Modeling DNA Structure, Elasticity and Deformations at the Base-pair Level

We present a generic model for DNA at the base-pair level. We use a variant of the Gay-Berne potential to represent the stacking energy between neighboring base-pairs. The sugar-phosphate backbones are taken into account by semi-rigid harmonic springs with a non-zero spring length. The competition of these two interactions and the introduction of a simple geometrical constraint leads to a stacked right-handed B-DNA-like conformation. The mapping of the presented model to the Marko-Siggia and the Stack-of-Plates model enables us to optimize the free model parameters so as to reproduce the experimentally known observables such as persistence lengths, mean and mean squared base-pair step parameters. For the optimized model parameters we measured the critical force where the transition from B- to S-DNA occurs to be approximately $140{pN}$. We observe an overstretched S-DNA conformation with highly inclined bases that partially preserves the stacking of successive base-pairs.Comment: 15 pages, 25 figures. submitted to PR

Planar and Poly-Arc Lombardi Drawings

In Lombardi drawings of graphs, edges are represented as circular arcs, and the edges incident on vertices have perfect angular resolution. However, not every graph has a Lombardi drawing, and not every planar graph has a planar Lombardi drawing. We introduce k-Lombardi drawings, in which each edge may be drawn with k circular arcs, noting that every graph has a smooth 2-Lombardi drawing. We show that every planar graph has a smooth planar 3-Lombardi drawing and further investigate topics connecting planarity and Lombardi drawings.Comment: Expanded version of paper appearing in the 19th International Symposium on Graph Drawing (GD 2011). 16 pages, 8 figure

Risk profiles and one-year outcomes of patients with newly diagnosed atrial fibrillation in India: Insights from the GARFIELD-AF Registry.

BACKGROUND: The Global Anticoagulant Registry in the FIELD-Atrial Fibrillation (GARFIELD-AF) is an ongoing prospective noninterventional registry, which is providing important information on the baseline characteristics, treatment patterns, and 1-year outcomes in patients with newly diagnosed non-valvular atrial fibrillation (NVAF). This report describes data from Indian patients recruited in this registry. METHODS AND RESULTS: A total of 52,014 patients with newly diagnosed AF were enrolled globally; of these, 1388 patients were recruited from 26 sites within India (2012-2016). In India, the mean age was 65.8 years at diagnosis of NVAF. Hypertension was the most prevalent risk factor for AF, present in 68.5% of patients from India and in 76.3% of patients globally (P < 0.001). Diabetes and coronary artery disease (CAD) were prevalent in 36.2% and 28.1% of patients as compared with global prevalence of 22.2% and 21.6%, respectively (P < 0.001 for both). Antiplatelet therapy was the most common antithrombotic treatment in India. With increasing stroke risk, however, patients were more likely to receive oral anticoagulant therapy [mainly vitamin K antagonist (VKA)], but average international normalized ratio (INR) was lower among Indian patients [median INR value 1.6 (interquartile range {IQR}: 1.3-2.3) versus 2.3 (IQR 1.8-2.8) (P < 0.001)]. Compared with other countries, patients from India had markedly higher rates of all-cause mortality [7.68 per 100 person-years (95% confidence interval 6.32-9.35) vs 4.34 (4.16-4.53), P < 0.0001], while rates of stroke/systemic embolism and major bleeding were lower after 1 year of follow-up. CONCLUSION: Compared to previously published registries from India, the GARFIELD-AF registry describes clinical profiles and outcomes in Indian patients with AF of a different etiology. The registry data show that compared to the rest of the world, Indian AF patients are younger in age and have more diabetes and CAD. Patients with a higher stroke risk are more likely to receive anticoagulation therapy with VKA but are underdosed compared with the global average in the GARFIELD-AF. CLINICAL TRIAL REGISTRATION-URL: http://www.clinicaltrials.gov. Unique identifier: NCT01090362

The ultrasonic ranging and data system for radiological surveys in the UMTRA (Uranium Mill Tailings Remedial Action) Project

The Ultrasonic Ranging and Data System (USRADS) was developed to allow radiation exposure data and positional information to be collected, stored and analyzed in a more efficient manner than currently employed on the (Uranium Mill Tailings Remedial Action (UMTRA) project. USRADS is a portable unit which employs ultrasonics, radio frequency transmissions, and a personal computer. Operational experience indicates that the system results in increased information about the property with decreased data analysis and transcription effort and only slightly more field effort. 5 refs., 3 figs., 2 tabs

The influence of peak shock stress on the high pressure phase transformation in zirconium

At high pressures zirconium is known to undergo a phase transformation from the hexagonal close packed (HCP) alpha phase to the simple hexagonal omega phase. Under conditions of shock loading, the high-pressure omega phase is retained upon release. However, the hysteresis in this transformation is not well represented by equilibrium phase diagrams and currently models that accurately represent such a solid-solid phase transformation coupled with the multi-phase plasticity likely under shock conditions do not exist. For this reason, the influence of peak shock stress on the retention of omega phase in Zr is explored in this study. In-situ VISAR measurements along with post-mortem metallographic and neutron diffraction characterization of soft recovered specimens have been utilized to quantify the volume fraction of retained omega phase, morphology of the shocked alpha and omega phases, and qualitatively understand the kinetics of this transformation. This understanding of the role of peak shock stress will be utilized to address physics to be encoded in our present macro-scale models

The influence of peak shock stress on the high pressure phase transformation in zirconium

At high pressures zirconium is known to undergo a phase transformation from the hexagonal close packed (HCP) alpha phase to the simple hexagonal omega phase. Under conditions of shock loading, the high-pressure omega phase is retained upon release. However, the hysteresis in this transformation is not well represented by equilibrium phase diagrams and currently models that accurately represent such a solid-solid phase transformation coupled with the multi-phase plasticity likely under shock conditions do not exist. For this reason, the influence of peak shock stress on the retention of omega phase in Zr is explored in this study. In-situ VISAR measurements along with post-mortem metallographic and neutron diffraction characterization of soft recovered specimens have been utilized to quantify the volume fraction of retained omega phase, morphology of the shocked alpha and omega phases, and qualitatively understand the kinetics of this transformation. This understanding of the role of peak shock stress will be utilized to address physics to be encoded in our present macro-scale models

Force-directed Lombardi-style graph drawing

A Lombardi drawing of a graph is defined as one in which vertices are represented as points, edges are represented as circular arcs between their endpoints, and every vertex has perfect angular resolution (angles between consecutive edges, as measured by the tangents to the circular arcs at the vertex, all have the same degree). We describe two algorithms that create “Lombardi-style” drawings (which we also call near-Lombardi drawings), in which all edges are still circular arcs, but some vertices may not have perfect angular resolution. Both of these algorithms take a force-directed, spring-embedding approach, with one using forces at edge tangents to produce curved edges and the other using dummy vertices on edges for this purpose. As we show, these approaches both produce near-Lombardi drawings, with one being slightly better at achieving near-perfect angular resolution and the other being slightly better at balancing vertex placements

Efeito da seleção para peso pós-desmama sobre indicadores da eficiência produtiva de vacas da raça Nelore Effects of selection for post weaning weight on Nellore cow productivity efficiency indicators

O objetivo deste estudo foi avaliar indicadores da eficiência produtiva de vacas Nelore selecionadas para peso pós-desmama, enfocados nas relações peso bezerro e peso da vaca, nos rebanhos controle (NeC), não-selecionados para peso pós-desmama, seleção (NeS) e tradicional (NeT). As análises envolveram 3929 e 3906 pesos dos bezerros aos 120 (P120) e 210 (P210) dias de idade, respectivamente. Os pesos das vacas àquelas idades também foram considerados, obtendo-se 3824 (PV120) e 3777 (PV210) registros, respectivamente, para 120 e 210 dias. A análise incluiu 183, 375 e 554 vacas dos rebanhos NeC, NeS e NeT, respectivamente. Para as análises utilizou-se o procedimento GLM/SAS, em modelos que incluíram os efeitos fixos de rebanho, ano e mês de nascimento, sexo do bezerro, idade da vaca ao parto e as interações rebanho x ano de nascimento e ano x mês de nascimento. Todos os efeitos foram significativos. Os resultados mostraram respostas correlacionadas positivas na seleção para peso pós-desmama nos pesos dos bezerros e, em menor magnitude, no peso das vacas. As relações peso bezerro e peso da vaca apresentaram valores médios ajustados de 249,0±2,1; 253,7±1,6; e 255,8±1,2 g/kg para R120 e 362,9±2,8; 368,5±2,1; e 374,6±1,7 para NeC, NeS e NeT em R210, respectivamente, indicando que, nas duas idades, os rebanhos NeS e NeT produziram mais quilogramas de bezerro por quilogramas de vaca, quando comparados ao NeC.<br>The objective of this study was to evaluate the productivity efficiency indicators of cows selected for post-weaning weight, with emphasis in the calf-cow weight ratios, in a controlled herd (NeC), unselected for post-weaning weight, selection (NeS) and conventional (NeT). The analysis involved 3929 and 3906 calves weights at the 120 (P120) and 210 (P210) days of age, respectively. The cow weights at those ages were also considered, and the recorded numbers were 3824 (PV120) and 3777 (PV210), respectively, for 120 and 210 days. The analysis included 183, 375 and 554 cows from NeC, NeS and NeT, respectively. The SAS/GLM procedure was used in the data analyses. The model included the effects of herd, year and month of birth, and sex of calf, age of cow at calving, and the interactions herd x year, and year x month of birth. All effects were significant. The results showed a positive correlated response in the selection for post weaning on the calf weights and, low response, on cow weights. The calf weight/cow weight ratios showed average adjusted values of 249.0±2.1, 253.7±1.6 and 255.8±1.2 g/kg for R120, and 362.9±2.8, 368.5±2.1 and 374.6±1.7 g/kg for NeC, NeS and NeT at R210, respectively, and indicated that, at both ages, the NeS and NeT herds produced more kg of calf by kg of cow when compared to NeC