Top 10 Biorxiv Papers Today in Epidemiology


2.004 Mikeys
#1. Evaluating a digital sepsis alert in a London multi-site hospital network: a natural experiment using electronic health record data
Kate Honeyford, Graham Cooke, Anne Kinderlerer, Elizabeth Williamson, Mark Gilchrist, Alison Holmes, Ben Glampson, Abdulrahim Mulla, Ceire Costelloe
Objective: To determine the impact of a digital sepsis alert on patient outcomes in a UK multi-site hospital network. Methods: A natural experiment utlising the phased introduction of a digital sepsis alert into a multi-site hospital network. Sepsis alerts were either visible to clinicans (the intervention group) or running silently and not visible (the control group). Inverse probability of treatment weighted multivariable logistic regression was used to estimate the effect of the intervention on patient outcomes. Outcomes: In-hospital 30-day mortality (all inpatients), prolonged hospital stay (≥7 days) and timely antibiotics (≤60 minutes of the alert) for patients who alerted in the Emergency Department. Results: The introduction of the alert was associated with lower odds of death (OR:0.76; 95%CI:(0.70, 0.84) n=21,183); lower odds of prolonged hospital stay ≥7 days (OR:0.93; 95%CI:(0.88, 0.99) n=9988); and in patients who required antibiotics, an increased odds of receiving timely antibiotics (OR:1.71; 95%CI:(1.57, 1.87)...
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BRCinfection: Can digital altering for sepsis in patient records improve outcome? Yes, including a reduction in mortality, according to work from @KHoneyfordStats and @DrCCostelloe Available as pre-print here https://t.co/DO1lJqJmXr
BRCinfection: Can digital alerting for sepsis in patient records improve outcome? Yes, including a reduction in mortality, according to work from @KHoneyfordStats and @DrCCostelloe Available as pre-print here https://t.co/DO1lJqJmXr
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Sample Sizes : [21183, 9988, 4622, 15056, 6127, 21183, 171, 214]
Authors: 9
Total Words: 7756
Unqiue Words: 2460

1.999 Mikeys
#2. Adding noise to Markov cohort models
Rowan Iskandar
Following its introduction over thirty years ago, the Markov state-transition cohort model has been used extensively to model population trajectories over time in decision modeling and cost-effectiveness studies. We recently showed that a cohort model represents the average of a continuous-time stochastic process on a multidimensional integer lattice governed by a master equation (ME), which represents the time-evolution of the probability function of a integer-valued random vector. From this theoretical connection, this study introduces an alternative modeling method, stochastic differential equation (SDE), which captures not only the mean behavior but also the variance. We first derive the continuous approximation to the master equation by relaxing integrality constraint of the state space in the form of Fokker Planck equation (FPE), which represents the time-evolution of the probability function of a real-valued random vector. Instead of working with the FPE, the SDE method constitutes time-evolution of the random vector of...
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R and Julia codes for examples in the manuscript titled "Adding noise to Markov cohort models."

Repository: SDE
User: rowaniskandar
Language: R
Stargazers: 0
Subscribers: 0
Forks: 0
Open Issues: 0
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Sample Sizes : None.
Authors: 1
Total Words: 6580
Unqiue Words: 1825

1.997 Mikeys
#3. Risk Factors Associated to Types of Gallstone Diagnosed at Ibnsina Gastroenterology center, Sudan
Mahasin Shaddad
Introduction: Gallstone disease (Cholelithiasis) affects 10 to 15% of the population of developed countries. Our study aimed to determine the risk factors associated to different types of gallstone in patients diagnosed in Khartoum State Ibnsina Gastroenterology Center. Methods: A facility-based prospective cross-sectional study was implemented on a convenient sample of 47 participants diagnosed with gallstone through ultrasonography in Ibnsina Gastroenterology center and who underwent surgical interventions for gallstone removal. A standardized interviewer-administrated research tool comprising three parts was used to collect data related to the characteristics of the participants, their medical presentation and examination as well as information on types of gallstone, surgical interventions and outcomes. The data were computerized through Epi-info7 and analyzed through SPSS 23. Descriptive statistics were firstly performed and association was tested through Chi square tests and ANOVA. A multinomial regression analysis...
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Sample Sizes : [47, 47, 47, 47, 47, 47, 47, 42, 47, 47, 47, 47, 47, 47, 47, 47, 13, 47, 47, 47, 47, 47, 47, 47, 47, 6, 16, 20, 42, 47]
Authors: 1
Total Words: 7354
Unqiue Words: 2838

1.997 Mikeys
#4. Drug safety in pregnancy: review of study approaches required by regulatory agencies
Andrea V Margulis, Mary S Anthony, Elena Rivero-Ferrer
Purpose of review: We reviewed postauthorization pregnancy safety studies requested by regulatory agencies to explore which study approaches have been typically requested and to what extent these have changed over time. Recent findings: The most common study approach requested by the US Food and Drug Administration (FDA) is pregnancy exposure registries (observational cohorts with prospective data collection), per the FDA's Postmarketing Requirements and Commitments (PMR/PMC) database. Since 2017, this requirement has often been paired with a request for a database study (observational study using preexisting electronic health care data), both approaches assessing pregnancy and fetal outcomes. From studies registered in the European Union electronic Register of Post-Authorisation Studies, we observed a similar number of pregnancy exposure registries and database studies, both approaches also assessing pregnancy and fetal outcomes. In requests for drugs approved since 2014, preference appears to have shifted toward studies using...
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Sample Sizes : None.
Authors: 3
Total Words: 6802
Unqiue Words: 1751

1.997 Mikeys
#5. Survival status and predictors of mortality among Breast cancer patients at Black lion specialized hospital, Adult oncology unit, Addis Ababa, Ethiopia, 2018. A retrospective follow-up study with survival analysis
Wondimeneh Shiferaw, Tefera Mulugeta, Habtamu Abera, Yared Asmare, Tadesse Yirga
Introduction: Breast cancer is a leading cause of death worldwide, and ranks as the fifth cause of death from all cancers, and the most common cause of cancer death in women in both developing and developed countries. Breast cancer ranks as the first most frequent cancer among women in Ethiopia. In spite of the high incidence and mortality rate, survival status among breast cancer patients was not determined in our country. Hence, this study aimed to assess survival status and predictor of mortality among breast cancer patients in Black Lion Specialized Hospital. Objective: the main aim of the study is to assess the survival status and predictor of mortality among Breast Cancer patients in Black Lion Specialized Hospital Adult Oncology Unit in 2018. Methods: An institution based retrospective longitudinal study was conducted in BLSH Adult Oncology Unit. All cases of breast cancer registered from January 1st 2012-December 30th, 2014 in BLSH were followed retrospectively for the six-year survival (until December 30th, 2017)....
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biorxivpreprint: Survival status and predictors of mortality among Breast cancer patients at Black lion specialized hospital, Adult oncology unit, Addis Ababa, Ethiopia, 2018. A retrospective follow-up study with survival analysis https://t.co/O8JDvWoitI #bioRxiv
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Sample Sizes : [627, 627, 627, 627, 627, 627]
Authors: 5
Total Words: 8690
Unqiue Words: 2735

1.997 Mikeys
#6. Anopheles bionomic, insecticide resistance and malaria transmission in southwest Burkina Faso: a pre-intervention study
Dieudonne Diloma SOMA, Barnabas Muhugnon Zogo, Anthony Some, Tchiekoi Bertin N, Domonbabele Francois de Sales Hien, Hermann Sie Pooda, Sanata Coulibaly, Jacques Edounou Gnambani, Ali Ouari, Karine Mouline, Amal Dahounto, Georges Anicet Ouedraogo, Florence Fournet, Alphonsine Amanan Koffi, Cedric Pennetier, Nicolas Moiroux, Roch Kounbobr Dabire
Background: The present study presents results of entomological surveys conducted to address the malaria vectors bionomic, insecticide resistance and transmission prior to the implementation of new strategies complement long-lasting insecticidal nets (LLINs) in the framework of a randomized control trial in southwest Burkina Faso. Methods: We conducted entomological surveys in 27 villages during the dry cold season (January 2017), dry hot season (March 2017) and rainy season (June 2017). We carried out hourly catches (from 17:00 to 09:00) inside and outside 4 houses in each village using the Human Landing Catch technique. Mosquitoes were identified using morphological taxonomic keys. Specimens belonging to the Anopheles gambiae complex and Funestus Group were identified using molecular techniques as well as detection of Plasmodium falciparum infection and insecticide resistance target-site mutations. Results: Eight Anopheles species were detected in the area. Anopheles funestus s.s was the main vector during the dry cold season....
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Sample Sizes : [1936, 481, 161, 13, 250, 3, 23, 221, 15, 220, 24, 897, 286, 62, 190, 31, 100, 59, 31, 25, 6, 16, 10, 3, 3, 7]
Authors: 17
Total Words: 10067
Unqiue Words: 3377

1.997 Mikeys
#7. Public health in genetic spaces: a statistical framework to optimize cluster-based outbreak detection
Connor Chato, Art Poon
In infectious disease epidemiology, clustering cases of infection in space and time is a standard method to identify and characterize outbreaks. Clustering cases by genetic similarity is analogous to spatial clustering, and may be more effective for pathogens transmitted at a relatively low rate by intimate contact. However, the statistical properties of genetic clustering in the context of outbreak detection are not well characterized and cluster-defining criteria are generally set to arbitrary values. We describe a new method to optimize the predictive value of a clustering method by optimizing its parameters to maximize the difference in the Akaike information criterion (AIC) between individual-weighted and null models of cluster growth. This approach mirrors solutions to the modifiable areal unit problem (MAUP): the statistical association between covariates and an outcome is contingent on how their spatial distribution is partitioned into units of observation. To evaluate our method, we analyzed the distributions of pairwise...
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biorxivpreprint: Public health in genetic spaces: a statistical framework to optimize cluster-based outbreak detection https://t.co/2RjW0KflSU #bioRxiv
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Sample Sizes : None.
Authors: 2
Total Words: 10499
Unqiue Words: 2674

1.997 Mikeys
#8. Evolution and expansion of multidrug resistant malaria in Southeast Asia: a genomic epidemiology study
William L Hamilton, Roberto Amato, Rob W van der Pluijm, Christopher G Jacob, Quang Huynh Hong, Thuy-Nhien Nguyen Thanh, Hien Tran Tinh, Bouasy Hongvanthong, Keobouphaphone Chindavongsa, Mayfong Mayxay, Rekol Huy, Rithea Leang, Cheah Huch, Lek Dysoley, Chanaki Amaratunga, Seila Suon, Rick M Fairhurst, Rupam Tripura, Thomas J Peto, Yok Sovann, Podjanee Jittamala, Borimas Hanboonkunupakarn, Sasithon Pukrittayakamee, Chau Nguyen Hoang, Mehul Dhorda, Ranitha Vongpromek, Chan S Xin Hui, Richard J Maude, Richard D Pearson, T Nguyen, Kirk Rockett, Eleanor Drury, Sonia Gonçalves, Nicholas J White, Nicholas P Day, Dominic P Kwiatkowski, Arjen M Dondorp, Olivo Miotto
Background: A multidrug resistant co-lineage of Plasmodium falciparum malaria, named KEL1/PLA1, spread across Cambodia c.2008-2013, causing high treatment failure rates to the frontline combination therapy dihydroartemisinin-piperaquine. Here, we report on the evolution and spread of KEL1/PLA1 in subsequent years. Methods: We analysed whole genome sequencing data from 1,673 P. falciparum clinical samples collected in 2008-2018 from northeast Thailand, Laos, Cambodia and Vietnam. By investigating genome-wide relatedness between parasites, we inferred patterns of shared ancestry in the KEL1/PLA1 population. Findings: KEL1/PLA1 spread rapidly from 2015 into all of the surveyed countries and now exceeds 80% of the P. falciparum population in several regions. The co-lineage parasites maintained a high level of genetic relatedness reflecting their common origin. However, several genetic subgroups have recently emerged within this lineage with diverse geographical distributions. Some of these emerging KEL1/PLA1 subgroups carry recent...
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Sample Sizes : [36, 19, 24]
Authors: 38
Total Words: 8149
Unqiue Words: 2318

1.997 Mikeys
#9. Comparison of two individual-based models for simulating HIV epidemics in a population with HSV-2 using as case study Yaoundé-Cameroon, 1989-1998
Diana M Hendrickx, Joao Sousa, Pieter JK Libin, Wim Delva, Jori Liesenborgs, Niel Hens, Viktor Müller, Anne-Mieke Vandamme
Mathematical modelling has been widely applied to better understand the transmission, treatment and prevention of infectious diseases. The comparison of different models is crucial for providing robust evidence for policy-makers because differences in model properties can influence their prediction. In this study, two individual-based models for simulating HIV epidemics and sexually transmitted infection (STI) co-factor effects, i.e. models developed with the Simpact Cyan 1.0 and StepSyn 1.0 frameworks, were compared. Simpact Cyan 1.0 uses a continuous-time implementation and is updated each time an event happens, while StepSyn 1.0 uses discrete daily or weekly time-steps and updates population, sexual links, and STI states at each time-step. Furthermore, there are differences in how stochastic processes are described, how individuals enter and leave the population, and in the formation and break-up of ties in the sexual network. We evaluated how these differences would affect survival and HIV prevalence curves during the course...
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Authors: 8
Total Words: 0
Unqiue Words: 0

1.997 Mikeys
#10. A model of tuberculosis clustering in low incidence countries reveals more on-going transmission in the United Kingdom than the Netherlands between 2010 and 2015.
Ellen Brooks-Pollock, Leon Danon, Hester Korthals Altes, Jennifer Davidson, Andrew M. T. Pollock, Dick van Soolingen, Colin Campbell, Maeve K. Lalor
Tuberculosis (TB) is a major public health threat, including in low TB incidence countries, through a combination of imported infection and onward transmission. Using data from the Enhanced Tuberculosis Surveillance system in the United Kingdom (UK) and the Netherlands (NL) Tuberculosis Register, we developed a mathematical model of TB importation and transmission in low-incidence settings. We apply this method to compare the effective reproduction number for TB, the contribution of importation and the role of superspreaders in the UK and the NL. We estimate that on average, between 2010 and 2015, a TB case generated 0.41(0.30,0.60) secondary cases in the UK, and 0.24(0.14,0.48) secondary cases in the NL. A majority of cases did not generate any secondary cases. Recent transmission accounted for 26% (21%,36%) of UK cases and 19%(11%,31%) of NL cases. We predict that reducing UK transmission rates to those observed in NL would result in 538(266,818) fewer cases annually in the UK. This methodology reveals common transmission...
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Authors: 8
Total Words: 6248
Unqiue Words: 1753

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