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The annals of applied statistics  2010;4(1):520-532.
To investigate whether treating cancer patients with erythropoiesis-stimulating agents (ESAs) would increase the mortality risk, Bennett et al. [Journal of the American Medical Association 299 (2008) 914–924] conducted a meta-analysis with the data from 52 phase III trials comparing ESAs with placebo or standard of care. With a standard parametric random effects modeling approach, the study concluded that ESA administration was significantly associated with increased average mortality risk. In this article we present a simple nonparametric inference procedure for the distribution of the random effects. We re-analyzed the ESA mortality data with the new method. Our results about the center of the random effects distribution were markedly different from those reported by Bennett et al. Moreover, our procedure, which estimates the distribution of the random effects, as opposed to just a simple population average, suggests that the ESA may be beneficial to mortality for approximately a quarter of the study populations. This new meta-analysis technique can be implemented with study-level summary statistics. In contrast to existing methods for parametric random effects models, the validity of our proposal does not require the number of studies involved to be large. From the results of an extensive numerical study, we find that the new procedure performs well even with moderate individual study sample sizes.
PMCID: PMC4321956
Bivariate beta; conditional permutation test; erythropoiesis-stimulating agents; logit-normal; two-level hierachical model
2.  Density estimation on multivariate censored data with optional Pólya tree 
Biostatistics (Oxford, England)  2013;15(1):182-195.
Analyzing the failure times of multiple events is of interest in many fields. Estimating the joint distribution of the failure times in a non-parametric way is not straightforward because some failure times are often right-censored and only known to be greater than observed follow-up times. Although it has been studied, there is no universally optimal solution for this problem. It is still challenging and important to provide alternatives that may be more suitable than existing ones in specific settings. Related problems of the existing methods are not only limited to infeasible computations, but also include the lack of optimality and possible non-monotonicity of the estimated survival function. In this paper, we proposed a non-parametric Bayesian approach for directly estimating the density function of multivariate survival times, where the prior is constructed based on the optional Pólya tree. We investigated several theoretical aspects of the procedure and derived an efficient iterative algorithm for implementing the Bayesian procedure. The empirical performance of the method was examined via extensive simulation studies. Finally, we presented a detailed analysis using the proposed method on the relationship among organ recovery times in severely injured patients. From the analysis, we suggested interesting medical information that can be further pursued in clinics.
PMCID: PMC3862208  PMID: 23902636
Multivariate survival analysis; Non-parametric Bayesian; Optional Pólya tree
3.  Landmark Estimation of Survival and Treatment Effect in a Randomized Clinical Trial 
In many studies with a survival outcome, it is often not feasible to fully observe the primary event of interest. This often leads to heavy censoring and thus, difficulty in efficiently estimating survival or comparing survival rates between two groups. In certain diseases, baseline covariates and the event time of non-fatal intermediate events may be associated with overall survival. In these settings, incorporating such additional information may lead to gains in efficiency in estimation of survival and testing for a difference in survival between two treatment groups. If gains in efficiency can be achieved, it may then be possible to decrease the sample size of patients required for a study to achieve a particular power level or decrease the duration of the study. Most existing methods for incorporating intermediate events and covariates to predict survival focus on estimation of relative risk parameters and/or the joint distribution of events under semiparametric models. However, in practice, these model assumptions may not hold and hence may lead to biased estimates of the marginal survival. In this paper, we propose a semi-nonparametric two-stage procedure to estimate and compare t-year survival rates by incorporating intermediate event information observed before some landmark time, which serves as a useful approach to overcome semi-competing risks issues. In a randomized clinical trial setting, we further improve efficiency through an additional calibration step. Simulation studies demonstrate substantial potential gains in efficiency in terms of estimation and power. We illustrate our proposed procedures using an AIDS Clinical Trial Protocol 175 dataset by estimating survival and examining the difference in survival between two treatment groups: zidovudine and zidovudine plus zalcitabine.
PMCID: PMC3960087  PMID: 24659838
Efficiency Augmentation; Kaplan Meier; Landmark Prediction; Semi-competing Risks; Survival Analysis
Contemporary clinical trials  2013;36(2):502-509.
Functional impairment, functional decline, and mobility loss are major public health problems in people with lower extremity peripheral artery disease (PAD). Few medical therapies significantly improve walking performance in PAD. We describe methods for the PROgenitor cell release Plus Exercise to improve functionaL performance in PAD (PROPEL) Study, a randomized controlled clinical trial designed to determine whether granulocyte-macrophage colony stimulating factor (GM-CSF) combined with supervised treadmill walking exercise improves six-minute walk distance more than GM-CSF alone, more than supervised treadmill exercise alone, and more than placebo plus attention control in participants with PAD, respectively. PROPEL Study participants are randomized to one of four arms in a 2 by 2 factorial design. The four study arms are GM-CSF plus supervised treadmill exercise, GM-CSF plus attention control, placebo plus supervised exercise therapy, or placebo plus attention control. The primary outcome is change in six-minute walk distance at 12-week follow-up. Secondary outcomes include change in brachial artery flow-mediated dilation (FMD), change in maximal treadmill walking time, and change in circulating CD34+ cells at 12-week follow-up. Outcomes are also measured at six-week and six-month follow-up. Results of the PROPEL Study will have important implications for understanding mechanisms of improving walking performance and preventing mobility loss in the large and growing number of men and women with PAD.
PMCID: PMC3939047  PMID: 24080099
5.  Detection of Pancreatic Ductal Adenocarcinoma in Mice by Ultrasound Imaging of Thymocyte Differentiation Antigen 1 
Gastroenterology  2013;145(4):885-894.e3.
Early detection of pancreatic ductal adenocarcinoma (PDAC) allows for surgical resection and increases patient survival times. Imaging agents that bind and amplify the signal of neovascular proteins in neoplasms can be detected by ultrasound, enabling accurate detection of small lesions. We searched for new markers of neovasculature in PDAC and assessed their potential for tumor detection by ultrasound molecular imaging.
Thymocyte Differentiation Antigen 1 (Thy1) was identified as a specific biomarker of PDAC neovasculature by proteomic analysis. Upregulation in PDAC was validated by immunohistochemical analysis of pancreatic tissue samples from 28 healthy individuals, 15 with primary chronic pancreatitis tissues, and 196 with PDAC. Binding of Thy1-targeted contrast microbubbles was assessed in cultured cells, in mice with orthotopic PDAC xenograft tumors expressing human Thy1 on the neovasculature, and on the neovasculature of a genetic mouse model of PDAC.
Based on immunohistochemical analyses, levels of Thy1 were significantly higher in the vascular of human PDAC than chronic pancreatitis (P=.007) or normal tissue samples (P<.0001). In mice, ultrasound imaging accurately detected human Thy1-positive PDAC xenografts, as well as PDACs that express endogenous Thy1 in genetic mouse models of PDAC.
We have identified and validated Thy1 as a marker of PDAC that can be detected by ultrasound molecular imaging in mice. The development of a specific imaging agent and identification of Thy1 as a new biomarker could aid in the diagnosis of this cancer and management of patients.
PMCID: PMC3783557  PMID: 23791701
Molecular imaging; pancreatic cancer; CD90; diagnostic test
6.  High-Throughput Sorting of the Highest Producing Cell via a Transiently Protein-Anchored System 
PLoS ONE  2014;9(7):e102569.
Developing a high-throughput method for the effecient selection of the highest producing cell is very important for the production of recombinant protein drugs. Here, we developed a novel transiently protein-anchored system coupled with fluorescence activated cell sorting (FACS) for the efficient selection of the highest producing cell. A furin cleavage peptide (RAKR) was used to join a human anti-epithelial growth factor antibody (αEGFR Ab) and the extracellular-transmembrane-cytosolic domains of the mouse B7-1 antigen (B7). The furin inhibitor can transiently switch secreted αEGFR Ab into a membrane-anchored form. After cell sorting, the level of membrane αEGFR Ab-RAKR-B7 is proportional to the amount of secreted αEGFR Ab in the medium. We further selected 23 αEGFR Ab expressing cells and demonstrated a high correlation (R2 = 0.9165) between the secretion level and surface expression levels of αEGFR Ab. These results suggested that the novel transiently protein-anchored system can easily and efficiently select the highest producing cells, reducing the cost for the production of biopharmaceuticals.
PMCID: PMC4103822  PMID: 25036759
7.  Proximal Superficial Femoral Artery Occlusion, Collateral Vessels, and Walking Performance in Peripheral Artery Disease 
JACC. Cardiovascular imaging  2013;6(6):687-694.
We studied associations of MRI-measured SFA occlusions with functional performance, leg symptoms, and collateral vessel number in PAD. We studied associations of collateral vessel number with functional performance in PAD.
Associations of magnetic resonance imaging (MRI)-detected superficial femoral artery (SFA) occlusion and collateral vessel number with functional performance among individuals with peripheral artery disease (PAD) have not been reported.
457 participants with an ankle brachial index (ABI) < 1.00 had MRI measurement of the proximal SFA with twelve consecutive 2.5 millimeter cross-sectional images. An occluded SFA was defined as an SFA in which at least one segment was occluded. A non-occluded SFA was defined as absence of any occluded slices. Collateral vessels were visualized with magnetic resonance angiography (MRA). Lower extremity functional performance was measured with the six-minute walk, four-meter walking velocity at usual and fastest pace, and the short physical performance battery (SPPB) (0-12 scale, 12=best).
Adjusting for age, sex, race, comorbidities, and other confounders, the presence of an SFA occlusion was associated with poorer six-minute walk performance (1,031 vs. 1,169 feet, P=0.006), slower fast-paced walking velocity (1.15 vs. 1.22 meters/second, P =0.042), and lower SPPB score (9.07 vs. 9.75, P=0.038) compared to the absence of an SFA occlusion. More numerous collateral vessels were associated with better six-minute walk performance (0-3 collaterals-1,064 feet, 4-7 collaterals-1,165 feet, ≥ 8 collaterals-1,246 feet, P trend=0.007), faster usual-paced walking speed (0-3 collaterals-0.84 meters/second, 4-7 collaterals-0.88 meters/second, ≥ 8 collaterals-0.91 meters/second, P trend=0.029), and faster rapid-paced walking speed (0-3 collaterals-1.17 meters/second, 4-7 collaterals-1.22 meters/second, ≥ 8 collaterals-1.29 meters/second, P trend=0.002), adjusting for age, sex, race, comorbidities, ABI, and other confounders.
Among PAD participants, MRI-visualized occlusions in the proximal SFA are associated with poorer functional performance, while more numerous collaterals are associated with better functional performance.
Clinical Trial ID
PMCID: PMC3766720  PMID: 23647796
atherosclerotic plaque; intermittent claudication; peripheral arterial disease; physical functioning
8.  Home‐Based Walking Exercise in Peripheral Artery Disease: 12‐Month Follow‐up of the Goals Randomized Trial 
We studied whether a 6‐month group‐mediated cognitive behavioral (GMCB) intervention for peripheral artery disease (PAD) participants, which promoted home‐based walking exercise, improved 6‐minute walk and other outcomes at 12‐month follow‐up, 6 months after completing the intervention, compared to a control group.
Methods and Results
We randomized PAD participants to a GMCB intervention or a control group. During phase I (months 1 to 6), the intervention used group support and self‐regulatory skills during weekly on‐site meetings to help participants adhere to home‐based exercise. The control group received weekly on‐site lectures on topics unrelated to exercise. Primary outcomes were measured at the end of phase I. During phase II (months 7 to 12), each group received telephone contact. Compared to controls, participants randomized to the intervention increased their 6‐minute walk distance from baseline to 12‐month follow‐up, (from 355.4 to 381.9 m in the intervention versus 353.1 to 345.6 m in the control group; mean difference=+34.1 m; 95% confidence interval [CI]=+14.6, +53.5; P<0.001) and their Walking Impairment Questionnaire (WIQ) speed score (from 36.1 to 46.5 in the intervention group versus 34.9 to 36.5 in the control group; mean difference =+8.8; 95% CI=+1.6, +16.1; P=0.018). Change in the WIQ distance score was not different between the 2 groups at 12‐month follow‐up (P=0.139).
A weekly on‐site GMCB intervention that promoted home‐based walking exercise intervention for people with PAD demonstrated continued benefit at 12‐month follow‐up, 6 months after the GMCB intervention was completed.
Clinical Trial Registration
URL: Unique identifier: NCT00693940.
PMCID: PMC4309051  PMID: 24850615
behavior change; exercise; mobility; peripheral artery disease; physical functioning
9.  Associations of Calf Skeletal Muscle Characteristics and Peripheral Nerve Function with Self-Perceived Physical Functioning and Walking Ability in Persons with Peripheral Arterial Disease 
We determined whether more adverse calf muscle characteristics and poorer peripheral nerve function were associated with impairments in self-perceived physical functioning and walking ability in persons with lower extremity peripheral arterial disease (PAD). Participants included 462 persons with PAD; measures included the ankle-brachial index (ABI), medical history, electrophysiologic characteristics of nerves, and computed tomography of calf muscle. Self-perceived physical functioning and walking ability were assessed using the 36-Item Short Form Health Survey (SF-36) and the Walking Impairment Questionnaire (WIQ). Results were adjusted for age, sex, race, ABI, body-mass index, comorbidities, and other confounders. Lower calf muscle area was associated with a poorer SF-36 physical function (PF) score (overall p trend<0.001, 33.76 PF score for the lowest quartile vs. 59.74 for the highest, pair wise p<0.001) and a poorer WIQ walking distance score (p trend=0.001, 29.71 WIQ score for the lowest quartile vs. 48.43 for the highest, pair wise p<0.001). Higher calf muscle percent fat was associated with a poorer SF-36 PF score (p trend<0.001, 53.76 PF score for the lowest quartile vs. 40.28 for the highest, pair wise p=0.009). Slower peroneal nerve conduction velocity was associated with a poorer WIQ speed score (p trend=0.023, 30.49 WIQ score for the lowest quartile vs. 40.48 for the highest, pair wise p=0.031). In summary, adverse calf muscle characteristics and poorer peripheral nerve function are associated significantly and independently with impairments in self-perceived physical functioning and walking ability in PAD persons.
PMCID: PMC4034534  PMID: 21471147
peripheral arterial disease; calf muscle characteristics; peripheral nerve function; quality of life
10.  Functional Production of a Soluble and Secreted Single-Chain Antibody by a Bacterial Secretion System 
PLoS ONE  2014;9(5):e97367.
Single-chain variable fragments (scFvs) serve as an alternative to full-length monoclonal antibodies used in research and therapeutic and diagnostic applications. However, when recombinant scFvs are overexpressed in bacteria, they often form inclusion bodies and exhibit loss of function. To overcome this problem, we developed an scFv secretion system in which scFv was fused with osmotically inducible protein Y (osmY), a bacterial secretory carrier protein, for efficient protein secretion. Anti-EGFR scFv (αEGFR) was fused with osmY (N- and C-termini) and periplasmic leader sequence (pelB) to generate αEGFR-osmY, osmY-αEGFR, and pelB-αEGFR (control), respectively. In comparison with the control, both the osmY-fused αEGFR scFvs were soluble and secreted into the LB medium. Furthermore, the yield of soluble αEGFR-osmY was 20-fold higher, and the amount of secreted protein was 250-fold higher than that of osmY-αEGFR. In addition, the antigen-binding activity of both the osmY-fused αEGFRs was 2-fold higher than that of the refolded pelB-αEGFR from inclusion bodies. Similar results were observed with αTAG72-osmY and αHer2-osmY. These results suggest that the N-terminus of osmY fused with scFv produces a high yield of soluble, functional, and secreted scFv, and the osmY-based bacterial secretion system may be used for the large-scale industrial production of low-cost αEGFR protein.
PMCID: PMC4019604  PMID: 24824752
11.  Comparative Effectiveness Study of Self-Directed Walking Exercise, Lower Extremity Revascularization, and Functional Decline in Peripheral Artery Disease 
Journal of vascular surgery  2013;57(4):990-996.e1.
Among individuals with peripheral artery disease (PAD), we compared annual change in six-minute walk performance between participants who neither underwent lower extremity revascularization nor walked for exercise (Group 1, reference), those who walked regularly for exercise (Group 2), and those who underwent lower extremity revascularization (Group 3).
Participants were recruited from Chicago-area vascular laboratories and followed annually. Change in six-minute walk was calculated beginning at the study visit preceding lower extremity revascularization or exercise behavior and continuing for one additional year after the therapy was reported. Results adjust for age, sex, race, comorbidities, and other confounders.
Of 348 PAD participants, 43 underwent revascularization during a median follow-up of 84 months. Adjusted annual declines in six-minute walk were Group 1: −96.6 feet/year, Group 2: −49.9 feet/year, and Group 3: −32.6 feet/year(p<.001). Forty-one percent of revascularizations were not associated with ankle brachial index (ABI) improvement. When Group 3 was limited to participants with ABI improvement of ≥ 0.15 after revascularization, annual adjusted changes in six-minute walk were Group 1:−97.7 feet/year; Group 2:−46.5 feet/year, and Group 3:+68.1 feet/year (P value<.001). When Group 3 was limited to participants without ABI improvement ≥ 0.15 after revascularization, annual adjusted changes in six-minute walk were Group 1:−99.2 feet/year, Group 2:−48.0 feet/year; and Group 3:−61.7 feet/year. (P value<.001).
A large proportion of PAD participants did not have an ABI improvement of at least 0.15 at their follow-up study visit after revascularization. The benefits of lower extremity revascularization in patients with PAD appear closely tied to improvements in the ABI after revascularization.
PMCID: PMC3612138  PMID: 23352363
Peripheral artery disease; intermittent claudication; physical functioning; exercise
12.  The Walking Impairment Questionnaire Stair-Climbing Score predicts mortality in men and women with peripheral arterial disease 
Journal of vascular surgery  2012;55(6):1662-73.e2.
The Walking Impairment Questionnaire (WIQ) measures self-reported walking distance, walking speed, and stair-climbing ability in men and women with lower extremity peripheral arterial disease (PAD). We determined whether poorer WIQ scores are associated with higher all-cause and cardiovascular disease (CVD) mortality in individuals with and without PAD.
1048 men and women with and without PAD were identified from Chicago-area medical centers. Participants completed the WIQ at baseline and were followed for a median of 4.5 years. Cox proportional hazards models were used to relate baseline WIQ scores with mortality, adjusting for age, sex, race, the ankle brachial index (ABI), comorbidities, and other covariates.
461 participants (44.0%) died during follow-up, including 158 deaths from cardiovascular disease. PAD participants in the lowest baseline quartile of the WIQ stair-climbing scores had higher all-cause mortality (HR = 1.70 [95% Confidence Interval (CI) 1.08-2.66, p=0.02] and higher CVD mortality (HR = 3.11 [95% CI 1.30 – 7.47, p=0.01]) compared to those with the highest baseline WIQ stair climbing score. Among PAD participants there were no significant associations of lower baseline WIQ distance or speed scores with rates of all-cause mortality (p for trend = 0.20 and 0.07, respectively) or CVD mortality (p for trend = 0.51 and p for trend = 0.33, respectively). Among non-PAD participants there were no significant associations of lower baseline WIQ stair climbing, distance, or speed score with rates of all-cause mortality (p for trend = 0.94, 0.69, and 0.26, respectively) or CVD mortality (p for trend = 0.28, 0.68, and 0.78, respectively).
Among participants with PAD, lower WIQ stair climbing scores are associated with higher all-cause and CVD mortality, independently of the ABI and other covariates.
PMCID: PMC3963605  PMID: 22608041
13.  Earlier Detection of Breast Cancer with Ultrasound Molecular Imaging in a Transgenic Mouse Model 
Cancer research  2013;73(6):1689-1698.
While there is an increasing role of ultrasound for breast cancer screening in patients with dense breast, conventional anatomical-ultrasound lacks sensitivity and specificity for early breast cancer detection. In this study we assessed the potential of molecular-ultrasound imaging, using clinically-translatable vascular endothelial growth factor receptor (VEGFR2)-targeted microbubbles (MBVEGFR2), to improve the diagnostic accuracy of ultrasound in earlier detection of breast cancer and ductal carcinoma in situ (DCIS) in a transgenic mouse model (FVB/N-Tg(MMTV-PyMT)634Mul). In vivo binding specificity studies (n=26 tumors) showed that ultrasound imaging signal was significantly higher (P<0.001) using MBVEGFR2 compared to non-targeted microbubbles and imaging signal significantly decreased (P<0.001) by blocking antibodies. Ultrasound molecular imaging signal significantly increased (P<0.001), when breast tissue (n=315 glands) progressed from normal (1.65±0.17 a.u.) to hyperplasia (4.21±1.16), DCIS (15.95±1.31) and invasive cancer (78.1±6.31) and highly correlated with ex vivo VEGFR2 expression (R2=0.84; 95% CI, 0.72, 0.91; P<0.001). At an imaging signal threshold of 4.6 a.u., ultrasound molecular imaging differentiated benign from malignant entities with a sensitivity of 84% (95% CI, 78, 88) and specificity of 89% (95% CI, 81, 94). In a prospective screening trail (n=63 glands) diagnostic performance of detecting DCIS and breast cancer was assessed and two independent readers correctly diagnosed malignant disease in >95% of cases and highly agreed between each other (ICC=0.98; 95% CI, 97, 99). These results suggest that VEGFR2-targeted ultrasound molecular imaging allows highly accurate detection of DCIS and breast cancer in transgenic mice and may be a promising approach for early breast cancer detection in women.
PMCID: PMC3602408  PMID: 23328585
Targeted ultrasound imaging; VEGFR2; breast cancer; early detection; microbubbles
14.  Superficial Femoral Artery Plaque and Functional Performance in Peripheral Arterial Disease 
JACC. Cardiovascular imaging  2011;4(7):730-739.
We studied associations of magnetic resonance imaging measurements of plaque area and relative percent lumen reduction in the proximal superficial femoral artery with functional performance among participants with peripheral arterial disease.
The clinical significance of directly imaged plaque characteristics in lower extremity arteries is not well established.
A total of 454 participants with an ankle brachial index <1.00 underwent magnetic resonance cross-sectional imaging of the proximal superficial femoral artery and completed a 6-min walk test, measurement of 4-m walking velocity at usual and fastest pace, and measurement of physical activity with a vertical accelerometer.
Adjusting for age, sex, race, body mass index, smoking, statin use, comorbidities, and other covariates, higher mean plaque area (1st quintile [least plaque]: 394 m, 2nd quintile: 360 m, 3rd quintile: 359 m, 4th quintile: 329 m, 5th quintile [greatest plaque]: 311 m; p trend <0.001) and smaller mean percent lumen area (1st quintile [greatest plaque]: 319 m, 2nd quintile: 330 m, 3rd quintile: 364 m, 4th quintile: 350 m, 5th quintile: 390 m; p trend <0.001) were associated with shorter distance achieved in the 6-min walk test. Greater mean plaque area was also associated with slower usual-paced walking velocity (p trend = 0.006) and slower fastest-paced 4-m walking velocity (p trend = 0.003). Associations of mean plaque area and mean lumen area with 6-min walk distance remained statistically significant even after additional adjustment for the ankle brachial index and leg symptoms.
Among participants with peripheral arterial disease, greater plaque burden and smaller lumen area in the proximal superficial femoral artery are associated independently with poorer functional performance, even after adjusting for the ankle brachial index and leg symptoms.
PMCID: PMC3906625  PMID: 21757163
atherosclerotic plaque intermittent claudication; peripheral arterial disease; physical functioning
15.  A group-mediated, home-based physical activity intervention for patients with peripheral artery disease: effects on social and psychological function 
PAD is a disabling, chronic condition of the lower extremities that affects approximately 8 million people in the United States. The purpose of this study was to determine whether an innovative home-based walking exercise program for patients with peripheral artery disease (PAD) improves self-efficacy for walking, desire for physical competence, satisfaction for physical functioning, social functioning, and acceptance of PAD related pain and discomfort.
The design was a 6-month randomized controlled clinical trial of 194 patients with PAD. Participants were randomized to 1 of 2 parallel groups: a home-based group-mediated cognitive behavioral walking intervention or an attention control condition.
Of the 194 participants randomized, 178 completed the baseline and 6-month follow-up visit. The mean age was 70.66 (±9.44) and was equally represented by men and women. Close to half of the cohort was African American. Following 6-months of treatment, the intervention group experienced greater improvement on self-efficacy (p = .0008), satisfaction with functioning (p = .0003), pain acceptance (p = .0002), and social functioning (p = .0008) than the control group; the effects were consistent across a number of potential moderating variables. Change in these outcomes was essentially independent of change in 6-minute walk performance.
Trial registration
[ Identifier: NCT00693940]
PMCID: PMC3910685  PMID: 24467875
Peripheral artery disease; Group-mediated intervention; Physical activity; Social function; Psychological function
When comparing a new treatment with a control in a randomized clinical study, the treatment effect is generally assessed by evaluating a summary measure over a specific study population. The success of the trial heavily depends on the choice of such a population. In this paper, we show a systematic, effective way to identify a promising population, for which the new treatment is expected to have a desired benefit, utilizing the data from a current study involving similar comparator treatments. Specifically, using the existing data, we first create a parametric scoring system as a function of multiple multiple baseline covariates to estimate subject-specific treatment differences. Based on this scoring system, we specify a desired level of treatment difference and obtain a subgroup of patients, defined as those whose estimated scores exceed this threshold. An empirically calibrated threshold-specific treatment difference curve across a range of score values is constructed. The subpopulation of patients satisfying any given level of treatment benefit can then be identified accordingly. To avoid bias due to overoptimism, we utilize a cross-training-evaluation method for implementing the above two-step procedure. We then show how to select the best scoring system among all competing models. Furthermore, for cases in which only a single pre-specified working model is involved, inference procedures are proposed for the average treatment difference over a range of score values using the entire data set, and are justified theoretically and numerically. Lastly, the proposals are illustrated with the data from two clinical trials in treating HIV and cardiovascular diseases. Note that if we are not interested in designing a new study for comparing similar treatments, the new procedure can also be quite useful for the management of future patients, so that treatment may be targeted towards those who would receive nontrivial benefits to compensate for the risk or cost of the new treatment.
PMCID: PMC3775385  PMID: 24058223
Cross-training-evaluation; Lasso procedure; Personalized medicine; Prediction; Ridge regression; Stratified medicine; Subgroup analysis; Variable selection
17.  Multiparametric Spectroscopic Photoacoustic Imaging of Breast Cancer Development in a Transgenic Mouse Model 
Theranostics  2014;4(11):1062-1071.
Objective: To evaluate the potential of multiparametric spectroscopic photoacoustic imaging using oxygen saturation, total hemoglobin, and lipid content to differentiate among four different breast histologies (normal, hyperplasia, ductal carcinoma in situ (DCIS), and invasive breast carcinoma) in a transgenic mouse model of breast cancer development.
Materials and Methods: Animal studies were approved by the Institutional Administrative Panel on Laboratory Animal Care. Mammary glands (n=251) of a transgenic mouse model of breast cancer development (FVB/N-Tg(MMTV-PyMT)634Mul) were imaged using B-mode ultrasound and spectroscopic photoacoustic imaging, analyzed for oxygen saturation, total hemoglobin, and lipid content, and processed for histological analysis. Statistical analysis was performed using one-way ANOVA, two-sample t-tests, logistic regression, and ROC analysis.
Results: Eighty-two normal, 12 hyperplastic, 96 DCIS, and 61 invasive breast carcinoma mammary glands were analyzed. Based on spectroscopic photoacoustic imaging, the oxygen saturation of hyperplasia (50.6%), DCIS (43.0%), and invasive carcinoma (46.2%) significantly increased compared to normal glands (35.5%, P <0.0001), while both total hemoglobin (P<0.01), and lipid content (P<0.0008) significantly decreased with advancing histology. In differentiating normal and hyperplasia from DCIS and invasive breast carcinoma, multiparametric imaging of oxygen saturation, lipid content, and raw photoacoustic signal at 750 nm provided an AUC value of 0.770.
Conclusion: Multiparametric spectroscopic photoacoustic imaging is feasible and allows detection of differences in concentration of tissue chromophores among different histologies in a transgenic mouse model of breast cancer development.
PMCID: PMC4173758  PMID: 25285161
Photoacoustic Imaging; Breast Cancer; Molecular Imaging; Spectroscopic.
18.  The Group Oriented Arterial Leg Study (GOALS) to improve walking performance in patients with peripheral arterial disease 
Contemporary clinical trials  2012;33(6):1311-1320.
People with lower extremity peripheral artery disease (PAD) have greater functional impairment and faster functional decline than those without PAD. We describe methods for the Group Oriented Arterial Leg Study (GOALS), an ongoing randomized controlled clinical trial designed to determine whether a Group-Mediated Cognitive Behavioral (GMCB) intervention improves functional performance in PAD participants, compared to a health education control condition. In GOALS, PAD participants are randomized to either an intervention or a health education control condition in a parallel design. Both conditions consist of weekly group sessions with other PAD participants. In the intervention, cognitive behavioral techniques are used to assist participants in setting and adhering to home-based walking exercise goals. Participants are encouraged to walk for exercise at home at least five days per week. In the control condition, participants receive lectures on health-related topics. After six months of on-site weekly sessions, participants are transitioned to telephone follow-up for another six months. Participants in the intervention are asked to continue home walking exercise. The primary outcome is change in six-minute walk performance between baseline and six-month follow-up. Secondary outcomes include change in six-minute walk performance at 12-month follow-up, and change in treadmill walking performance, the Walking Impairment Questionnaire, quality of life, and physical activity at six and 12-month follow-up. In conclusion, if our group-mediated cognitive behavioral intervention is associated with improved walking performance in individuals with PAD, results will have major public health implications for the large and growing number of people with PAD.
PMCID: PMC3502883  PMID: 23158112
Peripheral artery disease; intermittent claudication; clinical trial; exercise
19.  A unified inference procedure for a class of measures to assess improvement in risk prediction systems with survival data 
Statistics in medicine  2012;32(14):2430-2442.
Risk prediction procedures can be quite useful for the patient’s treatment selection, prevention strategy, or disease management in evidence-based medicine. Often, potentially important new predictors are available in addition to the conventional markers. The question is how to quantify the improvement from the new markers for prediction of the patient’s risk in order to aid cost–benefit decisions. The standard method, using the area under the receiver operating characteristic curve, to measure the added value may not be sensitive enough to capture incremental improvements from the new markers. Recently, some novel alternatives to area under the receiver operating characteristic curve, such as integrated discrimination improvement and net reclassification improvement, were proposed. In this paper, we consider a class of measures for evaluating the incremental values of new markers, which includes the preceding two as special cases. We present a unified procedure for making inferences about measures in the class with censored event time data. The large sample properties of our procedures are theoretically justified. We illustrate the new proposal with data from a cancer study to evaluate a new gene score for prediction of the patient’s survival.
PMCID: PMC3734387  PMID: 23037800
area under the receiver operating characteristic curve; C-statistic; Cox’s regression; integrated discrimination improvement; net reclassification improvement; risk prediction
20.  Inhibition of the angiogenesis and growth of Aloin in human colorectal cancer in vitro and in vivo 
Angiogenesis has been an attractive target for drug therapy. Aloin (AL), an natural compound derived from Aloe barbadensis Miller leaves, has been shown to possess anti-cancer potential activities. However, its roles in tumor angiogenesis and the involved molecular mechanism are unknown.
To evaluate the antiangiogenic and anticancer activities of AL, endothelial cell scratch, modified Boyden chamber inserts and tube formation assays were done in HUVECs, and MTT and Live-Dead assays were used to determine the proliferation inhibition and apoptosis induction of colorectal cancer cells in vitro. The inhibition effects of AL were further confirmed by a mouse xenograft model in vivo. The expression levels of STAT3 signaling pathway and that mediated-target genes were measured in HUVECs and SW620 cells by Western blots.
Here, we demonstrated that AL significantly inhibited HUVECs proliferation, migration and tube formation in vitro. Western blotting showed that AL suppressed activation of VEGF receptor (VEGFR) 2 and STAT3 phosphorylation in endothelial cells. In addition, the constitutively activated STAT3 protein, and the expression of STAT3-regulated antiapoptotic (Bcl-xL), proliferative (c-Myc), and angiogenic (VEGF) proteins were also down-regulated in response to AL in human SW620 cancer cells. Consistent with the above findings, AL inhibited tumor cell viability and induced cell apoptosis in vitro, and substantially reduced tumor volumes and weight in vivo mouse xenografts, without obviously toxicity.
Our studies provided the first evidence that AL may inhibit tumor angiogenesis and growth via blocking STAT3 activation, with the potential of a drug candidate for cancer therapy.
PMCID: PMC3722112  PMID: 23848964
Aloin; Angiogenesis; Tumor growth; Colorectal cancer; STAT3
21.  Utilizing the integrated difference of two survival functions to quantify the treatment contrast for designing, monitoring and analyzing a comparative clinical study 
Consider a comparative, randomized clinical study with a specific event time as the primary endpoint. In the presence of censoring, standard methods of summarizing the treatment difference are based on Kaplan-Meier curves, the logrank test and the point and interval estimates via Cox’s procedure. Moreover, for designing and monitoring the study, one usually utilizes an event-driven scheme to determine the sample sizes and interim analysis time points.
When the proportional hazards assumption is violated, the logrank test may not have sufficient power to detect the difference between two event time distributions. The resulting hazard ratio estimate is difficult, if not impossible, to interpret as a treatment contrast. When the event rates are low, the corresponding interval estimate for the “hazard ratio” can be quite large due to the fact that the interval length depends on the observed numbers of events. This may indicate that there is not enough information for making inferences about the treatment comparison even when there is no difference between two groups. This situation is quite common for a post marketing safety study. We need an alternative way to quantify the group difference.
Instead of quantifying the treatment group difference using the hazard ratio, we consider an easily interpretable and model-free parameter, the integrated survival rate difference over a pre-specified time interval, as an alternative. We present the inference procedures for such a treatment contrast. This approach is purely nonparametric and does not need any model assumption such as the proportional hazards. Moreover, when we deal with equivalence or non-inferiority studies and the event rates are low, our procedure would provide more information about the treatment difference. We used a cardiovascular trial data set to illustrate our approach.
The results using the integrated event rate differences have a heuristic interpretation for the treatment difference even when the proportional hazards assumption is not valid. When the event rates are low, for example, for the cardiovascular study discussed in the paper, the procedure for the integrated event rate difference provides tight interval estimates in contrast to those based on the event-driven inference method.
The design of a trial with the integrated event rate difference may be more complicated than that using the event-driven procedure. One may use simulation to determine the sample size and the estimated duration of the study.
The procedure discussed in the paper can be a useful alternative to the standard proportional hazards method in survival analysis.
PMCID: PMC3705645  PMID: 22914867
Equivalence study; Event-driven study; Kaplan-Meier curve; Non-inferiority trial; Post-market study; Proportional hazards estimate
22.  LILRA3 Is Associated with Benign Prostatic Hyperplasia Risk in a Chinese Population 
A recent prostate cancer (PCa) genome-wide association study (GWAS) identified rs103294, a single nucleotide polymorphism (SNP) located on LILRA3, a key component in the regulation of inflammatory inhibition, to be significantly associated with PCa risk in a Chinese population. Because inflammation may be a common etiological risk factor between PCa and benign prostatic hyperplasia (BPH), the current study was conducted to investigate the association of rs103294 with BPH risk. rs103294 was genotyped in a Chinese population of 426 BPH cases and 1,008 controls from Xinhua Hospital in Shanghai, China. Association between rs103294, BPH risk and clinicopathological traits were tested with adjustment for age. rs103294 was significantly associated with BPH risk with a p-value of 0.0067. Individuals with risk allele “C” had increased risk for BPH (OR = 1.34, 95% CI: 1.09–1.66). Stratified analysis revealed a stronger association risk for younger patients who are below 72 years old (OR = 1.51, 95% CI: 1.06–2.16). Our study represents the first effort to demonstrate that LILRA3 gene is significantly associated with BPH risk in a Chinese population. Our results support a common role of inflammation in the development of PCa and BPH. Additional studies are needed to further evaluate our results.
PMCID: PMC3676759  PMID: 23615473
benign prostatic hyperplasia (BPH); inflammation; LILRA3; single nucleotide polymorphism (SNP); Chinese
23.  On the covariate-adjusted estimation for an overall treatment difference with data from a randomized comparative clinical trial 
Biostatistics (Oxford, England)  2012;13(2):256-273.
To estimate an overall treatment difference with data from a randomized comparative clinical study, baseline covariates are often utilized to increase the estimation precision. Using the standard analysis of covariance technique for making inferences about such an average treatment difference may not be appropriate, especially when the fitted model is nonlinear. On the other hand, the novel augmentation procedure recently studied, for example, by Zhang and others (2008. Improving efficiency of inferences in randomized clinical trials using auxiliary covariates. Biometrics 64, 707–715) is quite flexible. However, in general, it is not clear how to select covariates for augmentation effectively. An overly adjusted estimator may inflate the variance and in some cases be biased. Furthermore, the results from the standard inference procedure by ignoring the sampling variation from the variable selection process may not be valid. In this paper, we first propose an estimation procedure, which augments the simple treatment contrast estimator directly with covariates. The new proposal is asymptotically equivalent to the aforementioned augmentation method. To select covariates, we utilize the standard lasso procedure. Furthermore, to make valid inference from the resulting lasso-type estimator, a cross validation method is used. The validity of the new proposal is justified theoretically and empirically. We illustrate the procedure extensively with a well-known primary biliary cirrhosis clinical trial data set.
PMCID: PMC3297822  PMID: 22294672
ANCOVA; Cross validation; Efficiency augmentation; Mayo PBC data; Semi-parametric efficiency
24.  Higher Body Mass Index is Associated with more Adverse Changes in Calf Muscle Characteristics in Peripheral Arterial Disease 
Journal of Vascular Surgery  2012;55(4):1015-1024.
To determine whether higher body mass index (BMI) is associated with more adverse lower extremity muscle characteristics at baseline and more adverse changes in muscle over time among participants with lower extremity peripheral arterial disease (PAD).
Longitudinal, observational study.
Academic medical center in Chicago.
Participants were 425 men and women with PAD and 261 without PAD.
Computed Tomography was used to measure calf muscle characteristics at baseline and every two years. Knee extension isometric strength, power, and six-minute walk were measured at baseline and annually. Baseline BMI categories were ideal (20-25 kg/m2), overweight (>25-30 kg/m2), and obese (>30 kg/m2). Analyses adjust for age, race, gender, ankle brachial index (ABI), comorbidities, and other covariates.
At baseline, among participants with PAD, higher BMI was associated with greater calf muscle area (ideal BMI: 5181 mm2, overweight: 5513 mm2, obese: 5695 mm2, p trend=0.0009), higher calf muscle percent fat (6.38%, 10.28%, 17.44% respectively, p trend<0.0001), lower calf muscle density (p trend<0.0001), and higher isometric knee extension strength (p trend=0.015). Among participants with PAD, higher BMI was associated with greater declines in calf muscle area p trend=0.030) and greater increases in calf muscle percent fat (p trend=0.023). Among participants without PAD, there were no significant associations of baseline BMI with changes in lower extremity muscle outcomes over time.
Among PAD participants, higher BMI is associated with greater calf muscle area at baseline. However, higher BMI is associated with more adverse calf muscle density and percent fat at baseline and greater declines in calf muscle area over time.
PMCID: PMC3319256  PMID: 22365177
We studied whether lower calf muscle density and poorer upper and lower extremity strength are associated with higher mortality rates in men and women with PAD.
Men and women with lower extremity peripheral arterial disease (PAD) have lower calf muscle density and reduced lower extremity strength compared to individuals without PAD.
At baseline, participants underwent measurement of calf muscle density with computed tomography in addition to knee extension power, and isometric knee extension, plantar flexion, and hand grip strength measures. Participants were followed annually for up to four years. Results are adjusted for age, sex, race, body mass index, the ankle brachial index (ABI), smoking, physical activity, and comorbidities.
Among 434 PAD participants, 103 (24%) died during a mean follow-up of 47.6 months. Lower calf muscle density was associated with higher all-cause mortality (lowest density tertile-hazard ratio (HR)=1.80 (95% Confidence Interval (CI)-1.07-3.03), 2nd tertile-HR=0.91 (95% CI-0.51-1.62); highest density tertile (HR=1.00), P trend=0.020) and higher cardiovascular disease mortality (lowest density tertile-HR=2.39 (95% CI-0.90-6.30), 2nd tertile-HR=0.85 (95% CI-0.27-2.71); highest density tertile (HR=1.00), P trend=0.047). Poorer plantar flexion strength (P trend=0.004), lower baseline leg power (P trend=0.046), and poorer handgrip (P trend=0.005) were associated with higher all-cause mortality.
These data demonstrate that lower calf muscle density and weaker plantar flexion strength, knee extension power, and hand grip are associated with increased mortality in participants with PAD, independently of the ABI and other confounders.
PMCID: PMC3465664  PMID: 22440216
Mortality; intermittent claudication; prognosis; Physical functioning

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