title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=942 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Self-compassion, ego-resiliency, coping with stress and the quality of life of parents of children with autism spectrum disorder link: https://peerj.com/articles/11198 last-modified: 2021-05-03 description: BackgroundThe literature shows a fairly coherent picture of the types of difficulties parents face. Adaptive both coping styles and resources, such as self-compassion and ego-resiliency, indicated as important predictors of the quality of life among parents of children with autism spectrum disorder. The aim of the study was to determine the links between self-compassion and ego-resiliency, coping with stress and quality of life among parents of children with autism spectrum disorder in a Polish sample (N = 76).MethodsA cross-sectional study was conducted. The CISS, Self-Compassion Scale-Short, Ego-Resiliency Scale, and Quality of Life Questionnaire were used.ResultsRegression analysis was carried out to address the research question. It was confirmed that both resources studied exhibited negative relations with emotion-oriented coping, while ego-resiliency was also positively correlated with task- and avoidance-oriented strategies. The hierarchical multiple regression conducted in three steps indicated that ego-resiliency (18%) and emotion-oriented (14%) were the strongest predictors of quality of life among parents of children with ASD.ConclusionsThe obtained results proved that ego-resiliency and a task-oriented coping strategy were important indicators of the quality of life of parents of children with ASD. creator: Anna Pyszkowska creator: Kamila Wrona uri: https://doi.org/10.7717/peerj.11198 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Pyszkowska and Wrona title: Lactobacillus reuteri TSR332 and Lactobacillus fermentum TSF331 stabilize serum uric acid levels and prevent hyperuricemia in rats link: https://peerj.com/articles/11209 last-modified: 2021-05-03 description: BackgroundUric acid (UA) is the end product of purine metabolism in the liver and is excreted by the kidneys. When purine metabolism is impaired, the serum UA level will be elevated (hyperuricemia) and eventually lead to gout. During evolution, humans and some primates have lost the gene encoding uricase, which is vital in UA metabolism. With the advances of human society, the prevalence of hyperuricemia has dramatically increased because of the refined food culture. Hyperuricemia can be controlled by drugs, such as allopurinol and probenecid. However, these drugs have no preventive effect and are associated with unpleasant side effects. An increasing number of probiotic strains, which are able to regulate host metabolism and prevent chronic diseases without harmful side effects, have been characterized. The identification of probiotic strains, which are able to exert beneficial effects on UA metabolism, will provide an alternative healthcare strategy for patients with hyperuricemia, especially for those who are allergic to anti-hyperuricemia drugs.MethodsTo elicit hyperuricemia, rats in the symptom control group (HP) were injected with potassium oxonate and fed a high-purine diet. Rats in the probiotic groups received the high-purine diet, oxonate injection, and supplements of probiotic strains TSR332, TSF331, or La322. Rats in the blank control group (C) received a standard diet (AIN-93G) and oxonate injection.ResultsPurine-utilizing strains of probiotics were screened using high-pressure liquid chromatography (HPLC) in vitro, and the lowering effect on serum UA levels was analyzed in hyperuricemia rats in vivo. We found that Lactobacillus reuteri strain TSR332 and Lactobacillus fermentum strain TSF331 displayed significantly strong assimilation of inosine (90%; p = 0.00003 and 59%; p = 0.00545, respectively) and guanosine (78%; p = 0.00012 and 51%; p = 0.00062, respectively) within 30 min in vitro. Further animal studies revealed that serum UA levels were significantly reduced by 60% (p = 0.00169) and 30% (p = 0.00912), respectively, in hyperuricemic rats treated with TSR332 and TSF331 for 8 days. Remarkably, TSR332 ameliorated the occurrence of hyperuricemia, and no evident side effects were observed. Overall, our study indicates that TSR332 and TSF331 are potential functional probiotic strains for controlling the development of hyperuricemia. creator: Yi-Wei Kuo creator: Shih-Hung Hsieh creator: Jui-Fen Chen creator: Cheng-Ruei Liu creator: Ching-Wei Chen creator: Yu-Fen Huang creator: Hsieh-Hsun Ho uri: https://doi.org/10.7717/peerj.11209 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Kuo et al. title: Molecular evidence for cross boundary spread of Salmonella spp. in meat sold at retail markets in the middle Mekong basin area link: https://peerj.com/articles/11255 last-modified: 2021-05-03 description: BackgroundThe surrounding areas of the middle Mekong basin, particularly along the border between Thailand and Lao People’s Democratic Republic (Lao PDR), are high-risk areas for many livestock-associated foodborne illnesses, especially salmonellosis. This study aimed to determine the prevalence and characteristics of Salmonella spp. contamination in pork, beef and chicken meats sold at retail markets in the Thailand-Laos border area surrounding the Thai-Lao Friendship Bridge I from January to May 2019. We focused on the prevalent serotypes, antimicrobial susceptibility profiles and the multilocus sequence type (MLST) genotypes of the collected Salmonella strains.ResultsFrom a total of 370 meat samples collected, 63% were positive for Salmonella, with the prevalence of 73%, 60% and 56% from pork, beef and chicken meat samples, respectively. Of all the positive samples, 53 serotypes were identified. Of these, Salmonella enterica serovar London accounted for the majority (27%), followed by serovars Corvallis (14%), and Rissen (6%). Resistance against tetracycline was found at the highest frequency (50%), followed by ampicillin (35%) and sulfamethoxazole-trimethoprim (28%). MLST revealed no evidence of shared genetic relatedness of Salmonella at retail sites among Thailand-Laos border zone. However, a diverse range of Salmonella genotypes were spread over the area. Besides, the persistence of the residential pathogen and sharing of the supply route within-country can be inferred.ConclusionsGiven the high levels of contamination of retail meats, regular disinfecting of all working areas and quality control checking at pre-retail stage must be applied to reduce the transmission of Salmonella and other foodborne pathogens to consumers. The findings of this study will make a significant contribution to the current understanding of Salmonella epidemiology to enhance food security in the region. creator: Dethaloun Meunsene creator: Thanaporn Eiamsam-ang creator: Prapas Patchanee creator: Ben Pascoe creator: Phacharaporn Tadee creator: Pakpoom Tadee uri: https://doi.org/10.7717/peerj.11255 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Meunsene et al. title: Prediction of DNA binding proteins using local features and long-term dependencies with primary sequences based on deep learning link: https://peerj.com/articles/11262 last-modified: 2021-05-03 description: DNA-binding proteins (DBPs) play pivotal roles in many biological functions such as alternative splicing, RNA editing, and methylation. Many traditional machine learning (ML) methods and deep learning (DL) methods have been proposed to predict DBPs. However, these methods either rely on manual feature extraction or fail to capture long-term dependencies in the DNA sequence. In this paper, we propose a method, called PDBP-Fusion, to identify DBPs based on the fusion of local features and long-term dependencies only from primary sequences. We utilize convolutional neural network (CNN) to learn local features and use bi-directional long-short term memory network (Bi-LSTM) to capture critical long-term dependencies in context. Besides, we perform feature extraction, model training, and model prediction simultaneously. The PDBP-Fusion approach can predict DBPs with 86.45% sensitivity, 79.13% specificity, 82.81% accuracy, and 0.661 MCC on the PDB14189 benchmark dataset. The MCC of our proposed methods has been increased by at least 9.1% compared to other advanced prediction models. Moreover, the PDBP-Fusion also gets superior performance and model robustness on the PDB2272 independent dataset. It demonstrates that the PDBP-Fusion can be used to predict DBPs from sequences accurately and effectively; the online server is at http://119.45.144.26:8080/PDBP-Fusion/. creator: Guobin Li creator: Xiuquan Du creator: Xinlu Li creator: Le Zou creator: Guanhong Zhang creator: Zhize Wu uri: https://doi.org/10.7717/peerj.11262 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Li et al. title: Assessing kinesthetic proprioceptive function of the upper limb: a novel dynamic movement reproduction task using a robotic arm link: https://peerj.com/articles/11301 last-modified: 2021-05-03 description: BackgroundProprioception refers to the perception of motion and position of the body or body segments in space. A wide range of proprioceptive tests exists, although tests dynamically evaluating sensorimotor integration during upper limb movement are scarce. We introduce a novel task to evaluate kinesthetic proprioceptive function during complex upper limb movements using a robotic device. We aimed to evaluate the test–retest reliability of this newly developed Dynamic Movement Reproduction (DMR) task. Furthermore, we assessed reliability of the commonly used Joint Reposition (JR) task of the elbow, evaluated the association between both tasks, and explored the influence of visual information (viewing arm movement or not) on performance during both tasks.MethodsDuring the DMR task, participants actively reproduced movement patterns while holding a handle attached to the robotic arm, with the device encoding actual position throughout movement. In the JR task, participants actively reproduced forearm positions; with the final arm position evaluated using an angle measurement tool. The difference between target movement pattern/position and reproduced movement pattern/position served as measures of accuracy. In study 1 (N = 23), pain-free participants performed both tasks at two test sessions, 24-h apart, both with and without visual information available (i.e., vision occluded using a blindfold). In study 2 (N = 64), an independent sample of pain-free participants performed the same tasks in a single session to replicate findings regarding the association between both tasks and the influence of visual information.ResultsThe DMR task accuracy showed good-to-excellent test–retest reliability, while JR task reliability was poor: measurements did not remain sufficiently stable over testing days. The DMR and JR tasks were only weakly associated. Adding visual information (i.e., watching arm movement) had different performance effects on the tasks: it increased JR accuracy but decreased DMR accuracy, though only when the DMR task started with visual information available (i.e., an order effect).DiscussionThe DMR task’s highly standardized protocol (i.e., largely automated), precise measurement and involvement of the entire upper limb kinetic chain (i.e., shoulder, elbow and wrist joints) make it a promising tool. Moreover, the poor association between the JR and DMR tasks indicates that they likely capture unique aspects of proprioceptive function. While the former mainly captures position sense, the latter appears to capture sensorimotor integration processes underlying kinesthesia, largely independent of position sense. Finally, our results show that the integration of visual and proprioceptive information is not straightforward: additional visual information of arm movement does not necessarily make active movement reproduction more accurate, on the contrary, when movement is complex, vision appears to make it worse. creator: Kristof Vandael creator: Tasha R. Stanton creator: Ann Meulders uri: https://doi.org/10.7717/peerj.11301 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Vandael et al. title: Association of sleep duration and sleep quality with hypertension in oil workers in Xinjiang link: https://peerj.com/articles/11318 last-modified: 2021-05-03 description: ObjectiveThe aim of this study is to explore sleep status and hypertension among oil workers in Xinjiang, China. It may provide new ideas and basis for the precise prevention and treatment of hypertension in occupational population.MethodsSleep status and hypertension were investigated in 3,040 workers by a multi-stage cluster sampling method in six oil field bases in Karamay City, Xinjiang. The Pittsburgh Sleep Quality Index was used to evaluate the sleep status of workers. Logistic regression was used to analyze the relationship between sleep duration and sleep quality, and hypertension. Stratified analysis was also performed.ResultsOur results show: 1. Insufficient sleep duration (OR = 1.51, 95% CI [1.19–1.90]) and poor sleep quality (OR = 1.78, 95% CI [1.33–2.38] were positively associated with hypertension. 2. Stratified analysis indicated insufficient sleep duration was associated with increased risk of hypertension in females (OR = 1.54, 95% CI [1.16–2.04]) than males (OR = 1.49, 95% CI [1.00–2.23]), and the risk of hypertension in the group <30 years old (OR = 9.03, 95% CI [2.32–35.15]) was higher than that in the group of 30–45 years old (OR = 1.59, 95% CI [1.14–2.20]). However, in the group > 45 years old, sleeping > 8 h was associated with increased risk of hypertension (OR = 3.36, 95% CI [1.42–7.91]). Oil workers doing shift work had a higher risk of hypertension (OR = 1.55, 95% CI [1.16–2.07]) to no shift work (OR = 1.48, 95% CI [1.02–2.15]). The risk of hypertension in the group with < 10 years of service (OR = 4.08, 95% CI [1.92–8.83]) was higher than that in the group with length of service of 10–20 years (OR = 2.79, 95% CI [1.59–4.86]). Poor sleep quality was associated with risk for hypertension in females (OR = 1.78, 95% CI [1.26–2.49]), those doing shift work (OR = 1.70, 95% CI [1.17–2.47]), those with length of service of > 20 years (OR = 1.64, 95% CI [1.18–2.27]). The risk of hypertension in the group 30–45 years old is higher than that in the group > 45 years old (OR30–45 years old = 1.71, 95% CI [1.10–2.66]; OR > 45 years old = 1.60, 95% CI [1.09–2.34]). ConclusionInsufficient sleep duration and poor sleep quality are the potential factors affecting hypertension in Xinjiang oil workers. creator: Fen Yang creator: Yuanyue Zhang creator: Ruiying Qiu creator: Ning Tao uri: https://doi.org/10.7717/peerj.11318 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Yang et al. title: Outcomes of critically ill end-stage kidney disease patients who underwent major surgery link: https://peerj.com/articles/11324 last-modified: 2021-05-03 description: PurposeEnd-stage kidney disease (ESKD) is a major worldwide health problem. Patients with ESKD are thought to have a significant risk for development of complications following an operation. However, the study of ESKD and its outcomes following major operations remains rare, particularly in critical illness. Therefore, this study aimed to demonstrate how the outcomes of ESKD patients were affected when they underwent a major operation and were admitted to the intensive care unit (ICU), compared with non-ESKD patients.MethodsA retrospective matched case cohort study was conducted in 122 critically ill surgical patients who underwent a major operation and were admitted to the ICU, during 2013 and 2016. Sixty-one ESKD patients who required long-term dialysis were enrolled and compared with 61 matched non-ESKD patients. The matching criteria were the same age interval (±5 years), gender, and type of operation. The ICU mortality was compared to the primary outcome of the study.ResultsPatients’ baseline characteristics between ESKD and non-ESKD were similar to a priori matching criteria and other demographics, except for pre-existing diabetes mellitus and hypertension, which were found significantly more in ESKD (p = 0.03 and 0.04, respectively). For operations, ESKD showed a higher grade of the American Society of Anesthesiologist (ASA) physical status (p < 0.001), but there were no differences for emergency surgery (p = 0.71) and duration of operation (p = 0.34). At ICU admission, the severity of illness measured by the Sequential Organ Failure Assessment (SOFA) score was greater in ESKD (8.9 ± 2.6 vs 5.6 ± 2.5; p < 0.001). However, after eliminating renal domain, SOFA non-renal score was equivalent (5.7 ± 2.2 vs 5.2 ± 2.3, p = 0.16). The ICU mortality was significantly higher in critically-ill surgical patients with ESKD than non-ESKD (23% vs 5%, p=0.007), along with hospital mortality rates (34% vs 10%, p = 0.002). The multivariable logistic regression analyses adjusted for age and SOFA non-renal score demonstrated that ESKD had a significant association with ICU and hospital mortality (adjOR = 5.59; 95%CI [1.49–20.88], p = 0.01 and adjOR = 4.55; 95%CI[1.67–12.44], p = 0.003, respectively).ConclusionPatients who underwent a major operation and needed intensive care admission with pre-existing ESKD requiring long-term dialysis were associated with greater mortality than patients without ESKD. More careful assessment before, during, and after major surgical procedures should be performed in this group of patients to improve post-operative outcomes. creator: Peerawitch Petchmak creator: Yuthapong Wongmahisorn creator: Konlawij Trongtrakul uri: https://doi.org/10.7717/peerj.11324 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Petchmak et al. title: Genetic diversity and population structure analysis in a large collection of white clover (Trifolium repens L.) germplasm worldwide link: https://peerj.com/articles/11325 last-modified: 2021-05-03 description: White clover is an important temperate legume forage with high nutrition. In the present study, 448 worldwide accessions were evaluated for the genetic variation and polymorphisms using 22 simple sequence repeat (SSR) markers. All the markers were highly informative, a total of 341 scored bands were amplified, out of which 337 (98.83%) were polymorphic. The PIC values ranged from 0.89 to 0.97 with an average of 0.95. For the AMOVA analysis, 98% of the variance was due to differences within the population and the remaining 2% was due to differences among populations. The white clover accessions were divided into different groups or subgroups based on PCoA, UPGMA, and STRUCTURE analyses. The existence of genetic differentiation between the originally natural and introduced areas according to the PCoA analysis of the global white clover accessions. There was a weak correlation between genetic relationships and geographic distribution according to UPGMA and STRUCTURE analyses. The results of the present study will provide the foundation for future breeding programs, genetic improvement, core germplasm collection establishment for white clover. creator: Feifei Wu creator: Sainan Ma creator: Jie Zhou creator: Chongyang Han creator: Ruchang Hu creator: Xinying Yang creator: Gang Nie creator: Xinquan Zhang uri: https://doi.org/10.7717/peerj.11325 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Wu et al. title: Local patterns of arbuscular mycorrhizal fungal diversity and community structure in a natural Toona ciliata var. pubescens forest in South Central China link: https://peerj.com/articles/11331 last-modified: 2021-05-03 description: Toona ciliata var. pubescens (Toona in Meliaceae) (Tc) is listed as an endangered species, and there are natural regeneration obstacles due to its long-term excessive exploitation and utilization. Arbuscular mycorrhizal fungi (AMF) can produce beneficial effects for plant growth and natural regeneration. However, the characteristics of the AMF community in natural Tc forests are poorly understood. The Illumina PE250 high-throughput sequencing method was used to study the characteristics of the AMF community in the rhizosphere soil and roots associated with three dominant tree species (Tc; Padus buergeriana, Pb; and Maesa japonica, Mj) in a natural Tc forest in Guanshan National Natural Reserve, South Central China. The results found that Glomeraceae was the most abundant AMF family in the rhizosphere soil and roots. Moreover, the relative abundance of Archaeosporaceae in rhizosphere soil was significantly larger than that in the roots; in contrast, the relative abundance of Glomeraceae in rhizosphere soil was significantly lower than that in the roots (p < 0.05). Regarding different tree species, the relative abundances of Acaulosporaceae and Geosiphonaceae were larger in Mj and Tc than in Pb. AMF operational taxonomic units (OTUs) were 1.30-, 1.43-, and 1.71-fold higher in the Tc, Pb, and Mj rhizosphere soil, respectively, than in the corresponding roots. Nevertheless, higher AMF community richness was found in the roots compared to that in the rhizosphere soil based on the Chao index. This finding indicated that AMF of a relatively high aggregation degree were in roots, and more AMF groups with relatively low abundance occurred in the rhizosphere soil, which correspondingly lowered the calculated richness index of the AMF community. A redundancy analysis showed that different soil chemical properties impacted variations in the AMF community characteristics differently. This study has great significance for the interpretation of AMF diversity survey and the application design of AMF in vegetation restoration. creator: Jianfeng Pan creator: Qiong Wang creator: Xiaoyan Guo creator: Xueru Jiang creator: Qiangqiang Cheng creator: Li Fu creator: Wei Liu creator: Lu Zhang uri: https://doi.org/10.7717/peerj.11331 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Pan et al. title: re-Searcher: GUI-based bioinformatics tool for simplified genomics data mining of VCF files link: https://peerj.com/articles/11333 last-modified: 2021-05-03 description: BackgroundHigh-throughput sequencing platforms generate a massive amount of high-dimensional genomic datasets that are available for analysis. Modern and user-friendly bioinformatics tools for analysis and interpretation of genomics data becomes essential during the analysis of sequencing data. Different standard data types and file formats have been developed to store and analyze sequence and genomics data. Variant Call Format (VCF) is the most widespread genomics file type and standard format containing genomic information and variants of sequenced samples.ResultsExisting tools for processing VCF files don’t usually have an intuitive graphical interface, but instead have just a command-line interface that may be challenging to use for the broader biomedical community interested in genomics data analysis. re-Searcher solves this problem by pre-processing VCF files by chunks to not load RAM of computer. The tool can be used as standalone user-friendly multiplatform GUI application as well as web application (https://nla-lbsb.nu.edu.kz). The software including source code as well as tested VCF files and additional information are publicly available on the GitHub repository (https://github.com/LabBandSB/re-Searcher). creator: Daniyar Karabayev creator: Askhat Molkenov creator: Kaiyrgali Yerulanuly creator: Ilyas Kabimoldayev creator: Asset Daniyarov creator: Aigul Sharip creator: Ainur Ashenova creator: Zhaxybay Zhumadilov creator: Ulykbek Kairov uri: https://doi.org/10.7717/peerj.11333 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2021 Karabayev et al.