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Integration between Genomic and Computational Statistical Surveys for the Screening of SNP Genetic Variants in Inflammatory Bowel Disease (IBD) Pediatric Patients*

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Computational Molecular Bioscience 2024年第3期14卷 146-191页

作者： Dago Dougba Noel Koffi N’Guessan Bénédicte sonia Dagnogo Olefongo Daramcoum Wentoin Alimata marie-Pierre Mauro Giacomelli Dagnogo Dramane Eboulé Ago Eliane Rebecca Yao Saraka Didier martial Diarrassouba Nafan Giovanni Malerba Raffaele Badolato Department of Clinical and Experimental Sciences University of Brescia Brescia Italy Angelo Nocivelli Institute of Molecular Medicine Childrens Hospital ASST Spedali Civili Brescia Italy Unit of Biostatistics and Biomathematics & Unit of Bioinformatics Department of Molecular and Translational Medicine University of Brescia Brescia Italy Biological Sciences Training and Research Unit Department of Genetic and Biochemistry Peleforo Gon Coulibaly University Korhogo Cte dIvoire Department of Neurosciences Biomedicine and Movement Sciences Section of Biology and Genetics University of Verona Verona Italy Biosciences Training and Research Unit Biology and Health Laboratory Felix Houphouet-Boigny University Abidjan Cte dIvoire

Inflammatory bowel diseases (IBD) are complex multifactorial disorders that include Crohn’s disease (CD) and ulcerative colitis (UC). Considering that IBD is a genetic and multifactorial disease, we screened for the distribution dynamism of IBD pathogenic genetic variants (single nucleotide polymorphisms;SNPs) and risk factors in four (4) IBD pediatric patients, by integrating both clinical exome sequencing and computational statistical approaches, aiming to categorize IBD patients in CD and UC phenotype. To this end, we first aligned genomic read sequences of these IBD patients to hg19 human genome by using bowtie 2 package. Next, we performed genetic variant calling analysis in terms of single nucleotide polymorphism (SNP) for genes covered by at least 20 read genomic sequences. Finally, we checked for biological and genomic functions of genes exhibiting statistically significant genetic variant (SNPs) by introducing Fitcon genomic parameter. Findings showed Fitcon parameter as normalizing IBD patient’s population variability, as well as inducing a relative good clustering between IBD patients in terms of CD and UC phenotypes. Genomic analysis revealed a random distribution of risk factors and as well pathogenic SNPs genetic variants in the four IBD patient’s genome, claiming to be involved in: i) Metabolic disorders, ii) Autoimmune deficiencies;iii) Crohn’s disease pathways. Integration of genomic and computational statistical analysis supported a relative genetic variability regarding IBD patient population by processing IBD pathogenic SNP genetic variants as opposite to IBD risk factor variants. Interestingly, findings clearly allowed categorizing IBD patients in CD and UC phenotypes by applying Fitcon parameter in selecting IBD pathogenic genetic variants. Considering as a whole, the study suggested the efficiency of integrating clinical exome sequencing and computational statistical tools as a right approach in discriminating IBD phenotypes as well as improvi

关键词： Inflammatory Bowel Disease (IBD) Crohn Disease (CD) Ulcerative Colitis (UC) Clinical Exome Analysis Computational Statistic SNP Genetic Variants

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Indomethacin but not a selective cyclooxygenase-2 inhibitor inhibits esophageal adenocarcinogenesis in rats

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World Journal of Gastroenterology 2012年第35期18卷 4866-4874页

作者： Paula Esquivias Antonio Morandeira Alfredo Escartín Carmelo Cebrián sonia Santander Francisco Esteva maría Asunción García-González Javier Ortego Angel lanas Elena Piazuelo CIBER Digestive and Hepatic Deseases Service of Surgery University Hospital "Lozano Blesa" Service of Pathology University Hospital "Lozano Blesa" Department of Medicine University of Zaragoza Service of Clinical Biochemistry University Hospital "Lozano Blesa" Aragon Health Science Institute Service of Gastroenterology University Hospital "Lozano Blesa"

AIM： To evaluate the effects of indomethacin [dual cyclooxygenase （COX）-I/COX-2 inhibitor] and 3-（3,4-difluorophenyl）-4-（4-（methylsulfonyl） phenyl）- 2-（5H）-furanone （MF-tricyclic）（COX-2 selective inhibi- tor） in a rat experimental model of Barrett＇s esophagus and esophageal ***： A total of 112 surviving post-surgery rats were randomly divided into three groups： the control group （n = 48）, which did not receive any treatment; the indomethacin group （n = 32）, which were given 2 mg/kg per day of the COX-I/COX-2 inhibitor; and the MF-tricyclic group （n = 32）, which received 10 mg/kg per day of the selective COX-2 inhibitor. Randomly se- lected rats were killed either 8 wk or 16 wk after sur- gery. The timing of the deaths was in accordance with a previous study performed in our group. Only rats that were killed at the times designated by the protocol were included in the study. We then assessed the histology and prostaglandin E2 （PGE2） expression levels in the rat esophagi. An additional group of eight animals that did not undergo esophagojejunostomy were included in order to obtain normal esophageal tissue as a control. RESUlTS： Compared to a control group with no treat- ment （vehicle-treated rats）, indomethacin treatment was associated with decreases in ulcerated esophageal mucosa （16% vs 35% and 14% vs 17%, 2 mo and 4 mo after surgery, respectively; P = 0.021）, length of intestinal metaplasia in continuity with anastomosis （2 4- 1.17 mm vs 2.29 ＋ 0.75 mm and 1.25 4- 0.42 mm vs 3.5 4- 1.54 mm, 2 mo and 4 mo after surgery, respec- tively; P = 0.007）, presence of intestinal metaplasia beyond anastomosis （20% vs 71.4% and 0% vs 60%, 2 mo and 4 mo after surgery, respectively; P = 0.009）, severity of dysplasia （0% vs 71.4% and 20% vs 85.7% high-grade dysplasia, 2 mo and 4 mo after surgery, re- spectively; P = 0.002）, and adenocarcinoma incidence （0% vs 57.1% and 0% vs 60%, 2 mo and 4 mo after surgery, respectively; P 〈 0.0001）. Treatment with the select

关键词： Intestinal metaplasia Esophageal adeno-carcinoma Indomethacin MF-tricyclic

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Determination and(Re)Parametrization of Rational Developable Surfaces

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Journal of Systems Science & Complexity 2015年第6期28卷 1426-1439页

作者： SHEN liyong PREZ-DíAZ sonia School of Mathematical Sciences University of Chinese Academy of Sciences Key laboratory of Mathematics Mechanization Academy of Mathematics and Systems Science Chinese Academy of Sciences Key laboratory of Big Data Mining and Knowledge management Chinese Academy of Sciences Dpto de Física y Matemáticas Universidad de Alcalá

The developable surface is an important surface in computer aided design, geometric modeling and industrial manufactory. It is often given in the standard parametric form, but it can also be in the implicit form which is commonly used in algebraic geometry. Not all algebraic developable surfaces have rational parametrizations. In this paper, the authors focus on the rational developable surfaces. For a given algebraic surface, the authors first determine whether it is developable by geometric inspection, and then give a rational proper parametrization in the affrmative case. For a rational parametric surface, the authors also determine the developability and give a proper reparametrization for the developable surface.

关键词： Parametrization proper rational developable surface reparametrization

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Inequalities for the Extended Best Polynomial Approximation Operator in Orlicz Spaces

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Acta Mathematica Sinica,English Series 2019年第2期35卷 185-203页

作者： sonia ACINAS Sergio FAVIER Felipe ZO Departamento de Matemática Facultad de Ciencias y Exactas NaturalesUniversidad Nacional de La Pampa Instituto de Matemática Aplicada San luis IMASLUniversidad Nacional de San Luis and CONICET Departamento de Matemática Universidad Nacional de San Luis

In this paper we pursue the study of the best approximation operator extended from l~Φ to l~φ, where φ denotes the derivative of the function Φ. We get pointwise convergence for the coefficients of the extended best approximation polynomials for a wide class of function f, closely related to the Calder′on–Zygmund class t_m^p(x) which had been introduced in 1961. We also obtain weak and strong type inequalities for a maximal operator related to the extended best polynomial approximation and a norm convergence result for the coefficients is derived. In most of these results, we have to consider Matuszewska–Orlicz indices for the function φ.

关键词： Orlicz spaces extended best polynomial approximation pointwise and norm convergence weak and strong type inequalities Orlicz indices

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Plant Growth-Promoting Traits in Rhizobacteria of Heavy Metal-Resistant Plants and Their Effects on Brassica nigra Seed Germination

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Pedosphere 2017年第3期27卷 511-526页

作者： Brenda ROMN-PONCE Diana Miryel REZA-VZQUEZ sonia GUTIRREZ-PAREDES maría de Jesús DE HARO-CRUZ Jessica MAlDONADO-HERNNDEZ Yanely BAHENA-OSORIO Paulina ESTRADA-DE lOS SANTOS En Tao WANG maría Soledad VSQUEZ-MURRIETA Instituto Politécnico Nacional Escuela Nacional de Ciencias Biológicas Prolongación Carpio y Plan de Ayala s/n Col.Santo Tomás Del.Miguel Hidalgo Ciudad de México

Phytoremediation is an emerging technology that uses plants and their associated microbes to clean up pollutants from the soil, water, and air. In order to select the plant growth-promoting rhizobacteria （PGPR） for phytoremediation of heavy metal contamination, 60 bacterial strains were isolated from the rhizosphere of two endemic plants, Prosopis laevigata and Spharealcea angustifolia, in a heavy metal-contaminated zone in Mexico. These rhizobacterial strains were characterized for the growth at different pH and salinity, extracellular enzyme production, solubilization of phosphate, heavy metal resistance, and plant growth-promoting （PGP） traits, including production of siderophores and indol-3-acetic acid （IAA）. Overall, the obtained rhizobacteria presented multiple PGP traits. These rhizoba^teria were also resistant to high levels of heavy metals （including As as a metalloid）（up to 480 mmol l-1 As（V）, 24 mmol l-1 Pb（II）, 21 mmol l-1 Cu（II）, and 4.5 mmol l-1 Zn（II））. Seven rhizobacterial strains with the best PGP traits were identified as members of Alcaligenes, Bacillus, Curtobacterium, and Microbacterium, and were selected for further bioassay. The inoculation of Brassica nigra seeds with Microbacteriurn sp. CE3R2, Microbacterium sp. NE1R5, Curtobacterium sp. NM1R1, and Microbacterium sp. NM3E9 facilitated the root development; they significantly improved the B. nigra seed germination and root growth in the presence of heavy metals such as 2.2 mmol l-1 Zn（II）. The rhizobacterial strains isolated in the present study had the potential to be used as efficient bioinoculants in phytorremediation of soils contaminated with multiple heavy metals.

关键词： bioinoculants endemic plants mine railings pH phytoremediation salinity

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Divergent foraging behavior in a hybrid zone： Darwin＇s tree finches （Camarhynchus spp.） on Floreana Island

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Current Zoology 2015年第1期61卷 181-190页

作者： Katharina J. PETERS sonia KlEINDORFER School of Biological Sciences Flinders University GPO Box 2100 Adelaide 5001 Australia

Hybrid speciation is increasingly recognized as a mechanism for novel evolutionary trajectories. However, we know very little about the ecology of a contact zone that has arisen in sympatry. This study examines the foraging behavior and fitness of two species of Darwin＇s tree finches （Camarhynchus parvulus, C pauper） and hybrid offspring on Floreana Island. Previous study showed that the percentage of hybrids in the tree finch population increased from 19% in 2005 to 41% in 2010, and their body and beak size increased by -5% （parental phenotype did not change）. In 2005-2006, all three tree finch groups （two paren- tal species and hybrid birds） used the same foraging substrate, technique, and height. By 2010-2013, the small tree finch C. par- vulus had changed its foraging technique and the medium tree finch C. pauper had changed its foraging height. Both parental species had higher body condition when foraging at （divergent） mean foraging heights per species but hybrid birds did not. We discuss the implications of conserving forest to facilitate vertical niche expansion and the role of hybridization for genetic persis- tence [Current Zoology 61 （1）： 181-190, 2015].

关键词： Hybridization Speciation Adaptive radiation Conservation Scalesia Ecological niche

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Second-order Sliding Mode Approaches for the Control of a Class of Underactuated Systems

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International Journal of Automation and computing 2015年第2期12卷 134-141页

作者： sonia Mahjoub Faical Mnif Nabil Derbel Advanced Control and Energy Management laboratory University of SfaxSfax Engineering School Department of Electrical and Computer Engineering Sultan Qaboos University

In this paper, first-order and second-order sliding mode controllers for underactuated manipulators are proposed. Sliding mode control(SMC) is considered as an effective tool in different studies for control systems. However, the associated chattering phenomenon degrades the system performance. To overcome this phenomenon and track a desired trajectory, a twisting, a supertwisting and a modified super-twisting algorithms are presented respectively. The stability analysis is performed using a lyapunov function for the proposed controllers. Further, the four different controllers are compared with each other. As an illustration, an example of an inverted pendulum is considered. Simulation results are given to demonstrate the effectiveness of the proposed approaches.

关键词： Underactuated manipulator sliding mode control twisting algorithm super-twisting algorithm inverted pendulum.

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Quality and Technological Properties of Gluten-Free Biscuits Made with Pachyrhizus ahipa Flour as a Novel Ingredient

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Food and Nutrition Sciences 2017年第1期8卷 70-83页

作者： maría Cecilia Doporto Fernanda Sacco sonia Z.Vina maría Alejandra García Centro de Investigación y Desarrollo en Criotecnología de Alimentos(CIDCA) Facultad Ciencias ExactasUniversidad Nacional de La Plata(UNLP)-CIC-PBA-CONICET La PlataLa PlataArgentina Curso Bioquímica y Fitoquímica Facultad Ciencias Agrarias y Forestales(UNLP)La PlataArgentina

The development of gluten-free foodstuffs with high nutritional quality components is an important objective to achieve. Pachyrhizus ahipa is one of the few leguminous species that produce edible tuberous roots with high nutritional value. Thus, the aim of this work was to formulate biscuits containing corn starch and 125 - 350 g·kg-1 of P. ahipa flour (AF) and to study the main physicochemical properties related to their nutritional and technological quality as well as their sensory acceptability. The formulation containing 250 g of AF kg-1 was selected for improving the product nutritional quality (i.e. higher protein content) without an extensive modification of textural properties. A formulation replacing corn starch by cassava flour (250 g·kg-1) was also analyzed. In this case, ahipa and cassava biscuits showed maximum force and energy required to bite twice and three times higher than the control, respectively. Slight variations were observed in color (E and browning index). The overall acceptability of biscuits formulated with both flours was better scored than the control by a sensory panel. Principal component analysis allowed to relate quality attributes, chemical composition, and sensory characteristics of biscuits containing cassava or ahipa flours. The results indicated that ahipa flour could satisfactorily substitute part of the corn starch used in the formulations of gluten-free biscuits.

关键词： Non-Traditional Flours Biscuits for Celiac Patients Chemical Composition Color and Texture Sensory Evaluation

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Morphotaxonomy and seasonal distribution of planktonic and benthic Prorocentrales in Karachi waters,Pakistan Northern Arabian Sea

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Chinese Journal of Oceanology and limnology 2013年第2期31卷 267-281页

作者： sonia MUNIR Zaib-un-nisa BURHAN Tahira NAZ P.J.A.SIDDIQUI Steve l.MORTON Centre of Excellence in marine Biology University of Karachi-75270Pakistan National Oceanic and Atmospheric Administrations 219 Fort Johnson RoadCharleston SC29412USA

Morphotaxonomy and seasonal abundance of dinoflagellates of the genera Prorocentrum and Mesoporos （Prorocentrales） were studied from nutrient-rich waters, Karachi Harbor and the mouth of the Manora Channel, Pakistan during May 2002-July 2003. Using both light and scanning electron microscopy, 13 species of Prorocentrales were identified according to cell shape, size, ornamentation of thecal plates, and architecture of apical platelets, apical pore area, marginal pores, and intercalary bands. P. sigmoides, P. arcuatum, P. scutellum, P. donghaiense, P. balticum, P. minimum, P. emarginatum, P. lima, P. faustiae, and Mesoporos perforatus constitute new records for sindh coast of Pakistan. The most abundant species were P. minimum/P, balticum （4.5x103 cells/l）, P. micans （1.1~103 cells/l）, P. gracile/P, sigmoides （2.5 x 102 cells/l） and P. donghaiense （6.6 x 103 cells/l） at temperatures of 29-31 ~C and salinities of 35-40. Maximum abundance was observed in winter and lower abundance in summer. There was no significant change in the distribution of species between stations except for the benthic species which occurred close to Karachi Harbor waters. Significant positive correlations were observed between Prorocentrum spp. and temperature （R2=0.27） and negative correlations with salinity （R2=-0.32） except for P. minimum and P. emarginatum which has negative correlation with temperature （R2=-0.24） and positive with salinity （R2=0.08, 0.19）. The finding of potential okadaic-acid producing species of benthic Prorocentrum call for monitoring for possible human health problems in this region.

关键词： ecology morphology planktonic/benthic Prorocentrales harmful algae scanning electronaaicroscopy northern Arabian Sea

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A Symbolic-Numeric Approach for Parametrizing Ruled Surfaces

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Journal of Systems Science & Complexity 2020年第3期33卷 799-820页

作者： PÉREZ-DÍAZ sonia SHEN li-Yong Dpto.de Física y Matemáticas Universidad de Alcalá28871-Alcaláde HenaresMadridSpain School of Mathematical Sciences University of Chinese Academy of SciencesBeijing 100049China

This paper presents symbolic algorithms to determine whether a given surface(implicitly or parametrically defined)is a rational ruled surface and find a proper parametrization of the ruled ***,in practical applications,one has to deal with numerical objects that are given approximately,probably because they proceed from an exact data that has been perturbed under some previous measuring process or *** these numerical objects,the authors adapt the symbolic algorithms presented by means of the use of numerical *** authors develop numeric algorithms that allow to determine ruled surfaces"close"to an input(not necessarily ruled)surface,and the distance between the input and the output surface is computed.

关键词： Implicit representation numeric algorithm ruled surface standard parametrization

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