bluuebunny/crossref_metadata_2025_split huggingface dataset:
How does the weekend catch-up sleep ratio affect the health and lifestyle of Korean adults? An age- and gender- matched study
Authors: Hwang In-Whi , Hwang Soo-Ji , Shen Jun-Hao , Kim Jisu , Lee Jung-Min 
Published: September 2023

AbstractThe purpose of this study was to investigate the association between various levels of physical activity, self-perception, cardiometabolic risk factors, and weekend catch-up sleep ratio (CSR). Using raw data from the Korea National Health and Nutrition Examination Survey 2018 – 2021, all participants were divided into three groups (< 1.0, 1.0 ≤ CSR < 1.5, or ≥ 1.5) by CSR, which is the value calculated by dividing weekend sleep time by weekday sleep time. After matching age and gender, 2,484 Korean adults were selected as study participants. Descriptive statistics, chi-square test, ANOVA, and multinomial logistic regression analysis were performed to analyze the data. The results showed a significant association between weekend CSR and socioeconomic status, physical activity, self-perception levels, and cardiometabolic risk factors. Specifically, compared to the reference group (1 ≤ CSR < 1.5), those with a CSR < 1 were 2.42 times more likely to live in a single-family house (OR = 2.42, 95% CI = 1.77 – 3.32) and 1.71 times more likely to engage in vigorous physical activity meeting WHO guidelines (OR = 1.71, 95% CI = 1.20 – 2.46). They were also 1.33 times more likely to perceive themselves as ‘obese’ (OR = 1.33, 95% CI = 1.00 – 1.76). Conversely, those in the CSR ≥ 1.5 group were 3.93 times more likely to be ‘pink-collar’ workers (OR = 3.93, 95% CI = 2.70 – 5.71), 1.72 times more likely to perceive their stress levels as ‘quite’ (OR = 1.72, 95% CI = 1.20 – 2.47), and 1.87 times more likely to have diabetes (OR = 1.87, 95% CI = 0.97 – 3.60). Alterations in CSR could indicate changes in physical activity levels, sedentary behavior duration, and other health indicators, ultimately influencing overall well-being. Therefore, a comprehensive healthcare approach incorporating CSR considerations is increasingly essential.
Data-driven Prior Elicitation for Bayes Factors in Cox Regression for Nine Subfields in Biomedicine
Authors: Linde Maximilian , Jochim Laura , Tendeiro Jorge N. , van Ravenzwaaij Don 
Published: September 2023

AbstractBiomedical research often utilizes Cox regression for the analysis of time-to-event data. The pervasive use of frequentist inference for these analyses implicates that the evidence for or against the presence (or absence) of an effect cannot be directly compared and that researchers must adhere to a predefined sampling plan. As an alternative, the use of Bayes factors improves upon these limitations, which is especially important for costly and time-consuming biomedical studies. However, Bayes factors involve their own difficulty of specifying priors for the parameters of the statistical model. In this article, we develop data-driven priors for Cox regression tailored to nine subfields in biomedicine. To this end, we extracted hazard ratios and associatedx% confidence intervals from the abstracts of large corpora of already existing studies within the nine biomedical subfields. We used these extracted data to inform priors for the nine subfields. All of our suggested priors are Normal distributions with means of 0 and standard deviations closely scattered around 1. We propose that researchers use these priors as reasonable starting points for their analyses.
Disruption of maternal IgA by prenatal antibiotics precedes intestinalE. colicolonization and late-onset sepsis in neonates
Authors: McDonald Katya , Browning Danielle , Greenfield Kara G. , Lin Kathryn , Meier Josephine , Butoryak Matthew , Sasaki Alexandria , Fandozzi Eva , Hand Tim , Megli Christina , Knoop Kathryn A. 
Published: September 2023

AbstractNeonates, particularly prematurely born neonates, are particularly vulnerable to enteric pathogens. Antibiotics are widely administered during pregnancy for off-label use and prevention, but the effect on neonatal physiology has not been well characterized. Maternally derived IgA provided in milk is a predominant protective measure in the intestinal lumen of the nursing offspring. The connection between the maternal intestine and mammary IgA responses has been observed, but understanding how clinical use of antibiotics effects mammary IgA remains unclear. Here we find that prenatal cephalosporin antibiotics, but not penicillins, decrease mammary IgA in dams, and limit the availability of IgA within the lumen of nursing offspring. Decreased IgA correlated with an outgrowth of commensalE. coliand increased colonization and translocation of pathogenE. coli.Moreover, antenatal cephalosporin administration was associated with increased mortality in a model of LOS that was associated with decreased mammary IgA. Futhermore, in a clinical cohort of at-risk infants, maternal broad spectrum antibiotic treatment, including cephalosporins, increased the risk of LOS in neonates in comparison to penicillin-based treatments. This was associated with reduced IgA in the milk, and we propose maternal administration of select antibiotics could disrupt mammary IgA, leading to increased risk of LOS in infants by allowing for pathogen colonization in the neonatal intestine.
Dietary road salt and monarch butterflies: minimal effects on larval growth, immunity, wing coloration, and migration to Mexico
Authors: Hund Amanda K , Mitchell Timothy S. , Ramirez Isabel , Zambre Amod , Hagg Lili , Stene Anne , Porter Karilyn , Carper Adrian , Agnew Lauren , Shephard Alex , Kobiela Megan , Oberhauser Karen , Taylor Orley R. , Snell-Rood Emilie 
Published: September 2023

AbstractThe spectacular migration of the monarch butterfly is under threat from the loss of habitat and the decline of their milkweed host plants. In the northern part of their range, roadsides could potentially produce millions of monarchs annually due to high densities of milkweed, however roadside milkweed can accumulate chemicals from roads, such as sodium from road salt. Controlled lab studies have shown mixed effects of sodium on monarch development: small increases can be beneficial as sodium is an important micronutrient in brain and muscle development, but large increases can sometimes decrease survival. It is unclear how dietary sodium affects performance in ecologically relevant conditions, and the migration itself. In this experiment, we raised monarchs outdoors, in migration-inducing conditions, on milkweed sprayed with three levels of sodium chloride. We released 2500 tagged monarchs and held an additional 250 for further lab assays. While our recovery rates to the wintering grounds were low (N = 7 individuals), individuals from all three sodium chloride treatments made it to Mexico. Butterflies reared on control milkweed and low salt concentrated sodium in their tissues, while those on high salt diets excreted sodium, suggesting levels were above a physiological optimum. There were no effects of treatment on wing coloration, survival, body size, immunity, or parasite prevalence. Taken together, our results suggest that monarchs are robust to levels of sodium in milkweeds found along roadsides, which is promising with respect to monarch conservation efforts that promote roadside habitat.Significance StatementMonarch butterflies are a flagship species for pollinator conservation, and were recently being listed as endangered by the IUCN. Roadside habitat is a target for monarch breeding habitat as they often have high densities of milkweed, the monarch hostplant. However, roadsides can also have high levels of pollutants, such as salt from deicing treatments. We reared monarch caterpillars on sodium treated milkweeds, measuring a suite of performance measures, and releasing nearly 2500 tagged monarchs for migration. We found little effect of salt on migration to Mexico, survival, body size, development time, parasite prevalence, immunity, or coloration. Monarchs appear robust to levels of sodium found in milkweed along roadsides, supporting the possibility of roadsides as habitat.
Centimeter-scale perfusable cultured meat with densely packed, highly aligned muscle fibers via hollow fiber bioreactor
Authors: Nie Minghao , Shima Ai , Takeuchi Shoji 
Published: September 2023

AbstractThe development of in-vitro biofabrication methods for producing cultured meat based on animal cells has been advancing, but replicating the texture of traditional meat in centimeter-scale has been a challenge. To address this, a method using a hollow fiber bioreactor (HFB) has been developed. The HFB contains semipermeable hollow fibers that act as artificial circulatory systems to deliver nutrients and oxygen uniformly to the tissue, along with microfabricated anchors for inducing cell alignment. With active perfusion, the biofabricated centimeter-scale chick muscle tissue shows elevated levels of marker protein expression and sarcomere formation across the whole tissue, along with improved texture and flavor. In the future, further scaling up of this approach using industrial robots has the potential to transform not only the cultured meat industry but also the tissue engineering fields aiming for the formation of large-scale artificial organs.
RNA binding proteins and glycoRNAs form domains on the cell surface for cell penetrating peptide entry
Authors: Perr Jonathan , Langen Andreas , Almahayni Karim , Nestola Gianluca , Chai Peiyuan , Lebedenko Charlotta G. , Volk Regan , Caldwell Reese M. , Spiekermann Malte , Hemberger Helena , Bisaria Namita , Tzelepis Konstantinos , Calo Eliezer , Möckl Leonhard , Zaro Balyn , Flynn Ryan A. 
Published: September 2023

AbstractThe composition and organization of the cell surface determine how cells interact with their environment. Traditionally, glycosylated transmembrane proteins were thought to be the major constituents of the external surface of the plasma membrane. Here, we provide evidence that a group of RNA binding proteins (RBPs) are present on the surface of living cells. These cell surface RBPs (csRBPs) precisely organize into well-defined nanoclusters that are enriched for multiple RBPs, glycoRNAs, and their clustering can be disrupted by extracellular RNase addition. These glycoRNA-csRBP clusters further serve as sites of cell surface interaction for the cell penetrating peptide TAT. Removal of RNA from the cell surface, or loss of RNA binding activity by TAT, causes defects in TAT cell internalization. Together, we provide evidence of an expanded view of the cell surface by positioning glycoRNA-csRBP clusters as a regulator of communication between cells and the extracellular environment.
Stabilization of RRBP1 mRNA via an m6A-dependent manner in prostate cancer constitutes a therapeutic vulnerability amenable to small-peptide inhibition of METTL3
Authors: Feng Yuqing , Li Zenghui , Zhu Jingwei , Zou Cheng , Tian Yu , Xiong Jiangling , He Qinju , Li Wenjun , Xu Hao , Xu Bin , Shi Junfeng , Zhang Dingxiao 
Published: September 2023

ABSTRACTMounting evidence has implicated the RNA m6A methylation catalyzed by METTL3 in a wide range of physiological and pathological processes, including tumorigenesis. The detailed m6A landscape and molecular mechanism of METTL3 in prostate cancer (PCa) remains ill-defined. We find that METTL3 is overexpressed in PCa and correlates with worse patient survival. Functional studies establish METTL3 as an oncoprotein dependent on its m6A enzymatic activity in both AR+ and AR- PCa cells. To dissect the regulatory network of m6A pathway in PCa, we map the m6A landscape in clinical tumor samples using m6A-seq and identify genome-wide METTL3-binding transcripts via RIP-seq. Mechanistically, we discover RRBP1 as a direct METTL3 target in which METTL3 stabilizesRRBP1mRNA in an m6A-dependent manner. RRBP1 positively correlates with METTL3 expression in PCa cohorts and exerts an oncogenic role in aggressive PCa cells. Leveraging the 3D structural protein-protein interaction between METTL3 and METTL14, we successfully develop two potential METTL3 peptide inhibitors (RM3 and RSM3) that effectively suppress cancer cell proliferationin vitroand tumor growthin vivo. Collectively, our study reveals a novel METTL3/m6A/RRBP1 axis in enhancing aggressive traits of PCa, which can be therapeutically targeted by small-peptide METTL3 antagonists.
A ubiquitin-specific, proximity-based labeling approach for the identification of ubiquitin ligase substrates
Authors: Mukhopadyay Urbi , Levantovsky Sophie , Gharbi Sarah , Stein Frank , Behrends Christian , Bhogaraju Sagar 
Published: September 2023

AbstractUbiquitination of proteins is central to protein homeostasis and other cellular processes including DNA repair, vesicular transport, cell-division etc. The process of ubiquitination is conserved from yeast to humans and is carried out by the sequential action of three enzymes: E1, E2 and E3. There are an estimated >600 E3 ligases in humans that execute ubiquitination of specific target proteins in a spatio-temporal manner to elicit desired signaling effects. Here, we developed a ubiquitin-specific proximity-based labeling method to selectively biotinylate substrates of a given ubiquitin ligase. Our method exploits the proximity and the relative orientation of the E3-ligase catalytic domain with respect to ubiquitin observed in the enzymatic intermediate-state structures of E3-E2∼Ub. By fusing the biotin ligase BirA and an Avi-tag variant to the candidate E3 ligase and ubiquitin, respectively, we were able to specifically enrichbona fidesubstrates and potential new substrates of a ligase using a one-step streptavidin pulldown under denaturing conditions. As proof-of-principle, we applied our method, which we named Ub-POD, to the RING E3 ligase RAD18. RAD18 ubiquitinates DNA-sliding clamp PCNA upon UV-induced DNA damage. We identified PCNA and several other critical players in the DNA damage repair pathway in a single RAD18 Ub-POD experiment. We went on to validate DNA replicase POLE as a possible new substrate of RAD18. Through RAD18 Ub-POD, we were also able to pin down the cellular localization of RAD18-mediated ubiquitination to the damaged DNA nuclear puncta using streptavidin immunofluorescence. Furthermore, we applied Ub-POD to TRAF6, another RING ubiquitin ligase involved in NF-κB signaling and successfully identified known and potentially new TRAF6 substrates. Finally, we adapted our method to the U-box-type E3 ubiquitin ligase CHIP to demonstrate that we can identify substrates of two major classes of mammalian ubiquitin ligases. We anticipate that our method and principle could be widely adapted to all classes of ubiquitin ligases to identify substrates and localize the cellular site(s) of ubiquitination.
MIC13 and SLP2 seed the assembly of MIC60-subcomplex to facilitate crista junction formation
Authors: Naha Ritam , Strohm Rebecca , Urbach Jennifer , Wittig Ilka , Reichert Andreas S. , Kondadi Arun Kumar , Anand Ruchika 
Published: September 2023

AbstractThe MICOS complex subunit MIC13 is essential for mitochondrial cristae organization. Mutations inMIC13cause severe mitochondrial hepato-encephalopathy displaying defective cristae morphology and loss of the MIC10-subcomplex. Here we identified stomatin-like protein 2 (SLP2) as an interacting partner of MIC13 and decipher a critical role of SLP2 as an auxiliary MICOS subunit, modulating cristae morphology. SLP2 provides a large interaction hub for MICOS subunits and loss of SLP2 leads to drastic alterations in cristae morphology. Double deletion of SLP2 and MIC13 showed reduced assembly of core MICOS subunit, MIC60 into MICOS and dispersion of MIC60-specific puncta, demonstrating a critical role of SLP2-MIC13 in MICOS assembly and crista junction (CJ) formation. We further identified that the mitochondrial i-AAA protease YME1L in coordination either with MIC13 or SLP2 differentially regulates MICOS assembly pathways thereby interlinking MIC13-specific or scaffolding-specific role of SLP2 with quality control and assembly of the MICOS complex. YME1L- depletion inMIC13KO could restore MIC10-subcomplex and reform the nascent CJ. Taken together, we propose ‘seeder’ model for MICOS assembly and CJ formation, where SLP2- MIC13 seed the assembly of MIC60 into MICOS complex and promote the formation of CJ by regulating the quality and stability of MIC10-subcomplex.
A Far-Red Fluorescent Probe to VisualizeStaphylococcus aureusin Patient Samples
Authors: Jantarug Krittapas , Tripathi Vishwachi , Morin Benedict , Iizuka Aya , Kuehl Richard , Morgenstern Mario , Clauss Martin , Khanna Nina , Bumann Dirk , Rivera-Fuentes Pablo 
Published: September 2023

AbstractStaphylococcus aureus (S. aureus)is the leading bacterial cause of death in high-income countries and can cause invasive infections at various body sites. These infections are associated with prolonged hospital stays, a large economic burden, considerable treatment failure, and mortality rates. So far, there is only limited knowledge about the specific locations whereS. aureusresides in the human body during various infections. Hence, the visualization ofS. aureusholds significant importance in microbiological research. Herein, we report the development and validation of a far-red-fluorescent probe to detectS. aureusin human biopsies from deep-seated infections. This probe displays strong fluorescence and low background in human tissues, outperforming current tools forS. aureusdetection. Several applications are demonstrated, including fixed- and live-cell imaging, flow cytometry, and super-resolution bacterial imaging.Abstract Figure
A function of Spalt major as a sequence-specific DNA binding transcription factor mediates repression ofknirpsin theDrosophilawing imaginal disc
Authors: Ostalé Cristina M. , del Prado Alicia , Esteban Nuria , López-Varea Ana , de Celis Jose F. 
Published: September 2023

ABSTRACTThe Spalt transcriptional regulators participate in a variety of cell fate decisions during multicellular development. Vertebrate Spalt proteins have been mostly associated to the organization of heterochromatic regions, but they also contribute regulatory functions through binding to A/T rich motives present in their target genes. The developmental processes in which theDrosophila spaltgenes participate are well known through genetic analysis, but the mechanism by which the Spalt proteins regulate transcription are still unknown. Furthermore, despite the prominent changes in gene expression associated to mutations in thespaltgenes, the specific DNA sequences they bind are also unknow. In this contribution we describe the analysis of a DNA fragment present in the regulatory region of theknirpsgene. Spalt proteins are candidate repressors ofknirpsexpression during the formation of the venation pattern in the wing disc, and here we identify a minimal conserved 30bp sequence that binds to Spalt major bothin vivoandin vitro. This sequence mediates transcriptional repression in the central region of the wing blade, constituting the first confirmed case of a direct regulatory interaction between Spalt major and its target DNA inDrosophila.
Bivalent mRNA vaccine effectiveness against COVID-19 infections, hospitalisations and deaths in Portugal: a cohort study based on electronic health records, September 2022 to May 2023
Authors: Machado Ausenda , Kislaya Irina , Soares Patricia , Magalhães Sarah , Rodrigues Ana Paula , Franco Rafael , Leite Pedro Pinto , Dias Carlos Matias , Nunes Baltazar 
Published: September 2023

AbstractIn Portugal, a bivalent COVID-19 vaccine booster was recommended for those with complete primary COVID-19 vaccination, starting on September 6 2022. This study aims to estimate the mRNA bivalent vaccine effectiveness (VE) against COVID-19 infection, hospitalisation and death in the Portuguese population aged 65 and more years with a follow-up of more than six months.MethodsWe used a cohort approach to analyse six electronic health registries using deterministic linkage. The follow-up period comprehend September 2022 to May 2023. The outcomes included SARS-CoV-2 infection, COVID-19-related hospitalisation and death. Individuals were considered vaccinated 14 days following a bivalent mRNA COVID-19 vaccine uptake. For each outcome, COVID-19 bivalent VE was estimated as one minus the confounder adjusted hazard ratio of bivalent vaccine vs no bivalent vaccine, estimated by Cox regression with time-dependent vaccine exposure.ResultsIn the ≥ 80 year-olds, bivalent VE was 23.2 (95%CI: 20.1 to 26.2), 41.3 (95%CI: 34.5 to 47.5) and 50.3 (44.6 to 55.3), against infection, COVID-19-related hospitalisation and death, respectively. In the 65-79 year-old, bivalent VE against infection was 37.7 (35.5 to 39.8), 58.5 (95%CI: 51.9 to 64.2) against hospitalisation and 65.1 (95%CI: 59 to 70.4) against death. Vaccine effectiveness decay was observed for both age groups and in all outcomes, up to 6 months of vaccine uptake.ConclusionsIn a population with a high risk of SARS-CoV-2 complications, we observed moderate bivalent VE estimates against severe COVID-19 and low protection against infection. The lower VE estimates observed in the ≥ 80 year-olds should be interpreted in light of the reference group used for the estimation, i.e., individuals with high vaccine coverage (both primary series and multiple boosters). Significant VE decay was observed up to six months of vaccine uptake, which should be considered when preparing future vaccination campaigns.
Applications of Data Characteristic AI-assisted Raman Spectroscopy in Pathological Classification
Authors: Chen Xun , Shen Jianghao , Liu Chang , Shi Xiaoyu , Feng Weichen , Sun Hongyi , Zhang Weifeng , Zhang Shengpai , Jiao Yuqing , Chen Jing , Hao Kun , Gao Qi , Li Yitong , Hong Weili , Wang Pu , Feng Limin , Yue Shuhua 
Published: September 2023

ABSTRACTRaman spectroscopy has been widely used for label-free biomolecular analysis of cell and tissue for pathological diagnosisin vitroandin vivo. AI technology facilitates disease diagnosis based on Raman spectroscopy including machine learning (PCA and SVM), manifold learning (UMAP) and deep learning (ResNet and AlexNet). However, it is not clear how to optimize the appropriate AI classification model for different types of Raman spectral data. Here, We selected five representative Raman spectral datasets, including endometrial carcinoma, hepatoma extracellular vesicles, bacteria, melanoma cell, diabetic skin, with different characteristics regarding sample size, spectral data size, Raman shift range, tissue sites, Kullback-Leibler (KL) divergence, and key Raman shifts, explore the performance of different AI models (e.g. PCA-SVM, SVM, UMAP-SVM, ResNet or AlexNet). Tissue sites mean that spectral collection sites from sample, KL divergence means the divergence between spectra of different types. We found that for dataset of large spectral data size, Resnet performed better than PCA-SVM and UMAP, for dataset of small spectral data size, PCA-SVM or UMAP performed better. We also optimized the network parameters (e.g. principal components, activation function, and loss function) of AI model based on data characteristics. Using AI classification models, the mean area under receiver operating characteristic curves (AUC) for representative datasets reached 0.966, with mean sensitivity of 89.6%, mean specificity of 95.4%, mean accuracy of 93.4%, and mean time expense of 5 seconds. By using data characteristic assisted AI classification model, the accuracy improve from 85.1% to 94.6% for endometrial carcinoma grading, from 77.l% to 90.7% for hepatoma extracellular vesicles detection, from 89.3% to 99.7% for melanoma cell detection, from 88.1% to 97.9% for bacterial identification, from 53.7% to 85.5% for diabetic skin screening. Furthermore, according to the saliency maps, we found classification-associated biomolecules (e.g. nucleic acid, tyrosine, tryptophan, cholesteryl ester, fatty acid, and collagen), which contribute to the pathological diagnosis classification. Data characteristic assisted AI classification model was demonstrated to improve the robustness and accuracy of Raman spectroscopy in pathological classification. Collectively, this study opens up new opportunities for accurate and rapid Raman optical biopsy.