FutureGRID: A Program for long-term research into GRID systems architecture

Proceedings of the 2003 UK e-Science All Hands Meeting, 31st August - 3rd September, Nottingham UKThis is a project to carry out research into long-term GRID architecture, in the University of Cambridge Computer Laboratory and the Cambridge eScience Center, with support from the Microsoft Research Laboratory, Cambridge. It is part of a larger vision for future systems architectures for public computing platforms, including both scientitic GRID and commodity level computing such as games, peer2peer computing and storage services and so forth, based on work in the laboratories in recent years into massively scaleable distributed systems for storage, computation, content distribution and collaboration[26]

Graphs Identified by Logics with Counting

We classify graphs and, more generally, finite relational structures that are identified by C2, that is, two-variable first-order logic with counting. Using this classification, we show that it can be decided in almost linear time whether a structure is identified by C2. Our classification implies that for every graph identified by this logic, all vertex-colored versions of it are also identified. A similar statement is true for finite relational structures. We provide constructions that solve the inversion problem for finite structures in linear time. This problem has previously been shown to be polynomial time solvable by Martin Otto. For graphs, we conclude that every C2-equivalence class contains a graph whose orbits are exactly the classes of the C2-partition of its vertex set and which has a single automorphism witnessing this fact. For general k, we show that such statements are not true by providing examples of graphs of size linear in k which are identified by C3 but for which the orbit partition is strictly finer than the Ck-partition. We also provide identified graphs which have vertex-colored versions that are not identified by Ck.Comment: 33 pages, 8 Figure

Dominant-negative calcium channel suppression by truncated constructs involves a kinase implicated in the unfolded protein response

Expression of the calcium channel Ca(V)2.2 is markedly suppressed by coexpression with truncated constructs of Ca(V)2.2. Furthermore, a two-domain construct of Ca(V)2.1 mimicking an episodic ataxia-2 mutation strongly inhibited Ca(V)2.1 currents. We have now determined the specificity of this effect, identified a potential mechanism, and have shown that such constructs also inhibit endogenous calcium currents when transfected into neuronal cell lines. Suppression of calcium channel expression requires interaction between truncated and full-length channels, because there is inter-subfamily specificity. Although there is marked cross-suppression within the Ca(V)2 calcium channel family, there is no cross-suppression between Ca(V)2 and Ca(V)3 channels. The mechanism involves activation of a component of the unfolded protein response, the endoplasmic reticulum resident RNA-dependent kinase (PERK), because it is inhibited by expression of dominant-negative constructs of this kinase. Activation of PERK has been shown previously to cause translational arrest, which has the potential to result in a generalized effect on protein synthesis. In agreement with this, coexpression of the truncated domain I of Ca(V)2.2, together with full-length Ca(V)2.2, reduced the level not only of Ca(V)2.2 protein but also the coexpressed alpha2delta-2. Thapsigargin, which globally activates the unfolded protein response, very markedly suppressed Ca(V)2.2 currents and also reduced the expression level of both Ca(V)2.2 and alpha2delta-2 protein. We propose that voltage-gated calcium channels represent a class of difficult-to-fold transmembrane proteins, in this case misfolding is induced by interaction with a truncated cognate Ca(V) channel. This may represent a mechanism of pathology in episodic ataxia-2

Importance of Spin-Orbit Interaction for the Electron Spin Relaxation in Organic Semiconductors

Despite the great interest organic spintronics has recently attracted, there is only a partial understanding of the fundamental physics behind electron spin relaxation in organic semiconductors. Mechanisms based on hyperfine interaction have been demonstrated, but the role of the spin-orbit interaction remains elusive. Here, we report muon spin spectroscopy and time-resolved photoluminescence measurements on two series of molecular semiconductors in which the strength of the spin-orbit interaction has been systematically modified with a targeted chemical substitution of different atoms at a particular molecular site. We find that the spin-orbit interaction is a significant source of electron spin relaxation in these materials

Visualizing the microscopic coexistence of spin density wave and superconductivity in underdoped NaFe1-xCoxAs

Although the origin of high temperature superconductivity in the iron pnictides is still under debate, it is widely believed that magnetic interactions or fluctuations play an important role in triggering Cooper pairing. Because of the relevance of magnetism to pairing, the question of whether long range spin magnetic order can coexist with superconductivity microscopically has attracted strong interests. The available experimental methods used to answer this question are either bulk probes or local ones without control of probing position, thus the answers range from mutual exclusion to homogeneous coexistence. To definitively answer this question, here we use scanning tunneling microscopy to investigate the local electronic structure of an underdoped NaFe1-xCoxAs near the spin density wave (SDW) and superconducting (SC) phase boundary. Spatially resolved spectroscopy directly reveal both the SDW and SC gap features at the same atomic location, providing compelling evidence for the microscopic coexistence of the two phases. The strengths of the SDW and SC features are shown to anti correlate with each other, indicating the competition of the two orders. The microscopic coexistence clearly indicates that Cooper pairing occurs when portions of the Fermi surface (FS) are already gapped by the SDW order. The regime TC < T < TSDW thus show a strong resemblance to the pseudogap phase of the cuprates where growing experimental evidences suggest a FS reconstruction due to certain density wave order. In this phase of the pnictides, the residual FS has a favorable topology for magnetically mediated pairing when the ordering moment of the SDW is small.Comment: 18 pages, 4 figure

Patients presenting with miliaria while wearing flame resistant clothing in high ambient temperatures: a case series

<p>Abstract</p> <p>Introduction</p> <p>Clothing can be a cause of occupational dermatitis. Frequent causes of clothing-related dermatological problems can be the fabric itself and/or chemical additives used in the laundering process, friction from certain fabrics excessively rubbing the skin, or heat retention from perspiration-soaked clothing in hot working environments. To the best of our knowledge, these are the first reported cases of miliaria rubra associated with prolonged use of flame resistant clothing in the medical literature.</p> <p>Case presentation</p> <p>We report 18 cases (14 men and 4 women, with an age range of 19 to 37 years) of moderate to severe skin irritation associated with wearing flame resistant clothing in hot arid environments (temperature range: 39 to 50°C, 5% to 25% relative humidity). We describe the medical history in detail of a 23-year-old Caucasian woman and a 31-year-old African-American man. A summary of the other 16 patients is also provided.</p> <p>Conclusions</p> <p>These cases illustrate the potential serious nature of miliaria with superimposed <it>Staphylococcus </it>infections. All 18 patients fully recovered with topical skin treatment and modifications to their dress ensemble. Clothing, in particular blend fabrics, must be thoroughly laundered to adequately remove detergent residue. While in hot environments, individuals with sensitive skin should take the necessary precautions such as regular changing of clothing and good personal hygiene to ensure that their skin remains as dry and clean as possible. It is also important that they report to their health care provider as soon as skin irritation or rash appears to initiate any necessary medical procedures. Miliaria rubra can take a week or longer to clear, so removal of exposure to certain fabric types may be necessary.</p

Annotation and query of tissue microarray data using the NCI Thesaurus

<p>Abstract</p> <p>Background</p> <p>The Stanford Tissue Microarray Database (TMAD) is a repository of data serving a consortium of pathologists and biomedical researchers. The tissue samples in TMAD are annotated with multiple free-text fields, specifying the pathological diagnoses for each sample. These text annotations are not structured according to any ontology, making future integration of this resource with other biological and clinical data difficult.</p> <p>Results</p> <p>We developed methods to map these annotations to the NCI thesaurus. Using the NCI-T we can effectively represent annotations for about 86% of the samples. We demonstrate how this mapping enables ontology driven integration and querying of tissue microarray data. We have deployed the mapping and ontology driven querying tools at the TMAD site for general use.</p> <p>Conclusion</p> <p>We have demonstrated that we can effectively map the diagnosis-related terms describing a sample in TMAD to the NCI-T. The NCI thesaurus terms have a wide coverage and provide terms for about 86% of the samples. In our opinion the NCI thesaurus can facilitate integration of this resource with other biological data.</p

What are we measuring? A critique of range of motion methods currently in use for Dupuytren's disease and recommendations for practice

Background: Range of motion is the most frequently reported measure used in practice to evaluate outcomes. A goniometer is the most reliable tool to assess range of motion yet, the lack of consistency in reporting prevents comparison between studies. The aim of this study is to identify how range of motion is currently assessed and reported in Dupuytren’s disease literature. Following analysis recommendations for practice will be made to enable consistency in future studies for comparability. This paper highlights the variation in range of motion reporting in Dupuytren’s disease. Methods: A Participants, Intervention, Comparison, Outcomes and Study design format was used for the search strategy and search terms. Surgery, needle fasciotomy or collagenase injection for primary or recurrent Dupuytren’s disease in adults were included if outcomes were monitored using range of motion to record change. A literature search was performed in May 2013 using subject heading and free-text terms to also capture electronic publications ahead of print. In total 638 publications were identified and following screening 90 articles met the inclusion criteria. Data was extracted and entered onto a spreadsheet for analysis. A thematic analysis was carried out to establish any duplication, resulting in the final range of motion measures identified. Results: Range of motion measurement lacked clarity, with goniometry reportedly used in only 43 of the 90 studies, 16 stated the use of a range of motion protocol. A total of 24 different descriptors were identified describing range of motion in the 90 studies. While some studies reported active range of motion, others reported passive or were unclear. Eight of the 24 categories were identified through thematic analysis as possibly describing the same measure, ‘lack of joint extension’ and accounted for the most frequently used. Conclusions: Published studies lacked clarity in reporting range of motion, preventing data comparison and meta-analysis. Percentage change lacks context and without access to raw data, does not allow direct comparison of baseline characteristics. A clear description of what is being measured within each study was required. It is recommended that range of motion measuring and reporting for Dupuytren’s disease requires consistency to address issues that fall into 3 main categories:- Definition of terms Protocol statement Outcome reportin

Validity of the Walter Reed Visual Assessment Scale to measure subjective perception of spine deformity in patients with idiopathic scoliosis

BACKGROUND: The Walter Reed Visual Assessment Scale (WRVAS) was designed to allow idiopathic scoliosis patients to describe their perception of their deformity. In a previous stduy, the scale has shown good correlation with magnitude of the curve METHODS: The study included 70 patients (60 women and 10 men), mean age 19.4 years (range 12–40), with idiopathic scoliosis. Each patient filled out the WRVAS and the SRS-22 questionnaire. Thoracic and lumbar curve angles were determined in standing X-rays and the largest was named Cobbmax. WRVAS internal consistency was assessed with Cronbach's alpha. Correlation coefficients were calculated between Cobbmax and the various WRVAS questions, and Cobbmax and the SRS-22 scales. The correlation between the WRVAS and SRS-22 was also determined RESULTS: Mean magnitudes were thoracic curve, 36.6° and lumbar curve, 33.2°; average Cobbmax was 37.9°. The mean total WRVAS score was 15.6. Mean scores for the various SRS-22 scales were function 4.6, pain 4.3, self-image 3.7, mental health 4.2, and total score 84.1. Internal consistency for the WRVAS was excellent (Cronbach's alpha, 0.9), and there were no signs of collinearity among the seven questions (tolerance range 0.2–0.5). All the items on the WRVAS correlated significantly with Cobbmax (correlation coefficients, 0.4 to 0.7). The correlation between the total WRVAS and total SRS-22 score was -0.54 (P = .0001) and between WRVAS total score and SRS-22 image domain score was -0.57 (p = 0.0001) CONCLUSION: The WRVAS showed excellent internal consistency and absence of collinearity. There was a highly significant correlation between the results of the test and the magnitude of the deformity. The WRVAS correlated significantly with the SRS-22 image scale. The WRVAS is a valid instrument to assess scoliosis patients perception of their deformit