Structures of small Ti- and V-doped Pt clusters : A GA-DFT study

AbstractHigh level GA-DFT searches are performed on small platinum clusters doped with early transition metal atoms, Ptx−yMy (M =Ti, V), where x=2–6, y=1, 2. Spin effects are studied and the global minimum structures are presented for the various spin multiplicities. It is found that varying spin can have significant effects on the pure Pt clusters, while spin has less effect for the doped clusters

Fast phylogeny of SARS-CoV-2 by compression

The compression method to assess similarity, in the sense of having a small normalized compression distance (NCD), was developed based on algorithmic information theory to quantify the similarity in files ranging from words and languages to genomes and music pieces. It has been validated on objects from different domains always using essentially the same software. We analyze the whole-genome phylogeny and taxonomy of the SARS-CoV-2 virus, which is responsible for causing the COVID-19 disease, using the alignment-free compression method to assess similarity. We compare the SARS-CoV-2 virus with a database of over 6500 viruses. The results suggest that the SARS-CoV-2 virus is closest in that database to the RaTG13 virus and rather close to the bat SARS-like coronaviruses bat-SL-CoVZXC21 and bat-SL-CoVZC45. Over 6500 viruses are identified (given by their registration code) with larger NCDs. The NCDs are compared with the NCDs between the mtDNA of familiar species. We address the question of whether pangolins are involved in the SARS-CoV-2 virus. The compression method is simpler and possibly faster than any other whole-genome method, which makes it the ideal tool to explore phylogeny. Here, we use it for the complex case of determining this similarity between the COVID-19 virus, SARS-CoV-2 and many other viruses. The resulting phylogeny and taxonomy closely resemble earlier results from by alignment-based methods and a machine-learning method, providing the most compelling evidence to date for the compression method, showing that one can achieve equivalent results both simply and quickly

A new quartet tree heuristic for hierarchical clustering

We present a new quartet tree heuristic for hierarchical clustering from weighted quartet topologies, and a standard manner to derive those from a given distance matrix. We do not assume that there is a true ternary tree that generated the quartet topologies or distances which we wish to recover as closely as possible. Our aim is to just model the input data as faithfully as possible by the quartet tree. Our method is capable of handling up to 60–80 objects in a matter of hours, while no existing quartet heuristic can directly compute a quartet tree of more than about 20–30 objects without running for years. The method is implemented and available as public software

String and M-theory Deformations of Manifolds with Special Holonomy

The R^4-type corrections to ten and eleven dimensional supergravity required by string and M-theory imply corrections to supersymmetric supergravity compactifications on manifolds of special holonomy, which deform the metric away from the original holonomy. Nevertheless, in many such cases, including Calabi-Yau compactifications of string theory and G_2-compactifications of M-theory, it has been shown that the deformation preserves supersymmetry because of associated corrections to the supersymmetry transformation rules, Here, we consider Spin(7) compactifications in string theory and M-theory, and a class of non-compact SU(5) backgrounds in M-theory. Supersymmetry survives in all these cases too, despite the fact that the original special holonomy is perturbed into general holonomy in each case.Comment: Improved discussion of SU(5) holonomy backgrounds. Other minor typos corrected. Latex with JHEP3.cls, 42 page

Constrained Willmore Surfaces

Constrained Willmore surfaces are conformal immersions of Riemann surfaces that are critical points of the Willmore energy $W=\int H^2$ under compactly supported infinitesimal conformal variations. Examples include all constant mean curvature surfaces in space forms. In this paper we investigate more generally the critical points of arbitrary geometric functionals on the space of immersions under the constraint that the admissible variations infinitesimally preserve the conformal structure. Besides constrained Willmore surfaces we discuss in some detail examples of constrained minimal and volume critical surfaces, the critical points of the area and enclosed volume functional under the conformal constraint.Comment: 17 pages, 8 figures; v2: Hopf tori added as an example, minor changes in presentation, numbering changed; v3: new abstract and appendix, several changes in presentatio

The Dynamic Structure of Thrombin in Solution

AbstractThe backbone dynamics of human α-thrombin inhibited at the active site serine were analyzed using R1, R2, and heteronuclear NOE experiments, variable temperature TROSY 2D [1H-15N] correlation spectra, and Rex measurements. The N-terminus of the heavy chain, which is formed upon zymogen activation and inserts into the protein core, is highly ordered, as is much of the double beta-barrel core. Some of the surface loops, by contrast, remain very dynamic with order parameters as low as 0.5 indicating significant motions on the ps-ns timescale. Regions of the protein that were thought to be dynamic in the zymogen and to become rigid upon activation, in particular the γ-loop, the 180s loop, and the Na+ binding site have order parameters below 0.8. Significant Rex was observed in most of the γ-loop, in regions proximal to the light chain, and in the β-sheet core. Accelerated molecular dynamics simulations yielded a molecular ensemble consistent with measured residual dipolar couplings that revealed dynamic motions up to milliseconds. Several regions, including the light chain and two proximal loops, did not appear highly dynamic on the ps-ns timescale, but had significant motions on slower timescales

Measles virus host invasion and pathogenesis

Measles virus is a highly contagious negative strand RNA virus that is transmitted via the respiratory route and causes systemic disease in previously unexposed humans and non-human primates. Measles is characterised by fever and skin rash and usually associated with cough, coryza and conjunctivitis. A hallmark of measles is the transient immune suppression, leading to increased susceptibility to opportunistic infections. At the same time, the disease is paradoxically associated with induction of a robust virus-specific immune response, resulting in lifelong immunity to measles. Identification of CD150 and nectin-4 as cellular receptors for measles virus has led to new perspectives on tropism and pathogenesis. In vivo studies in non-human primates have shown that the virus initially infects CD150+ lymphocytes and dendritic cells, both in circulation and in lymphoid tissues, followed by virus transmission to nectin-4 expressing epithelial cells. The abilities of the virus to cause systemic infection, to transmit to numerous new hosts via droplets or aerosols and to suppress the host immune response for several months or even years after infection make measles a remarkable disease. This review briefly highlights current topics in studies of measles virus host invasion and pathogenesis

SAFETY OF TRANSRADIAL CARDIAC CATHETERIZATION IN PATIENTS WITH END-STAGE LIVER DISEASE

The current study adopted McAdams’ multilayer framework as the basis to develop a psychological portrait of an elite athlete who was identified as being particularly “mentally tough.” The aim was to use this single case as an exemplar to demonstrate the utility of McAdams’ framework for understanding the complexity of sport performers across three domains of personality: dispositional traits, characteristic adaptations, and narrative identity. We operationalised these domains through the development of specific research questions and, subsequently, the collection and integration of the participant’s Big Five traits, personal strivings, coping strategies, and response to a life story interview. The results offered a comprehensive insight into the nature of one athlete’s personality that, in turn, informed conceptual perspectives of mental toughness in sport psychology literature and qualitatively supported emerging evidence of the validity of a three-layer framework in personality psychology. Specifically, the study’s design showed how a holistic approach to personality analysis can lead to a more complete psychological representation of competitors in sport, and people generally. It demonstrated how motivational, sociocultural, and meaning-making aspects of personality can complement a trait profile to achieving a satisfying assessment of the whole person

Which factors prognosticate rotational instability following lumbar laminectomy?

Purpose: Reduced strength and stiffness of lumbar spinal motion segments following laminectomy may lead to instability. Factors that predict shear biomechanical properties of the lumbar spine were previously published. The purpose of the present study was to predict spinal torsion biomechanical properties with and without laminectomy from a total of 21 imaging parameters. Method: Radiographs and MRI of ten human cadaveric lumbar spines (mean age 75.5, range 59-88 years) were obtained to quantify geometry and degeneration of the motion segments. Additionally, dual X-ray absorptiometry (DXA) scans were performed to measure bone mineral content and density. Facet-sparing lumbar laminectomy was performed either on L2 or L4. Spinal motion segments were dissected (L2-L3 and L4-L5) and tested in torsion, under 1,600 N axial compression. Torsion moment to failure (TMF), early torsion stiffness (ETS, at 20-40 % TMF) and late torsion stiffness (LTS, at 60-80 % TMF) were determined and bivariate correlations with all parameters were established. For dichotomized parameters, independent-sample t tests were used. Results: Univariate analyses showed that a range of geometric characteristics and disc and bone quality parameters were associated with torsion biomechanical properties of lumbar segments. Multivariate models showed that ETS, LTS and TMF could be predicted for segments without laminectomy (