Slides: Manuscript Writing Workshop 10-2-14

Part I: Principles of Effective Writing

Kristin Sainani, PhD Stanford University October 2, 2014

A few examples to start… n  This was the first sentence of an article in the Journal

of Clinical Oncology (Introduction section): n  “Adoptive cell transfer (ACT) immunotherapy is based

on the ex vivo selection of tumor-reactive lymphocytes, and their activation and numerical expression before reinfusion to the autologous tumor-bearing host.”

n  Ask Yourself: n  Is this sentence easy to understand? n  Is this sentence enjoyable and interesting to read?

And here’s the final sentence from the same article…

n  “Current studies in our laboratory are focused on the logistical aspects of generating autologous-cell based patient treatments, the genetic modification of lymphocytes with T-cell receptor genes and cytokine genes to change their specificity or improve their persistence, and the administration of antigen specific vaccines to augment the function of transferred cells.”

n  This is classic academic writing: boring, unreadable, written to obscure rather than to inform!

A classic hallmark of academic writing: spunky verbs become clunky nouns…

n  “Adoptive cell transfer (ACT) immunotherapy is based on the ex vivo selection of tumor-reactive lymphocytes, and their activation and numerical expression before reinfusion to the autologous tumor-bearing host.”

n  “Current studies in our laboratory are focused on the

logistical aspects of generating autologous-cell based patient treatments, the genetic modification of lymphocytes with T-cell receptor genes and cytokine genes to change their specificity or improve their persistence, and the administration of antigen specific vaccines to augment the function of transferred cells.”

“My professor friend told me that in his academic world, ‘publish or perish’ is really true. He doesn’t care if nobody reads it or understands it as long as it’s published.”

There’s a hint of truth here, n’est-ce pas?

From: Anne Ku. “The joys and pains of writing and editing,” Le Bon Journal, 2003 http://www.bonjournal.com/volume2/issue1writing.pdf

Another example…

Dysregulation of physiologic microRNA (miR) activity has been shown to play an important role in tumor initiation and progression, including gliomagenesis. Therefore, molecular species that can regulate miR activity on their target RNAs without affecting the expression of relevant mature miRs may play equally relevant roles in cancer.

From an article in Cell

Example


Note the use of nouns instead of verbs.

Example


Note the use of vague words.

Example


Note the use of unnecessary jargon and acronyms.

Example


Note the passive voice.

Example


Note the distance between the subject and the main verb of this sentence.

Possible rewrite…

n  Changes in microRNA expression play a role in cancer, including glioma. Therefore, events that disrupt microRNAs from binding to their target RNAs may also promote cancer.

Principles of effective writing

n  “Vigorous writing is concise. A sentence should contain no unnecessary words, a paragraph no unnecessary sentences, for the same reason that a drawing should have no unnecessary lines and a machine no unnecessary parts. This requires not that the writer make all his sentences short, or that he avoid all detail and treat his subjects only in outline, but that every word tell.”

-- Strunk and White, The Elements of Style

“The secret of good writing is to strip every sentence to its cleanest components. Every word that serves no function, every long word that could be a short word, every adverb that carries the same meaning that’s already in the verb, every passive construction that leaves the reader unsure of who is doing what—these are the thousand and one adulterants that weaken the strength of a sentence. And they usually occur in proportion to the education and rank.”

-- William Zinsser in On Writing Well, 1976



Three lessons: •  1. Cut unnecessary words and phrases; learn to

part with your words! •  2. Follow: subject + verb + object (active voice) •  3. Write with verbs: use strong verbs, avoid

turning verbs into nouns, and don’t bury the main verb!

Don’t be afraid to cut! •  1. Cut unnecessary words and phrases

Cut unnecessary words Example:

“This paper provides a review of the basic tenets of cancer biology study design, using as examples studies that illustrate the methodologic challenges or that demonstrate successful solutions to the difficulties inherent in biological research.”

s

and

“This paper reviews cancer biology study design, using examples that illustrate specific challenges and solutions.”

Cut unnecessary words Example:

“As it is well known, increased athletic activity has been related to a profile of lower cardiovascular risk, lower blood pressure levels, and improved muscular and cardio-respiratory performance.”

à

I

fitness.

“Increased athletic activity is associated with lower cardiovascular risk, lower blood pressure, and improved fitness.” “Increased athletic activity lowers cardiovascular risk and blood pressure, and improves fitness.” (stronger level of evidence)

is associated with

Cut unnecessary words

Hunt down and cast out all unneeded words that might slow your reader. n  Dead weight words and phrases (“as it is well known”, “as it

has been shown”, “it can be regarded that”) n  Empty words and phrases (“basic tenets of”, “methodologic”) n  Long words or phrases that could be short (“muscular and

cardiorespiratory performance”) n  Unnecessary jargon (“muscular and cardiorespiratory

performance”) n  Repetitive words or phrases (illustrate/demonstrate;

challenges/difficulties) n  Adverbs (very, really, quite, basically, generally)

Long words and phrases that could be short…

n  A majority of most n  A number of many n  Are of the same opinion agree n  Less frequently occurring rare n  All three of the the three n  Give rise to cause n  Due to the fact that because n  Have an effect on affect

Wordy version Crisp version

Cut unnecessary words

n  Be vigilant and ruthless

n  After investing much effort to put words on a page, we often find it hard to part with them.

But fight their seductive pull… n  Try the sentence without the extra words and

see how it’s better—conveys the same idea with more power

Cutting extra words

Example: “Brain injury incidence shows two peak

periods in almost all reports: rates are the highest in young people and the elderly.”

More punchà “Brain injury incidence peaks in the young

and the elderly.”

“I have only made this letter rather long

because I have not had time to make it shorter.” (“Je n'ai fait celle-ci plus longue que parceque je n'ai pas eu le loisir de la faire plus courte.”)

--Lettres provinciales, 16, Dec.14,1656 (though reference also attributed to St. Augustine, and

Cicero….)

Blaise Pascal on the elegance in brevity:

Practice: cut the clutter!

Anti-inflammatory drugs may be protective for the occurrence of Alzheimer’s Disease.

Possible rewrite

Anti-inflammatory drugs may protect against Alzheimer’s Disease.

Possible rewrite

Anti-inflammatory drugs may protect against Alzheimer’s Disease.

Practice

Clinical seizures have been estimated to occur in 0.5% to 2.3% of the neonatal population.

Possible rewrite

Clinical seizures occur in 0.5% to 2.3% of newborns.

Practice

To control infection with Mycobacterium tuberculosis (M. tb), a robust T cell-mediated immune response is necessary, and deficiency in this response predisposes an individual towards active TB.

Possible rewrite

A deficient T-cell response predisposes an individual to active TB.

Use active voice

•  2. Follow: subject + verb + object (active voice!)

Use active voice

“Subject verb object” “Subject verb object” “Subject verb object” “Subject verb object” or just… “Subject verb”

Use active voice

The passive voice…. n  Object-Verb-Subject or just Object-Verb n  Classic example: “Mistakes were made.” n  Passive verb = a form of the verb “to be” +

the past participle of the main verb n  The main verb must be a transitive verb

(that is, take an object).

Use active voice

Examples… Passive: My first visit to Boston will always be

remembered by me.

Active: I will always remember my first visit to Boston.

Object

Subject Verb

From: Strunk and White

Use active voice

"Cigarette ads were designed to appeal especially to children."

vs. "We designed the cigarette ads to appeal especially to

children.” Responsible party!

Use active voice

Passive: General dysfunction of the immune system has been suggested at the leukocyte level in both animal and human studies.

à

Active: Both human and animal studies suggest that diabetics have general immune dysfunction at the leukocyte level.

Use active voice

Passive: Increased promoter occupancy and transcriptional activation of p21 and other target genes were observed.

à

Active: We observed increased promoter occupancy and transcriptional activation of p21 and other target genes.

Practice: use the active voice

A recommendation was made by the DSMB committee that the study be halted.

In the active voice…

The DSMB committee recommended that the study be halted.

Major differences in the reaction times of the two study subjects were found.


We found major differences in the reaction times of the two study subjects.



The activation of Ca++ channels is induced by the depletion of endoplasmic reticulum Ca++ stores.


Depleting Ca++ from the endoplasmic reticulum activates Ca++ channels.

Use strong verbs

3. Write with verbs: •  use strong verbs •  avoid turning verbs into nouns •  don’t bury the main verb

Use strong verbs Verbs make sentences go! Compare: “Loud music came from speakers embedded in

the walls, and the entire arena moved as the hungry crowd got to its feet.”

With: “Loud music exploded from speakers embedded in the walls, and the entire arena shook as the hungry crowd leaped to its feet.”

Latter sentence from the novel: Bringing Down the House, Ben Mezrich

Use strong verbs Verbs make sentences go! Compare: “Loud music came from speakers embedded in

the walls, and the entire arena moved as the hungry crowd got to its feet.”

With: “Loud music exploded from speakers embedded in the walls, and the entire arena shook as the hungry crowd leaped to its feet.”

Latter sentence from the novel: Bringing Down the House, Ben Mezrich

Don’t turn verbs into nouns

Don’t kill verbs by turning them into nouns.


Example: During DNA damage, recognition of H3K4me3

by ING2 results in recruitment of Sin3/HDAC and repression of cell proliferation genes.


Example: During DNA damage, recognition of H3K4me3 by ING2 results in recruitment of Sin3/HDAC and repression of cell proliferation genes.

à During DNA damage, H3K4me3 recruits ING2 and Sin3/HDAC, which together repress cell proliferation genes. Say exactly who does what to whom!


Obtain estimates of

Has seen an expansion in

Provides a methodologic emphasis Take an assessment of

Weak verbs

Formerly spunky verbs transformed into boring nouns

estimate has expanded emphasizes methodology assess


Provide a review of

Offer confirmation of

Make a decision Shows a peak

review confirm decide peaks

Don’t bury the main verb

Keep the subject and main verb (predicate) close together at the start of the sentence…

n  Readers are waiting for the verb!

Don’t bury the main verb The case of the buried predicate… One study of 930 adults with multiple sclerosis (MS) receiving care in one of two managed care settings or in a fee-for-service setting found that only two-thirds of those needing to contact a neurologist for an MS-related problem in the prior 6 months had done so (Vickrey et al 1999).

predicate

subject

Don’t bury the main verb The case of the buried predicate…

One study found that, of 930 adults with multiple sclerosis (MS) who were receiving care in one of two managed care settings or in a fee-for-service setting, only two-thirds of those needing to contact a neurologist for an MS-related problem in the prior six months had done so (Vickrey et al 1999).

Practice: write with verbs

“The fear expressed by some teachers that students would not learn statistics well if they were permitted to use canned computer programs has not been realized in our experience. A careful monitoring of achievement levels before and after the introduction of computers in the teaching of our course revealed no appreciable change in students’ performances.”

Practice Exercises


Really long subject!

Passive voice

Practice Exercises


Buried predicate + boring verb

Really long subject! “hedge” word

Possible rewrite

Many teachers feared that the use of canned computer programs would prevent students from learning statistics. We monitored student achievement levels before and after the introduction of computers in our course and found no detriments in performance.

Take-home messages

Effective scientific writing conveys an idea clearly and concisely.

Scientific writing should be easy and even enjoyable to read.

Three key principles of effective writing: •  1. Cut all unnecessary words and phrases. •  2. Use the active voice (subject-verb-object). •  3. Write with verbs.

Editing Exercises, in groups of 2-3

Possible Answers (1)

n  H. pylori infection causes an acute increase in gastric acid (hyperchlorhydria) followed by a decrease (hypochlorhydria) that lasts up to eight months (1). Hypochlorhydria increases the host’s susceptibility to pathogens such as cholera, typhoid, and shigella (2). With such superinfections, the host may produce copious stool and emesis—the vehicles necessary to spread H. pylori. This may lead to malnutrition and chronic diarrhea (3).

n  Chronic H. pylori infection increases gastric pH. This elevated pH increases the host’s susceptibility to gastrointestinal superinfection, which may propagate H. pylori infection via diarrhea and vomiting.

Possible Answers (2)

n  There is no standard approach for assessing ulnar collateral flow prior to harvesting the radial artery. This review examines the benefits and drawbacks of common approaches.

n  We will examine the controversy surrounding methods for assessing ulnar collateral flow prior to harvesting the radial artery.

Possible Answer (3)

n  Breast cancer is the most common non-skin cancer in U.S women, with 267,000 new cases in 2003. Between 1975 and 2000 breast cancer prevalence increased by 4% in women over 40 but remained constant in those under 40. This suggests underlying genetic causes, given comparable screening patterns and lifestyle-related risk factors.

Part II: The Writing Process

Have you ever?

Got stuck on a paragraph for several hours?

Got stuck on one sentence for more

than an hour?

There are two kinds of stuck in writing!

n  1. Problems with the logic/ideas n  Can only be fixed by figuring out what you are

trying to say. n  Staring at the page will not help! n  Rearranging words on the page will not help!

n  2. Problems with the prose n  May be fixed by focusing on word order and word

choice.

Steps in the writing process:

1. Prewriting 2. Writing the first draft 3. Revision

What does your writing process look like now?

Proportionally, how much time do you think you spend on each step?

1. Prewriting 2. Writing 3. Revision

What I think it should be (roughly!):

1. Prewriting (70%) 2. Writing the first draft (10%) 3. Revision (20%)

1. Prewriting tips

Get organized first: n Don’t try to write and gather information simultaneously! n Gather and organize information BEFORE writing the first draft.

Develop a road-map

n  Arrange key facts and citations from the literature into a crude road map/outline BEFORE writing the first draft.

n  Think in paragraphs and sections…

Example “road-map”

Brainstorm away from the computer n  Write on the go!

n  While exercising (Turn off that ipod!) n  While driving alone (Turn off the radio!) n  While waiting in line (Put down the magazine!)

n  Work out take-home messages n  Organize your paper n  Write memorable lines

2. First draft tips: n  Don’t be a perfectionist! n  The goal of the first draft is to get the ideas

down in complete sentences in order. n  Focus on logical organization more than

sentence-level details.

n  Writing the first draft is the hardest step for most people. Minimize the pain by writing the first draft quickly and efficiently!

Example of first-draft writing:

Errors in publication occur when the authors have typos, omissions, or such poor writing of the methods that others cannot figure out what they did or reproduce their tables and figures. Sometimes there’s just so much to write up that errors will occur in almost every case.

Revised version:

Published papers frequently have typos, omissions, and otherwise poor documentation of methods. These errors make it impossible to figure out exactly what was done or to reproduce the results.

Example of first-draft writing: The finding of these HLA alleles may have some practical implications as well. Now we all divide up into those who carry archaic DNA and those who don’t. A potential implication is that people who carry archaic HLAs could be more prone to autoimmunity. Autoimmunity is associated with HLA factors. There could be downsides to archaic HLAs. Since we’ve evolved separately from Neanterdals for a few hundred thousand years, we may have evolved important differences in the proteins that interact with HLA. The archaic HLAs may interact more poorly with some of these proteins, potentially causing mistakes, like autoimmunity. “This is all just speculation. But we have been apart for all this time, so it would be very surprising if there weren’t differences,” Parham says. “It would solve a long-standing puzzle.”

Revised version:

Neanderthal (or Denisovan) proteins continue to live on and function inside us; and this may also have a downside, Parham notes. Neanderthals evolved separately from us for a few hundred thousands years, so their proteins may be somewhat mismatched to our immune systems and could play a role in autoimmune disease. Autoimmunity is poorly understood but known to be related to HLA types. “This is all just speculation. But we have been apart for all this time, so it would be very surprising if there weren’t differences,” Parham says. “It would solve a long-standing puzzle.”

Example of first-draft writing:

It’s also difficult to study the biology because the brain is so inaccessible. Cancer scientists can take out a tumor and look directly at the cells, but autism researchers cannot directly study brain cells (except on autopsy), let alone developing brain cells. Stanford is on the cutting edge of solving this problem—in fact, Dolmetsch’s solution is so innovative it seems straight out of a science fiction novel.

Revised version:

It’s also difficult to access the brain. Scientists can slice cancer cells out of a tumor and directly study them, but they can’t just scoop cells out of the brain, let alone the developing brain. Stanford is on the cutting edge of solving this problem—in fact, Dolmetsch’s solution seems straight out of a science fiction novel.

Final version (after outside editing!):

Another impediment: access to the brain. Scientists can slice cancer cells out of a tumor and study them directly, but they can't just scoop cells out of the brain. Stanford is on the forefront of solving this problem—in fact, Dolmetsch's solution seems straight out of a science fiction novel.

3. Tips on revision •  Read your work out loud •  Do a verb check •  Get rid of clutter •  Do an organizational review •  Get feedback from others •  Get editing help

Do a verb check Underline the main verb in each sentence. Watch out for: (1) lackluster verbs (e.g., There are many students who struggle with chemistry.) (2) passive verbs (e.g., The reaction was observed by her.) (3) buried verbs (e.g., A careful monitoring of achievement levels before and after the introduction of computers in the teaching of our course revealed no appreciable change in students’ performances.).

Do an organizational review

In the margins of your paper, tag each paragraph with a phrase or sentence that sums up the main point. Then move paragraphs around to improve logical flow and bring similar ideas together.

Get outside feedback

Ask someone outside your department to read your manuscript.

Without any technical background, they should easily grasp: -the main findings -take-home messages -significance of your work

Ask them to point out particularly hard-to-read sentences and paragraphs!

Part III: The Original Manuscript

Recommended order for writing an original manuscript

n  1. Tables and Figures n  2. Results n  3. Methods n  4. Introduction n  5. Discussion n  6. Abstract

What verb tense do I use?

*Use past tense for completed actions: We found that… Women were more likely to… Men smoked more cigarettes than… The average reaction time was…

*Use the present tense for assertions that continue to

be true, such as what the tables show, what you believe, and what the data suggest: Figure 1 shows… The findings confirm… The data suggest… We believe that this shows…

Tables and Figures tell the story of your manuscript.

Figures and tables should stand alone. The reader should not need to refer back to the main text.

Editors, reviewers, and readers may look first (and maybe only) at titles, abstracts, and tables and figures!

1. Tables and Figures

2. Results ≠ Raw Data n  The results section should: n  Summarize what the data show

n  Point out simple relationships n  Describe big-picture trends n  Cite figures or tables that present supporting

data

n  Avoid simply repeating the numbers that are already available in tables and figures.

Results section exercise, in groups of 2-3

Possible Answer

n  Results n  Table 1 shows the characteristics of the study

subjects. The groups were similar in age and socioeconomic status. Obese sedentary men were heavier and larger than both lean groups; and lean exercisers had significantly lower body fat then lean sedentary men. Lean exercisers had higher VO2 max (l·min-1) and better fitness than both sedentary groups.

n 

3. Methods and Materials

•  Give a clear overview of what was done •  Give enough information to replicate the study

(like a recipe!)

•  Be complete, but make life easy for your reader! 1.  Break into smaller sections with subheadings 2.  Cite a reference for commonly used methods 3.  Display in a flow diagram or table where possible

•  You may use jargon and the passive voice more liberally in the methods section

Who, what, when, where, how, and why…

Reprinted, with permission, from: Annesley TM. Who, what, when, where, how, and why: The ingredients in the recipe for a successful methods section. Clinical Chemistry. June 2010 vol. 56 no. 6, 897-901.

4. Introduction

n  Good News: The introduction is easier to write than you may realize!

n  Follows a fairly standard format n  Typically 3 paragraphs long

n  Recommended range: 2 to 5

n  It is not an exhaustive review of your general topic n  should focus on the specific hypothesis/aim of

your study

Introduction

Reproduced with permission from: Annesley TM. "It was a cold and rainy night." Set the scene with a good introduction. Clinical Chemistry. May 2010 56: 708-713. (Figure 1)

Introduction

1. What’s known 2. What’s unknown n  limitations and gaps in previous studies

3. Your burning question/hypothesis/aim 4. Your experimental approach 5. Why your experimental approach is new and different

and important (fills in the gaps)

Mimi Zeiger. Essentials of Writing Biomedical Research Papers, McGraw Hill Professional, 1999

Corresponds to roughly 3 paragraphs…

1. What’s known 2. What’s unknown n  limitations and gaps in previous studies

3. Your burning question 4. Your experimental approach 5. Why your experimental approach is new and different

and important (fills in the gaps)

≈ Paragraph 1

≈ Paragraph 2

≈ Paragraph 3

The relations between excess body weight and mortality, not only from all causes but also from cardiovascular disease, are well established.1,2,3,4,5,6 Although we have known for some time that excess weight is also an important factor in death from cancer,7 our knowledge of the magnitude of the relation, both for all cancers and for cancers at individual sites, and the public health effect of excess weight in terms of total mortality from cancer is limited. Previous studies have consistently shown associations between adiposity and increased risk of cancers of the endometrium, kidney, gallbladder (in women), breast (in postmenopausal women), and colon (particularly in men).8,9,10,11,12 Adenocarcinoma of the esophagus has been linked to obesity.11,13,14 Data on

cancers of the pancreas, prostate, liver, cervix, and ovary and on hematopoietic cancers are scarce or inconsistent.7,8,9,10,11,15,16,17 The lack of consistency may be attributable to the limited number of studies (especially those with prospective cohorts), the limited range and variable categorization of overweight and obesity among studies, bias introduced by reverse causality with respect to smoking-related cancers, and possibly real differences between the effects of overweight and obesity on the incidence of cancer and on the rates of death from some cancers.18,19

We conducted a prospective investigation in a large cohort of U.S. men and women to determine the relations between body-mass index (the weight in kilograms divided by the square of the height in meters) and the risk of death from cancer at specific sites. This cohort has been used previously to examine the association of body-mass index and death from any cause.5

Eugenia E. Calle, Ph.D., Carmen Rodriguez, M.D., M.P.H., Kimberly Walker-Thurmond, B.A., and Michael J. Thun, M.D. Overweight, Obesity, and Mortality from Cancer in a Prospectively Studied Cohort of U.S. Adults. N Engl J Med 2003; 348:1625-1638.

Introduction, Example

The relations between excess body weight and mortality, not only from all causes but also from cardiovascular disease, are well established.1,2,3,4,5,6 Although we have known for some time that excess weight is also an important factor in death from cancer,7 our knowledge of the magnitude of the relation, both for all cancers and for cancers at individual sites, and the public health effect of excess weight in terms of total mortality from cancer is limited. Previous studies have consistently shown associations between adiposity and increased risk of cancers of the endometrium, kidney, gallbladder (in women), breast (in postmenopausal women), and colon (particularly in men).8,9,10,11,12 Adenocarcinoma of the esophagus has been linked to obesity.11,13,14 Data on

cancers of the pancreas, prostate, liver, cervix, and ovary and on hematopoietic cancers are scarce or inconsistent.7,8,9,10,11,15,16,17 The lack of consistency may be attributable to the limited number of studies (especially those with prospective cohorts), the limited range and variable categorization of overweight and obesity among studies, bias introduced by reverse causality with respect to smoking-related cancers, and possibly real differences between the effects of overweight and obesity on the incidence of cancer and on the rates of death from some cancers.18,19

We conducted a prospective investigation in a large cohort of U.S. men and women to determine the relations between body-mass index (the weight in kilograms divided by the square of the height in meters) and the risk of death from cancer at specific sites. This cohort has been used previously to examine the association of body-mass index and death from any cause.5

What’s known What’s unknown What’s known What’s unknown

Gaps/limitations of previous studies

“This study will answer the question with better methods.”

Exogenous estrogens prevent or substantially retard the decrease in bone mineral density (BMD) that accompanies menopause [1]. However, it is unclear whether exogenous estrogens, administered as oral contraceptives (OCs), can modify premenopausal BMD. Several studies suggest that exposure to OCs during the premenopausal years has a favorable effect on BMD [2-10], whereas other studies show no effect [11-18]. Past studies of the relationship between OC use and BMD have several limitations. Studies have focused primarily on crude measures of OC use, such as current, past and never. These categories combine diverse types of OC use and may reduce the power to detect an effect. Many studies also failed to take into account lifestyle characteristics of study participants. Finally, few studies have considered an effect of OCs on BMD in women of races other than white. The aim of this study was to evaluate the associations of OCs with spine, hip and whole body BMD in black and white premenopausal women. Our primary hypothesis was that there would be an association between cumulative exposure to estrogen from OCs and BMD.

Introduction Example

Osteoporos Int. 2002 Nov;13(11):893-900.

Exogenous estrogens prevent or substantially retard the decrease in bone mineral density (BMD) that accompanies menopause [1]. However, it is unclear whether exogenous estrogens, administered as oral contraceptives (OCs), can modify premenopausal BMD. Several studies suggest that exposure to OCs during the premenopausal years has a favorable effect on BMD [2-10], whereas other studies show no effect [11-18]. Past studies of the relationship between OC use and BMD have several limitations. Studies have focused primarily on crude measures of OC use, such as current, past and never. These categories combine diverse types of OC use and may reduce the power to detect an effect. Many studies also failed to take into account lifestyle characteristics of study participants. Finally, few studies have considered an effect of OCs on BMD in women of races other than white. The aim of this study was to evaluate the associations of OCs with spine, hip and whole body BMD in black and white premenopausal women. Our primary hypothesis was that there would be an association between cumulative exposure to estrogen from OCs and BMD.

What’s known

What’s unknown/the research question

The lit. review

Gaps in previous research

This study

Introduction Section Exercise

Introduction Section Exercise, paragraph 1

n  Ovarian cancer is the deadliest gynecologic cancer with a high mortality rate that has remained unchanged in the past four decades. The dismal prognosis of ovarian cancer is in large part due to the acquired resistance to chemotherapy. Epithelial ovarian cancer, the most common type of ovarian cancer, is initially responsive to cisplatin therapy. The recurrent disease, however, is often refractory to treatment and leads to mortality. New strategies to overcome drug resistance are urgently needed in order to reduce the mortality rate of ovarian cancer.

n 

Introduction Section paragraph 2 n  The discovery of small interfering RNA (siRNA) by Fire and Mello

in 1998 has provided new avenues of combating resistant cancers. Silencing genes that are involved in drug resistance using RNA interference (RNAi) can allow for reversing cisplatin resistance in ovarian cancer. Successful treatment of ovarian cancer cells with multidrug resistance (MDR) gene-silencing siRNAs and cisplatin requires the development of novel vehicles that can specifically and effectively deliver cisplatin to cell nuclei and siRNAs to cell cytoplasms, respectively. We report here the first use of nanoscale metal-organic frameworks (NMOFs) for the co-delivery of cisplatin and pooled siRNAs to overcome drug re-sistance in ovarian cancer cells.

n 

Introduction Section paragraph 3 n  MOFs are an emerging class of self-assembled, porous materials whose

properties can be readily tuned by varying the molecular building blocks. When scaled down to the nano-regime, NMOFs serve as efficient nanocarriers for the delivery of imaging contrast agents and chemotherapeutics. We surmised that NMOFs represent a unique nanocarrier platform by virtue of their high porosity and controllable surface functionalities: the large pores of NMOFs can be used to load chemotherapeutics while the metal ions on the NMOF surfaces can be used to bind siRNAs. The simultaneous and efficient delivery of cisplatin and pooled siRNAs to ovarian cancer cells can allow for enhanced anticancer efficacy by blocking multiple drug resistance pathways. In this work, cisplatin and siRNA were sequentially loaded into UiO NMOFs by covalent attachment to bridging ligands inside the NMOFs and coordinating to metal sites on the NMOF surfaces, respectively. UiO NMOFs protect siRNAs from nuclease degradation, enhance siRNA cellular uptake, and promote siRNA escape from endosomes to silence MDR genes in cisplatin-resistant ovarian cancer cells. As a result, co-delivery of cisplatin and siRNAs with NMOFs led to an order of magnitude enhancement in chemotherapeutic efficacy in vitro, as indicated by cell viability assay, DNA laddering, and Annexin V staining.

n 

5. The Discussion section… •  Gives you the most freedom •  Gives you the most chance to put good

writing on display •  Is the most challenging to write

The Discussion

Follow your rules for good writing!

Invert the cone!

Answer the question asked. Support your conclusion (your data, others’ data) Defend your conclusion (anticipate criticisms) Give the “big-picture” take-home message

I.e., what do my results mean and why should anyone care?

• Start with: “WE FOUND THAT…” (or something similar) • Explain what the data mean (big-picture!) • State if the findings are novel

Key finding (answer to the question(s) asked in Intro.)

Key secondary findings

• Give possible mechanisms or pathways • Compare your results with other people’s results • Discuss how your findings support or challenge the

paradigm

Context

• Anticipate readers’ questions/criticisms • Explain why your results are robust Strengths and limitations

• Recommended confirmatory studies (“needs to be confirmed”)

• Point out unanswered questions and future directions What’s next

• Give the big-picture (human) implications of basic science findings

• Tell readers why they should care

The “so what?”: implicate, speculate, recommend

• Restate your main finding. • Give a final take-home message. Strong conclusion

LAST PARAGRAPH OF INTRODUCTION: The differences in health benefits between a carbohydrate-restricted

diet and a calorie- and fat-restricted diet are of considerable public interest. However, there is concern that a carbohydrate-restricted diet will adversely affect serum lipid concentrations.1 Previous studies demonstrating that healthy volunteers following a low-carbohydrate diet can lose weight have involved few subjects, and few used a comparison group that followed consensus guidelines for weight loss.2,3 The reported effects of a carbohydrate-restricted diet on risk factors for atherosclerosis have varied.2,3,4 We performed a study designed to test the hypothesis that severely obese subjects with a high prevalence of diabetes or the metabolic syndrome [a] would have a greater weight loss, [b] without detrimental effects on risk factors for atherosclerosis, while on a carbohydrate-restricted (low-carbohydrate) diet than on a calorie- and fat-restricted (low-fat) diet.

Discussion, example

Samaha FF, Iqbal N, Seshadri P, et al. A low-carbohydrate as compared with a low-fat diet in severe obesity. N Engl J Med 2003;348:2074-2081

The Discussion 1. We found that severely obese subjects with a high prevalence of diabetes and the metabolic syndrome lost more weight in a six-month period on a carbohydrate-restricted diet than on a fat- and calorie-restricted diet. [answer to a] The greater weight loss in the low-carbohydrate group suggests a greater reduction in overall caloric intake, rather than a direct effect of macronutrient composition. [mechanisms] However, the explanation for this difference is not clear. Subjects in this group may have experienced greater satiety on a diet with liberal proportions of protein and fat. However, other potential explanations include the simplicity of the diet and improved compliance related to the novelty of the diet. [possible mechanisms/unanswered questions]

2. Subjects in the low-carbohydrate group had greater decreases in triglyceride levels than did subjects in the low-fat group; nondiabetic subjects on the low-carbohydrate diet had greater increases in insulin sensitivity, and subjects with diabetes on this diet had a greater improvement in glycemic control. No adverse effects on other serum lipid levels were observed. [answer to b] Most studies suggest that lowering triglyceride levels has an overall cardiovascular benefit.14,15,16 Insulin resistance promotes such atherosclerotic processes as inflammation,17 decreased size of low-density lipoprotein particles,18 and endothelial dysfunction.19 Impaired glycemic control in subjects with other

features of the metabolic syndrome markedly increases the risk of coronary artery disease.20 As expected, we found that the amount of weight lost had a significant effect on the degree of improvement in these metabolic factors. [comparison to previous studies and paradigms] However, even after adjustment for the differences in weight loss between the groups, assignment to the low-carbohydrate diet predicted greater improvements in triglyceride levels and insulin sensitivity. [unexpected] Subjects who lost more than 5 percent of their base-line weight on a carbohydrate-restricted diet had greater decreases in triglyceride levels than those who lost a similar amount of weight while following a calorie- and fat-restricted diet.

[supporting details]

3. There was a consistent trend across weight-loss strata toward

a greater increase in insulin sensitivity in the low-carbohydrate

group, although these changes were small and were not significant within each stratum. [supporting details: dose/response] Although greater weight loss could not entirely account for the greater decrease in triglyceride levels and increase in insulin sensitivity in the low-carbohydrate group, we cannot definitively conclude that carbohydrate restriction alone accounted for this independent effect. [mechanisms] Other uncontrolled variables, such as the types of carbohydrates selected (e.g., the proportion of complex carbohydrates or the ratio of carbohydrate to fiber), or other unknown variables may have contributed to this effect. In addition, more precise measurements of insulin sensitivity than we used would be needed to confirm this effect of a carbohydrate-restricted diet. [limitations/future studies]

4. Many of our subjects were taking lipid-lowering medications and hypoglycemic agents. Although enrolling these subjects introduced confounding variables, it allowed the inclusion of subjects with the obesity-related medical disorders typically encountered in clinical practice. Analyses from which these subjects were excluded still revealed greater improvements in insulin sensitivity and triglyceride levels on a carbohydrate-restricted diet than on a fat- and calorie-restricted diet. [limitations and how they were addressed]

5. Our study included a high proportion of black subjects, a group previously underrepresented in lifestyle-modification studies. [strength] As compared with the white subjects, the black subjects had a smaller overall weight loss. Future studies should explore

whether greater weight loss in this population can be achieved by more effective incorporation of culturally sensitive dietary counseling. [future directions]

6. The high dropout rate in our study occurred very early and affected our findings. The very early dropout of these subjects may indicate that attrition most closely reflected base-line motivation to lose weight, rather than a response to the dietary intervention itself. [limitation]

7. Taken together, our findings demonstrate that severely obese subjects with a high prevalence of diabetes and the metabolic syndrome lost more weight during six months on a carbohydrate-restricted diet than on a calorie- and fat-restricted diet. The carbohydrate-restricted diet led to greater improvements in insulin sensitivity that were independent of weight loss and a greater reduction in triglyceride levels in subjects who lost more than 5 percent of their base-line weight. [conclusion; restate answers to a and b] These findings must be interpreted with caution, however, since the magnitude of the overall weight loss relative to our subjects' severe obesity was small, and it is unclear whether these benefits of a carbohydrate-restricted diet extend beyond six months. Furthermore, the high dropout rate and the small overall weight loss demonstrate that dietary adherence was relatively low in both diet groups. [big picture] This study proves a principle and does not provide clinical guidance; given the known benefits of fat restriction, future studies evaluating long-term cardiovascular outcomes are needed before a carbohydrate-restricted diet can be endorsed. [take-home message]

EXAMPLE 2: Low-Fat Dietary Pattern and Colorectal Cancer in The Women's Health Initiative Dietary Modification Trial.

INTRODUCTION The Women's Health Initiative (WHI) Dietary Modification Trial is a randomized

controlled trial designed in 1991-1992 to test whether a low-fat eating pattern with increased fruits, vegetables, and grains reduces the risk of breast cancer, colorectal cancer, or, secondarily, coronary heart disease in postmenopausal women. At that time, international comparisons suggested that countries with 50% lower fat intake than the US population had approximately one third the risk of colorectal cancer.1-2 Migration studies supported this hypothesis. Women migrating from countries with low fat consumption to countries with high fat consumption experienced the higher colorectal cancer rates of their new country.3-4 Fairly consistent evidence existed for an effect of dietary fat, vegetables and fruits, and grains on colorectal cancer risk from within-country observational studies,2, 5-8 although the protective effect of lower fat intake was no longer clear after adjusting for energy intake.2, 9 The WHI Dietary Modification Trial is the first randomized trial to directly address the health effects of a low-fat eating pattern in predominantly healthy postmenopausal women from diverse racial/ethnic, geographic, and socioeconomic backgrounds. This article reports the principal results for colorectal cancer. [the question

JAMA. 2006;295:643-654

Discussion: 1. An intervention aimed toward a low-fat eating pattern did not reduce colorectal cancer risk in postmenopausal women. [answer to the question asked] Despite a significant change in fat intake and increases in vegetable, fruit, and grain consumption, the intervention hazard ratio is in the direction of an increased risk. [supporting evidence from this trial] There were no substantial differences in tumor characteristics or in rates of bowel screening between groups. [supporting evidence] Although self-reported incidence of colorectal polyps or adenomas was lower in the intervention group, no evidence of a trend toward lower colorectal cancer risk with time in the intervention group was observed over the mean 8.1-year study

period.

2. These findings are consistent with the findings from the Polyp Prevention Trial,31 a secondary prevention trial of polyp recurrence, which had a similar goal for fat, fruit, and vegetable intake but also included a goal of 18 g/1000 kcal of dietary fiber.32 The Polyp Prevention Trial observed no effect on polyp recurrence in the 2079 participants followed up for 4 years.32 A small trial in Toronto, Ontario, of high fiber and low fat showed no effect on recurrence of neoplastic polyps, but, within an intensive counseling subgroup, concentrations of fecal bile acids appeared to be reduced.33 A small factorial trial in Australia of a low-fat intervention, -carotene supplementation, or wheat bran supplementation found no reduction in recurrence rates of adenomas but suggested that the combination of low fat and wheat bran reduced the transition from smaller to larger adenomas.34 [supporting evidence: other TRIALS]

3. Since the WHI Dietary Modification Trial was designed, the hypothesized relationship between dietary fat and risk of colorectal cancer has been questioned.35 More recently, higher red meat consumption has been associated with increased colorectal cancer risk,23, 36-39 particularly in the distal colon.23 The putative mechanism may be related to heme, the iron carrier of red meat, rather than to its fat content.23 In the WHI, the dietary intervention reduced red meat consumption (Table 2), with no apparent overall benefit on colorectal cancer risk but, perhaps, some shift in risk in distal vs proximal colon cancers. [consistency with the latest paradigm] [mechanisms: is red meat more important than fat?]

4. Mixed support exists for an influence of vegetables and fruits on colorectal cancer risk.37, 40-42 Some of the antioxidants they contain have not proved efficacious in reducing colorectal adenomas or preventing incident colorectal cancer in randomized trials.43-45 Regular consumption of alcohol has been associated with elevated risk of colorectal cancer in some prospective studies, particularly among persons with low folate status.46 This pattern was not found in the comparison group of this study. Observations in East Africa by Burkitt47 led to the hypothesis that very high fiber reduces colorectal cancer risk. This has mixed support from observational studies48-50 and polyp and adenoma recurrence trials.31, 33-34,51-52 A European trial found an adverse effect of soluble fiber on colorectal adenoma recurrence,51 while an Arizona trial found no effect of wheat bran supplement on colorectal adenoma recurrence.52 Our study is consistent with lack of association in that women in the intervention group modestly increased their fiber (Table 2) with no apparent benefit over 8.1 years of follow-up.

[existing paradigms: does fiber matter?]

5. The observed interactions between the intervention and baseline aspirin use, and between intervention and use of combined hormone therapy, are consistent with synergistic effects of a low-fat dietary pattern and these potentially protective agents. However, given the large number of interactions tested, these findings could also have occurred by chance.

[Could the null finding be wrong? Maybe low-fat diet matters for some groups]

6. From National Health and Nutrition Examination Survey (NHANES) data, in 1977, women reported consuming 40.5% of their energy from fat, while in 1987, the average was only 35.9%,54 and in 2000, the average was 33% (NHANES 1999-2000). Organizations including

the National Cancer Institute, American Cancer Society, and Institute for Cancer Prevention have recommended both lower fat intake and increased vegetable and fruit use.55-56 7. One explanation for a lack of intervention effect on colorectal cancer could be that the intervention did not achieve a large enough difference between the intervention and comparison groups. Although the changes achieved were substantial, and likely as large as could be achieved in a trial of free-living individuals, they fell short of the original design assumptions based on the Women's Health Trial studies.27 Using food frequency data, the WHI intervention on average achieved only about 70% of the designed reduction in fat. If design assumptions are revised to take into account this departure from goal, the predicted HR would have been 0.86, an effect size excluded by these results. The power to detect this effect size under the observed comparison group incidence rate and the achieved adherence is approximately 40%. [Could the null finding be wrong? Alternative explanations to no association]

8. Whether greater adherence, intervention of longer duration, or initiation of change at an earlier age would influence colorectal cancer risk remain unanswered questions. The self-reported first occurrence of polyps or adenomas was lower in dietary intervention women, suggesting that longer follow-up (currently planned) may reveal delayed benefit in favor of the intervention. Yet no time trends regarding colorectal cancer risk over 8 years

of follow-up have been seen. To the extent that the WHI Dietary Modification Trial intervention addressed the recommendations from national organizations, the current results suggest that changing dietary patterns to meet these recommendations in mid to late life will have limited or no benefit in preventing colorectal cancers in postmenopausal women. [Defending their results]

9. The strengths of this study are its randomized design, long-term follow-up, large numbers of participants, diversity of race/ethnicity and socioeconomic status, and high retention rate. The limitations of this study include not attaining intervention goals as designed for reducing fat intake or achieving large separation from the

comparison group in increased fruit, vegetable, or grain intake. Thus the potential intervention effect of the WHI low-fat dietary pattern may be underestimated. Furthermore, there was no study-specified colonoscopy, nor was there systematic screening for adenomatous

polyps; hence, the incidence of both colorectal cancer and polyps or adenomas would be underestimated. [Strengths and limitations]

10. In conclusion, there is no evidence that a low-fat dietary pattern intervention reduces colorectal cancer risk over an average of 8.1 years of follow-up. [Restatement of findings] Evidence from this study, along with that from polyp prevention trials, strongly suggests that lowering dietary fat intake and increasing fruit, vegetable, and fiber intake in mid to late life cannot be expected to reduce the

risk of colorectal cancer in this length of time. [Take-home message]

What NOT to do…

Don’t start your discussion like this! Discussion n  This meta-analysis is subject to a number of

limitations. The estimates of risk for melanoma subsequent to using sunlamps/sunbeds are based on published data in a series of 10 articles over a period of 20 years. A pooled analysis of original observations

taken in the 10 studies would have provided a more powerful approach …

The Discussion: verb tense

Past, when referring to study details, results, analyses, and background research:

•  We found that •  Subjects may have experienced •  Miller et al. found Present, when talking about what the data suggest:

The greater weight loss suggests The explanation for this difference is not clear. Potential explanations include

6. Abstract

Abstracts (ab=out, trahere=pull; “to pull out”) n  Overview of the main story n  Gives highlights from each section of the paper n  Limited length (100-300 words, typically)

n  Stands on its own n  Used, with title, for electronic search engines n  Most often, the only part people read

Abstract 1.  Background

2.  Question/aim/hypothesis n  “We asked whether,” “We hypothesized that,”…etc.

3.  Experiment(s) n  Quick summary of key materials and methods

4.  Results n  Key results found n  Minimal raw data (prefer summaries)

5.  Conclusion: The answer to the question asked/take-home message

6.  Implication, speculation, or recommendation Mimi Zeiger. Essentials of Writing Biomedical Research Papers, McGraw Hill Professional, 1999

Good references

n  Clinical Chemistry Guide to Scientific Writing: http://www.aacc.org/publications/clin_chem/ccgsw/Pages/default.aspx#

n  Mimi Zeiger. Essentials of Writing Biomedical Research Papers, McGraw Hill Professional

For more training:

Writing in the Sciences MOOC: https://class.stanford.edu/courses/Medicine/Sci-Write/Fall2014/about

Education

Slides: Manuscript Writing Workshop 10-2-14