A report of the U.S. environmental protection agency gene-tox program: Part I Host-mediated assay

The methodologies and status of the Host-Mediated Assay were reviewed using the published literature available up to June 1980. The Working Group reviewed 274 documents, including abstracts, research articles, review articles, and publicly available contracts and grant final reports. From this group, abstracts and reviews were rejected from critical evaluation. 77 documents were accepted and reviewed by the Working Group and the test results summarized.These selected documents yielded 208 chemicals that were evaluated in the host-mediated assay. Of these chemicals, 133 were mutagenic in this assay with one or more indicators. 76 chemicals, several of which are not considered to be carcinogenic, were not detected by any of the indicators. Of the 208 chemicals, 125 had been tested in carcinogenicity assay in rodents. 90, or 71%, of the carcinogens were detected as mutagens in the Host-Mediated Assay. In several cases, those carcinogens not detected may have been negative because of improper selection of the indicator.The Working Group concluded that the Host-Mediated Assay is an important test in mutagenicity/carcinogenicity research and that, by proper selection of protocols and indicators, valuable information can be gained that otherwise would be overlooked by strict, in vitro assays.     

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.     

The risk/safety assessment of transgenic crops: the transportability of data

This paper presents the activities and publications of Organisation for Economic Co-operation and Developments (OECD’s) Working Group on Harmonisation of Regulatory Oversight in Biotechnology and the Task Force for the Safety of Novel Foods and Feeds. The main outputs of the work are the Series of “consensus documents” of the respective groups. These documents compile information which is intended to be used by those involved in the business of risk/safety assessment. These documents are one means of ensuring the transportability of data amongst authorities. An increasing trend in both the Working Group and Task Force is to consider crop species which are relevant to tropical regions and therefore to countries that are not necessarily members of the OECD. For example, the Working Group has recently published a consensus document on bananas and plantains while the Task Force has published a document on cassava. This trend towards crops of greater interest in the tropics is likely to continue into the future.     

Unscheduled DNA synthesis tests. A report of the U.S. Environmental Protection Agency Gene-Tox Program

The utility of unscheduled DNA synthesis (UDS) testing for screening potentially hazardous chemicals was evaluated using the published papers and technical reports available to the UDS Work Group. A total of 244 documents were reviewed. Based on criteria defined in advance for evaluation of the results, 169 were rejected. From the 75 documents accepted, results were reviewed for 136 chemicals tested using autoradiographic approaches and for 147 chemicals tested using liquid scintillation counting (LSC) procedures; 38 chemicals were tested by both approaches to measure UDS. Since there were no documents available that provided detailed recommendations of UDS screening protocols or criteria for evaluating the results, the UDS Work Group presents suggested protocols and evaluation criteria suitable for measuring and evaluating UDS by autoradiography in primary rat hepatocytes and diploid human fibroblasts and by the LSC approach in diploid human fibroblasts. UDS detection is an appropriate system for inclusion in carcinogenicity and mutagenicity testing programs, because it measures the repair of DNA damage induced by many classes of chemicals over the entire mammalian genome. However, for this system to be utilized effectively, appropriate metabolic activation systems for autoradiographic measurements of UDS in human diploid fibroblasts must be developed, the nature of hepatocyte-to-hepatocyte variability in UDS responses must be determined, and the three suggested protocols must be thoroughly evaluated by using them to test a large number of coded chemicals of known in vivo mutagenicity and carcinogenicity.     

Computing fuzzy associations for the analysis of biological literature

The increase of information in biology makes it difficult for researchers in any field to keep current with the literature. The MEDLINE database of scientific abstracts can be quickly scanned using electronic mechanisms. Potentially interesting abstracts can be selected by matching words joined by Boolean operators. However this means of selecting documents is not optimal. Nonspecific queries have to be effected, resulting in large numbers of irrelevant abstracts that have to be manually scanned To facilitate this analysis, we have developed a system that compiles a summary of subjects and related documents on the results of a MEDLINE query. For this, we have applied a fuzzy binary relation formalism that deduces relations between words present in a set of abstracts preprocessed with a standard grammatical tagger. Those relations are used to derive ensembles of related words and their associated subsets of abstracts. The algorithm can be used publicly at http:// www.bork.embl-heidelberg.de/xplormed/.     

Behavioral and Psychological Factors in the Assessment and Treatment of Obesity Surgery Patients

Objective: To provide evidence‐based guidelines on the psychological and behavioral screening of weight loss surgery (WLS) candidates and the impact of psychosocial factors on behavior change after gastric bypass surgery. Research Methods and Procedures: The members of the Behavioral and Psychological subgroup of the Multidisciplinary Care Task Group conducted searches of MEDLINE and PubMed for articles related to WLS, behavior changes, and mental health, including quality of life (QOL) and behavior modification. Pertinent abstracts and literature were reviewed for references. A total of 198 abstracts were identified; 17 papers were reviewed in detail. Search periods were from 1980 to 2004. Results: We found a high incidence of depression, negative body image, eating disorders, and low QOL in severely obese patients. Our task subgroup recommended that all WLS candidates be evaluated by a licensed mental health care provider (i.e., psychiatrist, psychologist, or social worker), experienced in the treatment of severely obese patients and working within the context of a multidisciplinary care team. We also recommended development of pre‐ and postsurgical treatment plans that address psychosocial contraindications for WLS and potential barriers to postoperative success. Discussion: The psychological consequences of obesity can range from lowered self‐esteem to clinical depression. Rates of anxiety and depression are three to four times higher among obese individuals than among their leaner peers. A comprehensive multidisciplinary program that incorporates psychological and behavior change services can be of critical benefit in enhancing compliance, outcome, and QOL in WLS patients.     

XplorMed: a tool for exploring MEDLINE abstracts

The most frequent access to the MEDLINE database of scientific abstracts is by keyword search. However, this is often not sufficient because although the user might find all the useful abstracts, these are buried in hundreds that are irrelevant. The exploratory tool XplorMed has been developed to analyse the result of any MEDLINE query. It suggests main groups of related topics and documents, sparing the user the need of reading all abstracts.     

Could preoperative short-course radiotherapy be the treatment of choice for localized advanced rectal carcinoma?

Short-course preoperative radiotherapy (RT) is widely used in northern Europe for locally advanced resectable rectal cancer, but its role in the era of advanced imaging techniques is uncertain. Here, we reviewed articles and abstracts on SCRT published from 1974 through 2013 with the goal of identifying patients who might be best suited for short-course RT. We included relevant articles comparing surgery with or without preoperative radiation published before and after the advent of total mesorectal excision. We also analyzed two randomized trials directly comparing short-course RT with conventionally fractionated chemoradiation (the Polish Colorectal Study Group and the Trans-Tasman Radiation Oncology Group) that compared short-course RT with conventional chemoradiotherapy. We conclude from our review that short-course RT can be generally applied for operable rectal cancer and produces high rates of pelvic control with acceptable toxicity; it reduces local recurrence rates but does not increase overall survival. SCRT seems to be best used for tumors considered “low risk,” i.e., those that are >5 cm from the anal margin, without circumferential margin involvement, and involvement of fewer than 4 lymph nodes. Whether sequential chemotherapy can further improve outcomes remains to be seen, as does the best time for surgery (immediately or 6–8 weeks after RT). We further recommend that selection of patients for short-course RT should be based on findings from magnetic resonance imaging or transrectal ultrasonography.     

Inconsistent Definitions for Intention-To-Treat in Relation to Missing Outcome Data: Systematic Review of the Methods Literature

Background

Authors of randomized trial reports seem to hold a variety of views regarding the relationship between missing outcome data (MOD) and intention to treat (ITT). The objectives of this study were to systematically investigate how authors of methodology articles define ITT in the presence of MOD, how they recommend handling MOD under ITT, and to make a proposal for potential improvement in the definition and use of ITT in relation to MOD.

Methods and Findings

We systematically searched MEDLINE in February 2009 for methodological articles written in English that devoted at least one paragraph to ITT and two other paragraphs to either ITT or MOD. We excluded original trial reports, observational studies, and clinical systematic reviews. Working in teams of two, we independently extracted relevant information from each eligible article. Of 1007 titles and abstracts reviewed, 66 articles met eligibility criteria. Five (8%) did not provide a definition of ITT; 25 (38%) mentioned MOD but did not discuss its relationship to ITT; and 36 (55%) discussed the relationship of MOD with ITT. These 36 articles described one or more of three statements: complete follow-up is required for ITT (58%); ITT and MOD are separate issues (17%); and ITT requires a specific strategy for handling MOD (78%); 17 (47%) endorsed more than one relationship. The most frequently mentioned strategies for handling MOD within ITT were: using the last outcome carried forward (50%); sensitivity analysis (50%); and use of available data to impute missing data (46%).

Conclusion

We found that there is no consensus on the definition of ITT in relation to MOD. For conceptual clarity, we suggest that both reports of randomized trials and systematic reviews separately consider and describe how they deal with participants with complete data and those with MOD.     

Criteria for Patient Selection and Multidisciplinary Evaluation and Treatment of the Weight Loss Surgery Patient

Objective: To provide evidence‐based guidelines for patient selection and to recommend the medical and nutritional aspects of multidisciplinary care required to minimize perioperative and postoperative risks in patients with severe obesity who undergo weight loss surgery (WLS). Research Methods and Procedures: Members of the Multidisciplinary Care Task Group conducted searches of MEDLINE and PubMed for articles related to WLS in general and medical and nutritional care in particular. Pertinent abstracts and literature were reviewed for references. Multiple searches were carried out for various aspects of multidisciplinary care published between 1980 and 2004. A total of 3000 abstracts were identified; 242 were reviewed in detail. Results: We recommended multidisciplinary screening of WLS patients to ensure appropriate selection; preoperative assessment for cardiovascular, pulmonary, gastrointestinal, endocrine, and other obesity‐related diseases associated with increased risk for complications or mortality; preoperative weight loss and cessation of smoking; perioperative prophylaxis for deep vein thrombosis and pulmonary embolism (PE); preoperative and postoperative education and counseling by a registered dietitian; and a well‐defined postsurgical diet progression. Discussion: Obesity‐related diseases are often undiagnosed before WLS, putting patients at increased risk for complications and/or early mortality. Multidisciplinary assessment and care to minimize short‐ and long‐term risks include: comprehensive medical screening; appropriate pre‐, peri‐, and postoperative preparation; collaboration with multiple patient care disciplines (e.g., anesthesiology, pulmonary medicine, cardiology, and psychology); and long‐term nutrition education/counseling.     

Towards classifying species in systems biology papers using text mining

Background

In recent years high throughput methods have led to a massive expansion in the free text literature on molecular biology. Automated text mining has developed as an application technology for formalizing this wealth of published results into structured database entries. However, database curation as a task is still largely done by hand, and although there have been many studies on automated approaches, problems remain in how to classify documents into top-level categories based on the type of organism being investigated. Here we present a comparative analysis of state of the art supervised models that are used to classify both abstracts and full text articles for three model organisms.

Results

Ablation experiments were conducted on a large gold standard corpus of 10,000 abstracts and full papers containing data on three model organisms (fly, mouse and yeast). Among the eight learner models tested, the best model achieved an F-score of 97.1% for fly, 88.6% for mouse and 85.5% for yeast using a variety of features that included gene name, organism frequency, MeSH headings and term-species associations. We noted that term-species associations were particularly effective in improving classification performance. The benefit of using full text articles over abstracts was consistently observed across all three organisms.

Conclusions

By comparing various learner algorithms and features we presented an optimized system that automatically detects the major focus organism in full text articles for fly, mouse and yeast. We believe the method will be extensible to other organism types.

     

Lifestyle modifications to prevent and control hypertension. 2. Recommendations on obesity and weight loss. Canadian Hypertension Society,Canadian Coalition for High Blood Pressure Prevention and Control,Laboratory Centre for Disease Control at Health Canada,Heart and Stroke Foundation of Canada

OBJECTIVE: To provide updated, evidence-based recommendations concerning the effects of weight loss and maintenance of healthy weight on the prevention and control of hypertension in otherwise healthy adults (except pregnant women). OPTIONS: The main options are to attain and maintain a healthy body weight (body mass index [BMI] 20-25 kg/m2) or not to do so. For those at risk for hypertension, weight loss and maintenance of healthy weight may prevent the condition. For those who have hypertension, weight loss and maintenance of healthy weight may reduce or obviate the need for antihypertensive medications. OUTCOMES: The health outcome considered was change in blood pressure. Because of insufficient evidence, no economic outcomes were considered. EVIDENCE: A MEDLINE search was conducted for the years 1992-1996 with the terms hypertension and obesity in combination and antihypertensive therapy and obesity in combination. Other relevant evidence was obtained from the reference lists of the articles identified, from the personal files of the authors and through contacts with experts. The articles were reviewed, classified according to study design and graded according to level of evidence. VALUES: A high value was placed on the avoidance of cardiovascular morbidity and premature death caused by untreated hypertension. BENEFITS, HARMS AND COSTS: Weight loss and the maintenance of healthy body weight reduces the blood pressure of both hypertensive and normotensive people. The indirect benefits of a health body weight are well known. The negative effects of weight loss are primarily the frustrations associated with attaining and maintaining a healthy weight. The costs associated with weight loss programs were not measured in the studies reviewed. RECOMMENDATIONS: (1) It is recommended that health care professionals determine weight (in kilograms), height (in metres) and BMI for all adults. (2) To reduce blood pressure in the population at large, it is recommended that Canadians attain and maintain a healthy BMI (20-25). (3) All overweight hypertensive patients (BMI greater than 25) should be advised to reduce their weight. VALIDATION: These recommendations are similar to those of the World Hypertension League, the National High Blood Pressure Education Program Working Group on Primary Prevention of Hypertension, the Canadian Hypertension Society and the Canadian Coalition for High Blood Pressure Prevention and Control. They have not been clinically tested. SPONSORS: The Canadian Hypertension Society, the Canadian Coalition for High Blood Pressure Prevention and Control, the Laboratory Centre for Disease Control at Health Canada, and the Heart and Stroke Foundation of Canada.     

藻类DNA条形码研究进展

DNA barcode,又称为DNA条形码,是指利用短的标准DNA序列的核苷酸多样性进行物种的鉴定和快速识别.目前该方法在动物分类研究中应用广泛,其中线粒体的细胞色素c氧化酶亚基1(cytochrome c oxidase subunit 1,COI或cox 1)基因中的约700bp长度的一段被用来作为标准DNA片段.在陆地植物条形码研究中,生命-植物条形码联盟会(Consortium for the Barcode of Life-Plant Working Group,CBOL-Plant Working Group)近期推荐将植物叶绿体中的两个基因片段rbcL+ matK作为初步的陆生植物条形码,此组合能在70％的程度上进行植物物种的鉴别.在海藻的分类研究中,DNA条形码的应用较少,已有的研究主要集中在硅藻、红藻和褐藻,尚没有学者明确提出适合藻类的DNA条形码.总结了能够作为藻类DNA条形码的序列特点、应用流程及分析方法,综述了DNA条形码在藻类中的研究现状和存在的问题,展望了藻类DNA条形码的应用前景.     

Current Awareness: 9th International Symposium on Bioluminescence and Chemiluminescence,Marine Biological Laboratory,Woods Hole,MA, USA 4–8 October 1996 (remaining abstracts)

The following abstracts were not received in time to be included in the published collection of abstracts (J Biolumin Chemilumin 1996: 11:231-65). The three papers that follow were unable to be presented at the symposium and have not been peer reviewed. The symposium proceedings were published in the volume Bioluminescence and Chemiluminescence: Molecular Reporting with Photons, edited by J W Hastings, L J Kricka and PE Stanley, Chichester: Wiley,1997. © 1997 John Wiley & Sons, Ltd.     

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.     

History of the discovery of the mode of transmission of yellow fever virus

This essay documents and examines the historical circumstances and events surrounding the discovery of the mode of transmission of yellow fever virus in Cuba. Close scrutiny of the articles published by Walter Reed and his colleagues in 1900, 1901 and 1902 reveals their limitations as historic documents. Fortunately, other sources of information from that period survive in letters and documents written by individuals involved in the quest for the mode of transmission. Examination and comparison of those sources of information unveiled a fascinating story which reveals that misunderstandings engendered by published articles accorded merit where it was not fully due.     

Use of out-of-field contact shielding on patients in medical imaging: A review of current guidelines,recommendations and legislative documents

The use of patient contact-shielding has become a topic of intensive scientific debate. While it has been common practice during the last decades, some studies have questioned the efficiency of using such shielding while others have highlighted the inconsistencies in its application. The objective of this work is to review current recommendations and legislative documents on the use of out-of-field shielding in X-ray imaging, including those from national authorities and from international and national organisations and professional bodies.The review, performed within the framework of the activities of EURADOS Working Group 12, covers available recommendations on use of contact shielding in adult, pregnant and paediatric patients in general radiography, fluoroscopy, computed tomography, mammography and dental radiology. It includes a comprehensive search of 83 documents from 32 countries and 6 international organisations over the last 39 years. In general, using shielding is recommended only under two conditions: if it does not compromise the diagnostic task and the performance of the procedure and/or if it reassures the patient and comforters that they are appropriately protected against potentially harmful effects of radiation. There are very few specific regulatory requirements to use shielding in a particular imaging modality, although they may consider use of shielding either as part of good radiological practice or as requirements for availability of protective or ancillary tools, without further specification of their use. There is a wide variety of positions among documents that recommend out-of-field shielding, those that do not recommend it and those that are not specific. Therefore, evidence-based consensus is still needed to ensure best and consistent practice.     

Review of Cognitive Therapy and Dreams.

In this article I review the book, "Cognitive Therapy and Dreams" (see record 2004-00029-000). I came across this book as I was recently searching psychological abstracts for dreams and cognitive-behavioral therapy (CBT) and for hypnosis and CBT. Of the 9 references I found on dreams and CBT, all were in one issue of the Journal of Cognitive Psychotherapy: An International Quarterly (Vol. 16, No. 1). I read a good number of the hypnosis-CBT articles and books, and all were written to integrate CBT into the field of hypnosis. Conversely, the dream articles integrating dream work and CBT were written by a range of people, some with a primary interest in dreams, but some with a more central interest in cognitive therapy. Apparently, a few cognitive-behavioral therapists and researchers have taken some interest in dream work, whereas the hypnosis interest in CBT continues mostly outside the domain of CBT. The collection of the nine articles published in the journal was an impressive enough accomplishment that eight articles of this collection plus four additional articles are now published in this book. The fact that these articles are now in a book may encourage researchers to perform the necessary therapy outcome research to validate the integration of dream work and CBT. The book adds significantly to the journal by drawing a distinction between objectivist approaches (Part II) and constructivist approaches (Part III), a distinction that unifies the articles in this book. (PsycINFO Database Record (c) 2010 APA, all rights reserved)