The transcript assembly is essential for transcriptome studies trom next-generation sequencing data. However, there are still many faults of algorithms in the present assemblers, which should be largely improved in the future. According to the requirement of reference genome or not, the transcript assembly could be classified into the genome-guided and de novo methods. The two methods have different algorithms and implementation processes. The quality of assembled transcripts depends on a large number of factors, such as the PCR amplification, sequencing techniques, assembly algorithm and genome character. Here, we reviewed the present tools of transcript assembly and various indexes for assessing the quality of assembled transcripts, which would help biologists to determine which assembler should be used in their studies.
Algorithms ; Gene Expression Profiling ; Genome ; Genomics ; methods ; High-Throughput Nucleotide Sequencing ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Transcriptome

OBJECTIVE:To discuss our experience of switching use of immunosuppressive agents for patients after renal transplantation.METHODS:23 patients with chronic allograft dysfunction(CAD) were treated with tacrolimus + mycophenolate mofetil instead of cyclosporine A+ azathioprine.The change of renal function and the adverse effects were observed.RESULTS:The serum creatinine(Scr) level before and after therapy conversion were 167～478 ?mol?mL-1 with a mean value of(268?78) ?mol?mL-1 and 112～346 ?mol?mL-1 with a mean value of(174?65) ?mol?mL-1,respectively,showing significant difference in the t test(P

Gastric bronchogenic cysts （GBCs） is uncommon with atypical clinical features. It is difficult to diagnose by preoperative imaging examinations. Therefore , postoperative histopatho-logical examination is regarded as the golden bacteria in ultimate diagnosis. The treatment of GBCs：ultrasound-guided fine needle aspiration and endoscopic mucosal resection is only used for small GBCs with intra-cavity growth pattern. However , GBCs with extra-cavity growth pattern is featured with deeply anatomical position , large size , and prone on attaching to vital blood vessels and organs , which makes laparoscopic resection is the first choice in treatment. The authors introduce the diagnosis and treatment of a case of GBCs attaching to lesser curvature , in order to provide references for clinical diagnosis of GBCs.

Objective The aim of this study is to evaluate the efficacy and safety of preoperative CT-guided hardening agent localization.Methods From December 2010 to January 2012,27 patients with 29 solitary pulmonary nodules who had undergone CT-guided hardening agent localization and video-assisted thoracoscopic surgery (VATS) were studied.Results All cases were underwent CT-guided hardening agent localization successfully,and no patient had serious complication that required any intervention.The diameter of nodules ranged from 3 to 21 mm as measured by CT[mean (11.27 ± 6.32) mm].The distance between the center of nodule and visceral pleural ranged from 4 to 38 mm[mean (14.45 ± 4.32) mm].Conversion from VATS to thoracotomies was not necessary during the diagnostic resection procedure nodules.29 solitary pulmonary nodules underwent thoracoscopic wedge resection,and no intra-or postoperative mortality or morbidity was recorded.Conclusion CT-guided hardening agent localization before video-assisted thoracoscopic solitary pulmonary nodule resection is a safe and effective procedure for accurate diagnosis and resection of indeterminate solitary pulmonary nodules.

OBJECTIVE: To discuss whether a reduced dose of CsA was allowed yet without increase risk of rejection, and whether the incidence of CsA-related side effects be reduced while the curative effects be enhanced by combined use of Cyclosporine (CsA), prednisone and Mycophenolate Mofetil (MMF) in patients after renal transplantation. METHODS: In this comparative study, 213 renal allograft recipients receiving routine dose of CsA were compared with 176 cases receiving low dose CsA. RESULTS: The two groups showed no significant differences in renal function, incidence of rejection and human/kidney survival rate. However, the low dose CsA group showed a better total curative efficacy and significantly fewer incidences of ADRs. CONCLUSION: CsA, MMF and Pred used concomitantly in patients after renal transplantation allows for a reduced dose of CsA yet without increase the risk of acute rejection if with enough dose of MMF.

Objective: To establish the fingerprint chromatogram of Compound Renshen Injection (CRSI). Methods: HPLC with ZORBAX SB-C18[4.6(i.d)?250mm] column was used, the acetonitrile-water (gradient elution) as a mobile phase and detection wavelength at 203nm. Results: Indicating 27 peaks on the HPLC-fingerprint of CRSI. Conclusion: The method is simple and accurate with a good reproducibility and can be used as a quality control method for CRSI.

Objective To investigate the biological effects of 125I seeds and 60Co γ-rays on the non-small cell lung cancer cells A549 and the normal bronchial epithelium cells BEAS-2B.Methods A549 and BEAS-2B cells were irradiated with 125I seeds and 60Co γ-rays.The survival fraction was detected by colony formation assay.The cell cycle and cell apoptotic ratio were detected by flow cytometry.The expression of cell apoptotic related proteins was examined by western blot.Results After irradiation with different doses,the survival of A549 cells irradiated with 125I seeds was lower than that irradiated with γ-rays (t =6.06,9.42,4.90,P ＜0.05).After irradiation with 4 Gy of 125I seeds and 60Co γ-rays,the G1 phase percentages of A549 cells were 70.67％ ± 1.49％ and 59.59％ ± 0.71％ (t =10.77,P ＜ 0.05),and the apoptotic ratios of A549 cells were 18.09％ ±0.73％ and 9.81％ ±0.16％ (t =19.40,P＜ 0.05),respectively.125I seeds irradiation remarkably up-regulated the expressions of Bax and cleaved Caspase-3 proteins,down-regulated the expression of Bcl-2 proteins compared with 60Co γ-rays irradiation on A549 cells.However,the apoptotic ratio and the expressions of apoptosis-related proteins in BEAS-2B cells had little difference between two types of radiation.Conclusions The anti-proliferative effect of 125I seeds irradiation on A549 cell is more remarkably than that of 60Co γ-rays.The imbalance of Bcl-2/Bax ratio and the eventually activation of Caspase-3 proteins may play an important role in the anti-proliferative effect induced by the continuous low dose radiation of 125I-seeds.

AIM:To study whether the pulmonary infection of Escherichia coli (E.coli) interferes the glu-colipid metabolism in high-fat diet-induced obese mice.METHODS:High-fat diet-induced obese mice (n=48) and nor-mal chow-fed control mice ( n=48) were intranasally infused with 40 μL fluid containing 4 ×109 CFUs E.coli.The ser-um, periepididymal adipose tissue and liver were obtained at 0 d, 1 d, 2 d, 3 d and 4 d after infection.The body mass, periepididymal adipose tissue and liver were weighed , and the levels of fasting blood glucose (FBG), fasting blood insulin ( FINS) , free fatty acid ( FFA) and very-low-density lipoprotein ( VLDL) were measured by ELISA .The serum total cho-lesterol (TC), triglycerides (TG), high-density lipoprotein cholesterol (HDL-C) and low-density lipoprotein cholesterol ( LDL-C) , and hepatic TG contents were detected , and the hepatic steatosis was observed under microscope with oil red O staining.RESULTS:Compared with day 0, the body mass, fat mass and fat index were decreased significantly from day 1 to day 4 after infection (P<0.05).The levels of FBG, FINS and HOMA-IR were apparently raised from day 2 to day 4 af-ter infection (P<0.05).The contents of serum FFA, TG and VLDL were increased markedly from day 1 to day 4 after in-fection (P<0.05).However, the concentrations of serum TC, LDL-C and HDL-C were decreased obviously from day 1 to day 3 ( P<0.05 ) .The liver mass , liver index and TG content were significantly increased from day 1 to day 4 ( P<0.05 ) .Consistently , the lipid droplet accumulation in the liver cells was increased obviously at day 2 and day 4 after infec-tion.Compared with control group , except the levels of serum TC , LDL-C and HDL-C in obese group substantially de-creased, the other indexes were increased by different degrees during the whole experiment period (P<0.05).CONCLU-SION:Pulmonary infection of Escherichia coli exacerbates the disorder of glucose and lipid metabolism in high-fat diet-in-duced obese mice , which contributes the development of insulin resistance and hepatic steatosis .

Objective To evaluate the predictive value of tumor metabolic indexes measured by 18F-FDG PET/CT in recurrence of stage Ⅰ NSCLC after surgery.Methods A total of 85 patients (44 males,41 females,age (62.46± 10.38) years) in Shanghai Renji Hospital with stage Ⅰ NSCLC,who underwent 18F-FDG PET/CT and subsequent surgical resection,were retrospectively enrolled from April 2006 to December 2011.Gender,age,tumor size,pathology,SUVmax,MTV and TLG of the primary tumor were selected as variables.ROC curve analysis was used to analyze the cut off value.The prognostic significance of parameters for recurrence-free survival (RFS) was evaluated by univariate and multivariate analyses.Survival analysis was analyzed by Kaplan-Meier method.Results During follow-up period,tumor recurrence occurred in 21 patients (24.7％,21/85) and 11 patients (12.9％,11/85) died.The median follow-up period was 44 months.The median values of SUVmax,MTV and TLG were 4.100,3.048 cm3 and 7.970,respectively.Cut off values of SUVmax,MTV and TLG were 7.115,4.701 cm3 and 12.015 according to ROC curve analysis.Univariate Cox analysis showed that SUVmax(x2 =22.091),MTV (x2 =4.941) and TLG(x2 =10.488) were associated with RFS(all P＜0.05).But gender,age,tumor size,and pathology were not independent risk factors of recurrence (x2=0.248-3.888,all P＞0.05).Multivariate Cox analysis revealed that SUVmax(=16.902,HR=15.426,P＜0.05) and TLG (x2=6.029,HR=4.054,P＜0.05) were independent prognostic factors for recurrence.Kaplan-Meier survival analysis showed that the period of RFS in high SUVmax (＞ 7.115) group (x2=32.545,P＜0.05) and in high TLG (＞12.015) group (x2=12.665,P＜0.05) were lower than those in low SUVmax group and low TLG group.Conclusion The SUVmax and TLG measured by 18F-FDG PET/CT have significant value for predicting the recurrence of stage Ⅰ NSCLC.

Objective To analyze indications,complications and outcomes of amputation.Methods A total of 15 patients undergone amputation in field or at tent hospital were collected for analy-zing injury severity,place where amputation was done,whether open or closed amputation and stitch re-moval time. Results There were 9 males and 6 females.at an average age of 32 years(11-51years).There were 16 amputations including Gustilo IIIB in 2 patients, Gustilo IIIC in 9 and Tscheme Ⅲin 5 according to Gustiln classification or Tscheme classification.Four patients who received amputation in field or at tent hospital developed infection and had to receive amputation again at a higher level on the limb and drainage of open wounds because of a higher infection rate due to the amputation location.Ten patients received first amputation at higher levels with open wound at station hospital but only 2 manifested infected incision.High level amputation with one stage closure was done in 1 patient who was infected and suppurated after operation and even developed bacteremia. Conclusions Infection rate following am-putation 4n field and tent clinics is rather higher,so secondary open amputations should be performed at a higher level as soon as possible.One-time and high-level open amputation plays an important role in treat-ment of severe lower limb injuries following earthquake.