title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2021-07 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Developmental instability in wild Nigerian olive baboons (Papio anubis) link: https://peerj.com/articles/11832 last-modified: 2021-07-30 description: BackgroundDevelopmental instability in archaeological samples can be detected through analysis of skeletal and dental remains. During life, disruptions to biological internal homeostasis that occur during growth and development redirect bodily resources to returning to homeostasis and away from normal processes such as symmetrical development. Because dental enamel does not remodel in life, any deviations from normal development are left behind. Even subtle disturbances to developmental trajectory may be detected in asymmetrical development of traits, specifically a random variation in sides termed fluctuating asymmetry. Human dental fluctuating asymmetry studies are common, but here we investigate the permanent dentition of a non-human primate Papio anubis, for potential fluctuating asymmetry relative to sex, weaning, and reproductive maturity. The sample stems from an outlier population that lives in the wettest and most humid habitat of any studied baboon group.MethodsThe skulls of adult baboons were collected after their natural death in Gashaka Gumti National Park, Nigeria. The permanent dentition of antimeric teeth (paired) were measured for maximum length and breadth using standard methods. The metrics were analyzed to assess the presence of fluctuating asymmetry in adult permanent mandibular and maxillary dentition. Measurement error and other forms of asymmetry (antisymmetry, directional asymmetry) were considered and dental measures expressing true fluctuating asymmetry were used to address three research questions.ResultsMales exhibit greater fluctuating asymmetry than females, suggesting that males experience greater overall instability during the developmental period. While weaning is not more stressful than other life history stages for males and females (using the first molar fluctuating asymmetry index as a proxy compared to other teeth), it is more stressful for females than males. The onset of reproduction is also not more stressful than other life history stages for males and females (using the third molar fluctuating asymmetry index as a proxy compared to other teeth), but it is more stressful for males than females. We explore possible explanations for these findings in the discussion. creator: Kara C. Hoover creator: Emily Gelipter creator: Volker Sommer creator: Kris Kovarovic uri: https://doi.org/10.7717/peerj.11832 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Hoover et al. title: RNase H-dependent amplification improves the accuracy of rolling circle amplification combined with loop-mediated isothermal amplification (RCA-LAMP) link: https://peerj.com/articles/11851 last-modified: 2021-07-30 description: The hybrid method upon combining rolling circle amplification and loop-mediated isothermal amplification (RCA-LAMP) was developed to quantify very small amount of different type of RNAs, such as miRNAs. RCA-LAMP can help detect short sequences through padlock probe (PLP) circularization and exhibit powerful DNA amplification. However, one of the factors that determines the detection limit of RCA-LAMP is non-specific amplification. In this study, we improved the accuracy of RCA-LAMP through applying RNase H-dependent PCR (rhPCR) technology. In this method, the non-specific amplification was suppressed by using the rh primer, which is designed through blocking the modification at the 3′end to stop DNA polymerase reaction and replacing the 6th DNA molecule from the end with RNA using RNase H2 enzyme. Traditional RCA-LAMP amplified the non-specific amplicons from linear PLP without a targeting reaction, while RCA-LAMP with rh primer and RNase H2 suppressed the non-specific amplification. Conversely, we identified the risk posed upon conducting PLP cyclization reaction using Splint R ligase in the RNA-targeting step that occurred even in the RNA-negative condition, which is another factor determining the detection limit of RCA-LAMP. Therefore, this study contributes in improving the accuracy of RNA quantification using RCA-LAMP. creator: Takema Hasegawa creator: Diana Hapsari creator: Hitoshi Iwahashi uri: https://doi.org/10.7717/peerj.11851 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Hasegawa et al. title: Brain derived neurotrophic factor declines after complete curative resection in gastrointestinal cancer link: https://peerj.com/articles/11718 last-modified: 2021-07-30 description: BackgroundBrain derived neurotrophic factor (BDNF) is a neurotrophin involved in neural and metabolic diseases, but it is also one of the crucial factors in cancer development and metastases. In the current study, we investigated serum BDNF concentrations in patients that underwent surgical treatment for colorectal cancer or pancreatic cancer.MethodsSerum BDNF concentrations were measured with standard enzyme-linked immunosorbent assays, before and on the third day after the operation, in 50 consecutive patients with colorectal cancer and 25 patients with pancreatic cancer (tumours in the head of pancreas). We compared pre- and postoperative BDNF levels, according to the subsequent TNM stage, histologic stage, lymph node involvement, neuro- or angio-invasion, and resection range.ResultsIn the pancreatic cancer group, BDNF concentrations fell significantly postoperatively (p = 0.011). In patients that underwent resections, BDNF concentrations fell (p = 0.0098), but not in patients that did not undergo resections (i.e., laparotomy alone). There were significant pre- and postoperative differences in BDNF levels among patients with (p = 0.021) and without (p = 0.034) distant metastases. Significant reductions in BDNF were observed postoperatively in patients with small tumours (i.e., below the median size; p = 0.023), in patients with negative angio- or lymphatic invasion (p = 0.028, p = 0.011, respectively), and in patients with lymph node ratios above 0.17 (p = 0.043). In the colon cancer group, the serum BDNF concentrations significantly fell postoperatively in the entire group (p = 0.0076) and in subgroups of patients with or without resections (p = 0.034, p = 0.0179, respectively). Significant before-after differences were found in subgroups with angioinvasions (p = 0.050) and in those without neuroinvasions (p = 0.049). Considering the TNM stages, the postoperative BDNF concentration fell in groups with (p = 0.0218) and without (p = 0.034) distant metastases and in patients with tumours below the median size (p = 0.018).ConclusionOur results suggested that BDNF might play an important role in gastrointestinal cancer development. BDNF levels were correlated with tumour volume, and with neuro-, angio- and lymphatic invasions. In pancreatic cancer, BDNF concentrations varied according to the surgical procedure and they fell significantly after tumour resections. Thus, BDNF may serve as a potential marker of complete resections in underdiagnosed patients. However, this hypothesis requires further investigation. In contrast, no differences according to the procedure was made in patients with colon cancer. creator: Tomasz Guzel creator: Katarzyna Mech creator: Marzena Iwanowska creator: Marek Wroński creator: Maciej Słodkowski uri: https://doi.org/10.7717/peerj.11718 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Guzel et al. title: Validity and usefulness of the student-athletes’ motivation toward sport and academics questionnaire: a Bayesian multilevel approach link: https://peerj.com/articles/11863 last-modified: 2021-07-30 description: BackgroundReliable assessment and understanding of student-athletes’ motivation for dual careers are crucial to support their career development and transitions. The purpose of this research was to examine the validity and usefulness of the student-athletes’ motivation toward sport and academics questionnaire (SAMSAQ-PT) in the Brazilian higher education context. Four studies were performed.MethodsIn study one, conceptually and semantic translation of the questionnaire and Bayesian exploratory factor analysis were conducted. In study two, a Bayesian confirmatory factor analysis with an independent sample was performed. In study three, Bayesian multilevel modeling was applied to examine the construct validity of the questionnaire in a cross-sectional sample. In study four, the SAMSAQ-PT sensitiveness was examined in a longitudinal sample, and the results were interpreted based on multilevel regression and poststratification.ResultsAltogether the results provided evidence validity and usefulness of the SAMSAQ-PT in Brazilian student-athletes. The Brazilian student-athletes’ motivation scores were sensitive to the influence of sex, sport level, and type of university on career and sport motivation. SAMSAQ-PT estimate scores across an academic year showed a trend of stability in the scores, adjusting for sex, sport level, type of university, and student-athlete status.ConclusionThe SAMSAQ-PT proved to be a robust and valuable questionnaire, which could be used in Portuguese-speaking countries. The findings of the cross-sectional and longitudinal surveys urge to consider individual and contextual characteristics when investigating motivation of dual-career of athletes, also concerning the sex-related opportunities in university sports. Furthermore, there is a need for a call for action to promote and nurture the student-athletes motivation to remain engaged in both sports and educational commitments. creator: Ricardo T. Quinaud creator: Carlos E. Gonçalves creator: Kauana Possamai creator: Cristiano Zarbato Morais creator: Laura Capranica creator: Humberto M. Carvalho uri: https://doi.org/10.7717/peerj.11863 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Quinaud et al. title: CASPredict: a web service for identifying Cas proteins link: https://peerj.com/articles/11887 last-modified: 2021-07-30 description: Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated (Cas) proteins constitute the CRISPR-Cas systems, which play a key role in prokaryote adaptive immune system against invasive foreign elements. In recent years, the CRISPR-Cas systems have also been designed to facilitate target gene editing in eukaryotic genomes. As one of the important components of the CRISPR-Cas system, Cas protein plays an irreplaceable role. The effector module composed of Cas proteins is used to distinguish the type of CRISPR-Cas systems. Effective prediction and identification of Cas proteins can help biologists further infer the type of CRISPR-Cas systems. Moreover, the class 2 CRISPR-Cas systems are gradually applied in the field of genome editing. The discovery of Cas protein will help provide more candidates for genome editing. In this paper, we described a web service named CASPredict (http://i.uestc.edu.cn/caspredict/cgi-bin/CASPredict.pl) for identifying Cas proteins. CASPredict first predicts Cas proteins based on support vector machine (SVM) by using the optimal dipeptide composition and then annotates the function of Cas proteins based on the hmmscan search algorithm. The ten-fold cross-validation results showed that the 84.84% of Cas proteins were correctly classified. CASPredict will be a useful tool for the identification of Cas proteins, or at least can play a complementary role to the existing methods in this area. creator: Shanshan Yang creator: Jian Huang creator: Bifang He uri: https://doi.org/10.7717/peerj.11887 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Yang et al. title: Morphological variation of the relictual alveolar structures in the mandibles of baleen whales link: https://peerj.com/articles/11890 last-modified: 2021-07-30 description: Living baleen whales (mysticetes) are bulk filter feeders that use keratinous baleen plates to filter food from prey laden water. Extant mysticetes are born entirely edentulous, though they possess tooth buds early in ontogeny, a trait inherited from toothed ancestors. The mandibles of extant baleen whales have neither teeth nor baleen; teeth are resorbed in utero and baleen grows only on the palate. The mandibles of extant baleen whales also preserve a series of foramina and associated sulci that collectively form an elongated trough, called the alveolar groove. Despite this name, it remains unclear if the alveolar groove of edentulous mysticetes and the dental structures of toothed mammals are homologous. Here, we describe and quantify the anatomical diversity of these structures across extant mysticetes and compare their variable morphologies across living taxonomic groups (i.e., Balaenidae, Neobalaenidae, Eschrichtiidae, and Balaenopteridae). Although we found broad variability across taxonomic groups for the alveolar groove length, occupying approximately 60–80 percent of the mandible’s total curvilinear length (CLL) across all taxa, the relictual alveolar foramen showed distinct patterns, ranging between 15–25% CLL in balaenids, while ranging between 3–12% CLL in balaenopterids. This variability and the morphological patterning along the body of the mandible is consistent with the hypothesis that the foramina underlying the alveolar groove reflect relictual alveoli. These findings also lay the groundwork for future histological studies to examine the contents of these foramina and clarify their potential role in the feeding process. creator: Carlos Mauricio Peredo creator: Nicholas D. Pyenson uri: https://doi.org/10.7717/peerj.11890 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Peredo and Pyenson title: Fusion neural networks for plant classification: learning to combine RGB, hyperspectral, and lidar data link: https://peerj.com/articles/11790 last-modified: 2021-07-29 description: Airborne remote sensing offers unprecedented opportunities to efficiently monitor vegetation, but methods to delineate and classify individual plant species using the collected data are still actively being developed and improved. The Integrating Data science with Trees and Remote Sensing (IDTReeS) plant identification competition openly invited scientists to create and compare individual tree mapping methods. Participants were tasked with training taxon identification algorithms based on two sites, to then transfer their methods to a third unseen site, using field-based plant observations in combination with airborne remote sensing image data products from the National Ecological Observatory Network (NEON). These data were captured by a high resolution digital camera sensitive to red, green, blue (RGB) light, hyperspectral imaging spectrometer spanning the visible to shortwave infrared wavelengths, and lidar systems to capture the spectral and structural properties of vegetation. As participants in the IDTReeS competition, we developed a two-stage deep learning approach to integrate NEON remote sensing data from all three sensors and classify individual plant species and genera. The first stage was a convolutional neural network that generates taxon probabilities from RGB images, and the second stage was a fusion neural network that “learns” how to combine these probabilities with hyperspectral and lidar data. Our two-stage approach leverages the ability of neural networks to flexibly and automatically extract descriptive features from complex image data with high dimensionality. Our method achieved an overall classification accuracy of 0.51 based on the training set, and 0.32 based on the test set which contained data from an unseen site with unknown taxa classes. Although transferability of classification algorithms to unseen sites with unknown species and genus classes proved to be a challenging task, developing methods with openly available NEON data that will be collected in a standardized format for 30 years allows for continual improvements and major gains for members of the computational ecology community. We outline promising directions related to data preparation and processing techniques for further investigation, and provide our code to contribute to open reproducible science efforts. creator: Victoria M. Scholl creator: Joseph McGlinchy creator: Teo Price-Broncucia creator: Jennifer K. Balch creator: Maxwell B. Joseph uri: https://doi.org/10.7717/peerj.11790 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Scholl et al. title: Transcriptional landscape in rat intestines under hypobaric hypoxia link: https://peerj.com/articles/11823 last-modified: 2021-07-29 description: Oxygen metabolism is closely related to the intestinal homeostasis environment, and the occurrence of many intestinal diseases is as a result of the destruction of oxygen gradients. The hypobaric hypoxic environment of the plateau can cause dysfunction of the intestine for humans, such as inflammation. The compensatory response of the small intestine cells to the harsh environment definitely changes their gene expression. How the small intestine cells response the hypobaric hypoxic environment is still unclear. We studied the rat small intestine under hypobaric hypoxic conditions to explore the transcriptional changes in rats under acute/chronic hypobaric hypoxic conditions. We randomly divided rats into three groups: normal control group (S), acute hypobaric hypoxia group, exposing to hypobaric hypoxic condition for 2 weeks (W2S) and chronic hypobaric hypoxia group, exposing to hypobaric hypoxic condition for 4 weeks (W4S). The RNA sequencing was performed on the small intestine tissues of the three groups of rats. The results of principal component analysis showed that the W4S and W2S groups were quite different from the control group. We identified a total of 636 differentially expressed genes, such as ATP binding cassette, Ace2 and Fabp. KEGG pathway analysis identified several metabolic and digestive pathways, such as PPAR signaling pathway, glycerolipid metabolism, fat metabolism, mineral absorption and vitamin metabolism. Cogena analysis found that up-regulation of digestive and metabolic functions began from the second week of high altitude exposure. Our study highlights the critical role of metabolic and digestive pathways of the intestine in response to the hypobaric hypoxic environment, provides new aspects for the molecular effects of hypobaric hypoxic environment on intestine, and raises further questions about between the lipid metabolism disorders and inflammation. creator: Liuyang Tian creator: Zhilong Jia creator: Zhenguo Xu creator: Jinlong Shi creator: XiaoJing Zhao creator: Kunlun He uri: https://doi.org/10.7717/peerj.11823 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Tian et al. title: Early effects of crop tree management on undergrowth plant diversity and soil physicochemical properties in a Pinus massoniana plantation link: https://peerj.com/articles/11852 last-modified: 2021-07-29 description: BackgroundSoil and understory vegetation are vital components of forest ecosystems. Identifying the interaction of plantation management to vegetation and soil is crucial for developing sustainable plantation ecosystem management strategies. As one of the main measures of close-to-nature management of forest plantation, few studies have paid attention to the effect of crop tree management on the soil properties and understory vegetation.MethodsA 36-year-old Pinus massoniana plantation in Huaying city, Sichuan Province was taken as the research object to analyse the changes in undergrowth plant diversity and soil physicochemical properties under three different crop tree densities (100, 150, and 200 N/ha).ResultsOur results showed that the contents of available phosphorus, organic matter and hydrolysable nitrogen in the topsoil increased significantly after crop tree management, while content of available potassium decreased. The composition of shrub and herb layer was richer, and the dominant species were obviously replaced after crop tree management. The Shannon–Wiener index and Richness index of shrub layer, and the diversity of herb layer increased significantly after crop tree management. Herb layer diversity indexes and Richness index of shrub layer were closely related to soil organic matter, available phosphorus, hydrolysable nitrogen, available potassium, soil moisture and bulk density. As the main limiting factors for plant growth, nitrogen, phosphorus and potassium were closely related to plant diversity and to the distribution of the dominant species. At the initial stage of crop tree management, each treatment significantly improved the soil physicochemical properties and plant diversity of Pinus massoniana plantation, and the comprehensive evaluation was 200 N/ha >100 N/ha >150 N/ha >CK. Compared with other treatments, 200 N/ha had the best effect on improving the undergrowth environment of the Pinus massoniana plantation in the initial stage of crop tree management. creator: Qian Lyu creator: Yi Shen creator: Xianwei Li creator: Gang Chen creator: Dehui Li creator: Chuan Fan uri: https://doi.org/10.7717/peerj.11852 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Lyu et al. title: Sequence analysis and mRNA expression of prolactin receptor gene isoforms in different tissues of sheep during lactation and the post-weaning period link: https://peerj.com/articles/11868 last-modified: 2021-07-29 description: Few studies on mRNA expression of the prolactin receptor (PRLR) isoforms in different tissues of sheep were reported. The objective of this study was to analyze the gene sequence and mRNA expression of PRLR isoforms in the uterus, mammary gland, ovary, spleen and lymph tissue of ewes during the lactation and post-weaning periods. Ten lactating crossbred ewes (Dorper×Hu sheep) with twin lambs were used in this study. Five ewes were chosen randomly and slaughtered at mid-lactation (35 days after lambing). The remaining five ewes were slaughtered on the 5th day after weaning. Samples of uterus, mammary gland, ovary, spleen and lymph tissue were collected from each ewe to determine the mRNA expression of long PRLR (L-PRLR) and short PRLR (S-PRLR) by RT-qPCR. The physical and chemical properties, the similarity of the nucleotides L-PRLR and S-PRLR genes and the secondary and tertiary structure of the L-PRLR and S-PRLR proteins of sheep were analyzed. The results indicated that the predicted protein molecular weights of L-PRLR and S-PRLR are 65235.36 KD and 33847.48 KD, respectively, with isoelectric points of 5.12 and 8.34, respectively. The secondary protein structures of L-PRLR and S-PRLR are different. For L-PRLR these include alpha helix, extended strand and random coils and β-turns for which the content was 16.01%, 21%, 59.55% and 3.44%, respectively, whereas the secondary protein structures of S-PRLR contain only alpha helices, extended strand and random coils, comprising 18.24%, 30.07% and 48.99%, respectively. The L-PRLR and S-PRLR genes of the sheep (Ovis aries) had nucleotide sequences showing much similarity among ruminants. In these sheep, mRNA expression of L-PRLR and S-PRLR was highest in the uterus and differed between the uterus, ovary, mammary gland, spleen and lymph tissue. The mRNA expression of L-PRLR in lymph tissue was higher during lactation than in the post-weaning period (P < 0.01), whereas mRNA expression of S-PRLR in the uterus and the mammary gland was lower during lactation than during the post-weaning period (P < 0.01). In the uterus, mRNA expression of L-PRLR was higher than that of S-PRLR during lactation (P < 0.01) but there were no significant differences (P < 0.05) for the other five tissues. This study that the L-PRLR and S-PRLR proteins in ewes are mainly composed of extended fragments and random coils. The data also indicate that mRNA expression of L-PRLR and S-PRLR genes varies among different tissues in sheep and is higher in the uterus than in the ovary, spleen, mammary gland and lymph tissue throughout lactation and the post-weaning period. creator: Ruochen Yang creator: Chunhui Duan creator: Yunxia Guo creator: Yujing Ma creator: Nazi Niu creator: Yingjie Zhang creator: Yueqin Liu uri: https://doi.org/10.7717/peerj.11868 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Yang et al. title: Network analysis of miRNA targeting m6A-related genes in patients with esophageal cancer link: https://peerj.com/articles/11893 last-modified: 2021-07-29 description: BackgroundWe investigated the miRNA-m6A related gene network and identified a miRNA-based prognostic signature in patients with esophageal cancer using integrated genomic analysis.MethodsWe obtained expression data for m6A-related genes and miRNAs from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets. Survival analysis was conducted to identify potential prognostic biomarkers. LASSO Cox regression was performed to construct the overall survival (OS) associated prediction signature. We used the Kaplan–Meier (K–M) curve and receiver operating characteristic (ROC) curves to explore the signature’s efficiency and accuracy. Interactions between the m6A-related genes and miRNAs were identified in starBase3.0 and used to construct the miRNA-m6A related gene network.ResultsWe found that HNRNPC, YTHDF, ZC3H13, YTHDC2, and METTL14 were dysregulated in esophageal cancer tissues. Multivariate Cox regression analysis revealed that HNRNPC may be an independent risk factor for OS. Five hundred twenty-two potential upstream miRNAs were obtained from starBase3.0. Four miRNAs (miR-186, miR-320c, miR-320d, and miR-320b) were used to construct a prognostic signature, which could serve as a prognostic predictor independent from routine clinicopathological features. Finally, we constructed a key miRNA-m6A related gene network and used one m6A-related gene and four miRNAs associated with the prognosis. The results of our bioinformatics analysis were successfully validated in the human esophageal carcinoma cell lines KYSE30 and TE-1.ConclusionOur study identified a 4-miRNA prognostic signature and established a key miRNA-m6A related gene network. These tools may reliably assist with esophageal cancer patient prognosis. creator: Lili Li creator: Rongrong Xie creator: Qichun Wei uri: https://doi.org/10.7717/peerj.11893 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Li et al. title: Population and distribution of wild Asian elephants (Elephas maximus) in Phu Khieo Wildlife Sanctuary, Thailand link: https://peerj.com/articles/11896 last-modified: 2021-07-29 description: BackgroundThe populations of wild Asian elephants (Elephas maximus) have increased recently after a period of worldwide decline in protected areas. It is important to understand the dynamics and distribution of the remaining populations to ensure their conservation and prevent human-elephant conflicts.MethodsWe monitored the population distribution of elephants between 2016 and 2019 in the Phu Khieo Wildlife Sanctuary, Thailand. We set one hundred forty-nine camera trap locations; cameras recorded 38,834 photos over 6,896 trap nights. Elephants were captured in 4,319 photographs. The maximum entropy modeling software MaxEntwas used to identify elephants’ habitat preferences within 49 of the 149 total camera trap locations according to five environmental factors.ResultsOne hundred fourteen elephants were identified. We identified 30 adult males, 43 adult females, 14 sub-adult males, nine sub-adult females, 11 juveniles, and seven calves. The age structure ratio based on adult femaleswas 0.7:1:0.3:0.2:0.3:0.2, and the ratio of reproductive ability between adult females, juveniles, and calves was 1:0.2:0.1. A suitable elephant habitat was determined to be 1,288.9 km2 using Area Under the Curve (AUC). An AUC = 0.061 indicated good performance. Our model classified habitat preferences associated with elevation, forests, salt licks, human activity, and slope.ConclusionsAccording to our probability map this sanctuary can provide a suitable habitat for elephants. Our results indicate that effective management practices can protect wild Asian elephants in the region and reduce conflict between humans and elephants. creator: Nyi Nyi Phyo Htet creator: Rattanawat Chaiyarat creator: Nikorn Thongthip creator: Panat Anuracpreeda creator: Namphung Youngpoy creator: Phonlugsamee Chompoopong uri: https://doi.org/10.7717/peerj.11896 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Htet et al. title: Taxonomic and functional diversity of benthic macrofauna associated with rhodolith beds in SE Brazil link: https://peerj.com/articles/11903 last-modified: 2021-07-29 description: Rhodoliths are free-living and morphologically diverse marine calcareous algae commonly distributed over the continental shelf seafloor. They increase the seabed structural complexity and are of potential value as feeding and reproductive grounds for a myriad of marine fauna. The higher structural seabed complexity within rhodolith beds may also increase benthic diversity by creating microhabitats, but this relationship has been rarely explored within rhodolith beds worldwide. Here we compared benthic macrofaunal (>500 µm) structure on rhodolith beds (nodule epifauna) and within unconsolidated sediments (sediment infauna) under high and low-density beds to test whether rhodolith bed density and nodule morphology influenced macrofaunal assemblages. We observed that macrofaunal density on nodules (2538 ± 288.7 ind·m−2) was 15-fold higher when compared to sediments under those beds (166 ± 38.8 ind·m−2). Rhodolith bed density was positively related to macrofaunal density, composition, and functional diversity on the rhodoliths. Low-density beds (61 ± 27.1 nodules·m−2) with discoid-shape nodules were dominated by peracarid crustaceans whereas high-density beds (204 ± 18.7 nodules·m−2) with spheroidal nodules were dominated by Annelid polychaetes. The sediment macrofauna was also positively influenced by the density of rhodolith nodules, which increased sediment carbonate and organic quality (protein and lipids) under high-density beds. Macrofaunal functional diversity was generally higher on rhodoliths, with low similarity (low nestedness) and high taxa turnover between macrofaunal assemblages of rhodoliths and sediments. These findings indicate that rhodolith beds provide an unique habitat for benthic macrofaunal communities, with exclusive functional and taxonomic richness that are likely not typical in the unconsolidated sediment below these beds in SE Brazil. This study highlights the importance of protecting rhodolith beds from multiple sources of anthropogenic disturbance and exploration on continental shelves. creator: Patricia Sarcinelli Stelzer creator: Ana Carolina A. Mazzuco creator: Luiz Eduardo Gomes creator: João Martins creator: Sergio Netto creator: Angelo F. Bernardino uri: https://doi.org/10.7717/peerj.11903 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Stelzer et al. title: Why a landscape view is important: nearby urban and agricultural land affects bird abundances in protected areas link: https://peerj.com/articles/10719 last-modified: 2021-07-28 description: Protected areas are one of the primary conservation tools used worldwide. However, they are often embedded in a landscape that is intensely used by people, such as for agriculture or urban development. The proximity of these land-use types to protected areas can potentially affect the ecological effectiveness (or conservation effectiveness) of protected areas. In this article, we examine to what degree adjacent agricultural and urban land uses affect the ecological effectiveness of protected areas over the greater Gauteng region of South Africa. We selected 198 common, resident bird species, and analysed detection/non-detection data for these species collected over regular grid cells (approximately 61 km2 in area). For each species, we estimated abundance per grid cell with the Royle-Nichols model in relation to the proportion of protected area as a covariate. Our study focused on how this relationship between proportion of protected area and abundance (which we term the ‘protection–abundance relationship’) changed as a function of other land-use types in the grid cell. Specifically, we examined the interaction effects between protected area and both urban and agricultural land-use type per grid cell on bird abundance. We assigned each species to one of seven guilds, namely: frugivores, gleaners, granivores, ground-feeders, hawkers, predators and vegivores, and examined how the protection–abundance relationship varied across guilds in relation to agriculture and urban area. As urban area within a grid cell increased, the protection–abundance relationship became more positive for 58% of all species. At the level of guilds, the protection–abundance relationship became more positive for two guilds (granivores and ground-feeders), more negative for frugivores, and remained unchanged for the other four guilds (gleaners, hawkers, predators and vegivores). As agricultural area within a grid cell increased, the protection–abundance relationship became more positive for 49% of all species. At the guild level, the protection–abundance relationship became more positive for six guilds (frugivores, gleaners, ground-feeders, hawkers, predators and vegivores) and remained unchanged for the granivores. Our results show land-use type near protected areas modified the effect protected areas had on bird abundances, and hence the ecological effectiveness of protected areas. Our results suggest that protected areas should be viewed as constituents within the landscape, rather than islands of protection. creator: Gregory Duncan Duckworth creator: Res Altwegg uri: https://doi.org/10.7717/peerj.10719 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Duckworth and Altwegg title: Bioactive marine metabolites derived from the Persian Gulf compared to the Red Sea: similar environments and wide gap in drug discovery link: https://peerj.com/articles/11778 last-modified: 2021-07-28 description: Marine life has provided mankind with unique and extraordinary chemical structures and scaffolds with potent biological activities. Many organisms and secondary metabolites derived from fungi and symbionts are found to be more environmentally friendly to study than the marine corals per se. Marine symbionts such as Aspergillus sp., a fungus, which can be isolated and grown in the lab would be a potential and continuous source of bioactive natural compounds without affecting the marine environment. The Red Sea is known for its biodiversity and is well-studied in terms of its marine-derived bioactive metabolites. The harsh environmental conditions lead to the development of unique metabolic pathways. This, in turn, results in enhanced synthesis and release of toxic and bioactive chemicals. Interestingly, the Persian Gulf and the Gulf of Oman carry a variety of environmental stresses, some of which are similar to the Red Sea. When compared to the Red Sea, the Persian Gulf has been shown to be rich in marine fungi as well, and is, therefore, expected to contain elaborate and interesting bioactive compounds. Such compounds may or may not be similar to the ones isolated from the Red Sea environment. Astoundingly, there are a very limited number of studies on the bioactive portfolio of marine-derived metabolites from the Persian Gulf and the Gulf of Oman. In this perspective, we are looking at the Red Sea as a comparator marine environment and bioactive materials repertoire to provide a futuristic perspective on the potential of the understudied and possibly overlooked bioactive metabolites derived from the marine life of the Persian Gulf and the Gulf of Oman despite its proven biodiversity and harsher environmental stress. creator: Reham K. Abuhijjleh creator: Samiullah Shabbir creator: Ahmed M. Al-Abd creator: Nada H. Jiaan creator: Shahad Alshamil creator: Eman M. El-labbad creator: Sherief I. Khalifa uri: https://doi.org/10.7717/peerj.11778 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Abuhijjleh et al. title: Large chromosomal deletions and impaired homologous recombination repairing in HEK293T cells exposed to polychlorinated biphenyl 153 link: https://peerj.com/articles/11816 last-modified: 2021-07-28 description: BackgroundPolychlorinated biphenyls (PCBs) are persistent pollutants with carcinogenesis and mutagenesis effects which have been closely associated with PCBs-induced DNA damage. However, the detailed DNA damage events and corresponding pathway alterations under PCBs poisoning is still not well understood.MethodsWhole-genome sequencing (WGS) and RNA sequencing (RNA-seq) were used to explore genome wide variations and related pathway changes in HEK293T cells that challenged by 15 µM PCB153 for 96 h in vitro. Double strand breaks (DSBs) were measured by 53BP1 foci detection, altered pathways were confirmed by quantitative real-time PCR (qPCR).ResultsThe results indicated that abundant copy number variations (CNVs), including four duplications and 30 deletions, occurred in PCB153-exposed HEK293T cells. Multiple large fragment deletions (>1 Mb) involving up to 245 Mb regions on many chromosomes. Missense mutations were found in six tumor susceptibility genes, two of which are key members participating in homologous recombination (HR) repair response, BRCA1 and BRCA2. RNA-seq data showed that PCB153 poisoning apparently suppressedHR repairing genes. Besides, 15 µM PCB153 exposure significantly increased 53BP1 foci formation and effectively reduced BRCA1, RAD51B and RAD51C expression, indicating an elevated DSBs and impaired HR repairing.ConclusionThis study firstly reported multiple large chromosomal deletions and impaired HR repairing in PCB153-exposed HEK293T cells, which provided a new insight into the understanding of early response and the mechanism underlying PCB153 genotoxicity. The chromosomal instabilities might be related to the impaired HR repairing that induced by PCB153; however, further investigations, especially on actual toxic effects of human body, are needed to confirm such speculation. creator: Jiaci Li creator: Yaqing Jing creator: Yi Liu creator: Yawei Ru creator: Mingyan Ju creator: Yuxia Zhao creator: Guang Li uri: https://doi.org/10.7717/peerj.11816 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Li et al. title: A genomic perspective on the potential of termite-associated Cellulosimicrobium cellulans MP1 as producer of plant biomass-acting enzymes and exopolysaccharides link: https://peerj.com/articles/11839 last-modified: 2021-07-28 description: BackgroundLignocellulose is a renewable and enormous biomass resource, which can be degraded efficiently by a range of cocktails of carbohydrate-active enzymes secreted by termite gut symbiotic bacteria. There is an urgent need to find enzymes with novel characteristics for improving the conversion processes in the production of lignocellulosic-based products. Although various studies dedicated to the genus Cellulosimicrobium as gut symbiont, genetic potential related to plant biomass-acting enzymes and exopolysaccharides production has been fully untapped to date.MethodsThe cellulolytic bacterial strain MP1 was isolated from termite guts and identified to the species level by phenotypic, phylogenetic, and genomic analysis. To further explore genes related to cellulose and hemicellulose degradation, the draft genome of strain MP1 was obtained by using whole-genome sequencing, assembly, and annotation through the Illumina platform. Lignocellulose degrading enzymes and levan production in the liquid medium were also examined to shed light on bacterial activities.ResultsAmong 65 isolates obtained, the strain MP1 was the most efficient cellulase producer with cellulase activity of 0.65 ± 0.02 IU/ml. The whole genome analysis depicted that strain MP1 consists of a circular chromosome that contained 4,580,223 bp with an average GC content of 73.9%. The genome comprises 23 contigs including 67 rRNA genes, three tRNA genes, a single tmRNA gene, and 4,046 protein-coding sequences. In support of the phenotypic identification, the 16S rRNA gene sequence, average nucleotide identity, and whole-genome-based taxonomic analysis demonstrated that the strain MP1 belongs to the species Cellulosimicrobium cellulans. A total of 30 genes related to the degradation of cellulases and hemicellulases were identified in the C. cellulans MP1 genome. Of note, the presence of sacC1-levB-sacC2-ls operon responsible for levan and levan-type fructooligosaccharides biosynthesis was detected in strain MP1 genome, but not with closely related C. cellulans strains, proving this strain to be a potential candidate for further studies. Endoglucanases, exoglucanases, and xylanase were achieved by using cheaply available agro-residues such as rice bran and sugar cane bagasse. The maximum levan production by C. cellulans MP1 was 14.8 ± 1.2 g/l after 20 h of cultivation in media containing 200 g/l sucrose. To the best of our knowledge, the present study is the first genome-based analysis of a Cellulosimicrobium species which focuses on lignocellulosic enzymes and levan biosynthesis, illustrating that the C. cellulans MP1 has a great potential to be an efficient platform for basic research and industrial exploitation. creator: Nguyen Thi-Hanh Vu creator: Tung Ngoc Quach creator: Xuan Thi-Thanh Dao creator: Ha Thanh Le creator: Chi Phuong Le creator: Lam Tung Nguyen creator: Lam Tung Le creator: Cuong Cao Ngo creator: Ha Hoang creator: Ha Hoang Chu creator: Quyet-Tien Phi uri: https://doi.org/10.7717/peerj.11839 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Vu et al. title: Comparative development and ocular histology between epigean and subterranean salamanders (Eurycea) from central Texas link: https://peerj.com/articles/11840 last-modified: 2021-07-28 description: The salamander clade Eurycea from the karst regions of central Texas provides an ideal platform for comparing divergent nervous and sensory systems since some species exhibit extreme phenotypes thought to be associated with inhabiting a subterranean environment, including highly reduced eyes, while others retain an ancestral ocular phenotype appropriate for life above ground. We describe ocular morphology, comparing three salamander species representing two phenotypes—the surface-dwelling Barton Springs salamander (E. sosorum) and San Marcos salamander (E. nana) and the obligate subterranean Texas blind salamander (E. rathbuni) - in terms of structure and size of their eyes. Eyes were examined using confocal microscopy and measurements were made using ImageJ. Statistical analysis of data was carried out using R. We also provide a developmental series and track eye development and immunolocalization of Pax6 in E. sosorum and E. rathbuni. Adult histology of the surface-dwelling San Marcos salamander (E. nana) shows similarities to E. sosorum. The eyes of adults of the epigean species E. nana and E. sosorum appear fully developed with all the histological features of a fully functional eye. In contrast, the eyes of E. rathbuni adults have fewer layers, lack lenses and other features associated with vision as has been reported previously. However, in early developmental stages eye morphology did not differ significantly between E. rathbuni and E. sosorum. Parallel development is observed between the two phenotypes in terms of morphology; however, Pax6 labeling seems to decrease in the latter stages of development in E.rathbuni. We test for immunolabeling of the visual pigment proteins opsin and rhodopsin and observe immunolocalization around photoreceptor disks in E. nana and E. sosorum, but not in the subterranean E. rathbuni. Our results from examining developing salamanders suggest a combination of underdevelopment and degeneration contribute to the reduced eyes of adult E. rathbuni. creator: Ruben U. Tovar creator: Valentin Cantu creator: Brian Fremaux creator: Pedro Gonzalez Jr creator: Amanda Spikes creator: Dana M. García uri: https://doi.org/10.7717/peerj.11840 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Tovar et al. title: Bird-window collisions: Mitigation efficacy and risk factors across two years link: https://peerj.com/articles/11867 last-modified: 2021-07-28 description: BackgroundResearch on bird-window collision mitigation is needed to prevent up to a billion bird fatalities yearly in the U.S. At the University of Utah campus (Salt Lake City, Utah, USA), past research documented collisions, especially for Cedar Waxwings (Bombycilla cedrorum) drawn to fruiting ornamental pears in winter. Mirrored windows, which have a metallic coating that turns window exteriors into mirrors, had frequent collisions, which were mitigated when Feather Friendly®bird deterrent markers were applied. Bird-friendly windows–ORNILUX®ultraviolet (UV) and fritted windows–also reduced collisions when data were collected across fall and winter. Extending this prior research, we evaluated additional mitigation and tested the replicability of effects for pear trees, mirrored windows, and bird-friendly windows across two years.MethodsUsing published data from eight buildings monitored for collisions in year 1 (Fall and Winter, 2019–2020), we added another year of monitoring, Fall and Winter, 2020–2021. Between years, Feather Friendly®mitigation markers were added to collision-prone areas of two buildings, including both mirrored and transparent windows.ResultsThe two buildings that received new Feather Friendly®mitigation had significantly fewer collisions post-mitigation. Control areas also had nonsignificant decline in collisions. The interaction of area (mitigation vs. control) by time (year 1 vs. 2) was significant, based on generalized estimating equations (GEE). The total yearly collisions across all eight buildings declined from 39 to 23. A second GEE analysis of all 8 buildings showed that mirrored windows, pear trees, and bird-friendly windows were each significant when analyzed separately. The best-fit model showed more collisions for mirrored windows and fewer collisions for bird-friendly windows. We found pear tree proximity to be related to more collisions in winter than fall. In addition, pear trees showed reduced collisions from year 1 to 2, consistent with new mitigation for two of three buildings near pear trees.DiscussionFeather Friendly® markers can mitigate collisions with transparent windows, not only mirrored windows, compared to unmitigated areas over 2 years. Results also underscore the dangers of pear tree proximity and mirrored windows and the efficacy of bird-friendly windows. Thus, bird collisions can be prevented by window mitigation, permanent bird-friendly windows, and landscape designs that avoid creating ecological traps. creator: Barbara B. Brown creator: Sabrina Santos creator: Natalia Ocampo-Peñuela uri: https://doi.org/10.7717/peerj.11867 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Brown et al. title: Development of a homogeneous time-resolved FRET (HTRF) assay for the quantification of Shiga toxin 2 produced by E. coli link: https://peerj.com/articles/11871 last-modified: 2021-07-28 description: Shiga toxin-producing Escherichia coli (STEC) is a major intestinal pathogen and causes serious gastrointestinal illness, which includes diarrhea, hemorrhagic colitis, and life-threatening hemolytic uremic syndrome. The major virulence factors of STEC are Shiga toxins (Stx1 and Stx2), which belong to the AB-type toxin family. Among several subtypes of Stx1 and Stx2, the production of Stx2a is thought to be a risk factor for severe STEC infections, but Stx2a production levels vary markedly between STEC strains, even strains with the same serotype. Therefore, quantitative analyses of Stx2 production by STEC strains are important to understand the virulence potential of specific lineages or sublineages. In this study, we developed a novel Stx2 quantification method by utilizing homogeneous time-resolved fluorescence resonance energy transfer (HTRF) technology. To determine suitable “sandwich” assay conditions, we tested 6 combinations of fluorescence-labeled monoclonal antibodies (mAbs) specific to Stx2 and compared the HTRF signal intensities obtained at various incubation times. Through this analysis, we selected the most suitable mAb pair, one recognizing the A subunit and the other recognizing the B subunit, thus together detecting Stx holotoxins. The optimal incubation time was also determined (18 h). Then, we optimized the concentrations of the two mAbs based on the range for linearity. The established HTRF assay detected 0.5 ng/ml of the highly purified recombinant Stx2a and Stx2e proteins and the working range was 1–64 ng/ml for both Stx2a and Stx2e. Through the quantification analysis of Stx proteins in STEC cell lysates, we confirmed that other Stx2 subtypes (Stx2b, Stx2c, Stx2d and Stx2g) can also be quantified at a certain level of accuracy, while this assay system does not detect Stx2f, which is highly divergent in sequence from other Stx2 subtypes, and Stx1. As the HTRF protocol we established is simple, this assay system should prove useful for the quantitative analysis of Stx2 production levels of a large number of STEC strains. creator: Keiji Nakamura creator: Chikashi Tokuda creator: Hideyuki Arimitsu creator: Yoshiki Etoh creator: Mitsuhiro Hamasaki creator: Yuichiro Deguchi creator: Itsuki Taniguchi creator: Yasuhiro Gotoh creator: Yoshitoshi Ogura creator: Tetsuya Hayashi uri: https://doi.org/10.7717/peerj.11871 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Nakamura et al. title: Distribution and abundance of the land snail Pollicaria elephas (Gastropoda: Pupinidae) in limestone habitats in Perak, Malaysia link: https://peerj.com/articles/11886 last-modified: 2021-07-28 description: This study aimed to reveal the habitat variables that determine the distribution and abundance of the land snail Pollicaria elephas in limestone habitats in Perak, Malaysia. Seventeen plots were selected on a limestone hill to determine the effect of environmental variables on the abundance of this land snail. The environmental variables we considered included habitat (canopy cover and leaf litter thickness), topography (elevation, aspect, ruggedness, and slope), microclimate (soil temperature, air temperature, and humidity), and vegetation (abundance of respective vascular plant species). The correlation analyses suggested that the snails’ abundance was positively correlated with the abundance of the four vascular plant species: Diospyros toposia var. toposoides, Croton cascarilloides, Kibatalia laurifolia, and Mallotus peltatus. Plots with lower soil temperatures had more snails than plots with higher soil temperatures. Our results show that plots in the southern part of the limestone hill, in which P. elephas were absent, were similar in habitat, topography, microclimate, and vegetation to the plots in the northern part of the limestone hill, where specimens were mostly present. The absence of this species in suitable habitats may be due to their low dispersal ability rather than adverse environmental conditions. creator: Thor-Seng Liew creator: Chee-Chean Phung creator: Mohamad Afandi Mat Said creator: Pui Kiat Hoo uri: https://doi.org/10.7717/peerj.11886 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Liew et al. title: Honey bee (Apis mellifera) colony strength and its effects on pollination and yield in highbush blueberries (Vaccinium corymbosum) link: https://peerj.com/articles/11634 last-modified: 2021-07-27 description: Many pollination studies with honey bees have examined the effect of colony density on crop yield and yet overlook the effect of variation in the population size of these colonies. High colony density in northern highbush blueberry has been met with concerns from beekeepers who feel higher densities will intensify outbreaks of European foulbrood (EFB, Melissococcus plutonius, Truper and dé Clari), a honey bee brood disease. The purpose of this study was to confirm the prevalence of EFB in colonies pollinating blueberries and to determine whether field-level variation in the population of adult workers in colonies explained variation in blueberry fruit set and/or yield. We addressed these objectives over the course of two production seasons at 13 commercial blueberry fields in Oregon, USA, stocked with identical densities of 10 colonies/ha. We confirmed that all colonies had negligible symptoms of EFB at the start of blueberry pollination, but 53% of colonies in 2019 and 41% in 2020 had symptoms immediately following the pollination season. We also validated a method for rapidly assessing adult honey bee colony populations, namely by counting the rate of foragers returning to colonies, and it was found to be strongly correlated to true internal adult bee population independent of year and ambient temperature at the time of evaluation. Using returning forager counts, we determined there was considerable variation in the average population of colonies at each field, ranging from an estimated 10,300 to 30,700 adult worker bees per colony. While average colony strength did not predict variation in fruit set, it was related to variation in yield, independent of year. Our linear model of flight count (as a proxy for colony strength) predicts estimated yield increases of up to 25,000 kg/ha of blueberries could be achieved by colonies stronger than the recommended six frame minimum, suggesting that higher pollination benefits could be achieved without increasing hive density if stronger colonies are promoted. creator: Kennedy Judith Grant creator: Lisa DeVetter creator: Andony Melathopoulos uri: https://doi.org/10.7717/peerj.11634 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Grant et al. title: A new HSI denoising method via interpolated block matching 3D and guided filter link: https://peerj.com/articles/11642 last-modified: 2021-07-27 description: A new hyperspectral images (HSIs) denoising method via Interpolated Block-Matching and 3D filtering and Guided Filtering (IBM3DGF) denoising method is proposed. First, inter-spectral correlation analysis is used to obtain inter-spectral correlation coefficients and divide the HSIs into several adjacent groups. Second, high-resolution HSIs are produced by using adjacent three images to interpolate. Third, Block-Matching and 3D filtering (BM3D) is conducted to reduce the noise level of each group; Fourth, the guided image filtering is utilized to denoise HSI of each group. Finally, the inverse interpolation is applied to retrieve HSI. Experimental results of synthetic and real HSIs showed that, comparing with other state-of-the-art denoising methods, the proposed IBM3DGF method shows superior performance according to spatial and spectral domain noise assessment. Therefore, the proposed method has a potential to effectively remove the spatial/spectral noise for HSIs. creator: Ping Xu creator: Bingqiang Chen creator: Jingcheng Zhang creator: Lingyun Xue creator: Lei Zhu uri: https://doi.org/10.7717/peerj.11642 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Xu et al. title: Photosynthesis and respiration of the soft coral Xenia umbellata respond to warming but not to organic carbon eutrophication link: https://peerj.com/articles/11663 last-modified: 2021-07-27 description: Eutrophication with dissolved organic carbon (DOC) as a far under-investigated stressor, and ocean warming, can strongly affect coral reefs and hard corals as major reefs ecosystem engineers. However, no previous studies have investigated the metabolic responses of soft corals to DOC eutrophication, or its interaction with ocean warming. Thus, we investigated respiration and photosynthesis response of Xenia umbellata, a common mixotrophic soft coral from the Indo-pacific, to (1) three levels of DOC eutrophication simulated by glucose addition over the first 21 days of experiment and (2) ocean warming scenarios where the temperature was gradually increased from 26 °C (control condition) to 32 °C over another 24 days in an aquarium experiment. We found no significant difference in response to DOC treatments and all corals survived regardless of the DOC concentrations, whilst subsequent exposure to simulated ocean warming significantly decreased gross photosynthesis by approximately 50% at 30 °C, and 65% at 32 °C, net photosynthesis by 75% at 30 °C and 79% at 32 °C, and respiration by a maximum of 75% at 30 °C; with a slight increase at 32 °C of 25%. The ratio between gross photosynthesis and respiration decreased by the end of the warming period but remained similar between controls and colonies previously exposed to DOC. Our findings suggest that soft corals may be more resistant than hard corals to DOC eutrophication and in consequence, may potentially experiment in less magnitude the negative effects of increased temperature or subsequently both stressors. The results of this study may contribute to explain the successful role of soft corals in phase shifts as reported from many coral reefs. Where predicted declines in reef ecosystems health due to increased eutrophication levels can be exacerbated by future warming. creator: Susana Marcela Simancas-Giraldo creator: Nan Xiang creator: Meghan Moger Kennedy creator: Rassil Nafeh creator: Edoardo Zelli creator: Christian Wild uri: https://doi.org/10.7717/peerj.11663 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Simancas-Giraldo et al. title: MSBOTS: a multiple small biological organism tracking system robust against non-ideal detection and segmentation conditions link: https://peerj.com/articles/11750 last-modified: 2021-07-27 description: Accurately tracking a group of small biological organisms using algorithms to obtain their movement trajectories is essential to biomedical and pharmaceutical research. However, object mis-detection, segmentation errors and overlapped individual trajectories are particularly common issues that restrict the development of automatic multiple small organism tracking research. Extending on previous work, this paper presents an accurate and generalised Multiple Small Biological Organism Tracking System (MSBOTS), whose general feasibility is tested on three types of organisms. Evaluated on zebrafish, Artemia and Daphnia video datasets with a wide variety of imaging conditions, the proposed system exhibited decreased overall Multiple Object Tracking Precision (MOTP) errors of up to 77.59%. Moreover, MSBOTS obtained more reliable tracking trajectories with a decreased standard deviation of up to 47.68 pixels compared with the state-of-the-art idTracker system. This paper also presents a behaviour analysis module to study the locomotive characteristics of individual organisms from the obtained tracking trajectories. The developed MSBOTS with the locomotive analysis module and the tested video datasets are made freely available online for public research use. creator: Xiaoying Wang creator: Eva Cheng creator: Ian S. Burnett uri: https://doi.org/10.7717/peerj.11750 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Wang et al. title: Development of the breastfeeding support scale to measure breastfeeding support from lay and professional persons, and its predictive validity in Japan link: https://peerj.com/articles/11779 last-modified: 2021-07-27 description: BackgroundInternational and national organizations recommend exclusive breastfeeding for the first 6 months of life, but many women stop earlier. Lay and professional persons can support mothers’ efforts to overcome breastfeeding difficulties. Considering breastfeeding support to comprise emotional support, practical help, and information offered to women who desire to breastfeed (by professionals, family members, and others), we developed and tested a scale to measure it in Japan.MethodsA total of 31 items were generated by literature review and from the authors’ clinical experiences. Those items were tested with 243 mothers who visited public health centers in Tokyo for their infant’s health check-up 3 months after birth. Breastfeeding support and infant feeding status were then assessed 5 months after birth. All the data were collected by using self-administered questionnaires.ResultsOn the basis of the results of factor analysis, the number of items was reduced to 11. There were three factors: support from breastfeeding peers and from people in specifically named healthcare professions, practical help, and support from people the mother can rely on to help meet emotional needs and address breastfeeding concerns. Internal-consistency reliability (alpha) of scores on the 11-item scale was 0.83 when measured 3 months postpartum and 0.85 when measured 5 months postpartum. Higher scores on the 11-item scale 3 months postpartum were associated with more breastfeeding exclusivity both at that time (Kruskal–Wallis test, chi-squared = 14.871, df = 3, n = 211, p = 0.002, eta-squared = 0.071) and also 5 months postpartum (Kruskal–Wallis test, chi-squared = 8.556, df = 3, n = 159, p = 0.036, eta-squared = 0.054). Further, the area under the Receiver Operating Characteristic curve was 0.73 (95% CI [0.57–0.88]), which indicates that scores on the 11-item scale 3 months postpartum may be useful to predict which mothers will be less exclusive in breastfeeding 5 months postpartum. In conclusion, scores on this 11-item scale were reasonably reliable and valid for measuring breastfeeding support provided by lay and professional persons to mothers in Japan. Further research is required to evaluate this scale’s applicability in other settings. creator: Keiko Nanishi creator: Joseph Green creator: Hiroko Hongo uri: https://doi.org/10.7717/peerj.11779 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2021 Nanishi et al. title: Relationship between impulsivity and suicide among the rural elderly in China: a case-control psychological autopsy study link: https://peerj.com/articles/11801 last-modified: 2021-07-27 description: BackgroundThe relationship between impulsivity and suicide is inconsistent in different populations. Hence, the relationship between impulsivity and suicide still needs to be studied among the elderly population. The present study intends to explore the relationship between impulsivity and suicide among the rural Chinese elderly.MethodsA case-control psychological autopsy study was conducted from February 1, 2014 to December 18, 2015 among rural residents over the age of 60 who died by suicide. The sample consisted of 242 suicides as the case group and 242 living individuals as the control group. Data on demographic characteristics, impulsivity, previous history of suicide attempts, social support, negative life events, and suicidal behavior were collected.ResultsOur study found that impulsivity increased the risk of suicide. The case group showed a higher Barratt Impulsiveness Scale score compared with the control group (p < 0.001), which indicates that impulsivity was higher among the elderly suicides. In addition, regression analyses show that impulsivity (odds ratio: 1.03, 95% confidence interval: 1.01–1.06) is an independent risk factor of suicide, after controlling for the effects of marital status, education, family annual income, being left behind, social support, and negative life events. Finally, compared with elderly who do not have a history of attempted suicide, elderly with a history of attempted suicide showed higher impulsivity (p = 0.001). creator: Yunfang Zhou creator: Zhenyu Ma creator: Cun-Xian Jia creator: Liang Zhou uri: https://doi.org/10.7717/peerj.11801 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zhou et al. title: ptxD/Phi as alternative selectable marker system for genetic transformation for bio-safety concerns: a review link: https://peerj.com/articles/11809 last-modified: 2021-07-27 description: Antibiotic and herbicide resistance genes are the most common marker genes for plant transformation to improve crop yield and food quality. However, there is public concern about the use of resistance marker genes in food crops due to the risk of potential gene flow from transgenic plants to compatible weedy relatives, leading to the possible development of “superweeds” and antibiotic resistance. Several selectable marker genes such as aph, nptII, aaC3, aadA, pat, bar, epsp and gat, which have been synthesized to generate transgenic plants by genetic transformation, have shown some limitations. These marker genes, which confer antibiotic or herbicide resistance and are introduced into crops along with economically valuable genes, have three main problems: selective agents have negative effects on plant cell proliferation and differentiation, uncertainty about the environmental effects of many selectable marker genes, and difficulty in performing recurrent transformations with the same selectable marker to pyramid desired genes. Recently, a simple, novel, and affordable method was presented for plant cells to convert non-metabolizable phosphite (Phi) to an important phosphate (Pi) for developing cells by gene expression encoding a phosphite oxidoreductase (PTXD) enzyme. The ptxD gene, in combination with a selection medium containing Phi as the sole phosphorus (P) source, can serve as an effective and efficient system for selecting transformed cells. The selection system adds nutrients to transgenic plants without potential risks to the environment. The ptxD/Phi system has been shown to be a promising transgenic selection system with several advantages in cost and safety compared to other antibiotic-based selection systems. In this review, we have summarized the development of selection markers for genetic transformation and the potential use of the ptxD/Phi scheme as an alternative selection marker system to minimize the future use of antibiotic and herbicide marker genes. creator: Richard Dormatey creator: Chao Sun creator: Kazim Ali creator: Sajid Fiaz creator: Derong Xu creator: Alejandro Calderón-Urrea creator: Zhenzhen Bi creator: Junlian Zhang creator: Jiangping Bai uri: https://doi.org/10.7717/peerj.11809 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Dormatey et al. title: The importance of spawning behavior in understanding the vulnerability of exploited marine fishes in the U.S. Gulf of Mexico link: https://peerj.com/articles/11814 last-modified: 2021-07-27 description: The vulnerability of a fish stock to becoming overfished is dependent upon biological traits that influence productivity and external factors that determine susceptibility or exposure to fishing effort. While a suite of life history traits are traditionally incorporated into management efforts due to their direct association with vulnerability to overfishing, spawning behavioral traits are seldom considered. We synthesized the existing biological and fisheries information of 28 fish stocks in the U.S. Gulf of Mexico to investigate relationships between life history traits, spawning behavioral traits, management regulations, and vulnerability to fishing during the spawning season. Our results showed that spawning behavioral traits were not correlated with life history traits but improved identification of species that have been historically overfished. Species varied widely in their intrinsic vulnerability to fishing during spawning in association with a broad range of behavioral strategies. Extrinsic vulnerability was high for nearly all species due to exposure to fishing during the spawning season and few management measures in place to protect spawning fish. Similarly, several species with the highest vulnerability scores were historically overfished in association with spawning aggregations. The most vulnerable species included several stocks that have not been assessed and should be prioritized for further research and monitoring. Collectively, the results of this study illustrate that spawning behavior is a distinct aspect of fish ecology that is important to consider for predictions of vulnerability and resilience to fisheries exploitation. creator: Christopher R. Biggs creator: William D. Heyman creator: Nicholas A. Farmer creator: Shin’ichi Kobara creator: Derek G. Bolser creator: Jan Robinson creator: Susan K. Lowerre-Barbieri creator: Brad E. Erisman uri: https://doi.org/10.7717/peerj.11814 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: title: Effect of modified pomace on copper migration via riverbank soil in southwest China link: https://peerj.com/articles/11844 last-modified: 2021-07-27 description: To explore the effects of modified pomace on copper migration via the soil on the banks of the rivers in northern Sichuan and Chongqing, fruit pomace (P) and ethylene diamine tetra-acetic acid (EDTA) modified P (EP) were evenly added (1% mass ratio) to the soil samples of Guanyuan, Nanbu, Jialing, and Hechuan from the Jialing River; Mianyang and Suining from the Fu River; and Guangan and Dazhou from the Qu River. The geochemical characteristics and migration rules of copper in different amended soils were simulated by column experiment. Results showed that the permeation time of copper in each soil column was categorized as EP-amended > P-amended > original soil, and the permeation time of amended soil samples at different locations was Jialing > Suining > Mianyang > Guangan > Dazhou > Nanbu > Guanyuan > Hechuan. Meanwhile, the average flow rate of copper in each soil column showed a reverse trend with the permeation time. Copper in exchangeable, carbonate, and iron–manganese oxide forms decreased with the increase of vertical depth in the soil column, among which the most evident decreases appeared in the carbonate-bonding form. The copper accumulation in different locations presented a trend of Jialing > Suining > Mianyang > Guangan > Dazhou > Nanbu > Guangyuan > Hechuan, and the copper content under the same soil showed EP-amended > P-amended > original soil. The copper proportion of the carbonate form was the highest in each soil sample, followed by the exchangeable form. The proportions of iron-manganese oxide and organic matter forms were relatively small. A significant correlation was observed between the cation exchange capacity and the copper content in exchangeable and carbonate forms. Moreover, total organic carbon and copper contents were negatively correlated. creator: Lingyuan Chen creator: Touqeer Abbas creator: Lin Yang creator: Yao Xu creator: Hongyan Deng creator: Lei Hou creator: Wenbin Li uri: https://doi.org/10.7717/peerj.11844 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Chen et al. title: PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly link: https://peerj.com/articles/11845 last-modified: 2021-07-27 description: DNA de novo assembly can be used to reconstruct longer stretches of DNA (contigs), including genes and even genomes, from short DNA sequencing reads. Applying this technique to metagenomic data derived from archaeological remains, such as paleofeces and dental calculus, we can investigate past microbiome functional diversity that may be absent or underrepresented in the modern microbiome gene catalogue. However, compared to modern samples, ancient samples are often burdened with environmental contamination, resulting in metagenomic datasets that represent mixtures of ancient and modern DNA. The ability to rapidly and reliably establish the authenticity and integrity of ancient samples is essential for ancient DNA studies, and the ability to distinguish between ancient and modern sequences is particularly important for ancient microbiome studies. Characteristic patterns of ancient DNA damage, namely DNA fragmentation and cytosine deamination (observed as C-to-T transitions) are typically used to authenticate ancient samples and sequences, but existing tools for inspecting and filtering aDNA damage either compute it at the read level, which leads to high data loss and lower quality when used in combination with de novo assembly, or require manual inspection, which is impractical for ancient assemblies that typically contain tens to hundreds of thousands of contigs. To address these challenges, we designed PyDamage, a robust, automated approach for aDNA damage estimation and authentication of de novo assembled aDNA. PyDamage uses a likelihood ratio based approach to discriminate between truly ancient contigs and contigs originating from modern contamination. We test PyDamage on both on simulated aDNA data and archaeological paleofeces, and we demonstrate its ability to reliably and automatically identify contigs bearing DNA damage characteristic of aDNA. Coupled with aDNA de novo assembly, Pydamage opens up new doors to explore functional diversity in ancient metagenomic datasets. creator: Maxime Borry creator: Alexander Hübner creator: Adam B. Rohrlach creator: Christina Warinner uri: https://doi.org/10.7717/peerj.11845 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Borry et al. title: Distribution, source, water quality and health risk assessment of dissolved heavy metals in major rivers in Wuhan, China link: https://peerj.com/articles/11853 last-modified: 2021-07-27 description: Heavy metals are released into the water system through various natural processes and anthropogenic activities, thus indirectly or directly endangering human health. The distribution, source, water quality and health risk assessment of dissolved heavy metals (V, Mn, Fe, Co, Ni, Zn, As, Mo, Sb) in major rivers in Wuhan were analyzed by correlation analysis (CA), principal component analysis (PCA), heavy metal pollution index (HPI), hazard index (HI) and carcinogenic risk (CR). The results showed that the spatial variability of heavy metal contents was pronounced. PCA and CA results indicated that natural sources controlled Mn, Fe, Co, Ni and Mo, and industrial emissions were the dominant factor for V, Zn and Sb, while As was mainly from the mixed input of urban and agricultural activities. According to the heavy metal pollution index (HPI, ranging from 23.74 to 184.0) analysis, it should be noted that As and Sb contribute most of the HPI values. The health risk assessment using HI and CR showed that V and Sb might have a potential non-carcinogenic risk and As might have a potential carcinogenic risk to adults and children in the study area (CR value exceeded target risk 10−4). At the same time, it was worth noting that As might have a potential non-carcinogenic risk for children around QLR (HI value exceeded the threshold value 1). The secular variation of As and Sb should be monitor in high-risk areas. The results of this study can provide important data for improving water resources management efficiency and heavy metal pollution prevention in Wuhan. creator: Xingyong Zhang creator: Qixin Wu creator: Shilin Gao creator: Zhuhong Wang creator: Shouyang He uri: https://doi.org/10.7717/peerj.11853 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Zhang et al. title: Genome-wide association study of yield components in spring wheat collection harvested under two water regimes in Northern Kazakhstan link: https://peerj.com/articles/11857 last-modified: 2021-07-27 description: BackgroundBread wheat is the most important cereal in Kazakhstan, where it is grown on over 12 million hectares. One of the major constraints affecting wheat grain yield is drought due to the limited water supply. Hence, the development of drought-resistant cultivars is critical for ensuring food security in this country. Therefore, identifying quantitative trait loci (QTLs) associated with drought tolerance as an essential step in modern breeding activities, which rely on a marker-assisted selection approach.MethodsA collection of 179 spring wheat accessions was tested under irrigated and rainfed conditions in Northern Kazakhstan over three years (2018, 2019, and 2020), during which data was collected on nine traits: heading date (HD), seed maturity date (SMD), plant height (PH), peduncle length (PL), number of productive spikes (NPS), spike length (SL), number of kernels per spike (NKS), thousand kernel weight (TKW), and kernels yield per m2 (YM2). The collection was genotyped using a 20,000 (20K) Illumina iSelect SNP array, and 8,662 polymorphic SNP markers were selected for a genome-wide association study (GWAS) to identify QTLs for targeted agronomic traits.ResultsOut of the total of 237 discovered QTLs, 50 were identified as being stable QTLs for irrigated and rainfed conditions in the Akmola region, Northern Kazakhstan; the identified QTLs were associated with all the studied traits except PH. The results indicate that nine QTLs for HD and 11 QTLs for SMD are presumably novel genetic factors identified in the irrigated and rainfed conditions of Northern Kazakhstan. The identified SNP markers of the QTLs for targeted traits in rainfed conditions can be applied to develop new competitive spring wheat cultivars in arid zones using a marker-assisted selection approach. creator: Akerke Amalova creator: Saule Abugalieva creator: Adylkhan Babkenov creator: Sandukash Babkenova creator: Yerlan Turuspekov uri: https://doi.org/10.7717/peerj.11857 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Amalova et al. title: Proteomic analysis reveals some common proteins in the kidney stone matrix link: https://peerj.com/articles/11872 last-modified: 2021-07-27 description: BackgroundProteins are the most abundant component of kidney stone matrices and their presence may reflect the process of the stone’s formation. Many studies have explored the proteomics of urinary stones and crystals. We sought to comprehensively identify the proteins found in kidney stones and to identify new, reliable biomolecules for use in nephrolithiasis research.MethodsWe conducted bioinformatics research in November 2020 on the proteomics of urinary stones and crystals. We used the ClusterProfiler R package to transform proteins into their corresponding genes and Ensembl IDs. In each study we located where proteomic results intersected to determine the 20 most frequently identified stone matrix proteins. We used the Human Protein Atlas to obtain the biological information of the 20 proteins and conducted Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genome (KEGG) analysis to explore their biological functions. We also performed immunohistochemistry to detect the expression of the top five stone matrix proteins in renal tissue.ResultsWe included 19 relevant studies for analysis. We then identified 1,409 proteins in the stone matrix after the duplicates were removed. The 20 most-commonly identified stone matrix proteins were: S100A8, S100A9, uromodulin, albumin, osteopontin, lactotransferrin, vitamin K-dependent protein Z, prothrombin, hemoglobin subunit beta, myeloperoxidase, mannan-binding lectin serine protease 2, lysozyme C, complement C3, serum amyloid P-component, cathepsin G, vitronectin, apolipoprotein A-1, eosinophil cationic protein, fibrinogen alpha chain, and apolipoprotein D. GO and KEGG analysis revealed that these proteins were typically engaged in inflammation and immune response.Immunohistochemistry of the top five stone matrix proteins in renal tissue showed that the expression of S100A8, S100A9, and osteopontin increased, while uromodulin decreased in kidney stone patients. Albumin was rarely expressed in the kidney with no significant difference between healthy controls and kidney stone patients.ConclusionProteomic analysis revealed some common inflammation-related proteins in the kidney stone matrix. The role of these proteins in stone formation should be explored for their potential use as diagnostic biomarkers and therapeutic targets for urolithiasis. creator: Yuanyuan Yang creator: Senyuan Hong creator: Cong Li creator: Jiaqiao Zhang creator: Henglong Hu creator: Xiaolong Chen creator: Kehua Jiang creator: Fa Sun creator: Qing Wang creator: Shaogang Wang uri: https://doi.org/10.7717/peerj.11872 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Yang et al. title: HepGentox: a novel promising HepG2 reportergene-assay for the detection of genotoxic substances in complex mixtures link: https://peerj.com/articles/11883 last-modified: 2021-07-27 description: BackgroundIn risk assessment, genotoxicity is a key factor to determine the safety for the consumer. Most in vitro genotoxicity assays were developed for the assessment of pure substances. However, in recent years more attention has been given to complex mixtures, where usually low amounts of a substance are present. For high-throughput screening, a toxicologically sensitive assay should be used, covering a broad range of genotoxic substances and detecting them at low concentrations. HepG2 cells have been recommended as one of the prime candidates for genotoxicity testing, as they are p53 competent, less prone towards cytotoxic effects and tend to have some metabolic activity.MethodsA HepG2 liver cell line was characterized for its suitability for genotoxicity assessment. For this, a luciferase based reporter gene assay revolving around the p53 pathway was validated for the analysis of pure substances and of complex mixtures. Further, the cell’s capability to detect genotoxins correctly with and without an exogenous metabolizing system, namely rat liver S9, was assessed.ResultsThe assay proved to have a high toxicological sensitivity (87.5%) and specificity (94%). Further, the endogenous metabolizing system of the HepG2 cells was able to detect some genotoxins, which are known to depend on an enzymatic system. When complex mixtures were added this did not lead to any adverse effects concerning the assays performance and cytotoxicity was not an issue.DiscussionThe HepGentox proved to have a high toxicological sensitivity and specificity for the tested substances, with similar or even lower lowest effective concentration (LEC) values, compared to other regulatory mammalian assays. This combines some important aspects in one test system, while also being less time and material consuming and covering several genotoxicity endpoints. As the assay performs well with and without an exogenous metabolizing system, no animal liver fractions have to be used, which application is discussed controversially and is considered to be expensive and laborious in sample testing. Because of this, the HepGentox is suitable for a cost-efficient first screening approach to obtain important information with human cells for further approaches, with a relatively fast and easy method. Therefore, the HepGentox is a promising assay to detect genotoxic substances correctly in complex mixtures even at low concentrations, with the potential for a high throughput application. In a nutshell, as part of an in vitro bioassay test battery, this assay could provide valuable information for complex mixtures. creator: Elisabeth Pinter creator: Christina Friedl creator: Alexandra Irnesberger creator: Thomas Czerny creator: Tina Piwonka creator: Alfonso Peñarroya creator: Manfred Tacker creator: Elisabeth Riegel uri: https://doi.org/10.7717/peerj.11883 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Pinter et al. title: Between darkness and light: spring habitats provide new perspectives for modern researchers on groundwater biology link: https://peerj.com/articles/11711 last-modified: 2021-07-26 description: Springs are interfaces between groundwater and surface habitats and may play an important role in the study of subterranean animals. In this systematic evidence review and meta-analysis, we explore whether observations of stygobionts in springs are relevant and more common than observations of epigean animals in groundwater. We searched the Web of Science database for papers on groundwater fauna and spring fauna. For each paper we found, we recorded whether the paper reported the occurrence of typical stygobionts in springs, of surface animals in groundwater, or of the same taxa in both habitats. If so, we recorded how many such species were reported. We also recorded the scientific discipline of each study and the year of publication. Our search yielded 342 papers. A considerable number of these papers reported stygobionts in springs: 20% of papers dealing with groundwater fauna and 16% of papers dealing with spring fauna reported the occurrence of stygobionts in spring habitats. Both the number of papers that mentioned stygobionts in springs, and the number of stygobiont species that were documented in springs, were higher than equivalent measures for the occurrence of surface fauna underground. We also detected a positive relationship between year of publication and the number of reports of stygofauna in springs. To broaden the insights from biological research on underground environments, we suggest that springs should be considered not only as simple sampling points of stygobionts but also as core stygobiont habitats. creator: Raoul Manenti creator: Beatrice Piazza uri: https://doi.org/10.7717/peerj.11711 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Manenti and Piazza title: Genomics pipelines to investigate susceptibility in whole genome and exome sequenced data for variant discovery, annotation, prediction and genotyping link: https://peerj.com/articles/11724 last-modified: 2021-07-26 description: Over the last few decades, genomics is leading toward audacious future, and has been changing our views about conducting biomedical research, studying diseases, and understanding diversity in our society across the human species. The whole genome and exome sequencing (WGS/WES) are two of the most popular next-generation sequencing (NGS) methodologies that are currently being used to detect genetic variations of clinical significance. Investigating WGS/WES data for the variant discovery and genotyping is based on the nexus of different data analytic applications. Although several bioinformatics applications have been developed, and many of those are freely available and published. Timely finding and interpreting genetic variants are still challenging tasks among diagnostic laboratories and clinicians. In this study, we are interested in understanding, evaluating, and reporting the current state of solutions available to process the NGS data of variable lengths and types for the identification of variants, alleles, and haplotypes. Residing within the scope, we consulted high quality peer reviewed literature published in last 10 years. We were focused on the standalone and networked bioinformatics applications proposed to efficiently process WGS and WES data, and support downstream analysis for gene-variant discovery, annotation, prediction, and interpretation. We have discussed our findings in this manuscript, which include but not are limited to the set of operations, workflow, data handling, involved tools, technologies and algorithms and limitations of the assessed applications. creator: Zeeshan Ahmed creator: Eduard Gibert Renart creator: Saman Zeeshan uri: https://doi.org/10.7717/peerj.11724 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Ahmed et al. title: Clinical and perinatal outcomes of fresh single-blastocyst-transfer cycles under an early follicular phase prolonged protocol according to day of trigger estradiol levels link: https://peerj.com/articles/11785 last-modified: 2021-07-26 description: BackgroudThis study’s objectives were to compare the clinical, perinatal, and obstetrical outcomes of patients with different estradiol (E2) levels in fresh single-blastocyst-transfer (SBT) cycles under an early follicular phase prolonged regimen on the day of trigger.MethodsWe recruited patients in fresh SBT cycles (n = 771) undergoing early follicular phase prolonged protocols with β-hCG values above 10 IU/L between June 2016 and December 2018. Patients who met the inclusion and exclusion criteria were divided into four groups according to their serum E2 level percentages on the day of trigger: <25th, 25th–50th, 51st–75th, and >75th percentile groups.ResultsAlthough the rates of clinical pregnancy (85.57% (166/194)), embryo implantation 86.60% (168/194), ongoing pregnancy (71.13% (138/194)), and live birth (71.13% (138/194)) were lowest in the >75th percentile group, we did not observe any significant differences (all P > 0.05). We used this information to predict the rate of severe ovarian hyperstimulation syndrome (OHSS) area under the curve (AUC) = 72.39%, P = 0.029, cut off value of E2 = 2,893 pg/ml with the 75% sensitivity and 70% specificity. The 51st–75th percentile group had the highest rates of low birth weight infants (11.73% (19/162), P = 0.0408), premature delivery (11.43% (20/175), P = 0.0269), admission to the neonatal intensive care unit (NICU) (10.49% (17/162), P = 0.0029), twin pregnancies (8.57% (15/175), P = 0.0047), and monochorionic diamniotic pregnancies (8.57% (15/175); P = 0.001). We did not observe statistical differences in obstetrics complications, including gestational diabetes mellitus (GDM), gestational hypertension, placenta previa, premature rupture of membranes (PROM), and preterm premature rupture of membranes (PPROM).ConclusionWe concluded that serum E2 levels on the day of trigger were not good predictors of live birth rate or perinatal and obstetrical outcomes. However, we found that high E2 levels may not be conducive to persistent pregnancies. The E2 level on the day of trigger can still be used to predict the incidence of early onset severe OHSS in the fresh SBT cycle. creator: Yingfen Ying creator: Xiaosheng Lu creator: Huina Zhang creator: Samuel Kofi Arhin creator: Xiaohong Hou creator: Zefan Wang creator: Han Wu creator: Jieqiang Lu creator: Yunbing Tang uri: https://doi.org/10.7717/peerj.11785 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Ying et al. title: Responses of nitrogen efficiency and antioxidant system of summer maize to waterlogging stress under different tillage link: https://peerj.com/articles/11834 last-modified: 2021-07-26 description: Waterlogging was one of the main abiotic stresses affecting maize yield and growth in the North China Plain, while ridge tillage effectually improved soil environment, enhanced crop stress resistance to waterlogging, and increased grain yield of waterlogged maize. In order to explore the responses of nitrogen (N) efficiency and antioxidant system of summer maize to waterlogging stress under different tillage, a field experiment was conducted to explore N use efficiency, leaf activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), and malondialdehyde (MDA) content of waterlogged maize Denghai 605 (DH605) and Zhengdan 958 (ZD958) under different tillage system (ridge planting and flat planting). Our results showed that ridge tillage was beneficial to ameliorate waterlogging damages on antioxidant system by increasing SOD, POD, and CAT activities, and decreasing MDA content. Moreover, ridge tillage significantly increased N efficiency of waterlogged maize. N translocation amount (NTA), N translocation efficiency (NTE), N contribution proportion (NCP), N harvest index (NHI), and N use efficiency (NUE) of waterlogging treatment under ridge planting system (W-V3+R) for DH605 was increased by 108%, 69%, 60%, 8% and 16%, while ZD958 increased by 248%, 132%, 146%, 13% and 16%, respectively, compared to those of waterlogging treatment under flat planting system (W-V3). Ultimately, ridge tillage led to a significant yield improvement by 39% and 50% for DH605 and ZD958, respectively, compared to that of W-V3. In conclusion, ridge tillage was conducive to retard leaf aging, and enhance nitrogen efficiency, thereby resulting in a yield improvement of waterlogged summer maize. creator: Baizhao Ren creator: Juan Hu creator: Peng Liu creator: Bin Zhao creator: Jiwang Zhang uri: https://doi.org/10.7717/peerj.11834 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Ren et al. title: A bright idea—metabarcoding arthropods from light fixtures link: https://peerj.com/articles/11841 last-modified: 2021-07-26 description: Arthropod communities in buildings have not been extensively studied, although humans have always shared their homes with them. In this study we explored if arthropod DNA can be retrieved and metabarcoded from indoor environments through the collection of dead specimens in light fixtures to better understand what shapes arthropod diversity in our homes. Insects were collected from 45 light fixtures at the Centre for Biodiversity Genomics (CBG, Guelph, Canada), and by community scientists at 12 different residential homes in Southern Ontario. The CBG ground floor of the CBG showed the greatest arthropod diversity, especially in light fixtures that were continuously illuminated. The community scientist samples varied strongly by light fixture type, lightbulb used, time passed since lamp was last cleaned, and specimen size. In all cases, the majority of OTUs was not shared between samples even within the same building. This study demonstrates that light fixtures might be a useful resource to determine arthropod diversity in our homes, but individual samples are likely not representative of the full diversity. creator: Vasco Elbrecht creator: Angie Lindner creator: Laura Manerus creator: Dirk Steinke uri: https://doi.org/10.7717/peerj.11841 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Elbrecht et al. title: Nurses’ knowledge, attitude, and competence regarding palliative and end-of-life care: a path analysis link: https://peerj.com/articles/11864 last-modified: 2021-07-26 description: BackgroundNurses’ knowledge regarding palliative and end-of-life (EOL) care has been documented, but the competence of nurses in Taiwan has not been deeply analyzed and may affect the use of EOL care.PurposeWe aimed to (1) assess the palliative care knowledge, competence and attitude of nurses in a general hospital and (2) examine the paths connecting nurses’ demographic characteristics, previous experiences, knowledge, competence, and attitude.MethodA correlational, cross-sectional survey design was implemented to recruit 682 eligible nurses. The questionnaires included demographic information and palliative and EOL care knowledge, attitude, and competence scales. Path analysis was employed for statistical analysis using structural equation modeling.ResultsOverall, 76% of the questions assessing palliative and hospice knowledge were answered correctly. Nurses’ palliative attitudes were divided into “positive perception” and “negative perception”. “Positive perception” was highly correlated with competence (r = 0.48, p < 0.001), but “negative perception” was not significantly correlated with competence (r = −0.07, p = 0.25). “Positive perception” (β =  −0.01, p = 0.84) and competence (β =  0.02, p = 0.80) were not related to palliative knowledge. “Negative perception”, however, was negatively associated with palliative knowledge (β =  −0.20, p < 0.01).ConclusionsThis study suggests continuing education to decrease nurses’ “negative perception” attitude regarding the provision of information to patients and families to provide better palliative and EOL care.Implications for PracticeNurses’ attitudes and competences with respect to palliative care and EOL care are critical. Areas for further research and advanced palliative and EOL care-related education and training are suggested and may be applied in future clinical interventions. creator: Hung-Yu Lin creator: Chun-I Chen creator: Chu-Yun Lu creator: Shu-Chuan Lin creator: Chiung-Yu Huang uri: https://doi.org/10.7717/peerj.11864 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Lin et al. title: ensembleTax: an R package for determinations of ensemble taxonomic assignments of phylogenetically-informative marker gene sequences link: https://peerj.com/articles/11865 last-modified: 2021-07-26 description: BackgroundHigh-throughput sequencing of phylogenetically informative marker genes is a widely used method to assess the diversity and composition of microbial communities. Taxonomic assignment of sampled marker gene sequences (referred to as amplicon sequence variants, or ASVs) imparts ecological significance to these genetic data. To assign taxonomy to an ASV, a taxonomic assignment algorithm compares the ASV to a collection of reference sequences (a reference database) with known taxonomic affiliations. However, many taxonomic assignment algorithms and reference databases are available, and the optimal algorithm and database for a particular scientific question is often unclear. Here, we present the ensembleTax R package, which provides an efficient framework for integrating taxonomic assignments predicted with any number of taxonomic assignment algorithms and reference databases to determine ensemble taxonomic assignments for ASVs.MethodsThe ensembleTax R package relies on two core algorithms: taxmapper and assign.ensembleTax. The taxmapper algorithm maps taxonomic assignments derived from one reference database onto the taxonomic nomenclature (a set of taxonomic naming and ranking conventions) of another reference database. The assign.ensembleTax algorithm computes ensemble taxonomic assignments for each ASV in a data set based on any number of taxonomic assignments determined with independent methods. Various parameters allow analysts to prioritize obtaining either more ASVs with more predicted clade names or more robust clade name predictions supported by multiple independent methods in ensemble taxonomic assignments.ResultsThe ensembleTax R package is used to compute two sets of ensemble taxonomic assignments for a collection of protistan ASVs sampled from the coastal ocean. Comparisons of taxonomic assignments predicted by individual methods with those predicted by ensemble methods show that conservative implementations of the ensembleTax package minimize disagreements between taxonomic assignments predicted by individual and ensemble methods, but result in ASVs with fewer ranks assigned taxonomy. Less conservative implementations of the ensembleTax package result in an increased fraction of ASVs classified at all taxonomic ranks, but increase the number of ASVs for which ensemble assignments disagree with those predicted by individual methods.DiscussionWe discuss how implementation of the ensembleTax R package may be optimized to address specific scientific objectives based on the results of the application of the ensembleTax package to marine protist communities. While further work is required to evaluate the accuracy of ensemble taxonomic assignments relative to taxonomic assignments predicted by individual methods, we also discuss scenarios where ensemble methods are expected to improve the accuracy of taxonomy prediction for ASVs. creator: Dylan Catlett creator: Kevin Son creator: Connie Liang uri: https://doi.org/10.7717/peerj.11865 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Catlett et al. title: How C: N: P stoichiometry in soils and carbon distribution in plants respond to forest age in a Pinus tabuliformis plantation in the mountainous area of eastern Liaoning Province, China link: https://peerj.com/articles/11873 last-modified: 2021-07-26 description: Carbon distribution in plants and ecological stoichiometry in soils are important indicators of element cycling and ecosystem stability. In this study, five forest ages, young forest (YF), middle-aged forest (MAF), near-mature forest (NMF), mature forest (MF), and over-mature forest (OMF) in a Pinus tabuliformis plantation were chosen to illustrate interactions among the C: N: P stoichiometry in soils and carbon distribution in plants, in the mountainous area of eastern Liaoning, China. Carbon content was highest in the leaves of MAF (505.90 g⋅kg−1) and NMF (509.00 g⋅kg−1) and the trunks of YF (503.72 g⋅kg−1), MF (509.73 g⋅kg−1), and OMF (504.90 g⋅kg−1), and was lowest in the branches over the entire life cycle of the aboveground components (335.00 g⋅kg−1). The carbon content of the fine roots decreased with soil layer depth. In YF, MAF, and NMF carbon content of fine roots at 0.5 m was always higher than that of fine roots at 1 m; however, it was the opposite in MF and OMF. The carbon content of the leaves changed with forest age; however, carbon content of branches, trunks and fine roots did not change significantly. Soil total carbon (TC), total nitrogen (TN), total phosphorus (TP), and available phosphorus (AP) content was highest in the OMF. Soil TC, TN and AP content, and TC: TN, TC: TP and TN: TP ratio decreased with increasing soil depth. Soil TC, TN, and TP content had a significant effect on the carbon content of fine roots (p < 0.05). The leaf carbon content and soil element content changed obviously with forest age, and the soil TN, TP and AP increased, which might reduce the carbon content allocation of fine roots. creator: Lijiao Wang creator: Xin Jing creator: Jincheng Han creator: Lei Yu creator: Yutao Wang creator: Ping Liu uri: https://doi.org/10.7717/peerj.11873 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Wang et al. title: Inter-ethnic genetic variations and novel variant identification in the partial sequences of CYP2B6 gene in Pakistani population link: https://peerj.com/articles/11149 last-modified: 2021-07-23 description: BackgroundSome single nucleotide polymorphisms (SNPs) in the cytochrome P450 (CYP)2B6 gene lead to decreased enzyme activity and have an impact on drug metabolism. The present study was designed to investigate the patterns of genetic distinction across a hypervariable region of the CYP2B6 gene, known to contain important SNPs, i.e. rs4803419 and rs3745274, among five major ethnic groups of the Pakistani population.MethodsArlequin v3.5.DnaSPv6.12. and network 5 resources were used to analyze population genetic variance in the partial CYP2B6 gene sequences obtained from 104 human samples belonging to Punjabi, Pathan, Sindhi, Seraiki and Baloch ethnicities of Pakistan. The partial CYP2B6 gene region analyzed in the current study is previously known to possess important SNPs.ResultsThe data analyses revealed that genetic variance among samples mainly came from differentiation within the ethnic groups. However, significant genetic variation was also found among the various ethnic groups. The high pairwise Fst genetic distinction was observed between Seraiki and Sindhi ethnic groups (Fst = 0.13392, P-value = 0.026) as well as between Seraiki and Balochi groups (Fst = 0.04303, P-value = −0.0030). However, the degree of genetic distinction was low between Pathan and Punjabi ethnic groups. Some SNPs, including rs3745274 and rs4803419, which are previously shown in strong association with increased plasma Efavirenz level, were found in high frequency. Besides, a novel SNP, which was not found in dbSNP and Ensemble databases, was identified in the Balochi ethnicity. This novel SNP is predicted to affect the CYP2B6 splicing pattern.ConclusionThese results may have significant implications in Pakistani ethnicities in the context of drugs metabolized by CYP2B6, especially in Seraiki and Balochi ethnicity. The novel heterogeneous SNP, found in the present study, might lead to altered drug-metabolizing potential of CYP2B6 and, therefore, may be implicated in non-responder phenomenon. creator: Sagheer Ahmed creator: Hizbullah Khan creator: Asifullah Khan creator: Muhammad Hanif Bangash creator: Abrar Hussain creator: Mughal Qayum creator: Mohammad Hamid Hamdard uri: https://doi.org/10.7717/peerj.11149 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Ahmed et al. title: Phenotypic plasticity and evolution of thermal tolerance in bacteria from temperate and hot spring environments link: https://peerj.com/articles/11734 last-modified: 2021-07-23 description: Phenotypic plasticity allows individuals to respond to the selective forces of a new environment, followed by adaptive evolution. We do not know to what extent phenotypic plasticity allows thermal tolerance evolution in bacteria at the border of their physiological limits. We analyzed growth and reaction norms to temperature of strains of two bacterial lineages, Bacillus cereus sensu lato and Bacillus subtilis sensu lato, that evolved in two contrasting environments, a temperate lagoon (T) and a hot spring (H). Our results showed that despite the co-occurrence of members of both lineages in the two contrasting environments, norms of reactions to temperature exhibited a similar pattern only in strains within the lineages, suggesting fixed phenotypic plasticity. Additionally, strains from the H environment showed only two to three degrees centigrade more heat tolerance than strains from the T environment. Their viability decreased at temperatures above their optimal for growth, particularly for the B. cereus lineage. However, sporulation occurred at all temperatures, consistent with the known cell population heterogeneity that allows the Bacillus to anticipate adversity. We suggest that these mesophilic strains survive in the hot-spring as spores and complete their life cycle of germination and growth during intermittent opportunities of moderate temperatures. The limited evolutionary changes towards an increase in heat tolerance in bacteria should alert us of the negative impact of climate change on all biological cycles in the planet, which at its most basic level depends on microorganisms. creator: Enrique Hurtado-Bautista creator: Laura F. Pérez Sánchez creator: Africa Islas-Robles creator: Gustavo Santoyo creator: Gabriela Olmedo-Alvarez uri: https://doi.org/10.7717/peerj.11734 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Hurtado-Bautista et al. title: Impacts of heat stress and storm events on the benthic communities of Kenting National Park (Taiwan) link: https://peerj.com/articles/11744 last-modified: 2021-07-23 description: Over the past few decades, extreme events—such as ocean warming, typhoons, and coral bleaching—have been increasing in intensity and frequency, threatening coral reefs from the physiological to ecosystem level. In the present study, the impacts of rising seawater temperatures, typhoons, and coral bleaching events on benthic communities were seasonally assessed over a 21 month-period, using photo-transects at 11 sites in Kenting National Park (KNP), Taiwan. Between August 2015 and April 2017, seven typhoon events were recorded and in situ seawater temperatures in KNP reached a maximum of 31.2 °C, as opposed to an average maximum SST of 28.8 °C (2007–2016). The state and response of benthic communities to these events were interpreted based on the environmental conditions of KNP. The repeated storms lowered the levels of thermal stress during the 2015–2016 El Niño event and may have mitigated its impact on the Taiwanese coral reefs. However, storm-induced local shifts from coral to macro-algae dominance were observed. Storms may mitigate the negative effects of heatwaves, but the mechanical damage induced by the storms may also decrease the structural complexity of reefs and their associated diversity. Eventually, despite reef persistence, the composition and function of remnant communities may profoundly diverge from those in regions with less active storms. creator: Lauriane Ribas-Deulofeu creator: Vianney Denis creator: Pierre-Alexandre Château creator: Chaolun Allen Chen uri: https://doi.org/10.7717/peerj.11744 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Ribas-Deulofeu et al. title: Furongian (Jiangshanian) occurrences of radiodonts in Poland and South China and the fossil record of the Hurdiidae link: https://peerj.com/articles/11800 last-modified: 2021-07-23 description: The Furongian period represents an important gap in the fossil record of most groups of non-biomineralizing organisms, owing to a scarcity of Konservat-Lagerstätten of that age. The most significant of these deposits, the Jiangshanian strata of the Sandu Formation near Guole Township (Guangxi, South China), have yielded a moderately abundant, but taxonomically diverse soft-bodied fossil assemblage, which provides rare insights into the evolution of marine life at that time. In this contribution, we report the first discovery of a radiodont fossil from the Guole Konservat-Lagerstätte. The specimen is an incomplete frontal appendage of a possibly new representative of the family Hurdiidae. It is tentatively interpreted as composed of seven podomeres, six of which bearing laminiform endites. The best preserved of these endites is especially long, and it bears short auxiliary spines that greatly vary in size. This is the second occurrence of hurdiids and more generally radiodonts in the Furongian, the first being the external mould of an oral cone from Jiangshanian strata of the Wiśniówka Sandstone Formation in Poland. Restudy of this Polish specimen confirms that it belongs to a hurdiid radiodont and best compares to Peytoia. The family Hurdiidae includes the oldest (basal Cambrian Epoch 2) and youngest (Early Ordovician, possibly Early Devonian) representatives of the Radiodonta and as such, has the longest stratigraphical range of the group. Yet, hurdiids only became prominent components of marine ecosystems during the middle Cambrian (Miaolingian), and their fossil record in younger strata remains limited. creator: Xuejian Zhu creator: Rudy Lerosey-Aubril creator: Javier Ortega-Hernández uri: https://doi.org/10.7717/peerj.11800 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zhu et al. title: LncRNA NEAT1 regulated diabetic retinal epithelial-mesenchymal transition through regulating miR-204/SOX4 axis link: https://peerj.com/articles/11817 last-modified: 2021-07-23 description: AimEpithelial-mesenchymal transition (EMT) of retinal pigment epithelium (RPE) cells is the key of the development of diabetic retinopathy (DR), and lncRNA NEAT1 could accelerate EMT in diabetic nephropathy. Meanwhile, as a diabetes susceptibility gene, whether sex-determining region Y-related (SRY) high-mobility group box 4 (SOX4) has relationship with lncRNA NEAT1 in DR remains unclear.MethodsFirstly, NEAT1, SOX4 and miR-204 were evaluated by qRT-PCR (quantitative reverse-transcriptase PCR) under high glucose condition. Then, cell viability, proliferation, migration and invasion were respectively detected by MTT, BrdU staining, wound healing and transwell assay after NEAT1 knockdown or miR-204 overexpression. Also, the EMT-related proteins were examined by western blot and cell immunofluorescence assay. In order to confirm the relationship between miR-204 and NEAT1 or SOX4, dual luciferase reporter gene assay was conducted. At the same time, the protein levels of SOX4 and EMT-related proteins were investigated by immunohistochemistry in vivo.ResultsHigh glucose upregulated NEAT1 and SOX4 and downregulated miR-204 in ARPE19 cells. NEAT1 knockdown or miR-204 overexpression inhibited the proliferation and EMT progression of ARPE19 cells induced by high glucose. NEAT1 was identified as a molecular sponge of miR-204 to increase the level of SOX4. The effect of NEAT1 knockdown on the progression of EMT under high glucose condition in ARPE19 cells could be reversed by miR-204 inhibitor. Also, NEAT1 knockdown inhibited retinal EMT in diabetic mice.ConclusionNEAT1 regulated the development of EMT in DR through miR-204/SOX4 pathway, which could provide reference for clinical prevention and treatment. creator: Yang Yang creator: Jing Zhou creator: Wei hong Li creator: Zhi xiong Zhou creator: Xiao bo Xia uri: https://doi.org/10.7717/peerj.11817 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Yang et al. title: How fish traits and functional diversity respond to environmental changes and species invasion in the largest river in Southeastern China link: https://peerj.com/articles/11824 last-modified: 2021-07-23 description: BackgroundFreshwater fish populations are facing multiple stressors, including climate change, species invasion, and anthropogenic interference. Temporal studies of fish functional diversity and community assembly rules based on trait-environment relationships provide insights into fish community structure in riverine ecosystems.MethodsFish samples were collected in 2015 in the Min River, the largest freshwater riverine system in Southeastern China. Fish functional diversity was compared with the background investigation in 1979. Changes in functional richness, functional evenness, functional divergence, and functional beta diversity were analyzed. Relationships between functional diversity and environmental factors were modeled by random forest regression. Correlations between fish functional traits and environmental factors were detected by fourth-corner combined with RLQ analysis.ResultsFunctional richness was significantly reduced in 2015 compared with 1979. Functional beta diversity in 2015 was significantly higher than that in 1979, with functional nestedness being the driving component. Reduction of functional richness and domination of functional nestedness is associated with species loss. Trait convergence was the dominant mechanism driving the temporal changes of functional diversity. Precipitation, temperature, species invasion, and human population were the most significant factors driving fish functional diversity. Higher precipitation, higher temperature, and presence of invasive species were significantly associated with higher swimming factor and higher relative eye diameter, while the opposite environmental conditions were significantly associated with higher pectoral fin length and eurytopic water flow preference.ConclusionsEnvironmental filtering is the dominant temporal assembly mechanism shaping fish community structure. This work contributes to the understanding of temporal freshwater fish community assembly and the associations between fish functional structure and local environmental conditions, which will be informative for future freshwater fish conservation. creator: Li Lin creator: Weide Deng creator: Xiaoxia Huang creator: Yang Liu creator: Liangliang Huang creator: Bin Kang uri: https://doi.org/10.7717/peerj.11824 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Lin et al. title: Assessing the quantitative relationships between the impervious surface area and surface heat island effect during urban expansion link: https://peerj.com/articles/11854 last-modified: 2021-07-23 description: As an important component of underlying urban surfaces, the distribution pattern and density of the impervious surface area (ISA) play an important role in the generation of surface urban heat island (SUHI) effects. However, the quantitative and localized exploration of the ISA’s influence on SUHIs in the process of urban expansion from the perspective of temporal and spatial changes is still not clear. Based on multisource remote sensing data, the SUHI effect of urban expansion is revealed by using geospatial analysis methods such as profile, difference and regression analysis. The results show the following: (1) urban expansion plays a significant role in aggravating SUHIs. Overall, the ISA and land surface temperature (LST) have obvious consistency in terms of spatial distribution patterns. However, local spatial differentiation is significant. The areas with the highest LST were not concentrated in the downtown area with the highest ISA but were scattered in the cultivated land and exposed surface areas under development in the northern part of the city. (2) In general, the ISA can explain the spatial distribution of LST well, there is an obvious positive correlation between them, and the quadratic polynomial function is the best fitting model between them. (3) The density and spatial allocation of ecological elements, such as green space and water bodies, play an important role in alleviating SUHIs. This study found that the urban center with the highest ISA coverage rate has no significant SUHI due to the reasonable allocation of green space and water bodies. The research results can provide a scientific basis for future urban planning and ecological environment construction. creator: Xiaoliang Ma creator: Shuangyun Peng uri: https://doi.org/10.7717/peerj.11854 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Ma and Peng title: Genome-wide identification of alcohol dehydrogenase (ADH) gene family under waterlogging stress in wheat (Triticum aestivum) link: https://peerj.com/articles/11861 last-modified: 2021-07-23 description: BackgroundAlcohol dehydrogenase (ADH) plays an important role in plant survival under anaerobic conditions. Although some research about ADH in many plants have been carried out, the bioinformatics analysis of the ADH gene family from Triticum aestivum and their response to abiotic stress is unclear.MethodsA total of 22 ADH genes were identified from the wheat genome, and these genes could be divided into two subfamilies (subfamily I and subfamily II). All TaADH genes belonged to the Medium-chain ADH subfamily. Sequence alignment analysis showed that all TaADH proteins contained a conservative GroES-like domain and Zinc-binding domain. A total of 64 duplicated gene pairs were found, and the Ka/Ks value of these gene pairs was less than 1, which indicated that these genes were relatively conservative and did not change greatly in the process of duplication.ResultsThe organizational analysis showed that nine TaADH genes were highly expressed in all organs, and the rest of TaADH genes had tissue specificity. Cis-acting element analysis showed that almost all of the TaADH genes contained an anaerobic response element. The expression levels of ADH gene in waterlogging tolerant and waterlogging sensitive wheat seeds were analyzed by quantitative real-time PCR (qRT-PCR). This showed that some key ADH genes were significantly responsive to waterlogging stress at the seed germination stage, and the response of waterlogging tolerant and waterlogging sensitive wheat seeds to waterlogging stress was regulated by different ADH genes. The results may be helpful to further study the function of TaADH genes and to determine the candidate gene for wheat stress resistance breeding. creator: Changwei Shen creator: Jingping Yuan creator: Xingqi Ou creator: Xiujuan Ren creator: Xinhua Li uri: https://doi.org/10.7717/peerj.11861 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Shen et al. title: Effects of step length and cadence on hip moment impulse in the frontal plane during the stance phase link: https://peerj.com/articles/11870 last-modified: 2021-07-23 description: BackgroundAn excessive daily cumulative hip moment in the frontal plane (determined as the product of hip moment impulse in the frontal plane during the stance phase and mean number of steps per day) is a risk factor for the progression of hip osteoarthritis. Moreover, walking speed and step length decrease, whereas cadence increases in patients with hip osteoarthritis. However, the effects of step length and cadence on hip moment impulse in the frontal plane during the stance phase are not known. Therefore, this study aimed to examine the effects of step length and cadence on hip moment impulse in the frontal plane during the stance phase.MethodsWe used a public dataset (kinetic and kinematic data) of over-ground walking and selected 31 participants randomly from the full dataset of 57 participants. The selected participants walked at a self-selected speed and repeated the exercise 15 times. We analyzed the data for all 15 trials for each participant. Multiple regression analysis was performed with the hip moment impulse in the frontal plane during the stance phase as the dependent variable and step length and cadence as independent variables.ResultsThe adjusted R2 in this model was 0.71 (p < 0.001). The standardized partial regression coefficients of step length and cadence were 0.63 (t = 5.24; p < 0.001) and −0.60 (t =  − 4.58; p < 0.001), respectively.ConclusionsOur results suggest that low cadence, not short step length, increases the hip moment impulse in the frontal plane. Our findings help understand the gait pattern with low hip moment impulse in the frontal plane. creator: Takuma Inai creator: Tomoya Takabayashi creator: Mutsuaki Edama creator: Masayoshi Kubo uri: https://doi.org/10.7717/peerj.11870 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Inai et al. title: Detection of genomic regions associated malformations in newborn piglets: a machine-learning approach link: https://peerj.com/articles/11580 last-modified: 2021-07-22 description: BackgroundA significant proportion of perinatal losses in pigs occurs due to congenital malformations. The purpose of this study is the identification of genomic loci associated with fetal malformations in piglets.MethodsThe malformations were divided into two groups: associated with limb defects (piglet splay leg) and associated with other congenital anomalies found in newborn piglets. 148 Landrace and 170 Large White piglets were selected for the study. A genome-wide association study based on the gradient boosting machine algorithm was performed to identify markers associated with congenital anomalies and piglet splay leg.ResultsForty-nine SNPs (23 SNPs in Landrace pigs and 26 SNPs in Large White) were associated with congenital anomalies, 22 of which were localized in genes. A total of 156 SNPs (28 SNPs in Landrace; 128 in Large White) were identified for piglet splay leg, of which 79 SNPs were localized in genes. We have demonstrated that the gradient boosting machine algorithm can identify SNPs and their combinations associated with significant selection indicators of studied malformations and productive characteristics.Data availabilityGenotyping and phenotyping data are available at http://www.compubioverne.group/data-and-software/. creator: Siroj Bakoev creator: Aleksei Traspov creator: Lyubov Getmantseva creator: Anna Belous creator: Tatiana Karpushkina creator: Olga Kostyunina creator: Alexander Usatov creator: Tatiana V. Tatarinova uri: https://doi.org/10.7717/peerj.11580 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Bakoev et al. title: Variation in the skulls of Elgaria and Gerrhonotus (Anguidae, Gerrhonotinae) and implications for phylogenetics and fossil identification link: https://peerj.com/articles/11602 last-modified: 2021-07-22 description: BackgroundThere are limited data on intra- and interspecific osteological variation for many squamate clades. Those data are relevant for phylogenetic analyses that use osteological characters and for apomorphic identifications of fossils. We investigate whether morphological features in the skulls of extant gerrhonotine lizards can be used to distinguish taxa at the species- and genus-level and assess whether newly discovered intra- and interspecific osteological variation alters the utility of previously reported apomorphic features. We examined skulls of species belonging to the gerrhonotine genera Elgaria and Gerrhonotus. These genera contain 17 extant species, but the cranial osteology of only a few species was previously examined. As a result, intra- and interspecific osteological variation of these gerrhonotines is poorly understood.MethodsWe employed high-resolution x-ray computed tomography (CT) to scan 25 alcohol-preserved specimens. We provide data on the skulls of all eight species of Elgaria, four for the first time, and five species of Gerrhonotus, three for the first time. We examined 3-D reconstructed skulls of the scanned specimens as well as dry, traditionally prepared skeletons (when they were available).ResultsWe found that the purported diagnostic utility of many previously described morphological features is impacted because of substantial morphological variation between and within species. We present an assessment of osteological differences that may be useful to differentiate species of Elgaria and Gerrhonotus, many of which are present on isolated cranial elements commonly recovered as fossils, including the premaxilla, maxilla, parietal, pterygoid, prootic, dentary, and surangular. We demonstrate the importance of documenting patterns of osteological variation using large sample sizes, and the utility of examining disarticulated cranial elements of the squamate skull to identify diagnostic morphology. This study adds to a growing body of literature suggesting that extensive documentation of morphological variation is needed to further our understanding of the phylogenetic and diagnostic utility of morphological features across vertebrate clades. Efforts in that direction likely will benefit from examination of disarticulated skeletal elements. creator: David T. Ledesma creator: Simon G. Scarpetta creator: Christopher J. Bell uri: https://doi.org/10.7717/peerj.11602 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Ledesma et al. title: Comparative anatomy of the middle ear in some lizard species with comments on the evolutionary changes within Squamata link: https://peerj.com/articles/11722 last-modified: 2021-07-22 description: The skeleton of the middle ear of lizards is composed of three anatomical elements: columella, extracolumella, and tympanic membrane, with some exceptions that show modifications of this anatomy. The main function of the middle ear is transforming sound waves into vibrations and transmitting these to the inner ear. Most middle ear studies mainly focus on its functional aspects, while few describe the anatomy in detail. In lizards, the morphology of the columella is highly conservative, while the extracolumella shows variation in its presence/absence, size, and the number of processes present on the structure. In this work, we used diaphanized and double-stained specimens of 38 species of lizards belonging to 24 genera to study the middle ear’s morphology in a comparative framework. Results presented here indicate more variation in the morphology of the extracolumella than previously known. This variation in the extracolumella is found mainly in the pars superior and anterior processes, while the pars inferior and the posterior process are more constant in morphology. We also provide new information about the shape of gekkotan extracolumella, including traits that are diagnostic for the iguanid and gekkonid middle ear types. The data collected in this study were combined with information from published descriptive works. The new data included here refers to the length of the columella relative to the extracolumella central axis length, the general structure of the extracolumella, and the presence of the internal process. These characters were included in ancestral reconstruction analysis using Bayesian and parsimony approaches. The results indicate high levels of homoplasy in the variation of the columella-extracolumella ratio, providing a better understanding of the ratio variation among lizards. Additionally, the presence of four processes in the extracolumella is the ancestral state for Gekkota, Pleurodonta, and Xantusiidae, and the absence of the internal processes is the ancestral state for Gekkota, Gymnophthalmidae, and Scincidae; despite the fact that these groups convergently develop these character states, they could be used in combination with other characters to diagnose these clades. The posterior extension in the pars superior and an anterior process with some small and sharp projections is also a diagnostic trait for Gekkota. A more accurate description of each process of the extracolumella and its variation needs to be evaluated in a comprehensive analysis, including a greater number of species. Although the number of taxa sampled in this study is small considering the vast diversity of lizards, the results provide an overall idea of the amount of variation of the middle ear while helping to infer the evolutionary history of the lizard middle ear. creator: Paola María Sánchez-Martínez creator: Juan D. Daza creator: Julio Mario Hoyos uri: https://doi.org/10.7717/peerj.11722 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Sánchez-Martínez et al. title: Change in mental health, physical health, and social relationships during highly restrictive lockdown in the COVID-19 pandemic: evidence from Australia link: https://peerj.com/articles/11767 last-modified: 2021-07-22 description: BackgroundA novel coronavirus first reported in Wuhan City in China in 2019 (COVID-19) developed into a global pandemic throughout 2020. Many countries around the world implemented strict social distancing policies to curb the spread of the virus. In this study we aimed to examine potential change in mental/physical health and social relationships during a highly restrictive COVID-19 lockdown period in Australia during April 2020.MethodsOur survey (n = 1, 599) included questions about concerns, social behaviour, perceived change in relationship quality, social media use, frequency of exercise, physical health, and mental health during COVID-19 lockdown (April, 2020).ResultsWhen estimating their mental health for the previous year 13% of participants reported more negative than positive emotion, whereas this increased to 41% when participants reflected on their time during COVID-19 lockdown. A substantial proportion (39–54%) of participants reported deterioration in mental health, physical health, financial situation, and work productivity. However, most of these participants reported ’somewhat’ rather than ’a lot’ of deterioration, and many others reported ’no change’ (40–50%) or even ’improvement’ (6–17%). Even less impact was apparent for social relationships (68% reported ’no change’) as participants compensated for decreased face-to-face interaction via increased technology-mediated interaction.ConclusionsThe psychological toll of COVID-19 on Australians may not have been as large as other parts of the world with greater infection rates. Our findings highlight how technology-mediated communication can allow people to adequately maintain social relationships during an extreme lockdown event. creator: Shane L. Rogers creator: Travis Cruickshank uri: https://doi.org/10.7717/peerj.11767 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Rogers and Cruickshank title: Genome-wide identification and analysis of the YABBY gene family in Moso Bamboo (Phyllostachys edulis (Carrière) J. Houz) link: https://peerj.com/articles/11780 last-modified: 2021-07-22 description: BackgroundThe YABBY gene family is a family of small zinc finger transcription factors associated with plant morphogenesis, growth, and development. In particular, it is closely related to the development of polarity in the lateral organs of plants. Despite being studied extensively in many plant species, there is little information on genome-wide characterization of this gene family in Moso bamboo.MethodsIn the present study, we identified 16 PeYABBY genes, which were unequally distributed on 11 chromosomes, through genome-wide analysis of high-quality genome sequences of M oso bamboo by bioinformatics tools and biotechnological tools. Gene expression under hormone stress conditions was verified by quantitative real-time PCR (qRT-PCR) experiments.ResultsBased on peptide sequences and similarity of exon-intron structures, we classified the PeYABBY genes into four subfamilies. Analysis of putative cis-acting elements in promoters of these genes revealed that PeYABBYs contained a large number of hormone-responsive and stress-responsive elements. Expression analysis showed that they were expressed at a high level in Moso bamboo panicles, rhizomes, and leaves. Expression patterns of putative PeYABBY genes in different organs and hormone-treated were analyzed using RNA-seq data, results showed that some PeYABBY genes were responsive to gibberellin (GA) and abscisic acid (ABA), indicating that they may play an important role in plant hormone responses. Gene Ontology (GO) analyses of YABBY proteins indicated that they may be involved in many developmental processes, particularly high level of enrichment seen in plant leaf development. In summary, our results provide a comprehensive genome-wide study of the YABBY gene family in bamboos, which could be useful for further detailed studies of the function and evolution of the YABBY genes, and to provide a fundamental basis for the study of YABBY in Gramineae for resistance to stress and hormonal stress. creator: Ruifang Ma creator: Bin Huang creator: Zhinuo Huang creator: Zhijun Zhang uri: https://doi.org/10.7717/peerj.11780 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Ma et al. title: Alterations to arbuscular mycorrhizal fungal community composition is driven by warming at specific elevations link: https://peerj.com/articles/11792 last-modified: 2021-07-22 description: BackgroundGlobal warming can alter plant productivity, and community composition which has consequences for soil-plant associated microorganisms. Arbuscular mycorrhizal fungi (AMF) are distributed widely and form symbiotic relationships with more than 80% of vascular plants and play a key role in nutrient cycling processes at the ecosystem scale.MethodsA simulated warming experiment at multiple elevations (3,000, 3,500, 3,800, and 4,170 m) was conducted utilizing an in-situ open-top chamber (OTC) for exploring the effect of global warming on AMF community structure in the Qinghai-Tibet Plateau (QTP). This region has been identified as one of the most sensitive areas to climatic changes. Soil DNA was extracted and sequenced using next the Mi-Seq platform for diversity profiling.ResultsAMF richness was higher under the simulated warming chamber, however this only occurred in the elevation of 3,500 m. Warming did not alter other AMF alpha diversity indices (e.g. Shannon, Ace, and Simpson evenness index). Glomus and Acaulospora were the dominate AMF genera as assessed through their relative abundance and occurrence in control and warming treatments at the different elevations.ConclusionWarming changed significantly AMF community. The effects of warming on AMF community structure varied depend on elevations. Moreover, the occurrences of AMF in different genera were also presented the different responses to warming in four elevations. creator: Mei Yang creator: Zhaoyong Shi creator: Bede S. Mickan creator: Mengge Zhang creator: Libing Cao uri: https://doi.org/10.7717/peerj.11792 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Yang et al. title: Influenza A virus infection in turkeys induces respiratory and enteric bacterial dysbiosis correlating with cytokine gene expression link: https://peerj.com/articles/11806 last-modified: 2021-07-22 description: Turkey respiratory and gut microbiota play important roles in promoting health and production performance. Loss of microbiota homeostasis due to pathogen infection can worsen the disease or predispose the bird to infection by other pathogens. While turkeys are highly susceptible to influenza viruses of different origins, the impact of influenza virus infection on turkey gut and respiratory microbiota has not been demonstrated. In this study, we investigated the relationships between low pathogenicity avian influenza (LPAI) virus replication, cytokine gene expression, and respiratory and gut microbiota disruption in specific-pathogen-free turkeys. Differential replication of two LPAI H5N2 viruses paralleled the levels of clinical signs and cytokine gene expression. During active virus shedding, there was significant increase of ileal and nasal bacterial contents, which inversely corresponded with bacterial species diversity. Spearman’s correlation tests between bacterial abundance and local viral titers revealed that LPAI virus-induced dysbiosis was strongest in the nasal cavity followed by trachea, and weakest in the gut. Significant correlations were also observed between cytokine gene expression levels and relative abundances of several bacteria in tracheas of infected turkeys. For example, interferon γ/λ and interleukin-6 gene expression levels were correlated positively with Staphylococcus and Pseudomonas abundances, and negatively with Lactobacillus abundance. Overall, our data suggest a potential relationship where bacterial community diversity and enrichment or depletion of several bacterial genera in the gut and respiratory tract are dependent on the level of LPAI virus replication. Further work is needed to establish whether respiratory and enteric dysbiosis in LPAI virus-infected turkeys is a result of host immunological responses or other causes such as changes in nutritional uptake. creator: John M. Ngunjiri creator: Kara J.M. Taylor creator: Hana Ji creator: Michael C. Abundo creator: Amir Ghorbani creator: Mahesh KC creator: Chang-Won Lee uri: https://doi.org/10.7717/peerj.11806 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Ngunjiri et al. title: Predicted distribution of a rare and understudied forest carnivore: Humboldt marten (Martes caurina humboldtensis) link: https://peerj.com/articles/11670 last-modified: 2021-07-21 description: BackgroundMany mammalian species have experienced range contractions. Following a reduction in distribution that has resulted in apparently small and disjunct populations, the Humboldt marten (Martes caurina humboldtensis) was recently designated as federally Threatened and state Endangered. This subspecies of Pacific marten occurring in coastal Oregon and northern California, also known as coastal martens, appear unlike martens that occur in snow-associated regions in that vegetation associations appear to differ widely between Humboldt marten populations. We expected current distributions represent realized niches, but estimating factors associated with long-term occurrence was challenging for this rare and little-known species. Here, we assessed the predicted contemporary distribution of Humboldt martens and interpret our findings as hypotheses correlated with the subspecies’ niche to inform strategic conservation actions.MethodsWe modeled Humboldt marten distribution using a maximum entropy (Maxent) approach. We spatially-thinned 10,229 marten locations collected from 1996–2020 by applying a minimum distance of 500-m between locations, resulting in 384 locations used to assess correlations of marten occurrence with biotic and abiotic variables. We independently optimized the spatial scale of each variable and focused development of model variables on biotic associations (e.g., hypothesized relationships with forest conditions), given that abiotic factors such as precipitation are largely static and not alterable within a management context.ResultsHumboldt marten locations were positively associated with increased shrub cover (salal (Gautheria shallon)), mast producing trees (e.g., tanoak, Notholithocarpus densiflorus), increased pine (Pinus sp.) proportion of total basal area, annual precipitation at home-range spatial scales, low and high amounts of canopy cover and slope, and cooler August temperatures. Unlike other recent literature, we found little evidence that Humboldt martens were associated with old-growth structural indices. This case study provides an example of how limited information on rare or lesser-known species can lead to differing interpretations, emphasizing the need for study-level replication in ecology. Humboldt marten conservation would benefit from continued survey effort to clarify range extent, population sizes, and fine-scale habitat use. creator: Katie M. Moriarty creator: Joel Thompson creator: Matthew Delheimer creator: Brent R. Barry creator: Mark Linnell creator: Taal Levi creator: Keith Hamm creator: Desiree Early creator: Holly Gamblin creator: Micaela Szykman Gunther creator: Jordan Ellison creator: Janet S. Prevéy creator: Jennifer Hartman creator: Raymond Davis uri: https://doi.org/10.7717/peerj.11670 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: ©2021 Moriarty et al. title: Morphological observation and protein expression of fertile and abortive ovules in Castanea mollissima link: https://peerj.com/articles/11756 last-modified: 2021-07-21 description: Chinese chestnuts (Castanea mollissima Blume.) contain 12–18 ovules in one ovary, but only one ovule develops into a seed, indicating a high ovule abortion rate. In this study, the Chinese chestnut ‘Huaihuang’ was used to explore the possible mechanisms of ovule abortion with respect to morphology and proteomics. The morphology and microstructure of abortive ovules were found to be considerably different from those of fertile ovules at 20 days after anthesis (20 DAA). The fertile ovules had completely formed tissues, such as the embryo sac, embryo and endosperm. By contrast, in the abortive ovules, there were no embryo sacs, and wide spaces between the integuments were observed, with few nucelli. Fluorescence labelling of the nuclei and transmission electron microscopy (TEM) observations showed that cells of abortive ovules were abnormally shaped and had thickened cell walls, folded cell membranes, condensed cytoplasm, ruptured nuclear membranes, degraded nucleoli and reduced mitochondria. The iTRAQ (isobaric tag for relative and absolute quantitation) results showed that in the abortive ovules, low levels of soluble protein with small molecular weights were found, and most of differently expressed proteins (DEPs) were related to protein synthesis, accumulation of active oxygen free radical, energy synthesis and so on. These DEPs might be associated with abnormal ovules formation. creator: Bingshuai Du creator: Qing Zhang creator: Qingqin Cao creator: Yu Xing creator: Ling Qin creator: Kefeng Fang uri: https://doi.org/10.7717/peerj.11756 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Du et al. title: The effects of genetic drift and genomic selection on differentiation and local adaptation of the introduced populations of Aedes albopictus in southern Russia link: https://peerj.com/articles/11776 last-modified: 2021-07-21 description: BackgroundAsian tiger mosquito Aedes albopictus is an arbovirus vector that has spread from its native habitation areal in Southeast Asia throughout North and South Americas, Europe, and Africa. Ae. albopictus was first detected in the Southern Federal District of the Russian Federation in the subtropical town of Sochi in 2011. In subsequent years, this species has been described in the continental areas with more severe climate and lower winter temperatures.MethodsGenomic analysis of pooled Ae. albopictus samples collected in the mosquito populations in the coastal and continental regions of the Krasnodar Krai was conducted to look for the genetic changes associated with the spread and potential cold adaptation in Ae. albopictus.ResultsThe results of the phylogenetic analysis based on mitochondrial genomes corresponded well with the hypothesis that Ae. albopictus haplotype A1a2a1 was introduced into the region from a single source. Population analysis revealed the role of dispersal and genetic drift in the local adaptation of the Asian tiger mosquito. The absence of shared haplotypes between the samples and high fixation indices suggest that gene flow between samples was heavily restricted. Mitochondrial and genomic differentiation together with different distances between dispersal routes, natural and anthropogenic barriers and local effective population size reduction could lead to difficulties in local climatic adaptations due to reduced selection effectiveness. We have found genomic regions with selective sweep patterns which can be considered as having been affected by recent selection events. The genes located in these regions participate in neural protection, lipid conservation, and cuticle formation during diapause. These processes were shown to be important for cold adaptation in the previous transcriptomic and proteomic studies. However, the population history and relatively low coverage obtained in the present article could have negatively affect sweep detection. creator: Evgenii A. Konorov creator: Vyacheslav Yurchenko creator: Ivan Patraman creator: Alexander Lukashev creator: Nadezhda Oyun uri: https://doi.org/10.7717/peerj.11776 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Konorov et al. title: Leveraging the potential of nature to meet net zero greenhouse gas emissions in Washington State link: https://peerj.com/articles/11802 last-modified: 2021-07-21 description: The State of Washington, USA, has set a goal to reach net zero greenhouse gas emissions by 2050, the year around which the Intergovernmental Panel on Climate Change (IPCC) recommended we must limit global warming to 1.5 °C above that of pre-industrial times or face catastrophic changes. We employed existing approaches to calculate the potential for a suite of Natural Climate Solution (NCS) pathways to reduce Washington’s net emissions under three implementation scenarios: Limited, Moderate, and Ambitious. We found that NCS could reduce emissions between 4.3 and 8.8 MMT CO2eyr−1 in thirty-one years, accounting for 4% to 9% of the State’s net zero goal. These potential reductions largely rely on changing forest management practices on portions of private and public timber lands. We also mapped the distribution of each pathway’s Ambitious potential emissions reductions by county, revealing spatial clustering of high potential reductions in three regions closely tied to major business sectors: private industrial forestry in southwestern coastal forests, cropland agriculture in the Columbia Basin, and urban and rural development in the Puget Trough. Overall, potential emissions reductions are provided largely by a single pathway, Extended Timber Harvest Rotations, which mostly clusters in southwestern counties. However, mapping distribution of each of the other pathways reveals wider distribution of each pathway’s unique geographic relevance to support fair, just, and efficient deployment. Although the relative potential for a single pathway to contribute to statewide emissions reductions may be small, they could provide co-benefits to people, communities, economies, and nature for adaptation and resiliency across the state. creator: James C. Robertson creator: Kristina V. Randrup creator: Emily R. Howe creator: Michael J. Case creator: Phillip S. Levin uri: https://doi.org/10.7717/peerj.11802 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Robertson et al. title: Co-expression network and comparative transcriptome analysis for fiber initiation and elongation reveal genetic differences in two lines from upland cotton CCRI70 RIL population link: https://peerj.com/articles/11812 last-modified: 2021-07-21 description: Upland cotton is the most widely planted for natural fiber around the world, and either lint percentage (LP) or fiber length (FL) is the crucial component tremendously affecting cotton yield and fiber quality, respectively. In this study, two lines MBZ70-053 and MBZ70-236 derived from G. hirsutum CCRI70 recombinant inbred line (RIL) population presenting different phenotypes in LP and FL traits were chosen to conduct RNA sequencing on ovule and fiber samples, aiming at exploring the differences of molecular and genetic mechanisms during cotton fiber initiation and elongation stages. As a result, 249/128, 369/206, 4296/1198 and 3547/2129 up-/down- regulated differentially expressed genes (DGEs) in L2 were obtained at −3, 0, 5 and 10 days post-anthesis (DPA), respectively. Seven gene expression profiles were discriminated using Short Time-series Expression Miner (STEM) analysis; seven modules and hub genes were identified using weighted gene co-expression network analysis. The DEGs were mainly enriched into energetic metabolism and accumulating as well as auxin signaling pathway in initiation and elongation stages, respectively. Meanwhile, 29 hub genes were identified as 14-3-3ω, TBL35, GhACS, PME3, GAMMA-TIP, PUM-7, etc., where the DEGs and hub genes revealed the genetic and molecular mechanisms and differences during cotton fiber development. creator: Xiao Jiang creator: Liqiang Fan creator: Pengtao Li creator: Xianyan Zou creator: Zhen Zhang creator: Senmiao Fan creator: Juwu Gong creator: Youlu Yuan creator: Haihong Shang uri: https://doi.org/10.7717/peerj.11812 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Jiang et al. title: The predatory bug Orius strigicollis shows a preference for egg-laying sites based on plant topography link: https://peerj.com/articles/11818 last-modified: 2021-07-21 description: BackgroundOviposition site selection is an important factor in determining the success of insect populations. Orius spp. are widely used in the biological control of a wide range of soft-bodied insect pests such as thrips, aphids, and mites. Orius strigicollis (Heteroptera: Anthocoridae) is the dominant Orius species in southern China; however, what factor drives its selection of an oviposition site after mating currently remains unknown.MethodsHere, kidney bean pods (KBPs) were chosen as the oviposition substrate, and choice and nonchoice experiments were conducted to determine the preferences concerning oviposition sites on the KBPs of O. strigicollis. The mechanism of oviposition behavior was revealed through observation and measurement of oviposition action, the egg hatching rate, and the oviposition time.ResultsWe found that O. strigicollis preferred the seams of the pods for oviposition, especially the seams at the tips of the KBPs. Choice and nonchoice experiments showed that females did not lay eggs when the KBP tail parts were unavailable. The rates of egg hatching on different KBP parts were not significantly different, but the time required for females to lay eggs on the tip seam was significantly lower. Decreased oviposition time is achieved on the tip seam because the insect can exploit support points found there and gain leverage for insertion of the ovipositor.DiscussionThe preferences for oviposition sites of O. strigicollis are significantly influenced by the topography of the KBP surface. Revealing such behavior and mechanisms will provide an important scientific basis for the mass rearing of predatory bugs. creator: Chendi Yu creator: Jun Huang creator: Xiaoyun Ren creator: G Mandela Fernández-Grandon creator: Xiaowei Li creator: Muhammad Hafeez creator: Yaobin Lu uri: https://doi.org/10.7717/peerj.11818 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Yu et al. title: A simple mechanistic model of the invasive species Heracleum sosnowskyi propagule dispersal by wind link: https://peerj.com/articles/11821 last-modified: 2021-07-21 description: BackgroundInvasive species are one of the key elements of human-mediated ecosystem degradation and ecosystem services impairment worldwide. Dispersal of propagules is the first stage of plant species spread and strongly influences the dynamics of biological invasion. Therefore, distance prediction for invasive species spread is critical for invasion management. Heracleum sosnowskyi is one of the most dangerous invasive species with wind-dispersed propagules (seeds) across Eastern Europe. This study developed a simple mechanistic model for H. sosnowskyi propagule dispersal and their distances with an accuracy comparable to that of empirical measurements.MethodsWe measured and compared the propagule traits (terminal velocity, mass, area, and wing loading) and release height for H. sosnowskyi populations from two geographically distant regions of European Russia. We tested two simple mechanistic models: a ballistic model and a wind gradient model using identical artificial propagules. The artificial propagules were made of colored paper with a mass, area, wing loading, and terminal velocity close to those of natural H. sosnowskyi mericarps.ResultsThe wind gradient model produced the best results. The first calculations of maximum possible propagule transfer distance by wind using the model and data from weather stations showed that the role of wind as a vector of long-distance dispersal for invasive Heracleum species was strongly underestimated. The published dataset with H. sosnowskyi propagule traits and release heights allows for modeling of the propagules’ dispersal distances by wind at any geographical point within their entire invasion range using data from the closest weather stations. The proposed simple model for the prediction of H. sosnowskyi propagule dispersal by wind may be included in planning processes for managing invasion of this species. creator: Ivan Chadin creator: Igor Dalke creator: Denis Tishin creator: Ilya Zakhozhiy creator: Ruslan Malyshev uri: https://doi.org/10.7717/peerj.11821 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Chadin et al. title: A star is torn—molecular analysis divides the Mediterranean population of Poli’s stellate barnacle, Chthamalus stellatus (Cirripedia, Chtamalidae) link: https://peerj.com/articles/11826 last-modified: 2021-07-21 description: Poli’s stellate barnacle, Chthamalus stellatus Poli, populates the Mediterranean Sea, the North-Eastern Atlantic coasts, and the offshore Eastern Atlantic islands. Previous studies have found apparent genetic differences between the Atlantic and the Mediterranean populations of C. stellatus, suggesting possible geological and oceanographic explanations for these differences. We have studied the genetic diversity of 14 populations spanning from the Eastern Atlantic to the Eastern Mediterranean, using two nuclear genes sequences revealing a total of 63 polymorphic sites. Both genotype-based, haplotype-based and the novel SNP distribution population-based methods have found that these populations represent a geographic cline along the west to east localities. The differences in SNP distribution among populations further separates a major western cluster into two smaller clusters, the Eastern Atlantic and the Western Mediterranean. It also separates the major eastern cluster into two smaller clusters, the Mid-Mediterranean and Eastern Mediterranean. We suggested here environmental conditions like surface currents, water salinity and temperature as probable factors that have formed the population structure. We demonstrate that C. stellatus is a suitable model organism for studying how geological events and hydrographic conditions shape the fauna in the Mediterranean Sea. creator: Yaron Tikochinski creator: Sharon Tamir creator: Noa Simon-Blecher creator: Uzi Motro creator: Yair Achituv uri: https://doi.org/10.7717/peerj.11826 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Tikochinski et al. title: Dose-response relationship among body mass index, abdominal adiposity and atrial fibrillation in patients undergoing cardiac surgery: a meta-analysis of 35 cohorts link: https://peerj.com/articles/11855 last-modified: 2021-07-21 description: BackgroundWhether overweight increases the risk of postoperative atrial fibrillation (POAF) is unclear, and whether adiposity independently contributes to POAF has not been comprehensively studied. Thus, we conducted a meta-analysis to clarify the strength and shape of the exposure-effect relationship between adiposity and POAF.MethodsThe PubMed, Cochrane Library, and EMBASE databases were searched for revelant studies (randomized controlled trials (RCTs), cohort studies, and nest-case control studies) reporting data regarding the relationship between adiposity and the risk of POAF.ResultsThirty-five publications involving 33,271 cases/141,442 patients were included. Analysis of categorical variables showed that obesity (RR: 1.39, 95% CI [1.21–1.61]; P < 0.001), but not being underweight (RR: 1.44, 95% CI [0.90–2.30]; P = 0.13) or being overweight (RR: 1.03, 95% CI [0.95–1.11]; P = 0.48) was associated with an increased risk of POAF. In the exposure-effect analysis (BMI) was 1.09 (95% CI [1.05–1.12]; P < 0.001) for the risk of POAF. There was a significant linear relationship between BMI and POAF (Pnonlinearity = 0.44); the curve was flat and began to rise steeply at a BMI of approximately 30. Notably, BMI levels below 30 (overweight) were not associated with a higher risk of POAF. Additionally, waist obesity or visceral adiposity index was associated with the risk of POAF.ConclusionBased on the current evidence, our findings showed that high body mass index or abdominal adiposity was independently associated with an increased risk of POAF, while underweight or overweight might not significantly increase the POAF risk. creator: Menglu Liu creator: Kaibo Mei creator: Lixia Xie creator: Jianyong Ma creator: Peng Yu creator: Siquan Niu creator: Ya Xu creator: Yujie Zhao creator: Xiao Liu uri: https://doi.org/10.7717/peerj.11855 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Liu et al. title: The main stage of recovery after the end-Permian mass extinction: taxonomic rediversification and ecologic reorganization of marine level-bottom communities during the Middle Triassic link: https://peerj.com/articles/11654 last-modified: 2021-07-20 description: The recovery of marine life from the end-Permian mass extinction event provides a test-case for biodiversification models in general, but few studies have addressed this episode in its full length and ecological context. This study analyses the recovery of marine level-bottom communities from the end-Permian mass extinction event over a period of 15 Ma, with a main focus on the previously neglected main phase during the Middle Triassic. Our analyses are based on faunas from 37 lithological units representing different environmental settings, ranging from lagoons to inner, mid- and outer ramps. Our dataset comprises 1562 species, which belong to 13 higher taxa and 12 ecological guilds. The diversification pattern of most taxa and guilds shows an initial Early Triassic lag phase that is followed by a hyperbolic diversity increase during the Bithynian (early middle Anisian) and became damped later in the Middle Triassic. The hyperbolic diversity increase is not predicted by models that suggest environmental causes for the initial lag phase. We therefore advocate a model in which diversification is primarily driven by the intensity of biotic interactions. Accordingly, the Early Triassic lag phase represents the time when the reduced species richness in the wake of the end-Permian mass extinction was insufficient for stimulating major diversifications, whereas the Anisian main diversification event started when self-accelerating processes became effective and stopped when niche-crowding prevented further diversification. Biotic interactions that might drive this pattern include interspecific competition but also habitat construction, ecosystem engineering and new options for trophic relationships. The latter factors are discussed in the context of the resurgence of large carbonate platforms, which occurred simultaneously with the diversification of benthic communities. These did not only provide new hardground habitats for a variety of epifaunal taxa, but also new options for grazing gastropods that supposedly fed from microalgae growing on dasycladaceans and other macroalgae. Whereas we do not claim that changing environmental conditions were generally unimportant for the recovery of marine level-bottom communities, we note that their actual role can only be assessed when tested against predictions of the biotic model. creator: Evelyn Friesenbichler creator: Michael Hautmann creator: Hugo Bucher uri: https://doi.org/10.7717/peerj.11654 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Friesenbichler et al. title: Effects of fertilizer and biochar applications on the relationship among soil moisture, temperature, and N2O emissions in farmland link: https://peerj.com/articles/11674 last-modified: 2021-07-20 description: BackgroundDi-nitrogen oxide (N2O) emissions from soil may lead to nonpoint-source pollution in farmland. Improving the C and N content in the soil is an excellent strategy to reduce N2O emission and mitigate soil N loss. However, this method lacks a unified mathematical index or standard to evaluate its effect.MethodsTo quantify the impact of soil improvement (C and N) on N2O emissions, we conducted a 2-year field experiment using biochar as carbon source and fertilizer as nitrogen source, setting three treatments (fertilization (300 kg N ha−1), fertilization + biochar (30 t ha−1), control).ResultsResults indicate that after biochar application, the average soil water content above 20 cm increased by ∼26% and 26.92% in 2019, and ∼10% and 12.49% in 2020. The average soil temperature above 20 cm also increased by ∼2% and 3.41% in 2019. Fertigation significantly promotes the soil N2O emissions, and biochar application indeed inhibited the cumulation by approximately 52.4% in 2019 and 33.9% in 2020, respectively. N2O emissions strongly depend on the deep soil moisture and temperature (20–80 cm), in addition to the surface soil moisture and temperature (0–20 cm). Therefore, we established an exponential model between the soil moisture and N2O emissions based on theoretical analysis. We find that the N2O emissions exponentially increase with increasing soil moisture regardless of fertilization or biochar application. Furthermore, the coefficient a < 0 means that N2O emissions initially increase and then decrease. The aRU < aCK indicates that fertilization does promote the rate of N2O emissions, and the aBRU > aRU indicates that biochar application mitigates this rate induced by fertilization. This conclusion can be verified by the sensitivity coefficient (SCB of 1.02 and 14.74; SCU of 19.18 and 20.83). Thus, we believe the model can quantify the impact of soil C and N changes on N2O emissions. We can conclude that biochar does significantly reduce N2O emissions from farmland. creator: Xiao Wang creator: Ping Lu creator: Peiling Yang creator: Shumei Ren uri: https://doi.org/10.7717/peerj.11674 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Wang et al. title: Network pharmacology to investigate the pharmacological mechanisms of muscone in Xingnaojing injections for the treatment of severe traumatic brain injury link: https://peerj.com/articles/11696 last-modified: 2021-07-20 description: BackgroundXingnaojing injections (XNJI) are widely used in Chinese medicine to mitigate brain injuries. An increasing number of studies have shown that XNJI may improve neurological function. However, XNJI’s active ingredients and molecular mechanisms when treating traumatic brain injury (TBI) are unknown.MethodsXNJI’s chemical composition was acquisited from literature and the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database. We used the “absorption, distribution, metabolism, and excretion” (ADME) parameter-based virtual algorithm to further identify the bioactive components. We then screened data and obtained target information regarding TBI and treatment compounds from public databases. Using a Venn diagram, we intersected the information to determine the hub targets. Cytoscape was used to construct and visualize the network. In accordance with the hub proteins, we then created a protein–protein interaction (PPI) network using STRING 11.0. Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were analyzed according to the DAVID bioinformatics resource database (ver. 6.8). We validated the predicted compound’s efficacy using the experimental rat chronic constriction injury (CCI) model. The neuronal apoptosis was located using the TUNEL assay and the related pathways’ hub proteins were determined by PCR, Western blot, and immunohistochemical staining.ResultsWe identified 173 targets and 35 potential compounds belonging to XNJI. STRING analysis was used to illustrate the protein–protein interactions and show that muscone played a fundamental role in XNJI’s efficacy. Enrichment analysis revealed critical signaling pathways in these components’ potential protein targets, including PI3K/AKT1, NF-kB, and p53. Moreover, the hub proteins CASP3, BCL2L1, and CASP8 were also involved in apoptosis and were associated with PI3K/AKT, NF-kB, and p53 signaling pathways. We showed that muscone and XNJI were similarly effective 168 h after CCI, demonstrating that the muscone in XNJI significantly attenuated neuronal apoptosis through the PI3K/Akt1/NF-kB/P53 pathway.ConclusionWe verified the neuroprotective mechanism in muscone for the first time in TBI. Network pharmacology offers a new approach for identifying the potential active ingredients in XNJI. creator: Zhuohang Liu creator: Hang Li creator: Wenchao Ma creator: Shuyi Pan uri: https://doi.org/10.7717/peerj.11696 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Liu et al. title: Interventions to improve the well-being of family caregivers of patients on hemodialysis and peritoneal dialysis: a systematic review link: https://peerj.com/articles/11713 last-modified: 2021-07-20 description: BackgroundThe family caregivers of patients on hemodialysis (HD) and peritoneal dialysis (PD) typically experience higher burden than the general population because of the nature of tasks these caregivers need to carry out as a part of homecare. This fact influences both the caregivers’ quality of life and the quality of their care toward the patient. Thus, this study aimed to review the effectiveness and limitations of interventions in improving the well-being of family caregivers of patients on HD and PD.MethodologyA systematic review was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses and the Cochrane Handbook for Systematic Reviews of Interventions (version 5.1.0). The Cochrane Library, Cumulative Index to Nursing and Allied Health Literature, Embase, MEDLINE, VHL Regional Portal, Scopus, and Web of Science databases were searched queried for randomized controlled trials that developed interventions aimed at improving the well-being of family caregivers of patients undergoing HD and/or PD from 2009 to 2020. The study protocol was registered at the International Prospective Register of Systematic Reviews (registration no. CRD42020151161).ResultsSix studies met the inclusion criteria, all of which addressed caregivers of patients undergoing HD. All interventions reported in the included studies were carried out in group sessions, which addressed topics such as patient assistance and care, treatment complications, coping strategies, caregiver self-care practices, problem solving, and self-efficacy. The studies found significant improvement in the caregiver’s well-being.ConclusionsGroup session interventions are effective in improving the well-being of family caregivers of patients undergoing HD. In regard to PD, there is insufficient evidence to make recommendations for caregivers of patients with this treatment. creator: Ana Carolina Hovadick creator: Viviane Rodrigues Jardim creator: Constança Paúl creator: Adriana Pagano creator: Ilka Reis creator: Heloisa Torres uri: https://doi.org/10.7717/peerj.11713 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Hovadick et al. title: Lots of movement, little progress: a review of reptile home range literature link: https://peerj.com/articles/11742 last-modified: 2021-07-20 description: Reptiles are the most species-rich terrestrial vertebrate group with a broad diversity of life history traits. Biotelemetry is an essential methodology for studying reptiles as it compensates for several limitations when studying their natural history. We evaluated trends in terrestrial reptile spatial ecology studies focusing upon quantifying home ranges for the past twenty years. We assessed 290 English-language reptile home range studies published from 2000–2019 via a structured literature review investigating publications’ study location, taxonomic group, methodology, reporting, and analytical techniques. Substantial biases remain in both location and taxonomic groups in the literature, with nearly half of all studies (45%) originating from the USA. Snakes were most often studied, and crocodiles were least often studied, while testudines tended to have the greatest within study sample sizes. More than half of all studies lacked critical methodological details, limiting the number of studies for inclusion in future meta-analyses (55% of studies lacked information on individual tracking durations, and 51% lacked sufficient information on the number of times researchers recorded positions). Studies continue to rely on outdated methods to quantify space-use (including Minimum Convex Polygons and Kernel Density Estimators), often failing to report subtleties regarding decisions that have substantial impact on home range area estimates. Moving forward researchers can select a suite of appropriate analytical techniques tailored to their research question (dynamic Brownian Bridge Movement Models for within sample interpolation, and autocorrelated Kernel Density Estimators for beyond sample extrapolation). Only 1.4% of all evaluated studies linked to available and usable telemetry data, further hindering scientific consensus. We ultimately implore herpetologists to adopt transparent reporting practices and make liberal use of open data platforms to maximize progress in the field of reptile spatial ecology. creator: Matthew Crane creator: Inês Silva creator: Benjamin M. Marshall creator: Colin T. Strine uri: https://doi.org/10.7717/peerj.11742 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Crane et al. title: Inheritance of heat tolerance in perennial ryegrass (Lolium perenne, Poaceae): evidence from progeny array analysis link: https://peerj.com/articles/11782 last-modified: 2021-07-20 description: BackgroundHeat stress is considered one of the most important environmental factors influencing plant physiology, growth, development, and reproductive output. The occurrence and damage caused by heat stress will likely increase with global climate change. Thus, there is an urgent need to better understand the genetic basis of heat tolerance, especially in cool season plants.Materials and MethodsIn this study, we assessed the inheritance of heat tolerance in perennial ryegrass (Lolium perenne L. subspecies perenne) , a cool season grass, through a comparison of two parental cultivars with their offspring. We crossed plants of a heat tolerant cultivar (Kangaroo Valley) with plants of a heat sensitive cultivar (Norlea), to generate 72 F1 hybrid progeny arrays. Both parents and their progeny were then exposed to heat stress for 40 days, and their photosynthetic performance (Fv/Fm values) and leaf H2O2 content were measured.ResultsAs expected, Kangaroo Valley had significantly higher Fv/Fm values and significantly lower H2O2 concentrations than Norlea. For the F1 progeny arrays, values of Fv/Fm decreased gradually with increasing exposure to heat stress, while the content of H2O 2 increased. The progeny had a wide distribution of Fv/Fm and H 2O2 values at 40 days of heat stress. Approximately 95% of the 72 F1 progeny arrays had Fv/Fm values that were equal to or intermediate to the values of the two parental cultivars and 68% of the progeny arrays had H2O2 concentrations equal to or intermediate to their two parents.ConclusionResults of this study indicate considerable additive genetic variation for heat tolerance among the 72 progeny arrays generated from these crosses, and such diversity can be used to improve heat tolerance in perennial ryegrass cultivars. Our findings point to the benefits of combining physiological measurements within a genetic framework to assess the inheritance of heat tolerance, a complex plant response. creator: Wagdi S. Soliman creator: Ahmed M. Abbas creator: Stephen J. Novak creator: Masahiro Fujimori creator: Kazuhiro Tase creator: Shu-ichi Sugiyama uri: https://doi.org/10.7717/peerj.11782 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Soliman et al. title: Implications of the foliar phytochemical diversity of the avocado crop Persea americana cv. Hass in its susceptibility to pests and pathogens link: https://peerj.com/articles/11796 last-modified: 2021-07-20 description: Phytochemical diversity (PD) can be considered as a defensive trait; it can operate through single plant secondary metabolites or usually as complex mixtures of them. We tested the more diversity-better defense hypothesis correlating the leaf plant secondary metabolites (PSMs) with the incidence of plant enemies on Hass avocado trees. We expected a negative correlation between the occurrence of plant enemies and PD metrics. Also, as intraspecific PSMs polymorphisms in plant populations are common, we studied the incidence of plant enemies on Hass avocado trees representing chemical variants (chemotypes). We expected a differential incidence of plant enemies among trees grouped by their mono and sesquiterpene + phenylpropanoid chemotypes. We analyzed foliar hexane extracts from 236 trees in 17 orchards by gas chromatography and for the incidence of red mite, thrips, whitefly, avocado branch borer, fruit rot, scab, and peduncle collar blight. The predicted negative correlation between the plant enemies’ incidence and the phytochemical metrics did not occur. To determine the relationship between enemy incidence and chemotypes we grouped the trees by cluster analysis using a matrix of PSMs in each tree. Most trees were grouped under four out of 23 chemotypes. Branch borers attacked trees of low-frequency chemotypes more frequently than trees with common chemotypes. The incidence of five plant enemies was different among the predominant chemotypes. The hypothesis of more diversity-better defense was not supported by the correlations between the phytochemical diversity and the incidence of pests and pathogens in Hass avocado orchards. Based on our results, we hypothesize that phytochemical diversity function as a defensive trait relies more on differentiation among individuals in a population than on the sole increase of chemical diversity. Also, the differential incidence of pests and pathogens on trees classified by their foliar chemotypes implies that these susceptibility or resistance markers represent potential useful tools for Hass avocado orchard pest management. creator: Francisco J. Espinosa-García creator: Yolanda M. García-Rodríguez creator: Angel E. Bravo-Monzón creator: Ernesto V. Vega-Peña creator: Guillermo Delgado-Lamas uri: https://doi.org/10.7717/peerj.11796 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Espinosa-García et al. title: Precocious puberty in male wild boars: a possible explanation for the dramatic population increase in Germany and Europe link: https://peerj.com/articles/11798 last-modified: 2021-07-20 description: BackgroundThe wild boar population in Europe is steadily growing, one of the reasons for this increase probably being the high reproductive potential of this large mammal. Population management is important to stabilise wild boar numbers and a great deal of attention is focusing on the reasons, which might contribute to the high reproductive rates. Understanding the timing of puberty attainment provides information required for proper management practices. Knowledge of the earliest expected time of sexual maturation in male wild boars is limited, research being mostly focused on females. Previous hunting references indicate that sexual maturity in males occurs in the second year after birth. In contrast, male domestic pigs become sexually mature from about seven months of age. Thus, aims of this study were to investigate (1) whether there is a physiological ability for reproduction also in male wild boars of a younger age and (2) whether the body weight of wild boar males has a more important role than age in driving the maturation of the testis.MethodsMale wild boar individuals were sampled during hunting drives in the eastern part of Lower Saxony in Germany. Testes with epididymides from 74 males were collected and prepared for histological examination and immunohistochemistry. The reproductive status could be ascertained based on development/occurrence of different germ cell populations using histology and based on the immunohistochemical detection of the anti-Müllerian hormone and androgen receptor.ResultsIn this study, male wild boars aged nine to ten months already passed puberty and were able to reproduce if they had reached the appropriate body condition of about 29 kg dressed weight. Immunopositivity to the anti-Müllerian hormone in Sertoli cells was evident only in prepubertal animals and decreased with the onset of puberty. No immunoreaction was evident at postpuberty. The androgen receptor was detected in Sertoli cells, peritubular cells and Leydig cells, surprisingly already in Sertoli cells of prepubertal wild boars as well depending on body weight. Moreover, two-thirds of young males aged about ten months were precociously reproductively mature, showing histologically the presence of spermatozoa in testes and epididymides.ConclusionsAs piglets are mostly born in spring, also these young male individuals could target the heat of female wild boars in the winter months, resulting in the observed population increase. Therefore, a reduction in wild boar numbers should also focus on piglets of both sexes. creator: Claudia Maistrelli creator: Hanna Hüneke creator: Marion Langeheine creator: Oliver Keuling creator: Ursula Siebert creator: Ralph Brehm uri: https://doi.org/10.7717/peerj.11798 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Maistrelli et al. title: Clinical and prognostic relevance of CXCL12 expression in acute myeloid leukemia link: https://peerj.com/articles/11820 last-modified: 2021-07-20 description: BackgroundAccumulating studies have been made to understand the association between CXC chemokine ligand-12 (CXCL12)/CXC chemokine receptor 4 (CXCR4) and acute myeloid leukemia (AML). However, large-scale data analysis of potential relationship between CXCL12 and AML remains insufficient.MethodsWe collected abundant CXCL12 expression data and AML samples from several publicly available datasets. The CIBERSORT algorithm was used to quantify immune cell fractions and the online website of STRING was utilized for gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. The statistical analysis and graphical work were mainly performed via the R software.ResultsCXCL12 expression was extremely down-regulated in AML. Clinically, low CXCL12 expression was correlated with higher white blood cells (WBCs) (P < 0.0001), more blasts in bone marrow (BM) (P < 0.001) and peripheral blood (PB) (P < 0.0001), FLT3-internal tandem duplications (FLT3-ITD) (P = 0.010) and NPM1 mutations (P = 0.015). More importantly, reduced CXCL12 expression predicted worse overall survival (OS) and event-free survival (EFS) in all AML, non-M3-AML, and cytogenetically normal (CN)-AML patients in three independent cohorts. As for immune cell infiltration, high CXCL12 expressed groups tended to harbor more memory B cells and plasma cells infiltration while low CXCL12 expressed groups exhibited more eosinophils infiltration. GO enrichment and KEGG pathways analysis revealed the potential biological progress the gene participating in.ConclusionsCXCL12 is significantly down-regulated in AML and low CXCL12 expression is an independent and poor predictor of AML prognosis. CXCL12 expression level correlates with clinical and immune characteristics of AML, which could provide potential assistance for treatment. Prospective studies are needed to further validate the impact of CXCL12 expression before routine clinical application in AML. creator: Shi-sen Wang creator: Zi-jun Xu creator: Ye Jin creator: Ji-chun Ma creator: Pei-hui Xia creator: Xiangmei Wen creator: Zhen-wei Mao creator: Jiang Lin creator: Jun Qian uri: https://doi.org/10.7717/peerj.11820 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Wang et al. title: causalizeR: a text mining algorithm to identify causal relationships in scientific literature link: https://peerj.com/articles/11850 last-modified: 2021-07-20 description: Complex interactions among multiple abiotic and biotic drivers result in rapid changes in ecosystems worldwide. Predicting how specific interactions can cause ripple effects potentially resulting in abrupt shifts in ecosystems is of high relevance to policymakers, but difficult to quantify using data from singular cases. We present causalizeR (https://github.com/fjmurguzur/causalizeR), a text-processing algorithm that extracts causal relations from literature based on simple grammatical rules that can be used to synthesize evidence in unstructured texts in a structured manner. The algorithm extracts causal links using the relative position of nouns relative to the keyword of choice to extract the cause and effects of interest. The resulting database can be combined with network analysis tools to estimate the direct and indirect effects of multiple drivers at the network level, which is useful for synthesizing available knowledge and for hypothesis creation and testing. We illustrate the use of the algorithm by detecting causal relationships in scientific literature relating to the tundra ecosystem. creator: Francisco J. Ancin-Murguzur creator: Vera H. Hausner uri: https://doi.org/10.7717/peerj.11850 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Ancin-Murguzur and Hausner title: Novel sampling methods for monitoring Anopheles arabiensis from Eritrea link: https://peerj.com/articles/11497 last-modified: 2021-07-19 description: BackgroundStudies comparing novel collection methods for host seeking and resting mosquitoes A. arabiensis were undertaken in a village in Eritrea. Techniques included an odor baited trap, a novel tent-trap, human landing collection and three methods of resting collection. A technique for the collection of mosquitoes exiting vegetation is also described. Pre-gravid rates were determined by dissection of host seeking insects and post-prandial egg development among insects collected resting.ResultsOverall 5,382 host-seeking, 2,296 resting and 357 A. arabiensis exiting vegetation were collected. The Furvela tent-trap was the most efficient, risk-free method for the collection of outdoor host-seeking insects, whilst the Suna trap was the least effective method. Mechanical aspirators (the CDC backpack or the Prokopack aspirator) were superior to manual aspiration in a dark shelter but there was no advantage over manual aspiration in a well-lit one. An estimated two-thirds of newly-emerged mosquitoes went through a pre-gravid phase, feeding twice before producing eggs. Mosquitoes completed gonotrophic development in a dark shelter but left a well-lit shelter soon after feeding. One blood-fed female marked in the village was recaptured 2 days after release exiting vegetation close to the oviposition site and another, shortly after oviposition, attempting to feed on a human host 3 days after release. Exit rates of males from vegetation peaked 3 min after the initial male had left. Unfed and gravid females exited approximately 6 min after the first males.ConclusionsFurvela tent-traps are suitable for the collection of outdoor biting A. arabiensis in Eritrea whilst the Prokopack sampler is the method of choice for the collection of resting insects. Constructing well-lit, rather than dark, animal shelters, may encourage otherwise endophilic mosquitoes to leave and so reduce their survival and hence their vectorial capacity. creator: Jacques D. Charlwood creator: Amanuel Kidane Andegiorgish creator: Yonatan Estifanos Asfaha creator: Liya Tekle Weldu creator: Feven Petros creator: Lidia Legese creator: Robel Afewerki creator: Selam Mihreteab creator: Corey LeClair creator: Ayubo Kampango uri: https://doi.org/10.7717/peerj.11497 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Charlwood et al. title: The impact of curcumin derived polyphenols on the structure and flexibility COVID-19 main protease binding pocket: a molecular dynamics simulation study link: https://peerj.com/articles/11590 last-modified: 2021-07-19 description: The newly occurred SARS-CoV-2 caused a leading pandemic of coronavirus disease (COVID-19). Up to now it has infected more than one hundred sixty million and killed more than three million people according to 14 May 2021 World Health Organization report. So far, different types of studies have been conducted to develop an anti-viral drug for COVID-19 with no success yet. As part of this, silico were studied to discover and introduce COVID-19 antiviral drugs and results showed that protease inhibitors could be very effective in controlling. This study aims to investigate the binding affinity of three curcumin derived polyphenols against COVID-19 the main protease (Mpro), binding pocket, and identification of important residues for interaction. In this study, molecular modeling, auto-dock coupled with molecular dynamics simulations were performed to analyze the conformational, and stability of COVID-19 binding pocket with diferuloylmethane, demethoxycurcumin, and bisdemethoxycurcumin. All three compounds have shown binding affinity −39, −89 and −169.7, respectively. Demethoxycurcumin and bisdemethoxycurcumin showed an optimum binding affinity with target molecule and these could be one of potential ligands for COVID-19 therapy. And also, COVID-19 main protease binding pocket binds with the interface region by one hydrogen bond. Moreover, the MD simulation parameters indicated that demethoxycurcumin and bisdemethoxycurcumin were stable during the simulation run. These findings can be used as a baseline to develop therapeutics with curcumin derived polyphenols against COVID-19. creator: Aweke Mulu creator: Mulugeta Gajaa creator: Haregewoin Bezu Woldekidan creator: Jerusalem Fekadu W/mariam uri: https://doi.org/10.7717/peerj.11590 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 et al. title: Development of a preoperative index-based nomogram for the prediction of hypokalemia in patients with pituitary adenoma: a retrospective cohort study link: https://peerj.com/articles/11650 last-modified: 2021-07-19 description: ObjectiveTo develop and validate a preoperative index-based nomogram for the prediction of hypokalemia in patients with pituitary adenoma (PA).MethodsThis retrospective cohort study included 205 patients with PAs between January 2013 and April 2020 in the Sun Yat-sen Memorial Hospital, Guangzhou, China. The patients were randomly classified into either a training set (N = 143 patients) and a validation set (N = 62 patients) at a ratio of 7:3. Variables, which were identified by using the LASSO regression model were included for the construction of a nomogram, and a logistic regression analysis was used to calculate odds ratios (ORs) and 95% confidence intervals (CIs) in the training set. The area under the curve (AUC) was used to evaluate the performance of the nomogram for predicting hypokalemia. Multivariate logistic regression analysis with a restricted cubic spline analysis was conducted to identify a potential nonlinear association between the preoperative index and hypokalemia.ResultsThe incidence of hypokalemia was 38.05%. Seven preoperative indices were identified for the construction of the nomogram: age, type of PA, weight, activated partial thromboplastin time, urea, eosinophil percentage, and plateletocrit. The AUCs of the nomogram for predicting hypokalemia were 0.856 (95% CI [0.796–0.915]) and 0.652 (95% CI [0.514–0.790]) in the training and validation sets, respectively. Restricted cubic splines demonstrated that there was no nonlinear association between hypokalemia and the selected variables.ConclusionIn this study, we constructed a preoperative indices-based nomogram that can assess the risk of hypokalemia after the surgical treatment of pituitary adenomas. This nomogram may also help to identify high risk patients who require close monitoring of serum potassium. creator: Wenpeng Li creator: Lexiang Zeng creator: Deping Han creator: Shanyi Zhang creator: Bingxi Lei creator: Meiguang Zheng creator: Yuefei Deng creator: Lili You uri: https://doi.org/10.7717/peerj.11650 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Li et al. title: MALDI-TOF MS as a method for rapid identification of Phytophthora de Bary, 1876 link: https://peerj.com/articles/11662 last-modified: 2021-07-19 description: The number of described species of the oomycete genus Phytophthora is growing rapidly, highlighting the need for low-cost, rapid tools for species identification. Here, a collection of 24 Phytophthora species (42 samples) from natural as well as anthropogenic habitats were genetically identified using the internal transcribed spacer (ITS) and cytochrome c oxidase subunit I (COI) regions. Because genetic identification is time consuming, we have created a complementary method based on by matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS). Both methods were compared and hypothesis that the MALDI-TOF MS method can be a fast and reliable method for the identification of oomycetes was confirmed. Over 3500 mass spectra were acquired, manually reviewed for quality control, and consolidated into a single reference library using the Bruker MALDI Biotyper platform. Finally, a database containing 144 main spectra (MSPs) was created and published in repository. The method presented in this study will facilitate the use of MALDI-TOF MS as a complement to existing approaches for fast, reliable identification of Phytophthora isolates. creator: Matěj Božik creator: Marcela Mrázková creator: Karolína Novotná creator: Markéta Hrabětová creator: Petr Maršik creator: Pavel Klouček creator: Karel Černý uri: https://doi.org/10.7717/peerj.11662 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Božik et al. title: From data compilation to model validation: comparing three ecosystem models of the Tasman and Golden Bays, New Zealand link: https://peerj.com/articles/11712 last-modified: 2021-07-19 description: The Tasman and Golden Bays (TBGB) are a semi-enclosed embayment system in New Zealand that supports numerous commercial and recreational activities. We present three ecosystem models of the TBGB ecosystem with varying levels of complexity, aimed at contributing as tools to aid in understanding this ecosystem and its responses to anthropogenic and natural pressures. We describe the process of data compilation through to model validation and analyse the importance of knowledge gaps with respect to model dynamics and results. We compare responses in all three models to historical fishing, and analyse similarities and differences in the dynamics of the three models. We assessed the most complex of the models against initialisation uncertainty and sensitivity to oceanographic variability and found it most sensitive to the latter. We recommend that scenarios relating to ecosystem dynamics of the TBGB ecosystem include sensitivities, especially oceanographic uncertainty, and compare responses across all three models where it is possible to do so. creator: Vidette L. McGregor creator: Peter Horn creator: Adele Dutilloy creator: Samik Datta creator: Alice Rogers creator: Javier Porobic creator: Alistair Dunn creator: Ian Tuck uri: https://doi.org/10.7717/peerj.11712 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 McGregor et al. title: Assessment of agro-morphological, physiological and yield traits diversity among tropical rice link: https://peerj.com/articles/11752 last-modified: 2021-07-19 description: Rice (Oryza sativa L.) is an essential staple food crop, but the per acre average rice yield is less than its substantial potential in many countries. Rice breeders and growers would benefit from a robust genotypes with better morpho-physiological and yield-related traits. Here, seventy-four new rice genotypes were phenotyped over two years for their gas exchange and yield potential-related traits under Mississippi rice-growing conditions. A wide range of variability was observed among genotypes for all measured traits. Detailed phenotyping of rice genotypes revealed two key relationships that function together to contribute to yield potential under the southern US climate. The first one, grain yield, grain number, and spikelet fertility, showed considerable correlation (r = 0.45 to 0.79, p < 0.001) to harvest index. Conversely, days to anthesis had a high and negative correlation with harvest index (r = −0.79, p < 0.001), which suggests that selection for short duration genotypes with efficient partitioning could improve the yields under southern US climatic conditions. Additive response index revealed a higher positive association with yield traits (R2 = 0.59) than physiological (R2 = 0.28) and morphological traits (R2 = 0.21). Compared with the commercial genotype Rex, 21.6% and 47.3% of the rice genotypes had a higher gas exchange and yield response scores. IR08A172, IR07K142 and IR07F287 were ranked as high performers in physiological and yield response indices. Our study highlights that selection for short-duration yield-related traits with efficient sink capacity traits is desirable for future breeding programs. creator: Naqeebullah Kakar creator: Raju Bheemanahalli creator: Salah Jumaa creator: Edilberto Redoña creator: Marilyn L. Warburton creator: Kambham R. Reddy uri: https://doi.org/10.7717/peerj.11752 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: title: Pepper root rot resistance and pepper yield are enhanced through biological agent G15 soil amelioration link: https://peerj.com/articles/11768 last-modified: 2021-07-19 description: Pepper root rot is a serious soil-borne disease that hinders pepper production, and efforts are being made to identify biological agents that can prevent and control pepper root rot. Our group recently discovered and produced a biological agent, named G15, which reduces the diversity and richness of fungi and bacteria when applied to pepper fields. In the soil of the G15-treatment condition, the pathogenic fungus Fusarium was inhibited, while the richness of beneficial bacteria Rhodanobacter was increased. Also, the ammonia nitrogen level was decreased in the G15-treatment soil, and the pH, total carbon, and total potassium levels were increased. Compared to the control condition, pepper yield was increased in the treatment group (by 16,680 kg acre−1). We found that G15 could alter the microbial community structure of the pepper rhizosphere. These changes alter the physical and chemical properties of the soil and, ultimately, improve resistance to pepper root rot and increase pepper yield. creator: Xuejiang Zhang creator: Dazhao Yu creator: Hua Wang uri: https://doi.org/10.7717/peerj.11768 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zhang et al. title: Association between Dietary Inflammatory Index and Type 2 diabetes mellitus in Xinjiang Uyghur autonomous region, China link: https://peerj.com/articles/11159 last-modified: 2021-07-16 description: BackgroundDiet and inflammation have both been studied in relation to type 2 diabetes mellitus (T2DM). The aim of this cross-sectional study was to examine the association between the Dietary Inflammatory Index (DII®) and T2DM.MethodsSubjects were adults enrolled in the baseline study of the Xinjiang multi-ethnic natural population cohort and health follow-up study from January to May 2019. The study involved 5,105 subjects (58.7% men) between 35 and 74 years of age. The DII score was calculated from a data obtained via a food frequency questionnaire consisting of 127 food items.ResultsLogistic regression analyses were used to estimate the odds ratios (ORs) and 95% confidence intervals (95% CIs) of DII in relation to T2DM. After adjusting for potential confounders, compared to subjects in the 1st DII quintile, subjects in the 5th quintile (i.e., with the most pro-inflammatory diet) had higher odds of T2DM (OR = 3.27, 95%CI:2.38,4.50; p < 0.001).ConclusionsOur results suggest that a pro-inflammatory diet is associated with a higher risk of T2DM in this population of Chinese adults. creator: WenHui Fu creator: Hualian Pei creator: Nitin Shivappa creator: James R. Hebert creator: Tao Luo creator: Tian Tian creator: Dilibaier Alimu creator: Zewen Zhang creator: Jianghong Dai uri: https://doi.org/10.7717/peerj.11159 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Fu et al. title: Stable isotope analyses identify trophic niche partitioning between sympatric terrestrial vertebrates in coastal saltmarshes with differing oiling histories link: https://peerj.com/articles/11392 last-modified: 2021-07-16 description: Bioindicator species are commonly used as proxies to help identify the ecological effects of oil spills and other stressors. However, the utility of taxa as bioindicators is dependent on understanding their trophic niche and life history characteristics, as these factors mediate their ecological responses. Seaside sparrows (Ammospiza maritima) and marsh rice rats (Oryzomys palustris) are two ubiquitous terrestrial vertebrates that are thought to be bioindicators of oil spills in saltmarsh ecosystems. To improve the utility of these omnivorous taxa as bioindicators, we used carbon and nitrogen stable isotope analysis to quantify their trophic niches at saltmarshes in coastal Louisiana with differing oiling histories. We found that rats generally had lower trophic positions and incorporated more aquatic prey relative to seaside sparrows. The range of resources used (i.e.,trophic niche width) varied based on oiling history. Seaside sparrows had wider trophic niches than marsh rice rats at unoiled sites, but not at oiled sites. Trophic niche widths of conspecifics were less consistent at oiled sites, although marsh rice rats at oiled sites had wider trophic niches than rats at unoiled sites. These results suggest that past oiling histories may have imparted subtle, yet differing effects on the foraging ecology of these two co-occurring species. However, the temporal lag between initial oiling and our study makes identifying the ultimate drivers of differences between oiled and unoiled sites challenging. Even so, our findings provide a baseline quantification of the trophic niches of sympatric seaside sparrows and marsh rice rats that will aid in the use of these species as indicators of oiling and other environmental stressors in saltmarsh ecosystems. creator: Sydney Moyo creator: Hayat Bennadji creator: Danielle Laguaite creator: Anna A. Pérez-Umphrey creator: Allison M. Snider creator: Andrea Bonisoli-Alquati creator: Jill A. Olin creator: Philip C Stouffer creator: Sabrina S. Taylor creator: Paola C. López-Duarte creator: Brian J. Roberts creator: Linda Hooper-Bui creator: Michael J. Polito uri: https://doi.org/10.7717/peerj.11392 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Moyo et al. title: Dairy management practices associated with multi-drug resistant fecal commensals and Salmonella in cull cows: a machine learning approach link: https://peerj.com/articles/11732 last-modified: 2021-07-16 description: BackgroundUnderstanding the effects of herd management practices on the prevalence of multidrug-resistant pathogenic Salmonella and commensals Enterococcus spp. and Escherichia coli in dairy cattle is key in reducing antibacterial resistant infections in humans originating from food animals. Our objective was to explore the herd and cow level features associated with the multi-drug resistant, and resistance phenotypes shared between Salmonella, E. coli and Enterococcus spp. using machine learning algorithms.MethodsRandomly collected fecal samples from cull dairy cows from six dairy farms in central California were tested for multi-drug resistance phenotypes of Salmonella, E. coli and Enterococcus spp. Using data on herd management practices collected from a questionnaire, we built three machine learning algorithms (decision tree classifier, random forest, and gradient boosting decision trees) to predict the cows shedding multidrug-resistant Salmonella and commensal bacteria.ResultsThe decision tree classifier identified rolling herd average milk production as an important feature for predicting fecal shedding of multi-drug resistance in Salmonella or commensal bacteria. The number of culled animals, monthly culling frequency and percentage, herd size, and proportion of Holstein cows in the herd were found to be influential herd characteristics predicting fecal shedding of multidrug-resistant phenotypes based on random forest models for Salmonella and commensal bacteria. Gradient boosting models showed that higher culling frequency and monthly culling percentages were associated with fecal shedding of multidrug resistant Salmonella or commensal bacteria. In contrast, an overall increase in the number of culled animals on a culling day showed a negative trend with classifying a cow as shedding multidrug-resistant bacteria. Increasing rolling herd average milk production and spring season were positively associated with fecal shedding of multidrug- resistant Salmonella. Only six individual cows were detected sharing tetracycline resistance phenotypes between Salmonella and either of the commensal bacteria.DiscussionPercent culled and culling rate reflect the increase in culling over time adjusting for herd size and were associated with shedding multidrug resistant bacteria. In contrast, number culled was negatively associated with shedding multidrug resistant bacteria which may reflect producer decisions to prioritize the culling of otherwise healthy but low-producing cows based on milk or beef prices (with respect to dairy beef), amongst other factors. Using a data-driven suite of machine learning algorithms we identified generalizable and distant associations between antimicrobial resistance in Salmonella and fecal commensal bacteria, that can help develop a producer-friendly and data-informed risk assessment tool to reduce shedding of multidrug-resistant bacteria in cull dairy cows. creator: Pranav S. Pandit creator: Deniece R. Williams creator: Paul Rossitto creator: John M. Adaska creator: Richard Pereira creator: Terry W. Lehenbauer creator: Barbara A. Byrne creator: Xunde Li creator: Edward R. Atwill creator: Sharif S. Aly uri: https://doi.org/10.7717/peerj.11732 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Pandit et al. title: Structural and immunological characterization of an epitope within the PAN motif of ectodomain I in Babesia bovis apical membrane antigen 1 for vaccine development link: https://peerj.com/articles/11765 last-modified: 2021-07-16 description: BackgroundBovine babesiosis caused by Babesia bovis (B. bovis) has had a significant effect on the mobility and mortality rates of the cattle industry worldwide. Live-attenuated vaccines are currently being used in many endemic countries, but their wide use has been limited for a number of reasons. Although recombinant vaccines have been proposed as an alternative to live vaccines, such vaccines are not commercially available to date. Apical membrane antigen-1 (AMA-1) is one of the leading candidates in the development of a vaccine against diseases caused by apicomplexan parasite species. In Plasmodium falciparum (P. falciparum) AMA-1 (PfAMA-1), several antibodies against epitopes in the plasminogen, apple, and nematode (PAN) motif of PfAMA-1 domain I significantly inhibited parasite growth. Therefore, the purpose of this study was to predict an epitope from the PAN motif of domain I in the B. bovis AMA-1 (BbAMA-1) using a combination of linear and conformational B-cell epitope prediction software. The selected epitope was then bioinformatically analyzed, synthesized as a peptide (sBbAMA-1), and then used to immunize a rabbit. Subsequently, in vitro growth- and the invasion-inhibitory effects of the rabbit antiserum were immunologically characterized.ResultsOur results demonstrated that the predicted BbAMA-1 epitope was located on the surface-exposed α-helix of the PAN motif in domain I at the apex area between residues 181 and 230 with six polymorphic sites. Subsequently, sBbAMA-1 elicited antibodies capable of recognizing the native BbAMA-1 in immunoassays. Furthermore, anti-serum against sBbAMA-1 was immunologically evaluated for its growth- and invasion-inhibitory effects on B. bovis merozoites in vitro. Our results demonstrated that the rabbit anti-sBbAMA-1 serum at a dilution of 1:5 significantly inhibited (p < 0.05) the growth of B. bovis merozoites by approximately 50–70% on days 3 and 4 of cultivation, along with the invasion of merozoites by approximately 60% within 4 h of incubation when compared to the control groups.ConclusionOur results indicate that the epitope predicted from the PAN motif of BbAMA-1 domain I is neutralization-sensitive and may serve as a target antigen for vaccine development against bovine babesiosis caused by B. bovis. creator: Amarin Rittipornlertrak creator: Boondarika Nambooppha creator: Anucha Muenthaisong creator: Veerasak Punyapornwithaya creator: Saruda Tiwananthagorn creator: Yang-Tsung Chung creator: Bumduuren Tuvshintulga creator: Thillaiampalam Sivakumar creator: Naoaki Yokoyama creator: Nattawooti Sthitmatee uri: https://doi.org/10.7717/peerj.11765 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Rittipornlertrak et al. title: Vertical escape tactics and movement potential of orthoconic cephalopods link: https://peerj.com/articles/11797 last-modified: 2021-07-16 description: Measuring locomotion tactics available to ancient sea animals can link functional morphology with evolution and ecology over geologic timescales. Externally-shelled cephalopods are particularly important for their central roles in marine trophic exchanges, but most fossil taxa lack sufficient modern analogues for comparison. In particular, phylogenetically diverse cephalopods produced orthoconic conchs (straight shells) repeatedly through time. Persistent re-evolution of this morphotype suggests that it possesses adaptive value. Practical lateral propulsion is ruled out as an adaptive driver among orthoconic cephalopods due to the stable, vertical orientations of taxa lacking sufficient counterweights. However, this constraint grants the possibility of rapid (or at least efficient) vertical propulsion. We experiment with this form of movement using 3D-printed models of Baculites compressus, weighted to mimic hydrostatic properties inferred by virtual models. Furthermore, model buoyancy was manipulated to impart simulated thrust within four independent scenarios (Nautilus-like cruising thrust; a similar thrust scaled by the mantle cavity of Sepia; sustained peak Nautilus-like thrust; and passive, slightly negative buoyancy). Each model was monitored underwater with two submerged cameras as they rose/fell over ~2 m, and their kinematics were computed with 3D motion tracking. Our results demonstrate that orthocones require very low input thrust for high output in movement and velocity. With Nautilus-like peak thrust, the model reaches velocities of 1.2 m/s (2.1 body lengths per second) within one second starting from a static initial condition. While cephalopods with orthoconic conchs likely assumed a variety of life habits, these experiments illuminate some first-order constraints. Low hydrodynamic drag inferred by vertical displacement suggests that vertical migration would incur very low metabolic cost. While these cephalopods likely assumed low energy lifestyles day-to-day, they may have had a fighting chance to escape from larger, faster predators by performing quick, upward dodges. The current experiments suggest that orthocones sacrifice horizontal mobility and maneuverability in exchange for highly streamlined, vertically-stable, upwardly-motile conchs. creator: David J. Peterman creator: Kathleen A. Ritterbush uri: https://doi.org/10.7717/peerj.11797 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Peterman and Ritterbush title: Forgetting faces over a week: investigating self-reported face recognition ability and personality link: https://peerj.com/articles/11828 last-modified: 2021-07-16 description: BackgroundAlthough face recognition is now well studied, few researchers have considered the nature of forgetting over longer time periods. Here, I investigated how newly learned faces were recognised over the course of one week. In addition, I considered whether self-reported face recognition ability, as well as Big Five personality dimensions, were able to predict actual performance in a recognition task.MethodsIn this experiment (N = 570), faces were learned through short video interviews, and these identities were later presented in a recognition test (using previously unseen images) after no delay, six hours, twelve hours, one day, or seven days.ResultsThe majority of forgetting took place within the first 24 hours, with no significant decrease after that timepoint. Further, self-reported face recognition abilities were moderately predictive of performance, while extraversion showed a small, negative association with performance. In both cases, these associations remained consistent across delay conditions.DiscussionThe current work begins to address important questions regarding face recognition using longitudinal, real-world time intervals, focussing on participant insight into their own abilities, and the process of forgetting more generally. creator: Robin S.S. Kramer uri: https://doi.org/10.7717/peerj.11828 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Kramer title: Nacre morphology and chemical composition in Atlantic winged oyster Pteria colymbus (Röding, 1798) link: https://peerj.com/articles/11527 last-modified: 2021-07-15 description: The microstructure and nanostructure of nacre in Pteria colymbus were studied with high-resolution field emission scanning electron microscopy (FESEM). The tablets were found to be flat and polyhedral with four to eight sides, and lengths ranging from 0.6 to 3.0 µm. They consisted of nanocrystals 41 nm wide, growing in the same direction. X-ray diffraction showed the crystals to be mineral phase aragonite, which was confirmed by Raman spectroscopy. Fourier transform infrared spectroscopy identified a band at 1,786.95 cm−1 attributed to carboxylate (carbonyl) groups of the proteins present in the organic matrix as well as bands characteristic of calcium carbonate. X-ray fluorescence showed the nacre to contain 98% calcium carbonate, as well as minor elements (Si, Na, S and Sr) and trace elements (Mg, P, Cu, Al, Fe, Cl, K and Zn). creator: Pablo Santana creator: Dalila Aldana Aranda uri: https://doi.org/10.7717/peerj.11527 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Santana and Aldana Aranda title: Age, size and body condition do not equally reflect population response to habitat change in the common spadefoot toad Pelobates fuscus link: https://peerj.com/articles/11678 last-modified: 2021-07-15 description: Urbanization impacts biodiversity both directly through physical expansion over land, and indirectly due to land use conversion and human behaviors associated with urban areas. We assessed the response of a common spadefoot toad population (Pelobates fuscus) to habitat loss and fragmentation resulting from urban development by studying changes in size, body condition and age parameters. We compared samples collected in the early 2000s (sample A) and later on during 2012–2014 (sample B). The terrestrial habitats in the study area were severely reduced and fragmented due to the expansion of the human settlement. We found no significant differences in the age parameters between the two sampling periods; the median lifespan shortened from 3.5 (sample A) to 3.0 years (sample B), while the other age parameters were similar in both samples. In contrast, snout-vent length, body mass and body condition experienced a significant decrease over time. Our results suggest that changes in body size and body condition, rather than age parameters, better reflect the response of the common spadefoot toad population to declining habitat quality. Therefore, body measurements can provide reliable estimates of the impact of habitat degradation in amphibian populations. creator: Dan Cogălniceanu creator: Florina Stănescu creator: Diana Székely creator: Theodor-Sebastian Topliceanu creator: Ruben Iosif creator: Paul Székely uri: https://doi.org/10.7717/peerj.11678 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Cogălniceanu et al. title: Utilization of soil residual phosphorus and internal reuse of phosphorus by crops link: https://peerj.com/articles/11704 last-modified: 2021-07-15 description: Phosphorus (P) participates in various assimilatory and metabolic processes in plants. Agricultural systems are facing P deficiency in many areas worldwide, while global P demand is increasing. Pioneering efforts have made us better understand the more complete use of residual P in soils and the link connecting plant P resorption to soil P deficiency, which will help to address the challenging issue of P deficiency. We summarized the state of soil “residual P” and the mechanisms of utilizing this P pool, the possible effects of planting and tillage patterns, various fertilization management practices and phosphate-solubilizing microorganisms on the release of soil residual P and the link connecting leaf P resorption to soil P deficiency and the regulatory mechanisms of leaf P resorption. The utilization of soil residual P represents a great challenge and a good chance to manage P well in agricultural systems. In production practices, the combination of “optimal fertilization and agronomic measures” can be adopted to utilize residual P in soils. Some agricultural practices, such as reduced or no tillage, crop rotation, stubble retention and utilization of biofertilizers-phosphate-solubilizing microorganisms should greatly improve the conversion of various P forms in the soil due to changes in the balance of individual nutrients in the soil or due to improvements in the phosphatase profile and activity in the soil. Leaf P resorption makes the plant less dependent on soil P availability, which can promote the use efficiency of plant P and enhance the adaptability to P-deficient environments. This idea provides new options for helping to ameliorate the global P dilemma. creator: Mei Yang creator: Huimin Yang uri: https://doi.org/10.7717/peerj.11704 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Yang and Yang title: Assessing the diversity of whiteflies infesting cassava in Brazil link: https://peerj.com/articles/11741 last-modified: 2021-07-15 description: BackgroundThe necessity of a competent vector for transmission is a primary ecological factor driving the host range expansion of plant arthropod-borne viruses, with vectors playing an essential role in disease emergence. Cassava begomoviruses severely constrain cassava production in Africa. Curiously, begomoviruses have never been reported in cassava in South America, the center of origin for this crop. It has been hypothesized that the absence of a competent vector in cassava is the reason why begomoviruses have not emerged in South America.MethodsWe performed a country-wide whitefly diversity study in cassava in Brazil. Adults and/or nymphs of whiteflies were collected from sixty-six cassava fields in the main agroecological zones of the country. A total of 1,385 individuals were genotyped based on mitochondrial cytochrome oxidase I sequences.ResultsA high species richness was observed, with five previously described species and two putative new ones. The prevalent species were Tetraleurodes acaciae and Bemisia tuberculata, representing over 75% of the analyzed individuals. Although we detected, for the first time, the presence of Bemisia tabaci Middle East-Asia Minor 1 (BtMEAM1) colonizing cassava in Brazil, it was not prevalent. The species composition varied across regions, with fields in the Northeast region showing a higher diversity. These results expand our knowledge of whitefly diversity in cassava and support the hypothesis that begomovirus epidemics have not occurred in cassava in Brazil due to the absence of competent vector populations. However, they indicate an ongoing adaptation process of BtMEAM1 to cassava, increasing the likelihood of begomovirus emergence in this crop. creator: Cesar A.D. Xavier creator: Angélica Maria Nogueira creator: Vinicius Henrique Bello creator: Luís Fernando Maranho Watanabe creator: Tarsiane Mara Carneiro Barbosa creator: Miguel Alves Júnior creator: Leonardo Barbosa creator: José E.A. Beserra-Júnior creator: Alessandra Boari creator: Renata Calegario creator: Eduardo Silva Gorayeb creator: Jaime Honorato Júnior creator: Gabriel Koch creator: Gaus Silvestre de Andrade Lima creator: Cristian Lopes creator: Raquel Neves de Mello creator: Késsia Pantoja creator: Fábio Nascimento Silva creator: Roberto Ramos Sobrinho creator: Enilton Nascimento Santana creator: José Wilson Pereira da Silva creator: Renate Krause-Sakate creator: Francisco M. Zerbini uri: https://doi.org/10.7717/peerj.11741 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Xavier et al. title: Time series data analysis and ARIMA modeling to forecast the short-term trajectory of the acceleration of fatalities in Brazil caused by the corona virus (COVID-19) link: https://peerj.com/articles/11748 last-modified: 2021-07-15 description: ObjectiveThis paper incorporates the concept of acceleration to fatalities caused by the coronavirus in Brazil from time series data beginning on 17th March 2020 (the day of the first death) to 3rd February 2021 to explain the trajectory of the fatalities for the next six months using confirmed infections as the explanatory variable.MethodsAcceleration of the cases of confirmed infection and fatalities were calculated by using the concept of derivatives. Acceleration of fatality function was then determined from multivariate linear function and calculus chain rule for composite function with confirmed infections as an explanatory variable. Different ARIMA models were fitted for each acceleration of fatality function: the de-seasonalized Auto ARIMA Model, the adjusted lag model, and the auto ARIMA model with seasonality. The ARIMA models were validated. The most realistic models were selected for each function for forecasting. Finally, the short run six-month forecast was conducted on the trajectory of the acceleration of fatalities for all the selected best ARIMA models.ResultsIt was found that the best ARIMA model for the acceleration functions were the seasonalized models. All functions suggest a general decrease in fatalities and the pace at which this change occurs will eventually slow down over the next six months.ConclusionThe decreasing fatalities over the next six-month period takes into consideration the direct impact of the confirmed infections. There is an early increase in acceleration for the forecast period, which suggests an increase in daily fatalities. The acceleration eventually reduces over the six-month period which shows that fatalities will eventually decrease. This gives health officials an idea on how the fatalities will be affected in the future as the trajectory of confirmed COVID-19 infections change. creator: Akini James creator: Vrijesh Tripathi uri: https://doi.org/10.7717/peerj.11748 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 James and Tripathi title: Comparing audio- and video-delivered instructions in dispatcher-assisted cardiopulmonary resuscitation with drone-delivered automatic external defibrillator: a mixed methods simulation study link: https://peerj.com/articles/11761 last-modified: 2021-07-15 description: This study compared first responders’ cardiopulmonary resuscitation (CPR) performance when a dispatcher provides audio instructions only and when both audio and video instructions are given. In the simulation, an automatic external defibrillator (AED) was delivered via drone in response to a cardiac arrest occurring outside a hospital setting. Participants’ qualitative experiences were also explored.An exploratory sequential mixed methods design was used. AEDs were delivered to college students via drone with one group receiving both audio and video instructions and the other receiving audio-only instruction, and differences in CPR performance and accuracy were compared. After completion, focus group interview data were collected and analyzed. Video-based instruction was found to be more effective in the number of chest compressions (p < 0.01), chest compression rate (p < 0.01), and chest compression interruptions (p < 0.01). The accuracy of the video group for the chest compression region was high (p = 0.05). Participants’ experiences were divided into three categories: “unfamiliar but beneficial experience,” “met helper during a desperate and embarrassing situation,” and “diverse views on drone use.” Our results lay the groundwork for a development plan for providing emergency medical services using drones, as well as the preparation of guidelines for dispatchers on the provision of video instructions. creator: Hyun-Jung Kim creator: Jin-Hwa Kim creator: Dahye Park uri: https://doi.org/10.7717/peerj.11761 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Kim et al. title: Additive and multiplicative probabilistic models of infant looking times link: https://peerj.com/articles/11771 last-modified: 2021-07-15 description: Additive and multiplicative regression models of habituation were compared regarding the fit to looking times from a habituation experiment with infants aged between 3 and 11 months. In contrast to earlier studies, the current study considered multiple probability distributions, namely Weibull, gamma, lognormal and normal distribution. In the habituation experiment the type of contrast between the habituation and the test trial was varied (luminance, color or orientation contrast), crossed with the number of habituation trials (1, 3, 5, or 7 habituation trials) and crossed with three age cohorts (4, 7, 10 months). The initial mean LT to dark stimuli (around 3.7 s) was considerably shorter than the mean LT to green and gray stimuli (around 5 s). Infants showed the strongest dishabituation to changes from dark to bright (luminance contrast) and weak-to-no dishabituation to a 90-degrees rotation of the gray stimuli (orientation contrast). The dishabituation was stronger after five and seven habituation trials, but the result was not statistically robust. The gamma distribution showed the best fit in terms of log-likelihood and mean absolute error and the best predictive performance. Furthermore, the gamma distribution showed small correlations between parameters relative to other models. The normal additive model showed an inferior fit and medium correlations between the parameters. In particular, the positive correlation between the initial looking time (LT) and the habituation rate was likely responsible for a different interpretation relative to the multiplicative models of the main effect of age on the habituation rate. Otherwise, the additive and multiplicative models provided similar statistical conclusions. The performance of the model versions without pooling and with partial pooling across participants (also called random-effects, multi-level or hierarchical models) were compared. The latter type of models showed worse data fit but more precise predictions and reduced correlations between the parameters. The performance of model variants with auto-regressive time structures were explored but showed considerably worse fit. The performance of quadratic models that allowed non-monotonic changes in LTs were investigated as well. However, when fitted with LT data, these models did not produce non-monotonic change in LTs. The study underscores the utility of partial-pooling models in terms of providing more accurate predictions. Further, it agrees with previous research in that a multiplicative LT model is preferable. Nevertheless, the current results suggest that the impact of the choice of an additive model on the statistical inference is less dramatic then previously assumed. creator: Matuš Šimkovic creator: Birgit Träuble uri: https://doi.org/10.7717/peerj.11771 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Šimkovic and Träuble title: Efficacy of computational predictions of the functional effect of idiosyncratic pharmacogenetic variants link: https://peerj.com/articles/11774 last-modified: 2021-07-15 description: BackgroundPharmacogenetic variation is important to drug responses through diverse and complex mechanisms. Predictions of the functional impact of missense pharmacogenetic variants primarily rely on the degree of sequence conservation between species as a primary discriminator. However, idiosyncratic or off-target drug-variant interactions sometimes involve effects that are peripheral or accessory to the central systems in which a gene functions. Given the importance of sequence conservation to functional prediction tools—these idiosyncratic pharmacogenetic variants may violate the assumptions of predictive software commonly used to infer their effect.MethodsHere we exhaustively assess the effectiveness of eleven missense mutation functional inference tools on all known pharmacogenetic missense variants contained in the Pharmacogenomics Knowledgebase (PharmGKB) repository. We categorize PharmGKB entries into sub-classes to catalog likely off-target interactions, such that we may compare predictions across different variant annotations.ResultsAs previously demonstrated, functional inference tools perform variably across the complete set of PharmGKB variants, with large numbers of variants incorrectly classified as ‘benign’. However, we find substantial differences amongst PharmGKB variant sub-classes, particularly in variants known to cause off-target, type B adverse drug reactions, that are largely unrelated to the main pharmacological action of the drug. Specifically, variants associated with off-target effects (hence referred to as off-target variants) were most often incorrectly classified as ‘benign’. These results highlight the importance of understanding the underlying mechanism of pharmacogenetic variants and how variants associated with off-target effects will ultimately require new predictive algorithms.ConclusionIn this work we demonstrate that functional inference tools perform poorly on pharmacogenetic variants, particularly on subsets enriched for variants causing off-target, type B adverse drug reactions. We describe how to identify variants associated with off-target effects within PharmGKB in order to generate a training set of variants that is needed to develop new algorithms specifically for this class of variant. Development of such tools will lead to more accurate functional predictions and pave the way for the increased wide-spread adoption of pharmacogenetics in clinical practice. creator: Hannah McConnell creator: T. Daniel Andrews creator: Matt A. Field uri: https://doi.org/10.7717/peerj.11774 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 McConnell et al. title: Associations of individual and joint expressions of ERCC6 and ERCC8 with clinicopathological parameters and prognosis of gastric cancer link: https://peerj.com/articles/11791 last-modified: 2021-07-15 description: BackgroundExcision repair cross-complementing group 6 and 8 (ERCC6 and ERCC8) have been implicated in ailments such as genetic diseases and cancers. However, the relationship between individual and joint expressions of ERCC6/ERCC8 and clinicopathological parameters as well as prognosis of gastric cancer (GC) still remains unclear.MethodsIn this study, protein expressions of ERCC6, ERCC8 and ERCC6-ERCC8 were detected by immunohistochemistry (IHC) in 109 paired GC and para-cancerous normal tissue samples. The mRNA expression was detected in 36 pairs of tissue samples. IHC results and RNA-seq data extracted from The Cancer Genome Atlas (TCGA) were used to explore the clinical value of ERCC6 and ERCC8 expression in GC. We further conducted protein-protein interaction analysis, Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, gene set enrichment analysis, and gene-gene interaction analysis to explore the function and regulation networks of ERCC6 and ERCC8 in GC.ResultsIndividual and joint ERCC6/ERCC8 expression were significantly higher in adjacent normal mucosa compared with GC tissues. ERCC6 mRNA expression showed no difference in GC and paired tissues, while ERCC8 mRNA was significantly decreased in GC tissues. Protein expression of ERCC6, ERCC8, double negative ERCC6-ERCC8 and double positive ERCC6-ERCC8 and overexpressed ERCC6 mRNA were related to better clinicopathologic parameters, while overexpressed ERCC8 mRNA suggested worse parameters. Univariate survival analysis indicated that the OS was longer when ERCC6 protein expression and ERCC8 mRNA expression increased, and double negative ERCC6-ERCC8 expression was associated with a short OS. Bioinformatics analyses showed ERCC6 and ERCC8 were associated with nucleotide excision repair (NER) pathway, and six and ten gene sets were figured out to be related with ERCC6 and ERCC8, respectively. KEGG pathway showed that ERCC6/ERCC8 related gene sets were mainly involved in the regulation of PI3K/AKT/mTOR pathway. Direct physical interactions were found between ERCC6 and ERCC8.ConclusionsIndividual and joint expressions of ERCC6/ERCC8 were associated with clinical features of GC. Protein expression of ERCC6, ERCC6-ERCC8, and mRNA expression of ERCC8 were related to prognosis of GC. ERCC6 and ERCC8 primarily function in the NER pathway, and may regulate GC progression through the regulation of PI3K/AKT/mTOR pathway. creator: Jing Chen creator: Liang Li creator: Liping Sun creator: Yuan Yuan creator: Jingjing Jing uri: https://doi.org/10.7717/peerj.11791 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Chen et al. title: Relict groups of spiny frogs indicate Late Paleogene-Early Neogene trans-Tibet dispersal of thermophile faunal elements link: https://peerj.com/articles/11793 last-modified: 2021-07-15 description: BackgroundThe Himalaya-Tibet orogen (HTO) presents an outstanding geologically active formation that contributed to, and fostered, modern Asian biodiversity. However, our concepts of the historical biogeography of its biota are far from conclusive, as are uplift scenarios for the different parts of the HTO. Here, we revisited our previously published data set of the tribe Paini extending it with sequence data from the most western Himalayan spiny frogs Allopaa and Chrysopaa and using them as an indirect indicator for the potential paleoecological development of Tibet.MethodsWe obtained sequence data of two mitochondrial loci (16S rRNA, COI) and one nuclear marker (Rag1) from Allopaa samples from Kashmir Himalaya as well as Chrysopaa sequence data from the Hindu Kush available from GenBank to complement our previous data set. A Maximum likelihood and dated Bayesian gene tree were generated based on the concatenated data set. To resolve the inconsistent placement of Allopaa, we performed different topology tests.ResultsConsistent with previous results, the Southeast Asian genus Quasipaa is sister to all other spiny frogs. The results further reveal a basal placement of Chrysopaa relative to Allopaa and Nanorana with an estimated age of ca. 26 Mya. Based on the topology tests, the phylogenetic position of Allopaa as a sister clade to Chaparana seems to be most likely, resulting in a paraphyletic genus Nanorana and a separation from the latter clade around 20 Mya, although a basal position of Allopaa to the genus Nanorana cannot be entirely excluded. Both, the placements of Chrysopaa and Allopaa support the presence of basal Paini lineages in the far northwestern part of the HTO, which is diametrically opposite end of the HTO with respect to the ancestral area of spiny frogs in Southeast Asia. These striking distributional patterns can be most parsimoniously explained by trans-Tibet dispersal during the late Oligocene (subtropical Chrysopaa) respectively early Miocene (warm temperate Allopaa). Within spiny frogs, only members of the monophyletic Nanorana+Paa clade are adapted to the colder temperate climates, indicating that high-altitude environments did not dominate in the HTO before ca. 15 Mya. Our results are consistent with fossil records suggesting that large parts of Tibet were characterized by subtropical to warm temperate climates at least until the early Miocene. They contradict prevalent geological models of a highly uplifted late Paleogene proto-Plateau. creator: Sylvia Hofmann creator: Daniel Jablonski creator: Spartak N. Litvinchuk creator: Rafaqat Masroor creator: Joachim Schmidt uri: https://doi.org/10.7717/peerj.11793 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Hofmann et al. title: Single molecule, full-length transcript sequencing provides insight into the TPS gene family in Paeonia ostii link: https://peerj.com/articles/11808 last-modified: 2021-07-15 description: BackgroundThe tree peony (Paeonia section Moutan DC), one of the traditional famous flowers with both ornamental and medicinal value, was widely used in China. Surprisingly little is known about the full-length transcriptome sequencing in tree peony, limiting the research on its gene function and molecular mechanism. The trehalose phosphate phosphatase (TPS) family genes has been found to affect plant growth and development and the function of TPS genes in Paeonia ostii is unknown.MethodsIn our study, we performed single molecule, full-length transcript sequencing in P. ostii. 10 TPS family members were identified from PacBio sequencing for bioinformatics analysis and transcriptional expression analysis.ResultsA total of 230,736 reads of insert (ROI) sequences and 114,215 full-Length non-chimeric reads (FLNC) were obtained for further ORFs and transcription factors prediction, SSR analysis and lncRNA identification. NR, Swissprot, GO, COG, KOG, Pfam and KEGG databases were used to obtain annotation information of transcripts. 10 TPS family members were identified with molecular weights between 48.0 to 108.5 kD and isoelectric point between 5.61 to 6.37. Furthermore, we found that TPS family members contain conserved TPP or TPS domain. Based on phylogenetic tree analysis, PoTPS1 protein was highly similar to AtTPS1 protein in Arabidopsis. Finally, we analyzed the expression levels of all TPS genes in P. ostii and found PoTPS5 expressed at the highest level. In conclusion, this study combined the results of the transcriptome to systematically analyze the 10 TPS family members, and sets a framework for further research of this important gene family in development of tree peony. creator: Jing Sun creator: Tian Chen creator: Jun Tao uri: https://doi.org/10.7717/peerj.11808 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Sun et al. title: Genome-wide identification of candidate aquaporins involved in water accumulation of pomegranate outer seed coat link: https://peerj.com/articles/11810 last-modified: 2021-07-15 description: Aquaporins (AQPs) are a class of highly conserved integral membrane proteins that facilitate the uptake and transport of water and other small molecules across cell membranes. However, little is known about AQP genes in pomegranate (Punica granatum L.) and their potential role in water accumulation of the outer seed coat. We identified 38 PgrAQP genes in the pomegranate genome and divided them into five subfamilies based on a comparative analysis. Purifying selection played a role in the evolution of PgrAQP genes and a whole-genome duplication event in Myrtales may have contributed to the expansion of PgrTIP, PgrSIP, and PgrXIP genes. Transcriptome data analysis revealed that the PgrAQP genes exhibited different tissue-specific expression patterns. Among them, the transcript abundance of PgrPIPs were significantly higher than that of other subfamilies. The mRNA transcription levels of PgrPIP1.3, PgrPIP2.8, and PgrSIP1.2 showed a significant linear relationship with water accumulation in seed coats, indicating that PgrPIP1.3/PgrPIP2.8 located in the plasma membrane and PgrSIP1.2 proteins located on the tonoplast may be involved in water accumulation and contribute to the cell expansion of the outer seed coat, which then develops into juicy edible flesh. Overall, our results provided not only information on the characteristics and evolution of PgrAQPs, but also insights on the genetic improvement of outer seed coats. creator: Jianjian Liu creator: Gaihua Qin creator: Chunyan Liu creator: Xiuli Liu creator: Jie Zhou creator: Jiyu Li creator: Bingxin Lu creator: Jianrong Zhao uri: https://doi.org/10.7717/peerj.11810 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Liu et al. title: Developing a dementia inclusive hospital environment using an Integrated Care Pathway design: research protocol link: https://peerj.com/articles/11589 last-modified: 2021-07-14 description: People with dementia occupy 25% of the hospital beds. When they are admitted to hospitals their cognitive impairment is not considered in most of the cases. Some European and North American countries already have experience of implementing national plans about Alzheimer’s disease and dementia. However South European countries such as Spain are in the early stages. The aim of this study is to design an Integrated Care Pathway to adapt the hospital environment and processes to the needs of people with dementia and their caregivers, generating a sense of confidence, increasing their satisfaction and protecting them from potential harmful situations. This study uses King’s Fund Dementia Tool to assess the hospital environment and develop a continous improvement process. People with dementia, families, caregivers and healthcare staff will evaluate the different settings in order to provide guidance based on patient needs. Person-centred care, prudent healthcare and compassionate care are the conceptual framework of this care pathway. The implementation and evaluation of this research protocol will provide information about how to successfully design dementia interventions in a hospital environment within available resources in those contexts where dementia plans are in its infancy, as only around 15% of all states worldwide have currently designed a concise dementia national plan. creator: Jorge Riquelme-Galindo creator: Manuel Lillo-Crespo uri: https://doi.org/10.7717/peerj.11589 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Riquelme-Galindo and Lillo-Crespo title: Influence of the dental topical application of a nisin-biogel in the oral microbiome of dogs: a pilot study link: https://peerj.com/articles/11626 last-modified: 2021-07-14 description: Periodontal disease (PD) is one of the most widespread inflammatory diseases in dogs. This disease is initiated by a polymicrobial biofilm in the teeth surface (dental plaque), leading to a local inflammatory response, with gingivitis and/or several degrees of periodontitis. For instance, the prevention of bacterial dental plaque formation and its removal are essential steps in PD control. Recent research revealed that the antimicrobial peptide nisin incorporated in the delivery system guar gum (biogel) can inhibit and eradicate bacteria from canine dental plaque, being a promising compound for prevention of PD onset in dogs. However, no information is available regarding its effect on the dog’s oral microbiome. In this pilot study, the influence of the nisin-biogel on the diversity of canine oral microbiome was evaluated using next generation sequencing (NGS), aiming to access the viability of nisin-biogel to be used in long-term experiment in dogs. Composite toothbrushing samples of the supragingival plaque from two dogs were collected at three timepoints: T1—before any application of the nisin-biogel to the animals’ teeth surface; T2—one hour after one application of the nisin-biogel; and T3—one hour after a total of three applications of the nisin-biogel, each 48 hours. After that, microbial profiling was performed by NGS of the V3V4 16s rRNA region. After only one application of the nisin-biogel to the oral cavity of dogs, a statistically significant reduction in microbial diversity was observed (T2) as well as a reduction of some bacterial species potentially related with distinct stages of PD, when compared with samples collected before any application (T1). However, after a total of three nisin-biogel applications (T3), a recovery of the microbial diversity was detected. In conclusion, the nisin-biogel may influence the canine oral microbiome. A reduction in some bacterial species potentially related with distinct stages of PD was observed. This pilot study will help to design a controlled in vivo clinical trial to evaluate nisin-biogel effect on dental plaque progression and canine periodontal indices evolution in a long-term application period. creator: Eva Cunha creator: Sara Valente creator: Mariana Nascimento creator: Marcelo Pereira creator: Luís Tavares creator: Ricardo Dias creator: Manuela Oliveira uri: https://doi.org/10.7717/peerj.11626 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Cunha et al. title: LncRNA AC007255.1, an immune-related prognostic enhancer RNA in esophageal cancer link: https://peerj.com/articles/11698 last-modified: 2021-07-14 description: BackgroundGrowing evidence has suggested that enhancer RNAs (eRNAs), a set of long non-coding RNAs (lncRNAs) that were derived from active enhancer regions, play critical roles in regulating gene expression in human cancers. Nevertheless potential functions of eRNAs in esophageal cancer ESCA have not yet been expounded. Here, this study aimed to explore key prognostic eRNAs in ESCA.MethodsLncRNAs that were transcribed from active enhancer regions were analyzed utilizing the PreSTIGE algorithm, followed by prediction of their target genes. Based on the ESCA RNA-seq data from the TANRIC database, overall survival (OS)-related eRNAs were determined. The correlation between AC007255.1 expression and various clinical traits of ESCA was calculated. Functional enrichment analysis was presented based on its co-expressed genes. Based on the TIMER database, we analyzed correlations between AC007255.1 expression and immune infiltration levels. qRT-PCR was utilized to validate the expression of AC007255.1 and PRR15 in ESCA and normal tissues.ResultsTotally, 2,695 lncRNAs were transcribed from active enhancer regions. Among them, 33 were significantly related to OS. AC007255.1 was a key eRNA. PRR15 was a target gene of AC007255.1 (correlation coefficient r = 0.936). Patients with high AC007255.1 expression indicated poor OS time. There were significant correlations between AC007255.1 expression and clinical characteristics like pathological TNM, grade and stage. AC007255.1 was closely related to tight junction and neutrophil activation involved in immune response. Moreover, AC007255.1 expression was related to the infiltration levels of B cell, dendritic cell and neutrophil. qRT-PCR results confirmed that AC007255.1 and PRR15 were both up-regulated in ESCA tissues, and there was a positive correlation between the two.ConclusionOur findings identified a novel immune-related eRNA AC007255.1 in ESCA, which could be a promising prognostic factor for ESCA. creator: Qingqing Wang creator: Xiaoyan Yu creator: Ningning Yang creator: Lu Xu creator: Yunfeng Zhou uri: https://doi.org/10.7717/peerj.11698 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Wang et al. title: Ecological stoichiometric characteristics and influencing factors of carbon, nitrogen, and phosphorus in the leaves of Sophora alopecuroides L. in the Yili River Valley, Xinjiang link: https://peerj.com/articles/11701 last-modified: 2021-07-14 description: BackgroundSophora alopecuroides L. (S. alopecuroides L.) is a perennial herb widely distributed throughout Xinjiang, China. It is characterized by its rapid diffusion ability.MethodsTo reveal the ecological mechanism of the rapid spread of S. alopecuroides, and to elucidate the ecological stoichiometric characteristics of C, N, and P (and the influencing factors) in the leaves of S. alopecuroides, leaves were sampled from four habitats—forest, roadside, farmland, and desert—across the Yili River Valley. The variation rules of the ecological stoichiometric characteristics of C, N, and P in the leaves of S. alopecuroides were analyzed. Correlations between the ecological stoichiometric characteristics of leaves and environmental factors were examined using redundancy analysis (RDA).Results(1) The C, N, and P contents of S. alopecuroides leaves were 391.30–533.10 g/kg, 8.90–43.14 g/kg, and 0.71–2.04 g/kg, respectively, and the C/N, C/P, and N/P ratios were 10.34–4.94, 209.05–698.73, and 10.78–31.43 respectively. (2) The C content and C/P ratio of S. alopecuroides leaves were the highest in the desert habitat, leaf N content and N/P ratio were the highest in the forest habitat, leaf P content was the highest in the farmland habitat, and the leaf C/N ratio was the highest in the roadside habitat. (3) RDA showed that available potassium (AK) and pH were the main factors affecting the ecological stoichiometric characteristics of S. alopecuroides leaves in Yili Valley (p ≤ 0.05), and these factors were positively correlated with C, N, P, and N/P, and negatively correlated with C/P and C/N. AK was the dominant factor that affected the P content of S. alopecuroides leaves, and appropriate reduction of K fertilizer would be conducive to restraining the spread of S. alopecuroides. Soil C, N, P, and K content, soil organic matter (OM), nitrate nitrogen (NO3−-N), ammonium nitrogen (NH4+-N), and AK had no significant effect on the ecological stoichiometric characteristics of leaves (p > 0.05). creator: Yulu Zhang creator: Dong Cui creator: Yuhai Yang creator: Haijun Liu creator: Haijun Yang creator: Yang Zhao uri: https://doi.org/10.7717/peerj.11701 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2021 Zhang et al. title: Effects of salt stress levels on nutritional quality and microorganisms of alfalfa-influenced soil link: https://peerj.com/articles/11729 last-modified: 2021-07-14 description: BackgroundGlobally, there is a large amount of salinized land. These soils have varying degrees of salt stress, causing ionic toxicity and osmotic stress on plants. However, it is not clear how different degrees of salt stress affect plant nutrients and microbial communities. Thus, a comprehensive understanding of plant major nutrients and microbial communities response to salt stress is desirable.ResultsWe analyzed the main nutrients of the salt-tolerant ZhongMu No. 3 alfalfa variety planted in a salt stress environment. In mild and moderate group, the protein content and fatty acid content of alfalfa were the highest, indicating the best nutritional value. The severe group of salt stress affected the growth and development of alfalfa, as manifested by a decrease in the nutritional quality of alfalfa. Pseudomonas and Sphingobacterium that from alfalfa stem and leaf endophytes also increased with an increase in salt stress. In contrast, Sphingomonas, Methylobacterium, and Rhizobium decrease with increasing salt stress. Methylobacterium and Rhizobium have extremely significant differences in response to salt stress, and Exiquobacterium also shows significant differences.ConclusionsSoil salinity would be an important factor beyond which alfalfa nutrient quality and microbial community structure change. This study identified key levels of salt stress that may affect the nutrient quality and microbial community structure. These findings enhance our understanding of the effects of salt stress on the nutritional quality of alfalfa and provide a reference for the sustainable use of salinized soil in the future. creator: Qiang Lu creator: GenTu Ge creator: DuoWen Sa creator: ZhiJun Wang creator: MeiLing Hou creator: Yu Shan Jia uri: https://doi.org/10.7717/peerj.11729 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Lu et al. title: Test-retest reliability of a functional electromechanical dynamometer on swing eccentric hamstring exercise measures in soccer players link: https://peerj.com/articles/11743 last-modified: 2021-07-14 description: BackgroundThe use of a functional electromechanical dynamometer (FEMD) has been proposed as a valid and effective tool to evaluate specific movement patterns. The aim of this study was to determine the reliability of FEMD on swing eccentric hamstring exercise (SEHE) measures in soccer players.MethodsNineteen federated male soccer players (20.74 ± 4.04 years) performed the SEHE at three different isokinetic velocities (20–40–60 cm/s). These evaluations were conducted in four sessions, two for familiarization and two for registration. The average and maximum load (N) of the three isokinetic velocities was calculated from the values obtained from the FEMD (Dynasystem®, Bangalore).ResultsThe main results of this research showed that the reliability was high for the average load in the condition of 40 cm/s, presenting the highest ICC value (0.94). For maximum load, reliability was high in the condition of 20 cm/s. The manifestation of the most reliable load was the maximum load (ICC = 0.91–0.87).ConclusionsFEMD (Dynasystem®, Bangalore) is a reliable device to evaluate the eccentric strength of the hamstring muscles in soccer players. creator: Antonio Jesús Sánchez-Sánchez creator: Luis Javier Chirosa-Ríos creator: Ignacio Jesús Chirosa-Ríos creator: Agustín José García-Vega creator: Daniel Jerez-Mayorga uri: https://doi.org/10.7717/peerj.11743 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Sánchez-Sánchez et al. title: Role of ferroptosis-related genes in prognostic prediction and tumor immune microenvironment in colorectal carcinoma link: https://peerj.com/articles/11745 last-modified: 2021-07-14 description: Background and AimColorectal cancer (CRC) ranks the second most common cause of cancer-related mortality worldwide. Ferroptosis, a recently discovered form of programmed cell death different from other, raises promising novel opportunities for therapeutic intervention of CRC. This study intended to systematically assess the prognosis value and multiple roles of the ferroptosis-related genes in the tumor immune microenvironment of CRC.Materials and MethodsOf 1,192 CRC patients with complete information from the public datasets (TCGA CRC, GEO GSE39582 and GSE17538 cohorts) were selected for analysis. Firstly, K-means consensus clustering was performed to identify ferroptosis-associated subtypes in CRC patients. Subsequently, we constructed a risk signature based on ferroptosis-related genes in TCGA cohort and acquired its validation in two GEO cohorts. Additionally, we established a nomogram integrating the risk signature and clinical factors to improve risk assessment of CRC patients.ResultsFive molecular subtypes were identified by consensus clustering for ferroptosis-related genes. There were significant differences in the overall survival, immune cells infiltration status and PD1/PD-L1 mRNA among the five clusters. Then, a risk signature based on the ten-gene was constructed which could distinguish effectively high-risk group among CRC patients in both training and validation sets. The high-risk patients were more likely to have an inhibitory immune microenvironment and lower stemness features. A prognostic nomogram integrated risk signature and clinicopathological features could be used as a more accurate prognostic prediction visualization tool than TNM stage alone.ConclusionThis ferroptosis risk signature may accurately differentiate between different risk populations and predict the prognosis of CRC. Besides, this study elucidated the crucial role of ferroptosis in tumor immune microenvironment. creator: Chao Yang creator: Shuoyang Huang creator: Fengyu Cao creator: Yongbin Zheng uri: https://doi.org/10.7717/peerj.11745 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Yang et al. title: Molecular phylogenetic assessment of Spirobranchus kraussii-complex (Annelida: Serpulidae) from the Japanese Archipelago link: https://peerj.com/articles/11746 last-modified: 2021-07-14 description: Spirobranchus kraussii (Annelida: Serpulidae) was recognized as being widely distributed both in the Pacific and Atlantic Oceans. However, the sampling records far from its type locality (South Africa) have been questioned. Actually, recent molecular phylogenetic studies showed that S. kraussii contains genetically distinct species. In this study, we performed molecular phylogenetic analyses of S. cf. kraussii collected from Japan using the nucleotide sequences of a mitochondrial gene and two nuclear genes. Three lineages were recovered within Spirobranchus kraussii-complex in Japan, and one (Spirobranchus sp. 6) showed moderate genetic difference (approximately 4%) in the mitochondrial cytb gene sequence from Spirobranchus sp. 1, an undescribed sequenced species from Honshu Island, Japan. However, the nucleotide sequences of the 18S rRNA gene and ITS2 region were nearly indistinguishable. The other lineage was clearly distinct from the other previously sequenced species and is thus considered to be another distinct species of this species complex (Spirobranchus sp. 5). Although detailed morphological assessment of these lineages is necessary to define their taxonomic status, the present study provided further implications for the species diversity within the S. kraussii-complex. creator: Genki Kobayashi creator: Ryutaro Goto uri: https://doi.org/10.7717/peerj.11746 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Kobayashi and Goto title: Gene expression during THP-1 differentiation is influenced by vitamin D3 and not vibrational mechanostimulation link: https://peerj.com/articles/11773 last-modified: 2021-07-14 description: BackgroundIn injury or infection, monocytes migrate into the affected tissues from circulation and differentiate into macrophages which are subsequently involved in the inflammatory responses. Macrophage differentiation and activation have been studied in response to multiple chemokines and cytokines. However, mechanical, and physical stimuli can also influence macrophage differentiation, activation, cytokine production, and phagocytic activity.MethodsIn this study the macrophage differentiation from THP-1 monocytes was assessed upon the stimulation with 1,25-dihydroxyvitamin D3 and 1,000 Hz vibrations, using qPCR for quantification of transcript expression. Vitamin D binds the vitamin D receptor (VDR) and subsequently modulates the expression of a variety of genes in monocytes. The effects of the 1,000 Hz vibrational stimulation, and the combined treatment of vitamin D3 and 1000 Hz vibrations were unknown. The differentiation of macrophages was assessed by looking at transcription of macrophage markers (e.g., CD14, CD36), antigen presenting molecules (e.g., HLA-DRA), transcription factors (e.g., LEF-1, TCF7L2), and mechanosensors (e.g., PIEZO1 and PKD2).ResultsThe results showed that vitamin D3 induced THP-1 macrophage differentiation, which was characterized by upregulation of CD14 and CD36, downregulation of HLA-DRA, upregulation of the PKD2 (TRPP2), and an inverse relationship between TCF7L2 and LEF-1, which were upregulated and downregulated respectively. The 1,000 Hz vibrations were sensed from the cells which upregulated PIEZO1 and TCF3, but they did not induce expression of genes that would indicate macrophage differentiation. The mRNA transcription profile in the cells stimulated with the combined treatment was comparable to that of the cells stimulated by the vitamin only. The 1,000 Hz vibrations slightly weakened the effect of the vitamin for the regulation of CD36 and HLA-DMB in the suspension cells, but without causing changes in the regulation patterns. The only exception was the upregulation of TCF3 in the suspension cells, which was influenced by the vibrations. In the adherent cells, the vitamin D3 cancelled the upregulating effect of the 1,000 Hz vibrations and downregulated TCF3. The vitamin also cancelled the upregulation of PIEZO1 gene by the 1,000 Hz vibrations in the combined treatment.ConclusionThe mechanical stimulation with 1,000 Hz vibrations resulted in upregulation of PIEZO1 in THP-1 cells, but it did not affect the differentiation process which was investigated in this study. Vitamin D3 induced THP-1 macrophage differentiation and could potentially influence M2 polarization as observed by upregulation of CD36 and downregulation of HLA-DRA. In addition, in THP-1 cells undergoing the combined stimulation, the gene expression patterns were influenced by vitamin D3, which also ablated the effect of the mechanical stimulus on PIEZO1 upregulation. creator: Theodoros Simakou creator: Robin Freeburn creator: Fiona L. Henriquez uri: https://doi.org/10.7717/peerj.11773 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Simakou et al. title: Ambulacrarian insulin-related peptides and their putative receptors suggest how insulin and similar peptides may have evolved from insulin-like growth factor link: https://peerj.com/articles/11799 last-modified: 2021-07-14 description: BackgroundSome insulin/IGF-related peptides (irps) stimulate a receptor tyrosine kinase (RTK) that transfers the extracellular hormonal signal into an intracellular response. Other irps, such as relaxin, do not use an RTK, but a G-protein coupled receptor (GPCR). This is unusual since evolutionarily related hormones typically either use the same or paralogous receptors. In arthropods three different irps, i.e. arthropod IGF, gonadulin and Drosophila insulin-like peptide 7 (dilp7), likely evolved from a gene triplication, as in several species genes encoding these three peptides are located next to one another on the same chromosomal fragment. These arthropod irps have homologs in vertebrates, suggesting that the initial gene triplication was perhaps already present in the last common ancestor of deuterostomes and protostomes. It would be interesting to know whether this is indeed so and how insulin might be related to this trio of irps.MethodologyGenes encoding irps as well as their putative receptors were identified in genomes and transcriptomes from echinoderms and hemichordates.ResultsA similar triplet of genes coding for irps also occurs in some ambulacrarians. Two of these are orthologs of arthropod IGF and dilp7 and the third is likely a gonadulin ortholog. In echinoderms, two novel irps emerged, gonad stimulating substance (GSS) and multinsulin, likely from gene duplications of the IGF and dilp7-like genes respectively. The structures of GSS diverged considerably from IGF, which would suggest they use different receptors from IGF, but no novel irp receptors evolved. If IGF and GSS use different receptors, and the evolution of GSS from a gene duplication of IGF is not associated with the appearance of a novel receptor, while irps are known to use two different types of receptors, the ancestor of GSS and IGF might have acted on both types of receptors while one or both of its descendants act on only one. There are three ambulacrarian GPCRs that have amino acid sequences suggestive of being irp GPCRs, two of these are orthologs of the gonadulin and dilp7 receptors. This suggests that the third might be an IGF receptor, and that by deduction, GSS only acts on the RTK. The evolution of GSS from IGF may represent a pattern, where IGF gene duplications lead to novel genes coding for shorter peptides that activate an RTK. It is likely this is how insulin and the insect neuroendocrine irps evolved independently from IGF.ConclusionThe local gene triplication described from arthropods that yielded three genes encoding irps was already present in the last common ancestor of protostomes and deuterostomes. It seems plausible that irps, such as those produced by neuroendocrine cells in the brain of insects and echinoderm GSS evolved independently from IGF and, thus, are not true orthologs, but the result of convergent evolution. creator: Jan A. Veenstra uri: https://doi.org/10.7717/peerj.11799 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Veenstra title: Identification of consistent post-translational regulatory triplets related to oncogenic and tumour suppressive modulators in childhood acute lymphoblastic leukemia link: https://peerj.com/articles/11803 last-modified: 2021-07-14 description: BackgroundAcute lymphoblastic leukemia (ALL) is the most common type of childhood cancer. It can be caused by mutations that turn on oncogenes or turn off tumour suppressor genes. For instance, changes in certain genes including Rb and p53 are common in ALL cells. Oncogenes and TSGs may serve as a modulator gene to regulate the gene expression level via their respective target genes. To investigate the regulatory relationship between oncogenes, tumour suppressor genes and transcription factors at the post translational level in childhood ALL, we performed an integrative network analysis on the gene regulation in the post-translational level for childhood ALL based on many publicly available cancer gene expression data including TARGET and GEO database.MethodsWe collected 259 childhood ALL-related genes from the latest online leukemia database, Leukemia Gene Literature Database. These 259 genes were selected from a comprehensive systematic literature with experimental evidences. The identified and curated genes were also associated with patient survival cases and we incorporated this pediatric ALL-related gene list into our analysis. We extracted the known human TFs from the TRRUST database. Among 259 childhood ALL-related genes, 101 unique regulators were mapped to the list of oncogene and tumour suppressor genes (TSGs) from the ONGene and the TSGene databases, and these included 74 TSGs, 62 oncogenes and 46 TF genes.ResultsThe resulted regulation was presented as a hierarchical regulatory network with transcription factors (TFs) as intermediate regulators connecting the top modulators (oncogene and TSGs) to the common target genes. Cross-validation was applied to the results from the TARGET dataset by identifying the consistent regulatory motifs based on three independent ALL expression datasets. A three-layer regulatory network of consistent positive modulators in childhood ALL was constructed in which 74 modulators (40 oncogenes, 34 TSGs) are considered as the most important regulators. The middle layer and the bottom layer contain 34 TFs and 176 target genes, respectively. Oncogenes mostly participated in positive regulation of gene expression and the transcription process of RNA II polymerase, while TSGs were mainly involved in the negative regulation of gene expression. In addition, the oncogene-specific targets were enriched with regulators of the MAPK cascade while tumour suppressor-specific targets were associated with cell death.ConclusionThe results revealed that oncogenes and TSGs possess a different functional regulatory pattern with regard to not only their biological functions but also their specific target genes in childhood ALL cancer progression. Taken together, our findings could contribute to a better understanding of the important regulatory mechanisms and this method could be used to analyse the targeted genes at the post-translational level in childhood ALL through integrative network analysis. creator: YongKiat Wee creator: Yining Liu creator: Min Zhao uri: https://doi.org/10.7717/peerj.11803 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Wee et al. title: Conversion of alpine pastureland to artificial grassland altered CO2 and N2O emissions by decreasing C and N in different soil aggregates link: https://peerj.com/articles/11807 last-modified: 2021-07-14 description: BackgroundThe impacts of land use on greenhouse gases (GHGs) emissions have been extensively studied. However, the underlying mechanisms on how soil aggregate structure, soil organic carbon (SOC) and total N (TN) distributions in different soil aggregate sizes influencing carbon dioxide (CO2), and nitrous oxide (N2O) emissions from alpine grassland ecosystems remain largely unexplored.MethodsA microcosm experiment was conducted to investigate the effect of land use change on CO2and N2O emissions from different soil aggregate fractions. Soil samples were collected from three land use types, i.e., non-grazing natural grassland (CK), grazing grassland (GG), and artificial grassland (GC) in the Bayinbuluk alpine pastureland. Soil aggregate fractionation was performed using a wet-sieving method. The variations of soil aggregate structure, SOC, and TN in different soil aggregates were measured. The fluxes of CO2 and N2O were measured by a gas chromatograph.ResultsCompared to CK and GG, GC treatment significantly decreased SOC (by 24.9–45.2%) and TN (by 20.6–41.6%) across all soil aggregate sizes, and altered their distributions among soil aggregate fractions. The cumulative emissions of CO2 and N2O in soil aggregate fractions in the treatments of CK and GG were 39.5–76.1% and 92.7–96.7% higher than in the GC treatment, respectively. Moreover, cumulative CO2emissions from different soil aggregate sizes in the treatments of CK and GG followed the order of small macroaggregates (2–0.25 mm) > large macroaggregates (> 2 mm) > micro aggregates (0.25–0.053 mm) > clay +silt (< 0.053 mm), whereas it decreased with aggregate sizes decreasing in the GC treatment. Additionally, soil CO2 emissions were positively correlated with SOC and TN contents. The highest cumulative N2O emission occurred in micro aggregates under the treatments of CK and GG, and N2O emissions among different aggregate sizes almost no significant difference under the GC treatment.ConclusionsConversion of natural grassland to artificial grassland changed the pattern of CO2 emissions from different soil aggregate fractions by deteriorating soil aggregate structure and altering soil SOC and TN distributions. Our findings will be helpful to develop a pragmatic management strategy for mitigating GHGs emissions from alpine grassland. creator: Mei Zhang creator: Dianpeng Li creator: Xuyang Wang creator: Maidinuer Abulaiz creator: Pujia Yu creator: Jun Li creator: Xinping Zhu creator: Hongtao Jia uri: https://doi.org/10.7717/peerj.11807 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zhang et al. title: 2018 Survey of antimicrobial drug use and stewardship practices in adult cows on California dairies: post-Senate Bill 27 link: https://peerj.com/articles/11515 last-modified: 2021-07-13 description: BackgroundA survey of California (CA) dairies was performed in spring 2018 to characterize antimicrobial stewardship practices, antimicrobial drug (AMD) use, and health management of adult cows on CA dairies since the implementation of the Veterinary Feed Directive (VFD) and the CA Senate Bill 27 (SB 27). Effective January 1, 2017, the U.S. Food and Drug Administration (FDA) implemented regulatory changes requiring veterinary oversight for therapeutic uses of medically-important antimicrobial drugs (MIADs) administered in feed (VFD) and water (veterinary prescription). Similarly, effective January 1, 2018, the CA legislature enacted California Food and Agricultural Code (FAC) 14400–14408, formerly known as Senate Bill 27 (SB 27) requiring veterinary prescriptions for all other dosage forms of MIADs.MethodsThe questionnaire consisted of 43 questions partitioned into three sections to assess herd information, management practices, and AMD use and perspectives. The questionnaire was mailed to 1,282 grade A licensed dairies in CA and 149 responses (11.6%) were collected from 19 counties across the three defined regions of CA: Northern CA (NCA), Northern San Joaquin Valley (NSJV), and Greater Southern CA (GSCA).ResultsMost dairies reported treating all dry cows with intramammary AMD and/or teat sealant at the end of a lactation (87.2%). In 92.3% of dairies, producers relied on the veterinarian for information about AMD used to treat cows. Treatment duration for cows treated with AMD was based on the drug manufacturer’s label and veterinarian’s instructions in most dairies (98.6%). Most respondents to the survey confirmed having a valid veterinarian-client-patient-relationship (VCPR) for their dairies (91.7%), participated in animal welfare audit programs (81.8%) and dairy quality assurance programs (52.9%). Approximately 98.6% respondents were aware that all uses of MIADs in livestock required a veterinary feed directive (VFD) or prescription and are no longer sold over-the-counter (OTC) in CA since January 1, 2018. Multiple factor analysis (MFA) was performed and identified seven components composed of 21 variables (questions) that explained 99.7% of the total variance in the data. Hierarchical cluster analysis on the principal coordinates of the MFA based on conventional dairy survey responses identified two clusters characterized as large conventional dairies (median herd size: 1,265 cows) and mid-sized conventional dairies (median herd size: 715 cows) mostly in GSCA and NSJV. The organic dairies grouped into a single cluster of median herd size of 325 cows mostly in NCA.ConclusionsThe survey results contribute to the knowledge of AMD use and antimicrobial stewardship practices on CA dairies since the implementation of the SB 27 and VFD laws and provide useful information for future evaluation of resistance-related risk in adult cows. creator: Pius S. Ekong creator: Essam M. Abdelfattah creator: Emmanuel Okello creator: Deniece R. Williams creator: Terry W. Lehenbauer creator: Betsy M. Karle creator: Joan D. Rowe creator: Edith S. Marshall creator: Sharif S. Aly uri: https://doi.org/10.7717/peerj.11515 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Ekong et al. title: 2018 Survey of factors associated with antimicrobial drug use and stewardship practices in adult cows on conventional California dairies: immediate post-Senate Bill 27 impact link: https://peerj.com/articles/11596 last-modified: 2021-07-13 description: BackgroundAntimicrobial drugs (AMD) are critical for the treatment, control, and prevention of diseases in humans and food-animals. Good AMD stewardship practices and judicious use of AMD are beneficial to the preservation of animal and human health from antimicrobial resistance threat. This study reports on changes in AMD use and stewardship practices on California (CA) dairies, following the implementation of CA Senate Bill 27 (SB 27; codified as Food and Agricultural Code, FAC 14400–14408; here onward referred to as SB 27), by modeling the associations between management practices on CA conventional dairies and seven outcome variables relating to AMD use and stewardship practices following SB 27.MethodsA survey questionnaire was mailed to 1,282 grade A licensed dairies in CA in spring of 2018. Responses from 132 conventional dairies from 16 counties were included for analyses. Multivariate logistic regression models were specified to explore the associations between survey factors and six outcome variables: producers’ familiarity with the Food and Drug Administration’s (FDA), Silver Spring, WA, USA medically important antimicrobial drugs (MIAD) term; change in over-the-counter (OTC) AMD use; initiation or increased use of alternatives to AMD; changes to prevent disease outbreaks; changes in AMD costs; and better animal health post SB 27. We employed machine learning classification models to determine which of the survey factors were the most important predictors of good-excellent AMD stewardship practices of CA conventional dairy producers.ResultsHaving a valid veterinary-client-patient-relationship, involving a veterinarian in training employees on treatment protocols and decisions on AMDs used to treat sick cows, tracking milk and/or meat withdrawal intervals for treated cows, and participating in dairy quality assurance programs were positively associated with producers’ familiarity with MIADs. Use or increased use of alternatives to AMDs since 2018 was associated with decreased use of AMDs that were previously available OTC prior to SB 27. Important variables associated with good-excellent AMD stewardship knowledge by CA conventional dairy producers included having written or computerized animal health protocols, keeping a drug inventory log, awareness that use of MIADs required a prescription following implementation of SB 27, involving a veterinarian in AMD treatment duration determination, and using selective dry cow treatment.ConclusionsOur study identified management factors associated with reported AMD use and antimicrobial stewardship practices on conventional dairies in CA within a year from implementation of SB 27. Producers will benefit from extension outreach efforts that incorporate the findings of this survey by further highlighting the significance of these management practices and encouraging those that are associated with judicious AMD use and stewardship practices on CA conventional dairies. creator: Pius S. Ekong creator: Essam M. Abdelfattah creator: Emmanuel Okello creator: Deniece R. Williams creator: Terry W. Lehenbauer creator: Betsy M. Karle creator: Joan D. Rowe creator: Sharif S. Aly uri: https://doi.org/10.7717/peerj.11596 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Ekong et al. title: Scaling the effects of ocean acidification on coral growth and coral–coral competition on coral community recovery link: https://peerj.com/articles/11608 last-modified: 2021-07-13 description: Ocean acidification (OA) is negatively affecting calcification in a wide variety of marine organisms. These effects are acute for many tropical scleractinian corals under short-term experimental conditions, but it is unclear how these effects interact with ecological processes, such as competition for space, to impact coral communities over multiple years. This study sought to test the use of individual-based models (IBMs) as a tool to scale up the effects of OA recorded in short-term studies to community-scale impacts, combining data from field surveys and mesocosm experiments to parameterize an IBM of coral community recovery on the fore reef of Moorea, French Polynesia. Focusing on the dominant coral genera from the fore reef, Pocillopora, Acropora, Montipora and Porites, model efficacy first was evaluated through the comparison of simulated and empirical dynamics from 2010–2016, when the reef was recovering from sequential acute disturbances (a crown-of-thorns seastar outbreak followed by a cyclone) that reduced coral cover to ~0% by 2010. The model then was used to evaluate how the effects of OA (1,100–1,200 µatm pCO2) on coral growth and competition among corals affected recovery rates (as assessed by changes in % cover y−1) of each coral population between 2010–2016. The model indicated that recovery rates for the fore reef community was halved by OA over 7 years, with cover increasing at 11% y−1 under ambient conditions and 4.8% y−1 under OA conditions. However, when OA was implemented to affect coral growth and not competition among corals, coral community recovery increased to 7.2% y−1, highlighting mechanisms other than growth suppression (i.e., competition), through which OA can impact recovery. Our study reveals the potential for IBMs to assess the impacts of OA on coral communities at temporal and spatial scales beyond the capabilities of experimental studies, but this potential will not be realized unless empirical analyses address a wider variety of response variables representing ecological, physiological and functional domains. creator: Nicolas R. Evensen creator: Yves-Marie Bozec creator: Peter J. Edmunds creator: Peter J. Mumby uri: https://doi.org/10.7717/peerj.11608 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Evensen et al. title: Effect of genetic background on the evolution of Vancomycin-Intermediate Staphylococcus aureus (VISA) link: https://peerj.com/articles/11764 last-modified: 2021-07-13 description: Vancomycin-intermediate Staphylococcus aureus (VISA) typically arises through accumulation of chromosomal mutations that alter cell-wall thickness and global regulatory pathways. Genome-based prediction of VISA requires understanding whether strain background influences patterns of mutation that lead to resistance. We used an iterative method to experimentally evolve three important methicillin-resistant S. aureus (MRSA) strain backgrounds—(CC1, CC5 and CC8 (USA300)) to generate a library of 120 laboratory selected VISA isolates. At the endpoint, isolates had vancomycin MICs ranging from 4 to 10 μg/mL. We detected mutations in more than 150 genes, but only six genes (already known to be associated with VISA from prior studies) were mutated in all three background strains (walK, prs, rpoB, rpoC, vraS, yvqF). We found evidence of interactions between loci (e.g., vraS and yvqF mutants were significantly negatively correlated) and rpoB, rpoC, vraS and yvqF were more frequently mutated in one of the backgrounds. Increasing vancomycin resistance was correlated with lower maximal growth rates (a proxy for fitness) regardless of background. However, CC5 VISA isolates had higher MICs with fewer rounds of selection and had lower fitness costs than the CC8 VISA isolates. Using multivariable regression, we found that genes differed in their contribution to overall MIC depending on the background. Overall, these results demonstrated that VISA evolved through mutations in a similar set of loci in all backgrounds, but the effect of mutation in common genes differed with regard to fitness and contribution to resistance in different strains. creator: Michelle Su creator: Michelle H. Davis creator: Jessica Peterson creator: Claudia Solis-Lemus creator: Sarah W. Satola creator: Timothy D. Read uri: https://doi.org/10.7717/peerj.11764 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Su et al. title: Peach-Morchella intercropping mode affects soil properties and fungal composition link: https://peerj.com/articles/11705 last-modified: 2021-07-12 description: ObjectiveThis study aims to explore a three-dimensional planting mode in orchards and provide theoretical basis for the efficient peach-Morchella planting and soil management after Morchella cultivation.MethodsNext-generation sequencing was performed to investigate the variations in soil physicochemical properties, enzyme activities and fungal composition under peach-Morchella intercropping for one year and two years, by using the soil without peach-Morchella intercropping as the control group.ResultsPeach-Morchella intercropping decreased the soil bulk density, and significantly increased the maximum field capacity, non-capillary porosity and total porosity, organic matter, available potassium and available zinc, which together improved soil structure and soil fertility. Besides, the intercropping mode obviously enhanced soil enzyme activities and mineral absorption and transformation in peach orchard soils. The intercropping also resulted in a decline of soil fungal diversity, and the 2-year soil samples were of higher abundance of Zygomycota. More importantly, peach-Morchella intercropping elevated the yields of both peach and Morchella, bringing about obviously higher economic benefits.ConclusionContinuous peach-Morchella intercropping improves the soil structure and fertility while decreases soil fungal diversity, which can contribute to greater economic benefits of the peach orchard. Our findings shed new light on the intercropping-fungus-soil relationship, and may facilitate the further development of peach-Morchella intercropping. creator: Haiyan Song creator: Dong Chen creator: Shuxia Sun creator: Jing Li creator: Meiyan Tu creator: Zihong Xu creator: Ronggao Gong creator: Guoliang Jiang uri: https://doi.org/10.7717/peerj.11705 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Song et al. title: Genetic hypervariability of a Northeastern Atlantic venomous rockfish link: https://peerj.com/articles/11730 last-modified: 2021-07-12 description: BackgroundUnderstanding the interplay between climate and current and historical factors shaping genetic diversity is pivotal to infer changes in marine species range and communities’ composition. A phylogeographical break between the Atlantic and the Mediterranean has been documented for several marine organisms, translating into limited dispersal between the two basins.MethodsIn this study, we screened the intraspecific diversity of 150 individuals of the Madeira rockfish (Scorpaena maderensis) across its distributional range (seven sampling locations in the Atlantic and Mediterranean basins) using the mitochondrial control region and the nuclear S7 first intron.ResultsThe present work is the most comprehensive study done for this species, yielding no genetic structure across sampled locations and no detectable Atlantic-Mediterranean break in connectivity. Our results reveal deep and hyper-diverse bush-like genealogies with large numbers of singletons and very few shared haplotypes. The genetic hyper-diversity found for the Madeira rockfish is relatively uncommon in rocky coastal species, whose dispersal capability is limited by local oceanographic patterns. The effect of climate warming on the distribution of the species is discussed. creator: Sara M. Francisco creator: Rita Castilho creator: Cristina S. Lima creator: Frederico Almada creator: Francisca Rodrigues creator: Radek Šanda creator: Jasna Vukić creator: Anna Maria Pappalardo creator: Venera Ferrito creator: Joana I. Robalo uri: https://doi.org/10.7717/peerj.11730 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Francisco et al. title: Combined effects of biochar and chicken manure on maize (Zea mays L.) growth, lead uptake and soil enzyme activities under lead stress link: https://peerj.com/articles/11754 last-modified: 2021-07-12 description: The goal of the present work was to evaluate the additive effects of biochar and chicken manure on maize growth in Pb-contaminated soils. In this study, we conducted a pot experiment to investigate how biochar in soil (20, 40 g·kg−1), chicken manure in soil (20, 40 g·kg−1), or a combination of biochar and chicken manure in soil (each at 20 g·kg−1) effect maize growth, Pb uptake, leaves’ antioxidant enzymatic activities, and soil enzyme activities under artificial conditions to simulate moderate soil pollution (800 Pb mg·kg−1). The results showed that all biochar and/or chicken manure treatments significantly (P < 0.05) increased maize plant height, biomass, and superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) activity but decreased the malondialdehyde (MDA) content. These results indicated that amending the soil with biochar and/or chicken manure could alleviate Pb’s phytotoxicity. The biochar and/or chicken manure treatments remarkably decreased the Pb concentration in maize roots, stems, leaves, bioconcentration factor (BCF), translocation factor (TF), and available Pb concentration in the soil. Amending the soil with chicken manure alone was more effective at increasing maize growth and antioxidant enzymatic activity; the biochar treatment alone was more effective at inducing soil alkalinization and contributing to Pb immobilization. The combined use of biochar and chicken manure had an additive effect and produced the largest increases in maize growth, leaves’ antioxidant enzymatic activity, and soil enzyme activity. Their combined use also led to the most significant decreases in maize tissues Pb and soil available Pb. These results suggest that a combination of biochar and chicken manure was more effective at reducing soil Pb bioavailability and uptake by maize tissues, and increasing maize growth. This combination increased plant height by 43.23% and dry weight by 69.63% compared to the control. creator: Ling Liu creator: Jiwei Li creator: Guanghai Wu creator: Hongtao Shen creator: Guozhan Fu creator: Yanfang Wang uri: https://doi.org/10.7717/peerj.11754 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Liu et al. title: Long-term dynamics of Norovirus transmission in Japan, 2005–2019 link: https://peerj.com/articles/11769 last-modified: 2021-07-12 description: Norovirus continues to evolve, adjusting its pathogenesis and transmissibility. In the present study, we systematically collected datasets on Norovirus outbreaks in Japan from 2005 to 2019 and analyzed time-dependent changes in the asymptomatic ratio, the probability of virus detection, and the probability of infection given exposure. Reports of 1,728 outbreaks were published, and feces from all involved individuals, including those with asymptomatic infection, were tested for virus in 434 outbreaks. We found that the outbreak size did not markedly change over this period, but the variance in outbreak size increased during the winter (November–April). Assuming that natural history parameters did not vary over time, the asymptomatic ratio, the probability of virus detection, and the probability of infection given exposure were estimated to be 18.6%, 63.3% and 84.5%, respectively. However, a model with time-varying natural history parameters yielded better goodness-of-fit and suggested that the asymptomatic ratio varied by year. The asymptomatic ratio was as high as 25.8% for outbreaks caused by genotype GII.4 noroviruses. We conclude that Norovirus transmissibility has not changed markedly since 2005, and that yearly variation in the asymptomatic ratio could potentially be explained by the circulating dominant genotype. creator: Megumi Misumi creator: Hiroshi Nishiura uri: https://doi.org/10.7717/peerj.11769 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Misumi and Nishiura title: Inter- and intraspecific variation in the Artibeus species complex demonstrates size and shape partitioning among species link: https://peerj.com/articles/11777 last-modified: 2021-07-12 description: Neotropical leaf-nosed bats (family Phyllostomidae) are one of the most diverse mammalian families and Artibeus spp. is one of the most speciose phyllostomid genera. In spite of their species diversity, previous work on Artibeus crania using linear morphometrics has uncovered limited interspecific variation. This dearth of shape variation suggests that differences in cranial morphology are not contributing to niche partitioning across species, many of which are often found in sympatry. Using two-dimensional geometric morphometric methods on crania from eleven species from the Artibeus species complex, the current study demonstrates substantial cranial interspecific variation, sexual size and shape dimorphism, and intraspecific geographic variation. The majority of species were shown to have a unique size and shape, which suggests that each species may be taking advantage of slightly different ecological resources. Further, both sexual size and shape dimorphism were significant in the Artibeus species complex. Male and female Artibeus are known to have sex specific foraging strategies, with males eating near their roosts and females feeding further from their roosts. The presence of cranial sexual dimorphism in the Artibeus species complex, combined with previous work showing that different fruit size and hardness is correlated with different cranial shapes in phyllostomids, indicates that the males and females may be utilizing different food resources, leading to divergent cranial morphotypes. Additional field studies will be required to confirm this emergent hypothesis. Finally, significant geographical shape variation was found in a large intraspecific sample of Artibeus lituratus crania. However, this variation was not correlated with latitude and instead may be linked to local environmental factors. Additional work on ecology and behavior in the Artibeus species complex underlying the morphological variation uncovered in this study will allow for a better understanding of how the group has reached its present diversity. creator: Brandon P. Hedrick uri: https://doi.org/10.7717/peerj.11777 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Hedrick title: Seasonal variation in the diel activity of a dung beetle assemblage link: https://peerj.com/articles/11786 last-modified: 2021-07-12 description: The seasonal and diel variations of dung beetle species were studied in an Iberian mid-mountain locality to examine the interaction between these two temporal rhythms. We assume that a seasonal variation in the diel activity would support the notion that both rhythms may assist in achieving a quick and flexible response when the climatic conditions change. Data coming from 4,104 pitfall traps placed during 15 sampling periods and totalling 30 daily sampling cycles were analysed using circular statistics and General Linear Models. A wide variety of seasonal patterns are observed, highlighting those species with a clear unimodal or spring-autumn bimodal seasonal pattern. However, a midday diel pattern is the norm in most of the species, except in the case of those exhibiting a high body weight that prefer dusk or night periods. We hypothesize that most of the dung beetle species fly at noon to promote the passive heating of their muscle activity and minimize the metabolic energy expenditure. Results only partially support the seasonal variation in diel activity. Diel preferences are mainly manifested at the time of the year in which the abundance is greater. Approximately two-thirds of the considered species exhibit a similar diel activity along their seasonal active period. As consequence, a significant portion of the dung beetle species currently inhabiting Mediterranean mid-mountains are not able to use the daily variation in climatic conditions to limit the inconveniences of climate change. creator: Jorge M. Lobo creator: Eva Cuesta uri: https://doi.org/10.7717/peerj.11786 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Lobo and Cuesta title: Where three snail species attach while emersed in relation to heterogenous substrate temperatures underneath intertidal boulders link: https://peerj.com/articles/11675 last-modified: 2021-07-09 description: Mobile intertidal gastropods can employ behavioural thermoregulation to mitigate thermal stress, which may include retreating under boulders when emersed. However, little is known about how gastropod occupancy of under-boulder habitats is associated with any variations in substrate temperature that exist under boulders. Thermal imagery was used to measure the temperature of boulder lower surfaces and investigate how three snail species were associated at low tide with the maximum and average temperatures underneath grey siltstone and quartzite. Lower boulder surfaces had heterogeneous temperatures, with grey siltstone having temperature gradients and quartzite temperature showing mosaics. Temperature differences between the hottest and coolest gradient or mosaic locations were >5 °C; thus there was a range of temperatures that snails could interact with. All three snail species occupied cooler parts of temperature mosaics or gradients, avoiding the hottest areas. Stronger associations were detected on the hotter grey siltstone and for the more-thermally sensitive Nerita atramentosa and Diloma concameratum. Even though snails were associated with cooler areas, some individuals were still exposed to extreme substratum heat (>50 °C). These results suggest that gastropod thermoregulatory behaviour is far more complex than simply retreating underneath boulders at low tide, as there is also a range of under-boulder temperatures that they interact with. Untangling interactions between intertidal gastropods and heterogenous substrate temperatures is important given rocky seashores already represent a thermally-variable and potentially-stressful habitat, which may be exacerbated further given predictions of warming temperatures associated with climate change. creator: Nathan Janetzki creator: Kirsten Benkendorff creator: Peter G. Fairweather uri: https://doi.org/10.7717/peerj.11675 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Janetzki et al. title: Short-term high fat diet alters genes associated with metabolic and vascular dysfunction during adolescence in rats: a pilot study link: https://peerj.com/articles/11714 last-modified: 2021-07-09 description: BackgroundDiet-induced metabolic dysfunction precedes multiple disease states including diabetes, heart disease, and vascular dysfunction. The critical role of the vasculature in disease progression is established, yet the details of how gene expression changes in early cardiovascular disease remain an enigma. The objective of the current pilot project was to evaluate whether a quantitative assessment of gene expression within the aorta of six-week old healthy male Sprague-Dawley rats compared to those exhibiting symptoms of metabolic dysfunction could reveal potential mediators of vascular dysfunction.MethodsRNA was extracted from the aorta of eight rats from a larger experiment; four animals fed a high-fat diet (HFD) known to induce symptoms of metabolic dysfunction (hypertension, increased adiposity, fasting hyperglycemia) and four age-matched healthy animals fed a standard chow diet (CHOW). The bioinformatic workflow included Gene Ontology (GO) biological process enrichment and network analyses.ResultsThe resulting network contained genes relevant to physiological processes including fat and protein metabolism, oxygen transport, hormone regulation, vascular regulation, thermoregulation, and circadian rhythm. The majority of differentially regulated genes were downregulated, including several associated with circadian clock function. In contrast, leptin and 3-hydroxy-3-methylglutaryl-CoA synthase 2 (Hmgcs2) were notably upregulated. Leptin is involved in several major energy balance signaling pathways and Hmgcs2 is a mitochondrial enzyme that catalyzes the first reaction of ketogenesis.ConclusionTogether, these data describe changes in gene expression within the aortic wall of HFD rats with early metabolic dysfunction and highlight potential pathways and signaling intermediates that may impact the development of early vascular dysfunction. creator: Alex E. Mohr creator: Rebecca A. Reiss creator: Monique Beaudet creator: Johnny Sena creator: Jay S. Naik creator: Benjimen R. Walker creator: Karen L. Sweazea uri: https://doi.org/10.7717/peerj.11714 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Mohr et al. title: ERpred: a web server for the prediction of subtype-specific estrogen receptor antagonists link: https://peerj.com/articles/11716 last-modified: 2021-07-09 description: Estrogen receptors alpha and beta (ERα and ERβ) are responsible for breast cancer metastasis through their involvement of clinical outcomes. Estradiol and hormone replacement therapy targets both ERs, but this often leads to an increased risk of breast and endometrial cancers as well as thromboembolism. A major challenge is posed for the development of compounds possessing ER subtype specificity. Herein, we present a large-scale classification structure-activity relationship (CSAR) study of inhibitors from the ChEMBL database which consisted of an initial set of 11,618 compounds for ERα and 7,810 compounds for ERβ. The IC50 was selected as the bioactivity unit for further investigation and after the data curation process, this led to a final data set of 1,593 and 1,281 compounds for ERα and ERβ, respectively. We employed the random forest (RF) algorithm for model building and of the 12 fingerprint types, models built using the PubChem fingerprint was the most robust (Ac of 94.65% and 92.25% and Matthews correlation coefficient (MCC) of 89% and 76% for ERα and ERβ, respectively) and therefore selected for feature interpretation. Results indicated the importance of features pertaining to aromatic rings, nitrogen-containing functional groups and aliphatic hydrocarbons. Finally, the model was deployed as the publicly available web server called ERpred at http://codes.bio/erpred where users can submit SMILES notation as the input query for prediction of the bioactivity against ERα and ERβ. creator: Nalini Schaduangrat creator: Aijaz Ahmad Malik creator: Chanin Nantasenamat uri: https://doi.org/10.7717/peerj.11716 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Schaduangrat et al. title: Predicting temperature curve based on fast kNN local linear estimation of the conditional distribution function link: https://peerj.com/articles/11719 last-modified: 2021-07-09 description: Predicting the yearly curve of the temperature, based on meteorological data, is essential for understanding the impact of climate change on humans and the environment. The standard statistical models based on the big data discretization in the finite grid suffer from certain drawbacks such as dimensionality when the size of the data is large. We consider, in this paper, the predictive region problem in functional time series analysis. We study the prediction by the shortest conditional modal interval constructed by the local linear estimation of the cumulative function of $Y$Y given functional input variable $X$X. More precisely, we combine the $k$k-Nearest Neighbors procedure to the local linear algorithm to construct two estimators of the conditional distribution function. The main purpose of this paper is to compare, by a simulation study, the efficiency of the two estimators concerning the level of dependence. The feasibility of these estimators in the functional times series prediction is examined at the end of this paper. More precisely, we compare the shortest conditional modal interval predictive regions of both estimators using real meteorological data. creator: Ibrahim M. Almanjahie creator: Zoulikha Kaid creator: Ali Laksaci creator: Mustapha Rachdi uri: https://doi.org/10.7717/peerj.11719 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Almanjahie et al. title: Diversity and function of culturable actinobacteria in the root-associated of Salvia miltiorrhiza Bunge link: https://peerj.com/articles/11749 last-modified: 2021-07-09 description: The root-associated actinobacteria play important roles in plant growth, nutrient use, and disease resistance due to their functional diversity. Salvia miltiorrhiza is a critical medicinal plant in China. The root actinobacterial community structure has been studied; however, the functions of root-associated actinobacteria of S. miltiorrhiza have not been elucidated. This study aimed to decipher the diversity and function of the culturable root-associated actinobacteria in plant growth using culture-dependent technology and culturable microbe metagenomes. We isolated 369 strains from the root-associated actinobacteria, belonging to four genera, among which Streptomyces was dominant. Besides, the functional prediction revealed some pathways related to plant growth, nitrogen and phosphorus metabolism, and antagonistic pathogens. We systematically described the diversity and functions of the culturable root-associated actinobacteria community. Our results demonstrated that the culturable root-associated actinobacteria of S. miltiorrhiza have rich functionalities, explaining the possible contribution of culturable root-associated actinobacteria to S. miltiorrhiza’s growth and development. This study provides new insights into understanding the function of the culturable root-associated actinobacteria and can be used as a knowledge base for plant growth promoters and biological control agent development in agriculture. creator: Yu-Rui Wu creator: Cui-Bai Li creator: Yan-Hong Wu creator: Lan Li creator: Bo Li creator: Wen-Bo Li creator: Bu-Jin Ma creator: Zhu-Yun Yan uri: https://doi.org/10.7717/peerj.11749 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Wu et al. title: Genetic differentiation in the genus Characodon: implications for conservation and taxonomy link: https://peerj.com/articles/11492 last-modified: 2021-07-08 description: The subfamily Goodeinae is a group of fishes endemic to the Mexican highlands. Most of the species are restricted to small and isolated streams or springs. Within this subfamily, the genus Characodon is the earliest diverging lineage of which three species have been described: C. lateralis, C. audax, and C. garmani, with the latter, considered extinct. Characodon lateralis and C. audax are classed as endangered, and have been the subject of taxonomic controversy since their description: previous studies have recognized a genetic differentiation in two groups separated by the El Salto waterfall, but morphological analyses contradict these genetic results. We perform a phylogeographic study using the mitochondrial cytb gene and d-loop region to elucidate the evolutionary history of C. lateralis and C. audax. The results with both markers show the presence of two highly differentiated haplogroups; one distributed north and the other distributed south of the waterfall, with genetic distances of 1.7 and 13.1% with cytb and d-loop respectively, and divergence calculated to have occurred 1.41 Mya. Significant genetic structure was found within each haplogroup and suggests the existence of at least four Evolutionary Significant Units (ESUs) within the examined populations. The possible processes identified as contributing to the formation of differentiated genetic groups are isolation, low population size, recurrent bottlenecks, and the strong sexual selection exhibited by the genus. creator: Rosa G. Beltrán-López creator: Rodolfo Pérez-Rodríguez creator: Ofelia C. Montañez-García creator: Juan M. Artigas-Azas creator: Michael Köck creator: Adán F. Mar-Silva creator: Omar Domínguez-Domínguez uri: https://doi.org/10.7717/peerj.11492 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Beltrán-López et al. title: Light alters the impacts of nitrogen and foliar pathogens on the performance of early successional tree seedlings link: https://peerj.com/articles/11587 last-modified: 2021-07-08 description: Light limitation is a major driver of succession and an important determinant of the performance of shade-intolerant tree seedlings. Shade intolerance may result from a resource allocation strategy characterized by rapid growth and high metabolic costs, which may make shade-intolerant species particularly sensitive to nutrient limitation and pathogen pressure. In this study, we evaluated the degree to which nitrogen availability and fungal pathogen pressure interact to influence plant performance across different light environments. To test this, we manipulated nitrogen availability (high, low) and access by foliar fungal pathogens (sprayed with fungicide, unsprayed) to seedlings of the shade-intolerant tree, Liquidambar styraciflua, growing at low and high light availability, from forest understory to adjacent old field. Foliar fungal damage varied with light and nitrogen availability; in low light, increasing nitrogen availability tripled foliar damage, suggesting that increased nutrient availability in low light makes plants more susceptible to disease. Despite higher foliar damage under low light, spraying fungicide to exclude pathogens promoted 14% greater plant height only under high light conditions. Thus, although nitrogen availability and pathogen pressure each influenced aspects of plant performance, these effects were context dependent and overwhelmed by light limitation. This suggests that failure of shade-intolerant species to invade closed-canopy forest can be explained by light limitation alone. creator: Alexander Brown creator: Robert W. Heckman uri: https://doi.org/10.7717/peerj.11587 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Brown and Heckman title: Plastics in Porifera: The occurrence of potential microplastics in marine sponges and seawater from Bocas del Toro, Panamá link: https://peerj.com/articles/11638 last-modified: 2021-07-08 description: Microplastics (MP) are now considered ubiquitous across global aquatic environments. The ingestion of MP by fish and other marine vertebrates is well studied, but the ingestion of MP by marine invertebrates is not. Sponges (Phylum Porifera) are particularly understudied when it comes to MP ingestion, even though they are widely distributed across benthic habitats, can process large volumes of seawater, and can retain small particles within their water filtration systems. This study examines the presence of potential MP (PMP) in wild marine sponges and seawater collected in Bocas del Toro, Panamá. Subsurface seawater and tissue from six common Caribbean sponge species was collected in Saigon Bay, a heavily impacted, shallow-water coral reef. Seawater samples were filtered onto glass fiber filters to retain any PMP present and sponge tissue was digested with bleach, heated and filtered. Filters were examined using fluorescence microscopy to quantify PMP. An average of 107 ± 25 PMP L–1 was detected in seawater from Saigon Bay with particles ranging in size between 10 μm and ~3,000 μm. The number of PMP found in sponge tissue ranged between 6 ± 4 and 169 ± 71 PMP g–1 of dry tissue. Most particles found in sponge samples were very small (10–20 μm), but fibers greater than 5,000 μm were detected. Our results indicate that PMP exists within the tissues of the sponges we studied, but future studies should confirm the presence of MP in sponges using chemical analysis. Most importantly, the discrepancy between low levels of PMP in our sponge samples and high levels in the surrounding seawater highlights the potential for sponges to resist and/or egest MP. Finally, we provide a critical evaluation of our methods to improve their use in future MP work with benthic marine organisms. creator: Bailey R. Fallon creator: Christopher J. Freeman uri: https://doi.org/10.7717/peerj.11638 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Fallon and Freeman title: Flatfoot in Africa, the cirripede Chthamalus in the west Indian Ocean link: https://peerj.com/articles/11710 last-modified: 2021-07-08 description: Barnacles of the genus Chthamalus are commonly encountered rocky intertidal shores. The phylogeography of the different species in the Western Indian Ocean is unclear. Using morphological characteristics as well as the molecular markers mitochondrial cytochrome oxygenase subunit I (COI) and the nuclear sodium-potassium ATPase (NaKA), we identified four clades representing four species in the Western Indian Ocean and its adjacent seas. Among these species, a newly identified species, Chthamalus barilani, which was found in Madagascar, Zanzibar and Tanzania. Chthamalus from the coasts of Tanzania and Zanzibar is identified morphologically as C. malayensis, and clusters with C. malayensis from the Western Pacific and the Indo Malayan regions. C. malayensis is regarded as a group of four genetically differentiated clades representing four cryptic species. The newly identified African clade is genetically different from these clades and the pairwise distances between them justify the conclusion that it is an additional cryptic species of C. malayensis. This type of genetic analyses offers an advantage over morphological characterization and allowed us to reveal that another species, C. barnesi, which is known from the Red Sea, is also distributed in the Arabian Sea and the Persian Gulf. We could also confirm the presence of the South African species C. dentatus in the Mozambique channel. This represents the Northeastern limit of C. dentatus, which is usually distributed along the coast of southern Africa up to the Islands of Cape Verde in West Africa. Altogether, based on a combination of morphology and genetics, we distinct between four clusters of Chthamalus, and designate their distribution in the West Indian Ocean. These distinctions do not agree with the traditional four groups reported previously based merely on morphological data. Furthermore, these findings underline the importance of a combining morphological and genetics tools for constructing barnacle taxonomy. creator: Noa Simon-Blecher creator: Avi Jacob creator: Oren Levy creator: Lior Appelbaum creator: Shiran Elbaz-Ifrah creator: Yair Achituv uri: https://doi.org/10.7717/peerj.11710 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Simon-Blecher et al. title: Identification of a circadian gene signature that predicts overall survival in lung adenocarcinoma link: https://peerj.com/articles/11733 last-modified: 2021-07-08 description: BackgroundLung adenocarcinoma (LUAD) is one of the most common subtypes of lung cancer which is the leading cause of death in cancer patients. Circadian clock disruption has been listed as a likely carcinogen. However, whether the expression of circadian genes affects overall survival (OS) in LUAD patients remains unknown. In this article, we identified a circadian gene signature to predict overall survival in LUAD.MethodsRNA sequencing (HTSeq-FPKM) data and clinical characteristics were obtained for a cohort of LUAD patients from The Cancer Genome Atlas (TCGA). A multigene signature based on differentially expressed circadian clock-related genes was generated for the prediction of OS using Least Absolute Shrinkage and Selection Operator (LASSO)-penalized Cox regression analysis, and externally validated using the GSE72094 dataset from the GEO database.ResultsFive differentially expressed genes (DEGs) were identified to be significantly associated with OS using univariate Cox proportional regression analysis (P < 0.05). Patients classified as high risk based on these five DEGs had significantly lower OS than those classified as low risk in both the TGCA cohort and GSE72094 dataset (P < 0.001). Multivariate Cox regression analysis revealed that the five-gene-signature based risk score was an independent predictor of OS (hazard ratio > 1, P < 0.001). Receiver operating characteristic (ROC) curves confirmed its prognostic value. Gene set enrichment analysis (GSEA) showed that Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to cell proliferation, gene damage repair, proteasomes, and immune and autoimmune diseases were significantly enriched.ConclusionA novel circadian gene signature for OS in LUAD was found to be predictive in both the derivation and validation cohorts. Targeting circadian genes is a potential therapeutic option in LUAD. creator: Xinliang Gao creator: Mingbo Tang creator: Suyan Tian creator: Jialin Li creator: Wei Liu uri: https://doi.org/10.7717/peerj.11733 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Gao et al. title: A review of coral bleaching specimen collection, preservation, and laboratory processing methods link: https://peerj.com/articles/11763 last-modified: 2021-07-08 description: Under current climate warming predictions, the future of coral reefs is dire. With projected coral reef decline, it is likely that coral specimens for bleaching research will increasingly become a more limited resource in the future. By adopting a holistic approach through increased collaborations, coral bleaching scientists can maximize a specimen’s investigative yield, thus reducing the need to remove more coral material from the reef. Yet to expand a specimen’s utility for additional analytic methods, information on how corals are collected is essential as many methods are variably sensitive to upstream handling and processing. In an effort to identify common practices for coral collection, sacrifice, preservation, and processing in coral bleaching research, we surveyed the literature from the last 6.5 years and created and analyzed the resulting dataset of 171 publications. Since January 2014, at least 21,890 coral specimens were collected for bleaching surveys or bleaching experiments. These specimens spanned 122 species of scleractinian corals where the most frequently sampled were Acropora millepora, Pocillopora damicornis, and Stylophora pistillata. Almost 90% of studies removed fragments from the reef, 6% collected skeletal cores, and 3% collected mucus specimens. The most common methods for sacrificing specimens were snap freezing with liquid nitrogen, chemical preservation (e.g., with ethanol or nucleic acid stabilizing buffer), or airbrushing live fragments. We also characterized 37 distinct methodological pathways from collection to processing of specimens in preparation for a variety of physiological, -omic, microscopy, and imaging analyses. Interestingly, almost half of all studies used only one of six different pathways. These similarities in collection, preservation, and processing methods illustrate that archived coral specimens could be readily shared among researchers for additional analyses. In addition, our review provides a reference for future researchers who are considering which methodological pathway to select to maximize the utility of coral bleaching specimens that they collect. creator: Rowan H. McLachlan creator: Kerri L. Dobson creator: Emily R. Schmeltzer creator: Rebecca Vega Thurber creator: Andréa G. Grottoli uri: https://doi.org/10.7717/peerj.11763 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 McLachlan et al. title: Anti-inflammatory and antiaging properties of chlorogenic acid on UV-induced fibroblast cell link: https://peerj.com/articles/11419 last-modified: 2021-07-07 description: BackgroundSkin aging is the most common dermatological problem caused by intrinsic and extrinsic factor, such as exposure to (ultraviolet) UV rays. Chlorogenic acid (CA) is a phenolic compound which is known for its antioxidant properties against oxidative stress.ObjectiveThis study investigates the antiaging and anti-inflammatory properties of CA on UV-induced skin fibroblast cells.MethodsAnti-inflammatory properties of CA were assessed by measuring inflammatory-related proteins IL-1β and TNF-α, while antiaging properties of CA were assessed by measuring reactive oxygen species (ROS), apoptosis, live and necrotic cells, and COL-3 gene expression level.ResultsTreating UV-induced skin fibroblast cells with CA decreased the level of ROS, IL-1β, TNF-α, apoptotic cells, and necrotic cells and increased live cells and COL-3 gene expression.ConclusionCA has the potential as the protective compound against inflammation and aging by decreasing the level ROS, pro-inflammatory cytokines IL-1β and TNF-α, apoptotic cells, and necrotic cells and by increasing live cells and COL-3 gene expression. creator: Ermi Girsang creator: Chrismis N. Ginting creator: I Nyoman Ehrich Lister creator: Kamila yashfa Gunawan creator: Wahyu Widowati uri: https://doi.org/10.7717/peerj.11419 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Girsang et al. title: Analysis and forecasts for trends of COVID-19 in Pakistan using Bayesian models link: https://peerj.com/articles/11537 last-modified: 2021-07-07 description: BackgroundCOVID-19 is currently on full flow in Pakistan. Given the health facilities in the country, there are serious threats in the upcoming months which could be very testing for all the stakeholders. Therefore, there is a need to analyze and forecast the trends of COVID-19 in Pakistan.MethodsWe have analyzed and forecasted the patterns of this pandemic in the country, for next 30 days, using Bayesian structural time series models. The causal impacts of lifting lockdown have also been investigated using intervention analysis under Bayesian structural time series models. The forecasting accuracy of the proposed models has been compared with frequently used autoregressive integrated moving average models. The validity of the proposed model has been investigated using similar datasets from neighboring countries including Iran and India.ResultsWe observed the improved forecasting accuracy of Bayesian structural time series models as compared to frequently used autoregressive integrated moving average models. As far as the forecasts are concerned, on August 10, 2020, the country is expected to have 333,308 positive cases with 95% prediction interval [275,034–391,077]. Similarly, the number of deaths in the country is expected to reach 7,187 [5,978–8,390] and recoveries may grow to 279,602 [208,420–295,740]. The lifting of lockdown has caused an absolute increase of 98,768 confirmed cases with 95% interval [85,544–111,018], during the post-lockdown period. The positive aspect of the forecasts is that the number of active cases is expected to decrease to 63,706 [18,614–95,337], on August 10, 2020. This is the time for the concerned authorities to further restrict the active cases so that the recession of the outbreak continues in the next month. creator: Navid Feroze creator: Kamran Abbas creator: Farzana Noor creator: Amjad Ali uri: https://doi.org/10.7717/peerj.11537 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Feroze et al. title: Effects of exercise training with blood flow restriction on vascular function in adults: a systematic review and meta-analysis link: https://peerj.com/articles/11554 last-modified: 2021-07-07 description: BackgroundBlood flow restricted exercise (BFRE) improves physical fitness, with theorized positive effects on vascular function. This systematic review and meta-analysis aimed to report (1) the effects of BFRE on vascular function in adults with or without chronic health conditions, and (2) adverse events and adherence reported for BFRE.MethodologyFive electronic databases were searched by two researchers independently to identify studies reporting vascular outcomes following BFRE in adults with and without chronic conditions. When sufficient data were provided, meta-analysis and exploratory meta-regression were performed.ResultsTwenty-six studies were included in the review (total participants n = 472; n = 41 older adults with chronic conditions). Meta-analysis (k = 9 studies) indicated that compared to exercise without blood flow restriction, resistance training with blood flow restriction resulted in significantly greater effects on endothelial function (SMD 0.76; 95% CI [0.36–1.14]). No significant differences were estimated for changes in vascular structure (SMD −0.24; 95% CI [−1.08 to 0.59]). In exploratory meta-regression analyses, several experimental protocol factors (design, exercise modality, exercised limbs, intervention length and number of sets per exercise) were significantly associated with the effect size for endothelial function outcomes. Adverse events in BFRE studies were rarely reported.ConclusionThere is limited evidence, predominantly available in healthy young adults, on the effect of BFRE on vascular function. Signals pointing to effect of specific dynamic resistance exercise protocols with blood flow restriction (≥4 weeks with exercises for the upper and lower limbs) on endothelial function warrant further investigation. creator: Elisio A. Pereira-Neto creator: Hayley Lewthwaite creator: Terry Boyle creator: Kylie Johnston creator: Hunter Bennett creator: Marie T. Williams uri: https://doi.org/10.7717/peerj.11554 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Pereira-Neto et al. title: Impact of fertilization with reducing in nitrogen and phosphorous application on growth, yield and biomass accumulation of rice (Oryza sativa L.) under a dual cropping system link: https://peerj.com/articles/11668 last-modified: 2021-07-07 description: The current farming system in China is heavily reliant on synthetic fertilizers, which adversely affect soil quality and crop production. Therefore, the aim of this study was to assess the effect of different nitrogen (N) and phosphorous (P) fertilizer application rate on the growth, yield, and yield components of rice cultivars in the Binyang, Beiliu and Liucheng sites of southern China in the early (March to July) and late season (August to December). The study consisted of three fertilization regimes—CK (N0P0); N180P90 (180 kg N + 90 kg P2O5 ha−1) and N90P45 (90 kg N ha−1 + 45 kg P2O5)—conducted at each of three different experimental sites with four cultivars (Baixang 139, Y Liangyou 1, Guiyu 9, and Teyou 582). Results showed that the leaf area index (LAI) was 38.8% found higher in Guiyu 9 compared with Baxiang at reduced fertilization (N90P45). N90P45 resulted higher dry matter production at the heading (9411.2 kg ha−1) and maturity (15319.5 kg ha−1) stages in Teyou 582 at Beiliu. Fertilization (N180P90) had higher effective panicle number (4,158,800 panicle ha−1) and grains panicle−1 (113.84 grains) compared with other treatments. Teyou 582 treated with N90P45 and Y Liangyou 1 treated with N180P90 improved seed setting rate average by 82.91% and 72.17% compared with other treatments at Beiliu in both seasons, respectively. N0P0 and N90P45 increased the thousand-grain weight (TGW) of Y Liangyou 1 at Binyang (27.07 g) and Liucheng (27.84 g) during the early and late seasons, respectively. In Beiliu, the N90P45 treatment (6611.7 kg ha−1) of Teyou 582 increased grain yield compared with other treatments. Overall, our results suggested that reducing N and P at the ratio of 90:45 kg ha−1 in Teyou 582 and Y Liangyou 1 could increase rice grain yield and yield components. creator: Ke Wu creator: Izhar Ali creator: Huimin Xie creator: Saif Ullah creator: Anas Iqbal creator: Shangqing Wei creator: Liang He creator: QianYing Huang creator: Xiaoyan Wu creator: Fangwei Cheng creator: Ligeng Jiang uri: https://doi.org/10.7717/peerj.11668 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Wu et al. title: Comparative population genetics of swimming crab host (Portunus pelagicus) and common symbiotic barnacle (Octolasmis angulata) in Vietnam link: https://peerj.com/articles/11671 last-modified: 2021-07-07 description: BackgroundBy comparing spatial geographical structures of host populations with that of their symbionts light can be shed on their biological interactions, and the degree of congruence between host and symbiont phylogeographies should reflect their life histories and especially dispersal mechanisms.MethodsHere, we analyzed the genetic diversity and structure of a host, the blue swimming crab, Portunus pelagicus, and its symbiotic pedunculate barnacle Octolasmis angulata from six location sites representing three geographic regions (north, central and south) along the Vietnam coastline. High levels of congruence in their phylogeographic patterns were expected as they both undergo planktonic larval stages.ResultsBased on the COI mtDNA markers, O. angulata populations showed higher genetic diversity in comparison with their host P. pelagicus (number of haplotype/individuals, haplotype and nucleotide diversity are 119/192, 0.991 ± 0.002 and 0.02; and 89/160, 0.913 ± 0.02 and 0.015, respectively). Pairwise Fst and AMOVA analyses showed a more pronounced population structure in the symbiotic barnacle than in its crab host. The DAPC analyses identified three genetic clusters. However, both haplotype networks and scatter plots supported connectivity of the host and the symbiotic barnacle throughout their distribution range, except for low subdivision of southern population. Isolation by distance were detected only for the symbiont O. angulata (R2 = 0.332, P = 0.05), while dbMEM supported spatial structure of both partners, but only at MEM-1 (Obs. 0.2686, P < 0.01 and Obs. 0.2096, P < 0.01, respectively). creator: Binh Thuy Dang creator: Oanh Thi Truong creator: Sang Quang Tran creator: Henrik Glenner uri: https://doi.org/10.7717/peerj.11671 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Dang et al. title: NMDAR in bladder smooth muscle is not a pharmacotherapy target for overactive bladder in mice link: https://peerj.com/articles/11684 last-modified: 2021-07-07 description: Overactive bladder (OAB) is a common condition that affects a significant patient population. The N-methyl-D-aspartate receptor (NMDAR) has a role in developing bladder overactivity, pharmacological inhibition of which inhibits bladder overactivity. The common pathogenesis of OAB involves bladder smooth muscle (BSM) overactivity. In this study, a smooth muscle–specific NMDAR knockout (SMNRKO) mouse model was generated. The bladders from SMNRKO mice displayed normal size and weight with an intact bladder wall and well-arranged BSM bundles. Besides, SMNRKO mice had normal voiding patterns and urodynamics and BSM contractility, indicating that NMDAR in BSM was not essential for normal physiological bladder morphology and function. Unexpectedly, cyclophosphamide (CYP)-treated SMNRKO and wild-type (WT) mice had similar pathological changes in the bladder. Furthermore, SMNRKO mice displayed similar altered voiding patterns and urodynamic abnormalities and impaired BSM contractility compared with WT mice after CYP treatment. MK801 partially reversed the pathological bladder morphology and improved bladder dysfunction induced by CYP, but did not cause apparent differences between WT mice and SMNRKO mice, suggesting that NMDAR in BSM was not involved in pathological bladder morphology and function. Moreover, the direct instillation of NMDAR agonists or antagonists into the CYP-induced OAB did not affect bladder urodynamic function, indicating that NMDAR in BSM was not the pharmacotherapy target of MK801 for CYP-induced cystitis. The findings indicated that NMDAR in BSM was not essential for normal physiological or pathological bladder morphology and function, and MK801 improving pathological bladder function was not mediated by an action on NMDAR in BSM. creator: Xiang Xie creator: Chuang Luo creator: Jia Yu Liang creator: Run Huang creator: Jia Li Yang creator: Linlong Li creator: YangYang Li creator: Hongming Xing creator: Huan Chen uri: https://doi.org/10.7717/peerj.11684 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Xie et al. title: Construction and validation of a 15-gene ferroptosis signature in lung adenocarcinoma link: https://peerj.com/articles/11687 last-modified: 2021-07-07 description: BackgroundFerroptosis is a novel form of programmed cell death characterized by the excessive accumulation of intracellular iron and an increase in reactive oxygen species. Emerging studies have shown that ferroptosis plays a vital role in the progression of lung adenocarcinoma, but the effect of ferroptosis-related genes on prognosis has been poorly studied. The purpose of this study was to explore the prognostic value of ferroptosis-related genes.MethodsLung adenocarcinoma samples were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. The least absolute shrinkage and selection operator (LASSO) Cox regression algorithm was used to establish a predictive signature for risk stratification. Kaplan–Meier (K–M) survival analysis and receiver operating characteristic (ROC) curve analysis were conducted to evaluate the signature. We further explored the potential correlation between the risk score model and tumor immune status.ResultsA 15-gene ferroptosis signature was constructed to classify patients into different risk groups. The overall survival (OS) of patients in the high-risk group was significantly shorter than that of patients in the low-risk group. The signature could predict OS independent of other risk factors. Single-sample gene set enrichment analysis (ssGSEA) identified the difference in immune status between the two groups. Patients in the high-risk group had stronger immune suppression, especially in the antigen presentation process.ConclusionsThe 15-gene ferroptosis signature identified in this study could be a potential biomarker for prognosis prediction in lung adenocarcinoma. Targeting ferroptosis might be a promising therapeutic alternative for lung adenocarcinoma. creator: Guangxu Tu creator: Weilin Peng creator: Qidong Cai creator: Zhenyu Zhao creator: Xiong Peng creator: Boxue He creator: Pengfei Zhang creator: Shuai Shi creator: Yongguang Tao creator: Xiang Wang uri: https://doi.org/10.7717/peerj.11687 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Tu et al. title: Effects of different biomass materials as a salt-isolation layer on water and salt migration in coastal saline soil link: https://peerj.com/articles/11766 last-modified: 2021-07-07 description: The aim of this study was to find a material suited for the prevention of evaporative water loss and salt accumulation in coastal saline soils. One-dimensional vertical water infiltration and phreatic evaporation experiments were conducted using a silty loam saline soil. A 3-cm-thick layer of corn straw, biochar, and peat was buried at the soil depth of 20 cm, and a 6-cm-thick layer of peat was also buried at the same soil depth for comparison. The presence of the biochar layer increased the upper soil water content, but its ability to inhibit salt accumulation was poor, leading to a high salt concentration in the surface soil. The 3-cm-thick straw and 6-cm-thick peat layers were most effective to inhibit salt accumulation, which reduced the upper soil salt concentration by 96% and 93%, respectively. However, the straw layer strongly inhibited phreatic evaporation and resulted in low water content in the upper soil layer. Compared with the straw layer, the peat layer increased the upper soil water content. Thus, burying a 6-cm-thick peat layer in the coastal saline soil is the optimal strategy to retain water in the upper soil layer and intercept salt in the deeper soil layer. creator: Mao Yang creator: Runya Yang creator: Yanni Li creator: Yinghua Pan creator: Junna Sun creator: Zhenhua Zhang uri: https://doi.org/10.7717/peerj.11766 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Yang et al. title: Prevalence and risk of spinal pain among physiotherapists in Poland link: https://peerj.com/articles/11715 last-modified: 2021-07-06 description: BackgroundThe purpose of this study was to determine the prevalence, symptoms of, and risk factors for spinal pain in physiotherapists, as well as to analyse the correlation between these factors and the nature of the work, anthropometric features of the respondents, and the level of their physical activity.MethodsThe study was conducted among 240 physiotherapists (71 male and 169 female) with a mean age of 38.7 years. They were divided into three groups: physical therapy (37), kinesitherapy (158) and massage (45). Physiotherapists were evaluated with a specially designed questionnaire, the postural discomfort chart, the Neck Disability Index (NDI) questionnaire, and the Oswestry Disability Index (ODI) questionnaire.ResultsThe analysis showed a 91.7% incidence of spinal pain in physiotherapists (91.1% for kinesitherapy, 97.3% for physical therapy, and 88.9% for massage). The study revealed that 50.2% of physiotherapists indicated one to five pain episodes in their careers. Most respondents reported pain in the lumbosacral spine (82%) and the cervical spine (67%). Most respondents (58.5%) scored the pain as moderate (VAS scale). Carrying (62.6%) and torso bending (37.4%) were indicated as the causes of pain.ConclusionsPhysiotherapists demonstrate a high prevalence of spinal pain. Physical activity reduces the frequency of pain episodes. creator: Sebastian Glowinski creator: Aleksandra Bryndal creator: Agnieszka Grochulska uri: https://doi.org/10.7717/peerj.11715 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Glowinski et al. title: Prognostic factors and treatment of neuroendocrine tumors of the uterine cervix based on the FIGO 2018 staging system: a single-institution study of 172 patients link: https://peerj.com/articles/11563 last-modified: 2021-07-06 description: ObjectiveThis study aimed to explore the prognostic factors and outcomes of patients with neuroendocrine tumors (NETs) of the cervix and to determine appropriate treatment.MethodsA single-institution retrospective analysis of 172 patients with NETs was performed based on the new International Federation of Gynecology and Obstetrics (FIGO 2018) staging system.ResultsAmong the 172 eligible patients, 161 were diagnosed with small cell neuroendocrine carcinoma (SCNEC), six with large cell neuroendocrine carcinoma, four with typical carcinoid tumors and one with SCNEC combined with an atypical carcinoid tumor. According to the FIGO 2018 staging guidelines, 31 were stage I, 66 were stage II, 57 were stage III, and 18 were stage IV. The 5-year survival rates of patients with stage I–IV disease were 74.8%, 56.2%, 41.4% and 0%, respectively. The 5-year progression-free survival rates of patients with stage I–IV disease were 63.8%, 54.5%, 30.8% and 0%, respectively. In the multivariate analysis, advanced FIGO stage, large tumor and older age were identified as independent variables for 5-year survival in patients with stage I–IV disease. FIGO stage, tumor size and para-aortic lymph node metastasis were independent prognostic factors for 5-year progression-free survival in patients with stage I–IV disease. For the patients receiving surgery (n = 108), tumor size and pelvic lymph node metastasis were independent prognostic factors for 5-year survival, and pelvic lymph node metastasis for 5-year progression-free survival. In stage IVB, at least six cycles of chemotherapy (n = 7) was associated with significantly better 2-year OS (83.3% vs. 9.1%, p < 0.001) and 2-year PFS (57.1% vs. 0%, p = 0.01) than fewer than six cycles of chemotherapy(n = 11).ConclusionAdvanced FIGO stage, large tumor, older age and lymph node metastasis are independent prognostic factors for NETs of the cervix. The TP/TC and EP regimens were the most commonly used regimens, with similar efficacies and toxicities. Standardized and complete multimodality treatment may improve the survival of patients with NETs. creator: Jian Chen creator: Yang Sun creator: Li Chen creator: Lele Zang creator: Cuibo Lin creator: Yongwei Lu creator: Liang Lin creator: An Lin creator: Hu Dan creator: Yiyu Chen creator: Haixin He uri: https://doi.org/10.7717/peerj.11563 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Chen et al. title: NLRP3 inflammasome activation mediates sleep deprivation-induced pyroptosis in mice link: https://peerj.com/articles/11609 last-modified: 2021-07-06 description: BackgroundSleep deprivation (SD) has many deleterious health effects, including cognitive decline, work ability decline, inadequate alertness, etc. Neuroinflammation plays an important role in sleep deprivation. However, the underlying mechanism is still unclear.MethodsIn the present study, we detected the activation of microglia and apoptosis of nerve cells in sleep deprivation (SD) mice model using IHC, HE staining and TUNEL apoptosis assay. RT-PCR array data were used to detect the expression of inflammatory bodies in hippocampal CA1 region after sleep deprivation, to explore how NLRP3 inflammasome regulates neuronal apoptosis and how specific signaling pathways are involved in SD-induced activation of NLRP3/pyrosis axis.ResultsWe found the number of microglia significantly increased in SD mice, while this effect was blocked by sleep recovery. RT-PCR array data suggested that NLRP3 inflammasome, but not other inflammasomes, was obviously increased in hippocampus CA1 region after sleep deprivation. Mechanistically, we found that NLRP3 mediated the pyroptosis of neurocyte through GSDMD-dependent way , and P38 and ERK-MAPK signaling pathway is involved in SD-induced activation of NLRP3/pyroptosis axis. All these results suggested that MAPK/NLRP3 axis mediated SD-induced pyroptosis.ConclusionNLRP3 plays an important role in SD-induced neuroinflammation. Thus, NLRP3 inflammasome is expected to be a potential therapeutic target for SD-induced neuroinflammation. creator: Kun Fan creator: Jiajun Yang creator: Wen-Yi Gong creator: Yong-Chao Pan creator: Peibing Zheng creator: Xiao-Fang Yue uri: https://doi.org/10.7717/peerj.11609 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Fan et al. title: Comparative efficacy of different renin angiotensin system blockade therapies in patients with IgA nephropathy: a Bayesian network meta-analysis of 17 RCTs link: https://peerj.com/articles/11661 last-modified: 2021-07-06 description: BackgroundIgA nephropathy (IgAN) is still one of the most prevalent forms of primary glomerulonephritis globally. However, no guidelines have clearly indicated which kinds of renin angiotensin system blockade therapies (ACEIs or ARBs or their combination) in patients with IgAN result in a greater reduction in proteinuria and a better preservation of kidney function. Thus, we conducted a Bayesian network analysis to evaluate the relative effects of these three therapy regimens in patients with IgAN.MethodsThe protocol was registered in PROSPERO with ID CRD42017073726. We comprehensively searched the PubMed, the Cochrane Library, Embase, China Biology Medicine disc, WanFang and CNKI databases for studies published since 1993 as well as some grey literature according to PICOS strategies. Pairwise meta-analysis and Bayesian network analysis were conducted to evaluate the effect of different regimens.ResultsSeventeen randomized controlled trials (RCTs) involving 1,006 patients were analyzed. Co-administration of ACEIs and ARBs had the highest probability (92%) of being the most effective therapy for reducing proteinuria and blood pressure, but ACEIs would be the most appropriate choice for protecting kidney function in IgAN.ConclusionThe combination of ACEIs and ARBs seems to have a significantly better antiproteinuric effect and a greater reduction of blood pressure than ACEI or ARB monotherapy in IgAN. ACEIs appear to be a more renoprotective therapy regimen among three therapies. creator: Zhihao Huo creator: Huizhen Ye creator: Peiyi Ye creator: Guanqing Xiao creator: Zhe Zhang creator: Yaozhong Kong uri: https://doi.org/10.7717/peerj.11661 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Huo et al. title: Constructing high-order functional connectivity network based on central moment features for diagnosis of autism spectrum disorder link: https://peerj.com/articles/11692 last-modified: 2021-07-06 description: The sliding-window-based dynamic functional connectivity network (D-FCN) has been becoming an increasingly useful tool for understanding the changes of brain connectivity patterns and the association of neurological diseases with these dynamic variations. However, conventional D-FCN is essentially low-order network, which only reflects the pairwise interaction pattern between brain regions and thus overlooking the high-order interactions among multiple brain regions. In addition, D-FCN is innate with temporal sensitivity issue, i.e., D-FCN is sensitive to the chronological order of its subnetworks. To deal with the above issues, we propose a novel high-order functional connectivity network framework based on the central moment feature of D-FCN. Specifically, we firstly adopt a central moment approach to extract multiple central moment feature matrices from D-FCN. Furthermore, we regard the matrices as the profiles to build multiple high-order functional connectivity networks which further capture the higher level and more complex interaction relationships among multiple brain regions. Finally, we use the voting strategy to combine the high-order networks with D-FCN for autism spectrum disorder diagnosis. Experimental results show that the combination of multiple functional connectivity networks achieves accuracy of 88.06%, and the best single network achieves accuracy of 79.5%. creator: Qingsong Xie creator: Xiangfei Zhang creator: Islem Rekik creator: Xiaobo Chen creator: Ning Mao creator: Dinggang Shen creator: Feng Zhao uri: https://doi.org/10.7717/peerj.11692 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Xie et al. title: High expression of PIMREG predicts poor survival outcomes and is correlated with immune infiltrates in lung adenocarcinoma link: https://peerj.com/articles/11697 last-modified: 2021-07-06 description: BackgroundPIMREG is upregulated in multiple cancer types. However, the potential role of PIMREG in lung adenocarcinoma (LUAD) remains unclear. The present study aimed to explore its clinical significance in LUAD.MethodsUsing the Cancer Genome Atlas (TCGA) databases, we obtained 513 samples of LUAD and 59 normal samples from the Cancer Genome Atlas (TCGA) databases to analyze the relationship between PIMREG and LUAD. We used t and Chi-square tests to evaluate the level of expression of PIMREG and its clinical implication in LUAD. The prognostic value of PIMREG in LUAD was identified through the Kaplan–Meier method, Cox regression analysis, and nomogram. Gene set enrichment analysis (GSEA) and single-sample gene set enrichment analysis (ssGSEA) were performed to screen biological pathways and analyze the correlation of the immune infiltrating level with the expression of PIMREG in LUAD.ResultsPIMREG was highly expressed in patients with LUAD. Specifically, the level of PIMREG gradually increased from pathological stage I to IV. Further, we validated the higher expression of PIMREG expressed in LUAD cell lines. Moreover, PIMREG had a high diagnostic value, with an -AUC of 0.955. Kaplan–Meier survival and Cox regression analyses revealed that the high expression of PIMREG was independently associated with poor clinical outcomes. In our prognostic nomogram, the expression of PIMREG implied a significant prognostic value. Gene set enrichment analysis (GSEA) identified that the high expression PIMREG phenotype was involved in the mitotic cell cycle, mRNA splicing, DNA repair, Rho GTPase signaling, TP53 transcriptional regulation, and translation pathways. Next, we also explored the correlation of PIMREG and tumor-immune interactions and found a negative correlation between PIMREG and the immune infiltrating level of T cells, macrophages, B cells, dendritic cells (DCs) , and CD8+ T cells in LUAD.ConclusionsHigh levels of PIMREG correlated with poor prognosis and immune infiltrates in LUAD. creator: Feng Jiang creator: Min Liang creator: Xiaolu Huang creator: Wenjing Shi creator: Yumin Wang uri: https://doi.org/10.7717/peerj.11697 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Jiang et al. title: Quail eggs in artificial nests change their coloration when exposed to ambient conditions: implication for studies on nest predation link: https://peerj.com/articles/11725 last-modified: 2021-07-06 description: Quail eggs have been widely used in field experiments, mainly to study factors associated with the risk of nest predation. Some shortcomings of using quail eggs in this type of study have been previously addressed (e.g., these eggs might be too big for some predators of eggs of small birds). Here, we show experimental evidence of another shortcoming of the use of these eggs in field experiments. Quail eggs exposed to sunlight rapidly faded in colour after three days, both in the visible and UV spectra, and this change was related to the amount of solar radiation received. This caused changes in the camouflage of the eggs, which may be perceived by predators with different visual systems (dichromatic, trichromatic, and tetrachromatic (for both violet- and UV-sensitive species)). Therefore, the results of field studies of nest predation using quail eggs might be questioned in those cases in which the camouflage has been altered due to the rapid changes in coloration, as this can affect the resulting predation rates. We recommend that researchers planning to use quail eggs should perform a prospective assessment of changes in coloration of eggs exposed to environmental conditions in the nest sites used by the target species. creator: Gustavo Liñan Cembrano creator: Macarena Castro creator: Juan A. Amat creator: Alejandro Perez creator: Miguel Ángel Rendón creator: Cristina Ramo uri: https://doi.org/10.7717/peerj.11725 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Liñan Cembrano et al. title: The anatomy of the palate in Early Triassic Chaohusaurus brevifemoralis (Reptilia: Ichthyosauriformes) based on digital reconstruction link: https://peerj.com/articles/11727 last-modified: 2021-07-06 description: The palatal anatomy of ichthyosauriforms remains largely unknown. Here, the complete palate of the early-branching ichthyosauriform Chaohusaurus brevifemoralis is reconstructed and described for the first time with the assistance of high-resolution X-ray computed tomography (CT) scanning on the basis of the three-dimensionally preserved skull of its paratype (GMPKU-P-3086) from the Lower Triassic of South China. The reconstruction reveals new palatal features of C. brevifemoralis. The palatine contacts the jugal directly, which is observed in ichthyosauriforms for the first time. A single row of denticles is present on each side of the palate. The vomer exceeds the anterior and posterior margins of the internal naris. The pterygoid is posterior to the internal naris. The epipterygoid is present and the ectopterygoid is absent. creator: Ya-Lei Yin creator: Cheng Ji creator: Min Zhou uri: https://doi.org/10.7717/peerj.11727 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Yin et al. title: Serum albumin and albuminuria predict the progression of chronic kidney disease in patients with newly diagnosed type 2 diabetes: a retrospective study link: https://peerj.com/articles/11735 last-modified: 2021-07-06 description: BackgroundDiabetes-related kidney disease is associated with end-stage renal disease and a high mortality rate. However, data on risk factors associated with kidney disease in patients with newly diagnosed type 2 diabetes mellitus (DM) remains insufficient. The aim of the present study was to identify the risk factors significantly associated with chronic kidney disease progression in patients with newly diagnosed type 2 DM.MethodsWe reviewed a total of 254 consecutive patients who were newly diagnosed with type 2 diabetes at Nanjing First Hospital from January to December 2014. They were observed for two years, and baseline and biochemical variables were used to identify significant predictors of kidney failure progression. Kidney failure progression was defined as a ≥ 30% increase in serum creatine level.ResultsThe mean age of patients was 58.96 years, 37.4% were women, and 57.1% had hypertension. Kidney function progressed in 40 patients (15.75%). Multivariable logistic regression analyses showed that serum albumin (p = 0.015) and microalbuminuria (p < 0.001) were associated with kidney failure progression in patients with newly diagnosed type 2 DM. Those with lower estimated glomerular filtration rate (eGFR; 30–60 ml/min/1.73 m2) at baseline had lower serum albumin levels compared to those of patients with higher eGFR. The albuminuria levels were higher in patients with lower eGFR than in those with eGFR ≥ 90 ml/min/1.73 m2. Receiver operating characteristic curve analysis showed that the area under the curve was 0.754 (95% CI [0.670–0. 0.837]).ConclusionsThe overall rate of chronic kidney disease progression is relatively high, and low serum albumin and high albuminuria levels are associated with kidney failure progression in newly diagnosed diabetic patients. creator: Yujiao Li creator: Xiaobing Ji creator: Wenji Ni creator: Yong Luo creator: Bo Ding creator: Jianhua Ma creator: Jian Zhu uri: https://doi.org/10.7717/peerj.11735 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Li et al. title: Weight-dependent susceptibility of tilapia to tilapia lake virus infection link: https://peerj.com/articles/11738 last-modified: 2021-07-06 description: The emergence of tilapia lake virus (TiLV) has had a severely negative impact on global tilapia aquaculture. TiLV infection has been reported at different life stages of tilapia, with more emphasis on fry and fingerlings; however, the virulence and pathology of TiLV at different tilapia size remains unexplored. In this study, tilapias from a single spawning were raised to 5 g, 25 g, and 65 g, and subsequently challenged by the intraperitoneal injection and cohabitation of a virulent strain of TiLV. The cumulative mortality, viral load, and histopathology of the fish were determined until 22 days post-infection (dpi). The cumulative mortality of the 5 g, 25 g, and 65 g fish was 85% (±1.67), 55% (±2.89), and 51.67% (±7.49), respectively. At 14 dpi, the mean TiLV load in the liver of the 5 g fish was significantly higher than in the 25 g and 65 g fish. All the weight groups showed severe pathological changes in the liver, spleen, and intestine after TiLV infection, but no particular difference was otherwise noted during the study with the exception of higher pathological scores in the liver of the small fish at 14 dpi. Overall, this study indicated that small fish are more susceptible to TiLV infection than large fish. Although multiple factors, including environmental factors, farm management practices, strains of virus could contribute to different susceptibility of fish to viral infection, the present study provides the evidence to support that fish weight affects the mortality and clinical outcome during TiLV infection. More intensive measures such as strict biosecurity and disease surveillance during the susceptible weight should therefore be emphasized to reduce the impact of this virus. creator: Sri Rajiv Kumar Roy creator: Jidapa Yamkasem creator: Puntanat Tattiyapong creator: Win Surachetpong uri: https://doi.org/10.7717/peerj.11738 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Roy et al. title: Childhood maltreatment and suicidal ideation in Chinese children and adolescents: the mediation of resilience link: https://peerj.com/articles/11758 last-modified: 2021-07-06 description: BackgroundChildhood maltreatment could increase the risk of suicidal ideation (SI) in adolescents. However, the mediation of resilience in this association remains unclear.MethodsA population-based cross-sectional study has been done among 3,146 Chinese adolescents. We collected relevant information from the study participants by using self-administered questionnaire. Chinese version of the Childhood Trauma Questionnaire (CTQ), the Resilience Scale for Chinese Adolescents (RSCA), and the Beck Scale for Suicide Ideation (BSSI) were used to measure childhood maltreatment, resilience, and SI, respectively. Univariate and multivariate binary Logistic regression models were employed to estimate crude and adjusted associations between childhood maltreatment, resilience, and SI. Path analysis has subsequently been performed to measure the mediation of resilience in this association.ResultsMultivariate Logistic regression models revealed that compared to non-abused counterparts, adolescents who had ever experienced any type of childhood maltreatment was 1.74 times likely to report SI. Among the specific types of childhood maltreatment, emotional abuse showed the strongest association with SI (adjusted OR = 3.01, 95% CI [2.37–3.82]). Path model suggested that over one-third (39.8%) of the total association between childhood maltreatment and SI was mediated via resilience. Emotion regulation and interpersonal assistance were the most prominent mediators among all dimensions of resilience.ConclusionsResilience played as a significant mediator in the association between childhood maltreatment and SI. Resilience-oriented intervention measures could be considered for suicidal risk prevention among abused Chinese adolescents. creator: Xue Chen creator: Linling Jiang creator: Yi Liu creator: Hailiang Ran creator: Runxu Yang creator: Xiufeng Xu creator: Jin Lu creator: Yuanyuan Xiao uri: https://doi.org/10.7717/peerj.11758 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Chen et al. title: Shape familiarity modulates preference for curvature in drawings of common-use objects link: https://peerj.com/articles/11772 last-modified: 2021-07-06 description: Drawing is a way to represent common-use objects. The contour of an object is a salient feature that defines its identity. Preference for a contour (curved or angular) may depend on how familiar the resulting shape looks for that given object. In this research, we examined the influence of shape familiarity on preference for curved or sharp-angled drawings of common-use objects. We also examined the possibility that some individual differences modulated this preference. Preference for curvature was assessed with a liking rating task (Experiment 1) and with a two-alternative forced-choice task simulating approach/avoidance responses (Experiment 2). Shape familiarity was assessed with a familiarity selection task where participants selected the most familiar shape between the curved and the angular version for each object, or whether both shapes were equally familiar for the object. We found a consistent preference for curvature in both experiments. This preference increased when the objects with a curved shape were selected as the most familiar ones. We also found preference for curvature when participants selected the shape of objects as equally familiar. However, there was no preference for curvature or preference for angularity when participants selected the sharp-angled shapes as the most familiar ones. In Experiment 2, holistic and affective types of intuition predicted higher preference for curvature. Conversely, participants with higher scores in the unconventionality facet showed less preference for the curved drawings. We conclude that shape familiarity and individual characteristics modulate preference for curvature. creator: Erick G. Chuquichambi creator: Letizia Palumbo creator: Carlos Rey creator: Enric Munar uri: https://doi.org/10.7717/peerj.11772 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Chuquichambi et al. title: Short-chain soluble polyphosphate fertilizers increased soil P availability and mobility by reducing P fixation in two contrasting calcareous soils link: https://peerj.com/articles/11493 last-modified: 2021-07-05 description: Short-chain polyphosphate fertilizers have been increasingly applied in agriculture, but little is known about the chemical behaviors of polyphosphate in soils. Herein, a cylinder experiment was carried out to investigate the influences of different P types (i.e., mono-ammonium phosphate (MAP), phosphoric acid (PA) and ammonium polyphosphate (poly-P)) and their application methods (single vs split) on the mobility and availability of P in soil through a column millimeter-scale slice cutting method; meanwhile a soil microcosm experiment (560-day) was conducted to investigate the effects of different P types on phosphorus dynamic transformation. Polyphosphate addition significantly increased P mobility. The average distance of P downward movement (81.5 mm) in soil profile in the poly-P application treatment increased by 33.6% and 81.1%, respectively, compared to the MAP and PA treatments. Different P application methods also markedly influenced phosphorus mobility. For instance, the average distance of P vertical movement in the split P application treatment was 21.2% higher than in the single application treatment, indicating that split P addition significantly increased P downward movement. Moreover, polyphosphate application decreased soil P fixation by blocking the transformation of the applied-P from labile to recalcitrant forms (HCl-P and residual-P). Overall, our findings provide meaningful information to current phosphorus fertilization practice in increasing soil P mobility and bioavailability. We suggest that polyphosphate could be regarded as an alternative P source used in agriculture, and split polyphosphate application is recommended as an effective P fertilization strategy. creator: Jawad Ali Shah creator: Guixin Chu uri: https://doi.org/10.7717/peerj.11493 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Shah and Chu title: Geographic distribution modeling and taxonomy of Stephadiscus lyratus (Cothouny in Gould, 1846) (Charopidae) reveal potential distributional areas of the species along the Patagonian Forests link: https://peerj.com/articles/11614 last-modified: 2021-07-05 description: BackgroundStephadiscus lyratus (Couthouy in Gould, 1846), an endemic Charopidae from southern South America, was described from few dry shells. The distribution of this species is known on scattering occurrences, mainly from material deposited in museum collections. We provide here new information on anatomy, habitat, and microhabitat preferences and estimate the potential geographic distribution of the species to test if it is exclusively endemic to the Subpolar Magellanic Forest.MethodsFieldwork was carried out in the National Parks of the Patagonian Forests. Snails were photographed, measured, and dissected for anatomical studies; shells were studied with scanning electron microscopy. Estimation of the species geographical distribution (EGD) was obtained through correlative ecological niche modeling (ENM). We designed a calibration area a priori with known species points of occurrence in the Magellanic Subpolar Forests and borders of the Patagonian steppe. Seven bioclimatic variables of the WorldClim database were used. The best ENMs were calibrated and selected using a maximum entropy method with Maxent v3.3.3K through the R package “kuenm”. Candidate models were created by combining four values of regularization multiplier and all possible combinations of three feature classes. We evaluated candidate model performance based on significance (partial ROC), omission rates (E = 5%), and model complexity (AICc). From the best models obtained, a final model was transferred to a region “G” consisting of the calibration area plus the Valdivian Temperate Forests and whole Patagonian steppe, where we hypothesize that the species could be present. Finally, we obtained binary presence-absence maps. We quantified the proportion of the occurrence points and distribution range of S. lyratus in different land cover categories. To explore the degree of protection of S. lyratus’EGD, we quantified the proportion of its distributional range within protected areas.ResultsA be-lobed kidney, a close secondary ureter, the terminal portion of the uterus forming a compact glandular mass, and the vas deferens with a dilatation are new anatomical information that distinguishes this species. Stephadiscus lyratus inhabit cold native forest areas, mainly living on or under humid logs in contact with the ground. The main constraining variables to explain S. lyratus distribution in the EGD were BIO3, BIO12, BIO6, and BIO4. The potential area of distribution obtained almost duplicates their original range (140,454 km2) extending to the Valdivian Temperate forests mainly in Chile. Natural and semi-natural terrestrial vegetation was predominant in the potential area of distribution of S. lyratus. However, only 14.7% of this area occurs within current protected areas from Argentina and Chile. The ectothermic physiological traits of this species, low dispersal capacity, and its narrow habitat requirements turn S. lyratus into a potentially vulnerable species. creator: Maria Gabriela Cuezzo creator: Regina Gabriela Medina creator: Carolina Nieto uri: https://doi.org/10.7717/peerj.11614 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Cuezzo et al. title: Quantifying the effects of delisting wolves after the first state began lethal management link: https://peerj.com/articles/11666 last-modified: 2021-07-05 description: Predators and their protection are controversial worldwide. Gray wolves, Canis lupus, lost U.S. federal protection (delisting) and the State of Wisconsin began lethal management first among all states and tribes that regained authority over wolves. Here we evaluated the initial success of reaching the state’s explicit objective, “…to allow for a sustainable harvest that neither increases nor decreases the state’s wolf population…” We used official state figures for hunter-killed wolves, population estimates from April 2017–2020, and the latest peer-reviewed model of individual wolf survival to estimate additional deaths resulting from federal delisting. More than half of the additional deaths were predicted to be cryptic poaching under the assumption that this period resembled past periods of liberalized wolf-killing in Wisconsin. We used a precautionary approach to construct three conservative scenarios to predict the current status of this wolf population and a minimum estimate of population decline since April 2020. From our scenarios that vary in growth rates and additional mortality estimates, we expect a maximum of 695–751 wolves to be alive in Wisconsin by 15 April 2021, a minimum 27–33% decline in the preceding 12 months. This contradicts the state expectation of no change in the population size. We draw a conclusion about the adequacy of regulatory mechanisms under state control of wolves and discuss the particular governance conditions met in Wisconsin. We recommend greater rigor and independent review of the science used by agencies to plan wolf hunting quotas and methods. We recommend clearer division of duties between state wildlife agencies, legislatures, and courts. We recommend federal governments reconsider the practice of sudden deregulation of wolf management and instead recommend they consider protecting predators as non-game or transition more slowly to subnational authority, to avoid the need for emergency relisting. creator: Adrian Treves creator: Francisco J. Santiago-Ávila creator: Karann Putrevu uri: https://doi.org/10.7717/peerj.11666 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Treves et al. title: Genetic analysis and population structure of wild and cultivated wishbone flower (Torenia fournieri Lind.) lines related to specific floral color link: https://peerj.com/articles/11702 last-modified: 2021-07-05 description: BackgroundThe wishbone flower or Torenia fournieri Lind., an annual from tropical Indochina and southern China, is a popular ornamental plant, and many interspecific (T. fournieri × T. concolor) hybrid lines have been bred for the international market. The cultivated lines show a pattern of genetic similarity that correlates with floral color which informs on future breeding strategies. This study aimed to perform genetic analysis and population structure of cultivated hybrid lines comparing with closely related T. concolor wild populations.MethodsWe applied the retrotransposon based iPBS marker system for genotyping of a total of 136 accessions from 17 lines/populations of Torenia. These included 15 cultivated lines of three series: Duchess (A, B, C); Kauai (D, E, F, G, H, I, J); Little Kiss (K, L, M, N, P) and two wild T. concolor populations (Q and R). PCR products from each individual were applied to estimate the genetic diversity and differentiation between lines/populations.ResultsGenotyping results showed a pattern of genetic variation differentiating the 17 lines/populations characterized by their specific floral colors. The final PCoA analysis, phylogenetic tree construction, and Bayesian population structural bar plot all showed a clear subdivision of lines/populations analysed. The 15 cultivated hybrid lines and the wild population Q that collected from a small area showed the lowest genetic variability while the other wild population R which sampled from a larger area had the highest genetic variability.DiscussionThe extremely low genetic variability of 15 cultivated lines indicated that individual line has similar reduction in diversity/heterozygosity from a bottleneck event, and each retained a similar (but different from each other) content of the wild genetic diversity. The genetic variance for the two wild T. concolor populations could be due to our varied sampling methods. The two wild populations (Q, R) and the cultivated hybrid lines (I, K, M, N, P) are genetically more closely related, but strong positive correlations presented in cultivated lines A, C, E, M, and N. These results could be used to guide future Torenia breeding.ConclusionsThe genetic variation and population structure found in our study showed that cultivated hybrid lines had similar reduction in diversity/heterozygosity from a bottleneck event and each line retained a similar (but different from each other) content of the wild genetic diversity, especially when strong phenotypic selection of floral color overlaps. Generally, environmental factors could induce transposon activation and generate genetic variability which enabled the acceleration of the evolutionary process of wild Torenia species. Our study revealed that wild Torenia populations sampled from broad geographic region represent stronger species strength with outstanding genetic diversity, but selective breeding targeting a specific floral color decreased such genetic variability. creator: Shikai Guan creator: Qian Song creator: Jinye Zhou creator: Haixia Yan creator: Yuxiang Li creator: Zibin Zhang creator: Dayan Tao creator: Shuming Luo creator: Youqiang Pan uri: https://doi.org/10.7717/peerj.11702 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Guan et al. title: The effects of hip- and ankle-focused exercise intervention on dynamic knee valgus: a systematic review link: https://peerj.com/articles/11731 last-modified: 2021-07-05 description: BackgroundA range of non-contact injuries such as anterior cruciate ligament tear, and patellofemoral pain syndrome are caused by disordered knee joint loading from excessive dynamic knee valgus (DKV). Previous systematic reviews showed that DKV could be modified through the influence of hip strength and ankle range of motion. Therefore, the purpose of this systematic review was to examine the effects of exercise intervention which involved either top-down or bottom-up kinetic chains on minimizing DKV in male and female adults and adolescents, with and without existing knee pain.MethodologyElectronic searches were conducted in SAGE, Science Direct, SCOPUS, and Pubmed. The search strategy consisted of medical subject headings and free-text search keywords, synonyms and variations of ‘exercise intervention,’ ‘knee alignment,’ ‘dynamic knee valgus’, ‘knee abduction’ that were merged via the Boolean operator ‘AND’ and ‘OR’. The search was conducted on full-text journals that documented the impact of the exercise intervention program involving either the bottom-up or top-down DKV mechanism on the knee kinematics. Furthermore, exercise intervention in this review should last at least one week which included two or three sessions per week. This review also considered both men and women of all ages with a healthy or symptomatic knee problem. The risk of bias of the included studies was assessed by Cochrane risk assessment tool. The protocol of this review was registered at PROSPERO (registration number: CRD42021219121).ResultsTen studies with a total of 423 participants (male = 22.7%, female = 77.3%; adults = 249, adolescents = 123; pre-adolescent = 51) met the inclusion criteria of this review. Seven studies showed the significant effects of the exercise intervention program (range from two weeks to ten weeks) on reducing DKV. The exercise training in these seven studies focused on muscle groups directly attached to the knee joint such as hamstrings and gastrocnemius. The remaining three studies did not show significant improvement in DKV after the exercise intervention (range between eight weeks to twelve weeks) probably because they focused on trunk and back muscles instead of muscles crossing the knee joint.ConclusionExercises targeting specific knee-joint muscles, either from top-down or bottom-up kinetic chain, are likely to reduce DKV formation. These results may assist athletes and coaches to develop effective exercise program that could minimize DKV and ultimately prevent lower limb injuries. creator: Farhah Nadhirah Aiman Sahabuddin creator: Nazatul Izzati Jamaludin creator: Nurul Hidayah Amir creator: Shazlin Shaharudin uri: https://doi.org/10.7717/peerj.11731 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Sahabuddin et al. title: Description of three species of ophioplinthacids, including a new species, from a deep seamount in the Northwest Pacific Ocean link: https://peerj.com/articles/11566 last-modified: 2021-07-02 description: Five specimens of brittle star were collected from a deep-sea seamount in the Northwest Pacific, and identified into three species. One which is new to science, Ophioplinthaca grandisquama n. sp., can be easily distinguished from its congeners by the distinctly elongated and stout tentacle scales, stout and long disc spines, capitate with typically elongate to flaring head bearing numerous distinct thorns, radial shields roughly triangular and contiguous distally. One specimen was identified as Ophioplinthaca semele (Clark, 1949), which had been reported in Hawaii seamounts, is a new record of this species in the Northwest Pacific. The remaining specimen was an unknown species of Ophioplinthaca, with some different characteristics from other species of Ophioplinthaca. However, we, herein, prefer not to attach a name to this specimen until more morphological characteristics are available. The finding of this new species and two new records further enriches the distribution of Ophioplinthaca in the seamount of Northwest Pacific, providing useful information for marine protection in the cobalt-rich area. creator: Wanying Chen creator: Jieying Na creator: Dongsheng Zhang uri: https://doi.org/10.7717/peerj.11566 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Chen et al. title: Phosphate solubilizing rhizobacteria isolated from jujube ziziphus lotus plant stimulate wheat germination rate and seedlings growth link: https://peerj.com/articles/11583 last-modified: 2021-07-02 description: Jujube plant (Ziziphus lotus (L.) Desf.) can survive in arid climates and tolerates both biotic and abiotic stresses. Here, we isolated, for the first time in Morocco, nine phosphate solubilizing bacteria strains from jujube rhizosphere, designated J10 to J13, J15, & J153 to J156. Genotypic identification based on 16S rDNA sequencing, revealed six strains that belong to Pseudomonas (J10, J12, J13, J15, J153 and J154), two to Bacillus (J11 and J156), and one to Paenibacillus J155. Siderophores were produced by all strains. Proteases activity was missing in Pseudomonas sp. J153 & J154, whereas cellulase was restricted only to Pseudomonas sp. J10, Paenibacillus xylanexedens J155 and Bacillus cereus J156. Indole-3- acetic acid and ammonia were also produced by all strains, with a maxima of 204.28 µg mL−1 in Bacillus megaterium J11 and 0.33 µmol mL−1 in Pseudomonas sp. J153, respectively. Pseudomonas sp. J10 and B. cereus J156 grew on plates containing 1,500 µg mL−1 of nickel nitrate, while Pseudomonas sp. J153 withstood 1,500 µg mL−1 of either copper sulfate or cadmium sulfate. Phenotypic analysis of the potential of the isolates to promote early plant growth showed that wheat seeds inoculated with either P. moraviensis J12 or B. cereus J156 remarkably increased germination rate and seedlings growth. Lastly, antibiotic resistance profiling revealed that except for Pseudomonas sp. J11 and B. cereus J156, remaining strains displayed resistance at least to one of tested antibiotics. Collectively, Pseudomonas sp. J10, P. moraviensis J12, Pseudomonas sp. J153 and B. cereus J156, represent potential biofertilizers suitable for soils that are poor in P, and/or heavy metals contaminated. creator: Nidal Fahsi creator: Ismail Mahdi creator: Abdelhalem Mesfioui creator: Latefa Biskri creator: Abdelmounaaim Allaoui uri: https://doi.org/10.7717/peerj.11583 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Fahsi et al. title: Genome-wide analysis of genetic diversity and artificial selection in Large White pigs in Russia link: https://peerj.com/articles/11595 last-modified: 2021-07-02 description: Breeding practices adopted at different farms are aimed at maximizing the profitability of pig farming. In this work, we have analyzed the genetic diversity of Large White pigs in Russia. We compared genomes of historic and modern Large White Russian breeds using 271 pig samples. We have identified 120 candidate regions associated with the differentiation of modern and historic pigs and analyzed genomic differences between the modern farms. The identified genes were associated with height, fitness, conformation, reproductive performance, and meat quality. creator: Siroj Bakoev creator: Lyubov Getmantseva creator: Olga Kostyunina creator: Nekruz Bakoev creator: Yuri Prytkov creator: Alexander Usatov creator: Tatiana V. Tatarinova uri: https://doi.org/10.7717/peerj.11595 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Bakoev et al. title: Repression of ZCT1, ZCT2 and ZCT3 affects expression of terpenoid indole alkaloid biosynthetic and regulatory genes link: https://peerj.com/articles/11624 last-modified: 2021-07-02 description: Terpenoid indole alkaloids (TIAs) include several valuable pharmaceuticals. As Catharanthus roseus remains the primary source of these TIA pharmaceuticals, several research groups have devoted substantial efforts to increase production of these compounds by C. roseus. Efforts to increase TIA production by overexpressing positive regulators of TIA biosynthetic genes have met with limited success. This limited success might be due to the fact that overexpression of several positive TIA regulators turns on expression of negative regulators of TIA biosynthetic genes. Consequently, a more effective approach for increasing expression of TIA biosynthetic genes might be to decrease expression of negative regulators of TIA biosynthetic genes. Towards this end, an RNAi construct was generated that expresses a hairpin RNA carrying nucleotide fragments from three negative transcriptional regulators of TIA genes, ZCT1, ZCT2 and ZCT3, under the control of a beta-estradiol inducible promoter. Transgenic C. roseus hairy root lines carrying this ZCT RNAi construct exhibit significant reductions in transcript levels of all three ZCT genes. Surprisingly, out of eight TIA biosynthetic genes analyzed, seven (CPR, LAMT, TDC, STR, 16OMT, D4H and DAT) exhibited decreased rather than increased transcript levels in response to reductions in ZCT transcript levels. The lone exception was T19H, which exhibited the expected negative correlation in transcript levels with transcript levels of all three ZCT genes. A possible explanation for the T19H expression pattern being the opposite of the expression patterns of the other TIA biosynthetic genes tested is that T19H shunts metabolites away from vindoline production whereas the products of the other genes tested shunt metabolites towards vindoline metabolism. Consequently, both increased expression of T19H and decreased expression of one or more of the other seven genes tested would be expected to have similar effects on flux through the TIA pathway. As T19H expression is lower in the ZCT RNAi hairy root lines than in the control hairy root line, the ZCTs could act directly to inhibit expression of T19H. In contrast, ZCT regulation of the other seven TIA biosynthetic genes tested is likely to occur indirectly, possibly by the ZCTs turning off expression of a negative transcriptional regulator of some TIA genes. In fact, transcript levels of a negative TIA transcriptional regulator, GBF1, exhibited a strong, and statistically significant, negative correlation with transcript levels of ZCT1, ZCT2 and ZCT3. Together, these findings suggest that the ZCTs repress expression of some TIA biosynthetic genes, but increase expression of other TIA biosynthetic genes, possibly by turning down expression of GBF1. creator: Chun Yao Li creator: Susan I. Gibson uri: https://doi.org/10.7717/peerj.11624 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Li and Gibson title: First record of entomopathogenic nematodes from Yucatán State, México and their infectivity capacity against Aedes aegypti link: https://peerj.com/articles/11633 last-modified: 2021-07-02 description: BackgroundBiological control using entomopathogenic nematodes (EPN) has demonstrated good potential to contribute to the integral control of mosquito larvae, which as adults are vectors of diseases such as Dengue fever, Zika and Chikungunya. However, until now there are no records of the presence of EPN or their killing capacity in Yucatán state, southern México. The objectives of the current study were: (1) to report the entomopathogenic nematodes present in Yucatán soils and (2) to determine the killing capacity of the most frequent and abundant EPN against Aedes aegypti mosquito larvae and the microbial community developed by Ae. Aegypti exposed to this EPN.MethodsThe nematodes were collected by the insect trap technique using the great wax moth Galleria mellonella. Internal transcribed spacer (ITS), 28S gene of ribosomal DNA and phylogenetic analyses were performed to identify the EPN. For the bioassay, four concentrations of the most frequent and abundant EPN were tested: 1,260:1 infective juveniles (IJs) per mosquito larvae, 2,520 IJs:1, 3,780 IJs:1 and 5,040 IJs:1. High-throughput sequencing of the 16S rRNA gene was used to identify bacterial amplicon sequences in the mosquito larvae infected with EPN.ResultsSix isolates of Heterorhabditis were recovered from 144 soil samples. Heterorhabditis indica (four isolates) was the most frequent and abundant EPN, followed by Heterorhabditis n. sp. (two isolates). Both nematodes are reported for the first time for Yucatán state, Mexico. The concentration of 2,520 IJs:1 produced 80% of mosquito larvae mortality in 48 h. Representative members of Photorhabdus genus were numerically dominant (74%) in mosquito larvae infected by H. indica. It is most likely that these bacteria produce secondary toxic metabolites that enhance the mortality of these mosquito larvae. creator: Mariana B. Ávila-López creator: José Q. García-Maldonado creator: Héctor Estrada-Medina creator: David I. Hernández-Mena creator: Daniel Cerqueda-García creator: Víctor M. Vidal-Martínez uri: https://doi.org/10.7717/peerj.11633 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Ávila-López et al. title: Application of different building representation techniques in HEC-RAS 2-D for urban flood modeling using the Toce River experimental case link: https://peerj.com/articles/11667 last-modified: 2021-07-02 description: This paper presents the impact of the choice of building representation techniques and hydrodynamic models on urban flood simulations using HEC-RAS 2-D for the Toce River physical model. To this end, eight numerical models based on previous laboratory experiments were prepared to simulate unsteady urban flooding on each side of building units. Two simplified building layouts (aligned and staggered) were examined, where models were prepared for two different building representation techniques: Building Block (BB) and Building Resistance (BR). Water depth variation computations using the BR and BB techniques were compared to the laboratory measurements and previous studies in the literature. A statistical analysis was performed using both the Root Mean Square Error (RMSE) and the Pearson Product-Moment Correlation Coefficient (PPMCC) in order to evaluate the performance of the models. A sensitivity analysis showed that the proper mesh resolution and model parameter values were obtained. As far as the BR technique is concerned, it is well-suited for representing building units in numerical simulations using high Manning coefficients. Furthermore, this study confirms the importance of the BR technique, which should help researchers in using low-resolution Digital Elevation Models (DEMs) along with open-source programs. Moreover, the study aims to produce a deeper comprehension of numerical modeling and urban flooding. creator: Andam Mustafa creator: Michał Szydłowski uri: https://doi.org/10.7717/peerj.11667 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Mustafa and Szydłowski title: Confidence intervals for the difference between the coefficients of variation of Weibull distributions for analyzing wind speed dispersion link: https://peerj.com/articles/11676 last-modified: 2021-07-02 description: Wind energy is an important renewable energy source for generating electricity that has the potential to replace fossil fuels. Herein, we propose confidence intervals for the difference between the coefficients of variation of Weibull distributions constructed using the concepts of the generalized confidence interval (GCI), Bayesian methods, the method of variance estimates recovery (MOVER) based on Hendricks and Robey’s confidence interval, a percentile bootstrap method, and a bootstrap method with standard errors. To analyze their performances, their coverage probabilities and expected lengths were evaluated via Monte Carlo simulation. The simulation results indicate that the coverage probabilities of GCI were greater than or sometimes close to the nominal confidence level. However, when the Weibull shape parameter was small, the Bayesian- highest posterior density interval was preferable. All of the proposed confidence intervals were applied to wind speed data measured at 90-meter wind energy potential stations at various regions in Thailand. creator: Manussaya La-ongkaew creator: Sa-Aat Niwitpong creator: Suparat Niwitpong uri: https://doi.org/10.7717/peerj.11676 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 La-ongkaew et al. title: CGRP overexpression does not alter depression-like behavior in mice link: https://peerj.com/articles/11720 last-modified: 2021-07-02 description: BackgroundThe calcitonin gene-related peptide (CGRP) is a neuropeptide that is released from capsaicin-sensitive nerves as a potent vasodilator involved in nociceptive transmission. While CGRP has been rigorously studied for its role in migraines owing to its vasodilation and inflammation activities, the effects of CGRP overexpression on depressive-like behaviors remain insufficiently understood.MethodsIn the present study, we performed a battery of behavioral tests, including the social interaction test, open field test, and sucrose preference test, to evaluate social defeat stress using male C57BL6J or CGRP overexpression in transgenic (Tg) mice (CGRP Tg). We performed mRNA and protein analyses on the brain-derived neurotrophic factor (BDNF), phosphorylated Akt, mTOR, and p70S6K in the hippocampi.ResultsCGRP Tg mice showed increased levels of Bdnf mRNAs, low locomotor activity, and no deficits in social interaction, which indicate that CGRP Tg mice exhibit stress resistance and not depression. However, the open field test significantly decreased after 15-day social defeat stress exposure. We also evaluated depressive-like behavior using the sucrose preference and social interaction tests. Our data indicate that defeated CGRP Tg mice exhibited a depressive-like phenotype, which was inferred from increased social avoidance and reduced sucrose preference compared with non-defeated controls. Although stress exposure did not change the BDNF levels in CGRP Tg mice, it significantly decreased the expression levels of p-Akt, p-mTOR and p-p70S6K in the mice hippocampi. We conclude that CGRP-overexpressing Tg mice have normal sensitivity to stress and down-regulated hippocampal Akt/mTOR/p70S6K pathways. creator: Narumi Hashikawa-Hobara creator: Ami Otsuka creator: Chihiro Okujima creator: Naoya Hashikawa uri: https://doi.org/10.7717/peerj.11720 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Hashikawa-Hobara et al. title: Cytological analysis of tracheal wash and bronchoalveolar lavage fluid in health and respiratory disease in dromedary camels link: https://peerj.com/articles/11723 last-modified: 2021-07-02 description: BackgroundTracheal wash (TW) and bronchoalveolar lavage (BAL) have proven to be useful tools for the identification of disease-associated changes in the respiratory tract in human and different animal species. In the dromedary camel, little is known about cytological analysis of TW and BAL in health and disease. The aim of the present study was to evaluate the cytological composition of TW and BAL in health and respiratory disease in dromedary camels.MethodsTW and BAL samples were collected from dromedary camels and cytological analysis was performed by microscopic examination of prepared smears. Camels with clinical respiratory disease (n = 18) were compared with apparently healthy (control) camels (n = 9).ResultsIn the apparently healthy camels, differential cytological analysis of TW samples identified macrophages and neutrophils as the main cell populations with lesser proportions of lymphocytes and epithelial cells and very rare abundance of eosinophils and mast cells. In the TW of camels with respiratory disease, neutrophils were the most abundant cells followed by macrophages and lymphocytes. In the BAL of healthy camels, macrophages represented the main cell type followed by lymphocytes and neutrophils. In respiratory-diseased camels, BAL samples contained higher percentages of neutrophils with reduced percentages of macrophages and lymphocytes in comparison to camels from the control group. Collectively, the results of the current study revealed higher abundance of neutrophils in the TW and BAL from dromedary camels than many other veterinary species. The cytological patterns of TW and BAL from camels with respiratory diseases were characterized by increased proportion of neutrophils and decreased proportion of macrophages in comparison to healthy camels. The proportion of lymphocytes was also decreased in TW samples from diseased camels. creator: Turke Shawaf creator: Abdullah Almubarak creator: Naser Alhumam creator: Faisal Almathen creator: Jamal Hussen uri: https://doi.org/10.7717/peerj.11723 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Shawaf et al. title: Metabolism and transcriptome profiling provides insight into the genes and transcription factors involved in monoterpene biosynthesis of borneol chemotype of Cinnamomum camphora induced by mechanical damage link: https://peerj.com/articles/11465 last-modified: 2021-07-01 description: BackgroundThe borneol chemotype of Cinnamomum camphora (BCC), a monoterpene-rich woody plant species, is the sole source prescribed by the Chinese Pharmacopoeia for the production of natural D-borneol, a major monoterpene in BCC used for millennia as a topical analgesic in China. Nevertheless, the possible gene-regulatory roles of transcription factors (TFs) in BCC’s monoterpenoid biosynthesis remained unknown. Here, a joint analysis of the transcriptome and terpenoid metabolome of BCC induced by mechanical damage (MD) was used to comprehensively explore the interaction between TFs and terpene synthase (TPS) unigenes that might participate in monoterpene biosynthesis in BCC.ResultsGas chromatography–mass spectrometry analysis detected 14 monoterpenes and seven sesquiterpenes. All but two monoterpenes underwent a significantly increased accumulation after the MD treatment. RNA sequencing data revealed that 10 TPS, 82 MYB, 70 AP2/ERF, 38 BHLH, 31 WRKY, and 29 bZIP unigenes responded to the MD treatment. A correlation analysis revealed that three monoterpene synthase genes (CcTPS1, CcTPS3, CcTPS4) highly correlated with multiple monoterpenes, namely D-borneol, camphor, and bornyl acetate, which could be responsible for monoterpenoid biosynthesis in BCC. Furthermore, five WRKY, 15 MYB, 10 ERF/AP2, five bZIP, and two BHLH genes had strong, positive correlations with CcTPS1 or CcTPS4, judging by their high coefficient values (R2 > 0.8). The bioinformatics results were verified by quantitative real-time PCR.ConclusionThis study provides insight into the genes involved in the biosynthesis and regulation of monoterpene in BCC and thus provides a pool of candidate genes for future mechanistic analyses of how monoterpenes accumulate in BCC. creator: Zerui Yang creator: Chunzhu Xie creator: Yuying Huang creator: Wenli An creator: Shanshan Liu creator: Song Huang creator: Xiasheng Zheng uri: https://doi.org/10.7717/peerj.11465 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Yang et al. title: Dumpster diving for diatom plastid 16S rRNA genes link: https://peerj.com/articles/11576 last-modified: 2021-07-01 description: High throughput sequencing is improving the efficiency of monitoring diatoms, which inhabit and support aquatic ecosystems across the globe. In this study, we explored the potential of a standard V4 515F-806RB primer pair in recovering diatom plastid 16S rRNA sequences. We used PhytoREF to classify the 16S reads from our freshwater biofilm field sampling from three stream segments across two streams in south-eastern Australia and retrieved diatom community data from other, publicly deposited, Australian 16S amplicon datasets. When these diatom operational taxonomic units (OTUs) were traced using the default RDPII and NCBI databases, 68% were characterized as uncultured cyanobacteria. We analysed the 16S rRNA sequences from 72 stream biofilm samples, separated the chloroplast OTUs, and classified them using the PhytoREF database. After filtering the reads attributed to Bacillariophyta (relative abundance >1%), 71 diatom OTUs comprising more than 90% of the diatom reads in each stream biofilm sample were identified. Beta-diversity analyses demonstrated significantly different diatom assemblages and discrimination among river segments. To further test the approach, the diatom OTUs from our biofilm sampling were used as reference sequences to identify diatom reads from other Australian 16S rRNA datasets in the NCBI-SRA database. Across the three selected public datasets, 67 of our 71 diatom OTUs were detected in other Australian ecosystems. Our results show that diatom plastid 16S rRNA genes are readily amplified with existing 515F-806RB primer sets. Therefore, the volume of existing 16S rRNA amplicon datasets initially generated for microbial community profiling can also be used to detect, characterize, and map diatom distribution to inform phylogeny and ecological health assessments, and can be extended into a range of ecological and industrial applications. To our knowledge, this study represents the first attempt to classify freshwater samples using this approach and the first application of PhytoREF in Australia. creator: Krista L. Bonfantine creator: Stacey M. Trevathan-Tackett creator: Ty G. Matthews creator: Ana Neckovic creator: Han Ming Gan uri: https://doi.org/10.7717/peerj.11576 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Bonfantine et al. title: Analysis of ceRNA network of differentially expressed genes in FaDu cell line and a cisplatin-resistant line derived from it link: https://peerj.com/articles/11645 last-modified: 2021-07-01 description: BackgroundHypopharyngeal cancer accounts for 2% in head and neck cancers and has a poor prognosis. Cisplatin is a widely used chemotherapeutic drug in kinds of carcinomas, concluding hypopharyngeal cancer. However, the resistance of cisplatin appeared in recent years. Cisplatin-resistance has been partly explored before, but rarely in hypopharyngeal cancer.MethodsWe cultured the hypopharyngeal cancer cell (FaDu) and induced its cisplatin-resistant cell (FaDu/DDP4). Then we tested the differentially expressed genes (DEGs) between FaDu and FaDu/DDP4. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted on the DEGs, and we drew the ceRNA networks of DEGs. Finally, we chose eight miRNAs and six mRNAs for qRT-PCR to verify our microarray.ResultsWe induced cisplatin-resistant FaDu/DDP4 and proved its chemoresistance. The resistance index (RI) of FaDu/DDP4 was 2.828. DEGs contain 2,388 lncRNAs, 1,932 circRNAs, 745 mRNAs and 202 miRNAs. These 745 mRNAs were classified into three domains and 47 secondary GO terms. In KEGG pathway enrichment, the “TNF signaling pathway”, “IL-17 signaling pathway” and “JAK-STAT signaling pathway” were potentially significant signaling pathways. Then, 52 lncRNAs, 148 circRNAs, 155 mRNAs and 18 miRNAs were selected to draw the network. We noticed several potential targets (as miR-197-5p, miR-6808-5p, APOE, MMP1, S100A9 and CYP24A1). At last, the eight miRNAs and six mRNAs that are critical RNAs in ceRNA network were verified by qRT-PCR.ConclusionThe microarray helped to find DEGs in cisplatin-resistant hypopharyngeal cancer. TNF, IL-17 and JAK-STAT signaling pathways might be more significant for cisplatin-resistance. MiR-197-5p, miR-6808-5p, APOE, MMP1, S100A9 and CYP24A1 might be potential genes inducing resistance. creator: Gehou Zhang creator: Guolin Tan creator: Tieqi Li creator: Jingang Ai creator: Yexun Song creator: Zheng Zhou creator: Jian Xiao creator: Wei Li uri: https://doi.org/10.7717/peerj.11645 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Zhang et al. title: Comparative analysis of fatty acid metabolism based on transcriptome sequencing of wild and cultivated Ophiocordyceps sinensis link: https://peerj.com/articles/11681 last-modified: 2021-07-01 description: BackgroundOphiocordyceps sinensis is a species endemic to the alpine and high-altitude areas of the Qinghai-Tibet plateau. Although O. sinensis has been cultivated since the past few years, whether cultivated O. sinensis can completely replace wild O. sinensis remains to be determined.MethodsTo explore the differences of O. sinensis grown in varied environments, we conducted morphological and transcriptomic comparisons between wild and cultivated samples who with the same genetic background.ResultsThe results of morphological anatomy showed that there were significant differences between wild and cultivated O. sinensis, which were caused by different growth environments. Then, a total of 9,360 transcripts were identified using Illumina paired-end sequencing. Differential expression analysis revealed that 73.89% differentially expressed genes (DEGs) were upregulated in O. sinensis grown under natural conditions compared with that grown under artificial conditions. Functional enrichment analysis showed that some key DEGs related to fatty acid metabolism, including acyl-CoA dehydrogenase, enoyl-CoA hydratase, 3-ketoacyl-CoA thiolase, and acetyl-CoA acetyltransferase, were upregulated in wild O. sinensis. Furthermore, gas chromatography-mass spectrometry results confirmed that the fatty acid content of wild O. sinensis was significantly higher than that of cultivated O. sinensis and that unsaturated fatty acids accounted for a larger proportion.ConclusionThese results provide a theoretical insight to the molecular regulation mechanism that causes differences between wild and cultivated O. sinensis and improving artificial breeding. creator: Han Zhang creator: Pan Yue creator: Xinxin Tong creator: Tinghui Gao creator: Ting Peng creator: Jinlin Guo uri: https://doi.org/10.7717/peerj.11681 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zhang et al. title: A synthetic defective interfering SARS-CoV-2 link: https://peerj.com/articles/11686 last-modified: 2021-07-01 description: Viruses thrive by exploiting the cells they infect, but in order to replicate and infect other cells they must produce viral proteins. As a result, viruses are also susceptible to exploitation by defective versions of themselves that do not produce such proteins. A defective viral genome with deletions in protein-coding genes could still replicate in cells coinfected with full-length viruses. Such a defective genome could even replicate faster due to its shorter size, interfering with the replication of the virus. We have created a synthetic defective interfering version of SARS-CoV-2, the virus causing the Covid-19 pandemic, assembling parts of the viral genome that do not code for any functional protein but enable the genome to be replicated and packaged. This synthetic defective genome replicates three times faster than SARS-CoV-2 in coinfected cells, and interferes with it, reducing the viral load of infected cells by half in 24 hours. The synthetic genome is transmitted as efficiently as the full-length genome, suggesting the location of the putative packaging signal of SARS-CoV-2. A version of such a synthetic construct could be used as a self-promoting antiviral therapy: by enabling replication of the synthetic genome, the virus would promote its own demise. creator: Shun Yao creator: Anoop Narayanan creator: Sydney A. Majowicz creator: Joyce Jose creator: Marco Archetti uri: https://doi.org/10.7717/peerj.11686 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Yao et al. title: In silico-driven analysis of the Glossina morsitans morsitans antennae transcriptome in response to repellent or attractant compounds link: https://peerj.com/articles/11691 last-modified: 2021-07-01 description: BackgroundHigh-throughput sequencing generates large volumes of biological data that must be interpreted to make meaningful inference on the biological function. Problems arise due to the large number of characteristics p (dimensions) that describe each record [n] in the database. Feature selection using a subset of variables extracted from the large datasets is one of the approaches towards solving this problem.MethodologyIn this study we analyzed the transcriptome of Glossina morsitans morsitans (Tsetsefly) antennae after exposure to either a repellant (δ-nonalactone) or an attractant (ε-nonalactone). We identified 308 genes that were upregulated or downregulated due to exposure to a repellant (δ-nonalactone) or an attractant (ε-nonalactone) respectively. Weighted gene coexpression network analysis was used to cluster the genes into 12 modules and filter unconnected genes. Discretized and association rule mining was used to find association between genes thereby predicting the putative function of unannotated genes.Results and discussionAmong the significantly expressed chemosensory genes (FDR < 0.05) in response to Ɛ-nonalactone were gustatory receptors (GrIA and Gr28b), ionotrophic receptors (Ir41a and Ir75a), odorant binding proteins (Obp99b, Obp99d, Obp59a and Obp28a) and the odorant receptor (Or67d). Several non-chemosensory genes with no assigned function in the NCBI database were co-expressed with the chemosensory genes. Exposure to a repellent (δ-nonalactone) did not show any significant change between the treatment and control samples. We generated a coexpression network with 276 edges and 130 nodes. Genes CAH3, Ahcy, Ir64a, Or67c, Ir8a and Or67a had node degree values above 11 and therefore could be regarded as the top hub genes in the network. Association rule mining showed a relation between various genes based on their appearance in the same itemsets as consequent and antecedent. creator: Consolata Gakii creator: Billiah Kemunto Bwana creator: Grace Gathoni Mugambi creator: Esther Mukoya creator: Paul O. Mireji creator: Richard Rimiru uri: https://doi.org/10.7717/peerj.11691 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Gakii et al.