A robust genomic signature for the detection of colorectal cancer patients with microsatellite instability phenotype and high mutation frequency.

Microsatellite instability (MSI) occurs in 10-20% of colorectal tumours and is associated with good prognosis. Here we describe the development and validation of a genomic signature that identifies colorectal cancer patients with MSI caused by DNA mismatch repair deficiency with high accuracy. Microsatellite status for 276 stage II and III colorectal tumours has been determined. Full-genome expression data was used to identify genes that correlate with MSI status. A subset of these samples (n = 73) had sequencing data for 615 genes available. An MSI gene signature of 64 genes was developed and validated in two independent validation sets: the first consisting of frozen samples from 132 stage II patients; and the second consisting of FFPE samples from the PETACC-3 trial (n = 625). The 64-gene MSI signature identified MSI patients in the first validation set with a sensitivity of 90.3% and an overall accuracy of 84.8%, with an AUC of 0.942 (95% CI, 0.888-0.975). In the second validation, the signature also showed excellent performance, with a sensitivity 94.3% and an overall accuracy of 90.6%, with an AUC of 0.965 (95% CI, 0.943-0.988). Besides correct identification of MSI patients, the gene signature identified a group of MSI-like patients that were MSS by standard assessment but MSI by signature assessment. The MSI-signature could be linked to a deficient MMR phenotype, as both MSI and MSI-like patients showed a high mutation frequency (8.2% and 6.4% of 615 genes assayed, respectively) as compared to patients classified as MSS (1.6% mutation frequency). The MSI signature showed prognostic power in stage II patients (n = 215) with a hazard ratio of 0.252 (p = 0.0145). Patients with an MSI-like phenotype had also an improved survival when compared to MSS patients. The MSI signature was translated to a diagnostic microarray and technically and clinically validated in FFPE and frozen samples.

Selective and powerful stress gene expression in Arabidopsis in response to malondialdehyde.

The provenance, half-life and biological activity of malondialdehyde (MDA) were investigated in Arabidopsis thaliana. We provide genetic confirmation of the hypothesis that MDA originates from fatty acids containing more than two methylene-linked double bonds, showing that tri-unsaturated fatty acids are the in vivo source of up to 75% of MDA. The abundance of the combined pool of free and reversibly bound MDA did not change dramatically in stress, although a significant increase in the free MDA pool under oxidative conditions was observed. The half-life of infiltrated MDA indicated rapid metabolic turnover/sequestration. Exposure of plants to low levels of MDA using a recently developed protocol powerfully upregulated many genes on a cDNA microarray with a bias towards those implicated in abiotic/environmental stress (e.g. ROF1 and XERO2). Remarkably, and in contrast to the activities of other reactive electrophile species (i.e. small vinyl ketones), none of the pathogenesis-related (PR) genes tested responded to MDA. The use of structural mimics of MDA isomers suggested that the propensity of the molecule to act as a cross-linking/modifying reagent might contribute to the activation of gene expression. Changes in the concentration/localisation of unbound MDA in vivo could strongly affect stress-related transcription.

More is not always better-comparison of three instruments measuring volume of drinking in a sample of young men and their association with consequences

OBJECTIVE: In general population survey instruments that measure volume of drinking, additional questions and shorter reference periods yield higher volumes. Comparison studies have focused on volume but not on associations between volume and consequences. METHOD: From a cohort study on substance use risk factors (Cohort Study on Substance Use Risk Factors [C-SURF]), baseline data were analyzed for 5,074 young (approximately 20-year-old) men who were drinkers in the past 12 months. Volume of drinking was measured by a generic quantity-frequency (QF) instrument, an extended QF (separately for weekends and weekdays) instrument with 12-months recall, and a retrospective past-week diary. Associations of consequences with and without attribution of alcohol as a cause, Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition (DSM-IV), criteria for dependence, and DSM-5 alcohol use disorder in the past 12 months were analyzed. RESULTS: The generic QF measure resulted in lower volume compared with either the extended QF measure (more questions) or the retrospective diary (the most questions and the shortest recall period). For outcomes, however, the extended QF assessment performed the best and the diary the worst. CONCLUSIONS: Higher volume yields are not always better regarding associations with outcomes. The extended QF instrument better captures the variability of drinking. The retrospective diary performs poorly for associations because of the mismatch with the recall period for past-12-months consequences and the potential for misclassification of past-week abstainers and heavy drinkers because of an uncommon past week. Diaries are not recommended for research investigating individual associations between exposure and outcomes in young populations if consequences are measured with a sufficiently long interval to capture rare consequences. (J. Stud. Alcohol Drugs, 75, 880-888, 2014).

Depression with atypical features and increase in obesity, body mass index, waist circumference, and fat mass: a prospective, population-based study.

IMPORTANCE: Depression and obesity are 2 prevalent disorders that have been repeatedly shown to be associated. However, the mechanisms and temporal sequence underlying this association are poorly understood. OBJECTIVE: To determine whether the subtypes of major depressive disorder (MDD; melancholic, atypical, combined, or unspecified) are predictive of adiposity in terms of the incidence of obesity and changes in body mass index (calculated as weight in kilograms divided by height in meters squared), waist circumference, and fat mass. DESIGN, SETTING, AND PARTICIPANTS: This prospective population-based cohort study, CoLaus (Cohorte Lausannoise)/PsyCoLaus (Psychiatric arm of the CoLaus Study), with 5.5 years of follow-up included 3054 randomly selected residents (mean age, 49.7 years; 53.1% were women) of the city of Lausanne, Switzerland (according to the civil register), aged 35 to 66 years in 2003, who accepted the physical and psychiatric baseline and physical follow-up evaluations. EXPOSURES: Depression subtypes according to the DSM-IV. Diagnostic criteria at baseline and follow-up, as well as sociodemographic characteristics, lifestyle (alcohol and tobacco use and physical activity), and medication, were elicited using the semistructured Diagnostic Interview for Genetic Studies. MAIN OUTCOMES AND MEASURES: Changes in body mass index, waist circumference, and fat mass during the follow-up period, in percentage of the baseline value, and the incidence of obesity during the follow-up period among nonobese participants at baseline. Weight, height, waist circumference, and body fat (bioimpedance) were measured at baseline and follow-up by trained field interviewers. RESULTS: Only participants with the atypical subtype of MDD at baseline revealed a higher increase in adiposity during follow-up than participants without MDD. The associations between this MDD subtype and body mass index (β = 3.19; 95% CI, 1.50-4.88), incidence of obesity (odds ratio, 3.75; 95% CI, 1.24-11.35), waist circumference in both sexes (β = 2.44; 95% CI, 0.21-4.66), and fat mass in men (β = 16.36; 95% CI, 4.81-27.92) remained significant after adjustments for a wide range of possible cofounding. CONCLUSIONS AND RELEVANCE: The atypical subtype of MDD is a strong predictor of obesity. This emphasizes the need to identify individuals with this subtype of MDD in both clinical and research settings. Therapeutic measures to diminish the consequences of increased appetite during depressive episodes with atypical features are advocated.

Identification of CARDIAK, a RIP-like kinase that associates with caspase-1.

Members of the tumor necrosis factor receptor (TNFR) superfamily have an important role in the induction of cellular signals resulting in cell growth, differentiation and death. TNFR-1 recruits and assembles a signaling complex containing a number of death domain (DD)-containing proteins, including the adaptor protein TRADD and the serine/threonine kinase RIP, which mediates TNF-induced NF-kappa B activation. RIP also recruits caspase-2 to the TNFR-1 signaling complex via the adaptor protein RAIDD, which contains a DD and a caspase-recruiting domain (CARD). Here, we have identified a RIP-like kinase, termed CARDIAK (for CARD-containing interleukin (IL)-1 beta converting enzyme (ICE) associated kinase), which contains a serine/threonine kinase domain and a carboxy-terminal CARD. Overexpression of CARDIAK induced the activation of both NF-kappa B and Jun N-terminal kinase (JNK). CARDIAK interacted with the TNFR-associated factors TRAF-1 and TRAF-2, and a dominant-negative form of TRAF-2 inhibited CARDIAK-induced NF-kappa B activation. Interestingly, CARDIAK specifically interacted with the CARD of caspase-1 (previously known as ICE), and this interaction correlated with the processing of pro-caspase-1 and the formation of the active p20 subunit of caspase-1. Together, these data suggest that CARDIAK may be involved in NF-kappa B/JNK signaling and in the generation of the proinflammatory cytokine IL-1 beta through activation of caspase-1.

Assessment of Physical Activity and Energy Expenditure by GPS Combined With Accelerometry in Real-Life Conditions.

Background: Physical activity (PA) and related energy expenditure (EE) is often assessed by means of a single technique. Because of inherent limitations, single techniques may not allow for an accurate assessment both PA and related EE. The aim of this study was to develop a model to accurately assess common PA types and durations and thus EE in free-living conditions, combining data from global positioning system (GPS) and 2 accelerometers. Methods: Forty-one volunteers participated in the study. First, a model was developed and adjusted to measured EE with a first group of subjects (Protocol I, n = 12) who performed 6 structured and supervised PA. Then, the model was validated over 2 experimental phases with 2 groups (n = 12 and n = 17) performing scheduled (Protocol I) and spontaneous common activities in real-life condition (Protocol II). Predicted EE was compared with actual EE as measured by portable indirect calorimetry. Results: In protocol I, performed PA types could be recognized with little error. The duration of each PA type could be predicted with an accuracy below 1 minute. Measured and predicted EE were strongly associated (r = .97, P < .001). Conclusion: Combining GPS and 2 accelerometers allows for an accurate assessment of PA and EE in free-living situations.

Epidémiologie des cancers épithéliaux de la peau [Epidemiology of epithelial skin cancers]

With no less than 15,000 estimated new cases diagnosed per year, non melanomatous carcinomas are the commonest cutaneous cancers in the Swiss population. About 1 in 3 new cancer case is a basal (BCC) or a squamous cell carcinoma (SCC). Incidence rates are steadily increasing, faster for BCC than SCC. Rates are higher for men than women and increase exponentially with age. Systematic population-based registration of non melanomatous skin cancers faces many challenges that few cancer registries can meet. Rates of these cancers in Switzerland are among the highest in Europe. Primary and secondary nationwide prevention campaigns have been carried out for nearly 20 years with a focus on the deadliest cutaneous cancer: melanoma. However, detection of non melanomatous skin cancers benefits from these campaigns since prevention messages and means of early detection are similar for melanomas and other skin cancers.

Le couvent de Romainmôtier du début de l'époque clunisienne à la fin du XIIe siècle : étude archivistique, diplomatique et historique, suivie de l'édition du chatrier

Les chartes de l'ancien couvent de Romainmôtier constituent une source d'information essentielle pour l'histoire du Pays de Vaud aux Xe et XIe siècles. Toutefois, malgré leur importance, elles n'ont jamais fait l'objet d'une étude d'ensemble. Les historiens dépendent encore aujourd'hui de transcriptions partielles et fautives, imprimées au XIXe siècle. Afin de remédier à cette carence historiographique, Alexandre Pahud, qui a réuni l'ensemble des documents entre 888 et 1190, propose dans sa thèse de doctorat, soutenue à l'Université de Lausanne le 25 novembre 2008, une édition critique de tous ces textes, selon les principes de l'érudition moderne. Si les Archives cantonales vaudoises conservent la majeure partie de la documentation, d'autres institutions en Suisse et à l'étranger fournissent un apport substantiel concernant Romainmôtier avant le XIIIe siècle. Il s'agit en particulier des Archives de l'Etat de Fribourg, des Archives de l'Etat de Berne et de la Bibliothèque royale de Turin. En raison d'une importante dispersion des fonds, A. Pahud a entrepris de reconstituer le chartrier du couvent, tel qu'il devait exister à l'époque médiévale. Pour cela, il s'est basé sur les notes dorsales qui figurent au verso des parchemins, ainsi que sur les anciens inventaires. La méthode utilisée a permis de retrouver plusieurs chartes du début de l'an mil, sous la forme de copies intégrales, ainsi qu'une vingtaine de notices en allemand résumant des actes des Xe-XIIe siècles, tous ces textes étant demeurés inconnus des spécialistes. Ainsi, la thèse de A. Pahud démontre qu'il est possible d'apporter de nouveaux matériaux destinés à enrichir notre connaissance de cette période reculée et mal documentée au niveau local. En parallèle, l'auteur de la thèse a mené une expertise diplomatique des chartes de Romainmôtier, c'est-à-dire une étude de leurs caractéristiques matérielles et formelles. A l'examen, il apparaît que les moines ont davantage acquis de biens qu'ils n'en ont concédé à des tiers, symptôme d'un patrimoine en voie de formation. Les actes privés, qui relatent des transactions entre le monastère et ses voisins, représentent le 80% du corpus étudié. Ils sont rédigés tantôt au présent et à la première personne, tantôt au passé et à la troisième personne, lorsqu'ils ne mélangent pas les deux types de discours. Leur valeur juridique est assurée par une liste de témoins, à défaut de tout scellement. Dans la majorité des cas, un unique scribe établit son texte en une seule fois, après la cérémonie sanctionnant le transfert de propriété. Jusqu'en 1050, ce sont généralement des personnes extérieures à Romainmôtier qui instrumentent au profit du couvent; par la suite, les clunisiens reprennent à leur compte la confection des actes qui les concernent. Curieusement, on constate une disparition radicale de l'acte privé à Romainmôtier entre 1167 et 1198, phénomène qui tranche complètement sur la conjoncture régionale. Dans la dernière partie de sa thèse, A. Pahud présente une nouvelle histoire du couvent de Romainmôtier, qui aborde à la fois les questions politiques et les structures socioéconomiques. Durant le premier tiers du XIe siècle, les clunisiens de Romainmôtier bénéficient de la protection du dernier roi de Bourgogne, Rodolphe III (993-1032), qui fonde la puissance temporelle du monastère. A cette époque, l'institution est administrée directement par l'abbé de Cluny, Odilon, responsable de Romainmôtier à titre personnel. Cependant, la disparition de Rodolphe III, dont la succession est contestée, inaugure une période de grave insécurité dans nos régions. Ces troubles profitent avant tout aux seigneurs locaux, qui prennent appui sur un château pour imposer leur domination au détriment des pouvoirs ecclésiastiques. Au milieu du XIe siècle, les possessions de Romainmôtier, qui s'étendent de chaque côté du Jura, sont menacées par trois puissants lignages, les Grandson, les Salins et les Joux. Face à cette situation périlleuse, les religieux s'adressent tour à tour au pape, à l'empereur germanique, ainsi qu'aux comtes de Bourgogne, dépositaires d'une autorité publique en Franche-Comté. Mais bien souvent, les moines doivent transiger avec leurs adversaires, en passant avec eux des accords coûteux et fragiles. Cela n'empêche pas qu'une certaine coopération s'établisse à l'occasion avec le monde laïque, qui contribue par ses aumônes au développement économique du monastère. Romainmôtier tire ses principales ressources de l'agriculture, tant au Pays de Vaud qu'en Franche-Comté; le travail de la vigne est bien attesté sur La Côte, dès la fin du Xe siècle, tandis que l'élevage ne joue qu'un rôle secondaire; là où ils sont bien implantés, les moines parviennent à prendre le contrôle des moulins; à Salins (France), ils exploitent eux-mêmes le sel nécessaire à leurs besoins. L'ensemble de ces observations s'appuie sur des tableaux et des annexes, qui ajoutent à la critique interne des sources une dimension quantitative. Afin de divulguer les résultats obtenus, A. Pahud envisage de publier prochainement sa thèse dans les Mémoires et documents de la Société d'histoire de la Suisse romande.

Incidence of stent thrombosis and adverse cardiac events 5 years after sirolimus stent implantation in clinical practice.

BACKGROUND: The long-term incidence of stent thrombosis (ST) and complications after sirolimus-eluting stents (SES) implantation is still a matter of debate. METHOD: We conducted a systematic follow-up on the day of their 5-year SES implantation anniversary, in a series of consecutive real-world patients treated with a SES. The use of SES implantation was not restricted to "on-label" indications, and target lesions included in-stent restenosis, vein graft, left main stem locations, bifurcations, and long lesions. The Academic Research Consortium criteria were used for ST classification. RESULTS: Three hundred fifty consecutive patients were treated with SES between April and December 2002 in 3 Swiss hospitals. Mean age was 63 +/- 6 years, 78% were men, 20% presented with acute coronary syndrome, and 19% were patients with diabetes. Five-year follow-up was obtained in 98% of eligible patients. Stent thrombosis had occurred in 12 patients (3.6%) [definite 6 (1.8%), probable 1 (0.3%) and possible 5 (1.5%)]. Eighty-one percent of the population was free of complications. Major adverse cardiac events occurred in 74 (21%) patients and were as follows: cardiac death 3%, noncardiac death 4%, myocardial infarction 2%, target lesion revascularization 8%, non-target lesion revascularization target vessel revascularization 3%, coronary artery bypass graft 2%. Non-TVR was performed in 8%. CONCLUSION: Our data confirm the good long-term outcome of patients treated with SES. The incidence of complications and sub acute thrombosis at 5 years in routine clinical practice reproduces the results of prospective randomized trials.

Daily smoking as a marker of weight control practices among female adolescents

Purpose: There is evidence indicating that adolescent females smoke as a way to control weight. The aim of our research is to assess whether daily smoking is a marker for weight control practices among adolescent females. Methods: Data were drawn from the 2002 Swiss Multicenter Adolescent Survey on Health (SMASH02) data base, a survey including 7,548 [3,838 females] in-school adolescents aged 16-20 years in Switzerland. Among females self-reporting BMI (N _ 3,761), two groups were drawn: daily smokers (DS, N _ 1,273) included all those smoking at least 1 cigarette/day and never smokers (NS, N _ 1,888) included all those having never smoked. Former (N _ 177) and occasional (N _ 423) smokers were not included. Groups were compared on weight control practices (being on a diet, self-induced vomiting, use of doctor-prescribed or over-the-counter appetite suppressors) controlling for possible confounding variables (age, BMI, feeling fat, body image, use of other substances, depression, sport practice, academic track and perceived advanced puberty). Analyses were performed with STATA 9. Bivariate analyses are presented as point-prevalence and multivariate analysis (using logistic regression) are presented as adjusted odds ratio (AOR) and [95% confidence interval]. Results: In the bivariate analysis, DS females were significantly more likely (p _ 0.001) than NS to be on a diet (DS: 33.2%, NS: 22.2%), to self-induce vomiting (DS: 9.0%, NS: 3.3%), and to use doctor prescribed (DS: 2.3%, NS: 0.9%) or over-the-counter (DS: 3.2%, NS: 1.2%) appetite suppressors. In the multivariate analysis, DS females were more likely than NS to be on a diet (AOR: 1.40 [1.17/1.68]), to self-induce vomiting (AOR: 2.07 [1.45/2.97]), and to use doctor-prescribed appetite suppressors (AOR: 1.99 [1.00/ 3.96]). Conclusions: Weight control practices are more frequent among female daily smokers than among never smokers. This finding seems to confirm cigarette smoking as a way to control weight among adolescent females. Health professionals should inquire adolescent female smokers about weight control practices, and this association must be kept in mind when discussing tobacco cessation options with adolescent females. Sources of Support: The SMASH02 survey was funded by the Swiss Federal Office of Public Health and the participating cantons.

Endovascular aortic repair versus open surgical repair for descending thoracic aortic disease a systematic review and meta-analysis of comparative studies.

OBJECTIVES: The purpose of this study was to determine whether thoracic endovascular aortic repair (TEVAR) reduces death and morbidity compared with open surgical repair for descending thoracic aortic disease. BACKGROUND: The role of TEVAR versus open surgery remains unclear. Metaregression can be used to maximally inform adoption of new technologies by utilizing evidence from existing trials. METHODS: Data from comparative studies of TEVAR versus open repair of the descending aorta were combined through meta-analysis. Metaregression was performed to account for baseline risk factor imbalances, study design, and thoracic pathology. Due to significant heterogeneity, registry data were analyzed separately from comparative studies. RESULTS: Forty-two nonrandomized studies involving 5,888 patients were included (38 comparative studies, 4 registries). Patient characteristics were balanced except for age, as TEVAR patients were usually older than open surgery patients (p = 0.001). Registry data suggested overall perioperative complications were reduced. In comparative studies, all-cause mortality at 30 days (odds ratio [OR]: 0.44, 95% confidence interval [CI]: 0.33 to 0.59) and paraplegia (OR: 0.42, 95% CI: 0.28 to 0.63) were reduced for TEVAR versus open surgery. In addition, cardiac complications, transfusions, reoperation for bleeding, renal dysfunction, pneumonia, and length of stay were reduced. There was no significant difference in stroke, myocardial infarction, aortic reintervention, and mortality beyond 1 year. Metaregression to adjust for age imbalance, study design, and pathology did not materially change the results. CONCLUSIONS: Current data from nonrandomized studies suggest that TEVAR may reduce early death, paraplegia, renal insufficiency, transfusions, reoperation for bleeding, cardiac complications, pneumonia, and length of stay compared with open surgery. Sustained benefits on survival have not been proven.

Routine therapeutic drug monitoring in patients treated with 10-360 mg/day citalopram

From data collected during routine TDM, plasma concentrations of citalopram (CIT) and its metabolites demethylcitalopram (DCIT) and didemethylcitalopram (DDCIT) were measured in 345 plasma samples collected in steady-state conditions. They were from 258 patients treated with usual doses (20-60 mg/d) and from patients medicated with 80-360 mg/d CIT. Most patients had one or several comedications, including other antidepressants, antipsychotics, lithium, anticonvulsants, psychostimulants and somatic medications. Dose-corrected CIT plasma concentrations (C/D ratio) were 2.51 +/- 2.25 ng mL-1 mg-1 (n = 258; mean +/- SD). Patients >65 years had significantly higher dose-corrected CIT plasma concentrations (n = 56; 3.08 +/- 1.35 ng mL-1 mg-1) than younger patients (n = 195; 2.35 +/- 2.46 ng mL-1 mg-1) (P = 0.03). CIT plasma concentrations in the generally recommended dose range were [mean +/- SD, (median)]: 57 +/- 64 (45) ng/mL (10-20 mg/d; n = 64), 117 +/- 95 (91) ng/mL (21-60 mg/d; n = 96). At higher than usual doses, the following concentrations of CIT were measured: 61-120 mg/d CIT, 211 +/- 103 (190) ng/mL (n = 93); 121-200 mg/d: 339 +/- 143 (322) ng/mL (n = 70); 201-280 mg/d: 700 +/- 408 (565) ng/mL (n = 18); 281-360 mg/d: 888 +/- 620 (616) ng/mL (n = 4). When only one sample per patient (at the highest daily dose if repeated dosages) is considered, there is a linear and significant correlation (n = 48, r = 0.730; P < 0.001) between daily dose (10-200 mg/d) and CIT plasma concentrations. In experiments with dogs, DDCIT was reported to affect the QT interval when present at concentrations >300 ng/mL. In this study, DDCIT concentration reached 100 ng/mL in a patient treated with 280 mg/d CIT. Twelve other patients treated with 140-320 mg/d CIT had plasma concentrations of DDCIT within the range 52-73 ng/mL. In a subgroup comprised of patients treated with > or =160 mg/d CIT and with CIT plasma concentrations < or =300 ng/mL, and patients treated with < or =200 mg/d CIT and CIT plasma concentrations > or = 600 ng/mL, the enantiomers of CIT and DCIT were also analyzed. The highest S-CIT concentration measured in this subgroup was 327 ng/mL in a patient treated with 140 mg/d CIT, but the highest S-CIT concentration (632 ng/mL) was measured in patient treated with 360 mg/d CIT. In conclusion, there is a highly linear correlation between CIT plasma concentrations and CIT doses, well above the usual dose range.

Automated scoring of AFLPs using RawGeno v 2.0, a free R CRAN library.

Amplified Fragment Length Polymorphisms (AFLPs) are a cheap and efficient protocol for generating large sets of genetic markers. This technique has become increasingly used during the last decade in various fields of biology, including population genomics, phylogeography, and genome mapping. Here, we present RawGeno, an R library dedicated to the automated scoring of AFLPs (i.e., the coding of electropherogram signals into ready-to-use datasets). Our program includes a complete suite of tools for binning, editing, visualizing, and exporting results obtained from AFLP experiments. RawGeno can either be used with command lines and program analysis routines or through a user-friendly graphical user interface. We describe the whole RawGeno pipeline along with recommendations for (a) setting the analysis of electropherograms in combination with PeakScanner, a program freely distributed by Applied Biosystems; (b) performing quality checks; (c) defining bins and proceeding to scoring; (d) filtering nonoptimal bins; and (e) exporting results in different formats.