title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=179 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Genetic analysis of Pinna rudis L 1758 (Mollusca, Bivalvia, Pinnidae) in the Northwest Cabo Verde Islands (Central-East Atlantic) link: https://peerj.com/articles/18328 last-modified: 2025-01-08 description: The rough pen shell Pinna rudis Linnaeus, 1758 (family Pinnidae) is a mollusc with an Atlantic–Mediterranean distribution, typically inhabiting coarse sandy substrates. Habitat degradation is considered the primary cause of population decline, leading to the designation ‘Vulnerable’ in certain regions. In this study, we conducted a genetic analysis of populations of P. rudis from Cabo Verde and compared them with populations from the Mediterranean and Macaronesia. We based our analysis on two mitochondrial DNA markers, cytochrome oxidase I (COI) and 16S rRNA, and one nuclear marker, 28S rRNA. The results showed a strong genetic structuring among Macaronesia populations, with each island tending to have unique or exclusive haplotypes, though some sharing occurred between islands. We found significant genetic divergence between the population from Cabo Verde and the other sampled population, suggesting that P. rudis is not monotypic, but may include several cryptic species. Bayesian and maximum-likelihood phylogenetic analysis, including all Pinnidae species, indicated that P. rudis from Gorée Island (Senegal) and Baía das Gatas (São Vicente Island) might be undergoing speciation. The high genetic structure found for P. rudis could be influenced by hydrodynamic barriers, local currents and hydrographic isolation, in association with the short larval duration (planktotrophic) reported for this species. Altogether, our findings highlight significant genetic divergence in P. rudis populations, possibly supporting speciation events in the Cabo Verde archipelago among widely distributed taxonomic groups. creator: Evandro P. Lopes creator: Sarah Santos creator: Raquel Xavier creator: Joana L. Santos creator: M. Pilar Cabezas creator: Fernando Sequeira creator: António M. Santos uri: https://doi.org/10.7717/peerj.18328 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Lopes et al. title: Niche-related processes explain phylogenetic structure of acoustic bird communities in Mexico link: https://peerj.com/articles/18412 last-modified: 2025-01-08 description: Acoustic communities are acoustically active species aggregations within a habitat, where vocal interactions between species can interfere their communication. The acoustic adaptation hypothesis (AAH) explains how the habitat favors the transmission of acoustic signals. To understand how bird acoustic communities are structured, we tested the effect of habitat structure on the phylogenetic structure, and on the phylogenetic and vocal diversity of acoustic communities in a semi-arid zone of Mexico. From autonomous recordings in three types of vegetation (crop fields, tetecheras, and mesquiteras), which differ in terms of complexity and canopy openness, we evaluated sound attenuation, and estimated metrics of phylogenetic structure and diversity as well as acoustic diversity with the use of two indices. Mesquiteras showed greater vegetation density, more attenuation, more vocal diversity, as well as a phylogenetic structure that tended towards overdispersion, in contrast to crop fields that showed less vegetation density, less attenuation, less vocal diversity and more phylogenetic relatedness, while tetecheras showed intermediate patterns. Phylogenetic structure was explained by vegetation density and excess attenuation. The higher vocal diversity, phylogenetic structure tended towards overdispersion. These results suggest a role for environmental filters in the crop fields, where more closely related species with similar vocal characteristics coexist (supporting AAH), and probably competitive exclusion in the mesquiteras, where more distantly related species coexist, promoting vocal diversity. This study offers information about the influence of habitat on the acoustic community structure, which could inform our understanding of the distribution of species from acoustic perspective. creator: Christian D. Morán-Titla creator: Juan-Hector García-Chávez creator: Leonel Lopez-Toledo creator: Clementina González uri: https://doi.org/10.7717/peerj.18412 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Morán-Titla et al. title: The impact of a disaster medicine clinical training program on medical students’ disaster literacy link: https://peerj.com/articles/18800 last-modified: 2025-01-08 description: BackgroundThis study was conducted to assess how students’ disaster literacy was affected by the Disaster Medicine Clinical Training Program at the Izmir Democracy University Faculty of Medicine (IDUFM) during the academic year 2022–2023.MethodsUsing an experimental method involving experimental and control groups, measurements were made at different times. The sample consisted of 5th-year students at IDUFM for the experimental group, while the control group was composed of 3rd- and 4th-year students from different buildings with limited interaction with the experimental group. The clinical training program was organized to improve the clinical practice skills of students in the field of disaster medicine and provide theoretical information. Throughout their internship, the students were provided with a program including information on types of disasters, preparation, response, relief, emergency surgical procedures, hospital disaster plans, national and international organizations and institutions working in disasters, and other relevant topics. The Disaster Literacy Scale (DLS) was used to collect data. This scale is a self-report scale that was developed to evaluate knowledge levels about disasters. In this study, the scale was applied as a pretest and a posttest, and the obtained data were analyzed using independent samples and paired-sample t-tests.ResultThe DLS scores of the experimental group showed significant improvement after the training program compared to their pretest scores (Total Scale: p < 0.001, Damage Mitigation: p = 0.002, Preparation: p < 0.001, Response: p < 0.001, and Relief: p = 0.004). When comparing the posttest results of the experimental group with the control group, the experimental group demonstrated significantly higher scores in Total Scale (p = 0.01), Damage Mitigation (p = 0.02), Response (p = 0.03), and Relief (p < 0.001). However, no significant differences were observed between the experimental group’s pretest (T1) scores and the control group’s posttest (T3) scores (p > 0.05p > 0.05p > 0.05), indicating that the knowledge levels of the experimental and control groups were homogeneous prior to the training intervention. These findings confirm the effectiveness of the Disaster Medicine Training Program in improving disaster literacy and response skills among medical students.ConclusionThis study, which aimed to determine the effects of the Disaster Medicine Clinical Training Program on the disaster literacy of medical students, revealed that the program increased the literacy levels of the students and contributed to their responsible decision-making. It is thought that such education programs can make significant contributions to the effective management of healthcare services in disaster situations. creator: Aysel Başer creator: Zeynep Sofuoğlu uri: https://doi.org/10.7717/peerj.18800 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Başer and Sofuoğlu 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.