Search tips
Search criteria

Results 1-25 (444)

Clipboard (0)

Select a Filter Below

more »
Year of Publication
more »
1.  Patients with Old Age or Proximal Tumors Benefit from Metabolic Syndrome in Early Stage Gastric Cancer 
PLoS ONE  2014;9(3):e89965.
Metabolic syndrome and/or its components have been demonstrated to be risk factors for several cancers. They are also found to influence survival in breast, colon and prostate cancer, but the prognostic value of metabolic syndrome in gastric cancer has not been investigated.
Clinical data and pre-treatment information of metabolic syndrome of 587 patients diagnosed with early stage gastric cancer were retrospectively collected. The associations of metabolic syndrome and/or its components with clinical characteristics and overall survival in early stage gastric cancer were analyzed.
Metabolic syndrome was identified to be associated with a higher tumor cell differentiation (P = 0.036). Metabolic syndrome was also demonstrated to be a significant and independent predictor for better survival in patients aged >50 years old (P = 0.009 in multivariate analysis) or patients with proximal gastric cancer (P = 0.047 in multivariate analysis). No association was found between single metabolic syndrome component and overall survival in early stage gastric cancer. In addition, patients with hypertension might have a trend of better survival through a good control of blood pressure (P = 0.052 in univariate analysis).
Metabolic syndrome was associated with a better tumor cell differentiation in patients with early stage gastric cancer. Moreover, metabolic syndrome was a significant and independent predictor for better survival in patients with old age or proximal tumors.
PMCID: PMC3943843  PMID: 24599168
2.  Figure-Associated Text Summarization and Evaluation 
PLoS ONE  2015;10(2):e0115671.
Biomedical literature incorporates millions of figures, which are a rich and important knowledge resource for biomedical researchers. Scientists need access to the figures and the knowledge they represent in order to validate research findings and to generate new hypotheses. By themselves, these figures are nearly always incomprehensible to both humans and machines and their associated texts are therefore essential for full comprehension. The associated text of a figure, however, is scattered throughout its full-text article and contains redundant information content. In this paper, we report the continued development and evaluation of several figure summarization systems, the FigSum+ systems, that automatically identify associated texts, remove redundant information, and generate a text summary for every figure in an article. Using a set of 94 annotated figures selected from 19 different journals, we conducted an intrinsic evaluation of FigSum+. We evaluate the performance by precision, recall, F1, and ROUGE scores. The best FigSum+ system is based on an unsupervised method, achieving F1 score of 0.66 and ROUGE-1 score of 0.97. The annotated data is available at (
PMCID: PMC4313946  PMID: 25643357
3.  Characteristics of language impairment in Parkinson’s disease and its influencing factors 
Language impairment is relatively common in Parkinson’s disease (PD), but not all PD patients are susceptible to language problems. In this study, we identified among a sample of PD patients those pre-disposed to language impairment, describe their clinical profiles, and consider factors that may precipitate language disability in these patients.
A cross-sectional cohort of 31 PD patients and 20 controls were administered the Chinese version of the Western Aphasia Battery (WAB) to assess language abilities, and the Montreal Cognitive Assessment (MoCA) to determine cognitive status. PD patients were then apportioned to a language-impaired PD (LI-PD) group or a PD group with no language impairment (NLI-PD). Performance on the WAB and MoCA was investigated for correlation with the aphasia quotient deterioration rate (AQDR).
The PD patients scored significantly lower on most of the WAB subtests than did the controls. The aphasia quotient, cortical quotient, and spontaneous speech and naming subtests of the WAB were significantly different between LI-PD and NLI-PD groups. The AQDR scores significantly and positively correlated with age at onset and motor function deterioration.
A subset group was susceptible to language dysfunction, a major deficit in spontaneous speech. Once established, dysphasia progression is closely associated with age at onset and motor disability progression.
PMCID: PMC4328233
Aphasia quotient; Language function deterioration rate; Language impairment; Parkinson’s disease; Western aphasia battery
4.  Gastrotracheal fistula: Treatment with a covered elf-expanding Y-shaped metallic stent 
A 67-year-old man had a sev-ere cough and pulmonary infection for 1 wk before seeking evaluation at our hospital. He had undergone esophagectomy with gastric pull-up and radiotherapy for esophageal cancer 3 years previously. After admission to our hospital, gastroscopy and bronchoscopy revealed a fistulous communication between the posterior tracheal wall near the carina and the upper residual stomach. We measured the diameter of the trachea and bronchus and determined the site and size of the fistula using multislice computed tomography and gastroscopy. A covered self-expanding Y-shaped metallic stent was implanted into the trachea and bronchus. Subsequently, the fistula was closed completely. The patient tolerated the stent well and had good palliation of his symptoms.
PMCID: PMC4299322  PMID: 25624743
Gastrotracheal fistula; Y-shaped metallic stent; Esophageal cancer; Gastroesophageal surgery
5.  Genome Sequence of a Novel Recombinant Coxsackievirus A6 Strain from Shanghai, China, 2013 
Genome Announcements  2015;3(1):e01347-14.
A novel recombinant coxsackievirus A6 (CVA6) strain was isolated during a coxsackievirus A6 outbreak in Shanghai, China, in 2013. Genomic sequence and similarity plot analysis showed that the novel CVA6 strain shared higher similarity with a recent CVA4 strain rather than the recent CVA6 strain in the 2C and 3′ untranslated regions (UTRs).
PMCID: PMC4290982  PMID: 25573929
RUNX2, a key transcription factor for osteoblast differentiation, is regulated by ERK1/2 and p38 MAP kinase-mediated phosphorylation. However, the specific contribution of each kinase to RUNX2-dependent transcription is not known. Here we investigate ERK and p38 regulation of RUNX2 using a unique P-RUNX2-specific antibody. Both MAP kinases stimulated RUNX2 Ser319 phosphorylation and transcriptional activity. However, a clear preference for ERK1 versus p38α/β was seen when the ability of these MAPKs to phosphorylate and activate RUNX2 was compared. Similarly, ERK1 preferentially bound to a consensus MAPK binding site on RUNX2 that was essential for the activity of either kinase. To assess the relative contribution of ERK1/2 and p38 to osteoblast gene expression, MC3T3-E1 preosteoblast cells were grown in control or ascorbic acid (AA)-containing medium ± BMP2/7. AA-induced gene expression, which requires collagen matrix synthesis, was associated with parallel increases in P-ERK and RUNX2-S319-P in the absence of any changes in P-p38. This response was blocked by ERK, but not p38, inhibition. Significantly, in the presence of AA, BMP2/7 synergistically stimulated RUNX2 S319 phosphorylation and transcriptional activity without affecting total RUNX2 and this response was totally dependent on ERK/MAPK activity. In contrast, although p38 inhibition partially blocked BMP-dependent transcription, it did not affect RUNX2 S319 phosphorylation, suggesting the involvement of other phosphorylation sites and/or transcription factors in this response. Based on this work, we conclude that extracellular matrix and BMP regulation of RUNX2 phosphorylation and transcriptional activity in osteoblasts is predominantly mediated by ERK rather than p38 MAPKs.
PMCID: PMC4285380  PMID: 22072425
Osteoblast; transcription; phosphorylation; MAPK; Runx2
7.  Cross-Fostering Increases Th1/Th2 Expression in a Prenatal Dexamethasone Exposure Rat Model 
PLoS ONE  2014;9(12):e115554.
Prenatal dexamethasone exposure has been reported to increase allergy potential in childhood possibly by interference with normal immunological development in utero. This study investigated the effects of prenatal dexamethasone on T helper cell immune responses in a rat model.
Pregnant rats received either dexamethasone 0.1 mg/kg/day or normal saline from gestational day 14–21. Off-springs were cared for by their biological mother, or cross-fostered by the opposing group. Spleen and blood samples were collected at post-natal day 7 and 120 and tested for mRNA expression and plasma cytokine levels of Th1/Th2/Th17 immune response.
Both Th1 (T-bet) and Th2 (GATA-3) mRNA expression were shown to have a significant increase in the prenatal dexamethasone exposure group at day 120 (p<0.05). The plasma levels for Th1 (IFNγ and IL-2) and Th2 (IL-4, IL-5, IL-13) were found to have no significant differences between the two group (p>0.05). The mRNA expression of Th17 (RORγt) showed a significant decrease at post-natal day 120 as well as the plasma level of IL-17A at day 7 (11.21±1.67 vs. 6.23±1.06 pg/ml, p = 0.02). Cross-fostering by a dexamethasone exposed mother resulted in a significant increase in Th1/Th2 mRNA expression (p<0.05) and decrease of Th17.
Prenatal dexamethasone exposure increased Th1, Th2 and decreased Th17 expression. Cross-fostering by a dexamethasone exposed mother results in more prominent increase of Th1 and Th2 expression.
PMCID: PMC4272273  PMID: 25526616
8.  Clinical Features and Expressions of Foxp3 and IL-17 in Type 1 Autoimmune Pancreatitis in China 
Autoimmune pancreatitis (AIP) is a distinct type of pancreatitis associated with a presumed autoimmune mechanism. The aim of this study was to analyze the clinical features and expressions of forkhead box P3 (Foxp3) and interleukin-17 (IL-17) in type 1 AIP in China and to identify factors for differentiation of AIP from non-AIP chronic pancreatitis (CP).
We retrospectively reviewed pancreatic specimens with diagnosis of type 1 AIP and non-AIP CP at Sun Yat-Sen Memorial Hospital in China from January 2000 to December 2013. The clinical symptoms, serological data, imaging findings, histopathology, and immunohistochemical findings of Foxp3 and IL-17 in the 2 groups were analyzed.
Twenty-nine patients with type 1 AIP and 20 patients with non-AIP CP were enrolled. Obstructive jaundice was more common in type 1 AIP than in non-AIP CP (62.1% vs. 30.0%, P=0.042). The diffuse or segmental enlargement of the pancreas was more frequent in type 1 AIP than in non-AIP CP (72.4% vs. 40.0%, P=0.038). Histopathology of type 1 AIP presented dense lymphoplasmacytic infiltration, “snowstorm-like” fibrosis and abundant immunoglobulin (Ig) G4+ cells. Foxp3+ cells were more frequently observed in type 1 AIP than in non-AIP CP. IL-17+ cell infiltration was similar between the 2 groups. Furthermore, a positive correlation was found between Foxp3+ and IgG4+ cell counts in the pancreas of patients with type 1 AIP.
Type 1 AIP has distinctive symptoms, image, and pathological characteristics, which could be used for differentiation from non-AIP CP. Foxp3+ cells might be helpful to distinguish type 1 AIP from non-AIP CP.
PMCID: PMC4278699  PMID: 25553723
Forkhead Transcription Factors; Immunoglobulin G; Interleukin-17; Pancreatitis; Pancreatitis, Chronic
9.  Condensin suppresses recombination and regulates double-strand break processing at the repetitive ribosomal DNA array to ensure proper chromosome segregation during meiosis in budding yeast 
Molecular Biology of the Cell  2014;25(19):2934-2947.
Condensin undergoes a sequestration, release, and reloading cycle at the rDNA array in budding yeast meiosis. It regulates rDNA stability by suppressing double-strand break (DSB) formation and promoting DSB processing.
During meiosis, homologues are linked by crossover, which is required for bipolar chromosome orientation before chromosome segregation at anaphase I. The repetitive ribosomal DNA (rDNA) array, however, undergoes little or no meiotic recombination. Hyperrecombination can cause chromosome missegregation and rDNA copy number instability. We report here that condensin, a conserved protein complex required for chromosome organization, regulates double-strand break (DSB) formation and repair at the rDNA gene cluster during meiosis in budding yeast. Condensin is highly enriched at the rDNA region during prophase I, released at the prophase I/metaphase I transition, and reassociates with rDNA before anaphase I onset. We show that condensin plays a dual role in maintaining rDNA stability: it suppresses the formation of Spo11-mediated rDNA breaks, and it promotes DSB processing to ensure proper chromosome segregation. Condensin is unnecessary for the export of rDNA breaks outside the nucleolus but required for timely repair of meiotic DSBs. Our work reveals that condensin coordinates meiotic recombination with chromosome segregation at the repetitive rDNA sequence, thereby maintaining genome integrity.
PMCID: PMC4230583  PMID: 25103240
10.  Safety and Effects of the Vector for the Leber Hereditary Optic Neuropathy Gene Therapy Clinical Trial 
JAMA ophthalmology  2014;132(4):409-420.
We developed a novel strategy for treatment of Leber hereditary optic neuropathy (LHON) caused by a mutation in the nicotinamide adenine dinucleotide dehydrogenase subunit IV (ND4) mitochondrial gene.
To demonstrate the safety and effects of the gene therapy vector to be used in a proposed gene therapy clinical trial.
In a series of laboratory experiments, we modified the mitochondrial ND4 subunit of complex I in the nuclear genetic code for import into mitochondria. The protein was targeted into the organelle by agency of a targeting sequence (allotopic expression). The gene was packaged into adeno-associated viral vectors and then vitreally injected into rodent, nonhuman primate, and ex vivo human eyes that underwent testing for expression and integration by immunohistochemical analysis and blue native polyacrylamide gel electrophoresis. During serial follow-up, the animal eyes underwent fundus photography, optical coherence tomography, and multifocal or pattern electroretinography. We tested for rescue of visual loss in rodent eyes also injected with a mutant G11778A ND4 homologue responsible for most cases of LHON.
Ocular infection with recombinant adeno-associated viral vectors containing a wild-type allotopic human ND4 gene.
Expression of human ND4 and rescue of optic neuropathy induced by mutant human ND4.
We found human ND4 expressed in almost all mouse retinal ganglion cells by 1 week after injection and ND4 integrated into the mouse complex I. In rodent eyes also injected with a mutant allotopic ND4, wild-type allotopic ND4 prevented defective adenosine triphosphate synthesis, suppressed visual loss, reduced apoptosis of retinal ganglion cells, and prevented demise of axons in the optic nerve. Injection of ND4 in the ex vivo human eye resulted in expression in most retinal ganglion cells. Primates undergoing vitreal injection with the ND4 test article and followed up for 3 months had no serious adverse reactions.
Expression of our allotopic ND4 vector in the ex vivo human eye, safety of the test article, rescue of the LHON mouse model, and the severe irreversible loss of visual function in LHON support clinical testing with mutated G11778A mitochondrial DNA in our patients.
PMCID: PMC4266107  PMID: 24457989
11.  Prediction of protein-protein interactions from amino acid sequences using a novel multi-scale continuous and discontinuous feature set 
BMC Bioinformatics  2014;15(Suppl 15):S9.
Identifying protein-protein interactions (PPIs) is essential for elucidating protein functions and understanding the molecular mechanisms inside the cell. However, the experimental methods for detecting PPIs are both time-consuming and expensive. Therefore, computational prediction of protein interactions are becoming increasingly popular, which can provide an inexpensive way of predicting the most likely set of interactions at the entire proteome scale, and can be used to complement experimental approaches. Although much progress has already been achieved in this direction, the problem is still far from being solved and new approaches are still required to overcome the limitations of the current prediction models.
In this work, a sequence-based approach is developed by combining a novel Multi-scale Continuous and Discontinuous (MCD) feature representation and Support Vector Machine (SVM). The MCD representation gives adequate consideration to the interactions between sequentially distant but spatially close amino acid residues, thus it can sufficiently capture multiple overlapping continuous and discontinuous binding patterns within a protein sequence. An effective feature selection method mRMR was employed to construct an optimized and more discriminative feature set by excluding redundant features. Finally, a prediction model is trained and tested based on SVM algorithm to predict the interaction probability of protein pairs.
When performed on the yeast PPIs data set, the proposed approach achieved 91.36% prediction accuracy with 91.94% precision at the sensitivity of 90.67%. Extensive experiments are conducted to compare our method with the existing sequence-based method. Experimental results show that the performance of our predictor is better than several other state-of-the-art predictors, whose average prediction accuracy is 84.91%, sensitivity is 83.24%, and precision is 86.12%. Achieved results show that the proposed approach is very promising for predicting PPI, so it can be a useful supplementary tool for future proteomics studies. The source code and the datasets are freely available at for academic use.
PMCID: PMC4271571  PMID: 25474679
12.  A Conformation-Dependent Neutralizing Monoclonal Antibody Specifically Targeting Receptor-Binding Domain in Middle East Respiratory Syndrome Coronavirus Spike Protein 
Journal of Virology  2014;88(12):7045-7053.
Prophylactic and therapeutic strategies are urgently needed to combat infections caused by the newly emerged Middle East respiratory syndrome coronavirus (MERS-CoV). Here, we have developed a neutralizing monoclonal antibody (MAb), designated Mersmab1, which potently blocks MERS-CoV entry into human cells. Biochemical assays reveal that Mersmab1 specifically binds to the receptor-binding domain (RBD) of the MERS-CoV spike protein and thereby competitively blocks the binding of the RBD to its cellular receptor, dipeptidyl peptidase 4 (DPP4). Furthermore, alanine scanning of the RBD has identified several residues at the DPP4-binding surface that serve as neutralizing epitopes for Mersmab1. These results suggest that if humanized, Mersmab1 could potentially function as a therapeutic antibody for treating and preventing MERS-CoV infections. Additionally, Mersmab1 may facilitate studies of the conformation and antigenicity of MERS-CoV RBD and thus will guide rational design of MERS-CoV subunit vaccines.
IMPORTANCE MERS-CoV is spreading in the human population and causing severe respiratory diseases with over 40% fatality. No vaccine is currently available to prevent MERS-CoV infections. Here, we have produced a neutralizing monoclonal antibody with the capacity to effectively block MERS-CoV entry into permissive human cells. If humanized, this antibody may be used as a prophylactic and therapeutic agent against MERS-CoV infections. Specifically, when given to a person (e.g., a patient's family member or a health care worker) either before or after exposure to MERS-CoV, the humanized antibody may prevent or inhibit MERS-CoV infection, thereby stopping the spread of MERS-CoV in humans. This antibody can also serve as a useful tool to guide the design of effective MERS-CoV vaccines.
PMCID: PMC4054355  PMID: 24719424
13.  A robust data-driven approach for gene ontology annotation 
Gene ontology (GO) and GO annotation are important resources for biological information management and knowledge discovery, but the speed of manual annotation became a major bottleneck of database curation. BioCreative IV GO annotation task aims to evaluate the performance of system that automatically assigns GO terms to genes based on the narrative sentences in biomedical literature. This article presents our work in this task as well as the experimental results after the competition. For the evidence sentence extraction subtask, we built a binary classifier to identify evidence sentences using reference distance estimator (RDE), a recently proposed semi-supervised learning method that learns new features from around 10 million unlabeled sentences, achieving an F1 of 19.3% in exact match and 32.5% in relaxed match. In the post-submission experiment, we obtained 22.1% and 35.7% F1 performance by incorporating bigram features in RDE learning. In both development and test sets, RDE-based method achieved over 20% relative improvement on F1 and AUC performance against classical supervised learning methods, e.g. support vector machine and logistic regression. For the GO term prediction subtask, we developed an information retrieval-based method to retrieve the GO term most relevant to each evidence sentence using a ranking function that combined cosine similarity and the frequency of GO terms in documents, and a filtering method based on high-level GO classes. The best performance of our submitted runs was 7.8% F1 and 22.2% hierarchy F1. We found that the incorporation of frequency information and hierarchy filtering substantially improved the performance. In the post-submission evaluation, we obtained a 10.6% F1 using a simpler setting. Overall, the experimental analysis showed our approaches were robust in both the two tasks.
PMCID: PMC4243380  PMID: 25425037
14.  Association between miR-125a rs12976445 and survival in breast cancer patients 
MicroRNAs (miRNAs) act as an oncogene or a tumor suppressor by negatively regulating target genes. Genetic variants in miRNA genes confer susceptibility to cancer and risk of death in cancer patients. The aim of this study was to investigate whether miRNA polymorphisms were associated with survival in breast cancer patients. Five miRNA polymorphisms (miR-26a1 rs7372209, miR-125a rs12976445, miR-218 rs11134527, miR-423 rs6505162, and miR-608 rs4919510) were genotyped in 196 breast cancer patients. We found that miR-125a rs12976445 was significantly associated with survival in codominant, recessive, and dominant models. However, only association under the codominant model remained significant after adjustment for lymph node metastasis, TNM stage, estrogen receptor, and progesterone receptor. Furthermore, this effect remained in stratification analysis. In conclusion, our results provide evidence that miR-125a rs12976445 may serve as a prognostic biomarker for breast cancer. Further large-scale studies are required to confirm these findings.
PMCID: PMC4297354  PMID: 25628797
MicroRNA; miR-125a; polymorphism; breast cancer; prognosis
15.  Transcatheter arterial chemoembolization combined with radiofrequency ablation delays tumor progression and prolongs overall survival in patients with intermediate (BCLC B) hepatocellular carcinoma 
BMC Cancer  2014;14(1):849.
This study was designed to evaluate the effectiveness of radiofrequency ablation in patients with intermediate (BCLC B) stage hepatocellular carcinoma who underwent transcatheter arterial chemoembolization.
Included in this study were 211 patients with intermediate stage HCC who underwent initial transcatheter arterial chemoembolization and were potentially amendable for radiofrequency ablation (single tumor with diameter 5-8 cm, median 6.0 cm; 2–5 multiple nodules with diameter less than 5 cm) between January 2005 and December 2011. According to the inclusion and exclusion criteria, 55 patients were treated with following radiofrequency ablation, and the remaining 156 patients were treated with transcatheter arterial chemoembolization alone. The treatment effectiveness, local tumor control and survival outcome between the two groups were compared.
The complete tumor necrosis rate after treatment was 76.9% in combination group vs. 46.5% in transcatheter arterial chemoembolization alone group (P = 0.02). The major complication rate was 1.8% in combination group vs. 2.6% in transcatheter arterial chemoembolization alone group. Follow-up observation showed that the total tumor control rate was 74.5% in combination group versus 54.5% in transcatheter arterial chemoembolization alone group (P < 0.001). The 1-, 3- and 5-year survival rates in combination group were significantly higher than those in TACE alone group (P = 0.01).
Radiofrequency ablation following initial transcatheter arterial chemoembolization delays tumor progression and prolongs overall survival of patients with intermediate stage HCC tumors.
PMCID: PMC4256894  PMID: 25409554
Hepatocellular carcinoma; Transcatheter arterial chemoembolization; Radiofrequency ablation; Combination therapy; Survival
16.  Cytoplasmic and/or Nuclear Expression of β-Catenin Correlate with Poor Prognosis and Unfavorable Clinicopathological Factors in Hepatocellular Carcinoma: A Meta-Analysis 
PLoS ONE  2014;9(11):e111885.
The β-catenin is an important effector in WNT/β-catenin signaling pathway, which exerts a crucial role in the development and progression of hepatocellular carcinoma (HCC). Some researchers have suggested that the overexpression of β-catenin in cytoplasm and/or nucleus was closely correlated to metastasis, poor differentiation and malignant phenotype of HCC while some other researchers hold opposite point. So far, no consensus was obtained on the prognostic and clinicopathological significance of cytoplasmic/nuclear β-catenin overexpression for HCCs.
Systematic strategies were applied to search eligible studies in all available databases. Subgroup analyses, sensitivity analyses and multivariate analysis were performed. In this meta-analysis, we utilized either fixed- or random-effects model to calculate the pooled odds ratios (OR) and its 95% confidence intervals (CI).
A total of 22 studies containing 2334 cases were enrolled in this meta-analysis. Pooled data suggested that accumulation of β-catenin in cytoplasm and/or nucleus significantly correlated with poor 1-, 3- and 5-year OS and RFS. Moreover, nuclear accumulation combined with cytoplasmic accumulation of β-catenin tended to be associated with dismal metastasis and vascular invasion while cytoplasmic or nuclear expression alone showed no significant effect. Besides, no significant association was observed between cytoplasmic and/or nuclear β-catenin expression and poor differentiation grade, advanced TNM stage, liver cirrhosis, tumor size, tumor encapsulation, AFP and etiologies. Additional subgroup analysis by origin suggested that the prognostic value and clinicopathological significance of cytoplasmic and/or nuclear β-catenin expression was more validated in Asian population. Multivariate analyses of factors showed that cytoplasmic and/or nuclear β-catenin expression, as well as TNM stage, metastasis and tumor size, was an independent risk factors for OS and RFS.
Cytoplasmic and/or nuclear accumulation of β-catenin, as an independent prognostic factor, significantly associated with poor prognosis and deeper invasion of HCC, and could serve as a valuable prognostic predictor for HCC.
PMCID: PMC4234306  PMID: 25401330
17.  Computational Approaches for Predicting Biomedical Research Collaborations 
PLoS ONE  2014;9(11):e111795.
Biomedical research is increasingly collaborative, and successful collaborations often produce high impact work. Computational approaches can be developed for automatically predicting biomedical research collaborations. Previous works of collaboration prediction mainly explored the topological structures of research collaboration networks, leaving out rich semantic information from the publications themselves. In this paper, we propose supervised machine learning approaches to predict research collaborations in the biomedical field. We explored both the semantic features extracted from author research interest profile and the author network topological features. We found that the most informative semantic features for author collaborations are related to research interest, including similarity of out-citing citations, similarity of abstracts. Of the four supervised machine learning models (naïve Bayes, naïve Bayes multinomial, SVMs, and logistic regression), the best performing model is logistic regression with an ROC ranging from 0.766 to 0.980 on different datasets. To our knowledge we are the first to study in depth how research interest and productivities can be used for collaboration prediction. Our approach is computationally efficient, scalable and yet simple to implement. The datasets of this study are available at
PMCID: PMC4222920  PMID: 25375164
18.  Comparative Transcriptome Analysis of Two Oysters, Crassostrea gigas and Crassostrea hongkongensis Provides Insights into Adaptation to Hypo-Osmotic Conditions 
PLoS ONE  2014;9(11):e111915.
Environmental salinity creates a key barrier to limit the distribution of most aquatic organisms. Adaptation to osmotic fluctuation is believed to be a factor facilitating species diversification. Adaptive evolution often involves beneficial mutations at more than one locus. Bivalves hold great interest, with numerous species living in waters, as osmoconformers, who maintain the osmotic pressure balance mostly by free amino acids. In this study, 107,076,589 reads from two groups of Crassostrea hongkongensis were produced and the assembled into 130,629 contigs. Transcripts putatively involved in stress-response, innate immunity and cell processes were identified according to Gene ontology and KEGG pathway analyses. Comparing with the transcriptome of C. gigas to characterize the diversity of transcripts between species with osmotic divergence, we identified 182,806 high-quality single nucleotide polymorphisms (SNPs) for C. hongkongensis, and 196,779 SNPs for C. gigas. Comparison of 11,602 pairs of putative orthologs allowed for identification of 14 protein-coding genes that experienced strong positive selection (Ka/Ks>1). In addition, 45 genes that may show signs of moderate positive selection (1≥Ka/Ks>0.5) were also identified. Based on Ks ratios and divergence time between the two species published previously, we estimated a neutral transcriptome-wide substitution mutation rate of 1.39×10−9 per site per year. Several genes were differentially expressed across the control and treated groups of each species. This is the first time to sequence the transcriptome of C. hongkongensis and provide the most comprehensive transcriptomic resource available for it. The increasing amount of transcriptome data on Crassostrea provides an excellent resource for phylogenetic analysis. A large number of SNPs identified in this work are expected to provide valuable resources for future marker and genotyping assay development. The analysis of natural selection provides an innovative view on the adaptation within species and sets the basis for future genetic and evolutionary studies.
PMCID: PMC4219811  PMID: 25369077
19.  CD40-independent help by memory CD4 T cells induces pathogenic alloantibody but does not lead to long-lasting humoral immunity 
CD40/CD154 interactions are essential for productive antibody responses to T-dependent antigens. Memory CD4 T cells express accelerated helper functions and are less dependent on costimulation when compared to naïve T cells. Here we report that donor-reactive memory CD4 T cells can deliver help to CD40-deficient B cells and induce high titers of IgG alloantibodies that contribute to heart allograft rejection in CD40−/− heart recipients. While cognate interactions between memory helper T cells and B cells are crucial for CD40-independent help, this process is not accompanied by germinal center formation and occurs despite ICOS blockade. Consistent with the extrafollicular nature of T/B cell interactions, CD40-independent help fails to maintain stable levels of serum alloantibody and induce differentiation of long-lived plasma cells and memory B cells. In summary, our data suggest that while CD40-independent help by memory CD4 T cells is sufficient to induce high levels of pathogenic alloantibody, it does not sustain long-lasting anti-donor humoral immunity and B cell memory responses. This information may guide the future use of CD40/CD154 targeting therapies in transplant recipients containing donor-reactive memory T cells.
PMCID: PMC4019209  PMID: 24102790
memory T cells; alloantibody; CD40 costimulation
20.  Differentiating Benign from Malignant Bone Tumors Using Fluid-Fluid Level Features on Magnetic Resonance Imaging 
Korean Journal of Radiology  2014;15(6):757-763.
To analyze different fluid-fluid level features between benign and malignant bone tumors on magnetic resonance imaging (MRI).
Materials and Methods
This study was approved by the hospital ethics committee. We retrospectively analyzed 47 patients diagnosed with benign (n = 29) or malignant (n = 18) bone tumors demonstrated by biopsy/surgical resection and who showed the intratumoral fluid-fluid level on pre-surgical MRI. The maximum length of the largest fluid-fluid level and the ratio of the maximum length of the largest fluid-fluid level to the maximum length of a bone tumor in the sagittal plane were investigated for use in distinguishing benign from malignant tumors using the Mann-Whitney U-test and a receiver operating characteristic (ROC) analysis. Fluid-fluid level was categorized by quantity (multiple vs. single fluid-fluid level) and by T1-weighted image signal pattern (high/low, low/high, and undifferentiated), and the findings were compared between the benign and malignant groups using the χ2 test.
The ratio of the maximum length of the largest fluid-fluid level to the maximum length of bone tumors in the sagittal plane that allowed statistically significant differentiation between benign and malignant bone tumors had an area under the ROC curve of 0.758 (95% confidence interval, 0.616-0.899). A cutoff value of 41.5% (higher value suggests a benign tumor) had sensitivity of 73% and specificity of 83%.
The ratio of the maximum length of the largest fluid-fluid level to the maximum length of a bone tumor in the sagittal plane may be useful to differentiate benign from malignant bone tumors.
PMCID: PMC4248631  PMID: 25469087
Fluid-fluid level; Magnetic resonance imaging; Bone neoplasm
21.  Catalpol Suppresses Proliferation and Facilitates Apoptosis of OVCAR-3 Ovarian Cancer Cells through Upregulating MicroRNA-200 and Downregulating MMP-2 Expression 
Catalpol is expected to possess diverse pharmacological actions including anti-cancer, anti-inflammatory and hypoglycemic properties. Matrix metalloproteinase-2 (MMP-2) is closely related to the pathogenesis of ovarian cancer. In addition, microRNA-200 (miR-200) can modulate phenotype, proliferation, infiltration and transfer of various tumors. Here, OVCAR-3 cells were employed to investigate whether the effect of catalpol (25, 50 and 100 μg/mL) promoted apoptosis of ovarian cancer cells and to explore the potential mechanisms. Our results demonstrate that catalpol could remarkably reduce the proliferation and accelerate the apoptosis of OVCAR-3 cells. Interestingly, our findings show that catalpol treatment significantly decreased the MMP-2 protein level and increased the miR-200 expression level in OVCAR-3 cells. Further, microRNA-200 was shown to regulate the protein expression of MMP-2 in OVCAR-3 cells. It is concluded that catalpol suppressed cellular proliferation and accelerated apoptosis in OVCAR-3 ovarian cancer cells via promoting microRNA-200 expression levels and restraining MMP-2 signaling.
PMCID: PMC4264118  PMID: 25347277
catalpol; ovarian cancer; OVCAR-3 cell; MicroRNA-200; matrix metalloproteinase-2
22.  Vascular relaxation induced by Eucommiae Ulmoides Oliv. and its compounds Oroxylin A and wogonin: implications on their cytoprotection action 
The vascular relaxation action of Eucommiae Ulmoides Oliv. also known as Duzhong has been seen on arteries of the heart such as the aorta and the coronary artery which are elastic in nature. Duzhong is historically an active ingredient commonly used in hypertensive herbal prescriptions in China. This work investigated the vasodilating effect of Duzhong and its compounds (wogonin 10 μM and oroxylin-A) in the isolated intact rat heart, perfused retrograde according the method of Langendorff and the cytoprotective effect in EA.hy926 cell lines Coronary perfusion pressure was monitored with a pressure transducer connected to a side-arm of the aortic perfusion cannula. Duzhong induced vasorelaxation in a dose dependent manner, on precontracting the vessels with endothelin-1, Duzhong 10 mg/ml, wogonin 10 μM and oroxylin-A 10 μM could significantly lower the perfusion pressure in reference to positive control SNP, Duzhong induced vasodilation was not inhibited by L-NAME (nitric oxide inhibitor), but was significantly inhibited by Tetraethyl ammonium (TEA, a K+ channel blocker and almost abolished by potassium chloride. The underlying mechanism was carried out in EA.hy926 cell lines. When these cells were treated with H2O2, there was higher expression of NOX-4, TNF-α and COX-2 mRNA. However, wogonin treatment attenuated the mRNA of NOX-4, TNF-α and COX-2. Wogonin also upregulated the mRNA expression of CAT, SOD-1 and GSR in oxidative stress induced by H2O2 EA.hy926 cells. Duzhong and compounds can exert an in vitro relaxation effect of the coronary artery and improve the heart function in Langendorff apparatus. This action appears to be endothelium dependent but not NO mediated. Cell culture findings indicated that wogonin can exert vascular and cellular protection by scavenging Reactive Oxygen Species.
PMCID: PMC4238523  PMID: 25419347
Eucommiae Ulmoides Oliv.; endothelium; vasorelaxation; hypertension
23.  Analysis of start-up, retention, and adherence in ALS clinical trials 
Neurology  2013;81(15):1350-1355.
To investigate predictors of trial start-up times, high attrition, and poor protocol adherence in amyotrophic lateral sclerosis (ALS) trials.
Retrospective analysis of start-up times, retention, and protocol adherence was performed on 5 clinical studies conducted by the Northeast ALS Consortium and 50 ALS clinical trials identified by PubMed search. Predictors of start-up times were estimated by accelerated failure time models with random effects. Predictors of retention and protocol deviations were estimated by mixed-model logistic regression.
Median times for contract execution and institutional review board (IRB) approval were 105 days and 125 days, respectively. Contract execution was faster at sites with more ongoing trials (p = 0.005), and more full-time (p = 0.006) and experienced (p < 0.001) coordinators. IRB approval was faster at sites with more ongoing trials (p = 0.010) and larger ALS clinics (p = 0.038). Site activation after IRB approval was faster at sites with more full-time (p = 0.038) and experienced (p < 0.001) coordinators. Twenty-two percent of surviving participants withdrew before completing the trial. Better participant functional score at baseline was an independent predictor of trial completion (odds ratio 1.29, p = 0.002) and fewer protocol deviations (odds ratio 0.86, p = 0.030).
Delays in IRB review contribute the most to prolonged trial start-up times, and these timelines are faster in sites with more experienced staff. Strategies to improve protocol adherence and participants' retention may include enrolling people at early disease stages.
PMCID: PMC3806927  PMID: 24005339
24.  Multi-Surgeon, Multi-Site Validation of a Trajectory Planning Algorithm for Deep Brain Stimulation Procedures 
Deep brain stimulation, which is used to treat various neurological disorders, involves implanting a permanent electrode into precise targets deep in the brain. Reaching these targets safely is difficult because surgeons have to plan trajectories that avoid critical structures and reach targets within specific angles. A number of systems have been proposed to assist surgeons in this task. These typically involve formulating constraints as cost terms, weighting them by surgical importance, and searching for optimal trajectories, in which constraints and their weights reflect local practice. Assessing the performance of such systems is challenging because of the lack of ground truth and clear consensus on an optimal approach among surgeons. Due to difficulties in coordinating inter-institution evaluation studies, these have been performed so far at the sites at which the systems are developed. Whether or not a scheme developed at one site can also be used at another is thus unknown. In this article, we conduct a study that involves four surgeons at three institutions to determine whether or not constraints and their associated weights can be used across institutions. Through a series of experiments, we show that a single set of weights performs well for all surgeons in our group. Out of 60 trajectories, our trajectories were accepted by a majority of neurosurgeons in 95% of the cases and the average acceptance rate was 90%. This study suggests, albeit on a limited number of surgeons, that the same system can be used to provide assistance across multiple sites and surgeons.
PMCID: PMC4142093  PMID: 24833411
Deep brain stimulation; trajectory planning; computer-assisted surgery
25.  Reference Intervals of Total Bilirubin, ALT, AST, and Creatinine in Healthy Elderly Chinese 
The aim of this study was to establish the reference intervals (RIs) of total bilirubin (TBIL), alanine aminotransferase (ALT), aspartate transaminase (AST), and creatinine (CREA) for apparently healthy elderly (Han ethnicity) in Shuyang, China.
A total of 54 912 blood specimens from elderly residents age 65–104 years were collected by standard procedures in Shuyang county of Jiangsu province. TBIL, ALT, AST, and CREA for each participant were determined by automatic biochemical analyzer. Distribution and differences of TBIL, ALT, AST, and CREA were analyzed and compared between the elderly of the same age of different sexes and different ages of the same sex. RIs of TBIL, ALT, AST, and CREA were compared with the current RIs. The RIs and 95% confidence intervals were calculated using nonparametric method (2.5th–97.5th percentiles) according to the guideline of the Clinical and Laboratory Standards Institute.
RIs established for the healthy elderly include: TBIL 7.8~30.6 μmol/L for males and 7.3~26.1 μmol/L for females; ALT 8.7~47.3 U/L for males and 8.4~45.2 U/L for females; AST 15.7~46.9 U/L for males and 15.1~46.2 U/L for females; and CREA 45.1~100.9 μmol/L for males and 38.7~85.0 μmol/L for females. Reference intervals of TBIL, ALT, AST, and CREA for male elderly were higher than those of females, and values of CREA increased with increasing age.
We have established a panel of locally relevant RIs. It is necessary to establish scientific and reasonable RIs of TBIL, ALT, AST, and CREA for the healthy elderly in our region, which will provide a reference for clinicians and inspection officers.
PMCID: PMC4196892  PMID: 25272068
Alanine Transaminase; Creatinine; Reference Values

Results 1-25 (444)