BilKristal 2.0: A tool for pattern information extraction from crystal structures

Cataloged from PDF version of article.We present a revised version of the BilKristal tool of Okuyan et al. (2007). We converted the development environment into Microsoft Visual Studio 2005 in order to resolve compatibility issues. We added multi-core CPU support and improvements are made to graphics functions in order to improve performance. Discovered bugs are fixed and exporting functionality to a material visualization tool is added

Direct volume rendering of unstructured tetrahedral meshes using CUDA and OpenMP

Cataloged from PDF version of article.Direct volume visualization is an important method in many areas, including computational fluid dynamics and medicine. Achieving interactive rates for direct volume rendering of large unstructured volumetric grids is a challenging problem, but parallelizing direct volume rendering algorithms can help achieve this goal. Using Compute Unified Device Architecture (CUDA), we propose a GPU-based volume rendering algorithm that itself is based on a cell projection-based ray-casting algorithm designed for CPU implementations. We also propose a multicore parallelized version of the cell-projection algorithm using OpenMP. In both algorithms, we favor image quality over rendering speed. Our algorithm has a low memory footprint, allowing us to render large datasets. Our algorithm supports progressive rendering. We compared the GPU implementation with the serial and multicore implementations. We observed significant speed-ups that, together with progressive rendering, enables reaching interactive rates for large datasets

A tool for pattern information extraction and defect quantification from crystal structures

In this paper, we present a revised version of BilKristal 2.0 tool. We added defect quantification functionality to assess crystalline defects. We improved visualization capabilities by adding transparency support and runtime visibility sorting. Discovered bugs are fixed and small performance optimizations are made. New version program summary Program title: BilKristal 3.0 Catalogue identifier: ADYU-v3-0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYU-v3-0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 1868 923 No. of bytes in distributed program, including test data, etc.: 8854 507 Distribution format: tar.gz Programming language: C, C++, Microsoft.NET Framework 2.0 and OpenGL Libraries. Computer: Personal Computers with Windows operating system. Operating system: Windows XP or higher. RAM: 20-60 Megabytes. Classification: 8. Catalogue identifier of previous version: ADYU-v2-0 Journal reference of previous version: Comput. Phys. Comm. 185 (2014) 442 External routines: Microsoft.NET Framework 2.0. For the visualization tool, graphics card driver should also support OpenGL. Does the new version supersede the previous version?: Yes Nature of problem: Determining the crystal structure parameters of a material is a very important issue in crystallography. Knowing the crystal structure parameters helps the understanding of the physical behavior of material. For complex structures, particularly for materials which also contain local symmetry as well as global symmetry, obtaining crystal parameters can be very hard. Solution method: The tool extracts crystal parameters such as primitive vectors, basis vectors and identifies the space group from atomic coordinates of crystal structures. Reasons for new version: Additional features, Compatibility issues with newer development environments, Performance optimizations, Minor bug corrections. Summary of revisions:Defect quantification capability is added. The tool can process the imperfect crystal structures, finds and quantifies the crystalline defects. The tool is capable of finding positional defects, vacancy defects, substitutional impurities and interstitial impurities. The algorithms presented in [3] are used for defect quantification implementation.Transparency support is added to the visualization tool. Users are now allowed to set the transparency of each atom type individually.Runtime visibility sorting functionality is added to facilitate correct transparency computations.Visual Studio 2012 support is added. Visual Studio 2012 specific project files are created and the project is tested with this development environment.In visualization tool, an unused log file was created. This issue is corrected.In visualization tool, some OpenGL calls which are executed at every draw are changed to be executed only when they are needed, improving the visualization performance.Restrictions: Assumptions are explained in [1,2]. However, none of them can be considered as a restriction onto the complexity of the problem. Running time: The tool was able to process input files with more than a million atoms in less than 20 s on a PC with an Athlon quad-core CPU at 3.2 GHz using the default parameter values. References: [1] Erhan Okuyan, Ugur Güdükbay, Oguz Gülseren, Pattern information extraction from crystal structures, Comput. Phys. Comm. 176 (2007) 486. [2] Erhan Okuyan, Ugur Güdükbay, BilKristal 2.0: A tool for pattern information extraction from crystal structures, Comput. Phys. Comm. 185 (2014) 442. [3] Erhan Okuyan, Ugur Güdükbay, Ceyhun Bulutay, Karl-Heinz Heinig, MaterialVis: material visualization tool using direct volume and surface rendering techniques, J. Mol. Graphics Model. 50201450-60. © 2014 The Authors

BilKristal 4.0: A tool for crystal parameters extraction and defect quantification

In this paper, we present a revised version of BilKristal 3.0 tool. Raycast screenshot functionality is added to provide improved visual analysis. We added atomic distance analysis functionality to assess crystalline defects. We improved visualization capabilities by adding high level cut function definitions. Discovered bugs are fixed and small performance optimizations are made. © 2015 Elsevier B.V. All rights reserved

MaterialVis: Material visualization tool using direct volume and surface rendering techniques

Cataloged from PDF version of article.Visualization of the materials is an indispensable part of their structural analysis. We developed a visualization tool for amorphous as well as crystalline structures, called Material Vis. Unlike the existing tools, Material Vis represents material structures as a volume and a surface manifold, in addition to plain atomic coordinates. Both amorphous and crystalline structures exhibit topological features as well as various defects. Material Vis provides a wide range of functionality to visualize such topological structures and crystal defects interactively. Direct volume rendering techniques are used to visualize the volumetric features of materials, such as crystal defects, which are responsible for the distinct fingerprints of a specific sample. In addition, the tool provides surface visualization to extract hidden topological features within the material. Together with the rich set of parameters and options to control the visualization, Material Vis allows users to visualize various aspects of materials very efficiently as generated by modern analytical techniques such as the Atom Probe Tomography. (C) 2014 Elsevier Inc. All rights reserved

Pattern information extraction from crystal structures

Determining the crystal structure parameters of a material is an important issue in crystallography and material science. Knowing the crystal structure parameters helps in understanding the physical behavior of material. It can be difficult to obtain crystal parameters for complex structures, particularly those materials that show local symmetry as well as global symmetry. This work provides a tool that extracts crystal parameters such as primitive vectors, basis vectors and space groups from the atomic coordinates of crystal structures. A visualization tool for examining crystals is also provided. Accordingly, this work could help crystallographers, chemists and material scientists to analyze crystal structures efficiently. Program summary: Title of program: BilKristal. Catalogue identifier: ADYU_v1_0. Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADYU_v1_0. Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland. Licensing provisions: None. Programming language used: C, C++, Microsoft .NET Framework 1.1 and OpenGL Libraries. Computer: Personal Computers with Windows operating system. Operating system: Windows XP Professional. RAM: 20-60 MB. No. of lines in distributed program, including test data, etc.:899 779. No. of bytes in distributed program, including test date, etc.:9 271 521. Distribution format:tar.gz. External routines/libraries: Microsoft .NET Framework 1.1. For visualization tool, graphics card driver should also support OpenGL. Nature of problem: Determining crystal structure parameters of a material is a quite important issue in crystallography. Knowing the crystal structure parameters helps to understand physical behavior of material. For complex structures, particularly, for materials which also contain local symmetry as well as global symmetry, obtaining crystal parameters can be quite hard. Solution method: The tool extracts crystal parameters such as primitive vectors, basis vectors and identify the space group from atomic coordinates of crystal structures. Restrictions: Assumptions are explained in the paper. However, none of them can be considered as a restriction onto the complexity of the problem. Running time: All the examples presented in the paper take less than 30 seconds on a 2.4 GHz Pentium 4 computer. © 2007 Elsevier B.V. All rights reserved

Dynamic view-dependent visualization of unstructured tetrahedral volumetric meshes

Visualization of large volumetric datasets has always been an important problem. Due to the high computational requirements of volume-rendering techniques, achieving interactive rates is a real challenge. We present a selective refinement scheme that dynamically refines the mesh according to the camera parameters. This scheme automatically determines the impact of different parts of the mesh on the output image and refines the mesh accordingly, without needing any user input. The view-dependent refinement scheme uses a progressive mesh representation that is based on an edge collapse-based tetrahedral mesh simplification algorithm. We tested our view-dependent refinement framework on an existing state-of-theart volume renderer. Thanks to low overhead dynamic view-dependent refinement, we achieve interactive frame rates for rendering common datasets at decent image resolutions. © 2012 The Visualization Society of Japan

How to write a successful grant application: guidance provided by the European Society of Clinical Pharmacy.

Considering a rejection rate of 80–90%, the preparation of a research grant is often considered a daunting task since it is resource intensive and there is no guarantee of success, even for seasoned researchers. This commentary provides a summary of the key points a researcher needs to consider when writing a research grant proposal, outlining: (1) how to conceptualise the research idea; (2) how to find the right funding call; (3) the importance of planning; (4) how to write; (5) what to write, and (6) key questions for reflection during preparation. It attempts to explain the difficulties associated with finding calls in clinical pharmacy and advanced pharmacy practice, and how to overcome them. The commentary aims to assist all pharmacy practice and health services research colleagues new to the grant application process, as well as experienced researchers striving to improve their grant review scores. The guidance in this paper is part of ESCP’s commitment to stimulate "innovative and high-quality research in all areas of clinical pharmacy"

Prevalence of Subclinical Hypothyroidism among Patients with Acute Myocardial Infarction

Introduction. Subclinical hypothyroidism (SCH) is defined as a serum thyroid-stimulating hormone (TSH) level above the upper limit of normal despite normal levels of serum free thyroxine. There is growing evidence that SCH is associated with increased cardiovascular risk. We tried to investigate prevalence of SCH in acute myocardial infarction patients. Methods and Results. We evaluate free T3, free T4, and TSH levels of 604 patients (age 58.4) retrospectively, who have been admitted to the coronary intensive care unit between years 2004–2009 with the diagnosis of ST elevation (STEMI) or non-ST elevation acute myocardial infarction (NSTEMI). Mild subclinical hypothyroidism (TSH 4.5 to 9.9 mU/l) was present in 54 (8.94%) participants and severe subclinical hypothyroidism (TSH 10.0 to 19.9 mU/l) in 11 (1.82%). So 65 patients (10.76%) had TSH levels between 4.5 and 20. Conclusions. In conclusion, 65 patients (10.76%) had TSH levels between 4.5 and 20 in our study, and it is a considerable amount. Large-scale studies are needed to clarify the effects of SCH on myocardial infarction both on etiologic and prognostic grounds

Scope, content and quality of clinical pharmacy practice guidelines:a systematic review

Background Guidelines for pharmacy practitioners regarding various clinical pharmacy activities have been published ina number of countries. There is a need to review the guidelines and identify the scope of activities covered as a prelude todeveloping internationally acceptable common guidelines.Aim To review the scope of clinical pharmacy guidelines and assess the extent to which these guidelines conform to qualitystandards as per the AGREE II instrument.Method Medline, Embase, Guideline Central, International Pharmaceutical Abstracts, Google Scholar and Google (for greyliterature) were searched for the period 2010 to January 2023. Guidelines which focused on any health care setting and anyclinical pharmacy activity were included. Data were extracted and quality assessed independently by two reviewers usingthe English version of the AGREE II instrument.Results Thirty-eight guidelines were included, mostly originating from Australia (n = 10), Ireland (n = 8), UK (n = 7) andUSA (n = 5). Areas covered included medication reconciliation, medicines optimisation, medication management and transi-tion of care. As per the AGREE II assessment, the highest score was obtained for the scope and purpose domain and the low-est score for rigour of development, mainly due to non-consideration of literature/evidence to inform guideline development.Conclusion Clinical pharmacy guidelines development processes need to focus on all quality domains and should take asystematic approach to guideline development. Guidelines need to further emphasise person-centred care and clinical com-munication. There is a scope to harmonise the guidelines internationally considering the diverse practices, standards and legislations across different geographie