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1.  Coding and noncoding expression patterns associated with rare obesity-related disorders: Prader–Willi and Alström syndromes 
Advances in genomics and genetics  2015;2015(5):53-75.
Obesity is accompanied by hyperphagia in several classical genetic obesity-related syndromes that are rare, including Prader–Willi syndrome (PWS) and Alström syndrome (ALMS). We compared coding and noncoding gene expression in adult males with PWS, ALMS, and nonsyndromic obesity relative to nonobese males using readily available lymphoblastoid cells to identify disease-specific molecular patterns and disturbed mechanisms in obesity. We found 231 genes upregulated in ALMS compared with nonobese males, but no genes were found to be upregulated in obese or PWS males and 124 genes were downregulated in ALMS. The metallothionein gene (MT1X) was significantly downregulated in ALMS, in common with obese males. Only the complex SNRPN locus was disturbed (downregulated) in PWS along with several downregulated small nucleolar RNAs (snoRNAs) in the 15q11-q13 region (SNORD116, SNORD109B, SNORD109A, SNORD107). Eleven upregulated and ten downregulated snoRNAs targeting multiple genes impacting rRNA processing, developmental pathways, and associated diseases were found in ALMS. Fifty-two miRNAs associated with multiple, overlapping gene expression disturbances were upregulated in ALMS, and four were shared with obese males but not PWS males. For example, seven passenger strand microRNAs (miRNAs) (miR-93*, miR-373*, miR-29b-2*, miR-30c-1*, miR27a*, miR27b*, and miR-149*) were disturbed in association with six separate downregulated target genes (CD68, FAM102A, MXI1, MYO1D, TP53INP1, and ZRANB1). Cell cycle (eg, PPP3CA), transcription (eg, POLE2), and development may be impacted by upregulated genes in ALMS, while downregulated genes were found to be involved with metabolic processes (eg, FABP3), immune responses (eg, IL32), and cell signaling (eg, IL1B). The high number of gene and noncoding RNA disturbances in ALMS contrast with observations in PWS and males with nonsyndromic obesity and may reflect the progressing multiorgan pathology of the ALMS disease process.
doi:10.2147/AGG.S74598
PMCID: PMC4334166
hyperphagia; microarray analysis; gene; obesity; exon expression; miRNA expression
2.  Tripling the detection view of high-frequency linear-array-based photoacoustic computed tomography by using two planar acoustic reflectors 
Background
Linear-array-based photoacoustic computed tomography (PACT) suffers from a limited view. Circular scanning does increase the detection view angle but is time-consuming. Therefore, it is desirable to increase the detection view angle of linear-array-based PACT without sacrificing imaging speed.
Methods
Two planar acoustic reflectors placed at 120 degrees to each other were added to a linear-array-based PACT system. Each reflector redirects originally undetectable photoacoustic waves back to the transducer array elements, and together they triple the original detection view angle of the PACT system.
Results
Adding two reflectors increased the detection view angle from 80 to 240 degrees. As a comparison, a single-reflector PACT has a detection view angle of only 160 degrees. A leaf skeleton phantom with a rich vascular network was imaged with the double-reflector PACT, and most of its features were recovered.
Conclusions
The two acoustic reflectors triple the detection view angle of a linear-array-based PACT without compromising the original imaging speed. This nearly full-view detection capability produces higher-quality images than single-reflector PACT or conventional PACT without reflectors.
doi:10.3978/j.issn.2223-4292.2014.11.09
PMCID: PMC4312304
Photoacoustic computed tomography (PACT); linear transducer array; limited view; view angle; acoustic reflector
3.  Complete Genome Sequence of Human Enterovirus Strain 71 (EV71/Taipei/3118/2011), Isolated from a Patient in Taiwan 
Genome Announcements  2015;3(1):e01375-14.
This full-length genome sequence of human enterovirus strain 71 (EV71/Taipei/3118/2011) was isolated from a clinical patient in Taiwan in 2011. According to the phylogenetic analysis, the complete genome sequence in this study is part of the subgenotype C4.
doi:10.1128/genomeA.01375-14
PMCID: PMC4290987  PMID: 25573934
4.  Association between ADIPOQ +45T>G Polymorphism and Type 2 Diabetes: A Systematic Review and Meta-Analysis 
Recently, a number of studies have reported the association between the single nucleotide polymorphisms (SNPs) +45T>G polymorphism in the adiponectin (ADIPOQ) gene and type 2 diabetes mellitus (T2DM) risk, though the results are inconsistent. In order to obtain a more precise estimation of the relationship, a meta-analysis was performed. In this current study, the Medline, Embase, Pubmed, ISI Web of Knowledge, Ovid, Science Citation Index Expanded Database, Wanfang Database, and China National Knowledge Infrastructure were searched for eligible studies. Odds ratios (ORs) with 95% confidence intervals (CIs) were used to estimate the strength of association. Forty-five publications were included in the final meta-analysis with 9986 T2DM patients and 16,222 controls for ADIPOQ +45T>G polymorphism according to our inclusion and exclusion criteria. The +45T>G polymorphism was associated with an overall significantly increased risk of T2DM (G vs. T: OR = 1.18, 95% CI = 1.06–1.32; The dominant model: OR = 1.18, 95% CI = 1.03–1.33; The recessive model: OR = 1.47, 95% CI = 1.20–1.78; The homozygous model: OR = 1.62, 95% CI = 1.25–2.09; Except the heterozygous model: OR = 1.11, 95% CI = 0.98–1.24). Subgroup analysis revealed a significant association between the +45T>G polymorphism and T2D in an Asian population. Thus, this meta-analysis indicates that the G allele of the ADIPOQ +45T>G polymorphisms associated with a significantly increased risk of T2DM in the Asian population.
doi:10.3390/ijms16010704
PMCID: PMC4307270  PMID: 25561226
ADIPOQ; single nucleotide polymorphisms (SNPs); type 2 diabetes mellitus; meta-analysis
5.  A new modified Tsuge suture for flexor tendon repairs: the biomechanical analysis and clinical application 
Purpose
This study is to develop a new suturing technique for flexor tendon repair by modifying the extant Tsuge repair techniques and to use biomechanical analysis to compare the new method with four established repair techniques and evaluate its clinical efficacy in the repair of 47 flexor tendons in 22 patients.
Methods
The biomechanical analysis relied on 50 flexor digitorum profundus tendons harvested from fresh cadavers. The tendons were randomly divided into five groups, transected, and repaired by use of a 1. double-loop suture, 2. double modified locking Kessler, 3. four-strand Savage, 4. modified six-strand Savage, and 5. the new technique. The tensile force and breaking force of all repaired tendons were measured by static loading trials. For clinical application, 22 patients with acute flexor tendon injuries were treated with the new modified Tsuge suture and follow-up for more than 12 months.
Results
While differences in the tensile force and breaking force in the modified Tsuge sutures and modified six-strand Savage sutures were not statistically significant, static loading trials showed the tensile force, in the form of a 2-mm gap formation, and the breaking force of the new modified Tsuge sutures were, statistically, both higher than the ones characteristic of double-loop sutures, double modified locking Kessler, and four-strand Savage sutures. After 12 months, restored functions were observed in all the patients during the postoperative 12 months. Total active motion (TAM) score demonstrated that more than 90% fingers were estimated as excellent or good.
Conclusion
The new modified Tsuge sutures described here have evident higher tensile and breaking forces compared to other four-strand core suture techniques, suggesting, in turn, that this new technique is a good alternative for flexor tendon repairs in clinical applications.
doi:10.1186/s13018-014-0136-x
PMCID: PMC4305253  PMID: 25551285
Flexor tendon; Repair; Modified Tsuge; Biomechanics; Clinical practice
6.  Effectiveness of tranexamic acid in reducing blood loss in spinal surgery: a meta-analysis 
Background
The aim of present meta-analysis was to evaluate the effectiveness of tranexamic acid (TXA) use in reducing blood loss and the related thrombotic complications in spinal surgery.
Methods
Three databases (MEDLINE, EMBASE, and the Cochrane Library) were searched through October 2012 to identify the relevant randomized controlled trials (RCTs) regarding the TXA effective in spinal surgery. Mean differences (MDs) of blood loss, blood transfusions, and postoperative partial thromboplastic time (PTT), odds ratios (ORs) of blood transfusion and thrombotic complication in TXA-treated group compared to placebo group were extracted and combined using random-effect meta-analysis.
Results
A total of 6 RCTs comprising 411 patients were included in the meta-analysis according to the pre-defined selection criteria. TXA-treated group had significantly less amount of blood loss and blood transfusions per patient, and had smaller proportion of patients who required a blood transfusion compared with the placebo group. The use of TXA can significantly reduce the postoperative PTT with weighted MD of -1.59 [(95% confidence interval (CI):-3.07, -0.10] There is a null association between thrombosis complications and the use of TXA.
Conclusion
We conclude that the use of TXA in patients undergoing spinal surgery appears to be effective in reducing the amount of blood loss, the volume of blood transfusion, the transfusion rate, and the postoperative PTT. However, data were too limited for any conclusions regarding safety. More high-quality RCTs are required before recommending the administered of TXA in spinal surgery.
doi:10.1186/1471-2474-15-448
PMCID: PMC4326491  PMID: 25532706
Tranexamic acid; Spine; Surgery; Meta-analysis
7.  Selenium Supplementation for Autoimmune Thyroiditis: A Systematic Review and Meta-Analysis 
Many studies have reported that selenium (Se) has a close relationship with autoimmune thyroiditis (AIT). The therapeutic effect of Se supplementation in AIT treatment remains unclear. The objective of the present study was to determine the efficacy of Se supplementation for the treatment of AIT. A structured literature search was undertaken to identify all randomized controlled trials conducted in patients with AIT receiving Se supplementation or placebo. Nine studies enrolling a total of 787 patients were included. The results showed that Se supplementation with duration 6 months significantly dropped the TPOAb titers but did not decrease the TgAb titers. Patients assigned to Se supplementation for 12-month duration showed significantly lower TPOAb titers and TgAb titers. Patients after Se supplementation had a higher chance to improve the mood or well-being compared with controls. Se supplementation is associated with a significant decrease in TPOAb titers at 6 and 12 months; meanwhile, the TgAb titers can be dropped at 12 months. After Se supplementation treatment, patients had a higher chance to improve the mood without significant adverse events.
doi:10.1155/2014/904573
PMCID: PMC4276677  PMID: 25574167
8.  Evaluation of EEG Oscillatory Patterns and Cognitive Process during Simple and Compound Limb Motor Imagery 
PLoS ONE  2014;9(12):e114853.
Motor imagery (MI), sharing similar neural representations to motor execution, is regarded as a window to investigate the cognitive motor processes. However, in comparison to simple limb motor imagery, significantly less work has been reported on brain oscillatory patterns induced by compound limb motor imagery which involves several parts of limbs. This study aims to investigate differences of the electroencephalogram (EEG) patterns as well as cognitive process between simple limb motor imagery and compound limb motor imagery. Ten subjects participated in the experiment involving three tasks of simple limb motor imagery (left hand, right hand, feet) and three tasks of compound limb motor imagery (both hands, left hand combined with right foot, right hand combined with left foot). Simultaneous imagination of different limbs contributes to the activation of larger cortical areas as well as two estimated sources located at corresponding motor areas within beta rhythm. Compared with simple limb motor imagery, compound limb motor imagery presents a network with more effective interactions overlying larger brain regions, additionally shows significantly larger causal flow over sensorimotor areas and larger causal density over both sensorimotor areas and neighboring regions. On the other hand, compound limb motor imagery also shows significantly larger 10–11 Hz alpha desynchronization at occipital areas and central theta synchronization. Furthermore, the phase-locking value (PLV) between central and occipital areas of left/right hand combined with contralateral foot imagery is significantly larger than that of simple limb motor imagery. All these findings imply that there exist apparent intrinsic distinctions of neural mechanism between simple and compound limb motor imagery, which presents a more complex effective connectivity network and may involve a more complex cognitive process during information processing.
doi:10.1371/journal.pone.0114853
PMCID: PMC4260914  PMID: 25489941
9.  TERT promoter mutations are associated with distant metastases in upper tract urothelial carcinomas and serve as urinary biomarkers detected by a sensitive castPCR 
Oncotarget  2014;5(23):12428-12439.
TERT promoter C228T and C250T mutations occur in various malignancies including bladder cancer (BC) and may serve as urinary tumor markers. However, the mutation association with clinical variables in upper tract urothelial carcinomas (UTUCs) is unclear. There is also a lack of sensitive tools to detect the minor mutant TERT promoter in bulk urinary DNA. Here we analyzed 220 UTUC patients [98 with renal pelvic carcinoma (RPC) and 122 with ureter carcinoma (UC)] and developed a Competitive Allele-Specific TaqMan PCR (castPCR) for urinary assay. We identified C228T or C250T mutations in 42 of 98 (43%) RPC and 23 of 122 (19%) UC tumors. Distant metastases were significantly correlated with UTUC patients harboring TERT promoter mutations (P = 0.001). C228T were detected in 6/10 and 9/10 of urine samples from patients with mutation-carrying tumors using Sanger sequencing and castPCR, respectively. When urine samples from 70 BC patients were analyzed together, the sensitivity of urinary C228T assay was 89% and 50% for castPCR and Sanger sequencing, respectively (P < 0.001). Collectively, TERT promoter mutations occur in UTUCs with a high frequency in RPCs and predict distant metastasis. castPCR assays of the mutation are a useful tool for urine-based diagnostics of urological malignancies.
PMCID: PMC4322995  PMID: 25474136
Cancer biomarkers; Promoter mutations; Telomerase; TERT; UTUC
10.  A Thermostable Glucoamylase from Bispora sp. MEY-1 with Stability over a Broad pH Range and Significant Starch Hydrolysis Capacity 
PLoS ONE  2014;9(11):e113581.
Background
Glucoamylase is an exo-type enzyme that converts starch completely into glucose from the non-reducing ends. To meet the industrial requirements for starch processing, a glucoamylase with excellent thermostability, raw-starch degradation ability and high glucose yield is much needed. In the present study we selected the excellent Carbohydrate-Activity Enzyme (CAZyme) producer, Bispora sp. MEY-1, as the microbial source for glucoamylase gene exploitation.
Methodology/Principal Findings
A glucoamylase gene (gla15) was cloned from Bispora sp. MEY-1 and successfully expressed in Pichia pastoris with a high yield of 34.1 U/ml. Deduced GLA15 exhibits the highest identity of 64.2% to the glucoamylase from Talaromyces (Rasamsonia) emersonii. Purified recombinant GLA15 was thermophilic and showed the maximum activity at 70°C. The enzyme was stable over a broad pH range (2.2–11.0) and at high temperature up to 70°C. It hydrolyzed the breakages of both α-1,4- and α-1,6-glycosidic linkages in amylopectin, soluble starch, amylose, and maltooligosaccharides, and had capacity to degrade raw starch. TLC and H1-NMR analysis showed that GLA15 is a typical glucoamylase of GH family 15 that releases glucose units from the non-reducing ends of α-glucans. The combination of Bacillus licheniformis amylase and GLA15 hydrolyzed 96.14% of gelatinized maize starch after 6 h incubation, which was about 9% higher than that of the combination with a commercial glucoamylase from Aspergillus niger.
Conclusion/Significance
GLA15 has a broad pH stability range, high-temperature thermostability, high starch hydrolysis capacity and high expression yield. In comparison with the commercial glucoamylase from A. niger, GLA15 represents a better candidate for application in the food industry including production of glucose, glucose syrups, and high-fructose corn syrups.
doi:10.1371/journal.pone.0113581
PMCID: PMC4240638  PMID: 25415468
11.  Calretinin-positive L5a pyramidal neurons in the development of the paralemniscal pathway in the barrel cortex 
Molecular Brain  2014;7(1):84.
Background
The rodent barrel cortex has been established as an ideal model for studying the development and plasticity of a neuronal circuit. The barrel cortex consists of barrel and septa columns, which receive various input signals through distinct pathways. The lemniscal pathway transmits whisker-specific signals to homologous barrel columns, and the paralemniscal pathway transmits multi-whisker signals to both barrel and septa columns. The integration of information from both lemniscal and paralemniscal pathways in the barrel cortex is critical for precise object recognition. As the main target of the posterior medial nucleus (POm) in the paralemniscal pathway, layer 5a (L5a) pyramidal neurons are involved in both barrel and septa circuits and are considered an important site of information integration. However, information on L5a neurons is very limited. This study aims to explore the cellular features of L5a neurons and to provide a morphological basis for studying their roles in the development of the paralemniscal pathway and in information integration.
Results
1. We found that the calcium-binding protein calretinin (CR) is dynamically expressed in L5a excitatory pyramidal neurons of the barrel cortex, and L5a neurons form a unique serrated pattern similar to the distributions of their presynaptic POm axon terminals.
2. Infraorbital nerve transection disrupts this unique alignment, indicating that it is input dependent.
3. The formation of the L5a neuronal alignment develops synchronously with barrels, which suggests that the lemniscal and paralemniscal pathways may interact with each other to regulate pattern formation and refinement in the barrel cortex.
4. CR is specifically expressed in the paralemniscal pathway, and CR deletion disrupts the unique L5a neuronal pattern, which indicates that CR may be required for the development of the paralemniscal pathway.
Conclusions
Our results demonstrate that L5a neurons form a unique, input-dependent serrated alignment during the development of cortical barrels and that CR may play an important role in the development of the paralemniscal pathway. Our data provide a morphological basis for studying the role of L5a pyramidal neurons in information integration within the lemniscal and paralemniscal pathways.
doi:10.1186/s13041-014-0084-8
PMCID: PMC4246560  PMID: 25404384
Calretinin; L5a pyramidal neuron; Paralemniscal pathway; Posterior medial nucleus; Barrel cortex
12.  Exploring the Chemodiversity and Biological Activities of the Secondary Metabolites from the Marine Fungus Neosartorya pseudofischeri 
Marine Drugs  2014;12(11):5657-5676.
The production of fungal metabolites can be remarkably influenced by various cultivation parameters. To explore the biosynthetic potentials of the marine fungus, Neosartorya pseudofischeri, which was isolated from the inner tissue of starfish Acanthaster planci, glycerol-peptone-yeast extract (GlyPY) and glucose-peptone-yeast extract (GluPY) media were used to culture this fungus. When cultured in GlyPY medium, this fungus produced two novel diketopiperazines, neosartins A and B (1 and 2), together with six biogenetically-related known diketopiperazines,1,2,3,4-tetrahydro-2,3-dimethyl-1,4-dioxopyrazino[1,2-a]indole (3), 1,2,3,4-tetrahydro-2-methyl-3-methylene-1,4-dioxopyrazino[1,2-a]indole (4), 1,2,3,4-tetrahydro-2-methyl-1,3,4-trioxopyrazino[1,2-a] indole (5), 6-acetylbis(methylthio)gliotoxin (10), bisdethiobis(methylthio)gliotoxin (11), didehydrobisdethiobis(methylthio)gliotoxin (12) and N-methyl-1H-indole-2-carboxamide (6). However, a novel tetracyclic-fused alkaloid, neosartin C (14), a meroterpenoid, pyripyropene A (15), gliotoxin (7) and five known gliotoxin analogues, acetylgliotoxin (8), reduced gliotoxin (9), 6-acetylbis(methylthio)gliotoxin (10), bisdethiobis(methylthio) gliotoxin (11) and bis-N-norgliovictin (13), were obtained when grown in glucose-containing medium (GluPY medium). This is the first report of compounds 3, 4, 6, 9, 10 and 12 as naturally occurring. Their structures were determined mainly by MS, 1D and 2D NMR data. The possible biosynthetic pathways of gliotoxin-related analogues and neosartin C were proposed. The antibacterial activity of compounds 2–14 and the cytotoxic activity of compounds 4, 5 and 7–13 were evaluated. Their structure-activity relationships are also preliminarily discussed.
doi:10.3390/md12115657
PMCID: PMC4245550  PMID: 25421322
marine fungus; Neosartorya pseudofischeri; neosartin; diketopiperazine; antibacterial activity; cytotoxic activity
13.  Thermostability Improvement of a Streptomyces Xylanase by Introducing Proline and Glutamic Acid Residues 
Protein engineering is commonly used to improve the robustness of enzymes for activity and stability at high temperatures. In this study, we identified four residues expected to affect the thermostability of Streptomyces sp. strain S9 xylanase XynAS9 through multiple-sequence analysis (MSA) and molecular dynamic simulations (MDS). Site-directed mutagenesis was employed to construct five mutants by replacing these residues with proline or glutamic acid (V81P, G82E, V81P/G82E, D185P/S186E, and V81P/G82E/D185P/S186E), and the mutant and wild-type enzymes were expressed in Pichia pastoris. Compared to the wild-type XynAS9, all five mutant enzymes showed improved thermal properties. The activity and stability assays, including circular dichroism and differential scanning calorimetry, showed that the mutations at positions 81 and 82 increased the thermal performance more than the mutations at positions 185 and 186. The mutants with combined substitutions (V81P/G82E and V81P/G82E/D185P/S186E) showed the most pronounced shifts in temperature optima, about 17°C upward, and their half-lives for thermal inactivation at 70°C and melting temperatures were increased by >9 times and approximately 7.0°C, respectively. The mutation combination of V81P and G82E in adjacent positions more than doubled the effect of single mutations. Both mutation regions were at the end of long secondary-structure elements and probably rigidified the local structure. MDS indicated that a long loop region after positions 81 and 82 located at the end of the inner β-barrel was prone to unfold. The rigidified main chain and filling of a groove by the mutations on the bottom of the active site canyon may stabilize the mutants and thus improve their thermostability.
doi:10.1128/AEM.03458-13
PMCID: PMC3993148  PMID: 24463976
15.  Angiopoietin-1, Angiopoietin-2 and Bicarbonate as Diagnostic Biomarkers in Children with Severe Sepsis 
PLoS ONE  2014;9(9):e108461.
Severe pediatric sepsis continues to be associated with high mortality rates in children. Thus, an important area of biomedical research is to identify biomarkers that can classify sepsis severity and outcomes. The complex and heterogeneous nature of sepsis makes the prospect of the classification of sepsis severity using a single biomarker less likely. Instead, we employ machine learning techniques to validate the use of a multiple biomarkers scoring system to determine the severity of sepsis in critically ill children. The study was based on clinical data and plasma samples provided by a tertiary care center's Pediatric Intensive Care Unit (PICU) from a group of 45 patients with varying sepsis severity at the time of admission. Canonical Correlation Analysis with the Forward Selection and Random Forests methods identified a particular set of biomarkers that included Angiopoietin-1 (Ang-1), Angiopoietin-2 (Ang-2), and Bicarbonate (HCO) as having the strongest correlations with sepsis severity. The robustness and effectiveness of these biomarkers for classifying sepsis severity were validated by constructing a linear Support Vector Machine diagnostic classifier. We also show that the concentrations of Ang-1, Ang-2, and HCO enable predictions of the time dependence of sepsis severity in children.
doi:10.1371/journal.pone.0108461
PMCID: PMC4178003  PMID: 25255212
16.  Partial greater trochanter osteotomy for hip reduction in total hip arthroplasty for high dislocated hip: a preliminary report 
Background
Hip reduction in total hip arthroplasty for high dislocated hips is difficult. Various femur osteotomy procedures have been used for hip reduction, but these methods increase operative time and risk of nonunion. We investigated the efficacy of a novel partial greater trochanter osteotomy technique for hip reduction in total hip arthroplasty for patients with high hip dislocation.
Methods
Twenty-one patients (23 hips) with high dislocated hip were treated with total hip arthroplasty that included partial greater trochanter osteotomy, i.e., the upper 2/3 greater trochanter was resected, and the gluteus medius muscle attachment was spared. The clinical outcome was evaluated by comparing the Harris hip scores and radiographic exam results, obtained before surgery and at follow-ups.
Results
Follow-ups of 21 patients ranged from 13 to 56 months. The mean Harris hip score increased from preoperative 55.0 (36–69) to postoperative 86.1 (71–93; P = 0.00). The average preoperative leg length discrepancy in patients with unilateral high hip dislocation was 46 mm (28–65 mm); postoperatively leg length discrepancy was less than 1 cm in 11 patients, between 1 and 2 cm in 8 patients, and more than 2 cm in 2 patients. The average leg lengthening at the time of surgery was 36 mm (24–54 mm). Trendelenburg’s gait changed from positive to negative in 20 hips by the last follow-up. No nerve injury occurred postoperative.
Conclusion
Partial greater trochanter osteotomy is an effective method to render hip reduction in total hip arthroplasty for patients with high dislocation of the hip.
doi:10.1186/1471-2474-15-293
PMCID: PMC4174664  PMID: 25186094
Partial greater trochanter osteotomy; Hip reduction; High dislocated hip; Total hip arthroplasty
17.  siRNA-Mediated Suppression of Synuclein γ Inhibits MDA-MB-231 Cell Migration and Proliferation by Downregulating the Phosphorylation of AKT and ERK 
Journal of Breast Cancer  2014;17(3):200-206.
Purpose
Synuclein-γ (SNCG), which was initially identified as breast cancer specific gene 1, is highly expressed in advanced breast cancers, but not in normal or benign breast tissue. This study aimed to evaluate the effects of SNCG siRNA-treatment on breast cancer cells and elucidate the associated mechanisms.
Methods
Vectors containing SNCG and negative control (NC) siRNAs were transfected into MDA-MB-231 cells; mRNA levels were determined by real-time polymerase chain reaction. Cell proliferation was evaluated using the MTT assay, cell migration was assessed by the Transwell assay, apoptosis and cell cycle analyses were conducted with the flow cytometer, and Western blot analysis was performed to determine the relative levels of AKT, ERK, p-AKT, and p-ERK expression.
Results
SNCG mRNA levels were significantly reduced in MDA-MB-231 cells transfected with SNCG siRNA. Our results indicate that in SNCG siRNA-treated cells, cell migration and proliferation decreased significantly, apoptosis was induced, and the cell cycle was arrested. Western blot analysis indicated that the protein levels of p-AKT and p-ERK were much lower in the SNCG siRNA-treated groups, than in the control and NC groups.
Conclusion
SNCG siRNA could decrease the migration and proliferation of breast cancer cells by downregulating the phosphorylation of AKT and ERK.
doi:10.4048/jbc.2014.17.3.200
PMCID: PMC4197349  PMID: 25320617
Breast neoplasms; Extracellular signal-regulated MAP kinases; Human SNCG protein; Proto-oncogene proteins c-akt; Small interfering RNA
18.  The Feature Extraction Based on Texture Image Information for Emotion Sensing in Speech 
Sensors (Basel, Switzerland)  2014;14(9):16692-16714.
In this paper, we present a novel texture image feature for Emotion Sensing in Speech (ESS). This idea is based on the fact that the texture images carry emotion-related information. The feature extraction is derived from time-frequency representation of spectrogram images. First, we transform the spectrogram as a recognizable image. Next, we use a cubic curve to enhance the image contrast. Then, the texture image information (TII) derived from the spectrogram image can be extracted by using Laws' masks to characterize emotional state. In order to evaluate the effectiveness of the proposed emotion recognition in different languages, we use two open emotional databases including the Berlin Emotional Speech Database (EMO-DB) and eNTERFACE corpus and one self-recorded database (KHUSC-EmoDB), to evaluate the performance cross-corpora. The results of the proposed ESS system are presented using support vector machine (SVM) as a classifier. Experimental results show that the proposed TII-based feature extraction inspired by visual perception can provide significant classification for ESS systems. The two-dimensional (2-D) TII feature can provide the discrimination between different emotions in visual expressions except for the conveyance pitch and formant tracks. In addition, the de-noising in 2-D images can be more easily completed than de-noising in 1-D speech.
doi:10.3390/s140916692
PMCID: PMC4208194  PMID: 25207869
emotional feature extraction; emotion sensing; spectrogram; texture image information
19.  Polymeric immunoglobulin receptor expression is predictive of poor prognosis in glioma patients 
Although there have been recent advances in surgery, radiotherapy, and chemotherapy, the survival of patient with glioma remains poor. Increased expression of polymeric immunoglobulin receptor (pIgR) in tumor tissue has been detected in various cancer forms. However, the clinical relevance of pIgR in glioma remains unclear. The aim of this study was to assess the prognostic value of pIgR in patients with glioma after surgical resection. pIgR expression was evaluated by immunohistochemistry in paraffin-embedded glioma tissues from 146 patients. The relation between pIgR expression and clinicopathologic factors and long-term prognosis in these 146 patients was retrospectively examined. The prognostic significance of negative or positive pIgR exspression in glioma was assessed using Kaplan-Meier survival analysis and log-rank tests. Positive expression of pIgR was statistically significantly associated with poor prognosis of patients with glioma. Our results indicated that pIgR could be a novel predictor for poor prognosis of patients with glioma after surgical resection.
PMCID: PMC4161565  PMID: 25232405
Glioma; polymeric immunoglobulin receptor (pIgR); prognosis
20.  Prognostic role of microvessel density in patients with renal cell carcinoma: a meta-analysis 
Microvessel density (MVD), an indicator of angiogenesis, has been proposed to predict prognosis of patients with renal cell carcinoma (RCC), but its ability to predict survival of patients with RCC remains controversial. The present study sought to address this question rigorously by systematically reviewing the literature on MVD and RCC prognosis. We identified relevant studies in PubMed, EMBASE and the Cochrane Library, and two reviewers independently assessed study quality and extracted relevant data to compare survival based on MVD stratification in patients with RCC. We identified 15 studies that satisfied the inclusion criteria; eight studies assessed MVD in surgical samples by immunohistochemistry to label factor VIII; four studies, by immunohistochemistry to label CD34; two studies, CD31; and one study, CD105. Survival meta-analysis was performed using data pooled from 10 studies: five based on factor VIII, two based on CD34, two based on CD31 and one based on CD105. The overall survival hazard ratio describing the relationship between MVD and survival in all 10 pooled studies was 0.964 (95% CI: 0.873-1.065), while the individual hazard ratios for pooled studies based on factor VIII were 1.673 (95% CI: 0.860-3.252); CD34, 0.903 (95% CI: 0.853-0.956); and CD31, 0.926 (95% CI: 0.868-0.989). The corresponding result for the sole trial based on CD105 was 0.1759 (95% CI: 0.036-0.856). These findings suggest that MVD is not reliably associated with survival time of patients with RCC, which may reflect the need to take into account whether the microvasculature is differentiated or not. MVD as currently calculated may not be an ideal prognostic factor for patients with RCC.
PMCID: PMC4203198  PMID: 25337227
Microvessel density; renal cell carcinoma; prognosis; meta-analysis
22.  Full-Wave Iterative Image Reconstruction in Photoacoustic Tomography With Acoustically Inhomogeneous Media 
IEEE transactions on medical imaging  2013;32(6):1097-1110.
Existing approaches to image reconstruction in photoacoustic computed tomography (PACT) with acoustically heterogeneous media are limited to weakly varying media, are computationally burdensome, and/or cannot effectively mitigate the effects of measurement data incompleteness and noise. In this work, we develop and investigate a discrete imaging model for PACT that is based on the exact photoacoustic (PA) wave equation and facilitates the circumvention of these limitations. A key contribution of the work is the establishment of a procedure to implement a matched forward and backprojection operator pair associated with the discrete imaging model, which permits application of a wide-range of modern image reconstruction algorithms that can mitigate the effects of data incompleteness and noise. The forward and backprojection operators are based on the k-space pseudospectral method for computing numerical solutions to the PA wave equation in the time domain. The developed reconstruction methodology is investigated by use of both computer-simulated and experimental PACT measurement data.
doi:10.1109/TMI.2013.2254496
PMCID: PMC4114232  PMID: 23529196
Acoustic heterogeneity; iterative image reconstruction; optoacoustic tomography; photoacoustic tomography; thermoacoustic tomography
23.  TCAB1: a potential target for diagnosis and therapy of head and neck carcinomas 
Molecular Cancer  2014;13:180.
Background
WRAP53, including α, β and γ isoforms, plays an important role not only in the stability of p53 mRNA, but also in the assembly and trafficking of the telomerase holoenzyme. It has been considered an oncogene and is thought to promote the survival of cancer cells. The aim of this study was to detect the role of TCAB1 (except WRAP53α) in the occurrence and development of head and neck carcinomas.
Methods
Immunohistochemistry was used to detect the TCAB1 expression in clinical specimen sections and performed western blotting to check the TCAB1 expression levels in cell lines. TCAB1 was depleted using shRNA lentivirus and the knockdown efficiency was assessed using q-PCR and Western blotting. We performed CCK-8 assays and flow cytometry to check the cell proliferation potential and used the trans-well assay to test the invasion ability in vitro. Xenografts were used to detect the tumor formation potential in vivo. Moreover, we performed cDNA microarray to investigate the candidate factors involved in this process.
Results
We observed a notable overexpression of TCAB1 in head and neck carcinoma clinical specimens as well as in carcinoma cell lines. Knockdown of TCAB1 decreased the cellular proliferation potential and invasion ability in vitro. cDNA microarray analysis suggested the possible involvement of several pathways and factors associated with tumorigenesis and carcinoma development in the TCAB1-mediated regulation of cancers. Furthermore, the xenograft assay confirmed that the depletion of TCAB1 would inhibit tumor formation in nude mice. The immunohistochemistry results of the mice tumor tissue sections revealed that the cells in shTCAB1 xenografts showed decreased proliferation potential and increased apoptotic trend, meanwhile, the angiogenesis was inhibited in the smaller tumors form shTCAB1 cells.
Conclusions
Our study demonstrated that depletion of TCAB1 decreased cellular proliferation and invasion potential both in vitro and in vivo. The data indicated that TCAB1 might facilitate the occurrence and development of head and neck carcinomas. In future, TCAB1 might be useful as a prognostic biomarker or a potential target for the diagnosis and therapy of head and neck carcinomas.
doi:10.1186/1476-4598-13-180
PMCID: PMC4118648  PMID: 25070141
TCAB1; Head and neck cancers; Proliferation; Invasion; Biomarker
24.  MDRL lncRNA Regulates the Processing of miR-484 Primary Transcript by Targeting miR-361 
PLoS Genetics  2014;10(7):e1004467.
Long noncoding RNAs (lncRNAs) are emerging as new players in gene regulation, but whether lncRNAs operate in the processing of miRNA primary transcript is unclear. Also, whether lncRNAs are involved in the regulation of the mitochondrial network remains to be elucidated. Here, we report that a long noncoding RNA, named mitochondrial dynamic related lncRNA (MDRL), affects the processing of miR-484 primary transcript in nucleus and regulates the mitochondrial network by targeting miR-361 and miR-484. The results showed that miR-361 that predominantly located in nucleus can directly bind to primary transcript of miR-484 (pri-miR-484) and prevent its processing by Drosha into pre-miR-484. miR-361 is able to regulate mitochondrial fission and apoptosis by regulating miR-484 levels. In exploring the underlying molecular mechanism by which miR-361 is regulated, we identified MDRL and demonstrated that it could directly bind to miR-361 and downregulate its expression levels, which promotes the processing of pri-miR-484. MDRL inhibits mitochondrial fission and apoptosis by downregulating miR-361, which in turn relieves inhibition of miR-484 processing by miR-361. Our present study reveals a novel regulating model of mitochondrial fission program which is composed of MDRL, miR-361 and miR-484. Our work not only expands the function of the lncRNA pathway in gene regulation but also establishes a new mechanism for controlling miRNA expression.
Author Summary
Long non-coding RNAs (lncRNAs) have been shown to be involved in a wide range of biological functions. However, studies linking individual lncRNA to the mitochondrial fission program remain scarce. Also, it remains unknown whether lncRNAs can operate in the processing of miRNA primary transcript. Here, we provide causal evidence for the involvement of the lncRNA MDRL in the mitochondrial dynamics and the processing of miR-484 primary transcript in cardiomyocyte. We identified MDRL which can act as an endogenous ‘sponge’ that directly binds to miR-361 and downregulates its expression levels. miR-361 can directly bind to primary transcript of miR-484 and prevent its processing by Drosha into pre-miR-484. MDRL inhibits mitochondrial fission and apoptosis by miR-361 and miR-484. Our present study reveals a novel regulating model which is composed of MDRL, miR-361 and miR-484. Modulation of their levels may provide a new approach for tackling myocardial infarction.
doi:10.1371/journal.pgen.1004467
PMCID: PMC4109843  PMID: 25057983
25.  Morphological and Proteomic Analysis Reveal the Role of Pistil under Pollination in Liriodendron chinense (Hemsl.) Sarg 
PLoS ONE  2014;9(6):e99970.
Pollination is an important physiological process during which interaction between pollen and pistil occurs. This interaction could determine whether or not fertilization will occur and hence the ratio of plant seed setting. Liriodendron chinense (Hemsl.) Sarg. (L. chinense) exhibits a distinct phenomenon where seed setting ratio is not more than 10% in natural environment. To explore the origin of this phenomenon, we conducted a comparative morphological and proteomic analysis on L. chinense pistils upon pollination. The morphological analysis showed that pollen grows well in vitro, but much slower on pistil or nutrient medium containing pistil extract. Proteomic analysis showed that 493 proteins had changed the expression after pollination. Among them, 468 and 51 proteins were identified by isobaric tags for relative and absolute quantitation and two-dimensional gel electrophoresis respectively, and 26 proteins were common in the two methods. After proteins functional categorization, 66 differentially expressed proteins that are involved in reproduction process were found. Further analysis showed that among the reproductive process related proteins, protein disulfide-isomerase A6 and four embryo-defective proteins showed closer relations with the low seed setting phenomenon. The results indicated that the element from pistil might be the main reason leading to low seed setting in L. chinense, which will provide new insights in the mechanisms underlying L. chinense reproduction process.
doi:10.1371/journal.pone.0099970
PMCID: PMC4055720  PMID: 24924488

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