SEARCH · PubMed Health

Results for “Model interpretability”

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 955 records · Page 53Linked to original sources

PubMed1997

Electronic and Molecular Structures of Pentaammineruthenium Pyridine and Benzonitrile Complexes as a Function of Oxidation State.

The structural characterization of both Ru(II) and Ru(III) compounds containing Ru(NH(3))(5)(2+/3+) with pyridine or benzonitrile as the sixth ligand (L) is described. Crystal data for L = pyridine, [(NH(3))(5)Ru(NC(5)H(5))](SO(3)CF(3))(2) (1): orthorhombic space group Pbcn, Z = 4, a = 13.096(2) Å, b = 11.541(2) Å, c = 13.179(2) Å. For [(NH(3))(5)Ru(NC(5)H(5))]Cl(3).1.4H(2)O (2): orthorhombic space group Pnma, Z = 4, a = 22.667(12) Å, b = 7.095(2) Å, c = 10.097(8) Å. For L = benzonitrile, [(NH(3))(5)Ru(NCC(6)H(5))](SO(3)CF(3))(2) (3): monoclinic space group P2(1)/n, Z = 4, a = 9.561(1) Å, b = 18.424(4) Å, c = 12.181(1) Å, beta = 95.73(1) degrees. For [(NH(3))(5)Ru(NCC(6)H(5))](S(2)O(6))(3/2).2H(2)O (4): triclinic space group P&onemacr;, Z = 2, a = 7.8947(6) Å, b = 11.517(2) Å, c = 11.630(1) Å, alpha = 99.61(1) degrees, beta = 97.275(8) degrees, gamma = 102.25(1) degrees. The Ru(II)-N(L) and Ru(III)-N(L) distances are respectively 2.058(8) and 2.077(10) Å for L = pyridine and 1.945(5) and 2.025(4) Å for L = benzonitrile. The new data yield a comprehensive set of structural parameters for modeling and interpreting electron transfer barriers and for investigating the dependence of metal-ligand coupling on d(M)(-)(N), for which the results of INDO calculations are also reported here.

Journal Article↗

PubMed2001

Dielectric relaxation in an enzyme active site: molecular dynamics simulations interpreted with a macroscopic continuum model.

Dielectric relaxation plays an important role in many chemical processes in proteins, including acid-base titration, ligand binding, and charge transfer reactions. Its complexity makes experimental characterization difficult, and so, theoretical approaches are valuable. The comparison of molecular dynamics free energy simulations with simpler models such as a dielectric continuum model is especially useful for obtaining qualitative insights. We have analyzed a charge insertion process that models deprotonation or mutation of an important side chain in the active site of the enzyme aspartyl-tRNA synthetase. Complexes with the substrate aspartate and the analogue asparagine were studied. The resulting dielectric relaxation was found to involve both ligand and side chain rearrangements in the active site and to account for a large part of the overall charging free energy. With the continuum model, charge insertion is performed along a two-step pathway: insertion into a static environment, followed by relaxation of the environment. These correspond to different physical processes and require different protein dielectric constants. A low value of approximately 1 is needed for the static step, consistent with the parametrization of the molecular mechanics charge set used. A value of 3-6 (depending on the exact insertion site and the nature of the ligand) is needed to describe the dielectric relaxation step. This moderate value indicates that, for this system, the local protein polarizability in the active site is within at most a factor of 2 of that expected at nonspecific positions in a protein interior.

Aspartate-tRNA Ligase↗

PubMed2004

Detection of free nickel monocarbonyl, NiCO: rotational spectrum and structure.

Unsaturated transition metal carbonyls are important in processes such as organometallic synthesis, homogeneous catalysis, and photochemical decomposition of organometallics. In particular, a metal monocarbonyl offers a zeroth-order model for interpreting the chemisorption of a CO molecule on a metal surface in catalytic activation processes. Quite large numbers of theoretical papers have appeared which predict spectroscopic and structural properties of transition metal carbonyls. The nickel monocarbonyl NiCO has been one of the metal carbonyls most extensively studied by the theoretical calculations. At least 50 theoretical studies have been published on this simplest transition metal carbonyl up to the present time. However, experimental evidence of NiCO is much more sparse than theoretical predictions, and the actual structure of NiCO has never been determined by any experimental methods. This Communication reports the first preparation of free nickel monocarbonyl and observation of its rotational transitions. The NiCO molecule was generated by the sputtering reaction of a Ni cathode in the presence of CO. The accurate bond lengths of Ni-C and C-O were experimentally determined from isotopic data and were compared with the theoretical predictions for the first time.

Journal Article↗

PubMed2005

Time-scale- and temperature-dependent mechanical properties of viscoelastic poly(3,4-ethylenedioxythiophene) films.

The viscoelastic properties of thin films of poly(3,4-ethylenedioxythiophene) (PEDOT) have been studied using the method of acoustic impedance. The films were deposited on the Au electrodes of 10 MHz AT-cut quartz thickness shear mode resonators and exposed to acetonitrile solutions of 0.1 M TEABF4 and LiClO4. For p-doped films, admittance spectra as a function of potential (E), temperature (T), and time scale (frequency, via harmonics, in the range 10-110 MHz) were acquired. Shear modulus components extracted from these responses surprisingly showed virtually no variation with E (and thus film solvation) or with T, but the variation with frequency was dramatic. This qualitative behavior and the numerical values of the shear moduli contrast strongly with recently reported data for the related poly(3-hexylthiophene) system, which shares the same conducting spine but differs substantially in the substitution pattern. Accordingly, the models and interpretation for PEDOT are quite different: film dynamics are determined by free-volume effects, and side-chain motion is not a significant factor. Qualitatively similar potential and time-scale effects were seen for n-doped PEDOT, but the scope of the measurements was limited by film stability.

Journal Article↗

PubMed1997

A strategy for the incorporation of water molecules present in a ligand binding site into a three-dimensional quantitative structure--activity relationship analysis.

Water present in a ligand binding site of a protein has been recognized to play a major role in ligand-protein interactions. To date, rational drug design techniques do not usually incorporate the effect of these water molecules into the design strategy. This work represents a new strategy for including water molecules into a three-dimensional quantitative structure-activity relationship analysis using a set of glucose analogue inhibitors of glycogen phosphorylase (GP). In this series, the structures of the ligand-enzyme complexes have been solved by X-ray crystallography, and the positions of the ligands and the water molecules at the ligand binding site are known. For the structure-activity analysis, some water molecules adjacent to the ligands were included into an assembly which encompasses both the inhibitor and the water involved in the ligand-enzyme interaction. The mobility of some water molecules at the ligand binding site of GP gives rise to differences in the ligand-water assembly which have been accounted for using a simulation study involving force-field energy calculations. The assembly of ligand plus water was used in a GRID/GOLPE analysis, and the models obtained compare favorably with equivalent models when water was excluded. Both models were analyzed in detail and compared with the crystallographic structures of the ligand-enzyme complexes in order to evaluate their ability to reproduce the experimental observations. The results demonstrate that incorporation of water molecules into the analysis improves the predictive ability of the models and makes them easier to interpret. The information obtained from interpretation of the models is in good agreement with the conclusions derived from the structural analysis of the complexes and offers valuable insights into new characteristics of the ligands which may be exploited for the design of more potent inhibitors.

Binding Sites↗

PubMed2005

Solution-phase, triangular ag nanotriangles fabricated by nanosphere lithography.

A novel method to produce solution-phase triangular silver nanoparticles is presented. Ag nanoparticles are prepared by nanosphere lithography and are subsequently released into solution. The resulting nanoparticles are asymmetrically functionalized to produce either single isolated nanoparticles or dimer pairs. The structural and optical properties of Ag nanoparticles have been characterized. Mie theory and the Discrete Dipole Approximation method (DDA) have been used to model and interpret the optical properties of the released Ag nanoparticles.

Journal Article↗

PubMed2003

Quantitative description of human skin water dynamics by a disposition-decomposition analysis (DDA) of trans-epidermal water loss and epidermal capacitance.

BACKGROUND: In vivo water assessment would greatly benefit from a dynamical approach since the evaluation of common related variables such as trans-epidermal water loss or "capacitance" measurements is always limited to instantaneous data. Mathematical modelling is still an attractive alternative already attempted with bi-exponential empirical models. A classical two-compartment interpretation of such models raises a number of questions about the underlying fundamentals, which can hardly be experimentally confirmed. However, in a system analysis sense, skin water dynamics may be approached as an ensemble of many factors, impossible to discretize, but conceptually grouped in terms of feasible properties of the system. The present paper explores the applicability of this strategy to the in vivo water dynamics assessment. METHODS: From the plastic occlusion stress test (POST) skin water balance is assessed by modelling trans-epidermal water loss (TEWL) and "capacitance" data obtained at skin's surface. With system analysis (disposition-decomposition analysis) the distribution function, H(t), modelled as a sum of exponential terms, covers only the distribution characteristics of water molecules traversing the skin. This may correspond macroscopically to the experimental data accessed by "corneometry". Separately, the hyperbolic elimination function Q(TEWL) helps to characterise the dynamic aspects of water influx through the skin. DISCUSSION AND CONCLUSION: In the observable range there seems to be a linear relationship between the net amount of water lost at the surface by evaporation, and the capability of the system to replenish that loss. This may be a specific characteristic of the system related to what may be described as the skin's "intrinsic hydration capacity" (IHC) a new functional parameter only identified by this strategy. These new quantitative tools are expected to find different applicabilities (from the in vivo skin characterisation to efficacy testing) contributing to disclose the dynamical nature of the skin water balance process.

Adult↗

PubMed2002

Conflicting perspectives on shamans and shamanism: points and counterpoints.

Shamans' communities grant them privileged status to attend to those groups' psychological and spiritual needs. Shamans claim to modify their attentional states and engage in activities that enable them to access information not ordinarily attainable by members of the social group that has granted them shamanic status. Western perspectives on shamanism have changed and clashed over the centuries; this address presents points and counterpoints regarding what might be termed the demonic model, the charlatan model, the schizophrenia model, the soul flight model, the degenerative and crude technology model, and the deconstructionist model. Western interpretations of shamanism often reveal more about the observer than they do about the observed; in addressing this challenge, the study of shamanism could make contributions to cognitive neuroscience, social psychology, psychological therapy, and ecological psychology.

Awards and Prizes↗

PubMed2004

Method matters: effects of explicit versus implicit social comparisons on activation, behavior, and self-views.

The authors investigated the impact of explicit versus implicit social comparisons. Simply being primed with a superior or inferior standard (implicit comparison) produced contrast as evidenced by accessibility of self-knowledge (Study 2), intellectual performance (Study 3), and self-ratings (Study 4), inconsistent with the standard. However, when participants were explicitly asked to compare, increased accessibility of a similarity focus (Study 1) and self-knowledge, behavioral performance, and self-ratings congruent with the standard were obtained more easily, indicative of assimilation. Explicit comparisons produced assimilation when the self was seen as mutable (rather than immutable; Study 4), when behavioral consequences were measured immediately after the comparison (rather than later; Study 3), and when the participants described (rather than ranked) their intelligence (Study 5). These findings support the interpretation comparison model. Implications for resolution of empirical inconsistencies in the social comparison literature are discussed.

Adult↗

PubMed2000

The importance of theory: response to Brenner (2000)

L. Brenner's (2000) critique of I. Erev, T. S. Wallsten and D. V. Budescu (1994) focuses on their (a) use of a model to explain the paradox of the same data appearing to suggest over- and underconfidence, depending on how they are analyzed; (b) definitions of true judgment and error; and (c) specific use of judgments transformed to log-odds and a model formulated in those terms. The authors of the present article strongly disagree with the first point and discuss the importance of using models to interpret data. With regard to the second, the authors admit that the constructs of true judgment and error are poorly named but dispute L. Brenner's specific criticisms. Concerning the third, the authors had not claimed that the log-odds metric has any special status in judgment research and thus agree with L. Brenner's basic point.

Humans↗

PubMed2001

Stability of atmospheric CO2 levels across the Triassic/Jurassic boundary.

The Triassic/Jurassic boundary, 208 million years ago, is associated with widespread extinctions in both the marine and terrestrial biota. The cause of these extinctions has been widely attributed to the eruption of flood basalts of the Central Atlantic Magmatic Province. This volcanic event is thought to have released significant amounts of CO2 into the atmosphere, which could have led to catastrophic greenhouse warming, but the evidence for CO2-induced extinction remains equivocal. Here we present the carbon isotope compositions of pedogenic calcite from palaeosol formations, spanning a 20-Myr period across the Triassic/Jurassic boundary. Using a standard diffusion model, we interpret these isotopic data to represent a rise in atmospheric CO2 concentrations of about 250 p.p.m. across the boundary, as compared with previous estimates of a 2,000-4,000 p.p.m. increase. The relative stability of atmospheric CO2 across this boundary suggests that environmental degradation and extinctions during the Early Jurassic were not caused by volcanic outgassing of CO2. Other volcanic effects-such as the release of atmospheric aerosols or tectonically driven sea-level change-may have been responsible for this event.

Journal Article↗

PubMed2003

From gene networks to brain networks.

The brain's structural organization is so complex that 2,500 years of analysis leaves pervasive uncertainty about (i) the identity of its basic parts (regions with their neuronal cell types and pathways interconnecting them), (ii) nomenclature, (iii) systematic classification of the parts with respect to topographic relationships and functional systems and (iv) the reliability of the connectional data itself. Here we present a prototype knowledge management system (http://brancusi.usc.edu/bkms/) for analyzing the architecture of brain networks in a systematic, interactive and extendable way. It supports alternative interpretations and models, is based on fully referenced and annotated data and can interact with genomic and functional knowledge management systems through web services protocols.

Animals↗

PubMed1999

Urinary nickel concentrations and selected pregnancy outcomes in delivering women and their newborns among arctic populations of Norway and Russia.

The two objectives of this study were to compare urinary nickel excretion in pregnant women and their newborns living in the Murmansk and Arkhangelsk Counties of Russia with that in comparable Norwegian populations living in Finnmark and the city of Bergen and to assess the influence on pregnancy outcome of different risk variables, specifically urinary nickel concentrations and questionnaire-based anamnestic information. Life-style information and urine samples were collected from 50 consecutive mother-infant pairs from hospital delivery departments in three Russian and three Norwegian communities. Pregnancy outcomes were verified from medical records. Urinary nickel excretion was significantly higher in the Russian communities, independent of the presence of a nickel refinery as a local environmental source. The birth weight and mean body mass index of the newborn children (BMIC) were significantly lower (p < 0.001) in the Russian groups, with or without adjustment for gestational age. A multivariate linear regression analysis indicated that maternal urinary nickel concentration had no impact on birth weight. The maternal body mass index (BMI) and maternal height were positive explanatory variables; maternal urinary creatinine is suggested as a weak negative factor. Smoking was shown to be a strong negative predictor only in the Norwegian group among whom there was a significantly higher smoking frequency (p = 0.005). The significant contribution of a country factor in the predictive model is interpreted to indicate that a number of important risk factors for low birth weight were not identified.

Adolescent↗

PubMed2000

Simultaneous monitoring of atmospheric methane and speciated non-methane hydrocarbon concentrations using Peltier effect sub-ambient pre-concentration and gas chromatography.

Sub-ambient trapping, used to pre-concentrate atmospheric samples for non-methane hydrocarbon (NMHC) analysis by gas chromatography, can also be used to measure ambient methane concentrations. Above a sample volume of 40 ml, a dynamic equilibrium is established between ambient and trapped methane allowing for simultaneous quantitative determinations of methane and NMHC. The temperature stability of the trap is critical for quantitative methane analysis and this can be achieved by Peltier effect cooling. Simultaneous measurements of methane and NMHC reduce the equipment required for field trips and can ease the interpretation and modelling of atmospheric data. The feasibility for deployment of the system in remote locations was demonstrated by running the apparatus virtually unattended for a 5-day period. The correlations between the concentrations of methane, ethane and ethene measured during this period are discussed.

Air Pollutants↗

PubMed2005

Post-remediation evaluation of a LNAPL site using electrical resistivity imaging.

Present understanding of the earth's subsurface is most often derived from samples at discrete points (wells) and interpolations or models that interpret the space between these points. Electrical resistivity imaging techniques have produced an improved capability to map contaminants (especially NAPLs--NonAqueous Phase Liquids) away from traditional wells using actual field data. Electrical resistivity image data, confirmed by drilling, have demonstrated that LNAPL (Light NAPL--less dense than water, such as gasoline) contaminants exist outside of a delineated and remediated area in Golden, Oklahoma. The data also demonstrate that LNAPL exists between monitoring and remediation wells which indicate low contaminant levels when sampled. Additionally, the electrical images provided the drilling location with the highest concentration of hydrocarbon ever found on the site, even after two phases of remediation work had been performed, although the sampling protocols varied. The results indicate that current methods of post-remediation site characterization are inadequate for complete site characterization.

Electric Impedance↗

PubMed2003

Evaluation of an ion-exchange membrane for the purification of plasmid DNA.

Separation and purification of large quantities of plasmid DNA (pDNA) is a particularly difficult manufacturing issue because of the relatively low capacity, flow rate and purity observed using traditional bead-based chromatography. The objective of the present study was to evaluate the performance of anion-exchange membranes for the purification of pDNA from Escherichia coli lysate solution. The fate of host-cell protein and endotoxin relative to pDNA was measured and used to calculate recoveries, mass balances, dynamic capacities and purification factors as a function of the flow rate and loading volume of the lysate solution. Breakthrough curves were not sigmoidal and symmetric in shape. They rose sharply at first, and then slowly towards, but never reaching, saturation. Conversely, elution curves were independent of flow rate. pDNA bound tightly to the membranes, whereas protein and endotoxin did not. Dynamic binding capacity for pDNA was 20-25 times greater, and the flow rate was 55-550 times greater, than values observed for beads. However, some pDNA bound irreversibly to the membrane surface and was not removed completely during elution. The intrinsic rate of pDNA adsorption to the membrane was found to be rate-limiting, whereas effects of liquid-phase mass transfer and flow non-idealities were negligible. These results were interpreted using models of adsorption that included steric effects using the 'car-parking-problem' model, and surface residence time effects using the spreading model. This work demonstrated the advantages of ion-exchange membranes compared with beads for the purification of large biomolecules such as pDNA.

Adsorption↗

PubMed1999

Estimation of alveolar pressure during speech using direct measures of tracheal pressure.

The pressure in the alveoli of the lungs, created by the elastic recoil of the lungs and respiratory muscle activity, is referred to as alveolar pressure (Pa). The extent to which tracheal pressure (Pt) approximates Pa depends on the resistance to airflow offered by structures above and below the point at which tracheal pressure is measured. An understanding of the relationship among Pa, Pt, and upper and lower airway resistance, and how these values fluctuate during speech, could aid in interpretation and modeling of speech aerodynamics. The purpose of this study was to (a) obtain values for lower airway resistance (Rlow), (b) use these Rlow values to estimate Pa during speech, and (c) quantify the degree to which Pt approximates Pa during production of voiced and voiceless sounds, in comparison to inhalation. In addition, the results were discussed in terms of the degree to which the respiratory system functions as a pressure source. Tracheal pressure (obtained with tracheal puncture) and airflow were measured during sentence production in 6 subjects. Using a technique introduced in this paper, Rlow was determined from measures of tracheal pressure and flow obtained during a sudden change in upper airway resistance because of release of a voiceless plosive. Mean Rlow values ranged from 0.14 to 0.32 kPa/(l/s). Each subject's mean Rlow was used to derive a time-varying measure of Pa during speech from continuous measures of tracheal pressure and airflow. Pt was approximately 95% of Pa during phonation (i.e., when the vocal folds were adducted), 75% of Pa during release of the voiceless stop consonant /p/, and 55% of Pa during inhalation (i.e., when the vocal folds were abducted). Therefore, the degree to which the respiratory system functioned as an ideal pressure source varied during speech. The ability to estimate Pa provides a measure of the pressure produced by the respiratory system that is not influenced by laryngeal activity.

Adult↗

PubMed2001

High-voltage electron microscope high-temperature in situ straining experiments to study dislocation dynamics in intermetallics and quasicrystals.

The dynamic behaviour of dislocations in several intermetallic alloys, studied by in situ straining experiments in a high-voltage electron microscope, is compared at room temperature and at high temperatures. In contrast to room temperature, the dislocations move viscously at high temperatures, which is explained by diffusion processes in the dislocation cores. In quasicrystals, the viscous dislocation motion can be interpreted by models on the cluster scale.

Journal Article↗