bluuebunny/crossref_metadata_2025_split huggingface dataset:
Demographic and Clinical Factors Associated With SARS-CoV-2 Spike 1 Antibody Response Among Vaccinated US Adults: the C4R Study
Authors: Kim John S. , Sun Yifei , Balte Pallavi , Cushman Mary , Boyle Rebekah , Tracy Russell P. , Styer Linda M. , Bell Taison D. , Anderson Michaela R. , Allen Norrina B. , Schreiner Pamela J. , Bowler Russell P. , Schwartz David A. , Lee Joyce S. , Xanthakis Vanessa , Doyle Margaret F. , Regan Elizabeth A. , Make Barry J. , Kanaya Alka M. , Wenzel Sally E. , Coresh Josef , Isasi Carmen R. , Raffield Laura M. , Elkind Mitchell S. V. , Howard Virginia J. , Ortega Victor E. , Woodruff Prescott , Cole Shelley A. , Henderson Joel M. , Mantis Nicholas J. , Parker Monica M. , Demmer Ryan T. , Oelsner Elizabeth C. 
Published: February 2024

AbstractThis study investigates correlates of anti-S1 antibody response following COVID-19 vaccination in a U.S. population-based meta-cohort of adults participating in longstanding NIH-funded cohort studies. Anti-S1 antibodies were measured from dried blood spots collected between February 2021-August 2022 using Luminex-based microsphere immunoassays. Of 6245 participants, mean age was 73 years (range, 21-100), 58% were female, and 76% were non-Hispanic White. Nearly 52% of participants received the BNT162b2 vaccine and 48% received the mRNA-1273 vaccine. Lower anti-S1 antibody levels are associated with age of 65 years or older, male sex, higher body mass index, smoking, diabetes, COPD and receipt of BNT16b2 vaccine (vs mRNA-1273). Participants with a prior infection, particularly those with a history of hospitalized illness, have higher anti-S1 antibody levels. These results suggest that adults with certain socio-demographic and clinical characteristics may have less robust antibody responses to COVID-19 vaccination and could be prioritized for more frequent re-vaccination.
Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis
Authors: Mennillo Elvira , Kim Yang Joon , Lee Gyehyun , Rusu Iulia , Patel Ravi K. , Dorman Leah C. , Flynn Emily , Li Stephanie , Bain Jared L. , Andersen Christopher , Rao Arjun , Tamaki Stanley , Tsui Jessica , Shen Alan , Lotstein Madison L. , Rahim Maha , Naser Mohammad , Bernard-Vazquez Faviola , Eckalbar Walter , Cho Soo-jin , Beck Kendall , El-Nachef Najwa , Lewin Sara , Selvig Daniel R. , Terdiman Jonathan P. , Mahadevan Uma , Oh David Y. , Fragiadakis Gabriela K. , Pisco Angela , Combes Alexis J. , Kattah Michael G. 
Published: February 2024

AbstractUlcerative colitis (UC) is driven by immune and stromal subsets, culminating in epithelial injury. Vedolizumab (VDZ) is an anti-integrin antibody that is effective for treating UC. VDZ is known to inhibit lymphocyte trafficking to the intestine, but its broader effects on other cell subsets are less defined. To identify the inflammatory cells that contribute to colitis and are affected by VDZ, we perform single-cell transcriptomic and proteomic analyses of peripheral blood and colonic biopsies in healthy controls and patients with UC on VDZ or other therapies. Here we show that VDZ treatment is associated with alterations in circulating and tissue mononuclear phagocyte (MNP) subsets, along with modest shifts in lymphocytes. Spatial multi-omics of formalin-fixed biopsies demonstrates trends towards increased abundance and proximity of MNP and fibroblast subsets in active colitis. Spatial transcriptomics of archived specimens pre-treatment identifies epithelial-, MNP-, and fibroblast-enriched genes related to VDZ responsiveness, highlighting important roles for these subsets in UC.
Long-term exposure to ambient PM2.5, particulate constituents and hospital admissions from non-respiratory infection
Authors: Feng Yijing , Castro Edgar , Wei Yaguang , Jin Tingfan , Qiu Xinye , Dominici Francesca , Schwartz Joel 
Published: February 2024

AbstractThe association between PM2.5 and non-respiratory infections is unclear. Using data from Medicare beneficiaries and high-resolution datasets of PM2.5 and its constituents across 39,296 ZIP codes in the U.S between 2000 and 2016, we investigated the associations between annual PM2.5, PM2.5 constituents, source-specific PM2.5, and hospital admissions from non-respiratory infections. Each standard deviation (3.7-μg m−3) increase in PM2.5 was associated with a 10.8% (95%CI 10.8–11.2%) increase in rate of hospital admissions from non-respiratory infections. Sulfates (30.8%), Nickel (22.5%) and Copper (15.3%) contributed the largest weights in the observed associations. Each standard deviation increase in PM2.5 components sourced from oil combustion, coal burning, traffic, dirt, and regionally transported nitrates was associated with 14.5% (95%CI 7.6–21.8%), 18.2% (95%CI 7.2–30.2%), 20.6% (95%CI 5.6–37.9%), 8.9% (95%CI 0.3–18.4%) and 7.8% (95%CI 0.6–15.5%) increases in hospital admissions from non-respiratory infections. Our results suggested that non-respiratory infections are an under-appreciated health effect of PM2.5.
Timbral effects on consonance disentangle psychoacoustic mechanisms and suggest perceptual origins for musical scales
Authors: Marjieh Raja , Harrison Peter M. C. , Lee Harin , Deligiannaki Fotini , Jacoby Nori 
Published: February 2024

AbstractThe phenomenon of musical consonance is an essential feature in diverse musical styles. The traditional belief, supported by centuries of Western music theory and psychological studies, is that consonance derives from simple (harmonic) frequency ratios between tones and is insensitive to timbre. Here we show through five large-scale behavioral studies, comprising 235,440 human judgments from US and South Korean populations, that harmonic consonance preferences can be reshaped by timbral manipulations, even as far as to induce preferences for inharmonic intervals. We show how such effects may suggest perceptual origins for diverse scale systems ranging from the gamelan’s slendro scale to the tuning of Western mean-tone and equal-tempered scales. Through computational modeling we show that these timbral manipulations dissociate competing psychoacoustic mechanisms underlying consonance, and we derive an updated computational model combining liking of harmonicity, disliking of fast beats (roughness), and liking of slow beats. Altogether, this work showcases how large-scale behavioral experiments can inform classical questions in auditory perception.
Leisure engagement in older age is related to objective and subjective experiences of aging
Authors: Bone Jessica K. , Bu Feifei , Sonke Jill K. , Fancourt Daisy 
Published: February 2024

AbstractLeisure engagement has potential to slow health and functional decline in older age. However, the benefits of different leisure domains for different aspects of aging remains unclear. In 8771 older adults from the Health and Retirement Study (a longitudinal panel study), we measured engagement in physical, creative, cognitive, and community activities. Outcome-wide analyses used 23 aging experiences across seven domains eight years later (daily functioning, physical fitness, long-term physical health problems, heart health, weight, sleep, subjective perceptions of health). Physical activity was related to more positive experiences in all domains but heart health eight years later. Creative engagement was positively related to aging experiences in four domains longitudinally. Cognitive and community engagement were less consistently related to aging experiences. Physical and creative activities may influence important aging metrics, reducing age-related decline and keeping older adults functionally independent for longer, potentially limiting increasing healthcare costs.
Substrate promiscuity of inositol 1,4,5-trisphosphate kinase driven by structurally-modified ligands and active site plasticity
Authors: Márquez-Moñino María Ángeles , Ortega-García Raquel , Whitfield Hayley , Riley Andrew M. , Infantes Lourdes , Garrett Shane W. , Shipton Megan L. , Brearley Charles A. , Potter Barry V. L. , González Beatriz 
Published: February 2024

Abstractd-myo-inositol 1,4,5-trisphosphate (InsP3) is a fundamental second messenger in cellular Ca2+ mobilization. InsP3 3-kinase, a highly specific enzyme binding InsP3 in just one mode, phosphorylates InsP3 specifically at its secondary 3-hydroxyl group to generate a tetrakisphosphate. Using a chemical biology approach with both synthetised and established ligands, combining synthesis, crystallography, computational docking, HPLC and fluorescence polarization binding assays using fluorescently-tagged InsP3, we have surveyed the limits of InsP3 3-kinase ligand specificity and uncovered surprisingly unforeseen biosynthetic capacity. Structurally-modified ligands exploit active site plasticity generating a helix-tilt. These facilitated uncovering of unexpected substrates phosphorylated at a surrogate extended primary hydroxyl at the inositol pseudo 3-position, applicable even to carbohydrate-based substrates. Crystallization experiments designed to allow reactions to proceed in situ facilitated unequivocal characterization of the atypical tetrakisphosphate products. In summary, we define features of InsP3 3-kinase plasticity and substrate tolerance that may be more widely exploitable.
A neurophysiological basis for aperiodic EEG and the background spectral trend
Authors: Brake Niklas , Duc Flavie , Rokos Alexander , Arseneau Francis , Shahiri Shiva , Khadra Anmar , Plourde Gilles 
Published: February 2024

AbstractElectroencephalograms (EEGs) display a mixture of rhythmic and broadband fluctuations, the latter manifesting as an apparent 1/f spectral trend. While network oscillations are known to generate rhythmic EEG, the neural basis of broadband EEG remains unexplained. Here, we use biophysical modelling to show that aperiodic neural activity can generate detectable scalp potentials and shape broadband EEG features, but that these aperiodic signals do not significantly perturb brain rhythm quantification. Further model analysis demonstrated that rhythmic EEG signals are profoundly corrupted by shifts in synapse properties. To examine this scenario, we recorded EEGs of human subjects being administered propofol, a general anesthetic and GABA receptor agonist. Drug administration caused broadband EEG changes that quantitatively matched propofol’s known effects on GABA receptors. We used our model to correct for these confounding broadband changes, which revealed that delta power, uniquely, increased within seconds of individuals losing consciousness. Altogether, this work details how EEG signals are shaped by neurophysiological factors other than brain rhythms and elucidates how these signals can undermine traditional EEG interpretation.
Patterns in the temporal complexity of global chlorophyll concentration
Authors: Agarwal Vitul , Chávez-Casillas Jonathan , Inomura Keisuke , Mouw Colleen B. 
Published: February 2024

AbstractDecades of research have relied on satellite-based estimates of chlorophyll-a concentration to identify oceanographic processes and plan in situ observational campaigns; however, the patterns of intrinsic temporal variation in chlorophyll-a concentration have not been investigated on a global scale. Here we develop a metric to quantify time series complexity (i.e., a measure of the ups and downs of sequential observations) in chlorophyll-a concentration and show that seemingly disparate regions (e.g., Atlantic vs Indian, equatorial vs subtropical) in the global ocean can be inherently similar. These patterns can be linked to the regularity of chlorophyll-a concentration change and the likelihood of anomalous events within the satellite record. Despite distinct spatial changes in decadal chlorophyll-a concentration, changes in time series complexity have been relatively consistent. This work provides different metrics for monitoring the global ocean and suggests that the complexity of chlorophyll-a time series can be independent of its magnitude.
Stenus-inspired, swift, and agile untethered insect-scale soft propulsors
Authors: Ke Xingxing , Yong Haochen , Xu Fukang , Ding Han , Wu Zhigang 
Published: February 2024

AbstractMimicking living creatures, soft robots exhibit incomparable adaptability and various attractive new features. However, untethered insect-scale soft robots are often plagued with inferior controllability and low kinetic performance. Systematically inspired by the swift swingable abdomen, conducting canals for secretion transport, and body setae of Stenus comma, together with magnetic-induced fast-transformed postures, herein, we present a swift, agile untethered millimetre-scale soft propulsor propelling on water. The demonstrated propulsor, with a body length (BL) of 3.6 mm, achieved a recorded specific speed of ~201 BL/s and acceleration of ~8,372 BL/s2. The comprehensive kinetic performance of this propulsor surpasses those of previous ones at similar scales by several orders. Notably, we discovered momentum-transfer-induced over-biological on-demand braking (deceleration ~−5,010 BL/s2) and elucidated the underlying hydrodynamics. This work offers new insights into systematically bio-inspired artificial insect-scale soft robots, enabling them to push boundaries in performance, and potentially revolutionizing robot design, optimization, and control paradigms.
The intestinal digesta microbiota of tropical marine fish is largely uncultured and distinct from surrounding water microbiota
Authors: Soh Melissa , Tay Ywee Chieh , Lee Co Sin , Low Adrian , Orban Laszlo , Jaafar Zeehan , Seedorf Henning 
Published: February 2024

AbstractStudying the gut microbes of marine fishes is an important part of conservation as many fish species are increasingly threatened by extinction. The gut microbiota of only a small fraction of the more than 32,000 known fish species has been investigated. In this study we analysed the intestinal digesta microbiota composition of more than 50 different wild fish species from tropical waters. Our results show that the fish harbour intestinal digesta microbiota that are distinct from that of the surrounding water and that location, domestication status, and host intrinsic factors are strongly associated with the microbiota composition. Furthermore, we show that the vast majority (~97%) of the fish-associated microorganisms do not have any cultured representative. Considering the impact of the microbiota on host health and physiology, these findings underpin the call to also preserve the microbiota of host species, especially those that may be exposed to habitat destruction.
Synaptic dysfunction and extracellular matrix dysregulation in dopaminergic neurons from sporadic and E326K-GBA1 Parkinson’s disease patients
Authors: Rosh Idan , Tripathi Utkarsh , Hussein Yara , Rike Wote Amelo , Djamus Jose , Shklyar Boris , Manole Andreea , Houlden Henry , Winkler Jurgen , Gage Fred H. , Stern Shani 
Published: February 2024

AbstractParkinson’s disease (PD) is a neurodegenerative disease with both genetic and sporadic origins. In this study, we investigated the electrophysiological properties, synaptic activity, and gene expression differences in dopaminergic (DA) neurons derived from induced pluripotent stem cells (iPSCs) of healthy controls, sporadic PD (sPD) patients, and PD patients with E326K-GBA1mutations. Our results demonstrate reduced sodium currents and synaptic activity in DA neurons derived from PD patients with E326K-GBA1mutations, suggesting a potential contribution to PD pathophysiology. We also observed distinct electrophysiological alterations in sPD DA neurons, which included a decrease in synaptic currents. RNA sequencing analysis revealed unique dysregulated pathways in sPD neurons and E326K-GBA1neurons, further supporting the notion that molecular mechanisms driving PD may differ between PD patients. In agreement with our previous reports, Extracellular matrix and Focal adhesion pathways were among the top dysregulated pathways in DA neurons from sPD patients and from patients with E326K-GBA1mutations. Overall, our study further confirms that impaired synaptic activity is a convergent functional phenotype in DA neurons derived from PD patients across multiple genetic mutations as well as sPD. At the transcriptome level, we find that the brain extracellular matrix is highly involved in PD pathology across multiple PD-associated mutations as well as sPD.
Vitamin A deficiency impairs neutrophil-mediated control of Salmonella via SLC11A1 in mice
Authors: Lokken-Toyli Kristen L. , Diaz-Ochoa Vladimir E. , Camacho Lizbeth , Stull-Lane Annica R. , Van Hecke Amber E. R. , Mooney Jason P. , Muñoz Ariel D. , Walker Gregory T. , Hampel Daniela , Jiang Xiaowen , Labuda Jasmine C. , Depew Claire E. , McSorley Stephen J. , Stephensen Charles B. , Tsolis Renée M. 
Published: February 2024

AbstractIn sub-Saharan Africa, multidrug-resistant non-typhoidal Salmonella serovars are a common cause of fatal bloodstream infection. Malnutrition is a predisposing factor, but the underlying mechanisms are unknown. Here we show that vitamin A deficiency, one of the most prevalent micronutrient deficits afflicting African children, increases susceptibility to disseminated non-typhoidal Salmonella disease in mice and impairs terminal neutrophil maturation. Immature neutrophils had reduced expression of Slc11a1, a gene that encodes a metal ion transporter generally thought to restrict pathogen growth in macrophages. Adoptive transfer of SLC11A1-proficient neutrophils, but not SLC11A1-deficient neutrophils, reduced systemic Salmonella burden in Slc11a1−/− mice or mice with vitamin A deficiency. Loss of terminal granulopoiesis regulator CCAAT/enhancer-binding protein ϵ (C/EBPϵ) also decreased neutrophil-mediated control of Salmonella, but not that mediated by peritoneal macrophages. Susceptibility to infection increased in Cebpe−/−Slc11a1+/+ mice compared with wild-type controls, in an Slc11a1-expression-dependent manner. These data suggest that SLC11A1 deficiency impairs Salmonella control in part by blunting neutrophil-mediated defence.
On uniform stability and numerical simulations of complex valued neural networks involving generalized Caputo fractional order
Authors: Panda Sumati Kumari , Abdeljawad Thabet , Nagy A. M. 
Published: February 2024

AbstractThe dynamics and existence results of generalized Caputo fractional derivatives have been studied by several authors. Uniform stability and equilibrium in fractional-order neural networks with generalized Caputo derivatives in real-valued settings, however, have not been extensively studied. In contrast to earlier studies, we first investigate the uniform stability and equilibrium results for complex-valued neural networks within the framework of a generalized Caputo fractional derivative. We investigate the intermittent behavior of complex-valued neural networks in generalized Caputo fractional-order contexts. Numerical results are supplied to demonstrate the viability and accuracy of the presented results. At the end of the article, a few open questions are posed.
Interspecific recognition based on cuticular hydrocarbons mediates reproduction control in aphids
Authors: Li Yang , Parven Nousheen , Akimoto Shin-ichi 
Published: February 2024

AbstractThe preset study tested whether an aphid species can control its reproduction by recognizing the presence and density of a rival species. Acyrthosiphon pisum and Megoura crassicauda often coexist on the same leguminous plant. We established clonal colonies from each species and mixed colonies with one A. pisum and one M. crassicauda adult. There were no significant differences in the population growth patterns of the two species at 20 °C. However, mixed colonies increased faster and attained larger colony sizes than the clonal colonies. Thus, positive interspecific interactions were confirmed. A mixed colony was dominated by the members of a clone that produced a greater number of newborns in the initial stage, irrespective of the species. Thus, we confirmed the priority effect in the interspecific competition. To simulate the priority effect, 15 glass beads coated with the hexane extract of M. crassicauda aphids were attached to a cut leaf, to which one A. pisum adult was transferred. The presence of the hexane extract of M. crassicauda greatly reduced the reproductive rate of A. pisum adults. We conclude that aphids can control their reproduction by evaluating the relative density of rivals to fellow aphids based on the cuticular hydrocarbons.
Spatial linear transformer and temporal convolution network for traffic flow prediction
Authors: Xing Zhibo , Huang Mingxia , Li Wentao , Peng Dan 
Published: February 2024

AbstractAccurately obtaining accurate information about the future traffic flow of all roads in the transportation network is essential for traffic management and control applications. In order to address the challenges of acquiring dynamic global spatial correlations between transportation links and modeling time dependencies in multi-step prediction, we propose a spatial linear transformer and temporal convolution network (SLTTCN). The model is using spatial linear transformers to aggregate the spatial information of the traffic flow, and bidirectional temporal convolution network to capture the temporal dependency of the traffic flow. The spatial linear transformer effectively reduces the complexity of data calculation and storage while capturing spatial dependence, and the time convolutional network with bidirectional and gate fusion mechanisms avoids the problems of gradient vanishing and high computational cost caused by long time intervals during model training. We conducted extensive experiments using two publicly available large-scale traffic data sets and compared SLTTCN with other baselines. Numerical results show that SLTTCN achieves the best predictive performance in various error measurements. We also performed attention visualization analysis on the spatial linear transformer, verifying its effectiveness in capturing dynamic global spatial dependency.
Characterization of non-invasive oropharyngeal samples and nucleic acid isolation for molecular diagnostics
Authors: Hose Leonie , Schürmann Matthias , Mennebröcker Inga , Kim Rayoung , Busche Tobias , Goon Peter , Sudhoff Holger 
Published: February 2024

AbstractMolecular diagnostics is an increasingly important clinical tool, especially in routine sampling. We evaluated two non-invasive methods (oral swabs and mouthwashes) for sampling nucleic acids from the oral/pharyngeal area. We created a workflow from sample collection (n = 59) to RT-qPCR based analysis. The samples were further characterized in terms of their cellular composition as well as the purity, degradation and microbial content of the derived DNA/RNA. We determined the optimal housekeeping genes applicable for these types of samples. The cellular composition indicated that mouthwashes contained more immune cells and bacteria. Even though the protocol was not specifically optimized to extract bacterial RNA it was possible to derive microbial RNA, from both sampling methods. Optimizing the protocol allowed us to generate stable quantities of DNA/RNA. DNA/RNA purity parameters were not significantly different between the two sampling methods. Even though integrity analysis demonstrated a high level of degradation of RNA, corresponding parameters confirmed their sequencing potential. RT-qPCR analysis determined TATA-Box Binding Protein as the most favorable housekeeping gene. In summary, we have developed a robust method suitable for multiple downstream diagnostic techniques. This protocol can be used as a foundation for further research endeavors focusing on developing molecular diagnostics for the oropharyngeal cavity.