bluuebunny/crossref_metadata_2025 huggingface dataset:
Metabolic Syndrome and the Risk of Stroke in Middle-Aged Men
Authors: Kurl Sudhir , Laukkanen Jari A. , Niskanen Leo , Laaksonen David , Sivenius Juhani , Nyyssönen Kristiina , Salonen Jukka T.
Published: February 2006

Background and Purpose—

The metabolic syndrome, a clustering of disturbed glucose and insulin metabolism, obesity and abdominal fat distribution, dyslipidemia, and hypertension is associated with cardiovascular diseases. The aim of this study was to examine the relationship of metabolic syndrome, as defined by National Cholesterol Education Program (NCEP) and World Health Organization (WHO) criteria, with the risk for stroke.

Methods—

Population-based cohort study with an average follow-up of 14.3 years from eastern Finland. A total of 1131 men with no history of cardiovascular disease and diabetes at baseline participated. Sixty-five strokes occurred, of which 47 were ischemic strokes.

Results—

Men with the metabolic syndrome as defined by the NCEP criteria had a 2.05-fold (95% CI, 1.03 to 4.11;
P
=0.042) risk for all strokes and 2.41-fold (95% CI, 1.12 to 5.32;
P
=0.025) risk for ischemic stroke, after adjusting for socioeconomic status, smoking, alcohol, and family history of coronary heart disease. Additional adjustment for ischemic changes during exercise test, serum low-density lipoprotein cholesterol, plasma fibrinogen, energy intake for saturated fats, energy expenditure of leisure time physical activity, and white blood cell count, the results remained significant. The risk ratios among men with metabolic syndrome as defined by the WHO criteria were 1.82 (95% CI, 1.01 to 3.26;
P
=0.046) for all strokes and 2.16 (95% CI, 1.11 to 4.19;
P
=0.022) for ischemic stroke. After further adjustment, the respective risks were 2.08 (95% CI, 1.12 to 3.87;
P
=0.020) and 2.47 (95% CI, 1.21 to 5.07;
P
=0.013).

Conclusion—

The risk of any stroke is increased in men with metabolic syndrome, in the absence of stroke, diabetes and cardiovascular disease at baseline. Prevention of the metabolic syndrome presents a great challenge for clinicians with respect to stroke.
New Urbanism and Sprawl
Authors: Skaburskis Andrejs
Published: February 2006

This article presents an approach that has not been previously used for assessing claims regarding a development's impact on urban form and sprawl. The analysis shows that the Cornell new urbanist development increases suburban densities but not by nearly as much as would be inferred by analysis that simply compares the density of the development with that of the surrounding conventional suburbs. Most households living in the higher-density building types plan to eventually move to detached houses. If new urbanism, as it is expressed in the planning and design of Cornell, is to be a generalizable substitute to conventional suburban development, its projects will have to have a much larger proportion of single-family detached houses than the Cornell's 37 percent. New urbanists may best help reduce city spread by inducing households to move to and then to stay in single-family detached houses on smaller lots.
Travel Choice with No Alternative
Authors: Zhang Ming
Published: February 2006

Land use is expected to have a two-tiered effect on reducing automobile dependence. One is to enhance access to choices and the other to influence modal shifts away from driving. Existing studies have focused primarily on the second-tier effect. This article presents an empirical study of automobile dependence with emphasis on the identification of the first-tier effect. Using the Boston 1991 activitytravel survey data, the study jointly models travel choice set formation and mode choice decision. Automobile dependence is defined and measured as the probability that a traveler has the automobile as the only element in the choice set of travel modes. The study finds a wide variation in levels of automobile dependence along spatial and social dimensions. Elasticity estimates show that automobile dependence is highly sensitive to street network connectivity and to automobile availability, while population/job density and transit supply also matter. The study confirms the choice-enabling role of land use in reducing automobile dependence.
C/EBPα determines hematopoietic cell fate in multipotential progenitor cells by inhibiting erythroid differentiation and inducing myeloid differentiation
Authors: Suh Hyung Chan , Gooya John , Renn Katie , Friedman Alan D. , Johnson Peter F. , Keller Jonathan R.
Published: February 2006

C/EBPα is an essential transcription factor required for myeloid differentiation. While C/EBPα can act as a cell fate switch to promote granulocyte differentiation in bipotential granulocyte-macrophage progenitors (GMPs), its role in regulating cell fate decisions in more primitive progenitors is not known. We found increased numbers of erythroid progenitors and erythroid cells in C/EBPα–/– fetal liver (FL). Also, enforced expression of C/EBPα in hematopoietic stem cells resulted in a loss of erythroid progenitors and an increase in myeloid cells by inhibition of erythroid development and inducing myeloid differentiation. Conditional expression of C/EBPα in murine erythroleukemia (MEL) cells induced myeloid-specific genes, while inhibiting erythroid-specific gene expression including erythropoietin receptor (EpoR), which suggests a novel mechanism to determine hematopoietic cell fate. Thus, C/EBPα functions in hematopoietic cell fate decisions by the dual actions of inhibiting erythroid and inducing myeloid gene expression in multipotential progenitors.
SHP1 tyrosine phosphatase negatively regulates NPM-ALK tyrosine kinase signaling
Authors: Honorat Jean-François , Ragab Ashraf , Lamant Laurence , Delsol Georges , Ragab-Thomas Jeannie
Published: February 2006

Anaplastic large-cell lymphoma (ALCL) is frequently associated with the 2;5 translocation and expresses the NPM-ALK fusion protein, which possesses a constitutive tyrosine kinase activity. We analyzed SHP1 tyrosine phosphatase expression and activity in 3 ALK-positive ALCL cell lines (Karpas 299, Cost, and SU-DHL1) and in lymph node biopsies (n = 40). We found an inverse correlation between the level of NPM-ALK phosphorylation and SHP1 phosphatase activity. Pull-down and coimmunoprecipitation experiments demonstrated a SHP1/NPM-ALK association. Furthermore, confocal microscopy performed on ALCL cell lines and biopsy specimens showed the colocalization of the 2 proteins in cytoplasmic bodies containing Y664-phosphorylated NPM-ALK. Dephosphorylation of NPM-ALK by SHP1 demonstrated that NPM-ALK was a SHP1 substrate. Downregulation of SHP1 expression by RNAi in Karpas cells led to hyperphosphorylation of NPM-ALK, STAT3 activation, and increase in cell proliferation. Furthermore, SHP1 overexpression in 3T3 fibroblasts stably expressing NPM-ALK led to the decrease of NPM-ALK phosphorylation, lower cell proliferation, and tumor progression in nude mice. These findings show that SHP1 is a negative regulator of NPM-ALK signaling. The use of tissue microarrays revealed that 50% of ALK-positive ALCLs were positive for SHP1. Our results suggest that SHP1 could be a critical enzyme in ALCL biology and a potential therapeutic target.
Uncoupling of T-cell effector functions by inhibitory killer immunoglobulin–like receptors
Authors: Henel Gabriella , Singh Karnail , Cui Dapeng , Pryshchep Sergey , Lee Won-Woo , Weyand Cornelia M. , Goronzy Jörg J.
Published: February 2006

Killer immunoglobulin–like receptors (KIRs) are a family of regulatory cell-surface molecules expressed on natural killer (NK) cells and memory T-cell subsets. Their ability to prevent the formation of an activation platform and to inhibit NK cell activation is the basis of the missing self model of NK cell function. The benefits of KIR expression for T-cell biology are unclear. We studied how KIR2DL2 regulates T-cell function. Engagement of KIR2DL2 by the ligand human leukocyte antigen (HLA)–Cw3 did not affect conjugate formation between CD4+KIR2DL2+ T cells and superantigen-pulsed target cells or the development of mature immune synapses with lipid rafts. KIR2DL2 and the corresponding HLA-C ligand were initially recruited to the peripheral supramolecular activation cluster (pSMAC). Consequently, KIR2DL2 engagement did not inhibit the phosphorylation of early signaling proteins and T-cell–receptor (TCR)–mediated cytotoxicity or granule exocytosis. After 15-30 minutes, KIR2DL2 moved to the central supramolecular activation cluster (cSMAC), colocalizing with CD3. TCR synapses dissociated, and phosphorylated phospholipase C (PLC)–γ1, Vav1, and extracellular signal–regulated kinase 1/2 (ERK1/2) were reduced 90 minutes after stimulation. Gene array studies documented that the inhibition of late signaling events by KIR2DL2 affected transcriptional gene activation. We propose that KIRs on memory T cells operate to uncouple effector functions by modifying the transcriptional profile while leaving granule exocytosis unabated.
Dasatinib (BMS-354825) targets an earlier progenitor population than imatinib in primary CML but does not eliminate the quiescent fraction
Authors: Copland Mhairi , Hamilton Ashley , Elrick Lucy J. , Baird Janet W. , Allan Elaine K. , Jordanides Niove , Barow Martin , Mountford Joanne C. , Holyoake Tessa L.
Published: February 2006

Dasatinib (BMS-354825), a novel dual SRC/BCR-ABL kinase inhibitor, exhibits greater potency than imatinib mesylate (IM) and inhibits the majority of kinase mutations in IM-resistant chronic myeloid leukemia (CML). We have previously demonstrated that IM reversibly blocks proliferation but does not induce apoptosis of primitive CML cells. Here, we have attempted to overcome this resistance with dasatinib. Primitive IM-resistant CML cells showed only single-copy BCR-ABL but expressed significantly higher BCR-ABL transcript levels and BCR-ABL protein compared with more mature CML cells (P = .031). In addition, CrKL phosphorylation was higher in the primitive CD34+CD38– than in the total CD34+ population (P = .002). In total CD34+ CML cells, IM inhibited phosphorylation of CrKL at 16 but not 72 hours, consistent with enrichment of an IM-resistant primitive population. CD34+CD38– CML cells proved resistant to IM-induced inhibition of CrKL phosphorylation and apoptosis, whereas dasatinib led to significant inhibition of CrKL phosphorylation. Kinase domain mutations were not detectable in either IM or dasatinib-resistant primitive CML cells. These data confirm that dasatinib is more effective than IM within the CML stem cell compartment; however, the most primitive quiescent CML cells appear to be inherently resistant to both drugs.
Efficient inhibition of HIV-1 replication in human immature monocyte-derived dendritic cells by purified anti–HIV-1 IgG without induction of maturation
Authors: Holl Vincent , Peressin Maryse , Schmidt Sylvie , Decoville Thomas , Zolla-Pazner Susan , Aubertin Anne-Marie , Moog Christiane
Published: February 2006

During mucosal HIV transmission, immature dendritic cells (DCs) present in the mucosa are among the first cellular targets of the virus. Previous studies have analyzed the inhibition of HIV-1 transfer from human mature DCs to T lymphocytes by neutralizing IgG, but so far no in vitro data regarding the capacity of antibodies to inhibit HIV-1 infection of immature DCs have been reported. Here, we found an increased HIV-inhibitory activity of monoclonal IgG and purified polyclonal IgG when immature monocyte-derived dendritic cells (iMDDCs) were used as target cells instead of autologous blood lymphocytes. We showed that FcγRII is involved in the mechanism for inhibiting HIV-1 infection of iMDDCs by IgG, whereas no induction of maturation was detected at concentrations of IgG that result in a 90% reduction of HIV replication. After induction of FcγRI expression on iMDDCs by IFN-γ, an augmentation of the HIV-inhibitory activity of IgG, related to the expression of FcγRI, was observed. Taken together, our results demonstrate the participation of FcγRs in HIV-1 inhibition by IgG when iMDDCs are the targets. We propose that IgG is able to efficiently inhibit HIV-1 replication in iMDDCs and should be one of the components to be induced by vaccination.
Proteasome activity restricts lentiviral gene transfer into hematopoietic stem cells and is down-regulated by cytokines that enhance transduction
Authors: Santoni de Sio Francesca Romana , Cascio Paolo , Zingale Anna , Gasparini Mauro , Naldini Luigi
Published: February 2006

The therapeutic potential of hematopoietic stem cell (HSC) gene therapy can be fully exploited only by reaching efficient gene transfer into HSCs without compromising their biologic properties. Although HSCs can be transduced by HIV-derived lentiviral vectors (LVs) in short ex vivo culture, they display low permissivity to the vector, requiring cytokine stimulation to reach high-frequency transduction. Using stringent assays of competitive xenograft repopulation, we show that early-acting cytokines synergistically enhanced human HSC gene transfer by LVs without impairing engraftment and repopulation capacity. Using S-phase suicide assays, we show that transduction enhancement by cytokines was not dependent on cell cycle progression and that LVs can transduce quiescent HSCs. Pharmacologic inhibition of the proteasome during transduction dramatically enhanced HSC gene transfer, allowing the reach of very high levels of vector integration in their progeny in vivo. Thus, LVs are effectively restricted at a postentry step by the activity of this proteolytic complex. Unexpectedly, cytokine stimulation rapidly and substantially down-regulated proteasome activity in hematopoietic progenitors, highlighting one mechanism by which cytokines may enhance permissiveness to LV gene transfer. These findings demonstrate that antiviral responses ultimately mediated by proteasomes strongly limit the efficiency of HSC transduction by LVs and establish improved conditions for HSC-based gene therapy.
ICAM-2 mediates neutrophil transmigration in vivo: evidence for stimulus specificity and a role in PECAM-1–independent transmigration
Authors: Huang Miao-Tzu , Larbi Karen Y. , Scheiermann Christoph , Woodfin Abigail , Gerwin Nicole , Haskard Dorian O. , Nourshargh Sussan
Published: February 2006

ICAM-2 has been implicated in leukocyte transmigration in vitro, but there is little in vivo evidence to support this. To address this, neutrophil migration was investigated in ICAM-2–deficient mice (KO) and in wild-type (WT) mice treated with an anti–ICAM-2 blocking monoclonal antibody (mAb) (3C4). In a peritonitis model, IL-1β–induced accumulation of neutrophils was significantly reduced in mice treated with 3C4 (51% inhibition) and in KO mice (41% inhibition). In contrast, TNF-α– or thioglycolate-induced responses were not suppressed in KO mice. Analysis of IL-1β–induced leukocyte responses in cremasteric venules of KO animals by intravital microscopy indicated a defect in transmigration (44% inhibition) but not rolling or adhesion. As found before, TNF-α–induced leukocyte transmigration was unaltered in the KO mice. WT mice treated with the anti–ICAM-2 mAb also exhibited a selective reduction in leukocyte transmigration in response to IL-1β while an anti–ICAM-1 mAb inhibited both leukocyte adhesion and transmigration. Interestingly, mAb 3C4 significantly suppressed IL-1β–induced neutrophil transmigration in PE-CAM-1 KO animals in the peritonitis model but not in the cremaster muscle. The findings provide direct evidence for the involvement of ICAM-2 in neutrophil transmigration in vivo, though this role appears to be stimulus specific. Furthermore, ICAM-2 appears capable of mediating PECAM-1–independent leukocyte transmigration.
Epigenetics and airways disease
Authors: Adcock Ian M , Ford Paul , Ito Kazuhiro , Barnes P J
Published: February 2006

Epigenetics is the term used to describe heritable changes in gene expression that are not coded in the DNA sequence itself but by post-translational modifications in DNA and histone proteins. These modifications include histone acetylation, methylation, ubiquitination, sumoylation and phosphorylation. Epigenetic regulation is not only critical for generating diversity of cell types during mammalian development, but it is also important for maintaining the stability and integrity of the expression profiles of different cell types. Until recently, the study of human disease has focused on genetic mechanisms rather than on non-coding events. However, it is becoming increasingly clear that disruption of epigenetic processes can lead to several major pathologies, including cancer, syndromes involving chromosomal instabilities, and mental retardation. Furthermore, the expression and activity of enzymes that regulate these epigenetic modifications have been reported to be abnormal in the airways of patients with respiratory disease. The development of new diagnostic tools might reveal other diseases that are caused by epigenetic alterations. These changes, despite being heritable and stably maintained, are also potentially reversible and there is scope for the development of 'epigenetic therapies' for disease.
Effects of CPAP on right ventricular myocardial performance index in obstructive sleep apnea patients without hypertension
Authors: Dursunoglu Nese , Dursunoglu Dursun , Özkurt Sibel , Gür Sükrü , Özalp Güllü , Evyapan Fatma
Published: February 2006

Objectives

Obstructive sleep apnoea (OSA) might cause right ventricular dysfunction and pulmonary hypertension. We aimed to determine the effects of nasal continuous positive airway pressure (CPAP) therapy on right ventricular myocardial performance index (MPI) in OSA patients without hypertension.

Methods

49 subjects without hypertension, diabetes mellitus, any cardiac and pulmonary disease had overnight polysomnography and echocardiography. In 18 moderate-severe OSA (apnea-hypopnea index ≥ 15) patients, right ventricular free wall diameter (RVFWD) was measured by M-mode, and right ventricular MPI was calculated as (isovolumic contraction time+ isovolumic relaxation time) / pulmonary ejection time using Doppler at baseline and after 6 months CPAP therapy.

Results

Mean age was 46.5 ± 4.9 year. Patients had high body mass index (BMI: 30.6 ± 4,0 kg/m2), but there was no change in either BMI or blood pressures after 6 months. Right ventricular end-diastolic and end-systolic diameters were in normal limits at baseline, and did not change after CPAP usage. Baseline RVFWD (7.1 ± 2.1 mm) significantly decreased after CPAP therapy (6.2 ± 1.7 mm, p < 0.001). 15 of patients (83%) had right ventricular diastolic dysfunction at baseline, and it was completely improved in 11 of them (73%) by CPAP usage. Right ventricular global dysfunction was shown in 11 patients (61%) with a high MPI (62.2 ± 9.3%) at baseline; and MPI was significantly decreased after CPAP therapy (47.3 ± 8.4%, p < 0.0001), and it was completely corrected in 4 of them (36%).

Conclusion

CPAP therapy significantly decreases RVFWD and improves right ventricular diastolic and global functions (MPI) in OSA patients without hypertension.
Integrated analysis of gene expression by association rules discovery
Authors: Carmona-Saez Pedro , Chagoyen Monica , Rodriguez Andres , Trelles Oswaldo , Carazo Jose M , Pascual-Montano Alberto
Published: February 2006

Background

Microarray technology is generating huge amounts of data about the expression level of thousands of genes, or even whole genomes, across different experimental conditions. To extract biological knowledge, and to fully understand such datasets, it is essential to include external biological information about genes and gene products to the analysis of expression data. However, most of the current approaches to analyze microarray datasets are mainly focused on the analysis of experimental data, and external biological information is incorporated as a posterior process.

Results

In this study we present a method for the integrative analysis of microarray data based on the Association Rules Discovery data mining technique. The approach integrates gene annotations and expression data to discover intrinsic associations among both data sources based on co-occurrence patterns. We applied the proposed methodology to the analysis of gene expression datasets in which genes were annotated with metabolic pathways, transcriptional regulators and Gene Ontology categories. Automatically extracted associations revealed significant relationships among these gene attributes and expression patterns, where many of them are clearly supported by recently reported work.

Conclusion

The integration of external biological information and gene expression data can provide insights about the biological processes associated to gene expression programs. In this paper we show that the proposed methodology is able to integrate multiple gene annotations and expression data in the same analytic framework and extract meaningful associations among heterogeneous sources of data. An implementation of the method is included in the Enge ne software package.
PathSys: integrating molecular interaction graphs for systems biology
Authors: Baitaluk Michael , Qian Xufei , Godbole Shubhada , Raval Alpan , Ray Animesh , Gupta Amarnath
Published: February 2006

Background

The goal of information integration in systems biology is to combine information from a number of databases and data sets, which are obtained from both high and low throughput experiments, under one data management scheme such that the cumulative information provides greater biological insight than is possible with individual information sources considered separately.

Results

Here we present PathSys, a graph-based system for creating a combined database of networks of interaction for generating integrated view of biological mechanisms. We used PathSys to integrate over 14 curated and publicly contributed data sources for the budding yeast (S. cerevisiae) and Gene Ontology. A number of exploratory questions were formulated as a combination of relational and graph-based queries to the integrated database. Thus, PathSys is a general-purpose, scalable, graph-data warehouse of biological information, complete with a graph manipulation and a query language, a storage mechanism and a generic data-importing mechanism through schema-mapping.

Conclusion

Results from several test studies demonstrate the effectiveness of the approach in retrieving biologically interesting relations between genes and proteins, the networks connecting them, and of the utility of PathSys as a scalable graph-based warehouse for interaction-network integration and a hypothesis generator system. The PathSys's client software, named BiologicalNetworks, developed for navigation and analyses of molecular networks, is available as a Java Web Start application at http://brak.sdsc.edu/pub/BiologicalNetworks.
HotSwap for bioinformatics: A STRAP tutorial
Authors: Gille Christoph , Robinson Peter N
Published: February 2006

Background

Bioinformatics applications are now routinely used to analyze large amounts of data. Application development often requires many cycles of optimization, compiling, and testing. Repeatedly loading large datasets can significantly slow down the development process. We have incorporated HotSwap functionality into the protein workbench STRAP, allowing developers to create plugins using the Java HotSwap technique.

Results

Users can load multiple protein sequences or structures into the main STRAP user interface, and simultaneously develop plugins using an editor of their choice such as Emacs. Saving changes to the Java file causes STRAP to recompile the plugin and automatically update its user interface without requiring recompilation of STRAP or reloading of protein data. This article presents a tutorial on how to develop HotSwap plugins. STRAP is available at http://strapjava.de and http://www.charite.de/bioinf/strap.

Conclusion

HotSwap is a useful and time-saving technique for bioinformatics developers. HotSwap can be used to efficiently develop bioinformatics applications that require loading large amounts of data into memory.
Evolution of the NANOG pseudogene family in the human and chimpanzee genomes
Authors: Fairbanks Daniel J , Maughan Peter J
Published: February 2006

Background

The NANOG gene is expressed in mammalian embryonic stem cells where it maintains cellular pluripotency. An unusually large family of pseudogenes arose from it with one unprocessed and ten processed pseudogenes in the human genome. This article compares the NANOG gene and its pseudogenes in the human and chimpanzee genomes and derives an evolutionary history of this pseudogene family.

Results

The NANOG gene and all pseudogenes except NANOGP8 are present at their expected orthologous chromosomal positions in the chimpanzee genome when compared to the human genome, indicating that their origins predate the human-chimpanzee divergence. Analysis of flanking DNA sequences demonstrates that NANOGP8 is absent from the chimpanzee genome.

Conclusion

Based on the most parsimonious ordering of inferred source-gene mutations, the deduced evolutionary origins for the NANOG pseudogene family in the human and chimpanzee genomes, in order of most ancient to most recent, are NANOGP6, NANOGP5, NANOGP3, NANOGP10, NANOGP2, NANOGP9, NANOGP7, NANOGP1, and NANOGP4. All of these pseudogenes were fixed in the genome of the human-chimpanzee common ancestor. NANOGP8 is the most recent pseudogene and it originated exclusively in the human lineage after the human-chimpanzee divergence. NANOGP1 is apparently an unprocessed pseudogene. Comparison of its sequence to the functional NANOG gene's reading frame suggests that this apparent pseudogene remained functional after duplication and, therefore, was subject to selection-driven conservation of its reading frame, and that it may retain some functionality or that its loss of function may be evolutionarily recent.
Adaptive evolution of chloroplast genome structure inferred using a parametric bootstrap approach
Authors: Cui Liying , Leebens-Mack Jim , Wang Li-San , Tang Jijun , Rymarquis Linda , Stern David B , dePamphilis Claude W
Published: February 2006

Background

Genome rearrangements influence gene order and configuration of gene clusters in all genomes. Most land plant chloroplast DNAs (cpDNAs) share a highly conserved gene content and with notable exceptions, a largely co-linear gene order. Conserved gene orders may reflect a slow intrinsic rate of neutral chromosomal rearrangements, or selective constraint. It is unknown to what extent observed changes in gene order are random or adaptive. We investigate the influence of natural selection on gene order in association with increased rate of chromosomal rearrangement. We use a novel parametric bootstrap approach to test if directional selection is responsible for the clustering of functionally related genes observed in the highly rearranged chloroplast genome of the unicellular green alga Chlamydomonas reinhardtii, relative to ancestral chloroplast genomes.

Results

Ancestral gene orders were inferred and then subjected to simulated rearrangement events under the random breakage model with varying ratios of inversions and transpositions. We found that adjacent chloroplast genes in C. reinhardtii were located on the same strand much more frequently than in simulated genomes that were generated under a random rearrangement processes (increased sidedness; p < 0.0001). In addition, functionally related genes were found to be more clustered than those evolved under random rearrangements (p < 0.0001). We report evidence of co-transcription of neighboring genes, which may be responsible for the observed gene clusters in C. reinhardtii cpDNA.

Conclusion

Simulations and experimental evidence suggest that both selective maintenance and directional selection for gene clusters are determinants of chloroplast gene order.
Selecting cases from nuclear families for case-control association analysis
Authors: Moore Rachael M , Pinel Tracy , Zhao Jing Hua , March Ruth , Jawaid Ansar
Published: February 2006

We examine the efficiency of a number of schemes to select cases from nuclear families for case-control association analysis using the Genetic Analysis Workshop 14 simulated dataset. We show that with this simulated dataset comparing all affected siblings with unrelated controls is considerably more powerful than all of the other approaches considered. We find that the test statistic is increased by almost 3-fold compared to the next best sampling schemes of selecting all affected sibs only from families with affected parents (AFaff), one affected sib with most evidence of allele-sharing from each family (SF), and all affected sibs from families with evidence for linkage (AFL). We consider accounting for biological relatedness of samples in the association analysis to maintain the correct type I error. We also discuss the relative efficiencies of increasing the ratio of unrelated cases to controls, methods to confirm associations and issues to consider when applying our conclusions to other complex disease datasets.
Resampling methods to reduce the selection bias in genetic effect estimation in genome-wide scans
Authors: Wu Long Yang , Lee Sophia SF , Shi Haijiang Steven , Sun Lei , Bull Shelley B
Published: February 2006

Using the simulated data of Problem 2 for Genetic Analysis Workshop 14 (GAW14), we investigated the ability of three bootstrap-based resampling estimators (a shrinkage, an out-of-sample, and a weighted estimator) to reduce the selection bias for genetic effect estimation in genome-wide linkage scans. For the given marker density in the preliminary genome scans (7 cM for microsatellite and 3 cM for SNP), we found that the two sets of markers produce comparable results in terms of power to detect linkage, localization accuracy, and magnitude of test statistic at the peak location. At the locations detected in the scan, application of the three bootstrap-based estimators substantially reduced the upward selection bias in genetic effect estimation for both true and false positives. The relative effectiveness of the estimators depended on the true genetic effect size and the inherent power to detect it. The shrinkage estimator is recommended when the power to detect the disease locus is low. Otherwise, the weighted estimator is recommended.
Regulation of the human LAT gene by the Elf-1 transcription factor
Authors: Finco Timothy S , Justice-Healy Geri E , Patel Shivani J , Hamilton Victoria E
Published: February 2006

Background

TheLATgene encodes an intracellular adaptor protein that links cell-surface receptor engagement to numerous downstream signalling events, and thereby plays an integral role in the function of cell types that express the gene, including T cells, mast cells, natural killer cells, and platelets. To date, the mechanisms responsible for the transcriptional regulation of this gene have not been investigated.

Results

In this study we have mapped the transcriptional start sites for the humanLATgene and localized the 5' and 3' boundaries of the proximal promoter. We find that the promoter contains both positive and negative regulatory regions, and that two binding sites for the Ets family of transcription factors have a strong, positive effect on gene expression. Each site binds the Ets family member Elf-1, and overexpression of Elf-1 augmentsLATpromoter activity. The promoter also contains a Runx binding site adjacent to one of the Ets sites. This site, which is shown to bind Runx-1, has an inhibitory effect on gene expression. Finally, data is also presented indicating that the identified promoter may regulate cell-type specific expression.

Conclusion

Collectively, these results provide the first insights into the transcriptional regulation of theLATgene, including the discovery that the Ets transcription factor Elf-1 may play a central role in its expression.
The association between processes, structures and outcomes of secondary prevention care among VA ischemic heart disease patients
Authors: Ho P Michael , Prochazka Allan V , Magid David J , Sales Anne E , Grunwald Gary K , Hammermeister Karl E , Rumsfeld John S
Published: February 2006

Background

Hyperlipidemia and hypertension are well-established risk factors for recurrent cardiovascular events among patients with ischemic heart disease (IHD). Despite national recommendations, concordance with guidelines for LDL cholesterol and blood pressure remains inadequate. The objectives of this study were to 1) determine concordance rates with LDL cholesterol and BP recommendations; and 2) identify patient factors, processes and structures of care associated with guideline concordance among VA IHD patients.

Methods

This was a cross sectional study of veterans with IHD from 8 VA hospitals. Outcomes were concordance with LDL guideline recommendations (LDL<100 mg/dl), and BP recommendations (<140/90 mm Hg). Cumulative logit and hierarchical logistic regression analyses were performed to identify patient factors, processes, and structures of care independently associated with guideline concordance.

Results

Of 14,114 veterans with IHD, 55.7% had hypertension, 71.5% had hyperlipidemia, and 41.6% had both conditions. Guideline concordance for LDL and BP were 38.9% and 53.4%, respectively. However, only 21.9% of the patients achieved both LDL <100 mg/dl and BP <140/90 mm Hg. In multivariable analyses, patient factors including older age and the presence of vascular disease were associated with worse guideline concordance. In contrast, diabetes was associated with better guideline concordance. Several process of care variables, including higher number of outpatient visits, higher number of prescribed medications, and a recent cardiac hospitalization were associated with better guideline concordance. Among structures of care, having on-site cardiology was associated with a trend towards better guideline concordance.

Conclusion

Guideline concordance with secondary prevention measures among IHD patients remains suboptimal. It is hoped that the findings of this study can serve as an impetus for quality improvement efforts to improve upon secondary prevention measures and reduce the morbidity and mortality of patients with known IHD.
Setting directions for capacity building in primary health care: a survey of a research network
Authors: Ried Karin , Farmer Elizabeth A , Weston Kathryn M
Published: February 2006

Background

The South Australian Research Network 'SARNet' aims to build research capacity in primary health care, as part of a national government-funded strategy to integrate research into clinical practice. Internationally, research networks have been a fundamental part of research culture change, and a variety of network models exist. The 'SARNet' model uses a whole system, multidisciplinary approach to capacity building and supports individuals and groups. We undertook a descriptive baseline survey in order to understand the background and needs of SARNet members and to tailor network activities towards those needs.

Methods

A questionnaire survey, assessing members' professional background, research experience, and interest in research development and training, was sent to all members who joined the network in its first year. The visual 'research spider' tool was used to ascertain members' experience in ten core research skills, as well as their interest in developing these skills. Individuals were asked to classify themselves into one of four categories of researchers, based on previous research experience. These self-assessment categories ranged from non-participant to academic.

Results

Network membership was diverse. Of the 89 survey participants, 55% were general practitioners or allied health professionals. Overall, most survey respondents indicated little to moderate experience in 7 out of the 10 skills depicted in the 'research spider'. In comparison, respondents were generally highly interested in developing their research skills in all areas. Respondents' research skills correlated significantly with their self-assessed category of research participation (Spearman rank correlation, r = 0.82, p < 0.0005). Correlations between research category and publication record (Gamma association, γ = 0.53, p < 0.0005) or funding record (Gamma association, γ = 0.62, p < 0.0005) supported the internal validity of the survey instrument.

Conclusion

Literature describing evaluation of the impact of networks is scarce. Our survey questionnaire could provide a useful instrument for evaluation of both networks and capacity building initiatives. The survey including the 'research spider' tool provided valuable information about members' needs and interest in strategies to develop their research skills. Initial needs analyses as well as on-going evaluation of network activities are important to include into the business plans of research networks, in order to ensure the network's effectiveness and support of its membership.
Automated extraction protocol for quantification of SARS-Coronavirus RNA in serum: an evaluation study
Authors: Chiu Rossa WK , Jin Yongjie , Chung Grace TY , Lui Wing-bong , Chan Anthony TC , Lim Wilina , Dennis Lo YM
Published: February 2006

Background

We have previously developed a test for the diagnosis and prognostic assessment of the severe acute respiratory syndrome (SARS) based on the detection of the SARS-coronavirus RNA in serum by real-time quantitative reverse transcriptase polymerase chain reaction (RT-PCR). In this study, we evaluated the feasibility of automating the serum RNA extraction procedure in order to increase the throughput of the assay.

Methods

An automated nucleic acid extraction platform using the MagNA Pure LC instrument (Roche Diagnostics) was evaluated. We developed a modified protocol in compliance with the recommended biosafety guidelines from the World Health Organization based on the use of the MagNA Pure total nucleic acid large volume isolation kit for the extraction of SARS-coronavirus RNA. The modified protocol was compared with a column-based extraction kit (QIAamp viral RNA mini kit, Qiagen) for quantitative performance, analytical sensitivity and precision.

Results

The newly developed automated protocol was shown to be free from carry-over contamination and have comparable performance with other standard protocols and kits designed for the MagNA Pure LC instrument. However, the automated method was found to be less sensitive, less precise and led to consistently lower serum SARS-coronavirus concentrations when compared with the column-based extraction method.

Conclusion

As the diagnostic efficiency and prognostic value of the serum SARS-CoV RNA RT-PCR test is critically associated with the analytical sensitivity and quantitative performance contributed both by the RNA extraction and RT-PCR components of the test, we recommend the use of the column-based manual RNA extraction method.
The GCC repeat length in the 5'UTR of MRP1 gene is polymorphic: a functional characterization of its relevance for cystic fibrosis
Authors: Nicolis Elena , Pasetto Matteo , Cigana Cristina , Pradal Ugo , Assael Baroukh M , Melotti Paola
Published: February 2006

Background

Among the members of the ATP binding cassette transporter superfamily, MRPs share the closest homology with the CFTR protein, which is defective in CF disease. MRP1 has been proposed as a potential modifier gene and/or as novel target for pharmacotherapy of CF to explain the clinical benefits observed in some CF patients treated with the macrolide AZM. The 5'UTR of the MRP1 gene contains a GCC triplet repeat that could represent a polymorphic site and affect the activity of the promoter.

Methods

The MRP1 5' flanking region was amplified by PCR from 36 CF patients and 100 non-CF subjects and the number of GCC triplets of each allele was determined by sequence and electrophoretic analysis. We performed gene reporter studies in CF airway epithelial cells 16HBE14o-AS3, in basal conditions and in the presence of AZM.

Results

We found that the GCC repeat is polymorphic, ranging from 7 to 14 triplets either in CF or in non-CF subjects. Our data are preliminary and have to be confirmed on a larger population of CF subjects. The transcriptional activity of the proximal MRP1 5' regulatory region revealed no statistically significant correlations between the number of repeats and treatment with AZM.

Conclusion

We identified a novel polymorphism in the 5'UTR of MRP1 gene that provides multiple alleles in a gene relevant for multidrug resistance as well as for CF, determining that this region is transcriptionally active and that this activity does not appear to be influenced by AZM treatment.
Are mild head injuries as mild as we think? Neurobehavioral concomitants of chronic post-concussion syndrome
Authors: Sterr Annette , Herron Katherine A , Hayward Chantal , Montaldi Daniela
Published: February 2006

Background

Mild traumatic brain injury (MTBI) can sometimes lead to persistent postconcussion symptoms. One well accepted hypothesis claims that chronic PCS has a neural origin, and is related to neurobehavioral deficits. But the evidence is not conclusive. In the attempt to characterise chronic MTBI consequences, the present experiment used a group comparison design, which contrasted persons (a) with MTBI and PCS, (b) MTBI without PCS, and (c) matched controls. We predicted that participants who have experienced MTBI but show no signs of PCS would perform similar to controls. At the same time, a subgroup of MTBI participants would show PCS symptoms and only these volunteers would have poorer cognitive performance. Thereby, the performance deficits should be most noticeable in participants with highest PCS severity.

Method

38 patients with a single MTBI that had occurred at least 12 month prior to testing, and 38 matched controls, participated in the experiment. A combination of questionnaires and neuropsychological test batteries were used to assess the extent of PCS and related deficits in neurobehavioral performance.

Results

11 out of 38 MTBI participants (29%) were found to suffer from PCS. This subgroup of MTBI patients performed poorly on neuropsychological test batteries. Thereby, a correlation was found between PCS symptom severity and test performance suggesting that participants with more pronounced PCS symptoms performed worse in cognitive tasks. In contrast, MTBI patients with no PCS showed performed similar to matched control. We further found that loss of consciousness, a key criterion for PCS diagnosis, was not predictive of sustained PCS.

Conclusion

The results support the idea that MTBI can have sustained consequences, and that the subjectively experienced symptoms and difficulties in everyday situations are related to objectively measurable parameters in neurocognitive function.
Understanding the attitudes of the elderly towards enrolment into cancer clinical trials
Authors: Townsley Carol A , Chan Kelvin K , Pond Gregory R , Marquez Christine , Siu Lillian L , Straus Sharon E
Published: February 2006

Background

The optimal cancer treatment for an older population is largely unknown because of the low numbers of elderly patients accrued into clinical trials. This project focuses on the attitudes of the elderly about participation in clinical trials to determine if this is one of the barriers to the involvement of this population in clinical trials.

Methods

The first phase of this study was a self-administered questionnaire mailed to 425 elderly persons with cancer, selected from Princess Margaret Hospital oncology clinics. The second phase consisted of individual semi-structured interviews with cancer patients to assess their attitudes towards cancer, its management and enrolment into cancer clinical trials.

Results

Ninety-four patients responded to the survey giving a response rate of 22.1%. Three quarters of respondents stated that they would be willing to participate in a clinical trial. The factors that most influenced older patients' willingness to participate in a cancer study were recommendations from a cancer doctor and the chance that the study treatment may help them feel better. Seventeen survey responders participated in interviews. Common themes from these interviews included patient-physician communication, the referral process, and the role of age in cancer care decision-making.

Conclusion

Most elderly people, who responded to this survey, are willing to consider participation in cancer clinical trials however, elderly patients do not appear to actively seek clinical trials and few were informed of the availability of clinical trials. Physician barriers and availability of appropriate clinical trials may play a bigger role in preventing accrual of elderly cancer patients into trials.
Auditory change detection in schizophrenia: sources of activity, related neuropsychological function and symptoms in patients with a first episode in adolescence, and patients 14 years after an adolescent illness-onset
Authors: Oades Robert D , Wild-Wall Nele , Juran Stephanie A , Sachsse Jan , Oknina Ljubov B , Röpcke Bernd
Published: February 2006

Background

The event-related brain response mismatch negativity (MMN) registers changes in auditory stimulation with temporal lobe sources reflecting short-term echoic memory and frontal sources a deviance-induced switch in processing. Impairment, controversially present at the onset of schizophrenia, develops rapidly and can remain independent of clinical improvement. We examined the characteristics of the scalp-recorded MMN and related these to tests of short-term memory and set-shifting. We assessed whether the equivalent dipole sources are affected already at illness-onset in adolescence and how these features differ after a 14-year course following an adolescent onset. The strength, latency, orientation and location of frontal and temporal lobe sources of MMN activity early and late in the course of adolescent-onset schizophrenia are analysed and illustrated.

Methods

MMN, a measure of auditory change-detection, was elicited by short deviant tones in a 3-tone oddball-presentation and recorded from 32 scalp electrodes. Four dipole sources were placed following hypothesis-led calculations using brain electrical source analysis on brain atlas and MR-images. A short neuropsychological test battery was administered. We compared 28 adolescent patients with a first episode of schizophrenia and 18 patients 14 years after diagnosis in adolescence with two age-matched control groups from the community (n = 22 and 18, respectively).

Results

MMN peaked earlier in the younger than the older subjects. The amplitude was reduced in patients, especially the younger group, and was here associated with negative symptoms and slow set-shifting. In first-episode patients the temporal lobe sources were more ventral than in controls, while the left cingular and right inferior-mid frontal sources were more caudal. In the older patients the left temporal locus remained ventral (developmental stasis), the right temporal locus extended more antero-laterally (illness progression), and the right frontal source moved antero-laterally (normalised).

Conclusion

From the start of the illness there were differences in the dipole-model between healthy and patient groups. Separate characteristics of the sources of the activity differences showed an improvement, stasis or deterioration with illness-duration. The precise nature of the changes in the sources of MMN activity and their relationship to selective information processing and storage depend on the specific psychopathology and heterogeneous course of the illness.