How to Troubleshoot Apps for the Modern Connected Worker
Xerox2009
1. Identifying Biological Knowledge:
Three Possible Strategies
Anita de Waard
Disruptive Technologies Director,
Elsevier Labs, Amsterdam
Casimir Researcher,
UiL-OTS, Utrecht University
XRCE, Grenoble, 24 September 2009
4. Overview
Problem: too much discourse, tools are not yet good
enough...
1. First attempt: allow authors to validate entities
5. Overview
Problem: too much discourse, tools are not yet good
enough...
1. First attempt: allow authors to validate entities
2. Second attempt: discourse analysis
6. Overview
Problem: too much discourse, tools are not yet good
enough...
1. First attempt: allow authors to validate entities
2. Second attempt: discourse analysis
3. Third attempt: collaboration to identify hypotheses
10. Why Study Biological Discourse?
- There is too much of it!
- Text mining and ‘fact
extraction’ techniques are
gaining ground to tame this
tangle
11. Why Study Biological Discourse?
- There is too much of it!
- Text mining and ‘fact
extraction’ techniques are
gaining ground to tame this
tangle
- Emerging area of biological
natural language processing
(BioNLP): subfield of computational linguistics
12. Why Study Biological Discourse?
- There is too much of it!
- Text mining and ‘fact
extraction’ techniques are
gaining ground to tame this
tangle
- Emerging area of biological
natural language processing
(BioNLP): subfield of computational linguistics
- Main focus: identifying biological entities (genes,
proteins, drugs) and their relationships
14. Example state of the art: MEDIE
Alteration of nm23, P53, and S100A4 expression may
contribute to the development of gastric
15. Example state of the art: MEDIE
Alteration of nm23, P53, and S100A4 expression may
contribute to the development of gastric
Previous studies have implicated miR-34a as a tumor
suppressor gene whose transcription is activated by p53.
16. Example state of the art: MEDIE
Add this knowledge during authoring?
Alteration of nm23, P53, and S100A4 expression may
contribute to the development of gastric
Previous studies have implicated miR-34a as a tumor
suppressor gene whose transcription is activated by p53.
19. Improve time + quality of knowledgebase entry
- For database curators: save time and money
20. Improve time + quality of knowledgebase entry
- For database curators: save time and money
- For authors: lower the threshold to submitting papers with
metadata
21. Improve time + quality of knowledgebase entry
- For database curators: save time and money
- For authors: lower the threshold to submitting papers with
metadata
- Structured Digital Abstract: an editorial experiment to increase
the reach of online published articles
22. Improve time + quality of knowledgebase entry
- For database curators: save time and money
- For authors: lower the threshold to submitting papers with
metadata
- Structured Digital Abstract: an editorial experiment to increase
the reach of online published articles
- SDA encodes in a schema information contained in the article
23. expression of GSG1 stimulates TPAP targeting to the
ER, suggesting that interactions between the two
proteins lead to the redistribution of TPAP from the
cytosol to the ER.
MINT-6168263:
Gsg1 (uniprotkb:Q8R1W2), TPAP
(uniprotkb:Q9WVP6) and Calmegin
(uniprotkb:P52194) colocalize (MI:0403) by
cosedimentation (MI:0027)
MINT-6168204, MINT-6168178:
Gsg1 (uniprotkb:Q8R1W2) and TPAP
(uniprotkb:Q9WVP6) colocalize (MI:0403) by
fluorescence microscopy (MI:0416)
MINT-6167930:
Gsg1 (uniprotkb:Q8R1W2) physically interacts (MI:
24. expression of GSG1 stimulates TPAP targeting to the
ER, suggesting that interactions between the two
proteins lead to the redistribution of TPAP from the
cytosol to the ER.
MINT-6168263:
Gsg1 (uniprotkb:Q8R1W2), TPAP
(uniprotkb:Q9WVP6) and Calmegin
(uniprotkb:P52194) colocalize (MI:0403) by
cosedimentation (MI:0027)
MINT-6168204, MINT-6168178:
Gsg1 (uniprotkb:Q8R1W2) and TPAP
(uniprotkb:Q9WVP6) colocalize (MI:0403) by
fluorescence microscopy (MI:0416)
MINT-6167930:
Gsg1 (uniprotkb:Q8R1W2) physically interacts (MI:
25. expression of GSG1 stimulates TPAP targeting to the
ER, suggesting that interactions between the two
proteins lead to the redistribution of TPAP from the
cytosol to the ER.
MINT-6168263:
Gsg1 (uniprotkb:Q8R1W2), TPAP
(uniprotkb:Q9WVP6) and Calmegin
(uniprotkb:P52194) colocalize (MI:0403) by
cosedimentation (MI:0027)
MINT-6168204, MINT-6168178:
Gsg1 (uniprotkb:Q8R1W2) and TPAP
(uniprotkb:Q9WVP6) colocalize (MI:0403) by
fluorescence microscopy (MI:0416)
MINT-6167930:
Gsg1 (uniprotkb:Q8R1W2) physically interacts (MI:
26. expression of GSG1 stimulates TPAP targeting to the
ER, suggesting that interactions between the two
proteins lead to the redistribution of TPAP from the
cytosol to the ER.
MINT-6168263:
Gsg1 (uniprotkb:Q8R1W2), TPAP
(uniprotkb:Q9WVP6) and Calmegin
(uniprotkb:P52194) colocalize (MI:0403) by
cosedimentation (MI:0027)
MINT-6168204, MINT-6168178:
Gsg1 (uniprotkb:Q8R1W2) and TPAP
(uniprotkb:Q9WVP6) colocalize (MI:0403) by
fluorescence microscopy (MI:0416)
MINT-6167930:
Gsg1 (uniprotkb:Q8R1W2) physically interacts (MI:
27. expression of GSG1 stimulates TPAP targeting to the
ER, suggesting that interactions between the two
proteins lead to the redistribution of TPAP from the
cytosol to the ER.
MINT-6168263:
Gsg1 (uniprotkb:Q8R1W2), TPAP
(uniprotkb:Q9WVP6) and Calmegin
(uniprotkb:P52194) colocalize (MI:0403) by
cosedimentation (MI:0027)
MINT-6168204, MINT-6168178:
Gsg1 (uniprotkb:Q8R1W2) and TPAP
(uniprotkb:Q9WVP6) colocalize (MI:0403) by
fluorescence microscopy (MI:0416)
MINT-6167930:
Gsg1 (uniprotkb:Q8R1W2) physically interacts (MI:
29. How? Word Plugin
- Okkam4MsW: a Microsoft Word plugin interact with Web Services performing NLP
and semantic technologies to detect entities and contextual information
- The OKKAM repository is queried to get the right OKKAM id and alternative ids
(UniProt in this case)
5
30. How? Word Plugin
- Okkam4MsW: a Microsoft Word plugin interact with Web Services performing NLP
and semantic technologies to detect entities and contextual information
- The OKKAM repository is queried to get the right OKKAM id and alternative ids
(UniProt in this case)
5
38. What else is wrong with MEDIE?
Alteration of nm23, P53, and S100A4 expression may
contribute to the development of gastric
39. What else is wrong with MEDIE?
Alteration of nm23, P53, and S100A4 expression may
contribute to the development of gastric
Previous studies have implicated miR-34a as a tumor
suppressor gene whose transcription is activated by p53.
40. What else is wrong with MEDIE?
without some idea of the status of the
sentence, it cannot be interpreted!
Alteration of nm23, P53, and S100A4 expression may
contribute to the development of gastric
Previous studies have implicated miR-34a as a tumor
suppressor gene whose transcription is activated by p53.
42. Discourse Analysis
Underlying model of text mining systems:
- Scientific paper is ‘statement of pertinent facts’
- So: finding entities and relationships will give you a summary of
the knowledge within the paper
- However, information extracted this way is not very useful....
43. Discourse Analysis
Underlying model of text mining systems:
- Scientific paper is ‘statement of pertinent facts’
- So: finding entities and relationships will give you a summary of
the knowledge within the paper
- However, information extracted this way is not very useful....
Proposed approach: treat scientific paper as a persuasive text: specific
genre, with genre characteristics and allowed persuasive techniques:
- ‘these results suggest’ (depersonification)
- ‘as fig. 2a shows’ (evidence is in the data)
- ‘oncogenes produce a stress response [Serrano, 2003]’
References and data form a “folded array of successive defense lines, behind
which scientists ensconce themselves” (Latour, 1986)
46. Overall Research Questions
i. How can we model the discourse/suasive moves in a
biological paper?
ii. Can this model help enable automated epistemic
markup?
47. Overall Research Questions
i. How can we model the discourse/suasive moves in a
biological paper?
ii. Can this model help enable automated epistemic
markup?
iii. Can it improve knowledge representations of
collections of papers?
50. Discourse analysis
Segmentation and classification:
1. Parse text into discourse segments (edu’s) containing a
single rhetorical move (if possible...)
51. Discourse analysis
Segmentation and classification:
1. Parse text into discourse segments (edu’s) containing a
single rhetorical move (if possible...)
2. Determine categories or types of discourse segments
that have similar semantic/pragmatic properties
52. Discourse analysis
Segmentation and classification:
1. Parse text into discourse segments (edu’s) containing a
single rhetorical move (if possible...)
2. Determine categories or types of discourse segments
that have similar semantic/pragmatic properties
3. Look at a number of linguistic characteristics and see if
these segment types share those characteristics.
55. Segmentation
Goal: ‘one new thought per segment’:
Figure 4A shows that following RASV12 stimulation, p53
was stabilized and activated, and its target gene, p21cip1,
was induced in all cases, indicating an intact p53 pathway
in these cells.
56. Segmentation
Goal: ‘one new thought per segment’:
Figure 4A shows that following RASV12 stimulation, p53
was stabilized and activated, and its target gene, p21cip1,
was induced in all cases, indicating an intact p53 pathway
in these cells.
a. Figure 4a shows that
b. following RASV12 stimulation
c. p53 was stabilized and activated
d. and the target gene, p21cip1, was induced in all cases,
e. indicating an intact p53 pathway in these cells.
57. Segmentation
Goal: ‘one new thought per segment’:
Figure 4A shows that following RASV12 stimulation, p53
was stabilized and activated, and its target gene, p21cip1,
was induced in all cases, indicating an intact p53 pathway
in these cells.
a. Figure 4a shows that Intratextual
b. following RASV12 stimulation Method
c. p53 was stabilized and activated Result
d. and the target gene, p21cip1, was induced in all cases, Result
e. indicating an intact p53 pathway in these cells. Implication
58. Segmentation
Goal: ‘one new thought per segment’:
Figure 4A shows that following RASV12 stimulation, p53
was stabilized and activated, and its target gene, p21cip1,
was induced in all cases, indicating an intact p53 pathway
in these cells.
a. Figure 4a shows that Intratextual
b. following RASV12 stimulation Method
c. p53 was stabilized and activated Result
d. and the target gene, p21cip1, was induced in all cases, Result
e. indicating an intact p53 pathway in these cells. Implication
60. 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
61. 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:
62. 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:
Regulatory segments, acting as matrix sentences framing other segments:
65. Linguistic and structural properties
1. Position in text
- Section of the paper (Introduction, Results, Discussion)
- Beginning/middle/end of section
- First/second/third part of sentence
66. Linguistic and structural properties
1. Position in text
- Section of the paper (Introduction, Results, Discussion)
- Beginning/middle/end of section
- First/second/third part of sentence
2. Verb:
- Tense, aspect, voice
- Verb class: Thing (increase), Thing-Thing (inhibit),
Person-Thing (examine, observe, operate, implicate), Person: Report
- Lexicon
67. Linguistic and structural properties
1. Position in text
- Section of the paper (Introduction, Results, Discussion)
- Beginning/middle/end of section
- First/second/third part of sentence
2. Verb:
- Tense, aspect, voice
- Verb class: Thing (increase), Thing-Thing (inhibit),
Person-Thing (examine, observe, operate, implicate), Person: Report
- Lexicon
3. Metadiscourse markers [Hyland, 2003]:
- Connectives
- Endophorics, Evidentials
- Hedges, Boosters
- Person markers
75. Results:Verb Tense
- Realm of the Present:
Fact (82%), Hypothesis (71%), Implication (62%)
76. Results:Verb Tense
- Realm of the Present:
Fact (82%), Hypothesis (71%), Implication (62%)
- Realm of the Past:
Result (82%), Method (76%) - 50% Passive, of Method
50% Past Perfect
77. Results:Verb Tense
- Realm of the Present:
Fact (82%), Hypothesis (71%), Implication (62%)
- Realm of the Past:
Result (82%), Method (76%) - 50% Passive, of Method
50% Past Perfect
- Realm of the Modal:
44% in Hypothesis
78. Results:Verb Tense
- Realm of the Present:
Fact (82%), Hypothesis (71%), Implication (62%)
- Realm of the Past:
Result (82%), Method (76%) - 50% Passive, of Method
50% Past Perfect
- Realm of the Modal:
44% in Hypothesis
- Realm of the To-Infinitive:
50% is Goal, 75% of Goal is to-infinitive (Purpose Clause)
80. Results: Verb Type
- Thing - Thing: high in experimental (Method, Result)
and conceptual (Problem, Hypothesis, Fact,
Implication) segments:
‣ Need to differentiate between ‘concept’ things
and ‘experimental’ things!
81. Results: Verb Type
- Thing - Thing: high in experimental (Method, Result)
and conceptual (Problem, Hypothesis, Fact,
Implication) segments:
‣ Need to differentiate between ‘concept’ things
and ‘experimental’ things!
- Person - Implicate: high in Hypothesis, Implication,
Problem
82. Results: Verb Type
- Thing - Thing: high in experimental (Method, Result)
and conceptual (Problem, Hypothesis, Fact,
Implication) segments:
‣ Need to differentiate between ‘concept’ things
and ‘experimental’ things!
- Person - Implicate: high in Hypothesis, Implication,
Problem
- Person - Operate: high in Methods (90%)
83. Results: Verb Type
- Thing - Thing: high in experimental (Method, Result)
and conceptual (Problem, Hypothesis, Fact,
Implication) segments:
‣ Need to differentiate between ‘concept’ things
and ‘experimental’ things!
- Person - Implicate: high in Hypothesis, Implication,
Problem
- Person - Operate: high in Methods (90%)
- Person - Examine: high in Goal (87%)
85. Results: Metadiscourse Markers
- Causitive: high in Implications (therefore, thus),
- Comparison: high in Results (whereas, in contrast),
- Temporality: high in Methods (next, subsequently)
- Person markers: high in Methods (50%) and Results
- Boosters: high in Results (indeed, surprisingly,
interestingly)
- Hedges: high in Implication, Reg-Implication (raises the
possibility that, explains at least in part)
- but modals and ‘suggest’ verbs are left out
86. i. How can we model the discourse moves in a biological paper?
Discourse as a Fact-ory
hypothesis
problem
fact fact fact
87. i. How can we model the discourse moves in a biological paper?
Discourse as a Fact-ory
hypothesis
goal
to
problem
fact fact fact
88. i. How can we model the discourse moves in a biological paper?
Discourse as a Fact-ory
hypothesis
goal
to
problem
fact fact fact
89. i. How can we model the discourse moves in a biological paper?
Discourse as a Fact-ory
hypothesis
goal
to
problem
we
method
resulting in
result
fact fact fact
90. i. How can we model the discourse moves in a biological paper?
Discourse as a Fact-ory
hypothesis
goal
to
problem
we
method
resulting in
result
fact fact fact
91. i. How can we model the discourse moves in a biological paper?
Discourse as a Fact-ory
hypothesis
goal
to
problem
we
method
resulting in
result
suggests that
discussion
fact fact fact
implication
92. i. How can we model the discourse moves in a biological paper?
Discourse as a Fact-ory
hypothesis
goal
to
problem
we
method
resulting in
result
suggests that
discussion
fact fact fact
implication
93. i. How can we model the discourse moves in a biological paper?
Discourse as a Fact-ory
hypothesis
goal
to
problem
we
method
introduction
resulting in
result
suggests that
discussion
fact fact fact
implication
94. i. How can we model the discourse moves in a biological paper?
Discourse as a Fact-ory
hypothesis
goal
to
problem results
we
method
introduction
resulting in
result
suggests that
discussion
fact fact fact
implication
95. i. How can we model the discourse moves in a biological paper?
Discourse as a Fact-ory
hypothesis
goal
to
problem results
we
method
introduction
resulting in
result
suggests that
discussion
fact fact fact
implication
discussion
96. i. How can we model the discourse moves in a biological paper?
Discourse as a Fact-ory
hypothesis
goal
to
problem results
we
method
introduction
resulting in
result
suggests that
discussion
fact fact fact
implication
Shared view Own view discussion
97. i. How can we model the discourse moves in a biological paper?
Discourse as a Fact-ory
hypothetical realm: hypothesis realm of activity:
(might, would) (to test, to see)
goal
to
problem results
we realm of
method
introduction experience:
past
resulting in
result
suggests that
discussion realm of models:
fact fact fact present
implication
Shared view Own view discussion
98. ii. Is this useful for enabling automated epistemic markup?
99. ii. Is this useful for enabling automated epistemic markup?
✓ first efforts seem promising: simple markers (‘suggest’
verbs, connectives, etc.) already help:
100. ii. Is this useful for enabling automated epistemic markup?
✓ first efforts seem promising: simple markers (‘suggest’
verbs, connectives, etc.) already help:
6> It is thus emerging that A_1-42-induced memory deficits may
involve subtler neuronal alternations leading to synaptic deficits, prior
to frank neurodegeneration in AD brains.
101. ii. Is this useful for enabling automated epistemic markup?
✓ first efforts seem promising: simple markers (‘suggest’
verbs, connectives, etc.) already help:
6> It is thus emerging that A_1-42-induced memory deficits may
involve subtler neuronal alternations leading to synaptic deficits, prior
to frank neurodegeneration in AD brains.
TRIPLET(that A_1_GENE:+ - 42 - induced memory
deficits,involve,subtler neuronal alternations)
102. ii. Is this useful for enabling automated epistemic markup?
✓ first efforts seem promising: simple markers (‘suggest’
verbs, connectives, etc.) already help:
6> It is thus emerging that A_1-42-induced memory deficits may
involve subtler neuronal alternations leading to synaptic deficits, prior
to frank neurodegeneration in AD brains.
TRIPLET(that A_1_GENE:+ - 42 - induced memory
deficits,involve,subtler neuronal alternations)
103. ii. Is this useful for enabling automated epistemic markup?
✓ first efforts seem promising: simple markers (‘suggest’
verbs, connectives, etc.) already help:
6> It is thus emerging that A_1-42-induced memory deficits may
involve subtler neuronal alternations leading to synaptic deficits, prior
to frank neurodegeneration in AD brains.
TRIPLET(that A_1_GENE:+ - 42 - induced memory
deficits,involve,subtler neuronal alternations)
‣ issue: segment parsing is difficult!
104. ii. Is this useful for enabling automated epistemic markup?
✓ first efforts seem promising: simple markers (‘suggest’
verbs, connectives, etc.) already help:
6> It is thus emerging that A_1-42-induced memory deficits may
involve subtler neuronal alternations leading to synaptic deficits, prior
to frank neurodegeneration in AD brains.
TRIPLET(that A_1_GENE:+ - 42 - induced memory
deficits,involve,subtler neuronal alternations)
‣ issue: segment parsing is difficult!
‣ issue: verb tense is not always accessible
105. ii. Is this useful for enabling automated epistemic markup?
✓ first efforts seem promising: simple markers (‘suggest’
verbs, connectives, etc.) already help:
6> It is thus emerging that A_1-42-induced memory deficits may
involve subtler neuronal alternations leading to synaptic deficits, prior
to frank neurodegeneration in AD brains.
TRIPLET(that A_1_GENE:+ - 42 - induced memory
deficits,involve,subtler neuronal alternations)
‣ issue: segment parsing is difficult!
‣ issue: verb tense is not always accessible
‣ bionlp: not that much work on full text, since
commercial publishers are difficult :-)!
106. ii. Is this useful for enabling automated epistemic markup?
✓ first efforts seem promising: simple markers (‘suggest’
verbs, connectives, etc.) already help:
6> It is thus emerging that A_1-42-induced memory deficits may
involve subtler neuronal alternations leading to synaptic deficits, prior
to frank neurodegeneration in AD brains.
TRIPLET(that A_1_GENE:+ - 42 - induced memory
deficits,involve,subtler neuronal alternations)
‣ issue: segment parsing is difficult!
‣ issue: verb tense is not always accessible
‣ bionlp: not that much work on full text, since
commercial publishers are difficult :-)!
‣ possible challenge at biolink 2011: watch this space...
109. To investigate the possibility that
miR-372 and miR-373 suppress the
expression of LATS2, we...
KnownFact KnownFact
Concepts Hypothesis
110. 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
111. 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
112. Voorhoeve, 2006
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
113. Voorhoeve, 2006
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
Goal
Method Result Method Result
Data Data
Experiment 1 Experiment 2
114. Voorhoeve, 2006
To investigate the possibility that
miR-372 and miR-373 suppress the
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 cell
miR-373 effects on cell proliferation and tumors by inhibition of LATS2 expression, which
tumorigenicity, 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
115. Yabuta, JBioChem 2007
Voorhoeve, 2006 miR-372 and miR-373 target the
Lats2 tumor suppressor
To investigate the possibility that (Voorhoeve et al., 2006)
miR-372 and miR-373 suppress the
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 cell
miR-373 effects on cell proliferation and tumors by inhibition of LATS2 expression, which
tumorigenicity, 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
120. Future research:
‣ Need co-annotators to verify semantic types
‣ Need to scale up with more (types of) texts!
121. Future research:
‣ Need co-annotators to verify semantic types
‣ Need to scale up with more (types of) texts!
I. How is a scientific fact created, as it moves from a
hedged claim to a throughout successive citations?
122. Future research:
‣ Need co-annotators to verify semantic types
‣ Need to scale up with more (types of) texts!
I. How is a scientific fact created, as it moves from a
hedged claim to a throughout successive citations?
II. Can we identify a rhetorically successful text, using
these segments and characteristics?
123. Future research:
‣ Need co-annotators to verify semantic types
‣ Need to scale up with more (types of) texts!
I. How is a scientific fact created, as it moves from a
hedged claim to a throughout successive citations?
II. Can we identify a rhetorically successful text, using
these segments and characteristics?
III. Can we help authors create such texts (guidelines,
tools?
125. Improve ‘what is claimed about an entity’
insulin ::: maintaining glucose ... diabetes defect) to overcome
GB000841 homeostasis insulin resistance in maintaining
glucose homeostasis,
hyperglycemia and glucose
improve glucose intolerance able to increase
... in T2D is ...
homeostasis insulin secretion and improve
glucose homeostasis.
improves glucose ... SIRT1, whose administration
homeostasis to insulin-resistant animals
improves glucose homeostasis.
is capable glucose S15511 is a novel insulin
homeostasis sensitizer that is capable of
improving glucose homeostasis
in nondiabetic rats.
maintains glucose Pancreatic beta-cells possess a
homeostasis well-regulated insulin secretory
property that maintains
systemic glucose homeostasis.
may be glucose ... similar way to those of
involved homeostasis insulin, PANDER may be
involved in glucose homeostasis.
participates glucose Fine-tuning of insulin secretion
homeostasis from pancreatic beta-cells
participates in blood glucose
homeostasis.
126. Improve ‘what is claimed about an entity’
insulin ::: maintaining glucose ... diabetes defect) to overcome When insulin secretion cannot be increased adequately (type I diabetes
defect) to overcome insulin resistance in maintaining glucose homeostasis,
GB000841 homeostasis insulin resistance in maintaining hyperglycemia and glucose intolerance ensues. Insulin resistance and glucose
glucose homeostasis, intolerance has been well recognized in patients with advanced chronic
hyperglycemia and glucose kidney diseases (CKD).
improve glucose intolerance able to increase
... in T2D is ... .. Incretin metabolism is abnormal in T2D, evidenced by a decreased
incretin effect, reduction in nutrient-mediated secretion of GIP and GLP-1 in
homeostasis insulin secretion and improve T2D, and resistance to GIP. GLP-1, on the other hand, when administered
glucose homeostasis. intravenously in T2D is able to increase insulin secretion and improve glucose
homeostasis.
improves glucose ... SIRT1, whose administration SIRT1, a NAD(+)-dependent protein deacetylase that regulates transcription
factors involved in key cellular processes, has been implicated as a mediator
homeostasis to insulin-resistant animals of the beneficial effects of calorie restriction. In a recent issue of Nature,
improves glucose homeostasis. Milne et al. (2007) describe novel potent activators of SIRT1, whose
administration to insulin-resistant animals improves glucose homeostasis.
is capable glucose S15511 is a novel insulin S15511 is a novel insulin sensitizer that is capable of improving glucose
homeostasis in nondiabetic rats.... However, the mechanisms behind the insulin-
homeostasis sensitizer that is capable of sensitizing effect of S15511 are unknown. The aim of our study was to
improving glucose homeostasis explore whether S15511 improves insulin sensitivity in skeletal muscles.
in nondiabetic rats. S15511 treatment was associated with an increase in insulin-stimulated
glucose transport in type IIb well-regulatedtype I fibers were unaffected.
Pancreatic beta-cells possess a fibers, while insulin secretory property that
maintains glucose Pancreatic beta-cells possess a
maintains systemic glucose homeostasis. Although it has long been
homeostasis well-regulated insulin secretory thought that differentiated beta-cells are nearly static, recent studies
property that maintains have shown that beta-cell mass dynamically changes throughout the
systemic glucose homeostasis. lifetime. In this article, recent progress of regenerative medicine of the
pancreasresults showed that glucose up-regulated PANDER mRNA and
... Our is reviewed.
may be glucose ... similar way to those of
protein levels in a time- and dose-dependent manner in MIN6 cells and
involved homeostasis insulin, PANDER may be pancreatic islets. ...Because PANDER is expressed by pancreatic beta-cells
involved in glucose homeostasis. and in response to glucose in a similar way to those of insulin, PANDER may be
involved in glucose homeostasis.
participates glucose Fine-tuning of insulin secretion Fine-tuning of insulin secretion from pancreatic beta-cells participates in blood
glucose homeostasis. ... Our data identify miR124a and miR96 as novel
homeostasis from pancreatic beta-cells regulators of the expression of proteins playing a critical role in insulin
participates in blood glucose exocytosis and in the release of other hormones and neurotransmitters.
homeostasis.
127. Improve ‘what is claimed about an entity’
insulin ::: maintaining glucose ... diabetes defect) to overcome When insulin secretion cannot be increased adequately (type I diabetes
defect) to overcome insulin resistance in maintaining glucose homeostasis,
GB000841 homeostasis insulin resistance in maintaining hyperglycemia and glucose intolerance ensues. Insulin resistance and glucose
glucose homeostasis, intolerance has been well recognized in patients with advanced chronic
hyperglycemia and glucose kidney diseases (CKD).
improve glucose intolerance able to increase
... in T2D is ... .. Incretin metabolism is abnormal in T2D, evidenced by a decreased
incretin effect, reduction in nutrient-mediated secretion of GIP and GLP-1 in
homeostasis insulin secretion and improve T2D, and resistance to GIP. GLP-1, on the other hand, when administered
glucose homeostasis. intravenously in T2D is able to increase insulin secretion and improve glucose
homeostasis.
improves glucose ... SIRT1, whose administration SIRT1, a NAD(+)-dependent protein deacetylase that regulates transcription
factors involved in key cellular processes, has been implicated as a mediator
homeostasis to insulin-resistant animals of the beneficial effects of calorie restriction. In a recent issue of Nature,
improves glucose homeostasis. Milne et al. (2007) describe novel potent activators of SIRT1, whose
administration to insulin-resistant animals improves glucose homeostasis.
is capable glucose S15511 is a novel insulin S15511 is a novel insulin sensitizer that is capable of improving glucose
homeostasis in nondiabetic rats.... However, the mechanisms behind the insulin-
homeostasis sensitizer that is capable of sensitizing effect of S15511 are unknown. The aim of our study was to
improving glucose homeostasis explore whether S15511 improves insulin sensitivity in skeletal muscles.
in nondiabetic rats. S15511 treatment was associated with an increase in insulin-stimulated
glucose transport in type IIb well-regulatedtype I fibers were unaffected.
Pancreatic beta-cells possess a fibers, while insulin secretory property that
maintains glucose Pancreatic beta-cells possess a
maintains systemic glucose homeostasis. Although it has long been
homeostasis well-regulated insulin secretory thought that differentiated beta-cells are nearly static, recent studies
property that maintains have shown that beta-cell mass dynamically changes throughout the
systemic glucose homeostasis. lifetime. In this article, recent progress of regenerative medicine of the
pancreasresults showed that glucose up-regulated PANDER mRNA and
... Our is reviewed.
may be glucose ... similar way to those of
protein levels in a time- and dose-dependent manner in MIN6 cells and
involved homeostasis insulin, PANDER may be pancreatic islets. ...Because PANDER is expressed by pancreatic beta-cells
involved in glucose homeostasis. and in response to glucose in a similar way to those of insulin, PANDER may be
involved in glucose homeostasis.
participates glucose Fine-tuning of insulin secretion Fine-tuning of insulin secretion from pancreatic beta-cells participates in blood
glucose homeostasis. ... Our data identify miR124a and miR96 as novel
homeostasis from pancreatic beta-cells regulators of the expression of proteins playing a critical role in insulin
participates in blood glucose exocytosis and in the release of other hormones and neurotransmitters.
homeostasis.
129. A network of hypotheses and evidence
PHC undergo Growth arrest
30
130. A network of hypotheses and evidence
PHC undergo Growth arrest
Paper A:
implication
method fact
goal fact
results
30
131. A network of hypotheses and evidence
PHC undergo Growth arrest
Paper A:
implication
method fact
goal fact
results
data 1
data 2 data 3
30
132. A network of hypotheses and evidence
PHC undergo Growth arrest
Paper A: Paper B:
implication implication
method fact method fact
goal fact goal fact
results
results
data 1
data 4
data 2 data 3
data 5 data 6
30
133. A network of hypotheses and evidence
PHC undergo Growth arrest
Paper A: Paper B:
implication implication
method fact method fact
goal fact goal fact
results
results
data 1
data 4
data 2 data 3
data 5 data 6
30
134. A network of hypotheses and evidence
PHC undergo Growth arrest
Paper A: Paper B:
implication implication
method fact method fact
goal fact goal fact
results
results
data 1
data 4
data 2 data 3
data 5 data 6
30
135. A network of hypotheses and evidence
PHC undergo Growth arrest
Paper A: Paper B:
implication implication
g
n nin
method fact rpi method
de fact
un
goal fact goal fact
results
results
data 1
data 4
data 2 data 3
data 5 data 6
30
136. A network of hypotheses and evidence
PHC undergo Growth arrest
Paper A: Paper B:
implication implication
method fact method fact
goal fact goal fact
results
results
data 1
data 4
data 2 data 3
data 5 data 6
30
137. A network of hypotheses and evidence
PHC undergo Growth arrest
Paper A: Paper B:
implication implication
method method link
fact method fact
goal fact goal fact
results
results
data 1
data 4
data 2 data 3
data 5 data 6
30
142. HypER Working Group:
- Goal: Align and expand existing efforts on detection and
analysis of Hypotheses, Evidence & Relationships
- Partners:
- Harvard/MGH: SWAN, ARF
- Open University: Cohere
- Oxford University: CiTO, eLearning/Rhetoric
- DERI: SALT, aTags
- University of Trento: LiquidPub
- Xerox Research: XIP hypothesis identifier
- U Tilburg: ML for Science
- Elsevier, UUtrecht: Discourse analysis of biology
143. HypER Working Group:
- Goal: Align and expand existing efforts on detection and
analysis of Hypotheses, Evidence & Relationships
- Partners:
- Harvard/MGH: SWAN, ARF
- Open University: Cohere
- Oxford University: CiTO, eLearning/Rhetoric
- DERI: SALT, aTags
- University of Trento: LiquidPub
- Xerox Research: XIP hypothesis identifier
- U Tilburg: ML for Science
- Elsevier, UUtrecht: Discourse analysis of biology
144. HypER Working Group:
- Goal: Align and expand existing efforts on detection and
analysis of Hypotheses, Evidence & Relationships
- Partners:
- Harvard/MGH: SWAN, ARF
- Open University: Cohere
- Oxford University: CiTO, eLearning/Rhetoric
- DERI: SALT, aTags
- University of Trento: LiquidPub
- Xerox Research: XIP hypothesis identifier
- U Tilburg: ML for Science
- Elsevier, UUtrecht: Discourse analysis of biology
145. HypER Working Group:
- Goal: Align and expand existing efforts on detection and
analysis of Hypotheses, Evidence & Relationships
- Partners:
- Harvard/MGH: SWAN, ARF
- Open University: Cohere
- Oxford University: CiTO, eLearning/Rhetoric
- DERI: SALT, aTags
- University of Trento: LiquidPub
- Xerox Research: XIP hypothesis identifier
- U Tilburg: ML for Science
- Elsevier, UUtrecht: Discourse analysis of biology
146. HypER Working Group:
- Goal: Align and expand existing efforts on detection and
analysis of Hypotheses, Evidence & Relationships
- Partners:
- Harvard/MGH: SWAN, ARF
- Open University: Cohere
- Oxford University: CiTO, eLearning/Rhetoric
- DERI: SALT, aTags
- University of Trento: LiquidPub
- Xerox Research: XIP hypothesis identifier
- U Tilburg: ML for Science
- Elsevier, UUtrecht: Discourse analysis of biology
147. HypER Working Group:
- Goal: Align and expand existing efforts on detection and
analysis of Hypotheses, Evidence & Relationships
- Partners:
- Harvard/MGH: SWAN, ARF
- Open University: Cohere
- Oxford University: CiTO, eLearning/Rhetoric
- DERI: SALT, aTags
- University of Trento: LiquidPub
- Xerox Research: XIP hypothesis identifier
- U Tilburg: ML for Science
- Elsevier, UUtrecht: Discourse analysis of biology
148. HypER Working Group:
- Goal: Align and expand existing efforts on detection and
analysis of Hypotheses, Evidence & Relationships
- Partners:
- Hypothesis 22: Intramembrenous Aβ dimer may be toxic.
Harvard/MGH: SWAN, ARF
- Derived of these Abeta peptides never leave theessay explores the possibility they aare
Open from: POSTAT_CONTRIBUTION(This
fraction
University: Cohere
membrane lipid bilayer after
that
- generated,University: CiTO,their toxic effects by competing with and compromising
Oxford but instead exert eLearning/Rhetoric
the functions of intramembranous segments of membrane-bound proteins that serve
- many critical functions.
DERI: SALT, aTags
- University of Trento: LiquidPub
- Xerox Research: XIP hypothesis identifier
- U Tilburg: ML for Science
- Elsevier, UUtrecht: Discourse analysis of biology
150. HypER Activities: http://hyper.wik.is
Current activities:
- Aligning discourse ontologies: joint task with W3C HCLSSig
- Aligning architectures to exchange hypotheses + evidence
- Format for a rhetorical conference paper (SALT + abcde)
- Parser test of hypothesis identification tools on pharmacology corpus
151. HypER Activities: http://hyper.wik.is
Current activities:
- Aligning discourse ontologies: joint task with W3C HCLSSig
- Aligning architectures to exchange hypotheses + evidence
- Format for a rhetorical conference paper (SALT + abcde)
- Parser test of hypothesis identification tools on pharmacology corpus
Further interests:
- Better structure of evidence: MyExperiment, KeFeD, ...
- Granularity of annotation/access: entity, hypothesis, discussion?
154. Conclusion
Problem: too much discourse, tools are not yet good
enough...
1. First attempt: allow authors to validate entities -
pursue
155. Conclusion
Problem: too much discourse, tools are not yet good
enough...
1. First attempt: allow authors to validate entities -
pursue
2. Second attempt: discourse analysis - any help is
great!
156. Conclusion
Problem: too much discourse, tools are not yet good
enough...
1. First attempt: allow authors to validate entities -
pursue
2. Second attempt: discourse analysis - any help is
great!
3. Third attempt: collaboration to identify hypotheses:
do join!
158. References
Hyland, K. (2004). Disciplinary Discourses: Social Interactions in Academic
Writing, Addison Wesley Publishing Company, 2004.
Latour, B., and Woolgar, S. (1986). Laboratory Life: The Construction of
Scientific Facts. 2nd ed. Princeton, NJ: Princeton University Press, 1986. ISBN:
9780691028323.
Latour, B. (1987). Science in Action, How to Follow Scientists and Engineers
through Society, (Cambridge, Ma.: Harvard University Press, 1987)
159. Segmentation Criteria (summary)
Finite/
Grammatical role Segment? Example
Non-finite
The extent to which miRNAs specifically affect
Finite/Non-finite Subject N metastasis
Finite/Non-finite Direct Object Y these miRNAs are potential novel oncogenes
Phrase-level adjunct (restrictive and
Nonfinite N spanning a given miRNA genomic region
non-restrictive)
Nonfinite Clause-level adjunct Y by cloning eight miR-Vec plasmids
which is only active when tamoxifen is added (De
Finite Non-restrictive Phrase-level adjunct Y Vita et al, 2005) […]
Finite Restrictive Phrase-level adjunct N that we examined
which correlates with the reported ES-cell
Finite Clause-level adjunct Y expression pattern of the miR-371-3 cluster (Suh et
al, 2004)
160. Basic Segment Types
Segment Description Example
a known fact, generally
Fact mature miR-373 is a homolog of miR-372
without explicit citation
a proposed idea, not
Hypothesis This could for instance be a result of high mdm2 levels
supported by evidence
unresolved, contradictory, or However, further investigation is required to
Problem
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,
a restatement of the outcome all constructs yielded high expression levels of mature
Result
of an experiment miRNAs
an interpretation of the
our procedure is sensitive enough to detect mild growth
Implication results, in light of earlier
hypotheses and facts differences
162. Two Types of Derived Segment Types
‘Other-segments’, related to (referenced) other work:
163. Two Types of Derived Segment Types
‘Other-segments’, related to (referenced) other work:
- other-result: ‘they are also found in the FCX and other cortical structures
([Sokoloff et al., 1990]’
164. Two Types of Derived Segment Types
‘Other-segments’, related to (referenced) other work:
- other-result: ‘they are also found in the FCX and other cortical structures
([Sokoloff et al., 1990]’
- other-goal: ‘the role of D3 receptors in the control of motivation and affect
has been intensively studied [Heidbreder et al., 2005]’
165. Two Types of Derived Segment Types
‘Other-segments’, related to (referenced) other work:
- other-result: ‘they are also found in the FCX and other cortical structures
([Sokoloff et al., 1990]’
- other-goal: ‘the role of D3 receptors in the control of motivation and affect
has been intensively studied [Heidbreder et al., 2005]’
- other-implication: ‘D1 or, more likely, D5, receptors have been implicated in
mechanisms underlying long-term spatial memory [Hersi et al., 1995]’
166. Two Types of Derived Segment Types
‘Other-segments’, related to (referenced) other work:
- other-result: ‘they are also found in the FCX and other cortical structures
([Sokoloff et al., 1990]’
- other-goal: ‘the role of D3 receptors in the control of motivation and affect
has been intensively studied [Heidbreder et al., 2005]’
- other-implication: ‘D1 or, more likely, D5, receptors have been implicated in
mechanisms underlying long-term spatial memory [Hersi et al., 1995]’
Regulatory segments, acting as matrix sentences framing other segments:
167. Two Types of Derived Segment Types
‘Other-segments’, related to (referenced) other work:
- other-result: ‘they are also found in the FCX and other cortical structures
([Sokoloff et al., 1990]’
- other-goal: ‘the role of D3 receptors in the control of motivation and affect
has been intensively studied [Heidbreder et al., 2005]’
- other-implication: ‘D1 or, more likely, D5, receptors have been implicated in
mechanisms underlying long-term spatial memory [Hersi et al., 1995]’
Regulatory segments, acting as matrix sentences framing other segments:
- reg-hypothesis: ‘we hypothesized that ’
168. Two Types of Derived Segment Types
‘Other-segments’, related to (referenced) other work:
- other-result: ‘they are also found in the FCX and other cortical structures
([Sokoloff et al., 1990]’
- other-goal: ‘the role of D3 receptors in the control of motivation and affect
has been intensively studied [Heidbreder et al., 2005]’
- other-implication: ‘D1 or, more likely, D5, receptors have been implicated in
mechanisms underlying long-term spatial memory [Hersi et al., 1995]’
Regulatory segments, acting as matrix sentences framing other segments:
- reg-hypothesis: ‘we hypothesized that ’
- reg-implication: ‘These observations suggest that’
169. Two Types of Derived Segment Types
‘Other-segments’, related to (referenced) other work:
- other-result: ‘they are also found in the FCX and other cortical structures
([Sokoloff et al., 1990]’
- other-goal: ‘the role of D3 receptors in the control of motivation and affect
has been intensively studied [Heidbreder et al., 2005]’
- other-implication: ‘D1 or, more likely, D5, receptors have been implicated in
mechanisms underlying long-term spatial memory [Hersi et al., 1995]’
Regulatory segments, acting as matrix sentences framing other segments:
- reg-hypothesis: ‘we hypothesized that ’
- reg-implication: ‘These observations suggest that’
- intratextual: ‘Fig 4 shows that’
170. Two Types of Derived Segment Types
‘Other-segments’, related to (referenced) other work:
- other-result: ‘they are also found in the FCX and other cortical structures
([Sokoloff et al., 1990]’
- other-goal: ‘the role of D3 receptors in the control of motivation and affect
has been intensively studied [Heidbreder et al., 2005]’
- other-implication: ‘D1 or, more likely, D5, receptors have been implicated in
mechanisms underlying long-term spatial memory [Hersi et al., 1995]’
Regulatory segments, acting as matrix sentences framing other segments:
- reg-hypothesis: ‘we hypothesized that ’
- reg-implication: ‘These observations suggest that’
- intratextual: ‘Fig 4 shows that’
- intertextual: ‘reviewed in (Serrano, 1997)’
175. Linguistic and structural properties
1. Position in text
- Section of the paper (Introduction, Results, Discussion)
176. Linguistic and structural properties
1. Position in text
- Section of the paper (Introduction, Results, Discussion)
- Beginning/middle/end of section
177. Linguistic and structural properties
1. Position in text
- Section of the paper (Introduction, Results, Discussion)
- Beginning/middle/end of section
- First/second third part of sentence
178. Linguistic and structural properties
1. Position in text
- Section of the paper (Introduction, Results, Discussion)
- Beginning/middle/end of section
- First/second third part of sentence
2. Verb:
179. Linguistic and structural properties
1. Position in text
- Section of the paper (Introduction, Results, Discussion)
- Beginning/middle/end of section
- First/second third part of sentence
2. Verb:
- Tense, aspect, voice
180. Linguistic and structural properties
1. Position in text
- Section of the paper (Introduction, Results, Discussion)
- Beginning/middle/end of section
- First/second third part of sentence
2. Verb:
- Tense, aspect, voice
- Verb class (idiosyncratic)
181. Linguistic and structural properties
1. Position in text
- Section of the paper (Introduction, Results, Discussion)
- Beginning/middle/end of section
- First/second third part of sentence
2. Verb:
- Tense, aspect, voice
- Verb class (idiosyncratic)
- Lexicon
182. Linguistic and structural properties
1. Position in text
- Section of the paper (Introduction, Results, Discussion)
- Beginning/middle/end of section
- First/second third part of sentence
2. Verb:
- Tense, aspect, voice
- Verb class (idiosyncratic)
- Lexicon
3. Metadiscourse markers [Hyland, 2003]:
183. Linguistic and structural properties
1. Position in text
- Section of the paper (Introduction, Results, Discussion)
- Beginning/middle/end of section
- First/second third part of sentence
2. Verb:
- Tense, aspect, voice
- Verb class (idiosyncratic)
- Lexicon
3. Metadiscourse markers [Hyland, 2003]:
- Connectives
184. Linguistic and structural properties
1. Position in text
- Section of the paper (Introduction, Results, Discussion)
- Beginning/middle/end of section
- First/second third part of sentence
2. Verb:
- Tense, aspect, voice
- Verb class (idiosyncratic)
- Lexicon
3. Metadiscourse markers [Hyland, 2003]:
- Connectives
- Endophorics, Evidentials
185. Linguistic and structural properties
1. Position in text
- Section of the paper (Introduction, Results, Discussion)
- Beginning/middle/end of section
- First/second third part of sentence
2. Verb:
- Tense, aspect, voice
- Verb class (idiosyncratic)
- Lexicon
3. Metadiscourse markers [Hyland, 2003]:
- Connectives
- Endophorics, Evidentials
- Hedges, Boosters
186. Linguistic and structural properties
1. Position in text
- Section of the paper (Introduction, Results, Discussion)
- Beginning/middle/end of section
- First/second third part of sentence
2. Verb:
- Tense, aspect, voice
- Verb class (idiosyncratic)
- Lexicon
3. Metadiscourse markers [Hyland, 2003]:
- Connectives
- Endophorics, Evidentials
- Hedges, Boosters
- Person markers
190. Interpretation: 3 Realms of Science:
(1) Oncogene-induced senescence is (4b) transduction with either
Conceptual characterized by the appearance of miR-Vec-371&2 or miR-Vec-
V12
cells with a flat morphology that 373 prevents RAS -
realm express senescence associated (SA)- induced growth arrest in
-Galactosid a s e . primary human cells.
(2a) Indeed, (4a) Altogether, these data
show that
Experimental realm (2b) control RAS V12
-arrested (3b) very few cells showed
cells showed relatively high senescent morphology when
(3a) Consistent
abundance of flat cells transduced with either miR-
with the cell
expressing SA- - Vec-371&2, miR-Vec-373, or
growth assay, kd
Galactosidase control p53 .
(2c) (Figures
2G and 2H).
Data realm
(Figures)
191. Interpretation: 3 Realms of Science:
(1) Oncogene-induced senescence is (4b) transduction with either
Conceptual characterized by the appearance of miR-Vec-371&2 or miR-Vec-
V12
cells with a flat morphology that 373 prevents RAS -
realm express senescence associated (SA)- induced growth arrest in
-Galactosid a s e . primary human cells.
(2a) Indeed, (4a) Altogether, these data
show that
Experimental realm (2b) control RAS V12
-arrested (3b) very few cells showed
cells showed relatively high senescent morphology when
(3a) Consistent
abundance of flat cells transduced with either miR-
with the cell
expressing SA- - Vec-371&2, miR-Vec-373, or
growth assay, kd
Galactosidase control p53 .
(2c) (Figures
2G and 2H).
Data realm
(Figures)
192. Tense 1: Concepts vs. Experiment
(1) Oncogene-induced senescence is (4b) transduction with either
Concept realm
characterized by the appearance of miR-Vec-371&2 or miR-Vec-
V12
cells with a flat morphology that 373 prevents RAS -
express senescence associated (SA)- induced growth arrest in
-Galactosid a s e . primary human cells.
(2a) Indeed, (4a) Altogether, these data
show that
Experimental realm
(personal, past)
V12
(2b) control RAS -arrested (3b) very few cells showed
cells showed relatively high senescent morphology when
(3a) Consistent
abundance of flat cells transduced with either miR-
with the cell
expressing SA- - Vec-371&2, miR-Vec-373, or
growth assay, kd
Galactosidase control p53 .
(2c) (Figures
2G and 2H).
(nontverbal)
Data realm
(Figures)
193. Tense 2: Referral
past present future
Introduction Discussion
own paper
After Before current Current work After current
other work: present work: past
(= Results section)
work:
past
other papers
Other Work
194. Tense 1+ 2 = 3:
Claim,
fact
Conceptual
Experi
ment
Experiential
past present future
Reading time
