Top 10 Biorxiv Papers Today in Epidemiology


2.012 Mikeys
#1. Effects of body mass index on relationship status, social contact, and socioeconomic position: Mendelian Randomization study in UK Biobank
Laura D Howe, Roshni Kanayalal, Robin Beaumont, Alisha R Davies, Timothy M Frayling, Sean Harrison, Samuel Edward Jones, Franco Sassi, Andrew R Wood, Jess Tyrrell
Objective: To assess whether body mass index (BMI) has a causal effect on social and socioeconomic factors, including whether both high and low BMI can be detrimental. Design: Mendelian Randomization, using genetic variants for BMI to obtain unconfounded estimates, and non-linear Mendelian Randomization. Setting: UK Biobank. Participants: 378,244 men and women of European ancestry, mean age 57 (SD 8 years). Main outcome measures: Townsend deprivation index, income, age completed full time education, degree level education, job class, employment status, cohabiting relationship status, participation in leisure and social activities, visits from friends and family, and having someone to confide in. Results: Higher BMI was causally associated with higher deprivation, lower income, fewer years of education, lower odds of degree-level education and skilled employment. For example, a 1 SD higher genetically-determined BMI (4.8kg/m2 in UK Biobank) was associated with 1,660 UK pounds less income per annum [95%CI: 950, 2,380]. Non-linear...
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biorxivpreprint: Effects of body mass index on relationship status, social contact, and socioeconomic position: Mendelian Randomization study in UK Biobank https://t.co/ALODR336vl #bioRxiv
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Non-linear Mendelian randomization

Repository: nlmr
User: jrs95
Language: R
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Sample Sizes : [2600, 1494, 378244, 203886]
Authors: 10
Total Words: 9258
Unqiue Words: 2425

2.011 Mikeys
#2. Development of a Prediction Model for Incident Atrial Fibrillation using Machine Learning Applied to Harmonized Electronic Health Record Data
Premanand Tiwari, Kathryn L. Colborn, Derek E. Smith, Fuyong Xing, Debashis Ghosh, Michael A. Rosenberg
Atrial fibrillation (AF) is the most common sustained cardiac arrhythmia, whose early detection could lead to significant improvements in outcomes through appropriate prescription of anticoagulation. Although a variety of methods exist for screening for AF, there is general agreement that a targeted approach would be preferred. Implicit within this approach is the need for an efficient method for identification of patients at risk. In this investigation, we examined the strengths and weaknesses of an approach based on application of machine-learning algorithms to electronic health record (EHR) data that has been harmonized to the Observational Medical Outcomes Partnership (OMOP) common data model. We examined data from a total of 2.3M individuals, of whom 1.16% developed incident AF over designated 6-month time intervals. We examined and compared several approaches for data reduction, sample balancing (re-sampling) and predictive modeling using cross-validation for hyperparameter selection, and out-of-sample testing for...
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biorxivpreprint: Development of a Prediction Model for Incident Atrial Fibrillation using Machine Learning Applied to Harmonized Electronic Health Record Data https://t.co/b8AweCYkAF #bioRxiv
Datascience__: Development of a Prediction Model for Incident Atrial Fibrillation using Machine Learning Applied to Harmonized Electronic Health Record Data https://t.co/FhL14zsJlb #MachineLearning
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Sample Sizes : None.
Authors: 6
Total Words: 7990
Unqiue Words: 2994

2.003 Mikeys
#3. Emergence of the Zika virus Asian lineage in Angola
Sarah C Hill, Jocelyne Vasconcelos, Zoraima Neto, Domingos Jandondo, Líbia Zé-Zé, Renato Santana Aguiar, Joilson Xavier, Julien Thézé, Marinela Mirandela, Ana Luísa Micolo Cândido, Filipa Vaz, Cruz dos Santos Sebastião, Chieh-Hsi Wu, Moritz Kraemer, Adriana Melo, Bruno LF Schamber-Reis, Girlene S de Azevedo, Amilcar Tanuri, Luiza M Higa, Carina Clemente, Sara Pereira da Silva, Darlan da Silva Candido, Ingra M Claro, Domingos Quibuco, Cristóvão Domingos, Bárbara Pocongo, Alexander G Watts, Kamran Khan, Luiz CJ Alcantara, Ester Sabino, Eve Lackritz, Oliver G Pybus, Maria-João Alves, Joana Afonso, Nuno R Faria
Background: Zika virus (ZIKV) infections and suspected microcephaly cases have been recently reported in Angola, but no data are available on the origins, epidemiology, and diversity of the virus. Methods: Serum samples from 54 suspected ZIKV cases, 76 suspected microcephaly cases, and 24 mothers of infants with suspected microcephaly were received by the Angolan Ministry of Health. Computed tomographic brain imaging and serological assays (PRNT) were conducted on one microcephalic infant. All sera were tested for ZIKV by RT-qPCR. 349 samples from HIV+ patients and 336 samples from patients suspected of chikungunya virus or dengue virus infection were also tested. Portable sequencing was used to generate Angolan ZIKV genome sequences, including from a ZIKV+ neonate with microcephaly born in Portugal to an Angolan resident. Genetic and mobility data were analysed to investigate the date of introduction and geographic origin of ZIKV in Angola. Findings: Four autochthonous cases were ZIKV positive via RT-qPCR, with all positive...
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SeqComplete: #nanopores Emergence of the Zika virus Asian lineage in Angola | bioRxiv https://t.co/1mJaOnsenX, see more https://t.co/QGcZ4oAz3B
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Sample Sizes : [336, 24]
Authors: 35
Total Words: 6767
Unqiue Words: 2114

1.998 Mikeys
#4. Space-time clusters of dengue, chikungunya, and Zika cases in the city of Rio de Janeiro
Laís Picinini Freitas, Oswaldo Gonçalves Cruz, Rachel Lowe, Marilia Sá Carvalho
Brazil is a dengue-endemic country where all four dengue virus serotypes circulate and cause seasonal epidemics. Recently, chikungunya and Zika viruses were also introduced. In Rio de Janeiro city, the three diseases co-circulated for the first time in 2015-2016, resulting in what is known as the ‘triple epidemic’. In this study, we identify space-time clusters of dengue, chikungunya, and Zika, to understand the dynamics and interaction between these simultaneously circulating arboviruses in a densely populated and heterogeneous city. We conducted a spatio-temporal analysis of weekly notified cases of the three diseases in Rio de Janeiro city (July 2015 – January 2017), georeferenced by 160 neighbourhoods, using Kulldorff's scan statistic with discrete Poisson probability models. There were 26549, 13662, and 35905 notified cases of dengue, chikungunya, and Zika, respectively. The 17 dengue clusters and 15 Zika clusters were spread all over the city, while the 14 chikungunya clusters were more concentrated in the North and Downtown...
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Sample Sizes : [999]
Authors: 4
Total Words: 8164
Unqiue Words: 2606

1.997 Mikeys
#5. Capturing multiple-type interactions into practical predictors of type replacement following HPV vaccination
Irene Man, Kari Auranen, Jacco A. Wallinga, Johannes A. Bogaards
Current HPV vaccines target a subset of the oncogenic human papillomavirus (HPV) types. If HPV types compete during infection, vaccination may trigger replacement by the non-targeted types. Existing approaches to assess the risk of type replacement have focussed on detecting competitive interactions between pairs of vaccine and non-vaccine types. However, methods to translate any inferred pairwise interactions into predictors of replacement have been lacking. In this paper, we develop practical predictors of type replacement in a multi-type setting, readily estimable from pre-vaccination longitudinal or cross-sectional prevalence data. The predictors we propose for replacement by individual non-targeted types take the form of weighted cross hazard ratios of acquisition versus clearance, or aggregate odds ratios of coinfection with the vaccine types. We elucidate how the hazard-based predictors incorporate potentially heterogeneous direct and indirect type interactions by appropriately weighting type-specific hazards and show when...
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Repository: Prediction-method-type-replacement
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Authors: 4
Total Words: 7889
Unqiue Words: 2016

1.996 Mikeys
#6. Health workers' perspectives on the outcomes, enablers, and barriers to the implementation of HIV “Treat All” guidelines in Abuja Nigeria
Solomon Odafe, Kristen A. Stafford, Aliyu Gambo, Dennis Onotu, Mahesh Swaminathan, Ibrahim Dalhatu, Uzoma Ene, Ademola Oladipo, Ahmed Mukhtar, Ramat Ibrahim, Akipu Ehoche, Henry Debem, Andrew T. Boyd, Sunday Aboje, Bola Gobir, Manhattan Charurat
Introduction To improve access to lifesaving treatment for all people living with HIV (PLHIV), Nigeria implemented the Treat All guidelines in 2016. However, health workers' perspectives on the implementation of the guidelines have not been evaluated. Methods We conducted in-depth interviews to explore health workers' perspectives on the Treat All guidelines. Using purposive sampling, 20 health workers providing HIV patient care were recruited from six primary health care hospitals in Abuja to participate in semi-structured interviews. Data exploration was conducted using thematic content analysis. Results The five main themes that emerged were (1) the perceived benefits of guidelines use, (2) the perceived disadvantages of using the guidelines, (3) reported patients' response to guideline change, (4) perceived barriers/enablers to guideline use and (5) health workers' recommendations for improvement. Health workers perceived that the implementation of the Treat All guidelines has considerably improved patient care, particularly...
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Authors: 16
Total Words: 11270
Unqiue Words: 3222

1.996 Mikeys
#7. Enteropathogen seroepidemiology among children in low-resource settings
Benjamin F Arnold, Diana L Martin, Jane Juma, Harran Mkocha, John B Ochieng, Gretchen M Cooley, Richard Omore, E. Brook Goodhew, Jamae F Morris, Veronica Costantini, Jan Vinje, Patrick J Lammie, Jeffrey W Priest
Little is known about enteropathogen seroepidemiology among children in low-resource settings. We measured serological IgG response to eight enteropathogens ( Giardia duodenalis , Cryptosporidium parvum , Entamoeba histolytica , Salmonella enterica , enterotoxigenic Escherichia coli , Vibrio cholerae , Campylobacter jejuni , norovirus) using multiplex bead assays in cohorts from Haiti, Kenya, and Tanzania. By age 2 years, most children had evidence of exposure by IgG response to the pathogens studied. We discovered a shift in IgG distributions for many pathogens as children age, caused by boosting and waning from repeated exposures, which complicates interpretation of seroprevalence among older children. Longitudinal profiles revealed important variation in enteropathogen IgG response above seropositivity cutoffs, underscoring the importance of longitudinal designs to estimate seroincidence rates as a measure of force of infection. In longitudinal cohorts there was a linear relationship between seroprevalence and prospective...
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Sample Sizes : [199, 5]
Authors: 13
Total Words: 13202
Unqiue Words: 3024

1.996 Mikeys
#8. Benefits of improved air quality on aging lungs. Impacts of genetics and obesity
Anke Huels, Dorothea Sugiri, Michael J Abramson, Barbara Hoffmann, Holger Schwender, Katja Ickstadt, Ursula Kraemer, Tamara Schikowski
Introduction: The beneficial effect of improving air quality on lung function in the elderly remains unclear. We examined associations between decline in air pollutants and lung function and effect modifications by genetics and BMI in elderly German women. Methods: Data were analysed from the prospective SALIA cohort study (N=601). Spirometry was conducted at baseline (1985-1994; 55 years), in 2007-2010 and in 2012-2013. Air pollution concentrations at home addresses were determined for each time point using land-use regression models. GLI z-scores were calculated. Weighted genetic risk scores (GRS) were determined from lung function-related risk alleles and used to investigate interactions with improved air quality. Adjusted linear mixed models were fitted. Results: Air pollution levels decreased substantially during the study period. Reduction of air pollution was associated with an increase of z-scores for FEV1 and FEV1/FVC. For a decrease of 10 μg/m3 in NO2, the z-score for FEV1 increased by 0.14 (95%CI: 0.01; 0.26). However,...
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Sample Sizes : [601, 601]
Authors: 8
Total Words: 8086
Unqiue Words: 2763

1.996 Mikeys
#9. The effectiveness and cost effectiveness of a hospital avoidance program in a residential aged care facility
Hannah Carter, Xing Lee, Trudy Dwyer, Dee Jeffrey, Barbara O'Neill, Chris Doran, Lynne Parkinson, Sonya Osborne, Kerry Reid-Searl, Nicholas Graves
Background: Residential aged care facility residents experience high rates of hospital admissions which are stressful, costly and often preventable. Design: Prospective pre-post cohort study and decision model analysis. Intervention: A decision-support tool was implemented to enable nursing staff to detect, refer and quickly respond to early signals of a deteriorating resident. Advanced clinical skills training, new diagnostic equipment and guided support from clinical lead nurses and nurse practitioners was provided to support nursing staff in the delivery of appropriate sub-acute care. Outcome measures: Rate of hospital admissions; length of stay; incremental cost per QALY; net monetary benefit. Results: The hospital avoidance program was associated with a 19% reduction in annual hospital admissions and a 31% reduction in the average length of stay. When modelled in a cohort of 1,000 residents the program resulted in a total of 1,606 fewer hospital bed days per annum. This contributed to a total cost saving of $2.6 million and...
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Authors: 10
Total Words: 4910
Unqiue Words: 1484

1.996 Mikeys
#10. Healthcare related activity following kidney transplantation: an observational cohort study.
Eleanor C Murray, Jamie Traynor, Patrick Mark, Colin Geddes, David Kingsmore, Karen Stevenson, Marc Clancy, Peter Thomson
Introduction: Kidney transplantation offers superior quality of life and survival compared to dialysis although involves invasive procedures, hospitalisation, clinic attendances, and risk of intercurrent illness. In this study we demonstrate visually and numerically the breadth and depth of activity incurred by transplantation when considering the patient journey. Methods: Consecutive patients in the Glasgow Renal and Transplant Unit (UK) in receipt of a kidney transplant during 2015 were studied. Demographics and events of interest were collated from electronic patient records for 2 years following transplantation. Results: 132 patients were transplanted. The median number of clinical contact days over 2 years was 47; 12 in-patient days, 3 day ward attendances, and 28 out-patient appointments. 46% of clinical contact days occurred in the first 90 days. In-patient days, were higher in both BMI >30kg/m2 and in extended criteria donor subgroups. 64/132 (48.5%) experienced at least one clinically significant infection requiring...
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Sample Sizes : [62, 30, 99, 33, 40, 14, 16]
Authors: 8
Total Words: 5123
Unqiue Words: 1928

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