PMCC PMCC

Search tips
Search criteria

Advanced
Results 1-25 (51)
 

Clipboard (0)
None

Select a Filter Below

Journals
more »
Year of Publication
Document Types
1.  Experimental Pain and Opioid Analgesia in Volunteers at High Risk for Obstructive Sleep Apnea 
PLoS ONE  2013;8(1):e54807.
Background
Obstructive sleep apnea (OSA) is characterized by recurrent nocturnal hypoxia and sleep disruption. Sleep fragmentation caused hyperalgesia in volunteers, while nocturnal hypoxemia enhanced morphine analgesic potency in children with OSA. This evidence directly relates to surgical OSA patients who are at risk for airway compromise due to postoperative use of opioids. Using accepted experimental pain models, we characterized pain processing and opioid analgesia in male volunteers recruited based on their risk for OSA.
Methods
After approval from the Intitutional Review Board and informed consent, we assessed heat and cold pain thresholds and tolerances in volunteers after overnight polysomnography (PSG). Three pro-inflammatory and 3 hypoxia markers were determined in the serum. Pain tests were performed at baseline, placebo, and two effect site concentrations of remifentanil (1 and 2 µg/ml), an μ-opioid agonist. Linear mixed effects regression models were employed to evaluate the association of 3 PSG descriptors [wake after sleep onset, number of sleep stage shifts, and lowest oxyhemoglobin saturation (SaO2) during sleep] and all serum markers with pain thresholds and tolerances at baseline, as well as their changes under remifentanil.
Results
Forty-three volunteers (12 normal and 31 with a PSG-based diagnosis of OSA) were included in the analysis. The lower nadir SaO2 and higher insulin growth factor binding protein-1 (IGFBP-1) were associated with higher analgesic sensitivity to remifentanil (SaO2, P = 0.0440; IGFBP-1, P = 0.0013). Other pro-inflammatory mediators like interleukin-1β and tumor necrosis factor-α (TNF-α) were associated with an enhanced sensitivity to the opioid analgesic effect (IL-1β, P = 0.0218; TNF-α, P = 0.0276).
Conclusions
Nocturnal hypoxemia in subjects at high risk for OSA was associated with an increased potency of opioid analgesia. A serum hypoxia marker (IGFBP-1) was associated with hypoalgesia and increased potency to opioid analgesia; other pro-inflammatory mediators also predicted an enhanced opioid potency.
Trial Registration: ClinicalTrials.gov
NCT00672737.
doi:10.1371/journal.pone.0054807
PMCID: PMC3558510  PMID: 23382975
2.  Sex-specific cognitive deficits and regional brain volume loss in mice exposed to chronic, sublethal hypoxia 
Pediatric research  2011;70(1):15-20.
Male sex is an independent risk factor for long-term neurologic deficits in human preterm infants. Using a chronic, sublethal hypoxia (CSH) mouse model of preterm brain injury, we recently demonstrated acute brain volume loss with an increased male susceptibility to hippocampal volume loss and hypomyelination. We now characterize the long-term, sex-specific effects of CSH on cognition and brain growth. Neonatal mice were treated with CSH for 8 days, raised in normoxia thereafter and underwent behavioral testing at 6 weeks of age. Behavioral assays sensitive to hippocampal function were chosen. CSH-treated males had impairments in associative learning, spatial memory and long-term social memory compared to control males. In contrast, CSH-treated females were less impaired. Persistent reductions in hippocampal and cerebellar volumes were found in adult CSH-treated males while regional brain volumes in CSH-treated females were indistinguishable from controls. Similar to human preterm infants, males exposed to hypoxia are especially vulnerable to short-term and long-term deficits in cognition and brain growth.
doi:10.1203/PDR.0b013e31821b98a3
PMCID: PMC3547599  PMID: 21436761
3.  Graphical Procedures for Evaluating Overall and Subject-specific Incremental Values from New Predictors with Censored Event Time Data 
Biometrics  2011;67(4):1389-1396.
Summary
Quantitative procedures for evaluating added values from new markers over a conventional risk scoring system for predicting event rates at specific time points have been extensively studied. However, a single summary statistic, for example, the area under the receiver operating characteristic curve or its derivatives, may not provide a clear picture about the relationship between the conventional and the new risk scoring systems. When there are no censored event time observations in the data, two simple scatterplots with individual conventional and new scores for “cases” and “controls” provide valuable information regarding the overall and the subject-specific level incremental values from the new markers. Unfortunately, in the presence of censoring, it is not clear how to construct such plots. In this paper, we propose a nonparametric estimation procedure for the distributions of the differences between two risk scores conditional on the conventional score. The resulting quantile curves of these differences over the subject-specific conventional score provide extra information about the overall added value from the new marker. They also help us to identify a subgroup of future subjects who need the new predictors, especially when there is no unified utility function available for cost-risk-benefit decision making. The procedure is illustrated with two data sets. The first is from a well-known Mayo Clinic PBC liver study. The second is from a recent breast cancer study on evaluating the added value from a gene score, which is relatively expensive to measure compared with the routinely used clinical biomarkers for predicting the patient's survival after surgery.
doi:10.1111/j.1541-0420.2011.01600.x
PMCID: PMC3144297  PMID: 21504421
Discriminant analysis; Nonparametric function estimation; Prediction; Receiver operating characteristic curve
4.  Comparing costs associated with risk stratification rules for t-year survival 
Biostatistics (Oxford, England)  2011;12(4):597-609.
Accurate risk prediction is an important step in developing optimal strategies for disease prevention and treatment. Based on the predicted risks, patients can be stratified to different risk categories where each category corresponds to a particular clinical intervention. Incorrect or suboptimal interventions are likely to result in unnecessary financial and medical consequences. It is thus essential to account for the costs associated with the clinical interventions when developing and evaluating risk stratification (RS) rules for clinical use. In this article, we propose to quantify the value of an RS rule based on the total expected cost attributed to incorrect assignment of risk groups due to the rule. We have established the relationship between cost parameters and optimal threshold values used in the stratification rule that minimizes the total expected cost over the entire population of interest. Statistical inference procedures are developed for evaluating and comparing given RS rules and examined through simulation studies. The proposed procedures are illustrated with an example from the Cardiovascular Health Study.
doi:10.1093/biostatistics/kxr001
PMCID: PMC3169667  PMID: 21415016
Disease prognosis; Optimal risk stratification; Risk prediction
5.  Lower Extremity Nerve Function, Calf Skeletal Muscle Characteristics, and Functional Performance in Peripheral Arterial Disease 
Objectives
To determine whether poor lower extremity nerve function is associated with more adverse calf muscle characteristics and greater functional impairment in people with and without peripheral arterial disease (PAD).
Design
Cross-sectional
Setting
Three Chicago-area medical centers
Participants
413 participants with PAD (ankle-brachial index (ABI) <0.90) and 271 participants without PAD.
Measurements
Electrodiagnostic testing of the peroneal nerve was performed. Calf muscle cross-sectional area and percent fat were measured using computed tomography at 66.7% of the distance between the distal and proximal tibia. 6-minute walk performance was measured.
Results
Adjusting for age, sex, race, ABI, leg symptoms, smoking, physical activity, comorbidities, and other covariates, lower peroneal nerve conduction velocity (NCV) was associated with lower calf muscle area (1st quartile: 5571.1 mm2, 4th quartile: 4770.3 mm2, p-value<0.001) and poorer 6-minute walk distance (1st quartile: 989.2 ft, 4th quartile: 1210.8 ft, p-value<0.001) in non-diabetic PAD participants. Lower peroneal NCV was associated with lower calf muscle area (1st quartile: 5166.0 mm2, 4th quartile: 6003.8 mm2, p-value=0.014) and poorer 6-minute walk distance (1st quartile: 866.4 ft, 4th quartile: 1082.5 ft, p-value=0.012) in diabetic PAD participants as well. Among non-PAD participants, lower peroneal NCV was not associated with lower calf muscle area but was associated with poorer 6-minute walk distance in non-diabetic participants only (1st quartile 1317.0 ft, 4th quartile 1570.4 ft; p-trend<0.001).
Conclusion
Lower peroneal nerve function is associated with smaller calf muscle area in individuals with PAD and greater functional impairment in individuals with PAD. Future study is needed to determine whether improving peroneal NCV prevents loss of calf muscle and functional decline in PAD.
doi:10.1111/j.1532-5415.2011.03600.x
PMCID: PMC3222937  PMID: 22091499
Claudication; Muscles; Peripheral Nervous System; Peripheral Vascular Disease; Physical functioning
6.  Fast microbubble dwell-time based ultrasonic molecular imaging approach for quantification and monitoring of angiogenesis in cancer 
Purpose
To develop and test a fast ultrasonic molecular imaging technique for quantification and monitoring of angiogenesis in cancer.
Materials and methods
A new software algorithm measuring the dwell time of contrast microbubbles in near real-time (henceforth, fast method) was developed and integrated in a clinical ultrasound system. In vivo quantification and monitoring of tumor angiogenesis during anti-VEGF antibody therapy was performed in human colon cancer xenografts in mice (n=20) using the new fast method following administration of vascular endothelial growth factor receptor 2 (VEGFR2)-targeted contrast microbubbles. Imaging results were compared with a traditional destruction/replenishment approach (henceforth, traditional method) in an intra-animal comparison.
Results
There was excellent correlation (R2=0.93; P<0.001) between the fast method and the traditional method in terms of VEGFR2-targeted in vivo ultrasonic molecular imaging with significantly higher (P=0.002) imaging signal in colon cancer xenografts using VEGFR2-targeted compared to control non-targeted contrast microbubbles. The new fast method was highly reproducible (ICC=0.87). Following anti-angiogenic therapy, ultrasonic molecular imaging signal decreased by an average of 41±10%, whereas imaging signal increased by an average of 54±8% in non-treated tumors over a 72-hour period. Decreased VEGFR2 expression levels following anti-VEGF therapy were confirmed on ex vivo immunofluorescent staining.
Conclusions
Fast ultrasonic molecular imaging based on dwell time microbubble signal measurements correlates well with the traditional measurement method, and allows reliable in vivo monitoring of anti-angiogenic therapy in human colon cancer xenografts. The improved work-flow afforded by the new quantification approach may facilitate clinical translation of ultrasonic molecular imaging.
doi:10.3978/j.issn.2223-4292.2012.06.05
PMCID: PMC3430464  PMID: 22943043
Angiogenesis; cancer; ultrasound; microbubbles; molecular imaging; anti-VEGF therapy; dwell time
7.  Self-assembled poly(ε-caprolactone)-g-chondroitin sulfate copolymers as an intracellular doxorubicin delivery carrier against lung cancer cells 
The aim of this study was to utilize self-assembled polycaprolactone (PCL)-grafted chondroitin sulfate (CS) as an anticancer drug carrier. We separately introduced double bonds to the hydrophobic PCL and the hydrophilic CS. The modified PCL was reacted with the modified CS through a radical reaction (CSMA-g-PCL). The copolymer without doxorubicin (DOX) was noncytotoxic in CRL-5802 and NCI-H358 cells at a concentration ranging from 5–1000 μg/mL and DOX-loaded CSMA-g-PCL (Micelle DOX) had the lowest inhibitory concentration of 50% cell growth values against the NCI-H358 cells among test samples. The cellular uptake of Micelle DOX into the cells was confirmed by flow cytometric data and confocal laser scanning microscopic images. The in vivo tumor-targeting efficacy of Micelle DOX was realized using an NCI-H358 xenograft nude mouse model. The mice administered with Micelle DOX showed suppressed growth of the NCI-H358 lung tumor compared with those administered with phosphate-buffered saline and free DOX.
doi:10.2147/IJN.S33602
PMCID: PMC3418078  PMID: 22904627
chondroitin sulfate; poly(ε-caprolactone); amphiphilic copolymers; micelles; cellular uptake
8.  Physical Activity During Daily Life and Circulating Biomarker Levels in Patients with Peripheral Arterial Disease 
The American Journal of Cardiology  2008;102(9):1263-1268.
Higher levels of inflammation are associated with adverse outcomes in persons with lower extremity peripheral arterial disease (PAD). This study evaluated associations of physical activity during daily life with levels of inflammatory biomarkers, D-dimer, and homocysteine in persons with PAD. Participants were 244 men and women (mean age 74.4 years ± 8.2) with PAD (ankle brachial index (ABI) < .90). C reactive protein (CRP), Interleukin-6 (IL-6), soluble Intracellular Adhesion Molecule-1 (sICAM-1), soluble Vascular Cellular Adhesion Molecule-1 (sVCAM-1), D-dimer, and homocysteine were assessed at study entry. Physical activity was objectively assessed via a vertical accelerometer, which participants wore continuously for 7 days. After adjusting for age, sex, race, body mass index, smoking, comorbidities, ABI, and other potential confounders, higher physical activity levels were associated linearly and significantly with lower levels of all measured circulating biomarkers: sVCAM-1 (p trend = 0.001); D-Dimer (p trend = 0.005); homocysteine (p trend = 0.006); IL-6 (p trend = 0.010); CRP, (p trend = 0.028); sICAM-1 (p trend = 0.033). In conclusion, higher levels of physical activity were associated independently with lower levels of inflammatory markers, homocysteine, and D-dimer in PAD patients.
doi:10.1016/j.amjcard.2008.06.051
PMCID: PMC3404486  PMID: 18940304
9.  A Perturbation Method for Inference on Regularized Regression Estimates 
Analysis of high dimensional data often seeks to identify a subset of important features and assess their effects on the outcome. Traditional statistical inference procedures based on standard regression methods often fail in the presence of high-dimensional features. In recent years, regularization methods have emerged as promising tools for analyzing high dimensional data. These methods simultaneously select important features and provide stable estimation of their effects. Adaptive LASSO and SCAD for instance, give consistent and asymptotically normal estimates with oracle properties. However, in finite samples, it remains difficult to obtain interval estimators for the regression parameters. In this paper, we propose perturbation resampling based procedures to approximate the distribution of a general class of penalized parameter estimates. Our proposal, justified by asymptotic theory, provides a simple way to estimate the covariance matrix and confidence regions. Through finite sample simulations, we verify the ability of this method to give accurate inference and compare it to other widely used standard deviation and confidence interval estimates. We also illustrate our proposals with a data set used to study the association of HIV drug resistance and a large number of genetic mutations.
doi:10.1198/jasa.2011.tm10382
PMCID: PMC3404855  PMID: 22844171
High dimensional regression; Interval estimation; Oracle property; Regularized estimation; Resampling methods
10.  GLYCEMIC CONTROL BY A GLUCOSE MANAGEMENT SERVICE AND INFECTION RATES FOLLOWING LIVER TRANSPLANTATION 
Objective
Intensive glycemic control with a dedicated glucose management service (GMS) has been used to manage hyperglycemic inpatients. We present an analysis of glycemic control before and after introduction of a GMS and outcomes within one year after liver transplantation (LT).
Methods
A retrospective review of patients undergoing LT who were treated with insulin infusions post-LT, before and after introduction of a GMS. Outcome measures within one year post-LT included rejection, infection, prolonged ventilation, and graft survival. A multiple logistic regression was used to examine the relationship between GMS use and outcomes.
Results
73 (35 GMS, 38 non-GMS) recipients were included. The mean perioperative blood glucose in the GMS group was lower than non-GMS group: unadjusted by 31.1 mg/dL (p=0.001) and adjusted for pre-insulin drip glucose, age, gender, MELD-score (Model for End Stage Liver Disease), type of transplant by 23.4 mg/dL (p=0.020). There were 27 rejection episodes, 48 infections, 26 episodes of prolonged ventilation, and 64 with graft survival at one year. Infection rate in the GMS group was lower than for non-GMS group: unadjusted OR=0.28 (p=0.015), when adjusted for pre-drip glucose, pre-transplant glucose, age, gender, MELD score, type of transplant and diabetes status prior to transplantation OR=0.24 (95% CI, [0.06, 0.97], p=0.045). There were no significant associations between GMS group and rejection rates, prolonged ventilation, or graft survival.
Conclusions
In this study of LT patients, a GMS was associated with improved glycemic control and reduced postoperative infections. Further studies investigating effects of strict glycemic control after LT are warranted.
doi:10.4158/EP10343.OR
PMCID: PMC3158277  PMID: 21324822
11.  ESTIMATING SUBJECT-SPECIFIC DEPENDENT COMPETING RISK PROFILE WITH CENSORED EVENT TIME OBSERVATIONS 
Biometrics  2010;67(2):427-435.
SUMMARY
In a longitudinal study, suppose that the primary endpoint is the time to a specific event. This response variable, however, may be censored by an independent censoring variable or by the occurrence of one of several dependent competing events. For each study subject, a set of baseline covariates is collected. The question is how to construct a reliable prediction rule for the future subject’s profile of all competing risks of interest at a specific time point for risk-benefit decision makings. In this paper, we propose a two-stage procedure to make inferences about such subject-specific profiles. For the first step, we use a parametric model to obtain a univariate risk index score system. We then estimate consistently the average competing risks for subjects which have the same parametric index score via a nonparametric function estimation procedure. We illustrate this new proposal with the data from a randomized clinical trial for evaluating the efficacy of a treatment for prostate cancer. The primary endpoint for this study was the time to prostate cancer death, but had two types of dependent competing events, one from cardiovascular death and the other from death of other causes.
doi:10.1111/j.1541-0420.2010.01456.x
PMCID: PMC2970653  PMID: 20618311
Local likelihood function; Nonparametric function estimation; Perturbation-resampling method; Risk index score
12.  Fast microbubble dwell-time based ultrasonic molecular imaging approach for quantification and monitoring of angiogenesis in cancer 
Purpose
To develop and test a fast ultrasonic molecular imaging technique for quantification and monitoring of angiogenesis in cancer.
Materials and methods
A new software algorithm measuring the dwell time of contrast microbubbles in near real-time (henceforth, fast method) was developed and integrated in a clinical ultrasound system. In vivo quantification and monitoring of tumor angiogenesis during anti-VEGF antibody therapy was performed in human colon cancer xenografts in mice (n=20) using the new fast method following administration of vascular endothelial growth factor receptor 2 (VEGFR2)-targeted contrast microbubbles. Imaging results were compared with a traditional destruction/replenishment approach (henceforth, traditional method) in an intra-animal comparison.
Results
There was excellent correlation (R2=0.93; P<0.001) between the fast method and the traditional method in terms of VEGFR2-targeted in vivo ultrasonic molecular imaging with significantly higher (P=0.002) imaging signal in colon cancer xenografts using VEGFR2-targeted compared to control non-targeted contrast microbubbles. The new fast method was highly reproducible (ICC=0.87). Following anti-angiogenic therapy, ultrasonic molecular imaging signal decreased by an average of 41±10%, whereas imaging signal increased by an average of 54±8% in non-treated tumors over a 72-hour period. Decreased VEGFR2 expression levels following anti-VEGF therapy were confirmed on ex vivo immunofluorescent staining.
Conclusions
Fast ultrasonic molecular imaging based on dwell time microbubble signal measurements correlates well with the traditional measurement method, and allows reliable in vivo monitoring of anti-angiogenic therapy in human colon cancer xenografts. The improved work-flow afforded by the new quantification approach may facilitate clinical translation of ultrasonic molecular imaging.
doi:10.3978/j.issn.2223-4292.2012.06.05
PMCID: PMC3430464  PMID: 22943043
Angiogenesis; cancer; ultrasound; microbubbles; molecular imaging; anti-VEGF therapy; dwell time
13.  A fusion protein composed of receptor binding domain of vascular endothelial growth factor-A and constant region fragment of antibody: angiogenesis antagonistic activity 
Cytotechnology  2011;63(3):285-293.
Vascular endothelial growth factor (VEGF) promotes the growth of solid tumor mainly via VEGF receptor-1 and receptor-2, which are expressed preferentially in proliferating endothelial cells. Therefore, a strategy for simultaneous blockage of both VEGF receptors may have a useful therapeutic effect in tumor growth. In this study, we utilized a fusion protein which is composed of receptor binding domain of VEGF-A (RBDV) and the constant region fragment (Fc) of a human immunoglobulin G1 (IgG1), to interfere with the growth of human umbilical vein endothelial cells (HUVECs) via VEGF receptors. The results showed that RBDV-IgG1 Fc was able to bind with both VEGF receptor-1 and receptor-2. In addition, RBDV-IgG1 Fc could decrease VEGF-induced proliferation and tube formation among HUVECs. Moreover, the cytotoxic test showed RBDV-IgG1 Fc could also enhance the cytotoxic activity of human natural killing cells. The data are suggesting that the fusion protein, RBDV-IgG1 Fc, may have potential as an angiogenesis antagonist for future tumor therapy.
doi:10.1007/s10616-011-9340-2
PMCID: PMC3081053  PMID: 21461946
Vascular endothelial growth factor; Receptor binding domain of VEGF-A; Immunoglobulin; Fusion protein; Human umbilical vein endothelial cells
14.  Relation of Interleukin-6 and Vascular Cellular Adhesion Molecule-1 Levels to Functional Decline in Patients with Lower Extremity Peripheral Arterial Disease 
The American journal of cardiology  2011;107(9):1392-1398.
We determined whether persistently high levels of interleukin-6 (IL-6) or soluble vascular adhesion molecule (sVCAM-1) are associated with faster functional decline, compared to fluctuating or persistently low biomarker levels, among 255 participants with peripheral arterial disease (PAD). Participants underwent baseline and at least two annual follow-up measures of IL-6 and sVCAM-1. Participants were categorized as follows: Category 1- annual levels of IL-6 (or sVCAM-1) were in the lowest tertile for at least three study visits. Category 3- annual levels of IL-6 (or sVCAM-1) were in the highest tertile for at least three visits. Category 2- levels of IL-6 (or sVCAM-1) did not meet criteria for Groups 1 or 3. Six-minute walk, fastest paced four meter walking velocity, and the short physical performance battery (SPPB) were measured annually. Results were adjusted for age, sex, race, comorbidities, statins, physical activity, the ankle brachial index, and other confounders. Across IL-6 categories, average annual declines in six minute walk performance were Category 1: -21.4 feet, Category 2:-49.2 feet, and Category 3:-76.8 feet (p trend = 0.013) and average annual declines in the SPPB score were -0.18, -0.45, and -0.62, respectively (p trend = 0.022). Similar associations of IL-6 categories with decline in fastest paced walking velocity were observed (p trend = 0.034). There were no significant associations of sVCAM-1 categories with functional decline. In conclusion, among PAD participants, persistently high IL-6 levels are associated with faster functional decline compared to those with fluctuating or persistently low IL-6 levels.
doi:10.1016/j.amjcard.2011.01.007
PMCID: PMC3227858  PMID: 21371679
Inflammation; physical functioning; peripheral arterial disease; intermittent claudication
15.  Superficial Femoral Artery Plaque, the Ankle Brachial Index, and Leg Symptoms in Peripheral Arterial Disease: The Walking and Leg Circulation Study (WALCS) III 
Background
The clinical significance of magnetic resonance imaged (MRI) plaque characteristics in the superficial femoral artery (SFA) is not well established. We studied associations of the ankle brachial index (ABI) and leg symptoms with MRI-measured plaque area and percent lumen area in the SFA in participants with and without lower extremity peripheral arterial disease (PAD).
Methods and Results
Four hundred twenty-seven participants (393 with PAD) underwent plaque imaging of the first 30 millimeters of the SFA. Twelve 2.5 millimeter cross-sectional images of the SFA were obtained. Outcomes were normalized plaque area, adjusted for artery size (0–1 scale, 1=greatest plaque), and lumen area, expressed as a percent of the total artery area. Adjusting for age, sex, race, smoking, statins, cholesterol, and other covariates, lower ABI values were associated with higher normalized mean plaque area (ABI < 0.50:0.79; ABI 0.50 to 0.69:0.73; ABI 0.70 to 0.89:0.65; ABI 0.90 to 0.99:0.62; ABI 1.00 to 1.09:0.48; ABI 1.10–1.30:0.47 (P trend <0.001)) and smaller mean percent lumen area (P trend<0.001). Compared to PAD participants with intermittent claudication, asymptomatic PAD participants had lower normalized mean plaque area (0.72 vs. 0.65, p=0.005) and larger mean percent lumen area (0.30 vs. 0.36, p=0.01), adjusting for the ABI and other confounders.
Conclusions
Lower ABI values are associated with greater MRI-measured plaque burden and smaller lumen area in the first 30 millimeters of the SFA. Compared to PAD participants with claudication, asymptomatic PAD participants have smaller plaque area and larger lumen area in the SFA.
doi:10.1161/CIRCIMAGING.110.962183
PMCID: PMC3229716  PMID: 21436300
atherosclerosis; magnetic resonance imaging; peripheral vascular disease; plaque
16.  Analysis of randomized comparative clinical trial data for personalized treatment selections 
Biostatistics (Oxford, England)  2010;12(2):270-282.
Suppose that under the conventional randomized clinical trial setting, a new therapy is compared with a standard treatment. In this article, we propose a systematic, 2-stage estimation procedure for the subject-level treatment differences for future patient's disease management and treatment selections. To construct this procedure, we first utilize a parametric or semiparametric method to estimate individual-level treatment differences, and use these estimates to create an index scoring system for grouping patients. We then consistently estimate the average treatment difference for each subgroup of subjects via a nonparametric function estimation method. Furthermore, pointwise and simultaneous interval estimates are constructed to make inferences about such subgroup-specific treatment differences. The new proposal is illustrated with the data from a clinical trial for evaluating the efficacy and toxicity of a 3-drug combination versus a standard 2-drug combination for treating HIV-1–infected patients.
doi:10.1093/biostatistics/kxq060
PMCID: PMC3062150  PMID: 20876663
Cross-validation; HIV infection; Non-parametric function estimation; Personalized medicine; Subgroup analysis
17.  A signal processing approach for enriched region detection in RNA polymerase II ChIP-seq data 
BMC Bioinformatics  2012;13(Suppl 2):S2.
Background
RNA polymerase II (PolII) is essential in gene transcription and ChIP-seq experiments have been used to study PolII binding patterns over the entire genome. However, since PolII enriched regions in the genome can be very long, existing peak finding algorithms for ChIP-seq data are not adequate for identifying such long regions.
Methods
Here we propose an enriched region detection method for ChIP-seq data to identify long enriched regions by combining a signal denoising algorithm with a false discovery rate (FDR) approach. The binned ChIP-seq data for PolII are first processed using a non-local means (NL-means) algorithm for purposes of denoising. Then, a FDR approach is developed to determine the threshold for marking enriched regions in the binned histogram.
Results
We first test our method using a public PolII ChIP-seq dataset and compare our results with published results obtained using the published algorithm HPeak. Our results show a high consistency with the published results (80-100%). Then, we apply our proposed method on PolII ChIP-seq data generated in our own study on the effects of hormone on the breast cancer cell line MCF7. The results demonstrate that our method can effectively identify long enriched regions in ChIP-seq datasets. Specifically, pertaining to MCF7 control samples we identified 5,911 segments with length of at least 4 Kbp (maximum 233,000 bp); and in MCF7 treated with E2 samples, we identified 6,200 such segments (maximum 325,000 bp).
Conclusions
We demonstrated the effectiveness of this method in studying binding patterns of PolII in cancer cells which enables further deep analysis in transcription regulation and epigenetics. Our method complements existing peak detection algorithms for ChIP-seq experiments.
doi:10.1186/1471-2105-13-S2-S2
PMCID: PMC3375632  PMID: 22536865
18.  DECLINE IN FUNCTIONAL PERFORMANCE PREDICTS LATER INCREASED MOBILITY LOSS AND MORTALITY IN PERIPHERAL ARTERIAL DISEASE 
BACKGROUND
Associations of decline in functional performance with clinically-important outcomes in patients with peripheral arterial disease (PAD) are unknown.
OBJECTIVES
We hypothesized that greater two-year decline in office-based functional performance measures would be associated with greater mobility loss and mortality in people with PAD.
METHODS
440 men and women with PAD completed the six-minute walk test and measures of walking velocity at baseline and annually for two years. Participants were categorized into tertiles according to their functional decline between baseline and two-year follow-up and were followed annually after the functional change assessment. Cox proportional hazard models were used to assess relations between the two-year change in functional performance with later mortality and mobility loss, adjusting for age, sex, race, the ankle brachial index, comorbidities, and other confounders.
RESULTS
One hundred two participants (23.2%) died during a median follow-up of 44.5 months after functional change was assessed. Of 319 participants without baseline mobility disability, 60 (18.8%) developed mobility loss after functional change was assessed. Participants in the tertile with greatest six-minute walk decline had the highest subsequent mobility loss (Hazard Ratio (HR)=3.50, 95% Confidence Interval (CI)=1.56–7.85, p=0.002), all-cause mortality (HR=2.16, 95% CI=1.28–3.64, p=0.004), and cardiovascular disease (CVD) mortality (HR=2.45, 95% CI=1.08–5.54, p=0.031), compared to those with the smallest six-minute walk decline. Greater declines in fastest paced four-meter walking velocity were associated with higher mobility loss (P trend=0.018), all-cause mortality (P trend=0.01) and CVD mortality (P trend=0.004).
CONCLUSION
PAD participants with declining functional performance are at increased risk for later mobility loss and mortality.
doi:10.1016/j.jacc.2010.09.053
PMCID: PMC3222682  PMID: 21329843
peripheral vascular disease; mortality; physical functioning
19.  Liposome-based polymer complex as a novel adjuvant: enhancement of specific antibody production and isotype switch 
The aim of vaccination is to induce appropriate immunity against pathogens. Antibody-mediated immunity is critical for protection against many virus diseases, although it is becoming more evident that coordinated, multifunctional immune responses lead to the most effective defense. Specific antibody (Ab) isotypes are more efficient at protecting against pathogen invasion in different locations in the body. For example, compared to other Ab isotypes, immunoglobulin (Ig) A provides more protection at mucosal areas. In this study, we developed a cationic lipopolymer (liposome-polyethylene glycol-polyethyleneimine complex [LPPC]) adjuvant that strongly adsorbs antigens or immunomodulators onto its surface to enhance or switch immune responses. The results demonstrate that LPPC enhances uptake ability, surface marker expression, proinflammatory cytokine release, and antigen presentation in mouse phagocytes. In contrast to Freund’s adjuvant, LPPC preferentially activates Th1- immunity against antigens in vivo. With lipopolysaccharides or CpG oligodeoxynucleotides, LPPC dramatically enhances the IgA or IgG2A proportion of total Ig, even in hosts that have developed Th2 immunities and high IgG1 serum titers. Taken together, the results demonstrate that the LPPC adjuvant not only increases the immunogenicity of antigens but also modulates host immunity to produce an appropriate Ab isotype by combining with immunomodulators.
doi:10.2147/IJN.S28097
PMCID: PMC3277439  PMID: 22346354
liposome-PEG-PEI complex; adjuvant; class switch; immunomodulator; vaccine
20.  Adaptive index models for marker-based risk stratification 
We use the term “index predictor” to denote a score that consists of K binary rules such as “age > 60” or “blood pressure > 120 mm Hg.” The index predictor is the sum of these binary scores, yielding a value from 0 to K. Such indices as often used in clinical studies to stratify population risk: They are usually derived from subject area considerations. In this paper, we propose a fast data-driven procedure for automatically constructing such indices for linear, logistic, and Cox regression models. We also extend the procedure to create indices for detecting treatment–marker interactions. The methods are illustrated on a study with protein biomarkers as well as a large microarray gene expression study.
doi:10.1093/biostatistics/kxq047
PMCID: PMC3006126  PMID: 20663850
Degree of freedom; Index predictor; International prognostic index
21.  Ultrasound-Mediated Gene Delivery with Cationic Versus Neutral Microbubbles: Effect of DNA and Microbubble Dose on In Vivo Transfection Efficiency 
Theranostics  2012;2(11):1078-1091.
Objective: To assess the effect of varying microbubble (MB) and DNA doses on the overall and comparative efficiencies of ultrasound (US)-mediated gene delivery (UMGD) to murine hindlimb skeletal muscle using cationic versus neutral MBs.
Materials and Methods: Cationic and control neutral MBs were characterized for size, charge, plasmid DNA binding, and ability to protect DNA against endonuclease degradation. UMGD of a codon optimized firefly luciferase (Fluc) reporter plasmid to endothelial cells (1 MHz, 1 W/cm², 20% duty cycle, 1 min) was performed in cell culture using cationic, neutral, or no MBs. In vivo UMGD to mouse hindlimb muscle was performed by insonation (1 MHz, 2 W/cm², 50% duty cycle, 5 min) after intravenous administration of Fluc combined with cationic, neutral, or no MBs. Gene delivery efficiency was assessed by serial in vivo bioluminescence imaging. Efficiency of in vivo UMGD with cationic versus neutral MBs was systematically evaluated by varying plasmid DNA dose (10, 17.5, 25, 37.5, and 50 µg) while maintaining a constant MB dose of 1x108 MBs and by changing MB dose (1x107, 5x107, 1x108, or 5x108 MBs) while keeping a constant DNA dose of 50 µg.
Results: Cationic and size-matched control neutral MBs differed significantly in zeta potential with cationic MBs being able to bind plasmid DNA (binding capacity of 0.03 pg/MB) and partially protect DNA from nuclease degradation while neutral MBs could not. Cationic MBs enhanced UMGD compared to neutral MBs as well as no MB and no US controls both in cell culture (P < 0.001) and in vivo (P < 0.05). Regardless of MB type, in vivo UMGD efficiency increased dose-dependently with DNA dose and showed overall maximum transfection with 50 µg DNA. However, there was an inverse correlation (ρ = -0.90; P = 0.02) between DNA dose and the degree of enhanced UMGD efficiency observed with using cationic MBs instead of neutral MBs. The delivery efficiency advantage associated with cationic MBs was most prominent at the lowest investigated DNA dose (7.5-fold increase with cationic versus neutral MBs at a DNA dose of 10 µg; P = 0.02) compared to only a 1.4-fold increase at a DNA dose of 50 µg (P < 0.01). With increasing MB dose, overall in vivo UMGD efficiency increased dose-dependently with a maximum reached at a dose of 1x108 MBs with no further significant increase with 5x108 MBs (P = 0.97). However, compared to neutral MBs, cationic MBs enhanced UMGD efficiency the most at low MB doses. Relative enhancement of UMGD efficiency using cationic over neutral MBs decreased from a factor of 27 for 1x107 MBs (P = 0.02) to a factor of 1.4 for 1x108 MBs (P < 0.01) and no significant difference for 5x108 MBs.
Conclusions: Cationic MBs enhance UMGD to mouse skeletal muscle relative to neutral MBs but this is dependent on MB and DNA dose. The enhancement effect of cationic MBs on UMGD efficiency is more evident when lower doses of MBs or DNA are used, whereas the advantage of cationic MBs over neutral MBs is substantially reduced in the presence of excess MBs or DNA.
doi:10.7150/thno.4240
PMCID: PMC3516840  PMID: 23227124
Ultrasound; gene therapy; ultrasound-mediated gene delivery; microbubble; sonoporation.
22.  PATHOPHYSIOLOGIC CHANGES IN CALF MUSCLE PREDICT MOBILITY LOSS AT TWO-YEAR FOLLOW-UP IN MEN AND WOMEN WITH PERIPHERAL ARTERIAL DISEASE 
Circulation  2009;120(12):1048-1055.
BACKGROUND
Associations of pathophysiologic calf muscle characteristics with functional decline in people with lower extremity peripheral arterial disease (PAD) are unknown.
METHODS AND RESULTS
Three hundred seventy participants with PAD underwent baseline measurement of calf muscle area, density, and percent fat using computed tomography. Participants were followed annually for two years. The outcome of mobility loss was defined as becoming unable to walk ¼ mile or walk up and down one flight of stairs without assistance, among those without baseline mobility limitations. Additional outcomes were ≥ 20% decline in six-minute walk distance and becoming unable to walk for six minutes continuously among participants who walked continuously for six minutes at baseline. Adjusting for age, sex, race, body mass index, the ankle brachial index, smoking, physical activity, relevant medications, and comorbidities, lower calf muscle density (p trend < 0.001) and lower calf muscle area (p trend =0.039) were each associated with increased mobility loss rates. Compared to participants in the highest baseline tertiles, participants in the lowest tertile of calf muscle percent fat had a hazard ratio of 0.18 for incident mobility loss (95% CI = 0.06–0.55, p=0.003), and participants in the lowest tertile of muscle density had a 3.50 hazard ratio for incident mobility loss (95% CI= 1.28–9.57, p=0.015). No significant associations of calf muscle characteristics with six-minute walk outcomes were observed.
CONCLUSION
Our findings suggest that interventions to prevent mobility loss in PAD should focus on reversing pathophysiologic findings in calf muscle.
doi:10.1161/CIRCULATIONAHA.108.842328
PMCID: PMC3246405  PMID: 19738138
Intermittent claudication; mobility; peripheral arterial disease; physical functioning
23.  ZBRK1 acts as a metastatic suppressor by directly regulating MMP9 in cervical cancer 
Cancer research  2009;70(1):192-201.
ZBRK1, named after its structure of Zinc finger and BRCA1-interacting protein with KRAB domain-1 (ZBRK1), is a transcriptional repressor modulated by BRCA1. Recent evidence also indicated that ZBRK1 collaborated with BRCA1/CtIP to repress angiopoietin-1 expression in preventing over enlargement of blood vessels in tumors, suggesting that ZBRK1 may exert a critical role during tumor progression. However, a direct role of ZBRK1 in tumorigenesis and tumor progression remains obscure. Here we found that ZBRK1 expression was significantly lower in highly malignant cervical cancer cells than the counterpart normal tissue. Ectopic expression of ZBRK1 in HeLa cells significantly inhibits its neoplastic phenotypes including cell proliferation, soft-agar colony formation and tumor growth in nude mice. To explore its mechanisms, analyses of gene expression patterns of these cells revealed groups of genes not only critical for cell proliferation but also for cell motility being down regulated. Consistently, ectopic expression of ZBRK1 inhibits HeLa cells migration in cell migration and invasion assays in culture and metastatic assay in mice. Importantly, ZBRK1 directly represses transcription of the metastatic gene, MMP9, and the loss of ZBRK1 expression is inversely correlated to the elevated expression of MMP9 in cervical cancer specimens. Taken together, these results indicate that ZBRK1 may have a critical role as a tumor suppressor, especially in metastasis, through directly modulating metastatic genes such as MMP9.
doi:10.1158/0008-5472.CAN-09-2641
PMCID: PMC3237114  PMID: 19996286
24.  Leg Symptom Categories and Rates of Mobility Decline in Peripheral Arterial Disease 
Objectives
To determine whether asymptomatic lower extremity peripheral arterial disease (PAD) and leg symptoms other than intermittent claudication (IC) in PAD are associated with faster functional decline compared to people with both PAD and IC.
Design
Prospective, observational study.
Setting
Chicago-area medical center.
Participants
415 men and women with PAD followed annually for up to seven years.
Measurements
At baseline, PAD patients were categorized into symptom categories including IC, leg pain on exertion and rest, pain/carry on (participants walk through exertional leg pain), and always asymptomatic (participants who never experience exertional leg pain, even during the six-minute walk). Outcomes included mobility loss (becoming unable to walk ¼ mile or walk up and down one flight of stairs without assistance) and becoming unable to complete the six minute walk without stopping. Analyses adjust for age, sex, comorbidities, the ankle brachial index (ABI) and other confounders.
Results
Always asymptomatic PAD participants (hazard ratio (HR)=2.94, 95% Confidence Interval (CI)= 1.34-5.42, p=0.005) and those with leg pain on exertion and rest (HR=2.89, 95% CI=1.47-5.68, p=0.002) had increased mobility loss compared to participants with IC. PAD participants with leg pain/carry on were less likely (p=0.047) to become unable to walk for six minutes continuously without stopping, compared to participants with IC.
Conclusion
The ABI identifies asymptomatic PAD patients and those with atypical leg symptoms who are at risk for greater mobility decline than participants without PAD and PAD participants with IC.
doi:10.1111/j.1532-5415.2010.02941.x
PMCID: PMC3227868  PMID: 20550604
intermittent claudication; peripheral vascular disease; physical functioning
25.  LEG STRENGTH PREDICTS MORTALITY IN MEN BUT NOT IN WOMEN WITH PERIPHERAL ARTERIAL DISEASE 
Objective
To establish associations between leg strength and mortality in men and women with lower extremity peripheral arterial disease (PAD).
Design
Observational, prospective study.
Setting
Chicago area medical centers.
Subjects
Participants were 410 men and women with PAD age 55 and older followed for a mean of 60.0 months.
Interventions
Isometric knee extension, knee flexion, hip extension, and hip flexion were measured at baseline. Primary outcomes were all-cause and cardiovascular disease mortality. Cox proportional hazards models were used to assess relations between leg strength and all-cause and cardiovascular disease mortality among men and women, adjusting for age, race, comorbidities, smoking, body mass index, and the ankle brachial index.
Results
Among the 246 male participants, poorer baseline strength for knee flexion (P trend = .029), knee extension (P trend =.010), and hip extension (P trend = .013) were each associated independently with higher all-cause mortality. Poorer strength for knee flexion (P trend = .042) and hip extension (P trend = .029) were associated with higher cardiovascular mortality. Compared to those in the fourth (best) baseline knee flexion quartile, Hazard Ratios for all-cause and cardiovascular disease mortality among men in the 1st (poorest) knee flexion quartile were 2.23 (95% Confidence Interval (CI) = 1.02–4.87, P=.045) and 4.20 (95% CI = 1.12–15.79, P=.043), respectively. No significant associations of leg strength and all-cause mortality were identified among women.
Conclusions
Poorer leg strength is associated with increased mortality in men, but not women, with PAD. Future study is needed to determine whether interventions that increase leg strength improve survival in men with PAD.
doi:10.1016/j.jvs.2010.03.066
PMCID: PMC3222683  PMID: 20598471

Results 1-25 (51)