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Design optimization of multilayer perceptron neural network by ant colony optimization applied to engine emissions data

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Science China(Technological Sciences) 2019年第6期62卷 1055-1064页

作者： MARTINEZ-MORALES jose QUEJ-COSGAYA Hector LAGUNAS-jimenez jose PALACIOS-HERNANDEZ Elvia MORALES-SALDANA Jorge Faculty of Engineering Autonomous University of Campeche Campeche 24039 Mexico Faculty of Sciences Autonomous University of San Luis Potosi San Luis Potosi 78290 Mexico Faculty of Engineering Autonomous University of San Luis Potosi San Luis Potosi 78290 Mexico

A multilayer perceptron(MLP) artificial neural network(ANN) model has been optimized by the multi-objective ant colony optimization(MOACO) algorithm, which uses three objective functions. A sensitivity analysis to choose MOACO parameter values is carried out by calculating hypervolume metric, and the proposed approach adopts the Vlsekriterijumska Optimizacija I Kompromisno Resenje(VIKOR) decision method to choose final compromised solution on the Pareto front obtained from MOACO. As a result, we used the MLP-MOACO developed model to estimate the value of engine emissions of NOxin a four stroke, spark ignition(SI) gasoline engine and observed acceptable correlation coefficient(R^2) of 0.99978.

关键词： ant colony optimization multilayer perceptron artificial neural networks hypervolume engine emissions

Emerging concepts in the care of patients with cirrhosis and septic shock

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World Journal of Hepatology 2023年第4期15卷 497-514页

作者： jose Victor jimenez Guadalupe Garcia-Tsao Saad Saffo Section of Digestive Diseases Yale School of MedicineNew HavenCT 06520United States

Septic shock impacts approximately 6% of hospitalized patients with cirrhosis and is associated with high rates of morbidity and mortality. Although a number of landmark clinical trials have paved the way for incremental improvements in the diagnosis and management of septic shock in the general population, patients with cirrhosis have largely been excluded from these studies and critical knowledge gaps continue to impact the care of these individuals. In this review,we discuss nuances in the care of patients with cirrhosis and septic shock using a pathophysiology-based approach. We illustrate that septic shock may be challenging to diagnose in this population in the context of factors such as chronic hypotension, impaired lactate metabolism, and concomitant hepatic encephalopathy. Furthermore, we demonstrate that the application of routine interventions such as intravenous fluids, vasopressors, antibiotics, and steroids should be carefully considered among those with decompensated cirrhosis in light of hemodynamic, metabolic, hormonal, and immunologic disturbances. We propose that future research should include and characterize patients with cirrhosis in a systematic manner, and clinical practice guidelines may need to be refined accordingly.

关键词： Cirrhosis Septic shock Intravenous fluids Vasopressors Antibiotics Steroids

Alternative splicing enhances transcriptome complexity in desiccating seeds

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Journal of Integrative Plant Biology 2016年第12期58卷 947-958页

作者： Arunkumar Srinivasan jose M. jimenez-Gomez Fabio Fornara Wim J. J. Soppe Vittoria Brambilla Department of Plant Breeding and Genetics Max Planck Institute for Plant Breeding Research Cologne Germany Open Analytics Antwerp Belgium Institut Jean-Pierre Bourgin Institut National de la Recherche Agronomique Versailles France University of Milan Department of Biosciences Milano 20133 Italy University of Milan Department of Agricultural and Environmental Sciences via Celoria 220133 Milano Italy

Before being dispersed in the environment, mature seeds need to be dehydrated. The survival of seeds after dispersal depends on their low hydration in combination with high desiccation tolerance. These characteristics are estab- lished during seed maturation. Some key seed maturation genes have been reported to be regulated by alternative splicing （AS）. However, so far AS was described only for single genes and a comprehensive analysis of AS during seed maturation has been lacking. We investigated gene expression and AS during Arabidopsis thaliana seed development at a global level, before and after desiccation. Bioinformatics tools were developed to identify differentially spliced regions within genes. Our data suggest the importance and shows the peculiar features of AS during seed desiccation. We identified AS in 347o of genes that are expressed at both timepoints before and after desiccation. Most of these AS transcript variants had not been found before in other tissues. Among the AS genes some seed master regulators could be found. Interestingly, 6% of all expressed transcripts were not transcriptionally regulated during desiccation, but only modified by AS. We propose that AS should be more routinely taken into account in the analysis of transcriptomic data to prevent overlooking potentially important regulators.

关键词： Alternative splicing Arabidopsis thaliana seed desiccation

Metaheuristic post-optimization of the NIST repository of covering arrays

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CAAI Transactions on Intelligence Technology 2017年第1期2卷 31-38页

作者： jose Torres-jimenez Arturo Rodriguez-Cristerna CINVESYAV-Yamaulipas Information Technology Laboratory Km. 5.5 Carretera Cd. Victoria Yamaulipas Mexico

Construction of Covering Arrays （CA） with minimum possible number of rows is challenging. Often the available CA have redundant combinatorial interaction that could be removed to reduce the number of rows. This paper addresses the problem of removing redundancy of CA using a metaheuristic post- optimization （MPO） approach. Our approach consists of three main components： a redundancy detector （RD）; a row reducer （RR）; and a missing-combinations reducer （MCR）. The MCR is a metaheuristic component implemented using a simulated annealing algorithm. MPO was instantiated with 21,964 CA taken from the National Institute of Standards and Technology （NIST） repository. It is a remarkable result that this instantiation of MPO has delivered 349 new upper bounds for these CA.

关键词： Covering arrays NIST repository of covering arrays Metaheuristic post-processing algorithms

Discovery of unique African Helicobacter pylori CagAmultimerization motif in the Dominican Republic

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World Journal of Gastroenterology 2020年第45期26卷 7118-7130页

作者： Takaaki Ono Modesto Cruz Hiroyuki Nagashima Phawinee Subsomwong Junko Akada Takashi Matsumoto Tomohisa Uchida Rumiko Suzuki Celso Hosking jose A jimenez Abreu Yoshio Yamaoka Department of Environmental and Preventive Medicine Oita University Faculty of MedicineYufu 879-5593Japan Criminal Investigation Laboratory Oita Prefectural Police HeadquartersOita 870-1117Japan Institute of Microbiology and Parasitology IMPAFaculty of ScienceAutonomous University of Santo DomingoSanto Domingo 10103Dominican Republic Department of Biomedical Research National Institute of Medicine and Diagnostic ImagingSanto Domingo 10107Dominican Republic Department of Gastroenterology Hokkaido Cancer CenterSapporo 003-0804Japan Department of Molecular Pathology Oita University Faculty of MedicineYufu 879-5593Japan Dominican-Japanese Digestive Disease Center Dr Luis E.Aybar Health and Hygiene CitySanto Domingo 10302Dominican Republic Department of Medicine Gastroenterology and Hepatology SectionBaylor College of MedicineHoustonTX 77030United States

BACKGROUND Helicobacter pylori(***)colonizes the human stomach and is a major cause of peptic ulcer disease and gastric ***,although the prevalence of *** is high in Africa,the incidence of gastric cancer is low,and this phenomenon is called to be African *** CagA protein produced by *** is the most studied virulence *** carcinogenic potential of CagA is associated with the Glu-Pro-Ile-Tyr-Ala(EPIYA)patterns and CagAmultimerization(CM)*** To better understand the EPIYA patterns and CM motifs of the cagA *** Gastric mucosal biopsy specimens were obtained from 258 patients with dyspepsia living in the Dominican Republic,from which 120 *** strains were *** the bacterial DNA extraction,the EPIYA pattern and CM motif genotypes were determined using a polymerase chain reaction-based *** population structure of the Dominican Republic strains was analyzed using multilocus sequence typing(MLST).Peptic ulcer disease and gastric cancer were identified via endoscopy,and gastric cancer was confirmed by *** scores of the gastric mucosa were evaluated using the updated Sydney *** All CagA-positive strains carried the Western-type CagA according to the identified EPIYA ***-seven kinds of CM motifs were *** the typical Western CM motif(FPLKRHDKVDDLSKVG)was observed most frequently,the typical East Asian CM motif(FPLRRSAAVNDLSKVG)was not ***,“FPLRRSAKVEDLSKVG”,similar to the typical East Asian CM motif,was found in 21 *** this type was significantly more frequent in strains classified as hpAfrica1 using MLST analysis(P=0.034),we termed it Africa1-CM(Af1-CM).A few hpEurope strains carried the Af1-CM motif,but they had a significantly higher ancestral Africa1 component than that of those without the Af1-CM motif(P=0.030).In 30 cagA-positive strains,the"GKDKGPE"motif was observed immediately upstream of the EPIYA motif in

关键词： Helicobacter pylori CagA CagA 3'region CagA-multimerization motif Glu-Pro-Ile-Tyr-Ala motif Dominican Republic

Ground-Based LiDAR Improves Phenotypic Repeatability of Above-Ground Biomass and Crop Growth Rate in Wheat

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Plant Phenomics 2020年第1期2卷 138-148页

作者： David M.Deery Greg J.Rebetzke jose A.jimenez-Berni Anthony G.Condon David J.Smith Kathryn M.Bechaz William D.Bovill CSIRO Agriculture and Food CanberraACTAustralia CSIRO Agriculture and Food YancoNSWAustralia NSW Department of Primary Industries YancoNSWAustralia

Highly repeatable,nondestructive,and high-throughput measures of above-ground biomass(AGB)and crop growth rate(CGR)are important for wheat improvement *** study evaluates the repeatability of destructive AGB and CGR measurements in comparison to two previously described methods for the estimation of AGB from LiDAR:3D voxel index(3DVI)and 3D profile index(3DPI).Across three field experiments,contrasting in available water supply and comprising up to 98 wheat genotypes varying for canopy architecture,several concurrent measurements of LiDAR and AGB were made from jointing to *** correlations at discrete events between AGB and the LiDAR-derived biomass indices were significant,ranging from 0.31(P<0:05)to 0.86(P<0:0001),providing confidence in the LiDAR indices as effective surrogates for *** repeatability of the LiDAR biomass indices at discrete events was at least similar to and often higher than AGB,particularly under water *** correlations between calculated CGR for AGB and the LiDAR indices were moderate to high and varied between ***,across all experiments,the repeatabilities of the CGR derived from the LiDAR indices were appreciably greater than those for AGB,except for the 3DPI in the water-limited *** our experiments,the repeatability of either LiDAR index was consistently higher than that of AGB,both at discrete time points and when CGR was *** findings provide promising support for the reliable use of ground-based LiDAR,as a surrogate measure of AGB and CGR,for screening germplasm in research and wheat breeding.

关键词： Wheat Biomass LiDAR

Protein Bodies in Cotyledon Cells Exhibit Differential Patterns of Legumin-Like Proteins Mobilization during Seedling Germinating States

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American Journal of Plant Sciences 2013年第12期4卷 2444-2454页

作者： jose C. jimenez-Lopez Maria C. Hernandez-Soriano School of Agriculture and Food Sciences Faculty of Science The University of Queensland Saint Lucia Australia The UWA Institute of Agriculture The University of Western Australia Perth Australia Department of Biochemistry Cell and Molecular Biology of Plants Estacion Experimental del Zaidin (EEZ) National Council for Scientific Research (CSIC) Granada Spain

Olive (Olea europaea L.) tree is one of the most extensive and important agricultural crop in Mediterranean countries due to its beneficial health and nutritional properties and its high economic value. Currently, olive tree constitutes the sixth most important cultivated plant in the world, spreading from the Mediterranean region of origin to new production areas such as Australia, South and North America and South Africa. However, the mobilization processes of storage materials i.e. reserve proteins during seed germination, which are largely involved in essential physiological process including plant growth and development, remain poorly understood. Morphometric and immunohistochemistry analyses of protein bodies contained in olive seed storage tissues, cotyledon and endosperm, were performed by using different microscopy techniques, including light (bright-field and fluorescence) microscopy and transmission electron microscopy. Furthermore, we used legumin-like proteins (11S-type globulins) as a molecular marker to study the mobilization of reserve proteins from PBs of cotyledons at germinating seedling stages by using immunofluorescence assays. Results demonstrated that cotyledon and endosperm are characterized by distinct PBs populations containing legumin-like proteins, distinctly discriminated by the number of PBs per cell and tissue, size, immunofluorescence and histochemical staining. These features reflect differential PBs biogenesis during development and maturation processes in olive seed tissues endosperm and cotyledon, in relation to proteins (polypeptides) final composition, SSPs processing and/or packaging during seed maturation. Three different mobilization patterns of legumin-like proteins were identified for the first time in cotyledon PBs during seedling germinating process. Mature proteins composition and/or processing, cell types and enzyme composition and/or differential activation have been discussed as key features determining how proteins m

关键词： 11S Globulins Cotyledon Endosperm In Vitro Germination Legumin-Like Proteins Olea europaea L. Protein Bodies Seed Proteins Mobilization

The Explicitly Covariant Stress-Energy-Momentum Balance Equation for Electromagnetism in Material Media

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Journal of Physical Science and Application 2012年第4期2卷 123-127页

作者： Ignacio Campos Flores jose Luis jimenez Ramirez Miguel Angel Lopez Marino Departamento de Fisica Facultad de Ciencias Universidad Naeional Aut6noma de Mdxico Apartado Postal 21-463 Mexieo D.F. 04000 Mdxico Departamento de Fisica Division de Ciencias Basicas e Ingenieria Universidad Aut6noma Metropolitana Iztapalapa Av. SanRafael Atlixco # 186 Col. Vicentina Apartado Postal 21-463 Mexico D. F. 04000 Mexico Departamento de Ingenieria Tecnol6gico de Monterrey Campus Central de Veracruz Av. E. Garza Sada # 1 Apartado Postal 314 C6rdoba Veracruz 94500 Mexico

Beginning with the explicitly covariant Maxwell equations in media, we deduce an explicitly covariant stress-energy-momentum balance equation in material media. Proceeding in this way we avoid mixing external fields and self fields, as occurs if one begins with Lorentz＇s law, the most usual approach appearing in textbooks. Indeed our deduction implies a generalized force density in which the total fields appear. As an application of the present deduction, we discuss briefly the Abraham-Minkowski controversy, showing its relation to open or closed electromagnetic systems. This approach will be interesting for scholars as well as graduate students interested in conceptual problems of relativistic electromagnetism.

关键词： Maxwell's equations balance equation electromagnetic force density.

Genome sequencing and next-generation sequence data analysis: A comprehensive compilation of bioinformatics tools and databases

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American Journal of Molecular Biology 2013年第2期3卷 115-130页

作者： jose C. jimenez-Lopez Emma W. Gachomo Sweta Sharma Simeon O. Kotchoni Department of Biochemistry Cell and Molecular Biology of Plants Estacion Experimental del Zaidin High Council for Scientific Research (CSIC) Granada Spain Department of Biology Rutgers University Camden USA

Genomics has become a ground-breaking field in all areas of the life sciences. The advanced genomics and the development of high-throughput techniques have lately provided insight into whole-genome characterization of a wide range of organisms. In the post-genomic era, new technologies have revealed an outbreak of prerequisite genomic sequences and supporting data to understand genome wide functional regulation of gene expression and metabolic pathways reconstruction. However, the availability of this plethora of genomic data presents a significant challenge for storage, analyses and data management. Analysis of this mega-data requires the development and application of novel bioinformatics tools that must include unified functional annotation, structural search, and comprehensive analysis and identification of new genes in a wide range of species with fully sequenced genomes. In addition, generation of systematically and syntactically unambiguous nomenclature systems for genomic data across species is a crucial task. Such systems are necessary for adequate handling genetic information in the context of comparative functional genomics. In this paper, we provide an overview of major advances in bioinformatics and computational biology in genome sequencing and next-generation sequence data analysis. We focus on their potential applications for efficient collection, storage, and analysis of genetic data/information from a wide range of gene banks. We also discuss the importance of establishing a unified nomenclature system through a functional and structural genomics approach.

关键词： Databases Computational Biology Genomics Proteomics Next-Generation Sequencing