Cross sectional survey of multicentre clinical databases in the United Kingdom

Objectives To describe the multicentre clinical databases that exist in the United Kingdom, to report on their quality, to explore which organisational and managerial features are associated with high quality, and to make recommendations for improvements.Design Cross sectional survey, with interviews with database custodians and search of electronic bibliographic database (PubMed).Studies reviewed 105 clinical databases across the United Kingdom.Results Clinical databases existed in all areas of health care, but their distribution was uneven—cancer and surgery were better covered than mental health and obstetrics. They varied greatly in age, size, growth rate, and geographical areas covered. Their scope (and thus their potential uses) and the quality of the data collected also varied. The latter was not associated with any organisational characteristics. Despite impressive achievements, many faced substantial financial uncertainty. Considerable scope existed for improvements: greater use of nationally approved codes; more support from relevant professional organisations; greater involvement by nurses, allied health professionals, managers, and laypeople in database management teams; and more attention to data security and ensuring patient confidentiality. With some notable exceptions, the audit and research potential of most databases had not been realised: half the databases had each produced only four or fewer peer reviewed research articles.Conclusions At least one clinical database support unit is needed in the United Kingdom to provide assistance in organisation and management, information technology, epidemiology, and statistics. Without such an initiative, the variable picture of databases reported here is likely to persist and their potential not be realised.     

Cancer and the web

The applications of functional genomics, proteomics and informatics to cancer research have yielded a tremendous amount of information, which is growing all the time. Much of this information is available publicly on the Internet and ranges from general information about different cancers from a patient or clinical viewpoint, through to databases suitable for cancer researchers of all backgrounds, to very specific sites dedicated to individual genes or molecules. A simple search for 'cancer' from a typical Web browser search engine yields more than half a million hits; an even more specific search for 'leukaemia' (>40 000 hits) or 'p53' (>5700 hits) yields far too many hits to allow one to identify particular sites of interest. This review aims to provide a brief guide to some of the resources and databases that can be used as springboards to home in rapidly on information relevant to many fields of cancer research. As such, this article will not focus on a single website but hopes to illustrate some of the ways that postgenomic biology is revolutionizing cancer research. It will cover genomics and proteomics approaches that have been applied to studying global expression patterns in cancers, in addition to providing links ranging from general information about cancer to specific cancer gene mutation databases.     

An analysis of historical trends in classical biological control of arthropods suggests need for a new centralized database in the USA

The documentation of biological control agents targeting arthropods in the United States has historically been subject to less regulation relative to weed biological control releases. This study reviews publicly available databases to track environmental releases of biological control agents targeting arthropods in the United States. It then presents available data for the states with the most releases between 1962 and 2005: Hawaii, California and Florida. These data indicate a clear decline in rates of introduction since 1982 or 1994, depending on the source. Existing record-keeping systems offer incomplete or inconsistent data for evaluation because they were designed with limited goals, attempt to capture excessive detail and are thus impractical, or are insufficiently resourced. Existing databases cannot be used to answer meaningful questions regarding non-target effects of introduced control agents. Current databases are inappropriately designed and insufficiently resourced to meet today's research and regulatory needs. We propose and describe a new database system for classical biological control of arthropods.     

European approach to the Human Gene Project

In the history of gene mapping, which extends through most of the present century, Europe has played an important role. This has continued during the evolution of the 10 International Human Gene Mapping Workshops that have been held in seven different countries since 1973. Nationally coordinated programs have been a recent development, and several European countries, including the United Kingdom and Italy, have followed the lead of the United States in investing substantial sums of money in research on the human genome. In addition, the European Community has launched a multinational program of research on Human Genome Analysis to complement the various national initiatives. The particular approach in Europe has been to support those in the field by establishing resource centers for distributing biomaterials and accessing databases, by assisting in the training of scientists, and by funding programs of research directed at present needs in both physical and genetic mapping.     

国际糖生物学战略布局与研究前沿分析

糖生物学与细胞信号转导、发育、免疫等许多领域相关联,是全面、深入理解生命活动所必需的。本文通过分析各国在糖生物学领域的战略布局,并使用ISI Essential Science Indicators数据库和VOS Viewer软件从定量角度分析国际糖生物学领域的研究前沿,为我国制定糖生物学研究相关战略提供借鉴。     

Effectiveness of patient-targeted interventions to promote cancer screening among ethnic minorities: A systematic review

BackgroundCancer is a major public health problem due to its incidence, morbidity and mortality. A large proportion of cancer cases and deaths could be prevented through the implementation of cancer screening programmes. However, there are social inequalities in patient access to these programmes, especially in underserved communities and minority populations.ObjectiveTo identify, characterise and analyse the effectiveness of patient-targeted healthcare interventions to promote cancer screening programmes in ethnic minorities.MethodsA comprehensive search of bibliographic databases was conducted. The results of our systematic review were reported in accordance with the PRISMA guidelines.ResultsSeventeen articles were identified and included in the review. Sixteen of the seventeen studies were conducted in the United States and one was conducted in Israel. Fifteen of the seventeen interventions selected were effective in increasing cancer screening rates. Moreover, five of the seventeen studies found an improvement in cancer knowledge, awareness, self-efficacy, attitudes, intention and perceptions, and three studies found a positive change in health beliefs and barriers. The results show that culturally adapted interventions appear to increase the rate of participation in cancer screening. In addition, the effectiveness of the interventions seems to be related to the use of small media, one-on-one interactions, small group education sessions, reminder strategies, and strategies for reducing structural barriers and out-of-pocket costs.ConclusionCulturally adapted patient-targeted healthcare interventions can help to reduce racial or ethnic inequalities in access to cancer screening programmes. Further research is needed to develop interventions to promote adherence to cancer screening programmes with repeat testing and vigorous economic evaluation methodologies.     

Depositing electron microscopy maps

A meeting was held at the European Bioinformatics Institute (EBI) in Hinxton, United Kingdom to discuss recent progress in the development of EMD, a database for maps determined by electron microscopy that is now integrated with MSD, the macromolecular structure database at EBI. This meeting of representatives of many of the major image processing groups in electron microscopy also discussed possible software developments that would ease the documentation and deposition of such datasets. The meeting concluded with a strong endorsement of map deposition in electron microscopy and its linkage with the family of archival databases in biomedical research.     

Gene expression databases and data mining

The DNA microarray technology has arguably caught the attention of the worldwide life science community and is now systematically supporting major discoveries in many fields of study. The majority of the initial technical challenges of conducting experiments are being resolved, only to be replaced with new informatics hurdles, including statistical analysis, data visualization, interpretation, and storage. Two systems of databases, one containing expression data and one containing annotation data are quickly becoming essential knowledge repositories of the research community. This present paper surveys several databases, which are considered "pillars" of research and important nodes in the network. This paper focuses on a generalized workflow scheme typical for microarray experiments using two examples related to cancer research. The workflow is used to reference appropriate databases and tools for each step in the process of array experimentation. Additionally, benefits and drawbacks of current array databases are addressed, and suggestions are made for their improvement.     

Advancements in Input‐Output Models and Indicators for Consumption‐Based Accounting

The use of global, multiregional input‐output (MRIO) analysis for consumption‐based (footprint) accounting has expanded significantly over the last decade. Most of the global studies on environmental and social impacts associated with consumption or embodied in international trade would have been impossible without the rapid development of extended MRIO databases. We present an overview of the developments in the field of MRIO analysis, in particular as applied to consumption‐based environmental and social footprints. We first provide a discussion of research published on various global MRIO databases and the differences between them, before focusing on the virtual laboratory computing infrastructure for potentially making MRIO databases more accessible for collaborative research, and also for supporting greater sectoral and regional detail. We discuss work that includes a broader range of extensions, in particular the inclusion of social indicators in consumption‐based accounting. We conclude by discussing the need for the development of detailed nested MRIO tables for investigating linkages between regions of different countries, and the applications of the rapidly growing field of global MRIO analysis for assessing a country's performance toward the United Nations Sustainable Development Goals.     

Association between comorbidity and participation in breast and cervical cancer screening: A systematic review and meta-analysis

BackgroundComorbidity is associated with poor outcomes for cancer patients but it is less clear how it influences cancer prevention and early detection. This review synthesizes evidence from studies that have quantified the association between comorbidity and participation in breast and cervical screening.MethodsPubMed, CINAHL and EMBASE databases were systematically searched using key terms related to cancer screening and comorbidity for original research articles published between 1 January 1991 and 21 March 2016. Two reviewers independently screened 1283 studies that met eligibility criteria related to Population (adult, non-cancer populations), Exposure (comorbidity), Comparison (a ‘no comorbidity’ group), and Outcome (participation in breast cancer or cervical screening). Data was extracted and risk of bias assessed using a standardised tool from the 22 studies identified for inclusion (17 breast; 13 cervical). Meta-analyses were performed for participation in breast and cervical screening, stratified by important study characteristics.ResultsThe majority of studies were conducted in the United States. Results of individual studies were variable. Most had medium to high risk of bias. Based on the three “low risk of bias” studies, mammography screening was less common among those with comorbidity (pooled Odds Ratio 0.66, 95%CI 0.44–0.88). The one “low risk of bias” study of cervical screening reported a negative association between comorbidity and participation.ConclusionWhile a definitive conclusion could not be drawn, the results from high quality studies suggest that women with comorbidity are less likely to participate in breast, and possibly cervical, cancer screening.     

Conducting clinical research in the new NHS: the model of cancer. United Kingdom Coordinating Committee on Cancer Research.

The United Kingdom Coordinating Committee on Cancer Research represents the major organizations funding cancer research in the United Kingdom. The deliberations of a working party convened by the committee to evaluate recently expressed concerns that the changes in the NHS threaten research, especially clinical trials to evaluate new treatments, are reported. A survey of contributors to trials coordinated by the committee showed that half are now experiencing difficulties in continuing to participate in clinical trials. The two major problems identified were lack of time and of staff, especially for NHS staff in non-teaching hospitals. Recent changes in junior doctors'' hours and proposed reductions in the length of time for training will exacerbate this. It is possible to identify the direct and indirect excess costs of conducting research in the NHS, but currently the mechanism does not exist to designate funds specifically for this purpose. Consultation with the regional directors of research and development confirmed that the service increment for teaching and research is not the solution for this. Proposals are made to secure future clinical research in the NHS, including finance, indemnity, the licensing of new drugs, the greater use of nurse counsellors, and the value of cancer registries.     

Towards a virtual reality for plant-associated fungi in the United States and Canada

At present knowledge of fungal biodiversity in North America is scattered in diverse sources ranging from well-reviewed, comprehensive databases to unedited databases of reports from the literature, information on file cards, and uncomputerized reference collections. Resources available electronically were used to determine their relative importance in evaluating the plant-associated fungi known from the United States and to a lesser extent Canada. The results demonstrate that the literature provides the greatest information but that reference collections in the US National Fungus Collections contribute between 22–31% additional data. Little overlap exists between fungi isolated as endophytes and those reported in the literature or as reference collections. Eighty to 100% of the plant-associated fungi reported from Canada are accounted for in comprehensive resources for the United States. A comprehensive database of plant-associated fungi in Canada, the United States, and eventually Mexico would serve as a valuable resource for those making plant quarantine decisions.     

Emerging roles for cancer registries in cancer control

Cancer registries are a vital part of the national cancer effort to cut United States cancer mortality rates in half by the year 2000. Registries provide the data to focus programs and monitor progress. Success in meeting the year 2000 goal will require aggressive attention to the opportunities for prevention, early detection, treatment, and applied cancer control research, all of which complement the current emphasis on basic research.     

Atlas of Genetics and Cytogenetics in Oncology and Haematology, updated

The 'Atlas of Genetics and Cytogenetics in Oncology and Haematology' (http://www.infobiogen.fr/services/chromcancer) is an Internet database aimed at genes involved in cancer, cytogenetics and clinical entities in cancer, and cancer-prone diseases. It presents information in concise and updated reviews (cards) or longer texts (deep insights), a (new) case report section, a huge portal towards genetics and/or cancer databases, and teaching items in genetics for students in medicine and the sciences. This database is made for and by clinicians and researchers in the above-mentioned fields, who are encouraged to contribute. It deals with cancer research, genomics and cytogenomics. It is at the crossroads of research, post-university teaching and telemedicine. The Atlas is available at no cost.     

In-silico selection of cancer blood plasma proteins by integrating genomic and proteomic databases

Blood protein markers have been studied for the clinical management of cancer. Due to the large number of the proteins existing in blood, it is often necessary to pre-select potential protein markers before experimental studies. However, to date there is a lack of automated method for in-silico selection of cancer blood proteins that integrates the information from both genetic and proteomic studies in a cancer-specific manner. In this work, we synthesized both genomic and proteomic information from several open access databases and established a bioinformatic pipeline for in-silico selection of blood plasma proteins overexpressed in specific type of cancer. We demonstrated the workflow of this pipeline with an example of breast cancer, while the methodology was applicable for other cancer types. With this pipeline we obtained 10 candidate biomarkers for breast cancer. The proposed pipeline provides a useful and convenient tool for in-silico selection of candidate blood protein biomarkers for a variety of cancer research.     

Academic impact of a public electronic health database: bibliometric analysis of studies using the general practice research database

Background

Studies that use electronic health databases as research material are getting popular but the influence of a single electronic health database had not been well investigated yet. The United Kingdom''s General Practice Research Database (GPRD) is one of the few electronic health databases publicly available to academic researchers. This study analyzed studies that used GPRD to demonstrate the scientific production and academic impact by a single public health database.

Methodology and Findings

A total of 749 studies published between 1995 and 2009 with ‘General Practice Research Database’ as their topics, defined as GPRD studies, were extracted from Web of Science. By the end of 2009, the GPRD had attracted 1251 authors from 22 countries and been used extensively in 749 studies published in 193 journals across 58 study fields. Each GPRD study was cited 2.7 times by successive studies. Moreover, the total number of GPRD studies increased rapidly, and it is expected to reach 1500 by 2015, twice the number accumulated till the end of 2009. Since 17 of the most prolific authors (1.4% of all authors) contributed nearly half (47.9%) of GPRD studies, success in conducting GPRD studies may accumulate. The GPRD was used mainly in, but not limited to, the three study fields of “Pharmacology and Pharmacy”, “General and Internal Medicine”, and “Public, Environmental and Occupational Health”. The UK and United States were the two most active regions of GPRD studies. One-third of GRPD studies were internationally co-authored.

Conclusions

A public electronic health database such as the GPRD will promote scientific production in many ways. Data owners of electronic health databases at a national level should consider how to reduce access barriers and to make data more available for research.     

Clinical infrastructures to support proteomic studies of tissue and fluids in breast cancer

The Danish Breast Cancer Cooperative Group (DBCG) was established in 1977 with the aim to ensure optimal breast cancer diagnostics and therapeutic modalities on a nationwide basis. DBCG was organized in such a way so it represents a broad interdisciplinary collaboration with established clinical databases and biobanks. This review summarizes the infrastructures, such as those of the DBCG, that are required to facilitate translational research studies aiming at further diagnostic and therapeutic improvements through interactions directed at prevention, early diagnosis, and treatment of primary breast cancer.     

Occupational exposure to genotoxic agents.

Millions of workers in the United States are potentially exposed each year to hazardous chemicals, dusts, or fibers in occupational settings. Some of these agents are genotoxic and may cause genetic alterations in the somatic or germ cells of exposed workers. Such alterations, if they occur in proto-oncogenes or tumor suppressor genes, which are involved in controlling cell growth or differentiation, may lead to the development of cancer. Genetic alterations in germ cells may also lead to reproductive failure or genetic disorders in subsequent generations. It has been estimated that occupational exposure accounts for 4% of all human cancers and up to 30% of cancer among blue-collar workers. Approximately 20,000 cancer deaths each year are attributable to occupational exposure in the United States. Occupational cancer and reproductive abnormalities have been listed on the National Occupational Research Agenda master list of research priorities as major occupational diseases and injuries.     

A meta-analysis of sunburn and basal cell carcinoma risk

Basal cell carcinoma (BCC) is the most common cancer in the United States. Sunburn is a modifiable risk factor for BCC. The objective of this project was to synthesize research on BCC and sunburn to quantify the impact and severity of sunburn at different life stages on BCC risk in the general population. A systematic literature search of four electronic databases was conducted and data were extracted by two independent reviewers using standardized forms. Data from 38 studies were pooled using both dichotomous and dose-response meta-analytic methods. BCC risk increased with ever experiencing a sunburn in childhood (OR=1.43, 95% CI: 1.19, 1.72) and with ever experiencing a sunburn in life (OR= 1.40, 95% CI: 1.02, 1.45). Every five sunburns experienced per decade in childhood increased BCC risk by 1.86 (95% CI: 1.73, 2.00) times. Every five sunburns experienced per decade in adulthood increased BCC risk by 2.12 (95% CI: 1.75, 2.57) times and every five sunburns per decade of life increased BCC risk by 1.91 (95% CI: 1.42, 2.58) times. The data on sunburn exposure and BCC show that an increase in number of sunburns at any age increased the risk of BCC. This may inform future prevention efforts.     

微生物与肺癌研究的知识图谱构建及可视化分析

【背景】微生物与肺癌的发生发展密切相关，该领域研究已成为国内外持续关注的焦点。【目的】对微生物与肺癌相关的文献进行文献计量分析，分析该领域的研究现状和发展趋势，为后续研究提供参考。【方法】收集Web of Science Core Collection （WOSCC）、中国知网（China National Knowledge Infrastructure，CNKI）、万方（Wanfang）与维普（VIP database for Chinese technical periodicals，VIP）等数据库的文献数据，并通过CiteSpace和VOSviewer对其年发文量、国家/地区、关键词进行可视化分析。【结果】共收录中文文献143篇，英文文献278篇。中国是发文量最多的国家。关键词分析显示，肺癌、肠道微生物、免疫治疗等关键词是该领域的研究热点。【结论】在过去20年中人们已关注到微生物在肺癌致病机制、诊断和治疗中的作用。通过对比这些数据库发现，国内外关注的热点话题基本一致。但该领域仍处于早期发展阶段，研究相对不成熟，缺乏广泛密切的国际合作，未来应进一步加强对该领域前沿热点的深入研究。本文结果有助于研究人员进一步了解该领域前沿热点及发展趋势，为后续研究的深入探索提供参考。