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At least 937 records · Page 52Linked to original sources
PubMed2005

Biological validation of differentially expressed genes in chronic lymphocytic leukemia identified by applying multiple statistical methods to oligonucleotide microarrays.

Oligonucleotide microarrays are a powerful tool for profiling the expression levels of thousands of genes. Different statistical methods for identifying differentially expressed genes can yield different results. To our knowledge, no experimental test has been performed to decide which method best identifies genes that are truly differentially expressed. We applied three statistical methods (dChip, t-test on log-transformed data, and Wilcoxon test) to identify differentially expressed genes in previously untreated patients with chronic lymphocytic leukemia (CLL). We used a training set of Affymetrix Hu133A microarray data from 11 patients with unmutated immunoglobulin (Ig) heavy chain variable region (VH) genes and 8 patients with mutated Ig VH genes. Differential expression was validated using semiquantitative real-time polymerase chain reaction assays and by validating models to predict the somatic mutation status of an independent test set of nine CLL samples. The methods identified 144 genes that were differentially expressed between cases of CLL with unmutated compared with mutated Ig VH genes. Eighty genes were identified by Wilcoxon test, 60 by t-test, and 65 by dChip, but only 11 were identified by all three methods. Greater agreement was found between the t-test and the Wilcoxon test. Differential expression was validated by semiquantitative real-time polymerase chain reaction assays for 83% of individual genes, regardless of the statistical method. However, the Wilcoxon test gave the most accurate predictions on new samples, and dChip, the least accurate. We found that all three methods were equally good for finding differentially expressed genes, but they found different genes. The genes selected by the nonparametric Wilcoxon test are the most robust for predicting the status of new cases. A comprehensive list of all differentially expressed genes can only be obtained by combining the results of multiple statistical tests.

Algorithms↗
PubMed2006

Association between dietary patterns and anaemia in adults from Jiangsu Province in Eastern China.

The objective of the present study was to investigate the association between food patterns and anaemia among Chinese adults. It was a cross-sectional household survey undertaken in 2002. The sample contained 2849 men and women aged 20 years and above, and had a response rate of 89.0 %. Factor analysis was used to identify food patterns based on a food-frequency questionnaire. Logistic regression was used to relate food patterns to anaemia. A four-factor solution explained 30.5 % of the total variance. After adjusting for socio-demographic factors and four distinct food patterns, the 'traditional' (rice, vegetable, wheat flour), 'sweet tooth' (drinks, cake) and 'healthy' (whole grains, fruits, vegetables) patterns were independently associated with anaemia. 'Traditional' and 'sweet tooth' patterns were positively associated with anaemia, whereas the association with 'healthy' food pattern was negative. No association was observed between the 'macho' pattern (meat and alcohol) and anaemia. Compared with the lowest quartile (Q1) of the 'traditional' pattern, the highest quartile (Q4) had a higher risk of anaemia (men: odds ratio (OR) 2.60, 95 % CI 1.38, 4.88; women: OR 3.40, 95 % CI 2.14, 5.39). For the 'sweet tooth' pattern, compared with the lowest quartile (Q1), the OR of the highest quartile was 2.34 (95 % CI 1.47, 3.73) for men and 2.02 (95 %CI 1.31, 3.13) for women. The fourth quartile of healthy food was associated with a lower risk of anaemia (men: OR 0.50, 95 % CI 0.31, 0.79; women: OR 0.51, 95 % CI 0.34, 0.75). Women in the north had a higher risk of anaemia (OR 2.49, 95 %CI 1.80, 3.43). Food patterns were associated with anaemia in this area with a high prevalence of anaemia.

Adult↗
PubMed2007

Predictors and dietary consequences of frequent intake of high-sugar, low-nutrient foods in 1-year-old children participating in the ABIS study.

Foods rich in sugar have been suggested to contribute to the increasing prevalence of obesity in children. The aim of this report is to investigate the dietary pattern in 1-year-old children who frequently receive foods rich in sugar but low in nutrients and to study associated demographic and parental factors. During 1977-9, 21,700 infants were invited to participate in this prospective, population-based, longitudinal cohort study. Screening questionnaires were completed for 16,070 infants after delivery. Follow-up questionnaires from 10,762 children at 1 year of age are included in the analysis. It was found that 24% of the children received sweets/pastries more often than one or two times per week. They had a higher intake of French fries, potato crisps and cream as well as a lower intake of fruit and vegetables. A frequent intake of sugar-rich, low-nutrient foods was significantly associated with several maternal factors (high intake of sweets/pastries during pregnancy, young age, mother living alone) as well as presence of older siblings. Maternal smoking during pregnancy and maternal overweight were of borderline significance. Parental education level was inversely associated with the frequency of intake of sweets/pastries in the child. Children who frequently receive sweets/pastries also have an otherwise unfavourable dietary pattern. Several parental and demographic factors were associated with this feeding pattern, especially high intake of sweets/pastries during pregnancy. Screening of pregnant women for risk predictors like consumption of sweets/pastries, young age and smoking could be possible ways of identifying children at future risk for low dietary quality.

Beverages↗
PubMed1976

Survival of Salmonella east bourne and Salmonella typhimurium in chocolate.

Experiments were carried out to assess the reduction rate of two salmonella strains (S. eastbourne and S. typhimurium) in chocolate bars. After artificial contamination of chocolate, after 'conching', with about 10(6) S. eastbourne/g. this organism was still recovered after 9 months storage. The strain of S. typhimurium was less resistant. Both serotypes died off more rapidly in bitter chocolate than in milk chocolate. After contamination with a smaller dose (about 10(3)/g.) with these two serotypes, similar differences were observed.

Cacao↗
PubMed2003

Predictors of fatigue following the onset of infectious mononucleosis.

BACKGROUND: Infectious mononucleosis (IM) is a risk factor for chronic fatigue. Reduced activity is the most consistent factor found to be associated with poor outcome following the onset of infectious mononucleosis. However, little is known about the biological mechanisms involved in the pathogenesis of chronic fatigue following IM and no study, so far, has examined the relation between certain illness beliefs and poor outcome. This study explored immunological, endocrine, behavioural and cognitive responses to the acute illness and assessed which components of these groups of risk factors predicted a chronic course. METHOD: Using a prospective cohort design, 71 primary care patients with IM were enrolled onto the study and interviewed. Their recovery was explored by postal questionnaire up to 1 year later. RESULTS: In the univariate analysis, increased baseline levels of immune activation were associated with fatigue at baseline and 3 months. Cortisol levels were not associated with fatigue at any point. Using multivariate models of clinical and psychosocial baseline factors, severity of symptoms and illness perceptions were found to predict fatigue 3 months later. At 6 months, fatigue was best predicted by female gender and illness perceptions, and at 12 months by female gender and a symptoms-disability factor. CONCLUSIONS: In the multivariate analysis no factors were found to predict poor outcome at all time-points. Instead the pattern of predictors changed over time, partly but not completely consistent with our a priori predictions. Larger studies are needed to explore further the predictive nature of biopsychosocial factors in the pathogenesis of chronic fatigue related to IM. The psycho-behavioural predictors found in this study are amenable to intervention. Such interventions should be tested in randomized controlled trials.

Adult↗
PubMed1986

Cholinergic receptors in cognitive disorders.

Cholinergic receptors (muscarinic subtypes M1 and M2, and putative nicotinic binding) have been examined in the hippocampus obtained at autopsy from a variety of patients with cognitive disorders (Alzheimer's, Parkinson's, and Huntington's diseases, Down's Syndrome and alcoholic dementia) and compared with neurologically normal controls and cases of Motor Neuron disease. In all of the disorders associated with a pre-synaptic cortical cholinergic deficit reflected by an extensive loss of choline acetyltransferase (Alzheimer's disease, Parkinson's disease and Down's Syndrome) there was a substantial reduction in the binding of (3H) nicotine to the nicotinic receptor. By contrast reductions in both muscarinic subtypes (M1 and M2) were apparent to only a moderate extent in Alzheimer's disease, whereas in Parkinson's disease binding was significantly increased (apparently not in relation to anti-cholinergic drug treatment) in the non-demented but not demented cases. A further abnormality detected in Alzheimer's disease but not the other disorders investigated was a decrease in an endogenous inhibitor of nicotinic binding, the identity of which is as yet unknown but which may be a candidate for a possible endogenous modulator of the nicotinic receptor. These observations suggest that in Alzheimer's disease not only muscarinic but also nicotinic receptor function should be considered in relation both to future therapeutic strategies and, in the search for a clinical marker which might be of diagnostic value, to potential probes of the cortical cholinergic system.

Cognition Disorders↗
PubMed2005

X-ray absorption fine structure combined with X-ray fluorescence spectrometry. Improvement of spectral resolution at the absorption edges of 9-29 keV.

X-ray absorption near-edge structure (XANES) suffers from core-hole lifetime broadening at a higher energy absorption edge, such as Sn K (29 keV, Gamma(K) = 8.49 eV). To overcome this problem, emitted Sn Kalpha1 fluorescence from sample was counted using high-energy-resolution fluorescence spectrometer in the XANES measurements. Experimental energy resolution (5.0 eV) was consistent with theoretical values based on the Rowland configuration of the spectrometer. The absorption edge became steeper compared to conventional spectra. The white-line peak due to Sn(II) species became remarkably sharper and more intense in the Sn Kalpha1-detecting Sn K-edge XANES for Pt-Sn/SiO2. To support the semiclassical theory of resonant Raman scattering for the explanation of observed elimination of lifetime width, more resolved XANES data at Cu K, Pb L3, and Sn K in this work were convoluted (filtered) with a Lorentzian of each core-hole lifetime width. The processed data resembled generally well corresponding XANES spectrum measured in transmission mode. The verification based on ab initio XANES calculations was also performed.

Journal Article↗
PubMed2002

Development and evaluation of a personal particulate organic and mass sampler.

Accurate measurement of personal exposure to particulate matter and its constituents requires samplers that are accurate, compact, lightweight, inexpensive, and convenient to use. The personal particulate organic and mass sampler (PPOMS) has been developed to meet these criteria. The PPOMS uses activated carbon-impregnated foam as a combined 2.5-microm size-selective inlet and denuder for assessment of fine particle mass and organic carbon. Proof of the PPOMS concept has been established by comparing mass and organic carbon in particles collected with collocated samplers in Seattle, at a central outdoor site, and in residences. Daily particulate mass concentrations averaged 10.0 +/- 5.2, 12.0 +/- 5.3, and 11.2 +/- 5.1 microg m(-3) for the Federal Reference Method, the Harvard Personal Exposure Monitor, and the PPOMS, respectively, for 10 24-h sampling periods. During a series of PM2.5 indoor organic carbon (OC) measurements from single quartz filters, the apparent indoor OC averaged 7.7 +/- 0.8 microg of C m(-3), which was close to the indoor PM2.5 mass from collocated Teflon filters (7.3 +/- 2.3 microg of C m(-3)), indicating the presence of a large positive OC artifact. In collocated measurements, the PPOMS eliminated this artifact just as well as the integrated gas and particle sampler that incorporated a macroreticular polystyrene-divinylbenzene (XAD-4) resin-coated denuder, yielding OC concentrations of 2.5 +/- 0.4 and 2.4 +/- 1.0 microg of C m(-3), respectively. Thermal analysis for OC indicated that the indoor positive artifact was due to adsorption of gas-phase semivolatile organic compounds (SVOC). This study shows that the PPOMS design provides a 2.5-microm size-selective inlet that also prevents the adsorption of gas-phase SVOC onto quartz filters, thus eliminating the filter positive artifact The PPOMS meets a significant current challenge for indoor and personal sampling of particulate organic carbon. The PPOMS design can also simplify accurate ambient sampling for PM2.5.

Air Pollutants↗
PubMed2004

Will Lake Michigan lake trout meet the Great Lakes Strategy 2002 PCB reduction goal?

The Great Lakes Strategy 2002 establishes the long-term goal that all Great Lakes fish should be safe to eat without restriction. As an indicator of progress toward that goal, the Strategy specifies that lake trout PCBs will decline 25% from 2000 to 2007. We estimated the plausibility of achieving this near-term goal by examining a time-series of Lake Michigan lake trout PCB concentrations from 1972 to 2000. We used two different Bayesian approaches, Bayesian model averaging (BMA) and dynamic linear models (DLM), to model the trajectory of these historical data and forecast concentrations through 2007. Both approaches indicate that the probability of a 25% reduction from 2000 to 2007 is negligible. The most likely lake trout PCB declines predicted by the BMA and DLM over this time period are 6.8% and 8.9%, respectively. Our results suggest that declines in lake trout PCBs will be in the range of 5-10% assuming conditions similar to recent years. This rate of decline will be difficult to discern without adequate data collection. If sufficient data are not gathered to document further declines, then the relaxation of lake trout consumption advisories is indeed a long-term prospect.

Animals↗
PubMed2006

Modeling ozone and aerosol formation and transport in the pacific northwest with the community Multi-Scale Air Quality (CMAQ) modeling system.

The Community Multi-Scale Air Quality (CMAQ) modeling system was used to investigate ozone and aerosol concentrations in the Pacific Northwest (PNW) during hot summertime conditions during July 1-15, 1996. Two emission inventories (El) were developed: emissions for the first El were based upon the National Emission Trend 1996 (NET96) database and the BEIS2 biogenic emission model, and emissions for the second El were developed through a "bottom up" approach that included biogenic emissions obtained from the GLOBEIS model. The two simulations showed that elevated PM2.5 concentrations occurred near and downwind of the Interstate-5 corridor along the foothills of the Cascade Mountains and in forested areas of central Idaho. The relative contributions of organic and inorganic aerosols varied by region, but generally organic aerosols constituted the largest fraction of PM2.5. In wilderness areas near the 1-5 corridor, organic carbon from anthropogenic sources contributed approximately 50% of the total organic carbon with the remainder from biogenic precursors, while in wilderness areas in Idaho, biogenic organic carbon accounted for 80% of the total organic aerosol. Regional analysis of the secondary organic aerosol formation in the Columbia River Gorge, Central Idaho, and the Olympics/Puget Sound showed that the production rate of secondary organic carbon depends on local terpene concentrations and the local oxidizing capacity of the atmosphere, which was strongly influenced by anthropogenic emissions. Comparison with observations from 12 IMPROVE sites and 21 ozone monitoring sites showed that results from the two El simulations generally bracketed the average observed PM parameters and that errors calculated for the model results were within acceptable bounds. Analysis across all statistical parameters indicated that the NW-AIRQUEST El solution performed better at predicting PM2.5, PM1, and beta(ext) even though organic carbon PM was over-predicted, and the NET96 El solution performed better with regard to the inorganic aerosols. For the NW-AIRQUEST El solution, the normalized bias was 30% and the normalized absolute error was 49% for PM2.5 mass. The NW-AIRQUEST solution slightly overestimated peak hourly ozone downwind of urban areas, while the NET96 solution slightly underestimated peak values, and both solutions over-predicted average 03 concentrations across the domain by approximately 6 ppb.

Aerosols↗
PubMed2001

Hydrogenolysis of cyclohexane over Ir/SiO(2) catalyst: a mechanistic study of carbon--carbon bond cleavage on metallic surfaces.

The hydrogenolysis of cyclohexane catalyzed by supported Ir/SiO(2) has been studied to get mechanistic information on the elementary steps of C--C bond cleavage for cyclic saturated hydrocarbons. The reaction was studied under conditions in which no dehydrogenation to benzene occurs. When a mixture of cyclohexane and H(2) flows over a Ir/SiO(2) catalyst at 200 degrees C and for a H(2)/cyclohexane ratio superior to 40, methane, ethane, propane, n-butane, n-pentane, and n-hexane are identified to be primary products. The hydrogenolysis of ethane and n-hexane has also been studied to clarify several mechanistic questions. To account for the primary products in the above reactions, a mechanism is proposed in which the key step of the carbon--carbon bond cleavage occurs via concerted electronic transfer in dimetallacyclopentane intermediate. The comparison of product distributions in the hydrogenolysis of cyclohexane and that observed for n-hexane led to conclusions about the relative ease of carbon--carbon bond cleavage with respect to surface alkyl isomerization.

Journal Article↗
PubMed2002

Development and application of an indirect competitive enzyme-linked immunoassay for aflatoxin m(1) in milk and milk-based confectionery.

High-titer rabbit polyclonal antibodies to aflatoxin M(1) (AFM1) were produced by utilizing AFM1-bovine serum albumin (BSA) conjugate as an immunogen. An indirect competitive enzyme-linked immunosorbent assay was standardized for estimating AFM1 in milk and milk products. To avoid the influence of interfering substances present in the milk samples, it was necessary to prepare AFM1 standards in methanol extracts of certified reference material (CRM) not containing detectable AFM1 (< 0.05 ng/g). The reliability of the procedure was assessed by using CRM with AFM1 concentrations of < 0.5 and 0.76 ng/g. Also, assays of milk samples mixed with AFM1 ranging in concentration between 0.5 and 50 ng/L gave recoveries of > 93%. The relative cross-reactivity with aflatoxins (AF) and ochratoxin A, assessed as the amount of AFM1 necessary to cause 50% inhibition of binding, was 5% for AFB1 and much less for AFB2, AFG1, and AFG2; there was no reaction with ochratoxin A. AFM1 contamination was measured in retail milk and milk products collected from rural and periurban areas in Andhra Pradesh, India. Of 280 milk samples tested, 146 were found to contain < 0.5 ng/mL of AFM1; in 80 samples it varied from 0.6 to 15 ng/mL, in 42 samples from 16 to 30 ng/mL, and in 12 samples from 31 to 48 ng/mL. Most of the milk samples that contained high AFM1 concentrations were obtained from periurban locations. The results revealed a significant exposure of humans to AFM1 levels in India and thus highlight the need for awareness of risk among milk producers and consumers.

Aflatoxin M1↗
PubMed2003

Quantification of the predominant monomeric catechins in baking chocolate standard reference material by LC/APCI-MS.

Catechins are polyphenolic plant compounds (flavonoids) that may offer significant health benefits to humans. These benefits stem largely from their anticarcinogenic, antioxidant, and antimutagenic properties. Recent epidemiological studies suggest that the consumption of flavonoid-containing foods is associated with reduced risk of cardiovascular disease. Chocolate is a natural cocoa bean-based product that reportedly contains high levels of monomeric, oligomeric, and polymeric catechins. We have applied solid-liquid extraction and liquid chromatography coupled with atmospheric pressure chemical ionization-mass spectrometry to the identification and determination of the predominant monomeric catechins, (+)-catechin and (-)-epicatechin, in a baking chocolate Standard Reference Material (NIST Standard Reference Material 2384). (+)-Catechin and (-)-epicatechin are detected and quantified in chocolate extracts on the basis of selected-ion monitoring of their protonated [M + H](+) molecular ions. Tryptophan methyl ester is used as an internal standard. The developed method has the capacity to accurately quantify as little as 0.1 microg/mL (0.01 mg of catechin/g of chocolate) of either catechin in chocolate extracts, and the method has additionally been used to certify (+)-catechin and (-)-epicatechin levels in the baking chocolate Standard Reference Material. This is the first reported use of liquid chromatography/mass spectrometry for the quantitative determination of monomeric catechins in chocolate and the only report certifying monomeric catechin levels in a food-based Standard Reference Material.

Atmospheric Pressure↗