University of California, Davis

About: University of California, Davis is a education organization based out in Davis, California, United States. It is known for research contribution in the topics: Population & Poison control. The organization has 78770 authors who have published 180033 publications receiving 8064158 citations. The organization is also known as: UC Davis & UCD.

On sparse reconstruction from Fourier and Gaussian measurements

Abstract: This paper improves upon best-known guarantees for exact reconstruction of a sparse signal f from a small universal sample of Fourier measurements. The method for reconstruction that has recently gained momentum in the sparse approximation theory is to relax this highly nonconvex problem to a convex problem and then solve it as a linear program. We show that there exists a set of frequencies Ω such that one can exactly reconstruct every r-sparse signal f of length n from its frequencies in Ω, using the convex relaxation, and Ω has size k(r, n) = O(r log(n)·log 2 (r) log(r logn)) = O(r log 4 n ). A random set Ω satisfies this with high probability. This estimate is optimal within the log log n and log 3 r factors. We also give a relatively short argument for a similar problem with k(r, n) ≈ r[12 + 8 log(n/r)] Gaussian measurements. We use methods of geometric functional analysis and probability theory in Banach spaces, which makes our arguments quite short.

Analysis of the bread wheat genome using whole-genome shotgun sequencing

Abstract: Bread wheat (Triticum aestivum) is a globally important crop, accounting for 20 per cent of the calories consumed by humans. Major efforts are underway worldwide to increase wheat production by extending genetic diversity and analysing key traits, and genomic resources can accelerate progress. But so far the very large size and polyploid complexity of the bread wheat genome have been substantial barriers to genome analysis. Here we report the sequencing of its large, 17-gigabase-pair, hexaploid genome using 454 pyrosequencing, and comparison of this with the sequences of diploid ancestral and progenitor genomes. We identified between 94,000 and 96,000 genes, and assigned two-thirds to the three component genomes (A, B and D) of hexaploid wheat. High-resolution synteny maps identified many small disruptions to conserved gene order. We show that the hexaploid genome is highly dynamic, with significant loss of gene family members on polyploidization and domestication, and an abundance of gene fragments. Several classes of genes involved in energy harvesting, metabolism and growth are among expanded gene families that could be associated with crop productivity. Our analyses, coupled with the identification of extensive genetic variation, provide a resource for accelerating gene discovery and improving this major crop.

Public Participation in Scientific Research: a Framework for Deliberate Design

Abstract: Members of the public participate in scientific research in many different contexts, stemming from traditions as varied as participatory action research and citizen science. Particularly in conservation and natural resource management contexts, where research often addresses complex social-ecological questions, the emphasis on and nature of this participation can significantly affect both the way that projects are designed and the outcomes that projects achieve. We review and integrate recent work in these and other fields, which has converged such that we propose the term public participation in scientific research (PPSR) to discuss initiatives from diverse fields and traditions. We describe three predominant models of PPSR and call upon case studies suggesting that—regardless of the research context—project outcomes are influenced by (1) the degree of public participation in the research process and (2) the quality of public participation as negotiated during project design. To illustrate relationships between the quality of participation and outcomes, we offer a framework that considers how scientific and public interests are negotiated for project design toward multiple, integrated goals. We suggest that this framework and models, used in tandem, can support deliberate design of PPSR efforts that will enhance their outcomes for scientific research, individual participants, and social-ecological systems.

Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres

Abstract: Polyploidy often confers emergent properties, such as the higher fibre productivity and quality of tetraploid cottons than diploid cottons bred for the same environments. Here we show that an abrupt five- to sixfold ploidy increase approximately 60 million years (Myr) ago, and allopolyploidy reuniting divergent Gossypium genomes approximately 1-2 Myr ago, conferred about 30-36-fold duplication of ancestral angiosperm (flowering plant) genes in elite cottons (Gossypium hirsutum and Gossypium barbadense), genetic complexity equalled only by Brassica among sequenced angiosperms. Nascent fibre evolution, before allopolyploidy, is elucidated by comparison of spinnable-fibred Gossypium herbaceum A and non-spinnable Gossypium longicalyx F genomes to one another and the outgroup D genome of non-spinnable Gossypium raimondii. The sequence of a G. hirsutum A(t)D(t) (in which 't' indicates tetraploid) cultivar reveals many non-reciprocal DNA exchanges between subgenomes that may have contributed to phenotypic innovation and/or other emergent properties such as ecological adaptation by polyploids. Most DNA-level novelty in G. hirsutum recombines alleles from the D-genome progenitor native to its New World habitat and the Old World A-genome progenitor in which spinnable fibre evolved. Coordinated expression changes in proximal groups of functionally distinct genes, including a nuclear mitochondrial DNA block, may account for clusters of cotton-fibre quantitative trait loci affecting diverse traits. Opportunities abound for dissecting emergent properties of other polyploids, particularly angiosperms, by comparison to diploid progenitors and outgroups.