Negative psychological aspects of working with experimental animals in scientific research
The aim of the study was to reveal the negative psychological aspects of using animals by scientists and to determine whether the emotional tensions and stress are associated with performing experiments on animals. All 150 participants of the study conduct experiments on animals in their work. Computer-assisted web interviewing, was used to collect the data. Correlation matrices for factorial analysis of main component loads and cluster analysis have been calculated as grouping methods revealed two different categories of researchers, which were mostly distinguished by acceptance and aversion to animal testing and animal welfare. The main findings demonstrated, that there is a group of respondents who feel discomfort when performing experiments on animals. Especially young people involved in animal testing, feel remorse, emotional tension and helplessness.
Mamzer et al. (2021) Negative psychological aspects of working with experimental animals in scientific research. PeerJ 9:e11035 https://doi.org/10.7717/peerj.11035
Prevalence of depression and its impact on quality of life in frontline otorhinolaryngology nurses during the COVID-19 pandemic in China
Objective Exposure to the coronavirus disease 2019 (COVID-19) was associated with high risk of mental health problems among frontline nurses. This study examined the prevalence of depressive symptoms (depression hereafter) and its impact on quality of life (QOL) in otorhinolaryngology (ENT) nurses during the COVID-19 pandemic in China. Methods An online study was conducted between March 15 and March 20, 2020. Depression and QOL were assessed using standardized instruments. Results A total of 1,757 participants were recruited. The prevalence of depression was 33.75% (95% CI: 31.59%-35.97%). Results emerging from multiple logistic regression analysis showed that direct care of COVID-19 patients (OR: 1.441, 95% CI: 1.031–2.013, P = 0.032), and current smoking (OR: 2.880, 95% CI: 1.018–8.979, P = 0.048) were significantly associated with depression. After controlling for covariates, ENT nurses with depression had a lower overall QOL compared to those without depression (F(1, 1757)= 536.80, P < 0.001). Conclusions Depression was common among ENT nurses during the COVID-19 pandemic in China. Considering the negative impact of depression on QOL and care quality, regular screening for depression should be conducted in ENT nurses and treatment should be provided.
Tian et al. (2021) Prevalence of depression and its impact on quality of life in frontline otorhinolaryngology nurses during the COVID-19 pandemic in China. PeerJ 9:e11037 https://doi.org/10.7717/peerj.11037
Epidemiology of antimicrobial resistance (AMR) on California dairies: descriptive and cluster analyses of AMR phenotype of fecal commensal bacteria isolated from adult cows
Background This 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). Methods The 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. Results The 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%). Conclusions Our 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.
Abdelfattah et al. (2021) Epidemiology of antimicrobial resistance (AMR) on California dairies: descriptive and cluster analyses of AMR phenotype of fecal commensal bacteria isolated from adult cows. PeerJ 9:e11108 https://doi.org/10.7717/peerj.11108
Evaluating alternative hypotheses to explain the downward trend in the indices of the COVID-19 pandemic death rate
Background In 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. Methodology We state six testable alternative hypotheses, analyze their testable predictions using public domain data and evaluate their relative contributions to the downward trend. Results We 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. Conclusion The 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.
Shinde et al. (2021) Evaluating alternative hypotheses to explain the downward trend in the indices of the COVID-19 pandemic death rate. PeerJ 9:e11150 https://doi.org/10.7717/peerj.11150
An integrated model of seasonal changes in stock composition and abundance with an application to Chinook salmon
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.
Freshwater et al. (2021) An integrated model of seasonal changes in stock composition and abundance with an application to Chinook salmon. PeerJ 9:e11163 https://doi.org/10.7717/peerj.11163
Rainwater chemistry observation in a karst city: variations, influence factors, sources and potential environmental effects
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.
Environmental Contamination and Remediation
Zeng et al. (2021) Rainwater chemistry observation in a karst city: variations, influence factors, sources and potential environmental effects. PeerJ 9:e11167 https://doi.org/10.7717/peerj.11167
Long non-coding RNA taurine upregulated gene 1 is downregulated in osteoporosis and influences the osteogenic differentiation of bone marrow mesenchymal stem cells
Background With 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 Methods TUG1 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. Results Decreased 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. Conclusion The 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.
Teng et al. (2021) Long non-coding RNA taurine upregulated gene 1 is downregulated in osteoporosis and influences the osteogenic differentiation of bone marrow mesenchymal stem cells. PeerJ 9:e11251 https://doi.org/10.7717/peerj.11251
Development and validation of an oxidative stress—associated prognostic risk model for melanoma
Background Oxidative 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. Methods We 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. Results The 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.
Yang et al. (2021) Development and validation of an oxidative stress—associated prognostic risk model for melanoma. PeerJ 9:e11258 https://doi.org/10.7717/peerj.11258
Prediction and analysis of novel key genes ITGAX, LAPTM5, SERPINE1 in clear cell renal cell carcinoma through bioinformatics analysis
Background Clear 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. Methods Four 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. Results A 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. Conclusion ITGAX, LAPTM5, and SERPINE1 were identified as novel key candidate genes that could be used as prognostic biomarkers and potential therapeutic targets for CCRCC.
Sui et al. (2021) Prediction and analysis of novel key genes ITGAX, LAPTM5, SERPINE1 in clear cell renal cell carcinoma through bioinformatics analysis. PeerJ 9:e11272 https://doi.org/10.7717/peerj.11272
The impact of functional excess of footwear on the foot shape of 7-year-old girls and boys
Background Properly 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. Methods The 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. Results About 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. Conclusion A 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.
Puszczalowska-Lizis et al. (2021) The impact of functional excess of footwear on the foot shape of 7-year-old girls and boys. PeerJ 9:e11277 https://doi.org/10.7717/peerj.11277