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Biomedical subjects

Wei Chen

Publications and source records attributed to Wei Chen.

At least 217 records · Page 12Linked to original sources
PubMed2005

Intravenous acid fibroblast growth factor protects intestinal mucosal cells against ischemia-reperfusion injury via regulating Bcl-2/Bax expression.

AIM: To detect the effect of acid fibroblast growth factor (aFGF) on apoptosis and gene expression of bax and bcl-2 gene in rat intestine after ischemia/reperfusion (I/R) injury, and to explore the protective mechanisms of aFGF. METHODS: One hundred and eight Wistar rats were randomly divided into sham-operated control group (C) (n = 6), intestinal ischemia group (I) (n = 6), aFGF treatment group (A) (n = 48) and intestinal ischemia-reperfusion group (R) (n = 48). In group I, the animals were killed after 45 min of superior mesenteric artery (SMA) occlusion, while in groups R and A, the rats sustained 45 min of SMA occlusion and were then treated with normal saline and aFGF, respectively, sustained 15 min, 30 min, 1, 2, 6, 12, 24, or 48 h of reperfusion, respectively. In group C, SMA was separated, but without occlusion. Apoptosis in intestinal villus was determined with terminal deoxynucleotidyl transferase mediated dUTP-biotin nick-end labeling technique (TUNEL). Intestinal tissue samples were taken not only for detection of bax and bcl-2 gene expression by RT-PCR, but also for detection of bax and bcl-2 protein expression and distribution by immunohistochemical analysis. RESULTS: The rat survival rates in aFGF treated group were higher than group R (P<0.05) and the improvement of intestinal histological structures was observed at 2, 6, and 12 h after the reperfusion in group A compared with group R. The apoptotic rates were (41.17+/-3.49)%, (42.83+/-5.23)% and (53.33+/-6.92)% at 2, 6 and 12 h after reperfusion, respectively in group A, apparently less than those of group R at matched time points (50.67+/-6.95, 54.17+/-7.86, 64.33+/-6.47, respectively) (P<0.05). The bax gene transcription and translation were significantly decreased in group A vs group R, while mRNA and protein contents of Bcl-2 in group A were obviously higher than those in group R during 2-12 h period after reperfusion. CONCLUSION: The changes in histological structure and the increment of apoptotic rate indicated that the intestinal barrier was damaged after intestinal I/R injury, whilst intravenous aFGF could alleviate apoptosis induced by ischemia and reperfusion in rat intestinal tissues, in which genes of bax and bcl-2 might play important roles.

Animals↗
PubMed2005

Upconversion luminescence from CdSe nanoparticles.

Efficient upconversion luminescence has been observed from CdSe nanoparticles ranging in size from 2.5 to 6 nm. The upconversion luminescence exhibits a near-quadratic laser power dependence. Emissions from both excitons and trap states are observed in the upconversion and photoluminescence spectra, and in the upconversion luminescence the emission from the trap states is enhanced relative to the trap-state emission in the photoluminescence. The upconversion decay lifetimes are slightly longer than the photoluminescence decay lifetimes. Time-resolved spectral measurements indicate that this is due to the involvement of long decay components from surface or trap states. Both the photoluminescence and upconversion luminescence decrease in intensity with increasing temperature due mainly to thermal quenching. All the observations indicate that trap states work as emitters rather than as intermediate states for upconversion luminescence and that two-photon absorption is the likely excitation mechanism.

Cadmium Compounds↗
PubMed2005

Pivotal molecules of MHC I pathway in human primary hepatocellular carcinoma.

AIM: To investigate the expression of several important molecules involved in major histocompatibility complex (MHC) class I presentation pathway in primary hepatocellular carcinoma (HCC), and to determine whether cytotoxic T lymphocyte (CTL) vaccine therapy was suitable for HCC. METHODS: Labeled streptavidin biotin (LSAB) method of immunohistochemistry was used to study 33 HCC tissue specimens. RESULTS: Most HCC tissues and adjacent histological normal hepatocytes expressed HLA-I antigens,TAP, and B7, expression of B7 was especially strong, and there was no significant difference between them (P>0.05). CONCLUSION: The MHC class I presentation pathway in primary hepatocellular carcinoma may not be abnormal or dysfunctional, and CTL could kill these tumor cells. Thus, it is suitable and practicable to design and construct CTL vaccine against HCC.

Cancer Vaccines↗
PubMed2005

[Investigation of mesenchymal-epithelial transdifferentiation in the morphogenesis mechanism of embryonic epidermic cells].

OBJECTIVE: To study the relationship between the morphologic mechanism of human embryonic epidermic cells and mesenchymal-epithelial transformation (MET) and its modulation factor. METHODS: Morphological occurrence of epidermis was detected with histologic methods in earlier period [estimated gestational age (EGA) 6-14 weeks] human embryonic skin samples. At the same time, the characteristic expression and their distribution markers of mesenchymal cells [vimentin and alpha-smooth muscle actin (alpha-SMA)], embryonic specific epidermic protein CK8&18, specific protein of epidermic stem cell CK19, transforming growth factor-beta1) (TGF-beta1) and its receptor (TGFbetaRI) in embryonic epidermis were examined with immunohistochemistry and indirect-immunofluorescent doble-labelling method. RESULTS: During EAG 6-8 weeks, ectodermal cells containing Vim+/alpha-SMA(-) were found to transform into epidermal stem cells with CK8&18+/CK19+. In ectodermal cells, protein expression density of TGFbetaRI was moderate (+ +), while positive signal of TGFbeta1 was weak (+/-). After EGA10 weeks, epidermal cells showed typical morphological characteristics. CONCLUSIONS: At EGA 6-8 weeks, human embryonic skin epidermal cells began to form through MET, in which the signal pathway mediated by TGFbetaRI might play important roles, but the role of TGFbeta1 need to be further studied.

Cell Differentiation↗
PubMed2005

Advanced lipoprotein testing does not improve identification of subclinical atherosclerosis in young adults: the Bogalusa Heart Study.

BACKGROUND: The clinical value of advanced lipoprotein testing relative to traditional lipid testing remains controversial. To date, no studies have evaluated associations between advanced lipoprotein testing and subclinical atherosclerosis in healthy young adults. OBJECTIVE: To determine whether advanced lipoprotein testing using vertical-spin density-gradient ultracentrifugation better predicts carotid intima-media thickness, a validated measure of subclinical atherosclerosis, than does traditional lipoprotein testing in asymptomatic young adults. DESIGN: Cross-sectional community-based study. SETTING: Bogalusa, Louisiana. PARTICIPANTS: 311 randomly selected adults from the Bogalusa Heart Study who were 20 to 38 years of age. MEASUREMENTS: The authors performed advanced lipoprotein testing using vertical-spin density-gradient ultracentrifugation, traditional testing using enzymatic methods, and Friedewald formula estimation of low-density lipoprotein cholesterol levels. A certified reader blinded to lipoprotein results determined carotid intima-media thickness by B-mode ultrasonography. C-statistics from area under the receiver-operating characteristic curves (AUCs) derived from multivariable regression models were compared. RESULTS: Lipid values obtained with advanced lipoprotein testing did not predict carotid intima-media thickness better than traditionally measured lipid values in 236 participants for whom all data were available. A model using traditional lipoprotein measures (AUC, 0.754 [95% CI, 0.690 to 0.812]) did not differ significantly from a model using advanced lipoprotein measures (AUC, 0.779 [CI, 0.662 to 0.871]) for prediction of carotid intima-media thickness (P > 0.2). Subclass pattern of LDL, lipoprotein(a) cholesterol, intermediate-density lipoprotein cholesterol, high-density lipoprotein cholesterol subclasses, and very-low-density lipoprotein subclasses did not improve the performance of models for prediction of carotid intima-media thickness. LIMITATIONS: The study was cross-sectional, cardiac events were not determined, and only 1 method of advanced lipoprotein testing was used. CONCLUSIONS: Advanced lipoprotein testing using vertical-spin density-gradient ultracentrifugation did not improve prediction of carotid intima-media thickness in young adults and may not be useful for assessing cardiovascular risk in this population.

Adult↗
PubMed2005

Rise in insulin resistance is associated with escalated telomere attrition.

BACKGROUND: Insulin resistance predisposes to cardiovascular disease and shortens human lifespan. We therefore tested the hypothesis that a rise in insulin resistance in concert with gain in body mass is associated with accelerated white blood cell telomere attrition. METHODS AND RESULTS: We measured white blood cell telomere dynamics and age-related changes in insulin resistance and body mass index in young adults of the Bogalusa Heart Study. Over 10.1 to 12.8 years, the relative changes in telomere length were correlated with the homeostasis model assessment of insulin resistance (r=-0.531, P<0.001) and changes in the body mass index (r=-0.423, P<0.001). CONCLUSIONS: These findings provide the first tangible nexus of telomere biology with insulin resistance and adiposity in humans.

Adiposity↗
PubMed2005

CGHPRO -- a comprehensive data analysis tool for array CGH.

BACKGROUND: Array CGH (Comparative Genomic Hybridisation) is a molecular cytogenetic technique for the genome wide detection of chromosomal imbalances. It is based on the co-hybridisation of differentially labelled test and reference DNA onto arrays of genomic BAC clones, cDNAs or oligonucleotides, and after correction for various intervening variables, loss or gain in the test DNA can be indicated from spots showing aberrant signal intensity ratios. Now that this technique is no longer confined to highly specialized laboratories and is entering the realm of clinical application, there is a need for a user-friendly software package that facilitates estimates of DNA dosage from raw signal intensities obtained by array CGH experiments, and which does not depend on a sophisticated computational environment. RESULTS: We have developed a user-friendly and versatile tool for the normalization, visualization, breakpoint detection and comparative analysis of array-CGH data. CGHPRO is a stand-alone JAVA application that guides the user through the whole process of data analysis. The import option for image analysis data covers several data formats, but users can also customize their own data formats. Several graphical representation tools assist in the selection of the appropriate normalization method. Intensity ratios of each clone can be plotted in a size-dependent manner along the chromosome ideograms. The interactive graphical interface offers the chance to explore the characteristics of each clone, such as the involvement of the clones sequence in segmental duplications. Circular Binary Segmentation and unsupervised Hidden Markov Model algorithms facilitate objective detection of chromosomal breakpoints. The storage of all essential data in a back-end database allows the simultaneously comparative analysis of different cases. The various display options facilitate also the definition of shortest regions of overlap and simplify the identification of odd clones. CONCLUSION: CGHPRO is a comprehensive and easy-to-use data analysis tool for array CGH. Since all of its features are available offline, CGHPRO may be especially suitable in situations where protection of sensitive patient data is an issue. It is distributed under GNU GPL licence and runs on Linux and Windows.

Algorithms↗
PubMed2005

Autosomal genome scan for loci linked to blood pressure levels and trends since childhood: the Bogalusa Heart Study.

Genetic loci influencing the long-term levels and trends of blood pressure over time were investigated using 775 white siblings, ages 13 to 43 years, enrolled in the Bogalusa Heart Study, and 357 microsatellite markers on the 22 autosomal chromosomes. Subjects had been examined serially 2 to 12 times with 4365 serial observations over an average of 22 years from childhood to adulthood. Total and incremental area under the curve was calculated based on a cubic growth curve and used as long-term levels and trends, respectively. After adjusting for age, sex, and body mass index, heritability estimates of total area were 0.66 for systolic and 0.68 for diastolic blood pressure. Heritability of incremental area was 0.38 for systolic and 0.46 for diastolic blood pressure. Significant linkage to the total area of diastolic blood pressure (peak logarithm of odds [LOD]=3.9 at 73 cM) was observed on chromosome 2, with a region spanning from 44 cM to 103 cM showing supporting linkage evidence of LOD >3.0. In addition, suggestive linkage for total area of systolic (LOD=1.6 at 182 cM) and diastolic blood pressure (LOD=2.0 at 36 cM) on chromosome 4 and diastolic blood pressure incremental area (LOD=2.2 at 28 cM) on chromosome 18 was noted. Several hypertension candidate genes such as alpha-adducin, beta-adducin, sodium bicarbonate co-transporter, and G protein-coupled receptor kinase 4 are located in these regions. Linkage evidence found in this community-based study indicates that regions on these chromosomes harbor genetic loci that affect the propensity for development of hypertension from childhood.

Adolescent↗
PubMed2005

Inverse sodium hydride: density functional theory study of the large nonlinear optical properties.

"Inverse sodium hydride" (AdzH(+)Na-) is an alkalide compound synthesized in recent experiments containing the unusual charge distribution H+ and Na- (inverse charge state). The new class of compounds interests scientists to investigate their especial structures and properties. In this paper, the structures of three alkalides compounds, (Me)3NH(+)Na-, AdzH(+)Na-, and AdzLi(+)Na-, have been obtained in theory. Especially, the structure of AdzLi(+)Na- is still researched by experimental scientists. We investigated the NLO properties of the alkalides complexes for the first time and found that inverse sodium hydride AdzH(+)Na- has a considerably large NLO response beta0 = 5.7675 x 10(4) au by density functional theory (DFT). To understand the essential features of the large NLO properties, four related systems have been also calculated. Their first hyperpolarizabilities are beta0 = 7.357 x 10(3) au for (Me)3NH(+)Na-, beta0 = 3.9 au for (Me)3NH+, beta0 = 1.10 x 10(2) au for (Me)3NH(+)Cl-, and beta0 = 6.20681 x 10(5) au for AdzLi(+)Na-, respectively. By comparing, we found that, first, the Na- anion plays a crucial role in the considerably large first hyperpolarizability of inverse sodium hydride and, second, the first hyperpolarizability of inverse sodium hydride increases with the charge value of the sodium anion. The above results are useful for designing potential NLO materials.

Journal Article↗
PubMed2005

Ethanol potentiates HIV-1 gp120-induced apoptosis in human neurons via both the death receptor and NMDA receptor pathways.

Neuronal loss is a hallmark of AIDS dementia syndromes. Human immunodeficiency virus type I (HIV-1)-specific proteins may induce neuronal apoptosis, but the signal transduction of HIV-1 gp120-induced, direct neuronal apoptosis remains unclear. Ethanol (EtOH) is considered to be an environmental co-factor in AIDS development. However, whether EtOH abuse in patients with AIDS increases neuronal dysfunction is still uncertain. Using pure, differentiated, and post-mitotic NT2.N-derived human neurons, we investigated the mechanisms of HIV-1 and/or EtOH-related direct neuronal injury and the molecular interactions between HIV-1-specific proteins and EtOH. It was demonstrated that NT2.N neurons were susceptible to HIV-1 Bal (R5-tropic strain) gp120-induced direct cell death. Of importance, EtOH induced cell death in human neurons in a clinically-relevant dose range and EtOH strongly potentiated HIV-1 gp120-induced neuronal injury at low and moderate concentrations. Furthermore, this potentiation of neurotoxicity could be blocked by N-methyl-D-aspartate (NMDA) receptor subunit 2B (NR2B) antagonists. We analyzed human genomic profiles in these human neurons, using Affymetrix genomics technology, to elucidate the apoptotic pathways involved in HIV-1- and EtOH-related neurodegeneration. Our findings indicated significant over-expression of selected apoptosis functional genes. Significant up-regulation of TRAF5 gene expression may play an essential role in triggering potentiation by EtOH of HIV-1 gp120-induced neuronal apoptosis at early stages of interaction. These studies suggested that two primary apoptotic pathways, death receptor (extrinsic) and NMDA receptor (intrinsic)-related programmed cell-death pathways, are both involved in the potentiation by EtOH of HIV-1 gp120-induced direct human neuronal death. Thus, these data suggest rationally-designed, molecular targets for potential anti-HIV-1 neuroprotection.

AIDS Dementia Complex↗
PubMed2005

Study of pi halogen bonds in complexes C2H(4-n)Fn-ClF (n = 0-2).

The pi-halogen bond may be considered, in a broad sense, essentially a pi-hydrogen bond. Using the counterpoise-corrected potential energy surface method (interaction energy optimization), the stationary structures of the C2H(4-n)Fn-ClF (n = 0-2) complexes with all real frequencies have been obtained at the MP2/aug-cc-pVDZ level. For C2H(4-n)Fn-ClF (n = 0-2), the pi-halogen bond has a long distance and is elongated by the F substituent effect. The pi-halogen bond length order is 2.661 A for C2H4-ClF < 2.745 A for C2H3F-ClF < 2.766 A for g-C2H2F2-ClF < 2.8076 A for trans-C2H2F2-ClF < 2.8079 A for cis-C2H2F2-ClF. For three complexes C2H3F-ClF, g-C2H2F2-ClF, and cis-C2H2F2-ClF, the pi-halogen bonds are further shifted and sloped by the F substituent effect. The F substituent effect reduces also the interaction energy of the pi-halogen bond. The interaction energies are respectively -3.7 for C2H4-ClF, -2.8 for C2H3F-ClF, -2.3 for g-C2H2F2-ClF, -1.9 for cis-C2H2F2-ClF, and -1.8 kcal/mol for trans-C2H2F2-ClF, at the CCSD(T)/aug-cc-pVDZ level. The electron correlation contribution of the interaction energy is large for C2H(4-n)Fn-ClF (n = 0-2), which shows that the stabilities of the pi-halogen bond systems results primarily from the dispersion interaction. In the double F substituent systems, the interaction energy of the pi-halogen bond structure with a longer interaction distance is larger than that of the corresponding pi-hydrogen bond structure with a shorter interaction distance. This may be because there are the large electron correlation contributions of the interaction energy, and a secondary interaction between lone pairs of Cl atom and some atoms (H, C) with positive charges in the pi-halogen bond structure.

Chlorides↗
PubMed2005

[Monitoring retrograde adenoviral transgene expression in spinal cord and anterograde labeling of the peripheral nerves].

OBJECTIVE: Targeted adenoviral gene delivery from peripheral nerves was used to integrally analyse the characterization and time course of LacZ gene (AdLacZ) retrograde transfer to spinal cord and transgene product anterograde labeling of peripheral nerve. METHODS: Recombinant replication-defective adenovirus containing AdLacZ was administrated to the cut proximal stumps of median and tibial nerves in Wistar rats. Then the transected nerve was repaired with 10-0 nylon sutures. At different time point post-infection the spinal cords of C5 to T1 attached with DRGs and brachial plexuses, or L2 to L6 attached with DRGs and lumbosacral plexuses were removed. The removed spinal cord and DRCs were cut into 50 microm serial coronal sections and processed for X-gal staining and immunohistochemical staining. The whole specimens of brachial or lumbosacral plexuses attaching with their peripheral nerves were processed for X-gal staining. The number of X-gal stained neurons was counted and the initial detected time of retrograde labeling, peak time and persisting period of gene expression in DRG sensory neurons, spinal cord motor neurons and peripheral nerves were studied. RESULTS: The gene transfer was specifically targeted to the particular segments of spinal cord and DRGs, and transgene expression was strictly unilaterally corresponding to the infected nerves. Within the same nerve models, the initial detected time of gene expression was earliest in DRG neurons, then in the motor neurons and latest in peripheral nerves. The persisting duration of beta-gal staining was shortest in motor neurons, then in sensory neurons and longest in peripheral nerves. The initial detected time of beta-gal staining in median nerve models was earlier in median nerve models compared with that in the tibial nerve models. Although the initial detected time and the beginning of peak duration of beta-gal staining were not same, the decreasing time of beta-gal staining in motor and sensory neurons of the two nerve models were started at about the same day 8 post-infection. The labeled neurons were more in tibial nerve models than that in median nerve models. Within the same models, the labeled sensory neurons of DRGs were more than labeled motor neurons of ventral horn. The beta-gal staining was tender in median nerves than that in tibial nerves. However the persisting time of beta-gal staining was longer in tibial nerve models. CONCLUSION: The strong gene expression in neurons and PNS renders this system particularly attractive for neuroanatomical tracing studies. Furthermore this gene delivery method allowing specific targeting of motor and sensory neurons without damaging the spinal cord might offer potentialities for the gene therapy of peripheral nerve injury.

Adenoviridae↗
PubMed2005

[Allogeneic umbilical cord blood stem cell transplantation in Duchenne muscular dystrophy].

OBJECTIVE: To study the feasibility of treatment of Duchenne muscular dystrophy (DMD) with umbilical cord stem cell transplantation. METHODS: HLA matching was conducted for a 11-year-old DMD boy with family history was underwent umbilical cord blood stem cell transplantation and a sample of umbilical cord stem cells with 5 matched HLA sites was found in the cord blood bank with 27.32 x 10(8) nucleated cells, about 2.6 times that of the treatment dosage for him. After pretreatment with busulfan 14 mg/kg.d, cyclophosphamide 50 mg/kg.d, and rabbit anti-human thymocyte globulin 10 mg/kg.d, the allogeneic cord blood stem cells were transplanted intravenously. Cyclosporin A, methylprednisolone and MMF were used after the transplantation so as to prevent graft versus host reaction. Prostaglandin E1 was used to prevent Budd-Chiari syndrome, and ganciclovir was used to prevent cytomegalovirus infection. At the same time, Gran, granulocytic cell stimulating factor, and gammaglobulin were also used. Biochemistry test, including serum creatine kinase (CK), was conducted. Evidence of reconstruction of blood making, including conversion of blood type, was observed. PCR-STR analysis was used to observe the status of implantation of the donor umbilical cord blood stem cells. RESULTS: (1) 12 days after transplantation, the white blood cells (WBC) of peripheral blood were 0.5 x 10(9)/L, 14 days after, the numbers of WBC and neutrophils were 1.0 x 10(9)/L and 0.6 x 10(9)/L respectively. In 37 days, granulocytic cell stimulating factor was no more used, the peripheral blood WBC fluctuated around 3.34 approximately 12.2 x 10(9)/L. In the 27th day, the number of blood platelets was more than 20 x 10(9)/L and hemoglobin rose to 88 g/L. On the 24th day red blood cells transfusion was stopped. (2) In the 42nd day, the blood type of the patient transformed from type A before transplantation to type AB (the blood type of transplanted stem cells is type B). (3) PCR-STR test of the peripheral blood made 17, 26, and 42 days after transplantation showed that the gene type of the patient was mixed mosaic: The ratio of donor gradually increased from 40% approximately 45% to 55% approximately 65%. (4) In the 38th day I degrees GVHD appeared. (5) serum CK level declined from 6000 U/L to 600 approximately 2200 U/L. (6) In the 42nd day, physical examination revealed obviously improvement in walking, turning the body over, and standing up. CONCLUSION: This is first case of prospective clinical transplantation on DMD by allogeneic cord blood stem cell. Umbilical cord stem cell transplantation helps re-build blood-making function, and improve locomotive function with a mild GVHD reaction. The genotype of rebuilt blood is mosaic but the ratio of gene mosaic gradually turn from recipient gene type > donor gene type to recipient gene type < donor gene type. The serum CK level decreases significantly after transplantation, which may slow down the necrosis of muscle cell. DMD patient will be benefited by stem cell transplantation.

Child↗
PubMed2005

Contrasting effects of tetraethylammonium and 4-aminopyridine on the gastrointestinal function of mice.

Many different K+ channels have been identified in the gastrointestinal tract, and the two classical K+ channel blockers, tetraethylammonium and 4-aminopyridine, show different sensitivity for these channels. The aim of the present study was to compare the effects of tetraethylammonium and 4-aminopyridine on the gastrointestinal function of mice. 4-Aminopyridine (5 mg/kg, p.o.) inhibited, but tetraethylammonium (40 mg/kg, p.o.) enhanced, the intestinal propulsion of a charcoal suspension in conscious mice. Studies in vitro showed that perfusion of 5 mM 4-aminopyridine increased the maximal contractile force and minimal relaxation force, and decreased the amplitude and frequency of the peristaltic contraction of the isolated duodenum. However, perfusion of 5 mM tetraethylammonium increased the maximal contractile force, the minimal relaxation force and the amplitude of the contraction. The effects of tetraethylammonium and 4-aminopyridine on the duodenal contraction could be abolished completely by application of 5 microM verapamil. Our results in vivo and in vitro showed that tetraethylammonium and 4-aminopyridine had contrasting effects on the gastrointestinal function of mice.

4-Aminopyridine↗
PubMed2005

Impact of multiple cardiovascular risk factors on femoral artery intima-media thickness in asymptomatic young adults (the Bogalusa Heart Study).

Femoral artery intima-media thickness (IMT), like carotid IMT, is a surrogate indicator of atherosclerotic coronary and peripheral vascular diseases in middle-aged and older adults. Although risk factors for coronary artery disease are also associated with increased IMT, especially as measured in carotid arteries, there is a paucity of information with respect to the femoral artery in this regard in the asymptomatic, younger adult population. This study examined the impact of multiple risk factors on the common femoral artery IMT as measured by B-mode ultrasonography in 1,080 black and white subjects aged 24 to 43 years (71% white and 43% men) enrolled in the Bogalusa Heart Study. Femoral IMT showed gender difference (men more than women, p = 0.001), but no racial difference. In a multivariate model, systolic blood pressure, age, male gender, cigarette smoking, and total cholesterol/high-density lipoprotein cholesterol ratios related independently, in that order, to IMT. Mean IMT increased with an increasing number of risk factors defined as values above the age-, race-, and gender-specific 75th percentile of systolic blood pressure, waist circumference, total cholesterol/high-density lipoprotein cholesterol ratio, and insulin along with smoking status (p for trend = 0.003), with respective mean IMT values of 0.66, 0.69, 0.73, and 0.79 mm for 0, 1 to 2, 3, and 4 to 5 risk factors. The odds ratio for patients with >/=3 risk factors versus no risk factors having IMT in the top fifth percentile was 4.7 (p = 0.01). The observed adverse trend of increasing femoral IMT with an increasing number of risk factors in free-living, asymptomatic young subjects underscores the need for multiple risk factors profiling in early life. Further, ultrasonography of the femoral artery in conjunction with multiple risk factor profiling can be helpful in risk stratification.

Adult↗
PubMed2005

Comparison of seven methods for producing Affymetrix expression scores based on False Discovery Rates in disease profiling data.

BACKGROUND: A critical step in processing oligonucleotide microarray data is combining the information in multiple probes to produce a single number that best captures the expression level of a RNA transcript. Several systematic studies comparing multiple methods for array processing have used tightly controlled calibration data sets as the basis for comparison. Here we compare performances for seven processing methods using two data sets originally collected for disease profiling studies. An emphasis is placed on understanding sensitivity for detecting differentially expressed genes in terms of two key statistical determinants: test statistic variability for non-differentially expressed genes, and test statistic size for truly differentially expressed genes. RESULTS: In the two data sets considered here, up to seven-fold variation across the processing methods was found in the number of genes detected at a given false discovery rate (FDR). The best performing methods called up to 90% of the same genes differentially expressed, had less variable test statistics under randomization, and had a greater number of large test statistics in the experimental data. Poor performance of one method was directly tied to a tendency to produce highly variable test statistic values under randomization. Based on an overall measure of performance, two of the seven methods (Dchip and a trimmed mean approach) are superior in the two data sets considered here. Two other methods (MAS5 and GCRMA-EB) are inferior, while results for the other three methods are mixed. CONCLUSIONS: Choice of processing method has a major impact on differential expression analysis of microarray data. Previously reported performance analyses using tightly controlled calibration data sets are not highly consistent with results reported here using data from human tissue samples. Performance of array processing methods in disease profiling and other realistic biological studies should be given greater consideration when comparing Affymetrix processing methods.

Algorithms↗