PeerJ最新文献

{"title":"High speciation in the cryptic <i>Pristimantis celator</i> clade (Anura: Strabomantidae) of the Mira river basin, Ecuador-Colombia.","authors":"Mario H Yánez-Muñoz, Juan P Reyes-Puig, Carolina Reyes-Puig, Gabriela Lagla-Chimba, Christian Paucar-Veintimilla, Miguel A Urgiles-Merchán, Julio C Carrión-Olmedo","doi":"10.7717/peerj.18680","DOIUrl":"10.7717/peerj.18680","url":null,"abstract":"<p><p>Over the past decade, research in the montane forests of the Mira River basin, spanning Ecuador and Colombia, has identified it as crucial for the adaptive radiation of flora and fauna, shaped by its complex geological and climatic history. This study focuses on the phylogenetic and systematic revision of a frog clade initially labeled as <i>Pristimantis verecundus</i>, revealing significant cryptic diversity. Through detailed analyses of type material and expanded molecular sampling, we found that the original description actually included specimens representing two additional species, which are described herein. In this work, we discovered and formally described four new species within montane forests at elevations from 1,600 to 2,300 meters. Genetic distances of 3.34% to 14% and clear morphological differences underscore the clade's hidden diversity. We propose renaming the group <i>Pristimantis celator</i> clade within <i>Pristimantis myersi</i> species group and subgenus <i>Trachyphrynus</i>, aligning with phylogenetic evidence and resolving taxonomic ambiguities using the oldest available name, <i>Pristimantis celator</i> (Lynch, 1976). This reclassification includes 14 species, seven formally described, and seven as candidates, distributed across northwestern Ecuador and southwestern Colombia, particularly in Mira and Esmeraldas River basins. The study highlights the Andean orogeny's role in species diversification within <i>Pristimantis celator</i> clade, with geographic barriers like Cerro Golondrinas influencing genetic isolation. Genetic divergences exceeding 3.34% indicate evolutionary isolation across these landscapes. Our findings provide insights into montane ecosystem speciation, emphasizing vicariance, niche adaptation, and altitudinal gradients in shaping biodiversity. A polytomy among three well-supported clades within <i>Pristimantis myersi</i> species group is noted due to incomplete genetic data, yet distinctiveness and evolutionary relationships are affirmed. Cryptic diversity within <i>Pristimantis celator</i> clade links to unique orogenic and climatic conditions, highlighting conservation needs. Lastly, we provide a redescription of <i>Pristimantis verecundus</i> and species identification key to aid future research and conservation in this biogeographically influential region.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"13 ","pages":"e18680"},"PeriodicalIF":2.3,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11786716/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143080464","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":"Leveraging machine learning to uncover multi-pathogen infection dynamics across co-distributed frog families.","authors":"Daniele L F Wiley, Kadie N Omlor, Ariadna S Torres López, Celina M Eberle, Anna E Savage, Matthew S Atkinson, Lisa N Barrow","doi":"10.7717/peerj.18901","DOIUrl":"10.7717/peerj.18901","url":null,"abstract":"<p><strong>Background: </strong>Amphibians are experiencing substantial declines attributed to emerging pathogens. Efforts to understand what drives patterns of pathogen prevalence and differential responses among species are challenging because numerous factors related to the host, pathogen, and their shared environment can influence infection dynamics. Furthermore, sampling across broad taxonomic and geographic scales to evaluate these factors poses logistical challenges, and interpreting the roles of multiple potentially correlated variables is difficult with traditional statistical approaches. In this study, we leverage frozen tissues stored in natural history collections and machine learning techniques to characterize infection dynamics of three generalist pathogens known to cause mortality in frogs.</p><p><strong>Methods: </strong>We selected 12 widespread and abundant focal taxa within three ecologically distinct, co-distributed host families (Bufonidae, Hylidae, and Ranidae) and sampled them across the eastern two-thirds of the United States of America. We screened and quantified infection loads <i>via</i> quantitative PCR for three major pathogens: the fungal pathogen <i>Batrachochytrium dendrobatidis</i> (Bd), double-stranded viruses in the lineage <i>Ranavirus</i> (Rv), and the alveolate parasite currently referred to as Amphibian Perkinsea (Pr). We then built balanced random forests (RF) models to predict infection status and intensity based on host taxonomy, age, sex, geography, and environmental variables and to assess relative variable importance across pathogens. Lastly, we used one-way analyses to determine directional relationships and significance of identified predictors.</p><p><strong>Results: </strong>We found approximately 20% of individuals were infected with at least one pathogen (231 single infections and 25 coinfections). The most prevalent pathogen across all taxonomic groups was Bd (16.9%; 95% CI [14.9-19%]), followed by Rv (4.38%; 95% CI [3.35-5.7%]) and Pr (1.06%; 95% CI [0.618-1.82%]). The highest prevalence and intensity were found in the family Ranidae, which represented 74.3% of all infections, including the majority of Rv infection points, and had significantly higher Bd intensities compared to Bufonidae and Hylidae. Host species and environmental variables related to temperature were key predictors identified in RF models, with differences in importance among pathogens and host families. For Bd and Rv, infected individuals were associated with higher latitudes and cooler, more stable temperatures, while Pr showed trends in the opposite direction. We found no significant differences between sexes, but juvenile frogs had higher Rv prevalence and Bd infection intensity compared to adults. Overall, our study highlights the use of machine learning techniques and a broad sampling strategy for identifying important factors related to infection in multi-host, multi-pathogen systems.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"13 ","pages":"e18901"},"PeriodicalIF":2.3,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11786709/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143080705","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":"Biocontrol efficacy of <i>Bacillus licheniformis</i> and <i>Bacillus amyloliquefaciens</i> against rice pathogens.","authors":"Mohsin Tariq, Mehvish Zahoor, Tahira Yasmeen, Tahir Naqqash, Muhammad Abdul Rehman Rashid, Muhammad Abdullah, Abdul Rafay Rafiq, Marriam Zafar, Iqra Irfan, Ijaz Rasul","doi":"10.7717/peerj.18920","DOIUrl":"10.7717/peerj.18920","url":null,"abstract":"<p><p>Biocontrol is a cost-effective and eco-friendly approach to control plant pathogens using natural enemies. Antagonistic microorganisms or their derivatives specifically target the plant pathogens while minimizing the harm to non-target organisms. Bacterial blight and brown spot are the major rice diseases caused by <i>Xanthomonas oryzae</i> pv. <i>oryzae</i> (<i>Xoo</i>) and <i>Bipolaris oryzae</i> (<i>Bo</i>), respectively. This study was conducted to assess the plant growth-promoting potential and biocontrol activity of root-associated bacteria against the rice pathogens, <i>Xoo</i> and <i>Bo</i>. A total of 98 bacteria were isolated from rice roots and characterized for plant growth-promoting properties including phosphate solubilization, indole-3-acetic acid production, nitrogen fixation and biofilm formation. Based on these properties, 36 bacteria were selected and tested for biocontrol potential against rice pathogens <i>via</i> co-culturing antagonism assay. LE7 exhibited the maximum inhibition of 79%, while FR8, PE2, LE7, LR22 and LR28 also significantly reduced the growth of <i>Xoo</i>. Likewise, FR2, LR22, LR35 and LE7 significantly inhibited the growth of <i>Bo</i>, in which LR22 exhibited the maximum inhibition of 81%. Under controlled-conditions, LE7 and LR22 significantly reduced the disease incidence of <i>Xoo</i> and <i>Bo</i>, respectively, and improved the growth of rice. Full-length 16S rRNA gene sequencing of most potential bacterial isolates, LE7 and LR22, revealed their maximum identity with <i>Bacillus amyloliquefaciens</i> and <i>Bacillus licheniformis</i>, respectively. Application of <i>Bacillus</i> spp. as biocontrol agent represents enormous potential in rice farming. The most promising bacterial isolates could be used as bioinoculants for rice disease management and improved production in a sustainable manner.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"13 ","pages":"e18920"},"PeriodicalIF":2.3,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11786712/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143080812","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":"Hematopoietic stem cell discovery: unveiling the historical and future perspective of colony-forming units assay.","authors":"Nur Afizah Yusoff, Zariyantey Abd Hamid, Siti Balkis Budin, Izatus Shima Taib","doi":"10.7717/peerj.18854","DOIUrl":"10.7717/peerj.18854","url":null,"abstract":"<p><p>Stem cells are special cells with the distinctive capability to self-renew, forming a new pool of undifferentiated stem cells. They are also able to differentiate into lineage-specific cell types that are specialized and matured. Thus, stem cells are considered as the building blocks of tissues and organs in which they reside. Among the many types of stem cells, hematopoietic stem cells (HSCs) are the most studied adult stem cells and are considered as a promising source of cells for applications in the clinical and basic sciences. Historically, research on HSCs was initiated in the 1940s, where in a groundbreaking experiment, intravenously injected bone marrow (BM) cells prevented the death of irradiated mice by restoring blood cell production. Since then, HSCs have been studied and utilized in medical therapies and research for over several decades. Over time, more sophisticated tools have been developed to evaluate the behaviour of specifically purified subsets of hematopoietic cells that have the capacity to produce blood cells. One of the established tools is the colony-forming units (CFUs) assay. This assay facilitates the identification, enumeration, and analysis of colonies formed by differentiated hematopoietic stem and progenitor cells (HSPCs) from myeloid, erythroid and lymphoid lineages. Hence, the CFUs assay is a fundamental <i>in vitro</i> platform that allows functional studies on the lineage potential of an individual HSPCs. The outcomes of such studies are crucial in providing critical insights into hematopoiesis. In this review, we explore the fundamental discoveries concerning the CFUs assay by covering the following aspects: (i) the historical overview of the CFUs assay for the study of clonal hematopoiesis involving multilineage potential of HSPCs, (ii) its use in various experimental models comprising humans, mice/rodents, zebrafish and induced pluripotent stem cells (iPSCs) and (iii) research gaps and future direction concerning the role of CFUs assay in clinical and basic sciences. Overall, the CFUs assay confers a transformative platform for a better understanding of HSPCs biology in governing hematopoiesis.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"13 ","pages":"e18854"},"PeriodicalIF":2.3,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11786707/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143080443","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":"Correction factors for prey size estimation from PenguCams.","authors":"Owen Dabkowski, Ursula Ellenberg, Thomas Mattern, Klemens Pütz, Pablo Garcia Borboroglu","doi":"10.7717/peerj.18598","DOIUrl":"10.7717/peerj.18598","url":null,"abstract":"<p><p>The use of animal-borne cameras enables scientists to observe behaviours and interactions that have until now, gone unseen or rarely documented. Researchers can now analyse prey preferences and predator-prey interactions with a new level of detail. New technology allows researchers to analyse prey features before they are captured, adding a new dimension to existing prey analysis techniques, which have primarily relied on examining partially or fully digested prey through stomach flushing. To determine prey size, the video footage captured needs a correction factor (pixel:mm ratio) that allows researchers to measure prey dimensions using image measuring software and convert the pixels to actual measurements. This in turn will help estimating the prey energy content. This method requires a reference object with known dimensions (such as beak measurements) to ground truth your distance. Using PenguCams we determined the correction factor by measuring a 2 cm section of 1 mm grid paper from video footage taken at known distances (10, 20, 30, 40, 50, 60 cm) in different salinities ranging from air and fresh water, up to 35 psu in 5 psu increments while controlling for temperature and pressure. We found no significant difference between correction factors of water at different salinities. However, due to their considerable differences in refraction index, correction factors contrast between water and air. Linear equations modelled from correction factors at tested distances help predict correction factors between tested distances and, therefore, enable a wider application of this research. We provide examples from PenguCam footage taken of Humboldt (<i>Spheniscus humboldti</i>), Tawaki (<i>Eudyptes pachyrhynchus</i>) and King (<i>Aptenodytes patagonicus</i>) penguins to illustrate the use of identified correction factors. This study provides a tool for researchers to further enhance their understanding of predator-prey interactions.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"13 ","pages":"e18598"},"PeriodicalIF":2.3,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11784529/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143079878","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> comparative thermo-chemical aging and penetration analyses of bioactive glass-based dental resin infiltrates.","authors":"Syed Zubairuddin Ahmed, Abdul Samad Khan, Maram Alshehri, Fatimah Alsebaa, Fadak Almutawah, Moayad Mohammed Aljeshi, Asma Tufail Shah, Budi Aslinie Md Sabri, Sultan Akhtar, Mohamed Ibrahim Abu Hassan","doi":"10.7717/peerj.18831","DOIUrl":"10.7717/peerj.18831","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Teeth with small to moderate cavities can be repaired with enamel resin infiltrants, a form of dental restorative material. In dental materials, it is standard practice to include several filler particles for experimental use in dental resin infiltrates. The resin's BG particles penetrate the lesion and release ions that combine with saliva to provide a mineral-rich environment that can strengthen enamel and heal. This study aimed to compare resin infiltrants based on three types of bioactive glass materials and investigate the penetration depth, microleakage, and the effect of thermal and chemical aging.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Methodology: &lt;/strong&gt;A triethylene glycol dimethacrylate (TEGDMA) and urethane dimethacrylate (UDMA)-based experimental resin infiltrate was prepared. Initial mixing was done manually for 1 h at room temperature, followed by another mix for 30 min on a magnetic stirrer. This prepared resin, called \"PURE RESIN\" was then further incorporated with three different types of bioactive glasses, &lt;i&gt;i.e&lt;/i&gt;., Bioglass (45S5), boron-substituted (B-BG), and fluoride-substituted (F-BG). Initial manual mixing for 1 h, followed by ultrasonic mixing for 3 min and then proceeded for the final mixing on a magnetic stirrer for 24 h in a dark room at ambient temperature. Human-extracted teeth were demineralized, and the experimental resins were infiltrated on the demineralized surface. The surface area, pore size, and volume of the demineralized surface were measured. The microleakage and penetration depth were analyzed with the stereomicroscope and micro-CT, respectively. The samples were challenged with the pH cycle for 14 days, followed by a scanning electron microscope (SEM). Thermocycling (5,000 cycles) and chemical aging (4 weeks) were conducted, followed by microhardness, surface roughness, and SEM analyses. Statistical analyses were conducted after each test.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;The F-BG group achieved the highest initial and day 14 penetration coefficients. There was a superior dye penetration with the microleakage analysis in the F-BG group. The 45S5 group had the highest average penetration depth &lt;i&gt;via&lt;/i&gt; micro-CT analysis. After thermocycling and chemical aging, the micro-hardness was reduced (non-significantly) among all samples except the F-BG group in post-chemical aging analysis, whereas the surface roughness was significantly increased. SEM images showed the presence of micro-pits on the surfaces after the thermal and chemical aging.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusion: &lt;/strong&gt;The F-BG group achieved the highest initial and day 14 penetration coefficients. There was a superior dye penetration with the microleakage analysis in the F-BG group. The 45S5 group had the highest average penetration depth &lt;i&gt;via&lt;/i&gt; micro-CT analysis. After thermocycling and chemical aging, the micro-hardness was reduced (non-significantly) among all samples except the F-BG group in post-chemical aging analysis, whereas ","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"13 ","pages":"e18831"},"PeriodicalIF":2.3,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11784535/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143080694","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":"Clinical considerations on antimicrobial resistance potential of complex microbiological samples.","authors":"Norbert Solymosi, Adrienn Gréta Tóth, Sára Ágnes Nagy, István Csabai, Csongor Feczkó, Tamás Reibling, Tibor Németh","doi":"10.7717/peerj.18802","DOIUrl":"10.7717/peerj.18802","url":null,"abstract":"<p><p>Antimicrobial resistance (AMR) is one of our greatest public health challenges. Targeted use of antibiotics (ABs) can reduce the occurrence and spread of AMR and boost the effectiveness of treatment. This requires knowledge of the AB susceptibility of the pathogens involved in the disease. Therapeutic recommendations based on classical AB susceptibility testing (AST) are based on the analysis of only a fraction of the bacteria present in the disease process. Next and third generation sequencing technologies allow the identification of antimicrobial resistance genes (ARGs) present in a bacterial community. Using this metagenomic approach, we can map the antimicrobial resistance potential (AMRP) of a complex, multi-bacterial microbial sample. To understand the interpretiveness of AMRP, the concordance between phenotypic AMR properties and ARGs was investigated by analyzing data from 574 <i>Escherichia coli</i> strains of five different studies. The overall results show that for 44% of the studied ABs, phenotypically resistant strains are genotypically associated with a 90% probability of resistance, while for 92% of the ABs, the phenotypically susceptible strains are genotypically susceptible with a 90% probability. ARG detection showed a phenotypic prediction with at least 90% confidence in 67% of ABs. The probability of detecting a phenotypically susceptible strain as resistant based on genotype is below 5% for 92% of ABs. While the probability of detecting a phenotypically resistant strain as susceptible based on genotype is below 5% for 44% of ABs. We can assume that these strain-by-strain concordance results are also true for bacteria in complex microbial samples, and conclude that AMRP obtained from metagenomic ARG analysis can help choose efficient ABs. This is illustrated using AMRP by a canine external otitis sample.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"13 ","pages":"e18802"},"PeriodicalIF":2.3,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11784533/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143079906","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":"Correlation of diabetes and adverse outcomes in hospitalized COVID-19 patients admitted to a tertiary hospital in China during a small-scale COVID-19 outbreak.","authors":"Yu Li, Guanni Li, Jiahong Li, Zirui Luo, Yaxuan Lin, Ning Lan, Xiaodan Zhang","doi":"10.7717/peerj.18865","DOIUrl":"10.7717/peerj.18865","url":null,"abstract":"<p><strong>Background: </strong>The aim of this study was to investigate the impact of diabetes on mortality and adverse outcomes in COVID-19 patients and to analyse the associated risk factors.</p><p><strong>Methods: </strong>This is a retrospective cohort study in 500 hospitalized patients with COVID-19 infection (214 with diabetes and 286 without diabetes) admitted to a tertiary hospital in China from December 2022 to February 2023. Demographic information, clinical characteristics and outcomes were collected. Survival status was investigated at discharge and at 6 months after discharge.</p><p><strong>Results: </strong>The mortality rate of COVID-19 patients with diabetes was higher than the rate of non-diabetic COVID-19 patients, both at discharge, and at 6 months after discharge. Body mass index (BMI), C-reactive protein (CRP), pH, D-dimer, blood osmotic pressure, serum creatinine, white blood cell count, creatine kinase and hospitalization expenses were significantly different between diabetic group and non-diabetic group (<i>p</i> < 0.05). Compared with the survivors, non-survived COVID-19 patients with diabetes had worse diabetes control indicators, with random blood glucose increased by 3.58 mmol/L (<i>p</i> < 0.05), and fasting blood glucose increased by 2.77 mmol/L (<i>p</i> < 0.01). In addition, there were significant differences in age, heart rate, CRP, pH, potassium (K⁺), serum creatinine, white blood cell count, creatine kinase, the proportion with diabetic complications, treatment in ICU and mechanical ventilation between survivors and non-survivors of COVID-19 patients with diabetes. By multivariate logistic regression analysis, the death of COVID-19 patients with diabetes is positively correlated with age and CRP (<i>p</i> < 0.05), and has a trend towards significance with fasting blood glucose (<i>p</i> < 0.1).</p><p><strong>Conclusion: </strong>Infection with COVID-19 on the basis of diabetes can significantly increase mortality, which was further associated with diabetes control indicators.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"13 ","pages":"e18865"},"PeriodicalIF":2.3,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11781264/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143067154","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":"Clusters explaining the relation between menopause and self-reported periodontal disease: a cross-sectional study.","authors":"Hani T Fadel, Lujain A Qarah, Manal O Alharbi, Alla Al-Sharif, Doaa S Al-Harkan, Saba Kassim, Osama Abu-Hammad, Najla Dar-Odeh","doi":"10.7717/peerj.18861","DOIUrl":"10.7717/peerj.18861","url":null,"abstract":"<p><strong>Background: </strong>Menopause is an important milestone in the women's life continuum and is associated with potentially adverse effects, including those related to oral health. This study assessed self-reported periodontal disease in relation to menopausal status.</p><p><strong>Methods: </strong>A cross-sectional study involving a convenience sample of female university dental hospital attendees was conducted using a validated, self-administered, self-reported periodontal disease questionnaire. A two-step cluster analysis was used to categorize the participants based on menstrual period (MP) continuity, systemic diseases and age. Differences between clusters were analyzed using chi-square test.</p><p><strong>Results: </strong>From 112 included participants, three clusters resulted from the analysis: Cluster #1 (37 ± 8 years, no systemic diseases and continued MP), Cluster #2 (40 ± 10, with systemic diseases and continued MP) and Cluster #3 (54 ± 9, with systemic diseases and discontinued MP). Cluster #3 tended to have less optimal oral hygiene habits and more missing teeth (<i>p</i> > 0.05). Clusters #1 and #2 insignificantly reported more gingival bleeding, tooth sensitivity and calculus (<i>p</i> > 0.05). Cluster #3, on the other hand, presented with more self-reported oral dryness (<i>p</i> ≤ 0.05).</p><p><strong>Conclusions: </strong>Within study limits, clusters of menopausal women with systemic diseases reported high symptoms of periodontal disease that were not significantly different from younger individuals, with the exception of oral dryness.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"13 ","pages":"e18861"},"PeriodicalIF":2.3,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11781263/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143067135","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":"Super Partition: fast, flexible, and interpretable large-scale data reduction in R.","authors":"Katelyn J Queen, Malcolm Barrett, Joshua Millstein","doi":"10.7717/peerj.18580","DOIUrl":"10.7717/peerj.18580","url":null,"abstract":"<p><strong>Motivation: </strong>As data sets increase in size and complexity with advancing technology, flexible and interpretable data reduction methods that quantify information preservation become increasingly important.</p><p><strong>Results: </strong>Super Partition is a large-scale approximation of the original Partition data reduction algorithm that allows the user to flexibly specify the minimum amount of information captured for each input feature. In an initial step, Genie, a fast, hierarchical clustering algorithm, forms a super-partition, thereby increasing the computational tractability by allowing Partition to be applied to the subsets. Applications to high dimensional data sets show scalability to hundreds of thousands of features with reasonable computation times.</p><p><strong>Availability and implementation: </strong>Super Partition is a new function within the partition R package, available on the CRAN repository (https://cran.r-project.org/web/packages/partition/index.html).</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"13 ","pages":"e18580"},"PeriodicalIF":2.3,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11781262/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143067156","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}