Scientific Reading and Writing in English

Scientific Reading and Writing in English

Lectures on:

12/11 “Abstract”12/18 “References, Acknowledgements, and Front page” 12/25 “Cover letter”

Readings: “How to Write & Publish a Scientific Paper” by Robert A. Day, 5th Edition

Pin Ling ( 凌斌 ), Ph.D. Department of Microbiology & Immunology, NCKUext [email protected]

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.

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 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

The function of the abstract

the first contact to readers

Readers

A Good Abstract The Whole Paper

A Poor AbstractXThe Whole Paper

A good abstract delivers the paper’s key points “Concisely and Precisely”.






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)

The Organization of the abstract (II)

Pull out the key information from each part to form a paragraph.

Conclusions & Discussion

Results & Figures

Materials & Methods

Introduction & Purpose

Abstract (one paragraph)

Title (a sentence)







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

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 (g) => 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.






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. From the Division of Hematology-Oncology, Department of Medicine, Harold Simmons Cancer Center, University of TexasSouthwestern Medical Center, Dallas, Texas 75390

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.

Example of an informative abstract

One paragraph, 201 words

Introduction(Background)


Dissection of the abstract


Purpose(Question)



J Biol Chem. 2002 Jul 5;277(27):24331-9.


What was done


What was found



Answer& Implication



Suggestions for the abstract

Tips for the abstract

Use simple words and define abbreviations

Write short and simple sentences

Verb tenses

Continuity

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.

Tips for the abstract

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.

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 wordsUse 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

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

What you should include in the abstract section…5 elements

• The goal is to include all the important information in the paper.• Background (B)• Purpose (P)• Method (M)• Results (R)• Conclusion (C) Sometimes, sentences with the combination of two elements have to be used. (the shortest abstract I have seen: 2-3 paragraphs)

Two common forms of abstract

• A “structured” abstract includes headings that reflect the main elements of the paper. More explicit details are usually required.

• A single-paragraph abstract includes all the contents in a single text block.

Structured AbstractPrognostic Value of Myeloperoxidase in Patients with Chest Pain NEJM 349:1595-1604 October 23, 2003

Background Inflammation is linked to adverse outcomes in acute coronary syndromes. Myeloperoxidase, an abundant leukocyte enzyme, is elevated in culprit lesions that have fissured or ruptured in patients with sudden death from cardiac causes. Numerous lines of evidence suggest mechanistic links between myeloperoxidase and both inflammation and cardiovascular disease. (In this example, purpose and methods are combined)Methods We assessed the value of plasma levels of myeloperoxidase as a predictor of the risk of cardiovascular events in 604 sequential patients presenting to the emergency department with chest pain.

Results Initial plasma myeloperoxidase levels predicted the risk of myocardial infarction, even in patients who are negative for troponin T (<0.1 ng per milliliter) at base line (P<0.001). Myeloperoxidase levels at presentation also predicted the risk of major adverse cardiac events (myocardial infarction, the need for revascularization, or death) within 30 days and 6 months after presentation (P<0.001). In patients without evidence of myocardial necrosis (defined as those who were negative for troponin T), the base-line myeloperoxidase levels independently predicted the risk of major adverse coronary events at 30 days (unadjusted 2nd, 3rd, and 4th quartile odds ratios, 2.2 [95 percent confidence interval, 1.1 to 4.6], 4.2 [95 percent confidence interval, 2.1 to 8.4], and 4.1 [95 percent confidence interval, 2.0 to 8.4], respectively) and at 6 months.

Conclusions A single initial measurement of plasma myeloperoxidase independently predicts the early risk of myocardial infarction, as well as the risk of major adverse cardiac events in the ensuing 30-day and 6-month periods. Myeloperoxidase levels, in contrast to troponin T, creatine kinase MB isoform, and C-reactive protein levels, identified patients at risk for cardiac events in the absence of myocardial necrosis, highlighting its potential usefulness for risk stratification among patients who present with chest pain.

Example of an informative abstract

Informative Abstract

communicate specific information from the article include the purpose, methods, and scope of the

article. provide the article's results, conclusions, and

recommendations. are short -- from a paragraph to a page or two.

Usually informative abstracts are 10% or less of the length of the original piece.

allow readers to decide whether they want to read

the article

A single-paragraph abstract Indicative and informative abstracts

• Indicative (Descriptive) abstracts, stating what the paper is about, are usually for long review papers. (contain descriptive info: illustration of previous and current concepts)

• Informative abstracts are for most research papers (five elements).

Writing an Informative Abstract

• Be orderly, succinct, and concrete Use active verbs such as “report”, “propose”, and “analyze” rather than static verbs such as “is”, “are”, and “appears to be”. • State the core issue, research question, or objective of the research• Briefly describe the methods.• Interpret the results (supporting or against the hypothesis)• Draw conclusions and state implications

Format A

1. Introductory statement, including motivation/problem statement (sometimes not needed)

2. Approach : research methodology3. Results or other main points (absolutely essential)4. Concluding statement, telling what the results meanNote: including all the keywords in the abstract.

Format B

1. Re-establish the topic of the research2. Give the research problem and/or main objective

of the research (this usually comes first)3. Indicate the methodology used4. Present the main findings5. Present the main conclusions

1. Single paragraph, and concise.2. As a summary of work done, it is always written in

past tense.3. An abstract should stand on its own, and not refer to any

other part of the paper such as a figure or table.4. Focus on summarizing results---limit background info to

a sentence or two, if absolutely necessary.5. What you report in an abstract must be consistent with

what you reported in the paper.6. Correct spelling, clarity of sentences and phrases, and

proper reporting of quantities are just as important in an abstract as they are anywhere else.

Styles

The word limitation of abstract

• A limit of 200 or 250 words is usually implemented.

• MEDLINE truncate abstract text at 250 words: The conclusion and results parts of the abstract will often disappear if the truncation happens.

What do you expect in an ideal abstract

An introduction shorter enough to let you quickly understand the background of the study

A question specific enough to let you catch the center of the authors’ scientific pursuit.

An approach to answer or solve the question. A bottom line of the finding

What do you want to write in an abstract

An introduction shorter enough to let others quickly understand the background of the study

A question specific enough to let others catch the center of your scientific pursuit.

An approach to answer or solve the question. A bottom line of your finding

Qualities of a Good Abstract uses one or more well developed paragraphs: these are

unified, coherent, concise, and able to stand alone. uses an introduction/body/conclusion structure which

presents the article, paper, or report's purpose, results, conclusions, and recommendations in that order.

follows strictly the chronology of the article, paper, or report.

provides logical connections (or transitions) between the information included.

adds no new information, but simply summarizes the report.

is understandable to a wide audience. oftentimes uses passive verbs to downplay the author

and emphasize the information.

Steps for writing effective abstracts…1

Reread the paper with the goal of abstracting in mind. Look specifically for these main parts of the article:

purpose, methods, scope, results, conclusions, and recommendation.

Use the headings, outline heads, and table of contents as a guide.

If you're writing an abstract about another person's article, the introduction and the summary are good places to begin. These areas generally cover what the article emphasizes.

After you've finished rereading the article, write a rough draft without looking back at what you're abstracting. Don't merely copy key sentences from the article,

paper, or report: you'll put in too much or too little information.

Don't rely on the way material was phrased in the article, paper, or report: summarize information in a new way.


Revise your rough draft to correct weaknesses in organization. improve transitions from point to point. drop unnecessary information. add important information you left out. eliminate wordiness. fix errors in grammar, spelling, and

punctuation.


Print your final copy and read it again to catch any glitches that you find


Something helpful Using Commas Misplaced/dangling modifiers Transitional Words & Phrases

Using Comma My father went to the store for some dessert and bought ice

cream. My father went to the store for some dessert, bought ice

cream, and came home in time to see his favorite TV show. Comma? Yes. Three or more verb phrases describing the

action of the same subject need commas to separate them.

The text Who Built America? describes Reconstruction as a noble failure.

Comma? No. If Who Built America? was taken out of the sentence, when a reader reads "text," they would not know which text the writer means, so commas are not used when the title is in the sentence.

Practice using commas Because I was three hours short of graduation requirements I had to take a course

during the summer. Because I was three hours short of graduation requirements, I had to take a

course during the summer.The comma separates an introductory phrase or dependent clause from the rest of the sentence.

The weather according to last night's forecast will improve by Saturday. The weather, according to last night's forecast, will improve by Saturday.

The phrase "according to last night's forecast" interrupts the main clause, so it is set off by commas.

Students hurried to the campus store to buy their fall textbooks but several of the books were already out of stock.

Students hurried to the campus store to buy their fall textbooks, but several of the books were already out of stock.The comma separates an independent clause from a dependent clause.

My sister asked "Are you going to be on the phone much longer?" My sister asked, "Are you going to be on the phone much longer?"

The comma separates a direct quotation from the rest of the sentence.

Misplaced/dangling modifiers

Roger looked at twenty-five sofas shopping on Saturday. Obviously twenty-five sofas were not shopping on Saturday. Because "shopping

on Saturday" is meant to modify Roger, it should be right next to Roger, as follows: Shopping on Saturday, Roger looked at twenty-five sofas. The woman tore open the package she had just received with her fingernails. Had the woman really received the package with her fingernails? The writer meant

that she tore open the package with her fingernails. With her fingernails, the woman tore open the package she had just received. The waiter brought the pancakes to the table drenched in blueberry syrup. What's drenched according to the sentence? The waiter, the table, or the

pancakes? Actually, the pancakes were drenched: The waiter brought the pancakes, drenched in blueberry syrup, to the table. Lying in a heap on the closet floor, Jean found her son's dirty laundry. It sounds as if Jean was lying on the closet floor when she found her son's laundry! Jean found her son's dirty laundry lying in a heap on the closet floor.

Mechanism of Suppression of Non-transmissible Pneumonia in Mice Induced by Newcastle Disease Virus…J. Bacteriol.

Mechanism of Suppression of Non-transmissible Pneumonia induced in Mice by Newcastle…….

Characterization of Bacteria Causing Mastitis by Gas-Liquid Chromatography…J. Clinic. Micro.

Using a fiberoptic bronchoscope, dogs were immunized with sheep red blood cells.

Isolation of Antigens from Monkeys Using Complement-Fixation Techniques.

Misplaced/dangling modifiers

Transitional Words & Phrases

Using transitional words and phrases: helps papers read more smoothly by providing coherence (Although it helps, do not use too many of these)

Transitions indicate relations: supporting ideas may have followed by a list of "transitional" words and phrases that can connect those ideas:

Addition:also, besides, furthermore, in addition, moreover, again

Consequence:accordingly, as a result, consequently, hence, otherwise,so then, therefore, thus, thereupon

Summarizing:after all, all in all, all things considered, briefly, by and large, in any case, in any event, in brief, in conclusion, on the whole, in short, in summary, in the final analysis, in the long run, on balance, to sum up, to summarize, finally

Generalizing:as a rule, as usual, for the most part,generally, generally speaking, ordinarily, usually

Restatement:in essence, in other words, namely, that is, that is to say,in short, in brief, to put it differently

Contrast and Comparison:contrast, by the same token, conversely, instead, likewise,on one hand, on the other hand, on the contrary, rather,similarly, yet, but, however, still, nevertheless, in contrast

Sequence:at first, first of all, to begin with, in the first place, at the same time,for now, for the time being, the next step, in time, in turn, later on,meanwhile, next, then, soon, the meantime, later, while, earlier,simultaneously, afterward, in conclusion

Diversion:by the way, incidentally

Illustration:for example, for instance, for one thing

Similarity:likewise, similar, moreover

Direction:here, there, over there, beyond, nearly, opposite, under, above,to the left, to the right, in the distance

Transitional Words & Phrases

No complex sentences please

The health authority has been ordered to pay a million dollars to Mr. X who fell off a car roof and suffered severe head injuries because a doctor at the hospital failed to diagnose a skull fracture.

Is this a clear sentence?

Traps in connections

Corrections:The health authority has been ordered to pay $1,000,000 damages to Mr. X, who fell off a car roof and suffered severe head injuries, because a doctor at the hospital failed to diagnose a skull fracture.

Because a doctor at the hospital failed to diagnose a skull fracture after Mr. X fell off a car roof and suffered severe head injuries, the health authority has been ordered to pay him $1,000,000 damages.

The health authority has been ordered to pay $1,000,000 damages to Mr. X, because a doctor at the hospital failed to diagnose a skull fracture after he fell off a car roof and suffered severe head injuries.

Traps in metaphors

Grossly obese patients often fall in to this group.

Traps in metaphors

Correction:Grossly obese patients often are in this category.

Make it simple!

Blood was taken for analysis prior to sacrifice of the animal.

Make it simple

Correction:Blood was taken for analysis before the animal was killed.

Blood for later analysis was taken before the animal was killed.

Blood was taken for analysis prior to sacrifice of the animal.

Passive and active voice

The index finger of the surgeon was then inserted into the atrium. The valve was palpated.

Passive and active voice

Correction:The surgeon then put his finger into the atrium and palpated the valve.

The index finger of the surgeon was then inserted into the atrium. The valve was palpated.

I. Look up the papers (1) “Prolonged exposure of T cells to TNF down-regulates TCR zeta and expression of the TCR/CD3 complex at the cell surface. J Immunol. 2001 May 1;166(9):5495-507.”, or (2) Diverse hepatitis C virus glycoproteins mediate viral infection in a CD81-dependent manner. J Virol. 2004 Aug;78(16):8496-505.

List sentences that serve the functions of B, P, M, R, C.

2. Shorten the abstract to <150 words.

II. Write a 200 word abstract of your favorite project and be prepared to present to the class in next session.

Homework

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Scientific Reading and Writing in English