title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2022-03 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: A spotlight on non-host resistance to plant viruses link: https://peerj.com/articles/12996 last-modified: 2022-03-31 description: Plant viruses encounter a range of host defenses including non-host resistance (NHR), leading to the arrest of virus replication and movement in plants. Viruses have limited host ranges, and adaptation to a new host is an atypical phenomenon. The entire genotypes of plant species which are imperceptive to every single isolate of a genetically variable virus species are described as non-hosts. NHR is the non-specific resistance manifested by an innately immune non-host due to pre-existing and inducible defense responses, which cannot be evaded by yet-to-be adapted plant viruses. NHR-to-plant viruses are widespread, but the phenotypic variation is often not detectable within plant species. Therefore, molecular and genetic mechanisms of NHR need to be systematically studied to enable exploitation in crop protection. This article comprehensively describes the possible mechanisms of NHR against plant viruses. Also, the previous definition of NHR to plant viruses is insufficient, and the main aim of this article is to sensitize plant pathologists to the existence of NHR to plant viruses and to highlight the need for immediate and elaborate research in this area. creator: Avanish Rai creator: Palaiyur N. Sivalingam creator: Muthappa Senthil-Kumar uri: https://doi.org/10.7717/peerj.12996 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Rai et al. title: Potential roles of melatonin and ABA on apple dwarfing in semi-arid area of Xinjiang China link: https://peerj.com/articles/13008 last-modified: 2022-03-31 description: Dwarfing is a typic breeding trait for mechanical strengthening and relatively high yield in modern apple orchards. Clarification of the mechanisms associated with dwarfing is important for use of molecular technology to breed apple. Herein, we identified four dwarfing apple germplasms in semi-arid area of Xinjiang, China. The internodal distance of these four germplasms were significantly shorter than non-dwarfing control. Their high melatonin (MT) contents are negatively associated with their malondialdehyde (MDA) levels and oxidative damage. In addition, among the detected hormones including auxin (IAA), gibberellin (GA), brassinolide (BR), zeatin-riboside (ZR), and abscisic acid (ABA), only ABA and ZR levels were in good correlation with the dwarfing phenotype. The qPCR results showed that the expression of melatonin synthetic enzyme genes MdASMT1 and MdSNAT5, ABA synthetic enzyme gene MdAAO3 and degradative gene MdCYP707A, ZR synthetic enzyme gene MdIPT5 all correlated well with the enhanced levels of MT, ABA and the reduced level of of ZR in the dwarfing germplasms. Furthermore, the significantly higher expression of ABA marker genes (MdRD22 and MdRD29) and the lower expression of ZR marker genes (MdRR1 and MdRR2) in all the four dwarf germplasms were consistent with the ABA and ZR levels. Considering the yearly long-term drought occurring in Xinjiang, China, it seems that dwarfing with high contents of MT and ABA may be a good strategy for these germplasms to survive against drought stress. This trait of dwarfing may also benefit apple production and breeding in this semi-arid area. creator: Tianci Yan creator: Chuang Mei creator: Handong Song creator: Dongqian Shan creator: Yanzhao Sun creator: Zehui Hu creator: Lin Wang creator: Tong Zhang creator: Jixun Wang creator: Jin Kong uri: https://doi.org/10.7717/peerj.13008 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Yan et al. title: Dietary fatty acid patterns and risk of oesophageal squamous cell carcinoma link: https://peerj.com/articles/13036 last-modified: 2022-03-31 description: BackgroundTo characterize and examine the associations between dietary fatty acid intake patterns and the risk of oesophageal squamous cell carcinoma (ESCC).MethodsA total of 422 patients and 423 controls were recruited. Dietary fatty acids were entered into a factor analysis. Multivariable logistic regression and restricted cubic spline were used to evaluate the risk of ESCC specific for different dietary fatty acid patterns (FAPs). A forest plot was applied to show the association between FAPs and ESCC risk after stratification by lifestyle exposure factors (tobacco smoking, alcohol drinking, pickled food, fried food, hot food, hard food).ResultsThe factor analysis generated four major fatty acid patterns: a medium- and long-chain SFA (MLC-SFA) pattern; an even-chain unsaturated fatty acid (EC-UFA) pattern, a saturated fatty acid (SFA) pattern and an n-3 long-chain polyunsaturated fatty acid (n-3 LC-PUFA) pattern. In the multivariate-adjusted model, the odds ratios (ORs) with 95% confidence intervals (CIs) of ESCC were 2.07 (1.31, 3.26) and 0.53 (0.34, 0.81) for the highest versus the lowest tertiles of the EC-UFA pattern and n-3 LC-PUFA pattern, respectively. The MLC-SFA and SFA patterns were not associated with ESCC. An association between FAPs and ESCC risk after stratification by lifestyle exposure factors was also observed.ConclusionsOur study indicates that the EC-UFA pattern and n-3 LC-PUFA pattern intake are associated with ESCC, providing a potential dietary intervention for ESCC prevention. creator: Chanchan Hu creator: Zheng Lin creator: Zhiqiang Liu creator: Xuwei Tang creator: Jianyu Song creator: Jianbo Lin creator: Yuanmei Chen creator: Zhijian Hu uri: https://doi.org/10.7717/peerj.13036 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Hu et al. title: Effectiveness of digital mental health interventions for university students: an umbrella review link: https://peerj.com/articles/13111 last-modified: 2022-03-31 description: BackgroundPoor mental health among university students remains a pressing public health issue. Over the past few years, digital health interventions have been developed and considered promising in increasing psychological wellbeing among university students. Therefore, this umbrella review aims to synthesize evidence on digital health interventions targeting university students and to evaluate their effectiveness.MethodsA systematic literature search was performed in April 2021 searching PubMed, Psychology and Behavioural Science Collection, Web of Science, ERIC, and Scopus for systematic reviews and meta-analyses on digital mental health interventions targeting university students. The review protocol was registered in the International Prospective Register of Systematic Reviews PROSPERO [CRD42021234773].ResultsThe initital literature search resulted in 806 records of which seven remained after duplicates were removed and evaluated against the inclusion criteria. Effectiveness was reported and categorized into the following six delivery types: (a) web-based, online/computer-delivered interventions (b) computer-based Cognitive Behavior Therapy (CBT), (c) mobile applications and short message service (d) virtual reality interventions (e) skills training (f) relaxation and exposure-based therapy. Results indicated web-based online/computer delivered-interventions were effective or at least partially effective at decressing depression, anxiety, stress and eating disorder symptoms. This was similar for skills-training interventions, CBT-based intervention and mobile applications. However, digital mental health interventions using virtual reality and relaxation, exposure-based therapy was inconclusive. Due to the variation in study settings and inconsistencies in reporting, effectiveness was greatly dependent on the delivery format, targeted mental health problem and targeted purpose group.ConclusionThe findings provide evidence for the beneficial effect of digital mental health interventions for university students. However, this review calls for a more systematic approach in testing and reporting the effectiveness of digital mental health interventions. creator: Sophia Harith creator: Insa Backhaus creator: Najihah Mohbin creator: Huyen Thi Ngo creator: Selina Khoo uri: https://doi.org/10.7717/peerj.13111 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Harith et al. title: Insight into the cryptic diversity and phylogeography of the peculiar fried egg jellyfish Phacellophora (Cnidaria, Scyphozoa, Ulmaridae) link: https://peerj.com/articles/13125 last-modified: 2022-03-31 description: The fried egg jellyfish Phacellophora camtschatica (senso lato) is a morphologically peculiar and conspicuous species occurring mostly in the cold waters of the North Pacific. It is less common in the cold waters of the NW Atlantic, and occasionally has been reported in the Mediterranean, Arctic, East and South Pacific, and E, SW and NE Atlantic. However, sightings of this scyphozoan jellyfish have intensified during the past two to three decades in Macaronesia, the Iberian Peninsula and the Mediterranean. These jellyfish are known to be voracious predators of other jellies, but also of other taxa, including fish of commercial interest. Therefore, Phacellophora aggregations may threaten local fisheries, aquaculture, and local biodiversity structuring. We report the first known occurrences of Phacellophora in the Azores Islands, which apparently become more frequent in recent years of the past decade. We confirm, through DNA barcoding of COI and 16S mitochondrial markers, the genetic identity of Phacellophora occurring in the Azores (NE Atlantic). We reveal, with COI sequence data, three (potentially four) cryptic species within the Phacellophora camtschatica complex. Two Phacellophora species co-occur in the North Pacific. In the North Atlantic (and possibly in the Mediterranean) one or two distinct species exist. Three nominal species of the genus that are currently synonymized, with type localities in the N Pacific, NW Atlantic, and the Mediterranean, need reassessment. The morphotypes previously defined for the four putative species names given for Phacellophora might be eventually differentiated by the number and disposition of the marginal lappets of umbrellae. This morphologic character has to be further inspected in vouchers of the four genetic lineages of Phacellophora, to decide between the description of new species, and the resurrection of junior synonyms through the designation of neotypes with DNA Barcodes, to validate the identity of the cryptic taxa detected. More haplotype sampling is necessary across the distribution of the genus to further investigate the genetic diversity and phylogeographic history of Phacellophora. The high genetic relatedness of Phacellophora from the cold NW Atlantic and the sub-tropical shores of the Azores, revealed by 16S and COI sequence data, suggests a recent invasion, in terms of geologic time, of the temperate waters of the NE Atlantic (and possibly of the Mediterranean). The medusivorous habits of Phacellophora, and especially its predation on the mauve stinger (Pelagia spp.) which frequently blooms in Macaronesia and Mediterranean waters, could relate to the recent reports of Phacellophora in the Azores, Madeira, Canary Islands, and the Mediterranean.More investment, including on scientific staff, is necessary to catalog, DNA barcode and monitor jellyfish dynamics more accurately worldwide. creator: Carlos J. Moura creator: Nikolai Ropa creator: Bruno Ivo Magalhães creator: João M. Gonçalves uri: https://doi.org/10.7717/peerj.13125 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Moura et al. title: Continuous mutation of SARS-CoV-2 during migration via three routes at the beginning of the pandemic link: https://peerj.com/articles/12681 last-modified: 2022-03-30 description: BackgroundIt remains unclear how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection started, spread worldwide, and mutated to result in the present variants. This difficulty can be attributed to the limitations associated with the analytical methodology for presenting the differences among genomic sequences. In this study, we critically analysed the early data to explain the start and spread of the pandemic.MethodsObjective analyses of the RNA sequences of earlier variants of SARS-CoV-2 (up to September 1, 2020, available in DDBJ and GISAID) were performed using Principal Component Analysis (PCA). The results were compared with information on the collection dates and location. The PCA was also conducted for 12 variants of interest to the WHO as of September 2021, and compared with earlier data.ResultsThe pandemic began in Wuhan, China. This strain was suspected to be related to other reported animal viruses; however, they had a minimal similarity. The strain then spreads via three routes while accumulating mutations. Several viral subgroups were identified along the routes, each with a large number of patients reported, indicating high infectivity to humans. These routes were only confirmed by the early data analysis, because newer variants would have more mutations, and would be preferentially be examined by PCA if they were included. On the original axes found in the early variants, the newer variants revealed that they retained previously acquired mutations, which helped to reveal the viral ancestors of the newer variants. The rate of mutation was found to be comparable to that of the influenza H1N1 virus, which causes recurrent seasonal epidemics. Another threat imposed by SARS-CoV-2 is that if the pandemic cannot be contained, new variants may emerge annually, preventing herd immunity. creator: Tomokazu Konishi uri: https://doi.org/10.7717/peerj.12681 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Konishi title: Expression profiles and transcript properties of fast-twitch and slow-twitch muscles in a deep-sea highly migratory fish, Pseudocaranx dentex link: https://peerj.com/articles/12720 last-modified: 2022-03-30 description: Fast-twitch and slow-twitch muscles are the two principal skeletal muscle types in teleost with obvious differences in metabolic and contractile phenotypes. The molecular mechanisms that control and maintain the different muscle types remain unclear yet. Pseudocaranx dentex is a highly mobile active pelagic fish with distinctly differentiated fast-twitch and slow-twitch muscles. Meanwhile, P. dentex has become a potential target species for deep-sea aquaculture because of its considerable economic value. To elucidate the molecular characteristics in the two muscle types of P. dentex, we generated 122 million and 130 million clean reads from fast-twitch and slow-witch muscles using RNA-Seq, respectively. Comparative transcriptome analysis revealed that 2,862 genes were differentially expressed. According to GO and KEGG analysis, the differentially expressed genes (DEGs) were mainly enriched in energy metabolism and skeletal muscle structure related pathways. Difference in the expression levels of specific genes for glycolytic and lipolysis provided molecular evidence for the differences in energy metabolic pathway between fast-twitch and slow-twitch muscles of P. dentex. Numerous genes encoding key enzymes of mitochondrial oxidative phosphorylation pathway were significantly upregulated at the mRNA expression level suggested slow-twitch muscle had a higher oxidative phosphorylation to ensure more energy supply. Meanwhile, expression patterns of the main skeletal muscle developmental genes were characterized, and the expression signatures of Sox8, Myod1, Calpain-3, Myogenin, and five insulin-like growth factors indicated that more myogenic cells of fast-twitch muscle in the differentiating state. The analysis of important skeletal muscle structural genes showed that muscle type-specific expression of myosin, troponin and tropomyosin may lead to the phenotypic structure differentiation. RT-qPCR analysis of twelve DEGs showed a good correlation with the transcriptome data and confirmed the reliability of the results presented in the study. The large-scale transcriptomic data generated in this study provided an overall insight into the thorough gene expression profiles of skeletal muscle in a highly mobile active pelagic fish, which could be valuable for further studies on molecular mechanisms responsible for the diversity and function of skeletal muscle. creator: Huan Wang creator: Busu Li creator: Long Yang creator: Chen Jiang creator: Tao Zhang creator: Shufang Liu creator: Zhimeng Zhuang uri: https://doi.org/10.7717/peerj.12720 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wang et al. title: Oviducal gland transcriptomics of Octopus maya through physiological stages and the negative effects of temperature on fertilization link: https://peerj.com/articles/12895 last-modified: 2022-03-30 description: BackgroundElevated temperatures reduce fertilization and egg-laying rates in the octopus species. However, the molecular mechanisms that control the onset of fertilization and egg-laying in the octopus’ oviducal gland are still unclear; and the effect of temperature on the expression of key reproductive genes is unknown. This study aims to better understand the molecular bases of octopus fertilization and egg-laying, and how they are affected by elevated temperatures.MethodRNA-seq of oviducal glands was performed for samples before, during, and after fertilization and their transcriptomic profiles were compared. Also, at the fertilization stage, the optimal and thermal-stress conditions were contrasted. Expression levels of key reproductive genes were validated via RT-qPCR.ResultsIn mated females before egg-laying, genes required for the synthesis of spermine, spermidine, which may prevent premature fertilization, and the myomodulin neuropeptide were upregulated. Among the genes with higher expression at the fertilization stage, we found those encoding the receptors of serotonin, dopamine, and progesterone; genes involved in the assembly and motility of the sperm flagellum; genes that participate in the interaction between male and female gametes; and genes associated with the synthesis of eggshell mucoproteins. At temperatures above the optimal range for reproduction, mated females reduced the fertilization rate. This response coincided with the upregulation of myomodulin and APGW-amide neuropeptides. Also, genes associated with fertilization like LGALS3, VWC2, and Pcsk1 were downregulated at elevated temperatures. Similarly, in senescent females, genes involved in fertilization were downregulated but those involved in the metabolism of steroid hormones like SRD5A1 were highly expressed. creator: Oscar E. Juárez creator: Lousiana Arreola-Meraz creator: Edna Sánchez-Castrejón creator: Omar Hernando Avila-Poveda creator: Laura L. López-Galindo creator: Carlos Rosas creator: Clara E. Galindo-Sánchez uri: https://doi.org/10.7717/peerj.12895 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Juárez et al. title: Heart rate variability, mood and performance: a pilot study on the interrelation of these variables in amateur road cyclists link: https://peerj.com/articles/13094 last-modified: 2022-03-30 description: ObjectiveThe present study seeks to explore the relationship between measures of cycling training on a given day and the heart rate variability (HRV) and mood states obtained the following morning. The association between HRV and mood state is also studied, as is the relationship between internal and external measures of training.MethodsDuring a 6-week period, five recreational road cyclists collected 123 recordings of morning HRV and morning mood, and 66 recordings of training power and rate of perceived exertion (RPE). Training power was used as an external measure of performance and RPE as an internal measure of performance. The HRV parameters used in the study were the mean of RR intervals (mean RR) and the standard deviation of all RR intervals (SDNN) as time domain analysis, and the normalized high frequency band (HFnu), normalized low frequency band (LFnu) and the ratio between low and high frequency bands, as frequency domain analysis. Mood was measured using a 10-point cognitive scale.ResultsIt was found that the higher the training power on a given day, the lower the HFnu and the higher LF/HF were on the following morning. At the same time, results showed an inverse relationship between training and mood, so the tougher a training session, the lower the mood the following day. A relationship between morning HRV and mood was also found, so that the higher mean RR and HFnu, the more positive the mood (r = 0.497 and r = 0.420 respectively; p < 0.001). Finally, RPE correlated positively with external power load variables (IF: r = 0.545; p < 0.001).ConclusionAltogether, the results indicate a relationship between training of cyclists on a given day and their morning HRV and mood state on the following day. Mood and HRV also seem positively related. It is argued that developing a monitoring system that considers external and internal training loads, together with morning mood, could help understand the state of the individual, enabling feedback to athletes to facilitate the adaptation to training and to prevent problems associated with overtraining. However, more research is needed to further understand the association between the different variables considered. creator: Carla Alfonso creator: Lluis Capdevila uri: https://doi.org/10.7717/peerj.13094 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Alfonso and Capdevila title: RNA sequencing reveals the emerging role of bronchoalveolar lavage fluid exosome lncRNAs in acute lung injury link: https://peerj.com/articles/13159 last-modified: 2022-03-30 description: BackgroundBronchoalveolar lavage fluid (BALF) exosomes possess different properties in different diseases, which are mediated through microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), among others. By sequencing the differentially expressed lncRNAs in BALF exosomes, we seek potential targets for the diagnosis and treatment of acute lung injury (ALI).MethodsConsidering that human and rat genes are about 80% similar, ALI was induced using lipopolysaccharide in six male Wistar rats, with six rats as control (all weighing 200 ± 20 g and aged 6–8 weeks). BALF exosomes were obtained 24 h after ALI. The exosomes in BALF were extracted by ultracentrifugation. The differential expression of BALF exosomal lncRNAs in BALF was analyzed by RNA sequencing. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to predict the functions of differentially expressed lncRNAs, which were confirmed by reverse transcription–polymerase chain reaction.ResultsCompared with the control group, the ALI group displayed a higher wet/dry ratio, tumor necrosis factor-α levels, and interleukin-6 levels (all P < 0.001). The airway injection of exosomes in rats led to significant infiltration by neutrophils. A total of 2,958 differentially expressed exosomal lncRNAs were identified, including 2,524 upregulated and 434 downregulated ones. Five lncRNAs confirmed the reliability of the sequencing data. The top three GO functions were phagocytic vesicle membrane, regulation of receptor biosynthesis process, and I-SMAD binding. Salmonella infection, Toll-like receptor signaling pathway, and osteoclast differentiation were the most enriched KEGG pathways. The lncRNA–miRNA interaction network of the five confirmed lncRNAs could be predicted using miRDB.ConclusionsBALF-derived exosomes play an important role in ALI development and help identify potential therapeutic targets related to ALI. creator: Meijuan Song creator: Xiuwei Zhang creator: Yizhou Gao creator: Bing Wan creator: Jinqiang Wang creator: Jinghang Li creator: Yuanyuan Song creator: Xiaowei Shen creator: Li Wang creator: Mao Huang creator: Xiaowei Wang uri: https://doi.org/10.7717/peerj.13159 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Song et al. title: ExhauFS: exhaustive search-based feature selection for classification and survival regression link: https://peerj.com/articles/13200 last-modified: 2022-03-30 description: Feature selection is one of the main techniques used to prevent overfitting in machine learning applications. The most straightforward approach for feature selection is an exhaustive search: one can go over all possible feature combinations and pick up the model with the highest accuracy. This method together with its optimizations were actively used in biomedical research, however, publicly available implementation is missing. We present ExhauFS—the user-friendly command-line implementation of the exhaustive search approach for classification and survival regression. Aside from tool description, we included three application examples in the manuscript to comprehensively review the implemented functionality. First, we executed ExhauFS on a toy cervical cancer dataset to illustrate basic concepts. Then, multi-cohort microarray breast cancer datasets were used to construct gene signatures for 5-year recurrence classification. The vast majority of signatures constructed by ExhauFS passed 0.65 threshold of sensitivity and specificity on all datasets, including the validation one. Moreover, a number of gene signatures demonstrated reliable performance on independent RNA-seq dataset without any coefficient re-tuning, i.e., turned out to be cross-platform. Finally, Cox survival regression models were used to fit isomiR signatures for overall survival prediction for patients with colorectal cancer. Similarly to the previous example, the major part of models passed the pre-defined concordance index threshold 0.65 on all datasets. In both real-world scenarios (breast and colorectal cancer datasets), ExhauFS was benchmarked against state-of-the-art feature selection models, including L1-regularized sparse models. In case of breast cancer, we were unable to construct reliable cross-platform classifiers using alternative feature selection approaches. In case of colorectal cancer not a single model passed the same 0.65 threshold. Source codes and documentation of ExhauFS are available on GitHub: https://github.com/s-a-nersisyan/ExhauFS. creator: Stepan Nersisyan creator: Victor Novosad creator: Alexei Galatenko creator: Andrey Sokolov creator: Grigoriy Bokov creator: Alexander Konovalov creator: Dmitry Alekseev creator: Alexander Tonevitsky uri: https://doi.org/10.7717/peerj.13200 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Nersisyan et al. title: Machine learning driven by environmental covariates to estimate high-resolution PM2.5 in data-poor regions link: https://peerj.com/articles/13203 last-modified: 2022-03-30 description: PM2.5, which refers to fine particles with an equivalent aerodynamic diameter of less than or equal to 2.5 µm, can not only affect air quality but also endanger public health. Nevertheless, the spatial distribution of PM2.5 is not well understood in data-poor regions where monitoring stations are scarce. Therefore, we constructed a random forest (RF) model and a bagging algorithm model based on ground-monitored PM2.5 data, aerosol optical depth (AOD) and meteorological data, and auxiliary geographical variables to accurately estimate the spatial distribution of PM2.5 concentrations in Xinjiang during 2015–2020 at a resolution of 1 km. Through 10-fold cross-validation (CV), the RF model and bagging algorithm model were verified and compared. The results showed the following: (1) The RF model achieved better model performance and thus can be used to estimate the PM2.5 concentration at a relatively high resolution. (2) The PM2.5 concentrations were high in southern Xinjiang and low in northern Xinjiang. The high values were concentrated mainly in the Tarim Basin, while most areas of northern Xinjiang maintained low PM2.5 levels year-round. (3) The PM2.5 values in Xinjiang showed significant seasonality, with the seasonally averaged concentrations decreasing as follows: winter (71.95 µg m−3) > spring (64.76 µg m−3) > autumn (46.01 µg m−3) > summer (43.40 µg m−3). Our model provides a way to monitor air quality in data-scarce places, thereby advancing efforts to achieve sustainable development in the future. creator: XiaoYe Jin creator: Jianli Ding creator: Xiangyu Ge creator: Jie Liu creator: Boqiang Xie creator: Shuang Zhao creator: Qiaozhen Zhao uri: https://doi.org/10.7717/peerj.13203 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2022 Jin et al. title: Bioinformatical analysis identifies PDLIM3 as a potential biomarker associated with immune infiltration in patients with endometriosis link: https://peerj.com/articles/13218 last-modified: 2022-03-30 description: BackgroundEndometriosis is a chronic systemic disease, whose classic symptoms are pelvic pain and infertility. This disease seriously reduces the life quality of patients. The pathogenesis, recognition and treatment of endometriosis is still unclear, and cannot be over emphasized. The aim of our study was to investigate the potential biomarker of endometriosis for the mechanism and treatment.MethodsUsing GSE11691, GSE23339 and GSE5108 datasets, differentially expressed genes (DEGs) were identified between endometriosis and normal samples. The functions of DEGs were reflected by the analysis of gene ontology (GO), pathway enrichment and gene set enrichment analysis (GSEA). The LASSO regression model was performed to identify candidate biomarkers. The receiver operating characteristic curve (ROC) was used to evaluate discriminatory ability of candidate biomarkers. The predictive value of the markers in endometriosis were further validated in the GSE120103 dataset. Then, the expression level of biomarkers was detected by qRT-PCR and Western blot. Finally, the relationship between candidate biomarker expression and immune infiltration was estimated using CIBERSORT.ResultsA total of 42 genes were identified, which were mainly involved in cytokine–cytokine receptor interaction, systemic lupus erythematosus and chemokine signaling pathway. We confirmed PDLIM3 was a specific biomarker in endometriosis (AUC = 0.955) and validated in the GSE120103 dataset (AUC = 0.836). The mRNA and protein expression level of PDLIM3 in endometriosis tissue was significantly higher than normal. Immune cell infiltration analysis revealed that PDLIM3 was correlated with M2 macrophages, neutrophils, CD4+ memory resting T cells, gamma delta T cells, M1 Macrophages, resting mast cells, follicular helper T cells, activated NK cells, CD8+ T cells, regulatory T cells (Tregs), naive B cells, plasma cells and resting NK cells. creator: Lei Gan creator: Jiani Sun creator: Jing Sun uri: https://doi.org/10.7717/peerj.13218 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Gan et al. title: Long non-coding RNA SPRY4-IT1 promotes proliferation and metastasis in nasopharyngeal carcinoma cell link: https://peerj.com/articles/13221 last-modified: 2022-03-30 description: BackgroundLong non-coding RNA SPRY4 intronic transcript 1 (Lnc RNA SPRY4-IT1) was aberrant-expressed in various kinds of cancer. Increasing evidence demonstrated that lnc RNAs involved in tumorigenesis and metastasis. In this study, we aimed to explore the biological role of SPRY4-IT1 on the phenotype of nasopharyngeal carcinoma (NPC) in vitro and in vivo.MethodsThe expression level of SPRY4-IT1 in NPC cell lines were measured by quantitative real-time polymerase chain reaction (qRT-PCR). Cell Counting Kit-8 (CCK-8) and colony formation assay were used to detect cell proliferation. Wound-healing assay, transwell assay and animal experiment were performed to evaluate the ability of cell migration and metastasis. Cell cycle distribution and apoptosis were determined by flow cytometry. Western blotting and immunofluorescence were employed to identify protein expression.ResultsSPRY4-IT1 was significantly up-regulated in several NPC cell lines (6-10B, CNE-2, and HONE-1) compared with human immortalized nasopharyngeal epithelial cell (NP69). Silencing of SPRY4-IT1 inhibited proliferation, migration, and metastasis, and induced significant G2/M phase arrest and apoptosis. Western blotting showed that the expression levels of cell cycle-related proteins (cyclin B1, cdc2 and p-cdc2) were down-regulated and apoptosis-associated proteins (PARP, cleaved PARP and cleaved caspase-3) were up-regulated after knockdown of SPRY4-IT1. The expression level of E-cadherin was increased and the expression of Vimentin, Snail and Twist1 were decreased after the SPRY4-IT1 knockdown.ConclusionlncRNA SPRY4-IT1 played a significant role in NPC proliferation, migration and metastasis, suggesting that SPRY4-IT1 might be a potential therapeutic target for the treatment of NPC. creator: Yanfei Li creator: Zhenpeng Liao creator: Rong Wang creator: Zibin Liang creator: Zhihe Lin creator: Shiqi Deng creator: Lei Chen creator: Zhigang Liu creator: Shaoyan Feng uri: https://doi.org/10.7717/peerj.13221 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Li et al. title: Classifying the difficulty levels of working memory tasks by using pupillary response link: https://peerj.com/articles/12864 last-modified: 2022-03-29 description: Knowing the difficulty of a given task is crucial for improving the learning outcomes. This paper studies the difficulty level classification of memorization tasks from pupillary response data. Developing a difficulty level classifier from pupil size features is challenging because of the inter-subject variability of pupil responses. Eye-tracking data used in this study was collected while students solved different memorization tasks divided as low-, medium-, and high-level. Statistical analysis shows that values of pupillometric features (as peak dilation, pupil diameter change, and suchlike) differ significantly for different difficulty levels. We used a wrapper method to select the pupillometric features that work the best for the most common classifiers; Support Vector Machine (SVM), Decision Tree (DT), Linear Discriminant Analysis (LDA), and Random Forest (RF). Despite the statistical difference, experiments showed that a random forest classifier trained with five features obtained the best F1-score (82%). This result is essential because it describes a method to evaluate the cognitive load of a subject performing a task using only pupil size features. creator: Hugo Mitre-Hernandez creator: Jorge Sanchez-Rodriguez creator: Sergio Nava-Muñoz creator: Carlos Lara-Alvarez uri: https://doi.org/10.7717/peerj.12864 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Mitre-Hernandez et al. title: Responsiveness of domesticated goats towards various stressors following long-term cognitive test exposure link: https://peerj.com/articles/12893 last-modified: 2022-03-29 description: Current evidence suggests that frequent exposure to situations in which captive animals can solve cognitive tasks may have positive effects on stress responsiveness and thus on welfare. However, confounding factors often hamper the interpretation of study results. In this study, we used human-presented object-choice tests (in form of visual discrimination and reversal learning tests and a cognitive test battery), to assess the effect of long-term cognitive stimulation (44 sessions over 4–5 months) on behavioural and cardiac responses of female domestic goats in subsequent stress tests. To disentangle whether cognitive stimulation per se or the reward associated with the human–animal interaction required for testing was affecting the stress responsiveness, we conditioned three treatment groups: goats that were isolated for participation in human-presented cognitive tests and rewarded with food (‘Cognitive’, COG treatment), goats that were isolated as for the test exposure and rewarded with food by the experimenter without being administered the object-choice tests (‘Positive’, POS treatment), and goats that were isolated in the same test room but neither received a reward nor were administered the tests (‘Isolation’, ISO treatment). All treatment groups were subsequently tested in four stress tests: a novel arena test, a novel object test, a novel human test, and a weighing test in which goats had to enter and exit a scale cage. All treatment groups weretested at the same two research sites, each using two selection lines, namely dwarf goats, not selected for production traits, and dairy goats, selected for high productivity. Analysing the data with principal component analysis and linear mixed-effects models, we did not find evidence that cognitive testing per se (COG–POS contrast) reduces stress responsiveness of goats in subsequent stress tests. However, for dwarf goats but not for dairy goats, we found support for an effect of reward-associated human–animal interactions (POS–ISO contrast) at least for some stress test measures. Our results highlight the need to consider ontogenetic and genetic variation when assessing stress responsiveness and when interacting with goats. creator: Katrina Rosenberger creator: Michael Simmler creator: Jan Langbein creator: Christian Nawroth creator: Nina Keil uri: https://doi.org/10.7717/peerj.12893 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Rosenberger et al. title: Faecal DNA metabarcoding reveals novel bacterial community patterns of critically endangered Southern River Terrapin, Batagur affinis link: https://peerj.com/articles/12970 last-modified: 2022-03-29 description: Southern River Terrapin, Batagur affinis, is a freshwater turtle listed as critically endangered on the IUCN Red List since 2000. Many studies suggest that faecal DNA metabarcoding can shield light on the host-associated microbial communities that play important roles in host health. Thus, this study aimed to characterise and compare the faecal bacterial community between captive and wild B. affinis using metabarcoding approaches. A total of seven faeces samples were collected from captive (N = 5) and wild (N = 2) adult B. affinis aseptically, crossing the East and West coast of peninsular Malaysia. The DNA was extracted from the faeces samples, and the 16S rRNA gene (V3–V4 region) was amplified using polymerase chain reaction (PCR). The amplicon was further analysed using SILVA and DADA2 pipelines. In total, 297 bacterial communities taxonomic profile (phylum to genus) were determined. Three phyla were found in high abundance in all faeces samples, namely Firmicutes (38.69%), Bacteroidetes (24.52%), and Fusobacteria (6.95%). Proteobacteria were detected in all faeces samples (39.63%), except the wild sample, KBW3. Under genus level, Cetobacteriumwas found as the most abundant genus (67.79%), followed by Bacteroides (24.56%) and Parabacteroides (21.78%). The uncultured genus had the highest abundance (88.51%) even though not detected in the BK31 and KBW2 samples. The potential probiotic genera (75.00%) were discovered to be more dominant in B. affinis faeces samples. Results demonstrated that the captive B. affinis faeces samples have a greater bacterial variety and richness than wild B. affinis faeces samples. This study has established a starting point for future investigation of the gut microbiota of B. affinis. creator: Mohd Hairul Mohd Salleh creator: Yuzine Esa creator: Mohamad Syazwan Ngalimat creator: Pelf Nyok Chen uri: https://doi.org/10.7717/peerj.12970 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Mohd Salleh et al. title: Investigating effect of mutation on structure and function of G6PD enzyme: a comparative molecular dynamics simulation study link: https://peerj.com/articles/12984 last-modified: 2022-03-29 description: Several natural mutants of the human G6PD enzyme exist and have been reported. Because the enzymatic activities of many mutants are different from that of the wildtype, the genetic polymorphism of G6PD plays an important role in the synthesis of nucleic acids via ribulose-5-phosphate and formation of reduced NADP in response to oxidative stress. G6PD mutations leading to its deficiency result in the neonatal jaundice and acute hemolytic anemia in human. Herein, we demonstrate the molecular dynamics simulations of the wildtype G6PD and its three mutants to monitor the effect of mutations on dynamics and stability of the protein. These mutants are Chatham (A335T), Nashville (R393H), Alhambra (V394L), among which R393H and V394L lie closer to binding site of structural NADP+. MD analysis including RMSD, RMSF and protein secondary structure revealed that decrease in the stability of mutants is key factor for loss of their activity. The results demonstrated that mutations in the G6PD sequence resulted in altered structural stability and hence functional changes in enzymes. Also, the binding site, of structural NADP+, which is far away from the catalytic site plays an important role in protein stability and folding. Mutation at this site causes changes in structural stability and hence functional deviations in enzyme structure reflecting the importance of structural NADP+ binding site. The calculation of binding free energy by post processing end state method of Molecular Mechanics Poisson Boltzmann SurfaceArea (MM-PBSA) has inferred that ligand binding in wildtype is favorable as compared to mutants which represent destabilised protein structure due to mutation that in turn may hinder the normal physiological function. Exploring individual components of free energy revealed that the van der Waals energy component representing non-polar/hydrophobic energy contribution act as a dominant factor in case of ligand binding. Our study also provides an insight in identifying the key inhibitory site in G6PD and its mutants which can be exploited to use them as a target for developing new inhibitors in rational drug design. creator: Sadaf Rani creator: Fouzia Perveen Malik creator: Jamshed Anwar creator: Rehan Zafar Paracha uri: https://doi.org/10.7717/peerj.12984 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Rani et al. title: Synergistic effects of climate and landscape change on the conservation of Amazonian lizards link: https://peerj.com/articles/13028 last-modified: 2022-03-29 description: The leading causes of the worldwide decline in biodiversity are global warming, allied with natural habitat loss and fragmentation. Here, we propose an analysis of the synergistic effects of these two factors in 63 species of Amazonian lizards. We predicted that the high-climatic suitability areas of species would be significantly impacted by different deforestation scenarios and the resultant landscape structure and considered that forest-dwelling species would be especially susceptible to deforestation scenarios. We also pointed out species threatened by both drivers and suggested critical areas for their future conservation. According to our results, most species will face future reductions in suitable areas for their occurrence according to five different patterns, two of which represent significant risks for 15 species. Some of these species already deal with severe habitat loss and fragmentation of their current distribution ranges, whereas others will suffer a considerable area reduction related to future range shifts. We emphasize the importance of protected areas (PAs), especially indigenous lands, and the need to plan combined strategies involving PAs’ maintenance and possible implementation of ecological corridors. Finally, we highlight eight species of thermoconformer lizards that constitute present and future conservation concerns related to the combined effects of climate change and habitat loss and that should be carefully evaluated in extinction risk assessments. creator: Cássia de Carvalho Teixeira creator: Leonardo Carreira Trevelin creator: Maria Cristina dos Santos-Costa creator: Ana Prudente creator: Daniel Paiva Silva uri: https://doi.org/10.7717/peerj.13028 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Teixeira et al. title: Rapid parameter estimation for selective inversion recovery myelin imaging using an open-source Julia toolkit link: https://peerj.com/articles/13043 last-modified: 2022-03-29 description: BackgroundMagnetic resonance imaging (MRI) is used extensively to quantify myelin content, however computational bottlenecks remain challenging for advanced imaging techniques in clinical settings. We present a fast, open-source toolkit for processing quantitative magnetization transfer derived from selective inversion recovery (SIR) acquisitions that allows parameter map estimation, including the myelin-sensitive macromolecular pool size ratio (PSR). Significant progress has been made in reducing SIR acquisition times to improve clinically feasibility. However, parameter map estimation from the resulting data remains computationally expensive. To overcome this computational limitation, we developed a computationally efficient, open-source toolkit implemented in the Julia language.MethodsTo test the accuracy of this toolkit, we simulated SIR images with varying PSR and spin-lattice relaxation time of the free water pool (R1f) over a physiologically meaningful scale from 5% to 20% and 0.5 to 1.5 s−1, respectively. Rician noise was then added, and the parameter maps were estimated using our Julia toolkit. Probability density histogram plots and Lin’s concordance correlation coefficients (LCCC) were used to assess accuracy and precision of the fits to our known simulation data. To further mimic biological tissue, we generated five cross-linked bovine serum albumin (BSA) phantoms with concentrations that ranged from 1.25% to 20%. The phantoms were imaged at 3T using SIR, and data were fit to estimate PSR and R1f. Similarly, a healthy volunteer was imaged at 3T, and SIR parameter maps were estimated to demonstrate the reduced computational time for a real-world clinical example.ResultsEstimated SIR parameter maps from our Julia toolkit agreed with simulated values (LCCC > 0.98). This toolkit was further validated using BSA phantoms and a whole brain scan at 3T. In both cases, SIR parameter estimates were consistent with published values using MATLAB. However, compared to earlier work using MATLAB, our Julia toolkit provided an approximate 20-fold reduction in computational time.ConclusionsPresented here, we developed a fast, open-source, toolkit for rapid and accurate SIR MRI using Julia. The reduction in computational cost should allow SIR parameters to be accessible in clinical settings. creator: Nicholas J. Sisco creator: Ping Wang creator: Ashley M. Stokes creator: Richard D. Dortch uri: https://doi.org/10.7717/peerj.13043 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Sisco et al. title: NanoForms: an integrated server for processing, analysis and assembly of raw sequencing data of microbial genomes, from Oxford Nanopore technology link: https://peerj.com/articles/13056 last-modified: 2022-03-29 description: BackgroundNext Generation Sequencing (NGS) techniques dominate today’s landscape of genetics and genomics research. Though Illumina still dominates worldwide sequencing, Oxford Nanopore is one of the leading technologies currently being used by biologists, medics and geneticists across various applications. Oxford Nanopore is automated and relatively simple for conducting experiments, but generates gigabytes of raw data, to be processed by often ambiguous set of alternative bioinformatics command-line tools, and genomics frameworks which require a knowledge of bioinformatics to run.ResultsWe established an inter-collegiate collaboration across experimentalists and bioinformaticians in order to provide a novel bioinformatics tool, free for academics. This tool allows people without extensive bioinformatics knowledge to simply process their raw genome sequencing data. Currently, due to ICT resources’ maintenance reasons, our server is only capable of handling small genomes (up to 15 Mb). In this paper, we introduce our tool, NanoForms: an intuitive and integrated web server for the processing and analysis of raw prokaryotic genome data, coming from Oxford Nanopore. NanoForms is freely available for academics at the following locations: http://nanoforms.tech (webserver) and https://github.com/czmilanna/nanoforms (GitHub source repository). creator: Anna Czmil creator: Michal Wronski creator: Sylwester Czmil creator: Marta Sochacka-Pietal creator: Michal Cmil creator: Jan Gawor creator: Tomasz Wołkowicz creator: Dariusz Plewczynski creator: Dominik Strzalka creator: Michal Pietal uri: https://doi.org/10.7717/peerj.13056 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Czmil et al. title: Subject specific muscle synergies and mechanical output during cycling with arms or legs link: https://peerj.com/articles/13155 last-modified: 2022-03-29 description: BackgroundUpper (UL) and lower limb (LL) cycling is extensively used for several applications, especially for rehabilitation for which neuromuscular interactions between UL and LL have been shown. Nevertheless, the knowledge on the muscular coordination modality for UL is poorly investigated and it is still not known whether those mechanisms are similar or different to those of LL. The aim of this study was thus to put in evidence common coordination mechanism between UL and LL during cycling by investigating the mechanical output and the underlying muscle coordination using synergy analysis.MethodsTwenty-five revolutions were analyzed for six non-experts’ participants during sub-maximal cycling with UL or LL. Crank torque and muscle activity of eleven muscles UL or LL were recorded. Muscle synergies were extracted using nonnegative matrix factorization (NNMF) and group- and subject-specific analysis were conducted.ResultsFour synergies were extracted for both UL and LL. UL muscle coordination was organized around several mechanical functions (pushing, downing, and pulling) with a proportion of propulsive torque almost 80% of the total revolution while LL muscle coordination was organized around a main function (pushing) during the first half of the cycling revolution. LL muscle coordination was robust between participants while UL presented higher interindividual variability.DiscussionWe showed that a same principle of muscle coordination exists for UL during cycling but with more complex mechanical implications. This study also brings further results suggesting each individual has unique muscle signature. creator: Théo Cartier creator: Laurent Vigouroux creator: Elke Viehweger creator: Guillaume Rao uri: https://doi.org/10.7717/peerj.13155 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Cartier et al. title: Mechanisms and potential immune tradeoffs of accelerated coral growth induced by microfragmentation link: https://peerj.com/articles/13158 last-modified: 2022-03-29 description: Microfragmentation is the act of cutting corals into small pieces (~1 cm2) to accelerate the growth rates of corals relative to growth rates observed when maintaining larger-sized fragments. This rapid tissue and skeletal expansion technique offers great potential for supporting reef restoration, yet the biological processes and tradeoffs involved in microfragmentation-mediated accelerated growth are not well understood. Here we compared growth rates across a range of successively smaller fragment sizes in multiple genets of reef-building corals, Orbicella faveolata and Montastraea cavernosa. Our results confirm prior findings that smaller initial sizes confer accelerated growth after four months of recovery in a raceway. O. faveolata transcript levels associated with growth rate include genes encoding carbonic anhydrase and glutamic acid-rich proteins, which have been previously implicated in coral biomineralization, as well as a number of unannotated transcripts that warrant further characterization. Innate immunity enzyme activity assays and gene expression results suggest a potential tradeoff between growth rate after microfragmentation and immune investment. Microfragmentation-based restoration practices have had great success on Caribbean reefs, despite widespread mortality among wild corals due to infectious diseases. Future studies should continue to examine potential immune tradeoffs throughout the microfragmentation recovery period that may affect growout survival and disease transmission after outplanting. creator: Louis Schlecker creator: Christopher Page creator: Mikhail Matz creator: Rachel M. Wright uri: https://doi.org/10.7717/peerj.13158 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Schlecker et al. title: In vitro evaluation of probiotic properties of lactic acid bacteria isolated from the vagina of yak (Bos grunniens) link: https://peerj.com/articles/13177 last-modified: 2022-03-29 description: Bovine endometritis is an inflammatory disease of the uterus that occurs after parturition and can result in the destruction of uterine microecology, disruption of hormone secretion, and even infertility. Problems such as antibiotic residues, pathogen resistance, and microbiota dysbiosis caused by conventional antibiotic therapy cannot be ignored. According to the microecological balance theory, probiotics have the potential to prevent or cure endometritis in cattle. Probiotics can positively influence host physiology by regulating microecological imbalance, modulating immunity, and antagonizing pathogens. Since some probiotics contribute to host health only in their specific natural niches, lactic acid bacteria (LAB) from the vagina may have better potential to fight against vaginal and uterine infection. The yak (Bos grunniens) is an ancient and primitive livestock animal that is adapted to high altitude and harsh environments (cold, nutritional deficiencies, and hypoxia). However, to our knowledge, there have been no studies on yak vaginal LAB. Therefore, the purpose of this study was to isolate vaginal LAB from yak, evaluate and compare the probiotic potential and safety of the isolates, and help establish the probiotics library that can be used in the prevention and/or treatment of endometritis. Twenty-five vaginal swabs were collected from healthy yak and cultured in deMan, Rogosa, and Sharpe (MRS) broth. Tentative LAB strains were preliminarily determined through calcium dissolving zone and morphological identification, and the strains were then identified using 16S rRNA gene sequencing. The probiotics of the isolates were detected using cell aggregation, hydrophobicity, resistance to acid and bile salt, adhesion, and antibacterial activities. Additionally, antimicrobial susceptibility, hemolytic activity, and detection of potential virulence factors were determined in order to confirm the safety of these strains. Five isolates were identified: Leuconostoc mesenteroides, Lactobacillus plantarum, Enterococcus hirae, Lacticaseibacillus camelliae, and Lactobacillus mucosae. All isolates had certain growth resistance, aggregation ability, effective antimicrobial potency against Escherichia coli, Staphylococcus aureus, and Salmonella typhimurium, were sensitive to most antibiotics, and could effectively adhere to bovine endometrial epithelial cells (BEECs). None of the isolates showed hemolytic activity or harbored virulence factors. Our results indicated that the five isolates have considerable potential as probiotics that can be used to prevent and/or treat bovine endometritis. We speculate that a mixture of YD6, YD9, and YD25 may yield better results, although this would require extensive experiments to verify. creator: Qingli Zhang creator: Yangyang Pan creator: Meng Wang creator: Liang Sun creator: Yao Xi creator: Mei Li creator: Qiaoying Zeng uri: https://doi.org/10.7717/peerj.13177 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhang et al. title: Using cluster and rest redistribution set structures as alternatives to resistance training prescription method based on velocity loss thresholds link: https://peerj.com/articles/13195 last-modified: 2022-03-29 description: BackgroundThe purpose of this study was to compare the effects of cluster (CS), rest redistribution (RR) and traditional (TS) set configurations on acute neuromuscular performance, and to determine the viability of using CS and RR as alternatives to training prescription based on velocity loss (VL).MethodsThirty-one resistance-trained men performed, in a randomised order, three experimental sessions consisting of the squat (SQ) and bench press (BP) exercises performed against the 10-repetition maximum load using CS (three sets of six repetitions; 30 s of intra-set rest every two repetitions; 3 min of inter-set rest), RR (9 sets of two repetitions; 45 s of inter-set rest), and TS (3 sets of 6 repetitions; 3 min of inter-set rest), set configurations.ResultsLinear mixed-effects model analysis revealed that participants had significantly lower VL (p = 0.0005) during CS and RR than TS. Generalised mixed-effects model analysis yielded significant main effects of set structure (p < 0.0001; RR > CS > TS), exercise (p < 0.0001; SQ > BP), and set number (p = 0.0006; Set 1 > Set 2 > Set 3) for maintaining repetition velocity above a 20% VL threshold.ConclusionsThese findings suggest that CS and RR are effective at reducing the overall fatigue-included decrease in velocity compared to TS and allow the majority of repetitions to be completed with less than 20% VL. Therefore, both CS and RR can be used to manage fatigue during resistance training, and as alternatives to training prescription method based on 20% VL threshold. creator: Ivan Jukic creator: Eric R. Helms creator: Michael R. McGuigan creator: Amador García-Ramos uri: https://doi.org/10.7717/peerj.13195 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Jukic et al. title: Comprehensive analysis of the correlations of S100B with hypoxia response and immune infiltration in hepatocellular carcinoma link: https://peerj.com/articles/13201 last-modified: 2022-03-29 description: S100B has been found to be dysregulated in many cancers including hepatocellular carcinoma (HCC). However, the functions of S100B and its underlying mechanisms in HCC remain poorly understood, especially in the tumor microenvironment. In this study, functions enrichment analysis indicated that S100B expression was correlated with hypoxia and immune responses. We found that hypoxia could induce S100B expression in an HIF-1α-dependent manner in HepG2 cells. Luciferase reporter and ChIP-qRCR assays demonstrated that HIF-1α regulates S100B transcription by directly binding to hypoxia-response elements (HREs) of the S100B promoter. Functionally, knockdown of S100B reduces hypoxia-induced HepG2 cell invasion and migration. Furthermore, GSVA enrichment results displayed that S100B and its co-expressed genes were positively correlated with EMT pathway in HCC. Additionally, GO/KEGG cluster analysis results indicated that co-expressed genes of S100B were involved in biological processes of immune response and multiple tumor immune-related signaling pathways in HCC. S100B expression was positively correlated with multiple immune cells tumor infiltration and associated with chemokines/chemokine receptors and immune checkpoint genes. Moreover, S100B is predominantly expressed in immune cells, especially NK (Natural Killer) cell. In addition, the hub genes of S100B co-expression and hypoxia response in HepG2 cell were also associated with immune cells infiltration in HCC. Taken together, these findings provide a new insight into the complex networks between hypoxia response and immune cells infiltration in tumor microenvironment of liver cancer. S100B maybe serve as a novel target for future HCC therapies. creator: Jia Yan creator: Ya jun Huang creator: Qing yu Huang creator: Peng Xia Liu creator: Chang Shan Wang uri: https://doi.org/10.7717/peerj.13201 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Yan et al. title: Relation between lymphocyte to monocyte ratio and survival in patients with hypertrophic cardiomyopathy: a retrospective cohort study link: https://peerj.com/articles/13212 last-modified: 2022-03-29 description: BackgroundThe lymphocyte-to-monocyte ratio (LMR) has been proposed as a novel prognostic factor in malignancies and cardiovascular diseases. Our study aimed to ascertain whether LMR is a useful biomarker in discriminating the hypertrophic cardiomyopathy (HCM) patients at higher risk of all-cause mortality.MethodsThis retrospective study consisted of 354 adult HCM patients. Cox’s proportional hazards regression models were used to analyze the association between LMR and all-cause mortality. Smooth curve fitting was conducted to explore the linear relationship between LMR and all-cause mortality.ResultsDuring the follow-up, 44 patients reached the study endpoint. The all-cause mortality rate was 7.3 per 100 person-years in the first tertile and decreased across the three tertiles of LMR. With the first tertile as reference, adjusted hazard ratios (HR) for all-cause mortality were 0.43 for the second tertile (95% CI [0.20–0.91], p = 0.027) and 0.39 for the third tertile (95% CI [0.17–0.90], p = 0.028), respectively. Smooth curve fitting exhibited a nonlinear relationship between LMR values and all-cause mortality. For LMR < 6.5, per SD increase resulted in a significantly decreased risk of all-cause mortality by 62% (HR: 0.38, 95% CI [0.21–0.68]). For LMR ≥ 6.5, the all-cause mortality risk did not progressively increase. Stratified and subgroup analyses revealed similar results to the main analyses,andE-value analysis suggested robustness to unmeasured confounding.ConclusionsThe study demonstrated that LMR was an independent predictor of all-cause mortality in HCM patients, and LMR may be useful for identifying HCM patients at high mortality risk. creator: Zhonglan Chen creator: Ziqiong Wang creator: Youping Li creator: Xiaoping Chen creator: Sen He uri: https://doi.org/10.7717/peerj.13212 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Chen et al. title: The relationship between distal trunk morphology and object grasping in the African savannah elephant (Loxodonta africana) link: https://peerj.com/articles/13108 last-modified: 2022-03-28 description: BackgroundDuring reach-to-grasp movements, the human hand is preshaped depending on the properties of the object. Preshaping may result from learning, morphology, or motor control variability and can confer a selective advantage on that individual or species. This preshaping ability is known in several mammals (i.e., primates, carnivores and rodents). However, apart from the tongue preshaping of lizards and chameleons, little is known about preshaping of other grasping appendages. In particular, the elephant trunk, a muscular hydrostat, has impressive grasping skills and thus is commonly called a hand. Data on elephant trunk grasping strategies are scarce, and nothing is known about whether elephants preshape their trunk tip according to the properties of their food.MethodsTo determine the influence of food sizes and shapes on the form of the trunk tip, we investigated the morphology of the distal part of the trunk during grasping movements. The influence of food item form on trunk tip shape was quantified in six female African savannah elephants (Loxodonta africana). Three food item types were presented to the elephants (elongated, flat, and cubic), as well as three different sizes of cubic items. A total of 107 ± 10 grips per individual were video recorded, and the related trunk tip shapes were recorded with a 2D geometric morphometric approach.ResultsHalf of the individuals adjusted the shape of the distal part of their trunk according to the object type. Of the three elephants that did not preshape their trunk tip, one was blind and another was subadult.Discussion and perspectivesWe found that elephants preshaped their trunk tip, similar to the preshaping of other species’ hands or paws during reach-to-grasp movements. This preshaping may be influenced by visual feedback and individual learning. To confirm these results, this study could be replicated with a larger sample of elephants. creator: Julie Soppelsa creator: Emmanuelle Pouydebat creator: Maëlle Lefeuvre creator: Baptiste Mulot creator: Céline Houssin creator: Raphaël Cornette uri: https://doi.org/10.7717/peerj.13108 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Soppelsa et al. title: The association between sedentary behavior and low back pain in adults: a systematic review and meta-analysis of longitudinal studies link: https://peerj.com/articles/13127 last-modified: 2022-03-28 description: BackgroundLow back pain (LBP) is a common musculoskeletal problem globally. While spending a longer time in sedentary behaviors is linked to several health problems; the quantitative association between different amounts of sedentary time and LBP is still unknown. This study aims to systematically review studies that examined the association between sedentary behavior and LBP development and LBP-related outcomes.MethodsThis systematic review and meta-analysis retrieved journal articles published from inception to March 2020 and were obtained by searching bibliographical databases. We included longitudinal study designs, including adult (aged ≥18) individuals with nonspecific LBP, and reporting estimates of the association between sedentary behavior and LBP development and LBP-related outcomes (i.e., pain intensity and disability).ResultsSixteen longitudinal studies with 100,002 participants were included in this review (eight studies included in quantitative syntheses with 83,111 participants). The results of meta-analyses showed that a sedentary time of 3–<6 (Odds ratio (OR) 0.95, 95% CI [0.85–1.07]), 6–8 (OR 0.95, 95% CI [0.88–1.02]), and >8 (OR 0.92, 95% CI [0.85–1.00]) hours per day (h/d) was not associated with LBP development. A sedentary time of ≥3 h/d was associated with poor LBP-related disability (OR 1.24, 95% CI [1.02–1.51]), but not with pain intensity.ConclusionA meta-analyses of longitudinal studies indicated that sedentary behavior of different durations was not associated with LBP development. However, the results showed that sedentary behavior ≥3 h/d was associated with worse LBP-related disability. These conclusions are tentative as the evidence was derived from mostly fair-quality studies using subjective measures of sedentary behavior.Systematic review registrationPROSPERO (registration number CRD42018107078). creator: Hosam Alzahrani creator: Mansour Abdullah Alshehri creator: Msaad Alzhrani creator: Yasir S. Alshehri creator: Wesam Saleh A. Al Attar uri: https://doi.org/10.7717/peerj.13127 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Alzahrani et al. title: Polymorphism in a Neotropical toad species: ontogenetic, populational and geographic approaches to chromatic variation in Proceratophrys cristiceps (Müller, 1883) (Amphibia, Anura, Odontophrynidae) link: https://peerj.com/articles/12879 last-modified: 2022-03-25 description: Quantifying variability is important for understanding how evolution operates in polymorphic species such as those of the genus Proceratophrys Miranda-Ribeiro, 1920, which is widely distributed in South America. P. cristiceps distribution is limited to the Caatinga biome in Brazil. We examined its chromatic variation from a populational perspective, looking at different phenetic polymorphism levels and probable chromotypic association by applying statistical and GIS tools that could facilitate future taxonomic research regarding this and other species. We characterized P. cristiceps colour patterns and re-evaluated its geographic variation, highlighting potential consequences for the taxonomy of the genus. Our results revealed six principle chromotypes whose frequencies varied among sex and ontogenetic classes. Phenotypic expression appeared to respect defined proportions and evidenced selective value for the species. We conclude that individual variation, together with typological traditionalism may overestimate the polymorphic magnitude at the population level and cause taxonomic inflation. Our data support the usefulness of P. cristiceps as a model for microevolutionary studies. creator: Kleber Silva Vieira creator: Erivanna Karlene Santos Oliveira creator: Washington Luiz Silva Vieira creator: Rômulo Romeu Nóbrega Alves uri: https://doi.org/10.7717/peerj.12879 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Vieira et al. title: Research progress of aldehyde oxidases in plants link: https://peerj.com/articles/13119 last-modified: 2022-03-25 description: Plant aldehyde oxidases (AOs) are multi-functional enzymes, and they could oxidize abscisic aldehyde into ABA (abscisic acid) or indole acetaldehyde into IAA (indoleacetic acid) as the last step, respectively. AOs can be divided into four groups based on their biochemical and physiological functions. In this review, we summarized the recent studies about AOs in plants including the motif information, biochemical, and physiological functions. Besides their role in phytohormones biosynthesis and stress response, AOs could also involve in reactive oxygen species homeostasis, aldehyde detoxification and stress tolerance. creator: Jun Wu creator: Blair Moses Kamanga creator: Wenying Zhang creator: Yanhao Xu creator: Le Xu uri: https://doi.org/10.7717/peerj.13119 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wu et al. title: Are Toxoplasma-infected subjects more attractive, symmetrical, or healthier than non-infected ones? Evidence from subjective and objective measurements link: https://peerj.com/articles/13122 last-modified: 2022-03-25 description: BackgroundParasites are among the main factors that negatively impact the health and reproductive success of organisms. However, if parasites diminish a host’s health and attractiveness to such an extent that finding a mate becomes almost impossible, the parasite would decrease its odds of reproducing and passing to the next generation. There is evidence that Toxoplasma gondii (T. gondii) manipulates phenotypic characteristics of its intermediate hosts to increase its spread. However, whether T. gondii manipulates phenotypic characteristics in humans remains poorly studied. Therefore, the present research had two main aims: (1) To compare traits associated with health and parasite resistance in Toxoplasma-infected and non-infected subjects. (2) To investigate whether other people perceive differences in attractiveness and health between Toxoplasma-infected and non-infected subjects of both sexes.MethodsFor the first aim, Toxoplasma-infected (n = 35) and non-infected subjects (n = 178) were compared for self-perceived attractiveness, number of sexual partners, number of minor ailments, body mass index, mate value, handgrip strength, facial fluctuating asymmetry, and facial width-to-height ratio. For the second aim, an independent group of 205 raters (59 men and 146 women) evaluated the attractiveness and perceived health of facial pictures of Toxoplasma-infected and non-infected subjects.ResultsFirst, we found that infected men had lower facial fluctuating asymmetry whereas infected women had lower body mass, lower body mass index, a tendency for lower facial fluctuating asymmetry, higher self-perceived attractiveness, and a higher number of sexual partners than non-infected ones. Then, we found that infected men and women were rated as more attractive and healthier than non-infected ones.ConclusionsOur results suggest that some sexually transmitted parasites, such as T. gondii, may produce changes in the appearance and behavior of the human host, either as a by-product of the infection or as the result of the manipulation of the parasite to increase its spread to new hosts. Taken together, these results lay the foundation for future research on the manipulation of the human host by sexually transmitted pathogens and parasites. creator: Javier I. Borráz-León creator: Markus J. Rantala creator: Indrikis A. Krams creator: Ana Lilia Cerda-Molina creator: Jorge Contreras-Garduño uri: https://doi.org/10.7717/peerj.13122 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Borráz-León et al. title: Knowing the gap: medication use, adherence and blood pressure control among patients with hypertension in Indonesian primary care settings link: https://peerj.com/articles/13171 last-modified: 2022-03-25 description: BackgroundHypertension is a major risk factor for global disease burden, however, little is known regarding the profiles of patients with hypertension in Indonesian primary care settings.ObjectiveThis study aimed to profile medication use, adherence to medications and lifestyle modifications as well as blood pressure control among patients with hypertension in Indonesian primary health centres (PHCs).MethodsA cross-sectional study design used a structured data collection tool (questionnaire and checklist). Patients aged ≥18 years with a diagnosis of hypertension, and prescribed an antihypertensive medication, and attending follow-up visits in the five PHCs in Surabaya, Indonesia, during a two-week study period (May–October 2019) were included. Descriptive analyses summarised the data, while binary logistic regression provided any independent associations between adherence profiles and blood pressure control.ResultsOf 457 eligible patients, 276 patients consented: PHC A (n = 50/91), PHC B (n = 65/116), PHC C (n = 47/61), PHC D (n = 60/88), PHC E (n = 54/101), giving an overall response rate of 60.4%. Patients were mainly treated with a single antihypertensive medication, i.e., amlodipine (89.1%), and many had not achieved blood pressure targets (68.1%). A majority reported notable levels of non-adherence to medication (low/intermediate, 65.2%) and poor healthy lifestyle behaviours, particularly physical activity (inadequate, 87.7%) and discretionary salt use (regularly, 50.4%). Significant associations were found between low medication adherence, discretionary salt use and smoking, with blood pressure control.ConclusionsThe study findings provide the evidence needed to improve the current level of sub-optimal blood pressure management among patients with hypertension in these Indonesian primary care settings. Particular emphasis should be placed on antihypertensive medication adherence and healthy lifestyle behaviours through locally tailored hypertension-related interventions. creator: Adji Prayitno Setiadi creator: Anita Febriandini creator: Eltia Trinanda creator: Wiweka Aryaguna creator: Irene Mutho’atin Chusna creator: Yulia Nurlaili creator: Bruce Sunderland creator: Yosi Irawati Wibowo uri: https://doi.org/10.7717/peerj.13171 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Setiadi et al. title: Disturbance has lasting effects on functional traits and diversity of grassland plant communities link: https://peerj.com/articles/13179 last-modified: 2022-03-25 description: BackgroundLocalized disturbances within grasslands alter biological properties and may shift species composition. For example, rare species in established communities may become dominant in successional communities if they exhibit traits well-suited to disturbance conditions. Although the idea that plant species exhibit different trait ‘strategies’ is well established, it is unclear how ecological selection for specific traits may change as a function of disturbance. Further, there is little data available testing whether disturbances select for single trait-characters within communities (homogenization), or allow multiple trait-types to persist (diversification). We investigated how (a) traits and (b) functional diversity of post-disturbance gap communities compared to those in adjacent undisturbed grasslands, and (c) if altered functional diversity resulted in the homogenization or diversification of functional traits.MethodsHere we emulate the impacts of an extreme disturbance in a native grassland site. We measured plant community composition of twelve paired 50 × 50 cm plots (24 total) in Alberta, Canada. Each pair consisted of one undisturbed plot and one which had all plants terminated 2 years prior. We used species abundances and a local trait database to calculate community weighted means for maximum height, specific leaf area, specific root length, leaf nitrogen percent, and root nitrogen percent. To test the impacts of disturbance on community functional traits, we calculated functional diversity measures and compared them between disturbed and undisturbed communities.ResultsWithin 2 years, species richness and evenness in disturbed communities had recovered and was equivalent to undisturbed communities. However, disturbed and undisturbed communities had distinct community compositions, resulting in lower functional divergence in disturbed plots. Further, disturbance was linked to increases in community-weighted mean trait values for resource-acquisitive traits, such as specific leaf area, and leaf and root nitrogen.DiscussionDisturbance had lasting effects on the functional traits and diversity of communities, despite traditional biodiversity measures such as richness and evenness recovering within 2 years. The trait space of gap communities shifted compared to undisturbed communities such that gap communities were dominated by traits enhancing resource uptake and growth rates. Overall, these results show that short-term disturbance fundamentally changes the functional character of early-successional communities, even if they superficially appear recovered. creator: Ellen A. Smith creator: Emily M. Holden creator: Charlotte Brown creator: James F. Cahill Jr uri: https://doi.org/10.7717/peerj.13179 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Smith et al. title: A longitudinal study of risk factors associated with white spot disease occurrence in marine shrimp farming in Rayong, Thailand link: https://peerj.com/articles/13182 last-modified: 2022-03-25 description: BackgroundA longitudinal study was conducted to analyze farm characteristics, farm practices, and biosecurity measures that influenced the occurrence of white spot disease (WSD) in shrimp farming in Rayong, Thailand.MethodsData were collected using a structured interview schedule administered between October 2017 and September 2019. A generalized estimating equations (GEE) model was used to identify risk factors. From the 270 responses, 86 possible risk factors were analyzed using univariate and multivariate analysis.ResultsWe found that 17 possible risk factors were statistically significant with an alpha level of 1% and associated with WSD status. In the final model, multivariate analysis found that two independent variables were statistically significant. First, the absence of inclement weather during ponding was a statistically significant factor associated with WSD occurrence and it prevented WSD occurrence as the odds ratio (OR) was <1 (OR = 0.196, P = 1.3 × 10−5). Second, the separation of ponds into three specific types (cultured, water treatment, and pond for water reservoir) was significantly associated with WSD occurrence. Likewise, the presence of this ponding system was a protective factor against WSD (OR = 0.0828, P = 0.001).ConclusionsThe results of this study offer a reference for farmers and relevant authorities when addressing WSD occurrence in shrimp farming. In addition, our results can help relevant authorities in controlling WSD in other endemic areas. creator: Sompit Yaemkasem creator: Visanu Boonyawiwat creator: Manakorn Sukmak creator: Sukanya Thongratsakul creator: Chaithep Poolkhet uri: https://doi.org/10.7717/peerj.13182 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Yaemkasem et al. title: Acute kidney injury-attributable mortality in critically ill patients with sepsis link: https://peerj.com/articles/13184 last-modified: 2022-03-25 description: BackgroundTo assess whether acute kidney injury (AKI) is independently associated with hospital mortality in ICU patients with sepsis, and estimate the excess AKI-related mortality attributable to AKI.MethodsWe analyzed adult patients from two distinct retrospective critically ill cohorts: (1) Medical Information Mart for Intensive Care IV (MIMIC IV; n = 15,610) cohort and (2) Wenzhou (n = 1,341) cohort. AKI was defined by Kidney Disease: Improving Global Outcomes (KDIGO) criteria. We applied multivariate logistic and linear regression models to assess the hospital and ICU mortality, hospital length-of-stay (LOS), and ICU LOS. The excess attributable mortality for AKI in ICU patients with sepsis was further evaluated.ResultsAKI occurred in 5,225 subjects in the MIMIC IV cohort (33.5%) and 494 in the Wenzhou cohort (36.8%). Each stage of AKI was an independent risk factor for hospital mortality in multivariate logistic regression after adjusting for baseline illness severity. The excess attributable mortality for AKI was 58.6% (95% CI [46.8%–70.3%]) in MIMIC IV and 44.6% (95% CI [12.7%–76.4%]) in Wenzhou. Additionally, AKI was independently associated with increased ICU mortality, hospital LOS, and ICU LOS.ConclusionAcute kidney injury is an independent risk factor for hospital and ICU mortality, as well as hospital and ICU LOS in critically ill patients with sepsis. Thus, AKI is associated with excess attributable mortality. creator: Zhiyi Wang creator: Jie Weng creator: Jinwen Yang creator: Xiaoming Zhou creator: Zhe Xu creator: Ruonan Hou creator: Zhiliang Zhou creator: Liang Wang creator: Chan Chen creator: Shengwei Jin uri: https://doi.org/10.7717/peerj.13184 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wang et al. title: Crop damage by vertebrates in Latin America: current knowledge and potential future management directions link: https://peerj.com/articles/13185 last-modified: 2022-03-25 description: BackgroundCrop farming contributes to one of the most extensive land use activities in the world, and cropland areas continue to rise. Many vertebrate species feed on crops, which has caused an increase in human-wildlife conflicts in croplands. Crop-feeding damages the economy of local communities and causes retaliation against the responsible vertebrates in several forms, including lethal practices such as hunting and poisoning. Lethal control may cause the local extirpation of some species, affecting ecological processes and patterns. Therefore, it is necessary to find non-lethal alternatives that can protect both local economies and wildlife. Research has been conducted in Africa and Asia, focusing on elephants and primates, and the effectiveness of some non-lethal alternatives, such as chili-based repellents and beehives, is being investigated. However, there has been very little research on this topic in Central and South America. The goal of this review is to assess the current knowledge on crop damage by vertebrates in Central and South America and indicate future research directions.Survey methodologyWe reviewed the available scientific literature reporting crop damage by vertebrates in Central and South America, and the Caribbean, published between 1980 and 2020, through systematic searches on Web of Science, Scopus, and Google Scholar. We analyzed the temporal and geographical distributions of the studies, the crops and vertebrate species these studies considered, the crop protection techniques used, and their effectiveness.ResultsWe retrieved only 113 studies on crop damage by vertebrates in Latin America, but there was an increasing trend in the number of studies published over time. Most of the studies were conducted in Brazil, Argentina, Mexico, and Costa Rica. Four orders of mammals (Rodentia, Carnivora, Artiodactyla, and Primates) and four orders of birds (Passeriformes, Columbiformes, Psittaciformes, and Anseriformes) were the most common groups of crop-feeding vertebrates. The most prominent crop was corn, which was featured in 49% of the studies. Other notable crops include rice, sorghum, and sugarcane. The most reported method for protecting crops was lethal control through hunting or poisoning. Non-lethal techniques were found to be less prevalent. Less than half of the studies that mentioned the use of protection techniques indicated their effectiveness, and only 10 studies evaluated it by performing scientific experiments and reporting their results.ConclusionsCentral and South America is still underrepresented in research on vertebrate crop-feeding. There is a need for experimentation-based robust research to find crop protection techniques that minimize harm to vertebrates while effectively reducing damage to crops. While this is being studied, habitat loss and fragmentation need to be halted to prevent the native vertebrates from turning to crops for food. creator: Adrián Alejandro Cuesta Hermira creator: Fernanda Michalski uri: https://doi.org/10.7717/peerj.13185 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Alejandro Cuesta Hermira and Michalski title: A worldwide comparison of long-distance running training in 2019 and 2020: associated effects of the COVID-19 pandemic link: https://peerj.com/articles/13192 last-modified: 2022-03-25 description: ObjectiveThe goal of the present study was to investigate possible effects of the COVID-19 pandemic on long-distance running training.MethodsThis is a retrospective study with a within-subject design. We analyzed 10,703,690 records of running training during 2019 and 2020, from 36,412 athletes from around the world. The records were obtained through web scraping of a large social network for athletes on the internet. A potential long-distance runner was defined as a user of the social network who had a record of running at least one of the six World Marathon Majors by 2019.ResultsIn 2020, compared with 2019, in total there was a 3.6% decrease in the number of athletes running, a 7.5% decrease in the distance and 6.7% in the duration of running training. There were large variations in these variables throughout 2020, reaching 16% fewer athletes running weekly and 35% lower running distance (Cohen’s d = 0.34, p < 0.001) and 33% lower running duration (Cohen’s d = 0.30, p < 0.001) in September 2020. The beginning of the decrease in running training in the first quarter of 2020 coincides with the beginning of the adoption of measures to restrict the COVID-19 pandemic; but as of the second quarter of 2020, running training appears to have undergone variations unrelated to the preventive measures. Among the ten most represented countries in the dataset, running training in Brazil appears to have been the most affected by the COVID-19 pandemic and restriction measures.ConclusionThe wide variations in long-distance running training throughout 2020 are likely related to the COVID-19 pandemic. As for the total volume, the observed decreases of up to 7.5% in the outcome variables related to running training in 2020 could also be attributed to the COVID-19 pandemic, but other factors such as injury, illness or lack of interest, may also have contributed to these decreases. creator: Leonardo A. Afonseca creator: Renato N. Watanabe creator: Marcos Duarte uri: https://doi.org/10.7717/peerj.13192 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Afonseca et al. title: Benchmarking metagenomics classifiers on ancient viral DNA: a simulation study link: https://peerj.com/articles/12784 last-modified: 2022-03-24 description: Owing to technological advances in ancient DNA, it is now possible to sequence viruses from the past to track down their origin and evolution. However, ancient DNA data is considerably more degraded and contaminated than modern data making the identification of ancient viral genomes particularly challenging. Several methods to characterise the modern microbiome (and, within this, the virome) have been developed; in particular, tools that assign sequenced reads to specific taxa in order to characterise the organisms present in a sample of interest. While these existing tools are routinely used in modern data, their performance when applied to ancient microbiome data to screen for ancient viruses remains unknown. In this work, we conducted an extensive simulation study using public viral sequences to establish which tool is the most suitable to screen ancient samples for human DNA viruses. We compared the performance of four widely used classifiers, namely Centrifuge, Kraken2, DIAMOND and MetaPhlAn2, in correctly assigning sequencing reads to the corresponding viruses. To do so, we simulated reads by adding noise typical of ancient DNA to a set of publicly available human DNA viral sequences and to the human genome. We fragmented the DNA into different lengths, added sequencing error and C to T and G to A deamination substitutions at the read termini. Then we measured the resulting sensitivity and precision for all classifiers. Across most simulations, more than 228 out of the 233 simulated viruses were recovered by Centrifuge, Kraken2 and DIAMOND, in contrast to MetaPhlAn2 which recovered only around one third. Overall, Centrifuge and Kraken2 had the best performance with the highest values of sensitivity and precision. We found that deamination damage had little impact on the performance of the classifiers, less than the sequencing error and the length of the reads. Since Centrifuge can handle short reads (in contrast to DIAMOND and Kraken2 with default settings) and since it achieve the highest sensitivity and precision at the species level across all the simulations performed, it is our recommended tool. Regardless of the tool used, our simulations indicate that, for ancient human studies, users should use strict filters to remove all reads of potential human origin. Finally, we recommend that users verify which species are present in the database used, as it might happen that default databases lack sequences for viruses of interest. creator: Yami Ommar Arizmendi Cárdenas creator: Samuel Neuenschwander creator: Anna-Sapfo Malaspinas uri: https://doi.org/10.7717/peerj.12784 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Arizmendi Cárdenas et al. title: First fossil-leaf floras from Brunei Darussalam show dipterocarp dominance in Borneo by the Pliocene link: https://peerj.com/articles/12949 last-modified: 2022-03-24 description: The Malay Archipelago is one of the most biodiverse regions on Earth, but it suffers high extinction risks due to severe anthropogenic pressures. Paleobotanical knowledge provides baselines for the conservation of living analogs and improved understanding of vegetation, biogeography, and paleoenvironments through time. The Malesian bioregion is well studied palynologically, but there have been very few investigations of Cenozoic paleobotany (plant macrofossils) in a century or more. We report the first paleobotanical survey of Brunei Darussalam, a sultanate on the north coast of Borneo that still preserves the majority of its extraordinarily diverse, old-growth tropical rainforests. We discovered abundant compression floras dominated by angiosperm leaves at two sites of probable Pliocene age: Berakas Beach, in the Liang Formation, and Kampong Lugu, in an undescribed stratigraphic unit. Both sites also yielded rich palynofloral assemblages from the macrofossil-bearing beds, indicating lowland fern-dominated swamp (Berakas Beach) and mangrove swamp (Kampong Lugu) depositional environments. Fern spores from at least nine families dominate both palynological assemblages, along with abundant fungal and freshwater algal remains, rare marine microplankton, at least four mangrove genera, and a diverse rainforest tree and liana contribution (at least 19 families) with scarce pollen of Dipterocarpaceae, today’s dominant regional life form. Compressed leaves and rare reproductive material represent influx to the depocenters from the adjacent coastal rainforests. Although only about 40% of specimens preserve informative details, we can distinguish 23 leaf and two reproductive morphotypes among the two sites. Dipterocarps are by far the most abundant group in both compression assemblages, providing rare, localized evidence for dipterocarp-dominated lowland rainforests in the Malay Archipelago before the Pleistocene. The dipterocarp fossils include winged Shorea fruits, at least two species of plicate Dipterocarpus leaves, and very common Dryobalanops leaves. We attribute additional leaf taxa to Rhamnaceae (Ziziphus), Melastomataceae, and Araceae (Rhaphidophora), all rare or new fossil records for the region. The dipterocarp leaf dominance contrasts sharply with the family’s <1% representation in the palynofloras from the same strata. This result directly demonstrates that dipterocarp pollen is prone to strong taphonomic filtering and underscores the importance of macrofossils for quantifying the timing of the dipterocarps’ rise to dominance in the region. Our work shows that complex coastal rainforests dominated by dipterocarps, adjacent to swamps and mangroves and otherwise similar to modern ecosystems, have existed in Borneo for at least 4–5 million years. Our findings add historical impetus for the conservation of these gravely imperiled and extremely biodiverse ecosystems. creator: Peter Wilf creator: Xiaoyu Zou creator: Michael P. Donovan creator: László Kocsis creator: Antonino Briguglio creator: David Shaw creator: JW Ferry Slik creator: Joseph J. Lambiase uri: https://doi.org/10.7717/peerj.12949 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wilf et al. title: Genome-wide characterization and expression of the TLP gene family associated with Colletotrichum gloeosporioides inoculation in Fragaria × ananassa link: https://peerj.com/articles/12979 last-modified: 2022-03-24 description: BackgroundColletotrichum gloeosporioides, a soil-borne fungal pathogen, causes significant yield losses in many plants, including cultivated strawberry (Fragaria × ananassa, 2n = 8x = 56). Thaumatin-like proteins (TLPs) are a large and complex family of proteins that play a vital role in plant host defense and other physiological processes.MethodsTo enhance our understanding of the antifungal activity of F. × ananassa TLPs (FaTLP), we investigated the genome-wide identification of FaTLP gene families and their expression patterns in F. × ananassa plants upon pathogen infection. Moreover, we used RNA sequencing (RNA-seq) to detect the differences in the expression patterns of TLP genes between different resistant strawberry cultivars in response to C. gloeosporioides infection.ResultsIn total, 76 TLP genes were identified from the octoploid cultivated strawberry genome with a mean length of 1,439 bp. They were distributed on 24 F. × ananassa chromosomes. The FaTLP family was then divided into ten groups (Group I–X) according to the comparative phylogenetic results. Group VIII contained the highest number of TLP family genes. qRT-PCR analysis results indicated that FaTLP40, FaTLP41, FaTLP43, FaTLP68, and FaTLP75 were upregulated following C. gloeosporioides infection in the resistant octoploid strawberry.ConclusionsThe data showed some differences in TLP gene expression patterns across different resistant strawberry cultivars, as well as faster TLP defense responses to pathogenic fungi in resistant cultivars. This study will aid in the characterization of TLP gene family members found in octoploid strawberries and their potential biological functions in plants’ defenses against pathogenic fungi. creator: Yuchao Zhang creator: Lixiang Miao creator: Xiaofang Yang creator: Guihua Jiang uri: https://doi.org/10.7717/peerj.12979 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhang et al. title: A prognostic risk model based on DNA methylation levels of genes and lncRNAs in lung squamous cell carcinoma link: https://peerj.com/articles/13057 last-modified: 2022-03-24 description: BackgroundRecurrence is a risk factor for the prognosis of lung squamous carcinoma (LUSC). DNA methylation levels of RNAs are also associated with LUSC prognosis. This study aimed to construct a prognostic model with high performance in predicting LUSC prognosis using the methylation levels of lncRNAs and genes.MethodsThe differentially expressed RNAs (DERs) and differentially methylated RNAs (DMRs) between the recurrent and non-recurrent LUSC tissues in The Cancer Genome Atlas (TCGA; training dataset) were identified. Weighted correlation network analysis was performed to identify co-methylation networks. Differentially methylated genes and lncRNAs with opposite expression-methylation levels were used for the screening of prognosis-associated RNAs. The prognostic model was constructed and its performance was validated in the GSE39279 dataset.ResultsA total of 664 DERs and 981 DMRs (including 972 genes) in recurrent LUSC tissues were identified. Three co-methylation modules, including 226 differentially methylated genes, were significantly associated with LUSC. Among prognosis-associated RNAs, 18 DERs/DMRs with opposite methylation-expression levels were included in the methylation prognostic risk model. LUSC patients with high risk scores had a poor prognosis compared with patients who had low risk scores (TCGA: HR = 3.856, 95% CI [2.297–6.471]; GSE39279: HR = 3.040, 95% CI [1.435–6.437]). This model had a high accuracy in predicting the prognosis (AUC = 0.903 and 0.800, respectively), equivalent to the nomogram model inclusive of clinical variables.ConclusionsReferring to the methylation levels of the 16-RNAs might help to predict the survival outcomes in LUSC. creator: Weiqing Wang creator: Ming Xiang creator: Hui Liu creator: Xiao Chu creator: Zhaoyun Sun creator: Liang Feng uri: https://doi.org/10.7717/peerj.13057 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wang et al. title: Development of a Japanese version of the Psychological Ownership Scale link: https://peerj.com/articles/13063 last-modified: 2022-03-24 description: The present study addresses the need for a valid instrument for measuring dimensions of psychological ownership, including that of owned and non-owned objects, for use in the language and culture of Japan. Although the theory of psychological ownership has expanded self-extension theory, the most widely used scale of psychological ownership does not measure the extent to which one feels that it (the owned object) is a part of them. Thus, the present study aimed to develop a Japanese version of the Psychological Ownership Scale (POS-J) and examine its reliability and validity. Study 1 measured the POS-J of an owned object, finding the POS-J to have a two-factor structure (possession-self link and feeling of ownership) and its internal consistency and reliability to be adequate. Moreover, POS-J scores were positively correlated with perceived control and self-extension tendency, but not monetary value, indicating that conceptual validity was generally supported. To confirm whether the POS-J could be used for a non-owned object, Study 2 rephrased the expressions of item descriptions and examined the effect of imagining touching a non-owned object on the POS-J scores, showing that doing so increased the POS-J scores for the object. Our findings suggest that the POS-J is a reliable and valid measure of the psychological ownership of owned and non-owned objects for use in Japan. creator: Sayo Iseki creator: Kyoshiro Sasaki creator: Shinji Kitagami uri: https://doi.org/10.7717/peerj.13063 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Iseki et al. title: Increased cortisol levels caused by acute resistance physical exercise impair memory and learning ability link: https://peerj.com/articles/13000 last-modified: 2022-03-23 description: Acute physical exercise works as an activator of the responses of the human organism to stress. This is based on the activation of the hypothalamic–pituitary–adrenal (HPA) axis, affecting physical, physiological and psychological levels. This study aimed to analyse the effects of a single bout of high-intensity resistance exercise on cognitive-behavioural responses: visuo-spatial path learning and memory, as well as physiological responses (salivary cortisol levels). Nineteen healthy male military-trained powerlifting subjects were tested in a within-subject design on two experimental days with an interval of 48 h. The stress and cognitive variables were measured by cortisol levels and Ruff–Light trail-learning test (RULIT) test scores, respectively. The results showed the immediate influence of acute exercise on cortisol, with significantly higher cortisol levels found in subjects after completion of the acute resistance exercise. In addition, this study found a significant deterioration of memory and learning ability after a dose of intense resistance exercise. In conclusion, the study highlights the relative effects of resistance exercise on cortisol and cognitive performance depending on the intensity and type of the exercise, the moment of measurement and the cerebral areas implicated. creator: José-Luis Bermejo creator: Raúl Valldecabres creator: Israel Villarrasa-Sapiña creator: Gonzalo Monfort-Torres creator: Adrià Marco-Ahulló creator: Bruno Ribeiro Do Couto uri: https://doi.org/10.7717/peerj.13000 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Bermejo et al. title: Antioxidant defense system in the prefrontal cortex of chronically stressed rats treated with lithium link: https://peerj.com/articles/13020 last-modified: 2022-03-23 description: BackgroundThis study aimed to investigate the effects of lithium treatment on gene expression and activity of the prefrontal antioxidant enzymes: copper, zinc superoxide dismutase (SOD1), manganes superoxide dismutase (SOD2), catalase (CAT), and glutathione peroxidase (GPx) in animals exposed to chronic restraint stress (CRS).MethodsThe investigated parameters were quantified using real-time RT-PCR, Western blot analyses, and assays of enzyme activities.ResultsWe found that lithium treatment decreased gene expression of SOD2, as well as the activities of SOD1 and SOD2 in chronically stressed rats to the levels found in unstressed animals. However, lithium treatment in animals exposed to CRS increased prefrontal GPx activity to the levels found in unstressed animals.ConclusionsThese findings confirm that treatment with lithium induced the modulation of prefrontal antioxidant status in chronically stressed rats. Our results may be very important in biomedical research for understanding the role of lithium in maintaining the stability of prefrontal antioxidant defense system in neuropsychiatric disorders caused by chronic stress. creator: Ljubica Gavrilović creator: Nataša Popović creator: Vesna Stojiljković creator: Snežana Pejić creator: Ana Todorović creator: Predrag Vujović creator: Snežana B. Pajović uri: https://doi.org/10.7717/peerj.13020 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Gavrilović et al. title: Exploring the genome of Lactobacillaceae spp. Sy-1 isolated from Heterotrigona itama honey link: https://peerj.com/articles/13053 last-modified: 2022-03-23 description: BackgroundHoney produced by Heterotrigona itama is highly preferred among consumers due to its high-value as a functional food and beneficial lactic acid bacteria (LAB) reservoir. Fructophilic lactic acid bacteria (FLAB) are a group of LAB with unique growth characteristics and are regarded as promising producers of bioactive compounds. Hence, it is not surprising that LAB, especially FLAB, may be involved with the excellent bioactivity of H. itama honey. With the trending consumer preference for H. itama honey coupled with increasing awareness for healthy food, the genomic background of FLAB isolated from this honey must, therefore, be clearly understood. In this study, one FLAB strain designated as Sy-1 was isolated from freshly collected H. itama honey. Its FLAB behavior and genomic features were investigated to uncover functional genes that could add value to functional food.MethodsThe fructophilic characteristics of strain Sy-1 were determined, and the genome was sequenced using Illumina iSeq100 and Oxford Nanopore. The average nucleotide identity and phylogenetic analyses based on 16S rRNA, 92 core genes, and whole-genome sequence were performed to unravel the phylogenetic position of strain Sy-1. NCBI Prokaryotic Genome Annotation Pipeline annotated the genome, while the EggNOG-mapper, BLASTKoala, and GHOSTKoala were used to add functional genes and pathways information.ResultsStrain Sy-1 prefers D-fructose over D-glucose and actively metabolizes D-glucose in the presence of electron acceptors. Genomic annotation of strain Sy-1 revealed few genes involved in carbohydrate transport and metabolism, and partial deletion of adhE gene, in line with the characteristic of FLAB. The 16S rRNA gene sequence of strain Sy-1 showed the highest similarity to unknown LAB species isolated from the gut of honeybees. The phylogenetic analyses discovered that strain Sy-1 belonged to the Lactobacillaceae family and formed a separate branch closer to type strain from the genera of Acetilactobacillus and Apilactobacillus. The ANI analysis showed the similarity of the closest relative, Apilactobacillus micheneri Hlig3T. The assembled genome of Sy-1 contains 3 contigs with 2.03 Mbp and a 41% GC content. A total of 1,785 genes were identified, including 1,685 protein-coding genes, 68 tRNA, and 15 rRNA. Interestingly, strain Sy-1 encoded complete genes for the biosynthesis of folate and riboflavin. High-performance liquid chromatography analysis further confirmed the high production of folic acid (1.346 mg/L) by Sy-1.DiscussionBased on phylogenetic and biochemical characteristics, strain Sy-1 should be classified as a novel genus in the family of Lactobacillaceae and a new member of FLAB. The genome information coupled with experimental studies supported the ability of strain Sy-1 to produce high folic acid. Our collective findings support the suitable application of FLAB strain Sy-1 in the functional food and pharmaceutical industries. creator: Syariffah Nuratiqah Syed Yaacob creator: Fahrul Huyop creator: Mailin Misson creator: Roswanira Abdul Wahab creator: Nurul Huda uri: https://doi.org/10.7717/peerj.13053 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Syed Yaacob et al. title: Metagenomic investigation of the equine faecal microbiome reveals extensive taxonomic diversity link: https://peerj.com/articles/13084 last-modified: 2022-03-23 description: BackgroundThe horse plays crucial roles across the globe, including in horseracing, as a working and companion animal and as a food animal. The horse hindgut microbiome makes a key contribution in turning a high fibre diet into body mass and horsepower. However, despite its importance, the horse hindgut microbiome remains largely undefined. Here, we applied culture-independent shotgun metagenomics to thoroughbred equine faecal samples to deliver novel insights into this complex microbial community.ResultsWe performed metagenomic sequencing on five equine faecal samples to construct 123 high- or medium-quality metagenome-assembled genomes from Bacteria and Archaea. In addition, we recovered nearly 200 bacteriophage genomes. We document surprising taxonomic diversity, encompassing dozens of novel or unnamed bacterial genera and species, to which we have assigned new Candidatus names. Many of these genera are conserved across a range of mammalian gut microbiomes.ConclusionsOur metagenomic analyses provide new insights into the bacterial, archaeal and bacteriophage components of the horse gut microbiome. The resulting datasets provide a key resource for future high-resolution taxonomic and functional studies on the equine gut microbiome. creator: Rachel Gilroy creator: Joy Leng creator: Anuradha Ravi creator: Evelien M. Adriaenssens creator: Aharon Oren creator: Dave Baker creator: Roberto M. La Ragione creator: Christopher Proudman creator: Mark J. Pallen uri: https://doi.org/10.7717/peerj.13084 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Gilroy et al. title: Reference values for bone density and bone mineral content from 5 to 80 years old in a province of Chile link: https://peerj.com/articles/13092 last-modified: 2022-03-23 description: BackgroundThe assessment of bone health throughout the life cycle is essential to determine fracture risk. The objectives of the work were (a) compare bone mineral density and content with international references from the United States, (b) determine maximum bone mass, (c) propose references for bone health measurements from ages 5 to 80 years old.MethodsResearch was carried out on 5,416 subjects. Weight and height were measured. Body Mass Index (BMI) was calculated. The total body was scanned using dual energy X-ray absorptiometry (DXA). Information was extracted from the bone health measures (bone mineral density (BMD) and bone mineral content (BMC)) for both sexes, according to pediatric and adult software.Results and DiscussionDifferences were identified between the mean values of Chilean and American men for BMD (~0.03 to 0.11 g/cm2) and BMC (~0.15 to 0.46 g). Chilean females showed average values for BMD similar to the US references (~−0.01 to 0.02 g/cm2). At the same time, they were relatively higher for BMC (~0.07 to 0.33 g). The cubic polynomial regression model reflected a relationship between BMD and BMC with chronological age in both sexes. For males, R2 was higher (R2 = 0.72 and 0.75) than for females (R2 = 0.59 and 0.66). The estimate of maximum bone mass (MBM) for males emerged at 30 years old (1.45 ± 0.18 g/cm2 of BMD and 3.57 ± 0.60 g of BMC) and for females at age 28 (1.22 ± 0.13 g/cm2 of BMD and 2.57 ± 0.44 g of BMC). The LMS technique was used to generate smoothed percentiles for BMD and BMC by age and sex. Results showed that maximum bone mass occurred in females at age 28 and in males at 30. Reference values obtained from this research may be used to evaluate bone health, diagnose bone fragility and osteoporosis in individuals and regional population groups. creator: Marco Cossio-Bolanos creator: Rubén Vidal-Espinoza creator: Jose Fuentes-Lopez creator: Luis Felipe Castelli Correia de Campos creator: Cynthia Lee Andruske creator: Camilo Urra-Albornoz creator: Fernando Alvear Vasquez creator: Rossana Gomez-Campos uri: https://doi.org/10.7717/peerj.13092 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Cossio-Bolanos et al. title: A flexible and accurate method for electroencephalography rhythms extraction based on circulant singular spectrum analysis link: https://peerj.com/articles/13096 last-modified: 2022-03-23 description: Rhythms extraction from electroencephalography (EEG) signals can be used to monitor the physiological and pathological states of the brain and has attracted much attention in recent studies. A flexible and accurate method for EEG rhythms extraction was proposed by incorporating a novel circulant singular spectrum analysis (CiSSA). The EEG signals are decomposed into the sum of a set of orthogonal reconstructed components (RCs) at known frequencies. The frequency bandwidth of each RC is limited to a particular brain rhythm band, with no frequency mixing between different RCs. The RCs are then grouped flexibly to extract the desired EEG rhythms based on the known frequencies. The extracted brain rhythms are accurate and no mixed components of other rhythms or artifacts are included. Simulated EEG data based on the Markov Process Amplitude EEG model and experimental EEG data in the eyes-open and eyes-closed states were used to verify the CiSSA-based method. The results showed that the CiSSA-based method is flexible in alpha rhythms extraction and has a higher accuracy in distinguishing between the eyes-open and eyes-closed states, compared with the basic SSA method, the wavelet decomposition method, and the finite impulse response filtering method. creator: Hai Hu creator: Zihang Pu creator: Peng Wang uri: https://doi.org/10.7717/peerj.13096 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Hu et al. title: Growth and survival among Hawaiian corals outplanted from tanks to an ocean nursery are driven by individual genotype and species differences rather than preconditioning to thermal stress link: https://peerj.com/articles/13112 last-modified: 2022-03-23 description: The drastic decline in coral coverage has stimulated an interest in reef restoration, and various iterations of coral nurseries have been used to augment restoration strategies. Here we examine the growth of two species of Hawaiian Montipora that were maintained in mesocosms under either ambient or warmed annual bleaching conditions for two consecutive years prior to outplanting to determine whether preconditioning aided coral restoration efforts. Using coral trees to create a nearby ocean nursery, we examined whether: (1) previous ex situ mesocosm growth would mirror in situ coral tree nursery growth; and (2) thermal ex situ stress-hardening would predict future success during natural warming events in situ for corals moved from tanks to trees. For Montipora capitata, we found that variation in growth was explained primarily by genotype; growth rates in the mesocosms were similar to those in situ, irrespective of preconditioning. Variation in M. flabellata growth, however, was explained by both genotype and culture method such that an individual M. flabellata colony that grew well in the tanks did not necessarily perform as well on the coral trees. For both species, previous exposure to elevated temperatures in the mesocosms provided no benefit to either growth or survival during a warming event in the coral tree nursery compared to those grown in ambient temperatures. Overall, M. capitata performed better in the tree nursery with higher net growth, lower mortality, and was subject to less predation than M. flabellata. Our results show little benefit of the additional cost and time of stress-hardening these corals prior to outplanting because it is unlikely to aid resilience to future warming events. These results also suggest that selecting corals for restoration based on long-term genotype growth performance may be more effective for optimal outcomes but should be weighed against other factors, such as coral morphology, in situ nursery method, location, and other characteristics. creator: E. Michael Henley creator: Jessica Bouwmeester creator: Christopher P. Jury creator: Robert J. Toonen creator: Mariko Quinn creator: Claire V.A. Lager creator: Mary Hagedorn uri: https://doi.org/10.7717/peerj.13112 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Henley et al. title: Multilingual validation of the short form of the Unesp-Botucatu Feline Pain Scale (UFEPS-SF) link: https://peerj.com/articles/13134 last-modified: 2022-03-23 description: BackgroundPain is the leading cause of animal suffering, hence the importance of validated tools to ensure its appropriate evaluation and treatment. We aimed to test the psychometric properties of the short form of the Unesp-Botucatu Feline Pain Scale (UFEPS-SF) in eight languages.MethodsThe original scale was condensed from ten to four items. The content validation was performed by five specialists in veterinary anesthesia and analgesia. The English version of the scale was translated and back-translated into Chinese, French, German, Italian, Japanese, Portuguese and Spanish by fluent English and native speaker translators. Videos of the perioperative period of 30 cats submitted to ovariohysterectomy (preoperative, after surgery, after rescue analgesia and 24 h after surgery) were randomly evaluated twice (one-month interval) by one evaluator for each language unaware of the pain condition. After watching each video, the evaluators scored the unidimensional, UFEPS-SF and Glasgow composite multidimensional feline pain scales. Statistical analyses were carried out using R software for intra and interobserver reliability, principal component analysis, criteria concurrent and predictive validities, construct validity, item-total correlation, internal consistency, specificity, sensitivity, the definition of the intervention score for rescue analgesia and diagnostic uncertainty zone, according to the receiver operating characteristic (ROC) curve.ResultsUFEPS-SF intra- and inter-observer reliability were ≥0.92 and 0.84, respectively, for all observers. According to the principal component analysis, UFEPS-SF is a unidimensional scale. Concurrent criterion validity was confirmed by the high correlation between UFEPS-SF and all other scales (≥0.9). The total score and all items of UFEPS-SF increased after surgery (pain), decreased to baseline after analgesia and were intermediate at 24 h after surgery (moderate pain), confirming responsiveness and construct validity. Item total correlation of each item (0.68–0.83) confirmed that the items contributed homogeneously to the total score. Internal consistency was excellent (≥0.9) for all items. Both specificity (baseline) and sensitivity (after surgery) based on the Youden index was 99% (97–100%). The suggestive cut-off score for the administration of analgesia according to the ROC curve was ≥4 out of 12. The diagnostic uncertainty zone ranged from 3 to 4. The area under the curve of 0.99 indicated excellent discriminatory capacity of UFEPS-SF.ConclusionsThe UFEPS-SF and its items, assessed by experienced evaluators, demonstrated very good repeatability and reproducibility, content, criterion and construct validities, item-total correlation, internal consistency, excellent sensitivity and specificity and a cut-off point indicating the need for rescue analgesia in Chinese, French, English, German, Italian, Japanese, Portuguese and Spanish. creator: Stelio P.L. Luna creator: Pedro H.E. Trindade creator: Beatriz P. Monteiro creator: Nadia Crosignani creator: Giorgia della Rocca creator: Helene L.M. Ruel creator: Kazuto Yamashita creator: Peter Kronen creator: Chia Te Tseng creator: Lívia Teixeira creator: Paulo V. Steagall uri: https://doi.org/10.7717/peerj.13134 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Luna et al. title: Knowledge, attitudes and perceptions regarding human papillomavirus among university students in Hail, Saudi Arabia link: https://peerj.com/articles/13140 last-modified: 2022-03-23 description: BackgroundHuman papillomavirus (HPV) is a well-known cause of cervical cancer. The prevalence of HPV, insufficient preventive services, inadequate treatment access, socioeconomic conditions, certain cultural causes and values and opinions regarding cervical cancer have been established as factors contributing to the occurrence of cervical cancer in various parts of the world.ObjectiveTo determine university students’ knowledge, attitudes and perceptions regarding HPV and its vaccine.Material and MethodsThe present cross-sectional study included students enrolled at the University of Hail, Saudi Arabia. Data were collected from January to May 2020 using a previously validated 26-item questionnaire.ResultsA total of 386 participants responded to the survey; the response rate was 80%. The majority of the respondents (63%) were male and 332 (86%) respondents were single among the overall study population. Most respondents were aged 21–25 years (75.6%), followed by 26–30 years (12.7%). In total, 130 (33.7%) respondents reported that they had heard of HPV before, while 174 (45.1%) reported that HPV infections are rare in Saudi Arabia. Furthermore, 102 (26.4%) respondents thought that HPV causes genital warts, while almost 29.5% believed that HPV infection is a sexually transmitted disease. Nearly 76.2% of the respondents did not believe that HPV infection can occur without symptoms. Moreover, 53.4% of the respondents stated that they did not know the health problems associated with HPV infection, while 148 (38.8%) stated that cervical cancer is a health problem associated with HPV infection. When asked about their understanding of the HPV vaccine, nearly 267 (62.2%) respondents believed that there is no vaccine for HPV, while 239 (61.9%) believed that the vaccine does not minimise the risk of cervical cancer. In addition, the respondents reported that they would be far more likely to get an HPV vaccine if recommended by their doctors [relative importance index (RII) = 0.745], followed by their friends (RII = 0.675).ConclusionThe present findings provide a clear understanding of university students’ knowledge, perceptions and attitudes regarding HPV; this information can be used to raise awareness by developing an effective educational strategy. However, further research with a larger sample size is recommended; such efforts would also aid in the development of educational services for various age ranges. creator: Farhan Alshammari creator: Kashif Ullah Khan uri: https://doi.org/10.7717/peerj.13140 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Alshammari and Khan title: RapidHRV: an open-source toolbox for extracting heart rate and heart rate variability link: https://peerj.com/articles/13147 last-modified: 2022-03-23 description: Heart rate and heart rate variability have enabled insight into a myriad of psychophysiological phenomena. There is now an influx of research attempting using these metrics within both laboratory settings (typically derived through electrocardiography or pulse oximetry) and ecologically-rich contexts (via wearable photoplethysmography, i.e., smartwatches). However, these signals can be prone to artifacts and a low signal to noise ratio, which traditionally are detected and removed through visual inspection. Here, we developed an open-source Python package, RapidHRV, dedicated to the preprocessing, analysis, and visualization of heart rate and heart rate variability. Each of these modules can be executed with one line of code and includes automated cleaning. In simulated data, RapidHRV demonstrated excellent recovery of heart rate across most levels of noise (>=10 dB) and moderate-to-excellent recovery of heart rate variability even at relatively low signal to noise ratios (>=20 dB) and sampling rates (>=20 Hz). Validation in real datasets shows good-to-excellent recovery of heart rate and heart rate variability in electrocardiography and finger photoplethysmography recordings. Validation in wrist photoplethysmography demonstrated RapidHRV estimations were sensitive to heart rate and its variability under low motion conditions, but estimates were less stable under higher movement settings. creator: Peter A. Kirk creator: Alexander Davidson Bryan creator: Sarah N. Garfinkel creator: Oliver J. Robinson uri: https://doi.org/10.7717/peerj.13147 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Kirk et al. title: ATP11A promotes EMT by regulating Numb PRRL in pancreatic cancer cells link: https://peerj.com/articles/13172 last-modified: 2022-03-23 description: PurposeThe Numb protein plays a vital role in tumor development. The main aim of this study was to identify ATP11A, which is associated with the biological behavior of pancreatic cancer, and elucidate its relationship with Numb and the underlying mechanism behind this relationship.MethodsFirst, data retrieved from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEX) databases was used to investigate the expression of ATP11A mRNA and its relationship with Numb mRNA in pancreatic cancer. Western blot assays on 31 pairs of pancreatic cancer tissues and paracancerous tissues, and immunohistochemical assays on 81 pancreatic cancer specimens were performed in order to verify the expression of ATP11A in pancreatic cancer at the protein level. Next, ATP11A was overexpressed or knocked down to observe its effects on the invasion and migration ability of pancreatic cancer cells and the changes of downstream proteins. Rescue assays were conducted to determine the mechanism through which ATP11A affects Numb, ZEB1, Snail2 and other proteins. Furthermore, immunoprecipitation assays were performed to explore the interaction between ATP11A and Numb. Finally, pancreatic cancer cells were stimulated with TGFB1 and ATP11A expression was examined to explore whether the effect of ATP11A on EMT was TGFB dependent.ResultsAt the mRNA level, the expression of ATP11A in pancreatic cancer tissues was significantly higher than in normal pancreatic tissues (P < 0.001). ATP11A expression was also highly correlated with Numb expression (R = 0.676). At the protein level, ATP11A expression in pancreatic cancer tissues was significantly higher than that in paracancerous tissues (P = 0.0009), and high ATP11A expression was also correlated with a worse prognosis. Moreover, our results showed that ATP11A can promote the invasion and migration of pancreatic cancer cells. Additionally, ATP11A could positively regulate the expression of Numb PRRL, Snail2 and ZEB1 proteins. The rescue experiment results showed that the enhancement effect of ATP11A on ZEB1/Snail2 was suppressed by the specific knockdown of Numb PRRL. In addition, the immunoprecipitation results showed that ATP11A could specifically bind to Numb PRRL. The expression of ATP11A was also upregulated after TGFB stimulation, suggesting that the effect of ATP11A on EMT is TGFB dependent.ConclusionATP11A is significantly upregulated in pancreatic cancer tissues, where it promotes the invasion and migration ability of pancreatic cancer cells. It is also associated with adverse prognosis in pancreatic cancer. Furthermore, ATP11A affects the epithelial-to-mesenchymal transition (EMT) of pancreatic cancer by regulating the TGFB dependent Numb PRRL-ZEB1/Snail2 pathway. creator: Lin Chen creator: Jingtong Tang creator: Weiwei Sheng creator: Jian Sun creator: Yuteng Ma creator: Ming Dong uri: https://doi.org/10.7717/peerj.13172 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Chen et al. title: Novel decorating behaviour of silk retreats in a challenging habitat link: https://peerj.com/articles/12839 last-modified: 2022-03-22 description: Many ecological interactions of spiders with their potential prey and predators are affected by the visibility of their bodies and silk, especially in habitats with lower structural complexity that expose spiders. For instance, the surface of tree trunks harbours relatively limited structures to hide in and may expose residents to visual detection by prey and predators. Here we provide the first detailed description of the novel retreat building strategy of the tree trunk jumping spider Arasia mullion. Using fields surveys, we monitored and measured over 115 spiders and 554 silk retreats. These spiders build silk retreats on the exposed surface of tree trunks, where they remain as sedentary permanent residents. Furthermore, the spiders decorate the silk retreats with bark debris that they collect from the immediate surrounding. We discuss the role of silk decoration in the unusual sedentary behaviour of these spiders and the potential mechanisms that allow A. mullion to engineer their niche in a challenging habitat. creator: Alfonso Aceves-Aparicio creator: Donald James McLean creator: Zoe Wild creator: Jutta M. Schneider creator: Marie E. Herberstein uri: https://doi.org/10.7717/peerj.12839 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Aceves-Aparicio et al. title: Upside-down in volcanic ash: crown reconstruction of the early Permian seed fern Medullosa stellata with attached foliated fronds link: https://peerj.com/articles/13051 last-modified: 2022-03-22 description: Our understanding of fossil floras through geological time is mainly based on various differently preserved plant parts, often found isolated under restricted taphonomic circumstances. Preservation of whole plants is exceptionally rare in the geological record but provides the most reliable proof of ancient plants, especially those lacking a nearest living relative like the late Paleozoic pteridosperms. Among them, the medullosan seed ferns represent the largest and most essential systematic group. Medullosaleans are well known from the large Euramerican tropical swamp forests of Carboniferous age, but also from seasonally dry, clastic-soil habitats of Late Pennsylvanian–early Permian intramontane basins in central Europe. An exceptional taphonomic window that offered three-dimensional preservation of early Permian plants is located in Chemnitz, eastern Germany. Here, a forest ecosystem had been buried by pyroclastic deposits in a geological instant, 291 ± 2 Ma ago. Medullosaleans are both abundant and diverse in this striking autochthonous assemblage. The upper part of a Medullosa stellata var. typica individual broke at its top resulting from the overload of volcanic ash and was buried upside-down in the basal pyroclastics. The tree crown consists of the anatomically preserved apical stem, ten attached Alethopteris schneideri foliated fronds with Myeloxylon-type petioles and rachises. Though already discovered during the scientific excavation in 2010, the remarkable find required several years of preparation work, documentation, and reconstruction. The fronds were up to 3.5 m long, bifurcating, and bore numerous bipinnately compound pinnae preserved pulvinated in life position. The apical stem vascular system consists of a cylindrical peripheral vascular segment and up to 87 central accessory strands, each surrounded by manoxylic wood and secondary phloem. The reconstructed tree is supposed to have been self-supporting and of slender stature. Its architectural model is comparable to modern tree ferns or cycads and adapted to have grown in light-deficient lower-storey (sub-) tropical forests, usually not exceeding 15 m in height. Apical meristematic growth dominated, whereas only minor secondary growth occurred during ontogenesis. The densely attached frond bases followed a 3/8 phyllotaxis and were most likely abscised shortly after becoming photosynthetically inactive. A high water-conducting potential is assumed due to the tree’s cauline, petiolar and leaf vascular anatomies. Concerning the extensive leaf surface of the densely foliated fronds, considerable transpiration is hypothesised. Alethopteris schneideri foliage is stratigraphically significant for lower Permian (Asselian–Sakmarian) continental strata of central Europe, preferring habitats of wet clastic soils in sub-humid, seasonal palaeoclimate. The new insights provide a substantial step towards the first whole-plant concept of intramontane medullosaleans. creator: Ludwig Luthardt creator: Mathias Merbitz creator: Evgeny Fridland creator: Ronny Rößler uri: https://doi.org/10.7717/peerj.13051 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Luthardt et al. title: Mutation breeding of Aspergillus niger by atmospheric room temperature plasma to enhance phosphorus solubilization ability link: https://peerj.com/articles/13076 last-modified: 2022-03-22 description: BackgroundPhosphorus (P) is abundant in soils, including organic and inorganic forms. Nevertheless, most of P compounds cannot be absorbed and used by plants. Aspergillus niger v. Tiegh is a strain that can efficiently degrade P compounds in soils.MethodsIn this study, A. niger xj strain was mutated using Atmospheric Room Temperature Plasma (ARTP) technology and the strains were screened by Mo-Sb Colorimetry with strong P-solubilizing abilities.ResultsCompared with the A. niger xj strain, setting the treatment time of mutagenesis to 120 s, four positive mutant strains marked as xj 90–32, xj120–12, xj120–31, and xj180–22 had higher P-solubilizing rates by 50.3%, 57.5%, 55.9%, and 61.4%, respectively. Among them, the xj120–12 is a highly efficient P solubilizing and growth-promoting strain with good application prospects. The growth characteristics such as plant height, root length, and dry and fresh biomass of peanut (Arachis hypogaea L.) increased by 33.5%, 43.8%, 43.4%, and 33.6%, respectively. Besides available P, the chlorophyll and soluble protein contents also vary degrees of increase in the P-solubilizing mutant strains.ConclusionsThe results showed that the ARTP mutagenesis technology can improve the P solubilization abilities of the A. niger mutant strains and make the biomass of peanut plants was enhanced of mutant strains. creator: Qiuju Peng creator: Yang Xiao creator: Su Zhang creator: Changwei Zhou creator: Ailin Xie creator: Zhu Li creator: Aijuan Tan creator: Lihong Zhou creator: Yudan Xie creator: Jinyi Zhao creator: Chenglin Wu creator: Lei Luo creator: Jie Huang creator: Tengxia He creator: Ran Sun uri: https://doi.org/10.7717/peerj.13076 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Peng et al. title: E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces link: https://peerj.com/articles/13099 last-modified: 2022-03-22 description: BackgroundThe SARS-CoV-2 pandemic reverberated, posing health and social hygiene obstacles throughout the globe. Mutant lineages of the virus have concerned scientists because of convergent amino acid alterations, mainly on the viral spike protein. Studies have shown that mutants have diminished activity of neutralizing antibodies and enhanced affinity with its human cell receptor, the ACE2 protein.MethodsHence, for real-time measuring of the impacts caused by variant strains in such complexes, we implemented E-Volve, a tool designed to model a structure with a list of mutations requested by users and return analyses of the variant protein. As a proof of concept, we scrutinized the spike-antibody and spike-ACE2 complexes formed in the variants of concern, B.1.1.7 (Alpha), B.1.351 (Beta), and P.1 (Gamma), by using contact maps depicting the interactions made amid them, along with heat maps to quantify these major interactions.ResultsThe results found in this study depict the highly frequent interface changes made by the entire set of mutations, mainly conducted by N501Y and E484K. In the spike-Antibody complex, we have noticed alterations concerning electrostatic surface complementarity, breaching essential sites in the P17 and BD-368-2 antibodies. Alongside, the spike-ACE2 complex has presented new hydrophobic bonds.DiscussionMolecular dynamics simulations followed by Poisson-Boltzmann calculations corroborate the higher complementarity to the receptor and lower to the antibodies for the K417T/E484K/N501Y (Gamma) mutant compared to the wild-type strain, as pointed by E-Volve, as well as an intensification of this effect by changes at the protein conformational equilibrium in solution. A local disorder of the loop α1′/β1′, as well its possible effects on the affinity to the BD-368-2 antibody were also incorporated to the final conclusions after this analysis. Moreover, E-Volve can depict the main alterations in important biological structures, as shown in the SARS-CoV-2 complexes, marking a major step in the real-time tracking of the virus mutant lineages. E-Volve is available at http://bioinfo.dcc.ufmg.br/evolve. creator: Vitor Pimentel Dos Santos creator: André Rodrigues creator: Gabriel Dutra creator: Luana Bastos creator: Diego Mariano creator: José Gutembergue Mendonça creator: Yan Jerônimo Gomes Lobo creator: Eduardo Mendes creator: Giovana Maia creator: Karina dos Santos Machado creator: Adriano Velasque Werhli creator: Gerd Rocha creator: Leonardo Henrique França de Lima creator: Raquel de Melo-Minardi uri: https://doi.org/10.7717/peerj.13099 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Dos Santos et al. title: The dynamics of circulating SARS-CoV-2 lineages in Bogor and surrounding areas reflect variant shifting during the first and second waves of COVID-19 in Indonesia link: https://peerj.com/articles/13132 last-modified: 2022-03-22 description: BackgroundIndonesia is one of the Southeast Asian countries with high case numbers of COVID-19 with up to 4.2 million confirmed cases by 29 October 2021. Understanding the genome of SARS-CoV-2 is crucial for delivering public health intervention as certain variants may have different attributes that can potentially affect their transmissibility, as well as the performance of diagnostics, vaccines, and therapeutics.ObjectivesWe aimed to investigate the dynamics of circulating SARS-CoV-2 variants over a 15-month period in Bogor and its surrounding areas in correlation with the first and second wave of COVID-19 in Indonesia.MethodsNasopharyngeal and oropharyngeal swab samples collected from suspected patients from Bogor, Jakarta and Tangerang were confirmed for SARS-CoV-2 infection with RT-PCR. RNA samples of those confirmed patients were subjected to whole genome sequencing using the ARTIC Network protocol and sequencer platform from Oxford Nanopore Technologies (ONT).ResultsWe successfully identified 16 lineages and six clades out of 202 samples (male n = 116, female n = 86). Genome analysis revealed that Indonesian lineage B.1.466.2 dominated during the first wave (n = 48, 23.8%) while Delta variants (AY.23, AY.24, AY.39, AY.42, AY.43 dan AY.79) were dominant during the second wave (n = 53, 26.2%) following the highest number of confirmed cases in Indonesia. In the spike protein gene, S_D614G and S_P681R changes were dominant in both B.1.466.2 and Delta variants, while N439K was only observed in B.1.466.2 (n = 44) and B.1.470 (n = 1). Additionally, the S_T19R, S_E156G, S_F157del, S_R158del, S_L452R, S_T478K, S_D950N and S_V1264L changes were only detected in Delta variants, consistent with those changes being characteristic of Delta variants in general.ConclusionsWe demonstrated a shift in SARS-CoV-2 variants from the first wave of COVID-19 to Delta variants in the second wave, during which the number of confirmed cases surpassed those in the first wave of COVID-19 pandemic. Higher proportion of unique mutations detected in Delta variants compared to the first wave variants indicated potential mutational effects on viral transmissibility that correlated with a higher incidence of confirmed cases. Genomic surveillance of circulating variants, especially those with higher transmissibility, should be continuously conducted to rapidly inform decision making and support outbreak preparedness, prevention, and public health response. creator: Anggia Prasetyoputri creator: Anik B. Dharmayanthi creator: Syam B. Iryanto creator: Ade Andriani creator: Isa Nuryana creator: Andri Wardiana creator: Asep M. Ridwanuloh creator: Sri Swasthikawati creator: Hariyatun Hariyatun creator: Herjuno A. Nugroho creator: Idris Idris creator: Indriawati Indriawati creator: Zahra Noviana creator: Listiana Oktavia creator: Yuliawati Yuliawati creator: Masrukhin Masrukhin creator: Erwin F. Hasrianda creator: Linda Sukmarini creator: Fahrurrozi Fahrurrozi creator: Nova Dilla Yanthi creator: Alfi T. Fathurahman creator: Ari S. Wulandari creator: Ruby Setiawan creator: Syaiful Rizal creator: Ahmad Fathoni creator: Wien Kusharyoto creator: Puspita Lisdiyanti creator: Ratih A. Ningrum creator: Sugiyono Saputra uri: https://doi.org/10.7717/peerj.13132 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Prasetyoputri et al. title: The prognostic and clinicopathological significance of desmoglein 2 in human cancers: a systematic review and meta-analysis link: https://peerj.com/articles/13141 last-modified: 2022-03-22 description: ObjectiveThe survival and clinicopathological significance of desmoglein 2 (DSG2) in various cancers is controversial. Thus, we performed this systematic review and meta-analysis to explore the preliminary prognostic value of DSG2.MethodsEligible studies were identified from databases including PubMed, the Cochrane Library, Embase, Web of Science and Scopus. Hand searches were also conducted in relevant bibliographies. We then extracted and pooled hazard ratio (HR) of overall survival (OS) and odds ratio (OR) of clinicopathological features.ResultsA total of 11 eligible studies containing 1,488 patients were included. Our results demonstrated that in non-small cell lung cancer (NSCLC), high DSG2 expression is associated with poor OS. However, in digestive system cancer and female reproductive system cancer, there were no statistically significant associations between OS and DSG2.ConclusionsBased on the findings of this study, high DSG2 expression is associated with worse prognosis in patients with NSCLC, and thus DSG2 expression could be a biomarker for prognosis in NSCLC. creator: Jiantao Wang creator: Siyuan Hao creator: Junjie Gu creator: Sean G. Rudd creator: Yan Wang uri: https://doi.org/10.7717/peerj.13141 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wang et al. title: Bird protection treatments reduce bird-window collision risk at low-rise buildings within a Pacific coastal protected area link: https://peerj.com/articles/13142 last-modified: 2022-03-22 description: BackgroundIn North America, up to one billion birds are estimated to die annually due to collisions with glass. The transparent and reflective properties of glass present the illusion of a clear flight passage or continuous habitat. Approaches to reducing collision risk involve installing visual cues on glass that enable birds to perceive glass as a solid hazard at a sufficient distance to avoid it.MethodsWe monitored for bird-window collisions between 2013 and 2018 to measure response to bird protection window treatments at two low-rise buildings at the Alaksen National Wildlife Area in Delta, British Columbia, Canada. After 2 years of collision monitoring in an untreated state, we retrofitted one building with Feather Friendly® circular adhesive markers applied in a grid pattern across all windows, enabling a field-based assessment of the relative reduction in collisions in the 2 years of monitoring following treatment. An adjacent building that had been constructed with a bird protective UV-treated glass called ORNILUX® Mikado, was monitored throughout the two study periods. Carcass persistence trials were conducted to evaluate the likelihood that carcasses were missed due to carcass removal between scheduled searches.Results and ConclusionsAfter accounting for differences in area of glass between the two buildings, year, and observer effects, our best-fit model for explaining collision risk included the building’s treatment group, when compared to models that included building and season only. We found that the Feather Friendly® markers reduced collision risk at the retrofitted building by 95%. Collision incidence was also lower at the two monitored façades of the building with ORNILUX® glass compared to the building with untreated glass. Although more research is needed on the effectiveness of bird-protection products across a range of conditions, our results highlight the benefit of these products for reducing avian mortality due to collisions with glass. creator: Krista L. De Groot creator: Amy G. Wilson creator: René McKibbin creator: Sarah A. Hudson creator: Kimberly M. Dohms creator: Andrea R. Norris creator: Andrew C. Huang creator: Ivy B. J. Whitehorne creator: Kevin T. Fort creator: Christian Roy creator: Julie Bourque creator: Scott Wilson uri: https://doi.org/10.7717/peerj.13142 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 De Groot et al. title: Evaluation of change in trabecular bone structure surrounding dental implants by fractal dimension analysis and comparison with radiomorphometric indicators: a retrospective study link: https://peerj.com/articles/13145 last-modified: 2022-03-22 description: BackgroundThe trabecular bone surrounding dental implant show some structural changes during healing period. The purpose of this study is to observe the change in trabecular bone with fractal dimensional analysis from baseline to 3rd month of implant placement. It was also aimed to determine the correlation of fractal dimension (FD) change with morphometric indices, mandibular cortical index (MCI) and mandibular cortical width (MCW).MethodsDigital panoramic radiographs taken from 14 patients were evaluated in this study. A total of 30 implants which were placed on mandibular premolar or molar region were included. MCI and MCW assessments were made on baseline radiograph and FD were analyzed on baseline and 3rd month radiograph. FD change by time was recorded separately for every ROI. A paired sample t-test was used to evaluate the change between FD-baseline and FD-3rdmonth values. One-way ANOVA was used to determine the relationship between FD change and MCI. FD change and MCW measurements correlation was calculated by Pearson correlation analysisResultsFD value increased in 75 of 90 implant-adjacent regions evaluated in the 3rd month and it was observed that the FD values were statistically significantly increased in the mesial, distal and apical regions at the 3rd month measurements. There was no statistically significant relationship between mean FD change and MCI, and there was no correlation between mean FD change and MCW value.DiscussionThere are many studies evaluating the resorptive changes in bone. However, there are few studies investigating whether there is a correlation between pre- and post-operative trabecular pattern with MCI and MCW. The results of this study indicate that the implants have an improving effect on bone trabeculation in the region where they are placed. creator: Ilkim Karadag creator: Hasan Guney Yilmaz uri: https://doi.org/10.7717/peerj.13145 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Karadag and Yilmaz title: Transcription factor 7-like 2 single nucleotide polymorphisms rs290487 and rs290481 are associated with dyslipidemia in the Balinese population link: https://peerj.com/articles/13149 last-modified: 2022-03-22 description: BackgroundDyslipidemia is one of the major risks for the development of cardiovascular diseases which has been the leading cause of death in developing countries. Previously, common polymorphisms of the transcription factor 7-like 2 (TCF7L2) gene have been associated with altered lipid profiles. In this study, we investigated the associations of TCF7L2 SNPs, rs290487 and rs290481, with dyslipidemia and altered lipid profile in the Balinese.MethodsA total of 565 subjects from four locations in the Bali Province, Indonesia, were recruited. Serum lipid concentrations (triglycerides (TG), low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), total cholesterol (TC)) were measured using standard protocol. SNP genotyping was done using the amplification refractory system mutation polymerase chain reaction (ARMS-PCR) method.ResultsWe found the shifted major/minor allele frequencies of both SNPs (0.56 for rs290487 T allele, 0.53 for rs290481 T allele) in the Balinese, as compared to dbSNP. The rs290487 and rs290481 C alleles were significantly associated with dyslipidemia, particularly high TC and high LDL-C. These associations were independent of age, sex, population, obesity, diabetes mellitus, and high TyG index as a proxy for insulin resistance. The haplotype CC also showed similar association with these traits. Our findings indicate that TCF7L2 polymorphisms are associated with dyslipidemia and altered lipid profile in the Balinese. creator: Prisca C. Limardi creator: Sukma Oktavianthi creator: Lidwina Priliani creator: Retno Lestari creator: Made Ratna Saraswati creator: Ketut Suastika creator: Safarina G. Malik uri: https://doi.org/10.7717/peerj.13149 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Limardi et al. title: The biogeography of bent-toed geckos, Cyrtodactylus (Squamata: Gekkonidae) link: https://peerj.com/articles/13153 last-modified: 2022-03-22 description: The gekkonid genus Cyrtodactylus is the third largest vertebrate genus on the planet with well over 300 species that range across at least eight biogeographic regions from South Asia to Melanesia. The ecological and morphological plasticity within the genus, has contributed to its ability to disperse across ephemeral seaways, river systems, basins, land bridges, and mountain ranges—followed by in situ diversification within specific geographic areas. Ancestral ranges were reconstructed on a mitochondrial phylogeny with 346 described and undescribed species from which it was inferred that Cyrtodactylus evolved in a proto-Himalaya region during the early Eocene. From there, it dispersed to what is currently Indoburma and Indochina during the mid-Eocene—the latter becoming the first major center of origin for the remainder of the genus that seeded dispersals to the Indian subcontinent, Papua, and Sundaland. Sundaland became a second major center of radiation during the Oligocene and gave rise to a large number of species that radiated further within Sundaland and dispersed to Wallacea, the Philippines, and back to Indochina. One Papuan lineage dispersed west to recolonize and radiate in Sundaland. Currently, Indochina and Sundaland still harbor the vast majority of species of Cyrtodactylus. creator: L. Lee Grismer creator: Nikolay A. Poyarkov creator: Evan S.H. Quah creator: Jesse L. Grismer creator: Perry L. Wood Jr uri: https://doi.org/10.7717/peerj.13153 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Grismer et al. title: Comparative transcriptome analysis of cold-tolerant and -sensitive asparagus bean under chilling stress and recovery link: https://peerj.com/articles/13167 last-modified: 2022-03-22 description: BackgroundLow temperature is a type of abiotic stress that threatens the growth and yield of asparagus bean. However, the key genes and regulatory pathways involved in low temperature response in this legume are still poorly understood. Methodology. The present study analyzed the transcriptome of seedlings from two asparagus bean cultivars—Dubai bean and Ningjiang 3—using Illumina RNA sequencing (RNA-seq). Correlations between samples were determined by calculating Pearson correlation coefficients (PCC) and principal component analysis (PCA). Differentially expressed genes (DEGs) between two samples were identified using the DESeq package. Transcription factors (TF) prediction, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of DEGs were also performed.ResultsPhenotypes and physiological indices indicated that Ningjiang 3 seedlings tolerated cold better than Dubai bean seedlings, in contrast to adult stage. The transcriptome dynamics of the two cultivars were closely compared using Illumina RNA-seq following 0, 3, 12, and 24 h of cold stress at 5 °C and recovery for 3 h at 25 °C room temperature. Global gene expression patterns displayed relatively high correlation between the two cultivars (>0.88), decreasing to 0.79 and 0.81, respectively, at 12 and 24 h of recovery, consistent with the results of principal component analysis. The major transcription factor families identified from differentially expressed genes between the two cultivars included bHLH, NAC, C2H2, MYB, WRKY, and AP2/ERF. The representative GO enrichment terms were protein phosphorylation, photosynthesis, oxidation-reduction process, and cellular glucan metabolic process. Moreover, KEGG analysis of DEGs within each cultivar revealed 36 transcription factors enriched in Dubai bean and Ningjiang 3 seedlings under cold stress.ConclusionsThese results reveal new information that will improve our understanding of the molecular mechanisms underlying the cold stress response of asparagus bean and provide genetic resources for breeding cold-tolerant asparagus bean cultivars. creator: Mingjun Miao creator: Huaqiang Tan creator: Le Liang creator: Haitao Huang creator: Wei Chang creator: Jianwei Zhang creator: Ju Li creator: Yi Tang creator: Zhi Li creator: Yunsong Lai creator: Liang Yang creator: Huanxiu Li uri: https://doi.org/10.7717/peerj.13167 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Miao et al. title: N-mixture models provide informative crocodile (Crocodylus moreletii) abundance estimates in dynamic environments link: https://peerj.com/articles/12906 last-modified: 2022-03-21 description: Estimates of animal abundance provide essential information for population ecological studies. However, the recording of individuals in the field can be challenging, and accurate estimates require analytical techniques which account for imperfect detection. Here, we quantify local abundances and overall population size of Morelet’s crocodiles (Crocodylus moreletii) in the region of Calakmul (Campeche, Mexico), comparing traditional approaches for crocodylians (Minimum Population Size—MPS; King’s Visible Fraction Method—VFM) with binomial N-mixture models based on Poisson, zero-inflated Poisson (ZIP) and negative binomial (NB) distributions. A total of 191 nocturnal spotlight surveys were conducted across 40 representative locations (hydrologically highly dynamic aquatic sites locally known as aguadas) over a period of 3 years (2017–2019). Local abundance estimates revealed a median of 1 both through MPS (min–max: 0–89; first and third quartiles, Q1–Q3: 0–7) and VFM (0–112; Q1–Q3: 0–9) non-hatchling C. moreletii for each aguada, respectively. The ZIP based N-mixture approach shown overall superior confidence over Poisson and NB, and revealed a median of 6 ± 3 individuals (min = 0; max = 120 ± 18; Q1 = 0; Q3 = 18 ± 4) jointly with higher detectabilities in drying aguadas with low and intermediate vegetation cover. Extrapolating these inferences across all waterbodies in the study area yielded an estimated ~10,000 (7,000–11,000) C. moreletii present, highlighting Calakmul as an important region for this species. Because covariates enable insights into population responses to local environmental conditions, N-mixture models applied to spotlight count data result in particularly insightful estimates of crocodylian detection and abundance. creator: José António Lemos Barão-Nóbrega creator: Mauricio González-Jaurégui creator: Robert Jehle uri: https://doi.org/10.7717/peerj.12906 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Lemos Barão-Nóbrega et al. title: Individuals with fibromyalgia have a different gait pattern and a reduced walk functional capacity: a systematic review with meta-analysis link: https://peerj.com/articles/12908 last-modified: 2022-03-21 description: BackgroundThe aim of the present study was to perform a systematic review and meta-analysis comparing walking test performance and gait pattern between individuals with and without fibromyalgia (FM).MethodologyThis systematic review was registered in PROSPERO with the following reference: CRD42018116200.The search for the scientific articles in this systematic review was carried out using the MEDLINE, SCOPUS, PEDRO, CINHAL and WEB OF SCIENCE databases. A combination of three conceptual groups of terms was used: (1) fibromyalgia; (2) walk (performance) tests; and (3) gait analysis. The included articles were analyzed for both functional and pattern of walking data of patients with FM. In order to provide a better estimate of the difference between individuals with and without FM on gait, a meta-analysis was performed on the 6MWT (6-minute walk test).ResultsThirty-six studies were analyzed, with a total population of 4.078 participants (3.369 FM and 709 individuals without FM). From a functional point of view, the 6MWT distance covered by the group of individuals without FM was significantly greater than that of the individuals with FM in all the analyzed studies. In addition, when comparing the results obtained in the gait pattern analysis, it was observed that individuals with FM walked slower, with a shorter stride length and lower cadence compare to individuals without FM.ConclusionsIt is possible to affirm that individuals with FM perform walking tests differently than individuals without FM. It was observed that individuals with FM walk performing a cycle of shorter length and lower frequency, producing a slower gait, which results in a shorter distance traveled, in the same period of time, with respect to healthy subjects. creator: Elio Carrasco-Vega creator: María Ruiz-Muñoz creator: Antonio Cuesta-Vargas creator: Rita Pilar Romero-Galisteo creator: Manuel González-Sánchez uri: https://doi.org/10.7717/peerj.12908 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Carrasco-Vega et al. title: Exploring interactions between Beauveria and Metarhizium strains through co-inoculation and responses of perennial ryegrass in a one-year trial link: https://peerj.com/articles/12924 last-modified: 2022-03-21 description: Perennial ryegrass (Lolium perenne L.) possesses a high level of nutritional quality and is widely used as a forage species to establish permanent pastures in southern Chile. However, the productivity of most such pastures is limited by various environmental agents, such as insect pests and drought. In this context, our work stresses the need for elucidating the ability of fungal endophytes to establish interactions with plants, and to understand how these processes contribute to plant performance and fitness. Therefore, we evaluated the colonization and impact of two native strains of the endophytic insect-pathogenic fungus (EIPF) group isolated from permanent ryegrass pastures in southern Chile. Roots and seeds of ryegrass and scarabaeid larvae were collected from nine different ryegrass pastures in the Los Ríos region of southern Chile to specifically isolate EIPFs belonging to the genera Beauveria and Metarhizium. Fungal isolations were made on 2% water agar with antibiotics, and strains were identified by analyzing the entire internal transcribed spacer (ITS) 1-5.8S-ITS2 ribosomal DNA region. Four strains of Beauveria and 33 strains of Metarhizium were isolated only in scarabaeid larvae from ryegrass pastures across four sites. Experimental mini-pastures that were either not inoculated (control) or co-inoculated with conidia of the strains Beauveria vermiconia NRRL B-67993 (P55_1) and Metarhizium aff. lepidiotae NRRL B-67994 (M25_2) under two soil humidity levels were used. Ryegrass plants were randomly collected from the mini-pastures to characterize EIPF colonization in the roots by real-time PCR and fluorescence microscopy. Aboveground biomass was measured to analyze the putative impact of colonization on the mini-pastures’ aboveground phenotypic traits with R software using a linear mixed-effects model and the ANOVA statistical test. Seasonal variation in the relative abundance of EIPFs was observed, which was similar between both strains from autumn to spring, but different in summer. In summer, the relative abundance of both EIPFs decreased under normal moisture conditions, but it did not differ significantly under water stress. The aboveground biomass of ryegrass also increased from autumn to spring and decreased in summer in both the inoculated and control mini-pastures. Although differences were observed between moisture levels, they were not significant between the control and inoculated mini-pastures, except in July (fresh weight and leaf area) and October (dry weight). Our findings indicate that native strains of B. vermiconia NRRL B-67993 (P55_1) and M. aff. lepidiotae NRRL B-67994 (M25_2) colonize and co-exist in the roots of ryegrass, and these had little or no effect on the mini-pastures’ aboveground biomass; however, they could have other functions, such as protection against root herbivory by insect pests. creator: Milena Vera creator: Sarah Zuern creator: Carlos Henríquez-Valencia creator: Carlos Loncoman creator: Javier Canales creator: Frank Waller creator: Esteban Basoalto creator: Sigisfredo Garnica uri: https://doi.org/10.7717/peerj.12924 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Vera et al. title: Structural analysis of M1AP variants associated with severely impaired spermatogenesis causing male infertility link: https://peerj.com/articles/12947 last-modified: 2022-03-21 description: BackgroundImpaired meiosis can result in absence of sperm in the seminal fluid. This condition, namely non-obstructive azoospermia (NOA), is one of the reasons of male infertility. Despite the low number of studies on meiosis 1-associated protein (M1AP) in the literature, M1AP is known to be crucial for spermatogenesis. Recently, seven variants (five missense, one frameshift, one splice-site) have been reported in the M1AP gene as associated with NOA, cryptozoospermia and oligozoospermia in two separate studies. However, all missense variants were evaluated as variant of uncertain significance by these studies. Therefore, we aimed to analyze their structural impacts on the M1AP protein that could lead to NOA.MethodsWe firstly performed an evolutionary conservation analysis for the variant positions. Afterwards, a comprehensive molecular modelling study was performed for the M1AP structure. By utilizing this model, protein dynamics were sampled for the wild-type and variants by performing molecular dynamics (MD) simulations.ResultsAll variant positions are highly conserved, indicating that they are potentially important for function. In MD simulations, none of the variants led to a general misfolding or loss of stability in the protein structure, but they did cause severe modifications in the conformational dynamics of M1AP, particularly through changes in local interactions affecting flexibility, hinge and secondary structure.ConclusionsDue to critical perturbations in protein dynamics, we propose that these variants may cause NOA by affecting important interactions regulating meiosis, particularly in wild-type M1AP deficiency since the variants are reported to be homozygous or bi-allelic in the infertile individuals. Our results provided reasonable insights about the M1AP structure and the effects of the variants to the structure and dynamics, which should be further investigated by experimental studies to validate. creator: Umut Gerlevik creator: Mahmut Cerkez Ergoren creator: Osman Uğur Sezerman creator: Sehime Gulsun Temel uri: https://doi.org/10.7717/peerj.12947 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Gerlevik et al. title: The direct and indirect effects of a global pandemic on US fishers and seafood workers link: https://peerj.com/articles/13007 last-modified: 2022-03-21 description: The United States’ fishing and seafood industries experienced major shifts in consumer demand and social-distancing restrictions starting in March 2020, when the early stages of the COVID-19 pandemic were unfolding. However, the specific effects on fishers and seafood processors are less well known. Fishermen and seafood workers are potentially at risk during a pandemic given existing tight working quarters, seasonal work, and long hours. To address these concerns, and given a lack of data on the sector, we reviewed news articles, scientific articles, and white papers to assess the various effects of COVID-19 on US seafood workers. Here, we show that most COVID-19 cases among seafood workers occurred during summer 2020 and during the beginning of 2021. These cases were documented across coastal areas, with Alaska experiencing the largest number of cases and outbreaks. Seafood workers were about twice as likely to contract COVID-19 as workers in other parts of the overall US food system. We also documented a number of indirect effects of the pandemic. New social-distancing restrictions and policies limited crew size, resulting in longer hours and more physical taxation. Because of changes in demand and the closure of some processing plants because of COVID-19 outbreaks, economic consequences of the pandemic were a primary concern for fishers and seafood workers, and safety measures allowed for seafood price variation and losses throughout the pandemic. We also highlight a number of inequities in COVID-19 responses within the seafood sector, both along racial and gender lines. All of these conditions point to the diverse direct and indirect effects of the COVID-19 pandemic on fishers and seafood workers. We hope this work sets the foundation for future work on the seafood sector in relation to the COVID-19 pandemic, improving the overall workplace, and collecting systematic social and economic data on workers. creator: Easton R. White creator: Jill Levine creator: Amanda Moeser creator: Julie Sorensen uri: https://doi.org/10.7717/peerj.13007 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 White et al. title: Focus on Polish nurses’ health condition: a cross-sectional study link: https://peerj.com/articles/13065 last-modified: 2022-03-21 description: BackgroundThe nursing profession carries with it many negative factors and a high risk of developing chronic diseases, including overweight and obesity. According to statistics, the health condition of this professional group is much worse than that of the average population of the same age. As the largest and most trusted professional group in the world, nurses are critical to the health of any nation. The aim of the study was to assess the Polish nurse’s health condition based on real measurements of parameters important for the occurrence of metabolic diseases.MethodsThis is the cross-sectional, conducted among two age groups of Polish nurses (<50 years and ≥50 years). Study included the measurements with DXA, the assessment of glucose concentration and lipid profile, the measurement of blood pressure and socio-demographic data of the surveyed nurses.ResultsThe majority of respondents above 50 years old were nurses with elevated total cholesterol (79.3%), elevated LDL cholesterol (72.8%), 42.4% of studied nurses had hypertension.ConclusionIndividual, local and national measures to prevent and support the health of this professional group are needed. creator: Anna Bartosiewicz creator: Edyta Łuszczki creator: Pawel Jagielski creator: Lukasz Oleksy creator: Artur Stolarczyk creator: Katarzyna Dereń uri: https://doi.org/10.7717/peerj.13065 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Bartosiewicz et al. title: Cooperation between arbuscular mycorrhizal fungi and plant growth-promoting bacteria and their effects on plant growth and soil quality link: https://peerj.com/articles/13080 last-modified: 2022-03-21 description: The roles of arbuscular mycorrhizal fungi (AMF) and plant growth-promoting rhizobacteria (PGPR) in improving nutrition uptake and soil quality have been well documented. However, few studies have explored their effects on root morphology and soil properties. In this study, we inoculated Elymus nutans Griseb with AMF and/or PGPR in order to explore their effects on plant growth, soil physicochemical properties, and soil enzyme activities. The results showed that AMF and/or PGPR inoculation significantly enhanced aboveground and belowground vegetation biomass. Both single and dual inoculations were beneficial for plant root length, surface area, root branches, stem diameter, height, and the ratio of shoot to root, but decreased root volume and root average diameter. Soil total nitrogen, alkaline phosphatase, and urease activities showed significant growth, and soil electrical conductivity and pH significantly declined under the inoculation treatments. Specific root length showed a negative correlation with belowground biomass, but a positive correlation with root length and root branches. These results indicated that AMF and PGPR had synergetic effects on root morphology, soil nutrient availability, and plant growth. creator: Lu Yu creator: Hui Zhang creator: Wantong Zhang creator: Kesi Liu creator: Miao Liu creator: Xinqing Shao uri: https://doi.org/10.7717/peerj.13080 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Yu et al. title: Chikungunya virus time course infection of human macrophages reveals intracellular signaling pathways relevant to repurposed therapeutics link: https://peerj.com/articles/13090 last-modified: 2022-03-21 description: BackgroundChikungunya virus (CHIKV) is a mosquito-borne pathogen, within the Alphavirus genus of the Togaviridae family, that causes ~1.1 million human infections annually. CHIKV uses Aedes albopictus and Aedes aegypti mosquitoes as insect vectors. Human infections can develop arthralgia and myalgia, which results in debilitating pain for weeks, months, and even years after acute infection. No therapeutic treatments or vaccines currently exist for many alphaviruses, including CHIKV. Targeting the phagocytosis of CHIKV by macrophages after mosquito transmission plays an important role in early productive viral infection in humans, and could reduce viral replication and/or symptoms.MethodsTo better characterize the transcriptional response of macrophages during early infection, we generated RNA-sequencing data from a CHIKV-infected human macrophage cell line at eight or 24 hours post-infection (hpi), together with mock-infected controls. We then calculated differential gene expression, enriched functional annotations, modulated intracellular signaling pathways, and predicted therapeutic drugs from these sequencing data.ResultsWe observed 234 pathways were significantly affected 24 hpi, resulting in six potential pharmaceutical treatments to modulate the affected pathways. A subset of significant pathways at 24 hpi includes AGE-RAGE, Fc epsilon RI, Chronic myeloid leukemia, Fc gamma R-mediated phagocytosis, and Ras signaling. We found that the MAPK1 and MAPK3 proteins are shared among this subset of pathways and that Telmisartan and Dasatinib are strong candidates for repurposed small molecule therapeutics that target human processes. The results of our analysis can be further characterized in the wet lab to contribute to the development of host-based prophylactics and therapeutics. creator: Madison Gray creator: Israel Guerrero-Arguero creator: Antonio Solis-Leal creator: Richard A. Robison creator: Bradford K. Berges creator: Brett E. Pickett uri: https://doi.org/10.7717/peerj.13090 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Gray et al. title: A machine learning approach for identification of gastrointestinal predictors for the risk of COVID-19 related hospitalization link: https://peerj.com/articles/13124 last-modified: 2022-03-21 description: Background and aimCOVID-19 can be presented with various gastrointestinal symptoms. Shortly after the pandemic outbreak, several machine learning algorithms were implemented to assess new diagnostic and therapeutic methods for this disease. The aim of this study is to assess gastrointestinal and liver-related predictive factors for SARS-CoV-2 associated risk of hospitalization.MethodsData collection was based on a questionnaire from the COVID-19 outpatient test center and from the emergency department at the University Hospital in combination with the data from internal hospital information system and from a mobile application used for telemedicine follow-up of patients. For statistical analysis SARS-CoV-2 negative patients were considered as controls in three different SARS-CoV-2 positive patient groups (divided based on severity of the disease). The data were visualized and analyzed in R version 4.0.5. The Chi-squared or Fisher test was applied to test the null hypothesis of independence between the factors followed, where appropriate, by the multiple comparisons with the Benjamini Hochberg adjustment. The null hypothesis of the equality of the population medians of a continuous variable was tested by the Kruskal Wallis test, followed by the Dunn multiple comparisons test. In order to assess predictive power of the gastrointestinal parameters and other measured variables for predicting an outcome of the patient group the Random Forest machine learning algorithm was trained on the data. The predictive ability was quantified by the ROC curve, constructed from the Out-of-Bag data. Matthews correlation coefficient was used as a one-number summary of the quality of binary classification. The importance of the predictors was measured using the Variable Importance. A 2D representation of the data was obtained by means of Principal Component Analysis for mixed type of data. Findings with the p-value below 0.05 were considered statistically significant.ResultsA total of 710 patients were enrolled in the study. The presence of diarrhea and nausea was significantly higher in the emergency department group than in the COVID-19 outpatient test center. Among liver enzymes only aspartate transaminase (AST) has been significantly elevated in the hospitalized group compared to patients discharged home. Based on the Random Forest algorithm, AST has been identified as the most important predictor followed by age or diabetes mellitus. Diarrhea and bloating have also predictive importance, although much lower than AST.ConclusionSARS-CoV-2 positivity is connected with isolated AST elevation and the level is linked with the severity of the disease. Furthermore, using the machine learning Random Forest algorithm, we have identified the elevated AST as the most important predictor for COVID-19 related hospitalizations. creator: Peter Lipták creator: Peter Banovcin creator: Róbert Rosoľanka creator: Michal Prokopič creator: Ivan Kocan creator: Ivana Žiačiková creator: Peter Uhrik creator: Marian Grendar creator: Rudolf Hyrdel uri: https://doi.org/10.7717/peerj.13124 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Lipták et al. title: An issue of concern: unique truncated ORF8 protein variants of SARS-CoV-2 link: https://peerj.com/articles/13136 last-modified: 2022-03-21 description: Open reading frame 8 (ORF8) shows one of the highest levels of variability among accessory proteins in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of Coronavirus Disease 2019 (COVID-19). It was previously reported that the ORF8 protein inhibits the presentation of viral antigens by the major histocompatibility complex class I (MHC-I), which interacts with host factors involved in pulmonary inflammation. The ORF8 protein assists SARS-CoV-2 in evading immunity and plays a role in SARS-CoV-2 replication. Among many contributing mutations, Q27STOP, a mutation in the ORF8 protein, defines the B.1.1.7 lineage of SARS-CoV-2, engendering the second wave of COVID-19. In the present study, 47 unique truncated ORF8 proteins (T-ORF8) with the Q27STOP mutations were identified among 49,055 available B.1.1.7 SARS-CoV-2 sequences. The results show that only one of the 47 T-ORF8 variants spread to over 57 geo-locations in North America, and other continents, which include Africa, Asia, Europe and South America. Based on various quantitative features, such as amino acid homology, polar/non-polar sequence homology, Shannon entropy conservation, and other physicochemical properties of all specific 47 T-ORF8 protein variants, nine possible T-ORF8 unique variants were defined. The question as to whether T-ORF8 variants function similarly to the wild type ORF8 is yet to be investigated. A positive response to the question could exacerbate future COVID-19 waves, necessitating severe containment measures. creator: Sk. Sarif Hassan creator: Vaishnavi Kodakandla creator: Elrashdy M. Redwan creator: Kenneth Lundstrom creator: Pabitra Pal Choudhury creator: Tarek Mohamed Abd El-Aziz creator: Kazuo Takayama creator: Ramesh Kandimalla creator: Amos Lal creator: Ángel Serrano-Aroca creator: Gajendra Kumar Azad creator: Alaa A.A. Aljabali creator: Giorgio Palù creator: Gaurav Chauhan creator: Parise Adadi creator: Murtaza Tambuwala creator: Adam M. Brufsky creator: Wagner Baetas-da-Cruz creator: Debmalya Barh creator: Vasco Azevedo creator: Nikolas G. Bazan creator: Bruno Silva Andrade creator: Raner José Santana Silva creator: Vladimir N. Uversky uri: https://doi.org/10.7717/peerj.13136 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Hassan et al. title: State of biodiversity documentation in the Philippines: Metadata gaps, taxonomic biases, and spatial biases in the DNA barcode data of animal and plant taxa in the context of species occurrence data link: https://peerj.com/articles/13146 last-modified: 2022-03-21 description: Anthropogenic changes in the natural environment have led to alarming rates of biodiversity loss, resulting in a more urgent need for conservation. Although there is an increasing cognizance of the importance of incorporating biodiversity data into conservation, the accuracy of the inferences generated from these records can be highly impacted by gaps and biases in the data. Because of the Philippines’ status as a biodiversity hotspot, the assessment of potential gaps and biases in biodiversity documentation in the country can be a critical step in the identification of priority research areas for conservation applications. In this study, we systematically assessed biodiversity data on animal and plant taxa found in the Philippines by examining the extent of metadata gaps, taxonomic biases, and spatial biases in DNA barcode data while using species occurrence data as a backdrop of the ‘Philippines’ biodiversity. These barcode and species occurrence datasets were obtained from public databases, namely: GenBank, Barcode of Life Data System and Global Biodiversity Information Facility. We found that much of the barcode data had missing information on either records and publishing, geolocation, or taxonomic metadata, which consequently, can limit the usability of barcode data for further analyses. We also observed that the amount of barcode data can be directly associated with the amount of species occurrence data available for a particular taxonomic group and location–highlighting the potential sampling biases in the barcode data. While the majority of barcode data came from foreign institutions, there has been an increase in local efforts in recent decades. However, much of the contribution to biodiversity documentation only come from institutions based in Luzon. creator: Carmela Maria P. Berba creator: Ambrocio Melvin A. Matias uri: https://doi.org/10.7717/peerj.13146 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Berba and Matias title: Computational bioacoustics with deep learning: a review and roadmap link: https://peerj.com/articles/13152 last-modified: 2022-03-21 description: Animal vocalisations and natural soundscapes are fascinating objects of study, and contain valuable evidence about animal behaviours, populations and ecosystems. They are studied in bioacoustics and ecoacoustics, with signal processing and analysis an important component. Computational bioacoustics has accelerated in recent decades due to the growth of affordable digital sound recording devices, and to huge progress in informatics such as big data, signal processing and machine learning. Methods are inherited from the wider field of deep learning, including speech and image processing. However, the tasks, demands and data characteristics are often different from those addressed in speech or music analysis. There remain unsolved problems, and tasks for which evidence is surely present in many acoustic signals, but not yet realised. In this paper I perform a review of the state of the art in deep learning for computational bioacoustics, aiming to clarify key concepts and identify and analyse knowledge gaps. Based on this, I offer a subjective but principled roadmap for computational bioacoustics with deep learning: topics that the community should aim to address, in order to make the most of future developments in AI and informatics, and to use audio data in answering zoological and ecological questions. creator: Dan Stowell uri: https://doi.org/10.7717/peerj.13152 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Stowell title: Immediate and cumulative effects of upper-body isometric exercise on the cornea and anterior segment of the human eye link: https://peerj.com/articles/13160 last-modified: 2022-03-21 description: ObjectivesThe execution of isometric resistance training has demonstrated to cause changes in the ocular physiology. The morphology of the cornea and anterior chamber is of paramount importance in the prevention and management of several ocular diseases, and thus, understating the impact of performing isometric exercise on the eye physiology may allow a better management of these ocular conditions. We aimed to determine the short-term effects of 2-minutes upper-body isometric effort at two different intensities on corneal and anterior eye morphology.MethodsEighteen healthy young adults performed a 2-minutes isometric biceps-curl exercise against two loads relative to their maximum strength capacity (high-intensity and low-intensity) in a randomized manner. An Oculus Pentacam was used to measure the corneal morphology and anterior chamber parameters in both experimental conditions at baseline, during the isometric effort (after 30, 60, 90 and 120 seconds), and after 30 and 120 seconds of passive recovery.ResultsWe found that isometric effort causes an increase in pupil size (P < 0.001), and a decrease in the iridocorneal angle (P = 0.005), anterior chamber volume (P < 0.001) and K-flat (P < 0.001) during isometric effort, with these effects being more accentuated in high-intensity condition (P < 0.005 in all cases).Performing 2-minutes upper-body isometric effort did not alter anterior chamber depth, central corneal thickness, corneal volume, and K-steep (P > 0.05 in all cases).ConclusionsOur data exhibit that performing 2-minutes of upper-body isometric exercise modifies several parameters of the corneal morphology and anterior eye biometrics, with these changes being greater for the high-intensity exercise condition. The findings of this study may be of relevance for the prevention and management of corneal ectasias and glaucoma. creator: Jesus Vera creator: Beatriz Redondo creator: Rubén Molina creator: Amador García-Ramos creator: Raimundo Jiménez uri: https://doi.org/10.7717/peerj.13160 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Vera et al. title: Relationship between circadian genes and memory impairment caused by sleep deprivation link: https://peerj.com/articles/13165 last-modified: 2022-03-21 description: BackgroundSleep deprivation (SD)-induced cognitive impairment is highly prevalent worldwide and has attracted widespread attention. The temporal and spatial oscillations of circadian genes are severely disturbed after SD, leading to a progressive loss of their physiological rhythms, which in turn affects memory function. However, there is a lack of research on the role of circadian genes and memory function after SD. Therefore, the present study aims to investigate the relationship between circadian genes and memory function and provide potential therapeutic insights into the mechanism of SD-induced memory impairment.MethodsGene expression profiles of GSE33302 and GSE9442 from the Gene Expression Omnibus (GEO) were applied to identify differentially expressed genes (DEGs). Subsequently, both datasets were subjected to Gene Set Enrichment Analysis (GSEA) to determine the overall gene changes in the hippocampus and brain after SD. A Gene Oncology (GO) analysis and Protein-Protein Interaction (PPI) analysis were employed to explore the genes related to circadian rhythm, with their relationship and importance determined through a correlation analysis and a receiver operating characteristic curve (ROC), respectively. The water maze experiments detected behavioral changes related to memory function in SD rats. The expression of circadian genes in several critical organs such as the brain, heart, liver, and lungs and their correlation with memory function was investigated using several microarrays. Finally, changes in the hippocampal immune environment after SD were analyzed using the CIBERSORT in R software.ResultsThe quality of the two datasets was very good. After SD, changes were seen primarily in genes related to memory impairment and immune function. Genes related to circadian rhythm were highly correlated with engagement in muscle structure development and circadian rhythm. Seven circadian genes showed their potential therapeutic value in SD. Water maze experiments confirmed that SD exacerbates memory impairment-related behaviors, including prolonged escape latencies and reduced numbers of rats crossing the platform. The expression of circadian genes was verified, while some genes were also significant in the heart, liver, and lungs. All seven circadian genes were also associated with memory markers in SD. The contents of four immune cells in the hippocampal immune environment changed after SD. Seven circadian genes were related to multiple immune cells.ConclusionsIn the present study, we found that SD leads to memory impairment accompanied by changes in circadian rhythm-related genes. Seven circadian genes play crucial roles in memory impairment after SD. Naïve B cells and follicular helper T cells are closely related to SD. These findings provide new insights into the treatment of memory impairment caused by SD. creator: Peng Ke creator: Chengjie Zheng creator: Feng Liu creator: LinJie Wu creator: Yijie Tang creator: Yanqin Wu creator: Dongdong Lv creator: Huangli Chen creator: Lin Qian creator: Xiaodan Wu creator: Kai Zeng uri: https://doi.org/10.7717/peerj.13165 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Ke et al. title: Transcriptomics analysis of field-droughted pear (Pyrus spp.) reveals potential drought stress genes and metabolic pathways link: https://peerj.com/articles/12921 last-modified: 2022-03-18 description: Drought acts as a major abiotic stress that hinders plant growth and crop productivity. It is critical, as such, to discern the molecular response of plants to drought in order to enhance agricultural yields under droughts as they occur with increasing frequency. Pear trees are among the most crucial deciduous fruit trees worldwide, and yet the molecular mechanisms of drought tolerance in field-grown pear remain unclear. In this study, we analyzed the differences in transcriptome profiles of pear leaves, branches, and young fruits in irrigation vs field-drought conditions over the growing seasons. In total, 819 differentially expressed genes (DEGs) controlling drought response were identified, among which 427 DEGs were upregulated and 392 DEGs were downregulated. Drought responsive genes were enriched significantly in monoterpenoid biosynthesis, flavonoid biosynthesis, and diterpenoid biosynthesis. Fourteen phenylpropanoid, five flavonoid, and four monoterpenoid structural genes were modulated by field drought stress, thereby indicating the transcriptional regulation of these metabolic pathways in fruit exposed to drought. A total of 4,438 transcription factors (TFs) belonging to 30 TF families were differentially expressed between drought and irrigation, and such findings signal valuable information on transcriptome changes in response to drought. Our study revealed that pear trees react to drought by modulating several secondary metabolic pathways, particularly by stimulating the production of phenylpropanoids as well as volatile organic compounds like monoterpenes. Our findings are of practical importance for agricultural breeding programs, while the resulting data is a resource for improving drought tolerance through genetic engineering of non-model, but economically important, perennial plants. creator: Sheng Yang creator: Mudan Bai creator: Guowei Hao creator: Huangping Guo creator: Baochun Fu uri: https://doi.org/10.7717/peerj.12921 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Yang et al. title: The mRNA and miRNA profiles of goat bronchial epithelial cells stimulated by Pasteurella multocida strains of serotype A and D link: https://peerj.com/articles/13047 last-modified: 2022-03-18 description: Pasteurella multocida (P. multocida) is a zoonotic bacterium that predominantly colonizes the respiratory tract and lungs of a variety of farmed and wild animals, and causes severe respiratory disease. To investigate the characteristics of the host immune response induced by P. multocida strains of serotype A and D, high-throughput mRNA-Seq and miRNA-Seq were performed to analyze the changes in goat bronchial epithelial cells stimulated by these two serotypes of P. multocida for 4 h. Quantitative RT-PCR was used to validate the randomly selected genes and miRNAs. The results revealed 204 and 117 differentially expressed mRNAs (|log2(Fold-change)| ≥ 1, p-value < 0.05) in the P. multocida serotype A and D stimulated groups, respectively. Meanwhile, the number of differentially expressed miRNAs (|log2(Fold-change)| > 0.1, p-value < 0.05) were 269 and 290, respectively. GO and KEGG enrichment analyses revealed 13 GO terms (p-value < 0.05) and four KEGG pathways (p-value < 0.05) associated with immunity. In the serotype A-stimulated group, the immune-related pathways were the GABAergic synapse and Toll-like receptor signaling pathways, while in the serotype D-stimulated group, the immune-related pathways were the phagosome and B cell receptor signaling pathways. Based on the predicted results of TargetScan and miRanda, the differentially expressed mRNA–miRNA network of immune-related GO terms and KEGG pathways was constructed. According to the cell morphological changes and the significant immune-related KEGG pathways, it was speculated that the P. multocida serotype D strain-stimulated goat bronchial epithelial cells may induce a cellular immune response earlier than serotype A-stimulated cells. Our study provides valuable insight into the host immune response mechanism induced by P. multocida strains of serotype A and D. creator: Qi An creator: Si Chen creator: Luyin Zhang creator: Zhenxing Zhang creator: Yiwen Cheng creator: Haotian Wu creator: Ang Liu creator: Zhen Chen creator: Bin Li creator: Jie Chen creator: Yiying Zheng creator: Churiga Man creator: Fengyang Wang creator: Qiaoling Chen creator: Li Du uri: https://doi.org/10.7717/peerj.13047 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 An et al. title: The use of electromyography and kinematic measurements of the lumbar spine during ergonomic intervention among workers of the production line of a foundry link: https://peerj.com/articles/13072 last-modified: 2022-03-18 description: PurposeWorkers who perform repetitive movements are exposed to many risk factors leading to the occurrence of lumbar back pain. The aim of the research was to answer the question whether the ergonomic instruction conducted by a physiotherapist would change the tested range of motion of the segments of lumbar spine and the symmetry of the work of the torso and upper limbs muscles during work performed by foundry employees.MethodsThe study included 12 foundry production line workers with musculoskeletal pain. The workstation was built in the laboratory that perfectly simulates work on the production line. The workers performed two activities from their daily work, i.e. transferring and moving a casting. They were then given ergonomic instruction by a physiotherapist and performed the assigned tasks again. During the activities, the electromyographic signal from five muscles was recorded in terms of symmetry of their work. The maximum angular ranges of the motor segments of the lumbar spine were measured using gyroscopes.ResultsAfter the ergonomic instruction, the contralateral imbalance of muscle activity decreased statistically significantly during the first phase (p = 0.0004), second phase (p = 0.0002) and the third phase (p = 0.0069) of transferring the casting. While moving the casting , only erector spinae showed statistically significantly (p = 0.0131) more symmetrical work after the ergonomic instruction. During the transfer of the casting, statistically significantly lower values of the ranges of motion between the segments were obtained after carrying out the ergonomic instruction for the left (p = 0.0231) and right (p = 0.0032) lateral flexion. The ranges of movement between the segments differed statistically significantly for the flexion (p = 0.0117), extension (p = 0.0469) and left (p = 0.0031) and right lateral flexion movements (p = 0.0012).ConclusionConducting ergonomic instruction consisting in teaching the correct performance of a movement task reduced the contralateral imbalance of muscle activity and changes the ranges of movement of L1-S1 segments. The task of optimizing the load on the musculoskeletal system, including the lumbar spine, should be carried out by means of appropriate ergonomic instruction and multi-pronged measures, including analysis of the health of employees, their working environment and physical activity outside the workplace. Electromyography and measurements of the range of movement of the lumbar spine appear to be good tools for the evaluation of workplace ergonomics. creator: Anna Błaszczyk creator: Małgorzata B. Ogurkowska uri: https://doi.org/10.7717/peerj.13072 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Błaszczyk and Ogurkowska title: Complete chloroplast genome studies of different apple varieties indicated the origin of modern cultivated apples from Malus sieversii and Malus sylvestris link: https://peerj.com/articles/13107 last-modified: 2022-03-18 description: BackgroundApple is one of the most important temperate deciduous fruit trees worldwide, with a wide range of cultivation. In this study, we assessed the variations and phylogenetic relationships between the complete chloroplast genomes of wild and cultivated apples (Malus spp.).MethodWe obtained the complete chloroplast genomes of 24 apple varieties using next-generation sequencing technology and compared them with genomes of (downloaded from NCBI) the wild species.ResultThe chloroplast genome of Malus is highly conserved, with a genome length of 160,067–160,290 bp, and all have a double-stranded circular tetrad structure. The gene content and sequences of genomes of wild species and cultivated apple were almost the same, but several mutation hotspot regions (psbI-atpA, psbM-psbD, and ndhC-atpE) were detected in these genomes. These regions can provide valuable information for solving specific molecular markers in taxonomic research. Phylogenetic analysis revealed that Malus formed a new clade and four cultivated varieties clustered into a branch with M. sylvestris and M. sieversii, which indicated that M. sylvestris and M. sieversii were the ancestor species of the cultivated apple. creator: Xueli Li creator: Zhijie Ding creator: Haoyu Miao creator: Jinbo Bao creator: Xinmin Tian uri: https://doi.org/10.7717/peerj.13107 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Li et al. title: Two new glassfrogs (Centrolenidae: Hyalinobatrachium) from Ecuador, with comments on the endangered biodiversity of the Andes link: https://peerj.com/articles/13109 last-modified: 2022-03-18 description: BackgroundThe Tropical Andes is the world’s most biodiverse hotspot. This region contains >1,000 amphibian species, more than half of which are endemic. Herein we describe two new glassfrog species (Centrolenidae: Hyalinobatrachium) that we discovered within relatively unexplored and isolated localities of the Ecuadorian Andes.MethodsWe employed morphological, acoustic, and molecular methods to test the hypothesis that Hyalinobatrachium mashpi sp. nov and H. nouns sp. nov. are species new to science. Following standard methods, we generated mitochondrial sequences (16S) of 37 individuals in the genus Hyalinobatrachium. We inferred the phylogenetic relationships of the two new species in comparison to all other glassfrogs using Maximum Likelihood. In addition to describing the call of H. mashpi sp. nov., we performed a discriminant analysis of principal components (DAPC) with the advertisement call characteristics of several congeners.ResultsBased on an integrative taxonomy approach, we describe two new species. Morphological traits and the inferred phylogeny unambiguously place the new taxa in the genus Hyalinobatrachium. Both species are distinguished from other glassfrogs mainly by their dorsal coloration (i.e., dorsum lime green with small light yellow spots, head usually with interorbital bar) and transparent pericardium (i.e., the heart is visible through the ventral skin). The new species exhibit a high morphological similarity (i.e., cryptic) and occur within relatively close geographical proximity (closest aerial distance = 18.9 km); however, their uncorrected p distance for the mitochondrial gene 16S is 4.6–4.7%, a value that greatly exceeds the genetic distance between closely related species of centrolenid frogs. The DAPC revealed that the advertisement call of H. mashpi sp. nov. is acoustically distinct.DiscussionOur findings are congruent with several previous studies that report a high degree of endemism in the Toisán mountain range, which appears to be isolated from the main Andean cordillera for some amphibian groups. We recommend that both H. mashpi sp. nov. and H. nouns sp. nov. be listed as Endangered, following IUCN criteria. These new species provide another example of cryptic diversity in the Andes—further evidence that the region fosters much more biodiversity than we have the resources to catalog. Threatened by mining and other exploitative industries, these glassfrogs and many other yet-to-be-discovered Andean species highlight the dire need for effective conservation measures—especially in northwestern Ecuador. creator: Juan M. Guayasamin creator: Rebecca M. Brunner creator: Anyelet Valencia-Aguilar creator: Daniela Franco-Mena creator: Eva Ringler creator: Anderson Medina Armijos creator: Carlos Morochz creator: Lucas Bustamante creator: Ross J. Maynard creator: Jaime Culebras uri: https://doi.org/10.7717/peerj.13109 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Guayasamin et al. title: Metabolic adjustment and regulation of gene expression are essential for increased resistance to severe water deficit and resilience post-stress in soybean link: https://peerj.com/articles/13118 last-modified: 2022-03-18 description: BackgroundSoybean is the main oilseed crop grown in the world; however, drought stress affects its growth and physiology, reducing its yield. The objective of this study was to characterize the physiological, metabolic, and genetic aspects that determine differential resistance to water deficit in soybean genotypes.MethodsThree soybean genotypes were used in this study, two lineages (L11644 and L13241), and one cultivar (EMBRAPA 48-C48). Plants were grown in pots containing 8 kg of a mixture of soil and sand (2:1) in a greenhouse under sunlight. Soil moisture in the pots was maintained at field capacity until the plants reached the stage of development V4 (third fully expanded leaf). At this time, plants were subjected to three water treatments: Well-Watered (WW) (plants kept under daily irrigation); Water Deficit (WD) (withholding irrigation until plants reached the leaf water potential at predawn of −1.5 ± 0.2 MPa); Rewatered (RW) (plants rehydrated for three days after reached the water deficit). The WW and WD water treatments were evaluated on the eighth day for genotypes L11644 and C48, and on the tenth day for L13241, after interruption of irrigation. For the three genotypes, the treatment RW was evaluated after three days of resumption of irrigation. Physiological, metabolic and gene expression analyses were performed.ResultsWater deficit inhibited growth and gas exchange in all genotypes. The accumulation of osmolytes and the concentrations of chlorophylls and abscisic acid (ABA) were higher in L13241 under stress. The metabolic adjustment of lineages in response to WD occurred in order to accumulate amino acids, carbohydrates, and polyamines in leaves. The expression of genes involved in drought resistance responses was more strongly induced in L13241. In general, rehydration provided recovery of plants to similar conditions of control treatment. Although the C48 and L11644 genotypes have shown some tolerance and resilience responses to severe water deficit, greater efficiency was observed in the L13241 genotype through adjustments in morphological, physiological, genetic and metabolic characteristics that are combined in the same plant. This study contributes to the advancement in the knowledge about the resistance to drought in cultivated plants and provides bases for the genetic improvement of the soybean culture. creator: Adinan Alves da Silva creator: Cíntia Oliveira Silva creator: Vanessa do Rosario Rosa creator: Michel Filiphy Silva Santos creator: Kacilda Naomi Kuki creator: Maximiller Dal-Bianco creator: Rafael Delmond Bueno creator: Juraci Alves de Oliveira creator: Danielle Santos Brito creator: Alan Carlos Costa creator: Cleberson Ribeiro uri: https://doi.org/10.7717/peerj.13118 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Alves da Silva et al. title: High-performance pipeline for MutMap and QTL-seq link: https://peerj.com/articles/13170 last-modified: 2022-03-18 description: SummaryBulked segregant analysis implemented in MutMap and QTL-seq is a powerful and efficient method to identify loci contributing to important phenotypic traits. However, the previous pipelines were not user-friendly to install and run. Here, we describe new pipelines for MutMap and QTL-seq. These updated pipelines are approximately 5–8 times faster than the previous pipeline, are easier for novice users to use, and can be easily installed through bioconda with all dependencies.AvailabilityThe new pipelines of MutMap and QTL-seq are written in Python and can be installed via bioconda. The source code and manuals are available online (MutMap: https://github.com/YuSugihara/MutMap, QTL-seq: https://github.com/YuSugihara/QTL-seq). creator: Yu Sugihara creator: Lester Young creator: Hiroki Yaegashi creator: Satoshi Natsume creator: Daniel J. Shea creator: Hiroki Takagi creator: Helen Booker creator: Hideki Innan creator: Ryohei Terauchi creator: Akira Abe uri: https://doi.org/10.7717/peerj.13170 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Sugihara et al. title: Sensitivity of soil hydrogen uptake to natural and managed moisture dynamics in a semiarid urban ecosystem link: https://peerj.com/articles/12966 last-modified: 2022-03-17 description: The North American Monsoon season (June–September) in the Sonoran Desert brings thunderstorms and heavy rainfall. These rains bring cooler temperature and account for roughly half of the annual precipitation making them important for biogeochemical processes. The intensity of the monsoon rains also increase flooding in urban areas and rely on green infrastructure (GI) stormwater management techniques such as water harvesting and urban rain gardens to capture runoff. The combination of increased water availability during the monsoon and water management provide a broad moisture regime for testing responses in microbial metabolism to natural and managed soil moisture pulses in drylands. Soil microbes rely on atmospheric hydrogen (H2) as an important energy source in arid and semiarid landscapes with low soil moisture and carbon availability. Unlike mesic ecosystems, transient water availability in arid and semiarid ecosystems has been identified as a key limiting driver of microbe-mediated H2 uptake. We measured soil H2 uptake in rain gardens exposed to three commonly used water harvesting practices during the monsoon season in Tucson AZ, USA. In situ static chamber measurements were used to calculate H2 uptake in each of the three water harvesting treatments passive (stormwater runoff), active (stored rooftop runoff), and greywater (used laundry water) compared to an unaltered control treatment to assess the effects of water management practices on soil microbial activity. In addition, soils were collected from each treatment and brought to the lab for an incubation experiment manipulating the soil moisture to three levels capturing the range observed from field samples. H2 fluxes from all treatments ranged between −0.72 nmol m−2 s−1 and −3.98 nmol m−2 s−1 over the monsoon season. Soil H2 uptake in the greywater treatment was on average 53% greater than the other treatments during pre-monsoon, suggesting that the increased frequency and availability of water in the greywater treatment resulted in higher H2 uptake during the dry season. H2 uptake was significantly correlated with soil moisture (r = −0.393, p = 0.001, df = 62) and temperature (r = 0.345, p = 0.005, df = 62). Our findings suggest that GI managed residential soils can maintain low levels of H2 uptake during dry periods, unlike unmanaged systems. The more continuous H2 uptake associated with GI may help reduce the impacts of drought on H2 cycling in semiarid urban ecosystems. creator: Vanessa Buzzard creator: Dana Thorne creator: Juliana Gil-Loaiza creator: Alejandro Cueva creator: Laura K. Meredith uri: https://doi.org/10.7717/peerj.12966 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Buzzard et al. title: A comparative study of the capability of MSCs isolated from different human tissue sources to differentiate into neuronal stem cells and dopaminergic-like cells link: https://peerj.com/articles/13003 last-modified: 2022-03-17 description: BackgroundNeurodegenerative diseases are characterized by progressive neuronal loss and degeneration. The regeneration of neurons is minimal and neurogenesis is limited only to specific parts of the brain. Several clinical trials have been conducted using Mesenchymal Stem Cells (MSCs) from different sources to establish their safety and efficacy for the treatment of several neurological disorders such as Parkinson’s disease, multiple sclerosis and amyotrophic lateral sclerosis.AimThe aim of this study was to provide a comparative view of the capabilities of MSCs, isolated from different human tissue sources to differentiate into neuronal stem cell-like cells (NSCs) and possibly into dopaminergic neural- like cells.MethodsMesenchymal stem cells were isolated from human bone marrow, adipose, and Wharton’s jelly (WJ) tissue samples. Cells were characterized by flow cytometry for their ability to express the most common MSC markers. The differentiation potential was also assessed by differentiating them into osteogenic and adipogenic cell lineages. To evaluate the capacity of these cells to differentiate towards the neural stem cell-like lineage, cells were cultured in media containing small molecules. Cells were utilized for gene expression and immunofluorescence analysis at different time points.ResultsOur results indicate that we have successfully isolated MSCs from bone marrow, adipose tissue, and Wharton’s jelly. WJ-MSCs showed a slightly higher proliferation rate after 72 hours compared to BM and AT derived MSCs. Gene expression of early neural stem cell markers revealed that WJ-MSCs had higher expression of Nestin and PAX6 compared to BM and AT-MSCs, in addition to LMX expression as an early dopaminergic neural marker. Immunofluorescence analysis also revealed that these cells successfully expressed SOX1, SOX2, Nestin, TUJ1, FOXA2 and TH.ConclusionThese results indicate that the protocol utilized has successfully differentiated BM, AT and WJ-MSCs into NSC-like cells. WJ-MSCs possess a higher potential to transdifferentiate into NSC and dopaminergic-like cells. Thus, it might indicate that this protocol can be used to induce MSC into neuronal lineage, which provides an additional or alternative source of cells to be used in the neurological cell-based therapies. creator: Nidaa A. Ababneh creator: Ban Al-Kurdi creator: Fatima Jamali creator: Abdalla Awidi uri: https://doi.org/10.7717/peerj.13003 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Ababneh et al. title: An ODE model of yaws elimination in Lihir Island, Papua New Guinea link: https://peerj.com/articles/13018 last-modified: 2022-03-17 description: Yaws is a chronic infection that affects mainly the skin, bone and cartilage and spreads mostly between children. The new approval of a medication as treatment in 2012 has revived eradication efforts and now only few known localized foci of infection remain. The World Health Organization strategy mandates an initial round of total community treatment (TCT) with single-dose azithromycin followed either by further TCT or by total targeted treatment (TTT), an active case-finding and treatment of cases and their contacts. We develop the compartmental ODE model of yaws transmission and treatment for these scenarios. We solve for disease-free and endemic equilibria and also perform the stability analysis. We calibrate the model and validate its predictions on the data from Lihir Island in Papua New Guinea. We demonstrate that TTT strategy is efficient in preventing outbreaks but, due to the presence of asymptomatic latent cases, TTT will not eliminate yaws within a reasonable time frame. To achieve the 2030 eradication target, TCT should be applied instead. creator: Presley Kimball creator: Jacob Levenson creator: Amy Moore creator: Jan Rychtar creator: Dewey Taylor uri: https://doi.org/10.7717/peerj.13018 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Kimball et al. title: International football players with cerebral palsy maintained their physical fitness after a self-training program during the COVID-19 lockdown link: https://peerj.com/articles/13059 last-modified: 2022-03-17 description: BackgroundThe COVID-19 global pandemic caused a complete stop in sport participation which meant a detraining period for athletes. High-level athletes had to train at home guided by their coaches and conditioning trainers in an effort to maintain their physical fitness. The aim of maintaining the training adaptations and physical fitness during the COVID-19 mandatory lockdown was especially important for CP athletes, in which the detraining period was expected to cause early declines in motor function, poor coordination and muscle weakness due to their disability.MethodsThe present study assessed the effect of a guided self-training program on international CP football players’ physical fitness during the COVID-19 mandatory lockdown. Fifteen CP football players from the Spanish National Team participated in the study. An experimental design with a pre- (T1) and a post-intervention (T2) assessment was carried out, with a 12-week period of players’ self-training (divided in two periods of 6 weeks) which combined strength and endurance training. Physical performance assessment consisted in the free countermovement jump (CMJ), 5, 10 and 20-m sprint, the modified agility T-test (MAT) and a dribbling test. The Kruskal–Wallis test was used for between-group comparisons, while the Student’s paired t test or the Fisher Pitman permutation test, based on the normality of the data, were used for within-group comparisons.ResultsThe results showed no differences between sport classes (FT1, FT2 and FT3) in physical fitness change after the training program (Chi2 = 0.16 to 1.73; p = 0.42 to 0.92). Within-group comparisons showed an increase of jump height in the CMJ (4.19 cm [2.46, 5.93]; p < 0.001) and a maintenance of the 5, 10 and 20-m sprint, MAT and dribbling ability (<0.01 to 0.09 s; p = 0.19 to 0.97).DiscussionTo the authors’ knowledge, this is the first study that examined the physical fitness adaptations to a training program with CP football players. The results show that a 12-week guided self-training program without football-specific stimulus may be effective to maintain or even improve the specific physical performance of international CP football players during a non-competitive period (as the COVID-19 lockdown). This study reveals that CP football players are able to show adaptations to the strength and endurance training and this could be the basis for future research regarding training adaptations in CP football players. creator: Iván Peña-González creator: José Manuel Sarabia creator: Agustín Manresa-Rocamora creator: Manuel Moya-Ramón uri: https://doi.org/10.7717/peerj.13059 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Peña-González et al. title: Geometric morphometrics as a tool to understand biogeographical and evolutionary patterns in crane fly genus Ischnotoma Skuse (Diptera, Tipulidae) link: https://peerj.com/articles/13123 last-modified: 2022-03-17 description: BackgroundThe geometric morphometric analysis is applied for the first time for the family Tipulidae to distinguish evolutionary and biogeographical patterns on Ischnotoma species from Neotropical and Australian regions. We included 45 recognized species of the genus, representing its three subgenera I. (Icriomastax), I. (Ischnotoma), and I. (Neotipula). This paper aims to test if the three subgenera are recoverable using this set of morphometric data.MethodsTwenty-two landmarks were selected on the wing, mostly located on the radial and medial veins. A Regression Analysis, Principal Components Analysis (PCA), a Shape Coordinates PCA and a Canonical Variate Analysis (CVA) were used to test the variations among individuals, wing shape and groups.ResultsFor all analyses, the species of Ischnotoma (Neotipula) has a strong dissociation from the remaining species and the CVA shows a complete separation of the three subgenera. This study represents the first insight for a new assessment of Ischnotoma and the first step to giving a possible new status for I. (Neotipula). creator: Jéssica Gouvêa creator: Leonardo H. Gil-Azevedo uri: https://doi.org/10.7717/peerj.13123 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Gouvêa and Gil-Azevedo title: Screening of stable resistant accessions and identification of resistance loci to Barley yellow mosaic virus disease link: https://peerj.com/articles/13128 last-modified: 2022-03-17 description: BackgroundThe disease caused by Barley yellow mosaic virus (BaYMV) infection is a serious threat to autumn-sown barley (Hordeum vulgare L.) production in Europe, East Asia and Iran. Due to the rapid diversification of BaYMV strains, it is urgent to discover novel germplasm and genes to assist breeding new varieties with resistance to different BaYMV strains, thus minimizing the effect of BaYMV disease on barley cropping.MethodsA natural population consisting of 181 barley accessions with different levels of resistance to BaYMV disease was selected for field resistance identification in two separate locations (Yangzhou and Yancheng, Jiangsu Province, China). Additive main effects and multiplicative interaction (AMMI) analysis was used to identify accessions with stable resistance. Genome-wide association study (GWAS) of BaYMV disease resistance was broadly performed by combining both single nucleotide polymorphisms (SNPs) and specific molecular markers associated with the reported BaYMV disease resistance genes. Furthermore, the viral protein genome linked (VPg) sequences of the virus were amplified and analyzed to assess the differences between the BaYMV strains sourced from the different experimental sites.ResultsSeven barley accessions with lower standardized Area Under the Disease Progress Steps (sAUDPS) index in every environment were identified and shown to have stable resistance to BaYMV disease in each assessed location. Apart from the reported BaYMV disease resistance genes rym4 and rym5, one novel resistance locus explaining 24.21% of the phenotypic variation was identified at the Yangzhou testing site, while two other novel resistance loci that contributed 19.23% and 19.79% of the phenotypic variation were identified at the Yancheng testing site, respectively. Further analysis regarding the difference in the VPg sequence of the predominant strain of BaYMV collected from these two testing sites may explain the difference of resistance loci differentially identified under geographically distinct regions. Our research provides novel genetic resources and resistance loci for breeding barley varieties for BaMYV disease resistance. creator: Yuhan Pan creator: Juan Zhu creator: Yi Hong creator: Mengna Zhang creator: Chao Lv creator: Baojian Guo creator: Huiquan Shen creator: Xiao Xu creator: Rugen Xu uri: https://doi.org/10.7717/peerj.13128 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Pan et al. title: Positively selected genes in the hoary bat (Lasiurus cinereus) lineage: prominence of thymus expression, immune and metabolic function, and regions of ancient synteny link: https://peerj.com/articles/13130 last-modified: 2022-03-17 description: BackgroundBats of the genus Lasiurus occur throughout the Americas and have diversified into at least 20 species among three subgenera. The hoary bat (Lasiurus cinereus) is highly migratory and ranges farther across North America than any other wild mammal. Despite the ecological importance of this species as a major insect predator, and the particular susceptibility of lasiurine bats to wind turbine strikes, our understanding of hoary bat ecology, physiology, and behavior remains poor.MethodsTo better understand adaptive evolution in this lineage, we used whole-genome sequencing to identify protein-coding sequence and explore signatures of positive selection. Gene models were predicted with Maker and compared to seven well-annotated and phylogenetically representative species. Evolutionary rate analysis was performed with PAML.ResultsOf 9,447 single-copy orthologous groups that met evaluation criteria, 150 genes had a significant excess of nonsynonymous substitutions along the L. cinereus branch (P < 0.001 after manual review of alignments). Selected genes as a group had biased expression, most strongly in thymus tissue. We identified 23 selected genes with reported immune functions as well as a divergent paralog of Steep1 within suborder Yangochiroptera. Seventeen genes had roles in lipid and glucose metabolic pathways, partially overlapping with 15 mitochondrion-associated genes; these adaptations may reflect the metabolic challenges of hibernation, long-distance migration, and seasonal variation in prey abundance. The genomic distribution of positively selected genes differed significantly from background expectation by discrete Kolmogorov–Smirnov test (P < 0.001). Remarkably, the top three physical clusters all coincided with islands of conserved synteny predating Mammalia, the largest of which shares synteny with the human cat-eye critical region (CECR) on 22q11. This observation coupled with the expansion of a novel Tbx1-like gene family may indicate evolutionary innovation during pharyngeal arch development: both the CECR and Tbx1 cause dosage-dependent congenital abnormalities in thymus, heart, and head, and craniodysmorphy is associated with human orthologs of other positively selected genes as well. creator: Robert S. Cornman creator: Paul M. Cryan uri: https://doi.org/10.7717/peerj.13130 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Cornman and Cryan title: Inhibition of Connexin 43 reverses ox-LDL-mediated inhibition of autophagy in VSMC by inhibiting the PI3K/Akt/mTOR signaling pathway link: https://peerj.com/articles/12969 last-modified: 2022-03-16 description: BackgroundOxidized low-density lipoproteins (ox-LDL) may induce foam cell formation from the vascular smooth muscle cell (VSMC) by inhibiting VSMC autophagy. This process accelerates the formation of atherosclerosis (AS). Connexin 43 (Cx43), which is the most widely distributed connexin in VSMC is associated with autophagy. However, the mechanism of action and the involvement of Cx43 in ox-LDL-inhibited VSMC autophagy remain unclear.MethodsThe primary VSMC were obtained and identified, before primary VSMC were pretreated with an inhibitor (Cx43-specific inhibitor Gap26 and PI3K inhibitor LY294002) and stimulated with ox-LDL.ResultsOx-LDL not only inhibited autophagy in VSMC via downregulation of autophagy-related proteins (such as Beclin 1, LC3B, p62), but also increased Cx43 protein levels. Then we added Gap26 to VSMC in the ox-LDL+Gap26 group, in which autophagy-related proteins were increased and the accumulation of lipid droplets was reduced. These result suggested that an enhanced level of autophagy and an alleviation of lipid accumulation might be caused by inhibiting Cx43 in VSMC. The phosphorylation levels of PI3K, AKT, mTOR were increased by ox-LDL, thus down-regulating autophagy-related proteins. However, this situation was partially reversed by the Gap26. Moreover, Cx43 expression were decreased by LY294002 in ox-LDL-induced VSMCs.ConclusionInhibiting Cx43 may activate VSMC autophagy to inhibit foam cell formation by inhibiting the PI3K/AKT/mTOR signaling pathway. creator: Xuqing Qin creator: Wenjun He creator: Rui Yang creator: Luqian Liu creator: Yingying Zhang creator: Li Li creator: Junqiang Si creator: Xinzhi Li creator: Ketao Ma uri: https://doi.org/10.7717/peerj.12969 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Qin et al. title: Onyx disparamphis sp. n. (Nematoda, Desmodorida) from South Korea with a taxonomic review of the genus link: https://peerj.com/articles/13010 last-modified: 2022-03-16 description: A new free-living marine nematode Onyx disparamphis sp. n. (Nematoda, Desmodorida) is described from sandy littoral of Jeju Island, South Korea. The new species differs from all other Onyx species by the unusual amphideal fovea morphology in males (elongated loop). O. disparamphis relates to O. balochinensis, and O. brevispiculatum by having simple non-double terminal pharyngeal bulb and relatively small and straight, non-sigmoid supplementary organs, but differs from them by smaller body length, shorter cephalic setae, smaller terminal pharyngeal bulb, smaller spicules, number of supplementary organs and tail shape expressed as ratio tail length/anal diameter. The genus Onyx is revised with updated genus diagnosis, and an annotated list of 23 valid species is presented. Onyx ferox is considered species inquirenda because the species is known only from a sole immature female specimen, while within Onyx, the males provide the most important distinguishing characters such as enlarged and complicated amphids, supplementary organs and copulatory spicules. For species identification, a pictorial key consisting of illustrations of simplified icons of male heads and posterior body sections, as well as a table of the most important morphometric and numerical characters are provided. Geographical distribution and habitat specifity of Onyx species is analysed briefly. creator: Alexei V. Tchesunov creator: Raehyuk Jeong creator: Wonchoel Lee uri: https://doi.org/10.7717/peerj.13010 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Tchesunov et al. title: A SNP variation in an expansin (EgExp4) gene affects height in oil palm link: https://peerj.com/articles/13046 last-modified: 2022-03-16 description: Oil palm (Elaeis guineensis Jacq.), an Aracaceae family plant, is utilized for both consumable and non-consumable products, including cooking oil, cosmetics and biodiesel production. Oil palm is a perennial tree with 25 years of optimal harvesting time and a height of up to 18 m. However, harvesting of oil palm fruit bunches with heights of more than 2–3 meters is challenging for oil palm farmers. Thus, understanding the genetic control of height would be beneficial for using gene-based markers to speed up oil palm breeding programs to select semi-dwarf oil palm varieties. This study aims to identify Insertion/Deletions (InDels) and single nucleotide polymorphisms (SNPs) of five height-related genes, including EgDELLA1, EgGRF1, EgGA20ox1, EgAPG1 and EgExp4, in short and tall oil palm groups by PacBio SMRT sequencing technology. Then, the SNP variation’s association with height was validated in the Golden Tenera (GT) population. All targeted genes were successfully amplified by two rounds of PCR amplification with expected sizes that ranged from 2,516 to 3,015 base pair (bp), covering 5′ UTR, gene sequences and 3′ UTR from 20 short and 20 tall oil palm trees. As a result, 1,166, 909, 1,494, 387 and 5,384 full-length genomic DNA sequences were revealed by PacBio SMRT sequencing technology, from EgDELLA1, EgGRF1, EgGA20ox1, EgAPG1 and EgExp4 genes, respectively. Twelve variations, including eight InDels and four SNPs, were identified from EgDELLA1, EgGRF1, EgGA20ox1 and EgExp4. No variation was found for EgAPG1. After SNP through-put genotyping of 4 targeted SNP markers was done by PACE™ SNP genotyping, the association with height was determined in the GT population. Only the mEgExp4_SNP118 marker, designed from EgExp4 gene, was found to associate with height in 2 of 4 height-recordings, with p values of 0.0383 for height (HT)-1 and 0.0263 for HT-4. In conclusion, this marker is a potential gene-based marker that may be used in oil palm breeding programs for selecting semi-dwarf oil palm varieties in the near future. creator: Suthasinee Somyong creator: Phakamas Phetchawang creator: Abdulloh Kafa Bihi creator: Chutima Sonthirod creator: Wasitthee Kongkachana creator: Duangjai Sangsrakru creator: Nukoon Jomchai creator: Wirulda Pootakham creator: Sithichoke Tangphatsornruang uri: https://doi.org/10.7717/peerj.13046 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Somyong et al. title: Skin microbiota diversity among genetically unrelated individuals of Indian origin link: https://peerj.com/articles/13075 last-modified: 2022-03-16 description: BackgroundHuman skin harbors complex transient and resident microbial communities that show intra- & inter-individual variation due to various environmental and host-associated factors such as skin site, diet, age, gender, genetics, or the type and use of cosmetics. This variation remains largely uncharacterized in the Indian population; hence, the present study aims to characterize the variation in skin microbiota among individuals of Indian origin and quantify associations with age, diet, and geography.MethodsAxillary sweat samples from genetically unrelated individuals (N = 58) residing in the three geographical locations of Maharashtra, India, were collected using a sterile cotton swab. Bacterial DNA was extracted using a standard protocol and checked for quality. Variable regions (V3–V4) of the 16S rRNA gene were sequenced using the Illumina platform. We used standard methods from microbiota bioinformatics, including alpha and beta diversity, community typing, and differential abundance, to quantify the association of skin microbiota with age, diet, and geographical location.ResultsOur study indicated the prevalence of phyla- Firmicutes, Proteobacteria, and Actinobacteria, consistent with previous reports on skin microbiota composition of the world population level. The alpha diversity (Shannon index) was significantly associated with the age group (Kruskal–Wallis test, p = 0.02), but not with geography (p = 0.62) or diet (p = 0.74). The overall skin microbiota community composition was significantly associated with geographical location based on Community State Types (CST) analysis and PERMANOVA (R2 = 0.07, p = 0.01). Differential abundance analysis at the genus level indicated a distinctively high abundance of Staphylococcus and Corynebacterium among individuals of the Pune district. Pseudomonas and Anaerococcus were abundant in individuals from Ahmednagar whereas, Paenibacillus, Geobacillus, Virgibacillus, Jeotgalicoccus, Pullulanibacillus, Delsulfosporomusa, Citinovibrio, and Calditerricola were abundant in individuals from Nashik district.ConclusionOur work provides one of the first characterizations of skin microbiota variation in different sub-populations in India. The analysis quantifies the level of individuality, as contrasted to the other factors of age, geography, and diet, thus helping to evaluate the applicability of skin microbiota profiles as a potential biomarker to stratify individuals. creator: Renuka Potbhare creator: Ameeta RaviKumar creator: Eveliina Munukka creator: Leo Lahti creator: Richa Ashma uri: https://doi.org/10.7717/peerj.13075 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Potbhare et al. title: Whole-genome analysis of CGS, SAHH, SAMS gene families in five Rosaceae species and their expression analysis in Pyrus bretschneideri link: https://peerj.com/articles/13086 last-modified: 2022-03-16 description: Cystathionine γ-synthase (CGS), S-adenosyl-L-homocysteine hydrolase (SAHH), and S-adenosy-L-methionine synthetase (SAMS) play an important role in the regulation of plant growth, development, and secondary metabolism. In this study, a total of 6 CGS, 6 SAHH, and 28 SAMS genes were identified from five Rosaceae species (Pyrus bretschneideri, Prunus persica, Prunus mume, Fragaria vesca, and Malus domestica). The evolutionary relationship and microsynteny analysis in five Rosaceae species revealed that duplicated regions were conserved between three gene families (CGS, SAHH, SAMS). Moreover, the chromosomal locations, gene structures, conserved motifs, cis-elements, physicochemical properties, and Ka/Ks analysis were performed by using numerous bioinformatics tools. The expression of different organs showed that the CGS, SAHH and SAMS genes of pear have relatively high expression patterns in flowers and stems, except for PbCGS1. RNA-seq and qRT-PCR combined analysis showed that PbSAMS1 may be involved in the regulation of pear stone cell development. In summary, this study provides the basic information of CGS, SAHH and SAMS genes in five Rosaceae species, further revealing the expression patterns in the pear fruit, which provides the theoretical basis for the regulation of pear stone cells. creator: Yang Zhang creator: Decong Li creator: Xiaofeng Feng creator: Xinya Wang creator: Mengna Wang creator: Wenlong Han creator: Muhammad Aamir Manzoor creator: Guohui Li creator: Tianzhe Chen creator: Han Wang creator: Yongping Cai uri: https://doi.org/10.7717/peerj.13086 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhang et al. title: Identification of potential biomarkers of vascular calcification using bioinformatics analysis and validation in vivo link: https://peerj.com/articles/13138 last-modified: 2022-03-16 description: BackgroundVascular calcification (VC) is the most widespread pathological change in diseases of the vascular system. However, we know poorly about the molecular mechanisms and effective therapeutic approaches of VC.MethodsThe VC dataset, GSE146638, was downloaded from the Gene Expression Omnibus (GEO) database. Using the edgeR package to screen Differentially expressed genes (DEGs). Gene set enrichment analysis (GSEA) and gene set variation analysis (GSVA) were used to find pathways affecting VC. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were performed on the DEGs. Meanwhile, using the String database and Cytoscape software to construct protein-protein interaction (PPI) networks and identify hub genes with the highest module scores. Correlation analysis was performed for hub genes. Receiver operating characteristic (ROC) curves, expression level analysis, GSEA, and subcellular localization were performed for each hub gene. Expression of hub genes in normal and calcified vascular tissues was verified by quantitative reverse transcription PCR (RT-qPCR) and immunohistochemistry (IHC) experiments. The hub gene-related miRNA-mRNA and TF-mRNA networks were constructed and functionally enriched for analysis. Finally, the DGIdb database was utilized to search for alternative drugs targeting VC hub genes.ResultsBy comparing the genes with normal vessels, there were 64 DEGs in mildly calcified vessels and 650 DEGs in severely calcified vessels. Spp1, Sost, Col1a1, Fn1, and Ibsp were central in the progression of the entire VC by the MCODE plug-in. These hub genes are primarily enriched in ossification, extracellular matrix, and ECM-receptor interactions. Expression level results showed that Spp1, Sost, Ibsp, and Fn1 were significantly highly expressed in VC, and Col1a1 was incredibly low. RT-qPCR and IHC validation results were consistent with bioinformatic analysis. We found multiple pathways of hub genes acting in VC and identified 16 targeting drugs.ConclusionsThis study perfected the molecular regulatory mechanism of VC. Our results indicated that Spp1, Sost, Col1a1, Fn1, and Ibsp could be potential novel biomarkers for VC and promising therapeutic targets. creator: Chuanzhen Chen creator: Yinteng Wu creator: Hai-lin Lu creator: Kai Liu creator: Xiao Qin uri: https://doi.org/10.7717/peerj.13138 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Chen et al. title: Study on the differences of phyllosphere microorganisms between poplar hybrid offspring and their parents link: https://peerj.com/articles/12915 last-modified: 2022-03-15 description: The females and males of dioecious plants have evolved sex-specific characteristics in terms of their morphological and physiological properties. However, the differentiation of phyllosphere microorganism of dioecious plants between parents and hybrid offspring remain largely unexplored. Here, the phyllosphere bacterial and fungal community diversity and composition of female (Populus nigra ‘DH5’ (PNDH5)), male (P. simonii ‘DH4’ (PSDH4)), and the hybrid offspring (P. simonii × P. nigra ‘DH1’ (PSPNDH1), P. simonii × P. nigra ‘DH2’ (PSPNDH2), P. simonii × P. nigra ‘DH3’ (PSPNDH3)) were investigated using 16S rDNA/ITS rDNA gene-based Illumina NovaSeq 6000 sequencing. There was considerable variation of plant height, diameter at breast height, leaf area, length of petioles, leaf moisture content, and starch among different samples, and PSDH2 owned the highest plant height, diameter at breast height, and length of petioles. No distinct differences of phyllosphere bacterial community diversity were observed among PSDH4, PNDH5, PSPNDH1, PSPNDH2, and PSPNDH3; while, PSPNDH2 owned the highest fungal Pielou_e index, Shannon index, and Simpson index. Firmicutes and Ascomycota were the predominant phyllosphere bacterial and fungal community at the phylum level, respectively. Bacilli and Gammaproteobacteria were the two most dominant bacterial classes regardless of parent and the hybrid offspring. The predominant phyllosphere fungal community was Dothideomycetes at the class level. The NMDS demonstrated that phyllosphere microbial community obviously differed between parents and offspring, while the phyllosphere microbial community presented some similarities under different hybrid progeny. Also, leaf characteristics contributed to the differentiation of phyllosphere bacterial and fungal communities between parents and hybrid offspring. These results highlighted the discrimination of phyllosphere microorganisms on parent and hybrid offspring, which provided clues to potential host-related species in the phyllosphere environment. creator: Changjun Ding creator: Weixi Zhang creator: Yanbo Wang creator: Mi Ding creator: Xiaojiang Wang creator: Aiping Li creator: Dejun Liang creator: Xiaohua Su uri: https://doi.org/10.7717/peerj.12915 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Ding et al. title: CIAlign: A highly customisable command line tool to clean, interpret and visualise multiple sequence alignments link: https://peerj.com/articles/12983 last-modified: 2022-03-15 description: BackgroundThroughout biology, multiple sequence alignments (MSAs) form the basis of much investigation into biological features and relationships. These alignments are at the heart of many bioinformatics analyses. However, sequences in MSAs are often incomplete or very divergent, which can lead to poor alignment and large gaps. This slows down computation and can impact conclusions without being biologically relevant. Cleaning the alignment by removing common issues such as gaps, divergent sequences, large insertions and deletions and poorly aligned sequence ends can substantially improve analyses. Manual editing of MSAs is very widespread but is time-consuming and difficult to reproduce.ResultsWe present a comprehensive, user-friendly MSA trimming tool with multiple visualisation options. Our highly customisable command line tool aims to give intervention power to the user by offering various options, and outputs graphical representations of the alignment before and after processing to give the user a clear overview of what has been removed. The main functionalities of the tool include removing regions of low coverage due to insertions, removing gaps, cropping poorly aligned sequence ends and removing sequences that are too divergent or too short. The thresholds for each function can be specified by the user and parameters can be adjusted to each individual MSA. CIAlign is designed with an emphasis on solving specific and common alignment problems and on providing transparency to the user.ConclusionCIAlign effectively removes problematic regions and sequences from MSAs and provides novel visualisation options. This tool can be used to fine-tune alignments for further analysis and processing. The tool is aimed at anyone who wishes to automatically clean up parts of an MSA and those requiring a new, accessible way of visualising large MSAs. creator: Charlotte Tumescheit creator: Andrew E. Firth creator: Katherine Brown uri: https://doi.org/10.7717/peerj.12983 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Tumescheit et al. title: Diegoaelurus, a new machaeroidine (Oxyaenidae) from the Santiago Formation (late Uintan) of southern California and the relationships of Machaeroidinae, the oldest group of sabertooth mammals link: https://peerj.com/articles/13032 last-modified: 2022-03-15 description: Machaeroidinae is a taxonomically small clade of early and middle Eocene carnivorous mammals that includes the earliest known saber-toothed mammalian carnivores. Machaeroidine diversity is low, with only a handful of species described from North America and Asia. Here we report a new genus and species of machaeroidine, Diegoaelurus vanvalkenburghae, established on the basis of a nearly complete dentary with most of the dentition from the late Uintan (middle Eocene) portion of the Santiago Formation of southern California. The new taxon is the youngest known machaeroidine and provides the first evidence for the presence of multiple machaeroidine lineages, as it differs substantially from Apataelurus kayi, the only near-contemporaneous member of the group. Phylogenetic analysis indicates that Diegoaelurus is the sister taxon of Apataelurus, while older species are recovered as a monophyletic Machaeroides. Both phylogenetic results are relatively weakly supported. The new taxon extends the record of machaeroidines to the end of the Uintan, potentially tying machaeroidine extinction to the faunal turnover spanning the middle to late Eocene transition in North America. creator: Shawn P. Zack creator: Ashley W. Poust creator: Hugh Wagner uri: https://doi.org/10.7717/peerj.13032 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zack et al. title: Spinal-pelvic sagittal parameters in patients with gluteal muscle contracture: an imaging study link: https://peerj.com/articles/13093 last-modified: 2022-03-15 description: BackgroundGluteal muscle contracture (GMC) may cause abnormal spinal alignment as well as hip and pelvic deformities. The spine-pelvis alignment of GMC patients is unclear. This study aimed to describe the spine-pelvis sagittal alignment in patients with GMC and to explore the impact of GMC on the pathogenesis of low back pain (LBP).MethodsRadiological analysis was performed in 100 patients with GMC and 100 asymptomatic volunteers who acted as the control group. Sagittal parameters were measured by two independent raters and their averages were presented on lateral radiographs of the whole spine, including pelvic incidence (PI), sagittal vertical axis (SVA), pelvic tilt (PT), lumbar lordosis (LL), sacral slope (SS), thoracic kyphosis (TK), and the relationship between PI and LL (expressed as PI-LL). All cases were categorized into one of three classes based on the apex position of lumbar lordosis and were further divided into three groups by the PI value. The GMC and control parameters were compared and the correlations between the parameters in the GMC group were analysed.ResultsThe PI value of the GMC group was significantly less than that of the control group (42.38 ± 10.90° vs 45.68 ± 7.49°, P < 0.05). There was no difference found between the key parameters (SVA, PT, and PI-LL), which correlated with outcomes in adult deformity. No differences of SS were found between the two groups (P > 0.05). The GMC group showed lower average LL (42.77 ± 10.97° vs 46.41 ± 9.07°) and TK (17.34 ± 9.50° vs 20.45 ± 8.02°) compared with the control group (P < 0.05). LL was correlated with PI, SS, PT, TK (P < 0.01) and SVA (P < 0.05). TK and SVA were not correlated with any parameters except LL and pairwise correlations were found among PI, SS, and PT. There were no differences found between the distributions of the lumbar lordosis apex of GMC and the control but the range of SS in apex groups 3 and 4 did differ. GMC patients had the most small-PI value (44%) while approximately 64% of asymptomatic individuals had a normal PI. Interobserver variability was sufficient for all parameters calculated by the intraclass correlation coefficient (ICC).ConclusionsGluteal muscle contracture causes a low PI which may contribute to low back pain. Patients with GMC present the same global sagittal spinal-pelvic balance as asymptomatic individuals due to a compensatory mechanism through excessive flat lumbar and thoracic curves. Future studies on the relationship between spinal-pelvic sagittal and coronal alignment and low back pain are needed to understand the mechanical forces involved in the onset of GMC. creator: Jiyi Liu creator: Pengzhou Huang creator: Guanwei Jiang creator: Liang Gao creator: Mengdi Zhang creator: Xueping Dong creator: Wentao Zhang creator: Xintao Zhang uri: https://doi.org/10.7717/peerj.13093 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Liu et al. title: Freeze-drying can replace cold-chains for transport and storage of fecal microbiome samples link: https://peerj.com/articles/13095 last-modified: 2022-03-15 description: BackgroundThe transport and storage of samples in temperatures of minus 80 °C is commonly considered as the gold standard for microbiome studies. However, studies conducting sample collection at remote sites without a reliable cold-chain would benefit from a sample preservation method that allows transport and storage at ambient temperature.MethodsIn this study we compare alpha diversity and 16S microbiome composition of 20 fecal sample replicates from Damaraland mole-rats (Fukomys damarensis) preserved in a minus 80 °C freezer and transported on dry ice to freeze-dried samples that were stored and transported in ambient temperature until DNA extraction.ResultsWe found strong correlations between relative abundances of Amplicon Sequence Variants (ASVs) between preservation treatments of the sample, no differences in alpha diversity measures between the two preservation treatments and minor effects of the preservation treatment on beta diversity measures. Our results show that freeze-drying samples can be a useful method for cost-effective transportation and storage of microbiome samples that yields quantitatively almost indistinguishable results in 16S microbiome analyses as those stored in minus 80 °C. creator: Hanna M. Bensch creator: Conny Tolf creator: Jonas Waldenström creator: Daniel Lundin creator: Markus Zöttl uri: https://doi.org/10.7717/peerj.13095 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Bensch et al. title: Predicting population: development and validation of a new predictive nomogram for evaluating medication nonadherence risk in a type 2 diabetes link: https://peerj.com/articles/13102 last-modified: 2022-03-15 description: BackgroundDiabetes mellitus is a growing global health challenge and affects patients of all ages. Treatment aims to keep blood glucose levels close to normal and to prevent or delay complications. However, adherence to antidiabetic medicines is often unsatisfactory.PurposeHere, we established and internally validated a medication nonadherence risk nomogram for use in Chinese type 2 diabetes mellitus (T2DM) patients.MethodsThis cross-sectional study was carried out from July–December 2020 on randomly selected T2DM patients visiting a diabetes clinic and included 753 participants. Adherence was analyzed based on an eight-item Morisky Medication Adherence Scale (MMAS-8). Other data, including patient demographics, treatment, complications, and comorbidities, were also collected on questionnaires. Optimization of feature selection to develop the medication nonadherence risk model was achieved using the least absolute shrinkage and selection operator regression model (LASSO). A prediction model comprising features selected from LASSO model was designed by applying multivariable logistic regression analysis. The decision curve analysis, calibration plot, and C-index were utilized to assess the performance of the model in terms of discrimination, calibration, and clinical usefulness. Bootstrapping validation was applied for internal validation.ResultsThe prediction nomogram comprised several factors including sex, marital status, education level, employment, distance, self-monitoringofbloodglucose, disease duration, and dosing frequency of daily hypoglycemics (pills, insulin, or glucagon-like peptide-1). The model exhibited good calibration and good discrimination (C-index = 0.79, 95% CI [0.75–0.83]). In the validation samples, a high C-index (0.75) was achieved. Results of the decision curve analysis revealed that the nonadherence nomogram could be applied in clinical practice in cases where the intervention is decided at a nonadherence possibility threshold of 12%.ConclusionThe number of patients who adhere to anti-diabetes therapy was small. Being single male, having no formal education, employed, far from hospital, long disease duration, and taking antidiabetics twice or thrice daily, had significant negative correlation with medication adherence. Thus, strategies for improving adherence are urgently needed. creator: NaRen QiMuge creator: Xu Fang creator: Baocheng Chang creator: Dong Mei Li creator: Yuanyuan Li uri: https://doi.org/10.7717/peerj.13102 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 QiMuge et al. title: Biochemical analysis of collagens from the bone of lizardfish (Saurida tumbil Bloch, 1795) extracted with different acids link: https://peerj.com/articles/13103 last-modified: 2022-03-15 description: BackgroundLizardfish (Saurida tumbil Bloch, 1795) bone is a fish by-product generated during industrial surimi processing. This by-product is an important source of collagen production since the use of terrestrial animal-based collagens no longer sought due to concern regarding the transfer of infectious diseases and religious issues. Hence, this study was carried out to determine the biochemical analysis of collagens from the bone of lizardfish extracted with different acids.MethodsLizardfish bone collagens were extracted with various acids (i.e., acetic, lactic and citric acids). All extraction processes were conducted in a chiller room (4 °C). The extracted collagens were biochemically characterized, such as hydroxyproline content, Ultraviolet (UV) absorption, X-ray diffraction (XRD), Fourier transform infrared spectroscopy spectra (FTIR), Differential scanning calorimetry (DSC) and solubility in different pH values and NaCl concentrations.ResultsThe yield of extracted collagens ranged between 1.73% and 2.59%, with the highest (p < 0.05) observed in citric acid-extracted collagen (CaEC). Protein patterns confirmed that all-collagen samples had two identical subunits, α1 and α2, representing type I collagen. The highest whiteness value was found in acetic acid-extracted collagen (AaEC), but there was no significant difference (p ≥ 0.05) compared to lactic acid-extracted collagen (LaEC). UV absorption and XRD analysis reflected the characteristics of the collagen, as reported in the literature. For the FTIR, all acid-extracted collagen samples presented a triple helical structure. The thermal transition temperature (Tmax = 77.92–89.04 °C) was in accordance with collagen extracted from other fish species. All extracted collagens were highly soluble in acidic pH and low concentrations of NaCl (0–20 g/L). In conclusion, collagens extracted from lizardfish bone may be used as alternative sources of collagen in industrial settings, and AaEC would be considered superior in terms of the characteristics evaluated in this study. creator: Abdul Aziz Jaziri creator: Rossita Shapawi creator: Ruzaidi Azli Mohd Mokhtar creator: Wan Norhana Md. Noordin creator: Nurul Huda uri: https://doi.org/10.7717/peerj.13103 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Jaziri et al. title: Spring diet and energy intake of tundra swan (Cygnus columbianus) at the Yellow River National Wetland in Baotou, China link: https://peerj.com/articles/13113 last-modified: 2022-03-15 description: The Yellow River National Wetland in Baotou, China is an important resting and energy replenishment place for many migratory birds, such as tundra swan (Cygnus columbianus). The energy supply of food available at stopover sites plays an important role in the life cycle of migratory birds. In order to understand diet composition and energy supply of tundra swans for further protection of them, in this study, fecal of tundra swans (C. columbianus) were collected and fecal microhistological analysis was conducted to analyze the feeding habits and the energy supply. Results showed that: (1) tundra swans (C. columbianus) mainly fed on twelve species of plants from five families, including corn (Zea mays), quinoa (Chenopodium album) and rice (Oryza sativa), this is related to local crops and abundant plants. (2) The energy provided by crops to tundra swans (C. columbianus) was significantly higher than other abundant plants in wetlands (P < 0.05), corn and rice were the most consumed food, and other abundant wetland plants play complementary roles. (3) The daily energy intake of tundra swans (C. columbianus) was much higher than their daily energy consumption, the daily net energy intake of tundra swans (C. columbianus) was 855.51 ± 182.88 kJ (mean ± standard deviations). This suggested that the wetland provides energy for continue migrating to the tundra swan (C. columbianus). For further protection of tundra swans (C. columbianus) and other migratory birds, the Baotou Yellow River National Wetland environment and the surrounding farmland habitat should be protected. creator: Li Liu creator: Chao Du creator: Yan Sun creator: Wenjing Li creator: Jiyun Zhang creator: Litong Cao creator: Li Gao uri: https://doi.org/10.7717/peerj.13113 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Liu et al. title: Geomorphically controlled coral distribution in degraded shallow reefs of the Western Caribbean link: https://peerj.com/articles/12590 last-modified: 2022-03-14 description: The development of coral reefs results from the interaction between ecological and geological processes in space and time. Their difference in scale, however, makes it difficult to detect the impact of ecological changes on geological reef development. The decline of coral cover over the last 50 years, for example, has dramatically impaired the function of ecological processes on reefs. Yet given the limited-resolution of their Holocene record, it is uncertain how this will impact accretion and structural integrity over longer timescales. In addition, reports of this ecological decline have focused on intrinsic parameters such as coral cover and colony size at the expense of extrinsic ones such as geomorphic and environmental variables. Despite these problems, several attempts have been made to predict the long-term accretion status of reefs based entirely on the contemporary health status of benthic communities. Here we explore how this ecological decline is represented within the reef geomorphic structure, which represents the long-term expression of reef development. Using a detailed geomorphic zonation scheme, we analyze the distribution and biodiversity of reef-building corals in fringing-reef systems of the Mesoamerican Reef tract. We find a depth-related pattern in community structure which shows that the relative species distribution between geomorphic zones is statistically different. Despite these differences, contemporary coral assemblages in all zones are dominated by the same group of pioneer generalist species. These findings imply that first, coral species distribution is still controlled by extrinsic processes that generate the geomorphic zonation; second, that coral biodiversity still reflects species zonation patterns reported by early studies; and third that dominance of pioneer species implies that modern coral assemblages are in a prolonged post-disturbance adjustment stage. In conclusion, any accurate assessment of the future viability of reefs requires a consideration of the geomorphic context or risks miscalculating the impact of ecological changes on long-term reef development. creator: Alexis Enrique Medina-Valmaseda creator: Paul Blanchon creator: Lorenzo Alvarez-Filip creator: Esmeralda Pérez-Cervantes uri: https://doi.org/10.7717/peerj.12590 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Medina-Valmaseda et al. title: Identification of key microorganisms in facultative stabilization ponds from dairy industries, using metagenomics link: https://peerj.com/articles/12772 last-modified: 2022-03-14 description: Wastewater stabilization ponds are a natural form of wastewater treatment. Their low operation and maintenance costs have made them popular, especially in developing countries. In these systems, effluents are retained for long periods of time, allowing the microbial communities present in the ponds to degrade the organic matter present, using both aerobic and anaerobic processes. Even though these systems are widespread in low income countries, there are no studies about the microorganisms present in them and how they operate. In this study, we analised the microbial communities of two serial full-scale stabilization ponds systems using whole genome shotgun sequencing. First, a taxonomic profiling of the reads was performed, to estimate the microbial diversity. Then, the reads of each system were assembled and binned, allowing the reconstruction of 110 microbial genomes. A functional analysis of the genomes allowed us to find how the main metabolic pathways are carried out, and we propose several organisms that would be key to this kind of environment, since they play an important role in these metabolic pathways. This study represents the first genome-centred approach to understand the metabolic processes in facultative ponds. A better understanding of these microbial communities and how they stabilize the effluents of dairy industries is necessary to improve them and to minimize the environmental impact of dairy industries wastewater. creator: Jose M. Irazoqui creator: Maria F. Eberhardt creator: Maria M. Adjad creator: Ariel F. Amadio uri: https://doi.org/10.7717/peerj.12772 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Irazoqui et al. title: PhosVarDeep: deep-learning based prediction of phospho-variants using sequence information link: https://peerj.com/articles/12847 last-modified: 2022-03-14 description: Human DNA sequencing has revealed numerous single nucleotide variants associated with complex diseases. Researchers have shown that these variants have potential effects on protein function, one of which is to disrupt protein phosphorylation. Based on conventional machine learning algorithms, several computational methods for predicting phospho-variants have been developed, but their performance still leaves considerable room for improvement. In recent years, deep learning has been successfully applied in biological sequence analysis with its efficient sequence pattern learning ability, which provides a powerful tool for improving phospho-variant prediction based on protein sequence information. In the study, we present PhosVarDeep, a novel unified deep-learning framework for phospho-variant prediction. PhosVarDeep takes reference and variant sequences as inputs and adopts a Siamese-like CNN architecture containing two identical subnetworks and a prediction module. In each subnetwork, general phosphorylation sequence features are extracted by a pre-trained sequence feature encoding network and then fed into a CNN module for capturing variant-aware phosphorylation sequence features. After that, a prediction module is introduced to integrate the outputs of the two subnetworks and generate the prediction results of phospho-variants. Comprehensive experimental results on phospho-variant data demonstrates that our method significantly improves the prediction performance of phospho-variants and compares favorably with existing conventional machine learning methods. creator: Xia Liu creator: Minghui Wang creator: Ao Li uri: https://doi.org/10.7717/peerj.12847 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Liu et al. title: Textural quality, growth parameters and oxidative responses in Nile tilapia (Oreochromis niloticus) fed faba bean water extract diet link: https://peerj.com/articles/13048 last-modified: 2022-03-14 description: Texture is one of the key quality attributes used in the fresh and processed fish industry to assess product quality and consumer acceptability. To improve the textural quality of tilapia, we formulated the expanded pellet diet (EPD) and pellet diet (PD), both containing faba bean (Vicia faba, FB) water extract, a previously reported potential aquafeed additive to increase flesh texture. The common diet was used as a control. After Nile tilapia (Oreochromis niloticus) were fed three kinds of experimental diet for 120 days, muscle textural quality, growth parameters, oxidative response and immune parameters were analyzed. The results showed that there was no significant difference in the growth parameters between the three groups (P > 0.05). The highest measure of textural quality (hardness and chewiness) was found for the PD group, followed by the EPD and the control (P < 0.05). Less oxidative damage to the hepatopancreas and intestine was found in the EPD compared with the PD group, as demonstrated by the decreased levels of reactive oxygen species and increased levels of nicotinamide adenine dinucleotide and intestinal digestive enzyme activity (amylase and lipase). Taken together, this study highlights the potential usefulness in commercial settings of FB water extract for improving the textural quality of tilapia, and EPD containing faba bean water extract could be more advanced substitute for faba bean in tilapia culture in term of both effectiveness in textural quality improvement and health status enhancement compared with PD. creator: Yichao Li creator: Junming Zhang creator: Bing Fu creator: Jun Xie creator: Guangjun Wang creator: Jingjing Tian creator: Yun Xia creator: Ermeng Yu uri: https://doi.org/10.7717/peerj.13048 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Li et al. title: Full vaccination coverage and associated factors among children aged 12 to 23 months in remote rural area of Demba Gofa District, Southern Ethiopia link: https://peerj.com/articles/13081 last-modified: 2022-03-14 description: BackgroundFull vaccination refers to the administration of vaccines/antigens recommended for children in the first year of life. However, little is known about full vaccination in remote, rural Ethiopia. This study aimed to measure full vaccination coverage and associated factors among children aged 12 to 23 months in Demba Gofa District, Southern Ethiopia.MethodsA community-based cross-sectional study was conducted in April and May 2019 using a multistage sampling technique to select 677 mothers with children 12–23 months of age. Data was collected using a pre-tested structured questionnaire, and data were edited, coded, entered, and cleaned using Epi Info v3.1 and analyzed using SPSS v20. Bivariate and multivariable logistic regression was used to understand associations between dependent and independent variables.ResultsThree-hundred and nine children (47.0%) were fully vaccinated, 274 (41.7%) were partially vaccinated, and 74 (11.3%) were not vaccinated at all. Children were more likely to be vaccinated if decisions were made jointly with husbands (AOR = 1.88, 95% CI [1.06–3.34]), were made by mothers (AOR = 4.03, 95% CI [1.66–9.78]), followed postnatal care (AOR = 5.02, 95% CI [2.28–11.05]), if the child’s age for completing vaccination was known (AOR = 2.54, 95% CI [1.04–6.23]), and if vaccinations did not make the child sick (AOR = 0.32, 95% CI [0.16–0.64]).ConclusionFull vaccination coverage was less than average in the study district and far below the governmental target (90%) necessary for sustained control of vaccine-preventable diseases. Interventions targeted towards maternal healthcare decision-making, postnatal care, knowledge on vaccination timing, and importance should be prioritized to improve full vaccination coverage. A continuous supply of vaccination cards needs to be ensured to improve vaccination conditions. creator: Tadele Dana Darebo creator: Bahru Belachew Oshe creator: Chala Wegi Diro uri: https://doi.org/10.7717/peerj.13081 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Darebo et al. title: 3,4-dihydroxyphenylethyl alcohol glycoside reduces acetaminophen-induced acute liver failure in mice by inhibiting hepatocyte ferroptosis and pyroptosis link: https://peerj.com/articles/13082 last-modified: 2022-03-14 description: APAP is one of the most commonly used antipyretic and pain medications, but excessive use can cause liver toxicity and damage. 3,4-dihydroxyphenylethyl alcohol glycoside (DAG) is a component isolated from Sargentodoxa cuneata known to have anti-apoptotic, anti-oxidation and anti-inflammatory effects. However, the effects of DAG on acute liver failure (ALF) are largely unknown. The purpose of this study is to study the protective effects and mechanism of DAG on APAP-induced ALF in mice. We established an ALF model in adult male pathogen-free C57BL/6 mice treated with APAP (300 mg/kg) by intraperitoneal injection and resolved by 24 h. Hematoxylin and eosin (HE) staining was used to evaluate the pathological changes in mouse liver tissue. The infiltration of neutrophils in liver tissue and reactive oxygen species (ROS) in AML12 cells were analyzed by flow cytometry. The levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST), glutathione (GSH), malondialdehyde (MDA), catalase (CAT), and superoxide dismutase (SOD) were analyzed using relevant kits. Our results show that DAG reduced APAP-induced serum ALT and AST levels, histopathological changes, liver neutrophil infiltration and proinflammatory cytokines production, also attenuated the accumulation of MDA and the exhaustion of GSH, CAT and SOD. In vitro experiment indicated that DAG dose-dependently inhibited APAP-induced the levels of pro-inflammatory factors (IL-1β and IL18), and reactive oxygen species (ROS) and preventing GSH depletion in mouse AML12 hepatocytes. More interestingly, DAG inhibited the expression of ERK, HO-1, NLRP3, Caspase1 (p20) and Gasdermin-D and upregulated the expression of GPX4 in liver tissues and AML12hepatocytes. Therefore, our results indicate that DAG may act as a potential agent to treat ALF induced by APAP by inhibiting hepatocyte ferroptosis and pyroptosis. creator: Tianyu Liu creator: Lei Yang creator: Hejun Gao creator: Yuzhen Zhuo creator: Zhengwei Tu creator: Yongqin Wang creator: Jing Xun creator: Qi Zhang creator: Lanqiu Zhang creator: Ximo Wang uri: https://doi.org/10.7717/peerj.13082 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Liu et al. title: The application of sudoscan for screening microvascular complications in patients with type 2 diabetes link: https://peerj.com/articles/13089 last-modified: 2022-03-14 description: The aim of the study was to evaluate the performance of sudoscan in screening diabetic microvascular complications in patients with type 2 diabete mellitus (T2DM). 515 patients with T2DM aged from 23 to 89 years were included for analysis in our study. The mean age was 60.00 ± 11.37 years and the mean duration of T2DM was 8.44 ± 7.56 years. Electrochemical skin conductance (ESC) in hands and feet was evaluated by SUDOCAN. Diabetic peripheral neuropathy (DPN) was diagnosed in 378 patients (44.3%), diabetic kidney disease (DKD) in 161 patients (31.26%), diabetic retinopathy (DR) in 148 patients (28.74%). Hands and feet ESC was significantly and independently associated with the presence of DPN, DKD and DR. Patients with a lower ESC (<60 µS) had 5.63-fold increased likelihood of having DPN, 4.90-fold increased likelihood of having DKD, 1.01-fold increased likelihood of having DR, than those with a higher ESC. Age, duration of T2DM, smoking, renal function and vibration perception thresholds were negatively correlated with ESC. Sudoscan parameters were correlated with diabetic microvascular complications, especially with DPN. Sudoscan could be an effective screening tool in primary health care for early screening microvascular complications. creator: Kun Lin creator: Yixi Wu creator: Shuo Liu creator: Jiaqi Huang creator: Guishan Chen creator: Qiong Zeng uri: https://doi.org/10.7717/peerj.13089 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Lin et al. title: Integration of the metabolome and transcriptome reveals indigo biosynthesis in Phaius flavus flowers under freezing treatment link: https://peerj.com/articles/13106 last-modified: 2022-03-14 description: BackgroundIndigo-containing plant tissues change blue after a freezing treatment, which is accompanied by changes in indigo and its related compounds. Phaius flavus is one of the few monocot plants containing indigo. The change to blue after freezing was described to explore the biosynthesis of indigo in P. flavus.MethodsIn this study, we surveyed the dynamic change of P. flavus flower metabolomics and transcriptomics.ResultsThe non-targeted metabolomics and targeted metabolomics results revealed a total of 98 different metabolites, the contents of indole, indican, indigo, and indirubin were significantly different after the change to blue from the freezing treatment. A transcriptome analysis screened ten different genes related to indigo upstream biosynthesis, including three anthranilate synthase genes, two phosphoribosyl-anthranilate isomerase genes, one indole-3-glycerolphosphate synthase gene, five tryptophan synthase genes. In addition, we further candidate 37 cytochrome P450 enzyme genes, one uridine diphosphate glucosyltransferase gene, and 24 β-D-glucosidase genes were screened that may have participated in the downstream biosynthesis of indigo. This study explained the changes of indigo-related compounds at the metabolic level and gene expression level during the process of P. flavus under freezing and provided new insights for increasing the production of indigo-related compounds in P. flavus. In addition, transcriptome sequencing provides the basis for functional verification of the indigo biosynthesis key genes in P. flavus. creator: Yi-Ming Zhang creator: Yong Su creator: Zhong-wu Dai creator: Meng Lu creator: Wei Sun creator: Wei Yang creator: Sha-Sha Wu creator: Zhi-Ting Wan creator: Hui-Hua Wan creator: Junwen Zhai uri: https://doi.org/10.7717/peerj.13106 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhang et al. title: A review of the opportunities to support pollinator populations in South African cities link: https://peerj.com/articles/12788 last-modified: 2022-03-11 description: Globally insects are declining, but some guilds of pollinators are finding refuge in urban landscapes. The body of knowledge on urban pollinators is relatively mature, which means it is now possible to begin to make generalization. Unfortunately, studies do not represent climatic regions evenly and there is a gap in research from the African continent. This study aimed to address some of the gaps on urban pollination knowledge in South Africa and to identify opportunities to improve urban habitats for pollinators. We reviewed the international literature on urban pollinators and the South African literature on pollinators with a landscape ecology focus, drawing on literature with an emphasis on agricultural and ecosystem services. The findings show that some taxa (e.g. large-bodied, cavity nesting bees) will exploit urban environments increasing in abundance with urban intensity. Moderately sensitive taxa (such as small-bodied, ground-nesting bees) take advantage of urban environments only if local habitats are supportive of their needs for resource provision and habitat connectivity. The South African urban poor rely on pollination services for subsistence agriculture and the reproduction of wild-foraged medicines and food. Potential interventions to improve habitat quality include strategic mowing practices, conversion of turf-grass to floral rich habitats, scientific confirmation of lists of highly attractive flowers, and inclusion of small-scale flower patches throughout the urban matrix. Further research is needed to fill the Africa gap for both specialized and generalized pollinators (Diptera, Halictids, Lepidoptera and Hopliini) in urban areas where ornamental and indigenous flowering plants are valued. creator: Peta Brom creator: Les G. Underhill creator: Kevin Winter uri: https://doi.org/10.7717/peerj.12788 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Brom et al. title: Evolution analysis of FRIZZY PANICLE (FZP) orthologs explored the mutations in DNA coding sequences in the grass family (Poaceae) link: https://peerj.com/articles/12880 last-modified: 2022-03-11 description: FRIZZY PANICLE (FZP), an essential gene that controls spikelet differentiation and development in the grass family (Poaceae), prevents the formation of axillary bud meristems and is closely associated with crop yields. It is unclear whether the FZP gene or its orthologs were selected during the evolutionary process of grass species, which possess diverse spike morphologies. In the present study, we adopted bioinformatics methods for the evolutionary analysis of FZP orthologs in species of the grass family. Thirty-five orthologs with protein sequences identical to that of the FZP gene were identified from 29 grass species. Analysis of conserved domains revealed that the AP2/ERF domains were highly conserved with almost no amino acid mutations. However, species of the tribe Triticeae, genus Oryza, and C4 plants exhibited more significant amino acid mutations in the acidic C-terminus region. Results of the phylogenetic analysis showed that the 29 grass species could be classified into three groups, namely, Triticeae, Oryza, and C4 plants. Within the Triticeae group, the FZP genes originating from the same genome were classified into the same sub-group. When selection pressure analysis was performed, significant positive selection sites were detected in species of the Triticeae and Oryza groups. Our results show that the FZP gene was selected during the grass family’s evolutionary process, and functional divergence may have already occurred among the various species. Therefore, researchers investigating the FZP gene’s functions should take note of the possible presence of various roles in other grass species. creator: Jia Li creator: Litian Zhang creator: Rania G. Elbaiomy creator: Lilan Chen creator: Zhenrong Wang creator: Jie Jiao creator: Jiliang Zhu creator: Wanhai Zhou creator: Bo Chen creator: Salma A. Soaud creator: Manzar Abbas creator: Na Lin creator: Ahmed H. El-Sappah uri: https://doi.org/10.7717/peerj.12880 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Li et al. title: Antimicrobial resistance and virulence profiles of Enterobacterales isolated from two-finger and three-finger sloths (Choloepus hoffmanni and Bradypus variegatus) of Costa Rica link: https://peerj.com/articles/12911 last-modified: 2022-03-11 description: BackgroundWildlife has been recently recognized as an environmental reservoir for antimicrobial resistance (AMR). However, less information on this topic is available in animals released back into the wild after rehabilitation in wildlife facilities, compared with studies performed exclusively in captive or free-ranging wildlife. This study aimed to evaluate the potential influence of captivity and/or treatment while in captivity of wild sloths on the AMR and virulence profiles of sloths’ Enterobacterales.MethodsOral and rectal swab samples were collected from 39 two-finger (Choloepus hoffmanni) and three-finger sloths (Bradypus variegatus) of Costa Rica (n = 78) and analyzed using conventional bacteriological techniques. A generalized linear mixed model was applied to estimate the isolates’ multiple antimicrobial resistance and virulence indices as a function of animal status.ResultsA considerable level of resistance was detected, especially for Citrobacter youngae and Escherichia coli, with 17.5% of isolates classified as multidrug-resistant. Virulence indices of isolates from rehabilitated sloths were significantly higher than the ones from sloths being hand-reared for shorter periods.ConclusionsTo our knowledge, this is the first description of sloths’ antimicrobial resistant Enterobacterales, suggesting that sloths’ rehabilitation and consequent exposure to humans, may promote the selection of bacteria with higher virulence. Ultimately, these bacteria may represent a threat to human and animal health due to their zoonotic potential and AMR and virulence profiles. creator: Matilde Fernandes creator: Carla Nóbrega Carneiro creator: Ana Maria Villada Rosales creator: Miguel Grilo creator: Yolanda Ramiro creator: Eva Cunha creator: Telmo Nunes creator: Luís Tavares creator: Janet Sandi creator: Manuela Oliveira uri: https://doi.org/10.7717/peerj.12911 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Fernandes et al. title: The evolution of reproductive strategies in turtles link: https://peerj.com/articles/13014 last-modified: 2022-03-11 description: Optimal egg size theory assumes that changes in the egg and clutch are driven by selection, resulting in adjustments for the largest possible production of offspring with the highest fitness. Evidence supports the idea that large-bodied turtles tend to produce larger clutches with small and round eggs, while smaller species produce small clutches with large and elongated eggs. Our goals were to investigate whether egg and clutch size follow the predictions of egg size theory, if there are convergent reproductive strategies, and identify ecological factors that influence clutch and egg traits across all clades of living turtles. Using phylogenetic methods, we tested the covariance among reproductive traits, if they are convergent among different turtle lineages, and which ecological factors influence these traits. We found that both egg shape and size inversely correlate with clutch size, although with different evolutionary rates, following the predictions of the egg size theory. We also present compelling evidence for convergence among different turtle clades, over at least two reproductive strategies. Furthermore, climatic zone is the only ecological predictor to influence both egg size and fecundity, while diet only influences egg size. We conclude that egg and clutch traits in Testudines evolved independently several times across non-directly related clades that converged to similar reproductive strategies. Egg and clutch characteristics follow the trade-offs predicted by egg size theory and are influenced by ecological factors. Climatic zone and diet play an important role in the distribution of reproductive characteristics among turtles. creator: Gabriel Jorgewich-Cohen creator: Rafael S. Henrique creator: Pedro Henrique Dias creator: Marcelo R. Sánchez-Villagra uri: https://doi.org/10.7717/peerj.13014 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Jorgewich-Cohen et al. title: UAV spraying on citrus crop: impact of tank-mix adjuvant on the contact angle and droplet distribution link: https://peerj.com/articles/13064 last-modified: 2022-03-11 description: Adding tank-mix adjuvants into the spray mixture is a common practice to improve droplet distribution for field crops (e.g., rice, wheat, corn, etc.) when using Unmanned Aerial Vehicle (UAV) sprayers. However, the effectiveness of tank-mix adjuvant for UAV spraying in orchard crops is still an open problem, considering their special canopy structure and leaf features. This study aims to evaluate the effects of a typical tank-mix adjuvant concentrations (i.e., Nong Jian Fei (NJF)) on Contact Angle (CA) and droplet distribution in the citrus tree canopy. Three commonly used parameters, namely dynamic CA, droplet coverage, and Volume Median Diameter (VMD), are adopted for performance evaluation. The dynamic CAs on the adaxial surface of citrus leaves, for water-only and NJF-presence sprays, respectively, are measured with five concentration levels, where three replications are performed for each concentration. The sprays with 0.5‰ NJF are adopted in the field experiment for evaluating droplet distributions, where Water Sensitive Papers (WSPs) are used as collectors. Two multi-rotor UAVs (DJI T20 and T30) which consist of different sizes of pesticide tanks and rotor diameters are used as the spraying platforms. Both water-only and NJF-presence treatments are conducted for the two UAVs, respectively. The results of the CA experiment show that NJF addition can significantly reduce the CAs of the sprays. The sprays with 0.5‰ NJF obtain the lowest CA within the observing time, suggesting a better spread ability on solid surface (e.g., WSPs or/and leaves). With respect to the effects of NJF addition on individual UAVs, the field trial results indicate that NJF addition can remarkably increase both the droplet coverage and VMD at three canopy layers, except for T30 droplet coverage of the inside and bottom layers. Comparing the difference of droplet coverage between two UAVs, while significant difference is found in the same layer before NJF addition, there is no notable difference appearing in the outside and bottom layers after NJF addition. The difference of VMD in the same layer between two UAVs is not affected by NJF addition except for the bottom layer. These results imply that the differences of droplet coverage among different UAVs might be mitigated, thus the droplet distribution of some UAVs could be improved by adding a tank-mix adjuvant into the sprays. This hypothesis is verified by investigating the droplet penetration and the correlation coefficient (CC) of droplet coverage and VMD. After NJF addition, the total percentage of T20 droplet coverage in the bottom and inside layers is increased by 5%. For both UAVs, the CCs indicate that both droplet coverage and VMD increase at the same time in most cases after NJF addition. In conclusion, the addition of a tank-mix adjuvant with the ability to reduce CA of the sprays, can effectively improve droplet distribution using UAV spraying in the citrus canopy by increasing droplet coverage and VMD. creator: Yanhua Meng creator: Wanqiang Zhong creator: Cunjia Liu creator: Jinya Su creator: Jiyuan Su creator: Yubin Lan creator: Zhiguo Wang creator: Meimei Wang uri: https://doi.org/10.7717/peerj.13064 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Meng et al. title: The Significance of the preoperative lactate dehydrogenase/albumin Ratio in the Prognosis of Colon Cancer: a retrospective study link: https://peerj.com/articles/13091 last-modified: 2022-03-11 description: BackgroundWe explored the relationship between the platelet-lymphocyte ratio (PLR), the prognostic nutritional index (PNI), the lactate dehydrogenase-albumin ratio (LDH/albumin ratio; LAR), the controlling nutritional status (CONUT) score, and the long-term survival of colon cancer patients.MethodsWe conducted a retrospective analysis of the clinical data and follow-up materials of 126 patients with colon cancer who underwent surgical treatment in the Department of Gastrointestinal Surgery of Jiangnan University Affiliated Hospital from June 2012 to December 2015. The receiver operating characteristic curve (ROC) was used to distinguish the high ratio group from the low ratio group. The Kaplan Meier method was used to draw the survival curve in our survival analysis. The log rank test was used for the univariate analysis and the Cox multivariate regression analysis was used to analyze the correlation between preoperative PLR, PNI, LAR, conut scores, and overall survival (OS) and progression free survival (PFS) of patients with colon cancer.ResultsThe median follow-up time was 72 months. The OS rates at 3 and 5 years were 83.3% and 78.5%, respectively. The PFS rates at 3 and 5 years were 79.3% and 77.6%, respectively. The 3-year and 5-year OS rates in the low LAR group (≤4.91) were 90.9% and 87.1%, respectively, and were 56.0% and 44.0% in the high LAR group (>4.91) respectively. Univariate and multivariate analyses showed that the LAR value was correlated with OS and PFS (P < 0.05).ConclusionA high preoperative LAR is an independent predictor of the prognosis of colon cancer patients. creator: Zhihui Xie creator: Hui Zhou creator: Lei Wang creator: Yibo Wu uri: https://doi.org/10.7717/peerj.13091 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Xie et al. title: Comparison and correlation of cervical proprioception and muscle endurance in general joint hypermobility participants with and without non-specific neck pain—a cross-sectional study link: https://peerj.com/articles/13097 last-modified: 2022-03-11 description: BackgroundCervical proprioception and muscle endurance are essential for maintaining cervical functional joint stability. Proprioception and muscle endurance may be impaired in those with general joint hypermobility (GJH). Examining these aspects is crucial. This study’s aims are to (1) compare the cervical joint position error (JPE) and muscle endurance holding capacities in GJH individuals with and without non-specific neck pain (NSNP) (2) to assess the relationship between hypermobility Beighton scores, cervical JPE’s, and muscle endurance in GJH individuals with and without NSNP.MethodsIn this cross-sectional comparative study, 33 GJH participants with NSNP (mean age 21.7 ± 1.8 years) and 35 asymptomatic participants GJH (mean age 22.42 ± 1.7 years) participated. Beighton’s score of ≥4 of 9 tests was used as criteria to diagnose GJH. Cervical JPEs were estimated in degrees using a cervical range of motion device, and muscle endurance (flexor and extensor) were estimated in seconds using a stopwatch.ResultsGJH participants with NSNP showed significantly larger cervical JPEs (p < 0.001) and decreased muscle endurance holding times (p < 0.001) compared to asymptomatic participants. Beighton hypermobility scores showed a significant moderate positive correlation with cervical JPEs (flexion: r = 0.43, p = 0.013), left rotation: r = 0.47, p = 0.005, right rotation: r = 0.57, p = 0.001) in NSNP individuals. Also, Beighton hypermobility scores showed a moderate negative correlation with muscle endurance in NSNP (flexor muscles: r = −0.40, p = 0.020, extensor muscles: r = −0.41, p = 0.020, and asymptomatic individuals (flexor muscles: −0.34, p = 0.045, extensor muscles: r = −0.45, p = 0.007).ConclusionGJH individuals with NSNP showed increased cervical JPEs and reduced muscle endurance compared to asymptomatic. Individuals with GJH with higher Beighton scores demonstrated increased cervical JPEs and reduced neck muscle endurance holding ability. In clinical practice, therapists should be aware of these findings, incorporate proprioceptive and muscle endurance assessments, and formulate rehabilitation strategies for NSNP individuals with GJM. creator: Ravi Shankar Reddy creator: Jaya Shanker Tedla creator: Mastour Saeed Alshahrani creator: Faisal Asiri creator: Venkata Nagaraj Kakaraparthi uri: https://doi.org/10.7717/peerj.13097 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Reddy et al. title: Stage 2 registered report: investigating a preference for certainty in conversation among autistic adults link: https://peerj.com/articles/13110 last-modified: 2022-03-11 description: Social communication difficulties are a diagnostic feature in autism. These difficulties are sometimes attributed, at least in part, to impaired ability in making inferences about what other people mean. In this registered report, we tested a competing hypothesis that the communication profile of adults on the autism spectrum can be more strongly characterised by reduced confidence in making inferences in the face of uncertain information. We tested this hypothesis by comparing the performance of 102 autistic and 109 non-autistic adults on a test of implied meaning, using a test of grammaticality judgements as a control task. We hypothesised that autistic adults would report substantially lower confidence, allowing for differences in accuracy, than non-autistic adults on the test of implied meaning compared to the grammaticality test. However, our results did not suggest this. Instead, we found that accuracy and confidence were both reduced to a similar extent on the test of implied meaning in the autistic group compared to the control group, although these were only subtle differences. This pattern of results was specific to inference-making, as the autistic and non-autistic groups did not differ on the grammar test. This supports the idea that specific differences in pragmatic language processing can exist in autism in the absence of core language problems. Importantly, this pattern of results (differences on the test of implied meaning and no differences on the grammar test) was reversed in a group with self-reported reading difficulties, indicating that the differences in inference-making were specific to the autistic group. Lastly, we found relationships between Intolerance of Uncertainty, performance on the test of implied meaning, and self-reported social communication challenges. This supports the idea that discomfort with uncertainty plays a role in the pragmatic language and communication challenges in autism. creator: Alexander C. Wilson creator: Dorothy V.M. Bishop uri: https://doi.org/10.7717/peerj.13110 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wilson and Bishop title: Dissection of genetic architecture for tiller angle in rice (Oryza sativa. L) by multiple genome-wide association analyses link: https://peerj.com/articles/12674 last-modified: 2022-03-10 description: BackgroundThe rice plant architecture is determined by spatially and temporally domesticated tiller angle. The deeper insight into the genetic mechanism for rice plant architecture will allow more efficient light capture by increasing the planting density, reproducibility, and the ability to survive in a stressful environment.MethodsIn this study, a natural population of 795 genotypes further divided into japonica and indica subpopulations, was evaluated for tiller angle. A significant variation with a wide range was observed. Genome-wide association analysis was performed by the general linear model (GLM), and compressed mix linear model (cMLM) for three populations to disclose the genomic associations. The population principal components and kinship matrix in 1,000 permutations were used to remove the false positives. The candidate genes were evaluated for their functional annotations and specific molecular pathways. The sequencing-based haplotype analysis was further performed to reveal the functional variation among candidate genomic regions.ResultsAs a result, 37 significant QTLs with 93 annotated loci were identified. Among the loci, a known tiller angle controlling locus TAC1 was also identified. The introduction of the sequence pooling technique was observed fruitful to screen the 12 significant QTLs with 22 annotated loci. For ten of these loci, the functional variations were identified by haplotype analysis. These results were not only providing a better understanding of the genetic bases of rice plant architecture but also provide significant information for future breeding programs. creator: Muhammad Abdul Rehman Rashid creator: Rana Muhammad Atif creator: Yan Zhao creator: Farrukh Azeem creator: Hafiz Ghulam Muhu-Din Ahmed creator: Yinghua Pan creator: Danting Li creator: Yong Zhao creator: Zhanying Zhang creator: Hongliang Zhang creator: Jinjie Li creator: Zichao Li uri: https://doi.org/10.7717/peerj.12674 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Rashid et al. title: Genotypic variation in root architectural traits under contrasting phosphorus levels in Mediterranean and Indian origin lentil genotypes link: https://peerj.com/articles/12766 last-modified: 2022-03-10 description: The development of phosphorus-efficient crop cultivars boosts productivity while lowering eutrophication in the environment. It is feasible to improve the efficiency of phosphorus (P) absorption in lentils by enhancing phosphorus absorption through root architectural traits. The root architectural traits of 110 diverse lentil genotypes of Indian and Mediterranean origin were assessed, and the relationships between traits were investigated. In a hydroponics experiment, the lentil lines were examined at the seedling stage under two conditions: adequate P supply and deficient P supply. The Pearson correlation coefficients between root architectural traits and genetic diversity among lentil lines were assessed. To estimate variance components, a model (fixed factor) was used. In this experiment, both phosphorus (P) and genotype were fixed variables. Our lentil lines showed significant genetic variability and considerable genetic diversity for all traits under both treatments. The TRL (total root length) and PRL (primary root length) showed strong positive associations with all other characteristics excluding root average diameter (RAD) in both P treatments. In both P treatments, the RAD revealed a negative significant association with Total Root Tips (TRT), as well as total root volume (TRV) and total root forks (TRF) in the deficit conditions of P. Total root volume (TRV), total surface area (TSA), and total root tips had higher coefficient variance values. The first two principal components represented 67.88% and 66.19% of the overall variance in the adequate and deficit P treatments respectively. The Shannon-Weaver diversity index (H′) revealed that RAD, PRL, and TSA had more variability than TRT and TRF under both treatments. According to the Comprehensive Phosphorus Efficiency Measure (CPEM), the best five highly efficient genotypes are PLL 18-09, PLS 18-01, PLL 18-25, PLS 18-23, and PLL 18-07, while IG112131, P560206, IG334, L11-231, and PLS18-67 are highly inefficient genotypes. The above contrasting diverse lentil genotypes can be utilized to produce P-efficient lentil cultivars. The lentil germplasm with potentially favorable root traits can be suggested to evaluated for other abiotic stress to use them in crop improvement programme. The scientific breakthroughs in root trait phenotyping have improved the chances of establishing trait–allele relationships. As a result, genotype-to-phenotype connections can be predicted and verified with exceptional accuracy, making it easier to find and incorporate favourable nutrition-related genes/QTLs in to breeding programme. creator: Muraleedhar Aski creator: Reena Mehra creator: Gyan Prakash Mishra creator: Dharmendra Singh creator: Prachi Yadav creator: Neha Rai creator: Venkata Ravi Prakash Reddy creator: Arun Kumar MB creator: Renu Pandey creator: Madan Pal Singh creator: Gayacharan creator: Ruchi Bansal creator: Kuldeep Tripathi creator: Sripada M. Udupa creator: Shiv Kumar creator: Ashutosh Sarker creator: Harsh Kumar Dikshit uri: https://doi.org/10.7717/peerj.12766 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Aski et al. title: A versatile isothermal amplification assay for the detection of leptospires from various sample types link: https://peerj.com/articles/12850 last-modified: 2022-03-10 description: BackgroundLeptospirosis is a zoonotic disease caused by bacteria of the genus Leptospira that affects both humans and animals worldwide. Early detection of the pathogen in humans is crucial for early intervention and control of the progression of the disease to a severe state. It is also vitally important to be able to detect the presence of the pathogen in carrier animals to control the spread of the disease from the environment. Here we developed a simple and rapid loop-mediated isothermal amplification (LAMP) assay targeting the leptospiral secY gene.ResultsSeveral reaction conditions of the LAMP reaction were optimized to ensure efficient amplification of the target DNA. The sensitivity of the developed LAMP assay obtained using a pure Leptospira culture was 2 × 104 copies of genomic DNA per reaction (equivalent to 0.1 ng) for a 40-minute reaction time. No cross-reactions were observed in the LAMP reaction against a series of non-leptospiral bacteria, indicating a specific reaction. The applicability of the LAMP assay was demonstrated on human blood and urine specimens collected from suspected leptospirosis patients and rat kidney specimens collected from suspected leptospirosis outbreak areas and high-risk areas. The developed LAMP assay demonstrated a higher detection rate for leptospiral DNA compared with the polymerase chain reaction (PCR) assay, possibly due to the presence of inhibitory substances, especially in rat kidney specimens, to which the PCR method is more susceptible. The present findings also highlight the importance of urine sample collection from patients for routine monitoring of the disease.ConclusionsIn short, the developed LAMP assay can serve as a feasible alternative tool for the diagnosis of leptospirosis and be used for epidemiological and environmental surveillance of the disease, considering its robustness, rapidity, sensitivity, and specificity, as demonstrated in this study. creator: Shuhaidah Othman creator: Pui-Yuei Lee creator: Jia-Yong Lam creator: Noraini Philip creator: Nurul Natasya Azhari creator: Norliza Bahtiar Affendy creator: Siti Norbaya Masri creator: Vasantha Kumari Neela creator: Farah Shafawati Mohd-Taib creator: Hui-Yee Chee uri: https://doi.org/10.7717/peerj.12850 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Othman et al. title: Expression of IER3 in hepatocellular carcinoma: clinicopathology, prognosis, and potential regulatory pathways link: https://peerj.com/articles/12944 last-modified: 2022-03-10 description: BackgroundImmediate early response 3 (IER3) is correlated to the prognosis of several cancers, but the precise mechanisms underlying the regulation by IER3 of the occurrence and development of hepatocellular carcinoma (HCC) remain unknown.MethodsThe expression level of IER3 was examined by using in-house immunohistochemistry (IHC), public gene chip, and public RNA-sequencing (RNA-seq). The standardized mean difference (SMD) was calculated to compare the expression levels of IER3 between HCC patients and controls. The summary receiver operating characteristics (sROC) was plotted to comprehensively understand the discriminatory capability of IER3 between HCC and non-HCC group. The Kaplan–Meier curves and the combined hazard ratios (HRs) were used to determine the prognostic value of IER3 in HCC. Moreover, differentially expressed genes (DEGs) and co-expression genes (CEGs) were used to explored the molecular mechanisms of IER3 underlying HCC. hTFtarget was used to predict the transcription factors (TFs) of IER3. The binding site of TFs and the IER3 promoter region was forecasted using the JASPAR website. The relevant ChIP-seq data were used to determine whether TF peaks were present in the IER3 transcription initiation.ResultsA significantly increased expression of IER3 protein was found in HCC tissue relative to non-HCC tissue as detected by IHC (p < 0.001). Compared to 1,263 cases of non-HCC tissues, IER3 in 1483 cases of HCC tissues was upregulated (SMD = 0.42, 95% confidence interval [CI] [0.09–0.76]). The sROC showed that IER3 had a certain ability at differentiating HCC tissues (area under the curve (AUC) = 0.65, 95% CI [0.61–0.69]). Comprehensive analysis of the effect of IER3 on the prognosis of patients with HCC demonstrated that higher IER3 expression was associated with poor prognosis in HCC (HRs = 1.30, 95% CI [1.03–1.64]). Pathway enrichment analysis revealed that IER3-related genes were mostly enriched in the PI3K-Akt signaling pathway, cancer-related signaling pathways, the p53 signaling pathway, and other signaling pathways. Regulatory factor X5 (RFX5) was identified as a possible regulator of IER3-related TF.ConclusionIER3 may be a potential prognostic marker for HCC. The molecular mechanisms of IER3 in HCC warrant further study. creator: Fei-Yan He creator: Gang Chen creator: Rong-quan He creator: Zhi-Guang Huang creator: Jian-Di Li creator: Wei-Zi Wu creator: Ji-Tian Chen creator: Yu-Lu Tang creator: Dong-Ming Li creator: Shang-Ling Pan creator: Zhen-Bo Feng creator: Yi-wu Dang uri: https://doi.org/10.7717/peerj.12944 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 He et al. title: First observations of ovary regeneration in an amphipod, Ampelisca eschrichtii Krøyer, 1842 link: https://peerj.com/articles/12950 last-modified: 2022-03-10 description: BackgroundFemales of the gammaridean amphipod Ampelisca eschrichtii with signs of regenerating, previously atrophied ovaries were recovered from the northeastern shelf of Sakhalin Island (Okhotsk Sea, Russia). Ovarian regeneration was previously unknown for any amphipod species. A. eschrichtii have a predominantly 2-year life cycle (from embryo to adult death) and reproduce once between late winter or early spring at the age of 2 years. Occasionally, females survive to a third year. An adaptive value of extended survival among these females is likely to require that they are also reproductive.MethodsHistological sections from a second-year female with ovarian atrophy, a female with normal ovaries, a third-year female with ovarian regeneration, as well as testes of an immature and a sexually mature male were compared to determine the sources of cells of the germinal and somatic lines necessary for ovarian regeneration.ResultsOvarian regeneration in the third-year female began with the formation of a new germinal zone from germ cells preserved in the atrophied ovaries and eosinophilic cells of the previously starving second-year female. Eosinophilic cells form the mesodermal component of the germinal zone. A mass of these cells appeared in the second-year female that had atrophied ovaries and in large numbers on the intestine wall of the third-year female with regenerating ovaries. These eosinophilic cells appear to migrate into the regenerating ovaries.ConclusionsAll germ cells of the second-year female are not lost during ovarian atrophy and can be involved in subsequent ovarian regeneration. Eosinophilic cells involved in ovarian regeneration are of mesodermal origin. The eosinophilic cell morphologies are similar to those of quiescence cells (cells in a reversible state that do not divide but retain the ability to re-enter cell division and participate in regeneration). These histological data thus indicate that eosinophilic and germ cells of third-year females can participate in the regeneration of the ovaries to reproduce a second brood. The precursors of these third-year females (a small number the second-year females with an asynchronous [summer] breeding period and ovaries that have atrophied due to seasonal starvation) appear to possess sources of somatic and germ cells that are sufficient for ovarian regeneration and that may be adaptations to starvation stress. creator: Valentina B. Durkina creator: John W. Chapman creator: Natalia L. Demchenko uri: https://doi.org/10.7717/peerj.12950 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Durkina et al. title: Evaluation of the diagnostic and prognostic values of serum HSP90α in sepsis patients: a retrospective study link: https://peerj.com/articles/12997 last-modified: 2022-03-10 description: BackgroundSepsis is a serious syndrome that is caused by immune responses dysfunction and leads to high mortality. The abilities of heat shock protein 90α (HSP90α) in assessing the diagnosis and prognosis in patients with sepsis remain ill-defined to date. We conducted a study to reveal the possible clinical applications of HSP90α as biomarker for the diagnosis and prognosis in patients with sepsis.MethodsIn total, 150 patients of sepsis, 110 patients without sepsis admitted to ICU and 110 healthy subjects were involved in this study. The serum HSP90α contents, sequential organ failure assessment (SOFA) scores, procalcitonin (PCT), and short-term survival status of the participants were measured and compared. Logistic and linear regression models adjusting for potential confounders were used to examine the association of HSP90α with sepsis survival. Moreover, serum IL-1β, IL-18, MIP-3α, and ENA-78 were also determined. Finally, Spearman correlation analysis was employed to reveal a possible mechanism that HSP90α contributed to the short-term deaths.ResultsSerum HSP90α levels in sepsis patients were higher than those in ICU controls and healthy controls (P < 0.001), and even increased in patients who died within 28 days (P < 0.001). Logistic and linear regression models identified HSP90α was an independent risk factors for sepsis mortality. Receiver operating characteristic (ROC) analysis displayed that HSP90α had a considerable predictive performance for sepsis outcome, with an area under curve (AUC) value up to 0.79. Survival analysis demonstrated that the mortality of sepsis individuals at 28 days was positively associated with HSP90α levels, especially the levels of HSP90α were greater than 120 ng/mL (P < 0.001). Moreover, among sepsis patients, those who died had notably elevated cytokines, IL-1β, IL-18, and chemokines, MIP-3α, ENA-78, relative to survivors. Further correlation analysis demonstrated that there was a nominally positive correlation between HSP90α and IL-1β, IL-18, and MIP-3α.ConclusionHSP90α is of favorable clinical significance in sepsis diagnosis and prognosis, laying a foundation for future clinical applications. creator: Fuxing Li creator: Yulin Zhang creator: Bocheng Yu creator: Zihua Zhang creator: Yujuan Fan creator: Li Wang creator: Mingjing Cheng creator: Ping Yan creator: Weidong Zhao uri: https://doi.org/10.7717/peerj.12997 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Li et al. title: Effect of magnification factor by Galilean loupes on working posture of dental students in simulated clinical procedures: associations between direct and observational measurements link: https://peerj.com/articles/13021 last-modified: 2022-03-10 description: ObjectivesTo determine the effect of different levels of Galilean loupe magnification on working posture as measured by compliance with ergonomic posture positions, angular deviation from the neutral position of the neck, and muscle activation in the neck and upper back region during simulated clinical conditions.MethodsAn experimental laboratory study was performed in which the dependent variables were compliance with ergonomic posture requirements while performing simulated restorative procedures in Restorative Dentistry, angular deviation from the neutral position of the neck, and muscle activation in the neck and upper back. The independent variable was the level of Galilean loupe magnification, which was tested at four levels (naked eye, 2.5× magnification, 3.0× magnification, and 3.5× magnification). The cavity preparations and Class I composite resin restorations were performed on artificial first molars on a mannequin in a dental chair. The Compliance Assessment of Dental Ergonomic Posture Requirements (CADEP) was used for the postural analysis; as was an analysis of the angular deviation from the neutral position of the neck and surface electromyography. Working posture was recorded on video over the course of the procedure. Participants were filmed from three different angles. The Compliance Assessment of Dental Ergonomic Posture Requirements (CADEP) assessed compliance with ergonomic posture requirements. A locally produced posture assessment software analyzed angular deviation. Surface electromyography bilaterally assessed activation of the sternocleidomastoid, descending trapezius and ascending trapezius muscles. Two-factor analysis of variance (ANOVA) and either Tukey’s post-hoc test or the Games-Howell post-hoc test were performed (α = 0.05).ResultsDuring the cavity preparations and restorations, the use of Galilean loupes at all magnifications positively influenced working posture as measured by participants’ compliance with ergonomic posture positions (p < 0.01) and neck angulation (p < 0.01); the use of these loupes did not affect muscle activation in the regions evaluated (p > 0.05).ConclusionThe use of Galilean loupes had a positive effect on dental students’ working posture during the restoration procedures performed. creator: Júlia Margato Pazos creator: Simone Cecilio Hallak Regalo creator: Paulo de Vasconcelos creator: Juliana Alvares Duarte Bonini Campos creator: Patricia Petromilli Nordi Sasso Garcia uri: https://doi.org/10.7717/peerj.13021 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Pazos et al. title: Functional analysis of ARF1 from Cymbidium goeringii in IAA response during leaf development link: https://peerj.com/articles/13077 last-modified: 2022-03-10 description: BackgroundCymbidium is an economically important genus of flowering orchids cultivated in China because of showing graceful leaf shapes and elegant flower coloration. However, the deterioration of the ecological environment and the difficulty of conservation management have become increasing challenges for maintaining its germplasm resources. ARFs are critical transcription factors in the auxin signaling pathway and have been found to play pivotal roles in leaf growth and development in previous studies. However, their functions and mechanisms in Cymbidium goeringii remain to be clarified.MethodsThe sequence of the CgARF1 gene was analyzed by bioinformatics. The expression of this gene in different tissues and under IAA treatment was detected by quantitative real-time PCR analysis. The CgARF1 gene was overexpressed in wild-type Arabidopsis and Nicotiana benthamiana via the Agrobacterium infection method. Acetone-ethanol solvent extraction was applied for the determination of chlorophyll contents, and the contents of endogenous hormones were determined using the enzyme-linked immunosorbent assay technique.ResultsCgARF1 cloned from C. goeringii ‘Songmei’ was 2,049 bp in length and encoded 682 amino acids containing three typical domains: a B3 DNA binding domain, an Aux_resp domain and an AUX/IXX family domain. The expression pattern of CgARF1 in different tissues of C. goeringii showed that its expression was highest in the leaves and changed greatly under IAA treatment. Subcellular localization studies showed that the protein was mainly localized in the cell nucleus. CgARF1-overexpressing lines exhibited leaf senescence and a decreased chlorophyll content. Under IAA treatment, CgARF1 regulates the rooting length, rooting number and rooting rate from detached leaves. The levels of endogenous hormones in transgenic leaves were also significantly changed.ConclusionThese results indicated that CgARF1 overexpression is responsive to IAA treatment during leaf development. This study provides a foundation for future research on the function of the ARF gene family in C. goeringii. creator: Zihan Xu creator: Fangle Li creator: Meng Li creator: Yuanhao He creator: Yue Chen creator: Fengrong Hu uri: https://doi.org/10.7717/peerj.13077 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Xu et al. title: Effect of precipitation change on the photosynthetic performance of Phragmites australis under elevated temperature conditions link: https://peerj.com/articles/13087 last-modified: 2022-03-10 description: BackgroundAs a fundamental metabolism, leaf photosynthesis not only provides necessary energy for plant survival and growth but also plays an important role in global carbon fixation. However, photosynthesis is highly susceptible to environmental stresses and can be significantly influenced by future climate change.MethodsIn this study, we examined the photosynthetic responses of Phragmites australis (P. australis) to three precipitation treatments (control, decreased 30%, and increased 30%) under two thermal regimes (ambient temperature and +4 °C) in environment-controlled chambers.ResultsOur results showed that the net CO2 assimilation rate (Pn), maximal rate of Rubisco (Vcmax), maximal rate of ribulose-bisphosphate (RuBP) regeneration (Jmax) and chlorophyll (Chl) content were enhanced under increased precipitation condition, but were declined drastically under the condition of water deficit. The increased precipitation had no significant effect on malondialdehyde (MDA) content (p > 0.05), but water deficit drastically enhanced the MDA content by 10.1%. Meanwhile, a high temperature inhibited the positive effects of increased precipitation, aggravated the adverse effects of drought. The combination of high temperature and water deficit had more detrimental effect on P. australis than a single factor. Moreover, non-stomatal limitation caused by precipitation change played a major role in determining carbon assimilation rate. Under ambient temperature, Chl content had close relationship with Pn (R2 = 0.86, p < 0.01). Under high temperature, Pn was ralated to MDA content (R2 = 0.81, p < 0.01). High temperature disrupted the balance between Vcmax and Jmax (the ratio of Jmax to Vcmax decreased from 1.88 to 1.12) which resulted in a negative effect on the photosynthesis of P. australis. Furthermore, by the analysis of Chl fluorescence, we found that the xanthophyll cycle-mediated thermal dissipation played a major role in PSII photoprotection, resulting in no significant change on actual PSII quantum yield (ΦPSII) under both changing precipitation and high temperature conditions.ConclusionsOur results highlight the significant role of precipitation change in regulating the photosynthetic performance of P. australis under elevated temperature conditions, which may exacerbate the drought-induced primary productivity reduction of P. australis under future climate scenarios. creator: Linhong Teng creator: Hanyu Liu creator: Xiaonan Chu creator: Xiliang Song creator: Lianhui Shi uri: https://doi.org/10.7717/peerj.13087 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Teng et al. title: Feature screening for survival trait with application to TCGA high-dimensional genomic data link: https://peerj.com/articles/13098 last-modified: 2022-03-10 description: BackgroundIn high-dimensional survival genomic data, identifying cancer-related genes is a challenging and important subject in the field of bioinformatics. In recent years, many feature screening approaches for survival outcomes with high-dimensional survival genomic data have been developed; however, few studies have systematically compared these methods. The primary purpose of this article is to conduct a series of simulation studies for systematic comparison; the second purpose of this article is to use these feature screening methods to further establish a more accurate prediction model for patient survival based on the survival genomic datasets of The Cancer Genome Atlas (TCGA).ResultsSimulation studies prove that network-adjusted feature screening measurement performs well and outperforms existing popular univariate independent feature screening methods. In the application of real data, we show that the proposed network-adjusted feature screening approach leads to more accurate survival prediction than alternative methods that do not account for gene-gene dependency information. We also use TCGA clinical survival genetic data to identify biomarkers associated with clinical survival outcomes in patients with various cancers including esophageal, pancreatic, head and neck squamous cell, lung, and breast invasive carcinomas.ConclusionsThese applications reveal advantages of the new proposed network-adjusted feature selection method over alternative methods that do not consider gene-gene dependency information. We also identify cancer-related genes that are almost detected in the literature. As a result, the network-based screening method is reliable and credible. creator: Jie-Huei Wang creator: Cai-Rong Li creator: Po-Lin Hou uri: https://doi.org/10.7717/peerj.13098 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wang et al. title: The association between non-suicidal self-injury and negative life events in children and adolescents in underdeveloped regions of south-western China link: https://peerj.com/articles/12665 last-modified: 2022-03-09 description: BackgroundThe association between negative life events and Non-suicidal self-injury (NSSI) in children and adolescents has been extensively discussed. Nevertheless, little is known about the relationship between negative life events and repetition and severity of NSSI. This survey aims to understand the association between NSSI prevalence, severity, repetition and the negative life events in children and adolescents in underdeveloped regions in south-western China.MethodsIn this population-based cross-sectional study, 3,146 children and adolescents were included from underdeveloped regions of south-western China, and each of them requested to complete a self-assessment questionnaire. The Modified Version of Adolescents Self-Harm Scale (MASHS) and the Adolescent Self-rating negative Life Events Check-list were used to evaluate NSSI behaviors and negative life events, respectively. The statistical implementation of this study was carried out in the R statistical software, and the logistic regression analysis method was used to analyze the relationship between negative life events and adolescents’ non-suicidal self-injury behaviors.ResultsThe average age of all included participants was 13.31 years old. The lifetime prevalence of NSSI was 47.0% (95% CI [36.3–58.0%]). Gender, grade level and ASLEC was positively associated with NSSI. Further analysis revealed that, for all five dimensions of ASLEC, only interpersonal relationship factor (IRF) (OR 1.77 (95% CI [1.06–2.97])), health adaptation factor (HAF) (OR 2.08 (95% CI [1.31–3.31])) showed prominent association with NSSI. Multivariate Logistic regression models revealed that, repetitive NSSI (OR 4.54 (95% CI [3.66–5.63])) and NSSI severity (OR 9.01 (95% CI [6.11–13.29])) were positively associated with ASLEC.ConclusionNSSI is very common among children and adolescents in underdeveloped regions of south-western China. Negative life event are positively associated with NSSI, repeated NSSI, and severe NSSI. Negative life events centered intervention measures might be effective in reducing NSSI among school children and adolescents in underdeveloped regions of south-western China. creator: Fan Yang creator: Linling Jiang creator: Jing Miao creator: Xiufeng Xu creator: Hailiang Ran creator: Yusan Che creator: Die Fang creator: TianLan Wang creator: Yuanyuan Xiao creator: Jin Lu uri: https://doi.org/10.7717/peerj.12665 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Yang et al. title: Three new species of Microlaimus (Nematoda: Microlaimidae) from the South Atlantic link: https://peerj.com/articles/12734 last-modified: 2022-03-09 description: Three new species of Microlaimus are described from the continental shelf of the Campos Basin, southwest Atlantic, Brazil. Microlaimus campiensissp. n. differs from all other species in the presence of two anterior testes, slender spicules with enlarged proximal ends, 7–11 pre-cloacal papilliform supplements, and females with a pair of constriction structures, one on each branch of the ovary. Microlaimus alexandrisp. n. shows sexual dimorphism in the size of the amphidial fovea, which occupies 100% of the diameter of the corresponding area in the male; the buccal cavity provided with five teeth and a slightly cuticularized cuticular ring. Microlaimus vitoriussp. n. has four longitudinal-lateral rows of glands associated with small pores, one seta and three pores small pre-cloacal, and the gubernaculum has a triangular base. An amendment to the diagnosis of the genus is proposed, where the number of teeth was modified. creator: Rita C. Lima creator: Patrícia F. Neres creator: André M. Esteves uri: https://doi.org/10.7717/peerj.12734 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Lima et al. title: Isolation and transcriptome analysis of a biotechnologically promising Black Sea protist, Thraustochytrium aureum ssp. strugatskii link: https://peerj.com/articles/12737 last-modified: 2022-03-09 description: BackgroundMarine protists are an important part of the ocean ecosystem. They may possess unique sets of biosynthetic pathways and, thus, be promising model organisms for metabolic engineering for producing substances for the pharmaceutical, cosmetic, and perfume industries. Currently, full-genome data are available just for a limited number of protists hampering their use in biotechnology.MethodsWe characterized the morphology of a new cultured strain of Thraustochytriaceae isolated from the Black Sea ctenophore Beroe ovata using phase-contrast microscopy. Cell culture was performed in the FAND culture medium based on fetal bovine serum and DMEM. Phylogenetic analysis was performed using the 18S rRNA sequence. We also conducted a transcriptome assembly and compared the data with the closest species.ResultsThe protist belongs to the genus Thraustochytrium based on the 18S rRNA sequence analysis. We designated the isolated protist as T. aureum ssp. strugatskii. The closest species with the genome assembly is Schizochytrium aggregatum. Transcriptome analysis revealed the majority of the fatty acid synthesis enzymes.ConclusionOur findings suggest that the T. aureum ssp. strugatskii is a promising candidate for biotechnological use. Together with the previously available, our data would allow the establishment of an accurate phylogeny of the family Thraustochytriaceae. Also, it could be a reference point for studying the evolution of the enzyme families. creator: Dmitrii K. Konstantinov creator: Aleksei Menzorov creator: Olga Krivenko creator: Alexey V. Doroshkov uri: https://doi.org/10.7717/peerj.12737 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Konstantinov et al. title: Analysis of the role and mechanism of EGCG in septic cardiomyopathy based on network pharmacology link: https://peerj.com/articles/12994 last-modified: 2022-03-09 description: BackgroundSeptic cardiomyopathy (SC) is a common complication of sepsis that leads to an increase in mortality. The pathogenesis of septic cardiomyopathy is unclear, and there is currently no effective treatment. EGCG (epigallocatechin gallate) is a polyphenol that has anti-inflammatory, antiapoptotic, and antioxidative stress effects. However, the role of EGCG in septic cardiomyopathy is unknown.MethodsNetwork pharmacology was used to predict the potential targets and molecular mechanisms of EGCG in the treatment of septic cardiomyopathy, including the construction and analysis of protein-protein interaction (PPI) network, gene ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and molecular docking. The mouse model of septic cardiomyopathy was established after intraperitoneal injection of LPS (lipopolysaccharide). The myocardial protective effect of EGCG on septic mice is observed by cardiac ultrasound and HE staining. RT-PCR is used to verify the expression level of the EGCG target in the septic cardiomyopathy mouse model.ResultsA total of 128 anti-SC potential targets of EGCGareselected for analysis. The GO enrichment analysis and KEGG pathway analysis results indicated that the anti-SC targets of EGCG mainly participate in inflammatory and apoptosis processes. Molecular docking results suggest that EGCG has a high affinity for the crystal structure of six targets (IL-6 (interleukin-6), TNF (tumor necrosis factor), Caspase3, MAPK3 (Mitogen-activated protein kinase 3), AKT1, and VEGFA (vascular endothelial growth factor)), and the experimental verification result showed levated expression of these 6 hub targets in the LPS group, but there is an obvious decrease in expression in the LPS + EGCG group. The functional and morphological changes found by echocardiography and HE staining show that EGCG can effectively improve the cardiac function that is reduced by LPS.ConclusionOur results reveal that EGCG may be a potentially effective drug to improve septic cardiomyopathy. The potential mechanism by which EGCG improves myocardial injury in septic cardiomyopathy is through anti-inflammatory and anti-apoptotic effects. The anti-inflammatory and anti-apoptotic effects of EGCG occur not only through direct binding to six target proteins (IL-6,TNF-α, Caspase3, MAPK3, AKT1, and VEGFA) but also by reducing their expression. creator: Ji Wu creator: Zhenhua Wang creator: Shanling Xu creator: Yang Fu creator: Yi Gao creator: Zuxiang Wu creator: Yun Yu creator: Yougen Yuan creator: Lin Zhou creator: Ping Li uri: https://doi.org/10.7717/peerj.12994 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wu et al. title: Optimizing seawater temperature conditions to increase the productivity of ex situ coral nurseries link: https://peerj.com/articles/13017 last-modified: 2022-03-09 description: Large scale ex situ propagation of coral colonies for reef restoration is a relatively new and developing field. One of the many advantages of utilizing ex situ coral nurseries is the ability to optimize water quality conditions for coral health and survival. Slight alterations in environmental parameters (light, pH, temperature etc.) can affect the health and grow-out time of cultured coral, ultimately influencing production rates. However, corals are also subjected to pests associated with culture facilities such as ciliates, cyanobacterial blooms, and infectious diseases. Therefore, adjusting environmental parameters to optimize coral growth for a shorter ex situ residency time will lead to greater survival and faster restoration. Studies indicate that some coral species demonstrate parabolic tissue growth in response to increasing sea-surface temperatures until the maximum temperature tolerance is reached, whereafter they bleach. To maximize coral growth in Mote Marine Laboratory’s ex situ system, we tested the effect of two water temperature treatments (high temperature: 29.5 ± 0.03 °C; control: 25.2 ± 0.08 °C) on two coral species commonly used in reef restoration. To quantify this, we used four replicates of three genotypes each of Montastraea cavernosa (n = 12) and Acropora palmata (n = 12). Two-dimensional tissue area was recorded monthly using ImageJ and survival rates within each treatment were documented for 7 months. Results found that M. cavernosa had greater growth rates and equal survivorship in the high temperature treatment compared to the control treatment. A. palmata grew faster and had equal survivorship in the control treatment compared with the high temperature treatment. These results suggest that temperature preferences exist among coral species within ex situ systems and restoration practitioners should consider species-specific temperature regimes to maximize ex situ coral growth rates. This information is critical for optimizing production when corals are in the grow-out stage and should also be considered when designing ex situ systems to ensure temperature regulation can be controlled on a species-specific basis. creator: Dakotah E. Merck creator: Chelsea G. Petrik creator: Alicia A. Manfroy creator: Erinn M. Muller uri: https://doi.org/10.7717/peerj.13017 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Merck et al. title: Perfluoroalkyl acids in sediment and water surrounding historical fire training areas at Barksdale Air Force Base link: https://peerj.com/articles/13054 last-modified: 2022-03-09 description: Perfluoroalkyl acids (PFAAs) are environmentally persistent components of surfactants that consist of fully fluorinated carbon chains and a terminal sulfonate or carboxylate polar head moiety. Due to their unique amphiphilic properties, PFAAs are used in the manufacturing of products such as aqueous film forming foams (AFFF). There is cause for concern for PFAA contamination resulting from runoff and groundwater infiltration of AFFF that were used during fire training. This study analyzed water and sediment samples that were collected over a 13-month sampling period from bayous upstream and downstream of two former fire training areas located near Barksdale Air Force Base (BAFB); the occurrence and magnitude of PFAAs supported an aquatic ecological risk assessment of potential impacts of PFAAs at the site. Liquid chromatography coupled with mass spectrometry was used for determination of 6 PFAAs listed under the third Unregulated Contaminant Monitoring Rule (UCMR 3). Total PFAA concentrations in surface water and sediment samples ranged from 0 (ND) −7.1 ng/mL and 0 (ND) −31.4 ng/g, respectively. Perfluorooctanesulfonic acid (PFOS) and perfluorooctanoic acid (PFOA) were the predominant PFAAs detected. In general, perfluorosulfonates were quantified more frequently and at higher concentrations than perfluorocarboxylates. The perfluoroalkyl chain length of PFAAs also showed significant influence on PFAA concentrations when analyzed by Spearman’s rank correlation analysis. Some contamination we observed in surface water and sediment samples from reference locations could be a result of local runoff from the use of commercial products containing per- and poly-fluoroalkyl substances (PFAS), but AFFF appears to be the primary source given the close proximity of the historical fire training areas. creator: Rebecca S. Wilkinson creator: Heather A. Lanza creator: Adric D. Olson creator: Joseph F. Mudge creator: Christopher J. Salice creator: Todd A. Anderson uri: https://doi.org/10.7717/peerj.13054 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wilkinson et al. title: Expression of connexin-43 in surgical resections of primary tumor and lymph node metastases of squamous cell carcinoma and adenocarcinoma of the lung: a retrospective study link: https://peerj.com/articles/13055 last-modified: 2022-03-09 description: BackgroundConnexins are transmembrane proteins forming gap junctions between the cells, which allow intercellular communication. Significance of gap junctions and connexins in lung carcinoma is not yet understood. The objective of the study was to investigate immunohistochemical expression and the localization of connexin-43 (Cx43) in primary lung carcinoma and its lymphatic metastases.MethodsSurgical specimens of excised tumors from 88 patients (45 men and 43 women, 61.9 ± 7.4 years) with lung carcinoma (52 adenocarcinoma (AC), 36 squamous cell carcinoma (SqCC)) who were operated on at the University Hospital “Bezanijska Kosa” in a five-year period (2012–2016) were used. We conducted immunohistochemical staining for Cx43 and measured the degree of expression (percentage of positive cells and staining intensity) as well as localization of Cx43 in primary tumor and in lymphatic metastases.ResultsImmunohistochemical analysis of the primary tumors revealed that SqCC showed significantly higher percentage of tumor cells expressing Cx43 as well as higher staining intensity than AC (p < 0.001). Almost 70% of samples with SqCC showed high Cx43 expression, whereas AC showed no expression in more than 50% of cases. Localization of Cx43 expression was most often cytoplasmic (AC and SqCC) and combined membranous and cytoplasmic (SqCC) with very rare instances of nuclear localization (AC). Almost the same pattern in distribution, intensity, and localization of Cx43 expression was observed in the lymph node metastases; however, almost a third of AC cases changed the pattern of Cx43 expression in the metastasis compared to primary tumor.ConclusionThe results of this study showed that lung carcinomas express Cx43 in more than 65% of cases and that it was aberrantly localized (not membranous localization). We highlighted that SqCC expressed Cx43 more than did AC, both in primary tumor and lymphatic metastases. Further research is needed to establish whether Cx43 could be used as a prognostic biomarker in lung carcinoma. creator: Ivana Savic creator: Petar Milovanovic creator: Svetlana Opric creator: Nebojsa Ivanovic creator: Dejan Oprić uri: https://doi.org/10.7717/peerj.13055 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Savic et al. title: Environmental enrichment changes rabbits’ behavior, serum hormone level and further affects cecal microbiota link: https://peerj.com/articles/13068 last-modified: 2022-03-09 description: Many studies have shown that stress is associated with gut microbiota. Environmental enrichment (EE) could reduce stress in farm animals; however, limited information is available on the microbial community composition in rabbits raised with or without EE. This study aimed to identify EE influences on the behavior, serum hormonal levels, and cecal microbiota of rabbits. Two hundred Rex rabbits were segregated randomly within four cohorts (n = 50); reared for 76 d within standardized enclosures (non-enriched) or within cages containing a willow-stick (WS), rubber-duck (RD), or a can of beans (CB). The rabbits’ ingestive, rest, locomotion, exploratory, grooming, and abnormal behavior were observed. The serum hormone levels for rabbits were measured, and cecal specimens were sequencedfrom the V3–V4 region using 16S rRNA amplicons. Environmental enrichment increased feeding and drinking time, promoted exploratory behavior, and reduced abnormal behavior in rabbits. Insulin-like growth factor 1(IGF-1) levels of the enriched cohorts were elevated in comparison to the control cohort. Serum cortisol level for CB cohort was markedly reduced in comparison to the control cohort (p < 0.05), while dopamine levels for CB cohort peaked. Further, we found that EE mainly affected the dominant microbiota. Several families, such as Erysipelotrichaceae, Tannerellaceae, Enterobacteriaceae, Burkholderiaceae, and Prevotellaceae were markedly reduced within the CB cohort. Bacteria such as Alloprevotella, Bifidobacterium, Enterobacteriaceae, Parabacteroides, and Erysipelatoclostridium were identified as having negative associations with the presence of serum cortisol. EE influenced rabbit behavior and serum hormonal levels, and CB enrichment was the most suitable for rabbits. Further, cecal microbiota composition and diversity were affected by CB enrichment. These findings suggested that CB could be considered for use in rabbit husbandry. creator: Yang Feng creator: Huimei Fan creator: Xue Liang creator: Xiaofeng Wang creator: Guoyan Gao creator: Shuangbao Gun uri: https://doi.org/10.7717/peerj.13068 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Feng et al. title: Long-term consumption of artificial sweeteners does not affect cardiovascular health and survival in rats link: https://peerj.com/articles/13071 last-modified: 2022-03-09 description: BackgroundRecent epidemiological cohort studies have suggested that consumption of artificial sweeteners (AS) is associated with adverse cardiovascular events and mortality. However, these population association studies cannot establish a causal relationship. In this study we investigated the effect of long-term (1-year) consumption of AS (Equal and Splenda, two commonly used AS) on cardiovascular health and survival in rats.MethodsAdult Sprague-Dawley rats (both sexes, 4–5 months old) were randomized into the following 3 groups: control (n = 21), AS Equal (n = 21) and Splenda (n = 18). In the AS groups, Equal or Splenda was added to the drinking water (2-packets/250 ml), while drinking water alone was used in the control rats. The treatment was administered for 12 months. Cardiovascular function and survival were monitored in all animals.ResultsIt was found that rats in the AS groups consistently consumed more sweetened water than those in the control group. AS did not affect body weight, non-fasting blood cholesterol, triglycerides, blood pressure or pulse wave velocity. There were no significant differences in left ventricular wall thicknesses, chamber dimension, cardiac function or survival. AS did not affect heart rate or atrial effective refractory period. However, rats in both Equal and Splenda groups had prolonged PR intervals (63 ± 5ms in Equal, 68 ± 6 ms in Splenda, vs 56 ± 8 ms in control, p < 0.05) and a tendency of increased atrial fibrillation inducibility.ConclusionLong-term consumption of AS does not affect cardiovascular structure, function or survival but may cause some electrophysiological abnormalities with prolonged PR intervals and a tendency of increased atrial fibrillation inducibility in rats. creator: Satvinder K. Guru creator: Ying Li creator: Olga V. Savinova creator: Youhua Zhang uri: https://doi.org/10.7717/peerj.13071 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Guru et al. title: Full-length transcriptome analysis of Adiantum flabellulatum gametophyte link: https://peerj.com/articles/13079 last-modified: 2022-03-09 description: Ferns are important components of plant communities on earth, but their genomes are generally very large, with many redundant genes, making whole genome sequencing of ferns prohibitively expensive and time-consuming. This means there is a significant lack of fern reference genomes, making molecular biology research difficult. The gametophytes of ferns can survive independently, are responsible for sexual reproduction and the feeding of young sporophytes, and play an important role in the alternation of generations. For this study, we selected Adiantum flabellulatum as it has both ornamental and medicinal value and is also an indicator plant of acidic soil. The full-length transcriptome sequencing of its gametophytes was carried out using PacBio three-generation sequencing technology. A total of 354,228 transcripts were obtained, and 231,705 coding sequences (CDSs) were predicted, including 5,749 transcription factors (TFs), 2,214 transcription regulators (TRs) and 4,950 protein kinases (PKs). The transcripts annotated by non-redundant protein sequence database (NR), Kyoto encyclopedia of genes and genomes (KEGG), eukaryotic ortholog groups (KOG), Swissprot, protein family (Pfma), nucleotide sequence database (NT) and gene ontology (GO) were 251,501, 197,474, 193,630, 194,639, 195,956, 113,069 and 197,883, respectively. In addition, 138,995 simple sequence repeats (SSRs) and 111,793 long non-coding RNAs (lncRNAs) were obtained. We selected nine chlorophyll synthase genes for qRT-PCR, and the results showed that the full-length transcript sequences and the annotation information were reliable. This study can provide a reference gene set for subsequent gene expression quantification. creator: Zeping Cai creator: Zhenyu Xie creator: Luyao Huang creator: Zixuan Wang creator: Min Pan creator: Xudong Yu creator: Shitao Xu creator: Jiajia Luo uri: https://doi.org/10.7717/peerj.13079 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Cai et al. title: Immunogenicity mechanism of mRNA vaccines and their limitations in promoting adaptive protection against SARS-CoV-2 link: https://peerj.com/articles/13083 last-modified: 2022-03-09 description: Since the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19) in late 2019, hundreds of millions of people have been infected worldwide. There have been unprecedented efforts in acquiring effective vaccines to confer protection against the disease. mRNA vaccines have emerged as promising alternatives to conventional vaccines due to their high potency with the capacity for rapid development and low manufacturing costs. In this review, we summarize the currently available vaccines against SARS-CoV-2 in development, with the focus on the concepts of mRNA vaccines, their antigen selection, delivery and optimization to increase the immunostimulatory capability of mRNA as well as its stability and translatability. We also discuss the host immune responses to the SARS-CoV-2 infection and expound in detail, the adaptive immune response upon immunization with mRNA vaccines, in which high levels of spike-specific IgG and neutralizing antibodies were detected after two-dose vaccination. mRNA vaccines have been shown to induce a robust CD8+T cell response, with a balanced CD4+ TH1/TH2 response. We further discuss the challenges and limitations of COVID-19 mRNA vaccines, where newly emerging variants of SARS-CoV-2 may render currently deployed vaccines less effective. Imbalanced and inappropriate inflammatory responses, resulting from hyper-activation of pro-inflammatory cytokines, which may lead to vaccine-associated enhanced respiratory disease (VAERD) and rare cases of myocarditis and pericarditis also are discussed. creator: Mohd Zulkifli Salleh creator: Mohd Nor Norazmi creator: Zakuan Zainy Deris uri: https://doi.org/10.7717/peerj.13083 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Salleh et al. title: Distinct metabolic profiling is correlated with bisexual flowers formation resulting from exogenous ethephon induction in melon (Cucumis melo L.) link: https://peerj.com/articles/13088 last-modified: 2022-03-09 description: Melon (Cucumis melo L.) is an agronomically important vegetable. Most cultivars of melon are andromonoecious and bisexual flowers only emerged from the leaf axil of lateral branches. However, the regulatory mechanism contributing to the occurrence of bisexual flowers were still obscure. In this study, ethephon was applied in two common cultivars of melon. In control without ethephon treatment, no bisexual flower was made in the main stem. However, 6.56 ± 1.42 and 6.63 ± 0.55 bisexual flowers were respectively induced in main stem of ‘Yangjiaocui-QX’ and ‘Lvbao’ after ethephon treatment, and induced bisexual flowers distributed in 12–20 nodes of main stem. During the formation of bisexual flowers, 41 metabolites were significantly up-regulated and 98 metabolites were significantly down-regulated. According to the KEGG enrichment analysis of 139 different metabolites, a total of 30 pathways were mapped and KEGG terms of “Phenylalanine, tyrosine and tryptophan biosynthesis”, “Phenylalanine metabolism” and “Flavone and flavonol biosynthesis” were significantly enriched. In three significantly enriched KEGG terms, shikimic acid, L-tryptophan, L-phenylalanine, and kaempferol were significantly up-regulated while L-tyrosine, 4-hydroxycinnami acid and luteolin were significantly down-regulated in ET compared to CK. Different metabolites were also classified depend on major class features and 14 classes were acquired. The results of metabonomics and endogenous hormone identification indicated that ethylene could enhance the concentration of salicylic acid, methyl jasmonate, ABA and IAA. This study provided an important theoretical foundation for inducing bisexual flowers in main stem and breeding new varieties of melon in future. creator: Siyu Fang creator: Yaqian Duan creator: Lanchun Nie creator: Wensheng Zhao creator: Jiahao Wang creator: Jiateng Zhao creator: Liping Zhao creator: Lei Wang uri: https://doi.org/10.7717/peerj.13088 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Fang et al. title: A bZIP transcription factor, PqbZIP1, is involved in the plant defense response of American ginseng link: https://peerj.com/articles/12939 last-modified: 2022-03-08 description: American ginseng (Panax quinquefolius L.) is a perennial medicinal plant that has a long usage history in China. However, root rot, which is mainly caused by Fusarium solani can severely reduce the yield and quality of American ginseng, but no disease-resistant variety of American ginseng exists, and the resistance against this disease is not yet well understood. Thus, it is very urgent to analyze the interaction mechanism regulating the interactions between American ginseng and F. solani to mine disease resistance genes. Using transcriptome data and quantitative polymerase chain reaction (qPCR), we screened the transcription factor PqbZIP1 in response to induction by chitin. Yeast self-activation and subcellular localization experiments proved that PqbZIP1 showed transcriptional activity and was localized in the plant nucleus. In addition, qPCR showed that the highest relative expression level was in the roots, wherein chitin and F. solani inhibited and activated the expression of PqbZIP1, respectively, in American ginseng. Additionally, PqbZIP1 significantly inhibited the growth of the Pseudomonas syringae pv. tomato D36E strain in Nicotiana benthamiana, where expressing PqbZIP1 in N. benthamiana increased the jasmonic acid, salicylic acid, and abscisic acid content. Furthermore, PqbZIP1 expression was continually increased upon inoculation with F. solani. Hence, this study revealed that the PqbZIP1 transcription factor might mediate multiple hormonal signaling pathway to modulate root rot disease resistance in American ginseng, and provided important information to breed disease-resistant American ginseng. creator: Shanshan Yang creator: Xiaoxiao Zhang creator: Ximei Zhang creator: Yanmeng Bi creator: Weiwei Gao uri: https://doi.org/10.7717/peerj.12939 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Yang et al. title: Associations between the rs5498 (A > G) and rs281432 (C > G) polymorphisms of the ICAM1 gene and atherosclerotic cardiovascular disease risk, including hypercholesterolemia link: https://peerj.com/articles/12972 last-modified: 2022-03-08 description: BackgroundAtherosclerotic cardiovascular disease (ASCVD) originates from complex risk factors, including age, gender, dyslipidemia, obesity, race, genetic and genetic variation. ICAM1 gene polymorphisms are a significant risk factor for ASCVD. However, the impact of the rs5498 and rs281432 polymorphisms on the prevalence of hypercholesterolemia (HCL) has not been reported. Therefore, we determine the relationships between single nucleotide polymorphisms (SNPs), including rs5498 and rs281432 on Intercellular adhesion molecule 1 gene (ICAM1) and ASCVD susceptibility in patients with HCL.MethodsThe clinical characteristics of 278 participants were assessed, and classified to groups having HCL and without HCL. ICAM1 SNPs genotyping was performed by DNA sequencing, and ICAM1 expression was measured using real-time PCR.ResultsPositive dominant model rs5498 participants had twice the risk of HCL (95% confidence interval (CI): [1.24–3.23], P = 0.005). The frequency of the G allele in rs5498 was 1.69 times higher in participants with HCL than in controls (95% CI [1.15–2.47], P = 0.007). Participants with the rs5498 AG or GG variants and high ICAM1 mRNA expression (≥3.12) had 2.49 times the risk (95% CI [1.42–4.38], P = 0.001), and those with a high LDL-C concentration (≥3.36 mmol/L) had 2.09 times the risk (95% CI [1.19–3.66], P = 0.010) of developing ASCVD compared with those with low ICAM1 mRNA and LDL-C levels. Interestingly, participants carrying the rs5498 AG or GG variants who had tachycardia (resting heart rates (RHRs) >100 beats/min) had a 5.02-times higher risk than those with a lower RHR (95% CI [1.35–18.63], P = 0.016).ConclusionsIt may consider the G allele in ICAM1rs5498 is associated with a higher risk of ASCVD in Thai people with HCL, and is also positively associated with ICAM1 mRNA expression, LDL-C concentration, and RHR. creator: Naruemon Wechjakwen creator: Amornrat Aroonnual creator: Pattaneeya Prangthip creator: Ngamphol Soonthornworasiri creator: Pornpimol Panprathip Phienluphon creator: Jirayu Lainampetch creator: Karunee Kwanbunjan uri: https://doi.org/10.7717/peerj.12972 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wechjakwen et al. title: Microbial community spatial structures in Luzhou-flavored liquor pit muds with different brewing materials link: https://peerj.com/articles/12987 last-modified: 2022-03-08 description: BackgroundAlthough studies have shown that Bacteroidetes, Clostridiales, and Lactobacillales are the main components of the microbial community in pit mud during the brewing of Luzhou-flavored liquor, little is known about the effect of brewing materials on spatial structures of this microbiome.MethodsHigh-throughput sequencing of the V4–V5 region of prokaryotic 16S rRNA gene was performed to analyze the microbial community diversity and spatial heterogeneity in Luzhou-flavored liquor pit muds with different brewing ingredients. The structural characteristics and heterogeneous spatial distribution of the pit mud microbial communities were examined using bioinformatics and multivariate statistical analysis methods.ResultsOur results showed that Euryarchaeota, Actinobacteria, Bacteroidetes, Chlorobi, Chloroflexi, Firmicutes, Proteobacteria, Synergistetes, Tenericutes, and WWE1 were the dominant phyla in the pit mud microbiome. The Shannon and Simpson indices of the pit mud microbiome with three grains (M3G) in the upper layer were significantly lower than those in middle layer and bottom, whereas those of the pit mud microbiome with five grains (M5G) in bottom were significantly lower than those in middle layer (p < 0.05). There were significant differences in the microbial community compositions between the pit muds with different brewing ingredients and locations in the same pit (p < 0.05). T78 of Anaerolinaceae, Butyrivibrio, Dehalobacter_Syntrophobotulus, Desulfosporosinus, Asteroleplasma, and vadinCA02 of Synergistaceae were significantly enriched in M3G, whereas Prevotella, Vagococcus, Caldicoprobacter, Butyrivibrio, Coprococcus, Dorea, Sporanaerobacter, Tepidimicrobium, TissierellaSoehngenia, RFN20 of Erysipelotrichaceae, Sutterella, 125ds10 of Alteromonadales, Vibrio, and Sphaerochaeta were significantly enriched in M5G. This study provides a theoretical basis for exploring the influence of brewing ingredients in pit muds on the production of Luzhou-flavored liquor and the specific influence of pit mud microorganisms in different locations on liquor production. creator: Jinjin Li creator: Hongzhao Sun creator: Qian Wang creator: Yunfei Cai creator: Zhu Shi creator: Jianlei Jia creator: Lei Zheng creator: Ru Jiang creator: Lingmei Gao uri: https://doi.org/10.7717/peerj.12987 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Li et al. title: Abubidentin A, New Oleanane-type Triterpene Ester from Abutilon bidentatum and its antioxidant, cholinesterase and antimicrobial activities link: https://peerj.com/articles/13040 last-modified: 2022-03-08 description: BackgroundThis work describes the phytochemical and biological investigation of aerial parts of Abutilon bidentatum Hochst. Of Saudi origin.MethodologyPetroleum ether fraction of ethanolic extract A. bidentatum was fractionated on a silica gel column and further purified with different chromatographic procedures for the isolation of chemical compounds. The chemical structures of all the pure isolated compounds were elucidated by the interpretation of their spectral data using IR, UV, 1H, 13C NMR, and MS spectroscopy and chemical methods (alkaline hydrolysis) as well as comparison with data reported in the literature. The extract and isolated compounds were evaluated for antioxidant, cholinesterase inhibitory, and antimicrobial activities.ResultsA new oleanane-type triterpene ester, namely abubidentin A (3) (α, 3β, 30-trihydroxy-29-carboxy-olean-9(11), 12-diene-3-dotriacontanoate), along with two known compounds: 2-hydroxydocosanoic acid (1) and stigmasta-22-ene-3-β-ol (2) were isolated from the aerial parts of Abutilon bidentatum Hochst. (Malvaceae). Concerning the biological potential, the abubidentinA displayed antioxidant, cholinesterase inhibitory and antimicrobial activities. AbubidentinA possessed strong antioxidant activity against DPPH and ABTS+ radical scavenging assays. This new triterpene exhibited high inhibition against acetylcholinesterase (IC50 38.13 ± 0.07 µgmL−1) and butyrylcholinesterase (IC50 32.68 ± 0.37 µgmL−1). Abubidentin A displayed promising antimicrobial activity against Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus (125–150 µgmL−1).ConclusionThese findings suggest A. bidentatum can contribute as a source of new biologically active compounds, especially antioxidants and antimicrobial agents. creator: Gadah A. Al-Hamoud creator: Nawal M. Al-Musayeib creator: Musarat Amina creator: Sabrin R.M. Ibrahim uri: https://doi.org/10.7717/peerj.13040 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Al-Hamoud et al. title: Comparison of the composition and function of gut microbes between adult and juvenile Cipangopaludina chinensis in the rice snail system link: https://peerj.com/articles/13042 last-modified: 2022-03-08 description: Cipangopaludina chinensis is an important economic value snail species with high medicinal value. The gut microbes of aquatic animals plays a vital role in food digestion and nutrient absorption. Herein, we aimed at high-throughput sequencing of 16S rRNA to further investigate whether there were differences in the composition and function of gut microbes of adult and juvenile C. chinensis snails, as well as sediments. This study found that the microbial diversity of the sediment was significantly higher than that of the snails gut (P < 0.001), but there was no significant difference between the gut flora of adult and juvenile snails (P > 0.05). A total of 47 phyla and 644 genera were identified from all samples. Proteobacteria and Verrucomicrobia were the two dominant phyla in all samples, and overall relative abundances was 48.2% and 14.2%, respectively. Moreover, the relative abundances of Aeromonas and Luteolibacter in the gut of juvenile snails (30.8%, 11.8%) were higher than those of adults (27.7%, 10.6%) at the genus level (P > 0.05). Then, four indicator genera were found, namely Flavobacterium, Silanimonas, Geobacter and Zavarzinella, and they abundance in the gut of juvenile snails was significantly higher than that of adults (P < 0.05). This results imply the potential development of Silanimonas as a bait for juvenile snail openings. We observed that Aeromonas was the primary biomarker of the snail gut and sediments (P < 0.001), and it may be a cellulose-degrading bacteria. Function prediction revealed significantly better biochemical function in the snail gut than sediments (P < 0.001), but no significant differences in adult and juvenile snail (P > 0.05). In conclusion, studies show that the snail gut and sediment microbial composition differ, but the two were very similar. The microbial composition of the snail gut was relatively stable and has similar biological functions. These findings provide valuable information for in-depth understanding of the relationship between snails and environmental microorganisms. creator: Kangqi Zhou creator: Junqi Qin creator: Haifeng Pang creator: Zhong Chen creator: Yin Huang creator: Wenhong Li creator: Xuesong Du creator: Luting Wen creator: Xianhui Pan creator: Yong Lin uri: https://doi.org/10.7717/peerj.13042 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhou et al. title: Four new species of Ctenodrilus, Raphidrilus, and Raricirrus (Cirratuliformia, Annelida) in Japanese waters, with notes on their phylogenetic position link: https://peerj.com/articles/13044 last-modified: 2022-03-08 description: Four new species of annelids, Ctenodrilus japonicus sp. nov., Raphidrilus misakiensis sp. nov., Raphidrilus okinawaensis sp. nov., and Raricirrus anubis sp. nov., are described based on specimens collected from Japanese waters. Ctenodrilus japonicus sp. nov. inhabits the interstitial environment and can be distinguished from the other congeners by the following features: (i) total of 16 chaetigers, (ii) chaetigers 1–3 with stout hooks, (iii) minute body (approximately 1 mm in length), (iv) all parapodia with the same number of chaetae (two notochaetae; two neurochaetae), and (v) presence of dorsal and ventral papillae. Raphidrilus misakiensis sp. nov. lives under intertidal stones and can be distinguished from other congeners by having pectinate neurochaetae. Raphidrilus okinawaensis sp. nov. inhabits the interstitial environment and can be distinguished from other congeners by: (i) absence of annulation on the peristomium and achaetous segment and (ii) presence of a heart body in chaetigers 4–5. Raricirrus anubis sp. nov. inhabits whale bones and can be distinguished from other congeners by the following features: (i) presence of a heart body in chaetigers 9–14, (ii) presence of capillary neurochaetae on chaetiger 1, and (iii) presence of simple curved spines. A phylogenetic tree based on partial sequences of cytochrome c oxidase subunit I and 16S rRNA from the new species and other cirratulid worms showed that Raphidrilus is included in Cirratuliformia. This is the first record of Raphidrilus and Raricirrus from Japanese waters. creator: Naoto Jimi creator: Shinta Fujimoto creator: Yoshihiro Fujiwara creator: Kohei Oguchi creator: Toru Miura uri: https://doi.org/10.7717/peerj.13044 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Jimi et al. title: Essential…but also vulnerable? Work intensification, effort/reward imbalance, fatigue and psychological health of Spanish cargo drivers during the COVID-19 pandemic link: https://peerj.com/articles/13050 last-modified: 2022-03-08 description: ObjectiveThis study investigates the combined effect of the Effort/Reward Imbalance (ERI) model of stress and work intensification within the context of the COVID-19 pandemic on the psychological health (general and work-related fatigue, and psychological strain) of cargo drivers, one of the most demanded workforces during the first year of this pandemic.MethodsFor this cross-sectional research, the data provided by n = 1,013 professional drivers from the different 17 autonomous communities (regions) of Spain were analyzed. Participants answered a questionnaire composed of the short version of the Effort Reward Imbalance (ERI) questionnaire, a Work Intensification Scale (WIS) designed for this study, the fatigue subscale of the Checklist Individual Strength (CIS), the Need for Recovery after Work Scale (NFR), and the General Health Questionnaire (GHQ).ResultsHierarchical regression analyses show that both (ERI and work intensification) models significantly predict driver’s fatigue and psychological strain. The effect of work intensification exists above and beyond the effect of effort/reward imbalance, which has been previously related to the safety performance of cargo drivers.ConclusionsThese findings suggest that the ERI and work intensification models can be complementarily used, especially in scenarios introducing substantial changes in the work environment, such as the COVID-19 crisis. Also, the results of this study support the need to intervene in the working conditions of professional drivers in order to improve their psychological health and well-being during both pandemic and post-pandemic times, as crisis-related management interventions are necessary to promote health and safety in professional drivers in potentially similar contexts in the future. creator: Luis Montoro creator: Boris Cendales creator: Francisco Alonso creator: Adela Gonzalez-Marin creator: Ignacio Lijarcio creator: Javier Llamazares creator: Sergio A. Useche uri: https://doi.org/10.7717/peerj.13050 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Montoro et al. title: Effect of individualized weight management intervention on excessive gestational weight gain and perinatal outcomes: a randomized controlled trial link: https://peerj.com/articles/13067 last-modified: 2022-03-08 description: It is unclear whether weight management is still effective for pregnant women with excessive weight gain in the second or third trimester in China. This study adopted individualized weight management intervention for pregnant women with abnormal weight gain in the second or third trimester, to analyze the effect of intervention by observing the gestational weight gain and perinatal outcomes. This randomized controlled trial was performed at Aerospace Center Hospital. The obstetrician determined whether the pregnant women gained too much weight in the second or third trimester according to the Institute of Medicine guidelines, and randomly divided the pregnant women who gained too much weight in the second or third trimester into the intervention group or the control group according to the inclusion and exclusion criteria. The pregnant women in the intervention group and in the control group all received routine prenatal examination and diet nutrition education by the doctors in the Department of Obstetrics and Gynecology. The intervention group underwent individualized weight management, including individualized diet, exercise, psychological assessment, cognitive intervention and continuous communication, the whole process is tracked and managed by professional nutritionists. The obstetrician collected the prenatal examination data and pregnancy outcome data of all enrolled pregnant women. The primary outcome measure was weight gain during pregnancy. A generalized linear model and a logistic regression model were used to compare the outcomes between the two groups. In total, 348 pregnant women participated in this study with 203 in the intervention group and 145 in the control group. The whole gestational weight gain in the intervention group (15.8 ± 5.4 Kg) was lower than that in the control group (17.5 ± 3.6 Kg; adjusted β =  − 1.644; 95% CI [−2.660–−0.627]; P = 0.002). The percent of pregnant women with excessive weight gainbefore delivery was 54.2% (110/203) in the intervention group, which was lower than 69.7% (101/145) in the control group (adjusted RR = 0.468; 95% CI [0.284–0.769] P = 0.003). The pregnant women given the individualized weight management intervention from the second to the third trimester experienced less weight gain than that from the third trimester (15.5 ± 5.6 Kg vs. 16.2 ± 5.2 Kg), but without significant difference (P = 0.338). Lower rates of GDM, preeclampsia and gestational hypertension, higher rates of fetal distress and puerperal infection were observed in the intervention group than in the control group (all P < 0.05). Individualized weight management during the second or third trimesters is still beneficial for pregnant women who gain excessive weight and can decrease the associated adverse outcomes. creator: Mei-Yan Xu creator: Yan-Jun Guo creator: Li-Juan Zhang creator: Qing-Bin Lu uri: https://doi.org/10.7717/peerj.13067 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Xu et al. title: Increased level of FAM19A5 is associated with cerebral small vessel disease and leads to a better outcome link: https://peerj.com/articles/13101 last-modified: 2022-03-08 description: ObjectiveFAM19A5 plays an essential role in the development and acute or chronic inflammation of the central nervous system. The present study aimed to explore the association between FAM19A5 and cerebral small vessel disease (cSVD).MethodsA total of 344 recent small subcortical infarct (RSSI) patients and 265 healthy controls were included in this study. The difference in the FAM19A5 level between the two groups was compared and the correlation between FAM19A5 and cerebral infarction volume was analyzed. Also, the association between FAM19A5 and the total magnetic resonance imaging (MRI) burden with its imaging characteristics was explored. Moreover, the correspondence of FAM19A5 with the outcome was assessed via Δ National Institutes of Health Stroke Scale score (NIHSS) and the percentage of NIHSS improvement.ResultsFAM19A5 was highly expressed in the RSSI group (P = 0.023), showing a positive correlation with cerebral infarction volume (P < 0.01). It was positively correlated with total MRI cSVD burden (P < 0.001) and reflected the severity of white matter hyperintensity (WMH) (P < 0.01) and enlarged perivascular space (EPVS) (P < 0.01), but did not show any association with cerebral microbleed (CMB) and lacune. Moreover, FAM19A5 suggested a larger Δ NIHSS (P = 0.021) and NIHSS improvement percentage (P = 0.007).ConclusionSerum FAM19A5 was increased in RSSI and positively correlated with the infarct volume. It also reflects the total MRI burden of cSVD, of which the imaging characteristics are positively correlated with WMH and EPVS. In addition, higher FAM19A5 levels reflect better outcomes in RSSI patients. creator: Zhongnan Hao creator: Shaonan Yang creator: Ruihua Yin creator: Jin Wei creator: Yuan Wang creator: Xudong Pan creator: Aijun Ma uri: https://doi.org/10.7717/peerj.13101 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Hao et al. title: Response of soil microbial community to plant composition changes in broad-leaved forests of the karst area in Mid-Subtropical China link: https://peerj.com/articles/12739 last-modified: 2022-03-07 description: The rapid growth and expansion ofCryptomeria japonica (Thunb. ex L. f.) D. Don in karst area strongly affects plant composition of native deciduous broad-leaved forest, which seriously threat ecosystem function and service. Given the importance of soil microorganisms in regulating nutrients cycling and plant species coexistence, understanding soil microbial attributes and their relationships with soil and vegetation features in forests harboring different C. japonica abundance will help understanding the drivers of ecosystem function changes. Here we examined the diversity and composition of soil bacterial and fungal communities and their correlations with plant diversity as well as soil physicochemical properties in karst broad-leaved forests with different relative abundances of C. japonica (i.e., a high, moderate, low and no proportion level with a stem density of 1,487, 538, 156 and 0 plant/hm2, respectively) in Mid-Subtropical China. We found that soil pH decreased while soil water content (SWC), total nitrogen (TN), total phosphorus (TP) and total potassium (TK) tended to increase with the increase in C. japonica abundance. In contrast, soil available nitrogen (AN), available phosphorus (AP) and available potassium (AK) content declined by 26.1%∼49.3% under the high level of C. japonica abundance. A gradual decrease in relative abundance of Acidobacteria and Chloroflexi while a pronounced increase in relative abundance of Ascomycota and Basidiomycota were observed with increase of C. japonica abundance. Alternations in bacterial composition were closely related to changes in AP and AK, while the change of fungal structure was mainly related to SWC, soil organic carbon (SOC) and pH, indicating that bacterial community was sensitive to declines in soil available nutrients and fungal structure was sensitive to changes in soil physicochemical properties (i.e., pH and SWC) and organic carbon resource. Understory plants had the highest α-diversity in forest containing moderate abundance of C. japonica, which might be related to the high bacterial diversity. Our findings suggest conservation of soil bacterial and fungal taxa that are responsible for nutrients availability and carbon sequestration is of great significance for improving the resistance of natural deciduous broad-leaved forests to the rapid spread of C. japonica in karst areas. Moreover, Acidobacteria, Chloroflexi, Ascomycota and Basidiomycota are potential indicators for soil properties changes, which should be taken into consideration in karst forest managements. creator: Liling Liu creator: Ninghua Zhu creator: Guangyi Zhou creator: Peng Dang creator: Xiaowei Yang creator: Liqiong Qiu creator: Muyi Huang creator: Yingyun Gong creator: Suya Zhao creator: Jie Chen uri: https://doi.org/10.7717/peerj.12739 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Liu et al. title: Growth, maturity, and diet of the pearl whipray (Fontitrygon margaritella) from the Bijagós Archipelago, Guinea-Bissau link: https://peerj.com/articles/12894 last-modified: 2022-03-07 description: The pearl whipray Fontitrygon margaritella (Compagno & Roberts, 1984) is a common elasmobranch in coastal western African waters. However, knowledge on their life-history and trophic ecology remains limited. Therefore, we aimed to determine the growth, maturity and diet of F. margaritella from the Bijagós Archipelago in Guinea-Bissau. Growth was modelled with: von Bertalanffy, Gompertz and logistic functions. Model selection revealed no model significantly outperformed another. The sampled age ranged from less than 1 to 7 years (1.8 ± 1.9 cm, mean ± standard deviation) and size (disc width) ranged from 12.2 to 30.6 cm (18.7 ± 5.2 cm). Size-at-maturity was estimated at 20.3 cm (95% CI [18.8–21.8 cm]) for males and 24.3 cm for females (95% CI [21.9–26.5 cm]), corresponding ages of 2.2 and 3.9 years. The diet differed significantly among young-of-the-year (YOY), juveniles and adults (p = 0.001). Diet of all life stages consisted mainly of crustaceans (27.4%, 28.5%, 33.3%) and polychaetes (12.5%, 26.7%, 20.3%), for YOY, juveniles and adults respectively. This study shows that F. margaritella is relatively fast-growing, matures early and experiences ontogenetic diet shifts. These results contribute to status assessments and conservation efforts of F. margaritella and closely related species. creator: Owen N. Clements creator: Guido Leurs creator: Rob Witbaard creator: Ido Pen creator: Yvonne I. Verkuil creator: Laura L. Govers uri: https://doi.org/10.7717/peerj.12894 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Clements et al. title: Sea urchin harvest inside marine protected areas: an opportunity to investigate the effects of exploitation where trophic upgrading is achieved link: https://peerj.com/articles/12971 last-modified: 2022-03-07 description: BackgroundMarine protected areas (MPAs) usually have both positive effects of protection for the fisheries’ target species and indirect negative effects for sea urchins. Moreover, often in MPAs sea urchin human harvest is restricted, but allowed. This study is aimed at estimating the effect of human harvest of the sea urchin Paracentrotus lividus within MPAs, where fish exploitation is restricted and its density is already controlled by a higher natural predation risk. The prediction we formulated was that the lowest densities of commercial sea urchins would be found where human harvest is allowed and where the harvest is restricted, compared to where the harvest is forbidden.MethodsAt this aim, a collaborative database gained across five MPAs in Sardinia (Western Mediterranean, Italy) and areas outside was gathered collecting sea urchin abundance and size data in a total of 106 sites at different degrees of sea urchin exploitation: no, restricted and unrestricted harvest sites (NH, RH and UH, respectively). Furthermore, as estimates made in past monitoring efforts (since 2005) were available for 75 of the sampled sites, for each of the different levels of exploitation, the rate of variation in the total sea urchin density was also estimated.ResultsResults have highlighted that the lowest sea urchin total and commercial density was found in RH sites, likely for the cumulative effects of human harvest and natural predation. The overall rate of change in sea urchin density over time indicates that only NH conditions promoted the increase of sea urchin abundance and that current local management of the MPAs has driven towards an important regression of populations, by allowing the harvest. Overall, results suggest that complex mechanisms, including synergistic effects between natural biotic interactions and human pressures, may occur on sea urchin populations and the assessment of MPA effects on P. lividus populations would be crucial to guide management decisions on regulating harvest permits. Overall, the need to ban sea urchin harvest in the MPAs to avoid extreme reductions is encouraged, as inside the MPAs sea urchin populations are likely under natural predation pressures for the trophic upgrading. creator: Giulia Ceccherelli creator: Piero Addis creator: Fabrizio Atzori creator: Nicoletta Cadoni creator: Marco Casu creator: Stefania Coppa creator: Mario De Luca creator: Giuseppe Andrea de Lucia creator: Simone Farina creator: Nicola Fois creator: Francesca Frau creator: Vittorio Gazale creator: Daniele Grech creator: Ivan Guala creator: Mariano Mariani creator: Massimo SG Marras creator: Augusto Navone creator: Arianna Pansini creator: Pieraugusto Panzalis creator: Federico Pinna creator: Alberto Ruiu creator: Fabio Scarpa creator: Luigi Piazzi uri: https://doi.org/10.7717/peerj.12971 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Ceccherelli et al. title: A new Amazonian species of Allobates Zimmermann & Zimmermann, 1988 (Aromobatidae) with a trilled advertisement call link: https://peerj.com/articles/13026 last-modified: 2022-03-07 description: BackgroundCurrently, 58 species are assigned to the genus Allobates, with 70% of its diversity described just in the last two decades, with many additional species likely unnamed. The continuous description of these new species represents a fundamental step for resolving the taxonomy and ensuring the future conservation of the genus.MethodsUsing molecular, acoustic, and morphological evidences, we describe a new species of Allobates from Teles Pires River region, southern Amazonia, and provide accounts on the population of A. tapajos found sympatrically with the new species.ResultsThe new species is distinguished from its congeners by the coloration of thighs, venter, dorsum, and dark lateral stripe. It has four types of calls, with advertisement calls formed by relatively long trills with a mean duration of 2.29 s ± 0.65, mean of 39.93 notes ± 11.18 emitted at a mean rate of 17.49 ± 0.68 notes per second, and mean dominant frequency of 5,717 Hz ± 220.81. The genetic distance between the new species and its congeners in a fragment of the 16S mitochondrial fragment ranged between 13.2% (A. carajas) to 21.3% (A. niputidea). The sympatric Allobates population fits its morphology and acoustic with the nominal A. tapajos, but presents a relatively high genetic distance of nearly 6.5%, raising questions on the current taxonomy of this species. creator: Leandro A. Silva creator: Ricardo Marques creator: Henrique Folly creator: Diego J. Santana uri: https://doi.org/10.7717/peerj.13026 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Silva et al. title: Perception, knowledge, and attitude of medical doctors in Saudi Arabia about the role of physiotherapists in vestibular rehabilitation: a cross-sectional survey link: https://peerj.com/articles/13035 last-modified: 2022-03-07 description: ObjectivesThere is compelling scientific evidence about the role of physiotherapists in vestibular rehabilitation. However, patients with vestibular-associated dizziness and balance disturbances are seldom referred to physiotherapists in Saudi Arabia. Therefore, this study aims to achieve insight into perceptions, knowledge, attitudes, and referral practices among Saudi Arabian medical doctors relating to the role of physiotherapists in vestibular rehabilitation.MethodsA sample of 381 medical doctors practicing in Saudi Arabia participated in this nationwide cross-sectional study. The sample was obtained from 226 hospitals across 13 provinces of Saudi Arabia by stratified sampling method. The 23-item questionnaire developed by a team of experts was emailed to medical doctors practicing in various hospitals across Saudi Arabia.ResultsOut of 1,231 medical doctors invited, 381 medical doctors responded, giving a response rate of 30.9%. One hundred ninety-three (50.6%) medical doctors reported managing patients with vestibular rehabilitation. The most preferred specialist for managing patients with vestibular disorders was an Ear Nose Throat (ENT) specialist (n = 173, 89.6%). Related Sample Cochran’s Q test showed statistically significant difference between preferred specialist for managing patients with vestibular disorders (ENT specialists, physiotherapists, nurses, occupational therapists and audiologists) (χ2(4) = 482.476, p = 0.001). Out of 193 medical doctors, 153 (79.2%) reported no role of the physiotherapist in vestibular rehabilitation. One hundred forty-five (75.1%) of medical doctors reported that they were not aware of the role of physiotherapists in vestibular rehabilitation. Only 27 (15.5%) medical doctors reported referring patients with vestibular disorders to physiotherapists.ConclusionThe study reports that physiotherapy services are underutilized in vestibular rehabilitation due to limited referral from Saudi Arabian medical doctors. Therefore, there is a need to increase the awareness among Saudi Arabian doctors about the physiotherapist’s role in vestibular rehabilitation. creator: Danah Alyahya creator: Faizan Z. Kashoo uri: https://doi.org/10.7717/peerj.13035 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Alyahya and Kashoo title: Loss of gut microbial diversity in the cultured, agastric fish, Mexican pike silverside (Chirostoma estor: Atherinopsidae) link: https://peerj.com/articles/13052 last-modified: 2022-03-07 description: Teleost fish are the most diverse group of extant vertebrates and have varied digestive anatomical structures and strategies, suggesting they also possess an array of different host-microbiota interactions. Differences in fish gut microbiota have been shown to affect host development, the process of gut colonization, and the outcomes of gene-environment or immune system-microbiota interactions. There is generally a lack of studies on the digestive mechanisms and microbiota of agastric short-intestine fish however, meaning that we do not understand how changes in gut microbial diversity might influence the health of these types of fish. To help fill these gaps in knowledge, we decided to study the Mexican pike silverside (Chirostoma estor) which has a simplified alimentary canal (agastric, short-intestine, 0.7 gut relative length) to observe the diversity and metabolic potential of its intestinal microbiota. We characterized gut microbial populations using high-throughput sequencing of the V3 region in bacterial 16S rRNA genes while searching for population shifts resulting associated with fish development in different environments and cultivation methods. Microbiota samples were taken from the digesta, anterior and posterior intestine (the three different intestinal components) of fish that grew wild in a lake, that were cultivated in indoor tanks, or that were raised in outdoor ponds. Gut microbial diversity was significantly higher in wild fish than in cultivated fish, suggesting a loss of diversity when fish are raised in controlled environments. The most abundant phyla observed in these experiments were Firmicutes and Proteobacteria, particularly of the genera Mycoplasma, Staphylococcus, Spiroplasma, and Aeromonas. Of the 14,161 OTUs observed in this experiment, 133 were found in all groups, and 17 of these, belonging to Acinetobacter, Aeromonas, Pseudomonas, and Spiroplasma genera, were found in all samples suggesting the existence of a core C. estor microbiome. Functional metagenomic prediction of bacterial ecological functions using PICRUSt2 suggested that different intestinal components select for functionally distinct microbial populations with variation in pathways related to the metabolism of amino acids, vitamins, cofactors, and energy. Our results provide, for the first time, information on the bacterial populations present in an agastric, short-gut teleost with commercial potential and show that controlled cultivation of this fish reduces the diversity of its intestinal microbiota. creator: Jesús Mateo Amillano-Cisneros creator: Perla T. Hernández-Rosas creator: Bruno Gomez-Gil creator: Pamela Navarrete-Ramírez creator: María Gisela Ríos-Durán creator: Carlos Cristian Martínez-Chávez creator: David Johnston-Monje creator: Carlos Antonio Martínez-Palacios creator: Luciana Raggi uri: https://doi.org/10.7717/peerj.13052 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Amillano-Cisneros et al. title: Hydrogen sulphide alleviates Fusarium Head Blight in wheat seedlings link: https://peerj.com/articles/13078 last-modified: 2022-03-07 description: Hydrogen sulphide (H2S), a crucial gas signal molecule, has been reported to be involved in various processes related to development and adversity responses in plants. However, the effects and regulatory mechanism of H2S in controlling Fusarium head blight (FHB) in wheat have not been clarified. In this study, we first reported that H2S released by low concentrations of sodium hydrosulphide (NaHS) could significantly alleviate the FHB symptoms caused by Fusarium graminearum (F. graminearum) in wheat. We also used coleoptile inoculation to investigate the related physiological and molecular mechanism. The results revealed that FHB resistance was strongly enhanced by the H2S released by NaHS, and 0.3 mM was confirmed as the optimal concentration. H2S treatment dramatically reduced the levels of hydrogen peroxide (H2O2) and malondialdehyde (MDA) while enhancing the activities of antioxidant enzymes. Meanwhile, the relative expressions levels of defence-related genes, including PR1.1, PR2, PR3, and PR4, were all dramatically upregulated. Our results also showed that H2S was toxic to F. graminearum by inhibiting mycelial growth and spore germination. Taken together, the findings demonstrated the potential value of H2S in mitigating the adverse effects induced by F. graminearum and advanced the current knowledge regarding the molecular mechanisms in wheat. creator: Yuanyuan Yao creator: Wenjie Kan creator: Pengfei Su creator: Yan Zhu creator: Wenling Zhong creator: Jinfeng Xi creator: Dacheng Wang creator: Caiguo Tang creator: Lifang Wu uri: https://doi.org/10.7717/peerj.13078 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Yao et al. title: Growth regulators promote soybean productivity: a review link: https://peerj.com/articles/12556 last-modified: 2022-03-04 description: Soybean [Glycine max (L.) Merrill] is a predominant edible plant and a major supply of plant protein worldwide. Global demand for soybean keeps increasing as its seeds provide essential proteins, oil, and nutraceuticals. In a quest to meet heightened demands for soybean, it has become essential to introduce agro-technical methods that promote adaptability to complex environments, improve soybean resistance to abiotic stress , and increase productivity. Plant growth regulators are mainly exploited to achieve this due to their crucial roles in plant growth and development. Increasing research suggests the influence of plant growth regulators on soybean growth and development, yield, quality, and abiotic stress responses. In an attempt to expatiate on the topic, current knowledge, and possible applications of plant growth regulators that improve growth and yield have been reviewed and discussed. Notably, the application of plant growth regulators in their appropriate concentrations at suitable growth periods relieves abiotic stress thereby increasing the yield and yield components of soybean. Moreover, the regulation effects of different growth regulators on the morphology, physiology, and yield quality of soybean are discoursed in detail. creator: Hanna Amoanimaa-Dede creator: Chuntao Su creator: Akwasi Yeboah creator: Hang Zhou creator: Dianfeng Zheng creator: Hongbo Zhu uri: https://doi.org/10.7717/peerj.12556 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Amoanimaa-Dede et al. title: A combined association of serum uric acid, alanine aminotransferase and waist circumference with non-alcoholic fatty liver disease: a community-based study link: https://peerj.com/articles/13022 last-modified: 2022-03-04 description: BackgroundIncreasing evidence has supported that serum uric acid (SUA), alanine aminotransferase (ALT) and waist circumference (WC) are associated with the occurrence of non-alcoholic fatty liver disease (NAFLD). However, the combined role of these factors in early screening of NAFLD has not been investigated. We aimed to de lineate this role in a community-based population.MethodsBinary logistic regression was used to explore the correlations of SUA, ALT and WC with NAFLD risk. The goodness of fit and discriminative ability of the model were evaluated by the Hosmer-Lemeshow test and area under the receiver operating characteristic curve (AUROC), respectively.ResultsLogistic regression analysis indicated that elevated SUA (adjusted odds ratio (OR) = 2.44, 95% confidence interval (CI) [1.76–3.38]), ALT (adjusted OR = 4.98, 95% CI [3.41–7.27]) and WC (adjusted OR = 3.22, 95% CI [2.01–5.16]) were facilitating factors for incident NAFLD after fully adjusted for related confounders. In addition, the risk of NAFLD followed linear trend s with increasing levels of these three indicators (all Ptrend < 0.001). The risk assessment model consisting of SUA, ALT, WC and demographics showed useful discrimination by AUROC being 0.825 (95% CI [0.811–0.838]) and good performance of calibration (P = 0.561).ConclusionsSUA, ALT and WC were all associated with NAFLD, independent of known risk factors. The simple model composed of these indicators showed good performance in the Chinese population, which may be applicable for appraisal of NAFLD risk in primary healthcare. creator: Min Wang creator: Minxian Wang creator: Ru Zhang creator: Liuxin Zhang creator: Yajie Ding creator: Zongzhe Tang creator: Haozhi Fan creator: Hongliang Wang creator: Wei Zhang creator: Yue Chen creator: Jie Wang uri: https://doi.org/10.7717/peerj.13022 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wang et al. title: Morphological description and molecular identification of Myxobolus dajiangensis n. sp. (Myxozoa: Myxobolidae) from the gill of Cyprinus carpio in southwest China link: https://peerj.com/articles/13023 last-modified: 2022-03-04 description: BackgroundMyxosporean diversity is a hot topic since they are difficult to accurately identify and classify. Many Myxobolus parasites have been named as Myxobolus koi because of their similar morphological features with the species originally reported. However, the distinctions in fine morphological features, host specificity, and molecular data have given rise to the attention of researchers.MethodsThe classical morphometric and histological methods were used to describe the Myxobolus dajiangensis n. sp. in morphology. The common techniques in modern molecular biology and the methods of phylogenetic analyses were combined to identify the species.ResultsPlasmodia of interlamellar-vascular type were found in the vascular network of gill lamellae. Mature myxospores of M. dajiangensis n. sp. were elongated and pyriform from the frontal view. The myxospores were 14.8 ± 0.4 (13.9–15.6) µm in length, 8.0 ± 0.5 (7.2–9.1) µm in width, and 5.5 µm in thickness. The two polar capsules were pyriform and slightly different in length. The length of the larger polar capsules was 8.0 ± 0.4 (7.1–8.8) µm, and it was 7.4 ± 0.4 (6.1–8.0) µm for the smaller ones. The width of both polar capsules was 2.5 ± 0.2 (2.0–3.2) µm. The polar filaments within the polar capsules were each coiled nine to 11 turns. Comparative analysis of both the morphological and molecular data between the present speices and other similar species revealed that the present species is a novel species, Myxobolus dajiangensis n. sp. Also, M. koi (FJ710800) was misidentified and the congener with M. dajiangensis n. sp., depending on the secondary structures of SSU rRNA and phylogenetic analysis. Moreover, the cryptic species existed in the M. koi parasites. creator: Miao-miao Wang creator: Jin-ye Zhang creator: Yuan-jun Zhao uri: https://doi.org/10.7717/peerj.13023 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wang et al. title: Lung–brain ‘cross-talk’: systemic propagation of cytokines in the ARDS via the bloodstream using a blood transfusion model does not influence cerebral inflammatory response in pigs link: https://peerj.com/articles/13024 last-modified: 2022-03-04 description: BackgroundInterorgan cross-talk describes the phenomenon in which a primarily injured organ causes secondary damage to a distant organ. This cross-talk is well known between the lung and brain. One theory suggests that the release and systemic distribution of cytokines via the bloodstream from the primarily affected organ sets in motion proinflammatory cascades in distant organs. In this study, we analysed the role of the systemic distribution of cytokines via the bloodstream in a porcine ARDS model for organ cross-talk and possible inflammatory changes in the brain.MethodsAfter approval of the State and Institutional Animal Care Committee, acute respiratory distress syndrome (ARDS) induction with oleic acid injection was performed in seven animals. Eight hours after ARDS induction, blood (35–40 ml kg–1) was taken from these seven ‘ARDS donor’ pigs. The collected ‘ARDS donor’ blood was transfused into seven healthy ‘ARDS-recipient’ pigs. Three animals served as a control group, and blood from these animals was transfused into three healthy pigs after an appropriate ventilation period. All animals were monitored for 8 h using advanced cardiorespiratory monitoring. Postmortem assessment included cerebral (hippocampal and cortex) mediators of early inflammatory response (IL-6, TNF-alpha, iNOS, sLCN-2), wet-to-dry ratio and lung histology. TNF-alpha serum concentration was measured in all groups.ResultsARDS was successfully induced in the ‘ARDS donor’ group, and serum TNF-alpha levels were elevated compared with the ‘ARDS-recipient’ group. In the ‘ARDS-recipient’ group, neither significant ARDS alterations nor upregulation of inflammatory mediators in the brain tissue were detected after high-volume random allogenic ‘ARDS-blood’ transfusion. The role of the systemic distribution of inflammatory cytokines from one affected organ to another could not be confirmed in this study. creator: René Rissel creator: Moritz Schaefer creator: Jens Kamuf creator: Robert Ruemmler creator: Julian Riedel creator: Katja Mohnke creator: Miriam Renz creator: Erik K. Hartmann creator: Alexander Ziebart uri: https://doi.org/10.7717/peerj.13024 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Rissel et al. title: A comparative study of life skills, lifestyle habits and academic performance in health promoting and non-health promoting schools in the Autonomous Community of Aragon, Spain link: https://peerj.com/articles/13041 last-modified: 2022-03-04 description: BackgroundThere is insufficient evidence about the impact of health promoting schools on the student’s health and academic performance. The aim of this study was to compare the life skills, lifestyle habits and academic performance of 7th and 8th grade students registered in health promoting and non-health promoting schools in the Autonomous Community of Aragon.MethodsAn observational, descriptive, comparative study of the life skills, lifestyle habits and academic performance of 7th and 8th grade students registered in 43 randomly selected health promoting and non-health promoting schools was carried out. We used an adapted tool, which was validated through the expert panel technique, to evaluate the students’ life skills (self-efficacy, social skills and affect balance), lifestyle habits (diet, sleep, physical exercise, use of screen and substance abuse) and academic performance.ResultsThe socioeconomic level of the mothers and fathers of the students who attended non-health promoting schools was significantly higher than that of the parents of the adolescents who attended health promoting schools (p < 0.001). The students who attended non-health promoting schools had better self-efficacy, led a healthier life generally and achieved better academic results (p = 0.03).ConclusionsAs opposed to previous studies, which found a positive association between health promoting schools and life skills, lifestyle habits and academic performance, our findings suggest that the impact of these health programs on the students’ health and academic performance is limited. We recommend that the degree of implementation of health promotion programs in health promoting schools is systematically evaluated, and the health promoting school accreditation process and requirements reviewed, in order to ensure that the health of school children and adolescents is safeguarded and promoted in the short, medium and long term. creator: Beatriz Sánchez-Hernando creator: Ángel Gasch-Gallén creator: Isabel Antón-Solanas creator: Vicente Gea-Caballero creator: Raúl Juárez-Vela creator: Javier Gállego-Diéguez creator: María Inmaculada Carboneres-Tafaner creator: Emmanuel Echániz-Serrano creator: Laura Lasso-Olayo creator: Ivan Santolalla-Arnedo uri: https://doi.org/10.7717/peerj.13041 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Sánchez-Hernando et al. title: Analyzing the relationship between self-efficacy and impulsivity in amateur soccer referees link: https://peerj.com/articles/13058 last-modified: 2022-03-04 description: Soccer referees (SRs) are exposed to stressful situations during the competition that can affect decision-making, could be affected by impulsivity during the competition and therefore, require optimal psychological skills. The objective of this study was to ascertain and analyze the relationship between levels of impulsivity and self-efficacy of amateur SRs in the senior category. A total of 21 Spanish SRs participated in this study (age 23.57 ± 2.40 years and 7.81 ± 2.58 seasons of experience). Self-efficacy data were collected with the REFS questionnaire between 48 and 72 h before the competition. The impulsivity data were collected using the UPPS-P questionnaire 60 min before the start the competition. The results indicate that SRs with higher self-efficacy have lower levels of impulsivity, specifically in the dimensions of negative urgency (p < 0.01), positive urgency (p < 0.05), lack of premeditation (p < 0.001), and lack of perseverance (p < 0.001), as well as lower global impulsivity (p < 0.01). However, the SRs with the highest self-efficacy also obtained higher levels in the sensation seeking dimension (p < 0.05). In conclusion, the main finding of this study showed that self-efficacy is influenced by SR impulsivity prior to competition. These novel facts allow us to discover aspects related to decision-making in refereeing that can be trained to reach optimal levels. creator: José López-Aguilar creator: Rafael Burgueño creator: Alfonso Castillo-Rodriguez creator: Wanesa Onetti-Onetti uri: https://doi.org/10.7717/peerj.13058 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 López-Aguilar et al. title: Factors regulating growth pattern and condition factor of an amphibious fish Periophthalmus gracilis living in the Mekong Delta link: https://peerj.com/articles/13060 last-modified: 2022-03-04 description: Growth pattern and condition factor (CF) are essential to fish resource assessment but limited to Periophthalmus gracilis—an amphibious fish living in the mudflats along the Indo-Pacific regions, including the Mekong Delta (MD), Vietnam. This study lasted from April 2020 to March 2021 to verify if their growth pattern and CF change with sex, size, season, month and site. The total length and weight of 486 individuals (236 females and 250 males) were 2.9–5.9 cm and 0.13–1.66 g, respectively. The mudskipper displayed negative allometry as the slope value (b = 2.69 ± 0.06) obtained from length and weight (LWR) was significantly less than 3 (p < 0.01), indicating that most fish specimens were caught in the immature stage. The fish growth pattern did not change with sex as both males and females displayed negative allometry but varied by size since the mudskipper showed negative allometry in the immature group and isometry in the mature group. Likewise, growth type changed with season since fish showed negative allometry in the dry season but isometry in the wet season. As the slope value (b) varied by site and month, the mudskipper displayed spatiotemporal growth patterns, ranging from negative to positive allometry. The CF was impacted by sex as this value of females (1.09 ± 0.02) was higher than that of males (0.96 ± 0.01, p < 0.01). Besides, CF was regulated by fish length since this value was higher in the mature group (1.12 ± 0.03) than in the immature group (1.01 ± 0.01, p < 0.01). Likewise, CF was affected by season as this value was higher in the wet season (1.05 ± 0.02) than in the dry season (0.99 ± 0.01, p < 0.01). Although the CF varied with site and month variables (p < 0.01), this value (1.02 ± 0.01) was generally higher than 1, showing fish adapted well to their habitat. The fish length at first capture should be increased to exploit this species sustainably. creator: Quang Minh Dinh creator: Ton Huu Duc Nguyen creator: Ngon Trong Truong creator: Lam Nguyen-Ngoc uri: https://doi.org/10.7717/peerj.13060 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Dinh et al. title: An overview of the nutritional value, health properties, and future challenges of Chinese bayberry link: https://peerj.com/articles/13070 last-modified: 2022-03-04 description: Chinese bayberry (CB) is among the most popular and valuable fruits in China owing to its attractive color and unique sweet/sour taste. Recent studies have highlighted the nutritional value and health-related benefits of CB. CB has special biological characteristics of evergreen, special aroma, dioecious, nodulation, nitrogen fixation. Moreover, the fruits, leaves, and bark of CB plants harbor a number of bioactive compounds including proanthocyanidins, flavonoids, vitamin C, phenolic acids, and anthocyanins that have been linked to the anti-cancer, anti-oxidant, anti-inflammatory, anti-obesity, anti-diabetic, and neuroprotective properties and to the treatment of cardiovascular and cerebrovascular diseases. The CB fruits have been used to produce a range of products: beverages, foods, and washing supplies. Future CB-related product development is thus expected to further leverage the health-promoting potential of this valuable ecological resource. The present review provides an overview of the botanical characteristics, processing, nutritional value, health-related properties, and applications of CB in order to provide a foundation for further research and development. creator: Shuwen Zhang creator: Zheping Yu creator: Li Sun creator: Haiying Ren creator: Xiliang Zheng creator: Senmiao Liang creator: Xingjiang Qi uri: https://doi.org/10.7717/peerj.13070 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhang et al. title: Hurricane María drives increased indoor proliferation of filamentous fungi in San Juan, Puerto Rico: a two-year culture-based approach link: https://peerj.com/articles/12730 last-modified: 2022-03-03 description: Extensive flooding caused by Hurricane María in Puerto Rico (PR) created favorable conditions for indoor growth of filamentous fungi. These conditions represent a public health concern as contamination by environmental fungi is associated with a higher prevalence of inflammatory respiratory conditions. This work compares culturable fungal spore communities present in homes that sustained water damage after Hurricane María to those present in dry, non-flooded homes. We collected air samples from 50 houses in a neighborhood in San Juan, PR, 12 and 22 months after Hurricane María. Self-reported data was used to classify the homes as flooded, water-damage or dry non-flooded. Fungi abundances, composition and diversity were analyzed by culturing on two media. Our results showed no significant differences in indoor fungal concentrations (CFU/m3) one year after the Hurricane in both culture media studied (MEA and G25N). During the second sampling period fungal levels were 2.7 times higher in previously flooded homes (Median = 758) when compared to dry homes (Median = 283), (p-value < 0.005). Fungal profiles showed enrichment of Aspergillus species inside flooded homes compared to outdoor samples during the first sampling period (FDR-adjusted p-value = 0.05). In contrast, 22 months after the storm, indoor fungal composition consisted primarily of non-sporulated fungi, most likely basidiospores, which are characteristic of the outdoor air in PR. Together, this data highlights that homes that suffered water damage not only have higher indoor proliferation of filamentous fungi, but their indoor fungal populations change over time following the Hurricane. Ultimately, after nearly two years, indoor and outdoor fungal communities converged in this sample of naturally ventilated homes. creator: Lorraine N. Vélez-Torres creator: Benjamín Bolaños-Rosero creator: Filipa Godoy-Vitorino creator: Felix E. Rivera-Mariani creator: Juan P. Maestre creator: Kerry Kinney creator: Humberto Cavallin uri: https://doi.org/10.7717/peerj.12730 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Vélez-Torres et al. title: Back pain and body posture of non-professional Brazilian Jiu-Jitsu practitioners link: https://peerj.com/articles/12838 last-modified: 2022-03-03 description: BackgroundThe aim of the study was to assess the prevalence of back pain in non-professional Brazilian Jiu-Jitsu practitioners (NP-BJJ practitioners), and to assess the relationship between their back pain and postural disorders.MethodsThe study involved 61 subjects (age: 30.7 ± 4.9 years old; body mass: 79.4 ± 12.9 kg; body height: 179.6 ± 8.4 cm; 8 woman and 53 man), 31 who trained Brazilian Jiu-Jitsu (BJJ) and 30 subjects who had never trained any combat sport. The mean time of training BJJ in the study population was 3.9 ± 4.1 years. Postural assessments were conducted with the use of the photogrammetric method. The assessment of back pain and injuries was conducted with the Oswestry Disability Index (ODI) and with our proprietary questionnaire.ResultsAmong both populations, 37 subjects reported back pain. There were no differences in back pain location between the two groups or in functional state on the ODI. Significant differences between the groups in the values of the postural parameters (spinal height, length of kyphosis, length of lordosis, pelvis inclination angle) were observed. Statistically significant differences between the NP-BJJ practitioners with and without back pain in the length of the thoracic kyphosis and the differences in the height of the waist triangles were found.ConclusionsBoth in the study population and in the control group the spinal pain was minimal or moderate on the ODI. BJJ practitioners who reported back pain had characteristic postural changes in some of the analysed postural parameters in comparison to BJJ practitioners who did not report back pain. creator: Katarzyna Sędek creator: Aleksandra Truszczyńska-Baszak creator: Anna Katarzyna Cygańska creator: Justyna Drzał-Grabiec uri: https://doi.org/10.7717/peerj.12838 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Sędek et al. title: Titanium dioxide dental implants surfaces related oxidative stress in bone remodeling: a systematic review link: https://peerj.com/articles/12951 last-modified: 2022-03-03 description: BackgroundTitanium dioxide dental implants have a controversial effect on reactive oxygen species (ROS) production. ROS is necessary for cellular signal transmission and proper metabolism, but also has the ability to cause cell death as well as DNA, RNA, and proteins damage by excessive oxidative stress. This study aimed to systematically review the effect of titanium dioxide dental implant-induced oxidative stress and its role on the osteogenesis-angiogenesis coupling in bone remodeling.MethodsThis systematic review was performed conforming to preferred reporting items for systematic review and meta-analysis (PRISMA) model. Four different databases (PubMed, Science Direct, Scopus and Medline databases) as well as manual searching were adopted. Relevant studies from January 2000 till September 2021 were retrieved. Critical Appraisal Skills Programme (CASP) was used to assess the quality of the selected studies.ResultsOut of 755 articles, only 14 which met the eligibility criteria were included. Six studies found that titanium dioxide nanotube (TNT) reduced oxidative stress and promoted osteoblastic activity through its effect on Wnt, mitogen-activated protein kinase (MAPK) and forkhead box protein O1 (FoxO1) signaling pathways. On the other hand, three studies confirmed that titanium dioxide nanoparticles (TiO2NPs) induce oxidative stress, reduce ostegenesis and impair antioxidant defense system as a significant negative correlation was found between decreased SIR3 protein level and increased superoxide (O2•-). Moreover, five studies proved that titanium implant alloy enhances the generation of ROS and induces cytotoxicity of osteoblast cells via its effect on NOX pathway.ConclusionTiO2NPs stimulate a wide array of oxidative stress related pathways. Scientific evidence are in favor to support the use of TiO2 nanotube-coated titanium implants to reduce oxidative stress and promote osteogenesis in bone remodeling. To validate the cellular and molecular cross talk in bone remodeling of the present review, well-controlled clinical trials with a large sample size are required. creator: Elaf Akram Abdulhameed creator: Natheer H. Al-Rawi creator: Marzuki Omar creator: Nadia Khalifa creator: A.B. Rani Samsudin uri: https://doi.org/10.7717/peerj.12951 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Abdulhameed et al. title: LncRNA CCAT1 facilitates the proliferation, invasion and migration of human laryngeal squamous cell carcinoma cells via the miR-218-5p/BMI1 link: https://peerj.com/articles/12961 last-modified: 2022-03-03 description: Long non-coding RNAs (LncRNAs) are vital in the treatment of laryngeal squamous cell carcinoma (LSCC). This study estimated the mechanism of lncRNA CCAT1 (CCAT1) in LSCC cells. The expression of CCAT1 in the human laryngeal mucosal epithelial cells (HLCs) and LSCC cells (Hep-2 and TU177) was detected. CCK-8 and Transwell assays were used to evaluate the cell proliferative, migrative, and invasive abilities, respectively. The subcellular localization of CCAT1 was verified by RNA-FISH and cytoplasmic isolation assays. The targeted relationship among CCAT1, miR-218-5p, and BMI1 was verified by dual-luciferase assay. Expressions of miR-218-5p and BMI1 were detected by RT-qPCR. Our results depicted that CCAT1 was highly-expressed in Hep-2 and TU177 cells. Silencing CCAT1 inhibited the proliferation, migration, and invasion of Hep-2 and TU177 cells. Mechanically, CCAT1 regulated the BMI1 expression by competitively binding to miR-218-5p as a competing endogenous RNA (ceRNA), and thus facilitated the growth of Hep-2 and TU177 cells. Downregulation of miR-218-5p or upregulation of BMI1 inhibited the inhibitory effect of silencing CCAT1 on Hep-2 and TU177 cell proliferation, invasion, and migration. In conclusion, our study elicited that lncRNA CCAT1 facilitated the proliferation, migration, and invasion of Hep-2 and TU177 cells by sponging miR-218-5p and regulating the downstream BMI1. creator: Jing Hong creator: Ali Hong creator: Houshu Tu creator: Zhichao Wan creator: Yuqiao Deng creator: Chengcheng Deng creator: Bo Tao creator: Yanjin Yu creator: Lanfei Zhou uri: https://doi.org/10.7717/peerj.12961 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Hong et al. title: Transcriptome-wide identification and expression analysis of the KT/HAK/KUP family in Salicornia europaea L. under varied NaCl and KCl treatments link: https://peerj.com/articles/12989 last-modified: 2022-03-03 description: BackgroundThe KT/HAK/KUP (KUP) transporters play important roles in potassium (K+) uptake and translocation, regulation of osmotic potential, salt tolerance, root morphogenesis and plant development. However, the KUP family has not been systematically studied in the typical halophyte Salicornia europaea L., and the specific expression patterns of SeKUPs under NaCl condition and K+ deficiency are unknown.MethodsIn this study, SeKUPs were screened from PacBio transcriptome data of Salicornia europaea L. using bioinformatics. The identification, phylogenetic analysis and prediction of conserved motifs of SeKUPs were extensively explored. Moreover, the expression levels of 24 selected SeKUPs were assayed by real-time quantitative polymerase chain reaction (RT-qPCR).ResultsIn this study, a total of 24 putative SeKUPs were identified in S. europaea. Nineteen SeKUPs with the fixed domain EA[ML]FADL were used to construct the phylogenetic tree, and they were divided into four clusters (clusters I–IV). MEME analysis identified 10 motifs in S. europaea, and the motif analysis suggested that 19 of the identified SeKUPs had at least four K+ transporter motifs existed in all SeKUPs (with the exception of SeKUP-2). The RT-qPCR analysis showed that the expression levels of most SeKUPs were significantly up-regulated in S. europaea when they were exposed to K+ deficiency and high salinity, implying that these SeKUPs may play a key role in the absorption and transport of K+ and Na+ in S. europaea.DiscussionsOur results laid the foundation for revealing the salt tolerance mechanism of SeKUPs, and provided key candidate genes for further studies on the function of KUP family in S. europaea. creator: Jia Wei creator: Richard John Tiika creator: Guangxin Cui creator: Yanjun Ma creator: Hongshan Yang creator: Huirong Duan uri: https://doi.org/10.7717/peerj.12989 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wei et al. title: East palearctic treefrog past and present habitat suitability using ecological niche models link: https://peerj.com/articles/12999 last-modified: 2022-03-03 description: Ecological niche modeling is a tool used to determine current potential species’ distribution or habitat suitability models which can then be used to project suitable areas in time. Projections of suitability into past climates can identify locations of climate refugia, or areas with high climatic stability likely to contain the highest levels of genetic diversity and stable populations when climatic conditions are less suitable in other parts of the range. Modeling habitat suitability for closely related species in recent past can also reveal potential periods and regions of contact and possible admixture. In the east palearctic, there are five Dryophytes (Hylid treefrog) clades belonging to two groups: Dryophytes japonicus group: Clades A and B; and Dryophytes immaculatus group: Dryophytes immaculatus, Dryophytes flaviventris, and Dryophytes suweonensis. We used maximum entropy modeling to determine the suitable ranges of these five clades during the present and projected to the Last Glacial Maximum (LGM) and Last Interglacial (LIG) periods. We also calculated climatic stability for each clade to identify possible areas of climate refugia. Our models indicated suitable range expansion during the LGM for four clades with the exclusion of D. immaculatus. High climatic stability in our models corresponded to areas with the highest numbers of recorded occurrences in the present. The models produced here can additionally serve as baselines for models of suitability under climate change scenarios and indicate species ecological requirements. creator: Desiree Andersen creator: Irina Maslova creator: Zoljargal Purevdorj creator: Jia-Tang Li creator: Kevin R. Messenger creator: Jin-Long Ren creator: Yikweon Jang creator: Amaël Borzée uri: https://doi.org/10.7717/peerj.12999 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Andersen et al. title: Tracking multiple fish link: https://peerj.com/articles/13031 last-modified: 2022-03-03 description: Although the Multiple Object Tracking (MOT) task is a widely used experimental method for studying divided attention, tracking objects in the real world usually looks different. For example, in the real world, objects are usually clearly distinguishable from each other and also possess different movement patterns. One such case is tracking groups of creatures, such as tracking fish in an aquarium. We used movies of fish in an aquarium and measured general tracking performance in this task (Experiment 1). In Experiment 2, we compared tracking accuracy within-subjects in fish tracking, tracking typical MOT stimuli, and in a third condition using standard MOT uniform objects which possessed movement patterns similar to the real fish. This third condition was added to further examine the impact of different motion characteristics on tracking performance. Results within a Bayesian framework showed that tracking real fish shares similarities with tracking simple objects in a typical laboratory MOT task. Furthermore, we observed a close relationship between performance in both laboratory MOT tasks (typical and fish-like) and real fish tracking, suggesting that the commonly used laboratory MOT task possesses a good level of ecological validity. creator: Filip Děchtěrenko creator: Daniela Jakubková creator: Jiří Lukavský creator: Christina J. Howard uri: https://doi.org/10.7717/peerj.13031 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Děchtěrenko et al. title: Overexpression of the Tectona grandis TgNAC01 regulates growth, leaf senescence and confer salt stress tolerance in transgenic tobacco plants link: https://peerj.com/articles/13039 last-modified: 2022-03-03 description: NAC transcription factors play critical roles in xylem secondary development and in regulation of stress response in plants. NAC proteins related to secondary cell wall development were recently identified and characterized in Tectona grandis (teak), one of the hardwood trees of highest economic importance in the world. In this work, we characterized the novel TgNAC01 gene, which is involved in signaling pathways that mediate teak response to stress. Abscisic acid (ABA) increases TgNAC01 expression in teak plants. Therefore, this gene may have a role in signaling events that mediate ABA-dependent osmotic stress responsive in this plant species. Stable expression in tobacco plants showed that the TgNAC01 protein is localized in the cell nucleus. Overexpression of TgNAC01 in two out three independent transgenic tobacco lines resulted in increased growth, leaf senescence and salt tolerance compared to wild type (WT) plants. Moreover, the stress tolerance of transgenic plants was affected by levels of TgNAC01 gene expression. Water potential, gas exchange and chlorophyll fluorescence were used to determine salt stress tolerance. The 35S:TgNAC01-6 line under 300 mM NaCl stress responded with a significant increase in photosynthesis rate, stomatal conductance, transpiration and carboxylation efficiency, but lower water potential compared to WT plants. The data indicate that the TgNAC01 transcription factor acts as a transcriptional activator of the ABA-mediated regulation and induces leaf senescence. creator: Fernando Matias creator: Perla Novais de Oliveira creator: Olman Gómez-Espinoza creator: Esteban Galeano creator: Helaine Carrer uri: https://doi.org/10.7717/peerj.13039 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Matias et al. title: Lacunes and type 2 diabetes mellitus have a joint effect on cognitive impairment: a retrospective study link: https://peerj.com/articles/13069 last-modified: 2022-03-03 description: ObjectiveTo evaluate the joint effects of cerebral small vessel disease (CSVD)-related imaging biomarkers in patients of type 2 diabetes mellitus (T2DM) with cognitive impairment.MethodsThis study is a retrospective cohort study. A total of 227 participants (115 patients with T2DM and 112 healthy control subjects) were enrolled in this study. Cognitive function assessments were evaluated using the Mini-Mental State Examination and the Montreal Cognitive Assessment. The burden of CSVD markers, including the lacunes, white matter hyperintensities (WMH), cerebral microbleeds (CMBs), and enlarged perivascular spaces (PVS), was identified by magnetic resonance imaging and evaluated using small vessel disease (SVD) scores (0–4). The subjects were divided into two groups based on the results of the cognitive function assessments. The synergy index was used to estimate the biological interactions between T2DM and lacunes.ResultsThere was a significant correlation between T2DM and cognitive impairment (p < 0.001, χ2 test). In patients with diabetes, cognitive impairment was significantly associated with both the presence of lacunes (p < 0.01, χ2 test) and increased total SVD burden scores (p < 0.01, χ2 test). Regarding CMBs, only the existence of lobar CMBs was correlated with cognitive impairment (p < 0.05, χ2 test). The joint effect tended to be larger than the independent effects of T2DM and lacunes on cognitive impairment (adjusted odds ratio [OR]: 7.084, 95% CI [2.836–17.698]; synergy index: 10.018, 95% CI [0.344–291.414]).ConclusionsT2DM and the presence of lacunes are significantly correlated with cognitive impairment. There was a joint effect of T2DM and lacunes on cognitive impairment. creator: Hong Zhou creator: Jun Hu creator: Peihan Xie creator: Yulan Dong creator: Wen Chen creator: Huiting Wu creator: Yihong Jiang creator: Hao Lei creator: Guanghua Luo creator: Jincai Liu uri: https://doi.org/10.7717/peerj.13069 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhou et al. title: Soybean (Glycine max L. Merrill) responds to phosphorus application and rhizobium inoculation on Acrisols of the semi-deciduous forest agro-ecological zone of Ghana link: https://peerj.com/articles/12671 last-modified: 2022-03-02 description: Soybean cultivation in Ghana is limited mainly to the Guinea savanna and the forest/savanna transitional agro-ecological zones. Although soybean can be cultivated in the semi-deciduous forest zone, low soil pH and limited nodulation limit its productivity in this zone. In this study, a randomized complete block design, with four replications, was used to test if rhizobia inoculation and/or p-fertilizer could improve yield of soybean in the semi-deciduous forest zone. The residual effects of the treatments were tested on maize and soybean sequentially during the 2018 and 2019 cropping seasons. The inoculation study was repeated in 2020. Phosphorus and inoculation significantly (p = 0.0009) increased soybean grain yield in the 2018 cropping season by 88% and 108%, respectively over the control. Co-application of P and inoculant increased grain yield 3-fold over the control. Maize grain yield ranged from 4.3 t ha−1 in the control plots to 5.2 t ha−1 in treated plots but did not differ significantly among treatments. In 2020, the combined application of P and inoculant produced a significantly (0.002) higher yield than any of the other treatments. This demonstrates that soybean can be grown economically in the semi-deciduous forest agro-ecological zone of Ghana. Co-application of P and inoculant appeared cost-effective, in terms of return on investment. creator: Samuel Adjei-Nsiah creator: David Martei creator: Adam Yakubu creator: Jacob Ulzen uri: https://doi.org/10.7717/peerj.12671 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Adjei-Nsiah et al. title: The Female Athlete Triad—the impact of running and type of diet on the regularity of the menstrual cycle assessed for recreational runners link: https://peerj.com/articles/12903 last-modified: 2022-03-02 description: BackgroundThe Female Athlete Triad (FAT) included three interrelated conditions including disordered eating, amenorrhea, and osteoporosis. The American College of Sports Medicine updated the definition of FAT to reflect the interdependence of low energy availability with or without eating disorders. The main aim of the study was to assess the impact of recreational running on potential disturbances in the regularity of women’s menstrual cycles. Additionally, this work compared differences in the menstrual cycle between women runners and women who did not regularly practice sports. The respondents were also asked about the type of diet they consumed.MethodsA total of 360 women took part in the research. This group included 217 runners and 143 control. The authors’ questionnaire was used in the research.ResultsWhen compared to the control group, the runners had an increased frequency of menstrual cycles of <24 days (10.14% vs. 3.50%), fewer typical cycles of 25–31 days (75.58% vs. 86.71%), had fewer regular cycles per year (9.62 vs. 11.22), shorter duration of bleeding (4.79 vs. 5.27 days), and an increased frequency of painless menstruation (23.96% vs. 7.69%). A positive predictor of menstrual cycle disorders was the use of a ‘special diet’ (R:1.67; 95% C:0.47–2.87).ConclusionsThe runners had shorter and less regular monthly cycles and shorter and more often painless menstrual bleeding when compared to the control group. The frequency of menstrual disorders in runners was increased by following a ‘special diet’. The frequency of menstrual cycle disorders in runners, however, did not differ significantly from the control group. creator: Joanna Witkoś creator: Magdalena Hartman-Petrycka uri: https://doi.org/10.7717/peerj.12903 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Witkoś and Hartman-Petrycka title: Development and validation of a multi-parameter nomogram for predicting prostate cancer: a retrospective analysis from Handan Central Hospital in China link: https://peerj.com/articles/12912 last-modified: 2022-03-02 description: BackgroundTo explore the possible predicting factors related to prostate cancer and develop a validated nomogram for predicting the probability of patients with prostate cancer.MethodClinical data of 697 patients who underwent prostate biopsy in Handan Central Hospital from January 2014 to January 2020 were retrospectively collected. Cases were randomized into two groups: 80% (548 cases) as the development group, and 20% (149 cases) as the validation group. Univariate and multivariate logistic regression analyses were performed to determine the independent risk factors for prostate cancer. The nomogram prediction model was generated using the finalized independent risk factors. Decision curve analysis (DCA) and the area under receiver operating characteristics curve (ROC) of both development group and validation group were calculated and compared to validate the accuracy and efficiency of the nomogram prediction model. Clinical utility curve (CUC) helped to decide the desired cut-off value for the prediction model. The established nomogram with Prostate Cancer Prevention Trial Derived Cancer Risk Calculator (PCPT-CRC) and other domestic prediction models using the entire study population were compared.ResultsThe independent risk factors determined through univariate and multivariate logistic regression analyses were: age, tPSA, fPSA, PV, DRE, TRUS and BMI. Nomogram prediction model was developed with the cut-off value of 0.31. The AUC of development group and validation group were 0.856 and 0.797 respectively. DCA exhibits consistent observations with the findings. Through validating our prediction model as well as other three domestic prediction models based on the entire study population of 697 cases, our prediction model demonstrated significantly higher predictive value than all the other models.ConclusionThe nomogram for predicting prostate cancer can facilitate more accurate evaluation of the probability of having prostate cancer, and provide better ground for prostate biopsy. creator: Libin Nan creator: Kai Guo creator: Mingmin Li creator: Qi Wu creator: Shaojun Huo uri: https://doi.org/10.7717/peerj.12912 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Nan et al. title: Physiological stress and higher reproductive success in bumblebees are both associated with intensive agriculture link: https://peerj.com/articles/12953 last-modified: 2022-03-02 description: Free-living organisms face multiple stressors in their habitats, and habitat quality often affects development and life history traits. Increasing pressures of agricultural intensification have been shown to influence diversity and abundance of insect pollinators, and it may affect their elemental composition as well. We compared reproductive success, body concentration of carbon (C) and nitrogen (N), and C/N ratio, each considered as indicators of stress, in the buff-tailed bumblebee (Bombus terrestris). Bumblebee hives were placed in oilseed rape fields and semi-natural old apple orchards. Flowering season in oilseed rape fields was longer than that in apple orchards. Reproductive output was significantly higher in oilseed rape fields than in apple orchards, while the C/N ratio of queens and workers, an indicator of physiological stress, was lower in apple orchards, where bumblebees had significantly higher body N concentration. We concluded that a more productive habitat, oilseed rape fields, offers bumblebees more opportunities to increase their fitness than a more natural habitat, old apple orchards, which was achieved at the expense of physiological stress, evidenced as a significantly higher C/N ratio observed in bumblebees inhabiting oilseed rape fields. creator: Tatjana Krama creator: Ronalds Krams creator: Maris Munkevics creator: Jonathan Willow creator: Sergejs Popovs creator: Didzis Elferts creator: Linda Dobkeviča creator: Patrīcija Raibarte creator: Markus Rantala creator: Jorge Contreras-Garduño creator: Indrikis A. Krams uri: https://doi.org/10.7717/peerj.12953 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Krama et al. title: Influence of Lymphangio vascular (V) and perineural (N) invasion on survival of patients with resected esophageal squamous cell carcinoma (ESCC): a single-center retrospective study link: https://peerj.com/articles/12974 last-modified: 2022-03-02 description: BackgroundLymphangio vascular invasion (LVI) and perineural invasion (PNI) are associated with survival following resection for gastrointestinal cancer. But the relationship between LVI/PNI and survival of esophageal squamous cell carcinoma (ESCC) is still unclear. We aim to demonstrate the prognostic significance of LVI/PNI in ESCC.MethodsA total of 195 ESCC patients underwent curative surgery from 2012 to 2018 was collected in the 2nd Affiliated Hospital of Fujian Medical University. All the patients were divided into four groups based on the status of the neurovascular invasion: (1) neither LVI nor PNI (V0N0); (2) LVI alone (V1N0); (3) PNI alone (V0N1); (4) combined LVI and PNI (V1N1). First, the analysis included the Kaplan-Meier survival estimates with the Log rank test were performed to determine median overall survival (OS) in different groups divided according to the clinical factor, respectively. And the association between OS with multi clinical factors was examined using Cox regression analysis. Next, the risk factors for recurrence in patients with V1N1 were analyzed with univariate and multivariate logistic regression analyses, respectively.ResultsThe cases in V0N0, V1N0, V0N1, and V1N1 groups were 91 (46.7%), 62 (31.8%), 9 (4.6%) and 33 (16.9%), respectively. The OS in the four groups was different (P < 0.001). The 1-, 3- and 5-year OS in V0N0 group was higher than that in V1N1 group, respectively (1-year OS: 93.4% vs 75.8%, 3-year OS: 53.8 % vs 24.2%, 5-year OS: 48.1% vs 10.5%). The OS in stage I-II for patients with V1N1 was significantly lower than that in the other groups (V0N0, V1N0, V0N1) (P < 0.001). The postoperative adjuvant chemotherapy was a significant impact factor of OS for ESCC patients with V1N1 (P = 0.004). Lymphatic invasion and LVI were significantly prognosis factors associated (P = 0.036, P = 0.030, respectively). The ulcerative type is a risk factor for V1N1 occurance (P = 0.040).ConclusionsThe LVI and PNI are important prognosis factors for ESCC patients. ESCC patients with simultaneous lymphangio vascular and perineural invasion (V1N1) showed worse OS than patients with either lymphangio vascular or perineural invasion alone (V1N0 or V0N1) or none (V0N0). In addition, adjuvant chemotherapy may prolong the OS for ESCC patients with V1N1. creator: Chengke Xie creator: Zhiyao Chen creator: Jie Xu creator: Zhiyong Meng creator: Zhijun Huang creator: Jianqing Lin uri: https://doi.org/10.7717/peerj.12974 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Xie et al. title: Reliability and validity of the multi-point method and the 2-point method’s variations of estimating the one-repetition maximum for deadlift and back squat exercises link: https://peerj.com/articles/13013 last-modified: 2022-03-02 description: This study aimed at examining the concurrent validity and reliability of the multi-point method and the two-point method’s variations for estimating the one-repetition maximum (1RM) in the deadlift and squat exercises and to determine the accuracy of which optimal two loads can be used for the two-point method protocol. Thirteen resistance-trained men performed six sessions that consisted of two incremental loading tests (multi-point method: 20–40–60–80–90% and two-point method variations: 40–60%, 40–80%, 40–90%,60–80%, 60–90%) followed by 1RM tests. Both the multi-point method and the two-point method load variations showed reliable results for 1RM estimation (CV < 10%) squat and deadlift exercises. Session-session reliability was found to be low in deadlift (ICC: 0.171–0.335) and squat exercises (ICC: 0.235–0.479) of 40–60% and 60–80% in two-point methods. Deadlift (ICC: 0.815–0.996) and squat (ICC: 0.817–0.988) had high session-to-session reliability in all other methods. Regarding the validity of deadlift exercise, the multipoint method (R2 = 0.864) and two variations of the two-point method (R2 = 0.816 for 40–80%, R2 = 0.732 for 60–80%) showed very large correlations, whereas other two variations of the two-point method (R2 = 0.945 for 40–90%, R2 = 0.914 for 60–90%) showed almost perfect correlations with the actual 1RM. Regarding the validity of squat exercise, the multi-point method (R2 = 0.773) and two variations of the two-point method (R2 = 0.0847 for 60–80%, R2 = 0.705 for 40–90%) showed very large correlations, whereas 40–60% variation showed almost perfect correlation (R2 = 0.962) with the actual 1RM. In conclusion, whereas both the multi-point method and the two-point method load variations showed reliable results, the multiple-point method and most of the two-point methods’ load variations examined in this research provided an accurate (from large-moderate to perfect) estimate of the 1RM. Therefore, we recommend using the multi-point method and especially the two-point methods variations including higher relative loads to estimate 1RM. creator: Onat Çetin creator: Zeki Akyildiz creator: Barbaros Demirtaş creator: Yılmaz Sungur creator: Filipe Manuel Clemente creator: Florin Cazan creator: Luca Paolo Ardigò uri: https://doi.org/10.7717/peerj.13013 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Çetin et al. title: Relationship between the distribution of vegetation and the environment in the coastal embryo dunes of Jalisco, México link: https://peerj.com/articles/13015 last-modified: 2022-03-02 description: BackgroundThe poorly developed soils of the embryo dunes imply little capacity for plant support, however, the adaptation mechanisms of plants respond sensitively to environmental variations, even when these variations are small, which results in a set of specialized habitats and flora that are rarely shared with other terrestrial ecosystems. The coastal dunes of the Mexican Pacific remain vaguely studied, this is why this research explored the relationship between environmental properties and the presence of plant species in the embryo dunes of the coast of Jalisco, Mexico.MethodsTwenty-nine sites were sampled, one or two sites per embryo dune, with a random stratified design. Geomorphological and vegetation data were collected at site. Laboratory determinations included soil color, particle size, organic matter, pH, electrical conductivity, magnetite content, and moisture retention. Statistical analysis included correlation analysis to identify relationships between environmental variables; principal component analysis (PCA) and cluster analysis to group dune sites by environmental properties; canonical correspondence analysis (CCA) to determine a possible significant relationship between the presence of plant species and environmental variables; cluster analysis to group dune sites by presence/absence of plant species and correlate both clusters to validate the relationship between them, the salient aspects of this relationship were described and the spatial distribution of the groups was mapped.ResultsEleven plant species were identified, six of them exclusive to the embryo dunes and the rest ubiquitous. The incipient development of these soils is reflected in a low content of organic matter, silt, clay, and moisture retention, with scattered data on granulometry, electrical conductivity, organic matter, and magnetite. Some significant correlations were found between some environmental properties, and the CCA showed a significant relationship between the presence of plant species and environmental variables (p-value of the Monte Carlo test = 0.026). The cluster analysis of dune sites according to environmental variables and the cluster analysis by presence/absence of plant species produces the formation of five groups of sites with significant environmental differences and five groups of sites with significant floristic differences. A significant connection (r = 0.471, p = 0.01) between the two clustering schemes also evidences the meaningful relationship between the presence of plant species and the environmental characteristics of the embryo dunes of Jalisco, Mexico. Differences in habitat preferences were observed among plant species exclusive to the embryo dunes; thus, Abronia maritima, Uniola pittieri, and Pectis arenaria showed a preference for embryo dunes with poor edaphic conditions, in contrast to Okenia hypogaea, Canavalia rosea, and Scaevola plumieri, which were mostly found in embryo dunes with higher fertility. creator: Héctor Gerardo Frías-Ureña creator: José Ariel Ruiz-Corral creator: Miguel Ángel Macías-Rodríguez creator: Noé Durán creator: Diego Gonzalez creator: Fabio De Albuquerque creator: José Pablo Torres Morán uri: https://doi.org/10.7717/peerj.13015 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Frías-Ureña et al. title: Highly pathogenic avian influenza virus of the A/H5N8 subtype, clade 2.3.4.4b, caused outbreaks in Kazakhstan in 2020 link: https://peerj.com/articles/13038 last-modified: 2022-03-02 description: BackgroundLarge poultry die-offs happened in Kazakhstan during autumn of 2020. The birds’ disease appeared to be avian influenza. Northern Kazakhstan was hit first and then the disease propagated across the country affecting eleven provinces. This study reports the results of full-genome sequencing of viruses collected during the outbreaks and investigation of their relationship to avian influenza virus isolates in the contemporary circulation in Eurasia.MethodsSamples were collected from diseased birds during the 2020 outbreaks in Kazakhstan. Initial virus detection and subtyping was done using RT-PCR. Ten samples collected during expeditions to Northern and Southern Kazakhstan were used for full-genome sequencing of avian influenza viruses. Phylogenetic analysis was used to compare viruses from Kazakhstan to viral isolates from other world regions.ResultsPhylogenetic trees for hemagglutinin and neuraminidase show that viruses from Kazakhstan belong to the A/H5N8 subtype and to the hemagglutinin H5 clade 2.3.4.4b. Deduced hemagglutinin amino acid sequences in all Kazakhstan’s viruses in this study contain the polybasic cleavage site (KRRKR-G) indicative of the highly pathogenic phenotype. Building phylogenetic trees with the Bayesian phylogenetics results in higher statistical support for clusters than using distance methods. The Kazakhstan’s viruses cluster with isolates from Southern Russia, the Russian Caucasus, the Ural region, and southwestern Siberia. Other closely related prototypes are from Eastern Europe. The Central Asia Migratory Flyway passes over Kazakhstan and birds have intermediate stops in Northern Kazakhstan. It is postulated that the A/H5N8 subtype was introduced with migrating birds.ConclusionThe findings confirm the introduction of the highly pathogenic avian influenza viruses of the A/Goose/Guangdong/96 (Gs/GD) H5 lineage in Kazakhstan. This virus poses a tangible threat to public health. Considering the results of this study, it looks justifiable to undertake measures in preparation, such as install sentinel surveillance for human cases of avian influenza in the largest pulmonary units, develop a human A/H5N8 vaccine and human diagnostics capable of HPAI discrimination. creator: Asylulan Amirgazin creator: Alexandr Shevtsov creator: Talgat Karibayev creator: Maxat Berdikulov creator: Tamila Kozhakhmetova creator: Laura Syzdykova creator: Yerlan Ramankulov creator: Alexandr V. Shustov uri: https://doi.org/10.7717/peerj.13038 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Amirgazin et al. title: Lactococcus lactis secreting phage lysins as a potential antimicrobial against multi-drug resistant Staphylococcus aureus link: https://peerj.com/articles/12648 last-modified: 2022-03-01 description: BackgroundStaphylococcus aureus is an opportunistic Gram-positive bacterium that can form biofilm and become resistant to many types of antibiotics. The treatment of multi-drug resistant Staphylococcus aureus (MDRSA) infection is difficult since it possesses multiple antibiotic-resistant mechanisms. Endolysin and virion-associated peptidoglycan hydrolases (VAPGH) enzymes from bacteriophage have been identified as potential alternative antimicrobial agents. This study aimed to assess the ability of Lactococcus lactis NZ9000 secreting endolysin and VAPGH from S. aureus bacteriophage 88 to inhibit the growth of S. aureus PS 88, a MDRSA.MethodEndolysin and VAPGH genes were cloned and expressed in L. lactis NZ9000 after fusion with the SPK1 signal peptide for secretion. The recombinant proteins were expressed and purified, then analyzed for antimicrobial activity using plate assay and turbidity reduction assay. In addition, the spent media of the recombinant lactococcal culture was analyzed for its ability to inhibit the growth of the S. aureus PS 88.ResultsExtracellular recombinant endolysin (Endo88) and VAPGH (VAH88) was successfully expressed and secreted from L. lactis which was able to inhibit S. aureus PS 88, as shown by halozone formation on plate assays as well as inhibition of growth in the turbidity reduction assay. Moreover, it was observed that the spent media from L. lactis NZ9000 expressing Endo88 and VAH88 reduced the viability of PS 88 by up to 3.5-log reduction with Endo88 being more efficacious than VAH88. In addition, Endo88 was able to lyse all MRSA strains tested and Staphylococcus epidermidis but not the other bacteria while VAH88 could only lyse S. aureus PS 88.ConclusionRecombinant L. lactisNZ9000 expressing phage 88 endolysin may be potentially developed into a new antimicrobial agent for the treatment of MDRSA infection. creator: Carumathy Chandran creator: Hong Yun Tham creator: Raha Abdul Rahim creator: Swee Hua Erin Lim creator: Khatijah Yusoff creator: Adelene Ai-Lian Song uri: https://doi.org/10.7717/peerj.12648 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Chandran et al. title: Production of single cell oil by Yarrowia lipolytica JCM 2320 using detoxified desiccated coconut residue hydrolysate link: https://peerj.com/articles/12833 last-modified: 2022-03-01 description: Nowadays, the replacement of petro-diesel with biodiesel has raised the concern among the community for the utilization of improper feedstocks and the cost involved. However, these issues can be solved by producing single cell oil (SCO) from lignocellulosic biomass hydrolysates by oleaginous microorganisms. This study introduced Yarrowia lipolytica JCM 2320 with a desiccated coconut residue (DCR) hydrolysate (obtained from the 2% dilute sulphuric acid pretreatment) as a carbon source in generating SCO. However, common inhibitors formed during acid pretreatment of biomass such as five-hydroxymethylfurfural (HMF), furfural, acetic acid and levulinic acid resulting from the sugar degradations may have detrimental effects towards the fermentation process. To visualize the effect of inhibitors on Y. lipolytica, an inhibitory study was conducted by adding 0.5–5.0 g/L of potential inhibitors to the YPD (yeast, peptone and D-glucose) medium. It was found that the presence of furfural at 0.5 g/L would increase the lag phase, which beyond that was detrimental to Y. lipolytica. Furthermore, increasing the five-hydroxymethylfurfural (HMF) concentration would increase the lag phase of Y. lipolytica, whereas, for acetic acid and levulinic acid, it showed a negligible effect. Detoxification was hence conducted to remove the potential inhibitors from the DCR hydrolysate prior its utilization in the fermentation. To examine the possibility of using adsorption resins for the detoxification of DCR hydrolysate, five different resins were tested (Amberlite® XAD-4, Amberlite® XAD-7, Amberlite® IR 120, Amberlite® IRA 96 and Amberlite® IRA 402) with five different concentrations of 1%, 3%, 5%, 10% and 15% (w/v), respectively. At resin concentration of 10%, Amberlite® XAD-4 recorded the highest SCO yield, 2.90 ± 0.02 g/L, whereas the control and the conventional overliming detoxification method, recorded only 1.29 ± 0.01 g/L and 1.27 ± 0.02 g/L SCO accumulation, respectively. Moreover, the fatty acid profile of the oil produced was rich in oleic acid (33.60%), linoleic acid (9.90%), and palmitic acid (14.90%), which indicates the potential as a good biodiesel raw material. creator: Muhammad Fakhri Zainuddin creator: Chong Kar Fai creator: Mohd Shamzi Mohamed creator: Nor ’Aini Abdul Rahman creator: Murni Halim uri: https://doi.org/10.7717/peerj.12833 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zainuddin et al. title: Remarkable genomic diversity among Escherichia isolates recovered from healthy chickens link: https://peerj.com/articles/12935 last-modified: 2022-03-01 description: The genus Escherichia has been extensively studied and it is known to encompass a range of commensal and pathogenic bacteria that primarily inhabit the gastrointestinal tracts of warm-blooded vertebrates. However, the presence of E. coli as a model organism and potential pathogen has diverted attention away from commensal strains and other species in the genus. To investigate the diversity of Escherichia in healthy chickens, we collected fecal samples from antibiotic-free Lohmann Brown layer hens and determined the genome sequences of 100 isolates, 81 of which were indistinguishable at the HC0 level of the Hierarchical Clustering of Core Genome Multi-Locus Sequence Typing scheme. Despite initial selection on CHROMagar Orientation medium, which is considered selective for E. coli, in silico phylotyping and core genome single nucleotide polymorphism analysis revealed the presence of at least one representative of all major clades of Escherichia, except for E. albertii, Shigella, and E. coli phylogroup B2 and cryptic clade I. The most frequent phylogenomic groups were E. coli phylogroups A and B1 and E. ruysiae (clades III and IV). We compiled a collection of reference strains isolated from avian sources (predominantly chicken), representing every Escherichia phylogroup and species, and used it to confirm the phylogeny and diversity of our isolates. Overall, the isolates carried low numbers of the virulence and antibiotic resistance genes typically seen in avian pathogenic E. coli. Notably, the clades not recovered are ones that have been most strongly associated with virulence by other studies. creator: Nicholas M. Thomson creator: Rachel Gilroy creator: Maria Getino creator: Ebenezer Foster-Nyarko creator: Arnoud H.M. van Vliet creator: Roberto M. La Ragione creator: Mark J. Pallen uri: https://doi.org/10.7717/peerj.12935 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Thomson et al. title: Validity of using perceived exertion to assess muscle fatigue during resistance exercises link: https://peerj.com/articles/13019 last-modified: 2022-03-01 description: BackgroundThe rating of perceived exertion (RPE) is correlated with physiological variables. The purpose of this study was to assess the validity of using the Borg CR-10 scale and velocity to predict muscle fatigue assessed by surface electromyography during single joint resistance exercises.MethodsFifteen healthy males underwent different fatigue levels of unilateral elbow flexion (EF) and knee extension (KE), consisting of low, medium, and high volumes at 65% of their one-repetition maximum. The RPEs, spectral fatigue index (SFI), and mean velocity of the experimental exercises were assessed throughout the trials.ResultsSignificant differences in overall RPE (p < 0.001) and average SFI (p < 0.001) were observed between the conditions in both exercises. Significant changes in RPE and SFI (p < 0.001) were observed throughout the EF, whereas a SFI increase (p < 0.001) was only observed at the end point of KE. Multiple regression analyses revealed two significant models (p < 0.001) for the prediction of muscle fatigue during EF (R2 = 0.552) and KE (R2 = 0.377).ConclusionsMuscle fatigue resulted in similar increases in perceptual responses, demonstrating that RPE is useful for assessing fatigue when resistance exercise is performed. However, velocity changes may not reflect muscle fatigue correctly when exercise is no longer performed in an explosive manner. We recommend combining RPE responses with velocity changes to comprehensively assess muscle fatigue during clinical and sports situations. creator: Hanye Zhao creator: Takuya Nishioka creator: Junichi Okada uri: https://doi.org/10.7717/peerj.13019 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhao et al. title: Genome wide expression analysis of circular RNAs in mammary epithelial cells of cattle revealed difference in milk synthesis link: https://peerj.com/articles/13029 last-modified: 2022-03-01 description: Milk is an excellent source of nutrients for humans. Therefore, in order to enhance the quality and production of milk in cattle, it is interesting to examine the underlying mechanisms. A number of new investigations and research have found that, circRNA; a specific class of non-coding RNAs, is linked with the development of mammary gland and lactation. In the present study, genome wide identification and expression of the circRNAs in mammary epithelial cells of two distinct cattle breeds viz Jersey and Kashmiri at peak lactation was conducted. We reported 1554 and 1286 circRNA in Jersey and Kashmiri cattle, respectively, with 21 circRNAs being differentially expressed in the two breeds. The developmental genes of the established differentially expressed circRNAs were found to be largely enriched in antioxidant activity, progesterone, estradiol, lipid, growth hormone, and drug response. Certain pathways like MAPK, IP3K and immune response pathways were found significantly enriched in KEGG analysis. These results add to our understanding of the controlling mechanisms connected with the lactation process, as well as the function of circRNAs in bovine milk synthesis. Additionally, the comparative analysis of differentially expressed circRNAs showed significant conservation across different species. creator: Syed Mudasir Ahmad creator: Basharat Bhat creator: Zainab Manzoor creator: Mashooq Ahmad Dar creator: Qamar Taban creator: Eveline M. Ibeagha-Awemu creator: Nadeem Shabir creator: Mohd Isfaqul Hussain creator: Riaz A. Shah creator: Nazir A. Ganai uri: https://doi.org/10.7717/peerj.13029 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Syed et al. title: Characterization of amphoteric bentonite-loaded magnetic biochar and its adsorption properties for Cu2+ and tetracycline link: https://peerj.com/articles/13030 last-modified: 2022-03-01 description: To realize simultaneous adsorption of heavy metal and antibiotic pollutants by a BC-based recyclable material, Fe3O4 magnetic biochar (MBC) was prepared by co-precipitation method. Then different ratios of dodecyl dimethyl betaine (BS-12)-modified bentonite (BS-B) were loaded on the surfaces of biochar (BC) and MBC to prepare BS-B-loaded BC and MBC composites, called BS-B/BC and BS-B/MBC, respectively. The physicochemical and structural properties of the composites were characterized by scanning electron microscopy, Fourier transform infrared spectrometry, thermogravimetric analysis, specific surface area (SBET) analysis, and vibrating sample magnetometry, and the adsorption efficiencies of BS-B/BC and BS-B/MBC to Cu2+ and tetracycline (TC) were studied. The following results were obtained. (1) Compared with BS-B/BC, BS-B/MBC had decreased pH and cation exchange capacity (CEC) and increased SBET. The pH, CEC, and SBET of BS-B/BC and BS-B/MBC decreased with the increase in the BS-12 proportion of BS-B. The surface of BS-B/MBC became rough after Fe3O4 loading. (2) The residual rate of BS-B/MBC was higher than that of BS-B/BC after high-temperature combustion, and the residual rate decreased with the increase in the BS-12 proportion of BS-B. The 2D infrared spectra showed that Fe3O4 and BS-12 were modified on the surface of BS-B/MBC. MBC and BS-B/MBC had splendid magnetism and could be separated by external magnetic field. (3) Compared with unmagnetized ones, the adsorption effects of Cu2+ and TC on different BS-B/MBCs improved, and the average adsorption rate reached the largest value of 91.92% and 97.76%, respectively. Cu2+ and TC adsorptions were spontaneous, endothermic, and entropy-increasing processes. The pH and SBET of the material had a great influence on Cu2+ and TC adsorptions, respectively, than CEC. creator: Hongyan Deng creator: Haixia He creator: Wenbin Li creator: Touqeer Abbas creator: Zhifeng Liu uri: https://doi.org/10.7717/peerj.13030 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Deng et al. title: Violence, runaway, and suicide attempts among people living with schizophrenia in China: Prevalence and correlates link: https://peerj.com/articles/13033 last-modified: 2022-03-01 description: BackgroundPeople living with schizophrenia are at higher risk of disruptive behaviors, including violence, running away from home, and suicide attempts, which often co-occur and are highly correlated, yet seldom studied together. The current study investigated the frequency and correlates of disruptive behaviors among a Chinese community sample of individuals living with schizophrenia.MethodsA cross-sectional study was conducted among 400 individuals living with schizophrenia from 12 communities. Data about disruptive behaviors in the past 2 months was collected using self-designed questionnaires. Clinical characteristics including psychiatric symptoms, depression, anxiety, disability, and functioning were collected by internationally standardized assessment instruments.ResultsAbout one-fifth (21%) of the subjects had experienced at least one form of disruptive behavior in the past 2 months. Violence was the most commonly reported (17.25%), which included damaging property (15%) and physical violence toward others (7.5%); followed by running away (6.5%), and suicide attempts (4%). Logistic regression analysis suggested that medication non-adherence (OR = 4.96, 95% CI [1.79–13.72]), involuntary hospital admission (OR = 5.35, 95% CI [2.06–13.87]), depression (OR = 2.34, 95% CI [1.07–5.10]), and lower social functioning (OR = 0.97, 95% CI [0.93–0.99]) were independently associated with a higher risk of disruptive behaviors.ConclusionsThe overlap among three forms of disruptive behaviors warrants them to be assessed and studied together in clinical, research, and policy fields. The significant association between disruptive behaviors with medication non-adherence, involuntary admission, depression, and lower social functioning indicates the need for integrated, targeted, and needs-based intervention programs to be developed for the prevention and treatment of these disruptive behaviors. creator: Yixiang Long creator: Xiaoliang Tong creator: Michael Awad creator: Shijun Xi creator: Yu Yu uri: https://doi.org/10.7717/peerj.13033 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Long et al. title: SEPALLATA­-like genes of Isatis indigotica can affect the architecture of the inflorescences and the development of the floral organs link: https://peerj.com/articles/13034 last-modified: 2022-03-01 description: BackgroundThe architecture of inflorescence and the development of floral organs can influence the yield of seeds and have a significant impact on plant propagation. E-class floral homeotic MADS-box genes exhibit important roles in regulation of floral transition and differentiation of floral organs. Woad (Isatis indigotica) possesses unique inflorescence, floral organs and fruit. However, very little research has been carried out to determine the function of MADS-box genes in this medicinal cruciferous plant species.ResultsSEPALLATA orthologs in I. indigotica were cloned by degenerate PCR. The sequence possessing the highest identity with SEP2 and SEP4 of Arabidopsis were named as IiSEP2 and IiSEP4, respectively. Constitutive expression of IiSEP2 in Columbia (Col-0) ecotype of Arabidopsis led to early flowering, and the number of the flowers and the lateral branches was reduced, indicating an alteration in architecture of the inflorescences. Moreover, the number of the floral organs was declined, the sepals were turned into carpelloid tissues bearing stigmatic papillae and ovules, and secondary flower could be produced in apetalous terminal flowers. In 35S::IiSEP4-GFP transgenic Arabidopsis plants in Landsberg erecta (Ler) genetic background, the number of the floral organs was decreased, sepals were converted into curly carpelloid structures, accompanied by generation of ovules. Simultaneously, the size of petals, stamens and siliques was diminished. In 35S::IiSEP4-GFP transgenic plants of apetalous ap1 cal double mutant in Ler genetic background, the cauliflower phenotype was attenuated significantly, and the petal formation could be rescued. Occasionally, chimeric organs composed of petaloid and sepaloid tissues, or petaloid and stamineous tissues, were produced in IiSEP4 transgenic plants of apl cal double mutant. It suggested that overexpression of IiSEP4 could restore the capacity in petal differentiation. Silencing of IiSEP4 by Virus-Induced Gene Silencing (VIGS) can delay the flowering time, and reduce the number and size of the floral organs in woad flowers.ConclusionAll the results showed that SEPALLATA-like genes could influence the architecture of the inflorescence and the determinacy of the floral meristems, and was also related to development of the floral organs. creator: Yan-Qin Ma creator: Zuo-Qian Pu creator: Xiao-Min Tan creator: Qi Meng creator: Kai-Li Zhang creator: Liu Yang creator: Ye-Ye Ma creator: Xuan Huang creator: Zi-Qin Xu uri: https://doi.org/10.7717/peerj.13034 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Ma et al. title: Alterations of gut fungal microbiota in patients with rheumatoid arthritis link: https://peerj.com/articles/13037 last-modified: 2022-03-01 description: BackgroundRheumatoid arthritis (RA) is a systemic autoimmune disease, in addition, gut microbiota plays an important role in the etiology of RA. However, our understanding of alterations to the gut fungal microbiota in Chinese population with RA is still limited.MethodsSerum samples were obtained from 62 patients with RA, and 39 age- and gender-matched healthy controls (HCs). Fecal samples were obtained from 42 RA patients and 39 HCs. Fecal fungal microbiota targeting internal transcribed spacer region 2 (ITS2) rRNA genes was investigated using MiSeq sequencing, as well as their associations with some diagnostic biomarkers for RA.ResultsOur results showed that the fungal diversity did not alter in RA patients but taxonomic composition of the fecal fungal microbiota did. The gut mycobiota of RA patients was characterized by decreased abundance of Pholiota, Scedosporium, and Trichosporon. The linear discriminant analysis (LDA) effect size analysis (LEfSe) analysis identified several RA-enriched fungal genera, which were positively correlated with most RA biomarkers. Furthermore, since RA is an age- and gende-related disease, we classified RA patients into subgroups with age and gender and analyzed the sequencing results. Our data demonstrated that Wallemia and Irpex were the most discriminatory against RA patients over 60 years old, while Pseudeurotiaceae was the most discriminatory against female RA patients.ConclusionsThe case-control study presented here confirmed the alterations of gut fungal microbiota in Chinese patients with RA, and we speculated that the fungal dysbiosis may contribute to RA development. creator: Xiaoyu Sun creator: Yushuang Wang creator: Xinke Li creator: Meiling Wang creator: Jianyi Dong creator: Wei Tang creator: Zengjie Lei creator: Yuling Guo creator: Ming Li creator: Yuyuan Li uri: https://doi.org/10.7717/peerj.13037 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Sun et al.