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author:("holy, John")
1.  Seasonal Distribution and Historic Trends in Abundance of White Sharks, Carcharodon carcharias, in the Western North Atlantic Ocean 
PLoS ONE  2014;9(6):e99240.
Despite recent advances in field research on white sharks (Carcharodon carcharias) in several regions around the world, opportunistic capture and sighting records remain the primary source of information on this species in the northwest Atlantic Ocean (NWA). Previous studies using limited datasets have suggested a precipitous decline in the abundance of white sharks from this region, but considerable uncertainty in these studies warrants additional investigation. This study builds upon previously published data combined with recent unpublished records and presents a synthesis of 649 confirmed white shark records from the NWA compiled over a 210-year period (1800-2010), resulting in the largest white shark dataset yet compiled from this region. These comprehensive records were used to update our understanding of their seasonal distribution, relative abundance trends, habitat use, and fisheries interactions. All life stages were present in continental shelf waters year-round, but median latitude of white shark occurrence varied seasonally. White sharks primarily occurred between Massachusetts and New Jersey during summer and off Florida during winter, with broad distribution along the coast during spring and fall. The majority of fishing gear interactions occurred with rod and reel, longline, and gillnet gears. Historic abundance trends from multiple sources support a significant decline in white shark abundance in the 1970s and 1980s, but there have been apparent increases in abundance since the 1990s when a variety of conservation measures were implemented. Though the white shark's inherent vulnerability to exploitation warrants continued protections, our results suggest a more optimistic outlook for the recovery of this iconic predator in the Atlantic.
doi:10.1371/journal.pone.0099240
PMCID: PMC4053410  PMID: 24918579
2.  Does journal endorsement of reporting guidelines influence the completeness of reporting of health research? A systematic review protocol 
Systematic Reviews  2012;1:24.
Background
Reporting of health research is often inadequate and incomplete. Complete and transparent reporting is imperative to enable readers to assess the validity of research findings for use in healthcare and policy decision-making. To this end, many guidelines, aimed at improving the quality of health research reports, have been developed for reporting a variety of research types. Despite efforts, many reporting guidelines are underused. In order to increase their uptake, evidence of their effectiveness is important and will provide authors, peer reviewers and editors with an important resource for use and implementation of pertinent guidance. The objective of this study was to assess whether endorsement of reporting guidelines by journals influences the completeness of reporting of health studies.
Methods
Guidelines providing a minimum set of items to guide authors in reporting a specific type of research, developed with explicit methodology, and using a consensus process will be identified from an earlier systematic review and from the EQUATOR (Enhancing the QUAlity and Transparency Of health Research) Network’s reporting guidelines library. MEDLINE, EMBASE, the Cochrane Methodology Register and Scopus will be searched for evaluations of those reporting guidelines; relevant evaluations from the recently conducted CONSORT systematic review will also be included. Single data extraction with 10% verification of study characteristics, 20% of outcomes and complete verification of aspects of study validity will be carried out. We will include evaluations of reporting guidelines that assess the completeness of reporting: (1) before and after journal endorsement, and/or (2) between endorsing and non-endorsing journals. For a given guideline, analyses will be conducted for individual and the total sum of items. When possible, standard, pooled effects with 99% confidence intervals using random effects models will be calculated.
Discussion
Evidence on which guidelines have been evaluated and which are associated with improved completeness of reporting is important for various stakeholders, including editors who consider which guidelines to endorse in their journal editorial policies.
doi:10.1186/2046-4053-1-24
PMCID: PMC3482392  PMID: 22626029
Reporting guidelines; Evaluation; Systematic review; Completeness of reporting
3.  Investigator experiences with financial conflicts of interest in clinical trials 
Trials  2011;12:9.
Background
Financial conflicts of interest (fCOI) can introduce actions that bias clinical trial results and reduce their objectivity. We obtained information from investigators about adherence to practices that minimize the introduction of such bias in their clinical trials experience.
Methods
Email survey of clinical trial investigators from Canadian sites to learn about adherence to practices that help maintain research independence across all stages of trial preparation, conduct, and dissemination. The main outcome was the proportion of investigators that reported full adherence to preferred trial practices for all of their trials conducted from 2001-2006, stratified by funding source.
Results
844 investigators responded (76%) and 732 (66%) provided useful information. Full adherence to preferred clinical trial practices was highest for institutional review of signed contracts and budgets (82% and 75% of investigators respectively). Lower rates of full adherence were reported for the other two practices in the trial preparation stage (avoidance of confidentiality clauses, 12%; trial registration after 2005, 39%). Lower rates of full adherence were reported for 7 practices in the trial conduct (35% to 43%) and dissemination (53% to 64%) stages, particularly in industry funded trials. 269 investigators personally experienced (n = 85) or witnessed (n = 236) a fCOI; over 70% of these situations related to industry trials.
Conclusion
Full adherence to practices designed to promote the objectivity of research varied across trial stages and was low overall, particularly for industry funded trials.
doi:10.1186/1745-6215-12-9
PMCID: PMC3031202  PMID: 21226951
9.  Transparent and accurate reporting increases reliability, utility, and impact of your research: reporting guidelines and the EQUATOR Network 
BMC Medicine  2010;8:24.
Although current electronic methods of scientific publishing offer increased opportunities for publishing all research studies and describing them in sufficient detail, health research literature still suffers from many shortcomings. These shortcomings seriously undermine the value and utility of the literature and waste scarce resources invested in the research. In recent years there have been several positive steps aimed at improving this situation, such as a strengthening of journals' policies on research publication and the wide requirement to register clinical trials.
The EQUATOR (Enhancing the QUAlity and Transparency Of health Research) Network is an international initiative set up to advance high quality reporting of health research studies; it promotes good reporting practices including the wider implementation of reporting guidelines. EQUATOR provides free online resources http://www.equator-network.org supported by education and training activities and assists in the development of robust reporting guidelines. This paper outlines EQUATOR's goals and activities and offers suggestions for organizations and individuals involved in health research on how to strengthen research reporting.
doi:10.1186/1741-7015-8-24
PMCID: PMC2874506  PMID: 20420659
10.  Financial Conflicts of Interest Checklist 2010 for clinical research studies 
Open Medicine  2010;4(1):e69-e91.
Abstract
A conflict of interest is defined as “a set of conditions in which professional judgment concerning a primary interest (such as a patient’s welfare or the validity of research) tends to be unduly influenced by a secondary interest (such as financial gain)” [Thompson DF. Understanding financial conflicts of interest. N Engl J Med 1993;329(8):573–576]. Because financial conflict of interest (fCOI) can occur at different stages of a study, and because it can be difficult for investigators to detect their own bias, particularly retrospectively, we sought to provide funders, journal editors and other stakeholders with a standardized tool that initiates detailed reporting of different aspects of fCOI when the study begins and continues that reporting throughout the study process to publication. We developed a checklist using a 3-phase process of pre-meeting item generation, a stakeholder meeting and post-meeting consolidation. External experts (n = 18), research team members (n = 12) and research staff members (n = 4) rated or reviewed items for some or all of the 7 major iterations. The resulting Financial Conflicts of Interest Checklist 2010 consists of 4 sections covering administrative, study, personal financial, and authorship information, which are divided into 6 modules and contain a total of 15 items and their related sub-items; it also includes a glossary of terms. The modules are designed to be completed by all investigators at different points over the course of the study, and updated information can be appended to the checklist when it is submitted to stakeholder groups for review. We invite comments and suggestions for improvement at http://www.openmedicine.ca/fcoichecklist and ask stakeholder groups to endorse the use of the checklist.
PMCID: PMC3116675  PMID: 21686297
12.  Development of an Immunoglobulin M Capture-Based Enzyme-Linked Immunosorbent Assay for Diagnosis of Acute Infections with Bartonella henselae▿  
We describe the development of an immunoglobulin M-specific enzyme-linked immunosorbent assay for the detection of an early antibody response to Bartonella henselae, the causative agent of cat scratch disease, bacillary angiomatosis, and endocarditis. This assay discriminates between B. henselae-positive and -negative patient samples with sensitivity and specificity values of 100% and 97.1%, respectively.
doi:10.1128/CVI.00305-08
PMCID: PMC2643531  PMID: 19052161
13.  Helping editors, peer reviewers and authors improve the clarity, completeness and transparency of reporting health research 
BMC Medicine  2008;6:13.
Inadequate reporting is problematic for several reasons. If authors do not provide sufficient details concerning the conduct of their study, readers are left with an incomplete picture of what was done. As such, they are not able to judge the merits of the results and interpret them. The EQUATOR Network is a new initiative aimed at improving the clarity and transparency of reporting health research.
doi:10.1186/1741-7015-6-13
PMCID: PMC2438435  PMID: 18558004
14.  Guidelines for Reporting Health Research: The EQUATOR Network's Survey of Guideline Authors 
PLoS Medicine  2008;5(6):e139.
Iveta Simera and colleagues survey the authors of 37 guidelines on reporting health research.
doi:10.1371/journal.pmed.0050139
PMCID: PMC2443184  PMID: 18578566
17.  Editorial Independence in the Electronic Age: New Threats, Old Owners? 
Mens Sana Monographs  2008;6(1):226-236.
Editorial independence is crucial for the intellectual life of a scientific journal. A journal exists only as an idea created by authors and readers, with some editorial orchestration. Editorial independence can be compromised by pressure put on editors by their owners–whether commercial publishers or professional organizations. Both types of owners rely heavily on income from paid advertising in their print journals. Yet, the massive expansion of journal readership that has resulted due to the development of the Web has effected a marked shift in the readership of the journal, both geographically and intellectually, producing a new community of users who see only electronic versions of the journal. Commercial pressures on owners to satisfy the interests of the (mainly national and professional) print readership conflict with the editorial independence needed to respond to the vast Web constituency. This is a major source for compromise of editorial independence. Reduction of commercial pressures by transferring editorial costs to authors and by other cost-reducing models are discussed in this article.
doi:10.4103/0973-1229.40568
PMCID: PMC3190552  PMID: 22013360
Editorial Independence; Editorial Freedom; Editorial Integrity; Journal Profitability; Conflict of Interest; Electronic Publication; Pharmaceutical Advertising
18.  An editorial dissection 
Open Medicine  2007;1(3):e129-e130.
PMCID: PMC3113216
19.  Not all guidelines are created equal 
doi:10.1503/cmaj.060245
PMCID: PMC1402372
21.  Unnecessary exposure? 
doi:10.1503/cmaj.1050244
PMCID: PMC1373761  PMID: 16477070
22.  Guideline controversy 
doi:10.1503/cmaj.051662
PMCID: PMC1373715
23.  Lymphocytic choriomeningitis virus 
doi:10.1503/cmaj.051184
PMCID: PMC1266324  PMID: 16247097
24.  The Olivieri story, take three 
doi:10.1503/cmaj.051032
PMCID: PMC1247707

Results 1-25 (96)