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At least 649 records · Page 36Linked to original sources
PubMed2004

Ground based radon-222 observations and their application to atmospheric studies.

The aim of this paper is to review recent trends in the application of ground based radon observations to atmospheric research. In spite of over four decades of atmospheric radon monitoring, only in the past decade has the potential of this passive tracer been realised through a series of atmospheric model evaluation studies. Firstly, the key operational requirements for baseline radon detectors are briefly discussed, including lower limit of detection and response time. Then, current radon-related benchmarks for the evaluation of regional and global models are reviewed, with particular consideration given to the implications of data availability, resolution, site location and model spatial/temporal resolution. An 8-year subset of radon observations from the Cape Grim Baseline Air Pollution Station is used to suggest new benchmarks that exploit long-term data sets. Lastly an overview is presented of a technique that uses radon to estimate regional fluxes of climatically sensitive gases, with specific examples for CO2, CH4 and N2O.

Air Pollutants, Radioactive↗
PubMed1996

Structural prediction of A- and B-DNA duplexes based on coordinates of the phosphorus atoms.

The sequence-dependent structure of DNA double helices was studied extensively during the past 10 years. How the backbone structure correlates with the base structure in a duplex conformation is still an important yet open question. Using a set of reduced coordinates and a least-squares fitting procedure, we have developed a method to predict structures for B-DNA duplexes based on coordinates of the phosphorus atoms. This method can be used to predict all-atom structures for both bent and straight molecules. We estimated the accuracies of the predictions by studying a set of 10 oligonucleotides with their structures available from the Protein Data Bank. We used this method to construct a modeled structure for the bacteriophage lambda cro operator for which the phosphorus coordinates were known from 3.5-angstrum resolution crystal data (4CRO).

Bacteriophage lambda↗
PubMed2006

An iterative synthetic aperture imaging algorithm with correction of diffraction effects.

In this paper we present an iterative version of the synthetic aperture imaging algorithm extended synthetic aperture technique (ESAFT) proposed recently. The algorithm is based on a linear model that accounts for the distortions effects of an imaging system used for acquisition of ultrasonic data. Improved resolution (both lateral and temporal) in the reconstructed image is obtained as a result of minimizing the reconstruction mean square error. In this work, the minimization is extended to parameters that characterize expected amplitudes of each image element in the area of interest. An iterative optimization scheme is proposed, which in each step performs minimization of the reconstruction error based on the parameter matrix found in the previous step. Comparing to ESAFT, the proposed approach yields a significant improvement in resolution and a high degree of robustness with regard to initial choice of the parameter matrix. Performance of the proposed algorithm is evaluated using both real and simulated ultrasonic data.

Journal Article↗
PubMed1995

Refined structure of cytochrome b562 from Escherichia coli at 1.4 A resolution.

The structure of cytochrome b562 from Escherichia coli has been refined at 1.4 A resolution against X-ray data collected on a Picker four-circle diffractometer. The triclinic unit cell parameters are a = 33.68 A, b = 50.48 A, c = 32.67 A, alpha = 102.51 degrees, beta = 86.56 degrees and gamma = 107.01 degrees and there are two molecules in the asymmetric unit. A total of 138 cycles of restrained crystallographic refinement using the program PROLSQ were augmented at intermediate stages by two cycles of simulated annealing refinement using X-PLOR. The final crystallographic R-factor is 16.4% for data in the resolution range 6.0 A to 1.4 A for a model containing 1650 protein atoms, 86 heme atoms, 165 water molecules and four sulfate anions. The root-mean-square deviations from ideal bond lengths and angles are 0.012 A and 2.0 degrees, respectively. Each molecule consists of a bundle of four alpha-helices arranged in a simple up-down-up-down manner with a non-covalently bound heme group inserted between the first and fourth helices. In addition, there is a very short 3(10) helix in the 15-residue loop connecting the first and second pairs of helices. The two independent molecules show r.m.s. differences of 0.30 A for main-chain atoms and 0.88 A for all atoms. A detailed comparison with the structurally similar cytochrome c' from Rhodospirulum molishianum is presented. In addition, the titration behavior of cytochrome b562 in solution is discussed in terms of its molecular structure.

Biological Evolution↗
PubMed2000

Determination of the sedimentation coefficient distribution by least-squares boundary modeling.

A new method is presented for the calculation of apparent sedimentation coefficient distributions g*(s) for the size-distribution analysis of polymers in sedimentation velocity experiments. Direct linear least-squares boundary modeling by a superposition of sedimentation profiles of ideal nondiffusing particles is employed. It can be combined with algebraic noise decomposition techniques for the application to interference optical ultracentrifuge data at low loading concentrations with significant systematic noise components. Because of the use of direct boundary modeling, residuals are available for assessment of the quality of the fits and the consistency of the g*(s) distribution with the experimental data. The method can be combined with regularization techniques based on F statistics, such as used in the program CONTIN, or alternatively, the increment of s values can be adjusted empirically. The method is simple, has advantageous statistical properties, and reveals precise sedimentation coefficients. The new least-squares ls-g*(s) exhibits a very high robustness and resolution if data acquired over a large time interval are analyzed. This can result in a high resolution for large particles, and for samples with a high degree of heterogeneity. Because the method does not require a high frequency of scans, it can also be easily used in experiments with the absorbance optical scanning system. Published 2000 John Wiley & Sons, Inc.

Immunoglobulin G↗
PubMed1993

Data needed for improving the health of minorities.

Identified needs for minority health data, obstacles in obtaining the data, and potential solutions are reviewed. Vital statistics for whites and blacks have been available by states for many years. Recent revisions provide data on Hispanics, and new resolutions will provide data on Asian and Pacific Islander subgroups. But limitations persist in providing accurate statistics for minority subgroups. A major obstacle is the inadequacy of census denominator estimates, due to differential undercounts, paucity of postcensal estimates for states and localities, and the validity of the race and ethnicity data. Important issues revolve around quality, comparability, and intraperson variability of self-identification in determining race and ethnicity, versus external assessment. National survey data have oversampled for black and Hispanic minorities, but not others. The Disadvantaged Minority Health Improvement Act of 1990 provides some solutions, including an extramural grants program to strengthen minority statistics, which the National Center for Health Statistics has implemented to improve minority health assessment at all levels.

Adolescent↗
PubMed2006

Modeling of ligation-induced helix/loop displacements in myoglobin: toward an understanding of hemoglobin allostery.

Combining quantum and molecular mechanics (QM/MM) methods and protein structure prediction algorithms, helix and loop movements are computed along the pathway of CO dissociation from myoglobin (Mb). The results are compared with high-resolution crystallographic data using sequence-displacement graphs. These graphs provide an unbiased method for evaluating main-chain segmental motions; they resolve an apparent disagreement between two sets of high-resolution crystal structures for MbCO and deoxyMb. The QM/MM modeling of the CO deligation reproduces the experimentally observed spin states and photodissociated crystal structure. The principal effect of CO dissociation is shown to be a concerted rotation of the E and F helices, which hold the heme like a clamshell. The rotation is a response to deligation forces, which impel the F helix away from the heme because of the Fe spin conversion, and which allow the E helix to collapse toward the heme as nonbonded contacts on the distal side are relieved. Additional helix and loop displacements stem from these primary events. In particular, the CD loop is found to be repositioned as a result of steric interactions with the water molecule that becomes H-bonded to the distal histidine in deoxyMb. A similar EF rotation and CD loop displacement are proposed to be the first steps along the allosteric pathway from the R to the T state in hemoglobin.

Allosteric Regulation↗
PubMed2004

A phthalide with in vitro growth inhibitory activity from an oidiodendron strain.

A screening campaign was implemented utilizing capillary electrophoresis as a primary assay to discover binders to the cancer target Akt1 from a crude natural extract library. Fungal extracts with binding activities were characterized for biochemical inhibition of Akt1 to phosphorylate the downstream substrate protein Bad. One of the crude extracts with bioactivity selected for isolation and structure elucidation from fermentation of the fungal culture Oidiodendron sp. F01895 yielded a new trihydroxy phthalide (1). The structure of 1 was determined by a combination of 1D and 2D NMR spectroscopic data along with high-resolution mass spectrometric data. Compound 1 displays inhibition of Akt1 biochemical activity in vitro and confers growth inhibition on some cancer-derived cell lines in culture.

Antineoplastic Agents↗
PubMed2004

Phylo-VISTA: interactive visualization of multiple DNA sequence alignments.

MOTIVATION: The power of multi-sequence comparison for biological discovery is well established. The need for new capabilities to visualize and compare cross-species alignment data is intensified by the growing number of genomic sequence datasets being generated for an ever-increasing number of organisms. To be efficient these visualization algorithms must support the ability to accommodate consistently a wide range of evolutionary distances in a comparison framework based upon phylogenetic relationships. RESULTS: We have developed Phylo-VISTA, an interactive tool for analyzing multiple alignments by visualizing a similarity measure for multiple DNA sequences. The complexity of visual presentation is effectively organized using a framework based upon interspecies phylogenetic relationships. The phylogenetic organization supports rapid, user-guided interspecies comparison. To aid in navigation through large sequence datasets, Phylo-VISTA leverages concepts from VISTA that provide a user with the ability to select and view data at varying resolutions. The combination of multiresolution data visualization and analysis, combined with the phylogenetic framework for interspecies comparison, produces a highly flexible and powerful tool for visual data analysis of multiple sequence alignments. AVAILABILITY: Phylo-VISTA is available at http://www-gsd.lbl.gov/phylovista. It requires an Internet browser with Java Plug-in 1.4.2 and it is integrated into the global alignment program LAGAN at http://lagan.stanford.edu

Algorithms↗
PubMed2006

High-resolution large-scale mosaic imaging using multiphoton microscopy to characterize transgenic mouse models of human neurological disorders.

The thorough characterization of transgenic mouse models of human central nervous system diseases is a necessary step in realizing the full benefit of using animal models to investigate disease processes and potential therapeutics. Because of the labor- and resource-intensive nature of high-resolution imaging, detailed investigation of possible structural or biochemical alterations in brain sections has typically focused on specific regions of interest as determined by the researcher a priori. For example, Parkinson's disease researchers often focus imaging on regions of the brain expected to exhibit pathology such as the substantia nigra and striatum. Because of limitations in acquiring and storing high-resolution imaging data, additional data contained in the specimen is not usually acquired or disseminated/reported to the research community. Here we present a method of imaging large regions of brain at close to the resolution limit of light microscopy using a mosaic imaging technique in conjunction with multiphoton microscopy. These maps are being used to characterize several genetically modified animal models of neurological disease by filling the information "gap" among techniques such as magnetic resonance imaging and electron microscopic analysis.

Animals↗
PubMed1985

A comparative study of two nutrient data bases.

Reported dietary intake records of 18 infants, 22 young children, and 20 women were analyzed using the nutrient data base systems of the Second National Health and Nutrition Examination Survey (NHANES II) and the Nutrient Dietary Data Analysis (NDDA) System. Significant differences between the nutrient data bases were found in the calculations of potassium and niacin for infants and of energy and nine nutrients for women and children. The energy and nutrient composition of many commonly consumed food items in the two nutrient data base systems was different, even though the systems shared common data sources. Differences in the nutrient data bases were primarily due to the timing of data base updates, as well as to the differential use of industry, private, and government food analysis sources, procedural differences in data base updating, and random data entry error. Resolution of differences among nutrient data base systems may depend upon comprehensive reviews of all data base systems or the establishment of a national nutrient data base to serve as a standard for the professional.

Child, Preschool↗
PubMed1991

Analysis of the VNTR locus D1S80 by the PCR followed by high-resolution PAGE.

Allelic data for the D1S80 locus was obtained by using the PCR and subsequent analysis with a high-resolution, horizontal PAGE technique and silver staining. Compared with RFLP analysis of VNTR loci by Southern blotting, the approach described in this paper offers certain advantages: (1) discrete allele resolution, (2) minimal measurement error, (3) correct genotyping of single-band VNTR patterns, (4) a nonisotopic assay, (5) a permanent record of the electrophoretic separation, and (6) reduced assay time. In a sample of 99 unrelated Caucasians, the D1S80 locus demonstrated a heterozygosity of 80.8% with 37 phenotypes and 16 alleles. The distribution of genotypes is in agreement with expected values according to the Hardy-Weinberg equilibrium. Furthermore, the observed number of alleles and the level of heterozygosity, obtained through the protocol described here, were congruent with each other in accordance with the expectation of a mutation-drift equilibrium model for a single, homogeneous, random-mating population. Therefore, the analysis of D1S80 and similar VNTR loci by amplified fragment length polymorphism (AMP-FLP) may prove useful as models for population genetic issues for VNTR loci analyzed by RFLP typing via Southern blotting.

Blotting, Southern↗
PubMed2006

Spectrophotometric determination of acidity constants of alizarine red S in water, water-Brij-35 and water-SDS micellar media solutions.

The acidity constants of Alizarine Red S in water, water-Brij-35 and water-SDS micellar media solutions at 25 degrees C and an ionic strength of 0.1 M have been determined spectrophotometrically. To evaluate the pH-absorbance data, a resolution method based on the combination of soft- and hard-modeling is applied. The acidity constants of all related equilibria are estimated using the whole spectral fitting of the collected data to an established factor analysis model. DATAN program applied for determination of acidity constants. Results show that the pKa values of Alizarine Red S are influenced as the percentages of a neutral and an anionic surfactant such as Brij-35 and SDS, respectively, added to the solution of this reagent. Effect of surfactant on acidity constants and pure spectrum of each component are also discussed.

Anthraquinones↗
PubMed2004

Object dependency of resolution in reconstruction algorithms with interiteration filtering applied to PET data.

In this paper, we study the resolution properties of those algorithms where a filtering step is applied after every iteration. As concrete examples we take filtered preconditioned gradient descent algorithms for the Poisson log likelihood for PET emission data. For nonlinear estimators, resolution can be characterized in terms of the linearized local impulse response (LLIR). We provide analytic approximations for the LLIR for the class of algorithms mentioned above. Our expressions clearly show that when interiteration filtering (with linear filters) is used, the resolution properties are, in most cases, spatially varying, object dependent and asymmetric. These nonuniformities are solely due to the interaction between the filtering step and the Poisson noise model. This situation is similar to penalized likelihood reconstructions as studied previously in the literature. In contrast, nonregularized and postfiltered maximum-likelihood expectation maximization (MLEM) produce images with nearly "perfect" uniform resolution when convergence is reached. We use the analytic expressions for the LLIR to propose three different approaches to obtain nearly object independent and uniform resolution. Two of them are based on calculating filter coefficients on a pixel basis, whereas the third one chooses an appropriate preconditioner. These three approaches are tested on simulated data for the filtered MLEM algorithm or the filtered separable paraboloidal surrogates algorithm. The evaluation confirms that images obtained using our proposed regularization methods have nearly object independent and uniform resolution.

Algorithms↗
PubMed2002

Pattern-recognition methods to identify secondary structure within X-ray crystallographic electron-density maps.

The interpretation of macromolecular crystallographic electron-density maps is a difficult and traditionally a manual step in the determination of a protein structure. The visualization of information within an electron-density map can be extremely arduous owing to the amount and complexity of information present. The ability to see the overall fold and structure of the molecule is usually lost among all the detail, particularly with larger structures. This paper describes a novel method of analysis of electron density in real space that can determine the secondary structure of a protein within minutes without any user intervention. The method is able to work with poor data as well as good data at resolutions down to 3.5A and is integral to the functionality of QUANTA. This article describes the methodology of the pattern recognition and its use with a number of sets of experimental data.

Algorithms↗
PubMed2005

[Virtual otoscopy of middle ear structure and pathology].

OBJECTIVE: To assess the value of high-resolution CT data of the temporal bone for the virtual endoscopic (VE) visualization of the ossicular chain and the temporal bone. METHODS: Fifty patients with suspected lesions of middle ear underwent a high-resolution CT of the temporal bone with VE, seventeen patients were subsequently operated. CT examinations of the temporal bone were carried out using spiral equipment and endoscopic 3D processing was carried out on a separate workstation equipped with a flying through program. RESULTS: VE is valuable for the evaluation of ossicular dislocation, disruption and ossicular lysis, morphological anomalies of the malleus, incus, and stapes, as well as for evaluation of normal middle ear structures with high detail. The VE assessment in detecting ossicular disruption of chronic otitis media match the operation exploration perfectly (10 in 11 ears), whereas only 3 in 6 ears of cholesteatoma match the operation exploration. CONCLUSIONS: This image processing method can be used pre-operatively for the individual planning, simulation, and post-operatively for assessment of the position of implants.

Adolescent↗
PubMed2002

Atomic resolution (0.98 A) structure of eosinophil-derived neurotoxin.

Human eosinophil-derived neurotoxin (EDN) is a small, basic protein that belongs to the ribonuclease A superfamily. EDN displays antiviral activity and causes the neurotoxic Gordon phenomenon when injected into rabbits. Although EDN and ribonuclease A have appreciable structural similarity and a conserved catalytic triad, their peripheral substrate-binding sites are not conserved. The crystal structure of recombinant EDN (rEDN) has been determined at 0.98 A resolution from data collected at a low temperature (100 K). We have refined the crystallographic model of the structure using anisotropic displacement parameters to a conventional R-factor of 0.116. This represents the highest resolution structure of rEDN determined to date and is only the second ribonuclease structure to be determined at a resolution greater than 1.0 A. The structure provides a detailed picture of the conformational freedom at the various subsites of rEDN, and the water structure accounts for more than 50% of the total solvent content of the unit cell. This information will be crucial for the design of tight-binding inhibitors to restrain the ribonucleolytic activity of rEDN.

Binding Sites↗
PubMed1985

Temporal resolution in background noise.

Temporal resolution is measured with a normal-hearing subject and with a hard-of-hearing subject having reduced temporal resolution. The data produced in a masking-period pattern and those produced in a simplified method are compared for conditions with and without background noise. It seems that for normal-hearing subjects, temporal resolution is somewhat improved in a noisy background condition. However, it remains strongly reduced for the hearing impaired.

Adult↗