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1.  Comparison of classical and non‐classical cardiovascular risk factors influencing the patency of native arteriovenous fistulas after percutaneous transluminal angioplasty therapy among haemodialysis patients 
Postgraduate Medical Journal  2007;83(982):547-551.
Objective
To evaluate the classical and non‐classical cardiovascular risk factors that effect patency of native arteriovenous fistulas (AVF) in end stage renal disease (ESRD) patients who are undergoing regular haemodialysis treatment and have a percutaneous transluminal angioplasty (PTA) procedure.
Methods
All PTAs performed between 1 October 2002 and 30 September 2004 were identified from case notes and the computerised database and follow up to 31 March 2005. The definition of patency of AVF after PTA was including primary or secondary patencies. Risks were analysed to assess the influence on survival following PTAs of age, sex, serum cholesterol, serum triglyceride, diabetes, use of aspirin, current smoking and hypertension, serum albumin, serum calcium–phosphate product, intact parathyroid hormone (I‐PTH), and urea reduction ratio (URR).
Results
The patency rate of AVFs of all interventions was 65% at 6 months. Factors with poor patencies of AVFs after PTA procedures were higher serum calcium–phosphate product (p = 0.033), higher URR (p<0.001), lower serum albumin (p<0.001), non‐hypertension (p = 0.010) and “non‐smoker + ex‐smoker group” (p = 0.033). The hypertensive patients and current smokers had lower patency failure after PTAs (p<0.01 and p<0.05, respectively).
Conclusions
Unfavourable cumulative patency rates are observed in haemodialysis patients with higher URR, higher serum calcium–phosphate product and hypoalbuminaemia (lower serum albumin before the PTA procedure). Hypertension and current smoking were associated with better patency rates of AVF after PTA.
doi:10.1136/pgmj.2006.054908
PMCID: PMC2600117  PMID: 17675549
2.  Draft Genome Sequences of the Mycobacterium tuberculosis Clinical Strains A2 and A4, Isolated from a Relapse Patient in Taiwan 
Genome Announcements  2014;2(5):e00672-14.
The recurrence rate of Mycobacterium tuberculosis in Taiwan is 3%. Here, we present the draft genome sequences of M. tuberculosis strains A2 and A4 from a relapse patient. The draft genome sequences comprise 4,443,031 bp and 4,487,096 bp, revealing 4,220 and 4,143 coding sequences for A2 and A4, respectively, as well as 49 tRNA genes for the both isolates.
doi:10.1128/genomeA.00672-14
PMCID: PMC4155581  PMID: 25189576
3.  Carbon monoxide regulates the expression of the wound-inducible gene ipomoelin through antioxidation and MAPK phosphorylation in sweet potato 
Journal of Experimental Botany  2014;65(18):5279-5290.
Summary
A reduction in CO produced by IbHO occurs in leaves upon wounding and causes H2O2 generation and ERK phosphorylation. Defence systems are then switched on to protect plants from herbivores.
Carbon monoxide (CO), one of the haem oxygenase (HO) products, plays important roles in plant development and stress adaptation. However, the function of CO involved in wounding responses is seldom studied. A wound-inducible gene, ipomoelin (IPO), of sweet potato (Ipomoea batatas cv. Tainung 57) was used as a target to study the regulation of CO in wounding responses. After wounding for 1h, the endogenous CO content and IbHO expression level were significantly reduced in leaves. IPO expression upon wounding was prohibited by the HO activator hemin, whereas the HO inhibitor zinc protoporphyrin IX elevated IPO expression. The IPO expression induced by wounding, H2O2, or methyl jasmonate was inhibited by CO. CO also affected the activities of ascorbate peroxidase, catalase, and peroxidase, and largely decreased H2O2 content in leaves. CO inhibited the extracellular signal-regulated kinase (ERK) phosphorylation induced by wounding. IbMAPK, the ERK of sweet potato, was identified by immunoblotting, and the interaction with its upstream activator, IbMEK1, was further confirmed by bimolecular fluorescence complementation and co-immunoprecipitation. Conclusively, wounding in leaves repressed IbHO expression and CO production, induced H2O2 generation and ERK phosphorylation, and then stimulated IPO expression.
doi:10.1093/jxb/eru291
PMCID: PMC4157712  PMID: 25063862
Carbon monoxide; ERK phosphorylation; H2O2; ipomoelin; sweet potato; wounding.
4.  Draft Genome Sequence of the Mycobacterium tuberculosis Clinical Isolate C2, Belonging to the Latin American–Mediterranean Family 
Genome Announcements  2014;2(3):e00536-14.
Tuberculosis remains a major infectious disease in Taiwan. Here we present the draft genome sequence of the Mycobacterium tuberculosis C2 strain, belonging to the Latin American–Mediterranean lineage. The draft genome sequence comprises 4,453,307 bp with a G+C content of 65.6%, revealing 4,390 coding genes and 45 tRNA genes.
doi:10.1128/genomeA.00536-14
PMCID: PMC4047450  PMID: 24903871
5.  Comparing Risk of New Onset Diabetes Mellitus in Chronic Kidney Disease Patients Receiving Peritoneal Dialysis and Hemodialysis Using Propensity Score Matching 
PLoS ONE  2014;9(2):e87891.
Chronic kidney disease (CKD) patients are at risk for developing new-onset diabetes mellitus (NODM) even after hemodialysis (HD) and peritoneal dialysis (PD) treatment. It is not clear if the incidence for NODM is different in CKD patients receiving HD and PD. This study compared the risk of NODM in PD patients and HD patients.
Methods
All HD and PD patients in Taiwan Renal Registry Database from 1997 to 2005 were included and all patients were followed to December 31, 2008. The risk of NODM was analyzed in PD patients and propensity score matched HD patients using logistic regression for early type NODM (< = 6 months after dialysis) and Cox regression for late type NODM (>6 months after dialysis).
Results
A total of 2548 PD patients and 10192 HD patients who had no diabetes on the initiation of dialysis were analyzed. The incidence for NODM was 3.7 per 100 patient/year for HD and 2.4 for PD patients. HD patients are more at risk for developing early type NODM (p<0.001) with an adjusted odds ratio of 1.41 [95% confidence interval (CI) 1.12–1.78)]. HD patients are more at risk for late type NODM (p<0.001) with an adjusted hazard ratio of 2.01 (95% CI: 1.77–2.29). Patient’s age was negatively associated with risk of early type of NODM (p<0.001) but positively associated with risk of late type NODM (p<0.001).
Conclusions
Chronic kidney disease patients receiving hemodialysis are more at risk for developing new-onset diabetes mellitus compared to those receiving peritoneal dialysis.
doi:10.1371/journal.pone.0087891
PMCID: PMC3913687  PMID: 24504072
6.  Draft Genome Sequence of NDM-1-Producing Klebsiella pneumoniae Clinical Isolate 303K 
Genome Announcements  2013;1(6):e01069-13.
Multidrug-resistant New Delhi metallo-β-lactamase 1 (NDM-1)-producing bacteria have spread globally and become a major clinical and public health threat. We report here the draft genome sequence of the Klebsiella pneumoniae clinical isolate 303K, harboring an NDM-1 coding sequence.
doi:10.1128/genomeA.01069-13
PMCID: PMC3868859  PMID: 24356835
7.  Identification of Cytotoxic T Lymphocyte Epitopes on Swine Viruses: Multi-Epitope Design for Universal T Cell Vaccine 
PLoS ONE  2013;8(12):e84443.
Classical swine fever (CSF), foot-and-mouth disease (FMD) and porcine reproductive and respiratory syndrome (PRRS) are the primary diseases affecting the pig industry globally. Vaccine induced CD8+ T cell-mediated immune response might be long-lived and cross-serotype and thus deserve further attention. Although large panels of synthetic overlapping peptides spanning the entire length of the polyproteins of a virus facilitate the detection of cytotoxic T lymphocyte (CTL) epitopes, it is an exceedingly costly and cumbersome approach. Alternatively, computational predictions have been proven to be of satisfactory accuracy and are easily performed. Such a method enables the systematic identification of genome-wide CTL epitopes by incorporating epitope prediction tools in analyzing large numbers of viral sequences. In this study, we have implemented an integrated bioinformatics pipeline for the identification of CTL epitopes of swine viruses including the CSF virus (CSFV), FMD virus (FMDV) and PRRS virus (PRRSV) and assembled these epitopes on a web resource to facilitate vaccine design. Identification of epitopes for cross protections to different subtypes of virus are also reported in this study and may be useful for the development of a universal vaccine against such viral infections among the swine population. The CTL epitopes identified in this study have been evaluated in silico and possibly provide more and wider protection in compared to traditional single-reference vaccine design. The web resource is free and open to all users through http://sb.nhri.org.tw/ICES.
doi:10.1371/journal.pone.0084443
PMCID: PMC3866179  PMID: 24358361
8.  Monitoring the antigenic evolution of human influenza A viruses to understand how and when viruses escape from existing immunity 
BMC Research Notes  2013;6:227.
Background
The World Health Organization (WHO) organizes consultations in February and September of each year, spearheaded by an advisory group of experts to analyze influenza surveillance data generated by the WHO Global Influenza Surveillance and Response System (GISRS). The purpose of these consultations is to recommend the composition on influenza virus vaccines for the northern and southern hemispheres, respectively. The latest news of influenza viruses is made available to the public and updated on the WHO website. Although WHO discloses the manner in which it has made the recommendation, usually by considering epidemiological and clinical information to analyze the antigenic and genetic characteristics of seasonal influenza viruses, most individuals do not possess an understanding of antigenic drift and when it occurs.
Findings
We have constructed a web server, named Fluctrl, and implemented a pipeline whereby HA sequence data is downloaded from the Influenza Virus Resource at NCBI along with their isolation information including isolation year and location, which are parsed and managed in MySQL database. By analyzing the frequency of each amino acid residue of the HA1 domain expressed by the viruses on annual basis, users are able to obtain evolutionary dynamics of human influenza viruses corresponding with epidemics. Users are able to upload and analyze their HA1 sequences for generating evolutionary dynamics. In addition, a distribution of amino acid residues at a particular site is represented geographically to trace the location where antigenic variants are seeded.
Conclusions
Fluctrl is constructed for monitoring the antigenic evolution of human influenza A viruses. This tool is intended to inform the general public how and when influenza viruses evade the human body's immunity. Furthermore, leveraging the geographic information, the original locations of emerging influenza viruses can be traced. Fluctrl is freely accessible at http://sb.nhri.org.tw/fluctrl.
doi:10.1186/1756-0500-6-227
PMCID: PMC3689074  PMID: 23758844
9.  Comparing Survival between Peritoneal Dialysis and Hemodialysis Patients with Subclinical Peripheral Artery Disease: a 6-Year Follow-Up 
Peripheral artery disease (PAD) is known to be an increased mortality risk in patients with end-stage renal disease (ESRD). The aim of this study was to compare patient survival between patients with subclinical PAD undergoing peritoneal dialysis (PD) and hemodialysis (HD). Subclinical peripheral artery was defined as an ankle-brachial index of less than 0.9. This study was conducted from April 2005, and the observation period ended on 30 June 2011. At the end of the follow-up, the status of all patients was assessed and data on mortality were obtained for the entire cohort. A total of 91 patients (61 HD and 30 PD) were included for analyses in this study. Mortality rate was 60.0% (18/30) for PD and 52.5% (32/61) for HD. Kaplan-Meier estimate demonstrate that PD patients had a higher mortality rate than those underwent HD (log-rank p = 0.0039). Cox regression model demonstrated that PD was an independent predictor for further mortality in ESRD patients with subclinical peripheral artery disease.(p = 0.012, HR: 1.776, 95% CI: 1.136-2.775). In multivariate analysis, the HD group still had a greater survival than PD group (p = 0.005, HR:1.916, 95% CI: 1.218-3.015). In patients with subclinical peripheral artery disease, the patient survival is better in HD patients as compared with PD patients.
doi:10.7150/ijms.5091
PMCID: PMC3590604  PMID: 23471522
Survival; hemodialysis; peritoneal dialysis; peripheral artery disease.
10.  Association of response to hepatitis B vaccination and survival in dialysis patients 
BMC Nephrology  2012;13:97.
Background
The status of immunocompromised patients is well recognized in end stage renal disease (ESRD). As described recently, this acquired immune dysfunction in the uremic milieu may be one of the main pathogenic factors for mortality in ESRD. The aim of this study was to determine the relationship between the immune response following a hepatitis B vaccination (HBV vaccination) and the survival of maintenance dialysis patients.
Methods
A total of 156 patients (103 on hemodialysis and 53 on continuous ambulatory peritoneal dialysis) were recruited. After receiving a full dose of the HBV vaccination, all patients were followed up for to 5 years to evaluate the association of patient survival, cause of mortality, and immune response.
Results
The response rate to the hepatitis B vaccination was 70.5%. There was no significant association between the immune response and the 5-year survival rate (p =0.600) or between the post-vaccination anti-HBs titers and the 5-year survival rate (p = 0.201). The logistic prediction model with the coefficient as non-response following HBV vaccination, diabetes mellitus, old age, and low albumin level could significantly predict infection-cause mortality (sensitivity = 0.842, specificity = 0.937).
Conclusion
There was no significant association between the immune response to HBV vaccination and the 5-year survival rate. However, non-response following HBV vaccination might be associated with infection-cause mortality in dialysis patients.
doi:10.1186/1471-2369-13-97
PMCID: PMC3471045  PMID: 22935561
Hepatitis B vaccination; Immune response; Post-vaccination anti-HBs titers
11.  The risk for chronic kidney disease in patients with heart diseases: a 7-year follow-up in a cohort study in Taiwan 
BMC Nephrology  2012;13:77.
Background
The worldwide increasing trend of chronic kidney disease (CKD) is of great concern and the role of heart disease deserves longitudinal studies. This study investigated the risk of developing CKD among patients with heart diseases.
Methods
From universal insurance claims data in Taiwan, we retrospectively identified a cohort of 26005 patients with newly diagnosed heart diseases and 52010 people without such disease from the 2000–2001 claims. We observed prospectively both cohorts until the end of 2007 to measure CKD incidence rates in both cohorts and hazard ratios (HR) of CKD.
Results
The incidence of CKD in the cohort with heart disease was 4.1 times greater than that in the comparison cohort (39.5 vs. 9.65 per 10,000 person-years). However, the HR changed into 2.37 (95% confidence interval (CI) = 2.05 – 2.74) in the multivariate Cox proportional hazard model after controlling for sociodemographic characteristics and comorbidity. Compared with individuals aged < 40 years, the HRs for CKD ranged from 2.70 to 4.99 in older age groups. Significant estimated relative risks of CKD observed in our patients were also independently associated with hypertension (HR = 2.26, 95% CI = 1.94 - 2.63) and diabetes mellitus (HR = 2.44, 95% CI = 2.13 - 2.80), but not with hyperlipidemia (HR =1.13, 95% CI = 0.99-1.30).
Conclusions
This population study provides evidence that patients with heart disease are at an elevated risk of developing CKD. Hypertension and diabetes mellitus are also comorbidity associated with increasing the CKD risk independently.
doi:10.1186/1471-2369-13-77
PMCID: PMC3437200  PMID: 22863289
12.  Real-Time PCR Analysis of the Intestinal Microbiotas in Peritoneal Dialysis Patients 
Bifidobacterium and Lactobacillus can beneficially affect the host by producing acetic acid and lactic acid, which lower pH and thereby inhibit the growth of pathogens or allow the probiotic bacteria to compete with pathogens for epithelial adhesion sites and nutrients. The transmural migration of enteric organisms into the peritoneal cavity can cause peritonitis in peritoneal dialysis (PD) patients. We hypothesized that the composition of the intestinal microbiota with regard to Lactobacillus species and Bifidobacterium species differed between PD patients and healthy controls. The aim of the study was to investigate these differences by real-time PCR analysis of fecal samples. From 1 August 2009 to 31 March 2010, a total of 29 nondiabetic PD patients and 41 healthy controls from China Medical University Hospital were recruited after giving their informed consent. Fecal samples were collected from the PD patients and their age-matched counterparts in the morning using a standardized procedure. DNA extracted from these samples was analyzed by real-time PCR. All bifidobacteria, Bifidobacterium catenulatum, B. longum, B. bifidum, Lactobacillus plantarum, L. paracasei, and Klebsiella pneumoniae were less frequently detected in the patient samples. Dysbiosis (microbial imbalance) may impair intestinal barrier function and increase host vulnerability to pathogen invasion. Further studies are necessary to confirm our findings before clinical trials with probiotic supplementation in PD patients.
doi:10.1128/AEM.05605-11
PMCID: PMC3273023  PMID: 22179250
13.  A Novel puf-A Gene Predicted from Evolutionary Analysis Is Involved in the Development of Eyes and Primordial Germ-Cells 
PLoS ONE  2009;4(3):e4980.
Although the human genome project has been completed for some time, the issue of the number of transcribed genes with identifiable biological functions remains unresolved. We used zebrafish as a model organism to study the functions of Ka/Ks-predicted novel human exons, which were identified from a comparative evolutionary genomics analysis.
In this study, a novel gene, designated as puf-A, was cloned and functionally characterized, and its homologs in zebrafish, mouse, and human were identified as one of the three homolog clusters which were consisted of 14 related proteins with Puf repeats. Computer modeling of human Puf-A structure and a pull-down assay for interactions with RNA targets predicted that it was a RNA-binding protein. Specifically, Puf-A contained a special six Puf-repeat domain, which constituted a unique superhelix half doughnut-shaped Puf domain with a topology similar to, but different from the conventional eight-repeat Pumilio domain. Puf-A transcripts were uniformly distributed in early embryos, but became restricted primarily to eyes and ovaries at a later stage of development. In mice, puf-A expression was detected primarily in retinal ganglion and pigmented cells. Knockdown of puf-A in zebrafish embryos resulted in microphthalmia, a small head, and abnormal primordial germ-cell (PGC) migration. The latter was confirmed by microinjecting into embryos puf-A siRNA containing nanos 3′ UTR that expressed in PGC only. The importance of Puf-A in the maturation of germline stem cells was also implicated by its unique expression in the most primitive follicles (stage I) in adult ovaries, followed by a sharp decline of expression in later stages of folliculogenesis. Taken together, our study shows that puf-A plays an important role not only in eye development, but also in PGC migration and the specification of germ cell lineage. These studies represent an exemplary implementation of a unique platform to uncover unknown function(s) of human genes and their roles in development regulation.
doi:10.1371/journal.pone.0004980
PMCID: PMC2656619  PMID: 19319195

Results 1-13 (13)