Scientific Reading and Writing in English Lectures on: 12/01, 12/22 Abstract & Practice12/08, 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 ( ), Ph.D. Department of Microbiology & Immunology, NCKUext 5632lingpin@mail.ncku.edu.tw

How to prepare the abstract?Definition and function of the abstract

Organization of the abstract

Tips for writing the abstract

Example and practiceYour involvement is the key to success in this lecture. Speak Up!

The Structure of A Paper

TitleAbstractIntroductionMaterials & MethodsResults & FiguresDiscussionReferences

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 articlesto Pull Out

The function of the abstractThe first contact to readers ReadersA good abstract delivers the papers 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.

The Organization of the abstract (II)

Definition and function of the abstract

Organization of the abstract

Tips for writing the abstract

Example and practiceHow to prepare the abstract?

Tips for writing the abstractTiming to write the abstract

Length

Sentence structure & word choice

Other issues

The Structure of A Paper

TitleAbstractIntroductionMaterials & MethodsResults & FiguresDiscussionReferences

The order to write a paperWrite the main text first and then the overview sections

The length of the abstractOne 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 StructureWrite short and simple sentences

Short sentences are easy for readers to follow up.

By contrast, long sentences tend to make readers lost.

Word choice & AbbreviationsUse 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-kB 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 abstractVerb 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 practiceHow to prepare the abstract?

Example of an informative abstractRegulation of IkB Kinase (IKK)g/NEMO Function by IKKb-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. 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-1Introduction(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-2Purpose(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-3What 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-4What 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& ImplicationDissection of the abstract-5

Any suggestion for the abstract?

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.

Tips for the abstractUse simple words and define abbreviations

Write short and simple sentences

Verb tenses

Continuity

Signal Topics

Define the Abbreviations

Tips for the abstract

The Revised AbstractThe IkappaB kinase (IKK) complex includes the catalytic components IKKalpha (IKKa) and IKKbeta (IKKb) in addition to the scaffold protein IKKgamma (IKKg)/NEMO. Activation of the IKK complex results in the phosphorylation and subsequent degradation of IkappaB and the activation of the NF-kappaB (NF-kB) 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 IKKg/NEMO by IKKb. To address the significance of IKKb-mediated phosphorylation of IKKg/NEMO, we determined the sites in IKKg/NEMO that were phosphorylated by IKKb. We also assayed whether IKKg/NEMO phosphorylation was involved in modulating IKKb activity. Our result showed that IKKg/NEMO was rapidly phosphorylated following stimulation by tumor necrosis factor-alpha and interleukin-1 that activate the NF-kB pathway. IKKb was found to phosphorylate IKKg/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 IKKg/NEMO to stimulate IKKb kinase activity. These results indicate that the differential phosphorylation of IKKg/NEMO by IKKb and perhaps other kinases may be important in regulating IKK activity. One paragraph, 201=>191 wordsUse simple words & abbreviationsWrite short and simple sentencesVerb tensesSignal Topics

Common Problems in AbstractsExcessive 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 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.