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author:("Li, tingling")
1.  Inverse probability weighting for covariate adjustment in randomized studies 
Statistics in medicine  2013;33(4):555-568.
Covariate adjustment in randomized clinical trials has the potential benefit of precision gain. It also has the potential pitfall of reduced objectivity as it opens the possibility of selecting “favorable” model that yields strong treatment benefit estimate. Although there is a large volume of statistical literature targeting on the first aspect, realistic solutions to enforce objective inference and improve precision are rare. As a typical randomized trial needs to accommodate many implementation issues beyond statistical considerations, maintaining the objectivity is at least as important as precision gain if not more, particularly from the perspective of the regulatory agencies. In this article, we propose a two-stage estimation procedure based on inverse probability weighting to achieve better precision without compromising objectivity. The procedure is designed in a way such that the covariate adjustment is performed before seeing the outcome, effectively reducing the possibility of selecting a “favorable” model that yields a strong intervention effect. Both theoretical and numerical properties of the estimation procedure are presented. Application of the proposed method to a real data example is presented.
PMCID: PMC3899802  PMID: 24038458
clinical trials; covariate adjustment; efficiency; inverse probability weighting; objectivity
2.  Comparative Analysis of Super-Shedder Strains of Escherichia coli O157:H7 Reveals Distinctive Genomic Features and a Strongly Aggregative Adherent Phenotype on Bovine Rectoanal Junction Squamous Epithelial Cells 
PLoS ONE  2015;10(2):e0116743.
Shiga toxin-producing Escherichia coli O157:H7 (O157) are significant foodborne pathogens and pose a serious threat to public health worldwide. The major reservoirs of O157 are asymptomatic cattle which harbor the organism in the terminal recto-anal junction (RAJ). Some colonized animals, referred to as “super-shedders” (SS), are known to shed O157 in exceptionally large numbers (>104 CFU/g of feces). Recent studies suggest that SS cattle play a major role in the prevalence and transmission of O157, but little is known about the molecular mechanisms associated with super-shedding. Whole genome sequence analysis of an SS O157 strain (SS17) revealed a genome of 5,523,849 bp chromosome with 5,430 open reading frames and two plasmids, pO157 and pSS17, of 94,645 bp and 37,446 bp, respectively. Comparative analyses showed that SS17 is clustered with spinach-associated O157 outbreak strains, and belongs to the lineage I/II, clade 8, D group, and genotype 1, a subgroup of O157 with predicted hyper-virulence. A large number of non-synonymous SNPs and other polymorphisms were identified in SS17 as compared with other O157 strains (EC4115, EDL933, Sakai, TW14359), including in key adherence- and virulence-related loci. Phenotypic analyses revealed a distinctive and strongly adherent aggregative phenotype of SS17 on bovine RAJ stratified squamous epithelial (RSE) cells that was conserved amongst other SS isolates. Molecular genetic and functional analyses of defined mutants of SS17 suggested that the strongly adherent aggregative phenotype amongst SS isolates is LEE-independent, and likely results from a novel mechanism. Taken together, our study provides a rational framework for investigating the molecular mechanisms associated with SS, and strong evidence that SS O157 isolates have distinctive features and use a LEE-independent mechanism for hyper-adherence to bovine rectal epithelial cells.
PMCID: PMC4321836  PMID: 25664460
3.  Rapid Rise of Breast Magnetic Resonance Imaging Use: Trends from 2000-2011 
JAMA internal medicine  2014;174(1):114-121.
Breast MRI is highly sensitive for detecting breast cancer. Low specificity, high cost and little evidence regarding mortality benefits, however, limit recommendations for its use to high risk women. How breast MRI is actually used in community settings is not known.
To describe breast MRI trends and indications in a community setting.
Retrospective cohort study.
Large not-for-profit health plan and multi-specialty group medical practice, both in New England.
: 10,518 women age 20 and older enrolled in the health plan for at least one year who had ≥ 1 breast MRIs between January 1, 2000 and December 31, 2011.
Main outcomes
Breast MRI counts were obtained from claims data. Clinical indication (screening, diagnostic evaluation, staging/treatment, or surveillance) for each MRI in the claims data was determined by a prediction model developed from electronic medical records on a subset of participants. Breast cancer risk status was assessed using claims data and, for the subset, also through electronic medical record review.
: Breast MRI use increased more than 20-fold from 6.5 per 10,000 women in 2000 to its peak of 130.7 per 10,000 in 2009. Use declined and stabilized to 104.8 per 10,000 by 2011. Screening and surveillance, rare indications in 2000, together accounted for nearly 60% of MRI use by 2011; 30% had claims-based personal and 50% family history of breast cancer, while 4% of women had a genetic mutation noted. In the subset of women who had electronic medical records and received screening or surveillance MRIs, only 21% had evidence of meeting the American Cancer Society's (ACS's) criteria for breast MRI. Conversely, only half of women with documented deleterious genetic mutations received breast MRI screening.
Breast MRI use rose steeply over ten years and then stabilized, especially for screening and surveillance among women with family or personal history of breast cancer; the majority of women receiving screening and surveillance breast MRIs did not have evidence in their medical records meeting ACS criteria and many women with mutations were not screened. Efforts are needed to ensure that breast MRI use and documentation are focused on those women who will benefit most.
PMCID: PMC4145846  PMID: 24247482
4.  Statin Exposure Is Associated with Decreased Asthma-related Emergency Department Visits and Oral Corticosteroid Use 
Rationale: Statins, or HMG-CoA reductase inhibitors, may aid in the treatment of asthma through their pleiotropic antiinflammatory effects.
Objectives: To examine the effect of statin therapy on asthma-related exacerbations using a large population-based cohort.
Methods: Statin users aged 31 years or greater with asthma were identified from the Population-Based Effectiveness in Asthma and Lung population, which includes data from five health plans. Statin exposure and asthma exacerbations were assessed over a 24-month observation period. Statin users with a statin medication possession ratio greater than or equal to 80% were matched to non–statin users by age, baseline asthma therapy, site of enrollment, season at baseline, and propensity score, which was calculated based on patient demographics and Deyo-Charlson conditions. Asthma exacerbations were defined as two or more oral corticosteroid dispensings, asthma-related emergency department visits, or asthma-related hospitalizations. The association between statin exposure and each of the three outcome measures was assessed using conditional logistic regression.
Measurements and Main Results: Of the 14,566 statin users, 8,349 statin users were matched to a nonuser. After adjusting for Deyo-Charlson conditions that remained unbalanced after matching, among statin users, statin exposure was associated with decreased odds of having asthma-related emergency department visits (odds ratio [OR], 0.64; 95% confidence interval [CI], 0.53–0.77; P < 0.0001) and two or more oral corticosteroid dispensings (OR, 0.90; 95% CI, 0.81–0.99; P = 0.04). There were no differences in asthma-related hospitalizations (OR, 0.91; 95% CI, 0.66–1.24; P = 0.52).
Conclusions: Among statin users with asthma, statin exposure was associated with decreased odds of asthma-related emergency department visits and oral corticosteroid dispensings.
PMCID: PMC3863744  PMID: 24093599
HMG-CoA reductase inhibitors; asthma therapy; exacerbations
5.  Near real-time adverse drug reaction surveillance within population-based health networks: methodology considerations for data accrual 
This study describes practical considerations for implementation of near real-time medical product safety surveillance in a distributed health data network.
We conducted pilot active safety surveillance comparing generic divalproex sodium to historical branded product at 4 health plans from April – October 2009. Outcomes reported are all-cause emergency room (ER) visits and fractures. One retrospective data extract was completed (1/2002–6/2008), followed by seven prospective monthly extracts (1/2008–11/2009). To evaluate delays in claims processing, we used three analytic approaches: near real-time sequential analysis, sequential analysis with 1.5 month delay, and nonsequential (using final retrospective data). Sequential analyses used the maximized sequential probability ratio test. Procedural and logistical barriers to active surveillance were documented.
We identified 6,586 new users of generic divalproex sodium and 43,960 new users of the branded product. Quality control methods identified 16 extract errors, which were corrected. Near real-time extracts captured 87.5% of ER visits and 50.0% of fractures, which improved to 98.3% and 68.7% respectively with 1.5 month delay. We did not identify signals for either outcome regardless of extract timeframe; slight differences in the test statistic and relative risk estimates were found.
Near real-time sequential safety surveillance is feasible, but several barriers warrant attention. Data quality review of each data extract was necessary. Although signal detection was not affected by delay in analysis, when using a historical control group differential accrual between exposure and outcomes may theoretically bias near real-time risk estimates towards the null, causing failure to detect a signal.
PMCID: PMC3644310  PMID: 23401239
Drug Surveillance; Prospective Analysis; Analytic Methods
6.  Outcomes After Periodic Use of Inhaled Corticosteroids in Children 
Many children with persistent asthma use inhaled corticosteroids on a periodic basis. Clinical trials in adults suggest that periodic use of inhaled corticosteroids may be effective for patients with mild persistent asthma. However, scant information exists on the clinical outcomes of children with asthma who are using inhaled corticosteroids on a periodic basis in real-world settings.
This prospective cohort study compared clinical outcomes during a 12-month follow-up period between children with persistent asthma whose parents believed that they were supposed to use inhaled steroids either (a) periodically or (b) daily year-round at the start of the period. The clinical outcomes studied were (1) asthma-related emergency department (ED) visits or hospitalizations, (2) uncontrolled asthma based on health care and medication use, and (3) outpatient visits for asthma.
Patients and methods
The study population included children with persistent asthma from two health plans whose parents reported that they were using inhaled corticosteroids during a baseline telephone interview. The interviews collected information on whether the children’s parents believed they were supposed to use inhaled corticosteroids on a periodic or daily basis, as well as baseline asthma symptom status, sociodemographic, and behavioral variables. We used computerized databases to identify clinical events for each child during the 12 months after their baseline interview. Uncontrolled asthma was defined as any asthma-related ED visit or hospitalization, two or more oral steroid prescription fills, or four or more beta-agonists canisters filled during the 12-month period. We compared these outcomes between the periodic versus daily users of inhaled corticosteroids using logistic regression analyses. We conducted both (1) a traditional logistic regression analysis in which we adjusted for selection bias by including covariates such as age, asthma physical status, sociodemographic and behavioral variables, and history of asthma-related health care use during the year before interview and (2) an analysis using propensity scores to more fully adjust for selection bias.
Of a total of 476 children in the study, 55% of parents believed their children were supposed to be using inhaled corticosteroids on a periodic basis and 45% believed their children were supposed to be using them daily year-round based on the baseline parent interview. At baseline, periodic inhaled corticosteroid users had less severe asthma than daily users based on several measures including better asthma physical status scores on the Children’s Health Survey for Asthma (mean 87 ± 16.0 vs. 81 ± 17.4, p = < 0.0001). During the year before the baseline interview, periodic users compared with daily users were less likely to have an ED visit or hospitalization (10% vs. 23%, p = 0.0001) and less likely to have had five or more albuterol prescription fills (13% vs. 31%, p < 0.0001). During the follow-up year, those who believed inhaled steroids were for periodic use were less likely than those who believed inhaled steroids were for daily use to have an ED visit or hospitalization for asthma (OR 0.36, 95% CI: 0.18–0.73), even after adjusting for baseline asthma status and other covariates. Similarly, those who believed inhaled steroids were for periodic use were less likely to have uncontrolled asthma, OR 0.38 (95% CI: 0.24–0.62). Analyses using propensity score adjustment yielded similar results to the logistic regression analyses.
Children whose parents believed they were supposed to use inhaled corticosteroids on a periodic basis had less severe asthma at baseline than those whose parents believed they were supposed to be using them daily. Periodic users were less likely than daily users to have adverse asthma outcomes during 1-year follow-up. This suggests that clinicians may be applying appropriate selection criteria by choosing patients with less severe asthma for periodic inhaled corticosteroid regimens.
PMCID: PMC4004094  PMID: 19544175
asthma; periodic inhaled corticosteroids; children
7.  On weighting approaches for missing data 
We review the class of inverse probability weighting (IPW) approaches for the analysis of missing data under various missing data patterns and mechanisms. The IPW methods rely on the intuitive idea of creating a pseudo-population of weighted copies of the complete cases to remove selection bias introduced by the missing data. However, different weighting approaches are required depending on the missing data pattern and mechanism. We begin with a uniform missing data pattern (i.e., a scalar missing indicator indicating whether or not the full data is observed) to motivate the approach. We then generalize to more complex settings. Our goal is to provide a conceptual overview of existing IPW approaches and illustrate the connections and differences among these approaches.
PMCID: PMC3998729  PMID: 21705435
missing data; inverse probability weighting; missing at random; missing not at random; monotone missing; non-monotone missing
8.  Automated Detection and Classification of Type 1 Versus Type 2 Diabetes Using Electronic Health Record Data 
Diabetes Care  2013;36(4):914-921.
To create surveillance algorithms to detect diabetes and classify type 1 versus type 2 diabetes using structured electronic health record (EHR) data.
We extracted 4 years of data from the EHR of a large, multisite, multispecialty ambulatory practice serving ∼700,000 patients. We flagged possible cases of diabetes using laboratory test results, diagnosis codes, and prescriptions. We assessed the sensitivity and positive predictive value of novel combinations of these data to classify type 1 versus type 2 diabetes among 210 individuals. We applied an optimized algorithm to a live, prospective, EHR-based surveillance system and reviewed 100 additional cases for validation.
The diabetes algorithm flagged 43,177 patients. All criteria contributed unique cases: 78% had diabetes diagnosis codes, 66% fulfilled laboratory criteria, and 46% had suggestive prescriptions. The sensitivity and positive predictive value of ICD-9 codes for type 1 diabetes were 26% (95% CI 12–49) and 94% (83–100) for type 1 codes alone; 90% (81–95) and 57% (33–86) for two or more type 1 codes plus any number of type 2 codes. An optimized algorithm incorporating the ratio of type 1 versus type 2 codes, plasma C-peptide and autoantibody levels, and suggestive prescriptions flagged 66 of 66 (100% [96–100]) patients with type 1 diabetes. On validation, the optimized algorithm correctly classified 35 of 36 patients with type 1 diabetes (raw sensitivity, 97% [87–100], population-weighted sensitivity, 65% [36–100], and positive predictive value, 88% [78–98]).
Algorithms applied to EHR data detect more cases of diabetes than claims codes and reasonably discriminate between type 1 and type 2 diabetes.
PMCID: PMC3609529  PMID: 23193215
9.  Complete Genome Sequence of Mycobacterium avium subsp. paratuberculosis, Isolated from Human Breast Milk 
Genome Announcements  2014;2(1):e01252-13.
Mycobacterium avium subsp. paratuberculosis is the etiologic agent of Johne’s disease in ruminants and has also been associated with human Crohn’s disease. We report the complete genome sequence of M. avium subsp. paratuberculosis, isolated from the breast milk of a Crohn’s disease patient. This sequence has high identity with characterized strains recovered from cattle.
PMCID: PMC3916490  PMID: 24503996
10.  Evaluation of novel oral vaccine candidates and validation of a caprine model of Johne's disease 
Johne's disease (JD) caused by Mycobacterium avium subspecies paratuberculosis (MAP) is a major threat to the dairy industry and possibly some cases of Crohn's disease in humans. A MAP vaccine that reduced of clinical disease and/or reduced fecal shedding would aid in the control of JD. The objectives of this study were (1) to evaluate the efficacy of 5 attenuated strains of MAP as vaccine candidates compared to a commercial control vaccine using the protocol proposed by the Johne's Disease Integrated Program (JDIP) Animal Model Standardization Committee (AMSC), and (2) to validate the AMSC Johne's disease goat challenge model. Eighty goat kids were vaccinated orally twice at 8 and 10 weeks of age with an experimental vaccine or once subcutaneously at 8 weeks with Silirum® (Zoetis), or a sham control oral vaccine at 8 and 10 weeks. Kids were challenged orally with a total of approximately 1.44 × 109 CFU divided in two consecutive daily doses using MAP ATCC-700535 (K10-like bovine isolate). All kids were necropsied at 13 months post-challenge. Results indicated that the AMSC goat challenge model is a highly efficient and valid model for JD challenge studies. None of the experimental or control vaccines evaluated prevented MAP infection or eliminated fecal shedding, although the 329 vaccine lowered the incidence of infection, fecal shedding, tissue colonization and reduced lesion scores, but less than the control vaccine. Based on our results the relative performance ranking of the experimental live-attenuated vaccines evaluated, the 329 vaccine was the best performer, followed by the 318 vaccine, then 316 vaccine, 315 vaccine and finally the 319 vaccine was the worst performer. The subcutaneously injected control vaccine outperformed the orally-delivered mutant vaccine candidates. Two vaccines (329 and 318) do reduce presence of JD gross and microscopic lesions, slow progression of disease, and one vaccine (329) reduced fecal shedding and tissue colonization.
PMCID: PMC3941644  PMID: 24624365
Mycobacterium avium subsp paratuberculosis; vaccine efficacy; mutant vaccines; diagnostic tests; goats
11.  Sensitivity analysis for causal inference using inverse probability weighting 
Evaluation of impact of potential uncontrolled confounding is an important component for causal inference based on observational studies. In this article, we introduce a general framework of sensitivity analysis that is based on inverse probability weighting. We propose a general methodology that allows both non-parametric and parametric analyses, which are driven by two parameters that govern the magnitude of the variation of the multiplicative errors of the propensity score and their correlations with the potential outcomes. We also introduce a specific parametric model that offers a mechanistic view on how the uncontrolled confounding may bias the inference through these parameters. Our method can be readily applied to both binary and continuous outcomes and depends on the covariates only through the propensity score that can be estimated by any parametric or non-parametric method. We illustrate our method with two medical data sets.
PMCID: PMC3777387  PMID: 21770046
Causal inference; Inverse probability weighting; Propensity score; Sensitivity analysis; Uncontrolled confounding
12.  Effect of Vitamin D and Inhaled Corticosteroid Treatment on Lung Function in Children 
Rationale: Low vitamin D levels are associated with asthma and decreased airway responsiveness. Treatment with inhaled corticosteroids improves airway responsiveness and asthma control.
Objectives: To assess the effect of vitamin D levels on prebronchodilator FEV1, bronchodilator response, and responsiveness to methacholine (PC20, provocative concentration of methacholine producing a 20% decline in FEV1) in patients with asthma treated with inhaled corticosteroids.
Methods: We measured 25-hydroxyvitamin D levels in the serum of children with persistent asthma at the time of enrollment in the Childhood Asthma Management Program. We divided subjects into the vitamin D sufficiency (>30 ng/ml), insufficiency (20–30 ng/ml), and deficiency (<20 ng/ml) groups. Covariates included age, treatment, sex, body mass index, race, history of emergency department visits, hospitalizations, and season that vitamin D specimen was drawn. Our main outcome measures were change in prebronchodilator FEV1, bronchodilator response, and PC20 from enrollment to 8–12 months.
Measurements and Main Results: Of the 1,024 subjects, 663 (65%) were vitamin D sufficient, 260 (25%) were insufficient, and 101 (10%) were deficient. Vitamin D–deficient subjects were more likely to be older, African American, and have a higher body mass index compared with the vitamin D–sufficient and insufficient subjects. In the inhaled corticosteroid treatment group, prebronchodilator FEV1 increased from randomization to 12 months by 140 ml in the vitamin D–deficient group and prebronchodilator FEV1 increased by 330 ml in the vitamin D insufficiency group and by 290 ml in the vitamin D sufficiency group (P = 0.0072), in adjusted models.
Conclusions: In children with asthma treated with inhaled corticosteroids, vitamin D deficiency is associated with poorer lung function than in children with vitamin D insufficiency or sufficiency.
PMCID: PMC3480528  PMID: 22798322
asthma; vitamin D; lung function; forced expiratory volume; children
13.  Guillain-Barré Syndrome, Influenza Vaccination, and Antecedent Respiratory and Gastrointestinal Infections: A Case-Centered Analysis in the Vaccine Safety Datalink, 2009–2011 
PLoS ONE  2013;8(6):e67185.
Guillain-Barré Syndrome (GBS) can be triggered by gastrointestinal or respiratory infections, including influenza. During the 2009 influenza A (H1N1) pandemic in the United States, monovalent inactivated influenza vaccine (MIV) availability coincided with high rates of wildtype influenza infections. Several prior studies suggested an elevated GBS risk following MIV, but adjustment for antecedent infection was limited.
We identified patients enrolled in health plans participating in the Vaccine Safety Datalink and diagnosed with GBS from July 2009 through June 2011. Medical records of GBS cases with 2009–10 MIV, 2010–11 trivalent inactivated influenza vaccine (TIV), and/or a medically-attended respiratory or gastrointestinal infection in the 1 through 141 days prior to GBS diagnosis were reviewed and classified according to Brighton Collaboration criteria for diagnostic certainty. Using a case-centered design, logistic regression models adjusted for patient-level time-varying sources of confounding, including seasonal vaccinations and infections in GBS cases and population-level controls.
Eighteen confirmed GBS cases received vaccination in the 6 weeks preceding onset, among 1.27 million 2009–10 MIV recipients and 2.80 million 2010–11 TIV recipients. Forty-four confirmed GBS cases had infection in the 6 weeks preceding onset, among 3.77 million patients diagnosed with medically-attended infection. The observed-versus-expected odds that 2009–10 MIV/2010–11 TIV was received in the 6 weeks preceding GBS onset was odds ratio = 1.54, 95% confidence interval (CI), 0.59–3.99; risk difference = 0.93 per million doses, 95% CI, −0.71–5.16. The association between GBS and medically-attended infection was: odds ratio = 7.73, 95% CI, 3.60–16.61; risk difference = 11.62 per million infected patients, 95% CI, 4.49–26.94. These findings were consistent in sensitivity analyses using alternative infection definitions and risk intervals for prior vaccination shorter than 6 weeks.
After adjusting for antecedent infections, we found no evidence for an elevated GBS risk following 2009–10 MIV/2010–11 TIV influenza vaccines. However, the association between GBS and antecedent infection was strongly elevated.
PMCID: PMC3694016  PMID: 23840621
14.  Development of a Pharmacogenetic Predictive Test in asthma: proof of concept 
Pharmacogenetics and genomics  2010;20(2):86-93.
To assess the feasibility of developing a Combined Clinical and Pharmacogenetic Predictive Test, comprised of multiple single nucleotide polymorphisms (SNPs) that is associated with poor bronchodilator response (BDR).
We genotyped SNPs that tagged the whole genome of the parents and children in the Childhood Asthma Management Program (CAMP) and implemented an algorithm using a family-based association test that ranked SNPs by statistical power. The top eight SNPs that were associated with BDR comprised the Pharmacogenetic Predictive Test. The Clinical Predictive Test was comprised of baseline forced expiratory volume in 1 s (FEV1). We evaluated these predictive tests and a Combined Clinical and Pharmacogenetic Predictive Test in three distinct populations: the children of the CAMP trial and two additional clinical trial populations of asthma. Our outcome measure was poor BDR, defined as BDR of less than 20th percentile in each population. BDR was calculated as the percent difference between the prebronchodilator and postbronchodilator (two puffs of albuterol at 180 μg/puff) FEV1 value. To assess the predictive ability of the test, the corresponding area under the receiver operating characteristic curves (AUROCs) were calculated for each population.
The AUROC values for the Clinical Predictive Test alone were not significantly different from 0.50, the AUROC of a random classifier. Our Combined Clinical and Pharmacogenetic Predictive Test comprised of genetic polymorphisms in addition to FEV1 predicted poor BDR with an AUROC of 0.65 in the CAMP children (n= 422) and 0.60 (n= 475) and 0.63 (n= 235) in the two independent populations. Both the Combined Clinical and Pharmacogenetic Predictive Test and the Pharmacogenetic Predictive Test were significantly more accurate than the Clinical Predictive Test (AUROC between 0.44 and 0.55) in each of the populations.
Our finding that genetic polymorphisms with a clinical trait are associated with BDR suggests that there is promise in using multiple genetic polymorphisms simultaneously to predict which asthmatics are likely to respond poorly to bronchodilators.
PMCID: PMC3654515  PMID: 20032818
asthma; bronchodilator response; personalized medicine; pharmacogenetic test; predictive medicine
15.  Comparative safety of infliximab and etanercept on the risk of serious infections – Does the association vary by patient characteristics? 
Infliximab, a chimeric monoclonal anti-TNFα antibody, has been found to increase the risk of serious infections compared with the TNF receptor fusion protein etanercept in some studies. It is unclear whether the risk varies by patient characteristics. We conducted a study to address this question.
We identified members of Kaiser Permanente Northern California who initiated infliximab (n=793) or etanercept (n=2,692) in 1997–2007. Using a Cox model, we estimated the propensity score-adjusted hazard ratio (HR) and 95% confidence interval (CI) of serious infections requiring hospitalization or opportunistic infections comparing infliximab with etanercept following treatment initiation. We tested whether the adjusted HR differed by age, sex, race/ethnicity, body mass index, and smoking status.
The crude incidence rate of serious infections per 100 person-years was 5.4 (95% CI: 3.8, 7.5) in patients <65 years and 16.0 (10.4, 23.4) in patients ≥65 years during the first three months following treatment initiation. Compared with etanercept, the adjusted HR during this period was elevated for infliximab in patients <65 years (HR 3.01; 95% CI: 1.49, 6.07), but not in those ≥65 years (HR 0.94; 0.41, 2.13). Findings did not suggest that the HR varied by other patient characteristics examined.
An increased risk of serious infections associated with infliximab relative to etanercept did not appear to be modified by patients’ sex, race/ethnicity, body mass index, or smoking status. There was an indication that the increased risk might be limited to patients <65 years. Additional studies are warranted to verify or refute this finding.
PMCID: PMC3330193  PMID: 22411435
Anti-TNF agents; Database; Pharmacoepidemiology; Propensity score; Serious infections
16.  Metabolic engineering of Escherichia coli for high-specificity production of isoprenol and prenol as next generation of biofuels 
The isopentenols, including isoprenol and prenol, are excellent alternative fuels. However, they are not compounds largely accumulated in natural organism. The need for the next generation of biofuels with better physical and chemical properties impels us to develop biosynthetic routes for the production of isoprenol and prenol from renewable sugar. In this study, we use the heterogenous mevalonate-dependent (MVA) isoprenoid pathway for the synthesis of isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP) intermediates, and then convert IPP and DMAPP to isoprenol and prenol, respectively.
A mevalonate titer of 1.7 g/L was obtained by constructing an efficient MVA upper pathway in engineered E. coli. Different phosphatases and pyrophosphatases were investigated for their abilities in hydrolyzing the IPP and DMAPP. Consequently, ADP-ribose pyrophosphatase was found to be an efficient IPP and DMAPP hydrolase. Moreover, ADP-ribose pyrophosphatase from Bacillus subtilis (BsNudF) exhibited a equivalent substrate specificity towards IPP and DMAPP, while ADP-ribose pyrophosphatase from E. coli (EcNudF) presented a high substrate preference for DMAPP. Without the expression of any phosphatases or pyrophosphatases, a background level of isopentenols was synthesized. When the endogenous pyrophosphatase genes (EcNudF and yggV) that were capable of enhancing the hydrolyzation of the IPP and DMAPP were knocked out, the background level of isopentenols was still obtained. Maybe the synthesized IPP and DMAPP were hydrolyzed by some unknown hydrolases of E. coli. Finally, 1.3 g/L single isoprenol was obtained by blocking the conversion of IPP to DMAPP and employing the BsNudF, and 0.2 g/L ~80% prenol was produced by employing the EcNudF. A maximal yield of 12% was achieved in both isoprenol and prenol producing strains.
To the best of our knowledge, this is the first successful report on high-specificity production of isoprenol and prenol by microbial fermentation. Over 1.3 g/L isoprenol achieved in shake-flask experiments represents a quite encouraging titer of higher alcohols. In addition, the substrate specificities of ADP-ribose pyrophosphatases were determined and successfully applied for the high-specificity synthesis of isoprenol and prenol. Altogether, this work presents a promising strategy for high-specificity production of two excellent biofuels, isoprenol and prenol.
PMCID: PMC3654967  PMID: 23618128
Isoprenol; Prenol; Metabolic engineering; Escherichia coli; Biofuel
17.  Electrochemiluminescence energy transfer-promoted ultrasensitive immunoassay using near-infrared-emitting CdSeTe/CdS/ZnS quantum dots and gold nanorods 
Scientific Reports  2013;3:1529.
The marriage of energy transfer with electrochemiluminescence has produced a new technology named electrochemiluminescence energy transfer (ECL-ET), which can realize effective and sensitive detection of biomolecules. To obtain optimal ECL-ET efficiency, perfect energy overlapped donor/acceptor pair is of great importance. Herein, we present a sensitive ECL-ET based immunosensor for the detection of tumor markers, using energy tunable CdSeTe/CdS/ZnS double shell quantum dots (QDs) and gold nanorods (GNRs) as the donor and acceptor, respectively. Firstly a facile microwave-assisted strategy for the synthesis of green- to near-infrared-emitting CdSeTe/CdS/ZnS QDs with time- and component-tunable photoluminescence was proposed. And, on the basis of the adjustable optical properties of both CdSeTe/CdS/ZnS QDs and GNRs, excellent overlap between donor emission and acceptor absorption can be obtained to ensure effective ECL-ET quenching, thus improving the sensing sensitivity. This method represents a novel approach for versatile detection of biomolecules at low concentrations.
PMCID: PMC3607123  PMID: 23524874
18.  Quadratic semiparametric Von Mises calculus 
Metrika  2009;69(2-3):227-247.
We discuss a new method of estimation of parameters in semiparametric and nonparametric models. The method is based on U-statistics constructed from quadratic influence functions. The latter extend ordinary linear influence functions of the parameter of interest as defined in semiparametric theory, and represent second order derivatives of this parameter. For parameters for which the matching cannot be perfect the method leads to a bias-variance trade-off, and results in estimators that converge at a slower than n–1/2-rate. In a number of examples the resulting rate can be shown to be optimal. We are particularly interested in estimating parameters in models with a nuisance parameter of high dimension or low regularity, where the parameter of interest cannot be estimated at n–1/2-rate.
PMCID: PMC3475538  PMID: 23087487
Von Mises calculus; Semiparametric models; Missing data; Tangent space; Influence function; Rate of convergence
19.  Boosting the free fatty acid synthesis of Escherichia coli by expression of a cytosolic Acinetobacter baylyi thioesterase 
Thioesterases remove the fatty acyl moiety from the fatty acyl-acyl carrier proteins (ACPs), releasing them as free fatty acids (FFAs), which can be further used to produce a variety of fatty acid-based biofuels, such as biodiesel, fatty alcohols and alkanes. Thioesterases play a key role in the regulation of the fatty acid synthesis in Escherichia coli. Therefore, exploring more promising thioesterases will contribute to the development of industrial microbial lipids production.
We cloned and expressed a cytosolic Acinetobacter baylyi thioesterase (‘AcTesA) in E. coli by deleting its leader sequence. Protein sequence alignment, structure modeling and site-directed mutagenesis demonstrated that Ser10, Gly48, Asn77, Asp158 and His161 residues composed the active centre of ‘AcTesA. The engineered strain that overexpressed ‘AcTesA achieved a FFAs titer of up to 501.2 mg/L in shake flask, in contrast to only 20.5 mg/L obtained in wild-type E. coli, demonstrating that the expression of ‘AcTesA indeed boosted the synthesis of FFAs. The ‘AcTesA exhibited a substrate preference towards the C8-C16 acyl groups, with C14:0, C16:1, C12:0 and C8:0 FFAs being the top four components. Optimization of expression level of ‘AcTesA made the FFAs production increase to 551.3 mg/L. The FFAs production further increased to 716.1 mg/L by optimization of the culture medium. Fed-batch fermentation was also carried out to evaluate the FFAs production in a scaleable process. Finally, 3.6 g/L FFAs were accumulated within 48 h, and a maximal FFAs yield of 6.1% was achieved in 12–16 h post induction.
For the first time, an A. baylyi thioesterase was cloned and solubly expressed in the cytosol of E. coli. This leaderless thioesterase (‘AcTesA) was found to be capable of enhancing the FFAs production of E. coli. Without detailed optimization of the strain and fermentation, the finally achieved 3.6 g/L FFAs is encouraging. In addition, ‘AcTesA exhibited different substrate specificity from other thioesterases previously reported, and can be used to supply the fatty acid-based biofuels with high quality of FFAs. Altogether, this study provides a promising thioesterase for FFAs production, and is of great importance in enriching the library of useful thioesterases.
PMCID: PMC3524773  PMID: 23057831
Thioesterase; Acinetobacter baylyi; Escherichia coli; Free fatty acid; Substrate specificity; Active-site residues
20.  Purification and characterization of a novel plant lectin from Pinellia ternata with antineoplastic activity 
SpringerPlus  2012;1:13.
A novel Pinellia ternata lectin was purified from the bulbs of a Chinese herb Pinellia ternata using a combination of hydrophobic chromatography and DEAE-ion exchange chromatography. The lectin was found to be a homodimer of 12093.3 Da subunits as determined by gel filtration and MS. Biochemical characterization of the lectin revealed the existence of a glycoprotein, which contains 3.22% neutral sugars. The N-terminal 10-amino acid sequence of the lectin, QGVNISGQVK, has not been reported for other lectins. The lectin had a special agglutinating activity with mouse erythrocytes at a minimum concentration of 8.0 ug/ml. The lectin was stable in the pH range of pH 5–12 and temperatures up to 80°C for 30 min. The results of MTT experiment showed that the lectin had significant effect towards tumor cells, the maximum inhibition of cell proliferation with Sarcoma 180, HeLa and K562 cell line were 85.2%, 74.6% and 59.4% respectively. Experimental therapy in vivo also showed that PTL apparently inhibited transplanted tumor in mice. Flow cytometric analysis demonstrated that PTL inhibited the proliferation of Sarcoma 180 in a time- and dose-dependent manner through inhibiting the transition of G1/S and subsequently inducing G0/G1 cell cycle arrest. Thus, Pinellia ternata lectin displays a high potential for antitumor activity.
PMCID: PMC3725870  PMID: 23961344
Lectin; Pinellia ternata; Antineoplastic activity; Purification
21.  Propensity Score-based Sensitivity Analysis Method for Uncontrolled Confounding 
American Journal of Epidemiology  2011;174(3):345-353.
The authors developed a sensitivity analysis method to address the issue of uncontrolled confounding in observational studies. In this method, the authors use a 1-dimensional function of the propensity score, which they refer to as the sensitivity function (SF), to quantify the hidden bias due to unmeasured confounders. The propensity score is defined as the conditional probability of being treated given the measured covariates. Then the authors construct SF-corrected inverse-probability-weighted estimators to draw inference on the causal treatment effect. This approach allows analysts to conduct a comprehensive sensitivity analysis in a straightforward manner by varying sensitivity assumptions on both the functional form and the coefficients in the 1-dimensional SF. Furthermore, 1-dimensional continuous functions can be well approximated by low-order polynomial structures (e.g., linear, quadratic). Therefore, even if the imposed SF is practically certain to be incorrect, one can still hope to obtain valuable information on treatment effects by conducting a comprehensive sensitivity analysis using polynomial SFs with varying orders and coefficients. The authors demonstrate the new method by implementing it in an asthma study which evaluates the effect of clinician prescription patterns regarding inhaled corticosteroids for children with persistent asthma on selected clinical outcomes.
PMCID: PMC3202161  PMID: 21659349
confounding factors (epidemiology); inverse probability weighting; propensity score; sensitivity analysis; sensitivity function; uncontrolled confounding
22.  Higher Order Inference On A Treatment Effect Under Low Regularity Conditions 
Statistics & probability letters  2011;81(7):821-828.
We describe a novel approach to nonparametric point and interval estimation of a treatment effect in the presence of many continuous confounders. We show the problem can be reduced to that of point and interval estimation of the expected conditional covariance between treatment and response given the confounders. Our estimators are higher order U-statistics. The approach applies equally to the regular case where the expected conditional covariance is root-n estimable and to the irregular case where slower non-parametric rates prevail.
PMCID: PMC3088168  PMID: 21552339
Minimax; U-statistics; Influence functions; Nonparametric; Semi-parametric; Robust Inference
23.  A note on overadjustment in inverse probability weighted estimation 
Biometrika  2010;97(4):997-1001.
Standardized means, commonly used in observational studies in epidemiology to adjust for potential confounders, are equal to inverse probability weighted means with inverse weights equal to the empirical propensity scores. More refined standardization corresponds with empirical propensity scores computed under more flexible models. Unnecessary standardization induces efficiency loss. However, according to the theory of inverse probability weighted estimation, propensity scores estimated under more flexible models induce improvement in the precision of inverse probability weighted means. This apparent contradiction is clarified by explicitly stating the assumptions under which the improvement in precision is attained.
PMCID: PMC3371719  PMID: 22822256
Causal inference; Propensity score; Standardized mean
24.  Predicted Interval Plots (PIPS): A Graphical Tool for Data Monitoring of Clinical Trials 
Group sequential designs are often used in clinical trials to evaluate efficacy and/or futility. Many methods have been developed for different types of endpoints and scenarios. However, few of these methods convey information regarding effect sizes (e.g., treatment differences) and none uses prediction to convey information regarding potential effect size estimates and associated precision, with trial continuation. To address these limitations, Evans et al. (2007) proposed to use prediction and predicted intervals as a flexible and practical tool for quantitative monitoring of clinical trials. In this article, we reaffirm the importance and usefulness of this innovative approach and introduce a graphical summary, predicted interval plots (PIPS), to display the information obtained in the prediction process in a straightforward yet comprehensive manner. We outline the construction of PIPS and apply this method in two examples. The results and the interpretations of the PIPS are discussed.
PMCID: PMC3059316  PMID: 21423789
Clinical trials; Data monitoring; Interim analyses; Prediction; Predicted intervals
25.  Energy transfer dyads based on Nile Red 
Tetrahedron letters  2009;50(47):6442-6445.
This project was initiated to develop energy transfer dyads emitting in the 600 – 700 nm region by using Nile Red acceptors. Thus fluorescein- and BODIPY-based donors were linked to these acceptors via alkynes or triazoles. The product dyads (1 – 5) have energy transfer efficiencies of 77 – 97% in organic media.
PMCID: PMC2770174  PMID: 20160911
fluorophores; microwave reactions; Sonogashira coupling

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