest size of the genus (SVL of males 16.0–17.8 mm and females 22.9–24.4 mm), presence of a large palmar tubercle (occupying 2/4 of the palmar surface), 5.6–8.1% uncorrected p-distance from its sister clade (including A. teko, A. sp.1, and A. manaos) for the 16S mitochondrial gene, and 8.8% for the COI. The new species described here represents a newly discovered lineage. Of the 12 Amazophrynella species currently recognized, two were describe in the last century (A. bokermanni and A. minuta) and the remaining species were recently discovered and described (in the last six years), which underscores the degree to which species richness of Amazophrynella is underestimated. creator: Sarah Mângia creator: Ricardo Koroiva creator: Diego José Santana uri: https://doi.org/10.7717/peerj.9887 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Mângia et al. title: Endocranial anatomy of the ceratopsid dinosaur Triceratops and interpretations of sensory and motor function link: https://peerj.com/articles/9888 last-modified: 2020-09-18 description: Triceratops is one of the well-known Cretaceous ceratopsian dinosaurs. The ecology of Triceratops has been controversial because of its unique morphological features. However, arguments based on brain and inner ear structures have been scarce. In this study, two braincases (FPDM-V-9677 and FPDM-V-9775) were analyzed with computed tomography to generate three-dimensional virtual renderings of the endocasts of the cranial cavities and bony labyrinths. Quantitative analysis, including comparison of linear measurements of the degree of development of the olfactory bulb and inner ear, was performed on these virtual endocasts to acquire detailed neuroanatomical information. When compared with other dinosaurs, the olfactory bulb of Triceratops is relatively small, indicating that Triceratops had a reduced acuity in sense of smell. The lateral semicircular canal reveals that the basicranial axis of Triceratops is approximately 45° to the ground, which is an effective angle to display their horns as well as frill, and to graze. The semicircular canals of Triceratops are relatively smaller than those of primitive ceratopsians, such as Psittacosaurus and Protoceratops, suggesting that sensory input for the reflexive stabilization of gaze and posture of Triceratops was less developed than that of primitive ceratopsians. The cochlear length of Triceratops is relatively short when compared with other dinosaurs. Because cochlear length correlates with hearing frequency, Triceratops was likely adapted to hearing low frequencies. creator: Rina Sakagami creator: Soichiro Kawabe uri: https://doi.org/10.7717/peerj.9888 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Sakagami and Kawabe title: Genetic variation and selection in the major histocompatibility complex Class II gene in the Guizhou pony link: https://peerj.com/articles/9889 last-modified: 2020-09-18 description: The Guizhou pony (GZP) is an indigenous species of equid found in the mountains of the Guizhou province in southwest China. We selected four regions of the equine leukocyte antigen (ELA), including DQA, DRA, DQB, and DRB, and used them to assess the diversity of the major histocompatibility complex (MHC) class II gene using direct sequencing technology. DRA had the lowest dN/dS ratio (0.560) compared with the other three loci, indicating that DRA was conserved and could be conserved after undergoing selective processes. Nine DQA, five DQB, nine DRA, and seven DRB codons were under significant positive selection at the antigen binding sites (ABS), suggesting that the selected residues in ABS may play a significant role in the innate immune system of the GZP. Two GZP alleles were shared with Przewalski’s horse, and six older GZP haplotypes had a better relationship with other horse species by one or two mutational steps, indicating that the GZP may be a natural ancient variety of equid. The specific diversity of ABS and the numbers of unique haplotypes in the evolutionary process affords this species a better genetic fitness and ability to adapt to the native environment. creator: Chang Liu creator: Hongmei Lei creator: Xueqin Ran creator: Jiafu Wang uri: https://doi.org/10.7717/peerj.9889 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Liu et al. title: Native trees of Mexico: diversity, distribution, uses and conservation link: https://peerj.com/articles/9898 last-modified: 2020-09-18 description: BackgroundMexico is one of the most floristically rich countries in the world. Despite significant contributions made on the understanding of its unique flora, the knowledge on its diversity, geographic distribution and human uses, is still largely fragmented. Unfortunately, deforestation is heavily impacting this country and native tree species are under threat. The loss of trees has a direct impact on vital ecosystem services, affecting the natural capital of Mexico and people’s livelihoods. Given the importance of trees in Mexico for many aspects of human well-being, it is critical to have a more complete understanding of their diversity, distribution, traditional uses and conservation status. We aimed to produce the most comprehensive database and catalogue on native trees of Mexico by filling those gaps, to support their in situ and ex situ conservation, promote their sustainable use, and inform reforestation and livelihoods programmes.MethodsA database with all the tree species reported for Mexico was prepared by compiling information from herbaria and reviewing the available floras. Species names were reconciled and various specialised sources were used to extract additional species information, i.e. endemic status, threat status, availability in seed collections, reports on plant uses and conservation actions currently in place. With this information, a comprehensive catalogue of native trees from Mexico was redacted. Available georeferenced records were used to map each species distribution and perform spatial analyses to identify gaps of information and priority areas for their conservation and exploration.ResultsMexico has at least 2,885 native tree species, belonging to 612 genera and 128 families. Fabaceae is the most represented family and Quercus the most represented genus. Approximately 44% of tree species are endemic to the country. The southern part of the country showed the highest values of species richness. Six hundred and seventy-four species have at least one documented human use. In terms of conservation assessment, ca. 33% of species have been assessed by either the IUCN Red List (919) or the National protection catalogue “NORMA Oficial Mexicana NOM-059” (29) or both (45). Additionally, 98 species have been included in the CITES listing for protection. In terms of existing conservation efforts, 19% of species have ex situ protection in seed banks, while protected areas overlap with all the identified peaks of species richness, except for those in the states of Veracruz and Chiapas. This work constitutes a key milestone for the knowledge, management, and conservation of the Mexican native trees. The two areas with high density of tree species identified in Veracruz and Chiapas represent two priority areas for tree conservation in Mexico, where integrated in situ and ex situ conservation efforts should be focused. creator: Oswaldo Tellez creator: Efisio Mattana creator: Mauricio Diazgranados creator: Nicola Kühn creator: Elena Castillo-Lorenzo creator: Rafael Lira creator: Leobardo Montes-Leyva creator: Isela Rodriguez creator: Cesar Mateo Flores Ortiz creator: Michael Way creator: Patricia Dávila creator: Tiziana Ulian uri: https://doi.org/10.7717/peerj.9898 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Tellez et al. title: Life-history traits and intra-cohort divergence of clearhead icefish (Protosalanx chinensis), indicating cannibalism increased fitness link: https://peerj.com/articles/9900 last-modified: 2020-09-18 description: Cannibalism is considered one of the causes of intra-cohort size divergence in fish and is usually believed to result in increased fitness in terms of survival and reproduction, but direct evidence of this is lacking. Population demographics of the clearhead icefish (Protosalanx chinensis) from Lake Xingkai (Khanka) were investigated for one year. Size-frequencies exhibited a bimodal distribution from July through January, where the population diverged into an upper and a lower modal group based on size. Stomach content analysis confirmed the occurrence of cannibalism, where fish belonging to the larger, upper modal group preyed upon those of the smaller, lower modal group. We found P. chinensis does not spawn until all of the oocytes have reached maturity and then a single spawning event occurs although the oocytes may develope asynchronously in the ovary. Upper modal group females matured slightly earlier than those of the lower modal group, and reproductive investment was considerably greater in the upper modal group than the lower modal group. The lower modal males made up the majority of the population after the spawning period, which meant they may have few opportunities to participate in reproduction. Therefore, piscivory and cannibalism of P. chinensis appears to have increased fitness of the fish belonging to the upper modal group and greatly reduced the fitness of those belonging to the lower modal group. creator: Fujiang Tang creator: Wei Liu creator: Jilong Wang creator: James Henne uri: https://doi.org/10.7717/peerj.9900 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: ©2020 Tang et al. title: Different responses of plant N and P resorption to overgrazing in three dominant species in a typical steppe of Inner Mongolia, China link: https://peerj.com/articles/9915 last-modified: 2020-09-18 description: Nutrient resorption from senesced leaves is an important mechanism for nutrient conservation in plants. However, little is known about the effect of grazing on plant nutrient resorption from senesced leaves, especially in semiarid ecosystems. Here, we evaluated the effects of grazing on N and P resorption in the three most dominant grass species in a typical steppe in northern China. We identified the key pathways of grazing-induced effects on N and P resorption efficiency. Grazing increased N and P concentrations in the green leaves of Leymus chinensis and Stipa grandis but not in Cleistogenes squarossa. Both L. chinensis and S. grandis exhibited an increasing trend of leaf N resorption, whereas C. squarrosa recorded a decline in both leaf N and P resorption efficiency under grazing. Structural equation models showed that grazing is the primary driver of the changes in N resorption efficiency of the three dominant grass species. For L. chinensis, the P concentration in green and senesced leaves increased the P resorption efficiency, whereas the senesced leaf P concentration played an important role in the P resorption efficiency of C. squarrosa. Grazing directly drove the change in P resorption efficiency of S. grandis. Our results suggest that large variations in nutrient resorption patterns among plant species depend on leaf nutritional status and nutrient-use strategies under overgrazing, and indicate that overgrazing may have indirect effects on plant-mediated nutrient cycling via inducing shifts in the dominance of the three plant species. creator: Zhen Wang creator: Saheed Olaide Jimoh creator: Xiliang Li creator: Baoming Ji creator: Paul C. Struik creator: Shixian Sun creator: Ji Lei creator: Yong Ding creator: Yong Zhang uri: https://doi.org/10.7717/peerj.9915 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al. title: Sampling impacts the assessment of tooth growth and replacement rates in archosaurs: implications for paleontological studies link: https://peerj.com/articles/9918 last-modified: 2020-09-18 description: Dietary habits in extinct species cannot be directly observed; thus, in the absence of extraordinary evidence, they must be reconstructed with a combination of morphological proxies. Such proxies often include information on dental organization and function such as tooth formation time and tooth replacement rate. In extinct organisms, tooth formation times and tooth replacement rate are calculated, in part via extrapolation of the space between incremental lines in dental tissues representing daily growth (von Ebner Line Increment Width; VEIW). However, to date, little work has been conducted testing assumptions about the primary data underpinning these calculations, specifically, the potential impact of differential sampling and data extrapolation protocols. To address this, we tested a variety of intradental, intramandibular, and ontogentic sampling effects on calculations of mean VEIW, tooth formation times, and replacement rates using histological sections and CT reconstructions of a growth series of three specimens of the extant archosaurian Alligator mississippiensis. We find transect position within the tooth and transect orientation with respect to von Ebner lines to have the greatest impact on calculations of mean VEIW—a maximum number of VEIW measurements should be made as near to the central axis (CA) as possible. Measuring in regions away from the central axis can reduce mean VEIW by up to 36%, causing inflated calculations of tooth formation time. We find little demonstrable impact to calculations of mean VEIW from the practice of subsampling along a transect, or from using mean VEIW derived from one portion of the dentition to extrapolate for other regions of the dentition. Subsampling along transects contributes only minor variations in mean VEIW (<12%) that are dwarfed by the standard deviation (SD). Moreover, variation in VEIW with distance from the pulp cavity likely reflects idiosyncratic patterns related to life history, which are difficult to control for; however, we recommend increasing the number of VEIW measured to minimize this effect. Our data reveal only a weak correlation between mean VEIW and body length, suggesting minimal ontogenetic impacts. Finally, we provide a relative SD of mean VEIW for Alligator of 29.94%, which can be used by researchers to create data-driven error bars for tooth formation times and replacement rates in fossil taxa with small sample sizes. We caution that small differences in mean VEIW calculations resulting from non-standardized sampling protocols, especially in a comparative context, will produce inflated error in tooth formation time estimations that intensify with crown height. The same holds true for applications of our relative SD to calculations of tooth formation time in extinct taxa, which produce highly variable maximum and minimum estimates in large-toothed taxa (e.g., 718–1,331 days in Tyrannosaurus). creator: Jens C.D. Kosch creator: Lindsay E. Zanno uri: https://doi.org/10.7717/peerj.9918 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Kosch and Zanno title: Mesenchymal stem cell exosomes reverse acute lung injury through Nrf-2/ARE and NF-κB signaling pathways link: https://peerj.com/articles/9928 last-modified: 2020-09-18 description: Acute lung injury (ALI) is associated with histopathological diffuse alveolar damage. The potential role of mesenchymal stem cells (MSCs) in the treatment of various clinical disorders have been widely documented, such as those for ALI. Recent evidence has demonstrated that exosomes from endothelial progenitor cells can improve outcomes of the lipopolysaccharide (LPS)-induced ALI. However, there has been no research on the potential role of MSC-exosomes in the treatment of sepsis-induced ALI, which is worth further exploration. Thus, the objective of our study was to identify whether the MSC-exosomes could reverse ALI. The ALI model induced by LPS was established in this study. MTT assay was performed to test cell proliferation. Expression of inflammatory factors (TNF-α, IL-6, and IL-10) in the LPS-treated type II alveolar epithelial cells (AECs) (MLE-12) was detected by ELISA. After co-culture of MSC-exosomes with LPS-treated MLE-12 cells, we found that the cell proliferation of MLE-12 cells gradually increased. Furthermore, we selected five of the Nrf-2/ARE- and NF-κB signaling pathway-related genes to explore if MSC-exosomes could reverse LPS-induced ALI through Nrf-2/ARE and NF-κB signaling pathways. QRT-PCR and western blot experiment results showed that the expression of these five genes were significantly regulated after stimulation with high-concentration LPS and exosome intervention. Taken together, these findings highlighted the fact that MSC-exosomes could reverse ALI through the Nrf-2/ARE and NF-κB signaling pathways. The MSC-exosome may be the potential future therapeutic strategy for the treatment of ALI. creator: Jun Li creator: Xingqi Deng creator: Xiangling Ji creator: Xiaojun Shi creator: Zhiying Ying creator: Kan Shen creator: Dongwei Xu creator: Zhihui Cheng uri: https://doi.org/10.7717/peerj.9928 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Li et al. title: Potential COVID-19 papain-like protease PLpro inhibitors: repurposing FDA-approved drugs link: https://peerj.com/articles/9965 last-modified: 2020-09-18 description: Using the crystal structure of SARS-CoV-2 papain-like protease (PLpro) as a template, we developed a pharmacophore model of functional centers of the PLpro inhibitor-binding pocket. With this model, we conducted data mining of the conformational database of FDA-approved drugs. This search identified 147 compounds that can be potential inhibitors of SARS-CoV-2 PLpro. The conformations of these compounds underwent 3D fingerprint similarity clusterization, followed by docking of possible conformers to the binding pocket of PLpro. Docking of random compounds to the binding pocket of protease was also done for comparison. Free energies of the docking interaction for the selected compounds were lower than for random compounds. The drug list obtained includes inhibitors of HIV, hepatitis C, and cytomegalovirus (CMV), as well as a set of drugs that have demonstrated some activity in MERS, SARS-CoV, and SARS-CoV-2 therapy. We recommend testing of the selected compounds for treatment of COVID-19 creator: Valentina L. Kouznetsova creator: Aidan Zhang creator: Mahidhar Tatineni creator: Mark A. Miller creator: Igor F. Tsigelny uri: https://doi.org/10.7717/peerj.9965 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Kouznetsova et al. title: Radiolarian assemblages in the shelf area of the East China Sea and Yellow Sea and their ecological indication of the Kuroshio Current derivative branches link: https://peerj.com/articles/9976 last-modified: 2020-09-18 description: We analyzed the radiolarian assemblages of 59 surface sediment samples collected from the Yellow Sea and East China Sea of the northwestern Pacific. In the study region, the Kuroshio Current and its derivative branches exerted a crucial impact on radiolarian composition and distribution. Radiolarians in the Yellow Sea shelf showed a quite low abundance as no tests were found in 15 of 25 Yellow Sea samples. Radiolarians in the East China Sea shelf could be divided into three regional groups: the East China Sea north region group, the East China Sea middle region group, and the East China Sea south region group. The results of the redundancy analysis suggested that the Sea Surface Temperature and Sea Surface Salinity were primary environmental variables explaining species-environment relationship. The gradients of temperature, salinity, and species diversity reflect the powerful influence of the Kuroshio Current in the study area. creator: Hanxue Qu creator: Yong Xu creator: Jinbao Wang creator: Xin-Zheng Li uri: https://doi.org/10.7717/peerj.9976 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Qu et al. title: Development of a noninvasive photograph-based method for the evaluation of body condition in free-ranging brown bears link: https://peerj.com/articles/9982 last-modified: 2020-09-18 description: Body condition is an important determinant of health, and its evaluation has practical applications for the conservation and management of mammals. We developed a noninvasive method that uses photographs to assess the body condition of free-ranging brown bears (Ursus arctos) in the Shiretoko Peninsula, Hokkaido, Japan. First, we weighed and measured 476 bears captured during 1998–2017 and calculated their body condition index (BCI) based on residuals from the regression of body mass against body length. BCI showed seasonal changes and was lower in spring and summer than in autumn. The torso height:body length ratio was strongly correlated with BCI, which suggests that it can be used as an indicator of body condition. Second, we examined the precision of photograph-based measurements using an identifiable bear in the Rusha area, a special wildlife protection area on the peninsula. A total of 220 lateral photographs of this bear were taken September 24–26, 2017, and classified according to bear posture. The torso height:body/torso length ratio was calculated with four measurement methods and compared among bear postures in the photographs. The results showed torso height:horizontal torso length (TH:HTL) to be the indicator that could be applied to photographs of the most diverse postures, and its coefficient of variation for measurements was <5%. In addition, when analyzing photographs of this bear taken from June to October during 2016–2018, TH:HTL was significantly higher in autumn than in spring/summer, which indicates that this ratio reflects seasonal changes in body condition in wild bears. Third, we calculated BCI from actual measurements of seven females captured in the Rusha area and TH:HTL from photographs of the same individuals. We found a significant positive relationship between TH:HTL and BCI, which suggests that the body condition of brown bears can be estimated with high accuracy based on photographs. Our simple and accurate method is useful for monitoring bear body condition repeatedly over the years and contributes to further investigation of the relationships among body condition, food habits, and reproductive success. creator: Yuri Shirane creator: Fumihiko Mori creator: Masami Yamanaka creator: Masanao Nakanishi creator: Tsuyoshi Ishinazaka creator: Tsutomu Mano creator: Mina Jimbo creator: Mariko Sashika creator: Toshio Tsubota creator: Michito Shimozuru uri: https://doi.org/10.7717/peerj.9982 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Shirane et al. title: Soil fungal networks are more sensitive to grazing exclusion than bacterial networks link: https://peerj.com/articles/9986 last-modified: 2020-09-18 description: Soil microbial communities play a crucial role in ecological restoration, but it is unknown how co-occurrence networks within these communities respond to grazing exclusion. This lack of information was addressed by investigating the effects of eight years of grazing exclusion on microbial networks in an area of Stipa glareosa P. Smirn desert steppe in northern China. Here, we show that fungal networks were more sensitive to grazing exclusion than bacterial networks. Eight years of grazing exclusion decreased the soil fungal community stability via changes in plant composition and reductions in soil total organic carbon, in this case triggering negative effects on the S. glareosa desert steppe. The results provide new insights into the response mechanisms of soil microbes to grazing exclusion and offer possible solutions for management issues in the restoration of degraded desert steppe. creator: Lingling Chen creator: Jiajia Shi creator: Zhihua Bao creator: Taogetao Baoyin uri: https://doi.org/10.7717/peerj.9986 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Chen et al. title: Evidence of transfer of miRNAs from the diet to the blood still inconclusive link: https://peerj.com/articles/9567 last-modified: 2020-09-17 description: MicroRNAs (miRNAs) are short, non-coding, single-strand RNA molecules that act as regulators of gene expression in plants and animals. In 2012, the first evidence was found that plant miRNAs could enter the bloodstream through the digestive tract. Since then, there has been an ongoing discussion about whether miRNAs from the diet are transferred to blood, accumulate in tissues, and regulate gene expression. Different research groups have tried to replicate these findings, using both plant and animal sources. Here, we review the evidence for and against the transfer of diet-derived miRNAs from plants, meat, milk and exosome and their assimilation and putative molecular regulation role in the consuming organism. Some groups using both miRNAs from plant and animal sources have claimed success, whereas others have not shown transfer. In spite of the biological barriers that may limit miRNA transference, several diet-derived miRNAs can transfer into the circulating system and targets genes for transcription regulation, which adds arguments that miRNAs can be absorbed from the diet and target specific genes by regulating their expression. However, many other studies show that cross-kingdom transfer of exogenous miRNAs appears to be insignificant and not biologically relevant. The main source of controversy in plant studies is the lack of reproducibility of the findings. For meat-derived miRNAs, studies concluded that the miRNAs can survive the cooking process; nevertheless, our evidence shows that the bovine miRNAs are not transferred to human bloodstream. The most important contributions and promising evidence in this controversial field is the transference of milk miRNAs in exosomes and the finding that plant miRNAs in beebread regulate honeybee caste development, and cause similar changes when fed to Drosophila. MiRNAs encapsulated in exosomes ensure their stability and resistance in the harsh conditions presented in milk, bloodstream, and gastrointestinaltract to reinforce the idea of transference. Regardless of the model organism, the idea of source of miRNAs, or the approach—bioinformatics or in vivo—the issue of transfer of miRNAs from the diet remains in doubt. Our understanding of the cross-kingdom talk of miRNAs needs more research to study the transfer of “xenomiRs” from different food sources to complement and expand what we know so far regarding the interspecies transfer of miRNAs. creator: Fermín Mar-Aguilar creator: Alejandra Arreola-Triana creator: Daniela Mata-Cardona creator: Vianey Gonzalez-Villasana creator: Cristina Rodríguez-Padilla creator: Diana Reséndez-Pérez uri: https://doi.org/10.7717/peerj.9567 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Mar-Aguilar et al. title: Salinity impairs photosynthetic capacity and enhances carotenoid-related gene expression and biosynthesis in tomato (Solanum lycopersicum L. cv. Micro-Tom) link: https://peerj.com/articles/9742 last-modified: 2020-09-17 description: Carotenoids are essential components of the photosynthetic antenna and reaction center complexes, being also responsible for antioxidant defense, coloration, and many other functions in multiple plant tissues. In tomato, salinity negatively affects the development of vegetative organs and productivity, but according to previous studies it might also increase fruit color and taste, improving its quality, which is a current agricultural challenge. The fruit quality parameters that are increased by salinity are cultivar-specific and include carotenoid, sugar, and organic acid contents. However, the relationship between vegetative and reproductive organs and response to salinity is still poorly understood. Considering this, Solanum lycopersicum cv. Micro-Tom plants were grown in the absence of salt supplementation as well as with increasing concentrations of NaCl for 14 weeks, evaluating plant performance from vegetative to reproductive stages. In response to salinity, plants showed a significant reduction in net photosynthesis, stomatal conductance, PSII quantum yield, and electron transport rate, in addition to an increase in non-photochemical quenching. In line with these responses the number of tomato clusters decreased, and smaller fruits with higher soluble solids content were obtained. Mature-green fruits also displayed a salt-dependent higher induction in the expression of PSY1, PDS, ZDS, and LYCB, key genes of the carotenoid biosynthesis pathway, in correlation with increased lycopene, lutein, β-carotene, and violaxanthin levels. These results suggest a key relationship between photosynthetic plant response and yield, involving impaired photosynthetic capacity, increased carotenoid-related gene expression, and carotenoid biosynthesis. creator: Andrés Leiva-Ampuero creator: Mario Agurto creator: José Tomás Matus creator: Gustavo Hoppe creator: Camila Huidobro creator: Claudio Inostroza-Blancheteau creator: Marjorie Reyes-Díaz creator: Claudia Stange creator: Paulo Canessa creator: Andrea Vega uri: https://doi.org/10.7717/peerj.9742 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Leiva-Ampuero et al. title: Jatropha curcas ortholog of tomato MADS-box gene 6 (JcTM6) promoter exhibits floral-specific activity in Arabidopsis thaliana link: https://peerj.com/articles/9827 last-modified: 2020-09-17 description: BackgroundJatropha curcas L., a perennial oilseed plant, is considered as a promising feedstock for biodiesel production. Genetic modification of flowering characteristics is critical for Jatropha breeding. However, analysis of floral-specific promoters in Jatropha is limited.MethodsIn this study, we isolated the Jatropha ortholog of TM6 (JcTM6) gene from Jatropha flower cDNA library and detected the expression pattern of JcTM6 gene by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). We isolated a 1.8-kb fragment from the 5’ region of the JcTM6 gene and evaluated its spatiotemporal expression pattern in Arabidopsis using the β-glucuronidase (GUS) reporter gene and Arabidopsis ATP/ADP isopentenyltransferase 4 (AtIPT4) gene, respectively.ResultsJcTM6 was identified as a flower-specific gene in Jatropha. As expected, JcTM6 promoter was only active in transgenic Arabidopsis flowers with the strongest activity in stamens. Moreover, JcTM6:AtIPT4 transgenic Arabidopsis showed a phenotype of large flowers without any alterations in other organs. Furthermore, deletion of the region from –1,717 to –876 bp resulted in the disappearance of promoter activity in stamens but an increase in promoter activity in young leaves, sepals, and petals. Deletion analysis suggests that the –1,717- to –876-bp promoter fragment contains regulatory elements that confer promoter activity in stamens and inhibit activity in young leaves, sepals, and petals. creator: Jing-Xian Wang creator: Xin Ming creator: Yan-Bin Tao creator: Zeng-Fu Xu uri: https://doi.org/10.7717/peerj.9827 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2020 Wang et al. title: Association between serum and dietary antioxidant micronutrients and advanced liver fibrosis in non-alcoholic fatty liver disease: an observational study link: https://peerj.com/articles/9838 last-modified: 2020-09-17 description: BackgroundDespite clinical trials with antioxidant supplementation, few studies have been conducted to evaluate the nutritional status of antioxidant vitamins and minerals, and none have reported on the status of these serum antioxidants associated with the dietary intake of antioxidants by non-alcoholic fatty liver disease (NAFLD) patients.ObjectiveTo evaluate association between serum and dietetics antioxidants with liver fibrosis in patients with NAFLD.MethodsAcross-section analysis with out with 72 patients diagnosed with NAFLD. Hepatic fibrosis was measured by FibroScan®, and liver stiffness ≥7.9 kPa was considered to indicate advanced fibrosis. Retinol, alpha-tocopherol, ascorbic acid, beta-carotene, serum zinc, and selenium were evaluated, as was the dietary intake of these micronutrients in the previous 24 h (using 24-h dietary recall). The Mann–Whitney test was used to compare the fibrosis groups and, a linear regression analysis was performed to determine associated risk factors between age, sex, BMI, hepatic fibrosis, and serum antioxidants.ResultsA high proportion of inadequate serum retinol (20.8%), vitamin C (27%), and selenium (73.6%) was observed in the patients with NAFLD, in addition to a significant inadequacy of vitamin A (98.3%) and vitamin E (100%) intake. Patients with advanced liver fibrosis had reduced levels of serum retinol (P = 0.002), with liver fibrosis being the independent risk factor associated with serum retinol lower.ConclusionHepatic fibrosis was associated with a reduction in serum retinol and was reduced in advanced fibrosis. NAFLD patients showed an important serum deficiency and insufficient dietary intake of the evaluated micronutrients. creator: Juliana Moraes Coelho creator: Katia Cansanção creator: Renata de Mello Perez creator: Nathalie Carvalho Leite creator: Patrícia Padilha creator: Andrea Ramalho creator: Wilza Peres uri: https://doi.org/10.7717/peerj.9838 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Coelho et al. title: lcc: an R package to estimate the concordance correlation, Pearson correlation and accuracy over time link: https://peerj.com/articles/9850 last-modified: 2020-09-17 description: Background and ObjectiveObservational studies and experiments in medicine, pharmacology and agronomy are often concerned with assessing whether different methods/raters produce similar values over the time when measuring a quantitative variable. This article aims to describe the statistical package lcc, for are, that can be used to estimate the extent of agreement between two (or more) methods over the time, and illustrate the developed methodology using three real examples.MethodsThe longitudinal concordance correlation, longitudinal Pearson correlation, and longitudinal accuracy functions can be estimated based on fixed effects and variance components of the mixed-effects regression model. Inference is made through bootstrap confidence intervals and diagnostic can be done via plots, and statistical tests.ResultsThe main features of the package are estimation and inference about the extent of agreement using numerical and graphical summaries. Moreover, our approach accommodates both balanced and unbalanced experimental designs or observational studies, and allows for different within-group error structures, while allowing for the inclusion of covariates in the linear predictor to control systematic variations in the response. All examples show that our methodology is flexible and can be applied to many different data types.ConclusionsThe lcc package, available on the CRAN repository, proved to be a useful tool to describe the agreement between two or more methods over time, allowing the detection of changes in the extent of agreement. The inclusion of different structures for the variance-covariance matrices of random effects and residuals makes the package flexible for working with different types of databases. creator: Thiago P. Oliveira creator: Rafael A. Moral creator: Silvio S. Zocchi creator: Clarice G.B. Demetrio creator: John Hinde uri: https://doi.org/10.7717/peerj.9850 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Oliveira et al. title: Earthworms accelerate rice straw decomposition and maintenance of soil organic carbon dynamics in rice agroecosystems link: https://peerj.com/articles/9870 last-modified: 2020-09-17 description: BackgroundTo promote straw degradation, we inoculated returned farmland straw with earthworms (Pheretima guillelmi). Increasing the number of earthworms may generally alter soil organic carbon (SOC) dynamics and the biological activity of agricultural soils.MethodsWe performed soil mesocosm experiments with and without earthworms to assess the decomposition and microbial mineralization of returned straw and soil enzyme activity across different time periods.ResultsWhen earthworms were present in soil, the surface residues were completely consumed during the first four weeks, but when earthworms were absent, most of the residues remained on the soil surface after 18 weeks. On day 28, the SOC content was significantly higher in the treatment where both earthworms and residue had been added. The SOC content was lower in the treatment where earthworms but no residue had been added. The organic carbon content in water-stable macroaggregates showed the same trend. During the first 14 weeks, the soil basal respiration was highest in the treatments with both residues and earthworms. From weeks 14 to 18, basal respiration was highest in the treatments with residues but without earthworms. We found a significant positive correlation between soil basal respiration and soil dissolved organic carbon content. Earthworms increased the activity of protease, invertase, urease and alkaline phosphatase enzymes, but decreased β-cellobiohydrolase, β-glucosidase and xylosidase activity, as well as significantly reducing ergosterol content.ConclusionThe primary decomposition of exogenous rice residues was mainly performed by earthworms. Over a short period of time, they converted plant carbon into soil carbon and increased SOC. The earthworms played a key role in carbon conversion and stabilization. In the absence of exogenous residues, earthworm activity accelerated the decomposition of original organic carbon in the soil, reduced SOC, and promoted carbon mineralization. creator: Ke Song creator: Lijuan Sun creator: Weiguang Lv creator: Xianqing Zheng creator: Yafei Sun creator: William Terzaghi creator: Qin Qin creator: Yong Xue uri: https://doi.org/10.7717/peerj.9870 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Song et al. title: Wild meat hunting and use by sedentarised Baka Pygmies in southeastern Cameroon link: https://peerj.com/articles/9906 last-modified: 2020-09-17 description: As a result of sedentarisation many Baka Pygmies have changed their mobility patterns away from nomadic lifestyles to living in roadside villages. These settled groups are increasingly dependent on cultivated foods but still rely on forest resources. The level of dependence on hunting of wild animals for food and cash, as well as the hunting profiles of sedentarised Pygmy groups is little known. In this study we describe the use of wild meat in 10 Baka villages along the Djoum-Mintom road in southeastern Cameroon. From data collected from 1,946 hunting trips by 121 hunters, we show that most trips are of around 13 hours and a median of eight hours. A mean ± SD of 1.15 ± 1.11 animal carcasses are taken in a single trip; there was a positive correlation between duration of trips and carcasses. A total of 2,245 carcasses of 49 species of 24 animal families were taken in the study; species diversity was similar in all villages except one. Most hunted animals were mammals, with ungulates contributing the highest proportion. By species, just over half of the animal biomass extracted by all hunters in the studied villages was provided by four mammal species. Most animals were trapped (65.77% ± 16.63), followed by shot with guns (22.56% ± 17.72), other methods (8.69% ± 6.96) and with dogs (2.96% ± 4.49). A mean of 7,569.7 ± 6,103.4 kg yr−1 (2,080.8–19,351.4) were extracted per village, giving 75,697 kg yr−1 in total, which is equivalent to 123 UK dairy cattle. In all villages, 48.07% ± 17.58 of animals hunted were consumed by the hunter and his family, around 32.73% ± 12.55, were sold, followed by a lower percentage of carcasses partially sold and consumed (19.21% ± 17.02). Between 60% and 80% of carcasses belonged to the “least concern” category, followed by “near threatened”, “vulnerable” and, rarely “endangered”. The only endangered species hunted was the chimpanzee (Pan troglodytes). We suggest that hunting is a critical activity that provides a vital source of food for our study communities. Measured wild meat extraction levels are likely to be sustainable if hunter densities do not increase. creator: Eva Avila Martin creator: Guillermo Ros Brull creator: Stephan M. Funk creator: Luca Luiselli creator: Robert Okale creator: Julia E. Fa uri: https://doi.org/10.7717/peerj.9906 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Avila Martin et al. title: Estimating the impact of lock-down, quarantine and sensitization in a COVID-19 outbreak: lessons from the COVID-19 outbreak in China link: https://peerj.com/articles/9933 last-modified: 2020-09-17 description: In recent history, COVID-19 is one of the worst infectious disease outbreaks currently affecting humanity globally. Using real data on the COVID-19 outbreak from 22 January 2020 to 30 March 2020, we developed a mathematical model to investigate the impact of control measures in reducing the spread of the disease. Analyses of the model were carried out to determine the dynamics. The results of the analyses reveal that, using the data from China, implementing all possible control measures best reduced the rate of secondary infections. However, quarantine (isolation) of infectious individuals is shown to have the most dominant effect. This possibility emphasizes the need for extensive testing due to the possible prevalence of asymptomatic COVID-19 cases. creator: Obiora C. Collins creator: Kevin J. Duffy uri: https://doi.org/10.7717/peerj.9933 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Collins and Duffy title: Cocoa colonic phenolic metabolites are related to HDL-cholesterol raising effects and methylxanthine metabolites and insoluble dietary fibre to anti-inflammatory and hypoglycemic effects in humans link: https://peerj.com/articles/9953 last-modified: 2020-09-17 description: BackgroundIn many cocoa intervention studies, health outcomes are related to cocoa components without taking into account the bioavailability of the main bioactive components: phenolic compounds and methylxanthines.MethodsThe present work associates the results of bioavailability and randomised controlled crossover studies in humans carried out with similar cocoa products, so that the main phenol and methylxanthine metabolites observed in plasma and urine are associated to the health effects observed in the chronic studies. We outstand that doses of cocoa and consumption rate used are realistic. In the bioavailability study, a conventional (CC) and a methylxanthine-polyphenol rich (MPC) cocoa product were used, whereas in the chronic study a dietary fibre-rich (DFC) and a polyphenol-rich (PC) product were studied in healthy and cardiovascular risk subjects.Results and DiscussionThe main phenolic metabolites formed after CC and MPC intake, 5-(4′-hydroxyphenyl)-γ-valerolactone-3′-sulfate, 3′-methyl-epicatechin-5-sulfate, 4-hydroxy-5-(4′-hydroxyphenyl)valeric acid-sulfate, 5-phenyl-γ-valerolactone--sulfate and 5-(4′-hydroxyphenyl)-γ-valerolactone-3′-glucuronide, may contribute to the changes in cholesterol (and indirectly HDL-cholesterol) observed after the regular intake of both DFC and PC, in healthy and cardiovascular risk subjects, whereas 7-methylxanthine (the main cocoa methylxanthine metabolite) and theobromine, together with its content in insoluble dietary fibre, may be responsible for the decrease of IL-1β and hypoglycemic effects observed with DFC. With both phenolic and methylxanthine metabolites a strong dose–response effect was observed.ConclusionAfter the regular consumption of both DFC and PC, positive changes were observed in volunteer’s lipid profile, which may be related to the long-lasting presence of colonic phenolic metabolites in blood. In contrast, the anti-inflammatory and hypoglycemic effects were only observed with DFC, and these may be related to methylxanthine metabolites, and it is likely that insoluble dietary fibre may have also played a role. creator: Beatriz Sarriá creator: Miren Gomez-Juaristi creator: Sara Martínez López creator: Joaquín García Cordero creator: Laura Bravo creator: Mª Raquel Mateos Briz uri: https://doi.org/10.7717/peerj.9953 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Sarriá et al. title: Role of reactive oxygen species and isoflavonoids in soybean resistance to the attack of the southern green stink bug link: https://peerj.com/articles/9956 last-modified: 2020-09-17 description: Southern green stink bugs (Nezara viridula L.) are one of the major pests in many soybean producing areas. They cause a decrease in yield and affect seed quality by reducing viability and vigor. Alterations have been reported in the oxidative response and in the secondary metabolites in different plant species due to insect damage. However, there is little information available on soybean-stink bug interactions. In this study we compare the response of undamaged and damaged seeds by Nezara viridula in two soybean cultivars, IAC-100 (resistant) and Davis (susceptible), grown under greenhouse conditions. Pod hardness, H2O2 generation, enzyme activities in guaiacol peroxidase (GPOX), catalase (CAT) and superoxide dismutase (SOD) as well as lipoxygenase expression and isoflavonoid production were quantified. Our results showed a greater resistance of IAC-100 to pod penetration, a decrease in peroxide content after stink bug attack, and higher GPOX, CAT and SOD activities in seeds due to the genotype and to the genotype-interaction with the herbivory treatment. Induction of LOX expression in both cultivars and higher production of isoflavonoids in IAC-100 were also detected. It was then concluded that the herbivory stink bug induces pathways related to oxidative stress and to the secondary metabolites in developing seeds of soybean and that differences between cultivars hold promise for a plant breeding program. creator: Ivana Sabljic creator: Jesica A. Barneto creator: Karina B. Balestrasse creator: Jorge A. Zavala creator: Eduardo A. Pagano uri: https://doi.org/10.7717/peerj.9956 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Sabljic et al. title: Comparable behaviour of ring and little fingers due to an artificial reduction in thumb contribution to hold objects link: https://peerj.com/articles/9962 last-modified: 2020-09-17 description: BackgroundThe human hand plays a crucial role in accomplishing activities of daily living. The contribution of each finger in the human hand is remarkably unique in establishing object stabilization. According to the mechanical advantage hypothesis, the little finger tends to exert a greater normal force than the ring finger during a supination moment production task to stabilize the object. Similarly, during pronation, the index finger produces more normal force when compared with the middle finger. Hence, the central nervous system employs the peripheral fingers for torque generation to establish the equilibrium as they have a mechanical advantage of longer moment arms for normal force. In our study, we tested whether the mechanical advantage hypothesis is supported in a task in which the contribution of thumb was artificially reduced. We also computed the safety margin of the individual fingers and thumb.MethodologyFifteen participants used five-finger prismatic precision grip to hold a custom-built handle with a vertical railing on the thumb side. A slider platform was placed on the railing such that the thumb sensor could move either up or down. There were two experimental conditions. In the “Fixed” condition, the slider was mechanically fixed, and hence the thumb sensor could not move. In the “Free” condition, the slider platform on which the thumb sensor was placed could freely move. In both conditions, the instruction was to grasp and hold the handle (and the platform) in static equilibrium. We recorded tangential and normal forces of all the fingers.ResultsThe distribution of fingertip forces and moments changed depending on whether the thumb platform was movable (or not). In the free condition, the drop in the tangential force of thumb was counteracted by an increase in the normal force of the ring and little finger. Critically, the normal forces of the ring and little finger were statistically equivalent. The safety margin of the index and middle finger did not show a significant drop in the free condition when compared to fixed condition.ConclusionWe conclude that our results does not support the mechanical advantage hypothesis at least for the specific mechanical task considered in our study. In the free condition, the normal force of little finger was comparable to the normal force of the ring finger. Also, the safety margin of the thumb and ring finger increased to prevent slipping of the thumb platform and to maintain the handle in static equilibrium during the free condition. However, the rise in the safety margin of the ring finger was not compensated by a drop in the safety margin of the index and middle finger. creator: Banuvathy Rajakumar creator: Varadhan SKM uri: https://doi.org/10.7717/peerj.9962 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Rajakumar and SKM title: One becomes two: second species of the Euwallacea fornicatus (Coleoptera: Curculionidae: Scolytinae) species complex is established on two Hawaiian Islands link: https://peerj.com/articles/9987 last-modified: 2020-09-17 description: The cryptic species that make up the Euwallacea fornicatus species complex can be readily distinguished via their DNA sequences. Until recently, it was believed that the Hawaiian Islands had been invaded by only one of these cryptic species, E. perbrevis (tea shot hole borer; TSHB). However, following the 2016 deposition of a DNA sequence in the public repository GenBank, it became evident that another species, E. fornicatus (polyphagous shot hole borer; PSHB), had been detected in macadamia orchards on Hawaiʻi Island (the Big Island). We surveyed the two most-populous islands of Hawaiʻi, Big Island and Oʻahu, and herein confirm that populations of TSHB and PSHB are established on both. Beetles were collected using a variety of techniques in macadamia orchards and natural areas. Individual specimens were identified to species using a high-resolution melt assay, described herein and validated by subsequent sequencing of specimens. It remains unclear how long each species has been present in the state, and while neither is currently recognized as causing serious economic or ecological damage in Hawaiʻi, the similarity of the newly-confirmed PSHB population to other damaging invasive PSHB populations around the world is discussed. Although the invasive PSHB populations in Hawaiʻi and California likely have different geographic origins within the beetle’s native range, they share identical Fusarium and Graphium fungal symbionts, neither of which have been isolated from PSHB in that native range. creator: Paul F. Rugman-Jones creator: Michelle Au creator: Valeh Ebrahimi creator: Akif Eskalen creator: Conrad P.D.T. Gillett creator: David Honsberger creator: Deena Husein creator: Mark G. Wright creator: Fazila Yousuf creator: Richard Stouthamer uri: https://doi.org/10.7717/peerj.9987 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Rugman-Jones et al. title: Adaptive Metropolis-coupled MCMC for BEAST 2 link: https://peerj.com/articles/9473 last-modified: 2020-09-16 description: With ever more complex models used to study evolutionary patterns, approaches that facilitate efficient inference under such models are needed. Metropolis-coupled Markov chain Monte Carlo (MCMC) has long been used to speed up phylogenetic analyses and to make use of multi-core CPUs. Metropolis-coupled MCMC essentially runs multiple MCMC chains in parallel. All chains are heated except for one cold chain that explores the posterior probability space like a regular MCMC chain. This heating allows chains to make bigger jumps in phylogenetic state space. The heated chains can then be used to propose new states for other chains, including the cold chain. One of the practical challenges using this approach, is to find optimal temperatures of the heated chains to efficiently explore state spaces. We here provide an adaptive Metropolis-coupled MCMC scheme to Bayesian phylogenetics, where the temperature difference between heated chains is automatically tuned to achieve a target acceptance probability of states being exchanged between individual chains. We first show the validity of this approach by comparing inferences of adaptive Metropolis-coupled MCMC to MCMC on several datasets. We then explore where Metropolis-coupled MCMC provides benefits over MCMC. We implemented this adaptive Metropolis-coupled MCMC approach as an open source package licenced under GPL 3.0 to the Bayesian phylogenetics software BEAST 2, available from https://github.com/nicfel/CoupledMCMC. creator: Nicola F. Müller creator: Remco R. Bouckaert uri: https://doi.org/10.7717/peerj.9473 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Müller and Bouckaert title: Density and diversity of macroinvertebrates in Colombian Andean streams impacted by mining, agriculture and cattle production link: https://peerj.com/articles/9619 last-modified: 2020-09-16 description: BackgroundMining, agriculture and cattle production are activities that threaten the quality and quantity of water resources in the Colombian Andes. However, many drainage basins in this region have not been subjected to simultaneous evaluation of the impact these activities have on the density, diversity and composition of aquatic macroinvertebrates (AMI). The first two of these ecological variables are expected to decrease drastically from zones with no apparent impact towards areas with anthropogenic activity, which areas with mining will present the most impoverished AMI community.MethodsWe evaluated the density, diversity and composition dissimilarity of AMI in streams impacted by gold mining, agriculture and cattle production. Two reference streams were also studied. Six benthic samplings were conducted bimonthly (Feb 2014–Feb 2015) using a Surber net. Water samples were taken in order to make environmental evaluation among the aforementioned streams, including hydrological, physicochemical and bacteriological parameters (HPCB). Diversity was evaluated as the effective number of RTUs—recognizable taxonomic units—by comparing the richness, typical diversity, and effective number of the most abundant RTUs. Compositional dissimilarity was examined with nMDS and CCA analysis.ResultsA total of 7,483 organisms were collected: 14 orders, 42 families and 71 RTUs. Our prediction regarding the density and diversity of AMI (Reference > Cattle production > Agriculture > Mining) was partially fulfilled, since the agriculture-dominated stream presented a more impoverished AMI community than that of the gold mining stream. However, these streams presented lower diversity than the cattle production and reference streams, and the AMI density only differed significantly between one reference stream and the agriculture stream. The AMI composition in the agriculture-dominated stream clearly differed from that of the other streams.DiscussionThe observation of a more impoverished AMI community in agricultural production areas compared to those with mining or cattle production may reflect the importance of the remaining riparian vegetation, which was scarce at the stream with agricultural activity. Moreover, the low diversity, and mainly the reduced AMI richness, in the agriculture stream coincided with the absence of insect genera are intolerant to deterioration of the biological and physicochemical conditions of the water (e.g. Anacroneuria).ConclusionsThe results suggest that the local impact of agricultural activities may be of equal or greater magnitude than that of mining in terms of AMI density, diversity and composition, in the Colombian Andean riverscape. Future studies should systematically evaluate, throughout the annual cycle, the relative effects of the productive land use, the remaining native vegetation cover and the consequent changes in the HPCB parameters of the water on AMI communities in Colombian Andean basins. creator: Ana M. Meza-Salazar creator: Giovany Guevara creator: Lucimar Gomes-Dias creator: Carlos A. Cultid-Medina uri: https://doi.org/10.7717/peerj.9619 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Meza-Salazar et al. title: Psychometric properties of the Automatic Thoughts Questionnaire-8 in two Spanish nonclinical samples link: https://peerj.com/articles/9747 last-modified: 2020-09-16 description: BackgroundThe ATQ is a widely used instrument consisting of 30 items that assess the frequency of negative automatic thoughts. However, the extensive length of the ATQ could compromise its measurement efficiency in survey research. Consequently, an 8-item shortened version of the ATQ has been developed. This study aims to analyze the validity of the ATQ-8 in two Spanish samples.MethodThe ATQ-8 was administered to a total sample of 1,148 participants (302 undergraduates and 846 general online population). To analyze convergent construct validity, the questionnaire package also included the Dysfunctional Attitude Scale-Revised (DAS-R), Depression Anxiety and Stress Scale-21 (DASS-21), Acceptance Action Questionnaire-II (AAQ-II), Cognitive Fusion Questionnaire (CFQ), Generalized Pliance Questionnaire (GPQ), and Satisfaction with Life Scale (SWLS). To analyze internal consistency, we computed Cronbach’s alpha and McDonald’s omega. A confirmatory factor analysis was conducted to test the one-factor structure of the ATQ-8. In so doing, a robust diagonally weighted least square estimation method (Robust DWLS) was adopted using polychoric correlations. Afterward, we analyzed measurement invariance across samples, gender, groupage, and education level. Lastly, we evaluated convergent construct validity by computing Pearson correlations between the ATQ-8 and the remaining instruments.ResultsThe internal consistency across samples was adequate (alpha and omega = .89). The one-factor model demonstrated a good fit to the data (RMSEA = 0.10, 90% CI [0.089, 0.112], CFI = 0.98, NNFI = 0.97, and SRMR = 0.048). The ATQ-8 showed scalar metric invariance across samples, gender, groupage, and education level. The ATQ-8 scores were significantly associated with emotional symptoms (DASS-21), satisfaction with life (SWLS), dysfunctional schemas (DAS-R), cognitive fusion (CFQ), experiential avoidance (AAQ-II), and generalized pliance (GPQ). In conclusion, the Spanish version of the ATQ-8 demonstrated adequate psychometric properties in Spanish samples. creator: Francisco J. Ruiz creator: Miguel A. Segura-Vargas creator: Paula Odriozola-González creator: Juan C. Suárez-Falcón uri: https://doi.org/10.7717/peerj.9747 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ruiz et al. title: Dual-tasking effects on static and dynamic postural balance performance: a comparison between endurance and team sport athletes link: https://peerj.com/articles/9765 last-modified: 2020-09-16 description: In sports, postural balance control has been demonstrated to be one of the limiting factors of performance and a necessary component to achieve any sport technique. Team players (TP) must process and react to multiple external stimuli while executing at the same time the skills of the game. By contrast, endurance athletes (END) must perform the same gesture repetitively without a concurrent coordination of continuous stimuli-related actions. However, END are used to facilitate their physical performance by adopting cognitive strategies while performing their sport gesture. Therefore, we aimed to investigate static and dynamic balance performance in these two types of athletes, both in single and dual-task conditions. Nineteen END and sixteen TP underwent a static and a dynamic balance assessment on a dynamometric platform and an instrumented oscillating board, respectively. Among TP static but not dynamic postural balance performance was negatively affected by dual-tasking considering the area of the confidence ellipse (p < 0.001; d = 0.52) and the sway path mean speed (p < 0.001; d = 0.93). Conversely, END unaltered static balance performance but showed an overall improvement in the dynamic one when dual-tasking occurred. The limited human processing capacity accounted the worsening of the cognitive performance in both TP (p < 0.05; d = 0.22) and END (p < 0.001; d = 0.37). Although TP are more used coping dual tasking, the better performance of END could be accounted for by the employment of the external attentive focus (i.e. counting backward aloud) that called into play a strategy close to those adopted during training and competitions. These surprising results should be considered when driving and developing new trainings for team players in dual-tasking conditions. creator: Fabio Sarto creator: Giorgia Cona creator: Francesco Chiossi creator: Antonio Paoli creator: Patrizia Bisiacchi creator: Elisabetta Patron creator: Giuseppe Marcolin uri: https://doi.org/10.7717/peerj.9765 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Sarto et al. title: If you build it, they will come: rapid colonization by dragonflies in a new effluent-dependent river reach link: https://peerj.com/articles/9856 last-modified: 2020-09-16 description: BackgroundAquatic ecosystems are greatly altered by urban development, including the complete loss of natural habitat due to water diversions or channel burial. However, novel freshwater habitats also are created in cities, such as effluent-dependent streams that rely on treated wastewater for flow. It is unclear how diverse these novel ecosystems are, or how quickly aquatic species are able to colonize them. In this study, we (1) quantify odonate (Insecta, Odonata) colonization of a novel effluent-dependent river reach, (2) examine how drying events affect odonates in these novel habitats, and (3) explore whether effluent-dependent streams can support diverse odonate assemblages.MethodsWe conducted monthly odonate surveys at three sites along the Santa Cruz River (Tucson, AZ, USA) between June 2019 and May 2020. One site was in a long-established effluent-dependent reach (flowing since the 1970s) that served as a reference site and two sites were in a newly-established reach that began flowing on June 24, 2019 (it was previously dry). We compared odonate species richness, assemblage composition, and colonization patterns across these reaches, and examined how these factors responded to flow cessation events in the new reach.ResultsSeven odonate species were observed at the study sites in the new reach within hours of flow initiation, and species rapidly continued to arrive thereafter. Within 3 months, species richness and assemblage composition of adult odonates were indistinguishable in the new and reference reaches. However, drying events resulted in short-term and chronic reductions in species richness at one of the sites. Across all three sites, we found over 50 odonate species, which represent nearly 40% of species known from the state of Arizona.DiscussionOdonates were surprisingly diverse in the effluent-dependent Santa Cruz River and rapidly colonized a newly established reach. Richness levels remained high at study sites that did not experience drying events. These results suggest that consistent discharge of high-quality effluent into dry streambeds can be an important tool for promoting urban biodiversity. However, it remains to be seen how quickly and effectively less vagile taxa (e.g., mayflies, caddisflies) can colonize novel reaches. Effluent-dependent urban streams will always be highly managed systems, but collaboration between ecologists and urban planners could help to maximize aquatic biodiversity while still achieving goals of public safety and urban development. creator: Michael T. Bogan creator: Drew Eppehimer creator: Hamdhani Hamdhani creator: Kelsey Hollien uri: https://doi.org/10.7717/peerj.9856 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Bogan et al. title: Biological function of Klebsiella variicola and its effect on the rhizosphere soil of maize seedlings link: https://peerj.com/articles/9894 last-modified: 2020-09-16 description: BackgroundDeterioration of the ecological environment in recent years has led to increasing soil salinization, which severely affects the cultivation of agricultural crops. While research has focused on improving soil environment through the application of pollution-free microbial fertilizers, there are relatively few plant growth-promoting bacteria suitable for saline-alkali environments. Although Klebsiella variicola can adapt to saline-alkali environments to successfully colonize rhizosphere microenvironments, only a few studies have investigated its role in promoting crop growth. Its effect on the crop rhizosphere soil microenvironment is especially unclear.MethodsIn this study, the biological function of K. variicola and its colonization in maize seedling rhizosphere soil were studied in detail through selective media and ultraviolet spectrophotometry. The effects of K. variicola on the rhizosphere soil microenvironment and the growth of maize seedlings in saline-alkali and neutral soils were systematically analysed using the colorimetric method, the potassium dichromate volumetric method, and the diffusion absorption method.ResultsOur results showed that K. variicola played a role in indole acetic acid, acetoin, ammonia, phosphorus, and potassium production, as well as in nitrogen fixation. A high level of colonization was observed in the rhizosphere soil of maize seedlings. Following the application of K. variicola in neutral and saline-alkali soils, the nutrient composition of rhizosphere soil of maize seedlings increased in varying degrees, more notably in saline-alkali soil. The content of organic matter, alkali-hydrolysable nitrogen, available phosphorus, available potassium, alkaline phosphatase, sucrase, urease, and catalase increased by 64.22%, 117.39%, 175.64%, 28.63%, 146.08%, 76.77%, 86.60%, and 45.29%, respectively, insaline-alkalisoil.ConclusionK.variicola, therefore, performed a variety of biological functions to promote the growth of maize seedlings and effectively improve the level of soil nutrients and enzymes in the rhizosphere of maize seedlings, undersaline-alkali stress conditions. It played an important role in enhancing the rhizosphere microenvironment of maize seedlings under saline-alkali stress. creator: Lijuan Yang creator: Kejun Yang uri: https://doi.org/10.7717/peerj.9894 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Yang and Yang title: Entomopathogenic fungi decrease Rhizoctonia disease in potato in field conditions link: https://peerj.com/articles/9895 last-modified: 2020-09-16 description: Rhizoctonia potato disease is widespread in the world and causes substantial yield and quality losses in potato. This study aimed to evaluate the efficacy of entomopathogenic fungi Metarhizium robertsii and Beauveria bassiana in the inhibition of potato Rhizoctonia complex disease. The efficacy of the entomopathogenic fungi M. robertsii and B. bassiana in the defense of potato against Rhizoctonia disease (stem cancer, black scrulf and other forms of manifestation on tubers) was estimated under field conditions in Western Siberia. Preplanting treatment of the tubers with B. bassiana decreased Rhizoctonia disease in the stems and stolons. At the same time, treatment with M. robertsii did not cause a decrease in Rhizoctonia disease in these organs. However, both fungi decreased the sclerotium index on the tubers of new crops. We demonstrated two mechanisms of inhibition of Rhizoctonia solani by M. robertsii and B. bassiana, including (1) direct effect, expressed as inhibition of R. solani sclerotium formation in cocultivation assays, and (2) indirect effect, which is associated with increased peroxidase activity in potato roots under the influence of colonization by entomopathogenic fungi. We suggest that the treatment of seed tubers with B. basiana can effectively manage Rhizoctonia disease during the plant vegetative season and that both fungi significantly improve the quality of the new tuber crop. creator: Oksana G. Tomilova creator: Elena M. Shaldyaeva creator: Natalia A. Kryukova creator: Yulia V. Pilipova creator: Natalia S. Schmidt creator: Viktor P. Danilov creator: Vadim Y. Kryukov creator: Viktor V. Glupov uri: https://doi.org/10.7717/peerj.9895 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Tomilova et al. title: Community based actions save Yellow-spotted river turtle (Podocnemis unifilis) eggs and hatchlings flooded by rapid river level rises link: https://peerj.com/articles/9921 last-modified: 2020-09-16 description: The conservation and recovery of increasingly threatened tropical freshwater turtle populations depends on effective management plans and actions. Here we show that community-based actions saved Yellow-spotted river turtle (Podocnemis unifilis) eggs submerged by unseasonal flooding and ensured the release of hatchlings. We recovered 926 eggs and 65 premature hatchlings from 74 submerged nests at 16 flooded nesting areas along 75 km of waterways. The rescued eggs were transferred to a rearing center and incubated. Hatchlings emerged from eggs that had remained underwater for up to two days. Hatchlings were maintained in 250–500 L nursery tanks until yolk sac scars had closed. Healthy hatchlings were then immediately released around the original nesting areas. We released 599 hatchlings (60.4%) from 991 submerged eggs and hatchlings. Egg survival (61.7% (571/926)) was substantially less than hatchling survival (94.2% (599/636)) but within the expected range of values reported for this species. These findings suggest that Yellow-spotted river turtle eggs and embryos are resistant to short-term submersion, which could help explain the widespread distribution of this species across highly seasonal Amazonian rivers. Management plans should take the possible survival of submerged eggs into consideration as part of species conservation and recovery actions. creator: Darren Norris creator: Fernanda Michalski creator: James P. Gibbs uri: https://doi.org/10.7717/peerj.9921 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Norris et al. title: Ultraviolet-reflective film applied to windows reduces the likelihood of collisions for two species of songbird link: https://peerj.com/articles/9926 last-modified: 2020-09-16 description: Perhaps a billion birds die annually from colliding with residential and commercial windows. Therefore, there is a societal need to develop technologies that reduce window collisions by birds. Many current window films that are applied to the external surface of windows have human-visible patterns that are not esthetically preferable. BirdShades have developed a short wavelength (ultraviolet) reflective film that appears as a slight tint to the human eye but should be highly visible to many bird species that see in this spectral range. We performed flight tunnel tests of whether the BirdShades external window film reduced the likelihood that two species of song bird (zebra finch, Taeniopygia guttata and brown-headed cowbird, Molothrus ater) collide with windows during daylight. We paid particular attention to simulate the lighting conditions that birds will experience while flying during the day. Our results indicate a 75–90% reduction in the likelihood of collision with BirdShades-treated compared with control windows, in forced choice trials. In more ecologically relevant comparison between trials where all windows were either treated or control windows, the estimated reduction in probability of collision was 30–50%. Further, both bird species slow their flight by approximately 25% when approaching windows treated with the BirdShades film, thereby reducing the force of collisions if they were to happen. Therefore, we conclude that the BirdShades external window film will be effective in reducing the risk of and damage caused to populations and property by birds’ collision with windows. As this ultraviolet-reflective film has no human-visible patterning to it, the product might be an esthetically more acceptable low cost solution to reducing bird-window collisions. Further, we call for testing of other mitigation technologies in lighting and ecological conditions that are more similar to what birds experience in real human-built environments and make suggestions for testing standards to assess collision-reducing technologies. creator: John P. Swaddle creator: Lauren C. Emerson creator: Robin G. Thady creator: Timothy J. Boycott uri: https://doi.org/10.7717/peerj.9926 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Swaddle et al. title: Seasonal variations in leaf and branch trace elements and the influence of a 3-yr 100% rainfall exclusion on Pinus massoniana Lamb link: https://peerj.com/articles/9935 last-modified: 2020-09-16 description: BackgroundTrace elements are essential for the growth and survival of plants, and their concentrations and distributions in plants are effective reflections of ecological adaptation strategies. However, this aspect has seldom been addressed.MethodChanges in the leaf and branch trace elements of Pinus massoniana Lamb, induced by seasonal dynamics and in response to a 3-yr 100% rainfall exclusion, were evaluated.ResultsThe results showed that the concentrations of Fe, Cu, Zn, Cd, Ni and Cr in leaves of P. massoniana in the control group had high seasonal resolution. There were three groups according to their patterns over the growing season: (1) nutrient elements (Cu, Zn, Ni and Cd), which continuously decreased in concentration during the growing season, with the highest concentration in spring and the lowest in autumn; (2) accumulating element (Cr), which increased in concentration from spring to autumn; and (3) indifferent element (Fe), which increased in concentration from spring to summer and decreased in concentration from summer to autumn. The concentrations of trace elements in leaves and branches showed no significant differences with mild drought stress, except for Fe and Cr in leaves and Cr in branches, which significantly increased (p < 0.05) under the result of self-selection under mild drought stress. Therefore, the resultant seasonal and drought effects on trace element cycling in P. massoniana could provide theoretical support to respond to future climate change. creator: Tian Lin creator: Xuanmei Zheng creator: Huaizhou Zheng uri: https://doi.org/10.7717/peerj.9935 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Lin et al. title: Nitrogen form plays an important role in the growth of moso bamboo (Phyllostachys edulis) seedlings link: https://peerj.com/articles/9938 last-modified: 2020-09-16 description: BackgroundThis study aimed to gain an understanding of the growth response of Phyllostachys edulis (moso bamboo) seedlings to nitrogen (N) and potassium (K) to benefit nutrient management practices and the design of proper fertilizer in nursery cultivation.MethodsAn orthogonal array L8(4×24) was used to study the effects of N forms (NH4+, NO3−), N concentrations (8, 32 mmol/L), and K+concentrations (0, 0.5, 1.5, 3 mmol/L) on seedling height, leaf number, chlorophyll content (SPAD value), biomass, root systems, and N content of P. edulis seedlings. Plants were grown in vermiculite under controlled greenhouse conditions.ResultsOur study showed that N form played a significant role in the overall performance of P. edulis seedlings, followed by the effect of N and K+ concentrations. Among the N forms, NH4+ significantly improved the growth of P. edulis seedlings compared with NO3−. Seedling height, leaf number, chlorophyll SPAD value, biomass, and root system architecture (root length, root surface area, root volume, and root tips) were greater with 8 mmol/L of NH4+ treatments than with 32 mmol/L of NH4+treatments, whereas root diameter and N content of P. edulis seedlings were higher with 32 mmol/L of NH4+ than with 8 mmol/L of NH4+. K displayed inconsistent effects on the growth of P. edulis seedlings. Specifically, seedling height, leaf number, biomass and root volume increased when the K+ concentration was increased from 0 to 0.5 mmol/L, followed by a decrease when the K+ concentration was further increased from 0.5 to 3 mmol/L. Root average diameter of the seedlings was the highest with a K+ concentration of 1.5 mmol/L, and K had some inhibitory effects on the chlorophyll SPAD value of the seedlings. P. edulis seedlings performed well with 8 mmol/L NH4+and further tolerated a higher concentration of both NH4+ and NO3−, although excessive N could inhibit seedling growth. A lower concertation of K (≤ 0.5 mmol/L) promoted seedling growth and increasing K+ concentration in the nutrient solution did not alleviate the inhibitory effect of high N on the growth of P. edulis seedlings. Therefore, NH4+nitrogen as the main form of N fertilizer, together with a low concertation of K+, should be supplied in the cultivation and nutrient management practices of moso bamboo. creator: Na Zou creator: Ling Huang creator: Huijing Chen creator: Xiaofeng Huang creator: Qingni Song creator: Qingpei Yang creator: Tianchi Wang uri: https://doi.org/10.7717/peerj.9938 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zou et al. title: An empirical examination of sample size effects on population demographic estimates in birds using single nucleotide polymorphism (SNP) data link: https://peerj.com/articles/9939 last-modified: 2020-09-16 description: Sample size is a critical aspect of study design in population genomics research, yet few empirical studies have examined the impacts of small sample sizes. We used datasets from eight diverging bird lineages to make pairwise comparisons at different levels of taxonomic divergence (populations, subspecies, and species). Our data are from loci linked to ultraconserved elements and our analyses used one single nucleotide polymorphism per locus. All individuals were genotyped at all loci, effectively doubling sample size for coalescent analyses. We estimated population demographic parameters (effective population size, migration rate, and time since divergence) in a coalescent framework using Diffusion Approximation for Demographic Inference, an allele frequency spectrum method. Using divergence-with-gene-flow models optimized with full datasets, we subsampled at sequentially smaller sample sizes from full datasets of 6–8 diploid individuals per population (with both alleles called) down to 1:1, and then we compared estimates and their changes in accuracy. Accuracy was strongly affected by sample size, with considerable differences among estimated parameters and among lineages. Effective population size parameters (ν) tended to be underestimated at low sample sizes (fewer than three diploid individuals per population, or 6:6 haplotypes in coalescent terms). Migration (m) was fairly consistently estimated until <2 individuals per population, and no consistent trend of over-or underestimation was found in either time since divergence (T) or theta (Θ = 4Nrefμ). Lineages that were taxonomically recognized above the population level (subspecies and species pairs; that is, deeper divergences) tended to have lower variation in scaled root mean square error of parameter estimation at smaller sample sizes than population-level divergences, and many parameters were estimated accurately down to three diploid individuals per population. Shallower divergence levels (i.e., populations) often required at least five individuals per population for reliable demographic inferences using this approach. Although divergence levels might be unknown at the outset of study design, our results provide a framework for planning appropriate sampling and for interpreting results if smaller sample sizes must be used. creator: Jessica F. McLaughlin creator: Kevin Winker uri: https://doi.org/10.7717/peerj.9939 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 McLaughlin and Winker title: Galectin-3 not Galectin-9 as a candidate prognosis marker for hepatocellular carcinoma link: https://peerj.com/articles/9949 last-modified: 2020-09-16 description: BackgroundGalectins (Gal) are a family of protein that bind to the β-galactoside of glycoproteins. It modulates a variety of biological functions, such as tumor growth, angiogenesis and tumor metastasis. A series of experimental and clinical evidences have been reported to support a correlation between galectin expressions and neoplastic transformation, progression and prognosis. The objective of this study was to estimate the expression of Gal-3 and Gal-9 in order to evaluate their relation to hepatocellular carcinoma (HCC) -related clinical features and their prognostic values.MethodsWe evaluated Gal-3 and Gal-9 expression in 247 HCC patients by a tissue microarray immunohistochemistry method, then analyzed the relationship between expression levels of Gal-3 and Gal-9 protein and tumor parameters or clinical outcomes.ResultsThe Gal-3 expression was significantly higher in tumor tissues compared with adjacent non-tumor tissues (P < 0.001), while no significant differences of Gal-9 was detected (P = 0.222). A higher Gal-3 expression was significantly associated with lymph-vascular invasion (P = 0.049), poor histological differentiation (P = 0.016), and no cirrhosis (P = 0.040). In contrast, a lower Gal-9 expression was related to lymph-vascular invasion (P = 0.012) and poor histological differentiation (P = 0.002). Survival analysis showed that patients with higher Gal-3 expression had worse overall survival (P = 0.012) , however no correlation was found between Gal-9 expression and survival (P = 0.185). Multivariate analysis showed that multiple tumor (HR = 1.94, 95% CI [1.36–2.78]), tumor size ≥ 5 cm (HR = 1.51, 95% CI [1.07–2.12]), Lymph-vascular invasion (HR = 1.45, 95% CI [1.00–2.10]) and Gal-3 expression (HR = 1.57, 95% CI [1.06–2.33]) were independent influencing factors of prognosis in patients with hepatocellular carcinoma.ConclusionGal-3 was expected to serve as a novel prognostic marker of hepatocellular carcinoma, while Gal-9 expression was only related to tumor progression. creator: Fei Kong creator: Meishan Jin creator: Donghui Cao creator: Zhifang Jia creator: Yawen Liu creator: Jing Jiang uri: https://doi.org/10.7717/peerj.9949 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kong et al. title: Effect of concurrent training on trainability performance factors in youth elite golf players link: https://peerj.com/articles/9963 last-modified: 2020-09-16 description: BackgroundDue to the early specialization of golf players, examining the within session sequence of training should be considered to enhance performance and prevent injury risk. The present study analyzed the effects of an 18-week concurrent training developed before or after a specific golf session in adolescence elite golfers on several performance factors.MethodsSixteen right-handed male golfers, were randomly divided into two groups: after golf specific training (AG) (n = 8, age: 16.77 ± 0.58 years) and before golf specific training (BG) (n = 8, age: 16.93 ± 0.59 years). AG and BG players followed a concurrent physical conditioning program (CT) after or before the golf specific training, respectively. Body mass, body fat, muscle mass, jumping ability (CMJ), ball speed (Sball), golf movements screens (GMS), power in a golf swing-specific cable woodchop (Wmax) and the perceived training load (TL) in golf specific training (TL-G) and TL in CT (TL-CT) were measured on three separate occasions.ResultsBG demonstrates a lower TL-CT than AG (p < .001, ${\eta }_{p}^{2}=0.90$ηp2=0.90) along the training program without effects on TL-G, achieving significant percentage of change on CMJ (9.38%; p = .165; d = 0.73), GMS (50.52%; p = .41, d = 0.91), Wmax (16.93%; p = .001; d = 2.02) and Sball (1.82%; p = .018; d = 0.92) without interaction effects on anthropometric measures.ConclusionsPerforming CT sessions before the regular golf training can improve specific performance factors with a lower perceived TL than the same training carried out after the regular golf training. creator: Juan Carlos Redondo creator: Ana María de Benito creator: José María Izquierdo uri: https://doi.org/10.7717/peerj.9963 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Redondo et al. title: Assessing turbine passage effects on internal fish injury and delayed mortality using X-ray imaging link: https://peerj.com/articles/9977 last-modified: 2020-09-16 description: Knowledge on the extent and mechanisms of fish damage caused by hydropower facilities is important for the conservation of fish populations. Herein, we assessed the effects of hydropower turbine passage on internal fish injuries using X-ray technology. A total of 902 specimens from seven native European fish species were screened for 36 types of internal injuries and 86 external injuries evaluated with a previously published protocol. The applied systematic visual evaluation of X-ray images successfully detected skeletal injuries, swim bladder anomalies, emphysema, free intraperitoneal gas and hemorrhages. Injuries related to handling and to impacts of different parts of the hydropower structure could be clearly distinguished applying multivariate statistics and the data often explained delayed mortality within 96 h after turbine passage. The internal injuries could clearly be assigned to specific physical impacts resulting from turbine passage such as swim bladder rupture due to abrupt pressure change or fractures of skeletal parts due to blade-strike, fluid shear or severe turbulence. Generally, internal injuries were rarely depicted by external evaluation. For example, 29% of individuals with vertebral fractures did not present externally visible signs of severe injury. A combination of the external and internal injury evaluation allows quantifying and comparing fish injuries across sites, and can help to identify the technologies and operational procedures which minimize harm to fish in the context of assessing hydropower-related fish injuries as well as in assessing fish welfare. creator: Melanie Mueller creator: Katharina Sternecker creator: Stefan Milz creator: Juergen Geist uri: https://doi.org/10.7717/peerj.9977 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Mueller et al. title: Enrichment in conservative amino acid changes among fixed and standing missense variations in slowly evolving proteins link: https://peerj.com/articles/9983 last-modified: 2020-09-16 description: The process of molecular evolution has many elements that are not yet fully understood. Evolutionary rates are known to vary among protein coding and noncoding DNAs, and most of the observed changes in amino acid or nucleotide sequences are assumed to be non-adaptive by the neutral theory of molecular evolution. However, it remains unclear whether fixed and standing missense changes in slowly evolving proteins are more or less neutral compared to those in fast evolving genes. Here, based on the evolutionary rates as inferred from identity scores between orthologs in human and Rhesus Macaques (Macaca mulatta), we found that the fraction of conservative substitutions between species was significantly higher in their slowly evolving proteins. Similar results were obtained by using four different methods of scoring conservative substitutions, including three that remove the impact of substitution probability, where conservative changes require fewer mutations. We also examined the single nucleotide polymorphisms (SNPs) by using the 1000 Genomes Project data and found that missense SNPs in slowly evolving proteins also had a higher fraction of conservative changes, especially for common SNPs, consistent with more non-conservative substitutions and hence stronger natural selection for SNPs, particularly rare ones, in fast evolving proteins. These results suggest that fixed and standing missense variants in slowly evolving proteins are more likely to be neutral. creator: Mingrui Wang creator: Dapeng Wang creator: Jun Yu creator: Shi Huang uri: https://doi.org/10.7717/peerj.9983 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al. title: Interdependency of regulatory effects of iron and riboflavin in the foodborne pathogen Shigella flexneri determined by integral transcriptomics link: https://peerj.com/articles/9553 last-modified: 2020-09-15 description: Shigella flexneri is the causative agent of dysentery. For pathogens, iron is a critical micronutrient as its bioavailability is usually low in bacterial niches. This metal is involved in critical physiological processes mainly as a component of important metabolic molecules involved in redox reactions. Usually bacteria respond to fluctuations in iron availability to regulate iron acquisition and other iron-related functions. Recently the close metabolic feedback between iron and riboflavin, another pivotal biological redox agent, began to draw attention in bacteria. This is a widespread biological phenomenon, partly characterized by the coordination of regulatory responses to iron and riboflavin, probably owed to the involvement of these cofactors in common processes. Nonetheless, no systematic analyses to determine the extent of this regulatory effect have been performed in any species. Here, the transcriptomics responses to iron, riboflavin, iron in the presence of riboflavin and riboflavin in the presence of iron were assessed and compared in S. flexneri. The riboflavin regulon had a 43% overlap with the iron regulon. Notably, the presence of riboflavin highly increased the number of iron-responsive genes. Reciprocally, iron drastically changed the pool of riboflavin-responsive genes. Gene ontology (GO) functional terms enrichment analysis showed that biological processes were distinctively enriched for each subgroup of responsive genes. Among the biological processes regulated by iron and riboflavin were iron uptake, amino acids metabolism and electron transfer for ATP synthesis. Thus, iron and riboflavin highly affect the transcriptomics responses induced by each other in S. flexneri. GO terms analysis suggests that iron and riboflavin coordinately regulate specific physiological functions involving redox metabolism. creator: Luis Fernando Lozano Aguirre creator: Juan Carlos Salazar creator: José Ignacio Vásquez creator: Víctor Antonio García-Angulo uri: https://doi.org/10.7717/peerj.9553 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Lozano Aguirre et al. title: Differences in the support needs of children with developmental disabilities among groups of medical and behavioral needs link: https://peerj.com/articles/9557 last-modified: 2020-09-15 description: Background/AimsMedical and behavioral needs are relevant in organizing and providing support strategies that improve the quality of life for children, along with their families. The present study aims to examine the impact of medical and behavioral needs on the need for support of children with disabilities.MethodsHealth and education professionals were interviewed using the Supports Intensity Scale-Children’s version to estimate the support needs of 911 children and adolescents (5–16 years) with an intellectual disability, including 55.32% with an additional disability. For data analysis, a model for measuring support needs was specified, consisting of seven support needs factors and three method factors. In estimating the model, four groups of medical and behavioral needs were considered. The factor scores’ means of the groups were compared through t-tests.ResultsMedical and behavioral needs had an impact on overall support needs. Differences were found in all support domains for medical needs. The greatest influence of behavioral needs was found in the Social and School participation areas but was indistinguishable between the mild and moderate levels of needs.ConclusionsMedical and behavioral needs greatly affect the need for support in a child’s daily life, so they need to be considered a priority for support services. The importance of standardized assessments is emphasized to help develop support strategies. creator: Victor B. Arias creator: Virginia Aguayo creator: Miguel A. Verdugo creator: Antonio M. Amor uri: https://doi.org/10.7717/peerj.9557 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Arias et al. title: A prognostic long non-coding RNA-associated competing endogenous RNA network in head and neck squamous cell carcinoma link: https://peerj.com/articles/9701 last-modified: 2020-09-15 description: BackgroundThis study aimed to develop multi-RNA-based models using a competing endogenous RNA (ceRNA) regulatory network to provide survival risk prediction in head and neck squamous cell carcinoma (HNSCC).MethodsAll long non-coding RNA (lncRNA), microRNA (miRNA), and mRNA expression data and clinicopathological features related to HNSCC were derived from The Cancer Genome Atlas. Differentially expressed RNAs were calculated using R. Prognostic factors were identified using univariate Cox regression analysis. Functional analysis was performed using GO, KEGG pathways, and PPI network. Based on the results, we derived a risk signature and compared high- and low-risk subgroups using LASSO regression analysis. Survival analysis and the relationship between risk signature and clinicopathological features were performed using log-rank tests and Cox regression analysis. A ceRNA regulatory network was constructed, and prognostic lncRNAs and miRNA expression levels were validated in vitro and in vivo.ResultsA list of 207 lncRNAs, 18 miRNAs and 362 mRNAs related to overall survival was established. Five lncRNAs (HOTTIP, LINC00460, RMST, SFTA1P, and TM4SF19-AS1), one miRNA (hsa-miR-206), and one mRNA (STC2) were used to construct the ceRNA network. Three prognostic models contained 13 lncRNAs, eight miRNAs, and 17 mRNAs, which correlated with the patient status, disease-free survival (DFS), stage, grade, T stage, N stage, TP53 mutation status, angiolymphatic invasion, HPV status, and extracapsular spread. KEGG pathway analysis revealed significant enrichment of “Transcriptional misregulation in cancer” and “Neuroactive ligand-receptor interaction.” In addition, HOTTIP, LINC00460, miR-206 and STC2 were validated in GTEx data, GEO microarrays and six HNSCC cell lines.ConclusionsOur findings clarify the interaction of ceRNA regulatory networks and crucial clinicopathological features. These results show that prognostic biomarkers can be identified by constructing multi-RNA-based prognostic models, which can be used for survival risk prediction in patients with HNSCC. creator: Chengyao Zhang creator: Wei Cao creator: Jiawu Wang creator: Jiannan Liu creator: Jialiang Liu creator: Hao Wu creator: Siyi Li creator: Chenping Zhang uri: https://doi.org/10.7717/peerj.9701 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhang et al. title: Changes in muscle activity during the flexion and extension phases of arm cycling as an effect of power output are muscle-specific link: https://peerj.com/articles/9759 last-modified: 2020-09-15 description: Arm cycling is commonly used in rehabilitation settings for individuals with motor impairments in an attempt to facilitate neural plasticity, potentially leading to enhanced motor function in the affected limb(s). Studies examining the neural control of arm cycling, however, typically cycle using a set cadence and power output. Given the importance of motor output intensity, typically represented by the amplitude of electromyographic (EMG) activity, on neural excitability, surprisingly little is known about how arm muscle activity is modulated using relative workloads. Thus, the objective of this study was to characterize arm muscle activity during arm cycling at different relative workloads. Participants (n = 11) first completed a 10-second maximal arm ergometry sprint to determine peak power output (PPO) followed by 11 randomized trials of 20-second arm cycling bouts ranging from 5–50% of PPO (5% increments) and a standard 25 W workload. All submaximal trials were completed at 60 rpm. Integrated EMG amplitude (iEMG) was assessed from the biceps brachii, brachioradialis, triceps brachii, flexor carpi radialis, extensor carpi radialis and anterior deltoid of the dominant arm. Arm cycling was separated into two phases, flexion and extension, relative to the elbow joint for all comparisons. As expected, iEMG amplitude increased during both phases of cycling for all muscles examined. With the exception of the triceps brachii and extensor carpi radialis, iEMG amplitudes differed between the flexion and extension phases. Finally, there was a linear relationship between iEMG amplitude and the %PPO for all muscles during both elbow flexion and extension. creator: Carla P. Chaytor creator: Davis Forman creator: Jeannette Byrne creator: Angela Loucks-Atkinson creator: Kevin E. Power uri: https://doi.org/10.7717/peerj.9759 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Chaytor et al. title: Osteohistology and growth dynamics of the Brazilian noasaurid Vespersaurus paranaensis Langer et al., 2019 (Theropoda: Abelisauroidea) link: https://peerj.com/articles/9771 last-modified: 2020-09-15 description: Although the knowledge of bone histology of non-avian theropods has advanced considerably in recent decades, data about the bone tissue patterns, growth dynamics and ontogeny of some taxa such as abelisauroids are still limited. Here we describe the bone microstructure and growth dynamics of the Brazilian noasaurine Vespersaurus paranaensis using five femora and six tibiae and quantify the annual growth marks through retrocalculation of missing ones to estimate ontogenetic ages. The femoral series comprises four femoral histological classes (FHC I-IV), varying from two annuli or LAGs to seven LAGs. Femora show that sexual maturity was achieved around the seventh to tenth year of life, whereas the tibiae suggest it was earlier (around three to five years old). Tibiae represent three histological classes (THC I-III) displaying from three to nine LAGs. Two tibiae (THC III) exhibit an external fundamental system indicating that these specimens reached full skeletal size. The heterogeneous maturity observed in Vespersaurus hind limb bones could result from differential allometry scaling between femora and tibiae length with the body length. The predominant parallel-fibered bone matrix suggests that Vespersaurus grew more slowly than most theropods, including other abelisauroids, in a pattern shared with the noasaurines Masiakasaurus knopfleri from Madagascar and CPPLIP 1490 from Brazil. This deviation from the typical theropod growth pattern may be mainly correlated with small body size, but also may related to resource limitation imposed by the arid climate prevailing in southwestern Gondwana during Cretaceous. Moreover, given the ecological and phylogenetic similarities among these taxa, such features would probably be apomorphic within Noasauridae. creator: Geovane Alves de Souza creator: Marina Bento Soares creator: Arthur Souza Brum creator: Maria Zucolotto creator: Juliana M. Sayão creator: Luiz Carlos Weinschütz creator: Alexander W.A. Kellner uri: https://doi.org/10.7717/peerj.9771 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Souza et al. title: Effect of shooting experience on executive function: differences between experts and novices link: https://peerj.com/articles/9802 last-modified: 2020-09-15 description: BackgroundExecutive function (EF) plays an important role in controlling human actions. Shooting is a closed motor skill, characterized by high anti-interference ability and high mental intensity. However, the beneficial effects of closed exercises such as shooting on EF remain unclear.MethodsWe utilized an expert-novice paradigm and the Flanker task to examine the EF of shooting athletes. Participants were assigned into the novice group, expert group, or control group, based on the level of training and competition experience. Reaction time (RT) and accuracy of performance across the three groups were compared.ResultsFor the simple task, the control group showed a longer RT than the novice group, for all three inter-stimulus interval (ISI) conditions. Significant differences between the control and the expert groups were observed only at 300-ms and 400-ms ISIs. For the complex task, the control group exhibited a higher RT than the novice and expert groups at the 300- and 400-ms ISIs.ConclusionsThe self-control during performing closed motor skills in the environment determines that shooters have proficient anti-interference ability. This ability is uncorrelated with task type, but most likely is affected by reserved task response time. creator: Mingming Shao creator: Yinghui Lai creator: AnMin Gong creator: Yuan Yang creator: Tingting Chen creator: Changhao Jiang uri: https://doi.org/10.7717/peerj.9802 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Shao et al. title: Ground beetles (Coleoptera; Carabidae) as an indicator of ongoing changes in forest habitats due to increased water retention link: https://peerj.com/articles/9815 last-modified: 2020-09-15 description: This study, concerning the epigeic fauna of carabid beetles (Coleoptera; Carabidae), was conducted in the north-east of Poland, in an area which is part of the Dąbrówka Forest Subdistrict and has been included in the “Small water retention program for the Province of Warmia and Mazury in 2006–2015”. The purpose of the study was to assess the impact of the water retention implemented within the framework of the above program on assemblages of ground beetles. These insects are highly sensitive to any anthropogenically induced transformations. This analysis was based on the interactions among the analyzed insects caused by changes occurring in their habitat. During the 3-year study, 5,807 specimens representing 84 species were captured. The water storage had a significant influence on the structure of the Carabidae assemblages. Before the earthworks were constructed for the project, the beetle assemblages had comprised a large group of xerophilous species, whereas after the small retention reservoirs had been created, an increase in the contribution of hygrophilous species was noticed. The results indicate that the retention works cause alterations in the water and environmental conditions of the habitats, and thereby effect changes in the composition of Carabidae assemblages. Moreover, modification in water relations within a habitat causes long-term changes in the structural and functional diversity of the beetles. creator: Emilia Ludwiczak creator: Mariusz Nietupski creator: Agnieszka Kosewska uri: https://doi.org/10.7717/peerj.9815 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Ludwiczak et al. title: Effects of different ablation points of renal denervation on the efficacy of resistant hypertension link: https://peerj.com/articles/9842 last-modified: 2020-09-15 description: ObjectiveTo explore the blood pressure response to different ablation points of renal denervation (RDN) in patients with resistant hypertensionMethodsA total of 42 cases with resistant hypertension treated by RDN in our center from 2013 to 2015 were retrospectively analyzed. The patients were divided into two groups according to the different ablation points of RDN: the standard treatment group (spiral ablation from near to proximal, with less than 8 points per artery) and the intensive treatment group (from near to far by spiral ablation, with at least 8 points per artery), with 21 patients in each group. The ablation parameters, including points, impedance, actual wattage, and actual temperature, were recorded intraoperatively. Renal angiography was performed again after RDN. Ambulatory blood pressure (ABP) images were taken for all patients at the baseline and 6 months after operation.ResultsThe mean 24-h blood pressure of the standard treatment group was lower than that of the baseline (24-h systolic blood pressure decreased by 7.4 ± 10.6 mmHg and 24-h diastolic blood pressure decreased by 4.6  ± 6.1 mmHg), and the mean 24-h blood pressure decreased significantly from baseline to 6 months in the intensive treatment group (24–h systolic blood pressure decreased by 27.4 ±  11.4 mmHg, P < 0.0001; 24–h diastolic blood pressure decreased by 10.9 ±  9.6 mmHg, P = 0.005). There was a positive correlation between the decrease of systolic/diastolic 24-hour mean and the number of ablation points used in the procedure. The mean value of systolic and diastolic blood pressure was positively correlated with ablation points at 24-hour (R2 = 0.777 and 0.633 respectively, P < 0.01). There were no adverse events in either group after the operation and during the follow-up.ConclusionsRDN could significantly reduce BP in patients with resistant hypertension. Our study showed that the antihypertensive effect appeared to be positively correlated with the number of ablation points. creator: Hua Zhang creator: Ling-Yan Li creator: Rong-Xue Xiao creator: Ting-Chuan Zhang creator: Zong-Jun Liu creator: Jun-Qing Gao uri: https://doi.org/10.7717/peerj.9842 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2020 Zhang et al. title: Integrated jerk as an indicator of affinity for artificial agent kinematics: laptop and virtual reality experiments involving index finger motion during two-digit grasping link: https://peerj.com/articles/9843 last-modified: 2020-09-15 description: Uncanny valley research has shown that human likeness is an important consideration when designing artificial agents. It has separately been shown that artificial agents exhibiting human-like kinematics can elicit positive perceptual responses. However the kinematic characteristics underlying that perception have not been elucidated. This paper proposes kinematic jerk amplitude as a candidate metric for kinematic human likeness, and aims to determine whether a perceptual optimum exists over a range of jerk values. We created minimum-jerk two-digit grasp kinematics in a prosthetic hand model, then added different amplitudes of temporally smooth noise to yield a variety of animations involving different total jerk levels, ranging from maximally smooth to highly jerky. Subjects indicated their perceptual affinity for these animations by simultaneously viewing two different animations side-by-side, first using a laptop, then separately within a virtual reality (VR) environment. Results suggest that (a) subjects generally preferred smoother kinematics, (b) subjects exhibited a small preference for rougher-than minimum jerk kinematics in the laptop experiment, and that (c) the preference for rougher-than minimum-jerk kinematics was amplified in the VR experiment. These results suggest that non-maximally smooth kinematics may be perceptually optimal in robots and other artificial agents. creator: James Hirose creator: Atsushi Nishikawa creator: Yosuke Horiba creator: Shigeru Inui creator: Todd C. Pataky uri: https://doi.org/10.7717/peerj.9843 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Hirose et al. title: Assessing the prognostic scores for the prediction of the mortality of patients with acute-on-chronic liver failure: a retrospective study link: https://peerj.com/articles/9857 last-modified: 2020-09-15 description: BackgroundAcute-on-chronic liver failure (ACLF), which is characterized by rapid deterioration of liver function and multiorgan failure, has high mortality. This study was designed to identify prognostic scores to predict short-term and long-term outcome in patients with ACLF to facilitate early treatment and thereby improve patient survival.Materials and MethodsWe retrospectively analyzed 102 ACLF patients who were hospitalized in the gastroenterology department. The EASL-CLIF criteria were used to define the ACLF. The demographic characteristics and biochemical examination results of the patients were acquired, and seven scores (CTP score, MELD score, MELD-Na, CLIF ACLF score, CLIF-C OF score, and CLIF SOFA score) were calculated 24 h after admission. All patients were observed until loss to follow-up, death, or specific follow-up times (28 days, 3 months, and 6 months), which were calculated after the initial hospital admission. The receiver operating characteristic (ROC) curve was employed to estimate the power of six scores to forecast ACLF patients’ outcome.ResultsAll scores were distinctly higher in nonsurviving patients than in surviving patients and had predictive value for outcome in patients with ACLF at all time points (P < 0.050). The areas under the ROC curve (AUROCs) of the CLIF-SOFA score were higher than those of other scores at all time points. The comparison of the AUROC of the CLIF-SOFA score with other scores was statistically significant at 28 days (P < 0.050), which was the only time point at which it was greater than 0.800.ConclusionPatients with ACLF have high mortality. These six scores are effective tools for assessing the prognosis of ACLF patients. The CLIF-SOFA score is especially effective for evaluating 28-day mortality. creator: Yue Zhang creator: Yuan Nie creator: Linxiang Liu creator: Xuan Zhu uri: https://doi.org/10.7717/peerj.9857 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Zhang et al. title: Estimating the impact of mobility patterns on COVID-19 infection rates in 11 European countries link: https://peerj.com/articles/9879 last-modified: 2020-09-15 description: BackgroundAs governments across Europe have issued non-pharmaceutical interventions (NPIs) such as social distancing and school closing, the mobility patterns in these countries have changed. Most states have implemented similar NPIs at similar time points. However, it is likely different countries and populations respond differently to the NPIs and that these differences cause mobility patterns and thereby the epidemic development to change.MethodsWe build a Bayesian model that estimates the number of deaths on a given day dependent on changes in the basic reproductive number, R0, due to differences in mobility patterns. We utilise mobility data from Google mobility reports using five different categories: retail and recreation, grocery and pharmacy, transit stations, workplace and residential. The importance of each mobility category for predicting changes in R0 is estimated through the model.FindingsThe changes in mobility have a considerable overlap with the introduction of governmental NPIs, highlighting the importance of government action for population behavioural change. The shift in mobility in all categories shows high correlations with the death rates 1 month later. Reduction of movement within the grocery and pharmacy sector is estimated to account for most of the decrease in R0.InterpretationOur model predicts 3-week epidemic forecasts, using real-time observations of changes in mobility patterns, which can provide governments with direct feedback on the effects of their NPIs. The model predicts the changes in a majority of the countries accurately but overestimates the impact of NPIs in Sweden and Denmark and underestimates them in France and Belgium. We also note that the exponential nature of all epidemiological models based on the basic reproductive number, R0 cause small errors to have extensive effects on the predicted outcome. creator: Patrick Bryant creator: Arne Elofsson uri: https://doi.org/10.7717/peerj.9879 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Bryant and Elofsson title: Integrated analysis of the transcriptome-wide m6A methylome in preeclampsia and healthy control placentas link: https://peerj.com/articles/9880 last-modified: 2020-09-15 description: N6-methyladenosine (m6A) is the most prevalent modification in eukaryotic mRNA and potential regulatory functions of m6A have been shown by mapping the RNA m6A modification landscape. m6A modification in active gene regulation manifests itself as altered methylation profiles. The number of reports regarding to the profiling of m6A modification and its potential role in the placenta of preeclampsia (PE) is small. In this work, placental samples were collected from PE and control patients. Expression of m6A-related genes was investigated using quantitative real-time PCR. MeRIP-seq and RNA-seq were performed to detect m6A methylation and mRNA expression profiles. Gene ontology (GO) functional and Kyoto encyclopedia of genes and genomes (KEGG) pathway analyses were also conducted to explore the modified genes and their clinical significance. Our findings show that METTL3 and METTL14 were up-regulated in PE. In total, 685 m6A peaks were differentially expressed as determined by MeRIP-seq. Altered peaks of m6A-modified transcripts were primarily associated with nitrogen compound metabolic process, positive regulation of vascular-associated smooth muscle cell migration, and endoplasmic reticulum organisation. The m6A hyper-methylated genes of Wnt/β-catenin signalling pathway, mTOR signalling pathway, and several cancer-related pathways may contribute to PE. We also verified that the significant increase of HSPA1A mRNA and protein expression was regulated by m6A modification, suggesting m6A plays a key role in the regulation of gene expression. Our data provide novel information regarding m6A modification alterations in PE and help our understanding of the pathogenesis of PE. creator: Jin Wang creator: Fengchun Gao creator: Xiaohan Zhao creator: Yan Cai creator: Hua Jin uri: https://doi.org/10.7717/peerj.9880 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al. title: Effect of calcium on relieving berry cracking in grape (Vitis vinifera L.) ‘Xiangfei’ link: https://peerj.com/articles/9896 last-modified: 2020-09-15 description: Fruit cracking is a physiological disorder in many plant species that leads to severe economic losses. The aim of this study was to investigate the effect of calcium on fruit cracking and explore the underlying mechanisms. We studied the effect of exogenous calcium on grape berry cracking, calcium absorbance and distribution, and cell wall metabolism in the cracking-susceptible cultivar ‘Xiangfei’. Calcium significantly reduced the frequency of fruit cracking, increased the break force of the berry skin, and stimulated storage of calcium. In addition, calcium increased the content of protopectin and inhibited the increase in content of water-soluble pectin, by regulating the transcription and activities of enzymes associated with cell wall metabolism. Taken together, the results indicated that dipping grape berries in calcium solution is effective in preventing fruit cracking by stimulating calcium uptake, inhibiting cell wall disassembly, and promoting cell wall strengthening. creator: Jun Yu creator: Mingtao Zhu creator: Miao Bai creator: Yanshuai Xu creator: Shaogang Fan creator: Guoshun Yang uri: https://doi.org/10.7717/peerj.9896 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Yu et al. title: Proanthocyanidins reduce cellular function in the most globally diagnosed cancers in vitro link: https://peerj.com/articles/9910 last-modified: 2020-09-15 description: BackgroundGrowing evidence indicates that proanthocyanidins (PACs) may be effective in treating and preventing various cancers. The fundamental mechanism of PACs inhibiting the proliferation at cellular and molecular levels in most of the cancer types remains unclear.ObjectiveThe anticancer efficacy of PACs was investigated in vitro using three human cancer cell lines: human colorectal adenocarcinoma (HT-29), human breast carcinoma (MCF-7), and human prostatic adenocarcinoma (PC-3).MethodsCytotoxicity was evaluated by MTT assay, while cell proliferation was measured by trypan blue exclusion method. Cell migration was measured by wound healing assay, and DAPI staining was used to evaluate apoptotic nucleus morphology. RT-PCR was used to analyze the expression of Bax and Bcl-2, and caspase enzyme activity assay was measured by caspase colorimetric assay.ResultsPACs could inhibit both cellular viability and proliferation in a concentration- and time-dependent fashion in all investigated cells. Further, all tested cells showed similarly decreased migration after 24- and 48-h PAC treatment. We observed increased apoptotic nucleus morphology in treated cells (p ≤ 0.01). BAX expression significantly increased in HT-29 (p < 0.01), PC-3(p < 0.01), and MCF-7 (p < 0.05) cells, while BCL-2 expression significantly declined (p < 0.05). Caspase activities were significantly increased in all tested cancer cell lines after 24-h PAC treatment.ConclusionPACs may have potential therapeutic properties against colorectal, breast, and prostate cancer. creator: Sarah Albogami uri: https://doi.org/10.7717/peerj.9910 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Albogami title: Carbon emission and water use efficiency response to tillage methods and planting patterns of winter wheat in the North China Plain link: https://peerj.com/articles/9912 last-modified: 2020-09-15 description: BackgroundImplementing sustainable farming practices for winter wheat (Triticum aestivum L.) in the North China Plain may be a way to reduce carbon emissions. No tillage generally results in less net CO2 loss from farmland, but no tillage also reduces the grain yield and water use efficiency (WUE) of winter wheat. Wide-precision planting of winter wheat may enhance the grain yield and WUE; however, it is not known precisely how tillage and planting patterns affect CO2 exchange, grain yield and WUE.MethodsIn this study, two tillage methods (conventional tillage, T and no tillage, NT) and two planting patterns (conventional planting, C and wide-precision planting, W) were used in two consecutive winter wheat growing seasons.ResultsCompared with the T treatments, the NT treatments had significantly lower cumulative net CO2 emissions in 2015–2016 and 2016–2017 (30.8 and 21.3%, respectively), and had lower grain yields (9.0 and 9.4%, respectively) and WUE (6.0 and 7.2%, respectively). The W treatments had a compensating effect on grain yield failure and reduced cumulative net CO2 emissions more than C treatments, thereby increasing WUE, reducing carbon emissions per unit water consumption, and increasing the yield carbon utilization efficiency (YCUE). The lowest cumulative CO2 emissions and highest YCUE were observed for NT with W treatment. Results from this analogous tillage experiment indicated that NT and W farming practices provide an option for reducing carbon emissions and enhancing WUE and YCUE for sustainable winter wheat development. creator: Yuzhao Ma creator: Quanqi Li uri: https://doi.org/10.7717/peerj.9912 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ma and Li title: Development of a novel nanoflow liquid chromatography-parallel reaction monitoring mass spectrometry-based method for quantification of angiotensin peptides in HUVEC cultures link: https://peerj.com/articles/9941 last-modified: 2020-09-15 description: BackgroundThis study aimed to develop an analytical method using liquid chromatography tandem mass spectrometry (LC-MS/MS) for the determination of angiotensin (Ang) I, Ang (1-9), Ang II, Ang (1-7), Ang (1-5), Ang III, Ang IV in human umbilical vein endothelial cell (HUVEC) culture supernatant.MethodsHUVEC culture supernatant was added with gradient concentrations (0.05–1,000 ng/ml) of standard solutions of the Ang peptides. These samples underwent C18 solid-phase extraction and separation using a preconcentration nano-liquid chromatography mass spectrometry system. The target peptides were detected by a Q Exactive quadrupole orbitrap high-resolution mass spectrometer in the parallel reaction monitoring mode. Ang converting enzyme (ACE) in HUVECs was silenced to examine Ang I metabolism.ResultsThe limit of detection was 0.1 pg for Ang II and Ang III, and 0.5 pg for Ang (1-9), Ang (1-7), and Ang (1-5). The linear detection range was 0.1–2,000 pg (0.05–1,000 ng/ml) for Ang II and Ang III, and 0.5–2,000 pg (0.25–1,000 ng/ml) for Ang (1-9) and Ang (1-5). Intra-day and inter-day precisions (relative standard deviation) were <10%. Ang II, Ang III, Ang IV, and Ang (1-5) were positively correlated with ACE expression by HUVECs, while Ang I, Ang (1-7), and Ang (1-9) were negatively correlated.ConclusionThe nanoflow liquid chromatography-parallel reaction monitoring mass spectrometry-based methodology established in this study can evaluate the Ang peptides simultaneously in HUVEC culture supernatant. creator: Chuan He creator: Simiao Hu creator: Wanxing Zhou uri: https://doi.org/10.7717/peerj.9941 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 He et al. title: Numerical investigation of microbial quorum sensing under various flow conditions link: https://peerj.com/articles/9942 last-modified: 2020-09-15 description: Microorganisms efficiently coordinate phenotype expressions through a decision-making process known as quorum sensing (QS). We investigated QS amongst distinct, spatially distributed microbial aggregates under various flow conditions using a process-driven numerical model. Model simulations assess the conditions suitable for QS induction and quantify the importance of advective transport of signaling molecules. In addition, advection dilutes signaling molecules so that faster flow conditions require higher microbial densities, faster signal production rates, or higher sensitivities to signaling molecules to induce QS. However, autoinduction of signal production can substantially increase the transport distance of signaling molecules in both upstream and downstream directions. We present empirical approximations to the solutions of the advection–diffusion–reaction equation that describe the concentration profiles of signaling molecules for a wide range of flow and reaction rates. These empirical relationships, which predict the distribution of dissolved solutes along pore channels, allow to quantitatively estimate the effective communication distances amongst multiple microbial aggregates without further numerical simulations. creator: Heewon Jung creator: Christof D. Meile uri: https://doi.org/10.7717/peerj.9942 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Jung and Meile title: TET1 may contribute to hypoxia-induced epithelial to mesenchymal transition of endometrial epithelial cells in endometriosis link: https://peerj.com/articles/9950 last-modified: 2020-09-15 description: BackgroundEndometriosis (EMs) is a non-malignant gynecological disease, whose pathogenesis remains to be clarified. Recent studies have found that hypoxia induces epithelial-mesenchymal transition (EMT) as well as epigenetic modification in EMs. However, the relationship between EMT and demethylation modification under hypoxia status in EMs remains unknown.MethodsThe expression of N-cadherin, E-cadherin and TET1 in normal endometria, eutopic endometria and ovarian endometriomas was assessed by immunohistochemistry and immunofluorescence double staining. 5-hmC was detected by fluorescence-based ELISA kit using a specific 5-hmC antibody. Overexpression and inhibition of TET1 or hypoxia-inducible factor 2α (HIF-2α) were performed by plasmid and siRNA transfection. The expression of HIF-2α, TET1 and EMT markers in Ishikawa (ISK) cells (widely used as endometrial epithelial cells) was evaluated by western blotting. The interaction of HIF-2α and TET1 was analyzed by chromatin immunoprecipitation.ResultsDemethylation enzyme TET1 (ten-eleven translocation1) was elevated in glandular epithelium of ovarian endometrioma, along with the activation of EMT (increased expression of N-cadherin, and decreased expression of E-cadherin) and global increase of epigenetic modification marker 5-hmC(5-hydroxymethylcytosine). Besides, endometriosis lesions had more TET1 and N-cadherin co-localized cells. Further study showed that ISK cells exhibited enhanced EMT, and increased expression of TET1 and HIF-2α under hypoxic condition. Hypoxia-induced EMT was partly regulated by TET1 and HIF-2α. HIF-2α inhibition mitigated TET1 expression changes provoked by hypoxia.ConclusionsHypoxia induces the expression of TET1 regulated by HIF-2α, thus may promote EMT in endometriosis. creator: Jingni Wu creator: Xidie Li creator: Hongyan Huang creator: Xiaomeng Xia creator: Mengmeng Zhang creator: Xiaoling Fang uri: https://doi.org/10.7717/peerj.9950 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wu et al. title: Prophet forecasting model: a machine learning approach to predict the concentration of air pollutants (PM2.5, PM10, O3, NO2, SO2, CO) in Seoul, South Korea link: https://peerj.com/articles/9961 last-modified: 2020-09-15 description: Amidst recent industrialization in South Korea, Seoul has experienced high levels of air pollution, an issue that is magnified due to a lack of effective air pollution prediction techniques. In this study, the Prophet forecasting model (PFM) was used to predict both short-term and long-term air pollution in Seoul. The air pollutants forecasted in this study were PM2.5, PM10, O3, NO2, SO2, and CO, air pollutants responsible for numerous health conditions upon long-term exposure. Current chemical models to predict air pollution require complex source lists making them difficult to use. Machine learning models have also been implemented however their requirement of meteorological parameters render the models ineffective as additional models and infrastructure need to be in place to model meteorology. To address this, a model needs to be created that can accurately predict pollution based on time. A dataset containing three years worth of hourly air quality measurements in Seoul was sourced from the Seoul Open Data Plaza. To optimize the model, PFM has the following parameters: model type, changepoints, seasonality, holidays, and error. Cross validation was performed on the 2017–18 data; then, the model predicted 2019 values. To compare the predicted and actual values and determine the accuracy of the model, the statistical indicators: mean squared error (MSE), mean absolute error (MAE), root mean squared error (RMSE), and coverage were used. PFM predicted PM2.5 and PM10 with a MAE value of 12.6 µg/m3 and 19.6 µg/m3, respectively. PFM also predicted SO2 and CO with a MAE value of 0.00124 ppm and 0.207 ppm, respectively. PFM’s prediction of PM2.5 and PM10 had a MAE approximately 2 times and 4 times less, respectively, than comparable models. PFM’s prediction of SO2and CO had a MAE approximately five times and 50 times less, respectively, than comparable models. In most cases, PFM’s ability to accurately forecast the concentration of air pollutants in Seoul up to one year in advance outperformed similar models proposed in literature. This study addresses the limitations of the prior two PFM studies by expanding the modelled air pollutants from three pollutants to six pollutants while increasing the prediction time from 3 days to 1 year. This is also the first research to use PFM in Seoul, Korea. To achieve more accurate results, a larger air pollution dataset needs to be implemented with PFM. In the future, PFM should be used to predict and model air pollution in other regions, especially those without advanced infrastructure to model meteorology alongside air pollution. In Seoul, Seoul’s government can use PFM to accurately predict air pollution concentrations and plan accordingly. creator: Justin Shen creator: Davesh Valagolam creator: Serena McCalla uri: https://doi.org/10.7717/peerj.9961 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Shen et al. title: Seasonal and successional dynamics of size-dependent plant demographic rates in a tropical dry forest link: https://peerj.com/articles/9636 last-modified: 2020-09-14 description: Tropical forests are globally important for biodiversity conservation and climate change mitigation but are being converted to other land uses. Conversion of seasonally dry tropical forests (SDTF) is particularly high while their protection is low. Secondary succession allows forests to recover their structure, diversity and composition after conversion and subsequent abandonment and is influenced by demographic rates of the constituent species. However, how these rates vary between seasons for different plant sizes at different successional stages in SDTF is not known. The effect of seasonal drought may be more severe early in succession, when temperature and radiation are high, while competition and density-dependent processes may be more important at later stages, when vegetation is tall and dense. Besides, the effects of seasonality and successional stage may vary with plant size. Large plants can better compete with small plants for limiting resources and may also have a greater capacity to withstand stress. We asked how size-dependent density, species density, recruitment and mortality varied between seasons and successional stages in a SDTF. We monitored a chronosequence in Yucatan, Mexico, over six years in three 0.1 ha plots in each of three successional stages: early (3–5 years-old), intermediate (18–20 years-old) and advanced (>50 years-old). Recruitment, mortality and species gain and loss rates were calculated from wet and dry season censuses separately for large (diameter > 5 cm) and small (1–5 cm in diameter) plants. We used linear mixed-effects models to assess the effects of successional stage, seasonality and their changes through time on demographic rates and on plant and species density. Seasonality affected demographic rates and density of large plants, which exhibited high wet-season recruitment and species gain rates at the early stage and high wet-season mortality at the intermediate stage, resulting in an increase in plant and species density early in succession followed by a subsequent stabilization. Small plant density decreased steadily after only 5 years of land abandonment, whereas species density increased with successional stage. A decline in species dominance may be responsible for these contrasting patterns. Seasonality, successional stage and their changes through time had a stronger influence on large plants, likely because of large among-plot variation of small plants. Notwithstanding the short duration of our study, our results suggest that climate-change driven decreases in rainy season precipitation may have an influence on successional dynamics in our study forest as strong as, or even stronger than, prolonged or severe droughts during the dry season. creator: Irving Saenz-Pedroza creator: Richard Feldman creator: Casandra Reyes-García creator: Jorge A. Meave creator: Luz Maria Calvo-Irabien creator: Filogonio May-Pat creator: Juan M. Dupuy uri: https://doi.org/10.7717/peerj.9636 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Saenz-Pedroza et al. title: Rediscovery of Cyperus flavescens (Cyperaceae) on the northeast periphery of its range in Europe link: https://peerj.com/articles/9837 last-modified: 2020-09-14 description: In recent years, three large populations of Cyperus flavescens were found in Poland, the richest occurrence of this species in over 30 years. The goal of this research is to determine the habitat factors lead to the mass occurrence of C. flavescens and the present situation of that species and its habitat in Central Europe. Soil conditions of the three populations were studied. To determine the correlation between the occurrence and abundance of species and the chemical parameters of the soil, the DCA and CCA methods were used. The DCA of environmental Ellenberg values was made for all relevés known from Poland. The occurrence of C. flavescens in plant communities in Central Europe was studied. The maximum entropy method was used for potential distribution analysis of C. flavescens. All analyzed traits are important for this species and none has an advantage over another, so the environmental factor affecting the occurrence of C. flavescens is different from the tested. Analysis on Ellenberg values indicate that the longest gradients are temperature, moisture and nutrients. The analysis of vegetation data involving Cyperus flavescens available from Central Europe indicates that this species occurs mainly in the company of Juncus bufonius and Plantago intermedia, whereas other species of the Isoëto-Nanojuncetea class appear rarely. In MaxEnt analysis based on bioclimatic variables, the most important variable is BIO1 (Annual Mean Temperature). The results of our observation indicate that anthropogenic factors such as grazing livestock have a positive effect on the occurrence of the species. It is also very likely that the species is promoted by very warm summers with only short periods of heavy rains. A map of the potential distribution of C. flavescens in Central Europe created according historical and future data show an extension of the range of potential habitats to the north and east. creator: Paweł Marciniuk creator: Jolanta Marciniuk creator: Andrzej Łysko creator: Łukasz Krajewski creator: Justyna Chudecka creator: Janina Skrzyczyńska creator: Agnieszka Anna Popiela uri: https://doi.org/10.7717/peerj.9837 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Marciniuk et al. title: Potential role of cellular miRNAs in coronavirus-host interplay link: https://peerj.com/articles/9994 last-modified: 2020-09-14 description: Host miRNAs are known as important regulators of virus replication and pathogenesis. They can interact with various viruses through several possible mechanisms including direct binding of viral RNA. Identification of human miRNAs involved in coronavirus-host interplay becomes important due to the ongoing COVID-19 pandemic. In this article we performed computational prediction of high-confidence direct interactions between miRNAs and seven human coronavirus RNAs. As a result, we identified six miRNAs (miR-21-3p, miR-195-5p, miR-16-5p, miR-3065-5p, miR-424-5p and miR-421) with high binding probability across all analyzed viruses. Further bioinformatic analysis of binding sites revealed high conservativity of miRNA binding regions within RNAs of human coronaviruses and their strains. In order to discover the entire miRNA-virus interplay we further analyzed lungs miRNome of SARS-CoV infected mice using publicly available miRNA sequencing data. We found that miRNA miR-21-3p has the largest probability of binding the human coronavirus RNAs and being dramatically up-regulated in mouse lungs during infection induced by SARS-CoV. creator: Stepan Nersisyan creator: Narek Engibaryan creator: Aleksandra Gorbonos creator: Ksenia Kirdey creator: Alexey Makhonin creator: Alexander Tonevitsky uri: https://doi.org/10.7717/peerj.9994 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Nersisyan et al. title: Unexpected diversity in the host-generalist oribatid mite Paraleius leontonychus (Oribatida, Scheloribatidae) phoretic on Palearctic bark beetles link: https://peerj.com/articles/9710 last-modified: 2020-09-11 description: Bark beetles are feared as pests in forestry but they also support a large number of other taxa that exploit the beetles and their galleries. Among arthropods, mites are the largest taxon associated with bark beetles. Many of these mites are phoretic and often involved in complex interactions with the beetles and other organisms. Within the oribatid mite family Scheloribatidae, only two of the three nominal species of Paraleius have been frequently found in galleries of bark beetles and on the beetles themselves. One of the species, P. leontonychus, has a wide distribution range spanning over three ecozones of the world and is believed to be a host generalist, reported from numerous bark beetle and tree species. In the present study, phylogenetic analyses of one mitochondrial and two nuclear genes identified six well supported, fairly divergent clades within P. leontonychus which we consider to represent distinct species based on molecular species delimitation methods and largely congruent clustering in mitochondrial and nuclear gene trees. These species do not tend to be strictly host specific and might occur syntopically. Moreover, mito-nuclear discordance indicates a case of past hybridization/introgression among distinct Paraleius species, the first case of interspecific hybridization reported in mites other than ticks. creator: Sylvia Schäffer creator: Stephan Koblmüller uri: https://doi.org/10.7717/peerj.9710 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Schäffer and Koblmüller title: The impact of climate change on flow conditions and wetland ecosystems in the Lower Biebrza River (Poland) link: https://peerj.com/articles/9778 last-modified: 2020-09-11 description: Water plays a key role in the functioning of wetlands and a shortage or contamination of it leads to changes in habitat conditions and degradation of ecosystems. This article scrutinizes the impact of climate change on the hydrological characteristics of floods (maximum flow, duration, volume) in the River Biebrza wetlands (North-East Poland). We analysed the trends in duration and volume of flood and maximum discharges in the historical period 1970–2000 and predicted these for the future periods 2020–2050 and 2070–2100, respectively. Next we assessed the impact on the wetland ecosystems. The basis of our assessments consists of statistical analyses of hydrographs and calculations by the Soil and Water Assessment Tool hydrological model and considering nine bias-corrected climate models. The results indicate that both volume and duration of winter floods will keep increasing continuously under Representative Concentration Pathways 4.5 and 8.5. The reduction in peak annual floods is expected to decline slightly in both scenarios. On the other hand, the analysis of trends in mean and standard deviation revealed negligible tendencies in the datasets for summer and winter hydrological seasons within the three time frames analysed (1970–2000; 2020–2050; 2070–2100). We foresee several future implications for the floodplain ecosystems. Shifts in transversal ecosystem zonation parallel to the river will likely take place with more highly productive flood tolerant vegetation types. Nutrient availability and algal blooms during spring inundations will likely increase. Slowdown of organic matter turnover later in summer will lead to a higher peat accumulation rate. Logistical problems with summer mowing and removal of bushes in winter may enhance shrub encroachment. creator: Dorota Mirosław-Świątek creator: Paweł Marcinkowski creator: Krzysztof Kochanek creator: Martin J. Wassen uri: https://doi.org/10.7717/peerj.9778 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Mirosław-Świątek et al. title: Methylase-assisted subcloning for high throughput BioBrick assembly link: https://peerj.com/articles/9841 last-modified: 2020-09-11 description: The BioBrick standard makes possible iterated pairwise assembly of cloned parts without any depletion of unique restriction sites. Every part that conforms to the standard is compatible with every other part, thereby fostering a worldwide user community. The assembly methods, however, are labor intensive or inefficient compared to some newer ones so the standard may be falling out of favor. An easier way to assemble BioBricks is described herein. Plasmids encoding BioBrick parts are purified from Escherichia coli cells that express a foreign site-specific DNA methyltransferase, so that each is subsequently protected in vitro from the activity of a particular restriction endonuclease. Each plasmid is double-digested and all resulting restriction fragments are ligated together without gel purification. The ligation products are subsequently double-digested with another pair of restriction endonucleases so only the desired insert-recipient vector construct retains the capacity to transform E. coli. This 4R/2M BioBrick assembly protocol is more efficient and accurate than established workflows including 3A assembly. It is also much easier than gel purification to miniaturize, automate and perform more assembly reactions in parallel. As such, it should streamline DNA assembly for the existing community of BioBrick users, and possibly encourage others to join. creator: Ichiro Matsumura uri: https://doi.org/10.7717/peerj.9841 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Matsumura title: ProminTools: shedding light on proteins of unknown function in biomineralization with user friendly tools illustrated using mollusc shell matrix protein sequences link: https://peerj.com/articles/9852 last-modified: 2020-09-11 description: Biominerals are crucial to the fitness of many organism and studies of the mechanisms of biomineralization are driving research into novel materials. Biomineralization is generally controlled by a matrix of organic molecules including proteins, so proteomic studies of biominerals are important for understanding biomineralization mechanisms. Many such studies identify large numbers of proteins of unknown function, which are often of low sequence complexity and biased in their amino acid composition. A lack of user-friendly tools to find patterns in such sequences and robustly analyse their statistical properties relative to the background proteome means that they are often neglected in follow-up studies. Here we present ProminTools, a user-friendly package for comparison of two sets of protein sequences in terms of their global properties and motif content. Outputs include data tables, graphical summaries in an html file and an R-script as a starting point for data-set specific visualizations. We demonstrate the utility of ProminTools using a previously published shell matrix proteome of the giant limpet Lottia gigantea. creator: Alastair W. Skeffington creator: Andreas Donath uri: https://doi.org/10.7717/peerj.9852 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Skeffington and Donath title: Intergenerational implications of alcohol intake: metabolic disorders in alcohol-naïve rat offspring link: https://peerj.com/articles/9886 last-modified: 2020-09-11 description: Alcohol drinking may be associated with an increased risk of various metabolic diseases. Rat lines selectively bred for alcohol preference and alcohol avoidance constitute an interesting model to study inherited factors related to alcohol drinking and metabolic disorders. The aim of the present study was to compare the levels of selected laboratory biomarkers of metabolic disorders in blood samples from naïve offspring of Warsaw alcohol high-preferring (WHP), Warsaw alcohol low-preferring (WLP), and wild Wistar rats. Blood samples were collected from 3-month old (300–350 g) alcohol-naïve, male offspring of WHP (n = 8) and WLP rats (n = 8), as well as alcohol-naïve, male, wild Wistar rats. Markers of metabolic, hepatic, and pancreatic disorders were analysed (levels of homocysteine, glucose, total cholesterol, triglycerides and γ-glutamyl transferase (GGT), aspartate (AST), alanine aminotransferase (ALT), and amylase serum activities). Alcohol-naïve offspring of WHP, WLP, and wild Wistar rats differed significantly in the levels of triglycerides, total cholesterol, homocysteine, as well as in the activity of GGT, ALT, AST, and amylase enzymes. Most markers in the alcohol-naïve offspring of WHP rats were altered even thought they were never exposed to alcohol pre- or postnatally. This may suggest that parental alcohol abuse can have a detrimental influence on offspring vulnerability to metabolic disorders. creator: Pawel Mierzejewski creator: Alicja Zakrzewska creator: Julita Kuczyńska creator: Edyta Wyszogrodzka creator: Monika Dominiak uri: https://doi.org/10.7717/peerj.9886 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Mierzejewski et al. title: A prediction modeling based on SNOT-22 score for endoscopic nasal septoplasty: a retrospective study link: https://peerj.com/articles/9890 last-modified: 2020-09-11 description: BackgroundTo create a nomogram prediction model for the efficacy of endoscopic nasal septoplasty, and the likelihood of patient benefiting from the operation.MethodsA retrospective analysis of 155 patients with nasal septum deviation (NSD) was performed to develop a predictive model for the efficacy of endoscopic nasal septoplasty. Quality of life (QoL) data was collected before and after surgery using Sinonasal Outcome Test-22 (SNOT-22) scores to evaluate the surgical outcome. An effective surgical outcome was defined as a SNOT-22 score change ≥ 9 points after surgery. Multivariate logistic regression analysis was then used to establish a predictive model for the NSD treatment. The predictive quality and clinical utility of the predictive model were assessed by C-index, calibration plots, and decision curve analysis.ResultsThe identified risk factors for inclusion in the predictive model were included. The model had a good predictive power, with a AUC of 0.920 in the training group and a C index of 0.911 in the overall sample. Decision curve analysis revealed that the prediction model had a good clinical applicability.ConclusionsOur prediction model is efficient in predicting the efficacy of endoscopic surgery for NSD through evaluation of factors including: history of nasal surgery, preoperative SNOT-22 score, sinusitis, middle turbinate plasty, BMI, smoking, follow-up time, seasonal allergies, and advanced age. Therefore, it can be cost-effective for individualized preoperative assessment. creator: Xue-ran Kang creator: Bin Chen creator: Yi-sheng Chen creator: Bin Yi creator: Xiaojun Yan creator: Chenyan Jiang creator: Shulun Wang creator: Lixing Lu creator: Runjie Shi uri: https://doi.org/10.7717/peerj.9890 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kang et al. title: Nepenthes maximoides (Nepenthaceae) a new, critically endangered (possibly extinct) species in Sect. Alatae from Luzon, Philippines showing striking pitcher convergence with N. maxima (Sect. Regiae) of Indonesia link: https://peerj.com/articles/9899 last-modified: 2020-09-11 description: Nepenthes maximoides sp. nov. (Sect. Alatae) is described and assessed as Critically Endangered (Possibly Extinct) from Luzon, Philippines and appears unrecorded in 110 years. The spectacular, large, narrowly funnel-shaped upper pitchers, lids with recurved basal and filiform apical appendages, unlike any other species in the Philippines, closely resemble those of N. maxima (Sect. Regiae) of Sulawesi–New Guinea, likely due to convergent evolution. Following recent phylogenomic analysis, sect. Alatae is divided into two, Sect. Alatae sensu stricto of Luzon to Sibuyan (including N. maximoides), and Sect. Micramphorae, expanded and recircumscribed to encompass those species of the southern Visayas, and Mindanao. A key is provided to the six species now recognised in the newly narrowly recircumscribed Sect. Alatae. The number of Nepenthes species recorded from Luzon has increased from two in 2001, to eight in 2020, all but one of which are endemic to that island, and four of which appear to be point endemics. creator: Charles King creator: Martin Cheek uri: https://doi.org/10.7717/peerj.9899 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 King and Cheek title: First report of lionfish prey from Western Florida waters as identified by DNA barcoding link: https://peerj.com/articles/9922 last-modified: 2020-09-11 description: DNA barcoding was used to identify prey fragments recovered from the stomachs of lionfish harvested during the 2016 Sarasota Lionfish Derby. A total of 305 prey fragments were recovered from 50 stomachs (mean = 4.6 per stomach), of which 184 (60.3%) fragments could be identified to either species or genus when Cytochrome Oxidase I (COI) sequences were queried against the Barcode of Life Database. We identified 21 fish prey species which represented fourteen families and accounted for 95.7% of genetically identifiable prey items. The remaining prey items identified corresponded to six crustacean species. The four most common prey taxa in lionfish stomachs were Ptereleotris calliura (24.3%), an unidentified Microgobius species (20.4%), Diplectum formosum (14.3%), and Apogon aurolineatus (12.2%). The most frequently observed crustacean species, Metapenaeopsis goodei, was found in only three stomachs (6.1%). We also report eleven taxa as putative novel lionfish prey species, most of which are common in Florida waters. Sixteen prey items were identified as lionfish (P. volitans); however, it was not definitive whether these detections were due to cross contamination or cannibalization. This represents the first report of lionfish diets from Florida waters in the Eastern Gulf of Mexico based on barcoding efforts. Our results are largely congruent with previous COI barcoding based studies of lionfish diets, indicating these predators to be generalists exhibiting preferences for specific prey traits but with regional differences in their diets. creator: Carlos A. Santamaria creator: James Locascio creator: Taylor M. Greenan uri: https://doi.org/10.7717/peerj.9922 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Santamaria et al. title: Two new nematode species (Plectida: Leptolaimidae, Rhadinematidae) from Chatham Rise, New Zealand link: https://peerj.com/articles/9923 last-modified: 2020-09-11 description: Two new species of the order Plectida are described from Chatham Rise, New Zealand. Leptolaimus dififtinus sp. nov. is characterised by the short body 319–420 microns long, truncate labial region slightly offset from body contour and bearing conspicuous outer labial papillae, cephalic setae 1.3–1.4 microns long, amphid located 4–9 microns from anterior end, lateral alae originating from middle of buccal cavity length, female without supplements, male with precloacal and postcloacal pairs of subventral setae, nine tubular supplements (alveolar supplements absent), tubular supplements weakly S-shaped with pointed tip, spicules arcuate 24 microns or 1.4 cloacal body diameters long and dorsal gubernacular apophyses. Lavareda iramscotti sp. nov. is characterised by adult body length 3,023–3,121 microns long, eight longitudinal rows of body pores each with short papilla, cephalic setae 4–5 microns long, tail 146–165 microns long, male with spicules 54 microns long, gubernaculum with triangular apophyses, 20 precloacal supplements with bifid distal tips arranged in 9 + 1 + 10 pattern, female with vulva at 55% of body length from anterior and cuticularisation perpendicular to vagina at level of vulva. The present study provides the first record of a Leptolaimus species from the New Zealand region and the first description of a female specimen of the genus Lavareda. creator: Daniel Leduc uri: https://doi.org/10.7717/peerj.9923 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Leduc title: Antimicrobial and micronutrient interventions for the management of infants under 6 months of age identified with severe malnutrition: a literature review link: https://peerj.com/articles/9175 last-modified: 2020-09-10 description: BackgroundInfants under 6 months (U6M) contribute a significant proportion of the burden and mortality of severe malnutrition globally. Evidence of underlying aetiology in this population is sparse, but it is known that the group includes ex-preterm and low birthweight (LBW) infants. They represent a unique population given their dependence on breastmilk or a safe, secure alternative. Nutrition agencies and health providers struggle to make programming decisions on which interventions should be provided to this group based upon the 2013 WHO Guidelines for the ‘Management of Severe Acute Malnutrition in Infants and Young Children’ since there are no published interventional trial data focussed on this population. Interim guidance for this group might be informed by evidence of safety and efficacy in adjacent population groups.MethodologyA narrative literature review was performed of systematic reviews, meta-analyses and randomised controlled trials of antimicrobial and micronutrient interventions (antibiotics, deworming, vitamin A, vitamin D, iron, zinc, folic acid and oral rehydration solution (ORS) for malnutrition) across the population groups of low birthweight/preterm infants, infants under 6 months, infants and children over 6 months with acute malnutrition or through supplementation to breastfeeding mothers. Outcomes of interest were safety and efficacy, in terms of mortality and morbidity.ResultsNinety-four articles were identified for inclusion within this review. None of these studied interventions exclusively in severely malnourished infants U6M. 64% reported on the safety of studied interventions. Significant heterogeneity was identified in definitions of study populations, interventions provided, and outcomes studied. The evidence for efficacy and safety across population groups is reviewed and presented for the interventions listed.ConclusionsThe direct evidence base for medical interventions for severely malnourished infants U6M is sparse. Our review identifies a specific need for accurate micronutrient profiling and interventional studies of micronutrients and oral fluid management of diarrhoea amongst infants U6M meeting anthropometric criteria for severe malnutrition. Indirect evidence presented in this review may help shape interim policy and programming decisions as well as the future research agenda for the management of infants U6M identified as malnourished. creator: Timothy J. Campion-Smith creator: Marko Kerac creator: Marie McGrath creator: James A. Berkley uri: https://doi.org/10.7717/peerj.9175 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Campion-Smith et al. title: Evolutionary history of dimethylsulfoniopropionate (DMSP) demethylation enzyme DmdA in marine bacteria link: https://peerj.com/articles/9861 last-modified: 2020-09-10 description: Dimethylsulfoniopropionate (DMSP), an osmolyte produced by oceanic phytoplankton and bacteria, is primarily degraded by bacteria belonging to the Roseobacter lineage and other marine Alphaproteobacteria via DMSP-dependent demethylase A protein (DmdA). To date, the evolutionary history of DmdA gene family is unclear. Some studies indicate a common ancestry between DmdA and GcvT gene families and a co-evolution between Roseobacter and the DMSP-producing-phytoplankton around 250 million years ago (Mya). In this work, we analyzed the evolution of DmdA under three possible evolutionary scenarios: (1) a recent common ancestor of DmdA and GcvT, (2) a coevolution between Roseobacter and the DMSP-producing-phytoplankton, and (3) an enzymatic adaptation for utilizing DMSP in marine bacteria prior to Roseobacter origin. Our analyses indicate that DmdA is a new gene family originated from GcvT genes by duplication and functional divergence driven by positive selection before a coevolution between Roseobacter and phytoplankton. Our data suggest that Roseobacter acquired dmdA by horizontal gene transfer prior to an environment with higher DMSP. Here, we propose that the ancestor that carried the DMSP demethylation pathway genes evolved in the Archean, and was exposed to a higher concentration of DMSP in a sulfur-rich atmosphere and anoxic ocean, compared to recent Roseobacter eco-orthologs (orthologs performing the same function under different conditions), which should be adapted to lower concentrations of DMSP. creator: Laura Hernández creator: Alberto Vicens creator: Luis E. Eguiarte creator: Valeria Souza creator: Valerie De Anda creator: José M. González uri: https://doi.org/10.7717/peerj.9861 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Hernández et al. title: Consistent administration of cetuximab is associated with favorable outcomes in recurrent/metastatic head and neck squamous cell carcinoma in an endemic carcinogen exposure area: a retrospective observational study link: https://peerj.com/articles/9862 last-modified: 2020-09-10 description: BackgroundThis study aimed to analyze the clinical outcomes associated with patients with recurrent/metastatic head and neck squamous cell carcinoma (RM HNSCC) who received cetuximab-based chemotherapy in a real-world clinical setting.MethodsClinical data were extracted from RM HNSCC patients diagnosed between 2016 and 2019. Kaplan–Meier survival estimates and Cox proportional hazards model were used for survival analyses.ResultsOf 106 RM HNSCC patients (mean age = 55.1 years), 38.7% exhibited recurrent disease and 61.3% had metastatic disease. The majority of patients showed a habit of addictive substance use, including alcohol (67.0%), betel nuts (71.7%), or tobacco (74.5%). The primary tumor sites included the oral cavity (64.1%), hypopharynx (19.8%), and oropharynx (16.0%). The median number of cetuximab cycles for the 106 patients was 11 (2–24). The disease control rate (DCR) was 48.1%, and the overall response rate (ORR) was 28.3%. The median progression-free survival (PFS) and overall survival (OS) were 5.0 and 9.23 months, respectively. Patients treated with more than 11 cycles of cetuximab exhibited a longer median PFS and median OS than did patients treated with less than 11 cycles (median PFS: 7.0 vs. 3.0 months, p < 0.001; OS: 12.43 vs. 4.46 months, p = 0.001). Patients without previous concurrent chemoradiotherapy (CRT) had a better median PFS than did those with previous CRT (6.0 vs. 4.0 months, p = 0.046). Multivariable analysis revealed that perineural invasion and fewer cycles of cetuximab (<11 cycles) were independent risk factors associated with disease progression. In addition, the reduction in treatment cycles of cetuximab and advanced lymph node metastasis were independent prognostic factors predicting poorer overall survival.ConclusionOur study provides important real-world data regarding cetuximab-containing treatment in RM HNSCC. Consistent administration of cetuximab could be associated with more favorable outcomes in RM HNSCC in endemic carcinogen exposure areas. creator: Hui-Ching Wang creator: Pei-Lin Liu creator: Pei-Chuan Lo creator: Yi-Tzu Chang creator: Leong-Perng Chan creator: Tsung-Jang Yeh creator: Hui-Hua Hsiao creator: Shih-Feng Cho uri: https://doi.org/10.7717/peerj.9862 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al. title: A survey of RNA secondary structural propensity encoded within human herpesvirus genomes: global comparisons and local motifs link: https://peerj.com/articles/9882 last-modified: 2020-09-10 description: There are nine herpesviruses known to infect humans, of which Epstein–Barr virus (EBV) is the most widely distributed (>90% of adults infected). This ubiquitous virus is implicated in a variety of cancers and autoimmune diseases. Previous analyses of the EBV genome revealed numerous regions with evidence of generating unusually stable and conserved RNA secondary structures and led to the discovery of a novel class of EBV non-coding (nc)RNAs: the stable intronic sequence (sis)RNAs. To gain a better understanding of the roles of RNA structure in EBV biology and pathogenicity, we revisit EBV using recently developed tools for genome-wide motif discovery and RNA structural characterization. This corroborated previous results and revealed novel motifs with potential functionality; one of which has been experimentally validated. Additionally, since many herpesviruses increasingly rival the seroprevalence of EBV (VZV, HHV-6 and HHV-7 being the most notable), analyses were expanded to include all sequenced human Herpesvirus RefSeq genomes, allowing for genomic comparisons. In total 10 genomes were analyzed, for EBV (types 1 and 2), HCMV, HHV-6A, HHV-6B, HHV-7, HSV-1, HSV-2, KSHV, and VZV. All resulting data were archived in the RNAStructuromeDB (https://structurome.bb.iastate.edu/herpesvirus) to make them available to a wide array of researchers. creator: Ryan J. Andrews creator: Collin A. O’Leary creator: Walter N. Moss uri: https://doi.org/10.7717/peerj.9882 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Andrews et al. title: Evaluation of different culture media to support in vitro growth and biofilm formation of bacterial vaginosis-associated anaerobes link: https://peerj.com/articles/9917 last-modified: 2020-09-10 description: BackgroundBacterial vaginosis (BV) is one of the most common vaginal infections worldwide. It is associated with the presence of a dense polymicrobial biofilm on the vaginal epithelium, formed mainly by Gardnerella species. The biofilm also contains other anaerobic species, but little is known about their role in BV development.AimTo evaluate the influence of different culture media on the planktonic and biofilm growth of six cultivable anaerobes frequently associated with BV, namely Gardnerella sp., Atopobium vaginae, Lactobacillus iners, Mobiluncus curtisii, Peptostreptococcus anaerobius and Prevotella bivia.MethodsA total of nine different culture media compositions, including commercially available and chemically defined media simulating genital tract secretions, were tested in this study. Planktonic cultures and biofilms were grown under anaerobic conditions (10% carbon dioxide, 10% helium and 80% nitrogen). Planktonic growth was assessed by optical density measurements, and biofilm formation was quantified by crystal violet staining.ResultsSignificant planktonic growth was observed for Gardnerella sp., A. vaginae and L. iners in New York City III broth, with or without ascorbic acid supplementation. Biofilm quantification showed high in vitro biofilm growth for Gardnerella sp., P. anaerobius and P. bivia in almost all culture media excluding Brucella broth. Contrary, only New York City III broth was able to promote biofilm formation for A. vaginae, L. iners and M. curtisii.ConclusionsOur data demonstrate that New York City III broth relative to the other tested media is the most conducive for future studies addressing polymicrobial biofilms development as this culture medium allowed the formation of significant levels of single-species biofilms. creator: Aliona S. Rosca creator: Joana Castro creator: Nuno Cerca uri: https://doi.org/10.7717/peerj.9917 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Rosca et al. title: A multi-class classification model for supporting the diagnosis of type II diabetes mellitus link: https://peerj.com/articles/9920 last-modified: 2020-09-10 description: BackgroundNumerous studies have utilized machine-learning techniques to predict the early onset of type 2 diabetes mellitus. However, fewer studies have been conducted to predict an appropriate diagnosis code for the type 2 diabetes mellitus condition. Further, ensemble techniques such as bagging and boosting have likewise been utilized to an even lesser extent. The present study aims to identify appropriate diagnosis codes for type 2 diabetes mellitus patients by means of building a multi-class prediction model which is both parsimonious and possessing minimum features. In addition, the importance of features for predicting diagnose code is provided.MethodsThis study included 149 patients who have contracted type 2 diabetes mellitus. The sample was collected from a large hospital in Taiwan from November, 2017 to May, 2018. Machine learning algorithms including instance-based, decision trees, deep neural network, and ensemble algorithms were all used to build the predictive models utilized in this study. Average accuracy, area under receiver operating characteristic curve, Matthew correlation coefficient, macro-precision, recall, weighted average of precision and recall, and model process time were subsequently used to assess the performance of the built models. Information gain and gain ratio were used in order to demonstrate feature importance.ResultsThe results showed that most algorithms, except for deep neural network, performed well in terms of all performance indices regardless of either the training or testing dataset that were used. Ten features and their importance to determine the diagnosis code of type 2 diabetes mellitus were identified. Our proposed predictive model can be further developed into a clinical diagnosis support system or integrated into existing healthcare information systems. Both methods of application can effectively support physicians whenever they are diagnosing type 2 diabetes mellitus patients in order to foster better patient-care planning. creator: Kuang-Ming Kuo creator: Paul Talley creator: YuHsi Kao creator: Chi Hsien Huang uri: https://doi.org/10.7717/peerj.9920 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Kuo et al. title: KEYLINK: towards a more integrative soil representation for inclusion in ecosystem scale models. I. review and model concept link: https://peerj.com/articles/9750 last-modified: 2020-09-09 description: The relatively poor simulation of the below-ground processes is a severe drawback for many ecosystem models, especially when predicting responses to climate change and management. For a meaningful estimation of ecosystem production and the cycling of water, energy, nutrients and carbon, the integration of soil processes and the exchanges at the surface is crucial. It is increasingly recognized that soil biota play an important role in soil organic carbon and nutrient cycling, shaping soil structure and hydrological properties through their activity, and in water and nutrient uptake by plants through mycorrhizal processes. In this article, we review the main soil biological actors (microbiota, fauna and roots) and their effects on soil functioning. We review to what extent they have been included in soil models and propose which of them could be included in ecosystem models. We show that the model representation of the soil food web, the impact of soil ecosystem engineers on soil structure and the related effects on hydrology and soil organic matter (SOM) stabilization are key issues in improving ecosystem-scale soil representation in models. Finally, we describe a new core model concept (KEYLINK) that integrates insights from SOM models, structural models and food web models to simulate the living soil at an ecosystem scale. creator: Gaby Deckmyn creator: Omar Flores creator: Mathias Mayer creator: Xavier Domene creator: Andrea Schnepf creator: Katrin Kuka creator: Kris Van Looy creator: Daniel P. Rasse creator: Maria J.I. Briones creator: Sébastien Barot creator: Matty Berg creator: Elena Vanguelova creator: Ivika Ostonen creator: Harry Vereecken creator: Laura M. Suz creator: Beat Frey creator: Aline Frossard creator: Alexei Tiunov creator: Jan Frouz creator: Tine Grebenc creator: Maarja Öpik creator: Mathieu Javaux creator: Alexei Uvarov creator: Olga Vindušková creator: Paul Henning Krogh creator: Oskar Franklin creator: Juan Jiménez creator: Jorge Curiel Yuste uri: https://doi.org/10.7717/peerj.9750 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Deckmyn et al. title: Omics approaches in Allium research: Progress and way ahead link: https://peerj.com/articles/9824 last-modified: 2020-09-09 description: BackgroundThe genus Allium (Family: Amaryllidaceae) is an economically important group of crops cultivated worldwide for their use as a vegetable and spices. Alliums are also well known for their nutraceutical properties. Among alliums, onion, garlic, leek, and chives cultivated worldwide. Despite their substantial economic and medicinal importance, the genome sequence of any of the Allium is not available, probably due to their large genome sizes. Recently evolved omics technologies are highly efficient and robust in elucidating molecular mechanisms of several complex life processes in plants. Omics technologies, such as genomics, transcriptomics, proteomics, metabolomics, metagenomics, etc. have the potential to open new avenues in research and improvement of allium crops where genome sequence information is limited. A significant amount of data has been generated using these technologies for various Allium species; it will help in understanding the key traits in Allium crops such as flowering, bulb development, flavonoid biosynthesis, male sterility and stress tolerance at molecular and metabolite level. This information will ultimately assist us in speeding up the breeding in Allium crops.MethodIn the present review, major omics approaches, and their progress, as well as potential applications in Allium crops, could be discussed in detail.ResultsHere, we have discussed the recent progress made in Allium research using omics technologies such as genomics, transcriptomics, micro RNAs, proteomics, metabolomics, and metagenomics. These omics interventions have been used in alliums for marker discovery, the study of the biotic and abiotic stress response, male sterility, organ development, flavonoid and bulb color, micro RNA discovery, and microbiome associated with Allium crops. Further, we also emphasized the integrated use of these omics platforms for a better understanding of the complex molecular mechanisms to speed up the breeding programs for better cultivars.ConclusionAll the information and literature provided in the present review throws light on the progress and potential of omics platforms in the research of Allium crops. We also mentioned a few research areas in Allium crops that need to be explored using omics technologies to get more insight. Overall, alliums are an under-studied group of plants, and thus, there is tremendous scope and need for research in Allium species. creator: Kiran Khandagale creator: Ram Krishna creator: Praveen Roylawar creator: Avinash B. Ade creator: Ashwini Benke creator: Bharat Shinde creator: Major Singh creator: Suresh J. Gawande creator: Ashutosh Rai uri: https://doi.org/10.7717/peerj.9824 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Khandagale et al. title: Assessment of postoperative health functioning after knee arthroplasty in relation to pain catastrophizing: a 6-month follow-up cohort study link: https://peerj.com/articles/9903 last-modified: 2020-09-09 description: BackgroundKnee arthroplasty (KA) is a typically successful surgical procedure commonly performed to alleviate painin participants with end-stage knee osteoarthritis. Despite its beneficial effects, a significant proportion of individuals with KA continue experiencing persistent pain and functional limitations. The purpose of this study was to assess the postoperative outcomes after KA in relation to postoperative pain catastrophizing.MethodsParticipants were recruited at a domiciliary physiotherapy service, using a prospective, observational, hypothesis-generating cohort design. Participants were divided into two groups based on their Pain Catastrophizing Scale (PCS) total score (50th percentile), which resulted in high and low PCS groups. The primary outcome measure was the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC). In addition, quality of life, walking speed, physical performance, range of motion, and pain were measured. Outcome measures were collected at baseline (1 week postoperatively) and at follow-up (1, 3, and 6 months postoperatively).ResultsA total of 60 participants (21 total KA and 39 unicompartmental KA) were recruited. Individuals with a higher degree of pain catastrophizing showed significantly higher WOMAC total scores at every follow-up, indicating poorer health functioning (p < 0.01). Similarly, the high PCS group showed higher WOMAC pain, stiffness and disability subscale scores (p < 0.05), poorer quality of life (p < 0.01), and poorer physical performance (p < 0.05) at every follow-up. In addition, the high PCS group achieved a slower walking speed at baseline and at 3 months follow-up (p < 0.05), and a higher degree of pain at rest, on walking and on knee flexion at every follow-up (p < 0.01, p < 0.05 and p < 0.05, respectively) except for walking pain at 3 months follow-up. No significant differences were observed between groups in range of motion, except for active knee extension at the 6-month follow-up (p < 0.05). Effect size was large at 1 month follow-up in WOMAC total score (r = 0.578) and pain intensity during knee flexion (r = 0.529). Longitudinal analyses revealed different improvement trends during the rehabilitation process between groups, with a lack of significant improvements in the high PCS group between the 3- and 6-month follow-up in WOMAC total score, WOMAC pain, WOMAC disability, quality of life, physical performance, active knee extension and resting pain (p > 0.05).ConclusionThe results of the present study suggest that participants with high postoperative pain catastrophizing might have poorer outcomes during the rehabilitation process after KA. Future work should seek to clarify if this relationship is causal. creator: Marc Terradas-Monllor creator: Mirari Ochandorena-Acha creator: Julio Salinas-Chesa creator: Sergi Ramírez creator: Hector Beltran-Alacreu uri: https://doi.org/10.7717/peerj.9903 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Terradas-Monllor et al. title: Effect of nest age and habitat variables on nest survival in Marsh Harrier (Circus aeruginosus) in a fishpond habitat link: https://peerj.com/articles/9929 last-modified: 2020-09-09 description: BackgroundOne important anti‐predator strategy adopted by birds involves nest site selection and timing of breeding. Nest-site selection by marsh-nesting birds often involves nest concealment and water depth as key features influencing nest survival. Marsh Harrier (Circus aeruginosus) is an obligate ground nester, which sets it apart from other raptors. The aim of the present study was to identify for the first time possible temporal and habitat factors affecting nest survival in Marsh Harrier. Understanding features which affect nest survival are essential for assessing relevant conservation strategies.MethodsTo understand the relative contributions of different temporal and habitat variables to brood losses, it is useful to determine the daily survival rate (DSR). We examined 82 Marsh Harrier nests located on fishponds in eastern Poland, where predation is the main cause of nest loss. Six habitat variables were measured for each active nest. DSR was calculated using known-fate models with the RMark package.ResultsThe best-supported model predicted that DSR decreased with nest age and was positively affected by the water depth and the diameter of reed stems, but not by the height or density of vegetation at the nest site. The distances of nests to the fishpond dyke and to open water received no support in the models. The chances of nest survival were lower if a neighbouring nest had been depredated. This result suggests that the Marsh Harrier is more susceptible to mammalian than avian predation and confirms the high level of predator pressure in fishpond habitats. creator: Urszula Zaremba creator: Zbigniew Kasprzykowski creator: Artur Golawski uri: https://doi.org/10.7717/peerj.9929 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Zaremba et al. title: A descriptive study of random forest algorithm for predicting COVID-19 patients outcome link: https://peerj.com/articles/9945 last-modified: 2020-09-09 description: BackgroundThe outbreak of coronavirus disease 2019 (COVID-19) that occurred in Wuhan, China, has become a global public health threat. It is necessary to identify indicators that can be used as optimal predictors for clinical outcomes of COVID-19 patients.MethodsThe clinical information from 126 patients diagnosed with COVID-19 were collected from Wuhan Fourth Hospital. Specific clinical characteristics, laboratory findings, treatments and clinical outcomes were analyzed from patients hospitalized for treatment from 1 February to 15 March 2020, and subsequently died or were discharged. A random forest (RF) algorithm was used to predict the prognoses of COVID-19 patients and identify the optimal diagnostic predictors for patients’ clinical prognoses.ResultsSeven of the 126 patients were excluded for losing endpoints, 103 of the remaining 119 patients were discharged (alive) and 16 died in the hospital. A synthetic minority over-sampling technique (SMOTE) was used to correct the imbalanced distribution of clinical patients. Recursive feature elimination (RFE) was used to select the optimal subset for analysis. Eleven clinical parameters, Myo, CD8, age, LDH, LMR, CD45, Th/Ts, dyspnea, NLR, D-Dimer and CK were chosen with AUC approximately 0.9905. The RF algorithm was built to predict the prognoses of COVID-19 patients based on the best subset, and the area under the ROC curve (AUC) of the test data was 100%. Moreover, two optimal clinical risk predictors, lactate dehydrogenase (LDH) and Myoglobin (Myo), were selected based on the Gini index. The univariable logistic analysis revealed a substantial increase in the risk for in-hospital mortality when Myo was higher than 80 ng/ml (OR = 7.54, 95% CI [3.42–16.63]) and LDH was higher than 500 U/L (OR = 4.90, 95% CI [2.13–11.25]).ConclusionWe applied an RF algorithm to predict the mortality of COVID-19 patients with high accuracy and identified LDH higher than 500 U/L and Myo higher than 80 ng/ml to be potential risk factors for the prognoses of COVID-19 patients in the early stage of the disease. creator: Jie Wang creator: Heping Yu creator: Qingquan Hua creator: Shuili Jing creator: Zhifen Liu creator: Xiang Peng creator: Cheng’an Cao creator: Yongwen Luo uri: https://doi.org/10.7717/peerj.9945 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Wang et al. title: Correlation between obesity and clinicopathological characteristics in patients with papillary thyroid cancer: a study of 1579 cases: a retrospective study link: https://peerj.com/articles/9675 last-modified: 2020-09-08 description: ObjectiveTo explore the relationship between body mass index (BMI) and clinicopathological characteristics in patients with papillary thyroid carcinoma (PTC).MethodsThe clinical data of 1,579 patients with PTC, admitted to our hospital from May 2016 to March 2017, were retrospectively analyzed. According to the different BMI of patients, it can be divided into underweight recombination (BMI < 18.5 kg/m), normal body recombination (18.5 ≤ BMI < 24.0 kg/m2), overweight recombination (24.0 ≤ BMI < 28.0 kg/m2) and obesity group (BMI ≥ 28.0 kg/m2). The clinicopathological characteristics of PTC in patients with different BMIs group were compared.ResultsIn our study, the risk for extrathyroidal extension (ETE), advanced T stage (T III/IV), and advanced tumor-node-metastasis stage (TNM III/IV) in the overweight group were higher, with OR (odds ratio) = 1.99(1.41–2.81), OR = 2.01(1.43–2.84), OR = 2.94(1.42–6.07), respectively, relative to the normal weight group. The risk for ETE and T III/IV stage in the obese group were higher, with OR = 1.82(1.23–2.71) and OR = 1.82(1.23–2.70), respectively, relative to the normal weight group.ConclusionBMI is associated with the invasiveness of PTC. There is a higher risk for ETE and TNM III/IV stage among patients with PTC in the overweight group and for ETE among patients with PTC in the obese group. creator: Huijuan Wang creator: Pingping Wang creator: Yu Wu creator: Xiukun Hou creator: Zechun Peng creator: Weiwei Yang creator: Lizhao Guan creator: Linfei Hu creator: Jingtai Zhi creator: Ming Gao creator: Xiangqian Zheng uri: https://doi.org/10.7717/peerj.9675 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al. title: Advances and complications of regenerative medicine in diabetes therapy link: https://peerj.com/articles/9746 last-modified: 2020-09-08 description: The rapid development of technologies in regenerative medicine indicates clearly that their common application is not a matter of if, but of when. However, the regeneration of beta-cells for diabetes patients remains a complex challenge due to the plurality of related problems. Indeed, the generation of beta-cells masses expressing marker genes is only a first step, with maintaining permanent insulin secretion, their protection from the immune system and avoiding pathological modifications in the genome being the necessary next developments. The prospects of regenerative medicine in diabetes therapy were promoted by the emergence of promising results with embryonic stem cells (ESCs). Their pluripotency and proliferation in an undifferentiated state during culture have ensured the success of ESCs in regenerative medicine. The discovery of induced pluripotent stem cells (iPSCs) derived from the patients’ own mesenchymal cells has provided further hope for diabetes treatment. Nonetheless, the use of stem cells has significant limitations related to the pluripotent stage, such as the risk of development of teratomas. Thus, the direct conversion of mature cells into beta-cells could address this issue. Recent studies have shown the possibility of such transdifferentiation and have set trends for regeneration medicine, directed at minimizing genome modifications and invasive procedures. In this review, we will discuss the published results of beta-cell regeneration and the advantages and disadvantages illustrated by these experiments. creator: Olga Brovkina creator: Erdem Dashinimaev uri: https://doi.org/10.7717/peerj.9746 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Brovkina and Dashinimaev title: Cannonball jellyfish digestion: an insight into the lipolytic enzymes of the digestive system link: https://peerj.com/articles/9794 last-modified: 2020-09-08 description: The digestive system and metabolism of the cannonball jellyfish Stomolophus sp. 2 are not well-known. The digestion study was critical to explain its ecology and bloom success. Different enzymes are involved in food digestion, which hydrolyze carbohydrates, proteins, and lipids. This study detected lipolytic activity in enzymatic extracts from gastric pouches of Stomolophus sp. 2 collected in the summer of 2013 at Bahía de Kino, Sonora, México (28°47′47″N 111°57′25″W). Lipase/esterase activity showed optimal pH at 11.0 and 50–60 °C with a half-life (t1/2) of 33 min at 55 °C, whereas halotolerance of this activity was recorded from 0-4 M NaCl. Metal ions Ca2+ and Mn2+ did not affect the activity, but Mg2+ decreased it 14.2% ± 3.15, while chelating agents as ethylenediaminetetraacetic acid reduced the activity 8.55% ± 2.13. Inhibition of lipase/esterase activity with tetrahydrolipstatin and paraoxon-ethyl decreased the activity 18.2% ± 2.3, and 62.80% ± 0.74, respectively, whereas phenylmethanesulfonyl fluoride (a protease inhibitor) did not affect it. The enzyme displayed a higher specificity for short-chain triglycerides, but triolein, coconut oil, olive oil, and fish oil were hydrolyzed. For the first time, phospholipase activity from the gastric pouch of Stomolophus sp. 2 was detected using L-α-phosphatidylethanolamine from chicken egg yolk as a substrate. These results suggest that Stomolophus sp. 2 hydrolyze several kinds of lipids, and lipolytic enzymes are active at alkaline pH under different saline conditions, which may be essential to digest different preys. creator: Raul B. Martínez-Pérez creator: Jorge A. Rodríguez creator: Luis Alonso Leyva Soto creator: Pablo Gortáres-Moroyoqui creator: Lourdes M. Diaz-Tenorio uri: https://doi.org/10.7717/peerj.9794 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Martínez-Pérez et al. title: Resilience is inversely associated with self-harm behaviors among Chinese adolescents with childhood maltreatment link: https://peerj.com/articles/9800 last-modified: 2020-09-08 description: BackgroundAbundant studies have identified the association between childhood maltreatment and self-harm (SH), but little has been discussed with regard to the role of resilience in SH behaviors of adolescents who had experienced childhood maltreatment. In this study, we investigated if resilience, as well as its five dimensions, could present negative associations with presence, repetition, and severity of SH among maltreated and neglected adolescents in China.MethodsA cross-sectional survey including 2,084 maltreated teenagers aged from 10 to 17 years was conducted in southwest China Yunnan province. The Childhood Trauma Questionnaire (CTQ), The Resilience Scale for Chinese Adolescents (RSCA), and the Modified version of Adolescents Self-Harm Scale (MASHS) were adopted to measure childhood maltreatment experiences, psychological resilience, and SH behaviors of the respondents, respectively. Binary univariate and multivariate logistic regression models were employed to discuss the associations between resilience and occurrence, repetition, severity of SH.ResultsAmong the participants who met the criteria of CTQ, the prevalence rates of SH were 63.83%, 73.94%, 71.50%, 55.53%, and 58.21% for physical abuse (PA), emotional abuse (EA), sexual abuse (SA), physical neglect (PN), and emotional neglect (EN). Final regression model demonstrated that resilience was in general inversely associated with SH, repeated SH, and severe SH for all types of childhood maltreatment, with adjusted odds ratios (aORs) ranging from 0.29 (95% CI: 0.19-0.44) to 0.46 (95% CI: 0.26-0.81). Of the five dimensions of resilience, emotion regulation served as the strongest associated factor of SH among abused youths, regardless of maltreatment types. Besides, compared with those who had lower level of goal concentration and interpersonal assistance, subjects with higher resilience level reported significantly decreased risks of SH occurrence, SH repetition, and more severe SH, in adolescents who had experienced EA and PN.ConclusionsResilience showed inverse association with childhood maltreatment related SH in Chinese adolescents. These findings preliminarily indicated that interventions targeting on building up resilience, especially enhancing emotion regulation ability, improving goal concentration, and consolidating interpersonal assistance, could be effective in reducing SH risk, repetition, and severity in maltreated Chinese teenagers. creator: Xin Tian creator: Guangya Yang creator: Linling Jiang creator: Runxu Yang creator: Hailiang Ran creator: Fujia Xie creator: Xiufeng Xu creator: Jin Lu creator: Yuanyuan Xiao uri: https://doi.org/10.7717/peerj.9800 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Tian et al. title: A synthetic biosensor to detect peroxisomal acetyl-CoA concentration for compartmentalized metabolic engineering link: https://peerj.com/articles/9805 last-modified: 2020-09-08 description: BackgroundSub-cellular compartmentalization is used by cells to create favorable microenvironments for various metabolic reactions. These compartments concentrate enzymes, separate competing metabolic reactions, and isolate toxic intermediates. Such advantages have been recently harnessed by metabolic engineers to improve the production of various high-value chemicals via compartmentalized metabolic engineering. However, measuring sub-cellular concentrations of key metabolites represents a grand challenge for compartmentalized metabolic engineering.MethodsTo this end, we developed a synthetic biosensor to measure a key metabolite, acetyl-CoA, in a representative compartment of yeast, the peroxisome. This synthetic biosensor uses enzyme re-localization via PTS1 signal peptides to construct a metabolic pathway in the peroxisome which converts acetyl-CoA to polyhydroxybutyrate (PHB) via three enzymes. The PHB is then quantified by HPLC.ResultsThe biosensor demonstrated the difference in relative peroxisomal acetyl-CoA availability under various culture conditions and was also applied to screening a library of single knockout yeast mutants. The screening identified several mutants with drastically reduced peroxisomal acetyl-CoA and one with potentially increased levels. We expect our synthetic biosensors can be widely used to investigate sub-cellular metabolism and facilitate the “design-build-test” cycle of compartmentalized metabolic engineering. creator: Herbert M. Huttanus creator: Ryan S. Senger uri: https://doi.org/10.7717/peerj.9805 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Huttanus and Senger title: Identification of priority shorebird conservation areas in the Caribbean link: https://peerj.com/articles/9831 last-modified: 2020-09-08 description: Despite being geographically central to the Atlantic Americas Flyway for migratory birds, the Caribbean is often overlooked or underappreciated when addressing the conservation of North American shorebirds. To our knowledge, this is the first Caribbean-wide assessment of shorebird use in the region. We analyzed 211,013 shorebird species observations in the insular Caribbean from 2010–2019, representing 78,794 eBird checklists and cumulative total of 2.1 million shorebirds of 45 species. We conclude that priority areas for shorebird conservation include Humedal Sur de Pinar del Río (Humedal Sur de Los Palacios) in Cuba, and Monte Cristi in the Dominican Republic as they each likely support more than 20,000 shorebirds annually, and they host large abundances of geographic populations for particular taxa. Specifically, the former site hosts >10% of Short-billed Dowitchers (Limnodromus griseus griseus/hendersoni), and >1% of Black-bellied Plovers (Pluvialis squatarola cynosurae) and Wilson’s Plovers (Charadrius wilsonia wilsonia), while the latter site supports large numbers of Black-necked Stilts (Himantopus mexicanus). We also identified at least 15 additional sites that likely cross the 1% population threshold for one or more shorebird taxa. These sites may qualify for special international designations such as Important Bird and Biodiversity Areas or as part of the Western Hemisphere Shorebird Reserve Network; 11 of the 17 sites we identified do not hold either of these titles. Data on subspecific or geographic distributions of three species, Snowy Plover (C. nivosus), Black-necked Stilt, and Killdeer (C. vociferous), are insufficient to reveal if the sites with the highest abundances were mostly comprised of Caribbean populations or migrants, but the limited information suggests that they also likely exceed 1% thresholds on several islands. Based on our results, we recommend more extensive systematic surveys of shorebirds in the Caribbean, including research on turnover rates and movements between islands, as well as assimilation of shorebird survey data not yet included in the eBird portal. creator: Jessica R. Cañizares creator: J. Michael Reed uri: https://doi.org/10.7717/peerj.9831 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Cañizares and Reed title: A new basal ornithopod dinosaur from the Lower Cretaceous of China link: https://peerj.com/articles/9832 last-modified: 2020-09-08 description: A new basal ornithopod dinosaur, based on two nearly complete articulated skeletons, is reported from the Lujiatun Beds (Yixian Fm, Lower Cretaceous) of western Liaoning Province (China). Some of the diagnostic features of Changmiania liaoningensis nov. gen., nov. sp. are tentatively interpreted as adaptations to a fossorial behavior, including: fused premaxillae; nasal laterally expanded, overhanging the maxilla; shortened neck formed by only six cervical vertebrae; neural spines of the sacral vertebrae completely fused together, forming a craniocaudally-elongated continuous bar; fused scapulocoracoid with prominent scapular spine; and paired ilia symmetrically inclined dorsomedially, partially covering the sacrum in dorsal view. A phylogenetic analysis places Changmiania liaoningensis as the most basal ornithopod dinosaur described so far. It is tentatively hypothesized that both Changmiania liaoningensis specimens were suddenly entrapped in a collapsed underground burrow while they were resting, which would explain their perfect lifelike postures and the complete absence of weathering and scavenging traces. However, further behavioural inference remains problematic, because those specimens lack extensive sedimentological and taphonomic data, as it is also the case for most specimens collected in the Lujiatun Beds so far. creator: Yuqing Yang creator: Wenhao Wu creator: Paul-Emile Dieudonné creator: Pascal Godefroit uri: https://doi.org/10.7717/peerj.9832 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Yang et al. title: Cropland heterogeneity changes on the Northeast China Plain in the last three decades (1980s–2010s) link: https://peerj.com/articles/9835 last-modified: 2020-09-08 description: The Northeast China Plain is one of the major grain-producing areas of China because of its fertile black soil and large fields adapted for agricultural machinery. It has experienced some land-use changes, such as urbanization, deforestation, and wetland reclamation in recent decades. A comprehensive understanding of these changes in terms of the total cropping land and its heterogeneity during this period is important for policymakers. In this study, we used a series of cropland products at the 30-m resolution for the period 1980–2015. The heterogeneity for dominant cropland decreased slowly over the three decades, especially for the large pieces of cropland, showing a general trend of increased cropland homogeneity. The spatial patterns of the averaged heterogeneity index were nearly the same, varying from 0.5 to 0.6, and the most heterogeneous areas were mainly located in some separate counties. Cropland expansion occurred across most of Northeast China, while cropland shrinking occurred only in the northern and eastern sections of Northeast China and around the capital cities, in the flat areas. Also, changes in land use away from cropland mainly occurred in areas with low elevation (50–200 m) and a gentle slope (less than 1 degree). The predominant changes in cropland were gross gain and homogeneity, occurring across most of the area except capital cities and boundary areas. Possible reasons for the total cropland heterogeneity changes were urbanization, restoration of cropland to forest, and some government land-use policies. Moreover, this study evaluates the effectiveness of cropland policies influencing in Northeast China. creator: Xiaoxuan Liu creator: Le Yu creator: Qinghan Dong creator: Dailiang Peng creator: Wenbin Wu creator: Qiangyi Yu creator: Yuqi Cheng creator: Yidi Xu creator: Xiaomeng Huang creator: Zheng Zhou creator: Dong Wang creator: Lei Fang creator: Peng Gong uri: https://doi.org/10.7717/peerj.9835 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Liu et al. title: Reduced organizational skills in adults with ADHD are due to deficits in persistence, not in strategies link: https://peerj.com/articles/9844 last-modified: 2020-09-08 description: BackgroundAttention Deficit Hyperactivity Disorder (ADHD) is commonly associated with poor organizational skills, as per the definition of ADHD. However, the contribution of each of the following factors (and their interactions) to the aforementioned poor organization, while comparing individuals with and without ADHD, has not been analyzed in-depth: Work Organization; Communication Clarity; Punctuality; Goal-oriented behaviour; Assiduity; Workspace Organization; Strategies; and Attentiveness. The purpose is to examine the self-reported levels of organizational skills in adults with and without ADHD.MethodsSeven hundred seventy-four (n = 303 with a diagnosis of ADHD) adults from the community were recruited online. Participants completed a measure of organizational skills and a screening measure of ADHD.ResultsParticipants with a diagnosis of ADHD displayed lower scores than individuals without a diagnosis of ADHD on all organizational skills with the exception of using strategies to remain organized and learn new information. Higher levels of education were associated with higher levels of organizational skills. While there was no difference between males and females with ADHD, females without ADHD scored higher than males without ADHD.ConclusionThis study supports that individuals with ADHD can efficiently develop strategies, but may have difficulties using those strategies in a continuous manner. Suggestions to increase organizational skills in adults with ADHD are presented. creator: Guillaume Durand creator: Ioana-Smarandita Arbone creator: Monica Wharton uri: https://doi.org/10.7717/peerj.9844 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Durand et al. title: Identification of key modules and hub genes associated with lung function in idiopathic pulmonary fibrosis link: https://peerj.com/articles/9848 last-modified: 2020-09-08 description: BackgroundIdiopathic pulmonary fibrosis (IPF) is a chronic and progressive interstitial lung disease, characterized by a decline in lung function. To date, the pathophysiologic mechanisms associated with lung dysfunction remain unclear, and no effective therapy has been identified to improve lung function.MethodsIn the present study, we used weighted gene co-expression network analysis (WGCNA) to identify key modules and hub genes associated with lung function in IPF. Three datasets, containing clinical information, were downloaded from Gene Expression Omnibus. WGCNA was performed on the GSE32537 dataset. Differentially expressed gene s (DEGs) between IPF patients and healthy controls were also identified to filter hub genes. The relationship between hub genes and lung function was then validated using the GSE47460 and GSE24206 datasets.ResultsThe red module, containing 267 genes, was positively correlated with the St. George’s Respiratory Questionnaire score (r = 0.37, p < 0.001) and negatively correlated with the percent predicted forced vital capacity (FVC% predicted) (r =  − 0.46, p < 0.001) and the percent predicted diffusion capacity of the lung for carbon monoxide (Dlco% predicted) (r =  − 0.42, p < 0.001). Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis suggested that the genes in the red module were primarily involved in inflammation and immune pathways. Based on Module Membership and Gene Significance, 32 candidate hub genes were selected in the red module to construct a protein-protein interaction network . Based on the identified DEGs and the degree of connectivity in the network, we identified three hub genes, including interleukin 6 (IL6), suppressor of cytokine signaling-3 (SOCS3), and serpin family E member 1 (SERPINE1). In the GSE47460 dataset, Spearman correlation coefficients between Dlco% predicted and expression levels of IL6, SERPINE1, SOCS3 were –0.32, –0.41, and –0.46, respectively. Spearman correlation coefficients between FVC% predicted and expression levels of IL6, SERPINE1, SOCS3 were –0.29, –0.33, and –0.27, respectively. In the GSE24206 dataset, all three hub genes were upregulated in patients with advanced IPF.ConclusionWe identified three hub genes that negatively correlated with the lung function of IPF patients. Our results provide insights into the pathogenesis underlying the progressive disruption of lung function, and the identified hub genes may serve as biomarkers and potential therapeutictargets for the treatment of IPF patients. creator: Yuechong Xia creator: Cheng Lei creator: Danhui Yang creator: Hong Luo uri: https://doi.org/10.7717/peerj.9848 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Xia et al. title: Monthly drought prediction based on ensemble models link: https://peerj.com/articles/9853 last-modified: 2020-09-08 description: Drought is a natural hazard, which is a result of a prolonged shortage of precipitation, high temperature and change in the weather pattern. Drought harms society, the economy and the natural environment, but it is difficult to identify and characterize. Many areas of Pakistan have suffered severe droughts during the last three decades due to changes in the weather pattern. A drought analysis with the incorporation of climate information has not yet been undertaken in this study region. Here, we propose an ensemble approach for monthly drought prediction and to define and examine wet/dry events. Initially, the drought events were identified by the short term Standardized Precipitation Index (SPI-3). Drought is predicted based on three ensemble models i.e., Equal Ensemble Drought Prediction (EEDP), Weighted Ensemble Drought Prediction (WEDP) and the Conditional Ensemble Drought Prediction (CEDP) model. Besides, two weighting procedures are used for distributing weights in the WEDP model, such as Traditional Weighting (TW) and the Weighted Bootstrap Resampling (WBR) procedure. Four copula families (i.e., Frank, Clayton, Gumbel and Joe) are used to explain the dependency relation between climate indices and precipitation in the CEDP model. Among all four copula families, the Joe copula has been found suitable for most of the times. The CEDP model provides better results in terms of accuracy and uncertainty as compared to other ensemble models for all meteorological stations. The performance of the CEDP model indicates that the climate indices are correlated with a weather pattern of four meteorological stations. Moreover, the percentage occurrence of extreme drought events that have appeared in the Multan, Bahawalpur, Barkhan and Khanpur are 1.44%, 0.57%, 2.59% and 1.71%, respectively, whereas the percentage occurrence of extremely wet events are 2.3%, 1.72%, 0.86% and 2.86%, respectively. The understanding of drought pattern by including climate information can contribute to the knowledge of future agriculture and water resource management. creator: Muhammad Haroon Shaukat creator: Ijaz Hussain creator: Muhammad Faisal creator: Ahmad Al-Dousari creator: Muhammad Ismail creator: Alaa Mohamd Shoukry creator: Elsayed Elsherbini Elashkar creator: Showkat Gani uri: https://doi.org/10.7717/peerj.9853 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Shaukat et al. title: Usefulness of the cytokines expression of Th1/Th2/Th17 and urinary CD80 excretion in adult-onset minimal change disease link: https://peerj.com/articles/9854 last-modified: 2020-09-08 description: BackgroundMinimal change disease (MCD) is a common form of nephrotic syndrome in adults. However, the molecular mechanism underlying the pathogenesis of MCD remains incompletely understood. In this study, we aimed to investigate the role of the cytokines expression of Th1/Th2/Th17 and urinary CD80 excretion in adult-onset MCD patients.MethodsThe lymphocyte subsets, 34 cytokine levels of Th1/Th2/Th17, serum and urine concentrations of CD80, and expression of CD80 in glomeruli were analyzed in 28 cases (15 males and 13 females; average age: 34.1 years, age range: 18–56 years), including 10 patients with MCD in relapse, nine patients with MCD in remission and nine healthy controls.ResultsThere was no significant difference of CD3+CD4+ cells proportion among patients with MCD in relapse, MCD in remission and healthy controls (P = 0.802). The cytokine levels of GM-CSF and tumor necrosis factor (TNF)-related activation-induced cytokine (TRANCE) in patients with MCD in relapse increased 1.5 times higher than those in remission. An evident increase in the excretion of urinary CD80 was found in patients with relapsed MCD compared with those in remission (598.4 ± 115.8 vs 81.78 ± 7.04 ng/g creatinine, P < 0.001) and healthy controls (598.4 ± 115.8 vs 67.44 ±  8.94  ng/g creatinine, P < 0.001). CD80 expression was observed in podocyte of MCD patient in relapse by immunofluorescence technique.ConclusionsThe cytokines GM-CSF and TRANCE are increased and the urinary CD80 levels are elevated in adult-onset MCD patients in relapse, indicating a disorder of Th1/Th2/Th17 balance and that the elevated excretion of CD80 may underlie the pathogenesis and development of adult-onset MCD. creator: Ping Chen creator: Yan Chen creator: Maoqing Jiang creator: Yijun Mo creator: Huanhuan Ying creator: Xun Tang creator: Jun Zhang uri: https://doi.org/10.7717/peerj.9854 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Chen et al. title: Hypercarnivorous teeth and healed injuries to Canis chihliensis from Early Pleistocene Nihewan beds, China, support social hunting for ancestral wolves link: https://peerj.com/articles/9858 last-modified: 2020-09-08 description: Collaborative hunting by complex social groups is a hallmark of large dogs (Mammalia: Carnivora: Canidae), whose teeth also tend to be hypercarnivorous, specialized toward increased cutting edges for meat consumption and robust p4-m1 complex for cracking bone. The deep history of canid pack hunting is, however, obscure because behavioral evidence is rarely preserved in fossils. Dated to the Early Pleistocene (>1.2 Ma), Canis chihliensis from the Nihewan Basin of northern China is one of the earliest canines to feature a large body size and hypercarnivorous dentition. We present the first known record of dental infection in C. chihliensis, likely inflicted by processing hard food, such as bone. Another individual also suffered a displaced fracture of its tibia and, despite such an incapacitating injury, survived the trauma to heal. The long period required for healing the compound fracture is consistent with social hunting and family care (food-sharing) although alternative explanations exist. Comparison with abundant paleopathological records of the putatively pack-hunting Late Pleistocene dire wolf, Canis dirus, at the Rancho La Brea asphalt seeps in southern California, U.S.A., suggests similarity in feeding behavior and sociality between Chinese and American Canis across space and time. Pack hunting in Canis may be traced back to the Early Pleistocene, well before the appearance of modern wolves, but additional evidence is needed for confirmation. creator: Haowen Tong creator: Xi Chen creator: Bei Zhang creator: Bruce Rothschild creator: Stuart White creator: Mairin Balisi creator: Xiaoming Wang uri: https://doi.org/10.7717/peerj.9858 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Tong et al. title: Mechanisms of diversity maintenance in dung beetle assemblages in a heterogeneous tropical landscape link: https://peerj.com/articles/9860 last-modified: 2020-09-08 description: Background Anthropized landscapes play a crucial role in biodiversity conservation, as they encompass about 90% of the remaining tropical forest. Effective conservation strategies require a deep understanding of how anthropic disturbances determine diversity patterns across these landscapes. Here, we evaluated how attributes and assembly mechanisms of dung beetle communities vary across the Selva El Ocote Biosphere Reserve (REBISO) landscape.MethodsCommunity attributes (species diversity, abundance, and biomass) were assessed at the landscape scale, using spatial windows and vegetation classes. Windows were categorized as intact, variegated, or fragmented based on their percent cover of tropical forest. The vegetation classes analyzed were tropical forest, second-growth forest, and pastures.ResultsWe collected 15,457 individuals and 55 species. Variegated windows, tropical forests, and second-growth forests showed the highest diversity values, while the lowest values were found in intact windows and pastures. Landscape fragmentation was positively and strongly related to dung beetle diversity and negatively related to their abundance; biomass was positively associated with forest cover. Beta diversity was the primary driver of the high dung beetle diversity in the landscape analyzed.DiscussionThe landscape heterogeneity and its biodiversity-friendly matrix facilitate the complementarity of dung beetle assemblages in the Selva El Ocote Biosphere Reserve. Random processes govern beta diversity patterns in intact and variegated windows. Therefore, vegetation cover in the region is sufficient to maintain a continuous flow of dung beetles between forested landscape segments. However, intense anthropic disturbances acted as deterministic environmental filters in fragmented windows and pastures sites, leading to biotic homogenization processes. Our results suggest that increasing habitat variegation in highly fragmented sites is an effective strategy to prevent or buffer homogenization processes in the REBISO landscape. creator: Jose D. Rivera creator: Benigno Gómez creator: Darío A. Navarrete-Gutiérrez creator: Lorena Ruíz-Montoya creator: Leonardo Delgado creator: Mario E. Favila uri: https://doi.org/10.7717/peerj.9860 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Rivera et al. title: Climatic influence on the growth pattern of Panthasaurus maleriensis from the Late Triassic of India deduced from paleohistology link: https://peerj.com/articles/9868 last-modified: 2020-09-08 description: Metoposaurids are representatives of the extinct amphibian clade Temnospondyli, found on almost every continent exclusively in the Late Triassic deposits. Osteohistologically, it is one of the best-known temnospondyl groups, analyzed with a wide spectrum of methods, such as morphology, morphometry, bone histology or computed modelling. The least known member of Metoposauridae is Panthasaurus maleriensis from the Pranhita-Godavari basin in Central India, being geographically the most southern record of this family. For the first time the bone histology of this taxon was studied with a focus on the intraspecific variability of the histological framework and the relationship between the observed growth pattern and climatic and/or environmental conditions. The studied material includes thin-sections of five long bones, a rib, an ilium and an intercentrum belonging most likely to eight individuals ranging from different ontogenetic stages. All bones have a large medullary region with progressively increasing remodeling, surrounded by a lamellar-zonal tissue type. The primary cortex consists of parallel-fibered matrix showing various degrees of organization, less organized collagen fibers in the zones and higher organized in the annuli. Growth marks occur in the form of alternating zones and annuli in every bone except the ilium and the intercentrum. The vascularity becomes less dense towards the outermost cortex in all sampled limb bones. Towards the outermost cortex the zone thickness is decreasing, in contrast to the avascular annuli, that become thicker or are of the same thickness. The growth pattern of P. maleriensis is uniform and represents changes in ontogenetic development. Multiple resting lines are prominent in the outer annuli of the limb bones and the rib and they presumably indicate climatic and environmental influence on the growth pattern. Therefore, a prolonged phase of slowed-down growth occurred during the unfavorable phase, but a complete cessation of growth indicated by Lines of Arrested Growth (LAGs) is not recorded in the studied samples. Based on the histological framework we conclude that the climate had an impact on the growth pattern. As we do not see any LAGs in the Indian metoposaurid, we assume that the local climate was relatively mild in India during the Late Triassic. A similar prolonged phase of slowed down growth without the occurrence of LAGs was observed in Metoposaurus krasiejowensis from the Late Triassic of Krasiejów (Poland). This is in contrast to Moroccan metoposaurid Dutuitosaurus ouazzoui from the Late Triassic of Argana Basin, where LAGs are regularly deposited throughout ontogeny indicating most likely harsher climatic conditions. creator: Elżbieta M. Teschner creator: Sanjukta Chakravorti creator: Dhurjati P. Sengupta creator: Dorota Konietzko-Meier uri: https://doi.org/10.7717/peerj.9868 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Teschner et al. title: Development of limb bone laminarity in the homing pigeon (Columba livia) link: https://peerj.com/articles/9878 last-modified: 2020-09-08 description: BackgroundBirds show adaptations in limb bone shape that are associated with resisting locomotor loads. Whether comparable adaptations occur in the microstructure of avian cortical bone is less clear. One proposed microstructural adaptation is laminar bone in which the proportion of circumferentially-oriented vascular canals (i.e., laminarity) is large. Previous work on adult birds shows elevated laminarity in specific limb elements of some taxa, presumably to resist torsion-induced shear strain during locomotion. However, more recent analyses using improved measurements in adult birds and bats reveal lower laminarity than expected in bones associated with torsional loading. Even so, there may still be support for the resistance hypothesis if laminarity increases with growth and locomotor maturation.MethodsHere, we tested that hypothesis using a growth series of 17 homing pigeons (15–563 g). Torsional rigidity and laminarity of limb bones were measured from histological sections sampled from midshaft. Ontogenetic trends in laminarity were assessed using principal component analysis to reduce dimensionality followed by beta regression with a logit link function.ResultsWe found that torsional rigidity of limb bones increases disproportionately with growth, consistent with rapid structural compensation associated with locomotor maturation. However, laminarity decreases with maturity, weakening the hypothesis that high laminarity is a flight adaptation at least in the pigeon. Instead, the histological results suggest that low laminarity, specifically the relative proportion of longitudinal canals aligned with peak principal strains, may better reflect the loading history of a bone. creator: Rylee S. McGuire creator: Raffi Ourfalian creator: Kelly Ezell creator: Andrew H. Lee uri: https://doi.org/10.7717/peerj.9878 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 McGuire et al. title: Spatial ecology of little egret (Egretta garzetta) in Hong Kong uncovers preference for commercial fishponds link: https://peerj.com/articles/9893 last-modified: 2020-09-08 description: Many natural wetlands have been converted to human-influenced wetlands. In some instances, human-influenced wetlands could provide complementary habitats for waterbirds, compensating for the loss of natural wetlands. Inner Deep Bay in Hong Kong is composed of both natural and human-influenced wetlands and is under immense development pressure. From an ecology perspective, we need to understand if different wetland types play the same ecological role. To achieve this, we tracked nine little egrets (Egretta garzetta) using GPS loggers for 14 months to study their spatial ecology, home range, movement and habitat use. We found that over 88% of the home range of all individuals comprised of wetlands (commercial fishponds, mangrove, gei wai, channel, and intertidal mudflat). Among these wetland types, nearly all (seven of nine) individuals preferred commercial fishponds over other habitats in all seasons. Little egrets exhibited seasonal movement and habitat use among seasons, with largest home range, greatest movement, and most frequent visits to commercial fishponds in winter compared to spring and autumn. Our results highlight the significant role of commercial fishponds, providing a feeding ground for little egrets. However, other wetland types cannot be ignored, as they were also used considerably. These findings underscore the importance of maintaining a diversity of wetland types as alternative foraging and breeding habitats. creator: Chun-chiu Pang creator: Yik-Hei Sung creator: Yun-tak Chung creator: Hak-king Ying creator: Helen Hoi Ning Fong creator: Yat-tung Yu uri: https://doi.org/10.7717/peerj.9893 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Pang et al. title: Combating SARS-CoV-2: leveraging microbicidal experiences with other emerging/re-emerging viruses link: https://peerj.com/articles/9914 last-modified: 2020-09-08 description: The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Wuhan City, China, late in December 2019 is an example of an emerging zoonotic virus that threatens public health and international travel and commerce. When such a virus emerges, there is often insufficient specific information available on mechanisms of virus dissemination from animal-to-human or from person-to-person, on the level or route of infection transmissibility or of viral release in body secretions/excretions, and on the survival of virus in aerosols or on surfaces. The effectiveness of available virucidal agents and hygiene practices as interventions for disrupting the spread of infection and the associated diseases may not be clear for the emerging virus. In the present review, we suggest that approaches for infection prevention and control (IPAC) for SARS-CoV-2 and future emerging/re-emerging viruses can be invoked based on pre-existing data on microbicidal and hygiene effectiveness for related and unrelated enveloped viruses. creator: M. Khalid Ijaz creator: Syed A. Sattar creator: Joseph R. Rubino creator: Raymond W. Nims creator: Charles P. Gerba uri: https://doi.org/10.7717/peerj.9914 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Ijaz et al. title: Overexpression of KIAA1199 is an independent prognostic marker in laryngeal squamous cell carcinoma link: https://peerj.com/articles/9637 last-modified: 2020-09-07 description: BackgroundKIAA1199 is a recently identified novel gene that is upregulated in various human cancers with poor survival, but its role and the underlying mechanisms in laryngeal squamous cell carcinoma (LSCC) remain unknown. Here, we collected tissues from 105 cases of LSCC to investigate the relationships between KIAA1199 protein expression and clinical factors.MethodsWestern blotting and real-time quantitative PCR (RT-PCR) were used for detect the protein and mRNA expression of KIAA1199 in LSCC tissue. Immunohistochemistry (IHC) staining was used to detect the expression of KIAA1199. Patient clinical information, for instance sex, age, pathological differentiation, clinical region, T stage, N stage, clinical stage, operation type, neck lymph dissection, smoking status, and drinking status were recorded. Kaplan–Meier survival analysis and Cox analysis were applied to identify the relationship between KIAA1199 and LSCC.ResultsWestern blotting results showed KIAA1199 protein was significantly higher in tumor tissues vs. adjacent non-cancerous tissues (0.9385 ± 0.1363 vs. 1.838 ± 0.3209, P = 0.04). The KIAA1199 mRNA expression was considerably higher in tumor tissues (P < 0.001) than in adjacent non-cancerous tissues by RT-PCR. IHC results showed up-regulated KIAA1199 expression was related with some severe clinicopathological parameters: pathologic differentiation (P = 0.002), T stage (P < 0.001), N stage (P < 0.001), clinical stage (P < 0.001), survival time (P = 0.008) and survival status (P < 0.001). Kaplan–Meier survival analysis showed that patients with high KIAA1199 protein expression had poor overall survival (OS) (P < 0.05). Cox analysis suggested that the KIAA1199 protein expression constituted an independent prognostic marker for LSCC patients (P < 0.001).ConclusionOur findings revealed that KIAA1199 protein expression may be used to predict LSCC patient outcome. creator: Meixiang Huang creator: Feifei Liao creator: Yexun Song creator: Gang Zuo creator: Guolin Tan creator: Ling Chu creator: Tiansheng Wang uri: https://doi.org/10.7717/peerj.9637 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Huang et al. title: Characterization of the transcriptional response of Candida parapsilosis to the antifungal peptide MAF-1A link: https://peerj.com/articles/9767 last-modified: 2020-09-07 description: Candida parapsilosis is a major fungal pathogen that leads to sepsis. New and more effective antifungal agents are required due to the emergence of resistant fungal strains. MAF-1A is a cationic antifungal peptide isolated from Musca domestica that is effective against a variety of Candida species. However, the mechanism(s) of its antifungal activity remains undefined. Here, we used RNA-seq to identify differentially expressed genes (DEGs) in Candida parapsilosis following MAF-1A exposure. The early (6 h) response included 1,122 upregulated and 1,065 downregulated genes. Late (18 h) responses were associated with the increased expression of 101 genes and the decreased expression of 151 genes. Upon MAF-1A treatment for 18 h, 42 genes were upregulated and 25 genes were downregulated. KEGG enrichment showed that the DEGs in response to MAF-1A were mainly involved in amino acid synthesis and metabolism, oxidative phosphorylation, sterol synthesis, and apoptosis. These results indicate that MAF-1A exerts antifungal activity through interference with Candida parapsilosis cell membrane integrity and organelle function. This provides new insight into the interaction between Candida parapsilosis and this antimicrobial peptide and serves as a reference for future Candida parapsilosis therapies. creator: Rong Cheng creator: Wei Li creator: Klarke M. Sample creator: Qiang Xu creator: Lin Liu creator: Fuxun Yu creator: Yingjie Nie creator: Xiangyan Zhang creator: Zhenhua Luo uri: https://doi.org/10.7717/peerj.9767 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Cheng et al. title: A pilot feasibility randomized controlled trial on combining mind-body physical exercise, cognitive training, and nurse-led risk factor modification to reduce cognitive decline among older adults with mild cognitive impairment in primary care link: https://peerj.com/articles/9845 last-modified: 2020-09-07 description: ObjectivesTo examine the feasibility and preliminary effectiveness of (1) combining cognitive training, mind-body physical exercise, and nurse-led risk factor modification (CPR), (2) nurse-led risk factor modification (RFM), and (3) health advice (HA) on reducing cognitive decline among older adults with mild cognitive impairment (MCI).MethodsIt was a 3-arm open-labeled pilot randomized controlled trial in the primary care setting in Hong Kong. Nineteen older adults with MCI were randomized to either CPR (n = 6), RFM (n = 7), or HA (n = 6) for 6 months. The primary outcome was the feasibility of the study. Secondary outcomes included the Alzheimer’s Disease Assessment Scale-Cognitive Subscale (ADAS-Cog), the Montreal Cognitive Assessment Hong Kong version (HK-MoCA), the Clinical Dementia Rating (CDR), the Disability Assessment for Dementia (DAD), quality of life, depression, anxiety, physical activity, health service utilization, and diet.ResultsNineteen out the 98 potential patients were recruited, with a recruitment rate of 19% (95% CI [12–29]%, P = 0.243). The adherence rate of risk factor modification was 89% (95% CI [65–98]%, P = 0.139) for CPR group and 86% (95% CI [63–96]%, P = 0.182) for RFM group. In the CPR group, 53% (95% CI [36–70]%, P = 0.038) of the Tai Chi exercise sessions and 54% (95% CI [37–71]%, P = 0.051) of cognitive sessions were completed. The overall dropout rate was 11% (95% CI [2–34]%, P = 0.456). Significant within group changes were observed in HK-MoCA in RFM (4.50 ± 2.59, P = 0.008), cost of health service utilization in CPR (−4000, quartiles: −6800 to −200, P = 0.043), fish and seafood in HA (−1.10 ± 1.02, P = 0.047), and sugar in HA (2.69 ± 1.80, P = 0.015). Group × time interactions were noted on HK-MoCA favoring the RFM group (P = 0.000), DAD score favoring CPR group (P = 0.027), GAS-20 favoring CPR group (P = 0.026), number of servings of fish and seafood (P = 0.004), and sugar (P < 0.001) ate per day.ConclusionsIn this pilot study, RFM and the multi-domain approach CPR were feasible and had preliminary beneficial effects in older adults with MCI in primary care setting in Hong Kong.Trial registrationChinese Clinical Trial Registry (ChiCTR1800015324). creator: Zijun Xu creator: Dexing Zhang creator: Allen T.C. Lee creator: Regina W.S. Sit creator: Carmen Wong creator: Eric K.P. Lee creator: Benjamin H.K. Yip creator: Jennifer Y.S. Tiu creator: Linda C.W. Lam creator: Samuel Y.S. Wong uri: https://doi.org/10.7717/peerj.9845 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Xu et al. title: Adaptations to cursoriality and digit reduction in the forelimb of the African wild dog (Lycaon pictus) link: https://peerj.com/articles/9866 last-modified: 2020-09-07 description: BackgroundThe African wild dog (Lycaon pictus), an endangered canid native to southern and eastern Africa, is distinct among canids in being described as entirely tetradactyl and in its nomadic lifestyle and use of exhaustive predation to capture its prey instead of speed, strength, or stealth. These behavioral and morphological traits suggest a potentially unique set of adaptations.MethodsHere, we dissected the forelimbs of an adult male L. pictus specimen and performed detailed descriptions and quantitative analyses of the musculoskeletal anatomy.ResultsStatistical comparisons of muscle masses and volumes revealed that L. pictus has relatively smaller wrist rotators (mm. pronator teres, pronator quadratus, supinator) than any other included carnivoran taxon, suggesting adaptive pressures for antebrachial stability over rotatory movement in the carpus of L. pictus. While a complete digit I is absent in L. pictus, a vestigial first metacarpal was discovered, resulting in changes to insertions of mm. extensor digiti I et II, abductor (et opponens) digiti I and flexor digiti I brevis. Mm. anconeus, brachialis and flexor carpi ulnaris caput ulnare all have more extensive origins in L. pictus than other canids suggesting an emphasis on posture and elbow stability. M. triceps brachii caput laterale has a larger origin in L. pictus and m. triceps brachii caput longum has an additional accessory head. Electromyographic studies have shown this muscle is active during the stance phase of trotting and galloping and is important for storing elastic energy during locomotion. We interpret these differences in size and attachments of muscles in L. pictus as adaptations for long distance running in this highly cursorial species, likely important for exhaustive predation. Absence of a full digit I in L. pictus may increase speed and stride length; however, the retention of a vestigial digit permits the attachment of reduced pollical muscles which may provide additional stability and proprioception to the carpus. creator: Heather F. Smith creator: Brent Adrian creator: Rahul Koshy creator: Ryan Alwiel creator: Aryeh Grossman uri: https://doi.org/10.7717/peerj.9866 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Smith et al. title: Demographic and genetic characterization of harvested Corbicula fluminea populations link: https://peerj.com/articles/9657 last-modified: 2020-09-04 description: The freshwater clam Corbicula fluminea s.l. is an edible freshwater bivalve of economic value in Asia. The species has been particularly well studied in the invaded range. However, there is a lack of knowledge in its native range where it supports an increasing commercial harvest pressure. Among Asiatic countries, China accounts for 70% of known commercial harvest and aquaculture production. We aim to characterize here wild C. fluminea s.l populations exposed to commercial harvest pressure in Poyang Lake Basin. We found higher biomass, density and genetic diversity in lake populations compared to peripheral populations (i.e., lake tributaries). Given that lake habitats support more intense harvest pressure than peripheral habitats, we suggest that demographic and genetic differentiation among subpopulations may be influenced in some degree by different harvest pressure. In this regard, additional demographic and/or genetic changes related to increasing harvest pressure may place population at a higher risk of extirpation. Altogether, these results are especially relevant for maintaining populations at or above viable levels and must be considered in order to ensure the sustainability of the resource. creator: Weikai Wang creator: Xiongjun Liu creator: Noé Ferreira-Rodríguez creator: Weiwei Sun creator: Yanli Wu creator: Shan Ouyang creator: Chunhua Zhou creator: Xiaoping Wu uri: https://doi.org/10.7717/peerj.9657 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al. title: Five new pseudocryptic land planarian species of Cratera (Platyhelminthes: Tricladida) unveiled through integrative taxonomy link: https://peerj.com/articles/9726 last-modified: 2020-09-04 description: Background Cratera is a genus of land planarians endemic to the Brazilian Atlantic forest. The species of this genus are distinguished from each other by a series of external and internal characters, nonetheless they represent a challenging taxonomic issue due to the extreme alikeness of the species analysed in the present work. To resolve these difficulties, we have performed morphological analyses and used three nuclear markers (ribosomal 18S and 28S, Elongation Factor, a new anonymous marker named Tnuc813) and two mitochondrial fragments (Cytochrome c oxidase subunit I gene, and a fragment encompasing NADH deshydrogenase subunit 4 gene, trnF and the beginning of the Cytochrome c oxidase I gene) in an integrative taxonomic study.MethodsTo unveil cryptic species, we applied a molecular species delimitation approach based on molecular discovery methods, followed by a validation method. The putative species so delimited were then validated on the basis of diagnostic morphological features.ResultsWe discovered and described four new species, namely Cratera assu, C. tui, C. boja, and C. imbiri. A fifth new species, C. paraitinga was not highly supported by molecular evidence, but was described because its morphological attributes are unique. Our study documents for the genus Cratera the presence of a number of highly similar species, a situation that is present also in other genera of land planarians. The high number of poorly differentiated and presumably recent speciation events might be explained by the recent geological history of the area. creator: Ana Paula Goulart Araujo creator: Fernando Carbayo creator: Marta Riutort creator: Marta Álvarez-Presas uri: https://doi.org/10.7717/peerj.9726 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Araujo et al. title: Zonula occludens and nasal epithelial barrier integrity in allergic rhinitis link: https://peerj.com/articles/9834 last-modified: 2020-09-04 description: Allergic rhinitis (AR) is a common disease affecting 400 million of the population worldwide. Nasal epithelial cells form a barrier against the invasion of environmental pathogens. These nasal epithelial cells are connected together by tight junction (TJ) proteins including zonula occludens-1 (ZO-1), ZO-2 and ZO-3. Impairment of ZO proteins are observed in AR patients whereby dysfunction of ZOs allows allergens to pass the nasal passage into the subepithelium causing AR development. In this review, we discuss ZO proteins and their impairment leading to AR, regulation of their expression by Th1 cytokines (i.e., IL-2, TNF-α and IFN-γ), Th2 cytokines (i.e., IL-4 and IL-13) and histone deacetylases (i.e., HDAC1 and HDAC2). These findings are pivotal for future development of targeted therapies by restoring ZO protein expression and improving nasal epithelial barrier integrity in AR patients. creator: Che Othman Siti Sarah creator: Norasnieda Md Shukri creator: Noor Suryani Mohd Ashari creator: Kah Keng Wong uri: https://doi.org/10.7717/peerj.9834 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Siti Sarah et al. title: Risk factors for disease-related deterioration following diagnostic bronchoalveolar lavage procedures in diffuse lung disease: a case-control study link: https://peerj.com/articles/9864 last-modified: 2020-09-04 description: BackgroundAlthough the risk factors for diagnostic bronchoalveolar lavage (BAL)-induced acute exacerbations in patients with idiopathic pulmonary fibrosis (IPF) have been previously reported, no study has assessed these in patients with non-IPF. We aimed to identify the risk factors for BAL-induced disease deterioration (BAL-DD) in all types of diffuse lung disease.MethodsPatients with diffuse lung disease who underwent BAL at our hospital from April 2012 to November 2017 were retrospectively analyzed. The patient information, laboratory data, radiological findings, and BAL fluid analysis results in patients who developed BAL-DDs were compared with those in patients who did not.ResultsBAL-DDs occurred in 14 (3.3%) of the 429 patients included the study. The BAL-DD group had a significantly poorer performance status, higher C-reactive protein level, lower partial pressure of oxygen in the arterial blood at rest, greater proportion of desaturation on exertion and cases having followed a progressive clinical course before BAL, and more extensive consolidation and ground-glass opacity on chest high-resolution computed tomography (HRCT) than the non-BAL-DD group. A high total cell concentration and an increased number of eosinophils in the BAL fluid were more frequently found in patients with BAL-DD than in those without.ConclusionsPatients with decreased physical activity level, increased level of inflammatory markers, low oxygenation status, and extensive lung involvements on chest HRCT and following a progressive clinical course before BAL may be warned of the BAL-DD risk. Elevated eosinophil counts in the BAL fluid could be associated with the triggering of BAL-DDs. creator: Yuko Usagawa creator: Kosaku Komiya creator: Mari Yamasue creator: Kazuhiko Hashinaga creator: Eri Mizukami creator: Kenji Umeki creator: Shin-ichi Nureki creator: Masaru Ando creator: Kazufumi Hiramatsu creator: Jun-ichi Kadota uri: https://doi.org/10.7717/peerj.9864 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Usagawa et al. title: Platelet factor 4 inhibits human hair follicle growth and promotes androgen receptor expression in human dermal papilla cells link: https://peerj.com/articles/9867 last-modified: 2020-09-04 description: Platelet-rich plasma (PRP) has been reported recently as a potential therapeutic approach for alopecia, such as androgenetic alopecia, but the exact mechanisms and effects of specific components of this recipe remain largely unknown. In this study, we identified that platelet factor 4 (PF4), a component of PRP, significantly suppressed human hair follicle growth and restrained the proliferation of human dermal papilla cells (hDPCs). Furthermore, our results showed that PF4 upregulated androgen receptor (AR) in human dermal papilla cells in vitro and via hair follicle organ culture. Among the hair growth-promoting and DP-signature genes investigated, PF4 decreased the expression of Wnt5a, Wnt10b, LEF1, HEY1 and IGF-1, and increased DKK1 expression, but did not affect BMP2 and BMP4 expression. Collectively, Our data demonstrate that PF4 suppresses human hair follicle growth possibly via upregulating androgen receptor signaling and modulating hair growth-associated genes, which provides thought-provoking insights into the application and optimization of PRP in treating hair loss. creator: Ke Sha creator: Mengting Chen creator: Fangfen Liu creator: San Xu creator: Ben Wang creator: Qinqin Peng creator: Yiya Zhang creator: Hongfu Xie creator: Ji Li creator: Zhili Deng uri: https://doi.org/10.7717/peerj.9867 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Sha et al. title: Tuber melanosporum shapes nirS-type denitrifying and ammonia-oxidizing bacterial communities in Carya illinoinensis ectomycorrhizosphere soils link: https://peerj.com/articles/9457 last-modified: 2020-09-03 description: BackgroundNirS-type denitrifying bacteria and ammonia-oxidizing bacteria (AOB) play a key role in the soil nitrogen cycle, which may affect the growth and development of underground truffles. We aimed to investigate nirS-type denitrifying bacterial and AOB community structures in the rhizosphere soils of Carya illinoinensis seedlings inoculated with the black truffle (Tuber melanosporum) during the early symbiotic stage.MethodsThe C. illinoinensis seedlings inoculated with or without T. melanosporum were cultivated in a greenhouse for six months. Next-generation sequencing (NGS) technology was used to analyze nirS-type denitrifying bacterial and AOB community structures in the rhizosphere soils of these seedlings. Additionally, the soil properties were determined.ResultsThe results indicated that the abundance and diversity of AOB were significantly reduced due to the inoculation of T. melanosporum, while these of nirS-type denitrifying bacteria increased significantly. Proteobacteria were the dominant bacterial groups, and Rhodanobacter, Pseudomonas, Nitrosospira and Nitrosomonas were the dominant classified bacterial genera in all the soil samples. Pseudomonas was the most abundant classified nirS-type denitrifying bacterial genus in ectomycorrhizosphere soils whose relative abundance could significantly increase after T. melanosporum inoculation. A large number of unclassified nirS-type denitrifying bacteria and AOB were observed. Moreover, T. melanosporum inoculation had little effect on the pH, total nitrogen (TN), nitrate-nitrogen (NO${}_{3}^{-}$3−-N) and ammonium-nitrogen (NH${}_{4}^{+}$4+-N) contents in ectomycorrhizosphere soils. Overall, our results showed that nirS-type denitrifying bacterial and AOB communities in C. illinoinensis rhizosphere soils were significantly affected by T. melanosporum on the initial stage of ectomycorrhizal symbiosis, without obvious variation of soil N contents. creator: Zongjing Kang creator: Jie Zou creator: Yue Huang creator: Xiaoping Zhang creator: Lei Ye creator: Bo Zhang creator: Xiaoping Zhang creator: Xiaolin Li uri: https://doi.org/10.7717/peerj.9457 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kang et al. title: Expression profile analysis to predict potential biomarkers for glaucoma: BMP1, DMD and GEM link: https://peerj.com/articles/9462 last-modified: 2020-09-03 description: PurposeGlaucoma is the second commonest cause of blindness. We assessed the gene expression profile of astrocytes in the optic nerve head to identify possible prognostic biomarkers for glaucoma.MethodA total of 20 patient and nine normal control subject samples were derived from the GSE9944 (six normal samples and 13 patient samples) and GSE2378 (three normal samples and seven patient samples) datasets, screened by microarray-tested optic nerve head tissues, were obtained from the Gene Expression Omnibus (GEO) database. We used a weighted gene coexpression network analysis (WGCNA) to identify coexpressed gene modules. We also performed a functional enrichment analysis and least absolute shrinkage and selection operator (LASSO) regression analysis. Genes expression was represented by boxplots, functional geneset enrichment analyses (GSEA) were used to profile the expression patterns of all the key genes. Then the key genes were validated by the external dataset.ResultsA total 8,606 genes and 19 human optic nerve head samples taken from glaucoma patients in the GSE9944 were compared with normal control samples to construct the co-expression gene modules. After selecting the most common clinical traits of glaucoma, their association with gene expression was established, which sorted two modules showing greatest correlations. One with the correlation coefficient is 0.56 (P = 0.01) and the other with the correlation coefficient is −0.56 (P = 0.01). Hub genes of these modules were identified using scatterplots of gene significance versus module membership. A functional enrichment analysis showed that the former module was mainly enriched in genes involved in cellular inflammation and injury, whereas the latter was mainly enriched in genes involved in tissue homeostasis and physiological processes. This suggests that genes in the green–yellow module may play critical roles in the onset and development of glaucoma. A LASSO regression analysis identified three hub genes: Recombinant Bone Morphogenetic Protein 1 gene (BMP1), Duchenne muscular dystrophy gene (DMD) and mitogens induced GTP-binding protein gene (GEM). The expression levels of the three genes in the glaucoma group were significantly lower than those in the normal group. GSEA further illuminated that BMP1, DMD and GEM participated in the occurrence and development of some important metabolic progresses. Using the GSE2378 dataset, we confirmed the high validity of the model, with an area under the receiver operator characteristic curve of 85%.ConclusionWe identified several key genes, including BMP1, DMD and GEM, that may be involved in the pathogenesis of glaucoma. Our results may help to determine the prognosis of glaucoma and/or to design gene- or molecule-targeted drugs. creator: Dao wei Zhang creator: Shenghai Zhang creator: Jihong Wu uri: https://doi.org/10.7717/peerj.9462 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhang et al. title: Seed germination and early seedling survival of the invasive species Prosopis juliflora (Fabaceae) depend on habitat and seed dispersal mode in the Caatinga dry forest link: https://peerj.com/articles/9607 last-modified: 2020-09-03 description: BackgroundBiological invasion is one of the main threats to tropical biodiversity and ecosystem functioning. Prosopis juliflora (Sw) DC. (Fabales: Fabaceae: Caesalpinioideae) was introduced in the Caatinga dry forest of Northeast Brazil at early 1940s and successfully spread across the region. As other invasive species, it may benefit from the soils and seed dispersal by livestock. Here we examine how seed dispersal ecology and soil conditions collectively affect seed germination, early seedling performance and consequently the P. juliflora invasive potential.MethodsSeed germination, early seedling survival, life expectancy and soil attributes were examined in 10 plots located across three habitats (flooding plain, alluvial terrace and plateau) into a human-modified landscape of the Caatinga dry forest (a total of 12,000 seeds). Seeds were exposed to four seed dispersal methods: deposition on the soil surface, burial in the soil, passed through cattle (Boss taurus) digestive tracts and mixed with cattle manure and passed through mule (Equus africanus asinus × Equus ferus caballus) digestive tracts and mixed with mule manure. Seeds and seedlings were monitored through a year and their performance examined with expectancy tables.ResultsSoils differed among habitats, particularly its nutrient availability, texture and water with finely-textured and more fertile soils in the flooding plain. Total seed germination was relatively low (14.5%), with the highest score among seeds buried in the flooding plain (47.4 ± 25.3%). Seed dispersal by cattle and mule also positively impacted seed germination. Early seedling survival rate of P. juliflora was dramatically reduced with few seedlings still alive elapsed a year. Survival rate was highest in the first 30 days and declined between 30 and 60 days with stabilization at 70 days after germination in all seed treatments and habitats. However, survival and life expectancy were higher in the flooding plain at 75 days and lower in the plateau. Prosopis juliflora seedling survival and life expectancy were higher in the case seeds were mixed with cattle manure.SynthesisProsopis juliflora seeds and seedlings are sensitive to water stress and habitat desiccation. Therefore, they benefit from the humid soils often present across human-disturbed flooding plains. This plant also benefits from seed deposition/dispersal by livestock in these landscapes, since cattle manure represents a nutrient-rich and humid substrate for both seeds and seedlings. The quality of the seed dispersal service varies among livestock species, but this key mutualism between exotic species is due to the arillate, hard-coated and palatable seeds. Prosopis juliflora traits allow this species to take multiple benefits from human presence and thus operating as a human commensal. creator: Clóvis Eduardo de Souza Nascimento creator: Carlos Alberto Domingues da Silva creator: Inara Roberta Leal creator: Wagner de Souza Tavares creator: José Eduardo Serrão creator: José Cola Zanuncio creator: Marcelo Tabarelli uri: https://doi.org/10.7717/peerj.9607 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Nascimento et al. title: Comparative masticatory myology in anteaters and its implications for interpreting morphological convergence in myrmecophagous placentals link: https://peerj.com/articles/9690 last-modified: 2020-09-03 description: BackgroundEcological adaptations of mammals are reflected in the morphological diversity of their feeding apparatus, which includes differences in tooth crown morphologies, variation in snout size, or changes in muscles of the feeding apparatus. The adaptability of their feeding apparatus allowed them to optimize resource exploitation in a wide range of habitats. The combination of computer-assisted X-ray microtomography (µ-CT) with contrast-enhancing staining protocols has bolstered the reconstruction of three-dimensional (3D) models of muscles. This new approach allows for accurate descriptions of muscular anatomy, as well as the quick measurement of muscle volumes and fiber orientation. Ant- and termite-eating (myrmecophagy) represents a case of extreme feeding specialization, which is usually accompanied by tooth reduction or complete tooth loss, snout elongation, acquisition of a long vermiform tongue, and loss of the zygomatic arch. Many of these traits evolved independently in distantly-related mammalian lineages. Previous reports on South American anteaters (Vermilingua) have shown major changes in the masticatory, intermandibular, and lingual muscular apparatus. These changes have been related to a functional shift in the role of upper and lower jaws in the evolutionary context of their complete loss of teeth and masticatory ability.MethodsWe used an iodine staining solution (I2KI) to perform contrast-enhanced µ-CT scanning on heads of the pygmy (Cyclopes didactylus), collared (Tamandua tetradactyla) and giant (Myrmecophaga tridactyla) anteaters. We reconstructed the musculature of the feeding apparatus of the three extant anteater genera using 3D reconstructions complemented with classical dissections of the specimens. We performed a description of the musculature of the feeding apparatus in the two morphologically divergent vermilinguan families (Myrmecophagidae and Cyclopedidae) and compared it to the association of morphological features found in other myrmecophagous placentals.ResultsWe found that pygmy anteaters (Cyclopes) present a relatively larger and architecturally complex temporal musculature than that of collared (Tamandua) and giant (Myrmecophaga) anteaters, but shows a reduced masseter musculature, including the loss of the deep masseter. The loss of this muscle concurs with the loss of the jugal bone in Cyclopedidae. We show that anteaters, pangolins, and aardvarks present distinct anatomies despite morphological and ecological convergences. creator: Sérgio Ferreira-Cardoso creator: Pierre-Henri Fabre creator: Benoit de Thoisy creator: Frédéric Delsuc creator: Lionel Hautier uri: https://doi.org/10.7717/peerj.9690 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ferreira-Cardoso et al. title: Two new species of Pseudopimelodus Bleeker, 1858 (Siluriformes: Pseudopimelodidae) from the Magdalena Basin, Colombia link: https://peerj.com/articles/9723 last-modified: 2020-09-03 description: The family Pseudopimelodidae is widely distributed in South America and includes 51 described species organized in seven genera. Only two of four species of the genus Pseudopimelodus have been recorded for the trans-Andean basins of Colombia, Pseudopimelodus bufonius and P. schultzi, whose similarity in external morphology make their identification difficult. We performed a phylogenetic analysis using a fragment of the Cytochrome C Oxidase subunit 1 gene (COI), and analyzed osteological and traditional morphometric characters to study Pseudopimelodus from the Colombian trans-Andean region. Results provided strong support for two clades phylogenetically related to Pseudopimelodus, that showed clear-cut molecular, osteological, and morphometric differences from previously described bumblebee catfishes. Based on these results, we describe two Pseudopimelodus species from the Magdalena-Cauca River Basin: P. magnus sp. nov. with 43–44 vertebrae, dorsal-fin spine with serrations on its anterior margin; lateral margin of transverse process of the fourth vertebra of the Weberian complex forming an acute angle in ventral view and P. atricaudus sp. nov. with 39 vertebrae, dorsal-fin spine smooth on its anterior margin and a dark, vertical band covering 3/4 of the caudal fin with base of rays and tip of caudal-fin lobes hyaline. creator: Ana M. Restrepo-Gómez creator: José D. Rangel-Medrano creator: Edna J. Márquez creator: Armando Ortega-Lara uri: https://doi.org/10.7717/peerj.9723 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Restrepo-Gómez et al. title: Comprehensive genome analysis of a pangolin-associated Paraburkholderia fungorum provides new insights into its secretion systems and virulence link: https://peerj.com/articles/9733 last-modified: 2020-09-03 description: BackgroundParaburkholderia fungorum (P. fungorum) is a Gram-negative environmental species that has been commonly used as a beneficial microorganism in agriculture as an agent for biocontrol and bioremediation. Its use in agriculture is controversial as many people believe that it could harm human health; however, there is no clear evidence to support.MethodologyThe pangolin P. fungorum (pangolin Pf) genome has a genomic size of approximately 7.7 Mbps with N50 of 69,666 bps. Our study showed that pangolin Pf is a Paraburkholderia fungorum supported by evidence from the core genome SNP-based phylogenetic analysis and the ANI analysis. Functional analysis has shown that the presence of a considerably large number of genes related to stress response, virulence, disease, and defence. Interestingly, we identified different types of secretion systems in the genome of pangolin Pf, which are highly specialized and responsible for a bacterium’s response to its environment and in physiological processes such as survival, adhesion, and adaptation. The pangolin Pf also shared some common virulence genes with the known pathogenic member of the Burkholderiales. These genes play important roles in adhesion, motility, and invasion.ConclusionThis study may provide better insights into the functions, secretion systems and virulence of this pangolin-associated bacterial strain. The addition of this genome sequence is also important for future comparative analysis and functional work of P. fungorum. creator: Ka Yun Tan creator: Avirup Dutta creator: Tze King Tan creator: Ranjeev Hari creator: Rofina Y. Othman creator: Siew Woh Choo uri: https://doi.org/10.7717/peerj.9733 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Tan et al. title: DATMA: Distributed AuTomatic Metagenomic Assembly and annotation framework link: https://peerj.com/articles/9762 last-modified: 2020-09-03 description: BackgroundA prime objective in metagenomics is to classify DNA sequence fragments into taxonomic units. It usually requires several stages: read’s quality control, de novo assembly, contig annotation, gene prediction, etc. These stages need very efficient programs because of the number of reads from the projects. Furthermore, the complexity of metagenomes requires efficient and automatic tools that orchestrate the different stages.MethodDATMA is a pipeline for fast metagenomic analysis that orchestrates the following: sequencing quality control, 16S rRNA-identification, reads binning, de novo assembly and evaluation, gene prediction, and taxonomic annotation. Its distributed computing model can use multiple computing resources to reduce the analysis time.ResultsWe used a controlled experiment to show DATMA functionality. Two pre-annotated metagenomes to compare its accuracy and speed against other metagenomic frameworks. Then, with DATMA we recovered a draft genome of a novel Anaerolineaceae from a biosolid metagenome.ConclusionsDATMA is a bioinformatics tool that automatically analyzes complex metagenomes. It is faster than similar tools and, in some cases, it can extract genomes that the other tools do not. DATMA is freely available at https://github.com/andvides/DATMA. creator: Andres Benavides creator: Friman Sanchez creator: Juan F. Alzate creator: Felipe Cabarcas uri: https://doi.org/10.7717/peerj.9762 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Benavides et al. title: Generalized Linear Models outperform commonly used canonical analysis in estimating spatial structure of presence/absence data link: https://peerj.com/articles/9777 last-modified: 2020-09-03 description: BackgroundEcological communities tend to be spatially structured due to environmental gradients and/or spatially contagious processes such as growth, dispersion and species interactions. Data transformation followed by usage of algorithms such as Redundancy Analysis (RDA) is a fairly common approach in studies searching for spatial structure in ecological communities, despite recent suggestions advocating the use of Generalized Linear Models (GLMs). Here, we compared the performance of GLMs and RDA in describing spatial structure in ecological community composition data. We simulated realistic presence/absence data typical of many β-diversity studies. For model selection we used standard methods commonly used in most studies involving RDA and GLMs.MethodsWe simulated communities with known spatial structure, based on three real spatial community presence/absence datasets (one terrestrial, one marine and one freshwater). We used spatial eigenvectors as explanatory variables. We varied the number of non-zero coefficients of the spatial variables, and the spatial scales with which these coefficients were associated and then compared the performance of GLMs and RDA frameworks to correctly retrieve the spatial patterns contained in the simulated communities. We used two different methods for model selection, Forward Selection (FW) for RDA and the Akaike Information Criterion (AIC) for GLMs. The performance of each method was assessed by scoring overall accuracy as the proportion of variables whose inclusion/exclusion status was correct, and by distinguishing which kind of error was observed for each method. We also assessed whether errors in variable selection could affect the interpretation of spatial structure.ResultsOverall GLM with AIC-based model selection (GLM/AIC) performed better than RDA/FW in selecting spatial explanatory variables, although under some simulations the methods performed similarly. In general, RDA/FW performed unpredictably, often retaining too many explanatory variables and selecting variables associated with incorrect spatial scales. The spatial scale of the pattern had a negligible effect on GLM/AIC performance but consistently affected RDA’s error rates under almost all scenarios.ConclusionWe encourage the use of GLM/AIC for studies searching for spatial drivers of species presence/absence patterns, since this framework outperformed RDA/FW in situations most likely to be found in natural communities. It is likely that such recommendations might extend to other types of explanatory variables. creator: Lélis A. Carlos-Júnior creator: Joel C. Creed creator: Rob Marrs creator: Rob J. Lewis creator: Timothy P. Moulton creator: Rafael Feijó-Lima creator: Matthew Spencer uri: https://doi.org/10.7717/peerj.9777 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Carlos-Júnior et al. title: Comparing the gastrointestinal barrier function between growth-retarded and normal yaks on the Qinghai-Tibetan Plateau link: https://peerj.com/articles/9851 last-modified: 2020-09-03 description: BackgroundYak (Bos grunniens) is an ancient bovine species on the Qinghai-Tibetan Plateau. Due to extremely harsh condition in the plateau, the growth retardation of yaks commonly exist, which can reduce the incomes of herdsman. The gastrointestinal barrier function plays a vital role in the absorption of nutrients and healthy growth. Functional deficiencies of the gastrointestinal barrier may be one of the contributors for yaks with growth retardation.MethodsTo this end, we compared the growth performance and gastrointestinal barrier function of growth-retarded (GRY) and normal yaks (GNY) based on average daily gain (ADG), serum parameters, tissue slice, real-time PCR, and western blotting, with eight yaks in each group.ResultsGRY exhibited lower (P < 0.05) average daily gain as compared to GNY. The diamine oxidase, D-lactic acid, and lipopolysaccharide concentrations in the serum of GRY were significantly higher (P < 0.05) than those of GNY. Compared to GNY, the papillae height in the rumen of GRY exhibited lower (P = 0.004). In jejunum, with the exception of higher villus height, width, and surface area in GNY, numerical difference (P = 0.61) was detected between two groups for crypt depth. Both in rumen and jejunum, the mRNA expression of interleukin-1beta in GRY was markedly higher (P < 0.05) than that in GNY, but an opposite trend was found in interleukin-10 expression. Moreover, GRY showed a higher (P < 0.05) tumor necrosis factor-alpha mRNA expression in the rumen. The claudin-1 (CLDN1), occludin (OCLN), and zonula occludens-1 (ZO1) expressions of GRY in rumen and jejunum were significantly down-regulated (P < 0.05) as compared to GNY. The correlation analysis identified that in rumen and jejunum, there was a positive correlation between interleukin-10 and CLDN1, OCLN, and ZO1 mRNA expressions, but the tumor necrosis factor-alpha was negatively correlated with CLDN1, OCLN, and ZO1. In the rumen, the ADG was positively correlated with papillae surface area, and a same relationship between ADG and CLDN1, OCLN, and ZO1 expressions was found.ConclusionThe results indicated that the ruminal and jejunal barrier functions of GRY are disrupted as compared to GNY. In addition, our study provides a potential solution for promoting the growth of GRY by enhancing the gastrointestinal barrier function. creator: Jian Ma creator: Ali Mujtaba Shah creator: Zhisheng Wang creator: Rui Hu creator: Huawei Zou creator: Xueying Wang creator: Guang Cao creator: Quanhui Peng creator: Bai Xue creator: Lizhi Wang creator: Suonan Zhao creator: Xiangying Kong uri: https://doi.org/10.7717/peerj.9851 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ma et al. title: Collaborative networks enable the rapid establishment of serological assays for SARS-CoV-2 during nationwide lockdown in New Zealand link: https://peerj.com/articles/9863 last-modified: 2020-09-03 description: BackgroundSerological assays that detect antibodies to SARS-CoV-2 are critical for determining past infection and investigating immune responses in the COVID-19 pandemic. We established ELISA-based immunoassays using locally produced antigens when New Zealand went into a nationwide lockdown and the supply chain of diagnostic reagents was a widely held domestic concern. The relationship between serum antibody binding measured by ELISA and neutralising capacity was investigated using a surrogate viral neutralisation test (sVNT).MethodsA pre-pandemic sera panel (n = 113), including respiratory infections with symptom overlap with COVID-19, was used to establish assay specificity. Sera from PCR‑confirmed SARS-CoV-2 patients (n = 21), and PCR-negative patients with respiratory symptoms suggestive of COVID-19 (n = 82) that presented to the two largest hospitals in Auckland during the lockdown period were included. A two-step IgG ELISA based on the receptor binding domain (RBD) and spike protein was adapted to determine seropositivity, and neutralising antibodies that block the RBD/hACE‑2 interaction were quantified by sVNT.ResultsThe calculated cut-off (>0.2) in the two-step ELISA maximised specificity by classifying all pre-pandemic samples as negative. Sera from all PCR-confirmed COVID-19 patients were classified as seropositive by ELISA ≥7 days after symptom onset. There was 100% concordance between the two-step ELISA and the sVNT with all 7+ day sera from PCR‑confirmed COVID-19 patients also classified as positive with respect to neutralising antibodies. Of the symptomatic PCR-negative cohort, one individual with notable travel history was classified as positive by two-step ELISA and sVNT, demonstrating the value of serology in detecting prior infection.ConclusionsThese serological assays were established and assessed at a time when human activity was severely restricted in New Zealand. This was achieved by generous sharing of reagents and technical expertise by the international scientific community, and highly collaborative efforts of scientists and clinicians across the country. The assays have immediate utility in supporting clinical diagnostics, understanding transmission in high-risk cohorts and underpinning longer‑term ‘exit’ strategies based on effective vaccines and therapeutics. creator: Reuben McGregor creator: Alana L. Whitcombe creator: Campbell R. Sheen creator: James M. Dickson creator: Catherine L. Day creator: Lauren H. Carlton creator: Prachi Sharma creator: J. Shaun Lott creator: Barbara Koch creator: Julie Bennett creator: Michael G. Baker creator: Stephen R. Ritchie creator: Shivani Fox-Lewis creator: Susan C. Morpeth creator: Susan L. Taylor creator: Sally A. Roberts creator: Rachel H. Webb creator: Nicole J. Moreland uri: https://doi.org/10.7717/peerj.9863 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 McGregor et al. title: Structural and functional microbial diversity of sandy soil under cropland and grassland link: https://peerj.com/articles/9501 last-modified: 2020-09-02 description: BackgroundLand use change significantly alters soil organic carbon content and the microbial community. Therefore, in the present study, the effect of changing cropland to grassland on structural and functional soil microbial diversity was evaluated. The specific aims were (i) to identify the most prominent members of the fungal communities and their relevant ecological guild groups; (ii) to assess changes in the diversity of ammonia-oxidizing archaea; (iii) to determine the relationships between microbial diversity and selected physical and chemical properties.MethodsWe investigated microbial diversity and activity indicators, bulk density and the water-holding capacity of sandy soil under both cropland and 25-year-old grassland (formerly cropland) in Trzebieszów, in the Podlasie Region, Poland. Microbial diversity was assessed by: the relative abundance of ammonia-oxidizing archaea, fungal community composition and functional diversity. Microbial activity was assessed by soil enzyme (dehydrogenase, β-glucosidase) and respiration tests.ResultsIt was shown that compared to cropland, grassland has a higher soil organic carbon content, microbial biomass, basal respiration, rate of enzyme activity, richness and diversity of the microbial community, water holding capacity and the structure of the fungal and ammonia-oxidizing archaea communities was also altered. The implications of these results for soil quality and soil health are also discussed. The results suggest that grassland can have a significant phytosanitary capacity with regard to ecosystem services, due to the prominent presence of beneficial and antagonistic microbes. Moreover, the results also suggest that grassland use may improve the status of soil organic carbon and nitrogen dynamics, thereby increasing the relative abundance of fungi and ammonia-oxidizing archaea. creator: Magdalena Frąc creator: Jerzy Lipiec creator: Bogusław Usowicz creator: Karolina Oszust creator: Małgorzata Brzezińska uri: https://doi.org/10.7717/peerj.9501 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Frąc et al. title: Postcranial elements of small mammals as indicators of locomotion and habitat link: https://peerj.com/articles/9634 last-modified: 2020-09-02 description: Many studies have shown a correlation between postcranial anatomy and locomotor behavior in mammals, but the postcrania of small mammals (<5 kg) is often considered to be uninformative of their mode of locomotion due to their more generalized overall anatomy. Such small body size was true of all mammals during the Mesozoic. Anatomical correlates of locomotor behavior are easier to determine in larger mammals, but useful information can be obtained from the smaller ones. Limb bone proportions (e.g., brachial index) can be useful locomotor indicators; but complete skeletons, or even complete long bones, are rare for Mesozoic mammals, although isolated articular surfaces are often preserved. Here we examine the correlation of the morphology of long bone joint anatomy (specifically articular surfaces) and locomotor behavior in extant small mammals and demonstrate that such anatomy may be useful for determining the locomotor mode of Mesozoic mammals, at least for the therian mammals. creator: Christine M. Janis creator: Alberto Martín-Serra uri: https://doi.org/10.7717/peerj.9634 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Janis and Martín-Serra title: Extreme dispersal or human-transport? The enigmatic case of an extralimital freshwater occurrence of a Southern elephant seal from Indiana link: https://peerj.com/articles/9665 last-modified: 2020-09-02 description: Elephant seals (Mirounga spp.) are the largest living pinnipeds, and the spatial scales of their ecology, with dives over 1 km in depth and foraging trips over 10,000 km long, are unrivalled by their near relatives. Here we report the discovery of an incomplete Holocene age Southern elephant seal (M. leonina) rostrum from Indiana, USA. The surviving material are two casts of the original specimen, which was collected in a construction excavation close to the Wabash River near Lafayette, Indiana. The original specimen was mostly destroyed for radiometric dating analyses in the 1970s, which resulted in an age of 1,260 ± 90 years before the present. The existence of sediments in the original specimen suggests some type of post depositional fluvial transportation. The prevalent evidence suggests that this male Southern elephant seal crossed the equator and the Gulf of Mexico, and then entered the Mississippi River system, stranding far upriver in Indiana or adjacent areas, similar to other reported examples of lost marine mammals in freshwater systems. Based on potential cut marks, we cannot exclude human-mediated transportation or scavenging by Indigenous peoples as a contributing factor of this occurrence. The material reported here represents by far the northernmost occurrence of a Southern elephant seal in the Northern Hemisphere ever recorded. The unusual occurrence of a top marine predator >1,000 km from the closest marine effluent as a potential extreme case of dispersal emphasizes how marine invasions of freshwater systems have happened frequently through historical (and likely geological) time. creator: Ana M. Valenzuela-Toro creator: Maria H. Zicos creator: Nicholas D. Pyenson uri: https://doi.org/10.7717/peerj.9665 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: title: Peritumoral immune infiltrates in primary tumours are not associated with the presence of axillary lymph node metastasis in breast cancer: a retrospective cohort study link: https://peerj.com/articles/9779 last-modified: 2020-09-02 description: BackgroundThe axillary lymph nodes (ALNs) in breast cancer patients are the body regions to where tumoral cells most often first disseminate. The tumour immune response is important for breast cancer patient outcome, and some studies have evaluated its involvement in ALN metastasis development. Most studies have focused on the intratumoral immune response, but very few have evaluated the peritumoral immune response. The aim of the present article is to evaluate the immune infiltrates of the peritumoral area and their association with the presence of ALN metastases.MethodsThe concentration of 11 immune markers in the peritumoral areas was studied in 149 patients diagnosed with invasive breast carcinoma of no special type (half of whom had ALN metastasis at diagnosis) using tissue microarrays, immunohistochemistry and digital image analysis procedures. The differences in the concentration of the immune response of peritumoral areas between patients diagnosed with and without metastasis in their ALNs were evaluated. A multivariate logistic regression model was developed to identify the clinical-pathological variables and the peritumoral immune markers independently associated with having or not having ALN metastases at diagnosis.ResultsNo statistically significant differences were found in the concentrations of the 11 immune markers between patients diagnosed with or without ALN metastases. Patients with metastases in their ALNs had a higher histological grade, more lymphovascular and perineural invasion and larger-diameter tumours. The multivariate analysis, after validation by bootstrap simulation, revealed that only tumour diameter (OR = 1.04; 95% CI [1.00–1.07]; p = 0.026), lymphovascular invasion (OR = 25.42; 95% CI [9.57–67.55]; p < 0.001) and histological grades 2 (OR = 3.84; 95% CI [1.11–13.28]; p = 0.033) and 3 (OR = 5.18; 95% CI [1.40–19.17]; p = 0.014) were associated with the presence of ALN metastases at diagnosis. This study is one of the first to study the association of the peritumoral immune response with ALN metastasis. We did not find any association of peritumoral immune infiltrates with the presence of ALN metastasis. Nevertheless, this does not rule out the possibility that other peritumoral immune populations are associated with ALN metastasis. This matter needs to be examined in greater depth, broadening the types of peritumoral immune cells studied, and including new peritumoral areas, such as the germinal centres of the peritumoral tertiary lymphoid structures found in extensively infiltrated neoplastic lesions. creator: Carlos López creator: Ramón Bosch-Príncep creator: Guifré Orero creator: Laia Fontoura Balagueró creator: Anna Korzynska creator: Marcial García-Rojo creator: Gloria Bueno creator: Maria del Milagro Fernández-Carrobles creator: Lukasz Roszkowiak creator: Cristina Callau Casanova creator: M. Teresa Salvadó-Usach creator: Joaquín Jaén Martínez creator: Albert Gibert-Ramos creator: Albert Roso-Llorach creator: Andrea Gras Navarro creator: Marta Berenguer-Poblet creator: Montse Llobera creator: Júlia Gil Garcia creator: Bárbara Tomás creator: Vanessa Gestí creator: Eeva Laine creator: Benoít Plancoulaine creator: Jordi Baucells creator: Maryléne Lejeune uri: https://doi.org/10.7717/peerj.9779 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 López et al. title: Applied phylogeography of Cyclopia intermedia (Fabaceae) highlights the need for ‘duty of care’ when cultivating honeybush link: https://peerj.com/articles/9818 last-modified: 2020-09-02 description: BackgroundThe current cultivation and plant breeding of Honeybush tea (produced from members of CyclopiaVent.) do not consider the genetic diversity nor structuring of wild populations. Thus, wild populations may be at risk of genetic contamination if cultivated plants are grown in the same landscape. Here, we investigate the spatial distribution of genetic diversity within Cyclopia intermedia E. Mey.—this species is widespread and endemic in the Cape Floristic Region (CFR) and used in the production of Honeybush tea.MethodsWe applied High Resolution Melt analysis (HRM), with confirmation Sanger sequencing, to screen two non-coding chloroplast DNA regions (two fragments from the atpI-aptH intergenic spacer and one from the ndhA intron) in wild C. intermedia populations. A total of 156 individuals from 17 populations were analyzed for phylogeographic structuring. Statistical tests included analyses of molecular variance and isolation-by-distance, while relationships among haplotypes were ascertained using a statistical parsimony network.ResultsPopulations were found to exhibit high levels of genetic structuring, with 62.8% of genetic variation partitioned within mountain ranges. An additional 9% of genetic variation was located amongst populations within mountains, suggesting limited seed exchange among neighboring populations. Despite this phylogeographic structuring, no isolation-by-distance was detected (p > 0.05) as nucleotide variation among haplotypes did not increase linearly with geographic distance; this is not surprising given that the configuration of mountain ranges dictates available habitats and, we assume, seed dispersal kernels.ConclusionsOur findings support concerns that the unmonitored redistribution of Cyclopia genetic material may pose a threat to the genetic diversity of wild populations, and ultimately the genetic resources within the species. We argue that ‘duty of care’ principles be used when cultivating Honeybush and that seed should not be translocated outside of the mountain range of origin. Secondarily, given the genetic uniqueness of wild populations, cultivated populations should occur at distance from wild populations that is sufficient to prevent unintended gene flow; however, further research is needed to assess gene flow within mountain ranges. creator: Nicholas C. Galuszynski creator: Alastair J. Potts uri: https://doi.org/10.7717/peerj.9818 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Galuszynski and Potts title: Simulating highly disturbed vegetation distribution: the case of China’s Jing-Jin-Ji region link: https://peerj.com/articles/9839 last-modified: 2020-09-02 description: BackgroundSimulating vegetation distribution is an effective method for identifying vegetation distribution patterns and trends. The primary goal of this study was to determine the best simulation method for a vegetation in an area that is heavily affected by human disturbance.MethodsWe used climate, topographic, and spectral data as the input variables for four machine learning models (random forest (RF), decision tree (DT), support vector machine (SVM), and maximum likelihood classification (MLC)) on three vegetation classification units (vegetation group (I), vegetation type (II), and formation and subformation (III)) in Jing-Jin-Ji, one of China’s most developed regions. We used a total of 2,789 vegetation points for model training and 974 vegetation points for model assessment.ResultsOur results showed that the RF method was the best of the four models, as it could effectively simulate vegetation distribution in all three classification units. The DT method could only simulate vegetation distribution in units I and II, while the other two models could not simulate vegetation distribution in any of the units. Kappa coefficients indicated that the DT and RF methods had more accurate predictions for units I and II than for unit III. The three vegetation classification units were most affected by six variables: three climate variables (annual mean temperature, mean diurnal range, and annual precipitation), one geospatial variable (slope), and two spectral variables (Mid-infrared ratio of winter vegetation index and brightness index of summer vegetation index). Variables Combination 7, including annual mean temperature, annual precipitation, mean diurnal range and precipitation of driest month, produced the highest simulation accuracy.ConclusionsWe determined that the RF model was the most effective for simulating vegetation distribution in all classification units present in the Jing-Jin-Ji region. The RF model produced high accuracy vegetation distributions in classification units I and II, but relatively low accuracy in classification unit III. Four climate variables were sufficient for vegetation distribution simulation in such region. creator: Sangui Yi creator: Jihua Zhou creator: Liming Lai creator: Hui Du creator: Qinglin Sun creator: Liu Yang creator: Xin Liu creator: Benben Liu creator: Yuanrun Zheng uri: https://doi.org/10.7717/peerj.9839 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Yi et al. title: Prognostic implications of metabolism-associated gene signatures in colorectal cancer link: https://peerj.com/articles/9847 last-modified: 2020-09-02 description: Colorectal cancer (CRC) is one of the most common and deadly malignancies. Novel biomarkers for the diagnosis and prognosis of this disease must be identified. Besides, metabolism plays an essential role in the occurrence and development of CRC. This article aims to identify some critical prognosis-related metabolic genes (PRMGs) and construct a prognosis model of CRC patients for clinical use. We obtained the expression profiles of CRC from The Cancer Genome Atlas database (TCGA), then identified differentially expressed PRMGs by R and Perl software. Hub genes were filtered out by univariate Cox analysis and least absolute shrinkage and selection operator Cox analysis. We used functional enrichment analysis methods, such as Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and Gene Set Enrichment Analysis, to identify involved signaling pathways of PRMGs. The nomogram predicted overall survival (OS). Calibration traces were used to evaluate the consistency between the actual and the predicted survival rate. Finally, a prognostic model was constructed based on six metabolic genes (NAT2, XDH, GPX3, AKR1C4, SPHK1, and ADCY5), and the risk score was an independent prognostic prognosticator. Genetic expression and risk score were significantly correlated with clinicopathologic characteristics of CRC. A nomogram based on the clinicopathological feature of CRC and risk score accurately predicted the OS of individual CRC cancer patients. We also validated the results in the independent colorectal cancer cohorts GSE39582 and GSE87211. Our study demonstrates that the risk score is an independent prognostic biomarker and is closely correlated with the malignant clinicopathological characteristics of CRC patients. We also determined some metabolic genes associated with the survival and clinical stage of CRC as potential biomarkers for CRC diagnosis and treatment. creator: Yandong Miao creator: Qiutian Li creator: Jiangtao Wang creator: Wuxia Quan creator: Chen Li creator: Yuan Yang creator: Denghai Mi uri: https://doi.org/10.7717/peerj.9847 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Miao et al. title: Mayfly emergence production and body length response to hydrology in a tropical lowland stream link: https://peerj.com/articles/9883 last-modified: 2020-09-02 description: BackgroundHydrological impacts on aquatic biota have been assessed in numerous empirical studies. Aquatic insects are severely affected by population declines and consequent diversity loss. However, many uncertainties remain regarding the effects of hydrology on insect production and the consequences of energy transfer to the terrestrial ecosystem. Likewise, sublethal effects on insect morphology remain poorly quantified in highly variable environments. Here, we characterized monthly fluctuation in benthic and emerged biomass of Ephemeroptera in a tropical lowland stream. We quantified the proportion of mayfly production that emerges into the riparian forest. We also examined the potential morphological changes in Farrodes caribbianus (the most abundant mayfly in our samples) due to environmental stress.MethodsWe collected mayflies (nymphs and adults) in a first-order stream in Costa Rica. We compared benthic and adult biomass from two years’ worth of samples, collected with a core sampler (0.006 m2) and a 2 m2-emergence trap. The relationship between emergence and annual secondary production (E/P) was used to estimate the Ephemeroptera production that emerged as adults. A model selection approach was used to determine the relationship between environmental variables that were collected monthly and the emergent biomass. To determine potential departures from perfect bilateral symmetry, we evaluated the symmetry of two morphological traits (forceps and forewing) of F. caribbianus adults. We used Spearman’s rank correlation coefficients (ρ) to examine potential changes in adult body length as a possible response to environmental stress.ResultsBenthic biomass was variable, with peaks throughout the study period. However, peaks in benthic biomass did not lead to increases in mayfly emergence, which remained stable over time. Relatively constant mayfly emergence suggests that they were aseasonal in tropical lowland streams. Our E/P estimate indicated that approximately 39% and 20% (for 2002 and 2003, respectively) of the nymph production emerged as adults. Our estimated proportion of mayfly production transferred to terrestrial ecosystems was high relative to reports from temperate regions. We observed a strong negative response of F. caribbianus body length to increased hydrology (Spearman: ρ = −0.51, p < 0.001), while slight departures from perfect symmetry were observed in all traits.ConclusionOur two years study demonstrates that there was large temporal variability in mayfly biomass that was unrelated to hydrological fluctuations, but potentially related to trophic interactions (e.g., fish predation). Body length was a good indicator of environmental stress, which could have severe associated costs for mayfly fitness in ecosystems with high temporal variation. Our results highlight the complex ecological and evolutionary dynamics of tropical aquatic insects, and the intricate connection between aquatic and terrestrial ecosystems. creator: Pablo E. Gutiérrez-Fonseca creator: Alonso Ramírez uri: https://doi.org/10.7717/peerj.9883 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Gutiérrez-Fonseca and Ramírez title: Molecular characteristic of activin receptor IIB and its functions in growth and nutrient regulation in Eriocheir sinensis link: https://peerj.com/articles/9673 last-modified: 2020-09-01 description: Activin receptor IIB (ActRIIB) is a serine/threonine-kinase receptor binding with transforming growth factor-β (TGF-β) superfamily ligands to participate in the regulation of muscle mass in vertebrates. However, its structure and function in crustaceans remain unknown. In this study, the ActRIIB gene in Eriocheir sinensis (Es-ActRIIB) was cloned and obtained with a 1,683 bp open reading frame, which contains the characteristic domains of TGF-β type II receptor superfamily, encoding 560 amino acids. The mRNA expression of Es-ActRIIB was the highest in hepatopancreas and the lowest in muscle at each molting stage. After injection of Es-ActRIIB double-stranded RNA during one molting cycle, the RNA interference (RNAi) group showed higher weight gain rate, higher specific growth rate, and lower hepatopancreas index compared with the control group. Meanwhile, the RNAi group displayed a significantly increased content of hydrolytic amino acid in both hepatopancreas and muscle. The RNAi group also displayed slightly higher contents of saturated fatty acid and monounsaturated fatty acid but significantly decreased levels of polyunsaturated fatty acid compared with the control group. After RNAi on Es-ActRIIB, the mRNA expressions of five ActRIIB signaling pathway genes showed that ActRI and forkhead box O (FoxO) were downregulated in hepatopancreas and muscle, but no significant expression differences were found in small mother against decapentaplegic (SMAD) 3, SMAD4 and mammalian target of rapamycin. The mRNA expression s of three lipid metabolism-related genes (carnitine palmitoyltransferase 1β (CPT1β), fatty acid synthase, and fatty acid elongation) were significantly downregulated in both hepatopancreas and muscle with the exception of CPT1β in muscles. These results indicate that ActRIIB is a functionally conservative negative regulator in growth mass, and protein and lipid metabolism could be affected by inhibiting ActRIIB signaling in crustacean. creator: Jingan Wang creator: Kaijun Zhang creator: Xin Hou creator: Wucheng Yue creator: He Yang creator: Xiaowen Chen creator: Jun Wang creator: Chenghui Wang uri: https://doi.org/10.7717/peerj.9673 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al. title: Genomic diversity and evolution, diagnosis, prevention, and therapeutics of the pandemic COVID-19 disease link: https://peerj.com/articles/9689 last-modified: 2020-09-01 description: The coronavirus disease 19 (COVID-19) is a highly transmittable and pathogenic viral infection caused by a novel evolutionarily divergent RNA virus, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The virus first emerged in Wuhan, China in December 2019, and subsequently spreaded around the world. Genomic analyses revealed that this zoonotic virus may be evolved naturally but not a purposefully manipulated laboratory construct. However, currently available data are not sufficient to precisely conclude the origin of this fearsome virus. Comprehensive annotations of the whole-genomes revealed hundreds of nucleotides, and amino acids mutations, substitutions and/or deletions at different positions of the ever changing SARS-CoV-2 genome. The spike (S) glycoprotein of SARS-CoV-2 possesses a functional polybasic (furin) cleavage site at the S1-S2 boundary through the insertion of 12 nucleotides. It leads to the predicted acquisition of 3-O-linked glycan around the cleavage site. Although real-time RT-PCR methods targeting specific gene(s) have widely been used to diagnose the COVID-19 patients, however, recently developed more convenient, cheap, rapid, and specific diagnostic tools targeting antigens or CRISPR-Cas-mediated method or a newly developed plug and play method should be available for the resource-poor developing countries. A large number of candidate drugs, vaccines and therapies have shown great promise in early trials, however, these candidates of preventive or therapeutic agents have to pass a long path of trials before being released for the practical application against COVID-19. This review updates current knowledge on origin, genomic evolution, development of the diagnostic tools, and the preventive or therapeutic remedies of the COVID-19. We also discussed the future scopes for research, effective management, and surveillance of the newly emerged COVID-19 disease. creator: M. Nazmul Hoque creator: Abed Chaudhury creator: Md Abdul Mannan Akanda creator: M. Anwar Hossain creator: Md Tofazzal Islam uri: https://doi.org/10.7717/peerj.9689 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Hoque et al. title: Serum proteins differentially expressed in early- and late-onset preeclampsia assessed using iTRAQ proteomics and bioinformatics analyses link: https://peerj.com/articles/9753 last-modified: 2020-09-01 description: BackgroundPreeclampsia remains a serious disorder that puts at risk the lives of perinatal mothers and infants worldwide. This study assessed potential pathogenic mechanisms underlying preeclampsia by investigating differentially expressed proteins (DEPs) in the serum of patients with early-onset preeclampsia (EOPE) and late-onset preeclampsia (LOPE) compared with healthy pregnant women.MethodsBlood samples were collected from four women with EOPE, four women with LOPE, and eight women with normal pregnancies, with four women providing control samples for each preeclampsia group. Serum proteins were identified by isobaric tags for relative and absolute quantitation combined with liquid chromatography–tandem mass spectrometry. Serum proteins with differences in their levels compared with control groups of at least 1.2 fold-changes and that were also statistically significantly different between the groups at P < 0.05 were further analyzed. Bioinformatics analyses, including gene ontology and Kyoto Encyclopedia of Genes and Genomes signaling pathway analyses, were used to determine the key proteins and signaling pathways associated with the development of PE and to determine those DEPs that differed between women with EOPE and those with LOPE. Key protein identified by mass spectrometry was verified by enzyme linked immunosorbent assay (ELISA).ResultsCompared with serum samples from healthy pregnant women, those from women with EOPE displayed 70 proteins that were differentially expressed with significance. Among them, 51 proteins were significantly upregulated and 19 proteins were significantly downregulated. In serum samples from women with LOPE, 24 DEPs were identified , with 10 proteins significantly upregulated and 14 proteins significantly downregulated compared with healthy pregnant women. Bioinformatics analyses indicated that DEPs in both the EOPE and LOPE groups were associated with abnormalities in the activation of the coagulation cascade and complement system as well as with lipid metabolism. In addition, 19 DEPs in the EOPE group were closely related to placental development or invasion of tumor cells. Downregulationof pregnancy-specific beta-1-glycoprotein 9 (PSG9) in the LOPE group was confirmed by ELISA.ConclusionThe pathogenesis of EOPE and LOPE appeared to be associated with coagulation cascade activation, lipid metabolism, and complement activation. However, the pathogenesis of EOPE also involved processes associated with greater placental injury. This study provided several new proteins in the serum which may be valuable for clinical diagnosis of EOPE and LOPE, and offered potential mechanisms underpinning the development of these disorders. creator: Chengcheng Tu creator: Feng Tao creator: Ying Qin creator: Mingzhu Wu creator: Ji Cheng creator: Min Xie creator: Bing Shen creator: Junjiao Ren creator: Xiaohong Xu creator: Dayan Huang creator: Hongbo Chen uri: https://doi.org/10.7717/peerj.9753 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Tu et al. title: The effect of music on the perception of outdoor urban environment link: https://peerj.com/articles/9770 last-modified: 2020-09-01 description: Music may modify the impression of a visual environment. Most studies have explored the effect of music on the perception of various service settings, but the effect of music on the perception of outdoor environments has not yet been adequately explored. Music may make an environment more pleasant and enhance the relaxation effect of outdoor recreational activities. This study investigated the effect of music on the evaluation of urban built and urban natural environments. The participants (N = 94) were asked to evaluate five environments in terms of spatio-cognitive and emotional dimensions while listening to music. Two types of music were selected: music with a fast tempo and music with a slow tempo. In contrast with a previous study by Yamasaki, Yamada & Laukka (2015), our experiment revealed that there was only a slight and not significant influence of music on the evaluation of the environment. The effect of music was mediated by the liking of music, but only in the dimensions of Pleasant and Mystery. The environmental features of the evaluated locations had a stronger effect than music on the evaluation of the environments. Environments with natural elements were perceived as more pleasant, interesting, coherent, and mysterious than urban built environments regardless of the music. It is suggested that the intensity of music may be an important factor in addition to the research methodology, individual variables, and cultural differences. creator: Marek Franěk creator: Lukáš Režný creator: Denis Šefara uri: https://doi.org/10.7717/peerj.9770 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Franěk et al. title: Identification of a prognostic signature of nine metabolism-related genes for hepatocellular carcinoma link: https://peerj.com/articles/9774 last-modified: 2020-09-01 description: BackgroundHepatocellular carcinoma (HCC) is the fifth most common cancer. Since changes in liver metabolism contribute to liver disease development, it is necessary to build a metabolism-related prognostic model for HCC.MethodsWe constructed a metabolism-related-gene (MRG) signature comprising nine genes, which segregated HCC patients into high- and low-risk groups.ResultsThe survival rate (overall survival: OS; relapse-free survival; and progression-free survival) of patients in the low-risk group of The Cancer Genome Atlas (TCGA) cohort was significantly higher than that of patients in the high-risk group. The OS prognostic signature was validated in the International Cancer Genome Consortium independent cohort. The corresponding receiver operating characteristic curves of the model indicated that the signature had good diagnostic efficiency, in terms of improving OS over 1, 3, and 5 years. Hierarchical analysis demonstrated that the MRG signature was significantly associated with better prognosis in male patients, patients aged ≤ 65 years, and patients carrying the wild-type TP53 or CTNNB1 genes. A nomogram was established, and good performance and clinical practicability were confirmed. Additionally, using the GSE109211 dataset from the Gene Expression Omnibus database, we were able to verify that the nine genes in this MRG signature had different responses to sorafenib, suggesting that some of these MRGs may act as therapeutic targets for HCC.ConclusionsWe believe that these findings will add value in terms of the diagnosis, treatment, and prognosis of HCC. creator: Chaozhi Tang creator: Jiakang Ma creator: Xiuli Liu creator: Zhengchun Liu uri: https://doi.org/10.7717/peerj.9774 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Tang et al. title: Genome-wide identification and expression analyses of R2R3-MYB transcription factor genes from two Orchid species link: https://peerj.com/articles/9781 last-modified: 2020-09-01 description: MYB transcription factors play important roles in different plant biological processes during plant growth, development and stress response. In this study, 101 (DoMYB1-101) and 99 (PaMYB1-99) R2R3-MYB genes were identified in the genomes of Dendrobium officinale and Phalaenopsis aphrodite, respectively. To classify the isolated candidate genes, the R2R3-MYB genes from A. thaliana were selected as references. As a result, all identified DoMYB and PaMYB genes were classified into 22 subfamilies. Phylogenetic analysis revealed that S21 had the largest number of members of all the subfamilies. The numbers of introns, exons and conserved sequences in all of the identified genes are different. In addition, 20 DoMYB genes from six subfamilies were selected for further analysis of tissue-specific expression and responses to various abiotic stresses treatments. The results showed that all of the DoMYB genes in S4 and S19 subfamilies exhibited the highest relative expression levels in flowers. And five DoMYB genes including DoMYB31, DoMYB40, DoMYB49, DoMYB52 and DoMYB54, responded to the stress response. These results may provide useful information for further studies of the R2R3-MYB gene family. creator: Honghong Fan creator: Manli Cui creator: Ninghong Li creator: Xujuan Li creator: Yuxuan Liang creator: Lin Liu creator: Yongping Cai creator: Yi Lin uri: https://doi.org/10.7717/peerj.9781 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Fan et al. title: Range reduction of Oblong Rocksnail, Leptoxis compacta, shapes riverscape genetic patterns link: https://peerj.com/articles/9789 last-modified: 2020-09-01 description: Many freshwater gastropod species face extinction, including 79% of species in the family Pleuroceridae. The Oblong Rocksnail, Leptoxis compacta, is a narrow range endemic pleurocerid from the Cahaba River basin in central Alabama that has seen rapid range contraction in the last 100 years. Such a decline is expected to negatively affect genetic diversity in the species. However, precise patterns of genetic variation and gene flow across the restricted range of L. compacta are unknown. This lack of information limits our understanding of human impacts on the Cahaba River system and Pleuroceridae. Here, we show that L. compacta has likely seen a species-wide decline in genetic diversity, but remaining populations have relatively high genetic diversity. We also report a contemporary range extension compared to the last published survey. Our findings indicate that historical range contraction has resulted in the absence of common genetic patterns seen in many riverine taxa like isolation by distance as the small distribution of L. compacta allows for relatively unrestricted gene flow across its remaining range despite limited dispersal abilities. Two collection sites had higher genetic diversity than others, and broodstock sites for future captive propagation and reintroduction efforts should utilize sites identified here as having the highest genetic diversity. Broadly, our results support the hypothesis that range contraction will result in the reduction of species-wide genetic diversity, and common riverscape genetic patterns cannot be assumed to be present in species facing extinction risk. creator: Aaliyah D. Wright creator: Nicole L. Garrison creator: Ashantye’ S. Williams creator: Paul D. Johnson creator: Nathan V. Whelan uri: https://doi.org/10.7717/peerj.9789 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wright et al. title: Identification of risk factors for mortality associated with COVID-19 link: https://peerj.com/articles/9885 last-modified: 2020-09-01 description: ObjectivesCoronavirus Disease 2019 (COVID-19) has become a pandemic outbreak. Risk stratification at hospital admission is of vital importance for medical decision making and resource allocation. There is no sophisticated tool for this purpose. This study aimed to develop neural network models with predictors selected by genetic algorithms (GA).MethodsThis study was conducted in Wuhan Third Hospital from January 2020 to March 2020. Predictors were collected on day 1 of hospital admission. The primary outcome was the vital status at hospital discharge. Predictors were selected by using GA, and neural network models were built with the cross-validation method. The final neural network models were compared with conventional logistic regression models.ResultsA total of 246 patients with COVID-19 were included for analysis. The mortality rate was 17.1% (42/246). Non-survivors were significantly older (median (IQR): 69 (57, 77) vs. 55 (41, 63) years; p < 0.001), had higher high-sensitive troponin I (0.03 (0, 0.06) vs. 0 (0, 0.01) ng/L; p < 0.001), C-reactive protein (85.75 (57.39, 164.65) vs. 23.49 (10.1, 53.59) mg/L; p < 0.001), D-dimer (0.99 (0.44, 2.96) vs. 0.52 (0.26, 0.96) mg/L; p < 0.001), and α-hydroxybutyrate dehydrogenase (306.5 (268.75, 377.25) vs. 194.5 (160.75, 247.5); p < 0.001) and a lower level of lymphocyte count (0.74 (0.41, 0.96) vs. 0.98 (0.77, 1.26) × 109/L; p < 0.001) than survivors. The GA identified a 9-variable (NNet1) and a 32-variable model (NNet2). The NNet1 model was parsimonious with a cost on accuracy; the NNet2 model had the maximum accuracy. NNet1 (AUC: 0.806; 95% CI [0.693–0.919]) and NNet2 (AUC: 0.922; 95% CI [0.859–0.985]) outperformed the linear regression models.ConclusionsOur study included a cohort of COVID-19 patients. Several risk factors were identified considering both clinical and statistical significance. We further developed two neural network models, with the variables selected by using GA. The model performs much better than the conventional generalized linear models. creator: Yuetian Yu creator: Cheng Zhu creator: Luyu Yang creator: Hui Dong creator: Ruilan Wang creator: Hongying Ni creator: Erzhen Chen creator: Zhongheng Zhang uri: https://doi.org/10.7717/peerj.9885 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Yu et al.