Path constraints in semistructured data

International audienceWe consider semistructured data as multirooted edge-labelled directed graphs, and path inclusion constraints on these graphs. A path inclusion constraint pnot precedes, equalsq is satisfied by a semistructured data if any node reached by the regular query p is also reached by the regular query q. In this paper, two problems are mainly studied: the implication problem and the problem of the existence of a finite exact model. - We give a new decision algorithm for the implication problem of a constraint pnot precedes, equalsq by a set of bounded path constraints pinot precedes, equalsui where p, q, and the pi's are regular path expressions and the ui's are words, improving in this particular case, the more general algorithms of S. Abiteboul and V. Vianu, and N. Alechina et al. In the case of a set of word equalities ui≡vi, we provide a more efficient decision algorithm for the implication of a word equality u≡v, improving the more general algorithm of P. Buneman et al. We prove that, in this case, implication for nondeterministic models is equivalent to implication for (complete) deterministic ones. - We introduce the notion of exact model: an exact model of a set of path constraints Click to view the MathML source satisfies the constraint pnot precedes, equalsq if and only if this constraint is implied by Click to view the MathML source. We prove that any set of constraints has an exact model and we give a decidable characterization of data which are exact models of bounded path inclusion constraints sets

SERG Final report: Ecosystemic impacts of forest tent caterpillar outbreaks

The forest tent caterpillar (Malacosoma disstria) is a significant defoliator of hardwoods throughout Canada. Historically, infestations usually collapsed after one or two years of defoliation, but longer and more severe outbreaks have been observed in recent years, leading to mortality of both sugar maple and trembling aspen, and making the forest tent caterpillar another pest whose impacts are increasing under a changing climate. This project examines how forest tent caterpillar outbreaks influence soil ecosystems, in both temperate deciduous and mixed boreal forests. We will assess inputs to soil ecosystems associated with forest tent caterpillar outbreaks and determine impacts on soil arthropod communities and tree regeneration. We also examine the different sources of mortality of the forest tent caterpillar colonies during and after the outbreak. It will thus provide empirical data to assess effects of forest tent caterpillar outbreaks on forest ecosystems and successional processes as well as population dynamics throughout the outbreaking cycle. Results suggest that defoliation favours the growth of non-host saplings. They also suggest that sources of mortality change during the different parts of the outbreak. Results will also contribute to the development of novel silvicultural approaches taking into account the effects of forest tent caterpillar outbreaks on forest regeneration and the need to keep process promoting regulation of forest tent caterpillar populations. La livrée des forêts (Malacosoma disstria) est un défoliateur important des forêts feuillues du Canada. Dans le passé, les épidémies s’effondraient généralement après une ou deux années de défoliation sans causer de dommages significatifs à la forêt, mais l’observation récente d’épidémies plus longues et plus sévères, suivies de mortalité des tiges de peuplier faux-tremble et d’érable à sucre, suggèrent que les impacts de la livrée des forêts, comme de plusieurs autres insectes ravageurs, augmentent en raison des changements climatiques. Ce projet examine les effets d’une épidémie de livrée des forêts sur l’écosystème du sol dans deux écosystèmes forestiers: la forêt feuillue et la forêt boréale mixte. Nous examinerons les apports en nutriments au sol associés aux épidémies de livrée et évaluerons les effets sur la communauté d’arthropodes du sol et sur la régénération des arbres. Nous avons aussi examiné les sources de mortalité des colonies de livrée des forêts durant et après l’épidémie. Les résultats fourniront des données empiriques pour évaluer les impacts des épidémies de livrée sur les écosystèmes forestiers et les processus de succession écologiques ainsi que les dynamiques de populations à travers les cycles épidémiques. Les résultats suggèrent que la défoliation peut bénéficier la croissance des jeunes arbres non-hôtes. Ils suggèrent aussi que les sources de mortalité diffèrent lors des différentes parties du cycles épidémiques. Les résultats contribueront aussi au développement d’approches sylvicoles qui prennent en considération le rôle de la livrée dans la régénération des forêts

XML Security Views Revisited

International audienceIn this paper, we revisit the view based security framework for XML without imposing any of the previously considered restrictions on the class of queries, the class of DTDs, and the type of annotations used to dene the view. First, we show that the full class of Regular XPath queries is closed under query rewriting. Next, we address the problem of constructing a DTD that describes the view schema, which in general needs not be regular. We propose three dierent methods of ap- proximating the view schema and we show that the produced DTDs are indistinguishable from the exact schema (with queries from a class speci c for each method). Finally, we investigate problems of static analysis of security access specications

Clinical behavior and outcomes of breast cancer in young women with germline BRCA pathogenic variants

Càncer de mama; Genètica del càncerCáncer de mama; Genética del cáncerBreast cancer; Cancer geneticsYoung breast cancer (BC) patients carrying a germline BRCA pathogenic variant (mBRCA) have similar outcomes as non-carriers. However, the impact of the type of gene (BRCA1 vs. BRCA2) and hormone receptor status (positive [HR+] vs. negative [HR−]) on clinical behavior and outcomes of mBRCA BC remains largely unknown. This is an international, multicenter, hospital-based, retrospective cohort study that included mBRCA patients diagnosed, between January 2000 and December 2012, with stage I–III invasive early BC at age ≤40 years. From 30 centers worldwide, 1236 young mBRCA BC patients were included. Among 808 and 428 patients with mBRCA1 or mBRCA2, 191 (23.6%) and 356 (83.2%) had HR+tumors, respectively (P < 0.001). Median follow-up was 7.9 years. Second primary BC (P = 0.009) and non-BC malignancies (P = 0.02) were more frequent among mBRCA1 patients while distant recurrences were less frequent (P = 0.02). Irrespective of hormone receptor status, mBRCA1 patients had worse disease-free survival (DFS; adjusted HR = 0.76, 95% CI = 0.60–0.96), with no difference in distant recurrence-free interval (DRFI) and overall survival (OS). Patients with HR+ disease had more frequent distant recurrences (P < 0.001) and less frequent second primary malignancies (BC: P = 0.005; non-BC: P = 0.18). No differences in DFS and OS were observed according to hormone receptor status, with a tendency for worse DRFI (adjusted HR = 1.39, 95% CI = 0.94–2.05) in patients with HR+ BC. Type of mBRCA gene and hormone receptor status strongly impact BC clinical behavior and outcomes in mBRCA young patients. These results provide important information for patients’ counseling on treatment, prevention, and surveillance strategies.This study received partial financial support by grants from the Italian Ministry of Health - 5 × 1000 funds 2017 (no grant number), the Italian Association for Cancer Research (AIRC; MFAG 2020 ID 24698), and “Les Amis de l’Institut Bordet” foundation (no grant number). The funders had no role in the design and conduct of the study; collection, management, analysis, and interpretation of the data; preparation, review, or approval of the manuscript; and decision to submit the manuscript for publication. M.L. acknowledges the support from the European Society for Medical Oncology (ESMO) for a Translational Research Fellowship at the Institut Jules Bordet in Brussels (Belgium) at the time of study conduction. K.P. acknowledges the support from a predoctoral clinical ‘KOOR’ mandate from the University Hospitals Leuven (Leuven, Belgium). F.P.D. acknowledges the support for a postdoctoral clinical mandate (2017-034) from the not-for-profit organization ‘Foundation Against Cancer’ (Brussels, Belgium). A.H.P. acknowledges the support from Susan G. Komen and Breast Cancer Research Foundation (BCRF). J.H. acknowledges the support from the Carlos III National Health Institute funded by FEDER funds—a way to build Europe (PI16/11363). This research was presented in the Poster Spotlight session at the 2020 San Antonio Breast Cancer Symposium (SABCS), San Antonio, TX, United States of America, on 8–12 December 2020

Static analysis of XML security views and query rewriting

International audienceIn this paper, we revisit the view based security framework for XML without imposing any of the previously considered restrictions on the class of queries, the class of DTDs, and the type of annotations used to define the view. First, we study {\em query rewriting} with views when the classes used to define queries and views are Regular XPath and MSO. Next, we investigate problems of {\em static analysis} of security access specifications (SAS): we introduce the novel class of \emph{interval-bounded} SAS and we define three different manners to compare views (i.e. queries), with a security point of view. We provide a systematic study of the complexity for deciding these three comparisons, when the depth of the XML documents is bounded, when the document may have an arbitrary depth but the queries defining the views are restricted to guarantee the interval-bounded property, and in the general setting without restriction on queries and document

View update translation for XML

We study the problem of update translation for views on XML documents. More precisely, given an XML view definition and a user defined view update program, find a source update program that translates the view update without side effects on the view. Additionally, we require the translation to be defined on all possible source documents; this corresponds to Hegnerâ\u80\u99s notion of uniform translation. The existence of such translation would allow to update XML views without the need of materialization. The class of views we consider can remove parts of the document and rename nodes. Our update programs define the simultaneous application of a collection of atomic update operations among insertion/deletion of a subtree and node renaming. Such update programs are compatible with the XQuery Update Facility (XQUF) snapshot semantics. Both views and update programs are represented by recognizable tree languages. We present as a proof of concept a small fragment of XQUF that can be expressed by our update programs, thus allows for update propagation. Two settings for the update problem are studied: without source constraints, where all source updates are allowed, and with source constraints, where there is a restricted set of authorized source updates. Using tree automata techniques, we establish that without constraints, all view updates are uniformly translatable and the translation is tractable. In presence of constraints, not all view updates are uniformly translatable. However, we introduce a reasonable restriction on update programs for which uniform translation with constraints becomes possible

Impact of the Exposome on the Epigenome in Inflammatory Bowel Disease Patients and Animal Models

peer reviewedInflammatory bowel diseases (IBD) are chronic inflammatory disorders of the gastrointestinal tract that encompass two main phenotypes, namely Crohn’s disease and ulcerative colitis. These conditions occur in genetically predisposed individuals in response to environmental factors. Epigenetics, acting by DNA methylation, post-translational histones modifications or by non-coding RNAs, could explain how the exposome (or all environmental influences over the life course, from conception to death) could influence the gene expression to contribute to intestinal inflammation. We performed a scoping search using Medline to identify all the elements of the exposome that may play a role in intestinal inflammation through epigenetic modifications, as well as the underlying mechanisms. The environmental factors epigenetically influencing the occurrence of intestinal inflammation are the maternal lifestyle (mainly diet, the occurrence of infection during pregnancy and smoking); breastfeeding; microbiota; diet (including a low-fiber diet, high-fat diet and deficiency in micronutrients); smoking habits, vitamin D and drugs (e.g., IBD treatments, antibiotics and probiotics). Influenced by both microbiota and diet, short-chain fatty acids are gut microbiota-derived metabolites resulting from the anaerobic fermentation of non-digestible dietary fibers, playing an epigenetically mediated role in the integrity of the epithelial barrier and in the defense against invading microorganisms. Although the impact of some environmental factors has been identified, the exposome-induced epimutations in IBD remain a largely underexplored field. How these environmental exposures induce epigenetic modifications (in terms of duration, frequency and the timing at which they occur) and how other environmental factors associated with IBD modulate epigenetics deserve to be further investigated

Antiretroviral-naive and -treated HIV-1 patients can harbour more resistant viruses in CSF than in plasma

Objectives The neurological disorders in HIV-1-infected patients remain prevalent. The HIV-1 resistance in plasma and CSF was compared in patients with neurological disorders in a multicentre study. Methods Blood and CSF samples were collected at time of neurological disorders for 244 patients. The viral loads were >50 copies/mL in both compartments and bulk genotypic tests were realized. Results On 244 patients, 89 and 155 were antiretroviral (ARV) naive and ARV treated, respectively. In ARV-naive patients, detection of mutations in CSF and not in plasma were reported for the reverse transcriptase (RT) gene in 2/89 patients (2.2%) and for the protease gene in 1/89 patients (1.1%). In ARV-treated patients, 19/152 (12.5%) patients had HIV-1 mutations only in the CSF for the RT gene and 30/151 (19.8%) for the protease gene. Two mutations appeared statistically more prevalent in the CSF than in plasma: M41L (P = 0.0455) and T215Y (P = 0.0455). Conclusions In most cases, resistance mutations were present and similar in both studied compartments. However, in 3.4% of ARV-naive and 8.8% of ARV-treated patients, the virus was more resistant in CSF than in plasma. These results support the need for genotypic resistance testing when lumbar puncture is performe

Identification of a BRCA2-Specific modifier locus at 6p24 related to breast cancer risk

Common genetic variants contribute to the observed variation in breast cancer risk for BRCA2 mutation carriers; those known to date have all been found through population-based genome-wide association studies (GWAS). To comprehensively identify breast cancer risk modifying loci for BRCA2 mutation carriers, we conducted a deep replication of an ongoing GWAS discovery study. Using the ranked P-values of the breast cancer associations with the imputed genotype of 1.4 M SNPs, 19,029 SNPs were selected and designed for inclusion on a custom Illumina array that included a total of 211,155 SNPs as part of a multi-consortial project. DNA samples from 3,881 breast cancer affected and 4,330 unaffected BRCA2 mutation carriers from 47 studies belonging to the Consortium of Investigators of Modifiers of BRCA1/2 were genotyped and available for analysis. We replicated previously reported breast cancer susceptibility alleles in these BRCA2 mutation carriers and for several regions (including FGFR2, MAP3K1, CDKN2A/B, and PTHLH) identified SNPs that have stronger evidence of association than those previously published. We also identified a novel susceptibility allele at 6p24 that was inversely associated with risk in BRCA2 mutation carriers (rs9348512; per allele HR = 0.85, 95% CI 0.80-0.90, P = 3.9×10−8). This SNP was not associated with breast cancer risk either in the general population or in BRCA1 mutation carriers. The locus lies within a region containing TFAP2A, which encodes a transcriptional activation protein that interacts with several tumor suppressor genes. This report identifies the first breast cancer risk locus specific to a BRCA2 mutation background. This comprehensive update of novel and previously reported breast cancer susceptibility loci contributes to the establishment of a panel of SNPs that modify breast cancer risk in BRCA2 mutation carriers. This panel may have clinical utility for women with BRCA2 mutations weighing options for medical prevention of breast cancer