Enhancements to the GW space-time method

We describe the following new features which significantly enhance the power of the recently developed real-space imaginary-time GW scheme (Rieger et al., Comp. Phys. Commun. 117, 211 (1999)) for the calculation of self-energies and related quantities of solids: (i) to fit the smoothly decaying time/energy tails of the dynamically screened Coulomb interaction and other quantities to model functions, treating only the remaining time/energy region close to zero numerically and performing the Fourier transformation from time to energy and vice versa by a combination of analytic integration of the tails and Gauss-Legendre quadrature of the remaining part and (ii) to accelerate the convergence of the band sum in the calculation of the Green's function by replacing higher unoccupied eigenstates by free electron states (plane waves). These improvements make the calculation of larger systems (surfaces, clusters, defects etc.) accessible.Comment: 10 pages, 6 figure

OrChem - An open source chemistry search engine for Oracle®

<p>Abstract</p> <p>Background</p> <p>Registration, indexing and searching of chemical structures in relational databases is one of the core areas of cheminformatics. However, little detail has been published on the inner workings of search engines and their development has been mostly closed-source. We decided to develop an open source chemistry extension for Oracle, the de facto database platform in the commercial world.</p> <p>Results</p> <p>Here we present OrChem, an extension for the Oracle 11G database that adds registration and indexing of chemical structures to support fast substructure and similarity searching. The cheminformatics functionality is provided by the Chemistry Development Kit. OrChem provides similarity searching with response times in the order of seconds for databases with millions of compounds, depending on a given similarity cut-off. For substructure searching, it can make use of multiple processor cores on today's powerful database servers to provide fast response times in equally large data sets.</p> <p>Availability</p> <p>OrChem is free software and can be redistributed and/or modified under the terms of the GNU Lesser General Public License as published by the Free Software Foundation. All software is available via <url>http://orchem.sourceforge.net</url>.</p

LICSS - a chemical spreadsheet in microsoft excel

Abstract Background Representations of chemical datasets in spreadsheet format are important for ready data assimilation and manipulation. In addition to the normal spreadsheet facilities, chemical spreadsheets need to have visualisable chemical structures and data searchable by chemical as well as textual queries. Many such chemical spreadsheet tools are available, some operating in the familiar Microsoft Excel environment. However, within this group, the performance of Excel is often compromised, particularly in terms of the number of compounds which can usefully be stored on a sheet. Summary LICSS is a lightweight chemical spreadsheet within Microsoft Excel for Windows. LICSS stores structures solely as Smiles strings. Chemical operations are carried out by calling Java code modules which use the CDK, JChemPaint and OPSIN libraries to provide cheminformatics functionality. Compounds in sheets or charts may be visualised (individually or en masse), and sheets may be searched by substructure or similarity. All the molecular descriptors available in CDK may be calculated for compounds (in batch or on-the-fly), and various cheminformatic operations such as fingerprint calculation, Sammon mapping, clustering and R group table creation may be carried out. We detail here the features of LICSS and how they are implemented. We also explain the design criteria, particularly in terms of potential corporate use, which led to this particular implementation. Conclusions LICSS is an Excel-based chemical spreadsheet with a difference: • It can usefully be used on sheets containing hundreds of thousands of compounds; it doesn't compromise the normal performance of Microsoft Excel • It is designed to be installed and run in environments in which users do not have admin privileges; installation involves merely file copying, and sharing of LICSS sheets invokes automatic installation • It is free and extensible LICSS is open source software and we hope sufficient detail is provided here to enable developers to add their own features and share with the community.</p

Online Pattern Recognition for the ALICE High Level Trigger

The ALICE High Level Trigger has to process data online, in order to select interesting (sub)events, or to compress data efficiently by modeling techniques.Focusing on the main data source, the Time Projection Chamber (TPC), we present two pattern recognition methods under investigation: a sequential approach "cluster finder" and "track follower") and an iterative approach ("track candidate finder" and "cluster deconvoluter"). We show, that the former is suited for pp and low multiplicity PbPb collisions, whereas the latter might be applicable for high multiplicity PbPb collisions, if it turns out, that more than 8000 charged particles would have to be reconstructed inside the TPC. Based on the developed tracking schemes we show, that using modeling techniques a compression factor of around 10 might be achievableComment: Realtime Conference 2003, Montreal, Canada to be published in IEEE Transactions on Nuclear Science (TNS), 6 pages, 8 figure

Real Time Global Tests of the ALICE High Level Trigger Data Transport Framework

The High Level Trigger (HLT) system of the ALICE experiment is an online event filter and trigger system designed for input bandwidths of up to 25 GB/s at event rates of up to 1 kHz. The system is designed as a scalable PC cluster, implementing several hundred nodes. The transport of data in the system is handled by an object-oriented data flow framework operating on the basis of the publisher-subscriber principle, being designed fully pipelined with lowest processing overhead and communication latency in the cluster. In this paper, we report the latest measurements where this framework has been operated on five different sites over a global north-south link extending more than 10,000 km, processing a ``real-time'' data flow.Comment: 8 pages 4 figure

'Not to Be Harsh but Try Less to Relate to 'the Teens' and You'll Relate to Them More': Co-Designing Obesity Prevention Text Messages with Adolescents.

Text messages remain a preferred way for adolescents to communicate, and recent evidence suggests adolescents would like access to digital healthcare options. However, there is limited evidence for text messages to engage adolescent populations in obesity prevention behaviors. We aimed to co-design a bank of text messages that are evidence-based, acceptable, and engaging for adolescents. An established iterative mixed methods process, consisting of three phases, was used to develop the text message program. The first bank of 145 text messages was drafted based on current evidence, behavior change techniques, and input from researchers and health professionals. A survey was then administered to adolescents and professionals for review of text message content, usefulness, understanding, and age-appropriateness. An adolescent research assistant collaborated with the research team on all three phases. Forty participants (25 adolescents and 15 professionals) reviewed the initial bank of 145 text messages. On average, all reviewers agreed the text messages were easy to understand (13.6/15) and useful (13.1/15). In total, 107 text messages were included in the final text message bank to support behavior change and prevent obesity. This study may guide other researchers or health professionals who are seeking to engage adolescents in the co-design of health promotion or intervention content. Effectiveness of the text message program will be tested in a randomized controlled trial

Detection of IUPAC and IUPAC-like chemical names

Motivation: Chemical compounds like small signal molecules or other biological active chemical substances are an important entity class in life science publications and patents. Several representations and nomenclatures for chemicals like SMILES, InChI, IUPAC or trivial names exist. Only SMILES and InChI names allow a direct structure search, but in biomedical texts trivial names and Iupac like names are used more frequent. While trivial names can be found with a dictionary-based approach and in such a way mapped to their corresponding structures, it is not possible to enumerate all IUPAC names. In this work, we present a new machine learning approach based on conditional random fields (CRF) to find mentions of IUPAC and IUPAC-like names in scientific text as well as its evaluation and the conversion rate with available name-to-structure tools

Requirement for specific gravity and creatinine adjustments for urinary steroids and luteinizing hormone concentrations in adolescents

Objectives: Urinary hormone concentrations are often adjusted to correct for hydration status. We aimed to determine whether first morning void urine hormones in growing adolescents require adjustments and, if so, whether urinary creatinine or specific gravity (SG) are better adjustments. Design and Methods: The study population was adolescents aged 10.1 to 14.3 years initially who provided fasting morning blood samples at 0 and 12 months (n=343) and first morning urine every three months (n=644). Unadjusted, creatinine and SG-adjusted hormonal concentrations were compared by Deming regression and Bland-Altman analysis and grouped according to self-rated Tanner stage or chronological age. F-ratios for self-rated Tanner stages and age groups were used to compare unadjusted and adjusted hormonal changes in growing young adolescents. Correlations of paired serum and urinary hormonal concentration of unadjusted and creatinine and SG adjusted were also compared. Results: Fasting first morning void hormone concentrations correlated well and were unbiased between unadjusted or adjusted by either creatinine or SG. Urine creatinine concentration increases with Tanner stages, age and male gender whereas, urine SG was not influenced by Tanner stage, age or gender. Adjustment by creatinine or SG of urinary luteinizing hormone, estradiol, testosterone, dihydrotestosterone and dehydroepiandrosterone concentrations did not improve correlation with paired serum concentrations. Conclusions: Urine steroid and LH concentrations in first morning void samples of adolescents are not significantly influenced by hydration status and may not require adjustments; however, if desired, both creatinine and SG adjustments are equally suitable

A critical evaluation of automatic atom mapping algorithms and tools

The identification of the atoms which change their position in chemical reactions is an important knowledge within the field of Metabolic Engineering. This can lead to new advances at different levels from the reconstruction of metabolic networks to the classification of chemical reactions, through the identification of the atomic changes inside a reaction. The Atom Mapping approach was initially developed in the 1960s, but recently suffered important advances, being used in diverse biological and biotechnological studies. The main methodologies used for atom mapping are the Maximum Common Substructure and the Linear Optimization methods, which both require computational know-how and powerful resources to run the underlying tools. In this work, we assessed a number of previously implemented atom mapping frameworks, and built a framework able of managing the different data inputs and outputs, as well as the mapping process provided by each of these third-party tools. We evaluated the admissibility of the calculated atom maps from different algorithms, also assessing if with different approaches we were capable of returning equivalent atom maps for the same chemical reaction.ERDF -European Regional Development Fund(UID/BIO/04469/2013)info:eu-repo/semantics/publishedVersio