A study on using genetic niching for query optimisation in document retrieval

International audienceThis paper presents a new genetic approach for query optimisation in document retrieval. The main contribution of the paper is to show the effectiveness of the genetic niching technique to reach multiple relevant regions of the document space. Moreover, suitable merging procedures have been proposed in order to improve the retrieval evaluation. Experimental results obtained using a TREC sub-collection indicate that the proposed approach is promising for applications

Circulating vitamin D levels and colorectal cancer risk: a meta-analysis and systematic review of case-control and prospective cohort studies

The associations between circulating vitamin D concentrations and total and site-specific colorectal cancer (CRC) incidence have been examined in several epidemiological studies with overall inconclusive findings. The aim of this systematic review and meta-analysis of both case-control and prospective cohort studies was to evaluate the association between CRC and circulating levels of vitamin D. The main exposure and outcome were circulating total 25(OH)D and CRC, respectively, in the overall population (i.e., all subjects). Two reviewers, working independently, screened all the literature available to identify studies that met the inclusion criteria (e.g., case-control or prospective cohort studies, published in English, and excluding non-original papers). Data were pooled by the generic inverse variance method using a random or fixed effect model, as approriate. Heterogeneity was identified using the Cochran's Q-test and quantified by the I2 statistic. Results were stratified by study design, sex, and metabolite of vitamin D. Sensitivity and subgroup analyses were also performed. A total of 28 original studies were included for the quantitative meta-analysis. Meta-analyses comparing the highest vs lowest categories, showed a 39% lower risk between levels of total 25(OH)D and CRC risk (OR (95% CI): 0.61 (0.52; 0.71); 11 studies) in case-control studies; whereas a 20% reduced CRC risk in prospective cohort studies (HR (95% CI): 0.80 (0.66; 0.97); 6 studies). Results in women mirrored main results, whereas results in men were non-significant in both analyses. Our findings support an inverse association between circulating vitamin D levels and CRC risk

Impact of Tumor LINE-1 Methylation Level and Neoadjuvant Treatment and Its Association with Colorectal Cancer Survival

Recent studies suggest that long-interspersed nucleotide element-1 (LINE-1) hypomethylation is commonly found in colorectal cancer (CRC), and is associated with worse prognosis. However, the utility of LINE-1 methylation on the prognosis of CRC is still controversial, and may be due to the fact that some clinical and pathological features may affect LINE-1 methylation. Thus, the aim of this study was to assess the prognostic value of tumor LINE-1 methylation in CRC, through their association with the CRC clinical and pathological characteristics. Survival of sixty-seven CRC patients was evaluated according to the median of tumor LINE-1 methylation, as well as pathological and oncological variables. We also studied the association between LINE-1 methylation and pathological features, and finally, we assessed the overall and disease-free survival of LINE1 methylation, stratified by neoadjuvant treatment and further checked by multivariate Cox regression to assess the statistical interactions. LINE-1 was hypomethylated in the CRC tumor with respect to the tumor adjacent-free area (p < 0.05), without association with any other clinical and oncological features, nor with overall and disease-free survival rates for CRC. Relevantly, in neoadjuvant treatment, LINE-1 methylation was associated with survival rates. Thus, disease-free and overall survival rates of treated CRC patients were worse in the hypomethylated LINE-1 tumors than those with normal LINE-1 methylation (p = 0.004 and 0.0049, respectively). Indeed, LINE-1 was hypermethylated more in the treated patients than in the non-treated patients (p < 0.05). The present study showed that tumor LINE-1 hypomethylation was associated with worse survival rates in only treated patients. Our data suggest an interactive effect of neoadjuvant treatment and tumor LINE-1 methylation, which could be a specific-tissue biomarker to predict survival of the treated patients, and help to personalize treatment in CRC

Genetically predicted circulating B vitamins in relation to digestive system cancers

Funder: United Kingdom Research and Innovation Future Leaders Fellowship (MR/T043202/1)Funder: EC‐Innovative Medicines Initiative (BigData@Heart)Funder: Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (204623/Z/16/Z)Abstract: Background: Folate, vitamin B6 and vitamin B12 have been associated with digestive system cancers. We conducted a two-sample Mendelian randomisation study to assess the causality of these associations. Methods: Two, one and 14 independent single nucleotide polymorphisms associated with serum folate, vitamin B6 and vitamin B12 at the genome-wide significance threshold were selected as genetic instruments. Summary-level data for the associations of the vitamin-associated genetic variants with cancer were obtained from the UK Biobank study including 367,561 individuals and FinnGen consortium comprising up to 176,899 participants. Results: Genetically predicted folate and vitamin B6 concentrations were not associated with overall cancer, overall digestive system cancer or oesophageal, gastric, colorectal or pancreatic cancer. Genetically predicted vitamin B12 concentrations were positively associated with overall digestive system cancer (ORSD, 1.12; 95% CI 1.04, 1.21, p = 0.003) and colorectal cancer (ORSD 1.16; 95% CI 1.06, 1.26, p = 0.001) in UK Biobank. Results for colorectal cancer were consistent in FinnGen and the combined ORSD was 1.16 (95% CI 1.08, 1.25, p < 0.001). There was no association of genetically predicted vitamin B12 with any other site-specific digestive system cancers or overall cancer. Conclusions: These results provide evidence to suggest that elevated serum vitamin B12 concentrations are associated with colorectal cancer

Une Approche Possibiliste pour la Recherche d'Information (VSST 2004)

International audienceCe papier décrit une nouvelle approche pour un modèle de Recherche d'Information. Cette approche traduit à travers des réseaux Bayésiens naïfs des relations de dépendance entre les documents et les termes d'indexation quantifiables par deux mesures: la possibilité et la nécessité. Le processus de recherche restitue les documents plausiblement ou nécessairement pertinents à un besoin utilisateur. Ce besoin utilisateur est vu comme une nouvelle information à propager dans les réseaux

IRIT at TREC’2002: Filtering Track

The experiments we undertaken this year for TREC2002 Filtering track, are focussed on threshold calibration. We proposed a new approach to calibrate the dissemination threshold in an adaptive information filtering. It consists of optimizing a utility function represented by a linearized form of the probability distributions of the scores of the relevant and the non-relevant documents already filtered. The profiles are learned using the same method used last year. It is based on a reinforcement algorithm. We submitted results on three tasks: adaptive, batch and routing. 1 Information representation and filtering Our adaptive filtering model is inspired from the connectionist model Mercure [1]. The profile and the document are represented by a set of weighted terms. The filtering process consists of computing a relevance value RSV Retrieval Status Value. The document is delivered only if the RSV is greater than the dissemination threshold. A learning process is then carried out by modifying the profile and the dissemination threshold to be more efficient in the future. 1.1 System initialization The user profile is represented by a set of terms: p (0) �