title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=219 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Differences in cardiovascular disease mortality between northern and southern China under exposure to different temperatures: a systematic review link: https://peerj.com/articles/18355 last-modified: 2024-10-30 description: BackgroundDue to differences in climate and other environmental factors, exposure to different temperatures in China has different effects on the relative risk (RR) of cardiovascular disease (CVD) mortality. It is therefore important to compare the effects of exposure to different temperatures on CVD mortality in different regions of China.MethodsTo compare these effects, we performed a meta-analysis of 21 studies identified by a search of the Web of Science and China National Knowledge Infrastructure databases from January 1, 2014 to January 1, 2024. We performed the Cochran Q test and I2 statistics test to evaluate heterogeneity and Egger’s test to evaluate publication bias.ResultsThe pooled estimated size of the relationship between exposure to different temperatures and CVD mortality was 1.60 (95% confidence interval [CI]: [1.42–1.80]) for the extreme cold, 1.17 (95% CI [1.10–1.25]) for the extreme heat, and 1.16 (95% CI [1.10–1.24]) for extremely high diurnal temperature range (DTR). The Egger’s test showed potential publication bias in studies analyzing both the extreme cold and the extreme heat.DiscussionExtreme cold, extreme heat, and extremely high DTR are associated with an increase in CVD mortality in China, with extreme cold having the most significant effect. Residents of northern regions are more susceptible to high temperatures, while residents of southern regions are more sensitive to low temperatures. creator: Guangyu Zhai creator: Ziqing Jiang creator: Wenjuan Zhou uri: https://doi.org/10.7717/peerj.18355 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhai et al. title: Identification and validation of autophagy-related genes in Hirschsprung’s disease link: https://peerj.com/articles/18376 last-modified: 2024-10-30 description: BackgroundHirschsprung’s disease (HSCR) is a congenital disorder characterized by aganglionosis in the intermuscular and submucosal nerve plexuses of the gut, leading to impaired gastrointestinal function. Although the precise cause and pathophysiology of HSCR remain elusive, increasing evidence points to a significant role of autophagy in its development, warranting further investigation into its underlying mechanisms.MethodsThis study utilized publicly available microarray expression profiling datasets, GSE96854 and GSE98502, from the Gene Expression Omnibus (GEO). The R software (version 4.2.0) was employed to identify autophagy-related genes potentially showing differential expression in HSCR. Subsequent analyses included correlation analysis, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and protein-protein interaction (PPI) network analysis using the STRING database (version 11.0) and Cytoscape software (version 3.8.2). Ultimately, HSCR samples were used to verify the mRNA levels of important genes by quantitative real-time polymerase chain reaction (qRT-PCR) in a laboratory setting.ResultsWe have discovered 20 genes that are involved in autophagy and show variable expression. Among these genes, 15 are up-regulated and five are down-regulated. The enrichment analysis using the GO and KEGG pathways revealed a notable enrichment in pathways related to the control of autophagy. Nine hub genes were found via the investigation of the PPI network constructed from STRING database and module analysis using Cytoscape. Moreover, the concordance between SIRT1 expression in the HSCR model and the bioinformatics analysis of mRNA chip findings was validated using qRT-PCR.ConclusionUtilizing bioinformatics analysis, we identified 20 potential genes associated with Hirschsprung’s disease that play a role in autophagy. Notably, the upregulation of SIRT1 may profoundly influence the progression of HSCR by regulating autophagy-related pathways, offering a novel perspective on the disease’s pathogenesis. creator: Ting Yao creator: Zenghui Hao creator: Wei Fan creator: Jinbao Han creator: Shuyu Wang creator: Zaiqun Jiang creator: Yunting Wang creator: Xiao Qian Yang creator: Zhilin Xu uri: https://doi.org/10.7717/peerj.18376 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Yao et al. title: Optimization of fermentation conditions for physcion production of Aspergillus chevalieri BYST01 by response surface methodology link: https://peerj.com/articles/18380 last-modified: 2024-10-30 description: This study aimed to optimize the culture conditions of the termite-derived fungus Aspergillus chevalieri BYST01 for the production of physcion, a characteristic component of the traditional herb rhubarb, which has been commercially approved as a botanical fungicide in China. First, potato dextrose broth was screened as the suitable basal medium for further optimization, with an initial yield of 28.0 mg/L. Then, the suitable carbon source, fermentation time, temperature, pH value, and the rotary shaker speed for physcion production were determined using the one-variable-at-a-time method. Based on the results of single factors experiments, the variables with statistically significant effects on physcion production were further confirmed using the Plackett-Burman design (PBD). Among the five variables, temperature, initial pH, and rotary shaker speed were identified as significant factors (P < 0.05) for physcion productivity in the PDB and were further analyzed by response surface methodology (RSM). Finally, we found that the maximum physcion production (82.0 mg/L) was achieved under the following optimized conditions:initial pH 6.6, rotary shaker speed of 177 rpm, temperature of 28 °C, and glucose concentration of 30 g/L in PDB medium after 11 d of fermentation. The yield of physcion under the optimized culture conditions was approximately threefold higher than that obtained using the basal culture medium. Furthermore, the optimum fermentation conditions in the 5-L bioreactor achieved a maximal physcion yield of 85.2 mg/L within 8 d of fermentation. Hence, response surface methodology proved to be a powerful tool for optimizing physcion production by A. chevalieri BYST01. This study may be helpful in promoting the application of physcion produced by A. chevalieri BYST01 to manage plant diseases. creator: Shuxiang Zhang creator: Zhou Jiang creator: Suwen An creator: Xiaolan Jiang creator: Yinglao Zhang uri: https://doi.org/10.7717/peerj.18380 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhang et al. title: The role of microbiomes in cooperative detoxification mechanisms of arsenate reduction and arsenic methylation in surface agricultural soil link: https://peerj.com/articles/18383 last-modified: 2024-10-30 description: Microbial arsenic (As) transformations play a vital role in both driving the global arsenic biogeochemical cycle and determining the mobility and toxicity of arsenic in soils. Due to the complexity of soils, variations in soil characteristics, and the presence and condition of overlying vegetation, soil microbiomes and their functional pathways vary from site to site. Consequently, key arsenic-transforming mechanisms in soil are not well characterized. This study utilized a combination of high-throughput amplicon sequencing and shotgun metagenomics to identify arsenic-transforming pathways in surface agricultural soils. The temporal and successional variations of the soil microbiome and arsenic-transforming bacteria in agricultural soils were examined during tropical monsoonal dry and wet seasons, with a six-month interval. Soil microbiomes of both dry and wet seasons were relatively consistent, particularly the relative abundance of Chloroflexi, Gemmatimonadota, and Bacteroidota. Common bacterial taxa present at high abundance, and potentially capable of arsenic transformations, were Bacillus, Streptomyces, and Microvirga. The resulting shotgun metagenome indicated that among the four key arsenic-functional genes, the arsC gene exhibited the highest relative abundance, followed by the arsM, aioA, and arrA genes, in declining sequence. Gene sequencing data based on 16S rRNA predicted only the arsC and aioA genes. Overall, this study proposed that a cooperative mechanism involving detoxification through arsenate reduction and arsenic methylation was a key arsenic transformation in surface agricultural soils with low arsenic concentration (7.60 to 10.28 mg/kg). This study significantly advances our knowledge of arsenic-transforming mechanisms interconnected with microbial communities in agricultural soil, enhancing pollution control measures, mitigating risks, and promoting sustainable soil management practices. creator: Nattanan Rueangmongkolrat creator: Pichahpuk Uthaipaisanwong creator: Kanthida Kusonmano creator: Sasipa Pruksangkul creator: Prinpida Sonthiphand uri: https://doi.org/10.7717/peerj.18383 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Rueangmongkolrat et al. title: Using vessels of opportunity for determining important habitats of bottlenose dolphins in Port Phillip Bay, south-eastern Australia link: https://peerj.com/articles/18400 last-modified: 2024-10-30 description: Understanding species’ critical habitat requirements is crucial for effective conservation and management. However, such information can be challenging to obtain, particularly for highly mobile, wide-ranging species such as cetaceans. In the absence of systematic surveys, alternative economically viable methods are needed, such as the use of data collected from platforms of opportunity, and modelling techniques to predict species distribution in un-surveyed areas. The present study used data collected by ecotourism and other vessels of opportunity to investigate important habitats of a small, poorly studied population of bottlenose dolphins in Port Phillip Bay, south-eastern Australia. Using 16 years of dolphin sighting location data, an ensemble habitat suitability model was built from which physical factors influencing dolphin distribution were identified. Results indicated that important habitats were those areas close to shipping channels and coastlines with these factors primarily influencing the variation in the likelihood of dolphin presence. The relatively good performance of the ensemble model suggests that simple presence-background data may be sufficient for predicting the species distribution where sighting data are limited. However, additional data from the center of Port Phillip Bay is required to further support this contention. Important habitat features identified in the study are likely to relate to favorable foraging conditions for dolphins as they are known to provide feeding, breeding, and spawning habitat for a diverse range of fish and cephalopod prey species. The results of the present study highlight the importance of affordable community-based data collection, such as ecotourism vessels, for obtaining information critical for effective management. creator: Maddison J. Ledwidge creator: Jacquomo Monk creator: Suzanne J. Mason creator: John P. Y. Arnould uri: https://doi.org/10.7717/peerj.18400 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ledwidge et al. title: Kinematic differences between female national and provincial athletes in the tennis serve link: https://peerj.com/articles/18410 last-modified: 2024-10-30 description: BackgroundTennis, the second-largest ball game in the world, has a particularly wide audience. To date, little research has been conducted on the biomechanics of female serves.PurposeThe purpose of this study was to capture the key moments by using 1,000 frames/s high-speed video analysis, to analyze the kinematics of the serving techniques of national athletes and provincial athletes, to determine the differences between the two levels of athletes, and to provide theoretical references for the improvement of scientific training level.MethodsTen female athletes were selected as participants for this study, five of whom are national athletes, and the other are provincial athletes. Three-dimensional filming techniques were employed to capture videos of the first and second serve techniques. Simi Motion was applied to obtain the 3D kinematic data. Statistical analyses were performed using IBM SPSS Statistics 27.0, and Mann–Whitney U tests were conducted to determine differences between groups.ResultsSignificant differences in kinematics were found between national and provincial athletes. At the moment of the left knee’s minimum flexion (T2), in the first serve, national athletes had a smaller shoulder-hip vertical plane angle (−18.281 ± 6.142° vs. −25.631 ± 3.497°; p = 0.047) and a larger hip vertical plane rotation angle (−9.378 ± 4.263° vs. −0.470 ± 4.724°; p = 0.047). In the second serve, national athletes had a smaller hip horizontal plane rotation angle (−1.720 ± 4.683° vs. 24.146 ± 24.014°; p = 0.047) but a larger hip vertical plane rotation angle (−11.553 ± 1.949° vs. −0.422 ± 4.958°; p = 0.009). At the moment of impact (T4), in the second serve, national athletes’ batting position (0.296 ± 0.088 m vs. 0.446 ± 0.094 m; p = 0.047) was further back. Additionally, in the second serve, national athletes consistently had their body center of gravity further back at T2 (−0.106 ± 0.052 m vs. −0.018 ± 0.048 m; p = 0.028), T3 (0.002 ± 0.038 m vs. 0.132 ± 0.039 m; p = 0.009), and T4 (0.073 ± 0.050 m vs. 0.217 ± 0.034 m; p = 0.009).ConclusionsThe results of this study indicated several significant kinematic differences between national and provincial athletes, these variations were noted in the shoulder, hip, and body center of gravity. In summary, for the overall first and second serves, it is recommended that national athletes increase the horizontal plane angle of the shoulders and hips at T2, whereas provincial athletes decrease the horizontal plane angle of the shoulder–hip. In addition, provincial athletes need to increase the vertical plane angle of the hip joint, so that the top of the hip can be increased more, and provincial athletes need to be careful not to have the center of gravity too far in front of the body at T2, T3, and T4, so that it can hit the ball at a higher position to increase the swing speed. creator: Yan Chen creator: Tianyang Wang creator: Yuyan Zhao creator: Genghao Zhan creator: Yinchao Tang creator: Zefeng Wang uri: https://doi.org/10.7717/peerj.18410 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Chen et al. title: Development and internal and external validation of a nomogram model for predicting the risk of chronic kidney disease progression in IgA nephropathy patients link: https://peerj.com/articles/18416 last-modified: 2024-10-30 description: BackgroundIgA nephropathy (IgAN) is the most common primary glomerular disease in chronic kidney disease (CKD), exhibiting significant heterogeneity in both clinical and pathological presentations. We aimed to explore the risk factors influencing short-term prognosis (≥90 days) and to construct a nomogram model for evaluating the risk of CKD progression in IgAN patients.MethodsClinical and pathological data of patients diagnosed with IgAN through biopsy at two centers were retrospectively collected. Logistic regression was employed to analyze the training cohort dataset and identify the independent predictors to construct a nomogram model based on the final variables. The predictive model was validated both internally and externally, with its performance assessed using the area under the curve (AUC), calibration curves, and decision curve analysis.ResultsOut of the patients in the modeling group, 129 individuals (41.6%) did not achieve remission following 3 months of treatment, indicating a high risk of CKD progression. A multivariate logistic regression analysis demonstrated that body mass index, urinary protein excretion, and tubular atrophy/interstitial fibrosis were identified as independent predictors for risk stratification. A nomogram model was formulated utilizing the final variables. The AUCs for the training set, internal validation set, and external validation set were 0.746 (95% confidence intervals (CI) [0.691–0.8]), 0.764 (95% CI [0.68–0.85]), and 0.749 (95% CI [0.65–0.85]), respectively. The validation of the subgroup analysis also demonstrated a satisfactory AUC.ConclusionThis study developed and validated a practical nomogram that can individually predict short-term treatment outcomes (≥90 days) and the risk of CKD progression in IgAN patients. It provides reliable guidance for timely and personalized intervention and treatment strategies. creator: Ying Zhang creator: Zhixin Wang creator: Wenwu Tang creator: Xinzhu Yuan creator: Xisheng Xie uri: https://doi.org/10.7717/peerj.18416 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhang et al. title: Identification of common and specific cold resistance pathways from cold tolerant and non-cold tolerant mango varieties link: https://peerj.com/articles/18431 last-modified: 2024-10-30 description: Mango has frequently encountered severe climate and environmental challenges such as low temperatures, seriously affecting the sustainable development of the industry. In the study, physiological measurements showed that the activities of superoxide dismutase (SOD) and peroxidase (POD) were found to be higher in Jinhuang (JH) mango plants than those of Tainong (TN) mango plants under cold stress, indicating cold tolerant (JH) and non-cold tolerant (TN) mango varieties were firstly determined. Subsequently, transcriptomics showed 8,337 and 7,996 differentially expressed genes (DEGs) were respectively identified in JH and TN mango varieties treated at 4 °C for 36 h, while more DEGs (10,683 and 10,723) were screened when treated at 4 °C for 72 h. Quantitative real-time PCR (qRT-PCR) of the selected DEGs confirmed their transcriptional levels displayed agreement to the transcriptome data. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed two primary cold resistant regulation pathways, photosynthesis-antenna proteins pathway and photosynthesis pathway, were both significant annotated in the two mango varieties, indicating share the common regulation mechanism response to cold stress. However, five specific cold resistant pathways, such as amino acid and carbohydrate metabolisms, were identified in JH mango variety with cold stress for longer duration, indicating the specific regulation pathways in the cold tolerant mango varieties. Furthermore, 43 ethylene-responsive transcription factors (ERFs) were significantly annotated in JH mango after cold-treated for 72 h comparing with the control group, and three of them ERF109-1, ERF017-1 and ERF017-2 were highly expressed, which may play important regulatory roles in plant cold resistance. These results provided insights into the primary and specific molecular mechanisms of different mango varieties resistance to chill. creator: Jian-hua Wang creator: Xiaoyan Feng creator: Muhammad Aleem Ashraf creator: Yufeng Li creator: Yu Kong creator: Qiuliang Cai creator: Shuli Xian creator: Huixiang Yin creator: Nai-tong Yu uri: https://doi.org/10.7717/peerj.18431 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Wang et al. title: Reliability and validity of My Jump 2® app to measure the vertical jump in visually impaired five-a-side soccer athletes link: https://peerj.com/articles/18170 last-modified: 2024-10-29 description: BackgroundAlthough My Jump 2® consistently presented excellent values of reliability and validity when compared to force platforms (FPs) and contact mats, to date no scientific investigation assessed the validity and reliability of My Jump 2® to measure jump height in visually impaired five-a-side soccer athletes. Thus, the study aimed at analyzing the validity and reliability of the My Jump 2® to measure the vertical jump of five-a-side soccer athletes.MethodsTwelve visually impaired five-a-side soccer athletes, volunteered for this study. Each player performed five countermovement jumps (CMJs) and squat jumps (SJs) on a contact platform (CP) while they were simultaneously recorded using MyJump 2®.ResultsThere was almost perfect agreement between the My Jump 2® and the contact platform measurements of CMJ (intraclass correlation coefficient = 0.99; p < 0.001) and SJ (intraclass correlation coefficient = 0.99; p < 0.001), heights for athletes during the first and second measurement days. Bland-Altman analysis showed a bias of 0.25 ± 0.5 cm; maximum SD = 1.3; minimum SD = −0.88 for CMJ, while that Bland-Altman analysis showed bias 0.18 ± 0.5 cm; maximum SD = 1.3; minimum SD = −0.96, for SJ.ConclusionWe can conclude that the My Jump 2® is a valid and reliable method to measure CMJ and SJ in visually impaired five-a-side soccer athletes. creator: Julio Cesar Silva creator: Kalinne Fernandes Silva creator: Vitor Bruno Torres creator: Maria Socorro Cirilo-Sousa creator: Alexandre Igor Araripe Medeiros creator: Jacques Eanes Esmeraldo Melo creator: Gilmário Ricarte Batista uri: https://doi.org/10.7717/peerj.18170 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Silva et al. title: Risk factors for recovery from oculomotor nerve palsy after aneurysm surgery: a meta-analysis link: https://peerj.com/articles/18207 last-modified: 2024-10-29 description: BackgroundRisk factors for recovery from oculomotor nerve palsy (ONP) after aneurysm surgery explored by meta-analysis.MethodsThe PubMed, Embase, web of science, Cochrane library, China Knowledge, Wan fang, and VIP databases were searched for case-control or cohort studies on risk factors of oculomotor nerve palsy recovery after aneurysm surgery, with a cut-off date of 14 February 2024, and data were analyzed using Stata 15.ResultA total of 12 articles involving 866 individuals were included, meta-analysis results suggesting that gender (OR = 0.75, 95% CI [0.51–1.10]), age (OR = 1.00, 95% CI [0.93–1.07]), aneurysm size (OR = 0.85, 95% CI [−0.71 to 1.01]), treatment time (OR = 1.01, 95% CI [0.91–1.13]) is not a risk factor for recovery of motor nerve palsy after aneurysm surgery. Preoperative complete ONP (OR = 2.27, 95% CI [1.07–4.81]), surgery (OR = 9.88, 95% CI [2.53–38.57]), subarachnoid hemorrhage (OR = 1.29, 95% CI [1.06–1.56]) is a risk factor for recovery of motor nerve palsy after aneurysm surgery.ConclusionBased on the results of the studies we included, we found that complete ONP before surgery led to poorer recovery, but patients with post-operative and subarachnoid hemorrhage had better recovery. creator: Yuan Li creator: Ming Zhao creator: Xuemei Li creator: Tiejuan Liu creator: Lin Zheng creator: Deyu Hu creator: Tongyan Liu creator: Lingyun Zhou uri: https://doi.org/10.7717/peerj.18207 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li et al.