on the research paper, and the knowledge within
DESCRIPTION
Presentation on May 4th, 2011 at MITRE on Stories that persuade with Data; expanded version of talk at Harvard 'Reengineering the research paper'.TRANSCRIPT
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Stories, that persuade with data:On the research paper,
and the knowledge within
Anita de Waard, [email protected] Disruptive Technologies Director, Elsevier Labs
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Scientific papers are stories, that persuade with data.The Story of Goldilocks and the Three Bears
Story Part 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 domain
She 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 cellsSo, 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. Outcome
Episode 1
Data (Figure 1F),
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Scientific papers are stories, that persuade with data.The Story of Goldilocks and the Three Bears
Story Part 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 domain
She 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 cellsSo, 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. Outcome
Episode 1
Data (Figure 1F),
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Story grammar of fairytales:
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Story grammar 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.
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Story grammar 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.
F. Peinado, P. Gervas, and B. Diaz-Agudo, ʻA description logic ontology for fairy tale generationʼ, in Procs LREC. ELRA, (5 2004)
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Story grammar 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.
F. Peinado, P. Gervas, and B. Diaz-Agudo, ʻA description logic ontology for fairy tale generationʼ, in Procs LREC. ELRA, (5 2004)
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Story analysis of scientific text: ORB vs. Medium-grained structure
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See work at http://www.w3.org/wiki/HCLSIG/SWANSIOC
Story analysis of scientific text: ORB vs. Medium-grained structure
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Episode-level access through Linked Data standards:
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Episode-level access through Linked Data standards:
<ce:section id=#123>
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Episode-level access through Linked Data standards:
<ce:section id=#123> mice like cheesethis says
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Episode-level access through Linked Data standards:
<ce:section id=#123>
said @anita on April 5, 2011
mice like cheesethis says
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but we all know she was deluded then
Episode-level access through Linked Data standards:
<ce:section id=#123>
said @anita on April 5, 2011
mice like cheesethis says
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but we all know she was deluded then
Episode-level access through Linked Data standards:
<ce:section id=#123>
said @anita on April 5, 2011
the xml is fixed, but the structure is open!
mice like cheesethis says
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allows for layers of annotation
but we all know she was deluded then
Episode-level access through Linked Data standards:
<ce:section id=#123>
said @anita on April 5, 2011
the xml is fixed, but the structure is open!
mice like cheesethis says
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Satellite Format: LDR store for all our content
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Satellites: Provenance
Information about an annotation:-Who created it?,When? By what (version of a) tool?-Has it been reviewed? If so, when and by whom? Was it approved or rejected?
Use pav:createdOn and createdBy instead of dc:date and creator to reduce confusion:<tag:TaggingAnnotation rdf:about="#anno-1"> <tag:annotatesStatement rdf:resource="#stmt-1"/> <tag:score>0.8939283</tag:score><pav:createdOn>2010-07-23T15:45:00Z</pav:createdOn> <pav:createdBy rdf:resource= "http://data.elsevier.com/enh-services/ProjectCode/version"/> <tag:status rdf:resource= "http://data.elsevier.com/namespace/LDR-Satellite/TagAnnot-1/
VendorChecked"/></tag:TaggingAnnotation>
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Satellites: Fragments
Use XPointer for XML documents, Media Fragments for image, video, audio.XMLDocumentRegion, MediaRegion akin to Annotation Ontology Selectorsxpath1()* XPointer scheme so pointer can be dropped into any XPath engine and get back the section being annotated.Complex case – arbitrary string in document:
<rgn:XMLDocumentRegion rdf: about= "http://.../S0140-6736(95)90494-8#xpath-e(substring(id('sb-3')/p[2],15,6))">
<dct:isPartOf rdf:resource="http://.../S0140-6736(95)90494-8"/> <rgn:coveringXPath>id('sb-3')/p[2]</rgn:coveringXPath> <rgn:startingOffset>15</rgn:startingOffset> <rgn:stringLength>6</rgn:stringLength> <rgn:matchedString>biopsy</rgn:matchedString> <rgn:prefixString>Testing of the </rgn:prefixString> <rgn:suffixString>indicated nothing</rgn:suffixString></rgn:XMLDocumentRegion>
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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.
Scientific papers are stories, that persuade with data.
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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.
Scientific papers are stories, that persuade with data.
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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
Scientific papers are stories, that persuade with data.
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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
Scientific papers are stories, that persuade with data.
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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
Scientific papers are stories, that persuade with data.
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Realms of persuasive experimental discourse:
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(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 of persuasive experimental discourse:
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(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 of persuasive experimental discourse:
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(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 of persuasive experimental discourse:
‘State’ present tense
‘Narrative’ past tense
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Fact creation through citations:
To investigate the possibility that miR-372 and miR-373 suppress the expression of LATS2, we...
Therefore, these results point to LATS2 as a mediator of the miR-372 and miR-373 effects on cell proliferation and tumorigenicity,
Voorhoeve et al, Cell, 2006:
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Fact creation through citations:
To investigate the possibility that miR-372 and miR-373 suppress the expression of LATS2, we...
Therefore, these results point to LATS2 as a mediator of the miR-372 and miR-373 effects on cell proliferation and tumorigenicity,
Voorhoeve et al, Cell, 2006:
Hypothesis
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Fact creation through citations:
To investigate the possibility that miR-372 and miR-373 suppress the expression of LATS2, we...
Therefore, these results point to LATS2 as a mediator of the miR-372 and miR-373 effects on cell proliferation and tumorigenicity,
Voorhoeve et al, Cell, 2006:
Hypothesis
Implication
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... two miRNAs, miRNA-372 and-373, function as potential novel oncogenes in testicular germ cell tumors by inhibition of LATS2 expression, which suggests that Lats2 is an important tumor suppressor (Voorhoeve et al., 2006).
Raver-Shapira et.al, JMolCell 2007
Fact creation through citations:
To investigate the possibility that miR-372 and miR-373 suppress the expression of LATS2, we...
Therefore, these results point to LATS2 as a mediator of the miR-372 and miR-373 effects on cell proliferation and tumorigenicity,
Voorhoeve et al, Cell, 2006:
Hypothesis
Implication
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... two miRNAs, miRNA-372 and-373, function as potential novel oncogenes in testicular germ cell tumors by inhibition of LATS2 expression, which suggests that Lats2 is an important tumor suppressor (Voorhoeve et al., 2006).
Raver-Shapira et.al, JMolCell 2007
Fact creation through citations:
To investigate the possibility that miR-372 and miR-373 suppress the expression of LATS2, we...
Therefore, these results point to LATS2 as a mediator of the miR-372 and miR-373 effects on cell proliferation and tumorigenicity,
Voorhoeve et al, Cell, 2006:
Hypothesis
Implication
Cited Implication
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... two miRNAs, miRNA-372 and-373, function as potential novel oncogenes in testicular germ cell tumors by inhibition of LATS2 expression, which suggests that Lats2 is an important tumor suppressor (Voorhoeve et al., 2006).
Raver-Shapira et.al, JMolCell 2007
miR-372 and miR-373 target the Lats2 tumor suppressor (Voorhoeve et al., 2006)
Yabuta, JBioChem 2007:
Fact creation through citations:
To investigate the possibility that miR-372 and miR-373 suppress the expression of LATS2, we...
Therefore, these results point to LATS2 as a mediator of the miR-372 and miR-373 effects on cell proliferation and tumorigenicity,
Voorhoeve et al, Cell, 2006:
Hypothesis
Implication
Cited Implication
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... two miRNAs, miRNA-372 and-373, function as potential novel oncogenes in testicular germ cell tumors by inhibition of LATS2 expression, which suggests that Lats2 is an important tumor suppressor (Voorhoeve et al., 2006).
Raver-Shapira et.al, JMolCell 2007
miR-372 and miR-373 target the Lats2 tumor suppressor (Voorhoeve et al., 2006)
Yabuta, JBioChem 2007:
Fact creation through citations:
To investigate the possibility that miR-372 and miR-373 suppress the expression of LATS2, we...
Therefore, these results point to LATS2 as a mediator of the miR-372 and miR-373 effects on cell proliferation and tumorigenicity,
Voorhoeve et al, Cell, 2006:
Hypothesis
Implication
Cited Implication
Fact
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“[Y]ou can transform a fact into fiction or a fiction into fact just by adding or subtracting references [and data]”
– Bruno Latour, ‘Science in Action’,1987
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“[Y]ou can transform a fact into fiction or a fiction into fact just by adding or subtracting references [and data]”
– Bruno Latour, ‘Science in Action’,1987
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The logical structure of a scientific claim
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The logical structure of a scientific claim
- A Proposition P is about entities, relations, events, actions…
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The logical structure of a scientific claim
- A Proposition P is about entities, relations, events, actions…
- We define an Epistemic Evaluation of P to be EEs,v(P):
- S = Source = Holder, Basis:
- Holder: Author (A), Referent (N), Nameless referent (NN)
- Basis: Reasoning (R), Data (D), Unidentified (Ø)- V = Value = Certainly, Emphasis:
- Certainty: from 0 (uncertainty) to 3 (complete certainty)
- Emphasis: Focus (F: +/-), Surprise (S, +,-)
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The logical structure of a scientific claim
- A Proposition P is about entities, relations, events, actions…
- We define an Epistemic Evaluation of P to be EEs,v(P):
- S = Source = Holder, Basis:
- Holder: Author (A), Referent (N), Nameless referent (NN)
- Basis: Reasoning (R), Data (D), Unidentified (Ø)- V = Value = Certainly, Emphasis:
- Certainty: from 0 (uncertainty) to 3 (complete certainty)
- Emphasis: Focus (F: +/-), Surprise (S, +,-)
- Nested evaluations, e.g. “We question X’s suggestion that P” can be written as: EEA(EE’N(P)).
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The logical structure of a scientific claim
- A Proposition P is about entities, relations, events, actions…
- We define an Epistemic Evaluation of P to be EEs,v(P):
- S = Source = Holder, Basis:
- Holder: Author (A), Referent (N), Nameless referent (NN)
- Basis: Reasoning (R), Data (D), Unidentified (Ø)- V = Value = Certainly, Emphasis:
- Certainty: from 0 (uncertainty) to 3 (complete certainty)
- Emphasis: Focus (F: +/-), Surprise (S, +,-)
- Nested evaluations, e.g. “We question X’s suggestion that P” can be written as: EEA(EE’N(P)).
- If no explicit evaluation (“Water is wet”), of course, EE = Ø.
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How is this rhetoric instantiated?Rhetorical goal
Utterance {Proposition} S = H, B
V = C, E
Indicate lack of knowledge
{The role of untranslated exons in the CCR3 gene} has not been studied.
NN 0
Evaluate other work
Recently, CCR3 has been shown to {be upregulated on neutrophils by interferons in vitro [..]}
N, D 3
Offer hypotheses
it is thought that {these transcription factors affect transcription of the gene through interactions with the RNA transcription complex.}
NN, R 2
Interpret results these data suggested that {5' untranslated exon 1 may have a regulatory function.}
A, D 2
Assess validity of interpretations
Since {this was not the case with other lines,} {we suspect {it is integration-site specific}}
A, D 1
State correspondence to expectations
While we expected {the transcript to be about 1 kb in size (Figure 4A),} {two bands ~4 and 5 kb were apparent.}
A, D 2, S+
Comparison to other work
It is important that {this data be viewed with {what is known about other myeloid-specific promoters,}}
A,R/NN/D
2, F+
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One application: improve text mining:
insulin ::: GB000841
maintaining glucose homeostasis
... diabetes defect) to overcome insulin resistance in maintaining glucose homeostasis, hyperglycemia and glucose intolerance ...
improve glucose homeostasis
... in T2D is able to increase insulin secretion and improve glucose homeostasis.
improves glucose homeostasis
... SIRT1, whose administration to insulin-resistant animals improves glucose homeostasis.
is capable glucose homeostasis
S15511 is a novel insulin sensitizer that is capable of improving glucose homeostasis in nondiabetic rats.
maintains glucose homeostasis
Pancreatic beta-cells possess a well-regulated insulin secretory property that maintains systemic glucose homeostasis.
may be involved
glucose homeostasis
... similar way to those of insulin, PANDER may be involved in glucose homeostasis.
participates glucose homeostasis
Fine-tuning of insulin secretion from pancreatic beta-cells participates in blood glucose homeostasis.
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One application: improve text mining:
insulin ::: GB000841
maintaining glucose homeostasis
... diabetes defect) to overcome insulin resistance in maintaining glucose homeostasis, hyperglycemia and glucose intolerance ...
improve glucose homeostasis
... in T2D is able to increase insulin secretion and improve glucose homeostasis.
improves glucose homeostasis
... SIRT1, whose administration to insulin-resistant animals improves glucose homeostasis.
is capable glucose homeostasis
S15511 is a novel insulin sensitizer that is capable of improving glucose homeostasis in nondiabetic rats.
maintains glucose homeostasis
Pancreatic beta-cells possess a well-regulated insulin secretory property that maintains systemic glucose homeostasis.
may be involved
glucose homeostasis
... similar way to those of insulin, PANDER may be involved in glucose homeostasis.
participates glucose homeostasis
Fine-tuning of insulin secretion from pancreatic beta-cells participates in blood glucose homeostasis.
When insulin secretion cannot be increased adequately (type I diabetes defect) to overcome insulin resistance in maintaining glucose homeostasis, hyperglycemia and glucose intolerance ensues. Insulin resistance and glucose intolerance has been well recognized in patients with advanced chronic kidney diseases (CKD).
.. Incretin metabolism is abnormal in T2D, evidenced by a decreased incretin effect, reduction in nutrient-mediated secretion of GIP and GLP-1 in T2D, and resistance to GIP. GLP-1, on the other hand, when administered intravenously in T2D is able to increase insulin secretion and improve glucose homeostasis.
SIRT1, a NAD(+)-dependent protein deacetylase that regulates transcription factors involved in key cellular processes, has been implicated as a mediator of the beneficial effects of calorie restriction. In a recent issue of Nature, Milne et al. (2007) describe novel potent activators of SIRT1, whose administration to insulin-resistant animals improves glucose homeostasis.
S15511 is a novel insulin sensitizer that is capable of improving glucose homeostasis in nondiabetic rats.... However, the mechanisms behind the insulin-sensitizing effect of S15511 are unknown. The aim of our study was to explore whether S15511 improves insulin sensitivity in skeletal muscles. S15511 treatment was associated with an increase in insulin-stimulated glucose transport in type IIb fibers, while type I fibers were unaffected.
Pancreatic beta-cells possess a well-regulated insulin secretory property that maintains systemic glucose homeostasis. Although it has long been thought that differentiated beta-cells are nearly static, recent studies have shown that beta-cell mass dynamically changes throughout the lifetime. In this article, recent progress of regenerative medicine of the pancreas is reviewed.
... Our results showed that glucose up-regulated PANDER mRNA and protein levels in a time- and dose-dependent manner in MIN6 cells and pancreatic islets. ...Because PANDER is expressed by pancreatic beta-cells and in response to glucose in a similar way to those of insulin, PANDER may be involved in glucose homeostasis.
Fine-tuning of insulin secretion from pancreatic beta-cells participates in blood glucose homeostasis. ... Our data identify miR124a and miR96 as novel regulators of the expression of proteins playing a critical role in insulin exocytosis and in the release of other hormones and neurotransmitters.
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One application: improve text mining:
insulin ::: GB000841
maintaining glucose homeostasis
... diabetes defect) to overcome insulin resistance in maintaining glucose homeostasis, hyperglycemia and glucose intolerance ...
improve glucose homeostasis
... in T2D is able to increase insulin secretion and improve glucose homeostasis.
improves glucose homeostasis
... SIRT1, whose administration to insulin-resistant animals improves glucose homeostasis.
is capable glucose homeostasis
S15511 is a novel insulin sensitizer that is capable of improving glucose homeostasis in nondiabetic rats.
maintains glucose homeostasis
Pancreatic beta-cells possess a well-regulated insulin secretory property that maintains systemic glucose homeostasis.
may be involved
glucose homeostasis
... similar way to those of insulin, PANDER may be involved in glucose homeostasis.
participates glucose homeostasis
Fine-tuning of insulin secretion from pancreatic beta-cells participates in blood glucose homeostasis.
When insulin secretion cannot be increased adequately (type I diabetes defect) to overcome insulin resistance in maintaining glucose homeostasis, hyperglycemia and glucose intolerance ensues. Insulin resistance and glucose intolerance has been well recognized in patients with advanced chronic kidney diseases (CKD).
.. Incretin metabolism is abnormal in T2D, evidenced by a decreased incretin effect, reduction in nutrient-mediated secretion of GIP and GLP-1 in T2D, and resistance to GIP. GLP-1, on the other hand, when administered intravenously in T2D is able to increase insulin secretion and improve glucose homeostasis.
SIRT1, a NAD(+)-dependent protein deacetylase that regulates transcription factors involved in key cellular processes, has been implicated as a mediator of the beneficial effects of calorie restriction. In a recent issue of Nature, Milne et al. (2007) describe novel potent activators of SIRT1, whose administration to insulin-resistant animals improves glucose homeostasis.
S15511 is a novel insulin sensitizer that is capable of improving glucose homeostasis in nondiabetic rats.... However, the mechanisms behind the insulin-sensitizing effect of S15511 are unknown. The aim of our study was to explore whether S15511 improves insulin sensitivity in skeletal muscles. S15511 treatment was associated with an increase in insulin-stimulated glucose transport in type IIb fibers, while type I fibers were unaffected.
Pancreatic beta-cells possess a well-regulated insulin secretory property that maintains systemic glucose homeostasis. Although it has long been thought that differentiated beta-cells are nearly static, recent studies have shown that beta-cell mass dynamically changes throughout the lifetime. In this article, recent progress of regenerative medicine of the pancreas is reviewed.
... Our results showed that glucose up-regulated PANDER mRNA and protein levels in a time- and dose-dependent manner in MIN6 cells and pancreatic islets. ...Because PANDER is expressed by pancreatic beta-cells and in response to glucose in a similar way to those of insulin, PANDER may be involved in glucose homeostasis.
Fine-tuning of insulin secretion from pancreatic beta-cells participates in blood glucose homeostasis. ... Our data identify miR124a and miR96 as novel regulators of the expression of proteins playing a critical role in insulin exocytosis and in the release of other hormones and neurotransmitters.
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Other application: improve citations
time = t+1
Model of phenomenon
!
Model of phenomenon
time = t
?
Domain Model
(C) Ed Hovy
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Other application: improve citations
time = t+1
Model of phenomenon
!
Model of phenomenon
time = t
?
Domain Model
(C) Ed Hovy
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Other application: improve citations
time = t+1
Model of phenomenon
!
Model of phenomenon
time = t
?
Domain Model
Citation: • ‘Lifts’ claim from previous paper and add it to current paper
• We need ‘rules for legal lifting’:• Express author’s claim truly• Maintain (experimental) content• Apply appropriately
(C) Ed Hovy
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Other application: improve citations
time = t+1
Model of phenomenon
!
Model of phenomenon
time = t
?
Domain Model
Citation: • ‘Lifts’ claim from previous paper and add it to current paper
• We need ‘rules for legal lifting’:• Express author’s claim truly• Maintain (experimental) content• Apply appropriately
What does this mean?
(C) Ed Hovy
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17
Eventually: trace roots of a claim: how many independent data points is it based on?
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17
PHC Growth arrestundergo
Eventually: trace roots of a claim: how many independent data points is it based on?
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17
PHC Growth arrestundergo
Eventually: trace roots of a claim: how many independent data points is it based on?
Paper A:implication
results
method
goal
fact
fact
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17
PHC Growth arrestundergo
Eventually: trace roots of a claim: how many independent data points is it based on?
Paper A:implication
results
method
goal
fact
fact
data 1
data 2 data 3
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17
PHC Growth arrestundergo
Eventually: trace roots of a claim: how many independent data points is it based on?
Paper A:implication
results
method
goal
fact
fact
Paper B:
data 4
data 5 data 6
implication
results
method
goal
fact
fact
data 1
data 2 data 3
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17
PHC Growth arrestundergo
Eventually: trace roots of a claim: how many independent data points is it based on?
Paper A:implication
results
method
goal
fact
fact
Paper B:
data 4
data 5 data 6
implication
results
method
goal
fact
fact
data 1
data 2 data 3
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17
PHC Growth arrestundergo
Eventually: trace roots of a claim: how many independent data points is it based on?
Paper A:implication
results
method
goal
fact
fact
Paper B:
data 4
data 5 data 6
implication
results
method
goal
fact
fact
data 1
data 2 data 3
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17
PHC Growth arrestundergo
Eventually: trace roots of a claim: how many independent data points is it based on?
Paper A:implication
results
method
goal
fact
fact
Paper B:
data 4
data 5 data 6
implication
results
method
goal
fact
fact
underpinning
data 1
data 2 data 3
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17
PHC Growth arrestundergo
Eventually: trace roots of a claim: how many independent data points is it based on?
Paper A:implication
results
method
goal
fact
fact
Paper B:
data 4
data 5 data 6
implication
results
method
goal
fact
fact
data 1
data 2 data 3
![Page 60: On the research paper, and the knowledge within](https://reader034.vdocuments.us/reader034/viewer/2022042714/554ea4d6b4c9055f7b8b499a/html5/thumbnails/60.jpg)
17
PHC Growth arrestundergo
Eventually: trace roots of a claim: how many independent data points is it based on?
Paper A:implication
results
method
goal
fact
fact
Paper B:
data 4
data 5 data 6
implication
results
method
goal
fact
fact
data 1
data 2 data 3
method link
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Scientific papers are stories, that persuade with data.
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Scientific papers are stories, that persuade with data.
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Scientific papers are stories, that persuade with data.
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Sometimes the link to data is good:
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And sometimes it’s not so good:
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And sometimes it’s not so good:
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And sometimes it’s not so good:
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And sometimes it’s not so good:
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Can we make data-driven papers? Work done with Ed Hovy, Phil Bourne, Gully Burns and Cartic Ramakrishnan
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Can we make data-driven papers? Work done with Ed Hovy, Phil Bourne, Gully Burns and Cartic Ramakrishnan
1. Research: Each item in the system has metadata (including provenance) and relations to other data items added to it.
metadata
metadata
metadata
metadata
metadata
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Can we make data-driven papers? Work done with Ed Hovy, Phil Bourne, Gully Burns and Cartic Ramakrishnan
1. Research: Each item in the system has metadata (including provenance) and relations to other data items added to it.
metadata
metadata
metadata
metadata
metadata
2. Workflow: All data items created in the lab are added to a (lab-owned) workflow system.
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Can we make data-driven papers? Work done with Ed Hovy, Phil Bourne, Gully Burns and Cartic Ramakrishnan
1. Research: Each item in the system has metadata (including provenance) and relations to other data items added to it.
metadata
metadata
metadata
metadata
metadata
2. Workflow: All data items created in the lab are added to a (lab-owned) workflow system.
Rats were subjected to two grueling tests(click on fig 2 to see underlying data). These results suggest that the neurological pain pro-
3. Authoring: A paper is written in an authoring tool which can pull data with provenance from the workflow tool in the appropriate representation into the document.
![Page 73: On the research paper, and the knowledge within](https://reader034.vdocuments.us/reader034/viewer/2022042714/554ea4d6b4c9055f7b8b499a/html5/thumbnails/73.jpg)
Can we make data-driven papers? Work done with Ed Hovy, Phil Bourne, Gully Burns and Cartic Ramakrishnan
1. Research: Each item in the system has metadata (including provenance) and relations to other data items added to it.
metadata
metadata
metadata
metadata
metadata
2. Workflow: All data items created in the lab are added to a (lab-owned) workflow system.
4. Editing and review: Once the co-authors agree, the paper is ‘exposed’ to the editors, who in turn expose it to reviewers. Reports are stored in the authoring/editing system, the paper gets updated, until it is validated.
Review
Edit
Revise
Rats were subjected to two grueling tests(click on fig 2 to see underlying data). These results suggest that the neurological pain pro-
3. Authoring: A paper is written in an authoring tool which can pull data with provenance from the workflow tool in the appropriate representation into the document.
![Page 74: On the research paper, and the knowledge within](https://reader034.vdocuments.us/reader034/viewer/2022042714/554ea4d6b4c9055f7b8b499a/html5/thumbnails/74.jpg)
5. Publishing and distribution: When a paper is published, a collection of validated information is exposed to the world. It remains connected to its related data item, and its heritage can be traced.
Can we make data-driven papers? Work done with Ed Hovy, Phil Bourne, Gully Burns and Cartic Ramakrishnan
1. Research: Each item in the system has metadata (including provenance) and relations to other data items added to it.
metadata
metadata
metadata
metadata
metadata
2. Workflow: All data items created in the lab are added to a (lab-owned) workflow system.
4. Editing and review: Once the co-authors agree, the paper is ‘exposed’ to the editors, who in turn expose it to reviewers. Reports are stored in the authoring/editing system, the paper gets updated, until it is validated.
Review
Edit
Revise
Rats were subjected to two grueling tests(click on fig 2 to see underlying data). These results suggest that the neurological pain pro-
3. Authoring: A paper is written in an authoring tool which can pull data with provenance from the workflow tool in the appropriate representation into the document.
![Page 75: On the research paper, and the knowledge within](https://reader034.vdocuments.us/reader034/viewer/2022042714/554ea4d6b4c9055f7b8b499a/html5/thumbnails/75.jpg)
5. Publishing and distribution: When a paper is published, a collection of validated information is exposed to the world. It remains connected to its related data item, and its heritage can be traced.
Some other publisher
6. User applications: distributed applications run on this ‘exposed data’ universe.
Can we make data-driven papers? Work done with Ed Hovy, Phil Bourne, Gully Burns and Cartic Ramakrishnan
1. Research: Each item in the system has metadata (including provenance) and relations to other data items added to it.
metadata
metadata
metadata
metadata
metadata
2. Workflow: All data items created in the lab are added to a (lab-owned) workflow system.
4. Editing and review: Once the co-authors agree, the paper is ‘exposed’ to the editors, who in turn expose it to reviewers. Reports are stored in the authoring/editing system, the paper gets updated, until it is validated.
Review
Edit
Revise
Rats were subjected to two grueling tests(click on fig 2 to see underlying data). These results suggest that the neurological pain pro-
3. Authoring: A paper is written in an authoring tool which can pull data with provenance from the workflow tool in the appropriate representation into the document.
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One step: encouraging submission of structured workflows
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Another step: ScienceDirect app store
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Another step: ScienceDirect app store
- Eclipse SDK platform accessing all ScienceDirect/Scopus content
-Build applications on top of content-Offer to users in marketplace
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A third step: Executable Paper ChallengeGoal: invite computer science community to help develop formats that:
- add executable files and reproducible data to computer science papers;
- handle storage and validation of very large files
- help validation of data and code, and decrease the reviewer’s workload
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A third step: Executable Paper ChallengeGoal: invite computer science community to help develop formats that:
- add executable files and reproducible data to computer science papers;
- handle storage and validation of very large files
- help validation of data and code, and decrease the reviewer’s workload
![Page 81: On the research paper, and the knowledge within](https://reader034.vdocuments.us/reader034/viewer/2022042714/554ea4d6b4c9055f7b8b499a/html5/thumbnails/81.jpg)
In Summary:
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In Summary:1. Stories:
- ORB, Satellite: link to any part of content - bring it on!
![Page 83: On the research paper, and the knowledge within](https://reader034.vdocuments.us/reader034/viewer/2022042714/554ea4d6b4c9055f7b8b499a/html5/thumbnails/83.jpg)
In Summary:1. Stories:
- ORB, Satellite: link to any part of content - bring it on!
2. Persuasion:
- Logical structure for biological propositions; trace a claim through successive citations
![Page 84: On the research paper, and the knowledge within](https://reader034.vdocuments.us/reader034/viewer/2022042714/554ea4d6b4c9055f7b8b499a/html5/thumbnails/84.jpg)
In Summary:1. Stories:
- ORB, Satellite: link to any part of content - bring it on!
2. Persuasion:
- Logical structure for biological propositions; trace a claim through successive citations
3. Data:
- Better data linking, better structuring of methods.
![Page 85: On the research paper, and the knowledge within](https://reader034.vdocuments.us/reader034/viewer/2022042714/554ea4d6b4c9055f7b8b499a/html5/thumbnails/85.jpg)
In Summary:1. Stories:
- ORB, Satellite: link to any part of content - bring it on!
2. Persuasion:
- Logical structure for biological propositions; trace a claim through successive citations
3. Data:
- Better data linking, better structuring of methods.
In conclusion: is the research paper going away?
![Page 86: On the research paper, and the knowledge within](https://reader034.vdocuments.us/reader034/viewer/2022042714/554ea4d6b4c9055f7b8b499a/html5/thumbnails/86.jpg)
In Summary:1. Stories:
- ORB, Satellite: link to any part of content - bring it on!
2. Persuasion:
- Logical structure for biological propositions; trace a claim through successive citations
3. Data:
- Better data linking, better structuring of methods.
In conclusion: is the research paper going away?
I don’t think so! But it will be:
- Structured better: authors will need to justify claims directly
- Connected better: more traceable, better links to data and workflow components, and to other work
![Page 87: On the research paper, and the knowledge within](https://reader034.vdocuments.us/reader034/viewer/2022042714/554ea4d6b4c9055f7b8b499a/html5/thumbnails/87.jpg)
Thank you!
W3C group on Discourse Structure: http://www.w3.org/wiki/HCLSIG/SWANSIOC SciVerse: http://developer.sciverse.comPangea project: http://bit.ly/98haOw Parsing rhetoric: http://elsatglabs.com/labs/anita/Fact creation demo: http://elsatglabs.com/labs/anita/demos/LATSDemo102007/Methods Navigator: http://www.methodsnavigator.comSciVerse APIs: http://developer.sciverse.comExecutable Paper Challenge: http://www.executablepapers.com
Or mail me at: Anita de Waard, [email protected]