PhenoGeneRanker: A Tool for Gene Prioritization Using Complete Multiplex Heterogeneous Networks

Uncovering genotype-phenotype relationships is a fundamental challenge in genomics. Gene prioritization is an important step for this endeavor to make a short manageable list from a list of thousands of genes coming from high-throughput studies. Network propagation methods are promising and state of the art methods for gene prioritization based on the premise that functionally-related genes tend to be close to each other in the biological networks. In this study, we present PhenoGeneRanker, an improved version of a recently developed network propagation method called Random Walk with Restart on Multiplex Heterogeneous Networks (RWR-MH). PhenoGeneRanker allows multi-layer gene and disease networks. It also calculates empirical p-values of gene ranking using random stratified sampling of genes based on their connectivity degree in the network. We ran PhenoGeneRanker using multi-omics datasets of rice to effectively prioritize the cold tolerance-related genes. We observed that top genes selected by PhenoGeneRanker were enriched in cold tolerance-related Gene Ontology (GO) terms whereas bottom ranked genes were enriched in general GO terms only. We also observed that top-ranked genes exhibited significant p-values suggesting that their rankings were independent of their degree in the network

GENCODE: reference annotation for the human and mouse genomes in 2023.

GENCODE produces high quality gene and transcript annotation for the human and mouse genomes. All GENCODE annotation is supported by experimental data and serves as a reference for genome biology and clinical genomics. The GENCODE consortium generates targeted experimental data, develops bioinformatic tools and carries out analyses that, along with externally produced data and methods, support the identification and annotation of transcript structures and the determination of their function. Here, we present an update on the annotation of human and mouse genes, including developments in the tools, data, analyses and major collaborations which underpin this progress. For example, we report the creation of a set of non-canonical ORFs identified in GENCODE transcripts, the LRGASP collaboration to assess the use of long transcriptomic data to build transcript models, the progress in collaborations with RefSeq and UniProt to increase convergence in the annotation of human and mouse protein-coding genes, the propagation of GENCODE across the human pan-genome and the development of new tools to support annotation of regulatory features by GENCODE. Our annotation is accessible via Ensembl, the UCSC Genome Browser and https://www.gencodegenes.org

Post-kidney transplantation external iliac artery stenosis due to vascular clamp: report of a case

We report a case of right external iliac artery stenosis after kidney transplantation surgery caused by vascular clamp application injury. The patient presented with claudication of the ipsilateral lower limb and the lesion was diagnosed angiographically. The patient was treated with endovascular stent placement

Geochronology and sources of heavy metal pollution in sediments of Istanbul Strait (Bosporus) outlet area, SW Black Sea, Turkey

Geochemical and sedimentological analyses and radionuclide (Pb-210 and Cs-137) dating of three cores from the Bosporus outlet area of the Black Sea, north of Istanbul, were conducted to assess the sources and history of heavy metal pollution. The sedimentary succession in the shelf core KD12-01 consists mainly of clay (49-80%) and silt (15-41%). Radionuclide dating of the core indicates that it consists of old sediments that are uncontaminated with heavy metals. In contrast, cores KD12-04 and KD12-07 recovered from -350 m and -304 mm in the upper slope area represent sediments consisting of silt and clay that were deposited since at least the last 120 years and 60 years, respectively. The latter core contains two mass-flow units represented by relatively old sedimentary material according to the low 21 Pb activity and relatively low heavy metal contents. The upper 40 and 48 cm of cores KD 12-04 and KD 12-07 represent sediments deposited since 1970s and 1980s that are significantly polluted with Cu, Ni, Zn, Mo, Pb and Cr, Cu, Co, Ni, Mo, Pb, Zn, respectively. However, high Pb and Cr concentrations with high TOC contents date back to early part of the 20th century in core KD 12-04. The geochemical data, together with the high Cs-137 concentrations of the contaminated sediments, strongly suggest that the pollution is mainly delivered to the western and north western Black Sea by the large European rivers, from there transported to the study area by the rim current, and deposited in the sediments under anoxic conditions. (C) 2018 Elsevier Ltd. All rights reserved

Association of ST elevation with apical aneurysm in hypertrophic cardiomyopathy

AbstractObjectivesApical aneurysms in patients with hypertrophic cardiomyopathy (HCM) represent an underrecognized but clinically important subset of HCM patients. However it may be frequently missed by echocardiography because of poor image quality of left ventricular apex. We aimed to compare electrocardiographic STE in HCM patients with and without apical aneurysm.MethodsWe developed this clinical review using an extensive MEDLINE review of the literature and data from our laboratories; and some electrocardiographic parameters including STE were analysed in HCM patients with and without apical aneurysm.ResultsThere were 29 HCM patients without apical aneurysm (Group 1; 52.6±17.7years, 69% male) and 28 HCM patients with apical aneurysm (Group 2; 59.6±13.2years, 57% male). The STE in V4-6 derivations were statistically more frequent in patients with apical aneurysm compared to those without aneurysm (93% vs 7%, p<0.001). There was a positive correlation between the presence of the STE in V4-6 derivations and the presence of the apical aneurysm (Spearman's ρ=0.895, p<0.001).ConclusionsClinicians and specifically echocardiographers must pay special attention on the electrocardiography to correctly detect the frequently overlooked apical aneurysm in HCM patients, and should be careful for apical aneurysm particularly in the presence of STE in V4-6 derivations

Holocene sedimentary history of South Danamand?ra Lake: a peatland in west of ?stanbul, Catalca Peninsula, NW Turkey

This study investigates the sedimentological evolution of the South Danamandhra Lake (SDL) lake in ??atalca Peninsula, 70 km west of ??stanbul, using Georadar data and multiproxy analyses of five sediment cores. The lake is a 1.3-m deep, endorheic freshwater peatland, heavily colonised by common reed (Phragmites sp.). The multiproxy core investigations include a lithological core description and environmental magnetism, physical properties (gamma density and magnetic susceptibility), geochemical elemental, pollen and radiocarbon dating analyses. The lithological sequence in the lake consists of an upper peat unit and a lower sand-silt-clay unit. The peat unit is characterized by lower magnetic susceptibility, density and lithophile elements (K, Fe, Ti, and Zr) concentrations than the sand-silt-clay unit. Overall interpretation of the multiproxy data and the age-depth model suggest that the SDL was formed in a shallow depression of a fluvial channel at ca 10.9 cal kyr BP, and became a eutrophic lake at 8.1 cal kyr BP during the early Holocene warm period. Redox-sensitive element (i.e. Mn) distribution and mineral magnetic properties indicate that the peat unit has accumulated under anoxic conditions below a thin oxic surficial layer. Increase in the Taraxacum, Asteraceae, and Poaceae pollen percentages, together with high siliciclastic inputs in the lake, indicate that anthropogenic influence in the area started at 5.4 cal kyr BP