Research on anisotropy of fusion-produced protons and neutrons emission from high-current plasma-focus discharges.

The paper concerns fast protons and neutrons from D-D fusion reactions in a Plasma-Focus-1000U facility. Measurements were performed with nuclear-track detectors arranged in "sandwiches" of an Al-foil and two PM-355 detectors separated by a polyethylene-plate. The Al-foil eliminated all primary deuterons, but was penetrable for fast fusion protons. The foil and first PM-355 detector were penetrable for fast neutrons, which were converted into recoil-protons in the polyethylene and recorded in the second PM-355 detector. The "sandwiches" were irradiated by discharges of comparable neutron-yields. Analyses of etched tracks and computer simulations of the fusion-products behavior in the detectors were performed.

Note: Measurements of fast electrons in the TORE-SUPRA tokamak by means of modified Cherenkov-type diamond detector.

The Note reports on experimental studies of ripple born fast electrons within the TORE-SUPRA facility, which were performed by means of a modified measuring head equipped with diamond detectors designed especially for recording the electron-induced Cherenkov radiation. There are presented signals produced by fast electrons in the TORE-SUPRA machine, which were recorded during two experimental campaigns performed in 2010. Shapes of these electron-induced signals are considerably different from those observed during the first measurements carried out by the prototype Cherenkov probe in 2008. An explanation of the observed differences is given.

Development of a diagnostic technique based on Cherenkov effect for measurements of fast electrons in fusion devices.

A diagnostic technique based on the Cherenkov effect is proposed for detection and characterization of fast (super-thermal and runaway) electrons in fusion devices. The detectors of Cherenkov radiation have been specially designed for measurements in the ISTTOK tokamak. Properties of several materials have been studied to determine the most appropriate one to be used as a radiator of Cherenkov emission in the detector. This technique has enabled the detection of energetic electrons (70 keV and higher) and the determination of their spatial and temporal variations in the ISTTOK discharges. Measurement of hard x-ray emission has also been carried out in experiments for validation of the measuring capabilities of the Cherenkov-type detector and a high correlation was found between the data of both diagnostics. A reasonable agreement was found between experimental data and the results of numerical modeling of the runaway electron generation in ISTTOK.

Value of Gilliatt's pneumatic tourniquet test for diagnosis of carpal tunnel syndrome.

OBJECTIVES: In 1953, Gilliatt and Wilson described the pneumatic-tourniquet test to diagnose the carpal tunnel syndrome (CTS). It was originally carried out by inflating a brachial cuff at suprasystolic pressure, looking for the appearance of dysesthesiae; several authors later proposed to perform it at infrasystolic pressure, arguing that it would better reflect the elevated venous pressure supposed to be present in CTS. The purpose of this study was to compare both methods. METHODS: This prospective randomized controlled study included 49 patients and compared both methods to perform Gilliatt's test with more commonly used provocative tests (Tinel, Phalen, Durkan, and Weber). The following end-points were considered: typical clinical presentation, altered neurophysiological tests, abnormal ultrasound findings and early resolution of symptoms after surgical decompression. RESULTS: For all these end-points, no significant difference was observed in sensibility nor specificity, whether Gilliatt's test was performed supra- or infra-systolic. In addition, Gilliatt's test proved to have less diagnostic value than Phalen and Durkan tests for sensibility. CONCLUSION: This study did not permit to distinguish the two versions of Gilliatt's test but to open a discussion about the utility of such a test to diagnose the CTS.

Evolutionary inaccuracy of pairwise structural alignments.

MOTIVATION: Structural alignment methods are widely used to generate gold standard alignments for improving multiple sequence alignments and transferring functional annotations, as well as for assigning structural distances between proteins. However, the correctness of the alignments generated by these methods is difficult to assess objectively since little is known about the exact evolutionary history of most proteins. Since homology is an equivalence relation, an upper bound on alignment quality can be found by assessing the consistency of alignments. Measuring the consistency of current methods of structure alignment and determining the causes of inconsistencies can, therefore, provide information on the quality of current methods and suggest possibilities for further improvement. RESULTS: We analyze the self-consistency of seven widely-used structural alignment methods (SAP, TM-align, Fr-TM-align, MAMMOTH, DALI, CE and FATCAT) on a diverse, non-redundant set of 1863 domains from the SCOP database and demonstrate that even for relatively similar proteins the degree of inconsistency of the alignments on a residue level is high (30%). We further show that levels of consistency vary substantially between methods, with two methods (SAP and Fr-TM-align) producing more consistent alignments than the rest. Inconsistency is found to be higher near gaps and for proteins of low structural complexity, as well as for helices. The ability of the methods to identify good structural alignments is also assessed using geometric measures, for which FATCAT (flexible mode) is found to be the best performer despite being highly inconsistent. We conclude that there is substantial scope for improving the consistency of structural alignment methods. CONTACT: msadows@nimr.mrc.ac.uk SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Characteristics of four-channel Cherenkov-type detector for measurements of runaway electrons in the ISTTOK tokamak.

A diagnostics capable of characterizing the runaway and superthermal electrons has been developing on the ISTTOK tokamak. In previous paper, a use of single-channel Cherenkov-type detector with titanium filter for runaway electron studies in ISTTOK was reported. To measure fast electron populations with different energies, a prototype of a four-channel detector with molybdenum filters was designed. Test-stand studies of filters with different thicknesses (1, 3, 7, 10, 20, 50, and 100 µm) have shown that they should allow the detection of electrons with energies higher than 69, 75, 87, 95, 120, 181, and 260 keV, respectively. First results of measurements with the four-channel detector revealed the possibility to measure reliably different fast electrons populations simultaneously.

On the evolutionary origins of "Fold Space Continuity": a study of topological convergence and divergence in mixed alpha-beta domains.

Existing protein structure classifications group proteins by overall structural similarity at the highest level and by evolutionary relationships at the lowest level, deriving higher-level groups by pairwise structure comparison. For this to be successful requires that large changes in structure are relatively rare in evolution and that proteins with no detectable evolutionary relationship do not converge on similar global chain conformations since this creates conflicts between structural and evolutionary consistency. Analysis of global structural changes using core topological descriptions for 4261 domains from classes C and D of the SCOP database and new measures of topological distance and consistency of classification showed that the topological consistency of SCOP folds is highly variable with some folds having no consistent description and significant overlaps between groups including some members of separate folds with identical topological descriptions. Topological clustering shows that including sufficient indels to allow family members to be joined would also require joining several distinct folds. We conclude that evolutionary changes in the global topology of protein domains are the root cause of many difficulties for present approaches to structure classification using pairwise comparison. As a resolution we propose that a purely structural classification should be created using an approach similar to that adopted by the Gene Ontology in which proteins are assigned labels describing structure.

Cherenkov-type diamond detectors for measurements of fast electrons in the TORE-SUPRA tokamak.

The paper presents a schematic design and tests of a system applicable for measurements of fast electron pulses emitted from high-temperature plasma generated inside magnetic confinement fusion machines, and particularly in the TORE-SUPRA facility. The diagnostic system based on the registration of the Cherenkov radiation induced by fast electrons within selected solid radiators is considered, and electron low-energy thresholds for different radiators are given. There are some estimates of high thermal loads, which might be deposited by intense electron beams upon parts of the diagnostic equipment within the TORE-SUPRA device. There are some proposed measures to overcome this difficulty by the selection of appropriate absorption filters and Cherenkov radiators, and particularly by the application of a fast-moving reciprocating probe. The paper describes the measuring system, its tests, as well as some results of the preliminary measurements of fast electrons within TORE-SUPRA facility.

Mass- and energy-analyses of ions from plasma by means of a miniature Thomson spectrometer.

The paper presents an improved version of a miniature mass-spectrometer of the Thomson-type, which has been adopted for ion analysis near the dense plasma region inside a vacuum chamber. Problems connected with the separation of ions from plasma streams are considered. Input diaphragms and pumping systems, needed to ensure good vacuum inside the analyzing region, are described. The application of the miniature Thomson-type analyzer is illustrated by ion parabolas recorded in plasma-focus facility and rod plasma injector experiment. A quantitative analysis of the recorded ion parabolas is presented. Factors influencing accuracy of the ion analysis are discussed and methods of the spectrometer calibration are described.

The sequence-structure relationship and protein function prediction.

An incomplete understanding of protein sequence/structure/function relationships causes many difficulties for prediction methods. The highly complex nature of these relationships is a consequence of the interplay between physics and evolution that has been studied using a wide array of experimental and theoretical techniques. We review recent findings relating to conservation of sequence, structure and function and discuss their use in developing improved prediction methods.

Use of Cherenkov-type detectors for measurements of runaway electrons in the ISTTOK tokamak.

Gas, fluid, or solid Cherenkov-type detectors have been widely used in high-energy physics for determination of parameters of charged particles, which are moving with relativistic velocities. This paper presents experimental results on the detection of runaway electrons using Cherenkov-type detectors in the ISTTOK tokamak discharges. Such detectors have been specially designed for measurements of energetic electrons in tokamak plasma. The technique based on the use of the Cherenkov-type detectors has enabled the detection of energetic electrons (energies higher than 80 keV) and determination of their spatial and temporal parameters in the ISTTOK discharges. Obtained experimental data were found in adequate agreement to the results of numerical modeling of the runaway electron generation in ISTTOK.

Dirac fermions at the H point of graphite: magnetotransmission studies.

We report on far infrared magnetotransmission measurements on a thin graphite sample prepared by exfoliation of highly oriented pyrolytic graphite. In a magnetic field, absorption lines exhibiting a blueshift proportional to sqrt[B] are observed. This is a fingerprint for massless Dirac holes at the H point in bulk graphite. The Fermi velocity is found to be c[over ] =( 1.02+/-0.02) x 10(6) m/s and the pseudogap |Delta| at the H point is estimated to be below 10 meV. Although the holes behave to a first approximation as a strictly 2D gas of Dirac fermions, the full 3D band structure has to be taken into account to explain all the observed spectral features.

High-energy limit of massless Dirac fermions in multilayer graphene using magneto-optical transmission spectroscopy.

We have investigated the absorption spectrum of multilayer graphene in high magnetic fields. The low-energy part of the spectrum of electrons in graphene is well described by the relativistic Dirac equation with a linear dispersion relation. However, at higher energies (>500 meV) a deviation from the ideal behavior of Dirac particles is observed. At an energy of 1.25 eV, the deviation from linearity is approximately 40 meV. This result is in good agreement with the theoretical model, which includes trigonal warping of the Fermi surface and higher-order band corrections. Polarization-resolved measurements show no observable electron-hole asymmetry.

Benchmarking template selection and model quality assessment for high-resolution comparative modeling.

Comparative modeling is presently the most accurate method of protein structure prediction. Previous experiments have shown the selection of the correct template to be of paramount importance to the quality of the final model. We have derived a set of 732 targets for which a choice of ten or more templates exist with 30-80% sequence identity and used this set to compare a number of possible methods for template selection: BLAST, PSI-BLAST, profile-profile alignment, HHpred HMM-HMM comparison, global sequence alignment, and the use of a model quality assessment program (MQAP). In addition, we have investigated the question of whether any structurally defined subset of the sequence could be used to predict template quality better than overall sequence similarity. We find that template selection by BLAST is sufficient in 75% of cases but that there are examples in which improvement (global RMSD 0.5 A or more) could be made. No significant improvement is found for any of the more sophisticated sequence-based methods of template selection at high sequence identities. A subset of 118 targets extending to the lowest levels of sequence similarity was examined and the HHpred and MQAP methods were found to improve ranking when available templates had 35-40% maximum sequence identity. Structurally defined subsets in general are found to be less discriminative than overall sequence similarity, with the coil residue subset performing equivalently to sequence similarity. Finally, we demonstrate that if models are built and model quality is assessed in combination with the sequence-template sequence similarity that a extra 7% of "best" models can be found.

Longitudinal CSF and MRI biomarkers improve the diagnosis of mild cognitive impairment.

The diagnosis of Alzheimer's disease (AD) in patients with mild cognitive impairment (MCI) is limited because it is based on non-specific behavioral and neuroimaging findings. The lesions of Alzheimer's disease: amyloid beta (Abeta) deposits, tau pathology and cellular oxidative damage, affect the hippocampus in the earlier stages causing memory impairment. In a 2-year longitudinal study of MCI patients and normal controls, we examined the hypothesis that cerebrospinal fluid (CSF) markers for these pathological features improve the diagnostic accuracy over memory and magnetic resonance imaging (MRI)-hippocampal volume evaluations. Relative to control, MCI patients showed decreased memory and hippocampal volumes and elevated CSF levels of hyperphosphorylated tau and isoprostane. These two CSF measures consistently improved the diagnostic accuracy over the memory measures and the isoprostane measure incremented the accuracy of the hippocampal volume achieving overall diagnostic accuracies of about 90%. Among MCI patients, over 2 years, longitudinal hippocampal volume losses were closely associated with increasing hyperphosphorylated tau and decreasing amyloid beta-42 levels. These results demonstrate that CSF biomarkers for AD contribute to the characterization of MCI.

Landau level spectroscopy of ultrathin graphite layers.

Far infrared transmission experiments are performed on ultrathin epitaxial graphite samples in a magnetic field. The observed cyclotron resonance-like and electron-positron-like transitions are in excellent agreement with the expectations of a single-particle model of Dirac fermions in graphene, with an effective velocity of c=1.03 x 10(6) m/s.

[Wrist pain]. / Les syndromes douloureux du poignet.

Acute or chronic wrist pain is a relatively frequent complaint that may involve all age groups. The pain may be of osseous, articular, periarticular, neurologic, vascular origin, or be referred from the cervical spine, shoulder or elbow. The diagnosis should be oriented by a precise history and clinical examination. More specialised exams will be required according to clinical findings. Psychosocial and environmental influences need to be taken into consideration.

Prediction of novel and analogous folds using fragment assembly and fold recognition.

A number of new and newly improved methods for predicting protein structure developed by the Jones-University College London group were used to make predictions for the CASP6 experiment. Structures were predicted with a combination of fold recognition methods (mGenTHREADER, nFOLD, and THREADER) and a substantially enhanced version of FRAGFOLD, our fragment assembly method. Attempts at automatic domain parsing were made using DomPred and DomSSEA, which are based on a secondary structure parsing algorithm and additionally for DomPred, a simple local sequence alignment scoring function. Disorder prediction was carried out using a new SVM-based version of DISOPRED. Attempts were also made at domain docking and "microdomain" folding in order to build complete chain models for some targets.

Automated derivation and refinement of sequence length patterns for protein sequences using evolutionary computation.

Several stratagems are used in protein bioinformatics for the classification of proteins based on sequence, structure or function. We explore the concept of a minimal signature embedded in a sequence that defines the likely position of a protein in a classification. Specifically, we address the derivation of sparse profiles for the G-protein coupled receptor (GPCR) clan of integral membrane proteins. We present an evolutionary algorithm (EA) for the derivation of sparse profiles (signatures) without the need to supply a multiple alignment. We also apply an evolution strategy (ES) to the problem of pattern and profile refinement. Patterns were derived for the GPCR 'superfamily' and GPCR families 1-3 individually from starting populations of randomly generated signatures, using a database of integral membrane protein sequences and an objective function using a modified receiver operator characteristic (ROC) statistic. The signature derived for the family 1 GPCR sequences was shown to perform very well in a stringent cross-validation test, detecting 76% of unseen GPCR sequences at 5% error. Application of the ES refinement method to a signature developed by a previously described method [Sadowski, M.I., Parish, J.H., 2003. Automated generation and refinement of protein signatures: case study with G-protein coupled receptors. Bioinformatics 19, 727-734] resulted in a 6% increase of coverage for 5% error as measured in the validation test. We note that there might be a limit to this or any classification of proteins based on patterns or schemata.

Therapeutics and prion disease: can immunisation or drugs be effective?

Prion diseases are of considerable importance because of the threat of a variant form of Creutzfeldt Jakob disease that has emerged in recent years. Pre-clinical diagnosis of prion diseases still remains poor and effective therapies also do not exist at present. This review examines research on possible therapeutic strategies that might have potential benefits if applied before neurodegeneration has occurred.