Fast low-specific absorption rate B0 -mapping along projections at high field using two-dimensional radiofrequency pulses.

PURPOSE: At 7 Tesla (T), conventional static field (B0 ) projection mapping techniques, e.g., FASTMAP, FASTESTMAP, lead to elevated specific absorption rates (SAR), requiring longer total acquisition times (TA). In this work, the series of adiabatic pulses needed for slab selection in FASTMAP is replaced by a single two-dimensional radiofrequency (2D-RF) pulse to minimize TA while ensuring equal shimming performance. METHODS: Spiral gradients and 2D-RF pulses were designed to excite thin slabs in the small tip angle regime. The corresponding selection profile was characterized in phantoms and in vivo. After optimization of the shimming protocol, the spectral linewidths obtained after 2D localized shimming were compared with conventional techniques and published values from (Emir et al NMR Biomed 2012;25:152-160) in six different brain regions. RESULTS: Results on healthy volunteers show no significant difference (P > 0.5) between the spectroscopic linewidths obtained with the adiabatic (TA = 4 min) and the new low-SAR and time-efficient FASTMAP sequence (TA = 42 s). The SAR can be reduced by three orders of magnitude and TA accelerated six times without impact on the shimming performances or quality of the resulting spectra. CONCLUSION: Multidimensional pulses can be used to minimize the RF energy and time spent for automated shimming using projection mapping at high field. Magn Reson Med, 2014. © 2014 Wiley Periodicals, Inc.

Mass movement characterization using a reflexion and refraction seismic survey with the sloping local base level concept

This study proposes a new concept for upscaling local information on failure surfaces derived from geophysical data, in order to develop the spatial information and quickly estimate the magnitude and intensity of a landslide. A new vision of seismic interpretation on landslides is also demonstrated by taking into account basic geomorphic information with a numeric method based on the Sloping Local Base Level (SLBL). The SLBL is a generalization of the base level defined in geomorphology applied to landslides, and allows the calculation of the potential geometry of the landslide failure surface. This approach was applied to a large scale landslide formed mainly in gypsum and situated in a former glacial valley along the Rhone within the Western European Alps. Previous studies identified the existence of two sliding surfaces that may continue below the level of the valley. In this study. seismic refraction-reflexion surveys were carried out to verify the existence of these failure surfaces. The analysis of the seismic data provides a four-layer model where three velocity layers (<1000 ms(-1), 1500 ms(-1) and 3000 ms(-1)) are interpreted as the mobilized mass at different weathering levels and compaction. The highest velocity layer (>4000 ms(-1)) with a maximum depth of similar to 58 m is interpreted as the stable anhydrite bedrock. Two failure surfaces were interpreted from the seismic surveys: an upper failure and a much deeper one (respectively 25 and 50 m deep). The upper failure surface depth deduced from geophysics is slightly different from the results obtained using the SLBL, and the deeper failure surface depth calculated with the SLBL method is underestimated in comparison with the geophysical interpretations. Optimal results were therefore obtained by including the seismic data in the SLBL calculations according to the geomorphic limits of the landslide (maximal volume of mobilized mass = 7.5 x 10(6) m(3)).

EADock: docking of small molecules into protein active sites with a multiobjective evolutionary optimization.

In recent years, protein-ligand docking has become a powerful tool for drug development. Although several approaches suitable for high throughput screening are available, there is a need for methods able to identify binding modes with high accuracy. This accuracy is essential to reliably compute the binding free energy of the ligand. Such methods are needed when the binding mode of lead compounds is not determined experimentally but is needed for structure-based lead optimization. We present here a new docking software, called EADock, that aims at this goal. It uses an hybrid evolutionary algorithm with two fitness functions, in combination with a sophisticated management of the diversity. EADock is interfaced with the CHARMM package for energy calculations and coordinate handling. A validation was carried out on 37 crystallized protein-ligand complexes featuring 11 different proteins. The search space was defined as a sphere of 15 A around the center of mass of the ligand position in the crystal structure, and on the contrary to other benchmarks, our algorithm was fed with optimized ligand positions up to 10 A root mean square deviation (RMSD) from the crystal structure, excluding the latter. This validation illustrates the efficiency of our sampling strategy, as correct binding modes, defined by a RMSD to the crystal structure lower than 2 A, were identified and ranked first for 68% of the complexes. The success rate increases to 78% when considering the five best ranked clusters, and 92% when all clusters present in the last generation are taken into account. Most failures could be explained by the presence of crystal contacts in the experimental structure. Finally, the ability of EADock to accurately predict binding modes on a real application was illustrated by the successful docking of the RGD cyclic pentapeptide on the alphaVbeta3 integrin, starting far away from the binding pocket.

Small RNAs controlled by two-component systems.

Two-component systems (TCSs) allow bacteria to monitor diverse environmental cues and to adjust gene expression accordingly at the transcriptional level. It has been recently recognized that prokaryotes also regulate many genes and operons at a posttranscriptional level with the participation of small, noncoding RNAs which serve to control translation initiation and stability of target mRNAs, either directly by establishing antisense interactions or indirectly by antagonizing RNA-binding proteins. Interestingly, the expression of a subset of these small RNAs is regulated by TCSs and in this way, the small RNAs expand the scope of genetic control exerted by TCSs. Here we review the regulatory mechanisms and biological relevance ofa number of small RNAs under TCS control in Gram-negative and -positive bacteria. These regulatory systems govern, for instance, porin-dependent permeability of the outer membrane, quorum-sensing control of pathogenicity, or biocontrol activity. Most likely, this emerging and rapidly expanding field of molecular microbiology will provide more and more examples in the near future.

Early clarification processes in clients presenting with borderline personality disorder: Relations with symptom level and change

Clarification-Oriented Psychotherapy (COP), an integrative treatment form with a basis in process-experiential psychotherapy, is particularly relevant for clients with Personality Disorders (PDs). We argue here that two related core therapeutic COP principles, "dual action regulation" and "interactional games" have consequences for symptom severity and therapeutic outcome for clients with PDs. A high quality COP clarification process requires that client's interactional games may be quickly assessed and treated in all (preferably early) therapy sessions. These processes can be observed and measured using the observer-rated Bochum Process and Relationship Rating Scales (BPRRS) which measure both clients' and therapists' contributions to the quality of the clarification processes engaged in therapy. This measure has been successfully applied to COP-therapies, but not, as yet, to therapies other than experiential, nor to specific client populations such as borderline personality disorder. The present study is a first attempt to evaluate the application of COP processes to other therapies and populations. We measured action regulation and interactional games using the BPRRS during intake sessions of a 10-session psychodynamic treatment of borderline personality disorder for a total of N = 30 clients and N = 8 therapists. Significant relationships were found between the client's degree of interactional games and both pretherapy symptom level and symptom change across therapy. These results are discussed in the context of Clarification-Oriented Psychotherapy, and more generally Person-Centered and Process-Experiential Psychotherapies. The potential relevance of the findings for psychodynamic psychotherapists are explored as well as the potential usefulness of taking into account a detailed analysis of interactional games for the training of psychotherapists working with any model of therapy working with clients presenting with BPD.

Investigation of the Reproductibility of Third-Level Characteristics

The process of comparing a fingermark recovered from a crime scene with the fingerprint taken from a known individual involves the characterization and comparison of different ridge details on both the mark and the print. Fingerprints examiners commonly classify these characteristics into three different groups, depending on their level of discriminating power. It is commonly considered that the general pattern of the ridge flow constitutes first-level detail, specific ridge flow and minutiaes (e.g. ending ridges, bifurcations) constitutes second-level detail, and fine ridge details (e. g. pore positions and shapes) are described as third-level details.In this study, the reproducibility of a selection of third-level characteristics is investigated. The reproducibility of these features is examined on serveral recordings of a same finger, first acquired using only optical visualization techniques and second on impressions developed using common firngermark development techniques. Prior to the evaluation of the reproducibility of the considered characteristics, digital images of the fingerprints were recorded at two different resolutions (1000 and 2000 ppi). This allowed the study to also examine the influence of higher resolution on the considered characteristics. It was observed that the increase in the resolution did not result in better feature detection or comparison between images.The examination of the reproducibility of a selection of third-level characteristics showed that the most reproducible features observed were minutiae shapes and pore positions along the ridges.

Variations of the carcinoembryonic antigen level in the plasma of patients with gynecologie cancers during therapy

In 63 patients with histologically proved gynecologie carcinoma, circulating carcinoembryonic antigen (CEA) was determined by radioimmunoassay before and at two intervals after treatment. Thirty-one patients of 63 had CEA values over 2.5 ng. per milliliter before treatment. In general, the CEA levels were low compared to those found in endodermal carcinoma. The percentage of elevated CEA values was slightly higher in cases of carcinoma of the cervix and corpus uteri than in those of carcinoma of the ovary. All patients with CEA levels greater than 2.5 ng. per milliliter treated by complete surgical resection of tumor showed a drop of CEA levels to below 2.5 ng. per milliliter seven weeks after operation. In contrast, patients with palliative therapy showed no change in CEA values. About half of the patients treated with a complete course of internal and external radiotherapy showed a drop of CEA levels to below 2.5 ng. per milliliter, whereas the other patients showed fluctuating CEA values. No correlation between clinical status and evolution of CEA levels in these patients could be drawn at the present time. The CEA test seems to be of little value for the earl of diagnosis of gynecologie carcinoma but appears to be interesting for the evaluation of therapy and the follow-up of patients with diagnosed cases.

Postprandial thermogenesis at rest and during exercise in elderly men ingesting two levels of protein.

Seven elderly male subjects (69 +/- 3 yr, 67.8 +/- 9.2 kg, 24.5 +/- 3.6% body fat) lived for 12 consecutive weeks in a metabolic unit and maintained their weight with two different diets fed for 6 weeks each: Diet A, consisted of their habitual protein intake as determined on the outside by a dietary record (mean +/- SD, 1.12 +/- 0.22 g/kg d). Diet B was an isocaloric diet with reduced protein intake (70 mgN/kg d, i.e., 0.44 g protein/kg d) at the level of physiological protein requirement [7]. After 3 weeks on each diet, the thermogenic response to single meals A and B containing 38% of weight maintenance energy for each subject (731-994 kcal) was studied by indirect calorimetry under two situations: (1) at rest over a 4 hr period and (2) during graded exercise on a bicycle ergometer at four stepwise workloads (0,80, 200, and 300 kg/min). A postabsorptive control exercise was also performed in order to assess the net effect of the meal during exercise. Eating alone increased the energy expenditure by +0.18 +/- 0.07 kcal/min with meal A and +0.13 +/- 0.06 kcal/min with meal B. There was a positive correlation (r = 0.84, p less than 0.01) between the % energy derived from protein and the thermogenic response expressed as % of the energy content of test meal. Exercise failed to influence the thermogenic response to meals since the overall net increase in energy expenditure induced by the meals while exercising was not different from that obtained at rest: +0.22 +/- 0.17 kcal/min and +0.15 +/- 0.13 kcal/min with meal A and meal B, respectively. This study failed to show any interaction between exercise and postprandial thermogenesis in elderly individuals.

Estimating slope and level change in N=1 designs

The current study proposes a new procedure for separately estimating slope change and level change between two adjacent phases in single-case designs. The procedure eliminates baseline trend from the whole data series prior to assessing treatment effectiveness. The steps necessary to obtain the estimates are presented in detail, explained, and illustrated. A simulation study is carried out to explore the bias and precision of the estimators and compare them to an analytical procedure matching the data simulation model. The experimental conditions include two data generation models, several degrees of serial dependence, trend, level and/or slope change. The results suggest that the level and slope change estimates provided by the procedure are unbiased for all levels of serial dependence tested and trend is effectively controlled for. The efficiency of the slope change estimator is acceptable, whereas the variance of the level change estimator may be problematic for highly negatively autocorrelated data series.

Sclerotherapy of telangiectasias: a painless two-step technique.

BACKGROUND: Sclerotherapy of telangiectasias and reticular leg veins can be unpleasant and painful for some patients. OBJECTIVE: To determine pain level with two different sclerotherapy techniques in a prospective randomized trial. METHODS: Patients with symmetrical telangiectasias and reticular veins on both legs (C(1A) or (S)E(P)A(S)P(N1) were randomized to the standard (successive injections of chromated glycerin mixed with one-third lidocaine-epinephrine 1%) or two-step technique (first treating only reticular veins with a single injection at the base of each cluster of telangiectasias and then successively injecting all remaining telangiectasias a few minutes later. Pain was assessed using a 100-point visual analogue scale (0 = no pain, 100 = maximum pain). RESULTS: Data from 53 consecutive patients could be evaluated. The two-step technique was significantly less painful (28.2) than the standard technique (40.6, p < .001). CONCLUSION: The two-step technique with chromated glycerin mixed with one-third lidocaine-epinephrine 1% significantly reduces sclerotherapy pain. This may be a useful technique for patients who are particularly sensitive or afraid of sclerotherapy.

A system-level, molecular evolutionary analysis of mammalian phototransduction

Visual perception is initiated in the photoreceptor cells of the retina via the phototransduction system.This system has shown marked evolution during mammalian divergence in such complex attributes as activation time and recovery time. We have performed a molecular evolutionary analysis of proteins involved in mammalianphototransduction in order to unravel how the action of natural selection has been distributed throughout thesystem to evolve such traits. We found selective pressures to be non-randomly distributed according to both a simple protein classification scheme and a protein-interaction network representation of the signaling pathway. Proteins which are topologically central in the signaling pathway, such as the G proteins, as well as retinoid cycle chaperones and proteins involved in photoreceptor cell-type determination, were found to be more constrained in their evolution. Proteins peripheral to the pathway, such as ion channels and exchangers, as well as the retinoid cycle enzymes, have experienced a relaxation of selective pressures. Furthermore, signals of positive selection were detected in two genes: the short-wave (blue) opsin (OPN1SW) in hominids and the rod-specific Na+/Ca2+,K+ ion exchanger (SLC24A1) in rodents. The functions of the proteins involved in phototransduction and the topology of the interactions between them have imposed non-random constraints on their evolution. Thus, in shaping or conserving system-level phototransduction traits, natural selection has targeted the underlying proteins in a concerted manner.

Enhanced compressed sensing recovery with level set normals.

We propose a compressive sensing algorithm that exploits geometric properties of images to recover images of high quality from few measurements. The image reconstruction is done by iterating the two following steps: 1) estimation of normal vectors of the image level curves, and 2) reconstruction of an image fitting the normal vectors, the compressed sensing measurements, and the sparsity constraint. The proposed technique can naturally extend to nonlocal operators and graphs to exploit the repetitive nature of textured images to recover fine detail structures. In both cases, the problem is reduced to a series of convex minimization problems that can be efficiently solved with a combination of variable splitting and augmented Lagrangian methods, leading to fast and easy-to-code algorithms. Extended experiments show a clear improvement over related state-of-the-art algorithms in the quality of the reconstructed images and the robustness of the proposed method to noise, different kind of images, and reduced measurements.

Optimization of Snow Drifting Mitigation and Control Methods for Iowa Conditions Part II, TR-626, 2015

Blowing and drifting of snow is a major concern for transportation efficiency and road safety in regions where their development is common. One common way to mitigate snow drift on roadways is to install plastic snow fences. Correct design of snow fences is critical for road safety and maintaining the roads open during winter in the US Midwest and other states affected by large snow events during the winter season and to maintain costs related to accumulation of snow on the roads and repair of roads to minimum levels. Of critical importance for road safety is the protection against snow drifting in regions with narrow rights of way, where standard fences cannot be deployed at the recommended distance from the road. Designing snow fences requires sound engineering judgment and a thorough evaluation of the potential for snow blowing and drifting at the construction site. The evaluation includes site-specific design parameters typically obtained with semi-empirical relations characterizing the local transport conditions. Among the critical parameters involved in fence design and assessment of their post-construction efficiency is the quantification of the snow accumulation at fence sites. The present study proposes a joint experimental and numerical approach to monitor snow deposits around snow fences, quantitatively estimate snow deposits in the field, asses the efficiency and improve the design of snow fences. Snow deposit profiles were mapped using GPS based real-time kinematic surveys (RTK) conducted at the monitored field site during and after snow storms. The monitored site allowed testing different snow fence designs under close to identical conditions over four winter seasons. The study also discusses the detailed monitoring system and analysis of weather forecast and meteorological conditions at the monitored sites. A main goal of the present study was to assess the performance of lightweight plastic snow fences with a lower porosity than the typical 50% porosity used in standard designs of such fences. The field data collected during the first winter was used to identify the best design for snow fences with a porosity of 50%. Flow fields obtained from numerical simulations showed that the fence design that worked the best during the first winter induced the formation of an elongated area of small velocity magnitude close to the ground. This information was used to identify other candidates for optimum design of fences with a lower porosity. Two of the designs with a fence porosity of 30% that were found to perform well based on results of numerical simulations were tested in the field during the second winter along with the best performing design for fences with a porosity of 50%. Field data showed that the length of the snow deposit away from the fence was reduced by about 30% for the two proposed lower-porosity (30%) fence designs compared to the best design identified for fences with a porosity of 50%. Moreover, one of the lower-porosity designs tested in the field showed no significant snow deposition within the bottom gap region beneath the fence. Thus, a major outcome of this study is to recommend using plastic snow fences with a porosity of 30%. It is expected that this lower-porosity design will continue to work well for even more severe snow events or for successive snow events occurring during the same winter. The approach advocated in the present study allowed making general recommendations for optimizing the design of lower-porosity plastic snow fences. This approach can be extended to improve the design of other types of snow fences. Some preliminary work for living snow fences is also discussed. Another major contribution of this study is to propose, develop protocols and test a novel technique based on close range photogrammetry (CRP) to quantify the snow deposits trapped snow fences. As image data can be acquired continuously, the time evolution of the volume of snow retained by a snow fence during a storm or during a whole winter season can, in principle, be obtained. Moreover, CRP is a non-intrusive method that eliminates the need to perform man-made measurements during the storms, which are difficult and sometimes dangerous to perform. Presently, there is lots of empiricism in the design of snow fences due to lack of data on fence storage capacity on how snow deposits change with the fence design and snow storm characteristics and in the estimation of the main parameters used by the state DOTs to design snow fences at a given site. The availability of such information from CRP measurements should provide critical data for the evaluation of the performance of a certain snow fence design that is tested by the IDOT. As part of the present study, the novel CRP method is tested at several sites. The present study also discusses some attempts and preliminary work to determine the snow relocation coefficient which is one of the main variables that has to be estimated by IDOT engineers when using the standard snow fence design software (Snow Drift Profiler, Tabler, 2006). Our analysis showed that standard empirical formulas did not produce reasonable values when applied at the Iowa test sites monitored as part of the present study and that simple methods to estimate this variable are not reliable. The present study makes recommendations for the development of a new methodology based on Large Scale Particle Image Velocimetry that can directly measure the snow drift fluxes and the amount of snow relocated by the fence.

Gene expression patterns unveil a new level of molecular heterogeneity in colorectal cancer.

The recognition that colorectal cancer (CRC) is a heterogeneous disease in terms of clinical behaviour and response to therapy translates into an urgent need for robust molecular disease subclassifiers that can explain this heterogeneity beyond current parameters (MSI, KRAS, BRAF). Attempts to fill this gap are emerging. The Cancer Genome Atlas (TGCA) reported two main CRC groups, based on the incidence and spectrum of mutated genes, and another paper reported an EMT expression signature defined subgroup. We performed a prior free analysis of CRC heterogeneity on 1113 CRC gene expression profiles and confronted our findings to established molecular determinants and clinical, histopathological and survival data. Unsupervised clustering based on gene modules allowed us to distinguish at least five different gene expression CRC subtypes, which we call surface crypt-like, lower crypt-like, CIMP-H-like, mesenchymal and mixed. A gene set enrichment analysis combined with literature search of gene module members identified distinct biological motifs in different subtypes. The subtypes, which were not derived based on outcome, nonetheless showed differences in prognosis. Known gene copy number variations and mutations in key cancer-associated genes differed between subtypes, but the subtypes provided molecular information beyond that contained in these variables. Morphological features significantly differed between subtypes. The objective existence of the subtypes and their clinical and molecular characteristics were validated in an independent set of 720 CRC expression profiles. Our subtypes provide a novel perspective on the heterogeneity of CRC. The proposed subtypes should be further explored retrospectively on existing clinical trial datasets and, when sufficiently robust, be prospectively assessed for clinical relevance in terms of prognosis and treatment response predictive capacity. Original microarray data were uploaded to the ArrayExpress database (http://www.ebi.ac.uk/arrayexpress/) under Accession Nos E-MTAB-990 and E-MTAB-1026. © 2013 Swiss Institute of Bioinformatics. Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.

Persistence of Increased Eotaxin-1 (CCL11) Level in Tears of Patients Wearing Contact Lenses: A Long-Term Follow-Up Study.

BACKGROUND: Eotaxin-1 (CCL11) is a potent eosinophil chemotactic and activating peptide that may be implicated in the pathogenesis of chronic allergic eye disease and has been associated with the wearing of contact lenses (CL) in patients with contact lens papillary conjunctivitis (CLPC). The purpose of this study was to study eotaxin-1 expression in the tears of long-term CL wearers. PATIENTS AND METHODS: Tears were collected with glass capillaries from 15 patients (2 male, 13 female) with various degree of CLPC at 2-year intervals. CLPC severity was graded from 0 to 4 with reference to standard slit-lamp photographs of the superior tarsal conjunctiva. The eotaxin-1 level in the tears was measured by an ELISA, using mouse anti-human eotaxin monoclonal antibodies. RESULTS: The mean age was 32.5 ± 13.3 years (range: 17 - 69 years). The mean interval between the tear collections was 30 ± 4.8 months. The mean concentration of eotaxin was 2150 ± 477 pg/mL and 2486 ± 810 pg/mL for the first and second series, respectively. The difference was not statistically significant (paired Wilcoxon/Kruskal-Wallis, p = 0.803). The mean score of papilla grade was 1.26 ± 0.18 for the first sample and 1.40 ± 0.19 two years later. There was no significant difference of grading between the two time periods (paired Wilcoxon/Kruskal-Wallis, p = 0.751). CONCLUSIONS: the eotaxin-1 level remains up-regulated over a long time period in patients wearing CL, most of them with chronic CLPC. Eotaxin may play a role in the pathogenesis of contact lens intolerance.