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Search Results: 1 - 10 of 325325 matches for " K. Baca-López "
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Information-theoretical analysis of gene expression data to infer transcriptional interactions
Baca-López, K.;Hernández-Lemus, E.;Mayorga, M.;
Revista mexicana de física , 2009,
Abstract: the majority of human diseases are related with the dynamic interaction of many genes and their products as well as environmental constraints. cancer (and breast cancer in particular) is a paradigmatic example of such complex behavior. since gene regulation is a non-equilibrium process, the inference and analysis of such phenomena could be done following the tenets of non-equilibrium physics. the traditional programme in statistical mechanics consists in inferring the joint probability distribution for either microscopic states (equilibrium) or mesoscopic-states (non-equilibrium), given a model for the particle interactions (e.g. the potentials). an inverse problem in statistical mechanics, in the other hand, is based on considering a realization of the probability distribution of micro- or meso-states and used it to infer the interaction potentials between particles. this is the approach taken in what follows. we analyzed 261 whole-genome gene expression experiments in breast cancer patients, and by means of an information-theoretical analysis, we deconvolute the associated set of transcriptional interactions, i.e. we discover a set of fundamental biochemical reactions related to this pathology. by doing this, we showed how to apply the tools of non-linear statistical physics to generate hypothesis to be tested on clinical and biochemical settings in relation to cancer phenomenology.
Information-theoretical analysis of gene expression data to infer transcriptional interactions
K. Baca-López,E. Hernández-Lemus,M. Mayorga
Revista mexicana de física , 2009,
Abstract: La mayoría de las enfermedades humanas están relacionadas con la interacción de muchos genes, y con condicionantes ambientales, lo que las hace fenómenos complejos. El análisis de las interacciones bioquímicas relacionadas se basa frecuentemente en la consideración de las relaciones de regulación genética. Puesto que la regulación genética es un proceso fuera del equilibrio, la inferencia y el análisis de ésta puede hacerse siguiendo los principios de la termodinámica irreversible y la mecánica estadística fuera del equilibrio. El enfoque tradicional de la mecánica estadística es inferir la distribución de probabilidad conjunta para los estados del sistema en términos de un modelo para las interacciones. Un problema inverso en mecánica estadística consiste en considerar una realización de la distribución de probabilidad y emplearla para inferir las interacciones entre las partículas. Tomamos este enfoque para analizar 261 experimentos de expresión de mRNA de genoma completo, en pacientes con cáncer de mama y, a través de una medida basada en la teoría de la información descubrir el conjunto de interacciones transcripcionales asociadas. Mostramos como aplicar las herramientas de la física estadística no-lineal para generar hipótesis (es decir, el conjunto de interacciones inferidas) que pueden ser probadas en ensayos clínicos y bioquímicos con relación a la fenomenología del cáncer.
The role of master regulators in gene regulatory networks
E. Hernández-Lemus,K. Baca-López,R. Lemus,R. García-Herrera
Physics , 2015, DOI: 10.4279/PIP.070011
Abstract: Gene regulatory networks present a wide variety of dynamical responses to intrinsic and extrinsic perturbations. Arguably, one of the most important of such coordinated responses is the one of amplification cascades, in which activation of a few key-responsive transcription factors (termed master regulators, MRs) lead to a large series of transcriptional activation events. This is so since master regulators are transcription factors controlling the expression of other transcription factor molecules and so on. MRs hold a central position related to transcriptional dynamics and control of gene regulatory networks and are often involved in complex feedback and feedforward loops inducing non-trivial dynamics. Recent studies have pointed out to the myocyte enhancing factor 2C (MEF2C, also known as MADS box transcription enhancer factor 2, polypeptide C) as being one of such master regulators involved in the pathogenesis of primary breast cancer. In this work, we perform an integrative genomic analysis of the transcriptional regulation activity of MEF2C and its target genes to evaluate to what extent are these molecules inducing collective responses leading to gene expression deregulation and carcinogenesis. We also analyzed a number of induced dynamic responses, in particular those associated with transcriptional bursts, and nonlinear cascading to evaluate the influence they may have in malignant phenotypes and cancer.
The Role of Master Regulators in the Metabolic/Transcriptional Coupling in Breast Carcinomas
Karol Baca-López, Miguel Mayorga, Alfredo Hidalgo-Miranda, Nora Gutiérrez-Nájera, Enrique Hernández-Lemus
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0042678
Abstract: Metabolic transformations have been reported as involved in neoplasms survival. This suggests a role of metabolic pathways as potential cancer pharmacological targets. Modulating tumor's energy production pathways may become a substantial research area for cancer treatment. The significant role of metabolic deregulation as inducing transcriptional instabilities and consequently whole-system failure, is thus of foremost importance. By using a data integration approach that combines experimental evidence for high-throughput genome wide gene expression, a non-equilibrium thermodynamics analysis, nonlinear correlation networks as well as database mining, we were able to outline the role that transcription factors MEF2C and MNDA may have as main master regulators in primary breast cancer phenomenology, as well as the possible interrelationship between malignancy and metabolic dysfunction. The present findings are supported by the analysis of 1191 whole genome gene expression experiments, as well as probabilistic inference of gene regulatory networks, and non-equilibrium thermodynamics of such data. Other evidence sources include pathway enrichment and gene set enrichment analyses, as well as motif comparison with a comprehensive gene regulatory network (of homologue genes) in Arabidopsis thaliana. Our key finding is that the non-equilibrium free energies provide a realistic description of transcription factor activation that when supplemented with gene regulatory networks made us able to find deregulated pathways. These analyses also suggest a novel potential role of transcription factor energetics at the onset of primary tumor development. Results are important in the molecular systems biology of cancer field, since deregulation and coupling mechanisms between metabolic activity and transcriptional regulation can be better understood by taking into account the way that master regulators respond to physicochemical constraints imposed by different phenotypic conditions.
Whole Genome Gene Expression Analysis Reveals Casiopeína-Induced Apoptosis Pathways
Alejandra Idan Valencia-Cruz, Laura I. Uribe-Figueroa, Rodrigo Galindo-Murillo, Karol Baca-López, Anllely G. Gutiérrez, Adriana Vázquez-Aguirre, Lena Ruiz-Azuara, Enrique Hernández-Lemus, Carmen Mejía
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0054664
Abstract: Copper-based chemotherapeutic compounds Casiopeínas, have been presented as able to promote selective programmed cell death in cancer cells, thus being proper candidates for targeted cancer therapy. DNA fragmentation and apoptosis–in a process mediated by reactive oxygen species–for a number of tumor cells, have been argued to be the main mechanisms. However, a detailed functional mechanism (a model) is still to be defined and interrogated for a wide variety of cellular conditions before establishing settings and parameters needed for their wide clinical application. In order to shorten the gap in this respect, we present a model proposal centered in the role played by intrinsic (or mitochondrial) apoptosis triggered by oxidative stress caused by the chemotherapeutic agent. This model has been inferred based on genome wide expression profiling in cervix cancer (HeLa) cells, as well as statistical and computational tests, validated via functional experiments (both in the same HeLa cells and also in a Neuroblastoma model, the CHP-212 cell line) and assessed by means of data mining studies.
Polyamide Fibers Covered with Chlorhexidine: Thermodynamic Aspects  [PDF]
E. Giménez-Martín, M. López-Andrade, J. A. Moleón-Baca, M. A. López, A. Ontiveros-Ortega
Journal of Surface Engineered Materials and Advanced Technology (JSEMAT) , 2015, DOI: 10.4236/jsemat.2015.54021
Abstract: Results of dynamic and equilibrium of sorption of a reactive dye Remazol Brilliant Blue, and a bactericidal agent, Digluconate of Chlorhexidine over Polyamide fibers are presented with the aim of supplying the fiber with bactericidal properties. However, adsorption of Chlorhexidine onto Polyamide is scarce due to the lack of interactions between the reactive groups of the fiber and the antiseptic molecule. Therefore, in order to provide the fiber surface with anionic groups, fiber has been previously dyed with Remazol Brilliant Blue which increases the negative charge of the fiber surface due to the presence of its sulfonate end groups. Thermodynamic parameters of equilibrium sorption in the two situations, fiber/dye and fiber-dye/Chlorhexidine, have been analyzed, as function of the temperature, pH and concentration of the dye in the pretreatment. Results show that when sorption of Remazol Brilliant Blue reaches the value of about 50 mmol/ kg at the higher temperature and concentration tested, the amount of Chlorhexidine adsorbed exhibits its maximum value which is 6 mmol/kg. Both processes, adsorption of Remazol Brilliant Blue and adsorption of Chlorhexidine, fit well to Langmuir adsorption model, suggesting the existence of some kinds of specific interactions between adsorbent and adsorbate. Thermodynamic functions show that the interaction is endothermic and spontaneous in all the rage of temperature tested. The kinetic studies show that sorption of Remazol Brilliant Blue is better described by pseudo-first order model, while sorption of Chlorhexidine fits better to pseudo-second order model, and seems to be quicker process. According to the obtained results, chemical interaction between the vinyl-sulfone group of Remazol Brilliant Blue and the amine groups of Polyamide fiber, followed by electrostatic interactions between the guanine group of the Chlorhexidine and the sulfonate group of the dye must be considered in order to explain the adsorption process.
Situational Diagnosis of the Social Sphere of Elders Living in Retirement Homes  [PDF]
Verónica Benavides Pando, Martha Ornelas Contreras, Jesús Enrique Peinado Pérez, Juan Cristóbal Barrón Luján, Lepoldo Refugio López Baca
Advances in Aging Research (AAR) , 2015, DOI: 10.4236/aar.2015.42006
Abstract: A situational diagnosis of the social sphere of elder permanent residents at retirement homes in Chihuahua City was created with the aid of the Social Resource Scale instrument. From the 51 participants, there were 30 female and 21 male elders. The results and conclusions of the present study highlight two major needs: a systematic assessment of permanent residents in retirement homes and the implementation of a physical activation program. The proposed physical activation program must focus on both, the recovery of motor independence and the increase of socialization activities which allows members of the retired community to improve their daily routine performance and lessens the work load on their caretakers.
Características ecocardiográficas da cardiomiopatia n?o-compactada: diagnóstico perdido ou err?neo
Martínez-Baca López, Francisco;Alonso Bravo, Rosa Marisol;Rodríguez Huerta, Domingo Arturo;
Arquivos Brasileiros de Cardiologia , 2009, DOI: 10.1590/S0066-782X2009000800024
Abstract: non-compaction cardiomyopathy is a rare disease, anatomically characterized by a prominent trabecular pattern and deep intertrabecular recesses. its clinical manifestations include severe left ventricular dysfunction, arrhythmias, systemic embolism, and sudden death. in this report, two cases of patients of different ages with non-compaction cardiomyopathy are described: a male schoolboy whose pathology was associated with mitral stenosis and regurgitation and a 50-year-old female with history of high blood pressure and cardiac failure.
Fusión de un tercer molar mandibular con un cuarto molar supernumerario
López Carriches,C.; Leco Berrocal,I.; Baca Pérez-Bryan,R.;
Revista Espa?ola de Cirugía Oral y Maxilofacial , 2008, DOI: 10.4321/S1130-05582008000500005
Abstract: dental fusion is the union of two tooth buds that normally are separated, while gemination is defined as an attempt by a single tooth bud to divide. the fusion and gemination of molars is uncommon in permanent teeth. we report a clinical case of a right lower third molar fused to a supernumerary fourth molar in a 36-year-old male patient with repeated episodes of inflammation. after the radiologic study, the semi-impacted third molar was extracted under local anesthesia. the literature was reviewed.
Fusión de un tercer molar mandibular con un cuarto molar supernumerario Fusion of mandibular third molar with supernumerary fourth molar
C. López Carriches,I. Leco Berrocal,R. Baca Pérez-Bryan
Revista Espa?ola de Cirugía Oral y Maxilofacial , 2008,
Abstract: La fusión dental es la unión de dos gérmenes dentales normalmente separados, mientras que la geminación se define como el intento de división de un único germen dental. La fusión y geminación de molares es poco frecuente en la dentición permanente. Describimos un caso clínico de un tercer molar inferior derecho fusionado a un cuarto molar supernumerario en un paciente varón de 36 a os que ha presentado repetidos episodios de pericoronaritis. Tras el estudio radiológico se realiza la exodoncia del cordal semiincluido bajo anestesia local. Llevamos a cabo una revisión bibliográfica al respecto. Dental fusion is the union of two tooth buds that normally are separated, while gemination is defined as an attempt by a single tooth bud to divide. The fusion and gemination of molars is uncommon in permanent teeth. We report a clinical case of a right lower third molar fused to a supernumerary fourth molar in a 36-year-old male patient with repeated episodes of inflammation. After the radiologic study, the semi-impacted third molar was extracted under local anesthesia. The literature was reviewed.
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