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Integration of Known transcription Factor Binding Site Information and Gene Expression Data to Advance from Co-Expression to Co-Regulation

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Genomics, Proteomics & Bioinformatics 2007年第2期5卷 86-101页

作者： Maarten Clements Eugene P. van Someren theo A. Knijnenburg Marcel j.t. Reinders Information and Communication theory Group Faculty of Electrical Engineering Mathematics and Computer Science Delft University of Technology 2600 GA Delft the Netherlands.

the common approach to find co-regulated genes is to cluster genes based on gene expression. However, due to the limited information present in any dataset, genes in the same cluster might be co-expressed but not necessarily co-regulated. In this paper, we propose to integrate known transcription factor binding site information and gene expression data into a single clustering scheme. this scheme will find clusters of co-regulated genes that are not only expressed similarly under the measured conditions, but also share a regulatory structure that may explain their common regulation. We demonstrate the utility of this approach on a microarray dataset of yeast grown under different nutrient and oxygen limitations. Our integrated clustering method not only unravels many regulatory modules that are consistent with current biological knowledge, but also provides a more profound understanding of the underlying process. the added value of our approach, compared with the clustering solely based on gene expression, is its ability to uncover clusters of genes that are involved in more specific biological processes and are evidently regulated by a set of transcription factors.

关键词： gene clustering gene regulation binding motifs

Effect of hepatic artery embolization on liver hypertrophy response in a rabbit liver VX2tumor model

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Hepatobiliary & Pancreatic Diseases International 2013年第6期12卷 622-629页

作者： Krijn P van Lienden Lisette t Hoekstra jessica D van trigt joris j Roelofs Otto M van Delden thomas M van Gulik Department of RadiologyAcademic Medical Center University of Amsterdam Department of Surgery (Surgical Laboratory)Academic Medical Center University of Amsterdam Department of PathologyAcademic Medical Center University of Amsterdam

BACKGROUND:Portal vein embolization not only induces hypertrophy of the non-embolized liver,but also enhances tumor *** latter could be prevented by embolizing the hepatic arteries supplying the tumor-bearing liver *** study aimed to determine the effects of transcatheter arterial embolization(tAE)on tumor volume and liver regeneration in a rabbit VX2 tumor ***:twenty-three rabbits underwent subcapsular tumor implantation with a VX2 *** weeks after implantation,18 rabbits were used for tAE experiments,5were for sham *** response and liver regeneration response of the embolized cranial and non-embolized caudal liver lobes were assessed by Ct volumetry,liver to body weight index,and the amount of proliferating ***:All super-selective arterial tumor embolization procedures were performed *** embolization,the tumor volume increased after an initial steady *** tumor volume after embolization was smaller than that of the sham group,but this difference was not *** necrosis of the tumor,however,was seen after embolization,without damage of the surrounding liver *** was a significant atrophy response of the tumor bearing cranial lobe after super-selective arterial embolization of the tumor with a concomitant hypertrophy response of the non-embolized,caudal *** regeneration response was confirmed histologically by a significantly higher number of proliferating hepatocytes on the Ki-67 stained ***:Super-selective,bland arterial coil embolization causes massive necrosis of the tumor,despite increase of volume on Ct *** of the tumor bearing liver lobe is seen after arterial embolization of the tumor with a concomitant hypertrophy response of the non-embolized lobe,despite absence of histological damage of the tumor-surrounding liver parenchyma.

关键词： hypertrophy liver regeneration animal model transarterial embolization hepatic artery

Dietary fibre enrichment of supplemental feed modulates the development of the intestinal tract in suckling piglets

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journal of Animal Science and Biotechnology 2020年第1期11卷 183-193页

作者： H.M.j.van Hees M.Davids D.Maes S.Millet S.Possemiers L.A.den Hartog t.A.t.G.van Kempen G.P.j.janssens Department of Nutrition Genetics and EthologyGhent UniversityMerelbekeBelgium Research and Development Trouw NutritionAmersfoortThe Netherlands Department of Internal and Vascular Medicine Amsterdam University Medical CentreAmsterdamThe Netherlands Department of Reproduction Obstetrics and Herd HealthGhent UniversityMerelbekeBelgium ILVO Eenheid DierMelleBelgium BioActor MaastrichtThe Netherlands Animal Nutrition Wageningen University and ResearchWageningenThe Netherlands North Carolina State University RaleighNCUSA.

Background:Commercial pre-weaning diets are formulated to be highly digestible and nutrient-dense and contain low levels of dietary *** contrast,pigs in a natural setting are manipulating fibre-rich plant material from a young ***,dietary fibre affects gastrointestinal tract(GIt)development and health in older *** hypothesised that supplemental diets that contain vegetal fibres are accelerating GIt development in suckling piglets in terms of size and *** d 2 of life,sow-suckled piglets had access to a low fibre diet(CON),a diet with a fermentable long-chain arabinoxylan(lc-AXOS),a diet with a largely non-fermentable purified cellulose(CELL),or a diet containing both *** the initial 2 weeks,the control diet was a high-density milk replacer,followed by a dry and highly digestible creep *** weaning at 25 d,15 piglets from each treatment group,identified as eaters and originating from six or seven litters,were sacrificed for post-mortem examination of GIt morphology,small intestinal permeability and metabolic profile of the *** microbiota composition of the mid-colon was evaluated in a sub-set of ten ***:No major statistical interactions between the fibre sources were *** consumed the fibrecontaining milk supplements and creep diets *** size and small intestinal permeability was not *** intestinal fill was increased with lc-AXOS only,while relative large intestinal weight was increased with both fibre sources(Ptended to increase ileal DM content compared to CON(Pthe concentration of volatile fatty acids was increased in the caecum(Ption of ***-AXOS only stimulated caecal propionate(Pthe microbiota composition showed a high individual variation and limited dietary ***,CELL induced minor shifts in specific genera,with notable reductions of Escherichia-Sh

关键词： Dietary fibre Gut maturation Gut microbiota Suckling piglets

Cost projections for microwave plasma CO production using renewable energy

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journal of Energy Chemistry 2022年第8期31卷 507-513,I0014页

作者： Remko j.Detz Bob van der Zwaan Netherlands Organisation for Applied Scientific Research(tNO) Amsterdam 1043 NTThe Netherlands Faculty of Science(HIMS and IAS) University of AmsterdamAmsterdam 1090 GDThe Netherlands School of Advanced International Studies(SAIS) Johns Hopkins UniversityBologna 40126Italy

Successful deployment of renewable fuel production requires substantial cost reduction along the entire value chain of the underlying manufacturing *** improve their performance,renewable fuel production technologies should follow a cost-reducing learning *** this article,we adopt recent evidence that learning-by-doing is directly influenced by the technology unit size and explore three scenarios for microwave plasma CO_(2)conversion in which the learning rate varies between 10%,15%,and 20%.Our projections reveal that the total investments required to deploy this CO_(2)conversion technology at an exajoule scale decline from 83 down to 23 billion euros under a 10%increase in the value of the learning *** CO_(2) production costs in 2050 amount to 247–346€(2019)/t CO_(2),in which the range is determined by the value of the learning *** under substantial learning until 2050 the levelized CO production cost is unlikely to become competitive with conventional natural gas-based CO_(2) production processes,except when a CO_(2)tax is applied of up to 150€(2019)/t CO_(2).to optimally exploit effects of learning-by-doing,we recommend developing several CO production technologies simultaneously with multiple unit sizes,so as to improve the chance of ultimately selecting the process with the highest learning rate.

关键词： CO_(2)utilization Synthetic fuels Renewable chemicals Learning curves Unit size

Acute lung injury in mechanically ventilated patients with epidermal necrolysis:an exposed-unexposed retrospective cohort study

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Burns & trauma 2020年第1期8卷 30-33页

作者： S.Lalevée j.Catano S.Ingen-Housz-Oro M.Surenaud j.t.an van nhieu F.Schlemmer I.Bendib A.Mekontso-Dessap S.Hue N.de Prost Service de dermatologie AP-HPhoital Henri MondorCréteilFrance UniversitéParis Est Créteil INSERM U955IMRBF-94010 CréteilFrance Service de Médecine Intensive Réanimation Hoitaux Universitaires Henri MondorAssistance Publique-Hoitaux de ParisCréteil Cedex 94010France EA7379 EpidermE UPECCréteilFrance Centre de référence des dermatoses bulleuses toxiques et toxidermies graves tOXIBUL CréteilFrance Service d’Anatomopathologie AP-HPhoital Henri MondorCréteilFrance Unitéde Pneumologie Service de Médecine Intensive RéanimationHoitaux Universitaires Henri MondorAssistance Publique-Hoitaux de ParisCréteil Cedex 94010France Groupe de Recherche Clinique CARMAS Facultéde Santéde CréteilUniversitéParis Est CréteilCréteil Cedex 94010France AP-HP Département d’Hématologie et d’Immunologie biologiquesGroupe hospitalouniversitaire Chenevier MondorAssistance Publique-Hoitaux de Paris F-94010 CréteilFrance

to the Editor,During the acute phase of epidermal necrolysis(EN,including Stevens-johnson syndrome and toxic epidermal necrolysis),mucosal lesions involving the tracheo-bronchial tract have been reported[1,2]and approximately one in four EN patients develop acute respiratory failure and require endotracheal intubation and mechanical ventilation(MV)support[3].Asymptomatic respiratory sequelae may be detected on pulmonary function tests after the acute phase in as much as 50%of EN patients,possibly related to pulmonary lesions that occurred at the acute phase[4].

关键词： acute patients respiratory

Supplementing oat hulls to the diet of suckling piglets altered their intestinal tract and colonic microbiota development

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Animal Nutrition 2023年第1期12卷 284-296页

作者： Hubèrt M.j.van Hees Koen Chiers Leo A.den Hartog theo A.t.G.van Kempen Dominiek Maes Sam Millet Geert P.j.janssens Department of Veterinary and Biosciences Ghent UniversityMerelbekeBelgium trouw Nutrition Research and Development Amersfoortthe Netherlands Department of Pathology Ghent UniversityMerelbekeBelgium Animal Nutrition Wageningen University and ResearchWageningenthe Netherlands Department of Animal Science North Carolina State UniversityRaleighNCUSA Department of Reproduction Obstetrics and Herd HealthGhent UniversityMerelbekeBelgium ILVO(Flanders Research Institute for Agriculture Fisheries and Food)MelleBelgium

Current study evaluated the effect of a fine and coarsely ground insoluble dietary fibre source on the gastrointestinal development of suckling *** hulls(OH)were selected as a model feedstuff,rich in cellulose,lignin,and insoluble dietary *** experimental supplemental diets were formulated:a finely ground,low fibre and nutrient dense diet served as control(CON).For the 2 high fibre diets,15%heat-treated starch in CON was exchanged with OH,either finely(OH-f)or coarsely ground(OH-c).Litters of 10 primi-and multiparous sows(mean litter size 14.6±0.84)were *** a litter,experimental diets were allotted to triplets of 4 *** approximately 12 d of age,piglets’individual feed intakes were recorded 2 times per day when separated from their dam for 70 *** could suckle with their dam for the remainder of the *** d 24 and 25,from the total pool of 120 piglets,seven healthy well-eating piglets per treatment were selected for post-mortem evaluation,resulting in 14 replicates per *** of OH-c and OH-f did not impede clinical health and production performance of *** full stomach weights tended to be greater for OH-c compared to OH-f whereas CON was intermediate(P=0.083).Supplementing OH significantly increased ileal villus height and caecal dry matter concentration(Pthe colon,OH increased its length,contents weight,short-chain fatty acid concentration and reduced total bacterial count as well asγ-proteobacteria count and proportion(Pthe OH-c treatment specifically increased full gastrointestinal tract weight and caecum contents weight compared to piglets fed CON and ***,OH-c reduced colonic crypt depth when compared to OH-f(P=0.018).In conclusion,supplementing OH to a diet for suckling piglets exerted subtle developmental effects on gastrointestinal morphology and colonic microbial *** effects were largely independent from the particle size of the OH.

关键词： Oat hull Insoluble fibre Gastrointestinal development Suckling piglet

Bacterial inclusion bodies function as vehicles for dendritic cell-mediated t cell responses

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Cellular & Molecular Immunology 2020年第4期17卷 415-417页

作者： Sjoerd t.t.Schetters Wouter S.P.jong Laura j.W.Kruijssen H.B.van den Berg van Saparoea Steef Engels Wendy W.j.Unger Diane Houben joke M.M.den Haan joen Luirink Yvette van Kooyk Department of Molecular Cell Biology and Immunology Amsterdam UMCLocation VUmcAmsterdamThe Netherlands Abera Bioscience AB SolnaSweden Laboratory of Pediatrics Division of Pediatric Infectious Diseases and ImmunologyErasmus MC-Sophia Children’s HospitalRotterdamThe Netherlands Department of Molecular Cell Biology Section Molecular MicrobiologyFaculty of ScienceVU UniversityAmsterdamThe Netherlands

Immunogenic antigens for vaccination are often created through the production of recombinant proteins using Escherichia coli.1 As a side product,aggregates called inclusion bodies(IBs)are formed,containing largely misfolded forms of the overexpressed recombinant protein.2 the effect of IBs on the immune system and whether they can be used as effective vaccine products remain *** non-native conformation of proteins upon accumulation in IBs abrogates their use as vaccines aimed at generating high-affinity antibodies.3 However,IBs exhibit unique properties,including mechanical and thermal stability due to their intrinsic particulate nature,biocompatibility,high antigenic content,low toxicity and relative resistance to *** characteristics make IBs attractive as an antigenic vaccine formulation for t cell responses to linear *** IBs can trigger adaptive cellular responses initiated via uptake by dendritic cells for presentation to t cells is unknown.

关键词： vaccine attractive initiated

Using occupancy models to determine mammalian responses to landscape changes

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Integrative Zoology 2009年第2期4卷 232-239页

作者： jeremy M.NICHOLSON Frank t.van MANEN Department of Forestry Wildlifeand FisheriesUniversity of TennesseeKnoxvilleTennesseeUSA US Geological Survey Southern Appalachian Research BranchUniversity of TennesseeKnoxvilleTennesseeUSA

Determining impacts of anthropogenic landscape changes on wildlife populations is *** the challengesDetermining impacts of anthropogenic landscape changes on wildlife populations is *** the challenges of designing field studies to document conditions before and after landscape changes occur,assessment of popula-of designing field studies to document conditions before and after landscape changes occur,assessment of popula-tion responses(*** in population density)often provide poor inference because of sampling *** responses(*** in population density)often provide poor inference because of sampling *** of occupancy,however,only requires data on detection or non-detection of a species and might provideEstimation of occupancy,however,only requires data on detection or non-detection of a species and might provide better *** demonstrate the utility of occupancy models,we used data from an American black bear(Ursusbetter *** demonstrate the utility of occupancy models,we used data from an American black bear(Ursus americanus Pallas)population in North Carolina,USA to test our research hypothesis that documented declines inamericanus Pallas)population in North Carolina,USA to test our research hypothesis that documented declines in site occupancy of black bears would be greater near a new four-lane *** used multi-season occupancysite occupancy of black bears would be greater near a new four-lane *** used multi-season occupancy models to estimate site occupancy based on bear visitation to survey sites before and after completion of the newmodels to estimate site occupancy based on bear visitation to survey sites before and after completion of the new highway and as a function of distance to the *** occupancy declined from 0.81 to 0.35 between the twohighway and as a function of distance to the *** occupancy declined from 0.81 to 0.35 between the two s

关键词： landscape changes mammalian responses occupancy models transportation infrastructure Ursus americanus.

the Prognostic Value of Myocardial Deformation in Patients with Congenital Aortic Stenosis

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Congenital Heart Disease 2021年第3期16卷 221-232页

作者： Roderick W.j.van Grootel Allard t.van den Hoven Dan Bowen tijmen Ris jolien W.Roos-Hesselink Annemien E.van den Bosch Department of Cardiology Erasmus Medical CentreRotterdamThe Netherlands

Aims:to assess the prognostic value of left ventricular(LV)global longitudinal strain(GLS)and global longitudinal early diastolic strain rate(GLSre)with regard to cardiovascular events,as congenital aortic stenosis(AoS)is associated with significant mortality and morbidity but predictors for clinical outcome are *** analysis provides a robust and reproducible method for early detection of LV dysfunction,which might be of prognostic ***:this prospective study,included clinically stable patients with congenital AoS between 2011–*** GLS and GLSre was performed in the apical 4,3 and 2-chamber views using tomtec *** endpoint was a composite of death,heart failure,hospitalization,arrhythmia,thrombo-embolic events and ***:In total 138 patients were included(33[26–43]years,86(62%)male),NYHA class I:134(97%).Mean LV GLS was–15.3±3.2%,GLSre 0.66±0.18 s–*** correlated with Nt-proBNP,LV volumes and ejection fraction(strongest LV GLS with LV EF:r–0.539,ptrongest LV GLSre with age:r–0.376,pthe endpoint occurred in 53(38%)patients:4 patients died,9 developed heart failure,22 arrhythmias,8 thrombo-embolic events and 35 *** LV GLS(standardized HR(sHR 0.62(95%CI 0.47–0.81)and GLSre(sHR 0.62(95%CI 0.47–0.83)were associated with the *** multivariable analysis showed that both GLS and GLSre were associated independent of left atrial volume,Nt-proBNP and prior ***:Left ventricular GLS and GLSre are reduced in adult patients with congenital *** markers are associated with adverse cardiac events and have clear clinical relevance.

关键词： Speckle tracking echocardiography congenital aortic stenosis strain prognosis