bluuebunny/crossref_metadata_2025 huggingface dataset:
Using ECG Machine Learning for Detection of Cardiovascular Disease in African American Men and Women: the Jackson Heart Study
Authors: Pollard James D. , Haq Kazi T. , Lutz Katherine J. , Rogovoy Nichole M. , Paternostro Kevin A. , Soliman Elsayed Z. , Maher Joseph , Lima João A.C. , Musani Solomon , Tereshchenko Larisa G.
Published: July 2020

Background

Almost half of African American (AA) men and women have cardiovascular disease (CVD). Detection of prevalent CVD in barbershops would facilitate secondary prevention of CVD. We sought to investigate the cross-sectional association of prevalent CVD and sex with global electrical heterogeneity (GEH) and develop a tool for CVD detection.

Methods

Participants from the Jackson Heart Study (JHS) with analyzable ECGs (n=3,679; age, 62±12 years; 36% men) were included. QRS, T, and spatial ventricular gradient (SVG) vectors’ magnitude and direction, and traditional metrics were measured on 12-lead ECG. Linear regression and mixed linear models with random intercept were adjusted for cardiovascular risk factors, sociodemographic and anthropometric characteristics, type of median beat, and mean RR’ intervals. Random forests, convolutional neural network, and lasso models were developed in 80%, and validated in 20% samples.

Results

In fully adjusted models, women had a smaller spatial QRS-T angle (−12.2(−19.4 to-5.1)°;P=0.001), SAI QRST (−29.8(−39.3 to −20.3) mV*ms;P<0.0001), and SVG elevation (−4.5(−7.5 to −1.4)°;P=0.004) than men, but larger SVG azimuth (+16.2(10.5-21.9)°;P<0.0001), with a significant random effect between families (+20.8(8.2-33.5)°;P=0.001). SAI QRST was larger in women with CVD as compared to CVD-free women or men (+15.1(3.8-26.4) mV*ms;P=0.009). Men with CVD had smaller T area [by 5.1 (95%CI 1.2-9.0) mV*ms] than CVD-free men, but there were no differences when comparing women with CVD to CVD-free women. Machine-learning detected CVD with ROC AUC 0.69-0.74; plug-in-based model included only age and QRS-T angle.

Conclusions

GEH varies by sex. Sex modifies an association of GEH with CVD. Automated CVD detection is feasible.
Modeling the COVID-19 dissemination in the South Region of Brazil and testing gradual mitigation strategies
Authors: da Silva Rafael M.
Published: July 2020

This study aims to understand the features of the COVID-19 spread in the South Region of Brazil by estimating the Effective Reproduction Number (ERN)ℛefor the states of Paraná (PR), Rio Grande do Sul (RS), and Santa Catarina (SC). We used the SIRD (Susceptibles-Infectious-Recovered-Dead) model to describe the past data and to simulate strategies for the gradual mitigation of the epidemic curve by applying non-pharmacological measures. Besides the SIRD model does not include some aspects of COVID-19, as the symptomatic and asymptomatic subgroups of individuals and the incubation period, for example, in this work we intend to use a classical and easy to handle model to introduce a thorough method of adjustment that allows us to achieve reliable fitting for the real data and to obtain insights about the current trends for the pandemic in each locality. Our results demonstrate that for localities for which the ERN is about 2, only rigid measures are efficient to avoid overwhelming the health care system. These findings corroborate the relevance of keeping the value ofℛebelow 1 and applying containment measures early.
Nowcasting Influenza-like Illness Trends in Cameroon
Authors: Nsoesie Elaine O. , Oladeji Olubusola , Abah Aristide S. Abah , Ndeffo-Mbah Martial L.
Published: July 2020

Although acute respiratory infections are a leading cause of mortality in sub-Saharan Africa, surveillance of diseases such as influenza is mostly neglected. Evaluating the usefulness of influenza-like illness (ILI) surveillance systems and developing approaches for forecasting future trends is important for pandemic preparedness. We applied statistical and machine learning models to forecast 2012 to 2018 trends in ILI cases reported by the Cameroon Ministry of Health (MOH), using Google searches for influenza symptoms, treatments, natural or traditional remedies as well as, infectious diseases with a high burden (i.e., AIDS, malaria, tuberculosis). The variance explained by the models based on Google search data were 87.7%, 79.1% and 52.0% for the whole country, the Littoral and Centre regions respectively. Our study demonstrates the need for developing contextualized approaches when using digital data for disease surveillance and demonstrates the potential usefulness of search data for monitoring ILI in sub-Saharan African countries.
Dynamics of coagulopathy in patients with different COVID-19 severity
Authors: Kalinskaya Anna , Dukhin Oleg , Molodtsov Ivan , Maltseva Alexandra , Sokorev Denis , Elizarova Antonina , Sapozhnikova Olga , Glebova Ksenia , Stonogina Daria , Shakhidzhanov Soslan , Nikonov Evgeniy , Mazus Alexey , Spiridonov Ilia , Ataullakhanov Fazly , Margolis Leonid , Shpektor Alexander , Vasilieva Elena
Published: July 2020

With the progress of COVID-19 studies, it became evident that SARS-CoV-2 infection is often associated with thrombotic complications. The goal of our present study was to evaluate which component of clot formation process including endothelial function, platelets aggregation and plasma coagulation, as well as endogenous fibrinolysis in patients with COVID-19 correlates with the severity of the disease. We prospectively included 58 patients with COVID-19 and 47 healthy volunteers as a control group that we recruited before the pandemic started. It turns out that plasma coagulation with subsequent platelet aggregation, but not endothelial function, correlates with the severity of the COVID-19. IL-6 blockade may play a beneficial role in COVID-19 induced coagulopathy.
Laboratory findings that predict a poor prognosis in COVID-19 patients with diabetes: A meta-analysis
Authors: Lagunas-Rangel Francisco Alejandro , Chávez-Valencia Venice
Published: July 2020

Diabetes is one of the main comorbidities in patients infected with the SARS-CoV-2 virus, the causative agent of the new coronavirus disease 2019 (COVID-19). Because the presence of diabetes and COVID-19 in the same patient is related to a poor clinical prognosis and a high probability of death, it is necessary to determine what findings allow us to predict a good or bad resolution of the disease in order to opt for a traditional treatment or a more incisive one. In this way, in the present work we analyze which laboratory parameters showed differences in patients with COVID-19 and diabetes who recovered and in those who had complications or died.
Stroke survivors experience elevated levels of loneliness: a multi-year analysis of the National Survey for Wales
Authors: Byrne Christopher , Saville Christopher W. N. , Coetzer Rudi , Ramsey Richard
Published: July 2020

Despite clinical observation that stroke survivors frequently experience loneliness, there is no large-scale empirical evidence to support this observation. To address this issue, we completed two pre-registered analyses of a nationally representative annual survey that included a self-report measure of loneliness (N>21000). Across two separate cohorts, the results consistently showed that human stroke survivors report higher levels of loneliness compared to healthy individuals, and this relationship could not be accounted for by demographic factors (e.g., age, sex) or objective measures of social isolation (e.g., marital status, number of household members). These findings demonstrate that elevated levels of loneliness post-stroke are robust in that they replicate in large nationally representative samples and cannot be reduced to objective measures of social isolation. The work has clinical and societal relevance by suggesting that loneliness post-stroke is unlikely to be adequately “treated” if only the quantity and not the quality of social experiences are considered.
How was the Mental Health of Colombian people on March during Pandemics Covid19?
Authors: Chire Saire Josimar E.
Published: July 2020

Actual pandemic started with first cases in China and fast spread in Europe, Asia and the next continents became a global concern from March, so the most of countries ordered a lockdown to decrease infection rate forced people to stay at home. The first confirmed case was on March 6, during the next days more cases were confirmed by Minster of Health, the first death was on March 21, one day after of the announcement of lockdown in Colombia. During this period of waiting for what is going to happen people can develop mental stress as fear, sleep disorders so to analyze how was the behaviour on the population the present study is conducted using a Social Network as Twitter, Natural Language algorithms and Data Mining criterion’s. The findings confirmed the interest of covid19 was increasing daily, people was experimenting fear, anxiety, mental stress.
Prevalence of IgG and IgM antibodies to SARS-CoV-2 among clinic staff and patients
Authors: Asuquo Marcus Inyama , Effa Emmanuel , Otu Akaninyene , Ita Okokon , Udoh Ubong , Umoh Victor , Gbotosho Oluwabukola , Ikpeme Anthonia , Ameh Soter , Egbe William , Etok Margaret , Guck Jochen , Ekpenyong Andrew
Published: July 2020

The coronavirus disease 2019 (COVID-19) is now a pandemic with devastating social and economic consequences. The extent of the spread of COVID-19 within populations is uncertain since diagnostic tests have not been carried out on all eligible persons and doing such diagnostic tests on everyone is much less feasible in developing countries such as Nigeria. Tests for antibodies to SARS-CoV-2, the virus that causes COVID-19, are more affordable, readily available, and require minimal training than current diagnostic tests. Employing a seroepidemiological strategy, serological tests were conducted on 66 volunteering staff and patients at the University of Calabar Teaching Hospital (UCTH), a Federal Government owned tertiary healthcare facility, to determine the extent of exposure to SARS-CoV-2, from 17th to 25th June 2020. Using a COVID-19 IgG/IgM Rapid Test Cassette with emergency use authorization (EUA) from the Food and Drug Administration (FDA) of the United States, it was observed that of the 66 samples tested, 5 (7.6%) were both IgG and IgM positive and 17 (26%) were IgG positive. Moreover, for 44 of the 66 participants, simultaneous tests were carried out using a rapid test kit from a different manufacturer but without FDA-EUA and all the results completely matched with the FDA-EUA kit, except one case where the FDA-EUA kit showed positive for both IgG and IgM while the other kit was positive only for IgM. The 26% positive IgG indicates a high exposure rate for the hospital staff and patients and points to community transmission where the facility is situated. Hence, immediate activation of WHO guidelines for controlling community transmission is called for. These results can further serve as a pilot study to guide public health policies in response to COVID-19 pandemic in both the general population and in healthcare settings.
Forecasting COVID-19 cases using Machine Learning models
Authors: Tian Yuan , Luthra Ishika , Zhang Xi
Published: July 2020

As of April 26, 2020, more than 2,994,958 cases of COVID-19 infection have been confirmed globally, raising a challenging public health issue. A predictive model of the disease would help allocate medical resources and determine social distancing measures more efficiently. In this paper, we gathered case data from Jan 22, 2020 to April 14 for 6 countries to compare different models’ proficiency in COVID-19 cases prediction. We assessed the performance of 3 machine learning models including hidden Markov chain model (HMM), hierarchical Bayes model, and long-short-term-memory model (LSTM) using the root-mean-square error (RMSE). The LSTM model had the consistently smallest prediction error rates for tracking the dynamics of incidents cases in 4 countries. In contrast, hierarchical Bayes model provided the most realistic prediction with the capability of identifying a plateau point in the incidents growth curve.
Firearm Purchasing and Firearm Violence in the First Months of the Coronavirus Pandemic in the United States
Authors: Schleimer Julia P. , McCort Christopher D. , Pear Veronica A. , Shev Aaron , Tomsich Elizabeth , Asif-Sattar Rameesha , Buggs Shani , Laqueur Hannah S. , Wintemute Garen J.
Published: July 2020

Importance

Firearm violence is a significant public health and safety problem in the United States. A surge in firearm purchases following the onset of the coronavirus pandemic may increase rates of firearm violence.

Objective

To estimate the association between changes in firearm purchasing and interpersonal firearm violence during the coronavirus pandemic.

Design

Cross-sectional time series study. We estimate the difference between observed rates of firearm purchases and those predicted by seasonal autoregressive integrated moving average models. Using negative binomial models, we then estimate the association between excess firearm purchases and rates of interpersonal firearm violence within states, controlling for confounders.

Setting

The 48 contiguous states and the District of Columbia. Hawaii and Alaska are excluded due to missing or incomplete data.

Exposure

The difference between observed and expected rates of firearm purchases in March through May 2020, approximated by National Instant Criminal Background Check System records.

Main Outcome and Measure

Fatal and nonfatal injuries from interpersonal firearm violence, recorded in the Gun Violence Archive.

Results

We estimate that there were 2.1 million excess firearm purchases from March through May 2020—a 64.3% increase over expected volume, and an increase of 644.4 excess purchases per 100,000 population. We estimate a relative rate of death and injury from firearm violence of 1.015 (95% Confidence Interval (CI): 1.005 to 1.025) for every 100 excess purchases per 100,000, in models that incorporate variation in purchasing across states and control for effects of the pandemic common to all states. This reflects an increase of 776 fatal and nonfatal injuries (95% CI: 216 to 1,335) over the number expected had no increase in purchasing occurred.

Conclusions and Relevance

We find a significant increase in firearm violence in the United States associated with the coronavirus pandemic-related surge in firearm purchasing. Our findings are consistent with existing research. Firearm violence prevention strategies may be particularly important during the pandemic.

KEY POINTS

Question

Is the coronavirus-related surge in firearm purchasing associated with changes in rates of interpersonal firearm violence?

Findings

This cross-sectional time series study suggests the recent increase in firearm purchases—an estimated 2.1 million excess purchases nationally between March and May 2020—is associated with a statistically significant increase in firearm violence. We estimate an increase of 776 fatal and nonfatal injuries (95% CI: 216 to 1,335) in the US over the number expected for those months had there been no increase in purchasing.

Meaning

During the coronavirus pandemic, an acute increase in firearm access is associated with an increase in firearm violence.
Profiling cases with non-respiratory symptoms and asymptomatic SARS-CoV-2 infections in Mexico City
Authors: Bello-Chavolla Omar Yaxmehen , Antonio-Villa Neftali Eduardo , Vargas-Vázquez Arsenio , Fermín-Martínez Carlos A. , Márquez-Salinas Alejandro , Bahena-López Jessica Paola
Published: July 2020

ABSTRACT (50 WORDS)

We profiled cases with non-respiratory symptoms (NRS) and asymptomatic SARS-CoV-2 assessed within Mexico City’s Epidemiological Surveillance System. We show that initially asymptomatic or NRS cases have decreased risk of adverse COVID-19 outcomes compared to cases with respiratory symptoms. Comorbidity and age influence likelihood of developing symptoms in initially asymptomatic cases.
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

Introduction

The role of systemic corticosteroid as a therapeutic agent for patients with COVID-19 pneumonia is controversial.

Objective

The 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).

Methods

This 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.

Result

Among 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.

Conclusion

Among 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

Background & Aims

Aspirin 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.

Methods

Multiomics analysis identified networks and molecular targets regulated by aspirin which were validated in murine model and in patients with liver fibrosis.

Results

Biochemical/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).

Conclusions

Aspirin 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

Humans 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

Abstract

BACKGROUND & AIMS

The 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.

METHODS

Human 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).

RESULTS

Several 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.

CONCLUSIONS

Our 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

Behavioral 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

Non-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

HOXB13, 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

Background

Physical 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.

Methods

We 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.

Results

Senegal 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.

Conclusions

Our 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

BACKGROUND

Authorities 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.

METHODS

We 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.

FINDINGS

72 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.

INTERPRETATION

Theory-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

Laboratory 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

In 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

The 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

The 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.
Are Our COVID Warriors Cared-for Enough? A Nationwide Survey on Stress Among Doctors During the COVID-19 Pandemic
Authors: Nair Amritha , Menon Jagadeesh , Rammohan Ashwin , Hakeem Abdul R , Cherukuri Sathya D , Shanmugam Naresh , Rajakumar Akila , Reddy Mettu S , Kaliamoorthy Ilankumaran , Rela Mohamed
Published: July 2020

Limited and uneven accessibility to healthcare is a major impediment in the fight against the COVID-19 pandemic which continues on inexorably, across various parts of the globe. We conducted a nationwide survey of a large sample of Indian doctors to measure levels of perceived stress, identify risk factors for severe stress and assess their response to current issues related to safety and well-being of the HCP community. The survey found severely stressed doctors to be younger (<45years), of female gender working in the ICU setting and insecure regarding their finances. Concern regarding PPE shortages and ethical dilemmas of rationing care are factors inducing severe stress amongst doctors working in ICU settings. This is the first such survey done in the context of the COVID-19 pandemic from the Indian sub-continent. The findings have important implications on the International healthcare community, especially across Africa, Asia & South America where the contagion continues to wreak havoc. The survey has identified factors which adversely impact the mental health of doctors during this Pandemic. This can act as a valuable guide for governmental authorities, professional organisations and hospital managements to establish support systems at multiple levels for these “COVID Warriors”.
Oxygen and mortality in COVID-19 pneumonia: a comparative analysis of supplemental oxygen policies and health outcomes across 26 countries
Authors: Goyal Daniel K , Donnelly Harry , Kussner Albrecht , Neil James , Bhatti Sohail , Mansab Fatma
Published: July 2020

Introduction

Hypoxia is the main cause of morbidity and mortality in COVID-19. During the COVID-19 pandemic some countries have reduced access to supplemental oxygen (e.g. oxygen rationing), whereas other nations have maintained and even improved access to supplemental oxygen. We examined whether such variation in the access to supplemental oxygen had any bearing on mortality in COVID-19.

Methods

Three independent investigators searched for, identified and extracted the nationally recommended target oxygen levels for the commencement of oxygen in COVID-19 pneumonia from the 29 worst affected countries. Mortality estimates were calculated from three independent sources. We then applied linear regression analysis to examine for potential association between national targets for the commencement of oxygen and case fatality rates.

Results

Of the 26 nations included, 15 had employed conservative oxygen strategies to manage COVID-19 pneumonia. Of them, Belgium, France, USA, Canada, China, Germany, Mexico, Spain, Sweden and the UK guidelines advised commencing oxygen when oxygen saturations (SpO2) fell to 91% or less. Target SpO2 ranged from 92% to 95% in the other 16 nations. Linear regression analysis demonstrated a strong inverse correlation between the national target for the commencement of oxygen and national case fatality rates (Spearman’s Rho = −0.622, p < 0.001).

Conclusion

Our study highlights the disparity in oxygen provision for COVID-19 patients between the nations analysed, and indicates such disparity in access to supplemental oxygen may represent a modifiable factor associated with mortality during the pandemic.

Key Messages

What is already known?

There were no prospective clinical trials we could identify relating to COVID-19 and supplemental oxygen, nor any published studies examining access to supplemental oxygen and mortality in COVID-19.

There are a number of studies identifying an association with low oxygen saturations at presentation and mortality in COVID-19 pneumonia.

There is good quality evidence that a delay in the correction of hypoxia in pneumonia increases mortality.

What are the new findings?

This study highlights the different thresholds for commencing supplemental oxygen in patients with COVID-19 across 26 nations.

Those countries that provide better access to supplemental oxygen have a statistically significant lower mortality rate.

Our results support the consensus view that improving access to supplemental oxygen in COVID-19 pneumonia is likely to reduce mortality.
No official help is available - experience of parents and children with congenital heart disease during COVID-19
Authors: Marino Luise , Wagland Richard , Culliford David , Bharucha Tara , Sodergren Sam , Darlington Anne-Sophie
Published: July 2020

Purpose of the study
The purpose was to explore the experience, information, support needs and decision-making of parents with congenital heart disease (CHD) during the COVID-19 crisis.
Study design
On-line survey design
Setting
An on-line survey with open/closed questions to explore the experiences of parents of children, as well as children and young people (CYP) with CHD during the COVID-19 crisis
Patients
Parents of children with CHD and CYP
Results
184 parents and 36 CYP completed the survey. Parents worry about the virus (86.4%) vs. CYP (69.4%), whilst (89%) parents are vigilant for symptoms of the virus vs. CYP(69.4%). A thematic analysis of the qualitative comments covered 34 subthemes, forming eight-overarching themes: Virus 1)risk of infection, 2)information, guidance and advice, 3)change in health care provision, and 4)fears and anxieties; Lockdown and isolation 5)psychological and social impact, 6)keeping safe under lockdown, 7)provisions and dependence on others, 8)employment and income.
Conclusions
Parents and CYP were worried about the virus, although CYP less so. Parents and children however, were frustrated with the lack of specific and paediatric focused information and guidance, expressing disappointment with the adult centric information available. Parents also felt alone, especially with their concerns around the implications of cardiac service suspension and the implication for their childs health. In order to better support children and their families, resources need to be developed to address families and CYP concerns for their health during this pandemic.
Sub-epidemic model forecasts for COVID-19 pandemic spread in the USA and European hotspots, February-May 2020
Authors: Chowell Gerardo , Rothenberg Richard , Roosa Kimberlyn , Tariq Amna , Hyman James M. , Luo Ruiyan
Published: July 2020

Mathematical models have been widely used to understand the dynamics of the ongoing coronavirus disease 2019 (COVID-19) pandemic as well as to predict future trends and assess intervention strategies. The asynchronicity of infection patterns during this pandemic illustrates the need for models that can capture dynamics beyond a single-peak trajectory to forecast the worldwide spread and for the spread within nations and within other sub-regions at various geographic scales. Here, we demonstrate a five-parameter sub-epidemic wave modeling framework that provides a simple characterization of unfolding trajectories of COVID-19 epidemics that are progressing across the world at different spatial scales. We calibrate the model to daily reported COVID-19 incidence data to generate six sequential weekly forecasts for five European countries and five hotspot states within the United States. The sub-epidemic approach captures the rise to an initial peak followed by a wide range of post-peak behavior, ranging from a typical decline to a steady incidence level to repeated small waves for sub-epidemic outbreaks. We show that the sub-epidemic model outperforms a three-parameter Richards model, in terms of calibration and forecasting performance, and yields excellent short- and intermediate-term forecasts that are not attainable with other single-peak transmission models of similar complexity. Overall, this approach predicts that a relaxation of social distancing measures would result in continuing sub-epidemics and ongoing endemic transmission. We illustrate how this view of the epidemic could help data scientists and policymakers better understand and predict the underlying transmission dynamics of COVID-19, as early detection of potential sub-epidemics can inform model-based decisions for tighter distancing controls.