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At least 1,423 records · Page 79Linked to original sources
PubMed2005

Is the future for clinical trials internet-based? A cluster randomized clinical trial.

OBJECTIVE: To compare the efficiency and ease of use of internet data capture compared with conventional paper based data recording in the conduct of a clinical trial. DESIGN: Multicentre, cluster randomized clinical trial. SETTING: General practice in the UK. MAIN OUTCOME MEASURES: Timings for study landmarks, queries, data entry and monitoring time; Investigator Questionnaire Results. RESULTS: The internet-derived database was ready for release 33 days after the last patient visit compared with 48 days for the paper-derived database, despite much higher numbers of patients in the internet group. The mean times from visit to data entry were 10.2 (SD 18.9) days and 95.4 (SD 44.6) days respectively (P < 0.01). The mean times from a visit to a query being resolved were 121.4 (SD 58.3) days and 182.1 (SD 58.9) days respectively (P < 0.01). The post-study responses from investigators were positive. Seventy-one percent of centres said they would prefer to use the internet rather than paper CRFs for future studies. CONCLUSIONS: There were efficiency gains seen with the use of an internet-based system when compared with a paper-based system in terms data entry, query resolution and the time to the release of the database. The investigators' response to the internet system was generally favourable although on average investigators reported increased time spent on the study. Further efficiency might be gained with improved programming, increased investigator familiarity with the internet system, and with newly adapted working practices for sponsors' monitors and database personnel.

Clinical Trials as Topic↗
PubMed2001

Transthyretin stability as a key factor in amyloidogenesis: X-ray analysis at atomic resolution.

Transthyretin (TTR) amyloidosis is a conformational disturbance, which, like other amyloidoses, represents a life threat. Here, we report a TTR variant, TTR Thr119Met, that has been shown to have a protective role in the development of clinical symptoms in carriers of TTR Val30Met, one of the most frequent variants among TTR amyloidosis patients. In order to understand this effect, we have determined the structures of the TTR Val30Met/Thr119Met double mutant isolated from the serum of one patient and of both the native and thyroxine complex of TTR Thr119Met. Major conclusions are: (i) new H-bonds within each monomer and monomer-monomer inter-subunit contacts, e.g. Ser117-Ser117 and Met119-Tyr114, increase protein stability, possibly leading to the protective effect of the TTR Val30Met/Thr119Met variant when compared to the single variant TTR Val30Met. (ii) The mutated residue (Met119) extends across the thyroxine binding channel inducing conformational changes that lead to closer contacts between different dimers within the tetramer. The data, at atomic resolution, were essential to detect, for the first time, the subtle changes in the inter-subunit contacts of TTR, and explain the non-amyloidogenic potential of the TTR Thr119Met variant, improving considerably current research on the TTR amyloid fibril formation pathway.

Amino Acid Substitution↗
PubMed1996

Altered domain closure and iron binding in transferrins: the crystal structure of the Asp60Ser mutant of the amino-terminal half-molecule of human lactoferrin.

The crystal structure of a site-specific mutant of the N-terminal half-molecule of human lactoferrin, Lf(N), in which the iron ligand Asp60 has been mutated to Ser, has been determined at 2.05 A resolution in order to determine the effects of the mutation on iron binding and domain closure. Yellow monoclinic crystals of the D60S mutant, in its iron-bound form, were prepared, and have unit cell dimensions a = 110.2 A, b = 57.0 A, c = 55.2 A, beta = 97.6 degrees, space group C2, with one molecule of 333 residues in the asymmetric unit. The structure was determined by molecular replacement, using the wild-type Lf(N) as search model, and was refined by restrained least-squares methods. The final model, comprising 2451 protein atoms (from residues 2 to 315) one Fe3+ and one CO2-(3), and 107 water molecules, gives an R-factor of 0.175 for all data in the resolution range 20.0 to 2.05 A. The model conforms well with standard geometry, having root-mean-square deviations of 0.014 A and 1.2 degrees from standard bond lengths and angles. The structure of the D60S mutant deviates in two important respects from the parent Lf(N) molecule. At the mutation site the Ser side-chain neither binds to the iron atom nor makes any interdomain contact as the substituted Asp does; instead a water molecule fills the iron coordination site and participates in interdomain hydrogen bonding. The domain closure is also changed, with the D60S mutant having a more closed conformation. Consideration of crystal packing suggests that the altered domain closure is a genuine molecular property but both the iron coordination and interdomain contacts are consistent with weakened iron binding in the mutant. The implications for iron binding in transferrins generally are discussed.

Animals↗
PubMed1997

Validation of reconstructed bremsstrahlung spectra between 6 MV and 25 MV from measured transmission data.

We have previously investigated a method of high-energy x-ray spectral reconstruction from transmission data by direct resolution of a matrix system. This technique uses the spectral vectorial algebra formalism. The resolution has previously been tested on a 12 MV photon beam. To extend and to test the validity of the results to the entire radiotherapy energy range, we have performed the method on photon beams with nominal energies of 6, 12, 15, and 25 MV. The influence on the 6 MV spectrum of a 60 degrees built-in wedge has also been investigated to test the sensitivity of the method and the results are reported. To validate our reconstructed spectra, dosimetric quantities such as tissue phantom ratios (TPR), water-to-air stopping power ratios (S/p) air water, and quality indexes TPR 10 (20) have been calculated. The results show good agreement between the measured and calculated data. Mean mass energy absorption coefficient ratios for different materials have also been computed and compared to data published recently and the results are very close (within +/- 0.5%). Primary depth dose functions in water have also been computed to deduce primary dose attenuation coefficients.

Evaluation Studies as Topic↗
PubMed2001

Camel lactoferrin, a transferrin-cum-lactoferrin: crystal structure of camel apolactoferrin at 2.6 A resolution and structural basis of its dual role.

Camel lactoferrin is the first protein from the transferrin superfamily that has been found to display the characteristic functions of iron binding and release of lactoferrin as well as transferrin simultaneously. It was remarkable to observe a wide pH demarcation in the release of iron from two lobes. It loses 50 % iron at pH 6.5 and the remaining 50 % iron is released only at pH values between 4.0 and 2.0. Furthermore, proteolytically generated N and C-lobes of camel lactoferrin showed that the C-lobe lost iron at pH 6.5, while the N-lobe lost it only at pH less than 4.0. In order to establish the structural basis of this striking observation, the purified camel apolactoferrin was crystallized. The crystals belong to monoclinic space group C2 with unit cell dimensions a=175.8 A, b=80.9 A, c=56.4 A, beta=92.4 degrees and Z=4. The structure has been determined by the molecular replacement method and refined to an R-factor of 0.198 (R-free=0.268) using all the data in the resolution range of 20.0-2.6 A. The overall structure of camel apolactoferrin folds into two lobes which contain four distinct domains. Both lobes adopt open conformations indicating wide distances between the iron binding residues in the native iron-free form of lactoferrin. The dispositions of various residues of the iron binding pocket of the N-lobe of camel apolactoferrin are similar to those of the N-lobe in human apolactoferrin, while the corresponding residues in the C-lobe show a striking similarity with those in the C-lobes of duck and hen apo-ovotransferrins. These observations indicate that the N-lobe of camel apolactoferrin is structurally very similar to the N-lobe of human apolactoferrin and the structure of the C-lobe of camel apolactoferrin matches closely with those of the hen and duck apo-ovotransferrins. These observations suggest that the iron binding and releasing behaviour of the N-lobe of camel lactoferrin is similar to that of the N-lobe of human lactoferrin, whereas that of the C-lobe resembles those of the C-lobes of duck and hen apo-ovotransferrins. Hence, it correlates with the observation of the N-lobe of camel lactoferrin losing iron at a low pH (4.0-2.0) as in other lactoferrins. On the other hand, the C-lobe of camel lactoferrin loses iron at higher pH (7.0-6.0) like transferrins suggesting its functional similarity to that of transferrins. Thus, camel lactoferrin can be termed as half lactoferrin and half transferrin.

Animals↗
PubMed1986

Electron diffraction analysis of the M412 intermediate of bacteriorhodopsin.

High resolution electron diffraction data have been recorded for glucose-embedded purple membrane specimens in which bacteriorhodopsin (bR) has been trapped by cooling slowly to below--100 degrees C under continuous illumination. Thin films (OD approximately 0.7) of glucose-embedded membranes, prepared as a control, showed virtually 100% conversion to the M state, and stacks of such thin film specimens gave very similar x-ray diffraction patterns in the bR568 and the M412 state in most experiments. To be certain that any measured differences in diffraction intensity would be real, two independent sets of electron diffraction intensities were recorded for near-equatorial, i.e. (hkO), reflections. Little correlation was indeed observed between these two sets for delta F values at low resolution (15-5.0 A, 49 reflections), but the correlation coefficient is approximately 0.3 at high resolution (5.0-3.3 A, 218 reflections). Thus, while most of the measured difference is error, the mean delta F and the correlation coefficient can be used to estimate the smaller, true delta F due to structural changes occurring in the M state. The magnitude of this estimated true mean delta F is equal to what would be produced if approximately five to seven nonhydrogen atoms were moved to structurally uncorrelated (i.e., new) positions in the M state. Movements of a few amino acid side chains, and repositioning of atoms of the retinal group and the associated lysine side chain after trans-cis isomerization, are the most probable causes of the observed intensity changes in the M state. The difference Fourier map, calculated in projection at 3.5-A resolution, shows only very small peaks, the largest of which are confined, however, to the region of the protein.

Bacteriorhodopsins↗
PubMed1986

The role of magnetic resonance imaging techniques in the evaluation of orbital and ocular disease.

Technical developments have resulted in a great improvement in the quality of magnetic resonance imaging (MRI) of the orbit. With surface coil data acquisition spatial resolution of less than a millimetre can now be achieved, and contrast discrimination is such that the cortex and nucleus of the lens can be distinguished. The application of MRI to the diagnosis of orbital and ocular pathology was studied in a group of 51 patients with a wide range of pathology. Advantages of MRI over computed tomography (CT) included the avoidance of ionising radiation, the direct multiplanar facility and the use of flow-dependent sequences to identify pathological vessels without the need for contrast medium; although CT was superior in showing bone detail. Only a limited discrimination between different tumour types is possible by assessment of their MRI characteristics. Research is currently being directed towards achieving thinner slices, shorter data acquisition times and removal of the high signal from retrobulbar fat.

Adenoma↗
PubMedDate not supplied

Relationships of microsporidian genera, with emphasis on the polysporous genera, revealed by sequences of the largest subunit of RNA polymerase II (RPB1).

Molecular data have proved useful as an alternative to morphological data in showing the relationships of genera within the phylum Microsporidia, but until now have been available only for ribosomal genes. In previous studies protein-coding genes of microsporidia have been used only to assess their position in the evolution of eukaryotes. For the first time we report on the use of a protein-coding gene, the A-G region of the largest subunit of RNA polymerase II (RPB1) from 14 mainly polysporous species, to generate an alternative phylogeny for microsporidia. Using the amino acid sequences, the genera and species fell into the same main groupings as had been obtained with 16S rDNA sequences, but the RPB1 data provided better resolution within these groups. The results supported the pairings of Trachipleistophora hominis with Vavraia culicis and Pleistophora hippoglossoideos with Pleistophora typicalis. They also confirmed that the genus Pleistophora is not monophyletic and that it will be necessary to transfer Pleistophora ovariae and Pleistophora mirandellae into one or more other genera, as has already been effected for Pleistophora anguillarum.

Animals↗
PubMed1998

Quality of brain perfusion single-photon emission tomography images: multicentre evaluation using an anatomically accurate three-dimensional phantom.

The aim of the study was to evaluate the quality of routine brain perfusion single-photon emission tomography (SPET) images in Finnish nuclear medicine laboratories. Twelve laboratories participated in the study. A three-dimensional high resolution brain phantom (Data Spectrum's 3D Hoffman Brain Phantom) was filled with a well-mixed solution of technetium-99m (110 MBq), water and detergent. Acquisition, reconstruction and printing were performed according to the clinical routine in each centre. Three nuclear medicine specialists blindly evaluated all image sets. The results were ranked from 1 to 5 (poor quality-high quality). Also a SPET performance phantom (Nuclear Associates' PET/SPECT Performance Phantom PS 101) was filled with the same radioactivity concentration as the brain phantom. The parameters for the acquisition, the reconstruction and the printing were exactly the same as with the brain phantom. The number of detected "hot" (from 0 to 8) and "cold" lesions (from 0 to 7) was visually evaluated from hard copies. Resolution and contrast were quantified from digital images. Average score for brain phantom images was 2.7 +/- 0.8 (range 1.5-4.5). The average diameter of the "hot" cylinders detected was 16 mm (range 9.2-20.0 mm) and that of the "cold" cylinders detected, 11 mm (5.9-14.3 mm) according to visual evaluation. Quantification of digital images showed that the hard copy was one reason for low-quality images. The quality of the hard copies was good only in four laboratories and was amazingly low in the others when comparing it with the actual structure of the brain phantom. The described quantification method is suitable for optimizing resolution and contrast detectability of hard copies. This study revealed the urgent need for external quality assurance of clinical brain perfusion SPET images.

Brain↗
PubMed2003

Structure and mechanism of MT-ADPRase, a nudix hydrolase from Mycobacterium tuberculosis.

Nudix hydrolases are a family of proteins that contain the characteristic sequence GX(5)EX(7)REUXEEXG(I/L/V), the Nudix box. They catalyze the hydrolysis of a variety of nucleoside diphosphate derivatives such as ADP-ribose, Ap(n)A (3 </= n </= 6), NADH, and dATP. A number of Nudix hydrolases from several species, ranging from bacteria to humans, have been characterized, including, in some cases, the determination of their three-dimensional structures. The product of the Rv1700 gene of M. tuberculosis is a Nudix hydrolase specific for ADP-ribose (ADPR). We have determined the crystal structures of MT-ADPRase alone, and in complex with substrate, with substrate and the nonactivating metal ion Gd(3+), and in complex with a nonhydrolyzable ADPR analog and the activating metal ion Mn(2+). These structures, refined with data extending to resolutions between 2.0 and 2.3 A, showed that there are sequence differences in binding site residues between MT-ADPRase and a human homolog that may be exploited for antituberculosis drug development.

Adenosine Diphosphate Ribose↗
PubMed2000

Purification, crystallization and preliminary X-ray analysis of a complex between granulocyte colony-stimulating factor and its soluble receptor.

Crystals of the complex between granulocyte colony-stimulating factor and its soluble receptor were obtained by a vapour-diffusion method using ammonium sulfate as a precipitant. Addition of 1, 4-dioxane was critical in order to grow the crystals to sufficient sizes. Cryoprotection was essential in order to collect diffraction data at atomic resolution. Two kinds of crystal forms were obtained depending on the cryoprotectants. In a cryosolvent with the same salt concentration as in the crystallization conditions, the crystal belonged to the space group I4(1)22. At higher salt concentrations, the crystal was converted to a different space group P4(1)2(1)2 (P4(3)2(1)2) with the same unit-cell parameters.

Animals↗
PubMed2002

Twist and shear in beta-sheets and beta-ribbons.

The structures of the beta-sheets and the beta-ribbons have been analysed using high-resolution protein structure data. Systematic asymmetries measured in both parallel and antiparallel beta-structures include the sheet twist and the strand shear. In order to determine the origin of these asymmetries, numerous interactions and correlations were examined. The strongest correlations are observed for residues in antiparallel beta-sheets and beta-ribbons that form non-H-bonded pairs. For these residues, the sheet twist is correlated to the backbone phi angle but not to the psi angle. Our analysis supports the existence of an inter-strand C(alpha)H(alpha)...O weak H-bond, which, together with the CO...HN H-bond, constitutes a bifurcated H-bond that links neighbouring beta-strands. Residues of beta-sheets and beta-ribbons in high-resolution protein structures form a distinct region of the Ramachandran plot, which is determined by the formation of the bifurcated H-bond, the formation of an intra-strand O...H(alpha) non-bonded polar interaction, and an intra-strand O...C(beta) steric clash. Using beta-strands parameterised by phi-psi values from the allowed beta-sheet region of the Ramachandran plot, the shear and the right-hand twist can be reproduced in a simple model of the antiparallel and parallel beta-ribbon that models the bifurcated H-bonds specifically. The conformations of interior residues of beta-sheets are shown to be subsets of the conformations of residues of beta-ribbons.

Databases, Protein↗
PubMed2007

Comparison of nonuniform rotational distortion between mechanical IVUS and OCT using a phantom model.

Optical coherence tomography (OCT) is an optical analog of mechanical intravascular ultrasound (M-IVUS) with much higher spatial resolution. However, no data exist regarding the nonuniform rotational distortion (NURD) with OCT. The aim of the study was to investigate whether OCT generates less NURD relative to M-IVUS. A coronary artery phantom model was constructed with a rubber ring (3.68 mm in diameter), located at the distal end of the phantom. This model was also composed of eight equally spaced steel wires and an additional marker-wire. Two types of vascular phantoms were used, mild curve (90 degrees ) and acute curve (near 180 degrees ). Subsequent M-IVUS (n = 6) and OCT (n = 6) imaging was performed. Eight angles between eight wires, except the marker-wire, were measured from each image. These angles, measured with M-IVUS and OCT, were compared with those of high-resolution optical photography as a gold standard. The average in angle differences was significantly smaller in OCT compared with M-IVUS in the mild curve model (3.2 +/- 1.0 degrees vs, 6.9 +/- 2.1 degrees , p < 0.01). Compared with the latter model, the average in angle differences was exaggerated in the acute curve model with M-IVUS (9.1 +/- 0.9 degrees vs. 6.9 +/- 2.1 degrees , p < 0.05) but not with OCT (3.5 +/- 0.8 degrees vs. 3.2 +/- 1.0 degrees , p= not significant). OCT generates significantly less NURD compared with M-IVUS, especially in tortuous situation.

Artifacts↗
PubMedDate not supplied

A computerized approach for morphological analysis of the corpus callosum.

OBJECTIVE: A new technique for analyzing the morphology of the corpus callosum is presented, and it is applied to a group of elderly subjects. MATERIALS AND METHODS: The proposed approach normalizes subject data into the Talairach space using an elastic deformation transformation. The properties of this transformation are used as a quantitative description of the callosal shape with respect to the Talairach atlas, which is treated as a standard. In particular, a deformation function measures the enlargement/shrinkage associated with this elastic deformation. Intersubject comparisons are made by comparing deformation functions. RESULTS: This technique was applied to eight male and eight female subjects. Based on the average deformation functions of each group, the posterior region of the female corpus callosum was found to be larger than its corresponding region in the males. The average callosal shape of each group was also found, demonstrating visually the callosal shape differences between the two groups in this sample. CONCLUSION: The proposed methodology utilizes the full resolution of the data, rather than relying on global descriptions such as area measurements. The application of this methodology to an elderly group indicated sex-related differences in the callosal shape and size.

Aged↗
PubMed2000

Ab initio phasing of a 4189-atom protein structure at 1.2 A resolution.

The phase problem remains a key rate-limiting step in the determination of macromolecular X-ray structures. Direct methods, applying probability theory to the native data set, can routinely solve structures of up to about 200 non-H atoms, although much larger structures have been solved given sufficiently high resolution data and the presence of heavy atoms. Here it is shown that maximum-likelihood refinement of free-atom models with ARP/wARP can solve ab initio a much larger metalloprotein structure than the largest so far solved by conventional direct methods. The protein, OppA, is not naturally associated with metal ions but was co-crystallized with uranium.

Bacterial Proteins↗
PubMed2004

Expression, purification, crystallization and preliminary X-ray crystallographic analysis of pantothenate kinase from Mycobacterium tuberculosis.

Pantothenate kinase is an essential enzyme in the bacterial life cycle. It catalyzes the phosphorylation of pantothenate (vitamin B5) to 4'-phosphopantothenate, the first step in the coenzyme A biosynthetic pathway. The enzyme from Mycobacterium tuberculosis, MW 35.7 kDa, has been cloned, expressed, purified and crystallized in two different trigonal crystal forms, both belonging to space group P3(1)21. Two complete data sets of resolution 2.5 A (form I) and 2.9 A (form II) from crystals with unit-cell parameters a = b = 78.3, c = 115.45 A and a = b = 107.63, c = 89.85 A, respectively, were collected at room temperature on a home X-ray source. Structures of both crystal forms were solved for one subunit in the asymmetric unit by molecular replacement.

Bacterial Proteins↗
PubMed1997

Crystallization and preliminary X-ray analysis of bacteriophage lambda lysozyme in which all tryptophans have been replaced by aza-tryptophans.

After many unsuccessful attempts to crystallize the bacteriophage lambda lysozyme, a mutant where all the tryptophan residues have been replaced by aza-tryptophans has been crystallized by the vapor-diffusion method. The crystals are orthorhombic and belong to space group P2(1)2(1)2(1) with cell dimensions a = 73.01, b = 78.80, c = 82.31 A. Diffraction data were collected using synchrotron radiation sources. Crystals diffract to a resolution of 2.3 A. Data from two different platinum derivatives were also recorded to 2.8 and 2.5 A, respectively.

Journal Article↗
PubMed2006

Crystallization of the C-terminal head domain of the avian adenovirus CELO long fibre.

Avian adenovirus CELO contains two different fibres: fibre 1, the long fibre, and fibre 2, the short fibre. The short fibre is responsible for binding to an unknown avian receptor and is essential for infection of birds. The long fibre is not essential, but is known to bind the coxsackievirus and adenovirus receptor protein. Both trimeric fibres are attached to the same penton base, of which each icosahedral virus contains 12 copies. The short fibre extends straight outwards, while the long fibre emerges at an angle. The carboxy-terminal amino acids 579-793 of the avian adenovirus long fibre have been expressed with an amino-terminal hexahistidine tag and the expressed trimeric protein has been purified by nickel-affinity chromatography and crystallized. Crystals were grown at low pH using PEG 10,000 as precipitant and belonged to space group C2. The crystals diffracted rotating-anode Cu Kalpha radiation to at least 1.9 angstroms resolution and a complete data set was collected from a single crystal to 2.2 angstroms resolution. Unit-cell parameters were a = 216.5, b = 59.2, c = 57.5 angstroms, beta = 101.3 degrees, suggesting one trimer per asymmetric unit and a solvent content of 46%. The long fibre head does not have significant sequence homology to any other protein of known structure and molecular-replacement attempts with known fibre-head structures were unsuccessful. However, a map calculated using SIRAS phasing shows a clear trimer with a shape similar to known adenovirus fibre-head structures. Structure solution is in progress.

Capsid Proteins↗