bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chloroform associated with bone mineral density and bone mineral content in adults: a population-based cross-sectional research
Authors: Li Lin , Liu XK , Zhang Xia , Zhang Yan , Li Qing , Geng HF , Shi Li , Wang Ben , Qiu QQ , Yu TP , Sang YQ , Wang LY , Xu Wei , Liang Jun 
Published: August 2023

AbstractBackgroundAccording to a recent cross-sectional study, reduced Bone Mineral Density (BMD) in U.S. adults is associated with co-exposure to several Volatile Organic Compounds (VOCs), and contact with VOCs increases the risk of developing osteoporosis. However, the relationship between chloroform (an essential VOC component) and BMD remains unclear. Consequently, we aimed to explore the relationship between chloroform alone and Bone Mineral Density or Bone Mineral Content (BMD or BMC).MethodsHerein, 2,553 individuals aged 18 and above from the National Health and Nutrition Examination Surveys (NHANES) in 2009-2010, 2013-2014, and 2017-2020, were included. We employed two independent t-tests and multi-linear regression models to statistically assess the relationship between chloroform exposure and BMD/BMC in the spine and femoral area.ResultsA “V”-shaped correlation between chloroform exposure and BMD/BMC was observed in the unadjusted model, particularly in the Ward’s triangle and femoral neck as a whole. A negative correlation was specifically observed for the Ward’s triangle BMD/BMC and L4 BMD/BMC. On the other hand, in the adjusted model, a dominantly negative correlation between the L4 BMC and chloroform exposure was observed over a range of exposure levels. The subgroup analysis revealed a negative correlation between chloroform concentrations and BMC in the femur and spine, especially in women and the 65-80 age population.ConclusionOur study revealed a “V” shaped correlation between chloroform and BMD/BMC of the femur and spine in U.S. adults. This finding highlights the fact that prolonged exposure to chloroform may increase the risk of developing osteoporosis.
The Sidelines Effect on Minds: The Impact of Injury on Mental Health in National Collegiate Athletic Association Athletes
Authors: Axton Ruth A. , Crowell Nancy A. , Merenstein Daniel J. 
Published: August 2023

AbstractInjury and mental health are prevalent topics in among NCAA Division 1 (DI) student-athletes; however, there is limited literature regarding the impact of injury on student-athletes’ mental health. This study examined the impact of injury on social support and self-stigma and the relationship between athletic identity and self-stigma. A convenience sample survey yielded 101 responses from DI student-athletes. The survey was composed of demographic questions, Sarason Social Support Questionnaire, Self-Stigma for Seeking Self-Help Scale, and Athletic Identity Measurement Scale. There was no significant difference between injured and non-injured athletes in the mean scores of social support (t test p= 0.69) or self-stigma (t test p =0.92). There was a nonsignificant weak correlation between athletic identity and self-stigma. The results reveal that self-stigma is prevalent within this community, with an average score of 23.34 for all respondents. These conclusions can aid mental health professionals in providing support and education to student-athletes.
Work Attendance during Acute Respiratory Illness Before and During the COVID-19 Pandemic, United States, 2018–2022
Authors: Ahmed Faruque , Nowalk Mary Patricia , Zimmerman Richard K. , Bear Todd , Grijalva Carlos G. , Talbot H. Keipp , Florea Ana , Tartof Sara Y. , Gaglani Manjusha , Smith Michael , McLean Huong Q. , King Jennifer P. , Martin Emily T. , Monto Arnold S. , Phillips C. Hallie , Wernli Karen J. , Flannery Brendan , Chung Jessie R. , Uzicanin Amra 
Published: August 2023

AbstractSevere Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and influenza viruses can be transmitted by infected persons who are pre-symptomatic or symptomatic. To assess impact of the COVID-19 pandemic on work attendance during illness, we analyzed prospectively collected data from persons with acute respiratory illness (ARI) enrolled in a multi-state study during 2018–2022. Persons with prior experience working from home were significantly less likely than those without this experience to work onsite on the day before illness and during the first 3 days of illness; the effect was more pronounced for the COVID-19 pandemic period than the pre-pandemic influenza seasons. Persons with influenza or COVID-19 were significantly less likely to work onsite than persons with other ARIs. Among persons for whom positive COVID-19 test results were available by the second or third day of illness, few worked onsite. Work-from-home policies may reduce the likelihood of workplace exposures to respiratory viruses.Article’s summary lineWork-from-home policies may reduce the likelihood of workplace exposures to SARS-CoV-2 and influenza viruses.
An oligodendrocyte silencer element underlies the pathogenic impact of lamin B1 structural variants
Authors: Nmezi Bruce , Bey Guillermo Rodriguez , Oranburg Talia DeFrancesco , Dudnyk Kseniia , Lardo Santana M. , Herdman Nathan , Jacko Anastasia , Rubio Sandy , Alcocer Emanuel Loeza , Kofler Julia , Kim Dongkyeong , Rankin Julia , Kivuva Emma , Gutowski Nicholas , Schon Katherine , van den Ameele Jelle , Chinnery Patrick F. , Sousa Sérgio B. , Palavra Filipe , Toro Camilo , Pinto e Vairo Filippo , Saute Jonas , Pan Lisa , Alturkustani Murad , Hammond Robert , Gros-Louis Francois , Gold Michael , Park Yungki , Bernard Geneviève , Raininko Raili , Zhou Jian , Hainer Sarah J. , Padiath Quasar S. 
Published: August 2023

AbstractThe role of non-coding regulatory elements and how they might contribute to tissue type specificity of disease phenotypes is poorly understood. Autosomal Dominant Leukodystrophy (ADLD) is a fatal, adult-onset, neurological disorder that is characterized by extensive CNS demyelination. Most cases of ADLD are caused by tandem genomic duplications involving the lamin B1 gene (LMNB1) while a small subset are caused by genomic deletions upstream of the gene. Utilizing data from recently identified families that carryLMNB1gene duplications but do not exhibit demyelination, ADLD patient tissues, CRISPR modified cell lines and mouse models, we have identified a novel silencer element that is lost in ADLD patients and that specifically targets overexpression to oligodendrocytes. This element consists of CTCF binding sites that mediate three-dimensional chromatin looping involving theLMNB1and the recruitment of the PRC2 repressor complex. Loss of the silencer element in ADLD identifies a previously unknown role for silencer elements in tissue specificity and disease causation.
Assay for characterizing adsorption-properties of surfaces (APS) used for sample preparation prior to quantitative omics
Authors: Siebels Bente , Moritz Manuela , Hübler Diana , Gocke Antonia , Voß Hannah , Schlüter Hartmut 
Published: August 2023

ABSTRACTAnalytes during their journey from their natural sources to their identification and quantification are prone to adsorption to surfaces before they enter an analytical instrument, causing false quantities. This problem is especially severe in diverse omics. Here, thousands of analytes with a broad range of chemical properties and thus different affinities to surfaces are quantified within a single analytical run. For quantifying adsorption effects caused by surfaces of sample handling tools, an assay was developed, applying LC-MS/MS-based differential bottom-up proteomics and as probe a reference mixture of thousands of tryptic peptides, covering a broad range of chemical properties. The assay was tested by investigating the adsorption properties of several vials composed of polypropylene, including low-protein-binding polypropylene vials, borosilicate glass vials and low-retention glass vials. In total 3531 different peptides were identified and quantified across all samples and therefore used as probes. A significant number of hydrophobic peptides adsorbed on polypropylene vials. In contrast, only very few peptides adsorbed to low-protein-binding polypropylene vials. The highest number of peptides adsorbed to glass vials, driven by electrostatic as well as hydrophobic interactions. Calculation of the impact of the adsorption of peptides on differential quantitative proteomics showed significant false results. In summary, the new assay is suitable to characterize adsorption properties of surfaces getting into contact with analytes during sample preparation, thereby giving the opportunity to find parameters for minimizing false quantities.Insert Table of Contents artwork here
A robust genome and assembly with transcriptomic data from the striped scorpion,Centruroides vittatus
Authors: Yamashita Tsunemi , Rhoads Douglas D. , Pummill Jeff 
Published: August 2023

AbstractScorpions, a seemingly primitive, stinging arthropod taxa, are known to exhibit marked diversity in their venom components. These venoms are known for their human pathology, but also important as models for therapeutic and drug development applications. We report a high quality genome assembly and annotation of the striped bark scorpion,Centruroides vittatus, created with several shotgun libraries. The final assembly is 760 Mb in size, with a BUSCO score of 97.8%, a 30.85% GC, and a N50 of 2.35 Mb. We estimated 36,189 proteins with 37.32% assigned to GO terms in our GOanna analysis. We were able to map 2011 and 60 venom toxin genes to contigs and scaffolds, respectively. We were also able to identify expression differences between venom gland (telson) and body tissue (carapace) with 19 Sodium toxin and 14 Potassium toxin genes to 18 contigs and two scaffolds. This assembly along with our transcriptomic data, provides further data to investigate scorpion venom genomics.
Quantification of biases in predictions of protein-protein binding affinity changes upon mutations
Authors: Tsishyn Matsvei , Pucci Fabrizio , Rooman Marianne 
Published: August 2023

AbstractUnderstanding the impact of mutations on protein-protein binding affinity is a key objective for a wide range of biotechnological applications and for shedding light on disease-causing mutations, which are often located at protein-protein interfaces. Over the past decade, many computational methods using physics-based and/or machine learning approaches have been developed to predict how protein binding affinity changes upon mutations. They all claim to achieve astonishing accuracy on both training and test sets, with performances on standard benchmarks such as SKEMPI 2.0 that seem overly optimistic. Here we benchmarked eight well-known and well-used predictors and identified their biases and dataset dependencies, using not only SKEMPI 2.0 as a test set but also deep mutagenesis data on the SARS-CoV-2 spike protein in complex with the human angiotensin-converting enzyme 2. We showed that, even though most of the tested methods reach a significant degree of robustness and accuracy, they suffer from limited generalizability properties and struggle to predict unseen mutations. Interestingly, the generalizability problems are more severe for pure machine learning approaches while physics-based methods are less affected by this issue. Moreover, undesirable prediction biases towards specific mutation properties, the most marked being towards destabilizing mutations, are also observed and should be carefully considered by method developers. We conclude from our analyses that there is room for improvement in the prediction models and suggest ways to check, assess and improve their generalizability and robustness.
Remote ischemic conditioning modulates inflammatory response and metabolic pathways
Authors: Torres-Querol Coral , Pamplona Reinald , Arqué Gloria , Purroy Francisco 
Published: August 2023

ABSTRACTRemote ischemic conditioning (RIC) is an endogenous procedure that reduces ischemic injury by repeated transient mechanical obstruction of vessels at a remote limb. However, the specific mechanism of this protective phenomenon remains incompletely understood. We aimed to study perturbations in the brain and plasma metabolome following RIC as well as to identify potential novel inflammatory cytoprotective targets.A mouse model of transient focal cerebral ischemia by compressing the distal middle cerebral artery was used. Multiplex cytokine assay was performed in plasma samples. Blood plasma and brain samples were collected and metabolomes analyzed using non-targeted LC-MS.The analysis revealed a moderate impact on the brain metabolome compared to circulatory metabolites following RIC intervention. Interestingly, 3 plasma metabolites, Cer(42:3), HexCer(36:1) and TG(28:0), stood out as highly significantly upregulated. Moreover, RIC applied during the ischemia (RIPerC) and after the ischemia (RIPostC) protect against cerebral ischemia-reperfusion injury by modulating the peripheral immunomodulation.This study indicated that RIC neuroprotection is present in ischemic mice via the inflammatory response and metabolic changes both in the peripheral blood and ischemic brain.
Neural attentional filters and behavioural outcome follow independent individual trajectories over the adult life span
Authors: Tune Sarah , Obleser Jonas 
Published: August 2023

AbstractPreserved communication abilities promote healthy aging. To this end, the age-typical loss of sensory acuity might in part be compensated for by an individual’s preserved attentional neural filtering. Is such a compensatory brain–behaviour link longitudinally stable? Can it predict individual change in listening behaviour? We here show that individual listening behaviour and neural filtering ability follow largely independent developmental trajectories modelling electroencephalographic and behavioural data of N = 105 aging individuals (39–82 yrs). First, despite the expected decline in hearing- threshold–derived sensory acuity, listening-task performance proved stable over 2 years. Second, neural filtering and behaviour were correlated only within each separate measurement timepoint (T1, T2). Longitudinally, however, our results raise caution on attention-guided neural filtering metrics as predictors of individual trajectories in listening behaviour: Neither neural filtering at T1 nor its two-year change could predict individual two-year behavioural change, under a combination of modelling strategies.
A comparison of clustering models for inference of T cell receptor antigen specificity
Authors: Hudson Dan , Lubbock Alex , Basham Mark , Koohy Hashem 
Published: August 2023

AbstractThe vast potential sequence diversity of TCRs and their ligands has presented an historic barrier to computational prediction of TCR epitope specificity, a holy grail of quantitative immunology. One common approach is to cluster sequences together, on the assumption that similar receptors bind similar epitopes. Here, we provide an independent evaluation of widely used clustering algorithms for TCR specificity inference, observing some variability in predictive performance between models, and marked differences in scalability. Despite these differences, we find that different algorithms produce clusters with high degrees of similarity for receptors recognising the same epitope. Our analysis highlights an unmet need for improvement of complex models over a simple Hamming distance comparator, and strengthens the case for use of clustering models in TCR specificity inference.
MRI-based cell tracking of OATP-expressing cell transplants by pre-labeling with Gd-EOB-DTPA
Authors: Bhattacharyya Tapas , Mallett Christiane L. , Shapiro Erik M. 
Published: August 2023

AbstractPurposeTo detect cell transplants labeled with a clinical gadolinium-based contrast agent as hyperintense signals using a clinically familiar T1-weighted MRI protocol.MethodsHEK293 cells were stably transduced to express human OATP1B3, a hepatic transporter that transport Gd-EOB-DTPA into cells that express the transporters, the intracellular accumulation of which cells causes signal enhancement on T1-weighted MRI. Cells were labeled in media containing Gd-EOB-DTPA for MRI evaluation and indocyanine green for cryofluorescence tomography validation. Labeled cells were injected into chicken hearts, in vitro, after which MRI and cryofluorescence tomography were performed in tandem.ResultsOATP1B3-expressing cells had substantially reduced T1 following labeling with Gd-EOB-DTPA in culture. Following their implantation into chicken heart, these cells were easily identified in T1-weighted MRI. Cryofluorescence tomography validated that the areas of signal enhancement in MRI overlapped with areas of indocyanine green signal, indicating that signal enhancement was due to the transplanted cells.ConclusionOATP1B3-expressing cells can be pre-labeled with Gd-EOB-DTPA prior to injection into tissue, affording the use of clinically familiar T1-weighted MRI to robustly detect cell transplants.
Periods of environmental sensitivity couple larval behavior and development
Authors: Faerberg Denis F. , Aprison Erin Z. , Ruvinsky Ilya 
Published: August 2023

SummaryThe typical life cycle in most animal phyla includes a larval period that bridges embryogenesis and adulthood1. Despite the great diversity of larval forms, all larvae grow, acquire adult morphology and function, while navigating their habitats to obtain resources necessary for development. How larval development is coordinated with behavior remains substantially unclear. Here, we describe features of the iterative organization of larval stages that serve to assess the environment and procure resources prior to costly developmental commitments. We found that male-excreted pheromones accelerate2-4the onset of adulthood inC. eleganshermaphrodites by coordinately advancing multiple developmental events and growth during the last larval stage. The larvae are sensitive to the accelerating male pheromones only at the end of the penultimate larval stage, just before the acceleration begins. Other larval stages also contain windows of sensitivity to environmental inputs. Importantly, behaviors associated with search and consumption of food are distinct between early and late portions of larval stages. We infer that each larval stage inC. elegansis subdivided into two epochs: A) global assessment of the environment to identify the most suitable patch and B) consumption of sufficient food and acquisition of salient information for developmental events in the next stage. We predict that in larvae of other species behavior is also divided into distinct epochs optimized either for assessing the habitat or obtaining the resources. Thus, a major role of larval behavior is to coordinate the orderly progression of development in variable environments.“Life is what happens to you when you’re busy making other plans.”Allen Saunders (popularized by John Lennon)
Ontogeny of the organized nasopharynx-associated lymphoid tissue in rainbow trout
Authors: Garcia Benjamin J , Reyes Alexis , Martinez Chrysler , Serra dos Santos Yago , Salinas Irene 
Published: August 2023

AbstractUnderstanding the ontogeny of teleost mucosa-associated lymphoid tissues (MALT) is critical for determining the earliest timepoint for effective mucosal vaccination of young fish. Here, we describe the developmental sequence that leads to the formation of an organized MALT structure in rainbow trout, the organized nasopharynx-associated lymphoid tissue (O-NALT). Control rainbow trout were sampled between 340 and 1860 degree days (DD) and routine histology and immunofluorescence staining were used to determine cellular changes in immune cells in the nasal cavity as well as O-NALT formation. We identified that O-NALT is first seeded by CD8α+T cells at 700DD followed by IgM+B cells and CD4-2b+T cells at 1000DD. Histomorphologically, trout O-NALT is fully formed at 1400DD when it is composed of 67% CD4-2b+cells, 20% IgM+cells, 13% CD8α+T cells, and no IgT+B cells. Whole body gene expression analyses uncovered waves ofigmh,cd4-2b, andcd8aexpression that recapitulate the cellular seeding sequence of O-NALT by specific lymphocyte subsets. Our results indicate that 1) O-NALT formation results from a specific sequence of lymphocyte subset colonization pioneered by CD8α+T cells and 2) the presence of the full O-NALT structure at 1400DD may mark this timepoint as the earliest developmental stage at which mucosal vaccines can induce long lasting, specific immune responses.
Antigen Geometry Tunes Mast Cell Signaling Through Distinct FcεRI Aggregation and Structural Changes
Authors: Rinaldi Derek A. , Kanagy William K. , Kaye Hannah C. , Grattan Rachel M. , Lucero Shayna R. , Pérez Marelessis Palomino , Wester Michael J. , Lidke Keith A. , Wilson Bridget S. , Lidke Diane S. 
Published: August 2023

AbstractImmunoreceptor tyrosine-based activation motif (ITAM)-containing Fc receptors are critical components of the innate and adaptive immune systems. FcεRI mediates the allergic response via crosslinking of IgE-bound receptors by multivalent antigens. Yet, the underlying molecular mechanisms that govern the response of FcεRI to specific antigens remain poorly understood. We compared responses induced by two antigens with distinct geometries, high valency DNP-BSA and trivalent DF3, and found unique secretion and receptor phosphorylation profiles that are due to differential recruitment of Lyn and SHIP1. To understand how these two antigens can cause such markedly different outcomes, we used direct stochastic optical reconstruction microscopy (dSTORM) super-resolution imaging combined with Bayesian Grouping of Localizations (BaGoL) analysis to compare the nanoscale characteristics of FcεRI aggregates. DF3 aggregates were found to be smaller and more densely packed than DNP-BSA aggregates. Using lifetime-based Förster resonance energy transfer (FRET) measurements, we discovered that FcεRI subunits undergo structural rearrangements upon crosslinking with either antigen, and in response to interaction with monovalent antigen presented on a supported lipid bilayer. The extent of conformational change is positively correlated with signaling efficiency. Finally, we provide evidence for forces in optimizing FcεRI signaling, such that immobilizing DF3 on a rigid surface promoted degranulation while increasing DNP-BSA flexibility lowered degranulation. These results provide a link between the physical attributes of allergens, including size, shape, valency, and flexibility, and FcεRI signaling strength. Thus, the antigen modulates mast cell outcomes by creating unique aggregate geometries that tune FcεRI conformation, phosphorylation and signaling partner recruitment.Statement of SignificanceThis work elucidates the molecular mechanisms underlying differential FcεRI signaling responses induced by antigens of distinct geometries. By combining super-resolution imaging and biophysical techniques, we demonstrate that the physical attributes of allergens, including shape, flexibility, and valency, modulate mast cell signaling outcomes by altering FcεRI aggregate organization and conformational states. This provides novel insights into the structure-function relationships governing FcεRI signal transduction and its role in mast cell activation. Overall, this work establishes a link between allergen physical properties and immune receptor signaling at the molecular level, with important implications for understanding and regulating allergic responses.