bluuebunny/crossref_metadata_2025_split huggingface dataset:
Awake prone positioning and oxygen therapy in patients with COVID-19: The APRONOX study
Authors: Perez-Nieto Orlando R. , Escarraman-Martinez Diego , Guerrero-Gutierrez Manuel A. , Zamarron-Lopez Eder I. , Mancilla-Galindo Javier , Kammar-García Ashuin , Martinez-Camacho Miguel A. , Deloya-Tomás Ernesto , Sanchez-Diaz Jesús S. , Macías-García Luis A. , Soriano-Orozco Raúl , Cruz-Sánchez Gabriel , Salmeron-Gonzalez José D. , Toledo-Rivera Marco A. , Mata-Maqueda Ivette , Morgado-Villaseñor Luis A. , Martinez-Mazariegos Jenner J. , Ramirez Raymundo Flores , Medina-Estrada Josue L. , ñamendys-Silva Silvio A. 
Published: January 2021

ABSTRACTPurposeThe awake prone position (PP) strategy for patients with acute respiratory distress syndrome (ARDS) is a safe, simple, and cost-effective technique used to improve hypoxemia. We aimed to evaluate the relationship between awake PP (AP) and endotracheal intubation in patients with coronavirus disease (COVID-19).MethodsIn this retrospective, multicentre observational study conducted between 1 May and 12 June 2020 in 27 hospitals in Mexico and Ecuador, non-intubated patients with COVID-19 managed with AP or awake supine positioning (AS) were included to evaluate intubation and mortality risk in AP patients through logistic regression models; multivariable adjustment, propensity score analyses, and E-values were calculated to limit confounding. A CART model with cross-validation was also built. This study was registered at https://clinicaltrials.gov/ct2/show/NCT04407468Results827 non-intubated patients with COVID-19 in the AP (n=505) and AS (n=322) groups were included for analysis. Less patients in the AP group required endotracheal intubation (23.6% vs 40.4%) or died (20% vs 37.9%). AP was a protective factor for intubation even after multivariable adjustment (OR=0.39, 95%CI:0.28-0.56, p<0.0001, E-value=2.01), which prevailed after propensity score analysis (OR=0.32, 95%CI:0.21-0.49, p<0.0001, E-value=2.21), and mortality (adjusted OR=0.38, 95%CI:0.25-0.57, p<0.0001, E-value=1.98). The main variables associated with PP failure in AP patients were age, lower SpO2/FiO2, and management with a non-rebreather mask. In the CART model, only two variables were used: SpO2/FiO2 (F 97.7, p<0.001) and PP (X2 50.5, p<0.001), with an overall percentage of 75.2%.ConclusionPP in awake hospitalised patients with COVID-19 is associated with a lower risk of intubation and mortality.
How well do face masks protect the wearer compared to public perceptions?
Authors: O’Kelly Eugenia , Arora Anmol , Ward James , Clarkson P John 
Published: January 2021

AbstractIntroductionThere is a growing body of evidence to support the wearing of face masks to reduce spread of infectious respiratory pathogens, including SARS-CoV-2. However, the literature exploring the effectiveness of homemade fabric face masks is still in its infancy. Developing an evidence base is an important step to ensure that public policy is evidence based and truly effective.MethodsTwo methodologies were used in this study: quantitative fit testing of various face masks to indicate their effectiveness and a survey of 710 US residents about their perceptions of face mask effectiveness. N95, surgical and two fabric face masks were tested on an individual twenty five times each using a TSI 8038+ machine. Our survey was distributed by Qualtrics XM, asking participants to estimate the effectiveness of N95, surgical and fabric face masks.Results and DiscussionOur results indicate that fabric face masks blocked between 62.6% and 87.1% of fine particles, whereas surgical masks protected against an average of 78.2% of fine particles. N95 masks blocked 99.6% of fine particles. Survey respondents tended to underestimate the effectiveness of masks, especially fabric masks. Together these results suggest that fabric masks may be a useful tool in the battle against the COVID-19 pandemic and that increasing public awareness of the effectiveness of fabric masks may help in this endeavour.
REACT-1 round 8 final report: high average prevalence with regional heterogeneity of trends in SARS-CoV-2 infection in the community in England during January 2021
Authors: Riley Steven , Eales Oliver , Walters Caroline E. , Wang Haowei , Ainslie Kylie E. C. , Atchison Christina , Fronterre Claudio , Diggle Peter J. , Ashby Deborah , Donnelly Christl A. , Cooke Graham , Barclay Wendy , Ward Helen , Darzi Ara , Elliott Paul 
Published: January 2021

AbstractIn early January 2021, England entered its third national lockdown of the COVID-19 pandemic to reduce numbers of deaths and pressure on healthcare services, while rapidly rolling out vaccination to healthcare workers and those most at risk of severe disease and death. REACT-1 is a survey of SARS-CoV-2 prevalence in the community in England, based on repeated cross-sectional samples of the population. Between 6th and 22nd January 2021, out of 167,642 results, 2,282 were positive giving a weighted national prevalence of infection of 1.57% (95% CI, 1.49%, 1.66%). The R number nationally over this period was estimated at 0.98 (0.92, 1.04). Prevalence remained high throughout, but with suggestion of a decline at the end of the study period. The average national trend masked regional heterogeneity, with robustly decreasing prevalence in one region (South West) and increasing prevalence in another (East Midlands). Overall prevalence at regional level was highest in London at 2.83% (2.53%, 3.16%). Although prevalence nationally was highest in the low-risk 18 to 24 year old group at 2.44% (1.96%, 3.03%), it was also high in those over 65 years who are most at risk, at 0.93% (0.82%, 1.05%). Large household size, living in a deprived neighbourhood, and Black and Asian ethnicity were all associated with higher levels of infections compared to smaller households, less deprived neighbourhoods and other ethnicities. Healthcare and care home workers, and other key workers, were more likely to test positive compared to other workers. If sustained lower prevalence is not achieved rapidly in England, pressure on healthcare services and numbers of COVID-19 deaths will remain unacceptably high.
Frequency of hospitalization of infants with bronchiolitis during 2017 in Puerto Madryn, Argentina
Authors: L. Taire Damián , Pazos Bruno A. 
Published: January 2021

ABSTRACTIntroductionBronchiolitis is considered the most frequent disease in infants and still represents an important cause of morbidity and mortality worldwide. Despite its viral etiology, socioeconomic variables could influence the disease outcome. We aimed to determine the frequency of hospital discharge for bronchiolitis in a local Hospital in the city of Puerto Madryn, in the province of Chubut, Patagonia Argentina.Population and methodsWe performed a cross-sectional study that analyzed all hospitalized patients discharged for bronchiolitis in Hospital “Dr. Andrés R. Isola” during the year 2017 and based on data provided by the hospital administrative staff. The study variables were the length of stay, readmission rate and place of origin of hospitalized patients.ResultsA total of 120 patients were included. The median age was 4.45 months (3.9-5). The mean length-of-stay (LOS) was 7.30 days (5.52-9.08). Of the total number of patients, 24 (20%) had a LOS ≤3 days and 96 (80%) a >3 days. One hundred patients (88.33%) had no hospital readmissions and 10 patients (8.33%) had hospital readmissions. The median age of patients with readmissions was 4.2 months (2.69-5.71). The mean LOS during readmission was 17.3 days (5.25-29.35). Of the 120 hospitalized children, 100 infants (83.33%) live in areas identified as having “unsatisfied basic needs” in Puerto Madryn.ConclusionsThe overcrowding as a result of the demographic transformation on the frequency of hospitalization of infants with bronchiolitis was homogeneous within the Puerto Madryn population with “unsatisfied basic needs”.
Investigating the DNA methylation profile of e-cigarette use
Authors: Richmond Rebecca C , Rejon Carlos Sillero , Khouja Jasmine N , Prince Claire , Board Alexander , Sharp Gemma , Suderman Matthew , Relton Caroline L , Munafò Marcus , Gage Suzanne H 
Published: January 2021

AbstractRationale and objectivesLittle evidence exists on the health effects of e-cigarette use. DNA methylation may serve as a biomarker for exposure and could be predictive of future health risk. We aimed to investigate the DNA methylation profile of e-cigarette use.MethodsAmong 117 smokers, 117 non-smokers and 116 non-smoking vapers, we evaluated associations between e-cigarette use and epigenome-wide methylation from saliva. We tested associations between e-cigarette use and methylation scores known to predict smoking and smoking-related disease. We assessed the ability of a methylation score for predicting e-cigarette use and for discriminating lung cancer.Measurements and Main Results7 CpGs were identified in relation to e-cigarette use at p<1×10−5 and none at p<5.91×10−8. 13 CpGs were associated with smoking at p<1×10−5 and one at p<5.91×10−8. CpGs associated with e-cigarette use were largely distinct from those associated with smoking. There was strong enrichment of known smoking-related CpGs in the smokers but not the vapers. A methylation score for e-cigarette use showed poor prediction internally (AUC 0.55, 0.41-0.69) and externally (AUC 0.57, 0.36-0.74) compared with a smoking score (AUCs 0.80) and was less able to discriminate lung squamous cell carcinoma from adjacent normal tissue (AUC 0.64, 0.52-0.76 versus AUC 0.73, 0.61-0.85).ConclusionsThe DNA methylation profile for e-cigarette use is largely distinct from that of cigarette smoking, did not replicate in independent samples, and was unable to discriminate lung cancer from normal tissue. The extent to which methylation related to long-term e-cigarette use translates into chronic effects requires further investigation.Key MessagesWhat is the key question?Is there a DNA methylation signature of e-cigarette use and is it distinct from that of smoking?What is the bottom line?Smoke exposure is known to lead to widespread changes in DNA methylation which have been identified in different populations and samples, persist for many years after smoking cessation, and may act as a biomarker for smoking-related disease risk and mortality. Whether a similar methylation profile exists in relation to e-cigarette use has not been widely investigated.Why read on?We obtained saliva samples from 116 e-cigarette users and compared their DNA methylation profile with 117 smokers and 117 non-smokers. The e-cigarette users in this study had a minimal smoking history, and so we were able to distinguish the effects of e-cigarette use from those of smoke exposure. Overall, we found that the methylation profile associated with e-cigarette use is less pronounced and distinct from that associated with cigarette smoking.
Evaluation of the fluid-movement contribution to the oxygen transport in tissue
Authors: Liu Zhu , Wen Chenyu , Zhang Shi-Li 
Published: January 2021

AbstractThe model of diffusive O2transport from capillary to tissue was established by Krogh a century ago. This model is incomplete as it ignores the often inevitable convective O2transport via fluid movement. Here, we propose a one-dimensional physical-phenomenological model to evaluate the contribution of fluid movement to the O2transport in tissue. Both the O2gradient and the total O2flux are found to be sensitive to the fluid movement. For small flow rates with a Peclet numberPe< 1, a critical flow rate,udc, is introduced to characterize the contribution of fluid movement to the O2transport, as well as to evaluate the fluid contribution in O2-deficient tissues and the cytoplasm movement inside muscle fibers. During hemostasis, the O2flux contributed by the interstitial flow even below a rate of 2 μm/s, although negligible near the capillary, can be significant for the tissue residing far from the capillary. For an isolated intramyocyte mitochondrion, the cytoplasm movement can play a key role in the O2transport. These considerations point to the scenario of an external force to drive the fluid movement leading to an accelerated O2transport to sustain the mitochondrial consumption. Our model offers a comprehensive picture of the O2transport in tissue by including both the concentration gradient and the hydraulic pressure gradient. It predicts that even with a small external force, damaged tissues with higher permeability can yield larger rates of interstitial flow promoting O2transport for tissue recovery.HighlightsThe fluid movement can play a significant role in O2transport in tissue with high Prandtl numberν/D~ 103;A critical flow rate,udc, is introduced to evaluate the convective transport flux by the fluid in tissue for Pe < 1.O2transport in tissue is a result of the balance between hydraulic pressure gradient induced flux and concentration gradient induced flux.Our model indicates more O2pumped by convective transport into the O2-deficient region where the O2diffusive flux cannot penetrate.The cytoplasm movement can excite more O2flux to the mitochondria with higher myoglobin concentration.
The Similarity Structure of Real-World Memories
Authors: Tomita Tyler M. , Barense Morgan D. , Honey Christopher J. 
Published: January 2021

How do we mentally organize our memories of life events? Two episodes may be connected because they share a similar location, time period, activity, spatial environment, or social and emotional content. However, we lack an understanding of how each of these dimensions contributes to the perceived similarity of two life memories. We addressed this question with a data-driven approach, eliciting pairs of real-life memories from participants. Participants annotated the social, purposive, spatial, temporal, and emotional characteristics of their memories. We found that the overall similarity of memories was influenced by all of these factors, but to very different extents. Emotional features were the most consistent single predictor of overall memory similarity. Memories with different emotional tone were reliably perceived to be dissimilar, even when they occurred at similar times and places and involved similar people; conversely, memories with a shared emotional tone were perceived as similar even when they occurred at different times and places, and involved different people. A predictive model explained over half of the variance in memory similarity, using only information about (i) the emotional properties of events and (ii) the primary action or purpose of events. Emotional features may make an outsized contribution to event similarity because they provide compact summaries of an event’s goals and self-related outcomes, which are critical information for future planning and decision making. Thus, in order to understand and improve real-world memory function, we must account for the strong influence of emotional and purposive information on memory organization and memory search.SignificanceOur brains enable us to understand and act within the present, informed by previous, related life experience. But how are our life experiences organized so that one event can be related to another? Theories have suggested that we use spatiotemporal, social, causal, purposive, and emotional dimensions to inter-relate our memories; however, these organizing principles are usually studied using impersonal laboratory stimuli. Here, we mapped and modeled the connections between people’s own annotated life memories. We found that life events are linked by a variety of factors, but are predominantly connected in memory by their primary activity and emotional character. This highlights a need for theories of memory organization and retrieval to better account for the role of high-level actions and emotions.
Spatial spread of white-nose syndrome in North America, 2006-2018
Authors: Kramer Andrew M. , Mercier Alex , Maher Sean , Kumi-Ansu Yaw , Bowden Sarah , Drake John M. 
Published: January 2021

AbstractWhite-nose syndrome has caused massive mortality in multiple bat species and spread across much of North America, making it one of the most destructive wildlife diseases on record. This has also resulted in it being one of the most well-documented wildlife disease outbreaks, making it possible to look for changes in the pattern of spatial spread over time. We fit a series of spatial interaction models to the United States county-level observations of the pathogenic fungus,Pseudogymnoascus destructans, that causes white-nose syndrome. Models included the distance between caves, cave abundance, measures of winter length and winter onset, and species richness of all bats and hibernating bats only. We found that the best supported models included all of these factors, but that the particular structure and most informative covariates changed over the course of the outbreak, with winter length displacing winter onset as the most informative measure of winter conditions, and evidence for the effects total species richness and hibernation varying from year to year. We also found that weather had detectable effects on spread. While the effect sizes for cave abundance and species richness were relatively stable over the length of the outbreak, distance became less important as time went on. These findings indicate that although models produced early in the outbreak captured important and consistent aspects of the spatial spread of white-nose syndrome, there were also changes over time in the factors associated with spread, suggesting that forecasts may be improved by iterative model refinement.
Transcranial magnetic stimulation of right dorsolateral prefrontal cortex does not affect associative retrieval in healthy young or older adults
Authors: Hill Paul F. , Horne Erin D. , Koen Joshua D. , Rugg Michael D. 
Published: January 2021

AbstractWe examined whether post-retrieval monitoring processes supporting memory performance are more resource limited in older adults relative to younger individuals. We predicted that older adults would be more susceptible to an experimental manipulation that reduced the neurocognitive resources available to support post-retrieval monitoring. Young and older adults received transcranial magnetic stimulation (TMS) to the right dorsolateral prefrontal cortex (DLPFC) or a vertex control site during an associative recognition task. The right DLPFC was selected as a TMS target because the region is held to be a key member of a network of regions engaged during retrieval monitoring and is readily accessible to administration of TMS. We predicted that TMS to the right DLPFC would lead to reduced associative recognition accuracy, and that this effect would be more prominent in older adults. The results did not support this prediction. Recognition accuracy was significantly reduced in older adults relative to their younger counterparts but the magnitude of this age difference was unaffected following TMS to the right DLPFC or vertex. These findings suggest that TMS to the right DLPFC was insufficient to deplete the neurocognitive resources necessary to support post-retrieval monitoring.
pmVAE: Learning Interpretable Single-Cell Representations with Pathway Modules
Authors: Gut Gilles , Stark Stefan G. , Rätsch Gunnar , Davidson Natalie R. 
Published: January 2021

ABSTRACTMotivationDeep learning techniques have yielded tremendous progress in the field of computational biology over the last decade, however many of these techniques are opaque to the user. To provide interpretable results, methods have incorporated biological priors directly into the learning task; one such biological prior is pathway structure. While pathways represent most biological processes in the cell, the high level of correlation and hierarchical structure make it complicated to determine an appropriate computational representation.ResultsHere, we presentpathway module Variational Autoencoder(pmVAE). Our method encodes pathway information by restricting the structure of our VAE to mirror gene-pathway memberships. Its architecture is composed of a set of subnetworks, which we refer to as pathway modules. The subnetworks learn interpretable latent representations by factorizing the latent space according to pathway gene sets. We directly address correlation between pathways by balancing a module-specific local loss and a global reconstruction loss. Furthermore, since many pathways are by nature hierarchical and therefore the product of multiple downstream signals, we model each pathway as a multidimensional vector. Due to their factorization over pathways, the representations allow for easy and interpretable analysis of multiple downstream effects, such as cell type and biological stimulus, within the contexts of each pathway. We compare pmVAE against two other state-of-the-art methods on two single-cell RNA-seq case-control data sets, demonstrating that our pathway representations are both more discriminative and consistent in detecting pathways targeted by a perturbation.Availability and implementationhttps://github.com/ratschlab/pmvae
Effects of hydroelectric dam construction on spatio-temporal changes of land use land cover in Bui National Park, Ghana
Authors: Bempah Godfred , Boama Prince , Lu Changhu 
Published: January 2021

AbstractThe construction of hydroelectric dams in forest reserves has become a matter of concern for biodiversity conservationists. Visibly among which is the potential to cause changes in climate and land cover and subsequently affect fauna and flora composition. Spatio-temporal changes of climate and land cover in the Bui National Park was analyzed using indices calculations of the landscape based on land cover maps obtained from Landsat satellite images for pre-and post-dam construction periods. Significant changes in land cover following the dam construction were observed. Notable changes include the built-up areas and water body, which recorded an increase of 315.64 % and 4593.43 % respectively, while the forest area decreased. Significant reduction in rainfall (U = 24,ρ< 0.05) and increase in temperature (U = 22.5,ρ< 0.05) were observed between the pre-and post-dam construction periods. Increased human activities such as illegal mining, indiscriminate tree felling, uncontrolled cattle grazing and charcoal production within the reserve results from inadequate monitoring and law enforcement after the dam construction could likely compound the changes in land cover.
Zoomqa: Residue-Level Single-Model QA Support Vector Machine Utilizing Sequential and 3D Structural Features
Authors: Hippe Kyle , Lilley Cade , Berkenpas William , Kishaba Kiyomi , Cao Renzhi 
Published: January 2021

ABSTRACTMotivationThe Estimation of Model Accuracy problem is a cornerstone problem in the field of Bioinformatics. When predictions are made for proteins of which we do not know the native structure, we run into an issue to tell how good a tertiary structure prediction is, especially the protein binding regions, which are useful for drug discovery. Currently, most methods only evaluate the overall quality of a protein decoy, and few can work on residue level and protein complex. Here we introduce ZoomQA, a novel, single-model method for assessing the accuracy of a tertiary protein structure / complex prediction at residue level. ZoomQA differs from others by considering the change in chemical and physical features of a fragment structure (a portion of a protein within a radiusrof the target amino acid) as the radius of contact increases. Fourteen physical and chemical properties of amino acids are used to build a comprehensive representation of every residue within a protein and grades their placement within the protein as a whole. Moreover, ZoomQA can evaluate the quality of protein complex, which is unique.ResultsWe benchmark ZoomQA on CASP14, it outperforms other state of the art local QA methods and rivals state of the art QA methods in global prediction metrics. Our experiment shows the efficacy of these new features, and shows our method is able to match the performance of other state-of-the-art methods without the use of homology searching against database or PSSM matrix.Availabilityhttp://zoomQA.renzhitech.comContactcaora@plu.edu