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Intensity Data (intensity + data)
Kinds of Intensity Data Selected AbstractsCrystallization and preliminary X-ray studies of xylanase 10B from Thermotoga maritimaACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2003Ihsanawati Xylanases catalyze the hydrolysis of the ,-1,4-glycosidic bonds of xylan, which is the second most abundant component of plant cell walls after cellulose. The recombinant xylanase 10B from Thermotoga maritima MSB8 was prepared and crystallized by the sitting-drop vapour-diffusion method using 40,mM zinc acetate, 20,mM MES buffer pH 6.0 and 3% ethanol. Intensity data were collected to 2.5,Å resolution at beamline BL26B2 of SPring-8. Preliminary X-ray analysis showed that the crystal belongs to space group P21212, with unit-cell parameters a = 77.3, b = 80.6, c = 58.2,Å and one molecule per asymmetric unit. [source] A novel 40,kDa protein from goat mammary secretions: purification, crystallization and preliminary X-ray diffraction studiesACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2001P. Kumar A novel 40,kDa protein has been purified from dry secretions of the mammary gland of goats. The first 15 N-terminal residues were sequenced and showed a sequence identity of 30% to a novel 39,kDa whey protein from bovine mammary secretions. The protein was crystallized by the microdialysis method. Protein was dissolved to a concentration of 40,mg,ml,1 in 0.025,M Tris,HCl pH 8.0 and equilibrated with the same buffer containing 19%(v/v) ethanol. The crystals belong to the orthorhombic space group P212121, with unit-cell parameters a = 66.1, b = 107.8, c = 63.2,Å and one molecule per asymmetric unit. Intensity data were collected to 2.9,Å resolution, with a completeness of 95%. Since no similar model is available in the protein structure database, heavy-atom derivatives have been prepared and three-dimensional structure determination using the isomorphous replacement method is in progress. [source] Purification, crystallization and preliminary crystallographic study of haemoglobin from camel (Camelus dromedarius): a high oxygen-affinity lowland speciesACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 8 2009M. Balasubramanian Haemoglobin is a prototypical allosteric protein that is mainly involved in the transportation of oxygen from the lungs to tissues and of carbon dioxide back to the lungs in an intrinsically coordinated manner to maintain the viability of cells. Haemoglobin from Camelus dromedarius provides an interesting case study of adaptation to life in deserts at extremely high temperatures. An ambition to unravel the integrated structural and functional aspects of the casual survival of this animal at high temperatures led us to specifically work on this problem. The present work reports the preliminary crystallographic study of camel haemoglobin. Camel blood was collected and the haemoglobin was purified by anion-exchange chromatography and crystallized using the hanging-drop vapour-diffusion method under buffered high salt concentration using PEG 3350 as a precipitant. Intensity data were collected using a MAR 345 dtb image-plate detector system. Camel haemoglobin crystallized in the monoclinic space group P21, with one whole biological molecule (,2,2) in the asymmetric unit and unit-cell parameters a = 52.759, b = 116.782, c = 52.807,Å, , = 120.07°. [source] Purification, crystallization and preliminary crystallographic study of low oxygen-affinity haemoglobin from cat (Felis silvestris catus) in two different crystal formsACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 3 2009M. Balasubramanian Haemoglobin is a metalloprotein which plays a major role in the transportation of oxygen from the lungs to tissues and of carbon dioxide back to the lungs. The present work reports the preliminary crystallographic study of low oxygen-affinity haemoglobin from cat in different crystal forms. Cat blood was collected, purified by anion-exchange chromatography and crystallized in two different conditions by the hanging-drop vapour-diffusion method under unbuffered low-salt and buffered high-salt concentrations using PEG 3350 as a precipitant. Intensity data were collected using MAR345 and MAR345dtb image-plate detector systems. Cat haemoglobin crystallizes in monoclinic and orthorhombic crystal forms with one and two whole biological molecules (,2,2), respectively, in the asymmetric unit. [source] 3D Reconstruction of Real World Scenes Using a Low-Cost 3D Range ScannerCOMPUTER-AIDED CIVIL AND INFRASTRUCTURE ENGINEERING, Issue 7 2006Paulo Dias The article describes the mechanical and control issues addressed to physically achieve the 3D sensor used to acquire the data. It also presents the techniques used to process and merge range and intensity data to create textured polygonal models and illustrates the potential of such a unit. The result is a promising system for 3D modeling of real world scenes at a commercial price 10 or 20 times lower than current commercial 3D laser scanners. The use of such a system can simplify measurements of existing buildings and produce easily 3D models and ortophotos of existing structures with minimum effort and at an affordable price. [source] Fast set-up of doxycycline-inducible protein expression in human cell lines with a single plasmid based on Epstein,Barr virus replication and the simple tetracycline repressorFEBS JOURNAL, Issue 3 2007Markus Bach We have developed a novel plasmid vector, pEBTetD, for full establishment of doxycycline-inducible protein expression by just a single transfection. pEBTetD contains an Epstein,Barr virus origin of replication for stable and efficient episomal propagation in human cell lines, a cassette for continuous expression of the simple tetracycline repressor, and a cytomegalovirus-type 2 tetracycline operator (tetO2)-tetO2 promoter. As there is no integration of vector into the genome, clonal isolation of transfected cells is not necessary. Cells are thus ready for use 1 week after transfection; this contrasts with 3,12 weeks for other systems. Adequate regulation of protein expression was accomplished by abrogation of mRNA polyadenylation. In northern analysis of seven cDNAs coding for transport proteins, pools of transfected human embryonic kidney 293 cells showed on/off mRNA ratios in the order of 100 : 1. Cell pools were also analyzed for regulation of protein function. With two transport proteins of the plasma membrane, the on/off activity ratios were 24 : 1 and 34 : 1, respectively. With enhanced green fluorescent protein, a 23 : 1 ratio was observed based on fluorescence intensity data from flow cytometry. The unique advantage of our system rests on the unmodified tetracycline repressor, which is less likely, by relocation upon binding of doxycycline, to cause cellular disturbances than chimera of tetracycline repressor and eukaryotic transactivation domains. Thus, in a comprehensive comparison of on- and off-states, a steady cellular background is provided. Finally, in contrast to a system based on Flp recombinase, the set-up of our system is inherently reliable. [source] New procedures to decompose geomagnetic field variations and application to volcanic activitiyGEOPHYSICAL JOURNAL INTERNATIONAL, Issue 1 2008Ikuko Fujii SUMMARY We report the development of numerical procedures for extracting long-term geomagnetic field variations caused by volcanic activity from an observed geomagnetic field by using statistical methods. The newly developed procedures are to estimate the trend from the observed data, as well as variations of non-volcanic origin such as periodic components, components related to external geomagnetic variations and observational noise. We also aim at referring to data obtained at a remote standard geomagnetic observatory rather than using a temporarily installed reference site for reasons of data quality. Two different approaches,a Bayesian statistical method and a Kalman filter method,are applied to decompose the geomagnetic field data into four components for comparison. The number of filter coefficients and the degree of condition realizations are optimized on the basis of minimization of the information criteria. The two procedures were evaluated by using a synthetic data set. Generally, the results of both methods are equally sufficient. Subtle differences are seen at the first, several data points due to arbitrarily selected initial values in the case of the Kalman filter method and at the smaller residual for the Bayesian statistical method. The largest differences are in computation time and memory size. The Kalman filter method runs a thousand times faster on a testing workstation and requires less memory than the Bayesian method. The Kalman filter method was applied to the total intensity data at Kuchi-erabu-jima volcano. The result suggests that the procedure works reasonably well. [source] Symmetrization of diffraction peak profiles measured with a high-resolution synchrotron X-ray powder diffractometerJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 1 2006H. Hibino The asymmetry of diffraction peak profiles observed with a high-resolution synchrotron powder X-ray diffractometer has been successfully removed by a double deconvolution method. In the first step, the asymmetry caused by the axial divergence aberration of the diffractometer is removed by a whole-pattern deconvolution method based on an a priori theoretical model for the aberration. In the second step, the residual asymmetry, the origin of which can be ascribed to the aberrations of the beamline optics, is also removed by a whole-pattern deconvolution method, based on an empirical model derived from the analysis of experimental diffraction peak profiles of a standard Si powder (NIST SRM640b). The beamline aberration has been modelled by the convolution of a pseudo-Voigt or Voigt function with an exponential distribution function. It has been found that the angular dependence of the asymmetry parameter in the exponential function is almost proportional to tan,, which supports the idea that the residual asymmetry should be ascribed mainly to the intrinsic asymmetry in the spectroscopic distribution of the source X-ray supplied by the beamline optics of the synchrotron facility. Recently developed procedures of whole-pattern deconvolution have been improved to treat the singularity of the instrumental function in the measured angular range. Formulae for the whole-pattern deconvolution based on the Williamson,Hall-type dependence of the width parameter of the instrumental function have also been developed. The method was applied to the diffraction intensity data of a standard ZnO powder sample (NIST SRM674) measured with a high-resolution powder diffractometer on beamline BL4B2 at the Photon Factory. The structure parameters of ZnO were refined from the integrated peak intensities, which were extracted by an individual profile fitting method applying symmetric profile models. The refined structure parameters coincide fairly well with those obtained from single-crystal data. [source] A new technique for angle-dispersive powder diffraction using an energy-dispersive setup and synchrotron radiationJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 6 2004Yanbin Wang A new diffraction technique for combined angle- and energy-dispersive structural analysis and refinement (CAESAR), by collecting angle-dispersive data using a solid-state detector (SSD) and white synchrotron radiation, is introduced. By step scanning a well calibrated SSD over a limited 2, range, a series of one-dimensional energy-dispersive data (intensity versus energy) are obtained as a function of 2,. The entire intensity (Int) data set consists of several thousand channels covering a range of photon energies, E (up to ,150,keV), at each of the ,1000 2, steps, forming a 2,4 mega-element two-dimensional array, Int(E, 2,). These intensity data are then regrouped according to photon energies, which are defined in the multichannel SSD as individual channels, yielding a large number of intensity versus 2, (angle-dispersive) data sets, Int(E = const., 2,), each of which corresponds to a given photon energy or wavelength. The entire data set, selected subsets or composite scans can be used for multiple data set Rietveld refinement. Data collected both on ,-Al2O3 (a NIST diffraction standard) at ambient conditions and on a mixture of MgO and Au at high pressure were analyzed using the Rietveld technique, with varying schemes of data treatment. Furthermore, it is demonstrated that data within certain energy bands (,E/E = ±10%) may be binned together to improve counting statistics in a composite angle-dispersive scan, even when collected with much coarser scan steps of 0.1 or 0.2°. This technique is useful for high-pressure as well as general purpose powder diffraction studies that have limited X-ray access to the sample using synchrotron radiation. Several advantages are discussed. [source] Automated profile analysis for single-crystal diffraction dataJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 2 2003R. J. Angel An integration method for step-scanned single-crystal intensity data based upon fitting of the individual diffraction profiles by a pseudo-Voigt function is presented. Algorithms for both the recovery of weak intensities from data sets and the rejection of aberrant peak profiles are discussed. The ideas presented in this paper have been implemented in a software package for Microsoft Windows, WinIntegrStp, which is available at http://www.crystal.vt.edu/. [source] Particle surface temperature measurements with multicolor band pyrometryAICHE JOURNAL, Issue 1 2009Hong Lu Abstract A noncontact, color-band pyrometer, based on widely available, inexpensive digital imaging devices, such as commercial color cameras, and capable of pixel-by-pixel resolution of particle-surface temperature and emissivity is demonstrated and described. This diagnostic instrument is ideally suited to many combustion environments. The devices used in this method include color charge-coupled device (CCD), or complementary metal oxide semiconductor (CMOS) digital camera, or any other color-rendering camera. The color camera provides spectrally resolved light intensity data of the image, most commonly for three color bands (Red, Green, and Blue,), but in some cases for four or more bands or for a different set of colors. The CCD or CMOS sensor-mask combination has a specific spectral response curve for each of these color bands that spans the visible and often near infrared spectral range. A theory is developed, based on radiative heat transfer and camera responsivity that allows quantitative surface temperature distribution calculation, based on a photograph of an object in emitted light. Particle surface temperature calculation is corrected by heat transfer analysis with reflection between the particle and reactor wall for particles located in furnace environments, but such corrections lead to useful results only when the particle temperature is near or below the wall temperatures. Wood particle-surface temperatures were measured with this color-band pyrometry during pyrolysis and combustion processes, which agree well with thermocouple measured data. Particle-surface temperature data simultaneously measured from three orthogonal directions were also mapped onto the surface of a computer generated 3-D (three-dimensional) particle model. © 2008 American Institute of Chemical Engineers AIChE J, 2009 [source] Neutron Powder Diffraction Study of a Phase Transition in La0.68(Ti0.95Al0.05)O3JOURNAL OF THE AMERICAN CERAMIC SOCIETY, Issue 12 2006Roushown Ali Crystal structures and structural changes of the compound La0.68(Ti0.95Al0.05)O3 have been studied using neutron powder diffraction data and the Rietveld method in the temperature range from 25° to 592°C. The Rietveld profile-fitting analyses of the neutron data and the synchrotron diffraction profile revealed that the crystal symmetry of the low-temperature phase of La0.68(Ti0.95Al0.05)O3 is orthorhombic Cmmm (2ap× 2ap× 2ap; p: pseudo-cubic perovskite). The unit-cell and structural parameters were successfully refined with the orthorhombic Cmmm for the intensity data measured at 25°, 182°, and 286°C, and with the tetragonal P4/mmm (ap×ap× 2ap) for intensity data obtained at 388° and 592°C. The P4/mmm -to- Cmmm phase transition was found to be induced by tilting of the (TiAl)O6 octahedron. The tilt angle decreased with increasing temperature, reaching 0° at the Cmmm,P4/mmm transition temperature. [source] Comparative LC-MS: A landscape of peaks and valleysPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 4 2008Antoine H. P. America Dr. Abstract Quantitative proteomics approaches using stable isotopes are well-known and used in many labs nowadays. More recently, high resolution quantitative approaches are reported that rely on LC-MS quantitation of peptide concentrations by comparing peak intensities between multiple runs obtained by continuous detection in MS mode. Characteristic of these comparative LC-MS procedures is that they do not rely on the use of stable isotopes; therefore the procedure is often referred to as label-free LC-MS. In order to compare at comprehensive scale peak intensity data in multiple LC-MS datasets, dedicated software is required for detection, matching and alignment of peaks. The high accuracy in quantitative determination of peptide abundancies provides an impressive level of detail. This approach also requires an experimental set-up where quantitative aspects of protein extraction and reproducible separation conditions need to be well controlled. In this paper we will provide insight in the critical parameters that affect the quality of the results and list an overview of the most recent software packages that are available for this procedure. [source] Centrosymmetric and pseudo-centrosymmetric structures refined as non-centrosymmetricACTA CRYSTALLOGRAPHICA SECTION B, Issue 5 2006H. D. Flack The behaviour of the Flack parameter for centrosymmetric and pseudo-centrosymmetric crystal structures based on crystal structures published as being non-centrosymmetric is presented. It is confirmed for centrosymmetric structures that the value obtained for the Flack parameter is critically dependent on the Friedel coverage of the intensity data, approaching 0.5 for a coverage of 100% and sticking near the starting value for a coverage of 0%. For pseudo-centrosymmetric structures, even those very close to being centrosymmetric, it is found that it is often possible to obtain significant values of the Flack parameter. A theoretical basis for this surprising result is established. It has also been possible to establish an a priori estimate of the standard uncertainty of the Flack parameter based only on the chemical composition of the compound and the wavelength of the radiation. The paper concludes with preliminary presentations of bias in the Flack parameter and of inconsistent chemical and crystallographic data. [source] Characterization of diverse plant communities in Aspen Parkland rangeland using LiDAR dataAPPLIED VEGETATION SCIENCE, Issue 3 2007Jason G. Su Moss (1983) Abstract Question: How effective is high-resolution airborne LiDAR technology for quantifying biophysical characteristics of multiple community types within diverse rangeland environments? Location: Native Aspen Parkland vegetation in central Alberta, Canada. Methods: Vegetation within 117 reference plots stratified across eight types, including forest, shrubland, upland grassland and lowland meadow communities, were assessed in 2001 for the height, cover and density of vegetation within various strata (herb, shrub and tree layers). Actual ground data were subsequently compared against modelled values for each community type and strata derived from the analysis of airborne LiDAR data obtained in 2000. Results: LiDAR data were effective for quantifying vegetation height, cover and density of the overstory within closed- and open Populus forest communities. However, LiDAR measurements typically underestimated the height and cover of shrublands, as well as most of the herbaceous communities. Analysis of LiDAR intensity data indicated reflectance generally decreased as LiDAR sampling points moved upwards from the ground to the vegetation canopy. Conclusions: While LiDAR technology is useful for characterizing deciduous forest properties, the quantification of understory vegetation characteristics, as well as those of individual shrublands and grasslands, was more limiting. Further refinements in analysis methods are necessary to increase the reliability of characterizing these communities. [source] Decorrugation, edge detection, and modelling of total field magnetic observations from a historic town site, Yellowstone National Park, USAARCHAEOLOGICAL PROSPECTION, Issue 1 2010Steven D. Sheriff Abstract Cinnabar, Montana is a historic town site and railroad depot near the northern edge of Yellowstone National Park and was inhabited between 1883 and 1903. Remains of foundations and old photographs help determine the area of the town, but the south and east limits are unknown. We acquired total field magnetic intensity data to help determine the full extent of the town. Randomly distributed ferrous magnetic sources on the surface and typical noise associated with acquisition complicate the signal. To separate signal and noise we applied filtering and edge detection techniques common in the aeromagnetic industry to our data. Regional removal, decorrugation, upward continuation, and edge detection successfully separated signal and noise. Following filtering, we extracted two larger anomalies from the data set. For those two anomalies, we estimated the edges of their causative sources by calculating the maxima in the horizontal gradient of their anomalies and by inverse modelling those sources; both methods yield similar results. An archaeological test unit excavation within one of the anomalies clearly indicates the remains of buried domestic features, the foundation to a house or other building associated with the late nineteenth to early twentieth century use of Cinnabar. Thus the southeast extent of Cinnabar is greater than previously thought. The lack of surface indicators or adequate historic photography precluded the identification of this buried feature without the aid of the magnetic study. Copyright © 2009 John Wiley & Sons, Ltd. [source] Analysis of lattice-translocation disorder in the layered hexagonal structure of carboxysome shell protein CsoS1CACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2009Yingssu Tsai Lattice-translocation or crystal order,disorder phenomena occur when some layers or groups of molecules in a crystal are randomly displaced relative to other groups of molecules by a discrete set of vectors. In previous work, the effects of lattice translocation on diffraction intensities have been corrected by considering that the observed intensities are the product of the intensities from an ideal crystal (lacking disorder) multiplied by the squared magnitude of the Fourier transform of the set of translocation vectors. Here, the structure determination is presented of carboxysome protein CsoS1C from Halothiobacillius neapolitanus in a crystal exhibiting a lattice translocation with unique features. The diffraction data are fully accounted for by a crystal unit cell composed of two layers of cyclic protein hexamers. The first layer is fully ordered (i.e. has one fixed position), while the second layer randomly takes one of three alternative positions whose displacements are related to each other by threefold symmetry. Remarkably, the highest symmetry present in the crystal is P3, yet the intensity data (and the Patterson map) obey 6/m instead of symmetry; the intensities exceed the symmetry expected from combining the crystal space group with an inversion center. The origin of this rare phenomenon, known as symmetry enhancement, is discussed and shown to be possible even for a perfectly ordered crystal. The lattice-translocation treatment described here may be useful in analyzing other cases of disorder in which layers or groups of molecules are shifted in multiple symmetry-related directions. [source] A statistic for local intensity differences: robustness to anisotropy and pseudo-centering and utility for detecting twinningACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2003Jennifer E. Padilla A new approach to analyzing macromolecular single-crystal X-ray diffraction intensity statistics is presented. Instead of considering reflections in resolution shells, differences between local pairs of reflection intensities are taken and normalized separately. When the two reflections to be compared (having intensities I1 and I2, respectively) are chosen appropriately, the behavior of the parameter L = (I1 , I2)/(I1 + I2) is insensitive to phenomena that tend to confound traditional intensity statistics, such as anisotropic diffraction and pseudo-centering. The distributions and expected values for L take simple forms when the intensity data are from ordinary crystals or from perfectly twinned specimens. The robustness of the approach is demonstrated with examples using real proteins whose diffraction data appear aberrant by other methods of intensity analysis. The new statistic is better suited than other available methods for diagnosing perfect hemihedral twinning. [source] Preliminary X-ray diffraction studies of the external functional unit RtH2-e from the Rapana thomasianaACTA CRYSTALLOGRAPHICA SECTION D, Issue 11 2001M. Perbandt The `external' oxygenated functional unit RtH2-e of the Rapana hemocyanin subunit RHSS2 was isolated and crystallized. X-ray intensity data to 3.3,Å resolution have been collected at 100,K and the structure has been solved using the molecular-replacement method. The space group is assigned to be the tetragonal P43212, with unit-cell parameters a = b = 105.5, c = 375.0,Å. [source] Crystallization of the plant hormone receptors PYL9/RCAR1, PYL5/RCAR8 and PYR1/RCAR11 in the presence of (+)-abscisic acidACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 4 2010Nobuyuki Shibata Abscisic acid (ABA) is a plant hormone that plays key regulatory roles in physiological pathways for the adaptation of vegetative tissues to abiotic stresses such as water stress in addition to events pertaining to plant growth and development. The Arabidopsis ABA receptor proteins PYR/PYLs/RCARs form a START family that contains 14 members which are classified into three subfamilies (I,III). Here, purification, crystallization and X-ray data collection are reported for a member of each of the subfamilies, PYL9/RCAR1 from subfamily I, PYL5/RCAR8 from subfamily II and PYR1/RCAR11 from subfamily III, in the presence of (+)-abscisic acid. The three proteins crystallize in space groups P3121/P3221, P2 and P1, respectively. X-ray intensity data were collected to 1.9,2.6,Å resolution. [source] Purification and preliminary X-ray crystallographic studies of ,-microseminoprotein from human seminal plasmaACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 5 2009Vijay Kumar ,-Microseminoprotein (,-MSP) is a small cysteine-rich protein with a molecular mass of 10,kDa. It was first isolated from human seminal plasma and has subsequently been identified from several species. Comparison of the amino-acid sequences of ,-MSP proteins suggests that the protein is a rapidly evolving protein. The function of ,-MSP is poorly understood. Furthermore, no crystal structure has been reported of any ,-MSP; therefore, determination of the crystal structure of ,-MSP is the foremost task in order to understand the function of this protein completely. Here, the purification, crystallization and preliminary X-ray diffraction analysis of ,-MSP from human seminal plasma are described. The protein was purified using anion-exchange and size-exclusion chromatography and the purified protein was crystallized using 0.1,M ammonium sulfate, 0.1,M HEPES buffer pH 7.0 and 20%(w/v) PEG 3350. The crystals belonged to the tetragonal space group P4322 and contained three ,-MSP molecules in the asymmetric unit. X-ray intensity data were collected to 2.4,Å resolution. [source] Purification, crystallization and preliminary crystallographic analysis of Est-Y29: a novel oligomeric ,-lactamaseACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 3 2009SeungBum Kim ,-Lactam antibiotics such as penicillins and cephalosporins have a four-atom ring as a common element in their structure. The ,-lactamases, which catalyze the inactivation of these antibiotics, are of great interest because of their high incidence in pathogenic bacteria. A novel oligomeric class C ,-lactamase (Est-Y29) from a metagenomic library was expressed, purified and crystallized. The recombinant protein was expressed in Escherichia coli with an N-terminal 6×His tag and purified to homogeneity. EstY-29 was crystallized and X-ray intensity data were collected to 1.49,Å resolution using synchrotron radiation. [source] | ||||||||||||||||