title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=623
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Herbivore camping reshapes the taxonomy, function and network of pasture soil microbial communities
link: https://peerj.com/articles/14314
last-modified: 2022-11-09
description: Although the effects of herbivore camping on soil physicochemical properties have been studied, whether the effects alter the soil microbial communities (e.g., composition, functions, taxonomic and functional diversities, network) remain unknown, especially below the surface. Here, using paired subsoil samples from half month-camping and non-camping, we showed for the first time that camping significantly changed the relative abundance of 21 bacterial phylotypes and five fungal phylotypes. Specifically, we observed significant increases in the relative abundance of putative chitinase and terpenes vanillin-decomposition genes, nitrite reduction function (nirB, nasA), decreases in the relative abundance of putative carbon fixation genes (ackA, PGK, and Pak), starch-decomposition gene (dexB), gene coding nitrogenase (anfG), and tetracycline resistance gene (tetB) for bacterial communities, and significant decreases in the relative abundance of animal endosymbiont and increases in the relative abundance of litter saprotroph and endophyte for fungal communities. However, camping did not significantly impact the taxonomic and functional diversity. The niche restriction was the main driving force of bacterial and fungal community assembly. Compared to no camping, camping increased the stability of bacterial networks but decreased the stability of fungal networks. Camping exerted a positive effect on the network by compressing the niche width and reduced the change in the network by reducing the niche overlap. Our results suggest that camping restructures the soil microbial composition, function, and network, and provides a novel insight into the effect of animal camping on soil microbial communities in grassland.
creator: Puchang Wang
creator: Leilei Ding
creator: Fuxiang Li
creator: Jiafa Liao
creator: Mengya Wang
uri: https://doi.org/10.7717/peerj.14314
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Wang et al.

title: Development of a prediction model to estimate the 5-year risk of cardiovascular events and all-cause mortality in haemodialysis patients: a retrospective study
link: https://peerj.com/articles/14316
last-modified: 2022-11-09
description: BackgroundCardiovascular disease (CVD) is a major cause of mortality in patients on haemodialysis. The development of a prediction model for CVD risk is necessary to help make clinical decisions for haemodialysis patients. This retrospective study aimed to develop a prediction model for the 5-year risk of CV events and all-cause mortality in haemodialysis patients in China.MethodsWe retrospectively enrolled 398 haemodialysis patients who underwent dialysis at the dialysis facility of the General Hospital of Northern Theater Command in June 2016 and were followed up for 5 years. The composite outcome was defined as CV events and/or all-cause death. Multivariable logistic regression with backwards stepwise selection was used to develop our new prediction model.ResultsSeven predictors were included in the final model: age, male sex, diabetes, history of CV events, no arteriovenous fistula at dialysis initiation, a monocyte/lymphocyte ratio greater than 0.43 and a serum uric acid level less than 436 mmol/L. Discrimination and calibration were satisfactory, with a C-statistic above 0.80. The predictors lay nearly on the 45-degree line for agreement with the outcome in the calibration plot. A simple clinical score was constructed to provide the probability of 5-year CV events or all-cause mortality. Bootstrapping validation showed that the new model also has similar discrimination and calibration. Compared with the Framingham risk score (FRS) and a similar model, our model showed better performance.ConclusionThis prognostic model can be used to predict the long-term risk of CV events and all-cause mortality in haemodialysis patients. An MLR greater than 0.43 is an important prognostic factor.
creator: Aihong Zhang
creator: Lemuge Qi
creator: Yanping Zhang
creator: Zhuo Ren
creator: Chen Zhao
creator: Qian Wang
creator: Kaiming Ren
creator: Jiuxu Bai
creator: Ning Cao
uri: https://doi.org/10.7717/peerj.14316
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Zhang et al.

title: Age, adrenal steroids, and cognitive functioning in captive chimpanzees (Pan troglodytes)
link: https://peerj.com/articles/14323
last-modified: 2022-11-09
description: BackgroundDehydroepiandrosterone-sulfate is the most abundant circulating androgen in humans and other catarrhines. It is involved in several biological functions, such as testosterone production, glucocorticoid antagonist actions, neurogenesis and neuroplasticty. Although the role of dehydroepiandrosterone-sulfate (DHEAS) in cognition remains elusive, the DHEAS/cortisol ratio has been positively associated with a slower cognitive age-decline and improved mood in humans. Whether this relationship is found in nonhuman primates remains unknown.MethodsWe measured DHEAS and cortisol levels in serum of 107 adult chimpanzees to investigate the relationship between DHEAS levels and age. A subset of 21 chimpanzees was used to test the potential associations between DHEAS, cortisol, and DHEAS/cortisol ratio in cognitive function, taking into account age, sex, and their interactions. We tested for cognitive function using the primate cognitive test battery (PCTB) and principal component analyses to categorize cognition into three components: spatial relationship tasks, tool use and social communication tasks, and auditory-visual sensory perception tasks.ResultsDHEAS levels, but not the DHEAS/cortisol ratio, declined with age in chimpanzees. Our analyses for spatial relationships tasks revealed a significant, positive correlation with the DHEAS/cortisol ratio. Tool use and social communication had a negative relationship with age. Our data show that the DHEAS/cortisol ratio, but not DHEAS individually, is a promising predictor of spatial cognition in chimpanzees.
creator: Rafaela S.C. Takeshita
creator: Melissa K. Edler
creator: Richard S. Meindl
creator: Chet C. Sherwood
creator: William D. Hopkins
creator: Mary Ann Raghanti
uri: https://doi.org/10.7717/peerj.14323
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Takeshita et al.

title: Identification of quantitative trait loci of agronomic traits in bread wheat using a Pamyati Azieva × Paragon mapping population harvested in three regions of Kazakhstan
link: https://peerj.com/articles/14324
last-modified: 2022-11-09
description: BackgroundAlthough genome-wide association studies (GWAS) are an increasingly informative tool in the mining of new quantitative trait loci (QTLs), a classical biparental mapping approach is still a powerful, widely used method to search the unique genetic factors associated with important agronomic traits in bread wheat.MethodsIn this study, a newly constructed mapping population of Pamyati Azieva (Russian Federation) × Paragon (UK), consisting of 94 recombinant inbred lines (RILs), was tested in three different regions of Kazakhstan with the purpose of QTL identification for key agronomic traits. The RILs were tested in 11 environments of two northern breeding stations (Petropavlovsk, North Kazakhstan region, and Shortandy, Aqmola region) and one southeastern station (Almalybak, Almaty region). The following eight agronomic traits were studied: heading days, seed maturation days, plant height, spike length, number of productive spikes, number of kernels per spike, thousand kernel weight, and yield per square meter. The 94 RILs of the PAxP cross were genotyped using Illumina’s iSelect 20K single nucleotide polymorphism (SNP) array and resulted in the identification of 4595 polymorphic SNP markers.ResultsThe application of the QTL Cartographer statistical package allowed the identification of 53 stable QTLs for the studied traits. A survey of published studies related to common wheat QTL identification suggested that 28 of those 53 QTLs were presumably novel genetic factors. The SNP markers for the identified QTLs of the analyzed agronomic traits of common wheat can be efficiently applied in ongoing breeding activities in the wheat breeding community using a marker-assisted selection approach.
creator: Akerke Amalova
creator: Kanat Yermekbayev
creator: Simon Griffiths
creator: Saule Abugalieva
creator: Adylkhan Babkenov
creator: Elena Fedorenko
creator: Aigul Abugalieva
creator: Yerlan Turuspekov
uri: https://doi.org/10.7717/peerj.14324
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Amalova et al.

title: Using search trends to analyze web-based users’ behavior profiles connected with COVID-19 in mainland China: infodemiology study based on hot words and Baidu Index
link: https://peerj.com/articles/14343
last-modified: 2022-11-09
description: BackgroundMainland China, the world’s most populous region, experienced a large-scale coronavirus disease 2019 (COVID-19) outbreak in 2020 and 2021, respectively. Existing infodemiology studies have primarily concentrated on the prospective surveillance of confirmed cases or symptoms which met the criterion for investigators; nevertheless, the actual impact regarding COVID-19 on the public and subsequent attitudes of different groups towards the COVID-19 epidemic were neglected.MethodsThis study aimed to examine the public web-based search trends and behavior patterns related to COVID-19 outbreaks in mainland China by using hot words and Baidu Index (BI). The initial hot words (the high-frequency words on the Internet) and the epidemic data (2019/12/01–2021/11/30) were mined from infodemiology platforms. The final hot words table was established by two-rounds of hot words screening and double-level hot words classification. Temporal distribution and demographic portraits of COVID-19 were queried by search trends service supplied from BI to perform the correlation analysis. Further, we used the parameter estimation to quantitatively forecast the geographical distribution of COVID-19 in the future.ResultsThe final English-Chinese bilingual table was established including six domains and 32 subordinate hot words. According to the temporal distribution of domains and subordinate hot words in 2020 and 2021, the peaks of searching subordinate hot words and COVID-19 outbreak periods had significant temporal correlation and the subordinate hot words in COVID-19 Related and Territory domains were reliable for COVID-19 surveillance. Gender distribution results showed that Territory domain (the male proportion: 67.69%; standard deviation (SD): 5.88%) and Symptoms/Symptom and Public Health (the female proportion: 57.95%, 56.61%; SD: 0, 9.06%) domains were searched more by male and female groups respectively. The results of age distribution of hot words showed that people aged 20–50 (middle-aged people) had a higher online search intensity, and the group of 20–29, 30–39 years old focused more on Media and Symptoms/Symptom (proportion: 45.43%, 51.66%; SD: 15.37%, 16.59%) domains respectively. Finally, based on frequency rankings of searching hot words and confirmed cases in Mainland China, the epidemic situation of provinces and Chinese administrative divisions were divided into 5 levels of early-warning regions. Central, East and South China regions would be impacted again by the COVID-19 in the future.
creator: Shuai Jiang
creator: Changqiao You
creator: Sheng Zhang
creator: Fenglin Chen
creator: Guo Peng
creator: Jiajie Liu
creator: Daolong Xie
creator: Yongliang Li
creator: Xinhong Guo
uri: https://doi.org/10.7717/peerj.14343
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Jiang et al.

title: Treatment for dental erosion: a systematic review of in vitro studies
link: https://peerj.com/articles/13864
last-modified: 2022-11-08
description: BackgroundDental erosion is a chemical loss of the mineralized dental tissue caused by exposure to nonbacterial acids. Different treatment protocols have been adopted with the use of fluoride compounds to promote the formation of a layer of mineral precipitation in eroded lesions.AimThis systematic review aimed to evaluate the main treatments for dental erosion.MethodologyThis study followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines and recorded in the Open Science Framework database (OSF) under DOI 10.17605/OSF.IO/XMFNZ. The searches were conducted in six electronic databases (Pubmed, Embase, Web of Science, Cochrane, Scopus, Lilacs) and two grey literature sources (Google Scholar and OpenGrey). The eligibility criteria included in vitro studies that evaluated eroded teeth under treatment with some topical agent. Risk of bias assessment and qualitative synthesis were performed using the Cochrane collaboration’s tool for assessing risk of bias modified for in vitro studies.ResultsA total of 522 studies were identified, and only four studies that fulfilled our eligibility criteria were included in this review. Among these studies, three were considered to have a low risk of bias, and one to have a high risk of bias. Two studies evaluated the anti-erosion effect of fluoride toothpaste, and the other two assessed the action of casein phosphopeptide–amorphous calcium phosphate (CPP-ACP) on the surface of human teeth. Among the products analyzed, CPP-ACP was the only one that promoted a significant increase in enamel microhardness and reduced tooth wear.ConclusionBased on the in vitro studies included in this review, there was no anti-erosion effect after using different fluoride toothpaste. However, it should be considered that one of these studies presented a high risk of bias. On the other hand, studies with CPP-ACP showed anti-erosion efficacy when applied before or after erosive wear.
creator: Yago Gecy de Sousa Né
creator: Deiweson Souza-Monteiro
creator: Deborah Ribeiro Frazão
creator: María Olimpia Paz Alvarenga
creator: Walessa Alana Bragança Aragão
creator: NatháliaCarolina Fernandes Fagundes
creator: Renata Duarte de Souza-Rodrigues
creator: Rafael Rodrigues Lima
uri: https://doi.org/10.7717/peerj.13864
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Né et al.

title: Genomic, biochemical and expressional properties reveal strong conservation of the CLCA2 gene in birds and mammals
link: https://peerj.com/articles/14202
last-modified: 2022-11-08
description: Recent studies have revealed the dynamic and complex evolution of CLCA1 gene homologues in and between mammals and birds with a particularly high diversity in mammals. In contrast, CLCA2 has only been found as a single copy gene in mammals, to date. Furthermore, CLCA2 has only been investigated in few mammalian species but not in birds. Here, we established core genomic, protein biochemical and expressional properties of CLCA2 in several bird species and compared them with mammalian CLCA2. Chicken, turkey, quail and ostrich CLCA2 were compared to their mammalian orthologues using in silico, biochemical and expressional analyses. CLCA2 was found highly conserved not only at the level of genomic and exon architecture but also in terms of the canonical CLCA2 protein domain organization. The putatively prototypical galline CLCA2 (gCLCA2) was cloned and immunoblotting as well as immunofluorescence analyses of heterologously expressed gCLCA2 revealed protein cleavage, glycosylation patterns and anchoring in the plasma membrane similar to those of most mammalian CLCA2 orthologues. Immunohistochemistry found highly conserved CLCA2 expression in epidermal keratinocytes in all birds and mammals investigated. Our results suggest a highly conserved and likely evolutionarily indispensable role of CLCA2 in keratinocyte function. Its high degree of conservation on the genomic, biochemical and expressional levels stands in contrast to the dynamic structural complexities and proposed functional diversifications between mammalian and avian CLCA1 homologues, insinuating a significant degree of negative selection of CLCA2 orthologues among birds and mammals. Finally, and again in contrast to CLCA1, the high conservation of CLCA2 makes it a strong candidate for studying basic properties of the functionally still widely unresolved CLCA gene family.
creator: Florian Bartenschlager
creator: Nikolai Klymiuk
creator: Achim D. Gruber
creator: Lars Mundhenk
uri: https://doi.org/10.7717/peerj.14202
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Bartenschlager et al.

title: Prediction of Ross River virus incidence in Queensland, Australia: building and comparing models
link: https://peerj.com/articles/14213
last-modified: 2022-11-08
description: Transmission of Ross River virus (RRV) is influenced by climatic, environmental, and socio-economic factors. Accurate and robust predictions based on these factors are necessary for disease prevention and control. However, the complicated transmission cycle and the characteristics of RRV notification data present challenges. Studies to compare model performance are lacking. In this study, we used RRV notification data and exposure data from 2001 to 2020 in Queensland, Australia, and compared ten models (including generalised linear models, zero-inflated models, and generalised additive models) to predict RRV incidence in different regions of Queensland. We aimed to compare model performance and to evaluate the effect of statistical over-dispersion and zero-inflation of RRV surveillance data, and non-linearity of predictors on model fit. A variable selection strategy for screening important predictors was developed and was found to be efficient and able to generate consistent and reasonable numbers of predictors across regions and in all training sets. Negative binomial models generally exhibited better model fit than Poisson models, suggesting that over-dispersion in the data is the primary factor driving model fit compared to non-linearity of predictors and excess zeros. All models predicted the peak periods well but were unable to fit and predict the magnitude of peaks, especially when there were high numbers of cases. Adding new variables including historical RRV cases and mosquito abundance may improve model performance. The standard negative binomial generalised linear model is stable, simple, and effective in prediction, and is thus considered the best choice among all models.
creator: Wei Qian
creator: David Harley
creator: Kathryn Glass
creator: Elvina Viennet
creator: Cameron Hurst
uri: https://doi.org/10.7717/peerj.14213
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Qian et al.

title: Description of a new Pangasius (Valenciennes, 1840) species, from the Cauvery River extends distribution range of the genus up to South Western Ghats in peninsular India
link: https://peerj.com/articles/14258
last-modified: 2022-11-08
description: A new species of the genus Pangasius, is described based on 17 specimens collected from the Cauvery River, India. It can be distinguished from its sister species from South and Southeast Asia, by its widely placed, small and rounded vomerine and palatine tooth plates, longer maxillary and mandibular barbels, greater vertebrae count 50 (vs. 44–48), and smaller caudal peduncle depth (6.5–8.2% SL vs. 9.89–13.09% SL). The tooth plates of the new species closely resembles that of Pangasius macronema but can be clearly distinguished from the latter by having lesser gill rakers (16–19 vs. 36–45); a smaller eye (2.4–4.4% SL vs. 5.2–9.6% SL); and larger adipose-fin base (1.5–2.9% SL vs. 0.1–1.2% SL). The mitochondrial cytochrome c oxidase (COI) gene sequence of the new species shows the genetic divergence of 3.5% and 5.1% from P. pangasius and P. silasi respectively, the two sister species found in South Asia and India. The species delimitation approaches, Poisson Tree Processes (PTP) and assemble species by automatic partitioning (ASAP) clearly resolved that the P. icaria is distinct from its sister species. Phylogenetic position of the species with its sister species was evaluated using maximum likelihood and Bayesian analysis. The discovery of this previously unknown species of genus Pangasius from the Cauvery River of peninsular India indicates important biogeographical insight that this genus migrated till the southern division of Western Ghats.
creator: Kathirvelpandian P.V. Ayyathurai
creator: Paramasivam Kodeeswaran
creator: Vindhya Mohindra
creator: Rajeev K. Singh
creator: Charan Ravi
creator: Rahul Kumar
creator: BasheerSaidmuhammed Valaparambil
creator: Ajith Kumar Thipramalai Thangappan
creator: Joykrushna Jena
creator: Kuldeep K. Lal
uri: https://doi.org/10.7717/peerj.14258
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Ayyathurai et al.

title: A decade of invertebrate recruitment at Santa Catalina Island, California
link: https://peerj.com/articles/14286
last-modified: 2022-11-08
description: Marine fouling communities have long provided model systems for studying the ecology of community development, and settlement plates are the tool of choice for this purpose. Decades of plate deployments provide a baseline against which present-day trends can be interpreted, with one classic trend being the ultimate dominance of plates by colonial and encrusting taxa. Here we report the results of annual deployments of settlement plates from 2010 to 2021 in the shallow sub-tidal of southern California, where the recruitment of invertebrates and algae was recorded photographically, and resolved to functional group (solitary, encrusting, and arborescent) and the lowest taxon possible. The communities on these plates differed among years, with trends in abundances varying by functional group and taxon; solitary taxa consistently were abundant, but encrusting taxa declined in abundance. Seawater temperature and the subsurface concentration of chlorophyll a differed among years, and there was a weak inverse association between temperature and the abundances of encrusting taxa. Long-term increases in seawater temperature therefore could serve as a mechanism causing fouling communities to change. Because of the prominence of encrusting taxa in fouling communities, the shifts in abundance of this functional group reported here may portend ecologically significant changes in fouling communities exposed to warmer seawater because of an alleviation of competition for a classically limiting resource (i.e., space).
creator: Peter J. Edmunds
creator: Jessica Clayton
uri: https://doi.org/10.7717/peerj.14286
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Edmunds and Clayton