COMPARATIVE STUDY FOR MELANOMA SEGMENTATION IN SKIN LESION IMAGES

Melanoma is the leading cause of fatalities among skin can-cers and the discovery of the pathology in the early stagesis essential to increase the chances of cure. Computationalmethods through medical imaging are being developed tofacilitate the detection of melanoma. To interpret informa-tion in these images eciently, it is necessary to isolate theaected region. In our research, a comparison was made be-tween segmentation techniques, rstly a method based onthe Otsu algorithm, secondly the K-means clustering algo-rithm and nally,the U-net deep learning was developed.The tests performed on the PH2 images base had promisingresults, especially U-net

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London

Surgical site infection after gastrointestinal surgery in high-income, middle-income, and low-income countries: a prospective, international, multicentre cohort study

Background: Surgical site infection (SSI) is one of the most common infections associated with health care, but its importance as a global health priority is not fully understood. We quantified the burden of SSI after gastrointestinal surgery in countries in all parts of the world. Methods: This international, prospective, multicentre cohort study included consecutive patients undergoing elective or emergency gastrointestinal resection within 2-week time periods at any health-care facility in any country. Countries with participating centres were stratified into high-income, middle-income, and low-income groups according to the UN's Human Development Index (HDI). Data variables from the GlobalSurg 1 study and other studies that have been found to affect the likelihood of SSI were entered into risk adjustment models. The primary outcome measure was the 30-day SSI incidence (defined by US Centers for Disease Control and Prevention criteria for superficial and deep incisional SSI). Relationships with explanatory variables were examined using Bayesian multilevel logistic regression models. This trial is registered with ClinicalTrials.gov, number NCT02662231. Findings: Between Jan 4, 2016, and July 31, 2016, 13 265 records were submitted for analysis. 12 539 patients from 343 hospitals in 66 countries were included. 7339 (58·5%) patient were from high-HDI countries (193 hospitals in 30 countries), 3918 (31·2%) patients were from middle-HDI countries (82 hospitals in 18 countries), and 1282 (10·2%) patients were from low-HDI countries (68 hospitals in 18 countries). In total, 1538 (12·3%) patients had SSI within 30 days of surgery. The incidence of SSI varied between countries with high (691 [9·4%] of 7339 patients), middle (549 [14·0%] of 3918 patients), and low (298 [23·2%] of 1282) HDI (p < 0·001). The highest SSI incidence in each HDI group was after dirty surgery (102 [17·8%] of 574 patients in high-HDI countries; 74 [31·4%] of 236 patients in middle-HDI countries; 72 [39·8%] of 181 patients in low-HDI countries). Following risk factor adjustment, patients in low-HDI countries were at greatest risk of SSI (adjusted odds ratio 1·60, 95% credible interval 1·05–2·37; p=0·030). 132 (21·6%) of 610 patients with an SSI and a microbiology culture result had an infection that was resistant to the prophylactic antibiotic used. Resistant infections were detected in 49 (16·6%) of 295 patients in high-HDI countries, in 37 (19·8%) of 187 patients in middle-HDI countries, and in 46 (35·9%) of 128 patients in low-HDI countries (p < 0·001). Interpretation: Countries with a low HDI carry a disproportionately greater burden of SSI than countries with a middle or high HDI and might have higher rates of antibiotic resistance. In view of WHO recommendations on SSI prevention that highlight the absence of high-quality interventional research, urgent, pragmatic, randomised trials based in LMICs are needed to assess measures aiming to reduce this preventable complication

Aperçu du répertoire génomique des bactéries intracellulaires à l'aide de la génomique comparative

La première partie de ma thèse est une revue donnant un aperçu du répertoire génomique des bactéries intracellulaires et de leurs symbiotes. L'objectif de cette étude est d'explorer le processus permettant aux bactéries intracellulaires d'acquérir leur mode de vie spécifique. Nous avons commencé par examiner les données à propos de l'existence ancienne de bactéries intracellulaires, leur adaptation à leur hôte et les différences entre sympatrie et allopatrie. Une comparaison du contenu génomique de plusieurs bactéries avec différents modes de vie a révélé la capacité des bactéries à échanger des gènes à des degrés différents, en fonction de l'écosystème. La deuxième partie de ma thèse porte sur la séquence du génome de la souche Diplorickettsia massiliensis 20B qui est une bactérie intracellulaire obligatoire à Gram négatif isolée à partir des tiques de Slovaquie Ixodes ricinus. Dans ma troisième et dernière partie, nous exploré le répertoire du génome de Diplorickettsia massiliensis en le comparant aux génomes de bactéries phylogénétiquement très proches de Diplorickettsia massiliensis, issues de différentes niches. Ceci a permis de révélé son mode de vie allopatrique. Dans cette étude, nous avons comparé les caractéristiques du génome de Diplorickettsia massiliensis avec vingt-neuf espèces séquencées de Gammaproteobacteria (Legionella, Coxiella burnetii, Francisella tularensis et Rickettsiella grylli) en utilisant l'approche pangénomique multi-genre. Ce travail de thèse fournit des données originales et permet d’apporter plus de lumière sur la diversité des bactéries intracellulaires.The initial purpose of my thesis is to understand with the help of comparative genomics, genomic variations based on coexistence, by examining data on the ancient existence of intracellular bacteria, their host adaptation and the differences between sympatry and allopatry. The first part of my thesis is a review giving insight into intracellular bacterial genome repertoire and symbionts. The goal of this review is to explore how intracellular microbes acquire their specific lifestyle. Due to their different evolutionary trajectories, these bacteria have different genomic compositions. We reviewed data on the ancient existence of intracellular bacteria, their host adaptation and the differences between sympatry and allopatry. A comparison of the genomic contents of bacteria with certain lifestyles revealed the bacterial capacity to exchange genes to different extents, depending on the ecosystem. The second part of my thesis present about the genome sequence of Diplorickettsia massiliensis strain 20B which is an obligate intracellular, gram negative bacterium isolated from Ixodes ricinus ticks collected from Slovak. In the third part, we investigated the genome repertoire of Diplorickettsia massiliensis compared to closely related bacteria according to its niche, revealing its allopatric lifestyle. In this study, we compared the genomic features of Diplorickettsia massiliensis with twenty-nine sequenced Gammaproteobacteria species (Legionella strains, Coxiella burnetii strains, Francisella tularensis strains and Rickettsiella grylli) using multi-genus pangenomic approach. This thesis work provides original data and sheds light on intracellular bacterial diversity

Boolean analysis of the transcriptomic data to identify novel biomarkers of IVIG response

International audienceIntravenous immunoglobulin (IVIG) is used to treat several autoimmune and inflammatory diseases, but some patients are refractory to IVIG and require alternative treatments. Identifying a biomarker that could segregate IVIG responders from non-responders has been a subject of intense research. Unfortunately, previous transcriptomic studies aimed at addressing IVIG resistance have failed to predict a biomarker that could identify IVIG-nonresponders. Therefore, we used a novel data mining technique on the publicly available transcriptomic data of Kawasaki disease (KD) patients treated with IVIG to identify potential biomarkers of IVIG response. By studying the boolean patterns hidden in the expression profiles of KD patients undergoing IVIG therapy, we have identified new metabolic pathways implicated in IVIG resistance in KD. These pathways could be used as biomarkers to segregate IVIG nonresponders from responders prior to IVIG infusion. Also, boolean analysis of the transcriptomic data could be further extended to identify a universal biomarker that might predict IVIG response in other autoimmune diseases

Emerging extraction and diagnostic tools for detection of plant pathogens: Recent trends, challenges, and future scope

Plant pathogens are a serious threat to agriculture for long-term viability and cost loss of billions of dollars yearly. Many pathogens have been documented in the literature that infect a variety of crops. Nevertheless, new pathogens emerge and often result in disease outbreaks, leading to million-dollar losses. Currently, several diagnostic approaches with enhanced sensitivity and specificity for the identification of widespread and/or unknown plant pathogens are constantly being developed. Whereas the extensively used approaches for plant pathogen diagnostics are mostly serological and nucleic acid-based assays, many different nucleic acid-based approaches for amplifying target DNA/RNA have also emerged over time. However, these approaches lack precision, specificity, and rapidity, making them unsuitable for on-field analysis. As a result, there is a lot of interest arising in field-deployable point of care (POC) devices and artificial intelligence (AI)-assisted pathogens' detection accurately at an early stage within a minute. Similarly, development of a cell-lysis and purification-free DNA/RNA extraction process is also crucial for quick sample preparation for molecular diagnosis of plant pathogens at field level. In this review, we have discussed advanced tools that are trending not only to extract nucleic acids but also detect plant pathogens. We have also discussed critical challenges and future perspectives of disease diagnostic tools for plant pathogens' detection. In summary, advanced plant disease diagnostic tools can be helpful for routine monitoring of plant pathogens toward improving crop productivity and yield that can be used for improving the financial status of farmers.Web of Science2588185

Interplay between Liver X Receptor and Hypoxia Inducible Factor 1a Potentiates Interleukin-1b Production in Human Macrophages

International audienceLow-grade inflammation is constitutive of atherosclerosis, and anti-inflammatory therapy inhibiting interleukin-1β (IL-1β) reduces the rate of cardiovascular events. While cholesterol accumulation in atheroma plaque and macrophages is a major driver of the inflammatory process, the role of the LXR cholesterol sensors remains to be clarified. Murine and human macrophages were treated with LXR agonists for 48 h before Toll-like receptor (TLR) stimulation. Unexpectedly, we observe that, among other cytokines, LXR agonists selectively increase IL1B mRNA levels independently of TLR activation. This effect, restricted to human macrophages, is mediated by activation of HIF-1α through LXR. Accordingly, LXR agonists also potentiate other HIF-1α-dependent pathways, such as glycolysis. Treatment of human macrophages with carotid plaque homogenates also leads to induction of IL1B in an LXR-dependent manner. Thus, our work discloses a mechanism by which cholesterol and oxysterols trigger inflammation in atherosclerosis. This suggests perspectives to target IL-1β production in atherosclerotic patients