Talk on Epistemic Modality Modelling for dept of linguistics, University of Lethbridge, Lethbridge, Alberta

1. ‘These results suggest that...’
Knowledge Attribution in
Scientific Discourse
Anita de Waard
Disruptive Technologies Director, Elsevier Labs
Casimir Researcher, University of Utrecht
University of Lethbridge, April 2 2012
Monday, April 2, 2012

2. How a claim becomes a fact:
- Voorhoeve, 2006: “These miRNAs neutralize p53- mediated CDK
inhibition, possibly through direct inhibition of the expression of the
tumorsuppressor LATS2.”
- Kloosterman and Plasterk, 2006: “In a genetic screen, miR-372 and
miR-373 were found to allow proliferation of primary human cells that
express oncogenic RAS and active p53, possibly by inhibiting the tumor
suppressor LATS2 (Voorhoeve et al., 2006).”
- Yabuta et al., 2007: “[On the other hand,] 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).”
- Okada et al., 2011: “Two oncogenic miRNAs, miR-372 and miR-373,
directly inhibit the expression of Lats2, thereby allowing tumorigenic
growth in the presence of p53 (Voorhoeve et al., 2006).”
Monday, April 2, 2012

3. “[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
Text
Text
Monday, April 2, 2012

4. “[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
Text
Text
Monday, April 2, 2012

5. Research Questions:
Monday, April 2, 2012

6. Research Questions:
1. Can we find a model for epistemic evaluation and knowledge
attribution to describe all biological statements in a
straightforward way?
Monday, April 2, 2012

7. Research Questions:
1. Can we find a model for epistemic evaluation and knowledge
attribution to describe all biological statements in a
straightforward way?
2. If yes: can we detect this evaluation - manually, and
automatically?
Monday, April 2, 2012

8. Research Questions:
1. Can we find a model for epistemic evaluation and knowledge
attribution to describe all biological statements in a
straightforward way?
2. If yes: can we detect this evaluation - manually, and
automatically?
3. Is this model useful for examining the mechanism of ‘hedging
erosion’, does it show how a claim becomes validated after
being cited?
Monday, April 2, 2012

9. Method:
Monday, April 2, 2012

10. Method:
1.Model for epistemic evaluation?
Monday, April 2, 2012

11. Method:
1.Model for epistemic evaluation?
1.1.Parse text into discourse segments (Elementary Discourse
Units) containing a single rhetorical move (roughly, a clause)
Monday, April 2, 2012

12. Method:
1.Model for epistemic evaluation?
1.1.Parse text into discourse segments (Elementary Discourse
Units) containing a single rhetorical move (roughly, a clause)
1.2.Identify levels of epistemic evaluation
Monday, April 2, 2012

13. Method:
1.Model for epistemic evaluation?
1.1.Parse text into discourse segments (Elementary Discourse
Units) containing a single rhetorical move (roughly, a clause)
1.2.Identify levels of epistemic evaluation
1.3.Do a co-annotator study to see if these levels are shared
Monday, April 2, 2012

14. Method:
1.Model for epistemic evaluation?
1.1.Parse text into discourse segments (Elementary Discourse
Units) containing a single rhetorical move (roughly, a clause)
1.2.Identify levels of epistemic evaluation
1.3.Do a co-annotator study to see if these levels are shared
2. How to detect?
Monday, April 2, 2012

15. Method:
1.Model for epistemic evaluation?
1.1.Parse text into discourse segments (Elementary Discourse
Units) containing a single rhetorical move (roughly, a clause)
1.2.Identify levels of epistemic evaluation
1.3.Do a co-annotator study to see if these levels are shared
2. How to detect?
2.1.Identify markers of epistemic evaluation/knowledge
attribution
Monday, April 2, 2012

16. Method:
1.Model for epistemic evaluation?
1.1.Parse text into discourse segments (Elementary Discourse
Units) containing a single rhetorical move (roughly, a clause)
1.2.Identify levels of epistemic evaluation
1.3.Do a co-annotator study to see if these levels are shared
2. How to detect?
2.1.Identify markers of epistemic evaluation/knowledge
attribution
2.2.Work with computational linguists to see if these can be
found automatically
Monday, April 2, 2012

17. Method:
1.Model for epistemic evaluation?
1.1.Parse text into discourse segments (Elementary Discourse
Units) containing a single rhetorical move (roughly, a clause)
1.2.Identify levels of epistemic evaluation
1.3.Do a co-annotator study to see if these levels are shared
2. How to detect?
2.1.Identify markers of epistemic evaluation/knowledge
attribution
2.2.Work with computational linguists to see if these can be
found automatically
3. Useful for hedging erosion?
Monday, April 2, 2012

18. Method:
1.Model for epistemic evaluation?
1.1.Parse text into discourse segments (Elementary Discourse
Units) containing a single rhetorical move (roughly, a clause)
1.2.Identify levels of epistemic evaluation
1.3.Do a co-annotator study to see if these levels are shared
2. How to detect?
2.1.Identify markers of epistemic evaluation/knowledge
attribution
2.2.Work with computational linguists to see if these can be
found automatically
3. Useful for hedging erosion?
3.1.Perform a diachronic study of citation evaluation
Monday, April 2, 2012

19. Experimental Discourse
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.
Monday, April 2, 2012

20. Parsing Experimental Discourse
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.
Monday, April 2, 2012

21. Parsing Experimental Discourse
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.
Monday, April 2, 2012

22. Parsing Experimental Discourse
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.
Monday, April 2, 2012

23. Parsing Experimental Discourse
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.
Monday, April 2, 2012

24. Parsing Experimental Discourse
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.
Monday, April 2, 2012

25. Parsing Experimental Discourse
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.
Monday, April 2, 2012

26. Parsing Experimental Discourse
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.
Monday, April 2, 2012

27. Parsing Experimental Discourse
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.
Monday, April 2, 2012

28. Parsing Experimental Discourse
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.
Monday, April 2, 2012

29. Parsing Experimental Discourse
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.
Monday, April 2, 2012

30. Parsing Experimental Discourse
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.
Monday, April 2, 2012

31. Segment Types
Monday, April 2, 2012

32. Segment Types
Segment Description Example
Fact a known fact, generally without mature miR-373 is a homolog of miR-372
explicit citation
Hypothesis a proposed idea, not supported by This could for instance be a result of high
evidence mdm2 levels
Problem unresolved, contradictory, or However, further investigation is required to
unclear issue demonstrate the exact mechanism of LATS2
action
Goal research goal To identify novel functions of miRNAs,
Method experimental method Using fluorescence microscopy and luciferase
assays,
Result a restatement of the outcome of all constructs yielded high expression levels
an experiment of mature miRNAs
Implication an interpretation of the results, in our procedure is sensitive enough to detect
light of earlier hypotheses and facts mild growth differences
Monday, April 2, 2012

33. Segment Types
Segment Description Example
Fact a known fact, generally without mature miR-373 is a homolog of miR-372
explicit citation
Hypothesis a proposed idea, not supported by This could for instance be a result of high
evidence mdm2 levels
Problem unresolved, contradictory, or However, further investigation is required to
unclear issue demonstrate the exact mechanism of LATS2
action
Goal research goal To identify novel functions of miRNAs,
Method experimental method Using fluorescence microscopy and luciferase
assays,
Result a restatement of the outcome of all constructs yielded high expression levels
an experiment of mature miRNAs
Implication an interpretation of the results, in our procedure is sensitive enough to detect
light of earlier hypotheses and facts mild growth differences
‘Other-segments’, related to (referenced) other work - e.g. with reference
Monday, April 2, 2012

34. Segment Types
Segment Description Example
Fact a known fact, generally without mature miR-373 is a homolog of miR-372
explicit citation
Hypothesis a proposed idea, not supported by This could for instance be a result of high
evidence mdm2 levels
Problem unresolved, contradictory, or However, further investigation is required to
unclear issue demonstrate the exact mechanism of LATS2
action
Goal research goal To identify novel functions of miRNAs,
Method experimental method Using fluorescence microscopy and luciferase
assays,
Result a restatement of the outcome of all constructs yielded high expression levels
an experiment of mature miRNAs
Implication an interpretation of the results, in our procedure is sensitive enough to detect
light of earlier hypotheses and facts mild growth differences
‘Other-segments’, related to (referenced) other work - e.g. with reference
Regulatory segments, acting as matrix sentences framing other segments,
‘Altogether, this suggests that’
Monday, April 2, 2012

35. Realms in scholarly discourse:
place of hedging
Monday, April 2, 2012

36. Realms in scholarly discourse:
place of hedging
(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,
Monday, April 2, 2012

37. Realms in scholarly discourse:
place of hedging
(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
Monday, April 2, 2012

38. Realms in scholarly discourse:
place of hedging
(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),
Monday, April 2, 2012

39. Realms in scholarly discourse:
place of hedging
(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
(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),
Monday, April 2, 2012

40. Realms in scholarly discourse:
place of hedging
(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
(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),
Monday, April 2, 2012

41. Realms in scholarly discourse:
place of hedging
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
(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),
Monday, April 2, 2012

42. Realms in scholarly discourse:
place of hedging
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
(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
Monday, April 2, 2012

43. Realms in scholarly discourse:
place of hedging
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
(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
Monday, April 2, 2012

44. Hedging erosion in action
Monday, April 2, 2012

45. Hedging erosion in action
To investigate the possibility that
miR-372 and miR-373 suppress the
expression of LATS2, we...
Hypothesis
Monday, April 2, 2012

46. Hedging erosion in action
To investigate the possibility that
miR-372 and miR-373 suppress the
expression of LATS2, we...
KnownFact KnownFact
Concepts Hypothesis
Monday, April 2, 2012

47. Hedging erosion in action
To investigate the possibility that
miR-372 and miR-373 suppress the
expression of LATS2, we...
KnownFact KnownFact
Concepts Hypothesis
Goal
Method Result
Data
Experiment 1
Monday, April 2, 2012

48. Hedging erosion in action
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,
KnownFact KnownFact
Concepts Hypothesis Implication
Goal
Method Result
Data
Experiment 1
Monday, April 2, 2012

49. Hedging erosion in action
To investigate the possibility that
miR-372 and miR-373 suppress the
Voorhoeve, 2006
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,
KnownFact KnownFact
Concepts Hypothesis Implication
Goal
Method Result
Data
Experiment 1
Monday, April 2, 2012

50. Hedging erosion in action
To investigate the possibility that
miR-372 and miR-373 suppress the
Voorhoeve, 2006
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,
KnownFact KnownFact
Concepts Hypothesis Implication
Goal
Goal
Method Result Method Result
Data Data
Experiment 1 Experiment 2
Monday, April 2, 2012

51. Hedging erosion in action
To investigate the possibility that
miR-372 and miR-373 suppress the
Voorhoeve, 2006
expression of LATS2, we...
Raver-Shapira et.al, JMolCell 2007
Therefore, these results point to two miRNAs, miRNA-372 and-373, function as
LATS2 as a mediator of the miR-372 and potential novel oncogenes in testicular germ
miR-373 effects on cell proliferation and cell tumors by inhibition of LATS2 expression,
tumorigenicity, which suggests that Lats2 is an important
tumor suppressor (Voorhoeve et al., 2006).
KnownFact KnownFact
Concepts Hypothesis Implication Fact
Goal
Goal
Method Result Method Result
Data Data
Experiment 1 Experiment 2
Monday, April 2, 2012

52. Hedging erosion in action Yabuta, JBioChem 2007
miR-372 and miR-373 target the
To investigate the possibility that
miR-372 and miR-373 suppress the
Voorhoeve, 2006 Lats2 tumor suppressor
(Voorhoeve et al., 2006)
expression of LATS2, we...
Raver-Shapira et.al, JMolCell 2007
Therefore, these results point to two miRNAs, miRNA-372 and-373, function as
LATS2 as a mediator of the miR-372 and potential novel oncogenes in testicular germ
miR-373 effects on cell proliferation and cell tumors by inhibition of LATS2 expression,
tumorigenicity, which suggests that Lats2 is an important
tumor suppressor (Voorhoeve et al., 2006).
KnownFact KnownFact
Concepts Hypothesis Implication Fact
Goal
Goal
Method Result Method Result
Data Data
Experiment 1 Experiment 2
Monday, April 2, 2012

53. Hedging erosion in action Yabuta, JBioChem 2007
miR-372 and miR-373 target the
To investigate the possibility that
miR-372 and miR-373 suppress the
Voorhoeve, 2006 Lats2 tumor suppressor
(Voorhoeve et al., 2006)
expression of LATS2, we...
Raver-Shapira et.al, JMolCell 2007
Therefore, these results point to two miRNAs, miRNA-372 and-373, function as
LATS2 as a mediator of the miR-372 and potential novel oncogenes in testicular germ
miR-373 effects on cell proliferation and cell tumors by inhibition of LATS2 expression,
tumorigenicity, which suggests that Lats2 is an important
tumor suppressor (Voorhoeve et al., 2006).
KnownFact KnownFact
Concepts Hypothesis Implication Fact
Goal
Goal
Method Result Method Result
Data Data
Experiment 1 Experiment 2
http://elsatglabs.com/labs/anita/demos/LATSDemo102007/
Monday, April 2, 2012

54. Logical structure of epistemic evaluations:
Monday, April 2, 2012

55. Logical structure of epistemic evaluations:
For a Proposition P, an epistemically marked clause E is an
Evaluation of P, EV, B, S(P), with:
- V = Value:
3 = Assumed true, 2 = Probable, 1 = Possible,
0 = Unknown,
(- 1= possibly untrue, - 2 = probably untrue, -3 = assumed untrue)
- B = Basis:
Reasoning
Data
- S = Source:
A = speaker is author A, explicit
IA = speaker author, A, implicit
N = other author N, explicit
NN = other author NN, implicit
Monday, April 2, 2012

56. Logical structure of epistemic evaluations:
For a Proposition P, an epistemically marked clause E is an
Evaluation of P, EV, B, S(P), with:
- V = Value:
3 = Assumed true, 2 = Probable, 1 = Possible,
0 = Unknown,
(- 1= possibly untrue, - 2 = probably untrue, -3 = assumed untrue)
- B = Basis:
Reasoning
Data
- S = Source:
A = speaker is author A, explicit
IA = speaker author, A, implicit
N = other author N, explicit
NN = other author NN, implicit
Model suggested by Eduard Hovy,
Information Sciences Institute University South Califormia
Monday, April 2, 2012

57. Some examples:
Concept Values Example
Value 0 - Lack of knowledge: Thus, it remains to be determined if...
1 – Hypothetical: low certainty GATA-1 binding to exon 1 may affect transcription
start site function
2 – Dubitative: higher likelihood but suggesting the presence of lineage-specific elements.
short of complete certainty
3 – Doxastic: complete certainty, the 1.6 kb 5' flanking region of CCR3 has promoter
accepted/known/proven fact activity in vivo.
Basis R – Reasoning Therefore, one can argue…’
D – Data These results suggest…’
0 – Unidentified Studies report that…’
Source A - Author: Explicit mention of We hypothesize that…’; ‘Figure 2a shows that…
author/speaker or current paper as
source
N - Named external source, either …several reports have documented this expression
explicitly or as a reference [11-16,42].
IA - Implicit attribution to the author Electrophoretic mobility shift analysis revealed that…
NN – Nameless external source no eosinophil-specific transcription factors have been
reported…
0 – No source of knowledge transcription factors are the final common pathway
driving differentiation
Monday, April 2, 2012

58. Epistemic Markers
Monday, April 2, 2012

59. Epistemic Markers
- Modal auxiliary verbs (e.g. can, could, might)
Monday, April 2, 2012

60. Epistemic Markers
- Modal auxiliary verbs (e.g. can, could, might)
- Qualifying adverbs and adjectives (e.g. interestingly, possibly, likely,
potential, somewhat, slightly, powerful, unknown, undefined)
Monday, April 2, 2012

61. Epistemic Markers
- Modal auxiliary verbs (e.g. can, could, might)
- Qualifying adverbs and adjectives (e.g. interestingly, possibly, likely,
potential, somewhat, slightly, powerful, unknown, undefined)
- References, either external (e.g. ‘[Voorhoeve et al., 2006]’) or
internal (e.g. ‘See fig. 2a’).
Monday, April 2, 2012

62. Epistemic Markers
- Modal auxiliary verbs (e.g. can, could, might)
- Qualifying adverbs and adjectives (e.g. interestingly, possibly, likely,
potential, somewhat, slightly, powerful, unknown, undefined)
- References, either external (e.g. ‘[Voorhoeve et al., 2006]’) or
internal (e.g. ‘See fig. 2a’).
- Reporting/epistemic verbs (e.g. suggest, imply, indicate, show)
- either within the clause: ‘These results suggest that...’
- or in a subordinate clause governed by reporting-verb matrix
clause ‘{These results suggest that} indeed, this represents the true
endogenous activity.’
Monday, April 2, 2012

63. Markers v. Types: 1 paper, 640 segments
Value Modal Reporting Ruled Adverbs/ Referen None Total
Aux Verb by RV Adjectiv ces
es
Total value = 3 1 (0.5%) 81 (40%) 24 (12%) 7 (4%) 41 (20%) 47 (24%) 201(100%)
Total Value = 2 29 (51%) 23 (40%) 1 (2%) 4(7%) 57(100%)
Total Value = 1 9(27%) 11(33%) 11(33%) 1(3%) 1(3%) 33(100%)
Total Value = 0 9 (64%) 3 (21%) 1(7%) 1(7%) 14(100%)
Total No 16(37%) 3(7%) 0 3(7%) 22(50%) 44(100%)
Modality
Overall Total 10 (2%) 146(23%) 64(10%) 10(2%) 50(8%) 69(11%) 640(100%)
Monday, April 2, 2012

64. Markers v. Types: 1 paper, 640 segments
Value Modal Reporting Ruled Adverbs/ Referen None Total
Aux Verb by RV Adjectiv ces
es
Total value = 3 1 (0.5%) 81 (40%) 24 (12%) 7 (4%) 41 (20%) 47 (24%) 201(100%)
Total Value = 2 29 (51%) 23 (40%) 1 (2%) 4(7%) 57(100%)
Total Value = 1 9(27%) 11(33%) 11(33%) 1(3%) 1(3%) 33(100%)
Total Value = 0 9 (64%) 3 (21%) 1(7%) 1(7%) 14(100%)
Total No 16(37%) 3(7%) 0 3(7%) 22(50%) 44(100%)
Modality
Overall Total 10 (2%) 146(23%) 64(10%) 10(2%) 50(8%) 69(11%) 640(100%)
Monday, April 2, 2012

65. Markers v. Types: 1 paper, 640 segments
Value Modal Reporting Ruled Adverbs/ Referen None Total
Aux Verb by RV Adjectiv ces
es
Total value = 3 1 (0.5%) 81 (40%) 24 (12%) 7 (4%) 41 (20%) 47 (24%) 201(100%)
Total Value = 2 29 (51%) 23 (40%) 1 (2%) 4(7%) 57(100%)
Total Value = 1 9(27%) 11(33%) 11(33%) 1(3%) 1(3%) 33(100%)
Total Value = 0 9 (64%) 3 (21%) 1(7%) 1(7%) 14(100%)
Total No 16(37%) 3(7%) 0 3(7%) 22(50%) 44(100%)
Modality
Overall Total 10 (2%) 146(23%) 64(10%) 10(2%) 50(8%) 69(11%) 640(100%)
Monday, April 2, 2012

66. Markers v. Types: 1 paper, 640 segments
Value Modal Reporting Ruled Adverbs/ Referen None Total
Aux Verb by RV Adjectiv ces
es
Total value = 3 1 (0.5%) 81 (40%) 24 (12%) 7 (4%) 41 (20%) 47 (24%) 201(100%)
Total Value = 2 29 (51%) 23 (40%) 1 (2%) 4(7%) 57(100%)
Total Value = 1 9(27%) 11(33%) 11(33%) 1(3%) 1(3%) 33(100%)
Total Value = 0 9 (64%) 3 (21%) 1(7%) 1(7%) 14(100%)
Total No 16(37%) 3(7%) 0 3(7%) 22(50%) 44(100%)
Modality
Overall Total 10 (2%) 146(23%) 64(10%) 10(2%) 50(8%) 69(11%) 640(100%)
Monday, April 2, 2012

67. Reporting verbs vs. epistemic value:
Monday, April 2, 2012

68. Reporting verbs vs. epistemic value:
Value = 0 establish, (remain to be) elucidated,
(unknown) be (clear/useful), (remain to be) examined/determined,
describe, make difficult to infer, report
Value = 1 be important, consider, expect, hypothesize (5x),
(hypothetical) give insight, raise possibility that, suspect, think
Value = 2 appear, believe, implicate (2x), imply, indicate (12x),
(probable) play a role, represent, suggest (18x), validate (2x),
Value = 3 be able/apparent/important /positive/visible, compare
(presumed true) (2x), confirm (2x), define, demonstrate (15x), detect
(5x), discover, display (3x), eliminate, find (3x), identify
(4x), know, need, note (2x), observe (2x), obtain
(success/results- 3x), prove to be, refer, report(2x),
reveal (3x), see(2x), show(24x), study, view
Monday, April 2, 2012

69. Most prevalent clause type:
“These results suggest that...”
Monday, April 2, 2012

70. Most prevalent clause type:
“These results suggest that...”
Adverb/Connective thus, therefore, together, recently, in summary
Determiner/Pronoun it, this, these, we/our
Adjective previous, future, better
Noun phrase data, report, study, result(s); method or
reference
Modal form of ‘to be’, may, remain
Adjective often, recently, generally
Verb show, obtain, consider, view, reveal,
suggest, hypothesize, indicate, believe
Preposition that, to
Monday, April 2, 2012

71. Can we find this automatically?
‘Claimed knowledge updates’:
Work done with Agnes Sandor,
Xerox Research Europe
Monday, April 2, 2012

72. Preliminary steps towards
citation analysis:
Type Voorhoeve text Citing text
Method We subsequently created a human Voorhoeve et al. (116) employed a novel strategy by
miRNA expression library (miR-Lib) combining an miRNA vector library and corresponding
by cloning almost all annotated bar code array Using a novel retroviral miRNA
human miRNAs into our vector expression library,
(Rfam release 6) (Figure S3) Agami and co-workers performed a cell-based screen
Result we identified miR-372 and miR-372 and miR-373 were consequently found to permit
miR-373, each permitting proliferation and tumorigenesis of these primary cells
proliferation and tumorigenesis carrying both oncogenic RAS and wild-type p53,
of primary human cells that Voorhoeve et al. (2006) identified miR-372 and miR-373
harbor both oncogenic RAS miR-372 has been recently described as potential
and active wild - type p53. oncogene that collaborate with oncogenic RAS in
cellular transformation
Interpretat These miRNAs neutralize p53- probably through direct inhibition of the expression of the
ion mediated CDK inhibition, tumor-suppressor LATS2 and subsequent neutralization
possibly through direct of the p53 pathway.
inhibition of the expression of Compromised Lats2 functionality might reduce the
the tumor suppressor LATS2 . selective pressure for p53 inactivation during tumor
progressionRas activation.
Work done with Lucy Vanderwende, Microsoft Research
Monday, April 2, 2012

73. Conclusions:
Monday, April 2, 2012

74. Conclusions:
1. Can we find a model for epistemic evaluation and knowledge attribution
to describe all biological statements in a straightforward way?
- Yes: three-dimensional model - Value, Basis, Source;
- Four markers: modal auxiliaries, adverbs, references, reporting verbs;
- Correlation: reporting verbs + that = most prevalent marker;
value = 1: modal aux; value = 0: phrase; value = 3: refs or none
Monday, April 2, 2012

75. Conclusions:
1. Can we find a model for epistemic evaluation and knowledge attribution
to describe all biological statements in a straightforward way?
- Yes: three-dimensional model - Value, Basis, Source;
- Four markers: modal auxiliaries, adverbs, references, reporting verbs;
- Correlation: reporting verbs + that = most prevalent marker;
value = 1: modal aux; value = 0: phrase; value = 3: refs or none
2. If yes: can we detect this evaluation automatically?
- Early results are promising, needs more validation
Monday, April 2, 2012

76. Conclusions:
1. Can we find a model for epistemic evaluation and knowledge attribution
to describe all biological statements in a straightforward way?
- Yes: three-dimensional model - Value, Basis, Source;
- Four markers: modal auxiliaries, adverbs, references, reporting verbs;
- Correlation: reporting verbs + that = most prevalent marker;
value = 1: modal aux; value = 0: phrase; value = 3: refs or none
2. If yes: can we detect this evaluation automatically?
- Early results are promising, needs more validation
3. Is this model useful for examining the mechanism of ‘hedging erosion’,
does it show how a claim becomes validated after being cited?
- Probably! More work to be done...
Monday, April 2, 2012

77. Next steps:
Monday, April 2, 2012

78. Next steps:
1. Co-annotator validation of epistemic mark up: do we all agree on what
(the author says) is true, probable, possible, unknown?
Monday, April 2, 2012

79. Next steps:
1. Co-annotator validation of epistemic mark up: do we all agree on what
(the author says) is true, probable, possible, unknown?
2. Full-blown diachronic study: statistical validation for this trend?
Monday, April 2, 2012

80. Next steps:
1. Co-annotator validation of epistemic mark up: do we all agree on what
(the author says) is true, probable, possible, unknown?
2. Full-blown diachronic study: statistical validation for this trend?
3. Work with bioinformaticians:
- (Make OWL ontology) and add to formal knowledge representations, e.g.
Biological Expression Language add {V = 3, S = N, B = 0}:
- SET Evidence = "Arterial cells are highly susceptible to oxidative stress, which can induce
both necrosis and apoptosis (programmed cell death) [1,2]"
- biologicalProcess(GO:"response to oxidative stress") increases biologicalProcess
(GO:"apoptotic process")
- biologicalProcess(GO:"response to oxidative stress") increases biologicalProcess
(GO:necrosis)
- Improve triple search engines, e.g. compare in iHop:
- The Lats2 tumor suppressor protein has been implicated earlier in promoting p53
activation in response to mitotic apparatus stress {V = 2, S = NN, B = 0}
- Our findings reveal that miR-373 would be a potential oncogene and it participates
in the carcinogenesis of human esophageal cancer {V = 1/2?, S = A, B = D}
Monday, April 2, 2012

81. Acknowledgements:
Collaborators:
- Henk Pander Maat, Universiteit Utrecht
- Agnes Sandor, Xerox Research Europe
- Lucy Vanderwende, Microsoft Research
- Eduard H. Hovy, USC Information Sciences Institute
- Dexter Pratt, Biological Exchange Language
Funding:
- NWO/Casimir Subsidy, 2006-2010
- 2010+ - Elsevier Labs
Anita de Waard, a.dewaard@elsevier.com
http://elsatglabs.com/labs/anita
Monday, April 2, 2012

82. Tense and Mythology
Monday, April 2, 2012

83. Recursion/patterns of rhetoric:
Main moves in an experimental paper
Monday, April 2, 2012

84. Recursion/patterns of rhetoric:
Main moves in an experimental paper
Facts
Problem
Hypothesis
Monday, April 2, 2012

85. Recursion/patterns of rhetoric:
Main moves in an experimental paper
Facts
Problem
Hypothesis
Goal
Monday, April 2, 2012

86. Recursion/patterns of rhetoric:
Main moves in an experimental paper
Facts
Problem
Hypothesis
Goal
Method
Results
Monday, April 2, 2012

87. Recursion/patterns of rhetoric:
Main moves in an experimental paper
Facts
Problem
Hypothesis
Goal These results suggest that....
Method
Results
Monday, April 2, 2012

88. Recursion/patterns of rhetoric:
Main moves in an experimental paper
Facts
Problem
Implication
Hypothesis
Goal These results suggest that....
Method
Results
Monday, April 2, 2012

89. Recursion/patterns of rhetoric:
Main moves in an experimental paper
Facts
Concepts Problem
Implication
Hypothesis
Goal These results suggest that....
Method
Results
Monday, April 2, 2012

90. Recursion/patterns of rhetoric:
Main moves in an experimental paper
Facts
Concepts Problem
Implication
Hypothesis
Goal These results suggest that....
Method
Experiment
Results
Monday, April 2, 2012

91. Recursion/patterns of rhetoric:
Main moves in an experimental paper
Facts
Concepts Problem
Implication
Hypothesis
Transitions Goal These results suggest that....
Method
Experiment
Results
Monday, April 2, 2012

92. Mechanisms for realm transitions
Monday, April 2, 2012

93. Mechanisms for realm transitions
- Verb form change:
- Goal transitions:
- Regulatory segments:
Monday, April 2, 2012

94. 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:
Monday, April 2, 2012

95. 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:
Monday, April 2, 2012

96. 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).
Monday, April 2, 2012

97. Sentence-initial adverbials?
Monday, April 2, 2012

98. Sentence-initial adverbials?
- Not relevant for realm transitions:
- Relevant for realm transition?
Monday, April 2, 2012

99. Sentence-initial adverbials?
- Not relevant for realm transitions:
Furthermore, we confirmed the consistency of miRNA expression driven by
miRVec
by cloning eight miR-Vec plasmids expressing randomly chosen miRNAs.
With one exception, all constructs yielded high expression levels of mature
miRNAs (Figure S1).
Notably, very little pre-miRNA accumulation was detected in all cases,
indicating the efficient processing of the ectopically expressed miRNAs in the
cells.
- Relevant for realm transition?
Monday, April 2, 2012

100. Sentence-initial adverbials?
- Not relevant for realm transitions:
Furthermore, we confirmed the consistency of miRNA expression driven by
miRVec
by cloning eight miR-Vec plasmids expressing randomly chosen miRNAs.
With one exception, all constructs yielded high expression levels of mature
miRNAs (Figure S1).
Notably, very little pre-miRNA accumulation was detected in all cases,
indicating the efficient processing of the ectopically expressed miRNAs in the
cells.
-The third constructrealm transition? miR-Vec-371&2
Relevant for
did not overlap with
and encoded miRNA-373 and 373*.
Interestingly, the mature miR-373 is a homolog of miR-372,
and neither shares obvious homology with either miRNA-371 or miR-373*
(Fig.2D).
Monday, April 2, 2012

101. More general: verb form as realm indicator
Monday, April 2, 2012

102. More general: verb form as realm indicator
- Conceptual realm: ‘state’ (gnomic) present
‘Dopaminergic innervation plays a major role in the control of
mood and its perturbation’
Monday, April 2, 2012

103. More general: verb form as realm indicator
- Conceptual realm: ‘state’ (gnomic) present
‘Dopaminergic innervation plays a major role in the control of
mood and its perturbation’
- Experimental realm: ‘event’ past
‘Four out of seven cell lines expressed this cluster’,
‘Adult rats were individually housed for 2 days before
testing.’
Monday, April 2, 2012

104. More general: verb form as realm indicator
- Conceptual realm: ‘state’ (gnomic) present
‘Dopaminergic innervation plays a major role in the control of
mood and its perturbation’
- Experimental realm: ‘event’ past
‘Four out of seven cell lines expressed this cluster’,
‘Adult rats were individually housed for 2 days before
testing.’
- Argumentational realm: ‘instantaneous’ present; to-infinitive
‘These results suggest that...’, ‘To identify...’
Monday, April 2, 2012

105. More general: verb form as realm indicator
- Conceptual realm: ‘state’ (gnomic) present
‘Dopaminergic innervation plays a major role in the control of
mood and its perturbation’
- Experimental realm: ‘event’ past
‘Four out of seven cell lines expressed this cluster’,
‘Adult rats were individually housed for 2 days before
testing.’
- Argumentational realm: ‘instantaneous’ present; to-infinitive
‘These results suggest that...’, ‘To identify...’
- Discourse progression: ‘instantaneous’ present
‘Fig 2a shows that’, ‘see figure 7A’,
Monday, April 2, 2012

106. More general: verb form as realm indicator
- Conceptual realm: ‘state’ (gnomic) present
‘Dopaminergic innervation plays a major role in the control of
mood and its perturbation’
- Experimental realm: ‘event’ past
‘Four out of seven cell lines expressed this cluster’,
‘Adult rats were individually housed for 2 days before
testing.’
- Argumentational realm: ‘instantaneous’ present; to-infinitive
‘These results suggest that...’, ‘To identify...’
- Discourse progression: ‘instantaneous’ present
‘Fig 2a shows that’, ‘see figure 7A’,
- Reference to other work: present perfect - ‘finalised’ past
‘Previous work has demonstrated that VPCs are sensitive to
the levels of let-60/RAS (Han and Sternberg, 1990).’
Monday, April 2, 2012

107. ‘Referring Use of Tense’
Future
Monday, April 2, 2012

108. ‘Referring Use of Tense’
Concepts
‘Gnomic’ present
Future
Monday, April 2, 2012

109. ‘Referring Use of Tense’
Concepts
‘Gnomic’ present
Future
Experiment
Event past
Monday, April 2, 2012

110. ‘Referring Use of Tense’
Concepts
‘Gnomic’ present
Argumentation:
Instantaneous
present/To-inf
Future
Experiment
Event past
Monday, April 2, 2012

111. ‘Referring Use of Tense’
Concepts
‘Gnomic’ present
Argumentation:
Instantaneous
present/To-inf
Discourse
progression Future
Instantaneous
present
Experiment
Event past
Monday, April 2, 2012

112. ‘Referring Use of Tense’
Concepts
‘Gnomic’ present
Argumentation:
Instantaneous
present/To-inf
Other/Past
Work Discourse
Present progression Future
Instantaneous
present
Experiment
Event past
Monday, April 2, 2012

113. ‘Referring Use of Tense’
Concepts
‘Gnomic’ present
Argumentation:
Instantaneous
present/To-inf
Other/Past Future
Work Discourse Work
Present progression Future
Instantaneous
present
Experiment
Event past
Monday, April 2, 2012

114. Anecdotal excursion into mythological text:
Monday, April 2, 2012

115. Anecdotal excursion into mythological text:
Facts in the Endogenous small RNAs (miRNAs) I sing of golden-throned Hera whom Rhea
eternal regulate gene expression by mechanisms bare. Queen of the immortals is she, surpassing
conserved across metazoans. all in beauty: she is the sister and the wife of
present: loud-thundering Zeus, --the glorious one whom
all the blessed throughout high Olympus
reverence and honor.
Events in the Vehicle-treated animals spent equivalent Now the wooers turned to the dance and to
simple past: time investigating a juvenile in the first and gladsome song, and made them merry, and
second sessions in experiments conducted in waited till evening should come; and as they
the NAC and the striatum: T1 values were made merry dark evening came upon them.
122 ± 6 s and 114 ± 5 s.
Events with We also generated BJ/ET cells expressing And she took her mighty spear, tipped with
embedded the RASV12-ERTAM chimera gene, which sharp bronze, heavy and huge and strong,
is only active when tamoxifen is added (De wherewith she vanquishes the ranks of men-of
facts: Vita et al, 2005). warriors, with whom she is wroth, she, the
daughter of the mighty sire.
Attribution in miRNAs have emerged as important In this book I have had old stories written
the present regulators of development and control down, as I have heard them told by intelligent
processes such as cell fate determination and people, concerning chiefs who have held
perfect: cell death (Abrahante et al., 2003, Brennecke dominion in the northern countries, and who
et al., 2003, Chang et al., 2004, Chen et al., spoke the Danish tongue; and also concerning
2004, Johnston and Hobert, 2003, Lee et al., some of their family branches, according to
1993, ... what has been told me.
Implications These results indicate that although Now it is said that ever since then whenever
are hedged, & miR-372&3 confer complete protection to the camel sees a place where ashes have been
oncogene-induced senescence in a manner scattered, he wants to get revenge with his
present tense similar to p53 inactivation, the cellular enemy the rat and stomps and rolls in the ashes
+ that: response to DNA damage remains intact. hoping to get the rat.
Monday, April 2, 2012

116. Anecdotal excursion into mythological text:
Facts in the Endogenous small RNAs (miRNAs) I sing of golden-throned Hera whom Rhea
eternal regulate gene expression by mechanisms bare. Queen of the immortals is she, surpassing
conserved across metazoans. all in beauty: she is the sister and the wife of
present: loud-thundering Zeus, --the glorious one whom
all the blessed throughout high Olympus
reverence and honor.
Events in the Vehicle-treated animals spent equivalent Now the wooers turned to the dance and to
simple past: time investigating a juvenile in the first and gladsome song, and made them merry, and
second sessions in experiments conducted in waited till evening should come; and as they
the NAC and the striatum: T1 values were made merry dark evening came upon them.
122 ± 6 s and 114 ± 5 s.
Events with We also generated BJ/ET cells expressing And she took her mighty spear, tipped with
embedded the RASV12-ERTAM chimera gene, which sharp bronze, heavy and huge and strong,
is only active when tamoxifen is added (De wherewith she vanquishes the ranks of men-of
facts: Vita et al, 2005). warriors, with whom she is wroth, she, the
daughter of the mighty sire.
Attribution in miRNAs have emerged as important In this book I have had old stories written
the present regulators of development and control down, as I have heard them told by intelligent
processes such as cell fate determination and people, concerning chiefs who have held
perfect: cell death (Abrahante et al., 2003, Brennecke dominion in the northern countries, and who
et al., 2003, Chang et al., 2004, Chen et al., spoke the Danish tongue; and also concerning
2004, Johnston and Hobert, 2003, Lee et al., some of their family branches, according to
1993, ... what has been told me.
Implications These results indicate that although Now it is said that ever since then whenever
are hedged, & miR-372&3 confer complete protection to the camel sees a place where ashes have been
oncogene-induced senescence in a manner scattered, he wants to get revenge with his
present tense similar to p53 inactivation, the cellular enemy the rat and stomps and rolls in the ashes
+ that: response to DNA damage remains intact. hoping to get the rat.
Monday, April 2, 2012

117. Anecdotal excursion into mythological text:
Facts in the Endogenous small RNAs (miRNAs) I sing of golden-throned Hera whom Rhea
eternal regulate gene expression by mechanisms bare. Queen of the immortals is she, surpassing
conserved across metazoans. all in beauty: she is the sister and the wife of
present: loud-thundering Zeus, --the glorious one whom
all the blessed throughout high Olympus
reverence and honor.
Events in the Vehicle-treated animals spent equivalent Now the wooers turned to the dance and to
simple past: time investigating a juvenile in the first and gladsome song, and made them merry, and
second sessions in experiments conducted in waited till evening should come; and as they
the NAC and the striatum: T1 values were made merry dark evening came upon them.
122 ± 6 s and 114 ± 5 s.
Events with We also generated BJ/ET cells expressing And she took her mighty spear, tipped with
embedded the RASV12-ERTAM chimera gene, which sharp bronze, heavy and huge and strong,
is only active when tamoxifen is added (De wherewith she vanquishes the ranks of men-of
facts: Vita et al, 2005). warriors, with whom she is wroth, she, the
daughter of the mighty sire.
Attribution in miRNAs have emerged as important In this book I have had old stories written
the present regulators of development and control down, as I have heard them told by intelligent
processes such as cell fate determination and people, concerning chiefs who have held
perfect: cell death (Abrahante et al., 2003, Brennecke dominion in the northern countries, and who
et al., 2003, Chang et al., 2004, Chen et al., spoke the Danish tongue; and also concerning
2004, Johnston and Hobert, 2003, Lee et al., some of their family branches, according to
1993, ... what has been told me.
Implications These results indicate that although Now it is said that ever since then whenever
are hedged, & miR-372&3 confer complete protection to the camel sees a place where ashes have been
oncogene-induced senescence in a manner scattered, he wants to get revenge with his
present tense similar to p53 inactivation, the cellular enemy the rat and stomps and rolls in the ashes
+ that: response to DNA damage remains intact. hoping to get the rat.
Monday, April 2, 2012

118. Anecdotal excursion into mythological text:
Facts in the Endogenous small RNAs (miRNAs) I sing of golden-throned Hera whom Rhea
eternal regulate gene expression by mechanisms bare. Queen of the immortals is she, surpassing
conserved across metazoans. all in beauty: she is the sister and the wife of
present: loud-thundering Zeus, --the glorious one whom
all the blessed throughout high Olympus
reverence and honor.
Events in the Vehicle-treated animals spent equivalent Now the wooers turned to the dance and to
simple past: time investigating a juvenile in the first and gladsome song, and made them merry, and
second sessions in experiments conducted in waited till evening should come; and as they
the NAC and the striatum: T1 values were made merry dark evening came upon them.
122 ± 6 s and 114 ± 5 s.
Events with We also generated BJ/ET cells expressing And she took her mighty spear, tipped with
embedded the RASV12-ERTAM chimera gene, which sharp bronze, heavy and huge and strong,
is only active when tamoxifen is added (De wherewith she vanquishes the ranks of men-of
facts: Vita et al, 2005). warriors, with whom she is wroth, she, the
daughter of the mighty sire.
Attribution in miRNAs have emerged as important In this book I have had old stories written
the present regulators of development and control down, as I have heard them told by intelligent
processes such as cell fate determination and people, concerning chiefs who have held
perfect: cell death (Abrahante et al., 2003, Brennecke dominion in the northern countries, and who
et al., 2003, Chang et al., 2004, Chen et al., spoke the Danish tongue; and also concerning
2004, Johnston and Hobert, 2003, Lee et al., some of their family branches, according to
1993, ... what has been told me.
Implications These results indicate that although Now it is said that ever since then whenever
are hedged, & miR-372&3 confer complete protection to the camel sees a place where ashes have been
oncogene-induced senescence in a manner scattered, he wants to get revenge with his
present tense similar to p53 inactivation, the cellular enemy the rat and stomps and rolls in the ashes
+ that: response to DNA damage remains intact. hoping to get the rat.
Monday, April 2, 2012

119. Anecdotal excursion into mythological text:
Facts in the Endogenous small RNAs (miRNAs) I sing of golden-throned Hera whom Rhea
eternal regulate gene expression by mechanisms bare. Queen of the immortals is she, surpassing
conserved across metazoans. all in beauty: she is the sister and the wife of
present: loud-thundering Zeus, --the glorious one whom
all the blessed throughout high Olympus
reverence and honor.
Events in the Vehicle-treated animals spent equivalent Now the wooers turned to the dance and to
simple past: time investigating a juvenile in the first and gladsome song, and made them merry, and
second sessions in experiments conducted in waited till evening should come; and as they
the NAC and the striatum: T1 values were made merry dark evening came upon them.
122 ± 6 s and 114 ± 5 s.
Events with We also generated BJ/ET cells expressing And she took her mighty spear, tipped with
embedded the RASV12-ERTAM chimera gene, which sharp bronze, heavy and huge and strong,
is only active when tamoxifen is added (De wherewith she vanquishes the ranks of men-of
facts: Vita et al, 2005). warriors, with whom she is wroth, she, the
daughter of the mighty sire.
Attribution in miRNAs have emerged as important In this book I have had old stories written
the present regulators of development and control down, as I have heard them told by intelligent
processes such as cell fate determination and people, concerning chiefs who have held
perfect: cell death (Abrahante et al., 2003, Brennecke dominion in the northern countries, and who
et al., 2003, Chang et al., 2004, Chen et al., spoke the Danish tongue; and also concerning
2004, Johnston and Hobert, 2003, Lee et al., some of their family branches, according to
1993, ... what has been told me.
Implications These results indicate that although Now it is said that ever since then whenever
are hedged, & miR-372&3 confer complete protection to the camel sees a place where ashes have been
oncogene-induced senescence in a manner scattered, he wants to get revenge with his
present tense similar to p53 inactivation, the cellular enemy the rat and stomps and rolls in the ashes
+ that: response to DNA damage remains intact. hoping to get the rat.
Monday, April 2, 2012

120. Realms and planes: Patterns and Blends
Concepts
‘Present
Argumenta
tion:
present
Other/ Future
Past Discour Work
Present se Future
Present
Experiment
Past
Monday, April 2, 2012

121. Realms and planes: Patterns and Blends
Concepts
‘Present
Argumenta
tion:
present
Other/ Future
Past Discour Work
Present se Future
Present
Experiment
Past
Monday, April 2, 2012