bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Black Swan in clinical laboratory practice: the analytical error due to interferences in immunoassay methods
Authors: Clerico Aldo , Belloni Lucia , Carrozza Cinzia , Correale Mario , Dittadi Ruggero , Dotti Claudio , Fortunato Antonio , Vignati Giulio , Zucchelli Gian Carlo , Migliardi Marco 
Published: December 2017

Abstract
It is well known that the results of immunoassay methods can be affected by specific or non-specific interferences, ranging from 0.4% to 4.0%. The presence of interference may greatly compromise the accuracy of immunoassay analyses causing an error in the measurement, producing false-positive or false-negative results. From a clinical point of view, these analytical errors may have serious implications for patient care because they can cause misdiagnosis or inappropriate treatment. Unfortunately, it is a very difficult task to identify the irregular analytical errors related to immunoassay methods because they are not detectable by normal laboratory quality control procedures, are reproducible within the test system, may be clinically plausible and are relatively rare. The first line of defense against erroneous results is to use in laboratory practice only immunoassay systems with the highest level of robustness against interference. The second line of defense is always taking into account the possibility of interference in immunoassay results. A correct approach should be addressed on identification of samples at high risk of interference. The attainment of this goal requires a critical review of the test result in relation to patient’s clinical conditions and literature data, taking into account the analytical characteristics of the immunoassay system. The experts in immunoassay systems should make every effort to find some specific and reliable quality indicators for irregular analytical errors in order to better detect and monitor erroneous immunoassay results due to specific or non-specific interferences.
Pitting corpus-based classification models against each other: a case study for predicting constructional choice in written Estonian
Authors: Klavan Jane 
Published: December 2017

AbstractIn the context of constructional alternatives, we may assume that speakers’ choice between alternative forms is influenced by a multitude of factors. At the moment, multivariate statistical classification modelling seems to be the best tool available to capture this knowledge quantitatively. There is a vast array of techniques available. In this paper, two distinct modelling techniques are applied – logistic regression and naïve discriminative learning – to predict the choice between two constructional alternatives in written Estonian. One of the central questions in statistical modelling concerns the evaluation of model fit. It is proposed that for linguistic analysis, the performance of alternative corpus-based models can be evaluated by, first, pitting them against each other and second, pitting them against experimental data. Previous work on modelling constructional and lexical choice has focused on one of the two aspects. The present paper takes this line of analysis further by combining the two approaches.
Scale dependence of biotic homogenisation by urbanisation: a comparison of urban bird communities between central Argentina and northern Finland
Authors: Leveau Lucas M. , Jokimäki Jukka , Kaisanlahti-Jokimäki Marja-Liisa 
Published: December 2017

AbstractRecent studies showed contrasting results about the homogenising force of urbanisation on bird community composition at large and regional scales. We studied whether urbanisation promotes the homogenisation of wintering bird communities and if this varies when comparing towns located within a specific region and towns located in two different biomes of two countries. We used both similarity indices based on the presence/absence data and the abundance data in comparing communities. Processes governing bird community dissimilarity between urbanisation levels were examined with the partitioning of Sörensen index in species turnover and nestedness. We made bird surveys in town centres and suburban habitats of three cities located in the Pampean region of Argentina and in the boreal region of Finland using a single-visit study plot method. Rarefacted species richness did not differ amongst the town centres between the countries, but it was higher in the suburban areas of Argentina than in Finland. At the country-level comparison, we found a higher similarity amongst the town centres than amongst the suburban areas; whereas at the regional comparison, similarity between town centres was comparable to the similarity between suburban areas. The use of an abundance-based index produced a higher similarity between town centre communities of both countries than when using a presence-based index. The dissimilarity between habitats in Argentina was related to nestedness and to species turnover in Finland. Our results indicate that urban-based biotic homogenisation of bird communities is dependent on the scale used, being more evident when comparing cities of different biomes where the same and abundant bird species, such as sparrows and doves, dominate. At the regional scale, quite a high beta-diversity can still be found within urban habitats. Processes of community dissimilarity between urban habitats may differ according to the regional pool of species, being more related to nestedness toward the tropics.
Trends in High Nature Value farmland studies: A systematic review
Authors: Benedetti Yanina 
Published: December 2017

AbstractBackground. Since the High Nature Value (HNV) concept was defined in the early 1990s, several studies on HNV farmland has been increasing over the past 30 years in Europe, highlighting the interest by scientific community of HNV farming systems supporting biodiversity conservation. The aim of this study was to evaluate the trends and main gaps on HNV farmland peer-reviewed publications in order to contribute to the effectiveness of future research in this field. Methods. Searches were conducted using the databases Web of SciencesTM and Scopus in order to identify only peer-reviewed articles on HNV farmland, published prior to July 2017. The inclusion and exclusion criteria were developed a priori. Data as year, country, type of document, subject area, taxa studied and biodiversity metrics assessed were extracted and explored in order to analyse the spatial and temporal distribution of the concept, including the main topics addressed in HNV farmland literature. Results. After screening 308 original articles, 90 were selected for this review. HNV farmland studies involved several disciplines, mainly biodiversity and conservation and environmental sciences and ecology. Most peer-reviewed articles focused on HNV farming were conducted in Spain, Italy, Ireland and Portugal. The main studied taxa were plants and birds. Taxonomic diversity was the biodiversity metric more often used to assess the biodiversity status on HNV farmland areas. A positive correlation was found between HNV farmland area and HNV farmland studies conducted in respective countries. Discussion. The HNV farmland research subject is a relative novel approach, and this systematic review provides a comprehensive overview about the main topics in the HNV farmland peer-reviewed literature contributing to highlight the main gaps and provide some considerations in order to assist the performance of HNV farming systems and conservation policies, addressed to sustain high levels of biodiversity.
Simulated Cell Division Processes of the Xenopus Cell Cycle Pathway by Genomic Object Net
Authors: Matsui Mika , Fujita Sachie , Suzuki Shunichi , Matsuno Hiroshi , Miyano Satoru 
Published: December 2017

Summary Matsuno et al.[1] modeled and simulated that multicellular patterning by the Drosophila Delta-Notch signaling pathway by using the software “Genomic Object Net” which was developed based on hybrid functional Petri net (HFPN) architecture. In this model, cellular formation is fixed throughout the simulation. This paper constructs an HFPN model of the Xenopus cell cycle pathway, which includes the mechanism for cell division control as well as checkpoint processes. This model simulates dynamic cell division processes of the early Xenopus embryo, including the changes in cell division cycles from synchronous to asynchronous.
A Multi-Scale Modeling Concept and Computational Tools for the Integrative Analysis of Stationary Metabolic Data
Authors: Lieres Eric von , Petersen Sören , Wiechert Wolfgang 
Published: December 2017

SummaryMetabolic Engineering aims at the systematic analysis and targeted manipulation of the metabolism in biotechnologically utilized microorganisms [1,2]. Recently, consistent stationary in vivo data sets of intracellular metabolite concentrations, fluxes and specific enzyme activities have become available for this purpose [3,4]. For the integrative analysis of the metabolic data at hand, a novel multi-scale modeling concept, computeralgebraic methods and efficient numerical algorithms are proposed. The available metabolic data are typically afflicted with comparatively large measurement errors. Therefore, reliable comprehensive error estimations are essential for the reasonable interpretation of consecutive outcomes, such as simulation results. The concepts, methods and algorithms are first presented as universal methods and subsequently applied to the anaplerotic regulation in lysine-producing Corynebacterium glutamicum. A multi-scale model is set up, fitted to the available experimental data and validated by the prediction of further experiments. This model is capable of forecasting the quantitative effect of changes in the specific activity of anaplerotic enzymes, namely phosphoenolpyruvate carboxylase, pyruvate carboxylase and phosphoenolpyruvate carboxykinase, on lysine productivity and yield.
Integration of Data in Pathogenomics: Three Layers of cellular complexity and an XML-based Framework
Authors: Dünßer M. , Lampidis R. , Schmidt S. , Seipel D. , Dandekar T. 
Published: December 2017

Summary Integration of data in pathogenomics is achieved here considering three different levels of cellular complexity: (i) genome and comparative genomics, (ii) enzyme cascades and pathway analysis, (iii) networks including metabolic network analysis.After direct sequence annotation exploiting tools for protein domain annotation (e.g. AnDOM) and analysis of regulatory elements (e.g. the RNA analyzer tool) the analysis results from extensive comparative genomics are integrated for the first level, pathway alignment adds data for the pathway level, elementary mode analysis and metabolite databanks add to the third level of cellular complexity. For efficient data integration of all data the XML based platform myBSMLStudio2003 is discussed and developed here. It integrates XQuery capabilities, automatic scripting updates for sequence annotation and a JESS expert system shell for functional annotation. In the context of genome annotation platforms in place (GenDB, PEDANT) these different tools and approaches presented here allow improved functional genome annotation as well as data integration in pathogenomics.
Searching for ncRNAs in eukaryotic genomes: Maximizing biological input with RNAmotif
Authors: Collins Lesley J. , Macke Thomas J. , Penny David 
Published: December 2017

Summary Non-coding RNAs (ncRNAs) contain both characteristic secondary-structure and short sequence motifs. However, “complex” ncRNAs (RNA bound to proteins in ribonucleoprotein complexes) can be hard to identify in genomic sequence data. Programs able to search for ncRNAs were previously limited to ncRNA molecules that either align very well or have highly conserved secondary-structure. The RNAmotif program uses additional information to find ncRNA gene candidates through the design of an appropriate “descriptor” to model sequence motifs, secondary-structure and protein/RNA binding information. This enables searches of those ncRNAs that contain variable secondary-structure and limited sequence motif information. Applying the biologically-based concept of “positive and negative controls” to the RNAmotif search technique, we can now go beyond the testing phase to successfully search real genomes, complete with their background noise and related molecules. Descriptors are designed for two “complex” ncRNAs, the U5snRNA (from the spliceosome) and RNaseP RNA, which successfully uncover these sequences from some eukaryotic genomes. We include explanations about the construction of the input “descriptors” from known biological information, to allow searches for other ncRNAs. RNAmotif maximizes the input of biological knowledge into a search for an ncRNA gene and now allows the investigation of some of the hardest-to-find, yet important, genes in some very interesting eukaryotic organisms.
Matching of PDB chain sequences to information in public databases as a prerequisite for 3D functional site visualization
Authors: Dieterich Guido , Heinz Dirk W. , Reichelt Joachim 
Published: December 2017

Abstract The 3D structures of biomacromolecules stored in the Protein Data Bank [1] were correlated with different external, biological information from public databases. We have matched the feature table of SWISS-PROT [2] entries as well InterPro [3] domains and function sites with the corresponding 3D-structures. OMIM [4] (Online Mendelian Inheritance in Man) records, containing information of genetic disorders, were extracted and linked to the structures. The exhaustive all-against-all 3D structure comparison of protein structures stored in DALI [5] was condensed into single files for each PDB entry. Results are stored in XML format facilitating its incorporation into related software. The resulting annotation of the protein structures allows functional sites to be identified upon visualization.
Using gene networks to drug target identification
Authors: Jiang Zhenran , Zhou Yanhong 
Published: December 2017

Abstract The complete genome sequences have provided a plethora of potential drug targets. Gene network technique holds the promise of providing a conceptual framework for analysis of the profusion of biological data being generated on potential drug targets and providing insights to understand the biological regulatory mechanisms in diseases, which are playing an increasingly important role in searching for novel drug targets from the information contained in genomics. In this paper, we discuss some of the network-based approaches for identifying drug targets, with the emphasis on the gene network strategy. In addition, some of the relevant data resources and computational tools are given.
Identification of embryo specific human isoforms using a database of predicted alternative splice forms
Authors: Pospisil Heike 
Published: December 2017

Abstract Alternative splicing is one of the most important mechanisms to generate a large number of mRNA and protein isoforms from a small number of genes. Its study became one of the hot topics in computational genome analysis. The repository EASED (Extended Alternatively Spliced EST Database, http://eased.bioinf.mdc-berlin.de/) stores a large collection of splice variants predicted from comparing the human genome against EST databases. It enables finding new unpublished splice forms that could be interesting candidate genes for stage specific, diseases specific or tissue specific splicing. The main idea behind selecting specific splice forms is to compare the number and the origin of ESTs confirming one isoform with the number and the origin of ESTs confirming the opposite isoform. A measure asDcs is introduced to take into account the unequal distribution of ESTs per splice site on one hand, and the possible uncertainties due to the relatively low quality of EST data on the other hand. First, the number of ESTs per splice site is scaled with a modified Hill function. The measure asDcs computes in the second step the distance of each pair of ESTs from equipartition. Equipartition exists if for every number of adult ESTs the same number of embryonic ESTs. The effect of several input parameters for the scaling of true EST values is analysed and can be reproduced on http://cardigan.zbh.uni-hamburg.de/asDcs. Some of the obtained best scoring hits for selected parameters (transcription factor P65, drebrin, and fetuin) have been already described in literature as been involved in embryonic development. This result shows the plausibility of this approach and looks promising for the identification of unplublished embryo specific alternative splice sites in human.
A structural keystone for drug design
Authors: Rother Kristian , Dunkel Mathias , Michalsky Elke , Trissl Silke , Goede Andrean , Leser Ulf , Preissner Robert 
Published: December 2017

Abstract 3D-structures of proteins and potential ligands are the cornerstones of rational drug design. The first brick to build upon is selecting a protein target and finding out whether biologically active compounds are known. Both tasks require more information than the structures themselves provide. For this purpose we have built a web resource bridging protein and ligand databases. It consists of three parts: i) A data warehouse on annotation of protein structures that integrates many well-known databases such as Swiss-Prot, SCOP, ENZYME and others. ii) A conformational library of structures of approved drugs. iii) A conformational library of ligands from the PDB, linking the realms of proteins and small molecules. The data collection contains structures of 30,000 proteins, 5,000 different ligands from 70,000 ligand-protein complexes, and 2,500 known drugs. Sets of protein structures can be refined by criteria like protein fold, family, metabolic pathway, resolution and textual annotation. The structures of organic compounds (drugs and ligands) can be searched considering chemical formula, trivial and trade names as well as medical classification codes for drugs (ATC). Retrieving structures by 2D-similarity has been implemented for all small molecules using Tanimoto coefficients. For the drug structures, 110,000 structural conformers have been calculated to account for structural flexibility. Two substances can be compared online by 3D-superimposition, where the pair of conformers that fits best is detected. Together, these web-accessible resources can be used to identify promising drug candidates. They have been used in-house to find alternatives to substances with a known binding activity but adverse side effects.
Network integration of data and analysis of oncology interest
Authors: Romano P. , Bertolini G. , De Paoli F. , Fattore M. , Marra D. , Mauri G. , Merelli E. , Porro I. , Scaglione S. , Milanesi L. 
Published: December 2017

Summary The Human Genome Project has deeply transformed biology and the field has since then expanded to the management, processing, analysis and visualization of large quantities of data from genomics, proteomics, medicinal chemistry and drug screening. This huge amount of data and the heterogeneity of software tools that are used implies the adoption on a very large scale of new, flexible tools that can enable researchers to integrate data and analysis on the network. ICT technology standards and tools, like Web Services and related languages, and workflow management systems, can support the creation and deployment of such systems. While a number of Web Services are appearing and personal workflow management systems are also being more and more offered to researchers, a reference portal enabling the vast majority of unskilled researchers to take profit from these new technologies is still lacking. In this paper, we introduce the rationale for the creation of such a portal and present the architecture and some preliminary results for the development of a portal for the enactment of workflows of interest in oncology.
Noise in Genetic Toggle Switch Models
Authors: Andrecut M. , Kauffman S. A. 
Published: December 2017

Summary In this paper we study the intrinsic noise effect on the switching behavior of a simple genetic circuit corresponding to the genetic toggle switch model. The numerical results obtained from a noisy mean-field model are compared to those obtained from the stochastic Gillespie simulation of the corresponding system of chemical reactions. Our results show that by using a two step reaction approach for modeling the transcription and translation processes one can make the system to lock in one of the steady states for exponentially long times.
The implications for Bioinformatics of integration across physical scales
Authors: Hodgman T.C. , Ugartechea-Chirino Y. , Tansley G. , Dryden I. 
Published: December 2017

Abstract Bioinformatics blossomed with research developments in molecular biology. But as the focus of research moves back up the physical scale to the biology of whole multicellular organisms, there are new integration challenges. Data integration is a perennial theme that will not be explored here. Rather, we outline a survey of the types of data generated in whole organisms, putting particular emphasis on complex image capture, management and analysis, bio-systems modelling techniques at this higher scale, and approaches to integrating models across these physical scales. This change in biological focus raises certain challenges, one of which may be the need to retrain bioinformaticians in sciences pertaining to whole plants and animals.
Targeted Projection Pursuit Tool for Gene Expression Visualisation
Authors: Faith Joe , Brockway Michael 
Published: December 2017

Summary A tool is introduced that uses a novel technique to enable users to explore two-dimensional views of high dimensional gene expression data sets. Unlike other such tools, the interface is intuitive and efficient, allowing the user to easily select views that meet their requirements. The tool is tested on publicly available gene expression data sets and demonstrated to find views that show the seperation of gene expression data sets into classes more effectively than standard dimension-reduction methods.
The BioRSTM Integration and Retrieval System: An open system for distributed data integration
Authors: Kaps Andreas , Dyshlevoi Konstantin , Heumann Klaus , Jost Ralf , Kontodinas Ioannis , Wolff Martin , Hani Jean 
Published: December 2017

Summary Modern academic and industrial research in life sciences generates huge amounts of data and information. To extract knowledge from this information space, optimized integration and retrieval software tools are essential. In the last years, a number of academic as well as commercial systems have been developed to solve this problem. However, as scientific projects are distributed at different locations (e.g., subsidiaries of companies, academic partnerships), data exchange and availability must be realized in a way that avoids data replication.In this article, we describe a global solution for integrating distributed information by applying the BioRSTM Integration and Retrieval System and its inter-BioRS communication capability that goes beyond the standard issue of local data integration. Each site integrates and maintains locally generated data using a local copy of the BioRS software. Applying the inter-BioRS communication, all available BioRS instances can communicate with each other realizing a global network of integrated databanks. All databanks integrated in this network can be accessed from any site without any data replication. This open system allows the addition of new information and sites dynamically. However, access privileges for certain databanks can be maintained on a per user and databank level ensuring data security when required.