bluuebunny/crossref_metadata_2025 huggingface dataset:
Computational approaches to standard-compliant biofilm data for reliable analysis and integration
Authors: Sousa Ana Margarida , Ferreira Andreia , Azevedo Nuno F. , Pereira Maria Olivia , Lourenço Anália
Published: December 2017

The study of microorganism consortia, also known as biofilms, is associated to a number of applications in biotechnology, ecotechnology and clinical domains. Nowadays, biofilm studies are heterogeneous and data-intensive, encompassing different levels of analysis. Computational modelling of biofilm studies has become thus a requirement to make sense of these vast and ever-expanding biofilm data volumes.

The rationale of the present work is a machine-readable format for representing biofilm studies and supporting biofilm data interchange and data integration. This format is supported by the Biofilm Science Ontology (BSO), the first ontology on biofilms information. The ontology is decomposed into a number of areas of interest, namely: the Experimental Procedure Ontology (EPO) which describes biofilm experimental procedures; the Colony Morphology Ontology (CMO) which characterises morphologically microorganism colonies; and other modules concerning biofilm phenotype, antimicrobial susceptibility and virulence traits. The overall objective behind BSO is to develop semantic resources to capture, represent and share data on biofilms and related experiments in a regularized fashion manner. Furthermore, the present work also introduces a framework in assistance of biofilm data interchange and analysis - BiofOmics (http://biofomics.org) - and a public repository on colony morphology signatures - MorphoCol (http://stardust.deb.uminho.pt/morphocol).
Automatic knowledge extraction in sequencing analysis with multiagent system and grid computing
Authors: González Roberto , Zato Carolina , Benito Rocío , Bajo Javier , Hernández Jesús M. , De Paz Juan F. , Vera Vicente , Corchado Juan M.
Published: December 2017

Advances in bioinformatics have contributed towards a significant increase in available information. Information analysis requires the use of distributed computing systems to best engage the process of data analysis. This study proposes a multiagent system that incorporates grid technology to facilitate distributed data analysis by dynamically incorporating the roles associated to each specific case study. The system was applied to genetic sequencing data to extract relevant information about insertions, deletions or polymorphisms.
A Semi-Automated Approach for Anatomical Ontology Mapping
Authors: Petrov Peter , Krachunov Milko , Vassilev Dimitar
Published: December 2017

This paper presents a study in the domain of semi-automated and fully-automated ontology mapping. A process for inferring additional cross-ontology links within the domain of anatomical ontologies is presented and evaluated on pairs from three model organisms. The results of experiments performed with various external knowledge sources and scoring schemes are discussed.
On Comparison of SimTandem with State-of-the-Art Peptide Identification Tools, Efficiency of Precursor Mass Filter and Dealing with Variable Modifications
Authors: Novák Jiří , Hoksza David , Skopal Tomáš , Kohlbacher Oliver
Published: December 2017

The similarity search in theoretical mass spectra generated from protein sequence databases is a widely accepted approach for identification of peptides from query mass spectra produced by shotgun proteomics. Growing protein sequence databases and noisy query spectra demand database indexing techniques and better similarity measures for the comparison of theoretical spectra against query spectra. We employ a modification of previously proposed parameterized Hausdorff distance for comparisons of mass spectra. The new distance outperforms the original distance, the angle distance and state-of-the-art peptide identification tools OMSSA and X!Tandem in the number of identified peptides even though the q-value is only 0.001. When a precursor mass filter is used as a database indexing technique, our method outperforms OMSSA in the speed of search. When variable modifications are not searched, the search time is similar to X!Tandem. We show that the precursor mass filter is an efficient database indexing technique for high-accuracy data even though many variable modifications are being searched. We demonstrate that the number of identified peptides is bigger when variable modifications are searched separately by more search runs of a peptide identification engine. Otherwise, the false discovery rates are affected by mixing unmodified and modified spectra together resulting in a lower number of identified peptides. Our method is implemented in the freely available application SimTandem which can be used in the framework TOPP based on OpenMS.
Model checking software for phylogenetic trees using distribution and database methods
Authors: Requeno José Ignacio , Colom José Manuel
Published: December 2017

Model checking, a generic and formal paradigm stemming from computer science based on temporal logics, has been proposed for the study of biological properties that emerge from the labeling of the states defined over the phylogenetic tree. This strategy allows us to use generic software tools already present in the industry. However, the performance of traditional model checking is penalized when scaling the system for large phylogenies. To this end, two strategies are presented here. The first one consists of partitioning the phylogenetic tree into a set of subgraphs each one representing a subproblem to be verified so as to speed up the computation time and distribute the memory consumption. The second strategy is based on uncoupling the information associated to each state of the phylogenetic tree (mainly, the DNA sequence) and exporting it to an external tool for the management of large information systems. The integration of all these approaches outperforms the results of monolithic model checking and helps us to execute the verification of properties in a real phylogenetic tree.
BioNetLink - An Architecture for Working with Network Data
Authors: Klapperstück Matthias , Schreiber Falk
Published: December 2017

The visualization of biological data gained increasing importance in the last years. There is a large number of methods and software tools available that visualize biological data including the combination of measured experimental data and biological networks. With growing size of networks their handling and exploration becomes a challenging task for the user. In addition, scientists also have an interest in not just investigating a single kind of network, but on the combination of different types of networks, such as metabolic, gene regulatory and protein interaction networks. Therefore, fast access, abstract and dynamic views, and intuitive exploratory methods should be provided to search and extract information from the networks.

This paper will introduce a conceptual framework for handling and combining multiple network sources that enables abstract viewing and exploration of large data sets including additional experimental data. It will introduce a three-tier structure that links network data to multiple network views, discuss a proof of concept implementation, and shows a specific visualization method for combining metabolic and gene regulatory networks in an example.
Probabilistic Latent Semantic Analysis Applied to Whole Bacterial Genomes Identifies Common Genomic Features
Authors: Rusakovica J. , Hallinan J. , Wipat A. , Zuliani P.
Published: December 2017

The spread of drug resistance amongst clinically-important bacteria is a serious, and growing, problem [1]. However, the analysis of entire genomes requires considerable computational effort, usually including the assembly of the genome and subsequent identification of genes known to be important in pathology. An alternative approach is to use computational algorithms to identify genomic differences between pathogenic and non-pathogenic bacteria, even without knowing the biological meaning of those differences. To overcome this problem, a range of techniques for dimensionality reduction have been developed. One such approach is known as latent-variable models [2]. In latent-variable models dimensionality reduction is achieved by representing a high-dimensional data by a few hidden or latent variables, which are not directly observed but inferred from the observed variables present in the model. Probabilistic Latent Semantic Indexing (PLSA) is an extention of LSA [3]. PLSA is based on a mixture decomposition derived from a latent class model. The main objective of the algorithm, as in LSA, is to represent high-dimensional co-occurrence information in a lower-dimensional way in order to discover the hidden semantic structure of the data using a probabilistic framework.

In this work we applied the PLSA approach to analyse the common genomic features in methicillin resistant Staphylococcus aureus, using tokens derived from amino acid sequences rather than DNA. We characterised genome-scale amino acid sequences in terms of their components, and then investigated the relationships between genomes and tokens and the phenotypes they generated. As a control we used the non-pathogenic model Gram-positive bacterium Bacillus subtilis.
BacillusRegNet: A transcriptional regulation database and analysis platform for Bacillus species
Authors: Misirli Goksel , Hallinan Jennifer , Röttger Richard , Baumbach Jan , Wipat Anil
Published: December 2017

As high-throughput technologies become cheaper and easier to use, raw sequence data and corresponding annotations for many organisms are becoming available. However, sequence data alone is not sufficient to explain the biological behaviour of organisms, which arises largely from complex molecular interactions. There is a need to develop new platform technologies that can be applied to the investigation of whole-genome datasets in an efficient and cost-effective manner. One such approach is the transfer of existing knowledge from well-studied organisms to closely-related organisms. In this paper, we describe a system, BacillusRegNet, for the use of a model organism, Bacillus subtilis, to infer genome-wide regulatory networks in less well-studied close relatives. The putative transcription factors, their binding sequences and predicted promoter sequences along with annotations are available from the associated BacillusRegNet website (http://bacillus.ncl.ac.uk).
LmTDRM Database: A Comprehensive Database on Thiol Metabolic Gene/Gene Products in Listeria monocytogenes EGDe
Authors: Srinivas Vanishree , Gopal Shubha
Published: December 2017

There are a number of databases on the Listeria species and about their genome. However, these databases do not specifically address a set of network that is important in defence mechanism of the bacteria. Listeria monocytogenes EGDe is a well-established intracellular model organism to study host pathogenicity because of its versatility in the host environment. Here, we have focused on thiol disulphide redox metabolic network proteins, specifically in L. monocytogenes EGDe. The thiol redox metabolism is involved in oxidative stress mechanism and is found in all living cells. It functions to maintain the thiol disulphide balance required for protein folding by providing reducing power. Nevertheless, they are involved in the reversible oxidation of thiol groups in biomolecules by creating disulphide bonds; therefore, the term thiol disulphide redox metabolism (TDRM). TDRM network genes play an important role in oxidative stress mechanism and during host-pathogen interaction. Therefore, it is essential to have detailed information on these proteins with regard to other bacteria and its genome analysis to understand the presence of tRNA, transposons, and insertion elements for horizontal gene transfer. LmTDRM database is a new comprehensive web-based database on thiol proteins and their functions. It includes: Description, Search, TDRM analysis, and genome viewer. The quality of these data has been evaluated before they were aggregated to produce a final representation. The web interface allows for various queries to understand the protein function and their annotation with respect to their relationship with other bacteria. LmTDRM is a major step towards the development of databases on thiol disulphide redox proteins; it would definitely help researchers to understand the mechanism of these proteins and their interaction. Database URL: www.lmtdrm.com
Analyzing Phylogenetic Trees with Timed and Probabilistic Model Checking: The Lactose Persistence Case Study
Authors: Requeno José Ignacio , Colom José Manuel
Published: December 2017

Model checking is a generic verification technique that allows the phylogeneticist to focus on models and specifications instead of on implementation issues. Phylogenetic trees are considered as transition systems over which we interrogate phylogenetic questions written as formulas of temporal logic. Nonetheless, standard logics become insufficient for certain practices of phylogenetic analysis since they do not allow the inclusion of explicit time and probabilities. The aim of this paper is to extend the application of model checking techniques beyond qualitative phylogenetic properties and adapt the existing logical extensions and tools to the field of phylogeny. The introduction of time and probabilities in phylogenetic specifications is motivated by the study of a real example: the analysis of the ratio of lactose intolerance in some populations and the date of appearance of this phenotype.
Exceptional single strand DNA word symmetry: analysis of evolutionary potentialities
Authors: Afreixo Vera , Rodrigues João M. O. S. , Bastos Carlos A. C.
Published: December 2017

Some previous studies point to the extension of Chargaff’s second rule (the phenomenon of symmetry) to words of large length. However, in random sequences generated by an independent symbol model where the probability of occurrence of complementary nucleotides is the same, we expect that the phenomenon of symmetry holds for all word lengths. In this work, we measure the symmetry above that expected in independence contexts (exceptional symmetry), for several organisms: viruses; archaea; bacteria; eukaryotes. We also create 27 control scenarios with the same length of each genome under study. The results for each organism were compared to those obtained in control scenarios. We created a new organism genomic signature consisting of a vector of the measures of exceptional symmetry for words of lengths 1 through 12. We show that the proposed signature is able to capture essential relationships between organisms.
Geometric approach to string analysis for biosequence classification
Authors: Brimkov Boris
Published: December 2017

Tools that effectively analyze and compare sequences are of great importance in various areas of applied computational research, especially in the framework of molecular biology. In the present paper, we introduce simple geometric criteria based on the notion of string linearity and use them to compare DNA sequences of various organisms, as well as to distinguish them from random sequences. Several other theoretical and statistical results are outlined as well.

Our experiments reveal a substantial difference between biosequences and random sequences – the former having much higher deviation from linearity than the latter – as well as a general trend of increasing deviation from linearity between primitive and biologically complex organisms.
GITIRBio: A Semantic and Distributed Service Oriented- Architecture for Bioinformatics Pipeline
Authors: Castillo Luis F. , López-Gartner Germán , Isaza Gustavo A. , Sánchez Mariana , Arango Jeferson , Agudelo-Valencia Daniel , Castaño Sergio
Published: December 2017

The need to process large quantities of data generated from genomic sequencing has resulted in a difficult task for life scientists who are not familiar with the use of command-line operations or developments in high performance computing and parallelization. This knowledge gap, along with unfamiliarity with necessary processes, can hinder the execution of data processing tasks. Furthermore, many of the commonly used bioinformatics tools for the scientific community are presented as isolated, unrelated entities that do not provide an integrated, guided, and assisted interaction with the scheduling facilities of computational resources or distribution, processing and mapping with runtime analysis. This paper presents the first approximation of a Web Services platform-based architecture (GITIRBio) that acts as a distributed front-end system for autonomous and assisted processing of parallel bioinformatics pipelines that has been validated using multiple sequences. Additionally, this platform allows integration with semantic repositories of genes for search annotations. GITIRBio is available at: http://c-head.ucaldas.edu.co:8080/gitirbio
Specifications of Standards in Systems and Synthetic Biology
Authors: Schreiber Falk , Bader Gary D. , Golebiewski Martin , Hucka Michael , Kormeier Benjamin , Le Novère Nicolas , Myers Chris , Nickerson David , Sommer Björn , Waltemath Dagmar , Weise Stephan
Published: December 2017

Standards shape our everyday life. From nuts and bolts to electronic devices and technological processes, standardised products and processes are all around us. Standards have technological and economic benefits, such as making information exchange, production, and services more efficient. However, novel, innovative areas often either lack proper standards, or documents about standards in these areas are not available from a centralised platform or formal body (such as the International Standardisation Organisation).

Systems and synthetic biology is a relatively novel area, and it is only in the last decade that the standardisation of data, information, and models related to systems and synthetic biology has become a community-wide effort. Several open standards have been established and are under continuous development as a community initiative. COMBINE, the ‘COmputational Modeling in BIology’ NEtwork [1] has been established as an umbrella initiative to coordinate and promote the development of the various community standards and formats for computational models. There are yearly two meeting, HARMONY (Hackathons on Resources for Modeling in Biology), Hackathon-type meetings with a focus on development of the support for standards, and COMBINE forums, workshop-style events with oral presentations, discussion, poster, and breakout sessions for further developing the standards. For more information see http://co.mbine.org/.

So far the different standards were published and made accessible through the standards’ web-pages or preprint services. The aim of this special issue is to provide a single, easily accessible and citable platform for the publication of standards in systems and synthetic biology. This special issue is intended to serve as a central access point to standards and related initiatives in systems and synthetic biology, it will be published annually to provide an opportunity for standard development groups to communicate updated specifications.
Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2
Authors: Bergmann Frank T. , Cooper Jonathan , Le Novère Nicolas , Nickerson David , Waltemath Dagmar
Published: December 2017

The number, size and complexity of computational models of biological systems are growing at an ever increasing pace. It is imperative to build on existing studies by reusing and adapting existing models and parts thereof. The description of the structure of models is not sufficient to enable the reproduction of simulation results. One also needs to describe the procedures the models are subjected to, as recommended by the Minimum Information About a Simulation Experiment (MIASE) guidelines.

This document presents Level 1 Version 2 of the Simulation Experiment Description Markup Language (SED-ML), a computer-readable format for encoding simulation and analysis experiments to apply to computational models. SED-ML files are encoded in the Extensible Markup Language (XML) and can be used in conjunction with any XML-based model encoding format, such as CellML or SBML. A SED-ML file includes details of which models to use, how to modify them prior to executing a simulation, which simulation and analysis procedures to apply, which results to extract and how to present them. Level 1 Version 2 extends the format by allowing the encoding of repeated and chained procedures.
SBML Level 3 package: Hierarchical Model Composition, Version 1 Release 3
Authors: Smith Lucian P. , Hucka Michael , Hoops Stefan , Finney Andrew , Ginkel Martin , Myers Chris J. , Moraru Ion , Liebermeister Wolfram
Published: December 2017

Constructing a model in a hierarchical fashion is a natural approach to managing model complexity, and offers additional opportunities such as the potential to re-use model components. The SBML Level 3 Version 1 Core specification does not directly provide a mechanism for defining hierarchical models, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactical constructs. The SBML Hierarchical Model Composition package for SBML Level 3 adds the necessary features to SBML to support hierarchical modeling. The package enables a modeler to include submodels within an enclosing SBML model, delete unneeded or redundant elements of that submodel, replace elements of that submodel with element of the containing model, and replace elements of the containing model with elements of the submodel. In addition, the package defines an optional “port” construct, allowing a model to be defined with suggested interfaces between hierarchical components; modelers can chose to use these interfaces, but they are not required to do so and can still interact directly with model elements if they so chose. Finally, the SBML Hierarchical Model Composition package is defined in such a way that a hierarchical model can be “flattened” to an equivalent, non-hierarchical version that uses only plain SBML constructs, thus enabling software tools that do not yet support hierarchy to nevertheless work with SBML hierarchical models.
Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions
Authors: Hucka Michael , Bergmann Frank T. , Dräger Andreas , Hoops Stefan , Keating Sarah M. , Le Novère Nicolas , Myers Chris J. , Olivier Brett G. , Sahle Sven , Schaff James C. , Smith Lucian P. , Waltemath Dagmar , Wilkinson Darren J.
Published: December 2017

Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 5 of SBML Level 2. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org/.
Integrated Automatic Workflow for Phylogenetic Tree Analysis Using Public Access and Local Web Services
Authors: Damkliang Kasikrit , Tandayya Pichaya , Sangket Unitsa , Pasomsub Ekawat
Published: December 2017

At the present, coding sequence (CDS) has been discovered and larger CDS is being revealed frequently. Approaches and related tools have also been developed and upgraded concurrently, especially for phylogenetic tree analysis. This paper proposes an integrated automatic Taverna workflow for the phylogenetic tree inferring analysis using public access web services at European Bioinformatics Institute (EMBL-EBI) and Swiss Institute of Bioinformatics (SIB), and our own deployed local web services. The workflow input is a set of CDS in the Fasta format. The workflow supports 1,000 to 20,000 numbers in bootstrapping replication. The workflow performs the tree inferring such as Parsimony (PARS), Distance Matrix - Neighbor Joining (DIST-NJ), and Maximum Likelihood (ML) algorithms of EMBOSS PHYLIPNEW package based on our proposed Multiple Sequence Alignment (MSA) similarity score. The local web services are implemented and deployed into two types using the Soaplab2 and Apache Axis2 deployment. There are SOAP and Java Web Service (JWS) providing WSDL endpoints to Taverna Workbench, a workflow manager. The workflow has been validated, the performance has been measured, and its results have been verified. Our workflow’s execution time is less than ten minutes for inferring a tree with 10,000 replicates of the bootstrapping numbers. This paper proposes a new integrated automatic workflow which will be beneficial to the bioinformaticians with an intermediate level of knowledge and experiences. The all local services have been deployed at our portal http://bioservices.sci.psu.ac.th
Feature Fusion Based SVM Classifier for Protein Subcellular Localization Prediction
Authors: Rahman Julia , Mondal Nazrul Islam , Islam Khaled Ben , Hasan Al Mehedi
Published: December 2017

For the importance of protein subcellular localization in different branch of life science and drug discovery, researchers have focused their attentions on protein subcellular localization prediction. Effective representation of features from protein sequences plays most vital role in protein subcellular localization prediction specially in case of machine learning technique. Single feature representation like pseudo amino acid composition (PseAAC), physiochemical property model (PPM), amino acid index distribution (AAID) contains insufficient information from protein sequences. To deal with such problem, we have proposed two feature fusion representations AAIDPAAC and PPMPAAC to work with Support Vector Machine classifier, which fused PseAAC with PPM and AAID accordingly. We have evaluated performance for both single and fused feature representation of Gram-negative bacterial dataset. We have got at least 3% more actual accuracy by AAIDPAAC and 2% more locative accuracy by PPMPAAC than single feature representation.
Analysis of differential gene expression by RNA-seq data in brain areas of laboratory animals
Authors: Babenko Vladimir N. , Bragin Anatoly O. , Spitsina Anastasia M. , Chadaeva Irina V. , Galieva Elvira R. , Orlova Galina V. , Medvedeva Irina V. , Orlov Yuriy L.
Published: December 2017

Computer analysis of gene expression in the nervous system plays a fundamental role in biology, genetics, and neurosciences. We studied molecular and genetic mechanisms of enhanced aggressiveness in comparison with tolerant behaviour using experimental animal models developed at the Institute of Cytology and Genetics SB RAS. Grey rats (Rattus norvegicus) have been subjected to selection during several generations in two directions - friendly, tolerant behaviour towards man (tame grey rats) and increased aggressive behaviour. We used samples from hypothalamus, mesencephalic tegmentum and periaqueductum grey matter from brain areas of grey rats genetically selected by behaviour in many generations. The set of computer tools and data processing pipelines helped to find genes and gene regulation patterns related to behaviour patterns. RNAprofiling experiments revealed the lists of differentially expressed genes in the contrast samples as well as differentially spliced isoforms. The gene ontology categories of protein transport, phosphoproteins, and nucleotide binding are presented together with categories of transmission of nerve impulses and neuron development were identified. Differential alternative splicing events found in the brain areas studied are statistically significant. We discuss role of alternative splicing events for neurospecific genes in behaviour patterns as well as extension of brain transcriptomics profiling.
Current Progress of High-Throughput MicroRNA Differential Expression Analysis and Random Forest Gene Selection for Model and Non-Model Systems: an R Implementation
Authors: Zhang Jing , Hadj-Moussa Hanane , Storey Kenneth B.
Published: December 2017

MicroRNAs are short non-coding RNA transcripts that act as master cellular regulators with roles in orchestrating virtually all biological functions. The recent affordability and widespread use of high-throughput microRNA profiling technologies has grown along with the advancement of bioinformatics tools available for analysis of the mounting data flow. While there are many computational resources available for the management of data from genomesequenced animals, researchers are often faced with the challenge of identifying the biological implications of the daunting amount of data generated from these high-throughput technologies. In this article, we review the current state of highthroughput microRNA expression profiling platforms, data analysis processes, and computational tools in the context of comparative molecular physiology. We also present RBioMIR and RBioFS, our R package implementations for differential expression analysis and random forest-based gene selection. Detailed installation guides are available at kenstoreylab.com.
Satellite dependency of GNSS phase biases between receivers and between signals
Authors: Håkansson M.
Published: December 2017

The existence of hardware induced phase biases might influence the accuracy in precise positioning if not handled properly. This is extra problematic if the biases are dependent on the satellite tracked, as these biases no longer will be common between the satellites, and thus will not be absorbed by the receiver clock term of the positioning solution. In this paper, we carried out two studies to investigate whether there exists a satellite dependency of the relative phase biases. Even though small in size, satellite dependent variations were found in both cases. In the first case, relative receiver phase biases were studied, while relative phase biases between signals (e.g. between carrier phases from C/A-code and P-code tracking) were investigated in the second case. The biases in the first case had a size of 0.8 mm between the satellites with the largest and smallest values, and additionally showed temporal variations that were consistent over time. The corresponding sizes of the biases second case were 2 mm and 3.5 mm for GPS L1 and L2 respectively, and no temporal variations were found.
Fully populated VCM or the hidden parameter
Authors: Kermarrec G. , Schön S.
Published: December 2017

Least-squares estimates are trustworthy with minimal variance if the correct stochastic model is used. Due to computational burden, diagonal models that neglect correlations are preferred to describe the elevation dependency of the variance of GPS observations. In this contribution, an improved stochastic model based on a parametric function to take correlations between GPS phase observations into account is presented. Built on an adapted and flexible Mátern function accounting for spatiotemporal variabilities, its parameters can be fixed thanks to Maximum Likelihood Estimation or chosen apriori to model turbulent tropospheric refractivity fluctuations. In this contribution, we will show in which cases and under which conditions corresponding fully populated variance covariance matrices (VCM) replace the estimation of a tropospheric parameter. For this equivalence “augmented functional versus augmented stochastic model” to hold, the VCM should be made sufficiently largewhich corresponds to computing small batches of observations. A case study with observations from a medium baseline of 80 km divided into batches of 600 s shows improvement of up to 100 mm for the 3Drms when fully populated VCM are used compared with an elevation dependent diagonal model. It confirms the strong potential of such matrices to improve the least-squares solution, particularly when ambiguities are let float.
Requests for Help in a Multilingual Professional Environment Testimonies and Actantial Models
Authors: Lejot Eve
Published: December 2017

Professional multilingual environments using English as a lingua franca are prone to imbalances in communication, linguistic insecurity and rising tension. Non-native English speakers develop avoidance strategies in order to lessen their apprehension. To overcome these imbalances, this research aims to understand the relationships formed around languages focusing on the dynamics of integration and the requests for help. Guided by the actantial models of Greimas (1966), this qualitative study employs semiolinguistics and discourse analysis, including 19 narrative interviews with employees of Airbus and UNESCO in Hamburg, Germany in 2013. This methodology draws on actors connected through relationships of power and/or collaboration. The actantial models applied seek linguistic input through designational paradigms, shifters and modal occurrences. The actantial models illustrate how a good language competence provides a better understanding of one’s direct as well as passive environment. The learning process is shown to be a conduit to integration. The actantial model and discourse analysis shed light on the complex situation of multilingual communication settings by highlighting the influence of individuals’ linguistic skills. As a matter of fact, depending on the role of each individual in a given situation, lending a helping hand sometimes equates to upsetting the balance.
Anglophonic Influence in the Use of Sound Symbolism in Italian Disney Comics: A Corpus-based Analysis
Authors: Pischedda Pier Simone
Published: December 2017

This article will explore the linguistic implications of employing and creating sound symbolism (ideophones, onomatopoeia and interjections) in Italian Disney comics. It will endeavour to investigate the way sound symbolic forms in both imported Disney US comics and original Italian stories have profoundly influenced the development of Italian sound symbolism in the last century. The diachronic analysis is carried out thanks to the creation of a corpus of ideophones and interjections from 210 Disney stories published between 1932 and 2013. The corpus will allow the author to investigate how these forms have changed diachronically throughout the eighty years under investigation with the final aim of highlighting changes and patterns in both original and translated Italian stories. The unique status of ideophones, confirmed by language, sociological and neurological studies, has led to interesting experimentations but also to complicated dynamics. Certain linguistic settings seem to foster a better affinity towards the device- particularly if compared to Romance languages, such as Italian and Spanish, that often have to rely on Anglophone renditions. Anglicisation has indeed overshadowed previous original attempts. Nevertheless, recent creations, particularly from cartoonists, bear witness to a willingness to stretch language again in order to enhance language iconicity.
Covert Syncretism: The Reception of South Africa’s Sangoma Practise and Spirituality by “Double Faith” in the Contexts of Christianity and of Esotericism
Authors: Kleinhempel Ullrich Relebogilwe
Published: December 2017

South African Bantu mediumism (of “Sangoma” type) has moved from contexts in African Traditional Religion (ATR) and rural culture into South African Christianity, especially in the African Instituted Churches (AIC), which have adopted and transformed elements of mediumist practice and ritual. In recent years it has spread to urban culture and to white milieus in South Africa and Europe, where it is received in Esoteric contexts and beyond as a form of (alternative) “healing”. The spiritual aspects have been received as expressive of a “universal” spirituality, in particular by Jungian psychoanalysts. This reception involves reinterpretation in Jungian terms as by Ch. Bühler, which may be criticized as ambivalent. Although its concepts, phenomena and experiences exceed the Jungian or Esotericist frames of references, they are acknowledged by some, e.g., J.B.F. Laubscher. On an academic level this reception has been facilitated by approaches of anthropology of experience (V. Turner, W. Dilthey) in dissertations on the authors’ initiation and training as Sangomas, and by L-R.N. Mlisa and J.T. Wreford. In their itineraries of double spiritual or religious and therapeutic practice, epistemic repercussions on both sides and in their academic work are interesting, with observable transformations. Effects of “reductionism” can be observed where Sangomas in academia reframe their practice and its epistemic concepts in terms of Pragmatism or Positivitism or of Esotericism. However, the opposite can also be observed where cosmological and anthropological concepts encoded in Sangoma experience and practice have a transformative effect on the receiving milieus of Esoteric spirituality and Jungian psychoanalysis, and of wider audiences who participate through media of television and internet, literature as well as personal encounter and practice. Even this mediated “dual practice” provides avenues for reception and adaptation in both ways, leading to stimulating debate about cultural conditioning of perception and arcane realms of reality.
Monitoring Environmental Conditions with Low-Cost Single Board Computers
Authors: Maceli Monica , Cocciolo Anthony
Published: December 2017

Controlling environmental conditions is an important component in preserving archives and manuscripts, with building design and HVAC systems widely used to achieve the desired conditions. One tool used for monitoring HVAC systems is the datalogger, which stores data such as temperature and relative humidity. As such devices can be costly and inflexible, this work explores the creation of a do-it-yourself datalogger and compares its accuracy, reliability, extensibility, cost, and ease of use against a popular commercial device. Findings suggest that organizations with sufficiently technology-savvy staff can construct and employ a DIY monitor for approximately one-quarter the price of commercial options, although costs may rise over time for support and maintenance of such systems.
Fear of Discrimination: Net Neutrality and Product Differentiation on the Internet
Authors: Liu Xingyi
Published: December 2017

We study the impact of net neutrality on the content market with endogenous product differentiation. We show that when the Internet service provider is allowed to offer different connection qualities to content providers, it has incentives to favor contents that have a broader market feature. This biases content providers towards choosing those broader products, which may result in too little product differentiation in the content market. By eliminating the possibility of discrimination, net neutrality can reduce such distortion in the content market, and induce more efficient product choices. Net neutrality also raises social welfare if the extent of discrimination is relatively small compared to the extent of product differentiation.
Are the Aristotelian conversion rules easy for human thought?
Authors: López-Astorga Miguel
Published: December 2017

Drawing on the theory of ‘mental models’, I have previously shown that the valid syllogisms in the Aristotelian logical system, including all of its figures and moods, are very easy for the human mind. Indeed, they can even be used to predict inferences that people can make with quantified sentences. In this paper, I further argue that, if mental models theory is correct, then also the Aristotelian conversion rules are not hard for the human mind. My account here again focuses on the distinction made by the mental models theory between canonical and noncanonical models.
Clinical and Economic Outcomes of New Oral Anticoagulants in Orthopaedics
Authors: Lakic Dragana , Travica Jovana , Odalovic Marina , Tadic Ivana
Published: December 2017

Venous thromboembolism, including pulmonary embolism and deep vein thrombosis, is a significant factor in morbidity and mortality of patients. New oral anticoagulants, such as apixaban, dabigatran, and rivaroxaban, have recently demonstrated their safety and efficacy in patients undergoing major orthopaedic surgery. Selection of the appropriate drug should be adjusted according to patient needs. Major bleeding is rare with new oral anticoagulants and is comparable with the bleeding rate associated with low-molecular-weight heparins. Clinical data indicate that therapy with apixaban and rivaroxaban was more effective compared to enoxaparin, while dabigatran has a similar efficacy to enoxaparin. Cost-effectiveness studies of new oral anticoagulants showed that these medicines offer higher efficacy with acceptable costs for the healthcare system, even saving costs in certain cases. Clinical practice in Serbia reflects considerably more frequent use of traditional anticoagulant medication therapy compared to new oral anticoagulants.
Fatigue Crack Growth Testing and Evaluation for Aluminum Alloys at Temperatures of 25°C and −70°C
Authors: Liu M. D. , Xiong J. J.
Published: December 2017

This paper seeks to measure and evaluate crack growth behaviors and residual lives of aluminum alloys (AAs) 2524-T3 and 7050-T7452 subjected to fatigue loading at temperatures of 25°C and −70°C. Fatigue crack growth tests were performed on AAs 2524-T3 and 7050-T7452 subjected to constant-amplitude and actual random-spectra loading histories at temperatures of about 25°C and −70°C, respectively, to determine the crack growth behaviors and residual lives. The interaction mechanisms between cryogenic temperature and the fatigue load were deduced on the basis of the results of fractographic analysis. The crack growth behaviors and residual lives were evaluated and compared at both temperatures of 25°C and −70°C. Good correlation was achieved between the predictions and actual experiments.
Evaluation of Bearing Capacity of Fly-Ash Highway Subgrade Based on Model Test
Authors: Cui Wei , Zheng Xiao , Zhang Qian-qing
Published: December 2017

Based on the mechanical properties of fly ash (FA) and the similarity theory, a small-scale geomechanical model was virtually built for evaluating the actual bearing capacity of FA embankments. The embankment model was divided into two sides: the right was covered by a concrete surface and the left was uncovered. The monitoring results of stress and displacement in different depths of the model embankment during the loading process were both presented. In the process of testing on the covered right side, both the additional stress and displacement of soil in different depths increased with an increasing load. There was a significant increase of displacement under large loading in different depths of the covered side, which suggested that plastic failure may happen and would gradually develop from bottom to top. The limit-bearing capacity of the FA embankment covered by concrete surface yield from the model test can be adopted as 419 kN that was assumed to fulfil the requirements of traffic load. As to the uncovered left side, plastic failure was very likely to occur in the soil beneath the bearing plate with a certain applied load, which caused a decrease of additional stress. Plastic failure gradually develops from top to bottom of the uncovered side. The limit-bearing capacity of the FA embankment without the concrete surface can be taken as 193 kN that may not meet the requirement for the overloading of vehicles.
Insulin-Like Growth Factor II Targets the mTOR Pathway to Reverse Autism-Like Phenotypes in Mice
Authors: Steinmetz Adam B. , Stern Sarah A. , Kohtz Amy S. , Descalzi Giannina , Alberini Cristina M.
Published: December 2017

Autism spectrum disorder (ASD) is a developmental disability characterized by impairments in social interaction and repetitive behavior, and is also associated with cognitive deficits. There is no current treatment that can ameliorate most of the ASD symptomatology; thus, identifying novel therapies is urgently needed. We used male BTBRT+Itpr3tf/J (BTBR) mice, a model that reproduces most of the core behavioral phenotypes of ASD, to test the effects of systemic administration of insulin-like growth factor II (IGF-II), a polypeptide that crosses the blood–brain barrier and acts as a cognitive enhancer. We show that systemic IGF-II treatments reverse the typical defects in social interaction, cognitive/executive functions, and repetitive behaviors reflective of ASD-like phenotypes. In BTBR mice, IGF-II, via IGF-II receptor, but not via IGF-I receptor, reverses the abnormal levels of the AMPK-mTOR-S6K pathway and of active translation at synapses. Thus, IGF-II may represent a novel potential therapy for ASD.

SIGNIFICANCE STATEMENTCurrently, there is no effective treatment for autism spectrum disorder (ASD), a developmental disability affecting a high number of children. Using a mouse model that expresses most of the key core as well as associated behavioral deficits of ASD, that are, social, cognitive, and repetitive behaviors, we report that a systemic administration of the polypeptide insulin-like growth factor II (IGF-II) reverses all these deficits. The effects of IGF-II occur via IGF-II receptors, and not IGF-I receptors, and target both basal and learning-dependent molecular abnormalities found in several ASD mice models, including those of identified genetic mutations. We suggest that IGF-II represents a potential novel therapeutic target for ASD.
STUDI KARAKTERISTIK PASIEN TUBERKULOSIS DI PUSKESMAS SEBERANG ULU 1 PALEMBANG
Authors: Ismah Zata , Novita Emma
Published: December 2017

Abstrak

Analisis karakteristik penderita TB selain berguna untuk pengobatan juga berguna dalam memudahkan penemukan tersangka TB. Penelitian ini bertujuan untuk menganalisis karakteristik penderita TB. Desain studi yang digunakan adalah crossectional dengan sampel sebanyak 40 pasien TB yang berobat 3 bulan terakhir di Puskesmas Seberang Ulu 1 Palembang. Pengumpulan data dilakukan dengan kunjungan rumah ke pasien lalu dilakukan wawancara serta pemeriksaan fisik dan status kesehatan.  Hasil penelitian didapatkan bahwa karakteristik penderita TB paling banyak pada kelompok : usia produktif usia 12 – 35 tahun  dan  rentang usia dewasa 49 -  61 tahun; jenis kelamin laki-laki; pendidikan sekolah tingkat dasar; pekerjaan buruh; sosial ekonomi rendah; perokok aktif. Ditemukan 13.2% pasien TB dengan DM, 45% pasien TB dengan hipertensi, 47.5% pasien TB dengan anemia, 55% pasien TB dengan gizi kurang, 17.5% pasien memiliki riwayat keluarga menderita TB. Pasien kambuh sebanyak 12.5%; pasien yang putus OAT 17.5%; serta ditemukan tidak minum OAT sebanyak 15%.

 

Kata kunci: Karakteristik, Deskriptif, Tuberkulosis,                         

 

Abstracts

Analysis of characteristics TB disease besides useful for treatment is also useful to finding TB cases. This study aims to analyze characteristic of TB patients. This research used cross sectional study design with 40 TB patients treated last 3 months at Puskesmas Seberang Ulu 1 Palembang. Data collection was done with patient home visits, interview, physical examination health status. The results was most of characteristic TB patients in productive age group, maximum age 35 years, male gender, primary education, occupation was coolie, low socioeconomic, active smokers. TB Patients was founded 13.2% with DM; 45% TB patients with hypertension; 47.5% TB patients with anemia; 55% TB patients with malnutrition; 17.5% of patients had a family history of TB. Patients relapsed were 12.5%; OAT dropout patients were founded 17.5%; 15% patients were not OAT.

 

Keywords: Characteristics, Descriptive, Tuberculosis