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1.  Towards the bibliography of life 
ZooKeys  2011;151-166.
This paper discusses how we intend to take forward the vision of a Bibliography of Life in the ViBRANT project. The underlying principle of the Bibliography is to provide taxonomists and others with a freely accessible bibliography covering the whole of life. Such a bibliography has been achieved for specific study areas within taxonomy, but not for “life” as a whole.
The creation of such a comprehensive tool has been hindered by various social and technical issues. The social concerns focus on the willingness of users to contribute to the Bibliography. The technical concerns relate to the architecture required to deliver the Bibliography. These issues are discussed in the paper and approaches to addressing them within the ViBRANT project are described, to demonstrate how we can now seriously consider building a Bibliography of Life. We are particularly interested in the potential of the resulting tool to improve the quality of bibliographic references. Through analysing the large number of references in the Bibliography we will be able to add metadata by resolving known issues such as geographical name variations. This should result in a tool that will assist taxonomists in two ways. Firstly, it will be easier for them to discover relevant literature, especially pre-digital literature; and secondly, it will be easier for them to identify the canonical form for a citation
The paper also covers related issues relevant to building the tool in ViBRANT, including implementation and copyright, with suggestions as to how we could address them.
doi:10.3897/zookeys.150.2167
PMCID: PMC3234436  PMID: 22207811
bibliography; citation; reference manager
2.  Finding European bioethical literature: an evaluation of the leading abstracting and indexing services 
Journal of Medical Ethics  2004;30(3):299-303.
Objectives: In this study the author aimed to provide information for researchers to help them with the selection of suitable databases for finding medical ethics literature. The quantity of medical ethical literature that is indexed in different existing electronic bibliographies was ascertained.
Method: Using the international journal index Ulrich's Periodicals Directory, journals on medical ethics were identified. The electronic bibliographies indexing these journals were analysed. In an additional analysis documentalists indexing bioethical literature were asked to name European journals on medical ethics. The bibliographies indexing these journals were examined.
Results: Of 290 journals on medical ethics 173 were indexed in at least one bibliography. Current Contents showed the highest coverage with 66 (22.8%) journals indexed followed by MEDLINE (22.1%). By a combined search in the top ten bibliographies with the highest coverage, a maximum coverage of 45.2% of all journals could be reached. All the bibliographies showed a tendency to index more North American than European literature. This result was verified by the supplementary analysis of a sample of continental European journals. Here EMBASE covered the highest number of journals (20.6%) followed by the Russian Academy of Sciences Bibliographies (19.2%).
Conclusion: A medical ethics literature search has to be carried out in several databases in order to reach an adequate collection of literature. The databases one wishes to combine should be carefully chosen. There seems to be a regional bias in the most popular databases, favouring North American periodicals compared with European literature on medical ethics.
doi:10.1136/jme.2003.003269
PMCID: PMC1733872  PMID: 15173367
3.  Updating a bibliography using the related articles function within PubMed. 
Comprehensive bibliographies are useful for conducting reviews of the literature, and for assessing the progress within a field. These bibliographies may be broad and inclusive, or focused and precise in their inclusion criteria. In either case, the task of maintaining a complete bibliography within a particular area of research is made difficult by the diversity, complexity and huge volume of newly published literature. In an effort to effectively and automatically retrieve relevant literature, different search strategies and indexing tools have been developed, including the RELATED ARTICLES function provided with the PubMed system. In this paper, we report a program for incremental updates of a bibliography using the PubMed RELATED ARTICLES function. Given a highly specialized starting bibliography of experimental measurements of the structure of the 30S bacterial ribosomal subunit, the system was applied to find additional relevant references. For this particular task, the system has a recall of 75%, a strict precision of 32% and a partial precision of 42%. Our results are notable because although the RELATED ARTICLES function is purely statistical, it is nonetheless able to select a very narrowly defined set of articles from the literature. We discuss the tradeoffs between having a user to evaluate many articles of possible interest in a single session, versus asking a user to evaluate a small set of articles on a periodic basis.
PMCID: PMC2232162  PMID: 9929319
4.  Who cites non-English-language pharmaceutical articles? 
The Annals of Pharmacotherapy  2009;43(3):549-550.
PURPOSE
The objective was to determine a link between the number of non-English language references in the bibliographies of publications in international pharmaceutical journals and the geographic origin of these publications.
METHODS
A systematic prospective analysis of 7 international pharmaceutical journals in 2005–2006. All research articles whom corresponding author was a pharmacist were included. For each article, were recorded:
the geographic origin of the corresponding author (classified in: North America, Latin America, Oceania, Europe, Asia, others);
the title of the journal;
the number of non-English language references in the bibliography (classified in: Spanish, German, French, Portuguese, Dutch, Russian, Japanese, Chinese, others).
RESULTS
1,568 articles were included, corresponding to 45,949 bibliographic references, of whom 542 where non-English references. North America is the geographic zone of the world with the lowest rate of non-English language references in bibliographies of published articles; significant differences appear between North America and Europe, Latin America and Asia. A sub-analysis by countries shows that United States, United Kingdom, Australia and China present a specific low rate of non-English language references. The two journals with the lowest rate of non-English language references in bibliographies of published articles are edited in the USA.
CONCLUSIONS
Despite some limitations, this study shows that pharmacists from regions where English language is the only or predominant language are refractory to include non-English language references in the bibliographies of their publications. The fundamental reasons of this restriction are not clear.
doi:10.1345/aph.1L490
PMCID: PMC2852414  PMID: 19240258
Authorship; Language; Periodicals as Topic; statistics & numerical data; Pharmacists; English language; publication; pharmacy
5.  FlyBase: improvements to the bibliography 
Nucleic Acids Research  2012;41(Database issue):D751-D757.
An accurate, comprehensive, non-redundant and up-to-date bibliography is a crucial component of any Model Organism Database (MOD). Principally, the bibliography provides a set of references that are specific to the field served by the MOD. Moreover, it serves as a backbone to which all curated biological data can be attributed. Here, we describe the organization and main features of the bibliography in FlyBase (flybase.org), the MOD for Drosophila melanogaster. We present an overview of the current content of the bibliography, the pipeline for identifying and adding new references, the presentation of data within Reference Reports and effective methods for searching and retrieving bibliographic data. We highlight recent improvements in these areas and describe the advantages of using the FlyBase bibliography over alternative literature resources. Although this article is focused on bibliographic data, many of the features and tools described are applicable to browsing and querying other datasets in FlyBase.
doi:10.1093/nar/gks1024
PMCID: PMC3531214  PMID: 23125371
6.  Health aspects of Arctic exploration – Alaska’s medical history based on the research files of Dr. Robert Fortuine 
International Journal of Circumpolar Health  2013;72:10.3402/ijch.v72i0.21264.
Background
Robert Fortuine provided basic medical care to Alaska Native people, chronicled the Health Aspects of Arctic Exploration and through a number of influential publications, was the first to thoroughly document and analyse Alaska’s Medical History. This overview of his published work will provide the reader with a detailed overview, so that they can begin to explore Dr. Fortuine’s many published works in more detail.
Objective
This review will explore Alaska’s Medical History and the Health Aspects of Arctic Exploration through the research files and the 10 most significant publications of Dr. Robert Fortuine.
Design
Review of Dr. Fortuine’s major works and the master bibliography has over 3,000 references and 81 subjects. The master bibliography is a merger of 55 separate bibliographies, which provides a wealth of bibliographic information. This paper will describe his 10 most significant publications, 2 of which began as a journal issue.
Results
Dr. Fortuine was a prolific writer throughout his career, publishing 134 articles and books. He wrote papers and books on Alaska’s medical history, tuberculosis and health care delivery from Russian–America through the Public Health Service efforts in the territory and then the State of Alaska. The master bibliography has over 3,000 references and 81 subjects. This list has a significant number of entries for tuberculosis with almost one-third of the entries including this heading. Others dwell on the history of “pre-contact” health, the history of Alaska Native health care, the history of the Alaska Department of Health, especially the tuberculosis programme, the role of the US Public Health Service and traditional medicine. He completely reviewed every Governors’ and the US Surgeon General’s reports in regard to Alaska content. This paper describes his 10 most significant publications.
Conclusions
Robert Fortuine’s published works offer a wealth of information and insight into Alaska’s Medical History and the Health Aspects of Arctic Exploration. As is probably true for many historians, he began small, creating a bibliography and adapting a talk before tackling his first full-length book. Readers who sample his many works will be enriched and enlightened.
doi:10.3402/ijch.v72i0.21264
PMCID: PMC3748459  PMID: 23967418
medical history; arctic bibliography; health care delivery; access to health care; Alaska
7.  The Recurring Bibliographies Program of MEDLARS * 
Recurring bibliographies are by-products of the MEDLARS system which are prepared by the National Library of Medicine in collaboration with nonprofit scientific and professional societies and institutions and government agencies that represent a specialty area of biomedical research or practice. The sponsor generally assumes responsibility for the costs of publication and distribution. At present MEDLARS has a planned capacity of fifty such recurring bibliographies. The subject parameters and format are defined by the representatives of the sponsoring organization and the NLM Search, MeSH, and Index staffs. As citations are regularly put into the MEDLARS store, each one that qualifies for a recurring bibliography is identified and tagged by the computer with the number assigned to the pertinent RB. The MEDLARS store is searched for citations for a particular recurring bibliography according to the schedule specified by the sponsoring organization, and the output is printed from a GRACE tape.
PMCID: PMC198401  PMID: 5325816
8.  Whiplash: a selective annotated bibliography 
Objective:
To review the literature on whiplash injury including an overview, collision mechanics, pathophysiology, neurobehavioral, imaging, treatment/management, prognosis, outcomes, and litigation.
Design:
An annotated bibliography.
Methods:
A literature search of MEDLINE from 1987 to 1995 and CHIROLARS from 1900 to 1996, with emphasis on the last ten years, was performed. Conference proceedings and the personal files of the authors were searched for relevant citations. Key words utilized in the search were whiplash injury, acceleration/deceleration injury, neck pain, head pain, cognitive impairment, treatment, imaging, prognosis and litigation.
Results:
This annotated bibliography identifies key studies and potential models for future research.
Conclusions:
There is currently a lack of clinical consensus both in practice and in the literature regarding the evaluation and management of an episode of whiplash injury. This annotated bibliography has been developed in an attempt to provide an overview of the literature regarding various issues surrounding an episode of whiplash injury.
PMCID: PMC2485172
whiplash; neck pain; acceleration/deceleration; injury
9.  Annotated bibliography on participatory consultations to help aid the inclusion of marginalized perspectives in setting policy agendas 
The purpose of this bibliography is to present studies from peer-reviewed and grey literature that used consultations and other participatory strategies to capture a community’s perspective of their health priorities, and of techniques used to elevate participation from the implementation phase to a more upstream phase of prioritization, policymaking and agenda setting. The focus here is of those studies that worked with marginalized populations or sub-populations. This bibliography contains four areas of research. It begins by first offering some philosophical and conceptual frameworks that link participatory interventions with inclusive policy making or agenda setting, and a rationale for prioritizing marginalized populations in such an undertaking. After situating ourselves in this manner, the second section looks at various participatory instruments for participatory consultations, for reaching out to marginalized populations, and for communicating the results to policymakers. Two sets of distinctions are made here: one between external (non-invitation) and internal (stifling of opinions) exclusion, and between mere participation and from active inclusion within consultations and within the policies. In the third section, examples of consultations that created or changed policy in various jurisdictions are shared, followed by a final section on a reflective and evaluative look at the recruitment, instruments and examples. An earlier iteration of this bibliography was created to assist a multi-country research project by the author to inform the UN Post-2015 development framework of the views of several diverse and highly marginalized populations around the world on their health-related priorities.
doi:10.1186/s12939-014-0124-0
PMCID: PMC4279799  PMID: 25532831
Participation; Consultations; Inclusion; Marginalization; Post-2015; MDGs; Priorities; Frameworks; Methods
10.  Bibliography of Bioethics and Index Medicus: comparison of coverage, publication delay, and ease of recall for journal articles on bioethics. 
Citations selected from the bibliographies of recent texts, a specialized subject bibliography, and review articles were checked in both Cumulated Index Medicus (IM) and the Bibliography of Bioethics (BB) to compare coverage, publication delay, probable causes of indexing and retrieval failure, and the ease with which relevant citations were retrieved. The study also attempted to determine whether BB included appropriate articles from the MEDLINE database in a timely and systematic manner. While 98% of the IM citations appeared within a year of publication, 79% of the BB citations appeared two to three years after their publication dates. The average citation appeared twice as frequently in IM as in BB.
PMCID: PMC227691  PMID: 3315054
11.  Veterinary medicine books recommended for academic libraries 
This bibliography of in-print veterinary medical books published in English may be used as an acquisitions or evaluation tool for developing the monograph component of new veterinary medicine collections or existing science, technology, and medicine collections where veterinary medicine is in the scope of the collection. The bibliography is divided into 34 categories and consists of bibliographic information for 419 titles. The appendix contains an author/editor index. Prices for all entries are in US dollars, except where another currency is noted. The total cost of all books in the bibliography is $43,602.13 (US).
PMCID: PMC521519  PMID: 15494763
12.  Piriformis syndrome: an annotated bibliography 
Objective:
To review the literature on Piriformis Syndrome, including signs, symptoms, diagnosis, differential diagnosis, treatment and management.
Design:
An annotated bibliography.
Methods:
A literature search of MEDLINE from January 1987 to November 1996, MANTIS from 1990 to 1997, EMBASE from January 1986 to December 1996, and Index to Chiropractic Literature from 1985 to 1994. The key words utilized in the search were Piriformis, Piriformis Syndrome, and Piriformis Muscle. Only English language articles were selected.
Results:
This annotated bibliography identifies twelve case reports, four case series, nine commentaries, and one quasi experiment. Twenty of the articles were published in peer-reviewed journals.
Conclusions:
Future research should address diagnostic criteria, treatment protocols, and effectiveness of therapeutic options.
PMCID: PMC2485454
piriformis; muscle; syndrome
13.  Reasons Why Post-Trial Access to Trial Drugs Should, or Need not be Ensured to Research Participants: A Systematic Review 
Public Health Ethics  2011;4(2):160-184.
Background: researchers and sponsors increasingly confront the issue of whether participants in a clinical trial should have post-trial access (PTA) to the trial drug. Legislation and guidelines are inconsistent, ambiguous or silent about many aspects of PTA. Recent research highlights the potential importance of systematic reviews (SRs) of reason-based literatures in informing decision-making in medicine, medical research and health policy. Purpose: to systematically review reasons why drug trial participants should, or need not be ensured PTA to the trial drug and the uses of such reasons. Data sources: databases in science/medicine, law and ethics, thesis databases, bibliographies, research ethics books and included publications’ notes/bibliographies. Publication selection: a publication was included if it included a reason as above. See article for detailed inclusion conditions. Data extraction and analysis: two reviewers extracted and analyzed data on publications and reasons. Results: of 2060 publications identified, 75 were included. These mentioned reasons based on morality, legality, interests/incentives, or practicality, comprising 36 broad (235 narrow) types of reason. None of the included publications, which included informal reviews and reports by official bodies, mentioned more than 22 broad (59 narrow) types. For many reasons, publications differed about the reason’s interpretation, implications and/or persuasiveness. Publications differed also regarding costs, feasibility and legality of PTA. Limitations: reason types could be applied differently. The quality of reasons was not measured. Conclusion: this review captured a greater variety of reasons and of their uses than any included publication. Decisions based on informal reviews or sub-sets of literature are likely to be biased. Research is needed on PTA ethics, costs, feasibility and legality and on assessing the quality of reason-based literature.
doi:10.1093/phe/phr013
PMCID: PMC3133737  PMID: 21754950
14.  Routine Eye Examinations for Persons 20-64 Years of Age 
Executive Summary
Objective
The objective of this analysis was to determine the strength of association between age, gender, ethnicity, family history of disease and refractive error and the risk of developing glaucoma or ARM?
Clinical Need
A routine eye exam serves a primary, secondary, and tertiary care role. In a primary care role, it allows contact with a doctor who can provide advice about eye care, which may reduce the incidence of eye disease and injury. In a secondary care role, it can via a case finding approach, diagnose persons with degenerative eye diseases such as glaucoma and or AMD, and lead to earlier treatment to slow the progression of the disease. Finally in a tertiary care role, it provides ongoing monitoring and treatment to those with diseases associated with vision loss.
Glaucoma is a progressive degenerative disease of the optic nerve, which causes gradual loss of peripheral (side) vision, and in advanced disease states loss of central vision. Blindness may results if glaucoma is not diagnosed and managed. The prevalence of primary open angle glaucoma (POAG) ranges from 1.1% to 3.0% in Western populations, and from 4.2% to 8.8% in populations of African descent. It is estimated up to 50% of people with glaucoma are aware that they have the disease. In Canada, glaucoma disease is the second leading cause of blindness in people aged 50 years and older. Tonometry, inspection of the optic disc and perimetry are used concurrently by physicians and optometrists to make the diagnosis of glaucoma. In general, the evidence shows that treating people with increased IOP only, increased IOP and clinical signs of early glaucoma or with normal-tension glaucoma can reduce the progression of disease.
Age-related maculopathy (ARM) is a degenerative disease of the macula, which is a part of the retina. Damage to the macula causes loss of central vision affecting the ability to read, recognize faces and to move about freely. ARM can be divided into an early- stage (early ARM) and a late-stage (AMD). AMD is the leading cause of blindness in developed countries. The prevalence of AMD increases with increasing age. It is estimated that 1% of people 55 years of age, 5% aged 75 to 84 years and 15% 80 years of age and older have AMD. ARM can be diagnosed during fundoscopy (ophthalmoscopy) which is a visual inspection of the retina by a physician or optometrist, or from a photograph of the retina. There is no cure or prevention for ARM. Likewise, there is currently no treatment to restore vision lost due to AMD. However, there are treatments to delay the progression of the disease and further loss of vision.
The Technology
A periodic oculo-visual assessment is defined “as an examination of the eye and vision system rendered primarily to determine if a patient has a simple refractive error (visual acuity assessment) including myopia, hypermetropia, presbyopia, anisometropia or astigmatism.” This service includes a history of the presenting complaint, past medical history, visual acuity examination, ocular mobility examination, slit lamp examination of the anterior segment, ophthalmoscopy, and tonometry (measurement of IOP) and is completed by either a physician or an optometrist.
Review Strategy
The Medical Advisory Secretariat conducted a computerized search of the literature in the following databases: OVID MEDLINE, MEDLINE, In-Process & Other Non-Indexed Citations, EMBASE, INAHTA and the Cochrane Library. The search was limited to English-language articles with human subjects, published from January 2000 to March 2006. In addition, a search was conducted for published guidelines, health technology assessments, and policy decisions. Bibliographies of references of relevant papers were searched for additional references that may have been missed in the computerized database search. Studies including participants 20 years and older, population-based prospective cohort studies, population-based cross-sectional studies when prospective cohort studies were unavailable or insufficient and studies determining and reporting the strength of association or risk- specific prevalence or incidence rates of either age, gender, ethnicity, refractive error or family history of disease and the risk of developing glaucoma or AMD were included in the review. The Grading of Recommendations Assessment, Development and Evaluation (GRADE) system was used to summarize the overall quality of the body of evidence.
Summary of Findings
A total of 498 citations for the period January 2000 through February 2006 were retrieved and an additional 313 were identified when the search was expanded to include articles published between 1990 and 1999. An additional 6 articles were obtained from bibliographies of relevant articles. Of these, 36 articles were retrieved for further evaluation. Upon review, 1 meta-analysis and 15 population-based epidemiological studies were accepted for this review
Primary Open Angle Glaucoma
Age
Six cross-sectional studies and 1 prospective cohort study contributed data on the association between age and PAOG. From the data it can be concluded that the prevalence and 4-year incidence of POAG increases with increasing age. The odds of having POAG are statistically significantly greater for people 50 years of age and older relative to those 40 to 49 years of age. There is an estimated 7% per year incremental odds of having POAG in persons 40 years of age and older, and 10% per year in persons 49 years of age and older. POAG is undiagnosed in up to 50% of the population. The quality of the evidence is moderate.
Gender
Five cross-sectional studies evaluated the association between gender and POAG. Consistency in estimates is lacking among studies and because of this the association between gender and prevalent POAG is inconclusive. The quality of the evidence is very low.
Ethnicity
Only 1 cross-sectional study compared the prevalence rates of POAG between black and white participants. These data suggest that prevalent glaucoma is statistically significantly greater in a black population 50 years of age and older compared with a white population of similar age. There is an overall 4-fold increase in prevalent POAG in a black population compared with a white population. This increase may be due to a confounding variable not accounted for in the analysis. The quality of the evidence is low.
Refractive Error
Four cross-sectional studies assessed the association of myopia and POAG. These data suggest an association between myopia defined as a spherical equivalent of -1.00D or worse and prevalent POAG. However, there is inconsistency in results regarding the statistical significance of the association between myopia when defined as a spherical equivalent of -0.5D. The quality of the evidence is very low.
Family History of POAG
Three cross-sectional studies investigated the association between family history of glaucoma and prevalent POAG. These data suggest a 2.5 to 3.0 fold increase in the odds having POAG in persons with a family history (any first-degree relative) of POAG. The quality of the evidence is moderate.
Age-Related Maculopathy
Age
Four cohort studies evaluated the association between age and early ARM and AMD. After 55 years of age, the incidence of both early ARM and AMD increases with increasing age. Progression to AMD occurs in up to 12% of persons with early ARM. The quality of the evidence is low
Gender
Four cohort studies evaluated the association between gender and early ARM and AMD. Gender differences in incident early ARM and incident AMD are not supported from these data. The quality of the evidence is lows.
Ethnicity
One meta-analysis and 2 cross-sectional studies reported the ethnic-specific prevalence rates of ARM. The data suggests that the prevalence of early ARM is higher in a white population compared with a black population. The data suggest that the ethnic-specific differences in the prevalence of AMD remain inconclusive.
Refractive Error
Two cohort studies investigated the association between refractive error and the development of incident early ARM and AMD. The quality of the evidence is very low.
Family History
Two cross-sectional studies evaluated the association of family history and early ARM and AMD. Data from one study supports an association between a positive family history of AMD and having AMD. The results of the study indicate an almost 4-fold increase in the odds of any AMD in a person with a family history of AMD. The quality of the evidence, as based on the GRADE criteria is moderate.
Economic Analysis
The prevalence of glaucoma is estimated at 1 to 3% for a Caucasian population and 4.2 to 8.8% for a black population. The incidence of glaucoma is estimated at 0.5 to 2.5% per year in the literature. The percentage of people who go blind per year as a result of glaucoma is approximately 0.55%.
The total population of Ontarians aged 50 to 64 years is estimated at 2.6 million based on the April 2006 Ontario Ministry of Finance population estimates. The range of utilization for a major eye examination in 2006/07 for this age group is estimated at 567,690 to 669,125, were coverage for major eye exams extended to this age group. This would represent a net increase in utilization of approximately 440,116 to 541,551.
The percentage of Ontario population categorized as black and/or those with a family history of glaucoma was approximately 20%. Therefore, the estimated range of utilization for a major eye examination in 2006/07 for this sub-population is estimated at 113,538 - 138,727 (20% of the estimated range of utilization in total population of 50-64 year olds in Ontario), were coverage for major eye exams extended to this sub-group. This would represent a net increase in utilization of approximately 88,023 to 108,310 within this sub-group.
Costs
The total cost of a major eye examination by a physician is $42.15, as per the 2006 Schedule of Benefits for Physician Services.(1) The total difference between the treatments of early-stage versus late-stage glaucoma was estimated at $167. The total cost per recipient was estimated at $891/person.
Current Ontario Policy
As of November 1, 2004 persons between 20 years and 64 years of age are eligible for an insured eye examination once every year if they have any of the following medical conditions: diabetes mellitus type 1 or 2, glaucoma, cataract(s), retinal disease, amblyopia, visual field defects, corneal disease, or strabismus. Persons between 20 to 64 years of age who do not have diabetes mellitus, glaucoma, cataract(s), retinal disease, amblyopia, visual field defects, corneal disease, or strabismus may be eligible for an annual eye examination if they have a valid “request for major eye examination” form completed by a physician (other than that who completed the eye exam) or a nurse practitioner working in a collaborative practice. Persons 20-64 years of age who are in receipt of social assistance and who do not have one of the 8 medical conditions listed above are eligible to receive an eye exam once every 2 years as a non-OHIP government funded service. Persons 19 years of age or younger and 65 years of age or older may receive an insured eye exam once every year.
Considerations for Policy Development
As of July 17, 2006 there were 1,402 practicing optometrists in Ontario. As of December 31, 2005 there were 404 practicing ophthalmologists in Ontario. It is unknown how many third party payers now cover routine eye exams for person between the ages of 20 and 64 years of age in Ontario.
PMCID: PMC3379534  PMID: 23074485
15.  Manual Gene Ontology annotation workflow at the Mouse Genome Informatics Database 
The Mouse Genome Database, the Gene Expression Database and the Mouse Tumor Biology database are integrated components of the Mouse Genome Informatics (MGI) resource (http://www.informatics.jax.org). The MGI system presents both a consensus view and an experimental view of the knowledge concerning the genetics and genomics of the laboratory mouse. From genotype to phenotype, this information resource integrates information about genes, sequences, maps, expression analyses, alleles, strains and mutant phenotypes. Comparative mammalian data are also presented particularly in regards to the use of the mouse as a model for the investigation of molecular and genetic components of human diseases. These data are collected from literature curation as well as downloads of large datasets (SwissProt, LocusLink, etc.). MGI is one of the founding members of the Gene Ontology (GO) and uses the GO for functional annotation of genes. Here, we discuss the workflow associated with manual GO annotation at MGI, from literature collection to display of the annotations. Peer-reviewed literature is collected mostly from a set of journals available electronically. Selected articles are entered into a master bibliography and indexed to one of eight areas of interest such as ‘GO’ or ‘homology’ or ‘phenotype’. Each article is then either indexed to a gene already contained in the database or funneled through a separate nomenclature database to add genes. The master bibliography and associated indexing provide information for various curator-reports such as ‘papers selected for GO that refer to genes with NO GO annotation’. Once indexed, curators who have expertise in appropriate disciplines enter pertinent information. MGI makes use of several controlled vocabularies that ensure uniform data encoding, enable robust analysis and support the construction of complex queries. These vocabularies range from pick-lists to structured vocabularies such as the GO. All data associations are supported with statements of evidence as well as access to source publications.
doi:10.1093/database/bas045
PMCID: PMC3483533  PMID: 23110975
16.  Activity-based costing in services: literature bibliometric review 
SpringerPlus  2013;2:80.
This article is aimed at structuring a bibliography portfolio to treat the application of the ABC method in service and contribute to discussions within the scientific community. The methodology followed a three-stage procedure: Planning, execution and Synthesis. Also, the process ProKnow-C (Knowledge Process Development - Constructivist) was used in the execution stage. International databases were used to collect information (ISI Web of Knowledge and Scopus). As a result, we obtained a bibliography portfolio of 21 articles (with scientific recognition) dealing with the proposed theme.
doi:10.1186/2193-1801-2-80
PMCID: PMC3601252  PMID: 23518506
Bibliometrics; Bibliography portfolio; Costs; Services; Journals; 00–02
17.  Multi-morbidity of non communicable diseases and equity in WHO Eastern Mediterranean countries 
Introduction
Non communicable diseases are the biggest cause of death worldwide. Beside mortality, these diseases also cause high rates of morbidity and disability. Their high prevalence is generally associated to multi-morbidity. Because they need costly prolonged treatment and care, non communicable diseases have social and economical consequences that affect individuals, households and the whole society. They raise the equity problem between and within countries.
Methods and limitations
This annotated bibliography is a systematic review on multimorbidy of non communicable diseases and health equity in WHO Eastern Mediterranean countries. Medline/PubMed, EMBASE and other sources were used to get peer reviewed papers dealing with the review theme. The words/strings used for search and inclusion criteria were: multimorbidity, comorbidity, equity, non communicable diseases, chronic diseases, WHO Eastern Mediterranean and Arab countries.
Bibliography with annotations
According to the inclusion criteria, 26 papers were included in the present review. Generally, lack or paucity of publications was encountered in themes like headache, cancer and respiratory diseases. Of the 26 contributions selected, twelve dealt with comorbidity of depression and mental disorders with other chronic diseases. Another set of 11 publications was devoted to multimorbidity of diabetes, cardiovascular diseases (CVDs), hypertension, metabolic syndrome and obesity. Considering association of multimorbidity and social determinants, this review shows that female gender, low income, low level of education, old age and unemployed/retired are the most exposed to multimorbidity. It should also be stressed that, geographically, no contribution was issued from North African countries.
Non communicable diseases are one of the biggest challenges facing health decision makers in WHO Eastern Mediterranean countries where the multidimensional transition is boosting increases in multimorbidity of depression and mental diseases, cardiovascular diseases, diabetes, cancer and respiratory diseases among the whole population but with the highest burden among the least disadvantaged individuals or subpopulations. Health ministries in WHO Eastern Mediterranean countries should pay a particular attention to the association between equity and multimorbidity and opt for cost effective strategies based on early diagnosis and sensitisation for healthy diet, physical activity, no smoking and no alcohol.
doi:10.1186/1475-9276-12-60
PMCID: PMC3848740  PMID: 23961989
18.  Inflammatory bowel diseases and human reproduction: A comprehensive evidence-based review 
To evaluate the effects of inflammatory bowel diseases (IBDs) on human reproduction, we reviewed the current literature using a systematic search for published studies (articles and/or abstracts) without limits for English language. We searched on Medline (through PubMed), the Institute for Scientific Information, the Web of Science and the websites for the registration of controlled trials (http://controlled-trials.com/). Bibliographies of retrieved articles, books, expert opinion review articles and reviewed bibliographies from subject experts were manually searched. Titles and abstracts were screened initially, and potential relevant articles were identified and reviewed. Whenever possible, data were analyzed by comparing IBD patients vs healthy controls, and patients with active IBDs vs those with disease in remission. The effects of IBDs on female fertility, fertility in infertile couples, pregnancy and male infertility were examined separately. Patients with IBDs in remission have normal fertility. At the moment, there is no established guideline for the preservation of fertility in women with IBD undergoing surgery. Further data are needed regarding guidelines for the management of these patients. Data regarding IBDs and infertility are currently completely lacking. Considering the prevalence of intestinal pathology in young adults of childbearing age, this field is of great scientific and clinical interest, opening up important future perspectives. Another important and as yet unexplored point is the response to treatments for infertility in patients with IBDs. In particular, the question is whether the reproductive outcomes (clinical and biological) can be influenced by the IBD of one of the partners. The goals for successful reproductive outcomes in IBD population are correct counseling and disease remission. IBDs significantly affect several reproductive aspects of human (female, male, couple) reproduction. Further data are needed to develop guidelines for the clinical management of subjects of reproductive age with IBDs.
doi:10.3748/wjg.v20.i23.7123
PMCID: PMC4064059  PMID: 24966584
Inflammatory bowel diseases; Fertility; Infertility; Pregnancy
19.  Network-based statistical comparison of citation topology of bibliographic databases 
Scientific Reports  2014;4:6496.
Modern bibliographic databases provide the basis for scientific research and its evaluation. While their content and structure differ substantially, there exist only informal notions on their reliability. Here we compare the topological consistency of citation networks extracted from six popular bibliographic databases including Web of Science, CiteSeer and arXiv.org. The networks are assessed through a rich set of local and global graph statistics. We first reveal statistically significant inconsistencies between some of the databases with respect to individual statistics. For example, the introduced field bow-tie decomposition of DBLP Computer Science Bibliography substantially differs from the rest due to the coverage of the database, while the citation information within arXiv.org is the most exhaustive. Finally, we compare the databases over multiple graph statistics using the critical difference diagram. The citation topology of DBLP Computer Science Bibliography is the least consistent with the rest, while, not surprisingly, Web of Science is significantly more reliable from the perspective of consistency. This work can serve either as a reference for scholars in bibliometrics and scientometrics or a scientific evaluation guideline for governments and research agencies.
doi:10.1038/srep06496
PMCID: PMC4178292  PMID: 25263231
20.  Key Articles Related to Complementary and Alternative Medicine in Cardiovascular Disease 
Pharmacotherapy  2010;30(1):109.
Complementary and alternative medicine (CAM) therapy has gained popularity in America over the past several years, reflected in the increased utilization of these agents. Given the abundance of nontraditional products available to the public, clinicians should be made aware of the existing evidence relating to CAM therapy to better provide patient care in a meaningful manner. This bibliography paper compiled key articles specific to CAM therapy and cardiovascular disease, which include primary literature, review articles, consensus statements, and abstracts of landmark studies. Based on the numerous published reports available on this topic, this bibliography, as part I of II, focuses on the efficacy of CAM therapy in cardiovascular disease.
doi:10.1592/phco.30.1.109
PMCID: PMC4179498  PMID: 20030478
cardiovascular disease; complementary medicine; alternative medicine; nutraceutical; key articles; consensus statements
21.  A four-part working bibliography of neuroethics: part 2 – neuroscientific studies of morality and ethics 
Background
Moral philosophy and psychology have sought to define the nature of right and wrong, and good and evil. The industrial turn of the twentieth century fostered increasingly technological approaches that conjoined philosophy to psychology, and psychology to the natural sciences. Thus, moral philosophy and psychology became ever more vested to investigations of the anatomic structures and physiologic processes involved in cognition, emotion and behavior - ultimately falling under the rubric of the neurosciences. Since 2002, neuroscientific studies of moral thought, emotions and behaviors have become known as – and a part of – the relatively new discipline of neuroethics. Herein we present Part 2 of a bibliography of neuroethics from 2002–2013 addressing the “neuroscience of ethics” – studies of putative neural substrates and mechanisms involved in cognitive, emotional and behavioral processes of morality and ethics.
Methods
A systematic survey of the neuroethics literature was undertaken. Bibliographic searches were performed by accessing 11 databases, 8 literature depositories, and 4 individual journal searches, and employed indexing language for National Library of Medicine (NLM) Medical Subject Heading databases. All bibliographic searches were conducted using the RefWorks citation management program.
Results
This bibliography lists 397 articles, 65 books, and 52 book chapters that present (1) empirical/experimental studies, overviews, and reviews of neural substrates and mechanisms involved in morality and ethics, and/or (2) reflections upon such studies and their implications. These works present resources offering iterative descriptions, definitions and criticisms of neural processes involved in moral cognition and behaviors, and also provide a historical view of this field, and insights to its developing canon.
doi:10.1186/s13010-015-0022-0
PMCID: PMC4334407
Neuroethics; Neuroscience; Morality; Moral Psychology; Ethics; Bibliography
22.  Contact dermatitis and other skin conditions in instrumental musicians 
BMC Dermatology  2004;4:3.
Background
The skin is important in the positioning and playing of a musical instrument. During practicing and performing there is a permanent more or less intense contact between the instrument and the musician's skin. Apart from aggravation of predisposed skin diseases (e.g., atopic eczema or psoriasis) due to music-making, specific dermatologic conditions may develop that are directly caused by playing a musical instrument.
Methods
To perform a systematic review on instrument-related skin diseases in musicians we searched the PubMed database without time limits. Furthermore we studied the online bibliography "Occupational diseases of performing artist. A performing arts medicine bibliography. October, 2003" and checked references of all selected articles for relevant papers.
Results
The most prevalent skin disorders of instrumental musicians, in particular string instrumentalists (e.g., violinists, cellists, guitarists), woodwind players (e.g., flautists, clarinetists), and brass instrumentalists (e.g., trumpeters), include a variety of allergic contact sensitizations (e.g., colophony, nickel, and exotic woods) and irritant (physical-chemical noxae) skin conditions whose clinical presentation and localization are usually specific for the instrument used (e.g., "fiddler's neck", "cellist's chest", "guitar nipple", "flautist's chin"). Apart from common callosities and "occupational marks" (e.g., "Garrod's pads") more or less severe skin injuries may occur in musical instrumentalists, in particular acute and chronic wounds including their complications. Skin infections such as herpes labialis seem to be a more common skin problem in woodwind and brass instrumentalists.
Conclusions
Skin conditions may be a significant problem not only in professional instrumentalists, but also in musicians of all ages and ability. Although not life threatening they may lead to impaired performance and occupational hazard. Unfortunately, epidemiological investigations have exclusively been performed on orchestra musicians, though the prevalence of instrument-related skin conditions in other musician groups (e.g., jazz and rock musicians) is also of interest. The practicing clinician should be aware of the special dermatologic problems unique to the musical instrumentalist. Moreover awareness among musicians needs to be raised, as proper technique and conditioning may help to prevent affection of performance and occupational impairment.
doi:10.1186/1471-5945-4-3
PMCID: PMC416484  PMID: 15090069
23.  Annotated Bibliography on Equity in Health, 1980-2001 
The purposes of this bibliography are to present an overview of the published literature on equity in health and to summarize key articles relevant to the mission of the International Society for Equity in Health (ISEqH). The intent is to show the directions being taken in health equity research including theories, methods, and interventions to understand the genesis of inequities and their remediation. Therefore, the bibliography includes articles from the health equity literature that focus on mechanisms by which inequities in health arise and approaches to reducing them where and when they exist.
doi:10.1186/1475-9276-1-1
PMCID: PMC119369  PMID: 12234390
24.  Systematic review of orogenital HIV-1 transmission probabilities 
Background The objective was to assess the risk of HIV transmission from orogenital intercourse (OI).
Methods Systematic review of the literature on HIV-1 infectiousness through OI conducted according to MOOSE guidelines for reviews of observational studies. The PubMed database and bibliographies of relevant articles were searched to July 2007.
Results Of the titles, 56 214 were searched from which 10 potentially appropriate studies were identified; two additional studies were identified through bibliographies and one through discussion with experts. There were 10 included studies, providing estimates of transmission probabilities per-partner (n = 5), incidence per-partner (n = 3), per-study participant (n = 3, following initially seronegative individuals whose partners are of unknown serostatus) and per-act (n = 3). Only four of 10 studies reported non-zero estimates: two per-partner estimates (20%, 95% CI: 6–51, n = 10 and a model-based estimate, 1%, range 0.85–2.3%), one per-study participant estimate (0.37%, 95% CI: 0.10–1.34%) and one per-act estimate (0.04%, 95% CI: 0.01–0.17%). Upper bounds for the 95% CI for zero estimates tended to be relatively large due to the small study sample sizes: 9.0, 12.1 and 2.8% for per-partner; 4.7, 9.6 and 1.8 per 100 person-years for incidence per-partner; 4.4% per-study participant and 0.45 and 0.02% for per-act. Given the small number of studies, a meta-analysis was not considered appropriate.
Conclusions There are currently insufficient data to estimate precisely the risk from OI exposure. The low risk of transmission evident from identified studies means that more and larger studies would be required to provide sufficient evidence to derive more precise estimates.
doi:10.1093/ije/dyn151
PMCID: PMC2638872  PMID: 18664564
HIV; oral sex; orogenital intercourse; infectivity; transmission probability
25.  Development of a questionnaire to measure health-related quality of life (HRQoL) in patients with atrial fibrillation (AF-QoL) 
Background
The Health-Related Quality of Life (HRQoL) assessment in atrial fibrillation (AF) patients has traditionally been carried out in a poorly standardised fashion, or via the use of non disease-specific HRQoL questionnaires. The development of a HRQoL questionnaire with a good measuring performance will allow for a standardised assessment of the impact of this disease on the patient's daily living.
Methods
A bibliography review was conducted to identify the most relevant domains of daily living in AF patients. Subsequently, a focus group was created with the aid of cardiologists, and 17 patients were interviewed to identify the most-affected HRQoL domains. A qualitative analysis of the interview answers was performed, which was used to develop a pilot questionnaire administered to a 112-patient sample. Based on patient responses, an analysis was carried out following the statistical procedures defined by the Classical Test Theory (CTT) and the Item Response Theory (IRT). Reliablility was assessed via Cronbach's coefficient alpha and item-total score correlations. A factorial analysis was performed to determine the number of domains. For each domain, a Rasch analysis was carried out, in order to reduce and stand hierarchically the questionnaire items.
Results
By way of the bibliography review and the expert focus group, 10 domains were identified. The patient interviews allowed for the identification of 286 items that later were downsized to 40 items. The resultant preliminary questionnaire was administered to a 112-patient sample (pilot study). The Rasch analysis led to the definition of two domains, comprising 7 and 11 items respectively, which corresponded to the psychological and physical domains (18 items total), thereby giving rise to the initial AF-QoL-18 questionnaire. Cronbach's coefficient alpha was acceptable (0.91).
Conclusion
An initial HRQoL questionnaire, AFQoL-18, has been developed to assess HRQoL in AF patients.
doi:10.1186/1477-7525-5-37
PMCID: PMC1936414  PMID: 17610734

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