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Structure of the oligosaccharyl transferase complex at 12 Å resolution

STRUCTURE 2008年第3期16卷 432-440页

作者： Li, Hua Chavan, Manasi Schindelin, Hermann Lennarz, William J. Li, Huilin SUNY Stony Brook Inst Cell & Dev Biol Stony Brook NY 11794 USA SUNY Stony Brook Dept Biochem Stony Brook NY 11794 USA Brookhaven Natl Lab Dept Biol Upton NY 11973 USA Univ Wurzburg Inst Biol Struct D-97078 Wurzburg Germany Univ Wurzburg Rudolf Virchow Ctr Expt Biomed D-97078 Wurzburg Germany

Oligosaccharyl transferase (OT) catalyzes the transfer of a lipid-linked oligosaccharide to the nascent polypeptide emerging from the translocon. Currently, there is no structural information on the membrane-embedded OT complex, which consists of eight different polypeptide chains. We report a 12 angstrom resolution cryo-electron microscopy structure of OT from yeast. We mapped the locations of four essential OT subunits through a maltose-binding protein fusion strategy. OT was found to have a large domain in the lumenal side of encloplasmic reticulum where the catalysis occurs. The lumenal domain mainly comprises the catalytic Stt3p, the donor substrate-recognizing Wbp1p, and the acceptor substrate-recognizing Ost1p. A prominent groove was observed between these subunits, and we propose that the nascent polypepticle from the translocon threads through this groove while being scanned by the Ost1p subunit for the presence of the glycosylation sequon.

关键词： Carrier Proteins/genetics Cloning, Molecular Cryoelectron Microscopy Digitonin/pharmacology Hexosyltransferases/chemistry Hexosyltransferases/genetics Hexosyltransferases/metabolism image processing, computer-assisted/methods Imaging, Three-Dimensional Membrane Proteins/chemistry Membrane Proteins/genetics Membrane Proteins/metabolism Models, Biological Models, Molecular Molecular Weight Multiprotein Complexes/chemistry Protein Subunits/chemistry Recombinant Fusion Proteins/chemistry Recombinant Fusion Proteins/genetics Solubility/drug effects Yeasts/enzymology

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Placebo in emotional processing - Induced expectations of anxiety relief activate a generalized modulatory network

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NEURON 2005年第6期46卷 957-969页

作者： Petrovic, P Dietrich, T Fransson, P Andersson, J Carlsson, K Ingvar, M Karolinska Inst Karolinska Hosp Dept Clin Neurosci Cognit Neurophysiol Res Grp R2 01 S-17176 Stockholm Sweden

Placebo analgesia and reward processing share several features. For instance, expectations have a strong influence on the subsequent emotional experience of both. Recent imaging data indicate similarities in the underlying neuronal network. We hypothesized that placebo analgesia is a special case of reward processing and that placebo treatment could modulate emotional perception in the same way as does pain perception. The behavioral part of this study indicates that placebo treatment has an effect on how subjects perceive unpleasant pictures. Furthermore, event-related fMRI demonstrated that the same modulatory network, including the rostral anterior cingulate cortex and the lateral orbitofrontal cortex, is involved in both emotional placebo and placebo analgesia. These effects were correlated with the reported placebo effect and were predicted by the amount of treatment expectation induced on a previous day. Thus, the placebo effect may be considered to be a general process of modulation induced by the subjects' expectations.

关键词： Adult Anti-Anxiety Agents/therapeutic use Anxiety/drug therapy Anxiety/physiopathology Benzodiazepines/therapeutic use Brain Mapping Brain Mapping Emotions/drug effects Emotions/physiology Female Flumazenil/therapeutic use Humans image processing, computer-assisted/methods Magnetic Resonance Imaging/methods Nerve Net/blood supply Nerve Net/drug effects Nerve Net/physiology Oxygen/blood Photic Stimulation/methods Placebo Effect Placebos/pharmacology Time Factors

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An efficient TOF-SIMS image analysis with spatial correlation and alternating non-negativity-constrained least squares

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BIOINFORMATICS 2015年第5期31卷 753-760页

作者： Aram, Parham Shen, Lingli Pugh, John A. Vaidyanathan, Seetharaman Kadirkamanathan, Visakan Univ Sheffield Dept Automat Control & Syst Engn Sheffield S Yorkshire England Univ Sheffield Dept Chem & Biol Engn Sheffield S Yorkshire England

Motivation: Advances in analytical instrumentation towards acquiring high-resolution images of mass spectrometry constantly demand efficient approaches for data analysis. This is particularly true of time-of-flight secondary ion mass spectrometry imaging where recent advances enable acquisition of high-resolution data in multiple dimensions. In many applications, the distribution of different species from a sampled surface is spatially continuous in nature and a model that incorporates the spatial correlation across the surface would be preferable to estimations at discrete spatial locations. A key challenge here is the capability to analyse the high-resolution multidimensional data to extract relevant information reliably and efficiently. Results: We propose a framework based on alternating non-negativity-constrained least squares which accounts for the spatial correlation across the sample surface. The proposed method also decouples the computational complexity of the estimation procedure from the image resolution, which significantly reduces the processing time. We evaluate the performance of the algorithm with biochemical image datasets generated from mixture of metabolites.

关键词： Algorithms Computational Biology/methods Humans image processing, computer-assisted/methods Least-Squares Analysis Metabolomics/methods Spectrometry, Mass, Secondary Ion/methods

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Correcting data shifts in gel files created by model 377 DNA sequencers

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BIOTECHNIQUES 1998年第6期24卷 1002-1003页

作者： O'Brien, KM Ironside, MA Athanasiou, MC Basit, MA Evans, GA Garner, HR Univ Texas SW Med Ctr Eugene McDermott Ctr Human Growth & Dev Dallas TX 75235 USA

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Diffuse damage in pediatric traumatic brain injury: A comparison of automated versus operator-controlled quantification methods

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NEUROimage 2010年第3期50卷 1017-1026页

作者： Bigler, Erin D. Abildskov, Tracy J. Wilde, Elisabeth A. McCauley, Stephen R. Li, Xiaoqi Merkley, Tricia L. Fearing, Michael A. Newsome, Mary R. Scheibel, Randall S. Hunter, Jill V. Chu, Zili Levin, Harvey S. Brigham Young Univ Dept Psychol Provo UT 84602 USA Brigham Young Univ Ctr Neurosci Provo UT 84602 USA Univ Utah Dept Psychiat Salt Lake City UT USA Univ Utah Utah Brain Inst Salt Lake City UT USA Baylor Coll Med Dept Radiol Houston TX 77030 USA Baylor Coll Med Dept Neurol Houston TX 77030 USA Univ Texas Houston Sch Med Houston TX USA Baylor Coll Med Dept Pediat Hematol Oncol Sect Houston TX 77030 USA Hebrew SeniorLife Dept Med Neuropyschol Boston MA USA Texas Childrens Hosp EB Singleton Dept Diagnost Imaging Houston TX 77030 USA Baylor Coll Med Dept Neurol Houston TX 77030 USA Baylor Coll Med Dept Neurosurg Houston TX 77030 USA Michael E De Bakey Vet Affairs Med Ctr Houston TX USA

This investigation had two main objectives: 1) to assess the comparability Of volumes determined by operator-controlled image quantification with automated image analysis in evaluating atrophic brain changes related to traumatic brain injury (TBI) in children, and 2) to assess the extent of diffuse structural changes throughout the brain as determined by reduced volume of a brain Structure or region of interest (ROI). Operator-control led methods used ANALYZE (R) software for segmentation and tracing routines of pre-defined brain structures and Rots. For automated image analyses, the open-access FreeSurfer program was used. Sixteen children with moderate-to-severe TBI were compared to individually matched, typically developing control children and the Volumes of 18 brain structures and/or ROIs were compared between the two methods. Both methods detected atrophic changes but differed in the magnitude of the atrophic effect with the best agreement in subcortical Structures. The volumes of all brain structures/ROIs were smaller in the TBI group regardless of method used;overall effect size differences were minimal for caudate and putamen but moderate to large for all other measures. This is reflective of the diffuse nature of TBI and its widespread impact on structural brain integrity, indicating that both FreeSurfer and operator-control led methods can reliably assess cross-sectional volumetric changes in pediatric TBI. (C) 2010 Elsevier Inc. All rights reserved.

关键词： Adolescent Age Factors Automation Brain/pathology Brain Injuries/pathology Brain Injuries/pathology Caudate Nucleus/pathology Child Child, Preschool Female Humans image processing, computer-assisted/methods Infant Magnetic Resonance Imaging/methods Male Observer Variation Organ Size Putamen/pathology Severity of Illness Index Severity of Illness Index Software

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Different dynamics of performance and brain activation in the time course of perceptual learning

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NEURON 2008年第6期57卷 827-833页

作者： Yotsumoto, Yuko Watanabe, Takeo Sasaki, Yuka Massachusetts Gen Hosp Athinoula A Martinos Ctr Biomed Imaging Dept Radiol Charlestown MA 02129 USA Boston Univ Dept Psychol Boston MA 02215 USA CALTECH ERATO Shimojo Implicit Brain Funct Project Pasadena CA 91125 USA Harvard Univ Sch Med Dept Radiol Boston MA 02115 USA

Perceptual learning is regarded as a manifestation of experience-dependent plasticity in the sensory systems, yet the underlying neural mechanisms remain unclear. We measured the dynamics of performance on a visual task and brain activation in the human primary visual cortex (V1) across the time course of perceptual learning. Within the first few weeks of training, brain activation in a V1 subregion corresponding to the trained visual field quadrant and task performance both increased. However, while performance levels then saturated and were maintained at a constant level, brain activation in the corresponding areas decreased to the level observed before training. These findings indicate that there are distinct temporal phases in the time course of perceptual learning, related to differential dynamics of BOLD activity in visual cortex.

关键词： Adult Female Humans image processing, computer-assisted/methods Learning/physiology Magnetic Resonance Imaging/methods Male Nonlinear Dynamics Oxygen/blood Pattern Recognition, Visual/physiology Photic Stimulation/methods Time Factors Visual Cortex/blood supply Visual Cortex/physiology Visual Fields/physiology

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Accuracy of helical computed tomographic angiography for the diagnosis of colonic angiodysplasia

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GASTROENTEROLOGY 2000年第2期119卷 293-299页

作者： Junquera, F Quiroga, S Saperas, E Pérez-Lafuente, M Videla, S Alvarez-Castells, A Miró, JRA Malagelada, JR Autonomous Univ Barcelona Digest Syst Res Unit Hosp Gen Vall dHebron E-08035 Barcelona Spain Autonomous Univ Barcelona Dept Radiol Hosp Gen Vall dHebron E-08035 Barcelona Spain

Background & Aims: The diagnosis of colonic angiodysplasia is often challenging and relies on endoscopy or catheter angiography. We investigated whether computed tomographic angiography (CTA) contributes to the diagnosis of colonic angiodysplasia. methods: Twenty-eight patients with suspected bleeding from colonic angiodysplasia were prospectively evaluated. Gastrointestinal bleeding was investigated by colonoscopy plus visceral angiography and by CTA. The level of agreement between CTA and the former procedures was determined. Results: CTA images of diagnostic quality were obtained in 26 patients. Eighteen patients were diagnosed with colonic angiodysplasia by colonoscopy plus visceral angiography, and 14 by CTA (kappa = 0.68;P < 0.001). Sensitivity, specificity, and positive predictive values of CTA for detection of colonic angiodysplasia were 70%, 100%, and 100%, respectively. CTA signs including accumulation of vessels in the colonic wall, early filling vein, and supplying enlarged artery were present in 55%, 50%, and 22% of cases, respectively. None of these signs were present in the 8 patients with obscure gastrointestinal bleeding and negative diagnostic investigation of the digestive tract. Conclusions: CTA is a sensitive, specific, well-tolerated, and minimally invasive tool for the diagnosis of colonic angiodysplasia.

关键词： Aged Aged, 80 and over Angiodysplasia/radiography Angiography/methods Angiography/standards Colon/blood supply Colonic Diseases/radiography Female Gastrointestinal Hemorrhage/radiography Humans image processing, computer-assisted/methods image processing, computer-assisted/standards Male Middle Aged Prospective Studies Reproducibility of Results Tomography, X-Ray Computed/standards

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image processing techniques applied to excitation waves in the chicken retina

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methods-A COMPANION TO methods IN ENZYMOLOGY 2000年第4期21卷 317-323页

作者： Dahlem, MA Müller, SC Univ Magdeburg Inst Phys Expt Biophys Abt D-39016 Magdeburg Germany

image processing techniques are described in detail that are used to gain information about the dynamics of wave propagation in excitable media. We focus on a phenomenon called spreading depression (SD) observed in the chicken retina, but the techniques described here concern a large variety of excitable systems. Despite the impressive progress both in SD research of the past 50 years and, during nearly the same period, in the theory of self-organization of wave patterns, there is still little mutual overlap. However, the increasing demands for understanding complex systems, like neuronal tissue, require such theoretical concepts. Arguments are given why the chicken retina is a nearly perfect experimental system for assessing and further developing these concepts. (C) 2000 Academic Press.

关键词： Animals Central Nervous System/physiology Chickens image processing, computer-assisted/methods Microscopy, Video/instrumentation Microscopy, Video/methods Retina/physiology

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Template-O-Matic: A toolbox for creating customized pediatric templates

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NEUROimage 2008年第3期41卷 903-913页

作者： Wilke, Marko Holland, Scott K. Altaye, Mekibib Gaser, Christian Univ Tubingen Childrens Hosp Dept Pediat Neurol & Dev Med D-72076 Tubingen Germany Univ Tubingen Dept Neuroradiol CNS Sect Expt MR Tubingen Germany Childrens Hosp Med Ctr Imaging Res Ctr Cincinnati OH 45229 USA Univ Cincinnati Dept Pediat Cincinnati OH 45221 USA Univ Jena Dept Psychiat D-6900 Jena Germany

processing pediatric neuroimaging data is a challenge due to pervasive morphological changes that occur in the human brain during normal development. This is of special relevance when reference data is used as part of the processing approach, as in spatial normalization and tissue segmentation. Current approaches construct reference data (templates) by averaging brain images from a control group of subjects, or by creating custom templates from the group under study. In this technical note, we describe a new, and generalized method of constructing such appropriate reference data by statistically analyzing a large sample (n= 404) of healthy children, as acquired during the NIH MRI study of normal brain development. After eliminating non-contributing demographic variables, we modeled the effects of age (first, second, and third-order terms) and gender, for each voxel in gray matter and white matter. By appropriate weighting with the parameter estimates from these analyses, complete tissue maps can be generated automatically from this database to match a pediatric population selected for study. The algorithm is implemented in the form of a toolbox for the SPM5 image data processing suite, which we term Template-O-Matic. We compare the performance of this approach with the current method of template generation and discuss the implications of our approach. (C) 2008 Elsevier Inc. All rights reserved.

关键词： Adolescent Algorithms Brain/anatomy & histology Child Humans image processing, computer-assisted/methods image processing, computer-assisted/standards Magnetic Resonance Imaging Reference Standards

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Consistent sulcal parcellation of longitudinal cortical surfaces

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NEUROimage 2011年第1期57卷 76-88页

作者： Li, Gang Shen, Dinggang Univ N Carolina Dept Radiol Chapel Hill NC 27599 USA Univ N Carolina BRIC Chapel Hill NC 27599 USA

Automated accurate and consistent sulcal parcellation of longitudinal cortical surfaces is of great importance in studying longitudinal morphological and functional changes of human brains, since longitudinal cortical changes are normally very subtle, especially in aging brains. However, applying the existing methods (which were typically developed for cortical sulcal parcellation of a single cortical surface) independently to longitudinal cortical surfaces might generate longitudinally-inconsistent results. To overcome this limitation, this paper presents a novel energy function based method for accurate and consistent sulcal parcellation of longitudinal cortical surfaces. Specifically, both spatial and temporal smoothness are imposed in the energy function to obtain consistent longitudinal sulcal parcellation results. The energy function is efficiently minimized by a graph cut method. The proposed method has been successfully applied to sulcal parcellation of both real and simulated longitudinal inner cortical surfaces of human brain MR images. Both qualitative and quantitative evaluation results demonstrate the validity of the proposed method. (C) 2011 Elsevier Inc. All rights reserved.

关键词： Algorithms Brain Mapping/methods Brain Mapping/methods Cerebral Cortex/anatomy & histology Humans image processing, computer-assisted/methods

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