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PubMed1988

Prediction of the first variceal hemorrhage in patients with cirrhosis of the liver and esophageal varices. A prospective multicenter study.

We conducted a prospective study of 321 patients with cirrhosis of the liver and esophageal varices with no history of bleeding to see whether a comprehensive analysis of their clinical features and of the endoscopic appearances of their varices could help to identify those at highest risk for bleeding. Varices were classified endoscopically as suggested by the Japanese Research Society for Portal Hypertension. Patients were followed for 1 to 38 months (median, 23), during which 85 patients (26.5 percent) bled. Multiple regression analysis (Cox's model) revealed that the risk of bleeding was significantly related to the patient's modified Child class (an index of liver dysfunction based on serum albumin concentration, bilirubin level, prothrombin time, and the presence of ascites and encephalopathy), the size of the varices, and the presence of red wale markings (longitudinal dilated venules resembling whip marks) on the varices. A prognostic index based on these variables was devised that enabled us to identify a subset of patients with a one-year incidence of bleeding exceeding 65 percent. The index was prospectively validated on an independent sample of 75 patients with varices and no history of bleeding. We conclude that our prognostic index, which identifies groups of patients with one-year probabilities of bleeding ranging from 6 to 76 percent, can be used to identify candidates for prophylactic treatment.

Esophageal and Gastric Varices↗
PubMed2000

Soliton dynamics of symmetry-endowed two-soliton solutions of the nonlinear Schrodinger equation.

A comprehensive analysis is presented of the propagation of symmetry-endowed two-soliton solutions under the influence of various perturbations important in nonlinear optics. Thus, we begin by introducing the analytical expressions of these two-soliton solutions. Then, by considering perturbations which preserve the initial symmetry of the two-soliton solutions, the dependence of the soliton parameters on the propagation distance is determined by using an adiabatic perturbation method. As perturbations of this kind, important for soliton-based communication systems, we consider the bandwidth-limited amplification, nonlinear amplification, and amplitude and phase modulation. Moreover, the results obtained by the adiabatic perturbation method are compared with those obtained by direct numerical simulations of the corresponding governing differential equations. (c) 2000 American Institute of Physics.

Journal Article↗
PubMed2006

Elucidating the hard/soft acid/base principle: a perspective based on half-reactions.

A comprehensive analysis is presented for the acid-base double-exchange reaction as well as the associated acid-displacement and base-displacement "half-reactions" with the goal of elucidating the meaning of the hard/soft acid/base (HSAB) principle and the conditions for its validity. When electron-transfer effects are important and other effects are negligible, the HSAB principle is driven by the surpassing stability of the soft acid/soft base product. When electrostatic effects dominate the reactivity, the HSAB principle is driven by the surpassing stability of the hard acid/hard base product. Because electron-transfer effects favor soft/soft interactions, while electrostatic effects favor hard/hard interactions, acid-base exchange reactions may be used to determine whether a reagent's reactivity is dominated by electron-transfer or by electrostatic effects. Because electron-transfer and electrostatic considerations separately favor the HSAB principle whenever the electronic chemical potentials of the acids and bases involved in the reaction are similar, our analysis provides strong support for the HSAB principle. The electronic chemical potential measures the intrinsic strength of acids and bases.

Journal Article↗
PubMed2003

16. Immunologic lung disease.

This review summarizes the recent advances regarding pathogenesis, diagnosis, and treatment of immunological diseases of the lung. Rather than attempt a comprehensive analysis, we have focused on selected diseases that are of particular relevance to the practicing physician, and the material has been organized according to the dominant immunologic mechanisms underlying the disease. Because of the redundancy that characterizes the mammalian immune repertoire, this system of classification inevitably produces overlap but facilitates acquisition of what is otherwise a disparate collection of facts. The principal lung immunologic mechanisms are most broadly classified as innate or adaptive immune processes. Innate immunity includes neutrophils and complement that are important in diseases, such as pneumonia and the acute respiratory distress syndrome. Adaptive immunity involves T and B cells capable of recognizing discrete antigens. T(H)1- and T(H)2-dependent adaptive immune responses underlie some of the most common and important of lung diseases, including tuberculosis and asthma, respectively. Other important immunopathologic processes include granulomatous inflammation that characterizes sarcoidosis and Churg-Strauss vasculitis, and autoimmunity, which is characteristic of antiglomerular basement membrane disease and others.

Humans↗
PubMed2001

Predictors of left ventricular function after acute myocardial infarction: effects of time to treatment, patency, and body mass index: the GUSTO-I angiographic experience.

BACKGROUND: Despite the significant survival benefit associated with successful reperfusion therapy for acute myocardial infarction, global indices of outcome left ventricular function, such as ejection fraction, have often demonstrated little or no improvement. Although these measurements are confounded by numerous clinical, physiologic, and angiographic variables, no comprehensive analysis of this issue in a large series of patients is available. We used the Global Utilization of Streptokinase and Tissue Plasminogen Activator for Occluded Coronary Arteries (GUSTO-I) database to better understand this phenomenon by determining independent predictors of left ventricular function and their interplay with regard to outcome ventricular function and improvement in function during the initial postinfarction week. METHODS: Ninety-minute and 5- to 7-day posttreatment global and regional indices derived from left ventriculograms were analyzed from a population of 676 patients. These observations were combined with clinical data to describe independent determinants of ventricular function outcome. RESULTS: Clinical factors predictive of global and regional ventricular function as well as improvement in function between 90 minutes and 5 to 7 days included time to treatment, early infarct-related artery flow grade, and body mass index. These same factors contribute significantly to compensatory hyperkinesis of the noninfarct zone, which is critical to maintenance of global ventricular function during this time period. CONCLUSIONS: The ventricular function benefits of early complete reperfusion after myocardial infarction are readily demonstrable after adjustment for multiple covariables and include (1) maintenance of global ventricular function and (2) prevention or delay in ventricular dilatation.

Aged↗
PubMed2002

Effect of adenoviral titer and instillation pressure on gene transfer efficiency to arterial and venous grafts ex-vivo.

OBJECTIVE: Adenoviral-mediated gene transfer to arterial and venous grafts has potential in the treatment of a number of vascular diseases. Despite widespread use of these vectors to mediate gene transfer to blood vessel walls, the optimal transduction conditions for each type of vessel has yet to be determined. Our objective was to study the effect of adenoviral titer and instillation pressure on efficiency of gene transfer to arterial and venous grafts ex-vivo. METHODS: Jugular vein and carotid artery segments of 8 cm were harvested from Yorkshire Cross pigs. Tissue culture media or different titers of an adenoviral vector encoding human placental alkaline phosphatase (hpAP) were instilled into venous and arterial grafts at 0 mm Hg or 80 to 100 mm Hg of pressure and bathed externally in the same solution at 37 degrees C for 30 minutes. The grafts were rinsed, opened longitudinally, and incubated in culture media at 37 degrees C for 48 hours. Grafts were fixed and stained for hpAP transgene expression to quantitate percent luminal transduction or homogenized for alkaline phosphatase (AP) activity to determine total transmural transduction. RESULTS: For venous grafts, the percent luminal area stained for hpAP was greatest with 10(8) plaque-forming units/mL at 0 mm Hg (81% +/- 7%) and decreased with increasing titers (53% +/- 9% at 10(9) pfu/mL and 44% +/- 11% at 5 x 10(9) pfu/mL; n = 7; P <.05). No increase in percent luminal area stain was achieved with an instillation pressure of 80 to 100 mm Hg at any viral titer. The inverse finding was observed in arterial grafts. For arterial grafts, the greatest percent luminal area stained was achieved with 5 x 10(9) pfu/mL at 80 to 100 mm Hg (76% +/- 7%). An instillation pressure of 80 to 100 mm Hg increased the percent luminal area stained at 10(8) pfu/mL from 31% +/- 9% to 66% +/- 8% (n = 8; P =.01). For venous grafts, total AP activity peaked with 10(9) pfu/mL at 0 mm Hg and decreased with an instillation pressure of 80 to 100 mm Hg (30.6 +/- 9.7 U/mg versus 10.9 +/- 2.5 U/mg; n = 7; P <.01). However, for arterial grafts, total AP activity peaked with 5 x 10(9) pfu/mL (0 mm Hg) and increased with an instillation pressure of 80 to 100 mm Hg (32.8 +/- 9.9 U/mg versus 63.4 +/- 20.5 U/mg; n = 8; P <.05). CONCLUSION: High transduction efficiency can be achieved with adenoviral-mediated gene transfer of arterial and venous grafts. Gene transfer with the vascular graft's physiologic pressure conditions improved transduction efficiency for the artery (80 to 100 mm Hg) and vein (0 mm Hg). Comprehensive analysis of adenoviral transduction conditions is important to realize the full promise of adenoviral-mediated gene transfer.

Adenoviridae↗
PubMed2006

Simplifying data collection for process evaluation of community coalition activities--an electronic web-based application.

ISSUE ADDRESSED: It is important to document and measure coalition-based program activities in order to analyse and evaluate the process of program implementation. This paper describes the development and implementation of an electronic, web-based application to simplify data collection for this research process. METHODS: Childhood injury prevention project officers collaborated with injury prevention researchers to adapt a process log monitoring system initially developed by the Centers for Disease Control and Prevention to track coalition activities for evaluating community efforts to prevent cardiovascular disease. The adapted process log was converted into an electronic, web-based application that project officers completed daily. RESULTS: The web-based electronic log proved to be a practical tool that not only simplified the documentation and reporting processes for health professionals involved in the program, but also provided a rich source of data for subsequent comprehensive analysis of project implementation. CONCLUSION: Development, implementation and evaluation of this web-based process log, to the best of our knowledge, is the only program of its kind in use and provides a simple data collection solution for practitioners, policy makers and researchers involved in injury prevention programs and other community-based programs throughout the world.

Community Networks↗
PubMed2004

Isotopolog perturbation techniques for metabolic networks: metabolic recycling of nutritional glucose in Drosophila melanogaster.

Drosophila melanogaster strain Oregon-R(*) was grown on standard medium supplemented with [U-(13)C(6)]glucose. One to two days after hatching, flies were extracted with water. Glucose was isolated chromatographically from the extract and was analyzed by (13)C NMR spectroscopy. All (13)C signals of the isolated glucose were multiplets arising by (13)C(13)C coupling. Based on a comprehensive analysis of the coupling constants and heavy isotope shifts in glucose, the integrals of individual (13)C signal patterns afforded the concentrations of certain groups of (13)C isotopologs. These data were deconvoluted by a genetic algorithm affording the abundances of all single-labeled and of 15 multiply labeled isotopologs. Among the latter group, seven isotopologs were found at concentrations >0.1 mol % with [1,2-(13)C(2)]glucose as the most prominent species. The multiply (13)C-labeled glucose isotopologs are caused by metabolic remodeling of the proffered glucose via a complex network of catabolic and anabolic processes involving glycolysis and/or passage through the pentose phosphate, the Cori cycle and/or the citrate cycle. The perturbation method described can be adapted to a wide variety of experimental systems and isotope-labeled precursors.

Animals↗
PubMed2004

Large-scale cDNA transfection screening for genes related to cancer development and progression.

A large-scale assay was performed by transfecting 29,910 individual cDNA clones derived from human placenta, fetus, and normal liver tissues into human hepatoma cells and 22,926 cDNA clones into mouse NIH 3T3 cells. Based on the results of colony formation in hepatoma cells and foci formation in NIH 3T3 cells, 3,806 cDNA species (8,237 clones) were found to possess the ability of either stimulating or inhibiting cell growth. Among them, 2,836 (6,958 clones) were known genes, 372 (384 clones) were previously unrecognized genes, and 598 (895 clones) were unigenes of uncharacterized structure and function. A comprehensive analysis of the genes and the potential mechanisms for their involvement in the regulation of cell growth is provided. The genes were classified into four categories: I, genes related to the basic cellular mechanism for growth and survival; II, genes related to the cellular microenvironment; III, genes related to host-cell systemic regulation; and IV, genes of miscellaneous function. The extensive growth-regulatory activity of genes with such highly diversified functions suggests that cancer may be related to multiple levels of cellular and systemic controls. The present assay provides a direct genomewide functional screening method. It offers a better understanding of the basic machinery of oncogenesis, including previously undescribed systemic regulatory mechanisms, and also provides a tool for gene discovery with potential clinical applications.

Animals↗
PubMed2005

Impact of distal mutations on the network of coupled motions correlated to hydride transfer in dihydrofolate reductase.

A comprehensive analysis of the network of coupled motions correlated to hydride transfer in dihydrofolate reductase is presented. Hybrid quantum/classical molecular dynamics simulations are combined with a rank correlation analysis method to extract thermally averaged properties that vary along the collective reaction coordinate according to a prescribed target model. Coupled motions correlated to hydride transfer are identified throughout the enzyme. Calculations for wild-type dihydrofolate reductase and a triple mutant, along with the associated single and double mutants, indicate that each enzyme system samples a unique distribution of coupled motions correlated to hydride transfer. These coupled motions provide an explanation for the experimentally measured nonadditivity effects in the hydride transfer rates for these mutants. This analysis illustrates that mutations distal to the active site can introduce nonlocal structural perturbations and significantly impact the catalytic rate by altering the conformational motions of the entire enzyme and the probability of sampling conformations conducive to the catalyzed reaction.

Binding Sites↗
PubMed2005

High-dimensional and large-scale phenotyping of yeast mutants.

One of the most powerful techniques for attributing functions to genes in uni- and multicellular organisms is comprehensive analysis of mutant traits. In this study, systematic and quantitative analyses of mutant traits are achieved in the budding yeast Saccharomyces cerevisiae by investigating morphological phenotypes. Analysis of fluorescent microscopic images of triple-stained cells makes it possible to treat morphological variations as quantitative traits. Deletion of nearly half of the yeast genes not essential for growth affects these morphological traits. Similar morphological phenotypes are caused by deletions of functionally related genes, enabling a functional assignment of a locus to a specific cellular pathway. The high-dimensional phenotypic analysis of defined yeast mutant strains provides another step toward attributing gene function to all of the genes in the yeast genome.

Actins↗
PubMed2006

Symmetry-, time-, and temperature-dependent strength of carbon nanotubes.

Although the strength of carbon nanotubes has been of great interest, their ideal value has remained elusive both experimentally and theoretically. Here, we present a comprehensive analysis of underlying atomic mechanisms and evaluate the yield strain for arbitrary nanotubes at realistic conditions. For this purpose, we combine detailed quantum mechanical computations of failure nucleation and transition-state barriers with the probabilistic approach of the rate theory. The numerical results are then summarized in a concise set of equations for the breaking strain. We reveal a competition between two alternative routes of brittle bond breaking and plastic relaxation, determine the domains of their dominance, and map the nanotube strength as a function of chiral symmetry, tensile test time, and temperature.

Journal Article↗
PubMed2006

Post-Miocene expansion, colonization, and host switching drove speciation among extant nematodes of the archaic genus Trichinella.

Parasitic nematodes of the genus Trichinella cause significant food-borne illness and occupy a unique evolutionary position at the base of the phylum Nematoda, unlike the free-living nematode Caenorhabditis elegans. Although the forthcoming genome sequence of Trichinella spiralis can provide invaluable comparative information about nematode biology, a basic framework for understanding the history of the genus Trichinella is needed to maximize its utility. We therefore developed the first robust and comprehensive analysis of the phylogeny and biogeographic history of Trichinella using the variation in three genes (nuclear small-subunit rDNA, and second internal transcribed spacer, mitochondrial large-subunit rDNA, and cytochrome oxidase I DNA) from all 11 recognized taxa. We conclude that (i) although Trichinellidae may have diverged from their closest extant relatives during the Paleozoic, all contemporary species of Trichinella diversified within the last 20 million years through geographic colonization and pervasive host switching among foraging guilds of obligate carnivores; (ii) mammalian carnivores disseminated encapsulated forms from Eurasia to Africa during the late Miocene and Pliocene, and to the Nearctic across the Bering Land Bridge during the Pliocene and Pleistocene, when crown species ultimately diversified; (iii) the greatest risk to human health is posed by those species retaining an ancestral capacity to parasitize a wide range of hosts; and (iv) early hominids may have first acquired Trichinella on the African savannah several million years before swine domestication as their diets shifted from herbivory to facultative carnivory.

Animals↗
PubMed2006

Epizootics of wild fish induced by farm fish.

The continuing decline of ocean fisheries and rise of global fish consumption has driven aquaculture growth by 10% annually over the last decade. The association of fish farms with disease emergence in sympatric wild fish stocks remains one of the most controversial and unresolved threats aquaculture poses to coastal ecosystems and fisheries. We report a comprehensive analysis of the spread and impact of farm-origin parasites on the survival of wild fish populations. We mathematically coupled extensive data sets of native parasitic sea lice (Lepeophtheirus salmonis) transmission and pathogenicity on migratory wild juvenile pink (Oncorhynchus gorbuscha) and chum (Oncorhynchus keta) salmon. Farm-origin lice induced 9-95% mortality in several sympatric wild juvenile pink and chum salmon populations. The epizootics arise through a mechanism that is new to our understanding of emerging infectious diseases: fish farms undermine a functional role of host migration in protecting juvenile hosts from parasites associated with adult hosts. Although the migratory life cycles of Pacific salmon naturally separate adults from juveniles, fish farms provide L. salmonis novel access to juvenile hosts, in this case raising infection rates for at least the first approximately 2.5 months of the salmon's marine life (approximately 80 km of the migration route). Spatial segregation between juveniles and adults is common among temperate marine fishes, and as aquaculture continues its rapid growth, this disease mechanism may challenge the sustainability of coastal ecosystems and economies.

Animals↗
PubMed2000

Postsymbiotic plasmid acquisition and evolution of the repA1-replicon in Buchnera aphidicola.

Buchnera aphidicola is an obligate, strictly vertically transmitted, bacterial symbiont of aphids. It supplies its host with essential amino acids, nutrients required by aphids but deficient in their diet of plant phloem sap. Several lineages of Buchnera show adaptation to their nutritional role in the form of plasmid-mediated amplification of key-genes involved in the biosynthesis of tryptophan (trpEG) and leucine (leuABCD). Phylogenetic analyses of these plasmid-encoded functions have thus far suggested the absence of horizontal plasmid exchange among lineages of Buchnera. Here, we describe three new Buchnera plasmids, obtained from species of the aphid host families Lachnidae and Pemphigidae. All three plasmids belong to the repA1 family of Buchnera plasmids, which is characterized by the presence of a repA1-replicon responsible for replication initiation. A comprehensive analysis of this family of plasmids unexpectedly revealed significantly incongruent phylogenies for different plasmid and chromosomally encoded loci. We infer from these incongruencies a case of horizontal plasmid transfer in Buchnera. This process may have been mediated by secondary endosymbionts, which occasionally undergo horizontal transmission in aphids.

Bacterial Proteins↗
PubMed2000

Quantitative transcript imaging in normal and heat-shocked Drosophila embryos by using high-density oligonucleotide arrays.

Embryonic development in Drosophila is characterized by an early phase during which a cellular blastoderm is formed and gastrulation takes place, and by a later postgastrulation phase in which key morphogenetic processes such as segmentation and organogenesis occur. We have focused on this later phase in embryogenesis with the goal of obtaining a comprehensive analysis of the zygotic gene expression that occurs during development under normal and altered environmental conditions. For this, a functional genomic approach to embryogenesis has been developed that uses high-density oligonucleotide arrays for large-scale detection and quantification of gene expression. These oligonucleotide arrays were used for quantitative transcript imaging of embryonically expressed genes under standard conditions and in response to heat shock. In embryos raised under standard conditions, transcripts were detected for 37% of the 1,519 identified genes represented on the arrays, and highly reproducible quantification of gene expression was achieved in all cases. Analysis of differential gene expression after heat shock revealed substantial expression level changes for known heat-shock genes and identified numerous heat shock-inducible genes. These results demonstrate that high-density oligonucleotide arrays are sensitive, efficient, and quantitative instruments for the analysis of large scale gene expression in Drosophila embryos.

Animals↗
PubMed1981

C NMR chemical shift correlations in application of "tool of increasing electron demand" to stable long-lived carbocations: Comprehensive evaluation.

The reliability of (13)C NMR chemical shift correlations in the application of the "tool of increasing electron demand" to stable long-lived carbocationic systems is demonstrated by a comprehensive analysis of 22 stable aryl-substituted carbocationic systems. The observation of slopes of less than unity in such chemical shift correlations for several cationic systems has been attributed to additional charge delocalizing mechanisms present in the system (such as homoallylic, cyclopropyl, and pi conjugations). The onset of nonclassical sigma-delocalization in 2-aryl-2-norbornyl cations with electron withdrawing-substituents previously observed was further verified by using sigma(C+) substituent constants. Difficulties in relating the C(alpha)NMR shifts in different carbocationic systems are also discussed.

Journal Article↗
PubMed1991

Molecular characterization of severe hemophilia A suggests that about half the mutations are not within the coding regions and splice junctions of the factor VIII gene.

Hemophilia A is an X chromosome-linked disorder resulting from deficiency of factor VIII, an important protein in blood coagulation. A large number of disease-producing mutations have been reported in the factor VIII gene. However, a comprehensive analysis of the mutations has been difficult because of the large gene size, its many scattered exons, and the high frequency of de novo mutations. Recently, we have shown that nearly all mutations resulting in mild-to-moderate hemophilia A can be detected by PCR and denaturing gradient gel electrophoresis (DGGE). In this study, we attempted to discover the mutations causing severe hemophilia A by analyzing 47 unselected patients, 30 of whom had severe hemophilia and 17 of whom had mild-to-moderate disease. Using DGGE as a screening method, we analyzed 99% of the coding region, 94% of the splice junctions, the promoter region, and the polyadenylylation site of the gene. We found the mutation in 16 of 17 (94%) patients with mild-to-moderate disease but in only 16 of 30 (53%) patients with severe hemophilia A. Since DGGE after computer analysis appears to detect all mutations in a given fragment, the lower-than-expected yield of mutations in patients with severe disease is likely not due to failure of the detection method; it is probably due to the presence of mutations in DNA sequences outside the regions studied. Such sequences may include locus-controlling regions, other sequences within introns or outside the gene that are important for its expression, or another gene involved in factor VIII expression that is very closely linked to the factor VIII gene.

Amino Acid Sequence↗