Top 10 Biorxiv Papers Today in Epidemiology


2.05 Mikeys
#1. The ability of single genes vs full genomes to resolve time and space in outbreak analysis
Gytis Dudas, Trevor Bedford
Inexpensive pathogen genome sequencing has had a transformative effect on the field of phylodynamics, where ever increasing volumes of data have promised real-time insight into outbreaks of infectious disease. As well as the sheer volume of pathogen isolates being sequenced, the sequencing of whole pathogen genomes, rather than select loci, has allowed phylogenetic analyses to be carried out at finer time scales, often approaching serial intervals for infections caused by rapidly evolving RNA viruses. Despite its utility, whole genome sequencing of pathogens has not been adopted universally and targeted sequencing of loci is common in some pathogen-specific fields. In this study we aim to highlight the utility of sequencing whole genomes of pathogens by re-analysing a well-characterised collection of Ebola virus sequences in the form of complete viral genomes (~19kb long) or the rapidly evolving glycoprotein (GP, ~2kb long) gene. We quantify changes in phylogenetic, temporal, and spatial inference resolution as a result of this...
more | pdf
Figures
Tweets
Github

baltic - backronymed adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. Development is back on the evogytis/baltic branch (i.e. here).

Repository: baltic
User: evogytis
Language: Jupyter Notebook
Stargazers: 16
Subscribers: 1
Forks: 9
Open Issues: 0
Youtube
None.
Other stats
Sample Sizes : None.
Authors: 2
Total Words: 10273
Unqiue Words: 2787

2.01 Mikeys
#2. Landscape epidemiology of ash dieback
Marie Grosdidier, T. Scordia, Renaud Ioos, Benoit Marcais
Ash dieback caused by Hymenoscyphus fraxineus, an invasive alien pathogen, has been severely damaging European ash populations. Nevertheless, a large range of disease severities was observed at the landscape scale in the field. Several studies suggested that environment, such as climate, site conditions or local tree cover strongly affects ash dieback. We characterized the landscape epidemiology of the disease at two stages of the invasion process with spatio-temporal models using Bayesian models fitted by Integrated Nested Laplace Approximation (INLA). We first analyzed the effect of landscape features on the disease arrival and establishment stage at the scale of a village in NE France in 2012, 2 years after first report of the disease in the area and then, on the disease development stage in 2016-18. Landscape features had little impact on the disease at the establishment stage but strongly determined it further development. The local fragmentation of the tree cover was the most important factor with trees isolated or in hedges...
more | pdf
Figures
Tweets
biorxivpreprint: Landscape epidemiology of ash dieback https://t.co/Oc4yBQByry #bioRxiv
Github
None.
Youtube
None.
Other stats
Sample Sizes : None.
Authors: 4
Total Words: 8909
Unqiue Words: 2482

1.997 Mikeys
#3. Multiparasitism among Schoolchildren of Akonolinga, Nyong et Mfoumou Division, Centre Region of Cameroon
Martin Gaël OYONO, Leopold Gustave LEHMAN, Samuel FOSSO, Charles Felix BILONG BILONG
In Sub-Saharan Africa, school-age children are the most vulnerable to parasitic infections and are particularly exposed to multi-parasitism and its potential consequences. This study aimed at determining the intensity of multi-parasitism in Nyong et Mfoumou Division and identifying its determinants. A cross-sectional study took place from September 2017 to July 2018 among pupils of five (05) government schools from the Nyong et Mfoumou Division. Stool samples were collected from each child and examined for protozoan cysts, helminth eggs and larva while blood samples were collected for detection of Plasmodium spp and filarial blood stages. In addition, socio-demographic and school environment related information were documented. In total, 416 schoolchildren were recruited; out of which 309 (74.28%) were infected by at least one parasite species. 13 parasite species were found: 03 hemoparasites and 10 intestinal parasites. Plasmodium falciparum was the main hemoparasite (37.26%). Amongst intestinal parasites, Entamoeba coli were the...
more | pdf
Figures
None.
Tweets
biorxivpreprint: Multiparasitism among Schoolchildren of Akonolinga, Nyong et Mfoumou Division, Centre Region of Cameroon https://t.co/TfIs7ZSFdW #bioRxiv
Github
None.
Youtube
None.
Other stats
Sample Sizes : [207, 73, 72, 64, 76, 131]
Authors: 4
Total Words: 7380
Unqiue Words: 2458

1.997 Mikeys
#4. Seroprevalence of zoonotic diseases (leptospirosis and Japanese encephalitis) in swine in ten provinces of Vietnam: a Bayesian approach to estimate prevalence
Hu Suk Lee, To Long Thanh, Nguyen Khanh Ly, Hung Nguyen-Viet, Krishna K. Thakur, Delia Grace
Background Leptospirosis is an important zoonotic disease with a global distribution, affecting a wide range of mammalian animals and humans. Japanese encephalitis (JE) virus is the major vector-borne zoonotic disease in the Asia-Pacific region. The main objective of this study was to evaluate the seroprevalence of serovar-specific Leptospira and JE in swine from 10 provinces in Vietnam. Methods Samples were initially collected for swine influenza surveillance from March to April 2017 at large-scale farms (with at least 50 sows and/or 250 fattening pigs) with pigs that tested positive for influenza in the previous surveillance period (2015-16). Findings A total of 2,000 sera samples were analyzed from 10 provinces. Overall, the seroprevalence of leptospirosis was 21.05% (95% CI: 19.28-22.90) using a cut-off titer of ≥1:100. The apparent prevalence of JE was 73.45% (95% CI: 71.46-75.37) while the true prevalence was slightly higher (74.46%, 95% credible interval: 73.73-86.41). We found a relatively high presence of leptospirosis...
more | pdf
Figures
Tweets
biorxivpreprint: Seroprevalence of zoonotic diseases (leptospirosis and Japanese encephalitis) in swine in ten provinces of Vietnam: a Bayesian approach to estimate prevalence https://t.co/X1EsGV7M9v #bioRxiv
Github
None.
Youtube
None.
Other stats
Sample Sizes : None.
Authors: 6
Total Words: 6550
Unqiue Words: 2537

1.997 Mikeys
#5. Clinical pattern of antibiotic overuse and misuse in primary healthcare hospitals in the southwest of China
Yue Chang, Sarunyou Chusri, Rassamee Sangthong, Edward McNeil, Jiaqi Hu, Wei Du, Duan Li, Xingying Fan, Hanni Zhou, Virasakdi Chongsuvivatwong, Lei Tang
Purpose: Overuse and misuse of antibiotics are the primary risk factors for antibiotics resistance. Inadequate professional competence of primary care physicians might exacerbate these problems in China. This retrospective study aims to document the clinical pattern of antibiotics use and its overuse and misuse rates in rural primary care institutions, and to evaluate the association between antibiotics use and characteristics of the physicians and their patients. Methods: Medical records from 16 primary care hospitals in rural areas of Guizhou province, China were obtained from the Health Information System in 2018. Classification of incorrect and/or unnecessary use, escalated use and combined antibiotics use was based on the Guiding Principle of Clinical Use of Antibiotics (2015, China) and the standard of USA Centers for Disease Control and Prevention. Generalized Estimating Equations were employed to determine predictive factors for inappropriate antibiotics use. Results: A total of 74,648 antibiotics prescriptions were...
more | pdf
Figures
None.
Tweets
biorxivpreprint: Clinical pattern of antibiotic overuse and misuse in primary healthcare hospitals in the southwest of China https://t.co/yUZMLfInef #bioRxiv
Github
None.
Youtube
None.
Other stats
Sample Sizes : None.
Authors: 11
Total Words: 5395
Unqiue Words: 2241

1.997 Mikeys
#6. Self-reported sleep duration and daytime napping are associated with renal hyperfiltration and microalbuminuria in apparently healthy Chinese population
Yingnan Ye, Linxi ZHANG, Wenhua YAN, Anping WANG, Weiqing WANG, Zhengnan GAO, Xulei TANG, Li YAN, Qin WAN, Zuojie LUO, Guijun QIN, Lulu CHEN, Shiqing WANG, Yuxia Wang, Yiming MU
Background Sleep duration affects health in various way. The objective of this study was to investigate the relationship between sleep duration, daytime napping and kidney function in a middle-aged apparently healthy Chinese population. Methods According to self-reported total sleep and daytime napping duration, 33,850 participants aged 38 to 90 years old from 8 regional centers were divided into subgroups. Height, weight, waistline, hipline, blood pressure, biochemical index, FBG, PBG, HbA1c, creatinine and urinary albumin-creatinine ratio (UACR) were measured and recorded in each subject. Microalbuminuria was defined as UACR>=30 mg/g, CKD was defined as eGFR<60 ml/min and hyperfiltration was defined as eGFR>=135 ml/min. Multiple logistic regressions were applied to investigate associations between sleep and kidney function. Results Compared to participants with [7-8]h/day sleep, ORs of >9 h/day, (8, 9]h/day and <6h/day sleep for microalbuminuria were 1.317 (1.200-1.446, p<0.001), 1.215 (1.123-1.315, p<0.001) and 1.218...
more | pdf
Figures
Tweets
Github
None.
Youtube
None.
Other stats
Sample Sizes : None.
Authors: 15
Total Words: 8007
Unqiue Words: 2662

1.992 Mikeys
#7. Levels of knowledge and attitude on preconception care at public hospitals in Wolayita Zone, South Ethiopia
zemenu yohannes kassa, Zelalem Tenaw, Ayalew Astatkie, Melese Siyoum, Gezahegn Bekele, Kefyalew Taye, Shewangizaw Mekonnen, Zerai Kassaye
Abstract Introduction: Preconception care is vital for reducing and preventing maternal and child morbidity and mortality. This study was conducted to assess the levels and correlates of knowledge and attitude of preconception care among mothers who gave birth at public hospitals in Wolayita zone, South Ethiopia. Methodology: A hospital-based cross sectional study was conducted from January 01-February 30, 2017 on a sample of 370 mothers who gave birth at public hospitals in Wolayita zone. The mothers were selected using systematic random sampling and interviewed using pretested structured questionnaires. Data were analyzed using bivariate and multivariable techniques. Results: In this study 53% (95%CI: 47.8, 58.1) of mothers who gave birth at public hospitals had a good level of knowledge on preconception care, whereas 54.3% (95%CI: 49.2, 59.5) possessed positive attitude on preconception care. Women who have radio, planned pregnancy, and have participated in community meetings related to preconception care had significantly...
more | pdf
Figures
None.
Tweets
Github
None.
Youtube
None.
Other stats
Sample Sizes : None.
Authors: 8
Total Words: 0
Unqiue Words: 0

1.988 Mikeys
#8. Patterns and predictors of Staphylococcus aureus carriage during the first year of life; a longitudinal study
Gili Regev-Yochay, Aylana Reiss-Mandel, Carmit Rubin, Ayala Maayan-Metzger, Ilya Novikov, Haana Jaber, Mordechay Dolitzky, Laurence Freedman, Galia Rahav
Objectives: To determine the patterns of S. aureus carriage in the first year of life, its determinants and dynamics of transmission between mothers and infants. Methods: Prospective longitudinal cohort study of S. aureus carriage among mothers and their infants. Monthly screenings from pregnancy/birth through the first year of the infant's life. Medical and lifestyle data was collected. Infant S. aureus carriage was detected by rectal and nasal swabs and maternal carriage by nasal swabs. Multivariate analysis and an NLMixed model were used to determine predictors of carriage and S. aureus persistence. Results: 130 S. aureus carrier women and their 132 infants were included in the study. 93% of the infants acquired S. aureus sometime during the first year of life, 64% of them acquired the maternal strain, mostly (66%) during the first month of life. 70 women (52.50%) and 17 infants (14%) carried S. aureus persistently. Early acquisition of S. aureus carriage was associated with longer duration of initial carriage and was the most...
more | pdf
Figures
None.
Tweets
Github
None.
Youtube
None.
Other stats
Sample Sizes : None.
Authors: 9
Total Words: 0
Unqiue Words: 0

1.988 Mikeys
#9. Lifetime changes in CD4 count, viral load suppression and adherence among adolescents living with HIV in urban Peru
Carly Rodriguez, Lenka Kolevic, Alicia Ramos, Milagros Wong, Maribel Munoz, Kunjal Patel, Molly F Franke
Introduction: Viral load suppression and adherence to combined antiretroviral therapy (cART) have been shown to be lower in adolescents than in other age groups; however, this relationship has not been documented longitudinally from childhood to adolescence and has rarely been examined outside of high-resource settings and sub-Saharan Africa. To address this knowledge gap, we quantified longitudinal changes in CD4 cell count, viral load suppression, and cART adherence in adolescents living with HIV in urban, Peru. Methods: We conducted a retrospective chart review among adolescents ages 10-18 years on cART and receiving care at a large, public sector pediatric hospital as of December 2015. We abstracted clinical notes indicating nonadherence and viral load and CD4 counts from childhood to adolescence. We modeled the association between age and each outcome with restricted cubic splines accounting for multiple observations per person, and graphed study outcomes by age. Results: A median of 7.7 years (25th percentile=4.9, 75th...
more | pdf
Figures
None.
Tweets
Github
None.
Youtube
None.
Other stats
Sample Sizes : None.
Authors: 7
Total Words: 0
Unqiue Words: 0

1.988 Mikeys
#10. Multiple-serotype models of dengue virus transmission: simulation study and perspectives for the application of inference in epidemiological surveillance
Caetano Souto-Maior
With around 3 billion people at risk, dengue virus is endemic to many parts of the world. In the Brazilian city of Rio de Janeiro, surveillance measures require notification of new dengue virus cases, and are supplemented by serum collection from patients and sequencing of viral RNA. Phylogenetic analyses have been performed for all serotypes circulating in the country to identify viral genotypes, potentially identify new introductions, and compare viruses presently circulating in the country with those in the past, and of other countries. As a separate type of analysis, a number of mathematical models have been developed to describe dengue virus transmission -- particularly qualitative incidence or prevalence patterns -- although few have been tested. In this chapter, I show how different mathematical formulations could represent transmission of dengue virus by mosquitoes to humans, how the different model structures entail assumptions about the process, and how these affect outputs qualitatively. Inference from simulated data is...
more | pdf
Figures
Tweets
Github
None.
Youtube
None.
Other stats
Sample Sizes : None.
Authors: 1
Total Words: 16049
Unqiue Words: 4480

About

Assert is a website where the best academic papers on arXiv (computer science, math, physics), bioRxiv (biology), BITSS (reproducibility), EarthArXiv (earth science), engrXiv (engineering), LawArXiv (law), PsyArXiv (psychology), SocArXiv (social science), and SportRxiv (sport research) bubble to the top each day.

Papers are scored (in real-time) based on how verifiable they are (as determined by their Github repos) and how interesting they are (based on Twitter).

To see top papers, follow us on twitter @assertpub_ (arXiv), @assert_pub (bioRxiv), and @assertpub_dev (everything else).

To see beautiful figures extracted from papers, follow us on Instagram.

Tracking 99,586 papers.

Search
Sort results based on if they are interesting or reproducible.
Interesting
Reproducible
Feedback
Online
Stats
Tracking 99,586 papers.