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1.  Prediction of Multi-Type Membrane Proteins in Human by an Integrated Approach 
PLoS ONE  2014;9(3):e93553.
Membrane proteins were found to be involved in various cellular processes performing various important functions, which are mainly associated to their types. However, it is very time-consuming and expensive for traditional biophysical methods to identify membrane protein types. Although some computational tools predicting membrane protein types have been developed, most of them can only recognize one kind of type. Therefore, they are not as effective as one membrane protein can have several types at the same time. To our knowledge, few methods handling multiple types of membrane proteins were reported. In this study, we proposed an integrated approach to predict multiple types of membrane proteins by employing sequence homology and protein-protein interaction network. As a result, the prediction accuracies reached 87.65%, 81.39% and 70.79%, respectively, by the leave-one-out test on three datasets. It outperformed the nearest neighbor algorithm adopting pseudo amino acid composition. The method is anticipated to be an alternative tool for identifying membrane protein types. New metrics for evaluating performances of methods dealing with multi-label problems were also presented. The program of the method is available upon request.
doi:10.1371/journal.pone.0093553
PMCID: PMC3968155  PMID: 24676214
2.  Interaction of sleep quality and sleep duration on impaired fasting glucose: a population-based cross-sectional survey in China 
BMJ Open  2014;4(3):e004436.
Objectives
To explore the interactions of sleep quality and sleep duration and their effects on impaired fasting glucose (IFG) in Chinese adults.
Design
Cross-sectional survey.
Setting
Community-based investigation in Xuzhou, China.
Participants
15 145 Chinese men and women aged 18–75 years old who fulfilled the inclusion criteria.
Primary and secondary outcome measures
The Pittsburgh Sleep Quality Index was used to produce sleep quality categories of good, common and poor. Fasting blood glucose levels were assessed for IFG. Sleep duration was measured by average hours of sleep per night, with categories of <6, 6–8 and >8 h. The products of sleep and family history of diabetes, obesity and age were added to the logistic regression model to evaluate the addictive interaction and relative excess risk of interaction (RERI) on IFG. The attributable proportion (AP) of the interaction and the synergy index (S) were applied to evaluate the additive interaction of two factors. Bootstrap measures were used to calculate 95% CI of RERI, AP and S.
Results
The prevalence of IFG was greatest in those with poor sleep quality and short sleep duration (OR 6.37, 95% CI 4.66 to 8.67; p<0.001) compared with those who had good sleep quality and 6–8 h sleep duration, after adjusting for confounders. After adjusting for potential confounders RERI, AP and S values (and their 95% CI) were 1.69 (0.31 to 3.76), 0.42 (0.15 to 0.61) and 2.85 (2.14 to 3.92), respectively, for the interaction between poor sleep quality and short sleep duration, and 0.78 (0.12 to 1.43), 0.61 (0.26 to 0.87) and −65 (−0.94 to −0.27) for the interaction between good sleep quality and long sleep duration.
Conclusions
The results suggest that there are additive interactions between poor sleep quality and short sleep duration.
doi:10.1136/bmjopen-2013-004436
PMCID: PMC3963090  PMID: 24625639
Diabetes & Endocrinology; Epidemiology
3.  Isolation and Identification of Quercetin Degrading Bacteria from Human Fecal Microbes 
PLoS ONE  2014;9(3):e90531.
Quercetin has a wide range of biological properties. The gut microflora can often modulate its biological activity and their potential health effects. There still is a lack of information about gut bacteria involving in this process. The strains of gut microbes from human feces that can transform quercetin were isolated and identified by in vitro fermentation. The results showed that Escherichia coli, Stretococcus lutetiensis, Lactobacillus acidophilus, Weissella confusa, Enterococcus gilvus, Clostridium perfringens and Bacteroides fragilis have the various ability of degrading quercetin. Among them, C. perfringens and B. fragilis were discovered to have the strongest ability of degrading quercetin. Additionally, quercetin can't inhibit the growth of C. perfringens. In conclusion, many species of gut microbiota can degrade quercetin, but their ability are different.
doi:10.1371/journal.pone.0090531
PMCID: PMC3942438  PMID: 24594786
4.  DLC1-dependent parathyroid hormone–like hormone inhibition suppresses breast cancer bone metastasis 
The Journal of Clinical Investigation  2014;124(4):1646-1659.
Bone metastasis is a frequent complication of breast cancer that is often accelerated by TGF-β signaling; however, little is known about how the TGF-β pathway is regulated during bone metastasis. Here we report that deleted in liver cancer 1 (DLC1) is an important regulator of TGF-β responses and osteolytic metastasis of breast cancer cells. In murine models, breast cancer cells lacking DLC1 expression exhibited enhanced capabilities of bone metastasis. Knockdown of DLC1 in cancer cells promoted bone metastasis, leading to manifested osteolysis and accelerated death in mice, while DLC1 overexpression suppressed bone metastasis. Activation of Rho-ROCK signaling in the absence of DLC1 mediated SMAD3 linker region phosphorylation and TGF-β–induced expression of parathyroid hormone–like hormone (PTHLH), leading to osteoclast maturation for osteolytic colonization. Furthermore, pharmacological inhibition of Rho-ROCK effectively reduced PTHLH production and breast cancer bone metastasis in vitro and in vivo. Evaluation of clinical breast tumor samples revealed that reduced DLC1 expression was linked to elevated PTHLH expression and organ-specific metastasis to bone. Overall, our findings define a stroma-dependent paradigm of Rho signaling in cancer and implicate Rho–TGF-β crosstalk in osteolytic bone metastasis.
doi:10.1172/JCI71812
PMCID: PMC3973085  PMID: 24590291
5.  Primary tumor regression speed after radiotherapy and its prognostic significance in nasopharyngeal carcinoma: a retrospective study 
BMC Cancer  2014;14:136.
Background
To observe the primary tumor (PT) regression speed after radiotherapy (RT) in nasopharyngeal carcinoma (NPC) and evaluate its prognostic significance.
Methods
One hundred and eighty-eight consecutive newly diagnosed NPC patients were reviewed retrospectively. All patients underwent magnetic resonance imaging and fiberscope examination of the nasopharynx before RT, during RT when the accumulated dose was 46–50 Gy, at the end of RT, and 3–4 months after RT.
Results
Of 188 patients, 40.4% had complete response of PT (CRPT), 44.7% had partial response of PT (PRPT), and 14.9% had stable disease of PT (SDPT) at the end of RT. The 5-year overall survival (OS) rates for patients with CRPT, PRPT, and SDPT at the end of RT were 84.0%, 70.7%, and 44.3%, respectively (P < 0.001, hazard ratio [HR] = 2.177, 95% confidence interval [CI] = 1.480-3.202). The 5-year failure-free survival (FFS) and distant metastasis-free survival (DMFS) rates also differed significantly (87.8% vs. 74.3% vs. 52.7%, P = 0.001, HR = 2.148, 95% CI, 1.384-3.333; 91.7% vs. 84.7% vs. 66.1%, P = 0.004, HR = 2.252, 95% CI = 1.296-3.912). The 5-year local relapse–free survival (LRFS) rates were not significantly different (95.8% vs. 86.0% vs. 81.8%, P = 0.137, HR = 1.975, 95% CI, 0.976-3.995). By multivariate analyses, the PT regression speed at the end of RT was the only independent prognostic factor of OS, FFS, and DMFS (P < 0.001, P = 0.001, and P = 0.004, respectively). The 5-year FFS rates for patients with CRPT during RT and CRPT only at the end of RT were 80.2% and 97.1%, respectively (P = 0.033). For patients with persistent PT at the end of RT, the 5-year LRFS rates of patients without and with boost irradiation were 87.1% and 84.6%, respectively (P = 0.812).
Conclusions
PT regression speed at the end of RT was an independent prognostic factor of OS, FFS, and DMFS in NPC patients. Immediate strengthening treatment may be provided to patients with poor tumor regression at the end of RT.
doi:10.1186/1471-2407-14-136
PMCID: PMC3943409  PMID: 24571531
Nasopharyngeal carcinoma; Radiotherapy; Tumor regression; Survival
6.  Development of highly polymorphic simple sequence repeat markers using genome-wide microsatellite variant analysis in Foxtail millet [Setaria italica (L.) P. Beauv.] 
BMC Genomics  2014;15:78.
Background
Foxtail millet (Setaria italica (L.) Beauv.) is an important gramineous grain-food and forage crop. It is grown worldwide for human and livestock consumption. Its small genome and diploid nature have led to foxtail millet fast becoming a novel model for investigating plant architecture, drought tolerance and C4 photosynthesis of grain and bioenergy crops. Therefore, cost-effective, reliable and highly polymorphic molecular markers covering the entire genome are required for diversity, mapping and functional genomics studies in this model species.
Result
A total of 5,020 highly repetitive microsatellite motifs were isolated from the released genome of the genotype 'Yugu1’ by sequence scanning. Based on sequence comparison between S. italica and S. viridis, a set of 788 SSR primer pairs were designed. Of these primers, 733 produced reproducible amplicons and were polymorphic among 28 Setaria genotypes selected from diverse geographical locations. The number of alleles detected by these SSR markers ranged from 2 to 16, with an average polymorphism information content of 0.67. The result obtained by neighbor-joining cluster analysis of 28 Setaria genotypes, based on Nei’s genetic distance of the SSR data, showed that these SSR markers are highly polymorphic and effective.
Conclusions
A large set of highly polymorphic SSR markers were successfully and efficiently developed based on genomic sequence comparison between different genotypes of the genus Setaria. The large number of new SSR markers and their placement on the physical map represent a valuable resource for studying diversity, constructing genetic maps, functional gene mapping, QTL exploration and molecular breeding in foxtail millet and its closely related species.
doi:10.1186/1471-2164-15-78
PMCID: PMC3930901  PMID: 24472631
Microsatellite marker; SSR development; Polymorphism; Setaria italica
7.  Prediction of Aptamer-Target Interacting Pairs with Pseudo-Amino Acid Composition 
PLoS ONE  2014;9(1):e86729.
Aptamers are oligonucleic acid or peptide molecules that bind to specific target molecules. As a novel and powerful class of ligands, aptamers are thought to have excellent potential for applications in the fields of biosensing, diagnostics and therapeutics. In this study, a new method for predicting aptamer-target interacting pairs was proposed by integrating features derived from both aptamers and their targets. Features of nucleotide composition and traditional amino acid composition as well as pseudo amino acid were utilized to represent aptamers and targets, respectively. The predictor was constructed based on Random Forest and the optimal features were selected by using the maximum relevance minimum redundancy (mRMR) method and the incremental feature selection (IFS) method. As a result, 81.34% accuracy and 0.4612 MCC were obtained for the training dataset, and 77.41% accuracy and 0.3717 MCC were achieved for the testing dataset. An optimal feature set of 220 features were selected, which were considered as the ones that contributed significantly to the interacting aptamer-target pair predictions. Analysis of the optimal feature set indicated several important factors in determining aptamer-target interactions. It is anticipated that our prediction method may become a useful tool for identifying aptamer-target pairs and the features selected and analyzed in this study may provide useful insights into the mechanism of interactions between aptamers and targets.
doi:10.1371/journal.pone.0086729
PMCID: PMC3899287  PMID: 24466214
8.  NURBS: a database of experimental and predicted nuclear receptor binding sites of mouse 
Bioinformatics  2012;29(2):295-297.
Summary: Nuclear receptors (NRs) are a class of transcription factors playing important roles in various biological processes. An NR often impacts numerous genes and different NRs share overlapped target networks. To fulfil the need for a database incorporating binding sites of different NRs at various conditions for easy comparison and visualization to improve our understanding of NR binding mechanisms, we have developed NURBS, a database for experimental and predicted nuclear receptor binding sites of mouse (NURBS). NURBS currently contains binding sites across the whole-mouse genome of 8 NRs identified in 40 chromatin immunoprecipitation with massively parallel DNA sequencing experiments. All datasets are processed using a widely used procedure and same statistical criteria to ensure the binding sites derived from different datasets are comparable. NURBS also provides predicted binding sites using NR-HMM, a Hidden Markov Model (HMM) model.
Availability: The GBrowse-based user interface of NURBS is freely accessible at http://shark.abl.ku.edu/nurbs/. NR-HMM and all results can be downloaded for free at the website.
Contact: jwfang@ku.edu
doi:10.1093/bioinformatics/bts693
PMCID: PMC3546791  PMID: 23196988
9.  Cancer Prevention Health Services Research: An Emerging Field 
In October 2009, The University of Texas MD Anderson Cancer Center hosted a symposium, “Future Directions in Cancer Prevention and Control: Workforce Implications for Training, Practice, and Policy.” This article summarizes discussions and an Internet and literature review by the symposium's Health Services Infrastructure Working Group. We agree on the need for the recognition of Cancer Prevention Health Services Research (CP-HSR) as a unified research field. With advances in cancer screening and increased emphasis on preventive services under healthcare reform, there is a growing need for investigators with both cancer prevention and HSR expertise to consider the comparative effectiveness of cancer screening methods, the cost-effectiveness of early detection technologies, and the accessibility of preventive care for individuals at risk of cancer. Defining CP-HSR as a field will provide investigators with credibility and will serve to draw more researchers to the field. Increasing funding to train individuals in CP-HSR will be important to help meet the anticipated demand for investigators with this specialized multidisciplinary expertise.
doi:10.1007/s13187-012-0330-7
PMCID: PMC3880141  PMID: 22311693
Cancer prevention; Health service research; Cancer screening; Cost-effectiveness; Comparative effectiveness; Workforce
10.  The Molecular Detection and Clinical Significance of ALK Rearrangement in Selected Advanced Non-Small Cell Lung Cancer: ALK Expression Provides Insights into ALK Targeted Therapy 
PLoS ONE  2014;9(1):e84501.
Background
This study aimed to elucidate clinical significance of anaplastic lymphoma kinase (ALK) rearrangement in selected advanced non-small cell lung cancer (NSCLC), to compare the application of different ALK detection methods, and especially evaluate a possible association between ALK expression and clinical outcomes in crizotinib-treated patients.
Methods
ALK status was assessed by fluorescent in situ hybridization (FISH), immunohistochemistry (IHC) and quantitative RT-PCR (qRT-PCR) in 173 selected advanced NSCLC patients. Clinicopathologic data, genotype status and survival outcomes were analyzed. Moreover, the association of ALK expression with clinical outcomes was evaluated in ALK FISH-positive crizotinib-treated patients including two patients with concurrent epidermal growth factor receptor (EGFR) mutation.
Results
The positivity detection rate of ALK rearrangement by FISH, IHC and qRT-PCR was 35.5% (59/166), 35.7% (61/171), and 27.9% (34/122), respectively. ALK rearrangement was observed predominantly in young patients, never or light smokers, and adenocarcinomas, especially with signet ring cell features and poor differentiation. Median progression-free survival (PFS) of crizotinib-treated patients was 7.6 months. The overall survival (OS) of these patients was longer compared with that of crizotinib-naive or wild-type cohorts, but there was no significant difference in OS compared with patients with EGFR mutation. ALK expression did not associate with PFS; but, when ALK expression was analyzed as a dichotomous variable, moderate and strong ALK expression had a decreased risk of death (P = 0.026). The two patients with concomitant EGFR and ALK alterations showed difference in ALK expression, response to EGFR and ALK inhibitors, and overall survival.
Conclusions
Selective enrichment according to clinicopathologic features in NSCLC patients could highly improve the positivity detection rate of ALK rearrangement for ALK-targeted therapy. IHC could provide more clues for clinical trial design and therapeutic strategies for ALK-positive NSCLC patients including patients with double genetic aberration of ALK and EGFR.
doi:10.1371/journal.pone.0084501
PMCID: PMC3880316  PMID: 24404167
11.  A new free-hand pedicle screw placement technique with reference to the supraspinal ligament 
Journal of Biomedical Research  2013;28(1):64-70.
We sought to compare the safety and accuracy of a new free-hand pedicle screw placement technique to that of the conventional technique. One hundred fifty-three consecutive adult patients with simple fracture in the thoracic or/and lumbar spine were alternately assigned to either the new free-hand or the conventional group. In the new free-hand technique group, preoperative computerized tomography (CT) images were used to calculate the targeted medial-lateral angle of each pedicle trajectory and the pedicle screw was inserted perpendicular to the correspond-ing supraspinal ligament. In the conventional technique group, the medial-lateral and cranial-caudal angle of each pedicle trajectory was determined by intraoperatively under fluoroscopic guidance. The accuracy rate of pedicle screw placement, the time of intraoperative fluoroscopy, the operating time and the amount of blood loss during operation were respectively compared. All screws were analyzed by using intraoperative radiographs, intraoperative triggered electromyography (EMG) monitoring data, postoperative CT data and clinical outcomes. The accuracy rate of pedicle screw placement in the new free-hand technique group and the conventional technique group was 96.3% and 94.2% (P < 0.05), respectively. The intraoperative fluoroscopy time of the new technique group was less than that of the conventional technique group (5.37 seconds vs. 8.79 seconds, P < 0.05). However, there was no statistical difference in the operating time and the amount of blood loss during operation (P > 0.05). Pedicle screw placement with the free-hand technique which keeps the screw perpendicular to the supraspinal ligament is an accurate, reliable and safe technique to treat simple fracture in the thoracic or lumbar spine.
doi:10.7555/JBR.27.20130051
PMCID: PMC3904177  PMID: 24474966
spine fracture; pedicle screw placement; radiation exposure; supraspinal ligament; anatomy reference
12.  A More Desirable Balanced Polyunsaturated Fatty Acid Composition Achieved by Heterologous Expression of Δ15/Δ4 Desaturases in Mammalian Cells 
PLoS ONE  2013;8(12):e84871.
Arachidonic (ARA), eicosapentaenoic (EPA) and docosahexaenoic (DHA) acids are the most biologically active polyunsaturated fatty acids, but their biosyntheses in mammals are very limited. The biosynthesis of DHA is the most difficult, because this undergoes the Sprecher pathway–a further elongation step from docosapentaenoic acid (DPA), a Δ6-desaturase acting on a C24 fatty acid substrate followed by a peroxisomal chain shortening step. This paper reports the successful heterologous expression of two non-mammalian genes (with modification of codon usage), coding for Euglena gracilis Δ4-desaturase and Siganus canaliculatus Δ4-desaturase respectively, in mammalian cells (HEK293 cell line). Both of the Δ4-desaturases can efficiently function, directly converting DPA into DHA. Moreover, the cooperation of the E. gracilis Δ4-desaturase with C. elegans Δ15-desaturase (able to convert a number of n-6 PUFAs to their corresponding n-3 PUFAs) in transgenic HEK293 cells made a more desirable fatty acid composition – a drastically reduced n-6/n-3 PUFAs ratio and a high level of DHA as well as EPA and ARA. Our findings provide a basis for potential applications of the gene constructs for expression of Δ15/Δ4-desaturases in transgenic livestock to produce such a fatty acid profile in the related products, which certainly will bring benefit to human health.
doi:10.1371/journal.pone.0084871
PMCID: PMC3877351  PMID: 24391980
13.  Maturation of morphology, phenotype and functions of murine bone marrow-derived dendritic cells(DCs) induced by polysaccharide Kureha(PSK) 
Human Vaccines & Immunotherapeutics  2012;8(12):1808-1816.
The aim of this work was to evaluate the influence of protein-bound polysaccharide Kureha(PSK) on murine dendritic cells (DCs). These impacts of PSK on DCs from bone marrow derived DCs(BMDCs) were assessed with inverted phase contrast microscope, conventional scanning electron microscopy (SEM), transmission electron microscopy (TEM) for morphology, fluorescence activated cell sorting (FACS) analysis, cytochemistry assay for key surface molecules, FITC-dextran for phagocytosis, bio-assay and enzyme linked immunosorbent assay (ELISA) for cytokine production. We found that under the influence of PSK, immature DCs changed into mature DCs with decrease of antigens up-taking, simultaneously high expression of key surface molecules of the MHC classII,CD40, CD80, CD86 and CD83 as well as more production of IL-12p70 and tumor necrosis factor α (TNF-α). These data indicate that PSK could markedly promote maturation of DCs and this adjuvant-like activity may have potential therapeutic value in vaccine preparation.
doi:10.4161/hv.21993
PMCID: PMC3656070  PMID: 23032163
polysaccharide kureha; bone marrow derived DCs; maturation; modulation
14.  Disruption of Growth Factor Receptor–Binding Protein 10 in the Pancreas Enhances β-Cell Proliferation and Protects Mice From Streptozotocin-Induced β-Cell Apoptosis 
Diabetes  2012;61(12):3189-3198.
Defects in insulin secretion and reduction in β-cell mass are associated with type 2 diabetes in humans, and understanding the basis for these dysfunctions may reveal strategies for diabetes therapy. In this study, we show that pancreas-specific knockout of growth factor receptor–binding protein 10 (Grb10), which is highly expressed in pancreas and islets, leads to elevated insulin/IGF-1 signaling in islets, enhanced β-cell mass and insulin content, and increased insulin secretion in mice. Pancreas-specific disruption of Grb10 expression also improved glucose tolerance in mice fed with a high-fat diet and protected mice from streptozotocin-induced β-cell apoptosis and body weight loss. Our study has identified Grb10 as an important regulator of β-cell proliferation and demonstrated that reducing the expression level of Grb10 could provide a novel means to increase β-cell mass and reduce β-cell apoptosis. This is critical for effective therapeutic treatment of both type 1 and 2 diabetes.
doi:10.2337/db12-0249
PMCID: PMC3501856  PMID: 22923474
15.  The Environment, Not Space, Dominantly Structures the Landscape Patterns of the Richness and Composition of the Tropical Understory Vegetation 
PLoS ONE  2013;8(11):e81308.
The mechanisms driving the spatial patterns of species richness and composition are essential to the understanding of biodiversity. Numerous studies separately identify the contributions of the environment (niche process) and space (neutral process) to the species richness or composition at different scales, but few studies have investigated the contributions of both types of processes in the two types of data at the landscape scale. In this study, we partitioned the spatial variations in all, exotic and native understory plant species richness and composition constrained by environmental variables and space in 134 plots that were spread across 10 counties in Hainan Island in southern China. The 134 plots included 70 rubber (Hevea brasiliensis) plantation plots, 50 eucalyptus (Eucalyptus urophylla) plantation plots, and 14 secondary forest plots. RDA based variation partitioning was run to assess the contribution of environment and space to species richness and composition. The results showed that the environmental variables alone explained a large proportion of the variations in both the species richness and composition of all, native, and exotic species. The RDA results indicated that overstory composition (forest type here) plays a leading role in determining species richness and composition patterns. The alpha and beta diversities of the secondary forest plots were markedly higher than that of the two plantations. In conclusion, niche differentiation processes are the principal mechanisms that shape the alpha and beta diversities of understory plant species in Hainan Island.
doi:10.1371/journal.pone.0081308
PMCID: PMC3838366  PMID: 24278417
16.  P3DB 3.0: From plant phosphorylation sites to protein networks 
Nucleic Acids Research  2013;42(D1):D1206-D1213.
In the past few years, the Plant Protein Phosphorylation Database (P3DB, http://p3db.org) has become one of the most significant in vivo data resources for studying plant phosphoproteomics. We have substantially updated P3DB with respect to format, new datasets and analytic tools. In the P3DB 3.0, there are altogether 47 923 phosphosites in 16 477 phosphoproteins curated across nine plant organisms from 32 studies, which have met our multiple quality standards for acquisition of in vivo phosphorylation site data. Centralized by these phosphorylation data, multiple related data and annotations are provided, including protein–protein interaction (PPI), gene ontology, protein tertiary structures, orthologous sequences, kinase/phosphatase classification and Kinase Client Assay (KiC Assay) data—all of which provides context for the phosphorylation event. In addition, P3DB 3.0 incorporates multiple network viewers for the above features, such as PPI network, kinase-substrate network, phosphatase-substrate network, and domain co-occurrence network to help study phosphorylation from a systems point of view. Furthermore, the new P3DB reflects a community-based design through which users can share datasets and automate data depository processes for publication purposes. Each of these new features supports the goal of making P3DB a comprehensive, systematic and interactive platform for phosphoproteomics research.
doi:10.1093/nar/gkt1135
PMCID: PMC3965113  PMID: 24243849
17.  Glycated Hemoglobin Independently Predicts Stroke Recurrence within One Year after Acute First-Ever Non-Cardioembolic Strokes Onset in A Chinese Cohort Study 
PLoS ONE  2013;8(11):e80690.
Objective
Hyperglycemia is related to stroke. Glycated hemoglobin (HbA1c) can reflect pre-stroke glycaemia status. However, the information on the direct association between HbA1c and recurrence after non-cardioembolic acute ischemic strokes is rare and there is no consistent conclusion.
Methods
The ACROSS-China database comprised of 2186 consecutive first-ever acute ischemic stroke patients with baseline HbA1c values. After excluding patients who died from non-stroke recurrence and patients lost to follow up, 1817 and 1540 were eligible for 3-month and 1-year analyses, respectively. Multivariate Cox regression was performed to evaluate the associations between HbA1c and 3-month and 1-year stroke recurrence.
Results
The HbA1c values at admission were divided into 4 levels by quartiles: Q1 (<5.5%); Q2 (5.5 to <6.1%); Q3 (6.1% to <7.2%); and Q4 (≥7.2%). The cumulative recurrence rates were 8.3% and 11.0% for 3 months and 1 year, respectively. In multivariate analyses, when compared with Q1, the adjusted hazard ratios (AHRs) were 2.83 (95% confidence interval (CI) 1.28-6.26) in Q3 and 3.71(95% CI 1.68-8.21) in Q4 for 3-month stroke recurrence; 3.30 (95% CI 1.31-8.34) in Q3 and 3.35 (95% CI 1.36-8.21) in Q4 for 1-year stroke recurrence. Adding fasting plasma glucose in the multivariate analyses did not modify the association: AHRs were 2.75 (95% CI 1.24-6.11) in Q3 and 3.67 (95% CI 1.59-8.53) in Q4 for 3-month analysis; AHRs were 3.08 (95% CI 1.10-8.64) in Q3 and 3.31(95% CI 1.35-8.14) in Q4 for 1-year analysis.
Conclusions
A higher “normal” HbA1c level reflecting pre-stroke glycaemia status independently predicts stroke recurrence within one year after non-cardioembolic acute ischemic stroke onset. HbA1c is recommended as a routine test in acute ischemic stroke patients.
doi:10.1371/journal.pone.0080690
PMCID: PMC3827473  PMID: 24236195
18.  Cardiac arrest and cardiopulmonary resuscitation dysregulates the hypothalamic–pituitary–adrenal axis 
Cardiac arrest and cardiopulmonary resuscitation (CA/CPR) increase the risk for affective disorders in human survivors. Postischemic anxiety- and depressive-like behaviors have been documented in animal models of CA/CPR; however, the stability of post-CA/CPR anxiety-like behavior over time and the underlying physiologic mechanisms remain unknown. The hypothalamic–pituitary–adrenal (HPA) axis and the corticotropin releasing factor (CRF) system may mediate the pathophysiology of anxiety and depression; therefore, this study measured CA/CPR-induced changes in CRF receptor binding and HPA axis negative feedback. Mice were exposed to CA/CPR or SHAM surgery and assessed 7 or 21 days later. Consistent with earlier demonstrations of anxiety-like behavior 7 days after CA/CPR, increased anxiety-like behavior in the open field was also present 21 days after CA/CPR. On postoperative day 7, CA/CPR was associated with an increase in basal serum corticosterone concentration relative to SHAM, but this difference resolved by postoperative day 21. The Dexamethasone Suppression Test showed that the CA/CPR group had enhanced negative feedback compared with SHAM controls at postoperative day 21. Furthermore, there was a gradual increase in CRF1 receptor binding in the paraventricular nucleus of the hypothalamus and bed nucleus of the stria terminalis, as well as a transient decrease of both CRF1, and CRF2A receptors in the dorsal hippocampus. Therefore, sustained changes in activity of the HPA axis and the CRF system after CA/CPR may contribute to the postischemic increase in affective disorders.
doi:10.1038/jcbfm.2009.85
PMCID: PMC3815600  PMID: 19553908
cardiac arrest; corticosterone; CRF; dexamethasone; HPA; ischemia
19.  Fat-Specific DsbA-L Overexpression Promotes Adiponectin Multimerization and Protects Mice From Diet-Induced Obesity and Insulin Resistance 
Diabetes  2012;61(11):2776-2786.
The antidiabetic and antiatherosclerotic effects of adiponectin make it a desirable drug target for the treatment of metabolic and cardiovascular diseases. However, the adiponectin-based drug development approach turns out to be difficult due to extremely high serum levels of this adipokine. On the other hand, a significant correlation between adiponectin multimerization and its insulin-sensitizing effects has been demonstrated, suggesting a promising alternative therapeutic strategy. Here we show that transgenic mice overexpressing disulfide bond A oxidoreductase-like protein in fat (fDsbA-L) exhibited increased levels of total and the high-molecular-weight form of adiponectin compared with wild-type (WT) littermates. The fDsbA-L mice also displayed resistance to diet-induced obesity, insulin resistance, and hepatic steatosis compared with WT control mice. The protective effects of DsbA-L overexpression on diet-induced insulin resistance, but not increased body weight and fat cell size, were significantly decreased in adiponectin-deficient fDsbA-L mice (fDsbA-L/Ad−/−). In addition, the fDsbA-L/Ad−/− mice displayed greater activity and energy expenditure compared with adiponectin knockout mice under a high-fat diet. Taken together, our results demonstrate that DsbA-L protects mice from diet-induced obesity and insulin resistance through adiponectin-dependent and independent mechanisms. In addition, upregulation of DsbA-L could be an effective therapeutic approach for the treatment of obesity and its associated metabolic disorders.
doi:10.2337/db12-0169
PMCID: PMC3478538  PMID: 22807031
20.  Multiphoton tomographic imaging: a potential optical biopsy tool for detecting gastrointestinal inflammation and neoplasia 
Endoscopy is widely used to detect and remove premalignant lesions with the goal of preventing gastrointestinal (GI) cancers. Because current endoscopes do not provide cellular resolution, all suspicious lesions are biopsied and subjected to histological evaluation. Technologies that facilitate directed biopsies should decrease both procedure-related morbidity and cost. Here we explore the use of multiphoton microscopy (MPM), an optical biopsy tool that relies on intrinsic tissue emissions, to evaluate pathology in both experimental and human GI specimens, using hematoxylin and eosin (H&E)-stained sections from these tissues for comparison. After evaluating the entire normal mouse GI tract, MPM was used to investigate disease progression in mouse models of colitis and colorectal carcinogenesis. MPM provided sufficient histological detail to identify all relevant substructures in ex vivo normal GI tissue, visualize both acute and resolving stages of colitis, and show the progression of colorectal carcinogenesis. Next, ex vivo specimens from human subjects with celiac sprue, inflammatory bowel disease, and colorectal neoplasia were imaged by MPM. Finally, colonic mucosa in live anesthetized rats was imaged in vivo using a flexible endoscope prototype. In both animal models and human specimens, MPM images demonstrated a striking similarity to the results of H&E staining, as demonstrated by the 100% concordance achieved by the study pathologists’ diagnoses. In summary, MPM is a promising technique that accurately visualizes histology in fresh, unstained tissues. Our findings support the continued development of MPM as a technology to enhance the early detection of GI pathologies including premalignant lesions.
doi:10.1158/1940-6207.CAPR-12-0132
PMCID: PMC3491145  PMID: 22961775
21.  Effects of Ambient Particulate Matter on Human Breast Cancer: Is Xenogenesis Responsible? 
PLoS ONE  2013;8(10):e76609.
Background
Recently, evidence from several studies has revealed that air pollution is associated with the increased morbidity and mortality of breast cancer patients. However, to date, the underlying mechanism remains largely unclear. Considering the high prevalence of air pollution and breast cancer in China, it is necessary to understand how air pollution may affect breast cancer.
Methods
We analyzed 1,832 female patients who had resided in the same cities for at least 10 years prior to their diagnosis. Variables including demographic data as well as clinical and tumor characteristics, including the patient’s age at menarche, family history of breast cancer, tumor histopathological type, tumor size, lymph node metastasis, distant metastasis, histological grade, estrogen receptor (ER) status, progesterone receptor (PR) status and human epidermal growth factor receptor 2 (HER-2) status at the time of diagnosis were analyzed.
Results
Compared to patients residing in low-pollution areas, patients living in high-pollution areas demonstrated a younger age at menarche (p<0.001), a greater family history of breast cancer (p = 0.034) and more invasive cancers (p = 0.028) with higher tumor grades (p = 0.028) and estrogen receptor (ER)-positive status (p = 0.022). Differences in tumor grade were only found in ER-positive cases.
Conclusions
Our findings and clinical data indicate that long-term air pollution exposure may contribute to the development of breast cancer by playing the role of a xenoestrogen, and also provides new insight into the association between air pollution and the morbidity and mortality of breast cancer patients. Furthermore, it is urgently necessary to study the association between air pollution and breast cancer to improve the living quality and health of females, and applicable public health strategies may need to be established or modified as soon as possible.
doi:10.1371/journal.pone.0076609
PMCID: PMC3797842  PMID: 24146897
22.  Unilateral lymphadenopathy due to the use of granulocyte colony stimulating factor 
BMJ Case Reports  2011;2011:bcr0520114210.
A 36-year-old woman was admitted to our hospital after modified radical mastectomy operation. Adjuvant chemotherapy was administered using TAC regimen. Severe neutropenia occurred after chemotherapy. Granulocyte colony stimulating factor (G-CSF) was given to treat neutropenia. On the second day of G-CSF use, the patient complained of swelling of her neck on the left side, which subsided spontaneously after discontinuation of G-CSF medication. However, the same symptom recurred following G-CSF use on the second cycle of chemotherapy. B-mode ultrasound showed swollen lymph nodes and biopsy revealed no evidence of metastasis. Therefore, the unilateral lymphadenopathy is considered to be the side effect of G-CSF, which is very rare.
doi:10.1136/bcr.05.2011.4210
PMCID: PMC3185385  PMID: 22679312
23.  Metastasis of lung adenocarcinoma to the fifth distal phalange of right hand 
BMJ Case Reports  2011;2011:bcr0520114276.
A 46-year-old male was diagnosed of lung adenocarcinoma with right adrenal gland metastasis in January 2009, and underwent chemotherapy (DC (docetaxel and cisplatin) regimen) and stereotactic radiotherapy. In December 2009, whole brain radiotherapy was given to the patient due to brain metastasis. In January 2010, he complained of redness, swelling and tenderness of the fifth terminal phalange of his right hand. Open surgery and biopsy confirmed bone metastasis to the finger. The patient then received local injection of OK-432 combined with radiotherapy. The symptoms were greatly relieved after treatment and the patient has survived for 28 months at the time of this report.
doi:10.1136/bcr.05.2011.4276
PMCID: PMC3185394  PMID: 22679314
24.  The Brassica rapa FLC homologue FLC2 is a key regulator of flowering time, identified through transcriptional co-expression networks 
Journal of Experimental Botany  2013;64(14):4503-4516.
The role of many genes and interactions among genes involved in flowering time have been studied extensively in Arabidopsis, and the purpose of this study was to investigate how effectively results obtained with the model species Arabidopsis can be applied to the Brassicacea with often larger and more complex genomes. Brassica rapa represents a very close relative, with its triplicated genome, with subgenomes having evolved by genome fractionation. The question of whether this genome fractionation is a random process, or whether specific genes are preferentially retained, such as flowering time (Ft) genes that play a role in the extreme morphological variation within the B. rapa species (displayed by the diverse morphotypes), is addressed. Data are presented showing that indeed Ft genes are preferentially retained, so the next intriguing question is whether these different orthologues of Arabidopsis Ft genes play similar roles compared with Arabidopsis, and what is the role of these different orthologues in B. rapa. Using a genetical–genomics approach, co-location of flowering quantitative trait loci (QTLs) and expression QTLs (eQTLs) resulted in identification of candidate genes for flowering QTLs and visualization of co-expression networks of Ft genes and flowering time. A major flowering QTL on A02 at the BrFLC2 locus co-localized with cis eQTLs for BrFLC2, BrSSR1, and BrTCP11, and trans eQTLs for the photoperiod gene BrCO and two paralogues of the floral integrator genes BrSOC1 and BrFT. It is concluded that the BrFLC2 Ft gene is a major regulator of flowering time in the studied doubled haploid population.
doi:10.1093/jxb/ert264
PMCID: PMC3808329  PMID: 24078668
Brassica rapa; candidate gene mapping; expression quantitative trait loci (eQTL); FLOWERING LOCUS C (FLC).; flowering time; gene expression networks; genome triplication.
25.  Correction: Targeting Caspase-3 as Dual Therapeutic Benefits by RNAi Facilitating Brain-Targeted Nanoparticles in a Rat Model of Parkinson’s Disease 
PLoS ONE  2013;8(9):10.1371/annotation/5f08fe1e-8868-421c-92ea-1a4aa987d11f.
doi:10.1371/annotation/5f08fe1e-8868-421c-92ea-1a4aa987d11f
PMCID: PMC3765454  PMID: 24039675

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