bluuebunny/crossref_metadata_2025_split huggingface dataset:
Annotation and visualization of endogenous retroviral sequences using the Distributed Annotation System (DAS) and eBioX
Authors: Martínez Barrio Álvaro , Lagercrantz Erik , Sperber Göran O , Blomberg Jonas , Bongcam-Rudloff Erik 
Published: June 2009

Abstract

Background
The Distributed Annotation System (DAS) is a widely used network protocol for sharing biological information. The distributed aspects of the protocol enable the use of various reference and annotation servers for connecting biological sequence data to pertinent annotations in order to depict an integrated view of the data for the final user.

Results
An annotation server has been devised to provide information about the endogenous retroviruses detected and annotated by a specialized in silico tool called RetroTector. We describe the procedure to implement the DAS 1.5 protocol commands necessary for constructing the DAS annotation server. We use our server to exemplify those steps. Data distribution is kept separated from visualization which is carried out by eBioX, an easy to use open source program incorporating multiple bioinformatics utilities. Some well characterized endogenous retroviruses are shown in two different DAS clients. A rapid analysis of areas free from retroviral insertions could be facilitated by our annotations.

Conclusion
The DAS protocol has shown to be advantageous in the distribution of endogenous retrovirus data. The distributed nature of the protocol is also found to aid in combining annotation and visualization along a genome in order to enhance the understanding of ERV contribution to its evolution. Reference and annotation servers are conjointly used by eBioX to provide visualization of ERV annotations as well as other data sources. Our DAS data source can be found in the central public DAS service repository, http://www.dasregistry.org, or at http://loka.bmc.uu.se/das/sources.
The GENIUS Grid Portal and robot certificates: a new tool for e-Science
Authors: Barbera Roberto , Donvito Giacinto , Falzone Alberto , La Rocca Giuseppe , Milanesi Luciano , Maggi Giorgio Pietro , Vicario Saverio 
Published: June 2009

Abstract

Background
Grid technology is the computing model which allows users to share a wide pletora of distributed computational resources regardless of their geographical location. Up to now, the high security policy requested in order to access distributed computing resources has been a rather big limiting factor when trying to broaden the usage of Grids into a wide community of users. Grid security is indeed based on the Public Key Infrastructure (PKI) of X.509 certificates and the procedure to get and manage those certificates is unfortunately not straightforward. A first step to make Grids more appealing for new users has recently been achieved with the adoption of robot certificates.

Methods
Robot certificates have recently been introduced to perform automated tasks on Grids on behalf of users. They are extremely useful for instance to automate grid service monitoring, data processing production, distributed data collection systems. Basically these certificates can be used to identify a person responsible for an unattended service or process acting as client and/or server. Robot certificates can be installed on a smart card and used behind a portal by everyone interested in running the related applications in a Grid environment using a user-friendly graphic interface. In this work, the GENIUS Grid Portal, powered by EnginFrame, has been extended in order to support the new authentication based on the adoption of these robot certificates.

Results
The work carried out and reported in this manuscript is particularly relevant for all users who are not familiar with personal digital certificates and the technical aspects of the Grid Security Infrastructure (GSI). The valuable benefits introduced by robot certificates in e-Science can so be extended to users belonging to several scientific domains, providing an asset in raising Grid awareness to a wide number of potential users.

Conclusion
The adoption of Grid portals extended with robot certificates, can really contribute to creating transparent access to computational resources of Grid Infrastructures, enhancing the spread of this new paradigm in researchers' working life to address new global scientific challenges. The evaluated solution can of course be extended to other portals, applications and scientific communities.
A novel similarity-measure for the analysis of genetic data in complex phenotypes
Authors: Lagani Vincenzo , Montesanto Alberto , Di Cianni Fausta , Moreno Victor , Landi Stefano , Conforti Domenico , Rose Giuseppina , Passarino Giuseppe 
Published: June 2009

Abstract

Background
Recent technological advances in DNA sequencing and genotyping have led to the accumulation of a remarkable quantity of data on genetic polymorphisms. However, the development of new statistical and computational tools for effective processing of these data has not been equally as fast. In particular, Machine Learning literature is limited to relatively few papers which are focused on the development and application of data mining methods for the analysis of genetic variability. On the other hand, these papers apply to genetic data procedures which had been developed for a different kind of analysis and do not take into account the peculiarities of population genetics. The aim of our study was to define a new similarity measure, specifically conceived for measuring the similarity between the genetic profiles of two groups of subjects (i.e., cases and controls) taking into account that genetic profiles are usually distributed in a population group according to the Hardy Weinberg equilibrium.

Results
We set up a new kernel function consisting of a similarity measure between groups of subjects genotyped for numerous genetic loci. This measure weighs different genetic profiles according to the estimates of gene frequencies at Hardy-Weinberg equilibrium in the population. We named this function the "Hardy-Weinberg kernel".
The effectiveness of the Hardy-Weinberg kernel was compared to the performance of the well established linear kernel. We found that the Hardy-Weinberg kernel significantly outperformed the linear kernel in a number of experiments where we used either simulated data or real data.

Conclusion
The "Hardy-Weinberg kernel" reported here represents one of the first attempts at incorporating genetic knowledge into the definition of a kernel function designed for the analysis of genetic data. We show that the best performance of the "Hardy-Weinberg kernel" is observed when rare genotypes have different frequencies in cases and controls. The ability to capture the effect of rare genotypes on phenotypic traits might be a very important and useful feature, as most of the current statistical tools loose most of their statistical power when rare genotypes are involved in the susceptibility to the trait under study.
Computational annotation of UTR cis-regulatory modules through Frequent Pattern Mining
Authors: Turi Antonio , Loglisci Corrado , Salvemini Eliana , Grillo Giorgio , Malerba Donato , D'Elia Domenica 
Published: June 2009

Abstract

Background
Many studies report about detection and functional characterization of cis-regulatory motifs in untranslated regions (UTRs) of mRNAs but little is known about the nature and functional role of their distribution. To address this issue we have developed a computational approach based on the use of data mining techniques. The idea is that of mining frequent combinations of translation regulatory motifs, since their significant co-occurrences could reveal functional relationships important for the post-transcriptional control of gene expression. The experimentation has been focused on targeted mitochondrial transcripts to elucidate the role of translational control in mitochondrial biogenesis and function.

Results
The analysis is based on a two-stepped procedure using a sequential pattern mining algorithm. The first step searches for frequent patterns (FPs) of motifs without taking into account their spatial displacement. In the second step, frequent sequential patterns (FSPs) of spaced motifs are generated by taking into account the conservation of spacers between each ordered pair of co-occurring motifs. The algorithm makes no assumption on the relation among motifs and on the number of motifs involved in a pattern. Different FSPs can be found depending on different combinations of two parameters, i.e. the threshold of the minimum percentage of sequences supporting the pattern, and the granularity of spacer discretization. Results can be retrieved at the UTRminer web site: http://utrminer.ba.itb.cnr.it/. The discovered FPs of motifs amount to 216 in the overall dataset and to 140 in the human subset. For each FP, the system provides information on the discovered FSPs, if any. A variety of search options help users in browsing the web resource. The list of sequence IDs supporting each pattern can be used for the retrieval of information from the UTRminer database.

Conclusion
Computational prediction of structural properties of regulatory sequences is not trivial. The presented data mining approach is able to overcome some limits observed in other competitive tools. Preliminary results on UTR sequences from nuclear transcripts targeting mitochondria are promising and lead us to be confident on the effectiveness of the approach for future developments.
Databases of homologous gene families for comparative genomics
Authors: Penel Simon , Arigon Anne-Muriel , Dufayard Jean-François , Sertier Anne-Sophie , Daubin Vincent , Duret Laurent , Gouy Manolo , Perrière Guy 
Published: June 2009

AbstractBackgroundComparative genomics is a central step in many sequence analysis studies, from gene annotation and the identification of new functional regions in genomes, to the study of evolutionary processes at the molecular level (speciation, single gene or whole genome duplications, etc.) and phylogenetics. In that context, databases providing users high quality homologous families and sequence alignments as well as phylogenetic trees based on state of the art algorithms are becoming indispensable.MethodsWe developed an automated procedure allowing massive all-against-all similarity searches, gene clustering, multiple alignments computation, and phylogenetic trees construction and reconciliation. The application of this procedure to a very large set of sequences is possible through parallel computing on a large computer cluster.ResultsThree databases were developed using this procedure: HOVERGEN, HOGENOM and HOMOLENS. These databases share the same architecture but differ in their content. HOVERGEN contains sequences from vertebrates, HOGENOM is mainly devoted to completely sequenced microbial organisms, and HOMOLENS is devoted to metazoan genomes from Ensembl. Access to the databases is provided through Web query forms, a general retrieval system and a client-server graphical interface. The later can be used to perform tree-pattern based searches allowing, among other uses, to retrieve sets of orthologous genes. The three databases, as well as the software required to build and query them, can be used or downloaded from the PBIL (Pôle Bioinformatique Lyonnais) site athttp://pbil.univ-lyon1.fr/.
DoOPSearch: a web-based tool for finding and analysing common conserved motifs in the promoter regions of different chordate and plant genes
Authors: Sebestyén Endre , Nagy Tibor , Suhai Sándor , Barta Endre 
Published: June 2009

Abstract

Background
The comparative genomic analysis of a large number of orthologous promoter regions of the chordate and plant genes from the DoOP databases shows thousands of conserved motifs. Most of these motifs differ from any known transcription factor binding site (TFBS). To identify common conserved motifs, we need a specific tool to be able to search amongst them. Since conserved motifs from the DoOP databases are linked to genes, the result of such a search can give a list of genes that are potentially regulated by the same transcription factor(s).

Results
We have developed a new tool called DoOPSearch http://doopsearch.abc.hu for the analysis of the conserved motifs in the promoter regions of chordate or plant genes. We used the orthologous promoters of the DoOP database to extract thousands of conserved motifs from different taxonomic groups. The advantage of this approach is that different sets of conserved motifs might be found depending on how broad the taxonomic coverage of the underlying orthologous promoter sequence collection is (consider e.g. primates vs. mammals or Brassicaceae vs. Viridiplantae). The DoOPSearch tool allows the users to search these motif collections or the promoter regions of DoOP with user supplied query sequences or any of the conserved motifs from the DoOP database. To find overrepresented gene ontologies, the gene lists obtained can be analysed further using a modified version of the GeneMerge program.

Conclusion
We present here a comparative genomics based promoter analysis tool. Our system is based on a unique collection of conserved promoter motifs characteristic of different taxonomic groups. We offer both a command line and a web-based tool for searching in these motif collections using user specified queries. These can be either short promoter sequences or consensus sequences of known transcription factor binding sites. The GeneMerge analysis of the search results allows the user to identify statistically overrepresented Gene Ontology terms that might provide a clue on the function of the motifs and genes.
The Mycoplasma conjunctivae genome sequencing, annotation and analysis
Authors: Calderon-Copete Sandra P , Wigger George , Wunderlin Christof , Schmidheini Tobias , Frey Joachim , Quail Michael A , Falquet Laurent 
Published: June 2009

Abstract

Background
The mollicute Mycoplasma conjunctivae is the etiological agent leading to infectious keratoconjunctivitis (IKC) in domestic sheep and wild caprinae. Although this pathogen is relatively benign for domestic animals treated by antibiotics, it can lead wild animals to blindness and death. This is a major cause of death in the protected species in the Alps (e.g., Capra ibex, Rupicapra rupicapra).

Methods
The genome was sequenced using a combined technique of GS-FLX (454) and Sanger sequencing, and annotated by an automatic pipeline that we designed using several tools interconnected via PERL scripts. The resulting annotations are stored in a MySQL database.

Results
The annotated sequence is deposited in the EMBL database (FM864216) and uploaded into the mollicutes database MolliGen http://cbi.labri.fr/outils/molligen/ allowing for comparative genomics.

Conclusion
We show that our automatic pipeline allows for annotating a complete mycoplasma genome and present several examples of analysis in search for biological targets (e.g., pathogenic proteins).
Functional assessment of time course microarray data
Authors: Nueda María José , Sebastián Patricia , Tarazona Sonia , García-García Francisco , Dopazo Joaquín , Ferrer Alberto , Conesa Ana 
Published: June 2009

Abstract

Motivation
Time-course microarray experiments study the progress of gene expression along time across one or several experimental conditions. Most developed analysis methods focus on the clustering or the differential expression analysis of genes and do not integrate functional information. The assessment of the functional aspects of time-course transcriptomics data requires the use of approaches that exploit the activation dynamics of the functional categories to where genes are annotated.

Methods
We present three novel methodologies for the functional assessment of time-course microarray data. i) maSigFun derives from the maSigPro method, a regression-based strategy to model time-dependent expression patterns and identify genes with differences across series. maSigFun fits a regression model for groups of genes labeled by a functional class and selects those categories which have a significant model. ii) PCA-maSigFun fits a PCA model of each functional class-defined expression matrix to extract orthogonal patterns of expression change, which are then assessed for their fit to a time-dependent regression model. iii) ASCA-functional uses the ASCA model to rank genes according to their correlation to principal time expression patterns and assess functional enrichment on a GSA fashion. We used simulated and experimental datasets to study these novel approaches. Results were compared to alternative methodologies.

Results
Synthetic and experimental data showed that the different methods are able to capture different aspects of the relationship between genes, functions and co-expression that are biologically meaningful. The methods should not be considered as competitive but they provide different insights into the molecular and functional dynamic events taking place within the biological system under study.
A supervised learning approach for taxonomic classification of core-photosystem-II genes and transcripts in the marine environment
Authors: Tzahor Shani , Man-Aharonovich Dikla , Kirkup Benjamin C , Yogev Tali , Berman-Frank Ilana , Polz Martin F , Béjà Oded , Mandel-Gutfreund Yael 
Published: June 2009

Abstract

Background
Cyanobacteria of the genera Synechococcus and Prochlorococcus play a key role in marine photosynthesis, which contributes to the global carbon cycle and to the world oxygen supply. Recently, genes encoding the photosystem II reaction center (psbA and psbD) were found in cyanophage genomes. This phenomenon suggested that the horizontal transfer of these genes may be involved in increasing phage fitness. To date, a very small percentage of marine bacteria and phages has been cultured. Thus, mapping genomic data extracted directly from the environment to its taxonomic origin is necessary for a better understanding of phage-host relationships and dynamics.

Results
To achieve an accurate and rapid taxonomic classification, we employed a computational approach combining a multi-class Support Vector Machine (SVM) with a codon usage position specific scoring matrix (cuPSSM). Our method has been applied successfully to classify core-photosystem-II gene fragments, including partial sequences coming directly from the ocean, to seven different taxonomic classes. Applying the method on a large set of DNA and RNA psbA clones from the Mediterranean Sea, we studied the distribution of cyanobacterial psbA genes and transcripts in their natural environment. Using our approach, we were able to simultaneously examine taxonomic and ecological distributions in the marine environment.

Conclusion
The ability to accurately classify the origin of individual genes and transcripts coming directly from the environment is of great importance in studying marine ecology. The classification method presented in this paper could be applied further to classify other genes amplified from the environment, for which training data is available.
Case reports describing treatments in the emergency medicine literature: missing and misleading information
Authors: Richason Tiffany P , Paulson Stephen M , Lowenstein Steven R , Heard Kennon J 
Published: June 2009

Abstract

Background
Although randomized trials and systematic reviews provide the "best evidence" for guiding medical practice, many emergency medicine journals still publish case reports (CRs). The quality of the reporting in these publications has not been assessed.

Objectives
In this study we sought to determine the proportion of treatment-related case reports that adequately reported information about the patient, disease, interventions, co-interventions, outcomes and other critical information.

Methods
We identified CRs published in 4 emergency medicine journals in 2000–2005 and categorized them according to their purpose (disease description, overdose or adverse drug reactioin, diagnostic test or treatment effect). Treatment-related CRs were reviewed for the presence or absence of 11 reporting elements.

Results
All told, 1,316 CRs were identified; of these, 85 (6.5%; 95CI = 66, 84) were about medical or surgical treatments. Most contained adequate descriptions of the patient (99%; 95CI = 95, 100), the stage and severity of the patient's disease (88%; 95CI = 79, 93), the intervention (80%; 95CI = 70, 87) and the outcomes of treatment (90%; 95CI = 82, 95). Fewer CRs reported the patient's co-morbidities (45%; 95CI = 35, 56), concurrent medications (30%; 95CI = 21, 40) or co-interventions (57%; 95CI = 46, 67) or mentioned any possible treatment side-effects (33%; 95CI = 24, 44). Only 37% (95CI = 19, 38) discussed alternative explanations for favorable outcomes. Generalizability of treatment effects to other patients was mentioned in only 29% (95CI = 20, 39). Just 2 CRs (2.3%; 95CI = 1, 8) reported a 'denominator" (number of patients subjected to the same intervention, whether or not successful.

Conclusion
Treatment-related CRs in emergency medicine journals often omit critical details about treatments, co-interventions, outcomes, generalizability, causality and denominators. As a result, the information may be misleading to providers, and the clinical applications may be detrimental to patient care.
Study protocol: a cluster randomised controlled trial of a school based fruit and vegetable intervention – Project Tomato
Authors: Kitchen Meaghan S , Ransley Joan K , Greenwood Darren C , Clarke Graham P , Conner Mark T , Jupp Jennifer , Cade Janet E 
Published: June 2009

Abstract

Background
The School Fruit and Vegetable Scheme (SFVS) is an important public health intervention. The aim of this scheme is to provide a free piece of fruit and/or vegetable every day for children in Reception to Year 2. When children are no longer eligible for the scheme (from Year 3) their overall fruit and vegetable consumption decreases back to baseline levels. This proposed study aims to design a flexible multi-component intervention for schools to support the maintenance of fruit and vegetable consumption for Year 3 children who are no longer eligible for the scheme.

Method
This study is a cluster randomised controlled trial of Year 2 classes from 54 primary schools across England. The schools will be randomly allocated into two groups to receive either an active intervention called Project Tomato, to support maintenance of fruit intake in Year 3 children, or a less active intervention (control group), consisting of a 5 A DAY booklet. Children's diets will be analysed using the Child And Diet Evaluation Tool (CADET), and height and weight measurements collected, at baseline (Year 2) and 18 month follow-up (Year 4). The primary outcome will be the ability of the intervention (Project Tomato) to maintain consumption of fruit and vegetable portions compared to the control group.

Discussion
A positive result will identify how fruit and vegetable consumption can be maintained in young children, and will be useful for policies supporting the SFVS. A negative result would be used to inform the research agenda and contribute to redefining future strategies for increasing children's fruit and vegetable consumption.

Trial registration
Medical Research Council Registry code G0501297