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Missingness mechanism is in theory unverifiable based only on observed data. If there is a suspicion of missing not at random, researchers often perform a sensitivity analysis to evaluate the impact of various missingness mechanisms. In general, sensitivity analysis approaches require a full specification of the relationship between missing values and missingness probabilities. Such relationship can be specified based on a selection model, a pattern-mixture model or a shared parameter model. Under the selection modeling framework, we propose a sensitivity analysis approach using a nonparametric multiple imputation strategy. The proposed approach only requires specifying the correlation coefficient between missing values and selection (response) probabilities under a selection model. The correlation coefficient is a standardized measure and can be used as a natural sensitivity analysis parameter. The sensitivity analysis involves multiple imputations of missing values, yet the sensitivity parameter is only used to select imputing/donor sets. Hence, the proposed approach might be more robust against misspecifications of the sensitivity parameter. For illustration, the proposed approach is applied to incomplete measurements of level of preoperative Hemoglobin A1c, for patients who had high-grade carotid artery stenosisa and were scheduled for surgery. A simulation study is conducted to evaluate the performance of the proposed approach.

Continuous-time Markov models are commonly used to analyze longitudinal transitions between multiple disease states in panel data, where participants' disease states are only observed at multiple time points, and the exact state paths between observations are unknown. However, when covariate effects are incorporated and allowed to vary for different transitions, the number of potential parameters to estimate can become large even when the number of covariates is moderate, and traditional maximum likelihood estimation and subset model selection procedures can easily become unstable due to overfitting. We propose a novel regularized continuous-time Markov model with the elastic net penalty, which is capable of simultaneous variable selection and estimation for large number of parameters. We derive an efficient coordinate descent algorithm to solve the penalized optimization problem, which is fully automatic and data driven. We further consider an extension where one of the states is death, and time of death is exactly known but the state path leading to death is unknown. The proposed method is extensively evaluated in a simulation study, and demonstrated in an application to real-world data on airflow limitation state transitions.

Objectives To determine whether the relationship between anthropometric measurements of obesity and mortality varies according to age, race, and ethnicity in older women. Design Prospective cohort study of multiethnic postmenopausal women. Setting Women's Health Initiative (WHI) observational study and clinical trials in 40 clinics. Participants Postmenopausal women aged 50–79 participating in WHI (N = 161,808). Measurements Baseline height, weight, and waist circumference (WC) were measured, and body mass index (BMI) was calculated based on height and weight. Demographic, health, and lifestyle data from a baseline questionnaire were used as covariates. The outcome was adjudicated death (n = 18,320) during a mean follow-up of 11.4 ± 3.2 years. Results Hazard ratios (HRs) and 95% confidence intervals (95% CIs) indicated that ethnicity and age modified (P < .01) the relationship between obesity and mortality. Underweight was associated with higher mortality, but overweight or slight obesity was not a risk factor for mortality in most ethnic groups except for Hispanic women in the obesity I category (HR = 1.42, 95% CI = 1.04–1.95). BMI was not or was only weakly associated with mortality in individuals aged 70–79 (HR = 0.90, 95% CI = 0.85–0.95 for overweight; HR = 0.98, 95 CI = 0.92–1.06 for obese I; HR = 1.11, 95% CI = 1.00–1.23 for obese II; HR = 1.08, 95% CI = 0.92–1.26 for obese III). In contrast, higher central obesity measured using WC was consistently associated with higher mortality in all groups. Conclusion Underweight is a significant risk factor for mortality in older women, and healthy BMI ranges may need to be specific for age, race, and ethnicity. The findings support a consistent relationship between central obesity and mortality.

We consider the situation of estimating the marginal survival distribution from censored data subject to dependent censoring using auxiliary variables. We had previously developed a nonparametric multiple imputation approach. The method used two working proportional hazards (PH) models, one for the event times and the other for the censoring times, to define a nearest neighbor imputing risk set. This risk set was then used to impute failure times for censored observations. Here, we adapt the method to the situation where the event and censoring times follow accelerated failure time models and propose to use the Buckley-James estimator as the two working models. Besides studying the performances of the proposed method, we also compare the proposed method with two popular methods for handling dependent censoring through the use of auxiliary variables, inverse probability of censoring weighted and parametric multiple imputation methods, to shed light on the use of them. In a simulation study with time-independent auxiliary variables, we show that all approaches can reduce bias due to dependent censoring. The proposed method is robust to misspecification of either one of the two working models and their link function. This indicates that a working proportional hazards model is preferred because it is more cumbersome to fit an accelerated failure time model. In contrast, the inverse probability of censoring weighted method is not robust to misspecification of the link function of the censoring time model. The parametric imputation methods rely on the specification of the event time model. The approaches are applied to a prostate cancer dataset.

Objectives Tenofovir disoproxol fumarate (TDF) is increasingly used in HAART regimens of pregnant women, but limited data exist on pregnancy pharmacokinetics of chronically-dosed TDF. This study described tenofovir pharmacokinetics during pregnancy and postpartum.

Author(s): Aweeka, FT; Hu, C; Huang, L; Best, BM; Stek, A; Lizak, P; Burchett, SK; Read, JS; Watts, H; Mirochnick, M; Capparelli, EV; International Maternal Pediatric Adolescent AIDS Clinical Trials Group (IMPAACT) P1026s Protocol Team | Abstract: ObjectivesPregnancy results in physiological changes altering the pharmacokinetics of drugs metabolized by cytochrome P450 3A4 (CYP3A4). The urinary ratio of 6-β hydroxycortisol to cortisol (6βHF : F) is a marker of CYP3A4 induction. We sought to evaluate its change in antiretroviral (ARV)-treated HIV-1-infected women and to relate this change to ARV pharmacokinetics.MethodsWomen receiving various ARVs had pharmacokinetic evaluations during the third trimester of pregnancy (g30 weeks) and postpartum with determination of 6βHF : F carried out on the same days. The Wilcoxon signed rank test was used to compare the ratio antepartum to postpartum. The relationship between the change in ratio and the change in pharmacokinetics was analysed using Kendall's tau.Results6βHF : F ratios were available for 107 women antepartum, with 54 having postpartum values. The ratio was higher antepartum (P=0.033) (median comparison 1.35; 95% confidence interval 1.01, 1.81). For 71 women taking a protease inhibitor (PI), the antepartum vs. postpartum 6βHF : F comparison was marginally significant (P=0.058). When the change in the 6βHF : F ratio was related to the change in the dose-adjusted ARV area under the plasma concentration vs. time curve (AUC) between antepartum and postpartum, the 35 subjects in the lopinavir/ritonavir (LPV/r) arms demonstrated an inverse relationship (P=0.125), albeit this correlation did not reach statistical significance.ConclusionsA 35% increase in the urinary 6βHF : F ratio was measured during late pregnancy compared with postpartum, indicating that CYP3A induction occurs during pregnancy. The trend towards an inverse relationship between the change in the 6βHF : F ratio and the change in the LPV AUC antepartum vs. postpartum suggests that CYP3A induction may be one mechanism behind altered LPV exposure during pregnancy.

Background The current standard of care for initial staging of pediatric Ewing sarcoma (EWS) patients is to obtain a bilateral bone marrow aspiration and biopsy (BMAB). The incidence of bone marrow (BM) disease in patients deemed non-metastatic by conventional and metabolic imaging and the concordance of BM positivity with other clinical characteristics are not well established. Procedure This study is a multi-institutional retrospective review of newly diagnosed EWS patients less than 40 years of age with initial staging that included imaging and BMAB. Results A total of 116 patients were eligible with 85 patients considered non-metastatic and 31 considered metastatic by imaging. None of the 85 patients with non-metastatic disease were BMAB positive (0%; 95% CI: 0–4.2%); 13 of the 31 patients with metastases were BMAB positive (41.9%; 95% CI: 24.5–60.9%). Primary tumor size was significantly higher in patients with metastases (P = 0.017). Bone metastasis by imaging had high correlation with BMAB positivity (P = 0.0002). In addition, the number of bony metastatic sites was significantly higher in patients with a positive BMAB as compared to those with a negative BMAB (median 3.5 and 0.0, respectively; P

Background and Objectives Colonoscopy is the preferred method for colon cancer screening, but can miss polyps and flat neoplasms with low color contrast. The objective was to develop a new autofluorescence method that improves image contrast of colonic neoplasms.

The three-dimensional structure of a protein is organized around the packing of its secondary structure elements. Predicting the topology and constructing the geometry of structural motifs involving α-helices and/or β-strands are therefore key steps for accurate prediction of protein structure. While many efforts have focused on how to pack helices and on how to sample exhaustively the topologies and geometries of multiple strands forming a β-sheet in a protein, there has been little progress on generating native-like packings of helices on sheets. We describe a method that can generate the packing of multiple helices on a given β-sheet for αβα sandwich type protein folds. This method mines the results of a statistical analysis of the conformations of αβ2 motifs in protein structures to provide input values for the geometric attributes of the packing of a helix on a sheet. It then proceeds with a geometric builder that generates multiple arrangements of the helices on the sheet of interest by sampling through these values and performing consistency checks that guarantee proper loop geometry between the helices and the strands, minimal number of collisions between the helices, and proper formation of a hydrophobic core. The method is implemented as a module of ProteinShop. Our results show that it produces structures that are within 4–6 A RMSD of the native one, regardless of the number of helices that need to be packed, though this number may increase if the protein has several helices between two consecutive strands in the sequence that pack on the sheet formed by these two strands. Proteins 2011; Published 2011 Wiley-Liss, Inc.

UVB irradiation of epidermal keratinocytes results in the activation of the p38 mitogen-activated protein kinase (MAPK) pathway and subsequently activator protein-1 (AP-1) transcription factor activation and cyclooxygenase-2 (COX-2) expression. AP-1 and COX-2 have been shown to play functional roles in UVB-induced mouse skin carcinogenesis. In this study, the experimental approach was to express a dominant negative p38α MAPK (p38DN) in the epidermis of SKH-1 hairless mice and assess UVB-induced AP-1 activation, COX-2 expression, and the skin carcinogenesis response in these mice compared to wild-type littermates. We observed a significant inhibition of UVB-induced AP-1 activation and COX-2 expression in p38DN transgenic mice, leading to a significant reduction of UVB-induced tumor number and growth compared to wild-type littermates in a chronic UVB skin carcinogenesis model. A potential mechanism for this reduction in tumor number and growth rate is an inhibition of chronic epidermal proliferation, observed as reduced Ki-67 staining in p38DN mice compared to wild-type. Although we detected no difference in chronic apoptotic rates between transgenic and nontransgenic mice, analysis of acutely irradiated mice demonstrated that expression of the p38DN transgene significantly inhibited UVB-induced apoptosis of keratinocytes. These results counter the concerns that inhibition of p38 MAPK in a chronic situation could compromise the ability of the skin to eliminate potentially tumorigenic cells. Our data indicate that p38 MAPK is a good target for pharmacological intervention for UV-induced skin cancer in patients with sun damaged skin, and suggest that inhibition of p38 signaling reduces skin carcinogenesis by inhibiting COX-2 expression and proliferation of UVB-irradiated cells.

The three-dimensional structure of a protein is organized around the packing of its secondary structure elements. While much is known about the packing geometry observed between α-helices and between β-sheets, there has been little progress on characterizing helix-sheet interactions. We present an analysis of the conformation of αβ2 motifs in proteins, corresponding to all occurrences of helices in contact with two strands that are hydrogen-bonded. The geometry of the αβ2 motif is characterized by the azimuthal angle θ between the helix axis and an average vector representing the two strands, the elevation angle ψ between the helix axis and the plane containing the two strands, and the distance D between the helix and the strands. We observe that the helix tends to align to the two strands, with a preference for an antiparallel orientation if the two strands are parallel; this preference is diminished for other topologies of the β-sheet. Sidechain packing at the interface between the helix and the strands is mostly hydrophobic, with a preference for aliphatic amino acids in the strand and aromatic amino acids in the helix. From the knowledge of the geometry and amino acid propensities of αβ2 motifs in proteins, we have derived different statistical potentials that are shown to be efficient in picking native-like conformations among a set of non-native conformations in well-known decoy datasets. The information on the geometry of αβ2 motifs as well as the related statistical potentials has applications in the field of protein structure prediction.

We describe a method that can thoroughly sample a protein conformational space given the protein primary sequence of amino acids and secondary structure predictions. Specifically, we target proteins with β-sheets because they are particularly challenging for ab initio protein structure prediction because of the complexity of sampling long-range strand pairings. Using some basic packing principles, inverse kinematics (IK), and β-pairing scores, this method creates all possible β-sheet arrangements including those that have the correct packing of β-strands. It uses the IK algorithms of ProteinShop to move α-helices and β-strands as rigid bodies by rotating the dihedral angles in the coil regions. Our results show that our approach produces structures that are within 4–6 A RMSD of the native one regardless of the protein size and β-sheet topology although this number may increase if the protein has long loops or complex α-helical regions. Proteins 2010. © Published 2009 Wiley-Liss, Inc.

Frailty models are frequently used to analyse clustered survival data. The assumption of non-informative censoring is commonly used by these models, even though it may not be true in many situations. This article proposes a test for this assumption. It uses the estimated correlation between two types of martingale residuals, one from a model for failure and the other from a model for censoring. It distinguishes two types of censoring, namely withdrawal and the end of the study. Simulation studies show that the proposed test works well under various scenarios. For illustration, the test is applied to a data set for kidney disease patients from multiple dialysis centres.

This article deals with parameter estimation in the Cox proportional hazards model when covariates are measured with error. We consider both the classical additive measurement error model and a more general model which represents the mis-measured version of the covariate as an arbitrary linear function of the true covariate plus random noise. Only moment conditions are imposed on the distributions of the covariates and measurement error. Under the assumption that the covariates are measured precisely for a validation set, we develop a class of estimating equations for the vector-valued regression parameter by correcting the partial likelihood score function. The resultant estimators are proven to be consistent and asymptotically normal with easily estimated variances. Furthermore, a corrected version of the Breslow estimator for the cumulative hazard function is developed, which is shown to be uniformly consistent and, upon proper normalization, converges weakly to a zero-mean Gaussian process. Simulation studies indicate that the asymptotic approximations work well for practical sample sizes. The situation in which replicate measurements (instead of a validation set) are available is also studied.

Objectives The aim of the study was to describe emtricitabine pharmacokinetics during pregnancy and postpartum.

Objectives Our objective was to evaluate the pharmacokinetics of nelfinavir (NFV) (625 mg tablets) 1250 mg twice daily during pregnancy and postpartum. Methods The participants were HIV-1-infected pregnant women enrolled in P1026s and receiving NFV (625 mg tablets) 1250 mg twice daily as part of routine clinical care. Intensive steady-state 12-h NFV pharmacokinetic profiles were performed during pregnancy and postpartum. The target NFV area under the plasma concentration–time curve (AUC0–12) was ≥10th percentile NFV AUC0–12 in non-pregnant historical controls (18.5 μg h/mL). Results Of 27 patients receiving NFV, pharmacokinetic data were available for four (second trimester), 27 (third trimester) and 22 (postpartum) patients. The NFV maximum concentration (Cmax), 12-h post-dose concentration (C12) and AUC0–12 were significantly lower during the third trimester compared to postpartum (P≤0.03). The metabolite hydroxyl-tert-butylamide (M8) AUC0–12 and the M8/NFV AUC ratio were lower during the third trimester compared to postpartum (P