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At least 1,117 records · Page 62Linked to original sources
PubMed2000

Prostate-specific antigen levels in young white and black men 20 to 45 years old.

OBJECTIVES: To determine the prostate-specific antigen (PSA) levels and PSA change over time in young white and black men 20 to 45 years old. METHODS: The Department of Defense Serum Repository, a serum bank that stores all residual serum from the military human immunodeficiency virus screening program at -25 degrees C, was sampled to obtain a total of 588 black and 588 white subjects 20 to 45 years old. This was a retrospective study with only demographic data available on the studied subjects. The samples used for this study were collected between June 24, 1988 and June 12, 1996. Individuals with a history of prostate disease were excluded by query of a centralized Department of Defense diagnosis database. Three serum specimens evenly distributed over a mean of 6 years were selected for each individual to determine the free and total PSA levels and PSA velocity. The Hybritech Tandem-E PSA assay was used for the total PSA measurement, and the Hybritech Tandem-R assay was used for the free PSA measurement. RESULTS: The baseline serum PSA levels differed by race (P = 0.04). The median (25th, 75th percentile) baseline serum PSA levels for black men 20 to 29, 30 to 39, and 40 to 45 were 0.38 ng/mL (0.26, 0.61), 0.45 ng/mL (0.32, 0. 67), and 0.52 ng/mL (0.37, 0.73), respectively. The median baseline serum PSA levels for the same decade groups in white men were 0.38 ng/mL (0.27, 0.57), 0.45 ng/mL (0.28, 0.68), and 0.40 ng/mL (0.26, 0. 64), respectively. The PSA velocity was higher in white men than in black men (mean 2.8%/yr and 1.6%/yr, respectively, P = 0.032). CONCLUSIONS: These results suggest that although black men 20 to 45 years old have higher baseline serum PSA levels than white men of the same age, the PSA velocity is greater in young white than in young black men. Additional work is needed to determine the clinical significance of these findings.

Adult↗
PubMed1990

Mast cell biology.

Mast cells are the repository for histamine in the body. They influence the pathophysiology of allergic diseases, such as rhinitis, urticaria, and asthma; regulate bone formation and integrity; help repair and maintain connective tissue; promote wound healing; and probably contribute to the development and preservation of the endothelium and small blood vessels. Although they are found in all human tissue, mast cells are most prevalent at the interface between the host and its environment, that is, in the skin and in the mucosa of the upper and lower respiratory tracts and the gastrointestinal tract. Recent evidence suggests that two types of mast cells exist: (1) the connective tissue type, found primarily but not exclusively in loose connective tissue and skin, and (2) the mucosal type, found primarily in gastrointestinal mucosa and peripheral airways. The factors that produce this differentiation are not fully known. Although both mast cell types have IgE receptors that can be activated by allergens, differences between the two types exist in their responses to nonallergic signals, the mediators they release, their proteoglycan constituents, and the makeup of their granular enzymes. The importance of these biochemical differences to cellular functioning remains to be investigated.

Animals↗
PubMed2000

Involvement of follicular stem cells in forming not only the follicle but also the epidermis.

The location of follicular and epidermal stem cells in mammalian skin is a crucial issue in cutaneous biology. We demonstrate that hair follicular stem cells, located in the bulge region, can give rise to several cell types of the hair follicle as well as upper follicular cells. Moreover, we devised a double-label technique to show that upper follicular keratinocytes emigrate into the epidermis in normal newborn mouse skin, and in adult mouse skin in response to a penetrating wound. These findings indicate that the hair follicle represents a major repository of keratinocyte stem cells in mouse skin, and that follicular bulge stem cells are potentially bipotent as they can give rise to not only the hair follicle, but also the epidermis.

Animals↗
PubMed1996

Direct visualization of uridylate deletion in vitro suggests a mechanism for kinetoplastid RNA editing.

Deletion of uridylates from the 3'-most editing site of synthetic ATPase 6 pre-mRNA can be visualized directly by coincubation of a radiolabeled substrate RNA and a synthetic gRNA in 20S fractions of T.brucie mitochondrial lysates. Substrate RNA cleavage is gRNA directed and occurs 3' to the uridylates to be deleted. U residues appear to be sequentially removed from the 3' end of the 5' cleavage product prior to religation of the two pre-mRNA halves. gRNA/mRNA chimeric molecules are also produced. Time course experiments indicate that chimeras appear after cleavage intermediates and edited product. Furthermore, a mutant gRNA promotes formation of edited product but not detectable chimeras. Our results suggest a model for kinetoplastid RNA editing in which chimeric molecules are nonproductive end products of editing and not intermediates that serve as a repository for deleted U's.

Adenosine Triphosphatases↗
PubMed2001

Amino acid residue environments and predictions of residue type.

The determination of a protein's structure from the knowledge of its linear chain is one of the important problems that remains as a bottleneck in interpreting the rapidly increasing repository of genetic sequence data. One approach to this problem that has shown promise and given a measure of success is threading. In this approach contact energies between different amino acids are first determined by statistical methods applied to known structures. These contact energies are then applied to a sequence whose structure is to be determined by threading it through various known structures and determining the total threading energy for each candidate structure. That structure that yields the lowest total energy is then considered the leading candidate among all the structures tested. Additional information is often needed in order to support the results of threading studies, as it is well known in the field that the contact potentials used are not sufficiently sensitive to allow definitive conclusions. Here, we investigate the hypothesis that the environment of an amino acid residue realized as all those residues not local to it on the chain but sufficiently close spatially can supply information predictive of the type of that residue that is not adequately reflected in the individual contact energies. We present evidence that confirms this hypothesis and suggests a high order cooperativity between the residues that surround a given residue and how they interact with it. We suggest a possible application to threading.

Algorithms↗
PubMed2001

Drug design by machine learning: support vector machines for pharmaceutical data analysis.

We show that the support vector machine (SVM) classification algorithm, a recent development from the machine learning community, proves its potential for structure-activity relationship analysis. In a benchmark test, the SVM is compared to several machine learning techniques currently used in the field. The classification task involves predicting the inhibition of dihydrofolate reductase by pyrimidines, using data obtained from the UCI machine learning repository. Three artificial neural networks, a radial basis function network, and a C5.0 decision tree are all outperformed by the SVM. The SVM is significantly better than all of these, bar a manually capacity-controlled neural network, which takes considerably longer to train.

Algorithms↗
PubMed2000

Networking and expert-system analysis: next frontier in biomonitoring.

The extensive use of biomarkers in environment biomonitoring programmes has raised the problem of data management and intercomparison. A research project (Pollution Effect Network, PEN) is proposed here, consisting of the realisation of an on-line warehouse for biomarker data (http://www.muf.unipmn.it/pen). The web site will contain repository sections and expert system procedures able to integrate information from different biomarkers and provide ranking of the organism health status in terms of synthetic stress syndrome indexes. Researchers accessing the site will be able to submit and process their own data. This will allow common criteria in the evaluation of the biological effects of pollutants, and an intercomparison of biomonitoring data among different geographic areas and sentinel species.

Animals↗
PubMed2001

Heavy metal contamination of brown seaweed and sediments from the UK coastline between the Wear river and the Tees river.

The concentration of Fe, Mn, Zn, Cu, Pb, Ni, Cr, Cd, and Ag were determined in the brown alga Fucus vesiculosus and intertidal surface sediments from coastal locations of northeast England. Levels of heavy metals similar to those of polluted areas of the British coastline were detected. There is evidence of contamination (especially with Zn and Pb) in sediments from sites affected by colliery spoil and from the Wear estuary. The pelitic fraction ( < 63 microm) is usually more enriched in heavy metals, but it represents a very small percentage of the bulk samples. The fine-grained sand is a very important repository of contaminants especially where particles of colliery spoil, secondary mineral, and amorphous phases are present. Aqua regia-extracted Zn, Cu, and Pb in sediments are significantly correlated with those in seaweed. Despite the closure of all base metal and coal mines, and the cessation of many industrial activities in the region, sediments and brown algae are contaminated with heavy metals. The control site (Holy Island) and the Tees estuary appear to be the least affected.

Environmental Monitoring↗
PubMed2000

An unusual human IgM antibody with a protruding HCDR3 and high avidity for its peptide ligands.

The crystal structure of the Fv molecule from a human monoclonal IgM cryoglobulin (Mez) was determined at 2.6 A resolution. Amino acid sequences of framework regions (FR) of the Mez light (L) and heavy (H) chain variable domains (VL and VH) are highly similar to their counterparts in another human Fv (Pot) previously subjected to X-ray analysis in our laboratory. As expected, the three-dimensional (3-D) structures of FR are quite similar in the two proteins, as are four of the six complementarity-determining regions (CDRs): CDRs 1 and 2 for both L and H chains. Absence of Pro 95L from the LCDR3 loop in Mez VL (relative to Pot LCDR3) results in compression of this loop and creates more space in the VL-VH interface. In the two IgMs, HCDR3 conformations differ significantly from all previously defined conformations for these loops. Pot has a 12-residue HCDR3 that collapses to fill all available space in the VL-VH domain interface, resulting in the formation of a relatively flat platform for antigen binding. In Mez, the HCDR3 is two residues longer and is comprehensively different. A semi-rigid ascending segment dominated by a Pro-Pro-Tyr sequence protrudes out into solvent. The descending portion has the sequence Gly-Trp-Gly-Gly-Gly, which promotes high local flexibility. This segment folds across the VL-VH domain interface to interact with residues in LCDR3. These features partition the Mez active site into two compartments, a large cavity between VL and VH and a smaller cavity lined entirely by constituents of the three heavy chain CDRs. Such an unusual topographical feature indicates why the Mez IgM does not bind to the Fc portion of intact human IgG antibodies in immunoassays yet interacts with high avidity with many Fc-derived octapeptides. The cavities are expected to be the repositories for the Fc-derived peptides, while the semi-rigid protrusion of the Mez HCDR3 prevents the close approach of another macromolecule (e.g. intact IgG) to the active site.

Amino Acid Sequence↗
PubMed2001

Long-term data storage in DNA.

This article discusses how DNA might be used to store data. It is argued that, at present, DNA would be best employed as a long-term repository (thousands or millions of years). How data-containing DNA might be packaged and how the data might be encrypted, with particular attention to the encryption of written information, is also discussed. Various encryption issues are touched on, such as how data-containing DNA might be differentiated from genetic material, error detection, data compression and reading frame location. Finally, this article broaches the difficulty of constructing very large pieces of DNA in the laboratory and highlights some complications that might arise when attempting to transmit DNA-encrypted data to recipients who are a long period of time in the future.

Base Sequence↗
PubMed2002

The evolution of structural databases.

Starting with the Protein Data Bank (PDB) as a common ancestor, the evolution of structural databases has been driven by the rapprochement of the structural world and the practical applications. The result is an impressive number of secondary structural databases that is welcomed by structural biologists and bioinformaticians but runs the risk of producing an embarrassment of riches among non-specialist users. Given that any profit depends on the number of customers, efficient interfaces between many structural data banks must be available to make their contents easily accessible. Increasing the information content of central structural repositories might be the best way to guide users through the many, sometimes overlapping databases.

Computer Communication Networks↗
PubMed2001

Terpenoid indole alkaloid profile changes in Catharanthus pusillus during development.

The terpenoid indole alkaloid content of Catharanthus pusillus was investigated during development from young to old plants. Different plant organs were assessed showing that the new leaves were the main repository site with vindoline ( approximately 4.8 mg/g DW) and catharanthine ( approximately 2.2 mg/g DW) being the major metabolites with the highest yields at the second and third sampling time (51 and 70 days, respectively). The other samples analysed, from old, oldest and yellow leaves followed in accumulation levels. The roots and stems were the least accumulative organs, although for the case of tubotaiwine the root was the most important organ. It appeared that the alkaloid content changed coinciding with the different developmental stages of the plants, particularly at flowering and fruiting stages. Moreover, this species seems to constitute a precious source of the monomerics, vindoline and catharanthine, intermediates in the synthesis of the two important antitumor dimerics vincristine and vinblastine, which did not accumulate in this species.

Journal Article↗
PubMed2003

A human tissue and data resource: an overview of opportunities, challenges, and development of a provider/researcher partnership model.

As we continue to strive to apply the findings of in vitro and animal studies to human disease and transition from genomics to proteomics, we will experience an ever-increasing need for human tissues. A web based system that provides access to tissues repositories and associated data will best facilitate the access to these vital resources and the application of research information to human disease treatment. There are organizational and design requirements that must be addressed in the implementation of the infrastructures that are needed to implement such a system, with special attention paid to the protection of patient anonymity. This report describes the implementation of a prototype human tissue network in the hope of encouraging implementation of similar systems among other consortia of providers and researchers.

Animals↗
PubMed1997

QAV: querying entity-attribute-value metadata in a biomedical database.

Entity-attribute-value (EAV) data organization is increasingly used for knowledge representation for complex heterogeneous biomedical databases. When delivered in relation form for production applications the simplicity of EAV storage is offset by difficulty of set-based data retrieval. We describe a client-server application, QAV, that is designed to perform set-based query on the Columbia MED dataset, a large medical metadata repository that has been the focus of much research. QAV interacts with the user through a graphical front end and generates a series of SQL statements that are sent to the server for the actual data retrieval.

Algorithms↗
PubMed2001

Solute transport properties of compacted Ca-bentonite used in FEBEX project.

The present Spanish concept of a deep geological high level waste repository includes an engineered clay barrier around the canister. The clay presents a very high sorption capability for radionuclides and a very small hydraulic conductivity, so that the migration process of solutes is limited by sorption and diffusion processes. Therefore, diffusion and distribution coefficients in compacted bentonite (i.e. in "realistic" liquid to solid ratio conditions) are the main parameters that have to be obtained in order to characterise solute transport that could be produced after the canister breakdown. Through-Diffusion (TD) and In-Diffusion (ID) experiments with HTO, Sr, Cs and Se were carried out using compacted FEBEX bentonite, which is the reference material for the Spanish concept of radioactive waste disposal. Experiments were interpreted by means of available analytical solutions that allow the estimation of diffusion coefficients and, in some cases, distribution coefficients. Analytical solutions are simple to use, but rely on hypotheses that do not hold in all the experiments. These experiments were interpreted also using an automatic parameter estimation code that overcomes the limitations of analytical solutions. Numerical interpretation allows the simultaneous estimation of porosity, diffusion and distribution coefficients, accounts for the role of porous sinters and time-varying boundary concentrations, and can use different types of raw concentration data.

Adsorption↗
PubMed2001

Attempt to model laboratory-scale diffusion and retardation data.

Different approaches for measuring the interaction between radionuclides and rock matrix are needed to test the compatibility of experimental retardation parameters and transport models used in assessing the safety of the underground repositories for the spent nuclear fuel. In this work, the retardation of sodium, calcium and strontium was studied on mica gneiss, unaltered, moderately altered and strongly altered tonalite using dynamic fracture column method. In-diffusion of calcium into rock cubes was determined to predict retardation in columns. In-diffusion of calcium into moderately and strongly altered tonalite was interpreted using a numerical code FTRANS. The code was able to interprete in-diffusion of weakly sorbing calcium into the saturated porous matrix. Elution curves of calcium for the moderately and strongly altered tonalite fracture columns were explained adequately using FTRANS code and parameters obtained from in-diffusion calculations. In this paper, mass distribution ratio values of sodium, calcium and strontium for intact rock are compared to values, previously obtained for crushed rock from batch and crushed rock column experiments. Kd values obtained from fracture column experiments were one order of magnitude lower than Kd values from batch experiments.

Calcium↗
PubMed2001

UraniumVI sorption behavior on silicate mineral mixtures.

UraniumVI sorption experiments involving quartz and clinoptilolite, important mineral phases at the proposed US nuclear waste repository at Yucca Mountain, NV, were conducted to evaluate the ability of surface complexation models to predict UVI sorption onto mineral mixtures based on parameters derived from single-mineral experiments. The experiments were conducted at an initial UVI aqueous concentration of approximately 2.0 x 10(-7) mol.l-1 (0.1 mol.l-1 NaNO3 matrix) and over the pH range approximately 2.5 to approximately 9.5. The UVI solutions were reacted with either quartz or clinoptilolite only, or with mixtures of the two minerals. The experiments were carried out under atmospheric pCO2(g) conditions (in loosely capped containers) or under limited pCO2(g) (in capped containers or in a glove box). Data from sorption experiments on quartz at atmospheric pCO2 conditions were used to derive UVI binding constants for a diffuse-layer surface complexation model (DLM). The DLM was then used with surface area as a scaling factor to predict sorption of UVI onto clinoptilolite and clinoptilolite/quartz mixtures under both atmospheric and low pCO2 conditions. The calculations reproduced many aspects of the pH-dependent sorption behavior. If this approach can be demonstrated for natural mineral assemblages, it may be useful as a relatively simple method for improving radionuclide transport models in performance-assessment calculations.

Adsorption↗
PubMed2001

Modeling colloid transport for performance assessment.

The natural system is expected to contribute to isolation at the proposed high-level nuclear waste (HLW) geologic repository at Yucca Mountain, NV (YM). In developing performance assessment (PA) computer models to simulate long-term behavior at YM, colloidal transport of radionuclides has been proposed as a critical factor because of the possible reduced interaction with the geologic media. Site-specific information on the chemistry and natural colloid concentration of saturated zone groundwaters in the vicinity of YM is combined with a surface complexation sorption model to evaluate the impact of natural colloids on calculated retardation factors (RF) for several radioelements of concern in PA. Inclusion of colloids into the conceptual model can reduce the calculated effective retardation significantly. Strongly sorbed radionuclides such as americium and thorium are most affected by pseudocolloid formation and transport, with a potential reduction in RF of several orders of magnitude. Radioelements that are less strongly sorbed under YM conditions, such as uranium and neptunium, are not affected significantly by colloid transport, and transport of plutonium in the valence state is only moderately enhanced. Model results showed no increase in the peak mean annual total effective dose equivalent (TEDE) within a compliance period of 10,000 years, although this is strongly dependent on container life in the base case scenario. At longer times, simulated container failures increase and the TEDE from the colloidal models increased by a factor of 60 from the base case. By using mechanistic models and sensitivity analyses to determine what parameters and transport processes affect the TEDE, colloidal transport in future versions of the TPA code can be represented more accurately.

Adsorption↗