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.

Effect of age toxicokinetics among human volunteers exposed to propylene glycol monomethyl ether (PGME)

Rationale: Aging adults represent the fastest growing population segment in many countries. Physiological and metabolic changes in the aging process may alter how aging adults respond to exposures compared to younger workers. Current preventive workplace exposure measures may therefore not be sufficiently protective for the aging workforce. In a controlled human toxicokinetic study (exposure chamber; 12m3), the volunteers (n=11) were men and women over the age of 58 years and exposed to a commonly used, low neurotoxic glycol ether; PGME (CAS no. 107-98- 2) (50 ppm, 6 hours). Oxidative metabolism (Michaelis-Menten) is the major pathway and conjugation the minor in humans. Metabolites, conjugated and free PGME are eliminated through the kidneys, and the elimination kinetics is dose-dependent (0 order). Scope: (1) compare the toxicokinetic profile of PGME obtained in the aging volunteers (58- 62 years) to young volunteers (20-25 years) from a previous study; (2) Test the predictive power of an existing PGME toxicokinetic compartment model for aging persons against urinary PGME concentrations found in volunteers from our experimental study. Experimental procedure: Urine samples were collected before, every 2-hour during exposures for six hours, and ad-lib for additional 20 hours. Urinary analysis of free and total PGME was performed using capillary GC/FID. The toxicokinetic model (Berkley Madonna software) was ageadjusted. Results. Urinary free and total PGME concentration rose rapidly, and did not reach an apparent plateau level during exposure. Less conjugation was observed in the older group. The predictive model developed for the young group predicted well total PGME in the aging group but not free PGME. The age adjusted toxicokinetic model's Vmax1 had to be changed for the aging group, implying slower enzymatic pathway. Conclusion: The toxicokinetic model did not predict well if only the physiological parameters were adjusted for aging adults (existing model); a substance specific metabolic rate parameter was also needed.

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.

Ultrasound assessment of ocular vascular effects of repeated intravitreal injections of ranibizumab for wet age-related macular degeneration.

PURPOSE: Determine the effect of repeated intravitreal injections of ranibizumab (0.5 mg; 0.05 ml) on retrobulbar blood flow velocities (BFVs) using ultrasound imaging quantification in twenty patients with exudative age-related macular degeneration treated for 6 months. METHODS: Visual acuity (ETDRS), central macular thickness (OCT), peak-systolic, end-diastolic and mean-BFVs in central retinal (CRA), temporal posterior ciliary (TPCA) and ophthalmic (OA) arteries were measured before, 2 days, 3 weeks and 6 months after the first injection. Patients were examined monthly and received 1-5 additional injections depending on ophthalmologic examination results. RESULTS: Six months after the first injection, a significant increase in visual acuity 50.9 ± 25.9 versus 44.4 ± 21.7 (p < 0.01) and decrease in mean central macular thickness 267 ± 74 versus 377 ± 115 μm (p < 0.001) were observed compared to baseline. Although mean-BFVs decreased by 16%±3% in CRA and 20%±5% in TPCA (p < 0.001) 2 days after the first injection, no significant change was seen thereafter. Mean-BFVs in OA decreased by 19%±5% at week 3 (p < 0.001). However, the smallest number of injections (two injections) was associated with the longest time interval between the last injection and month 6 (20 weeks) and with the best return to baseline levels for mean-BFVs in CRA, suggesting that ranibizumab had reversible effects on native retinal vascular supply after its discontinuation. Moreover, a significant correlation between the number of injections and percentage of changes in mean-BFVs in CRA was observed at month 6 (R = 0.74, p < 0.001) unlike TPCA or OA. CONCLUSION: Ranibizumab could impair the native choroidal and retinal vascular networks, but its effect seems reversible after its discontinuation.

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.

Apparent ileal digestibility of amino acids in wet wheat protein and soya bean meal for growing pigs

Selostus: Kuivaamattoman vehnäproteiinin ja soijarouheen aminohappojen ohutsuolisulavuus sioilla

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.