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Salt Dependent Association of Novel Mutants of TATA-Binding Proteins to DNA:Predictions from Theory and Experiments

Communications in Computational Physics 2008年第5期3卷 1132-1153页

作者： johan H.Bredenberg Marcia O.Fenley Institute of Molecular Biophysics Florida State UniversityTallahasseeFL 32306USA. Department of Physics Florida State UniversityTallahasseeFL 32306USA.

The nonlinear Poisson-Boltzmann predictions of the salt-dependent association of proteins to DNA,SKpred,are fairly insensitive to the choice of atomic charges,radii,interior dielectric constant and treatment of the boundary between a biomolecule and the *** this study we show that the SKpred is highly correlated with the conformational adaptability of the partners involved in the biomolecular binding *** is demonstrated for the wild-type and mutant forms of the archaeon Pyrococcus woesi TATA-binding protein(PwTBP)in complex with DNA,on which we performed molecular mechanics energy minimizations with different protocols,and molecular dynamics simulations and then computed the SKpred on the resulting *** was found that the inter-molecular non bonded force field energy between the DNA and protein correlates linearly and significantly well with the *** correlation encompasses the wild-type and mutant variants of the PwTBP and provides us with a quick way to estimate the SKpred from a large ensemble of structures generated with Molecular Dynamics or Monte Carlo *** corresponding experimental SKobs should also correlate with the inter-molecular non bonded force field energy between the protein and DNA,given that the underlying mechanisms in binding and salt-dependent effects are in fact the main contributors in the association of proteins/peptides to nucleic *** show that it is possible to fit experiments versus the inter-molecular non bonded force field energy between the protein and DNA,and use this relation to predict the SKobs in absolute ***,we present two novel approaches to estimate both the SKpred and the SKobs for in silico modelled PwTBP novel mutants and even for TBPs from other *** is a simple but powerful tool to suggest new experiments on the TBP-DNA type of macromolecular *** conclude by suggesting some mutants and a possible biological interpretation of how changes in solvent

关键词： Poisson-Boltzmann equation electrostatics salt dependence binding molecular mechanics DNA TATA binding proteins.

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Study of industrially applied methods for verification, validation and uncertainty quantification of simulator models

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International Journal of Modeling, Simulation, and Scientific Computing 2015年第2期6卷 56-84页

作者： Magnus Eek Sogol Kharrazi Hampus Gavel johan Olvander Saab Aeronautics Linkoping SE-58188Sweden Swedish National Road and Transport Research Institute(VTI)Linkoping SE-58195Sweden Linkoping University Linkoping SE-58183Sweden

To better utilize the potential of system simulation models and simulators,industrially applicable methods for Verification,Validation and Uncertainty Quantification(VV&UQ)are *** paper presents an exploratory case study of VV&UQ techniques applied on models integrated in aircraft system simulators at Saab Aeronautics and in driving simulators at the Swedish National Road and Transport Research Institute(VTI).Results show that a large number of Verification and Validation(V&V)techniques are applied,some of which are promising for further development and use in simulator credibility *** the application of UQ,a large gap between academia and this part of industry has been identified,and simplified methods are *** applicability of the NASA Credibility Assessment Scale(CAS)at the studied organizations is also evaluated and it can be concluded that the CAS is considered to be a usable tool for achieving a uniform level of V&V for all models included in a simulator,although its implementation at the studied organizations requires tailoring and coordination.

关键词： Simulator credibility simulation model verification validation uncertainty quantification V&V VV&UQ NASA Credibility Assessment Scale

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Carbon nanotubes for electronics manufacturing and packaging:from growth to integration

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Advances in Manufacturing 2013年第1期1卷 13-27页

作者： johan Liu Di Jiang Yifeng Fu Teng Wang Department of Microtechnology and Nanoscience Chalmers University of Technology Key Laboratory of Advanced Display and System Applications and SMIT Center School of Automation and Mechanical Engineering Shanghai University SHT Smart High Tech AB Fysikgrnd 3412 96 GothenburgSweden

Carbon nanotubes （CNTs） possess excellent electrical, thermal and mechanical properties. They are light in weight yet stronger than most of the other materials. They can be made both highly conductive and semi-conductive. They can be made from nano-sized small catalyst particles and extend to tens of millimeters long. Since CNTs emerged as a hot topic in the early 1990s, numerous research efforts have been spent on the study of the various properties of this new material. CNTs have been proposed as alternative materials of potential excellence in a lot of applications such as electronics, chemical sensors, mechanical sensors/actuators and composite materials, etc. This paper reviews the use of CNTs particularly in electronics manufacturing and packaging field. The progresses of three most important applications, including CNT-based thermal interface materials, CNT-based interconnections and CNT-based cooling devices are reviewed. The growth and post-growth processing of CNTs for specific applications are introduced and the tai- loring of CNTs properties, i.e., electrical resistivity, thermal conductivity and strength, etc., is discussed with regard to specific application requirement. As the semiconductor industry is still driven by the need of getting smaller and faster, CNTs and the related composite systems as emerging new materials are likely to provide the solution to the future challenges as we make more and more complex electronics devices and systems.

关键词： Carbon nanotubes Electronicsmanufacturing Electronics packaging - Growth Integration

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Diagnosis and management of microscopic colitis

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World Journal of Gastroenterology 2008年第48期14卷 7280-7288页

作者： Curt Tysk johan Bohr Nils Nyhlin Anna Wickbom Sune Eriksson Department of Medicine Division of Gastroenterology rebro University Hospital and School of Health and Medical Sciences rebro University Department of Pathology rebro University Hospital

Microscopic colitis, comprising collagenous and lymphocytic colitis, is characterized clinically by chronic watery diarrhea, and a macroscopically normal colonic mucosa where diagnostic histopathological features are seen on microscoplc incidence of each disorder examination. The annual is 4-6/100000 inhabitants, with a peak incidence in 60-70-year-old individuals and a noticeable female predominance for collagenous colitis. The etiology is unknown. Chronic diarrhea, abdominal pain, weight loss, fatigue and fecal incontinence are common symptoms, which impair the health-related quality of life of the patient. There is an association with other autoimmune disorders such as celiac disease, diabetes mellitus, thyroid disorders and arthritis. Budesonide is the best-documented shortterm treatment, but the optimal long-term strategy needs further study. The long-term prognosis is good and the risk of complications including colonic cancer is low.

关键词： Microscopic colitis Collagenous colitis Lymphocytic colitis Chronic diarrhea Budesonide

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Subregion graph: A path planning acceleration structure for characters with various motion types in very large environments

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Computational Visual Media 2015年第2期1卷 105-118页

作者： Nicholas Mario Wardhana Henry johan Hock Soon Seah Multi-plAtform Game Innovation Centre(MAGIC) Nanyang Technological University School of Computer Engineering Nanyang Technological University Fraunhofer IDM NTU Nanyang Technological University

Modern computer graphics applications commonly feature very large virtual environments and diverse characters which perform different kinds of motions. To accelerate path planning in such a scenario, we propose the subregion graph data structure. It consists of subregions, which are clusters of locally connected waypoints inside a region, as well as subregion connectivities. We also present a fast algorithm to automatically generate a subregion graph from an enhanced waypoint graph map representation,which also supports various motion types and can be created from large virtual environments. Nevertheless,a subregion graph can be generated from any graphbased map representation. Our experiments show that a subregion graph is very compact relative to the input waypoint graph. By firstly planning a subregion path, and then limiting waypoint-level planning to this subregion path, over 8 times average speedup can be achieved, while average length ratios remain as low as102.5%.

关键词： path planning acceleration very large environments motion types abstraction

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Gastric accommodation assessed by ultrasonography

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World Journal of Gastroenterology 2006年第18期12卷 2825-2829页

作者： Odd Helge Gilja johan Lunding Trygve Hausken Hans Gregersen National Centre for Ultrasound in Gastroenterology Haukeland University HospitalInstitute of MedicineUniversity of BergenBergenNorway Center for Visceral Biomechanics and Pain Aalborg Hospitaland Center for Sensory-motor InteractionAalborg UniversityDenmark

Gastric accommodation is important for the understanding of the pathophysiology in functional dyspepsia and is also relevant for symptom generation in other disorders. The term gastric accommodation has at least three different meanings： The accommodation process, the accommodation reflex, and the accommodation response. The gastric accommodation process is a complex phenomenon that describes how the size of the gastric compartment changes in response to a meal. The electronic barostat is considered the gold standard in assessing gastric accommodation. Imaging methods, including MRI, SPECT, and ultrasonography may also be used, particularly in patients who are stress-responsive, e.g. functional dyspepsia patients, as a non-invasive and less stress-inducing method is favourable. Ultrasonography satisfies these criteria as it does not by itself distort the physiological response in stress-responsive individuals.

关键词： Ultrasonography Gastric accommodation Stomach Barostat Gastric relaxation 3D ultrasound

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A New Enantiornithes(Aves) from the Early Cretaceous of China

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Acta Geologica Sinica(English Edition) 2014年第4期88卷 1034-1040页

作者： johan DALSTT Per G.P.ERICSON Zhonge ZHOU Department of Vertebrate Zoology Swedish Museum of Natural History Department of Geological Sciences Stockholm University Institute of Vertebrate Paleontology and Paleoanthropology Chinese Academy of Sciences

A new bird from the early Cretaceous Yixian Formation of Liaoning, China is described. This new species, Grabauornis lingyuanensis, shares several synapomorphies with the Enantiornithes. The specimen is relatively well preserved. The skeletal morphology of Grabauornis bears close resemblance to that of other Chinese members of this clade. The brachial index （the ratio between the lengths of humerus and ulna） is 0.95, which is close to the average for enantiornithine birds. It indicates that Grabauornis was a rather good flyer, and the presence of an alula in the wing further testifies to this.

关键词： Enantiornithes Aves Early Cretaceous Yixian Formation Liaoning China

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Risk factors and outcomes for patients with pancreatic cancer undergoing surgical exploration without resection due to metastatic disease:A national cohort study

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Hepatobiliary & Pancreatic Diseases International 2022年第3期21卷 279-284页

作者： Emil Sahlstrom Paulina Bereza-Carlson johan Nilsson Bobby Tingstedt Bodil Andersson Department of Clinical Sciences Lund SurgeryLund UniversitySweden Department of Surgery Central Hospital KristianstadSweden Department of Translational Medicine Cardiothoracic surgery and bioinformaticsLund UniversitySweden Department of Thoracic and vascular surgery Skane University hospitalLundSweden Department of Surgery Skane University HospitalLundSweden

Background:Unresectable disease is sometimes diagnosed during surgery in patients with pancreatic ductal adenocarcinoma(PDAC).This study aimed to identify preoperative risk factors for metastatic disease diagnosed at surgical exploration and to investigate and compare survival in resected and nonresected ***:Patients were identified from the Swedish National Pancreatic and Periampullary Cancer Registry *** of metastatic disease were evaluated with a multivariable logistic regression model,and survival was evaluated with Kaplan-Meier estimates and log-rank ***:In total,1938 patients with PDAC were scheduled for *** unresectable situation was diagnosed intraoperatively in 399 patients(20.6%),including 234(12.1%)with metastasized *** risk factors for metastasis were involuntary weight loss(OR=1.72;95%CI:1.27-2.33)and elevated carbohydrate antigen 19-9(CA19-9)(35-599 U/m L,OR=1.79,95%CI:1.11-2.89;≥600 U/m L,OR=3.24,95%CI:2.04-5.17).Overall survival was lower among patients with metastasized disease than that among patients with a resectable tumor(P<0.001).Conclusions:Involuntary weight loss and an elevation of CA19-9 are preoperative risk factors for diagnosing metastasized disease during surgical exploration.

关键词： Pancreatic cancer Surgery Metastasized Exploration

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Reduced-particle size wheat bran and endoxylanase supplementation in broiler feed affect arabinoxylan hydrolysis and fermentation with broiler age differently

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Animal Nutrition 2023年第1期12卷 308-320页

作者： An Bautil Michael R.Bedford johan Buyse Christophe M.Courtin Laboratory of Food Chemistry and Biochemistry Department of Microbial and Molecular Systems(M2S)KU LeuvenLeuven3001Belgium AB Vista MarlboroughWiltshire SN84ANUnited Kingdom Laboratory of Livestock Physiology Department of BiosystemsKU LeuvenLeuven3001Belgium

Since the caecal microbiota of young broilers are not yet able to ferment the dietary fibre(DF)fraction of the feed to a large extent,increasing the accessibility of DF substrates along the gastrointestinal tract is crucial to benefit from the health stimulating metabolic end-products(*** acid)generated upon microbial DF ***,the present study aimed to evaluate the potential of reduced-particle size wheat bran(RPS-WB)and endoxylanases as feed additives to stimulate arabinoxylan(AX)hydrolysis and fermentation along the hindgut of young *** this end,RPS-WB and endoxylanase supplementation were evaluated in a 2×2 factorial design using a total of 256 male 1-d-old chicks(Ross 308).Broilers were assigned to 4 dietary treatments:a basal wheat-based diet with(1)no feed additives(control,CTRL),(2)an endoxylanase(XYL;Econase XT 25 at 0.10 g/kg diet),(3)1%wheat bran with an average reduced particle size of 297μm(RPS-WB)and(4)an endoxylanase and 1%RPS-WB(RPS-WB+XYL).Each dietary treatment was replicated 8 times and on d 10 and 28,respectively,24 and 16 broilers per treatment group were euthanised to analyse AX degradation,short-chain fatty acid production and digesta viscosity in the ileum and *** receiving XYL in their diet showed increased AX solubilisation and fermentation at both d 10 and 28 compared to the CTRL group(P<0.05).Adding RPS-WB to the diet stimulated wheat AX utilisation by the primary AX degraders in the caecum at 10 d of age compared to the CTRL group,as observed by the high AX digestibility coefficient for the RPS-WB supplemented group at this young age(P<0.05).At 28 d,RPS-WB supplementation lowered body-weight gains but increased butyric acid concentrations compared to the XYL and CTRL group(P<0.05).Although no synergistic effect for RPS-WB+XYL broilers was observed for AX hydrolysis and fermentation,these findings suggest that both additives can raise a dual benefit to the broiler as a butyrogenic effect and im

关键词： Broiler chicken Wheat bran Particle size reduction Xylanase Arabinoxylan fermentation

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Evolution of gastroenterology training

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World Journal of Gastroenterology 2009年第15期15卷 1793-1798页

作者： Hanna Telleman Trevlyn Felicity Burger Chris Jacob johan Mulder Department of Gastroenterology and Hepatology VU Medical Center Department of Gastroenterology Witwatersrand University

There have been rapid developments in gastroenterology(GE)over the last *** until the late 1980s,GE-training was incorporated in Internal Medicine *** introduction of endoscopy has necessitated the need for additional *** the world different national boards have developed their own curricula which will be discussed in this paper. Emphasis will be placed on the curriculum recently introduced in The *** internal medicine component has become a two-year requirement (Common Trunk)and the duration of training in GE has been extended to four *** of the growing complexity of GE,there are now four subspecialties:Interventional Endoscopy,Neuromotility, Oncology and Hepatology that trainees can choose *** subspecialties each have predefined specific *** World Gastroenterology Organization has drawn up a standard curriculum which can be of help to the boards in different countries. The curriculum emphasizes the knowledge and skill *** curriculum also defines the training recommendations,the requirements of training facilities and competence evaluation of fellows and facilities,while less is said about research,finance and the number of gastroenterologists *** the coming decades the curriculum will need to be revised *** of the curriculum will be the next challenge for the years to come.

关键词： Career Common Trunk Curriculum Endoscopy Fellow Fellowship Gastroenterology Hepatology Program Training

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