eVOC: a controlled vocabulary for unifying gene expression data.

Expression data contribute significantly to the biological value of the sequenced human genome, providing extensive information about gene structure and the pattern of gene expression. ESTs, together with SAGE libraries and microarray experiment information, provide a broad and rich view of the transcriptome. However, it is difficult to perform large-scale expression mining of the data generated by these diverse experimental approaches. Not only is the data stored in disparate locations, but there is frequent ambiguity in the meaning of terms used to describe the source of the material used in the experiment. Untangling semantic differences between the data provided by different resources is therefore largely reliant on the domain knowledge of a human expert. We present here eVOC, a system which associates labelled target cDNAs for microarray experiments, or cDNA libraries and their associated transcripts with controlled terms in a set of hierarchical vocabularies. eVOC consists of four orthogonal controlled vocabularies suitable for describing the domains of human gene expression data including Anatomical System, Cell Type, Pathology and Developmental Stage. We have curated and annotated 7016 cDNA libraries represented in dbEST, as well as 104 SAGE libraries,with expression information,and provide this as an integrated, public resource that allows the linking of transcripts and libraries with expression terms. Both the vocabularies and the vocabulary-annotated libraries can be retrieved from http://www.sanbi.ac.za/evoc/. Several groups are involved in developing this resource with the aim of unifying transcript expression information.

Particle orientation distribution in Y-Fe2O3magnetic tapes by Mössbauer and hysteresis loop measurements

The particle orientation in several Y-Fe2O3magnetic tapes has been quantitatively evaluated by using the data of both Mössbauer and hysteresis loop measurements performed in the three orthogonal directions. A texture function has been obtained as a development of real harmonics. The profile of the texture function gives the quality of the different magnetic tapes. A different degree of particle orientation at the surface of the tape is evidenced by means of conversion electron Mössbauer spectra.

Quantum critical effects in mean-field glassy systems

We consider the effects of quantum fluctuations in mean-field quantum spin-glass models with pairwise interactions. We examine the nature of the quantum glass transition at zero temperature in a transverse field. In models (such as the random orthogonal model) where the classical phase transition is discontinuous an analysis using the static approximation reveals that the transition becomes continuous at zero temperature.

Exposition des enfants à la fumée passive: le point sur des campagnes de sensibilisation

Enfants de moins de 10 ans fumant passivement 14 cigarettes ! D'avril 2010 à avril 2011, l'exposition de 148 enfants (81 garçons et 67 filles) a été testée: 10 enfants de moins d'un an, 25 de 1 à 5 ans, 19 de 5 à 10 ans, 30 de 10 à 15 ans et 64 de 15 à 18 ans. 10 d'entre eux sont des fumeurs et la plus jeune de 14 ans fume 10 cigarettes par jour. Leurs parents, ou parfois des jeunes eux-mêmes, ont commandé de manière volontaire, via les sites Internet des CIPRET Valais, Vaud et Genève, un badge MoNIC gratuit. Les résultats quant à l'exposition de ces enfants interpellent et méritent l'attention.Pour l'ensemble des enfants, la concentration moyenne de nicotine dans leur environnement intérieur mesurée via les dispositifs MoNIC est de 0,5 mg/m3, avec des maximums pouvant aller jusqu'à 21 mg/m3. Pour le collectif d'enfants âgés de moins de 10 ans (26 garçons et 28 filles; tous non-fumeurs), la concentration de nicotine n'est pas négligeable (moyenne 0,069 mg/m3, min 0, max 0,583 mg/m3). En convertissant ce résultat en équivalent de cigarettes inhalées passivement, nous obtenons des chiffres allant de 0 à 14 cigarettes par jour* avec une moyenne se situant à 1.6 cig/j. Encore plus surprenant, les enfants de moins d'un an (4 garçons et 6 filles) inhalent passivement, dans le cadre familial, en moyenne 1 cigarette (min 0, max 2.2). Pour les deux autres collectifs: 10-15 ans et 15-18 ans, les valeurs maximales avoisinent les 22 cigarettes. Notons cependant que ce résultat est influencé, ce qui n'est pas le cas des enfants plus jeunes, par le fait que ces jeunes sont également parfois des fumeurs actifs.* Quand la durée d'exposition dépassait 1 jour (8 heures), le nombre d'heures a toujours été divisé par 8 heures. Le résultat obtenu donne l'équivalent de cigarettes fumées passivement en huit heures. Il s'agit de ce fait d'une moyenne, ce qui veut dire que durant cette période les enfants ont pu être exposés irrégulièrement à des valeurs supérieures ou inférieures à cette moyenne. [Auteurs]

Second hand tobacco smoke exposure in Switzerland

A passive sampling device called Monitor of NICotine or "MoNIC", was constructed and evaluated by IST laboratory for determining nicotine in Second Hand Tobacco Smoke (SHTS) or Environmental Tobacco Smoke (ETS). Vapour nicotine was passively collected on a potassium bisulfate treated glass fibre filter as collection medium. Analysis of collected nicotine on the treated filter by gas chromatography equipped with Thermoionic-Specific Detector (GC-TSD) after liquid-liquid extraction of 1mL of 5N NaOH : 1 mL of n-heptane saturated with NH3 using quinoline as internal standard. Based on nicotine amount of 0.2 mg/cigarette as the reference, the inhaled Cigarette Equivalents (CE) by non-smokers can be calculated. Using the detected CE on the badge for non-smokers, and comparing with amount of nicotine and cotinine level in saliva of both smokers and exposed non-smokers, we can confirm the use of the CE concept for estimating exposure to ETS. The regional CIPRET (Center of information and prevention of the addiction to smoking) of different cantons (Valais (VS), Vaud (VD), Neuchâtel (NE) and Fribourg (FR)) are going to organize a big campaign on the subject of the passive addiction to smoking. This campaign took place in 2007-2008 and has for objective to inform clearly the Swiss population of the dangerousness of the passive smoke. More than 3'900 MoNIC badges were gracefully distributed to Swiss population to perform a self-monitoring of population exposure level to ETS, expressed in term of CE. Non-stimulated saliva was also collected to determine ETS biomarkers nicotine/cotinine levels of participating volunteers. Results of different levels of CE in occupational and non-occupational situations in relation with ETS were presented in this study. This study, unique in Switzerland, has established a base map on the population's exposure to SHTS. It underscored the fact that all the Swiss people involved in this campaign (N=1241) is exposed to passive smoke, from <0.2 cig/d (10.8%), 1-2 to more than 10 cig/d (89.2%). In the area of high exposure (15-38 cig/d), are the most workers in public restaurant, cafe, bar, disco. By monitoring ETS tracer nicotine and its biomarkers, salivary nicotine and cotinine, it is demonstrated that the MoNIC badge can serve as indicator of CE passive smoking. The MoNIC badge, accompanied with content of salivary nicotine/cotinine can serve as a tool of evaluation of the ETS passive smoking and contributes to supply useful data for future epidemiological studies. It is also demonstrated that the salivary nicotine (without stimulation) is a better biomarker of ETS exposure than cotinine.

Chaotic Kabanov formula for the Azéma martingales

We derive the chaotic expansion of the product of nth- and first-order multiple stochastic integrals with respect to certain normal martingales. This is done by application of the classical and quantum product formulae for multiple stochastic integrals. Our approach extends existing results on chaotic calculus for normal martingales and exhibits properties, relative to multiple stochastic integrals, polynomials and Wick products, that characterize the Wiener and Poisson processes.

Measuring brain perfusion with intravoxel incoherent motion (IVIM): Initial clinical experience.

PURPOSE: To evaluate the feasibility of intravoxel incoherent motion (IVIM) perfusion measurements in the brain with currently available imaging systems. MATERIALS AND METHODS: We acquired high in-plane resolution (1.2 × 1.2 mm(2) ) diffusion-weighted images with 16 different values of b ranging from 0 to 900 s/mm(2) , in three orthogonal directions, on 3T systems with a 32-multichannel receiver head coil. IVIM perfusion maps were extracted by fitting a double exponential model of signal amplitude decay. Regions of interest were drawn in pathological and control regions, where IVIM perfusion parameters were compared to the corresponding dynamic susceptibility contrast (DSC) parameters. RESULTS: Hyperperfusion was found in the nonnecrotic or cystic part of two histologically proven glioblastoma multiforme and in two histologically proven glioma WHO grade III, as well as in a brain metastasis of lung adenocarcinoma, in a large meningioma, and in a case of ictal hyperperfusion. A monoexponential decay was found in a territory of acute ischemia, as well as in the necrotic part of a glioblastoma. The IVIM perfusion fraction f correlated well with DSC CBV. CONCLUSION: Our initial report suggests that high-resolution brain perfusion imaging is feasible with IVIM in the current clinical setting. J. Magn. Reson. Imaging 2014;39:624-632. © 2013 Wiley Periodicals, Inc.

Direct three-dimensional myocardial strain tensor quantification and tracking using zHARP.

Images of myocardial strain can be used to diagnose heart disease, plan and monitor treatment, and to learn about cardiac structure and function. Three-dimensional (3D) strain is typically quantified using many magnetic resonance (MR) images obtained in two or three orthogonal planes. Problems with this approach include long scan times, image misregistration, and through-plane motion. This article presents a novel method for calculating cardiac 3D strain using a stack of two or more images acquired in only one orientation. The zHARP pulse sequence encodes in-plane motion using MR tagging and out-of-plane motion using phase encoding, and has been previously shown to be capable of computing 3D displacement within a single image plane. Here, data from two adjacent image planes are combined to yield a 3D strain tensor at each pixel; stacks of zHARP images can be used to derive stacked arrays of 3D strain tensors without imaging multiple orientations and without numerical interpolation. The performance and accuracy of the method is demonstrated in vitro on a phantom and in vivo in four healthy adult human subjects.

Inexperienced sonographers can successfully visualize and assess a three-dimensional image of the fetal face using a standardized ultrasound protocol.

Introduction: A standardized three-dimensional ultrasonographic (3DUS) protocol is described that allows fetal face reconstruction. Ability to identify cleft lip with 3DUS using this protocol was assessed by operators with minimal 3DUS experience. Material and Methods: 260 stored volumes of fetal face were analyzed using a standardized protocol by operators with different levels of competence in 3DUS. The outcomes studied were: (1) the performance of post-processing 3D face volumes for the detection of facial clefts; (2) the ability of a resident with minimal 3DUS experience to reconstruct the acquired facial volumes, and (3) the time needed to reconstruct each plane to allow proper diagnosis of a cleft. Results: The three orthogonal planes of the fetal face (axial, sagittal and coronal) were adequately reconstructed with similar performance when acquired by a maternal-fetal medicine specialist or by residents with minimal experience (72 vs. 76%, p = 0.629). The learning curve for manipulation of 3DUS volumes of the fetal face corresponds to 30 cases and is independent of the operator's level of experience. Discussion: The learning curve for the standardized protocol we describe is short, even for inexperienced sonographers. This technique might decrease the length of anatomy ultrasounds and improve the ability to visualize fetal face anomalies.

La fonction de la carte géographique : approche épistémologique ternaire

Under the referential of a ternary logic, with the two orthogonal concepts of information/signification, mediated by the third-included, the diagonal organizer of the cartographic communication, this article aims to cladify the pragmatical aspects of the map functionnality as a communication object. The interaction beween the meaning of its information and the information reciprocally contained in its signification, within a specified context and pertinence, implies a strong level of redundancy shared by producers and users of the map, a same system of scientific and ideological values to pass on the cartographic message. We are far from the objective cartographer who would fade away so to let the facts speaks "objectively" by themselves.

Protective role of early aquaporin 4 induction against postischemic edema formation.

Aquaporin 4 (AQP4) is a water channel involved in water movements across the cell membrane and is spatially organized on the cell surface in orthogonal array particles (OAPs). Its role in edema formation or resolution after stroke onset has been studied mainly at late time points. We have shown recently that its expression is rapidly induced after ischemia coinciding in time with an early swelling of the ischemic hemisphere. There are two isoforms of AQP4: AQP4-M1 and AQP4-M23. The ratio of these isoforms influences the size of the OAPs but the functional impact is not known. The role of the early induction of AQP4 is not yet known. Thrombin preconditioning in mice provides a useful model to study endogenous protective mechanisms. Using this model, we provide evidence for the first time that the early induction of AQP4 may contribute to limit the formation of edema and that the AQP4-M1 isoform is predominantly induced in the ischemic tissue at this time point. Although it prevents edema formation, the early induction of the AQP4 expression does not prevent the blood-brain barrier disruption, suggesting an effect limited to the prevention of edema formation possibly by removing of water from the tissue.

On the existence of bi-pyramidal central configurations of the n + 2-body problem with an n-gon base

Abstract. In this paper we prove the existence of central con gurations of the n + 2{body problem where n equal masses are located at the vertices of a regular n{gon and the remaining 2 masses, which are not necessarily equal, are located on the straight line orthogonal to the plane containing the n{gon passing through its center. Here this kind of central con gurations is called bi{pyramidal central con gurations. In particular, we prove that if the masses mn+1 and mn+2 and their positions satisfy convenient relations, then the con guration is central. We give explicitly those relations.

Autonomous Measurements of Bridge Pier and Abutment Scour using Motion-Sensing Radio Transmitters, TR-595, 2010

Two portable Radio Frequency IDentification (RFID) systems (made by Texas Instruments and HiTAG) were developed and tested for bridge scour monitoring by the Department of Civil and Environmental Engineering at the University of Iowa (UI). Both systems consist of three similar components: 1) a passive cylindrical transponder of 2.2 cm in length (derived from transmitter/responder); 2) a low frequency reader (~134.2 kHz frequency); and 3) an antenna (of rectangular or hexagonal loop). The Texas Instruments system can only read one smart particle per time, while the HiTAG system was successfully modified here at UI by adding the anti-collision feature. The HiTAG system was equipped with four antennas and could simultaneously detect 1,000s of smart particles located in a close proximity. A computer code was written in C++ at the UI for the HiTAG system to allow simultaneous, multiple readouts of smart particles under different flow conditions. The code is written for the Windows XP operational system which has a user-friendly windows interface that provides detailed information regarding the smart particle that includes: identification number, location (orientation in x,y,z), and the instance the particle was detected.. These systems were examined within the context of this innovative research in order to identify the best suited RFID system for performing autonomous bridge scour monitoring. A comprehensive laboratory study that included 142 experimental runs and limited field testing was performed to test the code and determine the performance of each system in terms of transponder orientation, transponder housing material, maximum antenna-transponder detection distance, minimum inter-particle distance and antenna sweep angle. The two RFID systems capabilities to predict scour depth were also examined using pier models. The findings can be summarized as follows: 1) The first system (Texas Instruments) read one smart particle per time, and its effective read range was about 3ft (~1m). The second system (HiTAG) had similar detection ranges but permitted the addition of an anti-collision system to facilitate the simultaneous identification of multiple smart particles (transponders placed into marbles). Therefore, it was sought that the HiTAG system, with the anti-collision feature (or a system with similar features), would be preferable when compared to a single-read-out system for bridge scour monitoring, as the former could provide repetitive readings at multiple locations, which could help in predicting the scour-hole bathymetry along with maximum scour depth. 2) The HiTAG system provided reliable measures of the scour depth (z-direction) and the locations of the smart particles on the x-y plane within a distance of about 3ft (~1m) from the 4 antennas. A Multiplexer HTM4-I allowed the simultaneous use of four antennas for the HiTAG system. The four Hexagonal Loop antennas permitted the complete identification of the smart particles in an x, y, z orthogonal system as function of time. The HiTAG system can be also used to measure the rate of sediment movement (in kg/s or tones/hr). 3) The maximum detection distance of the antenna did not change significantly for the buried particles compared to the particles tested in the air. Thus, the low frequency RFID systems (~134.2 kHz) are appropriate for monitoring bridge scour because their waves can penetrate water and sand bodies without significant loss of their signal strength. 4) The pier model experiments in a flume with first RFID system showed that the system was able to successfully predict the maximum scour depth when the system was used with a single particle in the vicinity of pier model where scour-hole was expected. The pier model experiments with the second RFID system, performed in a sandbox, showed that system was able to successfully predict the maximum scour depth when two scour balls were used in the vicinity of the pier model where scour-hole was developed. 5) The preliminary field experiments with the second RFID system, at the Raccoon River, IA near the Railroad Bridge (located upstream of 360th street Bridge, near Booneville), showed that the RFID technology is transferable to the field. A practical method would be developed for facilitating the placement of the smart particles within the river bed. This method needs to be straightforward for the Department of Transportation (DOT) and county road working crews so it can be easily implemented at different locations. 6) Since the inception of this project, further research showed that there is significant progress in RFID technology. This includes the availability of waterproof RFID systems with passive or active transponders of detection ranges up to 60 ft (~20 m) within the water–sediment column. These systems do have anti-collision and can facilitate up to 8 powerful antennas which can significantly increase the detection range. Such systems need to be further considered and modified for performing automatic bridge scour monitoring. The knowledge gained from the two systems, including the software, needs to be adapted to the new systems.

Effects of epitope modification on T cell receptor-ligand binding and antigen recognition by seven H-2Kd-restricted cytotoxic T lymphocyte clones specific for a photoreactive peptide derivative.

We tested for antigen recognition and T cell receptor (TCR)-ligand binding 12 peptide derivative variants on seven H-2Kd-restricted cytotoxic T lymphocytes (CTL) clones specific for a bifunctional photoreactive derivative of the Plasmodium berghei circumsporozoite peptide 252-260 (SYIPSAEKI). The derivative contained iodo-4-azidosalicylic acid in place of PbCS S-252 and 4-azidobenzoic acid on PbCS K-259. Selective photoactivation of the N-terminal photoreactive group allowed crosslinking to Kd molecules and photoactivation of the orthogonal group to TCR. TCR photoaffinity labeling with covalent Kd-peptide derivative complexes allowed direct assessment of TCR-ligand binding on living CTL. In most cases (over 80%) cytotoxicity (chromium release) and TCR-ligand binding differed by less than fivefold. The exceptions included (a) partial TCR agonists (8 cases), for which antigen recognition was five-tenfold less efficient than TCR-ligand binding, (b) TCR antagonists (2 cases), which were not recognized and capable of inhibiting recognition of the wild-type conjugate, (c) heteroclitic agonists (2 cases), for which antigen recognition was more efficient than TCR-ligand binding, and (d) one partial TCR agonist, which activated only Fas (C1)95), but not perforin/granzyme-mediated cytotoxicity. There was no correlation between these divergences and the avidity of TCR-ligand binding, indicating that other factors than binding avidity determine the nature of the CTL response. An unexpected and novel finding was that CD8-dependent clones clearly incline more to TCR antagonism than CD8-independent ones. As there was no correlation between CD8 dependence and the avidity of TCR-ligand binding, the possibility is suggested that CD8 plays a critical role in aberrant CTL function.

Phylogeography and recolonization of the Swiss Alps by the Valais shrew (Sorex antinorii), inferred with autosomal and sex-specific markers.

Using one male-inherited, one female-inherited and eight biparentally inherited markers, we investigate the population genetic structure of the Valais shrew (Sorex antinorii) in the Swiss Alps. Bayesian analysis on autosomal microsatellites suggests a clear genetic differentiation between two groups of populations. This geographically based structure is consistent with two separate postglacial recolonization routes of the species into Switzerland from Italian refugia after the last Pleistocene glaciations. Sex-specific markers also confirm genetic structuring among western and eastern areas, since very few haplotypes for either Y chromosome or mtDNA genome are shared between the two regions. Overall, these results suggest that two already well-differentiated genetic lineages colonized the Swiss Alps and came into secondary contact in the Rhône Valley. Low level of admixture between the two lineages is likely explained by the mountainous landscape structure of lateral valleys orthogonal to the main Rhône valley.