Who Has Used Internal Company Documents for Biomedical and Public Health Research and Where Did They Find Them?

Objective

To describe the sources of internal company documents used in public health and healthcare research.

Methods

We searched PubMed and Embase for articles using internal company documents to address a research question about a health-related topic. Our primary interest was where authors obtained internal company documents for their research. We also extracted information on type of company, type of research question, type of internal documents, and funding source.

Results

Our searches identified 9,305 citations of which 357 were eligible. Scanning of reference lists and consultation with colleagues identified 4 additional articles, resulting in 361 included articles. Most articles examined internal tobacco company documents (325/361; 90%). Articles using documents from pharmaceutical companies (20/361; 6%) were the next most common. Tobacco articles used documents from repositories; pharmaceutical documents were from a range of sources. Most included articles relied upon internal company documents obtained through litigation (350/361; 97%). The research questions posed were primarily about company strategies to promote or position the company and its products (326/361; 90%). Most articles (346/361; 96%) used information from miscellaneous documents such as memos or letters, or from unspecified types of documents. When explicit information about study funding was provided (290/361 articles), the most common source was the US-based National Cancer Institute. We developed an alternative and more sensitive search targeted at identifying additional research articles using internal pharmaceutical company documents, but the search retrieved an impractical number of citations for review.

Conclusions

Internal company documents provide an excellent source of information on health topics (e.g., corporate behavior, study data) exemplified by articles based on tobacco industry documents. Pharmaceutical and other industry documents appear to have been less used for research, indicating a need for funding for this type of research and well-indexed and curated repositories to provide researchers with ready access to the documents.     

Genetic analysis of idiopathic hemochromatosis using both qualitative (disease status) and quantitative (serum iron) information.

An ongoing family study of idiopathic hemochromatosis in Brittany, France, allowed us to investigate the segregation of this trait and its linkage and association to the HLA-A locus in 147 pedigrees, comprising 1,408 individuals with over 900 characterized for relevant biological parameters and typed for HLA. The joint consideration of affection status and serum iron concentration reveals no dominance effect on the latter trait and documents the increased information afforded by the consideration of a biological correlate of liability to affection for disease exhibiting incomplete penetrance. Our overall results are in general agreement with published results on a Utah family study.     

Retrieving mutation-specific information for human proteins in UniProt/Swiss-Prot Knowledgebase

The UniProt/Swiss-Prot Knowledgebase records about 30,500 variants in 5,664 proteins (Release 52.2). Most of these variants are manually curated single amino acid polymorphisms (SAPs) with references to the literature. In order to keep the list of published documents related to SAPs up to date, an automatic information retrieval method is developed to recover texts mentioning SAPs. The method is based on the use of regular expressions (patterns) and rules for the detection and validation of mutations. When evaluated using a corpus of 9,820 PubMed references, the precision of the retrieval was determined to be 89.5% over all variants. It was also found that the use of nonstandard mutation nomenclature and sequence positional correction is necessary to retrieve a significant number of relevant articles. The method was applied to the 5,664 proteins with variants. This was performed by first submitting a PubMed query to retrieve articles using gene or protein names and a list of mutation-related keywords; the SAP detection procedure was then used to recover relevant documents. The method was found to be efficient in retrieving new references on known polymorphisms. New references on known SAPs will be rendered accessible to the public via the Swiss-Prot variant pages.     

中国最受关注濒危物种保护现状快速评价的新方法探讨

本文尝试制订了一套评分标准, 对中国174个国家I级保护动植物物种和IUCN物种红色名录中极危(CR)、濒危(EN)级别的鸟类的保护成效进行了快速评价。选取种群数量和趋势、信息完善程度、模拟分布区中适宜生境面积变化趋势和模拟分布区被保护区覆盖程度等4个指标进行评分。数据来源包括公开发表的研究文献、遥感数据、实地调查和公众收集。结果表明, 174个物种的保护状况整体呈变差趋势, 4项指标平均值均为负值。单个物种保护状况改善的有26种, 维持原状的有32种, 变差的有116种。本文还对2000-2013年间发表的涉及746个受威胁物种的9,338篇研究文献进行了梳理, 结果表明被研究物种数和文献数都逐年上升, 但每年被研究的物种不到1/3。研究集中于明星物种和有经济价值的物种, 如大熊猫(Ailuropoda melanoleuca)的文献占了全部的11.33%, 大多数物种研究不足。分析表明即使是集中了最多保护资源的濒危物种, 其保护状况仍然是变差的。     

Distribution of information in biomedical abstracts and full-text publications

MOTIVATION: Full-text documents potentially hold more information than their abstracts, but require more resources for processing. We investigated the added value of full text over abstracts in terms of information content and occurrences of gene symbol--gene name combinations that can resolve gene-symbol ambiguity. RESULTS: We analyzed a set of 3902 biomedical full-text articles. Different keyword measures indicate that information density is highest in abstracts, but that the information coverage in full texts is much greater than in abstracts. Analysis of five different standard sections of articles shows that the highest information coverage is located in the results section. Still, 30-40% of the information mentioned in each section is unique to that section. Only 30% of the gene symbols in the abstract are accompanied by their corresponding names, and a further 8% of the gene names are found in the full text. In the full text, only 18% of the gene symbols are accompanied by their gene names.     

我国生态产品价值实现政策的配置与优化——基于政策文本分析

为促进城乡区域协调发展，推动地区生态产业化和产业生态化，完善生态产品价值实现的多元化路径和政策制度体系，对当前中央和地方政府发布的生态产品价值实现相关政策文本展开分析，并提出优化建议，为后续相关政策配置与优化提供参考。通过选取2019年-2022年8月间36份生态产品价值实现政策文本作为研究对象，构建政策工具-政策目标二维分析框架，借助质性分析工具Nvivo12对其进行量化分析和综合评价。研究发现，政策文件以通知和实施方案为主；政策工具覆盖较为全面，但内部存在分配不太协调的现象。政策目标维度中生态环境优美化受关注度较高，而生态产业高效化较少。工具-目标配置上，存在多对多的关系，不同政策目标对应的政策工具也存在差异。为进一步优化生态产品价值实现的政策供给，从政策工具上应以战略、具体规划为重点，平衡政策工具内部结构比例；从政策目标上应强调从金融和技术方面助推生态产品价值实现的同时，也需要加强法规管制力度，推出更专业化和可操作性的具体举措，因地制宜凸显区域化特色和差异，真正将生态产品价值实现政策落到实处，确保成果看得见摸得着。     

Walk,swim or fly? Locomotor mode predicts genetic differentiation in vertebrates

Limited dispersal is commonly used to explain differences in diversification rates. An obvious but unexplored factor affecting dispersal is the mode of locomotion used by animals. Whether individuals walk, swim or fly can dictate the type and severity of geographical barriers to dispersal, and determine the general range over which genetic differentiation might occur. We collated information on locomotion mode and genetic differentiation (F_ST) among vertebrate populations from over 400 published articles. Our results showed that vertebrate species that walk tend to have higher genetic differentiation among populations than species that swim or fly. Within species that swim, vertebrates in freshwater systems have higher genetic differentiation than those in marine systems, which is consistent with the higher number of species in freshwater environments. These results show that locomotion mode can impact gene flow among populations, supporting at a broad‐scale what has previously been proposed at smaller taxonomical scales.     

世界各国应对番茄褐色皱果病毒跨境传播采取的植物检疫措施分析及启示

[目的]为了防范番茄褐色皱果病毒（Tomato brown rugose fruit virus,ToBRFV）跨境传入我国,本文对世界各国应对ToBRFV跨境传播采取的植物检疫措施进行分析,以期为我国应对ToBRFV提供参考。[方法]通过查阅各国政府和国际组织官网、文献等资料,收集世界各国应对ToBRFV的相关信息,对其开展的早期预警、出台的植物检疫政策和防控措施等进行梳理和分析。[结果]为防范ToBRFV的快速蔓延风险,各国和组织通过将其列入警示名单、向WTO提交相关通报、发表相关文章等手段开展早期预警。为防止ToBRFV的传入和扩散,各国和组织快速出台将其列为官方管制对象、制修订相关进境检疫法律法规等植物检疫政策;从产地、出口前、进口后等方面制定了严格的防控措施。[结论]早识别、早应对是国际上应对ToBRFV跨境传播的关键举措,各国的检疫措施整体严格。建议我国继续关注ToBRFV发生动态、适时调整检疫措施、提高口岸检疫能力、开展调查监测。     

The response of the Italian press to AIDS: a 22-month analysis.

This study analyses the way in which the Italian press reported Acquired Immunodeficiency Syndrome (AIDS) over a 22-month period from September 1993 to June 1995, when no national AIDS information campaigns were made in Italy. During this period we collected, read, and categorized every article relating to Human Immunodeficiency Virus (HIV) and AIDS in fourteen newspapers and two news magazines with the highest national circulation. Articles were then assigned to one of six content categories: statistics, basic science, cure and vaccine, education/awareness and prevention issue, government or non-goverment organizations response, and people with AIDS (PWA) personal portrayals. A total of 4,228 articles referring to HIV/AIDS were identified. Analysis of the featured topics reveals several clear differences in the coverage of aspects of AIDS. The major category was represented by government or non-goverment organization response which accounted for 1,341 articles. Overall, this analysis suggests that, even long after the beginning of the epidemic, the press continues to see AIDS as an important issue. However, the articles explaining scientifically the AIDS epidemic were very few. The majority of AIDS-related information was spread in consequence of sensational events. Further analysis of PWA coverage shows that most articles discussed news that could provoke a negative feeling towards HIV-infected patients among the general population.     

Portrayal of the Human Resource Crisis and Accountability in Healthcare: A Qualitative Analysis of Ugandan Newspapers

Background

Uganda is one of the 57 countries with a critical shortage of health workers. The aim of this study was to determine how the human resources and health service crisis was covered in Ugandan newspapers and, in particular, how the newspapers attributed accountability for problems in the health services.

Methods

We collected all articles related to health workers and health services for the calendar year 2012 in the two largest national newspapers in Uganda (collection on daily basis) and in one local newspaper (collection on weekly basis). These articles were analysed qualitatively regarding the main themes covered and attribution of accountability.

Results

The two more urban national newspapers published 229 articles on human resources and health services in Uganda (on average over two articles per week), whereas the local more rural newspaper published only a single article on this issue in the 12 month period. The majority of articles described problems in the health service without discussing accountability. The question of accountability is raised in only 46% of articles (106 articles). The responsibility of the government was discussed in 50 articles (21%), and negligence, corruption and misbehaviour by individual health workers was reported in 56 articles (25%). In the articles about corruption (n=35), 60% (21 articles) mention corruption by health workers and 40% (14 articles) mention corruption by government officials. Six articles defended the situation of health workers in Uganda.

Conclusions

The coverage of accountability in the Ugandan newspapers surveyed is insufficient to generate informed debate on what political actions need to be taken to improve the crisis in health care and services. There exists not only an “inverse care law” but also an “inverse information law”: those sections of society with the greatest health needs and problems in accessing quality health care receive the least information about health services.     

How good are articles on adverse drug reactions?

A study was carried out of the quality and completeness of articles on adverse drug reactions: 5737 articles from 80 countries published between 1972 and 1979 were studied. Only 61% of the articles included information on the number of patients treated and the number with adverse drug reactions, yet these are essential for calculating the incidence of adverse reactions. In only 55% could the incidence of a particular adverse reaction be calculated. Great importance is placed on articles on adverse reactions, particularly those that report on many patients. Authors and editors should ensure that articles include the following information: drug regimens, numbers of patients treated, numbers of patients developing adverse reactions, and nature and incidence of adverse reactions.     

Hairpins in bookstacks: information retrieval from biomedical text

Current advances in high-throughput biology are accompanied by a tremendous increase in the number of related publications. Much biomedical information is reported in the vast amount of literature. The ability to rapidly and effectively survey the literature is necessary for both the design and the interpretation of large-scale experiments, and for curation of structured biomedical knowledge in public databases. Given the millions of published documents, the field of information retrieval, which is concerned with the automatic identification of relevant documents from large text collections, has much to offer. This paper introduces the basics of information retrieval, discusses its applications in biomedicine, and presents traditional and non-traditional ways in which it can be used.     

Examining the Impact of the National Institutes of Health Public Access Policy on the Citation Rates of Journal Articles

PurposeTo examine whether National Institutes of Health (NIH) funded articles that were archived in PubMed Central (PMC) after the release of the 2008 NIH Public Access Policy show greater scholarly impact than comparable articles not archived in PMC.MethodsA list of journals across several subject areas was developed from which to collect article citation data. Citation information and cited reference counts of the articles published in 2006 and 2009 from 122 journals were obtained from the Scopus database. The articles were separated into categories of NIH funded, non-NIH funded and whether they were deposited in PubMed Central. An analysis of citation data across a five-year timespan was performed on this set of articles.ResultsA total of 45,716 articles were examined, including 7,960 with NIH-funding. An analysis of the number of times these articles were cited found that NIH-funded 2006 articles in PMC were not cited significantly more than NIH-funded non-PMC articles. However, 2009 NIH funded articles in PMC were cited 26% more than 2009 NIH funded articles not in PMC, 5 years after publication. This result is highly significant even after controlling for journal (as a proxy of article quality and topic).ConclusionOur analysis suggests that factors occurring between 2006 and 2009 produced a subsequent boost in scholarly impact of PubMed Central. The 2008 Public Access Policy is likely to be one such factor, but others may have contributed as well (e.g., growing size and visibility of PMC, increasing availability of full-text linkouts from PubMed, and indexing of PMC articles by Google Scholar).     

Integrating image data into biomedical text categorization

Categorization of biomedical articles is a central task for supporting various curation efforts. It can also form the basis for effective biomedical text mining. Automatic text classification in the biomedical domain is thus an active research area. Contests organized by the KDD Cup (2002) and the TREC Genomics track (since 2003) defined several annotation tasks that involved document classification, and provided training and test data sets. So far, these efforts focused on analyzing only the text content of documents. However, as was noted in the KDD'02 text mining contest-where figure-captions proved to be an invaluable feature for identifying documents of interest-images often provide curators with critical information. We examine the possibility of using information derived directly from image data, and of integrating it with text-based classification, for biomedical document categorization. We present a method for obtaining features from images and for using them-both alone and in combination with text-to perform the triage task introduced in the TREC Genomics track 2004. The task was to determine which documents are relevant to a given annotation task performed by the Mouse Genome Database curators. We show preliminary results, demonstrating that the method has a strong potential to enhance and complement traditional text-based categorization methods.     

An audit of the BMJ's correspondence columns.

OBJECTIVE--To see whether some sections of the BMJ attract more comment than others, whether letters submitted in response to different sections of the journal are rejected at different rates, and whether the balance between letters that agree and disagree with articles in the published correspondence reflects that in submitted letters. DESIGN--Retrospective audit of letters submitted for publication in the correspondence columns of the BMJ in response to articles published between 1 January and 21 May 1989. SUBJECTS--A total of 1319 letters received by the journal, 974 submitted in response to the 1501 published articles and a further 345 raising new issues. MAIN OUTCOME MEASURES--The total numbers of letters submitted in response to the four main sections of the journal--editorials, news, papers, and middles--and the numbers published. Submitted and published letters were analysed according to whether they agreed or disagreed with articles. RESULTS--The overall rejection rate was 63% (831/1319), but among letters relating to articles it was 56% (543/974). Editorials and middles attracted proportionately more letters than papers, but letters relating to papers had a lower rejection rate (43% v 57% for editorials and 43% v 66% for middles). For all sections more letters disagreed than agreed, but a higher proportion of letters in response to editorials and middles disagreed than those submitted in response to papers (64% and 72% v 53%). Among the published letters, however, broadly equal numbers of letters agreed and disagreed with articles, irrespective of section. CONCLUSION--Those sections of the journal that aim at stimulating debate succeeded in attracting the most comment. The relative importance of original scientific research papers was reflected by the priority given to letters submitted in response to papers, and the final correspondence column was a balanced platform of debate despite an unequal submitted response in terms of letters that agreed and disagreed with different sections of the journal.     

Surgical scientific publication and the 1991-1995 war in Croatia

The aim of this study was to evaluate surgical scientific publication in relation to the 1991-1995 war in Croatia, based on the articles indexed in Medline database that were published in 1980-2005 period. The number of articles was extracted from PubMed and analysed with trend analysis, which is preferred analytic approach over calculation of crude publication rates. The results indicate sporadic pre-war output, which was almost completely reduced by the onset of war. During wartime, a significant increasing trend in the number of published surgical articles that were related to warfare was detected (p = 0.003). During the post-war period a gradual shift towards surgical articles that were not related to warfare was detected, also marked by the significant increasing trend (p = 0.027). Both trends were significantly steeper than the overall Croatian biomedical output, suggesting that surgical scientific articles were being published more dynamically than in other biomedical areas in Croatia. The results suggest that war in Croatia has had a strong modifying effect on the surgical scientific output.     

Effectively Communicating the Uncertainties Surrounding Ebola Virus Transmission

The current Ebola virus outbreak has highlighted the uncertainties surrounding many aspects of Ebola virus virology, including routes of transmission. The scientific community played a leading role during the outbreak—potentially, the largest of its kind—as many of the questions surrounding ebolaviruses have only been interrogated in the laboratory. Scientists provided an invaluable resource for clinicians, public health officials, policy makers, and the lay public in understanding the progress of Ebola virus disease and the continuing outbreak. Not all of the scientific communication, however, was accurate or effective. There were multiple instances of published articles during the height of the outbreak containing potentially misleading scientific language that spurred media overreaction and potentially jeopardized preparedness and policy decisions at critical points. Here, we use articles declaring the potential for airborne transmission of Ebola virus as a case study in the inaccurate reporting of basic science, and we provide recommendations for improving the communication about unknown aspects of disease during public health crises.     

Assessing the quality of newspaper medical advice columns for elderly readers

BACKGROUND: Medical advice columns in newspapers can provide a valuable service by educating the general public about important health-related issues. However, these columns may be harmful if the advice or information given in them is incomplete, inappropriate or misleading. The objective of this study was to assess the safety and appropriateness of advice given to elderly readers of newspapers in medical advice columns. METHODS: Medical advice columns published in Canadian newspapers in 1995 were identified from a CD-ROM database. The articles that were selected were published in English and contained medical advice pertinent to elderly people about topics that could be found in a textbook of geriatric medicine. Fifty articles, randomly selected from the 109 articles that met these criteria, were independently assessed by 5 geriatricians. A scoring system was used to rate the ability to determine to which population the article applied, how well fact was distinguished from opinion, the degree to which critical issues were addressed, the safety and the appropriateness of the advice. When the kappa statistic for inter-rater agreement was 0.74 or less, a 2-stage Delphi process was used in an attempt to reach consensus. RESULTS: Agreement (kappa > 0.74) was eventually achieved for 232 (92.8%) of the 250 ratings. In 4 (8%) of the articles there was a high probability that the advice given could be applied to the wrong patient population; in 7 (14%) there was a high probability that opinion might be interpreted as fact; and in 11 (22%) the major critical issues were not identified. Of greatest concern, however, the advice in 25 (50%) of the articles was judged to be inappropriate, and in 14 (28%) advice may have been dangerous and potentially life-threatening. INTERPRETATION: Although medical advice columns have the potential to improve the health of elderly readers, a significant percentage of these articles contain inappropriate or even potentially dangerous advice.