bluuebunny/crossref_metadata_2025 huggingface dataset:
A region on chicken chromosome 2 affects both egg white thinning and egg weight
Authors: Honkatukia Mervi , Tuiskula-Haavisto Maria , De Koning Dirk-Jan , Virta Anneli , Mäki-Tanila Asko , Vilkki Johanna
Published: June 2009

We describe the results from genetic dissection of a QTL region on chicken chromosome 2, shown to affect egg weight and quality in an earlier genome scan of an F2 intercross between two divergent egg layer lines. As the 90% confidence intervals for the detected QTL covered tens of centiMorgans, new analyses were needed. The datasets were reanalysed with denser marker intervals to characterise the QTL region. Analysis of a candidate gene from the original QTL region, vimentin, did not support its role in controlling egg white thinning. Even after reanalysis with additional seven markers in the QTL area, the 90% confidence intervals remained large or even increased, suggesting the presence of multiple linked QTL for the traits. A grid search fitting two QTL on chromosome 2 for each trait suggested that there are two distinct QTL areas affecting egg white thinning in both production periods and egg weight in the late production period. The results indicate possible pleiotropic effects of some of the QTL on egg quality and egg weight. However, it was not possible to make a distinction between close linkage versus pleiotropic effects.
Transformation of QTL genotypic effects to allelic effects
Authors: Nagamine Yoshitaka
Published: June 2009

The genotypic and allelic effect models are equivalent in terms of QTL detection in a simple additive model, but the QTL allelic model has the advantage of providing direct information for marker-assisted selection. However, the allelic matrix is four times as large as the genotypic IBD matrix, causing computational problems, especially in genome scans examining multiple positions. Transformation from genotypic to allelic effects, after estimating the genotypic effects with a smaller IBD matrix, can solve this problem. Although the validity of transformation from genotypic to allelic effects has been disputed, this work proves that transformation can successfully yield unique allelic effects when genotypic and allelic IBD matrixes exist.
Identification of quantitative trait loci associated with bone traits and body weight in an F2 resource population of chickens*
Authors: Schreiweis Melissa A. , Hester Patricia Y. , Moody Diane E.
Published: June 2009

Bone fractures at the end of lay are a significant problem in egg-laying strains of hens. The objective of the current study was to identify quantitative trait loci (QTL) associated with bone mineralization and strength in a chicken resource population. Layer (White Leghorn hens) and broiler (Cobb-Cobb roosters) lines were crossed to generate an F2 population of 508Â hens over seven hatches, and 26 traits related to bone integrity, including bone mineral density (BMD) and content (BMC), were measured. Genotypes of 120 microsatellite markers on 28 autosomal groups were determined, and interval mapping was conducted to identify QTL regions. Twenty-three tests representing three chromosomal regions (chromosomes 4, 10 and 27) contained significant QTL that surpassed the 5% genome-wise threshold, and 47 tests representing 15 chromosomes identified suggestive QTL that surpassed the 5% chromosome-wise threshold. Although no significant QTL influencing BMD and BMC were detected after adjusting for variation in body weight and egg production, multiple suggestive QTL were found. These results support previous experiments demonstrating an important genetic regulation of bone strength in chickens, but suggest the regulation may be due to the effects of multiple genes that each account for relatively small amounts of variation in bone strength.
The 20th anniversary of EMBnet: 20 years of bioinformatics for the Life Sciences community
Authors: D'Elia Domenica , Gisel Andreas , Eriksson Nils-Einar , Kossida Sophia , Mattila Kimmo , Klucar Lubos , Bongcam-Rudloff Erik
Published: June 2009

The EMBnet Conference 2008, focusing on 'Leading Applications and Technologies in Bioinformatics', was organized by the European Molecular Biology network (EMBnet) to celebrate its 20th anniversary. Since its foundation in 1988, EMBnet has been working to promote collaborative development of bioinformatics services and tools to serve the European community of molecular biology laboratories. This conference was the first meeting organized by the network that was open to the international scientific community outside EMBnet. The conference covered a broad range of research topics in bioinformatics with a main focus on new achievements and trends in emerging technologies supporting genomics, transcriptomics and proteomics analyses such as high-throughput sequencing and data managing, text and data-mining, ontologies and Grid technologies. Papers selected for publication, in this supplement to BMC Bioinformatics, cover a broad range of the topics treated, providing also an overview of the main bioinformatics research fields that the EMBnet community is involved in.
'Brukin2D': a 2D visualization and comparison tool for LC-MS data
Authors: Tsagkrasoulis Dimosthenis , Zerefos Panagiotis , Loudos George , Vlahou Antonia , Baumann Marc , Kossida Sophia
Published: June 2009

Background

Liquid Chromatography-Mass Spectrometry (LC-MS) is a commonly used technique to resolve complex protein mixtures. Visualization of large data sets produced from LC-MS, namely the chromatogram and the mass spectra that correspond to its compounds is the focus of this work.

Results

The in-house developed 'Brukin2D' software, built in Matlab 7.4, which is presented here, uses the compound data that are exported from the Bruker 'DataAnalysis' program, and depicts the mean mass spectra of all the chromatogram compounds from one LC-MS run, in one 2D contour/density plot. Two contour plots from different chromatograph runs can then be viewed in the same window and automatically compared, in order to find their similarities and differences. The results of the comparison can be examined through detailed mass quantification tables, while chromatogram compound statistics are also calculated during the procedure.

Conclusion

'Brukin2D' provides a user-friendly platform for quick, easy and integrated view of complex LC-MS data. The software is available at http://www.bioacademy.gr/bioinformatics/Brukin2d/index.html.
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

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

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

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

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

Background

Comparative 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.

Methods

We 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.

Results

Three 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

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

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

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

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

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

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
The burden of disease and injury in Iran 2003
Authors: Naghavi Mohsen , Abolhassani Farid , Pourmalek Farshad , Moradi Lakeh Maziar , Jafari Nahid , Vaseghi Sanaz , Mahdavi Hezaveh Niloufar , Kazemeini Hossein
Published: June 2009

Background

The objective of this study was to estimate the burden of disease and injury in Iran for the year 2003, using Disability-Adjusted Life Years (DALYs) at the national level and for six selected provinces.

Methods

Methods developed by the World Health Organization for National Burden of Disease (NBD) studies were applied to estimate disease and injury incidence for the calculation of Years of Life Lost due to premature mortality (YLL), Years Lived with Disability (YLD), and DALYs. The following adjustments of the NBD methodology were made in this study: a revised list with 213 disease and injury causes, development of new and more specific disease modeling templates for cancers and injuries, and adjustment for dependent comorbidity. We compared the results with World Health Organization (WHO) estimates for Eastern Mediterranean Region, sub-region B in 2002.

Results

We estimated that in the year 2003, there were 21,572 DALYs due to all diseases and injuries per 100,000 Iranian people of all ages and both sexes. From this total number of DALYs, 62% were due to disability premature deaths (YLD) and 38% were due to premature deaths (YLL); 58% were due to noncommunicable diseases, 28% – to injuries, and 14% – to communicable, maternal, perinatal, and nutritional conditions. Fifty-three percent of the total number of 14.349 million DALYs in Iran were in males, with 36.5% of the total due to intentional and unintentional injuries, 15% due to mental and behavioral disorders, and 10% due to circulatory system diseases; and 47% of DALYs were in females, with 18% of the total due to mental and behavioral disorders, 18% due to intentional and unintentional injuries, and 12% due to circulatory system diseases. The disease and injury causes leading to the highest number of DALYs in males were road traffic accidents (1.071 million), natural disasters (548 thousand), opioid use (510 thousand), and ischemic heart disease (434 thousand). The leading causes of DALYs in females were ischemic heart disease (438 thousand), major depressive disorder (420 thousand), natural disasters (419 thousand), and road traffic accidents (235 thousand). The burden of disease at the province level showed marked variability. DALY estimates by Iran's NBD study were higher than those for EMR-B by WHO.

Conclusion

The health and disease profile in Iran has made the transition from the dominance of communicable diseases to that of noncommunicable diseases and road traffic injuries. NBD results are to be used in health program planning, research, and resource allocation and generation policies and practices.
Early calcium increase triggers the formation of olfactory long-term memory in honeybees
Authors: Perisse Emmanuel , Raymond-Delpech Valérie , Néant Isabelle , Matsumoto Yukihisa , Leclerc Catherine , Moreau Marc , Sandoz Jean-Christophe
Published: June 2009

Background

Synaptic plasticity associated with an important wave of gene transcription and protein synthesis underlies long-term memory processes. Calcium (Ca2+) plays an important role in a variety of neuronal functions and indirect evidence suggests that it may be involved in synaptic plasticity and in the regulation of gene expression correlated to long-term memory formation. The aim of this study was to determine whether Ca2+is necessary and sufficient for inducing long-term memory formation. A suitable model to address this question is the Pavlovian appetitive conditioning of the proboscis extension reflex in the honeybeeApis mellifera,in which animals learn to associate an odor with a sucrose reward.

Results

By modulating the intracellular Ca2+concentration ([Ca2+]i) in the brain, we show that: (i) blocking [Ca2+]i increase during multiple-trial conditioning selectively impairs long-term memory performance; (ii) conversely, increasing [Ca2+]i during single-trial conditioning triggers long-term memory formation; and finally, (iii) as was the case for long-term memory produced by multiple-trial conditioning, enhancement of long-term memory performance induced by a [Ca2+]i increase depends onde novoprotein synthesis.

Conclusion

Altogether our data suggest that during olfactory conditioning Ca2+is both a necessary and a sufficient signal for the formation of protein-dependent long-term memory. Ca2+therefore appears to act as a switch between short- and long-term storage of learned information.
Challenges of Functional Imaging Research of Pain in Children
Authors: Sava Simona , Lebel Alyssa A , Leslie David S , Drosos Athena , Berde Charles , Becerra Lino , Borsook David
Published: June 2009

Functional imaging has revolutionized the neurosciences. In the pain field it has dramatically altered our understanding of how the brain undergoes significant functional, anatomical and chemical changes in patients with chronic pain. However, most studies have been performed in adults. Because functional imaging is non-invasive and can be performed in awake individuals, applications in children have become more prevalent, but only recently in the pain field. Measures of changes in the brains of children have important implications in understanding neural plasticity in response to acute and chronic pain in the developing brain. Such findings may have implications for treatments in children affected by chronic pain and provide novel insights into chronic pain syndromes in adults. In this review we summarize this potential and discuss specific concerns related to the imaging of pain in children.
The Alcohol Use Disorders Identification Test (AUDIT): reliability and validity of the Greek version
Authors: Moussas George , Dadouti Georgia , Douzenis Athanassios , Poulis Evangelos , Tselebis Athanasios , Bratis Dionisios , Christodoulou Christos , Lykouras Lefteris
Published: June 2009

Background

Problems associated with alcohol abuse are recognised by the World Health Organization as a major health issue, which according to most recent estimations is responsible for 1.4% of the total world burden of morbidity and has been proven to increase mortality risk by 50%. Because of the size and severity of the problem, early detection is very important. This requires easy to use and specific tools. One of these is the Alcohol Use Disorders Identification Test (AUDIT).

Aim

This study aims to standardise the questionnaire in a Greek population.

Methods

AUDIT was translated and back-translated from its original language by two English-speaking psychiatrists. The tool contains 10 questions. A score ≥ 11 is an indication of serious abuse/dependence. In the study, 218 subjects took part: 128 were males and 90 females. The average age was 40.71 years (± 11.34). From the 218 individuals, 109 (75 male, 34 female) fulfilled the criteria for alcohol dependence according to the Diagnostic and Statistical Manual of Mental Disorders, 4th edition (DSM-IV), and presented requesting admission; 109 subjects (53 male, 56 female) were healthy controls.

Results

Internal reliability (Cronbach α) was 0.80 for the controls and 0.80 for the alcohol-dependent individuals. Controls had significantly lower average scores (t test P < 0.001) when compared to the alcoholics. The questionnaire's sensitivity for scores >8 was 0.98 and its specificity was 0.94 for the same score. For the alcohol-dependent sample 3% scored as false negatives and from the control group 1.8% scored false positives. In the alcohol-dependent sample there was no difference between males and females in their average scores (t test P > 0.05).

Conclusion

The Greek version of AUDIT has increased internal reliability and validity. It detects 97% of the alcohol-dependent individuals and has a high sensitivity and specificity. AUDIT is easy to use, quick and reliable and can be very useful in detection alcohol problems in sensitive populations.
Breastfeeding in China: a review
Authors: Xu Fenglian , Qiu Liqian , Binns Colin W , Liu Xiaoxian
Published: June 2009

This review aims to describe changes in breastfeeding and summarise the breastfeeding rates, duration and reasons of discontinuing 'any breastfeeding' or 'exclusive breastfeeding' in P.R. China. Breastfeeding rates in China fell during the 1970s when the use of breast milk substitutes became widespread, and reached the lowest point in the 1980s. As a result many efforts were introduced to promote breastfeeding. The breastfeeding rate in China started to increase in the 1990s, and since the mid-1990s 'any breastfeeding' rates in the majority of cities and provinces, including minority areas, have been above 80% at four months. But most cities and provinces did not reach the national target of 'exclusive breastfeeding' of 80%. The 'exclusive breastfeeding' rates in minority areas were relatively lower than comparable inland provinces. The mean duration of 'any breastfeeding' in the majority of cities or provinces was between seven and nine months. The common reasons for ceasing breastfeeding, or introducing water or other infant food before four months, were perceived breast milk insufficiency, mother going to work, maternal and child illness and breast problems. Incorrect traditional perceptions have a strong adverse influence on 'exclusive breastfeeding' in less developed areas or rural areas. China is a huge country, geographically and in population size, and there is considerable ethnic diversity. Therefore breastfeeding rates in different parts of China can vary considerably.
The Symbiosis Interactome: a computational approach reveals novel components, functional interactions and modules in Sinorhizobium meliloti
Authors: Rodriguez-Llorente Ignacio , Caviedes Miguel A , Dary Mohammed , Palomares Antonio J , Cánovas Francisco M , Peregrín-Alvarez José M
Published: June 2009

Background

Rhizobium-Legume symbiosis is an attractive biological process that has been studied for decades because of its importance in agriculture. However, this system has undergone extensive study and although many of the major factors underpinning the process have been discovered using traditional methods, much remains to be discovered.

Results

Here we present an analysis of the 'Symbiosis Interactome' using novel computational methods in order to address the complex dynamic interactions between proteins involved in the symbiosis of the model bacteria Sinorhizobium meliloti with its plant hosts. Our study constitutes the first large-scale analysis attempting to reconstruct this complex biological process, and to identify novel proteins involved in establishing symbiosis. We identified 263 novel proteins potentially associated with the Symbiosis Interactome. The topology of the Symbiosis Interactome was used to guide experimental techniques attempting to validate novel proteins involved in different stages of symbiosis. The contribution of a set of novel proteins was tested analyzing the symbiotic properties of several S. meliloti mutants. We found mutants with altered symbiotic phenotypes suggesting novel proteins that provide key complementary roles for symbiosis.

Conclusion

Our 'systems-based model' represents a novel framework for studying host-microbe interactions, provides a theoretical basis for further experimental validations, and can also be applied to the study of other complex processes such as diseases.
Down-regulated miR-9 and miR-433 in human gastric carcinoma
Authors: Luo Hongchun , Zhang Hongbin , Zhang Zhenzhen , Zhang Xia , Ning Bo , Guo Jinjun , Nie Na , Liu Bo , Wu Xiaoling
Published: June 2009

Background

MircoRNAs(miRNAs) are short, endogenously non-coding RNAs. The abnormal expression of miRNAs may be valuable for the diagnosis and treatment of tumors.

Methods

To screening the special miRNAs in gastric carcinoma, expression level of miRNAs in gastric carcinoma and normal gaster samples were detected by miRNA gene chip. Then, the expressions of miR-9 and miR-433 in gastric carcinoma tissue and SGC7901 cell line were validated by qRT-PCR. GRB2 and RAB34, targets of miR-433 and miR-9 respectively, were detected by Western blot.

Results

We found 19 miRNAs and 7 miRNAs were down-regulated and up-regulated respectively. Compared with normal gaster samples, our data showed that miR-9 and miR-433 were down-regulated in gastric carcinoma. Meanwhile, we also found that miR-433 and miR-9 regulated the expression levels of GRB2 and RAB34 respectively.

Conclusion

Our data show miR-9 and miR-433 was down-regulated in gastric carcinoma. The targets of miR-433 and miR-9 were tumor-associated proteins GRB2 and RAB34 respectively. This result provided the related information of miRNAs in gastric carcinoma.
Contoured, prefabricated foot orthoses demonstrate comparable mechanical properties to contoured, customised foot orthoses: a plantar pressure study
Authors: Redmond Anthony C , Landorf Karl B , Keenan Anne‐Maree
Published: June 2009

Background

Foot orthoses have been demonstrated to be effective in the management of a range of conditions, but there is debate as to the benefits of customised foot orthoses over less expensive, prefabricated devices.

Methods

In a randomised, cross‐over trial, 15 flat‐footed participants aged between 18 and 45 years were provided with semi‐rigid, customised orthoses and semi‐rigid, contoured, prefabricated orthoses. Pressures and forces were measured using an in‐shoe system with subjects wearing shoes alone, wearing customised orthoses, and again when wearing contoured prefabricated orthoses. Two weeks acclimatisation was included between cross‐over of therapy. Repeated measures ANOVA models with post‐hoc, pair‐wise comparisons were used to test for differences.

Results

When compared to wearing shoes alone, wearing either the customised orthoses or the prefabricated orthoses was associated with increases in force and force time integrals in the midfoot region. Peak and maximum mean pressure and pressure‐time, and force‐time integrals were reduced in both the medial and lateral forefoot. There were, however, no significant differences between the customised orthoses and the prefabricated orthoses at any site.

Conclusion

There was a similar change in loading with both the semi‐rigid customised and the semi‐rigid prefabricated orthoses when compared to the shoe alone condition. However, while customised devices offered minor differences over prefabricated orthoses in some variables, these were not statistically significant. The results suggest that there may be only minor differences in the effects on plantar pressures between the customised and the less expensive prefabricated orthoses tested in this study, however further research is warranted.
A novel and universal method for microRNA RT-qPCR data normalization
Authors: Mestdagh Pieter , Van Vlierberghe Pieter , De Weer An , Muth Daniel , Westermann Frank , Speleman Frank , Vandesompele Jo
Published: June 2009

Gene expression analysis of microRNA molecules is becoming increasingly important. In this study we assess the use of the mean expression value of all expressed microRNAs in a given sample as a normalization factor for microRNA real-time quantitative PCR data and compare its performance to the currently adopted approach. We demonstrate that the mean expression value outperforms the current normalization strategy in terms of better reduction of technical variation and more accurate appreciation of biological changes.
Personal development planning: First-year Master of Pharmacy students' engagement with, and attitudes towards, reflective self-assessment
Authors: Dyke Janet E , Gidman Wendy K , Wilson Sarah E , Becket Gordon
Published: June 2009

Objectives

The aims of this study were to determine whether first-year Master of Pharmacy (MPharm) students would engage with an activity similar to pharmacists' continuing professional development, and to explore attitudes surrounding this task.

Methods

A paper version of the Royal Pharmaceutical Society of Great Britain's electronic template for recording continuing professional development was developed. Students were asked to use this paper version to record the planning, action and evaluation carried out while completing a written assignment. The records were assessed to determine any reflective self-assessment contained in the evaluation section, and whether this reflection related to the specified learning outcome and the planning and action stages. Six focus groups were run, during which the students discussed their reaction to completing these records. The study was carried out during the first semester with first-year undergraduate MPharm students in the School of Pharmacy and Pharmaceutical Sciences at the University of Central Lancashire in the UK.

Key findings

It was found that few students appeared to engage fully with the whole recording process. During focus-group sessions competence to self-assess was raised as an issue by students, and the value of the reflective process was questioned. Some students did recognize the value of undertaking and recording reflective self-assessment.

Conclusions

It appears that undergraduate students need a more gradual introduction to the process of reflective self-assessment. We suggest that the findings are linked to students' previous education experience and conclude there is a need for students to be encouraged to take ownership of their undergraduate learning, to gain confidence in self-assessment and to increase the value they place on reflection.