Migrating a Well-Established Longitudinal Cohort Database From Oracle SQL to Research Electronic Data Entry (REDCap): Data Management Research and Design Study

BACKGROUND: Providing user-friendly electronic data collection tools for large multicenter studies is key for obtaining high-quality research data. Research Electronic Data Capture (REDCap) is a software solution developed for setting up research databases with integrated graphical user interfaces for electronic data entry. The Swiss Mother and Child HIV Cohort Study (MoCHiV) is a longitudinal cohort study with around 2 million data entries dating back to the early 1980s. Until 2022, data collection in MoCHiV was paper-based. OBJECTIVE: The objective of this study was to provide a user-friendly graphical interface for electronic data entry for physicians and study nurses reporting MoCHiV data. METHODS: MoCHiV collects information on obstetric events among women living with HIV and children born to mothers living with HIV. Until 2022, MoCHiV data were stored in an Oracle SQL relational database. In this project, R and REDCap were used to develop an electronic data entry platform for MoCHiV with migration of already collected data. RESULTS: The key steps for providing an electronic data entry option for MoCHiV were (1) design, (2) data cleaning and formatting, (3) migration and compliance, and (4) add-on features. In the first step, the database structure was defined in REDCap, including the specification of primary and foreign keys, definition of study variables, and the hierarchy of questions (termed "branching logic"). In the second step, data stored in Oracle were cleaned and formatted to adhere to the defined database structure. Systematic data checks ensured compliance to all branching logic and levels of categorical variables. REDCap-specific variables and numbering of repeated events for enabling a relational data structure in REDCap were generated using R. In the third step, data were imported to REDCap and then systematically compared to the original data. In the last step, add-on features, such as data access groups, redirections, and summary reports, were integrated to facilitate data entry in the multicenter MoCHiV study. CONCLUSIONS: By combining different software tools-Oracle SQL, R, and REDCap-and building a systematic pipeline for data cleaning, formatting, and comparing, we were able to migrate a multicenter longitudinal cohort study from Oracle SQL to REDCap. REDCap offers a flexible way for developing customized study designs, even in the case of longitudinal studies with different study arms (ie, obstetric events, women, and mother-child pairs). However, REDCap does not offer built-in tools for preprocessing large data sets before data import. Additional software is needed (eg, R) for data formatting and cleaning to achieve the predefined REDCap data structure

Cohort profile: the Swiss Mother and Child HIV Cohort Study (MoCHiV)

Purpose: Prospective, multicentric observational cohort study in Switzerland investigating measures to prevent mother-to-child transmission in pregnant women with HIV (WWH) and assessing health and development of their exposed children as well as of children with HIV (CWH) in general. Participants: Between January 1986 and December 2022, a total of 1446 mother–child pairs were enrolled. During the same period, the study also registered 187 CWH and 521 HIV-exposed but uninfected children (HEU), for whom detailed maternal information was not available. Consequently, the cohort comprises a total of 2154 children. Findings to date: During these 37 years, research by the Swiss Mother and Child HIV Cohort Study (MoCHiV) and its international collaborators has strongly influenced the prevention of vertical transmission of HIV (eg, introduction and discontinuation of elective caesarean section, neonatal postexposure prophylaxis and breastfeeding). Contributions have also been made to the management of diagnostics (eg, p24 antigen assay) and the effects of antiretroviral treatment (eg, prematurity, growth) in HEU and CWH. Future plans: Most children present within the cohort are now HEU, highlighting the need to investigate other vertically transmitted pathogens such as hepatitis B and C viruses, cytomegalovirus orTreponema pallidum. In addition, analyses are planned on the longitudinal health status of CWH (eg, resistance and prolonged exposure to antiretroviral therapy), on social aspects including stigma in CWH and HEU, and on interventions to further optimise antenatal and postpartum care in WWH

Hyperoxemia and excess oxygen use in early acute respiratory distress syndrome: insights from the LUNG SAFE study

Contains fulltext : 218568.pdf (publisher's version ) (Open Access)BACKGROUND: Concerns exist regarding the prevalence and impact of unnecessary oxygen use in patients with acute respiratory distress syndrome (ARDS). We examined this issue in patients with ARDS enrolled in the Large observational study to UNderstand the Global impact of Severe Acute respiratory FailurE (LUNG SAFE) study. METHODS: In this secondary analysis of the LUNG SAFE study, we wished to determine the prevalence and the outcomes associated with hyperoxemia on day 1, sustained hyperoxemia, and excessive oxygen use in patients with early ARDS. Patients who fulfilled criteria of ARDS on day 1 and day 2 of acute hypoxemic respiratory failure were categorized based on the presence of hyperoxemia (PaO2 > 100 mmHg) on day 1, sustained (i.e., present on day 1 and day 2) hyperoxemia, or excessive oxygen use (FIO2 >/= 0.60 during hyperoxemia). RESULTS: Of 2005 patients that met the inclusion criteria, 131 (6.5%) were hypoxemic (PaO2 < 55 mmHg), 607 (30%) had hyperoxemia on day 1, and 250 (12%) had sustained hyperoxemia. Excess FIO2 use occurred in 400 (66%) out of 607 patients with hyperoxemia. Excess FIO2 use decreased from day 1 to day 2 of ARDS, with most hyperoxemic patients on day 2 receiving relatively low FIO2. Multivariate analyses found no independent relationship between day 1 hyperoxemia, sustained hyperoxemia, or excess FIO2 use and adverse clinical outcomes. Mortality was 42% in patients with excess FIO2 use, compared to 39% in a propensity-matched sample of normoxemic (PaO2 55-100 mmHg) patients (P = 0.47). CONCLUSIONS: Hyperoxemia and excess oxygen use are both prevalent in early ARDS but are most often non-sustained. No relationship was found between hyperoxemia or excessive oxygen use and patient outcome in this cohort. TRIAL REGISTRATION: LUNG-SAFE is registered with ClinicalTrials.gov, NCT02010073

Mortality and pulmonary complications in patients undergoing surgery with perioperative SARS-CoV-2 infection: an international cohort study

Background: The impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on postoperative recovery needs to be understood to inform clinical decision making during and after the COVID-19 pandemic. This study reports 30-day mortality and pulmonary complication rates in patients with perioperative SARS-CoV-2 infection. Methods: This international, multicentre, cohort study at 235 hospitals in 24 countries included all patients undergoing surgery who had SARS-CoV-2 infection confirmed within 7 days before or 30 days after surgery. The primary outcome measure was 30-day postoperative mortality and was assessed in all enrolled patients. The main secondary outcome measure was pulmonary complications, defined as pneumonia, acute respiratory distress syndrome, or unexpected postoperative ventilation. Findings: This analysis includes 1128 patients who had surgery between Jan 1 and March 31, 2020, of whom 835 (74·0%) had emergency surgery and 280 (24·8%) had elective surgery. SARS-CoV-2 infection was confirmed preoperatively in 294 (26·1%) patients. 30-day mortality was 23·8% (268 of 1128). Pulmonary complications occurred in 577 (51·2%) of 1128 patients; 30-day mortality in these patients was 38·0% (219 of 577), accounting for 81·7% (219 of 268) of all deaths. In adjusted analyses, 30-day mortality was associated with male sex (odds ratio 1·75 [95% CI 1·28–2·40], p\textless0·0001), age 70 years or older versus younger than 70 years (2·30 [1·65–3·22], p\textless0·0001), American Society of Anesthesiologists grades 3–5 versus grades 1–2 (2·35 [1·57–3·53], p\textless0·0001), malignant versus benign or obstetric diagnosis (1·55 [1·01–2·39], p=0·046), emergency versus elective surgery (1·67 [1·06–2·63], p=0·026), and major versus minor surgery (1·52 [1·01–2·31], p=0·047). Interpretation: Postoperative pulmonary complications occur in half of patients with perioperative SARS-CoV-2 infection and are associated with high mortality. Thresholds for surgery during the COVID-19 pandemic should be higher than during normal practice, particularly in men aged 70 years and older. Consideration should be given for postponing non-urgent procedures and promoting non-operative treatment to delay or avoid the need for surgery. Funding: National Institute for Health Research (NIHR), Association of Coloproctology of Great Britain and Ireland, Bowel and Cancer Research, Bowel Disease Research Foundation, Association of Upper Gastrointestinal Surgeons, British Association of Surgical Oncology, British Gynaecological Cancer Society, European Society of Coloproctology, NIHR Academy, Sarcoma UK, Vascular Society for Great Britain and Ireland, and Yorkshire Cancer Research

Decrease of condom use in heterosexual couples and its impact on pregnancy rates: the Swiss HIV Cohort Study (SHCS)

INTRODUCTION Following the 'Swiss statement' in 2008 it became an option to omit the use of condoms in serodiscordant couples and to conceive naturally. We analysed its impact on condom use and pregnancy events. METHODS In all, 3023 women (aged 18-49 years) participating in the Swiss HIV Cohort Study were included. Observation time was divided into pre- and post-Swiss statement phases (July 2005-December 2008 and January 2009-December 2019). We used descriptive statistics, Poisson interrupted time series analysis for pregnancy incidence, and logistic regression to identify predictors of live births, spontaneous and induced abortions. RESULTS Condomless sex in sexually active women increased from 25% in 2005 to 75% in 2019, while pregnancy incidence did not. Women after 2008 experienced higher spontaneous abortion rates (12.1% vs. 17.2%, p = 0.02) while induced abortion and live birth rates did not change significantly. Spontaneous abortions were more common in older women [adjusted odds ratio (aOR) = 1.4, 95% CI: 1.2-1.7, p < 0.001], in women consuming alcohol (aOR = 2.8, 95% CI: 1.9-4.1, p < 0.001) and in those with non-suppressed viral load (aOR = 0.2, 95% CI: 0.1-0.4, p ≤ 0.001). Induced abortions were more likely in women with depression (aOR = 3.4, 95% CI: 1.8-6.3, p < 0.001) and non-suppressed viral load (aOR = 0.3, 95% CI: 0.2-0.7, p = 0.003). CONCLUSIONS The publication of the Swiss statement resulted in more condomless sex in heterosexual women, but this did not result in a higher incidence of pregnancy. Maternal age and spontaneous abortion rates increased over time, while induced abortion rates were not significantly affected. Women living with HIV in Switzerland have an unmet need regarding family planning counselling

Decrease of condom use in heterosexual couples and its impact on pregnancy rates: the Swiss HIV Cohort Study (SHCS)

Following the 'Swiss statement' in 2008 it became an option to omit the use of condoms in serodiscordant couples and to conceive naturally. We analysed its impact on condom use and pregnancy events. In all, 3023 women (aged 18-49 years) participating in the Swiss HIV Cohort Study were included. Observation time was divided into pre- and post-Swiss statement phases (July 2005-December 2008 and January 2009-December 2019). We used descriptive statistics, Poisson interrupted time series analysis for pregnancy incidence, and logistic regression to identify predictors of live births, spontaneous and induced abortions. Condomless sex in sexually active women increased from 25% in 2005 to 75% in 2019, while pregnancy incidence did not. Women after 2008 experienced higher spontaneous abortion rates (12.1% vs. 17.2%, p = 0.02) while induced abortion and live birth rates did not change significantly. Spontaneous abortions were more common in older women [adjusted odds ratio (aOR) = 1.4, 95% CI: 1.2-1.7, p &lt; 0.001], in women consuming alcohol (aOR = 2.8, 95% CI: 1.9-4.1, p &lt; 0.001) and in those with non-suppressed viral load (aOR = 0.2, 95% CI: 0.1-0.4, p ≤ 0.001). Induced abortions were more likely in women with depression (aOR = 3.4, 95% CI: 1.8-6.3, p &lt; 0.001) and non-suppressed viral load (aOR = 0.3, 95% CI: 0.2-0.7, p = 0.003). The publication of the Swiss statement resulted in more condomless sex in heterosexual women, but this did not result in a higher incidence of pregnancy. Maternal age and spontaneous abortion rates increased over time, while induced abortion rates were not significantly affected. Women living with HIV in Switzerland have an unmet need regarding family planning counselling

Correction to: Potentially modifiable factors contributing to outcome from acute respiratory distress syndrome: the LUNG SAFE study (Intensive Care Medicine, (2016), 42, 12, (1865-1876), 10.1007/s00134-016-4571-5)

The members of the LUNG SAFE Investigators and the ESICM Trials Group were provided in such a way that they could not be indexed as collaborators on PubMed. The publisher apologizes for this error