title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=802 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: The structure and functional profile of ruminal microbiota in young and adult reindeers (Rangifer tarandus) consuming natural winter-spring and summer-autumn seasonal diets link: https://peerj.com/articles/12389 last-modified: 2021-11-24 description: BackgroundThe key natural area of Russian reindeer (Rangifer tarandus, Nenets breed) is arctic zones, with severe climatic conditions and scarce feed resources, especially in the cold winter season. The adaptation of reindeer to these conditions is associated not only with the genetic potential of the animal itself. The rumen microbiome provides significant assistance in adapting animals to difficult conditions by participating in the fiber digestion. The aim of our study is to investigate the taxonomy and predicted metabolic pathways of the ruminal microbiota (RM) during the winter–spring (WS) and summer–autumn (SA) seasons, in calves and adult reindeer inhabiting the natural pastures of the Yamalo-Nenetsky Autonomous District of the Russian Federation.MethodsThe RM in reindeer was studied using the Next Generation Sequencing method with the MiSeq (Illumina, San Diego, CA, USA) platform. Reconstruction and prediction of functional profiles of the metagenome, gene families, and enzymes were performed using the software package PICRUSt2 (v.2.3.0).ResultsThe nutritional value of WS and SA diets significantly differed. Crude fiber content in the WS diet was higher by 22.4% (p < 0.05), compared to SA, indicating possibly poorer digestibility and necessity of the adaptation of the RM to this seasonal change. A total of 22 bacterial superphyla and phyla were found in the rumen, superphylum Bacteroidota and phylum Firmicutes being the dominating taxa (up to 48.1% ± 4.30% and 46.1% ± 4.80%, respectively); while only two archaeal phyla presented as minor communities (no more then 0.54% ± 0.14% totally). The percentages of the dominating taxa were not affected by age or season. However, significant changes in certain minor communities were found, with seasonal changes being more significant than age-related ones. The percentage of phylum Actinobacteriota significantly increased (19.3-fold) in SA, compared to WS (p = 0.02) in adults, and the percentage of phylum Cyanobacteria increased up to seven-fold (p = 0.002) in adults and calves. Seasonal changes in RM can improve the ability of reindeer to withstand the seasons characterized by a low availability of nutrients. The PICRUSt2 results revealed 257 predicted metabolic pathways in RM: 41 pathways were significantly (p < 0.05) influenced by season and/or age, including the processes of synthesis of vitamins, volatile fatty acids, and pigments; metabolism of protein, lipids, and energy; pathogenesis, methanogenesis, butanediol to pyruvate biosynthesis, cell wall biosynthesis, degradation of neurotransmitters, lactic acid fermentation, and biosynthesis of nucleic acids. A large part of these changeable pathways (13 of 41) was related to the synthesis of vitamin K homologues.ConclusionThe results obtained improve our knowledge on the structure and possible metabolic pathways of the RM in reindeer, in relation to seasonal changes. creator: Elena Yildirim creator: Larisa Ilina creator: Georgy Laptev creator: Valentina Filippova creator: Evgeni Brazhnik creator: Timur Dunyashev creator: Andrey Dubrovin creator: Natalia Novikova creator: Daria Tiurina creator: Nikolay Tarlavin creator: Kasim Laishev uri: https://doi.org/10.7717/peerj.12389 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Yildirim et al. title: The reporting of p values, confidence intervals and statistical significance in Preventive Veterinary Medicine (1997–2017) link: https://peerj.com/articles/12453 last-modified: 2021-11-24 description: BackgroundDespite much discussion in the epidemiologic literature surrounding the use of null hypothesis significance testing (NHST) for inferences, the reporting practices of veterinary researchers have not been examined. We conducted a survey of articles published in Preventive Veterinary Medicine, a leading veterinary epidemiology journal, aimed at (a) estimating the frequency of reporting p values, confidence intervals and statistical significance between 1997 and 2017, (b) determining whether this varies by article section and (c) determining whether this varies over time.MethodsWe used systematic cluster sampling to select 985 original research articles from issues published in March, June, September and December of each year of the study period. Using the survey data analysis menu in Stata, we estimated overall and yearly proportions of article sections (abstracts, results-texts, results-tables and discussions) reporting p values, confidence intervals and statistical significance. Additionally, we estimated the proportion of p values less than 0.05 reported in each section, the proportion of article sections in which p values were reported as inequalities, and the proportion of article sections in which confidence intervals were interpreted as if they were significance tests. Finally, we used Generalised Estimating Equations to estimate prevalence odds ratios and 95% confidence intervals, comparing the occurrence of each of the above-mentioned reporting elements in one article section relative to another.ResultsOver the 20-year period, for every 100 published manuscripts, 31 abstracts (95% CI [28–35]), 65 results-texts (95% CI [61–68]), 23 sets of results-tables (95% CI [20–27]) and 59 discussion sections (95% CI [56–63]) reported statistical significance at least once. Only in the case of results-tables, were the numbers reporting p values (48; 95% CI [44–51]), and confidence intervals (44; 95% CI [41–48]) higher than those reporting statistical significance. We also found that a substantial proportion of p values were reported as inequalities and most were less than 0.05. The odds of a p value being less than 0.05 (OR = 4.5; 95% CI [2.3–9.0]) or being reported as an inequality (OR = 3.2; 95% CI [1.3–7.6]) was higher in the abstracts than in the results-texts. Additionally, when confidence intervals were interpreted, on most occasions they were used as surrogates for significance tests. Overall, no time trends in reporting were observed for any of the three reporting elements over the study period.ConclusionsDespite the availability of superior approaches to statistical inference and abundant criticism of its use in the epidemiologic literature, NHST is substantially the most common means of inference in articles published in Preventive Veterinary Medicine. This pattern has not changed substantially between 1997 and 2017. creator: Locksley L. McV. Messam creator: Hsin-Yi Weng creator: Nicole W. Y. Rosenberger creator: Zhi Hao Tan creator: Stephanie D. M. Payet creator: Mahishi Santbakshsing uri: https://doi.org/10.7717/peerj.12453 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Messam et al. title: Characterization of the morphology and complete mitochondrial genomes of Eupteryx minusula and Eupteryx gracilirama (Hemiptera: Cicadellidae: Typhlocybinae) from Karst area, Southwest China link: https://peerj.com/articles/12501 last-modified: 2021-11-24 description: BackgroundThe hemipteran insect family Cicadellidae (leafhoppers) includes >2,600 valid genera and >22,000 valid species worldwide, including >2,000 species in China. Typhlocybinae, second largest subfamilies of Cicadellidae, is widely distributed in the six major zoogeographic regions of the world, including >4,000 species worldwide and >1,000 species in China. Previously, morphological analysis are often effective to the way of taxonomy, but it did not combine with molecular biology. Therefore, morphology and mitochondrial genomes (mitogenomes) of two leafhopper species, Eupteryx (Eupteryx) minusculaLindberg, 1929 and Eupteryx (Stacla) graciliramaHou, Zhang & Huang, 2016 were studied and analyzed. This study analyzed the morphological and molecular characteristics of the two leafhoppers, and showed whether the results of the two identifications were consistent.MethodsBased on the method of comparison, mitogenomes and morphology were analyzed to prove the relationship between the two leafhoppers.ResultsAlthough two focal species are classified in two different subgenera of the same genus, they still share many morphological features, such as the moderately produced crown fore margin; the milky yellow apical part of scutellum; the pronotum, basal triangles of scutellum, and forewing are dark with several colorless patches on the surface; the light yellow face, without any spots or stripes, and so on. The circular mitogenomes are 16,944 bp long in E. minuscula (GenBank: MN910279) and 17,173 bp long in E. gracilirama (GenBank: MT594485). All of the protein-coding genes are starting with ATN, except for some in mitogenome, which has a single T or TAN as a stop codon. All tRNAs have the typical cloverleaf-shaped structure except for trnS1 (AGN) (E. minuscula) which has a reduced DHU arm. Moreover, these two mitogenomes have trnR with an unpaired base in the acceptor stem. The phylogenetic relationships between E. minuscula and E. gracilirama in respect to related lineages were reconstructed using Maximum likelihood and Maximum parsimony analyses.DiscussionThe result showed that the tribe Typhlocybini is a sister to the tribes Erythroneurini and Empoascini, and five genera, Bolanusoides, Typhlocyba, Eupteryx, Zyginella and Limassolla are forming a single clade. E. minuscula and E. gracilirama are clustered together, supporting the monophyly of the genus Eupteryx. The above conclusions are consistent with the traditional classification of the subfamily. creator: Zhouwei Yuan creator: Kangning Xiong creator: Ni Zhang creator: Can Li creator: Yuehua Song uri: https://doi.org/10.7717/peerj.12501 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Yuan et al. title: Proteomic profiling of the endogenous peptides of MRSA and MSSA link: https://peerj.com/articles/12508 last-modified: 2021-11-24 description: Staphylococcus aureus is a Gram-positive bacterium that can cause diverse skin and soft tissue infections. Methicillin-resistant Staphylococcus aureus (MRSA) can cause more severe infections than methicillin-susceptible Staphylococcus aureus (MSSA). Nevertheless, the physiological and metabolic regulation of MSSA and MRSA has not been well studied. In light of the increased interest in endogenous peptides and recognition of the important roles that they play, we studied the endogenous peptidome of MSSA and MRSA. We identified 1,065 endogenous peptides, among which 435 were differentially expressed (DE), with 292 MSSA-abundant endogenous peptides and 35 MRSA-abundant endogenous peptides. MSSA-abundant endogenous peptides have significantly enriched “VXXXK” motif of at the C-terminus. MSSA-abundant endogenous peptides are involved in penicillin-binding and immune responses, whereas MRSA-abundant endogenous peptides are associated with antibiotic resistance and increased toxicity. Our characterization of the peptidome of MSSA and MRSA provides a rich resource for future studies to explore the functional regulation of drug resistance in S. aureus and may also help elucidate the mechanisms of its pathogenicity and the development of treatments. creator: Haixia Tu creator: Fei Xu creator: Yiwei Cheng creator: Qianglong Pan creator: Xiao Cai creator: Shouxing Wang creator: Shuting Ge creator: Min Cao creator: Dongming Su creator: Yan Li uri: https://doi.org/10.7717/peerj.12508 license: https://creativecommons.org/licenses/by-nc/4.0/ rights: ©2021 Tu et al. title: Biomechanics of the medial meniscus in the osteoarthritic knee joint link: https://peerj.com/articles/12509 last-modified: 2021-11-24 description: BackgroundIncreased mechanical loading and pathological response of joint tissue to the abnormal mechanical stress can cause degradation of cartilage characteristic of knee osteoarthritis (OA). Despite osteoarthritis is risk factor for the development of meniscal lesions the mechanism of degenerative meniscal lesions is still unclear. Therefore, the aim of the study is to investigate the influence of medial compartment knee OA on the stress state and deformation of the medial meniscus.MethodsThe finite element method was used to simulate the stance phase of the gait cycle. An intact knee model was prepared based on magnetic resonance scans of the left knee joint of a healthy volunteer. Degenerative changes in the medial knee OA model were simulated by nonuniform reduction in articular cartilage thickness in specific areas and by a decrease in the material parameters of cartilage and menisci. Two additional models were created to separately evaluate the effect of alterations in articular cartilage geometry and material parameters of the soft tissues on the results. A nonlinear dynamic analysis was performed for standardized knee loads applied to the tibia bone.ResultsThe maximum von Mises stress of 26.8 MPa was observed in the posterior part of the medial meniscus body in the OA model. The maximal hoop stress for the first peak of total force was 83% greater in the posterior horn and only 11% greater in the anterior horn of the medial meniscus in the OA model than in the intact model. The reduction in cartilage thickness caused an increase of 57% in medial translation of the medial meniscus body. A decrease in the compressive modulus of menisci resulted in a 2.5-fold greater reduction in the meniscal body width compared to the intact model.ConclusionsHigher hoop stress levels on the inner edge of the posterior part of the medial meniscus in the OA model than in the intact model are associated with a greater medial translation of the meniscus body and a greater reduction in its width. The considerable increase in hoop stresses shows that medial knee OA may contribute to the initiation of meniscal radial tears. creator: Karol Daszkiewicz creator: Piotr Łuczkiewicz uri: https://doi.org/10.7717/peerj.12509 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Daszkiewicz and Łuczkiewicz title: Chemical profiling of root bark extract from Oplopanax elatus and its in vitro biotransformation by human intestinal microbiota link: https://peerj.com/articles/12513 last-modified: 2021-11-24 description: Oplopanax elatus (Nakai) Nakai, in the Araliaceae family, has been used in traditional Chinese medicine (TCM) to treat diseases as an adaptogen for thousands of years. This study established an ultra-performance liquid chromatography coupled with quadrupole time-of-flight tandem mass spectrometry (UPLC-Q-TOF/MS) method to identify chemical components and biotransformation metabolites of root bark extract from O. elatus. A total of 18 compounds were characterized in O. elatus extract, and 62 metabolites by human intestinal microbiota were detected. Two polyynes, falcarindiol and oplopandiol were recognized as the main components of O. elatus, whose metabolites are further illustrated. Several metabolic pathways were proposed to generate the detected metabolites, including methylation, hydrogenation, demethylation, dehydroxylation, and hydroxylation. These findings indicated that intestinal microbiota might play an essential role in mediating the bioactivity of O. elatus. creator: Jin-Yi Wan creator: Jing-Xuan Wan creator: Shilei Wang creator: Xiaolu Wang creator: Wenqian Guo creator: Han Ma creator: Yuqi Wu creator: Chong-Zhi Wang creator: Lian-Wen Qi creator: Ping Li creator: Haiqiang Yao creator: Chun-Su Yuan uri: https://doi.org/10.7717/peerj.12513 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Wan et al. title: Translation and psychometric validation of the Persian version of the Questionnaire on Smoking Urges for assessment of craving to smoke among university students link: https://peerj.com/articles/12531 last-modified: 2021-11-24 description: BackgroundEven though tobacco is one of the most preventable causes of death worldwide, it endangers more than 8 million people yearly. In this context, meta-analyses suggest that a significant part of the general Iranian population over 15 years of age smoke and that there is a need for good screening tools for smoking cravings and urges in Iran. The present study reported the translation and investigated the psychometric properties (i.e., factor structure, validity, and reliability) of the Persian version of the Questionnaire on Smoking Urges (QSU) with 12 items in the Iranian context.MethodThe translation process and content validity of the items were examined entirely in an expert panel using the Content Validity Index. The total sample of participants in which the translated version was tested consisted of 392 (172 female, 220 male, Mage = 22.31 years, SD = 2.90) university students who answered the QSU 12-item at the start of their participation in smoking cessation interventions. The QSU 12-item was firstly translated, then piloted using a subsample of 150 university students and finally validity and reliability of the instrument were investigated using a subsample of 242 participants. We tested the proposed models in the literature, that is, a 1-factor solution and a 2-factor solution with six items on each factor (Factor 1: desire/intention to smoke; Factor 2: relief of negative affect or withdrawal symptoms and anticipation of positive outcome). At last, we tested differences across differences in QSU-scores across different subgroups of individuals based on their demographics.ResultsThe results suggested that, in contrast to past studies, a modified 2-factor model, using five items for Factor 1 and 7 items for Factor 2, was the best fitting model (CFI = .95, RMSEA = .09, CI = 90%). Additionally, the QSU 12-item Persian version showed good convergent and divergent validity, internal consistency (Factor 1 = .94, Factor 2 = .97), ICC (average measure ICC = .95, CI = 95%, F(391, 4301) = 20.54, p < .001), concurrent validity (r = .71, p < .01), and discriminant validity (r = −.04, p > .05). Finally, subgroups based on gender, marital status, (un)employment, and educational level did not differed in their responses to the QSU 12-item.ConclusionThe Persian version of the QSU 12-item has satisfactory psychometric properties and, with a slight modification, it can be considered as a reliable and valid method to estimate smoking urges in the Iranian population. Moreover, the QSU 12-item seems appropriate to measure urge for smoking among groups of individuals with different sociodemographic backgrounds. Importantly, the QSU 12-item differentiates individuals’ desire and intention to smoke from their anticipated relief of negative affect or withdrawal symptoms, which can be important for personalizing interventions targeting individuals who want to quit smoking. creator: Maryam Kazemitabar creator: Danilo Garcia uri: https://doi.org/10.7717/peerj.12531 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Kazemitabar et al. title: Comparison of an exercise program with and without manual therapy for patients with chronic neck pain and upper cervical rotation restriction. Randomized controlled trial link: https://peerj.com/articles/12546 last-modified: 2021-11-24 description: BackgroundCervical exercise has been shown to be an effective treatment for neck pain, but there is still a need for more clinical trials evaluating the effectiveness of adding manual therapy to the exercise approach. There is a lack of evidence on the effect of these techniques in patients with neck pain and upper cervical rotation restriction.PurposeTo compare the effectiveness of adding manual therapy to a cervical exercise protocol for the treatment of patients with chronic neck pain and upper cervical rotation restriction.MethodsSingle-blind randomized clinical trial. Fifty-eight subjects: 29 for the Manual Therapy+Exercise (MT+Exercise) Group and 29 for the Exercise group. Neck disability index, pain intensity (0–10), pressure pain threshold (kPa), flexion-rotation test (°), and cervical range of motion (°) were measured at the beginning and at the end of the intervention, and at 3-and 6-month follow-ups. The MT+Exercise Group received one 20-min session of manual therapy and exercise once a week for 4 weeks and home exercise. The Exercise Group received one 20-min session of exercise once a week for 4 weeks and home exercise.ResultsThe MT+Exercise Group showed significant better values post-intervention in all variables: neck disability index: 0% patient with moderate, severe, or complete disability compared to 31% in the Exercise Group (p = 0.000) at 6-months; flexion-rotation test (p = 0.000) and pain intensity (p = 0.000) from the first follow-up to the end of the study; cervical flexion (p = 0.002), extension (p = 0.002), right lateral-flexion (p = 0.000), left lateral-flexion (p = 0.001), right rotation (p = 0.000) and left rotation (p = 0.005) at 6-months of the study, except for flexion, with significative changes from 3-months of follow up; pressure pain threshold from the first follow-up to the end of the study (p values range: 0.003–0.000).ConclusionFour 20-min sessions of manual therapy and exercise, along with a home-exercise program, was found to be more effective than an exercise protocol and a home-exercise program in improving the neck disability index, flexion-rotation test, pain intensity, and pressure pain threshold, in the short, medium, and medium-long term in patients with chronic neck pain and upper rotation restriction. Cervical range of motion improved with the addition of manual therapy in the medium and medium-long term. The high dropout rate may have compromised the external validity of the study. creator: Jacobo Rodríguez-Sanz creator: Miguel Malo-Urriés creator: María Orosia Lucha-López creator: Carlos López-de-Celis creator: Albert Pérez-Bellmunt creator: Jaime Corral-de-Toro creator: César Hidalgo-García uri: https://doi.org/10.7717/peerj.12546 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Rodríguez-Sanz et al. title: Thresholds of acidification impacts on macroinvertebrates adapted to seasonally acidified tropical streams: potential responses to extreme drought-driven pH declines link: https://peerj.com/articles/11955 last-modified: 2021-11-23 description: BackgroundDrought-driven acidification events of increasing frequency and severity are expected as a consequence of climate change, and these events may expose macroinvertebrate taxa to increased acidification beyond their tolerance levels. Recent work in lowland Costa Rica has shown that poorly-buffered tropical streams exhibit natural seasonal variation in pH, with extremely low levels (<4.5) after extreme dry seasons). Our goal was to determine the threshold of pH effects on survival of three tropical stream macroinvertebrate taxa.MethodsWe conducted laboratory mesocosm experiments to determine acidification effects (using diluted HCl) on three focal macroinvertebrate taxa collected from a poorly-buffered stream at La Selva Biological Station: (1) mayfly naiads (Ephemeroptera: Leptophlebiidae: Traverella holzenthali), (2) adult shrimp (Decapoda: Palaemonidae: Macrobrachium olfersii), and (3) larval midges (Diptera: Chironomidae). We also compared the effect of pH on survival and growth rates of larval midges from a poorly-buffered (pH 4.3–6.9) vs. a naturally well-buffered (pH 5.1–6.9) stream.Results/DiscussionMayfly and shrimp survival decreased between pH 4.0 and 3.5, overlapping with the range of lowest pH levels (3.6–4.0) recorded during a previous extreme El Niño Southern Oscillation event in 1998 and suggesting that increasingly extreme acidification events induced by climate change may negatively affect their survival. In contrast, survival of larval midges was unaffected by pH regimes at/above 3.5, indicating tolerance to pH levels experienced in poorly-buffered stream during seasonal acidification, which has presumably occurred over millennia. These findings highlight the potential importance of historical pH regimes in structuring macroinvertebrate communities. These results are relevant not only to lowland Neotropical streams, but also signal the need for further research in lotic ecosystems worldwide where drought-driven pH declines have been documented or are probable in the future. creator: Carissa Ganong creator: Minor Hidalgo Oconitrillo creator: Catherine Pringle uri: https://doi.org/10.7717/peerj.11955 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Ganong et al. title: Establishment and validation of an individualized macrophage-related gene signature to predict overall survival in patients with triple negative breast cancer link: https://peerj.com/articles/12383 last-modified: 2021-11-23 description: BackgroundRecently, researchers have classified highly heterogeneous triple negative breast cancer (TNBC) into different subtypes from different perspectives and investigated the characteristics of different subtypes to pursue individualized treatment. With the increase of immunotherapy and its preliminary application in TNBC treatment, the value of immune-related strategies in the treatment of TNBC has been initially reflected. Based thereon, this study plans to classify and further explore TNBC from the perspective of immune cell infiltration.MethodThe fractions of immune cells of TNBC patients were assessed by six immune component analysis methods in The Cancer Genome Atlas (TCGA) database. Hub genes significantly related to poor prognosis were verified by weighted gene co-expression network analysis (WGCNA) analysis, Lasso analysis, and univariate KM analysis. Two cohorts of TNBC patients with complete prognosis information were collected for validation analysis. Finally, the Genomics of Drug Sensitivity in Cancer (GDSC) database was adopted to ascertain the sensitivity differences of different populations based on hub-gene grouping to different chemotherapy drugs.ResultsFive hub genes (CD79A, CXCL13, IGLL5, LHFPL2, and PLEKHF1) of the key co-expression gene module could divide TNBC patients into two groups (Cluster A and Cluster B) based on consistency cluster analysis. The patients with Cluster A were responsible for significantly worse prognosis than the patients with Cluster B (P = 0.023). In addition, another classification method, PCoA, and two other datasets (GSE103091 and GSE76124), were used to obtain consistent results with previous findings, which verified the stability of the classification method and dataset in this study. The grouping criteria based on the previous results were developed and the accuracy of the cut-off values was validated. A prognosis model of TNBC patients was then constructed based on the grouping results of five hub genes and N staging as prognostic factors. The results of ROC and decision curve analyses showed that this model had high prediction accuracy and patients could benefit therefrom. Finally, GDSC database analysis proved that patients in Cluster A were more sensitive to Vinorelbine. Separate analysis of the sensitivity of patients in Cluster A to Gemcitabine and Vinorelbine showed that the patients in Cluster A exhibited higher sensitivity to Vinorelbine. We hypothesized that these five genes were related to gemcitabine resistance and they could serve as biomarkers for clinical drug decision-making after anthracene resistance and taxane resistance in patients with advanced TNBC.ConclusionThis study found five hub prognostic genes associated with macrophages, and a prognostic model was established to predict the survival of TNBC patients. Finally, these five genes were related to gemcitabine resistance in TNBC patients. creator: Peng Su creator: Ziqi Peng creator: Boyang Xu creator: Bowen Yang creator: Feng Jin uri: https://doi.org/10.7717/peerj.12383 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Su et al.