bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Hierarchical Model for eDNA Fate and Transport Dynamics Accommodating Low Concentration Samples
Authors: Augustine Ben C. , Hutchins Patrick R. , Jones Devin N. , Williams Jacob R. , Leinonen Eric , Sepulveda Adam J. 
Published: April 2024

AbstractEnvironmental DNA (eDNA) sampling is an increasingly important tool for answering ecological questions and informing aquatic species management; however, several factors currently limit the reliability of ecological inference from eDNA sampling. Two particular challenges are 1) determining species source location(s) and 2) accurately and precisely measuring low concentration eDNA samples in the presence of multiple sources of ecological and measurement variability. The recently introduced eDNA Integrating Transport and Hydrology (eDITH) model provides a framework for relating eDNA measurements to source locations in riverine networks, but little empirical work has been done to test and refine model assumptions or accommodate low concentration samples, that can be systematically undermeasured. To better understand eDNA fate and transport dynamics and our ability to reliably quantify low concentration samples, we developed a hierarchical model and used it to evaluate a fate and transport experiment. Our model addresses several low concentration challenges by modeling the number of copies in each PCR replicate as a latent variable with a count distribution and conditioning detection and quantification on replicate copy number. We provide evidence that the eDNA removal rate declined through time, estimating that over 80% of eDNA was removed over the first 10 meters, traversed in 41 seconds. After this initial period of rapid decay, eDNA decayed slowly with consistent detection through our farthest site 1km from the release location, traversed in 250 seconds. Our model further allowed us to detect extra-Poisson variation in the allocation of copies to replicates. We extended our hierarchical model to accommodate a continuous effect of inhibitors and used our model to provide evidence for the inhibitor hypothesis and explore the potential implications. While our model is not a panacea for all challenges faced when quantifying low-concentration eDNA samples, it provides a framework for a more complete accounting of uncertainty.
Learning from Machine Learning: advancing from static to dynamic facial function quantification
Authors: Kalavacherla Sandhya , Mills Morgan Davis , Greene Jacqueline J. 
Published: April 2024

AbstractObjectivesWe assess an open-source Python machine learning algorithm’s efficacy in image and video analysis of facial palsy (FP) patients.MethodsImages and videos of 60 patients with varying FP severities performing standard movements were obtained from MEEI Facial Palsy database. Landmarks generated on images by the open-source algorithm (adapted from OpenCV and Dlib libraries) and Emotrics (standard for two-dimensional FP analysis) were compared. Considering the human eye as the standard for accuracy, three raters marked perceived errors in each algorithm’s tracking of five facial features. Cumulative error distributions between both algorithms were compared via normalized root mean square error. FP severity and facial feature-specific error rates were compared using ANOVA tests. Raters also analyzed open-source algorithm-generated video landmarks; similar statistical comparisons between open-source algorithms’ image and video-based analyses were performed.ResultsCumulative error distribution between both algorithms’ image analyses was most robust for normal function; significant discrepancies were observed in mild/moderate flaccidity and nearly-normal/complete synkinesis. Both algorithms had similar error rates across all facial features (p=0.76) and FP severities (p=0.37). In the open-source algorithm’s video analysis, mild synkinesis (24.7%) and severe flaccidity (19.7%) had the highest error rates. Comparing image and video analyses generated by the open-source algorithm, video analyses had lower error rates across all FP severities (p<0.001).ConclusionsWe report for the first time the feasibility and relative accuracy of a Python open-source algorithm for dynamic facial landmark tracking in FP videos. The demonstrated superiority of landmark tracking with videos over images can improve objective FP quantification.
SLIRP promotes autoimmune diseases by amplifying antiviral signaling via positive feedback regulation
Authors: Ku Doyeong , Yang Yewon , Park Youngran , Jang Daesong , Lee Namseok , Lee Yong-ki , Lee Keonyong , Lee Jaeseon , Han Yeon Bi , Jang Soojin , Choi Se Rim , Ha You-Jung , Choi Yong Seok , Jeong Woo-Jin , Lee Yun Jong , Lee Kyung Jin , Cha Seunghee , Kim Yoosik 
Published: April 2024

SUMMARYThe abnormal innate immune response is a prominent feature underlying autoimmune diseases. One emerging factor that can trigger dysregulated immune activation is cytosolic mitochondrial double-stranded RNAs (mt-dsRNAs). However, the mechanism by which mt-dsRNAs stimulate immune responses remains poorly understood. Here, we discover SRA stem-loop interacting RNA binding protein (SLIRP) as a key amplifier of mt-dsRNA-triggered antiviral signals. In autoimmune diseases, SLIRP is commonly upregulated, and targeted knockdown of SLIRP dampens the interferon response. We find that the activation of melanoma differentiation-associated gene 5 (MDA5) by exogenous dsRNAs upregulates SLIRP, which then stabilizes mt-dsRNAs and promotes their cytosolic release to activate MDA5 further, augmenting the interferon response. Furthermore, the downregulation of SLIRP partially rescues the abnormal interferon-stimulated gene expression in autoimmune patients’ primary cells and makes cells vulnerable to certain viral infections. Our study unveils SLIRP as a pivotal mediator of interferon response through positive feedback amplification of antiviral signaling.
A method for recognizing motor imagery EEG signals based on high-quality lead selection
Authors: Du Xiuli , Wang Hanxing , Kong Meiya , Xi Meiling , Lv Yana 
Published: April 2024

AbstractIn the application of motor imagery brain-computer interface system, high-density leads bring redundant noise, which leads to time-consuming system operation and poor performance. A channel selection strategy based on brain function network is proposed. This method introduces Synchronization likelihood was used as a connection index to construct a motor imagery brain functional network, and the centrality analysis of the constructed network was used to select the combination of strong motor-related leads. Experiments were carried out on the EEG datasets dataset IVa of the 3rd International Brain-Computer Interface Competition and dataset I of the 4th International Brain-Computer Interface Competition, and 27 high-quality channels were selected from the 118 channels of dataset IVa, as well as 16 high-quality channels were selected from the 59 channels of dataset I. Finally, the CSP algorithm and support vector machine are used to extract features and classify. The experimental results show that the proposed channel selection strategy can greatly reduce the number of channels while obtaining higher recognition accuracy, which verifies the practicability and effectiveness of the proposed method.
Facilitators and barriers in the use of the electronic consultation register for Integrated Management of Childhood Illness in the health district of Toma, Burkina Faso: Perspectives of health care providers
Authors: Patrice Ngangue , Issaka Saouadogo , Safiata Kaboré Soutongnoma , Douglas Mbang Massom , Nestor Bationo , Seu Josiane , Ly Birama Apho 
Published: April 2024

AbstractBackgroundIn collaboration with the Ministry of Health and Public Hygiene (MHPH) of Burkina Faso (BF), the Foundation Terre des Hommes (Tdh) has developed the Integrated e-Diagnostic Approach (IeDA) project in BF since 2010 to strengthen the health system by digitalizing medical protocols, improving the quality of services and using data. We sought to identify and analyze the barriers and facilitators of using the electronic clinic registry (ECR) for the integrated management of childhood illness (IMCI) by healthcare providers (HCPs) in the health district of Toma, BF.MethodsWe conducted a descriptive and exploratory qualitative study. In-depth individual interviews were conducted with thirty-five (35) HCPs in the health district of Toma, BF, from the 1stto the 30thof December 2021. Thematic analysis of qualitative data according to the Braun & Clarke model was performed using NVivo 12 software and arranged along a social-ecological model.ResultsOur findings revealed that HCPs play an essential role in using ECR for IMCI. Many key facilitating factors have emerged regarding the use of IMCIs in primary health care (PHC) facilities, such as positive perceptions of the ECR, firm commitment and the involvement of HCPs, stakeholder support, collaborative networks with implementing partners, convenience, privacy, confidentiality and client trust, experience and confidence in using the system, and the satisfaction, motivation and competency of staff. In addition, the easy diagnosis offered by the ECR and the training of HCPs increased the acceptance and use of the ECR. Regarding barriers, HCPs complained about the tablet’s slowness, recurrent breakdowns, and increased workload.ConclusionThis study revealed that ECR has excellent potential to improve the quality of care and, in turn, reduce maternal and infant mortality. Although the satisfaction of the HCPs with the tool is positive, the actors of the Foundation Tdh, in collaboration with the MHPH, must work to optimize the application’s performance and reduce breakdowns and delays during consultations. This will allow the deployment of ECR in all BF health districts.
iGTP: Learning interpretable cellular embedding for inferring biological mechanisms underlying single-cell transcriptomics
Authors: Hsieh Kang-Lin , Zhang Kai , Chu Yan , Yu Lishan , Li Xiaoyang , Hu Nuo , Kawosa Isha , Pilié Patrick G. , Bhattacharya Pratip K. , Zhi Degui , Jiang Xiaoqian , Zhao Zhongming , Dai Yulin 
Published: April 2024

AbstractDeep-learning models like Variational AutoEncoder have enabled low dimensional cellular embedding representation for large-scale single-cell transcriptomes and shown great flexibility in downstream tasks. However, biologically meaningful latent space is usually missing if no specific structure is designed. Here, we engineered a novel interpretable generative transcriptional program (iGTP) framework that could model the importance of transcriptional program (TP) space and protein-protein interactions (PPI) between different biological states. We demonstrated the performance of iGTP in a diverse biological context using gene ontology, canonical pathway, and different PPI curation. iGTP not only elucidated the ground truth of cellular responses but also surpassed other deep learning models and traditional bioinformatics methods in functional enrichment tasks. By integrating the latent layer with a graph neural network framework, iGTP could effectively infer cellular responses to perturbations. Lastly, we applied iGTP TP embeddings with a latent diffusion model to accurately generate cell embeddings for specific cell types and states. We anticipate that iGTP will offer insights at both PPI and TP levels and holds promise for predicting responses to novel perturbations.
A deep generative model integrating single-cell time-frequency characteristics transformed from electrophysiological data with transcriptomic features
Authors: Furumichi Kazuki , Kojima Yasuhiro , Nomura Satoshi , Shimamura Teppei 
Published: April 2024

AbstractPatch-seq yields multi-modal data (e.g., transcriptomic and electrophysiological data) from single cells. However, currently used analytical methods are based on a few global electrophysiological features predefined from chronological potential changes and overlook the importance of time-frequency domain. In this study, we present LincSpectr, a deep neural network model that integrates transcriptomic and electrophysiological features with the latent variables of various variational autoencoders. This model combines the two modalities according to the connection between the latent variables of different modalities calculated by attention-like mechanisms and achieves cross-modal predictions and an inverse analysis. We discovered that the predicted electrophysiological features changed continuously along with their transcriptional profiles and that the neighborhood relationships between the latent states of the transcriptional profiles were consistent with those of the electrophysiological features. Inverse analysis of our model enabled the extraction of gene sets affecting specific time-frequency domains; some genes were likely to be involved in neural activity. Our approach represents a potential avenue to facilitate the discovery of molecular mechanisms underlying time-frequency activities in various cell types, enhancing our understanding of their roles in neural function.
Water deficit response in nodulated soybean roots: a comprehensive transcriptome and translatome network analysis
Authors: Sainz María Martha , Filippi Carla V , Eastman Guillermo , Sotelo-Silveira Mariana , Zardo Sofía , Martínez-Moré Mauro , Sotelo-Silveira José , Borsani Omar 
Published: April 2024

AbstractSoybean establishes a mutualistic interaction with nitrogen-fixing rhizobacteria, acquiring most of its nitrogen requirements through symbiotic nitrogen fixation. This crop is susceptible to water deficit; evidence suggests that its nodulation status—whether it is nodulated or not— can influence how it responds to water deficit. The translational control step of gene expression has proven relevant in plants subjected to water deficit. Here, we analyzed soybean roots’ differential responses to water deficit at transcriptional, translational, and mixed (transcriptional + translational) levels. Thus, the transcriptome and translatome of four combined-treated soybean roots were analyzed. We found hormone metabolism-related genes among the differentially expressed genes (DEGs) at the translatome level in nodulated and water-restricted plants. Also, weighted gene co-expression network analysis followed by differential expression analysis identified gene modules associated with nodulation and water deficit conditions. Protein-protein interaction network analysis was performed for subsets of mixed DEGs of the modules associated with the plant responses to nodulation, water deficit, or their combination. Our research reveals that the stand-out processes and pathways in the before-mentioned plant responses partially differ; terms related to glutathione metabolism and hormone signal transduction (2C protein phosphatases) were associated with the response to water deficit, terms related to transmembrane transport, response to abscisic acid, pigment metabolic process were associated with the response to nodulation plus water deficit. Still, two processes were common: galactose metabolism and branched-chain amino acid catabolism. A comprehensive analysis of these processes could lead to identifying new sources of tolerance to drought in soybean.
Extracellular electron transfer drives efficient H2-independent methylotrophic methanogenesis byMethanomassiliicoccus,a seventh order methanogen
Authors: Li Lingyan , Tian Xuping , Wang Xuemeng , Chen Chuan , Zhou Qi , Qi Lei , Li Jie , Xue Kai , Zhao Fangjie , Wang Yanfen , Dong Xiuzhu 
Published: April 2024

AbstractMethylotrophic methanogenesis is achieved via methyl group dismutation or H2reduction. This study reports extracellular electron droving efficient methylotrophic methanogenesis. The 7thorder methanogenMethanomassiliicoccus luminyensisexclusively implements H2-dependent methylotrophic methanogenesis, but strain CZDD1 isolated from paddy soil possessed a higher methane-producing rate in coculture withClostridium malenominatumCZB5 or the electrogenicGeobacter metallireducens.Chronoamperometry detected current production from CZB5, and current consumption accompanied CH4production in a methanol-containing electrochemical culture of CZDD1. This demonstrated thatM. luminyensiswas capable of both direct species electron transfer (DIET) and extracellular electron transfer (EET) in methylotrophic methanogenesis. EET and DIET also enabled CZDD1 to produce methane from dimethyl arsenate. Differential transcriptomic analysis on H2-versus EET- and DIET-cocultures suggested that a membrane-bound Fpo-like complex and archaella ofM. luminyensisCZDD1 could accept extracellular electrons. Given the ubiquitous environmental distribution ofMethanomassiliicoccusstrains, EET driven methylotrophic methanogenesis may contribute significantly to methane emission.
Gender, interdisciplinary graduate training, and confidence working in teams
Authors: Lu Lesa Tran , Blake Laura Palucki , Eyler Josh R. , Verduzco Rafael , Biswal Sibani Lisa , Bennett George N. , Silberg Jonathan J. 
Published: April 2024

AbstractTeamwork is recognized as critical to solving complex societal challenges related to energy, health, and sustainability. With graduate education, students often gain teamwork experience through a problem-focused approach where they are brought into existing collaborations to pursue research that is focused on studying questions that have already been identified. Here, we describe an interdisciplinary educational program where graduate students were tasked with leading team formation, problem identification, and research formulation. This “team-first” training approach used a two-year curriculum to bring together students enrolled in diverse engineering and science graduate programs and provided students with a pedagogical understanding of interdisciplinarity, nurtured the development of student communication skills across disciplines, fostered student-led team formation and idea development, and empowered students to forge new connections between research groups. Assessment of three cohorts immediately following curriculum completion (n = 36) revealed significant gains in confidence in teamwork (p < 0.001) when compared to a control group of academic peers (n = 74). These gains varied across demographic groups, with women in science, technology, engineering, and mathematics presenting the strongest gains. This finding illustrates the importance of exploring how interdisciplinary team curricula in graduate school could support overcoming the gender gap in confidence.SignificancePedagogical models for graduate education often neglect the importance of teamwork training. Here, we describe an interdisciplinary training program that was developed to bring together doctoral students from diverse science, technology, engineering, and mathematics disciplines for a two-year curriculum that focused on teamwork training through student-led team formation, problem identification, and research formulation. Following program participation, we measured participant confidence in teamwork relative to a peer group. Our findings reveal gains with confidence in teamwork, with women presenting the strongest increases without negative effects on other groups. This pedagogical approach represents a strategy to close gender gaps in professional role confidence while complementing the benefits of traditional disciplinary training approaches.
Patch-walking: Coordinated multi-pipette patch clamp for efficiently finding synaptic connections
Authors: Yip Mighten C. , Gonzalez Mercedes M. , Lewallen Colby F. , Landry Corey R. , Kolb Ilya , Yang Bo , Stoy William M. , Fong Ming-fai , Rowan Matthew J.M. , Boyden Edward S. , Forest Craig R. 
Published: April 2024

SummarySignificant technical challenges exist when measuring synaptic connections between neurons in living brain tissue. The patch clamping technique, when used to probe for synaptic connections, is manually laborious and time-consuming. To improve its efficiency, we pursued another approach: instead of retracting all patch clamping electrodes after each recording attempt, we cleaned just one of them and reused it to obtain another recording while maintaining the others. With one new patch clamp recording attempt, many new connections can be probed. By placing one pipette in front of the others in this way, one can “walk” across the tissue, termed “patch-walking.” We performed 136 patch clamp attempts for two pipettes, achieving 71 successful whole cell recordings (52.2%). Of these, we probed 29 pairs (i.e., 58 bidirectional probed connections) averaging 91µm intersomatic distance, finding 3 connections. Patch-walking yields 80-92% more probed connections, for experiments with 10-100 cells than the traditional synaptic connection searching method.MotivationRecognizing the manual labor and time-intensive nature of patch clamping when trying to find synaptic connections, we aim to improve its efficiency. We introduce a novel approach, termed “patch-walking,” where one patch clamping electrode is cleaned and reused, enabling the exploration of numerous connections with a single recording attempt and improving the efficiency of identifying synaptic connections.
Can Current Medical Examination Consumption Reduce Long-term Medical Expenses? - Analysis Based on CHARLS Data
Authors: Luo Juan , San Lulu , Han Sunian , Bi Liang , Ren Zhenpeng 
Published: April 2024

AbstractBackgroundWith the implementation of the healthy China strategy, physical examination, a means of preventing diseases, has gradually been valued by health care department. Can health examination effectively alleviate the pressure on residents’ medical expenses?MethodBased on the CHARLS2015 and CHARLS2018 databases, establishing an ordered multi-classification logistic regression model. To study the impact of residents’ health examination on the level of long-term medical expenditure.ResultsThe results show that adhere to health examination, long-term physical exercise and quit smoking and drinking can reduce residents’ medical expenses. The physical examination behavior of different populations was further discussed based on gender. The study found that the more physical examinations of male residents, the less medical expenses, while the number of physical examinations of women is not significant for reduce medical expenses.ConclusionTherefore, China should vigorously improve the enthusiasm of different residents to participate in health check-ups, give full play to health check-ups in disease prevention and to reduce individual’s medical expenses.