http://www.biomedcentral.com/bmcresnotes/ The most accessed research articles published by BMC Research Notes 2009-11-25T00:00:00Z This is an RSS newsfeed from BioMed Central It is intended to be used with an RSS reader. For more information about RSS newsfeeds from BioMed Central, visit http://www.biomedcentral.com/info/about/rss/ Background: Neuro-imaging studies demonstrate plasticity of cortical gray matter before and after practice for some motor and cognitive tasks in adults. Other imaging studies show functional changes after practice, but there is not yet direct evidence of how structural and functional changes may be related. A fundamental question is whether they occur at the same cortical sites, adjacent sites, or sites in other parts of a network.FindingsUsing a 3 T MRI, we obtained structural and functional images in adolescent girls before and after practice on a visual-spatial problem-solving computer game, Tetris. After three months of practice, compared to the structural scans of controls, the group with Tetris practice showed thicker cortex, primarily in two areas: left BAs 6 and 22/38. Based on fMRI BOLD signals, the Tetris group showed cortical activations throughout the brain while playing Tetris, but significant BOLD decreases, mostly in frontal areas, were observed after practice. None of these BOLD decreases, however, overlapped with the cortical thickness changes. Conclusion: Regional cortical thickness changes were observed after three months of Tetris practice. Over the same period, brain activity decreases were observed in several other areas. These data indicate that structural change in one brain area does not necessarily result in functional change in the same location, at least on the levels assessed with these MRI methods. http://www.biomedcentral.com/1756-0500/2/174 Richard Haier Sherif Karama Leonard Leyba Rex Jung BMC Research Notes 2009, 2:174 2009-09-01T00:00:00Z doi:10.1186/1756-0500-2-174 BMC Research Notes 1756-0500 2 174 2009-09-01T00:00:00Z XML Background: Research has shown that fecal biomarkers are useful to assess the activity of inflammatory bowel disease (IBD). The aim of the study is: to evaluate the efficacy of the fecal lactoferrin and calprotectin as indicators of inflammatory activity.FindingsA total of 78 patients presenting inflammatory bowel disease were evaluated. Blood tests, the Crohn's Disease Activity Index (CDAI), Mayo Disease Activity Index (MDAI), and Crohn's Disease Endoscopic Index of Severity (CDEIS) were used for the clinical and endoscopic evaluation. Two tests were performed on the fecal samples, to check the levels of calprotectin and lactoferrin. The performance of these fecal markers for detection of inflammation with reference to endoscopic and histological inflammatory activity was assessed and calculated sensitivity, specificity, accuracy.A total of 52 patient's samples whose histological evaluations showed inflammation, 49 were lactoferrin-positive, and 40 were calprotectin-positive (p = 0.000). Lactoferrin and calprotectin findings correlated with C-reactive protein in both the CD and UC groups (p = 0.006; p = 0.000), with CDAI values (p = 0.043; 0.010), CDEIS values in DC cases (p = 0,000; 0.000), and with MDAI values in UC cases (p = 0.000). Conclusion: Fecal lactoferrin and calprotectin are highly sensitive and specific markers for detecting intestinal inflammation. Levels of fecal calprotectin have a proportional correlation to the degree of inflammation of the intestinal mucosa. http://www.biomedcentral.com/1756-0500/2/221 Andrea Vieira Chia Bin Fang Ernani Geraldo Rolim Wilmar Artur Klug Flavio Steinwurz Lucio Giovanni Battista Rossini Paulo Azevedo Candelaria BMC Research Notes 2009, 2:221 2009-10-29T00:00:00Z doi:10.1186/1756-0500-2-221 BMC Research Notes 1756-0500 2 221 2009-10-29T00:00:00Z XML Background: Francisella tularensis is the etiologic agent of tularemia and is classified as a select agent by the Centers for Disease Control and Prevention. Currently four known subspecies of F. tularensis that differ in virulence and geographical distribution are recognized:tularensis (type A), holarctica (type B), mediasiatica, and novicida. Because of the Select Agent status and differences in virulence and geographical location, the molecular analysis of any clinical case of tularemia is of particular interest. We analyzed an unusual Francisella clinical isolate from a human infection in Arizona using multiple DNA-based approaches.FindingsWe report that the isolate is F. tularensis subsp. novicida, a subspecies that is rarely isolated. Conclusion: The rarity of this novicida subspecies in clinical settings makes each case study important for our understanding of its role in disease and its genetic relationship with other F. tularensis subspecies. http://www.biomedcentral.com/1756-0500/2/223 Dawn Birdsell Tasha Stewart Amy Vogler Elisabeth Lawaczeck Alisa Diggs Tammy Sylvester Jordan Buchhagen Raymond Auerbach Paul Keim David Wagner BMC Research Notes 2009, 2:223 2009-11-06T00:00:00Z doi:10.1186/1756-0500-2-223 BMC Research Notes 1756-0500 2 223 2009-11-06T00:00:00Z XML Background: The Smith-Waterman algorithm is one of the most widely used tools for searching biological sequence databases due to its high sensitivity. Unfortunately, the Smith-Waterman algorithm is computationally demanding, which is further compounded by the exponential growth of sequence databases. The recent emergence of many-core architectures, and their associated programming interfaces, provides an opportunity to accelerate sequence database searches using commonly available and inexpensive hardware.FindingsOur CUDASW++ implementation (benchmarked on a single-GPU NVIDIA GeForce GTX 280 graphics card and a dual-GPU GeForce GTX 295 graphics card) provides a significant performance improvement compared to other publicly available implementations, such as SWPS3, CBESW, SW-CUDA, and NCBI-BLAST. CUDASW++ supports query sequences of length up to 59K and for query sequences ranging in length from 144 to 5,478 in Swiss-Prot release 56.6, the single-GPU version achieves an average performance of 9.509 GCUPS with a lowest performance of 9.039 GCUPS and a highest performance of 9.660 GCUPS, and the dual-GPU version achieves an average performance of 14.484 GCUPS with a lowest performance of 10.660 GCUPS and a highest performance of 16.087 GCUPS. Conclusion: CUDASW++ is publicly available open-source software. It provides a significant performance improvement for Smith-Waterman-based protein sequence database searches by fully exploiting the compute capability of commonly used CUDA-enabled low-cost GPUs. http://www.biomedcentral.com/1756-0500/2/73 Yongchao Liu Douglas Maskell Bertil Schmidt BMC Research Notes 2009, 2:73 2009-05-06T00:00:00Z doi:10.1186/1756-0500-2-73 BMC Research Notes 1756-0500 2 73 2009-05-06T00:00:00Z XML Background: Hydrocephalus can be classified as purely obstructive, purely communicating or due to combinations of pathologies (obstruction in addition to defective absorption). Endoscopic third ventriculostomy (ETV) as an alternative to shunt procedures is an established treatment for obstructive hydrocephalus. However, patients who have combination of pathologies (complex hydrocephalus) could result in failure of ETV in spite of a patent stoma. The aim of this study was to prospectively evaluate the incidence of complex hydrocephalus in patients with obstructive hydrocephalus who failed an endoscopic third ventriculostomy.FindingsSeventy one patients of obstructive hydrocephalus who underwent ETV in our institution were included in this study. Aetiology of hydrocephalus included congenital aqueductal stenosis in 42 and tubercular meningitis (TBM) in 29 patients. Failure of ETV was seen in 15 (21%) patients. These 15 patients included 6 (14.3%) from the congenital group and 9 (31.0%) patients from the TBM group. Iohexol CT ventriculography confirmed a patent stoma (suggesting a complex hydrocephalus) in 10 (66.7%) out of the 15 failed ETV cases. The incidence of complex hydrocephalus was more common in TBM group (8/29 patients, 27.60%) compared to congenital group (2/42 patients, 4.8%). The complex hydrocephalus patients with a patent ETV stoma were successfully managed by a lumbar peritoneal (LP) shunt. Conclusion: Ten out of the 71 patients (14%) with obstructive hydrocephalus who underwent an ETV had a complex hydrocephalus, which was the major (66.7%) cause for failure of ETV. Improving methods to detect the exact type of hydrocephalus pre-operatively could increase success rate of ETV and avoid an unnecessary operative procedure (ETV). http://www.biomedcentral.com/1756-0500/2/137 Yad Yadav Gaurav Mukerji Vijay Parihar Mallika Sinha Sanjay Pandey BMC Research Notes 2009, 2:137 2009-07-16T00:00:00Z doi:10.1186/1756-0500-2-137 BMC Research Notes 1756-0500 2 137 2009-07-16T00:00:00Z XML Background: The fibroblast-populated 3D collagen matrix is a model of tissue and healing which has been used since the 1980's. It was hypothesized that anchorage disruption of the collagen matrix would produce p53-dependent apoptosis in the embedded fibroblasts, but results of hypothesis testing were variant.FindingsThe response of p53 to anchorage disruption in 3D culture or to UV irradiation in 2D culture was influenced both by fibroblast strain and culture conditions. It also was determined that data scatter in a collagen matrix contraction assay was related to fibroblast strain and possibly to technical factors, such as cell culture technician and/or number of matrices utilized. Subsequent analysis suggested that phenotypic drift and/or inter-strain genetic variability may have been responsible for the data scatter. In addition, several technical factors were identified that may have contributed to the scatter. Conclusion: Experimentation with human foreskin fibroblasts in both 2D and 3D culture can produce variant data. The underlying cause of the data scatter appears to be partially due to the biologic variability of the fibroblast. http://www.biomedcentral.com/1756-0500/2/229 Mark Carlson Amy Prall Jeremiah Gums Alex Lesiak Valerie Shostrom BMC Research Notes 2009, 2:229 2009-11-18T00:00:00Z doi:10.1186/1756-0500-2-229 BMC Research Notes 1756-0500 2 229 2009-11-18T00:00:00Z XML Background: Attributes of teams could affect the quality of care delivered in primary care. The aim of this study was to systematically review studies conducted within the UK NHS primary care that have measured team climate using the Team Climate Inventory (TCI), and to describe, if reported, the relationship between the TCI and measures of quality of care.FindingsThe databases MEDLINE, EMBASE, and CINAHL were searched. The reference lists of included article were checked and one relevant journal was hand-searched. Eight papers were included. Three studies used a random sample; the remaining five used convenience or purposive samples. Six studies were cross sectional surveys, whilst two were before and after studies. Four studies examined the relationship between team climate and quality of care. Only one study found a positive association between team climate and higher quality care in patients with diabetes, positive patient satisfaction and self-reported effectiveness. Conclusion: While the TCI has been used to measure team attributes in primary care settings in the UK it is difficult to generalise from these data. A small number of studies reported higher TCI scores being associated with only certain aspects of quality of care; reasons for the pattern of association are unclear. There are a number of methodological challenges to conducting such studies in routine service settings. Further research is needed in order to understand how to measure team functioning in relation to quality of care. http://www.biomedcentral.com/1756-0500/2/222 Teik Goh Martin Eccles BMC Research Notes 2009, 2:222 2009-10-29T00:00:00Z doi:10.1186/1756-0500-2-222 BMC Research Notes 1756-0500 2 222 2009-10-29T00:00:00Z XML Background: The shikimate pathway is an attractive target for the development of antitubercular agents because it is essential in Mycobacterium tuberculosis, the causative agent of tuberculosis, but absent in humans. M. tuberculosis aroE-encoded shikimate dehydrogenase catalyzes the forth reaction in the shikimate pathway. Structural and functional studies indicate that Lysine69 may be involved in catalysis and/or substrate binding in M. tuberculosis shikimate dehydrogenase. Investigation of the kinetic properties of mutant enzymes can bring important insights about the role of amino acid residues for M. tuberculosis shikimate dehydrogenase.FindingsWe have performed site-directed mutagenesis, steady-state kinetics, equilibrium binding measurements and molecular modeling for both the wild-type M. tuberculosis shikimate dehydrogenase and the K69A mutant enzymes. The apparent steady-state kinetic parameters for the M. tuberculosis shikimate dehydrogenase were determined; the catalytic constant value for the wild-type enzyme (50 s-1) is 68-fold larger than that for the mutant K69A (0.73 s-1). There was a modest increase in the Michaelis-Menten constant for DHS (K69A = 76 μM; wild-type = 29 μM) and NADPH (K69A = 30 μM; wild-type = 11 μM). The equilibrium dissociation constants for wild-type and K69A mutant enzymes are 32 (± 4) μM and 134 (± 21), respectively. Conclusion: Our results show that the residue Lysine69 plays a catalytic role and is not involved in substrate binding for the M. tuberculosis shikimate dehydrogenase. These efforts on M. tuberculosis shikimate dehydrogenase catalytic mechanism determination should help the rational design of specific inhibitors, aiming at the development of antitubercular drugs. http://www.biomedcentral.com/1756-0500/2/227 Valnes Rodrigues-Junior Ardala Breda Diogenes Santos Luiz Basso BMC Research Notes 2009, 2:227 2009-11-16T00:00:00Z doi:10.1186/1756-0500-2-227 BMC Research Notes 1756-0500 2 227 2009-11-16T00:00:00Z XML Background: The quantitative polymerase chain reaction (qPCR) is a widely utilized method for gene-expression analysis. However, insufficient material often compromises large-scale gene-expression studies. The aim of this study is to evaluate an RNA pre-amplification method to produce micrograms of cDNA as input for qPCR.FindingsThe linear isothermal Ribo-SPIA pre-amplification method (WT-Ovation; NuGEN) was first evaluated by measuring the expression of 20 genes in RNA samples from six neuroblastoma cell lines and of 194 genes in two commercially available reference RNA samples before and after pre-amplification, and subsequently applied on a large panel of 738 RNA samples extracted from neuroblastoma tumours. All RNA samples were evaluated for RNA integrity and purity. Starting from 5 to 50 nanograms of total RNA the sample pre-amplification method was applied, generating approximately 5 microgams of cDNA, sufficient to measure more than 1000 target genes. The results obtained from this study show a constant yield of pre-amplified cDNA independent of the amount of input RNA; preservation of differential gene-expression after pre-amplification without introduction of substantial bias; no co-amplification of contaminating genomic DNA; no necessity to purify the pre-amplified material; and finally the importance of good RNA quality to enable pre-amplification. Conclusion: Application of this unbiased and easy to use sample pre-amplification technology offers great advantage to generate sufficient material for diagnostic and prognostic work-up and enables large-scale qPCR gene-expression studies using limited amounts of sample material. http://www.biomedcentral.com/1756-0500/2/235 Joelle Vermeulen Stefaan Derveaux Steve Lefever Els De Smet Katleen De Preter Nurten Yigit Anne De Paepe Filip Pattyn Frank Speleman Jo Vandesompele BMC Research Notes 2009, 2:235 2009-11-25T00:00:00Z doi:10.1186/1756-0500-2-235 BMC Research Notes 1756-0500 2 235 2009-11-25T00:00:00Z XML Background: High-throughput screening of protein-protein interactions opens new systems biology perspectives for the comprehensive understanding of cell physiology in normal and pathological conditions. In this context, yeast two-hybrid system appears as a promising approach to efficiently reconstruct protein interaction networks at the proteome-wide scale. This protein interaction screening method generates a large amount of raw sequence data, i.e. the ISTs (Interaction Sequence Tags), which urgently need appropriate tools for their systematic and standardised analysis.FindingsWe develop pISTil, a bioinformatics pipeline combined with a user-friendly web-interface: (i) to establish a standardised system to analyse and to annotate ISTs generated by two-hybrid technologies with high performance and flexibility and (ii) to provide high-quality protein-protein interaction datasets for systems-level approach. This pipeline has been validated on a large dataset comprising more than 11.000 ISTs. As a case study, a detailed analysis of ISTs obtained from yeast two-hybrid screens of Hepatitis C Virus proteins against human cDNA libraries is also provided. Conclusion: We have developed pISTil, an open source pipeline made of a collection of several applications governed by a Perl script. The pISTil pipeline is intended to laboratories, with IT-expertise in system administration, scripting and database management, willing to automatically process large amount of ISTs data for accurate reconstruction of protein interaction networks in a systems biology perspective. pISTil is publicly available for download at http://sourceforge.net/projects/pistil. http://www.biomedcentral.com/1756-0500/2/220 Johann Pellet Laurene Meyniel Pierre-Olivier Vidalain Benoit de Chassey Lionel Tafforeau Vincent Lotteau Chantal Rabourdin-Combe Vincent Navratil BMC Research Notes 2009, 2:220 2009-10-29T00:00:00Z doi:10.1186/1756-0500-2-220 BMC Research Notes 1756-0500 2 220 2009-10-29T00:00:00Z XML