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

Effect of intra-uterine administration of Lactobacillus bacteria on the steroid hormone profile in sub-clinical endometritis affected cows

Infertility in bovines is a major cause of serious economic loss to the dairy farmers. A major reason for infertility is sub-clinical, retrograde uterine infections. Sub-clinical endometritis is endometrial inflammation without apparent clinical manifestation and usually without signs of infection. This condition may be due to uterine infections or an extended inflammatory period that exists after elimination of bacteria. At present, infertility treatment is mainly done with intrauterine antibacterials, antiseptics and less commonly by hormones. These days, the major problem faced by animal reproductive health workers is the multiple drug resistance pathogens because of the indiscriminate use of antibiotics.Therefore, a different approach for more effective treatment of subclinical endometritis with Lactobacilli and its role on the steroid hormone profile was studied. In the present study, estradiol-17 β values were lower in the sub-clinical endometritis  affected  cows.  Whereas,  intra-uterine administration of Lactobacillus bacteria caused significant increase in estradiol level in a cycle after treatment in cross- bred cows. Similarly, the circulating serum progesterone concentration was also found to be low in subclinical endometritis affected cows. These findings could be used for clinical and experimental interpretations. Further, the information on pulsatile release of gonadotropins and steroid hormones status, receptors and its control, the close relationship among hormones could be necessary for better understanding of the role of steroid hormones in sub-clinical uterine infections

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