bluuebunny/crossref_metadata_2025_split huggingface dataset:
COVID-19 SignSym: a fast adaptation of a general clinical NLP tool to identify and normalize COVID-19 signs and symptoms to OMOP common data model
Authors: Wang Jingqi , Abu-el-Rub Noor , Gray Josh , Pham Huy Anh , Zhou Yujia , Manion Frank J. , Liu Mei , Song Xing , Xu Hua , Rouhizadeh Masoud , Zhang Yaoyun 
Published: January 2021

Abstract
The COVID-19 pandemic swept across the world rapidly, infecting millions of people. An efficient tool that can accurately recognize important clinical concepts of COVID-19 from free text in electronic health records (EHRs) will be valuable to accelerate COVID-19 clinical research. To this end, this study aims at adapting the existing CLAMP natural language processing tool to quickly build COVID-19 SignSym, which can extract COVID-19 signs/symptoms and their 8 attributes (body location, severity, temporal expression, subject, condition, uncertainty, negation, and course) from clinical text. The extracted information is also mapped to standard concepts in the Observational Medical Outcomes Partnership common data model. A hybrid approach of combining deep learning-based models, curated lexicons, and pattern-based rules was applied to quickly build the COVID-19 SignSym from CLAMP, with optimized performance. Our extensive evaluation using 3 external sites with clinical notes of COVID-19 patients, as well as the online medical dialogues of COVID-19, shows COVID-19 SignSym can achieve high performance across data sources. The workflow used for this study can be generalized to other use cases, where existing clinical natural language processing tools need to be customized for specific information needs within a short time. COVID-19 SignSym is freely accessible to the research community as a downloadable package (https://clamp.uth.edu/covid/nlp.php) and has been used by 16 healthcare organizations to support clinical research of COVID-19.
Comparison of Efficacy of Povidone-Iodine, Ethanol, and an Aerosol Formulation of Silver Sulfadiazine in Controlling Microbial Burden on Sutures From Clean Surgeries
Authors: Prezzavento Gustavo E , Mas Carlos R , Achaval Rodríguez Juan , Juárez Calvi Rodrigo N , Piskulic Laura , Angelini Julia , Allasia María B , Smania Andrea M , Moyano Alejandro J 
Published: January 2021

AbstractIn the surgical suture, the implanted thread can be a source of microbial contamination. Implanted materials are frequently described as being substrates prone for biofilm development provoking surgical site infections. Treatment of postsurgical wounds with different topical antimicrobial agents is a current practice applied to every patient. However, to date, there is little evidence on the efficacy of different antiseptic treatments on suture materials in preventing environmental or skin bacterial adhesion and further infection. Here, the authors compared the ability of an aerosol formulation of silver sulfadiazine, vitamin A, and lidocaine (AF-SSD) and of two of the most frequently used topical treatments, povidone-iodine and ethanol, in eradicating or controlling the microbial contamination of suture threads in patients who have undergone clean surgeries. Postsurgical suture threads treated with AF-SSD showed a significantly reduced proportion of contaminated samples containing viable microbial cells compared with those treated with povidone-iodine or ethanol. Furthermore, those samples that were positive for bacterial growth showed a lesser number of viable cells in AF-SSD-treated sutures than those treated with povidone-iodine or ethanol. Confocal laser scanning microscopy showed that AF-SSD-treated postsurgical sutures presented significantly less attached microbial cells than povidone-iodine and ethanol, with scarce observable microbial cells on the surface of the suture. Taken together, the results suggest that treatment with AF-SSD is more effective than the other two antiseptics, and there is a potential for improvement in reducing the microbial burden of implanted materials such as the suture thread.
Completeness of the Gaia-verse – IV. The astrometry spread function of Gaia DR2
Authors: Everall Andrew , Boubert Douglas , Koposov Sergey E , Smith Leigh , Holl Berry 
Published: January 2021

ABSTRACT
Gaia Data Release 2 (DR2) published positions, parallaxes, and proper motions for an unprecedented 1331 909 727 sources, revolutionizing the field of Galactic dynamics. We complement this data with the astrometry spread function (ASF), the expected uncertainty in the measured positions, proper motions, and parallax for a non-accelerating point source. The ASF is a Gaussian function for which we construct the 5D astrometric covariance matrix as a function of position on the sky and apparent magnitude using the Gaia DR2 scanning law and demonstrate excellent agreement with the observed data. This can be used to answer the question ‘What astrometric covariance would Gaia have published if my star was a non-accelerating point source?’. The ASF will enable characterization of binary systems, exoplanet orbits, astrometric microlensing events, and extended sources that add an excess astrometric noise to the expected astrometry uncertainty. By using the ASF to estimate the unit weight error of Gaia DR2 sources, we demonstrate that the ASF indeed provides a direct probe of the excess source noise. We use the ASF to estimate the contribution to the selection function of the Gaia astrometric sample from a cut on astrometric_sigma5d_max showing high completeness for G &lt; 20 dropping to ${\lt} 1{{\ \rm per\ cent}}$ in underscanned regions of the sky for G = 21. We have added an ASF module to the python package scanninglaw (https://github.com/gaiaverse/scanninglaw) through which users can access the ASF.
A thermophysical and dynamical study of the Hildas, (1162) Larissa, and (1911) Schubart
Authors: Chavez Cristian F , Müller T G , Marshall J P , Horner J , Drass H , Carter B 
Published: January 2021

ABSTRACT
The Hilda asteroids are among the least studied populations in the asteroid belt, despite their potential importance as markers of Jupiter’s migration in the early Solar system. We present new mid-infrared observations of two notable Hildas, (1162) Larissa, and (1911) Schubart, obtained using the Faint Object infraRed CAmera for the SOFIA Telescope (FORCAST), and use these to characterize their thermal inertia and physical properties. For (1162) Larissa, we obtain an effective diameter of 46.5$^{+2.3}_{-1.7}$ km, an albedo of 0.12 ± 0.02, and a thermal inertia of 15$^{+10}_{-8}$ Jm−2 s1/2 K−1. In addition, our Larissa thermal measurements are well matched with an ellipsoidal shape with an axial ratio a/b = 1.2 for the most-likely spin properties. Our modelling of (1911) Schubart is not as refined, but the thermal data point towards a high-obliquity spin-pole, with a best fit a/b = 1.3 ellipsoidal shape. This spin-shape solution is yielding a diameter of 72$^{+3}_{-4}$ km, an albedo of 0.039± 0.02, and a thermal inertia below 30 Jm−2 s1/2 K−1 (or 10$^{+20}_{-5}$ Jm−2 s1/2 K−1). As with (1162) Larissa, our results suggest that (1911) Schubart is aspherical, and likely elongated in shape. Detailed dynamical simulations of the two Hildas reveal that both exhibit strong dynamical stability, behaviour that suggests that they are primordial, rather than captured objects. The differences in their albedos, along with their divergent taxonomical classification, suggests that despite their common origin, the two have experienced markedly different histories.
Selenomethionine ameliorates LPS-induced intestinal immune dysfunction in chicken jejunum
Authors: Cui Yuan , Qu Yingying , Yin Kai , Zhang Xintong , Lin Hongjin 
Published: January 2021

AbstractSelenomethionine (SeMet) is a widely used food supplement. However, the research on the effect of SeMet on intestinal immune function is not enough. Therefore, in this experiment, SeMet was added to the diet of chickens, and lipopolysaccharide (LPS) was used as harmful stimulation to study the effect of SeMet on intestinal immune function in chickens. We chose chicken jejunum as the research object. The results showed that LPS treatment decreased the expressions of selenoproteins and induced inflammatory reaction, cytokine disorder, decreases of immunoglobulin levels, heat shock protein expression disorder, and decreases of defensin expression levels in jejunum. However, dietary SeMet can effectively alleviate the above injury caused by LPS. Our results showed that SeMet could improve the intestinal immunity in chickens, and feeding SeMet could alleviate the intestinal immune dysfunction caused by LPS. The application range of SeMet in feed can be roughly given through our experiment; i.e. 0.35–0.5 mg/kg SeMet was effective. We speculated that dietary SeMet could effectively alleviate the intestinal immune dysfunction caused by harmful stimulation and help to resist the further damage caused by harmful stimulation.
Infectious Period of Severe Acute Respiratory Syndrome Coronavirus 2 in 17 Nursing Home Residents—Arkansas, June–August 2020
Authors: Surie Diya , Huang Jennifer Y , Brown Allison C , Gable Paige , Biedron Caitlin , Gilbert Sarah E , Garner Kelley , Bollinger Susan , Gulley Trent , Haney Tafarra , Lyons Amanda K , Beshearse Elizabeth , Gregory Christopher J , Sabour Sarah , Clemmons Nakia S , James Allison E , Tamin Azaibi , Reese Natashia , Perry-Dow K Allison , Brown Robin , Harcourt Jennifer L , Campbell Davina , Houston Hollis , Chakravorty Rohan , Paulick Ashley , Whitaker Brett , Murdoch Jordan , Spicer Lori , Stumpf Megan M , Mills Lisa , Coughlin Melissa M , Higdem Pamela , Rasheed Mohammad Ata Ur , Lonsway David , Bhatnagar Amelia , Kothari Atul , Anderson Karen , Thornburg Natalie J , Breaker Erin , Adamczyk Michelle , McAllister Gillian A , Halpin Alison L , Seely Kathryn A , Patil Naveen , McDonald L Clifford , Kutty Preeta K 
Published: January 2021

Abstract

Background
To estimate the infectious period of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in older adults with underlying conditions, we assessed duration of coronavirus disease 2019 (COVID-19) symptoms, reverse-transcription polymerase chain reaction (RT-PCR) positivity, and culture positivity among nursing home residents.

Methods
We enrolled residents within 15 days of their first positive SARS-CoV-2 test (diagnosis) at an Arkansas facility from July 7 to 15, 2020 and instead them for 42 days. Every 3 days for 21 days and then weekly, we assessed COVID-19 symptoms, collected specimens (oropharyngeal, anterior nares, and saliva), and reviewed medical charts. Blood for serology was collected on days 0, 6, 12, 21, and 42. Infectivity was defined by positive culture. Duration of culture positivity was compared with duration of COVID-19 symptoms and RT-PCR positivity. Data were summarized using measures of central tendency, frequencies, and proportions.

Results
We enrolled 17 of 39 (44%) eligible residents. Median participant age was 82 years (range, 58–97 years). All had ≥3 underlying conditions. Median duration of RT-PCR positivity was 22 days (interquartile range [IQR], 8–31 days) from diagnosis; median duration of symptoms was 42 days (IQR, 28–49 days). Of 9 (53%) participants with any culture-positive specimens, 1 (11%) severely immunocompromised participant remained culture-positive 19 days from diagnosis; 8 of 9 (89%) were culture-positive ≤8 days from diagnosis. Seroconversion occurred in 12 of 12 (100%) surviving participants with ≥1 blood specimen; all participants were culture-negative before seroconversion.

Conclusions
Duration of infectivity was considerably shorter than duration of symptoms and RT-PCR positivity. Severe immunocompromise may prolong SARS-CoV-2 infectivity. Seroconversion indicated noninfectivity in this cohort.
To stop or not to stop ‘culture’: determining the essential behavior of the government, church and public in fighting against COVID-19
Authors: Cordero Dalmacito A 
Published: January 2021

Abstract
Culture is a way of life. A recent correspondence emphasizes that it is a contributory factor in combatting the COVID-19 pandemic, and this must be considered by each government around the world. However, I argue that various elements in culture do not need to stop or else it will create public outrage. I therefore propose a win–win solution for both parties with the inclusion of the church that can serve as a framework for the sake of public health. It is primarily based on a kind of behavior that is needed to be embodied by the involved groups—‘supportive’ government, ‘creative’ church and an ‘adaptive’ public. These essential behaviors of all groups are possible to embody for a successful implementation of public health.
The evolving view of replay and its functions in wake and sleep
Authors: Findlay Graham , Tononi Giulio , Cirelli Chiara 
Published: January 2021

AbstractThe term hippocampal replay originally referred to the temporally compressed reinstantiation, during rest, of sequential neural activity observed during prior active wake. Since its description in the 1990s, hippocampal replay has often been viewed as the key mechanism by which a memory trace is repeatedly rehearsed at high speeds during sleep and gradually transferred to neocortical circuits. However, the methods used to measure the occurrence of replay remain debated, and it is now clear that the underlying neural events are considerably more complicated than the traditional narratives had suggested. “Replay-like” activity happens during wake, can play out in reverse order, may represent trajectories never taken by the animal, and may have additional functions beyond memory consolidation, from learning values and solving the problem of credit assignment to decision-making and planning. Still, we know little about the role of replay in cognition, and to what extent it differs between wake and sleep. This may soon change, however, because decades-long efforts to explain replay in terms of reinforcement learning (RL) have started to yield testable predictions and possible explanations for a diverse set of observations. Here, we (1) survey the diverse features of replay, focusing especially on the latest findings; (2) discuss recent attempts at unifying disparate experimental results and putatively different cognitive functions under the banner of RL; (3) discuss methodological issues and theoretical biases that impede progress or may warrant a partial revaluation of the current literature, and finally; (4) highlight areas of considerable uncertainty and promising avenues of inquiry.
Aquarium: open-source laboratory software for design, execution and data management
Authors: Vrana Justin , de Lange Orlando , Yang Yaoyu , Newman Garrett , Saleem Ayesha , Miller Abraham , Cordray Cameron , Halabiya Samer , Parks Michelle , Lopez Eriberto , Goldberg Sarah , Keller Benjamin , Strickland Devin , Klavins Eric 
Published: January 2021

AbstractAutomation has been shown to improve the replicability and scalability of biomedical and bioindustrial research. Although the work performed in many labs is repetitive and can be standardized, few academic labs can afford the time and money required to automate their workflows with robotics. We propose that human-in-the-loop automation can fill this critical gap. To this end, we present Aquarium, an open-source, web-based software application that integrates experimental design, inventory management, protocol execution and data capture. We provide a high-level view of how researchers can install Aquarium and use it in their own labs. We discuss the impacts of the Aquarium on working practices, use in biofoundries and opportunities it affords for collaboration and education in life science laboratory research and manufacture.
Anatomical variation of mesophyll conductance due to salt stress inPopulus cathayanafemales and males growing under different inorganic nitrogen sources
Authors: Liu Miao , Liu Xiucheng , Du Xuhua , Korpelainen Helena , Niinemets Ülo , Li Chunyang 
Published: January 2021

AbstractSynergistic regulation in leaf architecture and photosynthesis is essential for salt tolerance. However, how plant sex and inorganic nitrogen sources alter salt stress-dependent photosynthesis remains unknown. Leaf anatomical characteristics and photosynthesis of Populus cathayana Rehder females and males were investigated under salt stress conditions combined with nitrate NO3− and ammonium NH4+ supplies to clarify the underlying mechanisms. In salt-stressed females, we observed an increased mesophyll spongy cell density, a reduced chloroplast density, a decreased surface area of chloroplasts adjacent to the intercellular air space (Sc/S) and an increased mesophyll cell area per transverse section width (S/W), consequently causing mesophyll conductance (gm) and photosynthesis inhibition, especially under NH4+ supply. Conversely, males with a greater mesophyll palisade tissue thickness and chloroplast density, but a lower spongy cell density had lower S/W and higher Sc/S, and higher gm and photosynthesis. NH4+-fed females had a lower CO2 conductance through cell wall and stromal conductance perpendicular to the cell wall, but a higher chloroplast conductance from the cell wall (gcyt1) than females supplied with NO3−, whereas males had a higher chloroplast conductance and lower CO2 conductance through cell wall when supplied with NO3− instead of NH4+ under salt stress. These findings indicate sex-specific strategies in coping with salt stress related to leaf anatomy and gm under both types of nitrogen supplies, which may contribute to sex-specific CO2 capture and niche segregation.
The composition and function ofEnterococcus faecalismembrane vesicles
Authors: Afonina Irina , Tien Brenda , Nair Zeus , Matysik Artur , Lam Ling Ning , Veleba Mark , Koh Augustine , Rashid Rafi , Cazenave-Gassiot Amaury , Wenk Marcus , Wai Sun Nyunt , Kline Kimberly A. 
Published: January 2021

AbstractMembrane vesicles (MVs) contribute to various biological processes in bacteria, including virulence factor delivery, host immune evasion, and cross-species communication. MVs are frequently being discharged from the surface of both Gram-negative and Gram-positive bacteria during growth. In some Gram-positive bacteria, genes affecting MV biogenesis have been identified, but the mechanism of MV formation is unknown. InEnterococcus faecalis, a causative agent of life-threatening bacteraemia and endocarditis, neither mechanisms of MV formation nor their role in virulence has been examined. Since MVs of many bacterial species are implicated in host-pathogen interactions, biofilm formation, horizontal gene transfer, and virulence factor secretion in other species, we sought to identify, describe, and functionally characterize MVs fromE. faecalis. Here we show thatE. faecalisreleases MVs that possess unique lipid and protein profiles, distinct from the intact cell membrane, and are enriched in lipoproteins. MVs ofE. faecalisare specifically enriched in unsaturated lipids that might provide membrane flexibility to enable MV formation, providing the first insights into the mechanism of MV formation in this Gram-positive organism.
Reliance on polyfunctional tissue leads to a reproduction-immunity tradeoff due to inherent constraint
Authors: Gupta Vanika , Frank Ashley M. , Matolka Nick , Lazzaro Brian P. 
Published: January 2021

AbstractThe use of one tissue for multiple purposes can result in constraints, impaired function, and tradeoffs. The insect fat body performs remarkably diverse functions including metabolic control, reproductive provisioning, and systemic immune responses. Immunity and reproduction are observed to trade off in many organisms, although the mechanistic basis for the tradeoff is generally unknown. More generally, how do polyfunctional tissues simultaneously execute multiple distinct physiological functions? Using single-nucleus sequencing, we determined theDrosophila melanogasterfat body executes diverse basal functions with heterogenous cellular subpopulations. However, as an emergency function, the immune response engages the entire tissue. We found that reproductively active females exhibit impaired capacity to produce new protein in response to infection, resulting in the reproduction-immunity tradeoff. We suggest that such inherent internal limitations may provide a general explanation for the wide prevalence of physiological and evolutionary tradeoffs.
A genetic approach to dissect the role of prefoldins inArabidopsis
Authors: Blanco-Touriñán Noel , Esteve-Bruna David , Serrano-Mislata Antonio , María Esquinas Rosa , Resentini Francesca , Forment Javier , Carrasco-López Cristian , Novella-Rausell Claudio , Palacios Alberto , Carrasco Pedro , Salinas Julio , Blázquez Miguel Á. , Alabadí David 
Published: January 2021

SummaryThe prefoldin complex (PFDc) was identified in humans as co-chaperone of the cytosolic chaperonin TRiC/CCT. It is conserved in eukaryotes and is composed of subunits PFD1 to 6. PFDc-TRiC/CCT operates folding actin and tubulins. In addition to this function, PFDs participate in a wide range of cellular processes, both in the cytoplasm and in the nucleus, and their malfunction cause developmental alterations and disease in animals, and altered growth and environmental responses in yeast and plants. Genetic analyses in yeast indicate that not all functions performed by PFDs require the participation of the canonical complex. The lack of systematic genetic analyses in higher eukaryotes makes it difficult to discern whether PFDs participate in a particular process as canonical complex or in alternative configurations,i.e. as individual subunits or in other complexes. To tackle this question, and on the premise that the canonical complex cannot be formed if one subunit is missing, we have prepared anArabidopsismutant deficient in the six prefoldins, and compared various growth and environmental responses with those of the individualpfd. In this way, we demonstrate that the PFDc is required to delay flowering, for seed germination, or to respond to high salt stress, whereas two or more PFDs redundantly attenuate the response to osmotic stress. A coexpression analysis of differentially expressed genes in the sextuple mutant has identified several transcription factors, such as ABI5 or PIF4, acting downstream of PFDs. Furthermore, it has made possible to assign novel roles for PFDs, for instance, in the response to warm temperature.
Spatial organization of transcript elongation and splicing kinetics
Authors: Casill Alyssa D. , Haimowitz Adam J. , Kosmyna Brian , Query Charles C. , Ye Kenny , Gamble Matthew J. 
Published: January 2021

SummaryThe organization of the genome in three-dimensional space has been shown to play an important role in gene expression. Specifically, facets of genomic interaction such as topologically associated domains (TADs) have been shown to regulate transcription by bringing regulatory elements into close proximity1. mRNA production is an intricate process with multiple control points including regulation of Pol II elongation and the removal of non-coding sequences via pre-mRNA splicing2. The connection between genomic compartments and the kinetics of RNA biogenesis and processing has been largely unexplored. Here, we measure Pol II elongation and splicing kinetics genome-wide using a novel technique that couples nascent RNA-seq with a mathematical model of transcription and co-transcriptional RNA processing. We uncovered multiple layers of spatial organization of these rates: the rate of splicing is coordinated across introns within individual genes, and both elongation and splicing rates are coordinated within TADs, as are alternative splicing outcomes. Overall, our work establishes that the kinetics of transcription and splicing are coordinated by the spatial organization of the genome and suggests that TADs are a major platform for coordination of alternative splicing.