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1.  Using Functional Signature Ontology (FUSION) to Identify Mechanisms of Action for Natural Products 
Science signaling  2013;6(297):ra90.
A challenge for biomedical research is the development of pharmaceuticals that appropriately target disease mechanisms. Natural products can be a rich source of bioactive chemicals for medicinal applications but can act through unknown mechanisms and can be difficult to produce or obtain. To address these challenges, we developed a new marine-derived, renewable natural products resource and a method for linking bioactive derivatives of this library to the proteins and biological processes that they target in cells. We used cell-based screening and computational analysis to match gene expression signatures produced by natural products to those produced by siRNA and synthetic microRNA libraries. With this strategy, we matched proteins and microRNAs with diverse biological processes and also identified putative protein targets and mechanisms of action for several previously undescribed marine-derived natural products. We confirmed mechanistic relationships for selected short-interfering RNAs, microRNAs, and compounds with functional roles in autophagy, chemotaxis mediated by discoidin domain receptor 2, or activation of the kinase AKT. Thus, this approach may be an effective method for screening new drugs while simultaneously identifying their targets.
PMCID: PMC4075427  PMID: 24129700
2.  Modified posterior soft tissue repair for the prevention of early postoperative dislocation in total hip arthroplasty 
International Orthopaedics  2013;37(6):1039-1044.
Dislocation following total hip arthroplasty (THA) with the posterior approach has been quite a common and bothering complication. Previous researches suggest that careful repair of the posterior structures significantly reduces this risk. The purposes of the present study were to describe a modified posterior soft tissue repair procedure in THA using a suture anchor (TwinFix Ti 5.0, Smith & Nephew, Andover, MA) and evaluate the early postoperative dislocation rate.
From July 2004 to June 2008, 220 consecutive primary total hip arthroplasties were performed using the modified surgical approach. The average age in the group was 46.4 years (range from 21 to 90) at the time of the procedure. The rate of postoperative hip dislocation, as well as any signs of complications related to the technique, has been observed and analyzed in this study.
There was no postoperative dislocation following primary THA in 220 cases, and no signs of complications related to the technique, such as greater trochanteric fractures and sciatic nerve palsy, have been noted in any of the cases at their most recent follow-up.
These initial results demonstrate that the modified repair in THA using the suture anchor can serve as an effective and reliable mean for prevention of early postoperative dislocation
PMCID: PMC3664159  PMID: 23549842
3.  Human lung epithelial cells progressed to malignancy through specific oncogenic manipulations 
Molecular cancer research : MCR  2013;11(6):638-650.
We used CDK4/hTERT-immortalized normal human bronchial epithelial cells (HBECs) from several individuals to study lung cancer pathogenesis by introducing combinations of common lung cancer oncogenic changes (p53, KRAS, MYC) and followed the stepwise transformation of HBECs to full malignancy. This model demonstrated that: 1) the combination of five genetic alterations (CDK4, hTERT, sh-p53, KRASV12, and c-MYC) is sufficient for full tumorigenic conversion of HBECs; 2) genetically-identical clones of transformed HBECs exhibit pronounced differences in tumor growth, histology, and differentiation; 3) HBECs from different individuals vary in their sensitivity to transformation by these oncogenic manipulations; 4) high levels of KRASV12 are required for full malignant transformation of HBECs, however prior loss of p53 function is required to prevent oncogene-induced senescence; 5) over-expression of c-MYC greatly enhances malignancy but only in the context of sh-p53+KRASV12; 6) growth of parental HBECs in serum-containing medium induces differentiation while growth of oncogenically manipulated HBECs in serum increases in vivo tumorigenicity, decreases tumor latency, produces more undifferentiated tumors, and induces epithelial-to-mesenchymal transition (EMT); 7) oncogenic transformation of HBECs leads to increased sensitivity to standard chemotherapy doublets; 8) an mRNA signature derived by comparing tumorigenic vs. non-tumorigenic clones was predictive of outcome in lung cancer patients. Collectively, our findings demonstrate this HBEC model system can be used to study the effect of oncogenic mutations, their expression levels, and serum-derived environmental effects in malignant transformation, while also providing clinically translatable applications such as development of prognostic signatures and drug response phenotypes.
PMCID: PMC3687022  PMID: 23449933
p53; KRAS; c-MYC; immortalized human bronchial epithelial cell; in vitro transformation model of lung cancer; epithelial mesenchymal transition
4.  Synthesis, Characterization, In Vitro Cytotoxicity, and Apoptosis-Inducing Properties of Ruthenium(II) Complexes 
PLoS ONE  2014;9(5):e96082.
Two new Ru(II) complexes, [Ru(bpy)2(FAMP)](ClO4)2 1 and 2, are synthesized and characterized by elemental analysis, electrospray mass spectrometry, and 1H nuclear magnetic resonance. The in vitro cytotoxicities and apoptosis-inducing properties of these complexes are extensively studied. Complexes 1 and 2 exhibit potent antiproliferative activities against a panel of human cancer cell lines. The cell cycle analysis shows that complexes 1 and 2 exhibit effective cell growth inhibition by triggering G0/G1 phase arrest and inducing apoptosis by mitochondrial dysfunction. The in vitro DNA binding properties of the two complexes are investigated by different spectrophotometric methods and viscosity measurements.
PMCID: PMC4013043  PMID: 24804832
5.  Comparison of conventional medicine, TCM treatment, and combination of both conventional medicine and TCM treatment for patients with chronic obstructive pulmonary disease: study protocol of a randomized comparative effectiveness research trial 
Trials  2014;15:153.
Chronic obstructive pulmonary disease (COPD) affects millions worldwide. Although many therapies exist and are being developed to relieve symptoms and reduce mortality, few data are available to understand which of the therapeutic alternatives is the most cost-effective for COPD patients in everyday clinical practice, especially for traditional Chinese medicine (TCM). Comparative effectiveness research can help patients, clinicians, and decision-makers make best informed treatment decisions where such evidence was previously lacking. This study aims to compare the effectiveness and economic evaluation of three treatments: (1) conventional Western medicine; (2) TCM treatments, which have been evaluated and have certain effect; and (3) a combination of both conventional Western medicine and TCM treatments, and then determine which treatment is the most suitable for COPD patients.
A multicenter, pragmatic, randomized, controlled trial is adopted. A total of 360 patients will be recruited and randomly assigned to one of the three treatments group, with 120 in each group. Patients in the conventional Western medicine group will be given Salbutamol, Formoterol, Salmeterol/fluticasone, respectively, according to the guidelines. For the TCM group, patients will be given Bufei granule, Bu-Fei Jian-Pi granule, Bu-Fei Yi-Shen granule, and Yi-Qi Zi-Shen granule based on their corresponding TCM syndrome patterns, respectively. For the combination of conventional medicine and TCM treatments group, patients will be given a combination of conventional Western medicine and TCM granules. Treatments in each group are recognized as a whole comprehensive intervention. After the 26-week treatment, another 26 weeks will be followed up. The outcome measures including the frequency and duration of acute exacerbations, lung function, dyspnea, exercise capacity, quality of life, and economic evaluation will be assessed.
It is hypothesized that each of the three treatments will have beneficial effects in reducing the frequency and duration of acute exacerbations, improving exercise capacity and psychosocial function of COPD patients. In addition, the combination of conventional medicine and TCM treatments may be most suitable for COPD patients with better effectiveness and economic evaluation.
Trial registration NCT01836016.
PMCID: PMC4017822  PMID: 24885672
Chronic obstructive pulmonary disease; Comparative effectiveness research; Traditional Chinese medicine
6.  A Model-Based Approach to Identify Binding Sites in CLIP-Seq Data 
PLoS ONE  2014;9(4):e93248.
Cross-linking immunoprecipitation coupled with high-throughput sequencing (CLIP-Seq) has made it possible to identify the targeting sites of RNA-binding proteins in various cell culture systems and tissue types on a genome-wide scale. Here we present a novel model-based approach (MiClip) to identify high-confidence protein-RNA binding sites from CLIP-seq datasets. This approach assigns a probability score for each potential binding site to help prioritize subsequent validation experiments. The MiClip algorithm has been tested in both HITS-CLIP and PAR-CLIP datasets. In the HITS-CLIP dataset, the signal/noise ratios of miRNA seed motif enrichment produced by the MiClip approach are between 17% and 301% higher than those by the ad hoc method for the top 10 most enriched miRNAs. In the PAR-CLIP dataset, the MiClip approach can identify ∼50% more validated binding targets than the original ad hoc method and two recently published methods. To facilitate the application of the algorithm, we have released an R package, MiClip (, and a public web-based graphical user interface software ( for customized analysis.
PMCID: PMC3979666  PMID: 24714572
7.  Cross-sectional study of the relationship of peripheral blood cell profiles with severity of infection by adenovirus type 55 
BMC Infectious Diseases  2014;14:147.
The immunologic profiles of patients with human adenovirus serotype 55 (HAdV-55) infections were characterized in subjects diagnosed with silent infections (n = 30), minor infections (n = 27), severe infections (n = 34), and healthy controls (n = 30) during a recent outbreak among Chinese military trainees.
Blood was sampled at the disease peak and four weeks later, and samples were analyzed to measure changes in leukocyte and platelet profiles in patients with different severities of disease. Differential lymphocyte subsets and cytokine profiles were measured by flow cytometry and Luminex xMAP®, and serum antibodies were analyzed by ELISA and immunofluorescence staining.
Patients with severe HAdV infections had higher proportions of neutrophils and reduced levels of lymphocytes (p < 0.005 for both). Patients with minor and severe infections had significantly lower platelet counts (p < 0.005 for both) than those with silent infections. The silent and minor infection groups had higher levels of dendritic cells than the severe infection group. Relative to patients with silent infections, patients with severe infections had significantly higher levels of IL-17+CD4+ cells, decreased levels of IL-17+CD8+ cells, and higher levels of IFN-γ, IL-4, IL-10, and IFN-α2 (p < 0.001 for all comparisons).
Patients with different severities of disease due to HAdV-55 infection had significantly different immune responses. These data provide an initial step toward the identification of patients at risk for more severe disease and the development of treatments against HAdV-55 infection.
PMCID: PMC4000060  PMID: 24646014
Infectious diseases; Adenovirus; Immunopathology; Outbreak
8.  A 12-Gene Set Predicts Survival Benefits from Adjuvant Chemotherapy in Non-Small-Cell Lung Cancer Patients 
Prospectively identifying who will benefit from adjuvant chemotherapy (ACT) would improve clinical decisions for non-small-cell lung cancer (NSCLC) patients. In this study, we aim to develop and validate a functional gene set that predicts the clinical benefits of ACT in NSCLC.
Experimental Design
An 18-hub-gene prognosis signature was developed through a systems biology approach, and its prognostic value was evaluated in six independent cohorts. The 18-hub-gene set was then integrated with genome-wide functional (RNAi) data and genetic aberration data to derive a 12-gene predictive signature for ACT benefits in NSCLC.
Using a cohort of 442 Stage I–III NSCLC patients who underwent surgical resection, we identified an 18-hub-gene set which robustly predicted the prognosis of patients with adenocarcinoma in all validation datasets across four microarray platforms. The hub genes, identified through a purely data-driven approach, have significant biological implications in tumor pathogenesis, including NKX2-1, Aurora Kinase A, PRC1, CDKN3, MBIP, RRM2. The 12-gene predictive signature was successfully validated in two independent datasets (N=90 and N=176). The predicted benefit group showed significant improvement in survival after ACT (UT Lung SPORE data: hazard ratio=0.34, p=0.017; JBR.10 clinical trial data: hazard ratio=0.36, p=0.038), while the predicted non-benefit group showed no survival benefit for two datasets (hazard ratio=0.80, p=0.70; hazard ratio= 0.91, p=0.82).
This is the first study to integrate genetic aberration, genome-wide RNAi data, and mRNA expression data to identify a functional gene set that predicts which resectable patients with non-small-cell lung cancer will have a survival benefit with ACT.
PMCID: PMC3619002  PMID: 23357979
non-small-cell lung cancer; predictive gene signature; adjuvant chemotherapy; integrative analysis; hub genes
9.  27-Hydroxycholesterol Promotes Cell-autonomous ER-positive Breast Cancer Growth 
Cell reports  2013;5(3):637-645.
To date estrogen is the only known endogenous estrogen receptor (ER) ligand that promotes ER+ breast tumor growth. We report that the cholesterol metabolite 27-hydroxycholesterol (27HC) stimulates MCF-7 cell xenograft growth in mice. More importantly, in ER+ breast cancer patients, 27HC content in normal breast tissue is increased compared to that in cancer-free controls, and tumor 27HC content is further elevated. Increased tumor 27HC is correlated with diminished expression of CYP7B1, the 27HC metabolizing enzyme, and reduced expression of CYP7B1 in tumors is associated with poorer patient survival. Moreover, 27HC is produced by MCF-7 cells and it stimulates cell-autonomous, ER-dependent and GDNF-RET-dependent cell proliferation. Thus, 27HC is a locally-modulated, non-aromatized ER ligand that promotes ER+ breast tumor growth.
PMCID: PMC3950897  PMID: 24210818
10.  Antibiotic expected effectiveness and cost under real life microbiology: evaluation of ertapenem and ceftriaxone in the treatment of community-acquired pneumonia for elderly patients in Spain 
Clinical efficacy of antibiotics may be affected by changes in the susceptibility of microorganisms to antimicrobial agents. The purpose of this study is to assess how these changes could affect the initial efficacy of ertapenem and ceftriaxone in the treatment of community-acquired pneumonia (CAP) in elderly patients and the potential consequences this may have in health care costs.
Initial efficacy in elderly was obtained from a combined analysis of two multicenter, randomized studies. An alternative scenario was carried out using initial efficacy data according to the pneumonia severity index (PSI). Country-specific pathogens distribution was obtained from a national epidemiological study, and microbiological susceptibilities to first- and second-line therapies were obtained from Spanish or European surveillance studies. A decision analytic model was used to compare ertapenem versus ceftriaxone for CAP inpatient treatment. Inputs of the model were the expected effectiveness previously estimated and resource use considering a Spanish national health system perspective. Outcomes include difference in proportion of successfully treated patients and difference in total costs between ertapenem and ceftriaxone. The model performed one-way and probabilistic sensitivity analyses.
First-line treatment of CAP with ertapenem led to a higher proportion of successfully treated patients compared with ceftriaxone in Spain. One-way sensitivity analysis showed that length of stay was the key parameter of the model. Probabilistic sensitivity analysis showed that ertapenem can be a cost-saving strategy compared with ceftriaxone, with a 59% probability of being dominant (lower costs with additional health benefits) for both, elderly patients (>65 years) and patients with PSI >3.
The incorporation of the current antimicrobial susceptibility into the initial clinical efficacy has a significant impact in outcomes and costs in CAP treatment. The treatment with ertapenem compared with ceftriaxone resulted in better clinical outcomes and lower treatment costs for two segments of the Spanish population: elderly patients and patients with severe pneumonia (PSI >3).
PMCID: PMC3928454  PMID: 24611019
antibacterial agent; bacterial infection; cost-effectiveness analyses; drug costs; Spain; aged
11.  Statistical Methods for Integrating Multiple Types of High-Throughput Data 
Large-scale sequencing, copy number, mRNA, and protein data have given great promise to the biomedical research, while posing great challenges to data management and data analysis. Integrating different types of high-throughput data from diverse sources can increase the statistical power of data analysis and provide deeper biological understanding. This chapter uses two biomedical research examples to illustrate why there is an urgent need to develop reliable and robust methods for integrating the heterogeneous data. We then introduce and review some recently developed statistical methods for integrative analysis for both statistical inference and classification purposes. Finally, we present some useful public access databases and program code to facilitate the integrative analysis in practice.
PMCID: PMC3912747  PMID: 20652519
Integrative analysis; high-throughput data analysis; microarray
12.  Targeted zwitterionic near-infrared fluorophores for improved optical imaging 
Nature biotechnology  2013;31(2):10.1038/nbt.2468.
The signal-to-background ratio (SBR) is the key determinant of sensitivity, detectability, and linearity in optical imaging. As signal strength is often constrained by fundamental limits, background reduction becomes an important approach for improving SBR. We recently reported that a zwitterionic near-infrared (NIR) fluorophore, ZW800-1, exhibits low background. Here we show that this fluorophore provides much-improved SBR when targeted to cancer cells or proteins by conjugation with a cyclic RGD peptide, fibrinogen, or antibodies. ZW800-1 outperforms the commercially available NIR fluorophores IRDye800-CW and Cy5.5 in vitro for immunocytometry, histopathology and immunoblotting, and in vivo for image-guided surgery. In tumor model systems, tumor-to-background ratios of 17.2 are achieved after only 4 h post-injection, compared with 5.1 for IRDye800-CW and 2.7 for Cy5.5. Our results suggest that introducing zwitterionic properties into targeted fluorophores may be a general strategy for improving the SBR in diagnostic and therapeutic applications.
PMCID: PMC3568187  PMID: 23292608
13.  PIPE-CLIP: a comprehensive online tool for CLIP-seq data analysis 
Genome Biology  2014;15(1):R18.
CLIP-seq is widely used to study genome-wide interactions between RNA-binding proteins and RNAs. However, there are few tools available to analyze CLIP-seq data, thus creating a bottleneck to the implementation of this methodology. Here, we present PIPE-CLIP, a Galaxy framework-based comprehensive online pipeline for reliable analysis of data generated by three types of CLIP-seq protocol: HITS-CLIP, PAR-CLIP and iCLIP. PIPE-CLIP provides both data processing and statistical analysis to determine candidate cross-linking regions, which are comparable to those regions identified from the original studies or using existing computational tools. PIPE-CLIP is available at
PMCID: PMC4054095  PMID: 24451213
14.  dCLIP: a computational approach for comparative CLIP-seq analyses 
Genome Biology  2014;15(1):R11.
Although comparison of RNA-protein interaction profiles across different conditions has become increasingly important to understanding the function of RNA-binding proteins (RBPs), few computational approaches have been developed for quantitative comparison of CLIP-seq datasets. Here, we present an easy-to-use command line tool, dCLIP, for quantitative CLIP-seq comparative analysis. The two-stage method implemented in dCLIP, including a modified MA normalization method and a hidden Markov model, is shown to be able to effectively identify differential binding regions of RBPs in four CLIP-seq datasets, generated by HITS-CLIP, iCLIP and PAR-CLIP protocols. dCLIP is freely available at
PMCID: PMC4054096  PMID: 24398258
15.  Massive heterotopic ossification associated with late deficits in posterior wall of acetabulum after failed acetabular fracture operation 
Heterotopic ossification is a common postoperative complication of acetabular fracture. However, functionally significant heterotopic ossification with associated late bone defects in the posterior wall of the acetabulum is rare and challenging to treat. When heterotopic ossification is a late complication of failed acetabular fracture operation, it is disabling and may only be treated by THA. THA is highly susceptible to premature failure in young and active patients and may require numerous revisions.
Case presentation
This article describes a 40-year-old man with massive heterotopic ossification associated with late bone defects in the posterior wall of the acetabulum after a failed acetabular fracture operation. The primary fracture type was a 62-A2.3 fracture according to the AO/OTA Classification.Surgical excision and anatomical reconstruction of the acetabular wall using heterotopic ossific bone were performed 10 months after the fracture repair. Postoperatively, indomethacin was administered for prophylaxis against recurrence of heterotopic ossification, and hip range of motion was progressively increased. At 5 years and 6 months follow-up, the patient’s pain was relieved and hip function had recovered. Though radiography and CT showed minimal subchondral cysts and mild joint-space narrowing, there was no evidence of graft resorption, progressive posttraumatic osteoarthritis or necrosis of the femoral head.
To the authors’ knowledge, this is the first case of such a challenging condition. Although it is an extremely rare case, it provides an attractive option for avoiding THA, as the long-term follow-up shows a satisfactory outcome.
PMCID: PMC3877962  PMID: 24369897
Heterotopic ossification; Late bone defects; Posterior wall; Acetabulum; Acetabular fracture
16.  Application of Ni-Ti Alloy connector for the treatment of comminuted coronal plane supracondylar-condylar femoral fractures: a retrospective review of 21 patients 
Our preliminary retrospective study assessed outcomes after the use of Ni-Ti arched shape-memory connector (ASC) combined with partially threaded cancellous screws (PTCS) to repair coronal plane supracondylar-condylar femoral fractures.
Twenty-one patients (16 men and 5 women) with a mean age of 34.1 years (range, 28 to 44 years) with coronal plane supracondylar and condylar fractures of the distal femur were included in this study. Each patient underwent open reduction and internal fixation using the ASC and PTCS. Active functional exercises with restricted weight bearing were initiated the first postoperative day. A gradual increase in weight bearing status and range of motion was permitted and subjects progressed to full weight bearing by 8 weeks. Surgical time, blood loss, postoperative knee range of motion, American Knee Society Scores (KSS), and postoperative complications were assessed.
The mean surgical time was 75 mins (range, 45 to 100 mins) and average blood loss was 105 ml (range, 35 to 130 ml). Mean follow-up was 65 months (range, 22 to 90 months). No subjects demonstrated evidence of osteonecrosis or arthritis at the final follow-up. The mean KSS was excellent (≥85) in 8 subjects, good (70-84) in 11 subjects, and fair (60-69) in 2 subjects. The mean active range of motion of knee flexion at final follow-up was 100 degrees (range, 85 to 110 degrees).
ASC combined with PTCS can serve as an effective means for managing comminuted femoral fractures that extend from the condyle to the supracondylar region. However, further prospective comparative studies and biomechanical analyses are needed to evaluate long-term outcomes using these materials.
PMCID: PMC3878495  PMID: 24341860
Shape memory alloy; Treatment; Comminuted; Coronal plane; Femoral fracture
17.  Socioeconomic disparities in lung cancer treatment and outcome persist within a single academic medical center 
Clinical lung cancer  2012;13(6):448-457.
Socioeconomic disparities in treatment and outcomes of non-small cell lung cancer (NSCLC) are well established. To explore whether these differences are secondary to individual or institutional characteristics, we examined treatment selection and outcome in a diverse population treated at a single medical center.
Patient and Methods
We performed a retrospective analysis of consecutive patients diagnosed with NSCLC stages I-III from 2000-2005 at the University of Texas Southwestern Medical Center. Treatment selection was dichotomized as “standard” (surgery for stage I-II; surgery and/or radiation therapy for stage III) or “other.” Associations between patient characteristics (including socioeconomic status) and treatment selection were examined using logistic regression; associations between characteristics and overall survival were examined using Cox regression models and Kaplan-Meier survival analysis.
A total of 450 patients were included. Twenty-eight percent of patients had private insurance, 43% had Medicare, and 29% had an indigent care plan. The likelihood of receiving “standard” therapy was significantly associated with insurance type [indigent plan versus private insurance OR 0.13 (95% CI 0.04-0.43) for stage I-II; OR 0.38 (95% CI 0.14-1.00) for stage III]. For patients with stage I-II NSCLC, survival was associated with age, gender, insurance type (indigent plan versus private insurance HR 1.98; 95% CI 1.16-3.37), stage, and treatment selection. In stage III NSCLC, survival was associated with treatment selection.
Within a single academic medical center, socioeconomically disadvantaged patients with stage I-III NSCLC are less likely to receive “standard” therapy. Socioeconomically disadvantaged patients with stage I-II NSCLC have inferior survival independent of therapy.
PMCID: PMC3436959  PMID: 22512997
Surgery; radiation therapy; chemotherapy; underserved; minorities; socioeconomic disparities
18.  Selective laser sintering fabrication of nano-hydroxyapatite/poly-ε-caprolactone scaffolds for bone tissue engineering applications 
The regeneration of functional tissue in osseous defects is a formidable challenge in orthopedic surgery. In the present study, a novel biomimetic composite scaffold, here called nano-hydroxyapatite (HA)/poly-ε-caprolactone (PCL) was fabricated using a selective laser sintering technique. The macrostructure, morphology, and mechanical strength of the scaffolds were characterized. Scanning electronic microscopy (SEM) showed that the nano-HA/PCL scaffolds exhibited predesigned, well-ordered macropores and interconnected micropores. The scaffolds have a range of porosity from 78.54% to 70.31%, and a corresponding compressive strength of 1.38 MPa to 3.17 MPa. Human bone marrow stromal cells were seeded onto the nano-HA/PCL or PCL scaffolds and cultured for 28 days in vitro. As indicated by the level of cell attachment and proliferation, the nano-HA/PCL showed excellent biocompatibility, comparable to that of PCL scaffolds. The hydrophilicity, mineralization, alkaline phosphatase activity, and Alizarin Red S staining indicated that the nano-HA/PCL scaffolds are more bioactive than the PCL scaffolds in vitro. Measurements of recombinant human bone morphogenetic protein-2 (rhBMP-2) release kinetics showed that after nano-HA was added, the material increased the rate of rhBMP-2 release. To investigate the in vivo biocompatibility and osteogenesis of the composite scaffolds, both nano-HA/PCL scaffolds and PCL scaffolds were implanted in rabbit femur defects for 3, 6, and 9 weeks. The wounds were studied radiographically and histologically. The in vivo results showed that both nano-HA/PCL composite scaffolds and PCL scaffolds exhibited good biocompatibility. However, the nano-HA/PCL scaffolds enhanced the efficiency of new bone formation more than PCL scaffolds and fulfilled all the basic requirements of bone tissue engineering scaffolds. Thus, they show large potential for use in orthopedic and reconstructive surgery.
PMCID: PMC3818022  PMID: 24204147
osseous defects; orthopedic surgery; biomimetic composite scaffold; reconstructive surgery
19.  Structure-Activity Relationship of Nerve-Highlighting Fluorophores 
PLoS ONE  2013;8(9):e73493.
Nerve damage is a major morbidity associated with numerous surgical interventions. Yet, nerve visualization continues to challenge even the most experienced surgeons. A nerve-specific fluorescent contrast agent, especially one with near-infrared (NIR) absorption and emission, would be of immediate benefit to patients and surgeons. Currently, there are only three classes of small molecule organic fluorophores that penetrate the blood nerve barrier and bind to nerve tissue when administered systemically. Of these three classes, the distyrylbenzenes (DSBs) are particularly attractive for further study. Although not presently in the NIR range, DSB fluorophores highlight all nerve tissue in mice, rats, and pigs after intravenous administration. The purpose of the current study was to define the pharmacophore responsible for nerve-specific uptake and retention, which would enable future molecules to be optimized for NIR optical properties. Structural analogs of the DSB class of small molecules were synthesized using combinatorial solid phase synthesis and commercially available building blocks, which yielded more than 200 unique DSB fluorophores. The nerve-specific properties of all DSB analogs were quantified using an ex vivo nerve-specific fluorescence assay on pig and human sciatic nerve. Results were used to perform quantitative structure-activity relationship (QSAR) modeling and to define the nerve-specific pharmacophore. All DSB analogs with positive ex vivo fluorescence were tested for in vivo nerve specificity in mice to assess the effect of biodistribution and clearance on nerve fluorescence signal. Two new DSB fluorophores with the highest nerve to muscle ratio were tested in pigs to confirm scalability.
PMCID: PMC3767781  PMID: 24039960
20.  Identification of Breast Cancer Prognosis Markers via Integrative Analysis 
In breast cancer research, it is of great interest to identify genomic markers associated with prognosis. Multiple gene profiling studies have been conducted for such a purpose. Genomic markers identified from the analysis of single datasets often do not have satisfactory reproducibility. Among the multiple possible reasons, the most important one is the small sample sizes of individual studies. A cost-effective solution is to pool data from multiple comparable studies and conduct integrative analysis. In this study, we collect four breast cancer prognosis studies with gene expression measurements. We describe the relationship between prognosis and gene expressions using the accelerated failure time (AFT) models. We adopt a 2-norm group bridge penalization approach for marker identification. This integrative analysis approach can effectively identify markers with consistent effects across multiple datasets and naturally accommodate the heterogeneity among studies. Statistical and simulation studies demonstrate satisfactory performance of this approach. Breast cancer prognosis markers identified using this approach have sound biological implications and satisfactory prediction performance.
PMCID: PMC3389801  PMID: 22773869
Breast cancer prognosis; Gene expression; Marker identification; Integrative analysis; 2-norm group bridge
21.  Probe mapping across multiple microarray platforms 
Briefings in Bioinformatics  2011;13(5):547-554.
Access to gene expression data has become increasingly common in recent years; however, analysis has become more difficult as it is often desirable to integrate data from different platforms. Probe mapping across microarray platforms is the first and most crucial step for data integration. In this article, we systematically review and compare different approaches to map probes across seven platforms from different vendors: U95A, U133A and U133 Plus 2.0 from Affymetrix, Inc.; HT-12 v1, HT-12v2 and HT-12v3 from Illumina, Inc.; and 4112A from Agilent, Inc. We use a unique data set, which contains 56 lung cancer cell line samples—each of which has been measured by two different microarray platforms—to evaluate the consistency of expression measurement across platforms using different approaches. Based on the evaluation from the empirical data set, the BLAST alignment of the probe sequences to a recent revision of the Transcriptome generated better results than using annotations provided by Vendors or from Bioconductor's Annotate package. However, a combination of all three methods (deemed the ‘Consensus Annotation’) yielded the most consistent expression measurement across platforms. To facilitate data integration across microarray platforms for the research community, we develop a user-friendly web-based tool, an API and an R package to map data across different microarray platforms from Affymetrix, Illumina and Agilent. Information on all three can be found at
PMCID: PMC3431719  PMID: 22199380
microarray; gene expression; probe; integrated analysis; probe mapping
22.  Gene expression profile analysis of human intervertebral disc degeneration 
Genetics and Molecular Biology  2013;36(3):448-454.
In this study, we used microarray analysis to investigate the biogenesis and progression of intervertebral disc degeneration. The gene expression profiles of 37 disc tissue samples obtained from patients with herniated discs and degenerative disc disease collected by the National Cancer Institute Cooperative Tissue Network were analyzed. Differentially expressed genes between more and less degenerated discs were identified by significant analysis of microarray. A total of 555 genes were significantly overexpressed in more degenerated discs with a false discovery rate of < 3%. Functional annotation showed that these genes were significantly associated with membrane-bound vesicles, calcium ion binding and extracellular matrix. Protein-protein interaction analysis showed that these genes, including previously reported genes such as fibronectin, COL2A1 and β-catenin, may play key roles in disc degeneration. Unsupervised clustering indicated that the widely used morphology-based Thompson grading system was only marginally associated with the molecular classification of intervertebral disc degeneration. These findings indicate that detailed, systematic gene analysis may be a useful way of studying the biology of intervertebral disc degeneration.
PMCID: PMC3795174  PMID: 24130454
genes; intervertebral disc degeneration; molecular classification; protein-protein interaction
23.  Very Low Birth Weight Hospital Volume and Mortality – An Instrumental Variables Approach 
Medical Care  2012;50(8):714-721.
Previous studies of very low birth weight (VLBW) hospital volume effects on inhospital mortality have used standard risk-adjusted models that only account for observable confounders but not for self-selection bias due to unobservable confounders.
To assess the effects of hospital volume of VLBW infants on in-hospital mortality while explicitly accounting for unobservable confounders and self-selection bias using an instrumental-variables model.
The sample includes 4,553 VLBW infants born in 63 hospitals in 2000–2004 in New Jersey. We employ instrumental-variables analysis using as instruments the differences between the patient’s distances to the nearest low (<50 VLBW infants annually), moderate (51–100 infants annually) and high (>100 VLBW infants annually) volume hospitals. We evaluate several volume measures and adjust for observable infant and hospital characteristics.
We find beneficial volume effects on survival that are significantly underestimated in classical risk-adjusted models, under which low and moderate volumes compared to high volumes increase mortality odds by 1.8 and 1.88 times, respectively (risk ratios of 1.4 and 1.5, respectively). However, using an instrumental variables approach, we find that low and moderate volumes increase mortality odds by 5.42 and 3.51 times, respectively (risk ratios of 2.76 and 2.21, respectively). These findings suggest unobservable confounders that increase the selection of infants at a greater mortality risk into higher volume hospitals.
Accounting for unobserved self-selection bias reveals large survival benefits from delivering and treating VLBW infants at high-volume hospitals. This supports policies regionalizing the delivery and care for pregnancies at-risk for VLBW at high-volume hospitals.
PMCID: PMC3388172  PMID: 22437621
Very low birth weight; hospital volume; neonatal mortality; infant mortality; neonatal intensive care; instrumental variables
24.  Cytoplasmic TRADD Confers a Worse Prognosis in Glioblastoma12 
Neoplasia (New York, N.Y.)  2013;15(8):888-897.
Tumor necrosis factor receptor 1 (TNFR1)-associated death domain protein (TRADD) is an important adaptor in TNFR1 signaling and has an essential role in nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) activation and survival signaling. Increased expression of TRADD is sufficient to activate NF-κB. Recent studies have highlighted the importance of NF-κB activation as a key pathogenic mechanism in glioblastoma multiforme (GBM), the most common primary malignant brain tumor in adults.We examined the expression of TRADD by immunohistochemistry (IHC) and find that TRADD is commonly expressed at high levels in GBM and is detected in both cytoplasmic and nuclear distribution. Cytoplasmic IHC TRADD scoring is significantly associated with worse progression-free survival (PFS) both in univariate and multivariate analysis but is not associated with overall survival (n = 43 GBMs). PFS is a marker for responsiveness to treatment. We propose that TRADD-mediated NF-κB activation confers chemoresistance and thus a worse PFS in GBM. Consistent with the effect on PFS, silencing TRADD in glioma cells results in decreased NF-κB activity, decreased proliferation of cells, and increased sensitivity to temozolomide. TRADD expression is common in glioma-initiating cells. Importantly, silencing TRADD in GBM-initiating stem cell cultures results in decreased viability of stem cells, suggesting that TRADD may be required for maintenance of GBM stem cell populations. Thus, our study suggests that increased expression of cytoplasmic TRADD is both an important biomarker and a key driver of NF-κB activation in GBM and supports an oncogenic role for TRADD in GBM.
PMCID: PMC3730041  PMID: 23908590
25.  Distinct transcriptome profiles identified in normal human bronchial epithelial cells after exposure to γ-rays and different elemental particles of high Z and energy 
BMC Genomics  2013;14:372.
Ionizing radiation composed of accelerated ions of high atomic number (Z) and energy (HZE) deposits energy and creates damage in cells in a discrete manner as compared to the random deposition of energy and damage seen with low energy radiations such as γ- or x-rays. Such radiations can be highly effective at cell killing, transformation, and oncogenesis, all of which are concerns for the manned space program and for the burgeoning field of HZE particle radiotherapy for cancer. Furthermore, there are differences in the extent to which cells or tissues respond to such exposures that may be unrelated to absorbed dose. Therefore, we asked whether the energy deposition patterns produced by different radiation types would cause different molecular responses. We performed transcriptome profiling using human bronchial epithelial cells (HBECs) after exposure to γ-rays and to two different HZE particles (28Si and 56Fe) with different energy transfer properties to characterize the molecular response to HZE particles and γ-rays as a function of dose, energy deposition pattern, and time post-irradiation.
Clonogenic assay indicated that the relative biological effectiveness (RBE) for 56Fe was 3.91 and for 28Si was 1.38 at 34% cell survival. Unsupervised clustering analysis of gene expression segregated samples according to the radiation species followed by the time after irradiation, whereas dose was not a significant parameter for segregation of radiation response. While a subset of genes associated with p53-signaling, such as CDKN1A, TRIM22 and BTG2 showed very similar responses to all radiation qualities, distinct expression changes were associated with the different radiation species. Gene enrichment analysis categorized the differentially expressed genes into functional groups related to cell death and cell cycle regulation for all radiation types, while gene pathway analysis revealed that the pro-inflammatory Acute Phase Response Signaling was specifically induced after HZE particle irradiation. A 73 gene signature capable of predicting with 96% accuracy the radiation species to which cells were exposed, was developed.
These data suggest that the molecular response to the radiation species used here is a function of the energy deposition characteristics of the radiation species. This novel molecular response to HZE particles may have implications for radiotherapy including particle selection for therapy and risk for second cancers, risk for cancers from diagnostic radiation exposures, as well as NASA’s efforts to develop more accurate lung cancer risk estimates for astronaut safety. Lastly, irrespective of the source of radiation, the gene expression changes observed set the stage for functional studies of initiation or progression of radiation-induced lung carcinogenesis.
PMCID: PMC3680091  PMID: 23724988
Gene expression; HZE particles; Ionizing radiation; Human bronchial epithelial cells

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