Efficient Low Rank Matrix Recovery With Flexible Group Sparse Regularization

In this paper, we present a novel approach to the low rank matrix recovery (LRMR) problem by casting it as a group sparsity problem. Specifically, we propose a flexible group sparse regularizer (FLGSR) that can group any number of matrix columns as a unit, whereas existing methods group each column as a unit. We prove the equivalence between the matrix rank and the FLGSR under some mild conditions, and show that the LRMR problem with either of them has the same global minimizers. We also establish the equivalence between the relaxed and the penalty formulations of the LRMR problem with FLGSR. We then propose an inexact restarted augmented Lagrangian method, which solves each subproblem by an extrapolated linearized alternating minimization method. We analyze the convergence of our method. Remarkably, our method linearizes each group of the variable separately and uses the information of the previous groups to solve the current group within the same iteration step. This strategy enables our algorithm to achieve fast convergence and high performance, which are further improved by the restart technique. Finally, we conduct numerical experiments on both grayscale images and high altitude aerial images to confirm the superiority of the proposed FLGSR and algorithm

Quitosana e fungicidas no controle pós-colheita de Guignardia citricarpa e na qualidade de laranjas 'Pêra Rio'

Citrus fruits are affected by the black spot disease caused by the fungus Guignardia citricarpa. Chitosan can be used as covering for fruits and may delay the ripening process and inhibit the growth of some fungi. Thus, the control of citrus black spot using chitosan and the fungicides thiabendazole and imazalil was assessed in addition to the physicochemical quality of 'Pêra Rio' oranges. The oranges were immersed into chitosan, thiabendazole or imazalil, and in chitosan mixed with both fungicides. The fruits were then stored at 25 °C, 80% RH, for 7 days and, after this storage period, subjected to physicochemical analyses. Chitosan in association with the fungicides reduced black spot in 'Pêra Rio' oranges and delayed the change in the orange skin colour from green to yellow during the postharvest storage. Total soluble solids, titratable acidity, pH, ascorbic acid content and ratio were not influenced by the treatments. Thus, chitosan applied with the fungicides thiabendazole and imazalil showed potential to control the development of black spot lesions on 'Pêra Rio' oranges during the postharvest period.Os frutos cítricos são afetados pela pinta preta dos citros, causada pelo fungo Guignardia citricarpa. A quitosana pode ser utilizada como revestimento de frutos, sendo capaz de atrasar o processo de maturação e inibir o crescimento de fungos. Dessa maneira, o controle da pinta preta utilizando quitosana e os fungicidas tiabendazole e imazalil foi avaliado, assim como a qualidade físico-química de laranjas 'Pêra Rio'. Frutos de laranja foram imersos em quitosana, tiabendazole ou imazalil, e em quitosana em mistura com ambos os fungicidas. Os frutos foram armazenados a 25°C, 80% UR, por 7 dias e após o período de armazenamento foram submetidos a análises fisico-químicas. Quitosana em associação com os fungicidas reduziu o aparecimento da pinta preta em laranjas 'Pêra Rio' e atrasou a alteração de verde para amarelo da cor da casca das laranjas durante o armazenamento pós-colheita. Os sólidos solúveis totais, a acidez titulável, o pH, o ácido ascórbico e o ratio não sofreram influência dos tratamentos. Deste modo, a quitosana em aplicação com os fungicidas tiabendazol e imazalil aumentou o potencial de controle da pinta preta em laranjas 'Pêra Rio' em pós-colheita, mantendo a qualidade dos frutos cítricos.Fundação de Apoio à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

PhyloCSF: a comparative genomics method to distinguish protein-coding and non-coding regions

As high-throughput transcriptome sequencing provides evidence for novel transcripts in many species, there is a renewed need for accurate methods to classify small genomic regions as protein-coding or non-coding. We present PhyloCSF, a novel comparative genomics method that analyzes a multi-species nucleotide sequence alignment to determine whether it is likely to represent a conserved protein-coding region, based on a formal statistical comparison of phylogenetic codon models. We show that PhyloCSF's classification performance in 12-species _Drosophila_ genome alignments exceeds all other methods we compared in a previous study, and we provide a software implementation for use by the community. We anticipate that this method will be widely applicable as the transcriptomes of many additional species, tissues, and subcellular compartments are sequenced, particularly in the context of ENCODE and modENCODE

Testing the Coding Potential of Conserved Short Genomic Sequences

Proposed is a procedure to test whether a genomic sequence contains coding DNA, called a coding potential region. The procedure tests the coding potential of conserved short genomic sequence, in which the assumptions on the probability models of gene structures are relaxed. Thus, it is expected to provide additional candidate regions that contain coding DNAs to the current genomic database. The procedure was applied to the set of highly conserved human-mouse sequences in the genome database at the University of California at Santa Cruz. For sequences containing RefSeq coding exons, the procedure detected 91.3% regions having coding potential in this set, which covers 83% of the human RefSeq coding exons, at a 2.6% false positive rate. The procedure detected 12,688 novel short regions with coding potential at the false discovery rate <0.05; 65.7% of the novel regions are between annotated genes