MOSAIX: a tool to built large mosaics from GALEX images

Large sky surveys are providing a huge amount of information for studies of the interstellar medium, the galactic structure or the cosmic web. Setting into a common frame information coming from different wavelengths, over large fields of view, is needed for this kind of research. GALEX is the only nearly all-sky survey at ultraviolet wavelengths and contains fundamental information for all types of studies. GALEX field of view is circular embedded in a squared matrix of 3840 x 3840 pixels. This fact makes it hard to get GALEX images properly overlapped with the existing astronomical tools such as Aladin or Montage. We developed our own software for this purpose. In this article, we describe this software and makes it available to the community.Comment: 7 pages, including 8 figures, accepted by Astrophysics and Space Scienc

X-ray emission from stellar jets by collision against high-density molecular clouds: an application to HH 248

We investigate the plausibility of detecting X-ray emission from a stellar jet that impacts against a dense molecular cloud. This scenario may be usual for classical T Tauri stars with jets in dense star-forming complexes. We first model the impact of a jet against a dense cloud by 2D axisymmetric hydrodynamic simulations, exploring different configurations of the ambient environment. Then, we compare our results with XMM-Newton observations of the Herbig-Haro object HH 248, where extended X-ray emission aligned with the optical knots is detected at the edge of the nearby IC 434 cloud. Our simulations show that a jet can produce plasma with temperatures up to 10 MK, consistent with production of X-ray emission, after impacting a dense cloud. We find that jets denser than the ambient medium but less dense than the cloud produce detectable X-ray emission only at the impact onto the cloud. From the exploration of the model parameter space, we constrain the physical conditions (jet density and velocity, cloud density) that reproduce well the intrinsic luminosity and emission measure of the X-ray source possibly associated with HH 248. Thus, we suggest that the extended X-ray source close to HH 248 corresponds to the jet impacting on a dense cloud.Comment: Accepted for publication in ApJ. (12 pages, 12 figures

Master regulators of FGFR2 signalling and breast cancer risk.

The fibroblast growth factor receptor 2 (FGFR2) locus has been consistently identified as a breast cancer risk locus in independent genome-wide association studies. However, the molecular mechanisms underlying FGFR2-mediated risk are still unknown. Using model systems we show that FGFR2-regulated genes are preferentially linked to breast cancer risk loci in expression quantitative trait loci analysis, supporting the concept that risk genes cluster in pathways. Using a network derived from 2,000 transcriptional profiles we identify SPDEF, ERα, FOXA1, GATA3 and PTTG1 as master regulators of fibroblast growth factor receptor 2 signalling, and show that ERα occupancy responds to fibroblast growth factor receptor 2 signalling. Our results indicate that ERα, FOXA1 and GATA3 contribute to the regulation of breast cancer susceptibility genes, which is consistent with the effects of anti-oestrogen treatment in breast cancer prevention, and suggest that fibroblast growth factor receptor 2 signalling has an important role in mediating breast cancer risk.This is the final version of the article. It was originally published in Nature Communications here: http://www.nature.com/ncomms/2013/130917/ncomms3464/full/ncomms3464.html

Combined image and genomic analysis of high-grade serous ovarian cancer reveals PTEN loss as a common driver event and prognostic classifier.

BACKGROUND: TP53 and BRCA1/2 mutations are the main drivers in high-grade serous ovarian carcinoma (HGSOC). We hypothesise that combining tissue phenotypes from image analysis of tumour sections with genomic profiles could reveal other significant driver events. RESULTS: Automatic estimates of stromal content combined with genomic analysis of TCGA HGSOC tumours show that stroma strongly biases estimates of PTEN expression. Tumour-specific PTEN expression was tested in two independent cohorts using tissue microarrays containing 521 cases of HGSOC. PTEN loss or downregulation occurred in 77% of the first cohort by immunofluorescence and 52% of the validation group by immunohistochemistry, and is associated with worse survival in a multivariate Cox-regression model adjusted for study site, age, stage and grade. Reanalysis of TCGA data shows that hemizygous loss of PTEN is common (36%) and expression of PTEN and expression of androgen receptor are positively associated. Low androgen receptor expression was associated with reduced survival in data from TCGA and immunohistochemical analysis of the first cohort. CONCLUSION: PTEN loss is a common event in HGSOC and defines a subgroup with significantly worse prognosis, suggesting the rational use of drugs to target PI3K and androgen receptor pathways for HGSOC. This work shows that integrative approaches combining tissue phenotypes from images with genomic analysis can resolve confounding effects of tissue heterogeneity and should be used to identify new drivers in other cancers.This work was supported by Cancer Research UK [grant numbers A15601, A17197,A16561, A10124]; the University of Cambridge; National Institute for Health Research Cambridge Biomedical Research Centre and Academic Clinical Fellowship scheme (FCM); Cambridge Experimental Cancer Medicine Centre and Hutchison Whampoa Limited. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.This is the final published version. It first appeared at http://genomebiology.com/2014/15/12/526

Deregulation of hydroxybutyric acid metabolism provides diagnostic and prognostic biomarkers in ovarian high-grade serous carcinomas

Ovarian cancer is a heterogeneous disease of low prevalence but poor survival. Early diagnosis is critical for patients’ survival but often challenging because ovarian cancer symptoms are unclear and appear only in advanced stages of the disease. Finding more robust disease markers is therefore a clinical priority. Metabolomics is an emerging diagnostic tool that enables the detection of biomarkers reflecting alterations of tumor metabolism, a hallmark of cancer. We performed metabolomics profiling of serum and tumor tissue of high grade serous ovarian cancer (HGSOC) patients, and report novel diagnostic and prognostic biomarkers which indicate deregulation of hydroxybutyric acid (HBA) metabolism. The accumulation of HBA metabolites was associated with lower expression of succinic semialdehyde dehydrogenase (encoded by ALDH5A1), and with the presence of an epithelial-to-mesenchymal-transition (EMT) gene signature, implying a role for these metabolic alterations in cancer cell migration and invasion. In conclusion, our work reports the first comprehensive metabolomic investigation of HGSOC and proposes a new set of metabolites that can be used as diagnostic and prognostic biomarkers of the disease.This work was supported by the Academy of Finland post-doctoral fellow grants: MH decision 138201 and PG 265966. TA was supported by Academy of Finland (grants 272437, 269862, 279163, 292611) and Cancer Society of Finland. EIA is participant in the Charité Clinical Scientist Program funded by the Charité Universitätsmedizin Berlin and the Berlin Institute of Health

Immunophenotypes of pancreatic ductal adenocarcinoma: Meta-analysis of transcriptional subtypes.

Pancreatic ductal adenocarcinoma (PDAC) is the most common malignancy of the pancreas and has one of the highest mortality rates of any cancer type with a 5-year survival rate of <5%. Recent studies of PDAC have provided several transcriptomic classifications based on separate analyses of individual patient cohorts. There is a need to provide a unified transcriptomic PDAC classification driven by therapeutically relevant biologic rationale to inform future treatment strategies. Here, we used an integrative meta-analysis of 353 patients from four different studies to derive a PDAC classification based on immunologic parameters. This consensus clustering approach indicated transcriptomic signatures based on immune infiltrate classified as adaptive, innate and immune-exclusion subtypes. This reveals the existence of microenvironmental interpatient heterogeneity within PDAC and could serve to drive novel therapeutic strategies in PDAC including immune modulation approaches to treating this disease.This study was supported by the NIHR Oxford Biomedical Research Centre. CY is supported by a UK Medical Research Council Research Grant (MR/P02646X/1). MLD is funded by Wellcome Trust grant 100262Z/12/Z. SS is funded by a NIHR Academic Clinical Lecturership

The Risk of Contracting COVID-19 Is Not Increased in Patients With Celiac Disease

The World Health Organization declared coronavirus disease-2019 (COVID-19) a global pandemic in March 2020. Since then, there are more than 34 million cases of COVID-19 leading to more than 1 million deaths worldwide. Numerous studies suggest that celiac disease (CeD), a chronic immune-mediated gastrointestinal condition triggered by gluten, is associated with an increased risk of respiratory infections.1-3 However, how it relates to the risk of COVID-19 is unknown. To address this gap, we conducted a cross-sectional study to evaluate whether patients with self-reported CeD are at an increased risk of contracting COVID-19

CONTEXTO DA GESTANTE EM SITUAÇÃO DE RUA: A REALIDADE NO MUNICÍPIO DE RIO BRANCO – ACRE

This study aimed to demonstrate the context of homeless pregnant women living in the municipality of Rio Branco – Acre. This is an exploratory study with a qualitative approach conducted with nine women who had children on the streets. Data were collected through semi-structured interviews and analyzed through Bardin's content analysis. Most of the participants were aged 25 to 29 years, with low schooling, single, of brown race/skin color, had lived on the streets for more than ten years and had had an average of one homeless child. The motivation for choosing the streets was the fact that they sought to have more freedom, in addition to the use of drugs and scarce economic conditions. None had undergone prenatal care because they felt ashamed of their condition and feared that they would not be attended. Most of the babies were born in a hospital setting and all were given up for adoption. For them, homeless pregnancy was very difficult, as they faced many difficulties such as lack of food, adequate clothing and a comfortable place to rest. The results point to the need to establish more consistent public policies in order to meet the needs of pregnant women living on the streets in the region.Este estudio tuvo como objetivo demostrar el contexto de las mujeres embarazadas sin hogar que viven en el municipio de Rio Branco – Acre. Se trata de un estudio exploratorio con abordaje cualitativo realizado con nueve mujeres que tenían hijos en la calle. Los datos fueron recolectados a través de entrevistas semiestructuradas y analizados a través del análisis de contenido de Bardin. La mayoría de los participantes tenían entre 25 y 29 años, con baja escolaridad, solteros, de raza marrón / color de piel, habían vivido en las calles durante más de diez años y habían tenido un promedio de un niño sin hogar. La motivación para elegir las calles fue el hecho de que buscaban tener más libertad, además del uso de drogas y las escasas condiciones económicas. Ninguna había recibido atención prenatal porque se sentían avergonzadas de su condición y temían que no fueran atendidas. La mayoría de los bebés nacieron en un entorno hospitalario y todos fueron dados en adopción. Para ellas, el embarazo sin hogar fue muy difícil, ya que enfrentaron muchas dificultades, como la falta de alimentos, ropa adecuada y un lugar cómodo para descansar. Los resultados apuntan a la necesidad de establecer políticas públicas más consistentes para satisfacer las necesidades de las mujeres embarazadas que viven en las calles de la región.Objetivou-se demostrar o contexto das gestantes em situação de rua residentes no municipio de&nbsp; Rio Branco – Acre. Trata-se de um eestudo exploratório, de abordagem qualitativa realizado junto a nove mulheres que tiveram filhos em situação de rua. A coleta de dados se deu por meio de entrevista semiestruturada e analisados através da análise do conteúdo de Bardin. A maioria das participantes encontrava-se na faixa etária de 25 a 29 anos, com baixa escolaridade, solteiras, da raça/cor da pele parda, moravam nas ruas há mais de dez anos e haviam tido em média um filho em situação de rua. A motivação para a escolha das ruas&nbsp; foi o fato de buscarem ter mais liberdade, além do uso de drogas e as condições econômicas escassas. Nenhuma&nbsp; havia realizado o pré-natal por sentirem vergonha&nbsp; de sua condição e receio que não fossem atendidas. A maioria dos bebês nasceu em ambiente hospitalar e todos foram entregues para adoção. Para elas a gravidez em situação de rua foi muito difícil, pois enfrentaram muitas dificuldades como a falta de alimentos, roupas adequadas e local confortável para descansar. Os resultados apontam para a necessidade da constituição de políticas públicas mais consistentes afim de atender as necessidades das gestantes em situação de rua na região.Objetivou-se demostrar o contexto das gestantes em situação de rua residentes no municipio de  Rio Branco – Acre. Trata-se de um eestudo exploratório, de abordagem qualitativa realizado junto a nove mulheres que tiveram filhos em situação de rua. A coleta de dados se deu por meio de entrevista semiestruturada e analisados através da análise do conteúdo de Bardin. A maioria das participantes encontrava-se na faixa etária de 25 a 29 anos, com baixa escolaridade, solteiras, da raça/cor da pele parda, moravam nas ruas há mais de dez anos e haviam tido em média um filho em situação de rua. A motivação para a escolha das ruas  foi o fato de buscarem ter mais liberdade, além do uso de drogas e as condições econômicas escassas. Nenhuma  havia realizado o pré-natal por sentirem vergonha  de sua condição e receio que não fossem atendidas. A maioria dos bebês nasceu em ambiente hospitalar e todos foram entregues para adoção. Para elas a gravidez em situação de rua foi muito difícil, pois enfrentaram muitas dificuldades como a falta de alimentos, roupas adequadas e local confortável para descansar. Os resultados apontam para a necessidade da constituição de políticas públicas mais consistentes afim de atender as necessidades das gestantes em situação de rua na região

T. cruzi OligoC-TesT: A Simplified and Standardized Polymerase Chain Reaction Format for Diagnosis of Chagas Disease

Chagas disease (American trypanosomiasis) is caused by the protozoan parasite Trypanosoma cruzi and represents a major public health problem in Latin America. Furthermore, growing human population movements extend the disease distribution to regions outside the South American continent. Accurate diagnosis is crucial in patient care and in preventing transmission through blood transfusion, organ transplantation, or vertical transmission from mother to child. Routine diagnosis of Trypanosoma cruzi infection generally is based on detection of the host's antibodies against the parasite. However, antibody detection tests are liable to specificity problems and are of limited use in assessing treatment outcome and congenital infections. The introduction of the polymerase chain reaction (PCR) to amplify specific DNA sequences opened promising diagnostic perspectives. Despite its reported high sensitivity and specificity, broad use of the PCR technique in diagnosis of Chagas disease is hampered by its complexity and the lack of any standardization. We here present the development and evaluation of the T. cruzi OligoC-TesT, a simple and standardized dipstick format for detection of PCR amplified T. cruzi DNA. The new tool is an important step towards simplified and standardized molecular diagnosis of Chagas disease

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