QueryOR: a comprehensive web platform for genetic variant analysis and prioritization

Background: Whole genome and exome sequencing are contributing to the extraordinary progress in the study of human genetic variants. In this fast developing field, appropriate and easily accessible tools are required to facilitate data analysis. Results: Here we describe QueryOR, a web platform suitable for searching among known candidate genes as well as for finding novel gene-disease associations. QueryOR combines several innovative features that make it comprehensive, flexible and easy to use. Instead of being designed on specific datasets, it works on a general XML schema specifying formats and criteria of each data source. Thanks to this flexibility, new criteria can be easily added for future expansion. Currently, up to 70 user-selectable criteria are available, including a wide range of gene and variant features. Moreover, rather than progressively discarding variants taking one criterion at a time, the prioritization is achieved by a global positive selection process that considers all transcript isoforms, thus producing reliable results. QueryOR is easy to use and its intuitive interface allows to handle different kinds of inheritance as well as features related to sharing variants in different patients. QueryOR is suitable for investigating single patients, families or cohorts. Conclusions: QueryOR is a comprehensive and flexible web platform eligible for an easy user-driven variant prioritization. It is freely available for academic institutions at http://queryor.cribi.unipd.it/

Human myotonic dystrophy protein kinase effect in S. cerevisiae

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Nucleosynthesis And The Inhomogeneous Chemical Evolution Of The Carina Dwarf Galaxy

The detailed abundances of 23 chemical elements in nine bright red giant branch stars in the Carina dwarf spheroidal galaxy are presented based on high-resolution spectra gathered at the Very Large Telescope (VLT) and Magellan telescopes. A spherical model atmospheres analysis is applied using standard methods (local thermodynamic equilibrium and plane-parallel radiative transfer) to spectra ranging from 380 to 680 nm. Stellar parameters are found to be consistent between photometric and spectroscopic analyses, both at moderate and high resolution. The stars in this analysis range in metallicity from -2.9 < [Fe/H] < -1.3, and adopting the ages determined by Lemasle et al., we are able to examine the chemical evolution of Carina's old and intermediate-aged populations. One of the main results from this work is the evidence for inhomogeneous mixing in Carina and therefore for a poor statistical sampling of the supernova contributions when forming stars; a large dispersion in [Mg/Fe] indicates poor mixing in the old population, an offset in the [alpha/Fe] ratios between the old and intermediate-aged populations (when examined with previously published results) suggests that the second star formation event occurred in alpha-enriched gas, and one star, Car-612, seems to have formed in a pocket enhanced in SN Ia/II products. This latter star provides the first direct link between the formation of stars with enhanced SN Ia/II ratios in dwarf galaxies to those found in the outer Galactic halo (Ivans et al.). Another important result is the potential evidence for SNII driven winds. We show that the very metal-poor stars in Carina have not been enhanced in asymptotic giant branch or SN Ia products, and therefore their very low ratios of [Sr/Ba] suggests the loss of contributions from the early SNe II. Low ratios of [Na/Fe], [Mn/Fe], and [Cr/Fe] in two of these stars support this scenario, with additional evidence from the low [Zn/Fe] upper limit for one star. It is interesting that the chemistry of the metal-poor stars in Carina is not similar to those in the Galaxy, most of the other dwarf spheroidal galaxies, or the ultra faint dwarfs, and suggests that Carina may be at the critical mass where some chemical enrichments are lost through SN II driven winds.NSERCNSF AST 99-84073McDonald Observator

GASTon: A Graph-Exploration System for Indexing, Annotating and Visualizing PubMed Articles to Enhance the Analysis of Social deTerminants of Health

Many works have shown associations between social determinants of health (SDoH) –the social circumstances in which people live– and health-related outcomes. However, the lack of SDoH data increases the challenges in measuring and understanding their effect on people’s health and health systems. In this paper, we present GASTon, a system for the indexing, annotation, and graph-based rendering of PubMed information to enable the search and retrieval of SDoHs in scientific literature. Our work provides a way to associate specific concepts with peer-reviewed articles to simplify the search for social factors. It builds a knowledge graph based on PubMed publications and associates them with concepts extracted from the Unified Medical Language System (UMLS) Metathesaurus. GASTon allows a full-text search and graph-based navigation and supports an overview of the concepts and related publications. Moreover, the architecture allows scale-up thanks to its containerized nature and parallelizat ion capabilities. The system is open-source under the Apache V2 license

Salivary gland ultrasonography: a highly specific tool for the early diagnosis of primary Sjögren's syndrome

INTRODUCTION:Recently, a great interest has arisen for salivary gland ultrasonography (SGUS) as a valuable tool for the assessment of major salivary gland involvement in primary Sjögren's syndrome (pSS. The aims of this study were to test the accuracy of SGUS for the early detection of pSSand to compare the diagnostic performance of SGUS with minor salivary gland biopsy (MSGB) and unstimulated salivary flow (USFR) in this context. METHOD:Patients with suspected pSS and symptoms duration of ≤5 years were consecutively enrolled in this study. The diagnosis of pSS was made according to the AECG criteria. SGUS was performed by two radiologists blinded to the diagnosis and a previously reported ultrasound scoring system (De Vita et al. 1992, cut-off ≥ 1) was used to grade the echostructure alterations of the salivary glands. Statistical analysis was performed using SPSS v16. RESULTS: This study included 50 pSS patients and 57 controls with no-SS sicca symptoms. The mean(SD) age of the pSS group was lower than non-SS group (47(13) vs 53(12)yrs, p = 0.006). No further differences between the two groups were observed. Patients with pSS showed a significantly higher SGUS score in comparison with controls (mean(SD) = 2.1(1.8) vs 0.0(0.4), p = 0.000). The SGUS cut-off ≥ 1 showed a sensitivity (SE) of 66 %, a specificity (SP) of 98 %, a positive predictive value (PPV) of 97 % and a negative predictive value (NPV) of 73 % for pSS diagnosis. The SGUS score correlated also with patients' MSGB/FS and USFR. CONCLUSIONS: This study confirmed the good performance of SGUS for the early non-invasive diagnosis of pSS. Further research in larger international cohort of patients is mandatory in order to assess the role of SGUS in the diagnostic algorithm of pSS

Heparin-Modified Collagen Gels for Controlled Release of Pleiotrophin: Potential for Vascular Applications

A fast re-endothelialization, along with the inhibition of neointima hyperplasia, are crucial to reduce the failure of vascular bypass grafts. Implants modifications with molecules capable of speeding up the re-endothelialization process have been proposed over the last years. However, clinical trials of angiogenic factor delivery have been mostly disappointing, underscoring the need to investigate a wider array of angiogenic factors. In this work, a drug release system based on a type I collagen hydrogel has been proposed for the controlled release of Pleiotrophin (PTN), a cytokine known for its pro-angiogenetic effects. Heparin, in virtue of its ability to sequester, protect and release growth factors, has been used to better control the release of PTN. Performances of the PTN drug delivery system on endothelial (ECs) and smooth muscle cells (SMCs) have been investigated. Structural characterization (mechanical tests and immunofluorescent analyses of the collagen fibers) was performed on the gels to assess if heparin caused changes in their mechanical behavior. The release of PTN from the different gel formulations has been analyzed using a PTN-specific ELISA assay. Cell viability was evaluated with the Alamar Blue Cell Viability Assay on cells directly seeded on the gels (direct test) and on cells incubated with supernatant, containing the released PTN, obtained from the gels (indirect test). The effects of the different gels on the migration of both ECs and SMCs have been evaluated using a Transwell migration assay. Hemocompatibility of the gel has been assessed with a clotting/hemolysis test. Structural analyses showed that heparin did not change the structural behavior of the collagen gels. ELISA quantification demonstrated that heparin induced a constant release of PTN over time compared to other conditions. Both direct and indirect viability assays showed an increase in ECs viability while no effects were noted on SMCs. Cell migration results evidenced that the heparin/PTN-modified gels significantly increased ECs migration and decreased the SMCs one. Finally, heparin significantly increased the hemocompatibility of the collagen gels. In conclusion, the PTN-heparin-modified collagen here proposed can represent an added value for vascular medicine, able to ameliorate the biological performance, and integration of vascular grafts

Setup and Validation of a Targeted Next-Generation Sequencing Approach for the Diagnosis of Lysosomal Storage Disorders.

Lysosomal storage disorders (LSDs) are monogenic diseases, due to accumulation of specific undegraded substrates into lysosomes. LSD diagnosis could take several years because of both poor knowledge of these diseases and shared clinical features. The diagnostic approach includes clinical evaluations, biochemical tests, and genetic analysis of the suspected gene. In this study, we evaluated an LSD targeted sequencing panel as a tool capable to potentially reverse this classic diagnostic route. The panel includes 50 LSD genes and 230 intronic sequences conserved among 33 placental mammals. For the validation phase, 56 positive controls, 13 biochemically diagnosed patients, and nine undiagnosed patients were analyzed. Disease-causing variants were identified in 66% of the positive control alleles and in 62% of the biochemically diagnosed patients. Three undiagnosed patients were diagnosed. Eight patients undiagnosed by the panel were analyzed by whole exome sequencing: for two of them, the disease-causing variants were identified. Five patients, undiagnosed by both panel and exome analyses, were investigated through array comparative genomic hybridization: one of them was diagnosed. Conserved intronic fragment analysis, performed in cases unresolved by the first-level analysis, evidenced no candidate intronic variants. Targeted sequencing has low sequencing costs and short sequencing time. However, a coverage >60× to 80× must be ensured and/or Sanger validation should be performed. Moreover, it must be supported by a thorough clinical phenotyping

Human urinary bladder transitional cell carcinomas acquire the functional Fas ligand during tumor progression

The interaction between FasL on tumor cells and Fas on lymphocytes may represent a tumor immune escape mechanism. We explored FasL expression and function in human urinary bladder transitional cell carcinomas (TCCs). FasL expression was observed in situ in 45% of TCCs (n = 45) and was absent in normal urothelium (n = 20). A correlation existed between FasL expression and high tumor grade (0% in G1,14% in G2, and 75% in G3; P < 0.0001) and stage (13% in superficial Ta-T1 versus 81% in invasive T2-T4; P < 0.0001). FasL function was shown by the ability of two FasL-positive primary culture TCC cell lines (established from two FasL-positive invasive TCCs) to induce Fas-mediated killing not only of conventional Fas-sensitive targets (such as Jurkat cells or phytohemagglutinin-lymphoblasts), but also of autologous T lymphocytes generated in a mixed lymphocyte tumor-cell culture. In addition, an association between FasL expression by TCC cells and activated caspase-8, -9, and -3 expression by interferon-gamma-producing CD8-positive tumor-infiltrating lymphocytes was observed in situ. Our results show a functional expression of TCC-expressed FasL that correlates with tumor progression. These results suggest that TCC-expressed FasL may induce apoptosis of anti-tumor T lymphocytes in vivo, providing new insights on the mechanisms involved in bladder TCC progression

Synovial effusion and synovial fluid biomarkers in psoriatic arthritis to assess intraarticular tumor necrosis factor-α blockade in the knee joint

Introduction: Evaluation of synovial effusion (SE), synovial fluid (SF) and synovial tissue (ST) biomarkers in relation to disease activity indexes to assess the response to intraarticular (IA) tumor necrosis factor (TNF)-\u3b1 blockers in psoriatic arthritis (PsA). Methods: Systemic and local disease activity indexes (disease activity score [DAS]; the Ritchie articular index [mRAI], erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP); Thompson articular [THOMP] and joint articular [KJAI]-Index ) and ST samples were assessed at baseline, throughout treatment, and during the follow-up in 14 patients affected with PsA who underwent IA injections (0.5 ml - 12.5 mg) in the knee joint of etanercept (E) or placebo (P) once every two weeks for a ten week period. Total SF white blood cell (WBC) counts (WBC/ \u3bcl) and SF cytokine/chemokine (CK/CCK) levels were measured before IA-E at baseline, after IA-E, and as long as there were adequate amounts of SF for knee aspiration (post). Characterization of synovial mononuclear cell infiltration and synovial vessels was carried out in 8/14 knees by staining serial sections of synovial tissue biopsies for CD45, CD3, CD68, CD31 and CD105. Results: At baseline, CRP and/or ESR were significantly correlated with SF-CK (IL-1\u3b2, IL-1Ra, IL-6, IL-8) and CCK (CCL2, CCL3 and CCL4). Post-IA injections, there was a decrease in SE in the knees in which aspiration following IA-E injection was possible as well as a significant reduction in SF WBC/\u3bcl and in SF-CK (TNF-\u3b1, IL- 1\u3b2, IL-1Ra, IL-6 and IL-22). Pre- and post- IAE injections, there were significant correlations between ST markers and SF-CK (IL-1\u3b2 with CD45; IL-1\u3b2 and IL-6 with CD31) and between SF-CCK (CCL4 and CCL3 with CD3). At the end of the study, there was a significant reduction in disease activity indexes (CRP, DAS, RAI, THOMP, KJAI) as well as in the ST markers (CD45; CD3)

Outcome Prediction from Behaviour Change Intervention Evaluations using a Combination of Node and Word Embedding

Findings from randomized controlled trials (RCTs) of behaviour change interventions encode much of our knowledge on intervention efficacy under defined conditions. Predicting outcomes of novel interventions in novel conditions can be challenging, as can predicting differences in outcomes between different interventions or different conditions. To predict outcomes from RCTs, we propose a generic framework of combining the information from two sources - i) the instances (comprised of surrounding text and their numeric values) of relevant attributes, namely the intervention, setting and population characteristics of a study, and ii) abstract representation of the categories of these attributes themselves. We demonstrate that this way of encoding both the information about an attribute and its value when used as an embedding layer within a standard deep sequence modeling setup improves the outcome prediction effectiveness