PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “Integrative interaction”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 469 records · Page 26Linked to original sources
PubMed1994

MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers.

A computer program package called MEGA has been developed for estimating evolutionary distances, reconstructing phylogenetic trees and computing basic statistical quantities from molecular data. It is written in C++ and is intended to be used on IBM and IBM-compatible personal computers. In this program, various methods for estimating evolutionary distances from nucleotide and amino acid sequence data, three different methods of phylogenetic inference (UPGMA, neighbor-joining and maximum parsimony) and two statistical tests of topological differences are included. For the maximum parsimony method, new algorithms of branch-and-bound and heuristic searches are implemented. In addition, MEGA computes statistical quantities such as nucleotide and amino acid frequencies, transition/transversion biases, codon frequencies (codon usage tables), and the number of variable sites in specified segments in nucleotide and amino acid sequences. Advanced on-screen sequence data and phylogenetic-tree editors facilitate publication-quality outputs with a wide range of printers. Integrated and interactive designs, on-line context-sensitive helps, and a text-file editor make MEGA easy to use.

Algorithms↗
PubMed2000

PNAD-CSS: a workbench for constructing a protein name abbreviation dictionary.

MOTIVATION: Since their initial development, integration and construction of databases for molecular-level data have progressed. Though biological molecules are related to each other and form a complex system, the information is stored in the vast archives of the literature or in diverse databases. There is no unified naming convention for biological object, and biological terms may be ambiguous or polysemic. This makes the integration and interaction of databases difficult. In order to eliminate these problems, machine-readable natural language resources appear to be quite promising. We have developed a workbench for protein name abbreviation dictionary (PNAD) building. RESULTS: We have developed PNAD Construction Support System (PNAD-CSS), which offers various convenient facilities to decrease the construction costs of a protein name abbreviation dictionary of which entries are collected from abstracts in biomedical papers. The system allows the users to concentrate on higher level interpretation by removing some troublesome tasks, e.g. management of abstracts, extracting protein names and their abbreviations, and so on. To extract a pair of protein names and abbreviations, we have developed a hybrid system composed of the PROPER System and the PNAD System. The PNAD System can extract the pairs from parenthetical-paraphrases involved in protein names, the PROPER System identified these paris, with 98.95% precision, 95.56% recall and 97.58% complete precision. AVAILABILITY: PROPER System is freely available from http://www.hgc.inc.u-tokyo.ac.jp/service/tooldoc /KeX/intro.html. The other software are also available on request. Contact the authors. CONTACT: mikio@ims.u-tokyo.ac.jp

Databases, Factual↗
PubMed1996

Effect of aging on the click-rate induced facilitation of acoustic reflex thresholds.

Acoustic reflex thresholds are known to improve with an increase in the click-repetition rates from 50/sec to 300/sec. In the current study this improvement was used to evaluate auditory processing in older subjects. Acoustic reflex thresholds were obtained from 16 human adult ears within each of the following four groups: young male, young female (18-28 years), older male and older female (50-65 years). The probe tone frequency was 226 Hz and the intensity of the probe tone was 85 dB SPL (sound pressure level). Clicks were delivered ipsilaterally to each ear at repetition rates of 50, 100, 150, 200, and 300/sec. The mixed MANOVA revealed a significant effect for the repetition rate and a significant age and rate interaction. Rate integration in dB was computed by subtracting the highest acoustic reflex threshold from the lowest threshold of each ear. Statistical analyses revealed reduced rate integration in the older subjects, suggesting less efficient processing of faster stimuli within the acoustic reflex pathway.

Adolescent↗
PubMed2000

The motor and tail regions of myosin XV are critical for normal structure and function of auditory and vestibular hair cells.

Recessive mutations in myosin 15, a class XV unconventional myosin, cause profound congenital deafness in humans and both deafness and vestibular dysfunction in mice homozygous for the shaker 2 and shaker 2(J) alleles. The shaker 2 allele is a previously described missense mutation of a highly conserved residue in the motor domain of myosin XV. The shaker 2(J) lesion, in contrast, is a 14.7 kb deletion that removes the last six exons from the 3"-terminus of the Myo15 transcript. These exons encode a FERM (F, ezrin, radixin and moesin) domain that may interact with integral membrane proteins. Despite the deletion of six exons, Myo15 mRNA transcripts and protein are present in the post-natal day 1 shaker 2(J) inner ear, which suggests that the FERM domain is critical for the development of normal hearing and balance. Myo15 transcripts are first detectable at embryonic day 13.5 in wild-type mice. Myo15 transcripts in the mouse inner ear are restricted to the sensory epithelium of the developing cristae ampularis, macula utriculi and macula sacculi of the vestibular system as well as to the developing organ of Corti. Both the shaker 2 and shaker 2(J) alleles result in abnormally short hair cell stereocilia in the cochlear and vestibular systems. This suggests that Myo15 may be important for both the structure and function of these sensory epithelia.

Alleles↗
PubMed2003

InterDom: a database of putative interacting protein domains for validating predicted protein interactions and complexes.

Advances in proteomics technology have enabled new proteins to be discovered at an unprecedented speed, and high throughput experimental methods have been developed to detect protein interactions and complexes en masse. Such bottom-up, data-driven approach has resulted in data that may be uninformative or potentially errorful, requiring further validation and annotation. The InterDom database focuses on providing supporting evidence for the detected protein interactions based on putative protein domain interactions. Using an integrative approach, InterDom derives potential domain interactions by combining data from multiple sources, ranging from domain fusions, protein interactions and complexes, to scientific literature. The InterDom database is available at http://InterDom.lit.org.sg.

Databases, Protein↗
PubMed1993

Left ventricular diastolic function in the normal and diseased heart. Perspectives for the anesthesiologist (1).

Attempts to quantitatively describe ventricular function during diastole have been stimulated by the recognition that diastolic mechanics significantly influence overall cardiac performance, and that diastolic dysfunction may precede, or substantially contribute to, abnormalities of systolic function in various pathologic conditions (table 1). Indices of diastolic function can be derived invasively or noninvasively, and focus on the measurement of a diverse and complex set of separate, but intimately interrelated, processes that, while complementary, may not be directly comparable. Measurement of these indices is complicated, because diastolic function depends on several determinants: active, energy-dependent forces (isovolumic ventricular relaxation); passive and dynamic filling characteristics (chamber and myocardial stiffness); and extrinsic factors (left atrial function, ventricular interaction, valvular integrity, pericardial restraint, and myocardial blood flow), as well as other conditions that affect myocardial function during systole (preload, afterload, heart rate, and inotropic state). The diversity of events occurring during diastole indicates that a single index of diastolic function cannot adequately describe this period of the cardiac cycle, and the physiologic implications of diastolic dysfunction may be different, depending on the period of diastole affected (table 1). Thus, assessment of diastolic function is complicated, because of the heterogeneity of the event and the multiple factors that influence it. Despite the inherent potential limitations of indices describing diastolic function, these parameters provide useful references for evaluating the natural history of patients with diastolic heart failure, for assessing the benefits of therapeutic interventions of anesthetic actions, and for enhancing our knowledge of cardiac pathophysiology.

Anesthesiology↗
PubMed2001

Role of corticostriatal and nigrostriatal inputs in malonate-induced striatal toxicity.

The striatal neuronal loss evident following cellular metabolic compromise may be dependent upon the presence of glutamate and dopamine within the striatum. In order to investigate the relative roles of corticostriatal and nigrostriatal projections in malonate-induced neuronal loss, the extent of toxicity was quantified in animals with cortical lesions to deplete the striatum of glutamate, nigrostriatal lesions to deplete the striatum of dopamine, or both. We found that malonate-induced striatal toxicity was significantly reduced following lesions of either the glutamatergic or dopaminergic afferents to the striatum. The extent of attenuation following the loss of both inputs within the same animal was similar to that seen following lesions of either alone. These data suggest that malonate-induced toxicity in the striatum depends upon the integrity of interactive influences from both glutamatergic and dopaminergic afferents.

Adrenergic Agents↗
PubMed1998

The Primary Care Assessment Survey: tests of data quality and measurement performance.

OBJECTIVES: The authors examine the data quality and measurement performance of the Primary Care Assessment Survey (PCAS), a patient-completed questionnaire that operationalizes formal definitions of primary care, including the definition recently proposed by the Institute of Medicine Committee on the Future of Primary Care. METHODS: The PCAS measures seven domains of care through 11 summary scales: accessibility (organizational, financial), continuity (longitudinal, visit-based), comprehensiveness (contextual knowledge of patient, preventive counseling), integration, clinical interaction (clinician-patient communication, thoroughness of physical examinations), interpersonal treatment, and trust. Data from a study of Massachusetts state employees (n = 6094) were used to evaluate key measurement properties of the 11 PCAS scales. Analyses were performed on the combined population and for each of the 16 subgroups defined according to sociodemographic and health characteristics. RESULTS: The 11 PCAS scales demonstrated consistently strong measurement characteristics across all subgroups of this adult population. Tests of scaling assumptions for summated rating scales were well satisfied by all Likert-scaled measures. Assessment of data completeness, scale score dispersion characteristics, and inter-scale correlations provide strong evidence for the soundness of all scales, and for the value of separately measuring and interpreting these concepts. CONCLUSIONS: With public and private sector policies increasingly emphasizing the importance of primary care, the need for tools to evaluate and improve primary care performance is clear. The PCAS has excellent measurement properties, and performs consistently well across varied segments of the adult population. Widespread application of an assessment methodology, such as the PCAS, will afford an empiric basis through which to measure, monitor, and continuously improve primary care.

Adult↗
PubMed2006

Membrane and protein interactions of oxysterols.

PURPOSE OF REVIEW: Oxysterols, oxidation products of cholesterol, mediate numerous and diverse biological processes. The objective of this review is to explain some of the biochemical and cell biological properties of oxysterols based on their membrane biophysical properties and their interaction with integral and peripheral membrane proteins. RECENT FINDINGS: According to their biophysical properties, which can be distinct from those of cholesterol, oxysterols can promote or inhibit the formation of membrane microdomains or lipid rafts. Oxysterols that inhibit raft formation are cytotoxic. The stereo-specific binding of cholesterol to sterol-sensing domains in cholesterol homeostatic pathways is not duplicated by oxysterols, and some oxysterols are poor substrates for the pathways that detoxify cells of excess cholesterol. The cytotoxic roles of oxysterols are, at least partly, due to a direct physical effect on membranes involved in cholesterol-induced cell apoptosis and raft mediated cell signaling. Oxysterols regulate cellular functions by binding to oxysterol binding protein and oxysterol binding protein-related proteins. Oxysterol binding protein is a sterol-dependent scaffolding protein that regulates the extracellular signal-regulated kinase signaling pathway. According to a recently solved structure for a yeast oxysterol binding protein-related protein, Osh4, some members of this large family of proteins are likely sterol transporters. SUMMARY: Given the association of some oxysterols with atherosclerosis, it is important to identify the mechanisms by which their association with cell membranes and intracellular proteins controls membrane structure and properties and intracellular signaling and metabolism. Studies on oxysterol binding protein and oxysterol binding protein-related proteins should lead to new understandings about sterol-regulated signal transduction and membrane trafficking pathways in cells.

Animals↗
PubMed2003

Fgfr1 regulates patterning of the pharyngeal region.

Development of the pharyngeal region depends on the interaction and integration of different cell populations, including surface ectoderm, foregut endoderm, paraxial mesoderm, and neural crest. Mice homozygous for a hypomorphic allele of Fgfr1 have craniofacial defects, some of which appeared to result from a failure in the early development of the second branchial arch. A stream of neural crest cells was found to originate from the rhombomere 4 region and migrate toward the second branchial arch in the mutants. Neural crest cells mostly failed to enter the second arch, however, but accumulated in a region proximal to it. Both rescue of the hypomorphic Fgfr1 allele and inactivation of a conditional Fgfr1 allele specifically in neural crest cells indicated that Fgfr1 regulates the entry of neural crest cells into the second branchial arch non-cell-autonomously. Gene expression in the pharyngeal ectoderm overlying the developing second branchial arch was affected in the hypomorphic Fgfr1 mutants at a stage prior to neural crest entry. Our results indicate that Fgfr1 patterns the pharyngeal region to create a permissive environment for neural crest cell migration.

Alleles↗
PubMed2003

Star-unitary transformations: from dynamics to irreversibility and stochastic behavior.

We consider a simple model of a classical harmonic oscillator coupled to a field. In standard approaches, Langevin-type equations for bare particles are derived from Hamiltonian dynamics. These equations contain memory terms and are time-reversal invariant. In contrast, the phenomenological Langevin equations have no memory terms (they are Markovian equations) and give a time-evolution split in two branches (semigroups), each of which breaks time symmetry. A standard approach to bridge dynamics with phenomenology is to consider the Markovian approximation of the former. In this paper, we present a formulation in terms of dressed particles, which gives exact Markovian equations. We formulate dressed particles for Poincaré nonintegrable systems, through an invertible transformation operator Lambda introduced by Prigogine and co-workers. Lambda is obtained by an extension of the canonical (unitary) transformation operator U that eliminates interactions for integrable systems. Our extension is based on the removal of divergences due to Poincaré resonances, which breaks time symmetry. The unitarity of U is extended to "star unitarity" for Lambda. We show that Lambda-transformed variables have the same time evolution as stochastic variables obeying Langevin equations, and that Lambda-transformed distribution functions satisfy exact Fokker-Planck equations. The effects of Gaussian white noise are obtained by the nondistributive property of Lambda with respect to products of dynamical variables.

Journal Article↗
PubMed2004

Atomistic versus two-body central potential models of C(60): a comparative molecular dynamics study.

We report on an extensive molecular dynamics investigation of two models of C60. The first model is based on an effective pair, central potential obtained by integrating the interaction between two carbon atoms over the fullerene cages [L.A. Girifalco, J. Phys. Chem. 96, 858 (1992)]. The second model explicitly takes into account the discrete, "atomistic" structure of the C60 molecules; we study two different parametrizations of the carbon-carbon interaction, one identical to that employed in the Girifalco approach, the other borrowed from previous studies on graphite [A. Cheng and M.L. Klein, J. Phys. Chem. 95, 6750 (1991)]. We consider a temperature range spanning from 300 to 1900 K, and pressures up to 200 kbar. Results for the lattice spacing and several thermodynamic quantities, as well as for the radial distribution functions, are reported and compared among each other and with experimental data. The central pair model yields only semiquantitative predictions at typical ambient densities, whereas pressures are generally overestimated. Atomistic simulations reproduce to an overall quantitative level of accuracy the experimental C60 properties. A comparison is also made of the central versus the atomistic potential predictions, when using the same potential parameters in the carbon-carbon interaction. We discuss applications of the adopted modelizations to fullerene systems of current interest, as well as different strategies to optimize the values of the potential parameters.

Journal Article↗
PubMed1997

Characterization of AtSEC12 and AtSAR1. Proteins likely involved in endoplasmic reticulum and Golgi transport.

Transport of cargo proteins from the endoplasmic reticulum (ER) to the cis-Golgi network is mediated by protein-coated vesicles. The coat, called COPII coat, consists of proteins that are recruited from the cytosol and interact with integral membrane proteins of the ER. In yeast, both cytosolic proteins (Sec13/31, Sec23/24, and Sar1) and ER-associated proteins (Sec12 and others) have been purified and characterized and it has been possible to demonstrate transport vesicle formation in vitro. Arabidopsis thaliana homologs of Sar1 and Sec12 have recently been identified, but little is known about the properties of the proteins or their subcellular distribution. Here we demonstrate that AtSAR1, a 22-kD protein that binds GTP, and AtSEC12, a 43-kD GTP-exchange protein, are both associated with the ER. However, about one-half of the cellular AtSAR1 is present in the cytosol. When AtSAR1 is overexpressed in transgenic plants, the additional protein is also cytosolic. When tissue-culture cells are cold-shocked (12 h at 8 degrees C), AtSAR1 levels appeared to decline and a larger proportion of the total protein was found in the cytosol. Given the known function of AtSAR1 in yeast, we propose that the amount of ER-associated AtSAR1 is an indication of the intensity of the secretory process. Thus, we expect that such a cold shock will adversely affect ER-to-Golgi transport of proteins.

Arabidopsis↗
PubMed2006

Identification of novel quaternary domain interactions in the Hsp90 chaperone, GRP94.

The structural basis for the coupling of ATP binding and hydrolysis to chaperone activity remains a central question in Hsp90 biology. By analogy to MutL, ATP binding to Hsp90 is thought to promote intramolecular N-terminal dimerization, yielding a molecular clamp functioning in substrate protein activation. Though observed in studies with recombinant domains, whether such quaternary states are present in native Hsp90s is unknown. In this study, native subunit interactions in GRP94, the endoplasmic reticulum Hsp90, were analyzed using chemical cross-linking in conjunction with tandem mass spectrometry. We report the identification of two distinct intermolecular interaction sites. Consistent with previous studies, one site comprises the C-terminal dimerization domain. The remaining site represents a novel intermolecular contact between the N-terminal and middle (M) domains of opposing subunits. This N+M domain interaction was present in the nucleotide-empty, ADP-, ATP-, or geldanamycin-bound states and could be selectively disrupted upon addition of synthetic geldanamycin dimers. These results identify a compact, intertwined quaternary conformation of native GRP94 and suggest that intersubunit N+M interactions are integral to the structural biology of Hsp90.

Adenosine Diphosphate↗