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Transcript of Scientific Reading and Writing in English Lectures on: 12/01, 12/22 “Abstract” & Practice 12/08,...
Scientific Reading and Writing in
English
Lectures on:
12/01, 12/22 “Abstract” & Practice
12/08, 12/29 “References, Acknowledgements,
and Front page” & Practice
12/15, 1/05 “Cover letter” & Practice
Readings: “How to Write & Publish a Scientific Paper” by Robert A. Day, 6th Edition
Pin Ling ( 凌 斌 ), Ph.D.
Department of Microbiology & Immunology, NCKU
ext 5632
How to prepare the abstract?
Definition and function of the abstract
Organization of the abstract
Tips for writing the abstract
Example and practice
Your involvement is the key to success in this lecture. Speak Up!
The Structure of A Paper
Title
Abstract
Introduction
Materials & Methods
Results & Figures
Discussion
References
Read them first and decide to read the rest or not
What is the abstract?
Ab, Out trahere, to Pull To pull out the “key points” from the paper
An abstract can be viewed as a mini-version of the paper.
Two common types of Abstracts- Informative abstracts: most research papers
(five elements)- Indicative (Descriptive) abstracts: review articles
to Pull Out
The function of the abstract
The first contact to readers
Readers
A Good Abstract The Whole Paper
A Poor Abstract X The Whole Paper
A good abstract delivers the paper’s key points “Concisely” and “Precisely”.
How to prepare the abstract?
Definition and function of the abstract
Organization of the abstract
Tips for writing the abstract
Example and practice
The Organization of the abstract (I)
The organization of the (informative) abstract is similar to the organization of the paper.
It includes the key information from the paper :- Introduction - Purpose (Key Question)- Materials & Methods (What was done)- Results (What was found)- Conclusions & Discussion (Answer & Implication)
Pull out the key information from each part to form a paragraph.
Conclusions & Discussion
Results & Figures
Materials & Methods
Introduction & Purpose
Abstract (One paragraph)
Title (One sentence)
The Organization of the abstract (II)
Definition and function of the abstract
Organization of the abstract
Tips for writing the abstract
Example and practice
How to prepare the abstract?
Tips for writing the abstract
Timing to write the abstract
Length
Sentence structure & word choice
Other issues
The Structure of A Paper
Title
Abstract
Introduction
Materials & Methods
Results & Figures
Discussion
References
The order to write a paper
Write the main text first and then the overview sections
Abstract (One paragraph)
Title (One sentence)
Overview sectionsMain text
Conclusions & Discussion
Results & Figures
Materials & Methods
Introduction & Purpose
The length of the abstract
One paragraph (usually)
Most journals limit the length within 250 words. Some are even lesser.
*Check the journal submission rules
Do not add unimportant details or unnecessary words to fill up the space.
Add more details => Out of
=> Lost the
Sentence Structure
Write short and simple sentences
Short sentences are easy for readers to follow up.
By contrast, long sentences tend to make readers lost.
Word choice & Abbreviations
Use simple words. Avoid jargon.
Avoid noun clusters (try your best)e.g. Real-time quantitative polymerase chain
reaction (qPCR)
Rules of using abbreviations: Use standard (std) abbreviations => units of measurement, e.g. microgram (mg) => widely accepted, e.g. DNA & NF-B Define a non-std abbreviation the first time you use it. e.g. Epidermal Growth Factor Receptor (EGFR),
c-Jun N-terminal Kinase (JNK)
Other issues for writing the abstract
Verb tenses in the abstract = those in the paper. Present tense => Question & AnswerPast tense => What was done & What was found
ContinuityKeep clear continuity throughout the abstract
Signaling TopicsSignal the parts of an abstract by starting a new sentence and by stating the topic at the beginning of the sentence.
Definition and function of the abstract
Organization of the abstract
Tips for writing the abstract
Example and practice
How to prepare the abstract?
Regulation of IB Kinase (IKK)/NEMO Function by IKK-mediated Phosphorylation* Shashi Prajapati and Richard B. Gaynor‡ J Biol Chem. 2002 Jul 5;277(27):24331-9.
The IkappaB kinase (IKK) complex includes the catalytic components IKKalpha and IKKbetain addition to the scaffold protein IKKgamma/NEMO. Increases in the activity of the IKKcomplex result in the phosphorylation and subsequent degradation of IkappaB and the activation of the NF-kappaB pathway. Recent data indicate that the constitutive activation of the NF-kappaB pathway by the human T-cell lymphotrophic virus, type I, Tax protein leads to enhanced phosphorylation of IKKgamma/NEMO by IKKbeta. To address further the significance of IKKbeta-mediated phosphorylation of IKKgamma/NEMO, we determined the sites in IKKgamma/NEMO that were phosphorylated by IKKbeta, and we assayed whether IKKgamma/NEMO phosphorylation was involved in modulating IKKbeta activity. IKKgamma/NEMO is rapidly phosphorylated following treatment of cells with stimuli such as tumor necrosis factor-alpha and interleukin-1 that activate the NF-kappaB pathway. By using both in vitro and in vivo assays, IKKbeta was found to phosphorylate IKKgamma/NEMO predominantly in its carboxyl terminus on serine residue 369 in addition to sites in the central region of this protein. Surprisingly, mutation of these carboxyl-terminal serine residues increased the ability of IKKgamma/NEMO to stimulate IKKbeta kinase activity. These results indicate that the differential phosphorylation of IKKgamma/NEMO by IKKbeta and perhaps other kinases may be important in regulating IKK activity.
Example of an informative abstract
One paragraph, 201 words
The IkappaB kinase (IKK) complex includes the catalytic components IKKalpha and IKKbeta in addition to the scaffold protein IKKgamma/NEMO. Increases in the activity of the IKK complex result in the phosphorylation and subsequent degradation of IkappaB and the activation of the NF-kappaB pathway. Recent data indicate that the constitutive activation of the NF-kappaB pathway by the human T-cell lymphotrophic virus, type I, Tax protein leads to enhanced phosphorylation of IKKgamma/NEMO by IKKbeta. To address further the significance of IKKbeta-mediated phosphorylation of IKKgamma/NEMO, we determined the sites in IKKgamma/NEMO that were phosphorylated by IKKbeta, and we assayed whether IKKgamma/NEMO phosphorylation was involved in modulating IKKbeta activity. IKKgamma/NEMO is rapidly phosphorylated following treatment of cells with stimuli such as tumor necrosis factor-alpha and interleukin-1 that activate the NF-kappaB pathway. By using both in vitro and in vivo assays, IKKbeta was found to phosphorylate IKKgamma/NEMO predominantly in its carboxyl terminus on serine residue 369 in addition to sites in the central region of this protein. Surprisingly, mutation of these carboxyl-terminal serine residues increased the ability of IKKgamma/NEMO to stimulate IKKbeta kinase activity. These results indicate that the differential phosphorylation of IKKgamma/NEMO by IKKbeta and perhaps other kinases may be important in regulating IKK activity.
Dissection of the abstract-1
Introduction(Background)
The IkappaB kinase (IKK) complex includes the catalytic components IKKalpha and IKKbeta in addition to the scaffold protein IKKgamma/NEMO. Increases in the activity of the IKK complex result in the phosphorylation and subsequent degradation of IkappaB and the activation of the NF-kappaB pathway. Recent data indicate that the constitutive activation of the NF-kappaB pathway by the human T-cell lymphotrophic virus, type I, Tax protein leads to enhanced phosphorylation of IKKgamma/NEMO by IKKbeta. To address further the significance of IKKbeta-mediated phosphorylation of IKKgamma/NEMO, we determined the sites in IKKgamma/NEMO that were phosphorylated by IKKbeta, and we assayed whether IKKgamma/NEMO phosphorylation was involved in modulating IKKbeta activity. IKKgamma/NEMO is rapidly phosphorylated following treatment of cells with stimuli such as tumor necrosis factor-alpha and interleukin-1 that activate the NF-kappaB pathway. By using both in vitro and in vivo assays, IKKbeta was found to phosphorylate IKKgamma/NEMO predominantly in its carboxyl terminus on serine residue 369 in addition to sites in the central region of this protein. Surprisingly, mutation of these carboxyl-terminal serine residues increased the ability of IKKgamma/NEMO to stimulate IKKbeta kinase activity. These results indicate that the differential phosphorylation of IKKgamma/NEMO by IKKbeta and perhaps other kinases may be important in regulating IKK activity.
Dissection of the abstract-2
Purpose(Question)
The IkappaB kinase (IKK) complex includes the catalytic components IKKalpha and IKKbeta in addition to the scaffold protein IKKgamma/NEMO. Increases in the activity of the IKK complex result in the phosphorylation and subsequent degradation of IkappaB and the activation of the NF-kappaB pathway. Recent data indicate that the constitutive activation of the NF-kappaB pathway by the human T-cell lymphotrophic virus, type I, Tax protein leads to enhanced phosphorylation of IKKgamma/NEMO by IKKbeta. To address further the significance of IKKbeta-mediated phosphorylation of IKKgamma/NEMO, we determined the sites in IKKgamma/NEMO that were phosphorylated by IKKbeta, and we assayed whether IKKgamma/NEMO phosphorylation was involved in modulating IKKbeta activity. IKKgamma/NEMO is rapidly phosphorylated following treatment of cells with stimuli such as tumor necrosis factor-alpha and interleukin-1 that activate the NF-kappaB pathway. By using both in vitro and in vivo assays, IKKbeta was found to phosphorylate IKKgamma/NEMO predominantly in its carboxyl terminus on serine residue 369 in addition to sites in the central region of this protein. Surprisingly, mutation of these carboxyl-terminal serine residues increased the ability of IKKgamma/NEMO to stimulate IKKbeta kinase activity. These results indicate that the differential phosphorylation of IKKgamma/NEMO by IKKbeta and perhaps other kinases may be important in regulating IKK activity.
J Biol Chem. 2002 Jul 5;277(27):24331-9.
Dissection of the abstract-3
What was done
The IkappaB kinase (IKK) complex includes the catalytic components IKKalpha and IKKbeta in addition to the scaffold protein IKKgamma/NEMO. Increases in the activity of the IKK complex result in the phosphorylation and subsequent degradation of IkappaB and the activation of the NF-kappaB pathway. Recent data indicate that the constitutive activation of the NF-kappaB pathway by the human T-cell lymphotrophic virus, type I, Tax protein leads to enhanced phosphorylation of IKKgamma/NEMO by IKKbeta. To address further the significance of IKKbeta-mediated phosphorylation of IKKgamma/NEMO, we determined the sites in IKKgamma/NEMO that were phosphorylated by IKKbeta, and we assayed whether IKKgamma/NEMO phosphorylation was involved in modulating IKKbeta activity. IKKgamma/NEMO is rapidly phosphorylated following treatment of cells with stimuli such as tumor necrosis factor-alpha and interleukin-1 that activate the NF-kappaB pathway. By using both in vitro and in vivo assays, IKKbeta was found to phosphorylate IKKgamma/NEMO predominantly in its carboxyl terminus on serine residue 369 in addition to sites in the central region of this protein. Surprisingly, mutation of these carboxyl-terminal serine residues increased the ability of IKKgamma/NEMO to stimulate IKKbeta kinase activity. These results indicate that the differential phosphorylation of IKKgamma/NEMO by IKKbeta and perhaps other kinases may be important in regulating IKK activity.
Dissection of the abstract-4
What was found
The IkappaB kinase (IKK) complex includes the catalytic components IKKalpha and IKKbeta in addition to the scaffold protein IKKgamma/NEMO. Increases in the activity of the IKK complex result in the phosphorylation and subsequent degradation of IkappaB and the activation of the NF-kappaB pathway. Recent data indicate that the constitutive activation of the NF-kappaB pathway by the human T-cell lymphotrophic virus, type I, Tax protein leads to enhanced phosphorylation of IKKgamma/NEMO by IKKbeta. To address further the significance of IKKbeta-mediated phosphorylation of IKKgamma/NEMO, we determined the sites in IKKgamma/NEMO that were phosphorylated by IKKbeta, and we assayed whether IKKgamma/NEMO phosphorylation was involved in modulating IKKbeta activity. IKKgamma/NEMO is rapidly phosphorylated following treatment of cells with stimuli such as tumor necrosis factor-alpha and interleukin-1 that activate the NF-kappaB pathway. By using both in vitro and in vivo assays, IKKbeta was found to phosphorylate IKKgamma/NEMO predominantly in its carboxyl terminus on serine residue 369 in addition to sites in the central region of this protein. Surprisingly, mutation of these carboxyl-terminal serine residues increased the ability of IKKgamma/NEMO to stimulate IKKbeta kinase activity. These results indicate that the differential phosphorylation of IKKgamma/NEMO by IKKbeta and perhaps other kinases may be important in regulating IKK activity.
Answer&
Implication
Dissection of the abstract-5
The IkappaB kinase (IKK) complex includes the catalytic components IKKalpha and IKKbetain addition to the scaffold protein IKKgamma/NEMO. Increases in the activity of the IKK complex result in the phosphorylation and subsequent degradation of IkappaB and the activation of the NF-kappaB pathway. Recent data indicate that the constitutive activation of the NF-kappaB pathway by the human T-cell lymphotrophic virus, type I, Tax protein leads to enhanced phosphorylation of IKKgamma/NEMO by IKKbeta. To address further the significance of IKKbeta-mediated phosphorylation of IKKgamma/NEMO, we determined the sites in IKKgamma/NEMO that were phosphorylated by IKKbeta, and we assayed whether IKKgamma/NEMO phosphorylation was involved in modulating IKKbeta activity. IKKgamma/NEMO is rapidly phosphorylated following treatment of cells with stimuli such as tumor necrosis factor-alpha and interleukin-1 that activate the NF-kappaB pathway. By using both in vitro and in vivo assays, IKKbeta was found to phosphorylate IKKgamma/NEMO predominantly in its carboxyl terminus on serine residue 369 in addition to sites in the central region of this protein. Surprisingly, mutation of these carboxyl-terminal serine residues increased the ability of IKKgamma/NEMO to stimulate IKKbeta kinase activity. These results indicate that the differential phosphorylation of IKKgamma/NEMO by IKKbeta and perhaps other kinases may be important in regulating IKK activity.
Any suggestion for the abstract?
Tips for the abstract
1. Use simple words and define abbreviations
2. Write short and simple sentences
3. Verb tenses
4. Continuity
5. Signal Topics
Define the Abbreviations
The IkappaB kinase (IKK) complex includes the catalytic components IKKalpha (IKK) and IKKbeta (IKK) in addition to the scaffold protein IKKgamma (IKK)/NEMO. Increases in the activity of the IKK complex result in the phosphorylation and subsequent degradation of IkappaB and the activation of the NF-kappaB (NF-B) pathway. Recent data indicate that the constitutive activation of the NF-B kappaB pathway by the human T-cell lymphotrophic virus, type I, Tax protein leads to enhanced phosphorylation of IKKamma/NEMO by IKKbeta. To address further the significance of IKKbeta-mediated phosphorylation of IKKgamma/NEMO, we determined the sites in IKKgamma/NEMO that were phosphorylated by IKKbeta, and we assayed whether IKKgamma/NEMO phosphorylation was involved in modulating IKKbeta activity. IKKgamma/NEMO is rapidly phosphorylated following treatment of cells with stimuli such as tumor necrosis factor-alpha and interleukin-1 that activate the NF-appa B pathway. By using both in vitro and in vivo assays, IKKbeta was found to phosphorylate IKKgamma/NEMO predominantly in its carboxyl terminus on serine residue 369 in addition to sites in the central region of this protein. Surprisingly, mutation of these carboxyl-terminal serine residues increased the ability of IKKgamma/NEMO to stimulate IKKbeta kinase activity. These results indicate that the differential phosphorylation of IKKgamma/NEMO by IKKbeta and perhaps other kinases may be important in regulating IKK activity.
The IkappaB kinase (IKK) complex includes the catalytic components IKKalpha (IKK) and IKKbeta (IKK) in addition to the scaffold protein IKKgamma (IKK)/NEMO. Increases in the activity Activation of the IKK complex results in the phosphorylation and subsequent degradation of IkappaB and the activation of the NF-kappaB (NF-B) pathway. Recent data indicate that the constitutive activation of the NF-kB pathway by the human T-cell lymphotrophic virus, type I, Tax protein leads to enhanced phosphorylation of IKK/NEMO by IKK. To address further the significance of IKK-mediated phosphorylation of IKK/NEMO, we determined the sites in IKK/NEMO that were phosphorylated by IKK, and Wwe also assayed whether IKK/NEMO phosphorylation was involved in modulating IKK activity. We found that IKK/NEMO wasis rapidly phosphorylated following treatment of cells with stimuli such as stimulation by tumor necrosis factor-alpha and interleukin-1 that activate the NF-B pathway. By using both in vitro and in vivo assays, IKK was found to phosphorylate IKK/NEMO predominantly in its carboxyl terminus on serine residue 369 in addition to sites in the central region of this protein. Surprisingly, mutation of these carboxyl-terminal serine residues increased the ability of IKK/NEMO to stimulate IKK kinase activity. These results indicate that the differential phosphorylation of IKK/NEMO by IKK and perhaps other kinases may be important in regulating IKK activity.
Tips for the abstract
The Revised Abstract
The IkappaB kinase (IKK) complex includes the catalytic components IKKalpha (IKK) and IKKbeta (IKK) in addition to the scaffold protein IKKgamma (IKK)/NEMO. Activation of the IKK complex results in the phosphorylation and subsequent degradation of IkappaB and the activation of the NF-kappaB (NF-B) pathway. Recent data indicate that the constitutive activation of the NF-kB pathway by the human T-cell lymphotrophic virus, type I, Tax protein leads to enhanced phosphorylation of IKK/NEMO by IKK. To address the significance of IKK-mediated phosphorylation of IKK/NEMO, we determined the sites in IKK/NEMO that were phosphorylated by IKK We also assayed whether IKK/NEMO phosphorylation was involved in modulating IKK activity. Our result showed that IKK/NEMO was rapidly phosphorylated following stimulation by tumor necrosis factor-alpha and interleukin-1 that activate the NF-B pathway. IKK was found to phosphorylate IKK/NEMO predominantly in its carboxyl terminus on serine residue 369 in addition to sites in the central region of this protein. Surprisingly, mutation of these carboxyl-terminal serine residues increased the ability of IKK/NEMO to stimulate IKK kinase activity. These results indicate that the differential phosphorylation of IKK/NEMO by IKK and perhaps other kinases may be important in regulating IKK activity.
One paragraph, 201=>191 words
Use simple words & abbreviationsWrite short and simple sentencesVerb tensesSignal Topics
Common Problems in Abstracts
Excessive details (length) => make the abstract unreadable (the trees overshadow the forest)
Omitting the question or Stating the question vaguely => No goal for this work
Answer not stated => No ending
The Divided Abstract
Abstracts for conferences show a valuable contribution lure audiences to your talk
Follow the most of guidelines as abstracts of research papers.
To encourage speculation, alternative theories, and suggestion for further research, the conference abstract is not as strict as the abstract for research papers.
Abstracts for conferences (I)
Abstracts for conferences (II)
Several differences as below: => include more details for methods => display data in a table or a graph sometimes => include more implications (to indicate the importance of the work)
Abstracts for conferences self-destruct after a year.
If the paper is not published eventually, the details and data in the conference abstract can not be used because of no validation.
A Example of the Conference Abstract
Indicative (Descriptive) Abstracts
Usually for the review articles Tell readers what information the article
contains
Include the purpose, methods, and scope of the article
DO NOT provide results, conclusions, or recommendations
A Example of an indicative abstract
The IkappaB kinase (IKK) complex includes the catalytic components IKKalpha and IKKbeta
in addition to the scaffold protein IKKgamma/NEMO. Increases in the activity of the IKK
complex result in the phosphorylation and subsequent degradation of IkappaB and the
activation
of the NF-kappaB pathway. Recent data indicate that the constitutive activation of the NF-
kappaB pathway by the human T-cell lymphotrophic virus, type I, Tax protein leads to
enhanced phosphorylation of IKKgamma/NEMO by IKKbeta. To address further the
significance of IKKbeta-mediated phosphorylation of IKKgamma/NEMO, we determined the
sites in IKKgamma/NEMO that were phosphorylated by IKKbeta, and we assayed whether
IKKgamma/NEMO phosphorylation was involved in modulating IKKbeta activity.
IKKgamma/NEMO is rapidly phosphorylated following treatment of cells with stimuli such as
tumor necrosis factor-alpha and interleukin-1 that activate the NF-kappaB pathway. By using
both in vitro and in vivo assays, IKKbeta was found to phosphorylate IKKgamma/NEMO
predominantly in its carboxyl terminus on serine residue 369 in addition to sites in the central
region of this protein. Surprisingly, mutation of these carboxyl-terminal serine residues
increased the ability of IKKgamma/NEMO to stimulate IKKbeta kinase activity. These results
indicate that the differential phosphorylation of IKKgamma/NEMO by IKKbeta and perhaps
other kinases may be important in regulating IKK activity.