bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterizing particle dynamics in live imaging through stochastic physical models and machine learning
Authors: Nardi G. , Sano M. Santos , Bilay M. , Brelot A. , Olivo-Marin J.-C. , Lagache T. 
Published: December 2024

AbstractParticle dynamics determine the orchestration of molecular signaling in cellular processes. A wide range of subdiffusive motions has been described at the cell interior and membrane, corresponding to different environmental constraints. However, the standard methods for motion analysis, embedded in a diffusion-based framework, lack robustness for capturing the complexity of stochastic dynamics. This work develops a classification method to detect the five main stochastic laws modeling particle dynamics accurately. The method builds on machine-learning techniques that use features properly designed to capture the intrinsic geometric properties of trajectories governed by the different processes. This guarantees the accurate classification of observed dynamics in an interpretable and explainable framework. The main asset of this approach is its capability to distinguish different subdiffusive behaviors making it a privileged tool for biological investigations. The robustness to localization error and motion composition is proven, ensuring its reliability on experimental data. Moreover, the classification of composed trajectories is investigated, showing that the method can uncover the path’s mono-vs bi-dynamics nature. The method is used to study the dynamics of membrane receptors CCR5, involved in HIV infection. Comparing the basal state to an agonist-bound state which displays potent anti-HIV-1 activity, we show that the latter affects the natural dynamic state of receptors, thus clarifying the link between movement and receptor activation.
Ready-to-load MHC-I Nanoparticles for High-throughput T cell Screening Studies
Authors: Phan Hoang Anh T. , Hwang Daniel , Young Michael C. , Sun Shirley M. , Monos Dimitri S. , Sgourakis Nikolaos G. 
Published: December 2024

AbstractMHC-I proteins present epitopic peptides to CD8+ T cells to elicit multifaceted adaptive immune responses. The affinity and avidity of interactions between peptide-MHC molecules and T-cell receptors (TCR) are fundamental parameters that contribute to the induction of activated or anergic T cell states. Here, we present a loadable system, VLP-Open HLA, featuring a virus-like particle (VLP) that can accommodate up to 60 loadable HLA (HLA – human leukocyte antigen) molecules. HLA nanoparticles, pre-loaded with a placeholder ligand, allow efficient peptide exchange upon incubation with target peptides. We show that fluorescently tagged VLP-Open HLA particles can be used to stain antigen-specific CD8+ T cells, providing a screening tool for novel TCRs. Finally, we demonstrate that our system can induce activation of T cells in an antigen-specific manner. Our platform can be adapted to encompass multiple HLA allotypes and co-stimulatory molecules as mosaic nanoparticles, to enable a range of applications in experimental immunology.
Activation and signaling characteristics of the hydroxy-carboxylic acid 3 receptor identified in human neutrophils through a microfluidic flow cell technique
Authors: Forsman Huamei , Li Wenyan , Levin Neele K. , Karlsson Roger , Karlsson Anders , Dahlgren Claes , Sundqvist Martina 
Published: December 2024

AbstractHuman neutrophils express numerous G protein-coupled receptors (GPCRs) of importance for immune regulation. Several of the functionally known neutrophil GPCRs, are not part of the human neutrophil proteome. To identify GPCRs not earlier shown to be expressed in human neutrophils, we utilized a microfluidic flow cell technique in combination with subcellular granule fractionation and liquid chromatography-tandem mass spectrometry (LC-MS/MS). This approach added the hydroxy-carboxylic acid 3 receptor (HCA3R) to the human neutrophil proteome. The β-oxidation intermediate 3-hydroxy-octanoic acid (3-OH-C8) is the primary endogenous agonist for this receptor which is highly expressed in adipocytes where it has anti-lipolytic effects. Literature describing the role and function of HCA3R in human neutrophils is scarce. We now show that 3-OH-C8 as well the synthetic HCA3R agonist IBC 293 activate human neutrophils determined as an increase in the intracellular concentration of free calcium ions ([Ca2+]i) and activation of the NADPH oxidase. However, in contrast to the rise in [Ca2+]iwhich could be triggered in naïve neutrophils, pre-treatment of neutrophils was required for HCA3Rs to activate the NADPH oxidase. That is, the HCA3R-mediated NADPH oxidase activation occurred only in neutrophils pre-treated with either an actin cytoskeleton disrupter or an allosteric modulator targeting the GPCR termed free fatty acid receptor 2 (FFA2R). Our findings demonstrate that HCA3R is not only a new member of the human neutrophil proteome, but also exhibits functional activity with complex signaling pathways when stimulated with endogenous and synthetic HCA3R agonists.
Association of Epigenetic Age Acceleration with Early Stage Heart Failure: Sex-Specific Effects in the Project Baseline Health Study
Authors: Ashar Perisa , Cauwenberghs Nicholas , Kottilil Kalyani , Chatterjee Ranee , Pagidipati Neha , Douglas Pamela S. , Plowman R. Scooter , Hernandez Adrian F. , Mahaffey Kenneth W. , Haddad Francois , Shah Svati H. , Kwee Lydia Coulter ,   the Project Baseline Health Study Group
Published: December 2024

AbstractBackgroundEpigenetic age acceleration (EAA), defined as blood DNA methylation-derived biological age exceeding chronological age, has emerged as a potential biomarker of cardiovascular health and disease. EAA has been associated with symptomatic heart failure (HF); however, its connection to early-stage HF remains unclear. Moreover, the association of EAA with cardiovascular disease may differ by sex.MethodsWe analyzed participants from the Project Baseline Health Study, a deeply-phenotyped longitudinal cohort. HF staging was performed using echocardiographic measures and clinical criteria, classifying participants into stage 0/B0 (no HF risk factors), stage A (HF risk factors only, without structural cardiac abnormalities), and stage B1 (structural changes without HF symptoms). EAA was calculated as the residual of Horvath methylation epigenetic age regressed on chronological age. We compared EAA across HF stages using ANOVA models adjusted for sex, and in secondary analyses, investigated associations between EAA and echocardiographic parameters as well as sex-specific differences.ResultsAmong 1,338 participants (mean age: 49.2±15.4 years; 53.5% female), 41.7% were stage 0/B0 (n=558), 39.4% were stage A (n=527), and 18.9% were stage B1 (n=253). EAA tended to differ across HF stages (p=0.07), with higher EAA in stage B1 participants compared to those in stage 0/B0 or A. Sex-stratified models suggested that this trend was more pronounced in males than females. Among individual echocardiographic parameters, greater left ventricular posterior wall thickness was associated with higher EAA (p=0.046). In analyses restricted to stage A and B1 participants, higher EAA in B1 approached significance only in males (p=0.051).ConclusionsThese findings suggest that elevated EAA may occur even in the early, asymptomatic stages of HF, potentially reflecting underlying biological aging processes associated with early cardiac structural abnormalities. The effects may be sex-specific, with males showing a stronger relationship between EAA and stage B1 HF. Although validation through larger, longitudinal studies is necessary, our results support EAA as a potential biomarker for early cardiovascular risk assessment and underscore the need of considering sex differences in early HF pathophysiology.
Functional outcome, return to work and quality of life in patients with non-aneurysmal subarachnoid hemorrhage
Authors: Dronkers Wouter J. , Germans Menno R. , Post René , Coert Bert A. , Coutinho Jonathan M. , van den Berg René , Vandertop W. Peter , Verbaan Dagmar 
Published: December 2024

AbstractBackgroundNon-aneurysmal, non-traumatic subarachnoid hemorrhage (nSAH) refers to cases where a causative aneurysm cannot be identified. We studied six-months’ outcomes in nSAH patients.MethodsFrom a prospective SAH registry of all nSAH patients admitted between 2012 and 2023, relevant complications and outcomes were collected. Functional outcome and return-to-work at six months were assessed using the modified Rankin Scale (mRS), quality of life with the EuroQol-5Dimensions (EQ-5D) and Hospital Anxiety & Depression Scale (HADS), and an institutional 14-item questionnaire for assessment of residual symptoms.Results325 consecutive nSAH patients were included (191 non-perimesencephalic, non-aneurysmal subarachnoid hemorrhage [NPSAH]; 134 perimesencephalic subarachnoid hemorrhage [PMSAH]). 303 (93%; 179 NPSAH and 124 PMSAH) were available at follow-up (7 patients died). Favorable functional outcome (mRS-score 0-2) was reported in 271 (89%) patients and did not differ between NPSAH- and PMSAH. 141 (77%) patients returned to work, whereas only 71 (39%) patients reached their previous level of work. PMSAH patients were more likely to return to work (68/96 (71%) NPSAH and 73/87 (84%) PMSAH, respectively, p=0.01). Furthermore, PMSAH patients were more likely to fully return to work (p=.034). The mean (SD) EQ-5D and EQ-VAS scores were 0.827 (0.184) and 74 (16), respectively. The HADS-A and -D scores were deviant (score >7 points) in 53 (23%) and 48 (21%) patients, respectively. Only 39 patients (16%) denied experiencing residual symptoms. Increased fatigue (n=164; 68%), increased concentration difficulties (n=130; 54%), and increased forgetfulness (n=121; 50%) were the most frequently reported residual symptoms.ConclusionsThis study reveals that the majority of nSAH patients reports residual symptoms and did not return to their previous level of work at six months follow-up, despite a favorable functional outcome. These findings nuance the perception of a good outcome, as suggested in previous studies, warranting further research on possible rehabilitative interventions and counseling in these patients.
Assessing the impact of whole genome duplication on gene expression and regulation during arachnid development
Authors: Aase-Remedios Madeleine E. , Leite Daniel J. , Janssen Ralf , McGregor Alistair P. 
Published: December 2024

AbstractWhole genome duplication (WGD) generates new genetic material that can contribute to the evolution of the regulation of developmental processes and phenotypic diversification. A WGD occurred in an ancestor of arachnopulmonates (spiders, scorpions, and their relatives), which provides an important independent comparison to WGDs in other animal lineages like those in vertebrates and horseshoe crabs. After WGD, arachnopulmonates retained many duplicated copies (ohnologues) of developmental genes including clusters of homeobox genes, many of which have been inferred to have undergone subfunctionalisation. However, there has been little systematic analysis of gene regulatory sequences and comparison of the expression of ohnologues versus their single-copy orthologues between arachnids. Here we compare the regions of accessible chromatin and gene expression of ohnologues and single-copy genes during three embryonic stages between an arachnopulmonate arachnid, the spiderParasteatoda tepidariorum, and a non-arachnopulmonate arachnid, the harvestmanPhalangium opilio. We found that the expression of each spider ohnologue was lower than their single-copy orthologues in the harvestman providing evidence for subfunctionalisation. However, this was not reflected in a reduction in peaks of accessible chromatin because both spider ohnologues and single-copy genes had more peaks than the harvestman genes. We also found peaks of open chromatin that increased in the late stage associated with activation of genes expressed later during embryogenesis in both species. Taken together, our study provides the first genome-wide comparison of gene regulatory sequences and gene expression in arachnids and thus provides new insights into the impact of the arachnopulmonate WGD.Significance statementThe comparison of independent WGD events is essential to understanding their evolutionary outcomes. Here we examine gene expression and chromatin accessibility during the development of two arachnids, one of which underwent an ancient WGD. Our data provide the first direct comparison of the regulation of ohnologues and single-copy genes in arachnids.
Standardized methods for rearing a moth larva,Manduca sexta, in a laboratory setting
Authors: Spencer Emma K. , Miller Craig R. , Bull James 
Published: December 2024

AbstractThe larval tobacco hornworm,Manduca sexta, has been used in a laboratory setting for physiological studies and for pathogen virulence studies. This moth offers a much larger size than the commonly used wax moth (Galleria mellonella), and it can thus be used for a greater variety of assays, such as repeated sampling of the same individual, growth measurements, and tissue sampling. Yet their occasional use in research has led to a minimally documented set of rearing methods. To facilitate further adoption of this insect model, we expanded on previously reported protocols and developed our own rearing methods, which we report here. Our protocol requires little specialized equipment, with a cost less than $100/month for the feeding and maintenance of a laboratory colony of about five hundred larvae of differing instar phases. The low cost generalized equipment and supplies, and the simplification of the standardized protocols allows for an easy entry point for rearing tobacco hornworm populations. We also describe a few methods that are relevant to the uses of these organisms as infection models.
Syngap1 and the development of murine neocortical progenitor cells
Authors: Barão Soraia , Hong Ingie , Müller Ulrich , Huganir Richard L. 
Published: December 2024

AbstractSYNGAP1 is a major regulator of synaptic plasticity through its interaction with synaptic scaffold proteins and modulation of Ras and Rap GTPase signaling pathways.SYNGAP1mutations in humans are often associated with intellectual disability, epilepsy, and autism spectrum disorder.Syngap1heterozygous loss-of-function results in impaired LTP, premature maturation of dendritic spines, learning disabilities and seizures in mice. More recently, SYNGAP1 was shown to influence cortical neurogenesis and the proliferation of progenitors in human organoids. Here, we show that the absence or haploinsufficiency ofSyngap1does not influence the properties of neocortical progenitors and their cellular output in mice. This discrepancy highlights potential species-specific or methodological differences and raises important questions about the broader applicability of SYNGAP1’s role in neurogenesis.
Defining the molecular impacts of Humalite application on field-grown wheat (Triticum aestivumL.) using quantitative proteomics
Authors: Grubb Lauren E. , Talasila Mohana , Gorim Linda Y. , Uhrig R. Glen 
Published: December 2024

ABSTRACTIncreasing global food production demands have resulted in increased fertilizer usage, causing detrimental environmental impacts. Biostimulants, such as humic substances, are currently being applied as a strategy to increase plant nutrient-use efficiency and minimize environmental impacts within cropping systems. Humalite is a unique, naturally occurring coal-like substance found in deposits across southern Alberta. These deposits contain exceptionally high ratios of humic acids (>70%) and micronutrients due to their unique freshwater depositional environment. Humalite has begun to be applied to fields based on scientific data suggesting positive impacts on crop growth, yield and nutrient usage; however, little is known about the underlying molecular mechanisms of Humalite. Here, we report a quantitative proteomics approach to identify systems-level molecular changes induced by the addition of different Humalite application rates in field-grown wheat (Triticum aestivumL.) under three urea fertilizer application rates. In particular, we see wide-ranging abundance changes in proteins associated with several metabolic pathways and growth-related biological processes that suggest how Humalite modulates the plant molecular landscape. Overall, our results provide new, functional information that will help better inform agricultural producers on optimal biostimulant and fertilizer usage.
The impact of subunit type, alternative splicing, and auxiliary proteins on AMPA receptor trafficking
Authors: Couch Tyler , McCullock Tyler W. , MacLean David M. 
Published: December 2024

AbstractAMPA receptors underlie fast excitatory synaptic transmission in the mammalian nervous system and are critical for the expression of synaptic plasticity. Four genes encode the AMPA subunits, each subject to RNA editing and alternative splicing at multiple positions. In addition, each tetrameric AMPA receptor can harbor up to four auxiliary proteins, of which there are multiple types. Subunit type, alternative splicing, and auxiliary proteins are all known to affect AMPA receptor gating and trafficking. However, determining which factors dominate AMPA receptor trafficking requires high throughput assessment of trafficking across multiple conditions. Here, we deploy two such methods to assess the relative contribution of AMPA subunit type (GluA1 versus GluA2), alternative splicing (flip versus flop), and various transmembrane AMPA receptor regulatory proteins (TARPs) to AMPA receptor trafficking. We find that subunit type is the most important factor, with GluA2 showing much better surface expression than GluA1, and alternative splicing plays a secondary role, with flip subunits consistently outperforming flop variants in surface expression across all conditions. Type 1 TARPs (γ2-4 and γ8) enhance surface trafficking, while Type 2 TARPs (γ5 and γ7) reduced surface expression, although we could not detect differences within each type. These data will be a helpful resource in comparing surface expression across a variety of AMPA receptor compositions. Our assays will also enable high throughput assessment of novel disease-associated mutations, chimeras, and auxiliary and chaperone proteins.
Heterologous immunization strategy developed broadly reactive human monoclonal antibodies against the BK virus
Authors: Duty J. Andrew , Kraus Thomas , Kumar Madhu , Tortorella Nicolo A. , Jimoh Tajudeen O. , Pastrana Diana V. , Buck Christopher B. , Moran Thomas , Tortorella Domenico 
Published: December 2024

ABSTRACTBK polyomavirus (BKV) causes polyomavirus-associated nephropathy (PyVAN) and polyomavirus-associated hemorrhagic cystitis (PyVHC) following kidney transplantation and allogeneic hematopoietic stem cell transplantation (HST). BKV strains fall into four distinct genotypes (BKV-I, -II, -III, and -IV) with more than 80% of individuals are seropositive against BKV-I genotype, while the seroprevalence of the other four genotypes is lower. PyVAN and PyVHC occurs in immunosuppressed (e.g. transplant recipients) or immunomodulated (e.g. pregnant women) individuals. In the case of transplant patients, the sole treatment is to reduce immunosuppression, which increases the chance of graft failure. Multiple investigations have shown that polyclonal antibodies have a role in preventing or treating BKV-mediated sickness, implying that a broadly reactive monoclonal antibody (mAb) regimen targeting BKV could be used to limit virus propagation in varied patient populations. Thus, we utilized a heterologous immunization strategy using BKV genotype I-IV major capsid protein VP1 DNA in transgenic VelocImmune@ mice to generate broadly reactive anti-BKV antibodies. Hybridoma clones from the immunized mice were screened using high-throughput binding assays against VP1 of the various BK genotypes. The binding clones were then assessed for neutralization of BKV pseudoviruses consisting of the VP1 protein of the BKV-I, -II, -III, or -IV genotypes. Overall, the screening identified more than 170 genotype-specific mAbs, as well as 15 broadly cross-neutralizing mAbs against BKV-I, -II, -III, and - IV PsVs. The unique panel of broadly neutralizing mAbs could be utilized prophylactically or therapeutically to prevent or treat BKV-induced illnesses.
Associations of Cardiovascular-Kidney-Metabolic syndrome with premature mortality and life expectancies in US adults: a cohort study
Authors: Lei Lubi , Li Jingkuo , Wang Wei , Yu Yanwu , Pu Boxuan , Peng Yue , Zhang Lihua , Guo Yuanlin 
Published: December 2024

ABSTRACTBackgroundThe American Heart Association recently updated the Cardiovascular-Kidney-Metabolic (CKM) Health advisory, proposing a new framework for defining, staging, and predicting CKM risk. However, the prevalence and adverse effects of CKM stages remain insufficiently characterized.MethodsWe analyzed data from the National Health and Nutrition Examination Survey (NHANES) (1999–2018), including 18,350 US adults aged 20– 79 years. CKM syndrome encompasses subclinical or clinical cardiovascular disease (CVD), chronic kidney disease (CKD), and metabolic risk factors. Participants were categorized into four CKM stages based on clinical severity. We assessed associations of CKM stages with mortality risk and life expectancy.ResultsOnly 12.9% of participants were classified as CKM stage 0. The prevalence of CKM stages 1, 2, 3, and 4 was 23.1%, 53.6%, 3.6%, and 6.7%, respectively. Compared to CKM stage 0, individuals in stage 4 had a markedly higher risk of all-cause mortality (HR: 4.30, 95% CI: 2.95– 6.26) and lost 15.5 (12.5–19.8) years of life at age 50. Sex and racial/ethnic disparities were also observed.ConclusionsHigher CKM stages were strongly associated with increased mortality and reduced life expectancy. Our findings underscore the urgent need for enhanced CKM health management, social support, and policy interventions.Key MessagesWhat is already known on this topicMetabolic disorders, chronic kidney disease, and cardiovascular diseases are significantly associated with premature mortality. By taking into account the overlaps between cardiovascular-kidney-metabolic (CKM) syndrome, it is possible to improve risk stratification and employ an integrated approach to multimorbidity management.What this study adds?Only 12.6% of individuals had no CKM conditions, whereas approximately 50% of individuals had CKM stage 2, encompassing metabolic disorders, chronic kidney disease, or a combination of both.The estimated life expectancy of individuals with CKM stage 4 was 15.5 years lower than that of individuals with CKM stage 0 at the age of 50.How this study might affect research, practice or policy?Our results indicate that the CKM condition is prevalent among US adults. We advocate the implementation of the new staging system for the prevention and treatment of CKM syndrome.Life expectancy is reduced in adults who have a combination of metabolic risk factors, chronic kidney disease, or cardiovascular disease. We highlight the importance of incorporating a people-centered approach that includes the development of social support and policy, the integration of CKM health multidisciplinary management, and the enhancement of obesity management.