title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=97 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Analysis of factors influencing hookwire dislodgement in CT-guided hookwire localization: a retrospective study using variable importance analysis with a random forest model link: https://peerj.com/articles/19231 last-modified: 2025-04-16 description: BackgroundVideo-assisted thoracoscopic surgery (VATS) is a minimally invasive and safe procedure. However, lung deflation during the operation causes anatomic landmark distortion, complicating small nodules detection. Computed tomography (CT)-guided hookwire localization promotes the success rates of VATS, but faces issues with hookwire dislodgement, potentially losing intraoperative tumor reference. This study was conducted to identify the relative importance ranking of potential factors influencing dislodgement in CT-guided hookwire localization.MethodsThis retrospective study reviewed 123 cases of CT-guided hookwire localization followed by VATS resection. Variables analyzed included sex, age, nodule size, emphysema, chest wall/muscle/total depth, distance from the nodule (DNP) or wire tip to the pleura (DWP), procedure time, nodule subtypes, multiple localization, post-procedural hemorrhage, pneumothorax, nodule penetration, and time intervals between completion of procedure to initiation of surgery (PS interval). Variables were compared using chi-square tests or Mann-Whitney tests. A random forest model, enhanced with the Synthetic Minority Over-sampling Technique (SMOTE) for oversampling, was employed to determine the relative importance of each variable. The relative importance of variables was presented using the mean decrease Gini and mean decrease accuracy metrics. For sensitivity analysis, relative variable importance was analyzed using extreme gradient boosting (XGBoost) model, and the relative importance of variables was presented using the gain metric.ResultsAmong the 123 cases, dislodgement occurred in 15. In univariable analysis, only the PS interval was statistically significant (134.1 ± 73.1 vs. 104.1 ± 46.1 minutes in dislodgement or non-dislodgement, p = 0.031). The random forest and XGBoost model identified the top five important variables as the PS interval, DWP, DNP, total depth, and age. The top five factors demonstrated a distinct difference when compared to the other factors.ConclusionsThe study identified the PS interval as the most critical factor in hookwire dislodgement, along with DNP, DWP, total depth, and age. These results identified the presence of modifiable factors within the hospital and can assist practitioners and surgeons in recognizing the dislodgement risk of procedures based on various patient factors. creator: Kiook Baek creator: Jin Young Kim creator: Jung Hee Hong uri: https://doi.org/10.7717/peerj.19231 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Baek et al. title: The tadpole of Chiasmocleis altomontana (Anura: Microhylidae) link: https://peerj.com/articles/19220 last-modified: 2025-04-16 description: BackgroundDescribing the morphology of anuran larvae contributes towards filling gaps in taxonomy and natural history. This is especially relevant for explosive breeders, in which adults remain at the reproduction site for only a short period, while tadpoles may be more conspicuous. Here, we describe the larval external morphology and internal oral anatomy of the microhylid frog Chiasmocleis altomontana from near its type locality in southeastern Brazil.MethodsWe took 13 linear morphometric measurements of 11 tadpoles between stages 35 and 39 from four ponds. To compare the larval external morphology of the genus, we also built a morphospace based on the log-shape ratio of linear measurements provided by the original descriptions. To impute missing data, we used a trait imputation method that considered the phylogenetic relationships and a Brownian Motion model of multivariate trait evolution. Finally, we provide novel quantitative and qualitative data on the tadpole of Chiasmocleis anatipes based on museum specimens.ResultsThe tadpole of C. altomontana is the largest among the Atlantic Forest species and the second largest of the genus, after C. anatipes. Like all species of the genus, the tadpole of C. altomontana is exotrophic, suspension feeder, Orton type II, and occurs in lentic temporary environments. Overall, C. altomontana shows subtle differences in dorsal fin height, dorsal fin insertion, tail tip, and snout in lateral view from its congeners. The spiracle of C. anatipes is ventral, single, covering the vent tube, as in all other microhylids. The species has a larger tail and interorbital distance than its congeners. All species of the Atlantic Forest clade are clustered together in the morphospace, suggesting little disparity, while those of the Amazonian clade are more spread, suggesting higher morphological disparity. Chiasmocleis altomontana was close to its sister species, Chiasmocleis mantiqueira, while C. anatipes differs greatly in terms of shape from the remaining species of the genus. Our results can improve our understanding of the morphological diversity of microhylid tadpoles and reduce the diversity shortfall in anuran larval forms. creator: Leandro B. C. Menezes creator: Marcos R. Severgnini creator: Tiago L. Pezzuti creator: Michel V. Garey creator: Diogo B. Provete uri: https://doi.org/10.7717/peerj.19220 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Menezes et al. title: Optimization of cultural conditions for pectinase production by Diaporthe isolate Z1-1N and its pathogenicity on kiwifruit link: https://peerj.com/articles/19207 last-modified: 2025-04-16 description: Diaporthe Z1-1N, the primary causal agent of soft rot disease in kiwifruit, exhibited higher pectinase activity compared to cellulase activity in both in vitro and in vivo incubation models. To gain deeper insights into the role of pectinases in the pathogenicity of this fungus, we evaluated the effects of incubation temperature (ranging from 18 to 38 °C), duration (1 to 7 days), and medium pH (4.0 to 9.0) on the activities of two crucial pectinases: polygalacturonase (PG) and polymethylgalacturonase (PMG). Our single-factor experiments revealed that the optimal conditions for maximizing PMG yield were a pH of 7.5 and a temperature of 28 °C, with peak activity occurring after three days of incubation. Notably, PG activity peaked on the fourth day under the same pH and temperature conditions. Under the optimal conditions identified through an orthogonal experimental design, PMG exhibited higher activity than PG. Further analysis showed that temperature was the most influential factor on PMG activity, followed by incubation duration and pH. The lesion size caused by the purified pectinase extracts was 50% the lesion size that caused by the fungal mycelium of Diaporthe Z1-1N. These findings underscore the significance of PG and PMG as key virulence factors in the pathogenicity of Diaporthe Z1-1N, providing a solid scientific basis for future research into the functions of these enzymes. creator: Shu-Dong Zhang creator: Ling-Ling Chen creator: Chao-Yue Li creator: Xiao-Qing Long creator: Xue Yang creator: Xiao-Duo He creator: Li-Wen Du creator: Heng-Feng Yang creator: Li-Zhen Ling uri: https://doi.org/10.7717/peerj.19207 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhang et al. title: Azov-type spits: long-term monitoring of morphodynamics and vegetation in response to changing environment link: https://peerj.com/articles/18369 last-modified: 2025-04-16 description: BackgroundAzov-type spits (ATS) are unique landforms located along the Northern coast of the Sea of Azov (NA) that have no global analogs. They play a vital role in delivering essential ecosystem services and significantly contribute to the economy of southern Ukraine. ATS are highly sensitive and dynamically responsive to environmental changes, including global and local climate changes, rising sea levels, geological shifts in the Ukrainian crystalline shield, internal shifts in the Sea of Azov and various anthropogenic influences. These factors significantly shape the ATS, influencing their capacity to accumulate biogenic material and sediments, thereby impacting vegetation cover, resilience and functioning within their ecological context.MethodsOur study on ATS morphodynamics and vegetation changes is based on a 95-year dataset that incorporates retrospective vegetation maps (1927–1929, 1934, 1996–1999), grassland releves (1995–1999) and satellite imagery (1975–2022) using specific standardized indices (NDVI, NDWI, NDMI, Thermal). We employed Earth Remote Sensing (ERS) tools due to the impracticality of field research amid the ongoing military occupation of ATS territories. Climate change vulnerability was assessed by examining surface air temperature and precipitation changes for the periods 1900–2021 and 1991–2021.ResultsMeteorological data for NA shows a consistent climate change trend, including rising annual surface temperatures (1.14 ± 0.3 °C/100 years) and increased annual precipitation (98 ± 35 mm/100 years) over the last 120 years. Recent decades have witnessed intensified aridization, with up to a 15% drop in precipitation and a 0.8 °C per decade temperature increase, accompanied by increased evaporation. Our study reveals the ongoing transformation of ATS and their vegetation, primarily driven by inundation, aggravated by climate change and rising sea levels. ERS tools demonstrated their effectiveness in monitoring environmental changes under challenging circumstances, identifying general trends in the state of plant communities and validating our earlier forecasts for changes in vegetation cover. The increase in the area of halophytic meadow and marsh plant communities occurred alongside a certain decrease in their productivity, while the reduction in sandy-steppe plant community areas was accompanied by an increase in their productivity. The study provides a complex evaluation of the current anthropogenic impacts on the spits and their vegetation. creator: Oksana Tyshchenko creator: Volodymyr Tyshchenko creator: Svitlana Boychenko creator: Andrii Tarieiev creator: Vasyl Tkachenko uri: https://doi.org/10.7717/peerj.18369 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Tyshchenko et al. title: Potential relationship of the gut microbiome with testosterone level in men: a systematic review link: https://peerj.com/articles/19289 last-modified: 2025-04-15 description: The gut microbiome influences the metabolism and health of several organs beyond the gut and has recently gained considerable attention. The gut plays a central role in food digestion, absorption, nutrition, and general health. Hence, the gut microbiome has become a research subject for almost all health conditions. Imbalance or dysbiosis in the gut microbiome can cause different health issues in men, including reproductive and sexual health issues associated with testosterone levels. Several studies have investigated the relationship between the gut microbiome and testosterone levels. In this systematic review, we aimed to examine the relationship between the gut microbiome and testosterone levels in men. Literature searches were conducted by scanning PubMed, ProQuest, EBSCO, Taylor & Francis Online, Wiley Online, Springer Link, Web of Science, Google Scholar, and Science Direct databases for relevant keywords following the preferred reporting items for the systematic review guidelines. This review included cross-sectional, case-control, retrospective, and prospective cohort studies. Quality assessment was conducted using the Newcastle-Ottawa Scale. We found a significant positive correlation between the gut microbiome and testosterone levels in men. Several microbes play substantial roles in testosterone production. Mechanisms have been proposed as factors that contribute to testosterone levels, namely the hypothalamus-pituitary-gonad axis modulation, androgen metabolism, and intestinal homeostasis, by balancing the bone morphogenic protein (BMP) and the Wnt diverse microbiome. Ruminococcus showed a stronger correlation with testosterone levels than other microorganisms. The gut microbiome has complex correlations with testosterone metabolism. However, the microbiome with the most significant influence on testosterone levels cannot be easily identified and requires further research. creator: Cennikon Pakpahan creator: Geraldo Laurus creator: Markus Christian Hartanto creator: Rajender Singh creator: Ankur Saharan creator: Darmadi Darmadi creator: Andri Rezano creator: Gito Wasian uri: https://doi.org/10.7717/peerj.19289 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Pakpahan et al. title: Identification of single nucleotide polymorphisms (SNPs) potentially associated with residual feed intake in Qinchuan beef cattle by hypothalamus and duodenum RNA-Seq data link: https://peerj.com/articles/19270 last-modified: 2025-04-15 description: The regulation of residual feed intake (RFI) in beef cattle involves brain-gut mechanisms due to the interaction between neural signals in the brain and hunger or satiety in the gut. RNA-Seq data contain an extensive resource of untapped SNPs. Therefore, hypothalamic and duodenal tissues from ten extreme RFI individuals were collected, and transcriptome sequenced in this study. All the alignment data were combined according to RFI, and the SNPs in the same group were identified. A total of 270,410 SNPs were found in the high RFI group, and 255,120 SNPs were found in the low RFI group. Most SNPs were detected in the intronic region, followed by the intergenic region, and the exon region accounts for 1.11% and 1.38% in the high and low RFI groups, respectively. Prediction of high-impact SNPs and annotation of the genes in which they are located yielded 83 and 97 genes in the high-RFI and low-RFI groups, respectively. GO enrichment analysis of these genes revealed multiple NADH/NADPH-related pathways, with ND4, ND5, and ND6 significantly enriched as core subunits of NADH dehydrogenase (complex I), and is closely related to mitochondrial function. KEGG enrichment analysis of ND4, ND5, and ND6 genes was enriched in the thermogenic pathway. Multiple genes, such as ATP1A2, SLC9A4, and PLA2G5, were reported to be associated with RFI energy metabolism in the concurrent enrichment analysis. Protein-protein interaction analysis identified multiple potential candidate genes related to energy metabolism that were hypothesized to be potentially associated with the RFI phenotype. The results of this study will help to increase our understanding of identifying SNPs with significant genetic effects and their potential biological functions. creator: Zonghua Su creator: Chenglong Li creator: Chaoyun Yang creator: YanLing Ding creator: Xiaonan Zhou creator: Junjie Xu creator: Chang Qu creator: Yuangang Shi creator: Cong-Jun Li creator: Xiaolong Kang uri: https://doi.org/10.7717/peerj.19270 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Su et al. title: Comprehensive analysis of groundwater hydrochemistry and nitrate health risks in the Baiquan basin, Northern China link: https://peerj.com/articles/19233 last-modified: 2025-04-15 description: Groundwater is a crucial water source and strategic resource, essential for sustaining both urban and rural livelihoods, supporting economic and social development, and maintaining ecological balance. This study investigates the hydrochemical properties and controlling factors of groundwater in the Baiquan basin (BQB) by analyzing water quality data collected during both dry and wet periods. Additionally, the suitability of groundwater for drinking and agricultural irrigation was evaluated. The findings reveal that groundwater in BQB is generally weakly alkaline and primarily consists of hard-fresh water. Although there are seasonal variations in the main ion concentrations, HCO3− and Ca2+ are the predominant anions and cations, respectively. Consequently, the hydrochemical type is mainly HCO3-Ca⋅Mg type, with a secondary classification of SO4⋅Cl-Ca ⋅ Mg. The hydrochemical composition is primarily influenced by the dissolution of carbonate and silicate minerals, as well as cation exchange processes. Additionally, it is affected by anthropogenic inputs, particularly from the use of agricultural fertilizers. The water quality assessment results indicated that all water samples are classified as either good or moderate, with a significant majority falling into the good category. Additionally, the northern section of the BQB exhibited lower entropy weight water quality index (EWQI) values during the dry season in comparison to the wet season. For irrigated agriculture, groundwater in the BQB serves as a high-quality water source for irrigation throughout both the dry and rainy seasons. Furthermore, non-carcinogenic risks are notably concentrated in the north-western and south-eastern regions of the study area. Health risks associated with nitrates in groundwater are elevated during the rainy season. Notably, non-carcinogenic risks for infants were significantly high across both seasons and substantially exceeded those for children and adults. These results provide valuable scientific insights for the management and development of groundwater resources in the BQB. creator: Bo Li creator: Di Wu creator: Dalu Yu creator: Changsuo Li creator: Jinxiao Wang creator: Liting Xing creator: Shuai Gao creator: Zhe Zhang creator: Mingguo Wang creator: Yuwei Wang uri: https://doi.org/10.7717/peerj.19233 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Li et al. title: Endozoicomonas dominance and Vibrionaceae stability underpin resilience in urban coral Madracis auretenra link: https://peerj.com/articles/19226 last-modified: 2025-04-15 description: Coral resilience varies across species, with some exhibiting remarkable stability and adaptability, often mediated by their associated microbiomes. Given the species-specific nature of coral-microbiome interactions, investigating the microbiomes of urban-adapted corals provides critical insights into the health, dynamics, and functioning of coral holobionts. In this study, we examined the microbiome of Madracis auretenra, a Caribbean coral from Santa Marta, Colombia, across contrasting environmental conditions. Over two years, we compared the microbiomes of healthy and stressed coral colonies from two distinct reef habitats—urban and protected—using 16S rRNA gene sequencing (V4 region) to assess microbial diversity. Our findings revealed microbial richness and diversity were primarily influenced by seasonal and local factors rather than host-specific traits such as interaction with algae, health status, or microhabitat. These variations were not substantial enough to disrupt the overall microbial community structure, which remained stable across temporal and spatial scales. Dominant taxa included Endozoicomonas, along with Vibrionaceae and Rhodobacteraceae, which form dense ecological interaction networks. Notably, nutrient and oxygen levels emerged as key drivers of microbiome fluctuations, yet Vibrionaceae populations exhibited exceptional temporal stability. These findings highlight the presence of a well-structured and resilient coral microbiome with minimal seasonal variability, even in urban-influenced environments. We propose that the dominance of Endozoicomonas and the stability of Vibrionaceae populations play a pivotal role in maintaining microbiome balance, ultimately contributing to the ecological resilience of M. auretenra in dynamic reef habitats. creator: Jordan Ruiz-Toquica creator: Andrés Franco Herrera creator: Mónica Medina uri: https://doi.org/10.7717/peerj.19226 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ruiz-Toquica et al. title: Evidence of rare occurrences of the Phoenix effect in the Hawaiian corals Porites compressa and Montipora capitata following mortality induced by a marine heatwave link: https://peerj.com/articles/19225 last-modified: 2025-04-15 description: Coral bleaching is a common stress response to extreme temperatures experienced during marine heatwaves. Bleached corals are left vulnerable without the nutritional support of their algal symbionts, and can often suffer partial or complete mortality. Bleaching-induced mortality is often accompanied by colonization of turf algae over the dead coral skeleton, which can be difficult for corals to regrow over. The Phoenix effect is a phenomenon of rapid recovery of live coral tissue following mortality, which is hypothesized to occur via the regrowth of tissue from deep within the coral skeleton that expands over the top of dead portions. Here, we found that the Hawaiian corals Porites compressa and Montipora capitata can display rapid tissue recovery suggestive of the Phoenix effect. During a marine heatwave that occurred in 2015 in Kāne’ohe Bay, Hawai’i, USA, 237 individuals (including bleached and non-bleached phenotypes) were identified and monitored for mortality and recovery over the next 2–7 years. Nearly 16% of P. compressa individuals and 34% of M. capitata exhibited substantial partial mortality, and approximately half of these affected individuals of each species had bleached during the heatwave. Partial mortality following the 2015 heatwave was followed by turf algae colonization over the exposed skeleton. Of the colonies with substantial mortality, six colonies (10% of affected individuals; five P. compressa and one M. capitata) subsequently recovered to over 90% live coral tissue within 2 years (2017), with an additional three colonies (two P. compressa and one M. capitata) recovering within 4 years of the 2015 marine heatwave (2019). We qualify colonies with rapid tissue recovery as those that meet two criteria: (1) substantial partial mortality (≥40%) in the first 12 months following the initial 2015 marine heatwave, and (2) recovery of any amount of live tissue at anytime before 2022. Interestingly, only colonies that had bleached in 2015 exhibited rapid tissue recovery. A consecutive, yet less severe marine heatwave occurred in 2019, and none of the previously recovered colonies observed experienced significant tissue loss, suggesting these individuals remained resilient amidst a secondary heat stress exposure. This phenomenon is an example of remarkable recovery and resilience that may be informative for further study of mechanisms of coral tissue regeneration in two important reef-building coral species. creator: Katelyn G. Jones creator: Katie L. Barott uri: https://doi.org/10.7717/peerj.19225 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Jones and Barott title: Ginsenosides and gut microbiota: differential effects on healthy individuals and irritable bowel syndrome subtypes link: https://peerj.com/articles/19223 last-modified: 2025-04-15 description: BackgroundIrritable bowel syndrome (IBS) is a common gastrointestinal disorder with poorly understood mechanisms. Variations in gut microbiota composition are observed in different IBS subtypes. Ginsenosides have shown potential in alleviating IBS symptoms, but their interactions with gut microbiota in different IBS subtypes are not well studied.MethodsIn this study, we investigated the effects of ginsenosides on the gut microbiota of both healthy participants and participants suffering from IBS characterized by diarrhea (IBS-D) or constipation (IBS-C), using in vitro fermentation alongside 16S rRNA sequencing and bioinformatics analyses.ResultsThe analysis demonstrated that there were no statistically significant alterations in α- or β-diversity between the ginsenosides-treated and control groups across all models. However, the microbial composition assessment revealed the presence of 51 shared genera, with notable variations in composition and a significant enrichment of specific taxa. Specifically, the LEfSe analysis revealed that, following ginsenosides treatment, the healthy model groups exhibited significant enrichment of Stenotrophomonas and Achromobacter, while the IBS-D model groups demonstrated significant enrichment of Pseudomonas and Stenotrophomonas.ConclusionsThe results elucidate the distinctive microbial signatures associated with ginsenosides treatment across both healthy and IBS-D groups, underscoring the potential therapeutic efficacy of ginsenosides in modulating gut microbiota. This study highlights the necessity for further investigation into targeted microbiome therapies for IBS, which may facilitate the development of more personalized and efficacious treatment strategies for gastrointestinal health. creator: Zhi Du creator: Chengman Zhao creator: Jiabin Li creator: Yan Shen creator: Guofei Ren creator: Jieying Ding creator: Jing Peng creator: Xiaoli Ye creator: Jing Miao uri: https://doi.org/10.7717/peerj.19223 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Du et al.