title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=128 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Activation of autophagy is required for clearance of mitochondrial ROS in patients with asthenozoospermia link: https://peerj.com/articles/18827 last-modified: 2025-02-13 description: Autophagy is regarded as an essential process for maintaining cell homeostasis. However, its role in the regulation of sperm motility is still less understood. In this study, we found that mitochondrial oxidative species (mROS) levels were elevated, but ATP levels and mitochondrial membrane potential (MMP) levels were reduced in human sperm with low motility (also called asthenozoospermia, AS) as compared to normal human sperm (normal sperm, NS). Immunocytochemistry staining showed that LC3 was mainly located in the neck of sperm. Western blot analysis showed that AS patients had elevated levels of the autophagy-related proteins LC3, Atg5, Atg7, and Beclin1. Flow cytometry showed that 3-MA treatment reduced sperm motility and MMP, but increased mROS. The results indicate that autophagy is essential for the clearance of mROS in sperm and the maintenance of mitochondrial function. creator: Xiaona Wang creator: Shiyuan Huang creator: Yu Zhao creator: Hua Chen creator: Linzhi Yan creator: Hongshan Ge creator: Xinmei Wu uri: https://doi.org/10.7717/peerj.18827 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Wang et al. title: pandasPGS: a Python package for easy retrieval of Polygenic Score Catalog data link: https://peerj.com/articles/18985 last-modified: 2025-02-12 description: BackgroundThe Polygenic Score (PGS) Catalog is a public database dedicated to storing polygenic risk scores. To date, the database has included 5,022 polygenic risk scores associated with 656 different traits. Although the PGS Catalog offers an official resource representational state transfer (REST) application programming interface (API), there is no ready-made data client tailored for any specific programming language. Researchers are thus required to invest time in becoming familiar with the structure of the REST API and to implement a corresponding client in their programming language of choice to integrate PGS data into their analytical workflows.MethodsIn this work we introduce pandasPGS, a Python package that provides programmatic access to PGS Catalog data. After being called by the researcher, pandasPGS will automatically select the appropriate uniform resource locator (URL) and request the data based on the name and parameters of the called function, and merge the obtained pagination data. In addition, pandasPGS also provides further data pre-processing functions. According to the structure of the obtained data, it can convert the data into several hierarchical pandas.DataFrame objects, which is convenient for further analysis by researchers.ResultsThis tool allows researchers to easily analyze PGS Catalog data using Python. It alleviates the time cost for researchers to learn the REST APIs of PGS Catalog. The source codes can be found in https://github.com/tianzelab/pandaspgs, and the API documentations can be found in https://tianzelab.github.io/pandaspgs/. creator: Zheyu Zhang creator: Jintong Zhou creator: Tianze Cao creator: Yuexia Huang creator: Chu Huang creator: Yu Xia uri: https://doi.org/10.7717/peerj.18985 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zhang et al. title: PGSXplorer: an integrated nextflow pipeline for comprehensive quality control and polygenic score model development link: https://peerj.com/articles/18973 last-modified: 2025-02-12 description: The rapid development of next-generation sequencing technologies and genomic data sharing initiatives during the post-Human Genome Project-era has catalyzed major advances in individualized medicine research. Genome-wide association studies (GWAS) have become a cornerstone of efforts towards understanding the genetic basis of complex diseases, leading to the development of polygenic scores (PGS). Despite their immense potential, the scarcity of standardized PGS development pipelines limits widespread adoption of PGS. Herein, we introduce PGSXplorer, a comprehensive Nextflow DSL2 pipeline that enables quality control of genomic data and automates the phasing, imputation, and construction of PGS models using reference GWAS data. PGSXplorer integrates various PGS development tools such as PLINK, PRSice-2, LD-Pred2, Lassosum2, MegaPRS, SBayesR-C, PRS-CSx and MUSSEL, improving the generalizability of PGS through multi-origin data integration. Tested with synthetic datasets, our fully Docker-encapsulated tool has demonstrated scalability and effectiveness for both single- and multi-population analyses. Continuously updated as an open-source tool, PGSXplorer is freely available with user tutorials at https://github.com/tutkuyaras/PGSXplorer, making it a valuable resource for advancing precision medicine in genetic research. creator: Tutku Yaraş creator: Yavuz Oktay creator: Gökhan Karakülah uri: https://doi.org/10.7717/peerj.18973 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Yaraş et al. title: Hematology and clinical biochemistry reference intervals for companion pigs using the ADVIA 2120 and Cobas c501 link: https://peerj.com/articles/18968 last-modified: 2025-02-12 description: BackgroundThe majority of published reference intervals for hematology and clinical biochemistry in pigs are generated from a sample group that is demographically different from companion pigs, and as such may not be transferable. The goals of this study were to provide reference intervals generated from sexually mature companion pigs and to compare results based on age group, breed, and reproductive status. Reference intervals are ideally generated in the same laboratory in which patient samples are measured, since there is often bias in values generated from different instruments, but the cost and time commitment required to produce reference intervals may be prohibitive. If so, published reference intervals may be used cautiously as guidelines for interpretation.MethodsComplete blood count (CBC) and plasma biochemistry data were generated using the ADVIA 2120 hematology analyzer and Cobas c501 chemistry analyzer on blood samples collected from 94 sexually mature, clinically healthy companion pigs housed mostly in eastern Tennessee over a 5-year period. The majority (90/94) of samples were collected after sedation or general anesthesia. The age range of the reference sample group was 5 months to 11 years, including <1-year-old (n = 26), 1–2 years old (n = 26), and >2-years-old (n = 42). Reproductive status included intact females (n = 46), spayed females (n = 9), intact males (n = 15), and castrated males (n = 24). Breeds were predominantly Vietnamese potbellied mini pigs, American mini pigs, and mixed breed pigs.ResultsReference intervals are provided for routine CBC and plasma biochemistry values. The <1-year-old pigs were excluded from reference interval calculation for some values because their results were significantly different from pigs >1-year-old. These included red blood cell concentration, mean cell volume, mean cell hemoglobin, platelet count, mean platelet volume, lymphocyte concentrations by both automated and manual methods, and total protein by refractometry. Few significant differences were observed based on breed or reproductive status.DiscussionAge, breed, and reproductive status can affect some hematology and biochemistry results in companion pigs. If companion pig reference intervals are not available from the laboratory in which patient samples are measured, these published reference intervals may provide guidance for interpretation, although some methodologic variances are likely. creator: Deanna M. W. Schaefer creator: Ricardo Videla creator: Joe S. Smith creator: Pierre-Yves Mulon creator: Bente Flatland creator: Xiaojuan Zhu uri: https://doi.org/10.7717/peerj.18968 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Schaefer et al. title: Silicon mitigates the adverse effects of drought on Lolium perenne physiological, morphometric and anatomical characters link: https://peerj.com/articles/18944 last-modified: 2025-02-12 description: Limited water resources and natural drought may result in reduced water availability for the population’s needs and the maintenance of the proper vegetation condition. Understanding the impact of drought on turfgrass species is essential to developing strategies that enhance the adaptability of plants to drought stress. It is vital for maintaining green areas in cities under changing climatic conditions. Therefore, studies on the ability of turfgrasses to recover after periods of drought without irrigation are becoming increasingly essential. We conducted research to determine the possibility of reducing the negative impact of drought stress on the photosynthetic efficiency, the morphometric features of plant shoots and roots, and the distribution of biomass of Lolium perenne lawn cultivars in the initial period of growth by applying biostimulant with silicon. We also investigated how drought and silicon (Si) application affect the leaf and root anatomical structure of L. perenne plants. Studies on the influence of drought on the physiological, biometric parameters and anatomical characteristics of two L. perenne cultivars were carried out under two levels of soil moisture (well-watered plants—control and drought caused by the cessation of watering) and also two variants of Si application (with and without Si application). Plants were exposed to drought in the tillering phase for 21 days. After this time, all plants were provided with optimal soil moisture conditions for the next 14 days (recovery period). Measurements of physiological parameters and biometric features of plants were evaluated in four terms: after 7, 14 and 21 days of drought and after recovery. Drought stress in L. perenne cvs. resulted in decreasing values of physiological parameters, especially maximal fluorescence, the quantum efficiency of photosystem II and photosynthetic electron transport rate compared with the values of features in well-watered plants. These adverse impacts were reflected in decreased biomass-related traits: shoot number, shoots and roots biomass, as well as area and length of roots. The application of Si reduced the detrimental effects of drought by accelerating plant growth after stress and increasing the values of most of the investigated physiological parameters. Under drought stress conditions, Si application led to the development of two-cell-layer exodermis, which reduced the water losses in L. perenne roots and shoots and, as a result, improved the drought tolerance of plants. creator: Grażyna Mastalerczuk creator: Barbara Borawska-Jarmułowicz creator: Marzena Sujkowska-Rybkowska creator: Magdalena Bederska-Błaszczyk creator: Wojciech Borucki creator: Piotr Dąbrowski uri: https://doi.org/10.7717/peerj.18944 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Mastalerczuk et al. title: Effects of chemical fungicides combined with plant resistance inducers against Bipolaris sorokiniana in turfgrass link: https://peerj.com/articles/18943 last-modified: 2025-02-12 description: One of the most common and causative diseases problems disease in turfgrass areas in Türkiye is leaf blight, root and crown rot caused by Bipolaris sorokiniana. The fungus causes great damage especially in parks, refuges, and golf courses, and needs to be managed. This study aimed to determine some activators alone or in combination with effective fungicides at different doses against B. sorokiniana, to reduce the use of fungicides in the control of the disease. In the study, the effects of combinations of different doses of some fungicides with Lactobacillus acidophilus, Arthrobacter sp. and a harpin protein determined to be effective in in vitro studies were investigated in greenhouse and field conditions in two different provinces. The highest effect was obtained in the combination of (Lactobacillus acidophilus-(Azoxystrobin+Difenocazole)), which was used at the recommended dose (94.70% effect) and the recommended dose of Azoxystrobin+Difenocazole (92.57% effect). The (Lactobacillus acidophilus-(Azoxystrobin+Difenocazole 1st subdose)) application, in which a lower dose of fungicide was used, ranked 4th with an 89.50% effect. When Lactobacillus acidophilus, Arthrobacter sp. and Harpin were used alone, they were found to be 82.53%, 72.17%, and 66.63% effective against the disease, respectively. As a result, environmentally friendly low-dose fungicide, and activator combination (Lactobacillus acidophilus-(Azoxystrobin+Difenocazole 1. subdose)), and (Arthrobacter sp.-(Epoxiconazole+Pyraclostrobin 1st sub-dose)) applications were found to be promising in the control of B. sorokiniana in turfgrass areas. When considered only as an activator application, the 82.53% effect value obtained in Lactobacillus acidophilus applications was found to be promising for the disease. It can be recommended as a disease suppressant, and at the same time environmentally friendly application. creator: Filiz Ünal creator: İlker Kurbetli creator: Yeşim Eğerci creator: Aysun Cavusoglu uri: https://doi.org/10.7717/peerj.18943 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ünal et al. title: Lengthened partial repetitions elicit similar muscular adaptations as full range of motion repetitions during resistance training in trained individuals link: https://peerj.com/articles/18904 last-modified: 2025-02-12 description: PurposeResistance training using different ranges of motion may produce varying effects on musclular adaptations. The purpose of this study was to compare the effects of lengthened partial repetitions (LPs) vs. full range of motion (ROM) resistance training (RT) on muscular adaptations.MethodsIn this within-participant study, thirty healthy, resistance-trained participants had their upper extremities randomly assigned to either a lengthened partial or full ROM condition; all other training variables were equivalent between limbs. The RT intervention was an 8-week program targeting upper-body musculature. Training consisted of two training sessions per week, with four exercises per session and four sets per exercise. Muscle hypertrophy of the elbow flexors and elbow extensors was evaluated using B-mode ultrasonography at 45% and 55% of humeral length. Muscle strength-endurance was assessed using a 10-repetition-maximum test on the lat pulldown exercise, both with a partial and full ROM. Data analysis employed a Bayesian framework with inferences made from posterior distributions and the strength of evidence for the existence of a difference through Bayes factors.ResultsBoth muscle thickness and unilateral lat pulldown 10-repetition-maximum improvements were similar between the two conditions. Results were consistent across outcomes with point estimates close to zero, and Bayes factors (0.16 to 0.3) generally providing “moderate” support for the null hypothesis of equal improvement across interventions.ConclusionsTrainees seeking to maximize muscle size should likely emphasize the stretched position, either by using a full ROM or LPs during upper-body resistance training. For muscle strength-endurance, our findings suggest that LPs and full ROM elicit similar adaptations. creator: Milo Wolf creator: Patroklos Androulakis Korakakis creator: Alec Piñero creator: Adam E. Mohan creator: Tom Hermann creator: Francesca Augustin creator: Max Sapuppo creator: Brian Lin creator: Max Coleman creator: Ryan Burke creator: Jeff Nippard creator: Paul A. Swinton creator: Brad J. Schoenfeld uri: https://doi.org/10.7717/peerj.18904 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Wolf et al. title: Analysis of local and systemic side effects of bacillus Calmette-Guérin immunotherapy in bladder cancer: a retrospective study in Türkiye link: https://peerj.com/articles/18870 last-modified: 2025-02-12 description: BackgroundBladder cancer is a growing health concern, especially in developing countries like Türkiye. Intravesical Bacillus Calmette-Guérin (BCG) immunotherapy is essential for reducing recurrence and progression in non-muscle invasive bladder cancer (NMIBC). However, it can cause local and systemic adverse effects linked to bacterial virulence, allergic reactions, or nosocomial infections. Data from randomized studies on BCG side effects are limited, with severe cases often reported in case studies. This study investigates the association between intravesical BCG immunotherapy and its adverse effects.MethodsA retrospective analysis was conducted on 239 patients who underwent BCG immunotherapy between 2017 and 2024. Detailed demographic, clinical, and laboratory data were collected, and the adverse effects that developed following BCG therapy were evaluated. Descriptive statistics, including medians, counts, and percentage distributions, were calculated, and logistic regression analysis was performed to identify factors influencing the development of adverse effects.ResultsAdverse effects related to BCG immunotherapy were observed in 63.1% of the patients. The most common minor adverse effects were hematuria, dysuria, and cystitis, while major adverse effects included sepsis and lymphadenopathy. The analyses revealed that elevated aspartate aminotransferase (AST) levels and the presence of Escherichia coli and Enterococcus faecalis in urine cultures were significant risk factors for the development of adverse effects. Additionally, patients who underwent the 6th cycle of BCG therapy were found to have a higher risk of developing adverse effects compared to those who received fewer cycles.ConclusionBCG immunotherapy is an effective treatment method for NMIBC; however, the adverse effects that occur during treatment must be closely monitored. Elevated AST levels, the presence of specific pathogens in urine cultures, and the number of BCG doses administered are significant factors that increase the risk of adverse effects. These findings highlight the necessity for more careful monitoring throughout the treatment process. creator: Ilkay Akbulut creator: İlker Ödemiş creator: Sabri Atalay uri: https://doi.org/10.7717/peerj.18870 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Akbulut et al. title: The in vitro antimicrobial activity of linezolid against unconventional pathogens link: https://peerj.com/articles/18825 last-modified: 2025-02-12 description: Linezolid is an oxazolidinone antibiotic that is mainly permitted to treat Gram-positive bacterial infections. Recent studies have shown that linezolid also has antibacterial effects on several other bacteria outside the package insert, including Mycobacterium tuberculosis, non-tuberculous mycobacteria (NTM), Nocardia, Corynebacterium, and anaerobes, etc. Interestingly, linezolid also has an in vitro inhibitory effect on fungi. This review focuses on the in vitro antibacterial activity of linezolid against microorganisms outside its antibacterial spectrum. We mainly listed the number of the tested strains, the minimum inhibitory concentration (MIC) range, MIC50, and MIC90 of linezolid against those pathogens outside the package insert. The results showed that among these tested pathogens, linezolid displayed strong inhibitory effects against M. tuberculosis, Nocardia, and Corynebacterium, with an MIC range of ≤2 μg/mL. As for NTM, linezolid exhibited moderate to potent inhibitory effects against the strains of different species with an MIC range of 0.06–128 μg/mL. Moreover, linezolid was reported to have a species-dependent inhibitory effect on anaerobes at a concentration range of 0.003–16 μg/mL. Furthermore, linezolid could enhance azoles and amphotericin B’s antifungal activity on Candida synergistically. It is hoped that this analysis can provide data for expanding the application of linezolid, make the off-label drug use have more compelling evidence, and provide clues for the development of new drugs. creator: Ting Wang creator: Huiyue Zhang creator: Rui Feng creator: Jieru Ren creator: Xinping Xu creator: Shujuan Sun uri: https://doi.org/10.7717/peerj.18825 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Wang et al. title: Association between toxic heavy metals and noncancerous thyroid disease: a scoping review link: https://peerj.com/articles/18962 last-modified: 2025-02-11 description: BackgroundToxic heavy metals such as chromium (Cr), arsenic (As), cadmium (Cd), mercury (Hg), and lead (Pb) are known to be priority pollutants due to their high degrees of toxicity and widespread presence in the environment. This review aimed to explore the association between heavy metals and noncancerous thyroid diseases by synthesizing findings from observational and experimental studies. This review addressed a critical intersection of environmental health, endocrinology, and public health. The findings would be of interest to a wide range of disciplines given the ubiquitous presence of toxic heavy metals in the environment and their potential to disrupt endocrine systems. The evidence-based information from diverse fields generated from this review will provide insights into the health implications of heavy metal exposure on thyroid function and guide the necessary interdisciplinary research and collaborative interventions.MethodThree databases were searched, namely PubMed, Web of Science, and Scopus. The Arksey and O’Malley (2005) framework was used as a guide in conducting this scoping review. The reporting was carried out based on the Preferred Reporting Items for Systematic Reviews and the Meta-Analyses Extension for Scoping Reviews (PRISMA). The literature search retrieved 552 articles and 29 articles were included in the final review.ResultsAs high as 83% of the 29 included studies followed an observational study design while the rest were experimental animal studies. Among the observational studies, two-thirds (66%) were cross-sectional studies while the rest were case-control studies (31%) and cohort studies (n = 1, 3%). Few number of studies in this review reported a significant association between Cr, As, Cd, Hg, and Pb with noncancerous thyroid diseases (2, 3, 16, 8, and 12) while another few (5, 8, 9, 5, and 11) did not show any significant association.ConclusionA heterogeneous and diverse sample population in the included studies could have potentially led to mixed findings about the association between toxic heavy metals and thyroid diseases in this review. Therefore, future research should prioritize longitudinal studies and controlled clinical trials to better elucidate the causative mechanisms and long-term impact of heavy metal exposure on thyroid health. creator: Muhammad Ridzwan Rafi’i creator: Mohd Hasni Ja’afar creator: Azmawati Mohammed Nawi creator: Shahrul Azhar Md Hanif creator: Siti Najiha Md Asari uri: https://doi.org/10.7717/peerj.18962 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Rafi’i et al.