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OBJECTIVE: COPD is one of the major causes of morbidity and mortality worldwide and represents one of the most important issues for public health. Frequent exacerbations induce a faster decline in lung function and poorer quality of life, increase mortality, and have a socio-economic impact with a high burden in terms of resources and healthcare costs. The clinical trials evaluated the effect of mucolytics in COPD and showed that the long-term carbocysteine, associated with bronchodilators, anticholinergics, and steroids, reduces the frequency of exacerbations and improves the quality of life. PATIENTS AND METHODS: The aim of this prospective real-life study was to evaluate the long-term impact on exacerbations (at 1 year) in COPD patients treated with carbocysteine lysine salt (single dose of 2.7 g once a day) in addition to background therapy with or without inhaled steroids. RESULTS: In a total of 155 evaluable patients, our study showed that the addition of a single dose of carbocysteine lysine salt to background therapy determines a statistically significant reduction of the average number of exacerbations vs. the number observed in the previous year (from 1.97±0.10 to 1.03±0.11; p<0.01), irrespective of treatment with or without inhaled steroids. In particular, in patients with ≥2 exacerbations in the previous year, the addition of carbocysteine lysine salt resulted in a statistically significant reduction in the exacerbations rate from 69% to 33% and from 58% to 25%, respectively (p<0.01) in patients with or without inhaled steroids. CONCLUSIONS: In summary, our data highlighted the efficacy of long-term administration of a single daily dose of carbocysteine lysine salt (2.7 g/day) in reducing the number and rate of exacerbations in COPD patients, independently from the use of inhaled steroids. [ABSTRACT FROM AUTHOR]

Nausea and vomiting are common for runners during ultramarathons and often contribute to non-finishes. We aimed to determine the efficacy of ondansetron, a commonly used antiemetic, to treat nausea and vomiting in runners during an ultramarathon. Runners who had a previous history of frequent nausea or vomiting during races and entered in 160, 80, and 55 km ultramarathons in 2018 and 2019 were randomized in a double-blind fashion to 4 mg ondansetron or placebo capsules to use if they developed nausea or vomiting during the race with the ability to take three additional doses. Study participants completed a post-race online survey to assess medication use and efficacy. Of 62 study participants, 31 took either ondansetron (20) or placebo (11). In this small study, there were no group differences in those reporting any improvement in nausea and vomiting ( p = 0.26) or in the amount of improvement ( p = 0.15). We found no evidence that ondansetron capsules improve nausea and vomiting during ultramarathons.

Background: Human studies have demonstrated that olive oil phenolic compounds reduce inflammatory markers associated with chronic diseases., Objectives: To explore the anti-inflammatory effects of extra-virgin olive oil polyphenols in an experimental model of inflammatory bowel disease (IBD)., Methods: HLA-B27 transgenic rats were fed an AIN-76 diet containing 10% corn oil (CO) or extra-virgin olive oil with high (EVOO) or low phenolic content (ROO) for 3 months. Wild-type rats (WT) were fed the CO diet., Results: CO-fed HLA-B27 animals developed intestinal inflammation characterized by diarrhea, increased myeloperoxidase activity, and mucosal injury. None of these parameters were influenced by EVOO. Gene expression profiling indicated that proinflammatory pathways were upregulated in the colon mucosa of CO-fed HLA-B27 rats compared to WT, and this was further confirmed by RT-PCR for the iNOS, TNFα, and IL1β genes. EVOO significantly reduced TNFα gene expression in the colon mucosa and decreased total cholesterol blood levels compared to CO HLA-B27 rats (89.43 ± 3.66 vs. 111.5 ± 8.10 mg/dL, p < 0.05). This latter effect with EVOO was associated with reduced HMGCR and increased PPAR-α hepatic gene expression, compared to ROO., Conclusion: These data indicate that olive oil polyphenols do not control colon inflammation in HLA-B27 transgenic rats but exert a positive effect on blood lipids by reducing total cholesterol levels. This preliminary result suggests the need to explore the efficacy of EVOO rich in polyphenols as a complementary strategy for managing hypercholesterolemia and to potentially limit statin-associated myotoxicity., (© 2019 S. Karger AG, Basel.)

We investigate large-scale effects induced by external fields, phenomenologically interpreted as mass media, in multiagent models evolving with the microscopic dynamics of the binary naming game. In particular, we show that a single external field, broadcasting information at regular time intervals, can reverse the majority opinion of the population, provided the frequency and the effectiveness of the sent messages lie above well-defined thresholds. We study the phase structure of the model in the mean field approximation and in numerical simulations with several network topologies. We also investigate the influence on the agent dynamics of two competing external fields, periodically broadcasting different messages. In finite regions of the parameter space we observe periodic equilibrium states in which the average opinion densities are reversed with respect to naive expectations. Such equilibria occur in two cases: (i) when the frequencies of the competing messages are different but close to each other; (ii) when the frequencies are equal and the relative time shift of the messages does not exceed half a period. We interpret the observed phenomena as a result of the interplay between the external fields and the internal dynamics of the agents and conclude that, depending on the model parameters, the naming game is consistent with scenarios of first- or second-mover advantage (to borrow an expression from the jargon of business strategy).

Background: DNA copy number alterations (CNAs) and gene expression changes have amply been encountered in colorectal cancers (CRCs), but the extent at which CNAs affect gene expression, as well as their relevance for tumor development, are still poorly defined. Here we aimed at assessing the clinical relevance of these parameters in a 10 year follow-up study., Methods: Tumors and normal adjacent colon mucosa, obtained at primary surgery from 21 CRC patients, were subjected to (i) high-resolution array CGH (a-CGH) for the detection of CNAs and (ii) microarray-based transcriptome profiling for the detection of gene expression (GE) changes. Correlations between these genomic and transcriptomic changes and their associations with clinical and histopathological parameters were assessed with the aim to identify molecular signatures associated with disease-free survival of the CRC patients during a 10 year follow-up., Results: DNA copy number gains were frequently detected in chromosomes 7, 8q, 13, 19, 20q and X, whereas DNA copy number losses were frequently detected in chromosomes 1p, 4, 8p, 15, 17p, 18, 19 and 22q. None of these alterations were observed in all samples. In addition, we found that 2,498 genes were up- and that 1,094 genes were down-regulated in the tumor samples compared to their corresponding normal mucosa (p < 0.01). The expression of 65 genes was found to be significantly associated with prognosis (p < 0.01). Specifically, we found that up-regulation of the IL17RA, IGF2BP2 and ABCC2 genes, and of genes acting in the mTOR and cytokine receptor pathways, were strongly associated with a poor survival. Subsequent integrated analyses revealed that increased expression levels of the MMP9, BMP7, UBE2C, I-CAM, NOTCH3, NOTCH1, PTGES2, HMGB1 and ERBB3 genes were associated with copy number gains, whereas decreased expression levels of the MUC1, E2F2, HRAS and SIRT3 genes were associated with copy number losses. Pathways related to cell cycle progression, eicosanoid metabolism, and TGF-β and apoptosis signaling, were found to be most significantly affected., Conclusions: Our results suggest that CNAs in CRC tumor tissues are associated with concomitant changes in the expression of cancer-related genes. In other genes epigenetic mechanism may be at work. Up-regulation of the IL17RA, IGF2BP2 and ABCC2 genes, and of genes acting in the mTOR and cytokine receptor pathways, appear to be associated with a poor survival. These alterations may, in addition to Dukes' staging, be employed as new prognostic biomarkers for the prediction of clinical outcome in CRC patients.

Objective: The recent surge of new legislation regulating induced abortion in the United States is ostensibly motivated by the desire to protect women's health. To provide context for interpreting the risk of abortion, we compared abortion-related mortality to mortality associated with other outpatient surgical procedures and selected nonmedical activities., Methods: We calculated the abortion-related mortality rate during 2000-2009 using national data. We searched PubMed and other sources for contemporaneous data on mortality associated with other outpatient procedures commonly performed on healthy young women, marathon running, bicycling and driving., Results: The abortion-related mortality rate in 2000-2009 in the United States was 0.7 per 100,000 abortions. Studies in approximately the same years found mortality rates of 0.8-1.7 deaths per 100,000 plastic surgery procedures, 0-1.7deaths per 100,000 dental procedures, 0.6-1.2 deaths per 100,000 marathons run and at least 4 deaths among 100,000 cyclists in a large annual bicycling event. The traffic fatality rate per 758 vehicle miles traveled by passenger cars in the United States in 2007-2011 was about equal to the abortion-related mortality rate., Conclusions: The safety of induced abortion as practiced in the United States for the past decade met or exceeded expectations for outpatient surgical procedures and compared favorably to that of two common nonmedical voluntary activities. The new legislation restricting abortion is unnecessary; indeed, by reducing the geographic distribution of abortion providers and requiring women to travel farther for the procedure, these laws are potentially detrimental to women's health., (Copyright © 2014 Elsevier Inc. All rights reserved.)

"Rare" diseases are a family of different disorders or conditions affecting fewer than 1/2000 in the general population. Among them, 150 involve respiratory system. To date, most reviews in literature focuses on the more important pulmonary lung diseases without taking in account the overall framework and diagnostic and therapeutic algorithms that allow a correct comprehensive approach to these disorders. The aim of our review is to describe a possible global approach to the management of these diseases trying to take a picture of the overall complexity of the field. We also want to highlight the role played by research on rare diseases pathogenesis in revealing, at least in part, mechanisms underlying many of "more common" disorders with the purpose to update the current state of knowledge.

Aim: The aim of the study is to establish whether healthy full-term breastfed infants require supplemental vitamin D for proper bone mineralization., Methods: Bone mineralization was studied by performing ultrasound scans of 73 healthy full-term subjects at the age of 3 months. The infants were divided into three groups. Group A: breastfed without supplemental vitamin D (BF); group B: breastfed with supplement of 400 IU/day of vitamin D (BFD); group C: fed with formula (with and without supplemental vitamin D 400 IU/day) (FF). The values of mcSOS (m/sec) and mcBTT (µsec) were assessed in all subjects., Results: A statistically significant difference has been found between group A vs group B both in mcSOS (P=0.03) and in mcBTT (P=0.01) values and also between group A vs group C both in mcSOS (P=0.012) and in mcBTT (P=0.003) values. Significant differences between group B vs group C were not found. In 75% of subjects of group A mcSOS and mcBTT values were ≤ the 10th percentile, while in group B they were between the 10th and 50th percentile. In FF infants given supplemental vitamin D mcSOS and mcBTT values were between the 25th and 75th percentile., Conclusion: Human breast milk is an appropriate source of nutrition for the growth of healthy full-term newborns, but is poor in vitamin D as demonstrated by the impaired bone mineralization in the breastfed infants without supplemental vitamin D. The results presented demonstrate that exclusively breastfed infants require at least 400 IU/day of supplemental vitamin D.

Advances in high-throughput DNA sequencing technologies have determined an explosion in the number of sequenced bacterial genomes. Comparative sequence analysis frequently reveals evidences of homologous recombination occurring with different mechanisms and rates in different species, but the large-scale use of computational methods to identify recombination events is hampered by their high computational costs. Here, we propose a new method to identify recombination events in large datasets of whole genome sequences. Using a filtering procedure of the gene conservation profiles of a test genome against a panel of strains, this algorithm identifies sets of contiguous genes acquired by homologous recombination. The locations of the recombination breakpoints are determined using a statistical test that is able to account for the differences in the natural rate of evolution between different genes. The algorithm was tested on a dataset of 75 genomes of Staphylococcus aureus and 50 genomes comprising different streptococcal species, and was able to detect intra-species recombination events in S. aureus and in Streptococcus pneumoniae. Furthermore, we found evidences of an inter-species exchange of genetic material between S. pneumoniae and Streptococcus mitis, a closely related commensal species that colonizes the same ecological niche. The method has been implemented in an R package, Reco, which is freely available from supplementary material, and provides a rapid screening tool to investigate recombination on a genome-wide scale from sequence data.

Aim: To examine the links between quality of sleep and the severity of intestinal symptoms in irritable bowel syndrome (IBS)., Methods: One hundred and forty-two outpatients (110 female, 32 male) who met the Rome III criteria for IBS with no psychiatric comorbidity were consecutively enrolled in this study. Data on age, body mass index (BMI), and a set of life-habit variables were recorded, and IBS symptoms and sleep quality were evaluated using the questionnaires IBS Symptom Severity Score (IBS-SSS) and Pittsburgh Sleep Quality Index (PSQI). The association between severity of IBS and sleep disturbances was evaluated by comparing the global IBS-SSS and PSQI score (Pearson's correlation and Fisher's exact test) and then analyzing the individual items of the IBS-SSS and PSQI questionnaires by a unitary bowel-sleep model based on item response theory (IRT)., Results: IBS-SSS ranged from mild to severe (120-470). The global PSQI score ranged from 1 to 17 (median 5), and 60 patients were found to be poor sleepers (PSQI > 5). The correlation between the global IBS-SSS and PSQI score indicated a weak association (r = 0.2 and 95% CI: -0.03 to 0.35, P < 0.05), which becomes stronger using our unitary model. Indeed, the IBS and sleep disturbances severities, estimated as latent variables, resulted significantly high intra-subject correlation (posterior mean of r = 0.45 and 95% CI: 0.17 to 0.70, P < 0.05). Moreover, the correlations between patient features (age, sex, BMI, daily coffee and alcohol intake) and IBS and sleep disturbances were also analyzed through our unitary model. Age was a significant regressor, with patients ≤ 50 years old showing more severe bowel disturbances (posterior mean = -0.38, P < 0.05) and less severe sleep disturbances (posterior mean = 0.49, P < 0.05) than older patients. Higher daily coffee intake was correlated with a lower severity of bowel disturbances (posterior mean = -0.31, P < 0.05). Sex (female) and daily alcohol intake (modest) were correlated with less severe sleep disturbances., Conclusion: The unitary bowel-sleep model based on IRT revealed a strong positive correlation between the severity of IBS symptoms and sleep disturbances.

Vitamin D has an important role in bone-metabolism (and its deficiency can cause preterm osteopenia, craniotabe and rickets), but it has also non-calcitropic functions. In fact, vitamin D deficiency is correlated to chronic kidney disease, respiratory infections, type 1 diabetes, psoriasis, Crohn disease and neonatal hypocalcemia. Because of the vitamin D deficiency is a global problem, its role as a drug is fundamental for the human health in all ages.

Purpose: Epidemiological studies suggest that a moderate consumption of wine is associated with a reduced risk of cardiovascular diseases and with a reduced mortality for all causes, possibly due to increased antioxidant defences. The present intervention study was undertaken to evaluate the in vivo effects of wine polyphenols on gene expression in humans, along with their supposed antioxidant activity., Methods: Blood haemorheology and platelet function were also evaluated. In order to avoid interferences from alcohol, we used de-alcoholised wine (DAW) with different polyphenol content. A randomised cross-over trial of high-proanthocyanidin (PA) red DAW (500 mL/die, PA dose = 7 mg/kg b.w.) vs. low-PA rosé DAW (500 mL/die, PA dose = 0.45 mg/kg) was conducted in 21 post-menopausal women in Florence, Italy. Oxidative DNA damage by the comet assay and gene expression by microarray was measured in peripheral blood lymphocytes, collected during the study period. Blood samples were also collected for the evaluation of haematological, haemostatic, haemorheological, and inflammatory parameters., Results: The results of the present study provide evidence that consumption of substantial amounts of de-alcoholised wine for 1 month does not exert a protective activity towards oxidative DNA damage, nor modifies significantly the gene expression profile of peripheral lymphocytes, whereas it shows blood-fluidifying actions, expressed as a significant decrease in blood viscosity. However, this effect does not correlate with the dosage of polyphenols of the de-alcoholised wine., Conclusions: More intervention studies are needed to provide further evidence of the health-protective effects of wine proanthocyanidins.

Prenatal exposure to toxicants, such as maternal smoking, may impair cardiovascular autonomic maturation in infants. We recently showed that exposure of pregnant rats to a mild concentration of carbon monoxide (CO), a component of cigarette smoke, delays postnatal electrophysiological maturation of ventricular myocytes from newborns rats, likely predisposing to life-threatening arrhythmias. To get a comprehensive view of developmental molecular abnormalities induced, at cardiac level, by prenatal CO exposure, we used microarray analysis approach on the rat heart at 4, 7 and 20 days postnatal life. The relationship between molecular and functional alterations was investigated by assessing the ventricular expression of f-current, an electrophysiological marker of immature cardiac phenotype. Rats were prenatally exposed to 0 (CTR) or 150 p.p.m. CO and mRNA obtained from ventricular samples. Differential analysis and biological pathway analysis of microarray data were performed by using Newton's approach and the GENMAPP/MAPPFinder, respectively. The real-time RT-PCR reactions were performed by TaqMan probe-based chemistry. Freshly isolated patch-clamped ventricular cardiomyocytes were used to measure I(f). Genes and pathways controlling cell cycle and excitation-contraction coupling were significantly modified in CO-exposed rats. The higher effect was observed in cardiomyocytes harvested from 7-day-old rats, in which mRNA expression for crucial sarcomeric proteins (myosin and actin subunits, troponin I), transporters (Ca(2+) transporting ATPase) and enzymes (aldolase) were significantly downregulated. Accordingly, the molecular and functional expression of f-channels, which represents a marker of fetal ventricular phenotype, was transiently greater in CO-exposed rats (+200%) than in control ones. In conclusion, our study provides new insights into the molecular and functional mechanisms underlying cardiac maturation and its impairment by prenatal exposure to toxic components of smoking, such as CO.

Whether the beneficial effects of pomegranate are due to the ellagitannins or to their microbiota-derived urolithins is not known. Our objectives were to evaluate the effects of pomegranate intake and its main microbiota-derived metabolite urolithin-A (UROA) on colon inflammation and to assess whether UROA is the main anti-inflammatory compound. In addition, the effect of the inflammation on the phenolic metabolism was also explored. Male Fisher rats were fed with 250 mg kg(-1) day(-1) pomegranate extract (PE) or 15 mg kg(-1) day(-1) UROA for 25 days. Dextran sodium sulfate (5%) (DSS) was administered for the five last days and then rats were euthanized. DSS is a well-known model of inflammatory bowel disease. Colon tissue damage, microbiota changes, antioxidant status, prostaglandin E(2) (PGE(2)), nitric oxide production, inducible nitric oxide synthase (iNOS), prostaglandin E synthase (PTGES), gene expression (microarrays and RT-PCR) and polyphenol metabolism (LC-MS-MS) were evaluated. Both PE and UROA decreased inflammation markers (iNOS, cycloxygenase-2, PTGES and PGE(2) in colonic mucosa) and modulated favorably the gut microbiota. The G(1) to S cell cycle pathway was up-regulated in both groups. UROA group showed various down-regulated pathways, including that of the inflammatory response. PE, but not UROA, decreased oxidative stress in plasma and colon mucosa. Only UROA preserved colonic architecture. The normal formation of urolithins in PE-fed rats was prevented during inflammation. Our results suggest that UROA could be the most active anti-inflammatory compound derived from pomegranate ingestion in healthy subjects, whereas in colon inflammation, the effects could be due to the nonmetabolized ellagitannin-related fraction., (Copyright 2010 Elsevier Inc. All rights reserved.)

Background: Azoxymethane (AOM) or 1,2-dimethylhydrazine (DMH)-induced colon carcinogenesis in rats shares many phenotypical similarities with human sporadic colon cancer and is a reliable model for identifying chemopreventive agents. Genetic mutations relevant to human colon cancer have been described in this model, but comprehensive gene expression and genomic analysis have not been reported so far. Therefore, we applied genome-wide technologies to study variations in gene expression and genomic alterations in DMH-induced colon cancer in F344 rats., Methods: For gene expression analysis, 9 tumours (TUM) and their paired normal mucosa (NM) were hybridized on 4 x 44K Whole rat arrays (Agilent) and selected genes were validated by semi-quantitative RT-PCR. Functional analysis on microarray data was performed by GenMAPP/MappFinder analysis. Array-comparative genomic hybridization (a-CGH) was performed on 10 paired TUM-NM samples hybridized on Rat genome arrays 2 x 105K (Agilent) and the results were analyzed by CGH Analytics (Agilent)., Results: Microarray gene expression analysis showed that Defcr4, Igfbp5, Mmp7, Nos2, S100A8 and S100A9 were among the most up-regulated genes in tumours (Fold Change (FC) compared with NM: 183, 48, 39, 38, 36 and 32, respectively), while Slc26a3, Mptx, Retlna and Muc2 were strongly down-regulated (FC: -500; -376, -167, -79, respectively). Functional analysis showed that pathways controlling cell cycle, protein synthesis, matrix metalloproteinases, TNFalpha/NFkB, and inflammatory responses were up-regulated in tumours, while Krebs cycle, the electron transport chain, and fatty acid beta oxidation were down-regulated. a-CGH analysis showed that four TUM out of ten had one or two chromosomal aberrations. Importantly, one sample showed a deletion on chromosome 18 including Apc., Conclusion: The results showed complex gene expression alterations in adenocarcinomas encompassing many altered pathways. While a-CGH analysis showed a low degree of genomic imbalance, it is interesting to note that one of the alterations concerned Apc, a key gene in colorectal carcinogenesis. The fact that many of the molecular alterations described in this study are documented in human colon tumours confirms the relevance of DMH-induced cancers as a powerful tool for the study of colon carcinogenesis and chemoprevention.

The naturally occurring polyphenol resveratrol has been acknowledged with health-beneficial properties. Most of the studies dealing with its in vivo effects assay huge doses, not representative from a dietary point of view. Our aim was to ascertain whether resveratrol can exert anti-inflammatory activity in vivo at an attainable dietary dose. Rats were fed with 1 mg of resveratrol/kg/day (a human equivalent dose) for 25 days, and in the last 5 days, 5% dextran sulfate sodium (DSS) was administered to induce colitis. Effects on colon tissue damage, gut microbiota, reactive oxygen species, inflammatory markers and nitric oxide production as well as gene expression profile with microarrays were evaluated. Resveratrol increased lactobacilli and bifidobacteria as well as diminished the increase of enterobacteria upon DSS treatment. Resveratrol significantly protected the colonic mucosa architecture, reduced body weight loss, diminished the induced anemia and reduced systemic inflammation markers, colonic mucosa prostaglandin E(2), cycloxygenase-2, prostaglandin E synthase and nitric oxide levels. In addition, the expression of 2,655 genes in distal colon mucosa related to important pathways was varied. These results reinforce the concept of resveratrol as a dietary beneficial compound in intestinal inflammation at doses possibly attainable with resveratrol-enriched nutraceuticals.

Plant polyphenols, such as flavonoids, comprise many compounds, ranging from simple phenolic molecules (i.e. flavonols, anthocyanins) to polymeric structures with high molecular weight (as proanthocyanidins, PAs). We investigated the effects of flavonoids by feeding Wistar rats Arabidopsis thaliana seeds carrying mutations in key enzymes of the flavonoid biosynthetic pathway (15% w/w seeds for 4 weeks). The seeds used were: Ws-2 wild-type containing flavonols and PAs, tt3-4 mutant containing flavonols only, ban-5 accumulating flavonols and anthocyanins, tt4-8 mutant, deprived of flavonoids. DNA oxidative damage was significantly reduced only in the liver of rats fed tt3-4 mutant seeds. Microarray analysis of the liver revealed down-regulation of genes associated with oxidative stress, Krebs cycle, electron transport and proteasome degradation in all experimental groups compared to the tt4-8-fed reference rats; therefore, these effects were due to the flavonol content and not to high molecular weight compounds. We observed a down-regulation of inflammatory response genes in the colon mucosa in ban-5- fed rats, probably due to anthocyanin content. In conclusion, flavonols exhibited antioxidant effects at systemic level, whereas high molecular weight flavonoids affected only the colon, probably due to their limited absorption.

Motivation: Eu.Gene Analyzer is an easy-to-use, stand-alone application that allows rapid and powerful microarray data analysis in the context of biological pathways. Its intuitive graphical user interface makes it an easy and flexible tool, even for the first-time user. Eu.Gene supports a variety of array platforms, organisms and pathway ontologies, transparently deals with multiple nomenclature systems and seamlessly integrates data from different sources. Two different statistical methods, the Fisher Exact Test and the Gene Set Enrichment Analysis (GSEA), are implemented to identify biological pathways transcriptionally affected under experimental conditions. A suite of tools is offered to define, visualize and share custom non-redundant pathway sets. In conclusion, Eu.Gene Analyzer is a new software application that takes advantage of information from multiple pathway databases to build a comprehensive interpretation of experimental results in a simple, intuitive environment.

In order to discover potential markers of prognosis in colorectal cancer (CRC) we have determined gene expression profiles, using cDNA microarrays in CRC samples obtained from 19 patients in Dukes stages C and D, with favorable clinical course (Dukes C patients, survival >5 years after surgery, group A, n=7) or unfavorable clinical course (Dukes stage C and D patients, survival <5 years after surgery, group B, n=12). Gene expression was measured in RNA from each tumor, using a pool of equal amounts of RNA from all tumors as a reference. To identify and rank differentially expressed genes we used three different analytical methods: (i) Significance Analysis of Microarrays (SAM), (ii) Cox's Proportional Hazard Model, and (iii) Trend Filter (a mathematical method for the assessment of numerical trends). The level of expression of a gene in an individual tumor was regarded as of interest when that gene was identified as differentially expressed by at least two of these three methods. By these stringent criteria we identified eight genes (ITGB2, MRPS11, NPR1, TXNL2, PHF10, PRSS8, KCNK3, JAK3) that were correlated with prolonged survival after surgery. Pathway analysis showed that patients with favorable prognosis had several activated metabolic pathways (carbon metabolism, transcription, amino acid and nitrogen metabolism, signaling and fibroblast growth factor receptor pathways). To further validate individual gene expression findings, the RNA level of each gene identified as a marker with microarrays was measured by real-time RT-PCR in CRC samples from an independent group of 55 patients. In this set of patients the Cox Proportional Hazard Model analysis demonstrated a significant association between increased patient survival and low expression of ITGB2 (p = 0.011) and NPR1 (p = 0.023) genes.

Motivation: Microarray studies permit to quantify expression levels on a global scale by measuring transcript abundance of thousands of genes simultaneously. A difficulty when analysing expression measures is how to model variability for the whole set of genes. It is usually unrealistic to assume a common variance for each gene. Several approaches to model gene-specific variances are proposed. We take advantage of calibration experiments, in which the probes hybridized on the two channels come from the same population (self-self experiment). In this case it is possible to estimate the gene-specific variance, to be incorporated in comparative experiments on the same tissue, cellular line or species., Results: We present two approaches to introduce prior information on gene-specific variability from a calibration experiment: an empirical Bayes model and a full Bayesian hierarchical model. We apply the methods in the analysis of human lipopolysaccharide-stimulated leukocyte experiments., Availability: The calculations are implemented in WinBugs. The codes are available on request from the authors.

The possible association between radon exposure in dwellings and adult myeloid leukaemia had been explored in an Italian province by a case-control study. A total of 44 cases and 211 controls were selected from death certificates file. No association had been found in the original study (OR = 0.58 for > 185 vs 80 < or = Bq/cm). Here we reanalyse the data taking into account the measurement error of radon concentration and the presence of missing data. A Bayesian hierarchical model with error in covariates is proposed which allows appropriate imputation of missing values. The general conclusion of no evidence of association with radon does not change, but a negative association is not observed anymore (OR = 0.99 for > 185 vs 80 < or = Bq/cm). After adjusting for residential house radon and gamma radiation, and for the multilevel data structure, geological features of the soil is associated with adult myeloid leukaemia risk (OR = 2.14, 95 per cent Cr.I. 1.0-5.5)., (Copyright 2005 John Wiley & Sons, Ltd.)