bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel approach to identify the fingerprint of stroke gait using deep unsupervised learning
Authors: David Sina , Georgievska Sonja , Geng Cunliang , Liu Yang , Punt Michiel 
Published: December 2024

AbstractBackgroundThe gait pattern results from a complex interaction of several body parts, orchestrated by the (central) nervous system that controls the active and passive systems of the body. An impairment of gait due to a stroke results in a decline in quality of life and independence. Setting up efficient gait training requires an objective and wholesome assessment of the patient’s movement pattern to target individual gait alterations. However, current assessment tools are limited in their ability to capture the complexity of the movement and the amount of data acquired during gait analysis.AimsIn this study, we explore the potential of variational autoencoders (VAE) to learn and recognise different gait patterns within both, pathologic and healthy gait.MethodsFor this purpose, the lower-limb joint angles of 71 participants (29 stroke survivors, 42 healthy controls) were used to train and test a VAE.ResultsThe good reconstruction results (range r = 0.52 - 0.91, average normalized RMSE 23.36 % ± 4.13) indicate that VAEs extract meaningful information from the gait pattern. Furthermore, the extracted latent features are sensitive enough to distinguish between the gait patterns of stroke survivors and a healthy cohort (p<0.001).ConclusionsThe presented approach allows the assessment of gait data in an objective and wholesome manner, thereby integrating the individual characteristics of each person’s gait, making it a suitable tool for monitoring the progress of rehabilitation efforts.
Probiotics and synbiotics administered to young infants: perceptions and acceptability amongst carers and healthcare workers in Western Kenya
Authors: Otiti Mary Iwaret , Achienge Florence , Zaim Sevim , Nabwera Helen , Kariuki Simon , Allen Stephen 
Published: December 2024

AbstractBackgroundA contributory factor to childhood undernutrition is poor gut health occurring within the first 6-12 weeks of life despite exclusive breast feeding. Pro/synbiotic administration may protect gut health. A qualitative study was conducted amongst mothers/carers and healthcare workers (HCWs) to explore their perceptions and the acceptability of pro/synbiotics administration in early life.MethodsThis study was nested within a randomised, open, clinical trial of pro/synbiotics with 32 doses administered under supervision to infants between age 0-5 months in western Kenya. Semi-structured interviews were conducted with mothers/carers, Peer Mothers and health care workers (HCWs) selected by purposive critical and key informant sampling. Interviews were transcribed and analysed using a thematic coding framework.FindingsSatisfaction with pro/synbiotic administration was very high amongst all three groups. Commonly perceived benefits included protection from diseases, healthy growth of the infant and improved appetite. The main barriers were working mothers and other commitments making it difficult to stick to scheduled administration visits, adverse judgment and opinions in the community and lack of engagement of fathers. Insights were gained into different means of administering pro/synbiotics to young infants. Triangulation of findings of the mothers/carers with HCWs showed that most identified motivations and challenges were similar.ConclusionsPro/synbiotic administration was well-accepted by mothers/carers and HCWs and generally perceived to have health benefits. Administration of pro/synbiotics by mothers/carers themselves to their infants may be feasible and overcome logistical challenges. Greater efforts to sensitise and engage fathers and communities would likely be critical for a community-based program.
Ten-Second Cold Water Stress Test Differentiates Parkinson’s Disease From Multiple System Atrophy: A Pilot Study
Authors: Takahashi Makoto , Hagiwara Wataru , Itaya Sakiko , Abe Keisuke , Maeda Tetsuya , Inaba Akira , Orimo Satoshi 
Published: December 2024

AbstractBackgroundPatients with Parkinson’s disease (PD) often have cold hands and experience frostbite. The diagnostic criteria for multiple system atrophy (MSA) also describe cold and discolored hands, but in our clinical experience we have noticed that the hands are relatively warm. These symptoms are thought to be caused by autonomic dysfunction; however, the detailed mechanisms and differences in cold hands between MSA and PD remain unclear.ObjectivesTo identify an appropriate cold stimulation test to differentiate patients with PD and MSA using finger surface temperature (FST).MethodsWe included 27 and seven patients diagnosed with PD and MSA, respectively, at least 5 years after disease onset. After 15 minutes in a room with constant temperature and humidity, the patient’s hand was placed in cold water at 4°C for 10 seconds as the cold water stress test (10sec-CWST). FST was captured using a thermal imaging camera every minute for 15 minutes, and the recovery of FST was analyzed. The association between the clinical characteristics of each patient and the degree of FST recovery was examined.ResultsAll patients completed the 10sec-CWST without adverse events. Patients with PD showed a significantly slower recovery of FST after 7 minutes than that of those with MSA, with a maximum difference at 11 minutes (PD: 8.1±0.6°C; MSA: 10.5±0.3°C; p<0.01). FST recovery at 11 minutes was negatively correlated with the degree of resting hand tremor (r=-0.585, p<0.01).ConclusionsFST after 10sec-CWST may be safe and efficient test to differentiate PD and MSA.
CARS2Hypermethylation Is a Risk Factor for Stage B Heart Failure and Hospitalizations in the Project Baseline Health Study
Authors: Regan Jessica A. , Franklin Jordan , Kottilil Kalyani , Cauwenberghs Nicholas , Mahaffey Kenneth W. , Douglas Pamela S. , Rodriguez Fatima , Haddad Francois , Hernandez Adrian F. , Shah Svati H. , Kwee Lydia Coulter ,   the Project Baseline Health Study Group
Published: December 2024

AbstractThe heart is a metabolically active organ with high energy demands that depend on mitochondrial oxidative phosphorylation, however as the heart begins to fail there is metabolic inflexibility and changes in mitochondrial function. Epigenetic changes such as DNA methylation can modify the transcription of genes essential for normal mitochondrial function, however this has not been studied in Stage B or pre-heart failure (HF). In 752 participants from the Project Baseline Health Study, we tested differences in DNA methylation in mitochondrial-related genes for association with Stage B HF compared to Stage A (at-risk for HF). We then validated these findings in 918 participants from the CATHGEN study for risk of incident HF hospitalization. One region on chromosome 13 overlapping with the cysteinyl-tRNA synthetase 2 (CARS2) gene, containing five cytosine-phosphate-guanine (CpG) probes, was significantly associated with a small mean regional increase in DNA methylation in Stage B HF (0.63%, Stouffer p=0.005). In CATHGEN, oneCARS2probe, cg08289839, was significantly associated with time-to-incident HF hospitalization (adjusted HR 1.74 [95% CI 1.18-2.56], FDR p=0.02). In this study of epigenetic changes of mitochondrial genes, these results indicate thatCARS2DNAm may play a role in HF pathogenesis and should be studied in future HF research.
TFClassPredict: A Novel Deep Learning Framework for Transcription Factor Binding Site Analysis Using Evolutionarily Conserved DNA-Binding Domain Annotations
Authors: Timucin Cigdem Hazal , Ickes Christian , Conrads Karly , Harms Bendix Christian , Beißbarth Tim , Haubrock Martin 
Published: December 2024

AbstractTranscription factors (TFs) are proteins that regulate gene expression by binding to short specific sequences in DNA. The binding of TFs to DNA is actualized through their DNA-binding domains (DBDs). The interactions between TFs and DNA are fundamental for understanding gene regulation mechanisms, which form the basis of many cellular activities and processes. While many models have been developed to predict TF binding, there is a lack of a comprehensive model that accounts for the similarity of binding characteristics of TFs within the same DBD families. Our model, TFClassPredict, introduces a novel approach to identify transcription factor binding sites (TFBSs) based on the structural annotations of evolutionarily conserved DNA-binding domains (DBDs). By leveraging strong canonical binding patterns, TFClassPredict provides high-confidence predictions that are crucial for reliable regulatory analysis. By fine-tuning the DNABERT model, TFClassPredict was developed to classify DNA sequences across different hierarchical levels, with 6 Superclasses at the top level and 17 more specific Class-level annotations, reflecting different degrees of DBD similarity. TFClassPredict achieved high performance across both hierarchical levels, with an average AUC of 0.988, precision of 0.942, and recall of 0.906 at the SuperClass level, and an average AUC of 0.990, precision of 0.937, and recall of 0.914 at the Class-level. TFClassPredict demonstrated its ability to reveal distinct regulatory landscapes associated with cancer progression. The Class-level model is publicly available for use and can be accessed athttps://gitlab.gwdg.de/hti/tfclass_dnabert.
Inferring phenotypes of single cells based on the expression profiles of phenotype-associated marker genes in bulks and single cells
Authors: He Yin , Long Rongzhuo , Zhao Li , Wang Xiaosheng 
Published: December 2024

AbstractSingle-cell transcriptomes is advantageous in characterizing cell types and states, but not sufficient in describing cell phenotypes due to small cohorts in single-cell datasets. Thus, inferring single-cell phenotypes with the leverage of bulk data is practical. Here we proposed an algorithm for Single Cells’ Phenotype Prediction based on the expression profiles of phenotype-associated marker genes in bulks and single cells (ScPP). ScPP first analyzes bulk data to identify phenotype-associated marker genes. Next, ScPP evaluates the enrichment scores of the phenotype-associated marker gene sets in single cells using the AUCell algorithm. The single cells with the phenotype are defined as the intersection of the single cells with top α ranks according to the phenotype-associated AUC values and the single cells with bottom α ranks according to the opposite phenotype-associated AUC values. Finally, all single cells are determined as phenotype+, phenotype- or background. We demonstrated that ScPP could effectively recognize cell subpopulations with specific phenotypes, including tumor malignancy, estrogen receptor status, microsatellite instability, copy number variation, survival and immunotherapy response. Compared to the established algorithms (Scissor and scAB), ScPP displays more excellent predictive performance and needs less running time. Thus, ScPP is an effective and competitive tool for inferring cell phenotypes.
Thymic involution as an adaptive schedule for combating diverse pathogens
Authors: Iwasa Yoh , Matsuo Kosei 
Published: December 2024

AbstractDiverse naive T cells, produced in the thymus, migrate to peripheral tissues and help suppress pathogens upon activation. As we age, the thymus shrinks, reducing both the supply and diversity of naive T cells, which increases the time required to establish immunity against new pathogens. This process, called thymic involution, is considered a form of aging. In this study, we explore whether thymic involution might be an adaptive strategy. Over time, the immune system accumulates memory cells, reducing the need for new naive T cells to combat unfamiliar pathogens. We examine how the optimal rate of naive T cell production,h(t), declines with age, taking into account the cost of maintaining thymic activity. When pathogen encounter rates are equal,h(t) decreases exponentially with age. As pathogen encounter rates rise, the initial valueh(0) increases, but the rate declines more rapidly with age, reducing overall production. A higher pathogen diversity, a greater cost of fighting new pathogens, and a lower cost of maintenance increaseh(t). When pathogen encounter rates vary,h(t) decreases with age according to a power function.HighlightsThe thymus generates diverse naive T cells to recognize a wide range of pathogens.Thymic involution is considered an adaptive strategy, factoring in maintenance cost.If pathogen encounters are frequent, the rate starts high but quickly declines.The rate increases with the pathogen risk and decreases with the thymic cost.If pathogens vary in abundances, the rate decreases as a power function of age.
A comparison study between liquid- and vapor-fed anode zero-gap bioelectrolysis cells
Authors: Rohbohm Nils , Angenent Largus T. 
Published: December 2024

AbstractImproving microbial electrosynthesis could be one solution for transitioning towards sustainable chemical production, offering a pathway to convert CO2into valuable commodities from renewable energy sources. Therefore, we examined the performance differences between liquid- and vapor-fed anode zero-gap bioelectrochemical cells for electromethanogenesis, utilizing a membrane electrode assembly to enhance mass and ohmic transport. Focusing on CH4and H2production, we compared two ion-exchange membranes with the liquid-fed anode system and selected the best performing ion-exchange membrane for the vapor-fed anode system. Liquid-fed anode systems did not show significant differences in volumetric CH₄ production rates compared to vapor-fed anode systems, although the latter demonstrated advantages in reducing electrocatalyst degradation and maintaining stable cell voltages. The research underscores the need for further optimization to address performance losses and suggests potential for industrial applications of microbial electrosynthesis, highlighting the importance of catalyst protection.
Lifespan costs of reproduction increase during the Great Finnish Famine
Authors: Young Euan A. , Postma Erik , Lummaa Virpi , Dugdale Hannah L. 
Published: December 2024

ABSTRACTEvolutionary theory of aging predicts that women with increased reproductive effort live shorter lives, but evidence is inconsistent. These inconsistencies could be because environmental conditions influence how much reproductive behavior shapes a mother’s lifespan, i.e. their lifespan cost of reproduction. Using a structural equation measurement model, we compare how reproductive effort affects lifespan of 4,684 women exposed across different life-stages, or not at all, to the Great Finnish Famine. We find that lifespan costs of reproduction became higher in mothers exposed to the famine during reproduction, and for these mothers amounted to a decreased life expectancy of ~0.5 years per child. Conversely, reproductive behavior did not shape the lifespans of mothers not exposed to the famine, or exposed post-reproduction or during development. These results suggest environment-dependent reproductive costs, which provides a biological explanation for previous inconsistent findings, and demonstrate how reproductive behavior can be an important determinant of human lifespan.
Inflammatory Monocytes Increase Prior to Detectable HIV-1 Rebound Viremia
Authors: Farrell-Sherman Anna , de la Force Natalia , Prator Cecila , Valieris Renan , Azam Walker , Da Silva Israel , Deeks Steven G. , Thanh Cassandra , Bosch Ronald , Henrich Timothy J. , Cohn Lillian 
Published: December 2024

AbstractThe persistence of HIV-1 proviruses in latently infected cells allows viremia to resume upon treatment cessation. To characterize the resulting immune response, we compare plasma proteomics and single-cell transcriptomics of peripheral blood mononuclear cells (PBMCs) before, during, and after detectable plasma viremia. We observe unique transcriptional signatures prior to viral rebound including a significant increase in CD16++monocytes with increased anti-viral gene expression. Inflammatory proteins were identified in plasma after detectable rebound. Identifying early signals of imminent viral rebound after treatment cessation will aid in the development of strategies to prolong time to viral rebound and cure HIV-1.
Afadin-deficient retinas exhibit severe neuronal lamination defects but preserve visual functions
Authors: Ueno Akiko , Sakuta Konan , Ono Hiroki , Tokumoto Haruki , Watanabe Mikiya , Nishimoto Taketo , Konishi Toru , Mizuno Shunsuke , Miyoshi Jun , Takai Yoshimi , Tachibana Masao , Koike Chieko 
Published: December 2024

ABSTRACTNeural lamination is a common feature of the central nervous system (CNS), with several subcellular structures, such as adherens junctions (AJs), playing a role in this process. The retina is also heavily laminated, but it remains unclear how laminar formation impacts retinal cell morphology, synapse integrity, and overall retinal function. In this study, we demonstrate that the loss of afadin, a key component of AJs, leads to significant pathological changes. These include the disruption of outer retinal lamination and a notable decrease as well as mislocalization of photoreceptors, their outer segments, and photoreceptor synapses. Interestingly, despite these severe impairments, we recorded small local field potentials, including the a- and b-waves. We also classified ganglion cells into ON, ON-OFF, and OFF types based on their firing patterns in response to light stimuli. Additionally, we successfully characterized the receptive fields of certain retinal ganglion cells. Overall, these findings provide the first evidence that retinal circuit function can be partially preserved even when there are significant disruptions in retinal lamination and photoreceptor synapses. Our results indicate that retinas with severely altered morphology still retain some capacity to process light stimuli.
Afadin Sorts Different Retinal Neuron Types into Accurate Cellular Layers
Authors: Lum Matthew R. , Patel Sachin H. , Graham Hannah K. , Zhao Mengya , Yi Yujuan , Li Liang , Yao Melissa , La Torre Anna , Santina Luca Della , Han Ying , Hu Yang , Welsbie Derek S. , Duan Xin 
Published: December 2024

ABSTRACTNeurons use cell-adhesion molecules (CAMs) to interact with other neurons and the extracellular environment: the combination of CAMs specifies migration patterns, neuronal morphologies, and synaptic connections across diverse neuron types. Yet little is known regarding the intracellular signaling cascade mediating the CAM recognitions at the cell surface across different neuron types. In this study, we investigated the neural developmental role of Afadin1–4, a cytosolic adapter protein that connects multiple CAM families to intracellular F-actin. We introduced the conditional Afadin mutant5to an embryonic retinal Cre, Six3-Cre6–8. We reported that the mutants lead to the scrambled retinal neuron distribution, including Bipolar Cells (BCs), Amacrine Cells (ACs), and retinal ganglion cells (RGCs), across three cellular layers of the retina. This scrambled pattern was first reported here at neuron-type resolution. Importantly, the mutants do not display deficits for BCs, ACs, or RGCs in terms of neural fate specifications or survival. Additionally, the displayed RGC types still maintain synaptic partners with putative AC types, indicating that other molecular determinants instruct synaptic choices independent of Afadin. Lastly, there is a significant decline in visual function and mis-targeting of RGC axons to incorrect zones of the superior colliculus, one of the major retinorecipient areas. Collectively, our study uncovers a unique cellular role of Afadin in sorting retinal neuron types into proper cellular layers as the structural basis for orderly visual processing.
Cross comparison of imaging strategies of mitochondria inC. elegansduring aging
Authors: Kim Juri , Dutta Naibedya , Vega Matthew , Bong Andrew , Averbuhk Maxim , Barahona Rebecca Aviles , Alcala Athena , Holmes Jacob T. , Garcia Gilberto , Higuchi-Sanabria Ryo 
Published: December 2024

AbstractMitochondria are double membrane-bound organelles with pleiotropic roles in the cell, including energy production through aerobic respiration, calcium signaling, metabolism, proliferation, immune signaling, and apoptosis. Dysfunction of mitochondria is associated with numerous physiological consequences and drives various diseases, and is one of twelve biological hallmarks of aging, linked to aging pathology. There are many distinct changes that occur to the mitochondria during aging including changes in mitochondrial morphology, which can be used as a robust and simple readout of mitochondrial quality and function. Although mitochondrial morphology alone cannot be used to conclude the quality of mitochondria, it is highly correlated with mitochondrial function whereby mitochondria exhibit increased fragmentation with age in multiple cell types of the nematodeC. elegans.Thus,C. elegansserve as a robust model for rapidly measuring mitochondrial morphology changes during aging. To standardize imaging methods for mitochondrial morphology inC. elegans, we provide a detailed comparative characterization of several transgenic constructs, highlighting benefits and caveats for aging biology studies.Summary BlurbThis study evaluates mitochondrial imaging inC. elegansduring aging, comparing various transgenic constructs for tissue-specific mitochondrial visualization. The findings highlight technical considerations, imaging method standardization, and the utility ofC. elegansas a robust model for studying mitochondrial dynamics.
Entrepreneurial leadership and employee performance; the role of innovative work behavior among employees in the food and beverages industry
Authors: Adu Isaac Nyarko , Boakye Kwame Owusu , Yeboah Samuel , Twumasi Evelyn 
Published: December 2024

PurposeThis study seeks to examine the mediating role of innovative work behavior (IWB) in the relationship between entrepreneurial leadership (EL) and employee performance.Design/methodology/approachThe study adopted the cross-sectional research design of quantitative approach where data were collected from 344 employees in Ghana’s food and beverages industry. The retrieved data were analyzed using descriptive and inferential statistics (partial least squares structural equation modeling).FindingsMainly, the study revealed that IWB positively and significantly mediated the relationship between EL and contextual and task performance (TP). The study found that EL has a significant positive relationship with task and contextual performance (CP). This indicates that leaders who demonstrate entrepreneurial qualities, such as innovation, proactiveness and risk-taking, are likely to enhance their team’s ability to complete specific tasks effectively (TP) and contribute positively to the broader organizational environment (CP).Practical implicationsPractically, organizations that prioritize EL qualities among managers and supervisors in the form of providing training programs, coaching and mentorship opportunities that emphasize innovation, risk-taking and pro-activeness in decision-making significantly influence their employee performance.Originality/valueThe originality and value of this study lie in its comprehensive exploration of the relationship between EL, IWB and performance outcomes.