Efficient preconditioned stochastic gradient descent for estimation in latent variable models

Latent variable models are powerful tools for modeling complex phenomena involving in particular partially observed data, unobserved variables or underlying complex unknown structures. Inference is often difficult due to the latent structure of the model. To deal with parameter estimation in the presence of latent variables, well-known efficient methods exist, such as gradient-based and EM-type algorithms, but with practical and theoretical limitations. In this paper, we propose as an alternative for parameter estimation an efficient preconditioned stochastic gradient algorithm. Our method includes a preconditioning step based on a positive definite Fisher information matrix estimate. We prove convergence results for the proposed algorithm under mild assumptions for very general latent variables models. We illustrate through relevant simulations the performance of the proposed methodology in a nonlinear mixed effects model and in a stochastic block model

Www.airqualitynow.eu, a common website and air quality indices to compare cities across europe

International audienceAir quality is a public concern. This is partly due to the "right to know" principle embodied in European legislation. Despite this common legislation, the way air quality is being interpreted and communicated differs considerably. For specialists raw monitoring data for Europe are available but these are not usable by the general public. Easy to understand and internationally comparable air quality information from one city to another is scarce: there are almost as many air quality indices as air quality monitoring networks. The CITEAIR II project (Common information to European Air, INTERREG IVc) facilitates the comparison of urban air quality in near real-time by introducing common air quality indices at hourly, daily and annual scales and by developing a forecast for those indices for D+0 and D+1.The implementation was based on a common website www.airqualitynow.eu using readily available simple IT-solutions. This paper describes those tools which both aimed at presenting the air quality of the participating cities in a comparable way and not to replace more targeted local information. Their added value is to provide, for the first time, a European and comparable picture of the air quality in near real-time easily accessible through a common platform and presentation of the results. The website is designed to receive and display data from any city wanting to join. The main part is dedicated to compare the cities index values using different time scales (hourly, daily or annual) and two types of exposure thanks to a background and a traffic index. In addition, space is offered to cities for presenting themselves according to a common template, providing background information on their specific air pollution situation and associated reduction measures. Participating is easy: cities upload their data through ftp and the indices calculations are automatically made. The website provides a dynamic picture of the air quality and is updated each hour enticing viewers to make repeated visits. However, participation with only a daily update or with yearly data is feasible as wel

Nivolumab and brentuximab vedotin with or without bendamustine for R/R Hodgkin lymphoma in children, adolescents, and young adults

Children, adolescents, and young adults (CAYA) with relapsed/refractory (R/R) classic Hodgkin lymphoma (cHL) without complete metabolic response (CMR) before autologous hematopoietic cell transplantation (auto-HCT) have poor survival outcomes. CheckMate 744, a phase 2 study for CAYA (aged 5-30 years) with R/R cHL, evaluated a risk-stratified, response-adapted approach with nivolumab plus brentuximab vedotin (BV) followed by BV plus bendamustine for patients with suboptimal response. Risk stratification was primarily based on time to relapse, prior treatment, and presence of B symptoms. We present the primary analysis of the standard-risk cohort. Data from the low-risk cohort are reported separately. Patients received 4 induction cycles with nivolumab plus BV; those without CMR (Deauville score &gt;3, Lugano 2014) received BV plus bendamustine intensification. Patients with CMR after induction or intensification proceeded to consolidation (high-dose chemotherapy/auto-HCT per protocol). Primary end point was CMR any time before consolidation. Forty-four patients were treated. Median age was 16 years. At a minimum follow-up of 15.6 months, 43 patients received 4 induction cycles (1 discontinued), 11 of whom received intensification; 32 proceeded to consolidation. CMR rate was 59% after induction with nivolumab plus BV and 94% any time before consolidation (nivolumab plus BV ± BV plus bendamustine). One-year progression-free survival rate was 91%. During induction, 18% of patients experienced grade 3/4 treatment-related adverse events. This risk-stratified, response-adapted salvage strategy had high CMR rates with limited toxicities in CAYA with R/R cHL. Most patients did not require additional chemotherapy (bendamustine intensification). Additional follow-up is needed to confirm durability of disease control. This trial was registered at www.clinicaltrials.gov as #NCT02927769.</p

RNA modifications detection by comparative Nanopore direct RNA sequencing.

RNA molecules undergo a vast array of chemical post-transcriptional modifications (PTMs) that can affect their structure and interaction properties. In recent years, a growing number of PTMs have been successfully mapped to the transcriptome using experimental approaches relying on high-throughput sequencing. Oxford Nanopore direct-RNA sequencing has been shown to be sensitive to RNA modifications. We developed and validated Nanocompore, a robust analytical framework that identifies modifications from these data. Our strategy compares an RNA sample of interest against a non-modified control sample, not requiring a training set and allowing the use of replicates. We show that Nanocompore can detect different RNA modifications with position accuracy in vitro, and we apply it to profile m6A in vivo in yeast and human RNAs, as well as in targeted non-coding RNAs. We confirm our results with orthogonal methods and provide novel insights on the co-occurrence of multiple modified residues on individual RNA molecules.The Kouzarides laboratory is supported by Cancer Research UK (grant reference RG72100) and core support from the Wellcome Trust (core grant reference WT203144) and Cancer Research UK (grant reference C6946/A24843). PPA was supported by a Borysiewicz Biomedical Sciences postdoctoral fellowship (University of Cambridge) and AL by a COFUND Marie Skłodowska-Curie Actions postdoctoral fellowship (EMBL). FW and TS are supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK (FC001203), the UK Medical Research Council (FC001203), and the Wellcome Trust (FC001203). IB and V Miano are supported by Cancer Research UK (grant reference RG86786) and by the Joseph Mitchell Fund

A school-based physical activity program to improve health and fitness in children aged 6–13 years ("Kinder-Sportstudie KISS"): study design of a randomized controlled trial [ISRCTN15360785]

BACKGROUND: Childhood obesity is the result of a long lasting imbalance between energy intake and energy expenditure. A major contributing factor is physical inactivity which is closely linked to bone health, cardiovascular disease risk, fitness and psychological factors. The school seems to provide an excellent setting to enhance levels of physical activity (PA). However, there is insufficient data from previous school-based intervention trials on how to enhance overall PA. It is also unknown whether an intervention aimed at increasing PA is effective in improving the children's health. The purpose of this paper is to outline the design of a school-based randomized, controlled trial (RCT) aiming to increase overall PA and to improve fitness and health in 6- to 13-year-old children. METHODS/DESIGN: 15 schools were randomized to the intervention (n = 9) or the control (n = 6) group, stratified by geographic region (urban vs. rural) and by age (1(st )and 5(th )grade). Participation was given for all children in the intervention group since in this group the intervention was part of the normal school curriculum. The intervention during one academic year consisted of: 1. two additional physical education classes per week given by trained physical education teachers adding up to a total of five PA classes per week, 2. short PA breaks (2–5 min each) during academic lessons, 3. PA home work, and 4. adaptation of recreational areas around the school. All children underwent anthropometric measurements, blood pressure assessment, fitness testing, measurement of PA and they filled out questionnaires. At least 70% of all children agreed to blood sampling and measurements of body composition and bone mineral measurements by dual energy x-ray absorptiometry. The primary endpoints of the study after one year were an increase in total PA by accelerometry, an increase in aerobic fitness measured by the 20 m shuttle run, a decrease in percent body fat derived from skinfold measurements and an increase in quality of life as assessed by the child health questionnaire in the intervention group compared to the control group. Secondary outcomes were overall fitness, differences in body composition including body fat distribution, cardiovascular risk factors, psychosocial health, bone mineral content and density of femur, lumbar spine and total body and food intake. DISCUSSION: Our preliminary data suggest that the children were representative of Swiss children with respect to sex, socio-demographic status, and body mass index. Short-term results can be expected by the beginning of 2007. We hypothesized that our intervention will lead to an increase in PA, fitness and overall health. Based on our data, we aim to provide important information regarding the influence of such an intervention on these outcome measures in school-aged children and to provide nationwide guidelines to improve PA in children

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Extracorporeal Membrane Oxygenation for Severe Acute Respiratory Distress Syndrome associated with COVID-19: An Emulated Target Trial Analysis.

RATIONALE: Whether COVID patients may benefit from extracorporeal membrane oxygenation (ECMO) compared with conventional invasive mechanical ventilation (IMV) remains unknown. OBJECTIVES: To estimate the effect of ECMO on 90-Day mortality vs IMV only Methods: Among 4,244 critically ill adult patients with COVID-19 included in a multicenter cohort study, we emulated a target trial comparing the treatment strategies of initiating ECMO vs. no ECMO within 7 days of IMV in patients with severe acute respiratory distress syndrome (PaO2/FiO2 <80 or PaCO2 ≥60 mmHg). We controlled for confounding using a multivariable Cox model based on predefined variables. MAIN RESULTS: 1,235 patients met the full eligibility criteria for the emulated trial, among whom 164 patients initiated ECMO. The ECMO strategy had a higher survival probability at Day-7 from the onset of eligibility criteria (87% vs 83%, risk difference: 4%, 95% CI 0;9%) which decreased during follow-up (survival at Day-90: 63% vs 65%, risk difference: -2%, 95% CI -10;5%). However, ECMO was associated with higher survival when performed in high-volume ECMO centers or in regions where a specific ECMO network organization was set up to handle high demand, and when initiated within the first 4 days of MV and in profoundly hypoxemic patients. CONCLUSIONS: In an emulated trial based on a nationwide COVID-19 cohort, we found differential survival over time of an ECMO compared with a no-ECMO strategy. However, ECMO was consistently associated with better outcomes when performed in high-volume centers and in regions with ECMO capacities specifically organized to handle high demand. This article is open access and distributed under the terms of the Creative Commons Attribution Non-Commercial No Derivatives License 4.0 (http://creativecommons.org/licenses/by-nc-nd/4.0/)

Ototoxicité des aminosides et prédisposition génétique (influence des mutations de l'ADN mitochondrial)

PARIS-BIUP (751062107) / SudocSudocFranceF

Experiences of alcohol drinking among Swedish youths with type 1 diabetes

Background: Alcohol consumption in Europe and North America is greatest in 18-25-year-olds. This behaviour can be seen as a transitional stage from childhood to adulthood, where consuming alcohol is perceived as a typical feature of adult behaviour. Youths often start to consume alcohol when they are 14-15 years of age, and one in five youngsters around 15 years of age report binge drinking. Studies of alcohol consumption among youths with type 1 diabetes have not been undertaken but it is well known that, in these people, alcohol drinking can cause hypoglycaemia and worsen the capacity to feel and interpret the symptoms of hypoglycaemia. Aim: The overall aim was to explore experiences of alcohol consumption among youths with type 1 diabetes. Another objective was to identify strategies as to how they deal with situations when they drink alcohol. Methods: Semistructured interviews with ten 18-year-old youths with type 1 diabetes, using Burnard's content analysis method. Results: This study illustrates that informants strive for security, independence and control. Frequency of binge drinking did not seem to differ from rates in other teenagers. Informants exposed themselves to considerable risks and many had met with serious incidents. Moreover, the result exemplifies how symptoms of diabetic ketoacidosis (such as nausea and vomiting) can easily be misinterpreted as a hangover or gastroenteritis. Informants lacked age-appropriate knowledge about diabetes and the effects of alcohol, but had tested things out themselves; some involved their friends in their diabetes treatment. Moreover, three strategies occurred with the aim of normalisation and security: the 'low-consumption' strategy, the 'ambitious' strategy and the 'rather-high-than-dead' strategy. Fear of hypoglycaemia was a significant concern and the consequence was poor diabetes control. Conclusion: To increase youths' independence and security, the diabetes care team should provide adequate and relevant information about alcohol. Treatment plans might contain practical steps such as advice about responsible alcohol intake and adjustments of insulin and meals, and could also encourage young people with diabetes to carry diabetes ID and inform friends about hypoglycaemia (and how to handle situations involving alcohol).