93 Matching Annotations
  1. Mar 2019
  2. Feb 2019
  3. Jan 2019
  4. Jan 2018
    1. An interactive network of bibliographic connections between some central proteins of the circadian clock, along with links to some major model organisms.

      Circadian clock proteins

  5. Nov 2017
  6. Oct 2017
  7. Jun 2017
  8. May 2017
    1. I have for several weeks now been playing around with a multipaned browser and some php and javascripts in an attempt to tie PS into a usable patchwork. PS3x5 (working name ;) is analogous to taking notes on 3x5 cards. 1. Do your research. 2. Take notes and bibliography info on your 3x5s. 3. Sort, reorder, toss, the 3x5s to create your outline. 4. Write "stuff" to fill in between the 3x5s.    (04) Granular links remain in the finished document. All done in the context of a browser.

      PS Browser

  9. Mar 2017
  10. Jan 2017
  11. Oct 2016
  12. Jul 2016
    1. Earlier studies A number of previous studies, both snapshots and some with longitudinal elements, have shed light on different aspects of such type of journals, which for short we will call “indie” journals.

      Bibliography of "independent journals"

  13. Jun 2016
    1. hmed, Maurana, Engle,Uddin, & Glaus (1997)

      authorship matrix bibliography

    2. However, a diverse body of work on thesocially situated nature of scientific communication alreadyexists which points the way. This ranges from Crane’s(1969) pioneering analyses of invisible colleges throughLatour and Woolgar’s (1979) classic study of laboratory lifeat the Salk Institute to Traweek’s (1992) richly texturedethnography of the HEP community. In addition, the workof Schatz and colleagues on the Worm Community Systemproject, which was designed to capture the full range ofknowledge, formal and informal, of the community of mo-lecular biologists who study the nematode worm C. elegans(see: http://www.canis.uiuc.edu/projects/wcs/index.html)can provide useful insights; so, too, research into the mate-rial practices and social interactions of scientists working incollaboratories, such as the Upper Atmospheric ResearchCollaboratory (see: http://intel.si.umich.edu/crew/Research/resrch08.htm) or the Space, Physics & Aeronomy ResearchCollaboratory (see: http://intel.si.umich.edu/sparc/) at theUniversity of Michigan

      great bibliography on ethnographies of different disciplines

    3. The answer probably has to do with the relative intensityof socialization and oral communication (Traweek, 1992,pp. 120 –123), along with the character of the organizationalstructures and value systems, which define collaborations inlarge-scale, high-energy physics and biomedical research.

      Why is there less soul-searching about hyper-authorship in HEP? disciplinary differences

    4. owever, it isimportant to distinguish between generic job categories andthe specification of tasks performed; the contributorshipmodel is designed to record each individual’s actual input(e.g., experimental design, data collection, statistical analy-sis, final article revision), not job title (e.g., coprincipalinvestigator, technician, systems analyst), since the lattermay on occasion mask or inflate the former (Stern, 2000).

      Great point about movie credits: they are about job title, not contribution.

    5. Rennie, Yank, andEmanuel (1997) that the distinction between the two modesof credit allocation is inherently artificial. Consequently,they have argued for explicit description of all individualcontributions as a means of eliminating ambiguity. Such aproposal would remove both authorship and acknowledg-ment from the frame, a really quite significant break withscholarly publishing tradition. This alternative amounts to aradical model of authorship attribution in contrast to thestandard model

      Rennie, Yank, and Emanuel 1997 argue that acknowledgements and authorship can't be disentangled.

    6. Some journals place a limit on the numberof coauthors; for example, theDutch Journal of Medicinedoes not publish articles with more than six authors (Hoenet al., 1998).

      Journal that caps authorship with bibliography

    7. “sub-authorship collaboration” (Patel, 1973, p. 81),

      acknowledgements as "sub-authorship collaboration"

    8. twe should not assume too much in terms of common un-derstandings: the dividing line between the two classifica-tions, author and acknowledgee, is neither universally ap-preciated nor consistently applied. Cronin (1995, pp. 85–86), for instance, has shown that interpretative disputes arenot uncommon, and that some researchers feel that theyhave been denied their just deserts by being downgradedfrom coauthor to acknowledgee. A

      on boundary between authorship and acknowledgement

    9. Slone (1996), in a survey of “major research” articlespublished in theAmerican Journal of Roentgenology, foundthat undeserved coauthorship rose from 9% on papers withthree coauthors to 30% on papers with more than six coau-thors.

      another estimate of undeserved authorship

    10. Flanagin et al.(1998) developed a multivariate logistic regression model totest the hypothesis that coauthored articles (operationalizedas papers with six or more authors) were increasing at a rategreater than would be expected when confounding vari-ables, such as the number of centers, were taken into ac-count. They found that 19% of original research reports hadhonorific authors, individuals who were garnering phantomfodder for their curricula vitae. They also discovered that11% of articles had ghost authors, which means that quite afew individuals were not receiving due credit for theircreative or material contributions to the research process—“the ghostly inferred hosts of unnamed actors who shiftedinstruments about and exerted their muscular labor’(Shapin, 1995, p. 379). Their findings, based on surveys ofcorresponding authors, are in keeping with other estimatesof honorific authorship in the biomedical literature.

      Bibliography on ghost and guest authorship: flanagin et al 1998 and Shapin 1995, 379

      Used statistical methods and surveys to work out percentage of ghosts and uncredited authors.

    11. norificauthorship and data integrity, seem to be of especial concernto the biomedical community, given widespread media cov-erage of, and speculation about, fraudulent practice, theeffects of which, in both career and personal terms, can bedevastating (e.g., Kevles, 1998).

      about authorship scandals in biomedicine

    12. n the realm of periodical publications,the sovereignty of the standard model is being most hotlycontested in biomedical research fields, where intense levelsof professional collaboration and coauthorship are common-place (Croll, 1984; Rennie & Flanagin, 1994; Rennie, Yank,& Emanuel, 1997; Rennie & Yank, 1998; King, 2000).Proposals for reform, which seek to retire the concept ofauthorship and replace it with a scheme for the allocation ofspecific, task- or job-related credits (e.g., Squires, 1996;Smith, 1997) are not only being debated by editors andothers, but are being adopted by leading scientific journal

      On how credit and authorship is being debated in medical publishing (with bibliography)

    13. Rennie’s and Flanagin’s (1994, p. 469) beguilingly simplequestion: “. . . how many people can wield one pen?” S

      How many people can yield one pen? Question about authorship

    14. Some medical commentators (Rennie, Yank, &Emanuel, 1997, p. 582) have advocated abandoning theconcept of author altogether in favor of ‘contributors’ and‘guarantors,’ thereby freeing us “from the historical andemotional connotations of authorship.”

      bibliography on the emotional connotations of authorship

      Idea is to abandon it entirely, so as to avoid this trap.

    15. ouble-blind) peer review became an established component of thepost-war scientific bureaucracy (Chubin & Hackett, 1990,pp. 19 –24)

      history of peer review

    16. e well-estab-lished “conventions of impersonality” in scientific writing(Hyland, 1999, p. 355) and resulting in the erasure of styl

      on the flattening effect collaborative authorship has on style

    17. s not still common prac-tice in fields such as philosophy or women’s studies (Cro-nin, Davenport, & Martinson, 1997). By way of example,Endersby (1996) has analyzed trends in, and reasons for,collaboration and multiple authorship in the social sciences.Patel (1973) has described the growth of coauthorship insociological journals for the period 1895 to 1965. Bird(1997) has found evidence of coauthorship growth in theliterature of marine mammal science (1985–1993), whileKoehler et al. (1999) found that the average number ofauthors per article in theJournal of the American Society forInformation Science(previouslyAmerican Documentation)rose from approximately 1.2 in the 1950s to 1.8 in the1990s

      bibliography on coauthorship by field

    18. Beaver and Rosen (1978) have shown how the differentialrates of scientific institutionalization in France, England,and Germany are mirrored in the relative output of coau-thored papers.

      bibliography tying rate of coauthorship to professionalisation of science

    19. iking increase inrates of coauthorship, though the latter is only a partialindicator of the former: coauthorship and collaboration arenot coextensive (Katz & Martin, 1997, p. 1). This trend ismost noticeable in experimental high-energy physics(HEP), with its often very large teams and highly sophisti-cated collaborations (Kling & McKim, 2000). A similartrend, dating from the 1990s, can be seen in the biomedicalresearch literature, particularly with regard to publicationsarising from large, multi-institutional clinical trials (Rennie,Yank, & Emanuel, 1997; Horton, 1998). H

      bibliography on HEP (High Energy Physics) collaborations and Biomedicine

    20. o some extent, authorship has becomea collective activity, with numerous coauthors competingfor the byline, some of whom may not have written, strictlyspeaking, a single word of the associated work (McDonald,1995; Kassirer & Angell, 1991).

      extent to which authors may not have written a word in science (with bibliography)

    21. hapin (1995,p. 178) notes in his brilliant study of trust in 17th-centuryEnglish science,

      "Brilliant study of trust in 17th century English science"

    22. As Katzen (1980, p. 191) notes in heranalysis of early volumes of thePhilosophical Transac-tions:. . . no attempt is made to give prominence to the author ofthe article . . . there is generally no reference at all to theauthor in the heading that signals a new communication. Ifthe author is referred to in the title, it is likely to be in anoblique form . . . we are at the threshold between anony-mous and eponymous authorship

      Study of authorship in Philosophical transactions

    23. s Rennie and Flanagin(1994) remind us, there is no standard method for determin-ing order, nor any universalistic criteria for conferring au-thorship status:

      bibliography on authorship practices

    24. Foucault,1977,p.125

      Authorship bibliography

    25. Manguel(1997,pp.182–183)

      Authorship bibliography

    26. lphabetization through weightedlisting to reverse seniority (e.g., Spiegel & Keith-Spiegel,1970; Riesenberg & Lundberg, 1990).

      bibliography on authorship ranking and practices

    1. most systems try to adapt the paper-and-pen paradigm to the digital world. That’s why many systems suffer from several shortcomings inherent in the paper-and-pen paradigm.
    1. The growth in web-based learning materials and information sources has created requirement for systems that allow annotations to be attached to these new sources and, potentially, shared with other learners.
    1. Harter's (1978) finding that expectation of letter grades affected children's task motivation in ways similar to the various extrinsic rewards used in other stud- ies

      Harter 1978 showed that grades are extrinsic motivators. Harter, S. (1978). Pleasure derived from challenge and the effects of receiving grades on children's difficulty level choices. Child Development, 49, 788-799.



    1. p. 65

      Contains a survey of the authors' own research on each topic (self-handicapping, avoidance of help-seeking behaviour, avoidance of challenge, and cheating.

  14. Apr 2016
    1. White (1984, cited by Vaughan, 1991) reported on a study conducted at California State University in which two essays were tucked into a huge sample of essays and read a year apart by the same readers using a 6-point scale. The reading a year later produced scores that were identical to the first in only 20 per cent of the cases. The scores differed by one point or less in 58 per cent of cases and 2 points or less in 83 per cent of the cases. As White points out, a 1-point difference is generally considered unproblematic, but on a 6-point scale the difference between a 3 and a 4 is the difference between a pass and a fail. Obviously, then, changes in examiner severity/leniency over-time have implications for maintaining standards, and must be monitored. Research has been conducted into variations in examiner severity/leniency during the marking of a particular allocation of scripts, a marking period, and over more extended periods of time.

      intrarater reliability is only 20%

    2. (2004) notes that most research papers describe interrater reliability as though it is a single, universal concept. He argues this practice is imprecise and potentially misleading. The specific type of interrater reliability being discussed should be indicated. He categorises the most common statistical methods for reporting interrater reliability into one of three classes: consensus estimates; consistency estimates; and measurement estimates.

      Stemler 2004

    1. Manso (2011)

      MANSO, G. “Motivating Innovation.”Journal of Finance, Vol. 66 (2011)

    2. Lerner and Wulf’s (2007) study of corporate R&D lab heads.They show that higher levels of deferred compensation are associated with the production ofmore heavily cited patents, whereas short-term incentives bear no relationship to firm innovativeperformance

      LERNER,J.ANDWULF, J. “Innovation and Incentives: Evidence from Corporate R&D.”Review of Economics and Statistics,Vol. 89 (2007), pp. 634–644

    3. Tian and Wang (2010) show that start-up firms backed by morefailure-tolerant venture capitalists are more innovativeex post

      TIAN,X.ANDWANG, T.Y. “Tolerance for Failure and Corporate Innovation.” Working Paper, Indiana University, 2010

    4. Lazear (2000)



  15. Mar 2016
    1. Begg, C. B., & Berlin, J. A. (1988). Publication bias: A problem in interpreting medical data.Journal of theRoyal Statistical Society A, 151, 419–463.
    2. Gilbody, S. M., Song, F., Eastwood, A. J., & Sutton, A. (2000). The causes, consequences and detection ofpublication bias in psychiatry.Acta Psychiatrica Scandinavica, 102, 241–249
    3. Greenberg, S. A. (2009). How citation distortions create unfounded authority: Analysis of a citation net-work.British Medical Journal, 339, b2680
    4. Kennedy, D. (2004). The old file-drawer problem.Science, 305, 45
    5. Krzyzanowska, M. K., Pintilie, M., & Tannock, I. F. (2003). Factors associated with failure to publish largerandomized trials presented at an oncology meeting.Journal of the American Medical Association,290, 495–501
    6. Levine, T., Asada, K. J., & Carpenter, C. (2009). Sample sizes and effect sizes are negatively correlated inmeta-analyses: Evidence and implications of a publication bias against non-significant findings.Communication Monographs, 76, 286–302
    7. Marsh, H. W., Bornmann, L., Mutz, R., Daniel, H. D., & O’Mara, A. (2009). Gender effects in the peerreviews of grant proposals: A comprehensive meta-analysis comparing traditional and multilevelapproaches.Review of Educational Research, 79, 1290–1326
    8. Paris, G., De Leo, G., Menozzi, P., & Gatto, M. (1998). Region-based citation bias in science.Nature, 396,6708
    9. Rosenthal, R. (1979). The file drawer problem and tolerance for null results.Psychological Bulletin, 86,638–641


    10. Song, F. J., Parekh-Bhurke, S., Hooper, L., Loke, Y. K., Ryder, J. J., Sutton, A. J., et al. (2009). Extent ofpublication bias in different categories of research cohorts: A meta-analysis of empirical studies.BMCMedical Research Methodology, 9, 79
    11. Sterling, T. D. (1959). Publication decisions and their possible effects on inferences drawn from tests ofsignificance—Or vice versa.Journal of the American Statistical Association, 54, 30–34

      publication bias

    1. Osuna, C., Crux-Castro, L., & Sanz-Menedez, L. (2011). Overturning some assumptions about the effects ofevaluation systems on publication performance.Scientometrics, 86, 575–592

      evaluation systems and publication performance

    2. Silvertown, J., & McConway, K. J. (1997). Does ‘‘publication bias’’ lead to biased science?Oikos, 79(1),167–168.
    3. Yousefi-Nooraie, R., Shakiba, B., & Mortaz-Hejri, S. (2006). Country development and manuscript selec-tion bias: A review of published studies.BMC Medical Research Methodology, 6, 37

      On developing countries and science

    4. Evanschitzky, H., Baumgarth, C., Hubbard, R., & Armstrong, J. S. (2007). Replication research’s disturbingtrend.Journal of Business Research, 60(4), 411–415. doi

      replication research

    5. Ioannidis, J. P. A. (2008a). Perfect study, poor evidence: Interpretation of biases preceding study design.Seminars in Hematology, 45(3), 160–166

      effect of positive bias

    6. Feigenbaum, S., & Levy, D. M. (1996). Research bias: Some preliminary findings.Knowledge and Policy:The International Journal of Knowledge Transfer and Utilization, 9(2 & 3), 135–142.

      Positive bias

    7. Song, F., Parekh, S., Hooper, L., Loke, Y. K., Ryder, J., Sutton, A. J., et al. (2010). Dissemination andpublication of research findings: An updated review of related biases.Health Technology Assessment,14(8), 1–193. doi

      positive bias

    8. Formann, A. K. (2008). Estimating the proportion of studies missing for meta-analysis due to publicationbias.Contemporary Clinical Trials, 29(5), 732–739. doi

      estimate of positive bias in clinical trials.

    9. Fronczak, P., Fronczak, A., & Holyst, J. A. (2007). Analysis of scientific productivity using maximumentropy principle and fluctuation-dissipation theorem.Physical Review E, 75(2), 026103. doi:10.1103/PhysRevE.75.026103.

      On rising scientific productivity over shorter careers.

    10. Atkin, P. A. (2002). A paradigm shift in the medical literature.British Medical Journal, 325(7378),1450–1451

      On the rise of sexy terms like "paradigm shift" in abstracts.

    11. Bonitz, M., & Scharnhorst, A. (2001). Competition in science and the Matthew core journals.Sciento-metrics, 51(1), 37–54

      Matthew effect

  16. Feb 2014
    1. Legal Writing for the Courts: An Annotated Bibliography
      • Mechanics
      • Argument
      • Style
      • Writing and Editing Process
      • Legal Briefs
      • Samples