Application of Multi-SNP Approaches Bayesian LASSO and AUC-RF to Detect Main Effects of Inflammatory-Gene Variants Associated with Bladder Cancer Risk

The relationship between inflammation and cancer is well established in several tumor types, including bladder cancer. We performed an association study between 886 inflammatory-gene variants and bladder cancer risk in 1,047 cases and 988 controls from the Spanish Bladder Cancer (SBC)/EPICURO Study. A preliminary exploration with the widely used univariate logistic regression approach did not identify any significant SNP after correcting for multiple testing. We further applied two more comprehensive methods to capture the complexity of bladder cancer genetic susceptibility: Bayesian Threshold LASSO (BTL), a regularized regression method, and AUC-Random Forest, a machine-learning algorithm. Both approaches explore the joint effect of markers. BTL analysis identified a signature of 37 SNPs in 34 genes showing an association with bladder cancer. AUC-RF detected an optimal predictive subset of 56 SNPs. 13 SNPs were identified by both methods in the total population. Using resources from the Texas Bladder Cancer study we were able to replicate 30% of the SNPs assessed. The associations between inflammatory SNPs and bladder cancer were reexamined among non-smokers to eliminate the effect of tobacco, one of the strongest and most prevalent environmental risk factor for this tumor. A 9 SNP-signature was detected by BTL. Here we report, for the first time, a set of SNP in inflammatory genes jointly associated with bladder cancer risk. These results highlight the importance of the complex structure of genetic susceptibility associated with cancer risk.

Vers une gestion de la nature en termes d'action publique : analyse d'une dynamique d'appropriation des ressources végétales à Tobré, Nord Bénin

Cette étude se fonde sur des recherches ethnographiques menées autour de la mise en oeuvre d'une politique publique de gestion de la nature à Tobré, une région baatonu au Bénin. L'étude se place dans une dynamique d'appropriation des ressources naturelles en rapport avec l'entrée en jeu de multiples acteurs publics et privés dans l'arène locale de gestion de la nature. En effet, ces acteurs ont acquis ces dernières années de l'expérience et de l'efficacité à la faveur des changements institutionnels et politiques et s'incluent davantage dans le processus de décision au point de suppléer l'Etat dans les actions qui étaient ses prérogatives. L'étude met en lumière les rapports de conflits, de compétitions, de concurrence ou de compromis autour des enjeux sociaux, politiques et économiques de protection de la nature. Elle décrit et analyse les formes d'interactions entre les différents acteurs individuels, collectifs et institutionnels, afin de voir en quoi ces interactions participent du processus de mobilisation d'acteurs locaux et de confrontation de vision, qui finalement définit et oriente les politiques locales de protection de la nature. Pour atteindre cet objectif, l'étude mobilise des apports théoriques de plusieurs disciplines, notamment de la socio- anthropologie du développement, de l'histoire et de la sociologie politique. Elle repose également sur des données empiriques collectées à partir d'une combinaison d'outils techniques, des entretiens et des observations jusqu'au dépouillement de presse et des études de cas. Les principaux résultats montrent que les acteurs locaux, particulièrement les comités de gestion sont parvenus à inscrire la gestion des ressources naturelles dans l'espace public à travers les débats dans les médias, les forums, les marches de protestation, etc. De fait, ils ont été capables d'influer sur le processus de définition et de mise en oeuvre des politiques locales de protection de la nature et donc de reconfigurer l'arène locale de gestion des ressources naturelles. Ce qui amène l'Etat et ses services déconcentrés, en premier lieu les services des Eaux et Forêts et la mairie à pactiser avec ces différents comités, sans pour autant perdre de leur notoriété. Au contraire, ils participent de la gouvernance de l'ensemble des actions et permettent de mettre en place des formes de gestion négociée. - This is an ethnographic research on the implementation of a public policy for the management of natural resources in Tobre, a baatonu village in Benin. The study focuses on the dynamic of natural resources ownership in a context of multiple stakeholders in the public and private sectors. In recent years, these stakeholders have become more experienced and efficient as a result of several institutional and policy changes. The stakeholders are more involved in the decision making process to the point that they can complement the role of the State in natural resources management. This study highlights the conflicts, competition, or compromise associated with the social, political and economic constraints of nature conservation. The interactions between individual, collective and institutional stakeholders were analyzed, to understand their role in the process of mobilizing local stakeholders and confronting their visions. This process ultimately defines and guides local policies on the management of nature. To achieve this goal, this study combined theoretical approaches from developmental socio-anthropology, history and political sociology with empirical data collected using interviews, observations, newspapers analysis and case studies. The results show that local stakeholders, particularly the management committees, were successful at introducing the need for sustainable natural resource management in the mainstream public discourse through the media, forums, and demonstrations. They were able to influence the process of identifying and implementing local policies on nature conservancy. This has encouraged the State, through its forestry services, and the district mayors to collaborate with these committees in the shared governance of natural resources.

Investigação qualitativa e abordagem psico-cultural do desvio [Qualitative research and psycho-cultural approaches of deviance]

Qualitative research and psycho-cultural approaches to deviant behaviour¦In this paper, the authors discuss the relevance of some historical, theoretical and¦methodological features of qualitative research for a psycho-cultural approach to¦deviance. Specifically, three methods are presented: ethnography, life stories and¦grounded theory. Some common features of these methods are: their potentialities of¦articulation with other methods, their plasticity and their procedures grounded in¦research contexts, experiences and meanings lived by participants. The role of the¦researcher, as well as the constructed and dialogical characteristics of both process¦and products of research, are also emphasised in these approaches. In this way,¦qualitative methods seem particularly adequate to a psycho-cultural approach to¦deviance, allowing the research of "hidden" phenomena and an understanding of¦deviance that takes into account its cultural norms. Thus, qualitative research is as a¦methodological device which allows to get beyond the traditional ethnocentrism of psychology.

In the eye of the listener: pupil dilation elucidates discourse processing.

The current study investigated cognitive resource allocation in discourse processing by means of pupil dilation and behavioral measures. Short question-answer dialogs were presented to listeners. Either the context question queried a new information focus in the successive answer, or else the context query was corrected in the answer sentence (correction information). The information foci contained in the answer sentences were either adequately highlighted by prosodic means or not. Participants had to judge the adequacy of the focus prosody with respect to the preceding context question. Prosodic judgment accuracy was higher in the conditions bearing adequate focus prosody than in the conditions with inadequate focus prosody. Latency to peak pupil dilation was longer when new information foci were perceived compared to correction foci. Moreover, for the peak dilation, an interaction of focus type and prosody was found. Post hoc statistical tests revealed that prosodically adequate correction focus positions were processed with smaller peak dilation in comparison to all other dialog conditions. Thus, pupil dilation and results of a principal component analysis suggest an interaction of focus type and focus prosody in discourse processing.

Standards of care and novel approaches in the management of glioblastoma multiforme.

Glioblastoma multiforme (GBM) is the most common malignant primary brain tumor in adults. Standard therapeutic approaches provide modest improvement in the progression-free and overall survival, necessitating the investigation of novel therapies. We review the standard treatment options for GBM and evaluate the results obtained in clinical trials for promising novel approaches, including the inhibition of angiogenesis, targeted approaches against molecular pathways, immunotherapies, and local treatment with low voltage electric fields.

Explorando los discursos de las organizaciones

Después de comentar algunas de las orientaciones con que se estudian los discursos en las organizaciones (empresas o instituciones), presentamos dos clasificaciones discursivas, basadas respectivamente en el organigrama (formal / informal, horizontal / vertical, etc.) y en la función comunicativa (discursos técnico-científicos, organizativos, comerciales y protocolarios).También establecemos una tipología de intervenciones lingüísticas en organizaciones, según tomen como objeto de trabajo la estructura organizativa, los recursos humanos, el registro o un discurso particular.

Beyond Conditionality versus Cooperation: Power and Resistance in the Case of EU Mobility Partnerships and Swiss Migration Partnerships

Migration partnerships (MPs) have become a key instrument in global migration governance. In contrast to traditional unilateral approaches, MPs emphasize a more comprehensive and inclusive tackling of migration issues between countries of origin, transit, and destination. Due to this cooperation-oriented concept, most of the existing studies on MPs neglect power questions within partnerships in line with the official discourse, reflecting a broader trend in the international migration governance literature. Others take an instrumentalist view in analysing the power of partnerships or focus on soft power. Illustrated with the examples of the European Mobility Partnerships (EU MPs) and the Swiss Migration Partnerships (CH MPs), we conduct an analysis based on a concept of productive power drawing on post-structural and post-colonial insights. Our main argument is that in contrast to their seemingly consent-oriented and technical character, MPs are sites of intense (discursive) struggles, and (re-)produce meanings, subjects, and resistances. A productive power analysis allows us to move beyond the dichotomy in the literature between coercion and cooperation, as well as between power and resistance more broadly.

Stand dynamics modelling approaches for multicohort management of eastern Canadian boreal forests

Abstract

Combined approaches in large vestibular schwannomas: surgical and radiosurgical perspective

Purpose: The management of vestibular schwanommas (VS) is challenging, with microsurgery remaining the main treatment option. Planned subtotal resection is now being increasingly considered to reduce the risk of neurological deficits following complete resection. The residual part of the tumor can then be treated with Gamma Knife surgery (GKS) to achieve long-term growth control. Methods: This case series of 11 patients documents early results with planned subtotal resection followed by GKS in Lausanne University Hospital, between July 2010 and March 2012. We analyzed clinical symptoms and signs for all cases, as well as MRI and audiograms. Results: Mean age in this series was 50.3 years (range 24.1-73.4). Two patients (18.2%) had a stereotactic fractionated radiotherapy, which had failed to ensure tumor control, before the microsurgical intervention. The lesions were solid in 9 cases (81.8%), and mixed (solid and cystic) in 2 patients (18.2%). Presurgical tumor volume was of a mean of 18.5 cm3 (range 9.7-34.9 cm3). The mean duration between microsurgery and GKS was 10.5 months (range 4-22.8). The mean tumor volume at the time of GKS treatment was 4.9 cm3 (range 0.5- 12.8). A mean number of 20.7 isocenters was used (range 8-31). Nine patients received 12 Gy and 2 patients with 11 Gy at the periphery (at the 50% prescription isodose). We did not have any major complications in our series. Postoperative status showed no facial nerve deficits. Four patients with useful pre-operative hearing underwent surgery aiming to preserve the cochlear nerve function. Of these patients, the patient who had Gardner-Robertson (GR) class 1 before surgery, remained in GR class 1. Two patients improved after surgery, one changing from GR 5 to GR 3 and the other with slight improvement, remaining in the same GR 3 class. Mean follow-up after surgery was 15.4 months (range 4-31.2). One patient, who presented with secondary trigeminal neuralgia before surgery, had transitory facial hypoesthesia following surgery. No other neurological deficits were encountered. Following GKS, the patients had a mean follow-up of 5.33 months (range 1-13). No new neurological deficits were encountered. Conclusions: Our data suggest that planned subtotal resection followed by GKS has an excellent clinical outcome with respect to preservation of cranial nerves, and other neurological functions, and a good possibility of recovery of many of the pre-operative cranial nerve dysfunctions

Aggregation invariance in general clustering approaches

General clustering deals with weighted objects and fuzzy memberships. We investigate the group- or object-aggregation-invariance properties possessed by the relevant functionals (effective number of groups or objects, centroids, dispersion, mutual object-group information, etc.). The classical squared Euclidean case can be generalized to non-Euclidean distances, as well as to non-linear transformations of the memberships, yielding the c-means clustering algorithm as well as two presumably new procedures, the convex and pairwise convex clustering. Cluster stability and aggregation-invariance of the optimal memberships associated to the various clustering schemes are examined as well.

Are the World AIDS Conferences guilty of gender bias? Evidence from trends in the monitoring of WAC scientific discourse from 1989 to 2012

Background : The issue of gender is acknowledged as a key issue for the AIDS epidemic. World AIDS Conferences (WAC) have constituted a major discursive space for the epidemic. We sought to establish the balance regarding gender in the AIDS scientific discourse by following its development in the published proceedings of WAC. Fifteen successive WAC 1989-2012 served to establish a "barometer" of scientific interest in heterosexual and homo/bisexual men and women throughout the epidemic. It was hypothesised that, as in other domains of Sexual and Reproductive Health, heterosexual men would be "forgotten" partners. Method : Abstracts from each conference were entered in electronic form into an Access database. Queries were created to generate five categories of interest and to monitor their annual frequency. All abstract titles including the term "men" or "women" were identified. Collections of synonyms were systematically and iteratively developed in order to classify further abstracts according to whether they included terms referring to "homo/bisexual" or "heterosexual". Reference to "Mother to Child Transmission" (MTCT) was also flagged. Results : The category including "men", but without additional reference to "homo-bisexuel" (i.e. referring to men in general and/or to heterosexual men) consistently appears four times less often than the equivalent category for women. Excluding abstracts on women and MTCT has little impact on this difference. Abstracts including reference to both "men" and "homo-bisexual" emerge as the secondmost frequent category; presence of the equivalent category for women is minimal. Conclusion : The hypothesised absence of heterosexual men in the AIDS discourse was confirmed. Although the relative presence of homo-bisexual men and women as a focal subject may be explained by epidemiological data, this is not so in the case of heterosexual men and women. This imbalance has consequences for HIV prevention.

A comparison of Bayesian and frequentist approaches to incorporating external information for the prediction of prostate cancer risk.

We present the most comprehensive comparison to date of the predictive benefit of genetics in addition to currently used clinical variables, using genotype data for 33 single-nucleotide polymorphisms (SNPs) in 1,547 Caucasian men from the placebo arm of the REduction by DUtasteride of prostate Cancer Events (REDUCE®) trial. Moreover, we conducted a detailed comparison of three techniques for incorporating genetics into clinical risk prediction. The first method was a standard logistic regression model, which included separate terms for the clinical covariates and for each of the genetic markers. This approach ignores a substantial amount of external information concerning effect sizes for these Genome Wide Association Study (GWAS)-replicated SNPs. The second and third methods investigated two possible approaches to incorporating meta-analysed external SNP effect estimates - one via a weighted PCa 'risk' score based solely on the meta analysis estimates, and the other incorporating both the current and prior data via informative priors in a Bayesian logistic regression model. All methods demonstrated a slight improvement in predictive performance upon incorporation of genetics. The two methods that incorporated external information showed the greatest receiver-operating-characteristic AUCs increase from 0.61 to 0.64. The value of our methods comparison is likely to lie in observations of performance similarities, rather than difference, between three approaches of very different resource requirements. The two methods that included external information performed best, but only marginally despite substantial differences in complexity.

Oxidative stress in aging: advances in proteomic approaches

Aging is a gradual, complex process in which cells, tissues, organs, and the whole organism itself deteriorate in a progressive and irreversible manner that, in the majority of cases, implies pathological conditions that affect the individual"s Quality of Life (QOL). Although extensive research efforts in recent years have been made, the anticipation of aging and prophylactic or treatment strategies continue to experience major limitations. In this review, the focus is essentially on the compilation of the advances generated by cellular expression profile analysis through proteomics studies (two-dimensional [2D] electrophoresis and mass spectrometry [MS]), which are currently used as an integral approach to study the aging process. Additionally, the relevance of the oxidative stress factors is discussed. Emphasis is placed on postmitotic tissues, such as neuronal, muscular, and red blood cells, which appear to be those most frequently studied with respect to aging. Additionally, models for the study of aging are discussed in a number of organisms, such as Caenorhabditis elegans, senescence-accelerated probe-8 mice (SAMP8), naked mole-rat (Heterocephalus glaber), and the beagle canine. Proteomic studies in specific tissues and organisms have revealed the extensive involvement of reactive oxygen species (ROS) and oxidative stress in aging.