eCOMPAGT – efficient Combination and Management of Phenotypes and Genotypes for Genetic Epidemiology

<p>Abstract</p> <p>Background</p> <p>High-throughput genotyping and phenotyping projects of large epidemiological study populations require sophisticated laboratory information management systems. Most epidemiological studies include subject-related personal information, which needs to be handled with care by following data privacy protection guidelines. In addition, genotyping core facilities handling cooperative projects require a straightforward solution to monitor the status and financial resources of the different projects.</p> <p>Description</p> <p>We developed a database system for an efficient combination and management of phenotypes and genotypes (eCOMPAGT) deriving from genetic epidemiological studies. eCOMPAGT securely stores and manages genotype and phenotype data and enables different user modes with different rights. Special attention was drawn on the import of data deriving from TaqMan and SNPlex genotyping assays. However, the database solution is adjustable to other genotyping systems by programming additional interfaces. Further important features are the scalability of the database and an export interface to statistical software.</p> <p>Conclusion</p> <p>eCOMPAGT can store, administer and connect phenotype data with all kinds of genotype data and is available as a downloadable version at <url>http://dbis-informatik.uibk.ac.at/ecompagt</url>.</p

Cloudflow – A Framework for MapReduce Pipeline Development in Biomedical Research

The data-driven parallelization framework Hadoop MapReduce allows analysing large data sets in a scalable way. Since the development of MapReduce programs can be a time-intensive and challenging task, the application and usage of Hadoop in Biomedical Research is still limited. Here we resent Cloudflow, a high-level framework to hide the implementation details of Hadoop and to provide a set of building blocks to create biomedical pipelines in a more intuitive way. We demonstrate the benefit of Cloudflow on three different genetic use cases. It will be shown how the framework can be combined with the Hadoop workflow system Cloudgene and the cloud orchestration platform CloudMan to provide Hadoop pipelines as a service to everyone

Synthesis and characterization of cationic hydrogels from thiolated copolymers for independent manipulation of mechanical and chemical properties of cell substrates

Cells sense both mechanical and chemical properties in their environment and respond to these inputs with altered phenotypes. Precise and selective experimental manipulations of these environmental cues require biocompatible synthetic materials, for which multiple properties can be fine-tuned independently from each other. For example, cells typically show critical thresholds for cell adhesion as a function of substrate parameters such as stiffness and the degree of functionalization. However, the choice of tailor-made, defined materials to produce such cell adhesion substrates is still very limited. Here, a platform of synthetic hydrogels based on well-defined thiolated copolymers is presented. Therefore, four disulfide crosslinked hydrogels of different composition by free radical polymerization are prepared. After cleavage with dithiothreitol, four soluble copolymers P1–P4 with 0–96% cationic monomer content are obtained. P1 and P4 are then combined with PEGDA3500 as a crosslinker, to fabricate 12 hydrogels with variable elasticity, ranging from 8.1 to 26.3 kPa and cationic group concentrations of up to 350 µmol cm−3. Systematic analysis using COS7 cells shows that all of these hydrogels are nontoxic. However, successful cell adhesion requires both a minimal elasticity and a minimal cationic group concentration

Cloudflow – A Framework for MapReduce Pipeline Development in Biomedical Research

- The data-driven parallelization framework Hadoop MapReduce allows analysing large data sets in a scalable way. Since the development of MapReduce programs can be a time-intensive and challenging task, the application and usage of Hadoop in Biomedical Research is still limited. Here we present Cloudflow, a high-level framework to hide the implementation details of Hadoop and to provide a set of building blocks to create biomedical pipelines in a more intuitive way. We demonstrate the benefit of Cloudflow on three different genetic use cases. It will be shown how the framework can be combined with the Hadoop workflow system Cloudgene and the cloud orchestration platform CloudMan to provide Hadoop pipelines as a service to everyone. The framework is open source and free available at https://github.com/genepi/cloudflow. Document type: Conference objec

CONAN: copy number variation analysis software for genome-wide association studies

<p>Abstract</p> <p>Background</p> <p>Genome-wide association studies (GWAS) based on single nucleotide polymorphisms (SNPs) revolutionized our perception of the genetic regulation of complex traits and diseases. Copy number variations (CNVs) promise to shed additional light on the genetic basis of monogenic as well as complex diseases and phenotypes. Indeed, the number of detected associations between CNVs and certain phenotypes are constantly increasing. However, while several software packages support the determination of CNVs from SNP chip data, the downstream statistical inference of CNV-phenotype associations is still subject to complicated and inefficient in-house solutions, thus strongly limiting the performance of GWAS based on CNVs.</p> <p>Results</p> <p>CONAN is a freely available client-server software solution which provides an intuitive graphical user interface for categorizing, analyzing and associating CNVs with phenotypes. Moreover, CONAN assists the evaluation process by visualizing detected associations via Manhattan plots in order to enable a rapid identification of genome-wide significant CNV regions. Various file formats including the information on CNVs in population samples are supported as input data.</p> <p>Conclusions</p> <p>CONAN facilitates the performance of GWAS based on CNVs and the visual analysis of calculated results. CONAN provides a rapid, valid and straightforward software solution to identify genetic variation underlying the 'missing' heritability for complex traits that remains unexplained by recent GWAS. The freely available software can be downloaded at <url>http://genepi-conan.i-med.ac.at</url>.</p

High-Resolution EM Attacks Against Leakage-Resilient PRFs Explained - And An Improved Construction

Achieving side-channel resistance through Leakage Resilience (LR) is highly relevant for embedded devices where requirements of other countermeasures such as e.g. high quality random numbers are hard to guarantee. The main challenge of LR lays in the initialization of a secret pseudorandom state from a long-term key and public input. Leakage-Resilient Pseudo-Random Functions (LR-PRFs) aim at solving this by bounding side-channel leakage to non-exploitable levels through frequent re-keying. Medwed et al. recently presented an improved construction at ASIACRYPT 2016 which uses \u27unknown-inputs\u27 in addition to limited data complexity and correlated algorithmic noise from parallel S-boxes. However, a subsequent investigation uncovered a vulnerability to high-precision EM analysis on FPGA. In this paper, we follow up on the reasons why such attacks succeed on FPGAs. We find that in addition to the high spatial resolution, it is mainly the high temporal resolution which leads to the reduction of algorithmic noise from parallel S-boxes. While spatial resolution is less threatening for smaller technologies than the used FPGA, temporal resolution will likely remain an issue since balancing the timing behavior of signals in the nanosecond range seems infeasible today. Nonetheless, we present an improvement of the ASIACRYPT 2016 construction to effectively protect against EM attacks with such high spatial and high temporal resolution. We carefully introduce additional key entropy into the LR-PRF construction to achieve a high remaining security level even when implemented on FPGAs. With this improvement, we finally achieve side-channel secure LR-PRFs in a practical and simple way under verifiable empirical assumptions

Functional asymmetry and effective connectivity of the auditory system during speech perception is modulated by the place of articulation of the consonant – A 7 T fMRI study

To differentiate between stop-consonants, the auditory system has to detect subtle place of articulation (PoA) and voice-onset time (VOT) differences between stop-consonants. How this differential processing is represented on the cortical level remains unclear. The present functional magnetic resonance (fMRI) study takes advantage of the superior spatial resolution and high sensitivity of ultra-high-field 7 T MRI. Subjects were attentively listening to consonant–vowel (CV) syllables with an alveolar or bilabial stop-consonant and either a short or long VOT. The results showed an overall bilateral activation pattern in the posterior temporal lobe during the processing of the CV syllables. This was however modulated strongest by PoA such that syllables with an alveolar stop-consonant showed stronger left lateralized activation. In addition, analysis of underlying functional and effective connectivity revealed an inhibitory effect of the left planum temporale (PT) onto the right auditory cortex (AC) during the processing of alveolar CV syllables. Furthermore, the connectivity result indicated also a directed information flow from the right to the left AC, and further to the left PT for all syllables. These results indicate that auditory speech perception relies on an interplay between the left and right ACs, with the left PT as modulator. Furthermore, the degree of functional asymmetry is determined by the acoustic properties of the CV syllables

Long-term effects of an extensive cognitive training on personality development

Previous research found that cognitive training increases the Big Five personality trait openness to experience during and some weeks after the intervention. The present study investigated whether long-term changes happen in openness to experience and other personality traits after an extensive cognitive training of memory and perceptual speed. Method: Intervention group consisted of 204 adults (20-31 years and 65-80 years, 50% female), who received daily one-hour cognitive training sessions for about 100 days. The control group consisted of 86 adults (21-29 years and 65-82 years, 51% female), who received no cognitive training. All participants answered the NEO Five-Factor Inventory before and two years after the cognitive training. Latent change models were applied that controlled for age group (young vs. old) and gender. In the long-run the cognitive training did not affect changes in any facet of openness to experience. This was true for young and old participants as well as for men and women. Instead, the cognitive training lowered the general increase of conscientiousness. Conclusion: Even an extensive cognitive training on memory and perceptual speed does not serve as a sufficient intervention for enduring changes in openness to experiences or one of its facets. (DIPF/Orig.