bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficacy of Corticosteroids in Non-Intensive Care Unit Patients with COVID-19 Pneumonia from the New York Metropolitan region
Authors: Majmundar Monil , Kansara Tikal , Lenik Joanna Marta , Park Hansang , Ghosh Kuldeep , Doshi Rajkumar , Shah Palak , Kumar Ashish , Amin Hossam , Chaudhari Shobhana , Habtes Imnett 
Published: July 2020

AbstractIntroductionThe role of systemic corticosteroid as a therapeutic agent for patients with COVID-19 pneumonia is controversial.ObjectiveThe purpose of this study was to evaluate the effect of corticosteroids in non-intensive care unit (ICU) patients with COVID-19 pneumonia complicated by acute hypoxemic respiratory failure (AHRF).MethodsThis was a single-center retrospective cohort study, from the 16th March, 2020 to 30th April, 2020; final follow-up on 10th May, 2020. 265 patients consecutively admitted to the non-ICU wards with laboratory-confirmed COVID-19 pneumonia were screened for inclusion. 205 patients who developed AHRF (SpO2/FiO2 ≤ 440 or PaO2/FiO2 ≤ 300) were only included in the final study. Direct admission to the Intensive care unit (ICU), patients developing composite primary outcome within 24 hours of admission, and patients who never became hypoxic during their stay in the hospital were excluded. Patients divided into two cohort based on corticosteroid. The primary outcome was a composite of ICU transfer, intubation, or in-hospital mortality. Secondary outcomes were ICU transfer, intubation, in-hospital mortality, discharge, length of stay and daily trend of SpO2/FiO2 (SF) ratio from the index date. Cox-proportional hazard regression was implemented to analyze the time to event outcomes.ResultAmong 205 patients, 60 (29.27%) were treated with corticosteroid. The mean age was ∼57 years, and ∼75% were men. Thirteen patients (22.41%) developed a primary composite outcome in the corticosteroid cohort vs. 54 (37.5%) patients in the non-corticosteroid cohort (P=0.039). The adjusted hazard ratio (HR) for the development of the composite primary outcome was 0.15 (95% CI, 0.07 – 0.33; P <0.001). The adjusted hazard ratio for ICU transfer was 0.16 (95% CI, 0.07 to 0.34; P < 0.001), intubation was 0.31 (95% CI, 0.14 to 0.70; P – 0.005), death was 0.53 (95% CI, 0.22 to 1.31; P – 0.172), and discharge was 3.65 (95% CI, 2.20 to 6.06; P<0.001). The corticosteroid cohort had increasing SpO2/FiO2 over time compared to the non-corticosteroid cohort who experience decreasing SpO2/FiO2 over time.ConclusionAmong non-ICU patients hospitalized with COVID-19 pneumonia complicated by AHRF, treatment with corticosteroid was associated with a significantly lower risk of the primary composite outcome of ICU transfer, intubation, or in-hospital death.
Multi-omics analysis of aspirin treatment response in mice provide molecular insights and targets linked to liver fibrosis regression
Authors: Bhat Adil , Chaudhary Sudrishti , Yadav Gaurav , prasar Anupama , Bihari Chhagan , Maras Jaswinder Singh , Sarin Shiv K 
Published: July 2020

AbstractBackground & AimsAspirin has potent anti-platelet activities and possibly helps regression of fibrosis. We investigated antifibrotic mechanisms of aspirin in the murine CCl4model and in patients with hepatic fibrosis.MethodsMultiomics analysis identified networks and molecular targets regulated by aspirin which were validated in murine model and in patients with liver fibrosis.ResultsBiochemical/histopathological changes and hepatic fibrosis were greater in CCl4-treated mice compared to CCl4-aspirin (CCl4+ASA) or control mice (p<0.05). In CCl4+ASA mice, integrated proteome-metabolome analysis showed an increase in autophagy, drug metabolism, glutathione and energy metabolism (p<0.05) and decrease in inflammatory pathways, arachidonic acid and butanoate metabolism (p<0.05). Global cross-correlation analysis linked fibrosis markers with protein-metabolite pathways (r2>0.5, p<0.05). Liver proteome enrichment for immune clusters using blood transcription module correlated with histidine and tryptophan metabolism (r2>0.5, p<0.05). Aspirin decreased Ryanodine-receptor-2 (RYR2;oxidative-stress), Arginase-1 (ARG-1;urea cycle), Arachidonate-5-lipoxygenase (ALOX5;leukotriene metabolism), and Kynurenine-3-monooxygenase (KMO;tryptophan metabolism; p<0.05) which correlated with reduction in α-SMA, PDGFR-β and degree of hepatic fibrosis (r2>0.75; p<0.05) in animal and human studies, and, in-vitro analysis. Aspirin modulated intracellular-calcium and oxidative-stress levels by reducing RYR2 expression in activated LX-2 cells. It modulated the liver microbiome and its functions which also correlated with ARG1, ALOX5, RYR2 expression (r2>0.5, p<0.05). Metaproteome analysis showed significant microbiome similarity at phylum level in murine liver tissues and fecal samples. Aspirin increased the abundance of Firmicutes (Ruminococcaceae, Lachnospiraceae, and Clostridiaceae) and their functionality, as assessed by glycerol-3-phosphate dehydrogenase (NAD(P)(+) and dTMP-kinase activity (p<0.05).ConclusionsAspirin demonstrates broad beneficial effects following oxidative injury, inflammation, and hepatic fibrosis. Aspirin induces distinctive hepatic proteome/metabolome and intrahepatic microbiome changes which are indicative of fibrosis regression and could be further explored as therapeutic targets.
Behavioral and neural fusion of expectation with sensation
Authors: Panichello Matthew F. , Turk-Browne Nicholas B. 
Published: July 2020

AbstractHumans perceive expected stimuli faster and more accurately. However, the mechanism behind the integration of expectations with sensory information during perception remains unclear. We investigated the hypothesis that such integration depends on ‘fusion’ — the weighted averaging of different cues informative about stimulus identity. We first trained participants to map a range of tones onto faces spanning a male-female continuum via associative learning. These two features served as expectation and sensory cues to sex, respectively. We then tested specific predictions about the consequences of fusion by manipulating the congruence of these cues in psychophysical and fMRI experiments. Behavioral judgments and patterns of neural activity in auditory association regions revealed fusion of sensory and expectation cues, providing evidence for a precise computational account of how expectations influence perception.
Combinatorial transcriptional profiling of mouse and human enteric neurons identifies shared and disparate subtypesin situ
Authors: May-Zhang Aaron A. , Tycksen Eric , Southard-Smith Austin N. , Deal Karen K. , Benthal Joseph T. , Buehler Dennis P. , Adam Mike , Simmons Alan J. , Monaghan James R. , Matlock Brittany K. , Flaherty David K. , Potter S. Steven , Lau Ken S. , Southard-Smith E. Michelle 
Published: July 2020

AbstractBACKGROUND & AIMSThe enteric nervous system (ENS) coordinates essential intestinal functions through the concerted action of diverse enteric neurons (EN). However, integrated molecular knowledge of EN subtypes is lacking. To compare human and mouse ENs, we transcriptionally profiled healthy ENS from adult humans and mice. We aimed to identify transcripts marking discrete neuron subtypes and visualize conserved EN subtypes for humans and mice in multiple bowel regions.METHODSHuman myenteric ganglia and adjacent smooth muscle were isolated by laser-capture microdissection for RNA-Seq. Ganglia-specific transcriptional profiles were identified by computationally subtracting muscle gene signatures. Nuclei from mouse myenteric neurons were isolated and subjected to single-nucleus RNA-Seq (snRNA-Seq), totaling over four billion reads and 25,208 neurons. Neuronal subtypes were defined using mouse snRNA-Seq data. Comparative informatics between human and mouse datasets identified shared EN subtype markers, which were visualizedin situusing hybridization chain reaction (HCR).RESULTSSeveral EN subtypes in the duodenum, ileum, and colon are conserved between humans and mice based on orthologous gene expression. However, some EN subtype-specific genes from mice are expressed in completely distinct morphologically defined subtypes in humans. In mice, we identified several neuronal subtypes that stably express gene modules across all intestinal segments, with graded, regional expression of one or more marker genes.CONCLUSIONSOur combined transcriptional profiling of human myenteric ganglia and mouse EN provides a rich foundation for developing novel intestinal therapeutics. There is congruency among some EN subtypes, but we note multiple species differences that should be carefully considered when relating findings from mouse ENS research to human GI studies.Graphical Abstract
Field-based body temperatures reveal behavioral thermoregulation strategies of the Atlantic marsh fiddler crabMinuca pugnax
Authors: Hews Sarah , Allen Zahkeyah , Baxter Adrienne , Rich Jacquline , Sheik Zahida , Taylor Kayla , Wu Jenny , Zakoul Heidi , Brodie Renae 
Published: July 2020

AbstractBehavioral thermoregulation is an important defense against the negative impacts of climate change for ectotherms. In this study we examined the use of burrows by a common intertidal crab,Minuca pugnax, to control body temperature. To understand how body temperatures respond to changes in the surface temperature and explore how efficiently crabs exploit the cooling potential of burrows to thermoregulate, we measured body, surface, and burrow temperature data during low tide on Sapelo Island, GA in March, May, August, and September of 2019. We found that an increase in 1°C in the surface temperature led to a 0.70-0.71°C increase in body temperature for females and an increase in 0.75-0.77°C in body temperature for males. Body temperatures of small females were 0.3°C warmer than large females for the same surface temperature. Female crabs used burrows more efficiently for thermoregulation compared to the males. Specifically, an increase of 1°C in the cooling capacity (the difference between the burrow temperature and the surface temperature) led to an increase of 0.42-0.50°C for females and 0.34-0.35°C for males in the thermoregulation capacity (the difference between body temperature and surface temperature). The body temperature that crabs began to use burrows to thermoregulate was estimated to be around 24°C, which is far below the critical body temperatures that could lead to death. Many crabs experience body temperatures of 24°C early in the reproductive season, several months before the hottest days of the year. Because the use of burrows involves fitness trade-offs, these results suggest that warming temperatures could begin to impact crabs far earlier in the year than expected.
A Large-Scale Internal Validation Study of Unsupervised Virtual Trichrome Staining Technologies on Non-alcoholic Steatohepatitis Liver Biopsies
Authors: Levy Joshua J. , Azizgolshani Nasim , Andersen Michael J. , Suriawinata Arief , Liu Xiaoying , Lisovsky Mikhail , Ren Bing , Bobak Carly , Christensen Brock C. , Vaickus Louis J. 
Published: July 2020

AbstractNon-alcoholic steatohepatitis (NASH) is a fatty liver disease characterized by accumulation of fat in hepatocytes with concurrent inflammation and is associated with morbidity, cirrhosis and liver failure. After extraction of a liver core biopsy, tissue sections are stained with hematoxylin and eosin (H&E) to grade NASH activity, and stained with trichrome to stage fibrosis. Methods to computationally transform one stain into another on digital whole slide images (WSI) can lessen the need for additional physical staining besides H&E, reducing personnel, equipment, and time costs. Generative adversarial networks (GAN) have shown promise for virtual staining of tissue. We conducted a large-scale validation study of the viability of GANs for H&E to trichrome conversion on WSI (n=574). Pathologists were largely unable to distinguish real images from virtual/synthetic images given a set of twelve Turing Tests. We report high correlation between staging of real and virtual stains (ρ = 0.86; 95% CI: 0.84-0.88). Stages assigned to both virtual and real stains correlated similarly with a number of clinical biomarkers and progression to End Stage Liver Disease (Hazard Ratio HR = 2.06, CI 95% 1.36-3.12, P < 0.001 for real stains; HR = 2.02, CI 95% 1.40-2.92, p < 0.001 for virtual stains). Our results demonstrate that virtual trichrome technologies may offer a software solution that can be employed in the clinical setting as a diagnostic decision aid.
Loss of HOXB13 expression in neuroendocrine prostate cancer
Authors: Cheng Siyuan , Yang Shu , Shi Yingli , Shi Runhua , Yeh Yunshin , Yu Xiuping 
Published: July 2020

AbstractHOXB13, the most posterior HOX B gene, is primarily expressed in the prostate. Using immunohistochemical staining, we evaluated the expression of HOXB13 in prostatic tissues. We found that HOXB13 was expressed in both benign prostatic tissues and prostate adenocarcinoma (AdPCa) but its expression was reduced or lost in neuroendocrine prostate cancer (NEPCa). Additionally, using RNAseq data of HOXs in cell lines derived from various tissue origins, we established HOX codes for these tissue types. We applied the HOX codes to PCa samples and found that the majority of AdPCa samples sustained the prostate-specific HOX code but the majority of NEPCa samples lost it. Our analysis also showed that the NEPCa samples did not correlate well with the HOX codes of any other tissue type. This indicates that NEPCa tumors lose prostate identity but do not gain a clear-cut new tissue identity. Finally, we treated PCa cells with all trans retinoic acid and found that the reduced/lost HOXB13 expression can be reverted, as can AR and AR targets. Taken together, our data indicate that HOXB13 expression is reduced or lost in NEPCa and a loss of prostate-specific HOX code in NEPCa represents a loss of prostatic identity.
The projected impact of mitigation and suppression strategies on the COVID-19 epidemic in Senegal: A modelling study
Authors: Thompson Hayley A , Mboup Aminata , Cisse Badara , Nayagam Shevanthi , Watson Oliver J , Whittaker Charles , Walker Patrick G T , Ghani Azra C , Mboup Souleymane ,   With the Imperial College COVID-19 Response Team
Published: July 2020

AbstractBackgroundPhysical distancing measures that reduce social contacts have formed a key part of national COVID-19 containment and mitigation strategies. Many Sub-Saharan African nations are now facing increasing numbers of cases of COVID-19 and there is a need to understand what levels of measures may be required to successfully reduce transmission.MethodsWe collated epidemiological data along with information on key COVID-19 specific response policies and health system capacity estimates for services needed to treat COVID-19 patients in Senegal. We calibrated an age-structured SEIR model to these data to capture transmission dynamics accounting for demography, contact patterns, hospital capacity and disease severity. We simulated the impact of mitigation and suppression strategies focussed on reducing social contact rates.ResultsSenegal acted promptly to contain the spread of SARS-CoV-2 and as a result has reduced the reproduction number from 1.9 (95% CI 1.7-2.2) to 1.3 (95% CI 1.2-1.5), which has slowed but not fully interrupted transmission. We estimate that continued spread is likely to peak in October, and to overwhelm the healthcare system with an estimated 77,400 deaths (95% CI 55,270-100,700). Further reductions in contact rates to suppress transmission (Rt<1) could significantly reduce this burden on healthcare services and improve overall health outcomes.ConclusionsOur results demonstrate that Senegal has already significantly reduced transmission. Enhanced physical distancing measures and rapid scale up of hospital capacity is likely to be needed to reduce mortality and protect healthcare infrastructure from high levels of demand.
Health literacy in the general population in the context of epidemic or pandemic coronavirus outbreak situations: rapid scoping review
Authors: Matterne Uwe , Egger Nina , Tempes Jana , Tischer Christina , Lander Jonas , Dierks Marie-Luise , Bitzer Eva-Maria , Apfelbacher Christian 
Published: July 2020

SummaryBACKGROUNDAuthorities responded with contact restrictions and other measures to the global spread of SARS-CoV-2. Health literacy (HL) has been linked to health outcomes and refers to the ability to access, understand, appraise and apply health information in order to make good health decisions. When restrictions are gradually lifted, individual HL becomes essential to control the pandemic and to prevent the resumption of these restriction, should infection numbers surge again. The aim of this rapid scoping review, for which only studies from the general population were considered, was to describe the extent of existing research on HL in the context of previous coronavirus outbreaks (SARS-CoV-1, MERS-CoV and SARS-CoV-2). Facets of HL that were of particular interest were: type of assessment of HL (theory-based versus proxy assessment; validated instrument versus ad hoc assessment), domains of HL, interventions aiming to improve HL during outbreak situations, and HL surveillance during outbreak.METHODSWe searched two major databases and included publications of quantitative and qualitative studies in English and German on any type of research on the functional, critical and communicative domains of HL conducted in the context of the three outbreaks in the general population. We extracted and tabulated relevant data and narratively reported where and when the study was conducted, the design and method used, and how HL was measured.FINDINGS72 studies were included. Three investigated HL or explicitly referred to the concept of HL, 14 were guided by health behaviour theory. We did not find any study designed to develop or psychometrically evaluate pandemic HL instruments, or relate pandemic or general HL to a pandemic outcome, or any controlled intervention study. Type of assessment of the domains of HL varied widely.INTERPRETATIONTheory-driven observational studies as well as interventions, examining whether pandemic-related HL can be improved are needed. In addition, the development and validation of instruments that measure pandemic-related HL is desirable.
Laboratory-based surveillance of COVID-19 in the Greater Helsinki area, Finland, February-June 2020
Authors: Jarva H , Lappalainen M , Luomala O , Jokela P , Jääskeläinen AE , Jääskeläinen AJ , Kallio-Kokko H , Kekäläinen E , Mannonen L , Soini H , Suuronen S , Toivonen A , Savolainen-Kopra C , Loginov R , Kurkela S 
Published: July 2020

AbstractLaboratory registry data (80,791 specimens, 70,517 individuals) was used to characterise age- and sex-specific SARS-CoV-2 RT-PCR sampling frequency and positivity rate, and laboratory capacity building in Greater Helsinki, Finland during February-June 2020. While the number of positive cases was similar in males and females, the positivity rate was significantly higher in males. The highest incidence/100,000 was observed in those aged ≥80 years. The proportion of young adults in positive cases increased in late May 2020.
The effect of opening up the US on COVID-19 spread
Authors: Bryant Patrick , Elofsson Arne 
Published: July 2020

AbstractIn response to the pandemic development of the novel coronavirus (SARS-CoV-2), governments worldwide have implemented strategies of suppression by non-pharmaceutical interventions (NPIs). Such NPIs include social distancing, school closures, limiting international travel and complete lockdown. Worldwide the NPIs enforced to limit the spread of COVID-19 are now being lifted. Understanding how the risk increases when NPIs are lifted is important for decision making. Treating NPIs equally across countries and regions limits the possibility for modelling differences in epidemic response, as the response to the NPIs influences can vary between regions and this can affect the epidemic outcome, so do the strength and speed of lifting these. Our solution to this is to measure mobility changes from mobile phone data and their impacts on the basic reproductive number. We model the epidemic in all US states to compare the difference in outcome if NPIs are lifted or retained. We show that keeping NPIs just a few weeks longer has a substantial impact on the epidemic outcome.
Battle with COVID-19 Under Partial to Zero Lockdowns in India
Authors: Babbar Sakshi , Gilotra Arnauv 
Published: July 2020

AbstractThe cumulative records of COVID-19 are rapidly increasing day by day in India. The key question prevailing in minds of all is when will it get over? There have been several attempts in literature to address this question using time series, Machine learning, epidemiological and statistical models. However due to high level of uncertainty in the domain and lack of big historical data, the performance of these models suffer. In this work, we present an intuitive model that uses a combination of epidemiological model (SEIR) and mathematical curve fitting method to forecast spread of COVID-19 in India in future. By using the combination model, we get characteristics benefits of these models under limited knowledge and historical data about the novel Coronavirus. Instead of fixing parameters of the standard SEIR model before simulation, we propose to learn them from the real data set consisting of progression of Corona spread in India. The learning of model is carefully designed by understanding that available data set consist of records of cases under full, partial to zero lockdown phases in India. Hence, we make two separate predictions by our propose model. One under the situation of full lockdown in India and, other with partial to zero restrictions in India. With continued strict lockdown after May 03, 2020, our model predicted May 14, 2020 as the date of peak of Coronavirus in India. However, in current scenario of partial to zero lockdown phase in India, the peak of Coronavirus cases is predicted to be July 31, 2020. These two predictions presented in this work provide awareness among citizens of India on importance of control measures such as full, partial and zero lockdown and the spread of Corona disease infection rate. In addition to this, it is a beneficial study for the government of India to plan the things ahead.
A Novel Approach for Estimating the Final Outcome of Global Diseases Like COVID-19
Authors: Christopoulos Demetris T. 
Published: July 2020

AbstractThe existence of a universal law which maps the bell curve of daily cases to a sigmoid curve for cumulative ones is used for making robust estimations about the final outcome of a disease. Computations of real time effective reproduction rate are presented and its limited usefulness is derived. After using methods ESE & EDE we are able to find the inflection point of the cumulative curve under consideration and study its time evolution. Since mortality processes tend to follow a Gompertz distribution, we apply the properties of it and introduce novel estimations for both the time remaining after inflection time and the capacity of the curve. Special properties of sigmoid curves are used for assessing the quality of estimation and as indices for the cycle completion. Application is presented for COVID-19 evolution for most affected countries and the World.