The document discusses syntagmatic and paradigmatic analysis approaches for analyzing scientific texts and fairy tales. It provides examples of applying Vladimir Propp's syntagmatic analysis to characterize characters in fairy tales. Additionally, it draws an analogy between the rhetorical structure of speeches and the structure of scientific papers. Finally, it discusses how linked data could enable more flexible syntagmatic analysis of scientific articles by allowing layers of annotation to be added to fixed XML structures.

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 Linguistics
Saturday, March 26, 2011

2. Scientific papers are stories, that persuade
with data
2
Saturday, 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 (?)
2
Saturday, 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’
2
Saturday, March 26, 2011

5. Syntagmatic analysis of fairytales:
3
Saturday, 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.
3
Saturday, 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
3
Saturday, 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
3
Saturday, March 26, 2011

9. Syntagmatic analysis of science: story grammar
The Story of Goldilocks Story Grammar Paper The AXH Domain of Ataxin-1 Mediates
and the Three Bears Neurodegeneration through Its Interaction with Gfi-1/
Senseless Proteins
Once 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 of
forest. Pretty soon, she came setup the human protein
upon a house.
She knocked and, when no one Goal Theme Research Gain insight into how Atx-1's function contributes to SCA1
answered, goal pathogenesis. How these interactions might contribute to the
disease process and how they might cause toxicity in only a subse
she walked right in. of neurons play a role in the regulation of gene expression
Atx-1 may in SCA1 is not fully understood.
Attempt Hypothesis
At the table in the kitchen, there Name Episode 1 Name dAtX-1 and hAtx-1 Induce Similar Phenotypes When
were three bowls of porridge. Overexpressed in Files
Goldilocks was hungry. Subgoal Subgoal test the function of the AXH domain
She tasted the porridge from Attempt Method overexpressed dAtx-1 in flies using the GAL4/UAS system (Brand
the 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 drive
exclaimed. expression in the differentiated R1-R6 photoreceptor cells
(Mollereau et al., 2000 and O'Tousa et al., 1985), results in
neurodegeneration in the eye, as does overexpression of hAtx-1
[82Q]. Although at 2 days after eclosion, overexpression of either
So, she tasted the porridge Activity Data (data not shown),
Atx-1 does not show obvious morphological changes in the
from the second bowl. photoreceptor cells
This porridge is too cold, she Outcome Results both genotypes show many large holes and loss of cell integrity at
said 28 days
So, 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 induce
she said happily and eye abnormalities. The external structures of the eyes that
4 overexpress dAtx-1 show disorganized ommatidia and loss of
she ate it all up. Data interommatidial bristles
(Figure 1F),
Saturday, March 26, 2011

10. Syntagmatic analysis of science: story grammar
The Story of Goldilocks Story Grammar Paper The AXH Domain of Ataxin-1 Mediates
and the Three Bears Neurodegeneration through Its Interaction with Gfi-1/
Senseless Proteins
Once 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 of
forest. Pretty soon, she came setup the human protein
upon a house.
She knocked and, when no one Goal Theme Research Gain insight into how Atx-1's function contributes to SCA1
answered, goal pathogenesis. How these interactions might contribute to the
disease process and how they might cause toxicity in only a subse
she walked right in. of neurons play a role in the regulation of gene expression
Atx-1 may in SCA1 is not fully understood.
Attempt Hypothesis
At the table in the kitchen, there Name Episode 1 Name dAtX-1 and hAtx-1 Induce Similar Phenotypes When
were three bowls of porridge. Overexpressed in Files
Goldilocks was hungry. Subgoal Subgoal test the function of the AXH domain
She tasted the porridge from Attempt Method overexpressed dAtx-1 in flies using the GAL4/UAS system (Brand
the 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 drive
exclaimed. expression in the differentiated R1-R6 photoreceptor cells
(Mollereau et al., 2000 and O'Tousa et al., 1985), results in
neurodegeneration in the eye, as does overexpression of hAtx-1
[82Q]. Although at 2 days after eclosion, overexpression of either
So, she tasted the porridge Activity Data (data not shown),
Atx-1 does not show obvious morphological changes in the
from the second bowl. photoreceptor cells
This porridge is too cold, she Outcome Results both genotypes show many large holes and loss of cell integrity at
said 28 days
So, 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 induce
she said happily and eye abnormalities. The external structures of the eyes that
4 overexpress dAtx-1 show disorganized ommatidia and loss of
she ate it all up. Data interommatidial bristles
(Figure 1F),
Saturday, March 26, 2011

11. Rhetorical analogue to scientific structure:
5
Saturday, 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 one's 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.
5
Saturday, 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 one's 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.
5
Saturday, March 26, 2011

14. Syntagmatic analysis of scientific text:
ORB vs. Medium-grained structure
6
Saturday, March 26, 2011

15. Syntagmatic analysis of scientific text:
ORB vs. Medium-grained structure
6
Saturday, 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 cheese
Saturday, March 26, 2011

19. Syntagmatic enabler: Linked Data (for Elsevier)
said @anita
on March 28, 2011
this says
<ce:section id=#123> mice like cheese
Saturday, 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 cheese
Saturday, 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 cheese
Saturday, 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 cheese
Saturday, 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.”
8
Saturday, 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.”
8
Saturday, 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.”
8
Saturday, 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.”
8
Saturday, 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.
9
Saturday, 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.
9
Saturday, 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.
9
Saturday, 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.
9
Saturday, 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.
9
Saturday, 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.
9
Saturday, 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.
9
Saturday, 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.
9
Saturday, 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.
9
Saturday, 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.
9
Saturday, 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.
9
Saturday, 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 that
Saturday, 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),
Experiment
Saturday, 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),
Experiment
Saturday, 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
12
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49. Mechanisms for realm transitions
• Verb form change:
• Goal transitions:
• Regulatory segments:
12
Saturday, 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:
12
Saturday, 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:
12
Saturday, 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).
12
Saturday, 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
13
Saturday, 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 Realm
Paradigmatic:
•repeats itself many times
•‘fractal dimension’:
•course-grained: Introduction, Results, Discussion
•medium-grained: parallel with paradigmatic?
•fine-grained: level of clauses.
13
Saturday, 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 Realm
Paradigmatic: 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.
13
Saturday, March 26, 2011

56. Questions:
14
Saturday, 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?
14
Saturday, 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
14
Saturday, March 26, 2011