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PubMed2006

Stereo motion transparency processing implements an ecological smoothness constraint.

Transparent motion stimuli allow us to investigate how visual motion is processed in the presence of multiple sources of information. We used stereo random-dot kinematograms to determine how motion processing is affected by the difference in direction and depth of two overlapping motion components. Observers judged whether a noise dot display contained one or two directions of motion. For all disparity differences, performance did not change among angles greater than 60 degrees, but the ability to detect transparent motion fell dramatically as the direction difference decreased below 60 degrees. When a disparity difference was added between the two motion components, detection became easier. We compared these results to an ideal-observer model limited by stimulus uncertainty and low-level sources of internal noise. The resulting measure of efficiency--the ratio of human to model performance--reflects changes in how motion stimuli are being processed. A decrease of both the direction and disparity differences had the effect of decreasing efficiency. These results suggest that the mechanism processing transparent motion may implement a smoothness constraint that tends to combine similar motions into a single percept.

Depth Perception↗

PubMed2006

Limitations of the rigid planar nonpolarizable models of water.

We analyzed the ability of variants of the SPC/E and TIP4P types of water models to describe the temperature dependence of their second virial coefficients, liquid-vapor phase envelopes, and corresponding coexistence vapor pressure. We complete the characterization of the two most promising models by testing their adequacy to predict the structure of the 13 known crystalline phases of ice by (Parrinello-Rahman) isothermal-isobaric Monte Carlo simulations. While these models perform well for the description of properties to which their force fields were fitted (density, heat of vaporization, structure at the level of pair correlations), their transferability to the entire phase diagram is unsatisfactory, i.e., none could significantly mitigate the shortcomings of the original models. In fact, the most appropriate alternative appears to be the TIP4P-EW model, i.e., the recent reparametrization of the original TIP4P water model. Model parametrizations aimed at improving the description of ice behavior fail even in the description of the liquid phase.

Journal Article↗

PubMed2005

Two-phase computational fluid dynamics assessment of bubble plume in air-diffuser destratification.

Hydrodynamic flow patterns and behavior induced by bubble plumes in a linearly stratified fluid are studied. To optimize an air-diffuser destratification system, we used computational fluid dynamics software to develop a two-phase (air-water) destratification model. The model enables us to simulate complicated stratification conditions with different densities and source strengths. We conducted laboratory experiments to verify the model in thermally stratified fresh water. The computational fluid dynamics model performs well when the plume number ranges from 30 to 600. We successfully explain various phenomena, including the hydrodynamic behavior of bubble plumes and turbulent three dimension flow patterns. Our approach provides a level of detail not possible with other one-dimensional plume models. Contrary to the findings of other researchers, our experiments and computational fluid dynamics simulation indicate that the energy conversion efficiency increases as plume number increases; moreover, the three flow types do not occur in the same plume number regimes defined in other research. The difference is apparently due to the effect of the bubble size.

Air Movements↗

PubMed2004

Growth patterns reflect response to antiretroviral therapy in HIV-positive infants: potential utility in resource-poor settings.

Laboratory monitoring of HIV-infected children is the current standard of care in the United States to guide the appropriate use of antiretroviral therapy (ART). Although ART is becoming a reality in some developing countries, laboratory monitoring of ART is costly, necessitating creative approaches to monitoring. As an initial step to guide monitoring of HIV progression in low resource settings, we assessed the utility of the physical examination to predict clinical progression of HIV. We conducted a retrospective cohort study of HIV-infected children using data from Pediatric AIDS Clinical Trials Group Protocol 300. We developed a clinical predictive model, and compared the utility of the clinical model to the change in HIV RNA viral load as diagnostic tests of ART failure. The clinical model incorporated treatment regimen, age, and height velocity: a three-level clinical predictive model provided likelihood ratios of 0.3, 3.9, and 14. For decline in RNA the likelihood ratios were 0.2 (> 1 log decline), 1.4, and 3.5 (> log increase). We developed a simple clinical predictive model that was able to predict clinical progression of HIV after initiation of new ART. The clinical model performed similarly to using changes in HIV RNA viral load. These data should be validated internationally and prospectively, because the test subjects were from a resource rich environment and growth patterns in undernourished children may be impacted differently by HIV and its treatment. The model was most pertinent to children 36 months of age or younger, and was conducted in children receiving monotherapy and dual therapy.

Anti-HIV Agents↗

PubMed1996

Evaluation of various sets of acoustic cues for the perception of prevocalic stop consonants. II. Modeling and evaluation.

The purpose of the study presented in this paper and the accompanying paper [Smits et al., J. Acoust. Soc. Am. 100, 3852-3864 (1996)] is to evaluate whether detailed or gross time-frequency structures are more relevant for the perception of prevocalic stop consonants. To this end, first a perception experiment was carried out with "burst-spliced" stop-vowel utterances. This experiment is described in the accompanying paper. The present paper describes the second part of the investigation, i.e., the simulation of the behavior of the listeners in the perception experiment. First, a number of detailed and gross cues are measured on the stimuli. Next, these cues are mapped onto the observed perceptual data using a formal model of human classification behavior. The results show that in all cases the detailed cues, such as formant transitions, give a better account of the perceptual data than the gross cues, such as the global spectral tilt and its initial change. The best-performing models are interpreted in terms of the acoustic boundaries which are associated with the perceived linguistic contrast. These boundaries are highly interpretable linear functions of five or six acoustic cues, which give a quantitative description of the often-discussed "trade-off" relation between the various cues for perception of place of articulation in stop consonants.

Humans↗

PubMed2026

A weakly supervised deep learning-based recurrence prediction and risk stratification of lung adenocarcinoma from pathology whole-slide images.

BACKGROUND: Accurate prediction of postoperative recurrence in lung adenocarcinoma (LUAD) is essential for guiding clinical decision-making and improving patient outcomes. Although various predictive models have been developed, most rely on complex genomic analyses and high-dimensional clinical data. The complexity of these approaches substantially limits their feasibility for routine clinical use. To address this clinical challenge, this study aims to predict postoperative recurrence using routinely available hematoxylin and eosin (H&E)-stained images and characterize the associated biological features. METHODS: A total of 329 patients who underwent curative resection at the First Affiliated Hospital of Wenzhou Medical University (FHWMU) were retrospectively enrolled and randomly assigned to training and internal validation cohorts in a 7:3 ratio. An independent external validation cohort comprising 70 patients from the Clinical Proteomic Tumor Analysis Consortium (CPTAC) was included. Three patch-level feature extractors (Inception_V3, ResNet18, and DenseNet121) were evaluated within a weakly supervised multiple-instance learning (MIL) framework incorporating automated region-of-interest (ROI) detection on segmented whole-slide images (WSIs). Model performance was assessed using the area under the receiver operating characteristic curve (AUC), Kaplan-Meier (KM) survival analysis, and multivariable Cox proportional hazards regression. Transcriptomic profiling and gene set enrichment analysis (GSEA) were conducted to investigate biological differences between risk groups. RESULTS: The model achieved AUCs of 0.923 in the training cohort, 0.891 in the internal validation cohort, and 0.847 in the external validation cohort. The model effectively stratified patients into high- and low-risk groups with significantly different recurrence-free survival (RFS) across all cohorts (all P < 0.001) and retained prognostic value within AJCC stages I-III. Transcriptomic analyses revealed consistent enrichment of cell cycle-related pathways and neutrophil extracellular trap (NET) formation in high-risk patients across both institutional and CPTAC cohorts, aligning with distinct biological profiles of the model-derived risk stratification. CONCLUSIONS: This weakly supervised deep learning framework enables accurate and externally validated prediction of postoperative recurrence in LUAD using routinely available histopathological images, and integration of histopathological features with molecular analyses enhances biological interpretability. This work provides a clinically accessible and cost-effective tool for postoperative risk assessment in LUAD patients.

Humans↗

PubMed2006

Achromatic half-wave plate for submillimeter instruments in cosmic microwave background astronomy: experimental characterization.

An achromatic half-wave plate (HWP) to be used in millimeter cosmic microwave background (CMB) polarization experiments has been designed, manufactured, and tested. The design is based on the 5-plates Pancharatnam recipe and it works in the frequency range 85-185 GHz. A model has been used to predict the transmission, reflection, absorption, and phase shift as a function of frequency. The HWP has been tested by using coherent radiation from a back-wave oscillator to investigate its modulation efficiency and with incoherent radiation from a polarizing Fourier transform spectrometer (FTS) to explore its frequency behavior. The FTS measurements have been fitted with an optical performance model which is in excellent agreement with the data. A detailed analysis of the data also allows a precise determination of the HWP fast and slow axes in the frequency band of operation. A list of the HWP performance characteristics is reported including estimates of its cross polarization.

Journal Article↗

PubMed1996

Key influences on the professional socialisation and practice of students undertaking different pre-registration nurse education programmes in the United Kingdom.

A principal aim of pre-registration nurse education programmes is the process of effective socialisation of students into the professional role. Key influences on the professional socialisation and practice of students undertaking such programmes were explored using a semi-structured interview approach (N = 99). This work formed part of a major comparative study of outcomes of pre-registration nurse education programmes in the United Kingdom. Analysis revealed differences between the programmes regarding positive influences of the respective courses; therapeutic influences of the practice environment; modelling performance on exemplars of high quality practice; and the identification of teachers within the educational setting and nurses in practice as key persons. This study has confirmed that the positive influence of the education programmes and the practice environment as well as high quality role models from both education and practice establishments are critical to the professional socialisation of student nurses.

Curriculum↗

PubMed1996

Cortical dynamic tuning: the role of intrinsic connections, as revealed by modeling.

A current challenge in computational neuroscience is to elucidate the role of cortical circuitry in information processing and in generating motor output. Our understanding of the functional significance of specifically organized feedback connections is progressing rapidly as researchers establish the equivalence of theoretical models to biological neural circuits. Modeling studies of different neural structures, along with quantitative comparisons of model performance to biological data, have recently helped to identify the basic features of synaptic connectivity that may play important roles in cortical operations.

Animals↗

PubMed1998

Risk factors for treatment-related death in elderly patients with aggressive non-Hodgkin's lymphoma: results of a multivariate analysis.

PURPOSE: It has been suggested that age is associated with chemotherapy-related death in patients with non-Hodgkin's lymphoma (NHL) treated with doxorubicin-containing chemotherapy. The purpose of this study was to evaluate the relative influence of increasing age and other clinical parameters on the occurrence of treatment-related death in elderly patients with intermediate- or high-grade NHL treated with cyclophosphamide, doxorubicin, vincristine, and prednisone (CHOP) chemotherapy. METHODS: A retrospective study of patients 60 years of age or older with intermediate- or high-grade NHL treated with CHOP chemotherapy in a single cancer center. The following variables were recorded: age (60 to 69, 70 to 79, and 80 to 94 years), histology (Working Formulation [WF] D, E, F, G, and H), Ann Arbor stage, B symptoms, extranodal involvement, bulky disease (> 7 cm), performance status (Eastern Cooperative Oncology Group [ECOG] scale), International Prognostic Index (IPI score), serum lactate dehydrogenase (LDH) level and doxorubicin relative dose-intensity (RDI). The relationship between these features and treatment-related death was assessed in univariate and multivariate logistic regression analysis. RESULTS: From 1982 to 1991, 267 consecutive patients were treated. Median age was 70 years (range, 60 to 94 years). There were 35 toxic deaths. Sixty-three percent of the deaths occurred after the first cycle. Infection accounted for 82% of the toxic deaths. In the univariate analysis, the features associated with an increased risk of toxic death were ECOG performance status 2 to 4 (relative risk [RR], 7.82), B symptoms (RR, 3.38), diffuse large-cell histology (RR, 3.06), bulky disease (RR, 2.58), serum levels of LDH (RR, 2.53), and IPI score (RR, 2.46). The age groups did not show significance. In the regression model, performance status 2 to 4 was the only independent predictor of treatment-related death (RR, 3.52; 95% confidence interval [CI], 2.98 to 4.06). CONCLUSION: Our results show that in elderly patients with NHL treated with doxorubicin-based chemotherapy the risk for treatment-related death is associated with poor performance status rather than with increasing chronologic age.

Age Factors↗

PubMed2005

Simulation study of the contribution of oligomer/oligomer binding to capsid assembly kinetics.

The process by which hundreds of identical capsid proteins self-assemble into icosahedral structures is complex and poorly understood. Establishing constraints on the assembly pathways is crucial to building reliable theoretical models. For example, it is currently an open question to what degree overall assembly kinetics are dominated by one or a few most efficient pathways versus the enormous number theoretically possible. The importance of this question, however, is often overlooked due to the difficulties of addressing it in either theoretical or experimental practice. We apply a computer model based on a discrete-event simulation method to evaluate the contributions of nondominant pathways to overall assembly kinetics. This is accomplished by comparing two possible assembly models: one allowing growth to proceed only by the accretion of individual assembly subunits and the other allowing the binding of sterically compatible assembly intermediates any sizes. Simulations show that the two models perform almost identically under low binding rate conditions, where growth is strongly nucleation-limited, but sharply diverge under conditions of higher association rates or coat protein concentrations. The results suggest the importance of identifying the actual binding pattern if one is to build reliable models of capsid assembly or other complex self-assembly processes.

Biophysics↗

PubMed1996

A New Neural Model for Invariant Pattern Recognition.

For most of the pattern recognition applications, it is often required to correctly recognize patterns even if they have variations in position, rotation, and/or scale. In this paper, to achieve the goal of invariant pattern recognition we propose a new neural model which consists of a cascade connection of four two-dimensional layers. The first three layers of the neural model perform the processes of position normalization, rotation normalization and feature extraction, respectively. The last layer is responsible for both recognition job and scale normalization by specially designing its output neurons to possess a scale invariant property. Finally, simulation results are given to demonstrate that the proposed model is simple and effective for invariant pattern recognition. Copyright 1996 Elsevier Science Ltd

Journal Article↗

PubMed2003

Centric-minded templates for self-motion perception.

We propose a two-layer neuromorphic architecture by which motion field pattern, generated during locomotion, are processed by template detectors specialized for gaze-directed self-motion (expansion and rotation). The templates provide a gaze-centered computation for analyzing motion field in terms of how it is related to the fixation point (i.e., the fovea). The analysis is performed by relating the vectorial components of the act of motion to variations (i.e., asymmetries) of the local structure of the motion field. Notwithstanding their limited extension in space, such centric-minded templates extract, as a whole, global information from the input flow field, being sensitive to different local instances of the same global property of the vector field with respect to the fixation point; a quantitative analysis, in terms of vectorial operators, evidences this property as tuning curves for heading direction. Model performances, evaluated in several situations characterized by conditions of absence and presence of pursuit eye movements, validate the approach. We observe that the gaze-centered model provides an explicit testable hypothesis that can guide further explorations of visual motion processing in extrastriate cortical areas.

Computational Biology↗

PubMed2005

Use of risk-adjusted change in health status to assess the performance of integrated service networks in the Veterans Health Administration.

OBJECTIVE: Health outcome assessments have become an expectation of regulatory and accreditation agencies. We examined whether a clinically credible risk adjustment methodology for the outcome of change in health status can be developed for performance assessment of integrated service networks. STUDY DESIGN: Longitudinal study. SETTING: Outpatient. STUDY PARTICIPANTS: Thirty-one thousand eight hundred and twenty-three patients from 22 Veterans Health Administration (VHA) integrated service networks were followed for 18 months. MAIN MEASURE: The physical (PCS) and mental (MCS) component scales from the Veterans Rand 36-items Health Survey (VR-36) and mortality. The outcomes were decline in PCS (decline in PCS scores greater than -6.5 points or death) and MCS (decline in MCS scores greater than -7.9 points). RESULTS: Four thousand three hundred and twenty-eight (13.6%) patients showed a decline in PCS scores greater than -6.5 points, 4322 (13.5%) had a decline in MCS scores by more than -7.9 points, and 1737 died (5.5%). Multivariate logistic regression models were used to adjust for case-mix. The models performed reasonably well in cross-validated tests of discrimination (c-statistics = 0.72 and 0.68 for decline in PCS and MCS, respectively) and calibration. The resulting risk-adjusted rates of decline in PCS and MCS and ranks of the networks differed considerably from unadjusted ratings. CONCLUSION: It is feasible to develop clinically credible risk adjustment models for the outcomes of decline in PCS and MCS. Without adequate controls for case-mix, we could not determine whether poor patient outcomes reflect poor performance, sicker patients, or other factors. This methodology can help to measure and report the performance of health care systems.

Aged↗

PubMed2001

Protein family and fold occurrence in genomes: power-law behaviour and evolutionary model.

Global surveys of genomes measure the usage of essential molecular parts, defined here as protein families, superfamilies or folds, in different organisms. Based on surveys of the first 20 completely sequenced genomes, we observe that the occurrence of these parts follows a power-law distribution. That is, the number of distinct parts (F) with a given genomic occurrence (V) decays as F=aV(-b), with a few parts occurring many times and most occurring infrequently. For a given organism, the distributions of families, superfamilies and folds are nearly identical, and this is reflected in the size of the decay exponent b. Moreover, the exponent varies between different organisms, with those of smaller genomes displaying a steeper decay (i.e. larger b). Clearly, the power law indicates a preference to duplicate genes that encode for molecular parts which are already common. Here, we present a minimal, but biologically meaningful model that accurately describes the observed power law. Although the model performs equally well for all three protein classes, we focus on the occurrence of folds in preference to families and superfamilies. This is because folds are comparatively insensitive to the effects of point mutations that can cause a family member to diverge beyond detectable similarity. In the model, genomes evolve through two basic operations: (i) duplication of existing genes; (ii) net flow of new genes. The flow term is closely related to the exponent b and can accommodate considerable gene loss; however, we demonstrate that the observed data is reproduced best with a net inflow, i.e. with more gene gain than loss. Moreover, we show that prokaryotes have much higher rates of gene acquisition than eukaryotes, probably reflecting lateral transfer. A further natural outcome from our model is an estimation of the fold composition of the initial genome, which potentially relates to the common ancestor for modern organisms. Supplementary material pertaining to this work is available from www.partslist.org/powerlaw.

Animals↗

PubMed1995

Molecular and physiological effects of overexpressing striated muscle beta-tropomyosin in the adult murine heart.

Tropomyosins comprise a family of actin-binding proteins that are central to the control of calcium-regulated striated muscle contraction. To understand the functional role of tropomyosin isoform differences in cardiac muscle, we generated transgenic mice that overexpress striated muscle-specific beta-tropomyosin in the adult heart. Nine transgenic lines show a 150-fold increase in beta-tropomyosin mRNA expression in the heart, along with a 34-fold increase in the associated protein. This increase in beta-tropomyosin message and protein causes a concomitant decrease in the level of alpha-tropomyosin transcripts and their associated protein. There is a preferential formation of the alpha beta-heterodimer in the transgenic mouse myofibrils, and there are no detectable alterations in the expression of other contractile protein genes, including the endogenous beta-tropomyosin isoform. When expression from the beta-tropomyosin transgene is terminated, alpha-tropomyosin expression returns to normal levels. No structural changes were observed in these transgenic hearts nor in the associated sarcomeres. Interestingly, physiological analyses of these hearts using a work-performing model reveal a significant effect on diastolic function. As such, this study demonstrates that a coordinate regulatory mechanism exists between alpha- and beta-tropomyosin gene expression in the murine heart, which results in a functional correlation between alpha- and beta-tropomyosin isoform content and cardiac performance.

Animals↗

PubMed1993

A model of sporting performance constructed from autonomic nervous system responses.

Four autonomic nervous system (ANS) variables: skin potential and resistance, skin blood flow and temperature - plus instantaneous heart rate and respiratory frequency - were simultaneously recorded during sporting competitions. The performances of 15 marksmen and 7 archers were analysed by comparing the variations in the six parameters during a concentration phase prior to shooting and during the shooting (or active) phase proper. The results of the performances distinguished two groups of sportsmen: firstly, the best shots and secondly, the worst shots. Comparison of the autonomic responses between the groups showed statistically significant correlations among the ANS variables. This made possible a relationship between performance characteristics and a percepto-effector factor to be defined. More precisely, this factor was defined as the number of correlations of the measured variables in the two phases, concentration and shooting. A positive relationship was demonstrated--the higher the factor, the better the performance. In addition, the stability of the factor was greater within the best marksmen and archers group. A model of the temporal change of the percepto-effector factor in both groups was given in three dimensions. This modelling of performance characteristics gave a visual indication of the differences between best/worst performances.

Autonomic Nervous System↗

PubMed2005

Design and analysis of controllers for a double inverted pendulum.

A physical control problem is studied with the Hinfinity, and the micro methodology. The issues of modeling, uncertainty modeling, performance specification, controller design, and laboratory implementation are discussed. The laboratory experiment is a double inverted pendulum placed on a cart. The limitations in the system with respect to performance are the limitation in the control signal and the limitation of the movement of the cart. It is shown how these performance limitations will effect the design of Hinfinity and micro controllers for the system.

Algorithms↗