Consistency and precision of cancer reporting in a multiwave national panel survey

Abstract Background Many epidemiological studies rely on self-reported information, the accuracy of which is critical for unbiased estimates of population health. Previously, accuracy has been analyzed by comparing self-reports to other sources, such as cancer registries. Cancer is believed to be a well-reported condition. This paper uses novel panel data to test the consistency of cancer reports for respondents with repeated self-reports. Methods Data come from 978 adults who reported having been diagnosed with cancer in at least one of four waves of the Panel Study of Income Dynamics, 1999-2005. Consistency of cancer occurrence reports and precision of timing of onset were studied as a function of individual and cancer-related characteristics using logistic and ordered logistic models. Results Almost 30% of respondents gave inconsistent cancer reports, meaning they said they never had cancer after having said they did have cancer in a previous interview; 50% reported the year of diagnosis with a discrepancy of two or more years. More recent cancers were reported with a higher consistency and timing precision; cervical cancer was reported more inaccurately than other cancer types. Demographic and socio-economic factors were only weak predictors of reporting quality. Conclusions Results suggest that retrospective reports of cancer contain significant measurement error. The errors, however, are fairly random across different social groups, meaning that the results based on the data are not systematically biased by socio-economic factors. Even for health events as salient as cancer, researchers should exercise caution about the presumed accuracy of self-reports, especially if the timing of diagnosis is an important covariate.http://deepblue.lib.umich.edu/bitstream/2027.42/112656/1/12963_2010_Article_108.pd

Lead exposure and periodontitis in US adults

Lead is known to have significant effects on bone metabolism and the immune system. This study tested the hypothesis that lead exposure affects periodontitis in adults. Material and Methods:  This study used the data from the Third National Health and Nutrition Examination Survey (NHANES III, 1988–94). It analyzed data from 2500 men and 2399 women, 20–56 yr old, who received complete periodontal examination. Periodontitis was defined as the presence of > 20% of mesial sites with ≥ 4 mm of attachment loss. Lead exposure was grouped into three categories:  7 μg/dL. Covariates were cotinine levels, poverty ratio, race/ethnicity, education, bone mineral density, diabetes, calcium intake, dental visit, and menopause (for women). All analyses were performed separately for men and women and considering the effect design. Univariate, bivariate, and stratified analysis was followed by multivariable analysis by estimating prevalence ratios through poisson regression. Results:  After adjustment for confounders, the prevalence ratios, comparing those with a lead blood level of > 7 μg/dL to those with a lead blood level of < 3 μg/dL was 1.70 (95% confidence interval (CI): 1.02, 2.85) for men and 3.80 (95% CI: 1.66, 8.73) for women. Conclusion:  The lead blood level was positively and statistically associated with periodontitis for both men and women. Considering the public health importance of periodontitis and lead exposure, further studies are necessary to confirm this association.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/65253/1/j.1600-0765.2006.00913.x.pd

Structure-activity relationships of anthraquinone derivatives derived from bromaminic acid as inhibitors of ectonucleoside triphosphate diphosphohydrolases (E-NTPDases)

Reactive blue 2 (RB-2) had been characterized as a relatively potent ectonucleoside triphosphate diphosphohydrolase (E-NTPDase) inhibitor with some selectivity for NTPDase3. In search for the pharmacophore and to analyze structure-activity relationships we synthesized a series of truncated derivatives and analogs of RB-2, including 1-amino-2-sulfo-4-ar(alk)ylaminoanthraquinones, 1-amino-2-methyl-4-arylaminoanthraquinones, 1-amino-4-bromoanthraquinone 2-sulfonic acid esters and sulfonamides, and bis-(1-amino-4-bromoanthraquinone) sulfonamides, and investigated them in preparations of rat NTPDase1, 2, and 3 using a capillary electrophoresis assay. Several 1-amino-2-sulfo-4-ar(alk)ylaminoanthraquinone derivatives inhibited E-NTPDases in a concentration-dependent manner. The 2-sulfonate group was found to be required for inhibitory activity, since 2-methyl-substituted derivatives were inactive. 1-Amino-2-sulfo-4-p-chloroanilinoanthraquinone (18) was identified as a nonselective competitive blocker of NTPDases1, 2, and 3 (Ki 16–18 μM), while 1-amino-2-sulfo-4-(2-naphthylamino)anthraquinone (21) was a potent inhibitor with preference for NTPDase1 (Ki 0.328 μM) and NTPDase3 (Ki 2.22 μM). Its isomer, 1-amino-2-sulfo-4-(1-naphthylamino)anthraquinone (20), was a potent and selective inhibitor of rat NTPDase3 (Ki 1.5 μM)

A discriminative method for protein remote homology detection and fold recognition combining Top-n-grams and latent semantic analysis

<p>Abstract</p> <p>Background</p> <p>Protein remote homology detection and fold recognition are central problems in bioinformatics. Currently, discriminative methods based on support vector machine (SVM) are the most effective and accurate methods for solving these problems. A key step to improve the performance of the SVM-based methods is to find a suitable representation of protein sequences.</p> <p>Results</p> <p>In this paper, a novel building block of proteins called Top-<it>n</it>-grams is presented, which contains the evolutionary information extracted from the protein sequence frequency profiles. The protein sequence frequency profiles are calculated from the multiple sequence alignments outputted by PSI-BLAST and converted into Top-<it>n</it>-grams. The protein sequences are transformed into fixed-dimension feature vectors by the occurrence times of each Top-<it>n</it>-gram. The training vectors are evaluated by SVM to train classifiers which are then used to classify the test protein sequences. We demonstrate that the prediction performance of remote homology detection and fold recognition can be improved by combining Top-<it>n</it>-grams and latent semantic analysis (LSA), which is an efficient feature extraction technique from natural language processing. When tested on superfamily and fold benchmarks, the method combining Top-<it>n</it>-grams and LSA gives significantly better results compared to related methods.</p> <p>Conclusion</p> <p>The method based on Top-<it>n</it>-grams significantly outperforms the methods based on many other building blocks including N-grams, patterns, motifs and binary profiles. Therefore, Top-<it>n</it>-gram is a good building block of the protein sequences and can be widely used in many tasks of the computational biology, such as the sequence alignment, the prediction of domain boundary, the designation of knowledge-based potentials and the prediction of protein binding sites.</p

Socioeconomic status and health in the second half of life: findings from the German Ageing Survey

This study examined social inequalities in health in the second half of life. Data for empirical analyses came from the second wave of the German Ageing Survey (DEAS), an ongoing population-based, representative study of community dwelling persons living in Germany, aged 40–85 years (N = 2,787). Three different indicators for socioeconomic status (SES; education, income, financial assets as an indicator for wealth) and health (physical, functional and subjective health) were employed. It could be shown that SES was related to health in the second half of life: Less advantaged persons between 40 and 85 years of age had worse health than more advantaged persons. Age gradients varied between status indicators and health dimensions, but in general social inequalities in health were rather stable or increasing over age. The latter was observed for wealth-related absolute inequalities in physical and functional health. Only income-related differences in subjective health decreased at higher ages. The amount of social inequality in health as well as its development over age did not vary by gender and place of residence (East or West Germany). These results suggest that, in Germany, the influence of SES on health remains important throughout the second half of life

Metatranscriptomics reveal differences in in situ energy and nitrogen metabolism among hydrothermal vent snail symbionts

Despite the ubiquity of chemoautotrophic symbioses at hydrothermal vents, our understanding of the influence of environmental chemistry on symbiont metabolism is limited. Transcriptomic analyses are useful for linking physiological poise to environmental conditions, but recovering samples from the deep sea is challenging, as the long recovery times can change expression profiles before preservation. Here, we present a novel, in situ RNA sampling and preservation device, which we used to compare the symbiont metatranscriptomes associated with Alviniconcha, a genus of vent snail, in which specific host–symbiont combinations are predictably distributed across a regional geochemical gradient. Metatranscriptomes of these symbionts reveal key differences in energy and nitrogen metabolism relating to both environmental chemistry (that is, the relative expression of genes) and symbiont phylogeny (that is, the specific pathways employed). Unexpectedly, dramatic differences in expression of transposases and flagellar genes suggest that different symbiont types may also have distinct life histories. These data further our understanding of these symbionts' metabolic capabilities and their expression in situ, and suggest an important role for symbionts in mediating their hosts' interaction with regional-scale differences in geochemistry

The Ratio 1660/1690 cm−1 Measured by Infrared Microspectroscopy Is Not Specific of Enzymatic Collagen Cross-Links in Bone Tissue

In postmenopausal osteoporosis, an impairment in enzymatic cross-links (ECL) occurs, leading in part to a decline in bone biomechanical properties. Biochemical methods by high performance liquid chromatography (HPLC) are currently used to measure ECL. Another method has been proposed, by Fourier Transform InfraRed Imaging (FTIRI), to measure a mature PYD/immature DHLNL cross-links ratio, using the 1660/1690 cm−1 area ratio in the amide I band. However, in bone, the amide I band composition is complex (collagens, non-collagenous proteins, water vibrations) and the 1660/1690 cm−1 by FTIRI has never been directly correlated with the PYD/DHLNL by HPLC. A study design using lathyritic rats, characterized by a decrease in the formation of ECL due to the inhibition of lysyl oxidase, was used in order to determine the evolution of 1660/1690 cm−1 by FTIR Microspectroscopy in bone tissue and compare to the ECL quantified by HPLC. The actual amount of ECL was quantified by HPLC on cortical bone from control and lathyritic rats. The lathyritic group exhibited a decrease of 78% of pyridinoline content compared to the control group. The 1660/1690 cm−1 area ratio was increased within center bone compared to inner bone, and this was also correlated with an increase in both mineral maturity and mineralization index. However, no difference in the 1660/1690 cm−1 ratio was found between control and lathyritic rats. Those results were confirmed by principal component analysis performed on multispectral infrared images. In bovine bone, in which PYD was physically destructed by UV-photolysis, the PYD/DHLNL (measured by HPLC) was strongly decreased, whereas the 1660/1690 cm−1 was unmodified. In conclusion, the 1660/1690 cm−1 is not related to the PYD/DHLNL ratio, but increased with age of bone mineral, suggesting that a modification of this ratio could be mainly due to a modification of the collagen secondary structure related to the mineralization process

Multiple FadD Acyl-CoA Synthetases Contribute to Differential Fatty Acid Degradation and Virulence in Pseudomonas aeruginosa

A close interconnection between nutrient metabolism and virulence factor expression contributes to the pathophysiology of Pseudomonas aeruginosa as a successful pathogen. P. aeruginosa fatty acid (FA) degradation is complicated with multiple acyl-CoA synthetase homologs (FadDs) expressed in vivo in lung tissue during cystic fibrosis infections. The promoters of two genetically linked P. aeruginosa fadD genes (fadD1 and fadD2) were mapped and northern blot analysis indicated they could exist on two different transcripts. These FadDs contain ATP/AMP signature and FA-binding motifs highly homologous to those of the Escherichia coli FadD. Upon introduction into an E. coli fadD-/fadR- double mutant, both P. aeruginosa fadDs functionally complemented the E. coli fadD-/fadR- mutant, allowing degradation of different chain-length FAs. Chromosomal mutagenesis, growth analysis, induction studies, and determination of kinetic parameters suggested that FadD1 has a substrate preference for long-chain FAs while FadD2 prefers shorter-chain FAs. When compared to the wild type strain, the fadD2 mutant exhibited decreased production of lipase, protease, rhamnolipid and phospholipase, and retardation of both swimming and swarming motilities. Interestingly, fadD1 mutant showed only increased swarming motility. Growth analysis of the fadD mutants showed noticeable deficiencies in utilizing FAs and phosphatidylcholine (major components of lung surfactant) as the sole carbon source. This defect translated into decreased in vivo fitness of P. aeruginosa in a BALB/c mouse lung infection model, supporting the role of lipids as a significant nutrient source for this bacterium in vivo

An overview of NMR-based metabolomics to identify secondary plant compounds involved in host plant resistance

Secondary metabolites provide a potential source for the generation of host plant resistance and development of biopesticides. This is especially important in view of the rapid and vast spread of agricultural and horticultural pests worldwide. Multiple pests control tactics in the framework of an integrated pest management (IPM) programme are necessary. One important strategy of IPM is the use of chemical host plant resistance. Up to now the study of chemical host plant resistance has, for technical reasons, been restricted to the identification of single compounds applying specific chemical analyses adapted to the compound in question. In biological processes however, usually more than one compound is involved. Metabolomics allows the simultaneous detection of a wide range of compounds, providing an immediate image of the metabolome of a plant. One of the most universally used metabolomic approaches comprises nuclear magnetic resonance spectroscopy (NMR). It has been NMR which has been applied as a proof of principle to show that metabolomics can constitute a major advancement in the study of host plant resistance. Here we give an overview on the application of NMR to identify candidate compounds for host plant resistance. We focus on host plant resistance to western flower thrips (Frankliniella occidentalis) which has been used as a model for different plant species