‘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

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

“[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

TextText

Monday, April 2, 2012

“[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

TextText

Monday, April 2, 2012

Research Questions:

Monday, April 2, 2012

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

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

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

Method:

Monday, April 2, 2012

Method:1.Model for epistemic evaluation?

Monday, April 2, 2012

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

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

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

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

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

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

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

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 evaluationMonday, April 2, 2012

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.

Experimental Discourse

Monday, April 2, 2012

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.

Experimental DiscourseParsing

Monday, April 2, 2012

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.

Experimental Discourse

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.

Parsing

Monday, April 2, 2012

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.

Experimental Discourse

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

Parsing

Monday, April 2, 2012

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.

Experimental Discourse

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

Parsing

Monday, April 2, 2012

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.

Experimental Discourse

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

Parsing

Monday, April 2, 2012

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.

Experimental Discourse

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

Parsing

Monday, April 2, 2012

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.

Experimental Discourse

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

Parsing

Monday, April 2, 2012

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.

Experimental Discourse

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

Parsing

Monday, April 2, 2012

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.

Experimental Discourse

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

Parsing

Monday, April 2, 2012

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.

Experimental Discourse

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

Parsing

Monday, April 2, 2012

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.

Experimental Discourse

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

Parsing

Monday, April 2, 2012

Segment Types

Monday, April 2, 2012

Segment TypesSegment Description Example

Fact a known fact, generally without explicit citation

mature miR-373 is a homolog of miR-372

Hypothesis a proposed idea, not supported by evidence

This could for instance be a result of high mdm2 levels

Problem unresolved, contradictory, or unclear issue

However, further investigation is required to demonstrate the exact mechanism of LATS2 actionGoal research goal To identify novel functions of miRNAs,

Method experimental method Using fluorescence microscopy and luciferase assays,

Result a restatement of the outcome of an experiment

all constructs yielded high expression levels of mature miRNAs

Implication an interpretation of the results, in light of earlier hypotheses and facts

our procedure is sensitive enough to detect mild growth differences

Monday, April 2, 2012

Segment TypesSegment Description Example

Fact a known fact, generally without explicit citation

mature miR-373 is a homolog of miR-372

Hypothesis a proposed idea, not supported by evidence

This could for instance be a result of high mdm2 levels

Problem unresolved, contradictory, or unclear issue

However, further investigation is required to demonstrate the exact mechanism of LATS2 actionGoal research goal To identify novel functions of miRNAs,

Method experimental method Using fluorescence microscopy and luciferase assays,

Result a restatement of the outcome of an experiment

all constructs yielded high expression levels of mature miRNAs

Implication an interpretation of the results, in light of earlier hypotheses and facts

our procedure is sensitive enough to detect mild growth differences

‘Other-segments’, related to (referenced) other work - e.g. with reference

Monday, April 2, 2012

Segment TypesSegment Description Example

Fact a known fact, generally without explicit citation

mature miR-373 is a homolog of miR-372

Hypothesis a proposed idea, not supported by evidence

This could for instance be a result of high mdm2 levels

Problem unresolved, contradictory, or unclear issue

However, further investigation is required to demonstrate the exact mechanism of LATS2 actionGoal research goal To identify novel functions of miRNAs,

Method experimental method Using fluorescence microscopy and luciferase assays,

Result a restatement of the outcome of an experiment

all constructs yielded high expression levels of mature miRNAs

Implication an interpretation of the results, in light of earlier hypotheses and facts

our procedure is sensitive enough to detect 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

Realms in scholarly discourse: place of hedging

Monday, April 2, 2012

Realms in scholarly discourse: place of hedging

(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,

Monday, April 2, 2012

Realms in scholarly discourse: place of hedging

(1) Both seminomas and the EC component of nonseminomas share features with ES cells.

(2) b. the detection of miR-371-3 merely reflects its expression pattern in ES cells,

(2) a. To exclude that

Monday, April 2, 2012

Realms in scholarly discourse: place of hedging

(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

Monday, April 2, 2012

Realms in scholarly discourse: place of hedging

(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

Monday, April 2, 2012

Realms in scholarly discourse: place of hedging

(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

Monday, April 2, 2012

Realms in scholarly discourse: place of hedging

(3) c. miR-371-3 expression is a selective event during tumorigenesis.

(1) Both seminomas and the EC component of nonseminomas share features with ES cells.

(2) b. the detection of miR-371-3 merely reflects its expression pattern in ES cells,

(2) c. we tested by RPA miR-302a-d, another ES cells-specific miRNA cluster (Suh et al, 2004).

(3) a. In many of the miR-371-3 expressing seminomas and nonseminomas, miR-302a-d was undetectable (Figs S7 and S8),

Concepts, models, ‘facts’

(2) a. To exclude that (3) b. suggesting

Monday, April 2, 2012

Realms in scholarly discourse: place of hedging

(3) c. miR-371-3 expression is a selective event during tumorigenesis.

(1) Both seminomas and the EC component of nonseminomas share features with ES cells.

(2) b. the detection of miR-371-3 merely reflects its expression pattern in ES cells,

(2) c. we tested by RPA miR-302a-d, another ES cells-specific miRNA cluster (Suh et al, 2004).

(3) a. In many of the miR-371-3 expressing seminomas and nonseminomas, miR-302a-d was undetectable (Figs S7 and S8),

Concepts, models, ‘facts’

Experiment

(2) a. To exclude that (3) b. suggesting

Monday, April 2, 2012

Realms in scholarly discourse: place of hedging

(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

Monday, April 2, 2012

Hedging erosion in action

Monday, April 2, 2012

Hypothesis

To investigate the possibility that miR-372 and miR-373 suppress the

expression of LATS2, we...

Hedging erosion in action

Monday, April 2, 2012

Concepts

KnownFact KnownFact

Hypothesis

To investigate the possibility that miR-372 and miR-373 suppress the

expression of LATS2, we...

Hedging erosion in action

Monday, April 2, 2012

Concepts

KnownFact KnownFact

Experiment 1

Goal

Result

Data

Method

Hypothesis

To investigate the possibility that miR-372 and miR-373 suppress the

expression of LATS2, we...

Hedging erosion in action

Monday, April 2, 2012

Concepts

KnownFact KnownFact

Experiment 1

Goal

Result

Data

Method

Hypothesis

To investigate the possibility that miR-372 and miR-373 suppress the

expression of LATS2, we...

Implication

Therefore, these results point toLATS2 as a mediator of the miR-372 and miR-373 effects on cell proliferation and tumorigenicity,

Hedging erosion in action

Monday, April 2, 2012

Concepts

KnownFact KnownFact

Experiment 1

Goal

Result

Data

Method

Hypothesis

To investigate the possibility that miR-372 and miR-373 suppress the

expression of LATS2, we...

Implication

Therefore, these results point toLATS2 as a mediator of the miR-372 and miR-373 effects on cell proliferation and tumorigenicity,

Voorhoeve, 2006Hedging erosion in action

Monday, April 2, 2012

Concepts

KnownFact KnownFact

Experiment 1

Goal

Result

Data

Method

Goal

Experiment 2

Data

Method Result

Hypothesis

To investigate the possibility that miR-372 and miR-373 suppress the

expression of LATS2, we...

Implication

Therefore, these results point toLATS2 as a mediator of the miR-372 and miR-373 effects on cell proliferation and tumorigenicity,

Voorhoeve, 2006Hedging erosion in action

Monday, April 2, 2012

Concepts

KnownFact KnownFact

Experiment 1

Goal

Result

Data

Method

Goal

Experiment 2

Data

Method Result

Hypothesis

To investigate the possibility that miR-372 and miR-373 suppress the

expression of LATS2, we...

Implication

Therefore, these results point toLATS2 as a mediator of the miR-372 and miR-373 effects on cell proliferation and tumorigenicity,

Fact

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

Voorhoeve, 2006Hedging erosion in action

Monday, April 2, 2012

Concepts

KnownFact KnownFact

Experiment 1

Goal

Result

Data

Method

Goal

Experiment 2

Data

Method Result

Hypothesis

To investigate the possibility that miR-372 and miR-373 suppress the

expression of LATS2, we...

Implication

Therefore, these results point toLATS2 as a mediator of the miR-372 and miR-373 effects on cell proliferation and tumorigenicity,

Fact

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

Voorhoeve, 2006Hedging erosion in action

Monday, April 2, 2012

Concepts

KnownFact KnownFact

Experiment 1

Goal

Result

Data

Method

Goal

Experiment 2

Data

Method Result

Hypothesis

To investigate the possibility that miR-372 and miR-373 suppress the

expression of LATS2, we...

Implication

Therefore, these results point toLATS2 as a mediator of the miR-372 and miR-373 effects on cell proliferation and tumorigenicity,

Fact

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

Voorhoeve, 2006

http://elsatglabs.com/labs/anita/demos/LATSDemo102007/

Hedging erosion in action

Monday, April 2, 2012

Logical structure of epistemic evaluations:

Monday, April 2, 2012

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:ReasoningData

- S = Source:A = speaker is author A, explicitIA = speaker author, A, implicitN = other author N, explicitNN = other author NN, implicit

Monday, April 2, 2012

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:ReasoningData

- S = Source:A = speaker is author A, explicitIA = speaker author, A, implicitN = other author N, explicitNN = other author NN, implicit

Model suggested by Eduard Hovy, Information Sciences Institute University South Califormia

Monday, April 2, 2012

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 short of complete certainty

suggesting the presence of lineage-specific elements.

3 – Doxastic: complete certainty, accepted/known/proven fact

the 1.6 kb 5' flanking region of CCR3 has promoter 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 author/speaker or current paper as source

We hypothesize that…’; ‘Figure 2a shows that…

N - Named external source, either explicitly or as a reference

…several reports have documented this expression [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

Some examples:

Monday, April 2, 2012

Epistemic Markers

Monday, April 2, 2012

Epistemic Markers

- Modal auxiliary verbs (e.g. can, could, might)

Monday, April 2, 2012

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

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

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

Markers v. Types: 1 paper, 640 segments

ValueValue Modal Aux

Reporting Verb

Ruled by RV

Adverbs/Adjectives

References

None Total

Total value = 3Total value = 3 1 (0.5%) 81 (40%) 24 (12%) 7 (4%) 41 (20%) 47 (24%) 201(100%)

Total Value = 2Total Value = 2 29 (51%) 23 (40%) 1 (2%) 4(7%) 57(100%)

Total Value = 1Total Value = 1 9(27%) 11(33%) 11(33%) 1(3%) 1(3%) 33(100%)

Total Value = 0Total Value = 0 9 (64%) 3 (21%) 1(7%) 1(7%) 14(100%)

Total No Modality

16(37%) 3(7%) 0 3(7%) 22(50%) 44(100%)

Overall TotalOverall Total 10 (2%) 146(23%) 64(10%) 10(2%) 50(8%) 69(11%) 640(100%)

Monday, April 2, 2012

Markers v. Types: 1 paper, 640 segments

ValueValue Modal Aux

Reporting Verb

Ruled by RV

Adverbs/Adjectives

References

None Total

Total value = 3Total value = 3 1 (0.5%) 81 (40%) 24 (12%) 7 (4%) 41 (20%) 47 (24%) 201(100%)

Total Value = 2Total Value = 2 29 (51%) 23 (40%) 1 (2%) 4(7%) 57(100%)

Total Value = 1Total Value = 1 9(27%) 11(33%) 11(33%) 1(3%) 1(3%) 33(100%)

Total Value = 0Total Value = 0 9 (64%) 3 (21%) 1(7%) 1(7%) 14(100%)

Total No Modality

16(37%) 3(7%) 0 3(7%) 22(50%) 44(100%)

Overall TotalOverall Total 10 (2%) 146(23%) 64(10%) 10(2%) 50(8%) 69(11%) 640(100%)

Monday, April 2, 2012

Markers v. Types: 1 paper, 640 segments

ValueValue Modal Aux

Reporting Verb

Ruled by RV

Adverbs/Adjectives

References

None Total

Total value = 3Total value = 3 1 (0.5%) 81 (40%) 24 (12%) 7 (4%) 41 (20%) 47 (24%) 201(100%)

Total Value = 2Total Value = 2 29 (51%) 23 (40%) 1 (2%) 4(7%) 57(100%)

Total Value = 1Total Value = 1 9(27%) 11(33%) 11(33%) 1(3%) 1(3%) 33(100%)

Total Value = 0Total Value = 0 9 (64%) 3 (21%) 1(7%) 1(7%) 14(100%)

Total No Modality

16(37%) 3(7%) 0 3(7%) 22(50%) 44(100%)

Overall TotalOverall Total 10 (2%) 146(23%) 64(10%) 10(2%) 50(8%) 69(11%) 640(100%)

Monday, April 2, 2012

Markers v. Types: 1 paper, 640 segments

ValueValue Modal Aux

Reporting Verb

Ruled by RV

Adverbs/Adjectives

References

None Total

Total value = 3Total value = 3 1 (0.5%) 81 (40%) 24 (12%) 7 (4%) 41 (20%) 47 (24%) 201(100%)

Total Value = 2Total Value = 2 29 (51%) 23 (40%) 1 (2%) 4(7%) 57(100%)

Total Value = 1Total Value = 1 9(27%) 11(33%) 11(33%) 1(3%) 1(3%) 33(100%)

Total Value = 0Total Value = 0 9 (64%) 3 (21%) 1(7%) 1(7%) 14(100%)

Total No Modality

16(37%) 3(7%) 0 3(7%) 22(50%) 44(100%)

Overall TotalOverall Total 10 (2%) 146(23%) 64(10%) 10(2%) 50(8%) 69(11%) 640(100%)

Monday, April 2, 2012

Reporting verbs vs. epistemic value:

Monday, April 2, 2012

Reporting verbs vs. epistemic value:

Value = 0 (unknown)

establish, (remain to be) elucidated, be (clear/useful), (remain to be) examined/determined, describe, make difficult to infer, report

Value = 1 (hypothetical)

be important, consider, expect, hypothesize (5x), give insight, raise possibility that, suspect, think

Value = 2 (probable)

appear, believe, implicate (2x), imply, indicate (12x), play a role, represent, suggest (18x), validate (2x),

Value = 3 (presumed true)

be able/apparent/important /positive/visible, compare (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

Most prevalent clause type: “These results suggest that...”

Monday, April 2, 2012

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

Can we find this automatically?‘Claimed knowledge updates’:

Work done with Agnes Sandor, Xerox Research Europe

Monday, April 2, 2012

Preliminary steps towards citation analysis:

Work done with Lucy Vanderwende, Microsoft Research

Type Voorhoeve text Citing text

Method We subsequently created a human miRNA expression library (miR-Lib) by cloning almost all annotated human miRNAs into our vector (Rfam release 6) (Figure S3)

Voorhoeve et al. (116) employed a novel strategy by combining an miRNA vector library and corresponding bar code array Using a novel retroviral miRNA expression library,

Agami and co-workers performed a cell-based screen

Result we identified miR-372 and miR-373, each permitting proliferation and tumorigenesis of primary human cells that harbor both oncogenic RAS and active wild - type p53.

miR-372 and miR-373 were consequently found to permit proliferation and tumorigenesis of these primary cells carrying both oncogenic RAS and wild-type p53,

Voorhoeve et al. (2006) identified miR-372 and miR-373 miR-372 has been recently described as potential

oncogene that collaborate with oncogenic RAS in cellular transformation

Interpretation

These miRNAs neutralize p53- mediated CDK inhibition, possibly through direct inhibition of the expression of the tumor suppressor LATS2 .

probably through direct inhibition of the expression of the tumor-suppressor LATS2 and subsequent neutralization of the p53 pathway.

Compromised Lats2 functionality might reduce the selective pressure for p53 inactivation during tumor progressionRas activation.

Monday, April 2, 2012

Conclusions:

Monday, April 2, 2012

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

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

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

Next steps:

Monday, April 2, 2012

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

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

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

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

Tense and Mythology

Monday, April 2, 2012

Recursion/patterns of rhetoric: Main moves in an experimental paper

Monday, April 2, 2012

Recursion/patterns of rhetoric: Main moves in an experimental paper

Facts

Hypothesis

Problem

Monday, April 2, 2012

Recursion/patterns of rhetoric: Main moves in an experimental paper

Facts

Hypothesis

Problem

Goal

Monday, April 2, 2012

Recursion/patterns of rhetoric: Main moves in an experimental paper

Facts

Hypothesis

Problem

Method

Results

Goal

Monday, April 2, 2012

Recursion/patterns of rhetoric: Main moves in an experimental paper

Facts

Hypothesis

Problem

Method

Results

Goal These results suggest that....

Monday, April 2, 2012

Recursion/patterns of rhetoric: Main moves in an experimental paper

Facts

Hypothesis

Problem

Method

Results

Implication

Goal These results suggest that....

Monday, April 2, 2012

Recursion/patterns of rhetoric: Main moves in an experimental paper

Facts

Hypothesis

Problem

Method

Results

Implication

Goal These results suggest that....

Concepts

Monday, April 2, 2012

Recursion/patterns of rhetoric: Main moves in an experimental paper

Facts

Hypothesis

Problem

Method

Results

Implication

Goal These results suggest that....

Experiment

Concepts

Monday, April 2, 2012

Recursion/patterns of rhetoric: Main moves in an experimental paper

Facts

Hypothesis

Problem

Method

Results

Implication

Goal These results suggest that....Transitions

Experiment

Concepts

Monday, April 2, 2012

Mechanisms for realm transitions

Monday, April 2, 2012

Mechanisms for realm transitions

- Verb form change:

- Goal transitions:

- Regulatory segments:

Monday, April 2, 2012

Mechanisms for realm transitions

- Verb form change:

- Goal transitions:

- Regulatory segments:

Whereas all three cluster-expressing cell lines contained high wt-p53 levels,NTera2 has low wild-type p53 levels,and NCCIT lost one p53 allelewhile the second allele is mutated (Burger et al, 1998).

Monday, April 2, 2012

Mechanisms for realm transitions

- Verb form change:

- Goal transitions:

- Regulatory segments:

Whereas all three cluster-expressing cell lines contained high wt-p53 levels,NTera2 has low wild-type p53 levels,and NCCIT lost one p53 allelewhile the second allele is mutated (Burger et al, 1998).

Additionally, we made a corresponding microarray (miR-Array) containing all miR-Lib inserts,which allows the detection of miRNA effects on proliferation.To test the sensitivity of screens with miR-Lib and miR-Array,We transduced modified primary BJ fibroblasts expressing ecotropic receptor...

Monday, April 2, 2012

Mechanisms for realm transitions

- Verb form change:

- Goal transitions:

- Regulatory segments:

Whereas all three cluster-expressing cell lines contained high wt-p53 levels,NTera2 has low wild-type p53 levels,and NCCIT lost one p53 allelewhile the second allele is mutated (Burger et al, 1998).

Additionally, we made a corresponding microarray (miR-Array) containing all miR-Lib inserts,which allows the detection of miRNA effects on proliferation.To test the sensitivity of screens with miR-Lib and miR-Array,We transduced modified primary BJ fibroblasts expressing ecotropic receptor...

In accordance, we observed an approximately 4-fold increase in miR311 signal, indicating that our procedure is sensitive enough to detect mild growth differences (Fig 1E).

Monday, April 2, 2012

Sentence-initial adverbials?

Monday, April 2, 2012

Sentence-initial adverbials?

- Not relevant for realm transitions:

- Relevant for realm transition?

Monday, April 2, 2012

Sentence-initial adverbials?

- Not relevant for realm transitions:

- Relevant for realm transition?

Furthermore, we confirmed the consistency of miRNA expression driven by miRVecby 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.

Monday, April 2, 2012

Sentence-initial adverbials?

- Not relevant for realm transitions:

- Relevant for realm transition?

Furthermore, we confirmed the consistency of miRNA expression driven by miRVecby 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 construct did not overlap with miR-Vec-371&2 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

More general: verb form as realm indicator

Monday, April 2, 2012

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

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

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

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

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

‘Referring Use of Tense’

Future

Monday, April 2, 2012

‘Referring Use of Tense’Concepts

‘Gnomic’ present

Future

Monday, April 2, 2012

‘Referring Use of Tense’

Experiment Event past

Concepts‘Gnomic’ present

Future

Monday, April 2, 2012

‘Referring Use of Tense’

Argumentation:

Instantaneous present/To-inf

Experiment Event past

Concepts‘Gnomic’ present

Future

Monday, April 2, 2012

‘Referring Use of Tense’

Argumentation:

Instantaneous present/To-inf

Experiment Event past

Concepts‘Gnomic’ present

Discourse progressionInstantaneous

present

Future

Monday, April 2, 2012

‘Referring Use of Tense’

Argumentation:

Instantaneous present/To-inf

Experiment Event past

Concepts‘Gnomic’ present

Discourse progressionInstantaneous

present

Other/Past WorkPresent Future

Monday, April 2, 2012

‘Referring Use of Tense’

Argumentation:

Instantaneous present/To-inf

Experiment Event past

Concepts‘Gnomic’ present

Discourse progressionInstantaneous

present

Other/Past WorkPresent

Future WorkFuture

Monday, April 2, 2012

Anecdotal excursion into mythological text:

Monday, April 2, 2012

Facts in the eternal present:

Endogenous small RNAs (miRNAs) regulate gene expression by mechanisms conserved across metazoans.

I sing of golden-throned Hera whom Rhea bare. Queen of the immortals is she, surpassing all in beauty: she is the sister and the wife of loud-thundering Zeus, --the glorious one whom all the blessed throughout high Olympus reverence and honor.

Events in the simple past:

Vehicle-treated animals spent equivalent time investigating a juvenile in the first and second sessions in experiments conducted in the NAC and the striatum: T1 values were 122 ± 6 s and 114 ± 5 s.

Now the wooers turned to the dance and to gladsome song, and made them merry, and waited till evening should come; and as they made merry dark evening came upon them.

Events with embedded facts:

We also generated BJ/ET cells expressing the RASV12-ERTAM chimera gene, which is only active when tamoxifen is added (De Vita et al, 2005).

And she took her mighty spear, tipped with sharp bronze, heavy and huge and strong, wherewith she vanquishes the ranks of men-of warriors, with whom she is wroth, she, the daughter of the mighty sire.

Attribution in the present perfect:

miRNAs have emerged as important regulators of development and control processes such as cell fate determination and cell death (Abrahante et al., 2003, Brennecke et al., 2003, Chang et al., 2004, Chen et al., 2004, Johnston and Hobert, 2003, Lee et al., 1993, ...

In this book I have had old stories written down, as I have heard them told by intelligent people, concerning chiefs who have held dominion in the northern countries, and who spoke the Danish tongue; and also concerning some of their family branches, according to what has been told me.

Implications are hedged, & present tense + that:

These results indicate that although miR-372&3 confer complete protection to oncogene-induced senescence in a manner similar to p53 inactivation, the cellular response to DNA damage remains intact.

Now it is said that ever since then whenever the camel sees a place where ashes have been scattered, he wants to get revenge with his enemy the rat and stomps and rolls in the ashes hoping to get the rat.

Anecdotal excursion into mythological text:

Monday, April 2, 2012

Facts in the eternal present:

Endogenous small RNAs (miRNAs) regulate gene expression by mechanisms conserved across metazoans.

I sing of golden-throned Hera whom Rhea bare. Queen of the immortals is she, surpassing all in beauty: she is the sister and the wife of loud-thundering Zeus, --the glorious one whom all the blessed throughout high Olympus reverence and honor.

Events in the simple past:

Vehicle-treated animals spent equivalent time investigating a juvenile in the first and second sessions in experiments conducted in the NAC and the striatum: T1 values were 122 ± 6 s and 114 ± 5 s.

Now the wooers turned to the dance and to gladsome song, and made them merry, and waited till evening should come; and as they made merry dark evening came upon them.

Events with embedded facts:

We also generated BJ/ET cells expressing the RASV12-ERTAM chimera gene, which is only active when tamoxifen is added (De Vita et al, 2005).

And she took her mighty spear, tipped with sharp bronze, heavy and huge and strong, wherewith she vanquishes the ranks of men-of warriors, with whom she is wroth, she, the daughter of the mighty sire.

Attribution in the present perfect:

miRNAs have emerged as important regulators of development and control processes such as cell fate determination and cell death (Abrahante et al., 2003, Brennecke et al., 2003, Chang et al., 2004, Chen et al., 2004, Johnston and Hobert, 2003, Lee et al., 1993, ...

In this book I have had old stories written down, as I have heard them told by intelligent people, concerning chiefs who have held dominion in the northern countries, and who spoke the Danish tongue; and also concerning some of their family branches, according to what has been told me.

Implications are hedged, & present tense + that:

These results indicate that although miR-372&3 confer complete protection to oncogene-induced senescence in a manner similar to p53 inactivation, the cellular response to DNA damage remains intact.

Now it is said that ever since then whenever the camel sees a place where ashes have been scattered, he wants to get revenge with his enemy the rat and stomps and rolls in the ashes hoping to get the rat.

Anecdotal excursion into mythological text:

Monday, April 2, 2012

Facts in the eternal present:

Endogenous small RNAs (miRNAs) regulate gene expression by mechanisms conserved across metazoans.

I sing of golden-throned Hera whom Rhea bare. Queen of the immortals is she, surpassing all in beauty: she is the sister and the wife of loud-thundering Zeus, --the glorious one whom all the blessed throughout high Olympus reverence and honor.

Events in the simple past:

Vehicle-treated animals spent equivalent time investigating a juvenile in the first and second sessions in experiments conducted in the NAC and the striatum: T1 values were 122 ± 6 s and 114 ± 5 s.

Now the wooers turned to the dance and to gladsome song, and made them merry, and waited till evening should come; and as they made merry dark evening came upon them.

Events with embedded facts:

We also generated BJ/ET cells expressing the RASV12-ERTAM chimera gene, which is only active when tamoxifen is added (De Vita et al, 2005).

And she took her mighty spear, tipped with sharp bronze, heavy and huge and strong, wherewith she vanquishes the ranks of men-of warriors, with whom she is wroth, she, the daughter of the mighty sire.

Attribution in the present perfect:

miRNAs have emerged as important regulators of development and control processes such as cell fate determination and cell death (Abrahante et al., 2003, Brennecke et al., 2003, Chang et al., 2004, Chen et al., 2004, Johnston and Hobert, 2003, Lee et al., 1993, ...

In this book I have had old stories written down, as I have heard them told by intelligent people, concerning chiefs who have held dominion in the northern countries, and who spoke the Danish tongue; and also concerning some of their family branches, according to what has been told me.

Implications are hedged, & present tense + that:

These results indicate that although miR-372&3 confer complete protection to oncogene-induced senescence in a manner similar to p53 inactivation, the cellular response to DNA damage remains intact.

Now it is said that ever since then whenever the camel sees a place where ashes have been scattered, he wants to get revenge with his enemy the rat and stomps and rolls in the ashes hoping to get the rat.

Anecdotal excursion into mythological text:

Monday, April 2, 2012

Facts in the eternal present:

Endogenous small RNAs (miRNAs) regulate gene expression by mechanisms conserved across metazoans.

I sing of golden-throned Hera whom Rhea bare. Queen of the immortals is she, surpassing all in beauty: she is the sister and the wife of loud-thundering Zeus, --the glorious one whom all the blessed throughout high Olympus reverence and honor.

Events in the simple past:

Vehicle-treated animals spent equivalent time investigating a juvenile in the first and second sessions in experiments conducted in the NAC and the striatum: T1 values were 122 ± 6 s and 114 ± 5 s.

Now the wooers turned to the dance and to gladsome song, and made them merry, and waited till evening should come; and as they made merry dark evening came upon them.

Events with embedded facts:

We also generated BJ/ET cells expressing the RASV12-ERTAM chimera gene, which is only active when tamoxifen is added (De Vita et al, 2005).

And she took her mighty spear, tipped with sharp bronze, heavy and huge and strong, wherewith she vanquishes the ranks of men-of warriors, with whom she is wroth, she, the daughter of the mighty sire.

Attribution in the present perfect:

miRNAs have emerged as important regulators of development and control processes such as cell fate determination and cell death (Abrahante et al., 2003, Brennecke et al., 2003, Chang et al., 2004, Chen et al., 2004, Johnston and Hobert, 2003, Lee et al., 1993, ...

In this book I have had old stories written down, as I have heard them told by intelligent people, concerning chiefs who have held dominion in the northern countries, and who spoke the Danish tongue; and also concerning some of their family branches, according to what has been told me.

Implications are hedged, & present tense + that:

These results indicate that although miR-372&3 confer complete protection to oncogene-induced senescence in a manner similar to p53 inactivation, the cellular response to DNA damage remains intact.

Now it is said that ever since then whenever the camel sees a place where ashes have been scattered, he wants to get revenge with his enemy the rat and stomps and rolls in the ashes hoping to get the rat.

Anecdotal excursion into mythological text:

Monday, April 2, 2012

Facts in the eternal present:

Endogenous small RNAs (miRNAs) regulate gene expression by mechanisms conserved across metazoans.

I sing of golden-throned Hera whom Rhea bare. Queen of the immortals is she, surpassing all in beauty: she is the sister and the wife of loud-thundering Zeus, --the glorious one whom all the blessed throughout high Olympus reverence and honor.

Events in the simple past:

Vehicle-treated animals spent equivalent time investigating a juvenile in the first and second sessions in experiments conducted in the NAC and the striatum: T1 values were 122 ± 6 s and 114 ± 5 s.

Now the wooers turned to the dance and to gladsome song, and made them merry, and waited till evening should come; and as they made merry dark evening came upon them.

Events with embedded facts:

We also generated BJ/ET cells expressing the RASV12-ERTAM chimera gene, which is only active when tamoxifen is added (De Vita et al, 2005).

And she took her mighty spear, tipped with sharp bronze, heavy and huge and strong, wherewith she vanquishes the ranks of men-of warriors, with whom she is wroth, she, the daughter of the mighty sire.

Attribution in the present perfect:

miRNAs have emerged as important regulators of development and control processes such as cell fate determination and cell death (Abrahante et al., 2003, Brennecke et al., 2003, Chang et al., 2004, Chen et al., 2004, Johnston and Hobert, 2003, Lee et al., 1993, ...

In this book I have had old stories written down, as I have heard them told by intelligent people, concerning chiefs who have held dominion in the northern countries, and who spoke the Danish tongue; and also concerning some of their family branches, according to what has been told me.

Implications are hedged, & present tense + that:

These results indicate that although miR-372&3 confer complete protection to oncogene-induced senescence in a manner similar to p53 inactivation, the cellular response to DNA damage remains intact.

Now it is said that ever since then whenever the camel sees a place where ashes have been scattered, he wants to get revenge with his enemy the rat and stomps and rolls in the ashes hoping to get the rat.

Anecdotal excursion into mythological text:

Monday, April 2, 2012

Argumentation:

present

Experiment Past

Concepts‘Present

Discourse

Present

Other/Past

Present

Future WorkFuture

Realms and planes: Patterns and Blends

Monday, April 2, 2012

Argumentation:

present

Experiment Past

Concepts‘Present

Discourse

Present

Other/Past

Present

Future WorkFuture

Realms and planes: Patterns and Blends

Monday, April 2, 2012

Markers vs. TypesValue Basis Source Modal

Aux Reporting Verb

Ruled by RV

Adverbs/Adjectives

References

None Total

3 0 0 8 83 0 IA 5 2 2 93 0 N 8 5 2 8 2 253 0 NN 1 2 2 12 173 D A 20 1 16 2 393 D IA 33 6 1 9 17 623 D N 7 7 1 8 6 293 D NN 3 33 R IA 2 1 1 43 R NN 1 1Total value = 3

1 (0.5%)

81 (40%)

24 (12%)

7 (4%) 41 (20%)

47 (24%)

201(100%)2 0 N 1 1 2

2 0 NN 1 1 22 D 0 1 12 D A 1 12 D IA 22 17 1 402 D NN 1 12 R 0 2 1 1 42 R IA 2 1 32 R N 1 1 22 R NN 1 1Total Value = 2

0 29 (51%)

23 (40%)

1 (2%) 4(7%) 0 57(100%)1 0 0 1 1

1 0 NN 1 1 1 1 41 D IA 5 5 3 1 141 R A 2 2 5 91 R IA 1 1 21 R NN 2 1 3Total Value = 1

9(27%) 11(33%) 11(33%) 1(3%) 1(3%) 0 33(100%)0 0 0 6 1 7

0 0 N 1 1 20 D 0 1 10 D N 1 10 D NN 1 10 R A 1 10 R IA 1 1Total Value = 0

0 9 (64%) 3 (21%) 1(7%) 1(7%) 0 14(100%)Total

No Modalit

0 16 3 0 3 22 44Overall Total

10 (2%) 146(23%)

64(10%)

10(2%) 50(8%) 69(11%) 640(100%)

Monday, April 2, 2012