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author:("Zhou, sifeng")
1.  Outcomes of renal transplant recipients with BK virus infection and BK virus surveillance in the Auckland region from 2006 to 2012 
World Journal of Nephrology  2016;5(6):497-506.
To evaluate incidence, risk factors and treatment outcome of BK polyomavirus nephropathy (BKVN) in a cohort of renal transplant recipients in the Auckland region without a formal BK polyomavirus (BKV) surveillance programme.
A cohort of 226 patients who received their renal transplants from 2006 to 2012 was retrospectively reviewed.
Seventy-six recipients (33.6%) had a BK viral load (BKVL) test and 9 patients (3.9%) developed BKVN. Cold ischaemia time (HR = 1.18, 95%CI: 1.04-1.35) was found to be a risk factor for BKVN. Four recipients with BKVN had complete resolution of their BKV infection; 1 recipient had BKVL less than 625 copies/mL; 3 recipients had BKVL more than 1000 copies/mL and 1 had graft failure from BKVN. BKVN has a negative impact on graft function [median estimated glomerular filtration rate (eGFR) 22.5 (IQR 18.5-53.0) mL/min per 1.73 m2, P = 0.015), but no statistically significant difference (P = 0.374) in renal allograft function was found among negative BK viraemia group [median eGFR 60.0 (IQR 48.5-74.2) mL/min per 1.73 m2), positive BK viraemia without BKVN group [median eGFR 55.0 (IQR 47.0-76.0) mL/min per 1.73 m2] and unknown BKV status group [median eGFR 54.0 (IQR 43.8-71.0) mL/min per 1.73 m2]. The incidence and treatment outcomes of BKVN were similar to some centres with BKV surveillance programmes.
Recipients with BVKN have poorer graft function. Although active surveillance for BKV has been shown to be effective in reducing incidence of BKVN, it should be tailored specifically to that transplant centre based on its epidemiology and outcomes of BKVN, particularly in centres with limited resources.
PMCID: PMC5099595  PMID: 27872831
BK virus; BK polyomavirus nephropathy; Kidney transplantation; Screening
2.  Identifying Virulence-Associated Genes Using Transcriptomic and Proteomic Association Analyses of the Plant Parasitic Nematode Bursaphelenchus mucronatus 
Bursaphelenchus mucronatus (B. mucronatus) isolates that originate from different regions may vary in their virulence, but their virulence-associated genes and proteins are poorly understood. Thus, we conducted an integrated study coupling RNA-Seq and isobaric tags for relative and absolute quantitation (iTRAQ) to analyse transcriptomic and proteomic data of highly and weakly virulent B. mucronatus isolates during the pathogenic processes. Approximately 40,000 annotated unigenes and 5000 proteins were gained from the isolates. When we matched all of the proteins with their detected transcripts, a low correlation coefficient of r = 0.138 was found, indicating probable post-transcriptional gene regulation involved in the pathogenic processes. A functional analysis showed that five differentially expressed proteins which were all highly expressed in the highly virulent isolate were involved in the pathogenic processes of nematodes. Peroxiredoxin, fatty acid- and retinol-binding protein, and glutathione peroxidase relate to resistance against plant defence responses, while β-1,4-endoglucanase and expansin are associated with the breakdown of plant cell walls. Thus, the pathogenesis of B. mucronatus depends on its successful survival in host plants. Our work adds to the understanding of B. mucronatus’ pathogenesis, and will aid in controlling B. mucronatus and other pinewood nematode species complexes in the future.
PMCID: PMC5037770  PMID: 27618012
Bursaphelenchus mucronatus; virulence-associated gene; transcriptomic; proteomic
3.  Random rotation survival forest for high dimensional censored data 
SpringerPlus  2016;5(1):1425.
Recently, rotation forest has been extended to regression and survival analysis problems. However, due to intensive computation incurred by principal component analysis, rotation forest often fails when high-dimensional or big data are confronted. In this study, we extend rotation forest to high dimensional censored time-to-event data analysis by combing random subspace, bagging and rotation forest. Supported by proper statistical analysis, we show that the proposed method random rotation survival forest outperforms state-of-the-art survival ensembles such as random survival forest and popular regularized Cox models.
PMCID: PMC5001968  PMID: 27625979
Survival ensemble; Rotation forest; Time-to-event data; Censored data; High-dimensional data
4.  Rotation survival forest for right censored data 
PeerJ  2015;3:e1009.
Recently, survival ensembles have found more and more applications in biological and medical research when censored time-to-event data are often confronted. In this research, we investigate the plausibility of extending a rotation forest, originally proposed for classification purpose, to survival analysis. Supported by the proper statistical analysis, we show that rotation survival forests are able to outperform the state-of-art survival ensembles on right censored data. We also provide a C-index based variable importance measure for evaluating covariates in censored survival data.
PMCID: PMC4465950  PMID: 26082863
Survival analysis; Censored data; Survival ensemble; Medical decision making
5.  Large Unbalanced Credit Scoring Using Lasso-Logistic Regression Ensemble 
PLoS ONE  2015;10(2):e0117844.
Recently, various ensemble learning methods with different base classifiers have been proposed for credit scoring problems. However, for various reasons, there has been little research using logistic regression as the base classifier. In this paper, given large unbalanced data, we consider the plausibility of ensemble learning using regularized logistic regression as the base classifier to deal with credit scoring problems. In this research, the data is first balanced and diversified by clustering and bagging algorithms. Then we apply a Lasso-logistic regression learning ensemble to evaluate the credit risks. We show that the proposed algorithm outperforms popular credit scoring models such as decision tree, Lasso-logistic regression and random forests in terms of AUC and F-measure. We also provide two importance measures for the proposed model to identify important variables in the data.
PMCID: PMC4338292  PMID: 25706988
6.  Anti-Inflammatory Effect of IL-37b in Children with Allergic Rhinitis 
Mediators of Inflammation  2014;2014:746846.
Background. Interleukin-37 (IL-37), a newly described member of IL-1family, functioned as a fundamental inhibitor of innate inflammatory and immune responses, especially its isoform IL-37b. Objective. This study was undertaken to evaluate the expression and regulation of IL-37b in children with allergic rhinitis (AR). Methods. Forty children with AR and twenty-five normal controls were included. The relationship between IL-37b and Th1/2 cytokines production in serum and nasal lavage was examined by enzyme-linked immunosorbent assay (ELISA). Peripheral blood mononuclear cells (PBMCs) were purified for in vitro regulation experiment of IL-37b. Intranasal mometasone furoate was given in AR children and IL-37b change after one-month treatment was detected using ELISA. Results. We observed significantly decreased IL-37b expression levels in both serum and nasal lavage compared to controls. IL-37b was negatively correlated with Th2 cytokines. Our results also showed that IL-37b downregulated Th2 cytokine expressed by PBMCs and this modulation was through mitogen-activated protein kinase (MAPK) and phosphatidylinositol 3-kinase (PI3K) pathway. We also found that intranasal mometasone furoate therapy can promote nasal IL-37b expression. Conclusion. IL-37b may be involved in Th2 cytokine regulation in AR and its expression was related to the efficacy of intranasal steroid therapy.
PMCID: PMC4142748  PMID: 25177111
7.  Heat Shock Factor 2 Levels Are Associated with the Severity of Ulcerative Colitis 
PLoS ONE  2014;9(2):e88822.
Background and Aims
The morbidity of ulcerative colitis (UC) is increasing in China every year. In addition, there is a lack of accurate diagnostic indices with which to evaluate the activity of the disease. The aim of this study was to identify UC-associated proteins as biomarkers for the diagnosis, and objective assessment of disease activity.
Differential expression of serum proteins from UC patients compared to normal controls was analyzed by two-dimensional electrophoresis (2-DE) and matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF-MS). The expression of heat shock factor 2(HSF2)in colonic mucosa in Crohn's disease, Behcet's disease, ulcerative colitis, intestinal tuberculosis, infective enteritis, intestinal lymphoma, and normal controls was investigated by immunohistochemistry (IHC). The expression of the HSF2 in colonic mucosa of UC subjects with varying severity of disease was measured by real time-PCR and Western Blots. The expression of HSF2 was inhibited by HSF2 small interfering RNA (siRNA) transfection in Caco-2 cells. The concentrations of HSF2, IL-1β, and TNF-α in serum and IL-1β, and TNF-α in the supernatants of transfected Caco-2 cells were determined by ELISA.
HSF2 was differentially expressed in UC patients compared to normal controls. HSF2 expression was significantly higher in the intestinal mucosa of UC patients compared to other six groups. The results of immunohistochemistry, real time-PCR, Western Blots, and ELISA showed that the expression of HSF2 increased in parallel with the severity of UC. The serum concentration of HSF2 also positively correlated with levels of IL-1β and TNF-α. After down-regulation expression of HSF2 in Caco-2 cells by RNA interference, the productions of IL-1β and TNF-α stimulated by lipopolysaccharide (LPS) increased dramatically.
HSF2 appears to be a potential novel molecular marker for UC activity, and may provide a basis for studies on the pathogenesis and novel therapeutic targets for UC.
PMCID: PMC3923051  PMID: 24533153
8.  Efficacy of medical therapy in treatment of chronic rhinosinusitis 
Allergy & Rhinology  2012;3(1):e8-e12.
Uncomplicated chronic rhinosinusitis (CRS) is generally treated with medical therapy initially and surgery is contemplated only after medical therapy has failed. However, there is considerable variation in the medical treatment regimens used and studies defining their efficacy are few. The aim of this study was to determine the proportion of patients treated medically who responded sufficiently well so that surgery was not required. Subgroup analysis to identify clinical features that predicted a favorable response to medical therapy was also performed. Eighty patients referred to the Otorhinolaryngology Clinic at North Shore Hospital were treated with a standardized medical therapy protocol (oral prednisone for 3 weeks, oral antibiotics and ongoing saline lavage and intranasal budesonide spray). Symptom scores were collected before and after medical therapy. Clinical features such as presence of polyps, asthma, and aspirin hypersensitivity were recorded. Failure of medical therapy was defined as the persistence of significant CRS symptoms, and those patients who failed medical therapy were offered surgery. Follow-up data were available for 72 (90%) patients. Of this group, 52.5%, (95% CI, 42.7%, 62.2%) failed to respond adequately to medical therapy and were offered surgery. The remaining patients (37.5%) were successfully treated with medical therapy and did not require surgery at the time of follow-up. The premedical therapy symptom scores were significantly higher than the postmedical therapy symptom scores (p < 0.01). The symptom scores of those patients postmedical therapy who proceeded to have surgery were significantly higher than the group who responded well to maximum medical therapy (MMT) and did not require surgery (p < 0.0001). There were no significant differences in the proportion of patients with asthma, aspirin sensitivity, or polyps between the groups failing or not failing MMT. In approximately one-third of patients with CRS, medical therapy improved symptoms sufficiently so that surgical therapy was avoided. Patients with more severe symptoms tended not to respond as well as those with less severe symptoms. Long-term follow-up is required for the group of responders to determine how many will eventually relapse.
PMCID: PMC3404479  PMID: 22852131
Antibiotics; chronic rhinosinusitis; corticosteroid; intranasal steroid; macrolides; maximal medical therapy; medical therapy; prednisone; saline irrigation; symptom

Results 1-8 (8)