bluuebunny/crossref_metadata_2025_split huggingface dataset:
COVID-19 vaccine hesitancy among individuals with cancer, autoimmune diseases, and other serious comorbid conditions
Authors: Tsai Richard , Hervey John , Hoffman Kathleen D , Wood Jessica , Novack John , Johnson Jennifer , Deighton Dana C. , Loew Brian , Goldberg Stuart L 
Published: April 2021

AbstractBackgroundIndividuals with comorbid conditions have been disproportionately affected by COVID-19. Since regulatory clinical trials with COVID-19 vaccines excluded those with immunocompromising conditions, few patients with cancer and autoimmune diseases were enrolled. With limited vaccine safety data available, vulnerable populations may have conflicted vaccine attitudes.MethodsTo assess the incidence and reasons for COVID-19 vaccine hesitancy and to assess early vaccine safety, we conducted a cross-sectional online survey, fielded January 15, 2021 through February 22, 2021, with international participation (74% USA). A random sample of members of Inspire, an⍰online health⍰community⍰of over 2.2⍰million individuals⍰with comorbid conditions, completed a 55-item online survey.Results21,943 individuals completed the survey (100% with comorbidities including 27% cancer, 23% autoimmune diseases, 38% chronic lung diseases). 10% declared they would not, 4% stated they probably would not, and 5% were not sure they would agree to vaccination (hesitancy rate 19%). Factors associated with hesitancy included younger age, female gender, black-Pacific-Island-Native American heritage, less formal education, conservative political tendencies, resistance to masks or routine influenza vaccinations, and distrust of media coverage. 5501 (25%) had received at least one COVID-19 vaccine injection, including 29% of US participants. Following the first injection, 69% self-reported local and 40% systemic reactions, which increased following the second injection to 76% and 67%, respectively, with patterns mimicking clinical trials.ConclusionNearly one in five individuals with serious comorbid conditions harbor COVID-19 hesitancy. Early safety experiences among those who have been vaccinated should be reassuring.HighlightsIndividuals with serious comorbid conditions, including cancer, have been disproportionately affected by COVID-19 and therefore have been prioritized for vaccinationAn online survey of nearly 22,000 individuals with comorbid conditions revealed that nearly one in 5 expressed vaccine hesitancy.Reasons for hesitancy in this comorbid population mimicked surveys of the general population.Self-reported safety profiles among individuals with comorbid conditions were acceptable, and generally milder than reports in clinical trials among the general population.
Sex-specific metabolic pathways associate with Alzheimer’s Disease (AD) endophenotypes in the European Medical Information Framework for AD Multimodal Biomarker Discovery cohort
Authors: Xu Jin , Green Rebecca , Kim Min , Lord Jodie , Ebshiana Amera , Westwood Sarah , Baird Alison L , Nevado-Holgado Alejo J , Shi Liu , Hye Abdul , Snowden Stuart G. , Bos Isabelle , Vos Stephanie J. B. , Vandenberghe Rik , Teunissen Charlotte E. , Kate Mara Ten , Scheltens Philip , Gabel Silvy , Meersmans Karen , Blin Olivier , Richardson Jill , De Roeck Ellen Elisa , Engelborghs Sebastiaan , Sleegers Kristel , Bordet Régis , Rami Lorena , Kettunen Petronella , Tsolaki Magda , Verhey Frans R.J. , Alcolea Daniel , Lleó Alberto , Peyratout Gwendoline , Tainta Mikel , Johannsen Peter , Freund-Levi Yvonne , Frölich Lutz , Dobricic Valerija , Frisoni Giovanni B. , Molinuevo José Luis , Wallin Anders , Popp Julius , Martinez-Lage Pablo , Bertram Lars , Blennow Kaj , Zetterberg Henrik , Streffer Johannes , Visser Pieter Jelle , Lovestone Simon , Proitsi Petroula , Legido-Quigley Cristina 
Published: April 2021

AbstractBACKGROUNDPhysiological differences between males and females could contribute to the development of AD. Here, we examined metabolic pathways that may lead to precision medicine initiatives.METHODSWe explored whether sex modifies the association of 540 plasma metabolites with AD endophenotypes including diagnosis, CSF biomarkers, brain imaging, and cognition using regression analyses for 695 participants (377 females), followed by sex-specific pathway overrepresentation analyses, APOE ε4 stratification and assessment of metabolites’ discriminatory performance in AD.RESULTSIn females with AD, vanillylmandelate (tyrosine pathway) was increased and tryptophan betaine (tryptophan pathway) was decreased. The inclusion of these two metabolites (AUC = 0.83, SE = 0.029) to a baseline model (covariates + CSF biomarkers, AUC = 0.92, SE = 0.019) resulted in a significantly higher AUC of 0.96 (SE = 0.012). Kynurenate was decreased in males with AD (AUC = 0.679, SE = 0.046).CONCLUSIONSMetabolic sex-specific differences were reported, covering neurotransmission and inflammation pathways with AD endophenotypes. Two metabolites, in pathways related to dopamine and serotonin, associated to females, paving the way to personalised treatment.
Examining Recent Trends in the Racial Disparity Gap in Tap Water Consumption: NHANES 2011–2018
Authors: Rosinger Asher Y. , Patel Anisha I. , Weaks Francesca 
Published: April 2021

AbstractObjectiveAs tap water distrust has grown in the US with greater levels among Black and Hispanic households, we aimed to examine recent trends in not drinking tap water including the period covering the US Flint Water Crisis and racial/ethnic disparities in these trends.Design, Setting, and ParticipantsWe analyzed data from the cross-sectional National Health and Nutrition Examination Survey data (2011–2018) for 9,439 children aged 2-19 and 17,268 adults. Log-binomial regressions and marginal predicted probabilities examined US nationally-representative trends in tap and bottled water consumption overall and by race/ethnicity.ResultsAmong US children and adults, respectively, in 2017-2018 there was a 63% (adjusted prevalence ratio [PR]:1.63, 95%CI: 1.25-2.12, p<0.001) and 40% (PR:1.40, 95%CI: 1.16-1.69, p=0.001) higher prevalence of not drinking tap water compared to 2013-2014 (pre-Flint Water Crisis). For Black children and adults, the probability of not drinking tap water increased significantly from 18.1% (95%CI: 13.4-22.8) and 24.6% (95%CI: 20.7-28.4) in 2013–14 to 29.3% (95%CI: 23.5-35.1) and 34.5% (95%CI: 29.4-39.6) in 2017–2018. Among Hispanic children and adults, not drinking tap water increased significantly from 24.5% (95%CI: 19.4-29.6) and 27.1% (95%CI: 23.0-31.2) in 2013-14 to 39.7% (95%CI: 32.7-46.8) and 38.1% (95%CI: 33.0-43.1) in 2017-2018. No significant increases were observed among Asian or white persons between 2013-14 and 2017-18. Similar trends were found in bottled water consumption.ConclusionsThis study found persistent disparities in the tap water consumption gap from 2011–2018. Black and Hispanics’ probability of not drinking tap water increased following the Flint Water Crisis.
plantR: An R package and workflow for managing species records from biological collections
Authors: de Lima Renato A. F. , Sánchez-Tapia Andrea , Mortara Sara R. , Steege Hans ter , de Siqueira Marinez F. 
Published: April 2021

AbstractSpecies records from biological collections are becoming increasingly available online. This unprecedented availability of records has largely supported recent studies in taxonomy, biogeography, macroecology, and biodiversity conservation. Biological collections vary in their documentation and notation standards, which have changed through time. For different reasons, neither collections nor data repositories perform the editing, formatting, and standardization of the data, leaving these tasks to the final users of the species records (e.g. taxonomists, ecologists and conservationists). These tasks are challenging, particularly when working with millions of records from hundreds of biological collections.To help collection curators and final users perform those tasks, we introduceplantR, an open-source package that provides a comprehensive tool-box to manage species records from biological collections. The package is accompanied by the proposal of a reproducible workflow to manage this type of data in taxonomy, ecology, and biodiversity conservation. It is implemented inRand designed to handle relatively large data sets as fast as possible. Initially designed to handle plant species records, many of theplantRfeatures also apply to other groups of organisms, given that the data structure is similar.TheplantRworkflow includes tools to (1) download records from different data repositories, (2) standardize typical fields associated with species records, (3) validate the locality, geographical coordinates, taxonomic nomenclature, and species identifications, including the retrieval of duplicates across collections, and (4) summarize and export records, including the construction of species checklists with vouchers.OtherRpackages provide tools to tackle some of the workflow steps described above. But in addition to the new features and resources related to the data editing and validation, the greatest strength ofplantRis to provide a comprehensive and user-friendly workflow in one single environment, performing all tasks from data retrieval to export. Thus,plantRcan help researchers better assess data quality and avoid data leakage in a wide variety of studies using species records.
Juvenile emperor penguin range calls for extended conservation measures in the Southern Ocean
Authors: Houstin Aymeric , Zitterbart Daniel P. , Heerah Karine , Eisen Olaf , Planas-Bielsa Víctor , Fabry Ben , Bohec Céline Le 
Published: April 2021

AbstractTo protect the unique Southern Ocean biodiversity, conservation measures like marine protected areas (MPAs) are implemented based on the known habitat distribution of ecologically important species. However, distribution models focus on adults, neglecting that immatures animals can inhabit vastly different areas. Here, we show that current conservation efforts in the Southern Ocean are insufficient for ensuring the protection of the highly mobile Emperor penguin. We find that juveniles spend ∼90% of their time outside the boundaries of proposed and existing MPAs, and that their distribution extends far beyond (> 1500 km) the species’ extent of occurrence as defined by the International Union for Conservation of Nature. We argue that strategic conservation plans for Emperor penguin and long-lived ecologically important species must consider the dynamic habitat range of all age classes.
Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space
Authors: Xiong Lei , Tian Kang , Li Yuzhe , Zhang Qiangfeng Cliff 
Published: April 2021

ABSTRACTComputational tools for integrative analyses of diverse single-cell experiments are facing formidable new challenges including dramatic increases in data scale, sample heterogeneity, and the need to informatively cross-reference new data with foundational datasets. Here, we present SCALEX, a deep-learning method that integrates single-cell data by projecting cells into a batch-invariant, common cell-embedding space in a truly online manner (i.e., without retraining the model). SCALEX substantially outperforms online iNMF and other state-of-the-art non-online integration methods on benchmark single-cell datasets of diverse modalities, (e.g., scRNA-seq, scATAC-seq), especially for datasets with partial overlaps, accurately aligning similar cell populations while retaining true biological differences. We showcase SCALEX’s advantages by constructing continuously expandable single-cell atlases for human, mouse, and COVID-19 patients, each assembled from diverse data sources and growing with every new data. The online data integration capacity and superior performance makes SCALEX particularly appropriate for large-scale single-cell applications to build-upon previously hard-won scientific insights.
Fungal community turnover along steep environmental gradients from geothermal soils in Yellowstone National Park
Authors: Bazzicalupo Anna L. , Erlandson Sonya , Branine Margaret , Ratz Megan , Ruffing Lauren , Nguyen Nhu H. , Branco Sara 
Published: April 2021

AbstractGeothermal soils offer unique insight into the way extreme environmental factors shape communities of organisms. However, little is known about the fungi growing in these environments and in particular how localized steep abiotic gradients affect fungal diversity. We used metabarcoding to characterize soil fungi surrounding a hot spring-fed thermal creek with water up to 84 °C and pH 10 in Yellowstone National Park. We found a significant association between fungal communities and soil variable principal components, and we identify the key trends in co-varying soil variables that explain the variation in fungal community. Saprotrophic and ectomycorrhizal fungi community profiles followed, and were significantly associated with, different soil variable principal components, highlighting potential differences in the factors that structure these different fungal trophic guilds. In addition,in vitrogrowth experiments in four target fungal species revealed a wide range of tolerances to pH levels but not to heat. Overall, our results documenting turnover in fungal species within a few hundred meters suggest many co-varying environmental factors structure the diverse fungal communities found in the soils of Yellowstone National Park.
Altered drug metabolism and increased susceptibility to fatty liver disease in myotonic dystrophy
Authors: Dewald Zac , Gupta Andrew , Chembazhi Ullas V. , Kalsotra Auinash 
Published: April 2021

AbstractMyotonic Dystrophy type 1 (DM1), a prevalent muscular dystrophy affecting 1 in 2800 individuals, is associated with a toxic (CTG)nrepeat expansion in theDMPKgene. While DM1 affects multiple systems, recent studies highlight its link to liver pathology, glucose intolerance, and drug sensitivity. Our study focused on liver implications by creating a hepatocyte-specific DM1 mouse model. Expression of toxic RNA in hepatocytes sequestered muscleblind-like (MBNL) proteins, impacting hepatocellular activity. DM1-induced liver alterations included morphological changes, inflammation, necrosis, and fatty accumulation. Impaired drug metabolism and clearance were evident in DM1 mice and increased susceptibility to diet-induced fatty liver disease. Notably, alternative splicing of acetyl-CoA carboxylase 1 induced excessive lipid accumulation in DM1 livers, exacerbated by high-fat, high-sugar diets. These findings unveil disruptions in hepatic functions, predisposing DM1 livers to injury, fatty liver disease, and compromised drug clearance. Understanding these mechanisms is crucial for addressing the complex health challenges in DM1 patients and optimizing treatment strategies.
Sustained Oxygenation Accelerates Diabetic Wound Healing by Simultaneously Promoting Epithelialization and Angiogenesis, and Decreasing Tissue Inflammation
Authors: Guan Ya , Niu Hong , Liu Zhongting , Dang Yu , Shen Jie , Zayed Mohamed , Ma Liang , Guan Jianjun 
Published: April 2021

AbstractNon-healing diabetic wound is one of the most common complications for diabetic patients. Chronic hypoxia is among the prominent factors that delay the wound healing process. Therefore, sustained oxygenation to alleviate hypoxia is hypothesized to promote diabetic wound healing. Yet it cannot be achieved by current clinical approaches including hyperbaric oxygen therapy. Herein, we developed a sustained oxygenation system consisting of oxygen-release microspheres and a reactive oxygen species (ROS)-scavenging hydrogel. The hydrogel was used to capture the ROS that is elevated in the diabetic wounds, and that may be generated due to oxygen release. The sustainedly released oxygen augmented survival and migration of keratinocytes and dermal fibroblasts; promoted angiogenic growth factor expression, and angiogenesis in the diabetic wounds; and decreased M1 macrophage density. These effects led to a significant increase of wound closure rate. These findings reveal that sustained oxygenation alone without using drugs is capable of healing diabetic wounds.
Activity-dependent Golgi satellite formation in dendrites reshapes the neuronal surface glycoproteome
Authors: Govind Anitha P. , Jeyifous Okunola , Russell Theron A. , Yi Zola , Weigel Aubrey V. , Ramaprasad Abhijit , Newell Luke , Ramos William , Valbuena Fernando M. , Casler Jason C. , Yan Jing-Zhi , Glick Benjamin S. , Swanson Geoffrey T. , Lippincott-Schwartz Jennifer , Green William N. 
Published: April 2021

ABSTRACTActivity-driven changes in the neuronal surface glycoproteome are known to occur with synapse formation, plasticity and related diseases, but their mechanistic basis and significance are unclear. Here, we observed thatN-glycans on surface glycoproteins of dendrites shift from immature to mature forms containing sialic acid in response to increased neuronal excitation. In exploring the basis of theseN-glycosylation alterations, we discovered they result from the growth and proliferation of Golgi satellites scattered throughout the dendrite. Golgi satellites that formed with neuronal excitation were in close association with ER exit sites and early endosomes and contained glycosylation machinery without the Golgi structural protein, GM130. They functioned as distal glycosylation stations in dendrites, terminally modifying sugars either on newly synthesized glycoproteins passing through the secretory pathway, or on surface glycoproteins taken up from the endocytic pathway. These activities led to major changes in the dendritic surface of excited neurons, impacting binding and uptake of lectins, as well as causing functional changes in neurotransmitter receptors such as nicotinic acetylcholine receptors. Neural activity thus boosts the activity of the dendrite’s satellite micro-secretory system by redistributing Golgi enzymes involved in glycan modifications into peripheral Golgi satellites. This remodeling of the neuronal surface has potential significance for synaptic plasticity, addiction and disease.
Intrinsic Timescales Across the Basal Ganglia
Authors: Nougaret Simon , Fascianelli Valeria , Ravel Sabrina , Genovesio Aldo 
Published: April 2021

AbstractRecent studies have shown that neuronal stability over time can be estimated by the structure of the spike-count autocorrelation of neuronal populations. This estimation, called the intrinsic timescale, has been computed for several cortical areas and can be used to propose a cortical hierarchy reflecting a scale of temporal receptive windows between areas. In this study, we performed an autocorrelation analysis on neuronal populations of three basal ganglia (BG) nuclei, including the striatum and the subthalamic nucleus (STN), the input structures of the BG, and the external globus pallidus (GPe). The analysis was performed during the baseline period of a motivational visuomotor task in which monkeys had to apply different amounts of force to receive a different amount of reward. We found that the striatum and the STN have longer intrinsic timescales than the GPe. Moreover, our results allow for the placement of these subcortical structures within the already-defined scale of cortical temporal receptive windows. Estimates of intrinsic timescales are important in adding further constraints in the development of computational models of the complex dynamics among these nuclei and throughout cortico-BG-thalamo-cortical loops.
Selective abrogation of S6K2 maps lipid homeostasis as a survival vulnerability in MAPKi-resistant NRASMUTmelanoma
Authors: Lipchick Brittany , Guterres Adam N. , Chen Hsin-Yi , Zundell Delaine M. , Aguila Segundo Del , Reyes-Uribe Patricia I. , Basu Subhasree , Yin Xiangfan , Kossenkov Andrew V. , Lu Yiling , Mills Gordon B. , Liu Qin , Goldman Aaron R. , Murphy Maureen E. , Speicher David W. , Villanueva Jessie 
Published: April 2021

ABSTRACTAlthough oncogenic NRAS activates MAPK signaling, inhibition of the MAPK pathway is not therapeutically efficacious in NRAS-mutant tumors. Here we report that silencing the ribosomal protein S6 kinase 2 (S6K2), while preserving the activity of S6K1, perturbs lipid metabolism, enhances fatty acid unsaturation, and triggers lethal lipid peroxidation selectively in NRAS-mutant melanoma cells that are resistant to MAPK inhibition. S6K2 depletion induces ER stress, and PPARα activation, triggering cell death selectively in MAPKi-resistant melanoma. We show that combining PPARα agonists and polyunsaturated fatty acids phenocopies the effects of S6K2 abrogation, blocking tumor growth in PDX and immunocompetent mouse pre-clinical models. Collectively, our study establishes S6K2 and its effector subnetwork as promising targets for NRAS-mutant melanoma that are resistant to global MAPK pathway inhibitors.One Sentence SummaryS6K2 is a vulnerability in MAPK inhibitor-resistant NRAS-mutant melanoma
Within-host genetic micro-diversity ofMycobacterium tuberculosisand the link with tuberculosis disease features
Authors: Genestet Charlotte , Hodille Elisabeth , Massol François , Refrégier Guislaine , Barbry Alexia , Westeel Emilie , Lina Gérard , Ader Florence , Jacob Laurent , Dray Stéphane , Berland Jean-Luc , Venner Samuel , Dumitrescu Oana 
Published: April 2021

ABSTRACTTuberculosis (TB), caused byMycobacterium tuberculosis(Mtb) complex, is still the number one deadly contagious disease. Mtb infection results in a wide spectrum of clinical presentations and severity symptoms, but without proven Mtb genetic determinants. Thanks to a collection of 355 clinical isolates with associated patient’s clinical data, we showed that Mtb micro-diversity within patient isolates is strongly correlated with TB-associated severity scores. Interestingly, this diversity is driven by a selection pressure to adapt to different lifestyles related to the infection site. Taken together, these results provide a new insight to better understand TB pathophysiology. Furthermore, Mtb micro-diversity could be envisioned as a new prognostic tool to improve the management of TB patients.
Dissociation of early and late face-related processes in Autism Spectrum Disorder and Williams syndrome
Authors: Gomez Alice , Lio Guillaume , Costa Manuela , Sirigu Angela , Demily Caroline 
Published: April 2021

AbstractWilliams syndrome (WS) and Autism Spectrum Disorders (ASD) are psychiatric conditions associated with atypical but opposite face-to-face interactions patterns: WS patients overly stare at others, ASD individuals escape eye contact. Whether these behaviors result from dissociable visual processes within the occipito-temporal pathways is unknown.Using high-density electroencephalography, multivariate signal processing algorithms and a protocol designed to identify and extract evoked activities sensitive to facial cues, we investigated how WS (N=14), ASD (N=14) and neurotypical subjects (N=14) decode the information content of a face stimulus.We found two neural components in neurotypical participants, both strongest when the eye region was projected onto the subject’s fovea, simulating a direct eye contact situation, and weakest over more distant regions, reaching a minimum when the focused region was outside the stimulus face. The first component peaks at 170ms, an early signal known to be implicated in low-level face features. The second is identified later, 260ms post-stimulus onset and is implicated in decoding salient face social cues.Remarkably, both components were found distinctly impaired and preserved in WS and ASD. In WS, we could weakly decode the 170ms signal based on our regressor relative to facial features, probably due to their relatively poor ability to process faces’ morphology, while the late 260ms component was highly significant. The reverse pattern was observed in ASD participants who showed neurotypical like early 170ms evoked activity but impaired late evoked 260ms signal. Our study reveals a dissociation between WS and ASD patients and point at different neural origins for their social impairments.