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1.  Evaluation of a novel choanoid fluidized bed bioreactor for future bioartificial livers 
AIM: To construct and evaluate the functionality of a choanoid-fluidized bed bioreactor (CFBB) based on microencapsulated immortalized human hepatocytes.
METHODS: Encapsulated hepatocytes were placed in the constructed CFBB and circulated through Dulbecco’s Modified Eagle’s Medium (DMEM) for 12 h, and then through exchanged plasma for 6 h, and compared with encapsulated cells cultivated under static conditions in a spinner flask. Levels of alanine aminotransferase (ALT) and albumin were used to evaluate the CFBB during media circulation, whereas levels of ALT, total bilirubin (TBil), and albumin were used to evaluate it during plasma circulation. Mass transfer and hepatocyte injury were evaluated by comparing the results from the two experimental conditions. In addition, the viability and microstructure of encapsulated cells were observed in the different environments.
RESULTS: The bioartificial liver model based on a CFBB was verified by in vitro experiments. The viability of encapsulated cells accounting for 84.6% ± 3.7% in CFBB plasma perfusion was higher than the 74.8% ± 3.1% in the static culture group (P < 0.05) after 6 h. ALT release from cells was 29 ± 3.5 U/L vs 40.6 ± 3.2 U/L at 12 h (P < 0.01) in the CFBB medium circulation and static medium culture groups, respectively. Albumin secretion from cells was 234.2 ± 27.8 μg/1 × 107 cells vs 167.8 ± 29.3 μg/1 × 107 cells at 6 h (P < 0.01), 274.4 ± 34.6 μg/1 × 107 cells vs 208.4 ± 49.3 μg/1 × 107 cells (P < 0.05) at 12 h, in the two medium circulation/culture groups, respectively. Furthermore, ALT and TBil levels were 172.3 ± 24.1 U/L vs 236.3 ± 21.5 U/L (P < 0.05), 240.1 ± 23.9 μmol/L vs 241.9 ± 31.4 μmol/L (P > 0.05) at 6 h in the CFBB plasma perfusion and static plasma culture groups, respectively. There was no significant difference in albumin concentration between the two experimental plasma groups at any time point. The microstructure of the encapsulated hepatocytes remained healthier in the CFBB group compared with the static culture group after 6 h of plasma perfusion.
CONCLUSION: The CFBB can function as a bioartificial liver based on a bioreactor. The efficacy of this novel bioreactor is promising for the study of liver failure.
doi:10.3748/wjg.v20.i22.6869
PMCID: PMC4051926  PMID: 24944477
Choanoid; Fluidized bed; Bioreactor; Immortalized human hepatocytes; Bioartificial liver
2.  Phosphorylation of the TOR ATP binding domain by AGC kinase constitutes a novel mode of TOR inhibition 
The Journal of Cell Biology  2013;203(4):595-604.
AGC kinase–mediated phosphorylation of the TOR kinase reduces its activity and results in physiologically significant changes in TOR signalling in both yeast and human cells.
TOR (target of rapamycin) signaling coordinates cell growth, metabolism, and cell division through tight control of signaling via two complexes, TORC1 and TORC2. Here, we show that fission yeast TOR kinases and mTOR are phosphorylated on an evolutionarily conserved residue of their ATP-binding domain. The Gad8 kinase (AKT homologue) phosphorylates fission yeast Tor1 at this threonine (T1972) to reduce activity. A T1972A mutation that blocked phosphorylation increased Tor1 activity and stress resistance. Nitrogen starvation of fission yeast inhibited TOR signaling to arrest cell cycle progression in G1 phase and promoted sexual differentiation. Starvation and a Gad8/T1972-dependent decrease in Tor1 (TORC2) activity was essential for efficient cell cycle arrest and differentiation. Experiments in human cell lines recapitulated these yeast observations, as mTOR was phosphorylated on T2173 in an AKT-dependent manner. In addition, a T2173A mutation increased mTOR activity. Thus, TOR kinase activity can be reduced through AGC kinase–controlled phosphorylation to generate physiologically significant changes in TOR signaling.
doi:10.1083/jcb.201305103
PMCID: PMC3840928  PMID: 24247430
3.  Incidence of road traffic disabilities trending upwards in transitional China: a retrospective analysis from 1980 to 2005 
BMJ Open  2014;4(5):e004297.
Objective
To evaluate the change in incidence rates of road traffic disabilities from 1980 to 2005 in China.
Methods
We employed the 2006 China National Sample Survey on Disability to derive weighted number of persons with disabilities resulting from road crashes and weighted age-gender-specific population at risk by disability occurrence year. The annual incidence rate of road traffic disabilities and corresponding 95% CI were estimated. We used the World Population Prospects (WPP) and the death rate of people with disabilities (PWD) to estimate potential earlier loss of lives before 2006. Both WPP-adjusted and PWD-adjusted incidence rates of road traffic disabilities were further adjusted using the life table analysis.
Results
The WPP-adjusted incidence rate for road traffic disabilities increased over time from 1.50 (95% CI 1.47 to 1.52) in 1980 to 11.19 (95% CI 11.13 to 11.25) per 100 000 persons in 2005. The PWD-adjusted incidence rate also increased from 1.71 (95% CI 1.68 to 1.73) to 11.51 (95% CI 11.45 to 11.57) per 100 000 persons.
Conclusions
Road crashes disable thousands of Chinese and remain a significant population health and development problem. The increasing burden of road traffic disabilities calls for more efforts and specific strategies to improve road safety in China.
doi:10.1136/bmjopen-2013-004297
PMCID: PMC4025444  PMID: 24833679
Public Health; Epidemiology
4.  Hyperactivated Wnt Signaling Induces Synthetic Lethal Interaction with Rb Inactivation by Elevating TORC1 Activities 
PLoS Genetics  2014;10(5):e1004357.
Inactivation of the Rb tumor suppressor can lead to increased cell proliferation or cell death depending on specific cellular context. Therefore, identification of the interacting pathways that modulate the effect of Rb loss will provide novel insights into the roles of Rb in cancer development and promote new therapeutic strategies. Here, we identify a novel synthetic lethal interaction between Rb inactivation and deregulated Wg/Wnt signaling through unbiased genetic screens. We show that a weak allele of axin, which deregulates Wg signaling and increases cell proliferation without obvious effects on cell fate specification, significantly alters metabolic gene expression, causes hypersensitivity to metabolic stress induced by fasting, and induces synergistic apoptosis with mutation of fly Rb ortholog, rbf. Furthermore, hyperactivation of Wg signaling by other components of the Wg pathway also induces synergistic apoptosis with rbf. We show that hyperactivated Wg signaling significantly increases TORC1 activity and induces excessive energy stress with rbf mutation. Inhibition of TORC1 activity significantly suppressed synergistic cell death induced by hyperactivated Wg signaling and rbf inactivation, which is correlated with decreased energy stress and decreased induction of apoptotic regulator expression. Finally the synthetic lethality between Rb and deregulated Wnt signaling is conserved in mammalian cells and that inactivation of Rb and APC induces synergistic cell death through a similar mechanism. These results suggest that elevated TORC1 activity and metabolic stress underpin the evolutionarily conserved synthetic lethal interaction between hyperactivated Wnt signaling and inactivated Rb tumor suppressor.
Author Summary
Inactivation of Rb tumor suppressor is common in cancers. Therefore, identification of genes and pathways that are synthetic lethal with Rb will provide new insights into the role of Rb in cancer development and promote the development of novel therapeutic approaches. Here we identified a novel synthetic lethal interaction between Rb inactivation and hyperactivated Wnt signaling and showed that this synthetic lethal interaction is conserved in mammalian systems. We demonstrate that hyperactivated Wnt signaling activate TORC1 activity and induce excessive energy stress with inactivated Rb tumor suppressor, which underpins the evolutionarily conserved synthetic lethal interaction. This study provides novel insights into the interactions between the Rb, Wnt, and mTOR pathways in regulating cellular energy balance, cell growth, and survival.
doi:10.1371/journal.pgen.1004357
PMCID: PMC4014429  PMID: 24809668
5.  Human Body 3D Posture Estimation Using Significant Points and Two Cameras 
The Scientific World Journal  2014;2014:670953.
This paper proposes a three-dimensional (3D) human posture estimation system that locates 3D significant body points based on 2D body contours extracted from two cameras without using any depth sensors. The 3D significant body points that are located by this system include the head, the center of the body, the tips of the feet, the tips of the hands, the elbows, and the knees. First, a linear support vector machine- (SVM-) based segmentation method is proposed to distinguish the human body from the background in red, green, and blue (RGB) color space. The SVM-based segmentation method uses not only normalized color differences but also included angle between pixels in the current frame and the background in order to reduce shadow influence. After segmentation, 2D significant points in each of the two extracted images are located. A significant point volume matching (SPVM) method is then proposed to reconstruct the 3D significant body point locations by using 2D posture estimation results. Experimental results show that the proposed SVM-based segmentation method shows better performance than other gray level- and RGB-based segmentation approaches. This paper also shows the effectiveness of the 3D posture estimation results in different postures.
doi:10.1155/2014/670953
PMCID: PMC4032775  PMID: 24883422
6.  Binding to WGR Domain by Salidroside Activates PARP1 and Protects Hematopoietic Stem Cells from Oxidative Stress 
Antioxidants & Redox Signaling  2014;20(12):1853-1865.
Abstract
Aims: A component of the base excision repair pathway, poly(ADP-ribose) polymerase-1 (PARP1) functions in multiple cellular processes, including DNA repair and programmed cell death. We previously showed that Salidroside, a phenylpropanoid glycoside isolated from medicinal plants, prevented the loss of hematopoietic stem cells (HSCs) in native mice and rescued HSCs repopulating in transplanted recipients under oxidative stress. The aim of this study was to investigate the mechanism by which PARP1 activation by Salidroside maintains HSCs under oxidative stress. Results: We found that although there were no spontaneous defects in hematopoiesis in Parp1−/− mice, oxidative stress compromised the repopulating capacity of Parp1−/− HSCs in transplanted recipient mice. A biochemical study using truncated proteins lacking the defined functional domains of PARP1 showed that the tryptophan-glycine–arginine-rich (WGR) domain of PARP1 was critical for Salidroside binding and subsequent PARP1 activation under oxidative stress. Functionally, complementation of Parp1−/− HSCs with full-length PARP1WT, but not the PARP1R591K mutant in WGR domain restored Salidroside-stimulated PARP1 activation in vitro. Mechanistically, activated PARP1 by Salidroside enhanced the repopulating capacity of the stressed HSCs by accelerating oxidative DNA damage repair. Innovations and Conclusion: Our findings reveal the action of mechanism for Salidroside in PARP1 stimulation and a novel role of PARP1 activation in maintaining HSC function under oxidative stress. Antioxid. Redox Signal. 20, 1853–1865.
doi:10.1089/ars.2013.5600
PMCID: PMC3967359  PMID: 24294904
7.  Soybean GmMYB73 promotes lipid accumulation in transgenic plants 
BMC Plant Biology  2014;14:73.
Background
Soybean is one of the most important oil crops. The regulatory genes involved in oil accumulation are largely unclear. We initiated studies to identify genes that regulate this process.
Results
One MYB-type gene GmMYB73 was found to display differential expression in soybean seeds of different developing stages by microarray analysis and was further investigated for its functions in lipid accumulation. GmMYB73 is a small protein with single MYB repeat and has similarity to CPC-like MYB proteins from Arabidopsis. GmMYB73 interacted with GL3 and EGL3, and then suppressed GL2, a negative regulator of oil accumulation. GmMYB73 overexpression enhanced lipid contents in both seeds and leaves of transgenic Arabidopsis plants. Seed length and thousand-seed weight were also promoted. GmMYB73 introduction into the Arabidopsis try cpc double mutant rescued the total lipids, seed size and thousand-seed weight. GmMYB73 also elevated lipid levels in seeds and leaves of transgenic Lotus, and in transgenic hairy roots of soybean plants. GmMYB73 promoted PLDα1 expression, whose promoter can be bound and inhibited by GL2. PLDα1 mutation reduced triacylglycerol levels mildly in seeds but significantly in leaves of Arabidopsis plants.
Conclusions
GmMYB73 may reduce GL2, and then release GL2-inhibited PLDα1 expression for lipid accumulation. Manipulation of GmMYB73 may potentially improve oil production in legume crop plants.
doi:10.1186/1471-2229-14-73
PMCID: PMC3998039  PMID: 24655684
Fatty acids; GmMYB73; Seed size; Soybean; Lipid; Thousand-seed weight
8.  Embryonic oxygen enhances learning ability in hatchling lizards 
Frontiers in Zoology  2014;11:21.
Introduction
Producing smart offspring is an important fitness trait; individuals with enhanced cognitive ability should be more adept at responding to complex environmental demands. Cognitive ability can be influenced by conditions experienced during embryonic development. Although oxygen is necessary for embryonic development, availability can be limited within the nest environment because of substrate type, hydric conditions, and temperature. We do not yet understand, however, whether oxygen availability during embryonic development influences offspring fitness, especially cognitive ability. To address this question we incubated Mongolian Racerunner lizard (Eremias argus) eggs under hypoxic (12% O2), normoxic (21% O2), and hyperoxic conditions (30% O2).
Results
Hypoxia not only slowed hatching time, but also resulted in constrained cognitive ability relative to hatchlings experiencing normoxic or hyperoxic incubation conditions. Oxygen did not influence hatching success, body size or sprint speed of hatchlings.
Conclusions
Oxygen availability during embryonic development has important influences on incubation duration and cognitive ability of hatchling lizards. This study provides the first evidence that oxygen availability during embryonic development can modify cognitive ability of oviparous reptiles.
doi:10.1186/1742-9994-11-21
PMCID: PMC3973888  PMID: 24589451
Embryonic development; Oxygen concentration; Cognitive ability; Mongolian Racerunner lizard; Eremias argus
9.  The synergistic apoptotic interaction of panaxadiol and epigallocatechin gallate in human colorectal cancer cells 
Phytotherapy research : PTR  2012;27(2):272-277.
SUMMRY
Panaxadiol (PD) is a purified sapogenin of ginseng saponins, which exhibits anticancer activity. Epigallocatechin gallate (EGCG), a major catechin in green tea, is a strong botanical antioxidant. In this study, we investigated the possible synergistic anticancer effects of PD and EGCG on human colorectal cancer cells and explored the potential role of apoptosis in the synergistic activities. Effects of selected compounds on HCT-116 and SW-480 human colorectal cancer cells were evaluated by an MTS cell proliferation analysis. Cell cycle distribution and apoptotic effects were analyzed by flow cytometry after staining with PI/RNase or annexin V/PI. Cell growth was suppressed after treatment with PD (10 and 20 μM) for 48 h. When PD (10 and 20 μM) was combined with EGCG (10, 20 and 30 μM), significantly enhanced antiproliferative effects were observed in both cell lines. Combining 20 μM of PD with 20 μM and 30 μM of EGCG significantly decreased S-phase fractions of cells. In the apoptotic assay, the combination of PD and EGCG significantly increased the percentage of apoptotic cells compared with PD alone (P < 0.01). The synergistic apoptotic effects were also supported by docking analysis, which demonstrated that PD and EGCG bound in two different sites of the annexin V protein. Data from this study suggested that apoptosis might play an important role in the EGCG enhanced antiproliferative effects of PD on human colorectal cancer cells.
doi:10.1002/ptr.4707
PMCID: PMC3416950  PMID: 22566066
Panaxadiol; Epigallocatechin gallate; Antiproliferation; Cell cycle; Apoptosis; Docking analysis; Human colorectal cancer
10.  A Randomized, Controlled, Delayed Start Trial of GM1 Ganglioside in Treated Parkinson’s Disease Patients 
Journal of the neurological sciences  2012;324(1-2):140-148.
The present single center, double-blind, delayed start study was conducted to examine possible symptomatic and disease-modifying effects of GM1 ganglioside in Parkinson’s disease (PD). Seventy-seven subjects with PD were randomly assigned to receive GM1 for 120 weeks (early-start group) or placebo for 24 weeks followed by GM1 for 96 weeks (delayed-start group). Washout evaluations occurred at 1 and 2 years after the end of treatment. Seventeen additional subjects who received standard-of-care were followed for comparative information about disease progression. Primary outcome was change from baseline Unified Parkinson’s Disease Rating Scale (UPDRS) motor scores. At week 24, the early-start group had significant improvement in UPDRS motor scores vs. a significant worsening of scores in the delayed-start group. The early-start group also showed a sustained benefit vs. the delayed-start group at week 72 and at week 120. Both groups had significant symptom worsening during washout. This study provides evidence that GM1 use for 24 weeks was superior to placebo for improving motor symptoms and that extended GM1 use (up to 120 weeks) resulted in a lower than expected rate of symptom progression. The data from this small study suggest that GM1 may have symptomatic and potentially disease modifying effects on PD.
doi:10.1016/j.jns.2012.10.024
PMCID: PMC3532888  PMID: 23199590
Parkinson’s disease; GM1; Ganglioside; Treatment; Symptomatic; Disease Modification
11.  Unsafe riding practice among electric bikers in Suzhou, China: an observational study 
BMJ Open  2014;4(1):e003902.
Background
Electric bike (E-bike)-related deaths have been increasing rapidly in China and such injuries may be partly attributable to unsafe riding practice.
Objectives
To describe potentially unsafe riding behaviours among electric bikers (E-bikers) and to investigate factors influencing these practices in China.
Methods
In September 2012, a cross-sectional observation study including a speed measurement component was conducted in Wuzhong (an urban district) and Zhangjiagang (a rural district) of Suzhou, Jiangsu Province, China. Hand-held radar speed metres were used to read travelling speeds of E-bikes and a pro forma observation checklist was used to collect data on road riding practice. Mixed-effect logistic regressions were used to calculate adjusted ORs and 95% CIs for the association between speeding, road rule violations and helmet use and their influencing factors.
Results
Among 800 E-bikes with a speed reading, 70.9% exceeded the designed speed limit of 20 km/h. Among a further 20 647 E-bikers observed, 38.3% did not comply with the road rules when entering intersections; and only 2.2% wore helmets. No regional variation was identified between urban and rural areas. Male E-bikers were associated with more speeding and road rule violations, whereas riding a pedal-equipped E-bike was associated with less road rule violations and less helmet use.
Conclusions
Unsafe riding practices such as speeding, road rule violations and lack of helmet use were commonplace among E-bikers, especially among men. The study findings indicate that measures aimed at improving E-bike safety are required in China.
doi:10.1136/bmjopen-2013-003902
PMCID: PMC3902425  PMID: 24435891
Electric Bike; Cross Sectional Study; Behavior; Risk Factor Research; Driver
12.  Mutation of the retinoblastoma tumor suppressor gene sensitizes cancers to mitotic inhibitor induced cell death 
The retinoblastoma gene Rb is a prototype tumor suppressor, which encodes a protein that is inactivated in a broad range of human cancers through different mechanisms. Rb functions to regulate cell proliferation, differentiation, as well as cell death. Therefore, even though Rb inactivation promotes cancer development, this may also open up certain vulnerabilities of cancers that can potentially be targeted with drug intervention. Based on the assumption that cancers that have mutation, deletion, or rearrangement in the Rb locus represent strong loss of Rb function while cancers with WT Rb on average retain some Rb function, we searched Genomics of Drug Sensitivity in Cancer database to identify cancer drugs that are particularly effective to cancers with Rb genomic alterations. Three mitotic inhibitors were identified from this analysis. We further tested the effects of two mitotic inhibitors, Taxol and STLC, on prostate and breast cancer cells. We demonstrate that the Rb status affects cancer cell sensitivity to these mitotic drugs and that the sensitizing effects of Rb are mediated in part by its regulation of the cell cycle checkpoint protein Mad2. Since the mitotic inhibitors identified in our analysis inhibit mitosis through distinct targets, it is possible that the Rb functional status may serve as a general biomarker for cancer sensitivity to mitotic inhibitors. Because the Rb pathway is inactivated in a large number of human cancers, identification of agents that are particularly effective or ineffective based on the Rb status in cancers can potentially be used generally to matching patients with appropriate treatments to achieve better therapeutic outcome.
PMCID: PMC3902231  PMID: 24482737
Drug sensitivity; Rb; retinoblastoma tumor suppressor; Mad2; cell death; mitotic inhibitor; Taxol; S-Trityl-L-cysteine; STLC
13.  Functional inactivation of Rb sensitizes cancer cells to TSC2 inactivation induced cell Death 
Cancer letters  2012;328(1):36-43.
We showed previously that inactivation of TSC2 induces death in cancer cells lacking the Retinoblastoma (Rb) tumor suppressor under stress conditions, suggesting that inactivation of TSC2 can potentially be used as an approach to specifically kill cancers that have lost WT Rb. As Rb is often inactivated in cancers by overexpression of cyclin D1, loss of p16ink4a cdk inhibitor, or expression of viral oncoproteins, it will be interesting to determine if such functional inactivation of Rb would similarly sensitize cancer cells to TSC2 inactivation induced cell death. In addition, many cancers lack functional Pten, resulting in increased PI3K/Akt signaling that has been shown to modulate E2F-induced cell death. Therefore it will be interesting to test whether loss of Pten will affect TSC2 inactivation induced killing of Rb mutant cancer cells. Here, we show that overexpression of Cyclin D1 or the viral oncogene E1a sensitizes cancer cells to TSC2 knockdown induced cell death and growth inhibition. On the other hand, knockdown of p16ink4a sensitizes cancer cells to TSC2 knockdown induced cell death in a manner that is likely dependant on serum induction of Cyclin D1 to inactivate the Rb function. Additionally, we demonstrate that loss of Pten does not interfere with TSC2 knockdown induced cell death in Rb mutant cancer cells. Together, these results suggest that TSC2 is potentially a useful target for a large spectrum of cancer types with an inactivated Rb pathway.
doi:10.1016/j.canlet.2012.09.016
PMCID: PMC3494767  PMID: 23022476
Rb pathway; Cyclin D1; p16ink4a; E1a; Pten; TSC2
14.  Correction: Rapamycin Inhibits IGF-1-Mediated Up-Regulation of MDM2 and Sensitizes Cancer Cells to Chemotherapy 
PLoS ONE  2013;8(12):10.1371/annotation/f1a4d192-57b9-43fb-a248-379e0f5a46ca.
doi:10.1371/annotation/f1a4d192-57b9-43fb-a248-379e0f5a46ca
PMCID: PMC3866301
15.  Efficacy and safety of recombinant Mycobacterium tuberculosis ESAT-6 protein for diagnosis of pulmonary tuberculosis: A phase II trial 
Background
This study aimed to determine the efficacy and safety of recombinant Mycobacterium tuberculosis ESAT-6 protein for diagnosis of pulmonary tuberculosis (TB).
Material/Methods
A phase II trial was performed in 158 patients with pulmonary TB (145 initially-treated and 13 re-treated) and 133 healthy subjects. Skin testing was carried out by injecting purified protein derivative (PPD) (on left forearm) or recombinant ESAT-6 protein at a dosage of 2, 5, or 10 μg/mL (on the right forearm) in each subject. Reaction activity and adverse events were monitored at 24, 48, and 72 h following the injection. Receiver operating characteristic curves were plotted to determine the areas under the curves (AUCs) and the cut-off induration diameters for the optimal diagnostic performance.
Results
The reaction activity was significantly increased upon recombinant ESAT-6 injection in pulmonary TB patients compared with healthy subjects. In pulmonary TB patients, the reaction was dose-dependent, and at 48 h, 10 μg/mL recombinant ESAT-6 produced a reaction similar to that produced by PPD. The AUCs for a 10 μg/mL dosage were 0.9823, 0.9552, and 0.9266 for 24 h, 48 h, and 72 h, respectively, and the induration diameters of 4.5–5.5 mm were the optimal trade-off values between true positive rates and false positive rates. No serious adverse events occurred in any subjects.
Conclusions
Recombinant ESAT-6 protein is efficacious and safe for diagnosing pulmonary TB. Based on the reaction, performance, safety, and practicability, we recommend that 10 μg/mL at 48 h with an induration cut-off value of 5.0 mm be used.
doi:10.12659/MSM.889425
PMCID: PMC3836599  PMID: 24217560
pulmonary tuberculosis; recombinant ESAT-6 protein; skin testing; phase II trial
16.  Computational Prediction of Human Salivary Proteins from Blood Circulation and Application to Diagnostic Biomarker Identification 
PLoS ONE  2013;8(11):e80211.
Proteins can move from blood circulation into salivary glands through active transportation, passive diffusion or ultrafiltration, some of which are then released into saliva and hence can potentially serve as biomarkers for diseases if accurately identified. We present a novel computational method for predicting salivary proteins that come from circulation. The basis for the prediction is a set of physiochemical and sequence features we found to be discerning between human proteins known to be movable from circulation to saliva and proteins deemed to be not in saliva. A classifier was trained based on these features using a support-vector machine to predict protein secretion into saliva. The classifier achieved 88.56% average recall and 90.76% average precision in 10-fold cross-validation on the training data, indicating that the selected features are informative. Considering the possibility that our negative training data may not be highly reliable (i.e., proteins predicted to be not in saliva), we have also trained a ranking method, aiming to rank the known salivary proteins from circulation as the highest among the proteins in the general background, based on the same features. This prediction capability can be used to predict potential biomarker proteins for specific human diseases when coupled with the information of differentially expressed proteins in diseased versus healthy control tissues and a prediction capability for blood-secretory proteins. Using such integrated information, we predicted 31 candidate biomarker proteins in saliva for breast cancer.
doi:10.1371/journal.pone.0080211
PMCID: PMC3855806  PMID: 24324552
17.  An educational video to increase clinical trials enrollment among breast cancer patients 
Only 3% of women with breast cancer participate in cancer clinical trials nationwide. The lack of awareness about clinical trials is a significant barrier towards clinical trials participation. A study was conducted at a large urban Comprehensive Cancer Center to test (1) the effectiveness of an 18-min educational video on improving attitudes toward clinical trials and trials enrollment among new breast cancer patients seen at the Karmanos Cancer Institute, and (2) to assess racial differences in attitudes regarding clinical trials. Participants were randomized to either the educational intervention prior to their first oncology clinic appointment or to standard care. A baseline and 2-week post-intervention survey to assess attitudes toward clinical trials participation was completed by participants. Of 218 subjects recruited, 196 (55% white vs. 45% African American (AA)) eligible patients were included in the analysis. A small increase in therapeutic clinical trial enrollment was observed in the intervention arm but was not statistically significant (10.4% vs. 6.1%; P = 0.277). The intervention also did not result in a clear improvement in patients’ attitudes toward clinical trials at posttest. However, a lower enrollment rate for the AA women was noted after adjusting for stage (OR = 0.282, P = 0.049). Significantly more negative scores were noted in 3 out of the 5 baseline attitudinal scales for AA women. The educational video did not significantly increase enrollment in breast cancer clinical trials. The findings that AA women had significantly more negative attitudes toward clinical trials than white women may partially explain the racial disparity in enrollment. An educational video remains a simple and cost-effective way to educate patients. Future studies should focus on designing a new educational video to specifically target cultural and attitudinal barriers in the AA population to more effectively change attitudes and increase trial enrollment.
doi:10.1007/s10549-009-0311-7
PMCID: PMC3799768  PMID: 19152024
Clinical trials enrollment; Breast cancer; Educational video; Attitudes regarding clinical trials; Racial disparity
18.  Modulations of functional connectivity in the healthy and schizophrenia groups during task and rest 
NeuroImage  2012;62(3):1694-1704.
Connectivity analysis using functional magnetic resonance imaging (fMRI) data is an important area, useful for the identification of biomarkers for various mental disorders, including schizophrenia. Most studies to date have focused on resting data, while the study of functional connectivity during task and the differences between task and rest are of great interest as well. In this work, we examine the graph-theoretical properties of the connectivity maps constructed using spatial components derived from independent component analysis (ICA) for healthy controls and patients with schizophrenia during an auditory oddball task (AOD) and at extended rest. We estimate functional connectivity using the higher-order statistical dependence, i.e., mutual information among the ICA spatial components, instead of the typically used temporal correlation. We also define three novel topological metrics based on the modules of brain networks obtained using a clustering approach. Our experimental results show that although the schizophrenia patients preserve the small-world property, they present a significantly lower small-worldness during both AOD task and rest when compared to the healthy controls, indicating a consistent tendency towards a more random organization of brain networks. In addition, the task-induced modulations to topological measures of several components involving motor, cerebellum and parietal regions are altered in patients relative to controls, providing further evidence for the aberrant connectivity in schizophrenia.
doi:10.1016/j.neuroimage.2012.05.048
PMCID: PMC3408853  PMID: 22634855
Functional connectivity; graph theoretical analysis; spatial dependence; resting state; auditory oddball task; schizophrenia
19.  Prokaryotic Phylogenies Inferred from Whole-Genome Sequence and Annotation Data 
BioMed Research International  2013;2013:409062.
Phylogenetic trees are used to represent the evolutionary relationship among various groups of species. In this paper, a novel method for inferring prokaryotic phylogenies using multiple genomic information is proposed. The method is called CGCPhy and based on the distance matrix of orthologous gene clusters between whole-genome pairs. CGCPhy comprises four main steps. First, orthologous genes are determined by sequence similarity, genomic function, and genomic structure information. Second, genes involving potential HGT events are eliminated, since such genes are considered to be the highly conserved genes across different species and the genes located on fragments with abnormal genome barcode. Third, we calculate the distance of the orthologous gene clusters between each genome pair in terms of the number of orthologous genes in conserved clusters. Finally, the neighbor-joining method is employed to construct phylogenetic trees across different species. CGCPhy has been examined on different datasets from 617 complete single-chromosome prokaryotic genomes and achieved applicative accuracies on different species sets in agreement with Bergey's taxonomy in quartet topologies. Simulation results show that CGCPhy achieves high average accuracy and has a low standard deviation on different datasets, so it has an applicative potential for phylogenetic analysis.
doi:10.1155/2013/409062
PMCID: PMC3773407  PMID: 24073404
20.  Soybean GmbZIP123 gene enhances lipid content in the seeds of transgenic Arabidopsis plants 
Journal of Experimental Botany  2013;64(14):4329-4341.
Soybean is one of most important oil crops and a significant increase in lipid content in soybean seeds would facilitate vegetable oil production in the world. Although the pathways for lipid biosynthesis in higher plants have been uncovered, our understanding of regulatory mechanism controlling lipid accumulation is still limited. In this study, we identified 87 transcription factor genes with a higher abundance at the stage of lipid accumulation in soybean seeds. One of these genes, GmbZIP123, was selected to further study its function in regulation of lipid accumulation. Overexpression of GmbZIP123 enhanced lipid content in the seeds of transgenic Arabidopsis thaliana plants. The GmbZIP123 transgene promoted expression of two sucrose transporter genes (SUC1 and SUC5) and three cell-wall invertase genes (cwINV1, cwINV3, and cwINV6) by binding directly to the promoters of these genes. Consistently, the cell-wall invertase activity and sugar translocation were all enhanced in siliques of GmbZIP123 transgenic plants. Higher levels of glucose, fructose, and sucrose were also found in seeds of GmbZIP123 transgenic plants. These results suggest that GmbZIP123 may participate in regulation of lipid accumulation in soybean seeds by controlling sugar transport into seeds from photoautotrophic tissues. This study provides novel insights into the regulatory mechanism for lipid accumulation in seeds and may facilitate improvements in oil production in soybean and other oil crops through genetic manipulation of the GmbZIP123 gene.
doi:10.1093/jxb/ert238
PMCID: PMC3808315  PMID: 23963672
Cell-wall intertase; GmbZIP123 overexpression; seed lipid; soybean; sugar transport; sucrose transporter.
21.  Can Reptile Embryos Influence Their Own Rates of Heating and Cooling? 
PLoS ONE  2013;8(6):e67095.
Previous investigations have assumed that embryos lack the capacity of physiological thermoregulation until they are large enough for their own metabolic heat production to influence nest temperatures. Contrary to intuition, reptile embryos may be capable of physiological thermoregulation. In our experiments, egg-sized objects (dead or infertile eggs, water-filled balloons, glass jars) cooled down more rapidly than they heated up, whereas live snake eggs heated more rapidly than they cooled. In a nest with diel thermal fluctuations, that hysteresis could increase the embryo’s effective incubation temperature. The mechanisms for controlling rates of thermal exchange are unclear, but may involve facultative adjustment of blood flow. Heart rates of snake embryos were higher during cooling than during heating, the opposite pattern to that seen in adult reptiles. Our data challenge the view of reptile eggs as thermally passive, and suggest that embryos of reptile species with large eggs can influence their own rates of heating and cooling.
doi:10.1371/journal.pone.0067095
PMCID: PMC3691125  PMID: 23826200
22.  PMTED: a plant microRNA target expression database 
BMC Bioinformatics  2013;14:174.
Background
MicroRNAs (miRNAs) are identified in nearly all plants where they play important roles in development and stress responses by target mRNA cleavage or translation repression. MiRNAs exert their functions by sequence complementation with target genes and hence their targets can be predicted using bioinformatics algorithms. In the past two decades, microarray technology has been employed to study genes involved in important biological processes such as biotic response, abiotic response, and specific tissues and developmental stages, many of which are miRNA targets. Despite their value in assisting research work for plant biologists, miRNA target genes are difficult to access without pre-processing and assistance of necessary analytical and visualization tools because they are embedded in a large body of microarray data that are scattered around in public databases.
Description
Plant MiRNA Target Expression Database (PMTED) is designed to retrieve and analyze expression profiles of miRNA targets represented in the plethora of existing microarray data that are manually curated. It provides a Basic Information query function for miRNAs and their target sequences, gene ontology, and differential expression profiles. It also provides searching and browsing functions for a global Meta-network among species, bioprocesses, conditions, and miRNAs, meta-terms curated from well annotated microarray experiments. Networks are displayed through a Cytoscape Web-based graphical interface. In addition to conserved miRNAs, PMTED provides a target prediction portal for user-defined novel miRNAs and corresponding target expression profile retrieval. Hypotheses that are suggested by miRNA-target networks should provide starting points for further experimental validation.
Conclusions
PMTED exploits value-added microarray data to study the contextual significance of miRNA target genes and should assist functional investigation for both miRNAs and their targets. PMTED will be updated over time and is freely available for non-commercial use at http://pmted.agrinome.org.
doi:10.1186/1471-2105-14-174
PMCID: PMC3680227  PMID: 23725466
MiRNA; Microarray; Meta-analysis; Stress response
23.  Genistein induces G2/M cell cycle arrest and apoptosis via ATM/p53-dependent pathway in human colon cancer cells 
International Journal of Oncology  2013;43(1):289-296.
Soybean isoflavones have been used as a potential preventive agent in anticancer research for many years. Genistein is one of the most active flavonoids in soybeans. Accumulating evidence suggests that genistein alters a variety of biological processes in estrogen-related malignancies, such as breast and prostate cancers. However, the molecular mechanism of genistein in the prevention of human colon cancer remains unclear. Here we attempted to elucidate the anticarcinogenic mechanism of genistein in human colon cancer cells. First we evaluated the growth inhibitory effect of genistein and two other isoflavones, daidzein and biochanin A, on HCT-116 and SW-480 human colon cancer cells. In addition, flow cytometry was performed to observe the morphological changes in HCT-116/SW-480 cells undergoing apoptosis or cell cycle arrest, which had been visualized using Annexin V-FITC and/or propidium iodide staining. Real-time PCR and western blot analyses were also employed to study the changes in expression of several important genes associated with cell cycle regulation. Our data showed that genistein, daidzein and biochanin A exhibited growth inhibitory effects on HCT-116/SW-480 colon cancer cells and promoted apoptosis. Genistein showed a significantly greater effect than the other two compounds, in a time- and dose-dependent manner. In addition, genistein caused cell cycle arrest in the G2/M phase, which was accompanied by activation of ATM/p53, p21waf1/cip1 and GADD45α as well as downregulation of cdc2 and cdc25A demonstrated by q-PCR and immunoblotting assay. Interestingly, genistein induced G2/M cell cycle arrest in a p53-dependent manner. These findings exemplify that isoflavones, especially genistein, could promote colon cancer cell growth inhibition and facilitate apoptosis and cell cycle arrest in the G2/M phase. The ATM/p53-p21 cross-regulatory network may play a crucial role in mediating the anticarcinogenic activities of genistein in colon cancer.
doi:10.3892/ijo.2013.1946
PMCID: PMC3742162  PMID: 23686257
colon cancer; cancer chemoprevention; G2/M cell cycle arrest; isoflavones; p53
24.  Preclinical study and phase I clinical safety evaluation of recombinant Mycobacterium tuberculosis ESAT6 protein 
Background
To investigate the ability of rESAT6 to identify different mycobacteria-sensitized guinea pigs and its safety in preclinical and phase I clinical study.
Material/Methods
Guinea pigs were sensitized with different Mycobacteria. After sensitization, all animals were intradermally injected with rESAT6 and either PPD or PPD-B. At 24 h after the injection, the erythema of the injection sites were measured using a double-blind method. For the preclinical safety study, different doses of rESAT6 and BSA were given 3 times intramuscularly to guinea pigs. On day 14 after the final immunization, the guinea pigs were intravenously injected with the same reagents in the hind legs and the allergic reactions were observed. A single-center, randomized, open phase I clinical trial was employed. The skin test was conducted in 32 healthy volunteers aged 19–65 years with 0.1 μg, 0.5 μg, and 1 μg rESAT6. Physical examination and laboratory tests were performed before and after the skin test and adverse reactions were monitored. The volunteers’ local and systemic adverse reactions and adverse events were recorded for 7 days.
Results
Positive PPD or PPD-B skin tests were observed in all Mycobacteria-sensitized guinea pigs; the diameters of erythema were all >10 mm. The rESAT6 protein induced a positive skin test result in the guinea pigs sensitized with MTB, M. bovis, M. africanum and M. kansasii; the diameters of erythema were 14.7±2.0, 9.3±3.8, 18.7±2.4, and 14.8±4.2 mm, respectively. A negative skin test result was detected in BCG-vaccinated and other NTM-sensitized guinea pigs. The rESAT6 caused no allergic symptoms, but many allergic reactions, such as cough, dyspnea, and even death, were observed in the guinea pigs who were administered BSA. During the phase I clinical trial, no adverse reactions were found in the 0.1 μg rESAT6 group, but in the 0.5 μg rESAT6 group 2 volunteers reported pain and 1 reported itching, and in the 1 μg rESAT6 group there was 1 case of pain, 1 case of itching, and 1 case of blister. No other local or systemic adverse reactions or events were reported.
Conclusions
The rESAT6 can differentiate effectively among MTB infection, BCG vaccination, and NTM infection and is safe in healthy volunteers.
doi:10.12659/MSMBR.883912
PMCID: PMC3659126  PMID: 23676766
phase I clinical trial; recombinant protein; skin test; latent M. tuberculosis infection
25.  Caspase-mediated pro-apoptotic interaction of panaxadiol and irinotecan in human colorectal cancer cells 
Objectives
Panaxadiol (PD) is a purified sapogenin of ginseng saponins that exhibits anticancer activity. Irinotecan (IRN) is a second line anticancer drug, but clinical treatment with IRN is limited due to side effects. In this study, we investigated the possible synergistic anticancer effects of PD and IRN on human colorectal cancer cells and explored the potential role of apoptosis in the synergistic activities.
Key findings
The combination of PD and IRN significantly enhanced antiproliferative effects in HCT-116 cells (P < 0.05). Cell cycle analysis demonstrated that combining IRN treatment with PD significantly increased the G1-phase fractions of cells, compared with IRN treatment alone. In apoptotic assays, the combination of PD and IRN significantly increased the percentage of apoptotic cells compared with IRN alone (P < 0.01). Increased caspase 3 and caspase 9 activities were observed after treating with PD and IRN. The synergistic apoptotic effects were also supported by docking analysis, which demonstrated that PD and IRN bound two different chains of the caspase 3 protein.
Conclusions
Data from this study suggested that caspase 3- and caspase 9-mediated apoptosis may play an important role in the PD enhanced antiproliferative effects of IRN on human colorectal cancer cells.
doi:10.1111/j.2042-7158.2012.01463.x
PMCID: PMC3349342  PMID: 22471369
Irinotecan; panaxadiol; apoptosis; cell cycle; human colorectal cancer

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