Impact of the Conformational Variability of Oligopeptides on the Computational Prediction of Their CD Spectra

Although successful in the structural determination of ordered biomolecules, the spectroscopic investigation of oligopeptides in solution is hindered by their complex and rapidly changing conformational ensemble. The measured circular dichroism (CD) spectrum of an oligopeptide is an ensemble average over all microstates, severely limiting its interpretation, in contrast to ordered biomolecules. Spectral deconvolution methods to estimate the secondary structure contributions in the ensemble are still mostly based on databases of larger ordered proteins. Here, we establish how the interpretation of CD spectra of oligopeptides can be enhanced by the ability to compute the same observable from a set of atomic coordinates. Focusing on two representative oligopeptides featuring a known propensity toward an α-helical and β-hairpin motif, respectively, we compare and cross-validate the structural information coming from deconvolution of the experimental CD spectra, sequence-based de novo structure prediction, and molecular dynamics simulations based on enhanced sampling methods. We find that small conformational variations can give rise to significant changes in the CD signals. While for the simpler conformational landscape of the α-helical peptide de novo structure prediction can already give reasonabl

GoSam: A program for automated one-loop Calculations

The program package GoSam is presented which aims at the automated calculation of one-loop amplitudes for multi-particle processes. The amplitudes are generated in terms of Feynman diagrams and can be reduced using either D-dimensional integrand-level decomposition or tensor reduction, or a combination of both. GoSam can be used to calculate one-loop corrections to both QCD and electroweak theory, and model files for theories Beyond the Standard Model can be linked as well. A standard interface to programs calculating real radiation is also included. The flexibility of the program is demonstrated by various examples.Comment: 10 pages, Talk given at the International Workshop on Advanced Computing and Analysis Techniques in Physics Research (ACAT), Uxbridge, London, September 201

Early computed tomography coronary angiography in adults presenting with suspected acute coronary syndrome: the RAPID-CTCA RCT.

BACKGROUND: Acute coronary syndrome is a common medical emergency. The optimal strategy to investigate patients who are at intermediate risk of acute coronary syndrome has not been fully determined. OBJECTIVE: To investigate the role of early computed tomography coronary angiography in the investigation and treatment of adults presenting with suspected acute coronary syndrome. DESIGN: A prospective, multicentre, open, parallel-group randomised controlled trial with blinded end-point adjudication. SETTING: Thirty-seven hospitals in the UK. PARTICIPANTS: Adults (aged ≥ 18 years) presenting to the emergency department, acute medicine services or cardiology department with suspected or provisionally diagnosed acute coronary syndrome and at least one of the following: (1) a prior history of coronary artery disease, (2) a cardiac troponin level > 99th centile and (3) an abnormal 12-lead electrocardiogram. INTERVENTIONS: Early computed tomography coronary angiography in addition to standard care was compared with standard care alone. Participants were followed up for 1 year. MAIN OUTCOME MEASURE: One-year all-cause death or subsequent type 1 (spontaneous) or type 4b (stent thrombosis) myocardial infarction, measured as the time to such event adjudicated by two cardiologists blinded to the computerised tomography coronary angiography ( CTCA ) arm. Cost-effectiveness was estimated as the lifetime incremental cost per quality-adjusted life-year gained. RESULTS: Between 23 March 2015 and 27 June 2019, 1748 participants [mean age 62 years (standard deviation 13 years), 64% male, mean Global Registry Of Acute Coronary Events score 115 (standard deviation 35)] were randomised to receive early computed tomography coronary angiography (n = 877) or standard care alone (n = 871). The primary end point occurred in 51 (5.8%) participants randomised to receive computed tomography coronary angiography and 53 (6.1%) participants randomised to receive standard care (adjusted hazard ratio 0.91, 95% confidence interval 0.62 to 1.35; p = 0.65). Computed tomography coronary angiography was associated with a reduced use of invasive coronary angiography (adjusted hazard ratio 0.81, 95% confidence interval 0.72 to 0.92; p = 0.001) but no change in coronary revascularisation (adjusted hazard ratio 1.03, 95% confidence interval 0.87 to 1.21; p = 0.76), acute coronary syndrome therapies (adjusted odds ratio 1.06, 95% confidence interval 0.85 to 1.32; p = 0.63) or preventative therapies on discharge (adjusted odds ratio 1.07, 95% confidence interval 0.87 to 1.32; p = 0.52). Early computed tomography coronary angiography was associated with longer hospitalisations (median increase 0.21 days, 95% confidence interval 0.05 to 0.40 days) and higher mean total health-care costs over 1 year (£561 more per patient) than standard care. LIMITATIONS: The principal limitation of the trial was the slower than anticipated recruitment, leading to a revised sample size, and the requirement to compromise and accept a larger relative effect size estimate for the trial intervention. FUTURE WORK: The potential role of computed tomography coronary angiography in selected patients with a low probability of obstructive coronary artery disease (intermediate or mildly elevated level of troponin) or who have limited access to invasive cardiac catheterisation facilities needs further prospective evaluation. CONCLUSIONS: In patients with suspected or provisionally diagnosed acute coronary syndrome, computed tomography coronary angiography did not alter overall coronary therapeutic interventions or 1-year clinical outcomes, but it did increase the length of hospital stay and health-care costs. These findings do not support the routine use of early computed tomography coronary angiography in intermediate-risk patients with acute chest pain. TRIAL REGISTRATION: This trial is registered as ISRCTN19102565 and Clinical Trials NCT02284191. FUNDING: This project was funded by the National Institute for Health and Care Research (NIHR) Health Technology Assessment programme and will be published in full in Health Technology Assessment; Vol. 26, No. 37. See the NIHR Journals Library website for further project information

Real-world performance and accuracy of stress echocardiography: The EVAREST observational multi-centre study

Aims - Stress echocardiography is widely used to identify obstructive coronary artery disease. High accuracy is reported in expert hands but is dependent on operator training and image quality. The EVAREST study provides UK-wide data to evaluate real-world performance and accuracy of stress echocardiography. Methods and Results - Participants undergoing stress echocardiography for coronary artery disease were recruited from 31 hospitals. Participants were followed up through health records which underwent expert adjudication. Cardiac outcome was defined as anatomically or functionally-significant stenosis on angiography, revascularisation, medical management of ischaemia, acute coronary syndrome or cardiac-related death within six months. 5131 patients (55% male) participated with a median age of 65 years (IQR 57 – 74). 72.9% of studies used dobutamine and 68.5% were contrast studies. Inducible ischaemia was present in 19.3% of scans. Sensitivity and specificity for prediction of a cardiac outcome were 95.4% and 96.0%, respectively, with an accuracy of 95.9%. Sub-group analysis revealed high levels of predictive accuracy across a wide range of patient and protocol sub-groups, with the presence of a resting regional wall motion abnormalitiy significantly reducing the performance of both dobutamine (p<0.01) and exercise (p<0.05) stress echocardiography (p<0.05). Overall accuracy remained consistently high across all participating hospitals. Conclusion – Stress echocardiography has high accuracy across UK-based hospitals and thus indicates stress echocardiography is being delivered effectively in real-world practice, reinforcing its role as a first-line investigation in the assessment of patients with stable chest pain

Interplay of Structural Disorder and Short Binding Elements in the Cellular Chaperone Function of Plant Dehydrin ERD14.

Details of the functional mechanisms of intrinsically disordered proteins (IDPs) in living cells is an area not frequently investigated. Here, we dissect the molecular mechanism of action of an IDP in cells by detailed structural analyses based on an in-cell nuclear magnetic resonance experiment. We show that the ID stress protein (IDSP) A. thaliana Early Response to Dehydration (ERD14) is capable of protecting E. coli cells under heat stress. The overexpression of ERD14 increases the viability of E. coli cells from 38.9% to 73.9% following heat stress (50 °C × 15 min). We also provide evidence that the protection is mainly achieved by protecting the proteome of the cells. In-cell NMR experiments performed in E. coli cells show that the protective activity is associated with a largely disordered structural state with conserved, short sequence motifs (K- and H-segments), which transiently sample helical conformations in vitro and engage in partner binding in vivo. Other regions of the protein, such as its S segment and its regions linking and flanking the binding motifs, remain unbound and disordered in the cell. Our data suggest that the cellular function of ERD14 is compatible with its residual structural disorder in vivo

Les Houches 2013: Physics at TeV Colliders: Standard Model Working Group Report

This Report summarizes the proceedings of the 2013 Les Houches workshop on Physics at TeV Colliders. Session 1 dealt primarily with (1) the techniques for calculating standard model multi-leg NLO and NNLO QCD and NLO EW cross sections and (2) the comparison of those cross sections with LHC data from Run 1, and projections for future measurements in Run 2.Comment: Proceedings of the Standard Model Working Group of the 2013 Les Houches Workshop, Physics at TeV Colliders, Les houches 3-21 June 2013. 200 page

Top Partner Discovery in the T→tZT\to tZ channel at the LHC

In this paper we study the discovery potential of the LHC run II for heavy vector-like top quarks in the decay channel to a top and a $Z$ boson. Despite the usually smaller branching ratio compared to charged-current decays, this channel is rather clean and allows for a complete mass reconstruction of the heavy top. The latter is achieved in the leptonic decay channel of the $Z$ boson and in the fully hadronic top channel using boosted jet and jet substructure techniques. To be as model-independent as possible, a simplified model approach with only two free parameters has been applied. The results are presented in terms of parameter space regions for $3\sigma$ evidence or $5\sigma$ discovery for such new states in that channel.Comment: 24 pages, 8 figures, version 2 updated to JHEP 01 (2015) 08

Critical Role of Astrocytic Polyamine and GABA Metabolism in Epileptogenesis

Accumulating evidence indicate that astrocytes are essential players of the excitatory and inhibitory signaling during normal and epileptiform activity via uptake and release of gliotransmitters, ions, and other substances. Polyamines can be regarded as gliotransmitters since they are almost exclusively stored in astrocytes and can be released by various mechanisms. The polyamine putrescine (PUT) is utilized to synthesize GABA, which can also be released from astrocytes and provide tonic inhibition on neurons. The polyamine spermine (SPM), synthesized form PUT through spermidine (SPD), is known to unblock astrocytic Cx43 gap junction channels and therefore facilitate astrocytic synchronization. In addition, SPM released from astrocytes may also modulate neuronal NMDA, AMPA, and kainate receptors. As a consequence, astrocytic polyamines possess the capability to significantly modulate epileptiform activity. In this study, we investigated different steps in polyamine metabolism and coupled GABA release to assess their potential to control seizure generation and maintenance in two different epilepsy models: the low-[Mg(2+)] model of temporal lobe epilepsy in vitro and in the WAG/Rij rat model of absence epilepsy in vivo. We show that SPM is a gliotransmitter that is released from astrocytes and significantly contributes to network excitation. Importantly, we found that inhibition of SPD synthesis completely prevented seizure generation in WAG/Rij rats. We hypothesize that this antiepileptic effect is attributed to the subsequent enhancement of PUT to GABA conversion in astrocytes, leading to GABA release through GAT-2/3 transporters. This interpretation is supported by the observation that antiepileptic potential of the Food and Drug Administration (FDA)-approved drug levetiracetam can be diminished by specifically blocking astrocytic GAT-2/3 with SNAP-5114, suggesting that levetiracetam exerts its effect by increasing surface expression of GAT-2/3. Our findings conclusively suggest that the major pathway through which astrocytic polyamines contribute to epileptiform activity is the production of GABA. Modulation of astrocytic polyamine levels, therefore, may serve for a more effective antiepileptic drug development in the future

Left ventricular assessment with artificial intelligence increases the diagnostic accuracy of stress echocardiography

Aims: To evaluate whether left ventricular ejection fraction (LVEF) and global longitudinal strain (GLS), automatically calculated by artificial intelligence (AI), increases the diagnostic performance of stress echocardiography (SE) for coronary artery disease (CAD) detection. Methods and results SEs from 512 participants who underwent a clinically indicated SE (with or without contrast) for the evaluation of CAD from seven hospitals in the UK and US were studied. Visual wall motion scoring (WMS) was performed to identify inducible ischaemia. In addition, SE images at rest and stress underwent AI contouring for automated calculation of AI-LVEF and AI-GLS (apical two and four chamber images only) with Ultromics EchoGo Core 1.0. Receiver operator characteristic curves and multivariable risk models were used to assess accuracy for identification of participants subsequently found to have CAD on angiography. Participants with significant CAD were more likely to have abnormal WMS, AI-LVEF, and AI-GLS values at rest and stress (all P &amp;lt; 0.001). The areas under the receiver operating characteristics for WMS index, AI-LVEF, and AI-GLS at peak stress were 0.92, 0.86, and 0.82, respectively, with cut-offs of 1.12, 64%, and −17.2%, respectively. Multivariable analysis demonstrated that addition of peak AI-LVEF or peak AI-GLS to WMS significantly improved model discrimination of CAD [C-statistic (bootstrapping 2.5th, 97.5th percentile)] from 0.78 (0.69–0.87) to 0.83 (0.74–0.91) or 0.84 (0.75–0.92), respectively. Conclusion AI calculation of LVEF and GLS by contouring of contrast-enhanced and unenhanced SEs at rest and stress is feasible and independently improves the identification of obstructive CAD beyond conventional WMSI