137 Works

From Black Box to Shining Spotlight

Andrew J. Sage, Yang Liu & Joe Sato
We introduce a pair of Shiny web applications that allow users to visualize random forest prediction intervals alongside those produced by linear regression models. The apps are designed to help undergraduate students deepen their understanding of the role that assumptions play in statistical modeling by comparing and contrasting intervals produced by regression models with those produced by more flexible algorithmic techniques. We describe the mechanics of each approach, illustrate the features of the apps, provide...

Additional file 2 of Development and validation of an extended Cox prognostic model for patients with ER/PR+ and HER2− breast cancer: a retrospective cohort study

Yiqun Xie, Xizhou Li, Ying Wu, Wenting Cui & Yang Liu
Additional file 2: Appendix 2. Hazard ratios and their 95% confidence limits of Ki67, PR, ER, and age. Figure 1. Hazard ratios and their 95% confidence limits for a series of binary variables of Ki67. Figure 2. Hazard ratios and their 95% confidence limits for a series of binary variables of ER. Figure 3. Hazard ratios and their 95% confidence limits for a series of binary variables of PR. Figure 4. Hazard ratios and their...

Additional file 4 of Do in-service training materials for midwifery care providers in sub-Saharan Africa meet international competency standards? A scoping review 2000–2020

Joanne Welsh, Hashim Hounkpatin, Mechthild M. Gross, Claudia Hanson & Ann-Beth Moller
Supplementary Material 4

Additional file 4 of Do in-service training materials for midwifery care providers in sub-Saharan Africa meet international competency standards? A scoping review 2000–2020

Joanne Welsh, Hashim Hounkpatin, Mechthild M. Gross, Claudia Hanson & Ann-Beth Moller
Supplementary Material 4

Decision Modelling for Health Economic Evaluation - Exercises

Andrew Briggs

Additional file 1 of Inequalities in the impact of COVID-19-associated disruptions on tuberculosis diagnosis by age and sex in 45 high TB burden countries

C. Finn McQuaid, Marc Y. R. Henrion, Rachael M. Burke, Peter MacPherson, Rebecca Nzawa-Soko & Katherine C. Horton
Additional file 1: Model code and additional tables and Figs. Table S1. Country-specific tuberculosis notifications for 2013-2020 by age and sex. Table S2. Country-specific linear models for expected notifications. Fig. S1. Country-specific linear models for expected notifications. Table S3. Country-specific numbers of missed or delayed diagnoses. Table S4. Country-specific risk-ratios for disruption to tuberculosis notifications due to the pandemic for men compared to women (both aged ≥ 15 years). Table S5. Country-specific risk-ratios for disruption...

The pre-surgical factors that determine the decision to proceed to resection in children diagnosed with high-risk neuroblastoma in a resource limited setting

Jaques van Heerden, Mariana Kruger, Tonya Marianne Esterhuizen, Anel van Zyl, Marc Hendricks, Sharon Cox, Hansraj Mangray, Janet Poole, Gita Naidu, Ané Büchner, Mariza de Villiers, Jan du Plessis, Barry van Emmenes, Elmarie Matthews, Yashoda Manickchund & Derek Stanley Harrison
Surgical control has prognostic value in neuroblastoma (NB). Advanced NB is common at diagnosis in South Africa. We investigated the pre-surgery factors that influenced decisions to perform surgical resections. We included 204 patients with high-risk NB from a national retrospective study, who completed induction chemotherapy between 2000 and 2016. The median age was 32.4 months (IQR 15.1 − 53.5 months). Primary tumor resection was achieved in 76.9% of patients between 0-18 months of age, 51.8%...

Additional file 1 of Comparison of femoral mechanics before and after internal fixation removal and the effect of sclerosis on femoral stress: a finite element analysis

Yang Liu, Wenjie Song, Haoran Liang, Chaoxin Li, Wenjie Niu, Huifeng Shao, Yuze Wang, Ziquan Yang, Pengcui Li, Xiaogang Wu, Yong He, Xiaochun Wei & Wangping Duan
Additional file 1.

Additional file 2 of Comparison of femoral mechanics before and after internal fixation removal and the effect of sclerosis on femoral stress: a finite element analysis

Yang Liu, Wenjie Song, Haoran Liang, Chaoxin Li, Wenjie Niu, Huifeng Shao, Yuze Wang, Ziquan Yang, Pengcui Li, Xiaogang Wu, Yong He, Xiaochun Wei & Wangping Duan
Additional file 2.

Additional file 23 of Proteogenomic insights into the biology and treatment of pancreatic ductal adenocarcinoma

Yexin Tong, Mingjun Sun, Lingli Chen, Yunzhi Wang, Yan Li, Lingling Li, Xuan Zhang, Yumeng Cai, Jingbo Qie, Yanrui Pang, Ziyan Xu, Jiangyan Zhao, Xiaolei Zhang, Yang Liu, Sha Tian, Zhaoyu Qin, Jinwen Feng, Fan Zhang, Jiajun Zhu, Yifan Xu, Wenhui Lou, Yuan Ji, Jianyuan Zhao, Fuchu He, Yingyong Hou … & Chen Ding
Additional file 23: Table S1. Clinicopathologic Information and Multi-omics Data in PDAC Cohort. Table S1A Multi-omics information of PDAC cohort. Table S1B Clinicopathologic information of the 229 PDAC.

Data from: Clarifying life lost due to cold and heat: a new approach using annual time series.

Nirandeep Rehill, Ben Armstrong & Paul Wilkinson
Objective: To clarify whether deaths associated with hot and cold days are among the frail who would have died anyway in the next few weeks or months. Design: Time series regression analysis of annual deaths in relation to annual summaries of cold and heat. Setting: London, UK. Participants: 3 530 280 deaths from all natural causes among London residents between October 1949 and September 2006. Main outcome measures: Change in annual risk of death (all...

Data from: Safety and immunogenicity of H1/IC31®, an adjuvanted TB subunit vaccine, in HIV-infected adults with CD4+ Lymphocyte counts greater than 350 cells/mm3: a phase II, multi-centre, double-blind, randomized, placebo-controlled trial

Klaus Reither, Lynn Katsoulis, Trevor Beattie, Nicolene Gardiner, Nicole Lenz, Khadija Said, Elirehema Mfinanga, Christian Pohl, Katherine L. Fielding, Hannah Jeffery, Benjamin M. Kagina, Elisabeth J. Hughes, Thomas J. Scriba, Willem A. Hanekom, Søren T. Hoff, Peter Bang, Ingrid Kromann, Claudia Daubenberger, Peter Andersen & Gavin J. Churchyard
Background: Novel tuberculosis vaccines should be safe, immunogenic, and effective in various population groups, including HIV-infected individuals. In this phase II multi-centre, double-blind, placebo-controlled trial, the safety and immunogenicity of the novel H1/IC31 vaccine, a fusion protein of Ag85B-ESAT-6 (H1) formulated with the adjuvant IC31, was evaluated in HIV-infected adults. Methods: HIV-infected adults with CD4+ T cell counts >350/mm3 and without evidence of active tuberculosis were enrolled and followed until day 182. H1/IC31 vaccine or...

Data for: Rapid Assessment of Hearing Loss survey in Malawi

Tess Bright

Antenatal code list for: \"The effects of antenatal care, ethnicity and social deprivation on the risk of stillbirth in the UK: A cohort study using routinely collected data\"

Amanda Clery, Caroline Minnasian, Liam Smeeth & Rohini Mathur
A list of Read codes and entity types used to identify events in the Clinical Practice Research Datalink that identify the antenatal appointments women in the Pregnancy Register had. These were used to quantify the frequency and timing of antenatal care, the exposure variable for the study.

Data from: Understanding willingness to use oral pre-exposure prophylaxis for HIV prevention among men who have sex with men in China

Xia Wang, Adam Bourne, Pulin Liu, Jiangli Sun, Thomas Cai, Gitau Mburu, Matteo Cassolato, Bangyuan Wang & Wang Zhou
Background: Oral pre-exposure prophylaxis (PrEP) is recommended as an additional prevention choice for men who have sex with men (MSM) at substantial risk of HIV. The aim of this study was to evaluate the extent, and reasons, for MSM’s willingness to use oral PrEP in Wuhan and Shanghai, China. Methods: Between May and December 2015, a cross-sectional survey was conducted among 487 MSM recruited through snowball sampling in physical locations frequented by MSM and through...

Data from: A randomized feasibility trial comparing four antimalarial drug regimens to induce Plasmodium falciparum gametocytemia in the controlled human malaria infection model

Isaie J. Reuling, Lisanne A Van De Schans, Luc E Coffeng, Kjerstin Lanke, Lisette Meerstein-Kessel, Wouter Graumans, Geert-Jan Van Gemert, Karina Teelen, Rianne Siebelink-Stoter, Marga Van De Vegte-Bolmer, Quirijn De Mast, André J Van Der Ven, Karen Ivinson, Cornelus C Hermsen, Sake De Vlas, John Bradley, Katharine A Collins, Christian F Ockenhouse, James McCarthy, Robert W. Sauerwein & Teun Bousema
Background: Malaria elimination strategies require a thorough understanding of parasite transmission from human to mosquito. A clinical model to induce gametocytes to understand their dynamics and evaluate transmission-blocking interventions (TBI) is currently unavailable. Here, we explore the use of the well-established Controlled Human Malaria Infection model (CHMI) to induce gametocyte carriage with different antimalarial drug regimens. Methods: In a single centre, open-label randomised trial, healthy malaria-naive participants (aged 18–35 years) were infected with Plasmodium falciparum...

Behavioural change towards reduced intensity physical activity is disproportionately prevalent among adults with serious health issues or self-perception of high risk during the UK COVID-19 lockdown.

Chrissy Roberts, Nina Rogers, Naomi Waterlow, Hannah Brindle, Luisa Enria & Shelley Lees
Quantitative data on physical activity and health behaviours during the UK COVID-19 lockdown. The anonymous web-based survey was performed between 6th April and 22 April 2020, approximately mapping to weeks 3-5 of the lockdown in the UK. The main survey included 49 questions which covered a broad range of topics including (1) Demographics, (2) Health and Health Behaviours, (3) Adherence to COVID-19 Control measures, (4) Information sources used to learn about COVID-19, (5) Trust in...

Data from: The impact of long-term azithromycin on antibiotic resistance in HIV-associated chronic lung disease

Regina Esinam Abotsi, Mark P. Nicol, Grace McHugh, Victoria Simms, Andrea M. Rehman, Charmaine Barthus, Lucky G. Ngwira, Brenda Kwambana-Adams, Robert S Heyderman, Jon Ø Odland, Rashida A Ferrand & Felix S. Dube
Background: Selection for resistance to azithromycin (AZM) and other antibiotics such as tetracyclines and lincosamides remains a concern with long-term AZM use for treatment of chronic lung diseases (CLD). We investigated the impact of 48 weeks of AZM on the carriage and antibiotic resistance of common respiratory bacteria among children with HIV-associated CLD. Methods: Nasopharyngeal (NP) swabs and sputa were collected at baseline, 48 and 72 weeks from participants with HIV-associated CLD randomised to receive...

Clinical codelist - CPRD Gold - dementia diagnoses and subtypes

Charlotte Warren-Gash
Read codes for dementia subtypes.

Secondary data for a cluster-randomised trial of community-led delivery of HIV self-testing in Malawi (HIV Self-Testing Africa [STAR])

Pitchaya Peach Indravudh
The dataset was generated as part of a cluster-randomised trial, with group village heads as the unit of randomisation, of community-led delivery of HIV self-testing in Malawi. Endline data describe individual-level variables reported in an endline survey. These data underpin the mediation analysis for the trial.

Additional file 5 of Changes in concentrations of cervicovaginal immune mediators across the menstrual cycle: a systematic review and meta-analysis of individual patient data

Sean M. Hughes, Claire N. Levy, Ronit Katz, Erica M. Lokken, Melis N. Anahtar, Melissa Barousse Hall, Frideborg Bradley, Philip E. Castle, Valerie Cortez, Gustavo F. Doncel, Raina Fichorova, Paul L. Fidel, Keith R. Fowke, Suzanna C. Francis, Mimi Ghosh, Loris Y. Hwang, Mariel Jais, Vicky Jespers, Vineet Joag, Rupert Kaul, Jordan Kyongo, Timothy Lahey, Huiying Li, Julia Makinde, Lyle R. McKinnon … & Florian Hladik
Additional file 5: Figure S1. Assessment of publication bias. A Funnel plots. Symbols show the effect of the menstrual cycle (x-axis) and the standard error of that effect (y-axis, reversed). Each symbol shows an individual study. Vertical solid line shows no effect. Vertical dashed line shows the meta-estimate of effect. Diagonal dashed lines enclose the region expected to include 95% of studies based on the estimated meta-effect and the standard errors. B Results of Egger’s...

Additional file 3 of Changes in concentrations of cervicovaginal immune mediators across the menstrual cycle: a systematic review and meta-analysis of individual patient data

Sean M. Hughes, Claire N. Levy, Ronit Katz, Erica M. Lokken, Melis N. Anahtar, Melissa Barousse Hall, Frideborg Bradley, Philip E. Castle, Valerie Cortez, Gustavo F. Doncel, Raina Fichorova, Paul L. Fidel, Keith R. Fowke, Suzanna C. Francis, Mimi Ghosh, Loris Y. Hwang, Mariel Jais, Vicky Jespers, Vineet Joag, Rupert Kaul, Jordan Kyongo, Timothy Lahey, Huiying Li, Julia Makinde, Lyle R. McKinnon … & Florian Hladik
Additional file 3. Code and data. IPD from co-authors who agreed to share it, results of all analyses presented in the paper, and R code files necessary to reproduce the analysis and figures.

Additional file 2 of Cross-watershed distribution pattern challenging the elimination of Oncomelania hupensis, the intermediate host of Schistosoma japonicum, in Sichuan province, China

Shen Chen, Ding Lu, Lei Duan, Ben Ma, Chao Lv, Yin-long Li, Shen-ning Lu, Lan-hua Li, Liang Xu, Zi-song Wu, Shang Xia, Jing Xu, Yang Liu & Shan Lv
Additional file 2: Dataset S1. The 130 unique cox1 haplotypes of Oncomelania hupensis from this study including two outgroups

Registration Year

  • 2022
    72
  • 2021
    17
  • 2020
    7
  • 2019
    9
  • 2018
    8
  • 2017
    6
  • 2016
    5
  • 2015
    7
  • 2014
    3
  • 2013
    1

Resource Types

  • Dataset
    137

Affiliations

  • London School of Hygiene & Tropical Medicine
    137
  • Chinese Academy of Tropical Agricultural Sciences
    34
  • Sun Yat-sen University
    34
  • Zhejiang University
    34
  • Central South University
    34
  • Fudan University Shanghai Cancer Center
    34
  • Fairy Lake Botanical Garden
    34
  • Tangshan Gongren Hospital
    34
  • Shanghai University of Traditional Chinese Medicine
    34
  • Lund University
    34