title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=147 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Clinical characteristics of pathogens in children with community-acquired pneumonia were analyzed via targeted next-generation sequencing detection link: https://peerj.com/articles/18810 last-modified: 2025-01-08 description: BackgroundThe primary purpose of this study was to detect the pathogen species using targeted next-generation sequencing (tNGS) to investigate the characteristics of community-acquired pneumonia (CAP)-related pathogens in children in Xiantao city, Hubei province, China.MethodsA total of 1,527 children with CAP were prospectively recruited from our hospital between May 2022 and February 2023. Information on age and sex was collected from the medical records. Pathogen detection was performed using standard detection methods and tNGS.ResultsThe positive coincidence rate of standard detection methods and tNGS were 61.95% (946/1,527) and 97.05% (1,482/1,527), respectively. Among the 1,482 children with CAP, the numbers of bacteria, virus, chlamydia, and mycoplasma infection were 1,188, 975, 321, and 1, respectively. Co-existing species showed high prevalence in CAP, and the prevalence of children infected with only one pathogen was 20.31%. The numbers of children infected with two and three pathogens were the highest, accounting for 29.22% and 25.17%, respectively. Among the 44 pathogens detected using tNGS, 17 species of bacteria, 25 species of viruses, one species of chlamydia, and one species of mycoplasma were documented. Among all infectious pathogens, the top five were Haemophilus influenzae, Acinetobacter baumannii, Streptococcus pneumoniae, human herpes virus type 5 (HHV-5), and Mycoplasma pneumoniae. The results showed that pathogenic infections in children with CAP were related to age but not to gender.ConclusionThe infection pathogens in children with CAP were complex and the incidence of co-existence was observed to be high. The pathogens involved in CAP were closely related to the age of the child. In addition, tNGS was shown to better identify pathogens than the standard detection method, which is crucial for improving the accuracy of early CAP diagnosis and initiating appropriate treatment in a timely manner, ultimately enhancing treatment outcomes. creator: Junhua Zhao creator: Mingfeng Xu creator: Zheng Tian creator: Yu Wang uri: https://doi.org/10.7717/peerj.18810 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhao et al. title: The potential of serum elabela levels as a marker of diabetic retinopathy: results from a pilot cross-sectional study link: https://peerj.com/articles/18841 last-modified: 2025-01-08 description: BackgroundThe aim of this study is to examine the relationship between elabela (ELA), a recently identified peptide also known as Toddler and Apela, and diabetic retinopathy (DR). ELA, produced in various tissues, acts as a natural ligand for the apelin receptor (APJ). Upon reviewing the existing literature, only one study was found investigating ELA, one of the APJ ligands, in the pathogenesis of DR.MethodsIn our study the patient group comprising individuals diagnosed with type 2 diabetes mellitus (DM), categorized into three subgroups based on detailed fundus examination: those without DR (non-DR) (n = 20), non-proliferative DR (NPDR) (n = 20), and proliferative DR (PDR) (n = 20). A control group (n = 20) consisted of individuals without DM. Blood samples were collected during outpatient clinic admission to measure serum ELA levels, which were determined using a commercial ELISA kit.ResultsThe age, sex, and body mass index of the between groups were similar (p = 0.905, 0.985 and 0.241, respectively). The HbA1c levels of the between DM subgroups were similar (p = 0.199). Serum ELA levels were 217.19 ± 97.54 pg/mL in the non-DR group, 221.76 ± 93.12 pg/mL in the NPDR group, 302.35 ± 146.17 pg/mL in the PDR group and 216.49 ± 58.85 pg/mL in the control group. While ELA levels were higher in DM patients compared to the control group, this elevation did not reach statistical significance. Further analysis dividing DM patients into subgroups (non-DR, NPDR, and PDR) revealed higher ELA levels in the PDR group compared to the other subgroups, but this increase was not statistically significant.ConclusionDespite the absence of a significant difference in our study, the identification of elevated ELA levels in the PDR group offers valuable insights for future investigations exploring the association between DR and ELA. creator: Muhammed Seyithanoğlu creator: Selma Meşen creator: Aysegul Comez creator: Ali Meşen creator: Abdullah Beyoğlu creator: Yaşarcan Baykişi creator: Filiz Alkan Baylan uri: https://doi.org/10.7717/peerj.18841 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Seyithanoğlu et al. title: Deregulation mechanisms and therapeutic opportunities of p53-responsive microRNAs in diffuse large B-cell lymphoma link: https://peerj.com/articles/18661 last-modified: 2025-01-07 description: Here, we have discussed the molecular mechanisms of p53-responsive microRNAs dysregulation in response to genotoxic stress in diffuse large B-cell lymphoma (DLBCL) patients. The role of micro ribonucleic acids (microRNAs) in p53-signaling cellular stress has been studied. MicroRNAs are the small non-coding RNAs, which regulate genes expression at post-transcriptional level. Many of them play a crucial role in carcinogenesis and may act as oncogenes or suppressor of tumor growth. The understanding of the effect of p53-responsive microRNA dysregulation on oncogenesis achieved in recent decades opens wide opportunities for the diagnosis, prediction and of microRNA-based cancer therapy. Development of new bioinformatics tools and databases for microRNA supports DLBCL research. We overview the studies on the role of miRNAs in regulating gene expression associated with tumorigenesis processes, with particular emphasis on their role as tumor growth-suppressing factors. The starting point is a brief description of the classical microRNA biogenesis pathway and the role of p53 in regulating the expression of these molecules. We analyze various molecular mechanisms leading to this dysregulation, including mutations in the TP53 gene, DNA methylation, changes in host-genes expression or microRNA gene copy number, mutations in microRNA and microRNA biogenesis genes. creator: Elena N. Voropaeva creator: Yuriy L. Orlov creator: Anastasia B. Loginova creator: Olga B. Seregina creator: Vladimir N. Maksimov creator: Tatiana I. Pospelova uri: https://doi.org/10.7717/peerj.18661 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Voropaeva et al. title: Reproductive strategies in loggerhead sea turtle Caretta caretta: polyandry and polygyny in a Southwest Atlantic rookery link: https://peerj.com/articles/18714 last-modified: 2025-01-07 description: Sea turtles are highly migratory and predominantly inhabit oceanic environments, which poses significant challenges to the study of their life cycles. Research has traditionally focused on nesting females, utilizing nest counts and mark-recapture methods, while male behavior remains understudied. To address this gap, previous studies have analyzed the genotypes of females and hatchlings to indirectly infer male genotypes and evaluate the extent of multiple paternity within populations. Our research aimed to investigate the presence of multiple paternity in loggerhead turtle (Caretta caretta) nests for the first time in Brazil. We analyzed 534 hatchlings from 43 nests associated with 42 females during the 2017/18 to 2019/20 nesting seasons, using four highly polymorphic, species-specific microsatellite markers (nDNA). Parentage tests were conducted to reconstruct paternal genotypes and determine the rates of multiple paternity within clutches. Our results revealed that 72.09% of clutches were sired by multiple males, with contributions ranging from one to six males per clutch. Additionally, seven out of 88 males (7.95%) were found to have sired clutches from multiple females, with some males contributing to more than one clutch within and across breeding seasons. The breeding sex ratio (BSR) was calculated to be 2.09 males per female. While multiple paternity is a common phenomenon among sea turtles, this study is the first to document polyandry in loggerheads in Brazil and the first to provide evidence of polygyny in this species globally. This research establishes a crucial database for future studies in Brazil, with a focus on the BSR of the Southwest Atlantic subpopulation, offering essential insights for developing effective management strategies for this vulnerable population. creator: Laís Amorim creator: Lara Chieza creator: Jake A. Lasala creator: Sarah de Souza Alves Teodoro creator: Wesley D. Colombo creator: Ana Carolina Barcelos creator: Paula Rodrigues Lopes Guimarães creator: João Luiz Guedes da Fonseca creator: Ana Claudia Jorge Marcondes creator: Alexsandro Santos creator: Sarah Vargas uri: https://doi.org/10.7717/peerj.18714 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Amorim et al. title: Recognising depression in non-human primates: a narrative review of reported signs of depression link: https://peerj.com/articles/18766 last-modified: 2025-01-07 description: Major depressive disorder (depression) is a highly heterogenous human mental disorder that may have equivalents in non-human animals. Research into non-human depression teaches us about human depression and can contribute to enhance welfare of non-human animals. Here, we narratively review how signs of depression in non-human primates (NHPs) can be observed based on symptoms of the Diagnostic and Statistical Manual of Mental Disorders (DSM-5). Furthermore, we propose diagnostic criteria of NHP depression and we review reports on signs of depression in NHPs. We diagnose an NHP with depression when it shows a core sign (depressed mood or anhedonia) alongside at least three other DSM-5-derived signs of depression. Results show that four out of six observable signs of depression are present in NHPs, occasionally lasting for months. However, only a group of six NHPs in one study met our proposed criteria for a diagnosis of depression. We call for more research into the co-occurrence of depressive symptoms in individual NHPs to establish the prevalence of depression in NHPs. creator: Jonas C. P. van Oosten creator: Annemie Ploeger creator: Elisabeth H. M. Sterck uri: https://doi.org/10.7717/peerj.18766 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 van Oosten et al. title: Trunk muscle behaviors during the full-cycle stoop and squat lifting tasks link: https://peerj.com/articles/18797 last-modified: 2025-01-07 description: BackgroundLifting is generally considered as a risk factor for low back pain. A thorough investigation of the muscle function during lifting is essential for a better assessment of the potential risk of muscle impairment and towards improvements in lifting strategy. We aimed to compare the activities of the trunk muscles between the stoop and the squat lifting tasks.MethodsA surface electromyography device was used to measure the muscle activity during the full-cycle squat and the stoop lifting tasks of a 5-kg weight. Each task was divided into four stages: stage 1 was bending forward to reach the weight, stage 2 was lifting the weight up, stage 3 was lowering the weight down, and stage 4 was returning to the upright position. The maximum electromyographic (EMG) activities among different tasks and different stages were compared. Eighteen males aged 20–35 years without low back pain were included, with a mean age of 26.55 ± 2.12 years, body height of 175.18 ± 4.29 cm, body weight of 69.27 ± 4.29 kg, and BMI of 22.56 ± 0.87 kg/m2.ResultsDuring stoop lifting, the median values of the absolute EMG of the left multifidus were 53.96, 70.32, 51.08 and 64.14 uV from stage 1 to stage 4, which were all non-significantly lower than those during squat lifting for 79.84, 103.64, 71.72 and 95.72, respectively (P > 0.05). The absolute EMG was greatest during stage 2, then during stage 4, stages 1 and 3 came next (Effect size = 0.879, P < 0.001). The median values of the normalized EMG of each muscle during stoop lifting were also non-significantly lower than those during squat lifting at each stage (P > 0.05). The normalized EMG was also greatest during stage 2, then during stage 4, and was lowest during stages 1 and 3 (Effect size = 0.932, P < 0.001).ConclusionThe trunk muscles were similarly activated during squat and stoop lifting. During lowering the weight down, the trunk muscles were less activated than during extension to the upright position without weight in hands. These results could help to develop subject-specific strategies for lifting tasks to prevent or alleviate occupational low back pain. creator: Fumin Pan creator: Wei Wang creator: Chao Kong creator: Shibao Lu uri: https://doi.org/10.7717/peerj.18797 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Pan et al. title: Antimicrobial activity of Lactobacillus spp. isolated from fermented foods and their inhibitory effect against foodborne pathogens link: https://peerj.com/articles/18541 last-modified: 2025-01-06 description: Lactic acid bacteria (LAB), known for their health benefits, exhibit antimicrobial and antibiofilm properties. This study investigated the cell-free supernatant (CFS) of Lactobacillus spp., particularly L. plantarum KR3, against the common foodborne pathogens S. aureus, E. coli and Salmonella spp. Lactobacillus strains were isolated from cheese, pickles and yoghurt. They were then identified by morphological, physiological and biochemical characteristics and confirmed by 16S rRNA gene sequencing. Culture supernatants from seven lactobacilli isolates showed varying inhibitory activities. Notably, L. plantarum KR3 and L. pentosus had the highest bacteriocin gene counts. L. plantarum KR3 CFS demonstrated significant antibacterial activity, with inhibition zones of 20 ± 0.34 mm for S. aureus, 23 ± 1.64 mm for E. coli, and 17.1 ± 1.70 mm for Salmonella spp. The CFS also exhibited substantial antibiofilm activity, with 59.12 ± 0.03% against S. aureus, 83.50 ± 0.01% against E. coli, and 60. ± 0.04% against Salmonella spp., which were enhanced at the minimum inhibitory concentration (MIC). These results highlighted the potential of L. plantarum KR3 in antimicrobial applications, however, further research is needed to evaluate its viability and functional properties for probiotic use. Additionally, the CFS demonstrated exceptional thermal stability, reinforcing its promise as an antimicrobial agent. creator: Athraa Oudah Hussein creator: Khalida Khalil creator: Nurul Aqilah Mohd Zaini creator: Ahmed Khassaf Al Atya creator: Wan Syaidatul Aqma uri: https://doi.org/10.7717/peerj.18541 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Hussein et al. title: Contact zone of slow worms Anguis fragilis Linnaeus, 1758 and Anguis colchica (Nordmann, 1840) in Poland link: https://peerj.com/articles/18563 last-modified: 2025-01-06 description: BackgroundLegless lizards, the slow worms of the genus Anguis, are forming secondary contact zones within their Europe-wide distribution.MethodsWe examined 35 populations of A. fragilis and A. colchica to identify the level of morphological and genetic divergence in Poland. We applied a conventional study approach using metric, meristic, and categorial (coloration) features for a phenotype analysis, and two standard molecular markers, a mitochondrial (NADH-ubiquinone oxidoreductase chain 2; ND2) and a nuclear (V(D)J recombination-activating protein 1; RAG1) one.ResultsWe found clear differences between A. fragilis and A. colchica in molecular markers and phenotype—in meristic features, e.g., ear opening, number of scales rows around the body, and higher than so far known diversity in ND2 and RAG1 haplotypes. The presence of five hybrids was detected in three populations in the Polish part of the European contact zone. In all hybrids, homozygous alleles of RAG1 were detected, which suggests a back-crossing within the genus.ConclusionsThe ability to produce fertile offspring by A. fragilis x A. colchica hybrids shows inefficient mechanisms of reproductive isolation of the two legless lizards. The hybrids were indistinguishable from parental species in head proportions (principal components and discriminant analyses) but more resembling A. colchica in meristic traits. creator: Grzegorz Skórzewski creator: Bartosz Borczyk creator: Stanisław Bury creator: Daniel Kulik creator: Jan Kotusz uri: https://doi.org/10.7717/peerj.18563 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Skórzewski et al. title: Research progress on the impact of climate change on wheat production in China link: https://peerj.com/articles/18569 last-modified: 2025-01-06 description: It is crucial to elucidate the impact of climate change on wheat production in China. This article provides a review of the current climate change scenario and its effects on wheat cultivation in China, along with an examination of potential future impacts and possible response strategies. Against the backdrop of climate change, several key trends emerge: increasing temperature during the wheat growing season, raising precipitation, elevated CO2 concentration, and diminished radiation. Agricultural disasters primarily stem from oscillations in temperature and precipitation, with the northern wheat region being mostly affected. The impact on wheat production is manifested in a reduction in the area under cultivation, with the most rapid reduction in spring wheat, and a shift in the center of cultivation to the west. Furthermore, climate change accelerates the nutritional stage and shortens phenology. Climate change has also led to an increase in yields in the Northeast spring wheat region, the Northern spring wheat region, the Northwest spring wheat region, and the North China winter wheat region, and a decrease in yields in the middle and lower reaches of the Yangtze River winter wheat region, the Southwest winter wheat region, and the South China winter wheat region. To cope with climate change, Chinese wheat can adopt adaptation strategies and measures such as breeding different wheat varieties for different wheat-growing regions, implementing differentiated farmland management measures, promoting regional ecological farmland construction, and establishing scientific monitoring and early warning systems. While future climate change may stimulate wheat yield potential, it could cause climate-induced issues such as weeds, diseases, and pests worsen, thereby posing challenges to the sustainability of farmland. Moreover, it is essential to conduct comprehensive research on pivotal areas such as the microscopic mechanism of climate change and wheat growth, the comprehensive influence of multiple climate factors, and the application of new monitoring and simulation technologies. This will facilitate the advancement of related research and provide invaluable insights. creator: Yu-chen Fan creator: Ya-qi Yuan creator: Ya-chao Yuan creator: Wen-jing Duan creator: Zhi-qiang Gao uri: https://doi.org/10.7717/peerj.18569 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Fan et al. title: Reproductive management: conditioning, spawning and development of Peruvian grunt Anisotremus scapularis in southern Peru link: https://peerj.com/articles/18655 last-modified: 2025-01-06 description: The Peruvian grunt, Anisotremus scapularis, is beginning its domestication as a candidate species for marine aquaculture. The optimal management of fingerling production requires precise knowledge on early development. Herein, we report the methodology for capturing and conditioning wild specimens to find a viable broodstock. The speed of capture and transportation (about 30 min), the post capture preventive treatment (60 min with tetracycline), and the 6-days preventive antiparasitic treatment (29 ppm formalin) maximized survival and a rapid feeding adaptation. Progressive diets based on the copepod Emerita analoga, fish meal, pellets and processed feedstuff prompted the spontaneous broodstock spawning 7 months post-capture. The interannual spawning of this broodstock since September 2016 indicated the optimal control of its reproduction in captivity. The morphogenetic process of the embryo lasted 42 h at 18 °C compared to (31–41) h at 19 °C in northern Peruvian latitudes. The knowledge generated allowed us to work out broodstock and egg management protocols in southern Pacific latitudes (southern Peru and northern Chile). Such protocols would help to escalate larval and juvenile production and to alleviate fishing pressure on the overexploited Peruvian grunt population. creator: Renzo Pepe-Victoriano creator: Jordan I. Huanacuni creator: Pablo Presa creator: Luis Antonio Espinoza-Ramos uri: https://doi.org/10.7717/peerj.18655 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Pepe-Victoriano et al.