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At least 1,099 records · Page 61Linked to original sources
PubMed2001

[A quality control test of the image obtained with electronic portal imaging devices].

INTRODUCTION: A quality control of the digital image obtained from two electronic portal imaging devices is discussed. The devices are used to verify the radiotherapic treatment setup by comparing online images of the irradiated volume with those of the simulation devices. MATERIAL AND METHODS: Both iView and Target View devices, respectively installed on a dual energy SLi Precise Elekta and Saturne 42 Ge linear accelerators, consist of highly efficient phosphor screen and high quality videocamera, controlled by a workstation, able to generate digital portal images from few cGy doses. A phantom and software package are used to assess the spatial resolution and signal to noise ratio, and to compare tha data obtained. Spatial resolution and signal to noise ratio of both systems were studied as a function of energy, gantry angle and image acquisition parameters. RESULTS: The mean spatial resolutions obtained from the first 30 measurements were 0,265+/-0,012 and 0,220+/-0,010 lp/mm respectively for 6 and 18 MV of Saturne 42 (Target View) and 0,241+/-0,006 and 0,239+/-0,005 lp/mm for 4 and 6 MV of SLi (iView). Spatial resolution decreases as a function of energy, meanwhile there are no significant statistical differences as regards of the acquisition parameters; signal to noise ratio, instead, increases with integration time. Different values of the spatial resolution as a function of gantry angle are due to changes in the screen-camera distance and flexing of the detector housing. The quality control test is performed every 15 days by the technicians of our Radiotherapy Department. We set the reject level of spatial resolution and signal to noise ratio to be three standard deviations below the mean value obtained during the initial EPID characterization: if the measures fall below these values preventative maintenance is scheduled. CONCLUSIONS: The efficacy of the use electronic portal imaging devices for visualizing and quantifying the relative positions of anatomical structures within the radiation field depends on the image quality. It is therefore essential to devise quality control tests for the devices themselves, to guarantee an optimal level of system performance in a fast and efficient manner.

Equipment Design↗
PubMed2003

Sub-Angstrom resolution enzyme X-ray structures: is seeing believing?

Recent technical advances in crystallographic analysis, particularly highly focused and high brilliance synchrotron beam lines, have significantly improved the resolutions that are attainable for many macromolecular crystal structures. The Protein Data Bank (http://www.rcsb.org/pdb/) contains an increasing number of atomic resolution structures, which are providing a wealth of structural information that was not previously visible in lower resolution electron density maps. Here, we review the importance of visualizing hydrogen atoms and multiple sidechain conformations or anisotropy, as well as substrate strain, at sub-Angstrom resolution. The additional structural features that are visible in the electron density maps as a result of atomic resolution data provide a better understanding of the catalytic mechanisms of cholesterol oxidase, ribonuclease A, beta-lactamase, serine proteases, triosephosphate isomerase and endoglucanase.

Binding Sites↗
PubMed2025

DiCARN-DNase: enhancing cell-to-cell Hi-C resolution using dilated cascading ResNet with self-attention and DNase-seq chromatin accessibility data.

MOTIVATION: The spatial organization of chromatin is fundamental to gene regulation and essential for proper cellular function. The Hi-C technique remains the leading method for unraveling 3D genome structures, but the limited availability of high-resolution (HR) Hi-C data poses significant challenges for comprehensive analysis. Deep learning models have been developed to predict HR Hi-C data from low-resolution counterparts. Early Convolutional Neural Network (CNN)-based models improved resolution but struggled with issues like blurring and capturing fine details. In contrast, Generative Adversarial Network (GAN)-based methods encountered difficulties in maintaining diversity and generalization. Additionally, most existing algorithms perform poorly in cross-cell line generalization, where a model trained on one cell type is used to enhance HR data in another cell type. RESULTS: In this work, we propose Dilated Cascading Residual Network (DiCARN) to overcome these challenges and improve Hi-C data resolution. DiCARN leverages dilated convolutions and cascading residuals to capture a broader context while preserving fine-grained genomic interactions. Additionally, we incorporate DNase-seq data into our model, providing a robust framework that demonstrates superior generalizability across cell lines in HR Hi-C data reconstruction. AVAILABILITY AND IMPLEMENTATION: DiCARN is publicly available at https://github.com/OluwadareLab/DiCARN.

Chromatin↗
PubMed2002

Towards rapid and unique curve resolution of low-field NMR relaxation data: trilinear SLICING versus two-dimensional curve fitting.

In this work an alternative method, named SLICING, for two-dimensional and noniterative T(2) decomposition of low-field pulsed NMR data (LF-NMR) is proposed and examined. The method is based on the Direct Exponential Curve Resolution Algorithm (DECRA) proposed by W. Windig and A. Antalek (1997, Chemom. Intell. Lab. Syst.37, 241-254) and takes advantage of the fact that exponential decay functions, when translated in time, retain their characteristic relaxation times while only their relative amounts or concentrations change. By such simple translations (slicing) it is possible to create a new "pseudo" direction in the relaxation data and thus facilitate application of trilinear (multiway) data-analytical methods. For the application on LF-NMR relaxation data, the method has two basic requirements in practice: (1) two or more samples must be analyzed simultaneously and (2) all samples must contain the same qualities (i.e., identical sets of distinct T(2) values). In return, if these requirements are fulfilled, the SLICING (trilinear decomposition) method provides very fast and unique curve-resolution of multiexponential LF-NMR relaxation curves and, as a spin-off, calibrations to reference data referring to individual proton components require only scaling of the resulting unique concentrations. In this work the performance of the SLICING method (including multiple slicing schemes) is compared to a traditional two-dimensional curve fitting algorithm named MATRIXFIT through application to simulated data in a large-scale exhaustive experimental design and the results validated by application to two small real data sets. Finally a new algorithm, Principal Phase Correction (PPC) based on principal component analysis, is proposed for phase rotation of CPMG quadrature data, an important prerequisite to optimal SLICING analysis.

Algorithms↗
PubMed2002

A molecular phylogenetic study of the Palmae (Arecaceae) based on atpB, rbcL, and 18S nrDNA sequences.

Notoriously slow rates of molecular evolution and convergent evolution among some morphological characters have limited phylogenetic resolution for the palm family (Arecaceae). This study adds nuclear DNA (18S SSU rRNA) and chloroplast DNA (cpDNA; atpB and rbcL) sequence data for 65 genera of palms and characterizes molecular variation for each molecule. Phylogenetic relationships were estimated with maximum likelihood and maximum parsimony techniques for the new data and for previously published molecular data for 45 palm genera. Maximum parsimony analysis was also used to compare molecular and morphological data for 33 palm genera. Incongruence among datasets was detected between cpDNA and 18S data and between molecular and morphological data. Most conflict between nuclear and cpDNA data was associated with the genus Nypa. Several taxa showed relatively long branches with 18S data, but phylogenetic resolution of these taxa was essentially the same for 18S and cpDNA data. Base composition bias for 18S that contributed to erroneous phylogenetic resolution in other taxa did not seem to be present in Palmae. Morphological data were incongruent with all molecular data due to apparent morphological homoplasy for Caryoteae, Ceroxyloideae, Iriarteae, and Thrinacinae. Both cpDNA and nuclear 18S data firmly resolved Caryoteae with Borasseae of Coryphoideae, suggesting that at least some morphological characters used to place Caryoteae in Arecoideae are homoplastic. In this study, increased character sampling seems to be more important than increased taxon sampling; a comparison of the full (65-taxon) and reduced (45- and 33-taxon) datasets suggests little difference in core topology but considerably more nodal support with the increased character sample sizes. These results indicate a general trend toward a stable estimate of phylogenetic relationships for the Palmae. Although the 33-taxon topologies are even better resolved, they lack several critical taxa and are affected by incongruence between molecular and morphological data. As such, a comparison of results from the 45- and 33-taxon trees offers the best available reference for phylogenetic inference on palms.

Arecaceae↗
PubMed1987

Inhibitors of sterol synthesis. Spectral characterization of derivatives of 5 alpha-cholest-8(14)-en-3 beta-ol-15-one.

Described herein are the chemical syntheses of a number of deuterated derivatives of 5 alpha-cholest-8(14)-en-3 beta-ol-15-one. These include the [2,2,3 alpha,4,4,7,7,9 alpha,16,16-2H10]-, [7 alpha,9 alpha,16,16-2H4]-, [7,7,9 alpha,16,16-2H5]-, and [2,2,3 alpha,4,4-2H5]-analogs of the delta 8(14)-15-ketosterol. Also included are the syntheses of the 3 beta-acetate derivatives of the latter three deuterated analogs and of 5 alpha-cholest-8(14)-en-3 beta-ol-15-one, and 5 alpha-cholest-8(14)-en-3 alpha-ol-15-one. Low resolution mass spectral data on these compounds and on 5 alpha-cholest-8(14)-en-15-one, 5 alpha-cholest-8(14)-en-3 beta-ol-15-one, 5 alpha-cholest-8(14)-en-3 alpha-ol-15-one, 3 beta-benzoyloxy-5 alpha-cholest-8(14)-en-15-one, and the trimethylsilyl ethers of the free sterols have been presented. The results of these studies, supplemented with high resolution mass spectral data on five of these compounds, have been used to evaluate the electron impact mass spectral fragmentation of the delta 8(14)-15-ketosterols and their derivatives. Also presented herein are the results of 1H, 2H, and 13C nuclear magnetic resonance studies of 5 alpha-cholest-8(14)-en-3 beta-ol-15-one and its derivatives.

Chemical Phenomena↗
PubMed2003

Neuron classification based on temporal firing patterns by the dynamical analysis with changing time resolution (DCT) method.

Spike train data of many neurons can be obtained by multirecording techniques; however, the data make it difficult to estimate the connective structure in a large network. Neuron classification should be helpful in that regard, assuming that multiple neurons having similar connections with other neurons show a similar temporal firing pattern. We propose a novel method for classifying neurons based on temporal firing patterns of spike train data called the dynamical analysis with changing time resolution (DCT) method. The DCT method can evaluate temporal firing patterns by a simple algorithm with few arbitrary factors and automatically classify neurons by similarity of temporal firing patterns. In the DCT method, temporal firing patterns were objectively evaluated by analyzing their dependence on temporal resolution. We confirmed the effectiveness of the DCT method using actual spike train data.

Action Potentials↗
PubMed2007

Increase of accuracy in intraoperative navigation through high-resolution flat-panel volume computed tomography: experimental comparison with multislice computed tomography-based navigation.

HYPOTHESIS: High-resolution imaging, as provided by flat-panel-based volume computed tomography (fpVCT), could increase navigation accuracy and could therefore improve image-guided procedures or make novel navigated surgery concepts possible. BACKGROUND: Intraoperative navigation is an accepted tool in head and neck surgery. However, its use is limited in the lateral cranial base because of its low surgical accuracy. Surgical accuracy is substantially influenced by the resolution of the underlying data set. The fpVCT offers a resolution of nearly two times higher than multislice computed tomography (MSCT). Target registration error (TRE), as a measurement for surgical navigation accuracy, should decrease when navigation is based on fpVCT data sets. METHODS: An acrylic glass phantom with 37 fiducial points was scanned in a current MSCT and in an experimental fpVCT. Both data sets were imported in an optical navigation system. Five fiducial points were used for registration, and seven points were used for measuring TRE. The distance between the indicated pointer tip and the corresponding fiducial point in data set was measured as TRE. Registration and TRE measurement were repeated five times for each computed tomographic data set. Average TREs were calculated, and results were compared using t-test. RESULTS: The average TRE using MSCT (0.82 mm [standard deviation, 0.35 mm]) was significantly higher than that using fpVCT (0.46 mm [standard deviation, 0.22 mm]) (p < 0.01). CONCLUSION: Submillimeter surgical navigation accuracy is possible using high-resolution fpVCT. This could be highly beneficial in cranial base surgery navigation.

Humans↗
PubMed2002

Three-dimensional imaging of the inner ear by volume-rendered reconstructions of magnetic resonance data.

OBJECTIVE: To evaluate 3-dimensional inner ear visualization by volume rendering of high-resolution magnetic resonance data in patients with clinically suspected inner ear abnormality. DESIGN: Prospective comparative study of different postprocessing techniques, based on blinded film readings. SETTING: Tertiary referral hospital. SUBJECTS: Fifty patients (17 females and 33 males) aged 1 to 77 years (average age, 42 years) with sensorineural hearing loss, vertigo, and/or tinnitus. INTERVENTION: Postprocessing of magnetic resonance data to inner ear reconstructions by the use of volume rendering as well as maximum-intensity projection; caloric testing by electronystagmography. MAIN OUTCOME MEASURES: Film was read blindly by 4 radiologists using a 5-point parameter scale for image quality and diagnostic value. The assessibility of inner ear subsegments was evaluated. The specificity of volume-rendered reconstructions for detecting semicircular canal obliterations was assessed in a subgroup of 9 patients by caloric testing. The time required for data postprocessing as well as film reading was recorded by means of a stopwatch. RESULTS: Volume-rendered inner ear reconstructions were superior in image quality (P<.001), diagnostic value (P<.001), subsegment inner ear assessment (P<.01 to P<.001), and film reading time (P<.001) compared with maximum-intensity projections. The data postprocessing time was comparable for both techniques. Caloric weakness was noted in all patients assessed by electronystagmography. CONCLUSION: Volume rendering is the postprocessing technique of choice for 3-dimensional inner ear visualization, performing better than maximum-intensity projections with respect to various parameters.

Adolescent↗
PubMed1993

High-resolution electron crystallography of protein molecules.

Electron diffraction data and high-resolution images can now be used to obtain accurate, three-dimensional density maps of biological macromolecules. These density maps can be interpreted by building an atomic-resolution model of the structure into the experimental density. The Cowley-Moodie formalism of dynamical diffraction theory has been used to validate the use of kinematic diffraction theory (strictly, the weak phase object approximation) in producing such 3D density maps. Further improvements in the preparation of very flat (planar) specimens and in the retention of diffraction to a resolution of 0.2 nm or better could result in electron crystallography becoming as important a technique as X-ray crystallography currently is for the field of structural molecular biology.

Crystallography↗
PubMed2000

Crystallization, preliminary X-ray analysis of a native and selenomethionine D-hydantoinase from Thermus sp.

A D-hydantoinase from Thermus sp. was expressed in Escherichia coli, purified to homogeneity and crystallized both as native and Se-Met labelled protein. The crystals belong to the orthorhombic space group C222(1), with unit-cell parameters a = 125.9, b = 215.8, c = 207.5 A. A three-wavelength MAD data set was collected to 2.5 A resolution and a native data set was collected to 1.7 A resolution. Crystal packing and self-rotation calculations led to the assumption of six protomers per asymmetric unit, corresponding to a V(M) value of 2.28 A(3) Da(-1) and a solvent content of 46%. As each protomer contains nine Se-Met residues, 54 selenium sites per asymmetric unit were present and could be unambigously located in the course of the MAD experiment. This selenium substructure is one of the largest selenium substructures that have been solved to date. The resulting phases obtained at a high-resolution limit of 3.0 A could be extended to 1.7 A and refined by application of density-modification techniques, especially non-crystallographic symmetry.

Amidohydrolases↗
PubMed1993

Crystal structure of canine and bovine granulocyte-colony stimulating factor (G-CSF).

The crystal structures of recombinant canine and bovine granulocyte colony stimulating factor (G-CSF) have been determined by X-ray crystallography, using molecular replacement with recombinant human G-CSF as a model. G-CSF is a member of the cytokine family of glycoproteins that stimulate the differentiation and proliferation of blood cells. Human, bovine and canine G-CSF all have a molecular mass of about 19 kDa and share an amino acid sequence identity of about 80%. Two crystal forms of canine G-CSF have been solved. Form I recombinant canine G-CSF (rcG-CSFI; space group C2) contains one molecule in the asymmetric unit while form II canine G-CSF (rcG-CSFII; space group P2(1)) has two molecules in the asymmetric unit and bovine G-CSF (rbG-CSF; space group P2(1)2(1)2(1)) contains one molecule in the asymmetric unit. rcG-CSFI has been refined to an R factor of 20.7% with data to 2.3 A resolution and rcG-CSFII has been refined to an R factor of 19.3% with data to 2.2 A resolution. rbG-CSF has been refined to an R factor of 21.3% with data to 1.7 A resolution. The structure of human, canine and bovine G-CSF is an antiparallel 4-alpha-helical bundle with up-up-down-down connectivity. With the exception of one highly exposed loop (residues 66 to 74), the human, canine and bovine structures are very similar to each other. Using our series of G-CSF crystal structures we developed a function that describes the probability that a particular residue position (i) contributes to a G-CSF receptor binding site based on two principles, (1) high sequence conservation in the primary sequence of human, bovine, canine and murine G-CSF and (2) conservation of high solvent accessibility in the human, bovine and canine crystal structures. On the basis of this probability function as well as a comparison of G-CSF to the crystal structure of human growth hormone (hGH) complexed with the extracellular domain of the human growth hormone receptor (hGHbp), residues that contribute to potential G-CSF receptor binding sites are identified.

Amino Acid Sequence↗
PubMedDate not supplied

Web portal to an image database for high-resolution three-dimensional reconstruction.

The exponential increase of image data in high-resolution reconstructions by electron cryomicroscopy (cryoEM) has posed a need for efficient data management solutions in addition to powerful data processing procedures. Although relational databases and web portals are commonly used to manage sequences and structures in biological research, their application in cryoEM has been limited due to the complexity in accomplishing the dual tasks of interacting with proprietary software and simultaneously providing data access to users without database knowledge. Here, we report our results in developing web portal to SQL image databases used by the Image Management and Icosahedral Reconstruction System (IMIRS) to manage cryoEM images for subnanometer-resolution reconstructions. Fundamental issues related to the design and deployment of web portals to image databases are described. A web browser-based user interface was designed to accomplish data reporting and other database-related services, including user authentication, data entry, graph-based data mining, and various query and reporting tasks with interactive image manipulation capabilities. With an integrated web portal, IMIRS represents the first cryoEM application that incorporates both web-based data reporting tools and a complete set of data processing modules. Our examples should thus provide general guidelines applicable to other cryoEM technology development efforts.

Cryoelectron Microscopy↗
PubMed2003

Capillary zone electrophoresis with a dynamic double coating for analysis of carbohydrate-deficient transferrin in human serum: impact of resolution between disialo- and trisialotransferrin on reference limits.

Capillary electrophoresis with a dynamic double coating formed by charged polymeric reagents represents a very effective tool for the separation of iron-saturated transferrin (Tf) isoforms and thus the determination of carbohydrate-deficient transferrin (CDT) in human serum. The resolution between di- and trisialo-Tf is dependent on the applied voltage and capillary temperature. With a 50 microm inside diameter (ID) capillary of about 60 cm total length mounted into the P/ACE MDQ, 28 kV and 40 degrees C, the resolution of the two Tf isoforms is shown to be between 1.0 and 1.4, whereas with reduced voltage and/or temperature, increased resolution at the expense of elongated run times is observed. Best data with complete resolution (Rs > or = 1.4) are obtained at 20 kV and 30 degrees C. For the determination of CDT in serum, incomplete separation of di- and trisialo-Tf is demonstrated to have an impact on the reference limits. Analysis of the sera of 54 healthy individuals with no or moderate alcohol consumption and using valley-to-valley peak integration, the upper (lower) reference limits for CDT in relation to total Tf at the two power levels are 1.33 (0.52) and 1.57 (0.81)%, respectively, representing intervals that are significantly different (P < 0.001). Furthermore, the reference intervals are shown to be strongly dependent on the peak integration approach used. Valley-to-valley peak integration should only be employed for conditions with complete resolution between disialo- and trisialo-Tf.

Blood Chemical Analysis↗
PubMed2005

Rotationally resolved absorption cross sections of formaldehyde in the 28100-28500 cm(-1) (351-356 nm) spectral region: implications for in situ LIF measurements.

The rotationally resolved ultraviolet absorption cross sections for the 2(0)(0)4(1)(0) vibrational band of the A(1)A(2)-X(1)A(1) electronic transition of formaldehyde (HCHO) at an apodized resolution of 0.027 cm(-1) (approximately 0.0003 nm at 352 nm) over the spectral range 28100-28500 cm(-1) (351-356 nm) at 298 and 220 K, using Fourier transform spectroscopy, are first reported here. Accurate rotationally resolved cross sections are important for the development of in situ HCHO laser-induced fluorescence (LIF) instruments and for atmospheric monitoring. Pressure dependence of the cross sections between 75 and 400 Torr at 298 K was explored, and an average pressure broadening coefficient in dry air of 1.8 x 10(-4) cm(-1) Torr(-1) for several isolated lines is reported. Gaseous HCHO was quantitatively introduced into a flow cell by evaporating micron-sized droplets of HCHO solution, using a novel microinjector technique. The condensed-phase concentrations of HCHO were determined by iodometric titrations to an accuracy of <1%. Accuracy of the measured absorption cross sections is estimated to be better than +/-5%. Integrated and differential cross sections over the entire band at low resolution (approximately 1 cm(-1)) obtained with our calibration technique are in excellent agreement with previous measurements. A maximum differential cross section of 5.7 x 10(-19) cm(2) molecule(-1) was observed at high resolution-almost an order of magnitude greater than any previously reported data at low resolution.

Journal Article↗
PubMed2026

Plant species identification by genome skimming across the vascular plant tree of life.

Accurate species identification is essential for biodiversity conservation and sustainable use, yet standard plant DNA barcoding often fails to achieve species-level resolution. We present a large-scale empirical evaluation of genome skimming as a tool to improve plant species discrimination. Using standardised data from 1969 individuals representing 475 species from 32 genera across major lineages of the vascular plant tree of life, we compare conventional plastid + internal transcribed spacer (ITS) barcodes with genome skimming approaches. Standard barcoding using rbcL, matK, trnH-psbA and ITS resolved about half of species (49.3%), with six genera showing <&#x2009;25% species discrimination. By contrast, genome skimming enabled the recovery of complete plastid genomes, yielding 57.6% species discrimination. It also generated sufficient nuclear genomic data for additional resolution from k-mer analysis, achieving 66.8% species discrimination - an average gain of 17.5% over standard barcodes - while eliminating cases of extreme failure (<&#x2009;25% resolution). The recovery of complete plastomes and ribosomal DNAs from genome skims also ensures backward compatibility with existing barcode datasets. Our results demonstrate that genome skimming provides data that substantially improves species-level resolution across diverse plant lineages and offers a scalable, high-throughput approach for building comprehensive reference resources to support global biodiversity initiatives.

DNA Barcoding, Taxonomic↗
PubMed1994

Crystallization and preliminary X-ray crystallographic studies of recombinant human leukotriene A4 hydrolase complexed with bestatin.

Recombinant human leukotriene A4 hydrolase complexed with bestatin, an inhibitor of metalloprotease, has been crystallized by the hanging drop vapor diffusion method using 0.1 M phosphate buffer (pH 6.5) and 50 to 54% saturated ammonium sulfate. The orthorhombic crystals belong to the space group I222 or I2(1)2(1)2(1) with unit cell dimensions of a = 273.6 A, b = 261.3 A and c = 52.9 A. They diffract beyond 2.5 A resolution and a native data set up to 3 A resolution has been collected on an imaging plate Weissenberg camera using synchrotron radiation.

Amino Acid Sequence↗
PubMedDate not supplied

Photographic patterns in macular images: representation by a mathematical model.

Normal macular photographic patterns are geometrically described and mathematically modeled. Forty normal color fundus photographs were digitized. The green channel gray-level data were filtered and contrast enhanced, then analyzed for concentricity, convexity, and radial resolution. The foveal data for five images were fit with elliptic quadratic polynomials in two zones: a central ellipse and a surrounding annulus. The ability of the model to reconstruct the entire foveal data from selected pixel values was tested. The gray-level patterns were nested sets of concentric ellipses. Gray levels increased radially, with retinal vessels changing the patterns to star shaped in the peripheral fovea. The elliptic polynomial model could fit a high-resolution green channel foveal image with mean absolute errors of 6.1% of the gray-level range. Foveal images were reconstructed from small numbers of selected pixel values with mean errors of 7.2%. Digital analysis of normal fundus photographs shows finely resolved concentric elliptical foveal and star-shaped parafoveal patterns, which are consistent with anatomical structures. A two-zone elliptic quadratic polynomial model can approximate foveal data, and can also reconstruct it from small subsets, allowing improved macular image analysis.

Adult↗