title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2025-02 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Inhibitory effects of Trichoderma asperellum culture filtrates on pathogenic bacteria, Burkholderia pseudomallei link: https://peerj.com/articles/19051 last-modified: 2025-02-28 description: BackgroundBurkholderia pseudomallei is a soil- and water-dwelling bacterium that causes the life-threatening infection melioidosis. Patients typically acquire this infection through environmental exposure, so reducing B. pseudomallei levels in the environment could mitigate the risk of infection. Trichoderma asperellum is a biological control agent that synthesizes a diverse range of antimicrobial substances targeting other microorganisms. This study therefore examined the antibacterial and anti-biofilm activities of T. asperellum culture filtrate against B. pseudomallei.MethodsThe antibacterial activities of T. asperellum culture filtrates, collected at various time intervals, were assessed against B. pseudomallei using the agar well diffusion method. Subsequently, the minimum inhibitory concentrations (MICs), minimum bactericidal concentrations (MBCs), and anti-biofilm activities of the culture filtrate exhibiting the highest inhibitory effect were determined. Bactericidal efficacy was further evaluated via a time-kill assay. The mechanisms underlying inhibition were then investigated using scanning electron microscopy and crystal violet uptake assays.ResultsFiltrate collected from 7-day old cultures of T. asperellum (TD7) exhibited the strongest inhibitory effect on B. pseudomallei, with an inhibition zone of 30.33 ± 0.19 mm. The MIC of TD7 against B. pseudomallei was 7.81 ± 0.00 mg/mL and the MBC ranged from 7.81 ± 0.00 to 11.72 ± 1.75 mg/mL. Time-kill studies with TD7 confirmed its bactericidal activity, with complete elimination of B. pseudomallei occurring within 30 min treatment at 62.48 mg/mL (8xMIC) and 24 h treatment at 7.81 mg/mL (1xMIC). At a concentration of  7.81 mg/mL, TD7 also significantly reduced B. pseudomallei biofilm formation. Scanning electron microscopy revealed surface roughening and cell shrinkage of TD7-treated B. pseudomallei. TD7-treated bacteria were also found to absorb more crystal violet dye than untreated cells, indicating that TD7 might inhibit and kill B. pseudomallei by disrupting cell membrane permeability.ConclusionsOur findings demonstrate that T. asperellum culture filtrates possess bactericidal activity and effectively disrupt biofilm formation by B. pseudomallei. This suggests that T. asperellum could potentially be used to reduce the presence of B. pseudomallei in the environment and, consequently, lower the incidence of melioidosis. creator: Naritsara Roopkhan creator: Thotsapol Chaianunporn creator: Sorujsiri Chareonsudjai creator: Kanokporn Chaianunporn uri: https://doi.org/10.7717/peerj.19051 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Roopkhan et al. title: Main complaints identified by parents of children with developmental delays during the initial consultation: a 10-year all-case study link: https://peerj.com/articles/19044 last-modified: 2025-02-28 description: BackgroundIn Japan, the child development support initiative is one of the government’s daycare support programs for children with disabilities. Children, aged 0–6 years, who are not attending elementary school can participate in the initiative and receive various support. Reports on the approaches taken by private child development support centers and the guardians’ perceptions are increasing. Conversely, information from public child development support centers, which serve as places for initial developmental consultation, is extremely scarce. Moreover, there are no nationwide reports on the main complaints from each region, which are of concern to the parents. This study aimed to clarify children’s gender and age, presence of referral sources, and characteristics of the main complaints obtained during the initial consultation with parents of children with developmental delays, who used a public developmental support center in a medium-sized city in Tokyo.MethodsThis study included 1,241 parents of children with developmental delays (average 40.3 months, range 2–87 months). Five questions regarding each child’s characteristics (gender, age in months, and medical diagnosis), referral sources for the use of support centers, and main complaints that they would like to discuss at the initial consultation, were asked. The participants were asked to describe their main complaints (specific consultation details) as precisely as possible. From the free-form descriptions of the main complaints, 137 codes were extracted and grouped into 13 categories. Participants were divided into two groups according to the presence (n = 122) or absence (n = 1,119) of a medical diagnosis. The t-test, chi-square test, and Fisher’s exact probability test were used to examine differences between the two groups. Logistic regression analysis with forced entry was performed to examine whether the factors related to the main complaints raised by parents of children with developmental delays differed depending on the presence or absence of a medical diagnosis.ResultsThe most common chief complaint at the time of the initial consultation was “language development” (43.9%), followed by “childcare and preschool counseling” (15.4%), “hyperactivity/inattention” (13.9%), and “general developmental issues” (13.6%). The regression analysis revealed that gender, age (months), and general developmental issues were factors associated with the presence or absence of a medical diagnosis were gender, age in months, and general developmental issues. The odds ratios (95% confidence intervals) were 1.573 (1.056–2.343) for gender, 0.988 (0.976–1.000) for age (months), and 0.421 (0.200–0.886) for general developmental issues.ConclusionProfessionals involved in child development support are expected to have broad knowledge of various developmental issues as well as comprehensive knowledge of local childcare and schooling systems. creator: Yasuaki Kusumoto creator: Eri Takahashi creator: Kenji Takaki creator: Tadamitsu Matsuda creator: Osamu Nitta uri: https://doi.org/10.7717/peerj.19044 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Kusumoto et al. title: The relationship between renal function indicators and preeclampsia in the second trimester of pregnancy: a retrospective study link: https://peerj.com/articles/19027 last-modified: 2025-02-28 description: BackgroundTo investigate the relationship between serum renal function indicators and preeclampsia (PE) in pregnant women at second trimester of pregnancy, determine the optimal critical values of the above indicators, and further identify the independent risk factors of PE.MethodsWe assessed the renal function indicators in second trimesters of 137 pregnant women with PE and 137 normal pregnant women who delivered at Shijiazhuang Fourth Hospital between January 2020 to December 2022. Paired t-tests, paired Mann-Whitney U tests, and Chi-square tests were used to evaluate differences of clinical data between the two groups. Receiver operating characteristic (ROC) curves was employed to establish the optimal critical values of the above indicators. A 1:1 matched case-control logistic regression analysis was conducted to identify the independent risk factors for PE.ResultsThe levels of serum uric acid and the ratio of serum uric acid to serum creatinine were significantly higher in the PE group compared to the control (P < 0.001), while the serum creatinine levels were higher in control group (P = 0.002). The incidence of adverse maternal (P < 0.001) and neonatal outcomes (P < 0.001) in the PE group were higher than those in the control group. A ROC analysis based on the occurrence of PE showed that the levels of serum uric acid (P < 0.001), serum creatinine (P = 0.006) and the ratio of serum uric acid to serum creatinine (P < 0.001) were statistically significant. After adjusting for confounding factors, elevated serum uric acid (a OR = 1.012, 95% CI [1.005–1.019], P < 0.001) and an increased serum uric acid to serum creatinine ratio (a OR = 1.190, 95% CI [1.053–1.346], P = 0.005) were identified as independent risk factors for PE. There was no significant difference in renal function between maternal and newborn group in relation to the occurrence of adverse outcomes (P > 0.05 vs. all groups).ConclusionsThrough the analysis of renal function indicators in patients with PE in the second trimester of pregnancy and those in a normal control group, it is found that elevated serum uric acid and serum uric acid to serum creatinine ratio in PE individual may serve as indicative markers for the onset of PE. Targeting this subset of the population for monitoring and management during the second trimester could enhance the efficacy of medical interventions. creator: Mingwei Li creator: Wei Liu creator: Xizhenzi Fan creator: Wenhui Song creator: Achou Su creator: Xue Zhang creator: Thomas Zheng creator: Tianxiao Yu uri: https://doi.org/10.7717/peerj.19027 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Li et al. title: Dietary composition and feeding preference of Mantled guereza Colobus guereza (Rüppell, 1835), in Maze National Park, Ethiopia link: https://peerj.com/articles/18998 last-modified: 2025-02-28 description: Knowledge of feeding ecology is essential for effective management of a primate and its habitat. The Mantled guereza Colobus guereza is a predominantly folivorous monkey that occurs in different parts of eastern Africa, including the Maze National Park in Ethiopia. Despite many studies conducted in the area, there is no up-to-date data that was carried out on feeding ecology of the Colobus guereza. The aim of this study is to determine the dietary composition and feeding preference of the Colobus guereza in the park. To better understand this, we randomly selected three study groups along the Maze River. We used instantaneous scan sampling method to collect feeding data from September 2021–August 2022. We followed guerezas from 6:30 to 10:30 in the morning and 13:30 to 17:25 in the afternoon collecting feeding activity data between 5 min intervals during 10-min scan duration. Overall, guerezas were observed to eat eight plant species and unidentified invertebrates in the park. Of these, Trichilia emetica contributed the highest proportion accounted 53.36% and 27.83% in the wet and dry season respectively, while unidentified invertebrates were rarely utilized over the course of this study. We also found that young leaves were consumed more (n = 1,794, 75.31%) in the wet while mature leaves were eaten more (n = 1,215, 43.61%) over the other diet components in the dry season. These results suggest that the guerezas in the park exhibit temporal dietary flexibility. The observed dietary flexibility may be partly due to seasonal changes in availability of food plant parts in the groups’ home ranges in the park. Our results suggest that maintaining the park is critical to protect food plant species for this primate, which at present constitutes only a few. creator: Abraham Tolcha creator: Matewos Masne creator: Belayneh Ayechw uri: https://doi.org/10.7717/peerj.18998 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Tolcha et al. title: Diagnostic accuracy of fat pad sign, X-ray, and computed tomography in elbow trauma: implications for treatment choices—a retrospective study link: https://peerj.com/articles/18922 last-modified: 2025-02-28 description: IntroductionIdentifying skeletal injuries significantly impacts patient outcomes in trauma cases. This study aims to compare the diagnostic accuracy of X-ray (XR) and computed tomography (CT) in detecting elbow fractures among patients presenting at the emergency department (ED). Additionally, the study assesses the potential contribution of the fat pad sign to enhancing the diagnostic accuracy of XR images in identifying elbow fractures. The secondary aim focused on evaluating the precision of XR imaging in determining the necessity for surgical intervention among patients presenting with elbow trauma.MethodsConducted retrospectively at an ED within a secondary hospital, this study included patients with elbow trauma between January 1, 2017, and January 1, 2020, who underwent both XR and CT imaging of the elbow joint. Following the application of exclusion criteria, the analysis comprised 183 patients based on remaining image data.ResultsWhen comparing XR to CT for fracture detection, XR exhibited a sensitivity of 46.9%, specificity of 85.9%, positive predictive value (PPV) of 79.3%, negative predictive value (NPV) of 58.4%, area under the curve (AUC) of 0.664. Considering the fat pad sign in XR as a fracture indicator, the sensitivity is 60.2%, specificity is 81.2%, PPV is 78.7%, NPV is 63.9% and AUC is 0.707. A significant difference was found when comparing the AUCs obtained with and without considering the fat pad sign (p = 0.039). Regarding surgical treatment decision-making, XR showed a sensitivity of 50%, specificity of 100%, PPV of 95%, NPV of 100%, and an AUC of 0.750 when compared to CT.ConclusionThe findings indicate that XR alone is insufficient for detecting elbow fractures and determining the need for surgical treatment. Incorporating the fat pad sign improves the diagnostic accuracy of XR. In cases where suspicion of fracture is high, considering CT imaging is crucial to avoid missed diagnoses, prevent complications, and guide treatment decisions effectively. creator: Mustafa Ahmet Afacan creator: Koray Kaya Kilic creator: Aytun Temiz creator: İsmail Tayfur creator: Fatih Doganay uri: https://doi.org/10.7717/peerj.18922 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Afacan et al. title: Mapping the global distribution and conservation status of oases—ecosystems of pivotal biocultural relevance link: https://peerj.com/articles/18884 last-modified: 2025-02-28 description: BackgroundOases are azonal, highly productive, densely vegetated areas within drylands, often converted to agriculture, and characterized by significant biocultural diversity. Despite their importance, comprehensive information on the global distribution and biocultural diversity of oases has been lacking.MethodsTo address this gap, a detailed bibliographic search and random forest modeling were combined to create a global map of oases, with a focus on Asia and North Africa (ANA).ResultsIn the ANA region, oases cover 1.5% of the dryland area and are populated by 150 million people, with an additional 268 million people living nearby and most likely being dependent on them. Globally, oases contain more than 8,200 vertebrate species, of which 13% are classified as threatened. However, less than 0.5% of their total area is currently under protection, making oases one of the least conserved ecosystems worldwide. These findings highlight the distinct biocultural, ecological, and geopolitical importance of oases, which are increasingly threatened by climate change and direct human impacts. Despite their significance, oases remain undervalued, emphasizing an urgent need for developing adaptative strategies to sustainably manage these pivotal ecosystems. creator: Juan Antonio Hernández-Agüero creator: Mechthilde Falkenhahn creator: Jessica Hetzer creator: Karsten Wesche creator: Christiane Zarfl creator: Klement Tockner uri: https://doi.org/10.7717/peerj.18884 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Hernández-Agüero et al. title: Skin microbiota variation in Indian families link: https://peerj.com/articles/18881 last-modified: 2025-02-28 description: BackgroundIn India, joint families often encompass members spanning multiple generations cohabiting in the same household, thereby sharing the same ethnicity, genetics, dietary habits, lifestyles, and other living conditions. Such an extended family provides a unique opportunity to evaluate the effect of genetics and other confounding factors like geographical location, diet and age on the skin microbiota within and between families across three generations.MethodsThe present study involved seventy-two individuals from fifteen families from two geographical regions of Maharashtra, India. The 16S rRNA sequencing of V3–V4 regions was performed and the generated taxonomic profiles were used for downstream analysis.ResultsOur study highlights a significant difference in community composition (beta diversity) between families (PERMANOVA; p = 0.001) and geographical locations (p = 0.001). We observed geographical location-wise differences in the relative abundances Staphylococcus in the families from Pune (Wilcoxon test, p = 0.007), and Bacillus in the Ahmednagar families (Wilcoxon test, p = 0.004). When within and between-family comparisons of skin microbiota composition were carried out between different generations (G1–G2, G2–G3, and G1–G3); we observed skin microbiota tended to be more similar within than between families but this difference was not significant.ConclusionThis study underscores the diversity and commonalities in skin microbiota composition within and between families. Our result suggests that geographical location is significantly associated with the genus composition of skin microbiota, which is quantitatively unique for a family and likely explained by co-habitation. creator: Renuka Potbhare creator: Ameeta RaviKumar creator: Eveliina Munukka creator: Leo Lahti creator: Richa Ashma uri: https://doi.org/10.7717/peerj.18881 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Potbhare et al. title: Anthropogenic reverberations on the gut microbiome of dwarf chameleons (Bradypodion) link: https://peerj.com/articles/18811 last-modified: 2025-02-28 description: Exploration of the microbiome has been referred to as a final frontier in biological research. This is due to its precedence for generating insights on the holistic functioning of organismal biology by exploring the interactions between hosts and their associated symbiotic organisms. The microbiomes of many vertebrate groups still require exploration to advance current knowledge and fill previous knowledge gaps. This study generated initial descriptions of the bacterial microbiomes of three species of dwarf chameleon (Bradypodion) from the 16S rRNA gene region targeting the V3 and V4 hypervariable regions. This led to the successful identification of 1,073 and 4,502 independent amplicon sequence variants from buccal swab and faecal material samples, respectively. This newly acquired information is intended as a baseline for future work incorporating holobiont information. The diversity of microbial taxa suggests that the total dwarf chameleon microbiome is similar to other squamates investigated to date, as well as chelonians (Testudines). Microbial frequency differences were noted in comparison to crocodilians (Archosauria) and mammalian groups. Furthermore, this study aimed to examine the influence of habitat transformation on the composition of the microbiome in dwarf chameleons as each of the study species occupy both urban and natural habitats. Given that most urban habitats are highly transformed, the expectation was that microbial assemblages of the gastro-intestinal tracts of all three Bradypodion species would show significant differences between populations (i.e., natural, or urban). It was found, however, that the level of effect was contingent on species: B. melanocephalum populations showed noticeable microbiome differences between urban and natural populations; B. thamnobates showed variations in microbial community dispersions between populations; and B. setaroi showed no significant microbiome differences based on diversity metrics although some frequency differences, in microbiome composition, were observed between populations. We suggest that the magnitude of difference between the habitats occupied by the populations is a factor, given the apparent disparity between the natural and urban habitats for B. melanocephalum as compared to the other two species. creator: Matthew G. Adair creator: Krystal A. Tolley creator: Bettine Jansen van Vuuren creator: Jessica Marie da Silva uri: https://doi.org/10.7717/peerj.18811 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Adair et al. title: The Italian version of the extended Barcelona Music Reward Questionnaire (eBMRQ): a validation study and association with age, gender, and musicianship link: https://peerj.com/articles/18403 last-modified: 2025-02-28 description: BackgroundMusic is a primary source of pleasure for humans. Nevertheless, there is large interindividual variability in how individuals experience and derive pleasure from music and music-related activities. With this study we propose and validate the Italian version of the extended Barcelona Music Reward Questionnaire (eBMRQ), the most in-depth and comprehensive tool for investigating the diverse characterization of individual sensitivity to pleasure in music. In addition, we aim to investigate eBMRQ scores as a function of age, gender, and musicianship across Italian population.MethodsFor the validation process of the Italian eBMRQ, we first conducted forward and backward translation from the original English eBMRQ version. The new Italian version was then administered to 1,012 participants who were fluent in Italian from the north and the south of Italy through online surveys (age range 18–86 years old; M = 34.9, SD = 16.9, females 74%). Unrestricted confirmatory analysis was computed for both six-factor and single-factor models. The effect of gender, age, and musicianship on eBMRQ scores was analyzed through analysis of variance (ANOVA).ResultsThe quality assessment of the factor solution indicated that the Italian eBMRQ demonstrated acceptable quality and reliability, making it a valid tool for assessing sensitivity to music reward. All factors were significantly correlated with each other, in line with previous adaptations of the BMRQ. Our findings indicate that females reported higher music reward sensitivity compared to males, except for Social Reward subscale. Moreover, individual reward sensitivity was significantly higher among musicians and amateurs compared to non-musicians, although this trend did not emerge for Sensory-motor and Mood Regulation subscales. Also, overall musical reward sensitivity was negatively associated with age.ConclusionsThe results obtained suggest the feasibility of applying the Italian version of eBMRQ as a reliable tool in the field of affective and clinical music-related research. Furthermore, the significant associations we have highlighted between eBMRQ scores, gender, age, and musicianship contribute to emphasizing the significant impact of individual factors on music reward sensitivity. creator: Giulio Carraturo creator: Laura Ferreri creator: Gemma Cardona creator: Urbano Lorenzo-Seva creator: Antoni Rodriguez-Fornells creator: Elvira Brattico uri: https://doi.org/10.7717/peerj.18403 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Carraturo et al. title: Development and validation of a nomogram predicting multidrug-resistant tuberculosis risk in East China link: https://peerj.com/articles/19112 last-modified: 2025-02-27 description: ObjectiveMultidrug-resistant tuberculosis (MDR-TB) is a global health threat. Our study aimed to develop and externally validate a nomogram to estimate the probability of MDR-TB in patients with TB.MethodsA total of 453 patients with TB in Anhui Chest Hospital between January 2019 and December 2020 were included in the training cohort. In addition, 116 patients with TB from Anhui Provincial Hospital Infection District between January 2015 and November 2023 were included in the validation cohort. Multivariable logistic regression analysis was applied to build a predictive model by combining the feature selected in the least absolute shrinkage and selection operator regression model. The C-index, calibration plot, and decision curve analysis were implemented to evaluate the predictive model’s discrimination, calibration, and clinical practicality. Then, logistic regression and least absolute shrinkage and selection operator (LASSO) models were constructed using R software, and the accuracy, goodness of fit, and stability of the models were verified using the validation cohort.ResultsEight variables of patients with TB were selected using the best penalization parameter of the LASSO regression method, and the nomogram was established. The model displayed good discrimination with a C-index of 0.752 and good calibration. A high C-index value of 0.825 could still be reached in the validation cohort. The decision curve analysis demonstrated the clinical value of the model.ConclusionIn this study, we constructed the LASSO regression model based on eight clinical traits and outcomes of laboratory tests, providing a novel insight for evaluating MDR-TB. creator: Fang He creator: Shu Wang creator: Hua Wang creator: Xing Ding creator: Pengfei Huang creator: Xiaoyun Fan uri: https://doi.org/10.7717/peerj.19112 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 He et al. title: There’s the Rub: a narrative review of the benefits and complications associated with Vicks VapoRub use link: https://peerj.com/articles/19105 last-modified: 2025-02-27 description: BackgroundVicks VapoRub (VVR) is a globally popular over-the-counter remedy marketed for use as a topical antitussive and analgesic. This review seeks to provide health professionals and care providers with a thorough summary of the benefits and complications associated with VVR use reported in the medical literature, identify off-label consumer behaviors that might increase the risk of health complications, and encourage further research into over-the-counter (OTC) medications.MethodsThree databases—PubMed, Web of Science, and Embase—aided in creating a pool of 220 studies. For inclusion, studies had to discuss the therapeutic application of VVR in humans or a complication arising from its use.FindingsThirty-seven articles were found to meet inclusion criteria. Nine synthesis groups were created: three groups concern the product’s efficacy in regard to upper respiratory tract infection (URTI) symptom treatment (n = 7), onychomycosis treatment (n = 2), and in the context of wound care (n = 2). Six groups collate case reports that describe VVR-related complications, including VVR-associated lipid pneumonia (n = 11), ocular injury (n = 5), camphor toxicity (n = 5), dermatological conditions (n = 3), psychosis (n = 1), and respiratory distress (n = 1). The evidence around the use of VVR for the treatment of URTI symptoms and onychomycosis is limited and inconclusive. Even more limited cross-sectional data concerns its use in wound care. Many of the complications described in our study (e.g., multi-organ failure, ocular evisceration, severe pneumonia) involve product misuse. This review was designed to help guide patients on the safe and appropriate use of VVR (e.g., advising patients to avoid heating, ingesting, or intranasal/intrabuccal/ocular application of the product). In general, the severity of complications associated with misuse of VVR highlights the importance of complementary and alternative medicine disclosure and discussion. creator: Austin Valido creator: Ana Carolina Boncompagni creator: Michelle Tsang creator: Patricia Hume uri: https://doi.org/10.7717/peerj.19105 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Valido et al. title: Association between psychosocial stressors and temporomandibular disorders in clinical dental students: a cross-sectional study link: https://peerj.com/articles/19066 last-modified: 2025-02-27 description: BackgroundTemporomandibular disorders (TMDs) comprise an extensive spectrum of conditions that originate from diverse complex components of the temporomandibular joint. It is generally acknowledged that the biopsychosocial model is the preeminent framework for understanding the aetiology of TMDs. Anxiety, depression, and tension are among the psychological disorders that are commonly observed in dental students. The current research probed the propinquity of psychosocial stressors and TMD-like symptoms among clinical dental undergraduates residing in the Aseer region of Saudi Arabia, with a specific emphasis on the functional implications for their overall well-being.MethodsThis research included 89 clinical dentistry students who completed online questionnaires. The Patient-Reported Outcomes Measurement Information System (PROMIS) and Oral Health Impact Profile for Temporomandibular Disorders (OHIP-TMD) were used in these surveys. The trait-related attributes of TMD impacting the oral health profile were assessed using principal component analysis. Demographic factors for anxiety and TMD were examined using linear regression. The psychosocial and functional variables of the OHIP-TMD were compared with those of anxiety in the general regression system.ResultsThe mean Oral Health Impact Profile (OHIP) value was 0.60, with a standard deviation of 0.61, indicating that the majority of respondents reported no or infrequent impacts on their oral health profile. Gender was a significant predictor of OHIP scores (P < 0.05), with females reporting higher scores. Despite these higher scores among females, the overall impact on oral health remained minimal for most respondents. The average PROMIS score was 11.12, with a standard deviation of 3.84. The PROMIS regression analysis on demographic variables yielded an R2 value of 0.092, F(4,78) = 5.691, with significance at P < 0.05. Gender emerged as the most significant predictor of PROMIS scores (P < 0.05), with females reporting higher scores. Once again, despite the higher scores among females, the overall impact remained low for most respondents. An analysis using a general linear model revealed a significant correlation between heightened anxiety levels and an increase in both psychosocial problems and physical function.ConclusionAlthough the majority of respondents reported minimal impacts on their oral health, anxiety remained a significant issue among female clinical dentistry students at the College of Dentistry in Aseer Province, Kingdom of Saudi Arabia. This anxiety was closely linked with psychological distress and impaired oral physical function. Beyond the realm of dental health, anxiety also had a profound effect on academic performance and student engagement. Therefore, addressing student anxiety is essential for enhancing overall well-being and academic success. creator: Abdullah Alqarni creator: Jagadish Hosmani creator: Saeed Alassiri creator: Ali Mosfer A. Alqahtani creator: Ali Alfaifi creator: Shuayl Abdulaziz Al Jazea uri: https://doi.org/10.7717/peerj.19066 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Alqarni et al. title: Development of a prognostic model based on the ceRNA network in Triple-Negative Breast cancer link: https://peerj.com/articles/19063 last-modified: 2025-02-27 description: BackgroundTriple-negative breast cancer (TNBC) is an aggressive subtype with a poor prognosis. Although circular RNAs (circRNAs) have been implicated in cancer progression, their roles in TNBC remain poorly understood. In this study, we aimed to develop a prognostic model for TNBC by constructing a competing endogenous RNA (ceRNA) network. This network integrates circRNAs, long noncoding RNAs (lncRNAs), microRNAs (miRNAs), and messenger RNAs (mRNAs) to identify potential biomarkers and therapeutic targets for improving clinical outcomes.MethodsDifferentially expressed circRNAs, lncRNAs, and mRNAs were identified from GEO datasets (144 samples: 94 TNBC and 50 normal tissues). A ceRNA network was constructed, and key genes were validated using The Cancer Genome Atlas (TCGA) dataset (115 TNBC and 113 para-cancer tissues). Multivariate Cox regression analysis was performed to develop a prognostic model, and Gene Set Enrichment Analysis (GSEA) was performed to identify associated pathways.ResultsNine genes (SH3BGRL2, CA12, LRP8, NAV3, GFRA1, DCDC2, CDC7, ABAT, NPTX1) were identified as key factors in the prognostic model, which demonstrated an area under the curve (AUC) of 0.90. Patients classified as high-risk patients exhibited significantly shorter overall survival (median OS: 8.12 years vs. 9.51 years, P < 0.01). The mitogen-activated protein kinase (MAPK) signaling pathway was identified as a key regulatory pathway, with circRNAs (hsa_circ_0005455, hsa_circ_000632, hsa_circ_0001666, and hsa_circ_0000069) regulating CA12, GFRA1, and NPTX1 expression.ConclusionThis study developed a novel prognostic model based on a ceRNA network analysis, highlighting the critical role of circRNAs and the MAPK signaling pathway in TNBC progression. These findings offer valuable insights into potential biomarkers for TNBC prognosis and reveal promising therapeutic targets for improving patient outcomes. creator: Yimin Zhu creator: Jiayu Wang creator: Binghe Xu uri: https://doi.org/10.7717/peerj.19063 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhu et al. title: Neuropeptides from a praying mantis: what the loss of pyrokinins and tryptopyrokinins suggests about the endocrine functions of these peptides link: https://peerj.com/articles/19036 last-modified: 2025-02-27 description: BackgroundNeuropeptides play important roles in insects, but in many cases their functions remain obscure. Comparative neuropeptidome analyses may provide clues to what these functions might be. Praying mantises are predators and close relatives of cockroaches that are scavengers. Cockroach neuropeptidomes are well established, but little is known about mantis neuropeptides. The recently published genome assembly of the praying mantis Tenodera sinensis makes it Possible to change that.MethodsThe genome assembly from T. sinensis was analyzed for the presence of genes coding neuropeptides. For comparison, publicly available short read archives from this and other mantis species were also examined for the presence and expression of neuropeptides.ResultsAs a rule, the neuropeptidomes of the Mantodea and Blattodea are almost identical; praying mantises and cockroaches use very similar neuropeptides. However, there is one surprising exception. Praying mantises lack the receptors for pyrokinins, including those for the tryptopyrokinins. No typical pyrokinin genes were found, but some species do have a tryptopyrokinin gene, in others this has also been lost and, in one species it is a speudogene. For most praying mantises there is no information where tryptopyrokinin is expressed, but in Deroplatys truncata it is in the thorax and thus not in the suboesophageal ganglion, as in other insects. In the genomic short read archives of two species–out of 52–sequences were found for a tryptopyrokinin specific receptor. The phylogenetic position of those two species implies that the receptor gene was independently lost on multiple occasions. The loss of the tryptopyrokinin gene also happened more than once.DiscussionThe multiple independent losses of the pyrokinin receptors in mantises suggests that these receptors are irrelevant in praying mantises. This is very surprising, since expression of tryptopyrokinin is very strongly conserved in two neuroendocrine cells in the suboeosphageal ganglion. In those species for which this is known, the expression of its receptor is in the salivary gland. As a neuroendocrine, tryptopyrokinin is unlikely to acutely regulate salivation, which in other insects is regulated by well characterized neurons. If the action of tryptopyrokinin were to prime the salivary gland for subsequent salivation, it would make perfect sense for a praying mantis to lose this capacity, as they can not anticipate when they will catch their next prey. Priming the salivary gland days before it is actually needed would be energetically costly. The other pyrokinins are known to facilitate feeding and may in a similar fashion prime muscles needed for moving to the food source and digesting it. This hypothesis provides a good explanation as to why praying mantises do not need pyrokinins, and also what the function of these ubiquitous arthropod neuropeptides may be. creator: Jan A. Veenstra uri: https://doi.org/10.7717/peerj.19036 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Veenstra title: Exploring molecular variation and combining ability of local and exotic bread wheat genotypes under well-watered and drought conditions link: https://peerj.com/articles/18994 last-modified: 2025-02-27 description: Drought is one of the most environmental stressors, significantly affecting wheat production, particularly in the face of accelerating climate change. Therefore, developing drought-resistant, high-yielding wheat varieties is essential to ensure sustainable production and maintain global food security as the world population rapidly grows. This study aimed to evaluate the genetic variation of local and imported bread wheat genotypes through simple sequence repeat (SSR) markers and assess their combining ability to identify top-performing genotypes under both normal and drought-stress environments. SSR markers revealed significant genetic diversity among the parental genotypes, which were utilized to develop 28 F1 crosses utilizing diallel mating design. Field trials under well-watered and drought-stressed environments demonstrated that drought significantly reduced all measured agronomic traits. The genotypes were categorized into five clusters based on their drought tolerance, ranging from highly sensitive (group-E) to robustly drought-resistant (group-A). The local variety Sids-12 (P2) was identified as an excellent combiner for breeding shorter and early-maturing cultivars and Line-117 (P3), Line-144 (P4), and Line-123 (P5) for improving grain yield and related traits under drought conditions. The crosses P1×P5, P3×P8, P4×P5, and P6×P7 possessed superior performance under both conditions. Key traits, including plant height, grains per spike, 1,000-grain weight, and spikes per plant, displayed strong correlations with grain yield, providing an effective approach for indirect selection in drought-prone environments. creator: Mohamed I. Motawei creator: Mohamed M. Kamara creator: Medhat Rehan uri: https://doi.org/10.7717/peerj.18994 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Motawei et al. title: A nicotinamide metabolism-related gene signature for predicting immunotherapy response and prognosis in lung adenocarcinoma patients link: https://peerj.com/articles/18991 last-modified: 2025-02-27 description: BackgroundNicotinamide (NAM) metabolism fulfills crucial functions in tumor progression. The present study aims to establish a NAM metabolism-correlated gene (NMRG) signature to assess the immunotherapy response and prognosis of lung adenocarcinoma (LUAD).MethodsThe training set and validation set (the GSE31210 dataset) were collected The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO), respectively. Molecular subtypes of LUAD were classified by consensus clustering. Mutation landscape of the top 20 somatic genes was visualized by maftools package. Subsequently, differential expression analysis was conducted using the limma package, and univariate, multivariate and LASSO regression analyses were performed on the screened genes to construct a risk model for LUAD. Next, the MCP-counter, TIMER and ESTIMATE algorithms were utilized to comprehensively assess the immune microenvironmental profile of LUAD patients in different risk groups. The efficacy of immunotherapy and chemotherapy drugs was evaluated by TIDE score and pRRophetic package. A nomogram was created by integrating RiskScore and clinical features. The mRNA expressions of independent prognostic NMRGs and the migration and invasion of LUAD cells were measured by carrying out cellular assays.ResultsTwo subtypes (C1 and C2) of LUAD were classified, with C1 subtype showing a worse prognosis than C2. The top three genes with a high mutation frequency in C1 and C2 subtypes were TTN (45.25%), FLG (25.25%), and ZNF536 (19.8%). Four independent prognostic NMRGs (GJB3, CPA3, DKK1, KRT6A) were screened and used to construct a RiskScore model, which exhibited a strong predictive performance. High-risk group showed low immune cell infiltration, high TIDE score, and worse prognosis, and the patients in this group exhibited a high drug sensitivity to Cisplatin, Erlotinib, Paclitaxel, Saracatini, and CGP_082996. A nomogram was established with an accurate predictive and diagnostic performance. GJB3, DKK1, CPA3, and KRT6A were all high- expressed in LUAD cells, and silencing GJB3 inhibited the migration and invasion of LUAD cells.ConclusionA novel NMRG signature was developed, contributing to the prognostic evaluation and personalized treatment for LUAD patients. creator: Meng Wang creator: Wei Li creator: Fang Zhou creator: Zheng Wang creator: Xiaoteng Jia creator: Xingpeng Han uri: https://doi.org/10.7717/peerj.18991 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Wang et al. title: Climate change and tree cover loss affect the habitat suitability of Cedrela angustifolia: evaluating climate vulnerability and conservation in Andean montane forests link: https://peerj.com/articles/18799 last-modified: 2025-02-27 description: BackgroundBecause of illegal logging, habitat fragmentation, and high value timber Andean montane forest Cedrela species (such as Cedrela angustifolia), is endangered in Central and South America. Studying the effects of climate change and tree cover loss on the distribution of C. angustifolia will help us to understand the climatic and ecological sensitivity of this species and suggest conservation and restoration strategies.MethodsUsing ecological niche modeling with two algorithms (maximum entropy (MaxEnt) and Random Forest) under the ecological niche conservatism approach, we generated 16,920 models with different combinations of variables and parameters. We identified suitable areas for C. angustifolia trees under present and future climate scenarios (2040, 2070, and 2100 with SSP 3-7.0 and SSP 5-8.5), tree cover loss, and variables linked to soil and topography.ResultsOur results demonstrated 10 environmental variables with high percentage contributions and permutation importance; for example, precipitation seasonality exhibited the highest contribution to the current and future distribution of Cedrela angustifolia. The potential present distribution was estimated as 13,080 km2with tree cover loss and 16,148.5 km2without tree cover loss. From 2040 to 2100 the species distribution will decrease (from 22.16% to 36.88% with tree cover loss variation). The results indicated that Bolivia displayed higher habitat suitability than Ecuador, Peru, and Argentina. Finally, we recommend developing conservation management strategies that consider both protected and unprotected areas as well as the impact of land-use changes to improve the persistence of C. angustifolia in the future. creator: Fressia N. Ames-Martínez creator: Ivan Capcha Romero creator: Anthony Guerra creator: Janet Gaby Inga Guillen creator: Harold Rusbelth Quispe-Melgar creator: Esteban Galeano creator: Ernesto C. Rodríguez-Ramírez uri: https://doi.org/10.7717/peerj.18799 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ames-Martínez et al. title: Leveraging diverse cell-death patterns in diagnosis of sepsis by integrating bioinformatics and machine learning link: https://peerj.com/articles/19077 last-modified: 2025-02-26 description: BackgroundSepsis is a life-threatening disease causing millions of deaths every year. It has been reported that programmed cell death (PCD) plays a critical role in the development and progression of sepsis, which has the potential to be a diagnosis and prognosis indicator for patient with sepsis.MethodsFourteen PCD patterns were analyzed for model construction. Seven transcriptome datasets and a single cell sequencing dataset were collected from the Gene Expression Omnibus database.ResultsA total of 289 PCD-related differentially expressed genes were identified between sepsis patients and healthy individuals. The machine learning algorithm screened three PCD-related genes, NLRC4, TXN and S100A9, as potential biomarkers for sepsis. The area under curve of the diagnostic model reached 100.0% in the training set and 100.0%, 99.9%, 98.9%, 99.5% and 98.6% in five validation sets. Furthermore, we verified the diagnostic genes in sepsis patients from our center via qPCR experiment. Single cell sequencing analysis revealed that NLRC4, TXN and S100A9 were mainly expressed on myeloid/monocytes and dendritic cells. Immune infiltration analysis revealed that multiple immune cells involved in the development of sepsis. Correlation and gene set enrichment analysis (GSEA) analysis revealed that the three biomarkers were significantly associated with immune cells infiltration.ConclusionsWe developed and validated a diagnostic model for sepsis based on three PCD-related genes. Our study might provide potential peripheral blood diagnostic candidate biomarkers for patients with sepsis. creator: Mi Liu creator: Xingxing Gao creator: Hongfa Wang creator: Yiping Zhang creator: Xiaojun Li creator: Renlai Zhu creator: Yunru Sheng uri: https://doi.org/10.7717/peerj.19077 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Liu et al. title: Trueness and precision of complete denture digital impression compared to conventional impression: an in vitro study link: https://peerj.com/articles/19075 last-modified: 2025-02-26 description: BackgroundThis study aimed to compare the precision and trueness of digital impressions of the edentulous arch made with different scanners to conventional physical impressions.MethodsA total of 40 impressions of a completely edentulous maxillary arch model (n = 10) were made using different digital impressions with an extraoral scanner, E3 3Shape desktop scanner, as the reference scan, intraoral scanner (TRIOS IOS, and Medit IOS) and Vinyl Polysiloxane impressions (VPS) impression using a Computer-Aided Design and Computer-Aided Manufacturing (CAD-CAM) custom tray. The VPS impression was scanned with the desktop scanner to produce standard tessellation language (STL) files for comparison with the digital impressions made by the Desktop and intraoral scanners. The STL files were super-imposed to a desktop scan and to each other with the same group using Geomagic Control X Software to assess the trueness and precision, respectively. A t-test was conducted for statistical analysis with a significance level of 0.05.ResultsThe overall trueness, Medit had the highest deviation compared to the VPS and TRIOS groups with a P value of 0.0013 and <0.0001, respectively. In terms of overall precision, TRIOS had a lower deviation than the VPS group, with a P value of 0.0002. The TRIOS and Medit groups had statistically comparable results. The desktop scanner showed the highest precision in digitizing completely edentulous cases, followed by the TRIOS scanner. The Medit scanner’s trueness had the highest deviation compared to the VPS and TRIOS groups. creator: Yousif A. Al-Dulaijan creator: Haidar Alalawi creator: Mohammed M. Gad creator: Faisal D. Al-Qarni creator: Shaimaa M. Fouda creator: Passent Ellakany uri: https://doi.org/10.7717/peerj.19075 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Al-Dulaijan et al. title: Impact of online support of physical activity management using a wearable device on renal function in patients with acute coronary syndrome: a randomized controlled trial protocol link: https://peerj.com/articles/19067 last-modified: 2025-02-26 description: BackgroundAcute coronary syndromes (ACS) often cause rapid decline in renal and cardiac function. In patients with ACS, combined renal dysfunction is associated with increased overall mortality and cardiovascular events. Physical activity (PA) management may crucially contribute towards protection of renal function in patients with ACS. This article describes the study protocol of a randomized controlled trial (RCT) assessing whether online support for PA management using wearable devices and information communication technology for patients with ACS facing difficulties in participating in outpatient cardiac rehabilitation after discharge can protect renal function following disease onset.MethodsWe have designed a two-arm RCT with a 3-month follow-up period. The online support intervention incorporates monitoring of PA, pulse rate, and blood pressure using a wearable device with an accelerometer and a web application system, as well as periodic educational feedback and goal setting. The primary study endpoint is the estimated glomerular filtration rate based on serum cystatin C (eGFRcys). The intervention effect will be assessed using the eGFRcys at 3 months adjusted for baseline values. The secondary endpoints are the urine albumin/creatinine ratio, brain natriuretic peptide levels, average step count, peak oxygen uptake, quality of life, and incidence of adverse events.DiscussionThis RCT will provide evidence regarding the effectiveness of online support for PA management as a renal protection strategy following ACS onset. This novel strategy not only mitigates barriers impeding participation in outpatient cardiac rehabilitation and protects cardiac and renal function in patients with ACS, but also may contribute towards improving survival and recurrence rates, preventing dialysis, and reducing medical and long-term care costs.Trial registration:The trial was registered in the Japan Registry of Clinical Trials on July 5, 2024. The registration number is jRCT1022240014 (Impact of Online Support of Physical Activity Management Using a Wearable Device on Renal Function in Patients with Acute Coronary Syndrome). creator: Toshimi Sato creator: Daisuke Suzuki creator: Yuichiro Sasamoto creator: Masahiro Ono creator: Namiko Shishito creator: Kohko Kanazawa creator: Akihito Watanabe creator: Koichi Naito creator: Shinichiro Morishita creator: Masahiro Kohzuki uri: https://doi.org/10.7717/peerj.19067 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Sato et al. title: Exploratory analyses of the associations between Ki-67 expression, lymph node metastasis, and prognosis in patients with esophageal squamous cell cancer link: https://peerj.com/articles/19062 last-modified: 2025-02-26 description: BackgroundThe relationships between Ki-67/MKI67 expression, lymph node metastasis (LNM), vascular invasion (VI), and perineural invasion (PI) in esophageal squamous cell cancer (ESCC) remain unclear. This retrospective cohort study was performed to evaluate the prognostic value of Ki-67 expression and its association with LNM in patients with resected ESCC.MethodsThe analysis included 168 patients with ESCC with available Ki-67 protein expression data. The patients were divided into Ki-67 high-expression group (Ki-67 High, 93 cases) and Ki-67 low-expression (Ki-67 Low, 75 cases) groups. Associations between Ki-67 expression and ESCC pathological features was assessed using chi-square test. Overall survival (OS) was compared between the two groups using Kaplan–Meier survival analysis and Cox proportional hazards model.ResultsMedian follow-up duration was 33.5 months (range 3.0–60.0 months). High Ki-67 expression was significantly associated with poor OS in patients with ESCC compared to that of the low-expression in both univariate (hazard ratios (HR) = 3.42, 95% CI [2.22–5.27], P < 0.001) and multivariate analyses (HR = 1.98, 95% CI [1.33–2.94], P < 0.001). Furthermore, high Ki-67 expression was significantly associated with an increased risk of LNM (χ2 = 11.219, P = 0.011), VI (χ2 = 6.359, P = 0.012), and PI (χ2 = 8.877, P = 0.003).ConclusionsHigh Ki-67 protein expression is associated with poor prognosis in ESCC. Increased Ki-67 expression significantly increases the risk of LNM, VI, and PI in ESCC, and thus may serve as an indication for adjuvant therapy in ESCC management. creator: Jianqing Zheng creator: Bifen Huang creator: Ying Chen creator: Bingwei Zeng creator: Lihua Xiao creator: Min Wu uri: https://doi.org/10.7717/peerj.19062 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zheng et al. title: LTR retrotransposon-derived novel lncRNA2 enhances cold tolerance in Moso bamboo by modulating antioxidant activity and photosynthetic efficiency link: https://peerj.com/articles/19056 last-modified: 2025-02-26 description: In Moso bamboo, the mechanism of long terminal repeat (LTR) retrotransposon-derived long non-coding RNA (TElncRNA) in response to cold stress remains unclear. In this study, several Pe-TElncRNAs were identified from Moso bamboo transcriptome data. qRT-PCR analysis showed that the expression of a novel Pe-TElncRNA2 in Moso bamboo seedlings reached its highest level at 8 hours of cold treatment at 4 °C and was significantly higher in the stems compared to the leaves, roots, and buds. Furthermore, cellular localization analysis revealed that Pe-TElncRNA2 expression was significantly higher in the cytoplasm than in the nucleus. Pe-TElncRNA2 overexpression in Moso bamboo protoplasts showed that Pe-TElncRNA2 positively regulated the expression of FZR2, NOT3, ABCG44 and AGD6 genes. Further validation of this lncRNA in Arabidopsis thaliana enhanced antioxidant activities, as evidenced by increased superoxide dismutase (SOD) activity and proline content, as well as maximum photochemical efficiency PS II in dark-adapted leaves (Fv/Fm), in the transgenic plants compared to the wild-type controls. Conversely, malondialdehyde (MDA) content, a lipid peroxidation marker (a marker of oxidative stress), was significantly reduced in the transgenic plants. Notably, the expression levels of both Pe-TElncRNA2 and the genes that were regulated by this lncRNA were upregulated in the transgenic plants after two days of cold stress treatment. These findings elucidate the critical role of LTR retrotransposon-derived lncRNAs in mediating cold stress responses in Moso bamboo. creator: Jiamin Zhao creator: Yiqian Ding creator: Muthusamy Ramakrishnan creator: Long-Hai Zou creator: Yujing Chen creator: Mingbing Zhou uri: https://doi.org/10.7717/peerj.19056 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Zhao et al. title: Optimal input DNA thresholds for genome skimming in marine crustacean zooplankton link: https://peerj.com/articles/19054 last-modified: 2025-02-26 description: Crustacean zooplanktons are key secondary and tertiary producers in marine ecosystems, yet their genomic resources remain poorly understood. To advance biodiversity research on crustacean zooplankton, this study evaluated the effectiveness of genome skimming, a method that assembles genetic regions, including mitogenome, from shotgun genome sequencing data. Because the small amount of DNA available is a limitation in zooplankton genetics, different input DNA amounts (1 pg–10 ng) were prepared for library construction for genome skimming using two large species: Euphausia pacifica (Euphausiacea) and Calanus glacialis (Copepoda). Additionally, de novo assembly was used to obtain long contigs from short reads because reference-guided assembly can not be applied to all crustacean zooplankton. Evaluation of the raw sequence reads showed increased proportions of high-quality and distinct reads (low duplication levels) for large DNA inputs. By contrast, low sequence quality and high sequence duplication were observed for ≤ 10 pg DNA samples, owing to increased DNA amplification cycles. Complete mitogenomes, including all 37 genes, were successfully retrieved for ≥ 10 pg (E. pacifica) and ≥ 100 pg (C. glacialis) of DNA. Despite the large estimated genome sizes of these zooplankton species, only ≥ 1 and ≥ 3 M reads were sufficient for mitogenome assembly for E. pacifica and C. glacialis, respectively. Nuclear ribosomal repeats and histone 3 were identified in the assembled contigs. As obtaining sufficient DNA amounts (≥ 100 pg) is feasible even from small crustacean zooplankton, genome skimming is a powerful approach for robust phylogenetics and population genetics in marine zooplankton. creator: Junya Hirai uri: https://doi.org/10.7717/peerj.19054 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Hirai title: Assessment of urinary oxidative stress biomarkers associated with fine particulate matter (PM2.5) exposure in Chiang Mai, Thailand link: https://peerj.com/articles/19047 last-modified: 2025-02-26 description: BackgroundExposure to fine particulate matter (PM2.5) is known to increase oxidative stress, impacting health adversely. This study examines the relationship between PM2.5 exposure and oxidative stress biomarkers in Chiang Mai, Thailand.MethodsA pilot prospective observational study was conducted in Samoeng District, Chiang Mai, including 25 healthy participants (age 25–60 years). Urine samples were collected during high (March–April 2023) and low (May–July 2023) PM2.5 seasons. PM2.5 concentrations were monitored daily from the Northern Thailand Air Quality Health Index (NTAQHI) system. Biomarkers analyzed included 1-hydroxypyrene (1-OHP) using high-performance liquid chromatography (HPLC), malondialdehyde (MDA) via Spectrophotometry, and 8-epi-prostaglandin F2α (8-epi-PGF2α) with Enzyme-linked Immunosorbent Assay (ELISA). Statistical analysis was performed using IBM SPSS Statistics 22.0.ResultsSignificant increases in urinary 1-OHP, MDA, and 8-epi-PGF2α were observed during the high PM2.5 season compared to the low season. The mean concentration of PM2.5 was 67 µg/m3 during high pollution and 7 µg/m3 during low pollution. Elevated levels of these biomarkers indicate increased oxidative stress associated with higher PM2.5 exposure.ConclusionsThis study highlights a significant association between elevated PM2.5 levels and increased oxidative stress biomarkers in Chiang Mai, Thailand. The findings suggest that exposure to higher concentrations of PM2.5 contributes to oxidative stress, potentially leading to adverse health outcomes. creator: Shamsa Sabir creator: Surat Hongsibsong creator: Hataichanok Chuljerm creator: Wason Parklak creator: Sakaewan Ounjaijean creator: Puriwat Fakfum creator: Sobia Kausar creator: Kanokwan Kulprachakarn uri: https://doi.org/10.7717/peerj.19047 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Sabir et al. title: Association of Chinese visceral adiposity index with asymptomatic hyperuricemia incidence in type 2 diabetes: a cross-sectional study link: https://peerj.com/articles/19045 last-modified: 2025-02-26 description: BackgroundPrevious research has shown a correlation between high visceral fat levels and hyperuricemia incidence. The Chinese Visceral Adiposity Index (CVAI) assessed visceral fat status in the Chinese population. Our study investigates the correlation between CVAI and asymptomatic hyperuricemia in type 2 diabetes patients.MethodsThis cross-sectional study analyzed 1,588 hospitalized type 2 diabetes patients to investigate the association between CVAI and hyperuricemia. CVAI was included in the logistic regression analysis as both a continuous and categorical variable, and restricted cubic splines were used to assess the dose-response relationship. Additionally, subgroup analyses were performed to investigate potential interactions among variables. The predictive capability of CVAI was assessed using the receiver operating characteristic (ROC) curve based on the basic model.ResultsThe CVAI quartile group analysis revealed a higher prevalence of hyperuricemia with increasing CVAI levels. CVAI is significantly associated with hyperuricemia, as identified through multifactorial logistic regression analysis. After adjusting for all covariates, the odds ratios for CVAI in the second, third, and fourth quartiles were significantly higher than in the lowest quartile, with values of 2.688 (95% CI [1.301–5.554], p = 0.008), 2.752 (95% CI [1.320–5.739], p = 0.007), and 4.990 (95% CI [2.392–10.409], p < 0.001), respectively. No significant interactions were observed in the subgroup analysis. Incorporating CVAI into the basic model increased the ROC curve’s area under the curve to 0.714.ConclusionThis study found a positive correlation between CVAI and hyperuricemia incidence in type 2 diabetes patients. Consequently, CVAI may reliably indicate hyperuricemia in this patient population. creator: Qing Wang creator: Tian Liu creator: Changxin Jia creator: Ping Wang creator: Yangang Wang creator: Qing He uri: https://doi.org/10.7717/peerj.19045 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Wang et al. title: Prognostic nutritional index (PNI) as an influencing factor for in-hospital mortality in patients with stroke-associated pneumonia: a retrospective study link: https://peerj.com/articles/19028 last-modified: 2025-02-26 description: BackgroundStroke-associated pneumonia (SAP) significantly increases patients’ risk of death after stroke. The identification of patients at high risk for SAP remains difficult. Nutritional assessment is valuable for risk identification in stroke patients. The aim of this study was to evaluate the relationship between prognostic nutritional index (PNI) levels and in-hospital mortality in SAP patients.MethodsA total of 336 SAP patients who visited the Third People’s Hospital of Chengdu from January 2019 to December 2023 were included in this study, and PNI were calculated based on the results of admission examinations. Linear regression was used to analyze the influencing factors of baseline PNI in SAP patients. Logistic regression as well as restricted cubic splines (RCS) were used to analyze the relationship between baseline PNI levels and hospital mortality events in SAP patients. Receiver operating characteristic (ROC) curves were plotted to assess the predictive value of PNI for in-hospital mortality by area under the curve (AUC).ResultsThirty out of 336 SAP patients presented with in-hospital mortality and these patients had significantly lower PNI levels. In our study, PNI levels were influenced by age, body mass index, and total cholesterol. Increased PNI levels are an independent protective factor for the risk of in-hospital mortality in SAP patients (OR: 0.232, 95% CI [0.096–0.561], P = 0.001). There was a nonlinear correlation between PNI and in-hospital mortality events (P for nonlinear <0.001). In terms of predictive effect, PNI levels were more efficacious in predicting in-hospital mortality in SAP patients with higher sensitivity and/or specificity compared to individual indicators (AUC = 0.750, 95% CI [0.641–0.860], P < 0.001).ConclusionPNI levels in SAP patients were associated with the short-term prognosis of patients, and SAP patients with elevated PNI levels had a reduced risk of in-hospital mortality. creator: Ke Xie creator: Chuan Zhang creator: Shiyu Nie creator: Shengnan Kang creator: Zhong Wang creator: Xuehe Zhang uri: https://doi.org/10.7717/peerj.19028 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Xie et al. title: Effects of larval foam-making and prolonged terrestriality on morphology, nitrogen excretion and development to metamorphosis in a Leptodactylid frog link: https://peerj.com/articles/18990 last-modified: 2025-02-26 description: At ontogenetic transitions, animals often exhibit plastic variation in development, behavior and physiology in response to environmental conditions. Most terrestrial-breeding frogs have aquatic larval periods. Some species can extend their initial terrestrial period, as either a plastic embryonic response to balance trade-offs across environments or an enforced wait for rain that allows larvae to access aquatic habitats. Terrestrial larvae of the foam-nesting frog, Leptodactylus fragilis, can arrest development, make their own nest foam to prevent dehydration, and synthesize urea to avoid ammonia toxicity. These plastic responses enable survival during unpredictably long periods in underground nest chambers, waiting for floods to enable exit and continued development in water. However, such physiological and behavioral responses may have immediate and long-term carry-over effects across subsequent ecological and developmental transitions. We examined effects of prolonged terrestriality and larval foam-making activity on larval physiology, development, and metamorphosis in L. fragilis. We tested for changes in foam-making ability by measuring the nests larvae produced following complete removal of parental foam at different ages. We measured ammonia and urea levels in larval foam nests to assess nitrogen excretion patterns, testing for effects of larval age, soil hydration around parental nests, and repeated nest construction. We also assessed immediate and long-term effects of larval foam-making and prolonged terrestriality on larval morphology at water entry and development to metamorphosis. We found that larvae arrested development during prolonged time on land and even young larvae were able to effectively produce multiple foam nests. We found high ammonia concentrations in larval nests, very high urea excretion by developmentally arrested older larvae, and faster growth of larvae in water than while constructing nests. Nonetheless, sibling larvae had a similar aquatic larval period and size at metamorphosis, regardless of their nest-making activity and timing of water entry. Sibship size increased the size of larval foam nests, but reduced per-capita foam production and increased size at metamorphosis, suggesting maternal effects in cooperative groups. Metamorph size also decreased with aquatic larval period. Our results highlight the extent of larval ability to maintain and construct a suitable developmental environment and excrete N-waste as urea, which are both crucial for survival during enforced extensions of terrestriality. Our results suggest that the energetic reserves in large eggs are sufficient to meet metabolic costs of urea synthesis and foam production during developmental arrest over an extended period on land, with no apparent carry-over effects on fitness-relevant traits at metamorphosis. creator: Javier Méndez-Narváez creator: Karen M. Warkentin uri: https://doi.org/10.7717/peerj.18990 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Méndez-Narváez and Warkentin title: Shoe configuration effects on equine forelimb gait kinetics at a walk link: https://peerj.com/articles/18940 last-modified: 2025-02-26 description: The shift in vertical forces on the equine hoof surface by heart-bar, egg-bar, and wooden clog shoes can significantly impact gait kinetics. Hypotheses tested in this study were that vertical, braking, and propulsion peak force (PF) and impulse (IMP) are different while shod with heart-bar, egg-bar, open-heel, and wooden clog shoes, or while unshod, and the resultant ground reaction force vector (GRFYZ) has the longest duration of cranial angulation with open-heel shoes followed by unshod, then egg-bar and heart-bar shoes, and the shortest with wooden clog shoes. Forelimb GRFs were recorded as six non-lame, light-breed horses walked across a force platform (four trials/side) while unshod or with egg-bar, heart-bar, open-heel, or wooden clog shoes. Outcomes included vertical, braking, and propulsive peak forces (PFV, PFB, PFP) and impulses (IMPV, IMPB, IMPP), percent stance time to each PF, braking to vertical PF ratio (PFB/PFV), walking speed (m s−1), total stance time (ST) and percent of stance in braking and propulsion. The magnitude and direction of the resultant GRFYZ vectors were quantified at 5% stance increments. Kinetic measures were compared among shoeing conditions with a mixed effects model (p-value < 0.05). A random forest classifier algorithm was used to predict shoeing condition from kinetic outcome measures. All results are reported as mean ± SEM. Trial speed, 1.51 ± 0.02 m s−1, was not different among shoeing conditions. The PFV was lower with wooden clog (6.13 ± 0.1 N kg−1) versus egg-bar (6.35 ± 0.1 N kg−1) shoes or unshod (6.32 ± 0.1 N kg−1); the PFP was higher with wooden clog (0.81 ± 0.03 N kg−1) versus open-heel (0.71 ± 0.03 N kg−1) or egg-bar (0.75 ± 0.03 N kg−1) shoes or unshod (0.74 ± 0.03 N kg−1), and lower with open-heel compared to heart-bar shoes (0.77 ± 0.03 N kg−1). Both IMP B and IMPV were higher with open-heel shoes (−0.19 ± 0.008 N s kg−1, 3.28 ± 0.09 N s kg−1) versus unshod (−0.17 ± 0.008 N s kg−1, 3.16 ± 0.09 N s kg−1), and IMPV was higher with wooden clog shoes (3.26 ± 0.09 N s kg−1) versus unshod. With wooden clog shoes, PFB/PFV (0.12 ± 0.004) was higher than unshod (0.11 ± 0.004). Percent time to peak PFV, PFB, and PFP, and percent braking time were highest and percent propulsion time lowest with wooden clog shoes. The magnitude of the GRFYZ vector with the wooden clog shoe was the highest among shoeing conditions during the first stance half, lowest during the second stance half, highest during late propulsion, and had the most gradual braking to propulsion transition. Vectors were angled cranially with wooden clog shoes slightly longer than the others. Wooden clog shoes was the only shoeing condition accurately predicted from kinetic measures. Distinct, predictable changes in gait kinetics with wooden clog shoes may reduce stresses on hoof structures. Study results enhance knowledge about shoe effects on equine gait kinetics and cutting-edge measures to quantify them. creator: Rita Aoun creator: Zaneta Ogunmola creator: Anaïs Musso creator: Takashi Taguchi creator: Catherine Takawira creator: Mandi J. Lopez uri: https://doi.org/10.7717/peerj.18940 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Aoun et al. title: Development and validation of a prognostic nomogram for predicting poor outcomes following intravenous rt-PA in patients with acute ischemic stroke link: https://peerj.com/articles/18937 last-modified: 2025-02-26 description: BackgroundIntravenous administration of recombinant tissue plasminogen activator (rt-PA) within 4.5 h of symptom onset is a standard treatment for acute ischemic stroke (AIS). However, certain patients continue to develop unfavorable outcomes despite timely rt-PA therapy. Identifying those at high risk is essential for developing individualized care plans and establishing appropriate follow-up.MethodsThis retrospective study included AIS patients treated with intravenous rt-PA at 0.9 mg/kg at our center. Outcomes at three months were evaluated using the modified Rankin Scale (mRS). Patients with mRS scores ≤2 were considered to have favorable outcomes, and those with scores >2 were considered to have poor outcomes. Univariable analysis and stepwise logistic regression were used to identify independent predictors of poor prognosis, and a nomogram was subsequently developed. The model’s discriminative power was assessed with area under the receiver operating characteristic curves (AUC-ROC), and its calibration was examined using calibration plots. Decision curves and clinical impact curves were applied to determine clinical utility.ResultsAmong 392 enrolled patients, 77 had poor outcomes three months after rt-PA therapy. Fibrinogen (Fg), baseline NIHSS, and a history of hypertension emerged as independent predictors of poor prognosis. The nomogram achieved an AUC of 0.948 (95% CI [0.910–0.985]), with sensitivity of 0.900 and specificity of 0.916 in the training dataset, and an AUC of 0.959 (95% CI [0.907–1.000]), with sensitivity of 0.943 and specificity of 0.947 in the validation dataset. Calibration plots demonstrated close agreement between predicted and observed probabilities, and decision curves indicated a wide range of net benefit threshold probabilities.ConclusionsThis nomogram, incorporating baseline NIHSS, Fg, and a history of hypertension, accurately predicts poor three-month outcomes in AIS patients treated with intravenous rt-PA. Its ease of use may facilitate early risk stratification and assist clinicians in formulating more targeted management strategies and follow-up protocols for patients likely to experience unfavorable outcomes. creator: Fengjiao Zhang creator: Dan Zhao creator: Jing Zhang uri: https://doi.org/10.7717/peerj.18937 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhang et al. title: Deep-learning tool for early identification of non-traumatic intracranial hemorrhage etiology and application in clinical diagnostics based on computed tomography (CT) scans link: https://peerj.com/articles/18850 last-modified: 2025-02-26 description: BackgroundTo develop an artificial intelligence system that can accurately identify acute non-traumatic intracranial hemorrhage (ICH) etiology (aneurysms, hypertensive hemorrhage, arteriovenous malformation (AVM), Moyamoya disease (MMD), cavernous malformation (CM), or other causes) based on non-contrast computed tomography (NCCT) scans and investigate whether clinicians can benefit from it in a diagnostic setting.MethodsThe deep learning model was developed with 1,868 eligible NCCT scans with non-traumatic ICH collected between January 2011 and April 2018. We tested the model on two independent datasets (TT200 and SD 98) collected after April 2018. The model’s diagnostic performance was compared with clinicians’ performance. We further designed a simulated study to compare the clinicians’ performance with and without the deep learning system complements.ResultsThe proposed deep learning system achieved area under the receiver operating curve of 0.986 (95% CI [0.967–1.000]) on aneurysms, 0.952 (0.917–0.987) on hypertensive hemorrhage, 0.950 (0.860–1.000) on arteriovenous malformation (AVM), 0.749 (0.586–0.912) on Moyamoya disease (MMD), 0.837 (0.704–0.969) on cavernous malformation (CM), and 0.839 (0.722–0.959) on other causes in TT200 dataset. Given a 90% specificity level, the sensitivities of our model were 97.1% and 90.9% for aneurysm and AVM diagnosis, respectively. On the test dataset SD98, the model achieved AUCs on aneurysms and hypertensive hemorrhage of 0.945 (95% CI [0.882–1.000]) and 0.883 (95% CI [0.818–0.948]), respectively. The clinicians achieve significant improvements in the sensitivity, specificity, and accuracy of diagnoses of certain hemorrhage etiologies with proposed system complements.ConclusionsThe proposed deep learning tool can be an accuracy tool for early identification of hemorrhage etiologies based on NCCT scans. It may also provide more information for clinicians for triage and further imaging examination selection. creator: Meng Zhao creator: Wenjie Li creator: Yifan Hu creator: Ruixuan Jiang creator: Yuanli Zhao creator: Dong Zhang creator: Yan Zhang creator: Rong Wang creator: Yong Cao creator: Qian Zhang creator: Yonggang Ma creator: Jiaxi Li creator: Shaochen Yu creator: Ran Zhang creator: Yefeng Zheng creator: Shuo Wang creator: Jizong Zhao uri: https://doi.org/10.7717/peerj.18850 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zhao et al. title: Diversity and efficacy of insect sampling methods in an urban tropical dry forest of the Colombian Caribbean link: https://peerj.com/articles/18262 last-modified: 2025-02-26 description: Tropical dry forests (TDFs) are among the most threatened ecosystems in Colombia and globally. Characterized by distinct dry and wet seasons, TDFs support a rich diversity of flora and fauna and offer crucial ecosystem services, despite facing significant threats such as deforestation, urbanization and climate change. This study provides a comprehensive assessment of insect diversity within an urban TDF area in Puerto Colombia, Atlántico and in the Colombian Caribbean, by comparing three traditional sampling methods: Malaise traps, pitfall traps, and canopy fogging. In total, 3,135 insects were collected, representing 413 morphospecies across various trophic guilds. Our findings indicate that Malaise traps were the most effective in capturing a diverse range of species, followed by pitfall traps, while canopy fogging yielded the lowest species richness. Each method captured unique species, demonstrating that these methods are complementary in capturing the full spectrum of insect diversity in TDFs. Additionally, our study contributes valuable data on the taxonomic and functional diversity of insects in this continuously threatened ecosystem, underscoring the need for conservation efforts in urban and peri-urban TDFs. creator: Rodrigo Sarmiento-Garcés creator: Daniel Posada-Echeverría creator: Rafik Neme uri: https://doi.org/10.7717/peerj.18262 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Sarmiento-Garcés et al. title: Gestational overweight decreased risk of antepartum hemorrhage in pregnant women with complete placenta previa: a retrospective study link: https://peerj.com/articles/19091 last-modified: 2025-02-25 description: BackgroundAntepartum hemorrhage (APH) is associated with perinatal mortality and maternal morbidity. Previous studies have reported that obesity in pregnancy adversely influences both fetal and neonatal outcomes. This study aimed to investigate gestational overweight and the risk of APH in pregnant women with complete placenta previa (CPP).MethodsThis was a retrospective cohort study of pregnant women with CPP delivery at our hospital from 2013 to 2015. Outcomes were stratified according to APH and non-APH.ResultsOf 193 pregnancies with CPP, 40.4% (78) were diagnosed with APH. Maternal weight and BMI at delivery were significantly decreased in women with APH (61.15 ± 8.73 vs. 65.22 ± 7.80, 24.47 ± 3.12 vs. 26.21 ± 2.85; P = 0.001, P = 0.001; respectively), and the prevalence of overweight at delivery was higher in the non-APH group compared to those in the APH group (54.9% (62) vs. 39.7% (27); OR 2.18; 95%CI [1.16–4.11]). After adjusting for gestation week and other potential confounding factors, maternal weight and BMI were associated with the APH (OR 0.95, 95%CI [0.91–0.99]; 0.85, 95%CI [0.75–0.97], respectively).ConclusionAppropriate weight gain during pregnancy may decrease the risk of antepartum hemorrhage in pregnant women with complete placenta previa. creator: Jie Yang creator: Shaoxin Ye creator: Bihua Xuan creator: Zhengping Liu creator: Dazhi Fan uri: https://doi.org/10.7717/peerj.19091 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Yang et al. title: Prediction of cancer cell line-specific synergistic drug combinations based on multi-omics data link: https://peerj.com/articles/19078 last-modified: 2025-02-25 description: Compared to single-drug therapy, combination therapy involves the use of two or more drugs to reduce drug dosage, decrease drug toxicity, and improve treatment efficacy. We developed an extreme gradient boosting (XGBoost)-based drug-drug cell line prediction model (XDDC) to predict synergistic drug combinations. XDDC was based on XGBoost and used one of the largest drug combination datasets, NCI-ALMANAC. In XDDC, drug chemical structures, adverse drug reactions, and target information were selected as drug features; gene expression, methylation, mutations, copy number variations, and RNA interference data were used as cell line features; and pathway information was incorporated to link drug features and cell line features. XDDC improved the interpretability of drug combination features and outperformed other machine learning methods. It achieved an area under the curve (AUC) of 0.966 ± 0.002 and an AUPR of 0.957 ± 0.002 when cross-validated on NCI-ALMANAC data. Different types of omics data were evaluated and compared in the model. Literature and experimental verification confirmed some of our predictions. XDDC could help medical professionals to rapidly screen synergistic drug combinations against specific cancer cell lines. creator: Jiaqi Chen creator: Huirui Han creator: Lingxu Li creator: Zhengxin Chen creator: Xinying Liu creator: Tianyi Li creator: Xuefeng Wang creator: Qibin Wang creator: Ruijie Zhang creator: Dehua Feng creator: Lei Yu creator: Xia Li creator: Limei Wang creator: Bing Li creator: Jin Li uri: https://doi.org/10.7717/peerj.19078 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Chen et al. title: Sex differences in absolute and relative changes in muscle size following resistance training in healthy adults: a systematic review with Bayesian meta-analysis link: https://peerj.com/articles/19042 last-modified: 2025-02-25 description: BackgroundMuscle hypertrophy may be influenced by biological differences between males and females. This meta-analysis investigated absolute and relative changes in muscle size following resistance training (RT) between males and females and whether measures of muscle size, body region assessed, muscle fibre type, and RT experience moderate the results.MethodsStudies were included if male and female participants were healthy (18–45 years old) adults that completed the same RT intervention, and a measure of pre- to post-intervention changes in muscle size was included. Out of 2,720 screened studies, 29 studies were included in the statistical analysis. Bayesian methods were used to estimate a standardised mean difference (SMD), log response ratio (lnRR) with exponentiated percentage change (Exp. % Change of lnRR), and probability of direction (pd) for each outcome.ResultsAbsolute increases in muscle size slightly favoured males compared to females (SMD = 0.19 (95% HDI: 0.11 to 0.28); pd = 100%), however, relative increases in muscle size were similar between sexes (Exp. % Change of lnRR = 0.69% (95% HDI: −1.50% to 2.88%)). Outcomes were minimally influenced by the measure of muscle size and not influenced by RT experience of participants. Absolute hypertrophy of upper-body but not lower-body regions was favoured in males. Type I muscle fibre hypertrophy slightly favoured males, but Type II muscle fibre hypertrophy was similar between sexes.ConclusionOur findings strengthen the understanding that females have a similar potential to induce muscle hypertrophy as males (particularly when considering relative increases in muscle size from baseline) and findings of our secondary analyses should inform future research that investigates sex differences in highly trained participants and muscle fibre type-specific hypertrophy. creator: Martin C. Refalo creator: Greg Nuckols creator: Andrew J. Galpin creator: Iain J. Gallagher creator: D. Lee Hamilton creator: Jackson J. Fyfe uri: https://doi.org/10.7717/peerj.19042 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Refalo et al. title: Assessment of the potential of drug-drug interactions among population-based oldest-old people in Turkiye link: https://peerj.com/articles/19032 last-modified: 2025-02-25 description: BackgroundThe risk of potential drug‒drug interactions is highest in oldest-old people. Thus, the aim of this study was to investigate the frequency and type of potential drug‒drug interactions in population-based oldest-old people.MethodsThe type of study was descriptive. Ethical permission was obtained (13.04.2022/153). All participants were informed, and their written consent was obtained. The “oldest-old” were defined as those who were ≥85 years of age during the study period and living in Turkiye. These people were reached from every region of Turkiye via the snowball method and were visited at their homes. Data were collected via face-to-face interviews. Age, sex, city of residence, and generic names of regularly used medications were recorded. The medications used were analyzed according to the Beers 2019® Criteria and UpToDate® Lexicomp® drug interaction guides. SPSS was used for statistical analysis, and p < 0.05 was considered statistically significant.ResultsData were collected from the 549 oldest-old people throughout Turkiye. Among the participants, 61.2% (n = 336) were women. The median age of the women was 88.00 years (minimum = 85, maximum = 101), and the median age of the men was 88.00 years (minimum = 85, maximum = 102). The distributions of men and women in the different age groups were similar (p = 0.341). The distributions of men and women across regions were similar (p = 0.826), most of whom (n = 300, 54.6%) had ≥1 potential drug‒drug interaction, according to the UpToDate analysis. The median number of medications used continuously was 4.0 (minimum = 0, maximum = 19). The median number of potential drug‒drug interactions was 1.0 (minimum = 0, maximum = 21). As the number of medications used increased, the number of potential drug‒drug interactions also increased (r = 0.737; p = 0.001). The number of potential drug‒drug interactions decreased with increasing age (r = −0.104; p = 0.015). According to the Beers 2019® Criteria, potential drug‒drug interactions were detected in only eight patients. The concordance between the Beers 2019® Criteria and the UpToDate®Lexicomb® drug interaction data was poor compared with the number of potential drug‒drug interactions (kappa = 0.024, p < 0.001). Central nervous system medications are a common group that can cause potential drug‒drug interactions according to both guidelines. Moreover, potentially inappropriate medications defined by the Beers 2019® Criteria were the most common causes of potential drug‒drug interactions, according to UpToDate®Lexicomb® drug interactions. The frequency of potential drug‒drug interactions was found to be high in the population-based oldest-old people interviewed in Turkiye. It has been determined that the use of more than one guide in the evaluation of potential drug‒drug interactions is safer. creator: Fuat Nihat Özaydın creator: Ayşe Nilüfer Özaydın uri: https://doi.org/10.7717/peerj.19032 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Özaydın and Özaydın title: Morphofunctional changes in the immune system in colitis-associated colorectal cancer in tolerant and susceptible to hypoxia mice link: https://peerj.com/articles/19024 last-modified: 2025-02-25 description: BackgroundOne of the effective strategies for the treatment of tumor diseases, including colitis-associated colorectal cancer (CAC), is immunotherapy. During inflammation, NF-κB is activated, which is connected with the hypoxia-inducible factor—HIF, regulating the immune cells functioning and influences the CAC development. Organisms differ according to their hypoxia resistance and HIF expression. Therefore, the aim of the study was to characterize the thymus, spleen and mesenteric lymph nodes morphofunctional features, as well as changes in the subpopulation composition of peripheral blood cells and mesenteric lymph nodes in tolerant and susceptible to hypoxia C57Bl/6 mice in CAC.MethodsHypoxia tolerance was assessed by gasping time measurement in hypobaric decompression chamber. Based on the outcome, the mice were assigned to three groups characterized as ‘tolerant to hypoxia’, ‘normal’, and ‘susceptible to hypoxia’. A month after determining hypoxia resistance CAC was modeled by intraperitoneal azoxymethane (AOM) administration and three cycles of dextran sulfate sodium consumption. Mice were sacrificed on the 141st day after the AOM administration, a morphological, morphometric and immunohistochemical study of tumors, morphological and morphometric study of thymus and spleen, and subpopulation composition of peripheral blood cells and mesenteric lymph nodes assessment were carried out.ResultsTumors in tolerant and susceptible to hypoxia mice were represented by glandular intraepithelial neoplasia and adenocarcinomas, the area of which was larger in susceptible mice. Immunohistochemical study revealed a more pronounced Ki-67+ staining in tumors of susceptible mice. In CAC, only in tolerant mice, expansion of the thymic cortex was observed relative to the control group, while in susceptible ones, no changes were detected. Only in susceptible to hypoxia mice, spleen germinal centers of lymphoid follicles enlargement were observed. Only in susceptible mice during CAC, in comparison to the control group, the relative and absolute number of B-lymphocytes and relative—cytotoxic T-lymphocytes in blood increased. The relative cytotoxic T-lymphocytes and NK cells number in peripheral blood during CAC was higher in susceptible to hypoxia mice compared to tolerant ones. In susceptible to hypoxia mice, more pronounced changes in the mesenteric lymph nodes subpopulation composition of cells were revealed—only in them the absolute and relative number of B-lymphocytes and NK cells, the absolute number of cytotoxic T-lymphocytes increased, and the relative number of macrophages decreased.ConclusionsMorphofunctional differences in the thymus, spleen, mesenteric lymph nodes and blood immune cells reactions indicated the more pronounced immune response to the CAC development in susceptible to hypoxia mice, which should be taken into account in experimental studies. creator: Dzhuliia Dzhalilova creator: Maria Silina creator: Anna Kosyreva creator: Nikolai Fokichev creator: Olga Makarova uri: https://doi.org/10.7717/peerj.19024 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Dzhalilova et al. title: Comparison of fracture resistance between immediate and delayed composite restorations with or without fiber after root canal treatment: a field-emission-gun scanning electron microscope study link: https://peerj.com/articles/19018 last-modified: 2025-02-25 description: BackgroundThis study aimed to evaluate the fracture resistance of immediate and delayed restorations after root canal treatment (RCT).MethodsSixty human intact premolar teeth were used. Teeth were prepared disto-occlusally. After RCT, teeth were randomly divided into two groups according to restoration times (immediate or 3 months delayed). The three month delay was imitated by thermomechanical aging. Then, samples were divided into six subgroups (n = 10). While I (Composite resin), II (Flowable bulk-fill) and III (Ribbond+Flowable bulk-fill) were restored immediately, Groups IV, V and VI were restored with temporary filling material and stored in distilled. After subjected to thermo-cycling (2,500 cycles, 5–55 °C) and exposed to 60,000 cycles in a chewing simulator, Group IV (Composite resin), V (Flowable bulk-fill) and VI (Ribbond+Flowable bulk-fill) were restored. All of the teeth were fractured on the universal testing machine. Failure modes were analyzed using scanning electron microscope. Data were analyzed using the Shapiro-Wilk and two-way ANOVA tests (p < 0.05).ResultsThe highest fracture resistance was recorded in Group III while the lowest in Group VI. No statistically significant difference was observed among groups (p > 0.05). Most of the repairable fractures were seen in Groups I and II.ConclusionDelaying the permanent restorations of teeth for 3 months did not affect fracture resistance. However, it was suggested to avoid delaying restorations for obtaining repairable surfaces. creator: Zeynep Buket Kaynar creator: Gözde Akbal Dinçer creator: Nazmiye Donmez uri: https://doi.org/10.7717/peerj.19018 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Kaynar et al. title: Development of LAMP assay for early detection of Yersinia ruckeri in aquaculture link: https://peerj.com/articles/19015 last-modified: 2025-02-25 description: Yersinia ruckeri is the causative agent of yersiniosis or enteric red mouth disease (ERM) that causes significant economic losses in the salmonid aquaculture industry. Due to an increasing number of outbreaks, lack of effective vaccines and the bacteria’s ability to survive in the environment for long periods, there is a necessity for novel measures to control ERM. New techniques capable of rapidly detecting Y. ruckeri are critical to aid effective control programs. Molecular methods, like real-time polymerase chain reaction, can detect Y. ruckeri; however, that methodology is not field-deployable and cannot support local decision-making during an outbreak. We present a field-deployable molecular assay using loop mediated isothermal amplification (LAMP) and water filtering method for the detection of Y. ruckeri eDNA from water samples to improve current surveillance methods. The assay was optimised to amplify the glutamine synthetase gene (glnA) of Y. ruckeri in under 20 min. The assay demonstrated high specificity and sensitivity, as it did not amplify any non-target bacteria typically present in water sources. It achieved a limit of detection (LOD) of 0.5 × 10−7 ng/µl, significantly surpassing the LOD of 0.5 × 10−4 ng/µl obtained through conventional polymerase chain reaction (cPCR). When applied to environmental water samples spiked with transformed Escherichia coli containing the G-block of the Yersinia ruckeri (glnA) target gene, the Yr-LAMP method exhibited an analytical sensitivity of 0.08 cells/µl from the initial filtered water sample. Notably, the cumulative time for sample preparation and amplification was under 1 h. The simplicity of the developed field-deployable Yr-LAMP assay makes it suitable as a routine procedure to monitor fish for ERM infection. This will enable informed decision-making on mitigating pathogen prevalence in aquaculture farms. creator: Hoda Abbas creator: Nickala Best creator: Gemma Zerna creator: Travis Beddoe uri: https://doi.org/10.7717/peerj.19015 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Abbas et al. title: Role of contrast-enhanced ultrasound with time-intensity curve analysis about thyroid nodule and parenchyma for differentiating BRAF V600E mutation status link: https://peerj.com/articles/19006 last-modified: 2025-02-25 description: BackgroundThe BRAF V600E mutation was proven associated with papillary thyroid cancer (PTC) which has more aggressive behavior and could affect the outcome of PTC. The objective of this study was to observe more contrast-enhanced ultrasound (CEUS) time-intensity curve (TIC)—based quantitative parameters in nodules and surrounding parenchyma and analyze the association between the TIC-based quantitative parameters and BRAF V600E mutation status in patients with PTC.MethodsA retrospective analysis of 447 PTC patients was conducted. Prior to thyroidectomy or fine needle aspiration (FNA), all patients had CEUS and had their BRAF V600E mutations examined. Based on their mutation status, the patients were split into two groups. The two groups were compared in terms of sex, age, quantitative CEUS characteristics, pathological findings, vascular invasion, capsular invasion, and cervical lymph node metastases.ResultsA total of 240 patients were in the mutation negative group and 207 patients were in the BRAF mutation positive group. The BRAF-positive group exhibited significantly higher arrival time (AT) and time to peak enhancement (TTP) of the nodules, among other direct quantitative characteristics. The BRAF-positive mutant nodules showed significantly higher arrival time change and time to peak change compared to the surrounding parenchyma for indirect quantitative metrics.ConclusionThe time-dependent quantitative parameters of CEUS time intensity curve in nodules and surrounding parenchyma have clinical value in distinguishing BRAF V600E mutation positive nodules from gene mutation negative nodules. Quantitative CEUS characteristics may be beneficial in detecting the BRAF V600E mutation status and informing the subsequent clinical choice. creator: Zhipeng Hu creator: Rong Xue creator: Zhixi Liu creator: Liang Liu creator: Zheli Gong uri: https://doi.org/10.7717/peerj.19006 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Hu et al. title: When safety becomes the priority: defensive nursing practice and its associated factors among nurses in Egypt: a cross-sectional study link: https://peerj.com/articles/19005 last-modified: 2025-02-25 description: BackgroundDefensive nursing practices, which prioritize legal protection over patient care, are becoming increasingly common. This study aims to explore the prevalence and factors associated with defensive nursing practices among nurses in Egypt, considering the impact of workplace violence and legal threats.MethodsA descriptive cross-sectional study was conducted from February to April 2024 using a self-report online questionnaire. The target population included clinical nurses working in various hospitals in Egypt. A sample size of 1,267 nurses was achieved through convenience sampling. The questionnaire assessed demographic data, experiences of workplace violence, legal consequences, and defensive nursing practices, categorized into positive and negative behaviors.ResultsThe sample consisted of 1,267 nurses, predominantly female (75.9%), with a mean age of 28.57 years. Positive defensive practices, such as detailed documentation (79%) and thorough explanation of procedures (58.5%), were highly prevalent. Negative practices included avoiding high-risk procedures (15.9%) and patients more likely to file lawsuits (13.6%). Older nurses and those with higher educational qualifications were more likely to engage in positive defensive practices. Nurses who experienced workplace violence or legal threats were significantly more likely to avoid high-complication procedures.ConclusionThe study identified a high engagement in both positive and negative defensive practices among nurses in Egypt. These practices are influenced by factors such as age, education level, and experiences of workplace violence and legal threats. The findings underscore the need for strategies to support nurses, reduce reliance on defensive practices, and ensure better patient outcomes. creator: Ahmed Zaher creator: Yasmine M. Osman creator: Salwa Sayed creator: Sally Mohammed Farghaly Abdelaliem creator: Amany Anwar Saeed Alabdullah creator: Ahmed Hendy creator: Zainab Attia Abdallah creator: Mohammed Musaed Ahmed Al-Jabri creator: Abdelaziz Hendy uri: https://doi.org/10.7717/peerj.19005 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zaher et al. title: Redescription of Aspidosiphon (Paraspidosiphon) steenstrupii Diesing, 1859 (Sipuncula: Aspidosiphonidae) and the reinstatement of three species link: https://peerj.com/articles/19003 last-modified: 2025-02-25 description: Sipuncula, specifically the family Aspidosiphonidae, faces taxonomic challenges due to brief original descriptions and the poor condition or loss of the type material. Detailed standardized redescriptions are essential to understanding the diversification in this group. Herein, a comprehensive redescription of Aspidosiphon (Paraspidosiphon) steenstrupii based on an extensive material collection from the tropical Western Atlantic is provided. Based on morphological data and the analysis of COI sequences, we delimited A. (P.) steenstrupii morphologically, restricting its distribution to the tropical Western Atlantic. Also, the redescriptions and proposals for reinstatement of A. (P.) exostomum, A. (P.) ochrus, and A. (P.) speculator, previously considered junior synonyms of A. (P.) steenstrupii, are included. Furthermore, a comprehensive discussion on diagnostic morphological features to recognize aspidosiphonid species and a detailed revision of synonyms of A. (P.) steenstrupii are included. Notable differences in morphology and genetic data suggest the need for revising the taxonomic status of several synonyms within the family, highlighting underestimated diversity in sipunculans. creator: Itzahi Silva-Morales creator: Luis F. Carrera-Parra uri: https://doi.org/10.7717/peerj.19003 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Silva-Morales and Carrera-Parra title: Prediction of clinical deterioration within one year in chronic obstructive pulmonary disease using the systemic coagulation-inflammation index: a retrospective study employing multiple machine learning method link: https://peerj.com/articles/18989 last-modified: 2025-02-25 description: BackgroundInflammatory response and the coagulation system are pivotal in the pathogenesis of clinical deterioration in chronic obstructive pulmonary disease (COPD), prompting us to hypothesize that the systemic coagulation-inflammation (SCI) index is associated with clinical deterioration in COPD.MethodsA cohort of 957 COPD patients (mean age: 68.4 ± 7.8 years; 74.4% male) from January 2018 to December 2021 was analyzed. Six machine learning models (XGBoost, logistic regression, Random Forest, elastic net (ENT), support vector machine (SVM), and K-nearest neighbors (KNN)) were evaluated using accuracy, precision, recall, F1-score, and the area under the receiver operating characteristic curve (AUC-ROC).ResultsOur study encompassed 957 patients, out of which 171 were classified in the clinical deterioration of COPD (cd-COPD) cohort. Significant disparities in age, comorbidities like respiratory failure, C-reactive protein, lymphocyte count, red blood cell distribution width (RDW), SCI, procalcitonin (PCT), and D-dimer were depicted between the cd-COPD and non-cd-COPD groups. Concerning machine learning and model comparison, the SVM model showcased consistent performance and strong generalization capabilities on both the training and testing sets compared to the other five machine learning (ML) models. The SCI index, as the most influential predictor, demonstrated a median of 93.08 in cd-COPD compared to 81.67 in non-cd-COPD patients.ConclusionThe SCI is markedly elevated in cd-COPD patients compared to COPD patients, and SVM demonstrates reliable performance in cd-COPD prediction. creator: Ling Hou creator: Ming Min creator: Rui Hou creator: Wei Tan creator: Minghua Zhang creator: Qianfei Liu uri: https://doi.org/10.7717/peerj.18989 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Hou et al. title: Effects of sex and season (breeding and non-breeding) on microhabitat selection in Stejneger’s bamboo pitviper (Viridovipera stejnegeri) link: https://peerj.com/articles/18970 last-modified: 2025-02-25 description: Habitat quality and availability are crucial for the survival and reproduction of animal species. Intraspecific and seasonal differences in habitat selection reflect adaptations to changing biological requirements and environmental factors. To investigate the effects of season (breeding and non-breeding) and sex on microhabitat selection in snakes, here we employed field surveys to analyze microhabitat selection data for Stejneger’s bamboo pitviper (Viridovipera stejnegeri) across different sexes and seasons. Results indicated that although no significant difference was observed between groups, marked differences in certain microhabitat factors were noted. Specifically: (1) Non-breeding season females (NBF) displayed distinct differences in altitude, slope position, distance from roads compared to other groups. (2) Temperature exerted a lesser effect on non-breeding season individuals compared to breeding season individuals. Additionally, distance from roads only significantly impacted breeding season males, not females. (3) Regarding sexual differences, males and females differed in slope position and distance from residential sites, reflecting their distinct ecological requirements. Regarding seasons, differences in habitat selection between breeding and non-breeding seasons were primarily related to temperature, indicating behavioral changes linked to seasons. (4) Non-breeding season females exhibited the narrowest microhabitat niche width and the least microhabitat niche overlap with other groups, potentially due to their pronounced foraging requirements, which compel them to explore limited habitats with higher human disturbance but richer food sources. This study contributes novel insights into the habitat selection behaviors of snakes. creator: Songwen Tan creator: Yayong Wu creator: Jiajun Wang creator: Bing Lyu creator: Min Yu creator: He Zhang creator: Peng Guo creator: Lei Shi uri: https://doi.org/10.7717/peerj.18970 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Tan et al. title: Computational modelling reveals the influence of object similarity and proximity on visually guided movements link: https://peerj.com/articles/18953 last-modified: 2025-02-25 description: The paper aims to understand how humans reach for a single target object in multi-object scenes. In a previous empirical study, human subjects were asked to execute reaches to a single target among non-targets (choice reaching task). In the current work, we re-analysed the human data and implemented a neurobiologically-plausible cognitive robotics model (choice reaching with a LEGO arm robot, CoRLEGO) that mimics human reaches in the choice reaching task. The results from the experiment confirmed the commonly made assumption that proximity and similarity between objects (also termed perceptual grouping) affect the quality of the reaches. However, what was novel here was that modelling the reaches also allowed to temporally separate these factors, as the start of the movement was affected by both factors while the reach trajectory was affected only by proximity between target and distractor objects indicating that human information processing of visual stimuli applies these factors in a serial fashion. In particular, our model architecture and the optimised parameter settings suggest that object proximity directly influences the movement onset. In addition, our computational model confirmed this interpretation but also revealed that the relationship between the two factors may be affected by how the participants balanced speed (starting time of the movement) and accuracy of reaching (straightness of reaches). Future research will need to test whether this plausible prediction is correct. creator: Mandar Manjunath Patil creator: Dietmar Heinke creator: Fan Zhang uri: https://doi.org/10.7717/peerj.18953 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Patil et al. title: Analysis of biopsies of gastric cancer, intestinal and diffuse, and non-atrophic gastritis: an overview of loss of heterozygosity in Mexican patients link: https://peerj.com/articles/18928 last-modified: 2025-02-25 description: This study analyzed the loss of heterozygosity (LOH) effect on gastric cancer (GC) tumor samples from 21 Mexican patients, including diffuse (DGC) and intestinal (IGC) subtypes, as well as non-atrophic gastritis (NAG, control). Whole-genome high-density arrays were performed, and LOH regions were identified among the tissue samples. The differences in affected chromosomes were established among groups, with chromosomes 6 and 8 primarily affected in DGC and chromosomes 3, 16, and 17 in IGC. Functional pathway analysis revealed involvement in cancer-associated processes, such as signal transduction, immune response, and cellular metabolism. Five LOH-genes (IRAK1, IKBKG, PAK3, TKTL1, PRPS1) shared between GC and NAG suggest an early role in carcinogenesis. Specific genes were highlighted for Hallmarks of Cancer NAG-related genes (PTPRJ and NDUFS) were linked to cell proliferation and growth; IGC genes (GNAI2, RHOA, MAPKAPK3, MST1R) to genomic instability, metastasis, and arrest of cell death; and DGC genes to energy metabolism and immune evasion. These findings emphasize the role of LOH in GC pathogenesis and underscore the need for further research to understand LOH-affected genes and their diagnostic or evolution potential in cancer management. Portions of this text were previously published as part of a preprint (https://www.medrxiv.org/content/10.1101/2024.07.29.24311063v1). creator: Violeta Larios-Serrato creator: Hilda A. Valdez-Salazar creator: Javier Torres creator: Margarita Camorlinga creator: Patricia Piña-Sánchez creator: Fernando Minauro creator: Martha-Eugenia Ruiz-Tachiquín uri: https://doi.org/10.7717/peerj.18928 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Larios-Serrato et al. title: Efficacy and safety of low-molecular-weight-heparin plus citrate in nephrotic syndrome during continuous kidney replacement therapy: retrospective study link: https://peerj.com/articles/18919 last-modified: 2025-02-25 description: BackgroundNephrotic syndrome (NS) is a condition often necessitating continuous kidney replacement therapy (CKRT) due to severe edema and other complications. Anticoagulation is critical in CKRT to prevent filter clotting, with regional citrate anticoagulation (RCA) being the first-line method. However, the hypercoagulable state of NS may require alternative strategies. Optimal anticoagulation therapy in NS patients undergoing CKRT is lacking.MethodsThis retrospective observational study included 251 CKRT sessions from 122 NS patients treated at Nanfang Hospital, Southern Medical University, from January 2019 to December 2022. Patients were divided into three groups based on anticoagulation method: Low-molecular-weight-heparin (LMWH) alone, RCA alone, and RCA plus LMWH. Filter lifespan, incidence of filter clotting, and adverse events were assessed to evaluate the efficacy and safety profiles of each anticoagulation methods.ResultsThe combination of RCA and LMWH demonstrated a significantly longer mean filter lifespan and lower incidence of filter clotting compared to LMWH or RCA alone. RCA plus LMWH also showed a lower incidence of overall adverse events, particularly thrombosis, without an increase in bleeding complications. Multivariate Cox analysis indicated that RCA plus LMWH was particularly effective in patients with normal kidney function.ConclusionsRCA combined with LMWH provides a superior anticoagulation strategy in NS patients undergoing CKRT, with enhanced filter lifespan and reduced clotting and thrombotic events without increasing bleeding risk. Further research is needed to optimize dosing and validate these results in broader populations. creator: Di Wang creator: Mengqin Yang creator: Siyuan Li creator: Can Tang creator: Jun Ai creator: Diankun Liu uri: https://doi.org/10.7717/peerj.18919 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Wang et al. title: The avifauna of Ramanathapuram, Tamil Nadu along the Southeast coast of India: waterbird assessments and conservation implications across key sanctuaries and Ramsar sites link: https://peerj.com/articles/18899 last-modified: 2025-02-25 description: BackgroundWetlands, globally, face significant threats from human activities, and waterbirds, as key indicators of wetland health, are essential to maintaining ecological balance. Any long-term conservation measures should prioritize coordinated habitat preservation, wetland restoration, and sustainable management practices involving local communities. Monitoring and analyzing waterbird population trends are critical for understanding restoration, conservation, and management practices.MethodsThe present study was carried out in five bird sanctuaries Chitrangudi, Kanjirankulam (Ramsar sites), Therthangal, Sakkarakottai, and Mel-Kel Selvanoor of Tamil Nadu, Southeast coast of India, over one year (April 2022 to March 2023). Monthly surveys using direct and block methods, with additional fortnightly visits during the breeding season, were conducted from vantage points to record species diversity, nesting activity, and conservation threats. Assessments of the residential status, national status (SOIB), and Convention for Migratory species (CMS) status were done along with the alpha and beta biodiversity profiles, principal component analysis, Pearson correlation and other statistical methods performed to assess breeding waterbirds community structure. Threats to the breeding waterbirds were categorised into high, medium, and low impacts based on degree of severity and irreversibility.ResultsThe avifaunal checklist revealed a diversity of waterbird species utilizing the sanctuaries for breeding. Notable findings include two Near-Threatened species like, Asian Woolly-necked Stork Ciconia episcopus, and Spot-billed Pelican Pelecanus philippensis, where Asian Woolly-necked Stork recorded only in Therthangal Bird Sanctuary. Avifauna of each sanctuary with breeding waterbirds in parenthesis is as follows: Chitragundi 122 (13); Mel-Kel Selvanoor 117 (19); Therthangal 96 (23); Sakkarakottai 116 (17) and Kanjirankulam 123 (14). The breeding activity (incubation in nests) was from November to February except for Glossy Ibis and Oriental Darter whose breeding started in December; Spot-billed Duck and Knob-billed Duck breed only during January and February. Among the 131 species recorded from all the sanctuaries, 78% were resident birds; 27% were breeding waterbirds, and 21% were Winter visitors. The SOIB and CMS statuses underscore the necessity of implementing effective conservation measures to protect breeding habitats amid anthropogenic pressures. Water unavailability and nest tree unavailability in the sanctuaries are found to be the high degree threats to breeding waterbirds than others. This research provides critical baseline data for the forest department’s future wetland management plans. creator: Hameed Byju creator: Hegde Maitreyi creator: Raveendran Natarajan creator: Reshmi Vijayan creator: Balu Alagar Venmathi Maran uri: https://doi.org/10.7717/peerj.18899 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Byju et al. title: Comparative effectiveness of nonpharmacological interventions for the nutritional status of maintenance hemodialysis patients: a systematic review and network meta-analysis link: https://peerj.com/articles/19053 last-modified: 2025-02-24 description: ObjectiveWe aim to analyze the effects of different nonpharmacological interventions on the nutritional status of patients on maintenance hemodialysis (MHD).MethodsRandomized controlled trials (RCTs) conducted up to October 12, 2023 were searched in the Cochrane Library, Chinese National Knowledge Infrastructure, Wan Fang Database, VIP databases, and China Biomedical Literature Database. R and Review Manager software were used for data analysis, the quality of the literature was assessed using the Cochrane Risk Bias Tool RoB2.0, the reliability of evidence was evaluated using Grading of Recommendations, Assessment, Development, and Evaluation guidelines, and sources of heterogeneity were explored through sensitivity analyses. This study was registered in PROSPERO with registration number CRD42023458187.ResultsA total of 54 studies met the criteria, 3,861 patients were enrolled in this study, and 11 interventions were explored. The results of the network meta-analysis (NMA) showed that dietary intervention is the best intervention in terms of improving patients’ body mass index and serum albumin levels and health education is the best intervention in terms of improving patients’ hemoglobin levels.ConclusionThis NMA confirmed that different nonpharmacological interventions benefit the nutritional status of patients on MHD, providing novel insights for healthcare practitioners. However, high-quality RCTs should be designed to validate the stability of the level of evidence for different nonpharmacological interventions. creator: Xiaolan Ma creator: Chun Tang creator: Hong Tan creator: Jingmei Lei creator: Li Li uri: https://doi.org/10.7717/peerj.19053 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Ma et al. title: Tolerance and antioxidant response to heavy metals are differentially activated in Trichoderma asperellum and Trichoderma longibrachiatum link: https://peerj.com/articles/19016 last-modified: 2025-02-24 description: Heavy metal pollution reduces the community of soil microorganisms, including fungi from the genus Trichoderma, which are plant growth promotors and biological control agents. Because of potential effects on crop productivity, the toxic effects of heavy metals (HMs) in Trichoderma are of interest. However, there have been few studies on the biochemical and molecular response to oxidation caused by exposure to copper (Cu), chromium (Cr), and lead (Pb) and whether this antioxidant response is species-specific. In this study, we compared the tolerance of Trichoderma asperellum and Trichoderma longibrachiatum to Cu, Pb, and Cr and evaluated the expression of genes related to the antioxidant response, including glutathione peroxidase (GPX), catalase (CAT), and cysteine synthase (CYS) as well as the activity of peroxidase and catalase. The isolates of Trichoderma were selected because we previously reported them as promotors of plant growth and agents of biological control. Our results revealed that, with exposure to the three HMs, the Trichoderma cultures formed aggregates and the culture color changed according to the metal and the Trichoderma species. The tolerance index (TI) indicated that the two Trichoderma species were tolerant of HMs (Cu > Cr > Pb). However, the TI and conidia production revealed that T. longibrachiatum was more tolerant of HMs than T. asperellum. The three HMs caused oxidative damage in both Trichoderma species, but the enzyme activity and gene expression were differentially regulated based on exposure time (72 and 144 h) to the HMs and Trichoderma species. The main changes occurred in T. asperellum; the maximum expression of the GPX gene occurred at 144 h in response to all three HMs, whereas the CAT gene was upregulated at 72 h in response to Cu but downregulated at 144 h in response to all three HMs. The CYS gene was upregulated in response to the three metals. The peroxidase activity increased with all three HMs, but the catalase activity increased with Cu and Pb at 72 h and decreased at 144 h with Pb and Cr. In T. longibrachiatum, the GPX gene was upregulated with all three HMs at 72 h, the CAT gene was upregulated only with Pb at 72 h and was downregulated at 144 h with HMs. Cr and Cu upregulated CYS gene expression, but expression did not change with Pb. The peroxidase activity increased with Cu at 144 h and with Cr at 72 h, whereas Pb decreased the enzyme activity. In contrast, catalase activity increased with the three metals at 144 h. In conclusion, T. longibrachiatum was more tolerant of Cu, Cr, and Pb than was T. asperellum, but exposure to all three HMs caused oxidative damage to both Trichoderma species. Peroxidases and catalases were activated, and the expression of the genes GPX and CYS was upregulated, whereas the CAT gene was downregulated. These findings indicate that the antioxidant response to HMs was genetically modulated in each Trichoderma species. creator: Diego Helman Zapata-Sarmiento creator: Aida Araceli Rodríguez-Hernández creator: Gabriela Sepúlveda-Jiménez creator: Mario Rodríguez-Monroy uri: https://doi.org/10.7717/peerj.19016 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zapata-Sarmiento et al. title: Predictors of outcome among children with biliary atresia: a single centre trial link: https://peerj.com/articles/19001 last-modified: 2025-02-24 description: ObjectiveThis study aimed to investigate the predictive role of preoperative gamma-glutamyl transpeptidase (GGT) levels on the prognosis of neonatal biliary atresia (NBA) in patients who underwent the Kasai procedure.MethodsA retrospective analysis was conducted of patients with NBA who underwent the Kasai procedure at our hospital from 2017 to 2021. Patients were categorized into high (GGT > 300 IU/L) and GGT inadequate (GGT ≤ 300 IU/L) groups based on preoperative GGT levels. The influence of GGT levels on NBA prognosis was evaluated by comparing clinical data, age at operation, jaundice normalization, and survival outcomes between the groups.ResultsA total of 74 patients with NBA were included, with 59 in the high GGT group and 15 in the GGT inadequate group. Ages at the time of the Kasai procedure ranged from 31 to 106 days, with a median of 61 days; the average weight was 4.8 ± 1.1 kg. Two years post-procedure, 56 patients (75.7%) survived with their native liver (P < 0.0001). At 3 months post-procedure, alanine aminotransferase (ALT) levels were significantly higher in the GGT inadequate group compared to the high GGT group (3.5 times vs. 2.3 times the upper limit of normal, P = 0.0259). Significant differences in GGT levels persisted 1-month post-procedure (P = 0.0473). Jaundice clearance was significantly higher in the high GTT group (P = 0.0171) after 6 months. Multivariate logistic regression indicated a substantially higher mortality rate in the GGT inadequate group (P = 0.0452), with no significant age difference at operation (P = 0.8449). Preoperative GGT is a valuable predictor for NBA prognosis (area under the curve (AUC) 0.754, 95% confidence interval CI [0.640–0.847], P = 0.001, specificity 91.1%, and sensitivity 61.1%).ConclusionsHigh preoperative GGT levels predict better prognosis in patients with NBA undergoing Kasai operation. creator: Chaoxiang Ye creator: Wei Gao uri: https://doi.org/10.7717/peerj.19001 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ye and Gao title: Current trends in the epidemiology of multidrug-resistant and beta-lactamase-producing Pseudomonas aeruginosa in Asia and Africa: a systematic review and meta-analysis link: https://peerj.com/articles/18986 last-modified: 2025-02-24 description: Pseudomonas aeruginosa continues to be a significant contributor to high morbidity and mortality rates worldwide, particularly due to its role in severe infections such as hospital-acquired conditions, including ventilator-associated pneumonia and various sepsis syndromes. The global increase in antimicrobial-resistant (AMR) P. aeruginosa strains has made these infections more difficult to treat, by limiting the effective drug options available. This systematic review and meta-analysis aim to provide an updated summary of the prevalence of AMR P. aeruginosa over the past 5 years. A systematic search was performed across three major electronic databases—PubMed, ScienceDirect, and Web of Science—yielding 40 eligible studies published between 2018 and 2023. Using a random-effects model, our meta-analysis estimated that the overall prevalence of P. aeruginosa in Asia and Africa over the past 5 years was 22.9% (95% CI [14.4–31.4]). The prevalence rates for multidrug-resistant (MDR) and extensively drug-resistant (XDR) P. aeruginosa strains were found to be 46.0% (95% CI [37.1–55.0]) and 19.6% (95% CI [4.3–34.9]), respectively. Furthermore, the prevalence rates of extended-spectrum β-lactamase- and metallo-β-lactamase-producing P. aeruginosa were 33.4% (95% CI [23.6–43.2]) and 16.0% (95% CI [9.8–22.3]), respectively. Notably, resistance rates to β-lactams used for treating pseudomonal infections were alarmingly high, with rates between 84.4% and 100.0% for cephalosporins, and over 40% of P. aeruginosa isolates showed resistance to penicillins. Our analysis identified the lowest resistance rates for last-resort antimicrobials, with 0.3% (95% CI [0.0–1.3]) resistance to polymyxin B and 5.8% (95% CI [1.5–10.2]) to colistin/polymyxin E. The low resistance rates to polymyxins suggest that these antibiotics remain effective against MDR P. aeruginosa. However, the findings also highlight the critical public health threat posed by antimicrobial-resistant P. aeruginosa, particularly concerning β-lactam antibiotics. This underscores the need for effective and carefully planned intervention strategies, including the development of new antibiotics to address the growing challenge of resistance. Developing robust antibiotic treatment protocols is essential for better management and control of pseudomonal infections globally. Therefore, continued research and international collaboration is vital to tackle this escalating public health challenge. This study protocol was registered with the International Prospective Register of Systematic Reviews (PROSPERO), under registration number CRD42023412839. creator: Mohd Zulkifli Salleh creator: Nik Mohd Noor Nik Zuraina creator: Zakuan Zainy Deris creator: Zeehaida Mohamed uri: https://doi.org/10.7717/peerj.18986 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Salleh et al. title: Demographic compensation occurs in populations of Quercus oleoides Schltdl & Cham in fragments across an altitudinal gradient link: https://peerj.com/articles/18980 last-modified: 2025-02-24 description: BackgroundDemographic compensation is a complex process by which populations can compensate for the effects of anthropogenic disturbance and other environmental changes and restore growth-rate stability (λ » 1). Dynamic equilibrium is achieved when the growth rate [λ] is close to one. This enables a population to persist under changing environmental conditions. The demographics of fragmented populations provides an ideal model to explore the processes by which populations adapt through demographic compensation responses.AimsTo characterize the demographic of Quercus oleoides populations and detect the various processes that result from demographic compensation responses.MethodsWe established permanent plots in three Q. oleoides populations at which three annual transition stages were registered. These were survival probability, transition probability, and average reproduction (that is, the number of seed production by size class).ResultsThe λs of the three populations under study were >1.0 (P < 0.005). However, differences were found in the elasticity matrices, as well as in the life-table response experiment (LTRE) variation analyses.ConclusionsThe three Q. oleoides populations have shown to have affected a transition to demographic compensation and achieved demographic balance through different strategies in their vital rates. creator: Carlos Flores-Romero creator: Lázaro Rafael Sánchez-Velásquez creator: Miguel Equihua creator: María del Rosario Pineda López creator: Enrique Alarcón Gutiérrez creator: Yareni Perroni uri: https://doi.org/10.7717/peerj.18980 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Flores-Romero et al. title: Kaempferia chonburiensis (Zingiberaceae), a new species from Thailand based on morphological and molecular evidence link: https://peerj.com/articles/18948 last-modified: 2025-02-24 description: BackgroundKaempferia is a genus belonging to the ginger family. Currently, this genus is comprised of about 63 species, mainly distributed from India to Southeast Asia. During our fieldwork, a new species of Kaempferia was found in Chon Buri Province, Thailand. The objective of this article was to provide morphological evidence and confirm its relationships in Kaempferia through molecular phylogenetic analysis.MethodsPlant samples were collected from field sites and investigated by conventional taxonomy and molecular techniques. The phylogenetic trees were reconstructed using the maximum likelihood criterion and Bayesian inference. The morphological evolution was also examined to elaborate the relationships among representative Kaempferia taxa.ResultsKaempferia chonburiensis from southeastern Thailand is described and illustrated based on morphological features and its taxonomic placement was confirmed by molecular phylogenetic analyses and morphological evolution. An identification key is provided for the new Kaempferia species occurring in Thailand.ConclusionKaempferia chonburiensis is a new enumerated species of Kaempferia from Thailand. creator: Pornpimon Wongsuwan creator: Boonmee Phokham creator: Pantamith Rattanakrajang creator: Chayan Picheansoonthon creator: Suchada Sukrong uri: https://doi.org/10.7717/peerj.18948 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Wongsuwan et al. title: The large mammal fossil fauna of the Cradle of Humankind, South Africa: a review link: https://peerj.com/articles/18946 last-modified: 2025-02-24 description: South Africa’s Cradle of Humankind UNESCO World Heritage Site has remained the single richest source of hominin fossils for over ninety years. While its hominin specimens have been the subject of extensive research, the same is not true for its abundant faunal assemblages, despite their value in Plio-Pleistocene palaeoenvironmental reconstructions. Moreover, precise ages and depositional histories have been historically difficult to assess, though advancements in both relative and absolute dating techniques are changing this. This review explores the history of non-hominin large mammal faunal reporting, palaeoenvironmental reconstructions based on these fauna, and dating histories (with a focus on biochronology) at the following eight fossil-bearing sites of the Cradle that have been radiometrically dated with uranium-lead: Bolt’s Farm, Cooper’s Cave, Drimolen, Haasgat, Hoogland, Malapa, Sterkfontein and Swartkrans. Continued efforts to provide more precise and direct ages for sites using a variety of methods indicate that the bulk of Cradle deposits date to between 3 and 1.4 Ma. We find that, across almost all eight sites, there is little discussion or debate surrounding faunal reports, with some sites described by a single publication. Many of the reports are decades old with little review or reanalysis in the years following, emphasising the need for reviews such as this one. Our analysis of the data indicates that faunal-based paleoenvironmental reconstructions across sites commonly show a trend of wooded landscapes giving way to grasslands. We find that these reconstructions are primarily based on faunal abundance data, despite the availability of many other informative analytical techniques. The findings of this review highlight a need for more extensive and robust faunal reporting, as this will aid in understanding the context of these Cradle sites. creator: Megan Malherbe creator: Robyn Pickering creator: Deano Stynder creator: Martin Haeusler uri: https://doi.org/10.7717/peerj.18946 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Malherbe et al. title: Integrating adaptation pathways and Ostrom’s framework for sustainable governance of social-ecological systems in a changing world link: https://peerj.com/articles/18938 last-modified: 2025-02-24 description: Dynamic Adaptive Policy Pathway (DAPP) maps are used to plan management decisions in contexts of high uncertainty, such as those driven by environmental changes affecting critical assets. Recent discussions emphasize their relevance for addressing complex common-pool resource challenges, where diverse species, actors, and ecosystem services are intricately connected. However, designing DAPPs for such multifaceted social-ecological systems (SES) is challenging due to the extensive range of potential adaptation options. This study presents a general method to address these challenges by leveraging Ostrom’s theoretical frameworks for the governance of common pool resources—the Institutional Analysis & Development framework (IADF), the social-ecological systems framework (SESF), and the coupled infrastructure systems framework (CISF). These frameworks were used to design nested DAPP maps that structure a large number of adaptation actions across multiple levels of institutional arrangement (operational, collective-choice, constitutional), and then develop a mathematical model to analyze the dynamic robustness of a SES across all potential pathways. The method was applied to predict and understand DAPP maps for supporting the collective management of hedgerow networks delivering diverse ecosystem services. DAPP maps for two SES were compared—one rural and one peri-urban—in France’s agro-ecological landscapes of the Auvergne region. We further modeled the impact of climate change on hedgerows characterized by different size and species richness, revealing the sensitivity of these DAPP maps to transit between nine nested institutional arrangements. We discuss the methodological and practical implications of this approach for managing SES characterized by greater diversities of interconnected species, actors, and ecosystem services, highlighting its strengths and challenges in guiding adaptation under deep uncertainty. creator: Jean-Baptiste Pichancourt creator: Antoine Brias creator: Anne Bonis uri: https://doi.org/10.7717/peerj.18938 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Pichancourt et al. title: Alteration of primary cilia and intraflagellar transport 20 (IFT20) expression in oral squamous cell carcinoma (OSCC) cell lines link: https://peerj.com/articles/18931 last-modified: 2025-02-24 description: BackgroundAberrations in primary cilia expression and intraflagellar transport (IFT) protein function have been implicated in tumourigenesis. This study explores the relationship between the alteration of primary cilia and tumourigenesis by investigating primary cilia expression and the role of IFT20 in regulating matrix metalloproteinase 9 (MMP-9) expression in oral squamous cell carcinoma (OSCC) cell lines.MethodsThe frequency and length of primary cilia were determined in OKF6-TERT2 cells, HSC-2 cells, and HSC-3 cells using immunofluorescence. Additionally, primary cilia presence in non-proliferating OSCC cells was examined. OSCC cells were treated with either small interfering RNA (siRNA) negative control or siRNA targeting IFT20 for functional analysis. mRNA expression levels of IFT20 and MMP-9 were quantified using quantitative reverse transcription polymerase chain reaction (qRT-PCR).ResultsResults showed that HSC-2 cells exhibit abundant primary cilia when cultured in low serum media (2% serum) for 48 h, followed by serum starvation for over 72 h. No significant changes in cilia expression were observed in HSC-3 cells compared to OKF6-TERT2 cells. Ciliated cells were found in non-proliferating HSC-2 and HSC-3 cells. OSCC cells showed longer cilia than OKF6-TERT2 cells, indicating ciliary abnormalities. Changes in ciliation and cilium length of OSCC cells were accompanied by increased expression of IFT20, an intraflagellar transport protein crucial for the primary cilia assembly. However, IFT20 knockdown did not affect MMP-9 at the mRNA level in these cells.Conclusions.This study reveals the differences in primary cilia expression among OSCC cells. Furthermore, the increased abundance and elongation of primary cilia in OSCC cells are accompanied by elevated expression of IFT20. Nonetheless, IFT20 did not affect MMP-9 mRNA expression in OSCC cells. creator: Gulam Sakinah-Syed creator: Jia Shi Liew creator: Nazia Abdul Majid creator: Siti Amalina Inche Zainal Abidin uri: https://doi.org/10.7717/peerj.18931 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Sakinah-Syed et al. title: Comparing between virtual reality based pre-clinical implantation training and traditional learning methods link: https://peerj.com/articles/18891 last-modified: 2025-02-24 description: ObjectiveAs dental implanting becomes an increasing demand among patients with tooth loss, an efficient and effective training for students is to be necessary. In this case, we anticipate the possible application of virtual reality (VR) technology to pre-clinical implantation training (PCIT) in order to improve the students’ learning efficiency and effectiveness.MethodsThe study divided 20 subjects into two groups on average—VR based PCIT (experimental group) and traditional PCIT (control group) with the completion of the background survey (BS) before PCITs, to guarantee no apparent backgroud variation including learning of oral implantology and VR technology, learning habits, interests and hobbies, etc. All subjects received identical professional tests (T-1, T-2, T-3) before, in and after PCITs to assess the knowledge mastery condition and maintaining levels. Along with both PCITs, the subjective evaluation tests (SET) were distributed to collect the subjective feedback data so as to analyze the preference to each PCIT. Meanwhile the total interaction time, learning duration per subject were recorded for the performance analysis.ResultsThe results show that from T-1 to T-2 period, the score of VR based PCIT increased significantly (p < 0.05). And the results of SET show that subjects in VR based PCIT generally obtain over one score higher than the ones in traditional PCIT as for the items of “Convenience”, “Interest”, “Comfort”, “Confidence” and “Subjective initiative” except “Precision”. During both PCITs, VR based PCIT shows a shorter learning duration and sufficient one-on-one interaction opportunities.ConclusionCompared with traditional PCIT, VR based PCIT has obvious influence on enhancing students’ knowledge mastery, study willingness and learning efficiency. creator: Yangjie Li creator: Xu Chen creator: Yuan ding Huang creator: Qingqing He creator: Dize Li creator: Shanshan Hu creator: Peng Xu creator: Tao Chen creator: Xiongwen Ran uri: https://doi.org/10.7717/peerj.18891 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Li et al. title: Injecting structure-aware insights for the learning of RNA sequence representations to identify m6A modification sites link: https://peerj.com/articles/18878 last-modified: 2025-02-24 description: N6-methyladenosine (m6A) represents one of the most prevalent methylation modifications in eukaryotes and it is crucial to accurately identify its modification sites on RNA sequences. Traditional machine learning based approaches to m6A modification site identification primarily focus on RNA sequence data but often incorporate additional biological domain knowledge and rely on manually crafted features. These methods typically overlook the structural insights inherent in RNA sequences. To address this limitation, we propose M6A-SAI, an advanced predictor for RNA m6A modifications. M6A-SAI leverages a transformer-based deep learning framework to integrate structure-aware insights into sequence representation learning, thereby enhancing the precision of m6A modification site identification. The core innovation of M6A-SAI lies in its ability to incorporate structural information through a multi-step process: initially, the model utilizes a Transformer encoder to learn RNA sequence representations. It then constructs a similarity graph based on Manhattan distance to capture sequence correlations. To address the limitations of the smooth similarity graph, M6A-SAI integrates a structure-aware optimization block, which refines the graph by defining anchor sets and generating an awareness graph through PageRank. Following this, M6A-SAI employs a self-correlation fusion graph convolution framework to merge information from both the similarity and awareness graphs, thus producing enriched sequence representations. Finally, a support vector machine is utilized for classifying these representations. Experimental results validate that M6A-SAI substantially improves the recognition of m6A modification sites by incorporating structure-aware insights, demonstrating its efficacy as a robust method for identifying RNA m6A modification sites. creator: Yue Yu creator: Shuang Xiang creator: Minghao Wu uri: https://doi.org/10.7717/peerj.18878 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Yu et al. title: A conceptual replication of the Psychological Typhoon Eye effect in the aftermath of the Petrinja earthquake in Croatia link: https://peerj.com/articles/18682 last-modified: 2025-02-24 description: BackgroundThe Psychological Typhoon Eye (PTE) effect refers to the observation that those living in the epicenters of natural disasters or public emergencies exhibit lower levels of psychological distress than those living further away. The effect has been described in the aftermath of multiple public emergencies, including the 2008 Wenchuan earthquake. However, despite its potential importance for emergency relieve, this phenomenon has received little research attention and requires further replication. The goals of this study were to replicate the PTE effect using both the original items used in prior research and using the validated Depression, Anxiety, and Stress Scales (DASS).MethodsA cross-sectional survey was conducted following an earthquake with a magnitude of 6.4 on the Richter scale that occurred in December 2020 in Petrinja, Croatia. The sample consisted of 316 participants living in Croatia at the time of the earthquake. Questionnaires were administered through an online survey, including the DASS, the items used in previous research, and questionnaires measuring general and earthquake-specific coping. Exposure to the earthquake was operationalized as the degree of devastation participants had experienced (i.e., the degree of structural damage to their home as assessed by local authorities). In line with previous work, we tested for an inverse relationship between the experienced level of devastation and the different measures of psychological distress (i.e., the items used in previous work and the DASS).ResultsWe found no evidence for the PTE effect in our study. Instead, we observed a ripple effect, whereby those most affected by the earthquake showed the most psychological distress. We argue that the ripple effect, rather than the PTE effect, should be seen as the default psychological response pattern to natural disasters and emergencies. creator: Gaëtan Mertens creator: Marta Dürrigl uri: https://doi.org/10.7717/peerj.18682 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Mertens and Dürrigl title: A first trial to supplement local hardwood sawdust at the first soaking for the cultivation of Shiitake (Lentinula edodes) link: https://peerj.com/articles/18622 last-modified: 2025-02-24 description: Supplementation of the growing substrate has been reported to enhance the production of cultivated mushrooms; however, supplementation using nano-sized additives is not yet investigated on Shiitake (Lentinula edodes). The study investigated the potential of a nano-supplement (Lithovit®-Amino25) containing an admixture of 25% L-amino acids on shiitake cultivated on sawdust from locally available oak, maple, and apple trees (oak sawdust: OS, maple sawdust: MS, and apple sawdust: AS). Initially, sawdusts were enriched equally with wheat bran (WB) and at the first soaking, Lithovit®-Amino25 was applied at 5 g/L. Treatments were: T1: OS-WB (control), T2: OS-WB+ nano-amino, T3: MS-WB, T4: MS-WB+ nano-amino, T5: AS-WB, and T6: AS-WB+ nano-amino. Among non-supplemented substrates, complete mycelia run, fruiting, and harvest dates were faster in T1 than in T3 and T5. Complete mycelial development was delayed by 7, 5, 9, and 6 d in T3, T4, T5, and T6 compared to T1. The harvest date was delayed by 7.7–8.3 d on maple sawdust and by 10.5–12.7 d on apple sawdust compared to oak sawdust. However, nano-supplementation hastened fruiting and harvest dates (by 9.3 d) in T4 compared to T3. The biological yield of the second harvest was higher on supplemented than on non-supplemented maple and apple sawdusts. Only T1 and T2 showed consistency in production over two consecutive harvests. Nano-supplementation improved the total biological yield in T2, T4, and T6 by 9.8, 21.0, and 22.5%, respectively. Nevertheless, all treatments, except T4, had lower biological efficiencies compared with T1. In T4, results of stepwise regression showed a strong positive correlation (R2 = 0.96) between the total biological yield and mushroom weight at the second harvest. Supplementation caused a slight or significant improvement in pileus diameter and mushroom firmness and a significant improvement in mushroom’s crude protein (by 2.9–8.2% compared to T1) and fiber contents (by 1–2.3% compared to T1). In conclusion, supplemented maple sawdust would alternate oak sawdust for shiitake production, though other timings of supplementation might be further investigated to optimize production on this substrate. creator: Stephanie Nabhan creator: Soukayna Haidar Ahmad creator: Zeina El Sebaaly creator: Teodor Nedelin creator: Youssef Najib Sassine uri: https://doi.org/10.7717/peerj.18622 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Nabhan et al. title: Study on SARS-CoV-2 infection in middle-aged and elderly population infected with hepatitis virus: a cohort study in a rural area of northeast China link: https://peerj.com/articles/19021 last-modified: 2025-02-21 description: BackgroundTo investigate the symptoms, the level of antibody, the progression of liver disease after SARS-CoV-2 infection in middle-aged and elderly population infected with hepatitis virus.MethodsThe study was based on a cohort of high-risk liver cancer and the participants was recruited in April 2023. Blood sample were collected and information was obtained through questionnaires. Data on reinfection was obtained by follow-up until July 31, 2023. The SARS-CoV-2-specific neutralizing antibody and IgG were measured.ResultsA total of 599 participants infected with hepatitis virus were included and the mean age was 61.3 ± 7.4 years. The SARS-CoV-2 infection rate was 94.7%. Among the infected, 132 were asymptomatic, 435 were symptomatic, no severe cases occurred. Four months after infection, no difference was in liver function and aMAP score between the infected and uninfected. The infected had higher seropositivity rates of both antibodies than the uninfected (neutralizing antibody: uninfected: 93.7%, infected: 99.6%; IgG: uninfected: 59.4%, infected: 98.9%). The levels of both antibodies in the symptomatic were higher than those the asymptomatic and the uninfected (neutralizing antibody: uninfected: 0.75 AU/mL, asymptomatic: 15.46 AU/mL, symptomatic: 24.76 AU/mL; IgG: uninfected: 15.10 AU/mL, asymptomatic: 263.84 AU/mL, symptomatic: 291.83 AU/mL). By July 31, 2023, the incidence of reinfection was 17.5%.ConclusionsAlthough the infection rate of SARS-CoV-2 was high, no severe cases occurred. Omicron infection may not aggravate progression of hepatitis. Four months after infection, the population showed high positivity rate in neutralizing antibody and IgG. Monitoring of virus mutations and targeted prevention and care strategies is crucial for vulnerable populations. creator: Yuchen Pan creator: Zhifang Jia creator: Xinyi Yu creator: Haiyong Lv creator: Yangyu Zhang creator: Yanhua Wu creator: Jing Jiang uri: https://doi.org/10.7717/peerj.19021 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Pan et al. title: Effect of water-based aerobic training on anthropometric, biochemical, cardiovascular, and explosive strength parameters in young overweight and obese women: a randomized controlled trial link: https://peerj.com/articles/19020 last-modified: 2025-02-21 description: BackgroundObesity is a major health concern that raises the risk of chronic illnesses such as heart disease, diabetes, and metabolic disorders. Traditional workouts such as running or walking can be difficult for overweight individuals due to the heavy impact on joints, which causes discomfort and the possibility of injury. Water-based exercises offer a low-impact alternative that overweight people may find more tolerable. There is minimal research on the specific effects of structured water aerobic exercise on health markers in young overweight and obese women, despite the acknowledged benefits of physical activity for weight control and overall health. This study aimed to assess the effects of 10-week water-based aerobic training (thrice a week) on anthropometric, biochemical, cardiovascular parameters, and explosive strength in young overweight and obese women.MethodsIn a randomized controlled trial with a pre-to-post testing design, twenty-seven young overweight and obese women (age: 27 ± 1 years; body mass index (BMI) = 30.0 ± 3.1) were randomly assigned into experimental (EG: performing a water-based aerobic training, n = 16) or control (CG: maintaining their usual activities during the intervention, n = 11) groups. The pre- and post-intervention participants were assessed for their anthropometrics (body height, body weight, body mass index (BMI), body fat and circumferences), biochemical (fasting glycemia, total cholesterol, high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C) and triglyceride (TG)), cardiovascular parameters (resting blood pressure and resting heart rate (RHR)), and explosive strength of upper and lower limbs.ResultsEG showed reductions in body weight, BMI, %BF, fasting glycemia, and TG, along with improvements in HDL-C, LDL-C, RHR, and explosive strength (all p < 0.05; effect size (ES) = 0.180–1.512, trivial to large). In contrast, CG exhibited increases in body weight, BMI, fasting glycemia, LDL-C, and RHR (all p < 0.05; ES = 0.127–0.993, trivial to large), with no significant changes observed in other measured variables. EG showed superior post-test results in fasting glycemia (p < 0.0001; ES = 2.559, large), LDL-C (p < 0.0001; ES = 0.971, large), and explosive strength measures (0.003 ≤ p < 0.0001; ES = 1.145–1.311, large) compared to the CG.ConclusionsOur findings indicate that water-based aerobic training could be a useful program to enhance anthropometric, biochemical, cardiovascular, and explosive strength parameters in young overweight and obese women compared to inactive persons. creator: Imen Ben Cheikh creator: Hamza Marzouki creator: Okba Selmi creator: Bilel Cherni creator: Siwar Bouray creator: Ezdine Bouhlel creator: Anissa Bouassida creator: Beat Knechtle creator: Yung-Sheng Chen uri: https://doi.org/10.7717/peerj.19020 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ben Cheikh et al. title: Effects of Chinese traditional ethnic sports on sleep quality among the elderly: a systematic review and meta-analysis link: https://peerj.com/articles/19019 last-modified: 2025-02-21 description: ObjectiveSleep disorders affect approximately one-fifth of the global elderly population, with poor sleep quality among old adults linked to an increased risk of chronic conditions such as cardiovascular disease, diabetes, and hypertension. Chinese traditional ethnic sports have garnered significant attention for their potential to enhance sleep quality in older adults; however, the effectiveness of these interventions remains controversial. This meta-analysis sought to evaluate the impact of Chinese traditional sports on the quality of sleep among older adults.MethodsA systematic search of databases, including Web of Science, Pubmed, Embase, Cochrane, China National Knowledge Infrastructure (CNKI), Wanfang, and China Science and Technology Journal Database (VIP), was conducted to identify randomized controlled trials (RCTs) examining the effects of Chinese traditional ethnic sports on sleep quality in older adults. Two independent researchers screened the literature, extracted relevant data, and conducted a quantitative meta-analysis using Stata17 software. Subgroup analyses were performed, including forest and funnel plot generation, heterogeneity analysis, sensitivity analysis, and publication bias assessment.ResultsA total of ten studies met the inclusion criteria. The meta-analysis revealed that older adults who participated in Chinese traditional ethnic sports showed significantly lower total PSQI score s relative to non-participants (Hedges’s g = −0.60, 95% CI [−0.89 to −0.31], P < 0.05). Egger’s test suggested no significant publication bias. Sensitivity analyses revealed that the age of participants, intervention mode, frequency, and duration did not substantially affect the combined effect size. Significant improvements were observed in sleep quality (Hedges’s g = −1.06, 95% CI [−2.00 to −0.13], P < 0.05), sleep duration (Hedges’s g = −0.52, 95% CI [−0.87 to −0.17], P < 0.05), and sleep efficiency (Hedges’s g = −0.50, 95% CI [−0.81 to −0.18], P < 0.05).ConclusionChinese traditional ethnic sports are highly effective in improving the sleep quality of older individuals, demonstrating significant benefits in sleep quality, duration, and efficiency. Additionally, these interventions may reduce the reliance on sleep medications. creator: Jiahui Liu creator: Xiong-Wen Ke creator: Yi Lan creator: Diana Yuan creator: Weihao Zhang creator: Jian Sun uri: https://doi.org/10.7717/peerj.19019 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Liu et al. title: Rhamnolipids bio-production and miscellaneous applications towards green technologies: a literature review link: https://peerj.com/articles/18981 last-modified: 2025-02-21 description: Growing attention towards rhamnolipids (RLs) biosurfactants with antibacterial, antifungal, antivirus and antitumor potentials encourage future research in biotechnology and biomedicine fields. Economic production from waste materials, biodegradability and low toxicity makes RLs perform as green molecules that serve in sustainability and green technologies. This review aims to focus on bioproduction, detection and applications of rhamnolipids in pharmaceuticals, soil bioremediation, agriculture and food industries in addition to future perspectives. This will help to shed light on and update the existing knowledge of feasible and sustainable biosurfactant production depending on the fermentation processes. creator: Sanaa S.A. Kabeil creator: Amira M.G. Darwish creator: Soad A. Abdelgalil creator: Abdelaal Shamseldin creator: Abdallah Salah creator: Heba A.I.M. Taha creator: Shimaa Ismael Bashir creator: Elsayed E. Hafez creator: Hesham Ali El-Enshasy uri: https://doi.org/10.7717/peerj.18981 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Kabeil et al. title: The optimal training intervention for improving the change of direction performance of adolescent team-sport athletes: a systematic review and network meta-analysis link: https://peerj.com/articles/18971 last-modified: 2025-02-21 description: BackgroundDue to the influence of growth, adolescent team-sport athletes have the need to improve their change of direction (COD) performance and reduce the risk of anterior cruciate ligament (ACL) injuries during COD. However, the optimal intervention for improving COD performance has not yet been determined. ObjectiveTo quantitatively assess the effects of diverse training interventions on COD performance.MethodsA systematic search of five databases was conducted, adhering to the PRISMA guidelines. Randomized controlled trials that examined 10 distinct training interventions for COD performance in adolescent team-sport athletes were emphasized. Effect sizes were represented as standardized mean differences (SMD) with 95% credible intervals (CI). The Cochrane study risk assessment tool evaluated the risk of bias in the selected studies.ResultsOf the 36 studies analyzed, involving 1,125 participants. Eccentric overload training (EOT) (SMD = −2.06, 95% CI [−2.83 to −1.29]) emerged as the most effective training method for overall COD performance. Subgroup analysis shows that combined training (COM) (SMD = −2.14, 95% CI [−3.54 to −0.74]) was the best training intervention for COD performance with angles less than 90°. EOT (SMD = −2.84, 95% CI [−4.62 to −1.07]) also was two best training intervention for COD performance with angles greater than 90°.ConclusionsThe choice of training intervention should be determined based on the COD angle. When the COD angle exceeds 90° or is not restricted, EOT is the optimal intervention; however, this is not the case for angles below 90°. Further high-quality studies are needed in the future to validate these findings. Systematic review registration: PROSPERO CRD42024501819. creator: Yonghui Chen creator: Maiwulanjiang Tulhongjiang creator: Tianpeng Ling creator: Xinmiao Feng creator: Jing Mi creator: Ruidong Liu uri: https://doi.org/10.7717/peerj.18971 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Chen et al. title: Impact of self-efficacy and burnout on professional development of physical education teachers in the digital age: a systematic review link: https://peerj.com/articles/18952 last-modified: 2025-02-21 description: BackgroundThe professional development of teachers in the digital age will positively impact the effectiveness of physical education teaching. Exploring key factors such as self-efficacy, burnout, and digital technology is crucial to ensure the professional development of teachers.MethodsThe search was conducted in accordance with the PRISMA guidelines and utilized the following databases: Scopus, Web of Science, ProQuest, and Google Scholar. Inclusion and exclusion criteria: population, research methods, keywords, and time limit were described for this study. This article predominantly includes cross-sectional studies, so we have used the AXIS risk assessment methodology.ResultsThe study included ten articles, seven of which (70%) were quantitative. Three key findings emerged from this review: first, the studies on self-efficacy were more noteworthy than the studies on burnout. Second, female teachers were more expressive in their digital teaching, while male teachers had higher levels of self-efficacy in their digital teaching. Finally, the study explored various factors affecting self-efficacy and burnout in relation to digital teaching. The study demonstrated that professional development has a higher impact on physical education teachers’ self-efficacy, and in turn, self-efficacy reduces burnout. Additionally, burnout had a significant impact on professional development.ConclusionThis study describes the limitations of risk assessment and uses the AXIS tool to assess the methodological quality of this review report instead of using the risk of bias tool. The use of digital teaching methods can increase self-efficacy and alleviate burnout among physical education teachers. This review analyses the effects of digital technology, self-efficacy, and burnout on the career progression of physical education instructors and examines the implications for future developments. creator: Luhong Ma creator: Chen Soon Chee creator: Saidon Amri creator: Xuejiao Gao creator: Qinglei Wang creator: Nina Wang creator: Pan Liu uri: https://doi.org/10.7717/peerj.18952 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Ma et al. title: Proteomic and phosphoproteomic profilings reveal distinct cellular responses during Tilapinevirus tilapiae entry and replication link: https://peerj.com/articles/18923 last-modified: 2025-02-21 description: BackgroundTilapia Lake virus (TiLV) poses a significant threat to global tilapia aquaculture, causing high mortality rates and severe economic losses. However, the molecular mechanisms underlying TiLV-host interactions remain largely unexplored.MethodologyWe investigated the proteomic and phosphoproteomic changes in two piscine cell lines, E-11 and RHTiB cells, following TiLV inoculation at different time points. Differential protein expressions at 10-min and 24-h post infection were selected for constructing protein-protein interactions and analyzing enriched pathways related to the viral entry and replication.ResultsOur findings revealed significant alterations in protein expression and phosphorylation states, highlighting distinct responses between the cell lines. In E-11 cells, TiLV infection suppressed proteins involved in the Janus kinase-signal transducer and activator of transcription and Fas-associated death domain protein-tumor necrosis factor receptor-associated factor pathways, leading to activation of nucleotide oligomerization domain signaling and apoptosis. In RHTiB cells, TiLV suppressed host cellular metabolism by reducing protein phosphatase activity to facilitate early viral entry, while later stages of infection showed increased activity of myosin heavy chain 9 and enhanced host immune responses via phosphorylation of ribosomal protein L17 and GTPase immunity-associated protein 7 (GIMAP7).ConclusionOur study suggested that TiLV employs different strategies to manipulate host cellular pathways depending on the cell type. Further studies are essential to validate these findings and ultimately facilitate the development of effective antiviral strategies. creator: Tuchakorn Lertwanakarn creator: Matepiya Khemthong creator: Piyathip Setthawong creator: Narumon Phaonakrop creator: Sittiruk Roytrakul creator: Sekkarin Ploypetch creator: Win Surachetpong uri: https://doi.org/10.7717/peerj.18923 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Lertwanakarn et al. title: Construction and verification of a prognostic model for bladder cancer based on disulfidptosis-related angiogenesis genes link: https://peerj.com/articles/18911 last-modified: 2025-02-21 description: BackgroundBladder cancer (BLCA) is the most common malignancy of the urinary system and one of the most common cancers worldwide. This study seeks to examine the influence of angiogenesis-related genes (ARGs) linked to disulfidptosis on BLCA patients and to formulate a prognostic model for evaluating their prognosis and response to immunotherapy.MethodsThis study used sequencing data of BLCA in the Cancer Genome Atlas (TCGA) database. Unsupervised consensus clustering analysis, cox regression analysis, and least absolute shrinkage and selection operator (LASSO) regression analysis were used to screen hub genes and construct a related prognostic risk model. The receiver operating characteristic (ROC) curve and independent prognostic analysis were then used to verify the predictive performance of the signature genes. Clinical characteristics, immune status, and Tumor Mutation Burden (TMB) of the prognostic risk model were evaluated. The expression levels of model genes within standard bladder epithelial cell lines (SV-HUC-1) and bladder cancer cell lines (T24 and SW1710) were quantified through qRT-PCR.ResultsThe constructed prognostic risk model can be used as an independent risk indicator for BLCA and was validated in an external dataset. Immune cell infiltration analysis showed that CD8+T cells, Tregs and dendritic cells were significantly different between the two groups. A significant increase was observed in the Stromal score, Immune score and ESTIMATE score in the high-risk group compared with the low-risk group. The Immune Exclusion score and Tumor Immune Dysfunction and Exclusion (TIDE) score of the high-risk group were higher than those of the low-risk score group. Compared with the normal bladder epithelial cell line (SV-HUC-1), the expression levels of 2 model genes (COL5A2 and SCG2) in bladder cancer cell lines (T24 and SW1710) were significantly elevated.ConclusionThis study helps us understand the characteristics of disulfidptosis-related subgroups. The characteristics of disulfidptosis-related ARGs may be used to evaluate the prognosis and immunotherapy response of BLCA patients. creator: Zhihao Zhou creator: Yuwei Zhang creator: Yuhua Zhou creator: Jiayu Gu creator: Jufa Li creator: Jianfeng Shao creator: Ninghan Feng uri: https://doi.org/10.7717/peerj.18911 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zhou et al. title: Genetic structure and designing a preliminary core collection of Zizania latifolia in China based on 12 microsatellites markers link: https://peerj.com/articles/18909 last-modified: 2025-02-21 description: The genetic diversity and structure of wild crop relatives are crucial for their conservation and utilization in breeding programs. This study presents a comprehensive survey and collection of Zizania latifolia across its natural distribution range in China. Using 12 microsatellite markers, the genetic diversity of 357 wild Z. latifolia accessions from 25 populations was evaluated, revealing a high genetic diversity (He = 0.439). The genetic structure analysis indicated significant genetic differentiation among populations, with evidence of isolation by distance. CoreHunter3 and PowerMarker software were employed to design a preliminary core collection, and the final core collection comprised 92 wild accessions. The core collection was found to be representative of the original germplasm, ensuring the effective conservation of Z. latifolia’s genetic resources. This study would provide valuable insights for the development of conservation strategies and the utilization of Z. latifolia. creator: Xiangliang Lei creator: Xiaona Su creator: Chengchuan Zhou creator: Shaolin Jiang creator: Xiaoquan Yuan creator: Yao Zhao creator: Shaomei Jiang uri: https://doi.org/10.7717/peerj.18909 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Lei et al. title: Spatial and temporal trends in dung beetle research link: https://peerj.com/articles/18907 last-modified: 2025-02-21 description: Dung beetles are one of the most charismatic animal taxa. Their familiarity as ecosystem service providers is clear, but they also play a range of roles in a variety of different ecosystems worldwide. Here, we give an overview of the current state of dung beetle research and the changes in the prevalence of topics in a collated corpus of 4,145 peer-reviewed articles of dung beetle research, spanning from 1930 until 2024. We used a range of text-analysis tools, including topic modelling, to assess how the peer-reviewed literature on dung beetles has changed over this period. Most of the literature is split into three distinct, but related discourses–the agri/biological topics, the ecological topics, and the taxonomic topics. Publications on the ‘effect of veterinary chemicals’ and ‘nesting behaviour’ showed the largest drop over time, whereas articles relating to ‘ecosystem function’ had a meteoric rise from a low presence before the 2000’s to being the most prevelant topic of dung beetle research in the last two decades. Research into dung beetles is global, but is dominated by Europe and North America. However, the research from South America, Africa, and Australia ranges wider in topics. Research in temperate and tropical mixed forests, as well as grasslands, savanna and shrublands dominated the corpus, as would be expected from a group of species directly associated with large mammals. Our assessment of dung beetle research comes when ecosystem service provision is becoming more important and more dominant in the literature globally. This review therefore should be of direct interest to dung beetle researchers, as well as researchers working in agricultural, ecological, and taxonomic arenas globally. Research worldwide and across agri/biological, ecological, and taxonomic discourses is imperative for a continued understanding of how dung beetles and their ecosystem services are modified across rapidly changing natural and agricultural landscapes. creator: Zac Hemmings creator: Maldwyn J. Evans creator: Nigel R. Andrew uri: https://doi.org/10.7717/peerj.18907 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Hemmings et al. title: Potential role of ghrelin in neuroprotection and cognitive function: implications for diabetic cognitive impairment link: https://peerj.com/articles/18898 last-modified: 2025-02-21 description: Ghrelin is a class of brain and intestinal peptides. It regulates food intake and body glucose levels and maintains cellular homeostasis. In recent years, research has revealed that ghrelin may positively impact learning and memory. Despite ghrelin’s multiple functions in the central nervous system, its use as a therapeutic agent for neurologic dysfunction remains unclear. Diabetic cognitive impairment (DCI) is a severe neurological complication of diabetes mellitus. Its incidence is increasing as a comorbidity in endocrinology and neurology. Additionally, it is a risk factor for Alzheimer’ s disease (AD). Ghrelin levels are altered in patients with diabetes mellitus combined with cognitive impairment. Furthermore, modulation of ghrelin levels improved cognitive function in rats with DCI. These findings suggest the potential therapeutic importance of ghrelin in the pathogenesis of DCI. This article presents a comprehensive review of the pathogenesis of DCI and its potential modulation by ghrelin and its mimics. Furthermore, this study elucidates the therapeutic prospects of ghrelin and its mimics for DCI, aiming to identify novel therapeutic targets and research avenues for the prevention and management of DCI in the future. creator: Yuhan Zhang creator: Ruihua Zhang creator: Xin Wang creator: Leilei Shi creator: Hongzhe Zhu creator: Jiping Liu uri: https://doi.org/10.7717/peerj.18898 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zhang et al. title: Extending the fossil record of late Oligocene non-biting midges (Chironomidae, Diptera) of New Zealand link: https://peerj.com/articles/18893 last-modified: 2025-02-21 description: BackgroundThe modern chironomid fauna of New Zealand is diverse, highly endemic and reflects a complex biogeographical history. This fauna has been important for developing phylogenetic and biogeographic concepts including Brundin’s writings on transantarctic relationships but until now the fossil record to support these reconstructions has been very limited. Here we describe the first fossil species of Chironomidae, subfamily Orthocladiinae, from New Zealand, based on inclusions in amber from the late Oligocene Pomahaka Formation of the South Island.MethodsWe examined newly excavated fossil tree resin (amber) from the late Oligocene Pomahaka Formation in southern New Zealand for inclusions. Amber pieces containing chironomids were prepared and morphologically investigated using light-microscopy and µCT-scanning. Specimens were taxonomically evaluated using identification keys for modern adult chironomid midges. Habitus and key morphological features of each specimen were documented photographically and/or by line drawings.ResultsThirteen Chironomidae specimens from Pomahaka amber were identified as members of the subfamily Orthocladiinae Kieffer. Bryophaenocladius zealandiae sp. nov. Baranov is the first Southern Hemisphere fossil of the genus. Bryophaenocladius Thienemann, 1934 is absent from the extant fauna of the main islands of New Zealand; however, it may be present on the subantarctic Auckland Islands. Two incompletely preserved specimens are described as Morphotype 1 cf. Bryophaenocladius zealandiae. Based on a male adult, Pterosis extinctus sp. nov. Baranov is described as the first fossil record of the extant genus Pterosis Sublette and Wirth, today represented by a single endemic species on the New Zealand subantarctic Auckland Islands and Campbell Island. Two female adult specimens are described as Morphotype 2 cf. Metriocnemini. The new fossils of the genera Bryophaenocladius and Pterosis belong to chironomid taxa requiring terrestrial or semi-aquatic habitats for larval development, supporting the notion of a humid forest swamp paleoenvironment for the Pomahaka amber source forest. creator: Viktor O. Baranov creator: Jörg U. Hammel creator: Daphne E. Lee creator: Alexander R. Schmidt creator: Uwe Kaulfuss uri: https://doi.org/10.7717/peerj.18893 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Baranov et al. title: A375 melanoma-derived lactate controls A375 melanoma phenotypes by inducing macrophage M2 polarization via TCA cycle and TGF-β signaling link: https://peerj.com/articles/18887 last-modified: 2025-02-21 description: IntroductionMacrophage phenotypes have been linked to progression and prognosis of cutaneous melanoma. However, the association between Warburg effect in A375 melanoma and macrophages polarization, as well as the underlying mechanisms, remains less well documented.ObjectiveThe present study aimed to investigate the effect of lactate derived from A375 melanoma on macrophage polarization, melanoma phenotype responses and the underlying mechanisms.MethodsFlow cytometry was performed to evaluate the expression of M1 and M2 markers, cell cycle and apoptosis. Levels of transforming growth factor β (TGF-β) and tumor necrosis factor α (TNF-α) were determined with enzyme-linked immunosorbent assay (ELISA) kit. Proliferation and invasion were assessed by CCK8 and transwell assays, respectively. The extracellular acidification rate (ECAR) and oxygen consumption rate (OCR) were analyzed using an XF96 extracellular flux analyzer. Protein expressions were determined by Western blotting.ResultsOur results revealed that melanoma A375 conditioned medium (A375-CM) induced peripheral blood mononuclear cells (PBMCs) to polarize toward anti-inflammatory M2 macrophages. M2 markers CD206 and ARG1 expression increased, as did TGF-β secretion. Conversely, M1 marker CD68 expression decreased. Furthermore, hypoxia promoted macrophage M2 polarization induced by A375-CM. Elevated lactate level in PIG1-conditioned medium (PIG1-CM) induced M2 polarization, whereas the lactate transport inhibitor AZD3965 suppressed this effect in PBMCs cultured with A375-CM. Additionally, lactate derived from melanoma regulated M1/M2 polarization by the tricarboxylic acid (TCA) cycle instead of glycolysis. Significantly, polarized macrophages altered melanoma phenotypes including proliferation, clone formation, cell cycle, apoptosis, migration and invasion via TCA cycle and TGF-β.ConclusionOur data collectively demonstrate that lactate derived from melanoma facilitates polarization of M2 macrophages, which subsequently leads to modifications in melanoma phenotypes via TCA cycle and TGF-β signaling. creator: Qifei Wang creator: Yurui Shi creator: Zelian Qin creator: Mengli Xu creator: Jingyi Wang creator: Yuhao Lu creator: Zhenmin Zhao creator: Hongsen Bi uri: https://doi.org/10.7717/peerj.18887 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Wang et al. title: Integrated multiomics analysis highlights the immunosuppressive role of granulin precursor positive macrophages in hepatocellular carcinoma link: https://peerj.com/articles/18879 last-modified: 2025-02-21 description: It has been reported that tumor-associated macrophages (TAMs) play a complicated role in cancer occurrence and development, immune escape, and immune checkpoint blockade (ICB) resistance. However, the role of granulin precursor (GRN) highly expressed macrophages (hereafter refer to GRN+ macrophages) in hepatocellular carcinoma (HCC) remains poorly understood. Herein, we systematically integrated multiomics analysis of human tumor tissues to illustrate the functional role of GRN+ macrophages in HCC. GRN is selectively expressed by TAMs in different type of cancers including HCC, and was significantly associated with poor prognosis in several type of cancer. GRN was closely correlated with infiltration levels of most immune cells, especially the M2 macrophage cells in various cancers. In particular, both mRNA and protein expression level of GRN was significantly upregulated in HCC. Compared with tumor tissue, GRN was more significantly expressed in the stroma area between HCC tissues and adjacent non-tumor tissues. High expression of GRN was significantly correlated with M2-polarization of macrophages and T-cell exhaustion in HCC. GRN+ macrophages communicated with intratumoral immune cells, especially CD8+ T cells. Functionally, GRN+ macrophages contacted with CD8+ T cells, which inducing T-cell exhaustion. Our study offers a comprehensive understanding of the clinical relevance and immunological role of GRN+ macrophages in HCC, indicating its potential role as a promising target for immunotherapeutic strategies. creator: Jun Li creator: Weizhen Huang creator: Junjie Kuang creator: Siwei Zhou creator: Yi Li creator: Yuan Xia uri: https://doi.org/10.7717/peerj.18879 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Li et al. title: Cadmium toxicity on communities of ammonia-oxidizing microorganisms link: https://peerj.com/articles/18829 last-modified: 2025-02-21 description: The oxidation of ammonia to nitrite, which constitutes the initial and rate-limiting step in the nitrification process, plays a pivotal role in the transformation of ammonia within soil ecosystems. Due to its susceptibility to a range of pollutants, such as heavy metals, pesticides, and pharmaceuticals, nitrification serves as a valuable indicator in the risk assessment of chemical contaminants in soil environments. Here, we analyzed the effects of cadmium (Cd) treatment on soil potential nitrification rate (PNR), and the abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities. The results showed that, under 1 day incubation, the soil PNR with Cd 0.5 mg kg−1 was a little higher but not statistically significant than that with zero mg kg−1. Then, the soil PNR increased with the increasing Cd concentration from 0.5 to one mg kg−1, and continuously declined from 1 to 10 mg kg−1. Moreover, we predicted the bacterial functions of samples with hormetic Cd dose (one mg kg−1) by PICURSt (Phylogenetic Investigation of Communities Reconstruction of Unobserved States), and found that the expression of protein disulfide isomerase (PDI) increased with the hormetic Cd dose. PDI is known to enhance the activity of compounds containing –SH or –S–S which can help prevent oxidative damage to membranes. The soil PNR was significantly correlated with AOA abundance rather than AOB, even the abundance of AOB was higher than that of AOA, indicating that AOA functionally predominated over AOB. Our study effectively evaluated the Cd toxicity on soil microbial community and clearly illustrated the ecological niches of AOA and AOB in the agricultural soil system studied, which will be instructive for the sustainable development of agriculture. creator: Huan He creator: Lina Dang creator: Qian Yang creator: Ran Chen creator: Jianmei Yang creator: Jinshan Li creator: Qiang Zhu creator: Jiulan Dai uri: https://doi.org/10.7717/peerj.18829 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 He et al. title: Integrative taxonomy reveals three new species and one new record of Psychropotes (Holothuroidea, Elasipodida, Psychropotidae) from the Kermadec Trench region and the Wallaby-Zenith Fracture Zone link: https://peerj.com/articles/18806 last-modified: 2025-02-21 description: The holothuroid genus Psychropotes is the largest genus in the family Psychropotidae. Prior to this study, this genus contained 20 accepted species and was prominent representatives in the deep-sea benthic fauna at lower bathyal-abyssal depths throughout the global oceans, but it has been poorly studied in the hadal zone. Deep-sea holothuroids were collected in October 2022 to March 2023 by the joint China-New Zealand deep-diving scientific expedition to the Kermadec Trench in the South Pacific Ocean and the Wallaby-Zenith Fracture Zone in the East Indian Ocean at a depth of 6,018–6,605 m. Our examination of specimens of Psychropotes revealed three new species, which we described as Psychropotes diutiuscaudasp. nov., Psychropotes nigrimargariasp. nov., and Psychropotes asperatussp. nov. We also recorded Psychropotes depressa (Théel, 1882) for the first time from the Kermadec Arc at a depth of 1,620 m. We provide comprehensive descriptions of the morphological features and a taxonomic key for the genus Psychropotes. We also performed a phylogenetic analysis of the order Elasipodida based on COI sequences and the concatenated 16S-COI sequences. Intraspecific and interspecific genetic distances were calculated among Psychropotes Species based on COI sequences. Our phylogenetic analyses supported the assignment of three new species to the genus Psychropotes and their differentiation from congeners. The geographical distribution and global depth range of psychropotid species were summarized, and the results showed that the Pacific region had the highest species diversity. These findings contribute to the taxonomic diversity and patterns of geographical distribution in the family Psychropotidae. creator: Yunlu Xiao creator: Haibin Zhang uri: https://doi.org/10.7717/peerj.18806 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Xiao and Zhang title: The mountain papaya may be a possible reservoir of the Kashmir bee virus link: https://peerj.com/articles/18634 last-modified: 2025-02-21 description: BackgroundThe Kashmir bee virus (KBV) infects many species of Hymenoptera, including bees, wasps, and other pollinators, potentially contributing to honeybee population declines. KBV can cause death of bees. KBV can infect through both vertical transmission (from queen to larvae and vice versa) and horizontal transmission (via food contamination). Plants pollinated by bees may be a source of horizontal transmission, through fecal contamination of pollen and flowers by infected pollinators, both intra- and interspecifically. Pollinated plants constitute a source of KBV intra- and inter-species horizontal transmission, particularly by the contamination of pollen and flowers by feces of KBV-infected pollinators.ResultWe test for the presence of KBV sequences in the transcriptomes of Vasconcellea pubescens, a commercially valuable plant species known as mountain papaya. We mapped transcriptomes from fruit, leaves, and root tissues to the KBV reference genome with 91% coverage, from which we produced a consensus sequence denominated Kashmir bee virus ch. phylogenetic analysis revealed that KBV-Ch shares 97% nucleotide identity with the reference genome, and groups with other KBV strains isolated from Spain, Chile and New Zealand. creator: Jorge Y. Faúndez-Acuña creator: Diego Verdugo creator: David Vergara creator: Gerardo Olivares creator: Gabriel I. Ballesteros creator: Karla Quiroz creator: Carlos A. Villarroel creator: Gloria González uri: https://doi.org/10.7717/peerj.18634 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Faúndez-Acuña et al. title: Occurrence rate and risk factors for acute kidney injury after lung transplantation: a systematic review and meta-analysis link: https://peerj.com/articles/18364 last-modified: 2025-02-21 description: BackgroundCompared with other solid organ transplantation, the morbidity rate of acute kidney injury is higher in lung transplantation. Our research was designed to examine the occurrence rate and risk factors for acute kidney injury after lung transplantation through a systematic review and meta-analysis.MethodologyWe conducted a database search for case-control studies and cohort studies on the occurrence rate and risk factors for acute kidney injury after lung transplantation up to August 19, 2023. Stata 15.0 was used for data analysis.ResultsNineteen case-control or cohort studies were included, involving 1,755 cases of acute kidney injury after lung transplantation and 1,404 cases of non-acute kidney injury after lung transplantation. Based on the meta-analysis, the risk factors for acute kidney injury after lung transplantation included pulmonary fibrosis (OR, 1.34; CI [1.09–1.65]), hypertension (OR, 1.30; CI [1.07–1.58]), pre-op mechanical ventilation (OR, 3.30; CI [1.84–5.90]), pre-op extracorporeal membrane oxygenation (OR, 3.70; CI [2.51–5.45]), double lung transplantation (OR, 1.91; CI [1.45–2.53]), cardiopulmonary bypass support (OR, 1.82; CI [1.38–2.40]), cardiovascular events (OR, 1.50; CI [1.15–1.96]), intra-op hypotension (OR, 2.70; CI [1.42–5.14]), post-op extracorporeal membrane oxygenation (OR, 1.90; CI [1.20–3.01]), sepsis (OR, 3.20; CI [2.16–4.73]), dialysis (OR, 12.79; CI [6.11–26.8]).ConclusionsBased on the existing evidence, clinical professionals can implement early detection, diagnosis and treatment of patients with acute kidney injury after lung transplantation, to improve the quality of life of these patients. creator: Nuan Lee creator: Haoxing Ying uri: https://doi.org/10.7717/peerj.18364 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Lee and Ying title: Unravelling approaches to study macrophages: from classical to novel biophysical methodologies link: https://peerj.com/articles/19039 last-modified: 2025-02-20 description: Macrophages play crucial roles in immune responses and tissue homeostasis. Despite the fact that macrophages were described more than a century ago, they continue to be the cells of intensive interest. Advanced understanding of phenotypic diversity in macrophages holds great promise for development of cell-based therapeutic strategies. The introduction of innovative approaches in cell biology greatly enhances our ability to investigate the unique characteristics of macrophages. The review considers both classical methods to study macrophages and high-tech approaches, including single-cell sequencing, single-cell mass spectrometry, droplet microfluidics, scanning probe microscopy and atomic force spectroscopy. This review will be valuable both to specialists beginning their study of macrophages and to experienced scientists seeking to deepen their understanding of methods at the intersection of biological and physical sciences. creator: Polina Vishnyakova creator: Andrey Elchaninov creator: Timur Fatkhudinov creator: Dmitry Kolesov uri: https://doi.org/10.7717/peerj.19039 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Vishnyakova et al. title: Hydroxycinnamoyl-coenzyme A: tetrahydroxyhexanedioate hydroxycinnamoyl transferase (HHHT) from Phaseolus vulgaris L.: phylogeny, expression pattern, kinetic parameters, and active site analysis link: https://peerj.com/articles/19037 last-modified: 2025-02-20 description: BAHD acyl-coenzyme A (CoA) transferases comprise a large family of enzymes in plants which transfer an acyl group from a CoA thioester to hydroxyl or amine groups to form esters or amides, respectively. Clade Vb of this family primarily utilizes hydroxycinnamoyl-CoA as the acyl donor. These enzymes are involved in biosynthesis of diverse specialized metabolites with functions such as structure (e.g., lignin formation) and biotic/abiotic stress mitigation. The diversity of these enzymes has arisen from both divergent and convergent evolution, making it difficult to predict substrate specificity or enzyme function based on homology, and relatively few BAHD transferases have been characterized biochemically with respect to substrate specificity. We previously identified a hydroxycinnamoyl-CoA: tetrahydroxyhexanedioate hydroxycinnamoyl transferase (HHHT) from common bean capable of transferring hydroxycinnamic acids to mucic or saccharic acid to form the corresponding esters. Here, to better understand the structure/function relationships of this enzyme, we have further characterized it with respect to expression pattern, kinetic parameters, and predicted three-dimensional (3-D) structure and active site interactions with acceptor substrates. The hhht gene was expressed predominantly in leaves and to a lesser extent flowers and shoots. KM values did not vary greatly among donor or among acceptor substrates (generally less than two-fold), while kcat values were consistently higher for saccharic acid as substrate compared to mucic acid, leading to higher catalytic efficiency (as kcat/KM) for saccharic acid. Both acceptors had similar binding poses when docked into the active site, and the proximity of multiple hydroxyl groups to the catalytic His 150, especially for saccharic acid, might provide some insights into regiospecificity. These findings provide a foundation for better understanding how the 3-D structure of BAHD transferases relates to their substrate specificity, as we explore the chemistry of the active site and interactions with ligands. This could ultimately lead to better prediction of their function and ability to rationally design BAHD transferases to make useful and novel products. creator: Amanda Fanelli creator: Christina Stonoha-Arther creator: Michael L. Sullivan uri: https://doi.org/10.7717/peerj.19037 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Fanelli et al. title: Examination of a novel dietary fiber formulation on morphology and nutritional physiology of young male Sprague-Dawley rats fed a high fat diet link: https://peerj.com/articles/19029 last-modified: 2025-02-20 description: Western diets are a public health concern as excess intake of simple sugars and fatty foods, and consequently low consumption of fruits and vegetables, can contribute to obesity and other chronic diseases such as diabetes mellitus, metabolic syndrome, cardiovascular diseases, and cancer. Due to the high prevalence of diseases related to Western diets, the objective of this study was to evaluate whether the inclusion of a novel fiber-rich complex could prevent high fat diet-induced weight gain, adiposity, hyperglycemia, dyslipidemia, and oxidative stress in young male Sprague-Dawley rats, Rattus norvegicus. The novel fiber complex contained a blend of bioactive ingredients: 27% flaxseed, 15.9% wheat bran, 14.8% wheat germ, 10% psyllium, 13.1% brewer’s yeast, and 19.2% grapeseed flour. The study included 24 6-week-old rats divided into three groups that were fed either a control diet (C; standard rodent maintenance diet) containing fiber (3.8%g diet); high-fat diet (H) containing Solka Floc cellulose fiber (6.46%g diet); or high-fat diet in which 5% of the diet was replaced with the novel fiber complex (HF) (total fiber: 5%g fiber complex + 6.14%g Solka Floc). Rats in all diet groups gained significant weight during the 6-week feeding period (p < 0.001) consistent with normal growth. Whereas no differences were observed for blood lipids or beta-hydroxybutyrate, consumption of the H diet significantly increased adiposity (p < 0.001), liver triglycerides (p < 0.001), and fasting whole blood glucose concentrations (p < 0.001) in comparison to the C diet. These effects of high fat consumption were not prevented by the inclusion of the novel fiber complex in this experimental design. creator: Milena Figueiredo de Sousa creator: Jingyu Ling creator: Eduardo Asquieri creator: Corrie Whisner creator: Karen L. Sweazea uri: https://doi.org/10.7717/peerj.19029 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Figueiredo de Sousa et al. title: Do ambiguous images provide psychological insights? Testing a popular claim link: https://peerj.com/articles/19022 last-modified: 2025-02-20 description: Social media posts and websites claim that the way in which people perceive ambiguous images reveals insights into their personality and thinking style. To explore this notion, participants indicated the first image that they perceived in four ambiguous pictures (Duck-Rabbit, Younger-Older Woman, Rubin’s Vase and Horse-Seal), and completed a Five Factor personality measure along with scales relating to optimism, procrastination, holistic thinking, and decision-making style. Many of the claims received no empirical support and so constitute a new type of psychological myth. Future research could explore why these claims remain popular with the public and why people frequently share the material with others. In addition, several significant and interesting findings emerged, including associations between Duck-Rabbit, personality, and optimism, and Younger-Older Woman and age. Possible future research into these phenomena is discussed. creator: Richard Wiseman creator: Caroline Watt uri: https://doi.org/10.7717/peerj.19022 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Wiseman and Watt title: Evaluation of a seed drill for barley and vetch sowing as a function of varying seeding ratios link: https://peerj.com/articles/19014 last-modified: 2025-02-20 description: ObjectivesThe objective of this study was to evaluate the performance of a seed drill for seeding barley and vetch mixtures having different ratios and to determine their impact on plant emergence, yield and feed quality of component crops.MethodsThe laboratory and field experiments were conducted to determine the performance of the seeder using pure barley, common vetch, and their mixtures in ratios, namely 100:0, 0:100, 75:25, 50:50, 25:75. The seed flow and distribution uniformity across the rows were determined within laboratory conditions, while other response variables were assessed in the field conditions.ResultsThe coefficient of variation values of flow evenness for barley and vetch were found to be 1.0–5.5% and 0.3–2.1%, respectively. Seed distribution uniformity of each row unit were also determined ranging from 4.2% to 10.7% and from 0.4% to 1.4% for barley and vetch, respectively. The goodness criteria values ranged between 66.4%–86.0% for the laboratory tests while the corresponding values had a range of 78%–86% for field samples. Based on the findings in this work, the overall ranges of variation factor values were 0.43–1.28 and 0.36–0.77 for laboratory and field evaluations, respectively. Furthermore, the maximum yield was 42,620 kg ha−1, whereas the minimum dry material ratio was 16.93% recorded for pure barley crop.ConclusionsIt appears that the results in this work demonstrated that the seed drill could have a great potential to be used effectively for the seeding of barley as well as vetch mixtures as a function of various ratios to enhance the overall yield of the crop. creator: Arzu Yazgi creator: Tuncay Gunhan creator: Behcet Kir creator: Gulcan Demiroglu Topcu creator: Erdem Aykas uri: https://doi.org/10.7717/peerj.19014 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Yazgi et al. title: Dinosaur teeth from the Lower Cretaceous Jiufotang Formation of western Liaoning, China link: https://peerj.com/articles/19013 last-modified: 2025-02-20 description: Here, two dinosaur teeth are discovered from the Lower Cretaceous Jiufotang Formation in Longcheng, Chaoyang, western Liaoning, China. This discovery marks a new fossil site for the Jehol Biota, characterized by three-dimensionally preserved fossils. Based on comprehensive morphological comparisons, the teeth can be assigned to Theropoda and early-diverging Titanosauriformes. The theropod tooth, with a preserved length of 47.8 mm, represents a distinct taxon separate from Sinotyrannus, which is the only known large theropod dinosaur from the Jiufotang Formation. The titanosauriform tooth represents the youngest sauropod record within the Jehol Biota. These findings contribute to an increased dinosaur diversity within the Jiufotang Formation from ten taxa to 12. creator: Ya-Lei Yin creator: Yang Li creator: Jin Hu creator: Hong-Gang Zhang uri: https://doi.org/10.7717/peerj.19013 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Yin et al. title: A novel microbial agent reduces soil paclobutrazol residue, enhances enzyme activities and increases Ophiopogon japonicus production link: https://peerj.com/articles/19008 last-modified: 2025-02-20 description: BackgroundOphiopogon japonicus (O. japonicus) is a versatile plant valued for its medicinal, food, and ornamental properties. Its cultivation often involves the excessive use of paclobutrazol, leading to a series of environmental and agricultural problems such as soil contamination, nutrient depletion, and safety risks. However, there is currently no effective solution.MethodsBased on a novel microbial agent, Micrococcus yunnanensis strain HY001 (MYSH), field experiments were conducted in the main production area of O. japonicus. Soil paclobutrazol residue, soil enzyme activities, and the yield and dry matter ratio of O. japonicus were measured. Hierarchical partitioning (HP) was used to identify the relative importance of different variables, and partial least squares path modeling (PLS-PM) was applied to elucidate the mechanisms underlying MYSH’s effects on soil health and crop production.ResultsMYSH significantly reduced soil paclobutrazol residue by 75.18% over five months, compared to a natural degradation rate of 50.72% over a year. Compared to the control group, the MYSH-treated group enhanced soil sucrase activity, soil urease activity, and soil alkaline phosphatase activity, with rates of 47.81%, 46.70%, and 216.66%, respectively. Additionally, MYSH improved O. japonicus productivity, with a 94.75% increase in yield and a 17.64% increase in dry matter ratio. HP revealed that MYSH was the primary factor affecting the yield and dry matter ratio of O. japonicus, with relative importance of 47.75% and 42.28%, respectively. The key mechanism was that MYSH degraded soil paclobutrazol residue, which in turn influenced soil sucrase activity, ultimately impacting the yield of O. japonicus (p < 0.05).ConclusionsThis study demonstrates the dual role of MYSH as both an environmental remediation agent and a crop productivity enhancer for the first time. By reducing paclobutrazol residue and enhancing soil health and crop production, MYSH shows great potential for broader application in sustainable agricultural practices. This research highlights the efficacy of microbial agents in addressing agrochemical contamination and promoting sustainable farming, providing a valuable contribution to the development of eco-friendly agricultural solutions. creator: Xiaojun Jiang creator: Huadong Wang creator: Yi Huang creator: Hong Jin creator: Jianguo Ding creator: Lin Ma creator: Lei Zheng uri: https://doi.org/10.7717/peerj.19008 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Jiang et al. title: AI detectors are poor western blot classifiers: a study of accuracy and predictive values link: https://peerj.com/articles/18988 last-modified: 2025-02-20 description: The recent rise of generative artificial intelligence (AI) capable of creating scientific images presents a challenge in the fight against academic fraud. This study evaluates the efficacy of three free web-based AI detectors in identifying AI-generated images of western blots, which is a very common technique in biology. We tested these detectors on AI-generated western blot images (n = 48, created using ChatGPT 4) and on authentic western blots (n = 48, from articles published before the rise of generative AI). Each detector returned a very different sensitivity (Is It AI?: 0.9583; Hive Moderation: 0.1875; and Illuminarty: 0.7083) and specificity (Is It AI?: 0.5417; Hive Moderation: 0.8750; and Illuminarty: 0.4167), and the predicted positive predictive value (PPV) for each was low. This suggests significant challenges in confidently determining image authenticity based solely on the current free AI detectors. Reducing the size of western blots reduced the sensitivity, increased the specificity, and did not markedly affect the accuracy of the three detectors, and only slightly improved the PPV of one detector (Is It AI?). These findings highlight the risks of relying on generic, freely available detectors that lack sufficient reliability, and demonstrate the urgent need for more robust detectors that are specifically trained on scientific contents such as western blot images. creator: Romain-Daniel Gosselin uri: https://doi.org/10.7717/peerj.18988 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Gosselin title: Corona or hydrochloric acid modulates embryonic diapause in silkworms by activating different signaling pathways link: https://peerj.com/articles/18966 last-modified: 2025-02-20 description: BackgroundTo adapt to environmental changes, diapausing silkworm eggs remain dormant during the early stages of embryonic development. Various methods have been used to terminate silkworm egg diapause and promote egg hatching.MethodsTo elucidate the molecular mechanisms by which corona and other treatments terminate silkworm egg diapause, we collected eggs at 1, 6, and 20 h after treatments and sequenced their transcriptomes.ResultsThe results showed that both corona and hydrochloric acid (HCl) treatments effectively terminated diapause and promoted egg hatching, with corona treatment inducing faster hatching than HCl treatment. Differentially expressed gene (DEG) analysis revealed the presence of fewer DEGs at 1 h, with a marked increase observed at 6 and 20 h post treatment. Functional enrichment analysis showed that the FoxO signaling pathway was activated at 6 h, with more substantial gene expression changes observed after corona treatment. In addition, HCl treatment appeared to activate the heat shock protein and hormone-regulated pathways. Our study results provide a basis for further analysis of the molecular mechanisms underlying diapause termination in silkworm eggs. creator: Yuli Zhang creator: Guizheng Zhang creator: Mangui Jiang creator: Pingyang Wang creator: Xia Wang creator: Qiuying Cui creator: Quan Sun uri: https://doi.org/10.7717/peerj.18966 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhang et al. title: Changes in bacterial viability after preparation and storage of fecal microbiota transplantation solution using equine feces link: https://peerj.com/articles/18860 last-modified: 2025-02-20 description: BackgroundFecal microbiota transplantation (FMT) has been used as a treatment option for horses (Equus caballus) with gastrointestinal diseases. Several preparation and conservation protocols to improve bacterial survival have been studied in other species.MethodsThis study aimed to evaluate the impact of oxygen exposure and different protectant solutions on bacterial viability before and after freezing using horse feces. Fecal samples from 10 healthy horses were aliquoted and diluted in cryoprotectant solutions containing antioxidants (n = 40) or 10% glycerol (n = 40). Half of the aliquots from each dilution condition were prepared inside an anaerobic chamber, while the other half were prepared under ambient air conditions. Each sample was also analyzed fresh and after freezing at −20 °C for 90 days. Bacterial viability was assessed using flow cytometry. A mixed linear model and the Friedman and Wilcoxon tests were used depending on data distribution.ResultsFreeze-thawing decreased bacterial viability by 47% (mean ± SD: 51 ± 27% before, 27 ± 8% after; p < 0.001). Glycerol was superior to the cryoprotectant after freezing (32 ± 8% glycerol, 24 ± 8% cryoprotectant; p < 0.001). Oxygen exposure did not affect viability (p = 0.13). There was no statistical difference between protectant solutions in fresh samples (p = 0.16).ConclusionsFresh FMT solutions may be better for treating horses with dysbiosis, but if freezing cannot be avoided, glycerol should be used to dilute feces. creator: Julia A. Arantes creator: Rebecca Di Pietro creator: Mélanie Ratté creator: Luis G. Arroyo creator: Mathilde Leclère creator: Marcio C. Costa uri: https://doi.org/10.7717/peerj.18860 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Arantes et al. title: Future climate-driven habitat loss and range shift of the Critically Endangered whitefin swellshark (Cephaloscyllium albipinnum) link: https://peerj.com/articles/18787 last-modified: 2025-02-20 description: Climate change is driving many species to shift their geographical ranges poleward to maintain their environmental niche. However, for endemic species with restricted ranges, like the Critically Endangered whitefin swellshark (Cephaloscyllium albipinnum), endemic to southeastern Australia, such dispersal may be limited. Nevertheless, there is a poor understanding of how C. albipinnum might spatially adjust its distribution in response to climate change or whether suitable refugia exist for this species in the future. Therefore, to address this gap, this study utilised maximum entropy (MaxEnt) modelling to determine the potential distribution of suitable habitat for C. albipinnum under present-day (2010–2020) climate conditions and for future conditions, under six shared socioeconomic pathways (SSP1-1.9, SSP1-2.6, SSP2-4.5, SSP3-7.0, SSP4-6.0 and SSP5-8.5) for the middle (2040–2050) and end (2090–2100) of the century. Under present-day conditions (2010–2020), our model predicted a core distribution of potentially suitable habitat for C. albipinnum within the Great Australian Bight (GAB), with benthic primary productivity and surface ocean temperature identified as key distribution drivers. However, under all SSP scenarios, future projections indicated an expected range shift of at least 72 km, up to 1,087 km in an east-southeast direction towards Tasmania (TAS). In all future climate scenarios (except SSP1-1.9 by 2100), suitable habitat is expected to decline, especially in the high-emission scenario (SSP5-8.5), which anticipates a loss of over 70% of suitable habitat. Consequently, all future climate scenarios (except SSP1-1.9 by 2100) projected a decrease in suitable habitat within a currently designated marine protected area (MPA). These losses ranged from 0.6% under SSP1-1.9 by 2050 to a substantial 89.7% loss in coverage under SSP5-8.5 by 2100, leaving just 2.5% of suitable habitat remaining within MPAs. With C. albipinnum already facing a high risk of extinction, these findings underscore its vulnerability to future climate change. Our results highlight the urgency of implementing adaptive conservation measures and management strategies that consider the impacts of climate change on this species. creator: Kerry Brown creator: Robert Puschendorf uri: https://doi.org/10.7717/peerj.18787 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Brown and Puschendorf title: Disturbance history alters the development of the HPA axis in altricial nestling birds link: https://peerj.com/articles/18777 last-modified: 2025-02-20 description: Glucocorticoid (GC) hormones regulate the vertebrate stress response and are secreted by the hypothalamic–pituitary–adrenal (HPA) axis. Acute elevation of GCs is thought be adaptive because it promotes physiological and behavioural changes that allow animals to cope with disturbances. In contrast, chronic elevation of GCs is associated with reduced body condition, immune function, reproductive success, and survival. In adult birds, the effects of chronic stress have been well documented, including human-related disturbances. In contrast, the effects of chronic stress on nestlings have rarely been addressed. This is of interest, as many ecological or monitoring studies of wild birds require nestlings to be regularly handled. However, the consequences of repeated handling of nestlings on HPA axis function and body mass in wild birds remain poorly quantified. We examined whether daily exposure to handling stress increased corticosterone (the dominant avian glucocorticoid) secretion and reduced pre-fledging body mass relative to undisturbed control nestlings of the noisy miner (Manorina melanocephala), a native Australian passerine bird. Daily handling resulted in an elevated baseline and attenuated stress-induced corticosterone levels in disturbed 14-day nestlings, in comparison with control nestlings handled for the first time. Despite this, disturbed and control nestlings fledged at a similar body mass. Baseline and stress-induced corticosterone increased with nestling age but remained independent of nestling sex and hatching order. Our findings are some of the first to suggest that chronic handling stress causes physiological alterations to the development of the HPA axis in nestling birds, and our data suggest that researchers should minimise or account for handling stress in their experiments. These data also raise the possibility that other chronic stressors may have long term physiological consequences for the development of the HPA axis in nestling birds. creator: Ahmad Barati creator: Ondi L. Crino creator: Paul G. McDonald creator: Katherine L. Buchanan uri: https://doi.org/10.7717/peerj.18777 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Barati et al. title: A new firefly genus from South America, with seven new species, a new combination, and notes on the phylogeny of Lampyrinae: Lucidotini (Coleoptera: Lampyridae) link: https://peerj.com/articles/18967 last-modified: 2025-02-19 description: BackgroundLucidotini is a diverse tribe of lampyrine fireflies present throughout the New World, Europe, and Asia. Most of the over 30 genera have overlapping diagnoses, largely due to a lack of revisionary and phylogenetic studies. Widespread convergence in sensory morphology, traditionally used in genus-level diagnoses, further compounds the taxonomic issues surrounding the Lucidotini. Recent work has cast light on the value of terminalia and genitalic traits for Lucidotini taxonomy and called for a more thorough screening of morphological characters. Of special interest are basal outgrowths of the phallus (i.e., ventrobasal processes)—currently only known in Alychnus Kirsch and Photinus Laporte–that can be quite informative at the species level, but its variation within Lucidotini remains poorly studied. Most Lucidotini species remain only superficially described, while internal characters—including those of terminalia and genitalia—which could inform species identification and phylogenetic relatedness, remain unknown. Upon studying eight Lucidotini species superficially looking like Photinus and Photinoides McDermott—all of which bearing long ventrobasal processes–we raised the hypothesis that they belonged to a genus yet to be recognized.MethodsHere, we analyzed 97 morphological characters of 32 lampyrid species spanning 17 of 30 Lucidotini genera under Bayesian Inference.ResultsWe found evidence for the recognition and description of Saguassugen. nov. to include seven new species (Saguassu acutumsp. nov.,Saguassu grossiisp. nov.,Saguassu manauarasp. nov.,Saguassu rebellumsp nov.,Saguassu rourasp. nov.,Saguassu serratumsp. nov. and Saguassu sinuosumsp. nov.), in addition to Photinus dissidens Olivier ((transferred herein, thus generating Saguassu dissidenscomb. nov.), for which we also designate a lectotype and two paralectotypes). This previously neglected lineage of Lucidotini spans four South American biomes: Amazon, Atlantic Rainforest, Cerrado, and Pampa. Interestingly, Saguassu species span a gradient of morphologies related to signaling: from Lampyris-style ventrally bulging eyes, tiny antennae and no lanterns; intermediate eyes and antennae, with complete lanterns as in Photinus; to small eyes and long antennae and small lanterns as in many Lucidota Laporte. Saguassugen. nov. was consistently found closely related to the three other Lucidotini taxa with ventrobasal processes (i.e., Alychnus, Photinoides, and Photinus). We provide an occurrence map of and a dichotomous key to Saguassu species, thoroughly compare this genus with co-occurring Lucidotini genera, and suggest steps towards a revision of the Lucidotini tribe. creator: Jéssica Herzog Viana creator: André Silva Roza creator: Stephanie Vaz creator: Gareth Powell creator: Luiz Felipe Lima da Silveira uri: https://doi.org/10.7717/peerj.18967 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Viana et al. title: Beyond single-species models: leveraging multispecies forecasts to navigate the dynamics of ecological predictability link: https://peerj.com/articles/18929 last-modified: 2025-02-19 description: BackgroundForecasting the responses of natural populations to environmental change is a key priority in the management of ecological systems. This is challenging because the dynamics of multi-species ecological communities are influenced by many factors. Populations can exhibit complex, nonlinear responses to environmental change, often over multiple temporal lags. In addition, biotic interactions, and other sources of multi-species dependence, are major contributors to patterns of population variation. Theory suggests that near-term ecological forecasts of population abundances can be improved by modelling these dependencies, but empirical support for this idea is lacking.MethodsWe test whether models that learn from multiple species, both to estimate nonlinear environmental effects and temporal interactions, improve ecological forecasts compared to simpler single species models for a semi-arid rodent community. Using dynamic generalized additive models, we analyze time series of monthly captures for nine rodent species over 25 years.ResultsModel comparisons provide strong evidence that multi-species dependencies improve both hindcast and forecast performance, as models that captured these effects gave superior predictions than models that ignored them. We show that changes in abundance for some species can have delayed, nonlinear effects on others, and that lagged, nonlinear effects of temperature and vegetation greenness are key drivers of changes in abundance for this system.ConclusionsOur findings highlight that multivariate models are useful not only to improve near-term ecological forecasts but also to ask targeted questions about ecological interactions and drivers of change. This study emphasizes the importance of jointly modelling species’ shared responses to the environment and their delayed temporal interactions when teasing apart community dynamics. creator: Nicholas J. Clark creator: S. K. Morgan Ernest creator: Henry Senyondo creator: Juniper Simonis creator: Ethan P. White creator: Glenda M. Yenni creator: K. A. N. K. Karunarathna uri: https://doi.org/10.7717/peerj.18929 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Clark et al. title: Effects of transcranial direct current stimulation combined with motor relearning program on strength and balance in stroke patients link: https://peerj.com/articles/18925 last-modified: 2025-02-19 description: BackgroundA stroke is characterized by neurological deficits that result in compromised muscle strength and balance, impacting the overall wellbeing of the patient, including decreased quality of life, socialization and participation in daily activities. The aim of the study is to determine the effects of transcranial direct current stimulation combined with a motor relearning program on strength and balance in sub-acute stroke patients.MethodsThe randomized controlled trial involved 44 subacute stroke patients, randomly assigned to either the experimental group (n = 22) or control group (n = 22). The intervention included anodal transcranial direct current stimulation (tDCS) for the experimental group and sham stimulation with a motor relearning program for the control groups. Assessments were conducted using manual muscle testing for muscle strength and the Berg Balance Scale for balance at baseline, the fourth week, and the eighth week.ResultsThere were no statistically significant effects in the experimental group for either strength or balance (p-value > 0.05) but there were time effects for both variables especially during the intervention period in both the experimental and control groups.ConclusionThere does not appear to be any short term or long-term additional effects of anodal transcranial direct current stimulation on strength and balance in subacute stroke patients. creator: Muhammad Hamad Haleem creator: Mirza Obaid Baig creator: Turki Abualait creator: Woo-Kyoung Yoo creator: Sumaiyah Obaid creator: Shahid Bashir uri: https://doi.org/10.7717/peerj.18925 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Haleem et al. title: Purification and characterization of detergent stable alkaline lipase from Bacillus safensis TKW3 isolated from Tso Kar brackish water lake link: https://peerj.com/articles/18921 last-modified: 2025-02-19 description: Extensive and escalating research has been directed towards halozymes derived from halophiles thriving in extreme hypersaline environments, owing to their myriad industrial applications. These extremophiles have evolved various physiological and metabolic adaptations to endure such extremes, enhancing their industrial potential. Being a potential source of lipases, halophiles of extreme niches have emerged as a emerging research area. This interest has been fueled by the recognition that extreme environments serve as rich reservoirs of diverse cold-active alkaliphilic enzymes.MethodsBacillus safensis TKW3, isolated from brackish Lake Tso Kar of the Ladakh region, India, produced cold-adapted haloalkaliphilic lipase halozyme. The current study focused on the purification and biochemical characterisation of lipase derived from halophilic bacteria.ResultsThe lipase enzyme, purified to homogeneity, exhibited a molecular mass of 28 kDa as confirmed by SDS-PAGE analysis. The purification process yielded a purification fold of 12.01 and a final recovery rate of 29.9%. It demonstrated optimal activity at 30 °C and pH 9. The enzyme was evaluated and demonstrated to exhibit stability over a broad temperature range spanning from 5 °C to 55 °C, as well as a wide pH range of 7.0 to 9.0. Due to its stability across a diverse spectrum of pH values, surfactants, metal ions, and inhibitors, the enzyme appeared to hold significant promise for application within the leather and detergent sectors. Upon undergoing detergent compatibility tests spanning diverse temperature ranges, the lipase showcased compatibility with various commercial detergents, thereby presenting itself as an attractive candidate for inclusion in detergent formulations within the industry.ConclusionsThe lipase from B. safensis TKW3 exhibits promising attributes, including alkali stability, halophilicity, and a wide spectrum of substrate specificity, rendering it an attractive option for incorporation into detergent formulations within the detergent industry. As far as we are aware, this is the first report on the purification and characterization of lipase enzyme from bacterial halophiles in a Tso Kar brackish lake. creator: Tishu Devi creator: Srinivas Sistla creator: Rabiya T. Khan creator: Swadha Kailoo creator: Mansavi Bhardwaj creator: Shafaq Rasool uri: https://doi.org/10.7717/peerj.18921 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Devi et al. title: Investigating the role of IDO1 in tumors: correlating IDO1 expression with clinical pathological features and prognosis in lung adenocarcinoma patients link: https://peerj.com/articles/18776 last-modified: 2025-02-19 description: PurposeThis study aimed to investigate the role and expression patterns of IDO1 in various tumors, focusing on its correlation with clinical pathological characteristics and prognosis in patients specifically diagnosed with lung adenocarcinoma.MethodsPan-cancer analysis assessed IDO1 function across different tumor types. Bioinformatics tools, immunohistochemistry techniques, and statistical analyses were employed to evaluate IDO1 expression levels and their association with clinical pathological features and prognosis in patients with lung adenocarcinoma.ResultsIDO1 was found to be significantly overexpressed in various types of tumors, with higher levels correlating with poorer progression-free survival (PFS) and overall survival (OS). In lung adenocarcinoma patients, IDO1 protein was predominantly localized to the cytoplasm and cell membrane of tumor cells, with higher expression observed in tumor cells closer to normal lung tissue. Statistical analysis revealed no significant differences in IDO1 expression based on the patient’s clinical data, including gender, age, tumor location, allergy history, hypertension history, cardiovascular disease history, tumor history, diabetes (both type 1 and type 2), body mass index, smoking history, family history, alcohol history, and tumor maximum diameter (P > 0.05). However, IDO1 expression positively correlated with lymph node metastasis, pleural invasion, tumor recurrence, lower tumor differentiation, solid tumor components, preoperative chemotherapy, and clinical tumor, node, metastasis (TNM) staging (*P < 0.05), while negatively correlating with prior surgical history (*P < 0.05). Patients exhibiting high IDO1 expression levels demonstrated significantly worse PFS and OS (***P < 0.001 and **P = 0.003, respectively).ConclusionHigh IDO1 expression in lung adenocarcinoma correlates with increased tumor invasiveness, metastatic potential, advanced clinical stage, and poorer prognosis. creator: Zhidong Yin creator: Bohao Sun creator: Sisi Wang creator: Xi Xu creator: Lu Cheng creator: Yue Gao creator: Er Jin uri: https://doi.org/10.7717/peerj.18776 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Yin et al. title: Prevalence of chronic conditions in masters games athletes: predictors and comparison to the general population link: https://peerj.com/articles/18912 last-modified: 2025-02-18 description: BackgroundMasters athletes (MA) are typically considered healthier than age-matched non-athletes. However, limited evidence exists on the prevalence of chronic conditions in MA.MethodsMasters athletes competing at the 2017 Australian Masters Games (n = 4,848) and 2018 Pan Pacific Masters Games (n = 14,455) were invited to complete a survey collecting demographic and health information focused on chronic conditions. Age- and sex-adjusted prevalence of selected chronic conditions in MA was compared with Australian general population data.ResultsOverall, 817 MA (53.7 ± 10.6 y, 61% female) completed the survey with 48% reporting ≥1 chronic condition. Cardiovascular conditions were less prevalent in MA vs. the general population (11%, 95% CI [9–14%] vs. 30%), as were cardiovascular risk factors, anxiety, asthma, cancers, and depression. The prevalence of osteoarthritis in MA was, however, similar (11%, 95% CI [9–14%] vs. 14%). Older (>50 yr) vs. younger MA were more likely to report osteoarthritis (OR 2.17, 95% CI [1.35–3.48]) and heart conditions (OR 1.85, 95% CI [1.11–3.07]), while younger vs. older MA were more likely to report mental health conditions (OR 1.86, 95% CI [1.23–2.82]). Prevalence of mental health conditions was higher in female vs. male MA (17% 95% CI [13–20%] vs. 8% 95% CI [5–11%]) and younger vs. older MA (18% vs. 10%). Employed MA were less likely than MA who were not employed to report having one or more cancers (OR 0.33, 95% CI [0.16–0.69]), cardiovascular conditions (OR 0.47, 95% CI [0.29–0.79]) and hypertension (OR 0.36 95% CI [0.18–0.73]).ConclusionsCardiovascular and other chronic conditions prevalence was lower in MA compared to age-matched non-athletes, highlighting the value of promoting sport involvement in aging individuals as well as for continuation of participation in younger age groups into MA level. Greater participation of younger and female groups in masters sport to improve mental health, and inclusion of people who are not employed should be supported. creator: Fiona Halar creator: Helen O’Connor creator: Mike Climstein creator: Tania Prvan creator: Deborah Black creator: Peter Reaburn creator: Wendy Stuart-Smith creator: Xiaojing Sharon Wu creator: Janelle Gifford uri: https://doi.org/10.7717/peerj.18912 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Halar et al. title: A review of behavioral testing in decapod shrimp (Caridea) and prawns (Dendrobranchiata) with applications for welfare assessment in aquaculture link: https://peerj.com/articles/18883 last-modified: 2025-02-18 description: Evolving societal expectations are driving increasing interest in the welfare of decapod crustaceans, such as prawns and shrimp, grown in aquaculture. A key aspect of understanding an animal’s welfare-related needs is through assessing their behavior to determine how the animal is perceiving and interacting with their environment. Behavioral testing has been applied to livestock animals for decades, providing insight into their wants and needs to guide housing structure design and husbandry practices that improve their welfare. This review collated studies that have applied behavioral testing, primarily at the individual level, to decapod shrimp and prawns in the Dendrobranchiata and Caridea sub- and infra-orders respectively. This review aims to understand the types of assessments that can be successfully applied to these taxa, and what the results of testing may be able to inform us about in regard to the welfare of these species. While the sentience capabilities of these decapod taxa is still under debate, the behavioral testing applied to date across varying species demonstrates they exhibit preferences across multiple contexts, individual differences indicative of personality, cognitive capabilities, and behavioral indicators consistent with negative affective states. There is scope to learn from livestock welfare assessment using behavioral testing and increase the research focused on penaeid shrimp and prawn species of aquaculture interest. Application and validation of new behavioral tests can guide system optimization for aquaculture shrimp and prawns in relation to the welfare of the animals. creator: Dana L. M. Campbell creator: Caroline Lee uri: https://doi.org/10.7717/peerj.18883 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Campbell and Lee title: The micro-niche explains allotopy and syntopy in South American Liolaemus (Iguania: Liolaemidae) lizards link: https://peerj.com/articles/18979 last-modified: 2025-02-17 description: Species distribution models have been established as essential tools for projecting the effects of changing environmental conditions on species distribution across space and time. The microclimatic niche denotes the environmental conditions within a habitat at a small scale or localized area. These conditions have a direct influence on several ecological traits and on species distribution as these conditions determine which organisms can survive and/or reproduce. This study examines the microclimate data from four sites located in Northwestern Salta Province, Argentina. Four South American Liolaemus lizard species were found to inhabit these four sites in allotopy or syntopy, with Liolaemus irregularis inhabiting all four sites. Liolaemus irregularis is the sole Liolaemus species inhabiting Site 1; L. irregularis inhabits Site 2 in syntopy with L. multicolor; L. irregularis inhabits Site 3 in syntopy with L. yanalcu; and L. irregularis inhabits Site 4 in syntopy with L. albiceps. To characterize the four sites, a microclimate model was generated for an interval from 10 AM to 6 PM every day, for 10 years. The sites exhibited some differences in the combination of climatic and soil characteristics. Site 1 was characterized by low relative humidity, high temperature, high wind speed, and Cambisol soil type. Site 2 had high relative humidity, low temperature, moderate wind speed, and Andosol soil type. Site 3 had high relative humidity, high temperature, low wind speed, and Cambisol soil type. Site 4 had high relative humidity, low temperature, moderate wind speed, and Regosol soil type. Temperature, humidity, wind speed, soil type, and species diet influenced the presence of lizard species at each site. It is evident that microenvironmental conditions profoundly influence lizard distribution and biological interactions. creator: Andrés S. Quinteros creator: Sabrina N. Portelli uri: https://doi.org/10.7717/peerj.18979 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Quinteros and Portelli title: A retrospective study of the correlation between high serum ferritin levels and the risk of gestational diabetes mellitus in midpregnant women link: https://peerj.com/articles/18965 last-modified: 2025-02-17 description: AimsGestational diabetes mellitus (GDM) is any degree of glucose intolerance with onset or first detection during pregnancy, with an inconsistent association with serum ferritin (SF). We aimed to ascertain the relationship between SF and the risk of GDM in mid-pregnancy and provide evidence for implementing clinical individualized and reasonable iron supplementation regimens.MethodsA retrospective study was conducted to investigate 1,052 pregnant women at 24–28 weeks of gestation who were examined in the obstetrics department of The Fourth Hospital of Shijiazhuang from January 2019 to December 2021. Questionnaires were used to obtain the general information. The levels of serum ferritin (SF), serum calcium, glycated haemoglobin (HbA1c) and Oral-Glucose-Tolerance-Test (OGTT) were reviewed. The GDM was diagnosed by glucose tests. Multivariate logistic regression was used to determine the relationship between serum ferritin and GDM.ResultsCompared to the non-GDM group, the GDM group had significantly higher level of SF (13.95 (8.59–23.65) ng/mL vs. 12.11 (7.27–19.86) ng/mL, (p = 0.012)). While SF levels positively correlated with 1-hour plasma glucose levels (PG1H) (r = 0.061, p = 0.047), there was a negative correlation between SF and HbA1c levels (r =  − 0.078, p = 0.011). The risk of GDM with higher levels of SF was increased (1.010 (95% CI [1.001–1.020], p = 0.025)). In the univariate logistic regression model, the risk of GDM in pregnant women with high ferritin levels was 1.010 (95% CI [1.001–1.020], p = 0.025). After adjustment for age and pre-pregnancy body mass index (BMI), the risk of GDM was significantly increased by 44% and 42% respectively (adjusted odds ratio (AOR) = 1.440, 95% CI [1.025–2.023], p = 0.035), AOR = 1.420 (95% CI [1.011–1.995], p = 0.043). After multivariate adjustment for age and pre-pregnancy BMI, the results were moderately revised (AOR = 1.427, 95%CI [1.013–2.008], p = 0.042).ConclusionsElevated SF levels of mid-pregnancy was associated with risk of GDM, which may guide the implementation of pregnancy-specific supplementation to some extent with the support of further clinical trials. creator: Xizhenzi Fan creator: Pan Zhang creator: Lingli Wang creator: Wenhui Song creator: Achou Su creator: Tianxiao Yu uri: https://doi.org/10.7717/peerj.18965 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Fan et al. title: TaZFP 23, a new Cys2/His2-type zinc-finger protein, is a regulator of wheat (Triticum aestivum L.) growth and abiotic stresses link: https://peerj.com/articles/18956 last-modified: 2025-02-17 description: Wheat (Triticum aestivum L.) is an important food crop and one of the most important grains in the world. With the global climate change, wheat production is increasingly affected by abiotic stress, among which drought, salinity, and other factors have become the main abiotic stress factors restricting the efficient production of wheat. The C2H2-type zinc finger proteins are a common class of transcription factors in plants that play crucial roles in regulating plant growth and development as well as responses to stresses. In this study, the wheat C2H2-type zinc finger protein transcription factor TaZFP23 was cloned. Its full-length coding sequence was 720 bp encoding 239 amino acids. TaZFP23 is a typical C2H2-type zinc finger protein. It contains two C2H2 zinc finger domains and an EAR motif, without a transmembrane domain. Promoter cis-acting element analysis suggested that TaZFP23 might function in abiotic stress responses and plant hormone signal transduction. Subcellular localization and transcriptional activity assays indicated that TaZFP23 encoded a nuclear protein without self-activation activity. Overexpressing TaZFP23 in Arabidopsis thaliana showed that it negatively regulate d seed germination and plant growth under NaCl, mannitol, and ABA treatments. Additionally, TaZFP23 overexpression under NaCl and drought stress in Arabidopsis resulted in lower expression levels of several stress-related marker genes compared to those in wild-type plants. This research provides a foundation for further elucidating the functions of C2H2-type zinc finger protein genes and offers promising candidate genes for the development of stress-tolerant wheat cultivars. creator: Shunxing Ye creator: Yuzhou Tang uri: https://doi.org/10.7717/peerj.18956 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ye and Tang title: First wild boar density data from Araucaria forest in Patagonian Andes link: https://peerj.com/articles/18951 last-modified: 2025-02-17 description: As Sus scrofa is an invasive species in South America, it may have a significant impact on biodiversity. Evaluating this threat requires reliable data, and population density can serve as a critical measure. However, such data is currently lacking for the southern Andes region. To address this gap, we monitored wild boar density in the Villarrica National Park, located in the Andes of south-central Chile. This study area is notable not only for its challenging climatic conditions but also for its endangered Araucaria araucana forest, which provides abundant food resources during autumn seed fall. The density calculated for the entire study period was 1.4 individuals/km2, with no significant variation between cold and warm seasons. The encounter rate showed strongly monthly variations. Given that this represents the first density estimate for wild boar in this region, our findings emphasize the need for continued monitoring, particularly due to the potential threat to the ecosystem and the already endangered Araucaria forest. creator: Oscar Skewes creator: Annaluisa Kambas creator: Paula Gädicke creator: Oliver Keuling uri: https://doi.org/10.7717/peerj.18951 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Skewes et al. title: Caffeic acid phenethyl ester inhibits multispecies biofilm formation and cariogenicity link: https://peerj.com/articles/18942 last-modified: 2025-02-17 description: BackgroundCaffeic acid phenethyl ester (CAPE), a natural phenolic compound, has demonstrated antibacterial effects. Dental caries etiology is multifactorial, including a cariogenic biofilm containing multispecies bacteria. However, the antibacterial property of CAPE on multispecies biofilm is unclear. The aim of this study was to assess the effect of CAPE on the formation and cariogenicity in biofilm containing Streptococcus mutans, Streptococcus oralis, and Streptococcus mitis.MethodsS. mutans (ATCC 25175), S. oralis (ATCC 35037), and S. mitis (ATCC 49456T) were employed in this investigation. Each bacterial strain was cultured in the presence of CAPE, followed by susceptibility assessment through optical density measurements at a 600 nm wavelength. Multispecies biofilm formation was achieved by co-culturing S. mutans, S. oralis, and S. mitis at a 1:1:1 ratio on hydroxyapatite-coated 96-well plates. The anti-adherence activity of CAPE on multispecies biofilm was evaluated using a crystal violet staining assay. Cariogenic gene expression level and glucosyltransferase (GTF) function in CAPE-treated mixed bacteria were evaluated using real-time PCR and enzyme activity assay, respectively. The thickness and bacterial viability in CAPE-treated multispecies biofilm were examined using confocal laser scanning microscopy.ResultsCAPE demonstrated a significant antimicrobial effect on S. mutans, S. oralis, and S. mitis (p < 0.05). The inhibition concentration 50% (IC50) of CAPE against S. mutans, S. oralis, and S. mitis ranged from 1.6–6.4 mg/ml. CAPE significantly hindered the multispecies biofilm adherence (p < 0.05). Furthermore, the expression of genes involved in acidogenicity, aciduricity, sucrose-dependent adhesion and quorum sensing mechanism and GTF activity were significantly decreased in CAPE-treated mixed bacteria (p < 0.05). In a multispecies biofilm, CAPE significantly reduced its thickness and viable bacteria population (p < 0.05). In conclusion, CAPE exhibited antimicrobial, anti-adherence and anti-cariogenic effects within a multispecies biofilm. These findings suggest the potential use of CAPE as an adjunctive anti-cariogenic agent in future dental applications. creator: Paopanga Kokilakanit creator: Nonthakorn Dungkhuntod creator: Nitchadakorn Serikul creator: Sittichai Koontongkaew creator: Kusumawadee Utispan uri: https://doi.org/10.7717/peerj.18942 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Kokilakanit et al. title: Integrated transcriptome and metabolome analyses reveal the differentially expressed metabolites and genes involved in lipid in olive fruits link: https://peerj.com/articles/18941 last-modified: 2025-02-17 description: BackgroundOlive (Olea europaea L.) oil is well-known commercial product worldwide for its nutritional and therapeutic properties. The molecular mechanisms underlying lipid variations in different olive cultivars remain unclear.MethodsTo investigate the molecular mechanism involved in lipid synthesis and metabolism, untargeted metabolome and RNA-Seq analyses were performed based on two varieties of olive fruits, i.e., Kalinjot (JZ) with low oil content and Coratina (KLD) with high oil content.ResultsTotally, 38 lipid compounds of 375 differentially accumulated metabolites (DAMs) were identified in JZ and KLD fruits, with 24 metabolites showing higher contents in KLD than those in JZ. Integrated transcriptome and metabolome analyses identified 48 differentially expressed genes (DEGs) associated with six lipid DAMs from JZ and KLD fruits. The contents of decanoic acid, sphinganine, and leukotriene D4 in KLD fruits were 2.33, 1.91, and 1.53 times greater than that of JZ fruits, respectively. In particular, two BCCP, one ACC, seven KAR, one EAR, one FATA and one SPT genes were observed involving to the content and quality of lipids in olive fruits. These DEGs were associated with the pathways of fatty acid biosynthesis, arachidonic acid metabolism, and limonene degradation. This study provides a strong theoretical and experimental foundation for further revealing the molecular mechanisms regulating lipid synthesis and metabolism in different olive cultivars. creator: Jipeng Qu creator: Zhou Xu creator: Zhengsong Peng creator: Zhenyong Chen creator: Tao Chen creator: Chunbang Ding uri: https://doi.org/10.7717/peerj.18941 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Qu et al. title: Identification of potential insect ecological interactions using a metabarcoding approach link: https://peerj.com/articles/18906 last-modified: 2025-02-17 description: Species interactions are challenging to quantify, particularly when they happen cryptically. Molecular methods have become a key tool to uncover these interactions when they leave behind a DNA trace from the interacting organism (e.g., pollen on a bee) or when the taxa are still present but morphologically challenging to identify (e.g., microbial or fungal interactions). The decreasing costs of sequencing makes the mass analysis of thousands of target species possible. However, the challenge has shifted to selecting molecular markers which maximize information recovery while analyzing these data at broad biological scales. In this manuscript we use model arthropod groups to compare molecular markers and their analysis across life stages. We develop protocols for two ecologically and economically devastating pests, the spongy moth (Lymantria dispar dispar) and the emerald ash borer (Agrilus planipennis), and a group of pollinators including bees and wasps which regularly deposit eggs in “bee hotels” where the larvae develop. Using Illumina MiSeq and Oxford Nanopore MinION platforms we evaluate seven primer pairs for five molecular markers which target plants, fungi, microbes, insects, and parasitic phyla (e.g., nematodes). Our data reveals hundreds of potential ecological interactions and establishes generalized methods which can be applied across arthropod host taxa with recommendations on the appropriate markers in different systems. However, we also discuss the challenge of differentiating co-occurring DNA signals and true ecological interactions, a problem only starting to be recognized as eDNA from the environment accumulates on living organisms. creator: Nicole D. Borsato creator: Katherine Lunn creator: Nina R. Garrett creator: Alejandro José Biganzoli-Rangel creator: Daniel Marquina creator: Dirk Steinke creator: Robin Floyd creator: Elizabeth L. Clare uri: https://doi.org/10.7717/peerj.18906 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Borsato et al. title: Potential transoceanic dispersal of Geodia cf. papyracea and six new tetractinellid sponge species descriptions within the Hawaiian reef cryptofauna link: https://peerj.com/articles/18903 last-modified: 2025-02-17 description: Kāne‘ohe Bay has historically been known for the introduction of alien species from the Caribbean and the Western Indo-Pacific. Recent efforts that explore the reef cryptofauna have shown that in addition to the diversity of non-indigenous species, patch reef environments are rich with undescribed species. Here we integrate molecular phylogeny and systematics to distinguish introduced species from those that are potentially native or endemic. We focus on the order Tetractinellida and document the potential transoceanic dispersal of Geodia papyracea from the Caribbean to Hawai‘i. Our integrative approach allowed us to describe new species of Stelletta (Stelletta kela sp. nov., Stelletta hokunalohia sp. nov., Stelletta kuhapa sp. nov., Stelletta hokuwanawana sp. nov., Stelletta apapaola sp. nov.) and one new species of Stryphnus (Stryphnus huna sp. nov.); all collected from the reef cryptofauna via the use of Autonomous Reef Monitoring Structures. Specimens were barcoded using 28S and COI molecular markers, providing insights into the phenotypic plasticity of sponges and the phylogenetic placement of these new species based on morphological characters. Using both molecular phylogeny and traditional taxonomy enhances the accuracy of species identification and classification, contributing to a broader understanding of sponge biodiversity within the Hawaiian archipelago. creator: Rachel M. Nunley creator: Emily C. Rutkowski creator: Robert J. Toonen creator: Jan Vicente uri: https://doi.org/10.7717/peerj.18903 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Nunley et al. title: The effect of perioperative probiotics and synbiotics on postoperative infections in patients undergoing major liver surgery: a meta-analysis of randomized controlled trials link: https://peerj.com/articles/18874 last-modified: 2025-02-17 description: ObjectiveTo evaluate the effect of perioperative probiotics or synbiotics on the incidence of postoperative infections following major liver surgery.DesignMeta-analysisData sourcesPubMed, Embase, Scopus, and the Cochrane Library for relevant English-language studies published up to February 21st, 2024.Eligibility criteriaRandomized controlled trials evaluating perioperative probiotics or synbiotics for preventing postoperative infections in patients undergoing major liver surgery.Data extraction and synthesisOutcomes included postoperative infection incidence, antibiotic therapy duration, length of stay in intensive care unit (ICU) and hospital. A random-effect model was adopted for the meta-analysis. The quality of included studies was evaluated using the Cochrane risk of bias tool.ResultsTen studies involving 588 patients were included. Pooled analyses revealed that perioperative probiotics or synbiotics significantly reduced postoperative infection incidence (RR 0.36, 95% CI [0.24–0.54], P < 0.0001, I2 = 6%) and antibiotic therapy duration (MD −2.82, 95% CI [−3.13 to −2.51], P < 0.001, I2 = 0%). No significant differences were observed in length of stay in ICU (MD −0.25, 95% CI [−0.84–0.34], P = 0.41, I2 = 64%) or length of stay in hospital (MD −1.25, 95% CI [−2.74–0.25], P = 0.10, I2 = 56%).ConclusionsThis meta-analysis suggests that perioperative administration of probiotics or synbiotics may reduce the incidence of postoperative infections and duration of antibiotic therapy. Their use as adjunctive therapy during the perioperative period could be considered for patients undergoing major liver surgery. creator: Haopeng Wu creator: Zhihui Guan creator: Kai Zhang creator: Lingmin Zhou creator: Lanxin Cao creator: Xiongneng Mou creator: Wei Cui creator: Baoping Tian creator: Gensheng Zhang uri: https://doi.org/10.7717/peerj.18874 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Wu et al. title: Butterflies (Lepidoptera: Papilionoidea) of Georgia (Caucasus): annotated review of regional butterfly fauna with vernacular names index, notes on distribution and phenology link: https://peerj.com/articles/18720 last-modified: 2025-02-17 description: BackgroundIt is well known that butterflies are valuable indicators of environmental quality, given their existence in various habitats. Collecting and regularly updating data on species richness, abundance, and distribution of all butterfly species in the country is crucial for effective monitoring and conservation efforts, which can ultimately help minimise biodiversity losses. Since the last publication of the Georgian butterfly list, there have been numerous reports registering taxonomic revisions, nomenclatural changes or providing several new butterfly “cryptic species” based on genetic research. In the following article, based on a review of various sources of data, including existing literature and new, unpublished data, we present an annotated regional checklist of butterflies of Georgia, a country that is a part of the Caucasus ecoregion representing one of 36 biodiversity “hotspots”.MethodsA database with all reported species for Georgia was created by compiling information from critical reviews of all available literature reports, records submitted by contributors of three websites dedicated to butterfly fauna, and data deposited in the Global Biodiversity Information Facility (GBIF) database. Various specialised sources were used to extract vernacular species names (Georgian, Russian and English).ResultsThe updated list of butterflies from Georgia includes 244 species of the superfamily Papilionoidea recorded from almost 600 different locations. Nearly 25% of the 244 species were considered rare and extremely rare, while at the same time being at risk of potential extinction. For each species, we present brief phenological information, distribution in Georgia/Caucasus, occurrence status in each region of the country, thumbnails (ventral and dorsal view), as well as a list of vernacular names in Georgian, Russian and English. Regarding species that are reported in the literature as new, uncertain, or questionable in Georgia, we provide the relevant comments. In comparison to the other republics of Transcaucasia (Armenia, Azerbaijan), we noted a similar number of species. Our studies provide a robust baseline of data for further exploration of the Lepidoptera fauna of Georgia. This foundation should help to fill in the gaps in knowledge regarding regional species distribution, phenology, and habitat requirements. creator: Iwona Słowińska creator: Krzysztof Jonko uri: https://doi.org/10.7717/peerj.18720 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Słowińska and Jonko title: Broad-scale spatial distribution, microhabitat association and habitat partitioning of damselfishes (family Pomacentridae) on an Okinawan coral reef link: https://peerj.com/articles/18977 last-modified: 2025-02-14 description: Spatial distribution of coral reef fishes is related to diverse environmental variables. This study aimed to elucidate the (1) broad-scale spatial distribution, (2) microhabitat-scale substrate association, (3) degree of dependence on live corals and (4) habitat partitioning of 26 damselfish species on an Okinawan coral reef. Broad-scale analysis revealed that fish assemblages could be divided into three groups in relation to the degree of wave exposure, and the coverage of live corals as well as non-coralline substrates: (1) 11 species that were found in exposed reefs with greater coverage of rock; (2) nine species that that were found in inner reefs with greater coverage of live corals, dead corals and macroalgae; and (3) six species that were found in inner reefs with a greater coverage of sand. Microhabitat-scale analysis revealed that fish assemblages could be divided into six groups in relation to diverse microhabitat availability: (1) 12 species showed significant positive associations with rock; (2) two species showed significant positive associations with coral rubble; (3) two species showed significant positive associations with corymbose Acropora, Pocillopora and branching corals; (4) three species showed significant positive associations with branching Acropora; (5) three species showed significant positive associations with branching Acropora, branching Isopora and branching Porites; and (6) two species showed significant positive associations with staghorn Acropora and branching Millepora. The microhabitat-scale analysis also revealed that Pomacentrus amboinensis showed a significant positive association with branching Millepora, whereas Neopomacentrus anabatoides showed significant positive associations with branching Porites, foliose coral and dead branching Porites. Among the 26 species, nine species were categorized as obligate coral dwellers (>80% of the individuals were associated with live corals), and three species showed a greater degree of dependence on acroporid corals (>60% individuals were associated with acroporid coral). Niche overlap analysis revealed that 14 species showed relatively greater habitat partitioning with other species, whereas the remaining 12 species showed greater habitat overlaps among some species. These results suggest that broad-scale and microhabitat-scale habitat partitioning is one of the factors supporting coexistence in at least 14 species among the 26 species, and the effects of habitat diversity on the species coexistence of damselfishes should be incorporated to establish effective marine protected areas to preserve damselfish species diversity. creator: Atsushi Nanami uri: https://doi.org/10.7717/peerj.18977 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Nanami title: Preparation and analysis of quinoa active protein (QAP) and its mechanism of inhibiting Candida albicans from a transcriptome perspective link: https://peerj.com/articles/18961 last-modified: 2025-02-14 description: The globe cultivation and industrial production of quinoa have been steadily increasing. Nevertheless, the full potential of quinoa’s nutritional and economic benefits remains underexploited. This study investigates the isolation and purification of quinoa active protein (QAP) through the precipitation method using ammonium sulfate from a phosphate extraction solution. The purification process involved gel filtration chromatography with Sephadex G-75 and Sephadex G-50 columns to obtain QAP fractions exhibiting inhibitory effects against Candida albicans (C. albicans). A comprehensive series of experiments was undertaken to examine the antifungal properties of these fractions. Proteomic analysis was employed to elucidate the composition of the active proteins. Furthermore, the activities of succinate dehydrogenase, Ca2+-Mg2+-ATPase, and catalase in C. albicans following treatment with QAP were quantified using an enzyme-linked immunosorbent assay. The effects of QAP on the cell morphology of C. albicans cultured on Spider agar medium was further investigated using scanning electron microscopy (SEM). Furthermore, RNA-seq analysis was conducted to investigate the alterations in gene expression in C. albicans cells subjected to QAP treatment. To elucidate the functional significance of these expression changes, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were performed. Quantitative real-time polymerase chain reaction was subsequently employed to validate the observed changes in gene expression. Our findings demonstrate that QAP exhibits inhibitory effects against C. albicans, with a minimum inhibitory concentration of 182 µg/mL. Through proteomic analysis, a definitive set of 18 active quinoa proteins was identified. At the molecular level, genes associated with hyphal development, cell wall and membrane integrity, cellular respiration, and energy metabolism were found to be enriched. Protein–protein interaction (PPI) analysis revealed that these QAP inhibit the growth of C. albicans hyphae, compromise cell wall and membrane integrity, and suppress oxidative phosphorylation. These disruptions collectively impair normal cellular metabolic activities, thereby exerting an inhibitory effect on C. albicans. creator: Xufei Zhang creator: Chunmei Zheng creator: Wenxuan Ge creator: Xueying Li creator: Xiuzhang Wang creator: Yanxia Sun creator: Xiaoyong Wu uri: https://doi.org/10.7717/peerj.18961 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhang et al. title: Associations between physical activity and emotional and behavioural problems in Chinese children and adolescents with intellectual disabilities link: https://peerj.com/articles/18949 last-modified: 2025-02-14 description: Background and purposeEmotional and behavioural problems (EBPs) are the two main forms of mental health problems that hinder the social interactions, learning and daily living of children and adolescents with intellectual disabilities (ID). Studies have shown that sufficient moderate-to-vigorous physical activity (MVPA) is associated with mental health outcomes among children and adolescents with typically developing (TD). However, these associations have not been fully studied in children and adolescent with ID, especially in samples from China. Therefore, this study aimed to examine the associations between MVPA and EBPs in Chinese children and adolescents with ID.MethodsA cross-sectional survey was conducted with 116 students with ID (35.34% girls) aged 6–18 years. The wGT3-BT accelerometer was used to measure physical activity (PA), and the Chinese version of the parent-rated Strengths and Difficulties Questionnaire (SDQ) was used to assess the participants’ EBPs. A series of binary logical regression analyses was conducted to examine the ability of the MVPA guideline attainment in predicting EBPs in the total sample.ResultsThe descriptive results showed that 43.97% of children and adolescents with ID present with EBPs. After controlling for age, sex, ID severity and weight status, logistic regression analysis indicated that the participants who meet the MVPA guideline exhibited significantly lower odds ratio for emotional symptoms (OR = 0.334, 95% CI [0.114–0.975], p = 0.045), peer problems (OR = 0.071, 95% CI [0.015–0.328], p < 0.001) and total difficulties (OR = 0.192, 95% CI [0.069–0.535], p = 0.002) compared with those who did not meet the guidelines.ConclusionThe prevalence of EBPs in Chinese children and adolescents with ID remains high. Children and adolescents with ID meeting the MVPA guideline were more likely to have lower risks for emotional symptoms, peer problems and total difficulties than those who did not meet the guidelines. Future research adopting longitudinal or interventional designs to determine the relationships between PA and EBPs in this population are expected. creator: Yecheng Zhong creator: Junjie Zhou creator: Niuniu Li creator: Wenhong Xu creator: Jing Qi uri: https://doi.org/10.7717/peerj.18949 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zhong et al. title: Increased glycoprotein hormone yield in stably transfected CHO cells using human serum albumin signal peptide for beta-chains link: https://peerj.com/articles/18908 last-modified: 2025-02-14 description: Heterologous signal peptides enable increasing titers of recombinant proteins in mammalian cell culture. Four human heterodimeric glycoprotein hormones (follicle-stimulating hormone, FSH; luteinizing hormone, LH; chorionic gonadotropin, CG; and thyroid-stimulating hormone, TSH) were expressed in stably transfected CHO cells when varying signal peptides of their β-subunits. The signal peptide of human serum albumin proved to be the most effective for the glycoprotein hormone family. The cell specific productivity was increased for LH (2.5 pg/cell, 4-fold increase), TSH (1.6 pg/cell, 13-fold increase), and CG (1.0 pg/cell, 60%-increase). According to the Western blotting and quantitative PCR data, the productivity increase is associated with an increase in the efficiency of translation and translocation of β-subunits of hormones in the endoplasmic reticulum due to their coupling with the heterologous signal peptides. creator: Maria V. Sinegubova creator: Denis E. Kolesov creator: Ivan I. Vorobiev creator: Nadezhda A. Orlova uri: https://doi.org/10.7717/peerj.18908 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Sinegubova et al. title: Change in exercise capacity, physical activity and motivation for physical activity at 12 months after a cardiac rehabilitation program in coronary heart disease patients: a prospective, monocentric and observational study link: https://peerj.com/articles/18885 last-modified: 2025-02-14 description: BackgroundExercise capacity (EC) and physical activity (PA) are relevant predictors of mortality in patients with coronary heart disease (CHD) but the CHD-specific long-term trajectories of these outcomes after a cardiac rehabilitation (CR) program are not well known. The main objective of this study was to determine the mean change in EC (6-min walking test (6MWT) distance) in CHD patients at 12 months after a CR program compared to the end of the program. We also performed a series of exploratory analyses: (i) estimating the decile shifts and the typical (median) individual change for EC, PA (International Physical Activity Questionnaire-Short Form Metabolic Equivalent of Task (IPAQ-SF MET)-min/week), and motivation for PA (Echelle de Motivation envers l’Activité Physique en contexte de Santé (EMAPS) scores) over the 12-month follow-up period; (ii) characterizing the PA motivational profiles at the end of the program and 12 months after the program; (iii) characterizing the barriers to PA perceived at 12 months; and (iv) estimating the categories of changes in EC and PA over time and their potential predictors.MethodsEighty-three patients were recruited at the end of a CR program.ResultsFor an average patient, EC was trivially increased at 12 months. However, the decile shifts analysis did not confirm that the positive shift of the distribution of the performances over time was uniform. In contrast, we observed a significant decrease in PA between the end of the program and 12 months post-program but not between 6 and 12 months post-program when considering both the group of patients as a whole and the typical individual change. The results regarding motivation for PA were mixed, with significant and non-uniform shifts of the deciles towards scores depicting degrees of autonomous and controlled motivations as well as amotivation that would be more in favor of PA, but with no significant typical individual changes except for introjected regulation. Two motivational profiles were identified both at the end of the program and 12 months after the program: one with a very high level of autonomous motivation and a high level of introjected regulation; and another one with a high level of autonomous motivation and a moderate level of introjected regulation. Unfavorable weather, lack of time, fatigue, and fear of injury were the main barriers to PA at 12 months post-program. The change in EC and PA could be categorized into different classes without the possibility to determine any potential predictor of the assignment to a given class. Overall, these results suggest that clinicians managing a CR program with CHD patients as the one implemented in the present study may expect slightly positive or at least steady trajectories in EC, PA (after 6 months), and motivation for PA during the year after the program when considering the bulks of the distributions of patient scores. However, these global trajectories are actually the results of heterogeneous individual changes with some profiles of patients who could need a particular attention. creator: Paul Da Ros Vettoretto creator: Anne-Armelle Bouffart creator: Youna Gourronc creator: Anne-Charlotte Baron creator: Marie Gaume creator: Florian Congnard creator: Bénédicte Noury-Desvaux creator: Pierre-Yves de Müllenheim uri: https://doi.org/10.7717/peerj.18885 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Da Ros Vettoretto et al. title: Comparative mitogenomics of Cheiracanthium species (Araneae: Cheiracanthiidae) with phylogenetic implication and evolutionary insights link: https://peerj.com/articles/18314 last-modified: 2025-02-14 description: The genus Cheiracanthium C. L. Koch, 1839 is the most species-rich genus of the family Cheiracanthiidae. Given the unavailability of information on the evolutionary biology and molecular taxonomy of this genus, here we sequenced nine mitochondrial genomes (mitogenomes) of Cheiracanthium species, four of which were fully annotated, and conducted comparative analyses with other well-characterized Araneae mitogenomes. We also provide phylogenetic insights on the genus Cheiracanthium. The circular mitogenomes of the Cheiracanthium contain 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and one putative control region (CR). All genes show a high A+T bias, characterized by a negative AT skew and positive GC skew, along with numerous overlapped regions and intergenic spacers. Approximately half of the tRNAs lack TΨC and/or dihydrouracil (DHU) arm and are characterized with unpaired amino acid acceptor arms. Most PCGs used the standard ATN start codons and TAR termination codons. The mitochondrial gene order of Cheiracanthium differs significantly from the putative ancestral gene order (Limulus polyphemus). Our novel phylogenetic analyses infer Cheiracanthiidae to be the sister group of Salticidae in BI analysis, but as sister to the node with Miturgidae, Viridasiidae, Corinnidae, Selenopidae, Salticidae, and Philodromidae in ML analysis. We confirm that Cheiracanthium is paraphyletic, for the first time using molecular phylogenetic approaches, with the earliest divergence estimated at 67 Ma. Our findings enhance our understanding of Cheiracanthium taxonomy and evolution. creator: Zhaoyi Li creator: Feng Zhang uri: https://doi.org/10.7717/peerj.18314 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Li and Zhang title: Ankylosing spondylitis and kinesiophobia link: https://peerj.com/articles/19034 last-modified: 2025-02-13 description: BackgroundAnkylosing spondylitis (AS) is a chronic rheumatic disease that predominantly affects the axial skeleton, causing pain and functional impairment. Kinesiophobia, or fear of movement, is common in patients with chronic pain conditions and can significantly hinder treatment outcomes. This study aims to assess the level of kinesiophobia in AS patients and explore its relationship with demographic characteristics, disease duration, pain intensity, disease activity, and functional impairment.MethodsThis single-center study included 35 AS patients from July 2021 to July 2023. Patient demographics, disease duration, disease activity (BASDAI (Bath Ankylosing Spondylitis Disease Activity Index)), functionality (BASFI (Bath Ankylosing Spondylitis Functional Index)), pain intensity (VAS (Visual Analog Scale)), and kinesiophobia (TSK (Tampa Scale of Kinesiophobia)) were recorded and analyzed. Patients were categorized into low and high kinesiophobia groups based on TSK scores.ResultsOf the 35 AS patients, 15 (42.86%) had high kinesiophobia levels (TSK ≥37). Patients with high kinesiophobia had significantly higher BASDAI, BASFI, and VAS scores (p < 0.001) compared to those with low kinesiophobia. No significant relationship was found between kinesiophobia and age, gender, or disease duration (p > 0.05).ConclusionHigh levels of kinesiophobia in AS patients are associated with increased pain, disease activity, and functional impairment. Early interventions targeting kinesiophobia could improve treatment outcomes and patient functionality. creator: Ugur Ertem uri: https://doi.org/10.7717/peerj.19034 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Ertem title: The relationship of ulnar variance with pathologies detected by magnetic resonance imaging in patients with chronic or subacute wrist pain link: https://peerj.com/articles/18999 last-modified: 2025-02-13 description: BackgroundThis study aims to determine whether ulnar variance (UV) types are associated with chronic or subacute ulnar-side wrist pain using 3 Tesla (T) magnetic resonance imaging (MRI), and to investigate potential relationships between UV, clinical data, and MRI-detected findings.MethodsThis retrospective study included patients who presented with ulnar-side wrist pain for at least one month and underwent 3T MRI between January 2020 and October 2023. All demographic and clinical data, wrist radiography, and MRI images were obtained from computerized records. The patients were classified as having neutral-UV, negative-UV, and positive-UV.ResultsIn total, 272 patients were included in the analysis. Mean age was 40.57 ± 13.18 years and 63.60% (n = 173) of the subjects were female. Neutral UV was detected in 147 (54.04%) patients, negative UV in 106 (38.97%), and positive UV in 19 (6.99%). Patients in the negative-UV group were significantly younger than those in the neutral-UV and positive-UV groups (p = 0.013); however, the sex distribution was similar in all groups (p = 0.653). All patients with ulnar impingement were in the negative-UV group, whereas all subjects with ulnar impaction were in the positive-UV group (p < 0.001). Finally, triangular fibrocartilage complex (TFCC) ruptures were significantly more common in the positive-UV group (p = 0.023).ConclusionThere is a significant relationship between UV changes and ulnar impingement syndrome, ulnar impaction syndrome, and TFCC tears, which can be easily detected by MRI. The previously reported relationships between UV, sex, and other pathologies were not supported by our findings. creator: Süheyl Poçan creator: Levent Karakaş uri: https://doi.org/10.7717/peerj.18999 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Poçan and Karakaş title: Proteomics of stress-induced cardiomyopathy: insights from differential expression, protein interaction networks, and functional pathway enrichment in an isoproterenol-induced TTC mouse model link: https://peerj.com/articles/18984 last-modified: 2025-02-13 description: BackgroundsTakotsubo cardiomyopathy (TTC), also known as stress-induced cardiomyopathy, is a condition characterized by transient left ventricular dysfunction without coronary artery obstruction.MethodsWe utilized label-free quantitative proteomics to analyze protein expression in a murine model of TTC, induced by a high dose of isoproterenol (ISO) injection.ResultsWe found that a single high dose of ISO injection in mice could induce stress-related cardiac dysfunction.The proteomic analysis revealed 81 differentially expressed proteins (DEPs) between the ISO and control groups—39 were upregulated, and 42 were downregulated. Key pathways enriched by Gene Ontology (GO) analysis included collagen fibril organization, cholesterol biosynthesis, and elastic fiber assembly. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment indicated significant changes in unsaturated fatty acid biosynthesis, glutathione metabolism, steroid biosynthesis, and ferroptosis. Key hub proteins identified by the protein-protein interaction (PPI) network included Ntrk2, Fdft1, Serpine1, and Cyp1a1. Gene set enrichment analysis (GSEA) showed upregulation in terpenoid backbone biosynthesis, oxidative phosphorylation, and ferroptosis, with downregulation in pathways such as systemic lupus erythematosus and Rap1 signaling.ConclusionsThis study employed high-throughput liquid chromatography-tandem mass spectrometry (LC-MS/MS) to identify key proteins associated with energy metabolism, oxidative stress, inflammation, and cell death in TTC. These findings provide new insights into the molecular mechanisms of stress-induced myocardial injury and may offer potential therapeutic targets for mitigating cardiovascular damage under stress conditions. creator: Liuyang Tian creator: Botao Liu creator: Ying Ren creator: Jian Cui creator: Zhihua Pang uri: https://doi.org/10.7717/peerj.18984 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Tian et al. title: Captive-rearing changes the gut microbiota of the bumblebee Bombus lantschouensis native to China link: https://peerj.com/articles/18964 last-modified: 2025-02-13 description: Bumblebees play crucial roles as pollinators in both natural agricultural and ecological systems. Their health and overall fitness are significantly affected by the gut microbiota, which can maintain intestinal homeostasis in hosts by regulating their nutritional metabolism. However, information about the diversity of the gut microbiota and related functional changes during artificial rearing of native species is currently limited. This study investigated the dynamic remodeling of gut microbiota in the Chinese native bumblebee Bombus lantschouensis under captive rearing, supported by 16S rRNA amplicon sequencing of bacterial DNA. The typical microbial community composition of the bumblebee was detected in the gut of wild B. lantschouensis, with species of genus Gilliamella and Snodgrassella identified as the dominant strains. Conversely, the microbiota of the captive-reared group showed increased diversity and decreased abundance of certain species of microorganisms. The populations of Bifidobacterium, Saccharibacter, and Lactobacillus, including Firm-4 and Firm-5, were dramatically increased after captive-rearing and became the dominant bacteria, while Gilliamella and Snodgrassella were strikingly reduced. Notably, this study found that pathogenic bacteria appeared in the intestines of wild-caught B. lantschouensis and disappeared when the host was reared under captive conditions. This study shows microbial community changes in bumblebees and facilitates the study of physiological metabolism in the commercial rearing of insects. creator: Feng Zhou creator: Shuning Sun creator: Xinge Song creator: Yuying Zhang creator: Zhuanxia Li creator: Jiani Chen uri: https://doi.org/10.7717/peerj.18964 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zhou et al. title: Association between visceral fat and bone mineral density in perimenopausal women link: https://peerj.com/articles/18957 last-modified: 2025-02-13 description: BackgroundThe effects of visceral fat and body fat on osteoporosis (OP) have long been controversial. This study investigated the correlation between visceral fat and bone mineral density (BMD) in perimenopausal women aged 40–60. The goal was to evaluate the current state of BMD and its influencing factors, with the specific objective of establishing a foundation for preventing and treating osteoporosis in this demographic.MethodsThis case-control study included female participants (n = 330), aged 40–60 years, from the Health Management Center of Guilin Medical College Affiliated Hospital, China, between January 2020 to August 2023. Their BMD was assessed using an ultrasound bone mineral density meter, and the visceral fat area was determined utilizing a body composition analyzer. Furthermore, past medical history, dietary habits, and lifestyle factors were collected through a telephonic questionnaire survey. Additionally, we analyzed the baseline characteristics of the population, bone status and visceral fat status, and the relationship between these variables.ResultsAmong perimenopausal women with varying bone mineral density statuses, there was no significant difference regarding body fat percentage (p = 0.359). In contrast, a statistically significant difference was observed regarding visceral fat area (p < 0.001) and vitamin D (p < 0.001). The visceral fat area exhibited an inverse correlation with bone density (r = –0.313, p < 0.001). Additionally, mediation analysis outcomes did not support the hypothesis that visceral fat affects bone density through its influence on vitamin D levels (p = 0.92).ConclusionsAmong perimenopausal women, visceral fat is negatively associated with bone density, suggesting that the distribution of body fat rather than the total amount plays a pivotal role in the development of osteoporosis. These findings suggest the significance of regular physical exercise and the abdominal fat distribution for perimenopausal women. creator: Xu Tang creator: Ling Tang creator: Xiaolin Li creator: Jiejing Cao creator: Huanhuan Wang creator: Shujiao Liu creator: Yufang Yi creator: Zhiyong Zhang uri: https://doi.org/10.7717/peerj.18957 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Tang et al. title: Integrated genomic analysis of the stemness index signature of mRNA expression predicts lung adenocarcinoma prognosis and immune landscape link: https://peerj.com/articles/18945 last-modified: 2025-02-13 description: mRNA expression-based stemness index (mRNAsi) has been used for prognostic assessment in various cancers, but its application in lung adenocarcinoma (LUAD) is limited, which is the focus of this study. Low mRNAsi in LUAD predicted a better prognosis. Eight genes (GNG7, EIF5A, ANLN, FKBP4, GAPDH, GNPNAT1, E2F7, CISH) associated with mRNAsi were screened to establish a risk model. The differentially expressed genes between the high and low risk groups were mainly enriched in the metabolism, cell cycle functions pathway. The low risk score group had higher immune cell scores. Patients with lower TIDE scores in the low risk group had better immunotherapy outcomes. In addition, risk score was effective in assessing drug sensitivity of LUAD. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) data showed that eight genes were differentially expressed in LUAD cell lines, and knockdown of EIF5A reduced the invasion and migration ability of LUAD cells. This study designed a risk model based on the eight mRNAsi-related genes for predicting LUAD prognosis. The model accurately predicted the prognosis and survival of LUAD patients, facilitating the assessment of the sensitivity of patients to immunotherapy and chemotherapy. creator: Xingzhao Lu creator: Wei Du creator: Jianping Zhou creator: Weiyang Li creator: Zhimin Fu creator: Zhibin Ye creator: Guobiao Chen creator: Xian Huang creator: Yuliang Guo creator: Jingsheng Liao uri: https://doi.org/10.7717/peerj.18945 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Lu et al. title: Modified Early Warning Score (MEWS) combined with biomarkers in predicting 7-day mortality in traumatic brain injury patients in the emergency department: a retrospective cohort study link: https://peerj.com/articles/18936 last-modified: 2025-02-13 description: BackgroundTraumatic brain injury (TBI) is a leading cause of injury-related disability and death globally, which negatively affects individuals, families, and society. Predicting the risk for mortality among TBI patients is crucial in guiding further timely and effective treatment plans. Both the standard risk assessment tools and blood-based biomarkers are helpful in predicting outcomes among TBI patients. However, no studies have compared the predicting performance of the individual and combined indicators from the two major types.AimThis study aimed to compare the Modified Early Warning Score (MEWS), Red blood cell distribution width (RDW), and creatine in predicting 7-day mortality among TBI patients.MethodsA retrospective study was conducted in the emergency department of the First People’s Hospital of Changde, China, from January 1, 2023, to June 30, 2023. Data of 1,701 patients with TBI were obtained from the hospital’s electronic medical records. A logistic regression model was used to determine independent factors influencing 7-day mortality. The area under the curve (AUC) of the receiver operating characteristic curve (ROC) was calculated to compare the individual and combined effects of MEWS, RDW, and creatine in predicting 7-day mortality based on bootstrap resampling (500 times).ResultsAmong the 1,701 patients, 225 died, with a mortality rate of 13.23%. The multivariate analysis showed that the type of TBI lesion, MEWS, SBP, DBP, MAP, SpO2, temperature, RDW, and creatine were significantly associated with 7-day mortality. MEWS (AUC: 0.843) performed better than RDW (AUC: 0.785) and creatine (AUC: 0.797) in predicting 7-day mortality. MEWS+RDW (AUC: 0.898) performed better than MEWS+creatine (AUC: 0.875) and RDW+ creatine (AUC: 0.822) in predicting 7-day mortality. The combination of all three indicators, MEWS+RDW+creatine, showed the best predicting performance (AUC: 0.906).ConclusionMEWS performed best in predicting the 7-day mortality of TBI patients, and its predicting performance was improved when combined with blood-based biomarkers such as RDW and creatine. Our findings provide preliminary evidence supporting the combination of MEWS with blood-based biomarkers as a new method for predicting 7-day mortality in patients with TBI. creator: Shouzhen Zhu creator: Yongqiang Yang creator: Boling Long creator: Li Tong creator: Jinhua Shen creator: Xueqing Zhang uri: https://doi.org/10.7717/peerj.18936 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Zhu et al. title: Advances and insights for DKK3 in non-cancerous diseases: a systematic review link: https://peerj.com/articles/18935 last-modified: 2025-02-13 description: This review delves into the role of Dickkopf-3 (DKK3), a secreted glycoprotein and member of the Dickkopf family, in non-malignant diseases. DKK3 is particularly known for its regulatory effects on the Wnt signaling pathway, a critical mediator in various biological processes including cell proliferation, differentiation, and migration. Our review highlights DKK3’s influence in disorders of the cardiovascular, respiratory, renal, and muscular systems, where it contributes to disease progression by modulating these key biological processes. As an emerging biomarker, DKK3’s levels have been found to correlate with various disease states, underscoring its potential diagnostic and therapeutic implications. creator: Yao Sun creator: Zengli Xiao creator: Shuguang Yang creator: Chenxiao Hao creator: Huiying Zhao creator: Youzhong An uri: https://doi.org/10.7717/peerj.18935 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Sun et al. title: Making sense of fossils and artefacts: a review of best practices for the design of a successful workflow for machine learning-assisted citizen science projects link: https://peerj.com/articles/18927 last-modified: 2025-02-13 description: Historically, the extensive involvement of citizen scientists in palaeontology and archaeology has resulted in many discoveries and insights. More recently, machine learning has emerged as a broadly applicable tool for analysing large datasets of fossils and artefacts. In the digital age, citizen science (CS) and machine learning (ML) prove to be mutually beneficial, and a combined CS-ML approach is increasingly successful in areas such as biodiversity research. Ever-dropping computational costs and the smartphone revolution have put ML tools in the hands of citizen scientists with the potential to generate high-quality data, create new insights from large datasets and elevate public engagement. However, without an integrated approach, new CS-ML projects may not realise the full scientific and public engagement potential. Furthermore, object-based data gathering of fossils and artefacts comes with different requirements for successful CS-ML approaches than observation-based data gathering in biodiversity monitoring. In this review we investigate best practices and common pitfalls in this new interdisciplinary field in order to formulate a workflow to guide future palaeontological and archaeological projects. Our CS-ML workflow is subdivided in four project phases: (I) preparation, (II) execution, (III) implementation and (IV) reiteration. To reach the objectives and manage the challenges for different subject domains (CS tasks, ML development, research, stakeholder engagement and app/infrastructure development), tasks are formulated and allocated to different roles in the project. We also provide an outline for an integrated online CS platform which will help reach a project’s full scientific and public engagement potential. Finally, to illustrate the implementation of our CS-ML approach in practice and showcase differences with more commonly available biodiversity CS-ML approaches, we discuss the LegaSea project in which fossils and artefacts from sand nourishments in the western Netherlands are studied. creator: Isaak Eijkelboom creator: Anne S. Schulp creator: Luc Amkreutz creator: Dylan Verheul creator: Wouter Verschoof-van der Vaart creator: Sasja van der Vaart-Verschoof creator: Laurens Hogeweg creator: Django Brunink creator: Dick Mol creator: Hans Peeters creator: Frank Wesselingh uri: https://doi.org/10.7717/peerj.18927 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Eijkelboom et al. title: The impacts of climate change on the global range of Culicoides punctatus (Meigen, 1804) with notes on its status in Saudi Arabia link: https://peerj.com/articles/18916 last-modified: 2025-02-13 description: Biting midges, particularly Culicoides species, pose significant health risks to humans and animals due to their biting behavior and ability to transmit diseases. Understanding their behavior and distribution patterns is crucial for predicting and controlling the spread of viral infections. This study employs species distribution modeling to assess the environmental suitability and potential future distribution of Culicoides punctatus, a species known for causing allergic reactions in horses and acting as a vector for bluetongue virus (BTV) and African horse sickness virus (AHSV). Species occurrence records for C. punctatus were collected from the Global Biodiversity Information Facility (GBIF), and environmental data representing climate variables were obtained from WorldClim. The data were used to develop species distribution models and predict the potential distribution of C. punctatus in the Old World under different emission scenarios. The results indicate that C. punctatus has a wide occurrence across the Old World, with the highest number of records in Europe. The species distribution models highlight the influence of climate on the distribution of C. punctatus, suggesting that climate change could impact its range and potentially expand regions with endemic viral infections. The study emphasizes the need for proactive measures to monitor and manage the spread of viral infections associated with Culicoides midges. The integration of geographic information systems (GIS) and remote sensing technology has facilitated high-throughput analysis techniques, eliminating the need for invasive experiments and enabling the remote assessment of species’ habitats, land cover changes, and meteorology. Species distribution modeling, a powerful tool in ecological research, has been employed to predict the potential distribution of C. punctatus and assess its vulnerability to climate change. This study contributes to our understanding of the ecological implications of climate change on Culicoides midges and the associated viral infections. It provides valuable insights for designing effective management strategies, conservation efforts, and mitigation measures to minimize the impact of biting midges on human and animal health. Further research and monitoring are necessary to continuously update and refine these models in the face of changing environmental conditions. creator: Esam S. Al-Malki uri: https://doi.org/10.7717/peerj.18916 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Al-Malki 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. title: Comparison of 1-year mortality predictions from vendor-supplied versus academic model for cancer patients link: https://peerj.com/articles/18958 last-modified: 2025-02-11 description: PurposeThe Epic End of Life Care Index (EOLCI) predicts 1-year mortality for a general adult population using medical record data. It is deployed at various medical centers, but we are not aware of an independent validation. We evaluated its performance for predicting 1-year mortality in patients with metastatic cancer, comparing it against an academic machine learning model designed for cancer patients. We focused on this patient population because of their high short-term mortality risk and because we had access to the comparator model predictions.Materials and MethodsThis retrospective analysis included adult outpatients with metastatic cancer from four outpatient sites. Performance metrics included AUC for 1-year mortality and positive predictive value of high-risk score.ResultsThere were 1,399 patients included. Median age at first EOLCI prediction was 67 and 55% were female. A total of 1,283 patients were evaluable for 1-year mortality; of these, 297 (23%) died within 1 year. AUC for 1-year mortality for EOLCI and academic model was 0.73 (95% CI [0.70–0.76]) and 0.82 (95% CI [0.80–0.85]), respectively. Positive predictive value was 0.38 and 0.65, respectively.ConclusionThe EOLCI’s discrimination performance was lower than the vendor-stated value (AUC of 0.86) and the academic model’s performance. Vendor-supplied machine learning models should be independently validated, particularly in specialized patient populations, to ensure accuracy and reliability. creator: Michael F. Gensheimer creator: Jonathan Lu creator: Kavitha Ramchandran uri: https://doi.org/10.7717/peerj.18958 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Gensheimer et al. title: Efficacy of sacubitril/valsartan on improving clinical symptoms in patients with acute myocardial infarction complicated with heart failure: a retrospective study link: https://peerj.com/articles/18873 last-modified: 2025-02-11 description: BackgroundAcute myocardial infarction (AMI) significantly contributes to the progression of heart failure (HF). Standard treatment for HF has long been angiotensin-converting enzyme inhibitors (ACEIs), targeting the renin-angiotensin-aldosterone system (RAAS). Recent developments in HF management introduced sacubitril/valsartan (S/V), a novel angiotensin receptor-neprilysin inhibitor (ARNI), showing promising results in global trials. This study aimed to assess the efficacy of early S/V application compared to angiotensin-converting enzyme inhibitors (ACEIs) in reducing NT-proBNP levels and improving clinical outcomes, specifically focusing on dyspnea symptomatology, in Chinese patients with AMI complicated by HF.MethodsThis single-center, mixed methods study was conducted at Tangshan Gongren Hospital from January to December 2021, including 88 patients diagnosed with AMI and HF. Patients were divided into two groups: 31 received S/V, while 57 were treated with ACEIs. Data collection encompassed baseline demographic, clinical, and biochemical variables, NT-proBNP levels, blood pressure measurements, and dyspnea symptom severity. Follow-up assessments were conducted 1 year post-discharge to evaluate NT-proBNP levels, and symptom progression. Statistical analyses, including t-tests, Wilcoxon rank-sum tests, and chi-square tests, were performed to compare outcomes between the two groups.ResultsAt baseline, no significant differences were observed between the two groups in terms of demographic, lifestyle, and medical history. Although patients in the S/V group presented with more severe baseline renal impairment and cardiac dysfunction, there was no significant difference in NT-proBNP levels from admission to discharge. 1-year follow-up showed a trend towards reduced NT-proBNP levels in the S/V group, though this difference did not reach statistical significance. All patients in both groups reported improvements in dyspnea at discharge and at follow-up, with no significant inter-group difference. Notably, the S/V group demonstrated a more significant reduction in both systolic and diastolic blood pressure from admission to discharge compared to the ACEIs group.ConclusionsThis study found that S/V had similar effects to ACEIs in reducing NT-proBNP levels among Chinese patients with AMI complicated by HF, though S/V was associated with greater reductions in blood pressure. These findings suggest that while S/V may offer additional benefits in blood pressure management, its impact on cardiac biomarkers in acute settings may not significantly differ from ACEIs. Given the study’s limitations, including its single-center design, small sample size, and baseline differences. Further multi-center, randomized controlled trials are warranted to validate these findings and explore tailored treatment strategies for AMI patients with concurrent HF. creator: Guiping Wang creator: Ruolin Zhang creator: Xuyang Li creator: Shuping Zuo creator: Boheng Zhang creator: Yanan Zhao creator: Suya Sun creator: Juanjuan Zhang creator: Xiaokun Liu uri: https://doi.org/10.7717/peerj.18873 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Wang et al. title: Modelling asynchrony in phenology considering a dynamic representation of meteorological variables link: https://peerj.com/articles/18653 last-modified: 2025-02-11 description: Shifts in the timing of phenological events across many taxa and ecosystems are a result of climate change. Within a trophic network, phenological mismatches between interlinked species can have negative impacts for biodiversity, ecosystems, and the trophic network. Here we developed interaction indices that quantify the level of synchrony and asynchrony among groups of species in three interlinked trophic levels, as well as accounting for a dynamic representation of meteorology. Insect first flight, vegetation green-up and arrival of migrant birds were the phenological indicators, obtained from a combination of spatially and temporally explicit species observations from citizen science programmes and remote sensing platforms (i.e., Landsat). To determine phenological shifts in interlinked taxa we created and applied several phenological indices of synchrony-asynchrony, combining information from the phenological events and critical time windows of meteorological variables. To demonstrate our method of incorporating a meteorological component in our new interaction index, we implemented the relative sliding time window analysis, a stepwise regression model, to identify critical time windows preceding the phenological events on a yearly basis. The new indices of phenological change identified several asynchronies within trophic levels, allowing exploration of potential interactions based on synchrony among interlinked species. Our novel index of synchrony-asynchrony including a meteorological dimension could be highly informative and should open new pathways for studying synchrony among species and interaction networks. creator: Rubén de la Torre Cerro creator: Gourav Misra creator: Emily Gleeson creator: Guy Serbin creator: Jesko Zimmermann creator: Fiona Cawkwell creator: Astrid Wingler creator: Paul Holloway uri: https://doi.org/10.7717/peerj.18653 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 de la Torre Cerro et al. title: N. sphaeroides phycocyanin subunit Ns-α and Ns-β improve C. elegans antioxidative capacity via ROS-related regulation link: https://peerj.com/articles/18917 last-modified: 2025-02-10 description: Oxidative stress and damage to macromolecules due to free radicals such as reactive oxygen species (ROS) are commonly considered factors that can impair health. This study investigated the potential antioxidant properties of of two subunit proteins associated with the pigment-protein complex phycocyanin derived from Nostoc sphaeroides (Gexianmi). Bacterial expression vectors were separately constructed to induce the two engineering subunit proteins, Ns-α and Ns-β. These engineering proteins were then examined for their potential to enhance antioxidative capacity in Caenorhabditis elegans. Firstly, a proper concentration of the proteins Ns-α and Ns-β in vitro exhibited 2, 2-azino-bis 3-ethylbenzothiazoline-6-sulfonic acid (ABTS) radical scavenging activity. Secondly, while there were no other observed effects on the nematodes, those treated with the proteins showed significant improvements in motility and reduced levels of lipofuscin compared to the control group. Furthermore, thirdly, the treated nematodes demonstrated increased resistance to oxidation, as evidenced by the higher survivals under oxidative conditions induced by 5 mM H2O2. Notably, the treated nematodes exhibited decline in endogenous ROS levels, and the redox-related genes, such as SOD-3 and CAT-1, were down-regulated following consumption of the engineering proteins. Taken together, these findings suggest that engineering proteins Ns-α and Ns-β improve the antioxidative capacity of C. elegans by modulating ROS-related regulation, making them potential modulators in responding to oxidative stressors. creator: Xiaoyu Wu creator: Caiyun Zhang creator: Shuwen Zhou creator: Chao Cheng creator: Qing Fang uri: https://doi.org/10.7717/peerj.18917 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Wu et al. title: Enhancing active ingredient biosynthesis in Chinese herbal medicine: biotechnological strategies and molecular mechanisms link: https://peerj.com/articles/18914 last-modified: 2025-02-10 description: BackgroundChinese herbal medicine (CHM) is a fundamental component of traditional Chinese medical practice, offering a rich source of natural remedies with significant therapeutic potential. However, the scarcity of active ingredients and complex extraction procedures present substantial challenges to their widespread clinical application. This review aims to address this gap by exploring the potential of modern biotechnological advancements in enhancing the biosynthesis of these valuable compounds.MethodologyThe study takes a comprehensive approach, delving into the chemical composition of CHM’s active ingredients and elucidating their biosynthetic pathways and molecular regulatory mechanisms. Additionally, it surveys recent progress in extraction methodologies and evaluates engineering strategies aimed at synthetic production. This multifaceted analysis forms the foundation for examining the role of synthetic biology in augmenting CHM’s active ingredient synthesis.ResultsOur examination provides insights into the intricate biosynthetic pathways governing the formation of CHM’s active ingredients, as well as the complex molecular regulatory networks that underlie these processes. Furthermore, the review highlights advancements in extraction techniques, demonstrating their ability to streamline and enhance the isolation of these compounds. Engineering approaches for synthetic production, including metabolic engineering and synthetic biology tools, are assessed for their potential to overcome natural limitations and scale up production.ConclusionsBy integrating insights from biosynthesis, molecular regulation, extraction methodologies, and synthetic biology, this review establishes a robust theoretical framework for enhancing the production of CHM’s active ingredients. The proposed strategies and practical guidance aim to facilitate their broader utilization in modern medicine while promoting sustainability and accessibility within this invaluable medicinal heritage. creator: Ziyi Guo creator: Ning Yang creator: Delin Xu uri: https://doi.org/10.7717/peerj.18914 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Guo et al. title: A gene signature related to programmed cell death to predict immunotherapy response and prognosis in colon adenocarcinoma link: https://peerj.com/articles/18895 last-modified: 2025-02-10 description: BackgroundTumor development involves the critical role of programmed cell death (PCD), but the correlation between colon adenocarcinoma (COAD) and PCD-related genes is not clear.MethodsSubtyping analysis of COAD was performed by consensus clustering based on The Cancer Genome Atlas (TCGA), with the AC-ICAM queue from the cBioportal database as a validation set. Immune infiltration of the samples was evaluated using CIBERSORT and Microenvironment Cell Populations (MCP)-counter algorithms. Patients’ immunotherapy response was predicted by the TIDE and aneuploidy scores. Pathway enrichment analysis was conducted with gene set enrichment analysis (GSEA). A RiskScore model was established with independent prognostic PCD-related genes filtered by Cox regression analysis. The mafCompare function was used to compare the differences in mutation rates of somatic genes. Wound healing, transwell assays and Flow cytometer were applied to measure the cell migration, invasion and apoptosis.ResultsThe patients were grouped into S1 and S2 subtypes based on a total of 21 PCD genes associated with the prognostic outcomes of COAD. Specifically, patients of S1 subtype were mainly related to the pathway activation in tumor invasion and deterioration and had a worse prognosis. A RiskScore model was established based on six prognostic genes, including two protective genes (ATOH1, ZG16) and four risk genes (HSPA1A, SEMA4C, CDKN2A, ARHGAP4). Notably, silencing of CDKN2A inhibited the activity of migration and invasion and promoted apoptosis of tumor cells. Based on the RiskScore model, the patients were grouped into high- and low-risk groups. Independent prognostic factors, namely, Age, pathologic_M, pathologic_stage, and RiskScore, were integrated to develop a nomogram with strong good prediction performance. High-risk group had high-expressed immune checkpoint genes and higher TIDE scores, showing a strong immune escape ability and less active immunotherapy response. Compared to the low-risk group, TP53 exhibited a higher rate of somatic mutation in the high-risk group.ConclusionWe constructed a RiskScore model with six PCD-related genes for the prognostic assessment of COAD, providing a valuable insight into the exploration of new targets for the prognostic improvement in COAD. creator: Lei Zheng creator: Jia Lu creator: Dalu Kong creator: Yang Zhan uri: https://doi.org/10.7717/peerj.18895 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zheng et al. title: Microplastic effects on mouse colon in normal and colitis conditions: A literature review link: https://peerj.com/articles/18880 last-modified: 2025-02-10 description: BackgroundTaking into account the global spread of microplastic (MP) pollution, the problem of the MP impact on human health is relevant. MP enters the organism predominantly with water and food, and is mostly detected in the large intestine. Therefore, the connection between MP pollution and the increase in colitis is an important question. In order to assess the toxic and pathogenetic effects of MP, experimental studies were actively conducted during recent years, mainly on laboratory mice.ObjectivesThe aim of our review was to summarize and systematize the data on the MP effect on mice colon under normal conditions and during colitis in order to assess the role of MP in the development of intestinal diseases. This manuscript could be relevant for ecologists, experimental biologists, and physicians dealing with problems related to anthropogenic environmental changes and inflammatory bowel diseases.Survey MethodologyThe search was conducted based on PubMed data about original experimental studies of the MP effects on the colon of healthy mice and mice with colitis.ResultsIn healthy mice colon, MP can cause oxidative stress, increased permeability, immune cell infiltration, production of proinflammatory factors, and decreased mucus production. MP affects proliferation, apoptosis, and differentiation of epithelial cells, expression of tight junction components and glycocalyx, membrane transport, signaling pathways, metabolome, and intestinal microflora composition. In mice with acute and chronic experimental colitis, MP consumption leads to a more pronounced pathological process course.ConclusionsMP may be one of the factors contributing to the development of colitis in humans. However, further research is needed. creator: Natalia Zolotova creator: Dzhuliia Dzhalilova creator: Ivan Tsvetkov creator: Maria Silina creator: Nikolai Fokichev creator: Olga Makarova uri: https://doi.org/10.7717/peerj.18880 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zolotova et al. title: Nanoparticles modified bioceramic sealers on solubility, antimicrobial efficacy, pushout bond strength and marginal adaptation at apical-third of canal dentin link: https://peerj.com/articles/18840 last-modified: 2025-02-10 description: ObjectiveThe present study investigates the solubility, antimicrobial potency, pushout bond strength (PBS), and marginal adaptation of sealer modified using various nanoparticles (NPs) (silver, chitosan, HapNPs) to the root dentin at the apical third.MethodsForty-four human premolars were prepared for root canal treatment via a chemical mechanical approach. The teeth included were subsequently distributed into four groups based on the type of modified and unmodified sealers. Group 1 bioceramic (BC) sealer (Control), Group 2 (AgNPs modified BC sealer), Group 3 (CHNPs modified BC sealer), and Group 4 (HApNPs modified BC sealer). Solubility was assessed by making five samples and measured via precision balance. Antimicrobial testing against E. faecalis was performed using the Agar diffusion test. The bond strength and failure modes were assessed utilizing a universal testing machine and stereomicroscope respectively. A pair of specimens from each cohort was fixed to an aluminum stub to assess marginal adaptation via SEM at the apical third. Data analysis was performed utilizing one way ANOVA and followed by Tukey’s post hoc test (p < 0.05).ResultsSealers-modified HApNPs exhibited the lowest solubility (3.884 ± 0.15%) and strongest PBS (9.63 ± 0.12 MPa). Group 1 (Control) demonstrated highest solubility rate (6.144 ± 0.39%) and weakest bond strength (6.50 ± 0.09 MPa). All the modified sealers exhibited the largest zone of inhibition with no significant difference. Whereas the unmodified BC sealer group presented the smallest zone of bacterial inhibition.ConclusionMarginal adaptation of sealers does not affect the bond strength outcomes achieved. The incorporation of silver, chitosan, and hydroxyapatite nanoparticles into BC root canal sealers resulted in reduced solubility, enhanced antibacterial efficacy, and improved PBS compared to unmodified BC canal sealers. creator: Basil Almutairi creator: Fahad Alkhudhairy uri: https://doi.org/10.7717/peerj.18840 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Almutairi and Alkhudhairy title: The association between serum lipids at diagnosis and renal outcome in microscopic polyangiitis patients link: https://peerj.com/articles/18839 last-modified: 2025-02-10 description: ObjectivesMicroscopic polyangiitis (MPA) is a subgroup of ANCA-associated vasculitis (AAV), which is characterized by vascular endothelial cell damage caused by abnormally activated neutrophils. Dyslipidemia is associated with vascular endothelial cell injury, and the relationship between blood lipid levels and renal prognosis in MPA patients is not clear. We aim to investigate the correlation between blood lipid levels at diagnosis and renal prognosis in MPA patients.MethodsFirstly, we retrospectively included 110 patients diagnosed with MPA and the primary endpoint was the occurrence of end stage renal disease (ESRD). The association between blood lipids at diagnosis and renal outcome was evaluated with Cox regression analysis and survival analysis. Secondly, we explored the potential underlying mechanism of poor renal prognosis in patients with high triglycerides (TG) levels at diagnosis using data independent acquisition (DIA) quantitative proteomics.ResultsDuring a median follow-up period of 23 months, 44 out of 110 patients (40%) developed ESRD. High serum TG at diagnosis was associated with ESRD development after adjusting for several confounding factors including age, gender, body mass index (BMI), hypertension, diabetes mellitus, estimated glomerular filtration rate (eGFR) and Birmingham Vasculitis Activity Score (BVAS). Serum very low-density lipoprotein (VLDL) demonstrated a marginal trend towards association with ESRD development. MPA patients with TG >1.45 mmol/L or VLDL > 0.66 mmol/L had significantly higher risk of ESRD development than those with TG ≤ 1.45 mmol/L or VLDL ≤ 0.66 mmol/L. DIA quantitative proteomics analysis suggested that patients with elevated TG levels and severe MPA had an upregulation of profibrotic pathways, inflammatory signaling, and complement and coagulation cascades, in contrast to those with lower TG levels and milder disease severity.ConclusionsIn MPA patients, high TG or VLDL at diagnosis is associated with an increased risk of ESRD development. The potential mechanisms may be associated with the upregulation of profibrotic and inflammatory signaling pathways, and the activation of complement and coagulation cascades. creator: Zigui Zheng creator: Yujia Wang creator: Jingzhi Xie creator: Zhimin Chen creator: Bingjing Jiang creator: Yanfang Xu uri: https://doi.org/10.7717/peerj.18839 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zheng et al. title: Genome-wide survey and expression analysis of the OMT gene family in Stephania japonica link: https://peerj.com/articles/18600 last-modified: 2025-02-10 description: BackgroundO-methyltransferase (OMT) is an important rate-limiting enzyme that plays a vital role in synthesizing various key metabolites, such as benzylisoquinoline alkaloids (BIA). Nevertheless, there is a dearth of extensive research on the analysis of the OMT gene family in Stephania japonica, a main source of cepharanthine with an anti-coronavirus effect.MethodsTwo OMT family genes, SjCCoAOMT and SjCOMT, were identified from the high-quality genome of S. japonica during this investigation. Further analysis of SjCCoAOMT and SjCOMT genes involved chromosome distribution, gene structure, phylogenetic relationship, conserved motif, expression profile, quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) experiments an d cis-acting elements analysis.ResultsThere are six SjCCoAOMT members and fifty-two SjCOMT members in the genome of S. japonica, which are unevenly distributed on 11 chromosomes. OMTs could be clustered into SjCCoAOMT and SjCOMT subfamilies through phylogenetic relationship, consistent with the conserved motif and gene structure analysis results. The expression profile revealed SjCOMT11 and SjCOMT13 showed specific expression levels mainly in root. SjCOMT21, SjCOMT33 and SjCOMT37 were significantly expressed in the root and slightly expressed in the stem, bud and leaf. SjCOMT15 and SjCOMT45 were not only significantly expressed in root, but also expressed highly in leaf. Significantly enhanced expression of SjCOMT11, SjCOMT13, SjCOMT15, SjCOMT21, SjCOMT33, SjCOMT37, and SjCOMT45 suggested these OMTs are essential for cepharanthine synthesis in the S. japonica roots. Cis-acting element analysis revealed the potential roles of OMTs in S. japonica in growth, development, and resistance to stress. These findings provide insight into understanding the functions and characterization of OMTs from S. japonica and lay a foundation for further revealing the role of the OMT genes in the biosynthesis of cepharanthine. creator: Zenghao Bi creator: Tianxing He creator: Yuting Liang creator: Changqing Zhou creator: Yuetong Yu creator: Liang Leng uri: https://doi.org/10.7717/peerj.18600 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Bi et al. title: New record of Frilled shark Chlamydoselachus anguineus Garman, 1884 (Chondrichthyes: Hexanchiformes) in the South Pacific Ocean link: https://peerj.com/articles/18992 last-modified: 2025-02-07 description: Frilled sharks are rarely observed and limited information is available regarding their life history. The global number of records for these sharks does not exceed 40, with most sightings reported in the Western Pacific Ocean. In 1976, one specimen was recorded for the first time in the South East Pacific Ocean; however, this study provides new evidence for the presence of Chlamydoselachus anguineus in Chilean waters, extending its distribution range 850 km south of the previous record. The morphological features of all specimens from Chile are discussed, supplementing previous observations and adding to the existing knowledge on this species in the Pacific Ocean. creator: Maria J. Indurain creator: Angel Mancilla creator: Leandro Brizuela creator: Carolina Vargas-Caro creator: Carlos Bustamante uri: https://doi.org/10.7717/peerj.18992 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Indurain et al. title: Berberine-induced browning and energy metabolism: mechanisms and implications link: https://peerj.com/articles/18924 last-modified: 2025-02-07 description: Obesity has become a global pandemic. The approaches researched to prevent it include decreasing energy intake and/or enhancing energy expenditure. Therefore, research on brown adipose tissue is of great importance. Brown adipose tissue is characterized by its high mitochondrial content. Mitochondrial uncoupling protein 1 (UCP1) releases energy as heat instead of chemical energy. Thermogenesis increases energy expenditure. Berberine, a phytochemical widely used in Asian countries, has positive effects on body weight control. While the precise mechanisms behind this effect remain unclear, the adenosine monophosphate-activated protein kinase (AMPK) pathway is known to play a crucial role. Berberine activates AMPK through phosphorylation, significantly impacting brown adipose tissue by enhancing lipolytic activity and increasing the expression of UCP1, peroxisome proliferator-activated receptor γ-co-activator-1α (PGC1α), and PR domain containing 16 (PRDM16). While investigating the mechanism of action of berberine, both the AMPK pathway is being examined in more detail and alternative pathways are being explored. One such pathway is growth differentiation factor 15 (GDF15), known for its appetite-suppressing effect. Berberine’s low stability and bioavailability, which are the main obstacles to its clinical use, have been improved through the development of nanotechnological methods. This review examines the potential mechanisms of berberine on browning and summarizes the methods developed to enhance its effect. creator: Aslıhan Alpaslan Ağaçdiken creator: Zeynep Göktaş uri: https://doi.org/10.7717/peerj.18924 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Alpaslan Ağaçdiken and Göktaş title: Assessing the quality of life among African medical and health science students using the WHOQOL-BREF tool link: https://peerj.com/articles/18809 last-modified: 2025-02-07 description: BackgroundThe quality of life (QoL) among health professional students is available in the literature, yet there is a paucity of information concerning QoL among African students. The study aimed to measure the QoL with the World Health Organization Quality of Life-BREF (WHOQOL-BREF) tool among African medical and health science students.MethodsA cross-sectional study was conducted involving 349 African medical and health science students from various disciplines at the International African University in May 2024. A purposive sampling method was used to recruit participants from five different faculties. Data were collected using the WHOQOL-BREF tool, and analyzed using descriptive statistics, chi-square test and multiple linear regression to determine the predictors of QoL among students.ResultsThe overall QoL among 349 African medical and health science students was moderate, with a mean score of 67.5% ± 10.8%. The highest mean scores were observed in the physical health domain (69.3% ± 12.0%), while the lowest scores were in the environmental domain (62.9% ± 12.0%). The multiple regression analysis using demographic data as predictors of QoL revealed that dentistry students were significant predictors of higher overall QoL scores compared to other student groups (β = 7.059, p < 0.05), as well as specific QoL domains including physical health (β = 6.328), psychological health (β = 8.415), social relationships (β = 7.823), and environment (β = 7.017). Furthermore, students from the fields of laboratory sciences and medicine significantly predicted higher scores in the physical health domain (β = 5.223) and the psychological health domain (β = 4.433), respectively. Age was also a significant predictor; students aged between 20 and 23 years showed a positive impact on social relationship domain of QoL (β = 10.296). However, second year (β = −11.146), third year (β = −13.629), and fourth-year students (β = −10.144) exhibited lower social relationship domain of QoL scores.ConclusionStudents of medical and health sciences in Africa exhibited moderate quality of life (QoL). The findings indicate that dentistry students generally experience higher QoL across multiple domains, which contrasts with students from other disciplines, such as pharmacy and nursing. Age and academic year were also significant predictors of QoL, with younger students and those in their initial years of study reporting lower scores. These results align with existing literature and underscore the need for targeted interventions to support students, particularly those in high-stress disciplines or at earlier stages of their education. creator: Fatima Alzahra Galgam creator: Adil Abdalla creator: Mahmoud Shahin creator: Magda Yousif creator: Nahla Abdulrahman creator: Fatmah Alamoudi creator: Mehrunnisha Ahmad creator: Amira Yahia creator: Mohammad Sidiq creator: Aksh Chahal creator: Fuzail Ahmad creator: Mohammad Abu Shaphe creator: Gopal Nambi creator: Moattar Raza Rizvi creator: Faizan Kashoo uri: https://doi.org/10.7717/peerj.18809 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Galgam et al. title: Effect of intercropping Lolium perenne in Ziziphus jujuba orchards on soil quality in the canopy link: https://peerj.com/articles/18710 last-modified: 2025-02-07 description: The cultivation of Lingwu jujube traditionally employs clean tillage, leaving substantial gaps between rows and exposing almost 60% of the orchard to the elements. This method promotes rapid soil moisture evaporation, exacerbates soil erosion, and deteriorates the soil’s physicochemical properties. Consequently, there is a critical need for a more sustainable planting approach that optimally utilizes land resources. A pertinent question is whether varying densities of ryegrass intercropping can improve the uptake of nutrients and water by the jujube tree, the primary species in this ecosystem. In this context, a 2-year field experiment was conducted with three densities of perennial ryegrass intercropped with Lingwu jujube. The experiment assessed the impact on soil’s physical and chemical attributes beneath the jujube canopy, with a focus on correlating soil moisture, enzyme activity, and physical properties. The findings reveal that intercropping at a medium density most effectively enhanced the soil’s physical characteristics. Relative to monoculture, this approach increased the proportion of water-stable aggregates (0.5–0.25 mm) by 4.16%, decreased the soil’s fractal dimension by 0.46%, augmented the field water holding capacity by 14.78%, and significantly boosted soil enzyme activity. Furthermore, high-density ryegrass intercropping elevated the soil’s organic matter content by 36.09% and ameliorated both the pH and cation exchange capacity. Conversely, low-density intercropping raised soil moisture levels by 40.18% in the top 20 cm of the soil. Collectively, these results suggest that an optimal density of ryegrass in intercropping not only bolsters the moisture retention capabilities of soil in Lingwu jujube orchards but also enhances overall soil fertility. Therefore, the adoption of ryegrass and jujube tree intercropping is highly advisable in the ecologically sensitive and resource-constrained arid sandy regions of northern China, offering substantial practical benefits. creator: Yao Ma creator: Bin Cao creator: Xiaojia Wang creator: Weijun Chen uri: https://doi.org/10.7717/peerj.18710 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Ma et al. title: Sex differences in anaerobic performance in CrossFit® athletes: a comparison of three different all-out tests link: https://peerj.com/articles/18930 last-modified: 2025-02-05 description: BackgroundAthletic performance can be influenced by various factors, including those related to biological sex. Various scientific disciplines have studied the observed differences in athletic performance between men and women. Moreover, anaerobic performance refers to the capacity of the human body to generate energy quickly and efficiently during high-intensity and short-duration activities. It is associated with the ability to perform explosive actions and the capacity for rapid recovery between repeated efforts. Anaerobic performance is a determining factor for performance in high-intensity sports and those with predominantly lower intensity but intermittent peaks of higher intensity. One high-intensity sport that has experienced exponential growth and attracts increasing numbers of participants yearly is commercially known as CrossFit® (CF). Therefore, the primary purpose of this study was to determine the anaerobic performance differences between sexes in CF athletes in terms of absolute and relative values.MethodsA cross-sectional study was conducted over 2 weeks. Fifty CrossFit® athletes (25 men and 25 women) voluntarily participated in the study. They were subjected to body composition analysis and three maximal effort tests to measure anaerobic performance: a cycle ergometer test, a continuous jump test and a squat test.ResultsSignificant differences were found in all the variables of absolute peak power and relative to body mass in the three tests. In values adjusted to lean and muscle mass, significant differences were only found in the cycle ergometer test but not in the other two. In mean power variables, significant differences were found in all the variables studied, except for the mean power adjusted to muscle mass in the squat test. In conclusion, this study’s results indicate that differences between sexes in absolute and relative peak powers measured in all tests evaluated are explained by the amount of lean and muscle mass. However, mean powers show significant differences in all variables except for the one related to muscle mass in the squat test. creator: Tomás Ponce-García creator: Jerónimo García-Romero creator: Laura Carrasco-Fernández creator: Alejandro Castillo-Domínguez creator: Javier Benítez-Porres uri: https://doi.org/10.7717/peerj.18930 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Ponce-García et al. title: PyBootNet: a python package for bootstrapping and network construction link: https://peerj.com/articles/18915 last-modified: 2025-02-05 description: BackgroundNetwork analysis has emerged as a tool for investigating interactions among species in a community, interactions among genes or proteins within cells, or interactions across different types of data (e.g., genes and metabolites). Two aspects of networks that are difficult to assess are the statistical robustness of the network and whether networks from two different biological systems or experimental conditions differ.MethodsPyBootNet is a user-friendly Python package that integrates bootstrapping analysis and correlation network construction. The package offers functions for generating bootstrapped network metrics, statistically comparing network metrics among datasets, and visualizing bootstrapped networks. PyBootNet is designed to be accessible and efficient with minimal dependencies and straightforward input requirements. To demonstrate its functionality, we applied PyBootNet to compare correlation networks derived from study using a mouse model to investigate the impacts of Polycystic Ovary Syndrome (PCOS) on the gut microbiome. PyBootNet includes functions for data preprocessing, bootstrapping, correlation matrix calculation, network statistics computation, and network visualization.ResultsWe show that PyBootNet generates robust bootstrapped network metrics and identifies significant differences in one or more network metrics between pairs of networks. Our analysis of the previously published PCOS gut microbiome data also showed that our network analysis uncovered patterns and treatment effects missed in the original study. PyBootNet provides a powerful and extendible Python bioinformatics solution for bootstrapping analysis and network construction that can be applied to microbes, genes, metabolites and other biological data appropriate for network correlation comparison and analysis. creator: Shayan R. Akhavan creator: Scott T. Kelley uri: https://doi.org/10.7717/peerj.18915 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Akhavan and Kelley title: The effects of gluteal stretching vs. Lightback® on hip rotation range of motion and posterior chain flexibility in healthy subjects: a cross-over clinical trial link: https://peerj.com/articles/18523 last-modified: 2025-02-05 description: IntroductionHip range of motion (ROM) across various planes is necessary in sport-related activities. Static stretching was commonly used to improve hip ROM. The Lightback system, a novel compression device, has been developed to enhance hip mobility by applying controlled axial forces on the femur. This study aimed to evaluate the effectiveness of the Lightback system in improving hip ROM and posterior chain flexibility compared to conventional static stretching.MethodsA randomized cross-over trial was carried out in 31 physically active participants (62 lower limbs; n = 31 Lightback group (LBG) and n = 31 stretching group (SG)). Hip rotation at two positions of hip flexion (active and passive external (ER) and internal rotation (IR) at 0–90° hip flexion), total rotation ROM (TRROM), and the flexibility of the posterior chain (active knee extension test (AKE) and active straight leg raise (ASLR)) were measured before and after the stretching session.ResultsLBG demonstrated significantly greater improvements in hip ER and IR compared to the SG. Specifically, the LBG showed significant increases in active ER at 0° (p = 0.002) and 90° (p < 0.001) of hip flexion, as well as IR at 0° (p = 0.007) and 90° (p < 0.001). TRROM in neutral and at 90° of hip flexion also improved significantly in the LBG (p < 0.001). In passive ROM, the LBG exhibited significant increases in ER at 0° (p < 0.001), IR at 90° (p = 0.001), and TRROM at both positions (p < 0.001), compared to the SG. Regarding posterior chain flexibility, both groups improved in AKE and ASLR (p < 0.001), but the LBG showed a significantly larger effect in ASLR (p < 0.001), with no significant difference between groups in AKE.ConclusionThis study demonstrated that both the Lightback system and static gluteal stretching improved passive hip ROM. However, the Lightback system showed greater improvements in active ROM, particularly in external and internal rotation at various degrees of hip flexion, as well as in posterior chain flexibility. Notably, the Lightback system significantly enhanced large improvement in the ASLR test. creator: Charles Cotteret creator: Jaime Almazán-Polo creator: Fabien Guérineau creator: Ángel González de-la-Flor uri: https://doi.org/10.7717/peerj.18523 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Cotteret et al. title: Closing the gap while standing still: clinimetric properties of a low-cost balance platform and a user-friendly app for posturography link: https://peerj.com/articles/18299 last-modified: 2025-02-04 description: BackgroundThe Wii Balance Board (WBB) is used as a rehabilitation tool for balance or strength interventions and posturography in balance tasks. Nonetheless, implementation of posturography using the WBB in a clinical setting is hampered by required technical skills for signal processing to obtain meaningful balance measures. Therefore, this study aims to evaluate the concurrent validity and test–retest reliability of a WBB to measure center of pressure (COP) parameters and to provide an easy-to-use web application to improve implementation of posturography in clinical practice.MethodsA cross-sectional study was carried out including 30 healthy adults who performed repeated balance tasks including single and double leg standing still with eyes open or eyes closed. A WBB on top of a laboratory-grade force plate synchronously measured COP. Parameters based on COP displacement were calculated, including standard deviation of displacement, velocity, pathlength and 95% predicted ellipse area.ResultsThe concurrent validity of the WBB to measure COP in quiet standing still tasks was excellent for all parameters (Intraclass Correlation Coefficient (ICC) > 0.900, p < 0.001), apart from medio-lateral velocity (ICC = 0.571, p = 0.090 to ICC = 0.711, p = 0.057). For the single leg balance tasks, across the two measurements, all WBB COP derived parameters showed excellent correlations with COP parameters derived from a laboratory-grade force plate (ICC > 0.95, p < 0.001). Test–retest reliability of the WBB was poor (ICC below 0.5) to occasionally good (ICC between 0.75 to 0.90) for the COP parameters from quiet standing balance tasks. Comparable reliability was found for the repeated measurements of single leg standing still. Power spectra analysis of both force plates revealed larger measurement error by the WBB in medio-lateral direction in tasks requiring minimal postural adjustments.ConclusionThe WBB revealed excellent concurrent validity with a laboratory-grade force plate for balance tasks on a single leg or two legs for most COP parameters. The reliability was poor to moderate for most tasks, however comparable to the findings from the laboratory grade force plate. An open-source web application, employing R Shiny, was created to provide a tool to analyse COP parameters. Hereby, it was demonstrated that open-source scientific tools may help researchers to bridge the gap between scientific findings and clinical use of posturography. creator: Tom Vredeveld creator: John F. Stins creator: Annelies J. van Vliet creator: Vincent C.M. Tuinder creator: Stephan P.J. Ramaekers creator: Michel W. Coppieters creator: Annelies L. Pool-Goudzwaard uri: https://doi.org/10.7717/peerj.18299 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Vredeveld et al. title: Searching for a common host: parasitoids of Lema daturaphila on Datura stramonium in Central Mexico link: https://peerj.com/articles/18675 last-modified: 2025-02-03 description: BackgroundNatural enemies of herbivore insects can change the arms race between plants and insects. Their presence and abundance even can affect the co-evolution of interacting species. The annual herb Datura stramonium varies geographically in the extent of its direct defenses against herbivores. Its main specialist herbivore, Lema daturaphila, is adapted to cope with these defenses, but little is known about its natural enemies. Here, we determined the presence and incidence of L. daturaphila parasitoids as an initial step to explore other ecological and evolutionary relationships in a tri-trophic context.MethodsField collections of L. daturaphila eggs and larvae were performed during the summers of 2018 and 2019 in eleven natural populations of D. stramonium in central Mexico. We recorded their development to evaluate the emergence of parasitoids and their relationship with the abundance of herbivore individuals and environmental variables in each locality.ResultsWe found six parasitoid fly and wasp species that are new records for Mexico or the host. Throughout their distribution, the interaction varies widely among populations and years. In some localities, egg parasitoids dominate over larval parasitoids and vice versa, and they exert strong pressures on the survival of L. daturaphila’s populations. The abundance of Emersonella lemae, the egg parasitoid, is related to the clutch size of L. daturaphila and climatic conditions such as temperature, altitude, and precipitation. As an apparent defense strategy against parasitoid flies, larvae of L. daturaphila release their oral secretions, which contain alkaloids from D. stramonium. At a geographic scale, these findings change the scenario between the plant-herbivore interaction and open the field to explore the different selective pressures among populations. creator: Carol Estefanía Villanueva-Hernández creator: Juan Núñez-Farfán uri: https://doi.org/10.7717/peerj.18675 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Villanueva-Hernández and Núñez-Farfán