title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1145 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Changes in the gut microbiota during Asian particolored bat (Vespertilio sinensis) development link: https://peerj.com/articles/9003 last-modified: 2020-05-12 description: BackgroundThe gut microbiota is closely linked to host development, diet and health and is influenced by both the host and the environment. Although many studies have focused on the dynamics of the gut microbiota during development in captive animals, few studies have focused on the dynamics of the gut microbiota during development in wild animals, especially for the order Chiroptera.MethodsIn this study, we characterized the gut microbiota of the wild Asian particolored bat (Vespertilio sinensis) from 1 day to 6 weeks after birth. We explored the changes in their gut microbial community compositions, examined possible influencing factors, and predicted the feeding transition period.ResultsThe gut microbiota changed during the development of V. sinensis. The alpha diversity of the bats’ gut microbiota gradually increased but did not change significantly from the 1st day to the 4th week after birth; however, the alpha diversity decreased significantly in week 5, then stabilized. The beta diversity differed slightly in weeks 4–6. In week 4, the fecal samples showed the highest diversity in bacterial community composition. Thus, we predicted that the potential feeding transition period for V. sinensis may occur during week 4. Redundancy analysis showed that age and body mass index significantly affected the compositional changes of the gut microbiota in Asian particolored bats.ConclusionThe gut microbiota changed during the development of V. sinensis. We suggest that changes in the alpha and beta diversity during week 4 after birth indicate a potential feeding transition, highlighting the importance of diet in the gut microbiota during the development of V. sinensis. creator: Zhongwei Yin creator: Keping Sun creator: Aoqiang Li creator: Deyi Sun creator: Zhongle Li creator: Guohong Xiao creator: Jiang Feng uri: https://doi.org/10.7717/peerj.9003 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Yin et al. title: Extent, patterns and demographic correlates for physical fighting among school-attending adolescents in Namibia: examination of the 2013 Global School-based Health Survey link: https://peerj.com/articles/9075 last-modified: 2020-05-12 description: BackgroundPhysical fighting is particularly detrimental for young people, often affecting other areas of their developing lives, such as relationships with friends and family and participating in risky behaviors. We aim to quantify the amount of problematic physical fighting in Namibian adolescents and identify modifiable risk factors for intervention.MethodsWe used the Namibia 2013 Global School-based Student Health Survey (GSHS). This survey collects health-related information on school-attending adolescents in grades 7 to 12. We defined physical fighting as having participated in at least two physical fights in the 12 months prior to responding to the survey. Factors that may be associated with physical fighting were identified a prior based on the literature and included age, sex, anxiety, suicide planning, truancy, physical activity, bullying victimization, presence of supportive parental figures, presence of helpful peers, extent of social network, and food insecurity. Multivariable logistic regression models were created to identify factors associated with physical fighting.ResultsA total of 4,510 adolescents were included in the study. A total of 52.7% female. 16.9% of adolescents reported engaging in at least two physical fights in the previous year. Factors associated with an increased odds of physical fighting included having a suicide plan, anxiety, truancy, food deprivation and being bullied. Increased age and loneliness were associated with a decreased odds of physical fighting.ConclusionThis study identifies problematic physical fighting among adolescents in Namibia. We recommend public health and school-based programming that simultaneously targets risk behaviours and conflict resolution to reduce rates of physical fighting. creator: Laura E. Davis creator: Anne Abio creator: Michael Lowery Wilson creator: Masood Ali Shaikh uri: https://doi.org/10.7717/peerj.9075 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Davis et al. title: EEG based assessment of stress in horses: a pilot study link: https://peerj.com/articles/8629 last-modified: 2020-05-12 description: As has been hypothesized more than 20 years ago, data derived from Electroencephalography (EEG) measurements can be used to distinguish between behavioral states associated with animal welfare. In our current study we found a high degree of correlation between the modulation index of phase related amplitude changes in the EEG of horses (n = 6 measurements with three different horses, mare and gelding) and their facial expression, measured by the use of the horse grimace scale. Furthermore, the pattern of phase amplitude coupling (PAC) was significantly different between a rest condition and a stress condition in horses. This pilot study paves the way for a possible use of EEG derived PAC as an objective tool for the assessment of animal welfare. Beyond that, the method might be useful to assess welfare aspects in the clinical setting for human patients, as for example in the neonatal intensive care unit. creator: Nora V. de Camp creator: Mechthild Ladwig-Wiegard creator: Carola I.E. Geitner creator: Jürgen Bergeler creator: Christa Thöne-Reineke uri: https://doi.org/10.7717/peerj.8629 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 de Camp et al. title: Phylogenetic study of extirpated Korean leopard using mitochondrial DNA from an old skin specimen in South Korea link: https://peerj.com/articles/8900 last-modified: 2020-05-12 description: The leopard, Panthera pardus, is a threatened species in its range throughout the world. Although, historically, the Korean Peninsula had a high population density of leopards, they were extirpated from South Korea by 1970, leaving almost no genetic specimens. Traditionally, Korean leopards are classified as Panthera pardus orientalis; however, their classification is based only on locality and morphology. Therefore, there is a need for genetic studies to identify the phylogenetic status of Korean leopards at the subspecies level. Presently, no extant wild specimen is available from South Korea; therefore, we extracted genetic material from the old skin of a leopard captured in Jirisan, South Korea in the 1930s and conducted the first phylogenetic study of the South Korean leopard. A total of 726 bp of mitochondrial DNA, including segments of the NADH5 and control region, were amplified by PCR. A phylogenetic analysis of the fragment, along with sequences of nine leopard subspecies from GenBank revealed that the extinct South Korean leopard belonged to the Asian leopard group and in the same clade as the Amur leopard (Panthera pardus orientalis). Thus, the leopard that inhabited South Korea in the past was of the same subspecies as the Amur leopard population currently inhabiting the transboundary region of Russia, China, and North Korea. These results emphasize the importance of conserving the endangered wild Amur leopard population (estimated to be about 60–80 individuals) in Russia and China, for future restoration of leopards in the Korean Peninsula. creator: Jee Yun Hyun creator: Jang Hyuk Cho creator: Puneet Pandey creator: Mi-Sook Min creator: Kyung Seok Kim creator: Hang Lee uri: https://doi.org/10.7717/peerj.8900 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Hyun et al. title: Exploring environmental coverages of species: a new variable contribution estimation methodology for rulesets from the genetic algorithm for rule-set prediction link: https://peerj.com/articles/8968 last-modified: 2020-05-12 description: Variable contribution estimation for, and determination of variable importance within, ecological niche models (ENMs) remain an important area of research with continuing challenges. Most ENM algorithms provide normally exhaustive searches through variable space; however, selecting variables to include in models is a first challenge. The estimation of the explanatory power of variables and the selection of the most appropriate variable set within models can be a second challenge. Although some ENMs incorporate the variable selection rubric inside the algorithms, there is no integrated rubric to evaluate the variable importance in the Genetic Algorithm for Ruleset Production (GARP). Here, we designed a novel variable selection methodology based on the rulesets generated from a GARP experiment. The importance of the variables in a GARP experiment can be estimated based on the consideration of the prevalence of each environmental variable in the dominant presence rules of the best subset of models and its coverage. We tested the performance of this variable selection method based on simulated species with both weak and strong responses to simulated environmental covariates. The variable selection method generally performed well during the simulations with over 2/3 of the trials correctly identifying most covariates. We then predict the distribution of Toxostoma rufum (a bird with a cosmopolitan distribution) in the continental United States (US) and apply our variable selection procedure as a real-world example. We found that the distribution of T. rufum could be accurately modeled with 13 or 10 of 21 variables, using an UI cutoff of 0.5 or 0.25, respectively, arriving at parsimonious environmental coverages with good model accuracy. We also provide tools to simulate species distributions for testing ENM approaches using R. creator: Anni Yang creator: Juan Pablo Gomez creator: Jason K. Blackburn uri: https://doi.org/10.7717/peerj.8968 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Yang et al. title: EZH2/H3K27Me3 and phosphorylated EZH2 predict chemotherapy response and prognosis in ovarian cancer link: https://peerj.com/articles/9052 last-modified: 2020-05-12 description: BackgroundEZH2 acts as an oncogene through canonical pathway EZH2/H3K27Me3 and uncanonical pathway pAkt1/pS21EZH2 in many solid tumors including ovarian cancer. However, the clinical value of EZH2/H3K27Me3 and pAkt1/pS21EZH2 remain unclear. In the current study, we aim to investigate the correlation between these two pathways to clinical-pathological parameters and prognosis.MethodsEZH2, H3K27Me3, pAkt1 and pS21EZH2 expression were evaluated by tissue micro-array and immunohistochemistry in a cohort of ovarian cancer patients. The results were analyzed based on clinical characteristics and survival outcomes.ResultsEZH2, H3K27Me3, pAkt1 and pS21EZH2 were universally expressed in ovarian cancer specimens with a positive expression rate of 81.54% (53/65), 88.89% (48/54), 63.07% (41/65) and 75.38% (49/65). EZH2-pS21EZH2 (Spearman r = 0.580, P < 0.0001) and pS21EZH2-pAkt1 (Spearman r = 0.546, P < 0.0001) were closely correlated while EZH2- H3K27Me3 were less closely correlated (Spearman r = 0.307, P = 0.002). Low pS21EZH2 associated with better chemotherapy response (OR = 0.184; 95% CI [0.052–0.647], P = 0.008) according to logistic regression with an area under the curve of 0.789 (specificity 89.36%, sensitivity 68.42%) by ROC analysis and predicted improved progression-free survival (HR = 0.453; 95% CI [0.229–0.895], P = 0.023) as indicated by multivariate cox regression. A combination of EZH2low/H3K27Me3low status predicted better chemotherapy response (OR = 0.110; 95% CI [0.013–0.906], P = 0.040) and better progression-free survival (HR = 0.388; 95% CI [0.164–0.917], P = 0.031). The results suggested that EZH2/H3K27Me3 and pEZH2 predicted chemotherapy response and progression-free survival in ovarian cancer. creator: Si Sun creator: Qiang Yang creator: E Cai creator: Bangxing Huang creator: Feiquan Ying creator: Yiping Wen creator: Jing Cai creator: Ping Yang uri: https://doi.org/10.7717/peerj.9052 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Sun et al. title: Direct aortic route versus transaxillary route for transcatheter aortic valve replacement: a systematic review and meta-analysis link: https://peerj.com/articles/9102 last-modified: 2020-05-12 description: BackgroundThe transfemoral route is contraindicated in nearly 10% of transcatheter aortic valve replacement (TAVR) candidates because of unsuitable iliofemoral vessels. Transaxillary (TAx) and direct aortic (DAo) routes are the principal nonfemoral TAVR routes; however, few studies have compared their outcomes.MethodsWe performed a systematic review and meta-analysis to compare the rates of mortality, stroke, and other adverse events of TAx and DAo TAVR. The study was prospectively registered with PROSPERO (registration number: CRD42017069788). We searched Medline, PubMed, Embase, and Cochrane databases for studies reporting the outcomes of DAo or TAx TAVR in at least 10 patients. Studies that did not use the Valve Academic Research Consortium definitions were excluded. We included studies that did not directly compare the two approaches and then pooled rates of events from the included studies for comparison.ResultsIn total, 31 studies were included in the quantitative meta-analysis, with 2,883 and 2,172 patients in the DAo and TAx TAVR groups, respectively. Compared with TAx TAVR, DAo TAVR had a lower Society of Thoracic Surgery (STS) score, shorter fluoroscopic time, and less contrast volume use. The 30-day mortality rates were significantly higher in the DAo TAVR group (9.6%, 95% confidence interval (CI) = [8.4–10.9]) than in the TAx TAVR group (5.7%, 95% CI = [4.8–6.8]; P for heterogeneity <0.001). DAo TAVR was associated with a significantly lower risk of stroke in the overall study population (2.6% vs. 5.8%, P for heterogeneity <0.001) and in the subgroup of studies with a mean STS score of ≥8 (1.6% vs. 6.2%, P for heterogeneity = 0.005). DAo TAVR was also associated with lower risks of permanent pacemaker implantation (12.3% vs. 20.1%, P for heterogeneity = 0.009) and valve malposition (2.0% vs. 10.2%, P for heterogeneity = 0.023) than was TAx TAVR.ConclusionsDAo TAVR increased 30-day mortality rate compared with TAx TAVR; by contrast, TAx TAVR increased postoperative stroke, permanent pacemaker implantation, and valve malposition risks compared with DAo TAVR. creator: Hsiu-An Lee creator: I-Li Su creator: Shao-Wei Chen creator: Victor Chien-Chia Wu creator: Dong-Yi Chen creator: Pao-Hsien Chu creator: An-Hsun Chou creator: Yu-Ting Cheng creator: Pyng-Jing Lin creator: Feng-Chun Tsai uri: https://doi.org/10.7717/peerj.9102 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Lee et al. title: Early language competence, but not general cognitive ability, predicts children’s recognition of emotion from facial and vocal cues link: https://peerj.com/articles/9118 last-modified: 2020-05-12 description: The ability to accurately identify and label emotions in the self and others is crucial for successful social interactions and good mental health. In the current study we tested the longitudinal relationship between early language skills and recognition of facial and vocal emotion cues in a representative UK population cohort with diverse language and cognitive skills (N = 369), including a large sample of children that met criteria for Developmental Language Disorder (DLD, N = 97). Language skills, but not non-verbal cognitive ability, at age 5–6 predicted emotion recognition at age 10–12. Children that met the criteria for DLD showed a large deficit in recognition of facial and vocal emotion cues. The results highlight the importance of language in supporting identification of emotions from non-verbal cues. Impairments in emotion identification may be one mechanism by which language disorder in early childhood predisposes children to later adverse social and mental health outcomes. creator: Sarah Griffiths creator: Shaun Kok Yew Goh creator: Courtenay Fraiser Norbury uri: https://doi.org/10.7717/peerj.9118 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Griffiths et al. title: Analyzing bacterial community in pit mud of Yibin Baijiu in China using high throughput sequencing link: https://peerj.com/articles/9122 last-modified: 2020-05-12 description: “Yibin Baijiu” (YB) is a special Chinese strong-aroma Baijiu (CSAB) that originated in Yibin, a city in western China. YB is fermented in cellars lined with pit mud (PM), the microbiota in which may affect YB quality. In this study, high throughput sequencing of the 16S rRNA gene was used to demonstrate the bacterial community structure and diversity in PM of YB. In addition, the physicochemical characteristics of PM were also analyzed, including moisture content, pH, and available phosphorous, ammonia nitrogen, and humic acid levels. Results showed that Firmicutes was the dominant phylum in all PM samples with abundance > 70.0%, followed by Euryarchaeota (11.3%), Bacteroidetes (6.5%), Synergistetes (3.0%), Actinobacteria (1.4%), and Proteobacteria (1.2%). Furthermore, 14 different genera with average relative abundance of > 1% were detected. The Chao1 and Shannon indexes did not vary significantly between the sub-layer and middle-layer PM (P > 0.05). However, Linear discriminant analysis Effect Size (LEfSe) analysis showed that the relative abundance of Lactobacillus in the sub-layer PM was significantly higher than in middle-layer PM. pH differed significantly (P < 0.05) between the two groups. Canonical correspondence analysis revealed that bacterial community in PM correlated significantly with available phosphorous content and pH. Our study provides basic data for further elucidating the diversity of microbiota in the PM of YB and the potential mechanism of Baijiu production. creator: Li Chen creator: Yuzhu Li creator: Lei Jin creator: Li He creator: Xiaolin Ao creator: Shuliang Liu creator: Yong Yang creator: Aiping Liu creator: Shujuan Chen creator: Likou Zou uri: https://doi.org/10.7717/peerj.9122 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Chen et al. title: Community science participants gain environmental awareness and contribute high quality data but improvements are needed: insights from Bumble Bee Watch link: https://peerj.com/articles/9141 last-modified: 2020-05-12 description: Bumble Bee Watch is a community science program where participants submit photos of bumble bees from across Canada and the United States for expert verification. The data can be used to help better understand bumble bee biology and aid in their conservation. Yet for community science programs like this to be successful and sustainable, it is important to understand the participant demographics, what motivates them, and the outcomes of their participation, as well as areas that are working well or could be improved. It is also important to understand who verifies the submissions, who uses the data and their views on the program. Of the surveyed users, most participate to contribute to scientific data collection (88%), because of a worry about bees and a desire to help save them (80%), to learn more about species in their property (63%) or region (56%), and because of a personal interest (59%). About 77% report increased awareness of species diversity, while 84% report improvement in their identification skills. We found that 81% had at least one college or university degree. There were more respondents from suburban and rural areas than urban areas, but area did not affect numbers of submissions. While half were between 45 and 64 years of age, age did not influence motivation or number of submissions. Respondents were happy with the program, particularly the website resources, the contribution to knowledge and conservation efforts, the educational values, and the ability to get identifications. Areas for improvement included app and website functionality, faster and more detailed feedback, localized resources, and more communication. Most respondents participate rarely and have submitted fewer than ten records, although about five percent are super users who participate often and submit more than fifty records. Suggested improvements to the program may increase this participation rate. Indeed, increased recruitment and retention of users in general is important, and advertising should promote the outcomes of participation. Fifteen experts responded to a separate survey and were favorable of the program although there were suggestions on how to improve the verification process and the quality of the submitted data. Suggested research questions that could be asked or answered from the data included filling knowledge gaps (species diversity, ranges, habitat, phenology, floral associations, etc.), supporting species status assessments, effecting policy and legislation, encouraging habitat restoration and management efforts, and guiding further research. However, only about half have used data from the project to date. Further promotion of Bumble Bee Watch and community science programs in general should occur amongst academia, conservationists, policy makers, and the general public. This would help to increase the number and scope of submissions, knowledge of these species, interest in conserving them, and the overall program impact. creator: Victoria J. MacPhail creator: Shelby D. Gibson creator: Sheila R. Colla uri: https://doi.org/10.7717/peerj.9141 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 MacPhail et al.