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PubMed2002

HLA matching and hematopoietic cell transplant outcome.

The development of accurate and reproducible high-resolution DNA-based HLA typing methods has significantly improved the prospects for identifying well-matched donors for patients undergoing HCT, particularly those who lack a matched relative to serve as donor. Analysis of high-resolution typing data has shown that donor-recipient compatibility for HLA alleles is an important predictor of transplant outcome. The risk of graft failure is increased by patient incompatibility for HLA alleles expressed by the donor, and by the presence of patient anti-donor alloantibody. The impact of HLA class I and class II allele disparity on transplant outcome in unrelated HCT has been demonstrated in several large studies, and it is now evident that complete donor-recipient matching for HLA-A,-B,-C,-DRB1 and -DQB1 genes can significantly reduce the incidence of GVHD and risk of mortality. Patient-donor disparity for multiple HLA class I and class II alleles is clearly related to poor outcome, in terms of both risk of severe GVHD and mortality. Important questions for future investigation include elucidation of the relative importance of matching for different HLA genes ("permissive" versus "non-permissive" alleles), and the potential synergistic impact of multi-locus class I and II disparities.

B-Lymphocytes↗
PubMedDate not supplied

Contraceptive behavior of Jerusalem women seeking pregnancy counseling, 1980-1989.

BACKGROUND: Inconsistencies between intent and action in the area of birth control are often attributed, in both theory and medical practice, to female ignorance and lack of contraceptive skills. In the light of prevailing theories, this survey examines the contraceptive behavior of 1,425 Jerusalem clients of the Pregnancy Counseling and Follow-up Service. METHODS: The majority of clients were "in crisis" due to unplanned pregnancies and had turned to the counseling service for help in crisis resolution. The data are based on intake questionnaires and clinical records filled in by counselors. Recorded information included age, education, marital status, religious observance, previous pregnancies and abortions, contraceptives ever used and methods used prior to pregnancy, age of fetus, initial attitude, treatment process, and outcome. RESULTS: The results suggest that the women in the sample became pregnant not because they lacked the skills to avoid it, but because they failed to use those skills effectively. Younger, unmarried, and less educated women and those with many children were especially prone to risk-taking. They also waited longer than others before turning to counseling.

Adult↗
PubMed2003

Effects of distortions by A-tracts of promoter B-DNA spacer region on the kinetics of open complex formation by Escherichia coli RNA polymerase.

A-tracts in DNA due to their structural morphology distinctly different from the canonical B-DNA form play an important role in specific recognition of bacterial upstream promoter elements by the carboxyl terminal domain of RNA polymerase alpha subunit and, in turn, in the process of transcription initiation. They are only rarely found in the spacer promoter regions separating the -35 and -10 recognition hexamers. At present, the nature of the protein-DNA contacts formed between RNA polymerase and promoter DNA in transcription initiation can only be inferred from low resolution structural data and mutational and crosslinking experiments. To probe these contacts further, we constructed derivatives of a model Pa promoter bearing in the spacer region one or two An (n = 5 or 6) tracts, in phase with the DNA helical repeat, and studied the effects of thereby induced perturbation of promoter DNA structure on the kinetics of open complex (RPo) formation in vitro by Escherichia coli RNA polymerase. We found that the overall second-order rate constant ka of RPo formation, relative to that at the control promoter, was strongly reduced by one to two orders of magnitude only when the A-tracts were located in the nontemplate strand. A particularly strong 30-fold down effect on ka was exerted by nontemplate A-tracts in the -10 extended promoter region, where an involvement of nontemplate TG (-14, -15) sequence in a specific interaction with region 3 of sigma-subunit is postulated. A-tracts in the latter location caused also 3-fold slower isomerization of the first closed transcription complex into the intermediate one that precedes formation of RPo, and led to two-fold faster dissociation of the latter. All these findings are discussed in relation to recent structural and kinetic models of RPo formation.

Base Sequence↗
PubMed2002

Interpretations of the past and expectations for the future among Israeli and Palestinian youth.

This study was developed by a group of Israeli and Palestinian researchers for the purpose of examining social knowledge of young people in the conflicted region of the Middle East. The article examines the relations between measures of interpretations of the past (perceptions of legitimacy and emotional reactions toward the historical "narratives" of Israelis and Palestinians) and measures of expectations of the collective future, as reflected in conflict resolution beliefs. Data were collected from December 1999 to February 2000 (before the present crisis [2000-2002] in Jewish-Palestinian relations) among representative samples of high school students (Grades 10 and 12): 1,183 Palestinians in the Palestinian National Territories and 1,188 Israeli Jewish students. The results are discussed from developmental, social, and cultural perspectives.

Adolescent↗
PubMed1992

Design features and performance of a PET system for animal research.

The design features of a PET system designed for animal studies are described and its performance evaluated. The system employs a two-dimensional modular detector array consisting of bismuth germanate detector elements that are 3.5 mm (transaxially) by 6.25 mm (axially) by 30 mm (deep). These arrays are optically coupled to a pair of dual-photo-multiplier tubes (PMT). The detector ring is 64 cm in diameter with a field of view (FOV) of 40 cm by 5.4 cm axially, acquiring 15 slices at 3.4 mm spacing. These features include: (1) digitization of PMT signals from each block for improved position and energy discrimination of coincident events and (2) dual-window energy discrimination for simultaneous but separate acquisition of photopeak and scatter data. Intrinsic resolution averages 3.5 mm at the center of the FOV, while reconstructed resolution (ramp filter) ranges from 3.8 mm at the center of the FOV to 4.6 mm at an 8 cm radius. Axial resolution averages 4.4 and 4.9 mm and sensitivity averages 4.2 and 6.1 kcps/microCi/cc for cross planes and enhanced direct planes, respectively. Randoms fraction is high due to reduced interplane shielding, giving a peak true count rate of 103 kcps for a 10 cm cylinder. Scatter as a fraction of trues is 16% for a 10 cm cylinder at a lower energy threshold of 350 keV. All parameters are sensitive to energy threshold. Spatial resolution improves by 11% transaxially and 9% axially, scatter fraction drops to 10%, and overall sensitivity drops by 48% when the threshold value is increased from 350 keV to 450 keV.

Animals↗
PubMed1992

Structural and thermodynamic analysis of compensating mutations within the core of chicken egg white lysozyme.

High resolution crystal structures have been determined for six chicken-type lysozymes that were constructed to investigate putative intermediates in the evolution of the lysozymes of modern game birds (Malcolm, B. A., Wilson, K. P., Matthews, B. W., Kirsch, J. F., and Wilson, A. C. (1990) Nature 345, 86-89). The amino acid replacements include Thr-40----Ser, Ile-55----Val, and Ser-91----Thr, as well as combinations of these substitutions. Residues 40, 55, and 91 are buried within the core of chicken lysozyme. The replacements therefore involve the insertion and/or removal of methyl groups from the protein interior. The mutant proteins have normal activities, and their thermal stabilities span a range of 7 degrees C, with some variants more stable and some less stable than the naturally occurring forms. Comparison of the crystal structures shows the overall structures to be very similar, but there are differences in the packing of side chains in the region of the replacements. The x-ray coordinates were used to evaluate the repacking of side chains in the protein interior and to attempt to evaluate the contributions of the different energetic interactions toward the overall stability of each variant. The results illustrate how proteins can compensate for potentially destabilizing substitutions in different ways and underscore the importance of high resolution structural data if changes in protein thermostability due to changes in protein sequence are to be understood. The findings also suggest that protein stability can be increased by mutations that lower strain in the protein interior while maintaining total buried hydrophobic surface area.

Egg White↗
PubMed2005

[Imaging aid for thoracoscopic thymectomy; thymic vein visualization].

The spread and progress of thoracoscopic surgery has been remarkable. There are many important organs and blood vessels in the mediastinal space, thus, as inadvertent injury invites serious consequences, it is necessary to understand the anatomical position of existing structures. When enucleating the thymoma under a thoracoscope, one of the blood vessels to be careful about is the thymic vein. Therefore, we examined whether the thymic vein could be confirmed using a multidetector-row computed tomography (MD CT). We believed we could understand the anatomical position of the thymic vein by analyzing the high resolution slice data provided in MD CT using a work station. The diameter of the thymic is from a little less than 1 mm to 3 mm, and there were individual variations in position and the number of the vein. The thymic vein flowed into the left brachiocephalic vein in many cases. In some cases, the thymic vein flowed into the right internal thoracic vein or superior vena cava. It appears that visualization of the thymic vein could provide useful data when performing thoracoscopic thymectomy.

Adult↗
PubMed1990

Angelman syndrome: three molecular classes identified with chromosome 15q11q13-specific DNA markers.

Angelman syndrome (AS) and Prader-Willi syndrome (PWS) share a cytogenetic deletion of chromosome 15q11q13. To determine the extent of deletion in AS we analyzed the DNA of 19 AS patients, including two sib pairs, with the following chromosome 15q11q13--specific DNA markers: D15S9-D15S13, D15S17, D15S18, and D15S24. Three molecular classes were identified. Class I showed a deletion of D15S9-D15S13 and D15S18; class II showed a deletion of D15S9-D15S13; and in class III, including both sib pairs, no deletion was detected. These molecular classes appear to be identical to those observed in PWS. High-resolution cytogenetic data were available on 16 of the patients, and complete concordance between the presence of a cytogenetic deletion and a molecular deletion was observed. No submicroscopic deletions were detected. DNA samples from the parents of 10 patients with either a class I or a class II deletion were available for study. In seven of the 10 families, RFLPs were informative as to the parental origin of the deletion. In all informative families, the deleted chromosome 15 was observed to be of maternal origin. This finding is in contrast to the paternal origin of the deletions in PWS and is currently the only molecular difference observed between the two syndromes.

Abnormalities, Multiple↗
PubMed1987

Liver alcohol dehydrogenase.

The article deals with the structure and function of liver alcohol dehydrogenase and reviews mainly literature published after 1979, i.e., summarizes progress made in the field since Klinman presented her review on alcohol dehydrogenases. The emphasis will be on high-resolution crystallographic data, results obtained with metal-substituted enzyme derivatives, and on the mechanism and pH dependence of the catalytic reaction.

Alcohol Dehydrogenase↗
PubMed1987

Single crystals of hydrogenase from Desulfovibrio vulgaris Miyazaki F.

The hydrogenase solubilized from the particulate fraction from Desulfovibrio vulgaris Miyazaki F (IAM 12604) has been crystallized. Although the solubilized hydrogenase purified by the previous method (Yagi, T., Kimura, K., Daidoji, H., Sakai, F., Tamura, S., and Inokuchi, H. (1976) J. Biochem. (Tokyo) 79,661-671) revealed a single band upon disc electrophoresis, it could not be crystallized. The apparently homogeneous hydrogenase has been separated into three components of similar molecular weights by high performance liquid chromatography on DEAE-Toyopearl. Each hydrogenase component was successfully crystallized by means of the vapor diffusion method with polyethylene glycol or 2-methyl-2,4-pentanediol as a precipitating agent. Seeding procedure is necessary to grow an x-ray grade crystal. Preliminary x-ray experiments reveal that crystals grown from one component are in space group of P2(1)2(1)2(1) with a = 102.1(1), b = 126.8 (3), and c = 66.9(1) A. The unit cell volume of 8.66 X 10(5) A3 suggests that it contains one molecule/asymmetric unit (Vm = 2.43). The crystals grown from another component are in the same space group with a = 99.6(1), b = 126.8(3), c = 66.9(1) A, and the unit cell volume is 8.45 X 10(5) A3 (Vm = 2.37). The crystals diffract more than 2.5 A and are suitable for complete crystal analysis. Up to 4 A resolution native data have been collected on a diffractometer.

Chromatography, High Pressure Liquid↗
PubMed1981

Cryoenzymology.

A detailed understanding of the mechanism of enzyme action requires a correspondingly detailed knowledge of the structures of the intermediates and transition states on the catalytic pathway, as well as the kinetics and thermodynamics of their interconversion. Cryoenzymology, the use of subzero temperatures and fluid cryosolvents, has the potential to supply this type of information. In this article recent investigations illustrating the advantages of cryoenzymology are reviewed. The major advantage lies in the ability to accumulate and stabilize productive enzyme-substrate intermediates for sufficient lengths of time to allow the collection of high resolution structural data, e.g. by X-ray diffraction. In addition, intermediates which are not detectable under normal conditions, due to too short lifetimes and/or low concentrations, may be detected at low temperatures, in some cases through changes in the rate-limiting step. The method seems of rather general applicability, judging by the number of different types of enzymes, including oligomeric and membrane-associated ones, which have successfully been studied using cryoenzymology. In some cases, at least, good agreement between observations at subzero temperatures and normal conditions has been found, demonstrating the relevance of the technique. Potential limitations of the techniques, as well as questions regarding the effects on the protein structure, are also discussed.

Animals↗
PubMed1995

Comparison of relative changes in phosphatic metabolites and phospholipids after irradiation.

Measurements of phosphatic metabolites and phospholipids using 31P NMR spectroscopy were performed on tumor extracts at specific times before and after a priming dose of radiation at 32 or 65 Gy. At both doses, statistically significant increases in the high-energy phosphates PCr and ATP, relative to their primary hydrolysis product Pi, were detected at 24 h after irradiation. These spectral changes are consistent with an increased capacity for aerobic metabolism and oxidative phosphorylation. The changes coincide with a significant reduction in the hypoxic cell fraction and 50% tumor control dose measurements reported previously for the same tumor model. A significant increase in the ratio of phosphorylethanolamine to phosphorylcholine was also detected at 24 h. The ratio of ethanolamine-containing to choline-containing phospholipids increased significantly between 48 and 96 h. The spectral changes measured in this study coincide with the changes in the hypoxic state of the tumor after irradiation and are consistent with spectral measurements performed in vivo. The high-resolution spectroscopic data also identify specific metabolites contributing to spectral changes measured in vivo.

Animals↗
PubMed1994

Myocardial perfusion imaging using single-photon emission computed tomography.

Myocardial perfusion single-photon emission computed tomography (SPECT) provides three-dimensional physiological information to assess myocardial blood flow at stress and rest and myocardial viability. The availability of perfusion agents with different uptake mechanisms, thallium 201, technetium 99m-sestamibi, and 99mTc-teboroxime, has created considerable flexibility in how these agents are imaged and interpreted. The higher photon flux and fixed distribution of 99mTc sestamibi allows for multiple-gated acquisition, which yields the potential for the assessment of myocardial thickening. Pharmacological agents, such as dipyridamole, adenosine, and dobutamine, may be used with myocardial perfusion SPECT as an alternate stress procedure in patients who cannot exercise adequately. SPECT reconstruction is limited by the current lack of clinically implemented algorithms to compensate for photon scatter and attenuation or for finite spatial resolution. Data-based quantification procedures that compare a patient's results to a database of normal patients assist the diagnosticians in circumventing these limitations.

Algorithms↗
PubMed1996

Three-dimensional statistical analysis of sulcal variability in the human brain.

Morphometric variance of the human brain is qualitatively observable in surface features of the cortex. Statistical analysis of sulcal geometry will facilitate multisubject atlasing, neurosurgical studies, and multimodality brain mapping applications. This investigation describes the variability in location and geometry of five sulci surveyed in each hemisphere of six postmortem human brains placed within the Talairach stereotaxic grid. The sulci were modeled as complex internal surfaces in the brain. Heterogeneous profiles of three-dimensional (3D) variation were quantified locally within individual sulci. Whole human heads, sectioned at 50 micrometer, were digitally photographed and high-resolution 3D data volumes were reconstructed. The parieto-occipital sulcus, the anterior and posterior rami of the calcarine sulcus, the cingulate and marginal sulci, and the supracallosal sulcus were delineated manually on sagittally resampled sections. Sulcal outlines were reparameterized for surface comparisons. Statistics of 3D variation for arbitrary points on each surface were calculated locally from the standardized individual data. Additional measures of surface area, extent in three dimensions, surface curvature, and fractal dimension were used to characterize variations in sulcal geometry. Paralimbic sulci exhibited a greater degree of anterior-posterior variability than vertical variability. Occipital sulci displayed the reverse trend. Both trends were consistent with developmental growth patterns. Points on the occipital sulci displayed a profile of variability highly correlated with their 3D distance from the posterior commissure. Surface curvature was greater for the arched paralimbic sulci than for those bounding occipital gyri in each hemisphere. On the other hand, fractal dimension measures were remarkably similar for all sulci examined, and no significant hemispheric asymmetries were found for any of the selected spatial and geometric parameters. Implications of cortical morphometric variability for multisubject comparisons and brain mapping applications are discussed.

Aged↗
PubMed1996

Relative contribution of polar interactions and conformational compatibility to the binding of neurokinin-1 receptor antagonists.

Based on single residue substitutions, previous studies suggested that Gln165, His197, and His265 of the neurokinin-1 receptor interact directly with many nonpeptide antagonists, including CP-96,345. To further test this model, all three residues have been substituted simultaneously with alanine. The Q165A-H197A-H265A triple mutant bound CP-96,345 and eight analogs with similar affinity (2-20 microM), even though the same series of compounds bound to the wild-type receptor with affinities over a range of 1000-fold. These observations correspond exactly to the prediction of the binding site model. The micromolar binding affinity of all tested CP-96,345 analogs for the triple mutant seems to reflect solely van der Waals interactions, which suggests a significant contribution of conformational compatibility (or shape complementarity) to binding affinity. The primary role of conformational compatibility in ligand binding was consistent with the observation that simply transferring the residues involved in polar interactions with beta2-agonists into the neurokinin-1 receptor did not lead to increased binding affinity for the beta2-agonists. Taken together, these results support a general principle of ligand-receptor binding in which specific polar interactions can take place only if the overall ligand conformation is compatible with the stereochemistry of the binding pocket. In addition, double-residue and triple-residue substitutions, in combination with single-residue substitutions, can provide an alternative route to reveal multiple interactions that may not be detectable by single-residue substitutions and represent a novel approach to examine ligand-receptor interactions in the absence of high-resolution structural data.

Amino Acid Sequence↗
PubMed2004

Spectra and concentration profiles throughout the reaction of curing epoxy resins from near-infrared spectroscopy and multivariate curve resolution methods.

When applied to near-infrared (NIR) data, multivariate curve resolution methods, in particular alternating least squares (ALS), make it possible to calculate the concentration profiles and the spectra of all species involved in the reaction of curing epoxy resins. In this paper, the model reaction between phenyl glicidyl ether and aniline (2:1) was studied at 95 degrees C. A NIR spectrum was recorded every five minutes throughout the eight-hour reaction process. The data display rank deficiency. This problem was overcome by supplying additional information to the system in the form of known spectra of some reactants. The recovered spectra and concentration profiles satisfactorily reproduced the experimental data. In this way, 99.99% of the variance associated with the experimental matrix was reproduced. A value of 0.87% was obtained for lack of fit while the similarity coefficient r between the spectra recovered and the spectra corresponding to the three pure species involved in the reaction were PGE (r = 0.994), aniline (r = 0.994), and tertiary amine (r = 0.999). The maximum and minimum limits associated with the ALS solutions were calculated, which made it possible to limit to a considerable extent the ambiguity that is characteristic of these curve resolution methods.

Algorithms↗
PubMed1999

Reliable identification of large numbers of candidate SNPs from public EST data.

High-resolution genetic analysis of the human genome promises to provide insight into common disease susceptibility. To perform such analysis will require a collection of high-throughput, high-density analysis reagents. We have developed a polymorphism detection system that uses public-domain sequence data. This detection system is called the single nucleotide polymorphism pipeline (SNPpipeline). The analytic core of the SNPpipeline is composed of three components: PHRED, PHRAP and DEMIGLACE. PHRED and PHRAP are components of a sequence analysis suite developed to perform the semi-automated analysis required for large-scale genomes (provided courtesy of P. Green). Using these informatics tools, which examine redundant raw expressed sequence tag (EST) data, we have identified more than 3,000 candidate single-nucleotide polymorphisms (SNPs). Empiric validation studies of a set of 192 candidates indicate that 82% identify variation in a sample of ten Centre d'Etudes Polymorphism Humain (CEPH) individuals. Our results suggest that existing sequence resources may serve as a valuable source for identifying genetic variation.

Algorithms↗