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Scholarly Content




Martin Fenner
Department of Hematology,
Hemostaseology, Oncology
and Stem Cell Transplantation
Not by starting
from scratch ā€¦
ā€¦ but by adding a few
       missing pieces
Scholarly research is
content creation
Reading is often an intermediary
step in content creation
Reading is often an intermediary
step in content creation




                      Except ā€¦
Education
Health Care
Curiosity
These uses are often covered by
secondary literature

Review journals   Textbooks   Science blogs
Reading for content creation
Fulltext search of methods
                    section
Fulltext search of methods
                    section




               Why only
               Elsevier?
An alternative fulltext search
Table 3. Olaparib-Related Adverse Events Found in at Least 5% of the Safety Population, According to Olaparib Dose.*




 Adverse Event
                         <100 mg, Daily
                         or Twice Daily,
                         2 of Every 3 Wk
                             (N = 18)
                                               100 mg,
                                             Twice Daily,
                                           2 of Every 3 Wk
                                                (N = 4)
                                                                 100 mg,
                                                               Twice Daily,
                                                               Continuously
                                                                  (N = 5)
                                                                                    200 mg
                                                                                  Twice Daily,
                                                                                  Continuously
                                                                                    (N = 20)
                                                                                                      400 mg
                                                                                                    Twice Daily,
                                                                                                    Continuously
                                                                                                       (N = 8)
                                                                                                                         600 mg
                                                                                                                       Twice Daily,
                                                                                                                       Continuously
                                                                                                                          (N = 5)
                                                                                                                                          Total
                                                                                                                                         (N = 60)
                                                                                                                                                    Figures and
                                                                                                                                                    tables
                                                                number of patients/total number (percent)
 Anemia
     Grade 1āˆ’2               1 (6)              0                  0                 0                  0                 1 (20)          2 (3)
     Grade 3āˆ’4               0                  0                  0                  1 (5)             0                  0              1 (2)
 Lymphopenia
     Grade 1āˆ’2               0                  0                  0                 0                  0                  0               0
     Grade 3āˆ’4               0                  0                  0                  2 (10)            1 (12)             0              3 (5)
 Diarrhea
     Grade 1āˆ’2               0                  0                  0                  2 (10)            1 (12)             0              3 (5)
     Grade 3āˆ’4               0                  0                  0                 0                  0                  0               0
 Dyspepsia
     Grade 1āˆ’2               0                  0                  0                  1 (5)             1 (12)             2 (40)         4 (7)
     Grade 3āˆ’4               0                  0                  0                 0                  0                  0               0
 Nausea
     Grade 1āˆ’2               6 (33)             1 (25)             0                  7 (35)            0                  3 (60)        17 (28)
     Grade 3āˆ’4               0                  0                   0                0                  1 (12)             1 (20)         2 (3)
 Stomatitis
     Grade 1āˆ’2               0                  0                   0                 3 (15)            0                  0              3 (5)
     Grade 3āˆ’4               0                  0                   0                0                  0                  0               0
 Vomiting
     Grade 1āˆ’2               2 (11)             1 (25)              0                 5 (25)            0                  3 (60)        11 (18)
     Grade 3āˆ’4               0                  0                   0                0                  1 (12)             0              1 (2)
 Anorexia
     Grade 1āˆ’2               3 (17)             0                   0                 2 (10)            0                  2 (40)         7 (12)
     Grade 3āˆ’4               0                  0                   0                0                  0                  0               0
 Dysgeusia
     Grade 1āˆ’2               0                  2 (50)              0                 2 (10)            1 (12)             3 (60)         8 (13)
     Grade 3āˆ’4               0                  0                   0                0                  0                  0               0
 Fatigue
     Grade 1āˆ’2               3 (17)             0                  1 (20)             4 (20)            5 (62)             4 (80)        17 (28)
     Grade 3āˆ’4               0                  0                   0                 1 (5)             0                  0              1 (2)
 Dizziness
     Grade 1āˆ’2               0                  0                   0                 1 (5)             0                  1 (20)         2 (3)
     Grade 3āˆ’4               0                  0                   0                0                  1 (12)             0              1 (2)

* The listed adverse events were classified as being possibly, probably, or definitely related to olaparib in the safety population. No grade 5



Fong et al. Inhibition of poly(ADP-ribose) polymerase in tumors from
BRCA mutation carriers. N Engl J Med 2009;361:123-34
Content licensing can be
automated ā€¦
Section 107 contains a list of the various purposes for
which the reproduction of a particular work may be
considered fair, such as criticism, comment, news
reporting, teaching, scholarship, and research.
Copyright protects the particular way an author has
expressed himself. It does not extend to any ideas,
systems, or factual information conveyed in the work.
                                   U.S. Copyright Law


       ā€¦ but is confusing and too
  restrictive for many researchers
How many researchers ask for
               permissions?
CC license for tables and ļ¬gures
better solution for reuse
     Attribution


     Share Alike


     No derivative works


     Non-commercial
Table 2: Univariate associations between cancer and other patient characteristics
                                                                                                BMC Medicine
 Characteristic                                              Cancer patients                Non-cancer patients            Odds ratio           P
                                                          % or mean (sd)         n         % or mean (sd)       n
                                                                                                Research article
 Number of subjects
 TZD therapy                                                   32.5%
                                                                                126
                                                                                126            Association between0.09
                                                                                               25.3%
                                                                                                       877
                                                                                                       877   1.42     cancer prevalence a
    Pioglitazone
    Rosiglitazone
                                                               13.5%
                                                               19.1%
                                                                                126
                                                                                126
                                                                                               thiazolidinediones: results from the Verm
                                                                                               13.6%
                                                                                               11.9%
                                                                                                       877
                                                                                                       877
                                                                                                             0.99
                                                                                                             1.75
                                                                                                                    0.98
                                                                                                                    0.03
 Sulfonylurea therapy
 Biguanide therapy
                                                               34.9%
                                                               39.7%
                                                                                126
                                                                                126
                                                                                               System 877
                                                                                               38.2%
                                                                                               40.0%   877
                                                                                                             0.87
                                                                                                             0.99
                                                                                                                    0.48
                                                                                                                    0.94
 Nateglinide therapy                                            0.8%            126             Maria E Ramos-Nino*ā€ 10.62
                                                                                                0.5%    877   1.75    , Charles D MacLeanā€ 2
 Men                                                           42.1%            126             46.1%              877          0.85            0.40
 Age, years                                                 69.1 (10.2)         126           64.2 (12.1)          877          1.04           <0.001
 White ethnicity                                               97.6%            125              Address:
                                                                                                97.3%      1University of Vermont, Department of Pathology, Vermont 05405, USA, 2Univ
                                                                                                                   875          1.15            0.83
 A1C, mean %                                                  7.0 (1.3)         126            7.2 (1.3) USA and871
                                                                                                 05401,            3University of Vermont, College of Nursing and Health Sciences, Burlin
                                                                                                                                0.88            0.12
 Insulin therapy                                               15.9%            126             18.8% Maria E Ramos-Nino*0.81
                                                                                                 Email:            877                          0.43
                                                                                                                                 - Maria.Ramos@uvm.edu; Charles D MacLean - Charles.M
 Body mass index, kg/m2                                      32.7 (6.8)         125           34.0 (7.5) Littenberg - Benjamin.Littenberg@vtmednet.org
                                                                                                 Benjamin          865          0.97            0.06
 Alcohol drinking                                              25.4%            126             27.6%
                                                                                                 * Corresponding876             0.89
                                                                                                                    author ā€ Equal contributors  0.60
 Cigarette smoking                                             11.1%            126             17.8%              876          0.58            0.06
 Median annual income, $                                   15000ā€“29999          114         15000ā€“29999            813          1.02            0.75
 Duration of diabetes, years                                 10.2 (9.7)         124           10.2 (10.4)          829          1.00            0.98
 High comorbidity                                              71.4%            126             46.2%              877          2.91           <0.001
                                                                                                 Published: 21 June 2007                                                      Received: 4 No
 Number of prescription medications                           7.3 (4.3)         126            6.6 (3.7)           877          1.05            0.05
                                                                                                                                                                              Accepted: 21 Ju
 Number of anti-diabetic drugs                               1.2 (1.0)          126              BMC Medicine 2007, 5:17 doi:10.1186/1741-7015-5-17
                                                                                               1.2(0.9)            877          1.01            0.92
 Physical functional status                                 40.9 (13.7)         125           42.3 (12.7) is available from: http://www.biomedcentral.com/1741-7015/5/17
                                                                                                 This article      871          0.99            0.27
 Mental functional status                                   50.5 (10.5)         126           49.4 (10.9)          875          1.01            0.30
                                                                                                 Ā© 2007 Ramos-Nino et al; licensee BioMed Central Ltd.
                                                                                                 This is an Open Access article distributed under the terms of the Creative Commons Attribu
 sd, standard deviation; n, number of patients for which data were available; TZD, thiazolidinedione. permits unrestricted use, distribution, and reproduction in any medium, provided the o
                                                                                                 which




                           Tables from papers donā€˜t                                                              Abstract
                                                                                                                 Background: Peroxisome proliferator-activated receptors (P
                                                                                                                 drug targets for diabetes. Drugs that activate PPAR , such as


                       display well in presentations
                                                                                                                 widely used for treatment of Type 2 diabetes mellitus. PPAR
                                                                                                                 neoplastic role in several in vitro models, although conflicting
                                                                                                                 models. The effects of TZDs on cancer risk in humans needs
                                                                                                                 prescribed for long periods of time in patients with diabetes.
                                                                                                                 Methods: A total of 1003 subjects in community practice set
Provide table and ļ¬gure data ā€¦
Anorexia   Nausea   Vomiting   Dysgeusia

                        18%        13%
    28%       28%




ā€¦ and visualize them as needed
www.sciencemag.org/cgi/content/full/328/5979/710/DC1




                     Supporting Online Material for

                 A Draft Sequence of the Neandertal Genome
      Richard E. Green,* Johannes Krause, Adrian W. Briggs, Tomislav Maricic,
          Udo Stenzel, Martin Kircher, Nick Patterson, Heng Li, Weiwei Zhai,
  Markus Hsi-Yang Fritz, Nancy F. Hansen, Eric Y. Durand, Anna-Sapfo Malaspinas,
  Jeffrey D. Jensen, Tomas Marques-Bonet, Can Alkan, Kay PrĆ¼fer, Matthias Meyer,
HernƔn A. Burbano, Jeffrey M. Good, Rigo Schultz, Ayinuer Aximu-Petri, Anne Butthof,
Barbara Hƶber, Barbara Hƶffner, Madlen Siegemund, Antje Weihmann, Chad Nusbaum,
   Eric S. Lander, Carsten Russ, Nathaniel Novod, Jason Affourtit, Michael Egholm,
      Christine Verna, Pavao Rudan, Dejana Brajkovic, !eljko Kucan, Ivan Gu"ic,
         Vladimir B. Doronichev, Liubov V. Golovanova, Carles Lalueza-Fox,
Marco de la Rasilla, Javier Fortea, Antonio Rosas, Ralf W. Schmitz, Philip L. F. Johnson,
 Evan E. Eichler, Daniel Falush, Ewan Birney, James C. Mullikin, Montgomery Slatkin,
    Rasmus Nielsen, Janet Kelso, Michael Lachmann, David Reich,* Svante PƤƤbo*

 *To whom correspondence should be addressed. E-mail: green@eva.mpg.de (R.E.G.);
        reich@genetics.med.harvard.edu (D.R.); paabo@eva.mpg.de (S.P.)
                          Published 7 May 2010, Science 328, 710 (2010)
                                  DOI: 10.1126/science.1188021



This PDF file includes:

       Materials and Methods
       SOM Text
                                                      Access to
       Figs. S1 to S51
       Tables S1 to S58
       References                                 research data
www.sciencemag.org/cgi/content/full/328/5979/710/DC1




                                  Supporting Online Material for

                              A Draft Sequence of the Neandertal Genome
                   Richard E. Green,* Johannes Krause, Adrian W. Briggs, Tomislav Maricic,
                       Udo Stenzel, Martin Kircher, Nick Patterson, Heng Li, Weiwei Zhai,
               Markus Hsi-Yang Fritz, Nancy F. Hansen, Eric Y. Durand, Anna-Sapfo Malaspinas,
               Jeffrey D. Jensen, Tomas Marques-Bonet, Can Alkan, Kay PrĆ¼fer, Matthias Meyer,
             HernƔn A. Burbano, Jeffrey M. Good, Rigo Schultz, Ayinuer Aximu-Petri, Anne Butthof,
             Barbara Hƶber, Barbara Hƶffner, Madlen Siegemund, Antje Weihmann, Chad Nusbaum,
                Eric S. Lander, Carsten Russ, Nathaniel Novod, Jason Affourtit, Michael Egholm,
                   Christine Verna, Pavao Rudan, Dejana Brajkovic, !eljko Kucan, Ivan Gu"ic,
                      Vladimir B. Doronichev, Liubov V. Golovanova, Carles Lalueza-Fox,
             Marco de la Rasilla, Javier Fortea, Antonio Rosas, Ralf W. Schmitz, Philip L. F. Johnson,
              Evan E. Eichler, Daniel Falush, Ewan Birney, James C. Mullikin, Montgomery Slatkin,
                 Rasmus Nielsen, Janet Kelso, Michael Lachmann, David Reich,* Svante PƤƤbo*

              *To whom correspondence should be addressed. E-mail: green@eva.mpg.de (R.E.G.);
                     reich@genetics.med.harvard.edu (D.R.); paabo@eva.mpg.de (S.P.)
                                       Published 7 May 2010, Science 328, 710 (2010)
                                               DOI: 10.1126/science.1188021




 PDF with
             This PDF file includes:

                    Materials and Methods
                    SOM Text
                                                                   Access to
175 pages?
                    Figs. S1 to S51
                    Tables S1 to S58
                    References                                 research data
Video and
other multimedia content
Is supplementary information
the right format?
Or shouldnā€˜t research data
rather be stored in a repository?
DataCite




     Or shouldnā€˜t research data
rather be stored in a repository?
Why only
Connotea?
7880 papers?
Unique author identiļ¬ers help
 ļ¬nd research by same author
Encourage electronic letters

                                                                                                                       RESEARCH

                                      Adequacy of authorsā€™ replies to criticism raised in electronic
                                      letters to the editor: cohort study
                                      Peter C GĆøtzsche, director,1 Tony Delamothe, editor,2 Fiona Godlee, editor,2 Andreas Lundh, PhD student1

   1
    Nordic Cochrane Centre,           ABSTRACT                                                      publication of the research report. Guidelines for edi-
   Rigshospitalet and University of   Objective To investigate whether substantive criticism in     tors are also sparse.3-5
   Copenhagen, Dept 3343,
   Blegdamsvej 9, DK-2100             electronic letters to the editor, defined as a problem that      We have noticed that when the criticism is serious,
   Copenhagen, Denmark                could invalidate the research or reduce its reliability, is   such as suggesting a fatal flaw, authors sometimes
   2
     BMJ, BMA House, Tavistock        adequately addressed by the authors.                          avoid addressing it in their reply and instead discuss
   Square, London
                                      Design Cohort study.                                          minor issues, or they misrepresent their research or
   Correspondence to: P C GĆøtzsche
   pcg@cochrane.dk                    SettingBMJ between October 2005 and September 2007.           the criticism. It is not known how common evasive
                                      Inclusion criteria Research papers generating substantive     replies are or how often editors assess whether authors
   Cite this as: BMJ 2010;341:c3926                                                                 have addressed criticisms appropriately and honestly
   doi:10.1136/bmj.c3926
                                      criticism in the rapid responses section on bmj.com.
                                      Main outcome measures Severity of criticism (minor,           and ask for changes when this is not the case. We inves-
                                      moderate, or major) as judged by two editors and extent       tigated whether authors responded adequately to sub-
                                      to which the criticism was addressed by authors (fully,       stantive criticism after publication and whether the
                                      partly, or not) as judged by two editors and the critics.     critics and the editors were satisfied with the replies.
                                      Results A substantive criticism was raised against 105 of
                                      350 (30%, 95% confidence interval 25% to 35%)                 METHODS
                                      included research papers, and of these the authors had        Our objectives were to study whether substantive criti-
                                      responded to 47 (45%, 35% to 54%). The severity of the        cism in letters to the editor was adequately addressed
                                      criticism was the same in those papers as in the 58           by authors, and whether the replies were less adequate
                                      without author replies (mean score 2.2 in both groups,        when the criticism was serious. We defined substantive
                                      P=0.72). For the 47 criticisms with replies, there was no     criticism as a problem that could invalidate the
                                      relation between the severity of the criticism and the        research or reduce its reliability.
Manuscript writing
Writing is collaborative
References should be shared
during writing
Current writing tools are not
ideal for scholarly papers
Why fonts,    Why margins,
    font sizes?   line heights?




 Why no
document
structure?
Remember Publicon?
Facilitate reference creation
  Bollen, J., VanĀ de Sompel, H., Hagberg, A. & Chute, R. A
  principal component analysis of 39 scientiļ¬c impact measures.
  PloS ONE 4, e6022+ (2009).

J.Ā Bollen, H.Ā VanĀ de Sompel, A.Ā Hagberg, R.Ā Chute, PloS ONE 4,
e6022+ (2009).

Bollen Johan, Sompel Herbert, Hagberg Aric, Chute Ryan. A
principal component analysis of 39 scientiļ¬c impact measures. PloS
ONE. 2009;4:e6022+.

J.Ā Bollen, etĀ al. (2009). `A principal component analysis of 39
scientiļ¬c impact measures.'. PloS ONE 4(6):e6022+.
This important paper provides evidence that scientiļ¬c impact can
not be adequately measured by any single indicator.
tributing papers should also submit via the Web. Corresponding

 PNAS Information for Authors
authors of communicated and contributed papers will be pro-
vided a URL for ļ¬le submission after the member has initiated
the process by providing his or her endorsement and copies of
  REVISED November also be submitted online.
the reviews received. SI must  2009
   Digital Figures. Only TIFF, EPS, and high-resolution PDF for
Mac or PC are allowedSCOPE that will appear in the print
  PURPOSE AND for ļ¬gures
journal. (See Supporting Information below for online-only ma-
terial.) Color images must theinNational Academy of Sciences U
  The Proceedings of be RGB (red, green, blue) mode.
  (PNAS) publishes research reports, commentaries, perspecti    -
erably 1 column width (8.7 cm). Figures wider with 1 column
  and colloquium papers. In accordance than the guiding prin
should be between 10.5 and 18.0 cm wide. Numbers, letters,
  ples established be no smallerEllery Hale in 1914,and no publis
and symbols should
                      by George than 6 points (2 mm) PNAS
larger than 12 points (6 mm) after reduction and must be con- foreign
  brief ļ¬rst announcements of Academy membersā€™ and
  sociatesā€™ (hereafter referred to as members) more important c
sistent. Composite ļ¬gures must be preassembled. Figures must
be submitted as separate ļ¬les, notof work thatmanuscriptto a membe
  tributions to research and embedded in appears text.
See www.pnas.org/site/misc/digitalart.pdf oris a general science jour
  be of particular importance. PNAS contact pnas_spe-
cialist@dartmouthjournals.com.
            Facilitate ļ¬gure creation
  with a broad scientiļ¬c audience. All papers should be intellig
   Tables. Each table should have a brief title, be on a separate
page,this audience.
  to and be double-spaced. Tables must be submitted as sepa-
Facilitate discussion prior to
publication
Facilitate peer review
Facilitate peer review
By connecting the missing
pieces using open standards ā€¦
     ORCID         CSL       ā€¦

                         ā€¦
DataCite     DOI

                      Creative
   NLM DTD           Commons
ā€¦ more
authors will
be happy
http://blogs.plos.org/mfenner
Credits
http://www.ļ¬‚ickr.com/photos/dhammza/91435718/
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nasaNAS~5~5~24355~127738:Original-Members-of-GIRD
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http://dx.doi.org/10.1056/NEJM194806032382301
http://dx.doi.org/10.1038/nature09442
http://dx.doi.org/10.1371/journal.pone.0006022
http://dx.doi.org/10.1056/NEJMoa0900212
http://dx.doi.org/10.1186/1741-7015-5-17
http://www.jneurosci.org/cgi/reprint/30/32/10599
http://dx.doi.org/10.3791/2059Ā 
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Helping Researchers Create Scholarly Content

  • 1. Helping Researchers Create Scholarly Content Martin Fenner Department of Hematology, Hemostaseology, Oncology and Stem Cell Transplantation
  • 2. Not by starting from scratch ā€¦
  • 3. ā€¦ but by adding a few missing pieces
  • 5. Reading is often an intermediary step in content creation
  • 6. Reading is often an intermediary step in content creation Except ā€¦
  • 10. These uses are often covered by secondary literature Review journals Textbooks Science blogs
  • 12. Fulltext search of methods section
  • 13. Fulltext search of methods section Why only Elsevier?
  • 15.
  • 16.
  • 17. Table 3. Olaparib-Related Adverse Events Found in at Least 5% of the Safety Population, According to Olaparib Dose.* Adverse Event <100 mg, Daily or Twice Daily, 2 of Every 3 Wk (N = 18) 100 mg, Twice Daily, 2 of Every 3 Wk (N = 4) 100 mg, Twice Daily, Continuously (N = 5) 200 mg Twice Daily, Continuously (N = 20) 400 mg Twice Daily, Continuously (N = 8) 600 mg Twice Daily, Continuously (N = 5) Total (N = 60) Figures and tables number of patients/total number (percent) Anemia Grade 1āˆ’2 1 (6) 0 0 0 0 1 (20) 2 (3) Grade 3āˆ’4 0 0 0 1 (5) 0 0 1 (2) Lymphopenia Grade 1āˆ’2 0 0 0 0 0 0 0 Grade 3āˆ’4 0 0 0 2 (10) 1 (12) 0 3 (5) Diarrhea Grade 1āˆ’2 0 0 0 2 (10) 1 (12) 0 3 (5) Grade 3āˆ’4 0 0 0 0 0 0 0 Dyspepsia Grade 1āˆ’2 0 0 0 1 (5) 1 (12) 2 (40) 4 (7) Grade 3āˆ’4 0 0 0 0 0 0 0 Nausea Grade 1āˆ’2 6 (33) 1 (25) 0 7 (35) 0 3 (60) 17 (28) Grade 3āˆ’4 0 0 0 0 1 (12) 1 (20) 2 (3) Stomatitis Grade 1āˆ’2 0 0 0 3 (15) 0 0 3 (5) Grade 3āˆ’4 0 0 0 0 0 0 0 Vomiting Grade 1āˆ’2 2 (11) 1 (25) 0 5 (25) 0 3 (60) 11 (18) Grade 3āˆ’4 0 0 0 0 1 (12) 0 1 (2) Anorexia Grade 1āˆ’2 3 (17) 0 0 2 (10) 0 2 (40) 7 (12) Grade 3āˆ’4 0 0 0 0 0 0 0 Dysgeusia Grade 1āˆ’2 0 2 (50) 0 2 (10) 1 (12) 3 (60) 8 (13) Grade 3āˆ’4 0 0 0 0 0 0 0 Fatigue Grade 1āˆ’2 3 (17) 0 1 (20) 4 (20) 5 (62) 4 (80) 17 (28) Grade 3āˆ’4 0 0 0 1 (5) 0 0 1 (2) Dizziness Grade 1āˆ’2 0 0 0 1 (5) 0 1 (20) 2 (3) Grade 3āˆ’4 0 0 0 0 1 (12) 0 1 (2) * The listed adverse events were classified as being possibly, probably, or definitely related to olaparib in the safety population. No grade 5 Fong et al. Inhibition of poly(ADP-ribose) polymerase in tumors from BRCA mutation carriers. N Engl J Med 2009;361:123-34
  • 18. Content licensing can be automated ā€¦
  • 19. Section 107 contains a list of the various purposes for which the reproduction of a particular work may be considered fair, such as criticism, comment, news reporting, teaching, scholarship, and research. Copyright protects the particular way an author has expressed himself. It does not extend to any ideas, systems, or factual information conveyed in the work. U.S. Copyright Law ā€¦ but is confusing and too restrictive for many researchers
  • 20. How many researchers ask for permissions?
  • 21. CC license for tables and ļ¬gures better solution for reuse Attribution Share Alike No derivative works Non-commercial
  • 22. Table 2: Univariate associations between cancer and other patient characteristics BMC Medicine Characteristic Cancer patients Non-cancer patients Odds ratio P % or mean (sd) n % or mean (sd) n Research article Number of subjects TZD therapy 32.5% 126 126 Association between0.09 25.3% 877 877 1.42 cancer prevalence a Pioglitazone Rosiglitazone 13.5% 19.1% 126 126 thiazolidinediones: results from the Verm 13.6% 11.9% 877 877 0.99 1.75 0.98 0.03 Sulfonylurea therapy Biguanide therapy 34.9% 39.7% 126 126 System 877 38.2% 40.0% 877 0.87 0.99 0.48 0.94 Nateglinide therapy 0.8% 126 Maria E Ramos-Nino*ā€ 10.62 0.5% 877 1.75 , Charles D MacLeanā€ 2 Men 42.1% 126 46.1% 877 0.85 0.40 Age, years 69.1 (10.2) 126 64.2 (12.1) 877 1.04 <0.001 White ethnicity 97.6% 125 Address: 97.3% 1University of Vermont, Department of Pathology, Vermont 05405, USA, 2Univ 875 1.15 0.83 A1C, mean % 7.0 (1.3) 126 7.2 (1.3) USA and871 05401, 3University of Vermont, College of Nursing and Health Sciences, Burlin 0.88 0.12 Insulin therapy 15.9% 126 18.8% Maria E Ramos-Nino*0.81 Email: 877 0.43 - Maria.Ramos@uvm.edu; Charles D MacLean - Charles.M Body mass index, kg/m2 32.7 (6.8) 125 34.0 (7.5) Littenberg - Benjamin.Littenberg@vtmednet.org Benjamin 865 0.97 0.06 Alcohol drinking 25.4% 126 27.6% * Corresponding876 0.89 author ā€ Equal contributors 0.60 Cigarette smoking 11.1% 126 17.8% 876 0.58 0.06 Median annual income, $ 15000ā€“29999 114 15000ā€“29999 813 1.02 0.75 Duration of diabetes, years 10.2 (9.7) 124 10.2 (10.4) 829 1.00 0.98 High comorbidity 71.4% 126 46.2% 877 2.91 <0.001 Published: 21 June 2007 Received: 4 No Number of prescription medications 7.3 (4.3) 126 6.6 (3.7) 877 1.05 0.05 Accepted: 21 Ju Number of anti-diabetic drugs 1.2 (1.0) 126 BMC Medicine 2007, 5:17 doi:10.1186/1741-7015-5-17 1.2(0.9) 877 1.01 0.92 Physical functional status 40.9 (13.7) 125 42.3 (12.7) is available from: http://www.biomedcentral.com/1741-7015/5/17 This article 871 0.99 0.27 Mental functional status 50.5 (10.5) 126 49.4 (10.9) 875 1.01 0.30 Ā© 2007 Ramos-Nino et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribu sd, standard deviation; n, number of patients for which data were available; TZD, thiazolidinedione. permits unrestricted use, distribution, and reproduction in any medium, provided the o which Tables from papers donā€˜t Abstract Background: Peroxisome proliferator-activated receptors (P drug targets for diabetes. Drugs that activate PPAR , such as display well in presentations widely used for treatment of Type 2 diabetes mellitus. PPAR neoplastic role in several in vitro models, although conflicting models. The effects of TZDs on cancer risk in humans needs prescribed for long periods of time in patients with diabetes. Methods: A total of 1003 subjects in community practice set
  • 23. Provide table and ļ¬gure data ā€¦
  • 24. Anorexia Nausea Vomiting Dysgeusia 18% 13% 28% 28% ā€¦ and visualize them as needed
  • 25. www.sciencemag.org/cgi/content/full/328/5979/710/DC1 Supporting Online Material for A Draft Sequence of the Neandertal Genome Richard E. Green,* Johannes Krause, Adrian W. Briggs, Tomislav Maricic, Udo Stenzel, Martin Kircher, Nick Patterson, Heng Li, Weiwei Zhai, Markus Hsi-Yang Fritz, Nancy F. Hansen, Eric Y. Durand, Anna-Sapfo Malaspinas, Jeffrey D. Jensen, Tomas Marques-Bonet, Can Alkan, Kay PrĆ¼fer, Matthias Meyer, HernĆ”n A. Burbano, Jeffrey M. Good, Rigo Schultz, Ayinuer Aximu-Petri, Anne Butthof, Barbara Hƶber, Barbara Hƶffner, Madlen Siegemund, Antje Weihmann, Chad Nusbaum, Eric S. Lander, Carsten Russ, Nathaniel Novod, Jason Affourtit, Michael Egholm, Christine Verna, Pavao Rudan, Dejana Brajkovic, !eljko Kucan, Ivan Gu"ic, Vladimir B. Doronichev, Liubov V. Golovanova, Carles Lalueza-Fox, Marco de la Rasilla, Javier Fortea, Antonio Rosas, Ralf W. Schmitz, Philip L. F. Johnson, Evan E. Eichler, Daniel Falush, Ewan Birney, James C. Mullikin, Montgomery Slatkin, Rasmus Nielsen, Janet Kelso, Michael Lachmann, David Reich,* Svante PƤƤbo* *To whom correspondence should be addressed. E-mail: green@eva.mpg.de (R.E.G.); reich@genetics.med.harvard.edu (D.R.); paabo@eva.mpg.de (S.P.) Published 7 May 2010, Science 328, 710 (2010) DOI: 10.1126/science.1188021 This PDF file includes: Materials and Methods SOM Text Access to Figs. S1 to S51 Tables S1 to S58 References research data
  • 26. www.sciencemag.org/cgi/content/full/328/5979/710/DC1 Supporting Online Material for A Draft Sequence of the Neandertal Genome Richard E. Green,* Johannes Krause, Adrian W. Briggs, Tomislav Maricic, Udo Stenzel, Martin Kircher, Nick Patterson, Heng Li, Weiwei Zhai, Markus Hsi-Yang Fritz, Nancy F. Hansen, Eric Y. Durand, Anna-Sapfo Malaspinas, Jeffrey D. Jensen, Tomas Marques-Bonet, Can Alkan, Kay PrĆ¼fer, Matthias Meyer, HernĆ”n A. Burbano, Jeffrey M. Good, Rigo Schultz, Ayinuer Aximu-Petri, Anne Butthof, Barbara Hƶber, Barbara Hƶffner, Madlen Siegemund, Antje Weihmann, Chad Nusbaum, Eric S. Lander, Carsten Russ, Nathaniel Novod, Jason Affourtit, Michael Egholm, Christine Verna, Pavao Rudan, Dejana Brajkovic, !eljko Kucan, Ivan Gu"ic, Vladimir B. Doronichev, Liubov V. Golovanova, Carles Lalueza-Fox, Marco de la Rasilla, Javier Fortea, Antonio Rosas, Ralf W. Schmitz, Philip L. F. Johnson, Evan E. Eichler, Daniel Falush, Ewan Birney, James C. Mullikin, Montgomery Slatkin, Rasmus Nielsen, Janet Kelso, Michael Lachmann, David Reich,* Svante PƤƤbo* *To whom correspondence should be addressed. E-mail: green@eva.mpg.de (R.E.G.); reich@genetics.med.harvard.edu (D.R.); paabo@eva.mpg.de (S.P.) Published 7 May 2010, Science 328, 710 (2010) DOI: 10.1126/science.1188021 PDF with This PDF file includes: Materials and Methods SOM Text Access to 175 pages? Figs. S1 to S51 Tables S1 to S58 References research data
  • 29. Or shouldnā€˜t research data rather be stored in a repository?
  • 30. DataCite Or shouldnā€˜t research data rather be stored in a repository?
  • 31.
  • 33.
  • 35. Unique author identiļ¬ers help ļ¬nd research by same author
  • 36. Encourage electronic letters RESEARCH Adequacy of authorsā€™ replies to criticism raised in electronic letters to the editor: cohort study Peter C GĆøtzsche, director,1 Tony Delamothe, editor,2 Fiona Godlee, editor,2 Andreas Lundh, PhD student1 1 Nordic Cochrane Centre, ABSTRACT publication of the research report. Guidelines for edi- Rigshospitalet and University of Objective To investigate whether substantive criticism in tors are also sparse.3-5 Copenhagen, Dept 3343, Blegdamsvej 9, DK-2100 electronic letters to the editor, defined as a problem that We have noticed that when the criticism is serious, Copenhagen, Denmark could invalidate the research or reduce its reliability, is such as suggesting a fatal flaw, authors sometimes 2 BMJ, BMA House, Tavistock adequately addressed by the authors. avoid addressing it in their reply and instead discuss Square, London Design Cohort study. minor issues, or they misrepresent their research or Correspondence to: P C GĆøtzsche pcg@cochrane.dk SettingBMJ between October 2005 and September 2007. the criticism. It is not known how common evasive Inclusion criteria Research papers generating substantive replies are or how often editors assess whether authors Cite this as: BMJ 2010;341:c3926 have addressed criticisms appropriately and honestly doi:10.1136/bmj.c3926 criticism in the rapid responses section on bmj.com. Main outcome measures Severity of criticism (minor, and ask for changes when this is not the case. We inves- moderate, or major) as judged by two editors and extent tigated whether authors responded adequately to sub- to which the criticism was addressed by authors (fully, stantive criticism after publication and whether the partly, or not) as judged by two editors and the critics. critics and the editors were satisfied with the replies. Results A substantive criticism was raised against 105 of 350 (30%, 95% confidence interval 25% to 35%) METHODS included research papers, and of these the authors had Our objectives were to study whether substantive criti- responded to 47 (45%, 35% to 54%). The severity of the cism in letters to the editor was adequately addressed criticism was the same in those papers as in the 58 by authors, and whether the replies were less adequate without author replies (mean score 2.2 in both groups, when the criticism was serious. We defined substantive P=0.72). For the 47 criticisms with replies, there was no criticism as a problem that could invalidate the relation between the severity of the criticism and the research or reduce its reliability.
  • 39. References should be shared during writing
  • 40. Current writing tools are not ideal for scholarly papers
  • 41. Why fonts, Why margins, font sizes? line heights? Why no document structure?
  • 43. Facilitate reference creation Bollen, J., VanĀ de Sompel, H., Hagberg, A. & Chute, R. A principal component analysis of 39 scientiļ¬c impact measures. PloS ONE 4, e6022+ (2009). J.Ā Bollen, H.Ā VanĀ de Sompel, A.Ā Hagberg, R.Ā Chute, PloS ONE 4, e6022+ (2009). Bollen Johan, Sompel Herbert, Hagberg Aric, Chute Ryan. A principal component analysis of 39 scientiļ¬c impact measures. PloS ONE. 2009;4:e6022+. J.Ā Bollen, etĀ al. (2009). `A principal component analysis of 39 scientiļ¬c impact measures.'. PloS ONE 4(6):e6022+. This important paper provides evidence that scientiļ¬c impact can not be adequately measured by any single indicator.
  • 44. tributing papers should also submit via the Web. Corresponding PNAS Information for Authors authors of communicated and contributed papers will be pro- vided a URL for ļ¬le submission after the member has initiated the process by providing his or her endorsement and copies of REVISED November also be submitted online. the reviews received. SI must 2009 Digital Figures. Only TIFF, EPS, and high-resolution PDF for Mac or PC are allowedSCOPE that will appear in the print PURPOSE AND for ļ¬gures journal. (See Supporting Information below for online-only ma- terial.) Color images must theinNational Academy of Sciences U The Proceedings of be RGB (red, green, blue) mode. (PNAS) publishes research reports, commentaries, perspecti - erably 1 column width (8.7 cm). Figures wider with 1 column and colloquium papers. In accordance than the guiding prin should be between 10.5 and 18.0 cm wide. Numbers, letters, ples established be no smallerEllery Hale in 1914,and no publis and symbols should by George than 6 points (2 mm) PNAS larger than 12 points (6 mm) after reduction and must be con- foreign brief ļ¬rst announcements of Academy membersā€™ and sociatesā€™ (hereafter referred to as members) more important c sistent. Composite ļ¬gures must be preassembled. Figures must be submitted as separate ļ¬les, notof work thatmanuscriptto a membe tributions to research and embedded in appears text. See www.pnas.org/site/misc/digitalart.pdf oris a general science jour be of particular importance. PNAS contact pnas_spe- cialist@dartmouthjournals.com. Facilitate ļ¬gure creation with a broad scientiļ¬c audience. All papers should be intellig Tables. Each table should have a brief title, be on a separate page,this audience. to and be double-spaced. Tables must be submitted as sepa-
  • 45. Facilitate discussion prior to publication
  • 48. By connecting the missing pieces using open standards ā€¦ ORCID CSL ā€¦ ā€¦ DataCite DOI Creative NLM DTD Commons
  • 50.
  • 55. This presentation can be copied and distributed provided that proper credit is given.