Vaxvec: The first web-based recombinant vaccine vector database and its data analysis

A recombinant vector vaccine uses an attenuated virus, bacterium, or parasite as the carrier to express a heterologous antigen(s). Many recombinant vaccine vectors and related vaccines have been developed and extensively investigated. To compare and better understand recombinant vectors and vaccines, we have generated Vaxvec (http://www.violinet.org/vaxvec), the first web-based database that stores various recombinant vaccine vectors and those experimentally verified vaccines that use these vectors. Vaxvec has now included 59 vaccine vectors that have been used in 196 recombinant vector vaccines against 66 pathogens and cancers. These vectors are classified to 41 viral vectors, 15 bacterial vectors, 1 parasitic vector, and 1 fungal vector. The most commonly used viral vaccine vectors are double-stranded DNA viruses, including herpesviruses, adenoviruses, and poxviruses. For example, Vaxvec includes 63 poxvirus-based recombinant vaccines for over 20 pathogens and cancers. Vaxvec collects 30 recombinant vector influenza vaccines that use 17 recombinant vectors and were experimentally tested in 7 animal models. In addition, over 60 protective antigens used in recombinant vector vaccines are annotated and analyzed. User-friendly web-interfaces are available for querying various data in Vaxvec. To support data exchange, the information of vaccine vectors, vaccines, and related information is stored in the Vaccine Ontology (VO). Vaxvec is a timely and vital source of vaccine vector database and facilitates efficient vaccine vector research and development.     

实验动物品系数据库的建立

目的基于国内外部分实验动物数据库和文献,收集整理世界上现有的200多种共计26 000多个品系的实验动物数据,建立关系型检索数据库,使其成为世界上最大最全的实验动物品系数据库。方法构建基于My SQL数据库软件的中小型数据库,建立检索界面、录入界面和数据库接口。结果本文建立了实验动物品系数据库,已经收录小鼠品系数据21 596条;大鼠品系数据2062条;猴品系数据13条;地鼠品系数据2条;犬品系数据5条;兔品系数据5条。以后会逐步完善数据,实现实验动物品系数据库的定期更新。讨论该数据库的建立方便我国科研人员查阅和使用国内外实验动物品系资源,为引进欧美日等发达国家的实验动物品系资源提供链接。     

Evaluation of Cognitive Behavioral Interventions and Psychoeducation Implemented by Rehabilitation Specialists to Treat Fear-Avoidance Beliefs in Patients With Low Back Pain: A Systematic Review

Objectives

To systematically locate, critically appraise, and synthesize the available evidence regarding the effectiveness of cognitive behavioral therapies (CBTs) and psychoeducation that can be implemented by rehabilitation specialists to treat fear-avoidance beliefs in patients with acute, subacute, and chronic low back pain (LBP).

Effectiveness of Conservative,Surgical, and Postsurgical Interventions for Trigger Finger,Dupuytren Disease,and De Quervain Disease: A Systematic Review

Objectives

To provide an evidence-based overview of the effectiveness of conservative and (post)surgical interventions for trigger finger, Dupuytren disease, and De Quervain disease.

大连医科大学SCI论文榜数据库的建设

针对国内高校网站SCI论文榜现状,介绍了大连医科大学SCI论文榜的建设内容、特点,指出高校图书馆建库要从用户角度考虑,充分利用网络技术,在保证数据质量的前提下对数据进行二次加工,为用户提供尽可能多的内容和链接,方便用户浏览详细信息和利用相关资源。由于SCI论文榜数据质量要求较高,还要在技术和人力上做好充分准备,馆员需具备耐心、细致的特质。     

医院病理样本库管理系统的设计

目的:建立病理样本数据库,以规范病理样本管理流程,并为病理样本存储和研究提供工作平台。方法:病理样本库管理系统采用了J2EE、JSP及组件对象模型等技术,建立了病理样本库工作平台,实现了病理资源网络化、文档化及智能化。结果:该系统建立了病理样本管理系统架构和工作流程,为病理样本的收集、存储及分析提供了平台。结论:系统设计可提高样本检定结果的真实性和可信度,从而提高样本分析的准确性,为相关科室的信息化建设提供了良好的借鉴。     

Haplotype distribution in a forensic full mtDNA genome database of admixed Southern Brazilians and its association with self-declared ancestry and pigmentation traits

Background:The advent of massively parallel sequencing (MPS) applications focused on the generation of forensic-quality full mitochondrial genome sequences led to a popularization of the technique on a global scale. However, the lack of forensic-graded population databases has refrained a wider adoption of full genome sequences as the industry standard, despite its better discrimination capacity of individual maternal lineages.Purpose:This work describes a forensic-oriented full mtDNA genome database comprised of 480 samples from a Southern Brazilian population.Methods:A collection of mitochondrial sequences were obtained from low-pass, full genome DNA sequencing results. The complete sample set was evaluated regarding haplotype composition and distribution. Summary statistics and forensic parameters were calculated and are presented for the database, with detailed information concerning the impact of removing genetic information in the form of specific variants or increasingly larger genomic regions. Interpopulational analysis comparing haplotypical diversity in Brazilian and 26 worldwide populations was also performed. The association between mitochondrial genetic variability and phenotypic diversity was also evaluated in populations, with self-declared ancestry and three distinct phenotypic pigmentation traits (eyes, skin and hair colors) as parameters.Results:The presented database can be used to evaluate mitochondrial-related genetic evidence, providing LR values of up to 20,465 for unobserved haplotypes. Haplotype distribution in Southern Brazil seems to be different than the remaining of the country, with a larger contribution of maternal lines with European origin. Despite association can be found between lighter and darker phenotypes or self-declared ancestry and haplotype distribution, prediction models cannot be reliably proposed due to the admixed nature of the Brazilian population.Conclusions:The proposed database provides a basis for statistical calculation and frequency estimation of full mitochondrial genomes, and can be part of an integrated, representative, national database comprising most of the genetic diversity of maternal lineages in the country.     

Prevalence of total knee arthroplasty and its predictive factors in Japanese patients with rheumatoid arthritis: Analysis using the NinJa cohort

Objectives. The aim of this study was to clarify the prevalence and the predictive factors for undergoing total knee arthroplasty (TKA) among patients with rheumatoid arthritis (RA).

Methods. The data of 1,134 patients with RA who were enrolled in the Japanese nationwide cohort database NinJa in 2003 and consecutively followed up until 2009 were analyzed.

Results. Seventy-six patients underwent TKA during the observation period. The yearly progression of the modified Health Assessment Questionnaire or mHAQ score from 2003 to 2004, but not the yearly progression of the Disease Activity Score in 28 Joints or DAS28 or patient visual analog scale (VAS) score, was significantly higher in the patients who underwent TKA than those who did not.

Multivariate analysis showed that knee involvement in the disease, high Steinbrocker stage (III or IV), and high patient VAS score at the time of enrollment were powerful predictive factors, with hazard ratios of 4.01, 3.71, and 1.20, respectively.

According to survival analysis with TKA as an endpoint, patients with knee involvement in the disease at the time of enrollment had a significantly worse 5-year survival rate than did those without knee involvement (83.5% vs. 97.0%, respectively).

Conclusion. Several factors were elucidated as predictive factors for undergoing TKA among patients with RA.     

Balloon Aortic Valvuloplasty as a Bridge to Aortic Valve Replacement: A Contemporary Nationwide Perspective

ObjectivesThis study sought to use a national representative database to assess the incidence, predictors, and outcomes of balloon aortic valvuloplasty (BAV) as a bridge to transcatheter aortic valve replacement (TAVR) in contemporary practice.BackgroundNationwide data on the use and outcomes of BAV as a bridge to TAVR are limited.MethodsPatients who underwent BAV between January and June in 2015 and 2016 were identified in the National Readmission Database. We assessed rate of subsequent TAVR following BAV, and predictors and timing of subsequent TAVR. We then identified a group of patients who had direct TAVR (without prior BAV) in the original 2015 to 2016 National Readmission Database dataset. We compared in-hospital outcomes following TAVR between patients with prior bridging BAV and those undergoing direct TAVR.ResultsAmong the 3,691 included patients 1,426 (38.6%) had subsequent TAVR. Timing of TAVR was pre-discharge in 7.4%, within 30 days in 35%, between 31 and 90 days in 47%, between 91 and 180 days in 14%, and >180 days in 4%. Negative predictors of subsequent TAVR included prior defibrillator (odds ratio [OR]: 0.56; 95% confidence interval [CI]: 0.36 to 0.85), dementia (OR: 0.60; 95% CI: 0.46 to 0.79), malnutrition (OR: 0.64; 95% CI: 0.45 to 0.90), and malignancy (OR: 0.62; 95% CI: 0.47 to 0.82). In propensity-score matched cohorts of patients who underwent direct TAVR versus those with prior BAV, in-hospital mortality during TAVR admission was similar (3.7% vs. 3.5%; p = 0.91). Major complications, length of stay, and discharge disposition were also comparable. However, cost of the hospitalization was higher in the direct TAVR group.ConclusionsAbout 40% of BAV patients undergo subsequent TAVR mostly within 90 days. In-hospital outcomes of TAVR in these patients were comparable with propensity-score matched patients who underwent TAVR without prior BAV. Further investigations are needed to define the role of BAV in contemporary practice.