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1.  Physical Activity Increases Gains in and Prevents Loss of Physical Function: Results From the Lifestyle Interventions and Independence for Elders Pilot Study 
Background.
Physical activity (PA) appears to have a positive effect on physical function, however, studies have not examined multiple indices of physical function jointly nor have they conceptualized physical functioning as a state rather than a trait.
Methods.
About 424 men and women aged 70–89 were randomly assigned to complete a PA or a successful aging (SA) education program. Balance, gait speed, chair stand performance, grip strength, and time to complete the 400-m walk were assessed at baseline and at 6 and 12 months. Using hidden Markov model, empiric states of physical functioning were derived based on these performance measures of balance, strength, and mobility. Rates of gain and loss in physical function were compared between PA and SA.
Results.
Eight states of disability were identified and condensed into four clinically relevant states. State 1 represented mild disability with physical functioning, states 2 and 3 were considered intermediate states of disability, and state 4 severe disability. About 30.1% of all participants changed states at 6 months, 24.1% at 12 months, and 11.0% at both time points. The PA group was more likely to regain or sustain functioning and less likely to lose functioning when compared with SA. For example, PA participants were 20% more likely than the SA participants to remain in state 1.
Conclusion.
PA appears to have a favorable effect on the dynamics of physical functioning in older adults.
doi:10.1093/gerona/gls186
PMCID: PMC3593616  PMID: 22987794
Older adults; Physical activity; Randomized controlled trial; Physical functioning; Transitional states.
2.  All-or-none Suppression of B Cell Terminal Differentiation by Environmental Contaminant 2,3,7,8-Tetrachlorodibenzo-p-Dioxin 
Many environmental contaminants can disrupt the adaptive immune response. Exposure to the ubiquitous aryl hydrocarbon receptor (AhR) ligand 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and other agonists suppresses the antibody response. The underlying pathway mechanism by which TCDD alters B cell function is not well understood. The present study investigated the mechanism of AhR-mediated pathways and mode of suppression by which TCDD perturbs terminal differentiation of B cells to plasma cells and thereby impairs antibody production. An integrated approach combining computational pathway modeling and in vitro assays with primary mouse B cells activated by lipopolysaccharide was employed. We demonstrated that suppression of the IgM response by TCDD occurs in an all-or-none (binary) rather than graded mode: i.e., it reduces the number of IgM-secreting cells in a concentration-dependent manner without affecting the IgM content in individual plasma cells. The mathematical model of the gene regulatory circuit underpinning B cell differentiation revealed that two previously identified AhR-regulated pathways, inhibition of signaling protein AP-1 and activation of transcription factor Bach2, could account for the all-or-none mode of suppression. Both pathways disrupt the operation of a bistable-switch circuit that contains transcription factors Bcl6, Prdm1, Pax5, and Bach2 and regulates B cell fate. The model further predicted that by transcriptionally activating Bach2, TCDD might delay B cell differentiation and increase the likelihood of isotype switching, thereby altering the antibody repertoire. In conclusion, the present study revealed the mode and specific pathway mechanisms by which the environmental immunosuppressant TCDD suppresses B cell differentiation.
doi:10.1016/j.taap.2013.01.015
PMCID: PMC3594464  PMID: 23357550
TCDD; AhR; all-or-none; bistable; Bach2
3.  Symptom clusters in patients with head and neck cancer receiving concurrent chemoradiotherapy 
Oral oncology  2012;49(4):360-366.
SUMMARY
Objectives
This study is to identify symptom clusters for head and neck (HNC) patients treated with con-current chemoradiotherapy.
Patients and methods
A secondary data analysis of 684 HNC patients treated on the Radiation Therapy Oncology Group (RTOG) 0129 trial comparing different RT fractionation schedules with concurrent chemotherapy was used to examine clusters. Treatment-related symptoms were measured by clinicians at three time-points during and after chemoradiotherapy using the National Cancer Institute Common Toxicity Criteria v2.0. Exploratory factor analysis was applied to identify symptom clusters, which was further verified by confirmatory factor analysis. Coefficients of congruence and alpha coefficients were employed to examine generalizability of cluster structures over different time-points and in different subgroups.
Results
Two clusters were identified. The HNC specific cluster is composed of radiodermatitis, dysphagia, radiomucositis, dry mouth, pain, taste disturbance, and fatigue. The gastrointestinal (GI) cluster involves nausea, vomiting, and dehydration. With the exception of patients 65 years old or older, diagnosed with larynx cancer, or with stage III cancer, the two clusters were generalizable to different subgroups defined by age, gender, race, education, marital status, history of tobacco use, treatments, primary sites, disease stages, and tube feedings, as well as to the three symptom assessment time-points.
Conclusions
The data provides preliminary support for two stable clusters in patients with HNC. These findings may serve to inform the symptom management in clinical practice. Moreover, the findings necessitate future research to examine the generalizability of identified clusters in the late symptom phase or other treatment modalities, and to understand the underlying biological mechanism.
doi:10.1016/j.oraloncology.2012.10.004
PMCID: PMC3924732  PMID: 23168337
Head and neck neoplasms; Chemoradiotherapy; Symptom clusters; Symptoms
4.  AβPP-Selective BACE Inhibitors (ASBI): Novel Class of Therapeutic Agents for Alzheimer’s Disease 
A systematic approach was used to identify AβPP-selective BACE inhibitors (ASBI) and to evaluate their in vivo ability to modulate AβPP processing selectively. We identified a bioflavonoid nutritional supplement as a molecular lead that acts as an ASBI in cell models, and show that increasing brain levels of this bioflavonoid through a pro-drug approach leads to reduction of Aβ42 in an Alzheimer’s disease mouse model. ASBIs represent a novel class of candidate therapeutic agents for Alzheimer’s disease.
doi:10.3233/JAD-130578
PMCID: PMC3971881  PMID: 23948888
Alzheimer’s disease; AβPP; ASBI; galangin; pro-drug; rutin
5.  A Phosphorylation Tag for Uranyl Mediated Protein Purification and Photo Assisted Tag Removal 
PLoS ONE  2014;9(3):e91138.
Most protein purification procedures include an affinity tag fused to either the N or C-terminal end of the protein of interest as well as a procedure for tag removal. Tag removal is not straightforward and especially tag removal from the C-terminal end is a challenge due to the characteristics of enzymes available for this purpose. In the present study, we demonstrate the utility of the divalent uranyl ion in a new procedure for protein purification and tag removal. By employment of a GFP (green florescence protein) recombinant protein we show that uranyl binding to a phosphorylated C-terminal tag enables target protein purification from an E. coli extract by immobilized uranyl affinity chromatography. Subsequently, the tag can be efficiently removed by UV-irradiation assisted uranyl photocleavage. We therefore suggest that the divalent uranyl ion (UO22+) may provide a dual function in protein purification and subsequent C-terminal tag removal procedures.
doi:10.1371/journal.pone.0091138
PMCID: PMC3945016  PMID: 24599526
6.  c-Jun N-terminal kinase activation contributes to reduced connexin43 and development of atrial arrhythmias 
Cardiovascular Research  2012;97(3):589-597.
Aims
c-Jun N-terminal kinase (JNK) activation is implicated in cardiovascular diseases and ageing, which are linked to enhanced propensity to atrial fibrillation (AF). However, the contribution of JNK to AF remains unknown. Thus, we assessed the role of JNK in remodelling of gap junction connexin43 (Cx43) and development of AF.
Methods and results
AF induction, optical mapping, and biochemical assays were performed in young and aged New Zealand white rabbit left atria (LA) and cultured HL-1 atrial cells. In aged rabbit LA, pacing-induced atrial arrhythmias were dramatically increased and conduction velocity (CV) was significantly slower compared with young controls. Aged rabbit LA contained 120% more activated JNK and 54% less Cx43 than young LA. Young rabbits treated with JNK activator anisomycin also exhibited increased pacing-induced atrial arrhythmias and reduced Cx43 (by 34%), similar to that found in aged LA. In HL-1 cell cultures, anisomycin treatment for 16 h led to 42% reduction in Cx43, 24% reduction in CV, and an increased incidence of irregular rapid spontaneous activities. These effects were prevented by a specific JNK inhibitor, SP600125. Moreover, a 63% reduction in Cx43 after anisomycin treatment for 24 h led to further slowed CV (by 41%) along with dramatically increased irregular rapid spontaneous activity and highly discontinuous conduction. These JNK-induced functional abnormalities were completely reversed by overexpressed exogenous wild-type Cx43, but not by inactive Cx43.
Conclusion
JNK activation contributes to Cx43 reductions that promote development of AF. Modulation of JNK may be a potential novel therapeutic approach to prevent and treat AF.
doi:10.1093/cvr/cvs366
PMCID: PMC3567788  PMID: 23241357
Atrial fibrillation; JNK; Gap junction; Cell–cell communication
7.  Long-Term Results of RTOG 91-11: A Comparison of Three Nonsurgical Treatment Strategies to Preserve the Larynx in Patients With Locally Advanced Larynx Cancer 
Journal of Clinical Oncology  2012;31(7):845-852.
Purpose
To report the long-term results of the Intergroup Radiation Therapy Oncology Group 91-11 study evaluating the contribution of chemotherapy added to radiation therapy (RT) for larynx preservation.
Patients and Methods
Patients with stage III or IV glottic or supraglottic squamous cell cancer were randomly assigned to induction cisplatin/fluorouracil (PF) followed by RT (control arm), concomitant cisplatin/RT, or RT alone. The composite end point of laryngectomy-free survival (LFS) was the primary end point.
Results
Five hundred twenty patients were analyzed. Median follow-up for surviving patients is 10.8 years. Both chemotherapy regimens significantly improved LFS compared with RT alone (induction chemotherapy v RT alone: hazard ratio [HR], 0.75; 95% CI, 0.59 to 0.95; P = .02; concomitant chemotherapy v RT alone: HR, 0.78; 95% CI, 0.78 to 0.98; P = .03). Overall survival did not differ significantly, although there was a possibility of worse outcome with concomitant relative to induction chemotherapy (HR, 1.25; 95% CI, 0.98 to 1.61; P = .08). Concomitant cisplatin/RT significantly improved the larynx preservation rate over induction PF followed by RT (HR, 0.58; 95% CI, 0.37 to 0.89; P = .0050) and over RT alone (P < .001), whereas induction PF followed by RT was not better than treatment with RT alone (HR, 1.26; 95% CI, 0.88 to 1.82; P = .35). No difference in late effects was detected, but deaths not attributed to larynx cancer or treatment were higher with concomitant chemotherapy (30.8% v 20.8% with induction chemotherapy and 16.9% with RT alone).
Conclusion
These 10-year results show that induction PF followed by RT and concomitant cisplatin/RT show similar efficacy for the composite end point of LFS. Locoregional control and larynx preservation were significantly improved with concomitant cisplatin/RT compared with the induction arm or RT alone. New strategies that improve organ preservation and function with less morbidity are needed.
doi:10.1200/JCO.2012.43.6097
PMCID: PMC3577950  PMID: 23182993
8.  Adipose Deficiency of Nrf2 in ob/ob Mice Results in Severe Metabolic Syndrome 
Diabetes  2013;62(3):845-854.
Nuclear factor E2–related factor 2 (Nrf2) is a transcription factor that functions as a master regulator of the cellular adaptive response to oxidative stress. Our previous studies showed that Nrf2 plays a critical role in adipogenesis by regulating expression of CCAAT/enhancer-binding protein β and peroxisome proliferator–activated receptor γ. To determine the role of Nrf2 in the development of obesity and associated metabolic disorders, the incidence of metabolic syndrome was assessed in whole-body or adipocyte-specific Nrf2-knockout mice on a leptin-deficient ob/ob background, a model with an extremely positive energy balance. On the ob/ob background, ablation of Nrf2, globally or specifically in adipocytes, led to reduced white adipose tissue (WAT) mass, but resulted in an even more severe metabolic syndrome with aggravated insulin resistance, hyperglycemia, and hypertriglyceridemia. Compared with wild-type mice, WAT of ob/ob mice expressed substantially higher levels of many genes related to antioxidant response, inflammation, adipogenesis, lipogenesis, glucose uptake, and lipid transport. Absence of Nrf2 in WAT resulted in reduced expression of most of these factors at mRNA or protein levels. Our findings support a novel role for Nrf2 in regulating adipose development and function, by which Nrf2 controls the capacity of WAT expansion and insulin sensitivity and maintains glucose and lipid homeostasis.
doi:10.2337/db12-0584
PMCID: PMC3581189  PMID: 23238296
9.  Fluoroquinolone-Resistant Haemophilus parasuis Isolates Exhibit More Putative Virulence Factors than Their Susceptible Counterparts 
Journal of Clinical Microbiology  2013;51(9):3130-3131.
The prevalence of 23 putative virulence factors among fluoroquinolone-susceptible and -resistant Haemophilus parasuis isolates was analyzed. Putative hemolysin precursor, fimbrial assembly chaperone, and type I site-specific restriction modification system R subunit genes were more prevalent among fluoroquinolone-resistant H. parasuis isolates than among fluoroquinolone-susceptible H. parasuis isolates. Fluoroquinolone resistance may be associated with an increase in the presence of some virulence factors.
doi:10.1128/JCM.01102-13
PMCID: PMC3754668  PMID: 23784118
10.  Discovery of a Series of Thiazole Derivatives as Novel Inhibitors of Metastatic Cancer Cell Migration and Invasion 
ACS medicinal chemistry letters  2013;4(2):191-196.
Effective inhibitors of cancer cell migration and invasion can potentially lead to clinical applications as therapy to block tumor metastasis, the primary cause of death in cancer patients. To this end we have designed and synthesized a series of thiazole derivatives that showed potent efficacy against cell migration and invasion in metastatic cancer cells. The most effective compound, 5k, was found to have an IC50 value of 176 nM in the dose-dependent transwell migration assays in MDA-MB-231cells. At the dose of 10 μM, 5k also blocked about 80% of migration in HeLa and A549 cells and 60% of invasion of MDA-MB-231 cells. Importantly, the majority of the derivatives exhibited no apparent cytotoxicity in the clonogenic assays. The low to negligible inhibition of cell proliferation is a desirable property of these anti-migration derivatives because they hold promise of low toxicity to healthy cells as potential therapeutic agents. Mechanistic studies analyzing the actin cytoskeleton by microscopy demonstrate that compound 5k substantially reduced cellular f-actin, and prevented localization of fascin to actin-rich membrane protrusions. These results suggest that the anti-migration activity may result from impaired actin structures in protrusions that are necessary to drive migration.
doi:10.1021/ml300322n
PMCID: PMC3601768  PMID: 23526571
Thiazole derivatives; synthesis; anti-migration; anti-invasion; f-actin; fascin
11.  Comparison of Spectral and Image Morphological Analysis for Egg Early Hatching Property Detection Based on Hyperspectral Imaging 
PLoS ONE  2014;9(2):e88659.
The use of non-destructive methods to detect egg hatching properties could increase efficiency in commercial hatcheries by saving space, reducing costs, and ensuring hatching quality. For this purpose, a hyperspectral imaging system was built to detect embryo development and vitality using spectral and morphological information of hatching eggs. A total of 150 green shell eggs were used, and hyperspectral images were collected for every egg on day 0, 1, 2, 3 and 4 of incubation. After imaging, two analysis methods were developed to extract egg hatching characteristic. Firstly, hyperspectral images of samples were evaluated using Principal Component Analysis (PCA) and only one optimal band with 822 nm was selected for extracting spectral characteristics of hatching egg. Secondly, an image segmentation algorithm was applied to isolate the image morphologic characteristics of hatching egg. To investigate the applicability of spectral and image morphological analysis for detecting egg early hatching properties, Learning Vector Quantization neural network (LVQNN) was employed. The experimental results demonstrated that model using image morphological characteristics could achieve better accuracy and generalization than using spectral characteristic parameters, and the discrimination accuracy for eggs with embryo development were 97% at day 3, 100% at day 4. In addition, the recognition results for eggs with weak embryo development reached 81% at day 3, and 92% at day 4. This study suggested that image morphological analysis was a novel application of hyperspectral imaging technology to detect egg early hatching properties.
doi:10.1371/journal.pone.0088659
PMCID: PMC3923798  PMID: 24551130
12.  Homocysteine Level and Risk of Abdominal Aortic Aneurysm: A Meta-Analysis 
PLoS ONE  2014;9(1):e85831.
Objectives
Previous studies have reported inconsistent findings regarding the association between elevated plasma homocysteine (Hcy) levels and abdominal aortic aneurysm (AAA). We investigated this association between Hcy levels in patients with AAA and unaffected controls by conducting a meta-analysis and systematic review.
Methods
We conducted a systematic literature search (up to August 2013) of the PubMed database and Embase. We selected observational studies that evaluated Hcy levels in subjects with AAA compared to unaffected controls. Criteria for inclusion were the assessment of baseline Hcy and risk of AAA as an outcome. The results were presented as odd ratio (OR) and corresponding 95% confidence intervals (CI) comparing AAA patients to the control subjects.
Results
7 studies with 6,445 participants were identified and analyzed. Overall, elevated plasma Hcy was associated with an increased risk of AAA (3.29; 95% CI 1.66–6.51). The pooled adjusted OR from a random effect model of only men participants in the AAA compared with the control group was 2.36 (95% CI 0.63–8.82).
Conclusion
This meta-analysis and systematic review suggested that Hcy significantly increased the risk of AAA.
doi:10.1371/journal.pone.0085831
PMCID: PMC3897527  PMID: 24465733
13.  Development of loop-mediated isothermal amplification assay for specific and rapid detection of differential goat Pox virus and Sheep Pox virus 
BMC Microbiology  2014;14:10.
Background
Capripox viruses are economically important pathogens in goat and sheep producing areas of the world, with specific focus on goat pox virus (GTPV), sheep pox virus (SPPV) and the Lumpy Skin Disease virus (LSDV). Clinically, sheep pox and goat pox have the same symptoms and cannot be distinguished serologically. This presents a real need for a rapid, inexpensive, and easy to operate and maintain genotyping tool to facilitate accurate disease diagnosis and surveillance for better management of Capripox outbreaks.
Results
A LAMP method was developed for the specific differential detection of GTPV and SPPV using three sets of LAMP primers designed on the basis of ITR sequences. Reactions were performed at 62°C for either 45 or 60 min, and specificity confirmed by successful differential detection of several GTPV and SPPV isolates. No cross reactivity with Orf virus, foot-and-mouth disease virus (FMDV), A. marginale Lushi isolate, Mycoplasma mycoides subsp. capri, Chlamydophila psittaci, Theileria ovis, T. luwenshuni, T. uilenbergi or Babesia sp was noted. RFLP-PCR analysis of 135 preserved epidemic materials revealed 48 samples infected with goat pox and 87 infected with sheep pox, with LAMP test results showing a positive detection for all samples. When utilizing GTPV and SPPV genomic DNA, the universal LAMP primers (GSPV) and GTPV LAMP primers displayed a 100% detection rate; while the SPPV LAMP detection rate was 98.8%, consistent with the laboratory tested results.
Conclusions
In summary, the three sets of LAMP primers when combined provide an analytically robust method able to fully distinguish between GTPV and SPPV. The presented LAMP method provides a specific, sensitive and rapid diagnostic tool for the distinction of GTPV and SPPV infections, with the potential to be standardized as a detection method for Capripox viruses in endemic areas.
doi:10.1186/1471-2180-14-10
PMCID: PMC3942189  PMID: 24438089
Goat pox virus (GTPV); Sheep pox virus (SPPV); Inverted terminal repeat (ITR) regions; Loop-mediated isothermal amplification (LAMP); Differential diagnosis
14.  Associations between interleukin-1 gene polymorphisms and sepsis risk: a meta-analysis 
BMC Medical Genetics  2014;15:8.
Background
Previous epidemiological studies have presented conflicting evidence regarding associations between interleukin-1 (IL-1) polymorphisms and sepsis susceptibility. We have performed a meta-analysis to evaluate possible associations between IL-1 polymorphisms and sepsis risk.
Methods
Eligible literature was retrieved from PubMed, Embase and Web of Knowledge databases until Jun 15, 2013. The pooled odds ratio (OR) and 95% confidence interval (CI) were calculated using random-effects model in the overall and subgroup analysis based on ethnicity, sepsis severity and quality score.
Results
Eighteen studies addressing five IL-1 polymorphisms were included in this meta-analysis. For IL-1A-889 (rs1800587) polymorphism, significant association was observed in overall comparison for allelic effect (OR = 1.47, 95% CI = 1.01-2.13, P = 0.04). There were no significant associations between either IL-1B-511 (rs16944) or IL-1B-31 (rs1143627) and sepsis susceptibility in overall or subgroup analyses. For IL-1B + 3594 (rs143634) polymorphism, genotype TT decreased sepsis risk in overall analysis (OR = 0.59, 95% CI = 0.36-0.97, P = 0.04), as well as in Caucasian (OR = 0.57, 95% CI = 0.34-0.95, P = 0.03) and sepsis (OR = 0.55, 95% CI = 0.31-0.97, P = 0.04) subgroup analysis. For IL-1RN VNTR polymorphism, significant association was observed in overall comparison for allelic effect (OR = 1.40, 95% CI = 1.01-1.95, P = 0.04). Furthermore, the effect sizes of IL-1RN VNTR on sepsis risk increased with disease severity (septic shock OR > severe sepsis OR > sepsis OR).
Conclusions
Our meta-analysis indicated that IL-1A-889, IL-1B + 3954 and IL-1RN VNTR might be associated with sepsis susceptibility. However, further studies with larger sample sizes and from homogenous populations would be necessary to validate these findings.
doi:10.1186/1471-2350-15-8
PMCID: PMC3901334  PMID: 24428862
Sepsis; IL-1; Polymorphism; Meta-analysis
15.  Association Between Single-Nucleotide Polymorphisms of BRAF and Papillary Thyroid Carcinoma in a Chinese Population 
Thyroid  2013;23(1):38-44.
Background
Papillary thyroid cancer (PTC) is a common malignancy that frequently harbors a high prevalence of somatic mutations in the oncogenic BRAF gene. As a novel prognostic molecular marker, this gene has drawn much attention in recent years for its potential utility in the risk prognosis and management of PTC. However, the contribution of the germline variants in this gene to PTC remains unclear. The study herein was aimed to investigate the potential association between the inherited BRAF variants and PTC based on a case–control study.
Methods
We selected four single-nucleotide polymorphisms (SNPs) and took a systematic step to interrogate whether these SNPs of BRAF are associated with PTC risk by genotyping these SNPs from 368 patients with PTC and 564 healthy controls.
Results
In comparison of cases and controls for the four SNPs, no differences were observed in the genotypic and allelic frequencies, nor was there evidence of an association between BRAF SNPs and overall risk of PTC. After stratification, however, we found a significantly increased risk of PTC attributed to the SNP variants rs17161747, rs1042179, and rs3748093 for those with a family history of cancer, for smokers, and for both those of age <45 years and nondrinkers, respectively. Further, in the PTC cases, those carrying the rs3748093 variant seemed to be less susceptible to developing lymph node metastases, but more likely to suffer from PTC at an earlier age (<45 years).
Conclusions
These preliminary results may provide evidence for the involvement of the common genetic variants scattered throughout the BRAF oncogene in the prediction of PTC onset and progression. In the future, enlarging the number of samples and performing functional studies in this gene may help to validate whether the association truly exists.
doi:10.1089/thy.2012.0228
PMCID: PMC3539251  PMID: 22973979
16.  MiRNA-199a-3p Regulates C2C12 Myoblast Differentiation through IGF-1/AKT/mTOR Signal Pathway 
MicroRNAs constitute a class of ~22-nucleotide non-coding RNAs. They modulate gene expression by associating with the 3′ untranslated regions (3′ UTRs) of messenger RNAs (mRNAs). Although multiple miRNAs are known to be regulated during myoblast differentiation, their individual roles in muscle development are still not fully understood. In this study, we showed that miR-199a-3p was highly expressed in skeletal muscle and was induced during C2C12 myoblasts differentiation. We also identified and confirmed several genes of the IGF-1/AKT/mTOR signal pathway, including IGF-1, mTOR, and RPS6KA6, as important cellular targets of miR-199a-3p in myoblasts. Overexpression of miR-199a-3p partially blocked C2C12 myoblast differentiation and the activation of AKT/mTOR signal pathway, while interference of miR-199a-3p by antisense oligonucleotides promoted C2C12 differentiation and myotube hypertrophy. Thus, our studies have established miR-199a-3p as a potential regulator of myogenesis through the suppression of IGF-1/AKT/mTOR signal pathway.
doi:10.3390/ijms15010296
PMCID: PMC3907811  PMID: 24378853
miR-199a-3p; C2C12; muscle; myogenic differentiation
17.  An Efficient Method of Key-Frame Extraction Based on a Cluster Algorithm 
This paper proposes a novel method of key-frame extraction for use with motion capture data. This method is based on an unsupervised cluster algorithm. First, the motion sequence is clustered into two classes by the similarity distance of the adjacent frames so that the thresholds needed in the next step can be determined adaptively. Second, a dynamic cluster algorithm called ISODATA is used to cluster all the frames and the frames nearest to the center of each class are automatically extracted as key-frames of the sequence. Unlike many other clustering techniques, the present improved cluster algorithm can automatically address different motion types without any need for specified parameters from users. The proposed method is capable of summarizing motion capture data reliably and efficiently. The present work also provides a meaningful comparison between the results of the proposed key-frame extraction technique and other previous methods. These results are evaluated in terms of metrics that measure reconstructed motion and the mean absolute error value, which are derived from the reconstructed data and the original data.
doi:10.2478/hukin-2013-0063
PMCID: PMC3916911  PMID: 24511336
Motion Capture; ISODATA; Adaptive Threshold
19.  Long-Term Follow-Up of the RTOG 9501/Intergroup Phase III Trial: Postoperative Concurrent Radiation Therapy and Chemotherapy in High-Risk Squamous Cell Carcinoma of the Head & Neck 
Purpose
Previous analysis of this Intergroup trial demonstrated that with a median follow-up among surviving patients of 45.9 months, the concurrent postoperative administration of cisplatin and radiation therapy improved local-regional control and disease-free survival of patients who had high-risk resectable head and neck carcinomas. With a minimum of 10 years of follow-up potentially now available for all patients, these results are herein updated to examine long-term outcomes.
Methods and Materials
410 analyzable patients who had high-risk resected head and neck cancers were prospectively randomized to receive either radiation therapy (RT: 60 Gy in 6 weeks) or identical RT plus cisplatin, 100 mg/m2 i.v. on days 1, 22, and 43 (RT + CT).
Results
At 10 years, the local-regional failure rates were 28.8% vs. 22.3% (p=0.10), disease-free survival was 19.1% vs. 20.1% (p=0.25) and overall survival was 27.0% vs. 29.1% (p=0.31) for patients treated by RT vs. RT + CT respectively. In the unplanned subset analysis limited to patients who had microscopically involved resection margins and/or extracapsular spread of disease, local-regional failure occurred in 33.1% vs. 21.0% (p=0.02), disease-free survival was 12.3% vs. 18.4% (p=0.05) and overall survival was 19.6% vs. 27.1% (p=0.07) respectively.
Conclusion
At a median follow-up of 9.4 years for surviving patients no significant differences in outcome were observed in the analysis of all randomized eligible patients. However, analysis of the subgroup of patients who had either microscopically involved resection margins and/or extracapsular spread of disease showed improved local-regional control and disease-free survival with concurrent administration of chemotherapy. The remaining subgroup of patients who were enrolled only because they had tumor in 2 or more lymph nodes did not benefit from the addition of CT to RT.
doi:10.1016/j.ijrobp.2012.05.008
PMCID: PMC3465463  PMID: 22749632
20.  siRNA-targeted inhibition of growth hormone receptor in human colon cancer SW480 cells 
AIM: To determine the effects of RNAi-mediated inhibition of the growth hormone receptor (GHR) gene on tumors and colon cancer cells in vivo.
METHODS: Construction of a eukaryotic vector for human GHR expression, the pcDNA™6.2-GW/EmGFP-small interfering RNAs (siRNAs)-GHR plasmid, was used to inhibit GHR expression. Thirty-six BALB/c nude mice were randomly divided into groups and treated with normal saline (NS), recombinant plasmid (G2), growth hormone (GH), 5-fluorouracil (FU), G2+FU or G2+FU+GH. Each nude mouse was subcutaneously inoculated with 1×107 human colon cancer SW480 cells; the nude mice were weighed before inoculation and on the 2nd, 5th, 8th, 11th, 14th and 17th day after inoculation. All nude mice were sacrificed after 17 d. Each subcutaneous tumor was removed and studied. Tumor volume was measured on the 5th, 8th, 11th, 14th and 17th day after inoculation. The expression of GHR protein in the tumor tissue was detected by Western blotting analysis, and the differences in GHR mRNA expression in the tumor tissue were detected by real-time quantitative reverse transcription-polymerase chain reaction.
RESULTS: Compared to the control group, the weights of the inoculated nude mice on the 17th day after inoculation were: G2: 21.60 ± 0.71 g, GH: 21.64 ± 0.45 g, FU: 18.94 ± 0.47 g, FU+G2: 19.40 ± 0.60 g, G2+FU+GH: 21.04 ± 0.78 g vs NS: 20.68 ± 0.66 g, P < 0.05; the tumor volumes after the subcutaneous inoculation were: G2: 9.71 ± 3.82 mm3, FU: 11.54 ± 2.42 mm3, FU+G2: 11.42 ± 1.11 mm3, G2+FU+GH: 10.47 ± 1.02 mm3 vs NS: 116.81 ± 10.61 mm3, P < 0.05. Compared to the GH group, the tumor volumes were significantly decreased in the experimental groups. The GHR protein expression (G2: 0.39 ± 0.02, FU: 0.40 ± 0.02, FU+G2: 0.38 ± 0.01, G2+FU+GH: 0.39 ± 0.01 vs NS: 0.94 ± 0.02, P < 0.05) and the GHR mRNA expression (G2: 14.12 ± 0.10, FU: 15.15 ± 0.44, FU+G2: 16.46 ± 0.27, G2+FU+GH: 15.37 ± 0.57 vs NS: 12.63 ± 0.14, P < 0.05) were significantly decreased and increased, respectively, in the experimental groups.
CONCLUSION: Inhibition of GHR in human colon cancer SW480 cells resulted in anti-tumor effects in nude mice.
doi:10.3748/wjg.v19.i44.8108
PMCID: PMC3848161  PMID: 24307807
Growth hormone receptor; Small interfering RNAs; Colon cancer; Gene therapy; Signaling pathway
21.  Floral Transcriptome Sequencing for SSR Marker Development and Linkage Map Construction in the Tea Plant (Camellia sinensis) 
PLoS ONE  2013;8(11):e81611.
Despite the worldwide consumption and high economic importance of tea, the plant (Camellia sinensis) is not well studied in molecular biology. Under the few circumstances in which the plant is studied, C. sinensis flowers, which are important for reproduction and cross-breeding, receive less emphasis than investigation of its leaves or roots. Using high-throughput Illumina RNA sequencing, we analyzed a C. sinensis floral transcriptome, and 26.9 million clean reads were assembled into 75,531 unigenes averaging 402 bp. Among them, 50,792 (67.2%) unigenes were annotated with a BLAST search against the NCBI Non-Redundant (NR) database and 10,290 (16.67%) were detected that contained one or more simple sequence repeats (SSRs). From these SSR-containing sequences, 2,439 candidate SSR markers were developed and 720 were experimentally tested, validating 431 (59.9%) novel polymorphic SSR markers for C. sinensis. Then, a consensus SSR-based linkage map was constructed that covered 1,156.9 cM with 237 SSR markers distributed in 15 linkage groups. Both transcriptome information and the genetic map of C. sinensis presented here offer a valuable foundation for molecular biology investigations such as functional gene isolation, quantitative trait loci mapping, and marker-assisted selection breeding in this important species.
doi:10.1371/journal.pone.0081611
PMCID: PMC3841144  PMID: 24303059
22.  Taurolidine Lock Solutions for the Prevention of Catheter-Related Bloodstream Infections: A Systematic Review and Meta-Analysis of Randomized Controlled Trials 
PLoS ONE  2013;8(11):e79417.
Background
Catheter-related bloodstream infections (CRBSIs) are a significant cause of morbidity and mortality in critically ill patients, contributing to prolonged hospital stays and increased costs. Whether taurolidine lock solutions (TLS) are beneficial for the prevention of CRBSIs remains controversial. In this meta-analysis, we aim to assess the efficacy of TLS for preventing CRBSIs.
Methods
We conducted a systematic search of PubMed, EMBASE, and the Cochrane Central Register of Controlled Trials. Eligible studies included randomized controlled trials that reported on the effects of TLS for preventing CRBSIs. The primary outcome in these studies was catheter-related bloodstream infections, with microbial distribution of CRBSI and catheter-associated thrombosis as secondary outcomes. Data were combined using random-effects models owing to significant clinical heterogeneity.
Results
Six randomized controlled trials (RCTs) conducted from 2004 through 2013 involving 431 patients and 86,078 catheter-days were included in the review. TLS were significantly associated with a lower incidence of CRBSIs when compared to heparin lock solutions (Risk Ratio [RR], 0.34; 95% Confidence Interval [CI], 0.21–0.55). Use of TLS significantly decreased the incidence of CRBSIs from gram-negative (G−) bacteria (P = 0.004; RR, 0.27; CI, 0.11–0.65), and was associated with a non-significant decrease in gram-positive (G+) bacterial infections (P = 0.07; RR, 0.41; CI, 0.15–1.09). No significant association was observed with TLS and catheter-associated thrombosis (RR, 1.99; CI, 0.75–5.28).
Conclusions
The use of TLS reduced the incidence of CRBSIs without obvious adverse effects or bacterial resistance. However, the susceptibility of G+ and G- bacteria to taurolidine and the risk for catheter-associated thrombosis of TLS are indeterminate due to limited data. The results should be treated with caution due to the limited sample sizes and methodological deficiencies of included studies. Therefore, additional well-designed and adequately powered RCTs are needed to confirm these findings.
doi:10.1371/journal.pone.0079417
PMCID: PMC3836857  PMID: 24278133
23.  At Last: Erythropoietin as a Single Glycoform** 
doi:10.1002/anie.201206090
PMCID: PMC3500780  PMID: 23012228
erythropoietin; aspartylation; glycoprotein; total synthesis
24.  Analysis of Tissue Proteomes of the Gulf Killifish, Fundulus grandis, by 2D Electrophoresis and MALDI–TOF/TOF Mass Spectrometry 
The Gulf killifish, Fundulus grandis, is a small teleost fish that inhabits marshes of the Gulf of Mexico and demonstrates high tolerance of environmental variation, making it an excellent subject for the study of physiological and molecular adaptations to environmental stress. In the present study, two-dimensional (2D) gel electrophoresis and matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry were used to resolve and identify proteins from five tissues: skeletal muscle, liver, brain, heart, and gill. Of 864 protein features excised from 2D gels, 424 proteins were identified, corresponding to a 49% identification rate. For any given tissue, several protein features were identified as the same protein, resulting in a total of 254 nonredundant proteins. These nonredundant proteins were categorized into a total of 11 molecular functions, including catalytic activity, structural molecule, binding, and transport. In all tissues, catalytic activity and binding were the most highly represented molecular functions. Comparing across the tissues, proteome coverage was lowest in skeletal muscle, due to a combination of a low number of gel spots excised for analysis and a high redundancy of identifications among these spots. Nevertheless, the identification of a substantial number of proteins with high statistical confidence from other tissues suggests that F. grandis may serve as a model fish for future studies of environmental proteomics and ultimately help to elucidate proteomic responses of fish and other vertebrates to environmental stress.
doi:10.1093/icb/ics063
PMCID: PMC3475974  PMID: 22537935
25.  Deficiency in the nuclear factor E2-related factor 2 renders pancreatic β-cells vulnerable to arsenic-induced cell damage 
Toxicology and applied pharmacology  2012;264(3):315-323.
Chronic human exposure to inorganic arsenic (iAs), a potent environmental oxidative stressor, is associated with increased prevalence of Type 2 diabetes, where impairment of pancreatic β-cell function is a key pathogenic factor. Nuclear factor E2-related factor 2 (Nrf2) is a central transcription factor regulating cellular adaptive response to oxidative stress. However, persistent activation of Nrf2 in response to chronic oxidative stress, including inorganic arsenite (iAs3+) exposure, blunts glucose-triggered reactive oxygen species (ROS) signaling and impairs glucose-stimulated insulin secretion (GSIS). In the current study, we found that MIN6 pancreatic β-cells with stable knockdown of Nrf2 (Nrf2-KD) by lentiviral shRNA and pancreatic islets isolated from Nrf2-knockout (Nrf2−/−) mice exhibited reduced expression of several antioxidant and detoxification enzymes in response to acute iAs3+ exposure. As a result, Nrf2-KD MIN6 cells and Nrf2−/− islets were more susceptible to iAs3+ and monomethylarsonous acid (MMA3+)-induced cell damage, as measured by decreased cell viability, augmented apoptosis and morphological change. Pretreatment of MIN6 cells with Nrf2 activator tert-butylhydroquinone protected the cells from iAs3+-induced cell damage in an Nrf2-dependent fashion. In contrast, antioxidant N-acetyl cysteine protected Nrf2-KD MIN6 cells against acute cytotoxicity of iAs3+. The present study demonstrates that Nrf2-mediated antioxidant response is critical in the pancreatic β-cell defense mechanism against acute cytotoxicity by arsenic. The findings here, combined with our previous results on the inhibitory effect of antioxidants on ROS signaling and GSIS, suggest that Nrf2 plays paradoxical roles in pancreatic β-cell dysfunction induced by environmental arsenic exposure.
doi:10.1016/j.taap.2012.09.012
PMCID: PMC3478490  PMID: 23000044
arsenic; diabetes; pancreatic β-cell; islets; Nrf2; oxidative stress; cytotoxicity

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