Department Blog

Health Sciences Libraries

Experimental Design and Statistics

January 14th, 2015 by Mary Wood

ILAR Journal Volume 55(3): Experimental Design and Statistics

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The review articles in this issue discuss current methods of animal research to address what can be done to improve the quality of animal experiments, choice of animal model, and the systematic review and meta-analysis of animal experiments.

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Select articles:

Festing, Nevalainen
Design and Statistical Analysis of Animal Experiments: Introduction to this Issue

Bailoo, Reichlin, Würbel
Refinement of Experimental Design and Conduct in Laboratory Animal Research

Nevalainen
Animal Husbandry and Experimental Design

Festing
Evidence Should Trump Intuition by Preferring Inbred Strains to Outbred Stocks in Preclinical Research

O’Connor, Sargeant
Critical Appraisal of Studies Using Laboratory Animal Models

Hooijmans, IntHout, Ritskes-Hoitinga, Rovers
Meta-Analyses of Animal Studies: An Introduction of a Valuable Instrument to Further Improve Healthcare

de Vries, Wever, Avey, Stephens, Sena, Leenaars
Usefulness of Systematic Reviews of Animal Experiments for the Design of Preclinical and Clinical Studies

Garner
Significance of Meaning: Why Do Over 90% of Behavioral Neuroscience Results Fail to Translate to Humans, and What Can We Do to Fix It?

Fry
Teaching Experimental Design

Festing
Randomized Block Experimental Designs Can Increase the Power and Reproducibility of Laboratory Animal Experiments

Parker, Browne
Place of Experimental Design and Statistics in the 3Rs

Pearl
Making the Most of Clustered Data in Laboratory Animal Research Using Multi-Level Models

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Guidance for the Description of Animal Research in Scientific Publications
Committee members included Dr. Stephen W. Barthold (IOM), Center for Comparative Medicine, University of California, Davis

Users’ Guides to the Medical Literature

December 12th, 2014 by Mary Wood

Understanding systematic reviews and levels of evidence is challenging, and relating it to clinical decisions difficult.
JAMA since 1994 has attempted to further understanding and help clinicians by publishing Users’ Guides to the Medical Literature.
The effort continues, 20 years later.

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The most recent article :

Users’ Guides to the Medical Literature July 09, 2014
How to Read a Systematic Review and Meta-analysis and Apply the Results to Patient Care: Users’ Guides to the Medical Literature
Murad; Montori;  Ioannidis; et al
JAMA. 2014; 312(2):171-179. doi: 10.1001/jama.2014.5559

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Three options for finding the Users’ Guides to the Medical Literature articles:

for UC Davis affiliates

PubMed (use VPN if off campus)
Search: users guides to the medical literature
Select interesting title, click on gold UCeLinks button to get full text

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purchase 2008 edition

Users’ Guides to the Medical Literature: A Manual for Evidence-Based Clinical Practice, 2nd Edition
Gordon Guyatt, Drummond Rennie, Maureen O. Meade, and Deborah J. Cook
American Medical Association, 2008

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limited open access to 1994-2005 articles

Users’ Guides to Evidence-Based Practice
University Alberta, Center for Health Evidence, provide access to a 2005 set of Users’ Guides originally published as a series in the JAMA: the full text pre-publication version of the series on behalf of the Evidence-Based Medicine Working Group with permission from the journal.

Questions? hslref@ucdavis.edu

New OA Journal: Veterinary Medicine & Science

December 9th, 2014 by Mary Wood

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Wiley has a new open access journal :  Veterinary Medicine and Science

Veterinary Medicine and Science is an international open access journal which publishes original, high-quality, peer-reviewed articles on all aspects of Veterinary Medicine and Science relating to companion, production and zoo animals.

Publish for free : they are waiving the APC for the first 15 accepted articles

Publicity cites the following as reasons to publish with Veterinary Medicine Science :
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High standard, rigorous peer review
Quality and reputation, supported by Wiley’s network of prestigious journals and societies
Immediate open access
Fully compliant with all open access mandates
Authors retain copyright. Articles published under the Creative Commons Attribution (CC BY) License

Editor: Ed Hall MA VetMB, PhD, Dip-ECVIM-CA, MRCVS
Professor, Small Animal Internal Medicine, University of Bristol Veterinary School

Progress in Genetics and Genomics of Nonhuman Primates

December 11th, 2013 by Mary Wood

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.ILAR Journal Volume 54(2)
Progress in Genetics and Genomics of Nonhuman Primates

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The articles in this issue discuss the current understanding of the genetics and genomics of apes and old world monkeys.

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Articles include

Palermo et al. / Old World Monkeys and New Age Science: The Evolution of Nonhuman Primate Systems Virology

Shen et al. / The Essential Detail: The Genetics and Genomics of the Primate Immune Response

Tardif et al. /  IACUC Review of Nonhuman Primate Research

Systematic Reviews of Animal Studies

September 24th, 2013 by Mary Wood
Essay

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Citation: Hooijmans CR, Ritskes-Hoitinga M (2013)
Progress in Using Systematic Reviews of Animal Studies to Improve Translational Research.
PLoS Med 10(7): e1001482. doi:10.1371/journal.pmed.1001482
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…We summarize developments since 2002, focusing on the scientific rationale for systematic reviews of animal studies and the limitations and pitfalls. Moreover, we suggest further improvements in animal research to maximise its contribution to evidence-based translational research.
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Authors spoke on same topic at recent Cochrane Colloquium: “Synergy of systematic reviews of animal and clinical studies: towards evidence-based translational medicine”.  (program/abstracts)
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PLoS Biol: Statistical significance in animal studies

July 19th, 2013 by Mary Wood

The Shadow of Bias
July 16, 2013
Chase JM (2013) The Shadow of Bias. PLoS Biol 11(7): e1001608. doi:10.1371/journal.pbio.1001608

In a study by John Ioannidis and colleagues, the evaluation of 160 meta-analyses of animal studies on potential treatments for neurological disorders has revealed that the number of statistically significant results was too large to be true, suggesting biases…

pbio.1001608

Tsilidis KK, Panagiotou OA, Sena ES, Aretouli E, Evangelou E, Howells DW, Salman RA, Macleod MR, Ioannidis JP
(2013)
Evaluation of Excess Significance Bias in Animal Studies of Neurological Diseases
PLoS Biol 11(7): e1001609. doi:10.1371/journal.pbio.1001609

Author summary: Studies have shown that the results of animal biomedical experiments fail to translate into human clinical trials; this could be attributed either to real differences in the underlying biology between humans and animals, to shortcomings in the experimental design, or to bias in the reporting of results from the animal studies. We use a statistical technique to evaluate whether the number of published animal studies with “positive” (statistically significant) results is too large to be true…

IOM Workshop Summaries Released

April 3rd, 2013 by Mary Wood

Cognitive Rehabilitation Therapy for Traumatic Brain Injury: Model Study Protocols and Frameworks to Advance the State of the Science: Workshop Summary
Karin Matchett, Rapporteur; Board on the Health of Select Populations; Institute of Medicine

In October 2011, the Institute of Medicine (IOM) released the report Cognitive Rehabilitation Therapy for Traumatic Brain Injury: Evaluating the Evidence, assessing the published evidence for the effectiveness of using cognitive rehabilitation therapy (CRT) to treat people with traumatic brain injury (TBI). The Department of Defense (DoD) asked the IOM to evaluate CRT for traumatic brain injury in order to guide the DoD’s use and coverage in the Military Health System.

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Improving the Utility and Translation of Animal Models for Nervous System Disorders: Workshop Summary
Diana E. Pankevich, Theresa M. Wizemann, and Bruce M. Altevogt, Rapporteurs; Board on Health Sciences Policy; Institute of Medicine

On March 28 and 29, 2012, the Institute of Medicine Forum on Neuroscience and Nervous System Disorders convened the workshop “Improving Translation of Animal Models for Nervous System Disorders” to discuss potential opportunities for maximizing the translation of new therapies from animal models to clinical practice. The primary focus of the workshop was to examine mechanisms for increasing the efficiency of translational neuroscience research through discussions about how and when to use animal models most effectively and then best approaches for the interpretation of the data collected.

PeerJ – new open access journal

March 1st, 2013 by Mary Wood

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.PeerJ Publishes Its First Articles
from Press Release, Feb 12th 2013

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PeerJ, a new academic journal publisher, founded on the principles of affordability, innovation, and Open Access, published its first articles 2/12/13, launched by Jason Hoyt (formerly at Mendeley and Stanford University) and Peter Binfield (formerly at PLoS ONE)

Essential Features of PeerJ:

> Rapid, peer reviewed, ‘Open Access’ scholarly journal, using a Creative Commons license which means that all articles are entirely free to read, distribute, and reuse provided authors are properly attributed.

> Publication decisions are made only on scientific validity (not on perceived impact).

>  Uses a ‘Membership Model’ whereby authors become lifetime members, giving them the ability to freely publish their articles thereafter.

>  PeerJ has 800 Academic Editors, including 20 Advisory Board members (of which 5 are Nobel Laureates).

>  Encourages ‘open’ Peer Review (meaning that reviewers are encouraged to provide their names; authors are empowered to reproduce their peer review history alongside their published article).

>  By utilizing short, iterative development cycles, users will see the rapid development of new features and innovative functionality, dramatically improving the academic publication and reading experience.

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UC Davis scientists included in inaugural issue

EVALUATION OF ANIMAL CONTROL MEASURES ON PET DEMOGRAPHICS IN SANTA CLARA COUNTY, CALIFORNIA, 1993-2006Philip H. Kass 1, Karen L. Johnson2, Hsin-Yi Weng3

1 Dept of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA
2 National Pet Alliance, San Jose, CA
3 Dept of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN

REDUCED EXPRESSION OF GLYCOLATE OXIDASE LEADS TO ENHANCED DISEASE RESISTANCE IN RICEMawsheng Chern1, Wei Bai1,2, Xuewei Chen1,3, Patrick E. Canlas1, Pamela C. Ronald 1

1 Dept of Plant Pathology, University of California Davis, California
2 College of Life Sciences, Inner Mongolia Agricultural University, Huhhot, China
3 Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China

Two new veterinary books worth noting

February 6th, 2013 by Mary Wood

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Vandevelde, Marc
Manual of veterinary neuropathology essentials of theory and practice
Ames, Iowa : Wiley-Blackwell, 2012
Electronic Resources Internet

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Fischer, Martin S.
Dogs in motion
Dortmund : VDH Service GmbH, 2011
Carlson Health Sci Library 2nd copy in process
Carlson Health Sci Reserves SF 432 F535d 2011

Developing Data Attribution / Citation Practices & Standards

November 27th, 2012 by Mary Wood

For Attribution — Developing Data Attribution and Citation Practices and Standards
Summary of an International Workshop


..Paul F. Uhlir, Rapporteur
..Board on Research Data and Information
..Policy and Global Affairs
..National Research Council

..Read Full Text
..Jump to book’s table of contents to begin reading online for free

..The National Academies Press

Description:
The growth of electronic publishing of literature has created new challenges, such as the need for mechanisms for citing online references in ways that can assure discoverability and retrieval for many years into the future. The growth in online datasets presents related, yet more complex challenges. It depends upon the ability to reliably identify, locate, access, interpret, and verify the version, integrity, and provenance of digital datasets. Data citation standards and good practices can form the basis for increased incentives, recognition, and rewards for scientific data activities that in many cases are currently lacking in many fields of research…

The problem of citing online data is complicated by the lack of established practices for referring to portions or subsets of data. There are a number of initiatives in different organizations, countries, and disciplines already underway. An important set of technical and policy approaches have already been launched by the U.S. National Information Standards Organization (NISO) and other standards bodies regarding persistent identifiers and online linking…    Read More