Estuarine bivalve metabolic response mediated by environmental drivers
Humans are rapidly modifying environmental conditions in estuaries, which are among Earth’s most productive and dynamic ecosystems. Bivalve molluscs are key estuarine organisms, contributing to range of ecosystem functions and services, though human-induced environmental changes are affecting their behaviour, physiology, and fitness with implications at individual, population, community, and ecosystem levels. Understanding how estuarine bivalves respond and adapt to different environmental drivers will enable us to better predict change at multiple levels of biological organisation. In this study, we investigated the metabolites of a common and ecological important suspension-feeding bivalve in New Zealand, the cockle, Austrovenus stutchburyi. At seven of eight pre-established monitoring sites in a North Island estuary, we evaluated differences in cockle metabolite abundance, diversity, and composition, as well as relationships between cockle metabolites and environmental conditions. Our findings revealed differences in the abundance and diversity of cockle metabolites across sites, particularly in the metabolites alanine, aspartic acid, glutamic acid, glycine, proline, and succinic acid. The differences in metabolites across sites were mediated by the site-specific environmental conditions, in particular, the sediment’s mud content and organic matter. Differences in metabolites were most pronounced when comparing sites close to freshwater inputs versus sites located closer to the estuary mouth. In general, Austrovenus metabolite abundance was higher at sites with less signs of stress (i.e., close to the estuary mouth) and lower in sites with with higher mud content (i.e., close to freshwater inputs), while the metabolite diversity followed an inverse pattern. The metabolic responses of cockles appeared to be linked to processes such as feeding, oxygen regulation, and energy allocation. The observed metabolic trends highlight the complex interactions between cockles and their environment and provide insights into the metabolic responses of bivalves to the rapidly changing environment.
Lam-Gordillo et al. (2025) Estuarine bivalve metabolic response mediated by environmental drivers. PeerJ 13:e20357 https://doi.org/10.7717/peerj.20357
Effects of combined exercise training for adults with resistant major depression: a pilot study from the TRACE-RMD project
Background This pilot study analyzed the changes in body composition, cardiorespiratory fitness (CRF), biochemical profile, clinical symptoms, and quality of life (QoL) of adults with resistant major depression (RMD) following 12 weeks of combined exercise training. Methods Eighteen adults diagnosed with RMD (42.5 ± 9.9 years, 66.7% women) participated in a supervised exercise group (2 days/week). The combined exercise training consisted of low-to-moderate intensity aerobic interval exercise on a bicycle and strength-resistance exercises. All variables were assessed pre- and post-intervention, including clinical symptoms with the Montgomery-Åsberg Depression Rating Scale (MADRS), the Clinical Global Impressions Scale (CGI-S), the Sheehan Disability Scale (SDS), and health-related QoL with the Short Form-36. A symptom-limited cardiopulmonary exercise peak test was performed to evaluate CRF. Results The baseline results classified the participants as metabolically unhealthy with overweight/obesity, moderate depression, and low CRF and QoL. Following the intervention, there were no significant changes (P > 0.05) in body composition, the main CRF physiological variables, and the biochemical profile. However, regarding clinical symptoms, the MADRS (mean difference −8.31, 95% confidence interval (CI) [−15.1 to −1.5], P = 0.021), CGI-S (mean difference -1.17, 95% CI [−1.92 to −0.41], P = 0.006), and SDS (mean difference -5.46, 95% CI [−10.8 to −0.12], P = 0.046) scores decreased, and the domains of health-related QoL –general health (mean difference 13.8, 95% CI [2.9–24.8], P = 0.017), vitality (mean difference 10.4, 95% CI [0.26–20.5], P = 0.045), social functioning (mean difference 25.9, 95% CI [8.1–43.7], P = 0.008), and the mental component summary (mean difference 6.9, 95% CI [1.1–12.8], P = 0.024) increased. Conclusions A supervised combined exercise program in people with RMD may induce positive and beneficial changes in functionality and clinical and QoL variables, and maintain body composition, CRF, and the biochemical profile. These preliminary results highlight the critical role of supervised exercise, regardless of intensity, in improving clinical symptoms in people with RMD. This study was registered with the International Standard Randomized Controlled Trial Code NCT 05136027.
Tous-Espelosin et al. (2025) Effects of combined exercise training for adults with resistant major depression: a pilot study from the TRACE-RMD project. PeerJ 13:e20356 https://doi.org/10.7717/peerj.20356
Tryptophan-kynurenine pathway: a possible new mechanism for the prevention and treatment of reproductive system-related diseases
Tryptophan (Trp) is one of the essential amino acids, and its metabolic pathway is essential for the maintenance of normal human physiological activities. Among them, various metabolites and rate-limiting enzymes of the tryptophan-kynurenine metabolic pathway play important roles in inflammatory responses, immune regulation, energy metabolism, as well as neuroprotective and toxic effects. Abnormalities in tryptophan-kynurenine pathway metabolism thus inevitably lead to numerous pathological changes, such as reproductive disorders. It is noteworthy that the prevention and treatment of reproductive diseases are not currently focused on this pathway. In view of the increasing number of studies that have found abnormalities in the levels of key enzymes and metabolites of tryptophan-kynurenine in reproductive diseases, this article will focus on summarizing the molecular mechanisms and relevance of the pathway in reproductive diseases, as well as proposing new ideas for the prevention and treatment of reproductive diseases, including the use of inhibitors of the pathway and the regulation of tryptophan metabolism in the intestinal flora.
Ou et al. (2025) Tryptophan-kynurenine pathway: a possible new mechanism for the prevention and treatment of reproductive system-related diseases. PeerJ 13:e20342 https://doi.org/10.7717/peerj.20342
Latitudinal variations in morphometric traits and bioenergetic status of adult red squat lobsters Grimothea monodon (H. Milne Edwards, 1837) in the Southeast Pacific Ocean
Adults of the red squat lobster (Grimothea monodon) present two morphotypes (small-pelagic (SP) and large-benthic (LB)) in their wide geographic distribution range in the Southeastern Pacific Ocean (SEPO). In this marine ecosystem, they are exposed to conspicuous latitudinal variations in oceanographic and physicochemical parameters that affect their nutritional and fitness status. The objective of this study was to determine variations in the bioenergetic condition at the level of morphometric, sexual and biochemical traits of G. monodon, considering a wide spatial scale of their populations’ distribution along a latitudinal gradient (from 9°S to 36°S) in the SEPO. According to the environmental parameters, temperature and dissolved oxygen presented abrupt changes between 15°S–17°S, while chlorophyll and salinity showed a constant reduction along the latitudinal gradient. When environmental parameters were related to the size of the two morphotypes (SP, LB) of G. monodon, some trends of change were observed, while the relative condition factor showed significant differences along the latitudinal gradient. The biochemical condition of SP individuals showed an increasing trend in glucose from Chimbote to Chala, proteins showed abrupt changes in three zones (between Huacho-Lima, Lomitas, and Chala), and lipids showed a notable change between Lima-Cañete. In turn, in LB individual’s increases were recorded in all their biochemical constituents towards high latitudes. A slight variability in fatty acids was observed between SP individuals from the north (Chimbote, Huarmey, Huacho) and SP individuals from the south (Marcona, Chala, Planchada, Mollendo). In addition, significant latitudinal differences were observed in the fatty acids of the two morphotypes (SP, LP). The nutritional condition index (docosahexaenoic acid (DHA)/eicosapentaenoic acid (EPA) ratio) showed significant differences for the locality factor. Our findings revealed conspicuous differences in the bioenergetic condition of G. monodon adults at the latitudinal level. These variations were strongly linked to the predominant environmental conditions in the SEPO. It is consequently recommended that future sustainable exploitation models consider a physiological and ecosystemic approach that includes key aspects of the nutritional condition and its habitat, thus establishing, in real time, the health status of the natural populations of this resource.
Quispe-Machaca et al. (2025) Latitudinal variations in morphometric traits and bioenergetic status of adult red squat lobsters Grimothea monodon (H. Milne Edwards, 1837) in the Southeast Pacific Ocean. PeerJ 13:e20339 https://doi.org/10.7717/peerj.20339
The effect of endoscopic polidocanol carbon dioxide foam for internal hemorrhoids: a retrospective study
Aim This article aims to explore the effectiveness of polidocanol carbon dioxide foam as a therapy for internal hemorrhoids. Methods A retrospective analysis was conducted on 158 patients who received endoscopic polidocanol foam sclerotherapy for internal hemorrhoids between October 2022 and September 2023. Among the patients, 78 underwent endoscopic polidocanol sclerotherapy with polidocanol air foam (control group), while 80 received polidocanol carbon dioxide foam (study group). The primary outcomes of this study were clinical effect and the incidence of complications 1 month after surgery. Patient self-reports of anal bleeding and anal prolapse served as the foundation for establishing three categories of clinical efficacy criteria. The clinical effect was determined based on the efficacy index, which was employed to assess treatment effectiveness. The occurrence of several postoperative complications was documented, specifically including anal pain, anal swelling, urinary retention, perianal infection, ectopic embolization, and anal edema. Secondary outcomes encompassed the surgical cost, duration of hospital stay, and the administered dosage of polidocanol. Result The treatment success at the end of the sclerotherapy session in the study and control group were 85.0% and 83.3%, respectively (P = 0.829). One month following endoscopic sclerotherapy, the study group exhibited an effective rate of 98.8%, while the control group showed a rate of 98.0%. Compared with the clinical effects one month after surgery of the two groups of patients, postoperative complications, surgical cost, hospitalization time and the dosage of polidocanol, we found 11 patients with anal pain and 12 patients with anal swelling in the control group. Within the study group, three patients experienced anal pain, while four patients presented with anal swelling. The study group exhibited significantly fewer patients with anal pain and anal swelling compared to the control group (P < 0.05), and importantly, no severe complications were observed. Both groups exhibited comparable clinical effects, surgical costs, hospitalization durations, and dosages of polidocanol, with no statistically significant differences observed (all P > 0.05). Conclusion The clinical effectiveness of endoscopic polidocanol carbon dioxide foam is on par with that of polidocanol air foam. In sclerotherapy for internal hemorrhoids, the use of endoscopic polidocanol carbon dioxide foam can significantly decrease complications such as anal swelling and pain.
Xiang et al. (2025) The effect of endoscopic polidocanol carbon dioxide foam for internal hemorrhoids: a retrospective study. PeerJ 13:e20252 https://doi.org/10.7717/peerj.20252
Enhancing heatstroke prediction accuracy with interpretable machine learning: a multi-center data-driven approach
Background Heatstroke poses a significant threat to public health, frequently culminating in fatal outcomes. This study aimed to develop and validate an interpretable machine learning (ML) model to forecast heatstroke using clinical and laboratory data. Methods Data were collated from 24 hospitals spanning the years 2021 to 2023, with data from 2021 and 2022 comprising the training datasets and data from 2023 designated for validation. Model efficacy was quantified via the area under the receiver operating characteristic curve (AUROC) and calibration plots. Furthermore, the SHapley Additive exPlanations (SHAP) methodology was employed to elucidate the interpretability of the final model. Results The study encompassed 691 patients, with 176 in the training datasets and 80 in the testing datasets diagnosed with heatstroke. Among the nine ML models assessed, the gradient boosting machine (GBM) model demonstrated superior performance, achieving an AUROC of 0.971 in the training datasets and 0.836 in the testing datasets, and exhibiting substantial net benefits in decision curve analysis. Creatine kinase (CK)-MB was identified as the most impactful variable influencing the GBM model’s efficacy. Conclusion The ML model we developed demonstrates robust predictive capabilities for heatstroke, potentially aiding clinicians in the identification and management of patients at elevated risk.
Zeng et al. (2025) Enhancing heatstroke prediction accuracy with interpretable machine learning: a multi-center data-driven approach. PeerJ 13:e20377 https://doi.org/10.7717/peerj.20377
Feeding ecology and trophic interactions of the narrow-barred Spanish Mackerel (Scomberomorus commerson) in the Central Taiwan Strait
Understanding the foraging ecology of marine predators is essential for ecosystem-based fisheries management. This study examined the diet of the narrow-barred Spanish mackerel (Scomberomorus commerson) in the Central Taiwan Strait using stomach content and stable isotope analyses integrated with an isotopic mixing model. A total of 1,733 specimens were collected between January 2017 and March 2022. Stomach content analysis revealed that 79.8% had empty stomachs, while the remainder mainly contained semi-digested fish remains. Among identifiable prey, composition varied by size and season. Sardinella lemuru, Decapterus spp., and Trichiurus spp. dominated the diet of smaller individuals, while larger fish primarily consumed Decapterus spp. and Mene maculata. Sardinella lemuru and Trichiurus spp. were more abundant in summer and autumn–winter, respectively. In the meanwhile, Decapterus spp. remained important year-round. Isotopic analysis further revealed that Sardinella lemuru, Etrumeus micropus, Decapterus macarellus and Penaeidae (Metapenaeopsis barbata) were dominant prey in smaller size classes, while Encrasicholina punctifer, D. macarellus, Evynnis cardinalis, Trichiurus spp. and Uroteuthis spp. were prevalent in intermediate and larger individuals. The estimated trophic position (3.8–4.3; mean = 4.0) confirms that S. commerson functions as a top predator with opportunistic feeding behavior. These findings improve understanding of regional trophic dynamics and support sustainable fisheries management in the Central Taiwan Strait.
Cheng et al. (2025) Feeding ecology and trophic interactions of the narrow-barred Spanish Mackerel (Scomberomorus commerson) in the Central Taiwan Strait. PeerJ 13:e20350 https://doi.org/10.7717/peerj.20350
Does reef crest zone selection influence Acropora palmata (Lamarck, 1816) fragment survival and growth?
In this study, we evaluated the effects of the crest zones on the survival and growth of Acropora palmata fragments in four sites differentially impacted by multiple natural and anthropogenic stressors. The crests are in the northwest (Playa Baracoa and Rincón de Guanabo) and the south-central region (El Peruano and Mariflores in Jardines de la Reina National Park) of Cuba. We established a field-based experiment with 50 fragments placed in each crest, 25 fragments in the back crest zone and 25 in the fore crest zone, parallel to the shoreline. The water flow intensity was estimated in both crest zones, using the dissolution of plaster discs as an indicator. The survival and growth of fragments were significantly influenced by site-specific and microhabitat conditions. The survival of the A. palmata fragments was high (survival probability: >0.6) in all four crests. Fragments placed in the fore crest zone (p = 0.02) exhibited higher survival than those in the back crest zone. The growth rates were slower (−1.5 to 7.3 cm year−1) than those previously recorded for wild A. palmata colonies and were negatively affected (estimate = −6.1; p = 0.004) in the fore crest zone. The dissolution of the plaster discs did not indicate a marked gradient of water flow between the crest zones, during April and June, but it was significantly higher (p = 0.03) in the fore crest zone in December at El Peruano and Mariflores crests, indicating temporal variations during the monitoring periods. The dissolution of plaster discs, as a proxy for water flow, did not have a significant effect on fragment survival between zones. However, when the dissolution was below approximately 68%, growth declined slightly; above this threshold, growth increased, possibly by higher inferred water flow. At higher levels of water flow (dissolution of the plaster discs), the positive effect of temperature on growth was attenuated (p = 0.007), suggesting that under strong water flow heat may be dissipated. These results highlight the importance of conducting small-scale pilot studies to identify the microhabitat conditions and to select effective restoration sites. We recommend that future restoration efforts should integrate local ecological knowledge with in situ environmental measurements to enhance coral fragment survival and growth, and to improve the long-term success of restoration interventions under variable and changing reef conditions.
Ramos Romero et al. (2025) Does reef crest zone selection influence Acropora palmata (Lamarck, 1816) fragment survival and growth?. PeerJ 13:e20303 https://doi.org/10.7717/peerj.20303
Status and trends of giant clam populations demonstrate the effectiveness of village-based protection in American Sāmoa
Giant clams (subfamily Tridacninae) serve diverse ecological functions in coral reef ecosystems but have experienced severe populatiaon declines across much of their native ranges. Continued overharvesting, habitat degradation, and climate change impacts reinforce the need for updated population assessments and have prompted consideration for endangered species status. Here, we report a territory-wide evaluation of giant clam populations in American Sāmoa, integrating historical data (1994/95, 2002, and 2018) with new surveys conducted from 2022 to 2024 to assess the population status of these ecologically important bivalves. Using belt transects (50 m × 2 m at 10 m depth), we examined clam densities, size-class distributions, species composition, and population trends across six islands—Tutuila, Aunuʻu, Ofu, Olosega, Taʻū, and Muliāva. This study added 264 transects to the historical dataset and showed population densities of giant clams varied among islands but have remained relatively consistent over time. Using univariate and factorial ANOVAs of giant clam abundance and size data, we assessed spatial and temporal variation across American Sāmoa, and our analyses tested for effects of island, year, protection status, and their interactions. The lowest recent clam densities (83.5 individuals per hectare in 2022) were observed on the main island of Tutuila, where 98% of residents live. Mean clam density on Tutuila has increased from 14.1/ha in 1994/95, but the island has considerable variation amongst locations. Remote islands, such as Taʻū and Muliāva, showed higher densities, up to 812 and 1,166/ha, respectively. Most (96.7%) of giant clams found on transects were identified as Tridacna maxima, with infrequent occurrences of the cryptic species T. squamosa and T. noae, primarily within specific, village-managed protected areas. On Tutuila, surveys sites included a variety of jurisdictions and levels of management, with village protected areas and remote sites supporting both higher clam densities and larger individuals. Overall, inaccessible remote sites and those under traditional village enforcement significantly outperformed all other management strategies, including federally designated no-take zones. These findings suggest that empowering traditional Indigenous community stewardship may offer a viable alternative to blanket federal restrictions, and support the importance of localized, community-based management practices in American Sāmoa. We emphasize the need for more frequent monitoring across varying depths, anthropogenic influences, and management regimes to better understand the population dynamics of these valuable coral reef species.
Marra-Biggs et al. (2025) Status and trends of giant clam populations demonstrate the effectiveness of village-based protection in American Sāmoa. PeerJ 13:e20290 https://doi.org/10.7717/peerj.20290
Fast and robust estimate of bacterial genus novelty using the percentage of conserved proteins with unique matches (POCPu)
Accurate taxonomic assignment of bacterial genomes is essential for identifying novel taxa and for stable classification to enable robust comparison between studies. Bacterial genus delineation relies on multiple lines of evidence, including phylogenetic trees and metrics like the percentage of conserved proteins (POCP). POCP is widely used, but requires benchmarking in terms of both, computation and accuracy. We used 2,358,466 pairwise comparisons of proteomes derived from 4,767 genomes across 35 families to systematically assess POCP calculation and percentage of conserved proteins with unique matches (POCPu) which considers unique matches only. Both methods are 20x faster than the reference BLASTP when using the very-sensitive setting of DIAMOND. However, POCPu differentiates better within-genus from between-genera values, which improves bacterial genus assignment. This work facilitates comparative analysis of an increasingly larger number of genomes, providing a reliable metric to support genus delineation. The findings suggest that specific POCPu thresholds deviating from the reference 50% value are needed for certain families.
Pauvert et al. (2025) Fast and robust estimate of bacterial genus novelty using the percentage of conserved proteins with unique matches (POCPu). PeerJ 13:e20259 https://doi.org/10.7717/peerj.20259