bluuebunny/crossref_metadata_2025_split huggingface dataset:
Domestication and evolutionary histories of specialized gut symbionts across cephalotine ants
Authors: Cabuslay Christian , Wertz John T. , Béchade Benoît , Hu Yi , Braganza Sonali , Freeman Daniel , Pradhan Shreyansh , Mukhanova Maria , Powell Scott , Moreau Corrie , Russell Jacob A. 
Published: July 2024

AbstractThe evolution of animals and their gut symbionts is a complex phenomenon, obscured by lability and diversity. In social organisms, transmission of symbionts among relatives may yield systems with more stable associations. Here, we study the history of a social insect symbiosis involving cephalotine ants and their extracellular gut bacteria, which come predominantly from host‐specialized lineages. We perform multi‐locus phylogenetics for symbionts from nine bacterial orders, and map prior amplicon sequence data to lineage‐assigned symbiont genomes, studying distributions of rigorously defined symbionts across 20 host species. Based on monophyly and additional hypothesis testing, we estimate that these specialized gut bacteria belong to 18 distinct lineages, of which 15 have been successfully isolated and cultured. Several symbiont lineages showed evidence for domestication events that occurred later in cephalotine evolutionary history, and only one lineage was ubiquitously detected in all 20 host species and 48 colonies sampled with amplicon 16S rRNA sequencing. We found evidence for phylogenetically constrained distributions in four symbionts, suggesting historical or genetic impacts on community composition. Two lineages showed evidence for frequent intra‐lineage co‐infections, highlighting the potential for niche divergence after initial domestication. Nearly all symbionts showed evidence for occasional host switching, but four may, more often, co‐diversify with their hosts. Through our further assessment of symbiont localization and genomic functional profiles, we demonstrate distinct niches for symbionts with shared evolutionary histories, prompting further questions on the forces underlying the evolution of hosts and their gut microbiomes.
Spatial variation in genomic signatures of local adaptation during the cane toad invasion of Australia
Authors: Beer Marc A. , Trumbo Daryl R. , Rautsaw Rhett M. , Kozakiewicz Christopher P. , Epstein Brendan , Hohenlohe Paul A. , Alford Ross A. , Schwarzkopf Lin , Storfer Andrew 
Published: July 2024

AbstractAdaptive evolution can facilitate species' range expansions across environmentally heterogeneous landscapes. However, serial founder effects can limit the efficacy of selection, and the evolution of increased dispersal during range expansions may result in gene flow swamping local adaptation. Here, we study how genetic drift, gene flow and selection interact during the cane toad's (Rhinella marina) invasion across the heterogeneous landscape of Australia. Following its introduction in 1935, the cane toad colonised eastern Australia and established several stable range edges. The ongoing, more rapid range expansion in north‐central Australia has occurred concomitant with an evolved increase in dispersal capacity. Using reduced representation genomic data of Australian cane toads from the expansion front and from two areas of their established range, we test the hypothesis that high gene flow constrains local adaptation at the expansion front relative to established areas. Genetic analyses indicate the three study areas are genetically distinct but show similar levels of allelic richness, heterozygosity and inbreeding. Markedly higher gene flow or recency of colonisation at the expansion front have likely hindered local adaptation at the time of sampling, as indicated by reduced slopes of genetic‐environment associations (GEAs) estimated using a novel application of geographically weighted regression that accounts for allele surfing; GEA slopes are significantly steeper in established parts of the range. Our work bolsters evidence supporting adaptation of invasive species post‐introduction and adds novel evidence for differing strengths of evolutionary forces among geographic areas with different invasion histories.
Genomic stress in diseases stemming from defects in the second brain
Authors: Mombeek Lobke Marie M. , Boesmans Werend , Wilson David M. 
Published: July 2024

AbstractThis review discusses the less‐explored realm of DNA damage and repair within the enteric nervous system (ENS), often referred to as the “second brain.” While the central nervous system has been extensively studied for its DNA repair mechanisms and associated neuropathologies, the ENS, which can autonomously coordinate gastrointestinal function, experiences unique challenges and vulnerabilities related to its genome integrity. The susceptibility of the ENS to DNA damage is exacerbated by its limited protective barriers, resulting in not only endogenous genotoxic exposures, such as oxidative stress, but also exogenous threats, such as ingested environmental contaminants, local inflammatory responses, and gut dysbiosis. Here, we discuss the evidence for DNA repair defects in enteric neuropathies, most notably, the reported relationship between inherited mutations in RAD21 and LIG3 with chronic intestinal pseudo‐obstruction and mitochondrial gastrointestinal encephalomyopathy disorders, respectively. We also introduce the lesser‐recognized gastrointestinal complications in DNA repair syndromes, including conditions like Cockayne syndrome. The review concludes by pointing out the potential role of DNA repair defects in not only congenital disorders but also aging‐related gut dysfunction, as well as the crucial need for further research to establish direct causal links between DNA damage accumulation and ENS‐specific pathologic phenotypes.
Deep learning‐based hyperspectral technique identifies metastatic lymph nodes in oral squamous cell carcinoma—A pilot study
Authors: Li Qingxiang , Zhang Xueyu , Zhang Jianyun , Huang Hongyuan , Li Liangliang , Guo Chuanbin , Li Wei , Guo Yuxing 
Published: July 2024

AbstractAimsTo establish a system based on hyperspectral imaging and deep learning for the detection of cancer cells in metastatic lymph nodes.Main MethodsThe continuous sections of metastatic lymph nodes from 45 oral squamous cell carcinoma (OSCC) patients were collected. An improved ResUNet algorithm was established for deep learning to analyze the spectral curve differences between cancer cells and lymphocytes, and that between tumor tissue and normal tissue.Key FindingsIt was found that cancer cells, lymphocytes, and erythrocytes in the metastatic lymph nodes could be distinguished basing hyperspectral image, with overall accuracy (OA) as 87.30% and average accuracy (AA) as 85.46%. Cancerous area could be recognized by hyperspectral image and deep learning, and the average intersection over union (IOU) and accuracy were 0.6253 and 0.7692, respectively.SignificanceThis study indicated that deep learning‐based hyperspectral techniques can identify tumor tissue in OSCC metastatic lymph nodes, achieving high accuracy of pathological diagnosis, high work efficiency, and reducing work burden. But these are preliminary results limited to a small sample.
Prediction of proliferative diabetic retinopathy using machine learning in Latino and non‐Hispanic black cohorts with routine blood and urine testing
Authors: Goldstein Ayelet , Ding Kun , Carasquillo Onelys , Levine Barton , Hasan Aisha , Levine Jonathan 
Published: July 2024

AbstractPurposeThe objective was to predict proliferative diabetic retinopathy (PDR) in non‐Hispanic Black (NHB) and Latino (LA) patients by applying machine learning algorithms to routinely collected blood and urine laboratory results.MethodsElectronic medical records of 1124 type 2 diabetes patients treated at the Bronxcare Hospital eye clinic between January and December 2019 were analysed. Data collected included demographic information (ethnicity, age and sex), blood (fasting glucose, haemoglobin A1C [HbA1c] high‐density lipoprotein [HDL], low‐density lipoprotein [LDL], serum creatinine and estimated glomerular filtration rate [eGFR]) and urine (albumin‐to‐creatinine ratio [ACR]) test results and the outcome measure of retinopathy status. The efficacy of different machine learning models was assessed and compared. SHapley Additive exPlanations (SHAP) analysis was employed to evaluate the contribution of each feature to the model's predictions.ResultsThe balanced random forest model surpassed other models in predicting PDR for both NHB and LA cohorts, achieving an AUC (area under the curve) of 83%. Regarding sex, the model exhibited remarkable performance for the female LA demographic, with an AUC of 87%. The SHAP analysis revealed that PDR‐related factors influenced NHB and LA patients differently, with more pronounced disparity between sexes. Furthermore, the optimal cut‐off values for these factors showed variations based on sex and ethnicity.ConclusionsThis study demonstrates the potential of machine learning in identifying individuals at higher risk for PDR by leveraging routine blood and urine test results. It allows clinicians to prioritise at‐risk individuals for timely evaluations. Furthermore, the findings emphasise the importance of accounting for both ethnicity and sex when analysing risk factors for PDR in type 2 diabetes individuals.
A novel approach to calculate the required volume of air for bronchial blockers in young children
Authors: Zhu Change , Zhang Saiji , Zhang Mazhong , Wei Rong 
Published: July 2024

AbstractIntroductionBronchial blocker balloons inflated with small volumes of air increase balloon pressure, involving a risk of airway injury especially in young children. However, there are no established guidelines regarding the appropriate volumes of air required to provide safe bronchial occlusion.MethodsThis study aimed to introduce a novel method for calculating the amount of air required for safe bronchial blocker balloon occlusion for one lung anesthesia in young children. We included 79 pediatric patients who underwent video‐assisted thoracoscopic surgery at our hospital. Preoperatively, the balloon pressure and corresponding diameter of 5F bronchial blockers inflated with different volumes of air were measured. Intraoperatively, bronchial diameters measured by computerized tomographic scans were matched to the ex vivo measured balloon diameters. The quality of lung isolation, incidence of balloon repositioning, and airway injury were documented. Postoperatively, airway injury was evaluated through fiberoptic bronchoscopy.ResultsBalloon pressure and balloon diameter showed linear and nonlinear correlations with volume, respectively. The median lengths of the right and left mainstem bronchi were median (interquartile range) range: 5.3 mm (4.5–6.3) 2.7–8.15 and 21.8 (19.6–23.4) 14–29, respectively. Occluding the left mainstem bronchus required <1 mL of air, with a balloon pressure of 27 cm H2O. The isolation quality was high with no case of mucosal injury or displacement. Occluding the right mainstem bronchus required a median air volume of 1.3 mL, with a median balloon pressure of 44 cm H2O. One patient had poor lung isolation due to a tracheal bronchus and another developed mild and transient airway injury.ConclusionThe bronchial blocker cuff should be regarded as a high‐pressure balloon. We introduced a new concept for safe bronchial blocker balloon occlusion for one‐lung ventilation in small children.
Psychosis and help‐seeking behaviour–A systematic review of the literature
Authors: Skrobinska Laura , Newman‐Taylor Katherine , Carnelley Katherine 
Published: July 2024

AbstractPurposeMany people with psychosis do not seek help which delays access to recommended treatments. Duration of untreated psychosis is associated with poor healthcare outcomes and increased risk of relapse. The reasons why people delay accessing treatment remain unclear. This is the first systematic review to synthesise the literature examining professional and non‐professional help‐seeking in psychosis across clinical and subclinical populations.MethodsWe searched four databases (APA PsycINFO, APA PsycArticles, Medline and British Library EThOS) to generate a comprehensive account of the quantitative literature. Heterogeneity of measures precluded a meta‐analysis.ResultsWe identified 19 articles (including 9686 participants) that met criteria for the review. Help‐seeking in psychosis is associated with being female, having a higher level of education, and experiencing more than one symptom. People with psychosis report stigma, poor mental health literacy and lack of family support as key barriers. Clinicians report childhood physical abuse, insecure attachment and severity of psychosis as additional barriers. We also found differences in preferred sources of help across cultures. There is currently no consensus on reliable help‐seeking measures.ConclusionsThis is the first systematic review to examine help‐seeking behaviour in psychosis. Assertive and culturally sensitive engagement efforts should be targeted towards people with a history of early adversity, poor mental health literacy, limited social support and more severe psychosis.
The stem cell niche transcription factor ETHYLENE RESPONSE FACTOR 115 participates in aluminum‐induced terminal differentiation in Arabidopsis roots
Authors: Larsen Paul B. , He Shiyang , Meyer Taylor J. , Szurman‐Zubrzycka Miriam , Alfs Carolin , Kwasniewska Jolanta , Pervis Alexandra , Gajecka Monika , Veerabahu Aishwarya , Beaulieu Taylor R. , Bolaris Stephen C. , Eekhout Thomas , De Veylder Lieven , Abel Steffen , Szarejko Iwona , Murn Jernej 
Published: July 2024

AbstractAluminum‐dependent stoppage of root growth requires the DNA damage response (DDR) pathway including the p53‐like transcription factor SUPPRESSOR OF GAMMA RADIATION 1 (SOG1), which promotes terminal differentiation of the root tip in response to Al dependent cell death. Transcriptomic analyses identified Al‐induced SOG1‐regulated targets as candidate mediators of this growth arrest. Analysis of these factors either as loss‐of‐function mutants or by overexpression in the als3‐1 background shows ERF115, which is a key transcription factor that in other scenarios is rate‐limiting for damaged stem cell replenishment, instead participates in transition from an actively growing root to one that has terminally differentiated in response to Al toxicity. This is supported by a loss‐of‐function erf115 mutant raising the threshold of Al required to promote terminal differentiation of Al hypersensitive als3‐1. Consistent with its key role in stoppage of root growth, a putative ERF115 barley ortholog is also upregulated following Al exposure, suggesting a conserved role for this ATR‐dependent pathway in Al response. In contrast to other DNA damage agents, these results show that ERF115 and likely related family members are important determinants of terminal differentiation of the root tip following Al exposure and central outputs of the SOG1‐mediated pathway in Al response.
The Global Adolescent Fertility Decline is Counteracted by Increasing Teen Births in Sub‐Saharan Africa
Authors: Spoorenberg Thomas , Carlsen Ellen Øen , Flatø Martin , Stonawski Marcin , Skirbekk Vegard 
Published: July 2024

AbstractThere is a lack of understanding of the persistence of elevated teen fertility rates in certain regions and countries, in contrast to the significant decline observed in other regions globally. This report considers fertility trends among 15‐ to 19‐year olds in the period 1950–2020 and explores potential driving factors behind the significant shifts that occurred over this period. The countries where teen fertility remains high are those with fast‐growing populations, primarily located in sub‐Saharan Africa. Countries with higher teen fertility are typically characterized by limited use of modern contraception, lower education levels, and early marriage. Sub‐Saharan Africa has emerged as the world region with the most teen births, increasing its proportion of global teen births from 12 percent in 1950 to 47 percent in 2020, a time during which this region's share of the global adolescent (15–19) population grew from 7.5 percent to 19 percent. By 2035, 67 percent of all teen births globally are projected to occur in this region. Consequently, the future number of births to teenage mothers will to a large extent depend on the development in sub‐Saharan Africa over the coming decades.
Future temporal reference in spoken world Englishes
Authors: Bartels Birgit , Szmrecsanyi Benedikt 
Published: July 2024

AbstractThis study investigates how language‐internal constraints regulate the future temporal reference (FTR) alternation across nine varieties of English around the world. We specifically marshal Variation‐Based Distance & Similarity Modeling (VADIS) to calculate distances between the varieties under study as a function of the non‐correspondence of the ways in which language users choose between FTR variants. Our linguistic data come from the spoken component of the International Corpus of English: the dataset covers 500 future marker observations per variety of English (Ntotal = 4500), richly annotated for seven language‐internal constraints (such as polarity and sentence type). VADIS uncovers a number of probabilistic grammar differences between the varieties of English under study, which are subsequently correlated with four language‐external distance measures: geographical distance, travel time distance, population size and GDP per capita. Mantel correlation analysis shows that language‐internal distances do not correlate with language‐external distances.
Enhancing Efficiency in Collision Avoidance: A Study on Transfer Reinforcement Learning in Autonomous Ships’ Navigation
Authors: Wang Xinrui , Jin Yan 
Published: July 2024

Abstract
Collision avoidance in ships and robotic vehicles exemplifies a complex work process that necessitates effective scenario recognition and precise movement decision-making. Machine learning methods addressing such work processes generally involve learning from scratch, which is not only time-consuming but also demands significant computational resources. Transfer learning emerges as a potent strategy to enhance the efficiency of these engineering work processes by harnessing previously acquired knowledge from analogous tasks, thereby streamlining the learning curve for new challenges. This research delves into two critical questions central to optimizing transfer reinforcement learning for the work process of collision avoidance: (1) Which process features can be successfully transferred across varying work processes? (2) What methodologies support the efficient and effective transfer of these features? Our study employs simulation-based experiments in ship collision avoidance to address these questions, chosen for their intrinsic complexity and the varied feature recognition it demands. We investigate and compare two transfer learning techniques—feature extraction and finetuning—utilizing a lightweight convolutional neural network (CNN) model pretrained on a base case of a comparable work process. Pixel-level visual input is leveraged to cover different numbers of encountering ships and fix the input size for the model. This model adeptly demonstrates the feasibility of transferring essential features to newer work process scenarios. Further, to enhance realism and applicability, we introduce a simplified yet comprehensive ship dynamic model that considers the substantial effects of ship inertia, thereby refining the interaction between the model and its environment. The response time is embedded into the reward function design to be considered for policy training. Experimental outcomes underscore the transferability of diverse process features and evaluate the relative effectiveness of the employed transfer methods across different task settings, offering insights that could be extrapolated to other engineering work processes.
Swirler Design Parameter Impact on Lean Blowout, Pressure Loss, and Flame Liftoff
Authors: DeMarco Kevin J. , Polanka Marc D. , Bohan Brian T. 
Published: July 2024

Abstract
Swirl stabilized combustion is a common technique used in gas turbine engine combustors and is accomplished by introducing swirl into the inlet flow, which enhances mixing and stabilizes the combustion event. Coaxial swirlers introduce the fuel and air axially through concentric inlets and use vanes to impart a tangential component to either the fuel, air, or both flows. The present study conducted a parametric analysis of coaxial swirler design by manufacturing an array of 14 coaxial swirlers scaled for use in low flow, small engine operations which incorporated the same base design but varied the swirl number, Sn, by changing the vane angle between 0 deg and 63 deg, vane count between four and ten, and vane shape between traditional and helical. Each design was experimentally evaluated using nonpremixed air and propane at different flow conditions to correlate swirler design with lean blowout limits, pressure loss, and flame liftoff. Lean blowout was primarily influenced by swirl number, while vane count and shape had significant impact at Sn = 0.8 but little impact at Sn = 1.5. Pressure loss was unchanged below a Sn of 0.6, and unlike lean blowout, Sn had little impact at 0.8 but significant impact at 1.5. Additionally, an initial equation correlating pressure loss with swirler number, vane count, and mass flowrate was developed. Finally, flame liftoff was mainly driven by swirl number, with vane count and shape the next significant design parameters.
Experimental Study on Nonlinear Development Process of Oil-Filled Equipment Fire Under External Fire Source
Authors: Zhang Zhizhen , Zheng Xin , Yang Haiming , Chen Xuan , Chen Peng 
Published: July 2024

Abstract
The transformer is the key oil-filled equipment in the power system, and its fire behavior seriously affects the safe operation of the power grid. In this article, to analyze the fire development process and combustion behavior of oil-filled equipment, a mesoscale model of transformer equipment was constructed, and fire simulation experiments of transformer equipment under the action of external ignition sources were conducted. The flame temperature, flame height, heat release rate, oil temperature, and pressure were measured. The experimental results show that the oil-filled equipment fire presents the characteristics of nonlinear development. The fire can be divided into three stages: the ignition stage, the stable growth stage, and the combustion mutation stage. The transformer oil near the wall is pyrolyzed by the external heat source, and the combustible gas and transformer oil form a gas–liquid two-phase flow, which is the main reason for the nonlinear development of oil-filled equipment fires. The experimental results are of great significance for the safe operation and fire control of power system oil-filled equipment.