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1.  Discovery of Protein Complexes with Core-Attachment Structures from Tandem Affinity Purification (TAP) Data 
Journal of Computational Biology  2012;19(9):1027-1042.
Abstract
Many cellular functions involve protein complexes that are formed by multiple interacting proteins. Tandem Affinity Purification (TAP) is a popular experimental method for detecting such multi-protein interactions. However, current computational methods that predict protein complexes from TAP data require converting the co-complex relationships in TAP data into binary interactions. The resulting pairwise protein-protein interaction (PPI) network is then mined for densely connected regions that are identified as putative protein complexes. Converting the TAP data into PPI data not only introduces errors but also loses useful information about the underlying multi-protein relationships that can be exploited to detect the internal organization (i.e., core-attachment structures) of protein complexes. In this article, we propose a method called CACHET that detects protein complexes with Core-AttaCHment structures directly from bipartitETAP data. CACHET models the TAP data as a bipartite graph in which the two vertex sets are the baits and the preys, respectively. The edges between the two vertex sets represent bait-prey relationships. CACHET first focuses on detecting high-quality protein-complex cores from the bipartite graph. To minimize the effects of false positive interactions, the bait-prey relationships are indexed with reliability scores. Only non-redundant, reliable bicliques computed from the TAP bipartite graph are regarded as protein-complex cores. CACHET constructs protein complexes by including attachment proteins into the cores. We applied CACHET on large-scale TAP datasets and found that CACHET outperformed existing methods in terms of prediction accuracy (i.e., F-measure and functional homogeneity of predicted complexes). In addition, the protein complexes predicted by CACHET are equipped with core-attachment structures that provide useful biological insights into the inherent functional organization of protein complexes. Our supplementary material can be found at http://www1.i2r.a-star.edu.sg/∼xlli/CACHET/CACHET.htm; binary executables can also be found there. Supplementary Material is also available at www.liebertonline.com/cmb.
doi:10.1089/cmb.2010.0293
PMCID: PMC3440013  PMID: 21777084
algorithms; gene clusters; gene networks
2.  Chemical constituents from the aerial parts of Euphorbia sikkimensis and their bioactivities 
Phytochemical investigation of the aerial parts of Euphorbia sikkimensis led to the isolation of one new diterpenoids, named sikkimenoid E (1), together with thirteen other known compounds (2–14). Their structures were established by means of spectroscopic methods. Compound 2 was identified to be a trinortriterpenoid, and derived for the first time from a natural source. In this paper we reveal for the first time its comprehensive spectral data and NMR spectral assignment. Compound 4 showed antiangiogenic activity with an IC50 value of 5.66 µM in a zebrafish model, and compounds 5 and 6 exhibited cytotoxicity toward A549 cell line with IC50 values of 12.12 and 6.45 µM, respectively.
Electronic Supplementary Material
Supplementary material is available for this article at 10.1007/s13659-013-0006-y and is accessible for authorized users.
doi:10.1007/s13659-013-0006-y
PMCID: PMC4131670
Euphorbia sikkimensis; ingenol; trinortriterpenoid; tocopherol derivatives; bioactivities
3.  Chemical constituents from Munronia sinica and their bioactivities 
Two new minor constituents, musinisins A (1) and B (2), together with five known compounds (3–7), were isolated from the aerial parts of Munronia sinica. Their structures were established by means of spectroscopic methods and the absolute stereochemistry of 1 was determined by single crystal X-ray experiment. Compound 4 showed antiangiogenic activity evaluated by a zebrafish model and apoptosis-inducing effect on A549 lung cancer cells.
Electronic Supplementary Material
Supplementary material is available for this article at 10.1007/s13659-012-0001-8 and is accessible for authorized users.
doi:10.1007/s13659-012-0001-8
PMCID: PMC4131585
Munronia sinica; chemical constituent; musinisin; antiangiogenic activity
4.  Epigenetic and metabolic regulation of breast cancer stem cells*  
Breast cancer has a relatively high mortality rate in women due to recurrence and metastasis. Increasing evidence has identified a rare population of cells with stem cell-like properties in breast cancer. These cells, termed cancer stem cells (CSCs), which have the capacity for self-renewal and differentiation, contribute significantly to tumor progression, recurrence, drug resistance and metastasis. Clarifying the mechanisms regulating breast CSCs has important implications for our understanding of breast cancer progression and therapeutics. A strong connection has been found between breast CSCs and epithelial mesenchymal transition (EMT). In addition, recent studies suggest that the maintenance of the breast CSC phenotype is associated with epigenetic and metabolic regulation. In this review, we focus on recent discoveries about the connection between EMT and CSC, and advances made in understanding the roles and mechanisms of epigenetic and metabolic reprogramming in controlling breast CSC properties.
doi:10.1631/jzus.B1400172
PMCID: PMC4288940  PMID: 25559951
Cancer stem cells (CSCs); Epithelial mesenchymal transition (EMT); Epigenetic modification; Metabolic reprogramming; Breast cancer
5.  Hyperspectral Imaging for Mapping of Total Nitrogen Spatial Distribution in Pepper Plant 
PLoS ONE  2014;9(12):e116205.
Visible/near-infrared (Vis/NIR) hyperspectral imaging was employed to determine the spatial distribution of total nitrogen in pepper plant. Hyperspectral images of samples (leaves, stems, and roots of pepper plants) were acquired and their total nitrogen contents (TNCs) were measured using Dumas combustion method. Mean spectra of all samples were extracted from regions of interest (ROIs) in hyperspectral images. Random frog (RF) algorithm was implemented to select important wavelengths which carried effective information for predicting the TNCs in leaf, stem, root, and whole-plant (leaf-stem-root), respectively. Based on full spectra and the selected important wavelengths, the quantitative relationships between spectral data and the corresponding TNCs in organs (leaf, stem, and root) and whole-plant (leaf-stem-root) were separately developed using partial least-squares regression (PLSR). As a result, the PLSR model built by the important wavelengths for predicting TNCs in whole-plant (leaf-stem-root) offered a promising result of correlation coefficient (R) for prediction (RP = 0.876) and root mean square error (RMSE) for prediction (RMSEP = 0.426%). Finally, the TNC of each pixel within ROI of the sample was estimated to generate the spatial distribution map of TNC in pepper plant. The achievements of the research indicated that hyperspectral imaging is promising and presents a powerful potential to determine nitrogen contents spatial distribution in pepper plant.
doi:10.1371/journal.pone.0116205
PMCID: PMC4280196  PMID: 25549353
6.  Detecting temporal protein complexes from dynamic protein-protein interaction networks 
BMC Bioinformatics  2014;15(1):335.
Background
Proteins dynamically interact with each other to perform their biological functions. The dynamic operations of protein interaction networks (PPI) are also reflected in the dynamic formations of protein complexes. Existing protein complex detection algorithms usually overlook the inherent temporal nature of protein interactions within PPI networks. Systematically analyzing the temporal protein complexes can not only improve the accuracy of protein complex detection, but also strengthen our biological knowledge on the dynamic protein assembly processes for cellular organization.
Results
In this study, we propose a novel computational method to predict temporal protein complexes. Particularly, we first construct a series of dynamic PPI networks by joint analysis of time-course gene expression data and protein interaction data. Then a Time Smooth Overlapping Complex Detection model (TS-OCD) has been proposed to detect temporal protein complexes from these dynamic PPI networks. TS-OCD can naturally capture the smoothness of networks between consecutive time points and detect overlapping protein complexes at each time point. Finally, a nonnegative matrix factorization based algorithm is introduced to merge those very similar temporal complexes across different time points.
Conclusions
Extensive experimental results demonstrate the proposed method is very effective in detecting temporal protein complexes than the state-of-the-art complex detection techniques.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2105-15-335) contains supplementary material, which is available to authorized users.
doi:10.1186/1471-2105-15-335
PMCID: PMC4288635  PMID: 25282536
Dynamic protein-protein interaction; Gene expression; Stable interaction; Transient interaction; Protein complex
7.  PLW: Probabilistic Local Walks for detecting protein complexes from protein interaction networks 
BMC Genomics  2013;14(Suppl 5):S15.
Background
Many biological processes are carried out by proteins interacting with each other in the form of protein complexes. However, large-scale detection of protein complexes has remained constrained by experimental limitations. As such, computational detection of protein complexes by applying clustering algorithms on the abundantly available protein-protein interaction (PPI) networks is an important alternative. However, many current algorithms have overlooked the importance of selecting seeds for expansion into clusters without excluding important proteins and including many noisy ones, while ensuring a high degree of functional homogeneity amongst the proteins detected for the complexes.
Results
We designed a novel method called Probabilistic Local Walks (PLW) which clusters regions in a PPI network with high functional similarity to find protein complex cores with high precision and efficiency in O (|V| log |V| + |E|) time. A seed selection strategy, which prioritises seeds with dense neighbourhoods, was devised. We defined a topological measure, called common neighbour similarity, to estimate the functional similarity of two proteins given the number of their common neighbours.
Conclusions
Our proposed PLW algorithm achieved the highest F-measure (recall and precision) when compared to 11 state-of-the-art methods on yeast protein interaction data, with an improvement of 16.7% over the next highest score. Our experiments also demonstrated that our seed selection strategy is able to increase algorithm precision when applied to three previous protein complex mining techniques.
Availability
The software, datasets and predicted complexes are available at http://wonglkd.github.io/PLW
doi:10.1186/1471-2164-14-S5-S15
PMCID: PMC3852146  PMID: 24564427
8.  PIMT Prevents the Apoptosis of Endothelial Cells in Response to Glycated Low Density Lipoproteins and Protective Effects of Grape Seed Procyanidin B2 
PLoS ONE  2013;8(7):e69979.
Background
The development of diabetic angiopathy is associated with profound vascular endothelial cells (VEC) dysfunction and apoptosis. Glycated low density lipoproteins (gly-LDL) continuously produced in the setting of diabetic patients play an important role in causing VEC dysfunction and apoptosis. However, the underlying molecular mechanism remains largely elusive. Protein L-isoaspartyl methyltransferase (PIMT) is a widely expressed protein repair enzyme by multiple cell types of arterial wall including VEC. Our previous proteomic studies showed that the expression of PIMT was significantly decreased in the aorta of diabetic rats as compared with control rats and treatment with grape seed procyanidin extracts significantly increased the PIMT expression in diabetic rats. We hypothesized that PIMT plays a critical role in gly-LDL induced VEC apoptosis; grape seed procyanidin B2 (GSPB2) protect against gly-LDL induced VEC apoptosis through PIMT regulation.
Methods and Results
HUVEC transfected negative control and PIMT siRNA were treated with or without GSPB2 (10 µmol/L) for 48 h. Moreover, HUVEC of PIMT overexpression were stimulated by gly-LDL (50 µg/ml) in the presence or absence of GSPB2 (10 µmol/L) for 48 h. Our results showed that gly-LDL downregulated PIMT expression and PIMT overexpression or GSPB2 significantly attenuated gly-LDL induced VEC apoptosis. PIMT siRNA increased VEC apoptosis with up-regulation of p53, cytochrome c release, caspase-9 and caspase-3 activation. Mechanistically, overexpression of PIMT or GSPB2 increased the phosphorylation of ERK1/2 and GSK3β in the gly-LDL induced VEC.
Conclusion
In summary, our study identified PIMT as a key player responsible for gly-LDL induced VEC apoptosis and GSPB2 protect against gly-LDL induced VEC apoptosis by PIMT up-regulation. Targeting PIMT including use of GSPB2 could be turned into clinical application in the fighting against diabetic vascular complications.
doi:10.1371/journal.pone.0069979
PMCID: PMC3724603  PMID: 23922881
9.  Stress and Temperature Sensitivity of Photonic Crystals Resonant Cavity 
The Scientific World Journal  2013;2013:805470.
The temperature and stress characteristic of photonic band gap structure resonant cavities with square and graphite lattice have been studied by finite-difference time-domain method. The results show that the resonant cavities, both square and graphite lattice, have more and more resonant frequency with the cavity enlarging. And the curves between the resonant frequency and stress have better linearity. When the cavity enlarges enough, the curve between resonant frequency and temperature will become sectionalized line from nonlinear curve. Especially, the temperature sensitivity will be descending as the cavity is enlarging. Nevertheless, once some structures are put in the center of the cavity, the temperature sensitivity will be rising fast for this kind of cavity. Obviously, this character is convenient for us to achieve the specification measurement for temperature and stress.
doi:10.1155/2013/805470
PMCID: PMC3725802  PMID: 23935434
10.  Modulation of Brain Electroencephalography Oscillations by Electroacupuncture in a Rat Model of Postincisional Pain 
The present study aimed to investigate how ongoing brain rhythmical oscillations changed during the postoperative pain and whether electroacupuncture (EA) regulated these brain oscillations when it relieved pain. We established a postincisional pain model of rats with plantar incision to mimic the clinical pathological pain state, tested the analgesic effects of EA, and recorded electroencephalography (EEG) activities before and after the EA application. By analysis of power spectrum and bicoherence of EEG, we found that in rats with postincisional pain, ongoing activities at the delta-frequency band decreased, while activities at theta-, alpha-, and beta-frequency bands increased. EA treatment on these postincisional pain rats decreased the power at high-frequency bands especially at the beta-frequency band and reversed the enhancement of the cross-frequency coupling strength between the beta band and low-frequency bands. After searching for the PubMed, our study is the first time to describe that brain oscillations are correlated with the processing of spontaneous pain information in postincisional pain model of rats, and EA could regulate these brain rhythmical frequency oscillations, including the power and cross-frequency couplings.
doi:10.1155/2013/160357
PMCID: PMC3655616  PMID: 23710210
11.  Effects of nicotine stimulation on spikes, theta frequency oscillations, and spike-theta oscillation relationship in rat medial septum diagonal band Broca slices 
Acta Pharmacologica Sinica  2013;34(4):464-472.
Aim:
Spiking activities and neuronal network oscillations in the theta frequency range have been found in many cortical areas during information processing. The aim of this study is to determine whether nicotinic acetylcholine receptors (nAChRs) mediate neuronal network activity in rat medial septum diagonal band Broca (MSDB) slices.
Methods:
Extracellular field potentials were recorded in the slices using an Axoprobe 1A amplifier. Data analysis was performed off-line. Spike sorting and local field potential (LFP) analyses were performed using Spike2 software. The role of spiking activity in the generation of LFP oscillations in the slices was determined by analyzing the phase-time relationship between the spikes and LFP oscillations. Circular statistic analysis based on the Rayleigh test was used to determine the significance of phase relationships between the spikes and LFP oscillations. The timing relationship was examined by quantifying the spike-field coherence (SFC).
Results:
Application of nicotine (250 nmol/L) induced prominent LFP oscillations in the theta frequency band and both small- and large-amplitude population spiking activity in the slices. These spikes were phase-locked to theta oscillations at specific phases. The Rayleigh test showed a statistically significant relationship in phase-locking between the spikes and theta oscillations. Larger changes in the SFC were observed for large-amplitude spikes, indicating an accurate timing relationship between this type of spike and LFP oscillations. The nicotine-induced spiking activity (large-amplitude population spikes) was suppressed by the nAChR antagonist dihydro-β-erythroidine (0.3 μmol/L).
Conclusion:
The results demonstrate that large-amplitude spikes are phase-locked to theta oscillations and have a high spike-timing accuracy, which are likely a main contributor to the theta oscillations generated in MSDB during nicotine receptor activation.
doi:10.1038/aps.2012.180
PMCID: PMC4002786  PMID: 23474704
medial septum diagonal band of Broca; theta oscillations; spike; LFP; nicotinic acetylcholine receptor; nicotine; dihydro-β-erythroidine; brain slice; electrophysiology
12.  Prevalence of and risk factors for aspirin resistance in elderly patients with coronary artery disease 
Objective
To assess the prevalence of and related risk factors for aspirin resistance in elderly patients with coronary artery disease (CAD).
Methods
Two hundred and forty-six elderly patients (75.9 ± 7.4 years) with CAD who received daily aspirin therapy (≥ 75 mg) over one month were recruited. The effect of aspirin was assessed using light transmission aggregometry (LTA) and thrombelastography platelet mapping assay (TEG). Aspirin resistance was defined as ≥ 20% arachidonic acid (AA)-induced aggregation and ≥ 70% adenosine diphosphate (ADP)-induced aggregation in the LTA assay. An aspirin semi-responder was defined as meeting one (but not both) of the criteria described above. Based on the results of TEG, aspirin resistance was defined as ≥ 50% aggregation induced by AA.
Results
As determined by LTA, 23 (9.3%) of the elderly CAD patients were resistant to aspirin therapy; 91 (37.0%) were semi-responders. As determined by TEG, 61 patients (24.8%) were aspirin resistant. Of the 61 patients who were aspirin resistant by TEG, 19 were aspirin resistant according to LTA results. Twenty-four of 91 semi-responders by LTA were aspirin resistant by TEG. Multivariate logistic regression analysis revealed that elevated fasting serum glucose level (Odds ratio: 1.517; 95% CI: 1.176–1.957; P = 0.001) was a significant risk factor for aspirin resistance as determined by TEG.
Conclusions
A significant number of elderly patients with CAD are resistant to aspirin therapy. Fasting blood glucose level is closely associated with aspirin resistance in elderly CAD patients.
doi:10.3969/j.issn.1671-5411.2013.01.005
PMCID: PMC3627718  PMID: 23610570
Aspirin resistance; Coronary artery disease; Risk factors
13.  Effects of phlorizin on diabetic retinopathy according to isobaric tags for relative and absolute quantification–based proteomics in db/db mice 
Molecular Vision  2013;19:812-821.
Purpose
Diabetic retinopathy (DR) is a leading cause of vision loss in working-age people. To retard the development and progression of retina lesions, effective therapeutic strategies directed toward key molecular targets are desired. Phlorizin is effective in treating diabetic complications, but little is known about functional protein changes that may mediate its actions. The aim of this study was to identify retinal proteomic alterations in db/db mice treated with phlorizin.
Methods
We used C57BLKS/J db/db mice as a type 2 diabetic animal model, while C57BLKS/J db/m mice were selected as the control. Phlorizin (20 mg/kg bodyweight /d) was administrated to db/db mice for ten weeks. Serum fasting blood glucose and advanced glycation end products were determined. Meanwhile, retina cell apoptosis was determined with terminal transferase dUTP nick end labeling. Isobaric tags for relative and absolute quantification and subsequent liquid chromatography-tandem mass spectrometry (LC-MS/MS) were used to identify and profile retinal proteins among control, untreated diabetic, and phlorizin-treated db/db mice. The expression of glial fibrillary acidic protein was measured in retinas using western blotting analysis.
Results
Phlorizin treatment significantly reduced fasting blood glucose and levels of advanced glycation end products (p<0.05) and remarkably inhibited retina cell apoptosis and the expression of glial fibrillary acidic protein in the retinas of db/db mice. In addition, we identified 1,636 proteins from retina tissue in total, of which 348 proteins were differentially expressed in db/db mice compared with the controls. Only 60 proteins in the retinas of the db/db mice were found to be differentially changed following phlorizin treatment, including 33 proteins that were downregulated and 27 proteins that were upregulated. Most of these differentially changed proteins were involved in oxidative stress, apoptosis, energy metabolism, and signaling transduction.
Conclusions
Our study revealed the expression of proteins differentially changed after phlorizin therapy. These proteins are most likely to participate in the development and recovery of DR. Our findings help expand understanding of the mechanism underlying the onset and progression of DR, and provide novel targets for evaluating the effects of phlorizin therapy.
PMCID: PMC3626294  PMID: 23592918
14.  Proteomic Analysis of Aorta and Protective Effects of Grape Seed Procyanidin B2 in db/db Mice Reveal a Critical Role of Milk Fat Globule Epidermal Growth Factor-8 in Diabetic Arterial Damage 
PLoS ONE  2012;7(12):e52541.
Background
Atherosclerosis is one of the major complications of type 2 diabetic patients (T2DM), leading to morbidity and mortality. Grape seed procyanidin B2 (GSPB2) has demonstrated protective effect against atherosclerosis, which is believed to be, at least in part, a result of its antioxidative effects. The aim of this study is to identify the target protein of GSPB2 responsible for the protective effect against atherosclerosis in patients with DM.
Methods and Results
GSPB2 (30 mg/kg body weight/day) were administrated to db/db mice for 10 weeks. Proteomics of the aorta extracts by iTRAQ analysis was obtained from db/db mice. The results showed that expression of 557 proteins were either up- or down-regulated in the aorta of diabetic mice. Among those proteins, 139 proteins were normalized by GSPB2 to the levels comparable to those in control mice. Among the proteins regulated by GSPB2, the milk fat globule epidermal growth factor-8 (MFG-E8) was found to be increased in serum level in T2DM patients; the serum level of MFG-E8 was positively correlated with carotid-femoral pulse wave velocity (CF-PWV). Inhibition of MFG-E8 by RNA interference significantly suppressed whereas exogenous recombinant MFG-E8 administration exacerbated atherogenesis the db/db mice. To gain more insights into the mechanism of action of MFG-E8, we investigated the effects of MFG-E8 on the signal pathway involving the extracellular signal-regulated kinase (ERK) and monocyte chemoattractant protein-1 (MCP-1). Treatment with recombinant MFG-E8 led to increased whereas inhibition of MFG-E8 to decreased expression of MCP-1 and phosphorylation of ERK1/2.
Conclusion
Our data suggests that MFG-E8 plays an important role in atherogenesis in diabetes through both ERK and MCP-1 signaling pathways. GSPB2, a well-studied antioxidant, significantly inhibited the arterial wall changes favoring atherogenesis in db/db mice by down-regulating MFG-E8 expression in aorta and its serum level. Measuring MFG-E8 serum level could be a useful clinical surrogate prognosticating atherogenesis in DM patients.
doi:10.1371/journal.pone.0052541
PMCID: PMC3528673  PMID: 23285083
15.  Positive-unlabeled learning for disease gene identification 
Bioinformatics  2012;28(20):2640-2647.
Background: Identifying disease genes from human genome is an important but challenging task in biomedical research. Machine learning methods can be applied to discover new disease genes based on the known ones. Existing machine learning methods typically use the known disease genes as the positive training set P and the unknown genes as the negative training set N (non-disease gene set does not exist) to build classifiers to identify new disease genes from the unknown genes. However, such kind of classifiers is actually built from a noisy negative set N as there can be unknown disease genes in N itself. As a result, the classifiers do not perform as well as they could be.
Result: Instead of treating the unknown genes as negative examples in N, we treat them as an unlabeled set U. We design a novel positive-unlabeled (PU) learning algorithm PUDI (PU learning for disease gene identification) to build a classifier using P and U. We first partition U into four sets, namely, reliable negative set RN, likely positive set LP, likely negative set LN and weak negative set WN. The weighted support vector machines are then used to build a multi-level classifier based on the four training sets and positive training set P to identify disease genes. Our experimental results demonstrate that our proposed PUDI algorithm outperformed the existing methods significantly.
Conclusion: The proposed PUDI algorithm is able to identify disease genes more accurately by treating the unknown data more appropriately as unlabeled set U instead of negative set N. Given that many machine learning problems in biomedical research do involve positive and unlabeled data instead of negative data, it is possible that the machine learning methods for these problems can be further improved by adopting PU learning methods, as we have done here for disease gene identification.
Availability and implementation: The executable program and data are available at http://www1.i2r.a-star.edu.sg/∼xlli/PUDI/PUDI.html.
Contact: xlli@i2r.a-star.edu.sg or yang0293@e.ntu.edu.sg
Supplementary information: Supplementary Data are available at Bioinformatics online.
doi:10.1093/bioinformatics/bts504
PMCID: PMC3467748  PMID: 22923290
16.  Successful management of mucinous ovarian cancer by conservative surgery in week 6 of pregnancy: case report and literature review 
Purpose
The management of ovarian cancer during pregnancy is still a big challenge, mostly due to the reciprocal impacts between cancer and pregnancy. The objective of this article is to present a rare case of maternal ovarian adenocarcinoma and review published similar cases about this clinical condition.
Materials and methods
Here we report a rare case of maternal ovarian adenocarcinoma detected during gestational week 6, with good pregnancy outcome treated with conservative surgery.
Results and discussion
A case of maternal ovarian adenocarcinoma (stage I) was detected in week 6 of pregnancy receiving conservative surgery without chemotherapy. In week 39 of pregnancy, due to relapse of the cancer, the patient underwent excision of the isolated tumor, and gave birth to a healthy baby through cesarian section. After that, the patient received cytoreductive surgery associated with six chemotherapy. The patient was finally diagnosed as epithelial ovarian cancer stage IIIC, and had survived more than 5 years without relapse. The successful experience from this case suggested that pregnancy complicated with early ovarian cancer receiving conservative surgery could continue to pregnancy and the effect of cesarian section followed with cytoreductive surgery associated with six chemotherapy at full term was still satisfied.
doi:10.1007/s00404-012-2490-4
PMCID: PMC3439607  PMID: 22850888
Pregnancy; Ovarian cancer; Cytoreductive surgery; Chemotherapy
17.  Reversion of P-Glycoprotein-Mediated Multidrug Resistance in Human Leukemic Cell Line by Diallyl Trisulfide 
Multidrug resistance (MDR) is the major obstacle in chemotherapy, which involves multiple signaling pathways. Diallyl trisulfide (DATS) is the main sulfuric compound in garlic. In the present study, we aimed to explore whether DATS could overcome P-glycoprotein-(P-gp-)mediated MDR in K562/A02 cells, and to investigate whether NF-κB suppression is involved in DATS-induced reversal of MDR. MTT assay revealed that cotreatment with DATS increased the response of K562/A02 cells to adriamycin (the resistance reversal fold was 3.79) without toxic side effects. DATS could enhance the intracellular concentration of adriamycin by inhibiting the function and expression of P-gp, as shown by flow cytometry, RT-PCR, and western blot. In addition, DATS resulted in more K562/A02 cell apoptosis, accompanied by increased expression of caspase-3. The expression of NF-κB/p65 (downregulation) was significantly linked to the drug-resistance mechanism of DATS, whereas the expression of IκBα was not affected by DATS. Our findings demonstrated that DATS can serve as a novel, nontoxic modulator of MDR, and can reverse the MDR of K562/A02 cells in vitro by increasing intracellular adriamycin concentration and inducing apoptosis. More importantly, we proved for the first time that the suppression of NF-κB possibly involves the molecular mechanism in the course of reversion by DATS.
doi:10.1155/2012/719805
PMCID: PMC3418761  PMID: 22919419
18.  Impact of genital warts on health related quality of life in men and women in mainland China: a multicenter hospital-based cross-sectional study 
BMC Public Health  2012;12:153.
Background
Information on the health-related quality of life (HRQoL) of patients with genital warts (GW) in populations in mainland China is still limited. The aim of the study was to use a generic instrument to measure the impact of genital warts on HRQoL in men and women in this setting.
Methods
A multi-centre hospital-based cross-sectional study across 18 centers in China was conducted to interview patients using the European quality of life-5 dimension (EQ-5D) instrument; respondents' demographic and clinical data were also collected.
Results
A total of 1,358 GW patients (612 men, 746 women) were included in the analysis, with a mean age of 32.0 ± 10.6 years. 56.4% of the patients reported some problems in the dimension of Anxiety/Depression (highest), followed by Pain/Discomfort (24.7%) and Mobility (3.5%). The overall visual analogue scale (VAS) score of the study population was found to be 65.2 ± 22.0, and the EQ-5D index score was found to be 0.843 ± 0.129 using Japanese preference weights (the Chinese preference was unavailable yet). Patients with lower VAS means and EQ-5D index scores were more often female, living in urban area, and suffering multiple GW (all p values < 0.05), but the values did not differ notably by age (p values > 0.05).
Conclusions
The HRQoL of patients with GW was substantially lower, compared to a national representative general population in China (VAS = ~80); the findings of different subgroups are informative for future GW prevention and control efforts.
doi:10.1186/1471-2458-12-153
PMCID: PMC3359232  PMID: 22381149
19.  A point mutation in the DNA-binding domain of HPV-2 E2 protein increases its DNA-binding capacity and reverses its transcriptional regulatory activity on the viral early promoter 
Background
The human papillomavirus (HPV) E2 protein is a multifunctional DNA-binding protein. The transcriptional activity of HPV E2 is mediated by binding to its specific binding sites in the upstream regulatory region of the HPV genomes. Previously we reported a HPV-2 variant from a verrucae vulgaris patient with huge extensive clustered cutaneous, which have five point mutations in its E2 ORF, L118S, S235P, Y287H, S293R and A338V. Under the control of HPV-2 LCR, co-expression of the mutated HPV E2 induced an increased activity on the viral early promoter. In the present study, a series of mammalian expression plasmids encoding E2 proteins with one to five amino acid (aa) substitutions for these mutations were constructed and transfected into HeLa, C33A and SiHa cells.
Results
CAT expression assays indicated that the enhanced promoter activity was due to the co-expressions of the E2 constructs containing A338V mutation within the DNA-binding domain. Western blots analysis demonstrated that the transiently transfected E2 expressing plasmids, regardless of prototype or the A338V mutant, were continuously expressed in the cells. To study the effect of E2 mutations on its DNA-binding activity, a serial of recombinant E2 proteins with various lengths were expressed and purified. Electrophoresis mobility shift assays (EMSA) showed that the binding affinity of E2 protein with A338V mutation to both an artificial probe with two E2 binding sites or HPV-2 and HPV-16 promoter-proximal LCR sequences were significantly stronger than that of the HPV-2 prototype E2. Furthermore, co-expression of the construct containing A338V mutant exhibited increased activities on heterologous HPV-16 early promoter P97 than that of prototype E2.
Conclusions
These results suggest that the mutation from Ala to Val at aa 338 is critical for E2 DNA-binding and its transcriptional regulation.
doi:10.1186/1471-2199-13-5
PMCID: PMC3307029  PMID: 22333459
HPV-2; E2; DNA-binding; Transcriptional regulation; Promoter
20.  Blood hemoperfusion with resin adsorption combined continuous veno-venous hemofiltration for patients with multiple organ dysfunction syndrome 
BACKGROUND:
Blood hemoperfusion with resin adsorption can clean larger molecules that exceed the molecular weight cutoff of combined continuous veno-venous hemofiltration (CVVH). Hence blood hemoperfusion with resin adsorption combined CVVH (HP+CVVH) has higher ability of mediator clearance, and can improve clinical outcomes in theory. This study aimed to investigate the effect of blood hemoperfusion with resin adsorption combined continuous veno-venous hemofiltration (HP+CVVH) on plasm cytokines like TNF-α, IL-1β, IL-6, cellular immunity and prognosis in patients with multiple organ dysfunction syndrome (MODS).
METHODS:
This was a prospective, randomized clinical trial. A total of 30 patients who had been diagnosed with MODS were enrolled in this study. Patients were randomly allocated to routine treatment+HP+CVVH group (treatment group) and routine treatment+only CVVH group (control group). In the treatment group, patients received blood hemoperfusion with resin adsorption for 2 hours, and then received CVVH for 10 hours every day. In the control group, patients received CVVH for 12 hours only every day. The patients in the two groups received blood purification therapy for three days. The plasma of patients in the treatment group was obtained at 0, 2, 12, 24, 26, 36, 48, 50, 60 hours, 5th day, 7th day and 10th day, respectively. The plasma of patients in the control group was obtained at 0, 12, 24, 36, 48, 60 hours, 5th day, 7th day and 10th day, respectively. APACHE II score, T-lymphocytes subpopulations, blood lactate acid concentration, heart rate, breathing rate, and oxygenation index were observed.
RESULTS:
Plasma cytokines like TNF-α, IL-1β, IL-6 decreased markedly after HP (P<0.01); T-lymphocytes subpopulations CD3+, CD4+, CD8+, CD4+/CD8+ increased after HP+CVVH or only CVVH. The plasma concentrations of TNF-α, IL-1β and IL-6 in the two groups were not markedly different at 12, 36, and 50 hours. But on the 5th day, the plasma concentrations of TNF-α, IL-1β and IL-6 in the treatment group were lower than those in the control group (P<0.05). On the 28th day, 5 patients died in the treatment group, and 6 patients in the control group.
CONCLUSIONS:
Both HP+CVVH and CVVH can clean plasma cytokines like TNF-α, IL-1β, and IL-6, and improve cellular immunity and clinical symptoms and signs of patients. Compared with only CVVH, the plasma concentrations of TNF-α, IL-1β and IL-6 were lower on the 5th day, and patients have an increased survival rate on the 28 day in the HP+CVVH group.
doi:10.5847/wjem.j.issn.1920-8642.2012.01.008
PMCID: PMC4129815  PMID: 25215038
Hemoperfusion with resin adsorption; Continuous veno-venous hemofiltration; Multiple organ dysfunction syndrome; Cytokines
21.  Clinical features and risk factors for severe and critical pregnant women with 2009 pandemic H1N1 influenza infection in China 
Background
2009 pandemic H1N1 (pH1N1) influenza posed an increased risk of severe illness among pregnant women. Data on risk factors associated with death of pregnant women and neonates with pH1N1 infections are limited outside of developed countries.
Methods
Retrospective observational study in 394 severe or critical pregnant women admitted to a hospital with pH1N1 influenza from Sep. 1, 2009 to Dec. 31, 2009. rRT-PCR testing was used to confirm infection. In-hospital mortality was the primary endpoint of this study. Univariable logistic analysis and multivariate logistic regression analysis were used to investigate the potential factors on admission that might be associated with the maternal and neonatal mortality.
Results
394 pregnant women were included, 286 were infected with pH1N1 in the third trimester. 351 had pneumonia, and 77 died. A PaO2/FiO2 ≤ 200 (odds ratio (OR), 27.16; 95% confidence interval (CI), 2.64-279.70) and higher BMI (i.e. ≥ 30) on admission (OR, 1.26; 95% CI, 1.09 to 1.47) were independent risk factors for maternal death. Of 211 deliveries, 146 neonates survived. Premature delivery (OR, 4.17; 95% CI, 1.19-14.56) was associated neonatal mortality. Among 186 patients who received mechanical ventilation, 83 patients were treated with non-invasive ventilation (NIV) and 38 were successful with NIV. The death rate was lower among patients who initially received NIV than those who were initially intubated (24/83, 28.9% vs 43/87, 49.4%; p = 0.006). Septic shock was an independent risk factor for failure of NIV.
Conclusions
Severe hypoxemia and higher BMI on admission were associated with adverse outcomes for pregnant women. Preterm delivery was a risk factor for neonatal death among pregnant women with pH1N1 influenza infection. NIV may be useful in selected pregnant women without septic shock.
doi:10.1186/1471-2334-12-29
PMCID: PMC3311613  PMID: 22292815
Pregnant women; Neonate; Pandemic H1N1 influenza; Mortality; Non-invasive ventilation
22.  Antiviral Therapy and Outcomes of Patients with Pneumonia Caused by Influenza A Pandemic (H1N1) Virus 
PLoS ONE  2012;7(1):e29652.
Background
There is limited data on the clinical outcome of patients with pandemic H1N1 (pH1N1) pneumonia who received oseltamivir treatment, especially when the treatment was administered more than 48 hours after symptom onset.
Methods
During the pandemic in 2009, a cohort of pH1N1 influenza pneumonia was built in China, and their clinical information was collected systematically, and analyzed with Cox models.
Results
920 adults and 541 children with pneumonia who didn't receive corticosteroids were analyzed. In-hospital mortality was higher in adults who did not receive antiviral therapy (18.2%) than those with who received oseltamivir ≤ 2days (2.9%), between 2–5 days (4.6%) and >5 days after illness onset (4.9%), p<0.01. A similar trend was observed in pediatric patients. Cox regression showed that at 60 days after symptoms onset, 11 patients (10.8%) who did not receive antivirals died versus 4 (1.8%), 18 (3.3%), and 23 (3.7%) patients whose oseltamivir treatment was started ≤ 2days, between 2–5days, and >5 days, respectively. For males patients, aged ≥ 14 years and baseline PaO2/FiO2<200, oseltamivir administration reduced the mortality risk by 92.1%, 88% and 83.5%, respectively. Higher doses of oseltamivir (>3.8 mg/kg/d) did not improve clinical outcome (mortality, higher dose 2.5% vs standard dose 2.8%, p>0.05).
Conclusions
Antiviral therapy might reduce mortality of patients with pH1N1 pneumonia, even when initiated more than 48 hours after onset of illness. Greater protective effects might be in males, patients aged 14–60 years, and patients with PaO2/FiO2<200.
doi:10.1371/journal.pone.0029652
PMCID: PMC3262784  PMID: 22276122
23.  Construction of co-complex score matrix for protein complex prediction from AP-MS data 
Bioinformatics  2011;27(13):i159-i166.
Motivation: Protein complexes are of great importance for unraveling the secrets of cellular organization and function. The AP-MS technique has provided an effective high-throughput screening to directly measure the co-complex relationship among multiple proteins, but its performance suffers from both false positives and false negatives. To computationally predict complexes from AP-MS data, most existing approaches either required the additional knowledge from known complexes (supervised learning), or had numerous parameters to tune.
Method: In this article, we propose a novel unsupervised approach, without relying on the knowledge of existing complexes. Our method probabilistically calculates the affinity between two proteins, where the affinity score is evaluated by a co-complexed score or C2S in brief. In particular, our method measures the log-likelihood ratio of two proteins being co-complexed to being drawn randomly, and we then predict protein complexes by applying hierarchical clustering algorithm on the C2S score matrix.
Results: Compared with existing approaches, our approach is computationally efficient and easy to implement. It has just one parameter to set and its value has little effect on the results. It can be applied to different species as long as the AP-MS data are available. Despite its simplicity, it is competitive or superior in performance over many aspects when compared with the state-of-the-art predictions performed by supervised or unsupervised approaches.
Availability: The predicted complex sets in this article are available in the Supplementary information or by sending email to asckkwoh@ntu.edu.sg
Contact: xlli@i2r.a-star.edu.sg
Supplementary information: Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/btr212
PMCID: PMC3117344  PMID: 21685066
24.  Effects of Oplopanax horridus on Human Colorectal Cancer Cells 
Anticancer research  2010;30(2):295-302.
Aim
In this study, we investigated the inhibitive effects of Oplopanax horridus extract (OhE) and its fractions (OhF1, OhF2, OhF3, OhF4 and OhF5) on the growth of human colorectal cancer cells and the possible mechanisms.
Materials and Methods
The anti-proliferative effects were evaluated by MTS cell proliferation assay. Apoptotic effects and cell cycle distribution were analyzed by flow cytometry after staining with Annexin V/PI or PI/RNase.
Results
After treatment for 48 hr, OhE, OhF4 and OhF5 (10–100 μg/ml) inhibited proliferation of HCT-116, SW-480 and HT-29 cell lines. And cell growth decreased most with the treatment of OhF4. On the other hand, OhF1, OhF2 and OhF3 were not observed to have obvious suppressive effects on these cell lines at concentrations of 10–100 μg/ml. OhE, OhF4 and OhF5 (1–10 μg/ml) noticeably induced apoptosis time- and concentration-dependently compared to the control at the same time point. Treatement with OhE, OhF4 or OhF5 (1–10 μg/ml) for 24 hr distinctly induced the G2/M phase arrest of the cell cycle in a dose-dependent manner. The trend of increasing cyclin A and cyclin B1 were similar to the increase of G2/M phase cells in all treated groups.
Conclusion
These results showed that OhE had potential anti-proliferation effects on human colorectal cancer cells, and the active components were enriched in the fractions OhF4 and OhF5. The anticancer mechanism of OhE, OhF4 and OhF5 might be attributed to the induction of apoptotic cells and the regulation of cell cycle transition.
PMCID: PMC3057088  PMID: 20332432
Oplopanax horridus; human colorectal cancer; anti-proliferation; apoptosis; cell cycle; cyclin A; cyclin B1
25.  Improving Anticancer Activities of Oplopanax horridus Root Bark Extract by Removing Water-soluble Components 
Phytotherapy research : PTR  2010;24(8):1166-1174.
Oplopanax horridus is used as a folk medicine by natives in the Northern Pacific coast of North America. This experiment studied the anti-proliferative effects of the extract of O. horridus root bark and its fractions chromatographed from Dianion HP20 resin column with water, 30, 50, 70 and 100% ethanol on human breast cancer MCF-7 cells and non-small cell lung cancer (NSCLC) cells. The role of O. horridus in the cell cycle and apoptosis of MCF-7 cells was also investigated. The results showed that the 70% and 100% ethanol fractions demonstrated more potent anti-proliferative effects than the total extract on both cell lines. The anti-proliferative effects may result from the enrichment of active constituents detected by the HPLC. The IC50 of the total extract, 50, 70, and 100% ethanol fractions for anti-proliferation on MCF-7 cells were 248.4, 123.1, 44.0, and 31.5 μg/mL, respectively, and on NSCLC cells were 125.3, 271.1, 17.6, and 23.2 μg/mL, respectively. On the other hand, the water and 30% ethanol fractions significantly promoted cell proliferation on MCF-7 cells at concentrations > 100 μg/mL, suggesting that the hydrophilic fractions should be removed from the extract when used for cancer chemoprevention in order to achieve desirable activities. The effects of the total extract on cell cycle and apoptosis were similar to that of the 100% ethanol fraction because of the similarity of their chemical composition. At higher concentrations, the apoptotic effects of the 70% ethanol fraction are more significant. Data from this study suggested that the 70% and 100% ethanol fractions are active anti-proliferative fractions and that induction of apoptosis is the mechanism involved in the anti-proliferative effect observed.
doi:10.1002/ptr.3061
PMCID: PMC3057089  PMID: 20077432
Oplopanax horridus; anti-proliferative effect; human breast cancer MCF-7 cells; non-small cell lung cancer (NSCLC) cells; apoptosis; cell cycle

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