Geophysical Investigations for Hydrogeological Characterization at the Kappelen Test Site (Switzerland)

Vertical electric soundings, 2D resistivity imaging and several logging measurements were performed at Kappelen test site to identify the various geolelectric facies that allowed determining the tabular and horizontal structure of the aquifer. The surface-based geoelectric methods allowed for a reliable characterization of the overall structure and the geometry of the aquifer, while geophysical logging methods allowed for inferring detailed hydrogeophysical characteristics, such as the electrical resistivity, total porosity, global and matrix density and hydraulic conductivity. The synoptic interpretation and integration of this broad and diverse database allows for constraining the key hydrological characteristics and hence forms the basis for the detailed hydraulic modelling of flow and transport process.

Test of four colon cancer risk-scores in formalin fixed paraffin embedded microarray gene expression data.

BACKGROUND: Prognosis prediction for resected primary colon cancer is based on the T-stage Node Metastasis (TNM) staging system. We investigated if four well-documented gene expression risk scores can improve patient stratification. METHODS: Microarray-based versions of risk-scores were applied to a large independent cohort of 688 stage II/III tumors from the PETACC-3 trial. Prognostic value for relapse-free survival (RFS), survival after relapse (SAR), and overall survival (OS) was assessed by regression analysis. To assess improvement over a reference, prognostic model was assessed with the area under curve (AUC) of receiver operating characteristic (ROC) curves. All statistical tests were two-sided, except the AUC increase. RESULTS: All four risk scores (RSs) showed a statistically significant association (single-test, P < .0167) with OS or RFS in univariate models, but with HRs below 1.38 per interquartile range. Three scores were predictors of shorter RFS, one of shorter SAR. Each RS could only marginally improve an RFS or OS model with the known factors T-stage, N-stage, and microsatellite instability (MSI) status (AUC gains < 0.025 units). The pairwise interscore discordance was never high (maximal Spearman correlation = 0.563) A combined score showed a trend to higher prognostic value and higher AUC increase for OS (HR = 1.74, 95% confidence interval [CI] = 1.44 to 2.10, P < .001, AUC from 0.6918 to 0.7321) and RFS (HR = 1.56, 95% CI = 1.33 to 1.84, P < .001, AUC from 0.6723 to 0.6945) than any single score. CONCLUSIONS: The four tested gene expression-based risk scores provide prognostic information but contribute only marginally to improving models based on established risk factors. A combination of the risk scores might provide more robust information. Predictors of RFS and SAR might need to be different.

HIERFSTAT, a package for R to compute and test hierarchical F-statistics

The package HIERFSTAT for the statistical software R, created by the R Development Core Team, allows the estimate of hierarchical F-statistics from a hierarchy with any numbers of levels. In addition, it allows testing the statistical significance of population differentiation for these different levels, using a generalized likelihood-ratio test. The package HIERFSTAT is available at http://www.unil.ch/popgen/softwares/hierfstat.htm.

Altered vision during motion: an unusual symptom of cerebellar dysfunction, quantifiable by a simple clinical test.

PURPOSE: To report a series of patients with cerebellar dysfunction and altered vision during motion, and to quantify their visual impairment in motion with a simple clinical test. METHODS: Twenty consecutive patients suffering from cerebellar dysfunction and altered vision during motion were examined between 1994 and 2007. A control group consisted of 20 age- and sex-matched healthy people. All patients had a full neuro-ophthalmic examination. Near visual acuity (NVA) was measured at rest (static NVA) and during chair rotation (dynamic NVA). Distance visual acuity (DVA) was measured at rest (static DVA) and during rotation of the patient's head (dynamic DVA). RESULTS: Only four of the 20 patients reported altered vision during motion spontaneously. The remaining 16 patients admitted this unusual visual disturbance only when asked specifically. All patients exhibited abnormal eye movements, including saccadic smooth pursuit (20/20), dysmetric saccades (15/20), nystagmus (19/20) and impaired suppression of vestibulo-ocular reflex (VOR) (20/20). During rotation of the examination chair (dynamic NVA), the drop in NVA averaged 5.6 lines (range 1-10 lines). During rotation of the patient's head (dynamic DVA), the drop in DVA averaged only 2.5 lines (range 0-10 lines). For the control group, there was no significant drop in NVA under dynamic conditions. CONCLUSION: Patients with cerebellar dysfunction rarely complain spontaneously of altered vision during motion. However, specific questioning may bring up this unusual symptom. The use of a simple clinical test, consisting of NVA measurement during rotation of the examination chair (dynamic NVA), allows practitioners to quantify the level of visual impairment in patients presenting altered VOR modulation.

Lats2, a novel regulator of Elongin BC ubiquitin ligase

Résumé : Le Large tumor suppressor, Lats2, est une protéine humaine homologue au suppresseur de tumeur Warts (Lats) de Drosophila melanogaster, qui réprime la prolifération des cellules en altérant leur cycle au niveau des transitions Gl/S et G2/M, et en induisant l'apoptose. Pourtant, la voie moléculaire par laquelle Lats2, une sériase-thréonine kinase, déclenche l'arrêt du cycle cellulaire, est toujours inconnue. Notre équipe a d'abord déterminé que Lats2 était un gène de réponse à la protéine p53 (Kostic et al., 2000). Par la suite, nous avons identifié des protéines interagissant avec Lats2, notamment les modules de reconnaissance du substrat des ligases Colline E3 (des protéines contenant Socs box ou F box) ainsi que deux Bous-unités du Signalosome CSN: CSN4 et CSNS. En outre, Lats2 est connue pour s'associer au Super-complexe composé de CSN et des ligases Colline E3 (Rongere, thesis, 2004; Rongere, unpublished results, 2005). Le travail présenté ici sur Lats2 a confirmé que cette protéine est une kinase associée à CSN. Nous avons caractérisé les interactions spécifiques de domaines de Lats2 avec hSocs3, hWsb 1 (des protéines Socs box) et hFBX-7 (une protéine F box), ainsi que les conséquences physiologiques des interactions avec hSocs3, hWsb1 et hSocs1. Des expériences de GST pull-down ont montré que les deux domaines, N-terminal et kinase, de Lats2 interagissent avec hSocs3, hWsb1 et hFBX-7, ce qui suggère aussi que l'ensemble de la protéine Lats2 est impliqué dans ces interactions. Une étude approfondie des interactions entre Lats2 et hSocs3 indique que le domaine kinase de Lats2 interagit avec la région de hSocs3 contenant un domaine SH2, situé en amont du domaine Socs box de hSocs3. Par ailleurs, Lats2 phosphoryle des régions spécifiques entre les domaines N-terminal et SH2 (Sl), et, entre les domaines SH2 et Socs box (S3) de la protéine hSocs3. Ces résultats révèlent que hSocs3 est un.nouveau substrat de Lats2. Des modifications de l'activité kinase ont aussi révélé que la protéine sauvage Lats2 (wt Lats2) était capable de phosphoryler hSocs3, alors qu'un mutant dead du domaine kinase Lats (poche ATP délétée, Lats2OATP) non. L'analyse des mutations a permis d'identifier deux résidus sériase situés aux positions 1441145 (S3), spécifiquement phosphorylés par wt Lats2. La phosphorylation des protéines représentant un signal de dégradation protéolytique, nous avons envisagé que Lats2 pouvait cibler hSocs3 pour une dégradation protéasomale. Lorsque wt Lats2 est surexprimée dans des cellules HEK293T et COS7, la demi-vie de hSocs3, un élément de la ligase Elongine BC-Colline É3 (ligase EBC), diminue significativement, effet que n'a pas la surexpression de Lats2OATP. De plus, la stabilité de hSocs3 dépend de la phosphorylation des résidus sériase aux positions 144/145 par wt Lats2. Bien que les sites de phosphorylation ne soient pas définis pour les deux autres modules de reconnaissance du substrat de la ligase EBC: hWsb 1 et hSocsl, leurs demi-vies diminuent également quand wt Lats2 est surexprimée. Pour les tests in vivo, nous avons synthétisé des esiRNA pour diminuer l'expression du gène endogène lats2, ce qui a entraîné une augmentation d'un facteur 2 de la demi-vie de hSocs3 et de hWsbl dans les cellules HEK293T. En conclusion, nos résultats suggérent que Lats2, une kinase associée au CSN, est un nouveau régulateur de la fonction des ligases EBC, agissant sur le renouvellement des protéines hSocs3, hSocs1 et hWsb1. Ainsi, Lats2 altère la spécificité et la capacité des ligases EBC, régulant par là même la stabilité de nombreuses protéines, ciblées par les ligases EBC pour une dégradation protéasomale. D'autres études devraient révéler si la modification observée de la fonction de la ligase EBC par Lats2, associée au Super-complexe, est également responsable du renouvellement des régulateurs du cycle cellulaire et des changements dans ce même cycle observés lors de la surexpression de Lats2. Summary : The Large tumor suppressor 2 (Lats2) is a human homologue of the Drosophila melanogaster tumor suppressor Warts (Cats) who negatively regulates cell proliferation by altering cell cycle Gl/S and G2/M transition and inducing apoptosis. However, the molecular pathway by which Lats2, a serine-threonine kinase, mediates cell cycle arrest is still unknown. Lats2 was initially identified to be a p53 response gene by our group (Kostic et al., 2000). Subsequently, our group identified interacting candidates of Lats2, including substrate recognition modules of Cullin-based E3 ligases (Socs box or F-box containing proteins) as well as two subunits of the Signalosome (CSN), CSN4 and CSNS. Additionally, Lats2 was shown to associate with a Super-complex, composed of CSN and Cullin-based E3 ligases (Rongere, thesis, 2004; Rongere, unpublished results, 2005) We hypothesized that Lats2 may perform its physiological function through interaction with CSN and Cullin-based E3 ligases. The present work on Lats2 has confirmed that Lats2 is a CSN associated kinase. We defined the domain specific interactions of Lats2 with hSocs3, hWsb1 (Sots box proteins) and hFBX-7 (F box protein), as well as the physiological consequences of interaction with hSocs3, hWsb1 and hSocs1. Both the N-terminal and the kinase domains of Lats2 interact with full-length hSocs3, hWsb1 and hFBX-7, determined in GST pull-down assays suggesting that full-length Lats2 protein is involved in interactions. Refinement of the Lats2 interaction with hSocs3 indicated that the kinase domain of Lats2 interacts with a region of hSocs3 containing a SH2 domain located upstream of the Socs box domain of the hSocs3. Moreover, Lats2 phosphorylated specific regions between the N-terminal and SH2 domain (S l) as well as between the SH2 domain and Socs box domain of hSocs3 (S3).These results indicate that hSocs3 is a novel Lats2 substrate. The kinase assay has also demonstrated that wt Lats2 was able to phosphorylate hSocs3, but not Lats2 kinase dead mutant (deleted ATP pocket, Lats20ATP). Mutational analysis identified two serine residues located at positions 144/145 (S3) to be specifically phosphorylated by wt Lats2. Phosphorylation of proteins has been shown to be a signal for proteolytic degradation of many characterized proteins. Thus we hypothesized that Lats2 could target hSocs3 for proteasomal degradation. When wt Lats2 was over-expressed in HEK293T cells and COST cells, the half-life of hSocs3, as a component of Elongin BC Cullin-based E3 ubiquitin ligase (EBC ligase), decreased significantly. In contrast, aver-expression of the Lats2OATP did not alter the half-life of hSocs3. Furthermore, the stability of hSocs3 depended on phosphorylation of serine residues at positions 144/145 by wt Lats2. Although the sites of phosphorylation were not defined for two other substrate recognition modules of EBC ligasehWsbl and hSocsl, their half-lives also decreased when wt Lats2 was over-expressed. To test in vivo, we synthesized esiRNA to knock-down endogenous Lats2 and subsequently we measured the half-lives of hSocs3 and hVVsb l . Here we demonstrated that the half-lives of hSocs3 and hWsbl were increased by the factor of two in Lats2-depleted HEK293T cells. In conclusion, our findings suggest that Lats2, a CSN associated kinase, is a novel regulator of EBC ligase function by regulating the turn-over of hSocs3, hSocs1 and hWsb1. Thus, Lats2 alters the specificity and capacity of EBC ligases regulating thereby the stability of numerous proteins which are targeted by EBC ligases for proteasomal degradation. Further studies should reveal whether the observed modulation of EBC ligase function by Lats2 associated with a Super-complex is also responsible for the turn-over of cell cycle regulators and the observed alteration in cell cycle by Lats2 over-expression.

A new blood-based screening test for colorectal cancer: a pilot study

Background: Colorectal cancer (CRC) can be cured when diagnosed in its early or precancerous (adenoma) stages. Mostly due to poor compliance towards invasive screening procedures, detection rates for adenoma and early CRCs are still low. Available non-invasive screening tests have unfortunately low sensitivity and specificity performances. Therefore, there is a large unmet need calling for a cost-effective, reliable and non-invasive test to screen for early neoplastic and pre-neoplastic lesions. Objective: To develop a routine screening test based on a nucleic acids multi-gene assay performed on peripheral blood mononuclear cells (PBMCs) that can detect early CRCs and adenomas. Methods: 116 patients (mean age: 55 years; range: 18 to 74 years; female/male ration 0.98) were included in this pilot, nonblinded, colonoscopy-controlled study. Colonoscopy revealed 21 patients with CRC, 30 patients with adenoma bigger than 1 cm, 24 patients with inflammatory bowel disease (IBD) and 41 patients had no neoplastic or inflammatory lesions. Blood samples were taken from each patient the day of the colonoscopy and PBMCs were purified. Total RNA was extracted following standard procedures. Multiplex RT-qPCR was applied on 92 different candidate biomarkers. Different univariate and multivariate statistical methods were applied on these candidates, and among them, 57 biomarkers with significant p values (<0.01, Wilcoxon test) were selected, including ADAMTS1, MMP9, CXCL10, CXCR4, VEGFA and CDH1. Two distinct biomarker signatures are used to separate patients without neoplastic lesion from those with cancer (named COLOX 1 test), respectively from those with adenoma (named COLOX 2 test). Result: COLOX 1 and 2 tests have successfully separated patients without neoplastic lesion from those with CRC (sensitivity 70%, specificity 90%, AUC 0.88), respectively from those with adenoma bigger than 1cm (sensitivity 61%, specificity 80%, AUC 0.80). 6/24 patients in the IBD group have a positive COLOX 1 test. Conclusion: These two COLOX tests demonstrated an acceptable sensitivity and a high specificity to detect the presence of CRCs and adenomas bigger than 1 cm. The false positives COLOX 1 test in IBD patients could possibly be due to the chronic inflammatory state. A prospective, multicenter, pivotal study is underway in order to confirm these promising results in a larger cohort.

The trail making test as a screening instrument for driving performance in older drivers; a translational research.

BACKGROUND: In many countries, primary care physicians determine whether or not older drivers are fit to drive. Little, however, is known regarding the effects of cognitive decline on driving performance and the means to detect it. This study explores to what extent the trail making test (TMT) can provide indications to clinicians about their older patients' on-road driving performance in the context of cognitive decline. METHODS: This translational study was nested within a cohort study and an exploratory psychophysics study. The target population of interest was constituted of older drivers in the absence of important cognitive or physical disorders. We therefore recruited and tested 404 home-dwelling drivers, aged 70 years or more and in possession of valid drivers' licenses, who volunteered to participate in a driving refresher course. Forty-five drivers also agreed to undergo further testing at our lab. On-road driving performance was evaluated by instructors during a 45 minute validated open-road circuit. Drivers were classified as either being excellent, good, moderate, or poor depending on their score on a standardized evaluation of on-road driving performance. RESULTS: The area under the receiver operator curve for detecting poorly performing drivers was 0.668 (CI95% 0.558 to 0.778) for the TMT-A, and 0.662 (CI95% 0.542 to 0.783) for the TMT-B. TMT was related to contrast sensitivity, motion direction, orientation discrimination, working memory, verbal fluency, and literacy. Older patients with a TMT-A ≥ 54 seconds or a TMT-B ≥ 150 seconds have a threefold (CI95% 1.3 to 7.0) increased risk of performing poorly during the on-road evaluation. TMT had a sensitivity of 63.6%, a specificity of 64.9%, a positive predictive value of 9.5%, and a negative predictive value of 96.9%. CONCLUSION: In screening settings, the TMT would have clinicians uselessly consider driving cessation in nine drivers out of ten. Given the important negative impact this could have on older drivers, this study confirms the TMT not to be specific enough for clinicians to justify driving cessation without complementary investigations on driving behaviors.

Dealing with clients' diversity in test situations: Client categorisations in psychologists' accounts of their practices

Reducing a test administration to standardised procedures reflects the test designers' standpoint. However, from the practitioners' standpoint, each client is unique. How do psychologists deal with both standardised test administration and clients' diversity? To answer this question, we interviewed 17 psychologists working in three public services for children and adolescents about their assessment practices. We analysed the numerous "client categorisations" they produced in their accounts. We found that they had shared perceptions about their clients' diversity, and reported various non-standard practices that complemented standardised test administration, but also differed from them or were even forbidden. They seem to experience a dilemma between: (a) prescribed and situated practices; (b) scientific and situated reliability; (c) commutative and distributive justice. For practitioners, dealing with clients' diversity this is a practical problem, halfway between a problem-solving task and a moral dilemma.

Passive knee-extension test to measure hamstring tightness: influence of gravity correction

CONTEXT: A passive knee-extension test has been shown to be a reliable method of assessing hamstring tightness, but this method does not take into account the potential effect of gravity on the tested leg. OBJECTIVE: To compare an original passive knee-extension test with 2 adapted methods including gravity's effect on the lower leg. DESIGN: Repeated measures. SETTING: Laboratory. PARTICIPANTS: 20 young track and field athletes (16.6 ± 1.6 y, 177.6 ± 9.2 cm, 75.9 ± 24.8 kg). INTERVENTION: Each subject was tested in a randomized order with 3 different methods: In the original one (M1), passive knee angle was measured with a standard force of 68.7 N (7 kg) applied proximal to the lateral malleolus. The second (M2) and third (M3) methods took into account the relative lower-leg weight (measured respectively by handheld dynamometer and anthropometrical table) to individualize the force applied to assess passive knee angle. MAIN OUTCOME MEASURES: Passive knee angles measured with video-analysis software. RESULTS: No difference in mean individualized applied force was found between M2 and M3, so the authors assessed passive knee angle only with M2. The mean knee angle was different between M1 and M2 (68.8 ± 12.4 vs 73.1 ± 10.6, P < .001). Knee angles in M1 and M2 were correlated (r = .93, P < .001). CONCLUSIONS: Differences in knee angle were found between the original passive knee-extension test and a method with gravity correction. M2 is an improved version of the original method (M1) since it minimizes the effect of gravity. Therefore, we recommend using it rather than M1.

How to screen for problematic cannabis use in population surveys: an evaluation of the Cannabis Use Disorders Identification Test (CUDIT) in a Swiss sample of adolescents and young adults.

BACKGROUND/AIMS: Cannabis use is a growing challenge for public health, calling for adequate instruments to identify problematic consumption patterns. The Cannabis Use Disorders Identification Test (CUDIT) is a 10-item questionnaire used for screening cannabis abuse and dependency. The present study evaluated that screening instrument. METHODS: In a representative population sample of 5,025 Swiss adolescents and young adults, 593 current cannabis users replied to the CUDIT. Internal consistency was examined by means of Cronbach's alpha and confirmatory factor analysis. In addition, the CUDIT was compared to accepted concepts of problematic cannabis use (e.g. using cannabis and driving). ROC analyses were used to test the CUDIT's discriminative ability and to determine an appropriate cut-off. RESULTS: Two items ('injuries' and 'hours being stoned') had loadings below 0.5 on the unidimensional construct and correlated lower than 0.4 with the total CUDIT score. All concepts of problematic cannabis use were related to CUDIT scores. An ideal cut-off between six and eight points was found. CONCLUSIONS: Although the CUDIT seems to be a promising instrument to identify problematic cannabis use, there is a need to revise some of its items.

Does Direct Democracy Matters for Political Parties : An Empirical Test in the Swiss Cantons

According to most political scientists and commentators, direct democracy seems to weaken political parties. Our empirical analysis in the 26 Swiss cantons shows that this thesis in its general form cannot be maintained. Political parties in cantons with extensive use of referendums and initiatives are not in all respects weaker than parties in cantons with little use of direct democratic means of participation. On the contrary, direct democracy goes together with more professional and formalized party organizations. Use of direct democracy is associated with more fragmented and volatile party systems, and with greater support for small parties, but causal interpretations of these relationships are difficult.

Inferring transport characteristics in a fractured rock aquifer by combining single-hole ground-penetrating radar reflection monitoring and tracer test data

Investigations of solute transport in fractured rock aquifers often rely on tracer test data acquired at a limited number of observation points. Such data do not, by themselves, allow detailed assessments of the spreading of the injected tracer plume. To better understand the transport behavior in a granitic aquifer, we combine tracer test data with single-hole ground-penetrating radar (GPR) reflection monitoring data. Five successful tracer tests were performed under various experimental conditions between two boreholes 6 m apart. For each experiment, saline tracer was injected into a previously identified packed-off transmissive fracture while repeatedly acquiring single-hole GPR reflection profiles together with electrical conductivity logs in the pumping borehole. By analyzing depth-migrated GPR difference images together with tracer breakthrough curves and associated simplified flow and transport modeling, we estimate (1) the number, the connectivity, and the geometry of fractures that contribute to tracer transport, (2) the velocity and the mass of tracer that was carried along each flow path, and (3) the effective transport parameters of the identified flow paths. We find a qualitative agreement when comparing the time evolution of GPR reflectivity strengths at strategic locations in the formation with those arising from simulated transport. The discrepancies are on the same order as those between observed and simulated breakthrough curves at the outflow locations. The rather subtle and repeatable GPR signals provide useful and complementary information to tracer test data acquired at the outflow locations and may help us to characterize transport phenomena in fractured rock aquifers.

La consultation pour le test sérologique de dépistage VIH : enjeux pour le couple et pour le médecin

La pratique du test au centre de dépistage anonyme VIH de la Policlinique médicale universitaire de Lausanne semble indiquer que de plus en plus de personnes demandent à être testées, souvent au moment inaugural de la constitution de la vie du couple. L'indication au test de dépistage devrait être le résultat d'une négociation entre le patient et son médecin. Ce dernier est en outre confronté à la complexité des enjeux sociétaux et éthiques que le test représente. Il s'agit d'une tâche difficile, d'autant plus que la requête d'un test n'implique pas le seul devenir du sujet, mais aussi, dans la dimension sexuelle, le devenir de la personne qu'il rencontre. L'avènement du Sida a modifié la vie du couple en rendant la sexualité plus problématique et en donnant un caractère impératif l'exigence de négociation entre les partenaires du couple. La pratique de la prévention révèle aussi comment le Sida met en jeu la responsabilité que les médecins ont de négocier avec leurs patients, à l'instar de ce que ces derniers devraient faire avec leur partenaire dans un but de protection.

Calibration of high-resolution geophysical data with tracer test measurements to improve hydrological predictions

Relationships between porosity and hydraulic conductivity tend to be strongly scale- and site-dependent and are thus very difficult to establish. As a result, hydraulic conductivity distributions inferred from geophysically derived porosity models must be calibrated using some measurement of aquifer response. This type of calibration is potentially very valuable as it may allow for transport predictions within the considered hydrological unit at locations where only geophysical measurements are available, thus reducing the number of well tests required and thereby the costs of management and remediation. Here, we explore this concept through a series of numerical experiments. Considering the case of porosity characterization in saturated heterogeneous aquifers using crosshole ground-penetrating radar and borehole porosity log data, we use tracer test measurements to calibrate a relationship between porosity and hydraulic conductivity that allows the best prediction of the observed hydrological behavior. To examine the validity and effectiveness of the obtained relationship, we examine its performance at alternate locations not used in the calibration procedure. Our results indicate that this methodology allows us to obtain remarkably reliable hydrological predictions throughout the considered hydrological unit based on the geophysical data only. This was also found to be the case when significant uncertainty was considered in the underlying relationship between porosity and hydraulic conductivity.