bluuebunny/crossref_metadata_2025_split huggingface dataset:
The importance of supplementary immunisation activities to prevent measles outbreaks during the COVID-19 pandemic in Kenya
Authors: Mburu CN , Ojal J , Chebet R , Akech D , Karia B , Tuju J , Sigilai A , Abbas K , Jit M , Funk S , Smits G , van Gageldonk PGM , van der Klis FRM , Tabu C , Nokes DJ ,   LSHTM CMMID COVID-19 Working Group, Scott JAG , Flasche S , Adetifa IMO 
Published: August 2020

AbstractBackgroundThe COVID-19 pandemic has disrupted routine measles immunisation and supplementary immunisation activities (SIAs) in most countries including Kenya. We assessed the risk of measles outbreaks during the pandemic in Kenya as a case study for the African Region.MethodsCombining measles serological data, local contact patterns, and vaccination coverage into a cohort model, we predicted the age-adjusted population immunity in Kenya and estimated the probability of outbreaks when contact-reducing COVID-19 interventions are lifted. We considered various scenarios for reduced measles vaccination coverage from April 2020.FindingsIn February 2020, when a scheduled SIA was postponed, population immunity was close to the herd immunity threshold and the probability of a large outbreak was 22% (0-46). As the COVID-19 restrictions to physical contact are lifted, from December 2020, the probability of a large measles outbreak increased to 31% (8-51), 35% (16-52) and 43% (31-56) assuming a 15%, 50% and 100% reduction in measles vaccination coverage. By December 2021, this risk increases further to 37% (17-54), 44% (29-57) and 57% (48-65) for the same coverage scenarios respectively. However, the increased risk of a measles outbreak following the lifting of restrictions on contact can be overcome by conducting an SIA with ≥ 95% coverage in under-fives.InterpretationWhile contact restrictions sufficient for SAR-CoV-2 control temporarily reduce measles transmissibility and the risk of an outbreak from a measles immunity gap, this risk rises rapidly once physical distancing is relaxed. Implementing delayed SIAs will be critical for prevention of measles outbreaks once contact restrictions are fully lifted in Kenya.FundingThe United Kingdom’s Medical Research Council and the Department for International Development
Causes of false-negative rapid diagnostic tests for symptomatic malaria in the DRC
Authors: Parr Jonathan B. , Kieto Eddy , Phanzu Fernandine , Mansiangi Paul , Mwandagalirwa Kashamuka , Mvuama Nono , Landela Ange , Atibu Joseph , Efundu Solange Umesumbu , Olenga Jean W. , Thwai Kyaw Lay , Morgan Camille E. , Denton Madeline , Poffley Alison , Juliano Jonathan J. , Mungala Pomie , Likwela Joris L. , Sompwe Eric M. , Tshefu Antoinette K. , N’Siala Adrien , Kalonji Albert 
Published: August 2020

ABSTRACTBackgroundThe majority of Plasmodium falciparum malaria diagnoses in Africa are made using rapid diagnostic tests (RDTs) that detect histidine-rich protein 2. Increasing reports of false-negative RDT results due to parasites with deletions of the pfhrp2 and/or pfhrp3 genes (pfhrp2/3) raise concern about existing malaria diagnostic strategies. We previously identified pfhrp2-negative parasites among asymptomatic children in the Democratic Republic of the Congo (DRC), but their impact on diagnosis of symptomatic malaria is unknown.MethodsWe performed a cross-sectional study of false-negative RDTs in symptomatic subjects in 2017. Parasites were characterized by microscopy; RDT; pfhrp2/3 genotyping and species-specific PCR assays; a multiplex bead-based immunoassay; and/or whole-genome sequencing.ResultsAmong 3,627 symptomatic subjects, we identified 427 (11.8%) RDT-/microscopy+ cases. Parasites from eight (0.2%) samples were initially classified as putative pfhrp2/3 deletions by PCR, but antigen testing and whole-genome sequencing confirmed the presence of intact genes. Malaria prevalence was high (57%) and non-falciparum co-infection common (15%). HRP2-based RDT performance was satisfactory and superior to microscopy.ConclusionsSymptomatic malaria due to pfhrp2/3-deleted P. falciparum was not observed in the DRC.Ongoing HRP2-based RDT use is appropriate for the detection of falciparum malaria in the DRC.
PRELIMINARY ASSESSMENT OF STRUCTURE AND COLLECTIVE DOSE FROM CT EXAMINATIONS RELATED TO COVID-19 DIAGNOSTICS IN THE RUSSIAN FEDERATION IN MARCH - JUNE 2020
Authors: Vodovatov A.V. , Romanovich I.K. , Istorik O.A. , Eremina L.A. , Morozov S.P. , Ryzhov S.A. , Berkovich G.V. , Kamyshanskaya I.G. , Trufanov G.E. , Chipiga L.A. , Druzhinina P. S. , Biblin A.M. , Akhmatdinov R.R. , Basek I.V. , Karatetskiy A.A. , Merkulov D. V. , Ispravnikova Yu.S. , Pritz V.V. , Polishchuk N.S. , Mukhortova A.N , Pyzyrev V.G. 
Published: August 2020

AbstractThe use of computed tomography (CT) for the diagnostics of COVID-19 in the Russian Federation led to significant changes in the structure of X-ray diagnostics and levels of medical exposure of the patients. This study was aimed at the preliminary operative assessment of changes in the structure and collective dose from CT examinations in several representative hospitals, regions and on the level of the Russian Federation. The results of the study indicate that during the transformation of hospitals from general medical practice into dedicated COVID-19 facilities, the number of CT examinations increased up to 30%; the collective dose from CT exams increased up to a factor of 1.5. During a partial transformation of a medical facility into the hospital with separate COVID-19 departments, the increase in the number of CT examinations in the facility was more significant (up to a factor of 2 or more). These numbers correspond to 1.5 - 2.5 chest CT examinations (from 1 to 6) per patient admitted to hospital with COVID-19 diagnosis; and 1.2 chest CT examinations per patient in outpatient facilities, including a mandatory CT scan for the staging of COVID-19. The collective dose from CT examinations in the Russian Federation for March-June period of 2020 increased by the factor of 2 (from 16k man-Sv to 32k man-Sv); the collective dose of COVID-19 patients was about 12k man-Sv. For a more detailed and reliable assessment of the dynamics of changes in the structure of diagnostic radiology and levels of radiation exposure of patients in the Russian Federation, data collection in the regions of the Russian Federation and individual medical facilities will continue.
COVID-19 hospitalisation rates rise exponentially with age, inversely proportional to thymic T-cell production
Authors: Palmer Sam , Cunniffe Nik , Donnelly Ruairí 
Published: August 2020

AbstractHere we report that COVID-19 hospitalisation rates follow an exponential relationship with age, doubling for every 16 years of age or equivalently increasing by 4.5% per year of life (R2=0.98). This mirrors the well studied exponential decline of both thymus volume and T-cell production, which halve every 16 years. COVID-19 can therefore be added to the list of other diseases with this property, including those caused by MRSA, MERS-CoV, West Nile virus, Streptococcus Pneumonia and certain cancers, such as chronic myeloid leukemia and brain cancers. In addition, incidence of severe disease and mortality due to COVID-19 are both higher in men, consistent with the degree to which thymic involution (and the decrease in T-cell production with age) is more severe in men compared to women. Since these properties are shared with some non-contagious diseases, we hypothesised that the age-dependence does not come from social-mixing patterns, i.e. that the probability of hospitalisation given infection rises exponentially, doubling every 16 years. A Bayesian analysis of daily hospitalisations, incorporating contact matrices, found that this relationship holds for every age group except for the under 20s. While older adults have less contacts than young adults, our analysis suggests that there is an approximate cancellation between the effects of less contacts for the elderly and higher infectiousness due to a higher probability of developing severe disease. Our model fitting suggests under 20s have 49-75% additional immune protection beyond that predicted by strong thymus function alone, consistent with increased juvenile cross-immunity from other viruses. We found no evidence for differences between age groups in susceptibility to infection or infectiousness to others (given disease state), i.e. the only important factor in the age-dependence of hospitalisation rates is the probability of hospitalisation given infection. These findings suggest the existence of a T-cell exhaustion threshold, proportional to thymic output, and that clonal expansion of peripheral T-cells does not affect disease risk. The strikingly simple inverse relationship between risk and thymic T-cell output adds to the evidence that thymic involution is an important factor in the decline of the immune system with age and may also be an important clue in understanding disease progression, not just for COVID-19 but other diseases as well.
Stratification of Systemic Lupus Erythematosus Patients with Gene Expression Data Reveals Expression of Distinct Immune Pathways
Authors: Deokar Aditi 
Published: August 2020

AbstractSystemic lupus erythematosus (SLE) is the tenth leading cause of death in females 15-24 years old in the US. The diversity of symptoms and immune pathways expressed in SLE patients causes difficulties in treating SLE as well as in new clinical trials. This study used unsupervised learning on gene expression data from adult SLE patients to separate patients into clusters. The dimensionality of the gene expression data was reduced by three separate methods (PCA, UMAP, and a simple linear autoencoder) and the results from each of these methods were used to separate patients into six clusters with k-means clustering. The clusters revealed three separate immune pathways in the SLE patients that caused SLE. These pathways were: (1) high interferon levels, (2) high autoantibody levels, and (3) dysregulation of the mitochondrial apoptosis pathway. Mitochondrial apoptosis has not been investigated before to our knowledge as a standalone cause of SLE, independent of autoantibody production, and mitochondrial proteins could be investigated as a therapeutic target for SLE in the future.
Recommendations for Primary Prevention of Skin Melanoma
Authors: Tasa Tõnis , Puustusmaa Mikk , Tõnisson Neeme , Kolk Berit , Padrik Peeter 
Published: August 2020

AbstractMelanoma (MEL) is an aggressive form of skin cancer, causing over 60,000 deaths every year and it is considered one of the fastest-growing cancer forms. Genome-wide association studies have identified numerous genetic variants (SNPs) independently associated with MEL. The effects of such SNPs can be combined into a single polygenic risk score (PRS). Stratification of individuals according to PRS could be introduced to the primary prevention of melanoma. Our aim was to combine PRS with health behavior recommendations to develop a personalized recommendation for primary prevention of melanoma.Previously published PRS models for predicting the risk of melanoma were collected from the literature. Models were validated on the UK Biobank dataset consisting of a total of 487,410 quality-controlled genotypes with 3791 prevalent and 2345 incident cases. The best performing sex-specific models were selected based on the AUC in prevalent data and independently validated on an independent UKBB incident dataset for females and males separately. The best performing model included 28 SNPs. The C-index of the best performing model in the dataset was 0.59 (0.009) and hazard ratio (HR) per unit of PRS was 1.38 (standard error of log (HR) = 0.03) for both males and females.We performed absolute risk simulations on the Estonian population and developed individual risk-based clinical follow-up recommendations. Both models were able to identify individuals with more than a 2-fold risk increase. The observed 10-year risks of developing melanoma for individuals in the 99th percentile exceeded the risk of individuals in the 1st percentile more than 4.5-fold.We have developed a PRS-based recommendations pipeline for individual health behavior suggestions to support melanoma prevention.
COVID-19 Cases and Testing in 53 Prison Systems
Authors: Lemasters Katherine , McCauley Erin , Nowotny Kathryn , Brinkley-Rubinstein Lauren 
Published: August 2020

AbstractBackgroundCOVID-19 has entered United States prison systems at alarming rates. Disparities in social and structural determinants of health disproportionately affect those experiencing incarceration, making them more vulnerable to COVID-19. Additionally, prisons are sites of congregate living, making it impossible to practice social distancing, and most prisons have relied only on incremental measures to reduce risk and spread of COVID-19. To more fully understand the impact that COVID-19 is having on incarcerated populations, it is critical to have systematic data on testing, test positivity, cases, and case fatality. Using data from the COVID Prison Project, we present data on 53 prison systems COVID-19 testing, test positivity, case, and case fatality by state and compare these data with each state’s general population.ResultsMany states are not reporting full information on COVID testing with some also not reporting on case fatality. Among those reporting data, there is a wide variation between testing, test positivity, and case rates within prison systems and as compared to the general population. However, when more tests are deployed more cases are identified with the majority of state prisons having higher case rates than their general population.ConclusionsThese findings underscore the need for the implementation and study of COVID-19 mitigation and surveillance strategies to flatten the COVID-19 curve in prisons across the country. We call for future research to build on this data from the COVID Prison Project to protect the health of our nations’ often forgotten residents.
Spontaneous Cervical Artery Dissection: A Case Series
Authors: Basgaran Amedra , Hsu Catherine Hsiao-wei , Sivagnanaratnam Aravinth 
Published: August 2020

AbstractCervical artery dissection refers to dissection of the vertebral or carotid arteries, and accounts for up to 20% of strokes in those under 45. Antithrombotic therapy is therefore essential to limit thrombosis at the site of injury and distal neuronal damage. However, the exact choice of drugs, timing and duration of therapy remain a challenging decision.A review of data was conducted on three cases of unprovoked cervical dissection at our stroke center between 2017 and 2020. They include bilateral internal carotid artery dissection, right vertebral artery dissection, and left internal carotid artery dissection.Three key outcomes were identified: narrowing, occlusion and pseudoaneurysm; such outcomes dictated our management approach. Two patients were given antiplatelet therapy for at least one year. The patient with bilateral dissection was perceived to have higher thromboembolic risk, due to the presence of a free-floating thrombus. Thus, he was anticoagulated for a year, and thereafter given antiplatelet therapy.The evidence behind long-term management of carotid artery dissection remains equivocal. There is no strong evidence favouring anticoagulation over antiplatelets or vice versa. Anticoagulation tends to be preferred in cases of severe stenosis, occlusion or pseudoaneurysm, to reduce the risk of thromboembolic phenomena. Anti-platelets are preferred where there is a high risk of haemorrhagic transformation or contraindication to anticoagulation. The duration of secondary prevention is similarly unclear. Advances in radiology and increased follow-up have resulted in uncertainty on the management of incomplete healing at the six-month point. Varying clinical practice has been identified and there is a lack of a clear guideline. We propose continuing antithrombotic therapy in cases of incomplete healing, as in our case series. Nevertheless, we require more data on the subject and thus suggest an initial nation-wide survey to compare the different management strategies followed by large-scale retrospective analyses comparing long-term outcomes.
The urgent need for phased university reopenings to mitigate the spread of COVID-19 and conserve institutional resources: A modeling study
Authors: Rennert Lior , Kalbaugh Corey A. , McMahan Christopher , Shi Lu , Colenda Christopher C. 
Published: August 2020

AbstractIntroductionRecent outbreaks of COVID-19 in universities across the United States highlight the difficulties in containing the spread of COVID-19 on college campuses. While research has shown that mitigation strategies such as frequent student testing, contact tracing, and isolation of confirmed and suspected cases can detect early outbreaks, such mitigation strategies may have limited effectiveness if large outbreaks occur. A phased reopening is a practical intervention to limit early outbreaks, conserve institutional resources, and ensure proper safety protocols are in place before the return of additional students to campus.MethodsWe develop dynamic compartmental transmission models of SARS-CoV-2 to assess the impact of a phased reopening and pre-arrival testing on minimizing outbreaks (measured by daily infections) and conserving university resources (measured by isolation bed capacity). We assume that one-third of the student population returns to campus each month as part of the phased reopening, and that pre-arrival testing removes 90% of infections at the semester start. We assume an on-campus population of N = 7500, an active COVID-19 prevalence of 2% at baseline, and that 60% of infected students require isolation for an average period of 11 days. We vary the reproductive number (Rt) between 1.25 and 4 to represent the effectiveness of alternative mitigation strategies throughout the semester, where Rt is constant or improving throughout the semester (ranging from 4 to 1.25).ResultsCompared to pre-arrival testing only or neither intervention, phased reopening with pre-arrival testing reduced peak daily infections by 6% and 18% (Rt=1.25), 44% and 48% (Rt=2.5), 63% and 64% (Rt=4), and 72% and 74% (improving Rt), respectively, and reduced the proportion of on-campus beds needed for isolation from 10%-25% to 5%-9% across different values of Rt.ConclusionPhased reopening with pre-arrival testing substantially reduces the peak number of daily infections throughout the semester and conserves university resources compared to strategies involving the simultaneous return of all students to campus. Phased reopenings allow institutions to improve safety protocols, adjust for factors that drive outbreaks, and if needed, preemptively move online before the return of additional students to campus, thus preventing unnecessary harm to students, institutional faculty and staff, and local communities.
DNA Methylation Architecture of the ACE2 gene in Nasal Cells
Authors: Cardenas Andres , Rifas-Shiman Sheryl L. , Sordillo Joanne E. , DeMeo Dawn L. , Baccarelli Andrea A , Hivert Marie-France , Gold Diane R , Oken Emily 
Published: August 2020

ABSTRACTSevere Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has led to the global coronavirus disease 2019 (COVID-19) pandemic. SARS-CoV-2 enters cells via angiotensin-Converting Enzyme 2 (ACE2) receptors, highly expressed in nasal epithelium with parallel high infectivity.1,2 The nasal epigenome is in direct contact with the environment and could explain COVID-19 disparities by reflecting social and environmental influences on ACE2 regulation. We collected nasal swabs from anterior nares of 547 children, measured DNA methylation (DNAm), and tested differences at 15 ACE2 CpGs by sex, age, race/ethnicity and epigenetic age. ACE2 CpGs were differentially methylated by sex with 12 sites having lower DNAm (mean=12.71%) and 3 sites greater DNAm (mean=1.45%) among females relative to males. We observed differential DNAm at 5 CpGs for Hispanic females (mean absolute difference=3.22%) and lower DNAm at 8 CpGs for Black males (mean absolute difference=1.33%), relative to white participants. Longer DNAm telomere length was associated with greater ACE2 DNAm at 11 and 13 CpGs among males (mean absolute difference=7.86%) and females (mean absolute difference=8.21%), respectively. Nasal ACE2 DNAm differences could contribute to our understanding COVID-19 severity and disparities reflecting upstream environmental and social influences.
An exploratory analysis of the association between moral injury and mental healthcare-seeking attitudes and behaviors in returning veterans of the Iraq and Afghanistan wars
Authors: Lewis Chad 
Published: August 2020

AbstractObjectivesThis study examines the degree to which veterans who have experienced more “moral injury” are less likely to seek the mental healthcare services they may urgently need.MethodsThe sampling frame for this study included American veterans of the Iraq and/or Afghanistan wars aged 25-44. Participants were recruited into the study by posting a call for participants to social media platforms such as Facebook and LinkedIn. A web link was provided to direct them to an anonymous online survey. We then collected data assessing veterans’ combat experiences, healthcare-seeking attitudes and behaviors, and various sociodemographic data. No identifying information was collected, and an Institutional Review Board exemption was granted under DHHS Regulatory Category II by the George Washington University’s Office of Human Research Study.ResultsThe results from the Inventory of Attitudes toward Seeking Mental Health Services (IASMHS) clearly showed that moral injury was associated with more negative mental health services-seeking attitudes in all measurable areas. Those respondents scoring higher on the Moral Injury Events Scale (MIES) were presumably less likely to acknowledge their psychological problems, more likely to have fear of anticipated stigma from loved ones if they were to seek mental health treatment, and less willing and able to seek out mental health treatment when needed.ConclusionsIt is probable that we will not be able to reach a significant number of veterans suffering from moral injury unless we dedicate further research in the area of developing effective techniques to recruit veterans suffering from moral injury into mental health treatment programs by taking their specific symptoms (independent of PTSD) into consideration.