bluuebunny/crossref_metadata_2025 huggingface dataset:
BacillOndex: An Integrated Data Resource for Systems and Synthetic Biology
Authors: Misirli Goksel , Wipat Anil , Mullen Joseph , James Katherine , Pocock Matthew , Smith Wendy , Allenby Nick , Hallinan Jennifer S.
Published: December 2017

BacillOndex is an extension of the Ondex data integration system, providing a semantically annotated, integrated knowledge base for the model Gram-positive bacterium Bacillus subtilis. This application allows a user to mine a variety of B. subtilis data sources, and analyse the resulting integrated dataset, which contains data about genes, gene products and their interactions. The data can be analysed either manually, by browsing using Ondex, or computationally via a Web services interface. We describe the process of creating a BacillOndex instance, and describe the use of the system for the analysis of single nucleotide polymorphisms in B. subtilis Marburg. The Marburg strain is the progenitor of the widely-used laboratory strain B. subtilis 168. We identified 27 SNPs with predictable phenotypic effects, including genetic traits for known phenotypes. We conclude that BacillOndex is a valuable tool for the systems-level investigation of, and hypothesis generation about, this important biotechnology workhorse. Such understanding contributes to our ability to construct synthetic genetic circuits in this organism.
Applying the Tuple Space-Based Approach to the Simulation of the Caspases, an Essential Signalling Pathway
Authors: Cárdenas-García Maura , González-Pérez Pedro Pablo
Published: December 2017

Apoptotic cell death plays a crucial role in development and homeostasis. This process is driven by mitochondrial permeabilization and activation of caspases. In this paper we adopt a tuple spaces-based modelling and simulation approach, and show how it can be applied to the simulation of this intracellular signalling pathway. Specifically, we are working to explore and to understand the complex interaction patterns of the caspases apoptotic and the mitochondrial role. As a first approximation, using the tuple spacesbased in silico approach, we model and simulate both the extrinsic and intrinsic apoptotic signalling pathways and the interactions between them. During apoptosis, mitochondrial proteins, released from mitochondria to cytosol are decisively involved in the process. If the decision is to die, from this point there is normally no return, cancer cells offer resistance to the mitochondrial induction.
Inter-STOP symbol distances for the identification of coding regions
Authors: Bastos Carlos A. C. , Afreixo Vera , Garcia Sara P. , Pinho Armando J.
Published: December 2017

In this study we explore the potential of inter-STOP symbol distances for finding coding regions in DNA sequences. We use the distance between STOP symbols in the DNA sequence and a chi-square statistic to evaluate the nonhomogeneity of the three possible reading frames and the occurrence of one long distance in one of the frames. The results of this exploratory study suggest that inter-STOP symbol distances have strong ability to discriminate coding regions in prokaryotes and simple eukaryotes.
Improving the performance of Transposable Elements detection tools
Authors: Loureiro Tiago , Camacho Rui , Vieira Jorge , Fonseca Nuno A.
Published: December 2017

Transposable Elements (TE) are sequences of DNA that move and transpose within a genome. TEs, as mutation agents, are quite important for their role in both genome alteration diseases and on species evolution. Several tools have been developed to discover and annotate TEs but no single tool achieves good results on all different types of TEs. In this paper we evaluate the performance of several TEs detection and annotation tools and investigate if Machine Learning techniques can be used to improve their overall detection accuracy. The results of an in silico evaluation of TEs detection and annotation tools indicate that their performance can be improved by using machine learning constructed classifiers.
An Evolutionary and Visual Framework for Clustering of DNA Microarray Data
Authors: Castellanos-Garzón José A. , Díaz Fernando
Published: December 2017

This paper presents a case study to show the competence of our evolutionary and visual framework for cluster analysis of DNA microarray data. The proposed framework joins a genetic algorithm for hierarchical clustering with a set of visual components of cluster tasks given by a tool. The cluster visualization tool allows us to display different views of clustering results as a means of cluster visual validation. The results of the genetic algorithm for clustering have shown that it can find better solutions than the other methods for the selected data set. Thus, this shows the reliability of the proposed framework.
Re-annotation of the genome sequence of Helicobacter pylori 26695
Authors: Resende Tiago , Correia Daniela M. , Rocha Miguel , Rocha Isabel
Published: December 2017

Helicobacter pylori is a pathogenic bacterium that colonizes the human epithelia, causing duodenal and gastric ulcers, and gastric cancer. The genome of H. pylori 26695 has been previously sequenced and annotated. In addition, two genome-scale metabolic models have been developed. In order to maintain accurate and relevant information on coding sequences (CDS) and to retrieve new information, the assignment of new functions to Helicobacter pylori 26695s genes was performed in this work. The use of software tools, on-line databases and an annotation pipeline for inspecting each gene allowed the attribution of validated EC numbers and TC numbers to metabolic genes encoding enzymes and transport proteins, respectively. 1212 genes encoding proteins were identified in this annotation, being 712 metabolic genes and 500 non-metabolic, while 191 new functions were assignment to the CDS of this bacterium. This information provides relevant biological information for the scientific community dealing with this organism and can be used as the basis for a new metabolic model reconstruction.
Integrated visualization of a multi-omics study of starvation in mouse intestine
Authors: Iersel Martijn P. van , Sokolović Milka , Lenaerts Kaatje , Kutmon Martina , Bouwman Freek G. , Lamers Wouter H. , Mariman Edwin C.M. , Evelo Chris T.
Published: December 2017

Our understanding of complex biological processes can be enhanced by combining different kinds of high-throughput experimental data, but the use of incompatible identifiers makes data integration a challenge. We aimed to improve methods for integrating and visualizing different types of omics data. To validate these methods, we applied them to two previous studies on starvation in mice, one using proteomics and the other using transcriptomics technology. We extended the PathVisio software with new plugins to link proteins, transcripts and pathways. A low overall correlation between proteome and transcriptome data was detected (Spearman rank correlation: 0.21). At the level of individual genes, correlation was highly variable. Many mRNA/protein pairs, such as fructose biphosphate aldolase B and ATP Synthase, show good correlation. For other pairs, such as ferritin and elongation factor 2, an interesting effect is observed, where mRNA and protein levels change in opposite directions, suggesting they are not primarily regulated at the transcriptional level. We used pathway diagrams to visualize the integrated datasets and found it encouraging that transcriptomics and proteomics data supported each other at the pathway level. Visualization of the integrated dataset on pathways led to new observations on gene-regulation in the response of the gut to starvation. Our methods are generic and can be applied to any multi-omics study. The PathVisio software can be obtained at http://www.pathvisio.org. Supplemental data are available at http://www.bigcat.unimaas.nl/data/jib-supplemental/, including instructions on reproducing the pathway visualizations of this manuscript.
A Query Suggestion Workflow for Life Science IR-Systems
Authors: Esch Maria , Chen Jinbo , Weise Stephan , Hassani-Pak Keywan , Scholz Uwe , Lange Matthias
Published: December 2017

Information Retrieval (IR) plays a central role in the exploration and interpretation of integrated biological datasets that represent the heterogeneous ecosystem of life sciences. Here, keyword based query systems are popular user interfaces. In turn, to a large extend, the used query phrases determine the quality of the search result and the effort a scientist has to invest for query refinement.

In this context, computer aided query expansion and suggestion is one of the most challenging tasks for life science information systems. Existing query front-ends support aspects like spelling correction, query refinement or query expansion. However, the majority of the front-ends only make limited use of enhanced IR algorithms to implement comprehensive and computer aided query refinement workflows.

In this work, we present the design of a multi-stage query suggestion workflow and its implementation in the life science IR system LAILAPS. The presented workflow includes enhanced tokenisation, word breaking, spelling correction, query expansion and query suggestion ranking. A spelling correction benchmark with 5,401 queries and manually selected use cases for query expansion demonstrate the performance of the implemented workflow and its advantages compared with state-of-the-art systems.
The Topology of the Growing Human Interactome Data
Authors: Janjić Vuk , Pržulj Nataša
Published: December 2017

We have long moved past the one-gene-one-function concept originally proposed by Beadle and Tatum back in 1941; but the full understanding of genotype-phenotype relations still largely relies on the analysis of static, snapshot-like, interaction data sets. Here, we look at what global patterns can be uncovered if we simply trace back the human interactome network over the last decade of protein-protein interaction (PPI) screening. We take a purely topological approach and find that as the human interactome is getting denser, it is not only gaining in structure (in terms of now being better fit by structured network models than before), but also there are patterns in the way in which it is growing: (a) newly added proteins tend to get linked to existing proteins in the interactome that are not know to interact; and (b) new proteins tend to link to already well connected proteins. Moreover, the alignment between human and yeast interactomes spanning over 40% of yeast’s proteins - that are involved in regulation of transcription, RNA splicing and other cellcycle- related processes-suggests the existence of a part of the interactome which remains topologically and functionally unaffected through evolution. Furthermore, we find a small sub-network, specific to the “core” of the human interactome and involved in regulation of transcription and cancer development, whose wiring has not changed within the human interactome over the last 10 years of interacome data acquisition. Finally, we introduce a generalisation of the clustering coefficient of a network as a new measure called the cycle coefficient, and use it to show that PPI networks of human and model organisms are wired in a tight way which forbids the occurrence large cycles.
Profiling of Genetic Switches using Boolean Implications in Expression Data
Authors: Çakır M. Volkan , Binder Hans , Wirth Henry
Published: December 2017

Correlation analysis assuming coexpression of the genes is a widely used method for gene expression analysis in molecular biology. Yet growing extent, quality and dimensionality of the molecular biological data permits emerging, more sophisticated approaches like Boolean implications.

We present an approach which is a combination of the SOM (self organizing maps) machine learning method and Boolean implication analysis to identify relations between genes, metagenes and similarly behaving metagene groups (spots). Our method provides a way to assign Boolean states to genes/metagenes/spots and offers a functional view over significantly variant elements of gene expression data on these three different levels. While being able to cover relations between weakly correlated entities Boolean implication method also decomposes these relations into six implication classes.

Our method allows one to validate or identify potential relationships between genes and functional modules of interest and to assess their switching behaviour. Furthermore the output of the method renders it possible to construct and study the network of genes. By providing logical implications as updating rules for the network it can also serve to aid modelling approaches.
Identifying interactions between chemical entities in biomedical text
Authors: Lamurias Andre , Ferreira João D. , Couto Francisco M.
Published: December 2017

Interactions between chemical compounds described in biomedical text can be of great importance to drug discovery and design, as well as pharmacovigilance. We developed a novel system, “Identifying Interactions between Chemical Entities” (IICE), to identify chemical interactions described in text. Kernel-based Support Vector Machines first identify the interactions and then an ensemble classifier validates and classifies the type of each interaction. This relation extraction module was evaluated with the corpus released for the DDI Extraction task of SemEval 2013, obtaining results comparable to stateof- the-art methods for this type of task. We integrated this module with our chemical named entity recognition module and made the whole system available as a web tool at www.lasige.di.fc.ul.pt/webtools/iice.
Systems Biology Graphical Notation: Process Description language Level 1 Version 1.3
Authors: Moodie Stuart , Le Novère Nicolas , Demir Emek , Mi Huaiyu , Villéger Alice
Published: December 2017

The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail.

The SBGN Process Description language represents biological entities and processes between these entities within a network. SBGN PD focuses on the mechanistic description and temporal dependencies of biological interactions and transformations. The nodes (elements) are split into entity nodes describing, e.g., metabolites, proteins, genes and complexes, and process nodes describing, e.g., reactions and associations. The edges (connections) provide descriptions of relationships (or influences) between the nodes, such as consumption, production, stimulation and inhibition. Among all three languages of SBGN, PD is the closest to metabolic and regulatory pathways in biological literature and textbooks, but its well-defined semantics offer a superior precision in expressing biological knowledge.
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core
Authors: Hucka Michael , Bergmann Frank T. , Hoops Stefan , Keating Sarah M. , Sahle Sven , Schaff James C. , Smith Lucian P. , 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 1 of SBML Level 3 Core. 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/.
The Systems Biology Markup Language (SBML) Level 3 Package: Layout, Version 1 Core
Authors: Gauges Ralph , Rost Ursula , Sahle Sven , Wengler Katja , Bergmann Frank T.
Published: December 2017

Many software tools provide facilities for depicting reaction network diagrams in a visual form. Two aspects of such a visual diagram can be distinguished: the layout (i.e.: the positioning and connections) of the elements in the diagram, and the graphical form of the elements (for example, the glyphs used for symbols, the properties of the lines connecting them, and so on). For software tools that also read and write models in SBML (Systems Biology Markup Language) format, a common need is to store the network diagram together with the SBML representation of the model. This in turn raises the question of how to encode the layout and the rendering of these diagrams. The SBML Level 3 Version 1 Core specification does not provide a mechanism for explicitly encoding diagrams, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactical constructs. The Layout package for SBML Level 3 adds the necessary features to SBML so that diagram layouts can be encoded in SBML files, and a companion package called SBML Rendering specifies how the graphical rendering of elements can be encoded.

The SBML Layout package is based on the principle that reaction network diagrams should be described as representations of entities such as species and reactions (with direct links to the underlying SBML elements), and not as arbitrary drawings or graphs; for this reason, existing languages for the description of vector drawings (such as SVG) or general graphs (such as GraphML) cannot be used.
The Systems Biology Markup Language (SBML) Level 3 Package: Flux Balance Constraints
Authors: Olivier Brett G. , Bergmann Frank T.
Published: December 2017

Constraint-based modeling is a well established modelling methodology used to analyze and study biological networks on both a medium and genome scale. Due to their large size, genome scale models are typically analysed using constraint-based optimization techniques. One widely used method is Flux Balance Analysis (FBA) which, for example, requires a modelling description to include: the definition of a stoichiometric matrix, an objective function and bounds on the values that fluxes can obtain at steady state.

The Flux Balance Constraints (FBC) Package extends SBML Level 3 and provides a standardized format for the encoding, exchange and annotation of constraint-based models. It includes support for modelling concepts such as objective functions, flux bounds and model component annotation that facilitates reaction balancing. The FBC package establishes a base level for the unambiguous exchange of genome-scale, constraint-based models, that can be built upon by the community to meet future needs (e. g. by extending it to cover dynamic FBC models).
Managing and Documenting Legacy Scientific Workflows
Authors: Acuña Ruben , Chomilier Jacques , Lacroix Zoé
Published: December 2017

Scientific legacy workflows are often developed over many years, poorly documented and implemented with scripting languages. In the context of our cross-disciplinary projects we face the problem of maintaining such scientific workflows. This paper presents the Workflow Instrumentation for Structure Extraction (WISE) method used to process several ad-hoc legacy workflows written in Python and automatically produce their workflow structural skeleton. Unlike many existing methods, WISE does not assume input workflows to be preprocessed in a known workflow formalism. It is also able to identify and analyze calls to external tools. We present the method and report its results on several scientific workflows.
Integrating data from heterogeneous DNA microarray platforms
Authors: Valente Eduardo , Rocha Miguel
Published: December 2017

DNA microarrays are one of the most used technologies for gene expression measurement. However, there are several distinct microarray platforms, from different manufacturers, each with its own measurement protocol, resulting in data that can hardly be compared or directly integrated. Data integration from multiple sources aims to improve the assertiveness of statistical tests, reducing the data dimensionality problem. The integration of heterogeneous DNA microarray platforms comprehends a set of tasks that range from the re-annotation of the features used on gene expression, to data normalization and batch effect elimination. In this work, a complete methodology for gene expression data integration and application is proposed, which comprehends a transcript-based re-annotation process and several methods for batch effect attenuation. The integrated data will be used to select the best feature set and learning algorithm for a brain tumor classification case study. The integration will consider data from heterogeneous Agilent and Affymetrix platforms, collected from public gene expression databases, such as The Cancer Genome Atlas and Gene Expression Omnibus.
Estimation of biomass composition from genomic and transcriptomic information
Authors: Santos Sophia , Rocha Isabel
Published: December 2017

Given the great potential impact of the growing number of complete genome-scale metabolic network reconstructions of microorganisms, bioinformatics tools are needed to simplify and accelerate the course of knowledge in this field. One essential component of a genomescale metabolic model is its biomass equation, whose maximization is one of the most common objective functions used in Flux Balance Analysis formulations. Some components of biomass, such as amino acids and nucleotides, can be estimated from genome information, providing reliable data without the need of performing lab experiments. In this work a java tool is proposed that estimates microbial biomass composition in amino acids and nucleotides, from genome and transcriptomic information, using as input files sequences in FASTA format and files with transcriptomic data in the csv format. This application allows to obtain the results rapidly and is also a user-friendly tool for users with any or little background in informatics (http://darwin.di.uminho.pt/biomass/). The results obtained using this tool are fairly close to experimental data, showing that the estimation of amino acid and nucleotide compositions from genome information and from transcriptomic data is a good alternative when no experimental data is available.
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016
Authors: Schreiber Falk , Bader Gary D. , Gleeson Padraig , Golebiewski Martin , Hucka Michael , Novère Nicolas Le , Myers Chris , Nickerson David , Sommer Björn , Waltemath Dagmar
Published: December 2017

Standards are essential to the advancement of science and technology. In systems and synthetic biology, numerous standards and associated tools have been developed over the last 16 years. This special issue of the Journal of Integrative Bioinformatics aims to support the exchange, distribution and archiving of these standards, as well as to provide centralised and easily citable access to them.
New insights into genotype–phenotype correlation in individuals with different level of general non-specific reactivity of an organism
Authors: Mulik Alexander , Novochadov Valery , Bondarev Alexander , Lipnitskaya Sofya , Ulesikova Irina , Shatyr Yulia
Published: December 2017

The objective of the study was to investigate the genetic basis of general non-specific reactivity of an organism. Systematic search in PubMedCentral, PDB, KEGG and SNP databases identified a set of genes and their polymorphisms that can determine pain sensitivity and therefore the level of general non-specific reactivity of the human organism. Six SNPs were selected for genotyping kit design; 230 healthy volunteers were enrolled in the study. It was revealed that very high pain threshold was associated with allele A in rs1851048 and allele C in rs6777055. High level of general non-specific reactivity of an organism was associated with allele G in rs2562456 (OR=1.804, CI=1.139-2.857, p=0.011) and allele C in rs6923492 (OR=1.582, CI=1.071-2.335, p=0.021). Low level of general non-specific reactivity of an organism was associated with allele T in rs6923492 (OR=0.351, CI=0.154-0.799, p=0.010). A set of genes and single-nucleotide polymorphisms associated with the pain sensitivity and indirectly with the level of general non-specific reactivity of human organism were determined. The identified correlations reveal some molecular mechanisms of general non-specific reactivity of an organism variability and can guide further research in this area.
Genomic Islands: an overview of current software tools and future improvements
Authors: Soares Siomar de Castro , Oliveira Letícia de Castro , Jaiswal Arun Kumar , Azevedo Vasco
Published: December 2017

Microbes are highly diverse and widely distributed organisms. They account for ~60% of Earth’s biomass and new predictions point for the existence of 1011 to 1012 species, which are constantly sharing genes through several different mechanisms. Genomic Islands (GI) are critical in this context, as they are large regions acquired through horizontal gene transfer. Also, they present common features like genomic signature deviation, transposase genes, flanking tRNAs and insertion sequences. GIs carry large numbers of genes related to specific lifestyle and are commonly classified in Pathogenicity, Resistance, Metabolic or Symbiotic Islands. With the advent of the next-generation sequencing technologies and the deluge of genomic data, many software tools have been developed that aim to tackle the problem of GI prediction and they are all based on the prediction of GI common features. However, there is still room for the development of new software tools that implements new approaches, such as, machine learning and pangenomics based analyses. Finally, GIs will always hold a potential application in every newly invented genomic approach as they are directly responsible for much of the genomic plasticity of bacteria.
A Machine Learning Approach for MicroRNA Precursor Prediction in Retro-transcribing Virus Genomes
Authors: Demirci Müşerref Duygu Saçar , Toprak Mustafa , Allmer Jens
Published: December 2017

Identification of microRNA (miRNA) precursors has seen increased efforts in recent years. The difficulty in experimental detection of pre-miRNAs increased the usage of computational approaches. Most of these approaches rely on machine learning especially classification. In order to achieve successful classification, many parameters need to be considered such as data quality, choice of classifier settings, and feature selection. For the latter one, we developed a distributed genetic algorithm on HTCondor to perform feature selection. Moreover, we employed two widely used classification algorithms libSVM and random forest with different settings to analyze the influence on the overall classification performance. In this study we analyzed 5 human retro virus genomes; Human endogenous retrovirus K113, Hepatitis B virus (strain ayw), Human T lymphotropic virus 1, Human T lymphotropic virus 2, Human immunodeficiency virus 2, and Human immunodeficiency virus 1. We then predicted pre-miRNAs by using the information from known virus and human pre-miRNAs. Our results indicate that these viruses produce novel unknown miRNA precursors which warrant further experimental validation.
miRquant 2.0: an Expanded Tool for Accurate Annotation and Quantification of MicroRNAs and their isomiRs from Small RNA-Sequencing Data
Authors: Kanke Matthew , Baran-Gale Jeanette , Villanueva Jonathan , Sethupathy Praveen
Published: December 2017

Small non-coding RNAs, in particular microRNAs, are critical for normal physiology and are candidate biomarkers, regulators, and therapeutic targets for a wide variety of diseases. There is an ever-growing interest in the comprehensive and accurate annotation of microRNAs across diverse cell types, conditions, species, and disease states. Highthroughput sequencing technology has emerged as the method of choice for profiling microRNAs. Specialized bioinformatic strategies are required to mine as much meaningful information as possible from the sequencing data to provide a comprehensive view of the microRNA landscape. Here we present miRquant 2.0, an expanded bioinformatics tool for accurate annotation and quantification of microRNAs and their isoforms (termed isomiRs) from small RNA-sequencing data. We anticipate that miRquant 2.0 will be useful for researchers interested not only in quantifying known microRNAs but also mining the rich well of additional information embedded in small RNA-sequencing data.
Performance of GPS sidereal filters during a satellite outage
Authors: Atkins C. , Ziebart M. K.
Published: December 2017

Sidereal filtering is the name of a technique used to reduce the effect of multipath interference on a GPS position time series associated with a static or quasi-static antenna. This article assesses the impact of a GPS satellite outage on the performance of a sidereal filter. Two different types of sidereal filter are tested: a position-domain sidereal filter (PDSF) and an observation-domain sidereal filter (ODSF). A satellite outage is simulated at two static receivers with contrasting antenna types and multipath environments. At both stations, the ODSF is more effective than a PDSF at removing multipath error over averaging intervals under around 200 seconds in length whether there is an outage or not. However, difference in the performance of the two types of sidereal filter was much more significant at the station more prone to multipath interference. The results are particularly relevant for applications where high-rate precise point positioning (PPP) is used for monitoring: If a PDSF is applied, then errors due to highfrequency multipath interference may still alias into the resulting position time series if a satellite outage occurs and possibly increasing the false alarm rate. In contrast, an ODSF is likely to perform better in such circumstances.
The System of Means for Overcoming the Crisis – Based on an Empirical Examination at Companies in Budapest and Békés County, Hungary
Authors: Chovan Brigitta , Poór József , Juhász Tímea
Published: December 2017

The economic crisis started in 2008 had a significant negative impact on employment in most sectors. During the research authors sought the answer to the question which employment systems were applied for overcoming the crisis at companies in Budapest and Békés County. To examine this, the authors compiled the questionnaire in co-operation with the Hungarian Chamber of Commerce and Industry and the Management and HR Research Centre of Szent István University.

The authors’ questionnaire findings also provide a proof for the fact that by creating and implementing the suitable human resource management models and by promoting them widely, the changes due to the current economic circumstances will be manageable and the increase in the competitiveness of organizations will be ensured.

One of the ways to decrease the personnel costs is to apply atypical employment forms. This form of employment is becoming more and more popular among employers; yet, despite the achievements, those questioned still prefer traditional employment forms.
Succesfull International Negotiations
Authors: Cichosz Izabela
Published: December 2017

Today’s concept of economic globalization is predicated and centered around a sustainable development various economic systems which focus on their ability to achieve the best possible results today without jeopardizing the ability of national economies to meet their needs in the future. Beginning with the fact that globalization has become a pre-requisite for most companies today, regardless of its size or scope of operations, I will, in this paper talk about the theoretical issues that surround globalization of an economy, different types and stages of international transactions and the business communications that go on within these internationalization stages.
The Impact of Perceived Ethical Leadership and Organizational Culture on Job Satisfaction with the Mediating Role of Organizational Commitment in Private Educational Sector of Islamabad, Pakistan
Authors: Rizwan Muhammad , Zeeshan Chaudhary , Mahmood Saba
Published: December 2017

The current study inspects the relationship among ethical leadership, organizational culture and job satisfaction with the mediating role of an organizational commitment in private educational sector of Islamabad, Pakistan. For this study data is collected through a survey of 210 employees of the education sector of Pakistan in October, 2016. The data is analyzed using SPSS 20.0 software through different statistical tests. The findings established the positive relationships among organizational culture, ethical leadership and job satisfaction with the mediating role of an organizational commitment. It is also observed that ethical leadership and organizational culture increases the job performance. The findings of the current study propose teachers and managers to encourage ethical leadership and create a positive culture to enhance organizational commitment and job satisfaction.
Adherence to growth hormone therapy in children and its potential barriers
Authors: Mohseni Shahrzad , Heydari Zahra , Qorbani Mostafa , Radfar Mania
Published: December 2017

Background:

One of the main concerns in chronic diseases such as growth hormone (GH) deficiency is adherence to the treatment, which significantly affects treatment outcomes.

Methods:

This cross-sectional study was conducted among 169 GH recipient children (2–12 years) and teens (13–19 years) referred to a GH distributing teaching pharmacy. The eight-item Morisky Medication Adherence Scale (MMAS) and auto-compliance method were used for the assessment of patients’ adherence to GH. The potential barriers to GH therapy adherence and medication persistence were also explored.

Results:

Based on the MMAS method, 56.7% of the children and 57.9% of the adolescent groups were adherent to GH therapy. Conversely, according to the auto-compliance method almost all the patients were adherent in the children (95.2%) and adolescent (95.5%) groups. Forgetting to take the injection or refill the prescription, being away from home, exhaustion from long-term injection, drug shortage and inaccessibility to the pharmacy were barriers found to be significantly associated with a low adherence in the children group. While in the adolescent group, forgetting to take the injection, painful injection, concern about long-term complications and exhaustion from long-term injection revealed a significant association with low adherence. Persistence with GH therapy was reported in 75.3% and 67% of children and adolescent patients, respectively.

Conclusions:

The current study revealed that overall adherence of the study population is low. Considering the barriers with significant association with adherence, different strategies can be incorporated to enhance adherence to GH therapy, i.e. providing early patient and parent education and support, medication reminder systems and longer duration of GH prescriptions.
The first trimester aneuploidy biochemical markers in IVF/ICSI patients have no additional benefit compared to spontaneous conceptions in the prediction of pregnancy complications
Authors: Szymusik Iwona , Kosinski Przemyslaw , Kosinska-Kaczynska Katarzyna , Warzecha Damian , Karwacka Anetta , Kaczynski Bartosz , Wielgos Miroslaw
Published: December 2017

Objectives:

The aim of this study was to determine if the levels of biochemical aneuploidy markers in in vitro fertilisation (IVF)/intracytoplasmic sperm injection (ICSI) pregnancies differ from those in spontaneous pregnancies and to verify if biochemical markers could predict pregnancy outcome in IVF/ICSI gestations.

Methods:

This was a prospective observational study performed in a group of 551 patients who underwent a combined first trimester prenatal screening (ultrasound scan and serum markers). All patients were divided into two groups according to the mode of conception: IVF/ICSI pregnancies (study group) and spontaneous conceptions (control group). The concentrations of first trimester biochemical markers were presented as multiples of median (MoM) and were compared between the study and control groups. Analysed pregnancy complications included: preterm delivery (PTD), small for gestational age (SGA), gestational hypertension (GH), preeclampsia (PE) and gestational diabetes (GDM).

Results:

The analysis was performed on 183 IVF/ICSI and 368 spontaneously conceived gestations, with complete data regarding obstetric outcome. There were no significant differences in the concentrations of biochemical markers between the analysed groups. Pregnancy-associated plasma protein-A (PAPP-A) levels were lower in hypertensive than in normotensive patients, although the difference was not significant. Twenty-three patients had GDM (12.5%), 16 had GH or PE (8.7%), SGA was diagnosed in 18 (9.8%) and 25 delivered preterm (13.6%).

Conclusions:

The trend for lower PAPP-A MoM was visible in all affected patients, although the results did not reach statistical significance. The first trimester biochemical markers in assisted reproduction technique (ART) pregnancies do not seem to have additional effect on predicting the risk of pregnancy complications.
Influence of α-lipoic acid on morphology of organs of rabbits fed a high fat diet with the addition of oxidised rapeseed oil
Authors: Stawiarska-Pięta Barbara , Zalejska-Fiolka Jolanta , Wyszyńska Magdalena , Kleczka Anna , Janiga Beata , Grzegorzak Natalia , Birkner Ewa
Published: December 2017

Introduction: The aim of the study was to assess the influence of α-lipoic acid (ALA) on the morphology of the aorta and liver of rabbits fed high fat diet with addition of oxidised (ORO) and non-oxidised rapeseed oil (N-ORO).

Material and Methods: The study was conducted on male chinchilla rabbits divided into six groups. The control group (C) was fed a breeding standard diet (BSD), group I received BSD with the addition of ALA in the dose of 10 mg/kg b.w., groups II and III received BSD enriched with 10% addition of N-ORO or ORO, whereas rabbits from groups IV and V received BSD with 10% addition of N-ORO or ORO and ALA.

Results: Addition of ORO caused necrosis and steatosis of hepatocytes, as well as atherosclerotic plaques of various intensification in the aorta. In the liver of rabbits from group II (N-ORO) infiltrations of mononuclear cells was observed in the area of liver triads and between liver lobules. The beneficial influence of ALA was demonstrated in rabbits fed a diet containing N-ORO or ORO. In case of ORO, the activity of ALA was not fully effective.

Conclusion: Diet supplementation with ALA counteracts the changes generated in the liver and aorta under increased exposure to higher fat content in diet, in particular thermally treated fats.
Saving America’s Endangered Recordings:NEDCC’s Conservation Ethic for the Preservation of Significant Audio Media
Authors: Martin Julie
Published: December 2017

Audio recordings may be the most endangered of Americas collections, due to rapidly deteriorating media material, the scarcity of equipment for playback, and the diminishing numbers of professionals who have the skills for repairing legacy equipment and reformatting audio using traditional analog methods. The evidence for the size of the problem may be found in a variety of studies prompted by the National Recording Preservation Act of 2000 (H.R.4846). The resulting National Recording Preservation Plan by the Library of Congress and the Council on Library and Information Resources (CLIR) was released in 2012.
Interest in screening examinations among cancer patients
Authors: Humeniuk Ewa , Dąbska Olga , Pawlikowska-Łagód Katarzyna , Goś Anna , Matuska Małgorzata
Published: December 2017

Aim. To determine the influence of socio-demographic variables on attendance rate at screening examinations in cancer patients. Material and methods. The research group comprised of 100 cancer patients. The method applied in the research was a diagnostic survey. The research instrument was the authors‘ own questionnaire specially compiled to measure cancer patients‘ interest in screening examinations. The research material was analysed with the statistical packet STATISTICA 12 and Microsoft Office Excel software. Significance level was assumed at p<0.05 to determine statistically significant differences and dependencies. A Chi2 test was used in the research. Results. The surveyed patients mostly did not participate in screening examinations aimed at diagnosing cancer (66%). Their Age (p=0.05), gender (p=0.003) and place of residence (p=0.04) determined their participation rate in screening tests. The patients‘ marital status (p=0.47), education (p=0.85) and economic status (p=0.13) did not affect their willingness to attend screening examinations. Conclusions. The process of cancer incidence and death rate limitation requires greater participation of the population in prevention programmes.
The comparison of cardiovascular risk factors prevalence among Catholics and Seventh-day Adventists living in southern Poland
Authors: Majda Anna , Zalewska-Puchała Joanna , Bodys-Cupak Iwona , Kamińska Alicja , Suder Marcin
Published: December 2017

Introduction. A review literature concerning the religious affiliation and that of cardiovascular disease did not show any clear correlations between these variables. Aim. To determine selected cardiovascular risk factors and the risk of a cardiovascular event among Seventh-day Adventists (SDA) and Catholics. Material and Methods. A cross-sectional study was carried out in the years 2014-2015 among 252 people, including 118 Seventhday Adventists and 134 Catholics over 18 years of age, residents of southern Poland. The results of the following were analysed: anthropometric measurements, an interview questionnaire, physical examination and laboratory tests, as well as the SCORE scale. Results. The mean concentration of homocysteine and triglycerides in Catholics was significantly higher than in Adventists. Adventists had significantly higher blood pressure and mean HDL cholesterol concentration than Catholics. On the basis of BMI, overweight and obesity were ascertained in a somewhat greater percentage of Catholics than Adventists, and on the basis of waist circumference, android obesity was found to be more common in Catholics than in Adventists. Conclusions. Based on the SCORE scale, the risk of a cardiovascular event was significantly higher in Catholics than in Adventists.
A Review of the Relationship between Novelty, Intrinsic Motivation and Reinforcement Learning
Authors: Siddique Nazmul , Dhakan Paresh , Rano Inaki , Merrick Kathryn
Published: December 2017

This paper presents a review on the tri-partite relationship between novelty, intrinsic motivation and reinforcement learning. The paper first presents a literature survey on novelty and the different computational models of novelty detection, with a specific focus on the features of stimuli that trigger a Hedonic value for generating a novelty signal. It then presents an overview of intrinsic motivation and investigations into different models with the aim of exploring deeper co-relationships between specific features of a novelty signal and its effect on intrinsic motivation in producing a reward function. Finally, it presents survey results on reinforcement learning, different models and their functional relationship with intrinsic motivation.
Artificial learners adopting normative conventions from human teachers
Authors: Cederborg Thomas
Published: December 2017

This survey provides an overview of implemented systems, theoretical work, as well as studies of biological systems relevant to the design of artificial learners trying to figure out what a human teacher would like them to do. Implementations of artificial learners are covered, with a focus on experiments trying to find better interpretations of human behavior, as well as algorithms that autonomously improve a model of the teacher. A distinction is made between learners trying to interpret teacher behavior in order to learn what the teacher would like the learner to do on the one hand, and learners whose explicit or implicit goal is to get something from the teacher on the other hand (for example rewards, or knowledge about how the world works). The survey covers the former type of systems. Human teachers are covered, focusing on studies that say something concrete about how one should interpret the behavior of a human teacher that is interacting with an artificial learner. Certain types of biological learners are interesting as inspiration for the types of artificial systems we are concerned with. The survey focus on studies of biological learners adopting normative conventions, as well as joint intentionality team efforts.
“What Kind of Death?”: On the Phaedo’s double topic
Authors: Thanassas Panagiotis
Published: December 2017

The Socratic instruction (64b) to clarify “what kind of death” a philosopher would deserve suggests two different notions of “death” in the Phaedo: physical demise and philosophy. This double meaning makes it possible for the Platonic Socrates to address a dual audience with a dual purpose: His interlocutors will receive consolation, while the perceptive reader will focus on practicing philosophy on the basis of the hypothesis of Forms. Socrates’ final words can also be illuminated as a vindication of his adherence to logos: the cock to Asclepius has to be offered as a sign of gratitude for healing misology.
Structuring a Program in Elite Professional Soccer
Authors: Walker Gary J. , Hawkins Richard
Published: December 2017

THIS ARTICLE DISCUSSES THE PROCESSES THAT ARE UNDERTAKEN BY THE CONDITIONING COACHES OF ELITE SOCCER CLUBS WHEN PLANNING THE TRAINING PROGRAM FOR PROFESSIONAL PLAYERS. TO SUCCESSFULLY MANAGE THE TRAINING REQUIREMENTS OF A SQUAD OF PLAYERS THROUGHOUT A SEASON, IT IS IMPORTANT TO STRUCTURE TRAINING APPROPRIATELY USING STRATEGIES TO IDENTIFY THE INDIVIDUAL NEEDS OF PLAYERS, ENSURING THAT THOSE REQUIREMENTS ARE MET WITHIN THE CONSTRAINTS OF THE ANNUAL CALENDAR. THE OVERALL AIM IS TO MAXIMIZE SQUAD AVAILABILITY WHILE OPTIMIZING PLAYER READINESS FOR MATCHES, ENSURING THAT EACH PLAYER HAS THE PHYSICAL CAPABILITY TO IMPLEMENT THE REQUIRED TACTICS SUCCESSFULLY.