bluuebunny/crossref_metadata_2025 huggingface dataset:
Expanding community engagement in HIV clinical trials: a pilot study using crowdsourcing
Authors: Day Suzanne , Mathews Allison , Blumberg Meredith , Vu Thi , Mason Hailey , Rennie Stuart , Kuruc JoAnne D. , Gay Cynthia L. , Margolis David M. , Tucker Joseph D.
Published: April 2020

Objective:

To assess the potential for crowdsourcing to complement and extend community advisory board (CAB) feedback on HIV clinical trials. Crowdsourcing involves community members attempting to solve a problem and then sharing solutions.

Methods:

CAB and crowdsourced approaches were implemented in the context of a phase 1 HIV antibody trial to collect feedback on informed consent, participation experiences, and fairness. CAB engagement was conducted through group discussions with members of an HIV CAB. Crowdsourcing involved open events intended to engage the local community, including interactive video modules, animated vignettes, and a creative idea contest. Open coding and analysis of emergent themes were conducted to compare CAB and crowdsourced feedback.

Results:

The crowdsourcing activities engaged 61 people across three events; nine people engaged in CAB feedback. Compared with CAB participants, crowdsourcing participants had lower levels of education and income, and higher levels of disability and unemployment. Overlap in CAB and crowdsourced feedback included recommendations for enhancing communication and additional support for trial participants. Crowdsourcing provided more detailed feedback on the impact of positive experiences and socio-economic factors on trial participation. CAB feedback included greater emphasis on institutional regulations and tailoring trial procedures. Crowdsourced feedback emphasized alternative methods for learning about trials and concerns with potential risks of trial participation.

Conclusion:

Conducting crowdsourcing in addition to CAB engagement can yield a broader range of stakeholder feedback to inform the design and conduct of HIV clinical trials.

Video abstract:

http://links.lww.com/QAD/B707
Generation of HIV-1-infected patients’ gene-edited induced pluripotent stem cells using feeder-free culture conditions
Authors: Ye Lin , Wang Jiaming , Teque Fernando , Xie Fei , Tan Yuting , Kan Yuet Wei , Levy Jay A.
Published: April 2020

Objectives:

The discovery of induced pluripotent stem cells (iPSC) has brought promise to regenerative medicine as it breaks the ethical barrier of using embryonic stem cells. Such cell culture-derived patient-specific autologous stem cells are needed for transplantation. Here we report deriving HIV-1-infected patients’ iPSC lines under transgene-free methods and under feeder-free and xeno-free culture conditions to meet the requirement for clinical application.

Methods and results:

We have reprogrammed patients’ peripheral blood mononuclear cells with EBNA1/OriP episomal vectors, or a defective and persistent Sendai virus vector (SeVdp) to ensure a nonintegrating iPSC generation. Both single picked and pooled iPSC lines demonstrated high pluripotency and were able to differentiate into various lineage cells in vivo. The established cell lines could be modified by genetic editing using the TALENs or CRISPR/Cas 9 technology to have a bi-allelic CCR5Δ32 mutations seamlessly. All generated iPSC lines and modified cell lines had no evidence of HIV integration and maintained normal karyotype after expansion.

Conclusions:

This study provides a reproducible simple procedure for generating therapeutic grade iPSCs from HIV-infected patients and for engineering these cells to possess a naturally occurring genotype for resistance to HIV-1 infection when differentiated into immune cells.
CD300a identifies a CD4+ memory T cell subset with a higher susceptibility to HIV-1 infection
Authors: Vitallé Joana , Tarancón-Díez Laura , Jiménez-Leon María R. , Terrén Iñigo , Orrantia Ane , Roca-Oporto Cristina , López-Cortés Luis , Ruiz-Mateos Ezequiel , Zenarruzabeitia Olatz , Borrego Francisco
Published: April 2020

Human CD300a is known to promote the infection by dengue and other enveloped viruses and is overexpressed on CD4+ T cells from HIV-1-infected patients. We found that infected CD4+RA− T cells from untreated HIV-1-infected patients were mostly CD300a+. Furthermore, CD300a expressing CD4+RA− T cells from healthy donors were significantly more infected by HIV-1 in vitro than CD300a− cells. CD300a might represent a biomarker of susceptibility to HIV-1 infection on memory CD4+ T lymphocytes.
Characteristics and outcomes of extracorporeal life support in pediatric trauma patients
Authors: Behr Christopher A. , Strotmeyer Stephen J. , Swol Justyna , Gaines Barbara A.
Published: April 2020

BACKGROUND

Extracorporeal life support utilizing extracorporeal membrane oxygenation (ECMO) techniques has been used in the pediatric population for numerous indications, but its use in trauma has been understudied. We sought to examine the indications, characteristics, and outcomes of children placed on ECMO for trauma and hypothesized that outcomes would be equivalent to those of patients placed on ECMO for other indications.

METHODS

We performed a retrospective review of all pediatric trauma patients in the Extracorporeal Life Support Organization registry from 1989 to 2018. Patient characteristics, indications for ECMO, pre- and post-ECMO ventilator settings and blood chemistry, complications, and survival rates were examined. Categories were stratified by mode: venovenous (VV), veno-arterial (VA), or conversion. Data were analyzed using SPSS software, with significance considered at p value less than 0.05.

RESULTS

We identified 573 patients with a median age of 4.82 years. The majority of patients (62.3%) were male and on VA support (54.5%). Drowning (38.7%) was the most common mechanism, followed by burns (21.1%) and thoracic trauma (17.8%). Complication rates were high (81.9%), with the most frequent types being cardiovascular, mechanical, and hemorrhagic. Incidences of complications (overall and by type) were similar to those reported in other Extracorporeal Life Support Organization cohorts. Overall survival was 55.3% and was significantly higher (p = 0.00) for patients on VV (74.3%) compared with those on VA (41.7%), even when controlling for mechanism.

CONCLUSION

Survival and complication rates of pediatric trauma patients on ECMO are comparable to those reported for other indications. Trauma should not be considered a contraindication for ECMO.

LEVEL OF EVIDENCE

Therapeutic, level V.
Measuring aggregation in parasite populations
Authors: McVinish R. , Lester R. J. G.
Published: April 2020

Aggregation, a fundamental feature of parasite distributions, has been measured using a variety of indices. We use the definition that parasite–host systemAis more aggregated than parasite–host systemBif any given proportion of the parasite population is concentrated in a smaller proportion of the host populationAthan of host populationB. This leads to indices based on the Lorenz curve such as the Gini index (Poulin’sD), coefficient of variation and the Hoover index, all of which measure departure from a uniform distribution. The Hoover index is particularly useful because it can be interpreted directly in terms of parasites and hosts. An alternative view of aggregation is degree of departure from a Poisson (or random) distribution, as used in the index of dispersion and the negative binomialk. These and Lloyd’s mean crowding index are reinterpreted and connected back to Lorenz curves. Aggregation has occasionally been defined as the slope from Taylor’s law, although the slope appears unrelated to other indices. The Hoover index may be the method of choice when data points are available, and the coefficient of variation when only variance and mean are given.
Using free association networks to extract characteristic patterns of affect dynamics
Authors: Dover Yaniv , Moore Zohar
Published: April 2020

The dynamics of human affect in day-to-day life are an intrinsic part of human behaviour. Yet, it is difficult to observe and objectively measure how affect evolves over time with sufficient resolution. Here, we suggest an approach that combines free association networks with affect mapping, to gain insight into basic patterns of affect dynamics. This approach exploits the established connection in the literature between association networks and behaviour. Using extant rich data, we find consistent patterns of the dynamics of the valence and arousal dimensions of affect. First, we find that the individuals represented by the data tend to feel a constant pull towards an affect-neutral global equilibrium point in the valence–arousal space. The farther the affect is from that point, the stronger the pull. We find that the drift of affect exhibits high inertia, i.e. is slow-changing, but with occasional discontinuous jumps of valence. We further find that, under certain conditions, another metastable equilibrium point emerges on the network, but one which represents a much more negative and agitated state of affect. Finally, we demonstrate how the affect-coded association network can be used to identify useful or harmful trajectories of associative thoughts that otherwise are hard to extract.
Passage through exceptional point: case study
Authors: Znojil Miloslav
Published: April 2020

The description of unitary evolution using non-Hermitian but ‘hermitizable’ Hamiltonians
H
is feasible via an
ad hoc
metric
Θ
 = 
Θ
(
H
) and a (non-unique) amendment 〈
ψ
1
|
ψ
2
〉 → 〈
ψ
1
|
Θ
|
ψ
2
〉 of the inner product in Hilbert space. Via a proper fine-tuning of
Θ
(
H
) this opens the possibility of reaching the boundaries of stability (i.e. exceptional points) in many quantum systems sampled here by the fairly realistic Bose–Hubbard (BH) and discrete anharmonic oscillator (AO) models. In such a setting, it is conjectured that the EP singularity can play the role of a quantum phase-transition interface between different dynamical regimes. Three alternative ‘AO ↔ BH’ implementations of such an EP-mediated dynamical transmutation scenario are proposed and shown, at an arbitrary finite Hilbert-space dimension
N
, exact and non-numerical.
Toward a genetic system in the marine cyanobacterium Prochlorococcus
Authors: Laurenceau Raphaël , Bliem Christina , Osburne Marcia S. , Becker Jamie W. , Biller Steven J. , Cubillos-Ruiz Andres , Chisholm Sallie W.
Published: April 2020

As the smallest and most abundant primary producer in the oceans, the cyanobacterium

Prochlorococcus

is of interest to diverse branches of science. For the past 30 years, research on this minimal phototroph has led to a growing understanding of biological organization across multiple scales, from the genome to the global ocean ecosystem. Progress in understanding drivers of its diversity and ecology, as well as molecular mechanisms underpinning its streamlined simplicity, has been hampered by the inability to manipulate these cells genetically. Multiple attempts have been made to develop an efficient genetic transformation method for

Prochlorococcus

over the years; all have been unsuccessful to date, despite some success with their close relative,

Synechococcus

. To avoid the pursuit of unproductive paths, we report here what has not worked in our hands, as well as our progress developing a method to screen the most efficient electroporation parameters for optimal DNA delivery into

Prochlorococcus

cells. We also report a novel protocol for obtaining axenic colonies and a new method for differentiating live and dead cells. The electroporation method can be used to optimize DNA delivery into any bacterium, making it a useful tool for advancing transformation systems in other genetically recalcitrant microorganisms.
Cytoplasmic flows caused by actomyosin contraction drive interkinetic nuclear migration
Authors: Badugu Amarendra , Käch Andres
Published: April 2020

Interkinetic nuclear migration (IKNM) is the process by which the nucleus migrates between apical and medial surfaces of pseudostratified epithelia. Previous studies have proposed force generating mechanisms, acting primarily on the nucleus. Having observed in drosophila wing discs that cytoplasmic components (lipid droplets and mitochondria) migrate alongside the nucleus, we used live imaging and particle tracking to demonstrate that the cytoplasm flows are responsible for the nucleus migration. We identify that nuclear migration in mitotic cells is preceded by a fast basal-to-apical flow of cytoplasm occurring over short time scales. We further show that, for the migration of basally located nuclei to an apical position, a slower flow of cytoplasm is responsible over a longer time scale. Our findings indicate that these flows are driven by acto-myosin contractile forces. These flows increase the hydrostatic pressure under the nucleus to exert a lifting force, much like a piston in a hydraulic cylinder.
A systematic review to assess seizure risk with chloroquine therapy in persons with epilepsy
Authors: Pati Sandipan
Published: April 2020

Background

The goal of this systematic review is to assess the published literature for seizure risk with chloroquine therapy in persons with and without epilepsy. With the COVID-19 pandemic, there is a desperate need for therapy against the SARS CoV-2 virus. Chloroquine is one proposed medication that has received substantial public attention. However, drug labeling in the package insertion states that persons with epilepsy have the risk of chloroquine provoking seizures, and this has increased questions and anxiety in the epilepsy community.

Methods

PubMed (1970 to March 27, 2020) and the Embase (1970 to March 27, 2020) were searched with the terms chloroquine and seizure or epilepsy. Selected studies were reviewed, and the adverse drug reaction was classified.

Results

Only nine out of 27 studies were deemed eligible for systematic analysis. Out of the nine studies, only one was a prospective study (N=109), two were case series (N=6), and the remaining 6 were case reports. The dose of chloroquine ranged between 100-500 mg/day, except in one patient, the seizure was after taking 1000 mg. The strength of causality for the drug causing seizures in healthy and persons with epilepsy was mostly possible or unlikely, and none were certain. The only clinical trial that evaluated seizure risk with chloroquine failed to find any significant relation.

Conclusion

Although the drug insertion label states an increased risk of seizure, the systematic review highlights that such a statement is not supported by any class I studies but by anecdotal case reports. The only randomized clinical study revealed that seizures were not associated with an increased blood level of chloroquine or its metabolite. The present systematic review should provide reassurance to busy clinicians and persons with epilepsy that chloroquine, if prescribed to treat COVID-19, lacks any substantial evidence to suggest that the medication increases the risk of seizure.
The first month of the COVID-19 outbreak in 46 sub-Saharan African countries. A comparative analysis of growth rates
Authors: Prince Martin J. , Alem Atalay , Chibanda Dixon , Fairall Lara , Fekadu Abebaw , Hanlon Charlotte , Lund Crick , Leather Andy , Petersen Inge , Verhey Ruth , Wurie Haja
Published: April 2020

Background

The COVID-19 outbreak in sub-Saharan African countries started after those in Asia, Europe and North America, on 28th February 2020. The susceptibility to infection of populations in that region has been debated. Outbreaks on the scale of those seen elsewhere would pose substantial challenges. There are reasons for concern that transmission may be high and difficult to control, rapidly exceeding capacity to meet the needs for hospitalization and critical care.

Methods

We obtained data on daily new confirmed cases for all 46 countries from the World Health Organization, and used these to model and visualize growth trajectories using an AutoRegressive Integrated Moving Average (ARIMA) model. We then estimated doubling times from growth rates estimated from Poisson regression models, and by back counting from the most recent observation. We also calculated the time from 1st to 50th case, and the time from 5th to 100th case. These indicators were compared with the same summary indicators of growth at the same stage of the outbreak in highly affected European countries.

Results

Kenya was the only country with clear evidence of exponential growth. Nineteen countries had either reported no cases, were in the first few days of the outbreak, or had reported fewer than 10 cases over a period of two or more weeks. For the remaining 27 countries we identified four growth patterns: slow linear growth, more rapid linear growth, variable growth patterns over the course of the outbreak, and early signs of possible exponential growth. For those in the last three groups, doubling times ranged from 3 to 4 days, times from 1st to 50th case from 12 to 29 days, and from 5th to 100th case from eight to 15 days. These early indicators are comparable to those in European countries that have gone on to have substantial outbreaks, and time to 50th case was shorter suggesting lesser effectiveness of contact-tracing and quarantine in the early phase.

Conclusion

The 46 sub-Saharan African countries, home to over one billion people, are at a tipping point with clear potential for the outbreak to follow a similar course as in HIC in the global north. Radical population-level physical distancing measures may be required, but their impact on poor, disadvantaged and vulnerable people and communities need mitigating. Health systems in the region need urgent technical and material support, with testing, personal protection, and hospital/ critical care.
Non synonymous substitutions in HIV-1 GAG are frequent in epitopes outside the major hydrophobic region and associated with subtype differences
Authors: Olusola Babatunde A. , Olaleye David O. , Odaibo Georgina N.
Published: April 2020

In 2018, an estimated 38 million people lived with HIV-1 infection resulting in 770,000 deaths. More than 50% of this infection and its associated deaths occurred in Sub-Saharan Africa. There is the need to develop an HIV-1 vaccine if the epidemic would be effectively controlled. Cytotoxic T Lymphocytes (CTL) epitopes within the Major Hydrophobic Region (MHR) have been shown to be highly immunogenic and immuno-dominant. These conserved epitopes have recently been the focus of vaccines studies. Despite the West African epicenter having one of the highest numbers of diverse circulating HIV-1 strains, very few longitudinal studies have checked the frequencies of CTL immune escape variants on epitopes within and without the MHR for HIV-1 strains circulating in the region.

In this study we describe non-synonymous substitutions within and without the MHR of HIV-1 GAG genes isolated from 10 infected Nigerians at the early stages of HIV-1 infection. Furthermore, we analyzed these substitutions longitudinally in five infected individuals from the early stages of infection up until when antibodies become detectable. We identified 3 non synonymous substitutions within the MHR of HIV-1 GAG genes isolated from the early HIV infected individuals. Fourteen and nineteen mutations outside the MHR were observed before and after detection of antibodies respectively while 4 mutations were found within the MHR. These substitutions include previously mapped CTL epitope immune escape mutants. CTL immune pressure likely leave different footprints on HIV-1 GAG epitopes within and outside the MHR. This information is crucial for future vaccine designs for use in the West African region.
Nasopharyngeal Colonization, Associated Factors and Antimicrobial Resistance ofStreptococcus pneumoniaeamong Children under 5 Years of Age in the Southwestern Colombia
Authors: Gámez Gustavo , Rojas Juan Pablo , Cardona Santiago , Castillo Juan David , Palacio María Alejandra , Mejía Luis Fernando , Torres José Luis , Contreras Jaime , Muñoz Laura Mery , Criales Javier , Vélez Luis Felipe , Forero Angélica María , Zúñiga Yulieth Alexandra , Cuastumal María Eugenia , Acevedo Leidy Johanna , de Jesús Molina Álvaro , Bolivar Johan Alexis , Gómez-Mejia Alejandro , Morales Jessica Lorena , Hammerschmidt Sven
Published: April 2020

Streptococcus pneumoniaediseases are important causes of children death worldwide. Nasopharyngeal carriage of this pathobiont promotes bacterial spread and infections in the community. Here, a cross-sectional surveillance study was done to determine the proportion of nasopharyngeal colonization, antimicrobial susceptibility profile and associated factors in pediatric outpatients (southwestern Colombia, 2019). Data on factors associated with pneumococcal nasopharyngeal carriage were obtained through survey-based interviews. Nasopharyngeal swabs were collected and bacteria were microbiologically characterized. Antimicrobial susceptibility tests were done by VITEK-2. A logistic regression analysis was performed to examine associated factors. Tests with ap-value <0.05 were considered statistically significant. 452 children from the southwestern Colombia were examined and 41.8% carriedS. pneumoniae. A higher pneumococcal carriage frequency was observed among participants <2-years and in individuals belonging to indigenous communities, which were not immunized against pneumococcus, because of lacking established immunization schemes. Additionally, children attending child-care institutions were also highly colonized by pneumococci.S. pneumoniaeshowed 57.7% non-susceptibility to benzyl-penicillin (meningitis-cut); 45.5% intermediate-sensitivity to benzyl-penicillin (oral-cut) and 21.7% to cefotaxime; and resistance to erythromycin (40.7%), tetracycline (36.0%), trimethoprim/sulfamethoxazole (24.9%), clindamycin (24.3%) and ceftriaxone (27.0%). The proportion of 41.8% of participants carryingS. pneumoniaeshows a scenario with the presence of strains resistant to different antimicrobial agents (MDR and XDR), which constitutes important reservoirs of bacterial transmission by children <5-years in the southwest of Colombia. This situation could potentially lead to an onset of pneumococcal diseases. Hence, the need to expand conjugate pneumococcal immunization in the community and ensure compliance with established immunization schedules.
Preliminary study to identify severe from moderate cases of COVID-19 using NLR&RDW-SD combination parameter
Authors: Wang Changzheng , Deng Rongrong , Gou Liyao , Fu Zhongxiao , Zhang Xiaomei , Shao Feng , Wang Guanzhen , Fu Weiyang , Xiao Jianping , Ding Xiao , Li Tao , Xiao Xiulin , Li Chengbin
Published: April 2020

Objectives

Investigate the characteristics and rules of hematology changes in patients with COVID-19, and explore the possibility to identify moderate and severe patients using conventional hematology parameters or combined parameters.

Methods

The clinical data of 45 moderate and severe type patients with SARS-CoV-2 infections in Jingzhou Central Hospital from January 23 to February 13, 2020 were collected. The epidemiological indexes, clinical symptoms and laboratory test results of the patients were retrospectively analyzed. Those parameters with significant differences between the two groups were analyzed, and the combination parameters with best diagnostic performance were selected using the LDA method.

Results

Of the 45 patients with COVID-19 (35 moderate and 10 severe cases), 23 were male and 22 female, aged 16-62 years. The most common clinical symptoms were fever (89%) and dry cough (60%). As the disease progressed, WBC, Neu#, NLR, PLR, RDW-CV and RDW-SD parameters in the severe group were significantly higher than that in the moderate group (P<0.05); meanwhile, Lym#, Eos#, HFC%, RBC, HGB and HCT parameters in the severe group were significantly lower than that in the moderate group (P<0.05). For NLR, the AUC, the best cut-off value, the sensitivity and the specificity were 0.890, 13.39, 83.3% and 82.4% respectively, and for PLR, the AUC, the best cut-off, the sensitivity and the specificity were 0.842, 267.03, 83.3% and 74.0% respectively. The combined parameter NLR&RDW-SD had the best diagnostic efficiency (AUC was 0.938) and when the cut-off value was 1.046, the sensitivity and the specificity were 90.0% and 84.7% respectively, followed by the fitting parameter NLR&RDW-CV (AUC = 0.923). When the cut-off value was 0.62, the sensitivity and the specificity for distinguishing severe type from moderate cases of COVID-19 were 90.0% and 82.4% respectively.

Conclusions

The combined parameter NLR&RDW-SD is the best hematology index and can help clinicians to predict the severity of COVID-19 patients, and it can be used as a useful indicator to help prevent and control the epidemic.
Associations of clinical characteristics and antiviral drugs with viral RNA clearance in patients with COVID-19 in Guangzhou, China: a retrospective cohort study
Authors: Chen Xudan , Zhang Yuying , Zhu Baoyi , Zeng Jianwen , Hong Wenxin , He Xi , Chen Jingfeng , Zheng Haipeng , Qiu Shuang , Deng Ying , Chan Juliana CN , Wang Jian
Published: April 2020

Background

The novel coronavirus disease 2019 (COVID-19) characterized by respiratory symptoms has become a global pandemic although factors influencing viral RNA clearance remained unclear to inform optimal isolation period and treatment strategies.

Methods

In this retrospective study, we included patients with confirmed COVID-19 admitted to Guangzhou Eighth People’s Hospital from 20th January 2020 to 15th March 2020. The associations of clinical characteristics and treatment regimens on time to viral RNA clearance were analyzed.

Results

We examined 284 consecutive COVID-19 cases, accounting for 82% of confirmed cases in Guangzhou during this period. At the time of reporting (20th March 2020), 276 (97.2%) had recovered and were discharged from hospital with a median hospital stay of 18 days (interquartile range [IQR]:13-24). Overall, 280 patients achieved viral RNA clearance with a median length of 12 days (IQR: 8-16) after onset of illness. Amongst them, 66.1% had viral RNA cleared within 14 days, and 89.3% within 21 days. Older age, severity of disease, time lag from illness onset to hospital admission, high body temperature, and corticosteroid use were associated with delayed clearance of viral RNA. None of the antiviral regimens (chloroquine, oseltamivir, arbidol, and lopinavir/ritonavir) improved viral RNA clearance. The use of lopinavir/ritonavir was associated with delayed clearance of viral RNA after adjusting for confounders.

Conclusion

In patients with COVID-19, isolation for a minimum of 21 days after onset of illness may be warranted, while the use of antiviral drugs does not enhance viral RNA clearance.

Brief Summary

Viral RNA was cleared in 89% of the COVID-19 patients within 21 days after illness onset. The use of antiviral drugs (chloroquine, oseltamivir, arbidol, and lopinavir/ritonavir) did not shorten viral RNA clearance, especially in non-serious cases.
Forecasting Covid-19 Outbreak Progression in Italian Regions: A model based on neural network training from Chinese data
Authors: Distante Cosimo , Pereira Igor Gadelha , Gonçalves Luiz M. Garcia , Piscitelli Prisco , Miani Alessandro
Published: April 2020

Background

Epidemiological figures of Covid-19 epidemic in Italy are worse than those observed in China.

Methods

We modeled the Covid-19 outbreak in Italian Regions vs. Lombardy to assess the epidemics progression and predict peaks of new daily infections and total cases by learning from the entire Chinese epidemiological dynamics. We trained an artificial neural network model, a modified auto-encoder with Covid-19 Chinese data, to forecast epidemic curve of the different Italian regions, and use the susceptible–exposed–infected–removed (SEIR) compartment model to predict the spreading and peaks. We have estimated the basic reproduction number (R0) - which represents the average number of people that can be infected by a person who has already acquired the infection - both by fitting the exponential growth rate of the infection across a 1-month period, and also by using a day by day assessment, based on single observations.

Results

The expected peak of SEIR model for new daily cases was at the end of March at national level. The peak of overall positive cases is expected by April 11th in Southern Italian Regions, a couple of days after that of Lombardy and Northern regions. According to our model, total confirmed cases in all Italy regions could reach 160,000 cases by April 30th and stabilize at a plateau.

Conclusions

Training neural networks on Chinese data and use the knowledge to forecast Italian spreading of Covid-19 has resulted in a good fit, measured with the mean average precision between official Italian data and the forecast.
COVID-19 in India: Predictions, Reproduction Number and Public Health Preparedness
Authors: Rai Balram , Shukla Anandi , Dwivedi Laxmi Kant
Published: April 2020

Introduction

The COVID-19 has emerged as a global concern for public health due to large scale outbreak. The number of confirmed cases has also been increased in India in past few weeks. The predictions for the COVID-19 can provide insights into the epidemiology of the disease, which helps policymakers to check health system capacities.

Methods

We obtained data on daily confirmed, recovered and deaths cases for a period of 21 days and have implemented the exponential growth model to predict the future cases for all the three components. The mathematical model was used to calculate the average reproduction number and herd immunity. We estimated the number of active cases till 30th of April. We have also tried to analyze the public health capacity to combat COVID-19 in India.

Results

If the exponential growth in number of cases continue then the total number of active cases will be 2,49,635 until the end of April. The reproduction number for COVID-19 in India was found to be 2.56 and herd immunity as 61%. The cumulative cases predicted by the mathematical model was 1,20,203.

Discussion

This prediction provides an alarming situation for India in terms of public health preparedness. The number of tests is needed to increase to detect all the cases of COVID-19 in India. Though some serious preventive measures have been implemented, but India should be ready to face any sudden community outbreak.
Real-time forecasts and risk assessment of novel coronavirus (COVID-19) cases: A data-driven analysis
Authors: Chakraborty Tanujit , Ghosh Indrajit
Published: April 2020

The coronavirus disease 2019 (COVID-19) has become a public health emergency of international concern affecting 201 countries and territories around the globe. As of April 4, 2020, it has caused a pandemic outbreak with more than 11,16,643 confirmed infections and more than 59,170 reported deaths worldwide. The main focus of this paper is two-fold: (a) generating short term (real-time) forecasts of the future COVID-19 cases for multiple countries; (b) risk assessment (in terms of case fatality rate) of the novel COVID-19 for some profoundly affected countries by finding various important demographic characteristics of the countries along with some disease characteristics. To solve the first problem, we presented a hybrid approach based on autoregressive integrated moving average model and Wavelet-based forecasting model that can generate short-term (ten days ahead) forecasts of the number of daily confirmed cases for Canada, France, India, South Korea, and the UK. The predictions of the future outbreak for different countries will be useful for the effective allocation of health care resources and will act as an early-warning system for government policymakers. In the second problem, we applied an optimal regression tree algorithm to find essential causal variables that significantly affect the case fatality rates for different countries. This data-driven analysis will necessarily provide deep insights into the study of early risk assessments for 50 immensely affected countries.
A Recursive Bifurcation Model for Predicting the Peak of COVID-19 Virus Spread in United States and Germany
Authors: Shen Julia
Published: April 2020

Prediction on the peak time of COVID-19 virus spread is crucial to decision making on lockdown or closure of cities and states. In this paper we design a recursive bifurcation model for analyzing COVID-19 virus spread in different countries. The bifurcation facilitates a recursive processing of infected population through linear least-squares fitting. In addition, a nonlinear least-squares fitting is utilized to predict the future values of infected populations. Numerical results on the data from three countries (South Korea, United States and Germany) indicate the effectiveness of our approach.
Diminishing Marginal Benefit of Social Distancing in Balancing COVID-19 Medical Demand-to-Supply
Authors: Liu Pai , Beeler Payton , Chakrabarty Rajan K.
Published: April 2020

Social distancing has been adopted as a non-pharmaceutical intervention to prevent the COVID-19 pandemic from overwhelming the medical resources across the United States (US). The catastrophic socio-economic impacts of this intervention could outweigh its benefits if the timing and duration of implementation are left uncontrolled and ill-strategized. Here we investigate the dynamics of social distancing on age-stratified US population and benchmark its effectiveness in reducing the burden on hospital and ICU beds. Our findings highlight the diminishing marginal benefit of social distancing, characterized by a linear decrease in medical demands against an exponentially increasing social distancing duration. We determine an optimal intermittent social-to-no-distancing ratio of 5:1 corresponding to ∼80% reduction in healthcare demands – beyond this ratio, benefit of social distancing diminishes to a negligible level.

COVID-19 Medical Demand Forecast

https://eece.wustl.edu/chakrabarty-group/covid/
Sero-epidemiological evaluation of malaria transmission in The Gambia before and after mass drug administration
Authors: Wu Lindsey , Mwesigwa Julia , Affara Muna , Bah Mamadou , Correa Simon , Hall Tom , Beeson James G. , Tetteh Kevin K.A. , Kleinschmidt Immo , D’Alessandro Umberto , Drakeley Chris
Published: April 2020

Background

As The Gambia aims to achieve elimination by 2030, serological assays are a useful surveillance tool to monitor trends in malaria incidence and evaluate community-based interventions.

Methods

Within a mass drug administration (MDA) study in The Gambia, where reduced malaria infection and clinical disease were observed after the intervention, a serological sub-study was conducted in four study villages. Spatio-temporal variation in transmission was measured with a panel of recombinant Pf antigens on a multiplexed bead-based assay. Village-level antibody levels were quantified as under-15 sero-prevalence, sero-conversion rates, and age-adjusted antibody acquisition rates. Antibody levels prior to MDA were assessed for association with persistent malaria infection after community chemoprophylaxis.

Results

Seasonal changes in antibodies to Etramp5.Ag1 were observed in children under 15 in two transmission settings – the West Coast and Upper River Regions (4·32% and 31·30% Pf prevalence, respectively). At the end of the malaria season, short-lived antibody responses to Etramp5.Ag1, GEXP18, HSP40.Ag1, EBA175 RIII-V, and Rh2.2030 were lower amongst 1-15 year olds in the West Coast compared to the Upper River, reflecting known differences in transmission. Prior to MDA, individuals in the top 50th percentile of antibody levels had two-fold higher odds of clinical malaria during the transmission season, consistent with previous findings where individuals infected pre-MDA had 2-fold higher odds of re-infection post-MDA.

Conclusion

Serological markers can serve dual functions as indicators of malaria exposure and incidence. Further studies, particularly cluster randomised trials, can help establish standardised serological protocols to measure transmission across endemic settings.
Standardization and Age-Distribution of COVID-19: Implications for Variability in Case Fatality and Outbreak Identification
Authors: Fisman David N. , Greer Amy L. , Tuite Ashleigh R.
Published: April 2020

Background

Epidemiological data from the COVID-19 pandemic has demonstrated variability in attack rates by age, and country-to-country variability in case fatality ratio (CFR).

Objective

To use direct and indirect standardization for insights into the impact of age-specific under-reporting on between-country variability in CFR, and apparent size of COVID-19 epidemics.

Design

Post-hoc secondary data analysis (“case studies”), and mathematical modeling.

Setting

China, global.

Interventions

None.

Measurements

Data were extracted from a sentinel epidemiological study by the Chinese Center for Disease Control (CCDC) that describes attack rates and CFR for COVID-19 in China prior to February 12, 2020. Standardized morbidity ratios (SMR) were used to impute missing cases and adjust CFR. Age-specific attack rates and CFR were applied to different countries with differing age structures (Italy, Japan, Indonesia, and Egypt), in order to generate estimates for CFR, apparent epidemic size, and time to outbreak recognition for identical age-specific attack rates.

Results

SMR demonstrated that 50-70% of cases were likely missed during the Chinese epidemic. Adjustment for under-recognition of younger cases decreased CFR from 2.4% to 0.8% (assuming 50% case ascertainment in older individuals). Standardizing the Chinese epidemic to countries with older populations (Italy, and Japan) resulted in larger apparent epidemic sizes, higher CFR and earlier outbreak recognition. The opposite effect was demonstrated for countries with younger populations (Indonesia, and Egypt).

Limitations

Secondary data analysis based on a single country at an early stage of the COVID-19 pandemic, with no attempt to incorporate second order effects (ICU saturation) on CFR.

Conclusion

Direct and indirect standardization are simple tools that provide key insights into between-country variation in the apparent size and severity of COVID-19 epidemics.

Funding

The research was supported by a grant to DNF from the Canadian Institutes for Health Research (2019 COVID-19 rapid researching funding OV4-170360).
Implementation of a Novel Remote Physician SBRT Coverage Process during the Coronavirus Pandemic
Authors: Price Alex , Henke Lauren E. , Maraghechi Borna , Kim Taeho , Spraker Matthew B. , Hugo Geoffrey D. , Robinson Clifford G. , Knutson Nels C.
Published: April 2020

INTRODUCTION

During the COVID-19 pandemic, alternative methods of care are needed to reduce the relative risk of transmission in departments. Also needed is the ability to provide vital radiation oncological care if radiation oncologists (RO) are reallocated to other departments. We implemented a novel remote RO SBRT coverage practice, requiring it to be reliable, of high audio and visual quality, timely, and the same level of specialty care as our current in-person treatment coverage practice.

METHODS

All observed failure modes were recorded during implementation over the first 15 sequential fractions. The time from CBCT to treatment was calculated before and after implementation to determine timeliness of remote coverage. Image quality metrics were calculated between the imaging console screen and the RO’s shared screen. Comfort levels with audio/visual communication as well as overall comfort in comparison to in-person RO coverage was evaluated using Likert scale surveys after treatment.

RESULTS

Remote RO SBRT coverage was successfully implemented in 14/15 fractions with 3 observed process failures that were all corrected before treatment. Average times of pre-treatment coverage before and after implementation were 8.74 and 8.51min, respectively. The cross correlation between the imaging console screen and RO’s shared screen was r=0.96 and lag was 0.05s. The average value for all survey questions was above 4.5, approaching in-person RO coverage comfort levels.

CONCLUSIONS

Our novel method of remote RO SBRT coverage permits reduced personnel and patient interactions surrounding RT procedures. This may help to reduce transmission of COVID-19 in our department and provides a means for SBRT coverage if ROs are reallocated to other areas of the hospital for COVID-19 support.
Next weeks of SARS-CoV-2: Projection model to predict time evolution scenarios of accumulated cases in Spain
Authors: Monleon-Getino Antonio , Canela-Soler Jaume
Published: April 2020

Background and objectives

SARS-CoV-2 is a new type of coronavirus that can affect people and causes respiratory disease, COVID-19. It is affecting the entire planet and we focus in Spain, where the first case was detected at the end of January 2020 and in recent weeks it has increased in many cases. We need predictive models in order to be efficient and take actions. The general goal of this work is present a new model of SARS-CoV-2 to predict different scenarios of accumulated cases in Spain.

Material and methods

In this short report is used a model proposed previously, based on a parametric model Weibull and in a the library BDSbiost3 developed in R to infer and predict different scenarios of the evolution of SARS-CoV-2 for the accumulated cases in Spain after the spread that affects Spain detected at the end of January of this year.

Results

In the analyses presented, projective curves have been generated for the evolution of accumulated cases in which they reach about 4,000 cases or about 15,000 cases, for which the lines of the day in which the value for 90 will be reached can be seen vertically 90, 95 and 99% of the asymptote (maximum number of cases, from that day they will begin to descend or remain the same), that is why the vertical lines would indicate the brake of the disease. For the worst-case scenario, it takes 118, 126 or 142 days to reach the maximum number of cases (n = 15,000) to reach 90, 95 and 99% of the asymptote (maximum number of cases), respectively. This means translated in a time scale that in the worst case the virus will not stop its progress, in Spain, until summer 2020, hopefully before.

Comments and conclusions

This model could be used to plan the resources and see if the policies or means dedicated to the virus are slowing the progress of the virus or it is necessary to implement others that are more effective, and can also validate a method for future outbreaks of diseases such as these.
COVID-19 pandemics modeling with SEIR(+CAQH), social distancing, and age stratification. The effect of vertical confinement and release in Brazil
Authors: Lyra Wladimir , Nascimento José-Dias do , Belkhiria Jaber , de Almeida Leandro , Chrispim Pedro Paulo M. , de Andrade Ion
Published: April 2020

The ongoing COVID-19 epidemics poses a particular challenge to low and middle income countries, making some of them consider the strategy of “vertical confinement”. In this strategy, contact is reduced only to specific groups (like age groups) that are at increased risk of severe disease following SARS-CoV-2 infection. We aim to assess the feasibility of this scenario as an exit strategy for the current lockdown in terms of its ability to keep the number of cases under the health care system capacity. We developed a modified SEIR model, including confinement, asymptomatic transmission, quarantine and hospitalization. The population is subdivided into 9 age groups, resulting in a system of 72 coupled nonlinear differential equations. The rate of transmission is dynamic and derived from the observed delayed fatality rate; the parameters of the epidemics are derived with a Markov chain Monte Carlo algorithm. We used Brazil as an example of middle income country, but the results are easily generalizable to other countries considering a similar strategy. We find that starting from 60% horizontal confinement, an exit strategy on May 1st of confinement of individuals older than 60 years old and full release of the younger population results in 400 000 hospitalizations, 50 000 ICU cases, and 120 000 deaths in the 50-60 years old age group alone. The health care system avoids collapse if the 50-60 years old are also confined, but our model assumes an idealized lockdown where the confined are perfectly insulated from contamination, so our numbers are a conservative lower bound. Our results discourage confinement by age as an exit strategy.
Acceptance of and preference for COVID-19 vaccination in healthcare workers: a comparative analysis and discrete choice experiment
Authors: Fu Chuanxi , wei Zheng , Zhu Fengchang , Pei Sen , Li Shunping , Zhang Liuren , Sun Xiaohui , Wu Yue , Liu Ping , Jit Mark
Published: April 2020

Background

A major obstacle to successful coronavirus disease (COVID-19) vaccine rollout is vaccine hesitancy. Acceptance of and preferences for COVID-19 vaccination among healthcare workers (HCWs) is critical, because they are a key target group for vaccination programs, and they are also highly influential to vaccine uptake in the wider population. This study sought to comparatively determine the acceptance of and preference for COVID-19 vaccination among HCWs and the general population.

Methods

An Internet-based, region-stratified discrete-choice experiment was conducted among 352 HCWs and 189 general population respondents recruited in March 2020 from 26 Chinese provinces. We accessed knowledge of disease, attitude towards and acceptance of COVID-19 vaccination. Several attributes (related to COVID-19 disease, COVID-19 vaccination and one social acceptance) were identified as key determinants of vaccine acceptance.

Results

HCWs had a more in-depth understanding of COVID-19 and showed a higher willingness to accept COVID-19 vaccines with lower effectiveness and/or more severe adverse effects compared to the general population. 76.4% of HCWs (vs 72.5% of the general population) expressed willingness to receive vaccination (χ2=2.904, p=0.234). High levels of willingness to accept influenza (65.3%) and pneumococcal (55.7%) vaccination were also seen in HCWs. Future COVID-19 disease incidence (OR: 4.367, 95% CI 3.721–5.126), decisions about vaccination among social contacts of respondents (OR 0.398, 95% CI 0.339–0.467), and infection risk >30% (OR 2.706, 95% CI 1.776–2.425) significantly increased the probability of vaccination acceptance in HCWs.

Conclusion

Multi-component interventions to address the key determinants of hesitancy in both HCWs and in the general population should be considered for COVID-19 vaccination programs.