A specialized learner for inferring structured cis-regulatory modules

BACKGROUND: The process of transcription is controlled by systems of transcription factors, which bind to specific patterns of binding sites in the transcriptional control regions of genes, called cis-regulatory modules (CRMs). We present an expressive and easily comprehensible CRM representation which is capable of capturing several aspects of a CRM's structure and distinguishing between DNA sequences which do or do not contain it. We also present a learning algorithm tailored for this domain, and a novel method to avoid overfitting by controlling the expressivity of the model. RESULTS: We are able to find statistically significant CRMs more often then a current state-of-the-art approach on the same data sets. We also show experimentally that each aspect of our expressive CRM model space makes a positive contribution to the learned models on yeast and fly data. CONCLUSION: Structural aspects are an important part of CRMs, both in terms of interpreting them biologically and learning them accurately. Source code for our algorithm is available at

Analyzing ChIP-chip Data Using Bioconductor

Analyzing ChIP-chip Data Using Bioconducto

Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data

Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is rapidly replacing chromatin immunoprecipitation combined with genome-wide tiling array analysis (ChIP-chip) as the preferred approach for mapping transcription-factor binding sites and chromatin modifications. The state of the art for analyzing ChIP-seq data relies on using only reads that map uniquely to a relevant reference genome (uni-reads). This can lead to the omission of up to 30% of alignable reads. We describe a general approach for utilizing reads that map to multiple locations on the reference genome (multi-reads). Our approach is based on allocating multi-reads as fractional counts using a weighted alignment scheme. Using human STAT1 and mouse GATA1 ChIP-seq datasets, we illustrate that incorporation of multi-reads significantly increases sequencing depths, leads to detection of novel peaks that are not otherwise identifiable with uni-reads, and improves detection of peaks in mappable regions. We investigate various genome-wide characteristics of peaks detected only by utilization of multi-reads via computational experiments. Overall, peaks from multi-read analysis have similar characteristics to peaks that are identified by uni-reads except that the majority of them reside in segmental duplications. We further validate a number of GATA1 multi-read only peaks by independent quantitative real-time ChIP analysis and identify novel target genes of GATA1. These computational and experimental results establish that multi-reads can be of critical importance for studying transcription factor binding in highly repetitive regions of genomes with ChIP-seq experiments

An Integrated Pipeline for the Genome-Wide Analysis of Transcription Factor Binding Sites from ChIP-Seq

ChIP-Seq has become the standard method for genome-wide profiling DNA association of transcription factors. To simplify analyzing and interpreting ChIP-Seq data, which typically involves using multiple applications, we describe an integrated, open source, R-based analysis pipeline. The pipeline addresses data input, peak detection, sequence and motif analysis, visualization, and data export, and can readily be extended via other R and Bioconductor packages. Using a standard multicore computer, it can be used with datasets consisting of tens of thousands of enriched regions. We demonstrate its effectiveness on published human ChIP-Seq datasets for FOXA1, ER, CTCF and STAT1, where it detected co-occurring motifs that were consistent with the literature but not detected by other methods. Our pipeline provides the first complete set of Bioconductor tools for sequence and motif analysis of ChIP-Seq and ChIP-chip data

Magnetic crystals and helical liquids in alkaline-earth fermionic gases

The joint action of a synthetic gauge potential and of atomic contact repulsion in a one-dimensional alkaline-earth(-like) fermionic gas with nuclear spin I leads to the existence of a hierarchy of fractional insulating and conducting states with intriguing properties. We unveil the existence and the features of those phases by means of both analytical bosonization techniques and numerical methods based on the density-matrix renormalization group algorithm. In particular, we show that the gapless phases can support helical modes, whereas the gapped states, which appear under certain conditions, are characterised both by density and magnetic order. Several distinct features emerge solely for spin I larger than 1/2, thus making their study with cold-atoms unique. We will finally argue that these states are related to the properties of an unconventional fractional quantum Hall effect in the thin-torus limit. The properties of this hierarchy of states can be experimentally studied in state-of-the-art cold-atom laboratories

Open Cell Aluminum Foams Produced by Polymer Impregnation Method

In this study, open cell aluminum foams were produced using the polymer impregnating method. This method consists of slurry preparation, template coating, drying, burning and finally sintering. Physical properties of the open cell aluminum foams were characterized. Microstructures were investigated utilizing optical and scanning electron microscopy. Cu $K_{α}$ was used as X-ray source in phase analysis. The hardness of the foams was measured by applying Vickers hardness test. An ideal foam coating was achieved using the slurry having 60% solid content mixed with a speed of 1000 rpm for 3 h. The polyurethane foam was burned out at 500C and ideal sintering parameters were 620C for 4 or 7 h. The foam densities containing 60% solid were found to be 0.12-0.15 g/$cm^3$. The porosity values were calculated to be in the range of 94.4-95.5%. Micro hardness values were 30.3-34.7 Hv

İlk ve orta adolesan dönemdeki erkek sıçanlara uygulanan 900-megahertz elektromanyetik alanın dalak üzerine etkileri: Biyokimyasal ve histopatolojik çalışma

Aim: Adolescents are at risk due to the intensive use of mobile phones. The aim of this study was to investigate the histopathological and biochemical effects of 900-Megahertz electromagnetic field on spleen in late adolescent period, exposed during periods of early and mid-adolescence. Material and Methods: In this study, 24 Sprague Dawley 21-day-old male rats were divided into control (n=8), sham (n=8) and electromagnetic field groups (n=8). Control group rats were not subjected to any application. Electromagnetic field group rats were taken into the electromagnetic field cage and were exposed to 900-Megahertz electromagnetic field (1 hour per day for 25 days). Sham group rats were taken into the electromagnetic field cages but were not exposed to electromagnetic field. At the end of the treatment, all animals were sacrificed by cervical dislocation method and the spleens were removed. After histological procedures, tissue sections were taken and stained with hematoxylin-eosin and periodic acid Schiff. Histopathological evaluation was performed on the spleen tissues. Oxidative stress parameters including lipid peroxidation, superoxide dismutase, glutathione and catalase levels were investigated via biochemical analysis. Results: Histopathological evaluation revealed megakaryocyte cells, enlarged white pulps and dilated sinusoids in spleen tissues of adolescent rats in electromagnetic field group. According to biochemical analysis results, it was determined that glutathione and lipid peroxidation values were increased, but superoxide dismutase and catalase values were decreased. Conclusion: It can be said that the 900-Megahertz electromagnetic field applied in adolescent period caused morphological changes on spleen tissue and caused oxidative stress in male rats. © 2019, Duzce University Medical School. All rights reserved

The Effect of 900-Megahertz Electromagnetic Field Exposure in the First and Middle Adolescent Period on the Spleen in Male Rats: A Biochemical and Histopathological Study

Aim: Adolescents are at risk due to the intensive use of mobile phones. The aim of this study was to investigate the histopathological and biochemical effects of 900-Megahertz electromagnetic field on spleen in late adolescent period, exposed during periods of early and mid-adolescence. Material and Methods: In this study, 24 Sprague Dawley 21-day-old male rats were divided into control (n=8), sham (n=8) and electromagnetic field groups (n=8). Control group rats were not subjected to any application. Electromagnetic field group rats were taken into the electromagnetic field cage and were exposed to 900-Megahertz electromagnetic field (1 hour per day for 25 days). Sham group rats were taken into the electromagnetic field cages but were not exposed to electromagnetic field. At the end of the treatment, all animals were sacrificed by cervical dislocation method and the spleens were removed. After histological procedures, tissue sections were taken and stained with hematoxylin-eosin and periodic acid Schiff. Histopathological evaluation was performed on the spleen tissues. Oxidative stress parameters including lipid peroxidation, superoxide dismutase, glutathione and catalase levels were investigated via biochemical analysis. Results: Histopathological evaluation revealed megakaryocyte cells, enlarged white pulps and dilated sinusoids in spleen tissues of adolescent rats in electromagnetic field group. According to biochemical analysis results, it was determined that glutathione and lipid peroxidation values were increased, but superoxide dismutase and catalase values were decreased. Conclusion: It can be said that the 900-Megahertz electromagnetic field applied in adolescent period caused morphological changes on spleen tissue and caused oxidative stress in male rats. © 2019, Duzce University Medical School. All rights reserved