95,693 research outputs found
Patterns of genetic diversity and linkage disequilibrium in a highly structured Hordeum vulgare association-mapping population for the Mediterranean basin
Population structure and genome-wide linkage disequilibrium (LD) were investigated in 192 Hordeum vulgare accessions providing a comprehensive coverage of past and present barley breeding in the Mediterranean basin, using 50 nuclear microsatellite and 1,130 DArT® markers. Both clustering and principal coordinate analyses clearly sub-divided the sample into five distinct groups centred on key ancestors and regions of origin of the germplasm. For given genetic distances, large variation in LD values was observed, ranging from closely linked markers completely at equilibrium to marker pairs at 50 cM separation still showing significant LD. Mean LD values across the whole population sample decayed below r 2 of 0.15 after 3.2 cM. By assaying 1,130 genome-wide DArT® markers, we demonstrated that, after accounting for population substructure, current genome coverage of 1 marker per 1.5 cM except for chromosome 4H with 1 marker per 3.62 cM is sufficient for whole genome association scans. We show, by identifying associations with powdery mildew that map in genomic regions known to have resistance loci, that associations can be detected in strongly stratified samples provided population structure is effectively controlled in the analysis. The population we describe is, therefore, shown to be a valuable resource, which can be used in basic and applied research in barle
Structured Sparsity Models for Multiparty Speech Recovery from Reverberant Recordings
We tackle the multi-party speech recovery problem through modeling the
acoustic of the reverberant chambers. Our approach exploits structured sparsity
models to perform room modeling and speech recovery. We propose a scheme for
characterizing the room acoustic from the unknown competing speech sources
relying on localization of the early images of the speakers by sparse
approximation of the spatial spectra of the virtual sources in a free-space
model. The images are then clustered exploiting the low-rank structure of the
spectro-temporal components belonging to each source. This enables us to
identify the early support of the room impulse response function and its unique
map to the room geometry. To further tackle the ambiguity of the reflection
ratios, we propose a novel formulation of the reverberation model and estimate
the absorption coefficients through a convex optimization exploiting joint
sparsity model formulated upon spatio-spectral sparsity of concurrent speech
representation. The acoustic parameters are then incorporated for separating
individual speech signals through either structured sparse recovery or inverse
filtering the acoustic channels. The experiments conducted on real data
recordings demonstrate the effectiveness of the proposed approach for
multi-party speech recovery and recognition.Comment: 31 page
Experimental damage detection in a wind turbine blade model using principal components of response correlation functions
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Behavioral synthesis from VHDL using structured modeling
This dissertation describes work in behavioral synthesis involving the development of a VHDL Synthesis System VSS which accepts a VHDL behavioral input specification and performs technology independent synthesis to generate a circuit netlist of generic components. The VHDL language is used for input and output descriptions. An intermediate representation which incorporates signal typing and component attributes simplifies compilation and facilitates design optimization.A Structured Modeling methodology has been developed to suggest standard VHDL modeling practices for synthesis. Structured modeling provides recommendations for the use of available VHDL description styles so that optimal designs will be synthesized.A design composed of generic components is synthesized from the input description through a process of Graph Compilation, Graph Criticism, and Design Compilation. Experiments were performed to demonstrate the effects of different modeling styles on the quality of the design produced by VSS. Several alternative VHDL models were examined for each benchmark, illustrating the improvements in design quality achieved when Structured Modeling guidelines were followed
Learning the optimal scale for GWAS through hierarchical SNP aggregation
Motivation: Genome-Wide Association Studies (GWAS) seek to identify causal
genomic variants associated with rare human diseases. The classical statistical
approach for detecting these variants is based on univariate hypothesis
testing, with healthy individuals being tested against affected individuals at
each locus. Given that an individual's genotype is characterized by up to one
million SNPs, this approach lacks precision, since it may yield a large number
of false positives that can lead to erroneous conclusions about genetic
associations with the disease. One way to improve the detection of true genetic
associations is to reduce the number of hypotheses to be tested by grouping
SNPs. Results: We propose a dimension-reduction approach which can be applied
in the context of GWAS by making use of the haplotype structure of the human
genome. We compare our method with standard univariate and multivariate
approaches on both synthetic and real GWAS data, and we show that reducing the
dimension of the predictor matrix by aggregating SNPs gives a greater precision
in the detection of associations between the phenotype and genomic regions
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