bluuebunny/crossref_metadata_2025 huggingface dataset:
Automated COVID-19 Detection from Chest X-Ray Images: A High Resolution Network (HRNet) Approach
Authors: Ahmed Sifat , Hossain Tonmoy , Hoque Oishee Bintey , Sarker Sujan , Rahman Sejuti , Shah Faisal Muhammad
Published: September 2020

The pandemic, originated by novel coronavirus 2019 (COVID-19), continuing its devastating effect on the health, well-being, and economy of the global population. A critical step to restrain this pandemic is the early detection of COVID-19 in the human body, to constraint the exposure and control the spread of the virus. Chest X-Rays are one of the non-invasive tools to detect this disease as the manual PCR diagnosis process is quite tedious and time-consuming. In this work, we propose an automated COVID-19 classifier, utilizing available COVID and non-COVID X-Ray datasets, along with High Resolution Network (HRNet) for feature extraction embedding with the UNet for segmentation purposes. To evaluate the proposed dataset, several baseline experiments have been performed employing numerous deep learning architectures. With extensive experiment, we got 99.26% accuracy, 98.53% sensitivity, and 98.82% specificity with HRNet which surpasses the performances of the existing models. Our proposed methodology ensures unbiased high accuracy, which increases the probability of incorporating X-Ray images into the diagnosis of the disease.
Predictors of healthcare worker burnout during the COVID-19 pandemic
Authors: Ferry Amy V , Wereski Ryan , Strachan Fiona E , Mills Nicholas L
Published: September 2020

Objective

We aim to provide a ‘snapshot’ of the levels of burnout, anxiety, depression and distress among healthcare workers during the COVID-19 pandemic.

Design, setting, participants

We distributed an online survey via social media in June 2020 that was open to any UK healthcare worker. The primary outcome measure was symptoms of burnout as measured using the Copenhagen Burnout Inventory (CBI). Secondary outcomes of depression, anxiety and distress as measured using the Patient Health Questionnaire-9, General Anxiety Scale-7, and Impact of Events Scale-Revised were recorded along with subjective measures of stress. Multivariate logistic regression analysis was performed to identify factors associated with burnout, depression, anxiety and distress.

Results

Of 539 persons responding to the survey, 90% were female, and 26% were aged 41-50 years, 53% were nurses. Participants with moderate-to-severe burnout were younger (49% [206/424] versus 33% [38/115] under 40 years, P=0.004), and more likely to have pre-existing comorbidities (21% versus 12%, P=0.031). They were twice as likely to have been redeployed from their usual role (22% versus 11%; adjusted odds ratio [OR] 2.2, 95% confidence interval [CI] 1.5-3.3, P=0.042), or to work in an area dedicated to COVID-19 patients (50% versus 32%, adjusted OR 1.6, 95% CI 1.4-1.8, P<0.001), and were almost 4-times more likely to have previous depression (24% versus 7%; adjusted OR 3.6, 95% CI 2.2-5.9, P=0.012). A supportive workplace team and male sex protected against burnout reducing the odds by 40% (adjusted OR 0.6, 95% CI 0.5-0.7, P<0.001) and 70% (adjusted OR 0.3, 95% CI 0.2-0.5, P=0.003), respectively.

Conclusion

Independent predictors of burnout were younger staff, redeployment to a new working area, working with patients with confirmed COVID-19 infection, and being female or having a previous history of depression. Evaluation of existing psychological support interventions is required with targeted approaches to ensure support is available to those most at risk.
Towards a digital solution: Predicting public take-up of Singapore’s contact tracing mobile application during the COVID-19 crisis
Authors: Saw Young Ern , Tan Edina Y-Q , Liu Jessica S , Liu Jean CJ
Published: September 2020

In the global outbreak of coronavirus disease 2019 (COVID-19), new digital solutions have been developed for infection control. In particular, contact tracing mobile applications provide a means for governments to manage both health and economic concerns. As public reception is paramount to success, we conducted a systematic examination of sociodemographic characteristics that predict downloads of a contact tracing application. Participants were 505 adults who completed a web-based survey in Singapore, the site of the first contact tracing application (TraceTogether). We found that persons who had already changed their lifestyles on account of the pandemic were more likely to download the application. Network analyses revealed that contact tracing downloads was associated with using hand sanitizers, avoiding public transport, and preferring outdoor over indoor venues during the pandemic. However, demographic and situational characteristics were not significant predictors of application downloads. Together, these findings provide a base for policy makers to promote the uptake of digital contact tracing.

Highlights

Worldwide, digital contact tracing has been introduced to control the spread of coronavirus disease 2019 (COVID-19).

In a survey of 505 participants, we investigated sociodemographic factors predicting voluntary downloads of a contact tracing mobile application.

Use of the contact tracing application was predicted by the extent to which an individual had modified his / her behaviors because of the outbreak.

Network analyses revealed that application usage was associated with using hand sanitizers, avoiding public transport, and preferring outdoor over indoor venues.

No demographic factor significantly predicted application usage.
Ethnic disparities in COVID-19 mortality in Mexico: a cross-sectional study based on national data
Authors: Ibarra-Nava Ismael , Flores-Rodriguez Kathia G. , Ruiz-Herrera Violeta , Ochoa-Bayona Hilda C. , Salinas-Zertuche Alfonso , Padilla-Orozco Magaly , Salazar-Montalvo Raul G.
Published: September 2020

Objective

To analyze the mortality associated with ethnicity, particularly of Indigenous peoples, in a large sample of patients with COVID-19 in Mexico.

Design

National, cross-sectional study.

Setting

Mexico.

Participants

416546 adult patients; 4178 Indigenous peoples with COVID-19 were the primary population under study.

Main outcome measures

The primary outcome was mortality from COVID-19 up to August 3rd, 2020. Logistic regression was used to calculate odds ratios while adjusting for confounders.

Results

Among all patients with COVID-19, whether hospitalized or not, a higher proportion of Indigenous peoples died compared to non-Indigenous people (16.5% vs 11.1%, respectively). Among hospitalized patients, a higher proportion of Indigenous peoples died (37.1%) compared to non-Indigenous peoples (36.3%). Deaths outside the hospital were also higher among Indigenous peoples (3.7% vs 1.7%). A higher proportion of Indigenous peoples died in both the private and public health care sectors. The adjusted odds ratio for COVID-19 mortality among Indigenous peoples with COVID-19 was 1.13 (95% confidence interval 1.03 to 1.24). The adjusted odds ratio for COVID-19 mortality among Indigenous peoples with COVID-19 was higher among those who received only ambulatory care (1.55, 95% confidence interval 1.24 to 1.92).

Conclusions

In the large sample of patients with COVID-19, the findings suggest that Indigenous peoples in Mexico have a higher risk of death from COVID-19, especially outside the hospital. These findings suggest Indigenous peoples lack access to care more so than non-Indigenous people during the COVID-19 pandemic in Mexico. More research is needed regarding the impact of the COVID-19 among racial and ethnic minorities in Mexico.
Covid-19 Social Distancing Interventions by State Mandate and their Correlation to Mortality in the United States
Authors: McCafferty Sean , Ashley Sean
Published: September 2020

Background

Evaluate the correlation between U.S. state mandated social interventions and Covid-19 mortality using a retrospective analysis of Institute for Health Metrics and Evaluation (IHME) data.

Methods

Twenty-seven (27) states in the United States were selected on June 17, 2020 from IHME data which had clearly defined and dated establishment of statewide mandates for social distancing measures to include: School closures, Prohibition on mass gatherings, business closures, stay at home orders, severe travel restrictions, and closure of non-essential businesses. The state Covid-19 mortality prevalence was defined as total normalized deaths to the peak daily mortality rate. The state mortality prevalence was correlated to the total number of mandates-days from their date of establishment to the peak daily mortality date. The slope of the maximum daily mortality rate was also correlated to mandate-days.

Results

The standardized mortality per state to the initial peak mortality rate did not demonstrate a discernable correlation to the total mandate days (R2 = 0.000006, p= 0.995). The standardized peak mortality rate per state suggested a slight correlation to the total mandate days (R2 = 0.053,p=0.246), but was not statistically significant. There was a significant correlation between standardized mortality and state population density (R2 = 0.524,p=0.00002).

Conclusions

The analysis appears to suggest no mandate effective reduction in Covid-19 mortality nor a reduction in Covid-19 mortality rate to its defined initial peak when interpreting the mean-effect of the mandates as present in the data. A strong correlation to population density suggests human interaction frequency does affect the total mortality and maximum mortality rate.

Trial Registration

Public data is not patient specific and made available for public download on IHME Websites which can be used, shared, modified or built upon by non-commercial users via the Creative Commons Attribution-NonCommercial 4.0 International License. https://creativecommons.org/licenses/by-nc/4.0/

Précis

The mean-effects of Covid-19 mandated social interventions were found to have no affect the maximum slope of the daily mortality nor the overall mortality but did correlate to the population density.
Beyond Six Feet: A Guideline to Limit Indoor Airborne Transmission of COVID-19
Authors: Bazant Martin Z. , Bush John W. M.
Published: September 2020

The revival of the world’s economy is being predicated on the Six-Foot Rule, a guideline that offers little protection from pathogen-bearing droplets sufficiently small to be continuously mixed through an indoor space. The importance of indoor, airborne transmission of COVID-19 is now widely recognized; nevertheless, no quantitative measures have been proposed to protect against it. In this article, we build upon models of airborne disease transmission in order to derive a safety guideline that would impose a precise upper bound on the “cumulative exposure time”, the product of the number of occupants and their time in an enclosed space. We demonstrate the manner in which this bound depends on the ventilation rate and dimensions of the room; the breathing rate, respiratory activity and face-mask use of its occupants; and the infectiousness of the respiratory aerosols, a disease-specific parameter that we estimate from available data. Case studies are presented, implications for contact tracing considered, and appropriate caveats enumerated.
A longitudinal study of SARS-CoV-2 infected patients shows high correlation between neutralizing antibodies and COVID-19 severity
Authors: Legros Vincent , Denolly Solène , Vogrig Manon , Boson Bertrand , Rigaill Josselin , Pillet Sylvie , Grattard Florence , Gonzalo Sylvie , Verhoeven Paul , Allatif Omran , Berthelot Philippe , Pélissier Carole , Thierry Guillaume , Botelho-Nevers Elisabeth , Paul Stéphane , Walzer Thierry , Cosset François-Loïc , Bourlet Thomas , Pozzetto Bruno
Published: September 2020

Understanding the immune responses elicited by SARS-CoV-2 infection is critical in terms of protection from re-infection and, thus, for public health policy and for vaccine development against the COVID-19. Here, using either live SARS-CoV-2 particles or retroviruses pseudotyped with the SARS-CoV-2 S viral surface protein (Spike), we studied the neutralizing antibody (nAb) response in serum specimens from a cohort of 140 SARS-CoV-2 qPCR-confirmed patients, including patient with mild symptoms but also more severe form including those that require intensive care. We show that nAb titers were strongly correlated with disease severity and with anti-Spike IgG levels. Indeed, patients from intensive care units exhibited high nAb titers, whereas patients with milder disease symptoms displayed heterogenous nAb titers and asymptomatic or exclusive outpatient care patients had no or poor nAb levels. We found that the nAb activity in SARS-CoV-2-infected patients displayed a relatively rapid decline after recovery, as compared to individuals infected with alternative coronaviruses. We show the absence of cross-neutralization between endemic coronaviruses and SARS-CoV-2, indicating that previous infection by human coronaviruses may not generate protective nAb against SARS-CoV-2 infection. Finally, we found that the D614G mutation in the Spike protein, which has recently been identified as the major variant now found in Europe, does not allow neutralization escape. Altogether, our results contribute to the understanding of the immune correlate of SARS-CoV-2 induced disease and claim for a rapid evaluation of the role of the humoral response in the pathogenesis of SARS-CoV-2.
Seroprevalence of SARS-CoV-2 in slums and non-slums of Mumbai, India, during June 29-July 19, 2020
Authors: Malani Anup , Shah Daksha , Kang Gagandeep , Lobo Gayatri Nair , Shastri Jayanthi , Mohanan Manoj , Jain Rajesh , Agrawal Sachee , Juneja Sandeep , Imad Sofia , Kolthur Ullas
Published: September 2020

Objective

Estimate seroprevalence in representative samples from slum and non-slum communities in Mumbai, India, a mega-city in a low or middle-income country and test if prevalence is different in slums.

Design

After geographically-spaced community sampling of households, one individual per household was tested for IgG antibodies to SARS-CoV-2 N-protein in a two-week interval.

Setting

Slum and non-slum communities in three wards, one each from the three main zones of Mumbai.

Participants

Individuals over age 12 who consent to and have no contraindications to venipuncture were eligible. 6,904 participants (4,202 from slums and 2,702 from non-slums) were tested.

Main outcome measures

The primary outcomes were the positive test rate for IgG antibodies to the SARS-CoV-2 N-protein by demographic group (age and gender) and location (slums and non-slums). The secondary outcome is seroprevalence at slum and non-slum levels. Sera was tested via chemiluminescence (CLIA) using Abbott Diagnostics ArchitectTM N-protein based test. Seroprevalence was calculated using weights to match the population distribution by age and gender and accounting for imperfect sensitivity and specificity of the test.

Results

The positive test rate was 54.1% (95% CI: 52.7 to 55.6) and 16.1% (95% CI: 14.9 to 17.4) in slums and non-slums, respectively, a difference of 38 percentage points (P < 0.001). Accounting for imperfect accuracy of tests (e.g., sensitivity, 0.90; specificity 1.00), seroprevalence was as high as 58.4% (95% CI: 56.8 to 59.9) and 17.3% (95% CI: 16 to 18.7) in slums and non-slums, respectively.

Conclusions

The high seroprevalence in slums implies a moderate infection fatality rate. The stark difference in seroprevalence across slums and non-slums has implications for the efficacy of social distancing, the level of herd immunity, and equity. It underlines the importance of geographic specificity and urban structure in modeling SARS-CoV-2.
in utero HIV exposure and the early nutritional environment influence neurodevelopment in infants before age three: findings from an evidenced review and meta-analysis
Authors: White Marina , Connor Kristin L.
Published: September 2020

The developing brain is especially vulnerable to infection and suboptimal nutrition during the pre- and early postnatal periods. Exposure to maternal HIV infection and antiretroviral therapies (ART) in utero and during breastfeeding can adversely influence infant (neuro)developmental trajectories. How early life nutrition may be optimised to improve neurodevelopmental outcomes for infants who are HIV/ART-exposed has not been well characterised. We conducted an up-to-date evidence review and meta-analysis on the influence of HIV exposure in utero and during breastfeeding, and early life nutrition, on infant neurodevelopmental outcomes before age three. We report that exposure to maternal HIV infection/ART may adversely influence expressive language development, in particular, and these effects may be detectable within the first three years of life. Further, while male infants may be especially vulnerable to HIV/ART exposure, few studies overall reported sex-comparisons, and whether there are sex-dependent effects of HIV exposure on neurodevelopment remains a critical knowledge gap to fill. Lastly, early life nutrition interventions, including daily maternal multivitamin supplementation during the perinatal period, may improve neurodevelopmental outcomes for infants who are HIV-exposed. Our findings suggest that the early nutritional environment may be leveraged to improve early neurodevelopmental trajectories in infants who have been exposed to HIV in utero. A clear understanding of how this environment should be optimised is key for developing targeted nutrition interventions during critical developmental periods in order to mitigate adverse outcome later in life, and should be a priority of future research.
Evaluation of production lots of a rapid point-of-care lateral flow serological test intended for identification of IgM and IgG against the N-terminal part of the spike protein (S1) of SARS-CoV-2
Authors: Hoffman Tove , Kolstad Linda , Rönnberg Bengt , Lundkvist Åke
Published: September 2020

Background and objectives

Several antibody tests are available to detect SARS-CoV-2 specific antibodies, many of which address different antigens. Rapid point-of-care (POC) tests have been doubted due to an eventual risk of production errors, although it is unstudied whether such error would affect test sensitivity and/or specificity. We aimed to evaluate two separate production lots of a commercially available test intended for rapid detection of IgM and IgG against the N-terminal part of the SARS-CoV-2 spike protein (S1).

Materials and methods

Serum samples from individuals with confirmed SARS-CoV-2 infection, by RT-PCR and/or serology, and pre-COVID-19 negative control sera gathered from a biobank during 2018 were collected. The presence of anti-S1 IgM/IgG was verified by an in-house Luminex-based serological assay, serving as reference method. The index test was a commercially available rapid POC-test (the COVID-19 IgG/IgM Rapid Test Cassette [Zhejiang Orient Gene Biotech Co Ltd, Huzhou, Zhejiang, China/Healgen Scientific, LLC, U.S.A.]).

Results

One hundred samples were verified positive for anti-S1 IgG (median fluorescence intensity (MFI) ≥900) and 74 for anti-S1 IgM (MFI ≥700), confirmed by RT-PCR (n=90) and/or serology (n=89). None of the negative controls (n=200; MFI <300) had SARS-CoV-2 anti-S1 IgM, while one tested positive for SARS-CoV-2 anti-S1 IgG. For the two lots, the sensitivities of the rapid test were 93.2% (69/74; 95% CI: 85.1% – 97.1%) and 87.8% (65/74; 95% CI: 78.5% – 93.5%) for IgM, respectively 93.0% (93/100; 95% CI: 86.3% – 96.6%) and 100.0% for IgG (100/100; 95% CI: 96.3% – 100.0%). The specificity for both lots was 100% for IgM (200/200; 95% CI: 98.1% – 100%) and 99.5% for IgG (199/200; 95% CI: 97.2% – 99.9%). The positive predictive value was 100% for IgM and 98.9% and 99.0% for IgG. The negative predictive value was 95.7% and 97.6% for IgM, and 96.6% and 100.0% for IgG.

Conclusion

The rapid POC-test used in this study is suitable to assess SARS-CoV-2 anti-S1 specific IgM/IgG, as a measure of previous virus exposure on an individual level. While the specificity was not affected by production lot, external validation of separate lots of rapid POC-tests is encouraged to ensure high sensitivity before market introduction.
Assessment of the Publication Trends of COVID-19 Systematic Reviews and Randomized Controlled Trials
Authors: Taito Shunsuke , Kataoka Yuki , Ariie Takashi , Oide Shiho , Tsujimoto Yasushi
Published: September 2020

Background

During the COVID-19 pandemic, the number of studies listed in The National Library of Medicine registry (ClinicalTrials.gov) and preprints in medRxiv for COVID-19 has grown rapidly. In this study, we clarified the publication trends of randomized controlled trials (RCTs) and systematic reviews (SRs) regarding COVID-19. Methods: We conducted a cross-sectional study by investigating the number of SRs and RCTs on topics related to COVID-19 practice published in PubMed and medRxiv between January 1 and June 30, 2020. We calculated the ratio of the number of RCTs to that of SRs for this study period, as in a previous study. Results: The SR/RCT ratio in PubMed increased from 9.0 in March to 102 in June. In medRxiv, the SR/RCT ratio rose from 7.7 in March to 16.5 in June Discussion: The SR/RCT ratio increased and was much higher than that of 0.871 in 2017 found in a previous review of all medical research. During the study period, the trend in the COVID-19 publications comprised a more rapid increase in the number of SRs than RCTs
The impact of the COVID-19 pandemic on mental health in the general population – a comparison between Germany and the UK
Authors: Knolle Franziska , Ronan Lisa , Murray Graham K.
Published: September 2020

Background

The COVID-19 pandemic has led to dramatic social and economic changes in daily life. First studies report an impact on mental health of the general population showing increased levels of anxiety, stress and depression. In this study, we compared the impact of the pandemic on two culturally and economically similar European countries: the UK and Germany.

Methods

Participants (UK=241, German=541) completed an online-survey assessing COVID-19 exposure, impact on financial situation and work, substance and media consumption, mental health using the tSymptom-Check-List-27 (SCL-27) and the Schizotypal Personality Questionnaire.

Results

We found distinct differences between the two countries. UK responders reported a stronger direct impact on health, financial situation and families. UK responders had higher clinical scores on the SCL-27, and higher prevalence. Interestingly, German responders were less hopeful for an end of the pandemic and more concerned about their life-stability.

Conclusion

As 25% of both German and UK responders reported a subjective worsening of the general psychological symptoms and 20-50% of German and UK responders reached the clinical cut-off for depressive and dysthymic symptoms as well as anxieties, it specifically shows the need for tailored intervention systems to support large proportions of the general public.
Are digital technology interventions effective to reduce loneliness in older adults? A systematic review and meta-analysis
Authors: Shah Syed Ghulam Sarwar , Nogueras David , Woerden Hugo Cornelis van , Kiparoglou Vasiliki
Published: September 2020

Objective

To review the latest literature on the effectiveness of DTIs in reducing loneliness in (older) adults.

Data Sources

Electronic searches in PubMed, Medline, CINAHL, EMBASE and Web of Science covering publication period from 1 January 2010 to 31 July 2019.

Subjects

Adult men and women

Design

Systematic review and meta-analysis

Main Outcome Measure

Loneliness.

Study Selection

Primary studies that used DTIs for tackling loneliness in adults (aged ≥18 years) with follow-up measurements at least three months or more and publication in the English language.

Data Extraction and Synthesis

Two researchers independently screened articles and extracted data on several variables: participants, interventions, comparators and outcomes. Data was extracted on the primary outcome i.e. loneliness measured at the baseline and follow-up measurements at three, four, six and twelve months after the intervention.

Results

Six studies were selected from 4939 articles screened. Selected studies included 5 clinical trials (4 RCTs and 1 quasi experimental study) and one before and after study, which enrolled 646 participants (men =154 (24%), women =427 (66%), no gender information =65 (10%) with average age between 73 and 78 years (SD 6-11). Five clinical trials were included in the meta-analysis and standardised mean differences (SMD) were calculated for each trial and pooled across studies using a random effects model. The overall effect estimates were not statistically significant in follow-up measurements at three months (SMD= 0.02, 95% CI= −0.36, 0.40; P=0.92), four months (SMDs= −1.11, 95% CI= - 2.60, 0.38; P=0.14) and six months (SMD= −0.11, 95% CI= −0.54, 0.32; P=0.61). The quality of evidence was very low to moderate in these trials.

Conclusions

There is insufficient evidence to make conclusions that DTIs are effective in reducing loneliness in older adults. Future research may consider RCTs with larger sample sizes and longer duration of interventions and follow-up.
The impact of the COVID-19 pandemic on wellbeing and cognitive functioning of older adults
Authors: De Pue Sarah , Gillebert Céline , Dierckx Eva , Vanderhasselt Marie-Anne , De Raedt Rudi , Van den Bussche Eva
Published: September 2020

COVID-19 took a heavy toll on older adults. In Belgium, by the end of August, 93% of deaths due to COVID-19 were aged 65 or older. Similar trends were observed in other countries. As a consequence, older adults were identified as a group at risk, and strict governmental restrictions were imposed on them. This has caused concerns about their mental health. Using an online survey, this study established the impact of the COVID-19 pandemic on adults aged 65 years or older, and which factors moderate this impact. Participants reported a significant decrease in activity level, sleep quality and wellbeing during the COVID-19 pandemic. Depression was strongly related to reported declines in activity level, sleep quality, wellbeing and cognitive functioning. Our study shows that the COVID-19 pandemic had a severe impact on the mental health of older adults. This implies that this group at risk requires attention of governments and healthcare.
Additive Compendium Map of Outbreak Risk Determinants of West Nile Virus in Europe at NUTS3
Authors: Gayle Alberto Alexander
Published: September 2020

Annual emergence of West Nile virus depends on a complex transmission chain. Predictive efforts are consequently confounded by time-varying associations and scale-dependent effect variability. SHAP (SHaply Additive Explanation) is a novel AI-driven solution with potential to overcome this. SHAP takes a high-performance XGBoost model and deductively imputes the marginal contribution of each feature with respect to the log relative risk associated with the local XGBoost prediction (an additive model). The resulting effect matrix is dimensionally identical to the original data but IID and homogenized in terms of units, scale, and interpretation. Such “synthetic data” can therefore serve as surrogate to allow for high-power statistical analyses. Here, we applied SHAP to a database consisting of high-resolution data from various domains – climate, environment, economic, sociodemographic, vector and host distribution – to derive an effect matrix of WNV outbreak risk determinants in Europe. This effect data proved superior to the original, nominal data in predictive tasks and delivered qualitatively compelling, domain-specific risk mappings. Further applications are discussed and others are invited to experiment.
Data-Driven Inference of COVID-19 Clinical Prognosis
Authors: Salas Joaquín , Pulido Dagoberto , Montoya Omar , Ruiz Isaac
Published: September 2020

Knowing the most likely clinical prognosis for a patient infected with SARS-Cov-2 could offer guidelines for tracking their medical evolution, improving attention, and assigning resources. Aiming to assess a patient’s status quantitatively, we explore the analysis of existing clinical information using data-driven methods. Our goal is to extract the characteristics distinguishing between those COVID-19 patients that improve and those who die. In our approach, we select the relevant features using the algorithm of Boruta, a wrapper framework that takes input from classifiers generating relevance assessment of the predictors. Using the extracted features, we train machine learning classifiers, including Random Forests, Support Vector Machine, Extreme Gradient Boosting, and Neural Networks. We assess the performance of the classifiers using Precision-Recall and ROC analysis, establishing the ranges at which risk assessment permits effective decision-making. Our research highlights that local regions present unique sets of essential features, that it is possible to construct effective classifiers based on clinical data, and that an ensemble of classifiers results in the best performing discriminant.
Changes in social behavior over time in the COVID-19 pandemic
Authors: Sheehan Megan M. , Pfoh Elizabeth R. , Speaker Sidra , Rothberg Michael B.
Published: September 2020

Public health recommendations aimed at limiting spread of SARS-CoV-2 have encouraged social distancing and masks as economies across the United States re-open. Understanding adherence to these guidelines will inform further efforts to reduce transmission. In this repeated cross-sectional survey study, we describe changes in social behavior in Ohio during periods of declining and rising cases. While essential activities remained consistent over time, more individuals attended gatherings of 10 or more people as cases rose, particularly in the 18-29 age group. A majority of individuals wore masks. It appears necessary to continue limiting gatherings and encourage mask-wearing, particularly among younger groups.
Validation of smartphone-based assessments of depressive symptoms using the Remote Monitoring Application in Psychiatry (ReMAP)
Authors: Goltermann Janik , Emden Daniel , Leehr Elisabeth J. , Dohm Katharina , Redlich Ronny , Dannlowski Udo , Hahn Tim , Opel Nils
Published: September 2020

Smartphone-based symptom monitoring has gained increased attention in psychiatric research as a cost-efficient tool for prospective and ecologically valid assessments based on participants’ self-reports. However, a meaningful interpretation of smartphone-based assessments requires knowledge on their psychometric properties; especially their validity. Here, we conducted a systematic investigation of the validity of smartphone-based assessments of affective symptoms by using the smartphone appRemote Monitoring Application in Psychiatry(ReMAP). Beck Depression Inventory (BDI), and single-item mood and sleep information was assessed via the ReMAP app and validated with stationary (nonsmartphone) BDI scores and clinician-rated depression severity using the Hamilton Depression Rating Scale (HDRS).

We found overall high comparability between smartphone-based and stationary BDI scores (ICC=.921, p<.001, n=173). Smartphone-based BDI further correlated with stationary HDRS ratings of depression severity (r=.783, p<.001, n=51). Higher agreement between smartphone and stationary assessments was found in affective disorder patients as compared to healthy controls, and anxiety disorder patients. Highly comparable agreement between delivery formats was found across age and gender groups. Similarly, smartphone-based single-item self-ratings of mood correlated with BDI sum scores (r=-.538, p<.001, n=168), while smartphone-based single-item sleep duration correlated with the sleep item of the BDI (r=-.310, p<.001, n=166).

The present findings demonstrate that smartphone-based monitoring of depressive symptoms via the ReMAP app provides valid assessments of depressive symptomatology and therefore represents a useful tool for prospective digital phenotyping in affective disorder patients in clinical and research applications.
Systematic Review and Meta-Analysis Identifies Significant Relationships Between Anxiety Disorders and Daytime Lower Urinary Tract Symptoms
Authors: Mahjani Behrang , Koskela Lotta Renström , Batuure Anita , Mahjani Christina Gustavsson , Janecka Magdalena , Hultman Christina M. , Reichenberg Abraham , Buxbaum Joseph D. , Akre Olof , Grice Dorothy E.
Published: September 2020

Background

Clinically, lower urinary tract symptoms (LUTS), such as voiding symptoms, overactive bladder, and interstitial cystitis, are associated with anxiety disorders. However, the existing evidence for the overlap of these conditions has not been systematically evaluated. The aim of this study was to examine this relationship.

Methods

We conducted a systematic review and meta-analysis to examine the relationship between LUTS and anxiety. We searched for articles published from January 1990 to July 2019 in PubMed, CENTRAL, PsycINFO, and Google Scholar. Outcomes were anxiety-related disorders and symptoms “clinical anxiety”) and subtypes of LUTS. We performed random-effect meta-analyses, and inspected funnel plots and applied the Egger’s test to evaluate publication bias. We followed PRISMA guidelines and recorded our protocol on PROSPERO (ID=CRD42019118607).

Results

We identified 814 articles, of which 94 fulfilled inclusion criteria and 23 had sufficient data for meta-analysis. The odds ratio for clinical anxiety among individuals with LUTS was 2.87 (95% CI: 2.38,3.46, P < 0.001). Very few studies looked at LUTS among individuals ascertained for clinical anxiety, but there appear to be significantly elevated odds ratio here as well. A large I2value suggests high heterogeneity between studies.

Conclusions

The results demonstrate a clinically significant association between clinical anxiety and LUTS. There were limited data on youth, which should motivate further study in this area. Understanding the co-occurrence of these conditions will lead to better prevention and interventions to ameliorate the progression of the symptoms and to improve quality of life.
A Comparison of Covid-19 Patient Characteristics Before versus After Partial Lockdown in Vietnam
Authors: Vo Hoang-Long , Vu Kim-Duy
Published: September 2020

Background

Given the Covid-19’ sudden rapid spread in the community since 25 July 2020, an updated analysis of Covid-19 cases was conducted to examine the differences of characteristics of Covid-19 patients before versus after partial lockdown end in Vietnam.

Methods

Data of 569 Covid-19 patients confirmed SARS-CoV-2 infection from 23 January to 31 July was collected from available official databases. We divided Covid-19 situation timeline into two main periods, before lockdown end (23 January – 22 April) and after lockdown end (23 April – 31 July).

Results

We found significant variations in the distribution of Covid-19 patients among different provinces between two periods. Covid-19 confirmed patients were older in the time after lockdown end compared to in the period before lockdown end by a median of 5 years. All discharged Covid-19 patients and no Covid-19 death were in the phase before lockdown, while post lockdown period had still remained significant patients being under treatment, especially reported first fatalities. The number of Covid-19 patients who returned from other countries (excluding China) slightly increased through two stages (p >0.05), partially showing that the continuous volume of people returning Vietnam from abroad during the Covid-19 epidemic.

Conclusions

Our analysis indicated demographic and epidemiological disparity of Covid-19 patients before versus after loosening the national partial lockdown in Vietnam. It is important to suggest that, proactive efforts in Covid-19 control after partial lockdown end will be effective when the measures to closely control and monitor repatriation and immigration via the borders of Vietnam are strictly enforced.

What is already known on this topic

Most of Covid-19 confirmed patients in Vietnam were acquired overseas.

In Vietnam, Covid-19 epidemic had the low estimated reproduction ratio (R0) and SARS-CoV-2 spread was on the downward trend before July 25.

What this study adds

Covid-19 confirmed patients were older in the time after lockdown end compared to in the period before lockdown end by a median of 5 years.

All discharged Covid-19 patients and no Covid-19 death were in the phase before lockdown, while post lockdown period had still remained significant patients being under treatment, especially reported first fatalities.

Continuous volume of people returning Vietnam from abroad through two stages during the Covid-19 epidemic.

Our analysis might be considered as a prompt reference source for further in-depth surveys to understand the adaptive models of Covid-19 patients among different provinces.
CIP2A interacts with TopBP1 and is selectively essential for DNA damage-induced basal-like breast cancer tumorigenesis
Authors: Laine Anni , Nagelli Srikar G. , Farrington Caroline , Butt Umar , Cvrljevic Anna N. , Vainonen Julia P. , Feringa Femke M. , Grönroos Tove J. , Gautam Prson , Khan Sofia , Sihto Harri , Qiao Xi , Pavic Karolina , Connolly Denise C. , Kronqvist Pauliina , Elo Laura L. , Maurer Jochen , Wennerberg Krister , Medema Rene H. , Joensuu Heikki , Peuhu Emilia , de Visser Karin , Narla Goutham , Westermarck Jukka
Published: September 2020

Despite saturated genetic profiling of breast cancers, oncogenic drivers for the clinically challenging basal-like breast cancer (BLBC) subtype are still poorly understood. Here, we demonstrate that CIP2A is selectively essential for DNA damage-induced initiation of mouse BLBC tumors, but not of other cancer types. Mechanistically, CIP2A was discovered genome-widely the closest functional homologue for DNA-damage proteins TopBP1, RHNO, POLQ, NBN and PARP1. CIP2A directly interacts with the ATR-activation domain of TopBP1, and dampens both, chromatin binding of TopBP1 and RAD51, and G2/M checkpoint in DNA-damaged cells. CIP2A also drives BLBC-associated proliferative MYC and E2F1 signaling. Consistently with high DNA-damage response activity BLBCs, and CIP2A’s novel role in checkpoint signaling, CIP2A was found essential for DNA-damaged, and BRCA-mutant BLBC cells. Selective role for CIP2A as BLBC driver was supported by association of high CIP2A expression with poor patient prognosis only in BLBC, but not in other breast cancer types. Therapeutically, small molecule reactivators of PP2A (SMAPs) phenocopy CIP2A-dependent DNA damage response, and inhibitin vivogrowth of patient-derived BLBC xenograft. In summary, we discover sub-type selective essential role for CIP2A in BLBC initiation and maintenance that can be explained by its newly discovered association with DNA-damage response, coordinated with regulation of proliferative signaling. The results also identify therapeutic strategy for CIP2A-dependent BLBCs.
Whole-exome imputation within UK Biobank powers rare coding variant association and fine-mapping analyses
Authors: Barton Alison R. , Sherman Maxwell A. , Mukamel Ronen E. , Loh Po-Ru
Published: September 2020

Exome association studies to date have generally been underpowered to systematically evaluate the phenotypic impact of very rare coding variants. We leveraged extensive haplotype sharing between 49,960 exome-sequenced UK Biobank participants and the remainder of the cohort (total N~500K) to impute exome-wide variants at high accuracy (R2>0.5) down to minor allele frequency (MAF) ~0.00005. Association and fine-mapping analyses of 54 quantitative traits identified 1,189 significant associations (P<5 x 10-8) involving 675 distinct rare protein-altering variants (MAF<0.01) that passed stringent filters for likely causality; 600 of the 675 variants (89%) were not present in the NHGRI-EBI GWAS Catalog. We replicated the effect directions of 28 of 28 height-associated variants genotyped in previous exome array studies, including missense variants in newly-associated collagen genes COL16A1 and COL11A2. Across all traits, 49% of associations (578/1,189) occurred in genes with two or more hits; follow-up analyses of these genes identified long allelic series containing up to 45 distinct likely-causal variants within the same gene (on average exhibiting 93%-concordant effect directions). In particular, 24 rare coding variants in IFRD2 independently associated with reticulocyte indices, suggesting an important role of IFRD2 in red blood cell development, and 11 rare coding variants in NPR2 (a gene previously implicated in Mendelian skeletal disorders) exhibited intermediate-to-strong effects on height (0.18-1.09 s.d.). Our results demonstrate the utility of within-cohort imputation in population-scale GWAS cohorts, provide a catalog of likely-causal, large-effect coding variant associations, and foreshadow the insights that will be revealed as genetic biobank studies continue to grow.
healthcareCOVID: A national cross-sectional observational study identifying risk factors for developing suspected or confirmed COVID-19 in UK healthcare workers
Authors: Kua J , Patel R , Nurmi E , Tian S , Gill H , Wong DJN , Moorley C , Nepogodiev D , Ahmad I , El-Boghdadly K
Published: September 2020

Objective

To establish the prevalence and risk factors for the development of suspected or confirmed coronavirus disease 2019 (COVID-19) infection among healthcare workers (HCWs) in the United Kingdom (UK).

Design

Cross-sectional observational study.

Setting

UK-based primary and secondary care.

Participants

HCWs aged ≥18 years working between 1 February and 25 May 2020.

Main outcome measures

A composite endpoint of laboratory-confirmed diagnosis of SARS-CoV-2, or self-isolation or hospitalisation due to suspected or confirmed COVID-19.

Results

Of 6152 eligible responses, the composite endpoint was present in 1806 (29.4%) HCWs, of whom 49 (0.8%) were hospitalised, 459 (7.5%) tested positive for SARS-CoV-2, and 1776 (28.9%) reported self-isolation. The strongest risk factor associated with the presence of the primary composite endpoint was increasing frequency of contact with suspected or confirmed COVID-19 cases without adequate personal protective equipment (PPE): “Never” (reference), “Rarely” (adjusted odds ratio 1.06, (95% confidence interval: 0.87 to 1.29)), “Sometimes” (1.7 (1.37 to 2.10)), “Often” (1.84 (1.28 to 2.63)), “Always” (2.93, (1.75 to 5.06)). Additionally, several comorbidities (cancer, respiratory disease, and obesity); working in a ‘doctors’ role; using public transportation for work; regular contact with suspected or confirmed COVID-19 patients; and lack of PPE were also associated with the presence of the primary endpoint. 1382 (22.5%) HCWs reported lacking access to PPE items while having clinical contact with suspected or confirmed COVID-19 cases. Overall, between 11,870 and 21,158 days of self-isolation were required by the cohort, equalling approximately 71 to 127 working days lost per 1000 working days.

Conclusions

Suspected or confirmed COVID-19 was more common in HCWs than in the general population. Risk factors included inadequate PPE, which was reported by nearly a quarter of HCWs. Governments and policymakers must ensure adequate PPE is available as well as developing strategies to mitigate risk for high-risk HCWs during future COVID-19 waves.
Do Lockdowns Bring about Additional Mortality Benefits or Costs? Evidence based on Death Records from 300 Million Chinese People
Authors: Qi Jinlei , Zhang Dandan , Zhang Xiang , Yin Peng , Liu Jiangmei , Pan Yuhang , Takana Tanakao , Xie Peiyu , Wang Zhaoguang , Liu Shuocen , Gao George F. , He Guojun , Zhou Maigeng
Published: September 2020

After the COVID-19 outbreak, China immediately adopted stringent lockdown policies to contain the virus. Using comprehensive death records covering around 300 million Chinese people, we estimate the impacts of city and community lockdowns on non-COVID-19 mortality outside of Wuhan. Employing a difference-in-differences method, we find that lockdowns reduced the number of non-COVID-19 deaths by 4.9% (cardiovascular deaths by 6.2%, injuries by 9.2%, and non-COVID-19 pneumonia deaths by 14.3%). The health benefits are likely driven by significant reductions in air pollution, traffic, and human interactions. A back-of-the-envelope calculation shows that more than 32,000 lives could have been saved from non-COVID-19 diseases/causes during the 40 days of the lockdown on which we focus. The results suggest that the rapid and strict virus countermeasures not only effectively controlled the spread of COVID-19 but also brought about massive unintended public health benefits. These findings can help better inform policymakers around the world about the benefits and costs of city and community lockdowns policies in dealing with the COVID-19 pandemic.
Backward and Hopf bifurcation analysis of an SEIRS COVID-19 epidemic model with saturated incidence and saturated treatment response
Authors: Oluyori David A. , Pérez Ángel G. C. , Okhuese Victor A. , Akram Muhammad
Published: September 2020

In this work, we further the investigation of an SEIRS model to study the dynamics of the Coronavirus Disease 2019 pandemic. We derive the basic reproduction number R0 and study the local stability of the disease-free and endemic states. Since the condition R0 < 1 for our model does not determine if the disease will die out, we consider the backward bifurcation and Hopf bifurcation to understand the dynamics of the disease at the occurrence of a second wave and the kind of treatment measures needed to curtail it. Our results show that the limited availability of medical resources favours the emergence of complex dynamics that complicates the control of the outbreak.
Participatory syndromic surveillance as a tool for tracking COVID-19 in Bangladesh
Authors: Mahmud Ayesha S. , Chowdhury Shayan , Sojib Kawsar Hossain , Chowdhury Anir , Quader Md. Tanvir , Paul Sangita , Saidy Md. Sheikh , Uddin Ramiz , Engø-Monsen Kenth , Buckee Caroline
Published: September 2020

Limitations in laboratory diagnostic capacity and reporting delays have hampered efforts to mitigate and control the ongoing coronavirus disease 2019 (COVID-19) pandemic globally. To augment traditional lab and hospital-based surveillance, Bangladesh established a participatory surveillance system for the public to self-report symptoms consistent with COVID-19 through multiple channels. Here, we report on the use of this system, which received over 3 million responses within two months, for tracking the COVID-19 outbreak in Bangladesh. Although we observe considerable noise in the data and initial volatility in the use of the different reporting mechanisms, the self-reported syndromic data exhibits a strong association with lab-confirmed cases at a local scale. Moreover, the syndromic data also suggests an earlier spread of the outbreak across Bangladesh than is evident from the confirmed case counts, consistent with predicted spread of the outbreak based on population mobility data. Our results highlight the usefulness of participatory syndromic surveillance for mapping disease burden generally, and particularly during the initial phases of an emerging outbreak.