bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ebbie: automated analysis and storage of small RNA cloning data using a dynamic web server
Authors: Ebhardt H Alexander , Wiese Kay C , Unrau Peter J 
Published: April 2006

Abstract

Background
DNA sequencing is used ubiquitously: from deciphering genomes[1] to determining the primary sequence of small RNAs (smRNAs) [2–5]. The cloning of smRNAs is currently the most conventional method to determine the actual sequence of these important regulators of gene expression. Typical smRNA cloning projects involve the sequencing of hundreds to thousands of smRNA clones that are delimited at their 5' and 3' ends by fixed sequence regions. These primers result from the biochemical protocol used to isolate and convert the smRNA into clonable PCR products. Recently we completed a smRNA cloning project involving tobacco plants, where analysis was required for ~700 smRNA sequences[6]. Finding no easily accessible research tool to enter and analyze smRNA sequences we developed Ebbie to assist us with our study.

Results

Ebbie is a semi-automated smRNA cloning data processing algorithm, which initially searches for any substring within a DNA sequencing text file, which is flanked by two constant strings. The substring, also termed smRNA or insert, is stored in a MySQL and BlastN database. These inserts are then compared using BlastN to locally installed databases allowing the rapid comparison of the insert to both the growing smRNA database and to other static sequence databases. Our laboratory used Ebbie to analyze scores of DNA sequencing data originating from an smRNA cloning project[6]. Through its built-in instant analysis of all inserts using BlastN, we were able to quickly identify 33 groups of smRNAs from ~700 database entries. This clustering allowed the easy identification of novel and highly expressed clusters of smRNAs. Ebbie is available under GNU GPL and currently implemented on http://bioinformatics.org/ebbie/

Conclusion

Ebbie was designed for medium sized smRNA cloning projects with about 1,000 database entries [6–8].Ebbie can be used for any type of sequence analysis where two constant primer regions flank a sequence of interest. The reliable storage of inserts, and their annotation in a MySQL database, BlastN[9] comparison of new inserts to dynamic and static databases make it a powerful new tool in any laboratory using DNA sequencing. Ebbie also prevents manual mistakes during the excision process and speeds up annotation and data-entry. Once the server is installed locally, its access can be restricted to protect sensitive new DNA sequencing data. Ebbie was primarily designed for smRNA cloning projects, but can be applied to a variety of RNA and DNA cloning projects[2, 3, 10, 11].
Classification of protein quaternary structure by functional domain composition
Authors: Yu Xiaojing , Wang Chuan , Li Yixue 
Published: April 2006

AbstractBackgroundThe number and the arrangement of subunits that form a protein are referred to as quaternary structure. Quaternary structure is an important protein attribute that is closely related to its function. Proteins with quaternary structure are called oligomeric proteins. Oligomeric proteins are involved in various biological processes, such as metabolism, signal transduction, and chromosome replication. Thus, it is highly desirable to develop some computational methods to automatically classify the quaternary structure of proteins from their sequences.ResultsTo explore this problem, we adopted an approach based on the functional domain composition of proteins. Every protein was represented by a vector calculated from the domains in the PFAM database. The nearest neighbor algorithm (NNA) was used for classifying the quaternary structure of proteins from this information. The jackknife cross-validation test was performed on the non-redundant protein dataset in which the sequence identity was less than 25%. The overall success rate obtained is 75.17%. Additionally, to demonstrate the effectiveness of this method, we predicted the proteins in an independent dataset and achieved an overall success rate of 84.11%ConclusionCompared with the amino acid composition method and Blast, the results indicate that the domain composition approach may be a more effective and promising high-throughput method in dealing with this complicated problem in bioinformatics.
An analysis of the Sargasso Sea resource and the consequences for database composition
Authors: Tress Michael L , Cozzetto Domenico , Tramontano Anna , Valencia Alfonso 
Published: April 2006

Abstract

Background
The environmental sequencing of the Sargasso Sea has introduced a huge new resource of genomic information. Unlike the protein sequences held in the current searchable databases, the Sargasso Sea sequences originate from a single marine environment and have been sequenced from species that are not easily obtainable by laboratory cultivation. The resource also contains very many fragments of whole protein sequences, a side effect of the shotgun sequencing method.
These sequences form a significant addendum to the current searchable databases but also present us with some intrinsic difficulties. While it is important to know whether it is possible to assign function to these sequences with the current methods and whether they will increase our capacity to explore sequence space, it is also interesting to know how current bioinformatics techniques will deal with the new sequences in the resource.

Results
The Sargasso Sea sequences seem to introduce a bias that decreases the potential of current methods to propose structure and function for new proteins. In particular the high proportion of sequence fragments in the resource seems to result in poor quality multiple alignments.

Conclusion
These observations suggest that the new sequences should be used with care, especially if the information is to be used in large scale analyses. On a positive note, the results may just spark improvements in computational and experimental methods to take into account the fragments generated by environmental sequencing techniques.
A FERM-adjacent (FA) region defines a subset of the 4.1 superfamily and is a potential regulator of FERM domain function
Authors: Baines Anthony J 
Published: April 2006

Abstract

Background
Proteins containing FERM domains comprise a diverse group of eukaryotic proteins that bind membrane proteins and lipids. In doing so, they organise membrane microstructure, and coordinate the disposition of signalling and cell adhesion complexes. In protein 4.1R, phosphorylation adjacent to the FERM domain regulates its activity, and membrane mechanical properties.

Results
A novel sequence domain has been detected in a subset of proteins that contain FERM domains. This subset includes the true 4.1 proteins, some tyrosine phosphatases, rho-GEF proteins and type II transmembrane proteins, as well as some uncharacterised FERM proteins. This FERM-adjacent region is always closely proximate to the C-terminal of the FERM domain. This sequence is likely to be folded with elements of α and β structure. The FERM-adjacent region of 4.1R contains serine residues phosphorylated by PKC and PKA; these appear conserved in about half of all other FERM-adjacent regions. Phylogenetic analyses indicate that all proteins containing a FERM-adjacent region arose from a single ancestor after FERM domains had started to proliferate in genomes of animals, plants and mycetozoa.

Conclusion
The FERM-adjacent region defines a subset of the FERM proteins in animals. The conservation of motifs in this region that are potential substrates for kinases together with the known regulatory phosphorylation of 4.1R in this region raises the possibility that the FERM-adjacent region is a regulatory adaptation in this subset of the FERM proteins.
Genotyping of Bacillus anthracis strains based on automated capillary 25-loci Multiple Locus Variable-Number Tandem Repeats Analysis
Authors: Lista Florigio , Faggioni Giovanni , Valjevac Samina , Ciammaruconi Andrea , Vaissaire Josée , le Doujet Claudine , Gorgé Olivier , De Santis Riccardo , Carattoli Alessandra , Ciervo Alessandra , Fasanella Antonio , Orsini Francesco , D'Amelio Raffaele , Pourcel Christine , Cassone Antonio , Vergnaud Gilles 
Published: April 2006

Abstract

Background
The genome of Bacillus anthracis, the etiological agent of anthrax, is highly monomorphic which makes differentiation between strains difficult. A Multiple Locus Variable-number tandem repeats (VNTR) Analysis (MLVA) assay based on 20 markers was previously described. It has considerable discrimination power, reproducibility, and low cost, especially since the markers proposed can be typed by agarose-gel electrophoresis. However in an emergency situation, faster genotyping and access to representative databases is necessary.

Results
Genotyping of B. anthracis reference strains and isolates from France and Italy was done using a 25 loci MLVA assay combining 21 previously described loci and 4 new ones. DNA was amplified in 4 multiplex PCR reactions and the length of the resulting 25 amplicons was estimated by automated capillary electrophoresis. The results were reproducible and the data were consistent with other gel based methods once differences in mobility patterns were taken into account. Some alleles previously unresolved by agarose gel electrophoresis could be resolved by capillary electrophoresis, thus further increasing the assay resolution. One particular locus, Bams30, is the result of a recombination between a 27 bp tandem repeat and a 9 bp tandem repeat. The analysis of the array illustrates the evolution process of tandem repeats.

Conclusion
In a crisis situation of suspected bioterrorism, standardization, speed and accuracy, together with the availability of reference typing data are important issues, as illustrated by the 2001 anthrax letters event. In this report we describe an upgrade of the previously published MLVA method for genotyping of B. anthracis and apply the method to the typing of French and Italian B. anthracis strain collections. The increased number of markers studied compared to reports using only 8 loci greatly improves the discrimination power of the technique. An Italian strain belonging to the B branch was described, and two new branches, D and E, are proposed. Owing to the upgrading achieved here, precise genotyping can now be produced either by automated capillary electrophoresis, or by the more accessible but slower and for some markers slightly less accurate agarose gel methodology.
A ketogenic diet as a potential novel therapeutic intervention in amyotrophic lateral sclerosis
Authors: Zhao Zhong , Lange Dale J , Voustianiouk Andrei , MacGrogan Donal , Ho Lap , Suh Jason , Humala Nelson , Thiyagarajan Meenakshisundaram , Wang Jun , Pasinetti Giulio M 
Published: April 2006

Abstract

Background
The cause of neuronal death in amyotrophic lateral sclerosis (ALS) is uncertain but mitochondrial dysfunction may play an important role. Ketones promote mitochondrial energy production and membrane stabilization.

Results
SOD1-G93A transgenic ALS mice were fed a ketogenic diet (KD) based on known formulations for humans. Motor performance, longevity, and motor neuron counts were measured in treated and disease controls. Because mitochondrial dysfunction plays a central role in neuronal cell death in ALS, we also studied the effect that the principal ketone body, D-β-3 hydroxybutyrate (DBH), has on mitochondrial ATP generation and neuroprotection. Blood ketones were > 3.5 times higher in KD fed animals compared to controls. KD fed mice lost 50% of baseline motor performance 25 days later than disease controls. KD animals weighed 4.6 g more than disease control animals at study endpoint; the interaction between diet and change in weight was significant (p = 0.047). In spinal cord sections obtained at the study endpoint, there were more motor neurons in KD fed animals (p = 0.030). DBH prevented rotenone mediated inhibition of mitochondrial complex I but not malonate inhibition of complex II. Rotenone neurotoxicity in SMI-32 immunopositive motor neurons was also inhibited by DBH.

Conclusion
This is the first study showing that diet, specifically a KD, alters the progression of the clinical and biological manifestations of the G93A SOD1 transgenic mouse model of ALS. These effects may be due to the ability of ketone bodies to promote ATP synthesis and bypass inhibition of complex I in the mitochondrial respiratory chain.
Crossmodal attention effects on brain responses to different stimulus classes
Authors: Nager Wido , Estorf Kaija , Münte Thomas F 
Published: April 2006

Abstract

Background
Attending to a point in space in one modality may facilitate processing to information from the same region in another modality. The involvement of sensory-specific cortical areas in intramodal and crossmodal selective spatial attention can be assessed with event-related brain potentials (ERPs).
ERPs were recorded in two groups of young participants (each n = 11). Stimulus sequences comprised visual standard stimuli (p = 0.4, a white square), visual deviant stimuli (p = 0.05, a white square with small black rectangle) and visual novel stimuli (p = 0.05, different multicolored checkerboards) as well as auditory standard (p = 0.4, 800 Hz tone), deviant (p = 0.05, 900 Hz tone), and novel (p = 0.05, random combination of three sine-wave tones) stimuli, occurring in random order at locations 30 degrees left and right of a fixation point. The "auditory group" of participants attended either to the left or to the right speaker in order to respond to the infrequent auditory deviants at that location by a speeded button press. Visual stimuli were irrelevant for this group. The "visual group" had the analogue task for the visual modality. For these participants auditory stimuli were irrelevant throughout the experiment.

Results
ERPs showed a typical enhancement of early sensory specific components by intramodal spatial attention (visual group: visual P1 and N1; auditory group: auditory Nd). Crossmodal spatial attention effects included a modulation of the Nd to auditory standards in the visual group and a modulation of the P1 to visual novels and N1 for visual standards for the auditory group. Similar to previous studies crossmodal spatial attention effects on visual standard and novel stimuli also included a frontocentral positivity in the 200–400 ms range that was not seen for intramodal spatial visual attention suggesting involvement of later supramodal areas.

Conclusion
These findings are consistent with an action of crossmodal spatial attention on early, sensory specific processing stages.
Percutaneous septal ablation for left mid-ventricular obstructive hypertrophic cardiomyopathy: a case report
Authors: Tengiz Istemihan , Ercan Ertugrul , Alioglu Emin , Turk Ugur O 
Published: April 2006

Abstract

Background
Mid-ventricular obstructive hypertrophic cardiomyopathy (MVOHC) is a rare type of cardiomyopathy. The diagnosis is based on the hourglass appearance on the left ventriculogram and the presence of pressure gradient between apical and basal chamber of the ventriculum on the hemodynamic assessment.

Case presentation
The present case represents successful percutaneous treatment with septal ablation to patient with MVOHC associated with systolic anterior motion of the mitral valve and obstruction at both the mid-ventricular and outflow levels.

Conclusion
Alcohol septal ablation has been proposed as less invasive alternatives to surgery in patients with MVOHC.
Endothelial nitric oxide synthase gene polymorphism (Glu298Asp) and development of pre-eclampsia: a case-control study and a meta-analysis
Authors: Yu Christina KH , Casas Juan P , Savvidou Makrina D , Sahemey Manpreet K , Nicolaides Kypros H , Hingorani Aroon D 
Published: April 2006

Abstract

Background
Pre-eclampsia is thought to have an important genetic component. Recently, pre-eclampsia has been associated in some studies with carriage of a common eNOS gene Glu298Asp polymorphism, a variant that leads to the replacement of glutamic acid by aspartic acid at codon 298.

Method
Healthy women with singleton pregnancies were recruited from 7 district general hospitals in London, UK. Women at high risk of pre-eclampsia were screened by uterine artery Doppler velocimetry at 22–24 weeks of gestation and maternal blood was obtained to genotype the eNOS Glu298Asp polymorphism. Odds ratios (OR) and 95%CI, using logistic regression methods, were obtained to evaluate the association between the Glu298Asp polymorphism and pre-eclampsia. A meta-analysis was then undertaken of all published studies up to November 2005 examining the association of eNOS Glu298Asp genotype and pre-eclampsia.

Results
89 women with pre-eclampsia and 349 controls were included in the new study. The Glu298Asp polymorphism in a recessive model was not significantly associated with pre-eclampsia (adjusted-OR: 0.83 [95%CI: 0.30–2.25]; p = 0.7). In the meta-analysis, under a recessive genetic model (1129 cases & 2384 controls) women homozygous for the Asp298 allele were not at significantly increased risk of pre-eclampsia (OR: 1.28 [95%CI: 0.76–2.16]; p = 0.34). A dominant model (1334 cases & 2894 controls) was associated with no increase of risk of pre-eclampsia for women carriers of the Asp298 allele (OR: 1.12 [95%CI: 0.84–1.49]; p = 0.42).

Conclusion
From the data currently available, the eNOS Glu298Asp polymorphism is not associated with a significant increased risk of pre-eclampsia. However, published studies have been underpowered, much larger studies are needed to confirm or refute a realistic genotypic risk of disease, but which might contribute to many cases of pre-eclampsia in the population.
Is comorbidity in adolescence a predictor for adult low back pain? A prospective study of a young population
Authors: Hestbaek Lise , Leboeuf-Yde Charlotte , Kyvik Kirsten O 
Published: April 2006

Abstract

Background
It has previously been shown that low back pain (LBP) often presents already in the teenage years and that previous LBP predicts future LBP. It is also well documented that there is a large degree of comorbidity associated with LBP, both in adolescents and adults. The objective of this study is to gain a deeper insight into the etiology of low back pain and to possibly develop a tool for early identification of high-risk groups. This is done by investigating whether different types of morbidity in adolescence are associated with LBP in adulthood.

Methods
Almost 10,000 Danish twins born between 1972 and 1982 were surveyed by means of postal questionnaires in 1994 and again in 2002. The questionnaires dealt with various aspects of general health, including the prevalence of LBP, classified according to number of days affected during the previous year (0, 1–7, 8–30, >30). The predictor variables used in this study were LBP, headache, asthma and atopic disease at baseline; the outcome variable was persistent LBP (>30 days during the past year) at follow-up. Associations between morbidity in 1994 and LBP in 2002 were investigated.

Results
LBP, headache and asthma in adolescence were positively associated with future LBP. There was no association between atopic disease and future LBP. Individuals with persistent LBP at baseline had an odds ratio of 3.5 (2.8–4.5) for future LBP, while the odds ratio for those with persistent LBP, persistent headache and asthma was 4.5 (2.5–8.1). There was a large degree of clustering of these disorders, but atopic disease was not part of this pattern.

Conclusion
Young people from 12 to 22 years of age with persistent LBP during the previous year have an odds ratio of 3.5 persistent LBP eight years later. Both headache and asthma are also positively associated with future LBP and there is a large clustering of LBP, headache and asthma in adolescence.
Linking community pharmacy dispensing data to prescribing data of general practitioners
Authors: Florentinus Stefan R , Souverein Patrick C , Griens Fabiënne AMG , Groenewegen Peter P , Leufkens Hubert GM , Heerdink Eibert R 
Published: April 2006

Abstract

Background
Databases are frequently used for pharmacoepidemiological research. However, most of these databases consist either of prescribing, dispensing or administrative data and therefore lack insight in the interaction between the several health professionals around the patient.

Methods
To determine the success rate of linking records from the dispensing database of the Foundation for Pharmaceutical Statistics to the prescribing database of the second Dutch national survey of general practice, conducted by NIVEL (Netherlands Institute for Health Services Research), a deterministic record linkage approach was used with patient and prescription characteristics as matching variables between the two databases.

Results
The catchment area included 123 community pharmacies, 90 GP practices and approximately 170,000 unique patients. Overall 110,102 (64.8%) unique patients were linked using the matching variables patient's gender, year of birth, the 4-digit part of the postal code, date of dispensing/prescribing and ATC-code. The final database contains of the 110,102 both prescribing data from 83 GP practices and dispensing data of 112 community pharmacies.

Conclusion
This study shows that linkage of dispensing to prescribing data is feasible with a combination of patient characteristics, such as gender, year of birth and postal code, and prescription characteristics like prescription date and ATC-code. We obtained a linkage proportion of 64.8% resulting in complete prescribing and dispensing history of 110,102 patients. This offers an opportunity to gain insight in the mechanisms and factors influencing drug utilisation in general practice.
Severity of self-reported diseases and symptoms in Denmark
Authors: Iburg Kim Moesgaard , Rasmussen Niels Kristian , Avlund Kirsten 
Published: April 2006

Abstract
Objective
To estimate and rank the relative severity of self-reported diseases and symptoms in Denmark.

Method
The 1994 Danish Health and Morbidity Survey collected data from 5,472 Danes older than 16 years of age. Interviews (response frequency: 79%) gave information on diseases and symptoms; a self-administered SF-36 questionnaire (response frequency: 64%) provided information on health-related quality of life. The severity of diseases and symptoms was represented by the health-related quality of life scores that individuals suffering from particular diseases and symptoms obtained on the single dimensions of the SF-36 and on a combined sum of all dimensions. We applied logistic regression to control for the influence of sex, age and socio-economic status on the SF-36 score. We also analysed the interaction between socio-economic status and diseases on the SF-36 score.

Results
Females, more frequently than males, reported on all symptoms and all disease groups except injuries. People with relatively low levels of education reported most diseases, especially musculoskeletal and cardiovascular diseases, more frequently than people with higher education. Age-adjusted mean SF-36 scores for all dimensions combined showed that the symptoms of melancholy/depression and breathing difficulties, psychiatric disorders and respiratory diseases scored lowest (i.e. were most often associated with worse health). Females had lower SF-36 combined scores (worse health) than males on all symptoms. We found interaction between socio-economic status and respiratory diseases and musculoskeletal diseases on the SF-36 score. SF-36 scores also indicated significantly worse health among Danes with low education and income levels compared to those with higher education and income.

Conclusion
In 1994 the Danes most frequently reported musculoskeletal symptoms and diseases. Psychiatric disorders and respiratory diseases were identified as the most severe reported diseases. Due to the interaction between socio-economic status and some diseases, severity estimates should be interpreted with caution or stratified by socio-economic groups.