bluuebunny/crossref_metadata_2025_split huggingface dataset:
Why (and how) COVID-19 could move us closer to the “health information for all” goal
Authors: Capocasa Marco , Anagnostou Paolo , Bisol Giovanni Destro 
Published: July 2020

SummaryIn this manuscript, we present an analysis of open access (OA) rates of papers concerning COVID-19 and other important human diseases, whose results helped develop an evidence-based scalable strategy aimed at increasing the full and timely access to medical literature. We show that COVID-19 papers are much more openly available (OA rate of 89.5%) than those concerning the four most recent viral outbreaks (Avian influenza, Middle East Respiratory Syndrome, Severe Acute Respiratory Syndrome, Swine influenza; OA rates (from 26.2% to 51.3%) and the ten non COVID-19 disease categories responsible for the highest number of deaths worldwide (OA rates from 44.0% for “Maternal and neonatal disorders” to 58.9% for “Respiratory infections and tuberculosis”). This evidence confronts us with an inevitable question: how can we bridge the gap between OA rates for COVID-19 and other high-impact human diseases? Based on empirical data and projections, we show that it is possible to increase substantially immediate OA to publicly-funded research and complement more demanding initiatives for access to medical literature in developing countries working on the sharing of post-prints at individual, group and multi stakeholder partnership level. However, to make our plan effective in bringing us closer to the “health information for all” goal a more widespread culture of cooperation is fundamental. We argue that the lesson taught by COVID-19 is a unique opportunity to raise awareness among researchers and stakeholders about the importance of open science for human health and to demonstrate that a real change is now possible.
Shared Component Analysis
Authors: de Cheveigné Alain 
Published: July 2020

AbstractThis paper proposes Shared Component Analysis (SCA) as an alternative to Principal Component Analysis (PCA) for the purpose of dimensionality reduction of neuroimaging data. The trend towards larger numbers of recording sensors, pixels or voxels leads to richer data, with finer spatial resolution, but it also inflates the cost of storage and computation and the risk of overfitting. PCA can be used to select a subset of orthogonal components that explain a large fraction of variance in the data. This implicitly equates variance with relevance, and for neuroimaging data such as electroencephalography (EEG) or magnetoencephalography (MEG) that assumption may be inappropriate if (latent) sources of interest are weak relative to competing sources. SCA instead assumes that components that contribute to observable signals on multiple sensors are of likely interest, as may be the case for deep sources within the brain as a result of current spread. In SCA, steps of normalization and PCA are applied iteratively, linearly transforming the data such that components more widely shared across channels appear first in the component series. The paper explains the motivation, defines the algorithm, evaluates the outcome, and sketches a wider strategy for dimensionality reduction of which this algorithm is an example. SCA is intended as a plug-in replacement for PCA for the purpose of dimensionality reduction.
Aspirin prescribing in cardiovascular disease in middle-aged and older adults in Ireland: findings from The Irish Longitudinal Study on Ageing
Authors: Moriarty Frank , Barry Alan , Kenny Rose Anne , Fahey Tom 
Published: July 2020

AbstractBackgroundAspirin use for cardiovascular indications is widespread despite evidence not supporting use in patients without cardiovascular disease (CVD). This study characterises aspirin prescribing among people aged ≥50 years in Ireland for primary and secondary prevention, and factors associated with prescription.MethodsThis cross-sectional study includes participants from wave 3 (2014-2015) of The Irish Longitudinal Study on Ageing. We identified participants reporting use of prescribed aspirin, other antiplatelets/anticoagulants, and doctor-diagnosed CVD (MI, angina, stroke, TIA) and other cardiovascular conditions. We examined factors associated with aspirin use for primary and secondary prevention in multivariate regression. For a subset, we also examined 10-year cardiovascular risk (using the Framingham general risk score) as a predictor of aspirin use.ResultsAmong 6,618 participants, the mean age was 66.9 years (SD 9.4) and 55.6% (3,679) were female. Prescribed aspirin was reported by 1,432 participants (21.6%), and 77.6% of aspirin users had no previous CVD. Among participants with previous CVD, 17% were not prescribed aspirin/another antithrombotic. This equates to 201,000 older adults nationally using aspirin for primary prevention, and 16,000 with previous CVD not prescribed an antithrombotic. Among those without CVD, older age, male sex, free health care, and more GP visits were associated with aspirin prescribing. Cardiovascular risk was significantly associated with aspirin use (adjusted relative risk 1.15, 95%CI 1.08-1.23, per 1% increase in cardiovascular risk).ConclusionAlmost four-fifths of people aged ≥50 years on aspirin have no previous CVD, equivalent to 201,000 adults nationally, however prescribing appears rational in targeting higher cardiovascular risk patients.
An effective COVID-19 response in South America: the Uruguayan Conundrum
Authors: Moreno Pilar , Moratorio Gonzalo , Iraola Gregorio , Fajardo Álvaro , Aldunate Fabián , Pereira-Gómez Marianoel , Perbolianachis Paula , Costábile Alicia , López-Tort Fernando , Simón Diego , Salazar Cecilia , Ferrés Ignacio , Díaz-Viraqué Florencia , Abin Andrés , Bresque Mariana , Fabregat Matías , Maidana Matías , Rivera Bernardina , Cruces María E. , Rodríguez-Duarte Jorge , Scavone Paola , Alegretti Miguel , Nabón Adriana , Gagliano Gustavo , Rosa Raquel , Henderson Eduardo , Bidegain Estela , Zarantonelli Leticia , Piattoni Vanesa , Greif Gonzalo , Francia María E. , Robello Carlos , Durán Rosario , Brito Gustavo , Bonnecarrere Victoria , Sierra Miguel , Colina Rodney , Marin Mónica , Cristina Juan , Ehrlich Ricardo , Paganini Fernando , Cohen Henry , Radi Rafael , Barbeito Luis , Badano José L. , Pritsch Otto , Fernández Cecilia , Arim Rodrigo , Batthyány Carlos ,   Interinstitutional COVID-19 Working Group.
Published: July 2020

ABSTRACTBackgroundSouth America has become the new epicenter of the COVID-19 pandemic with more than 1.1M reported cases and >50,000 deaths (June 2020). Conversely, Uruguay stands out as an outlier managing this health crisis with remarkable success.MethodsWe developed a molecular diagnostic test to detect SARS-CoV-2. This methodology was transferred to research institutes, public hospitals and academic laboratories all around the country, creating a “COVID-19 diagnostic lab network”. Uruguay also implemented active epidemiological surveillance following the “Test, Trace and Isolate” (TETRIS) strategy coupled to real-time genomic epidemiology.ResultsThree months after the first cases were detected, the number of positive individuals reached 826 (23 deaths, 112 active cases and 691 recovered). The Uruguayan strategy was based in a close synergy established between the national health authorities and the scientific community. In turn, academia rapidly responded to develop national RT-qPCR tests. Consequently, Uruguay was able to perform ∼1,000 molecular tests per day in a matter of weeks. The “COVID-19 diagnostic lab network” performed more than 54% of the molecular tests in the country. This, together with real- time genomics, were instrumental to implement the TETRIS strategy, helping to contain domestic transmission of the main outbreaks registered so far.ConclusionsUruguay has successfully navigated the first trimester of the COVID-19 health crisis in South America. A rapid response by the scientific community to increase testing capacity, together with national health authorities seeking out the support from the academia were fundamental to successfully contain, until now, the COVID-19 outbreak in the country.
Trends in Angiotensin Receptor Blocker Use Among those at Risk for COVID-19 Morbidity and Mortality in the United States
Authors: Perez Alexandra , Speth Robert , Saavedra Juan 
Published: July 2020

ABSTRACTImportanceAssessment of the use of angiotensin receptor blockers (ARBs) in the United States provides insight into prescribing practices, and may inform guidelines, policy measures and research during the COVID-19 pandemic.ObjectiveTo evaluate trends in ARB use among adults in the United States who have preexisting conditions and sociodemographic risk factors that put them at a higher risk of SARS-CoV-2 infection and COVID-19-related complications and mortality.Design, setting and participantsThis study uses the nationally representative cross-sectional data from the 2005-2018 National Health and Nutrition Examination Survey (NHANES). Participants included 39,749 non-institutionalized U.S. civilian adults who were 20 years and older and those with the most common preexisting conditions and risk factors reported among patients with COVID-19.Main outcomes and measuresUse of ARBs in the prior 30 days from survey interview.ResultsARB use ranged from 7.4% [95% CI, 6.5%-8.4%] to 26.2% [95% CI, 19.4%-34.4%] among those with one or two metabolic, renal, respiratory, and/or cardiovascular diseases. Among individuals with the three most common preexisting conditions in patients with COVID-19 including hypertension, diabetes and obesity, ARB use was higher among the elderly, females, non-Hispanic whites, and those with health insurance coverage.Conclusions and relevanceIn this nationally representative survey, ARB use was found to be widespread, but unevenly distributed among individuals with conditions and sociodemographic risk factors that place them at a higher risk of COVID-19 morbidity and mortality.Key PointsQuestionWhat is the prevalence of angiotensin receptor blocker (ARB) use among individuals at higher risk of COVID-19-related complications?FindingsIn a cross-sectional study with data from 39,749 adult participants of the National Health and Nutrition Examination Survey, ARB use ranged between 7.4% and 26.2% among those with one or two respiratory, metabolic, renal and/or cardiovascular diseases. Significant disparities in ARB use were found in participants with preexisting conditions and sociodemographic factors that place them at a higher risk of COVID-19 morbidity and mortality.MeaningARB use is widespread and disproportionate in the United States among people at higher risk of COVID-19 complications.
Eyes wide open: regulation of arousal by temporal expectations
Authors: Shalev Nir , Nobre Anna C. 
Published: July 2020

AbstractTo perform a task continuously over an extended period of time, it is necessary to maintain an adequate level of arousal. In cognitive research, traditional studies have used repetitive, monotonous tasks to learn about the dynamics of arousal in tasks that require sustained vigilance, such as driving or monitoring a factory line. To date, studies have rarely considered whether observers use task-embedded regularities in such continuous contexts to anticipate events and regulate arousal accordingly. In the current study, we explored whether arousal is an adaptive process that reacts to temporal stimulus predictability. Across two experiments, we used pupillometry as a proxy measure of arousal in human observers performing continuous tasks. Within the tasks, we manipulated the temporal predictability of relevant events by presenting stimuli either in a fixed rhythm or at varied intervals. Temporal predictability led to the lowering of tonic levels of arousal. Trial-wise temporal structures led to short-scale changes in pupil size related to temporal anticipation. Accordingly, we suggest that arousal is sensitive to varying levels of temporal predictability and dynamically adapts to task demands to bring about performance benefits as well as energetic efficiencies overall.Statement of RelevancePeople often have to sustain focus and high levels of performance on extended and non-stimulating tasks (e.g., driving, sowing, monitoring data acquisition). A critical factor to the success (or failure) in sustained performance is arousal – the ‘energetic state’ of the cognitive system. Here we used pupil dilation as a proxy to study levels of arousal during sustained performance on monotonous tasks. We reveal that arousal is dynamically regulated to support performance according to an important fundamental property of any task: its temporal structure. When the timing of task-relevant events is predictable, arousal levels fluctuate accordingly, saving energy overall while also optimally guiding performance. Our study and findings add ecological validity to the study of temporal expectations, by moving investigations beyond typical trial-by-trial designs. They also carry significant implications for clinical studies relying on sustained performance tasks.
Evolution of regulatory signatures in primate cortical neurons at cell type resolution
Authors: Kozlenkov Alexey , Vermunt Marit W. , Apontes Pasha , Li Junhao , Hao Ke , Sherwood Chet C. , Hof Patrick R. , Ely John J. , Wegner Michael , Mukamel Eran A. , Creyghton Menno P. , Koonin Eugene V. , Dracheva Stella 
Published: July 2020

ABSTRACTThe human cerebral cortex contains many cell types that likely underwent independent functional changes during evolution. However, cell type-specific regulatory landscapes in the cortex remain largely unexplored. Here we report epigenomic and transcriptomic analyses of the two main cortical neuronal subtypes, glutamatergic projection neurons and GABAergic interneurons, in human, chimpanzee and rhesus macaque. Using genome-wide profiling of the H3K27ac histone modification, we identify neuron-subtype-specific regulatory elements that previously went undetected in bulk brain tissue samples. Human-specific regulatory changes are uncovered in multiple genes, including those associated with language, autism spectrum disorder and drug addiction. We observe preferential evolutionary divergence in neuron-subtype-specific regulatory elements and show that a substantial fraction of pan-neuronal regulatory elements undergo subtype-specific evolutionary changes. This study sheds light on the interplay between regulatory evolution and cell-type-dependent gene expression programs, and provides a resource for further exploration of human brain evolution and function.SIGNIFICANCEThe cerebral cortex of the human brain is a highly complex, heterogeneous tissue that contains many cell types which are exquisitely regulated at the level of gene expression by non-coding regulatory elements, presumably, in a cell-type-dependent manner. However, assessing the regulatory elements in individual cell types is technically challenging, and therefore, most of the previous studies on gene regulation were performed with bulk brain tissue. Here we analyze two major types of neurons isolated from the cerebral cortex of humans, chimpanzees and rhesus macaques, and report complex patterns of cell-type-specific evolution of the regulatory elements in numerous genes. Many genes with evolving regulation are implicated in language abilities as well as psychiatric disorders.
Sensorimotor functional connectivity: a neurophysiological factor related to BCI performance
Authors: Vidaurre Carmen , Haufe Stefan , Jorajuría Tania , Müller Klaus-Robert , Nikulin Vadim V. 
Published: July 2020

AbstractBrain-Computer Interfaces (BCIs) are systems that allow users to control devices using brain activity alone. However, the ability of participants to command BCIs varies from subject to subject. For BCIs based on the modulation of sensorimotor rhythms as measured by means of electroen-cephalography (EEG), about 20% of potential users do not obtain enough accuracy to gain reliable control of the system. This lack of efficiency of BCI systems to decode user’s intentions requires the identification of neuro-physiological factors determining ‘good’ and ‘poor’ BCI performers. Given that the neuronal oscillations, used in BCI, demonstrate rich a repertoire of spatial interactions, we hypothesized that neuronal activity in sensorimotor areas would define some aspects of BCI performance. Analyses for this study were performed on a large dataset of 80 inexperienced participants. They took part in calibration and an online feedback session in the same day. Undirected functional connectivity was computed over sensorimotor areas by means of the imaginary part of coherency. The results show that post-as well as pre-stimulus connectivity in the calibration recordings is significantly correlated to online feedback performance inμand feedback frequency bands. Importantly, the significance of the correlation between connectivity and BCI feedback accuracy was not due to the signal-to-noise ratio of the oscillations in the corresponding post and pre-stimulus intervals. Thus, this study shows that BCI performance is not only dependent on the amplitude of sensorimotor oscillations as shown previously, but that it also relates to sensorimotor connectivity measured during the preceding training session. The presence of such connectivity between motor and somatosensory systems is likely to facilitate motor imagery, which in turn is associated with the generation of a more pronounced modulation of sen-sorimotor oscillations (manifested in ERD/ERS) required for the adequate BCI performance. We also discuss strategies for the up-regulation of such connectivity in order to enhance BCI performance.
RápidoPGS: A rapid polygenic score calculator for summary GWAS data without a test dataset
Authors: Reales Guillermo , Vigorito Elena , Kelemen Martin , Wallace Chris 
Published: July 2020

AbstractMotivationPolygenic scores (PGS) aim to genetically predict complex traits at an individual level. PGS are typically trained on genome-wide association summary statistics and require an independent test dataset to tune parameters. More recent methods allow parameters to be tuned on the training data, removing the need for independent test data, but approaches are computationally intensive. Based on fine-mapping principles, we present RápidoPGS, a flexible and fast method to compute PGS requiring summary-level GWAS datasets only, with little computational requirements and no test data required for parameter tuning.ResultsWe show that RápidoPGS performs slightly less well than two out of three other widely-used PGS methods (LDpred2, PRScs, and SBayesR) for case-control datasets, with median r2difference: −0.0092, −0.0042, and 0.0064, respectively, but up to 17,000-fold faster with reduced computational requirements. RápidoPGS is implemented in R and can work with user-supplied summary statistics or download them from the GWAS catalog.Availability and implementationOur method is available with a GPL license as an R package fromGitHub.
Structural and Genetic Determinants of Convergence in theDrosophilatRNA Structure-Function Map
Authors: Phillips Julie Baker , Ardell David H. 
Published: July 2020

AbstractThe evolution of tRNA multigene families remains poorly understood, exhibiting unusual phenomena such as functional conversions of tRNA genes through anticodon shift substitutions. We improved FlyBase tRNA gene annotations from twelveDrosophilaspecies, incorporating previously identified ortholog sets to compare substitution rates across tRNA bodies at single-site and base-pair resolution. All rapidly evolving sites fell within the same metal ion-binding pocket, that lies at the interface of the two major stacked helical domains. We applied our tRNA Structure-Function Mapper (tSFM) method independently to eachDrosophilaspecies and one outgroup speciesMusca domesticaand found that, although predicted tRNA structure-function maps are generally highly conserved in flies, one tRNA Class-Informative Feature (CIF) within the rapidly-evolving ion-binding pocket — Cytosine 17 (C17), ancestrally informative for lysylation identity — independently gained asparaginylation identity and substituted in parallel across tRNAAsnparalogs at least once, possibly multiple times, during evolution of the genus. InD. melanogaster, most tRNALysand tRNAAsngenes are co-arrayed in one large heterologous gene cluster, suggesting that heterologous gene conversion as well as structural similarities of tRNA-binding interfaces in the closely related asparaginyl-tRNA synthetase (AsnRS) and lysyl-tRNA synthetase (LysRS) proteins may have played a role in these changes. A previously identified Asn-to-Lys anticodon shift substitution inD. ananassaemay have arisen to compensate for the convergent and parallel gains of C17 in tRNAAsnparalogs in that lineage. Our results underscore the functional and evolutionary relevance of our tRNA structure-function map predictions and illuminate multiple genomic and structural factors contributing to rapid, parallel and compensatory evolution of tRNA multigene families.
Distribution of Epsilon-Polylysine Synthetases in Coryneform Bacteria Isolated from Cheese and Human Skin
Authors: Jiang Xinglin , Radko Yulia , Gren Tetiana , Palazzotto Emilia , Jørgensen Tue Sparholt , Cheng Tao , Xian Mo , Weber Tilmann , Lee Sang Yup 
Published: July 2020

ABSTRACTEpsilon-polylysine (ε-PL) is an antimicrobial commercially produced byStreptomycesfermentation and widely used in Asian countries for food preservation. Here we discovered a gene from cheese bacteriumCorynebacterium variabilethat showed high similarity to the ε-PL synthetase fromStreptomycesin terms of enzymatic domain architecture and gene context. By cloning it intoStreptomyces coelicolorwith aStreptomyces albulusε-PL synthetase promoter, we confirmed that its product is indeed ε-PL. A comprehensive sequence analysis suggests that ε-PL synthetases are widely spread among coryneform bacteria isolated from cheese and human skin; 14 out of 15Brevibacteriumisolates and 10 out of 12Corynebacteriumisolates contain Pls gene. This discovery raises the possibility that ε-PL as a bioactive secondary metabolite might be produced and play a role in the cheese and skin ecosystems.IMPORTANCEEvery year, microbial contamination causes billions of tons of food wasted and millions of cases of foodborne illness. ε-PL is an excellent food preservative as it is potent, wide spectrum and is heat stable and biodegradable. It has not been accepted by all countries (e.g those in the EU) partially because it was not a natural composition of food but rather originated from the soil bacteriaStreptomyces, a famous producer of various antibiotic drugs and toxins. The unexpected finding of ε-PL synthetases in cheese and skin bacteria suggests that ε-PL may naturally exist in cheese and on our skin.