bluuebunny/crossref_metadata_2025 huggingface dataset:
7000 years of turnover: historical contingency and human niche construction shape the Caribbean's Anthropocene biota
Authors: Kemp Melissa E. , Mychajliw Alexis M. , Wadman Jenna , Goldberg Amy
Published: May 2020

The human-mediated movement of species across biogeographic boundaries—whether intentional or accidental—is dramatically reshaping the modern world. Yet humans have been reshaping ecosystems and translocating species for millennia, and acknowledging the deeper roots of these phenomena is important for contextualizing present-day biodiversity loss, ecosystem functioning and management needs. Here, we present the first database of terrestrial vertebrate species introductions spanning the entire anthropogenic history of a system: the Caribbean. We employ this approximately 7000-year dataset to assess the roles of historical contingency and priority effects in shaping present-day community structure and conservation outcomes, finding that serial human colonization events contributed to habitat modifications and species extinctions that shaped the trajectories of subsequent species introductions by other human groups. We contextualized spatial and temporal patterns of species introductions within cultural practices and population histories of Indigenous, colonial and modern human societies, and show that the taxonomic and biogeographic diversity of introduced species reflects diversifying reasons for species introductions through time. Recognition of the complex social and economic structures across the 7000-year human history of the Caribbean provides the necessary context for interpreting the formation of an Anthropocene biota.
Experimental evidence that matching habitat choice drives local adaptation in a wild population
Authors: Camacho Carlos , Sanabria-Fernández Alberto , Baños-Villalba Adrián , Edelaar Pim
Published: May 2020

Matching habitat choice is a unique, flexible form of habitat choice based on self-assessment of local performance. This mechanism is thought to play an important role in adaptation and population persistence in variable environments. Nevertheless, the operation of matching habitat choice in natural populations remains to be unequivocally demonstrated. We investigated the association between body colour and substrate use by ground-perching grasshoppers (
Sphingonotus azurescens
) in an urban mosaic of dark and pale pavements, and then performed a colour manipulation experiment to test for matching habitat choice based on camouflage through background matching. Naturally, dark and pale grasshoppers occurred mostly on pavements that provided matching backgrounds. Colour-manipulated individuals recapitulated this pattern, such that black-painted and white-painted grasshoppers recaptured after the treatment aggregated together on the dark asphalt and pale pavement, respectively. Our study demonstrates that grasshoppers adjust their movement patterns to choose the substrate that confers an apparent improvement in camouflage given their individual-specific colour. More generally, our study provides unique experimental evidence of matching habitat choice as a driver of phenotype–environment correlations in natural populations and, furthermore, suggests that performance-based habitat choice might act as a mechanism of adaptation to changing environments, including human-modified (urban) landscapes.
COVID-19: disease pathways and gene expression changes predict methylprednisolone can improve outcome in severe cases
Authors: Draghici Sorin , Nguyen Tuan-Minh , Sonna Larry A , Ziraldo Cordelia , Vanciu Radu L , Fadel Raef , Morrison Austin , Ramesh Mayur , Mor Gil
Published: May 2020

Background. Current management efforts of COVID-19 include: early diagnosis, use of antivirals and immune modulation. After the initial viral phase of the illness, identification of the patients developing cytokine storm syndrome is critical. Treatment of this hyper-inflammation in these patients using existing, approved therapies with proven safety profiles could address the immediate need to reduce the rising mortality.
Methods. Using data from an A549 cell line, primary human bronchial epithelial (NBHE), as well as from COVID-19-infected lung, we compare the changes in the gene expression, pathways and mechanisms between SARS-CoV2, influenza A, and respiratory syncytial virus.
Results. We identified FDA-approved drugs that could be repurposed to help COVID-19 patients with severe symptoms related to hyper-inflammation. An important finding is that drugs in the same class will not achieve similar effects. For instance methylprednisolone and prednisolone were predicted to be effective in reverting many of the changes triggered by COVID-19, while other closely related steroids, such as prednisone or dexamethasone, were not. An independent clinical study evaluated 213 subjects, 81 (38%) and 132 (62%) in pre-and post-methylprednisolone groups, respectively. The composite end point was composed of escalation to intensive care units, need for mechanical ventilation, and death. The composite endpoint occurred at a significantly lower rate in post-methylprednisolone group compared to pre-methylprednisolone group (34.9% vs. 54.3%, p=0.005).
Conclusion. Clinical results confirmed the efficacy of the in silico prediction that indicated methyl- prednisolone could improve outcomes in severe COVID-19. These findings are important for any future pandemic regardless of the virus.
Predictive value of Altmetric Score on prospective citation and bibliometric impact: rise of a new argot
Authors: Robinson David BT , Powell Arfon GMT , Waterman Jennifer , Hopkins Luke , James Osian P , Egan Richard J , Lewis Wyn G
Published: May 2020

Background

Bibliometric and Altmetric analyses provide important but alternative perspectives regarding research article impact. This study aimed to establish whether Altmetric Score (AS) was associated with citation rate, independent of bibliometrics.

Method

Citations for a previously reported cohort of 100 most cited articles associated with the keyword “Surgery” (2018, Powellet al), were collected and a three-year interval Citation Gain (iCG) evaluated. Previous citation count, Citation Rate Index (CRI), AS, five-year Impact Factor, and Oxford Centre for Evidence Based Medicine (OCEBM) levels were used to classify citation rate prospect.

Results

During follow-up, the median iCG was 161 (IQR 83–281), with 73 and 62 articles receiving an increase in CRI and AS, respectively. Median CRI and AS increase were 2.8 (−0.1–7.7) and 3 (0–4), respectively. Receiver-Operator-Characteristic (ROC) analysis revealed that CRI (AUC 0.86 (95% CI 0.79–0.93), p<0.001) and AS (Area Under Curve (AUC) 0.65 (95% CI 0.55–0.76), p=0.008) were associated with higher iCG. AS critical threshold ≥ 2.0 was associated with better iCG when dichotomised at iCG median (OR=4.94, 95% CI 1.99–12.26, p=0.001) and iCG Upper Quartile (UQ, OR=4.13, 95% CI 1.60–10.66, p=0.003). Multivariable analysis identified that only CRI was independently associated with iCG when dichotomised at the median (OR 18.22, 95% CI 6.70–49.55, p<0.001) and UQ (OR 19.30, 95% CI 4.23–88.15, p<0.001).

Conclusion

Citation Rate Indices and Altmetric Scores are important predictors of interval Citation Gain, and better at predicting future citations than the historical and established Impact Factor and OCEBM quality of evidence descriptors.
Estimating the cost-of-illness associated with the COVID-19 outbreak in China from January to March 2020
Authors: Jin Huajie , Wang Haiyin , Li Xiao , Zheng Weiwei , Ye Shanke , Zhang Sheng , Zhou Jiahui , Pennington Mark
Published: May 2020

Background COVID-19, an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), swept through China in 2019-2020, with over 80,000 confirmed cases reported by end of March 2020. This study estimates the economic burden of COVID-19 in 31 provincial-level administrative regions in China between January and March 2020.

Methods The healthcare and societal cost of COVID-19 was estimated using bottom-up approach. The main cost components included identification, diagnosis and treatment of COVID-19, compulsory quarantine and productivity losses for all affected residents in China during the study period. Input data were obtained from government reports, clinical guidelines, and other published literature. The primary outcomes were total health and societal costs. Costs were reported in both RMB and USD (2019 value).

Outcomes The total estimated healthcare and societal cost associated with the outbreak is 4.26 billion RMB (0.62 billion USD) and 2,647 billion RMB (383 billion USD), respectively. The main components of routine healthcare costs are inpatient care (41.0%) and medicines (30.9%). The main component of societal costs is productivity losses (99.8%). Hubei province incurred the highest healthcare cost (83.2%) whilst Guangdong province incurred the highest societal cost (14.6%).

Interpretation This review highlights a large economic burden of the recent COVID-19 outbreak in China. These findings will aid policy makers in making informed decisions about prevention and control measures for COVID-19.

Funding The author(s) received no financial support for the research, authorship, and/or publication of this article.
A Human-Pathogen SEIR-P Model for COVID-19 Outbreak under different intervention scenarios in Kenya
Authors: Ojiambo Viona Nakhulo , Kimathi Mark , Mwalili Samuel , Gathungu Duncan , Mbogo Rachel
Published: May 2020

This work describes the mathematical modelling and dynamics of a novel Coronavirus disease 2019 (COVID-19) in Kenya. The mathematical model assumes Human-Human infection as well as Human-Pathogen interaction. Using the SEIR (Susceptible-Exposed-Infected-Recovered) compartmental model with additional component of the pathogen,we simulated the dynamics of COVID-19 outbreak and impact of different control measures. The resulting system of ordinary differential equations (ODEs) are directly solved using a combination of fourth and fifth-order Runge-Kutta methods. Simulation results indicate that non-pharmaceutical measures such as school closure, social distancing and movement restriction emphatically flatten the epidemic peak curve hence leading to a smaller number of overall disease cases.
Endothelial-protective effects of a G-protein-biased sphingosine-1 phosphate receptor-1 agonist, SAR247799, in type-2 diabetes rats and a randomized placebo-controlled patient trial.
Authors: Bergougnan Luc , Andersen Grit , Plum-Moerschel Leona , Evaristi Maria Francesca , Poirier Bruno , Tardat Agnes , Ermer Marcel , Herbrand Theresa , Arrubla Jorge , Coester Hans Veit , Sansone Roberto , Heiss Christian , Vitse Olivier , Hurbin Fabrice , Boiron Rania , Benain Xavier , Radzik David , Janiak Philip , Muslin Anthony J , Hovsepian Lionel , Kirkesseli Stephane , Deutsch Paul , Parkar Ashfaq A
Published: May 2020

SAR247799 is a G-protein-biased sphingosine-1 phosphate receptor-1 (S1P1) agonist designed to activate endothelial S1P1 and provide endothelial-protective properties, while limiting S1P1 desensitization and consequent lymphocyte-count reduction associated with higher doses. A dose-response study in diabetic rats with 5-week SAR247799 treatment demonstrated, at sub-lymphocyte-reducing doses, renal function and endothelial biomarker improvements and was used to select doses for human investigation. Type-2 diabetes patients, enriched for endothelial dysfunction (flow-mediated dilation, FMD<7%) (n=54), were randomized, in two sequential cohorts, to 28-day once-daily treatment with SAR247799 (1 or 5 mg in ascending cohorts), placebo or 50 mg sildenafil (positive control) in a 5:2:2 ratio per cohort. The maximum FMD change from baseline versus placebo for all treatments was reached on day 35; mean differences versus placebo were 0.60% (95% CI -0.34%-1.53%; p=0.203) for 1 mg SAR247799, 1.07% (95% CI 0.13%-2.01%; p=0.026) for 5 mg SAR247799 and 0.88% (95% CI -0.15%-1.91%; p=0.093) for 50 mg sildenafil. Both doses of SAR247799 were well tolerated, did not affect blood pressure, and were associated with minimal-to-no lymphocyte reduction and small-to-moderate heart rate decrease. These data provide the first human evidence for endothelial-protective properties of S1P1 activation, with SAR247799 being at least as effective as the clinical benchmark, sildenafil.
Trends in snakebite mortality in India from 2000 to 2019 in a nationally representative mortality study
Authors: Suraweera Wilson , Warrell David , Whitaker Romulus , Menon Geetha R , Rodrigues Rashmi , Hang Fu Sze , Begum Rehana , Sati Prabha , Piyasena Kapila , Bhatia Mehak , Brown Patrick , Jha Prabhat
Published: May 2020

The World Health Organization call to halve global snakebite deaths by 2030 will requires substantial progress in India. We analyzed 2,833 snakebite deaths from 611,483 verbal autopsies in the nationally representative Indian Million Death Study from 2001-14, and conducted a systematic literature review from 2000-19 covering 87,590 snakebites. We estimate that India had 1.2 million snakebite deaths (average 58,000/year) from 2000-19. Nearly half occurred at ages 30-69 years and over a quarter in children <15 years. Most occurred at home in rural areas. About 70% occurred in eight higher-burden states and half during the rainy season and at low altitude. The risk of an Indian dying from snakebite before age 70 is about 1 in 250, but notably higher in some areas. More crudely, we estimate 1.11-1.77 million bites occurred in 2015, of which 70% showed symptoms of envenomation. Prevention and treatment strategies might substantially reduce snakebite mortality in India.
An Age and Space Structured SIR Model Describing the Covid-19 Pandemic
Authors: Colombo Rinaldo M , Garavello Mauro , Marcellini Francesca , Rossi Elena
Published: May 2020

We present an epidemic model capable of describing key features of the present Covid-19 pandemic. While capturing several qualitative properties of the virus spreading, it allows to compute the basic reproduction number, the number of deaths due to the virus and various other statistics. Numerical integrations are used to illustrate the relevance of quarantine and the role of care houses.
The Seasonal End of Human Coronavirus Hospital Admissions with Implications for SARS-CoV-2
Authors: Evangelista Alan T.
Published: May 2020

The seasonality of influenza viruses and endemic human coronaviruses was tracked over an 8-year period to assess key epidemiologic reduction points in disease incidence for an urban area in the northeast United States. Patients admitted to a pediatric hospital with worsening respiratory symptoms were tested using a multiplex PCR assay from nasopharyngeal swabs. The additive seasonal effects of outdoor temperatures and indoor relative humidity (RH) were evaluated. The 8-year average peak activity of human coronaviruses occurred in the first week of January, when droplet and contact transmission was enabled by the low indoor RH of 20–30%. Previous studies have shown that an increase in RH to 50% has been associated with markedly reduced viability and transmission of influenza virus and animal coronaviruses. As disease incidence was reduced by 50% in early March, to 75% in early April, to greater than 99% at the end of April, a relationship was observed from colder temperatures in January with a low indoor RH to a gradual increase in outdoor temperatures in April with an indoor RH of 45–50%. As a lipid-bound, enveloped virus with similar size characteristics to endemic human coronaviruses, SARS-CoV-2 should be subject to the same dynamics of reduced viability and transmission with increased humidity. In addition to the major role of social distancing, the transition from lower to higher indoor RH with increasing outdoor temperatures could have an additive effect on the decrease in SARS-CoV-2 cases in May. Over the 8-year period of this study, human coronavirus activity was either zero or > 99% reduction in the months of June through September, and the implication would be that SARS-Cov-2 may follow a similar pattern.
Comparative Analysis of the Application of Behavioural Insights of 33 Worldwide Governments on the Landing Pages of their COVID-19 Official Websites and their Impact on the Growth Scale of the Pandemic
Authors: Cecchi-Dimeglio Paola , Kitson-Pantano Raphaela , Luu David , Cabon Yann
Published: May 2020

The COVID-19 crisis has seen over a third of the world population locked down and this article has sought to understand human behaviour in response to a historical and unprecedented global pandemic. Through the analysis 18 behavioural mechanisms present on the landing pages of the websites of 33 institutional governments from March 1st til May 1st 2020 compared to the WHO data on the number of COVID-19 cases and deaths per million for each country, the authors show that a behavioural consensus was observed across all 33 countries and that Individual and Social nudges had no impact. Whilst the decisions in essentially every country on Earth, were taken with the same aim: to limit population movements and social life, two aggravating factors of the spread of the virus, only the environmental nudges effectively helped slow the virus growth scale. The authors explain the rationale behind these results and suggest that people seek information beyond governmental websites that they generally mistrust. They further suggest using Scientists as role models to encourage governmental website's traffic and designing recursive nudges to increase the impact of individual and social interventions. Together with the new phases of the spread of the virus will come new rules and guidance. Public health policies need to address behavioural change of the population on a global scale in a more targeted manner and it is hoped that this paper will provide some insight on how to do so.
Development and validation of chest CT-based imaging biomarkers for early stage COVID-19 screening
Authors: Mao Xuanyu , Liu Xiao-Ping , Xiong Miao , Yang Xu , Jin Xiaoqing , Li Zhiqiang , Zhou Shuang , Chang Hang
Published: May 2020

Coronavirus Disease 2019 (COVID-19) is currently a global pandemic, and the early screening of COVID-19 is one of the key factors for COVID-19 control and treatment. Here, we developed and validated chest CT-based imaging biomarkers for COVID-19 patient screening. We identified the vasculature-like signals from CT images and found that, compared to healthy and community acquired pneumonia (CAP) patients, the COVID-19 patients revealed significantly higher abundance of these signals. Furthermore, unsupervised feature learning leads to the discovery of clinical-relevant imaging biomarkers from the vasculature-like signals for accurate and sensitive COVID-19 screening that has been double-blindly validated in an independent hospital (sensitivity: 0.941, specificity: 0.904, AUC: 0.952). Our findings could open a new avenue to assist screening of COVID-19 patients.
Global Analysis of an SEIRS Model for COVID-19 Capturing Saturated Incidence with Treatment Response
Authors: Oluyori David A. , Adebayo Helen O. , Pérez Ángel G. C.
Published: May 2020

Sequel to V. A. Okhuese [Mathematical Predictions for COVID-19 as a Global Pandemic, medRxiv, 2020, https://doi.org/10.1101/2020.03.19.20038794], who studied the dynamics of COVID-19 using an SEIRUS model. We consider an SEIRS model capturing saturated incidence with treatment response. In this theoretical model, we assumed that the treatment response is proportional to the number of infected as long as the incidence cases are within the capacity of the healthcare system, after which the value becomes constant, when the number of confirmed cases exceed the carrying capacity of the available medical facilities. Thus, we obtain the reproduction number stating that when R0 is less than a critical value R, the disease-free equilibrium is globally asymptotically stable. Also, we studied the existence of the local and global stability of the disease-free and endemic equilibria and found that the kind of treatment response and inhibitory measures deployed in tackling the COVID-19 pandemic determines whether the disease will die out or become endemic.
Differential Effects of Intervention Timing on COVID-19 Spread in the United States
Authors: Pei Sen , Kandula Sasikiran , Shaman Jeffrey
Published: May 2020

Assessing the effects of early non-pharmaceutical interventions1-5 on COVID-19 spread in the United States is crucial for understanding and planning future control measures to combat the ongoing pandemic6-10. Here we use county-level observations of reported infections and deaths11, in conjunction with human mobility data12 and a metapopulation transmission model13,14, to quantify changes of disease transmission rates in US counties from March 15, 2020 to May 3, 2020. We find significant reductions of the basic reproductive numbers in major metropolitan areas in association with social distancing and other control measures. Counterfactual simulations indicate that, had these same control measures been implemented just 1-2 weeks earlier, a substantial number of cases and deaths could have been averted. Specifically, nationwide, 61.6% [95% CI: 54.6%-67.7%] of reported infections and 55.0% [95% CI: 46.1%-62.2%] of reported deaths as of May 3, 2020 could have been avoided if the same control measures had been implemented just one week earlier. We also examine the effects of delays in re-implementing social distancing following a relaxation of control measures. A longer response time results in a stronger rebound of infections and death. Our findings underscore the importance of early intervention and aggressive response in controlling the COVID-19 pandemic.
Trust, threats, and consequences of the COVID-19 pandemic in Norway and Sweden: A comparative survey
Authors: Helsingen Lise M. , Refsum Erle , Gjostein Dagryn Kyte , Loberg Magnus , Bretthauer Michael , Kalager Mette , Emilsson Louise
Published: May 2020

Objectives: Norway and Sweden, two neighboring countries with similar populations, health care systems and socioeconomics, have reacted differently to the COVID-19 pandemic. Norway closed all kindergartens, schools and universities, and banned sports and cultural activities, while Sweden kept most institutions and trainings facilities open. We aimed to compare peoples' attitudes towards authorities and control measures, and effects on life in Norway and Sweden.
Design: Anonymous web-based surveys for individuals age 15 or older distributed through Facebook using the snowball method.
Setting: Norway and Sweden, mid-March to mid-April, 2020.
Participants: Altogether, 3,508 individuals participated in the survey; 3000 in Norway and 508 in Sweden. 79% of the participants were women, 60% of the Norwegians and 47% of the Swedes were between 30-49 years, and around 45% of the participants in both countries had more than 4 years of higher education.
Outcome measures: Perceived threat of the pandemic, views on infection control measures, and impact on daily life. We performed descriptive analyses of the responses and compared the two countries.
Results: People had high trust in the health services in both countries, but differed in the degree of trust in their government (17% had high trust in Norway and 37% in Sweden). More Norwegians than Swedes agreed that school closure was a good measure (66% Norway and 18% in Sweden), and that countries with open schools were irresponsible (65% in Norway and 23% in Sweden). About the same amount responded that COVID-19 was a large to very large threat to the population (53% in Norway and 58% in Sweden), whereas more Norwegians than Swedes responded that the threat from repercussions of the mitigation measures were large or very large (71% in Norway and 56% in Sweden). Compliance with infection preventive measures was high and similar in the two countries (more than 98%). In Norway, 69% lived a more sedentary life during the pandemic versus 50% in Sweden; and Norwegians reported they ate more than Swedes (44% in Norway and 33% in Sweden).
Conclusion: Sweden, with less restrictive measures against the COVID-19 pandemic, had a higher level of trust in the authorities, while Norwegians reported a more negative lifestyle during the pandemic. The level of trust in the health care system and self-reported compliance with preventive measures was high in both countries.
Empirical Assessment of COVID-19 Crisis Standards of Care Guidelines
Authors: Jezmir Julia L. , Bharadwaj Maheetha , Kishore Sandeep P. , Winkler Marisa , Diephuis Bradford , Kim Edy Y. , Feldman William B.
Published: May 2020

Background

Several states have released Crisis Standards of Care (CSC) guidelines for the allocation of scarce critical care resources. Most guidelines rely on Sequential Organ Failure Assessment (SOFA) scores to maximize lives saved, but states have adopted different stances on whether to maximize long-term outcomes (life-years saved) by accounting for patient comorbidities.

Methods

We compared 4 representative state guidelines with varying approaches to comorbidities and analyzed how CSC prioritization correlates with clinical outcomes. We included 27 laboratory-confirmed COVID-19 patients admitted to ICUs at Brigham and Women’s Hospital from March 12 to April 3, 2020. We compared prioritization algorithms from New York, which assigns priority based on SOFA alone; Maryland, which uses SOFA plus severe comorbidities; Pennsylvania, which uses SOFA plus major and severe comorbidities; and Colorado, which uses SOFA plus a modified Charlson comorbidity index.

Results

In pairwise comparisons across all possible pairs, we found that state guidelines frequently resulted in tie-breakers based on age or lottery: New York 100% of the time (100% resolved by lottery), Pennsylvania 86% of the time (18% by lottery), Maryland 93% of the time (35% by lottery), and Colorado: 32% of the time (10% by lottery). The prioritization algorithm with the strongest correlation with 14-day outcomes was Colorado (rs = −0.483. p = 0.011) followed by Maryland (rs = −0. 394, p =0.042), Pennsylvania (rs = −0.382, p = 0.049), and New York (rs = 0). An alternative model using raw SOFA scores alone was moderately correlated with outcomes (rs = −0.448, p = 0.019).

Conclusions

State guidelines for scarce resource allocation frequently resulted in identical priority scores, requiring tie-breakers based on age or lottery. These findings suggest that state CSC guidelines should be further assessed empirically to understand whether they meet their goals.
Performance of progressive and adaptive COVID-19 exit strategies: a stress test analysis for managing intensive care unit rates
Authors: van Wees Jan-Diederik , van der Kuip Martijn , Osinga Sander , van Westerloo David , Tanck Michael , Hanegraaf Maurice , Pluymaekers Maarten , Leeuwenburgh Olwijn , van Bijsterveldt Lonneke , Verreijdt Pien , Brunner Logan , Tutu van Furth Marceline
Published: May 2020

Background: In May 2020, many European countries have begun to introduce an exit strategy for the coronavirus disease 2019 (COVID-19) pandemic which involves relaxing social distancing measures. Predictive epidemiological modeling indicates that chances for resurgence are high. However, parametrization of the epidemiological nature of COVID-19 and the effect of relaxing social distancing is not well constrained, resulting in highly uncertain outcomes in view of managing future intensive care unit (ICU) needs.
Methods and findings: For performance analysis of exit strategies we developed an open-source ensemble-based Susceptible-Exposed-Infectious-Removed (SEIR) model. It takes into account uncertainties for the COVID-19 parametrization and social distancing measures. The model is calibrated to data of the outbreak and lockdown phase. For the exit phase, the model includes the capability to activate an emergency brake, reinstating lockdown conditions. Alternatively, the model uses an adaptive COVID-19 cruise control (ACCC) capable to retain a targeted ICU level. The model is demonstrated for the Netherlands and we analyzed progressive and adaptive exit strategies through a stress test of managing ICU rates. The progressive strategy reflects the outcome of social and economic pressure to use one-way steering toward progressively relaxing measures at an early stage. It is marked by a high probability for the activation of the emergency brake due to an unsolicited growth of ICU needs in the following months. Alternatively, the two-way steering ACCC can flatten ICU needs in a more gradual way and avoids activation of the emergency brake. It also performs well for seasonal variation in the reproduction number of severe acute respiratory syndrome-coronavirus.
Conclusions: The adaptive strategy (ACCC) is favored, as it avoids the use of the emergency brake at the expense of small steps of restrictive measures and allows the exploration of riskier and potentially rewarding measures in the future pathways of the exit strategy.
Psoriasis is associated with elevated gut IL-1α and intestinal microbiome alterations: results of a cross-sectional study from Central Asia.
Authors: Yegorov Sergey , Babenko Dmitriy , Kozhakhmetov Samat , Akhmaltdinova Lyudmila , Kadyrova Irina , Nurgozhina Ayaulym , Nurgaziyev Madiyar , Good Sara Victoria , Hortelano Gonzalo H. , Yermekbayeva Bakytgul , Kushugulova Almagul
Published: May 2020

Objective: Psoriasis is a chronic inflammatory condition that predominantly affects the skin and is associated with extracutaneous disorders, such as inflammatory bowel disease and arthritis. Changes in gut immunology and microbiota are important drivers of proinflammatory disorders and could play a role in the pathogenesis of psoriasis. Therefore, we explored whether psoriasis in a Central Asian cohort is associated with alterations in select immunological markers and/or microbiota of the gut.
Setting: We assessed correlates of psoriasis in a community from Kazakhstan.
Participants: Outpatients, aged 30-45 years, of a dermatology clinic presenting with plaque, guttate or palmoplantar psoriasis (n=20), and age-sex matched subjects without psoriasis (n=20).
Design: We undertook a cross-sectional study of stool samples. Stool supernatant was subjected to multiplex ELISA to assess the concentration of 47 cytokines and immunoglobulins and to 16S rRNA gene sequencing to characterize microbial diversity in both psoriasis+ participants and controls.
Results: The psoriasis+ group tended to have higher concentrations of most analytes in stool (29/47=61.7%) and gut IL-1α was significantly elevated (4.19-fold, p=0.007) compared to controls. Psoriasis was associated with alterations in gut Firmicutes, including elevated Faecalibacterium and decreased Oscillibacter and Roseburia abundance, but no association was observed between gut microbial diversity or Firmicutes/Bacteroidetes ratios and disease status.
Conclusions: Psoriasis may be associated with gut inflammation and dysbiosis. Studies are warranted to explore the use of gut microbiome-focused therapies in the management of psoriasis in this under-studied population.
COVID-19: Spatial Analysis of Hospital Case-Fatality Rate in France
Authors: SOURIS Marc , Gonzalez Jean-Paul
Published: May 2020

When the population risk factors and reporting systems are similar, the assessment of the case-fatality (or lethality) rate (ratio of cases to deaths) represents a perfect tool for analyzing, understanding and improving the overall efficiency of the health system.
The objective of this article is to estimate the influence of the hospital care system on lethality in metropolitan France during the inception of the COVID-19 epidemic, by analyzing the spatial variability of the hospital case-fatality rate between French districts (i.e. French departements).
The results show that the higher case-fatality rates observed by districts are mostly related to the level of morbidity, therefore to the overwhelming of the healthcare systems during the acute phases of the epidemic. However, the magnitude of this increase of case-fatality rate represents less than 10 per cent of the average case-fatality rate and cannot explain the magnitude of the variations in case-fatality rate reported per country by international organizations or information sites. These differences can only be explained by the systems for reporting cases and deaths, which, indeed, vary greatly from country to country, and not attributed to the care or treatment of patients, even during hospital stress due to epidemic peaks.
Similar incidence of Coronavirus Disease 2019 (COVID-19) in patients with rheumatic diseases with and without hydroxychloroquine therapy
Authors: Macias Juan , Gonzalez-Moreno Paz , Sanchez-Garcia Esther , Morillo-Verdugo Ramon , Dominguez-Quesada Carmen , Pinilla Ana , Macho MaMar , Martinez MaVictoria , Gonzalez-Serna Alejandro , Corma Anais , Real Luis Miguel , Pineda Juan Antonio
Published: May 2020

Background: Hydroxychloroquine is currently being tested as post-exposure prophylaxis against coronavirus disease 2019 (COVID-19) in several ongoing clinical trials.
Objective: To compare the incidence of COVID-19 in Spanish patients with autoimmune rheumatic diseases treated with and without hydroxychloroquine.
Methods: Retrospective electronic record review, from February 27th to April 16th, of patients with autoimmune inflammatory diseases followed at two academic tertiary care hospitals in Seville, Spain. The cumulative incidence of COVID-19, confirmed or suspected, was compared between patients with and without hydroxychloroquine as part of their treatment of autoimmune inflammatory diseases.
Results: Among 722 included subjects, 290 (40%) were receiving hydroxychloroquine. During the seven-week study period, five (1.7% [95% CI: 0.5%-4.0%] cases of COVID-19 were registered among patients with hydroxychloroquine and five (1.2% [0.4%-2.7%]) (p=0.523) in without hydroxychloroquine. COVID-19 was confirmed by PCR in one (0.3%, 95% CI 0.008-1.9%) patient with hydroxychloroquine and two (0.5%, 95% CI 0.05%-1.6%) without hydroxychloroquine (p=1.0). One patient on hydroxychloroquine and two subjects without hydroxychloroquine were admitted to the hospital, none of them required to be transferred to the intensive care unit and no patient died during the episode.
Conclusions: The incidence and severity of COVID-19 among patients with autoimmune rheumatic diseases with and without hydroxychloroquine was not significantly different. Hydroxychloroquine does not seem to be an appropriate therapy for post-exposure prophylaxis against COVID-19.
COVID-19 Infection Forecasting based on Deep Learning in Iran
Authors: Azarafza Mehdi , Azarafza Mohammad , Tanha Jafar
Published: May 2020

Since December 2019 coronavirus disease (COVID-19) is outbreak from China and infected more than 4,666,000 people and caused thousands of deaths. Unfortunately, the infection numbers and deaths are still increasing rapidly which has put the world on the catastrophic abyss edge. Application of artificial intelligence and spatiotemporal distribution techniques can play a key role to infection forecasting in national and province levels in many countries. As methodology, the presented study employs long short-term memory-based deep for time series forecasting, the confirmed cases in both national and province levels, in Iran. The data were collected from February 19, to March 22, 2020 in provincial level and from February 19, to May 13, 2020 in national level by nationally recognised sources. For justification, we use the recurrent neural network, seasonal autoregressive integrated moving average, Holt winter's exponential smoothing, and moving averages approaches. Furthermore, the mean absolute error, mean squared error, and mean absolute percentage error metrics are used as evaluation factors with associate the trend analysis. The results of our experiments show that the LSTM model is performed better than the other methods on the collected COVID-19 dataset in Iran
When Can Elimination of SARS-CoV-2 Infection be Assumed? Simulation Modelling in a Case Study Island Nation
Authors: Wilson Nick , Parry Matthew , Verrall Ayesha J , Baker Michael G , Schwehm Markus , Eichner Martin
Published: May 2020

Aims: We aimed to determine the length of time from the last detected case of SARS-CoV-2 infection before elimination can be assumed at a country level in an island nation.
Methods: A stochastic version of the SEIR model CovidSIM v1.1 designed specifically for COVID-19 was utilised. It was populated with data for the case study island nation of New Zealand (NZ) along with relevant parameters sourced from the NZ and international literature. This included a testing level for symptomatic cases of 7,800 tests per million people per week.
Results: It was estimated to take between 27 and 33 days of no new detected cases for there to be a 95% probability of epidemic extinction. This was for effective reproduction numbers (Re) in the range of 0.50 to 1.0, which encompass such controls as case isolation (the shorter durations relate to low Re values). For a 99% probability of epidemic extinction, the equivalent time period was 37 to 44 days. In scenarios with lower levels of symptomatic cases seeking medical attention and lower levels of testing, the time period was up to 53 to 91 days (95% level).
Conclusions: In the context of a high level of testing, a period of around one month of no new notified cases of COVID-19 would give 95% certainty that elimination of SARS-CoV-2 transmission had been achieved.
Plasma and Fecal Metabolite Profiles in Autism Spectrum Disorder
Authors: Needham Brittany D. , Adame Mark D. , Serena Gloria , Rose Destanie R. , Preston Gregory M. , Conrad Mary C. , Campbell A. Stewart , Donabedian David H. , Fasano Alessio , Ashwood Paul , Mazmanian Sarkis K.
Published: May 2020

Autism Spectrum Disorder (ASD) is a neurodevelopmental condition with hallmark behavioral manifestations including impaired social communication and restricted repetitive behavior. In addition, many affected individuals display metabolic imbalances, immune dysregulation, gastrointestinal (GI) dysfunction, and altered gut microbiome compositions. We sought to better understand non-behavioral features of ASD by determining molecular signatures in peripheral tissues. Herein, we present the untargeted metabolome of 231 plasma and 97 fecal samples from a large cohort of children with ASD and typically developing (TD) controls. Differences in lipid, amino acid, and xenobiotic metabolism discriminate ASD and TD samples. We reveal correlations between specific metabolite profiles and clinical behavior scores, and identify metabolites particularly associated with GI dysfunction in ASD. These findings support a connection between GI physiology, metabolism, and complex behavioral traits, and may advance discovery and development of molecular biomarkers for ASD.
Genome-wide effects of the antimicrobial peptide apidaecin on translation termination
Authors: Mangano Kyle , Florin Tanja , Shao Xinhao , Klepacki Dorota , Chelysheva Irina , Ignatova Zoya , Gao Yu , Mankin Alexander S. , Vázquez-Laslop Nora
Published: May 2020

Biochemical studies suggested that the antimicrobial peptide apidaecin (Api) inhibits protein synthesis by binding in the nascent peptide exit tunnel and trapping the release factor associated with a terminating ribosome. The mode of Api action in bacterial cells had remained unknown. Here, genome-wide analysis revealed that Api arrests translating ribosomes at stop codons and causes pronounced queuing of the trailing ribosomes. By sequestering the available release factors, Api promotes pervasive stop codon bypass, leading to expression of proteins with C-terminal extensions. Api-mediated translation arrest leads to futile activation of the ribosome rescue systems. Understanding the unique mechanism of Api action in living cells may facilitate development of new medicines and research tools for genome exploration.
An updated global COI barcode reference data set for Fall Armyworm (Spodoptera frugiperda) and first record of this species in Bhutan
Authors: Mahat Kiran , Mitchell Andrew , Zangpo Tshelthrim
Published: May 2020

We report the first detection of Fall Armyworm (FAW),Spodoptera frugiperda(Smith, 1797), in Bhutan. FAW feeds on more than 300 plant species and is a serious pest of many. It has been spreading through Africa since 2016 and Asia since 2018. In Bhutan, this species was first detected in maize fields in the western part of the country in September 2019 and subsequently found infesting maize crop in southern parts of the country in December 2019 and April 2020. Using morphological and molecular techniques the presence of the first invading populations ofS. frugiperdain Bhutan is confirmed through this study. We present an updated reference DNA barcode data set for FAW comprising 374 sequences, which can be used to reliably identify this serious pest species, and discuss some of the reasons why such compiled reference data sets are necessary, despite the publicly availability of the underlying data. We also report on a second armyworm species, the Northern Armyworm,Mythimna separata(Walker, 1865), in rice, maize and other crops in eighteen districts of Bhutan.
Workstation benchmark of Spark Capable Genome Analysis ToolKit 4 Variant Calling
Authors: Hansen Marcus H. , Simonsen Anita T. , Ommen Hans B. , Nyvold Charlotte G.
Published: May 2020

Background

Rapid and practical DNA-sequencing processing has become essential for modern biomedical laboratories, especially in the field of cancer, pathology and genetics. While sequencing turn-over time has been, and still is, a bottleneck in research and diagnostics, the field of bioinformatics is moving at a rapid pace – both in terms of hardware and software development. Here, we benchmarked the local performance of three of the most important Spark-enabled Genome analysis toolkit 4 (GATK4) tools in a targeted sequencing workflow: Duplicate marking, base quality score recalibration (BQSR) and variant calling on targeted DNA sequencing using a modest hyperthreading 12-core single CPU and a high-speed PCI express solid-state drive.

Results

Compared to the previous GATK version the performance of Spark-enabled BQSR and HaplotypeCaller is shifted towards a more efficient usage of the available cores on CPU and outperforms the earlier GATK3.8 version with an order of magnitude reduction in processing time to analysis ready variants, whereas MarkDuplicateSpark was found to be thrice as fast. Furthermore, HaploTypeCallerSpark and BQSRPipelineSpark were significantly faster than the equivalent GATK4 standard tools with a combined ∼86% reduction in execution time, reaching a median rate of ten million processed bases per second, and duplicate marking was reduced ∼42%. The called variants were found to be in close agreement between the Spark and non-Spark versions, with an overall concordance of 98%. In this setup, the tools were also highly efficient when compared execution on a small 72 virtual CPU/18-node Google Cloud cluster.

Conclusion

In conclusion, GATK4 offers practical parallelization possibilities for DNA sequence processing, and the Spark-enabled tools optimize performance and utilization of local CPUs. Spark utilizing GATK variant calling is several times faster than previous GATK3.8 multithreading with the same multi-core, single CPU, configuration. The improved opportunities for parallel computations not only hold implications for high-performance cluster, but also for modest laboratory or research workstations for targeted sequencing analysis, such as exome, panel or amplicon sequencing.
OPTIONAL VACCINE UTILIZATION HAS A MALE GENDER PREFERENCE – A RECORD BASED ANALYSIS FROM A TERTIARY CARE CENTRE OF EASTERN INDIA
Authors: Panigrahi Sandeep Kumar , Maiti Anumita , Epari Venkatarao
Published: May 2020

Background And Objectives

Optional vaccines find an important place in immunization today. This study attempts to find out the trend of optional vaccine utilization, over the past three years in the immunization clinic of a tertiary care centre and to find out the association of gender disparity with the utilization of these vaccines.

Methods

The retrospective study was conducted during October to December 2016 using the register based secondary data of October 2013 to September 2016. Month wise utilization of optional vaccines (Pneumococcal, influenza, typhoid, varicella, hepatitis A and MMR) and measles was captured. Analysis was done using Stata 12.1 SE.

Results

An increasing trend of utilization was seen for all vaccines including optional vaccines. The mean doses received by male children was significantly more for all optional vaccines (unlike all vaccines taken together) as well as for individual vaccines like Pneumococcal, influenza, typhoid, MMR, hepatitis A (p<0.05), but not for varicella and measles vaccine (p>0.05).

Conclusion

Gender disparity (preference for male children) was present for all optional vaccines except varicella, and not in case of measles vaccine used in universal immunization program selected as control.

Author’s note

What is already known on this subject

Differences in uptake are related to various factors in national immunization program of India.

Optional vaccines are not a part of the national immunization program,

There is no clarity regarding pattern and trend of use and gender differences, if any for optional vaccines.

What this study adds

Trend of optional vaccine uptake is on the rise reflecting increasing demand among parents.

Gender differences do not exist for vaccines covered under national immunization program, as seen for Measles vaccine, probably because of universalization.

Preference for male children exists for most of the optional vaccines (even for MMR) probably because of the cost involved.

Gender disparity was absent in Varicella, probably because of fear of parents for scar marks on face of their girl child.
Metamorphosis of COVID-19 Pandemic
Authors: Saif Farhan
Published: May 2020

We show phase-wise growth of COVID 19 pandemic and explain it by comparing real time data with Discrete Generalized Growth model and Discrete Generalized Richard Model. The comparison of COVID 19 is made for China, Italy, Japan and the USA. The mathematical techniques makes it possible to calculate the rate of exponential growth of active cases, estimates the size of the outbreak, and measures the deviation from the exponential growth indicating slowing down effect. The phase-wise pandemic evolution following the real time data of active cases defines the impact-point when the preventive steps, taken to eradicate the pandemic, becomes effective. The study is important to devise the measures to handle emerging threat of similar COVID-19 outbreaks in other countries, especially in the absence of a medicine.