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At least 559 records · Page 31Linked to original sources
PubMed1996

[Development of a clinical-radiological CD-ROM database for focal lesions of the liver].

PURPOSE: The development of a CD-ROM database for continuous acquisition and archiving of interesting radiologic cases is described. As a pilot study radiologic images of focal lesions of the liver were collected. METHODS: The database runs on a PC (80486 DX2, 66 MHz, 16 MB RAM), which is connected to the clinic network, a high quality x-ray scanner and a CD-ROM writer. Radiologic images can be inserted into the database either by scanner or by image transfer via network. The database is designed using Access 2.0. Well documented cases were chosen retrospectively, manipulated and archived. RESULTS: 308 images of 12 focal lesions with a capacity of 802 MB were stored on CD-ROM. Per case a storage capacity of 40-75 MB is necessary for image raw material, 15-25 MB are necessary for the postprocessed data. Spatial resolution is 190 dpi (3000 pixel/40 cm). Clinical data, radiological diagnosis coded by modified ACR index and a compressed icon of the images are stored on PC, the image data are stored on CD-ROM. 2.5 hours per case are needed for the complete acquisition, manipulation and archiving procedure, but improved hardware configuration can reduce the time significantly. CONCLUSION: The described database allows continuous archiving of interesting radiologic cases on PC. ACR index is suited for a quick search of a specific combination of radiologic images and diagnosis from different modalities.

Angiography↗
PubMed1982

Lipofuscin: resolution of discrepant fluorescence data.

Lipofuscin granules (age pigments) emit yellow light under ultraviolet excitation in the fluorescence microscope. The reported blue emission maximum of extracts of lipofuscin-laden cells may result from instrumental bias. The major fluorescent components that accumulate with age in these lysosomal residual bodies of human retinal pigment epithelium are yellow-emitting fluorophores. Different age-related fluorophores, which do emit blue light, are derived from other intracellular sources. A reevaluation of the connection between blue-emitting lipid peroxidation products and the age-related lipofuscin granules of classical pathology is necessary.

Adult↗
PubMed1997

Oversampling data acquisition to improve resolution of digitized signals.

The ability to capture analog signals in a digital format suitable for subsequent storage, processing and analysis by a computer has revolutionized many scientific fields, including biomechanics. In the process of going from the analog signal to its digital representation, it is essential to maintain as much of the original signal content as possible. There is always a loss of information associated with the conversion from analog to digital, independently of how it is actually performed. The only possibility to reduce the loss of information is to increase the number of states or the resolution of the digital signal. The method presented here, based on the same theory used in oversampling analog to digital converters, is applicable to digital signals acquired using any converter. In most situations this method provides a feasible and inexpensive technique to significantly improve the amplitude resolution of the analog to digital conversion. This can be of fundamental importance when the information of interest is small in amplitude compared to the overall signal, or when subsequent ill-conditioned operations, like the computation of the derivatives of the signal, are to be performed.

Analog-Digital Conversion↗
PubMed2003

In-house measurement of the sulfur anomalous signal and its use for phasing.

Five test structures (orthorhombic and trigonal trypsin, cubic and rhombohedral insulin and thaumatin) have been solved by the SAD (single-wavelength anomalous diffraction) method using highly redundant data collected at 100 K with a CCD detector, rotating-anode generator and three-circle goniometer. The very weak anomalous scattering (primarily from sulfur) was sufficient to locate all the anomalous scatterers using the integrated direct and Patterson methods in SHELXD. These positions and occupancies were used without further refinement to estimate phases that were extended to native (in-house) resolution by the sphere of influence algorithm in SHELXE. The final map correlation coefficients relative to the anisotropically refined structures were in the range 0.81-0.97. The use of highly redundant medium-resolution laboratory data for sulfur-SAD phasing combined with high-resolution synchrotron native data for phase expansion and structure refinement clearly has considerable potential.

Algorithms↗
PubMed2001

Crystallization and X-ray diffraction measurements on recombinant molbindin, MopII, from Clostridium pasteurianum.

Clostridium pasteurianum carries three genes termed mopI, II and III encoding three molbindin isoforms, one of which has been cloned, the gene product expressed in high yield and crystallized using the hanging-drop vapour-diffusion method. Well ordered monoclinic crystals in two different crystal forms, both with space group C2, were obtained in the presence and absence of Na(2)MoO(4) and Na(2)WO(4). Ligand-bound MopII crystallized with polyethylene glycol (PEG) 400 as a precipitant, whereas apo MopII required PEG 6000. High-resolution diffraction data were collected for ligand-bound MopII structures using synchrotron radiation to 1.8 and 1.6 A resolution for the molybdate and tungstate complexes, respectively. Data were collected on apoMopII crystals to a resolution of 1.8 A in-house.

Bacterial Proteins↗
PubMed2001

Complex of rat transthyretin with tetraiodothyroacetic acid refined at 2.1 and 1.8 A resolution.

The crystal structure of rat transthyretin (rTTR) complex with 3,5,3',5'-tetraiodothyroacetic acid (T4Ac) was determined at 1.8 A resolution with low temperature synchrotron data collected at CHESS. The structure was refined to R = 0.207 and Rfree = 0.24 with the use of 8-1.8 A data. The additional 8000 reflections from the incomplete 2.1-1.8 data shell, included in the refinement, reduced the Rfree index by 1.3%. Structure comparison with the model refined against the complete 8-2.1 A data revealed no differences in the ligand orientation and the conformation of the polypeptide chain in the core regions. However, the high-resolution data included in the refinement improved the model in the flexible regions poorly defined with the lower resolution data. Also additional sixteen water molecules were found in the difference map calculated with the extended data. The structure revealed both forward and reverse binding of tetraiodothyroacetic acid in one binding site and two modes of forward ligand binding in the second site, with the phenolic iodine atoms occupying different sets of the halogen binding pockets.

Animals↗
PubMed2001

Structure of a serine protease proteinase K from Tritirachium album limber at 0.98 A resolution.

X-ray diffraction data at atomic resolution to 0.98 A with 136 380 observed unique reflections were collected using a high quality proteinase K crystals grown under microgravity conditions and cryocooled. The structure has been refined anisotropically with REFMAC and SHELX-97 with R-factors of 11.4 and 12.8%, and R(free)-factors of 12.4 and 13.5%, respectively. The refined model coordinates have an overall rms shifts of 0.23 A relative to the same structure determined at room temperature at 1.5 A resolution. Several regions of the main chain and the side chains, which were not observed earlier have been seen more clearly. For example, amino acid 207, which was reported earlier as Ser has been clearly identified as Asp. Furthermore, side-chain disorders of 8 of 279 residues in the polypeptide have been identified. Hydrogen atoms appear as significant peaks in the F(o) - F(c) difference electron density map accounting for an estimated 46% of all hydrogen atoms at 2sigma level. Furthermore, the carbon, nitrogen, and oxygen atoms can be differentiated clearly in the electron density maps. Hydrogen bonds are clearly identified in the serine protease catalytic triad (Ser-His-Asp). Furthermore, electron density is observed for an unusual, short hydrogen bond between aspartic acid and histidine in the catalytic triad. The short hydrogen bond, designated "catalytic hydrogen bond", occurs as part of an elaborate hydrogen bond network, involving Asp of the catalytic triad. Though unusual, these features seem to be conserved in other serine proteases. Finally there are clear electron density peaks for the hydrogen atoms associated with the Ogamma of Ser 224 and Ndelta1 of His 69.

Ascomycota↗
PubMed2006

Ab initio determination of solid-state nanostructure.

Advances in materials science and molecular biology followed rapidly from the ability to characterize atomic structure using single crystals. Structure determination is more difficult if single crystals are not available. Many complex inorganic materials that are of interest in nanotechnology have no periodic long-range order and so their structures cannot be solved using crystallographic methods. Here we demonstrate that ab initio structure solution of these nanostructured materials is feasible using diffraction data in combination with distance geometry methods. Precise, sub-ångström resolution distance data are experimentally available from the atomic pair distribution function (PDF). Current PDF analysis consists of structure refinement from reasonable initial structure guesses and it is not clear, a priori, that sufficient information exists in the PDF to obtain a unique structural solution. Here we present and validate two algorithms for structure reconstruction from precise unassigned interatomic distances for a range of clusters. We then apply the algorithms to find a unique, ab initio, structural solution for C60 from PDF data alone. This opens the door to sub-ångström resolution structure solution of nanomaterials, even when crystallographic methods fail.

Journal Article↗
PubMed2005

The BrainIT Group: concept and current status 2004.

INTRODUCTION: An open collaborative international network has been established which aims to improve inter-centre standards for collection of high-resolution, neurointensive care data on patients with traumatic brain injury. The group is also working towards the creation of an open access, detailed and validated database that will be useful for hypothesis generation. In Part A, we describe the underlying concept of the group and it's aims and in Part B we describe the current status of the groups development. METHODS: Four group meetings funded by the EEC have enabled definition of a "Core Dataset" to be collected from all centres regardless of specific project aim. A form based feasibility study was conducted and a prospective data collection exercise of core data using PC and hand held computer based methods is in progress. FINDINGS: A core-dataset was defined and can be downloaded from the BrainIT web-site (go to "Core dataset" link at: www.brainit.org). A form based feasibility study was conducted showing the overall feasibility for collection of the core data elements was high. Software tools for collection of the core dataset have been developed. Currently, 130 patient's data from 16 European centres have been recruited to the joint database as part of an EEC funded proof of concept study. INTERPRETATION: The BrainIT network provides a more standardised and higher resolution data collection mechanism for research groups, organisations and the device industry to conduct multicentre trials of new health care technology in patients with traumatic brain injury.

Brain Injuries↗
PubMed2000

Purification of a D-hydantoinase using a laboratory-scale streamline phenyl column as the initial step.

A D-hydantoinase from Thermus sp. was overexpressed in Escherichia coli and purified to homogeneity for subsequent crystallization. The purification was performed with hydrophobic interaction chromatography as the capture step followed by anion-exchange chromatography and gel permeation chromatography as intermediate purification and polishing steps, respectively. The hydrophobic interaction step was done in fluidized bed mode in a laboratory-scale Streamline column made from conventional laboratory equipment. The whole purification protocol could be finished within one day. The purified enzyme crystallizes. The crystals are suitable for X-ray protein structure analysis and diffract to at least 2.3 A resolution. Complete data sets have been measured up to 2.6 A resolution. The X-ray structure is currently being solved.

Amidohydrolases↗
PubMed2003

Minimally invasive silicon probe for electrical impedance measurements in small animals.

It is commonly accepted that electrical impedance provides relevant information about the physiological condition of living tissues. Currently, impedance measurements are performed with relatively large electrodes not suitable for studies in small animals due to their poor spatial resolution and to the damage that they cause to the tissue. A minimally invasive needle shaped probe for electrical impedance measurements of living tissues is presented in this paper. This micro-probe consists of four square platinum electrodes (300 microm x 300 microm) on a silicon substrate (9 mm x 0.6 mm x 0.5 mm) and has been fabricated by using standard Si microelectronic techniques. The electrodes are not equally spaced in order to optimise the signal strength and the spatial resolution. Characterisation data obtained indicate that these probes provide high spatial resolution (measurement radius <4 mm) with a useful wide frequency band going from 100 Hz to 100 kHz. A series of in vivo experiments in rat kidneys subjected to ischemia was performed to demonstrate the feasibility of the probes and the measurement system. The impedance modulus and phase were measured at 1 kHz since this frequency is sufficiently low to permit the study of the extracellular medium. The extracellular pH and K+ were also simultaneously measured by using commercial miniaturised Ion Selective Electrodes. The induced ischemia period (45 min) resulted in significant changes of all measured parameters (Delta/Z/ approximately 65%; DeltapH approximately 0.8; DeltaK+ approximately 30 mM).

Animals↗
PubMed2001

Two novel procedures for automatic resolution of two-way data from coupled chromatography.

In order to deal with the problem of simultaneous qualitative and quantitative analysis of the complicated samples in analytical chemistry, two novel procedures for automatic resolution of two-way data from coupled chromatography were developed in this work. The first can be used to determine automatically the number of components involved in a certain peak cluster. The second method is an iterative resolution procedure named the stepwise key spectrum selection which has also been developed to resolve automatically the spectra and chromatographic profiles of every component in the peak cluster investigated. The results obtained from simulated and real data show that the proposed methods perform fairly well.

Journal Article↗
PubMed2002

Inner chromatogram projection (ICP) for resolution of GC-MS data with embedded chromatographic peaks.

The chromatographic peak located inside another peak in the time direction is called an embedded or inner peak in contradistinction with the embedding peak, which is called an outer peak. The chemical components corresponding to inner and outer peaks are called inner and outer components, respectively. This special case of co-eluting chromatograms was investigated using chemometric approaches taking GC-MS as an example. A novel method, named inner chromatogram projection (ICP), for resolution of GC-MS data with embedded chromatographic peaks is derived. Orthogonal projection resolution is first utilized to obtain the chromatographic profile of the inner component. Projection of the two-way data matrix columnwise-normalized along the time direction to the normalized profile of the inner component found is subsequently performed to find the selective m/z points, if they exist, which represent the chromatogram of the outer component by itself. With the profiles obtained, the mass spectra can easily be found by means of a least-squares procedure. The results for both simulated data and real samples demonstrate that the proposed method is capable of achieving satisfactory resolution performance not affected by the shapes of chromatograms and the relative positions of the components involved.

Journal Article↗
PubMed2005

A Hamilton-Jacobi-Bellman approach to high angular resolution diffusion tractography.

This paper describes a new framework for white matter tractography in high angular resolution diffusion data. A direction-dependent local cost is defined based on the diffusion data for every direction on the unit sphere. Minimum cost curves are determined by solving the Hamilton-Jacobi-Bellman using an efficient algorithm. Classical costs based on the diffusion tensor field can be seen as a special case. While the minimum cost (or equivalently the travel time of a particle moving along the curve) and the anisotropic front propagation frameworks are related, front speed is related to particle speed through a Legendre transformation which can severely impact anisotropy information for front propagation techniques. Implementation details and results on high angular diffusion data show that this method can successfully take advantage of the increased angular resolution in high b-value diffusion weighted data despite lower signal to noise ratio.

Algorithms↗