An Optimal Linear Time Algorithm for Quasi-Monotonic Segmentation

Monotonicity is a simple yet significant qualitative characteristic. We consider the problem of segmenting a sequence in up to K segments. We want segments to be as monotonic as possible and to alternate signs. We propose a quality metric for this problem using the l_inf norm, and we present an optimal linear time algorithm based on novel formalism. Moreover, given a precomputation in time O(n log n) consisting of a labeling of all extrema, we compute any optimal segmentation in constant time. We compare experimentally its performance to two piecewise linear segmentation heuristics (top-down and bottom-up). We show that our algorithm is faster and more accurate. Applications include pattern recognition and qualitative modeling.Comment: This is the extended version of our ICDM'05 paper (arXiv:cs/0702142

Antimicrobial activity of biogenically produced spherical Se-nanomaterials embedded in organic material against Pseudomonas aeruginosa and Staphylococcus aureus strains on hydroxyapatite-coated surfaces

In an effort to prevent the formation of pathogenic biofilms on hydroxyapatite (HA)-based clinical devices and surfaces, we present a study evaluating the antimicrobial efficacy of Spherical biogenic Se-Nanostructures Embedded in Organic material (Bio Se-NEMO-S) produced by Bacillus mycoides SelTE01 in comparison with two different chemical selenium nanoparticle (SeNP) classes. These nanomaterials have been studied as potential antimicrobials for eradication of established HA-grown biofilms, for preventing biofilm formation on HA-coated surfaces and for inhibition of planktonic cell growth of Pseudomonas aeruginosa NCTC 12934 and Staphylococcus aureus ATCC 25923. Bio Se-NEMO resulted more efficacious than those chemically produced in all tested scenarios. Bio Se-NEMO produced by B. mycoides SelTE01 after 6 or 24 h of Na 2 SeO 3 exposure show the same effective antibiofilm activity towards both P. aeruginosa and S. aureus strains at 0.078 mg ml −1 (Bio Se-NEMO 6 ) and 0.3125 mg ml −1 (Bio Se-NEMO 24 ). Meanwhile, chemically synthesized SeNPs at the highest tested concentration (2.5 mg ml −1 ) have moderate antimicrobial activity. The confocal laser scanning micrographs demonstrate that the majority of the P. aeruginosa and S. aureus cells exposed to biogenic SeNPs within the biofilm are killed or eradicated. Bio Se-NEMO therefore displayed good antimicrobial activity towards HA-grown biofilms and planktonic cells, becoming possible candidates as new antimicrobials

Centralizers of maximal regular subgroups in simple Lie groups and relative congruence classes of representations

In the paper we present a new, uniform and comprehensive description of centralizers of the maximal regular subgroups in compact simple Lie groups of all types and ranks. The centralizer is either a direct product of finite cyclic groups, a continuous group of rank 1, or a product, not necessarily direct, of a continuous group of rank 1 with a finite cyclic group. Explicit formulas for the action of such centralizers on irreducible representations of the simple Lie algebras are given.Comment: 27 page

Zidovudine and dideoxynucleosides deplete wild-type mitochondrial DNA levels and increase deleted mitochondrial DNA levels in cultured Kearns-Sayre syndrome fibroblasts

AbstractKearns-Sayre syndrome is the most commonly diagnosed mitochondrial cytopathy and produces severe neuromuscular symptoms. The most frequent cause is a mitochondrial DNA deletion that removes a 4977-base pair segment of DNA that includes several genes encoding for respiratory chain subunits. Treatment of AIDS patients with nucleoside analogs has been reported to cause mtDNA depletion and myopathies. Here, we report that azidothymidine, dideoxyguanosine, and dideoxycytidine cause a depletion of wild-type mtDNA while increasing the levels of deleted mitochondria DNA in Kearns-Sayre syndrome fibroblasts. The result of these effects is a large increase in the relative amounts of ΔmtDNA in comparison to wild type mtDNA. We found that Kearns-Sayre syndrome fibroblasts are a mixed population of cells with deleted mtDNA comprising from 0 to over 20% of the total mtDNA in individual cells. Treatment of cloned cell lines with dideoxycytidine did not result in increased levels of ΔmtDNA. The results suggest that nucleoside analogs may act to increase the average ΔmtDNA levels in a mixed population of cells by preferentially inhibiting the proliferation of cells with little or no ΔmtDNA. This raises the possibility that modulation of deleted mtDNA levels may occur by similar mechanisms in vivo, in response to the influence of exogenous agents

Removal of the phage-shock protein PspB causes reduction of virulence in Salmonella enterica serovar Typhimurium independently of NRAMP1

The phage-shock protein (Psp) system is believed to manage membrane stress in all Enterobacteriaceae and has recently emerged as being important for virulence in several pathogenic species of this phylum. The core of the Psp system consists of the pspA-D operon and the distantly located pspG gene. In Salmonella enterica serovar Typhimurium (S. Typhimurium), it has recently been reported that PspA is essential for systemic infection of mice, but only in NRAMP1(+) mice, signifying that attenuation is related to coping with divalent cation starvation in the intracellular environment. In the present study, we investigated the contribution of individual psp genes to virulence of S. Typhimurium. Interestingly, deletion of the whole pspA-D set of genes caused attenuation in both NRAMP1(+) and NRAMP1(-) mice, indicating that one or more of the psp genes contribute to virulence independently of NRAMP1 expression in the host. Investigations of single gene mutants showed that knock out of pspB reduced virulence in both types of mice, while deletion of pspA only caused attenuation in NRAMP1(+) mice, and deletion of pspD had a minor effect in NRAMP1(-) mice, while deletions of either pspC or pspG did not affect virulence. Experiments addressed at elucidating the role of PspB in virulence revealed that PspB is dispensable for uptake to and intracellular replication in cultured macrophages and resistance to complement-induced killing. Furthermore, the Psp system of S. Typhimurium was dispensable during pIV-induced secretin stress. In conclusion, our results demonstrate that removal of PspB reduces virulence in S. Typhimurium independently of host NRAMP1 expression, demonstrating that PspB has roles in intra-host survival distinct from the reported contributions of PspA

A Heuristic Based on the Intrinsic Dimensionality for Reducing the Number of Cyclic DTW Comparisons in Shape Classification and Retrieval Using AESA

Cyclic Dynamic Time Warping (CDTW) is a good dissimilarity of shape descriptors of high dimensionality based on contours, but it is computationally expensive. For this reason, to perform recognition tasks, a method to reduce the number of comparisons and avoid an exhaustive search is convenient. The Approximate and Eliminate Search Algorithm (AESA) is a relevant indexing method because of its drastic reduction of comparisons, however, this algorithm requires a metric distance and that is not the case of CDTW. In this paper, we introduce a heuristic based on the intrinsic dimensionality that allows to use CDTW and AESA together in classification and retrieval tasks over these shape descriptors. Experimental results show that, for descriptors of high dimensionality, our proposal is optimal in practice and significantly outperforms an exhaustive search, which is the only alternative for them and CDTW in these tasks

Exome-wide association study of pancreatic cancer risk

We conducted a case-control exome-wide association study to discover germline variants in coding regions that affect risk for pancreatic cancer, combining data from 5 studies. We analyzed exome and genome sequencing data from 437 patients with pancreatic cancer (cases) and 1922 individuals not known to have cancer (controls). In the primary analysis, BRCA2 had the strongest enrichment for rare inactivating variants (17/437 cases vs 3/1922 controls) (P=3.27x10(-6); exome-wide statistical significance threshold P<2.5x10(-6)). Cases had more rare inactivating variants in DNA repair genes than controls, even after excluding 13 genes known to predispose to pancreatic cancer (adjusted odds ratio, 1.35, P=.045). At the suggestive threshold (P<.001), 6 genes were enriched for rare damaging variants (UHMK1, AP1G2, DNTA, CHST6, FGFR3, and EPHA1) and 7 genes had associations with pancreatic cancer risk, based on the sequence-kernel association test. We confirmed variants in BRCA2 as the most common high-penetrant genetic factor associated with pancreatic cancer and we also identified candidate pancreatic cancer genes. Large collaborations and novel approaches are needed to overcome the genetic heterogeneity of pancreatic cancer predisposition

Anemia, iron status, and associated protective and risk factors among children and adolescents aged 3 to 19 years old from four First Nations communities in Quebec

Objectives: Anemia and iron deficiency (ID) are frequent among Indigenous children of Canada, but few data are available in Quebec. The present study aimed to characterize anemia and ID prevalence and associated protective and risk factors among First Nations youth in Quebec. Methods: The 2015 First Nations (JES!-YEH!) pilot study was conducted among children and adolescents (3 to 19 years; n=198) from four First Nations communities in Quebec. Blood and urine samples and anthropometric measurements were collected. Hemoglobin (Hb), serum ferritin (SF), plasma hs-CRP, and urinary cotinine levels were measured. Factors associated with anemia and ID (including traditional and market food consumption) were assessed using an interview-administered food frequency questionnaire, based on which nutritional intakes were calculated. Structural equation models were used totest associations. Results: The prevalence of anemia and ID was elevated (16.8% and 20.5% respectively). Traditional meat, fruit, and fruit juice (naturaland powdered)—via their positive association with vitamin C intake—were the only food variables positively associated with SF (coefficient [95% CI] 0.017 [0.000, 0.114]; 0.090 [0.027, 0.161]; and 0.237 [0.060, 0.411]). Male sex was also associated with higher SF (0.295 [0.093, 0.502]). Inflammation status (hs-CRP > 5 mg/L) was inversely associated with Hb (−0.015 [−0.025,−0.005]), whereas SF was positively associated with Hb (0.066 [0.040, 0.096]). Fruit and juice consumption was also positively associated with Hb, via vitamin C intake and SF (0.004 [0.001, 0.010]; 0.008 [0.003, 0.017]). Conclusions: Interventions fostering healthier food environments as well as higher consumption of traditional meats and foods naturally rich in vitamin C, which is known to enhance iron absorption, and fighting inflammation could contribute to decrease the high prevalence of anemia and ID in this young Indigenous population.Objectifs : L’anémie et la carence en fer sont fréquentes chez les enfants autochtones au Canada, mais peu de données sont disponibles au Québec. La présente étude visait à caractériser la prévalence de l’anémie et de la carence en fer et les facteurs protecteurs et des risques associés chez des jeunes des Premières Nations du Québec. Méthodes : En 2015, l’étude pilote Jeunes Environnement et Santé (JES! - YEH!) a été menée chez des enfants et des adolescents (3 à 19 ans,n= 198) de quatre communautés de Premières Nations au Québec. Des échantillons de sang et d’urine et des mesures anthropométriques ont été recueillis. Les concentrations d’hémoglobine, de ferritine sérique, de hs-CRP plasmatique et decotinine urinaire ont été mesurées. Les facteurs associés à l’anémie et à la carence en fer (y compris la consommation d’aliments traditionnels et de marché) ont été évalués à l’aide de questionnaires de fréquences alimentaires administré par un assistant de recherche, à partir desquels les apports nutritionnels ont été calculés. Des modèles d’équations structurelles ont été utilisés pour tester les associations. Résultats : La prévalence de l’anémie et de la carence en fer était élevée (16,8 % et 20,5 % respectivement). La viande traditionnelle, les fruits et les jus de fruits (naturels et en poudre) − par l’intermédiaire de leur association positive avec l’apport en vitamine C − étaient les seules variables alimentaires positivement associées à la ferritine sérique (coefficient [IC à 95 %] : 0,017 [0,000, 0,114]; 0,090 [0,027, 0,161]; et 0,237 [0,060, 0,411]). Le sexe masculin était également associé à une ferritine sérique plus élevée (0,295 [0,093, 0,502]). Le statut inflammatoire (hs-CRP > 5 mg/L) était inversement associé à l’hémoglobine (−0,015 [−0,025,−0,005]) alors que la ferritine sérique était positivement associée à l’hémoglobine (0,066 [0,040, 0,096]). La consommation de fruits et de jus était aussi positivement associée à l’hémoglobine via l’apport en vitamine C et la ferritine sérique (0,004 [0,001, 0,010]; 0,008 [0,003, 0,017]). Conclusions : Les interventions favorisant des environnements alimentaires plus sains ainsi qu’une consommation plus élevée de viandes et d’aliments traditionnels naturellement riches en vitamine C, qui sont connus d’améliorer l’absorption de fer, ainsi que luttant contre l’inflammation pourraient contribuer à diminuer la prévalence élevée d’anémie et de la carence en fer dans cette jeune population autochtone

Method for fabricating submicron silicide structures on silicon using a resistless electron beam lithography process

Abstract : A novel resistless lithography process using a conventional electron beam system is presented. Metallic lines with widths of less than 50 nm were produced on silicon substrates. The process is based on localized heating with a focused electron beam of thin platinum layers deposited on silicon. It is demonstrated that silicide formation occurs at the Pt-Si interface. By using a dilute solution of aqua regia, it is possible to obtain a sufficient difference in etch rates between exposed and unexposed regions of the platinum thin film to selectively remove only the unexposed areas