Monotone Constrained Tensor-product B-spline with application to screening studies

When different markers are responsive to different aspects of a disease, combination of multiple markers could provide a better screening test for early detection. It is also resonable to assume that the risk of disease changes smoothly as the biomarker values change and the change in risk is monotone with respect to each biomarker. In this paper, we propose a boundary constrained tensor-product B-spline method to estimate the risk of disease by maximizing a penalized likelihood. To choose the optimal amount of smoothing, two scores are proposed which are extensions of the GCV score (O'Sullivan et al. (1986)) and the GACV score (Ziang and Wahba (1996)) to incorporate linear constraints. Simulation studies are carried out to investigate the performance of the proposed estimator and the selection scores. In addidtion, sensitivities and specificities based ona pproximate leave-one-out estimates are proposed to generate more realisitc ROC curves. Data from a pancreatic cancer study is used for illustration.

A BAYESIAN HIERARCHICAL MODEL FOR CONSTRAINED DISTRIBUTED LAG FUNCTIONS: ESTIMATING THE TIME COURSE OF HOSPITALIZATION ASSOCIATED WITH AIR POLLUTION EXPOSURE

Numerous time series studies have provided strong evidence of an association between increased levels of ambient air pollution and increased levels of hospital admissions, typically at 0, 1, or 2 days after an air pollution episode. An important research aim is to extend existing statistical models so that a more detailed understanding of the time course of hospitalization after exposure to air pollution can be obtained. Information about this time course, combined with prior knowledge about biological mechanisms, could provide the basis for hypotheses concerning the mechanism by which air pollution causes disease. Previous studies have identified two important methodological questions: (1) How can we estimate the shape of the distributed lag between increased air pollution exposure and increased mortality or morbidity? and (2) How should we estimate the cumulative population health risk from short-term exposure to air pollution? Distributed lag models are appropriate tools for estimating air pollution health effects that may be spread over several days. However, estimation for distributed lag models in air pollution and health applications is hampered by the substantial noise in the data and the inherently weak signal that is the target of investigation. We introduce an hierarchical Bayesian distributed lag model that incorporates prior information about the time course of pollution effects and combines information across multiple locations. The model has a connection to penalized spline smoothing using a special type of penalty matrix. We apply the model to estimating the distributed lag between exposure to particulate matter air pollution and hospitalization for cardiovascular and respiratory disease using data from a large United States air pollution and hospitalization database of Medicare enrollees in 94 counties covering the years 1999-2002.

Enumerating constrained elementary flux vectors of metabolic networks

The concept of elementary vector is generalised to the case where the steady-state space of the metabolic network is not a flux cone but is a general polyhedron due to further inhomogeneous constraints on the flows through some of the reactions. On one hand, this allows to selectively enumerate elementary modes which satisfy certain optimality criteria and this can yield a large computational gain compared with full enumeration. On the other hand, in contrast to the single optimum found by executing a linear program, this enables a comprehensive description of the set of alternate optima often encountered in flux balance analysis. The concepts are illustrated on a metabolic network model of human cardiac mitochondria.

Discordant responses to potent antiretroviral treatment in previously naive HIV-1-infected adults initiating treatment in resource-constrained countries: the antiretroviral therapy in low-income countries (ART-LINC) collaboration

OBJECTIVES: To assess the frequency of and risk factors for discordant responses at 6 months on highly active antiretroviral therapy (HAART) in previously treatment-naive HIV patients from resource-limited countries. METHODS: The Antiretroviral Therapy in Low-Income Countries Collaboration is a network of clinics providing care and treatment to HIV-infected patients in Africa, Latin America, and Asia. Patients who initiated therapy between 1996 and 2004, were aged 16 years or older, and had a baseline CD4 cell count were included in this analysis. Responses were defined based on plasma viral load (PVL) and CD4 cell count at 6 months as complete virologic and immunologic (VR(+)IR(+)), virologic only (VR(+)IR(-)), immunologic only (VR(-)IR(+)), and nonresponse (VR(-)IR(-)). Multinomial logistic regression was used to assess the association between therapy responses and clinical and demographic variables. RESULTS: Of the 3111 patients eligible for analysis, 1914 had available information at 6 months of therapy: 1074 (56.1%) were VR(+)IR(+), 364 (19.0%) were VR(+)IR(-), 283 (14.8%) were (VR(-)IR(+)), and 193 (10.1%) were VR(-)IR(-). OF THE 3111 patients eligible for analysis, 1914 had available information at 6 months of therapy: 1074 (56.1%) were VRIR, 364 (19.0%) were VRIR, 283 (14.8%) were (VRIR), and 193 (10.1%) were VRIR. Compared with complete responders, virologic-only responders were older, had a higher baseline CD4 cell count, had a lower baseline PVL, and were more likely to have received a nonstandard HAART regimen; immunologic-only responders were younger, had a lower baseline CD4 cell count, had a higher baseline PVL, and were more likely to have received a protease inhibitor-based regimen. CONCLUSIONS: The frequency of and risk factors for discordant responses were comparable to those observed in developed countries. Longer follow-up is needed to assess the long-term impact of discordant responses on mortality in these resource-limited settings.

New sst4/5-selective somatostatin peptidomimetics based on a constrained tryptophan scaffold

The synthesis and biological evaluation of four peptidomimetic analogs of somatostatin based on a constrained Trp residue, 3-amino-indolo[2,3-c]azepin-2-one (Aia), are reported. It is shown that dipeptidomimetics with a D-Aia-Lys sequence, functionalized with N- and C-terminal aromatic substituents, display a good selectivity for both sst4 and sst5. This study allowed us to identify a new highly potent sst5 agonist with good selectivity over the other receptors, except versus sst4.

Unifying energy minimization and mutual information maximization for robust 2D/3D registration of X-ray and CT images

Similarity measure is one of the main factors that affect the accuracy of intensity-based 2D/3D registration of X-ray fluoroscopy to CT images. Information theory has been used to derive similarity measure for image registration leading to the introduction of mutual information, an accurate similarity measure for multi-modal and mono-modal image registration tasks. However, it is known that the standard mutual information measure only takes intensity values into account without considering spatial information and its robustness is questionable. Previous attempt to incorporate spatial information into mutual information either requires computing the entropy of higher dimensional probability distributions, or is not robust to outliers. In this paper, we show how to incorporate spatial information into mutual information without suffering from these problems. Using a variational approximation derived from the Kullback-Leibler bound, spatial information can be effectively incorporated into mutual information via energy minimization. The resulting similarity measure has a least-squares form and can be effectively minimized by a multi-resolution Levenberg-Marquardt optimizer. Experimental results are presented on datasets of two applications: (a) intra-operative patient pose estimation from a few (e.g. 2) calibrated fluoroscopic images, and (b) post-operative cup alignment estimation from single X-ray radiograph with gonadal shielding.

Vibro-acoustical analysis and design of a multiple-layer constrained viscoelastic damping structure

The goal of this research is to provide a framework for vibro-acoustical analysis and design of a multiple-layer constrained damping structure. The existing research on damping and viscoelastic damping mechanism is limited to the following four mainstream approaches: modeling techniques of damping treatments/materials; control through the electrical-mechanical effect using the piezoelectric layer; optimization by adjusting the parameters of the structure to meet the design requirements; and identification of the damping material’s properties through the response of the structure. This research proposes a systematic design methodology for the multiple-layer constrained damping beam giving consideration to vibro-acoustics. A modeling technique to study the vibro-acoustics of multiple-layered viscoelastic laminated beams using the Biot damping model is presented using a hybrid numerical model. The boundary element method (BEM) is used to model the acoustical cavity whereas the Finite Element Method (FEM) is the basis for vibration analysis of the multiple-layered beam structure. Through the proposed procedure, the analysis can easily be extended to other complex geometry with arbitrary boundary conditions. The nonlinear behavior of viscoelastic damping materials is represented by the Biot damping model taking into account the effects of frequency, temperature and different damping materials for individual layers. A curve-fitting procedure used to obtain the Biot constants for different damping materials for each temperature is explained. The results from structural vibration analysis for selected beams agree with published closed-form results and results for the radiated noise for a sample beam structure obtained using a commercial BEM software is compared with the acoustical results of the same beam with using the Biot damping model. The extension of the Biot damping model is demonstrated to study MDOF (Multiple Degrees of Freedom) dynamics equations of a discrete system in order to introduce different types of viscoelastic damping materials. The mechanical properties of viscoelastic damping materials such as shear modulus and loss factor change with respect to different ambient temperatures and frequencies. The application of multiple-layer treatment increases the damping characteristic of the structure significantly and thus helps to attenuate the vibration and noise for a broad range of frequency and temperature. The main contributions of this dissertation include the following three major tasks: 1) Study of the viscoelastic damping mechanism and the dynamics equation of a multilayer damped system incorporating the Biot damping model. 2) Building the Finite Element Method (FEM) model of the multiple-layer constrained viscoelastic damping beam and conducting the vibration analysis. 3) Extending the vibration problem to the Boundary Element Method (BEM) based acoustical problem and comparing the results with commercial simulation software.

Gender and the use of antiretroviral treatment in resource-constrained settings: findings from a multicenter collaboration

AIMS: To compare the gender distribution of HIV-infected adults receiving highly active antiretroviral treatment (HAART) in resource-constrained settings with estimates of the gender distribution of HIV infection; to describe the clinical characteristics of women and men receiving HAART. METHODS: The Antiretroviral Therapy in Lower-Income Countries, ART-LINC Collaboration is a network of clinics providing HAART in Africa, Latin America, and Asia. We compared UNAIDS data on the gender distribution of HIV infection with the proportions of women and men receiving HAART in the ART-LINC Collaboration. RESULTS: Twenty-nine centers in 13 countries participated. Among 33,164 individuals, 19,989 (60.3%) were women. Proportions of women receiving HAART in ART-LINC centers were similar to, or higher than, UNAIDS estimates of the proportions of HIV-infected women in all but two centers. There were fewer women receiving HAART than expected from UNAIDS data in one center in Uganda and one center in India. Taking into account heterogeneity across cohorts, women were younger than men, less likely to have advanced HIV infection, and more likely to be anemic at HAART initiation. CONCLUSIONS: Women in resource-constrained settings are not necessarily disadvantaged in their access to HAART. More attention needs to be paid to ensuring that HIV-infected men are seeking care and starting HAART.

A REGIONAL ASSESSMENT OF GROUNDWATER AVAILABILITY AS CONSTRAINED BY LOCAL HYDROGEOLOGY AND ENVIRONMENTAL LIMITS TO STREAMFLOW DEPLETION

Groundwater pumping from aquifers in hydraulic connection with nearby streams is known to cause adverse impacts by decreasing flows to levels below those necessary to maintain aquatic ecosystems. The recent passage of the Great Lakes--St. Lawrence River Basin Water Resources Compact has brought attention to this issue in the Great Lakes region. In particular, the legislation requires the Great Lakes states to enact measures for limiting water withdrawals that can cause adverse ecosystem impacts. This study explores how both hydrogeologic and environmental flow limitations constrain groundwater availability in the Great Lakes Basin. A methodology for calculating maximum allowable pumping rates is presented. Groundwater availability across the basin is shown to be constrained by a combination of hydrogeologic yield and environmental flow limitations varying over both local and regional scales. The results are sensitive to factors such as pumping time and streamflow depletion limits as well as streambed conductance. Understanding how these restrictions constrain groundwater usage and which hydrogeologic characteristics and spatial variables have the most influence on potential streamflow depletions has important water resources policy and management implications.

Compliance of the L5-S1 spinal unit: a comparative study between an unconstrained and a partially constrained system

A comparison between an unconstrained and a partially constrained system for in vitro biomechanical testing of the L5-S1 spinal unit was conducted. The objective was to compare the compliance and the coupling of the L5-S1 unit measured with an unconstrained and a partially constrained test for the three major physiological motions of the human spine. Very few studies have compared unconstrained and partially constrained testing systems using the same cadaveric functional spinal units (FSUs). Seven human L5-S1 units were therefore tested on both a pneumatic, unconstrained, and a servohydraulic, partially constrained system. Each FSU was tested along three motions: flexion-extension (FE), lateral bending (LB) and axial rotation (AR). The obtained kinematics on both systems is not equivalent, except for the FE case, where both motions are similar. The directions of coupled motions were similar for both tests, but their magnitudes were smaller in the partially constrained configuration. The use of a partially constrained system to characterize LB and AR of the lumbosacral FSU decreased significantly the measured stiffness of the segment. The unconstrained system is today's "gold standard" for the characterization of FSUs. The selected partially constrained method seems also to be an appropriate way to characterize FSUs for specific applications. Care should be taken using the latter method when the coupled motions are important.