PANACEA (Platform for Automatic, Normalised Annotation and Cost-Effective Acquisition of Language Resources for Human Language Technologies)

The objective of PANACEA is to build a factory of LRs that automates the stages involved in the acquisition, production, updating and maintenance of LRs required by MT systems and by other applications based on language technologies, and simplifies eventual issues regarding intellectual property rights. This automation will cut down the cost, time and human effort significantly. These reductions of costs and time are the only way to guarantee the continuous supply of LRs that MT and other language technologies will be demanding in the multilingual Europe.

Evolving from inferences to decisions in the interpretation of scientific evidence

Le travail d'un(e) expert(e) en science forensique exige que ce dernier (cette dernière) prenne une série de décisions. Ces décisions sont difficiles parce qu'elles doivent être prises dans l'inévitable présence d'incertitude, dans le contexte unique des circonstances qui entourent la décision, et, parfois, parce qu'elles sont complexes suite à de nombreuse variables aléatoires et dépendantes les unes des autres. Etant donné que ces décisions peuvent aboutir à des conséquences sérieuses dans l'administration de la justice, la prise de décisions en science forensique devrait être soutenue par un cadre robuste qui fait des inférences en présence d'incertitudes et des décisions sur la base de ces inférences. L'objectif de cette thèse est de répondre à ce besoin en présentant un cadre théorique pour faire des choix rationnels dans des problèmes de décisions rencontrés par les experts dans un laboratoire de science forensique. L'inférence et la théorie de la décision bayésienne satisfont les conditions nécessaires pour un tel cadre théorique. Pour atteindre son objectif, cette thèse consiste de trois propositions, recommandant l'utilisation (1) de la théorie de la décision, (2) des réseaux bayésiens, et (3) des réseaux bayésiens de décision pour gérer des problèmes d'inférence et de décision forensiques. Les résultats présentent un cadre uniforme et cohérent pour faire des inférences et des décisions en science forensique qui utilise les concepts théoriques ci-dessus. Ils décrivent comment organiser chaque type de problème en le décomposant dans ses différents éléments, et comment trouver le meilleur plan d'action en faisant la distinction entre des problèmes de décision en une étape et des problèmes de décision en deux étapes et en y appliquant le principe de la maximisation de l'utilité espérée. Pour illustrer l'application de ce cadre à des problèmes rencontrés par les experts dans un laboratoire de science forensique, des études de cas théoriques appliquent la théorie de la décision, les réseaux bayésiens et les réseaux bayésiens de décision à une sélection de différents types de problèmes d'inférence et de décision impliquant différentes catégories de traces. Deux études du problème des deux traces illustrent comment la construction de réseaux bayésiens permet de gérer des problèmes d'inférence complexes, et ainsi surmonter l'obstacle de la complexité qui peut être présent dans des problèmes de décision. Trois études-une sur ce qu'il faut conclure d'une recherche dans une banque de données qui fournit exactement une correspondance, une sur quel génotype il faut rechercher dans une banque de données sur la base des observations faites sur des résultats de profilage d'ADN, et une sur s'il faut soumettre une trace digitale à un processus qui compare la trace avec des empreintes de sources potentielles-expliquent l'application de la théorie de la décision et des réseaux bayésiens de décision à chacune de ces décisions. Les résultats des études des cas théoriques soutiennent les trois propositions avancées dans cette thèse. Ainsi, cette thèse présente un cadre uniforme pour organiser et trouver le plan d'action le plus rationnel dans des problèmes de décisions rencontrés par les experts dans un laboratoire de science forensique. Le cadre proposé est un outil interactif et exploratoire qui permet de mieux comprendre un problème de décision afin que cette compréhension puisse aboutir à des choix qui sont mieux informés. - Forensic science casework involves making a sériés of choices. The difficulty in making these choices lies in the inévitable presence of uncertainty, the unique context of circumstances surrounding each décision and, in some cases, the complexity due to numerous, interrelated random variables. Given that these décisions can lead to serious conséquences in the admin-istration of justice, forensic décision making should be supported by a robust framework that makes inferences under uncertainty and décisions based on these inferences. The objective of this thesis is to respond to this need by presenting a framework for making rational choices in décision problems encountered by scientists in forensic science laboratories. Bayesian inference and décision theory meets the requirements for such a framework. To attain its objective, this thesis consists of three propositions, advocating the use of (1) décision theory, (2) Bayesian networks, and (3) influence diagrams for handling forensic inference and décision problems. The results present a uniform and coherent framework for making inferences and décisions in forensic science using the above theoretical concepts. They describe how to organize each type of problem by breaking it down into its différent elements, and how to find the most rational course of action by distinguishing between one-stage and two-stage décision problems and applying the principle of expected utility maximization. To illustrate the framework's application to the problems encountered by scientists in forensic science laboratories, theoretical case studies apply décision theory, Bayesian net-works and influence diagrams to a selection of différent types of inference and décision problems dealing with différent catégories of trace evidence. Two studies of the two-trace problem illustrate how the construction of Bayesian networks can handle complex inference problems, and thus overcome the hurdle of complexity that can be present in décision prob-lems. Three studies-one on what to conclude when a database search provides exactly one hit, one on what genotype to search for in a database based on the observations made on DNA typing results, and one on whether to submit a fingermark to the process of comparing it with prints of its potential sources-explain the application of décision theory and influ¬ence diagrams to each of these décisions. The results of the theoretical case studies support the thesis's three propositions. Hence, this thesis présents a uniform framework for organizing and finding the most rational course of action in décision problems encountered by scientists in forensic science laboratories. The proposed framework is an interactive and exploratory tool for better understanding a décision problem so that this understanding may lead to better informed choices.

Resistance to nucleoside analog reverse transcriptase inhibitors mediated by human immunodeficiency virus type 1 p6 protein.

Resistance of human immunodeficiency virus type 1 (HIV-1) to antiretroviral agents results from target gene mutation within the pol gene, which encodes the viral protease, reverse transcriptase (RT), and integrase. We speculated that mutations in genes other that the drug target could lead to drug resistance. For this purpose, the p1-p6(gag)-p6(pol) region of HIV-1, placed immediately upstream of pol, was analyzed. This region has the potential to alter Pol through frameshift regulation (p1), through improved packaging of viral enzymes (p6(Gag)), or by changes in activation of the viral protease (p6(Pol)). Duplication of the proline-rich p6(Gag) PTAP motif, necessary for late viral cycle activities, was identified in plasma virus from 47 of 222 (21.2%) patients treated with nucleoside analog RT inhibitor (NRTI) antiretroviral therapy but was identified very rarely from drug-naïve individuals. Molecular clones carrying a 3-amino-acid duplication, APPAPP (transframe duplication SPTSPT in p6(Pol)), displayed a delay in protein maturation; however, they packaged a 34% excess of RT and exhibited a marked competitive growth advantage in the presence of NRTIs. This phenotype is reminiscent of the inoculum effect described in bacteriology, where a larger input, or a greater infectivity of an organism with a wild-type antimicrobial target, leads to escape from drug pressure and a higher MIC in vitro. Though the mechanism by which the PTAP region participates in viral maturation is not known, duplication of this proline-rich motif could improve assembly and packaging at membrane locations, resulting in the observed phenotype of increased infectivity and drug resistance.

The impact of pre- and post-natal contexts on immunity, glucocorticoids and oxidative stress resistance in wild and domesticated grey partridges

Genetic background, prenatal and post-natal early-life conditions influence the development of interconnected physiological systems and thereby shape the phenotype. Certain combinations of genotypes and pre- and post-natal conditions may provide higher fitness in a specific environmental context. Here, we investigated how grey partridges Perdix perdix of two strains (wild and domesticated) cope physiologically with pre- and post-natal predictable vs. unpredictable food supply. Food unpredictability occurs frequently in wild environments and requires physiological and behavioural adjustments. Well-orchestrated and efficient physiological systems are presumably more vital in a wild environment as compared to captivity. We thus predicted that wild-strain grey partridges have a stronger immunity, glucocorticoid (GC) stress response and oxidative stress resistance (OSR) than domesticated birds, which have undergone adaptations to captivity. We also predicted that wild-strain birds react more strongly to environmental stimuli and, when faced with harsh prenatal conditions, are better able to prepare their offspring for similarly poor post-natal conditions than birds of domesticated origin. We found that wild-strain offspring were physiologically better prepared for stressful situations as compared to the domesticated strain. They had a high GC stress response and a high OSR when kept under predictable food supply. Wild-strain parents reacted to prenatal unpredictable food supply by lowering their offspring's GC stress response, which potentially lowered GC-induced oxidative pressure. No such pattern was evident in the domesticated birds. Irrespective of strain and prenatal feeding scheme, post-natal unpredictable food supply boosted immune indices, and GC stress response was negatively related to antibody response in females and to mitochondrial superoxide production. Wild-strain grey partridge showed fitness-relevant physiological advantages and appeared to prepare their offspring for the prospective environment. Negative relationships between GC stress response, immunity and oxidative indices imply a pivotal role of an organism's oxidative balance and support the importance of considering multiple physiological systems simultaneously.

A novel and divergent role of granzyme a and B in resistance to helminth infection.

Granzyme (gzm) A and B, proteases of NK cells and T killer cells, mediate cell death, but also cleave extracellular matrices, inactivate intracellular pathogens, and induce cytokines. Moreover, macrophages, Th2 cells, regulatory T cells, mast cells, and B cells can express gzms. We recently reported gzm induction in human filarial infection. In this study, we show that in rodent filarial infection with Litomosoides sigmodontis, worm loads were significantly reduced in gzmA×B and gzmB knockout mice during the whole course of infection, but enhanced only early in gzmA knockout compared with wild-type mice. GzmA/B deficiency was associated with a defense-promoting Th2 cytokine and Ab shift, enhanced early inflammatory gene expression, and a trend of reduced alternatively activated macrophage induction, whereas gzmA deficiency was linked with reduced inflammation and a trend toward increased alternatively activated macrophages. This suggests a novel and divergent role for gzms in helminth infection, with gzmA contributing to resistance and gzmB promoting susceptibility.

ECG interpretation during the acute phase of coronary syndromes: in need of improvement?

QUESTION UNDER STUDY: Emergency room (ER) interpretation of the ECG is critical to assessment of patients with acute coronary syndromes (ACS). Our aim was to assess its reliability in our institution, a tertiary teaching hospital. METHODS: Over a 6-month period all consecutive patients admitted for ACS were included in the study. ECG interpretation by emergency physicians (EPs) was recorded on a preformatted sheet and compared with the interpretation of two specialist physicians (SPs). Discrepancies between the 2 specialists were resolved by an ECG specialist. RESULTS: Over the 6-month period, 692 consecutive patients were admitted with suspected ACS. ECG interpretation was available in 641 cases (93%). Concordance between SPs was 87%. Interpretation of normality or abnormality of the ECG was concordant between EPs and SPs in 475 cases (74%, kappa = 0.51). Interpretation of ischaemic modifications was concordant in 69% of cases, and as many ST segment elevations were unrecognised as overdiagnosed (5% each). The same findings occurred for ST segment depressions and negative T waves (12% each). CONCLUSIONS: Interpretation of the ECG recorded during ACS by 2 SPs was discrepant in 13% of cases. Similarly, EP interpretation was discrepant from SP interpretation in 25% of cases, equally distributed between over- and underdiagnosing of ischaemic changes. The clinical implications and impact of medical education on ECG interpretation require further study.

Lower thigh subcutaneous and higher visceral abdominal adipose tissue content both contribute to insulin resistance.

It is well known that visceral adipose tissue (VAT) is associated with insulin resistance (IR). Considerable debate remains concerning the potential positive effect of thigh subcutaneous adipose tissue (TSAT). Our objective was to observe whether VAT and TSAT are opposite, synergistic or additive for both peripheral and hepatic IR. Fifty-two volunteers (21 male/31 female) between 30 and 75 years old were recruited from the general population. All subjects were sedentary overweight or obese (mean BMI 33.0 ± 3.4 kg/m(2)). Insulin sensitivity was determined by a 4-h hyperinsulinemic-euglycemic clamp with stable isotope tracer dilution. Total body fat and lean body mass were determined by dual X-ray absorptiometry. Abdominal and mid-thigh adiposity was determined by computed tomography. VAT was negatively associated with peripheral insulin sensitivity, while TSAT, in contrast, was positively associated with peripheral insulin sensitivity. Subjects with a combination of low VAT and high TSAT had the highest insulin sensitivity, subjects with a combination of high VAT and low TSAT were the most insulin resistant. These associations remained significant after adjusting for age and gender. These data confirm that visceral excess abdominal adiposity is associated with IR across a range of middle-age to older men and women, and further suggest that higher thigh subcutaneous fat is favorably associated with better insulin sensitivity. This strongly suggests that these two distinct fat distribution phenotypes should both be considered in IR as important determinants of cardiometabolic risk.

Colon-specific deletion of epithelial sodium channel causes sodium loss and aldosterone resistance.

Aldosterone promotes electrogenic sodium reabsorption through the amiloride-sensitive epithelial sodium channel (ENaC). Here, we investigated the importance of ENaC and its positive regulator channel-activating protease 1 (CAP1/Prss8) in colon. Mice lacking the αENaC subunit in colonic superficial cells (Scnn1a(KO)) were viable, without fetal or perinatal lethality. Control mice fed a regular or low-salt diet had a significantly higher amiloride-sensitive rectal potential difference (∆PDamil) than control mice fed a high-salt diet. In Scnn1a(KO) mice, however, this salt restriction-induced increase in ∆PDamil did not occur, and the circadian rhythm of ∆PDamil was blunted. Plasma and urinary sodium and potassium did not change with regular or high-salt diets or potassium loading in control or Scnn1a(KO) mice. However, Scnn1a(KO) mice fed a low-salt diet lost significant amounts of sodium in their feces and exhibited high plasma aldosterone and increased urinary sodium retention. Mice lacking the CAP1/Prss8 in colonic superficial cells (Prss8(KO)) were viable, without fetal or perinatal lethality. Compared with controls, Prss8(KO) mice fed regular or low-salt diets exhibited significantly reduced ∆PDamil in the afternoon, but the circadian rhythm was maintained. Prss8(KO) mice fed a low-salt diet also exhibited sodium loss through feces and higher plasma aldosterone levels. Thus, we identified CAP1/Prss8 as an in vivo regulator of ENaC in colon. We conclude that, under salt restriction, activation of the renin-angiotensin-aldosterone system in the kidney compensated for the absence of ENaC in colonic surface epithelium, leading to colon-specific pseudohypoaldosteronism type 1 with mineralocorticoid resistance without evidence of impaired potassium balance.

Identification of a key lysine residue in heat shock protein 90 required for azole and echinocandin resistance in Aspergillus fumigatus.

Heat shock protein 90 (Hsp90) is an essential chaperone involved in the fungal stress response that can be harnessed as a novel antifungal target for the treatment of invasive aspergillosis. We previously showed that genetic repression of Hsp90 reduced Aspergillus fumigatus virulence and potentiated the effect of the echinocandin caspofungin. In this study, we sought to identify sites of posttranslational modifications (phosphorylation or acetylation) that are important for Hsp90 function in A. fumigatus. Phosphopeptide enrichment and tandem mass spectrometry revealed phosphorylation of three residues in Hsp90 (S49, S288, and T681), but their mutation did not compromise Hsp90 function. Acetylation of lysine residues of Hsp90 was recovered after treatment with deacetylase inhibitors, and acetylation-mimetic mutations (K27A and K271A) resulted in reduced virulence in a murine model of invasive aspergillosis, supporting their role in Hsp90 function. A single deletion of lysine K27 or an acetylation-mimetic mutation (K27A) resulted in increased susceptibility to voriconazole and caspofungin. This effect was attenuated following a deacetylation-mimetic mutation (K27R), suggesting that this site is crucial and should be deacetylated for proper Hsp90 function in antifungal resistance pathways. In contrast to previous reports in Candida albicans, the lysine deacetylase inhibitor trichostatin A (TSA) was active alone against A. fumigatus and potentiated the effect of caspofungin against both the wild type and an echinocandin-resistant strain. Our results indicate that the Hsp90 K27 residue is required for azole and echinocandin resistance in A. fumigatus and that deacetylase inhibition may represent an adjunctive anti-Aspergillus strategy.

Partial gene deletion of endothelial nitric oxide synthase predisposes to exaggerated high-fat diet-induced insulin resistance and arterial hypertension.

Nitric oxide (NO) plays a major role in the regulation of cardiovascular and metabolic homeostasis, as evidenced by insulin resistance and arterial hypertension in endothelial NO synthase (eNOS) null mice. Extrapolation of these findings to humans is difficult, however, because eNOS gene deficiency has not been reported. eNOS gene polymorphism and impaired NO synthesis, however, have been reported in several cardiovascular disease states and could predispose to insulin resistance. High-fat diet induces insulin resistance and arterial hypertension in normal mice. To test whether partial eNOS deficiency facilitates the development of insulin resistance and arterial hypertension during metabolic stress, we examined effects of an 8-week high-fat diet on insulin sensitivity (euglycemic clamp) and arterial pressure in eNOS(+/-) mice. When fed a normal diet, these mice had normal insulin sensitivity and were normotensive. When fed a high-fat diet, however, eNOS(+/-) mice developed exaggerated arterial hypertension and had fasting hyperinsulinemia and a 35% lower insulin-stimulated glucose utilization than control mice. The partial deletion of the eNOS gene does not alter insulin sensitivity or blood pressure in mice. When challenged with nutritional stress, however, partial eNOS deficiency facilitates the development of insulin resistance and arterial hypertension, providing further evidence for the importance of this gene in linking metabolic and cardiovascular disease.

On metapopulation resistance to drift and extinction.

The spatial configuration of metapopulations (numbers, sizes, and localization of patches) affects their ability to resist demographic extinction and genetic drift, but sometimes with opposite effects. Small and isolated patches, for instance, contribute marginally to demography but may play a large role in genetics by maintaining a sizeable amount of genetic variance among demes. In source-sink systems, similarly, connectivity may be beneficial in terms of effective size, but detrimental in terms of survival, by lowering the reproductive value of source populations. How to reconcile these opposite effects? Here we propose an analytical framework that integrates fixation time (ability to resist genetic drift) and extinction time (ability to resist demographic extinction) into a single index of resistance, measuring the ability of a metapopulation to maintain its demo-genetic integrity. We then illustrate with numerical examples how conflicting demands may be resolved.

Gluco-incretins regulate beta-cell glucose competence by epigenetic silencing of Fxyd3 expression.

BACKGROUND/AIMS: Gluco-incretin hormones increase the glucose competence of pancreatic beta-cells by incompletely characterized mechanisms. METHODS: We searched for genes that were differentially expressed in islets from control and Glp1r-/-; Gipr-/- (dKO) mice, which show reduced glucose competence. Overexpression and knockdown studies; insulin secretion analysis; analysis of gene expression in islets from control and diabetic mice and humans as well as gene methylation and transcriptional analysis were performed. RESULTS: Fxyd3 was the most up-regulated gene in glucose incompetent islets from dKO mice. When overexpressed in beta-cells Fxyd3 reduced glucose-induced insulin secretion by acting downstream of plasma membrane depolarization and Ca++ influx. Fxyd3 expression was not acutely regulated by cAMP raising agents in either control or dKO adult islets. Instead, expression of Fxyd3 was controlled by methylation of CpGs present in its proximal promoter region. Increased promoter methylation reduced Fxyd3 transcription as assessed by lower abundance of H3K4me3 at the transcriptional start site and in transcription reporter assays. This epigenetic imprinting was initiated perinatally and fully established in adult islets. Glucose incompetent islets from diabetic mice and humans showed increased expression of Fxyd3 and reduced promoter methylation. CONCLUSIONS/INTERPRETATION: Because gluco-incretin secretion depends on feeding the epigenetic regulation of Fxyd3 expression may link nutrition in early life to establishment of adult beta-cell glucose competence; this epigenetic control is, however, lost in diabetes possibly as a result of gluco-incretin resistance and/or de-differentiation of beta-cells that are associated with the development of type 2 diabetes.