diXa: a data infrastructure for chemical safety assessment.

Motivation: The field of toxicogenomics (the application of '-omics' technologies to risk assessment of compound toxicities) has expanded in the last decade, partly driven by new legislation, aimed at reducing animal testing in chemical risk assessment but mainly as a result of a paradigm change in toxicology towards the use and integration of genome wide data. Many research groups worldwide have generated large amounts of such toxicogenomics data. However, there is no centralized repository for archiving and making these data and associated tools for their analysis easily available.

Gene expression profiling of flaxseed in mouse lung tissues-modulation of toxicologically relevant genes.

Background: Flaxseed (FS), a nutritional supplement consisting mainly of omega-3 fatty acids and lignan phenolics has potent anti-inflammatory, anti-fibrotic and antioxidant properties. The usefulness of flaxseed as an alternative and complimentary treatment option has been known since ancient times. We have shown that dietary FS supplementation ameliorates oxidative stress and inflammation in experimental models of acute and chronic lung injury in mice resulting from diverse toxicants.

HLA-A and HLA-DRB1 amino acid polymorphisms are associated with susceptibility and protection to pulmonary tuberculosis in a Greek population.

Background: Pulmonary tuberculosis remains the single deadliest infectious disease causing high mortality in humans leading to 1.4 million deaths annually. Inherited genetic factors may explain why some people resist infection more successfully than others.

DTI based diagnostic prediction of a disease via pattern classification.

The paper presents a method of creating abnormality classifiers learned from Diffusion Tensor Imaging (DTI) data of a population of patients and controls. The score produced by the classifier can be used to aid in diagnosis as it quantifies the degree of pathology. Using anatomically meaningful features computed from the DTI data we train a non-linear support vector machine (SVM) pattern classifier.

Dietary curcumin increases antioxidant defenses in lung, ameliorates radiation-induced pulmonary fibrosis, and improves survival in mice.

The effectiveness of lung radiotherapy is limited by radiation tolerance of normal tissues and by the intrinsic radiosensitivity of lung cancer cells. The chemopreventive agent curcumin has known antioxidant and tumor cell radiosensitizing properties. Its usefulness in preventing radiation-induced pneumonopathy has not been tested previously.

Dietary flaxseed prevents radiation-induced oxidative lung damage, inflammation and fibrosis in a mouse model of thoracic radiation injury.

Flaxseed (FS) has high contents of omega-3 fatty acids and lignans with antioxidant properties. Its use in preventing thoracic X-ray radiation therapy (XRT)-induced pneumonopathy has never been evaluated. We evaluated FS supplementation given to mice given before and post-XRT.

Measuring brain lesion progression with a supervised tissue classification system.

Brain lesions, especially White Matter Lesions (WMLs), are associated with cardiac and vascular disease, but also with normal aging. Quantitative analysis of WML in large clinical trials is becoming more and more important. In this paper, we present a computer-assisted WML segmentation method, based on local features extracted from conventional multi-parametric Magnetic Resonance Imaging (MRI) sequences.

SKDM human leukocyte antigen (HLA) tool: A comprehensive HLA and disease associations analysis software.

The immensely polymorphic and gene-rich landscape of the major histocompatibility complex on chromosome 6 necessitates a thorough and consistent investigation of its constituting elements. The human leukocyte antigens (HLAs) are an example of such polymorphic elements, implicated in many immune-based diseases. So far, analyses of HLA molecules in the context of diseases have been ad hoc, frequently incomplete, and extremely cumbersome.

Association of variants of the interleukin-23 receptor gene with susceptibility to pediatric Crohn's disease.

Background & Aims: Recently an association was shown between the single nucleotide polymorphism (SNP), rs11209026, within the interleukin-23 receptor (IL23R) locus and Crohn's disease (CD) as a consequence of a genome-wide association study of this disease in adults. We examined the effects of this and other previously reported SNPs at this locus with respect to CD in children.

Methods: By using data from our ongoing genome-wide association study in our cohort of 142 pediatric CD patients and 281 matched controls, we investigated the association of the previously reported SNPs at the IL23R locus with the childhood form of this disease.

Combining multi-species genomic data for microRNA identification using a Naive Bayes classifier.

Motivation: Most computational methodologies for microRNA gene prediction utilize techniques based on sequence conservation and/or structural similarity. In this study we describe a new technique, which is applicable across several species, for predicting miRNA genes. This technique is based on machine learning, using the Naive Bayes classifier.