Data sharing and reanalysis of randomized controlled trials in leading biomedical journals with a full data sharing policy: survey of studies published in the BMJ and PLOS Medicine

Objectives To explore the effectiveness of data sharing by randomized controlled trials (RCTs) in journals with a full data sharing policy and to describe potential difficulties encountered in the process of performing reanalyses of the primary outcomes. Design Survey of published RCTs. Setting PubMed/Medline. Eligibility criteria RCTs that had been submitted and published by The BMJ and PLOS Medicine subsequent to the adoption of data sharing policies by these journals. Main outcome measure The primary outcome was data availability, defined as the eventual receipt of complete data with clear labelling. Primary outcomes were reanalyzed to assess to what extent studies were reproduced. Difficulties encountered were described. Results 37 RCTs (21 from The BMJ and 16 from PLOS Medicine) published between 2013 and 2016 met the eligibility criteria. 17/37 (46%, 95% confidence interval 30% to 62%) satisfied the definition of data availability and 14 of the 17 (82%, 59% to 94%) were fully reproduced on all their primary outcomes. Of the remaining RCTs, errors were identified in two but reached similar conclusions and one paper did not provide enough information in the Methods section to reproduce the analyses. Difficulties identified included problems in contacting corresponding authors and lack of resources on their behalf in preparing the datasets. In addition, there was a range of different data sharing practices across study groups. Conclusions Data availability was not optimal in two journals with a strong policy for data sharing. When investigators shared data, most reanalyses largely reproduced the original results. Data sharing practices need to become more widespread and streamlined to allow meaningful reanalyses and reuse of data

Do tests devised to detect recent HIV-1 infection provide reliable estimates of incidence in Africa?

International audienceThe objective of this study was to assess the performance of 4 biologic tests designed to detect recent HIV-1 infections in estimating incidence in West Africa (BED, Vironostika, Avidity, and IDE-V3). These tests were assessed on a panel of 135 samples from 79 HIV-1-positive regular blood donors from Abidjan, C?d'Ivoire, whose date of seroconversion was known (Agence Nationale de Recherches sur le SIDA et les H?tites Virales 1220 cohort). The 135 samples included 26 from recently infected patients (180 days), and 15 from patients with clinical AIDS. The performance of each assay in estimating HIV incidence was assessed through simulations. The modified commercial assays gave the best results for sensitivity (100% for both), and the IDE-V3 technique gave the best result for specificity (96.3%). In a context like Abidjan, with a 10% HIV-1 prevalence associated with a 1% annual incidence, the estimated test-specific annual incidence rates would be 1.2% (IDE-V3), 5.5% (Vironostika), 6.2% (BED), and 11.2% (Avidity). Most of the specimens falsely classified as incident cases were from patients infected for >180 days but <1 year. The authors conclude that none of the 4 methods could currently be used to estimate HIV-1 incidence routinely in C?d'Ivoire but that further adaptations might enhance their accuracy

Long‐term surveillance biopsy: Is it necessary after pediatric heart transplant?

Due to limited and conflicting data in pediatric patients, long‐term routine surveillance endomyocardial biopsy (RSB) in pediatric heart transplant (HT) remains controversial. We sought to characterize the rate of positive RSB and determine factors associated with RSB‐detected rejection. Records of patients transplanted at a single institution from 1995 to 2015 with >2 year of post‐HT biopsy data were reviewed for RSB‐detected rejections occurring >2 year post‐HT. We illustrated the trajectory of significant rejections (ISHLT Grade ≥3A/2R) among total RSB performed over time and used multivariable logistic regression to model the association between time and risk of rejection. We estimated Kaplan‐Meier freedom from rejection rates by patient characteristics and used the log‐rank test to assess differences in rejection probabilities. We identified the best‐fitting Cox proportional hazards regression model. In 140 patients, 86% did not have any episodes of significant RSB‐detected rejection >2 year post‐HT. The overall empirical rate of RSB‐detected rejection >2 year post‐HT was 2.9/100 patient‐years. The percentage of rejection among 815 RSB was 2.6% and remained stable over time. Years since transplant remained unassociated with rejection risk after adjusting for patient characteristics (OR = 0.98; 95% CI 0.78‐1.23; P = 0.86). Older age at HT was the only factor that remained significantly associated with risk of RSB‐detected rejection under multivariable Cox analysis (P = 0.008). Most pediatric patients did not have RSB‐detected rejection beyond 2 years post‐HT, and the majority of those who did were older at time of HT. Indiscriminate long‐term RSB in pediatric heart transplant should be reconsidered given the low rate of detected rejection.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/147767/1/petr13330_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/147767/2/petr13330.pd

Monitoring of SARS-CoV-2 in wastewater: what normalisation for improved understanding of epidemic trends?

SARS-CoV-2 RNA quantification in wastewater has emerged as a relevant additional means to monitor the COVID-19 pandemic. However, the concentration can be affected by black water dilution factors or movements of the sewer shed population, leading to misinterpretation of measurement results. The aim of this study was to evaluate the performance of different indicators to accurately interpret SARS-CoV-2 in wastewater. Weekly/bi-weekly measurements from three cities in France were analysed from February to September 2021. The concentrations of SARS-CoV-2 gene copies were normalised to the faecal-contributing population using simple sewage component indicators. To reduce the measurement error, a composite index was created to combine simultaneously the information carried by the simple indicators. The results showed that the regularity (mean absolute difference between observation and the smoothed curve) of the simple indicators substantially varied across sampling points. The composite index consistently showed better regularity compared to the other indicators and was associated to the lowest variation in correlation coefficient across sampling points. These findings suggest the recommendation for the use of a composite index in wastewater-based epidemiology to compensate for variability in measurement results

18-Month Effectiveness of Short-Course Antiretroviral Regimens Combined with Alternatives to Breastfeeding to Prevent HIV Mother-to-Child Transmission

OBJECTIVE: We assessed the 18-month effectiveness of short-course (sc) antiretroviral peripartum regimens combined with alternatives to prolonged breastfeeding to prevent mother-to-child transmission (MTCT) of HIV-1 in Abidjan, Côte d'Ivoire. METHODOLOGY: HIV-1 infected pregnant women received from >/=32-36 weeks of gestation scZidovudine (ZDV)+/-Lamivudine (3TC)+single-dose Nevirapine (sdNVP) at delivery within the ANRS 1201/1202 DITRAME-Plus cohort (2001-2003). Neonates received a sdNVP+7-day ZDV prophylaxis. Two infant-feeding interventions were systematically offered free of charge: formula-feeding or exclusive shortened breastfeeding with early cessation from four months. The reference group was the ANRS 049a DITRAME cohort (1994-2000) exposed to scZDV from 36 weeks, then to prolonged breastfeeding. Pediatric HIV infection was defined by a positive plasma HIV-1 RNA at any age, or if aged >/=18 months, a positive HIV-1 serology. Turnbull estimates of cumulative transmission risks (CTR) and effectiveness (HIV-free survival) were compared by exposure group using a Cox model. FINDINGS: Among 926 live-born children enrolled, 107 (11.6%) were HIV-infected at 18 months. CTRs were 22.3% (95% confidence interval[CI]:16-30%) in the 238 ZDV long-term breastfed reference group, 15.9% (CI:10-27%) in the 169 ZDV+sdNVP shortened breastfed group; 9.4% (CI:6-14%) in the 195 ZDV+sdNVP formula-fed group; 6.8% (CI:4-11%) in the 198 ZDV+3TC+sdNVP shortened breastfed group, and 5.6% (CI:2-10%) in the 126 ZDV+3TC+sdNVP formula-fed group. Each combination had a significantly higher effectiveness than the ZDV long-term breastfed group except for ZDV+sdNVP shortened breastfed children, ranging from 51% (CI:20-70%) for ZDV+sdNVP formula fed children to 63% (CI:40-80%) for ZDV+3TC+NVPsd shortened breastfed children, after adjustment for maternal eligibility for antiretroviral therapy (ART), home delivery and low birth-weight. Substantial MTCT risk reductions are reachable in Africa, even in short-term breastfed children. The two sc antiretroviral combinations associated to any of the two infant feeding interventions, formula-feeding and shortened breastfeeding, reduce significantly MTCT with long-term benefit until age 18 months and without increasing mortality

Estimation de l'incidence de l'infection par le VIH en Afrique (application à la Côte d'Ivoire)

L'épidémie de VIH/SIDA se répand de manière dramatique en Afrique subsaharienne. Connaître l'incidence de l'infection par le VIH (vitesse de production des nouvelles infections) est un enjeu majeur pour la surveillance de cette épidémie. L'objectif de ce mémoire est de proposer des outils performants pour estimer l'incidence du VIH dans le contexte africain. Nous développons une méthode pour l'estimer chez les femmes à partir de données de prévalence chez les femmes enceintes. Nous étudions également la performance sur des sujets africains des tests de détection d'infections récentes (TIR) développés dans des pays occidentaux. Nous montrons que notre méthode d'estimation permet d'estimer avec précision les tendances de l'incidence au cours du temps et par classe d'âge, mais qu'elle est moins performante pour les valeurs quantitatives. Nous montrons également que les TIRs ne sont pas adaptés pour estimer l'incidence du VIH en Afrique, et donnons des pistes de recherche pour les améliorer.The HIV/AIDS epidemic have been fast growing for more than two decades in Africa. It is a major issue for HIV surveillance to know the incidence of HIV infection (speed of acquisition of new infections). The objective of this work is to propose effective methods to estimate HIV incidence in the African context. We developped a method for estimating HIV incidence among women using serial HIV prevalence data from pregnant women, and studied the performance on African subjects of tests recent infections (TRI) developed among Caucasian. We showed that our method estimated correctly incidence time trends by age groups, but that quantitative values have to be interpreted with caution. We also showed that TRIs were not adapted to estimate HIV incidence in Africa and we gave several research leads to improve it.BORDEAUX2-BU Santé (330632101) / SudocSudocFranceF

Estimation de l'incidence de l'infection par le VIH en Afrique (application à la Côte d'Ivoire)

L'épidémie de VIH/SIDA se répand de manière dramatique en Afrique subsaharienne. Connaître l'incidence de l'infection par le VIH (vitesse de production des nouvelles infections) est un enjeu majeur pour la surveillance de cette épidémie. L'objectif de ce mémoire est de proposer des outils performants pour estimer l'incidence du VIH dans le contexte africain. Nous développons une méthode pour l'estimer chez les femmes à partir de données de prévalence chez les femmes enceintes. Nous étudions également la performance sur des sujets africains des tests de détection d'infections récentes (TIR) développés dans des pays occidentaux. Nous montrons que notre méthode d'estimation permet d'estimer avec précision les tendances de l'incidence au cours du temps et par classe d'âge, mais qu'elle est moins performante pour les valeurs quantitatives. Nous montrons également que les TIRs ne sont pas adaptés pour estimer l'incidence du VIH en Afrique, et donnons des pistes de recherche pour les améliorer.The HIV/AIDS epidemic have been fast growing for more than two decades in Africa. It is a major issue for HIV surveillance to know the incidence of HIV infection (speed of acquisition of new infections). The objective of this work is to propose effective methods to estimate HIV incidence in the African context. We developped a method for estimating HIV incidence among women using serial HIV prevalence data from pregnant women, and studied the performance on African subjects of tests recent infections (TRI) developed among Caucasian. We showed that our method estimated correctly incidence time trends by age groups, but that quantitative values have to be interpreted with caution. We also showed that TRIs were not adapted to estimate HIV incidence in Africa and we gave several research leads to improve it.BORDEAUX2-BU Santé (330632101) / SudocSudocFranceF

Lewis antigen expression and other pathogenic factors in the presence of atrophic chronic gastritis in a european population

To study the relationship between Helicobacter pylori cagA and vacA status and the expression of Lewis (Le) antigens and between these characteristics and atrophic chronic gastritis (ACG), H. pylori infection was assessed by culture and by histologic and serologic tests, cagA and vacA were assessed by a polymerase chain reaction-based reverse hybridization assay, and bacterial Le expression was assessed by immunoblotting. ACG was any form of antral or fundic atrophy with or without intestinal metaplasia. Of the 215 isolates, 64% were cagA(+) and 100% were vacA(+) (s1m1, 42%; s1m2, 29%; s2m2, 29%; and s2m1, 0). Le typing of 155 isolates showed that 6 (4%) were Le(x), 31 (20%) were Le(y), 87 (56%) were Le(x,y), and 31 (20%) were neither Le(x) nor Le(y). Two main clusters of isolates were identified by multiple correspondence analysis: s1a/m1/cagA(+)/Le(x)+/Le(y) +( n = 44; 29.7%) and s2/m2a/cagA(-)/Le(y)+or Le(x)-/Le(y)- (n = 29; 19.7%). Among patients with ACG, 54% of their isolates were from cluster s1m1/cagA(+)/Le(x)+/Le(y)+, which was associated with the presence of ACG (odds ratio, 7.4; 95% confidence interval, 1.5-37.0)