bluuebunny/crossref_metadata_2025 huggingface dataset:
Prediction and control of COVID-19 infection based on a hybrid intelligent model
Authors: Zhang Gengpei , Liu Xiongding
Published: October 2020

The coronavirus (COVID-19) is a highly infectious disease that emerged in the late December 2019 in Wuhan, China, and it has caused a worldwide outbreak, which represents a major threat to global health. It is important to design prediction research and control strategies to crush its exploding. In this study, a hybrid intelligent model is proposed to simulate the spreading dynamics of COVID-19. First, considering the control measures, such as government investment, media publicity, medical treatment and law enforcement. The infection rates are optimized by genetic algorithm (GA), then a modified susceptible-infected-quarantined-recovered (SIQR) model is proposed, then the long short-term memory (LSTM) is imbedded into the SIQR model to design the hybrid intelligent model to further optimize other parameters of the system model to obtain the optimal predictive model and control measures. This study provide a reliable model to predict cases of infection and death, and reasonable suggestion to control COVID-19.
Tracking changes in reporting of epidemiological data during the COVID-19 pandemic in Southeast Asia: an observational study during the first wave
Authors: Amit Arianna Maever L. , Pepito Veincent Christian F. , Gutierrez Bernardo , Rawson Thomas
Published: October 2020

Background

When a new pathogen emerges, consistent case reporting is critical for public health surveillance. Tracking cases geographically and over time is key for understanding the spread of an infectious disease and how to effectively design interventions to contain and mitigate an epidemic. In this paper we describe the reporting systems on COVID-19 in Southeast Asia during the first wave in 2020, and highlight the impact of specific reporting methods.

Methods

We reviewed key epidemiological variables from various sources including a regionally comprehensive dataset, national trackers, dashboards, and case bulletins for 11 countries during the first wave of the epidemic in Southeast Asia. We recorded timelines of shifts in epidemiological reporting systems. We further described the differences in how epidemiological data are reported across countries and timepoints, and the accessibility of epidemiological data.

Findings

Our findings suggest that countries in Southeast Asia generally reported precise and detailed epidemiological data during the first wave of the COVID-19 pandemic. However, changes in reporting were frequent and varied across data and countries. Changes in reporting rarely occurred for demographic data such as age and sex, while reporting shifts for geographic and temporal data were frequent. We also found that most countries provided COVID-19 individual-level data daily using HTML and PDF, necessitating scraping and extraction before data could be used in analyses.

Interpretation

Countries have different reporting systems and different capacities for maintaining consistent reporting of epidemiological data. As the pandemic progresses, governments may also change their priorities in data sharing. Our study thus highlights the importance of more nuanced analyses of epidemiological data of COVID-19 within and across countries because of the frequent shifts in reporting. Further, most countries provide data on a daily basis but not always in a readily usable format. As governments continue to respond to the impacts of COVID-19 on health and the economy, data sharing also needs to be prioritised given its foundational role in policymaking, and the implementation and evaluation of interventions.

Funding

The work was supported through an Engineering and Physical Sciences Research Council (EPSRC) (https://epsrc.ukri.org/) Systems Biology studentship award (EP/G03706X/1) to TR. This project was also supported in part by the Oxford Martin School.

The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Development and validation of multivariable machine learning algorithms to predict risk of cancer in symptomatic patients referred urgently from primary care
Authors: Savage Richard S , Messenger Mike , Neal Richard D , Ferguson Rosie , Johnston Colin , Lloyd Katherine L , Neal Matthew D , Sansom Nigel , Selby Peter , Sharma Nisha , Shinkins Bethany , Skinner Jim R , Tully Giles , Duffy Sean , Hall Geoff
Published: October 2020

Background

Urgent Suspected Cancer (Two Week Wait, 2WW) referrals have improved early cancer detection but are increasingly a major burden on NHS services. This has been exacerbated by the COVID-19 pandemic.

Method

We developed and validated tests to assess the risk of any cancer for 2WW patients. The tests use routine blood measurements (FBC, U&E, LFTs, tumour markers), combining them using machine learning and statistical modelling. Algorithms were developed and validated for nine 2WW pathways using retrospective data from 371,799 referrals to Leeds Teaching Hospitals Trust (development set 224,669 referrals, validation set 147,130 referrals). A minimum set of blood measurements were required for inclusion, and missing data were modelled internally by the algorithms.

Results

We present results for two clinical use-cases. In use-case 1, the algorithms identify 20% of patients who do not have cancer and may not need an urgent 2WW referral. In use-case 2, they identify 90% of cancer cases with a high probability of cancer that could be prioritised for review.

Conclusions

Combining a panel of widely available blood markers produces effective blood tests for cancer for NHS 2WW patients. The tests are affordable, can be deployed rapidly to any NHS pathology laboratory with no additional hardware requirements.
Seasonal and Daytime Variation in Multiple Immune Parameters in Humans: Evidence from 329,261 Participants of the UK Biobank Cohort
Authors: Wyse Cathy , O’Malley G , Coogan Andrew N. , Smith Daniel J.
Published: October 2020

Background

Seasonal disease outbreaks are perennial features of human infectious disease but the factors generating these patterns are unclear. In animal studies, seasonal and circadian (daily) rhythms in immune function generate periodicity in vulnerability to disease, although it is not known whether the same applies to humans. Making use of extensive data from the UK Biobank cohort, we investigate seasonal and daytime variability in multiple immune parameters (inflammatory markers, white blood cell counts and antibody titres), and test for associations with a wide range of environmental and lifestyle factors.

Methods and Findings

Markers of inflammation (CRP), and white blood cell counts were measured between 8am and 7pm over a 4-year time period in 329,261 participants in UK Biobank. Individual-level data were linked to other factors that vary over seasonal and daily cycles, including changes in day length, outdoor temperature and vitamin D at the time the blood sample was collected. Analyses were further adjusted for potentially confounding lifestyle factors. Seasonal patterns were evident in lymphocyte and neutrophil counts, and CRP, but not monocytes, and these were independent of lifestyle, demographic and environmental factors. All the immune parameters assessed demonstrated significant daytime variation that was independent of confounding factors.

Conclusions

At a population level, human immune parameters vary across season and across time of day, independent of multiple confounding factors. Both season and time of day are fundamental dimensions of immune function that should be considered in all studies of immuno-prophylaxis and disease transmission. Strategic alignment of human activities to seasons and times of the day when we are less susceptible to infection could be an important additional tool for limiting population-level impacts of infectious diseases.
Evaluation of User Experiences for the Clean Team Ghana Container-Based Sanitation Service in Kumasi, Ghana
Authors: Tidwell James B. , Nyarko Kwabena B. , Ross Ian , Dwumfour-Asare Bismark , Scott Pippa
Published: October 2020

There is a lack of affordable and acceptable sanitation solutions for dense, low-income urban settlements. One option that has been proposed is container-based sanitation, where a sealed cartridge installed in a free-standing toilet is regularly changed and adequately separates users from their excreta. Though container-based toilets are considered a safely managed sanitation solution that meets the Sustainable Development Goal for sanitation, little is known about user experiences to inform how such a solution should be viewed by governments. We conducted a longitudinal prospective cohort study of changes in objective and subjective measures of sanitation quality due to the Clean Team Ghana (CTG) container- based toilet service in Kumasi, Ghana from June to December 2019. We collected data immediately prior to installation of a toilet and 10 weeks afterwards for 292 customers. Most initially used public toilets with good structural quality, but sometimes had poor cleanliness, a lack of handwashing facilities, and required a 14.3 minute mean round trip time to use. The evaluation found that CTG delivers a high-quality service that positively impacts the quality of life of CTG customers, as well as saving them money, reducing gender gaps in quality of life, and addressing the needs of those with physical disabilities. Satisfaction with CTG toilet and service characteristics was high, with the largest increases for satisfaction with smell, comfort, disgust, and privacy. Women in particular were positively impacted both for explicitly gendered indicators like the ability to practice menstrual hygiene management, and other indicators where women scored lower than men at baseline, including ease of access, ease of use, and cleanliness. Use of the service also benefitted those who had been unable to use a toilet for physical or social reasons beforehand. Problems with the CTG service, such as leaking, filling, smelling, or not being replaced as scheduled, were reported by fewer than 10% of customers. While one product or service does not fit the needs of all customers, this evaluation supports the growing body of evidence that container-based sanitation provides a service valued by users and acceptable to policymakers in dense urban settlements.
COVID-19 Infections Following Physical School Reopening
Authors: Miron Oren , Yu Kun-Hsing , Wilf-Miron Rachel , Kohane Isaac S. , Davidovitch Nadav
Published: October 2020

Background

School reopened in August-September 2020 and their effect on COVID-19 infections is unclear.

Methods

We examined Coronavirus Disease-19 incidence following school reopening in Florida.

Results

We found that counties teaching physically had 1.2-fold incidence increase in elementary schools and 1.3-fold increase in high schools, while counties teaching remotely had no increase.

Conclusions

Our results suggest that counties teaching physically could consider teaching remotely, especially in high school, until it is safe to teach physically.

What was known

Schools reopened in August-September 2020, with some teaching remotely, since the effect of physical reopening on COVID-19 infections is unclear.

What we added

counties teaching physically had 1.2-fold incidence increase in elementary schools and 1.3-fold increase in high schools. This suggests that counties teaching physically could consider teaching remotely instead, especially at the high school level.
Preliminary Estimates of Years of Life Lost (YLL) Due to COVID-19 in India
Authors: Indrayan Abhaya , Mishra Aman , Pathak Mona
Published: October 2020

Objectives

More than 7 million cases of COVID have been detected in India by the middle of October 2020 and more than 100 thousand deaths have occurred. In this communication, we present an estimate of the years of life lost (YLL) due to COVID-19 so far and the projection for the full year so that the health damage by this new disease can be compared with some other ailments.

Design

Records based study

Method

The YLL by one premature death is the expectation of life at that age. To calculate YLL, the age-wise distribution of COVID cases and deaths was obtained from the official sources of the government of India. Similar calculations were done for the general population from all causes for comparison.

Results

A total of more than 2 million years of life have already lost due to COVID-19 and the pattern indicates that we may end up with nearly 4 million YLL due to this disease in India. This is nearly 20 years lost per COVID death, 303 years lost per 1000 cases of COVID, and about 3 years lost per 1000 population in a full year. The age-group 50–59 years has been particularly affected. Other important findings are summarized as key messages.

Conclusion

The years of life lost so far and anticipated in full-year are enormous but may still be lower compared with some other causes such as road injuries.
Airborne Pathogens in a Heterogeneous World: Superspreading & Mitigation
Authors: Kirkegaard Julius B. , Mathiesen Joachim , Sneppen Kim
Published: October 2020

Epidemics are regularly associated with reports of superspreading: single individuals infecting many others. How do we determine if such events are due to people inherently being biological superspreaders or simply due to random chance? We present an analytically solvable model for airborne diseases which reveal the spreading statistics of epidemics in socio-spatial heterogeneous spaces and provide a baseline to which data may be compared. In contrast to classical SIR models, we explicitly model social events where airborne pathogen transmission allows a single individual to infect many simultaneously, a key feature that generates distinctive output statistics. We find that diseases that have a short duration of high infectiousness can give extreme statistics such as 20 % infecting more than 80 %, depending on the socio-spatial heterogeneity. Quantifying this by a distribution over sizes of social gatherings, tracking data of social proximity for university students suggest that this can be a approximated by a power law. Finally, we study mitigation efforts applied to our model. We find that the effect of banning large gatherings works equally well for diseases with any duration of infectiousness, but depends strongly on socio-spatial heterogeneity.
Clinical Presentation, Complication and Outcome of Black Stone (Paraphenylene Diamine) Poisoning
Authors: Abro Hakim Ali , Chandio Sultan Ahmed , Jalbani Azizullah , Buriro Sheeraz Ali , Saeed Aafia , Shaukat Faizan
Published: October 2020

Introduction

In recent time, developing countries of South Asia and Africa have seen significant increase in ingestion of Para-Phenylene Diamine (PPD), locally known as Kala Pathar, either accidental or for suicide. Through this study, we aim to study the clinical presentations and outcomes among patients who have ingested PPD.

Method

This retrospective case series study was conducted in a tertiary care hospital of Pakistan, from April 2013 to August 2017. Data of patients of PPD poisoning was archived from the hospital’s medical records. Around 174 consecutive cases were included in the study. Patients were evaluated based on self-administrated proforma.

Result

Out of 174 cases of PPD poisoning that were identified, 57(32.8%) were males and 117(67.2%) were females. The mean age ± SD (range) of the patients was 24.16±9 (10 to 70) years. Approximately 170 (97.8%) patients used PPD for suicidal intention. The most common presentation was facial swelling which was present in 144(82.8%) patients followed by dysphagia in 143(82.2%) patients. Complications include metabolic acidosis in 50 (28.7%) patients and aspiration pneumonia in 36 (20.7%) patients. A total of 101 (58%) improved, while others were either referred or left against medical advice (LAMA).

Conclusion

Increasing incidence of ingestion of PPD for suicide warrants the regulatory authorities to restrict the use of PPD in hair dyes and implement strict measures to educate masses and curtail the easy access of such poisonous substances among common people.
Low serum vitamin D level and COVID-19 infection and outcomes, a multivariate meta-analysis
Authors: Chen Jie , Xie Lixia , Yuan Ping , Ma Jianyong , Yu Peng , Zheng Chunhua , Liu Xiao
Published: October 2020

Objective

This study aimed to determine whether serum vitamin D is independently associated with COVID-19 infection and outcomes in patients with COVID-19.

Methods

We identified relevant studies by searching the PubMed, Embase, and medRxiv databases from December 2019 to October 1, 2020. Odds ratios (ORs) were pooled using random-effects models. Only reports with multivariate adjusted results were included to avoid the impact of potential confounding factors.

Results

A total of six studies with 377,265 patients were identified. Overall, in the categorical analysis, a low serum vitamin D level was associated with an increased risk of COVID-19 infection (OR: 1.47, 95% CI: 1.09- 1.97, I2=81%), hospitalization (OR: 1.83, 95% CI: 1.22-2.74, I2=0%), but not in-hospital death (OR: 2.73, 95% CI: 0.27-27.61). Notably, when vitamin D level was analyzed as a continuous variable, each 5 ng/ml increase in vitamin D level was not associated with any increased risk of COVID-19 infection (OR: 1.04, 95% CI: 0.96-1.12, I2=74%) or in-hospital death (OR: 1.02, 95% CI: 0.93-1.12).

Conclusions

Low serum vitamin D is associated with an increased risk of COVID-19 infection and hospitalization. In-hospital death showed a tendency to be increased in COVID-19 patients with low vitamin D levels. The ongoing clinical trials for evaluation of vitamin D supplementation will be key to the validation of this adjunctive treatment for COVID-19 patients.
Reducing Covid-19 risk in schools: a qualitative examination of staff and family views and concerns
Authors: Lorenc Ava , Kesten Joanna M , Kidger Judi , Langford Rebecca , Horwood Jeremy
Published: October 2020

Background

The Covid-19 pandemic has necessitated schools implementing Covid-19 risk-reduction measures.

Methods

We investigated young people, parent and school staff attitudes towards secondary school Covid-19 mitigation measures. Recruitment used school communication, community organisations and snowball sampling. Audio recorded online/phone individual/group interviews lasted 45 minutes. Interviews focused on social distancing, hand-hygiene and testing. Team framework analysis used interview notes and transcripts.

Results

Participants were 13 school staff, 20 parents and 17 young people. Concerns about Covid-19 risk at school, especially to vulnerable individuals, were outweighed by perceived risks of not returning to school. Some teachers anticipated guilt around being a potential ‘spreader’. Participants saw school mitigation measures as an acceptable and pragmatic solution to the impossibility of social distancing, although anticipated challenges in changing habitual behaviour. Participants supported school Covid-19 testing but identified the need to consider data security and stigma. Staff were concerned about unintended consequences of risk-reduction strategies and widening inequalities.

Conclusion

Families and staff supported Covid-19 mitigation measures in schools. Clear messaging and engendering collective responsibility are important for compliance and success. However, schools and policy makers should consider unintended consequences of measures, supporting vulnerable individuals and those with additional needs, and avoiding widening inequalities.
Baseline phenotype and 30-day outcomes of people tested for COVID-19: an international network cohort including >3.32 million people tested with real-time PCR and >219,000 tested positive for SARS-CoV-2 in South Korea, Spain and the United States
Authors: Golozar Asieh , Lai Lana YH , Sena Anthony G. , Vizcaya David , Schilling Lisa M. , Huser Vojtech , Nyberg Fredrik , Duvall Scott L. , Morales Daniel R. , Alshammari Thamir M , Abedtash Hamed , Ahmed Waheed-Ul-Rahman , Alser Osaid , Alghoul Heba , Zhang Ying , Gong Mengchun , Guan Yin , Areia Carlos , Jonnagaddala Jitendra , Shah Karishma , Lane Jennifer C.E. , Prats-Uribe Albert , Posada Jose D. , Shah Nigam H. , Subbian Vignesh , Zhang Lin , Fernandes Abrahão Maria Tereza , Rijnbeek Peter R. , You Seng Chan , Casajust Paula , Roel Elena , Recalde Martina , Fernández-Bertolín Sergio , Andryc Alan , Thomas Jason A. , Wilcox Adam B. , Fortin Stephen , Blacketer Clair , DeFalco Frank , Natarajan Karthik , Falconer Thomas , Spotnitz Matthew , Ostropolets Anna , Hripcsak George , Suchard Marc , Lynch Kristine E. , Matheny Michael E. , Williams Andrew , Reich Christian , Duarte-Salles Talita , Kostka Kristin , Ryan Patrick B. , Prieto-Alhambra Daniel
Published: October 2020

Early identification of symptoms and comorbidities most predictive of COVID-19 is critical to identify infection, guide policies to effectively contain the pandemic, and improve health systems’ response. Here, we characterised socio-demographics and comorbidity in 3,316,107persons tested and 219,072 persons tested positive for SARS-CoV-2 since January 2020, and their key health outcomes in the month following the first positive test. Routine care data from primary care electronic health records (EHR) from Spain, hospital EHR from the United States (US), and claims data from South Korea and the US were used. The majority of study participants were women aged 18-65 years old. Positive/tested ratio varied greatly geographically (2.2:100 to 31.2:100) and over time (from 50:100 in February-April to 6.8:100 in May-June). Fever, cough and dyspnoea were the most common symptoms at presentation. Between 4%-38% required admission and 1-10.5% died within a month from their first positive test. Observed disparity in testing practices led to variable baseline characteristics and outcomes, both nationally (US) and internationally. Our findings highlight the importance of large scale characterization of COVID-19 international cohorts to inform planning and resource allocation including testing as countries face a second wave.
Causes of death in mental health service users during the first wave of the COVID-19 pandemic: South London and Maudsley data from March to June 2020, compared with 2015-2019
Authors: Stewart Robert , Jewell Amelia , Broadbent Matthew , Bakolis Ioannis , Das-Munshi Jayati
Published: October 2020

The COVID-19 pandemic is likely to have had a particularly high impact on the health and wellbeing of people with pre-existing mental disorders. This may include higher than expected mortality rates due to severe infections themselves, due to other comorbidities, or through increased suicide rates during lockdown. However, there has been very little published information to date on causes of death in mental health service users. Taking advantage of a large mental healthcare database linked to death registrations, we describe numbers of deaths within specific underlying-cause-of-death groups for the period from 1st March to 30th June in 2020 and compare these with the same four-month periods in 2015-2019. In past and current service users, there were 2561 deaths in March-June 2020, compared to an average of 1452 for the same months in 2015-19: an excess of 1109. The 708 deaths with COVID-19 as the underlying cause in 2020 accounted for 63.8% of that excess. The remaining excess was accounted for by unnatural/unexplained deaths and by deaths recorded as due to neurodegenerative conditions, with no excess in those attributed to cancer, circulatory disorders, digestive disorders, respiratory disorders, or other disease codes. Of 295 unexplained deaths in 2020 with missing data on cause, 162 (54.9%) were awaiting a formal death notice (i.e. the group that included deaths awaiting a coroner’s inquest) – an excess of 129 compared to the average of previous years, accounting for 11.6% of the excess in total deaths.
Serologic SARS-CoV-2 testing in healthcare workers with positive RT-PCR test or Covid-19 related symptoms
Authors: Visci Giovanni , Lodi Vittorio , Bonfiglioli Roberta , Lazzarotto Tiziana , Violante Francesco S. , Boffetta Paolo
Published: October 2020

Background

Limited information is available on prevalence and determinants of serologic response to SARS-CoV-2 infection among healthcare workers (HCWs).

Methods

We analyzed the results of serologic testing with chemiluminescence immunoassay analyzer (CLIA), lateral flow immunoassay (LFIA) and enzyme-linked immunosorbent assay (ELISA) test among 544 HCWs with at least one positive RT-PCR test and 157 HCWs with Covid-19 related symptoms without a positive RT-PCR test from public hospitals in Bologna, Northern Italy. Tests were performed between March and August 2020. We fitted multivariate logistic regression models to identify determinants of positive serology.

Results

The sensitivity of SARS-CoV-2 was 75.2% (LFIA) and 90.6% (CLIA). No differences in seropositivity were observed by sex, while older HCWs had higher positivity than other groups, and nurses had higher positivity compared to physicians, but not other HCWs. An estimated 73.4% of HCWs with Covid-19 symptoms without RT-PCR test were not infected with SARS-CoV-2.

Conclusions

Our study provides the best available data on sensitivity of serologic tests and on determinants of serologic response among HCWs positive for SARS-CoV-2, and provide evidence on the low specificity of Covid-19 related symptoms to identify infected HCWs.

The sensitivity of SARS-CoV-2 lateral flow immunoassay serology in healthcare workers (HCWs) was 75.2%. Older HCWs and nurses had higher positivity than other groups. An estimated 73.4% of HCWs with Covid-19 symptoms without RT-PCR test were not infected with SARS-CoV-2.
Gene validation and remodelling using proteogenomics ofPhytophthora cinnamomi, the causal agent of Dieback
Authors: Andronis Christina E. , Hane James K. , Bringans Scott , Hardy Giles E. S. , Jacques Silke , Lipscombe Richard , Tan Kar-Chun
Published: October 2020

Phytophthora cinnamomiis a pathogenic oomycete that causes plant dieback disease across a range of natural ecosystems and in many agriculturally important crops on a global scale. An annotated draft genome sequence and annotation is publicly available (JGI Mycocosm) and suggests 26,131 gene models. In this study, soluble mycelial, extracellular (secretome) and zoospore proteins ofP. cinnamomiwere exploited to refine the genome by correcting gene annotations and discovering novel genes. By implementing the diverse set of sub-proteomes into a generated proteogenomics pipeline, we were able to improve theP. cinnamomigenome. Liquid chromatography mass spectrometry was used to obtain high confidence peptides with spectral matching to both the annotated genome and a generated 6-frame translation. 2,764 annotations from the draft genome were confirmed by spectral matching. Using a proteogenomic pipeline, mass spectra were used to edit theP. cinnamomigenome and allowed identification of 23 new gene models and 60 edited gene features using high confidence peptides obtained by mass spectrometry, suggesting a rate of incorrect annotations of 3% of the detectable proteome. The novel features were further validated by total peptide support, alongside functional analysis including the use of Gene Ontology and functional domain identification. We demonstrated the use of spectral data in combination with our proteogenomics pipeline can be used to improve the genome of important plant diseases and identify biologically relevant missed genes. This study presents the first use of spectral data to edit and manually annotate an oomycete pathogen.
A modular approach to integrating multiple data sources into real-time clinical prediction for pediatric diarrhea
Authors: Brintz Ben J. , Haaland Benjamin , Howard Joel , Chao Dennis L. , Proctor Joshua L. , Khan Ashraful I. , Ahmed Sharia M. , Keegan Lindsay T. , Greene Tom , Keita Adama Mamby , Kotloff Karen L. , Platts-Mills James A. , Nelson Eric J. , Levine Adam C. , Pavia Andrew T. , Leung Daniel T.
Published: October 2020

Traditional clinical prediction models focus on parameters of the individual patient. For infectious diseases, sources external to the patient, including characteristics of prior patients and seasonal factors, may improve predictive performance. We describe the development of a predictive model that integrates multiple sources of data in a principled statistical framework using a post-test odds formulation. Our method enables electronic real-time updating and flexibility, such that components can be included or excluded according to data availability. We apply this method to the prediction of etiology of pediatric diarrhea, where “pre-test” epidemiologic data may be highly informative. Diarrhea has a high burden in low-resource settings, and antibiotics are often over-prescribed. We demonstrate that our integrative method outperforms traditional prediction in accurately identifying cases with a viral etiology, and show that its clinical application, especially when used with an additional diagnostic test, could result in a 61% reduction in inappropriately prescribed antibiotics.
Plasmodium falciparum artemisinin-resistant K13 mutations confer a sexual-stage transmission advantage that can be overcome with atovaquone-proguanil
Authors: Pava Zuleima , Mok Sachel , Collins Katharine A. , Rebelo Maria , Watts Rebecca E. , Robinson Gregory J. , Wang Claire Y.T. , Mitchell Hayley , Lynch Sean , Gower Jeremy , Webb Lachlan , McEwan Sam , Odedra Anand , Barber Bridget , Marquart Louise , Dixon Matthew W.A. , Moehrle Joerg J. , Fidock David A. , McCarthy James S.
Published: October 2020

Containing the spread of artemisinin (ART)-resistant Plasmodium falciparum will be assisted by improved understanding of its human-to-mosquito transmission. We compared gametocyte dynamics among field isolates containing K13 mutations conferring ART resistance and K13 wild-type parasites. In Pailin, Cambodia, the male to female gametocyte ratio was higher among K13 mutant infections compared to K13 wild-type infections. We also investigated the effects of artesunate and atovaquone-proguanil on the transmissibility of an ART-resistant K13 mutant strain, Cam3.IIR539T, in a volunteer infection study. Gametocyte production was higher after a single dose of artesunate (2 mg/kg) in volunteers infected with ART-resistant compared to ART-sensitive parasites. Despite the presence of gametocytes in volunteers infected with ART-resistant parasites, there was no infection observed in Anopheles stephensi mosquitoes after atovaquone-proguanil treatment. We report transmission determinants of ART-resistant infections that could be advantageous over ART-sensitive infections. Moreover, we show additional benefits of treating ART-resistant infections with atovaquone-proguanil treatment.
Comparison of Japanese nurse practitioner-led care and physician trainees-led care on patients’ length of stay in a secondary emergency department: A retrospective study
Authors: Uranaka Keiichi , Takaira Hitoshi , Shinohara Ryoji , Yamagata Zentaro
Published: October 2020

Objectives

We compared nurse practitioner-led care and physician trainees-led care on patients’ length of stay in a secondary emergency department in Japan.

Methods

This observational research utilized a secondary data analysis of medical records. Participants (N = 1,419; mean age = 63.9 ± 23.4 years; 52.3% men) were patients who were transferred to the emergency department by an ambulance between April 2016 and March 2018 in western Tokyo. Multiple linear regression analyses were performed with the length of stay as the dependent variable and the factors related to the length of stay, including medical care leaders, as the independent variable to compare Japanese nurse practitioner-led care and physician trainees-led care on patients’ length of stay.

Results

Approximately half of the patients (n = 763; 53.8%) received Japanese nurse practitioner-led care. Patients’ length of stay was significantly shorter by six minutes in the Japanese nurse practitioner-led care group than the physician trainees-led care group.

Conclusion

Patients’ length of stay was significantly shorter by six minutes in the Japanese nurse practitioner group than the physician trainees’ group. This time difference suggests that the medical care led by Japanese nurse practitioners is more efficient. In the future, the cost-effectiveness of Japanese nurse practitioner medical care, safety, and patient satisfaction should be examined in a multi-institutional joint study.
Can intersectionality help with understanding and tackling health inequalities? Perspectives of professional stakeholders
Authors: Holman Daniel , Salway Sarah , Bell Andrew , Beach Brian , Adebajo Adewale , Ali Nuzhat , Butt Jabeer
Published: October 2020

The concept of ‘intersectionality’ is increasingly employed within public health arenas, particularly in North America, and is often heralded as offering great potential to advance health inequalities research and action. Given persistently poor progress towards tackling health inequalities, and recent calls to reframe this agenda in the UK and Europe, the possible contribution of intersectionality deserves attention. Yet, no existing research has examined professional stakeholder understandings and perspectives on applying intersectionality to this field. In this paper we seek to address that gap, drawing upon a consultation survey and workshop undertaken in the UK. The survey included both researchers (n=53) and practitioners (n=20) with varied roles and levels of engagement in research and evaluation. Topics included: familiarity with the term and concept ‘intersectionality’, relevance to health inequalities work, and issues shaping its uptake. Respondents were also asked to comment on two specific policy suggestions; targeting and tailoring interventions to intersectional sub-groups, and evaluating the intersectional effects of policies. 23 people attended the face-to-face workshop. The aims of the workshop were to: share examples of applying intersectionality within health inequalities research and practice; understand the views of research and practice colleagues on potential contributions and challenges; and identify potential ways to promote intersectional approaches. Findings indicated a generally positive response to the concept and a cautiously optimistic assessment that intersectional approaches could be valuable. However, opinions were mixed and various challenges were raised, especially around whether intersectionality research is necessarily critical and transformative and, accordingly, how it should be operationalised methodologically. Nonetheless, there was general agreement that intersectionality is concerned with diverse inequalities and the systems of power that shape them. We position intersectionality within the wider context of health inequalities policy and practice, suggesting potential ways forward for the approach in the UK context.
A methodological blueprint to identify COVID-19 vulnerable locales by socioeconomic factors, developed using South Korean data
Authors: Weinstein Bayarmagnai , da Silva Alan R. , Kouzoukas Dimitrios E. , Bose Tanima , Kim Gwang-Jin , Correa Paola A. , Pondugula Santhi , Kim Jihoo , Carpenter David O.
Published: October 2020

COVID-19 has more severely impacted socioeconomically (SES) disadvantaged populations. Lack of SES measurements and inaccurately identifying high-risk locales can hamper COVID-19 mitigation efforts. Using South Korean COVID-19 incidence data (January 20 through July 1, 2020) and established social theoretical approaches, we identified COVID-19-specific SES factors. Principal component analysis created composite indexes for each SES factor, while Geographically Weighted Negative Binomial Regressions mapped a continuous surface of COVID-19 risk for South Korea. High area morbidity, risky health behaviours, crowding, and population mobility elevated area risk for COVID-19, while improved social distancing, healthcare access, and education decreased it. Our results indicated that falling SES-related COVID-19 risks and spatial shift patterns over three consecutive time periods reflected the implementation of reportedly effective public health interventions. While validating earlier studies, this study introduced a methodological blueprint for precision targeting of high-risk locales that is globally applicable for COVID-19 and future pandemics.
Controlled randomized clinical trial on using Ivermectin with Doxycycline for treating COVID-19 patients in Baghdad, Iraq
Authors: Hashim Hashim A. , Maulood Mohammed F. , Rasheed Anwar M. , Fatak Dhurgham F. , Kabah Khulood K. , Abdulamir Ahmed S.
Published: October 2020

Objectives

COVID-19 patients suffer from the lack of curative therapy. Hence, there is an urgent need to try repurposed old drugs on COVID-19.

Methods

Randomized controlled study on 70 COVID-19 patients (48 mild-moderate, 11 severe, and 11 critical patients) treated with 200ug/kg PO of Ivermectin per day for 2-3 days along with 100mg PO doxycycline twice per day for 5-10 days plus standard therapy; the second arm is 70 COVID-19 patients (48 mild-moderate and 22 severe and zero critical patients) on standard therapy. The time to recovery, the progression of the disease, and the mortality rate were the outcome-assessing parameters.

Results

among all patients and among severe patients, 3/70 (4.28%) and 1/11 (9%), respectively progressed to a more advanced stage of the disease in the Ivermectin-Doxycycline group versus 7/70 (10%) and 7/22 (31.81%), respectively in the control group (P>0.05). The mortality rate was 0/48 (0%), 0/11 (0%), and 2/11 (18.2%) in mild-moderate, severe, and critical COVID-19 patients, respectively in Ivermectin-Doxycycline group versus 0/48 (0%), and 6/22 (27.27%) in mild-moderate and severe COVID-19 patients, respectively in standard therapy group (p=0.052). Moreover, the mean time to recovery was 6.34, 20.27, and 24.13 days in mild-moderate, severe, and critical COVID-19 patients, respectively in Ivermectin-Doxycycline group versus 13.66 and 24.25 days in mild-moderate and severe COVID-19 patients, respectively in standard therapy group (P<0.01).

Conclusions

Ivermectin with doxycycline reduced the time to recovery and the percentage of patients who progress to more advanced stage of disease; in addition, Ivermectin with doxycycline reduced mortality rate in severe patients from 22.72% to 0%; however, 18.2% of critically ill patients died with Ivermectin and doxycycline therapy. Taken together, the earlier administered Ivermectin with doxycycline, the higher rate of successful therapy.
Community pharmacists Awareness and Attitude toward Counterfeit medicine in Khartoum Locality: Cross Sectional Survey
Authors: Wagiealla Wala W. , Shantier Shaza W. , Abureid Imad O. , Gadkariem Elrasheed A.
Published: October 2020

Background

Counterfeit medicines (CFMs) are a global problem with significant and well-documented consequences for global health and patient safety. Pharmacists, as healthcare professionals, have a vital role in combating CFMs via ensuring the effectiveness and safety of any imported and dispensed medicines.

Objectives

The aim of the present study was to assess the extent, awareness and attitude of pharmacists in Sudan towards CFMs.

Methods

A cross-sectional study was conducted applying pretested and structured questionnaire and the awareness and attitude were assessed statistically.

Results

A total of 229 participants have enrolled in the study. The majority of the respondents (76%) were found to be aware about the term CFMs during practice. 59% reported their ability to distinguish CFMs from the packaging feature and cost. Unavailability of medicine and inadequate regulatory bodies control were mentioned as the main leading factors for the spread of CFMs. 86% of the respondents reported knowing that there are pharmacists who deal with counterfeit medicines believing that they are unethical (76%). 69% of the respondents mentioned pharmacists to have vital role in combating CFMs spread through increasing knowledge and education. 62% of the participants were found to have a fair awareness about CFMs. Furthermore, 56% of them showed a good attitude toward CFMs.

Conclusion

Current literature includes gaps in knowledge and attitude towards CFMs. Therefore attention and concentrated efforts are required on the part of the government, drug manufacturers and health care providers’ especially pharmaceutical analysts to ensure that only drugs of acceptable quality reach the patient.
A2B-COVID: A method for evaluating potential SARS-CoV-2 transmission events
Authors: Illingworth Christopher J. R. , Hamilton William L. , Jackson Chris , Popay Ashley , Meredith Luke , Houldcroft Charlotte J. , Hosmillo Myra , Jahun Aminu , Routledge Matthew , Warne Ben , Caller Laura , Caddy Sarah , Yakovleva Anna , Hall Grant , Khokhar Fahad A. , Feltwell Theresa , Pinckert Malte L. , Georgana Iliana , Chaudhry Yasmin , Curran Martin , Parmar Surendra , Sparkes Dominic , Rivett Lucy , Jones Nick K. , Sridhar Sushmita , Forrest Sally , Dymond Tom , Grainger Kayleigh , Workman Chris , Gkrania-Klotsas Effrossyni , Brown Nicholas M. , Weekes Michael P. , Baker Stephen , Peacock Sharon J. , Gouliouris Theodore , Goodfellow Ian , Angelis Daniela De , Török M. Estée
Published: October 2020

Identifying linked cases of infection is a key part of the public health response to viral infectious disease. Viral genome sequence data is of great value in this task, but requires careful analysis, and may need to be complemented by additional types of data. The Covid-19 pandemic has highlighted the urgent need for analytical methods which bring together sources of data to inform epidemiological investigations. We here describe A2B-COVID, an approach for the rapid identification of linked cases of coronavirus infection. Our method combines knowledge about infection dynamics, data describing the movements of individuals, and novel approaches to genome sequence data to assess whether or not cases of infection are consistent or inconsistent with linkage via transmission. We apply our method to analyse and compare data collected from two wards at Cambridge University Hospitals, showing qualitatively different patterns of linkage between cases on designated Covid-19 and non-Covid-19 wards. Our method is suitable for the rapid analysis of data from clinical or other potential outbreak settings.
What does the COVID-19 pandemic mean for the next decade of onchocerciasis control and elimination?
Authors: Hamley Jonathan I.D. , Blok David J. , Walker Martin , Milton Philip , Hopkins Adrian D. , Hamill Louise C. , Downs Philip , de Vlas Sake J. , Stolk Wilma A. , Basáñez Maria-Gloria
Published: October 2020

Background

Mass drug administration (MDA) of ivermectin for onchocerciasis has been disrupted by the SARS-CoV-2 (COVID-19) pandemic. Mathematical modelling can help predict how missed/delayed MDA will affect short-term epidemiological trends and elimination prospects by 2030.

Methods

Two onchocerciasis transmission models (EPIONCHO-IBM and ONCHOSIM) are used to simulate microfilarial prevalence trends, elimination probabilities, and age-profiles of Onchocerca volvulus microfilarial prevalence and intensity, for different treatment histories and transmission settings, assuming no interruption, a 1-year (2020) or 2-year (2020–2021) interruption. Biannual MDA or increased coverage upon MDA resumption are investigated as remedial strategies.

Results

Programmes with shorter MDA histories and settings with high pre-intervention endemicity will be the most affected. Biannual MDA is more effective than increasing coverage for mitigating COVID-19’s impact on MDA. Programmes which had already switched to biannual MDA should be minimally affected. In high transmission settings with short treatment history, a 2-year interruption could lead to increased microfilarial load in children (EPIONCHO-IBM) or adults (ONCHOSIM).

Conclusions

Programmes with shorter (annual MDA) treatment histories should be prioritised for remedial biannual MDA. Increases in microfilarial load could have short- and long-term morbidity and mortality repercussions. These results can guide decision-making to mitigate the impact of COVID-19 on onchocerciasis elimination.
Agreement between DSM-IV and DSM-5 measures of substance use disorders in a sample of adult substance users
Authors: Livne Ofir , Stohl Malka , Shmulewitz Dvora , Mannes Zachary , Hasin Deborah
Published: October 2020

Aim

In DSM-5, definitions of substance use disorders (SUD) were changed considerably from DSM-IV, yet little is known about how well DSM-IV and DSM-5 SUD diagnoses agree with each other within a series of individuals with substance use problems.

Methods

Prevalences and chance-corrected agreement of DSM-5 SUD and DSM-IV substance dependence were evaluated in 588 adult substance users, interviewed by clinician interviewers using the semi-structured Psychiatric Research Interview for Substance and Mental Disorders (PRISM-5). Alcohol, tobacco, cannabis, cocaine, heroin, opioid, sedative, and stimulant use disorders were examined. Cohen’s kappa was used to assess agreement between DSM-5 and DSM-IV SUD (including abuse or dependence), DSM-5 SUD and DSM-IV dependence, and DSM-5 moderate-to-severe SUD and DSM-IV dependence.

Results

Agreement between DSM-5 and DSM-IV SUD was excellent for alcohol, cocaine, heroin, opioids, sedatives, and stimulants (κ=0.84; 0.91; 0.99; 0.96; 0.92; 0.97; respectively) and substantial for alcohol and tobacco (κ=0.75; 0.80, respectively). Agreement between DSM-5 SUD and DSM-IV substance dependence was excellent for cocaine, heroin, opioids, sedatives, and stimulants (κ=0.89; 0.97; 0.90; 0.88; 0.94, respectively) and substantial for alcohol, tobacco, and cannabis (κ=0.75; 0.69; 0.63, respectively). Agreement between moderate and severe DSM-5 SUD and DSM-IV dependence was excellent across all substances.

Conclusion

Findings suggest that while care should always be used in interpreting the results of studies using different methods, studies relying on DSM-IV or DSM-5 SUD diagnostic criteria can be considered to offer similar information and thus can be compared when accumulating a body of evidence on a particular issue regarding substance use.