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1.  Reactive Transformation and Increased BDNF Signaling by Hippocampal Astrocytes in Response to MK-801 
PLoS ONE  2015;10(12):e0145651.
MK-801, also known as dizocilpine, is a noncompetitive N-methyl-D-aspartic acid (NMDA) receptor antagonist that induces schizophrenia-like symptoms. While astrocytes have been implicated in the pathophysiology of psychiatric disorders, including schizophrenia, astrocytic responses to MK-801 and their significance to schizotypic symptoms are unclear. Changes in the expression levels of glial fibrillary acid protein (GFAP), a marker of astrocyte activation in response to a variety of pathogenic stimuli, were examined in the hippocampus of rats treated with the repeated MK-801 injection (0.5 mg/10ml/kg body weight for 6 days) and in primary cultured hippocampal astrocytes incubated with MK-801 (5 or 20 μM for 24 h). Moreover, the expression levels of BDNF and its receptors TrkB and p75 were examined in MK-801-treated astrocyte cultures. MK-801 treatment enhanced GFAP expression in the rat hippocampus and also increased the levels of GFAP protein and mRNA in hippocampal astrocytes in vitro. Treatment of cultured hippocampal astrocytes with MK-801 enhanced protein and mRNA levels of BDNF, TrkB, and p75. Collectively, our results suggest that hippocampal astrocytes may contribute to the pathophysiology of schizophrenia symptoms associated with NMDA receptor hypofunction by reactive transformation and altered BDNF signaling.
PMCID: PMC4689377  PMID: 26700309
2.  A simple feature construction method for predicting upstream/downstream signal flow in human protein-protein interaction networks 
Scientific Reports  2015;5:17983.
Signaling pathways play important roles in understanding the underlying mechanism of cell growth, cell apoptosis, organismal development and pathways-aberrant diseases. Protein-protein interaction (PPI) networks are commonly-used infrastructure to infer signaling pathways. However, PPI networks generally carry no information of upstream/downstream relationship between interacting proteins, which retards our inferring the signal flow of signaling pathways. In this work, we propose a simple feature construction method to train a SVM (support vector machine) classifier to predict PPI upstream/downstream relations. The domain based asymmetric feature representation naturally embodies domain-domain upstream/downstream relations, providing an unconventional avenue to predict the directionality between two objects. Moreover, we propose a semantically interpretable decision function and a macro bag-level performance metric to satisfy the need of two-instance depiction of an interacting protein pair. Experimental results show that the proposed method achieves satisfactory cross validation performance and independent test performance. Lastly, we use the trained model to predict the PPIs in HPRD, Reactome and IntAct. Some predictions have been validated against recent literature.
PMCID: PMC4673612  PMID: 26648121
3.  The role of Lin28b in myeloid and mast cell differentiation and mast cell malignancy 
Leukemia  2015;29(6):1320-1330.
Mast cells are critical components of the innate immune system and important for host defense, allergy, autoimmunity, tissue regeneration, and tumor progression. Dysregulated mast cell development leads to systemic mastocytosis, a clinically variable but often devastating family of hematologic disorders. Here we report that induced expression of Lin28, a heterochronic gene and pluripotency factor implicated in driving a fetal hematopoietic program, caused mast cell accumulation in adult mice in target organs such as the skin and peritoneal cavity. In vitro assays revealed a skewing of myeloid commitment in LIN28B-expressing hematopoietic progenitors, with increased levels of LIN28B in common myeloid and basophil-mast cell progenitors altering gene expression patterns to favor cell fate choices that enhanced mast cell specification. In addition, LIN28B-induced mast cells appeared phenotypically and functionally immature, and in vitro assays suggested a slowing of mast cell terminal differentiation in the context of LIN28B upregulation. Finally, interrogation of human mast cell leukemia samples revealed upregulation of LIN28B in abnormal mast cells from patients with systemic mastocytosis (SM). This work identifies Lin28 as a novel regulator of innate immune function and a new protein of interest in mast cell disease.
PMCID: PMC4456252  PMID: 25655194
4.  Comparison of intravascular ultrasound guided versus angiography guided drug eluting stent implantation: a systematic review and meta-analysis 
Intravascular ultrasound (IVUS) can be a useful tool during drug-eluting stents (DES) implantation as it allows accurate assessment of lesion severity and optimal treatment planning. However, numerous reports have shown that IVUS guided percutaneous coronary intervention is not associated with improved clinical outcomes, especially in non-complex patients and lesions.
We searched the literature in Medline, the Cochrane Library, and other internet sources to identify studies that compare clinical outcomes between IVUS-guided and angiography-guided DES implantation. Random-effects model was used to assess treatment effect.
Twenty eligible studies with a total of 29,068 patients were included in this meta-analysis. The use of IVUS was associated with significant reductions in major adverse cardiovascular events (MACE, odds ratios [OR] 0.77, 95 % confidence intervals [CI] 0.71-0.83, P < 0.001), death (OR 0.62, 95 % CI 0.54-0.71, p < 0.001), and stent thrombosis (OR 0.59, 95 % CI: 0.47-0.73, P < 0.001). The benefit was also seen in the repeated analysis of matched and randomized studies. In stratified analysis, IVUS guidance appeared to be beneficial not only in patients with complex lesions or acute coronary syndromes (ACS) but also patients with mixed lesions or presentations (MACE: OR 0.69, 95 % CI: 0.60-0.79, p < 0.001, OR 0.81, 95 % CI 0.74-0.90, p < 0.001, respectively). By employing meta-regression analysis, the benefit of IVUS is significantly pronounced in patients with complex lesions or ACS with respect to death (p = 0.048).
IVUS guidance was associated with improved clinical outcomes, especially in patients with complex lesions admitted with ACS. Large, randomized clinical trials are warranted to identify populations and lesion characteristics where IVUS guidance would be associated with better outcomes.
PMCID: PMC4647753  PMID: 26577590
Intravascular ultrasound; Angiography; Drug-eluting stent; Meta-analysis
5.  Precise let-7 expression levels balance organ regeneration against tumor suppression 
eLife  null;4:e09431.
The in vivo roles for even the most intensely studied microRNAs remain poorly defined. Here, analysis of mouse models revealed that let-7, a large and ancient microRNA family, performs tumor suppressive roles at the expense of regeneration. Too little or too much let-7 resulted in compromised protection against cancer or tissue damage, respectively. Modest let-7 overexpression abrogated MYC-driven liver cancer by antagonizing multiple let-7 sensitive oncogenes. However, the same level of overexpression blocked liver regeneration, while let-7 deletion enhanced it, demonstrating that distinct let-7 levels can mediate desirable phenotypes. let-7 dependent regeneration phenotypes resulted from influences on the insulin-PI3K-mTOR pathway. We found that chronic high-dose let-7 overexpression caused liver damage and degeneration, paradoxically leading to tumorigenesis. These dose-dependent roles for let-7 in tissue repair and tumorigenesis rationalize the tight regulation of this microRNA in development, and have important implications for let-7 based therapeutics.
eLife digest
The development of animals is guided by the expression of certain genes at critical moments. Many different mechanisms control development; in one of them, the expression of genes can be decreased by molecules called microRNAs. In particular, the group of microRNAs called let-7 has been intensively studied in roundworms and fruit flies. Although mammals have extremely similar let-7 microRNAs they seem to be more important during adulthood.
Previous studies using cells grown in the laboratory have shown that mammalian let-7 microRNAs decrease cell proliferation and cell growth. Furthermore, in mouse models of various cancers, let-7 microRNAs often reduce tumour growth when they are supplied to adult mice. Therefore, overall the let-7 group has been classified as genes that act to suppress tumors, and thus protect mice (and most likely humans too) from cancers. However, in-depth analysis of let-7 microRNAs was still missing.
Wu and Nguyen et al. have now studied mice with liver cancer using strains where they were able to regulate the levels of let-7. These mice overproduce a strong cancer-inducing gene in the liver; half were used as controls and the other half were further engineered to have moderately elevated levels of let-7 expression. Most of the control mice got large cancerous tumors, but only a few mice in the other group developed cancers and the tumors were smaller. This confirmed that let-7 hinders tumor formation.
Wu and Nguyen et al. also observed that the protected mice were less able to regenerate their liver tissues. Further experiments showed that deleting just two out of ten let-7 microRNAs enhanced the mice’s ability to regenerate liver tissue after injury. These findings indicate that let-7 microRNAs slow down the growth of both cancerous and normal cells. Lastly, when let-7 levels were raised to very high levels for a prolonged amount of time this actually led to liver damage and subsequent tumor formation.
This last observation may have important consequences for possible cancer therapies. Some scientists have shown that providing extra let-7 can slow or even reverse tumour growth, but the findings here clearly point out that too much let-7 could actually worsen the situation. Since the let-7 family comprises a handful of microRNAs in mammals, in the future it will also be important to find out to what extent these molecules play overlapping roles and how much they differ.
PMCID: PMC4716837  PMID: 26445246
let-7; regeneration; cancer; liver; microRNA; MYC; Mouse
6.  Robustness of cell cycle control and flexible orders of signaling events 
Scientific Reports  2015;5:14627.
The highly robust control of cell cycles in eukaryotes enables cells to undergo strictly ordered G1/S/G2/M phases and respond adaptively to regulatory signals; however the nature of the robustness remains obscure. Specifically, it is unclear whether events of signaling should be strictly ordered and whether some events are more robust than others. To quantitatively address the two questions, we have developed a novel cell cycle model upon experimental observations. It contains positive and negative E2F proteins and two Cdk inhibitors, and is parameterized, for the first time, to generate not only oscillating protein concentrations but also periodic signaling events. Events and their orders reconstructed under varied conditions indicate that proteolysis of cyclins and Cdk complexes by APC and Skp2 occurs highly robustly in a strict order, but many other events are either dispensable or can occur in flexible orders. These results suggest that strictly ordered proteolytic events are essential for irreversible cell cycle progression and the robustness of cell cycles copes with flexible orders of signaling events, and unveil a new and important dimension to the robustness of cell cycle control in particular and to biological signaling in general.
PMCID: PMC4588580  PMID: 26419873
7.  TALEN mediated somatic mutagenesis in murine models of cancer 
Cancer research  2014;74(18):5311-5321.
Cancer genome sequencing has identified numerous somatic mutations whose biological relevance is uncertain. In this study, we used genome-editing tools to create and analyze targeted somatic mutations in murine models of liver cancer. TALEN were designed against β-catenin (Ctnnb1) and Apc, two commonly mutated genes in hepatocellular carcinoma (HCC), to generate isogenic HCC cell lines. Both mutant cell lines exhibited evidence of Wnt pathway dysregulation. We asked if these TALENs could create targeted somatic mutations after hydrodynamic transfection (HDT) into mouse liver. TALENs targeting β-catenin promoted endogenous HCC carrying the intended gain-of-function mutations. However, TALENs targeting Apc were not as efficient in inducing in vivo homozygous loss-of-function mutations. We hypothesized that hepatocyte polyploidy might be protective against TALEN-induced loss of heterozygosity (LOH), and indeed Apc gene editing was less efficient in tetraploid than in diploid hepatocytes. To increase efficiency, we administered adenoviral Apc TALENs and found that we could achieve a higher mutagenesis rate in vivo. Our results demonstrate that genome-editing tools can enable the in vivo study of cancer genes and faithfully recapitulate the mosaic nature of mutagenesis in mouse cancer models.
PMCID: PMC4167541  PMID: 25070752
Hepatocellular carcinoma; TALEN; genome-editing; cancer
8.  Big Data in Chemical Toxicity Research: The Use of High-Throughput Screening Assays To Identify Potential Toxicants 
Chemical Research in Toxicology  2014;27(10):1643-1651.
High-throughput screening (HTS) assays that measure the in vitro toxicity of environmental compounds have been widely applied as an alternative to in vivo animal tests of chemical toxicity. Current HTS studies provide the community with rich toxicology information that has the potential to be integrated into toxicity research. The available in vitro toxicity data is updated daily in structured formats (e.g., deposited into PubChem and other data-sharing web portals) or in an unstructured way (papers, laboratory reports, toxicity Web site updates, etc.). The information derived from the current toxicity data is so large and complex that it becomes difficult to process using available database management tools or traditional data processing applications. For this reason, it is necessary to develop a big data approach when conducting modern chemical toxicity research. In vitro data for a compound, obtained from meaningful bioassays, can be viewed as a response profile that gives detailed information about the compound’s ability to affect relevant biological proteins/receptors. This information is critical for the evaluation of complex bioactivities (e.g., animal toxicities) and grows rapidly as big data in toxicology communities. This review focuses mainly on the existing structured in vitro data (e.g., PubChem data sets) as response profiles for compounds of environmental interest (e.g., potential human/animal toxicants). Potential modeling and mining tools to use the current big data pool in chemical toxicity research are also described.
PMCID: PMC4203392  PMID: 25195622
9.  Low Serum Hepatitis B Surface Antigen Level Predicts Compensated Cirrhosis Caused by Chronic Hepatitis B in HBeAg Positive Patients in East China 
Hepatitis Monthly  2015;15(8):e29183.
Serum hepatitis B surface antigen (HBsAg) levels are associated with fibrosis in patients with chronic hepatitis B (CHB) infection.
The aim of our study was to evaluate serum HBsAg level as a biomarker for compensated cirrhosis in hepatitis B e antigen (HBeAg) positive CHB patients.
Patients and Methods:
Two-hundred and one HBeAg-positive Chinese CHB patients with or without cirrhosis were enrolled in this retrospective study. Cirrhosis was diagnosed based on liver biopsy. Furthermore, patients with decompensated cirrhosis were excluded. A statistical analysis was performed regarding the association between serum HBsAg level and compensated cirrhosis.
Patients with compensated cirrhosis had a significantly lower mean serum HBsAg level compared to those without cirrhosis (3.27 Log10 IU/mL VS 4.17 Log10 IU/mL, P < 0.001). Furthermore, examining the correlation with compensated cirrhosis revealed that lower level of serum HBsAg was a significant factor in multivariate analysis. The area under the receiver operating characteristics curve of serum HBsAg was 0.856 for compensated cirrhosis. A positive predictive value of 66.2% and negative predictive value of 90.7% were obtained with a cut-off value of < 3.60 Log10 IU/mL (4000 IU/mL) of serum HBsAg. Moreover, the rate of compensated cirrhosis increased to 75.0% after combining with APRI > 2.
In HBeAg positive CHB patients, low serum HBsAg level is a useful predictor of compensated cirrhosis.
PMCID: PMC4546813  PMID: 26322110
Hepatitis B Surface Antigens; Liver Cirrhosis; Hepatitis B e Antigens; Hepatitis B; Chronic
10.  Clinical efficacy of dexmedetomidine versus propofol in children undergoing magnetic resonance imaging: a meta-analysis 
Dexmedetomidine, as a sole or combinable sedative, has served in pediatric sedation undergoing MRI. However, clinical effects of dexmedetomidine are still controversial. This meta-analysis was to assess the effects between dexmedetomidine and propofol in children undergoing MRI, especially outcomes and adverse events of patients. Multiple Electronic Database searched including MEDLINE, Embase and the Cochrane library, and updated to April 2015. All statistical analysis utilized review manager to perform, the Cochrane collaboration’s software preparation and maintenance of Cochrane systematic reviews. Five trials with a total of 337 patients were included. Compared with propofol group, dexmedetomidine significantly increased the recovery time (WMD: 10.70 min; 95% CI: 4.26-17.13; P = 0.001). The duration of sedation did not appear to decrease for the patients who received dexmedetomidine than for those who received propofol (WMD: 19.96 min; 95% CI: -4.12-44.04; P = 0.1). There were statistically significant increased in the pediatric anesthesia emergence Delirium scores of 5-min after awakening (WMD: 2.40; 95% CI: 1.00 to 3.81; P = 0.0008) and 10-min after awakening (WMD: 3.06; 95% CI: 1.81 to 4.31; P < 0.00001) in patients who were treated with dexmedetomidine than propofol. Improved the prognosis of patients, nonetheless, dexmedetomidine must have an indispensable role to undergoing pediatric MRI scanning. Compared with propofol, however, dexmedetomidine did not induce the duration of sedation and might lead to a longer recovery time.
PMCID: PMC4612785  PMID: 26550100
Dexmedetomidine; propofol; general anesthetics; children; MRI; randomized controlled trials; meta-analysis
11.  Lin28b is sufficient to drive liver cancer and necessary for its maintenance in murine models 
Cancer cell  2014;26(2):248-261.
Lin28a/b are RNA-binding proteins that influence stem cell maintenance, metabolism, and oncogenesis. Poorly differentiated, aggressive cancers often overexpress Lin28, but its role in tumor initiation or maintenance has not been definitively addressed. We report that LIN28B overexpression is sufficient to initiate hepatoblastoma and hepatocellular carcinoma in murine models. We also detected Lin28b overexpression in MYC-driven hepatoblastomas, and liver-specific deletion of Lin28a/b reduced tumor burden, extended latency, and prolonged survival. Both intravenous siRNA against Lin28b and conditional Lin28b deletion reduced tumor burden and prolonged survival. Igf2bp proteins are upregulated and Igf2bp3 is required in the context of LIN28B overexpression to promote growth. Thus, multiple murine models demonstrate that Lin28b is both sufficient to initiate liver cancer and necessary for its maintenance.
PMCID: PMC4145706  PMID: 25117712
12.  Novel Two-Dimensional Mechano-Electric Generators and Sensors Based on Transition Metal Dichalcogenides 
Scientific Reports  2015;5:12854.
Transition metal dichalcogenides (TMDCs), such as MoS2 and WSe2, provide two-dimensional atomic crystals with semiconductor band gap. In this work, we present a design of new mechano-electric generators and sensors based on transition metal dichalcogenide nanoribbon PN junctions and heterojunctions. The mechano-electric conversion was simulated by using a first-principle calculation. The output voltage of MoS2 nanoribbon PN junction increases with strain, reaching 0.036 V at 1% strain and 0.31 V at 8% strain, much larger than the reported results. Our study indicates that the length, width and layer number of TMDC nanoribbon PN junctions have an interesting but different impact on the voltage output. Also, the results indicate that doping position and concentration only cause a small fluctuation in the output voltage. These results have been compared with the mechano-electric conversion of TMDC heterojunctions. Such novel mechano-electric generators and sensors are very attractive for applications in future self-powered, wearable electronics and systems.
PMCID: PMC4523874  PMID: 26238461
13.  The influence of the CYP2C19*10 allele on clopidogrel activation and CYP2C19*2 genotyping 
Pharmacogenetics and genomics  2014;24(8):381-386.
The polymorphic hepatic enzyme CYP2C19 catalyzes the metabolism of clinically important drugs such as clopidogrel, proton-pump inhibitors, and others and clinical pharmacogenetic testing for clopidogrel is increasingly common. The CYP2C19*10 SNP is located 1 bp upstream the CYP2C19*2 SNP. Despite the low frequency of the CYP2C19*10 allele, its impact on metabolism of CYP2C19 substrates and CYP2C19*2 genotyping makes it an important SNP to consider for pharmacogenetic testing of CYP2C19. However, the effect of the CYP2C19*10 allele on clopidogrel metabolism has not been explored to date. We measured the enzymatic activity of the CYP2C19.10 protein against clopidogrel. The catalytic activity of CYP2C19.10 in the biotransformation of clopidogrel and 2-oxo-clopidgorel was significantly decreased relative to wild type CYP2C19.1B. We also report that the CYP2C19*10 SNP interferes with the CYP2C19*2 TaqMan® genotyping assay, resulting in miscalling of CYP2C19*10/*2 as CYP2C19*2/*2. Our data provide evidence of CYP2C19.10’s reduced metabolism of clopidogrel and 2-oxo-clopidogrel.
PMCID: PMC4090277  PMID: 24945780
CYP2C19*10; Clopidogrel; Pharmacokinetic; Pharmacogenetic; genotyping
14.  Precore/basal core promoter mutants quantification throughout phases of hepatitis B virus infection by Simpleprobe 
AIM: To investigate precore/basal core promoter (PC/BCP) mutants throughout hepatitis B virus (HBV) infection and to determine their relationship to hepatitis B early antigen (HBeAg) titers.
METHODS: We enrolled 191 patients in various stages of HBV infection at the Huashan Hospital and the Taizhou Municipal Hospital from 2010 to 2012. None of the patients received antiviral therapy. HBV DNA from serum, was quantified by real-time PCR. The HBV genotype was determined by direct sequencing of the S gene. We used the Simpleprobe ultrasensitive quantitative method to detect PC/BCP mutants in each patient. We compared the strain number, percentage, and the changes in PC/BCP mutants in different phases, and analyzed the relationship between PC/BCP mutants and HBeAg by multiple linear regression and logistic regression.
RESULTS: Patients with HBV infection (n = 191) were assigned to groups by phase: Immune tolerance (IT) = 55, Immune clearance (IC) = 67, Low-replicative (LR) = 49, and HBeAg-negative hepatitis (ENH) = 20. Of the patients (male, 112; female, 79) enrolled, 122 were HBeAg-positive and 69 were HBeAg-negative. The median age was 33 years (range: 18-78 years). PC and BCP mutation detection rates were 84.82% (162/191) and 96.86% (185/191), respectively. In five HBeAg-negative cases, we detected double mutation G1896A/G1899A. The logarithm value of PC mutant quantities (log10 PC) significantly differed in IT, IC, and LR phases, as well as in the ENH phase (F = 49.350, P < 0.001). The logarithm value of BCP mutant quantities (log10 BCP) also differed during the four phases (F = 25.530, P < 0.001). Log10 PC and log10 BCP values were high in the IT and IC phases, decreased in the LR phase, and increased in the ENH phase, although the absolute value at this point remained lower than that in the IT and IC phases. PC mutant quantity per total viral load (PC%) and BCP mutant quantity per total viral load (BCP%) differed between phases (F = 20.040, P < 0.001; F = 10.830, P < 0.001), with PC% and BCP% gradually increasing in successive phases. HBeAg titers negatively correlated with PC% (Spearman’s rho = -0.354, P < 0.001) and BCP% (Spearman’s rho = -0.395, P < 0.001). The negative correlation between PC% and HBeAg status was significant (B = -5.281, P = 0.001), but there was no such correlation between BCP% and HBeAg status (B = -0.523, P = 0.552).
CONCLUSION: PC/BCP mutants become predominant in a dynamic and continuous process. Log10 PC, log10 BCP, PC% and BCP% might be combined to evaluate disease progression. PC% determines HBeAg status.
PMCID: PMC4458774  PMID: 26074702
Precore mutant; Basal core promoter mutant; Hepatitis B virus; Quantification; Hepatitis B early antigen titers
15.  Triptolide Attenuates Podocyte Injury by Regulating Expression of miRNA-344b-3p and miRNA-30b-3p in Rats with Adriamycin-Induced Nephropathy 
Objectives. We investigated the action of triptolide in rats with adriamycin-induced nephropathy and evaluated the possible mechanisms underlying its protective effect against podocyte injury. Methods. In total, 30 healthy male Sprague-Dawley rats were randomized into three groups (normal group, model group, and triptolide group). On days 7, 28, 42, and 56, 24 h urine samples were collected. All rats were sacrificed on day 56, and their blood and renal tissues were collected for determination of biochemical and molecular biological parameters. Expression of miRNAs in the renal cortex was analyzed by a biochip assay and RT-PCR was used to confirm observed differences in miRNA levels. Results. Triptolide decreased proteinuria, improved renal function without apparent adverse effects on the liver, and alleviated renal pathological lesions. Triptolide also elevated the nephrin protein level. Furthermore, levels of miR-344b-3p and miR-30b-3p were elevated in rats with adriamycin-induced nephropathy, while triptolide treatment reversed the increase in the expression of these two miRNAs. Conclusions. These results suggest that triptolide may attenuate podocyte injury in rats with adriamycin-induced nephropathy by regulating expression of miRNA-344b-3p and miRNA-30b-3p.
PMCID: PMC4452866  PMID: 26078766
16.  Retrospective analysis of individual risk factors for urethrocutaneous fistula after onlay hypospadias repair in pediatric patients 
To retrospectively identify the individual risk factors for the urethrocutaneous fistula (UCF) in pediatric patients after hypospadias repair (HR) with onlay island flap urethroplasty.
A total of 167 patients who underwent primary HR at Nanjing Medical University Affiliated Children Hospital from January 2009 to December 2012 were enrolled. Clinical data including the patient’ age at HR, hypospadias type and urethral defect length were documented.
Among 167 patients, 12.6% patients (n = 21) developed UCF after HR. Postoperative UCF occurred in 3.9% (3/76) cases at age of 0–2 years, 14.3% (9/63) at 2–4 years, 20.0% (2/10) at 4–6 years and 38.9% (7/18) at 6–12 years. The incidences of UCF were 12.0% (3/25), 11.4% (5/132) and 30.0% (3/10) for distal, middle and proximal types of hypospadias. As to the urethral defect length, the incidences of UCF were 8.2% (5/61) in patients with a length of ≤ 2 cm, 12.8% (9/70) in 2-3 cm, 22.6% (7/31) in 3–4 cm and 0% (0/5) in above 4 cm. Older age at HR was significantly associated with the high incidence of UCF formation (P = 0.004), while the hypospadias type and urethral defect length did not affect it (P = 0.264 and P = 0.312, respectively).
The patient’ age at HR was a risk factor for the UCF formation after HR, and treatment of HR within two years old might be with the least incidence of UCF.
PMCID: PMC4422430  PMID: 25903765
Hypospadias; Urethrocutaneous fistula; Risk factors; Onlay island flap
17.  Common defects of mitochondria and iron in neurodegeneration and diabetes (MIND): A paradigm worth exploring 
Biochemical pharmacology  2013;88(4):573-583.
A popular, if not centric, approach to the study of an event is to first consider that of the simplest cause. When dissecting the underlying mechanisms governing idiopathic diseases, this generally takes the form of an ab initio genetic approach. To date, this genetic ‘smoking gun’ has remained elusive in diabetes mellitus and for many affected by neurodegenerative diseases. With no single gene, or even subset of genes, conclusively causative in all cases, other approaches to the etiology and treatment of these diseases seem reasonable, including the correlation of a systems’ predisposed sensitivity to particular influence. In the cases of diabetes mellitus and neurodegenerative diseases, overlapping themes of mitochondrial influence or dysfunction and iron dyshomeostasis are apparent and relatively consistent. This mini-review discusses the influence of mitochondrial function and iron homeostasis on diabetes mellitus and neurodegenerative disease, namely Alzheimer’s disease. Also discussed is the incidence of diabetes accompanied by neuropathy and neurodegeneration along with neurodegenerative disorders prone to development of diabetes. Mouse models containing multiple facets of this overlap are also described alongside current molecular trends attributed to both diseases. As a way of approaching the idiopathic and complex nature of these diseases we are proposing the consideration of a MIND (mitochondria, iron, neurodegeneration, and diabetes) paradigm in which systemic metabolic influence, iron homeostasis, and respective genetic backgrounds play a central role in the development of disease.
PMCID: PMC3972369  PMID: 24361914
18.  Critical Evaluation of Human Oral Bioavailability for Pharmaceutical Drugs by Using Various Cheminformatics Approaches 
Pharmaceutical research  2013;31(4):1002-1014.
Oral bioavailability (%F) is a key factor that determines the fate of a new drug in clinical trials. Traditionally, %F is measured using costly and time -consuming experimental tests. Developing computational models to evaluate the %F of new drugs before they are synthesized would be beneficial in the drug discovery process.
We employed Combinatorial Quantitative Structure-Activity Relationship approach to develop several computational %F models. We compiled a %F dataset of 995 drugs from public sources. After generating chemical descriptors for each compound, we used random forest, support vector machine, k nearest neighbor, and CASE Ultra to develop the relevant QSAR models. The resulting models were validated using five-fold cross-validation.
The external predictivity of %F values was poor (R2=0.28, n=995, MAE=24), but was improved (R2=0.40, n=362, MAE=21) by filtering unreliable predictions that had a high probability of interacting with MDR1 and MRP2 transporters. Furthermore, classifying the compounds according to the %F values (%F<50% as “low”, %F≥50% as ‘high”) and developing category QSAR models resulted in an external accuracy of 76%.
In this study, we developed predictive %F QSAR models that could be used to evaluate new drug compounds, and integrating drug-transporter interactions data greatly benefits the resulting models.
PMCID: PMC3955412  PMID: 24306326
oral bioavailability; intestinal membrane transporter; QSAR; drugs
19.  The Use of Pseudo-equilibrium Constant Affords Improved QSAR Models of Human Plasma Protein Binding 
Pharmaceutical research  2013;30(7):1790-1798.
To develop accurate in silico predictors of Plasma Protein Binding (PPB).
Experimental PPB data were compiled for over 1,200 compounds. Two endpoints have been considered: (1) fraction bound (%PPB); and (2) the logarithm of a pseudo binding constant (lnKa) derived from %PPB. The latter metric was employed because it reflects the PPB thermodynamics and the distribution of the transformed data is closer to normal. Quantitative Structure-Activity Relationship (QSAR) models were built with Dragon descriptors and three statistical methods.
Five-fold external validation procedure resulted in models with the prediction accuracy (R2) of 0.67±0.04 and 0.66±0.04, respectively, and the mean absolute error (MAE) of 15.3±0.2% and 13.6±0.2%, respectively. Models were validated with two external datasets: 173 compounds from DrugBank, and 236 chemicals from the US EPA ToxCast project. Models built with lnKa were significantly more accurate (MAE of 6.2–10.7%) than those built with %PPB (MAE of 11.9–17.6%) for highly bound compounds both for the training and the external sets.
The pseudo binding constant (lnKa) is more appropriate for characterizing PPB binding than conventional %PPB. Validated QSAR models developed herein can be applied as reliable tools in early drug development and in chemical risk assessment.
PMCID: PMC4363124  PMID: 23568522
machine learning; %PPB; drug fraction bound; ADMET; pharmacokinetics
20.  Magnetic Resonance Imaging with Superparamagnetic Iron Oxide Fails to Track the Long-term Fate of Mesenchymal Stem Cells Transplanted into Heart 
Scientific Reports  2015;5:9058.
MRI for in vivo stem cell tracking remains controversial. Here we tested the hypothesis that MRI can track the long-term fate of the superparamagnetic iron oxide (SPIO) nanoparticles labelled mesenchymal stem cells (MSCs) following intramyocardially injection in AMI rats. MSCs (1 × 106) from male rats doubly labeled with SPIO and DAPI were injected 2 weeks after myocardial infarction. The control group received cell-free media injection. In vivo serial MRI was performed at 24 hours before cell delivery (baseline), 3 days, 1, 2, and 4 weeks after cell delivery, respectively. Serial follow-up MRI demonstrated large persistent intramyocardial signal-voids representing SPIO during the follow-up of 4 weeks, and MSCs did not moderate the left ventricular dysfunction. The TUNEL analysis confirmed that MSCs engrafted underwent apoptosis. The histopathological studies revealed that the site of cell injection was infiltrated by inflammatory cells progressively and the iron-positive cells were macrophages identified by CD68 staining, but very few or no DAPI-positive stem cells at 4 weeks after cells transplantation. The presence of engrafted cells was confirmed by real-time PCR, which showed that the amount of Y-chromosome-specific SRY gene was consistent with the results. MRI may not reliably track the long-term fate of SPIO-labeled MSCs engraftment in heart.
PMCID: PMC4356978  PMID: 25762186
21.  Lin28 and let-7 in cell metabolism and cancer 
Translational Pediatrics  2015;4(1):4-11.
Malignant cells exhibit major metabolic alterations. The regulatory gene networks that regulate metabolism and the impact of these alterations on overall cellular fitness deserve further exploration. The let-7 microRNAs and their antagonists, the Lin28 RNA-binding proteins, are well-known for controlling the timing of embryonic development. This pathway has recently been shown to regulate glucose metabolism in adult mice and to reprogram metabolism during tissue injury and repair. In addition, many lines of evidence have established that Lin28 is an oncogene that drives tumorigenesis in part by suppressing let-7. The metabolic underpinnings of this oncogenic program are just beginning to be uncovered. Here, we will review the current understanding of how Lin28 exerts regenerative and oncogenic effects through metabolic mechanisms.
PMCID: PMC4729067  PMID: 26835354
Lin28, let-7; cancer; regeneration; metabolism
22.  Predicting Drug-induced Hepatotoxicity Using QSAR and Toxicogenomics Approaches 
Chemical research in toxicology  2011;24(8):1251-1262.
Quantitative Structure-Activity Relationship (QSAR) modeling and toxicogenomics are used independently as predictive tools in toxicology. In this study, we evaluated the power of several statistical models for predicting drug hepatotoxicity in rats using different descriptors of drug molecules, namely their chemical descriptors and toxicogenomic profiles. The records were taken from the Toxicogenomics Project rat liver microarray database containing information on 127 drugs ( The model endpoint was hepatotoxicity in the rat following 28 days of exposure, established by liver histopathology and serum chemistry. First, we developed multiple conventional QSAR classification models using a comprehensive set of chemical descriptors and several classification methods (k nearest neighbor, support vector machines, random forests, and distance weighted discrimination). With chemical descriptors alone, external predictivity (Correct Classification Rate, CCR) from 5-fold external cross-validation was 61%. Next, the same classification methods were employed to build models using only toxicogenomic data (24h after a single exposure) treated as biological descriptors. The optimized models used only 85 selected toxicogenomic descriptors and had CCR as high as 76%. Finally, hybrid models combining both chemical descriptors and transcripts were developed; their CCRs were between 68 and 77%. Although the accuracy of hybrid models did not exceed that of the models based on toxicogenomic data alone, the use of both chemical and biological descriptors enriched the interpretation of the models. In addition to finding 85 transcripts that were predictive and highly relevant to the mechanisms of drug-induced liver injury, chemical structural alerts for hepatotoxicity were also identified. These results suggest that concurrent exploration of the chemical features and acute treatment-induced changes in transcript levels will both enrich the mechanistic understanding of sub-chronic liver injury and afford models capable of accurate prediction of hepatotoxicity from chemical structure and short-term assay results.
PMCID: PMC4281093  PMID: 21699217
Quantitative Structure Activity Relationship (QSAR) modeling; toxicogenomics; biological descriptors; hepatotoxicity
23.  Lin28 enhances tissue repair by reprogramming cellular metabolism 
Cell  2013;155(4):778-792.
Regeneration capacity declines with age, but why juvenile organisms show enhanced tissue repair remains unexplained. Lin28a, a highly-conserved RNA binding protein expressed during embryogenesis, plays roles in development, pluripotency and metabolism. To determine if Lin28a might influence tissue repair in adults, we engineered the reactivation of Lin28a expression in several models of tissue injury. Lin28a reactivation improved hair regrowth by promoting anagen in hair follicles, and accelerated regrowth of cartilage, bone and mesenchyme after ear and digit injuries. Lin28a inhibits let-7 microRNA biogenesis; however let-7 repression was necessary but insufficient to enhance repair. Lin28a bound to and enhanced the translation of mRNAs for several metabolic enzymes, thereby increasing glycolysis and oxidative phosphorylation (OxPhos). Lin28a-mediated enhancement of tissue repair was negated by OxPhos inhibition, whereas a pharmacologically-induced increase in OxPhos enhanced repair. Thus, Lin28a enhances tissue repair in some adult tissues by reprogramming cellular bioenergetics.
PMCID: PMC3917449  PMID: 24209617
24.  AdaBoost Based Multi-Instance Transfer Learning for Predicting Proteome-Wide Interactions between Salmonella and Human Proteins 
PLoS ONE  2014;9(10):e110488.
Pathogen-host protein-protein interaction (PPI) plays an important role in revealing the underlying pathogenesis of viruses and bacteria. The need of rapidly mapping proteome-wide pathogen-host interactome opens avenues for and imposes burdens on computational modeling. For Salmonella typhimurium, only 62 interactions with human proteins are reported to date, and the computational modeling based on such a small training data is prone to yield model overfitting. In this work, we propose a multi-instance transfer learning method to reconstruct the proteome-wide Salmonella-human PPI networks, wherein the training data is augmented by homolog knowledge transfer in the form of independent homolog instances. We use AdaBoost instance reweighting to counteract the noise from homolog instances, and deliberately design three experimental settings to validate the assumption that the homolog instances are effective to address the problems of data scarcity and data unavailability. The experimental results show that the proposed method outperforms the existing models and some predictions are validated by the findings from recent literature. Lastly, we conduct gene ontology based clustering analysis of the predicted networks to provide insights into the pathogenesis of Salmonella.
PMCID: PMC4212833  PMID: 25330226
Identification of Endocrine Disrupting Chemicals is one of the important goals of environmental chemical hazard screening. We report on the development of validated in silico predictors of chemicals likely to cause Estrogen Receptor (ER)-mediated endocrine disruption to facilitate their prioritization for future screening. A database of relative binding affinity of a large number of ERα and/or ERβ ligands was assembled (546 for ERα and 137 for ERβ). Both single-task learning (STL) and multi-task learning (MTL) continuous Quantitative Structure-Activity Relationships (QSAR) models were developed for predicting ligand binding affinity to ERα or ERβ. High predictive accuracy was achieved for ERα binding affinity (MTL R2=0.71, STL R2=0.73). For ERβ binding affinity, MTL models were significantly more predictive (R2=0.53, p<0.05) than STL models. In addition, docking studies were performed on a set of ER agonists/antagonists (67 agonists and 39 antagonists for ERα, 48 agonists and 32 antagonists for ERβ, supplemented by putative decoys/non-binders) using the following ER structures (in complexes with respective ligands) retrieved from the Protein Data Bank: ERα agonist (PDB ID: 1L2I), ERα antagonist (PDB ID: 3DT3), ERβ agonist (PDB ID: 2NV7), ERβ antagonist (PDB ID: 1L2J). We found that all four ER conformations discriminated their corresponding ligands from presumed non-binders. Finally, both QSAR models and ER structures were employed in parallel to virtually screen several large libraries of environmental chemicals to derive a ligand- and structure-based prioritized list of putative estrogenic compounds to be used for in vitro and in vivo experimental validation.
PMCID: PMC3775906  PMID: 23707773
Endocrine Disrupting Chemicals; Estrogen Receptor; Quantitative Structure-Activity Relationships modeling; Multi-Task Learning; Docking; Virtual Screening

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