PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “Model explainability”

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 397 records · Page 22Linked to original sources

Wild bird mortality and West Nile virus surveillance: biases associated with detection, reporting, and carcass persistence.

Surveillance targeting dead wild birds, in particular American crows (Corvus brachyrhynchos), plays a critical role in West Nile virus (WNV) surveillance in the United States. Using crow decoy surrogates, detection and reporting of crow carcasses within urban and rural environments of DeKalb County, Georgia were assessed for potential biases that might occur in the county's WNV surveillance program. In each of two replicated trials, during July and September 2003, 400 decoys were labeled with reporting instructions and distributed along randomly chosen routes throughout designated urban and rural areas within DeKalb County. Information-theoretic methods were used to compare alternative models incorporating the effects of area and trial on probabilities of detection and reporting. The model with the best empirical support included the effects of area on both detection and reporting of decoys. The proportion of decoys detected in the urban area (0.605, SE=0.024) was approximately twice that of the rural area (0.293, SE=0.023), and the proportion of decoys reported in the urban area (0.273, SE=0.023) was approximately three times that of the rural area (0.103, SE=0.028). These results suggest that human density and associated factors can substantially influence dead crow detection and reporting and, thus, the perceived distribution of WNV. In a second and separate study, the persistence and fate of American crow and house sparrow (Passer domesticus) carcasses were assessed in urban and rural environments in Athens-Clarke, Madison, and Oconee counties, Georgia. Two replicated trials using 96 carcasses of each species were conducted during July and September 2004. For a portion of the carcasses, motion sensitive cameras were used to monitor scavenging species visits. Most carcasses (82%) disappeared or were decayed by the end of the 6-day study. Carcass persistence averaged 1.6 days in rural areas and 2.1 days in urban areas. We analyzed carcass persistence rates using a known-fate model framework in program MARK. Model selection based on Akaike's Information Criteria (AIC) indicated that the best model explaining carcass persistence rates included species and number of days of exposure; however, the model including area and number of days of exposure received approximately equal support. Model-averaged carcass persistence rates were higher for urban areas and for crow carcasses. Six mammalian and one avian species were documented scavenging upon carcasses. Dead wild birds could represent potential sources of oral WNV exposure to these scavenging species. Species composition of the scavenger assemblage was similar in urban and rural areas but "scavenging pressure" was greater in rural areas.

Animals↗

Predictors of change in exercise capacity after comprehensive COPD inpatient rehabilitation.

BACKGROUND: In order to evaluate the factors associated with change in exercise capacity after comprehensive inpatient Pulmonary Rehabilitation (IPR) we studied 132 consecutive adults with Chronic Obstructive Pulmonary Disease (COPD) recovering from an acute exacerbation. MATERIAL/METHODS: Lung function, arterial blood gases, and respiratory muscle strength were measured at baseline. Perceived breathlessness (B), 6-minute walk distance (6MWD), dyspnea at rest and post-exertion (D), hospital anxiety and depression (HAD), and health-related quality of life were assessed before (T0) and after (T1) IPR. The patients were divided into two groups depending on the change in 6MWD: Improvers (IM at least +54 meters after IPR, n=81) or Non-Improvers (NIM, less than 54 meters or no change, n=51). RESULTS: At T1 61% of the patients showed improvement as here defined. The IM group showed lower 6MWD and higher B and resting-D at T0 than NIM (p<0.05). A stepwise multiple regression analysis was performed using 6MWD change as the dependent variable. and anthropometric and physiological measures at T0 as the independent variables. This regression model explained 26% of the 6MWD-change; 6MWD and PaO2 significantly contributed to this model. CONCLUSIONS: In COPD patients recovering from an acute exacerbation, the predicted change in exercise capacity using anthropometric, demographic, clinical, and physiological variables after 2 weeks of comprehensive IPR is likely to be low. The baseline level of exercise performance and arterial oxygenation show the most consistent correlation with change in walking ability in these patients.

Aged↗

Single-molecule unzippering experiments on DNA and Peyrard-Bishop-Dauxois model.

In this paper, we rely on a nonlinear Peyrard-Bishop-Dauxois (PBD) model. This mechanical model explains DNA dynamics assuming only transversal oscillations of nucleotides. The potential energy for the hydrogen bonds, connecting AT or CG base pairs, is modeled by a Morse potential. This potential is characterized by the depth D and the inverse width a of the Morse potential well. We discuss one type of single molecule manipulation experiments, which we call unzippering experiments. It is explained that the highest values of two essential parameters of the PBD model, the parameters D and a, can be determined according to the results of those experiments. This statement is supported by theoretical calculations. We show that the inverse width of the Morse potential well a has been overestimated so far. The smallest value for this parameter is determined according to the PBD model, which means that a rather narrow interval can be assumed. Also, we give an idea how to determine the optimal value of the parameter a.

Computer Simulation↗

Rhythmic performance during a whole body movement: dynamic analysis of force-time curves.

The purpose of this study was to investigate rhythmic performance during two-legged hopping in place. In particular, it was tested whether (a) timing control is independent of force control, (b) a dynamic timer model explains rhythmic performance, and (c) it is a force related parameter that carries the timing information. Eleven participants performed two-legged hopping at their preferred hopping frequency (PHF) and at two hopping frequencies set by an external rhythmic stimulus as lower (LHF) and higher (HHF) than their PHF, respectively. A force plate was used to record the ground reaction force (GRF) time curves during two-legged hopping. The primary temporal and force related parameters determined from the GRF-time curves were the durations of the cycle of movement (t(cycle)), of the contact phase (t(contact)), of the flight phase (t(flight)), the magnitude of peak force (Fz(peak)) and the rate of peak force development (RFD). Control of t(cycle) was independent of force control as shown by the non-significant correlations between t(cycle) and the force parameters of the GRF-time curve. Lag 1 autocorrelations of t(cycle) were not significant in any of the HF, thereby a dynamic timer model is considered to explain the timing of t(cycle) during two-legged hopping. RFD varied more than any other GRF-time curve parameter, exhibited consistent significant strong correlations with the GRF-time curve parameters and significant negative lag 1 autocorrelations in PHF, thus, it was highlighted as the potent timing control parameter. Finally, we provide a practical application for the optimization of rhythmic performance.

Adult↗

Age differences in stress, social resources, and well-being in middle and older age.

The present study examines the interrelationships among the constructs of social resources, stress, and well-being in middle-aged and older adults. Two samples of 489 middle-aged adults (41-43 years) and 449 older adults (61-63 years) from the Interdisciplinary Longitudinal Study of Adult Development were compared with respect to the availability of social resources, levels of stress, and well-being. The data were used to construct separate structural equation models explaining the influence of stress and social resources on well-being in the two groups. The results indicate higher levels of health-related stress and similar levels of social resources in the older group. Structural equation models and examination of total and indirect effects confirmed that a stress-suppression model has the best fit in explaining the interrelationships between stress, social resources, and well-being. There was a strong effect of stress on well-being, no direct effect of social resources on well-being, and a mediating effect of stress on well-being. The relative contributions of stress and resources to well-being were comparable between age groups.

Adult↗

Noise-induced Min phenotypes in E. coli.

The spatiotemporal oscillations of the Escherichia coli proteins MinD and MinE direct cell division to the region between the chromosomes. Several quantitative models of the Min system have been suggested before, but no one of them accounts for the behavior of all documented mutant phenotypes. We analyzed the stochastic reaction-diffusion kinetics of the Min proteins for several E. coli mutants and compared the results to the corresponding deterministic mean-field description. We found that wild-type (wt) and filamentous (ftsZ-) cells are well characterized by the mean-field model, but that a stochastic model is necessary to account for several of the characteristics of the spherical (rodA-) and phospathedylethanolamide-deficient (PE-) phenotypes. For spherical cells, the mean-field model is bistable, and the system can get trapped in a non-oscillatory state. However, when the intrinsic noise is considered, only the experimentally observed oscillatory behavior remains. The stochastic model also reproduces the change in oscillation directions observed in the spherical phenotype and the occasional gliding of the MinD region along the inner membrane. For the PE- mutant, the stochastic model explains the appearance of randomly localized and dense MinD clusters as a nucleation phenomenon, in which the stochastic kinetics at low copy number causes local discharges of the high MinD(ATP) to MinD(ADP) potential. We find that a simple five-reaction model of the Min system can explain all documented Min phenotypes, if stochastic kinetics and three-dimensional diffusion are accounted for. Our results emphasize that local copy number fluctuation may result in phenotypic differences although the total number of molecules of the relevant species is high.

Adenosine Triphosphatases↗

Prediction of Henry's law constants by a quantitative structure property relationship and neural networks.

Multiple linear regression analysis and neural networks were employed to develop predictive models for Henry's law constants (HLCs) for organic compounds of environmental concern in pure water at 25 degrees C, using a set of quantitative structure property relationship (QSPR)-based descriptors to encode various molecular structural features. Two estimation models were developed from a set of 303 compounds using 10 and 12 descriptors, one of these models using two descriptors to account for hydrogen-bonding characteristics explicitly; these were validated subsequently on an external set of 54 compounds. For each model, a linear regression and neural network version was prepared. The standard errors of the linear regression models for the training data set were 0.262 and 0.488 log(H(cc)) units, while those of the neural network analogues were lower at 0.202 and 0.224, respectively; the linear regression models explained 98.3% and 94.3% of the variance in the development data, respectively, the neural network models giving similar quality results of 99% and 98.3%, respectively. The various descriptors used describe connectivity, charge distribution, charged surface area, hydrogen-bonding characteristics, and group influences on HLC values.

Journal Article↗

Silence is liberating: removing the handcuffs on grammatical expression in the manual modality.

Grammatical properties are found in conventional sign languages of the deaf and in unconventional gesture systems created by deaf children lacking language models. However, they do not arise in spontaneous gestures produced along with speech. The authors propose a model explaining when the manual modality will assume grammatical properties and when it will not. The model argues that two grammatical features, segmentation and hierarchical combination, appear in all settings in which one human communicates symbolically with another. These properties are preferentially assumed by speech whenever words are spoken, constraining the manual modality to a global form. However, when the manual modality must carry the full burden of communication, it is freed from the global form it assumes when integrated with speech--only to be constrained by the task of symbolic communication to take on the grammatical properties of segmentation and hierarchical combination.

Adult↗

The rate of DNA evolution: effects of body size and temperature on the molecular clock.

Observations that rates of molecular evolution vary widely within and among lineages have cast doubts on the existence of a single "molecular clock." Differences in the timing of evolutionary events estimated from genetic and fossil evidence have raised further questions about the accuracy of molecular clocks. Here, we present a model of nucleotide substitution that combines theory on metabolic rate with the now-classic neutral theory of molecular evolution. The model quantitatively predicts rate heterogeneity and may reconcile differences in molecular- and fossil-estimated dates of evolutionary events. Model predictions are supported by extensive data from mitochondrial and nuclear genomes. By accounting for the effects of body size and temperature on metabolic rate, this model explains heterogeneity in rates of nucleotide substitution in different genes, taxa, and thermal environments. This model also suggests that there is indeed a single molecular clock, as originally proposed by Zuckerkandl and Pauling [Zuckerkandl, E. & Pauling, L. (1965) in Evolving Genes and Proteins, eds. Bryson, V. & Vogel, H. J. (Academic, New York), pp. 97-166], but that it "ticks" at a constant substitution rate per unit of mass-specific metabolic energy rather than per unit of time. This model therefore links energy flux and genetic change. More generally, the model suggests that body size and temperature combine to control the overall rate of evolution through their effects on metabolism.

Animals↗

Prediction of dimethyl disulfide levels from biosolids using statistical modeling.

Two statistical models were used to predict the concentration of dimethyl disulfide (DMDS) released from biosolids produced by an advanced wastewater treatment plant (WWTP) located in Washington, DC, USA. The plant concentrates sludge from primary sedimentation basins in gravity thickeners (GT) and sludge from secondary sedimentation basins in dissolved air flotation (DAF) thickeners. The thickened sludge is pumped into blending tanks and then fed into centrifuges for dewatering. The dewatered sludge is then conditioned with lime before trucking out from the plant. DMDS, along with other volatile sulfur and nitrogen-containing chemicals, is known to contribute to biosolids odors. These models identified oxidation/reduction potential (ORP) values of a GT and DAF, the amount of sludge dewatered by centrifuges, and the blend ratio between GT thickened sludge and DAF thickened sludge in blending tanks as control variables. The accuracy of the developed regression models was evaluated by checking the adjusted R2 of the regression as well as the signs of coefficients associated with each variable. In general, both models explained observed DMDS levels in sludge headspace samples. The adjusted R2 value of the regression models 1 and 2 were 0.79 and 0.77, respectively. Coefficients for each regression model also had the correct sign. Using the developed models, plant operators can adjust the controllable variables to proactively decrease this odorant. Therefore, these models are a useful tool in biosolids management at WWTPs.

Air Pollutants↗

Long-term growth and water balance predictions for a mountain ash (Eucalyptus regnans) forest catchment subject to clear-felling and regeneration.

We used a physically based ecohydrological model to predict the water balance and growth responses of a mountain ash (Eucalyptus regnans F. Muell.) forest catchment to clear-felling and regeneration. The model, Topog-IRM, was applied to a 0.53 km(2) catchment for a 3-year pretreatment period, and a 20-year period following clear-felling and reseeding of 78% of the catchment area. Simulations were evaluated by comparing observed and predicted streamflows, rainfall interception and soil water values. The model faithfully simulated observed temporal patterns of overstory live stem carbon gain and produced a leaf area trajectory consistent with field observations. Cumulative throughfall was predicted within 1% of observations over an 18-year period. Over a 4-year period, predicted soil water storage in the upper 1.5 m of soil agreed well with field observations. There was fair correspondence between observed and predicted daily streamflows, and the model explained 76% of the variation in monthly flows. Over the 23-year simulation period, the model overpredicted cumulative streamflow by 6%. We argue that there is a useful role for physically based ecohydrological models in the management of mountain ash forest catchments that cannot be satisfied by simple empirical approaches.

Journal Article↗

The differential impact of academic self-regulatory methods on academic achievement among university students with and without learning disabilities.

Although research on academic self-regulation has proliferated in recent years, no studies have investigated the question of whether the perceived usefulness and the use of standard self-regulated learning strategies and compensation strategies provide a differential prediction of academic achievement for university students with and without learning disabilities (LD). We developed and tested a model explaining interrelationships among self-regulatory variables and grade point average (GPA) using structural equation modeling and multiple group analysis for students with LD (n = 53) and without LD (n = 421). Data were gathered using a new instrument, the Learning Strategies and Study Skills survey. The results of this study indicate that students with LD differed significantly from students without LD in the relationships between their motivation for and use of standard self-regulated learning strategies and compensation strategies, which in turn provided a differential explanation of academic achievement for students with and without LD. These paths of influence and idiosyncrasies of academic self-regulation among students with LD were interpreted in terms of social cognitive theory, metacognitive theory, and research conducted in the LD field.

Adaptation, Psychological↗

Determinants of volatile general anesthetic potency: a preliminary three-dimensional pharmacophore for halogenated anesthetics.

We investigated the molecular basis for the immobilizing activity of halogenated volatile anesthetics using comparative molecular field analysis. In vivo potency data (expressed as minimum alveolar concentrations) for 69 structurally diverse anesthetics were obtained from the literature. The drugs were randomly divided into a training set (n = 52) used to derive the activity model and a test set (n = 17) used to independently assess the model's predictive power. The anesthetic structures were aligned so as to maximize their similarity in molecular shape and electrostatic potential to the most potent drug in the group, CF2H-(CF2)3-CH2OH. The conformers and alignments of the anesthetics with maximum similarity (calculated as Carbo indices) were retained and used to derive the comparative molecular field analysis models. The final model explained 94.2% of the variance in the observed activities of the training set compounds. The model showed good predictive capability for both the training set (cross-validated r2 = 0.705) and randomly excluded test set anesthetics (r2 = 0.837). Three-dimensional pharmacophoric maps were derived to identify the spatial distribution of key areas where steric and electrostatic interactions are important in determining immobilizing activity of the halogenated drugs and were compared with our previously published maps obtained for nonhalogenated volatile anesthetics.

Anesthetics, General↗

Modelling the influence of fat-free mass and physical activity on the decline in maximal oxygen uptake with age in older humans.

The purpose of this study was to use an allometric model (maximal oxygen uptake (VO2,max) = FFMbeta1 x PAbeta2 x exp(beta0 + beta3 age + beta4 sex) x epsilon) to determine the influence of fat-free mass (FFM), physical activity (PA), sex and age on VO2,max in older men (n = 152) and women (n = 146) aged 55-86 years. VO2,max was measured during a fatigue-limited treadmill test, FFM was determined from skinfold thickness and physical activity by the Minnesota Leisure Time Physical Activity questionnaire. The model was linearised by taking the natural logarithm of VO2,max, FFM and physical activity. Variables were selected using multiple linear regression (P < 0.05). The sex variable was not significant (P = 0.062). The model explained 72.1% of the variance in VO2,max. Significant individual coefficients were incorporated into the model yielding the following expression: VO2,max = FFM0.971 x PA0.026 x exp(-2.48-0.015age). Therefore, FFM and physical activity were significant factors contributing to the changes in VO2,max with age. In addition, controlling for FFM and physical activity abolished sex differences in VO2,max. The rate of decline in VO2,max (after accounting for FFM and physical activity) with age, was approximately 15% per decade.

Aged↗

Global and specific relational models in the experience of social interactions.

Two studies demonstrated that global and relationship-specific models of self and other are correlated but not redundant constructs. Relationship-specific models were operationalized in terms of significant role relationships (Study 1) and salient relationships (i.e., frequent interactions; Study 2). Longitudinal analyses (Study 1) suggested that specific models generalized to global ones over time and that global models had a small but significant effect in shaping specific models over time. Through an event-sampling method, Study 2 assessed the quality and intimacy of daily interactions over a 7-day period. In hierarchical linear modeling analyses, both global and specific relational models explained the experience of daily interactions within relationships. This research highlighted that relational or attachment models can be considered global and specific representational structures, reflecting relational and individual differences.

Adolescent↗

[Interaction of rubomycin and its aglycone with DNA studied by fluorescent methods].

The fluorescent characteristics of rubomycin as dependent on the environmental conditions (different solvents, acidity of the medium, ionic strength) were studied. A model explaining suppression of the rubomycin fluorescence on the antibiotic interaction with DNA is described. The model confirmed intercalation and preferable binding with purines as compared to pyrimidines. The constants of rubomycin and aglycone interaction with DNA were determined. The use of the antibiotic concentrations less than 10(-6) M allowed the determination of a higher constant characterizing "strong binding". The nonlinearity of the curve of DNA titration with the antibiotic plotted on the Scatchard coordinates indicates the heterogeneity of the binding sites. The constant of the aglycone binding to DNA was approximately 2 orders lower at the same number of the binding sites in one molecule. The decrease in the constant of rubomycin interaction with DNA of an increased ionic strength and the low constant of the aglycone interaction with DNA as compared to that of the antibiotic itself confirmed the suggestion that there formed a bond between the amino sugar and the phosphate groups.

Animals↗

[Kinetics of breast neoplasms].

Breast cancer is a disease moderately responsive to chemotherapy. While its curability is inversely related to the tumor burden, a relevant number of patients still progress to metastatic disease even after adjuvant chemotherapy. Also, high-dose chemotherapy appears promising, but can not yet be considered ultimately curative of breast cancer. Different variables, biological, kinetic and treatment-related, account for the clinical behaviour of this disease. In order to improve its curability, they will all need to be taken into account in planning future treatment strategies. One of the most effective ways to understand and predict the clinical behaviour of breast cancer is the development of appropriate mathematical models explaining its growth-patterns. Aim of this paper is to review the two fundamental models, the exponential and the Gompertzian. The exponential model is at the basis of the Skipper-Schabel and the Goldie-Coldman hypotheses, while the Norton-Simon hypothesis has been formulated from the gompertzian model. The latter appears to better fit the vast amount of clinical data which are presently available: from Bloom's analysis of untreated breast cancer patients, to the results of large clinical trials, to the data emerged from the recent meta-analysis. Characteristic of a gompertzian growth pattern is that exponential growth is matched by exponential retardation of growth. In 1943 Delbruck and Luria demonstrated that random mutations could account for the development of virus resistance in bacteria and were able to estimate the rate of mutation as a function of the growth rate of bacteria. Shortly after Law demonstrated that resistance to methotrexate in murine leukemia occurred similarly. The concept of combination chemotherapy actually derived from the idea that cancer cells could be resistant to chemotherapy even before exposure to it. Goldie and Coldman applied the Delbruck/Luria model to hypothesize the use of non cross-resistant alternating combination chemotherapy as a better way to eliminate the risk of resistance. They also suggested that many different drugs were to be used as soon as possible, when the tumor size is still small. Most of their predictions were based on the Skipper/Schabel model of the exponential growth of cancer and on its deriving log-kill model. A large amount of clinical data are now suggesting that the behaviour of breast cancer is best described by gompertzian growth: in particular, gompertzian growth is a tenable model of breast cancer growth for both the unperturbed and the perturbed (by treatment) states.(ABSTRACT TRUNCATED AT 400 WORDS)

Breast Neoplasms↗

Association between indoor residential contamination with methyl parathion and urinary para-nitrophenol.

Methyl parathion, a pesticide listed by the U.S. Environmental Protection Agency in Toxicity Category I (i.e., most toxic), is not licensed for indoor use, and human exposure has resulted in the deaths of infants and children. From January 1991 through November 1994, an unlicensed pesticide applicator sprayed the interior of more than 200 homes in Lorain County, Ohio, with methyl parathion. To measure the environmental contamination this spraying caused, we measured methyl parathion in residential samples (air filtration and surface wipe) collected from a subset of 64 homes. To measure human exposure, we collected urine samples from 142 people living in these homes and measured urinary levels of para-nitrophenol, a methyl parathion metabolite. We then used a generalized estimating equation to evaluate the association between residential contamination and human exposure. The model included the age of the resident, the number of days between pesticide application and sample collection, and air and surface-wipe methyl parathion concentrations. As expected, the air and surface-wipe concentrations each had a significant inverse relationship with the number of days between application and sample collection. The model explained 65.7% of the variation in urinary para-nitrophenol concentrations. The form of this model could be used to estimate urine p-nitrophenol in residents exposed to methyl parathion in situations where urine specimens are not available. We recommend site-specific validation of this model.

Adolescent↗