Global asymmetry of many-qubit correlations: A lattice gauge theory approach

We introduce a novel bridge between the familiar gauge field theory approaches used in many areas of modern physics such as quantum field theory and the SLOCC protocols familiar in quantum information. Although the mathematical methods are the same the meaning of the gauge group will be different. The measure we introduce, `twist', is constructed as a Wilson loop from a correlation induced holonomy. The measure can be understood as the global asymmetry of the bipartite correlations in a loop of three or more qubits; if the holonomy is trivial (the identity matrix), the bipartite correlations can be globally untwisted using general local qubit operations, the gauge group of our theory, which turns out to be the group of Lorentz transformations familiar from special relativity. If it is not possible to globally untwist the bipartite correlations in a state globally using local operations, the twistedness is given by a non-trivial element of the Lorentz group, the correlation induced holonomy. We provide several analytical examples of twisted and untwisted states for three qubits, the most elementary non-trivial loop one can imagine.Comment: 13 pages, 3 figures, title changed, results and content remain unchange

Antibody-based detection of protein phosphorylation status to track the efficacy of novel therapies using nanogram protein quantities from stem cells and cell lines

This protocol describes a highly reproducible antibody-based method that provides protein level and phosphorylation status information from nanogram quantities of protein cell lysate. Nanocapillary isoelectric focusing (cIEF) combines with UV-activated linking chemistry to detect changes in phosphorylation status. As an example application, we describe how to detect changes in response to tyrosine kinase inhibitors (TKIs) in the phosphorylation status of the adaptor protein ​CrkL, a major substrate of the oncogenic tyrosine kinase ​BCR-​ABL in chronic myeloid leukemia (CML), using highly enriched CML stem cells and mature cell populations in vitro. This protocol provides a 2.5 pg/nl limit of protein detection (<0.2% of a stem cell sample containing <104 cells). Additional assays are described for phosphorylated tyrosine 207 (pTyr207)-​CrkL and the protein tyrosine phosphatase ​PTPRC/​CD45; these assays were developed using this protocol and applied to CML patient samples. This method is of high throughput, and it can act as a screen for in vitro cancer stem cell response to drugs and novel agents

New disease outbreak affects two dominant sea urchin species associated with Australian temperate reefs

Diseases of sea urchins have been implicated in dramatic transitions of marine ecosystems. Although no definitive causal agent has been found for many of these outbreaks, mostare hypothesised to be waterborne and bacterial. Here we show the first report of a novel diseaseaffecting at least 2 species of urchins off the south-eastern coast of Australia. The aetiologicalagent, identified via a range of molecular techniques, immuno-histology and inoculation experi-ments, was found to be the opportunistic pathogen Vibrio anguillarum . The disease appears to betemperature-dependent, with a faster transmission rate and increase in prevalence during ex -perimental trials conducted at higher temperatures. Furthermore, analysis of long-term field datasuggests that it may have already reached epidemic proportions. With the increases in ocean temperatures brought about by climate change, this novel urchin disease may pose a severe problem for the organisms associated with the temperate reefs off Australia and/or the ecosystemas a whole

Does a monetary incentive improve the response to a postal questionnaire in a randomised controlled trial? : the MINT incentive study

Background: Sending a monetary incentive with postal questionnaires has been found to improve the proportion of responders, in research in non-healthcare settings. However, there is little research on use of incentives to improve follow-up rates in clinical trials, and existing studies are inconclusive. We conducted a randomised trial among participants in the Managing Injuries of the Neck Trial (MINT) to investigate the effects on the proportion of questionnaires returned and overall non-response of sending a £5 gift voucher with a follow-up questionnaire. Methods: Participants in MINT were randomised to receive either: (a) a £5 gift voucher (incentive group) or (b) no gift voucher (no incentive group), with their 4 month or 8 month follow-up questionnaire. We recorded, for each group, the number of questionnaires returned, the number returned without any chasing from the study office, the overall number of non-responders (after all chasing efforts by the study office), and the costs of following up each group. Results: 2144 participants were randomised, 1070 to the incentive group and 1074 to the no incentive group. The proportion of questionnaires returned (RR 1.10 (95% CI 1.05, 1.16)) and the proportion returned without chasing (RR 1.14 (95% CI 1.05, 1.24) were higher in the incentive group, and the overall non-response rate was lower (RR 0.68 (95% CI 0.53, 0.87)). Adjustment for injury severity and hospital of recruitment to MINT made no difference to these results, and there were no differences in results between the 4-month and 8-month follow up questionnaires. Analysis of costs suggested a cost of £67.29 per additional questionnaire returned. Conclusion: Monetary incentives may be an effective way to increase the proportion of postal questionnaires returned and minimise loss to follow-up in clinical trials

SSIPTools: Software and Methodology for Surface Site Interaction Point (SSIP) Approach and Applications.

We present the SSIPTools suite of programs. SSIPTools is a collection of software modules enabling the use of the Surface Site Interaction Point (SSIP) molecular descriptors, used for the modeling of noncovalent interactions in neutral organic molecules. It contains an implementation of the workflow for the generation of the SSIP descriptors, as well as the Functional Group Interaction Profiles (FGIPs) and Solvent Similarity Indexes (SSIs) applications, based on the SSIMPLE (Surface Site Interaction model for the Properties of Liquids at Equilibria) approach.Engineering and Physical Sciences Research Council (EP/M506485/1

Cardiovascular disease biomarkers are associated with declining renal function in type 2 diabetes

Aims/hypothesis: We investigated whether biochemical cardiovascular risk factors and/or markers of subclinical cardiovascular disease were associated with the development of reduced renal function in people with type 2 diabetes. Methods: A cohort of 1066 Scottish men and women aged 60–74 years with type 2 diabetes from the Edinburgh Type 2 Diabetes Study were followed up for a median of 6.7 years. New-onset reduced renal function was defined as two eGFRs <60 ml−1 min−1 (1.73 m)−2 at least 3 months apart with a > 25% decline from baseline eGFR. Ankle brachial pressure index (ABI), N-terminal pro-B-type natriuretic peptide (NT-proBNP) and high-sensitivity troponin T (hsTnT) were measured at baseline. Pulse wave velocity (PWV) and carotid intima media thickness were measured 1 year into follow-up. Data were analysed using Cox proportional hazards models. Results: A total of 119 participants developed reduced renal function during follow-up. ABI, PWV, NT-proBNP and hsTnT were all associated with onset of decline in renal function following adjustment for age and sex. These associations were attenuated after adjustment for additional diabetes renal disease risk factors (systolic BP, baseline eGFR, albumin:creatinine ratio and smoking pack-years), with the exception of hsTnT which remained independently associated (HR 1.51 [95% CI 1.22, 1.87]). Inclusion of hsTnT in a predictive model improved the continuous net reclassification index by 0.165 (0.008, 0.286). Conclusions/interpretation: Our findings demonstrate an association between hsTnT, a marker of subclinical cardiac ischaemia, and subsequent renal function decline. Further research is required to establish the predictive value of hsTnT and response to intervention

19F NMR spectroscopy monitors ligand binding to recombinantly fluorine-labelled b'x from human protein disulphide isomerase (hPDI)

We report a protein-observe (19)F NMR-based ligand titration binding study of human PDI b'x with ?-somatostatin that also emphasises the need to optimise recombinant protein fluorination when using 5- or 6-fluoroindole. This study highlights a recombinant preference for 5-fluoroindole over 6-fluoroindole; most likely due to the influence of fluorine atomic packing within the folded protein structure. Fluorination affords a single (19)F resonance probe to follow displacement of the protein x-linker as ligand is titrated and provides a dissociation constant of 23 ± 4 ?M

Cytochrome P450 site of metabolism prediction from 2D topological fingerprints using GPU accelerated probabilistic classifiers.

BACKGROUND: The prediction of sites and products of metabolism in xenobiotic compounds is key to the development of new chemical entities, where screening potential metabolites for toxicity or unwanted side-effects is of crucial importance. In this work 2D topological fingerprints are used to encode atomic sites and three probabilistic machine learning methods are applied: Parzen-Rosenblatt Window (PRW), Naive Bayesian (NB) and a novel approach called RASCAL (Random Attribute Subsampling Classification ALgorithm). These are implemented by randomly subsampling descriptor space to alleviate the problem often suffered by data mining methods of having to exactly match fingerprints, and in the case of PRW by measuring a distance between feature vectors rather than exact matching. The classifiers have been implemented in CUDA/C++ to exploit the parallel architecture of graphical processing units (GPUs) and is freely available in a public repository. RESULTS: It is shown that for PRW a SoM (Site of Metabolism) is identified in the top two predictions for 85%, 91% and 88% of the CYP 3A4, 2D6 and 2C9 data sets respectively, with RASCAL giving similar performance of 83%, 91% and 88%, respectively. These results put PRW and RASCAL performance ahead of NB which gave a much lower classification performance of 51%, 73% and 74%, respectively. CONCLUSIONS: 2D topological fingerprints calculated to a bond depth of 4-6 contain sufficient information to allow the identification of SoMs using classifiers based on relatively small data sets. Thus, the machine learning methods outlined in this paper are conceptually simpler and more efficient than other methods tested and the use of simple topological descriptors derived from 2D structure give results competitive with other approaches using more expensive quantum chemical descriptors. The descriptor space subsampling approach and ensemble methodology allow the methods to be applied to molecules more distant from the training data where data mining would be more likely to fail due to the lack of common fingerprints. The RASCAL algorithm is shown to give equivalent classification performance to PRW but at lower computational expense allowing it to be applied more efficiently in the ensemble scheme.The authors would like to thank Unilever for funding. We thank Dr. Guus Duchateau, Leo van Buren and Prof. Werner Klaffke for useful discussions in the development of this work.This is the final version. It was first published by Chemistry Central at http://www.jcheminf.com/content/6/1/29

A national survey of clinical practice for the management of whiplash-associated disorders in UK emergency departments

Objective: To undertake a national survey to determine current practice for the management of whiplash injuries in UK emergency departments (ED). Methods: Postal questionnaire survey. 316 lead consultants from all UK ED with annual new attendances of over 50 000 people were asked to indicate the use of a range of treatments and the frequency with which these treatments were used. Samples of written advice were requested and content analysis was conducted and compared with survey responses. Results: The response rate was 79% (251/316). The intervention most frequently used was verbal advice to exercise, reported by 84% of respondents for most or all cases, and advice against the use of a collar (83%). Other treatments reported as being used frequently were written advice and anti-inflammatory medication. 106 consultants (42%) provided a sample of written materials. Reference to expected recovery and encouragement for early return to activities were included in less than 6%. Nearly 50% of written materials contained information on how to use a soft collar and 61% contained information on solicitors and pursuing a personal injury claim. There were important differences between reported verbal behaviours and written advice. Conclusion: Verbal advice is the primary method for managing whiplash injuries in ED and is usually supplemented by written advice. Within individual hospitals there is a lack of consistency between verbal and written advice. The promotion of personal injury claims is a common feature of written advice. Research is required to develop effective and consistent models of advice