Putative role of Brugada syndrome genes in familial atrial fibrillation.

OBJECTIVE: Familial atrial fibrillation (FAF), a not uncommon arrhythmia of the atrium, is characterized by heritability, early onset and absence of other heart defects. The molecular and genetic basis is still not completely clear and genetic diagnosis cannot be achieved in about 90% of patients. In this study, we present the results of genetic screening by next generation sequencing in affected Russian families. PATIENTS AND METHODS: Sixty subjects (18 probands and 42 relatives) with a clinical diagnosis of FAF were enrolled in the study. Since AF frequently associates with other cardiomyopathies, we included all genes that were known to be associated with these disorders at the time of our study. All probands were therefore systematically screened for 47 genes selected from the literature. RESULTS: Our study revealed that seven variants co-segregated with the clinical phenotype in seven families. Interestingly, four out of six genes and three out of seven variants have already been associated with Brugada syndrome in the literature. CONCLUSIONS: To our knowledge, this is the first report of association of the CACNA1C, CTNNA3, PKP2, ANK2 and SCN10A genes with FAF; it is also the first study in Russian families.

Feasibility of feature-based indexing, clustering, and search of clinical trials. A case study of breast cancer trials from ClinicalTrials.gov.

BACKGROUND: When standard therapies fail, clinical trials provide experimental treatment opportunities for patients with drug-resistant illnesses or terminal diseases. Clinical Trials can also provide free treatment and education for individuals who otherwise may not have access to such care. To find relevant clinical trials, patients often search online; however, they often encounter a significant barrier due to the large number of trials and in-effective indexing methods for reducing the trial search space. OBJECTIVES: This study explores the feasibility of feature-based indexing, clustering, and search of clinical trials and informs designs to automate these processes. METHODS: We decomposed 80 randomly selected stage III breast cancer clinical trials into a vector of eligibility features, which were organized into a hierarchy. We clustered trials based on their eligibility feature similarities. In a simulated search process, manually selected features were used to generate specific eligibility questions to filter trials iteratively. RESULTS: We extracted 1,437 distinct eligibility features and achieved an inter-rater agreement of 0.73 for feature extraction for 37 frequent features occurring in more than 20 trials. Using all the 1,437 features we stratified the 80 trials into six clusters containing trials recruiting similar patients by patient-characteristic features, five clusters by disease-characteristic features, and two clusters by mixed features. Most of the features were mapped to one or more Unified Medical Language System (UMLS) concepts, demonstrating the utility of named entity recognition prior to mapping with the UMLS for automatic feature extraction. CONCLUSIONS: It is feasible to develop feature-based indexing and clustering methods for clinical trials to identify trials with similar target populations and to improve trial search efficiency.

Changes in a nanoparticle's spectroscopic signal mediated by the local environment.

Using a first-principles theoretical model the adsorption of a methyl radical on different sized silver nanoparticles is compared to the adsorption of the same radical on model surfaces. Calculations of our structural, dynamical and electronic properties indicated that small changes in the local environment will lead to small changes in infrared (IR) wavenumbers, but in dramatic changes in the IR signal. Our calculations indicate the lower the adsorption site coordination, the higher is the signal strength, suggesting that small changes in the electronic charge distribution will result in bigger changes in the polarizability and hence in the spectroscopic signal intensity. This effect explains, among others, the signal magnification observed for nanoparticles in surface enhanced Raman spectroscopic (SERS) experiments.

Size effects on silver nanoparticles' properties.

In this work a systematic study of the dependence of the structural, electronic, and vibrational properties on nanoparticle size is performed. Based on our total energy calculations we identified three characteristic regimes associated with the nanoparticle's dimensions: (i) below 1.5 nm (100 atoms) where remarkable molecular aspects are observed; (ii) between 1.5 and 2.0 nm (100 and 300 atoms) where the molecular behavior is influenced by the inner core crystal properties; and (iii) above 2.0 nm (more than 300 atoms) where the crystal properties are preponderant. In all considered regimes the nanoparticle's surface modulates its properties. This modulation decreases with the increasing of the nanoparticle's size.

Semiconductor nanoparticle modeling via density functional theory.

In this work, a 2.0 nm nanoparticle (low limit synthesized system) is compared to possible simplified models: passivated clusters, small (1.3 nm) nanoparticles and sets of plane surfaces. Our density functional theory results suggest that even when geometric aspects are properly described by the simplifications considered, electronic properties might be very different, especially when edge atoms are not properly taken into account in the nanoparticle's modeling. In addition, we propose a protocol that might help future theoretical descriptions of nanoparticles.

Furan interaction with the Si(001)-(2 × 2) surface: structural, energetics, and vibrational spectra from first-principles.

In this work we employ the state of the art pseudopotential method, within a generalized gradient approximation to the density functional theory, to investigate the adsorption process of furan on the silicon (001) surface. A direct comparison of different adsorption structures with x-ray photoelectron spectroscopy (XPS), ultra-violet photoelectron spectroscopy (UPS), high resolution electron energy loss spectroscopy (HREELS), near edge x-ray absorption fine structure (NEXAFS), and high resolution spectroscopy experimental data allows us to identify the [4+2 ] cycloaddition reaction as the most probable adsorbate. In addition, theoretical scanning tunnelling microscopy (STM) images are presented, with a view to contributing to further experimental investigations.

Role of surfactant molecules in magnetic fluid: comparison of Monte Carlo simulation and electron magnetic resonance.

We investigate a magnetic fluid composed of magnetite nanoparticles surfacted with dodecanoic acid molecules and stably dispersed in a hydrocarbon solvent. A comparison between Monte Carlo simulation and different experimental techniques allows us to validate our methodology and investigate the behavior of the surfactant molecules. Our analysis, based on the Langmuir model, suggests that the surfactant grafting number on isolate nanoparticles increases with the nanoparticle concentration, while the grafting on agglomerated nanoparticles presents a more complicated behavior. Our results suggests that, if properly coated and at a certain concentration range, colloids can become stable even in the presence of agglomerates. The role of the Hamaker constant, which controls the van der Waals interaction intensity, was also investigated. We have found that the ratio between grafting and Hamaker constant governs the level of nanoparticle agglomeration.

Maleic anhydride adsorption on silicon (001).

The adsorption of maleic anhydride on the Si(001) surface has been investigated using the first-principles pseudopotential formalism. Our total-energy calculations suggest that maleic anhydride (C2H2-C2O3) adsorbs preferentially through a [2+2] cycloaddition of the C=C bond ([2+2]) with an adsorption energy of around 42 kcal/mol. Besides the [2+2] configuration we have also considered other possible coverages and adsorption models, including the adsorption on inter-row and intrarow dimer sites. Based on the analysis of the relative stability of different adsorption models, we propose the formation of mixed domains, containing the [2+2] unit and an interdimer unit. The comparison of our calculated electronic band structure, vibrational modes, and scanning tunneling microscopy images for the [2+2] and the favored interdimer adsorbed structures corroborate our proposed mixed domain model.