Ultrafast electron diffraction pattern simulations using GPU technology. Applications to lattice vibrations.

Graphical processing units (GPUs) offer a cost-effective and powerful means to enhance the processing power of computers. Here we show how GPUs can greatly increase the speed of electron diffraction pattern simulations by the implementation of a novel method to generate the phase grating used in multislice calculations. The increase in speed is especially apparent when using large supercell arrays and we illustrate the benefits of fast encoding the transmission function representing the atomic potentials through the simulation of thermal diffuse scattering in silicon brought about by specific vibrational modes.The research leading to these results has received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007–2013)/ERC grant agreement 291522-3DIMAGE and the Seventh Framework Programme of the European Commission: ESTEEM2 (Enabling Science and Technology through European Electron Microscopy), contract number 312483. The work was also supported by the EPSRC through EP/HO17712

A Further Unique Chondroitin Sulfate from the shrimp Litopenaeus vannamei with Antithrombin Activity that Modulates Acute Inflammation

The detailed structure of a further Chondroitin Sulfate from Litopenaeus vannamei shrimp (sCS) is described. The backbone structure was established by 1H/13C NMR, which identified 3-O-sulfated GlcA, 4-O-sulfated GalNAc, 6-O-sulfated GalNAc, and 4,6-di-O-sulfated GalNAc residues. GlcA is linked to GalNAc 4,6 di S and GlcA 3S is linked to GalNAc 4S, GalNAc 4,6 di-S and GalNAc6S residues. The anticoagulant properties of this sCS were evaluated by activated partial thromboplastin time, anti-IIa, anti-Xa and anti-heparin cofactor II-mediated activities, and sCS failed to stabilise antithrombin in a fluoresence shift assay. The anti-inflammatory effect of sCS was explored using a model of acute peritonitis, followed by leukocyte count and measurement of the cytokines, IL-1β, IL-6 and TNF-α. The compound showed low clotting effects, but high anti-IIa activity and HCII-mediated thrombin inhibition. Its anti-inflammatory effect was shown by leukocyte recruitment inhibition and a decrease in pro-inflammatory cytokine levels. Although the biological role of sCS remains unknown, its properties indicate that it is suitable for studies of multi-potent molecules obtained from natural sources

Innovator resilience potential: A process perspective of individual resilience as influenced by innovation project termination

Innovation projects fail at an astonishing rate. Yet, the negative effects of innovation project failures on the team members of these projects have been largely neglected in research streams that deal with innovation project failures. After such setbacks, it is vital to maintain or even strengthen project members’ innovative capabilities for subsequent innovation projects. For this, the concept of resilience, i.e. project members’ potential to positively adjust (or even grow) after a setback such as an innovation project failure, is fundamental. We develop the second-order construct of innovator resilience potential, which consists of six components – self-efficacy, outcome expectancy, optimism, hope, self-esteem, and risk propensity – that are important for project members’ potential of innovative functioning in innovation projects subsequent to a failure. We illustrate our theoretical findings by means of a qualitative study of a terminated large-scale innovation project, and derive implications for research and management

New Physics in Bs -> J/psi phi: a General Analysis

Recently, the CDF and D0 collaborations measured indirect CP violation in Bs -> J/psi phi and found a hint of a signal. If taken at face value, this can be interpreted as a nonzero phase of Bs-Bsbar mixing (beta_s), in disagreement with the standard model, which predicts that beta_s ~= 0. In this paper, we argue that this analysis may be incomplete. In particular, there can be new physics (NP) in the bbar -> sbar c cbar decay. If so, the value of beta_s is different than for the case in which NP is assumed to be present only in the mixing. We have examined several models of NP and found that, indeed, there can be significant contributions to the decay. These effects are consistent with measurements in B -> J/psi K* and Bd -> J/psi Ks. Due to the NP in the decay, polarization-dependent indirect CP asymmetries and triple-product asymmetries are predicted in Bs -> J/psi phi.Comment: 28 pages, JHEP, no figures. Considerable changes made. Abstract and main text of paper modified to alter presentation. Appendix added. References added. Conclusions unchanged

The influence of urban green systems on the Urban Heat Island effect in London

Urban areas are typically warmer than rural ones. This is mainly due to denser configuration dominated by impermeable surfaces such as buildings and roads, compared to rural areas which are less densely built and mainly dominated by open spaces. Rapid urban expansion in dense cities bares direct impact on surface and air temperature patterns within street canyons; a phenomena which is known as the Urban Heat Island (UHI) effect. Thus, several UK city councils such as Birmingham, Manchester, and London have started to develop strategies aiming at enhancing urban green systems (UGS) through trees, green walls and green roofs. Some of those strategies include considering the green space factor, and increasing green areas within the cities to improve street canyon microclimate and reduce UHI. The Mayor of London has adopted a strategy for London 2050 aspiring to transform it to be the greenest city in the world by increasing the green areas up to 50%. This paper investigates the influence of increasing the UGS percentage which is considered as a key solution to mitigate UHI effect which will, in turn, provide thermally comfortable outdoor environments for pedestrians. The investigation is undertaken by comparing the morphology of precincts and streets in relation to air temperature, mean radiant temperature and surface temperature within Oxford Street canyons in London city centre; being one of the world’s busiest streets. The results from this research demonstrate that different UGS interventions with varying percentage are required depending on particular canyon orientations and geometries. The study found that, in general, more trees would have significant thermal comfort effect followed by living façade, while high albedo pavement (HAP) came last. However, HAP had high influence on improving thermal comfort in North-South orientated streets with minor variance to trees and living facades which, changing their percentage levels was insignificant

Serum osteoprotegerin is associated with pulse pressure in kidney transplant recipients

Pulse pressure (PP) reflects increased large artery stiffness, which is caused, in part, by arterial calcification in patients with chronic kidney disease. PP has been shown to predict both cardiovascular and cerebrovascular events in various patient populations, including kidney transplant (KTX) recipients. Osteoprotegerin (OPG) is a marker and regulator of arterial calcification, and it is related to cardiovascular survival in hemodialysis patients. Here we tested the hypothesis that OPG is associated with increased pulse pressure. We cross-sectionally analyzed the association between serum OPG and PP in a prevalent cohort of 969 KTX patients (mean age: 51 +/- 13 years, 57% male, 21% diabetics, mean eGFR 51 +/- 20 ml/min/1.73 m2). Independent associations were tested in a linear regression model adjusted for multiple covariables. PP was positively correlated with serum OPG (rho = 0.284, p < 0.001). Additionally, a positive correlation was seen between PP versus age (r = 0.358, p < 0.001), the Charlson Comorbidity Index (r = 0.232, p < 0.001), serum glucose (r = 0.172, p < 0.001), BMI (r = 0.133, p = 0.001) and serum cholesterol (r = 0.094, p = 0.003). PP was negatively correlated with serum Ca, albumin and eGFR. The association between PP and OPG remained significant after adjusting for multiple potentially relevant covariables (beta = 0.143, p < 0.001). We conclude that serum OPG is independently associated with pulse pressure in kidney transplant recipients

Neutral Gauge Boson Contributions to the Dimuon Charge Asymmetry in B Decays

Recently, the D0 Collaboration measured the CP-violating like-sign dimuon charge asymmetry in neutral B decays, finding a 3.2sigma difference from the standard-model (SM) prediction. A non-SM charge asymmetry a_sl^s suggests a new-physics (NP) contribution to Bs-Bsbar mixing. In this case, in order to explain the measured value of a_sl^s within its 1sigma range, NP must be present in Gamma_12^s, the absorptive part of the mixing. In this paper, we examine whether such an explanation is possible in models with flavor-changing Z (ZFCNC) or Z' (Z'FCNC) gauge bosons. The models must also reproduce the measured values of the indirect CP asymmetry S_psi-phi in Bs -> J/psi phi, and Delta Gamma_s, the Bs-Bsbar width difference. We find that the ZFCNC model cannot reproduce the present measured values of S_psi-phi and a_sl^s within their 1sigma ranges. On the other hand, in the Z'FCNC model, the values of all three observables can be simultaneously reproduced.Comment: 18 pages, 7 figures, JHEP format. Some ZFCNC equations corrected, ZFCNC analysis redone, references added, conclusions unchange

Should Research Ethics Encourage the Production of Cost-Effective Interventions?

This project considers whether and how research ethics can contribute to the provision of cost-effective medical interventions. Clinical research ethics represents an underexplored context for the promotion of cost-effectiveness. In particular, although scholars have recently argued that research on less-expensive, less-effective interventions can be ethical, there has been little or no discussion of whether ethical considerations justify curtailing research on more expensive, more effective interventions. Yet considering cost-effectiveness at the research stage can help ensure that scarce resources such as tissue samples or limited subject popula- tions are employed where they do the most good; can support parallel efforts by providers and insurers to promote cost-effectiveness; and can ensure that research has social value and benefits subjects. I discuss and rebut potential objections to the consideration of cost-effectiveness in research, including the difficulty of predicting effectiveness and cost at the research stage, concerns about limitations in cost-effectiveness analysis, and worries about overly limiting researchers’ freedom. I then consider the advantages and disadvantages of having certain participants in the research enterprise, including IRBs, advisory committees, sponsors, investigators, and subjects, consider cost-effectiveness. The project concludes by qualifiedly endorsing the consideration of cost-effectiveness at the research stage. While incorporating cost-effectiveness considerations into the ethical evaluation of human subjects research will not on its own ensure that the health care system realizes cost-effectiveness goals, doing so nonetheless represents an important part of a broader effort to control rising medical costs

Enriching Peptide Libraries for Binding Affinity and Specificity Through Computationally Directed Library Design

Peptide reagents with high affinity or specificity for their target protein interaction partner are of utility for many important applications. Optimization of peptide binding by screening large libraries is a proven and powerful approach. Libraries designed to be enriched in peptide sequences that are predicted to have desired affinity or specificity characteristics are more likely to yield success than random mutagenesis. We present a library optimization method in which the choice of amino acids to encode at each peptide position can be guided by available experimental data or structure-based predictions. We discuss how to use analysis of predicted library performance to inform rounds of library design. Finally, we include protocols for more complex library design procedures that consider the chemical diversity of the amino acids at each peptide position and optimize a library score based on a user-specified input model.National Institute of General Medical Sciences (U.S.) (Award R01 GM110048

Minimal change in structural, functional and inflammatory markers of lung disease in newborn screened infants with cystic fibrosis at one year

BACKGROUND: With the widespread introduction of newborn screening for cystic fibrosis (CF), there has been considerable emphasis on the need to develop objective markers of lung health that can be used during infancy. We hypothesised that in a newborn screened (NBS) UK cohort, evidence of airway inflammation and infection at one year would be associated with adverse structural and functional outcomes at the same age. METHODS: Infants underwent lung function testing, chest CT scan and bronchoscopy with bronchoalveolar lavage (BAL) at 1 year of age when clinically well. Microbiology cultures were also available from routine cough swabs. RESULTS: 65 infants had lung function, CT and BAL. Mean (SD) lung clearance index and forced expiratory volume in 0.5 s z-scores were 0.9(1.2) and -0.6(1.1) respectively; median Brody II CF-CT air trapping score on chest CT =0 (interquartile range 0-1, maximum possible score 27). Infants isolating any significant pathogen by 1 yr of age had higher LCI z-score (mean difference 0.9; 95%CI:0.4-1.4; p = 0.001) and a trend towards higher air trapping scores on CT (p = 0.06). BAL neutrophil elastase was detectable in 23% (10/43) infants in whom BAL supernatant was available. This did not relate to air trapping score on CT. CONCLUSIONS: In this UK NBS cohort at one year of age, lung and airway damage is much milder and associations between inflammation, abnormal physiology and structural changes were at best weak, contrary to our hypothesis and previously published reports. Continued follow-up will clarify longer term implications of these very mild structural, functional and inflammatory changes