Simple method for detection of MYH11 DNA rearrangements in patients with inv(16)(p13q22) and acute myeloid leukemia.

The pericentric inversion on chromosome 16 [inv(16)(p13q22)] and related t(16;16)(p13;q22) are recurrent aberrations associated with acute myeloid leukemia (AML) M4 Eo. Both abberations result in a fusion of the core binding factor beta (CBFB) and smooth muscle myosin heavy chain gene (MYH11). A selected genomic 6.9-kb BamHl probe detects MYH11 DNA rearrangements in 18 of 19 inv(16)/t(16;16) patients tested using HindIII digested DNA. The rearranged fragments were not detectable after remission in two cases tested, while they were present after relapse in one of these two cases tested.

A new alternative method for testing skin irritation using a human skin model: a pilot study.

Studies assessing skin irritation to chemicals have traditionally used laboratory animals; however, such methods are questionable regarding their relevance for humans. New in vitro methods have been validated, such as the reconstructed human epidermis (RHE) model (Episkin®, Epiderm®). The comparison (accuracy) with in vivo results such as the 4-h human patch test (HPT) is 76% at best (Epiderm®). There is a need to develop an in vitro method that better simulates the anatomo-pathological changes encountered in vivo. To develop an in vitro method to determine skin irritation using human viable skin through histopathology, and compare the results of 4 tested substances to the main in vitro methods and in vivo animal method (Draize test). Human skin removed during surgery was dermatomed and mounted on an in vitro flow-through diffusion cell system. Ten chemicals with known non-irritant (heptylbutyrate, hexylsalicylate, butylmethacrylate, isoproturon, bentazon, DEHP and methylisothiazolinone (MI)) and irritant properties (folpet, 1-bromohexane and methylchloroisothiazolinone (MCI/MI)), a negative control (sodiumchloride) and a positive control (sodiumlaurylsulphate) were applied. The skin was exposed at least for 4h. Histopathology was performed to investigate irritation signs (spongiosis, necrosis, vacuolization). We obtained 100% accuracy with the HPT model; 75% with the RHE models and 50% with the Draize test for 4 tested substances. The coefficients of variation (CV) between our three test batches were <0.1, showing good reproducibility. Furthermore, we reported objectively histopathological irritation signs (irritation scale): strong (folpet), significant (1-bromohexane), slight (MCI/MI at 750/250ppm) and none (isoproturon, bentazon, DEHP and MI). This new in vitro test method presented effective results for the tested chemicals. It should be further validated using a greater number of substances; and tested in different laboratories in order to suitably evaluate reproducibility.

Modeling complex wells with the multi-scale finite-volume method

In this paper, an extension of the multi-scale finite-volume (MSFV) method is devised, which allows to Simulate flow and transport in reservoirs with complex well configurations. The new framework fits nicely into the data Structure of the original MSFV method,and has the important property that large patches covering the whole well are not required. For each well. an additional degree of freedom is introduced. While the treatment of pressure-constraint wells is trivial (the well-bore reference pressure is explicitly specified), additional equations have to be solved to obtain the unknown well-bore pressure of rate-constraint wells. Numerical Simulations of test cases with multiple complex wells demonstrate the ability of the new algorithm to capture the interference between the various wells and the reservoir accurately. (c) 2008 Elsevier Inc. All rights reserved.

The profiling of false identity documents: a promising method to fight identity fraud

Under the influence of intelligence-led policing models, crime analysis methods have known of important developments in recent years. Applications have been proposed in several fields of forensic science to exploit and manage various types of material evidence in a systematic and more efficient way. However, nothing has been suggested so far in the field of false identity documents.This study seeks to fill this gap by proposing a simple and general method for profiling false identity documents which aims to establish links based on their visual forensic characteristics. A sample of more than 200 false identity documents including French stolen blank passports, counterfeited driving licenses from Iraq and falsified Bulgarian driving licenses was gathered from nine Swiss police departments and integrated into an ad hoc developed database called ProfID. Links detected automatically and systematically through this database were exploited and analyzed to produce strategic and tactical intelligence useful to the fight against identity document fraud.The profiling and intelligence process established for these three types of false identity documents has confirmed its efficiency, more than 30% of documents being linked. Identity document fraud appears as a structured and interregional criminality, against which material and forensic links detected between false identity documents might serve as a tool for investigation.

Screening for foetal malformations: performance of routine ultrasonography in the population of the Swiss Canton of Vaud.

OBJECTIVE: To determine the sensitivity of ultrasonography in screening for foetal malformations in the pregnant women of the Swiss Canton of Vaud. STUDY DESIGN: Retrospective study over a period of five years. METHOD: We focused our study on 512 major or minor clinically relevant malformations detectable by ultrasonography. We analysed the global sensitivity of the screening and compared the performance of the tertiary centre with that of practitioners working in private practice or regional hospitals. RESULTS: Among the 512 malformations, 181 (35%) involved the renal and urinary tract system, 137 (27%) the heart, 71 (14%) the central nervous system, 50 (10%) the digestive system, 42 (8%) the face and 31 (6%) the limbs. Global sensitivity was 54.5%. The lowest detection rate was observed for cardiac anomalies, with only 23% correct diagnoses. The tertiary centre achieved a 75% detection rate in its outpatient clinic and 83% in referred patients. Outside the referral centre, the diagnostic rate attained 47%. CONCLUSIONS: Routine foetal examination by ultrasonography in a low-risk population can detect foetal structural abnormalities. Apart from the diagnosis of cardiac abnormalities, the results in the Canton of Vaud are satisfactory and justify routine screening for malformations in a low-risk population. A prerequisite is continuing improvement in the skills of ultrasonographers through medical education.

Overuse of upper gastrointestinal endoscopy in a country with open-access endoscopy: a prospective study in primary care.

BACKGROUND: This prospective observational study was aimed at evaluating the appropriateness of use of upper gastrointestinal endoscopy (UGE) in primary care in a country with open access to and high availability of the procedure. METHODS: Outpatients were consecutively included in two clinical settings: Setting A (20 primary care physicians during 4 weeks) and B (university-based outpatient clinic during 3 weeks). In patients undergoing UGE, appropriateness of referral was judged by explicit Swiss criteria developed by the RAND/UCLA panel method. RESULTS: Patient visits (8135) were assessed. Six hundred eleven patients complained of upper gastrointestinal symptoms. Physicians decided to perform UGE in 63 of these patients. Twenty-five (40%) of the endoscopies were rated appropriate, 7 (11%) equivocal, and 31 (49%) inappropriate. Overuse of UGE occurred in 5.1% (setting A: 4.7%; setting B:6.5%; p = 0.39) of the patients who presented with upper gastrointestinal symptoms. The decision to perform UGE in previously untreated dyspeptic patients was the most common clinical situation resulting in overuse. CONCLUSIONS: Inappropriate use of UGE is high in Switzerland. However, to better reflect primary care decision making, overuse should be related not only to patients referred for a medical test, but also to the number of patients who complain of the symptoms that would be investigated by the procedure.

An Efficient Segmentation Method for Ultrasound Images based on a Semi-supervised Approach and Patch-based Features

Segmenting ultrasound images is a challenging problemwhere standard unsupervised segmentation methods such asthe well-known Chan-Vese method fail. We propose in thispaper an efficient segmentation method for this class ofimages. Our proposed algorithm is based on asemi-supervised approach (user labels) and the use ofimage patches as data features. We also consider thePearson distance between patches, which has been shown tobe robust w.r.t speckle noise present in ultrasoundimages. Our results on phantom and clinical data show avery high similarity agreement with the ground truthprovided by a medical expert.

New trapping method to survey for presence of the Etruscan shrew Suncus etruscus, the smallest mammal

The presence of the Etruscan shrew Suncus etruscus is hard to prove where its predator, the barn owl Tyto alba, is absent, because most live traps are not triggered by it. I therefore developed a new trapping method involving a feeding period of 1 week followed by one night of trapping using modified Trip Trap traps. I show here in detail how I caught four Etruscan shrews in 2010 with 24 traps in the Valley of Dora Baltea (Piemonte, Italy). In 2011, another 11 Etruscan shrews were caught in Piemonte and Lombardia, Italy, and Ticino, Switzerland. The proposed new method is useful for establishing the presence of the species.

A pseudo-spectral method for simulating of poro-elastic seismic wave propagation in complex borehole environments

We present a novel numerical approach for the comprehensive, flexible, and accurate simulation of poro-elastic wave propagation in cylindrical coordinates. An important application of this method is the modeling of complex seismic wave phenomena in fluid-filled boreholes, which represents a major, and as of yet largely unresolved, computational problem in exploration geophysics. In view of this, we consider a numerical mesh consisting of three concentric domains representing the borehole fluid in the center, the borehole casing and the surrounding porous formation. The spatial discretization is based on a Chebyshev expansion in the radial direction, Fourier expansions in the other directions, and a Runge-Kutta integration scheme for the time evolution. A domain decomposition method based on the method of characteristics is used to match the boundary conditions at the fluid/porous-solid and porous-solid/porous-solid interfaces. The viability and accuracy of the proposed method has been tested and verified in 2D polar coordinates through comparisons with analytical solutions as well as with the results obtained with a corresponding, previously published, and independently benchmarked solution for 2D Cartesian coordinates. The proposed numerical solution also satisfies the reciprocity theorem, which indicates that the inherent singularity associated with the origin of the polar coordinate system is handled adequately.

A new method to measure rolling resistance in treadmill cycling.

The purpose of this study was to evaluate a new method of measuring rolling resistance in treadmill cycling and to establish its sensitivity and reproducibility. One participant was asked to keep a bicycle in equilibrium on a treadmill without pedalling at a constant speed of 5.56 m x s(-1), which was held in place in the front by a dynamometer. For each condition, the method consisted of 11 measurements of the force required to hold the cycle at different treadmill slopes (0-10%, increment 1%). The coefficient of rolling resistance was calculated based on the forces applied to the bicycle in equilibrium. To test the sensitivity of the method, the bicycle was successively equipped with three tyre types (700 x 28, 700 x 23, 700 x 22) and inflation pressure was set at 150, 300, 600, 900, and 1100 kPa. To test the reproducibility of the method, a second experimenter repeated all measurements done with the 700 x 23 tyres. The method was sensitive enough to detect an effect of both tyre type and inflation pressure (P < 0.001: two-way ANOVA). The measurement of the coefficient of rolling resistance by two separate experimenters resulted in a small bias of 0.00029 (95% CI, -0.00011 to 0.00068). In conclusion, the new method is sensitive and reliable, as well as being simple and affordable.

A filtering method to correct time-lapse 3D ERT data and improve imaging of natural aquifer dynamics

We have developed a processing methodology that allows crosshole ERT (electrical resistivity tomography) monitoring data to be used to derive temporal fluctuations of groundwater electrical resistivity and thereby characterize the dynamics of groundwater in a gravel aquifer as it is infiltrated by river water. Temporal variations of the raw ERT apparent-resistivity data were mainly sensitive to the resistivity (salinity), temperature and height of the groundwater, with the relative contributions of these effects depending on the time and the electrode configuration. To resolve the changes in groundwater resistivity, we first expressed fluctuations of temperature-detrended apparent-resistivity data as linear superpositions of (i) time series of riverwater-resistivity variations convolved with suitable filter functions and (ii) linear and quadratic representations of river-water-height variations multiplied by appropriate sensitivity factors; river-water height was determined to be a reliable proxy for groundwater height. Individual filter functions and sensitivity factors were obtained for each electrode configuration via deconvolution using a one month calibration period and then the predicted contributions related to changes in water height were removed prior to inversion of the temperature-detrended apparent-resistivity data. Applications of the filter functions and sensitivity factors accurately predicted the apparent-resistivity variations (the correlation coefficient was 0.98). Furthermore, the filtered ERT monitoring data and resultant time-lapse resistivity models correlated closely with independently measured groundwater electrical resistivity monitoring data and only weakly with the groundwater-height fluctuations. The inversion results based on the filtered ERT data also showed significantly less inversion artefacts than the raw data inversions. We observed resistivity increases of up to 10% and the arrival time peaks in the time-lapse resistivity models matched those in the groundwater resistivity monitoring data.

Detecting long-range chromatin interactions using the chromosome conformation capture sequencing (4C-seq) method.

Eukaryotic transcription is tightly regulated by transcriptional regulatory elements, even though these elements may be located far away from their target genes. It is now widely recognized that these regulatory elements can be brought in close proximity through the formation of chromatin loops, and that these loops are crucial for transcriptional regulation of their target genes. The chromosome conformation capture (3C) technique presents a snapshot of long-range interactions, by fixing physically interacting elements with formaldehyde, digestion of the DNA, and ligation to obtain a library of unique ligation products. Recently, several large-scale modifications to the 3C technique have been presented. Here, we describe chromosome conformation capture sequencing (4C-seq), a high-throughput version of the 3C technique that combines the 3C-on-chip (4C) protocol with next-generation Illumina sequencing. The method is presented for use in mammalian cell lines, but can be adapted to use in mammalian tissues and any other eukaryotic genome.