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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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Intracranial pressure is elevated at 24h post-stroke inmice

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Neuroprotection 2024年第1期2卷 60-64页

作者： Kirby E.Warren rebecca J.Hood Fredrick R.Walker Neil J.Spratt School of Biomedical Sciences and Pharmacy University of NewcastleCallaghanAustralia Hunter Medical Research Institute NewLambton HeightsAustralia School of Biomedicine Discipline of Anatomy and PathologyFaculty of Health and Medical SciencesThe University of AdelaideAdelaideAustralia Department of Neurology John Hunter HospitalNewLambton HeightsAustralia

Background:It has long been assumed that post-stroke intracranial pressure(ICP)elevation occurs because of large infarct and edema ***,we have repeatedly shown IcP elevation at 24 h post-stroke in the presence of little to no edema in *** processes are often conserved across species and types of ***,we aimed to determine if an ICP rise occurs at 24 h post-stroke in the presence of small infarct and edema volumes in ***:Mice were randomized by random number table to either photothrombotic stroke or sham surgery(n=15).Epidural ICP was recorded using a fiber optic catheter at 1 h post-stroke(baseline)and between 23 and ***:ICP was significantly higher at 24 h compared to baseline in stroke animals(n=6;10.71±6.45mmHg vs.3.74±2.20mmHg,respec-tively;p=0.03).ICP at 24 h was also significantly higher in stroke mice compared to sham(n=6;3.45±1.43mmHg;p=0.02).There was no change in ICP in sham mice(p=0.9).Edema volumes in stroke animals were small(0.04±0.04 mm3)and unlikely to have caused significant ICP ***:This study provides evidence of an edema-independent ICP elevation following small ischemic stroke in *** occurrence of this rise supports our findings in other species and suggests it is caused by a previously undescribed mechanism.

关键词： cerebraledema intracranial pressure ischemic stroke

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Impaired cellulose decomposition in a headwater stream receiving subsurface agricultural drainage

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Ecological Processes 2022年第1期11卷 845-861页

作者： rebecca Poisson Adam G.Yates Department of Geography Western UniversityLondonONCanada Department of Biology University of WaterlooWaterloo University200 University Avenue WestWaterlooON N2L 3G1Canada

Background:Agricultural development of former wetlands has resulted in many headwater streams being sourced by subsurface agricultural drainage *** drainage inputs can significantly influence stream environmental conditions,such as temperature,hydrology,and water chemistry,that drive ecological ***,ecological assessments of subsurface drainage impacts are *** assessed the impact of an agricultural drainage system on cellulose decomposition and benthic respiration using a paired stream study in a headwater branch of Nissouri Creek,in Ontario,*** first order segments sourced by a spring-fed marsh and a cropped field with subsurface drainage,as well as the adjoining trunk segment,were sampled over a year using the cotton strip assay to measure cellulose decomposition and benthic ***:Assessments of cellulose decomposition revealed a one-third reduction in the drainage-sourced segment compared to marsh-sourced *** segment differences in cellulose decomposition were associated with reduced summer temperatures in the drainage-sourced *** of stream cooling from the drainage-sourced segment were transmitted downstream as cellulose decomposition was slower than expected throughout the drainage-sourced segment and for several hundred meters down the adjoining trunk *** respiration only differed between the drainage-and marsh-sourced segments in spring,when stream temperatures were ***:Our findings suggest there may be a widespread reduction in cellulose decomposition in streams across similar agricultural regions where subsurface drainage is ***,cooling of streams receiving significant amounts of water inputs from subsurface drainage systems may impart increased resiliency to future climate warming.

关键词： Stream Agriculture Cotton strip assay Seasonality Organic matter breakdown Benthic respiration

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Nanoparticles for targeted cancer radiotherapy

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Nano Research 2020年第11期13卷 2887-2897页

作者： Roger M.Pallares rebecca J.Abergel Chemical Sciences Division Lawrence Berkeley National LaboratoryBerkeleyCA94720USA Department of Nuclear Engineering University of CaliforniaBerkeleyCA94720USA

Radiotherapy,where ionizing radiation is locally delivered either through an external beam or by surgically implanting radionuclide-based seeds in the tumor,is one of the gold standard treatments for *** to the non-selective nature of radiation,healthy tissue surrounding the cancerous region is usually affected by the ***,new strategies,including targeted alpha therapy,are being studied to improve the selectivity of the treatment and minimize side *** challenges,however,limit the current development of targeted radiotherapy,such as the functionalization of the therapeutic agent with targeting vectors and controlling the release of recoiling *** offer unique opportunities as drug delivery vehicles,since they are biocompatible,enhance the cellular uptake of drugs,and are easily functionalized with targeting *** this review,we examine how nanoparticles can be used for targeted radiotherapy,either as sensitizers of external beams or as delivery vehicles for therapeutic *** describe the clinical relevance of different types of nanoparticles,followed by an analysis of how these nanoconstructs can solve some of the main limitations of conventional ***,we critically discuss the current situation of nanoparticle-based radiotherapy in clinical settings and challenges that need to be overcome in the future for further development of the field.

关键词： radiotherapy targeted cancer radiotherapy nanoparticles cancer targeted alpha therapy external beam

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Simulated perturbation in the sea-to-air flux of dimethylsulfi de and the impact on polar climate

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Journal of Oceanology and Limnology 2021年第1期39卷 110-121页

作者： Bo QU Albert JGABRIC rebecca JACKSON School of Science Nantong UniversityNantong 226219China School of Environment and Science Griffi th UniversityBrisbane 4111QLDAustralia

Marine biogenic emission of dimethylsulfi de(DMS)has been well recognized as the main natural source of reduced sulfur to the remote marine atmosphere and has the potential to aff ect climate,especially in the polar *** used a global climate model(GCM)to investigate the impact on atmospheric chemistry from a change to the contemporary DMS fl ux to that which has been projected for the late 21 st *** perturbed simulation corresponded to conditions that pertained to a tripling of equivalent CO 2,which was estimated to occur by year 2090 based on current worst-case greenhouse gas emission *** changes in zonal mean DMS fl ux were applied to 50°S–70°S Antarctic(ANT)and 65°N–80°N Arctic(ARC)*** results indicate that there are clearly diff erent impacts after perturbation in the southern and northern polar *** quantities related to the sulfur cycle show a higher increase in ***,most sulfur compounds have higher peaks in *** perturbation in DMS fl ux leads to an increase of atmospheric DMS of about 45%in ANT and 33.6%in *** sulfur dioxide(SO 2)vertical integral increases around 43%in ANT and 7.5%in ***(SO 4)vertical integral increases by 17%in ANT and increases around 6%in *** emissions increases by 21%in ANT and increases by 9.7%in ***,oxidation of DMS by OH increases by 38.2%in ARC and by 15.17%in *** optical depth(AOD)increases by 4%in the ARC and by 17.5%in the ANT,and increases by 22.8%in austral *** importance of the perturbation of the biogenic source to future aerosol burden in polar regions leads to a cooling in surface temperature of 1 K in the ANT and 0.8 K in the ***,polar regions in the Antarctic Ocean will have a higher off setting eff ect on warming after DMS fl ux perturbation.

关键词： dimethylsulfi de(DMS) sulfur dioxide DMS sea-to-air fl ux perturbation global climate model(GCM) polar region

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Retinoprotective compounds,current efficacy,and future prospective

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Neural Regeneration Research 2023年第12期18卷 2619-2622页

作者： Rachele Marino rebecca Sappington Marco Feligioni Laboratory of Neuronal Cell Signaling EBRI Rita Levi-Montalcini FoundationRomeItaly Department of Neurobiology and Anatomy Wake Forest School of MedicineAtrium Health Wake Forest Baptist Medical CenterWinston-SalemNCUSA Department of Ophthalmology Wake Forest School of MedicineWinston-SalemNCUSA Department of Neurorehabilitation Sciences Casa di Cura IgeaMilanItaly

Retinal dysfunction is the most common cause of vision loss in several retinal *** has been estimated a great increase in these pathologies that are becoming more globally widespread and numerous over time,also supported by the life expectancy *** different types of retinopathies,we can account some that share causes,symptoms,and treatment including diabetic retinopathy,age-related macular degeneration,glaucoma,and retinitis *** changes,environmental factors,and genetic predisposition might be some of the main causes that drive retinal tissue to chronic inflammation and neurodegeneration in these *** treatments available on the market contain compounds that efficiently ameliorate some of the important clinical features of these pathologies like stabilization of the intraocular pressure,reduction of eye inflammation,control of eye oxidative stress which are considered the major molecular mechanisms related to retinal ***,the most commonly used drugs are antiinflammatories,such as corticosteroids,antioxidant,hypotonic molecules and natural neuroprotective ***,these drugs,which are fundamental to treating disease symptoms,are not capable to cure the pathologies and so they are not life-changing for *** review provided an overview of current treatments on the market,but more interestingly,wants to be a quick window on the new treatments that are now in clinical ***,it has been here highlighted that the recent technical enhancement of the investigation methods to identify the various retinopathies causes might be used as a sort of“precise medicine”approach to tailor the identification of molecular pathways involved and potentially study a dedicated treatment for each *** approach includes the use of cutting-edge technologies like gene therapy and metabolomics.

关键词： age-related macular degeneration anti-inflammatory drugs antioxidants diabetic retinopathy glaucoma neuroprotective compounds retinitis pigmentosa retinopathies vision loss

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Histones, histone chaperones and nucleosome assembly

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Protein & Cell 2010年第7期1卷 607-612页

作者： rebecca J.Burgess Zhiguo Zhang Department of Biochemistry and Molecular Biology Mayo Clinic College of Medicine200 First Street SWRochesterMN 55905USA

Chromatin structure governs a number of cellular processes including DNA replication,transcription,and DNA *** DNA replication,chromatin structure including the basic repeating unit of chromatin,the nucleosome,is temporarily disrupted,and then reformed immediately after the passage of the replication *** coordinated process of nucleosome assembly during DNA replication is termed replication—coupled nucleosome *** of this process can lead to genome instability,a hallmark of cancer ***,addressing how replication-coupled nucleosome assembly is regulated has been of great ***,we review the current status of this growing field of interest,highlighting recent advances in understanding the regulation of this important process by the dynamic interplay of histone chaperones and histone modifications.

关键词： nucleosome chaperones assembly

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Geographic variation in sexual selection and implications for speciation in the Barn Swallow

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Chinese Birds 2015年第1期5卷 30-42页

作者： Elizabeth SC Scordato rebecca J Safran Department of Ecology and Evolutionary Biology The University of Colorado

Barn Swallows(Hirundo rustica), a group of passerine birds comprised of six closely related subspecies, are well known throughout their nearly worldwide distribution, in part because of their close association with human settlements.A tractable species for both individual-based and population-level studies, Barn Swallows are a prominent model system in evolutionary, ecological, and behavioral research. Here we review work on sexual selection and population divergence in this species complex, focusing on comparative studies among populations and *** summarize variation in the targets of mate choice and in the information conveyed by sexually selected traits, and conclude that the benefits advertised by different traits may vary geographically. Finally, we consider the role of sexual selection as a driver of population divergence in this widespread and phenotypically variable species complex.

关键词： Barn Swallow Geographic variation Natural selection Sexual selection Speciation Tail streamers Ventral color

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Change Point Detection for Process Data Analytics Applied to a Multiphase Flow Facility

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Computer Modeling in Engineering & Sciences 2023年第3期134卷 1737-1759页

作者： rebecca Gedda Larisa Beilina Ruomu Tan Department of Mathematical Sciences Chalmers University of TechnologySE-42196GothenburgSweden and ABB Corporate Research CentreLadenburgGermany Department of Mathematical Sciences Chalmers University of Technology and University of GothenburgGothenburgSweden ABB Corporate Research Center LadenburgGermany

Change point detection becomes increasingly important because it can support data analysis by providing labels to the data in an unsupervised *** the context of process data analytics,change points in the time series of process variables may have an important indication about the process *** example,in a batch process,the change points can correspond to the operations and phases defined by the batch *** identifying change points can assist labelling the time series *** unsupervised algorithms have been developed for change point detection,including the optimisation approachwhich minimises a cost functionwith certain penalties to search for the change *** Bayesian approach is another,which uses Bayesian statistics to calculate the posterior probability of a specific sample being a change *** paper investigates how the two approaches for change point detection can be applied to process data *** addition,a new type of cost function using Tikhonov regularisation is proposed for the optimisation approach to reduce irrelevant change points caused by randomness in the *** novelty lies in using regularisation-based cost functions to handle ill-posed problems of noisy *** results demonstrate that change point detection is useful for process data analytics because change points can produce data segments corresponding to different operating modes or varying conditions,which will be useful for other machine learning tasks.

关键词： Change point detection unsupervisedmachine learning optimisation Bayesian statistics Tikhonov regularisation

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Reconciling concepts, theory, and empirical patterns surrounding cascade reinforcement

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Current Zoology 2016年第2期62卷 131-134页

作者： rebecca C. FULLER Department of Animal Biology University of Illinois Urbana IL 61801 USA

IntroductionReinforcement is a critically important process in speciation. It has been credited with often completing speciation, and it is unique in that natural selection directly favors the evolution of reproductive isolating barriers. Reinforcement occurs when selection favors increased prezygotic isolation between two lineages in order to avoid maladaptive hybridization in areas of sympatry （Noor 1999; Servedio and Noor 2003; Coyne and Orr 2004）.

关键词：调和加固梯级

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