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1.  Ubiquitin-Binding Site 2 of ataxin-3 prevents its proteasomal degradation by interacting with Rad23 
Nature communications  2014;5:4638.
Polyglutamine repeat expansion in ataxin-3 causes neurodegeneration in the most common dominant ataxia, Spinocerebellar Ataxia Type 3 (SCA3). Since reducing levels of disease proteins improves pathology in animals, we investigated how ataxin-3 is degraded. Here we show that, unlike most proteins, ataxin-3 turnover does not require its ubiquitination, but is regulated by Ubiquitin-Binding Site 2 (UbS2) on its N terminus. Mutating UbS2 decreases ataxin-3 protein levels in cultured mammalian cells and in Drosophila melanogaster by increasing its proteasomal turnover. Ataxin-3 interacts with the proteasome-associated proteins Rad23A/B through UbS2. Knockdown of Rad23 in cultured cells and in Drosophila results in lower levels of ataxin-3 protein. Importantly, reducing Rad23 suppresses ataxin-3-dependent degeneration in flies. We present a mechanism for ubiquitination-independent degradation that is impeded by protein interactions with proteasome-associated factors. We conclude that UbS2 is a potential target through which to enhance ataxin-3 degradation for SCA3 therapy.
doi:10.1038/ncomms5638
PMCID: PMC4237202  PMID: 25144244
Deubiquitinase; Drosophila; Neurodegeneration; Neuroprotection; Polyglutamine; Proteasome; hHR23; Spinocerebellar Ataxia; Ubiquitin
2.  Impact of Age, Race and Ethnicity on Dialysis Patient Survival and Kidney Transplantation Disparities 
American journal of nephrology  2014;39(3):183-194.
Background
Prior studies show that African-American and Hispanic dialysis patients have lower mortality risk than whites. Recent age-stratified analyses suggest this survival advantage may be limited to younger age groups, but did not concurrently compare Hispanic, African-American, and white patients, nor account for differences in nutritional and inflammatory status as potential confounders. Minorities experience inequities in kidney transplantation access, but it is unknown whether these racial/ethnic disparities differ across age groups.
Methods
The associations between race/ethnicity with all-cause mortality and kidney transplantation were separately examined among 130,909 adult dialysis patients from a large national dialysis organization (entry period 2001-2006, follow-up through 2009) within 7 age categories using Cox proportional hazard models adjusted for case-mix and malnutrition and inflammatory surrogates.
Results
African-Americans had similar mortality vs. whites in younger age groups (18-40 years), but decreased mortality in older age groups (>40 years). In contrast, Hispanics had lower mortality vs. whites across all ages. In sensitivity analyses using competing risk regression to account for differential kidney transplantation rates across racial/ethnic groups, the African-American survival advantage was limited to >60 year old age categories. African-Americans and Hispanics were less likely to undergo kidney transplantation from all donor types vs. whites across all ages, and these disparities were even more pronounced for living donor kidney transplantations (LDKT).
Conclusions
Hispanic dialysis patients have greater survival vs. whites across all ages; in African-Americans, this survival advantage is limited to patients >40 years old. Minorities are less likely to undergo kidney transplantation, particularly LDKT, across all ages.
doi:10.1159/000358497
PMCID: PMC4024458  PMID: 24556752
Race; Ethnicity; Disparities; Survival; Transplantation
3.  Deep RNA sequencing reveals a high frequency of alternative splicing events in the fungus Trichoderma longibrachiatum 
BMC Genomics  2015;16(1):54.
Background
Alternative splicing is crucial for proteome diversity and functional complexity in higher organisms. However, the alternative splicing landscape in fungi is still elusive.
Results
The transcriptome of the filamentous fungus Trichoderma longibrachiatum was deep sequenced using Illumina Solexa technology. A total of 14305 splice junctions were discovered. Analyses of alternative splicing events revealed that the number of all alternative splicing events (10034), intron retentions (IR, 9369), alternative 5’ splice sites (A5SS, 167), and alternative 3’ splice sites (A3SS, 302) is 7.3, 7.4, 5.1, and 5.9-fold higher, respectively, than those observed in the fungus Aspergillus oryzae using Illumina Solexa technology. This unexpectedly high ratio of alternative splicing suggests that alternative splicing is important to the transcriptome diversity of T. longibrachiatum. Alternatively spliced introns had longer lengths, higher GC contents, and lower splice site scores than constitutive introns. Further analysis demonstrated that the isoform relative frequencies were correlated with the splice site scores of the isoforms. Moreover, comparative transcriptomics determined that most enzymes related to glycolysis and the citrate cycle and glyoxylate cycle as well as a few carbohydrate-active enzymes are transcriptionally regulated.
Conclusions
This study, consisting of a comprehensive analysis of the alternative splicing landscape in the filamentous fungus T. longibrachiatum, revealed an unexpectedly high ratio of alternative splicing events and provided new insights into transcriptome diversity in fungi.
Electronic supplementary material
The online version of this article (doi:10.1186/s12864-015-1251-8) contains supplementary material, which is available to authorized users.
doi:10.1186/s12864-015-1251-8
PMCID: PMC4324775  PMID: 25652134
Alternative splicing; Fungi; RNA-Seq; Intron retention; Transcriptome; Trichoderma longibrachiatum
4.  Diagnostic accuracy of high resolution melting analysis for detection of KRAS mutations: a systematic review and meta-analysis 
Scientific Reports  2014;4:7521.
Increasing evidence points to a negative correlation between KRAS mutations and patients' responses to anti-EGFR monoclonal antibody treatment. Therefore, patients must undergo KRAS mutation detection to be eligible for treatment. High resolution melting analysis (HRM) is gaining increasing attention in KRAS mutation detection. However, its accuracy has not been systematically evaluated. We conducted a meta-analysis of published articles, involving 13 articles with 1,520 samples, to assess its diagnostic accuracy compared with DNA sequencing. The quality of included articles was assessed using the revised Quality Assessment for Studies of Diagnostic Accuracy (QUADAS-2) tools. Random effects models were applied to analyze the performance of pooled characteristics. The overall sensitivity and specificity of HRM were 0.99 (95% confidence interval [CI]: 0.98–1.00) and 0.96 (95%CI: 0.94–0.97), respectively. The area under the summary receiver operating characteristic curve was 0.996. High sensitivity and specificity, less labor, rapid turn-around and the closed-tube format of HRM make it an attractive choice for rapid detection of KRAS mutations in clinical practice. The burden of DNA sequencing can be reduced dramatically by the implementation of HRM, but positive results still need to be sequenced for diagnostic confirmation.
doi:10.1038/srep07521
PMCID: PMC4268648  PMID: 25515911
5.  High Amylose Resistant Starch Diet Ameliorates Oxidative Stress, Inflammation, and Progression of Chronic Kidney Disease 
PLoS ONE  2014;9(12):e114881.
Inflammation is a major mediator of CKD progression and is partly driven by altered gut microbiome and intestinal barrier disruption, events which are caused by: urea influx in the intestine resulting in dominance of urease-possessing bacteria; disruption of epithelial barrier by urea-derived ammonia leading to endotoxemia and bacterial translocation; and restriction of potassium-rich fruits and vegetables which are common sources of fermentable fiber. Restriction of these foods leads to depletion of bacteria that convert indigestible carbohydrates to short chain fatty acids which are important nutrients for colonocytes and regulatory T lymphocytes. We hypothesized that a high resistant starch diet attenuates CKD progression. Male Sprague Dawley rats were fed a chow containing 0.7% adenine for 2 weeks to induce CKD. Rats were then fed diets supplemented with amylopectin (low-fiber control) or high fermentable fiber (amylose maize resistant starch, HAM-RS2) for 3 weeks. CKD rats consuming low fiber diet exhibited reduced creatinine clearance, interstitial fibrosis, inflammation, tubular damage, activation of NFkB, upregulation of pro-inflammatory, pro-oxidant, and pro-fibrotic molecules; impaired Nrf2 activity, down-regulation of antioxidant enzymes, and disruption of colonic epithelial tight junction. The high resistant starch diet significantly attenuated these abnormalities. Thus high resistant starch diet retards CKD progression and attenuates oxidative stress and inflammation in rats. Future studies are needed to explore the impact of HAM-RS2 in CKD patients.
doi:10.1371/journal.pone.0114881
PMCID: PMC4260945  PMID: 25490712
6.  Acute and Delayed Protective Effects of Pharmacologically Induced Hypothermia in an Intracerebral Hemorrhage Stroke Model of Mice 
Neuroscience  2013;252:489-500.
Hemorrhagic stroke, including intracerebral hemorrhage (ICH), is a devastating subtype of stroke; yet, effective clinical treatment is very limited. Accumulating evidence has shown that mild to moderate hypothermia is a promising intervention for ischemic stroke and ICH. Current physical cooling methods, however, are less efficient and often impractical for acute ICH patients. The present investigation tested pharmacologically induced hypothermia (PIH) using the second generation neurotensin receptor (NTR) agonist HPI-201 (formerly known as ABS-201) in an adult mouse model with ICH. Acute or delayed administrations of HPI-201 (2 mg/kg bolus injection followed by 2 injections of 1 mg/kg, i.p.) were initiated at 1 or 24 hrs after ICH. HPI-201 induced mild hypothermia within 30 min and maintained body and brain temperatures at 32.7±0.4°C for at least 6 hrs without causing observable shivering. With the 1 hr delayed treatment, HPI-201-induced PIH significantly reduced ICH-induced cell death and brain edema compared to saline-treated ICH animals. When HPI-201-induced hypothermia was initiated 24 hrs after the onset of ICH, it still significantly attenuated brain edema, cell death and blood brain barrier breakdown. HPI-201 significantly decreased the expression of MMP-9, reduced caspase-3 activation, and increased Bcl-2 expression in the ICH brain. Moreover, ICH mice received 1-hr delayed HPI-201 treatment performed significantly better in the neurological behavior test 48 hrs after ICH. All together, these data suggest that systemic injection of HPI-201 is an effective hypothermic strategy that protects the brain from ICH injury with a wide therapeutic window. The protective effect of this PIH therapy is partially mediated through the alleviation of apoptosis and neurovascular damage. We suggest that pharmacological hypothermia using the newly developed neurotensin analogs is a promising therapeutic treatment for ICH.
doi:10.1016/j.neuroscience.2013.07.052
PMCID: PMC3961766  PMID: 23912033
Intracerebral hemorrhage; pharmacological hypothermia; PIH; neurotensin receptor; ABS-201; HPI-201
7.  Association of Serum Phosphorus Concentration with Mortality in Elderly and Non-Elderly Hemodialysis Patients 
Objective
Hypo- and hyperphosphatemia have each been associated with increased mortality in maintenance hemodialysis (MHD) patients. There has not been previous evaluation of a differential relationship between serum phosphorus level and death risk across varying age groups in MHD patients.
Design and Settings
In a 6-year cohort of 107,817 MHD patients treated in a large dialysis organization, we examined the association between serum phosphorus levels with all-cause and cardiovascular mortality within 5 age categories (15-<45, 45-<65, 65-<70, 70-<75 and ≥75 years old) using Cox proportional hazards model adjusted for case-mix covariates and malnutrition inflammation complex syndrome (MICS) surrogates.
Main outcome measure
all-cause and cardiovascular mortality.
Results
The overall mean age of the cohort was 60±16 years, among whom there were 45% women, 35% Blacks and 58% diabetics. The time averaged serum phosphorus level (mean ± SD) within each age category was 6.26±1.4, 5.65±1.2, 5.26±1.1, 5.11±1.0 and 4.88±1.0 mg/dl, respectively (P for trend <0.001). Hyperphosphatemia (>5.5 mg/dl) was consistently associated with increased all-cause and cardiovascular mortality risks across all age categories including after adjustment for case-mix and MICS-related covariates. In fully adjusted models, a low serum phosphorus level (<3.5 mg/dl) was associated with increased all-cause mortality only in elderly MHD patients ≥65 years old (hazard ratio [HR] (95% confidence interval[CI]): 1.21(1.07-1.37), 1.13(1.02-1.25), and 1.28(1.2-1.37) for patients 65-<70, 70-<75, and ≥75 years old, respectively], but not in younger patients (<65 years old). A similar differential for cardiovascular mortality of serum phosphorus levels between old and young age groups was observed.
Conclusions
The association between hyperphosphatemia and mortality is similar across all age groups of MHD patients, whereas hypophosphatemia is associated with increased mortality only in elderly MHD patients. Preventing very low serum phosphorus levels in elderly dialysis patients may be associated with better outcomes, which needs to be examined in future studies.
doi:10.1053/j.jrn.2013.01.018
PMCID: PMC3735629  PMID: 23631888
hemodialysis; mortality; phosphorus; elderly
8.  Nuclear Import of Transcription Factor BR-C Is Mediated by Its Interaction with RACK1 
PLoS ONE  2014;9(10):e109111.
The transcription factor Broad Complex (BR-C) is an early ecdysone response gene in insects and contains two types of domains: two zinc finger domains for the activation of gene transcription and a Bric-a-brac/Tramtrack/Broad complex (BTB) domain for protein-protein interaction. Although the mechanism of zinc finger-mediated gene transcription is well studied, the partners interacting with the BTB domain of BR-C has not been elucidated until now. Here, we performed a yeast two-hybrid screen using the BTB domain of silkworm BR-C as bait and identified the receptor for activated C-kinase 1 (RACK1), a scaffolding/anchoring protein, as the novel partner capable of interacting with BR-C. The interaction between BR-C and RACK1 was further confirmed by far-western blotting and pull-down assays. Importantly, the disruption of this interaction, via RNAi against the endogenous RACK1 gene or deletion of the BTB domain, abolished the nuclear import of BR-C in BmN4 cells. In addition, RNAi against the endogenous PKC gene as well as phosphorylation-deficient mutation of the predicted PKC phosphorylation sites at either Ser373 or Thr406 in BR-C phenocopied RACK1 RNAi and altered the nuclear localization of BR-C. However, when BTB domain was deleted, phosphorylation mimics of either Ser373 or Thr406 had no effect on the nuclear import of BR-C. Moreover, mutating the PKC phosphorylation sites at Ser373 and Thr406 or deleting the BTB domain significantly decreased the transcriptional activation of a BR-C target gene. Given that RACK1 is necessary for recruiting PKC to close and phosphorylate target proteins, we suggest that the PKC-mediated phosphorylation and nuclear import of BR-C is determined by its interaction with RACK1. This novel finding will be helpful for further deciphering the mechanism underlying the role of BR-C proteins during insect development.
doi:10.1371/journal.pone.0109111
PMCID: PMC4184850  PMID: 25280016
9.  Impact of age on survival predictability of bone turnover markers in hemodialysis patients 
Nephrology Dialysis Transplantation  2013;28(10):2535-2545.
Background
Abnormalities in serum alkaline phosphatase (ALP) and intact parathyroid hormone (PTH) concentrations, as biochemical markers of bone turnover in dialysis patients, correlate with increased mortality in maintenance hemodialysis (MHD) patients. Changes in bone turnover rate vary with age. The mortality predictability of serum ALP and PTH levels in MHD patients may be different across ages.
Methods
We examined differences across four age groups (18 to <45, 45 to <65, 65 to <75 and ≥75 years) in the mortality predictability of serum ALP and PTH in 102 149 MHD patients using Cox models.
Results
Higher serum ALP levels were associated with higher mortality across all ages; however, the ALP–mortality association was much stronger in young patients (<45 years) compared with older patients. The association between higher serum PTH levels and mortality was stronger in older patients compared with the younger groups. Serum PTH levels were incrementally associated with mortality only in middle-aged and elderly patients (≥45 years). Compared with patients with serum PTH 150 to <300pg/mL, the death risks were higher in patients with serum PTH 300 to <600pg/mL [HRs (95% CI): 1.05 (1.01–1.10), 1.15 (1.10–1.21) and 1.25 (1.19–1.31) for patients 45 to <65, 65 to <75 and ≥75 years, respectively], and ≥600pg/mL [HRs(95% CI): 1.07 (1.01–1.14), 1.31(1.21–1.42) and 1.45(1.33–1.59) for age categories 45 to <65, 65 to <75 and ≥75 years, respectively]. However, no significant association between higher serum PTH levels and mortality was observed in patients <45 years.
Conclusions
There are important differences in mortality-predictability of serum ALP and PTH in older MHD patients compared with their younger counterparts. The effect of age needs to be considered when interpreting the prognostic implications of serum ALP and PTH levels.
doi:10.1093/ndt/gft290
PMCID: PMC3784839  PMID: 23904397
age; alkaline phosphatase; bone turnover markers; hemodialysis; parathyroid hormone
10.  Biosensors for hepatitis B virus detection 
World Journal of Gastroenterology : WJG  2014;20(35):12485-12492.
A biosensor is an analytical device used for the detection of analytes, which combines a biological component with a physicochemical detector. Recently, an increasing number of biosensors have been used in clinical research, for example, the blood glucose biosensor. This review focuses on the current state of biosensor research with respect to efficient, specific and rapid detection of hepatitis B virus (HBV). The biosensors developed based on different techniques, including optical methods (e.g., surface plasmon resonance), acoustic wave technologies (e.g., quartz crystal microbalance), electrochemistry (amperometry, voltammetry and impedance) and novel nanotechnology, are also discussed.
doi:10.3748/wjg.v20.i35.12485
PMCID: PMC4168081  PMID: 25253948
Biosensor; Hepatitis B virus; Diagnosis; Detection; Quartz crystal microbalance
11.  Citalopram Enhances Neurovascular Regeneration and Sensorimotor Functional Recovery after Ischemic Stroke in Mice 
Neuroscience  2013;247:1-11.
Recent clinical trials have demonstrated that treatment with selective serotonin reuptake inhibitors (SSRIs) after stroke enhances motor functional recovery; however, the underlying mechanisms remain to be further elucidated. We hypothesized that daily administration of the clinical drug citalopram would produce these functional benefits via enhancing neurovascular repair in the ischemic peri-infarct region. To test this hypothesis, focal ischemic stroke was induced in male C57/B6 mice by permanent ligation of distal branches of the middle cerebral artery to the barrel cortex and 7-min occlusion of the bilateral common carotid arteries. Citalopram (10 mg/kg, i.p.) was injected 24 hrs after stroke and daily thereafter. To label proliferating cells, bromo-deoxyuridine was injected daily beginning 3 days after stroke. Immunohistochemical and functional assays were performed to elucidate citalopram-mediated cellular and sensorimotor changes after stroke. Citalopram treatment had no significant effect on infarct formation or edema 3 days after stroke; however, citalopram-treated mice had better functional recovery than saline-treated controls 3 and 14 days after stroke in the adhesive removal test. Increased expression of brain derived neurotrophic factor was detected in the peri-infarct region 7 days after stroke in citalopram-treated animals. The number of proliferating neural progenitor cells and the distance of neuroblast migration from the sub-ventricular zone towards the ischemic cortex were significantly greater in citalopram-treated mice at 7 days after stroke. Immunohistochemical staining and co-localization analysis showed that citalopram-treated animals generated more new neurons and microvessels in the peri-infarct region 21 and 28 days after stroke. Taken together, these results suggest that citalopram promotes post-stroke sensorimotor recovery likely via enhancing neurogenesis, neural cell migration and the microvessel support in the peri-infarct region of the ischemic brain.
doi:10.1016/j.neuroscience.2013.04.011
PMCID: PMC3916088  PMID: 23590907
Ischemic stroke; SSRI; Citalopram; Neurogenesis; Angiogenesis
12.  Does practice size matter? Review of effects on quality of care in primary care 
The British Journal of General Practice  2013;63(614):e604-e610.
Background
There is a trend towards consolidating smaller primary care practices into larger practices worldwide. However, the effects of practice size on quality of care remain unclear.
Aim
This review aims to systematically appraise the effects of practice size on the quality of care in primary care.
Design and setting
A systematic review and narrative synthesis of studies examining the relationship between practice size and quality of care in primary care.
Method
Quantitative studies that focused on primary care practices or practitioners were identified through PubMed, CINAHL, Embase, Cochrane Library, CRD databases, ProQuest dissertations and theses, conference proceedings, and MedNar databases, as well as the reference lists of included studies. Independent variables were team or list size; outcome variables were measures of clinical processes, clinical outcomes, or patient-reported outcomes. A narrative synthesis of the results was conducted.
Results
The database search yielded 371 articles, of which 34 underwent quality assessment, and 17 articles (13 cross-sectional studies) were included. Ten studies examined the association of practice size and clinical processes, but only five found associations of larger practices with selected process measures such as higher specialist referral rates, better adherence to guidelines, higher mammography rates, and better monitoring of haemoglobin A1c. There were mixed results for cytology and pneumococcal coverage. Only one of two studies on clinical outcomes found an effect of larger practices on lower random haemoglobin A1 value. Of the three studies on patient-reported outcomes, smaller practices were consistently found to be associated with satisfaction with access, but evidence was inconsistent for other patient-reported outcomes evaluated.
Conclusion
There is limited evidence to support an association between practice size and quality of care in primary care.
doi:10.3399/bjgp13X671588
PMCID: PMC3750799  PMID: 23998840
health facility size; primary care; quality of health care
13.  Risk stratification and rapid geriatric screening in an emergency department – a quasi-randomised controlled trial 
BMC Geriatrics  2014;14:98.
Background
To determine if risk stratification followed by rapid geriatric screening in an emergency department (ED) reduced functional decline, ED reattendance and hospitalisation.
Method
This was a quasi-randomised controlled trial. Patients were randomised by the last digit of their national registration identity card (NRIC). Odd number controls received standard ED care; even number patients received geriatric screening, followed by intervention and/or onward referrals. Patients were followed up for 12 months.
Results
There were 500 and 280 patients in the control and intervention groups. The intervention group had higher Triage Risk Screening Tool (TRST) scores (34.3% vs 25.4% TRST ≥3, p = 0.01) and lower baseline Instrumental Activity of Daily Living (IADL) scores (22.84 vs 24.18, p < 0.01). 82.9% of the intervention group had unmet needs; 62.1% accepted our interventions. Common positive findings were fall risk (65.0%), vision (61.4%), and footwear (58.2%). 28.2% were referred to a geriatric clinic and 11.8% were admitted. 425 (85.0%) controls and 234 (83.6%) in the intervention group completed their follow-up. After adjusting for TRST and baseline IADL, the intervention group had significant preservation in function (Basic ADL -0.99 vs -0.24, p < 0.01; IADL -2.57 vs +0.45, p < 0.01) at 12 months. The reduction in ED reattendance (OR0.75, CI 0.55-1.03, p = 0.07) and hospitalization (OR0.77, CI0.57-1.04, p = 0.09) were not significant, however the real difference would have been wider as 21.2% of the control group received geriatric screening at the request of the ED doctor. A major limitation was that a large proportion of patients who were randomized to the intervention group either refused (18.8%) or left the ED before being approached (32.0%). These two groups were not followed up, and hence were excluded in our analysis.
Conclusion
Risk stratification and focused geriatric screening in ED resulted in significant preservation of patients’ function at 12 months.
Trial registration
National Healthcare Group (NHG) Domain Specific Review Board (DSRB) C/09/023. Registered 5th March 2009.
doi:10.1186/1471-2318-14-98
PMCID: PMC4161268  PMID: 25178312
Geriatric screening; Elderly; Emergency department; Risk stratification
14.  Attribute Reduction Based on Property Pictorial Diagram 
The Scientific World Journal  2014;2014:109706.
This paper mainly studies attribute reduction which keeps the lattice structure in formal contexts based on the property pictorial diagram. Firstly, the property pictorial diagram of a formal context is defined. Based on such diagram, an attribute reduction approach of concept lattice is achieved. Then, through the relation between an original formal context and its complementary context, an attribute reduct of complementary context concept lattice is obtained, which is also based on the property pictorial diagram of the original formal context. Finally, attribute reducts in property oriented concept lattice and object oriented concept lattice can be acquired by the relations of attribute reduction between these two lattices and concept lattice of complementary context. In addition, a detailed illustrative example is presented.
doi:10.1155/2014/109706
PMCID: PMC4163284  PMID: 25247200
15.  RAD51 potentiates synergistic effects of chemotherapy with PCI-24781 and cis-diamminedichloroplatinum on gastric cancer 
World Journal of Gastroenterology : WJG  2014;20(29):10094-10107.
AIM: To explore the efficacy of PCI-24781, a broad-spectrum, hydroxamic acid-derived histone deacetylase inhibitor, in the treatment of gastric cancer (GC).
METHODS: With or without treatment of PCI-24781 and/or cis-diamminedichloroplatinum (CDDP), GC cell lines were subjected to functional analysis, including cell growth, apoptosis and clonogenic assays. Chromatin immunoprecipitation and luciferase reporter assays were used to determine the interacting molecules and the activity of the enzyme. An in vivo study was carried out in GC xenograft mice. Cell culture-based assays were represented as mean ± SD. ANOVA tests were used to assess differences across groups. All pairwise comparisons between tumor weights among treatment groups were made using the Tukey-Kramer method for multiple comparison adjustment to control experimental-wise type I error rates. Significance was set at P < 0.05.
RESULTS: PCI-24781 significantly reduced the growth of the GC cells, enhanced cell apoptosis and suppressed clonogenicity, and these effects synergized with the effects of CDDP. PCI-24781 modulated the cell cycle and significantly reduced the expression of RAD51, which is related to homologous recombination. Depletion of RAD51 augmented the biological functions of PCI-24781, CDDP and the combination treatment, whereas overexpressing RAD51 had the opposite effects. Increased binding of the transcription suppressor E2F4 on the RAD51 promoter appeared to play a major role in these processes. Furthermore, significant suppression of tumor growth and weight in vivo was obtained following PCI-24781 treatment, which synergized with the anticancer effect of CDDP.
CONCLUSION: These data suggest that RAD51 potentiates the synergistic effects of chemotherapy with PCI-24781 and CDDP on GC.
doi:10.3748/wjg.v20.i29.10094
PMCID: PMC4123338  PMID: 25110436
Chemotherapy; Combination; Gastric cancer; Histone deacetylase inhibitor; Homologous recombination
16.  A Novel Concept Acquisition Approach Based on Formal Contexts 
The Scientific World Journal  2014;2014:136324.
As an important tool for data analysis and knowledge processing, formal concept analysis (FCA) has been applied to many fields. In this paper, we introduce a new method to find all formal concepts based on formal contexts. The amount of intents calculation is reduced by the method. And the corresponding algorithm of our approach is proposed. The main theorems and the corresponding algorithm are examined by examples, respectively. At last, several real-life databases are analyzed to demonstrate the application of the proposed approach. Experimental results show that the proposed approach is simple and effective.
doi:10.1155/2014/136324
PMCID: PMC4132318  PMID: 25147834
17.  Celastrol may have an anti-atherosclerosis effect in a rabbit experimental carotid atherosclerosis model 
Background: Celastrol may have an anti-atherosclerosis effect. This study aimed to investigate if celastrol had an anti-AS effect using a rabbit experimental carotid atherosclerosis model. Methods: Forty male Japanese white rabbits were divided into the sham group (normal diet), the model group (high fat diet), the group treated with celastrol (high fat diet) and the group treated with atorvastatin (high fat diet) randomly. The rabbits fed a high fat diet underwent balloon injury of the right common carotid artery and were treated with dimethyl sulfoxide (DMSO) (the model group, 3.5 ml/kg/d), celastrol and its dissolvent DMSO (the celastrol group, 1 mg/kg/d and 3.5 ml/kg/d) and atorvastatin and its dissolvent DMSO (the atorvastatin group, 2.5 mg/kg/d and 3.5 ml/kg/d) for 12 weeks by gavage. Results: The ratio of the plaque area and the arterial wall cross-section area in the celastrol group was significantly less than the model group (P < 0.001), and there was no significant difference compared with the atorvastatin group. The serum level of LDL-C of the celastrol group was significantly lower than the model group (P = 0.014), and there was no significant difference compared with the atorvastatin group. The expression of VEGF in the celastrol group was significantly less compared with the model group (P = 0.014), whereas the expression of VEGF in the atorvastatin group and the model group showed no significant differences. Conclusion: Our findings suggest that celastrol effectively reduced the plaque ratio, decreased the serum levels of LDL and downregulated the expression of VEGF, suggesting an anti-AS effect of celastrol.
PMCID: PMC4132129  PMID: 25126165
Celastrol; carotid artery disease; balloon injury; low-density lipoprotein cholesterol; vascular endothelial growth factor
18.  Hyperphosphatemia is a combined function of high serum PTH and high dietary protein intake in dialysis patients 
Kidney International Supplements  2013;3(5):462-468.
Elevated serum phosphorus is associated with higher death risk in hemodialysis patients. Previous studies have suggested that both higher serum parathyroid hormone (PTH) level and higher dietary protein intake may contribute to higher serum phosphorus levels. However, it is not well known how these two factors simultaneously contribute to the combined risk of hyperphosphatemia in real patient-care scenarios. We hypothesized that the likelihood of hyperphosphatemia increases across higher serum PTH and higher normalized protein catabolic rate (nPCR) levels, a surrogate of protein intake. Over an 8-year period (July 2001–June 2009), we identified 69,355 maintenance hemodialysis patients with PTH, nPCR, and phosphorus data in a large dialysis provider. Logistic regression models were examined to assess the association between likelihood of hyperphosphatemia (serum phosphorus >5.5 mg/dl) and serum PTH and nPCR increments. Patients were 61±15 years old and included 46% women, 33% blacks, and 57% diabetics. Both higher serum PTH level and higher protein intake were associated with higher risk of hyperphosphatemia in dialysis patients. Compared with patients with PTH level 150–<300 pg/ml and nPCR level 1.0–<1.2 g/kg/day, patients with iPTH>600 pg/ml and nPCR>1.2 g/kg/day had a threefold higher risk of hyperphosphatemia (OR: 3.17, 95% CI: 2.69–3.75). Hyperphosphatemia is associated with both higher dietary protein intake and higher serum PTH level in maintenance hemodialysis patients. Worsening or resistant hyperphosphatemia may be an under-appreciated consequence of secondary hyperparathyroidism independent of dietary phosphorus load. Management of hyperphosphatemia should include diligent correction of hyper-parathyroidism while maintaining adequate intake of high protein foods with low phosphorus content.
doi:10.1038/kisup.2013.96
PMCID: PMC4089743  PMID: 25019031
chronic kidney disease (CKD); hemodialysis; hyperphosphatemia; parathyroid hormone; phosphorus; protein intake
19.  Preparation of clinical-grade 89Zr-panitumumab as a positron emission tomography biomarker for evaluating epidermal growth factor receptor-targeted therapy 
Panitumumab is a fully human monoclonal antibody approved for the treatment of epidermal growth factor receptor (EGFR) positive colorectal cancer. Recently, panitumumab has been radiolabeled with 89Zr and evaluated for its potential to be used as immuno-positron emission tomography (PET) probe for EGFR positive cancers. Interesting preclinical results published by several groups of researchers have prompted us to develop a robust procedure for producing clinical-grade 89Zr-panitumumab as an immuno-PET probe to evaluate EGFR-targeted therapy. In this process, clinical-grade panitumumab is bio-conjugated with desferrioxamine chelate and subsequently radiolabeled with 89Zr resulting in high radiochemical yield (>70%, n=3) and purity (>98%, n=3). All quality control (QC) tests were performed according to United States Pharmacopeia specifications. QC tests showed that 89Zr-panitumumab met all specifications for human injection. Herein, we describe a step-by-step method for the facile synthesis and QC tests of 89Zr-panitumumab for medical use. The entire process of bioconjugation, radiolabeling, and all QC tests will take about 5h. Because the synthesis is fully manual, two rapid, in-process QC tests have been introduced to make the procedure robust and error free.
doi:10.1002/jlcr.3134
PMCID: PMC3982615  PMID: 24448743
89Zr-immuno-PET; Clinical production; Panitumumab; PET imaging
20.  BRAF Mutations in Patients with Non-Small Cell Lung Cancer: A Systematic Review and Meta-Analysis 
PLoS ONE  2014;9(6):e101354.
Background
BRAF mutations have been well described in non-small cell lung cancer (NSCLC) for several years, but the clinical features of patients harboring BRAF mutations are still not well described. We performed a meta-analysis to identify common clinical features in NSCLC patients carrying BRAF mutations.
Methods
We identified clinical studies that examined the association between BRAF mutations and features of NSCLC within PubMed, Embase and ISI Science Citation Index database up to October 2013. The effect size of clinical features was estimated by odds ratios (ORs) with 95% confidence interval (CI) for each study, using a fixed-effects or random-effects model.
Results
Ten studies with a total of 5599 NSCLC patients were included. There was a 3% (170/5599) BRAF mutation rate. BRAF mutations in NSCLC were significantly associated with adenocarcinomas (ADCs) (compared with non-ADCs, OR = 4.96, 95%CI = 2.29–10.75). There were no significant differences in gender, smoking and stage in patients with and without BRAF mutations. The BRAFV600E mutation was more frequent in women than non-BRAFV600E mutations (OR = 0.27, 95%CI = 0.12–0.59), and was closely related to never smokers (OR = 0.14, 95%CI = 0.05–0.42).
Conclusions
These findings have important implications for the prediction of the NSCLC sub-types more accurately combined with other genetic changes.
doi:10.1371/journal.pone.0101354
PMCID: PMC4076330  PMID: 24979348
21.  Cell based therapies for ischemic stroke: From basic science to bedside 
Progress in neurobiology  2013;115:92-115.
Cell therapy is emerging as a viable therapy to restore neurological function after stroke. Many types of stem/progenitor cells from different sources have been explored for their feasibility and efficacy for the treatment of stroke. Transplanted cells not only have the potential to replace the lost circuitry, but also produce growth and trophic factors, or stimulate the release of such factors from host brain cells, thereby enhancing endogenous brain repair processes. Although stem/progenitor cells have shown a promising role in ischemic stroke in experimental studies as well as initial clinical pilot studies, cellular therapy is still at an early stage in humans. Many critical issues need to be addressed including the therapeutic time window, cell type selection, delivery route, and in vivo monitoring of their migration pattern. This review attempts to provide a comprehensive synopsis of preclinical evidence and clinical experience of various donor cell types, their restorative mechanisms, delivery routes, imaging strategies, future prospects and challenges for translating cell therapies as a neurorestorative regimen in clinical applications.
doi:10.1016/j.pneurobio.2013.11.007
PMCID: PMC4038267  PMID: 24333397
Stem cells; Cell-based therapies; Ischemic stroke; Neurorestoration
22.  Sodium-dependent phosphate cotransporters and phosphate-induced calcification of vascular smooth muscle cells: Redundant roles for PiT-1 and PiT-2 
Objective
Elevated serum phosphate has emerged as a major risk factor for vascular calcification. The sodium-dependent phosphate cotransporter, PiT-1, was previously shown to be required for phosphate-induced osteogenic differentiation and calcification of cultured human VSMCs, but its importance in vascular calcification in vivo, as well as the potential role of its homologue, PiT-2, have not been determined. We investigated the in vivo requirement for PiT-1 in vascular calcification using a mouse model of chronic kidney disease, and the potential compensatory role of PiT-2 using in vitro knockdown and over-expression strategies.
Approach and Results
Mice with targeted deletion of PiT-1 in VSMCs were generated (PiT-1Δsm). PiT-1 mRNA levels were undetectable whereas PiT-2 mRNA levels were increased 2 fold in the vascular aortic media of PiT-1Δsm compared to PiT-1flox/flox control. When arterial medial calcification was induced in PiT-1Δsm and PiT-1flox/flox by chronic kidney disease followed by dietary phosphate loading, the degree of aortic calcification was not different between genotypes, suggesting compensation by PiT-2. Consistent with this possibility, VSMCs isolated from PiT-1Δsm mice had no PiT-1 mRNA expression, increased PiT-2 mRNA levels, and no difference in sodium-dependent phosphate uptake or phosphate-induced matrix calcification compared to PiT-1flox/flox VSMCs. Knockdown of PiT-2 decreased phosphate uptake and phosphate-induced calcification of PiT-1Δsm VSMCs. Furthermore, over-expression of PiT-2 restored these parameters in human PiT-1-deficient VSMCs.
Conclusions
PiT-2 can mediate phosphate uptake and calcification of VSMCs in the absence of PiT-1. Mechanistically, PiT-1 and PiT-2 appear to serve redundant roles in phosphate-induced calcification of vascular smooth muscle cells.
doi:10.1161/ATVBAHA.113.302249
PMCID: PMC4009978  PMID: 23968976
PiT-1; PiT-2; phosphate; vascular smooth muscle cell; vascular calcification
23.  Zirconium-89 Labeled Panitumumab: a Potential Immuno-PET Probe for HER1-Expressing Carcinomas 
Nuclear medicine and biology  2013;40(4):451-457.
Introduction
Anti-HER1 monoclonal antibody (mAb), panitumumab (Vectibix®) is a fully human mAb approved by the FDA for the treatment of epidermal growth factor receptor (EGFR, HER1)-expressing colorectal cancers. By combining the targeted specificity of panitumumab with the quantitative in vivo imaging capabilities of PET, we evaluated the potential of 89Zr-DFO-panitumumab PET/CT imaging and performed non-invasive, in vivo imaging of HER1 expression and estimated human dosimetry.
Methods
Panitumumab was radiolabeled with 89Zrusing a derivative of desferrioxamine (DFO-Bz-NCS) and with 111In using CHX-A″ DTPA as bifunctional chelators. Comparative biodistribution/dosimetry of both radiotracers was performed in non-tumor bearing athymic nude mice (n= 2 females and n=2 males) over 1-week following i.v. injection of either using 89Zr-DFO-panitumumab or 111In-CHX-A″-DTPA-panitumumab. Micro-PET/CT imaging of female athymic nude mice bearing human breast cancer tumors (n=5 per tumor group) with variable HER1-expression very low (BT-474), moderate (MDA-MB-231), and very high (MDA-MB-468) was performed at over 1 week following i.v. injection of 89Zr-DFO-panitumumab.
Results
Radiochemical yield and purity of 89Zr-Panitumumab was > 70% and > 98% respectively with specific activity 150 ± 10 MBq/mg of panitumumab in a ~ 4 hr synthesis time. Biodistribution of 111In-CHX-A″ DTPA -panitumumab and 89Zr-DFO-panitumumab in athymic non-tumor bearing nude mice displayed similar percent injected dose per gram of tissue with prominent accumulation of both tracers in the lymph nodes, a known clearance mechanism of panitumumab. Also exhibited was prolonged blood pool with no evidence of targeted accumulation in any organ. Human radiation dose estimates showed similar biodistributions with estimated human effective doses of 0.578 and 0.183 mSv/MBq for 89Zr-DFO-panitumumab and 111In-CHX-A″-DTPA –panitumumab, respectively. Given the potential quantitative and image quality advantages of PET, imaging of tumor bearing mice was only performed using 89Zr-DFO-panitumumab. Immuno-PET imaging of 89Zr-DFO-panitumumab in mice bearing breast cancer xenograft tumors with variable HER1 expression showed high tumor uptake (SUV > 7) in the MDA-MB-468 high HER1-expressing mice and a strong correlation between HER1-expression level and tumor uptake (R2= 0.857, p<0.001).
Conclusions
89Zr-DFO-panitumumab can prepared with high radiochemical purity and specific activity. 89Zr-DFO-panitumumab microPET/CT showed uptake corresponding to HER-1 expression. Due to poor clearance, initial dosimetry estimates suggest that only a low dose 89Zr-DFO-panitumumab shows favorable human dosimetry; however due to high tumor uptake, the use of 89Zr-DFO-panitumumab is expected to be clinically feasible.
doi:10.1016/j.nucmedbio.2013.01.007
PMCID: PMC3637856  PMID: 23454247
24.  Effect of Back Massage Intervention on Anxiety, Comfort, and Physiologic Responses in Patients with Congestive Heart Failure 
Abstract
Background
Patients suffering from congestive heart failure (CHF) frequently feel physical suffering and anxiety.
Objectives
The researchers investigated whether back massage could reduce anxiety, discomfort, and physical suffering in patients with CHF. The effects of gender and severity-dependent response of back massage on anxiety and discomfort in patients were also analyzed.
Design
The study used a quasi-experimental design with one group pretest and posttest.
Participants
Sixty-four participants were recruited in southern Taiwan.
Outcome measures
The modified State Anxiety Inventory, the discomfort Visual Analogue Scale, electronic blood pressure (BP) gauges, stethoscopes and the pulse oximetry were used in this study.
Results
The participants' systolic BP (F (3, 189)=18.91, p<0.01), diastolic BP (F (3, 189)=13.40, p<0.01), heart rate (F (3, 189)=26.28, p<0.01), and respiratory rates (F (3, 189)=5.77, p<0.01) were significantly decreased after back massage. Oxygen saturation levels showed significant increases (F (3, 189)=42.82, p<0.01). Male participants revealed a more significant reduction in anxiety than the female participants (F (1, 50)=7.27, p=0.01). Those with more severe heart failure and greater levels of anxiety (F (2, 61)=4.31, p=0.02) and systolic BP (F (2, 61)=3.86, p=0.03) demonstrated significantly greater responses to back massage.
Conclusions
Back massage significantly reduced anxiety in the study population. Systolic BP decreased to a greater degree in the male participants, particularly in those with severe heart failure and greater levels of anxiety and higher systolic BP. This study was conducted without a control group. Randomized clinical trials are needed to validate the effectiveness of back massage on patients with CHF.
doi:10.1089/acm.2011.0873
PMCID: PMC3651680  PMID: 23186129
25.  RNAi silencing of the SoxE gene suppresses cell proliferation in silkworm BmN4 cells 
Molecular Biology Reports  2014;41(7):4769-4781.
The transcription factor SoxE is mainly expressed in the gonad and involved in the regulation of gonad development and sex determination in animals. Here, we used the silkworm ovary-derived BmN4-SID1 cell line to survey the roles of the silkworm SoxE protein (BmSoxE) and predict its candidate binding targets. RNAi-mediated silencing of BmSoxE expression suppressed cell proliferation in BmN4-SID1 cells. A further cell cycle analysis revealed that this inhibition of cell proliferation was largely due to cell cycle arrest in G1 phase when BmSoxE expression was blocked in BmN4-SID1 cells. Genome-wide microarray expression analyses demonstrated that the expression levels of a set of genes were significantly altered following BmSoxE RNAi. More than half of these genes contained conserved binding sites for HMG box domain of the Sox proteins and were predicted to be candidate binding targets for BmSoxE. Importantly, some of the candidate targets may be associated with the effect of BmSoxE on cell proliferation. Several candidate target genes showed gonad-specific expression in silkworm larvae. Taken together, these data demonstrate that BmSoxE is required for cell proliferation in silkworm BmN4-SID1 cells and provide valuable information for further investigations of the molecular control exerted by the BmSoxE protein over cell proliferation and gonad development in the silkworm.
Electronic supplementary material
The online version of this article (doi:10.1007/s11033-014-3348-6) contains supplementary material, which is available to authorized users.
doi:10.1007/s11033-014-3348-6
PMCID: PMC4066180  PMID: 24723138
Silkworm; SoxE; RNAi; Cell proliferation; Target

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