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Rare germline copy number variants in colorectal cancer predisposition characterized by exome sequencing analysis

Journal of Genetics and Genomics 2018年第1期45卷 41-45页

作者： Sebastia Franch-Exposito Clara Esteban-Jurado Pilar Garre Isabel Quintanilla Saray Duran-Sanchon Marcos Diaz-Gay Laia Bonjoch Miriam Cuatrecasas Esther Samper Jenifer Munoz Teresa Ocana Sabela Carballal Maria Lopez-Ceron Antoni Castells Maria Vila-Casadesus Sophia Derdak Steven Laurie Sergi Beltran Jaime carvajal Luis Bujanda Clara Ruiz-Ponte Jordi Camps Meritxell Gironella juan jose lozano Francesc Balaguer Joaquin Cubiella Trinidad Caldes Sergi Castellvi-Bel Gastroenterology Department Hospital Clinic de Barcelona August Pi i Sunyer Biomedical Research Institute CIBER of Hepatic and Digestive Diseases University of Barcelona Barcelona 08036 Spain Molecular Oncology Laboratory Hospital Clinico San Carlos Health Research Institute of the Hospital Clinico San Carlos Madrid 28040 Spain Department of Pathology Hospital Clinic de Barcelona Barcelona 08036 Spain EPICOLON consortium Bioinformatics Platform CIBER of Hepatic and Digestive Diseases Barcelona 08036 Spain National Center of Genomic Analysis Science Park of Barcelona Barcelona 08028 Spain Andalusian Developmental Biology Institute CSIC-Pablo de Olavide University-Andalusian Regional Government SeviUa 41013 Spain Gastroenterology Department Hospital Donostia-Biodonostia Institute CIBER of Hepatic and Digestive Diseases University of the Basque Country (UPV/EHU) San Sebastian 20080 Spain Galician Public Foundation of Genomic Medicine (FPGMX) CIBER of Rare Diseases Genomics Medicine Group Hospital Clinico Universitario University of Santiago de Compostela Santiago de Cornpostela 15706 Spain Castroenterology Department Complexo Hospitalario Universitario de Ourense Ourense Biomedical Research Institute Ourense 32005 Spain

Colorectal cancer （CRC） is one of the most common neoplasms and an important cause of mortality worldwide （http：//globocan. ***]）. Approximately 35% of the variation in CRC susceptibility is likely due to heritable factors （Lichtenstein et al., 2000}. Genetic variations in the human genome include single nucleotide variants （SNVs）, short insertions and deletions, and larger structural variants resulting in gain or loss of genomic DNA larger than 1 kb, such as copy number variants （CNVs）. Leaving aside the importance of CNVs in sporadic tumor development, these variants can also be present in the germline DNA of healthy individuals from the general population and be considered polymorphic.

关键词： CRC TTF

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A PREDICTOR MODIFICATION TO THE EBDF METHOD FOR STIFF SYSTEMS

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Journal of Computational Mathematics 2011年第2期29卷 199-214页

作者： Elisabete Alberdi juan jose Anza Lea Artibai Ikastetxea Xemein Avenue 19 48270 Markina-Xemein (Vizcaya) Spain Department of Applied Mathematics ETS de Ingenieria de Bilbao Universidad del Pais Vasco Alameda de Urquijo s/n 48013 Bilbao Spain

In this paper we modify the EBDF method using the NDFs as predictors instead of BDFs. This modification, that we call ENDF, implies the local truncation error being smaller than in the EBDF method without losing too much stability. We will also introduce two more changes, called ENBDF and EBNDF methods. In the first one, the NDF method is used as the first predictor and the BDF as the second predictor. In the EBNDF, the BDF is the first predictor and the NDF is the second one. In both modifications the local truncation error is smaller than in the EBDF. Moreover, the EBNDF method has a larger stability region than the EBDF.

关键词： Backward differentiation formula (BDF) EBDF Predictor Stability Stiff Systems.

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Phenotypic plasticity in Drosophila cactophilic species the effect of competition, density, and breeding sites

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Insect Science 2017年第4期24卷 675-683页

作者： juan jose Fanara Victoria Werenkraut Departamento de Ecologia Genetica y Evolucion Instituto de Ecologia GeneUca y Evolucion de Buenos Aires (CONICET-UBA) Facultad de Ciencias Exactas y Naturales Ciudad Universitaria Pabellon II Universidad de Buenos Aires Buenos Aires Laboratorio Ecotono Centro Regional Universitario Bariloche Universidad Nacional del ComahuelINIBIOMA-CONICET Quintral 1250 Bariloche Rio Negro Argentina

Changes in the environmental conditions experienced by naturally occurring populations are frequently accompanied by changes in adaptive traits allowing the organ- ism to cope with environmental unpredictability. Phenotypic plasticity is a major aspect of adaptation and it has been involved in population dynamics of interacting species. In this study, phenotypic plasticity （i,e., environmental sensitivity） of morphological adap- tive traits were analyzed in the cactophilic species Drosophila buzzatii and Drosophila koepferae （Diptera： Drosophilidae） considering the effect of crowding conditions （low and high density）, type of competition （intraspecific and interspecific competition） and cacti hosts （Opuntia and Columnar cacti）. All traits （wing length, wing width, thorax length, wing loading and wing aspect） showed significant variation for each environmental factor considered in both Drosophila species. The phenotypic plasticity pattern observed for each trait was different within and between these cactopbilic Drosophila species depending on the environmental factor analyzed suggesting that body size-related traits respond almost independently to environmental heterogeneity. The effects of ecological factors analyzed in this study are discussed in order to elucidate the causal factors investigated （type of com- petition, crowding conditions and alternative host） affecting the election of the breeding site and/or the range of distribution of these cactophilic species.

关键词： adaptation body size colonization Drosophila cactophilic species wingaspect wing loading

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THE INTEGRATION OF STIFF SYSTEMS OF ODEs USING NDFs AND MEBDFs

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Journal of Computational Mathematics 2013年第2期31卷 175-189页

作者： Elisabete Alberdi Celaya juan jose Anza Department of Applied Mathematics EUIT de Minas y Obras P(tblicas Universidad del Pals Vasco UPV/EHU Colina de Beurko s/n 48902 Barakaldo Spain Department of Applied Mathematics ETS de Ingenieria de Bilbao Universidad del Pals Vasco UPV/EHU Alameda de Urquijo s/n 48013 Bilbao Spain

In this paper we modify the MEBDF method using the NDFs as predictors instead of the BDFs. We have done it in three different ways： changing both predictors of the MEBDF, changing only the first predictor and changing only the second one. We have called the new methods MENDF, MENBDF and MEBNDF respectively. The new methods are A-stable up to order 4 and the stability properties of the new methods are better than the MEBDF method.

关键词： BDF NDF MEBDF Stiff ODEs Stability.

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A neural network to predict reactor core behaviors

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Nuclear Science and Techniques 2014年第1期25卷 75-80页

作者： juan jose Ortiz-Servin David A.Pelta jose Alejro Castillo Instituto Nacional de Investigaciones Nucleares Carretera Mexico Toluca S/NLa Marquesa OcoyoacacEstado de Mexico ETS Ingenieria Informatica y Telecomunicaciones Universidad de GranadaC/Daniel Saucedo Aranda

The global fuel management problem in BWRs(Boiling Water Reactors) can be understood as a very complex optimization problem,where the variables represent design decisions and the quality assessment of each solution is done through a complex and computational expensive *** last aspect is the major impediment to perform an extensive exploration of the design space,mainly due to the time lost evaluating non promising *** this work,we show how we can train a Multi-Layer Perceptron(MLP) to predict the reactor behavior for a given *** trained MLP is able to evaluate the configurations immediately,thus allowing performing an exhaustive evaluation of the possible configurations derived from a stock of fuel lattices,fuel reload patterns and control rods *** our particular problem,the number of configurations is approximately 7.7×10^(10);the evaluation with the core simulator would need above 200 years,while only 100hours were required with our approach to discern between bad and good *** later were then evaluated by the simulator and we confirm the MLP *** good core configurations reached the energy requirements,satisfied the safety parameter constrains and they could reduce uranium enrichment costs.

关键词：神经网络预测行为质量评估堆芯沸水反应堆多层感知器 MLP 优化问题

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Impact of endoscopic ultrasound-guided fine needle biopsy for diagnosis of pancreatic masses

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World Journal of Gastroenterology 2007年第2期13卷 289-293页

作者： Julio Iglesias-Garcia Enrique Dominguez-Munoz Antonio lozano-Leon Ihab Abdulkader jose Larino-Noia jose Antunez Jeronimo Forteza Gastroenterology Department University Hospital Santiago de Compostela Spain Foundation for Research in Digestive Diseases Santiago de Compostela Spain Foundation for Research in Digestive Diseases Santiago de Compostela Spain Pathology Department University Hospital Santiago de Compostela Spain

AIM： To evaluate the diagnostic accuracy of histological evaluation of pancreatic tissue samples obtained by a modified method for recovering and processing the endoscopic ultrasound （EUS）-guided fine needle aspiration （FNA） material in the differential diagnosis of pancreatic solid masses. METHODS： Sixty-two consecutive patients with pancreatic masses were prospectively studied. EUS was performed by the linear scanning Pentax FG-38UX echoendoscope. Three FNAs （22G needle） were carried out during each procedure. The materials obtained with first and second punctures were processed for cytological study. Haterials of the third puncture were recovered into 10% formol solution by careful injection of saline solution through the needle, and processed for histological study. RESULTS： Length of the core specimen obtained for histological analysis was 6.5±5.3 mm （range 1-22 mm）. Cytological and histological samples were considered as adequate in 51 （82.3%） and 52 cases （83.9%）, respectively. Overall sensitivity of both pancreatic cytology and histology for diagnosis of malignancy was 68.4%. Conbary to cytology, histology was able to diagnose tumours other than adenocarcinomas, and all cases of inflammatory masses. Combination of cytology and histology allowed obtaining an adequate sample in 56 cases （90.3%）, with a global sensitivity of 84.21%, specificity of 100% and an overall accuracy of 90.32%. The complication rate was 1.6%.CONCLUSION： Adequate pancreatic core specimens for histological examination can be obtained by EUS-guided FNA. This technique is mainly useful for the diagnosis of different types of pancreatic tumours and evaluation of benign diseases.

关键词： Endoscopic ultrasound Fine needle aspiration Cytology Biopsy Pancreatic cancer

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Selective intestinal decontamination for the prevention of early bacterial infections after liver transplantation

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World Journal of Gastroenterology 2016年第26期22卷 5950-5957页

作者： Elena Resino Rafael San-juan jose Maria Aguado Unit of Infectious Diseases 12 de Octubre University Hospital

Bacterial infection in the first month after liver transplantation is a frequent complication that poses a serious risk for liver transplant recipients as contributes substantially to increased length of hospitalization and hospital costs being a leading cause of death in this period. Most of these infections are caused by gramnegative bacilli, although gram-positive infections, especially Enterococcus sp. constitute an emerging infectious problem. This high rate of early postoperative infections after liver transplant has generated interest in exploring various prophylactic approaches to surmount this problem. One of these approaches is selective intestinal decontamination(SID). SID is a prophylactic strategy that consists of the administration of antimicrobials with limited anaerobicidal activity in order to reduce the burden of aerobic gram-negative bacteria and/or yeast in the intestinal tract and so prevent infections caused by these organisms. The majority of studies carried out to date have found SID to be effective in the reduction of gram-negative infection, but the effect on overall infection is limited due to a higher number of infection episodes by pathogenic enterococci and coagulase-negative staphylococci. However, difficulties in general extrapolation of the favorable results obtained in specific studies together with the potential risk of selection of multirresistant microorganisms has conditioned controversy about the routinely application of these strategies in liver transplant recipients.

关键词： Selective intestinal decontamination Liver transplant Infection Gram-negative bacterial infection Gram-positive bacterial infection Multirresistant

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Effect of genistein supplementation of thawing medium on characteristics of frozen human spermatozoa

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Asian Journal of Andrology 2010年第3期12卷 431-441,I0012页

作者： juan Carlos Martinez-Soto juan de DiosHourcade Alfonso Gutierrez-Adan jose Lorenzo Landeras Joaquin Gadea Department of Physiology School of Veterinary Murcia University Murcia 30100 Spain IVI- MURCIA Murcia 30007 Spain Department of Animal Reproduction INIA Madrid 28040 Spain

In this study, we evaluated the effects of genistein supplementation of the thawing extender on frozen-thawed human semen parameters. We analyzed the effect of supplementation on sperm motility, capacitation （membrane lipid disorder）, reactive oxygen species （ROS） generation, chromatin condensation and DNA damage. Using this preliminary information, it maybe possible to improve the cryopreservation process and reduce the cellular damage. We have confirmed that the isoflavone genistein （10 μmol L-1） has antioxidant properties on the frozen-thawed spermatozoa. This results in a decreased ROS production that shows a slight improvement in the sperm motility, and decreases the membrane lipid disorder and DNA damage caused by cryopreservation. These results suggest an effect of genistein on sperm functionality that could be of interest for assisted reproduction treatments using frozen- thawed human spermatozoa, but further studies will be necessary to confirm our findings and to evaluate the possible clinical applications.

关键词： antioxidants cryopreservation DNA damage genistein isoflavones sperm motility

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Brent *** Texas Intermediate in the US petro derivatives price formation

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Petroleum Science 2024年第1期21卷 729-739页

作者： Alejandro Almeida Antonio A.Golpe juan Manuel Martín-Alvarez jose Carlos Vides Universidad Internacional de La Rioja Department of Quantitative Methods for Economics and BusinessLa RiojaSpain University of Huelva Department of Economics and Centro de Estudios Avanzados en FisicaMatematicas y Computacion and ICEIHuelvaSpain Complutense University of Madrid Department of Applied and Structural Economics and History and ICEIMadridSpain

In this paper,we apply the spatial panel model to explore the relationship between the dynamic of two types of crude oil prices(WTI and Brent crude oil)and their refined products over *** the turbulent months of 2011,when Cushing Oklahoma had reached capacity and the crude oil export ban removal in 2015 as breakpoints,we apply this method both in the full sample and the three resultant ***,results suggest our results show that both WTI and Brent display very similar behaviour with the refined ***,when attending to each regime,results derived from the first and third regimes are quite similar to the full sample ***,during the second regime,Brent crude oil became the benchmark in the petrol market,and it influenced the distillate ***,our model can let us determine the price-setters and price-followers in the price formation mechanism through refined *** results possess important considerations to policymakers and the market participants and the price formation.

关键词： Crude oil prices Spatial panel model Refined products Price formation

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Photosynthetic and Molecular Markers of CO_2-mediated Photosynthetic Downregulation in Nodulated Alfalfa

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Journal of Integrative Plant Biology 2013年第8期55卷 721-734页

作者： Alvaro Sanz-Sez Gorka Erice Iker Aranjuelo Ricardo Aroca juan Manuel Ruíz-lozano Jone Aguirreolea juan Jos Irigoyen Manuel Sanchez-Diaz Department of Plant Biology University of NavarraPamplonaE-31008Spain Department of Plant Biology University of BarcelonaBarcelonaE-8028Spain Department of Plant Biology University of Illinois at Urbana-Champaign61801USA Agrobiotechnology Institute Public University of NavarraMutilva BajaE-31192Spain Department of Soil Microbiology and Symbiotic Systems Zaidin Experimental Station(CSIC)GranadaE-18008.Spain

Elevated CO2 leads to a decrease in potential net photosynthesis in long-term experiments and thus to a reduction in potential growth. This process is known as photosynthetic downregulation. There is no agreement on the definition of which parameters are the most sensitive for detecting CO2 acclimation. In order to investigate the most sensitive photosynthetic and molecular markers of CO2 acclimation, the effects of elevated CO2, and associated elevated temperature were analyzed in alfalfa plants inoculated with different Sinorhizobium meliloti strains. Plants （Medicago sativa L. cv. Aragon） were grown in summer or autumn in temperature gradient greenhouses （TGG）. At the end of the experiment, all plants showed acclimation in both seasons, especially under elevated summer temperatures. This was probably due to the lower nitrogen （N） availability caused by decreased N2-fixation under higher temperatures. Photosynthesis measured at growth CO2 concentration, rubisco in vitro activity and maximum rate of carboxylation were the most sensitive parameters for detecting downregulation. Severe acclimation was also related with decreases in leaf nitrogen content associated with declines in rubisco content （large and small subunits） and activity that resulted in a drop in photosynthesis. Despite the sensitivity of rubisco content as a marker of acclimation, it was not coordinated with gene expression, possibly due to a lag between gene transcription and protein translation.

关键词： Carbon dioxide Medicago sativa (alfalfa) photosynthetic downregulation RbcL and RbcS Sinorhizobium meliloti.

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