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SuperSAGE digital expression analysis of differential growth rate in a European sea bass population

Aquaculture and Fisheries 2019年第1期4卷 17-26页

作者： Bruno Louro Rute S.T.Martins Patricia I.S.Pinto Richard Reinhardt dirk-jan de koning Adelino V.M.Canario deborah M.Power CCMAR-Centre of Marine Sciences University of AlgarveCampus de GambelasFaro 8005-139Portugal Max Planck Genome Centre Carl-von-Linne-Weg 10Köln 50829Germany The Roslin Institute and R(D)SVS University of EdinburghEaster BushMidlothian EH259RGScotland UK department of Animal Breeding and Genetics Swedish University of Agricultural SciencesBox 7023Uppsala 75007Sweden

One of the goals of the aquaculture industry is to understand and control growth associated traits through selective *** the present study the molecular basis of growth heterogeneity in the European sea bass(Dicentrarchus labrax)was *** establish growth heterogeneity in a group of hatchery bred sea bass individuals were tagged and their specific growth rates(SGR)determined at monthly *** expression in the brain,liver and white muscle from fish with the most divergent sustained SGR(6 individuals of the first and last quartile)was assessed using SuperSAGE(Serial Analysis Gene Expression)combined with next generation SOLiD4 sequencing.A total of approx.11 million edited tags(26 bp),on average 2 million tags per SAGE library,that represented 47.071 unique transcripts were *** of transcripts in fish with high and low SGR yielded 344,698 and 601 differently expressed tags(0.01%false discovery rate and 4-fold change)in brain,liver and muscle,*** tags were mapped onto the sea bass genome and approximately one third of the tags could be assigned to annotated *** enrichment analysis revealed in liver,muscle and brain intricate gene expression changes in endocrine regulatory pathways involved in growth,metabolic and the stress axis,underlying divergent SGR in sea bass.

关键词： European sea bass Specific growth rate Gene expression SuperSAGE Pathways

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Utilization of fly ash from coal-fired power plants in China

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Journal of Zhejiang University-Science A(Applied Physics & Engineering) 2008年第5期9卷 681-687页

作者： Eva SELIC jan-dirk HERBELL Waste Management Engineering Department of Mechanical Engineering University of Duisburg-Essen Duisburg 47057 Germany

The rapidly increasing demand for energy in China leads to the construction of new power plants all over the country. Coal, as the main fuel resource of those power plants, results in increasing problems with the disposal of solid residues from combustion and off gas cleaning. This investigation describes chances for the utilization of fly ash from coal-fired power plants in China. After briefly comparing the situation in China and Germany, the status of aluminum recycling from fly ash and the ad- vantages for using fly ash in concrete products are introduced. Chemical and physical analyses of Chinese fly ash samples, e.g., X-ray diffraction (XRD), ICP (Inductive Coupled Plasma) and particle size analysis, water requirement, etc. are presented. Rea- sonable amounts of aluminum were detected in the samples under investigation, but for recovery only sophisticated procedures are available up to now. Therefore, simpler techniques are suggested for the first steps in the utilization of Chinese fly ash.

关键词： Fly ash utilization Aluminum recycling Concrete Chemical and physical analyses

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Diagnostic utility of faecal biomarkers in patients with irritable bowel syndrome

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World Journal of Gastroenterology 2014年第2期20卷 363-375页

作者： jan Dabritz Jason Musci dirk Foell Gastrointestinal Research in Inflammation and Pathology Murdoch Children’s Research InstituteThe Royal Children’s Hospital MelbourneParkville 3052VICAustralia department of Paediatrics Melbourne Medical SchoolUniversity of MelbourneParkville 3052VICAustralia department of Paediatric Rheumatology and Immunology University Children’s Hospital Munster48149 MunsterGermany

Irritable bowel syndrome(IBS)is a common functional gastrointestinal(GI)disorder characterized by unspecific *** clinical practice it is crucial to distinguish between non-inflammatory functional problems and inflammatory,malignant or infectious diseases of the GI *** between these involves the use of clinical,radiological,endoscopic,histological and serological techniques,which are invasive,expensive,time-consuming and/or hindered by inaccuracies arising from subjective components.A range of faecal markers now appears to have the potential to greatly assist in the differentiation of inflammatory bowel disease(IBD)and *** markers of neutrophil influx into the mucosa are reliable indicators of intestinal inflammation and their role has been mainly studied in discriminating IBD from non-IBD conditions(including IBS)rather than organic from non-organic *** proteins of the S100 family(S100A12,calprotectin)are amongst the most promising faecal biomarkers of *** leukocyte degranulation markers(lactoferrin,polymorphonuclear elastase and myeloperoxidase)have also been suggested as diagnostic tools for the differentiation of IBD and *** recently,additional proteins,including granins,defensins and matrix-metalloproteases,have been discussed as differential diagnostic markers in IBD and *** this review,some of the most promising faecal markers,which have the potential to differentiate IBD and IBS and to advance diagnostic practices,will be discussed.

关键词： S100A12 Calprotectin Lactoferrin M2-pyruvate kinase Polymorphonuclear elastase defensins Granins Irritable bowel syndrome

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Quark-Novae Ia in the Hubble diagram: implications for dark energy

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Research in Astronomy and Astrophysics 2014年第5期14卷 497-519页

作者： Rachid Ouyed Nico koning denis Leahy jan E.Staff Daniel T.Cassidy department of Physics and Astronomy University of Calgary 2500 University Drive NWCalgary Alberta T2N 1N4 Canada department of Physics and Astronomy Macquarie University NSW 2109 Australia department of Engineering Physics McMaster University Hamilton Ontario L8S 4L7 Canada

The accelerated expansion of the Universe was proposed through the use of Type-Ia supernovae （SNe） as standard candles. The standardization depends on an empirical correlation between the stretch/color and peak luminosity of the light curves. The use of Type-Ia SNe as standard candles rests on the assumption that their properties （and this correlation） do not vary with redshift. We consider the possibility that the majority of Type-Ia SNe are in fact caused by a Quark-Nova detonation in a tight neutron-star-CO-white-dwarf binary system, which forms a Quark-Nova Ia （QN-Ia）. The spin-down energy injected by the Quark-Nova remnant （the quark star） contributes to the post-peak light curve and neatly explains the observed correlation between peak luminosity and light curve shape. We demonstrate that the parameters describing QN-Ia are NOT constant in redshift. Simulated QN-Ia light curves provide a test of the stretch/color correlation by comparing the true distance modulus with that determined using SN light curve fitters. We determine a correction between the true and fitted distance moduli, which when applied to Type-Ia SNe in the Hubble diagram recovers the ΩM = 1 cosmology. We conclude that Type-Ia SNe observations do not necessitate the need for an accelerating expansion of the Universe （if the observed SNe Ia are dominated by QNe Ia） and by association the need for dark energy.

关键词： dark energy -- cosmology observations -- supernovae general

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Fluid-rock interaction in retrograde granulites of the Southern Marginal Zone,Limpopo high grade terrain,South Africa

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Geoscience Frontiers 2014年第5期5卷 673-682页

作者： jan Marten Huizenga dirk van Reenen Jacques L.R.Touret Unit of Environmental Sciences and Management North-West UniversityPrivate Bag X60012520South Africa Economic Geology Research Institute(EGRU) School of Earth and Environmental SciencesJames Cook UniversityTownsvilleQLD 4811Australia department of Geology University of JohannesburgJohannesburgSouth Africa Institut de Mineralogie.de Physique des Materiaux et de Cosmochimie(IMPMC) Sorbonne Universites UPMC Univ Paris 06UMR CNRS 7590 Museum National d'Histoire Naturelle.IRD UMR 206.4 Place Jussieu.F-75005

Fluid infiltration into retrograde granulites of the Southern Marginal Zone （Limpopo high grade terrain） is exemplified by hydration reactions, shear zone hosted metasomatism, and lode gold mineralisation. Hydration reactions include the breakdown of cordierite and orthopyroxene to gedrite ＋ kyanite, and anthophyllite, respectively. Metamorphic petrology, fluid inclusions, and field data indicate that a low H2O-activity carbon-saturated CO2-rich and a saline aqueous fluid infiltrated the Southern Marginal Zone during exhumation. The formation of anthophyllite after orthopyroxene established a regional retrograde anthophyllite-in isograd and occurred at P-Tconditions of -6 kbar and 610 ℃, which fixes the minimum mole fraction of H20 in the CO2-rich fluid phase at ~ 0.1. The maximum H20 mole fraction is fixed by the lower temperature limit （~800 ℃） for partial melting at -0.3. C-O-H fluid calculations show that the CO2-rich fluid had an oxygen fugacity that was 0.6 log10 units higher than that of the fayalite-magnetite- quartz buffer and that the CO2/（CO2＋CH4） mole ratio of this fluid was 1. The presence of dominantly relatively low density CO2-rich fluid inclusions in the hydrated granulites indicates that the fluid pressure was less than the lithostatic pressure. This can be explained by strike slip faulting and/or an increase of the rock permeability caused by hydration reactions.

关键词： GranuliteFluidLimpopoRetrogradeSouthern Marginal Zone

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Gene expression,transcription factor binding and histone modification predict leaf adaxial-abaxial polarity related genes

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Horticultural Plant Journal 2024年第4期10卷 971-982页

作者： Wei Sun Zhicheng Zhang Guusje Bonnema Xiaowu Wang Aalt dirk jan van Dijk State Key Laboratory of Vegetable Biobreeding Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing 100081China Sino-Dutch Joint Lab of Vegetable Genomics Beijing 100081China Bioinformatics Group Wageningen University and Research6708 PB Wageningenthe Netherlands Plant Breeding Wageningen University and Research6708 PB Wageningenthe Netherlands Biosystems Data Analysis Swammerdam Institute for Life SciencesUniversity of Amsterdam1090 GE Amsterdamthe Netherlands

Leaf adaxial-abaxial(ad-abaxial)polarity is crucial for leaf morphology and function,but the genetic machinery governing this process remains *** uncover critical genes involved in leaf ad-abaxial patterning,we applied a combination of in silico prediction using machine learning(ML)and experimental analysis.A Random Forest model was trained using genes known to influence ad-abaxial polarity as ground *** expression data from various tissues and conditions as well as promoter regulation data derived from transcription factor chromatin immunoprecipitation sequencing(ChIP-seq)was used as input,enabling the prediction of novel ad-abaxial polarity-related genes and additional transcription *** to this,available and newly-obtained transcriptome data enabled us to identify genes differentially expressed across leaf ad-abaxial *** on these analyses,we obtained a set of 111 novel genes which are involved in leaf ad-abaxial *** explore implications for vegetable crop breeding,we examined the conservation of expression patterns between Arabidopsis and Brassica rapa using single-cell *** results demonstrated the utility of our computational approach for predicting candidate genes in crop *** findings expand the understanding of the genetic networks governing leaf ad-abaxial differentiation in agriculturally important vegetables,enhancing comprehension of natural variation impacting leaf morphology and development,with demonstrable breeding applications.

关键词： Machine learning Leaf polarity Arabidopsis thaliana Brassica rapa Transcription factor

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Value of macrobiopsies and transanal endoscopic microsurgery in the histological work-up of rectal neoplasms:A retrospective study

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World Journal of Gastrointestinal Oncology 2017年第6期9卷 251-256页

作者： Guus MJ Bokkerink Gert-jan van der Wilt dirk de Jong Han HJM van Krieken Robert P Bleichrodt Johannes HW de Wilt Andreas JA Bremers department of Surgery Radboud University Nijmegen Medical Center department of Health Evidence Radboud University Nijmegen Medical Center department of Gastroenterology Radboud Uni-versity Nijmegen Medical Center department of Pathology Radboud University Nijmegen Medical Center department of of Surgery Saint Francis Hospital

To evaluate a step up approach: Taking macrobiopsies and performing excision biopsies in patients with suspected rectal cancer in which biopsies taken though the flexible endoscope showed benign histology. METHODSPatients with a rectal neoplasm who underwent flexible endoscopy and biopsies were included. In case of benign biopsies rigid rectoscopy and macrobiopsies were employed. If this failed to prove malignancy, transanal endoscopic microsurgery (TEM) was used in a final effort to establish a certain preoperative diagnosis. The preoperative results were compared with the findings after surgical excision and follow up to calculate the reliability of this algorithm. RESULTSOne hundred and thirty-two patients were included. One hundred and ten patients with a carcinoma and 22 with an adenoma. Seventy-five of 110 carcinomas were proven malignant after flexible endoscopy. With the addition of rigid endoscopy and taking of macrobiopsies, this number increased to 89. Performing TEM excision biopsies further enlarged the number of proven malignancies to 100. CONCLUSIONThe step-up approach includes taking macrobiopsies through the rigid rectoscope and performing excision biopsies using transanal endoscopic microsurgery in addition to flexible endoscopy. This approach, reduced the number of missed preoperative malignant diagnoses from 32% to 9%.

关键词： Rectal cancer Histology Biopsy Macrobiopsy Transanal endoscopic microsurgery Sampling error

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Improved patient reported outcomes with functional articulating spacers in two-stage revision of the infected hip

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World Journal of Orthopedics 2020年第12期11卷 595-605页

作者： Ewout S Veltman dirk jan F Moojen Rudolf W Poolman department of Orthopaedic and Trauma Surgery OLVGAmsterdam 1091ACNetherlands Orthopaedic and Trauma Surgery OLVGAmsterdam 1091ACNetherlands department of Orthopaedic Surgery and Joint Research OLVGAmsterdam 1091ACNetherlands

BACKGROUND Two-stage revision arthroplasty with an antibiotic-loaded spacer is the treatment of choice in chronically infected total hip *** spacers can be functional articulating or *** results of these spacers have scarcely been *** To compare retrospectively the patient reported outcome and infection eradication rate after two-stage revision arthroplasty of the hip with the use of a functional articulating or prefabricated *** All patients with two-stage revision of a hip prosthesis at our hospital between 2003 and 2016 were included in this retrospective cohort *** were divided into two groups;patients treated with a functional articulating spacer or with a prefabricated *** completed the Hip Osteoarthritis Outcome Score and the EQ-5D-3L(EQ-5D)and the EQ-5D quality of life thermometer(EQVAS)*** outcomes were patient reported outcome and infection eradication after two-stage *** results of both groups were compared to the patient acceptable symptom state for primary arthroplasty of the *** outcomes were complications during spacer treatment and at final *** statistics,mean and range are used to represent the demographics of the *** numerical variables,students’t-tests were used to assess the level of significance for differences between the groups,with 95%confidence intervals;for binary outcome,we used Fisher’s exact *** We consecutively treated 55 patients with a prefabricated spacer and 15 patients with a functional articulating spacer of the *** infection eradication rates for functional articulating and prefabricated spacers were 93%and 78%,respectively(P>0.05).With respect to the functional outcome,the Hip Osteoarthritis Outcome Score(HOOS)and its subscores(all P<0.01),the EQ-5D(P<0.01)and the EQVAS scores(P<0.05)were all significantly better for patients successfully treated with a functional articulating

关键词： Two-stage revision Periprosthetic joint infection Hip arthroplasty Functional articulating spacer Prefabricated spacer Patient reported outcome

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3D U-Net Segmentation Improves Root System Reconstruction from 3D MRI Images in Automated and Manual Virtual Reality Work Flows

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Plant Phenomics 2023年第3期5卷 598-611页

作者： Tobias Selzner jannis Horn Magdalena Landl Andreas Pohlmeier dirk Helmrich Katrin Huber jan Vanderborght Harry Vereecken Sven Behnke Andrea Schnepf Forschungszentrum Juelich GmbH Agrosphere(IBG-3)JuelichGermany Autonomous Intelligence Systems Group University of BonnBonnGermany Forschungszentrum Juelich GmbH Juelich Supercomputing CenterJuelichGermany

Magnetic resonance imaging(MRI)is used to image root systems grown in opaque ***,reconstruction of root system architecture(RSA)from 3-dimensional(3D)MRI images is *** resolution and poor contrast-to-noise ratios(CNRs)hinder automated ***,manual reconstruction is still widely ***,we evaluate a novel 2-step work flow for automated RSA *** the first step,a 3D U-Net segments MRI images into root and soil in *** the second step,an automated tracing algorithm reconstructs the root systems from the segmented *** evaluated the merits of both steps for an MRI dataset of 8 lupine root systems,by comparing the automated reconstructions to manual reconstructions of unaltered and segmented MRI images derived with a novel virtual reality *** found that the U-Net segmentation offers profound benefits in manual reconstruction:reconstruction speed was doubled(+97%)for images with low CNR and increased by 27%for images with high *** root lengths were increased by 20%and 3%,***,we propose to use U-Net segmentation as a principal image preprocessing step in manual work *** root length derived by the tracing algorithm was lower than in both manual reconstruction methods,but segmentation allowed automated processing of otherwise not readily usable MRI ***,model-based functional root traits revealed similar hydraulic behavior of automated and manual *** studies will aim to establish a hybrid work flow that utilizes automated reconstructions as scaffolds that can be manually corrected.

关键词： Root utilize otherwise

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Melody Generator: A device for Algorithmic Music Construction

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Journal of Software Engineering and Applications 2010年第7期3卷 683-695页

作者： dirk-jan Povel 不详

This article describes the development of an application for generating tonal melodies. The goal of the project is to ascertain our current understanding of tonal music by means of algorithmic music generation. The method followed consists of four stages: 1) selection of music-theoretical insights, 2) translation of these insights into a set of principles, 3) conversion of the principles into a computational model having the form of an algorithm for music generation, 4) testing the “music” generated by the algorithm to evaluate the adequacy of the model. As an example, the method is implemented in Melody Generator, an algorithm for generating tonal melodies. The program has a structure suited for generating, displaying, playing and storing melodies, functions which are all accessible via a dedicated interface. The actual generation of melodies, is based in part on constraints imposed by the tonal context, i.e. by meter and key, the settings of which are controlled by means of parameters on the interface. For another part, it is based upon a set of construction principles including the notion of a hierarchical organization, and the idea that melodies consist of a skeleton that may be elaborated in various ways. After these aspects were implemented as specific sub-algorithms, the device produces simple but well-structured tonal melodies.

关键词： Principles of Tonal Music Construction Algorithmic Composition Synthetic Musicology Computational Model Realbasic OOP Melody Meter Key

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