Testing for linearity

linearitytesting

Threshold autoregression with a near unit root

unit root;autoregressive models

Statistical Models of Treatment Effects in Chronic Hepatitis B and C

This thesis regards treatment effects in patients with chronic hepatitis B and C, and focuses on the tools that are used to analyse these effects. In this introduction the clinical background of hepatitis B and C along with the current treatment options are described. Clinical questions arisen from the effects of treatment are stated and the current state of art of statistical models to study these effects is provided

The grid bootstrap and the autoregressive model

bootstrap;autoregressive models

Factors associated with ethnical disparity in overall survival for patients with hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is an important cause of cancer-related death worldwide. Ethnical disparity in overall survival has been demonstrated for HCC patients in the United States (U.S.). We aimed to evaluate the contributors to this survival disparity. The SEER database was used to identify HCC patients from 2004 to 2012. Kaplan-Meier curves and Cox proportional hazard models were used to evaluate overall survival by ethnicity and the contributors to ethnical survival disparity. A total of 33 062 patients were included: 15 986 Non-Hispanic Whites, 6535 Hispanic Whites, 4842 African Americans, and 5699 Asians. Compared to Non-Hispanic Whites, African Americans had worse survival (HR, 1.18; 95%CI, 1.14-1.23), while Asians had a better survival (HR, 0.85; 95%CI, 0.82-0.89), and Hispanic Whites had a similar survival (HR, 1.01; 95%CI, 0.97-1.05). Multivariate Cox analysis identified that tumor presentation- and treatment-related factors significantly contributed to the ethnical survival disparity. Especially, tumor size was the most important contributor (HR, 1.11; 95%CI, 1.07-1.16). There is no ethnical survival disparity in patients undergoing liver transplantation and sub-analysis of patients within the Milan criteria for liver transplantation demonstrated no significant survival disparity between African Americans and non-Hispanic Whites in transplantation adjustment analysis (HR, 1.23; 95%CI, 1.11-1.35 in non-adjustment analysis to HR, 1.05; 95%CI, 0.95-1.15 after adjustment). Finally, no important contributor to the superior overall survival in Asians was identified. In conclusion, poor tumor presentation at diagnosis, limited benefit from resection and restricted utilization of liver transplantation are important contributors to poorer survival of African Americans with HCC

Bias and temperature dependence of the 0.7 conductance anomaly in Quantum Point Contacts

The 0.7 (2e^2/h) conductance anomaly is studied in strongly confined, etched GaAs/GaAlAs quantum point contacts, by measuring the differential conductance as a function of source-drain and gate bias as well as a function of temperature. We investigate in detail how, for a given gate voltage, the differential conductance depends on the finite bias voltage and find a so-called self-gating effect, which we correct for. The 0.7 anomaly at zero bias is found to evolve smoothly into a conductance plateau at 0.85 (2e^2/h) at finite bias. Varying the gate voltage the transition between the 1.0 and the 0.85 (2e^2/h) plateaus occurs for definite bias voltages, which defines a gate voltage dependent energy difference $\Delta$. This energy difference is compared with the activation temperature T_a extracted from the experimentally observed activated behavior of the 0.7 anomaly at low bias. We find \Delta = k_B T_a which lends support to the idea that the conductance anomaly is due to transmission through two conduction channels, of which the one with its subband edge \Delta below the chemical potential becomes thermally depopulated as the temperature is increased.Comment: 9 pages (RevTex) with 9 figures (some in low resolution

Transition to turbulence and effect of initial conditions on three-dimensional compressible mixing in planar blast-wave-driven systems

Perturbations on an interface driven by a strong blast wave grow in time due to a combination of Rayleigh–Taylor, Richtmyer–Meshkov, and decompression effects. In this paper, results from three-dimensional (3D) numerical simulations of such a system under drive conditions to be attainable on the National Ignition Facility [E. M. Campbell, Laser Part. Beams 9, 209 (1991)] are presented. Using the multiphysics, adaptive mesh refinement, higher order Godunov Eulerian hydrocode, Raptor [L. H. Howell and J. A. Greenough, J. Comput. Phys. 184, 53 (2003)], the late nonlinear instability evolution, including transition to turbulence, is considered for various multimode perturbation spectra. The 3D post-transition state differs from the 2D result, but the process of transition proceeds similarly in both 2D and 3D. The turbulent mixing transition results in a reduction in the growth rate of the mixing layer relative to its pretransition value and, in the case of the bubble front, relative to the 2D result. The post-transition spike front velocity is approximately the same in 2D and 3D. Implications for hydrodynamic mixing in core-collapse supernovae are discussed.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/87764/2/056317_1.pd

ITPA polymorphisms are associated with hematological side effects during antiviral therapy for chronic HCV infection

Background/Objective Genetic polymorphisms in the inosine triphosphatase (ITPA) gene have been associated with the protection from early ribavirin(RBV)-induced hemolytic anemia among patients with chronic hepatitis C virus (HCV) infection. The aim of the present study was to investigate the association between the functional ITPA variants and hematological side effects during antiviral therapy with pegylated interferon (PegIFN) and RBV. Patients and Methods This cohort study included all consecutive Caucasian patients treated for chronic HCV infection with PegIFN and RBV between 2000 and 2009 for whom a serum sample was available for genetic testing. The predicted inosine triphosphate pyrophosphatase (ITPase) activity was based on the genotypes of the SNPs rs1127354 and rs7270101. Decline in hemoglobin (Hb) during antiviral therapy, as well as dose reductions, blood transfusions and use of erythropoietin were assessed. Results In total, 213 patients were included. The predicted ITPase activity was normal among 152 (71%) patients; 61 (29%) patients had ITPase deficiency. By multivariable linear regression, RBV dose in mg per kilogram (Beta 0.09, 95%CI 0.04-0.13, p<0.001) and normal ITPase activity (Beta 0.89, 95%CI 0.64-1.14, p<0.001) were associated with more Hb decline at week 4 of treatment. Patients with normal ITPase activity underwent more dose adjustments of RBV than patients with ITPase deficiency (19(13%) vs 1(2%),p = 0.014) and received erythropoietin more frequently (12 (8%) vs 0 (0%),p = 0.024). Conclusion Genetic variants in the ITPA gene protected against RBV treatment-induced anemia among Caucasian patients with chronic HCV infection. Patients with normal ITPase activity underwent more dose reductions of RBV and received erythropoietin more frequently

Erythrocyte Inosine triphosphatase activity: A potential biomarker for adverse events during combination antiretroviral therapy for HIV

The purine analogues tenofovir and abacavir are precursors of potential substrates for the enzyme Inosine 5’-triphosphate pyrophosphohydrolase (ITPase). Here, we investigated the association of ITPase activity and ITPA genotype with the occurrence of adverse events (AEs) during combination antiretroviral therapy (cART) for human immunodeficiency virus (HIV) infection. In 393 adult HIV-seropositive patients, AEs were defined as events that led to stop of cART regimen. ITPase activity 4 mmol IMP/mmol Hb/hour was considered as normal. ITPA genotype was determined by testing two ITPA polymorphisms: c.94C>A (p. Pro32Thr, rs1127354) and c.124+21A>C (rs7270101). Logistic regression analysis determined odds ratios for developing AEs. In tenofovir-containing regimens decreased ITPase activity was associated with less AEs (p = 0.01) and longer regimen duration (p = 0.001). In contrast, in abacavir-containing regimens decreased ITPase activity was associated with more AEs (crude p = 0.02) and increased switching of medication due to AEs (p = 0.03). ITPA genotype wt/wt was significantly associated with an increase in the occurrence of AEs in tenofovir-containing regimens. Decreased ITPase activity seems to be protective against occurrence of AEs in tenofovir-containing cART, while it is associated with an increase in AEs in abacavir-containing regimens

Effective interaction between helical bio-molecules

The effective interaction between two parallel strands of helical bio-molecules, such as deoxyribose nucleic acids (DNA), is calculated using computer simulations of the "primitive" model of electrolytes. In particular we study a simple model for B-DNA incorporating explicitly its charge pattern as a double-helix structure. The effective force and the effective torque exerted onto the molecules depend on the central distance and on the relative orientation. The contributions of nonlinear screening by monovalent counterions to these forces and torques are analyzed and calculated for different salt concentrations. As a result, we find that the sign of the force depends sensitively on the relative orientation. For intermolecular distances smaller than $6\AA$ it can be both attractive and repulsive. Furthermore we report a nonmonotonic behaviour of the effective force for increasing salt concentration. Both features cannot be described within linear screening theories. For large distances, on the other hand, the results agree with linear screening theories provided the charge of the bio-molecules is suitably renormalized.Comment: 18 pages, 18 figures included in text, 100 bibliog