A syntagmatic/Paradigmatic analysis of scientific text
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Transcript of A syntagmatic/Paradigmatic analysis of scientific text
Syntagmatic/paradigmatic analysis of scientific text
Anita de Waard, [email protected] Disruptive Technologies Director, Elsevier Labs
University of Utrecht, Institute of Linguistics
HCLS Scientific Discourse CallMarch 28 2011
Saturday, March 26, 2011
Scientific papers are stories, that persuade with data
2
Saturday, March 26, 2011
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
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
Syntagmatic analysis of fairytales:
3
Saturday, March 26, 2011
Syntagmatic analysis of fairytales:
3
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.
Saturday, March 26, 2011
Syntagmatic analysis of fairytales:
3
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 fairytale”. The list contains 150 elements, distributed over six tables:1. Initial Situation2. Preparatory Section3. Complication4. Donors5. From the Entry of the Helper to the End of the First Move6. Beginning of the Second Move
Saturday, March 26, 2011
Syntagmatic analysis of fairytales:
3
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 fairytale”. The list contains 150 elements, distributed over six tables:1. Initial Situation2. Preparatory Section3. Complication4. Donors5. From the Entry of the Helper to the End of the First Move6. Beginning of the Second Move
F. Peinado, P. Gervas, and B. Diaz-Agudo, ʻA description logic ontology for fairy tale generationʼ, in Proceedings of LREC. ELRA, (5 2004)
Saturday, March 26, 2011
Syntagmatic analysis of science: story grammar
4
The Story of Goldilocks and the Three Bears
Story Grammar Paper The AXH Domain of Ataxin-1 Mediates 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
Setting
Objects of study the Drosophila Atx-1 homolog (dAtx-1) which lacks a polyQ tract,
She went for a walk in the forest. Pretty soon, she came upon a house.
Location
Setting
Experimental setup
studied and compared in vivo effects and interactions to those of the human protein
She knocked and, when no one answered,
Goal Theme Researchgoal
Gain insight into how Atx-1's function contributes to SCA1 pathogenesis. How these interactions might contribute to the disease process and how they might cause toxicity in only a subset of neurons in SCA1 is not fully understood.she walked right in. Attempt
Theme
Hypothesis Atx-1 may play a role in the regulation of gene expression
At the table in the kitchen, there were three bowls of porridge.
Name Episode 1 Name dAtX-1 and hAtx-1 Induce Similar Phenotypes When Overexpressed in Files
Goldilocks was hungry. Subgoal
Episode 1
Subgoal test the function of the AXH domainShe tasted the porridge from the first bowl.
Attempt
Episode 1
Method overexpressed dAtx-1 in flies using the GAL4/UAS system (Brand and Perrimon, 1993) and compared its effects to those of hAtx-1.
This porridge is too hot! she exclaimed.
Outcome
Episode 1
Results Overexpression of dAtx-1 by Rhodopsin1(Rh1)-GAL4, which drives 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 Atx-1 does not show obvious morphological changes in the photoreceptor cells
So, she tasted the porridge from the second bowl.
Activity
Episode 1
Data (data not shown),
This porridge is too cold, she said
Outcome
Episode 1
Results both genotypes show many large holes and loss of cell integrity at 28 days
So, she tasted the last bowl of porridge.
Activity
Episode 1
Data (Figures 1B-1D).
Ahhh, this porridge is just right, she said happily and
Outcome
Episode 1
Results Overexpression of dAtx-1 using the GMR-GAL4 driver also induces eye abnormalities. The external structures of the eyes that overexpress dAtx-1 show disorganized ommatidia and loss of interommatidial bristles she ate it all up.
Episode 1
Data (Figure 1F), Saturday, March 26, 2011
Syntagmatic analysis of science: story grammar
4
The Story of Goldilocks and the Three Bears
Story Grammar Paper The AXH Domain of Ataxin-1 Mediates 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
Setting
Objects of study the Drosophila Atx-1 homolog (dAtx-1) which lacks a polyQ tract,
She went for a walk in the forest. Pretty soon, she came upon a house.
Location
Setting
Experimental setup
studied and compared in vivo effects and interactions to those of the human protein
She knocked and, when no one answered,
Goal Theme Researchgoal
Gain insight into how Atx-1's function contributes to SCA1 pathogenesis. How these interactions might contribute to the disease process and how they might cause toxicity in only a subset of neurons in SCA1 is not fully understood.she walked right in. Attempt
Theme
Hypothesis Atx-1 may play a role in the regulation of gene expression
At the table in the kitchen, there were three bowls of porridge.
Name Episode 1 Name dAtX-1 and hAtx-1 Induce Similar Phenotypes When Overexpressed in Files
Goldilocks was hungry. Subgoal
Episode 1
Subgoal test the function of the AXH domainShe tasted the porridge from the first bowl.
Attempt
Episode 1
Method overexpressed dAtx-1 in flies using the GAL4/UAS system (Brand and Perrimon, 1993) and compared its effects to those of hAtx-1.
This porridge is too hot! she exclaimed.
Outcome
Episode 1
Results Overexpression of dAtx-1 by Rhodopsin1(Rh1)-GAL4, which drives 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 Atx-1 does not show obvious morphological changes in the photoreceptor cells
So, she tasted the porridge from the second bowl.
Activity
Episode 1
Data (data not shown),
This porridge is too cold, she said
Outcome
Episode 1
Results both genotypes show many large holes and loss of cell integrity at 28 days
So, she tasted the last bowl of porridge.
Activity
Episode 1
Data (Figures 1B-1D).
Ahhh, this porridge is just right, she said happily and
Outcome
Episode 1
Results Overexpression of dAtx-1 using the GMR-GAL4 driver also induces eye abnormalities. The external structures of the eyes that overexpress dAtx-1 show disorganized ommatidia and loss of interommatidial bristles she ate it all up.
Episode 1
Data (Figure 1F), Saturday, March 26, 2011
5
Rhetorical analogue to scientific structure:
Saturday, March 26, 2011
5
Aristotle QuintilianQuintilian Scientific Paper
prooimion Introduction/ exordium
The introduction of a speech, where one announces the subject and purpose of the discourse, and where one usually employs the persuasive appeal to ethos in order to establish credibility with the audience.
Introduction: positioning
prothesisStatement of Facts/narratio
The speaker here provides a narrative account of what has happened and generally explains the nature of the case.
Introduction: research question
Summary/ propostitio
The propositio provides a brief summary of what one is about to speak on, or concisely puts forth the charges or accusation. Summary of contents
pistis Proof/ confirmatio
The main body of the speech where one offers logical arguments as proof. The appeal to logos is emphasized here.
Results
Refutation/ refutatio
As the name connotes, this section of a speech was devoted to answering the counterarguments of one's opponent. Related Work
epilogos peroratio Following the refutatio and concluding the classical oration, the peroratio conventionally employed appeals through pathos, and often included a summing up.
Discussion: summary, implications.
Rhetorical analogue to scientific structure:
Saturday, March 26, 2011
5
Aristotle QuintilianQuintilian Scientific Paper
prooimion Introduction/ exordium
The introduction of a speech, where one announces the subject and purpose of the discourse, and where one usually employs the persuasive appeal to ethos in order to establish credibility with the audience.
Introduction: positioning
prothesisStatement of Facts/narratio
The speaker here provides a narrative account of what has happened and generally explains the nature of the case.
Introduction: research question
Summary/ propostitio
The propositio provides a brief summary of what one is about to speak on, or concisely puts forth the charges or accusation. Summary of contents
pistis Proof/ confirmatio
The main body of the speech where one offers logical arguments as proof. The appeal to logos is emphasized here.
Results
Refutation/ refutatio
As the name connotes, this section of a speech was devoted to answering the counterarguments of one's opponent. Related Work
epilogos peroratio Following the refutatio and concluding the classical oration, the peroratio conventionally employed appeals through pathos, and often included a summing up.
Discussion: summary, implications.
Rhetorical analogue to scientific structure:
Saturday, March 26, 2011
6
Syntagmatic analysis of scientific text: ORB vs. Medium-grained structure
Saturday, March 26, 2011
6
Syntagmatic analysis of scientific text: ORB vs. Medium-grained structure
Saturday, March 26, 2011
Syntagmatic enabler: Linked Data (for Elsevier)
Saturday, March 26, 2011
Syntagmatic enabler: Linked Data (for Elsevier)
<ce:section id=#123>
Saturday, March 26, 2011
Syntagmatic enabler: Linked Data (for Elsevier)
<ce:section id=#123> mice like cheesethis says
Saturday, March 26, 2011
Syntagmatic enabler: Linked Data (for Elsevier)
<ce:section id=#123>
said @anita on March 28, 2011
mice like cheesethis says
Saturday, March 26, 2011
but we all know she was wrong then
Syntagmatic enabler: Linked Data (for Elsevier)
<ce:section id=#123>
said @anita on March 28, 2011
mice like cheesethis says
Saturday, March 26, 2011
but we all know she was wrong then
Syntagmatic enabler: Linked Data (for Elsevier)
<ce:section id=#123>
said @anita on March 28, 2011
the xml is fixed, but the structure is open!
mice like cheesethis says
Saturday, March 26, 2011
allows for layers of annotation
but we all know she was wrong then
Syntagmatic enabler: Linked Data (for Elsevier)
<ce:section id=#123>
said @anita on March 28, 2011
the xml is fixed, but the structure is open!
mice like cheesethis says
Saturday, March 26, 2011
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
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
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
(narrative) TIME
Saturday, March 26, 2011
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
(narrative) TIME
(narrative) THEME
Saturday, March 26, 2011
Paradigmatic approach for science
9
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 m i R - 3 7 1 - 3 e x p r e s s i n g s e m i n o m a s a n d nonseminomas, miR-302a-d was undetectable (Figs S7 and S8), suggesting that miR-371-3 expression is a selective event during tumorigenesis.
Saturday, March 26, 2011
Paradigmatic approach for science
9
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 m i R - 3 7 1 - 3 e x p r e s s i n g s e m i n o m a s a n d nonseminomas, miR-302a-d was undetectable (Figs S7 and S8), suggesting that miR-371-3 expression is a selective event during tumorigenesis.
Both seminomas and the EC component of nonseminomas share features with ES cells.To exclude thatthe 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 thatmiR-371-3 expression is a selective event during tumorigenesis.
Saturday, March 26, 2011
Paradigmatic approach for science
9
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 m i R - 3 7 1 - 3 e x p r e s s i n g s e m i n o m a s a n d nonseminomas, miR-302a-d was undetectable (Figs S7 and S8), suggesting that miR-371-3 expression is a selective event during tumorigenesis.
Both seminomas and the EC component of nonseminomas share features with ES cells.To exclude thatthe 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 thatmiR-371-3 expression is a selective event during tumorigenesis.
Fact
Saturday, March 26, 2011
Paradigmatic approach for science
9
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 m i R - 3 7 1 - 3 e x p r e s s i n g s e m i n o m a s a n d nonseminomas, miR-302a-d was undetectable (Figs S7 and S8), suggesting that miR-371-3 expression is a selective event during tumorigenesis.
Both seminomas and the EC component of nonseminomas share features with ES cells.To exclude thatthe 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 thatmiR-371-3 expression is a selective event during tumorigenesis.
Fact
Hypothesis
Saturday, March 26, 2011
Paradigmatic approach for science
9
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 m i R - 3 7 1 - 3 e x p r e s s i n g s e m i n o m a s a n d nonseminomas, miR-302a-d was undetectable (Figs S7 and S8), suggesting that miR-371-3 expression is a selective event during tumorigenesis.
Both seminomas and the EC component of nonseminomas share features with ES cells.To exclude thatthe 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 thatmiR-371-3 expression is a selective event during tumorigenesis.
Fact
Hypothesis
Method
Saturday, March 26, 2011
Paradigmatic approach for science
9
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 m i R - 3 7 1 - 3 e x p r e s s i n g s e m i n o m a s a n d nonseminomas, miR-302a-d was undetectable (Figs S7 and S8), suggesting that miR-371-3 expression is a selective event during tumorigenesis.
Both seminomas and the EC component of nonseminomas share features with ES cells.To exclude thatthe 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 thatmiR-371-3 expression is a selective event during tumorigenesis.
Fact
Hypothesis
Method
Result
Saturday, March 26, 2011
Paradigmatic approach for science
9
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 m i R - 3 7 1 - 3 e x p r e s s i n g s e m i n o m a s a n d nonseminomas, miR-302a-d was undetectable (Figs S7 and S8), suggesting that miR-371-3 expression is a selective event during tumorigenesis.
Both seminomas and the EC component of nonseminomas share features with ES cells.To exclude thatthe 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 thatmiR-371-3 expression is a selective event during tumorigenesis.
Fact
Hypothesis
Method
Result
Implication
Saturday, March 26, 2011
Paradigmatic approach for science
9
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 m i R - 3 7 1 - 3 e x p r e s s i n g s e m i n o m a s a n d nonseminomas, miR-302a-d was undetectable (Figs S7 and S8), suggesting that miR-371-3 expression is a selective event during tumorigenesis.
Both seminomas and the EC component of nonseminomas share features with ES cells.To exclude thatthe 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 thatmiR-371-3 expression is a selective event during tumorigenesis.
Fact
Hypothesis
Method
Result
Implication
Goal
Saturday, March 26, 2011
Paradigmatic approach for science
9
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 m i R - 3 7 1 - 3 e x p r e s s i n g s e m i n o m a s a n d nonseminomas, miR-302a-d was undetectable (Figs S7 and S8), suggesting that miR-371-3 expression is a selective event during tumorigenesis.
Both seminomas and the EC component of nonseminomas share features with ES cells.To exclude thatthe 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 thatmiR-371-3 expression is a selective event during tumorigenesis.
Fact
Hypothesis
Method
Result
Implication
Goal
Reg-Implication
Saturday, March 26, 2011
Paradigmatic approach for science
9
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 m i R - 3 7 1 - 3 e x p r e s s i n g s e m i n o m a s a n d nonseminomas, miR-302a-d was undetectable (Figs S7 and S8), suggesting that miR-371-3 expression is a selective event during tumorigenesis.
Both seminomas and the EC component of nonseminomas share features with ES cells.To exclude thatthe 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 thatmiR-371-3 expression is a selective event during tumorigenesis.
Fact
Hypothesis
Method
Result
Implication
Goal
Reg-Implication
Conceptual knowledge
Saturday, March 26, 2011
Paradigmatic approach for science
9
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 m i R - 3 7 1 - 3 e x p r e s s i n g s e m i n o m a s a n d nonseminomas, miR-302a-d was undetectable (Figs S7 and S8), suggesting that miR-371-3 expression is a selective event during tumorigenesis.
Both seminomas and the EC component of nonseminomas share features with ES cells.To exclude thatthe 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 thatmiR-371-3 expression is a selective event during tumorigenesis.
Fact
Hypothesis
Method
Result
Implication
Goal
Reg-Implication
Conceptual knowledge
ExperimentalEvidence
Saturday, March 26, 2011
Realms in experimental discourse:
Saturday, March 26, 2011
(1) Both seminomas and the EC component of nonseminomas share features with ES cells.
(2) b. the detection of miR-371-3 merely reflects its expression pattern in ES cells,
Realms in experimental discourse:
Saturday, March 26, 2011
(1) Both seminomas and the EC component of nonseminomas share features with ES cells.
(2) b. the detection of miR-371-3 merely reflects its expression pattern in ES cells,
(2) a. To exclude that
Realms in experimental discourse:
Saturday, March 26, 2011
(1) Both seminomas and the EC component of nonseminomas share features with ES cells.
(2) b. the detection of miR-371-3 merely reflects its expression pattern in ES cells,
(2) c. we tested by RPA miR-302a-d, another ES cells-specific miRNA cluster (Suh et al, 2004).
(3) a. In many of the miR-371-3 expressing seminomas and nonseminomas, miR-302a-d was undetectable (Figs S7 and S8),
(2) a. To exclude that
Realms in experimental discourse:
Saturday, March 26, 2011
(1) Both seminomas and the EC component of nonseminomas share features with ES cells.
(2) b. the detection of miR-371-3 merely reflects its expression pattern in ES cells,
(2) c. we tested by RPA miR-302a-d, another ES cells-specific miRNA cluster (Suh et al, 2004).
(3) a. In many of the miR-371-3 expressing seminomas and nonseminomas, miR-302a-d was undetectable (Figs S7 and S8),
(2) a. To exclude that (3) b. suggesting that
Realms in experimental discourse:
Saturday, March 26, 2011
(3) c. miR-371-3 expression is a selective event during tumorigenesis.
(1) Both seminomas and the EC component of nonseminomas share features with ES cells.
(2) b. the detection of miR-371-3 merely reflects its expression pattern in ES cells,
(2) c. we tested by RPA miR-302a-d, another ES cells-specific miRNA cluster (Suh et al, 2004).
(3) a. In many of the miR-371-3 expressing seminomas and nonseminomas, miR-302a-d was undetectable (Figs S7 and S8),
(2) a. To exclude that (3) b. suggesting that
Realms in experimental discourse:
Saturday, March 26, 2011
(3) c. miR-371-3 expression is a selective event during tumorigenesis.
(1) Both seminomas and the EC component of nonseminomas share features with ES cells.
(2) b. the detection of miR-371-3 merely reflects its expression pattern in ES cells,
(2) c. we tested by RPA miR-302a-d, another ES cells-specific miRNA cluster (Suh et al, 2004).
(3) a. In many of the miR-371-3 expressing seminomas and nonseminomas, miR-302a-d was undetectable (Figs S7 and S8),
Concepts, models, ‘facts’
(2) a. To exclude that (3) b. suggesting that
Realms in experimental discourse:
Saturday, March 26, 2011
(3) c. miR-371-3 expression is a selective event during tumorigenesis.
(1) Both seminomas and the EC component of nonseminomas share features with ES cells.
(2) b. the detection of miR-371-3 merely reflects its expression pattern in ES cells,
(2) c. we tested by RPA miR-302a-d, another ES cells-specific miRNA cluster (Suh et al, 2004).
(3) a. In many of the miR-371-3 expressing seminomas and nonseminomas, miR-302a-d was undetectable (Figs S7 and S8),
Concepts, models, ‘facts’
Experiment
(2) a. To exclude that (3) b. suggesting that
Realms in experimental discourse:
Saturday, March 26, 2011
(3) c. miR-371-3 expression is a selective event during tumorigenesis.
(1) Both seminomas and the EC component of nonseminomas share features with ES cells.
(2) b. the detection of miR-371-3 merely reflects its expression pattern in ES cells,
(2) c. we tested by RPA miR-302a-d, another ES cells-specific miRNA cluster (Suh et al, 2004).
(3) a. In many of the miR-371-3 expressing seminomas and nonseminomas, miR-302a-d was undetectable (Figs S7 and S8),
Concepts, models, ‘facts’
Experiment
Transitions(2) a. To exclude that (3) b. suggesting that
Realms in experimental discourse:
Saturday, March 26, 2011
Paradigmatic analysis of clausesConceptual 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 deficit in recognition induced by a delay.By contrast, the preferential D2 antagonist, 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,
and underpin their pertinence as targets for antipsychotic agents.
11
Saturday, March 26, 2011
Mechanisms for realm transitions
12
Saturday, March 26, 2011
Mechanisms for realm transitions• Verb form change:
• Goal transitions:
• Regulatory segments:
12
Saturday, March 26, 2011
Mechanisms for realm transitions• Verb form change:
• Goal transitions:
• Regulatory segments:
Whereas all three cluster-expressing cell lines contained high wt-p53 levels,NTera2 has low wild-type p53 levels,and NCCIT lost one p53 allelewhile the second allele is mutated (Burger et al, 1998).
12
Saturday, March 26, 2011
Mechanisms for realm transitions• Verb form change:
• Goal transitions:
• Regulatory segments:
Whereas all three cluster-expressing cell lines contained high wt-p53 levels,NTera2 has low wild-type p53 levels,and NCCIT lost one p53 allelewhile the second allele is mutated (Burger et al, 1998).
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...
12
Saturday, March 26, 2011
Mechanisms for realm transitions• Verb form change:
• Goal transitions:
• Regulatory segments:
Whereas all three cluster-expressing cell lines contained high wt-p53 levels,NTera2 has low wild-type p53 levels,and NCCIT lost one p53 allelewhile the second allele is mutated (Burger et al, 1998).
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...
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
Paradigmatic vs syntagmatic axes: use both?
!
!
Experimental Realm
Syntagmatic Axis
Paradigmatic axis
This issue was addressed….
! Infusion of the highly selective D3 antagonists…!
A similar increase of recognition was obtained upon injection …!
Though D3 receptor antagonists can enhance cognitive function,
D3 receptors modulating social recognition are localized in FCX,
!
These data suggest that !
Conceptual Realm !
their sites of action remain unexplored.
13
Saturday, March 26, 2011
Paradigmatic vs syntagmatic axes: use both?
!
!
Experimental Realm
Syntagmatic Axis
Paradigmatic axis
This issue was addressed….
! Infusion of the highly selective D3 antagonists…!
A similar increase of recognition was obtained upon injection …!
Though D3 receptor antagonists can enhance cognitive function,
D3 receptors modulating social recognition are localized in FCX,
!
These data suggest that !
Conceptual Realm !
their sites of action remain unexplored.
13
Paradigmatic: •repeats itself many times•‘fractal dimension’:
•course-grained: Introduction, Results, Discussion•medium-grained: parallel with paradigmatic?•fine-grained: level of clauses.
Saturday, March 26, 2011
Paradigmatic vs syntagmatic axes: use both?
!
!
Experimental Realm
Syntagmatic Axis
Paradigmatic axis
This issue was addressed….
! Infusion of the highly selective D3 antagonists…!
A similar increase of recognition was obtained upon injection …!
Though D3 receptor antagonists can enhance cognitive function,
D3 receptors modulating social recognition are localized in FCX,
!
These data suggest that !
Conceptual Realm !
their sites of action remain unexplored.
13
Paradigmatic: •repeats itself many times•‘fractal dimension’:
•course-grained: Introduction, Results, Discussion•medium-grained: parallel with paradigmatic?•fine-grained: level of clauses.
Syntagmatic: • single line?• order is essential•‘medium-grained - ‘story components’
Saturday, March 26, 2011
Questions:
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Saturday, March 26, 2011
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
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
[email protected]://elsatglabs.com/labs/anita
Saturday, March 26, 2011