Use of IU parallel computing resources and high performance file systems - July 2013 to Dec 2014

This report details use of IU's parallel computing resources and high performance file systems from July 2013 through December 2014

North-South cooperation through BIOTA: An interdisciplinary monitoring programme in arid and semi-arid southern Africa

Connecting disciplines in a north– South collaboration has many advantages: mutualisms evolve, synergies are created and spin-offs emerge. The BIOTA South (Biodiversity Monitoring Transect Analysis in southern Africa) programme, with its long-term vision to generate knowledge of biodiversity along a north–south transect in southern Africa, is providing opportunities for research, technology transfer and capacity building while focusing on potential solutions for critical challenges that face this environmentally vulnerable part of the subcontinen

Electronically highly cubic conditions for Ru in alpha-RuCl3

We studied the local Ru 4d electronic structure of alpha-RuCl3 by means of polarization dependent x-ray absorption spectroscopy at the Ru-L2,3 edges. We observed a vanishingly small linear dichroism indicating that electronically the Ru 4d local symmetry is highly cubic. Using full multiplet cluster calculations we were able to reproduce the spectra excellently and to extract that the trigonal splitting of the t2g orbitals is -12 $\pm10$ meV, i.e. negligible as compared to the Ru 4d spin-orbit coupling constant. Consistent with our magnetic circular dichroism measurements, we found that the ratio of the orbital and spin moments is 2.0, the value expected for a Jeff = 1/2 ground state. We have thus shown that as far as the Ru 4d local properties are concerned, alpha-RuCl3 is an ideal candidate for the realization of Kitaev physics

Comparison of Multi-Sample Variant Calling Methods for Whole Genome Sequencing

Rapid advancement of next-generation sequencing (NGS) technologies has facilitated the search for genetic susceptibility factors that influence disease risk in the field of human genetics. In particular whole genome sequencing (WGS) has been used to obtain the most comprehensive genetic variation of an individual and perform detailed evaluation of all genetic variation. To this end, sophisticated methods to accurately call high-quality variants and genotypes simultaneously on a cohort of individuals from raw sequence data are required. On chromosome 22 of 818 WGS data from the Alzheimer's Disease Neuroimaging Initiative (ADNI), which is the largest WGS related to a single disease, we compared two multi-sample variant calling methods for the detection of single nucleotide variants (SNVs) and short insertions and deletions (indels) in WGS: (1) reduce the analysis-ready reads (BAM) file to a manageable size by keeping only essential information for variant calling ("REDUCE") and (2) call variants individually on each sample and then perform a joint genotyping analysis of the variant files produced for all samples in a cohort ("JOINT"). JOINT identified 515,210 SNVs and 60,042 indels, while REDUCE identified 358,303 SNVs and 52,855 indels. JOINT identified many more SNVs and indels compared to REDUCE. Both methods had concordance rate of 99.60% for SNVs and 99.06% for indels. For SNVs, evaluation with HumanOmni 2.5M genotyping arrays revealed a concordance rate of 99.68% for JOINT and 99.50% for REDUCE. REDUCE needed more computational time and memory compared to JOINT. Our findings indicate that the multi-sample variant calling method using the JOINT process is a promising strategy for the variant detection, which should facilitate our understanding of the underlying pathogenesis of human diseases

Современное состояние и перспективы развития ООПТ Томской области

В работе дана характеристика сети особо охраняемых природных территорий Томской области, ее роли в поддержании эколого-хозяйственного баланса области. Определены этапы формирования сети ООПТ. Дан анализ географического разнообразия сети ООПТ и представленности ее в административных районах области. Определена роль сети ООПТ в сохранении редких и исчезающих видов растений и животных. Разработана и реализована методика комплексной оценки эффективности сети ООПТ. Предложены пути ее развития и оптимизации.In work the characteristic of the network of specially protected natural territories of the Tomsk region, its role in maintaining ecological and economic balance of the region. The stages of forming a network of protected areas. The analysis of the geographic diversity of the PA network and its representation in the administrative districts of the region. Defined the role of the network of protected areas in the conservation of rare and endangered species of plants and animals. Developed and implemented a methodology of comprehensive evaluation of the effectiveness of the PA network. The proposed ways of its development and optimization

Serum concentrations of cortisol, interleukin 6, leptin and adiponectin predict stress induced insulin resistance in acute inflammatory reactions

Introduction Inflammatory stimuli are causative for insulin resistance in obesity as well as in acute inflammatory reactions. Ongoing research has identified a variety of secreted proteins that are released from immune cells and adipocytes as mediators of insulin resistance; however, knowledge about their relevance for acute inflammatory insulin resistance remains limited. In this study we aimed for a clarification of the relevance of different insulin resistance mediating factors in an acute inflammatory situation. Methods Insulin resistance was measured in a cohort of 37 nondiabetic patients undergoing cardiac surgery by assessment of insulin requirement to maintain euglycaemia and repeated measurements of an insulin glycaemic index. The kinetics of cortisol, interleukin 6 (IL6), tumour necrosis factor alpha (TNF alpha), resistin, leptin and adiponectin were assessed by repeated measurements in a period of 48 h. Results Insulin resistance increased during the observation period and peaked 22 h after the beginning of the operation. IL6 and TNF alpha displayed an early increase with peak concentrations at the 4-h time point. Serum levels of cortisol, resistin and leptin increased more slowly and peaked at the 22-h time point, while adiponectin declined, reaching a base at the 22-h time point. Model assessment identified cortisol as the best predictor of insulin resistance, followed by IL6, leptin and adiponectin. No additional information was gained by modelling for TNF alpha, resistin, catecholamine infusion rate, sex, age, body mass index (BMI), operation time or medication. Conclusions Serum cortisol levels are the best predictor for inflammatory insulin resistance followed by IL6, leptin and adiponectin. TNF alpha, and resistin have minor relevance as predictors of stress dependent insulin resistance