title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=930 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Epidemiology of antimicrobial resistance (AMR) on California dairies: descriptive and cluster analyses of AMR phenotype of fecal commensal bacteria isolated from adult cows link: https://peerj.com/articles/11108 last-modified: 2021-04-20 description: BackgroundThis study describes the occurrence of antimicrobial resistance (AMR) in commensal Escherichia coli and Enterococcus/Streptococcus spp. (ES) isolated from fecal samples of dairy cows and assesses the variation of AMR profiles across regions and seasons following the implementation of the Food and Agricultural Code (FAC) Sections 14400–14408 (formerly known as Senate Bill, SB 27) in California (CA).MethodsThe study was conducted on ten dairies distributed across CA’s three milk sheds: Northern California (NCA), Northern San Joaquin Valley (NSJV), and the Greater Southern California (GSCA). On each study dairy, individual fecal samples were collected from two cohorts of lactating dairy cows during the fall/winter 2018 and spring/summer 2019 seasons. Each cohort comprised of 12 cows per dairy. The fecal samples were collected at enrollment before calving (close-up stage) and then monthly thereafter for four consecutive time points up to 120 days in milk. A total of 2,171 E. coli and 2,158 ES isolates were tested for antimicrobial susceptibility using the broth microdilution method against a select panel of antimicrobials.ResultsThe E. coli isolates showed high resistance to florfenicol (83.31% ± 0.80) and sulphadimethoxine (32.45%), while resistance to ampicillin (1.10% ± 0.21), ceftiofur (1.93% ± 0.29), danofloxacin (4.01% ± 0.42), enrofloxacin (3.31% ± 0.38), gentamicin (0.32% ± 0.12) and neomycin (1.61% ± 0.27) had low resistance proportions. The ES isolates were highly resistant to tildipirosin (50.18% ± 1.10), tilmicosin (48% ± 1.10), tiamulin (42%) and florfenicol (46% ± 1.10), but were minimally resistant to ampicillin (0.23%) and penicillin (0.20%). Multidrug resistance (MDR) (resistance to at least 1 drug in ≥3 antimicrobial classes) was observed in 14.14% of E. coli isolates and 39% of ES isolates. Escherichia coli isolates recovered during winter showed higher MDR prevalence compared to summer isolates (20.33% vs. 8.04%). A higher prevalence of MDR was observed in NSJV (17.29%) and GSCA (15.34%) compared with NCA (10.10%).ConclusionsOur findings showed high rates of AMR to several drugs that are not labeled for use in lactating dairy cattle 20 months of age or older. Conversely, very low resistance was observed for drugs labeled for use in adult dairy cows, such as cephalosporins and penicillin. Overall, our findings identified important differences in AMR by antimicrobial class, region and season. creator: Essam M. Abdelfattah creator: Pius S. Ekong creator: Emmanuel Okello creator: Tapakorn Chamchoy creator: Betsy M. Karle creator: Randi A. Black creator: David Sheedy creator: Wagdy R. ElAshmawy creator: Deniece R. Williams creator: Daniela Califano creator: Luis Fernando Durán Tovar creator: Jonathan Ongom creator: Terry W. Lehenbauer creator: Barbara A. Byrne creator: Sharif S. Aly uri: https://doi.org/10.7717/peerj.11108 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Abdelfattah et al. title: Evaluating alternative hypotheses to explain the downward trend in the indices of the COVID-19 pandemic death rate link: https://peerj.com/articles/11150 last-modified: 2021-04-20 description: BackgroundIn the ongoing Covid-19 pandemic, in the global data on the case fatality ratio (CFR) and other indices reflecting death rate, there is a consistent downward trend from mid-April to mid-November. The downward trend can be an illusion caused by biases and limitations of data or it could faithfully reflect a declining death rate. A variety of explanations for this trend are possible, but a systematic analysis of the testable predictions of the alternative hypotheses has not yet been attempted.MethodologyWe state six testable alternative hypotheses, analyze their testable predictions using public domain data and evaluate their relative contributions to the downward trend.ResultsWe show that a decline in the death rate is real; changing age structure of the infected population and evolution of the virus towards reduced virulence are the most supported hypotheses and together contribute to major part of the trend. The testable predictions from other explanations including altered testing efficiency, time lag, improved treatment protocols and herd immunity are not consistently supported, or do not appear to make a major contribution to this trend although they may influence some other patterns of the epidemic.ConclusionThe fatality of the infection showed a robust declining time trend between mid April to mid November. Changing age class of the infected and decreasing virulence of the pathogen were found to be the strongest contributors to the trend. creator: Sonali Shinde creator: Pratima Ranade creator: Milind Watve uri: https://doi.org/10.7717/peerj.11150 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Shinde et al. title: An integrated model of seasonal changes in stock composition and abundance with an application to Chinook salmon link: https://peerj.com/articles/11163 last-modified: 2021-04-20 description: Population-specific spatial and temporal distribution data are necessary to identify mechanisms regulating abundance and to manage anthropogenic impacts. However the distributions of highly migratory species are often difficult to resolve, particularly when multiple populations’ movements overlap. Here we present an integrated model to estimate spatially-stratified, seasonal trends in abundance and population composition, using data from extensive genetic sampling of commercial and recreational Chinook salmon (Oncorhynchus tshawytscha) fisheries in southern British Columbia. We use the model to estimate seasonal changes in population-specific standardized catch per unit effort (a proxy for abundance) across six marine regions, while accounting for annual variability in sampling effort and uncertain genetic stock assignment. We also share this model as an R package stockseasonr for application to other regions and species. Even at the relatively small spatial scales considered here, we found that patterns in seasonal abundance differed among regions and stocks. While certain locations were clearly migratory corridors, regions within the Salish Sea exhibited diverse, and often weak, seasonal patterns in abundance, emphasizing that they are important, year-round foraging habitats. Furthermore, we found evidence that stocks with similar freshwater life histories and adult run timing, as well as relatively proximate spawning locations, exhibited divergent distributions. Our findings highlight subtle, but important differences in how adult Chinook salmon use marine habitats. Down-scaled model outputs could be used to inform ecosystem-based management efforts by resolving the degree to which salmon overlap with other species of concern, as well as specific fisheries. More broadly, variation in stock-specific abundance among regions indicates efforts to identify mechanisms driving changes in size-at-maturity and natural mortality should account for distinct marine distributions. creator: Cameron Freshwater creator: Sean C. Anderson creator: Terry D. Beacham creator: Wilf Luedke creator: Catarina Wor creator: Jackie King uri: https://doi.org/10.7717/peerj.11163 license: http://www.nationalarchives.gov.uk/doc/open-government-licence/ rights: title: Rainwater chemistry observation in a karst city: variations, influence factors, sources and potential environmental effects link: https://peerj.com/articles/11167 last-modified: 2021-04-20 description: The rainwater chemistry and related air contaminants are used to investigate the rainwater ions sources, variations, and influence factors from 2012 to 2014 in Guiyang city (the typical karst urban area of Southwest China). According to temporal rainwater ion concentrations, the obvious variations were presented in the study period, such as Ca2+ (125∼6,652 μeq L−1) and SO42− (11∼4,127 μeq L−1). Consequently, Ca2+, Mg2+, SO42− and Cl− are considered as the leading ions. Three critical influencing factors of rainwater ions concentrations, including sources variations, rainfall amount and long-distance migration (rainfall amount > 100 mm) are identified. Based on the typical ionic ratios, source identification suggested that anthropogenic inputs mainly contributed to F−, NO3− and SO42−, while the dusts (crustal sources) are the primary sources of Mg2+, Ca2+ and K+. Cl− Enrichment in long-distance transport is the main contributor of Cl−. According to the observation of high level of total wet acid deposition, the more detailed spatio-temporal monitoring of rainfall-related acid deposition (particularly sulfur deposition) is required to understand its potential environmental effects in the aquatic ecosystem of the earth surface. creator: Jie Zeng creator: Guilin Han uri: https://doi.org/10.7717/peerj.11167 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Zeng and Han title: Long non-coding RNA taurine upregulated gene 1 is downregulated in osteoporosis and influences the osteogenic differentiation of bone marrow mesenchymal stem cells link: https://peerj.com/articles/11251 last-modified: 2021-04-20 description: BackgroundWith aging, an imbalance in bone remodeling leading to increased bone resorption and decreased bone formation is thought to contribute to osteoporosis. Osteoblastic differentiation of bone marrow mesenchymal stem cells (BMMSCs) plays a vital role in the pathogenesis of osteoporosis. However, the detailed molecular mechanisms of osteoporosis remain incompletely understood. Given that long non-coding RNA taurine upregulated gene 1 (lnc TUG1) plays a critical role in the osteogenic differentiation, and microRNA-23b (miR-23b) as a putative sponge for lnc TUG1 has upregulated expression in osteoporosis. Therefore, this study investigated the roles of TUG1/miR-23b in osteoporotic pathology.Material and MethodsTUG1 and miR-23b expression in the plasma of osteoporotic patients were evaluated by quantitative real-time PCR (qRT-PCR). The osteogenic differentiation in human BMMSCs was evaluated by qRT-PCR, western blot, Alizarin red staining after knockdown of TUG1 by small interfering RNA (siRNA) treatment.ResultsDecreased expression of TUG1 and increased expression of miR-23b evident in the plasma of patients with osteoporosis than in that of age- and sex-matched healthy controls. Additionally, increased miR-23b expression inhibited runt-related transcription factor 2 (RUNX2), osteocalcin, and osteopontin expression and reduced calcified nodule formation based on the results of qRT-PCR, western blot, and Alizarin Red S staining.ConclusionThe study for the first time reported that silence of lncRNA TUG1 significantly suppressed the osteogenic differentiation of BMMSCs possibly by targeting the miR-23b/RUNX2 signaling pathway. This mechanism of TUG1/miR-23b/RUNX2 signaling within the osteogenic differentiation of BMMSCs might provide new insight for the development of lncRNA-directed diagnostic and therapeutic strategies for osteoporosis. creator: Zhaowei Teng creator: Yun Zhu creator: Qinggang Hao creator: Xiaochao Yu creator: Yirong Teng creator: Qiaoning Yue creator: Xiguang Zhang creator: Sheng Lu uri: https://doi.org/10.7717/peerj.11251 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2021 Teng et al. title: Development and validation of an oxidative stress—associated prognostic risk model for melanoma link: https://peerj.com/articles/11258 last-modified: 2021-04-20 description: BackgroundOxidative stress (OS) is key to various diseases and is implicated in cancer progression and oncogenesis. However, the potential diagnostic value of OS-related genes in skin cutaneous melanoma (SKCM) remains unclear.MethodsWe used data of RNA sequencing from 471 tumor tissues and one healthy tissue acquired from The Cancer Genome Atlas (TCGA)-SKCM cohort. The Genome Tissue Expression database was used to acquire transcriptome data from 812 healthy samples. OS-related genes that were differentially expressed between SKCM and healthy samples were investigated and 16 prognosis-associated OS genes were identified. The prognostic risk model was built using univariate and Cox multivariate regressions. The prognostic value of the hub genes was validated in the GSE65904 cohort, which included 214 SKCM patients.ResultsThe overall survival rate of SKCM patients in the high-risk group was decreased compared to the low-risk group. In both TCGA and GSE65904 cohorts, the ROC curves suggested that our prognostic risk model was more accurate than other clinicopathological characteristics to diagnose SKCM. Moreover, risk score and nomograms associated with the expression of hub genes were developed. These presented reiterated our prognostic risk model. Altogether, this study provides novel insights with regards to the pathogenesis of SKCM. The 16 hub genes identified may help in SKCM prognosis and individualized clinical treatment. creator: Yu Yang creator: Xuan Long creator: Kun Li creator: Guiyun Li creator: Xiaohong Yu creator: Ping Wen creator: Jun Luo creator: Xiaobin Tian creator: Jinmin Zhao uri: https://doi.org/10.7717/peerj.11258 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Yang et al. title: Prediction and analysis of novel key genes ITGAX, LAPTM5, SERPINE1 in clear cell renal cell carcinoma through bioinformatics analysis link: https://peerj.com/articles/11272 last-modified: 2021-04-20 description: BackgroundClear Cell Renal Cell Carcinoma (CCRCC) is the most aggressive subtype of Renal Cell Carcinoma (RCC) with high metastasis and recurrence rates. This study aims to find new potential key genes of CCRCC.MethodsFour gene expression profiles (GSE12606, GSE53000, GSE68417, and GSE66272) were downloaded from the Gene Expression Omnibus (GEO) database. The TCGA KIRC data was downloaded from The Cancer Genome Atlas (TCGA). Using GEO2R, the differentially expressed genes (DEG) in CCRCC tissues and normal samples were analyzed. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed in DAVID database. A protein-protein interaction (PPI) network was constructed and the hub gene was predicted by STRING and Cytoscape. GEPIA and Kaplan-Meier plotter databases were used for further screening of Key genes. Expression verification and survival analysis of key genes were performed using TCGA database, GEPIA database, and Kaplan-Meier plotter. Receiver operating characteristic (ROC) curve was used to analyze the diagnostic value of key genes in CCRCC, which is plotted by R software based on TCGA database. UALCAN database was used to analyze the relationship between key genes and clinical pathology in CCRCC and the methylation level of the promoter of key genes in CCRCC.ResultsA total of 289 up-regulated and 449 down-regulated genes were identified based on GSE12606, GSE53000, GSE68417, and GSE66272 profiles in CCRCC. The upregulated DEGs were mainly enriched with protein binding and PI3K-Akt signaling pathway, whereas down-regulated genes were enriched with the integral component of the membrane and metabolic pathways. Next, the top 35 genes were screened out from the PPI network according to Degree, and three new key genes ITGAX, LAPTM5 and SERPINE1 were further screened out through survival and prognosis analysis. Further results showed that the ITGAX, LAPTM5, and SERPINE1 levels in CCRCC tumor tissues were significantly higher than those in normal tissues and were associated with poor prognosis. ROC curve shows that ITGAX, LAPTM5, and SERPINE1 have good diagnostic value with good specificity and sensitivity. The promoter methylation levels of ITGAX, LAPTM5 and SERPINE1 in CCRCC tumor tissues were significantly lower than those in normal tissues. We also found that key genes were associated with clinical pathology in CCRCC.ConclusionITGAX, LAPTM5, and SERPINE1 were identified as novel key candidate genes that could be used as prognostic biomarkers and potential therapeutic targets for CCRCC. creator: Yingli Sui creator: Kun Lu creator: Lin Fu uri: https://doi.org/10.7717/peerj.11272 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Sui et al. title: The impact of functional excess of footwear on the foot shape of 7-year-old girls and boys link: https://peerj.com/articles/11277 last-modified: 2021-04-20 description: BackgroundProperly fitted shoes can support the development of growing feet and prevent problems and pathologies, not only in childhood, but also in adulthood. This points to the need to conduct research on the impact of shoe fitting on the structure of the foot in order to raise awareness and importance of this problem, to enable proper decisions regarding the purchase and use of shoes. The aim of this study was to analyze indoor footwear fit and its impact on foot structure in 7-year-old schoolchildren.MethodsThe CQ-ST podoscope and the Clevermess device were used for measurements. The analysis was carried out using the Mann Whitney U test, Wilcoxon signed-rank test, Chi-square test, regression analysis.ResultsAbout 40% of girls and boys had shoes that were incorrectly fitted in length, while as many as 74% of girls and 66% of boys wore shoes that were incorrectly fitted in width. Regression analysis demonstrated a statistically significant influence of the footwear length on longitudinal arch of the right and left foot and the transverse arch of the right foot. In boys, the length of the shoes shows associations with the right and left hallux valgus angle.ConclusionA significant percentage of the studied 7-year-olds, regardless of gender, wears inappropriately fitted shoes. In both sexes, the length of the footwear influenced the longitudinal arch of the right and left foot and the transverse arch of the right foot. Due to the deformity of the first metatarsophalangeal joint, the boys with hallux valgus require footwear which is wider and therefore their shoes need to be bigger in size. creator: Ewa Puszczalowska-Lizis creator: Aleksandra Lukasiewicz creator: Sabina Lizis creator: Jaroslaw Omorczyk uri: https://doi.org/10.7717/peerj.11277 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Puszczalowska-Lizis et al. title: Anti-atherosclerotic vaccination against Porphyromonas gingivalis as a potential comparator of statin in mice link: https://peerj.com/articles/11293 last-modified: 2021-04-20 description: BackgroundPorphyromonas gingivalis (Pg) is an oral anaerobe which damages teeth and periodontal tissues. Its body infection is known to cause chronic inflammation, thereby inducing an early stage of atherosclerosis through humoral immune actions. Hence, vaccination by immunizing the proteins of P. gingivalis (Pg) post sonication with heating may prevent atherosclerosis. This study aimed to compare the effect of its vaccination with statin, which effectively prevents atherosclerosis by lowering lipids.MethodsThe vaccine was produced by sonicating P. gingivalis through heating, and a total of 32 male APOE-/-mice (8-week old) were subjected Western diet for 8 weeks, in order to induce atherosclerosis in a physiological manner. Then, the mice were grouped to undergo four treatment conditions (i.e., no treatment, pitavastatin, vaccine, or pitavastatin with vaccine). Vaccination was conducted through nasal immunization and confirmed by a Pg-specific humoral immune reaction. Then, half of the mice in each group were orally injected with P. gingivalis for the next 5 weeks while the other half remained uninfected, generating a total of eight groups (n = 4/group). The mice were sacrificed at 3 weeks after the last injection. After harvesting the aorta, Oil Red O staining of en face was conducted with imaging and image analysis, and plaque formation was quantitatively determined.ResultsCompared to no treatment, the vaccination through nasal immunization significantly reduced the atherosclerotic plaque sizes in APOE -/- mice under Western diet to the comparable level of statin group. When both vaccine and statin were used, no clear synergistic effect was observed as opposed to expectation.ConclusionsThis study revealed that nasal immunization of heat shock P. gingivalis has a significant impact on the prevention of arteriosclerosis and acts as a potential comparator of statin. creator: Hyun-Su Ha creator: Tae Young Kim creator: Soo Jung Han creator: Hak-Joon Sung creator: Kyoung Yul Seo creator: Jong-Won Ha uri: https://doi.org/10.7717/peerj.11293 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Ha et al. title: Characteristics of craniofacial morphology and factors affecting them in patients with isolated cleft palate link: https://peerj.com/articles/11297 last-modified: 2021-04-20 description: BackgroundMyriad maxillo-mandibular occlusal relationships are observed in patients with isolated cleft palate (ICP), unlike in patients with other cleft types, such as cleft lip and palate.ObjectivesThis study aimed to categorise the characteristics of craniofacial morphology in patients with ICP, and investigate the clinical factors affecting these categorised morphological characteristics.MethodsThirty-six girls with ICP (age (mean ± SD): 5.36 ± 0.36 years) underwent cephalometric measurement. Their craniofacial morphology was categorised using cluster analysis. Profilograms were created and superimposed onto the standard Japanese profilograms to visualise the morphological characteristics of each group (cluster). The mean values and variations in the linear and angular measurements of each group were compared with the Japanese standards and statistically analysed using Dunnett’s test after the analysis of variance. Fisher’s exact test was used to analyse the differences between the cleft types (cleft in the hard and/or soft palate) and skills of the operating surgeons in the groups.ResultsCluster analysis of craniofacial morphologies in patients with ICP resulted in the formation of three categories: the first cluster exhibited a relatively harmonious anteroposterior relationship between the maxilla and the mandible (22.2%); the second cluster exhibited crossbite owing to a significantly smaller maxilla (33.3%); and the third cluster exhibited a smaller mandible with posterior rotation showing skeletal class II malocclusion (44.4%). Differences in cleft types and surgeons were not associated with the distribution of patients in each cluster.ConclusionsPatients with ICP exhibited characteristic morphological patterns, such as bimaxillary retrusion or severe mandibular retrusion, besides the anterior crossbite frequently found in patients with cleft lip and palate . Understanding the typical morphological characteristics could enable better diagnostic categorisation of patients with ICP, which may eventually improve orthodontic treatment planning. creator: Kyoko Tsuji creator: Naoto Haruyama creator: Shunsuke Nomura creator: Naohisa Murata creator: Keigo Yoshizaki creator: Takeshi Mitsuyasu creator: Hiroyuki Nakano creator: Seiji Nakamura creator: Yoshihide Mori creator: Ichiro Takahashi uri: https://doi.org/10.7717/peerj.11297 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Tsuji et al.