Numerical implementation and oceanographic application of the thermodynamic potentials of liquid water, water vapour, ice, seawater and humid air – Part 2: The library routines

The SCOR/IAPSO<sup>1</sup> Working Group 127 on Thermodynamics and Equation of State of Seawater has prepared recommendations for new methods and algorithms for numerical estimation of the the thermophysical properties of seawater. As an outcome of this work, a new International Thermodynamic Equation of Seawater (TEOS–10) was endorsed by IOC/UNESCO<sup>2</sup> in June 2009 as the official replacement and extension of the 1980 International Equation of State, EOS-80. As part of this new standard a source code package has been prepared that is now made freely available to users via the World Wide Web. This package includes two libraries referred to as the SIA (Sea-Ice-Air) library and the GSW (Gibbs SeaWater) library. Information on the GSW library may be found on the TEOS-10 web site (<a href="http://www.TEOS-10.org" target="_blank">http://www.TEOS-10.org</a>). This publication provides an introduction to the SIA library which contains routines to calculate various thermodynamic properties as discussed in the companion paper. The SIA library is very comprehensive, including routines to deal with fluid water, ice, seawater and humid air as well as equilibrium states involving various combinations of these, with equivalent code developed in different languages. The code is hierachically structured in modules that support (i) almost unlimited extension with respect to additional properties or relations, (ii) an extraction of self-contained sub-libraries, (iii) separate updating of the empirical thermodynamic potentials, and (iv) code verification on different platforms and between different languages. Error trapping is implemented to identify when one or more of the primary routines are accessed significantly beyond their established range of validity. The initial version of the SIA library is available in Visual Basic and FORTRAN as a supplement to this publication and updates will be maintained on the TEOS-10 web site. <br><br> <sup>1</sup>SCOR/IAPSO: Scientific Committee on Oceanic Research/International Association for the Physical Sciences of the Oceans<br> <sup>2</sup>IOC/UNESCO: Intergovernmental Oceanographic Commission/United Nations Educational, Scientific and Cultural Organizatio

Operationalization of interactive Multilingual Access Gateways (iMAGs) in the Traouiero project

International audienceWe will explain and demonstrate iMAGs (interactive Multilingual Access Gateways), in particular on a scientific laboratory web site and on the Greater Grenoble (La Métro) web site. This bilingual presentation has been obtained using an iMAG. Presentation This presentation is an adaptation and update of an article presented as a demonstration only to TALN-2010. The names of the files have been kept the same, although their contents are slightly different. The iMAG concept has been proposed by Ch. Boitet and V. Bellynck in 2006 (Boitet & al. 2008, Boitet & al. 2005), and reached prototype status in November 2008, with a first demonstration on the LIG laboratory Web site. It has been adapted to the DSR (Digital Silk Road) Web site in April 2009, and then to more than 50 other Web sites. These first prototypes are extensions of the SECTra_w (Huynh & al. 2008) online translation corpora support system. Since the beginning of 2011, we are operationalizing this software with a view to deploy it as a multilingual access infrastructure, in the context of the French ANR (National Agency for Research) Traouiero " emergence " project. An iMAG is an interactive Multilingual Access Gateway very much like Google Translate at first sight: one gives it a URL (starting Web site) and an access language and then navigates in that access language. When the cursor hovers over a segment (usually a sentence or a title), a palette shows the source segment and proposes to contribute by correcting the target segment, in effect post-editing an MT result. With Google Translate, the page does not change after contribution, and if another page contains the same segment, its translation is still the rough MT result, not the polished post-edited version. The more recent Google Translation Toolkit enables one to MT-translate and then post-edit online full Web pages from sites such as Wikipedia, but again the corrected segments don't appear when one later browses the Wikipedia page in the access language. By contrast, an iMAG is dedicated to an elected Web site, or rather to the elected sublanguage defined by one or more URLs and their textual content. It contains a translation memory (TM) and a specific, preterminological dictionary (pTD), both dedicated to the elected sublanguage. Segments are pretranslated not by a unique MT system, but by a (selectable) set of MT systems. Systran and Google are mainly used now, but specialized systems developed from the postedited part of the TM, and based on Moses, will be also used in the future. The powerful online contributive platforms SECTra_w and PIVAX (Nguyen & al. 2007) are used to support the TMs and pTDs. Translated pages are built with the best segment translations available so far. While reading a translated page, it is possible not only to contribute to the segment under the cursor, but also to seamlessly switch to SECTra_w online post-editing environment, equipped with proactive dictionary help and good filtering and search-and-replace functions, and then back to the reading context. A translation relay is being implemented to define the iMAGs or other translation gateways used by an elected Web site, select and parameterize the MT systems and translation routes used for various language pairs, and manage users, groups, projects (some contributions may be organized, other opportunistic), and access rights. Finally, MT systems tailored to the selected sublanguage can be built (by combinations of empirical and expert methods) from the TM and the pTD dedicated to a given elected Web site. That approach will inherently raise the linguistic and terminological quality of the MT results, hopefully converting them from rough into raw translations. The demonstration will use some iMAGs created by the AXiMAG startup for various Web sites, such as those of the LIG lab (http://service.aximag.fr:8180/xwiki/bin/view/imag/liglab) and of La Metro (Greater Grenoble) web site (http://service.aximag.fr:8180/xwiki/bin/view/imag/lametro), where access in Chinese and English was enabled in 2010 for the Shanghai Expo

From design to implementation - The Joint Asia Diabetes Evaluation (JADE) program: A descriptive report of an electronic web-based diabetes management program

<p>Abstract</p> <p>Background</p> <p>The Joint Asia Diabetes Evaluation (JADE) Program is a web-based program incorporating a comprehensive risk engine, care protocols, and clinical decision support to improve ambulatory diabetes care.</p> <p>Methods</p> <p>The JADE Program uses information technology to facilitate healthcare professionals to create a diabetes registry and to deliver an evidence-based care and education protocol tailored to patients' risk profiles. With written informed consent from participating patients and care providers, all data are anonymized and stored in a databank to establish an Asian Diabetes Database for research and publication purpose.</p> <p>Results</p> <p>The JADE electronic portal (e-portal: <url>http://www.jade-adf.org</url>) is implemented as a Java application using the Apache web server, the mySQL database and the Cocoon framework. The JADE e-portal comprises a risk engine which predicts 5-year probability of major clinical events based on parameters collected during an annual comprehensive assessment. Based on this risk stratification, the JADE e-portal recommends a care protocol tailored to these risk levels with decision support triggered by various risk factors. Apart from establishing a registry for quality assurance and data tracking, the JADE e-portal also displays trends of risk factor control at each visit to promote doctor-patient dialogues and to empower both parties to make informed decisions.</p> <p>Conclusions</p> <p>The JADE Program is a prototype using information technology to facilitate implementation of a comprehensive care model, as recommended by the International Diabetes Federation. It also enables health care teams to record, manage, track and analyze the clinical course and outcomes of people with diabetes.</p

SePaCS—a web-based application for classification of seroreactivity profiles

Immunogenic antigen sets possess high potential for minimally invasive disease detection and monitoring. For various diseases, including cancer, appropriate antigen sets have already been detected in blood sera of patients. Typically, a large number of sera from diseased and unaffected persons is screened for the antigens of interest. Sophisticated statistical learning approaches are trained on the resulting data set to classify sera as either tumor or normal sera. We developed a web-based application, called ‘Seroreactivity Profile Classification Service’ (SePaCS) that enables clinical groups to carry out analyzes of training sets and predictions of unclassified seroreactivity profiles with minimal effort. SePaCS provides a broad range of classification methods: four versions of a Naïve Bayes Classifier, Support Vector Machines with a radial basis function kernel, Linear Discriminant Analysis, and Diagonal Discriminant Analysis. The computed results are summarized in a PDF file. We demonstrate the functionality of SePaCS exemplarily for meningioma, a generally benign intracranial tumor. As a second example, we evaluated SePaCS on glioma, a malignant brain tumor. SePaCS is freely available at http://www.bioinf.uni-sb.de/sepacs

IMGD: an integrated platform supporting comparative genomics and phylogenetics of insect mitochondrial genomes

<p>Abstract</p> <p>Background</p> <p>Sequences and organization of the mitochondrial genome have been used as markers to investigate evolutionary history and relationships in many taxonomic groups. The rapidly increasing mitochondrial genome sequences from diverse insects provide ample opportunities to explore various global evolutionary questions in the superclass Hexapoda. To adequately support such questions, it is imperative to establish an informatics platform that facilitates the retrieval and utilization of available mitochondrial genome sequence data.</p> <p>Results</p> <p>The Insect Mitochondrial Genome Database (IMGD) is a new integrated platform that archives the mitochondrial genome sequences from 25,747 hexapod species, including 112 completely sequenced and 20 nearly completed genomes and 113,985 partially sequenced mitochondrial genomes. The Species-driven User Interface (SUI) of IMGD supports data retrieval and diverse analyses at multi-taxon levels. The Phyloviewer implemented in IMGD provides three methods for drawing phylogenetic trees and displays the resulting trees on the web. The SNP database incorporated to IMGD presents the distribution of SNPs and INDELs in the mitochondrial genomes of multiple isolates within eight species. A newly developed comparative SNU Genome Browser supports the graphical presentation and interactive interface for the identified SNPs/INDELs.</p> <p>Conclusion</p> <p>The IMGD provides a solid foundation for the comparative mitochondrial genomics and phylogenetics of insects. All data and functions described here are available at the web site <url>http://www.imgd.org/</url>.</p

Men Health Seeking Behaviour: A literature review

Gender equality between males and females is a Sustainable Development Goal (SDG) that the nation must address. However, compared to women, the health status of men lags. The objectives are to describe and summarize the factors influencing men's health-seeking behaviour in various health problems from published literature. Methods: The literature search was performed using online databases in Scopus, Web of Science and ScienceDirect. Findings: In a total of  22 studies that fulfilled the inclusion criteria, the factors identified were predisposing factors (socio-demographic, health belief), enabling factors (healthcare services and facilities, alternative medicine, social support), and need factors (perceived need). Keywords: Men; Health-seeking; Factors; Review eISSN: 2398-4287 © 2022. The Authors. Published for AMER ABRA cE-Bs by e-International Publishing House, Ltd., UK. This is an open access article under the CC BYNC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). Peer–review under responsibility of AMER (Association of Malaysian Environment-Behaviour Researchers), ABRA (Association of Behavioural Researchers on Asians/Africans/Arabians) and cE-Bs (Centre for Environment-Behaviour Studies), Faculty of Architecture, Planning &amp; Surveying, Universiti Teknologi MARA, Malaysia. DOI: https://doi.org/10.21834/ebpj.v7i20.348

Predicting domain-domain interaction based on domain profiles with feature selection and support vector machines

<p>Abstract</p> <p>Background</p> <p>Protein-protein interaction (PPI) plays essential roles in cellular functions. The cost, time and other limitations associated with the current experimental methods have motivated the development of computational methods for predicting PPIs. As protein interactions generally occur via domains instead of the whole molecules, predicting domain-domain interaction (DDI) is an important step toward PPI prediction. Computational methods developed so far have utilized information from various sources at different levels, from primary sequences, to molecular structures, to evolutionary profiles.</p> <p>Results</p> <p>In this paper, we propose a computational method to predict DDI using support vector machines (SVMs), based on domains represented as interaction profile hidden Markov models (ipHMM) where interacting residues in domains are explicitly modeled according to the three dimensional structural information available at the Protein Data Bank (PDB). Features about the domains are extracted first as the Fisher scores derived from the ipHMM and then selected using singular value decomposition (SVD). Domain pairs are represented by concatenating their selected feature vectors, and classified by a support vector machine trained on these feature vectors. The method is tested by leave-one-out cross validation experiments with a set of interacting protein pairs adopted from the 3DID database. The prediction accuracy has shown significant improvement as compared to <it>InterPreTS </it>(Interaction Prediction through Tertiary Structure), an existing method for PPI prediction that also uses the sequences and complexes of known 3D structure.</p> <p>Conclusions</p> <p>We show that domain-domain interaction prediction can be significantly enhanced by exploiting information inherent in the domain profiles via feature selection based on Fisher scores, singular value decomposition and supervised learning based on support vector machines. Datasets and source code are freely available on the web at <url>http://liao.cis.udel.edu/pub/svdsvm</url>. Implemented in Matlab and supported on Linux and MS Windows.</p

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704), PhyML has been widely used (>2500 citations in ISI Web of Science) because of its simplicity and a fair compromise between accuracy and speed. In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program. First, we introduce a new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves. The parsimony criterion is used here to filter out the least promising topology modifications with respect to the likelihood function. The analysis of a large collection of real nucleotide and amino acid data sets of various sizes demonstrates the good performance of this method. Second, we describe a new test to assess the support of the data for internal branches of a phylogeny. This approach extends the recently proposed approximate likelihood-ratio test and relies on a nonparametric, Shimodaira-Hasegawa-like procedure. A detailed analysis of real alignments sheds light on the links between this new approach and the more classical nonparametric bootstrap method. Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phym

Identifying DNA-binding proteins by combining support vector machine and PSSM distance transformation

Background: DNA-binding proteins play a pivotal role in various intra- and extra-cellular activities ranging from DNA replication to gene expression control. Identification of DNA-binding proteins is one of the major challenges in the field of genome annotation. There have been several computational methods proposed in the literature to deal with the DNA-binding protein identification. However, most of them can't provide an invaluable knowledge base for our understanding of DNA-protein interactions. Results: We firstly presented a new protein sequence encoding method called PSSM Distance Transformation, and then constructed a DNA-binding protein identification method (SVM-PSSM-DT) by combining PSSM Distance Transformation with support vector machine (SVM). First, the PSSM profiles are generated by using the PSI-BLAST program to search the non-redundant (NR) database. Next, the PSSM profiles are transformed into uniform numeric representations appropriately by distance transformation scheme. Lastly, the resulting uniform numeric representations are inputted into a SVM classifier for prediction. Thus whether a sequence can bind to DNA or not can be determined. In benchmark test on 525 DNA-binding and 550 non DNA-binding proteins using jackknife validation, the present model achieved an ACC of 79.96%, MCC of 0.622 and AUC of 86.50%. This performance is considerably better than most of the existing state-of-the-art predictive methods. When tested on a recently constructed independent dataset PDB186, SVM-PSSM-DT also achieved the best performance with ACC of 80.00%, MCC of 0.647 and AUC of 87.40%, and outperformed some existing state-of-the-art methods. Conclusions: The experiment results demonstrate that PSSM Distance Transformation is an available protein sequence encoding method and SVM-PSSM-DT is a useful tool for identifying the DNA-binding proteins. A user-friendly web-server of SVM-PSSM-DT was constructed, which is freely accessible to the public at the web-site on http://bioinformatics.hitsz.edu.cn/PSSM-DT/