PeerJ最新文献

{"title":"Close neighbors, not intruders: investigating the role of tank bromeliads in shaping faunal microbiomes.","authors":"Rodolfo Martínez-Mota, Antonio Acini Vásquez-Aguilar, Dolores Hernández-Rodríguez, Emilio A Suárez-Domínguez, Thorsten Krömer","doi":"10.7717/peerj.19376","DOIUrl":"https://doi.org/10.7717/peerj.19376","url":null,"abstract":"<p><strong>Background: </strong>Tropical montane cloud forests contain high levels of epiphyte diversity. Epiphytic tank bromeliads play an important role in the functioning of these ecosystems and provide a microhabitat for many species of invertebrates. Microbial ecology theory suggests that the environment serves as a source of microbes for animals, but the contribution of this factor to the composition of an animal microbiome varies. In this study, we examined the extent to which tank bromeliads (<i>Tillandsia multicaulis</i>) serve as a source of microbes for two species of fly larvae in a cloud forest fragment in central Veracruz, Mexico.</p><p><strong>Methods: </strong>We used 16S rRNA sequencing to characterize the bacterial communities in the organic matter within bromeliad tanks and in the whole bodies (surface and gut) of larvae from two fly taxa (<i>Austrophorocera</i> sp., Tachinidae, and <i>Copestylum</i> sp., Syrphidae) that inhabit these bromeliads. To assess the contribution of bromeliads to the microbiome of the fly larvae, we conducted fast expectation-maximization microbial source tracking (FEAST) analysis.</p><p><strong>Results: </strong>The bacterial communities in bromeliad tanks were primarily composed of Pseudomonadota, Acidobacteriota, Bacteroidota, Verrucomicrobiota, and Spirochaetota. Similarly, communities of the fly larvae contained Pseudomonadota, Bacteroidota, Bacillota, and Actinomycetota. Bromeliad tanks exhibited the highest bacterial richness, followed by <i>Copestylum</i> and <i>Austrophorocera</i> larvae. Beta diversity analyses indicated that bacterial communities clustered by species. We found a modest contribution of bromeliads to the fly microbiome, with nearly 30% of the larvae microbiome traced to the organic matter deposited in the tanks.</p><p><strong>Conclusions: </strong>Our data suggest that the microbiome of flies, which inhabit tank bromeliads during their larval stage, is nourished to some extent by the bacterial communities present in the organic matter within the tank.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"13 ","pages":"e19376"},"PeriodicalIF":2.3,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12068248/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144047549","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deep learning-based fine-grained assessment of aneurysm wall characteristics using 4D-CT angiography.","authors":"Teerawat Kumrai, Takuya Maekawa, Yixuan Chen, Yoshie Sugiyama, Masatoshi Takagaki, Shigeo Yamashiro, Katsumi Takizawa, Tsutomu Ichinose, Fujimaro Ishida, Haruhiko Kishima","doi":"10.7717/peerj.19393","DOIUrl":"https://doi.org/10.7717/peerj.19393","url":null,"abstract":"<p><strong>Purpose: </strong>This study proposes a novel deep learning-based approach for aneurysm wall characteristics, including thin-walled (TW) and hyperplastic-remodeling (HR) regions.</p><p><strong>Materials and methods: </strong>We analyzed fifty-two unruptured cerebral aneurysms employing 4D-computed tomography angiography (4D-CTA) and intraoperative recordings. The TW and HR regions were identified in intraoperative images. The 3D trajectories of observation points on aneurysm walls were processed to compute a time series of 3D speed, acceleration, and smoothness of motion, aiming to evaluate the aneurysm wall characteristics. To facilitate point-level risk evaluation using the time-series data, we developed a convolutional neural network (CNN)-long- short-term memory (LSTM)-based regression model enriched with attention layers. In order to accommodate patient heterogeneity, a patient-independent feature extraction mechanism was introduced. Furthermore, unlabeled data were incorporated to enhance the data-intensive deep model.</p><p><strong>Results: </strong>The proposed method achieved an average diagnostic accuracy of 92%, significantly outperforming a simpler model lacking attention. These results underscore the significance of patient-independent feature extraction and the use of unlabeled data.</p><p><strong>Conclusion: </strong>This study demonstrates the efficacy of a fine-grained deep learning approach in predicting aneurysm wall characteristics using 4D-CTA. Notably, incorporating an attention-based network structure proved to be particularly effective, contributing to enhanced performance.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"13 ","pages":"e19393"},"PeriodicalIF":2.3,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12068254/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144023464","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>In vitro</i> feasibility of bovine and canine whole blood and commercially prepared canine packed red blood cells as a source of xenotransfusion in swine (<i>Sus scrofa domestica</i>).","authors":"Victoria Diaz, Deanna M W Schaefer, Pierre-Yves Mulon, Xiaojuan Zhu, Joe Smith, Luca Giori, Chiara Hampton","doi":"10.7717/peerj.19436","DOIUrl":"https://doi.org/10.7717/peerj.19436","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;b&gt;Background:&lt;/b&gt; Since sourcing porcine blood donors for emergent transfusions to porcine patients is difficult, bovine or canine blood donors might represent alternative sources. The primary objective of this study was to determine the frequency of incompatible major (CMMa) and minor (CMMi) crossmatches by the standard saline agglutination tube method (SSA) between bovine whole blood (bWB) and whole blood from commercial pigs (pWB), and canine universal donor whole blood or commercially-prepared packed red blood cells (pRBCs) with whole blood from companion pigs. A secondary objective was determining the agreement between the reference method (SSA) and a quick slide (QS) method. &lt;b&gt;Methods:&lt;/b&gt; Blood was collected from 12 heifers, seven companion pigs, and eight commercial-cross pigs. A0 blood typing was performed for all porcine samples. Bovine blood was pooled into eight bags each containing three crossmatch-compatible individuals. Canine blood included whole blood from three canine blood donors (DEA 1.1, 5, 7 negative, and DEA 4 positive), and three bags each of DEA 1.1 negative and DEA 1.1 positive pRBCs. Crossmatch pairs were performed for bovine-to-porcine (&lt;i&gt;n&lt;/i&gt; = 64) and canine-to-porcine (&lt;i&gt;n&lt;/i&gt; = 63) samples. Incompatibility was defined as any agglutination or hemolysis on either CMMa and CMMi and reported separately. Complete incompatibility was defined as incompatibility of both CMMa and CMMi on the same pair. Kappa statistics tested the agreement between SSA and QS (significance at &lt;i&gt;P&lt;/i&gt; &lt; 0.05). &lt;b&gt;Results:&lt;/b&gt; For bWB and pWB, agglutination was observed in 9.4% of CMMa and 100% of CMMi &lt;i&gt;via&lt;/i&gt; SSA. Incompatibility on CMMa of bWB was more frequent with porcine blood type \"0\" (&lt;i&gt;P&lt;/i&gt; = 0.0107) than with type \"A\", whereas porcine blood group had no effect on CMMi results. All canine-to-porcine CMMa were incompatible with SSA and showed hemolysis severe enough to prevent evaluation of agglutination. The accuracy of QS at detecting incompatibilities was 87.5% in CMMa and 98.4% in CMMi in bovine-to-porcine samples. Agreement between SSA and QS methods was fair (&lt;i&gt;k&lt;/i&gt; = 0.36) for bovine-to-porcine CMMa but could not be calculated for CMMi due to lack of compatible matches. Because all canine-to-porcine CMMa were incompatible, the effects of the porcine blood group on incompatibility, accuracy of QS, and agreement between SSA and QS could not be calculated for CMMa. For CMMi, the agreement between tests was poor (&lt;i&gt;k&lt;/i&gt; = 0). &lt;b&gt;Discussion:&lt;/b&gt; When a xenotransfusion to a pig is indicated, bWB appears to be suitable based on &lt;i&gt;in vitro&lt;/i&gt; CMMa testing, whereas canine blood products are contraindicated for &lt;i&gt;in vivo&lt;/i&gt; administration to swine based on absolute CMMa incompatibility and incidence of hemolysis. &lt;i&gt;In vivo&lt;/i&gt; studies are needed to elucidate the clinical significance of CMMi incompatibilities. Based on these results, QS cannot be accurately used as a surrogate of SSA in pretransfusion testing for ","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"13 ","pages":"e19436"},"PeriodicalIF":2.3,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12068249/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143973345","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of 12-week integrative neuromuscular training on muscular fitness and sex differences in response to intervention in five- to six-year-old preschoolers.","authors":"Zhihai Wang, Jiayu Zang, Zhaohong Wang, Daniel T P Fong, Dan Wang","doi":"10.7717/peerj.19417","DOIUrl":"https://doi.org/10.7717/peerj.19417","url":null,"abstract":"<p><strong>Objectives: </strong>This study examined the effects of a 12-week integrative neuromuscular training (INT) program on muscular fitness in male and female five- to six-year-old preschoolers.</p><p><strong>Methods: </strong>Thirty preschoolers were randomly assigned to either an experimental group (EG; <i>n</i> = 15; age = 5.3 ± 0.5 years, body height = 115.3 ± 5.2 cm, body mass = 20.7 ± 2.6 kg) or a control group (CG; <i>n</i> = 15; age = 5.2 ± 0.4 years, body height = 118.5 ± 4.9 cm, body mass = 22.6 ± 2.7 kg) participating in a 12-week INT program and regular physical education classes three times per week, respectively. Upper extremity maximal strength (grip strength test) and power (tennis ball throwing test), core endurance strength (one-minute sit-up test), and lower extremity power (standing long jump test) were assessed at the baseline (T0), Week 6 (T6), and Week 12 (T12). Data were analyzed using an independent samples T-test and a two-way repeated-measures ANOVA.</p><p><strong>Results: </strong>Significant interaction effects between the EG and CG were observed for grip strength, tennis ball throws, one-minute sit-ups, and standing long jumps (<i>p</i> < 0.001). Relative to the CG, the EG demonstrated significant improvements in all muscular fitness at T6 and T12 (<i>p</i> < 0.05). However, no significant interaction was found between the time and the sex (<i>p</i> > 0.05).</p><p><strong>Conclusions: </strong>These findings suggested that a 12-week INT program can more effectively enhance the muscular fitness of 5-6-year-old preschoolers compared to regular physical education classes, serving as an effective and efficient supplement to physical education for this age group. Furthermore, there is no evidence of sex -specific differences in the development of muscular fitness among 5-6-year-old preschoolers under the INT program.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"13 ","pages":"e19417"},"PeriodicalIF":2.3,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12066101/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144019570","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Host specificity of gastrointestinal parasites in free-ranging sloths from Costa Rica.","authors":"Ezequiel A Vanderhoeven, Madeleine Florida, Rebecca N Cliffe, José Guzmán, Juliana Notarnicola, Tyler R Kartzinel","doi":"10.7717/peerj.19408","DOIUrl":"https://doi.org/10.7717/peerj.19408","url":null,"abstract":"<p><p>The diversity and host specificity of gastrointestinal parasites infecting free-ranging sloths is poorly known. We compared gastrointestinal parasites of two sloth species from Costa Rica-three-fingered sloths (<i>Bradypus variegatus</i>) and two-fingered sloths (<i>Choloepus hoffmanni</i>)-for the first time in both a primary forest and an urban habitat. We asked whether host-parasite interactions were predominantly structured by host identity, the habitats in which hosts occurred, or both. Coproparasitology revealed protozoa and nematode eggs from both host species, but cestode eggs were recorded only in <i>C. hoffmanni</i>. We found eight parasitic morphotypes in 38 samples, which matches the total number of these parasites described in sloths over the past 100 years. We found no significant difference in overall parasite richness between sloth species or habitats, but the parasite richness of <i>C. hoffmanni</i> was 2-fold greater in the primary forest <i>vs</i>. urban habitat. As no parasite sharing was observed between sloth species, we found strong and significant differences in parasite composition between host species regardless of habitat. In <i>B. variegatus</i>, we observed eggs of four nematode taxa (Spirocercidae, Subuluroidea, Spirurida, Ascaridida) and cysts of Eimeriidae (Apicomplexa). By contrast, in <i>C. hoffmanni</i>, we observed cestodes (Anoplocephalidae), a different nematode from the family Spirocercidae, and also different cysts of Eimeriidae (Apicomplexa). Many rare taxa were recorded only in samples from the primary forest, and these did not match any sloth parasites that had been previously described in the literature, suggesting that at least some could be undescribed species. Together, these results highlight the paucity of comparative parasitology involving tropical wildlife, the importance of characterizing host-parasite transmission networks, and the potential relevance of intermediate hosts that may be relevant to sloth health.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"13 ","pages":"e19408"},"PeriodicalIF":2.3,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12066103/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144031195","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Allelopathic effects and composition of aqueous extracts from different parts of <i>Galinsoga parviflora</i> Cav. on <i>Medicago sativa</i> L. and <i>Avena sativa</i> L.","authors":"Shipu Cheng, Fanru Xu, Zhiyong Lu, Huairui Xu, Mengqi Cai, Juan Sun, Yufang Xu","doi":"10.7717/peerj.19378","DOIUrl":"https://doi.org/10.7717/peerj.19378","url":null,"abstract":"<p><strong>Background: </strong><i>Galinsoga parviflora</i> Cav. is a high-risk invasive plant that seriously threatens the development of grasslands in southern China. However, the allelopathic effects on <i>Medicago sativa</i> L. and <i>Avena sativa</i> L., which are widely cultivated forages around the world, have not been reported.</p><p><strong>Methods: </strong>To explore the allelopathic mechanism of <i>G. parviflora</i>, the allelopathic effects of aqueous extracts from different parts of <i>G</i>. <i>parviflora</i> on <i>M. sativa</i> and <i>A. sativa</i> were investigated. The germination rate (GR), germination potential (GP), seedling height, fresh weight, and chlorophyll content of <i>M. sativa</i> and <i>A. sativa</i> seedlings were measured to elucidate the allelopathy of <i>G. parviflora</i> on the two forages. Based on the five indicators, synthetical allelopathic effects (SAE) of extracts was also calculated. In addition, the allelopathic components of the extracts in <i>G. parviflora</i> were quantitatively revealed by untargeted metabolomics detection. Furthermore, two key allelopathic substances, 1,4-cyclohexanedicarboxylic acid (CHDA) and trehalose, were selected to explore the inhibitory effect on two notorious weed species in China, such as gramineous <i>Digitaria sanguinalis</i> L. and broad-leaved <i>Amaranthus retroflexus</i> L.</p><p><strong>Result: </strong>(1) The inhibitory effects of aqueous extracts from different parts of <i>G. parviflora</i> on recipient plants were different, the root was the weakest, and the whole plants was the strongest, with the values of synthetical allelopathic effects (SAE) on <i>M. sativa</i> at the highest concentration being -0.12 and -0.40, respectively. (2) Compared with <i>A. sativa</i>, <i>M. sativa</i> was generally more susceptible to the extracts. (3) The differences in the content of CHDA or trehalose might be a reason why extracts from different parts of <i>G. parviflora</i> exhibited different allelopathic effects. (4) The herbicidal activity test of key allelopathic substances found that CHDA has a strong inhibitory effect on the germination of <i>D. sanguinalis</i> and almost does not affect <i>M. sativa</i> and <i>A. sativa</i>. Thus, this discovery not only revealed allelopathic effects and components in different parts of <i>G. parviflora</i>, but provided scientific evidence for weed control based on natural plant extracts in the future.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"13 ","pages":"e19378"},"PeriodicalIF":2.3,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12066104/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144037633","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Oral health status, oral hygiene behaviors, and caries risk assessment of individuals with special needs: a comparative study of Pakistan and Saudi Arabia.","authors":"Osama Khattak, Farooq Ahmad Chaudhary, Shahzad Ahmad, Muhammad Amber Fareed, Shazia Iqbal, Asma Shakoor, Mohammed Nadeem Baig, Haifa Ali Almutairi, Rakhi Issrani, Azhar Iqbal","doi":"10.7717/peerj.19286","DOIUrl":"https://doi.org/10.7717/peerj.19286","url":null,"abstract":"<p><strong>Background: </strong>Individuals with disabilities often experience greater challenges in managing oral diseases, including dental caries and periodontal conditions, due to functional limitations. This study aims to: (1) assess the oral health status of disabled individuals in Pakistan and Saudi Arabia, (2) evaluate their oral hygiene knowledge and behaviors, and (3) determine their caries risk using the Caries Management by Risk Assessment (CAMBRA) protocol.</p><p><strong>Methods: </strong>A cross-sectional study was conducted on 189 participants aged 13 years and older, including both young people and adults with hearing, visual, or intellectual disabilities from Pakistan and Saudi Arabia between September 2023 and April 2024. The participants were recruited from the Institute of Special Education, Pakistan, and the Saudi Institute of Rehabilitation Medicine, Saudi Arabia. Intraoral examinations and bitewing radiographs assessed oral health, including Decayed, Missing, and Filled Teeth (DMFT) index, Gingival Index, visible plaque, and molar alignment. A self-administered questionnaire gathered sociodemographic data and evaluated oral hygiene knowledge and behaviors. Caries risk was analyzed using the CAMBRA tool. Data were analyzed using descriptive statistics, Chi-square tests, and binary logistic regression.</p><p><strong>Results: </strong>The mean DMFT score was 6.30 (SD = 1.83), with a statistically significant difference between Pakistan and Saudi Arabia (<i>p</i> = 0.007). Gingival health was fair to poor in 47% of participants, while 43.4% exhibited bleeding on probing and 34.9% had visible plaque. Class III malocclusion affected approximately 30% of participants in both countries. Tooth brushing frequency showed a significant difference between the two groups (<i>p</i> = 0.005). Most participants (76% in Pakistan, 62% in Saudi Arabia) were classified as high caries risk. Deep pits and fissures (69.4%) and frequent snacking (63.8%) were the main risk factors in Pakistan, while frequent snacking (71.6%) and heavy plaque (60.4%) were prevalent in Saudi Arabia. Saudi participants had a significantly higher likelihood of being in the high-risk group for caries (OR = 1.86, 95% CI [0.95-3.65], <i>p</i> = 0.04).</p><p><strong>Conclusion: </strong>The disabled individuals in both countries face significant oral health challenges, with high caries risk and poor oral hygiene practices. Targeted preventive measures and improved dental care access are essential to addressing these disparities.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"13 ","pages":"e19286"},"PeriodicalIF":2.3,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12066100/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144036524","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genotypic and phenotypic characterization of thermo-sensitive genic male sterile (TGMS) rice lines using simple sequence repeat (SSR) markers and population structure analysis.","authors":"B Nagendra Naidu, Manonmani Swaminathan, Pushpam Ramamoorthy, Kumaresan Dharmalingam, Raveendran Muthurajan, Selvi Duraisamy, Nivedha Rakkimuthu, Abirami Subramanian, Rithesh Natarajan, Bonipas Antony John","doi":"10.7717/peerj.18975","DOIUrl":"https://doi.org/10.7717/peerj.18975","url":null,"abstract":"<p><p>Thermo-sensitive genic male sterile (TGMS) lines in rice are crucial for hybrid breeding, enhancing genetic diversity by eliminating the need for manual emasculation and restorer genes. These lines induce sterility at high temperatures and restore fertility at low temperatures, in contrast to cytoplasmic male sterility (CMS) systems that require specific restorative genes. This temperature-sensitive mechanism allows for greater flexibility in pairing parent lines, increasing genetic diversity and enabling recombination of beneficial traits in hybrids. A randomized block design (RBD) with three replications was employed for the evaluation of these TGMS rice lines. This study investigates the molecular diversity and genetic variability among TGMS rice lines. Traits such as single plant yield, grains per panicle, glume angle, and pollen fertility showed significant phenotypic and genotypic variation, indicated by high coefficients of variation (PCV and GCV), heritability estimates, and genetic advance as a percentage of mean (GAM). These results highlight substantial genetic variation and selection potential. Euclidean distance matrix analysis of morphological data revealed notable genetic differences. TNAU 137S 1 and TNAU 137S 2 were the most genetically similar, while TNAU 112S and TNAU 114S showed the greatest divergence. Principal component analysis (PCA) revealed distinct genetic profiles among lines such as TNAU 136S, TNAU 113S, TNAU 142S, and TNAU 126S, important for hybrid development. Molecular diversity analysis using simple sequence repeat (SSR) markers identified 90 alleles and eight genetic clusters. Bayesian analysis further confirmed two major subpopulations with significant genetic divergence. These findings support the selective use of parent lines for hybrid rice breeding.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"13 ","pages":"e18975"},"PeriodicalIF":2.3,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12066105/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144049578","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of an immune-related gene signature applying Ridge method for improving immunotherapy responses and clinical outcomes in lung adenocarcinoma.","authors":"Zhen Chen, Yongjun Zhang","doi":"10.7717/peerj.19121","DOIUrl":"https://doi.org/10.7717/peerj.19121","url":null,"abstract":"<p><strong>Background: </strong>Lung adenocarcinoma (LUAD) is a major cause of cancer mortality. Considering the critical role of tumor infiltrating lymphocytes in effective immunotherapy, this study was designed to screen molecular markers related to tumor infiltrating cells in LUAD, aiming to improve immunotherapy response during LUAD therapy.</p><p><strong>Methods: </strong>The ConsensusClusterPlus method was used for clustering immune molecular subtypes of LUAD. Immune cell infiltration and immunotherapeutic potential in each subtype was evaluated employing single-sample gene set enrichment analysis (ssGSEA), Tumor Immune Dysfunction and Exclusion (TIDE), and Immunophenoscore (IPS). Immune-related co-expression modules were classified by weighted gene co-expression network analysis (WGCNA) analysis. The sequencing data of immune-related genes were comprehensively analyzed by introducing a new computational framework and 10 machine learning algorithms (a total of 101 combinations) to determine the prognostic genes, which were further combined to develop an immune prognostic signature (IMMPS) using the stepCox and Ridge methods. The expression of the signature genes was validated by quantitative real-time PCR (qRT-PCR).</p><p><strong>Results: </strong>Samples from The Cancer Genome Atlas dataset (TCGA-LUAD) were divided into two subtypes (immunosuppressive subgroup C1 and immune-activated subgroup C2); notably, the C2 subgroup was more likely to benefit from immunotherapy (<i>p</i> < 0.05). An IMMPS developed based on seven immune infiltrating cell-related genes (<i>SEMA7A, EFHD2, CHST11, SLC24A4, MAL, JCHAIN</i>, and <i>SCARF1</i>) could accurately predict the overall survival of LUAD in five LUAD cohorts, with an average C-index higher than 0.69. LUAD patients with a low IMMPS value had a higher immune cell infiltration (<i>p</i> < 0.05). In addition, the IMMPS exhibited better prediction performance in comparison to 154 published gene signatures, suggesting that the IMMPS was an independent prognostic risk factor for evaluating the overall survival of LUAD patients. Since <i>BTNL9</i> was the most relevant immune checkpoint gene, <i>in vitro</i> experiment showed that the expression of the seven key genes (<i>SEMA7A, EFHD2, CHST11, SLC24A4, MAL, JCHAIN</i>, and <i>SCARF1</i>) in LUAD cell lines was consistent with that in normal lung epithelial cells after inhibiting <i>BTNL9</i> expression (<i>p</i> < 0.05).</p><p><strong>Conclusions: </strong>Our results contributed to a better understanding of immunological characteristics of LUAD. The IMMPS could serve as a promising tool for improving the clinical outcome of patients suffering from LUAD.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"13 ","pages":"e19121"},"PeriodicalIF":2.3,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12066106/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144041367","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Screen time exposure and academic performance, anxiety, and behavioral problems among school children.","authors":"Mohammad Sidiq, Balamurugan Janakiraman, Faizan Kashoo, Rayan Jastania, Abdullah Ibrahim Alhusayni, Abdullah Alzahrani, Aksh Chahal, Alagappan Thiyagarajan, Imran Khan, Chandan Kumar, Rajkumar Krishnan Vasanthi, Fahad Alanazi, Mehrunnisha Ahmad, Chhavi Arora Sehgal, Shabnam Khan, Mshari Alghadier","doi":"10.7717/peerj.19409","DOIUrl":"https://doi.org/10.7717/peerj.19409","url":null,"abstract":"<p><strong>Background: </strong>The growth of the digital landscape has surely outpaced research on the effects of screen media on the health, learning, and development of children. The potential risk-to-benefit ratio of screen media exposure for education and entertainment purposes warrants further exploration. Therefore, we aimed to investigate the relationships between screen time and academic performance, anxiety, and outdoor playing among school children in India.</p><p><strong>Methods: </strong>A total of 537 parents responded to this online survey and reported approximately 537 Indian school children (mean age 10.9 years) from five schools. Data was collected using an e-questionnaire which consisted of a socio-demographic domain, recreational activities, self-reported physical measures, academic performance, information related to children's screen time, the Spence Children Anxiety Scale (SCAS), and the Pediatric Symptom Checklist (parent version) instruments. We employed multivariate linear regression models to estimate the association between children's screen time and the predictor variables with 0.05 alpha as level of significance.</p><p><strong>Results: </strong>The mean screen time was 3.06 ± 1.22 h/day, the average duration of outdoor play per week was 11.23 ± 4.1 h, and the mean body mass index (BMI) was 18.2 ± 3.2. Screen time (h) in a typical week was positively correlated with BMI, the SCAS anxiety score, and behavioral problems and negatively correlated with academic performance. School children's screen time was a predictor of their BMI, behavioral symptoms, and academic performance according to the linear regression analysis.</p><p><strong>Conclusion: </strong>Our findings pointed out that screen time was associated with increased BMI, behavioral problems and poor academic performance. These insights shall be used for development of targeted tailored interventions and strategies to reduce childhood obesity related to screen time. Further research is necessary to rule out the influence of other intricate factors, such as sleep, parental practices, family connectedness, and supervision of parents. The careful use of digital media must serve as a positive force in children's educational and developmental trajectories.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"13 ","pages":"e19409"},"PeriodicalIF":2.3,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12066102/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144004965","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}