title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=900 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Clinical, serological and epidemiological features of hepatitis A in León, Nicaragua link: https://peerj.com/articles/11516 last-modified: 2021-06-21 description: Background and ObjectivesTo monitor and document the endemicity and disease burden of acute hepatitis A in the area of an ongoing vaccine effectiveness study in León, Nicaragua.MethodsAt community health centres in León, all children, adolescents and young adults presenting with jaundice and/or other clinical signs of hepatitis were offered free serologic screening (hepatitis A, B and C) and blood tests for liver enzymes and bilirubin. Clinical and socioeconomic data were collected with a structured questionnaire. Diagnosis of acute hepatitis A was confirmed by anti-HAV IgM testing. Using logistic regression we compared the characteristics and living conditions of acute hepatitis A cases with those of non-cases.ResultsOf 557 eligible subjects enrolled between May 2006 and March 2010, 315 (56.6%) were diagnosed with hepatitis A, 80.6% of them ≤10 years and five >18 years of age. No severe cases were encountered. Apart from jaundice (95.6%) and other signs of hepatitis A (fever, pale stool, dark urine, nausea, vomiting, anorexia), two thirds of patients had moderately raised liver enzymes. Cases occurred throughout the year, with highest incidences from August to March. Poor sanitary conditions and crowding were the main risk factors.ConclusionsIn the study area, hepatitis A is still highly endemic in young and school age children living in low socioeconomic conditions. There are, however, first indications that the endemicity level is shifting from high to high-intermediate. creator: Sophie Jaisli creator: Orlando Mayorga creator: Nadia Flores creator: Sandra de Berti creator: Gustav Frösner creator: Christian Herzog creator: Marcel Zwahlen creator: Sereina A. Herzog uri: https://doi.org/10.7717/peerj.11516 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Jaisli et al. title: Clostridium butyricum relieve the visceral hypersensitivity in mice induced by Citrobacter rodentium infection with chronic stress link: https://peerj.com/articles/11585 last-modified: 2021-06-21 description: BackgroundVisceral hypersensitivity is a common symptom in patients with post-infectious irritable bowel syndrome (PI-IBS), and change of the microbiota is a vital etiological factor of it. Clostridium butyricum (C. butyricum) is one of the probiotics which is reported as the active components in the treatment of IBS, especially IBS with diarrhea. Citrobacter rodentium (C. rodentium) is an enteropathogenic bacteria which can produce self-limiting colitis in mice, which have been used to produce a PI-IBS-like mice model. Whether C. butyricum could influence the visceral hypersensitivity and gut microbiota of PI-IBS is still unknown. Our study aimed to examine whether the intervention of C. butyricum or antibiotics could affect the etiology of visceral hypersensitivity.MethodsC57BL/6 male mice were gavaged with the C. rodentium to induce a infective colitis. The C. butyricum and antibiotic compound were used to intervene the infected mice 3 days later. A 9-day chronic water avoidance stress (WAS) process was implemented to help induce the visceral hypersensitivity. The abdominal withdrawal reflex (AWR) score was assayed to indicate the visceral hypersensitivity of different groups. On the 7th, 14th, and 30th days after infection, mice feces were collected and high-throughput sequencing was carried out to analyze their gut microbiota.ResultsCombined, the C. rodentium infection plus chronic stress (WAS) could induce the visceral hypersensitivity in mice. Treatment of the C. butyricum after C. rodentium infection could relieve visceral hypersensitivity of mice, while no difference was observed in the antibiotic treatment group. The gut microbiota diversity of C. rodentium infected mice was similar to the uninfected mice, while there were different microbial communities structure between them. The Shannon and Chao indexes significantly decreased in the antibiotic treatment group compared to other groups at 7th, 14th, and 30th days post-infection, while treatment of C. butyricum could maintain the indexes within normal range. At day 14 after infection, the structure of microbiota headed towards normality after the C. butyricum treatment. After the WAS, the Shannon and Chao indexes of the control group decreased and the structure of microbiota changed. The C. butyricum treatment could prevent these changes of the gut microbiota induced by WAS.ConclusionC. butyricum could relieve the visceral hypersensitivity in mice induced by C. rodentium infection plus chronic stress. It could also remodel the microbiota change caused by the infection and chronic stress. It may be a more effective treatment strategy for PI-IBS than antibiotics. creator: Tengfei Wang creator: Lixiang Li creator: Shiyang Li creator: Hongyu Zhao creator: Junyan Qu creator: Yanan Xia creator: Yanqing Li uri: https://doi.org/10.7717/peerj.11585 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Wang et al. title: Grab what you can—an evaluation of spatial replication to decrease heterogeneity in sediment eDNA metabarcoding link: https://peerj.com/articles/11619 last-modified: 2021-06-21 description: Environmental DNA methods such as metabarcoding have been suggested as possible alternatives or complements to the current practice of morphology-based diversity assessment for characterizing benthic communities in marine sediment. However, the source volume used in sediment eDNA studies is several magnitudes lower than that used in morphological identification. Here, we used data from a North Sea benthic sampling station to investigate to what extent metabarcoding data is affected by sampling bias and spatial heterogeneity. Using three grab parallels, we sampled five separate sediment samples from each grab. We then made five DNA extraction replicates from each sediment sample. Each extract was amplified targeting both the 18S SSU rRNA V1–V2 region for total eukaryotic composition, and the cytochrome c oxidase subunit I (COI) gene for metazoans only. In both datasets, extract replicates from the same sediment sample were significantly more similar than different samples from the same grab. Further, samples from different grabs were less similar than those from the same grab for 18S. Interestingly, this was not true for COI metabarcoding, where the differences within the same grab were similar to the differences between grabs. We also investigated how much of the total identified richness could be covered by extract replicates, individual sediment samples and all sediment samples from a single grab, as well as the variability of Shannon diversity and, for COI, macrofaunal biotic indices indicating environmental status. These results were largely consistent with the beta diversity findings, and show that total eukaryotic diversity can be well represented using 18S metabarcoding with a manageable number of biological replicates. Based on these results, we strongly recommend the combination of different parts of the surface of single grabs for eDNA extraction as well as several grab replicates, or alternatively box cores or similar. This will dilute the effects of dominating species and increase the coverage of alpha diversity. COI-based metabarcoding consistency was found to be lower compared to 18S, but COI macrofauna-based indices were more consistent than direct COI alpha diversity measures. creator: Jon T. Hestetun creator: Anders Lanzén creator: Thomas G. Dahlgren uri: https://doi.org/10.7717/peerj.11619 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Hestetun et al. title: Recovery of antimicrobial susceptibility in methicillin-resistant Staphylococcus aureus (MRSA): a retrospective, epidemiological analysis in a secondary care hospital, Sapporo, Japan link: https://peerj.com/articles/11644 last-modified: 2021-06-21 description: Anti-methicillin-resistant Staphylococcus aureus (MRSA) drugs are critical final options for treating MRSA infection. This study investigated the percentage of all S. aureus isolates that are resistant to methicillin and also MRSA susceptibility to other antimicrobial agents in the JR Sapporo Hospital inpatient service. The inpatient service MRSA percentages for Japan, Hokkaido, and JR Sapporo Hospital from 2010–2019 were compared, exploring the annual rate of change in the MRSA percentage. We also investigated the antimicrobial use density (AUD) and its relationship with MRSA antimicrobial susceptibility in the JR Sapporo Hospital during 2019. The MRSA percentage in JR Sapporo Hospital was 61.5% (95% CI [52.6–69.7]) in 2010 but was only 51.6% (95% CI [41.6–61.5]) in 2019, which is a 1.43% (95% CI [0.42–2.43]) annual decrease (p = 0.05). Regarding the MRSA antimicrobial susceptibility rate in JR Sapporo Hospital, the highest rates of annual increase were seen for minocycline (3.11% (95% CI [2.25–3.94])) followed by fosfomycin (2.85% (95% CI [1.83–3.85])). Positive correlations with the AUD of anti-MRSA drugs were identified for susceptibility to erythromycin (p < 0.01), clindamycin (p = 0.002), and levofloxacin (p = 0.0005). A recovery of MRSA antimicrobial susceptibility was observed in our antibiogram dataset. Our study supports the potential for appropriate antimicrobial agent use in reviving MRSA antimicrobial susceptibility. creator: Yuji Koike creator: Hiroshi Nishiura uri: https://doi.org/10.7717/peerj.11644 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Koike and Nishiura title: Retinal dysfunction induced in a mouse model of unilateral common carotid artery occlusion link: https://peerj.com/articles/11665 last-modified: 2021-06-21 description: BackgroundRetinal ischemic stresses are associated with the pathogenesis of various retinal vascular diseases. To investigate pathological mechanisms of retinal ischemia, reproducible, robust and clinically significant experimental rodent models are highly needed. Previously, we established a stable murine model of chronic hypoperfusion retinal injuries by permanent unilateral common carotid artery occlusion (UCCAO) and demonstrated chronic pathological processes in the ischemic retina after the occlusion; however, retinal functional deficits and other acute retinal ischemic injuries by UCCAO still remain obscure. In this study, we attempted to examine retinal functional changes as well as acute retinal ischemic alterations such as retinal thinning, gliosis and cell death after UCCAO.MethodsAdult mice (male C57BL/6, 6–8 weeks old) were subjected to UCCAO in the right side, and retinal function was primarily measured using electroretinography for 14 days after the surgery. Furthermore, retinal thinning, gliosis and cell death were investigated using optical coherence tomography, immunohistochemistry and TUNEL assay, respectively.ResultsFunctional deficits in the unilateral right retina started to be seen 7 days after the occlusion. Specifically, the amplitude of b-wave dramatically decreased while that of a-wave was slightly affected. 14 days after the occlusion, the amplitudes of both waves and oscillatory potentials were significantly detected decreased in the unilateral right retina. Even though a change in retinal thickness was not dramatically observed among all the eyes, retinal gliosis and cell death in the unilateral right retina were substantially observed after UCCAO.ConclusionsAlong with previous retinal ischemic results in this model, UCCAO can stimulate retinal ischemia leading to functional, morphological and molecular changes in the retina. This model can be useful for the investigation of pathological mechanisms for human ischemic retinopathies and furthermore can be utilized to test new drugs for various ischemic ocular diseases. creator: Deokho Lee creator: Heonuk Jeong creator: Yukihiro Miwa creator: Ari Shinojima creator: Yusaku Katada creator: Kazuo Tsubota creator: Toshihide Kurihara uri: https://doi.org/10.7717/peerj.11665 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Lee et al. title: Chemical defense in developmental stages and adult of the sea star Echinaster (Othilia) brasiliensis link: https://peerj.com/articles/11503 last-modified: 2021-06-18 description: To date, evidence regarding the performance of secondary metabolites from larval stages of sea stars as an anti-predation defense relates only to a few species/specimens from a few geographic ranges. Unfortunately, this hinders a comprehensive global understanding of this inter-specific predator-prey interaction. Here, we present laboratory experimental evidence of chemical defense action in the early developmental stages and adults of the sea star Echinaster (Othilia) brasiliensis from Brazil against sympatric and allopatric invertebrate consumers. Blastulae, early and late brachiolarias of E. (O.) brasiliensis were not consumed by the sympatric and allopatric crabs Mithraculus forceps. Blastulae were also avoided by the sympatric and allopatric individuals of the anemone Anemonia sargassensis, but not the larval stages. Extracts from embryos (blastula) and brachiolarias of E. (O.) brasiliensis from one sampled population (João Fernandes beach) significantly inhibited the consumption by sympatric M. forceps, but not by allopatric crabs and A. sargassensi anemone. In this same site, extracts from adults E. (O.) brasiliensis significantly inhibited the consumption by sympatric and allopatric specimens of the crab in a range of concentrations. Whereas equivalent extract concentrations of E. (O.) brasiliensis from other population (Itaipu beach)inhibited the predation by allopatric M. forceps, while sympatric individuals of this crab avoided the only the higher level tested. Then, early stages and adult specimens of E. (O.) brasiliensis can be chemically defended against consumers, but this action is quite variable, depending on the type (anemone or crab) and the origin of the consumer (sympatric or allopatric). creator: Renato Crespo Pereira creator: Daniela Bueno Sudatti creator: Thaise S.G. Moreira creator: Carlos Renato R. Ventura uri: https://doi.org/10.7717/peerj.11503 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Pereira et al. title: Dynamics of rumen bacterial composition of yak (Bos grunniens) in response to dietary supplements during the cold season link: https://peerj.com/articles/11520 last-modified: 2021-06-18 description: This study aimed to explore the rumen bacterial community of yak in response to dietary supplements during the cold season. In addition, the rumen fermentation products were also analyzed. Twenty-one female domestic yaks were randomly divided into three groups i.e., pure grazing (GG) group, grazing plus oats hay supplement (OG) group, and grazing plus concentrate supplement group (CG). Rumen contents were collected after 90 days to assess rumen fermentation parameters and bacterial community. The GC group presented higher concentrations of ammonia nitrogen (P < 0.001), and total volatile fatty acids (TVFA) (P < 0.001), and lower rumen pH (P < 0.001) compared to other experimental groups. The CG group displayed higher proportions of propionate, butyrate, isobutyrate, and isovalerate while lower A/P ratio compared to other experimental groups. Shannon, Chao1, and ACE values were significantly lower in the OG group compared to GG and CG groups. Anosim test showed significant differences in bacterial community structure between groups but the PCA plot was not very informative to see these differences. Bacteroidetes, Proteobacteria, and Firmicutes were the three dominant phyla in all groups. The genera Oscillospira was more abundant in GG and OG groups. Higher relative abundance of Ruminococcus and Clostridium was observed in the GG group, while Ruminobacter, Corynebacterium, and Selenomonas were more abundant in the CG group. These findings will help in improving our understanding of rumen bacteria in yaks in response to changes in diet. creator: Anum Ali Ahmad creator: Jian Bo Zhang creator: Zeyi Liang creator: Chao Yang creator: Qudratullah Kalwar creator: Tariq Shah creator: Mei Du creator: Ishaq Muhammad creator: Juanshan Zheng creator: Ping Yan creator: Xue-Zhi Ding creator: Ruijun Long uri: https://doi.org/10.7717/peerj.11520 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Ahmad et al. title: Evolutionary and ecological processes influencing chemical defense variation in an aposematic and mimetic Heliconius butterfly link: https://peerj.com/articles/11523 last-modified: 2021-06-18 description: Chemical defences against predators underlie the evolution of aposematic coloration and mimicry, which are classic examples of adaptive evolution. Surprisingly little is known about the roles of ecological and evolutionary processes maintaining defence variation, and how they may feedback to shape the evolutionary dynamics of species. Cyanogenic Heliconius butterflies exhibit diverse warning color patterns and mimicry, thus providing a useful framework for investigating these questions. We studied intraspecific variation in de novo biosynthesized cyanogenic toxicity and its potential ecological and evolutionary sources in wild populations of Heliconius erato along environmental gradients, in common-garden broods and with feeding treatments. Our results demonstrate substantial intraspecific variation, including detectable variation among broods reared in a common garden. The latter estimate suggests considerable evolutionary potential in this trait, although predicting the response to selection is likely complicated due to the observed skewed distribution of toxicity values and the signatures of maternal contributions to the inheritance of toxicity. Larval diet contributed little to toxicity variation. Furthermore, toxicity profiles were similar along steep rainfall and altitudinal gradients, providing little evidence for these factors explaining variation in biosynthesized toxicity in natural populations. In contrast, there were striking differences in the chemical profiles of H. erato from geographically distant populations, implying potential local adaptation in the acquisition mechanisms and levels of defensive compounds. The results highlight the extensive variation and potential for adaptive evolution in defense traits for aposematic and mimetic species, which may contribute to the high diversity often found in these systems. creator: Anniina L. K. Mattila creator: Chris D. Jiggins creator: Øystein H. Opedal creator: Gabriela Montejo-Kovacevich creator: Érika C. Pinheiro de castro creator: W. Owen McMillan creator: Caroline Bacquet creator: Marjo Saastamoinen uri: https://doi.org/10.7717/peerj.11523 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Mattila et al. title: The impact of mental and somatic stressors on physical activity and sedentary behaviour in adults with type 2 diabetes mellitus: a diary study link: https://peerj.com/articles/11579 last-modified: 2021-06-18 description: BackgroundAdopting an active lifestyle is key in the management of type 2 diabetes mellitus (T2DM). Nevertheless, the majority of individuals with T2DM fails to do so. Additionally, individuals with T2DM are likely to experience mental (e.g., stress) and somatic (e.g., pain) stressors. Research investigating the link between these stressors and activity levels within this group is largely lacking. Therefore, current research aimed to investigate how daily fluctuations in mental and somatic stressors predict daily levels of physical activity (PA) and sedentary behaviour among adults with T2DM.MethodsIndividuals with T2DM (N = 54) were instructed to complete a morning diary assessing mental and somatic stressors and to wear an accelerometer for 10 consecutive days. The associations between the mental and somatic stressors and participants’ levels of PA and sedentary behaviour were examined using (generalized) linear mixed effect models.ResultsValid data were provided by 38 participants. We found no evidence that intra-individual increases in mental and somatic stressors detrimentally affected participants’ activity levels. Similarly, levels of sedentary behaviour nor levels of PA were predicted by inter-individual differences in the mental and somatic stressors. creator: Louise Poppe creator: Annick L. De Paepe creator: Dimitri M.L. Van Ryckeghem creator: Delfien Van Dyck creator: Iris Maes creator: Geert Crombez uri: https://doi.org/10.7717/peerj.11579 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Poppe et al. title: Design and analysis of statistical probability distribution and non-parametric trend analysis for reference evapotranspiration link: https://peerj.com/articles/11597 last-modified: 2021-06-18 description: Accurate estimates of reference evapotranspiration are critical for water-resource management strategies such as irrigation scheduling and operation. Therefore, knowledge of events such as spatial and temporal reference evapotranspiration (ETo) and their related principle of statistical probability theory plays a vital role in amplifying sustainable irrigation planning. Spatiotemporal statistical probability distribution and its associated trends have not yet has explored in Pakistan. In this study, we have two objectives: (1) to determine the most appropriate statistical probability distribution that better describes ETo on mean monthly and seasons wise estimates for the design of irrigation system in Khyber Pakhtunkhwa, and (2) to check the trends in ETo on a monthly, seasonal, and annual basis. To check the ETo trends, we used the modified version of the Mann-Kendall and Sen Slope. We used Bayesian Kriging for spatial interpolation and propose a practical approach to the design and study of statistical probability distributions for the irrigation system and water supplies management. Also, the scheme preeminent explains ETo, on a monthly and seasonal basis. The statistical distribution that showed the best fit ETo result occupying 58.33% and 25% performance for the design of irrigation scheme in the entire study region on the monthly level was Johnson SB and Generalized Pareto, respectively. However, according to the Anderson-Darling (AD) and Kolmogorov–Smirnov (KS) goodness of fit measure, seasonal ETo estimates were preferably suited to the Burr, Johnson SB & Generalized Extreme Value. More research work must be conduct to assess the significance of this study to other fields. In conclusion, these findings might be helpful for water resource management and policymaker in future operations. creator: Sajid Gul creator: Jingli Ren creator: Neal Xiong creator: Muhammad Asif Khan uri: https://doi.org/10.7717/peerj.11597 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Gul et al.