On Binary Matroid Minors and Applications to Data Storage over Small Fields

Locally repairable codes for distributed storage systems have gained a lot of interest recently, and various constructions can be found in the literature. However, most of the constructions result in either large field sizes and hence too high computational complexity for practical implementation, or in low rates translating into waste of the available storage space. In this paper we address this issue by developing theory towards code existence and design over a given field. This is done via exploiting recently established connections between linear locally repairable codes and matroids, and using matroid-theoretic characterisations of linearity over small fields. In particular, nonexistence can be shown by finding certain forbidden uniform minors within the lattice of cyclic flats. It is shown that the lattice of cyclic flats of binary matroids have additional structure that significantly restricts the possible locality properties of $\mathbb{F}_{2}$-linear storage codes. Moreover, a collection of criteria for detecting uniform minors from the lattice of cyclic flats of a given matroid is given, which is interesting in its own right.Comment: 14 pages, 2 figure

Integrated genomic analyses of ovarian carcinoma

A catalogue of molecular aberrations that cause ovarian cancer is critical for developing and deploying therapies that will improve patients’ lives. The Cancer Genome Atlas project has analysed messenger RNA expression, microRNA expression, promoter methylation and DNA copy number in 489 high-grade serous ovarian adenocarcinomas and the DNA sequences of exons from coding genes in 316 of these tumours. Here we report that high-grade serous ovarian cancer is characterized by TP53 mutations in almost all tumours (96%); low prevalence but statistically recurrent somatic mutations in nine further genes including NF1, BRCA1, BRCA2, RB1 and CDK12; 113 significant focal DNA copy number aberrations; and promoter methylation events involving 168 genes. Analyses delineated four ovarian cancer transcriptional subtypes, three microRNA subtypes, four promoter methylation subtypes and a transcriptional signature associated with survival duration, and shed new light on the impact that tumours with BRCA1/2 (BRCA1 or BRCA2) and CCNE1 aberrations have on survival. Pathway analyses suggested that homologous recombination is defective in about half of the tumours analysed, and that NOTCH and FOXM1 signalling are involved in serous ovarian cancer pathophysiology.National Institutes of Health (U.S.) (Grant U54HG003067)National Institutes of Health (U.S.) (Grant U54HG003273)National Institutes of Health (U.S.) (Grant U54HG003079)National Institutes of Health (U.S.) (Grant U24CA126543)National Institutes of Health (U.S.) (Grant U24CA126544)National Institutes of Health (U.S.) (Grant U24CA126546)National Institutes of Health (U.S.) (Grant U24CA126551)National Institutes of Health (U.S.) (Grant U24CA126554)National Institutes of Health (U.S.) (Grant U24CA126561)National Institutes of Health (U.S.) (Grant U24CA126563)National Institutes of Health (U.S.) (Grant U24CA143882)National Institutes of Health (U.S.) (Grant U24CA143731)National Institutes of Health (U.S.) (Grant U24CA143835)National Institutes of Health (U.S.) (Grant U24CA143845)National Institutes of Health (U.S.) (Grant U24CA143858)National Institutes of Health (U.S.) (Grant U24CA144025)National Institutes of Health (U.S.) (Grant U24CA143866)National Institutes of Health (U.S.) (Grant U24CA143867)National Institutes of Health (U.S.) (Grant U24CA143848)National Institutes of Health (U.S.) (Grant U24CA143843)National Institutes of Health (U.S.) (Grant R21CA135877

Metatranscriptomics reveals metabolic adaptation and induction of virulence factors by Haemophilus parasuis during lung infection

International audienceAbstractHaemophilus parasuis is a common inhabitant of the upper respiratory tract of pigs, and the causative agent of Glässer’s disease. This disease is characterized by polyserositis and arthritis, produced by the severe inflammation caused by the systemic spread of the bacterium. After an initial colonization of the upper respiratory tract, H. parasuis enters the lung during the early stages of pig infection. In order to study gene expression at this location, we sequenced the ex vivo and in vivo H. parasuis Nagasaki transcriptome in the lung using a metatranscriptomic approach. Comparison of gene expression under these conditions with that found in conventional plate culture showed generally reduced expression of genes associated with anabolic and catabolic pathways, coupled with up-regulation of membrane-related genes involved in carbon acquisition, iron binding and pathogenesis. Some of the up-regulated membrane genes, including ABC transporters, virulence-associated autotransporters (vtaAs) and several hypothetical proteins, were only present in virulent H. parasuis strains, highlighting their significance as markers of disease potential. Finally, the analysis also revealed the presence of numerous antisense transcripts with possible roles in gene regulation. In summary, this data sheds some light on the scarcely studied in vivo transcriptome of H. parasuis, revealing nutritional virulence as an adaptive strategy for host survival, besides induction of classical virulence factors

Comparing Two Implementations of a Complete and Backtrack-Free Interactive Configurator

A product configurator should be complete and backtrack free in the sense that the user can choose freely between any valid configuration and will be prevented from making choices that no valid configuration satisfies. In this paper, we experimentally evaluate a symbolic and search-based implementation of an interactive product configuration algorithm with these properties. Our results show that the symbolic approach often has several orders of magnitude faster response time than the search-based approach due to the precompilation of a symbolic representation of the solution space. Moreover, the difference between the average and worst response time for the symbolic approach is typically within a factor of two, whereas it for the search-based approach may be more than two orders of magnitude

Comparing Two Implementations of a Complete and Backtrack-Free Interactive Configurator

A product configurator should be complete and backtrack free in the sense that the user can choose freely between any valid configuration and will be prevented from making choices that no valid configuration satisfies. In this paper, we experimentally evaluate a symbolic and search-based implementation of an interactive product configuration algorithm with these properties. Our results show that the symbolic approach often has several orders of magnitude faster response time than the search-based approach due to the precompilation of a symbolic representation of the solution space. Moreover, the di#erence between the average and worst response time for the symbolic approach is typically within a factor of two, whereas it for the search-based approach may be more than two orders of magnitude

Fast backtrack-free product configuration using a precompiled solution space representation

In this paper we describe a two-phase approach to interactive product configuration. In the first phase, a compressed symbolic representation of the set of valid configurations (the solution space) is compiled offline. In the second phase, this representation is embedded in an online configurator and utilized for fast, complete, and backtrack-free interactive product configuration. The main advantage of our approach compared to online search-based approaches is that we avoid searching for valid solutions in each iteration of the interactive configuration process. The computationally hard part of the problem is fully solved in the offline phase given that the produced symbolic representation is small. The employed symbolic representation is Binary Decision Diagrams (BDDs). More than a decade of research in formal verification has shown that BDDs often compactly encode formal models of systems encountered in practice. To our experience this is also the case for product models. Often the compiled BDD is small enough to be embedded directly in hardware. Our research has led to the establishment of a spin-off company called Configit Software A/S. Configit has developed software for writing product models in a strongly typed language and has patented a particularly efficient symbolic representation called Virtual Tables

Microclimate monitoring system for irrigation water optimization using IoT

The new notion of Agri (from ‘Agre’, latin for Land) – Culture (latin for Cultivation) is what made the transition of human race from primitive hunter-gatherers to more civilized and ordered societies. The invention of agriculture can be regarded as a key point in the timeline and dawn of modern civilization as we know it today. With the advent of digital electronics, we are now capable of carefully device systems to make any processes more optimized and generate significantly higher output, this is also true for the agriculture sector and many works are carried out recently aimed towards this objective and even created a new domain of precision agriculture. In this research work, an IoT-based system was developed that enables the farmers to monitor various micro-climatic parameters and assess the irrigation water requirement. The soil moisture and temperature were sensed with the aid of sensors and were fed to the LoRA system, in the receiver side, data is analyzed for the estimation of evapotranspiration. The global evapotranspiration was estimated using Cropwat software. The sensor data were analyzed using Mcguinnes-Bordne formulation and the outcome of this research work paves the way towards the estimation of the evapotranspiration in the microclimate environment