A syntagmatic/Paradigmatic analysis of scientific text
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Talk for HCLS SiG on Scientific Discourse by Anita de Waard

Talk for HCLS SiG on Scientific Discourse by Anita de Waard

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  • 1. Syntagmatic/paradigmatic analysis of scientific text HCLS Scientific Discourse Call March 28 2011 Anita de Waard, a.dewaard@elsevier.com Disruptive Technologies Director, Elsevier Labs University of Utrecht, Institute of LinguisticsSaturday, March 26, 2011
  • 2. Scientific papers are stories, that persuade with data 2Saturday, March 26, 2011
  • 3. Scientific papers are stories, that persuade with data 1.Syntagmatic approach (Tropp)/ story grammar (Rumelhart, Thorndyke): ‘‘systematic assignment of constituent structure” • Sequential components • Order in text is key factor • Granularity: one or more paragraphs (?) 2Saturday, March 26, 2011
  • 4. Scientific papers are stories, that persuade with data 1.Syntagmatic approach (Tropp)/ story grammar (Rumelhart, Thorndyke): ‘‘systematic assignment of constituent structure” • Sequential components • Order in text is key factor • Granularity: one or more paragraphs (?) 2.Paradigmatic approach: “groups of relations between actors and events are sought throughout the text” (Lévi-Strauss, 1955) • Groups are found throughout the text • Relationship types between actors/events are key • Granularity: ‘shortest possible sentences’ 2Saturday, March 26, 2011
  • 5. Syntagmatic analysis of fairytales: 3Saturday, March 26, 2011
  • 6. Syntagmatic analysis of fairytales: According to Propp, main characters (or dramatis personae) that are occuring in a fairy tale may be the following: 1. Hero: a character that seeks something; 2. Villain: opposes or actively blocks the heroʼs quest; 3. Donor: provides the hero with an object of magical properties; 4. Dispatcher: sends the hero on his/her quest via a message; 5. False Hero: disrupts the heroʼs success by making false claims; 6. Helper: aids the hero; 7. Princess: acts as the reward for the hero and the object of the villainʼs plots; 8. Her Father: acts to reward the hero for his effort. 3Saturday, March 26, 2011
  • 7. Syntagmatic analysis of fairytales: According to Propp, main characters (or dramatis personae) that are occuring in a fairy tale may be the following: 1. Hero: a character that seeks something; 2. Villain: opposes or actively blocks the heroʼs quest; 3. Donor: provides the hero with an object of magical properties; 4. Dispatcher: sends the hero on his/her quest via a message; 5. False Hero: disrupts the heroʼs success by making false claims; 6. Helper: aids the hero; 7. Princess: acts as the reward for the hero and the object of the villainʼs plots; 8. Her Father: acts to reward the hero for his effort. Morphology of the Folktale, Propp:“list of all the elements of the fairy tale”. The list contains 150 elements, distributed over six tables: 1. Initial Situation 2. Preparatory Section 3. Complication 4. Donors 5. From the Entry of the Helper to the End of the First Move 6. Beginning of the Second Move 3Saturday, March 26, 2011
  • 8. Syntagmatic analysis of fairytales: According to Propp, main characters (or dramatis personae) F. Peinado, P. Gervas, and B. Diaz-Agudo, ʻA description logic ontology for fairy tale that are occuring in a fairy tale may be the following: generationʼ, in Proceedings of LREC. ELRA 1. Hero: a character that seeks something; (5 2004) 2. Villain: opposes or actively blocks the heroʼs quest; 3. Donor: provides the hero with an object of magical properties; 4. Dispatcher: sends the hero on his/her quest via a message; 5. False Hero: disrupts the heroʼs success by making false claims; 6. Helper: aids the hero; 7. Princess: acts as the reward for the hero and the object of the villainʼs plots; 8. Her Father: acts to reward the hero for his effort. Morphology of the Folktale, Propp:“list of all the elements of the fairy tale”. The list contains 150 elements, distributed over six tables: 1. Initial Situation 2. Preparatory Section 3. Complication 4. Donors 5. From the Entry of the Helper to the End of the First Move 6. Beginning of the Second Move 3Saturday, March 26, 2011
  • 9. Syntagmatic analysis of science: story grammarThe Story of Goldilocks Story Grammar Paper The AXH Domain of Ataxin-1 Mediatesand the Three Bears Neurodegeneration through Its Interaction with Gfi-1/ Senseless ProteinsOnce upon a time Time Setting Background The mechanisms mediating SCA1 pathogenesis are still not fully understood, but some general principles have emerged.a little girl named Goldilocks Characters Objects of study the Drosophila Atx-1 homolog (dAtx-1) which lacks a polyQ tract,She went for a walk in the Location Experimental studied and compared in vivo effects and interactions to those offorest. Pretty soon, she came setup the human proteinupon a house.She knocked and, when no one Goal Theme Research Gain insight into how Atx-1s function contributes to SCA1answered, goal pathogenesis. How these interactions might contribute to the disease process and how they might cause toxicity in only a subseshe walked right in. of neurons play a role in the regulation of gene expression Atx-1 may in SCA1 is not fully understood. Attempt HypothesisAt the table in the kitchen, there Name Episode 1 Name dAtX-1 and hAtx-1 Induce Similar Phenotypes Whenwere three bowls of porridge. Overexpressed in FilesGoldilocks was hungry. Subgoal Subgoal test the function of the AXH domainShe tasted the porridge from Attempt Method overexpressed dAtx-1 in flies using the GAL4/UAS system (Brandthe first bowl. and Perrimon, 1993) and compared its effects to those of hAtx-1.This porridge is too hot! she Outcome Results Overexpression of dAtx-1 by Rhodopsin1(Rh1)-GAL4, which driveexclaimed. expression in the differentiated R1-R6 photoreceptor cells (Mollereau et al., 2000 and OTousa et al., 1985), results in neurodegeneration in the eye, as does overexpression of hAtx-1 [82Q]. Although at 2 days after eclosion, overexpression of eitherSo, she tasted the porridge Activity Data (data not shown), Atx-1 does not show obvious morphological changes in thefrom the second bowl. photoreceptor cellsThis porridge is too cold, she Outcome Results both genotypes show many large holes and loss of cell integrity atsaid 28 daysSo, she tasted the last bowl of  Activity Data (Figures 1B-1D).porridge.Ahhh, this porridge is just right, Outcome Results Overexpression of dAtx-1 using the GMR-GAL4 driver also induceshe said happily and eye abnormalities. The external structures of the eyes that 4 overexpress dAtx-1 show disorganized ommatidia and loss ofshe ate it all up.   Data interommatidial bristles (Figure 1F),Saturday, March 26, 2011
  • 10. Syntagmatic analysis of science: story grammarThe Story of Goldilocks Story Grammar Paper The AXH Domain of Ataxin-1 Mediatesand the Three Bears Neurodegeneration through Its Interaction with Gfi-1/ Senseless ProteinsOnce upon a time Time Setting Background The mechanisms mediating SCA1 pathogenesis are still not fully understood, but some general principles have emerged.a little girl named Goldilocks Characters Objects of study the Drosophila Atx-1 homolog (dAtx-1) which lacks a polyQ tract,She went for a walk in the Location Experimental studied and compared in vivo effects and interactions to those offorest. Pretty soon, she came setup the human proteinupon a house.She knocked and, when no one Goal Theme Research Gain insight into how Atx-1s function contributes to SCA1answered, goal pathogenesis. How these interactions might contribute to the disease process and how they might cause toxicity in only a subseshe walked right in. of neurons play a role in the regulation of gene expression Atx-1 may in SCA1 is not fully understood. Attempt HypothesisAt the table in the kitchen, there Name Episode 1 Name dAtX-1 and hAtx-1 Induce Similar Phenotypes Whenwere three bowls of porridge. Overexpressed in FilesGoldilocks was hungry. Subgoal Subgoal test the function of the AXH domainShe tasted the porridge from Attempt Method overexpressed dAtx-1 in flies using the GAL4/UAS system (Brandthe first bowl. and Perrimon, 1993) and compared its effects to those of hAtx-1.This porridge is too hot! she Outcome Results Overexpression of dAtx-1 by Rhodopsin1(Rh1)-GAL4, which driveexclaimed. expression in the differentiated R1-R6 photoreceptor cells (Mollereau et al., 2000 and OTousa et al., 1985), results in neurodegeneration in the eye, as does overexpression of hAtx-1 [82Q]. Although at 2 days after eclosion, overexpression of eitherSo, she tasted the porridge Activity Data (data not shown), Atx-1 does not show obvious morphological changes in thefrom the second bowl. photoreceptor cellsThis porridge is too cold, she Outcome Results both genotypes show many large holes and loss of cell integrity atsaid 28 daysSo, she tasted the last bowl of  Activity Data (Figures 1B-1D).porridge.Ahhh, this porridge is just right, Outcome Results Overexpression of dAtx-1 using the GMR-GAL4 driver also induceshe said happily and eye abnormalities. The external structures of the eyes that 4 overexpress dAtx-1 show disorganized ommatidia and loss ofshe ate it all up.   Data interommatidial bristles (Figure 1F),Saturday, March 26, 2011
  • 11. Rhetorical analogue to scientific structure: 5Saturday, March 26, 2011
  • 12. Rhetorical analogue to scientific structure: Aristotle Quintilian Scientific Paper The introduction of a speech, where one announces the Introduction subject and purpose of the discourse, and where one usually Introduction: prooimion / exordium employs the persuasive appeal to ethos in order to positioning establish credibility with the audience. Statement of The speaker here provides a narrative account of what has Introduction: research prothesis Facts/narratio happened and generally explains the nature of the case. question Summary/ The propositio provides a brief summary of what one is about   propostitio to speak on, or concisely puts forth the charges or accusation. Summary of contents The main body of the speech where one offers logical Proof/ pistis confirmatio arguments as proof. The appeal to logos is emphasized Results here. Refutation/ As the name connotes, this section of a speech was devoted to   refutatio answering the counterarguments of ones opponent. Related Work Following the refutatio and concluding the classical oration, the Discussion: summary, epilogos peroratio  peroratio conventionally employed appeals through pathos, and often included a summing up. implications. 5Saturday, March 26, 2011
  • 13. Rhetorical analogue to scientific structure: Aristotle Quintilian Scientific Paper The introduction of a speech, where one announces the Introduction subject and purpose of the discourse, and where one usually Introduction: prooimion / exordium employs the persuasive appeal to ethos in order to positioning establish credibility with the audience. Statement of The speaker here provides a narrative account of what has Introduction: research prothesis Facts/narratio happened and generally explains the nature of the case. question Summary/ The propositio provides a brief summary of what one is about   propostitio to speak on, or concisely puts forth the charges or accusation. Summary of contents The main body of the speech where one offers logical Proof/ pistis confirmatio arguments as proof. The appeal to logos is emphasized Results here. Refutation/ As the name connotes, this section of a speech was devoted to   refutatio answering the counterarguments of ones opponent. Related Work Following the refutatio and concluding the classical oration, the Discussion: summary, epilogos peroratio  peroratio conventionally employed appeals through pathos, and often included a summing up. implications. 5Saturday, March 26, 2011
  • 14. Syntagmatic analysis of scientific text:ORB vs. Medium-grained structure 6Saturday, March 26, 2011
  • 15. Syntagmatic analysis of scientific text:ORB vs. Medium-grained structure 6Saturday, March 26, 2011
  • 16. Syntagmatic enabler: Linked Data (for Elsevier)Saturday, March 26, 2011
  • 17. Syntagmatic enabler: Linked Data (for Elsevier) <ce:section id=#123>Saturday, March 26, 2011
  • 18. Syntagmatic enabler: Linked Data (for Elsevier) this says <ce:section id=#123> mice like cheeseSaturday, March 26, 2011
  • 19. Syntagmatic enabler: Linked Data (for Elsevier) said @anita on March 28, 2011 this says <ce:section id=#123> mice like cheeseSaturday, March 26, 2011
  • 20. Syntagmatic enabler: Linked Data (for Elsevier) but we all know she was wrong then said @anita on March 28, 2011 this says <ce:section id=#123> mice like cheeseSaturday, March 26, 2011
  • 21. Syntagmatic enabler: Linked Data (for Elsevier) the xml is fixed, but the structure is open! but we all know she was wrong then said @anita on March 28, 2011 this says <ce:section id=#123> mice like cheeseSaturday, March 26, 2011
  • 22. Syntagmatic enabler: Linked Data (for Elsevier) the xml is fixed, but the structure is open! allows for layers of annotation but we all know she was wrong then said @anita on March 28, 2011 this says <ce:section id=#123> mice like cheeseSaturday, March 26, 2011
  • 23. Paradigmatic analysis of fairytales: The Structural Study of Myth, Claude Lévi-Strauss The Jnl of American Folklore, 68(270) pp. 428-44, 1955, “the true constituent units of a myth are not the isolated relations but bundles of such relations and it is only as bundles that these relations can be put to use and combined so as to produce a meaning. Relations pertaining to the same bundle may appear diachronically at remote intervals, but when we have succeeded in grouping them together, we have reorganized our myth according to a time referent of a new nature corresponding to the prerequisite of the initial hypothesis, namely,a two-dimensional time referent which is simultaneously diachronical and synchronical and which accordingly integrates the characteristics of the langue on one hand, and those of the parole on the other.” 8Saturday, March 26, 2011
  • 24. Paradigmatic analysis of fairytales: The Structural Study of Myth, Claude Lévi-Strauss The Jnl of American Folklore, 68(270) pp. 428-44, 1955, “the true constituent units of a myth are not the isolated relations but bundles of such relations and it is only as bundles that these relations can be put to use and combined so as to produce a meaning. Relations pertaining to the same bundle may appear diachronically at remote intervals, but when we have succeeded in grouping them together, we have reorganized our myth according to a time referent of a new nature corresponding to the prerequisite of the initial hypothesis, namely,a two-dimensional time referent which is simultaneously diachronical and synchronical and which accordingly integrates the characteristics of the langue on one hand, and those of the parole on the other.” 8Saturday, March 26, 2011
  • 25. Paradigmatic analysis of fairytales: The Structural Study of Myth, Claude Lévi-Strauss The Jnl of American Folklore, 68(270) pp. 428-44, 1955, “the true constituent units of a myth are not the isolated relations but bundles of such relations and it is only as bundles that these relations can be put to use and combined so as to produce a meaning. Relations pertaining to the same bundle may appear diachronically at remote intervals, but when we have succeeded in grouping them together, we have reorganized our myth according to a time referent of a new nature corresponding to the prerequisite of the initial hypothesis, namely,a two-dimensional time referent which is simultaneously diachronical and synchronical and which accordingly integrates the characteristics of the langue on one (narrative) TIME hand, and those of the parole on the other.” 8Saturday, March 26, 2011
  • 26. Paradigmatic analysis of fairytales: The Structural Study of Myth, Claude Lévi-Strauss The Jnl of American Folklore, 68(270) pp. 428-44, 1955, (narrative) THEME “the true constituent units of a myth are not the isolated relations but bundles of such relations and it is only as bundles that these relations can be put to use and combined so as to produce a meaning. Relations pertaining to the same bundle may appear diachronically at remote intervals, but when we have succeeded in grouping them together, we have reorganized our myth according to a time referent of a new nature corresponding to the prerequisite of the initial hypothesis, namely,a two-dimensional time referent which is simultaneously diachronical and synchronical and which accordingly integrates the characteristics of the langue on one (narrative) TIME hand, and those of the parole on the other.” 8Saturday, March 26, 2011
  • 27. Paradigmatic approach for science Both seminomas and the EC component of nonseminomas share features with ES cells. To exclude that the detection of miR-371-3 merely reflects its expression pattern in ES cells, we tested by RPA miR-302a-d, another ES cells-specific miRNA cluster (Suh et al, 2004). In many of the miR-371-3 expressing seminomas and nonseminomas, miR-302a-d was undetectable (Figs S7 and S8), suggesting that miR-371-3 expression is a selective event during tumorigenesis. 9Saturday, March 26, 2011
  • 28. Paradigmatic approach for science Both seminomas and the EC component of Both seminomas and the EC component of nonseminomas share features with ES cells. nonseminomas share features with ES cells. To exclude thatthat detection of miR-371-3 merely To exclude the reflects its expression pattern in ES cells,reflects its the detection of miR-371-3 merely we tested by RPA miR-302a-d, another ES cells-specific expression pattern in ES cells, miRNA cluster RPA miR-302a-d, another ES cells- we tested by (Suh et al, 2004). In many of the m i R - 3 7 miRNAx p r e s s(Suh et e m2004). a s a n d specific 1 - 3 e cluster i n g s al, i n o m nonseminomas, miR-302a-d was undetectable (Figs In many of the miR-371-3 expressing seminomas S7 and S8), suggesting that miR-371-3undetectable and nonseminomas, miR-302a-d was expression is a selective event during tumorigenesis. (Figs S7 and S8), suggesting that miR-371-3 expression is a selective event during tumorigenesis. 9Saturday, March 26, 2011
  • 29. Paradigmatic approach for science Both seminomas and the EC component of Both seminomas and the EC component of Fact nonseminomas share features with ES cells. nonseminomas share features with ES cells. To exclude thatthat detection of miR-371-3 merely To exclude the reflects its expression pattern in ES cells,reflects its the detection of miR-371-3 merely we tested by RPA miR-302a-d, another ES cells-specific expression pattern in ES cells, miRNA cluster RPA miR-302a-d, another ES cells- we tested by (Suh et al, 2004). In many of the m i R - 3 7 miRNAx p r e s s(Suh et e m2004). a s a n d specific 1 - 3 e cluster i n g s al, i n o m nonseminomas, miR-302a-d was undetectable (Figs In many of the miR-371-3 expressing seminomas S7 and S8), suggesting that miR-371-3undetectable and nonseminomas, miR-302a-d was expression is a selective event during tumorigenesis. (Figs S7 and S8), suggesting that miR-371-3 expression is a selective event during tumorigenesis. 9Saturday, March 26, 2011
  • 30. Paradigmatic approach for science Both seminomas and the EC component of Both seminomas and the EC component of Fact nonseminomas share features with ES cells. nonseminomas share features with ES cells. To exclude thatthat detection of miR-371-3 merely To exclude the reflects its expression pattern in ES cells,reflects its the detection of miR-371-3 merely we tested Hypothesis by RPA miR-302a-d, another ES cells-specific expression pattern in ES cells, miRNA cluster RPA miR-302a-d, another ES cells- we tested by (Suh et al, 2004). In many of the m i R - 3 7 miRNAx p r e s s(Suh et e m2004). a s a n d specific 1 - 3 e cluster i n g s al, i n o m nonseminomas, miR-302a-d was undetectable (Figs In many of the miR-371-3 expressing seminomas S7 and S8), suggesting that miR-371-3undetectable and nonseminomas, miR-302a-d was expression is a selective event during tumorigenesis. (Figs S7 and S8), suggesting that miR-371-3 expression is a selective event during tumorigenesis. 9Saturday, March 26, 2011
  • 31. Paradigmatic approach for science Both seminomas and the EC component of Both seminomas and the EC component of Fact nonseminomas share features with ES cells. nonseminomas share features with ES cells. To exclude thatthat detection of miR-371-3 merely To exclude the reflects its expression pattern in ES cells,reflects its the detection of miR-371-3 merely we tested Hypothesis by RPA miR-302a-d, another ES cells-specific expression pattern in ES cells, miRNA cluster RPA miR-302a-d, another ES cells- we tested by (Suh et al, 2004). In many of the m i R - 3 7 miRNAx p r e s s(Suh et e m2004). a s a n d specific 1 - 3 e cluster i n g s al, i n o m Method nonseminomas, miR-302a-d was undetectable (Figs In many of the miR-371-3 expressing seminomas S7 and S8), suggesting that miR-371-3undetectable and nonseminomas, miR-302a-d was expression is a selective event during tumorigenesis. (Figs S7 and S8), suggesting that miR-371-3 expression is a selective event during tumorigenesis. 9Saturday, March 26, 2011
  • 32. Paradigmatic approach for science Both seminomas and the EC component of Both seminomas and the EC component of Fact nonseminomas share features with ES cells. nonseminomas share features with ES cells. To exclude thatthat detection of miR-371-3 merely To exclude the reflects its expression pattern in ES cells,reflects its the detection of miR-371-3 merely we tested Hypothesis by RPA miR-302a-d, another ES cells-specific expression pattern in ES cells, miRNA cluster RPA miR-302a-d, another ES cells- we tested by (Suh et al, 2004). In many of the m i R - 3 7 miRNAx p r e s s(Suh et e m2004). a s a n d specific 1 - 3 e cluster i n g s al, i n o m Method nonseminomas, miR-302a-d was undetectable (Figs In many of the miR-371-3 expressing seminomas S7 and S8), suggesting that miR-371-3undetectable and nonseminomas, miR-302a-d was expression Result is a selective event during tumorigenesis. (Figs S7 and S8), suggesting that miR-371-3 expression is a selective event during tumorigenesis. 9Saturday, March 26, 2011
  • 33. Paradigmatic approach for science Both seminomas and the EC component of Both seminomas and the EC component of Fact nonseminomas share features with ES cells. nonseminomas share features with ES cells. To exclude thatthat detection of miR-371-3 merely To exclude the reflects its expression pattern in ES cells,reflects its the detection of miR-371-3 merely we tested Hypothesis by RPA miR-302a-d, another ES cells-specific expression pattern in ES cells, miRNA cluster RPA miR-302a-d, another ES cells- we tested by (Suh et al, 2004). In many of the m i R - 3 7 miRNAx p r e s s(Suh et e m2004). a s a n d specific 1 - 3 e cluster i n g s al, i n o m Method nonseminomas, miR-302a-d was undetectable (Figs In many of the miR-371-3 expressing seminomas S7 and S8), suggesting that miR-371-3undetectable and nonseminomas, miR-302a-d was expression Result is a selective event during tumorigenesis. (Figs S7 and S8), suggesting that miR-371-3 expression is a selective event during Implication tumorigenesis. 9Saturday, March 26, 2011
  • 34. Paradigmatic approach for science Both seminomas and the EC component of Both seminomas and the EC component of Fact nonseminomas share features with ES cells. nonseminomas share features with ES cells. To exclude thatthat detection of miR-371-3 merely To exclude the Goal reflects its expression pattern in ES cells,reflects its the detection of miR-371-3 merely we tested Hypothesis by RPA miR-302a-d, another ES cells-specific expression pattern in ES cells, miRNA cluster RPA miR-302a-d, another ES cells- we tested by (Suh et al, 2004). In many of the m i R - 3 7 miRNAx p r e s s(Suh et e m2004). a s a n d specific 1 - 3 e cluster i n g s al, i n o m Method nonseminomas, miR-302a-d was undetectable (Figs In many of the miR-371-3 expressing seminomas S7 and S8), suggesting that miR-371-3undetectable and nonseminomas, miR-302a-d was expression Result is a selective event during tumorigenesis. (Figs S7 and S8), suggesting that miR-371-3 expression is a selective event during Implication tumorigenesis. 9Saturday, March 26, 2011
  • 35. Paradigmatic approach for science Both seminomas and the EC component of Both seminomas and the EC component of Fact nonseminomas share features with ES cells. nonseminomas share features with ES cells. To exclude thatthat detection of miR-371-3 merely To exclude the Goal reflects its expression pattern in ES cells,reflects its the detection of miR-371-3 merely we tested Hypothesis by RPA miR-302a-d, another ES cells-specific expression pattern in ES cells, miRNA cluster RPA miR-302a-d, another ES cells- we tested by (Suh et al, 2004). In many of the m i R - 3 7 miRNAx p r e s s(Suh et e m2004). a s a n d specific 1 - 3 e cluster i n g s al, i n o m Method nonseminomas, miR-302a-d was undetectable (Figs In many of the miR-371-3 expressing seminomas S7 and S8), suggesting that miR-371-3undetectable and nonseminomas, miR-302a-d was expression Result is a selective event during tumorigenesis. (Figs S7 and S8), suggesting that Reg-Implication miR-371-3 expression is a selective event during Implication tumorigenesis. 9Saturday, March 26, 2011
  • 36. Paradigmatic approach for science Conceptual Both seminomas and the EC component of Both seminomas and the EC component of knowledge Fact nonseminomas share features with ES cells. nonseminomas share features with ES cells. To exclude thatthat detection of miR-371-3 merely To exclude the Goal reflects its expression pattern in ES cells,reflects its the detection of miR-371-3 merely we tested Hypothesis by RPA miR-302a-d, another ES cells-specific expression pattern in ES cells, miRNA cluster RPA miR-302a-d, another ES cells- we tested by (Suh et al, 2004). In many of the m i R - 3 7 miRNAx p r e s s(Suh et e m2004). a s a n d specific 1 - 3 e cluster i n g s al, i n o m Method nonseminomas, miR-302a-d was undetectable (Figs In many of the miR-371-3 expressing seminomas S7 and S8), suggesting that miR-371-3undetectable and nonseminomas, miR-302a-d was expression Result is a selective event during tumorigenesis. (Figs S7 and S8), suggesting that Reg-Implication miR-371-3 expression is a selective event during Implication tumorigenesis. 9Saturday, March 26, 2011
  • 37. Paradigmatic approach for science Conceptual Both seminomas and the EC component of Both seminomas and the EC component of knowledge Fact nonseminomas share features with ES cells. nonseminomas share features with ES cells. To exclude thatthat detection of miR-371-3 merely To exclude the Goal reflects its expression pattern in ES cells,reflects its the detection of miR-371-3 merely we tested Hypothesis by RPA miR-302a-d, another ES cells-specific expression pattern in ES cells, miRNA cluster RPA miR-302a-d, another ES cells- we tested by (Suh et al, 2004). In many of the m i R - 3 7 miRNAx p r e s s(Suh et e m2004). a s a n d specific 1 - 3 e cluster i n g s al, i n o m Method Experimental nonseminomas, miR-302a-d was undetectable (Figs In many of the miR-371-3 expressing seminomas Evidence S7 and S8), suggesting that miR-371-3undetectable and nonseminomas, miR-302a-d was expression Result is a selective event during tumorigenesis. (Figs S7 and S8), suggesting that Reg-Implication miR-371-3 expression is a selective event during Implication tumorigenesis. 9Saturday, March 26, 2011
  • 38. Realms in experimental discourse:Saturday, March 26, 2011
  • 39. Realms in experimental discourse: (1) Both seminomas (2) b. the detection of and the EC component miR-371-3 merely of nonseminomas share reflects its expression features with ES cells. pattern in ES cells,Saturday, March 26, 2011
  • 40. Realms in experimental discourse: (1) Both seminomas (2) b. the detection of and the EC component miR-371-3 merely of nonseminomas share reflects its expression features with ES cells. pattern in ES cells, (2) a. To exclude thatSaturday, March 26, 2011
  • 41. Realms in experimental discourse: (1) Both seminomas (2) b. the detection of and the EC component miR-371-3 merely of nonseminomas share reflects its expression features with ES cells. pattern in ES cells, (2) a. To exclude that (2) c. we tested by RPA (3) a. In many of the miR-371-3 miR-302a-d, another ES expressing seminomas and cells-specific miRNA cluster nonseminomas, miR-302a-d was (Suh et al, 2004). undetectable (Figs S7 and S8),Saturday, March 26, 2011
  • 42. Realms in experimental discourse: (1) Both seminomas (2) b. the detection of and the EC component miR-371-3 merely of nonseminomas share reflects its expression features with ES cells. pattern in ES cells, (2) a. To exclude that (3) b. suggesting that (2) c. we tested by RPA (3) a. In many of the miR-371-3 miR-302a-d, another ES expressing seminomas and cells-specific miRNA cluster nonseminomas, miR-302a-d was (Suh et al, 2004). undetectable (Figs S7 and S8),Saturday, March 26, 2011
  • 43. Realms in experimental discourse: (1) Both seminomas (2) b. the detection of (3) c. miR-371-3 and the EC component miR-371-3 merely expression is a of nonseminomas share reflects its expression selective event during features with ES cells. pattern in ES cells, tumorigenesis. (2) a. To exclude that (3) b. suggesting that (2) c. we tested by RPA (3) a. In many of the miR-371-3 miR-302a-d, another ES expressing seminomas and cells-specific miRNA cluster nonseminomas, miR-302a-d was (Suh et al, 2004). undetectable (Figs S7 and S8),Saturday, March 26, 2011
  • 44. Realms in experimental discourse: Concepts, models, ‘facts’ (1) Both seminomas (2) b. the detection of (3) c. miR-371-3 and the EC component miR-371-3 merely expression is a of nonseminomas share reflects its expression selective event during features with ES cells. pattern in ES cells, tumorigenesis. (2) a. To exclude that (3) b. suggesting that (2) c. we tested by RPA (3) a. In many of the miR-371-3 miR-302a-d, another ES expressing seminomas and cells-specific miRNA cluster nonseminomas, miR-302a-d was (Suh et al, 2004). undetectable (Figs S7 and S8),Saturday, March 26, 2011
  • 45. Realms in experimental discourse: Concepts, models, ‘facts’ (1) Both seminomas (2) b. the detection of (3) c. miR-371-3 and the EC component miR-371-3 merely expression is a of nonseminomas share reflects its expression selective event during features with ES cells. pattern in ES cells, tumorigenesis. (2) a. To exclude that (3) b. suggesting that (2) c. we tested by RPA (3) a. In many of the miR-371-3 miR-302a-d, another ES expressing seminomas and cells-specific miRNA cluster nonseminomas, miR-302a-d was (Suh et al, 2004). undetectable (Figs S7 and S8), ExperimentSaturday, March 26, 2011
  • 46. Realms in experimental discourse: Concepts, models, ‘facts’ (1) Both seminomas (2) b. the detection of (3) c. miR-371-3 and the EC component miR-371-3 merely expression is a of nonseminomas share reflects its expression selective event during features with ES cells. pattern in ES cells, tumorigenesis. (2) a. To exclude that Transitions (3) b. suggesting that (2) c. we tested by RPA (3) a. In many of the miR-371-3 miR-302a-d, another ES expressing seminomas and cells-specific miRNA cluster nonseminomas, miR-302a-d was (Suh et al, 2004). undetectable (Figs S7 and S8), ExperimentSaturday, March 26, 2011
  • 47. Paradigmatic analysis of clauses Conceptual discourse Connecting discourse Experimental discourse Though D3 receptor antagonists can enhance cognitive function, their sites of action remain unexplored. This issue was addressed employing a model of social recognition in rats, and the actions of D3 antagonists were compared to D1 agonists that likewise possess pro-cognitive properties. Infusion of the highly selective D3 antagonists, S33084 and SB277,011 (0.04-2.5 µg/side), into the frontal cortex (FCX) dose-dependently reversed the By contrast, the preferential D2 a delay. deficit in recognition induced byantagonist, L741,626 (0.63-5.0) had no effect. The action of S33084 was regionally specific inasmuch as its injection into the nucleus accumbens or striatum was ineffective. These data suggest that D3 receptors modulating social recognition are localized in FCX, 11 and underpin their pertinence as targets for antipsychotic agents.Saturday, March 26, 2011
  • 48. Mechanisms for realm transitions 12Saturday, March 26, 2011
  • 49. Mechanisms for realm transitions • Verb form change: • Goal transitions: • Regulatory segments: 12Saturday, March 26, 2011
  • 50. Mechanisms for realm transitions • Verb form change: Whereas all three cluster-expressing cell lines contained high wt-p53 levels, NTera2 has low wild-type p53 levels, and NCCIT lost one p53 allele while the second allele is mutated (Burger et al, 1998). • Goal transitions: • Regulatory segments: 12Saturday, March 26, 2011
  • 51. Mechanisms for realm transitions • Verb form change: Whereas all three cluster-expressing cell lines contained high wt-p53 levels, NTera2 has low wild-type p53 levels, and NCCIT lost one p53 allele while the second allele is mutated (Burger et al, 1998). • Goal transitions: Additionally, we made a corresponding microarray (miR-Array) containing all miR-Lib inserts, which allows the detection of miRNA effects on proliferation. To test the sensitivity of screens with miR-Lib and miR-Array, We transduced modified primary BJ fibroblasts expressing ecotropic receptor... • Regulatory segments: 12Saturday, March 26, 2011
  • 52. Mechanisms for realm transitions • Verb form change: Whereas all three cluster-expressing cell lines contained high wt-p53 levels, NTera2 has low wild-type p53 levels, and NCCIT lost one p53 allele while the second allele is mutated (Burger et al, 1998). • Goal transitions: Additionally, we made a corresponding microarray (miR-Array) containing all miR-Lib inserts, which allows the detection of miRNA effects on proliferation. To test the sensitivity of screens with miR-Lib and miR-Array, We transduced modified primary BJ fibroblasts expressing ecotropic receptor... • Regulatory segments: In accordance, we observed an approximately 4-fold increase in miR311 signal, indicating that our procedure is sensitive enough to detect mild growth differences (Fig 1E). 12Saturday, March 26, 2011
  • 53. Paradigmatic vs syntagmatic axes: use both? Paradigmatic Conceptual Realm axis Though D3 receptor antagonists ! ! can enhance cognitive function, D3 receptors modulating social recognition are localized in FCX, their sites of action remain unexplored. ! This issue was These data suggest that addressed…. ! Syntagmatic Axis ! Infusion of the highly selective D3 antagonists…! A similar increase of recognition was obtained upon injection …! Experimental Realm 13Saturday, March 26, 2011
  • 54. Paradigmatic vs syntagmatic axes: use both? Paradigmatic Conceptual Realm axis Though D3 receptor antagonists ! ! can enhance cognitive function, D3 receptors modulating social recognition are localized in FCX, their sites of action remain unexplored. ! This issue was These data suggest that addressed…. ! Syntagmatic Axis ! Infusion of the highly selective D3 antagonists…! A similar increase of recognition was obtained upon injection …! Experimental RealmParadigmatic:•repeats itself many times•‘fractal dimension’: •course-grained: Introduction, Results, Discussion •medium-grained: parallel with paradigmatic? •fine-grained: level of clauses. 13Saturday, March 26, 2011
  • 55. Paradigmatic vs syntagmatic axes: use both? Paradigmatic Conceptual Realm axis Though D3 receptor antagonists ! ! can enhance cognitive function, D3 receptors modulating social recognition are localized in FCX, their sites of action remain unexplored. ! This issue was These data suggest that addressed…. ! Syntagmatic Axis ! Infusion of the highly selective D3 antagonists…! A similar increase of recognition was obtained upon injection …! Experimental RealmParadigmatic: Syntagmatic:•repeats itself many times • single line?•‘fractal dimension’: • order is essential •course-grained: Introduction, Results, Discussion •‘medium-grained - ‘story components’ •medium-grained: parallel with paradigmatic? •fine-grained: level of clauses. 13Saturday, March 26, 2011
  • 56. Questions: 14Saturday, March 26, 2011
  • 57. Questions: • What structures are useful to identify: •“Biological events”? •Modality/epistemic evaluation? • How do we connect to text structure? • Apply post-hoc or let authors create? • What new tools can we build on top of this? 14Saturday, March 26, 2011
  • 58. Questions: • What structures are useful to identify: •“Biological events”? •Modality/epistemic evaluation? • How do we connect to text structure? • Apply post-hoc or let authors create? • What new tools can we build on top of this? a.dewaard@elsevier.com http://elsatglabs.com/labs/anita 14Saturday, March 26, 2011