gllvm 2.0: fast fitting of advanced ordination methods and joint species distribution models
Background Over the past decade, joint species distribution models (JSDMs) and model-based ordination have emerged as powerful tools for the analysis of community ecology data. Generalized linear latent variable models (GLLVMs) offer a flexible framework for multivariate analysis of a wide range of data types, based on including a small number of latent variables to perform dimension reduction while accounting for residual correlation between species. Fast estimation methods The R package gllvm implements a wide range of GLLVMs, with estimation performed via fast approximate likelihood-based techniques; including the recently proposed extended variational approximation, which is applicable to almost any combination of response type and link function. Since its original development and accompanying software paper, the gllvm package has undergone a significant overhaul, consolidating its place as a general framework for joint modeling of community ecology datasets. Expanded functionalities Some of the key new features of gllvm include model-based constrained and concurrent ordination methods, capacity to account for nested/hierarchical sampling designs, and (phylogenetic) random effects. On top of this, other notable improvements include a great expansion of the response types that it can handle, enhanced capabilities of GLLVM inference, selection and prediction, and an easier-to-use interface for model fitting.
Korhonen et al. (2025) gllvm 2.0: fast fitting of advanced ordination methods and joint species distribution models. PeerJ 13:e20338 https://doi.org/10.7717/peerj.20338
Revisiting the Poison Dart Frog Ameerega ingeri (Anura: Dendrobatidae): external morphology, tadpoles, natural history, distribution, advertisement call, phylogenetic position and conservation
Many amphibian species have been described based solely on preserved specimens, leaving significant gaps in our understanding of their behavior, natural history, population status, and phylogenetic relationships—factors essential for effective conservation. Ameerega ingeri, a dark poison frog originally believed to be endemic to Colombia, exemplifies this challenge. Described from only four specimens, its coloration in life, ecological traits, and distribution remained poorly understood for decades, leading to taxonomic confusion with closely related species. In this study, we revisit A. ingeri by providing new distribution records that extend its known range, along with detailed morphological and acoustic descriptions, dietary analysis, and population data. By integrating molecular and acoustic data with ecological and natural history observations, we clarify its taxonomic identity and distinguish it from congeners. Furthermore, we assess its conservation status based on updated occurrence and population data, and propose its inclusion in a threat category according to IUCN criteria. Our findings enhance the understanding of dendrobatid diversity and highlight the importance of field-based research on poorly known and potentially threatened species to support informed conservation strategies.
Diaz-Ricaurte et al. (2025) Revisiting the Poison Dart Frog Ameerega ingeri (Anura: Dendrobatidae): external morphology, tadpoles, natural history, distribution, advertisement call, phylogenetic position and conservation. PeerJ 13:e20078 https://doi.org/10.7717/peerj.20078
Retrospective on decadal progress of the NOAA/NPS ocean noise reference station network
The National Oceanic and Atmospheric Administration (NOAA), in partnership with the U.S. National Park Service (NPS), established the Ocean Noise Reference Station Network (NRS) in 2014 as a foundational component of NOAA’s Ocean Noise Strategy. This long-term effort aims to characterize baseline ocean ambient sound conditions across diverse marine environments and to inform management of noise impacts on protected species and habitats within U.S. waters. The NRS is now composed of 13 autonomous passive acoustic monitoring stations strategically positioned across the U.S. Exclusive Economic Zone (EEZ), extending from Arctic regions to tropical waters in depths ranging from 33 to 4,790 m. These locations include several National Marine Sanctuaries and National Parks, such as the recently designated Chumash Heritage National Marine Sanctuary off the coast of California. Each station is equipped to continuously sample low-frequency underwater sound at five kHz, enabling the detection of anthropogenic, geophysical, and biological acoustic signals. To date the network has sampled over 72 years of calibrated acoustic data. The spatial breadth and consistent methodology of the NRS allow for comparative acoustic assessments across diverse marine ecosystems. In addition to applied research functions, the NRS has served as a platform for education and training, offering opportunities for students to develop skills for marine science and data analysis. Looking forward, the NRS project team is focused on network expansion, improved data delivery, and broader integration with collaborative scientific initiatives. NRS recordings are being archived in partnership with NOAA’s National Centers for Environmental Information to enhance accessibility and long-term utility. Efforts are underway to develop standardized metadata and summary products to accompany raw audio files, making the data more usable for a wide range of stakeholders in the ocean science community. The NRS is evolving into a fully integrated national framework for ocean sound monitoring that supports scientific inquiry, management decision-making, national security interests, and public engagement with ocean acoustic environments.
Haver et al. (2025) Retrospective on decadal progress of the NOAA/NPS ocean noise reference station network. PeerJ 13:e20382 https://doi.org/10.7717/peerj.20382
Alleviation of cold stress impacts on grapes by the chitosan-salicylic acid nanocomposite (CS-SA NCs) application
Low temperature is a major abiotic stressor that limits the distribution of various fruit tree species worldwide. In this study, the effects of chitosan-salicylic acid nanocomposite (CS-SA NCs) treatment were evaluated on antioxidant enzyme activity, the antioxidant pool, and membrane stability indices in the grapevine cultivar ‘Flame seedless’ under cold stress conditions. Prolonged exposure to cold, compared to the control, led to a reduction in maximum fluorescence (Fm), variable fluorescence (Fv), the ratio of photochemical to non-photochemical use of light energy in photosystem II (Fv/F0), and the ratio of variable fluorescence to maximum fluorescence (Fv/Fm). Levels of chlorophylls, carotenoids, total soluble protein content, antioxidant enzyme activity, ascorbate, and glutathione activity significantly decreased with increasing cold stress duration. Electrolyte leakage, malondialdehyde, and hydrogen peroxide content increased by 75%, 60%, and 80%, respectively, after 16 hours of cold stress compared to the control. Nanocomposite treatment significantly enhanced antioxidant activity and stabilized membranes under cold stress by reducing electrolyte leakage and malondialdehyde release. Overall, CS-SA NCs act as a biological stimulant and can be effectively used to improve the physiological and biochemical responses of grapevines under cold stress. Further research is needed to gain a comparative understanding of various physiological responses, which will help guide the application of this nanocomposite in extension services and field production systems.
Aazami et al. (2025) Alleviation of cold stress impacts on grapes by the chitosan-salicylic acid nanocomposite (CS-SA NCs) application. PeerJ 13:e20368 https://doi.org/10.7717/peerj.20368
Human-mediated dispersal of Geniotrigona thoracica (Apidae: Meliponini) colonies promotes high genetic diversity and reduces population structuring in managed populations
The stingless bee Geniotrigona thoracica is a key managed pollinator in Southeast Asia, valued for its honey, propolis, and colony trade. In Thailand, frequent human-mediated movement of colonies raises concerns about its effects on genetic diversity and population structure. We analysed variation in mitochondrial (COI and 16S rRNA) and nuclear (five microsatellite loci) markers from 70 colonies sampled across 17 meliponaries in seven southern provinces. Microsatellite data revealed high genetic diversity and low nuclear differentiation (K = 1; Fst = 0.0024–0.1219; all P > 0.05), with extensive gene flow (Nm = 3.60–207.83) among provinces. In contrast, mitochondrial markers indicated moderate-to-high differentiation (Fst = 0.619), consistent with mito-nuclear discordance arising from sex-biased. Managed colonies exhibited elevated heterozygosity and allelic richness, likely reflecting admixture from colony exchange, while unique haplotypes in certain provinces suggest introductions from external sources. Significant inbreeding was detected only in Yala, possibly linked to habitat loss and reduced effective population size. Our findings indicate that current meliponicultural practices maintain high genetic diversity in G. thoracica despite mitochondrial structuring, but increasing colony movement between genetically distinct populations may risk erosion of local adaptations, underscoring the need for genetic screening prior to translocation.
Duangphakdee et al. (2025) Human-mediated dispersal of Geniotrigona thoracica (Apidae: Meliponini) colonies promotes high genetic diversity and reduces population structuring in managed populations. PeerJ 13:e20460 https://doi.org/10.7717/peerj.20460
High abundance of Early Miocene sea cows from Qatar shows repeated evolution of seagrass ecosystem engineers in Eastern Tethys
Coastal ecosystems that include seagrasses are potential carbon sinks that require strategic conservation of top trophic consumers, such as dugongs, to maintain their function. It is unclear, however, how long seagrass ecosystems have persisted in geologic time because their fossil record is poor, although the record of their associated vertebrate consumers offers useful proxies. Here we describe an area of dense Early Miocene dugongid remains from Qatar. We documented over 172 sites in <1 km2 from one stratigraphic level, including material representing a new species of fossil dugongine dugongid. This taxon is unrelated to coeval Early Miocene dugongids from India and the Eastern Tethys and it is distantly related to extant dugongs, which occupy seagrass habitats of the Persian or Arabian Gulf (hereafter ‘Gulf’) today. The monodominant assemblage in this area likely reflects a single fossil dugongid taxon and matches the ecological diversity and geospatial distribution of modern-day live-dead assemblages in the Gulf. This fossil site from Qatar shows that the Gulf has repeatedly evolved sea cow communities with different taxa over the past 20 million years and coincides with an Early Miocene marine biodiversity hotspot in Arabia, prior to its eastward shift to the Indo-Australian Archipelago where dugongs continue to thrive today.
Pyenson et al. (2025) High abundance of Early Miocene sea cows from Qatar shows repeated evolution of seagrass ecosystem engineers in Eastern Tethys. PeerJ 13:e20030 https://doi.org/10.7717/peerj.20030
Differential effects of physical activity on cognitive and motor performance in obese young adults
The rising prevalence of obesity among young adults presents significant health challenges, particularly due to its adverse effects on cognitive function and physical mobility. This cross-sectional study examined the effects of physical activity on cognitive performance and gait speed in obese individuals aged 18 to 25 years. Seventy-six participants were categorized as either physically active or sedentary based on the Global Physical Activity Questionnaire. All enrolled participants completed the study, and no data were missing. Anthropometric data, including body mass, height, waist circumference, and hip circumference, were collected using standardized procedures. Cognitive assessments included the Trail Making Test, Stroop Color and Word Test, Hand Reaction Time Test, and Logical Memory Test. Gait speed was evaluated using the 10-meter walk test. The physically active group showed significantly better results in logical memory, executive function, and all Stroop test conditions (p < 0.05). No group differences were found in reaction time, Stroop interference score, or gait speed (p > 0.05). These findings suggest that higher physical activity levels are linked to better cognitive performance, highlighting the value of promoting physical activity in young adults with obesity. The lack of observed differences in gait speed and reaction time may indicate that these functions are less sensitive to early changes or require longer periods of inactivity to decline in this population.
Sa-nguanmoo et al. (2025) Differential effects of physical activity on cognitive and motor performance in obese young adults. PeerJ 13:e20481 https://doi.org/10.7717/peerj.20481
Effects of core stability exercises on balance among Chinese children and youth with intellectual disabilities
Background Children and youth with intellectual disabilities (IDs) are at risk of falls due to balance problems. Objective This study was conducted to assess the effects of six weeks of core stability exercises on balance in this population. Methods Thirty-five participants with IDs from a special school were selected. Static and dynamic balance were assessed by the one-legged stance test (OLS) and lower quarter Y balance test (YBT-LQ), respectively. Results Core stability exercises significantly improved static balance with eyes opened (EO) on firm (FI) ground (t = −5.269, P < 0.001) and dynamic balance in all three directions (left leg: anterior: t = −3.197, P = 0.005; posteromedial: t = − 4.608, P < 0.001; posterolateral: t = −4.706, P < 0.001; right leg: anterior: t = −3.324, P = 0.004; posteromedial: t = −5.614, P < 0.001; posterolateral: t = −5.905, P < 0.001). Conclusions Six weeks of core stability exercises significantly improved the static balance of children and youth with IDs under EO and FI conditions, as well as all three directions of dynamic balance. Future studies with multiple measurement points are warranted to examine the long-term effectiveness of this training on balance in this population.
Qi et al. (2025) Effects of core stability exercises on balance among Chinese children and youth with intellectual disabilities. PeerJ 13:e20454 https://doi.org/10.7717/peerj.20454
Single-cell RNA-seq reveals breast cancer heterogeneity and identifies TCP1 as a therapeutic target in breast cancer
Breast cancer is composed of diverse cell populations, and this intratumoral heterogeneity profoundly affects clinical behavior. Here, we leveraged single cell RNA sequencing (scRNA-seq) of 68 breast cancer specimens to dissect tumor heterogeneity at high resolution. Unsupervised clustering identified all major cell types of the tumor microenvironment (TME)—including malignant epithelial cells, fibroblasts, T cells, macrophages, endothelial cells, and others—with striking variability in their proportions across molecular subtypes. For example, a BRCA1-mutant triple-negative breast cancer (TNBC) sample showed dense immune infiltration, whereas an estrogen receptor (ER)-positive tumor was mostly epithelial, consistent with known subtype differences in immunogenicity. We applied inference of copy number variations (inferCNV) to distinguish malignant epithelial cells, identifying ~90,000 tumor cells with significant copy-number aberrations enriched for cancer hallmark pathways. Re-clustering of these malignant cells revealed five discrete subpopulations. Notably, a KRT17-positive subcluster displayed the highest stemness score and a distinctive ETS-family transcription factor (ERG) regulon, suggesting a stem-like phenotype. Using The Cancer Genome Atlas (TCGA) cohort, we found that genes upregulated in this KRT17+ subpopulation, particularly NFKBIA, PDLIM4, and TCP1 stratified patient survival. An 8-gene risk signature derived from the KRT17 program segregated patients into high- and low-risk groups with markedly different outcomes. High-risk tumors were characterized by an immunosuppressive TME enriched in M2-like macrophages, whereas low-risk tumors more often harbored lymphocyte-predominant infiltrates. Focusing on TCP1, a chaperonin subunit upregulated in high-risk tumors, we demonstrate that TCP1 knockdown in breast cancer cell lines substantially impairs cell migration (~50% reduction in wound closure) and invasion (P < 0.01). These findings reveal functionally distinct malignant cell states within breast cancer and identify TCP1 as a promising therapeutic target to disrupt aggressive, stem-like tumor cell programs, ultimately guiding more personalized treatment strategies.
Wu et al. (2025) Single-cell RNA-seq reveals breast cancer heterogeneity and identifies TCP1 as a therapeutic target in breast cancer. PeerJ 13:e20451 https://doi.org/10.7717/peerj.20451
Knowledge, attitude, and practice toward perioperative neurocognitive disorders among healthcare workers in Shandong, China: a cross-sectional study
Background Perioperative neurocognitive disorders (PND) refer to neurocognitive abnormalities detected during the perioperative period, currently including postoperative delirium, delayed neurocognitive recovery, postoperative neurocognitive disorder, and both mild and major cognitive impairments. It is a prevalent complication among surgical patients, particularly in older populations. Moreover, PND can have a profound effect on the quality of life for these patients. PND has been previously reported to occur with a prevalence of 10–54% during the first few weeks following surgery, and when persistent at the time of discharge or in the longer term, PND may increase mortality. Therefore, it is of considerable importance for healthcare professionals to accurately identify the occurrence of PND and implement appropriate management measures. This research aims to investigate the knowledge, attitude, and practice (KAP) of healthcare workers concerning perioperative neurocognitive disorders (PND) in Shandong Province, China. Methods This cross-sectional study recruited healthcare workers from twelve hospitals in Shandong Province, China, utilizing self-administered questionnaires distributed between February and May 2025. There are 12 items in the knowledge dimension, and the total score range for this dimension is 0 to 12 points. There are a total of seven items in the attitude dimension, and the total score range for this dimension is 7 to 35 points. There are a total of nine items in the practice dimension, and the total score range for this dimension is from 9 to 45 points. Results The analysis included a total of 309 valid questionnaires, which represents an impressive 87.78% response rate. Among them, a total of 193 doctors (62.5%) and 116 nurses (37.5%) participated in the survey, respectively. The PND knowledge score was 9.14 (SD = 2.85, range = 0–12). The PND attitudes score was 30.89 (SD = 3.81, range = 7–35). The PND practices score was 36.16 (SD = 7.77, range = 9–45). Furthermore, Path analysis indicated that participants’ knowledge of PND among healthcare workers had a direct and positive effect on their attitudes (β = 0.545, P < 0.001) and practices towards PND (β = 0.230, P = 0.002). And attitudes towards PND also had a direct and positive effect on practices (β = 0.238, P = 0.001). In addition, the knowledge exerted an indirect effect on practice through attitudes (β = 0.581, P = 0.003). Conclusions Healthcare practitioners have sufficient knowledge, and they demonstrate positive attitudes and adopt proactive approaches regarding PND. The understanding and perspectives of healthcare workers are closely linked to their actions towards PND. Educational training is pivotal in shaping their knowledge, attitude, and practice.
Zhang et al. (2025) Knowledge, attitude, and practice toward perioperative neurocognitive disorders among healthcare workers in Shandong, China: a cross-sectional study. PeerJ 13:e20450 https://doi.org/10.7717/peerj.20450