A screening methodology based on Random Forests to improve the detection of gene�Cgene interactions

The search for susceptibility loci in gene–gene interactions imposes a methodological and computational challenge for statisticians because of the large dimensionality inherent to the modelling of gene–gene interactions or epistasis. In an era in which genome-wide scans have become relatively common, new powerful methods are required to handle the huge amount of feasible gene–gene interactions and to weed out false positives and negatives from these results. One solution to the dimensionality problem is to reduce data by preliminary screening of markers to select the best candidates for further analysis. Ideally, this screening step is statistically independent of the testing phase. Initially developed for small numbers of markers, the Multifactor Dimensionality Reduction (MDR) method is a nonparametric, model-free data reduction technique to associate sets of markers with optimal predictive properties to disease. In this study, we examine the power of MDR in larger data sets and compare it with other approaches that are able to identify gene–gene interactions. Under various interaction models (purely and not purely epistatic), we use a Random Forest (RF)-based prescreening method, before executing MDR, to improve its performance. We find that the power of MDR increases when noisy SNPs are first removed, by creating a collection of candidate markers with RFs. We validate our technique by extensive simulation studies and by application to asthma data from the European Committee of Respiratory Health Study II.     

Diverse associations of microalbuminuria with C-reactive protein, interleukin-18 and soluble CD 40 ligand in male essential hypertensive subjects

BACKGROUND: Microalbuminuria (MA) and low-grade inflammation constitute emerging markers of subclinical atherosclerosis. We investigated whether urinary albumin excretion, expressed as the albumin-to-creatinine ratio (ACR), is associated with high sensitivity C-reactive protein (hs-CRP), interleukin (IL)-18, and soluble CD40 ligand (sCD40L), in hypertensive subjects. METHODS: The study population consisted of 108 nondiabetic male patients with newly diagnosed untreated stage I to II essential hypertension (aged 44.6 years, office blood pressure [BP] 148/95 mm Hg). According to ACR values determined as the average of two nonconsecutive overnight spot urine samples, subjects were divided into microalbuminurics (n = 28) (mean ACR = 30 to 300 mg/g) and normoalbuminurics (n = 80) (mean ACR <30 mg/g). RESULTS: Although microalbuminurics as compared to normoalbuminuric hypertensives had greater hs-CRP levels (2.55 +/- 1.18 v 1.45 +/- 0.52 mg/L, P < .0001), independently of confounding factors, these two groups did not differ regarding IL-18 and sCD40L values (P = not significant [NS] for both cases). In the entire population, ACR exhibited a positive correlation with hs-CRP (r = 0.623, P < .0001), whereas there was no association with both IL-18 and sCD40L (P = NS for both cases). When multiple linear regression analysis was performed, it was revealed that age, body mass index, office systolic BP, total cholesterol, and hs-CRP levels were significant independent predictors of the ACR (P < .05). CONCLUSIONS: In essential hypertensive subjects, MA is accompanied by elevated hs-CRP levels, but not by augmented IL-18 and sCD40L concentrations, suggesting activation of different inflammatory pathways in the progression of renal and cardiovascular atherosclerotic disease. The pathophysiologic mechanisms of these associations remain to be further elucidated in future studies.     

A rare RET gene exon 8 mutation is found in two Greek kindreds with familial medullary thyroid carcinoma: implications for screening

OBJECTIVE: Familial medullary thyroid carcinoma (FMTC) is caused by germ-line mutations in the RET proto-oncogene. These mutations concern mainly cysteine residues in exons 10 and 11, whereas noncysteine mutations in exons 13-16 are rare. Mutations in other exons have been reported only in isolated families. In this study we have analysed the RET gene in two FMTC families negative for mutations in the above exons. DESIGN: We have analysed exons 7-19 and 21 in one index patient from each family using DNA sequencing. PATIENTS: Twenty-eight subjects from both families were clinically assessed and subsequently molecularly analysed for the presence of RET gene mutations. RESULTS: We have found the mutation c.1597G-->T (Gly533Cys) in two Greek families with FMTC. The mutation was detected in all seven MTC patients of both families as well as in 13 asymptomatic relatives in the heterozygote state, although one of the patients was also a homozygote due to consanguinity. The mutation shows a wide clinical heterogeneity, as there are carrier patients with age of diagnosis ranging from 23 to 88 years. CONCLUSIONS: It is likely that this mutation causes FMTC, as no other mutation was found in the RET gene, the mutation co-segregates with FMTC, and family members without the mutation are clinically unaffected. As the same point mutation was previously found in a large Brazilian family, it may be present in other populations as well. Therefore, exon 8 of RET should be screened in FMTC families with no identified common RET mutations.     

Structure-antileukemic activity relationship study of B- and D-ring modified and nonmodified steroidal esters of 4-methyl-3-N,N-bis(2-chloroethyl)amino benzoic acid: a comparative study

This study was designed as a rational continuation of our research regarding the functional requirements essential for the antileukemic activity of compounds comprising an alkylating moiety and a modified steroid. The steroidal esteric derivatives of 4-methyl-3-N,N-bis(2-chloroethyl)amino benzoic acid were tested on leukemias P388 and L1210 in vivo and in normal human lymphocytes in vitro. Among them the B-lactamic steroidal esters proved more potent antileukemic agents than the 7-oxidized and those with a simple B-ring, but not more effective inducers of DNA damage and cell cycle arrest in vitro. We speculate that these results indicate a different mechanism of action induced by the lactamized B steroidal ring, in comparison to the 7-keto or the D-lactamic groups, which involves the interaction of the -NHCO- moiety with cellularcomponents essential for tumor growth. 4-Methyl-3-N,N-bis(2-chloroethyl)amino benzoic acid proved a more proper module for the B-lactams than chlorambucil and phenyl acetic acid's nitrogen mustard probably because the esteric bond is less cleaved by the esterases, resulting in an increased concentration of the drug in the vinicity of the target site essential for an antineoplasmatic response.     

Transcatheter closure of patent foramen ovale during a radiofrequency ablation procedure

A 43-year-old woman was undergoing radiofrequency catheter ablation of a symptomatic supraventricular tachycardia when a patent foramen ovale (PFO) was detected with passage of the diagnostic electrocatheter into the left atrium. Prior echocardiographic studies had been unrevealing. Upon questioning during the procedure, the patient now admitted to frequent and disabling daily migraine attacks, while her family described two recent brief episodes of disorientation and dysarthria, consistent with transient ischemic attacks. The patient was informed of the option of future closure of the PFO, but she insisted on having this done concurrently with her ablation procedure. After successful ablation of the slow pathway considered responsible for the supraventricular tachycardia, an Amplatzer closure device was utilized and the PFO was successfully closed during the same procedure. A postprocedural transesophageal echocardiogram showed complete sealing of the PFO, while over the ensuing 10 months the patient reported virtual elimination of her daily attacks of migrainous headaches, limited to a single episode the day after the procedure and none thereafter.     

Composition and chemical health hazards of the most common electronic cigarette liquids in nine European countries

Abstract

Background: The aim of the present study was to identify the composition and reported chemical health hazards of the most common electronic cigarette liquids (e-liquids) in nine European Union (EU) Member States (MS) prior to adoption of the Tobacco Product Directive (TPD).

Materials and methods: Within the Horizon2020, EUREST-PLUS study, 122 of the most commonly sold e-liquids in 9 EU MS were randomly selected and purchased. A quantitative and qualitative chemical analysis was performed using a previously validated based gas chromatography–mass spectrometry and liquid chromatography–mass spectrometry method. The most commonly detected compounds were then divided according to the Danger Globally Harmonized System of Classification and Labelling of Chemicals (GHS) and Warning GHS codes.

Results: Within our qualitative analysis, 171 different compounds were detected. Discrepancies in measured versus reported nicotine concentration were identified. Forty-one (85.4%) of the most commonly detected compounds were registered with Warning GHS codes, 11 with Danger GHS codes and 9 with both codes. Of the total number of the detected compounds, 293 were attributable to fruits flavor, followed by tobacco flavor (204), nonalcoholic drinks (n?=?64), desserts–sweets (n?=?50), menthol – mint (n?=?42) and alcohol (n?=?39). Menthol which is classified as a strong irritant to skin and eye was the most frequently detected compound.

Conclusion: A large plethora of compounds with varying warning codes was identified in e-cigarette samples. The systematic monitoring and chemical evaluation of e-liquids are warranted, so as to ensure consumer protection.     

Increased plasma concentration of surfactant protein D in chronic periodontitis independent of SFTPD genotype: potential role as a biomarker

Surfactant protein (SP) D belongs to the family of collectins, which are humoral molecules of the innate immune system. Collectins belong to pattern recognition receptors and are present in plasma and on mucosal surfaces and recognize several microbial components, the pathogen-associated molecular patterns (PAMPs). While SP-A is primarily expressed in the lung, expression of SP-D is more widely detected including different mucosal surfaces and in serum. Therefore, SP-D is considered a functional candidate in chronic periodontitis. The present study sought to investigate whether plasma concentration of SP-D is altered in chronic periodontitis and whether polymorphisms within the SFTPD gene (Met11Thr, Ala160Thr and Ser270Thr) are associated with chronic periodontitis. The study population comprised 105 patients with chronic periodontitis and 122 healthy, unrelated control individuals. SP-D Plasma concentrations were determined using enzyme-linked immunosorbent assay test. Genotyping of SFTPD polymorphisms was performed by polymerase chain reaction and restriction fragment length polymorphism analysis. Plasma concentrations were significantly increased in patients with chronic periodontitis compared with the controls. The median plasma concentrations were 81.6 ng/ml in the patients and 52.6 ng/ml in the controls (P = 0.00051). In contrast, the three SFTPD polymorphisms displayed no significant association with chronic periodontitis; thus, the increased plasma concentrations were independent on the genotype. The study showed significantly increased SP-D plasma concentrations in patients with chronic periodontitis compared with healthy controls. Thus, SP-D can potentially be used as a biomarker for chronic periodontitis. As no significant associations of SFTPD gene polymorphisms could be detected, other mechanisms influencing SP-D serum/plasma expression might exist.