Biomedical subjects

Angel Rubio

Publications and source records attributed to Angel Rubio.

28 records · Page 2Linked to original sources

PubMed2003

Bound excitons in time-dependent density-functional theory: optical and energy-loss spectra.

A robust and efficient frequency dependent and nonlocal exchange correlation f(xc)(r,r(');omega) is derived by imposing time-dependent density-functional theory (TDDFT) to reproduce the many-body diagrammatic expansion of the Bethe-Salpeter polarization function. As an illustration, we compute the optical spectra of LiF, SiO2, and diamond and the finite momentum transfer energy-loss spectrum of LiF. The TDDFT results reproduce extremely well the excitonic effects embodied in the Bethe-Salpeter approach, both for strongly bound and resonant excitons. We provide a working expression for f(xc) that is fast to evaluate and easy to implement.

Journal Article↗

PubMed2003

GARBAN: genomic analysis and rapid biological annotation of cDNA microarray and proteomic data.

SUMMARY: Genomic Analysis and Rapid Biological ANnotation (GARBAN) is a new tool that provides an integrated framework to analyze simultaneously and compare multiple data sets derived from microarray or proteomic experiments. It carries out automated classifications of genes or proteins according to the criteria of the Gene Ontology Consortium at a level of depth defined by the user. Additionally, it performs clustering analysis of all sets based on functional categories or on differential expression levels. GARBAN also provides graphical representations of the biological pathways in which all the genes/proteins participate. AVAILABILITY: http://garban.tecnun.es.

Algorithms↗

PubMed2003

Optical and loss spectra of carbon nanotubes: depolarization effects and intertube interactions.

We performed ab initio calculations of the anisotropic dielectric response of small-diameter single-walled carbon nanotubes in the framework of time-dependent density-functional theory. The calculated optical spectra are in very good agreement with experiment, both concerning absolute peak positions and anisotropy effects. The latter can only be described correctly when crystal local-field effects ("depolarization" effects) are fully taken into account. Moreover, interactions between the tubes can strongly modify their absorption and electron energy-loss spectra.

Journal Article↗

PubMed2003

Time-dependent density-functional approach for biological chromophores: the case of the green fluorescent protein.

We performed first-principles calculations of the optical response of the green fluorescent protein (GFP) within a combined quantum-mechanical molecular-mechanics and time-dependent density-functional theory approach. The computed spectra are in excellent agreement with experiments assuming the presence of two, protonated and deprotonated, forms of the photoreceptor in a approximately 4:1 ratio, which supports the conformation model of photodynamics in GFP. Furthermore, we discuss charge transfer, isomerization, and environment effects. The present approach allows for systematic studies of excited-state electron-ion dynamics in biological systems.

Anions↗

PubMed2003

Functional proteomics of nonalcoholic steatohepatitis: mitochondrial proteins as targets of S-adenosylmethionine.

Recent work shows that S-adenosylmethionine (AdoMet) helps maintain normal liver function as chronic hepatic deficiency results in spontaneous development of steatohepatitis and hepatocellular carcinoma. The mechanisms by which these nontraditional functions of AdoMet occur are unknown. Here, we use knockout mice deficient in hepatic AdoMet synthesis (MAT1A(-/-)) to study the proteome of the liver during the development of steatohepatitis. One hundred and seventeen protein spots, differentially expressed during the development of steatohepatitis, were selected and identified by peptide mass fingerprinting. Among them, 12 proteins were found to be affected from birth, when MAT1A(-/-) expression is switched on in WT mouse liver, to the rise of histological lesions, which occurs at approximately 8 months. Of the 12 proteins, 4 [prohibitin 1 (PHB1), cytochrome c oxidase I and II, and ATPase beta-subunit] have known roles in mitochondrial function. We show that the alteration in expression of PHB1 correlates with a loss of mitochondrial function. Experiments in isolated rat hepatocytes indicate that AdoMet regulates PHB1 content, thus suggesting ways by which steatohepatitis may be induced. Importantly, we found the expression of these mitochondrial proteins was abnormal in obob mice and obese patients who are at risk for nonalcoholic steatohepatitis.

Animals↗

PubMed2002

Patching and tearing single-wall carbon-nanotube ropes into multiwall carbon nanotubes.

Bundles of single-wall carbon nanotubes (SWCNTs) coalesce forming multiwall carbon nanotubes (MWCNTs), containing from two to six nested tubes, under thermal treatment at high temperatures [(2200-2400) degrees C]. This structural transformation is confirmed by extensive molecular dynamics (MD) simulations. The simulations suggest a "patching-and-tearing" mechanism for the single-wall-to-multiwall transformation underlying the "concerted" coalescence of the tubes that begins with their polymerization. Tubes of different sizes and chiralities are considered.

Journal Article↗

PubMed2002

Anisotropy and interplane interactions in the dielectric response of graphite.

We determined the anisotropic dielectric response of graphite by means of time-dependent density-functional theory and high-resolution valence electron energy-loss spectroscopy. The calculated loss function was in very good agreement with the experiment for a wide range of momentum-transfer orientations with respect to the graphitic basal planes, provided that local-field effects were included in the response. The calculations also showed strong effects of the interlayer Coulomb interaction on the total pi+sigma plasmon. This finding must be taken into account for the explanation of recent loss spectra of carbon nanotube materials.

Journal Article↗

PubMed2002

Excitonic effects in solids described by time-dependent density-functional theory.

Starting from the many-body Bethe-Salpeter equation we derive an exchange-correlation kernel f(xc) that reproduces excitonic effects in bulk materials within time-dependent density functional theory. The resulting f(xc) accounts for both self-energy corrections and the electron-hole interaction. It is static, nonlocal, and has a long-range Coulomb tail. Taking the example of bulk silicon, we show that the -alpha/q(2) divergency is crucial and can, in the case of continuum excitons, even be sufficient for reproducing the excitonic effects and yielding excellent agreement between the calculated and the experimental absorption spectrum.

Journal Article↗

PubMed2002

Predicting atypia inside endometrial polyps.

OBJECTIVE: To evaluate the efficacy of color Doppler exploration for assessing atypia inside endometrial polyps. METHODS: A prospective study was conducted in a tertiary university hospital. Eight hundred six patients with endometrial polyps were studied with color Doppler sonography, and the resistive index inside the polyp stalk was obtained. The patients were then referred for hysteroscopic resection, and pathologic analysis was performed. RESULTS: Thirty-five polyps with sonographic indications of atypia were pathologically confirmed. Sonographic indications of atypia inside 16 polyps were not confirmed. Three nonquestionable endometrial polyps had atypia inside them. CONCLUSIONS: Low Doppler resistance is highly predictive of atypia inside endometrial polyps.

Endometrial Neoplasms↗

PubMedDate not supplied

Correlation between gene expression and GO semantic similarity.

This research analyzes some aspects of the relationship between gene expression, gene function, and gene annotation. Many recent studies are implicitly based on the assumption that gene products that are biologically and functionally related would maintain this similarity both in their expression profiles as well as in their Gene Ontology (GO) annotation. We analyze how accurate this assumption proves to be using real publicly available data. We also aim to validate a measure of semantic similarity for GO annotation. We use the Pearson correlation coefficient and its absolute value as a measure of similarity between expression profiles of gene products. We explore a number of semantic similarity measures (Resnik, Jiang, and Lin) and compute the similarity between gene products annotated using the GO. Finally, we compute correlation coefficients to compare gene expression similarity against GO semantic similarity. Our results suggest that the Resnik similarity measure outperforms the others and seems better suited for use in Gene Ontology. We also deduce that there seems to be correlation between semantic similarity in the GO annotation and gene expression for the three GO ontologies. We show that this correlation is negligible up to a certain semantic similarity value; then, for higher similarity values, the relationship trend becomes almost linear. These results can be used to augment the knowledge provided by clustering algorithms and in the development of bioinformatic tools for finding and characterizing gene products.

Algorithms↗