Permutationally Invariant Polynomial Potential Energy Surfaces for Tropolone and H and D atom Tunneling Dynamics

We report permutationally invariant polynomial (PIP) fits to energies and gradients for 15-atom tropolone. These include standard, augmented, and fragmented PIP bases. Approximately 6600 energies and associated gradients are obtained from direct-dynamics calculations using DFT/B3LYP/6-31+G(d) supplemented by grid calculations spanning an energy range up to roughly 35 000 cm-1. Three fragmentation schemes are investigated with respect to efficiency and fit precision. In addition several fits are done with reduced weight for gradient data relative to energies. These do result in more precision for the H-transfer barrier height. Properties of the fits such as stationary points, harmonic frequencies and the barrier to H-atom transfer are reported and compared to direct calculations. A 1-d model to obtain the tunneling splitting for the ground vibrational state and qualitative predictions for excited vibrational states is employed. Several 1-d double well fits to the PES are developed and used to extrapolate H and D atom tunneling splittings to values at the CCSD(T)-F12 barrier. The level of agreement is within expectations for the method adapted and the level of the electronic structure theory employed

Some recent advances in nanomechanical testing: High strain rates, variable temperatures, fatigue and stress relaxation, combinatorial experimentation

In the first part of the talk, I will present two recently developed platforms for high temperature nanomechanical testing. The first platform allows for variable temperature and variable strain rate testing of micropillars in situ in the scanning electron microscope. By utilizing an intrinsically displacement-controlled micro-compression setup, which applies displacement using a miniaturized piezo-actuator, we’ve recently extended the attainable range of strain rates to up to~ 103 s−1, and enabled cyclic loading up to 107 cycles and load relaxation tests. Stable, variable temperature indentation/micro-compression in the range of -45°C to 600°C is achieved through independent heating and temperature monitoring of both the indenter tip and sample and by cooling the instrument frame. A second system allows for measurements at lower loads ex-situ in a dedicated vacuum chamber in the range of -150 °C to 700 °C. The cryo temperature is achieved by means of a liquid nitrogen line, while the high temperature is generated by three independent heat sources for the sample and the two tips of the differential displacement measurement system, establishing an infrared bath in the measurement area. In the second part several case studies will be presented. Using these new capabilities, we examine the plasticity of electrodeposited nanocrystalline Nickel, of combinatorial thin film libraries, of hard nanocrystalline ceramic thin films. Activation parameters such as activation volume and activation energy were determined and discussed in view of the most probable deformation mechanism. High strain rates and cyclic fatigue tests were performed on nanocrystalline Ni. The strain rate sensitivity seems to increase for strain rates higher than 10 s-1 suggesting a change in deformation mechanism with increasing strain rate. Cyclic fatigue tests up to 1 million cycles were performed on nanocrystalline Ni microbeams and compared with existing data from literature. Combinatorial libraries of bulk metallic glasses were synthesized by a combination of gradient sputtering and evaporation. Hardness and Young’s modulus was mapped as a function of temperate, strain rate and composition. The results are discussed in the light of shear band kinetics. Finally, a wide range of chromium nitride-based hard coatings was investigated using in situ micro-cantilever bending and compression testing. This allowed the first direct measurement of the high temperature compressive strength and fracture toughness

The General Solution of Bianchi Type VIIhVII_h Vacuum Cosmology

The theory of symmetries of systems of coupled, ordinary differential equations (ODE) is used to develop a concise algorithm in order to obtain the entire space of solutions to vacuum Bianchi Einstein Field Equations (EFEs). The symmetries used are the well known automorphisms of the Lie algebra for the corresponding isometry group of each Bianchi Type, as well as the scaling and the time re-parametrization symmetry. The application of the method to Type VII_h results in (a) obtaining the general solution of Type VII_0 with the aid of the third Painlev\'{e} transcendental (b) obtaining the general solution of Type $VII_h$ with the aid of the sixth Painlev\'{e} transcendental (c) the recovery of all known solutions (six in total) without a prior assumption of any extra symmetry (d) The discovery of a new solution (the line element given in closed form) with a G_3 isometry group acting on T_3, i.e. on time-like hyper-surfaces, along with the emergence of the line element describing the flat vacuum Type VII_0 Bianchi Cosmology.Comment: latex2e source file, 27 pages, 2 tables, no fiure

Manifesto of computational social science

The increasing integration of technology into our lives has created unprecedented volumes of data on society's everyday behaviour. Such data opens up exciting new opportunities to work towards a quantitative understanding of our complex social systems, within the realms of a new discipline known as Computational Social Science. Against a background of financial crises, riots and international epidemics, the urgent need for a greater comprehension of the complexity of our interconnected global society and an ability to apply such insights in policy decisions is clear. This manifesto outlines the objectives of this new scientific direction, considering the challenges involved in it, and the extensive impact on science, technology and society that the success of this endeavour is likely to bring about.The publication of this work was partially supported by the European Union’s Seventh Framework Programme (FP7/2007–2013) under grant agreement No. 284709, a Coordination and Support Action in the Information and Communication Technologies activity area (‘FuturICT’ FET Flagship Pilot Project). We are grateful to the anonymous reviewers for the insightful comments.Publicad

A dynamic folded hairpin conformation is associated with α-globin activation in erythroid cells

We investigate the three-dimensional (3D) conformations of the α-globin locus at the single-allele level in murine embryonic stem cells (ESCs) and erythroid cells, combining polymer physics models and high-resolution Capture-C data. Model predictions are validated against independent fluorescence in situ hybridization (FISH) data measuring pairwise distances, and Tri-C data identifying three-way contacts. The architecture is rearranged during the transition from ESCs to erythroid cells, associated with the activation of the globin genes. We find that in ESCs, the spatial organization conforms to a highly intermingled 3D structure involving non-specific contacts, whereas in erythroid cells the α-globin genes and their enhancers form a self-contained domain, arranged in a folded hairpin conformation, separated from intermingling flanking regions by a thermodynamic mechanism of micro-phase separation. The flanking regions are rich in convergent CTCF sites, which only marginally participate in the erythroid-specific gene-enhancer contacts, suggesting that beyond the interaction of CTCF sites, multiple molecular mechanisms cooperate to form an interacting domain

A multivariable prognostic score to guide systemic therapy in early-stage HER2-positive breast cancer: a retrospective study with an external evaluation

Background: In early-stage HER2-positive breast cancer, escalation or de-escalation of systemic therapy is a controversial topic. As an aid to treatment decisions, we aimed to develop a prognostic assay that integrates multiple data types for predicting survival outcome in patients with newly diagnosed HER2-positive breast cancer. Methods: We derived a combined prognostic model using retrospective clinical–pathological data on stromal tumour-infiltrating lymphocytes, PAM50 subtypes, and expression of 55 genes obtained from patients who participated in the Short-HER phase 3 trial. The trial enrolled patients with newly diagnosed, node-positive, HER2-positive breast cancer or, if node negative, with at least one risk factor (ie, tumour size >2 cm, histological grade 3, lymphovascular invasion, Ki67 >20%, age ≤35 years, or hormone receptor negativity), and randomly assigned them to adjuvant anthracycline plus taxane-based combinations with either 9 weeks or 1 year of trastuzumab. Trastuzumab was administered intravenously every 3 weeks (8 mg/kg loading dose at first cycle, and 6 mg/kg thereafter) for 18 doses or weekly (4 mg/kg loading dose in the first week, and 2 mg/kg thereafter) for 9 weeks, starting concomitantly with the first taxane dose. Median follow-up was 91·4 months (IQR 75·1–105·6). The primary objective of our study was to derive and evaluate a combined prognostic score associated with distant metastasis-free survival (the time between randomisation and distant recurrence or death before recurrence), an exploratory endpoint in Short-HER. Patient samples in the training dataset were split into a training set (n=290) and a testing set (n=145), balancing for event and treatment group. The training set was further stratified into 100 iterations of Monte-Carlo cross validation (MCCV). Cox proportional hazard models were fit to MCCV training samples using Elastic-Net. A maximum of 92 features were assessed. The final prognostic model was evaluated in an independent combined dataset of 267 patients with early-stage HER2-positive breast cancer treated with different neoadjuvant and adjuvant anti-HER2-based combinations and from four other studies (PAMELA, CHER-LOB, Hospital Clinic, and Padova) with disease-free survival outcome data. Findings: From Short-HER, data from 435 (35%) of 1254 patients for tumour size (T1 vs rest), nodal status (N0 vs rest), number of tumour-infiltrating lymphocytes (continuous variable), subtype (HER2-enriched and basal-like vs rest), and 13 genes composed the final model (named HER2DX). HER2DX was significantly associated with distant metastasis-free survival as a continuous variable (p<0·0001). HER2DX median score for quartiles 1–2 was identified as the cutoff to identify low-risk patients; and the score that distinguished quartile 3 from quartile 4 was the cutoff to distinguish medium-risk and high-risk populations. The 5-year distant metastasis-free survival of the low-risk, medium-risk, and high-risk populations were 98·1% (95% CI 96·3–99·9), 88·9% (83·2–95·0), and 73·9% (66·0–82·7), respectively (low-risk vs high-risk hazard ratio [HR] 0·04, 95% CI 0·0–0·1, p<0·0001). In the evaluation cohort, HER2DX was significantly associated with disease-free survival as a continuous variable (HR 2·77, 95% CI 1·4–5·6, p=0·0040) and as group categories (low-risk vs high-risk HR 0·27, 0·1–0·7, p=0·005). 5-year disease-free survival in the HER2DX low-risk group was 93·5% (89·0–98·3%) and in the high-risk group was 81·1% (71·5–92·1). Interpretation: The HER2DX combined prognostic score identifies patients with early-stage, HER2-positive breast cancer who might be candidates for escalated or de-escalated systemic treatment. Future clinical validation of HER2DX seems warranted to establish its use in different scenarios, especially in the neoadjuvant setting. Funding: Instituto Salud Carlos III, Save the Mama, Pas a Pas, Fundación Científica, Asociación Española Contra el Cáncer, Fundación SEOM, National Institutes of Health, Agenzia Italiana del Farmaco, International Agency for Research on Cancer, and the Veneto Institute of Oncology, and Italian Association for Cancer Research

Management and outcomes of patients with left atrial appendage thrombus prior to percutaneous closure

Altres ajuts: Fundación Interhospitalaria para la Investigación Cardiovascular (FIC Foundation); Abbott.Objective: Left atrial appendage (LAA) thrombus has heretofore been considered a contraindication to percutaneous LAA closure (LAAC). Data regarding its management are very limited. The aim of this study was to analyse the medical and invasive treatment of patients referred for LAAC in the presence of LAA thrombus. Methods: This multicentre observational registry included 126 consecutive patients referred for LAAC with LAA thrombus on preprocedural imaging. Treatment strategies included intensification of antithrombotic therapy (IAT) or direct LAAC. The primary and secondary endpoints were a composite of bleeding, stroke and death at 18 months, and procedural success, respectively. Results: IAT was the preferred strategy in 57.9% of patients, with total thrombus resolution observed in 60.3% and 75.3% after initial and subsequent IAT, respectively. Bleeding complications and stroke during IAT occurred in 9.6% and 2.9%, respectively, compared with 3.8% bleeding and no embolic events in the direct LAAC group before the procedure. Procedural success was 90.5% (96.2% vs 86.3% in direct LAAC and IAT group, respectively, p=0.072), without cases of in-hospital thromboembolic complications. The primary endpoint occurred in 29.3% and device-related thrombosis was found in 12.8%, without significant difference according to treatment strategy. Bleeding complications at 18 months occurred in 22.5% vs 10.5% in the IAT and direct LAAC group, respectively (p=0.102). Conclusion: In the presence of LAA thrombus, IAT was the initial management strategy in half of our cohort, with initial thrombus resolution in 60% of these, but with a relatively high bleeding rate (∼10%). Direct LAAC was feasible, with high procedural success and absence of periprocedural embolic complications. However, a high rate of device-related thrombosis was detected during follow-up

Machine Learning Framework to Identify Individuals at Risk of Rapid Progression of Coronary Atherosclerosis : From the PARADIGM Registry

Background Rapid coronary plaque progression (RPP) is associated with incident cardiovascular events. To date, no method exists for the identification of individuals at risk of RPP at a single point in time. This study integrated coronary computed tomography angiography-determined qualitative and quantitative plaque features within a machine learning (ML) framework to determine its performance for predicting RPP. Methods and Results Qualitative and quantitative coronary computed tomography angiography plaque characterization was performed in 1083 patients who underwent serial coronary computed tomography angiography from the PARADIGM (Progression of Atherosclerotic Plaque Determined by Computed Tomographic Angiography Imaging) registry. RPP was defined as an annual progression of percentage atheroma volume 651.0%. We employed the following ML models: model 1, clinical variables; model 2, model 1 plus qualitative plaque features; model 3, model 2 plus quantitative plaque features. ML models were compared with the atherosclerotic cardiovascular disease risk score, Duke coronary artery disease score, and a logistic regression statistical model. 224 patients (21%) were identified as RPP. Feature selection in ML identifies that quantitative computed tomography variables were higher-ranking features, followed by qualitative computed tomography variables and clinical/laboratory variables. ML model 3 exhibited the highest discriminatory performance to identify individuals who would experience RPP when compared with atherosclerotic cardiovascular disease risk score, the other ML models, and the statistical model (area under the receiver operating characteristic curve in ML model 3, 0.83 [95% CI 0.78-0.89], versus atherosclerotic cardiovascular disease risk score, 0.60 [0.52-0.67]; Duke coronary artery disease score, 0.74 [0.68-0.79]; ML model 1, 0.62 [0.55-0.69]; ML model 2, 0.73 [0.67-0.80]; all P&lt;0.001; statistical model, 0.81 [0.75-0.87], P=0.128). Conclusions Based on a ML framework, quantitative atherosclerosis characterization has been shown to be the most important feature when compared with clinical, laboratory, and qualitative measures in identifying patients at risk of RPP

Search for the standard model Higgs boson decaying into two photons in pp collisions at sqrt(s)=7 TeV

A search for a Higgs boson decaying into two photons is described. The analysis is performed using a dataset recorded by the CMS experiment at the LHC from pp collisions at a centre-of-mass energy of 7 TeV, which corresponds to an integrated luminosity of 4.8 inverse femtobarns. Limits are set on the cross section of the standard model Higgs boson decaying to two photons. The expected exclusion limit at 95% confidence level is between 1.4 and 2.4 times the standard model cross section in the mass range between 110 and 150 GeV. The analysis of the data excludes, at 95% confidence level, the standard model Higgs boson decaying into two photons in the mass range 128 to 132 GeV. The largest excess of events above the expected standard model background is observed for a Higgs boson mass hypothesis of 124 GeV with a local significance of 3.1 sigma. The global significance of observing an excess with a local significance greater than 3.1 sigma anywhere in the search range 110-150 GeV is estimated to be 1.8 sigma. More data are required to ascertain the origin of this excess.Comment: Submitted to Physics Letters