How to Write a Manuscript Get Your Paper Accepted

How to write a manuscript Get your paper accepted

Edanz free manuscript writing educational materials Edanz Group Ltd October 2010

Presentation
 Introduction  Section One: Preparations before writing

 Section Two: Manuscript structure
 Section Three: Tips for getting accepted

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Why publish?
 To share your research findings and opinions with the international research community
 Publication success is linked to funding success and career advancement  Many PhD programs require candidates to achieve a set number of peer-reviewed publications
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Publish or perish
Funding Bodies

Grant Writing
Journal Publication

Scientists / Clinicians

 Regularly publishing research findings ensures ongoing grant support for new research
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Increased competition
1400 1200

1000
800

%

Journal numbers
Journal submissions

600 400 200 0

1990 1992 1994 1996 1998 2000 2002 2004 2006 2008

Year

Relative growth from 100% baseline in 1990
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Section One Preparations before writing
 How to identify hot topics

 Study design
 What do journal editors want?  Choosing an appropriate journal

 Ethical issues

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How to identify hot topics

Look for clues— unexplained findings, controversies

Read the literature, including related fields

Attend international meetings

Greater interest = Greater competition Identify your advantages and use them
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Study design Get it right first time
      Have an hypothesis or research question Use appropriate methods and controls Ensure sample sizes are large enough Use appropriate statistical tests Remove investigator/researcher/patient bias Comply with ethical requirements

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What do journal editors want?
Good quality science  Robust to peer review  Well designed and executed original research

 Findings of interest to the journal’s readership
 Work in an active research area (=citations!)

 Work that advances the field in some way
 Compliance with ethical regulations

 Clear, concise writing
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Journal Selection
 Can be the difference between success and rejection  What is the main focus of your research and who will be interested in it?  What are its strengths and weaknesses?

 How significant are your findings?
 Are your findings preliminary or are they sufficient to make a story?  How widely will your research appeal? To researchers in the same field or to the broader scientific community?
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Journal Selection
What should you consider?
      Publishing frequency Impact factor Target audience Aims and scope Rejection rate Lead times     Access (open or subscriber) Prior publications Publication fees Publication types

How do these relate to your publication needs?
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Publication ethics
Unethical behavior could lead to rejection and a possible ban from a target journal. Multiple submissions Redundant publications Plagiarism Data fabrication and falsification Improper use of human subjects and animals in research Improper author contribution

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Section Two Manuscript structure
 The ‘write’ order  Title  Abstract and keywords  Introduction  Materials and Methods  Results  Display items  Statistics  Discussion and Conclusions  References

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The ‘write’ order
IMRaD manuscripts: for maximum clarity and consistency, write in this order:
 Methods  Results  Introduction  Discussion  Title  Abstract
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Write during the research Write after selecting your target journal

The importance of your title

Hook to catch readers

Sells your manuscript to the editor

Relevant readers increase citations

Journal editors like citations
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A good title
 Convey the main findings of the research  Be specific and concise without focusing on only one part of the content  Avoid jargon, non-standard abbreviations and unnecessary detail  Comply with character limits  Some journals also require a short running title
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A good title
Poor  Degeneration of neurons in the CA3 and DG following OA administration: involvement of a MAPK-dependent pathway in regional-specific neuronal degeneration Better  Region-specific neuronal degeneration after okadaic acid administration  MAP kinase-dependent neuronal degeneration after okadaic acid administration
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A good title
“Tumor-host cell interactions in the bone disease of myeloma”

“Development of pharmacotherapies for drug addiction: a Rosetta Stone approach”
“Reprogramming bacteria to seek and destroy an herbicide” “Stress, memory and amygdala”
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Abstract
Many researchers will only read the abstract so must be able to ‘stand alone’ Must give an accurate summary of your research, and enough information so that readers can understand:
What you did Why you did it What your findings are Why your findings are useful and important
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Abstract
General rules for abstracts:  Within the word limit  Avoid technical jargon  Avoid abbreviations unless necessary

 Avoid references
 Structured or unstructured? Always consult the target journal’s Guide for Authors to determine allowable length, style and abbreviations

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Abstract Structured
Risk factors and mortality in patients with nosocomial staphylococcus aureus bacteremia

2 sentences 2 sentences

5 sentences

1 sentence

BACKGROUND: Infections due to methicillin-resistant Staphylococcus aureus have become increasingly common in hospitals worldwide. S aureus continues to be a cause of nosocomial bacteremia. METHODS: We analyzed the clinical significance (mortality) of MRSA and methicillinsusceptible S aureus bacteremia in a retrospective cohort study in a 2900-bed tertiary referral medical center. Survival and logistic regression analyses were used to determine the risk factors and prognostic factors of mortality. RESULTS: During the 15-year period, 1148 patients were diagnosed with nosocomial S aureus bacteremia. After controlling potential risk factors for MRSA bacteremia on logistic regression analysis, service, admission days prior to bacteremia, age, mechanical ventilator, and central venous catheter (CVC) were independent risk factors for MRSA. The crude mortality rate of S aureus bacteremia was 44.1%. The difference between the mortality rates of MRSA (49.8%) and MSSA bacteremia (27.6%) was 22.2% (P < .001). Upon logistic regression analysis, the mortality with MRSA bacteremia was revealed to be 1.78 times higher than MSSA (P < .001). The other predicted prognostic factors included age, neoplasms, duration of hospital stay after bacteremia, presence of mechanical ventilator, and use of CVC. CONCLUSIONS: Resistance to methicillin was an important independent prognostic factor for patients with S aureus bacteremia. PMID: 18313513 [PubMed - indexed for MEDLINE]; Am J Infect Control. 2008 Mar;36(2):118-22.

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Keywords
Abstracts are often followed by a list of keywords selected by the authors  Choosing appropriate keywords is important for indexing purposes  Your manuscript can more easily identified, read and cited  Keywords should be specific to your manuscript  General terms should be avoided  Many medical journal require MeSH terms
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Keywords
Manuscript title: Region-specific neuronal degeneration after okadaic acid administration Poor keywords: neuron, brain, OA (as an abbreviation), regional-specific neuronal degeneration, signaling Better keywords:

okadaic acid, hippocampus, neuronal degeneration, MAP kinase signaling
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Introduction
 Must give the reader enough background information to put your work into context  Enough information to understand the rationale for your study is all that is required  Do not write a comprehensive literature review of the field  Do cite reviews that readers can refer to if they want more information

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Introduction
 Define technical and non-familiar terms

 Present “the problem”, research question and/or hypotheses to explain the rationale for the study
 Briefly explain how you addressed this problem and what was achieved (1–2 sentences for each)  Citations must be balanced, current and relevant

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A complement-dependent balance between hepatic ischemia/reperfusion injury and liver regeneration in mice
Songqing He, Carl Atkinson, Fei Qiao, Katherine Cianflone, Xiaoping Chen and Stephen Tomlinson

Introduction
Liver resection has become an increasingly safe procedure, but certain procedures remain high risk, such as massive liver resection and small-forsize (SFS) liver transplantation. Massive hepatic resection is the only option for some patients…. The failure of a partial liver to regenerate is considered a critical contributing factor in postsurgical primary liver dysfunction and liver failure, and minimal viable liver volume required for regeneration, following either massive liver resection or SFS transplantation, is an important concept... Thus, although the studies outlined above indicate that complement inhibition represents a potential therapeutic strategy to protect against hepatic IRI, the important role of complement in liver regeneration would appear to be a contraindication for such a strategy in the context of liver resection and SFS liver transplantation, even though IRI is associated with impaired regeneration… In the current study, we investigated the role of complement in the relationship between hepatic IRI and liver regeneration using 3 murine models: a warm total hepatic IRI model (similar to the Pringle maneuver), a 70% PHx model, and a combined IRI/PHx model designed to recreate clinical massive liver resection under the Pringle maneuver. In these studies, we used the complement inhibitor CR2–complement component…
The Journal of Clinical Investigation (doi:10.1172/JCT38289; reproduced with permission)

Statement of the problem

Background

Rationale

What was done

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Materials and methods What you did
 Clear subheadings for methods/materials  Describe methods in the past tense  Novel methods must be described in sufficient detail for a capable researcher to reproduce the experiment  Give manufacturers/suppliers and their locations  Describe any statistical tests used  Established methods can be referenced

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Proapoptotic signaling induced by RIG-I and MDA-5 results in type I interferon-independent apoptosis in human melanoma cells.
Robert Besch, Hendrik Poeck, Tobias Hohenauer et al.

Materials described first

Reagents and antibodies. Anti–caspase-3, anti–caspase-8 (1C12), anti–caspase-9, anti–Bcl-xL, anti–Bcl-w, and HRP-conjugated secondary antibodies were obtained from New England Biolabs. Anti–cytochrome c (clone 7H8.2C12) was from BD Biosciences. Anti-Noxa (N-15) antibody was from Santa Cruz Biotechnology Inc. Anti–Bcl-2 (Ab-1) and anti-p53 (Ab-6) antibodies were from Merck Biosciences. Anti–IPS-1 antibody was obtained from Bethyl Laboratories Inc. Anti–β-actin (AC-15) and anti-Puma (bbc3) antibodies were purchased from Sigma-Aldrich. PCR primers and siRNAs were purchased from MWG Biotech. Immunostimulatory and siRNAs. Poly(I:C) was purchased from Amersham Biosciences. 5′-Triphosphate– conjugated RNAs (pppRNAs) were transcribed in vitro from DNA templates as described in ref. 6. They contained a T7 RNA Polymerase consensus promoter sequence followed by the sequence of interest to be transcribed (MEGAshortscript Kit; Ambion). Reactions were treated with DNAse I (Ambion… siRNAs were designed according to published guidelines (48, 49) 3′ Overhangs were carried out as two deoxythymidine residues (dTdT). Sequences of specific siRNAs are listed in Supplemental Table 1. Nonsilencing control siRNAs were designed to contain random sequences that do not match within the human genome... Cell culture. Human melanoma cell lines were a gift of M. Herlyn (Wistar Institute, Philadelphia, Pennsylvania, USA)… Analysis of lung metastasis. For metastasis analysis at day 10, we isolated genomic DNA from lungs. Mouse lungs were reduced to small pieces and digested overnight at 56°C in a buffer containing 10 mM Tris, pH 8.0, 100 mM NaCl, 1 mM EDTA, 1% SDS, 0.5 mg/ml Pronase E (Sigma-Aldrich), and 150 μg/ml Protease K (Sigma-Aldrich). Genomic DNA was purified by phenol/chloroform extraction. The amount of human and murine DNA was determined by quantitative PCR using the LightCycler TaqMan Master Kit (Roche) together with the Universal Probe Library system (Roche). A 72-bp portion in the second intron of the human β-actin… Statistics. For statistical analysis, 2-tailed Student’s t test was used to assess the significance of mean differences. Differences were considered significant at a P value of 0.05 or less.
The Journal of Clinical Investigation (doi:10.1172/JCI37155; reproduced with permission)

Suppliers

References to save space

Clear subheadings

Statistical test information

Detailed information given

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Results What did you find?
 Assemble your findings in a logical order to ‘make a story’  Present your findings in subsections (the same as those in your methods section)  Present complementary evidence when possible  Describe results in the past tense  Refer to figures and tables in the present tense  Do not discuss implications — do that in the discussion section  Do not duplicate data among figures, tables and text  Show the results of statistical analyses, (e.g., p values) in the text

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Proapoptotic signaling induced by RIG-I and MDA-5 results in type I interferon–independent apoptosis in human melanoma cells
Robert Besch, Hendrik Poeck et al

Clear subheadings

Graphics used to show data with only brief descriptions in text

pppRNA and poly(I:C) induce apoptosis in melanoma cells. We tested the ability of RIG-I and MDA-5 ligands to induce cell death in human melanoma cell lines. Five cell lines derived from advanced melanomas (vertical growth phase or metastatic origin) were analyzed. Activation of RIG-I and MDA-5 by pppRNA1 and poly(I:C) strongly reduced viability from 100% in controls to 20%–50% within 24 hours (Figure ​(Figure1A).1 A). Viability was reduced due to induction of apoptosis as determined by staining with annexin V. Apoptosis strictly required intracellular delivery, as neither pppRNAs nor poly(I:C) without transfection were active (Figure ​(Figure1B).1 B). Different pppRNAs were tested, and all reduced cell viability (Figure ​(Figure1C).1 C). The 5′-triphosphate moiety was required, since synthetic RNAs carrying a free OH group at the 5′ end (e.g., OH-RNA1) had no effect (Figure ​(Figure1C,1 C, left panel). Strong dose-dependent reduction of viability was observed for poly(I:C) (Figure ​(Figure1C,1 C, right panel). Reduced viability was reflected in an increased number of cells undergoing apoptosis (Figure ​(Figure1D).1 D). Confirming the onset of apoptosis, caspase-3 was activated in cells transfected with pppRNAs or poly(I:C) but not in cells exposed to pppRNA or poly(I:C) in the absence of transfection reagent (Figure ​(Figure1E).1 E). Together, these results show high sensitivity of human melanoma cell lines toward apoptosis induction by pppRNAs or poly(I:C) when delivered to the cytosol. Apoptosis induction by pppRNA and poly(I:C) involves IPS-1 but is independent of IFN signaling. The RNA ligands pppRNA and poly(I:C) both induced IFN-β expression in melanoma cells (Figure ​(Figure3A).3A). Silencing of RIG-I and MDA-5 confirmed that induction of IFN-β by pppRNA and poly(I:C) required RIG-I and MDA-5, respectively, and that both required…

It is clear what was compared with what

Melanoma cells are more sensitive to RIG-I– and MDA-5–induced apoptosis than primary cells. We next compared healthy primary cells of the skin with melanoma cells to evaluate tumor specificity of apoptosis induction by RIG-I and MDA-5. Primary human melanocytes, primary fibroblasts, and primary keratinocytes were significantly less sensitive to pppRNA and poly(I:C) compared with melanoma cells (Figure ​(Figure7A).7A).
The Journal of Clinical Investigation (doi:10.1172/JCI37155; reproduced with permission)

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Display items Tables and figures
 Some readers will only look at the figures and their legends  Figures and tables are the best way to present your results  Data shown in figures and tables must be easy to interpret — use separate panels if necessary  Avoid redundancies or duplication  Clearly label all components  Show trendlines, scale bars and statistical significance  Legends must be able to ‘stand alone’: write them in the present tense (except when describing methods)  Comply with journal guidelines on display items

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Display items Tables and figures
 Tables are a great way to present large amounts of necessary data with minimal description required
Clear concise heading

Data divided into categories for clarity
Percentages as well as absolute values

Part of a table in a paper published in The Journal of Clinical Investigation (doi:10.1172/JCI37622; reproduced with permission)

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Display items Tables and figures
Trend lines Clear, ‘stand alone’ legend
Figure 5 RCP knockdown attenuates tumor formation and metastasis. Effects of RCP inhibition on tumor growth using (A) MCF7 cells in nude mice and (B) MB231 cells in NOD-SCID mice are shown. (A) Left panel shows mean tumor volume plotted as a function of time (mean ± SEM). Right panel shows tumor weight plotted at 5 weeks; mean weight indicated by solid line. (B) Left panel, tumor weight plotted at indicated number of weeks; mean weight indicated by solid line. Right panel, the average number of lung micrometastases per section is shown. (C) Representative lung sections and fluorescently imaged whole lungs (right panel) of NOD-SCID mice are shown. Micrometastases are indicated by arrows. Scale bars: 200 μm.

Multi-panel: different kinds of data grouped together in a single figure Complicated data separated into simpler components

Scale bars

The Journal of Clinical Investigation (doi:10.1172/JCI37622; reproduced with permission)

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Statistics
A man has one hand in boiling water…

The other hand in freezing water…

He is comfortable—on average…

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Statistics
Today, few professional activities are untouched by statistical thinking, and most academic disciplines use it … Statistical thinking is a way of recognizing that our observations of the world can never be totally accurate; they are always somewhat uncertain…
Rowntree D (1981). Statistics without tears. A primer for non-mathematicians. Penguin Books Ltd., London, England

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Statistics
Statistical analysis is at the heart of scientific inquiry Consider statistical analysis when you design your study. Before you start your research.

Data collection

Data analysis

Interpretation

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Statistics Poor statistics
Poor statistics
Poor study design e.g., sample size is too small Poor analysis Poor interpretation Data are valid

Re-analysis or re-interpretation Difficult to recover… Revise manuscript

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Statistics Basics
Reporting statistics in your manuscript:

 Consult a statistical expert about which test to use!  Clearly describe the statistical tests used to analyze data  Give the software, version number and maker  Only use the word “significant’ when describing statistically significant differences Alternatives: notable, substantial, marked  P not enough for “significant”? Describe as a “trend”
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Statistics Questions
Ask yourself these questions during study design:

What are the independent and dependent variables? What is the scale of measurement of the study variables? Consider sample number for power analysis i.e., how many samples will you need? Have I met the assumptions of the statistical test selected?

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Statistics Details
Reporting statistics in your manuscript:

 Indicate the parameters described, e.g., “means±S.D”  Give the numerator and denominator with percentages, e.g., “40% (100/250)”  Report p values, e.g., use “p=0.0035” rather than “p<0.05”  Do you have a correction for multiple testing?  Check target journal for P, P, p or p.

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Statistics A few rules
 Use appropriate amount of precision: Life expectancy of 22.085 years → 22 years Data should be rounded when presented NOT when analyzed Always give numerator and denominator. E.g., 25% (650/2958) Avoid using percentages to summerise small samples Be very clear with percentages within subgroups: “Of the 1000 patients, 800 (80%) were women; (31%) had a BMI of…” “Of the 1000 patients, 800 (80%) were women; of these, 250 (31%) had a BMI of…”
Book  As a full guide see the excellent book: How to report statistics in medicine by Thomas A. Lang and Michelle Secic (ACP Press, Second Edition)
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A complement-dependent balance between hepatic ischemia/reperfusion injury and liver regeneration in mice
Songqing He, Carl Atkinson et al

Methods Data type defined Statistical tests clearly described

Results

Statistics. Data are expressed as mean ± SD. Significant differences between groups were determined by ANOVA, with a Bonferroni correction for continuous variable and multiple groups. Two-tailed Student’s t test was used for the comparison of a normally distributed continuous variable between 2 groups. For the survival studies, Kaplan-Meier logrank analysis was performed. P values of less than 0.05 were considered statistically significant.

ALT levels were significantly lower at 24 and 48 hours after PHx in low-dose CR2-Crry–treated mice compared with those in salinetreated controls…. Compared with WT mice, surviving C3–/– mice had significantly increased hepatic injury and an impaired proliferative response (Figure 7, B–E)...

Significance threshold defined

‘significant’ only used for statistical significance

Figure 7 Opposing effects of high- and low-dose complement inhibition on hepatic injury and regeneration in a model incorporating both IRI and PHx. Mice were treated with normal saline or CR2-Crry at a dose of either 0.25 mg or 0.08 mg immediately after surgery. C3–/– mice received no treatment. All determinations made 48 hours after I/R and PHx. (A) Mouse survival. (B) Serum ALT levels. (C) Histological quantification of hepatic necrosis and injury determined on a scale of 0–4. (D) Assessment of regeneration by BrdU incorporation. (E) Restitution of liver weight. (F) MPO content in liver samples. #P < 0.05, ##P < 0.01 versus WT group; **P < 0.01 versus WT group (similar to WT normal saline group); ††P < 0.01 versus all other groups; *P < 0.05, **P < 0.01 versus WT group. Results are expressed as mean ± SD; n = 6–10.

Significance indicated in figure/table legend
The Journal of Clinical Investigation (doi:10.1172/JCI38289; reproduced with permission)

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Discussion What does it all mean?
Restate your research question and/or any hypotheses presented in the introduction Summarize your main findings—make it clear how your study has advanced the field Begin with your most important finding Past tense to describe results (current and published) Present tense to describe their implications Minimize repetition with other sections Describe inconsistencies with other papers Describe the limitations of your study
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Discussion
Be humble Don’t overstate the importance of your results

Our findings prove that…

Our findings show that…
Our findings suggest that…
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Conclusions
 Restate key findings and their significance
 Propose future studies that might follow on from your current study  Give the reader a ‘take-home’ message
“ we can now conduct quantitative and functional genetic studies in natural populations” (Science)
“Hopefully, more prospective, randomized, clinical trials will address these concerns and reinforce the efficacy of tropical antimicrobial therapy” (Curr Infect Dis Rep) “further, the structures reported here highlight the complex network of proteinprotein and protein-DNA interaction…” (Nature)
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RCP is a human breast cancer–promoting gene with Ras-activating function
Jinqiu Zhang, Xuejing Liu et al

Restate the question/problem Restate main findings Put in context of previous work Use ‘suggests’ and ‘may’

Discussion Genome-wide microarray analysis of primary tumors has enabled the discovery of novel, clinically relevant tumor subtypes defined by unique patterns of gene expression. More recently, however, the inverse of this concept has been explored through bottom-up analytical strategies that seek to identify gene subtypes with functional roles in tumorigenesis… In the present work, we have built on this concept of data integration and functional discovery and identified RCP, located on the 8p11–12 recurrent breast cancer amplicon, as a novel breast-cancer promoting gene with Ras-activating potential…. Amplification of the 8p11–12 locus has been observed in approximately 10%–25% of breast tumor cases and 15% of breast cancer cell lines and has been associated with poor patient survival and short interval to distant metastasis. Recently, this amplicon has been the focus of several functional genomics investigations involving primary breast tumors and cell lines. Using a highresolution BAC microarray specific for chromosome 8p, Gelsi-Boyer and colleagues… However, that the growth and metastatic properties of the tumor xenografts were dependent on the endogenous expression of RCP suggests an “oncogene addiction–like” scenario, whereby RCP may play a vital role in the maintenance and potentiation of the malignant and metastatic phenotype… In conclusion, through integrated genomic analysis, we identified RCP as a candidate oncogene at the 8p11–12 amplicon, with expression levels significantly correlated with aggressive breast cancer behavior…

Restate main findings Future research plans

The broader involvement of RCP in the pathogenesis of human cancers and the mechanisms underlying its oncogenic effects will be the focus of future investigations.

The Journal of Clinical Investigation (doi:10.1172/JCI37622; reproduced with permission)

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Acknowledgments
Your chance to acknowledge anyone who has helped with the study: Individuals who did not qualify for authorship based on ICMJE criteria Any researchers that supplied materials or reagents Anyone who provided technical assistance Anyone who helped with the preparation of the manuscript or provided a critical assessment of it Funding bodies State why each individual is being acknowledged
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References
 Always format your references: check your target journal’s Guide for Authors for the appropriate format

Harvard style or Vancouver style or APA
 Formatting is required both in text and in the references section  Use a reference manager like Endnote. Makes it easy to edit, reformat, add or remove references

 Some journal limit the number of references: check your target journal’s Guide for Authors

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Section Three Tips for getting accepted
Your cover letter Recommending reviewers Language Good writing Common language problems What do reviewers look for? Submission Final checks Post-referee revisions Checklist

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Cover letters
 Journal Editors receive hundreds of manuscripts each month  They don’t have time to read each manuscript  Society journal editors are especially busy as they are usually practicing researchers too

Your cover Letter is an opportunity to get the journal editor’s attention
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Cover letters
Competition for publication space and for editors’ attention is very high It is not enough to send a manuscript to a journal editor like this:
Dear Editor-in-Chief, I am sending you our manuscript entitled “Large Scale Analysis of Cell Cycle Regulators in bladder cancer” by A. Honda, K. Tanaka, J. Suzuki, and myself. We would like to have the manuscript considered for publication in Pathobiology. Please let me know of your decision at your earliest convenience. With my best regards, Sincerely yours, Shinsuke Izumi, PhD
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Your cover letter
General rules for cover letters: Address to the editor personally Begin by giving your manuscript title and publication type

Give a brief background, rationale and description of results
 Explain why your findings are important and why they would be of interest to the journal’s target audience  Consult the journal’s Guide for Authors for cover letter requirements (e.g., disclosures, statements, potential reviewers) Give corresponding author details

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Your cover letter
Dear Dr Lisberger, Please find enclosed our manuscript entitled “Amyloid-like inclusions in the brains of Huntington’s disease patients”, by McGowan et al., which we would like to submit for publication as a Research Paper in Neuroscience. Recent immunohistochemical studies have revealed the presence of neuronal inclusions containing an N-terminal portion of the mutant huntingtin protein and ubiquitin in the brain tissues of Huntington’s disease (HD) patients; however, the role of these inclusions in the disease process has remained unclear. One suspected disease-causing mechanism in Huntington’s disease and other polyglutamine disorders is the potential for the mutant protein to undergo a conformational change to a more stable anti-parallel β-sheet structure… To confirm if the immunohistochemically observed huntingtin- and ubiquitin-containing inclusions display amyloid features, we performed Congo red staining and both polarizing and confocal microscopy on post-mortem human brain tissues obtained from five HD patients, two AD patients, and two normal controls. Congo red staining revealed a small number of amyloid-like inclusions showing green birefringence by polarized microscopy, in a variety of cortical regions.... ….detected inclusions observed in parallel sections, suggesting that only a relatively small proportion of inclusions in HD adopt an amyloid-like structure.

Give the background to the research Explain what was done and what was found

We believe our findings would appeal to a broad audience, such as the readership of Neuroscience. As a wide-reaching journal publishing original research on all aspects of neuroscience…
We confirm that this manuscript has not been published elsewhere and is not under consideration by another journal. All authors have approved the manuscript and agree with submission to Neuroscience. We have read and have abided by the statement of ethical standards for manuscripts submitted to Neuroscience. The authors have no conflicts of interest to declare. Please address all correspondence to….

Explain why this is interesting to the journal’s readership
Conforms to the journal’s requirements

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Reviewers Recommendations and exclusions
Recommend  Your work supports their hypotheses and ideas  Your research builds on their work  International collaborators in the same field

Exclude
 Researchers working on the same research question

 Your study refutes their work
 The findings in your manuscript are are opposite to their findings or ideas
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Language
Journal editors are overloaded with quality manuscripts. They may make decisions on manuscripts based on formal criteria, like grammar or spelling. Don't get rejected for avoidable mistakes: make sure your manuscript looks perfect
A senior executive at a large international publishing house

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Language screening
Introduction of language screening protocols to check submissions

 Editors don’t want to send poorly written manuscripts for peer review  Editors receive enough well written submissions to reject poorly written manuscripts
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Language
Some journals are very clear regarding their English requirements, and about what happens to manuscripts that do not meet their standards…

European Polymer Journal
Language and Style: Manuscripts should be written in English in a clear and concise manner. Manuscripts which are not written in fluent English will be rejected automatically without refereeing.

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Scientific writing
Good scientific writing possesses the following three “C”s:

Clarity
Conciseness Correctness (accuracy)
Key points: Be as brief as possible without omitting essential details Be as specific as possible
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Scientific writing Common problems
Avoid: Spelling and grammatical errors Insufficient detail/vagueness

Repetition
Redundancy

Ambiguity
Inconsistency

They annoy editors, peer reviewers and readers
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Language Common English problems
Tense Articles Plural or singular Proper nouns Hyphen or dash That/which Making comparisons Respectively Between or among Nomenclature Such as/namely Etc. Asian fonts UK or US spelling Presenting numbers

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Language Dash or hyphen
Hyphen (-): for joining usually separate words
Incorrect use can lead to ambiguity

twenty-four hour reactions
is different to twenty four-hour reactions

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Language Dash or hyphen
En dash (–): means “through.” October 28–29; pp. 2–5. (don’t use ~) Em dash (—): Used to break a sentence, introduce something, or introduce an afterthought. These two metals—that is, titanium and magnesium— are very light.

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Language Asian fonts
Be careful of Asian fonts such as MS Mincho and SimSum Do not use Asian fonts in your manuscripts For example:

、 ，；（）× ％ ＜
Why not?

＞℃

Because they look like this on some computers: □ or ?

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Simple is best
Use simple language: it is often clearer, more precise and more concise than using more complex language Say what you mean in as few words as possible Delete unnecessary words

Avoid circular sentences, redundancies and repetition
One sentence: one idea

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Language UK or US spelling
Be consistent
Check the journal’s Guide for Authors
Generally, American journals require US spelling and British journals require British spelling, but many accept either form as long as the spelling used is consistent
fibre centre labelling colour or or or or fiber center labeling color

Exceptions: Ministry of Health, Labour and Welfare; your references
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Language Comparisons
Frequently made in the results sections of papers Compare “like” with “like” Do not be vague Use with, not to The material from the river bank was compared with the landfill.

The material from the river bank was compared with that from the landfill.
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Language Comparisons
Expression levels of p53 in smokers were compared with nonsmokers

Expression levels of p53 in smokers were compared with p53 levels in non-smokers

Expression levels of p53 in smokers were compared with those in non-smokers

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Language Comparisons
 Relative terms, such as more, higher and greater, require a reference for comparison

Use “than” or “compared with”
Reactions with the new machine were faster. than what?

Reactions with the new machine were faster than those with the old machine.

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Language Between or among
Use between for comparisons of two groups …the only difference between the original molecule and the new molecule is...
Use among for comparisons of more than two groups ..significant differences were observed in the H values among bio, fully- and semi-synthetic…

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Language Respectively
Use to refer to two corresponding lists, but not more For example:
Oxygen detector flow 85 mL/min Nitrogen detector flow 7 mL/min Hydrogen detector flow 4 mL/min

Oxygen, Nitrogen and Hydrogen detector flows were set at 85, 7 and 4 mL/min, respectively.

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Language Presenting numbers
AMA Manual of Style is a good guide: Spell out numbers one through nine, numerals for 10 and up EXCEPT Units of measurement, times, and dates: 2 mL; 1996
Beginning of a sentence Fifteen days previously…NOT: 15 days previously A mixture of numbers in one sentence: The sample included 34 men with type A blood, 15 with type B and 3 with type AB. Differentiating consecutive numbers: Five, 50-kg women….NOT 5, 50-kg women Large numbers in general expressions: A hundred; several thousand….
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Language Presenting numbers
Spacing No space between numeral and percent sign: 48% Space between numeral and unit of measurement: 178 mm
Decimals Use zero before decimal: 0.28 mL BUT Not when reporting P values: P= .04 Rates, proportions and fractions Use the virgule (/) for proportions, colon (:) for ratios About 1/3 of samples… the ratio was 3:4.5… The rate averaged 40/100,000 people…BUT  Spell out noun-modifying fractions: Half the cases showed…..; a two-thirds majority…
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Language Such as or namely
such as: to give examples

….there were other factors, such as nutrient status, primary production, microbial biomass, and coagulation processes.
namely: to define …we used certified reference materials, namely C36 n-alkane and phenanthrene, obtained from…

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Language Colon or semi-colon
The colon “:” is used to introduce a list or a clause that explains what precedes it Semicolon “;” is used to separate the items in a list too long for commas or where commas could be ambiguous. Use ‘and’ before the last item in the list. There are a number of journals for surgery manuscripts: Surgery, produced by Elsevier; Journal of Surgery, produced by NMS; British Journal of Surgery…

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Language Colon or semi-colon
Use a semicolon to join two sentences that are not independent

In previous sediments of all salinities, MeHg production was highest at previous sediment depths just below the oxic/anoxic transition; that is, depths where microbial sulfate reduction was present, but where sulfide, which inhibits methylation, was relatively low.

One sentence is too long; but the two sentences must be connected

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Language Minimizing errors
The internet can help you Google Scholar to check for word usage Check your target journal’s home page for full instructions MS Word Track changes function Comment function Find (and replace) to check for consistency Word Count function Spell Check (but be careful)  Custom Dictionaries (provided by some academic societies for specific fields)  Online glossaries provided by academic societies
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Reviewers What do they look for?
Is the manuscript sufficiently novel? Is the manuscript of broad enough interest?

Aims and Scope Impact Factor

Novelty Significance

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Reviewers About the research
Are the methods used appropriate? Are any additional experiments/analyses necessary? Are the statistical tests used appropriate? Are all possible interpretations of the data considered?

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Reviewers About the manuscript
Are the rationale and objectives defined? Is enough background given to understand the rationale? Could a capable researcher reproduce the experiments? Are the results clearly explained and in the best format? Are the findings described in context? Are the limitations discussed? Are the conclusions supported? Is the literature cited appropriate?

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Submission Final checks
 Critically self-evaluate—could anything be done better?  Double check the Guide for Authors  Are all files in the correct file format and of the appropriate resolution or size?  Is your spelling/grammar correct?  Do you have contact information for all authors?  Have you completed online registration?  Or have you prepared the requested number of print copies plus CD?  Have you written a persuasive cover letter?

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Revisions Post-referee revisions
Rejection from journals is an important part of the publication process It is not a negative experience

It exists to ensure that your paper is as scientifically robust and complete as possible before joining the ‘collective knowledge’ as part of the literature
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Revisions Post-referee revisions
Reasons for rejection:  Inappropriate target journal  Poor study design  Poor written language  Inappropriate or incompletely explained methodology

 Inappropriate statistical tests
 Incorrect description or overstatement of results

 Lack of balance or detail in introduction and/or discussion
 Lack of novelty
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Revisions Post-referee revisions
Only 1.5% of papers are immediately accepted without need for any revisions

Complete rejection Journal editor decision

Rejection with major revisions
Rejection with minor revisions

Acceptance

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Revisions Post-referee revisions
When revising your manuscript: Address all points raised by the editor and/or reviewers Describe the revisions in your response letter  Perform any additional experiments or analyses requested (unless you feel that they would not add to the strength of your paper: explain why not in your response letter)  Provide a polite and scientific rebuttal to any points or comments you disagree with Differentiate comments and responses in your letter Clearly show the major revisions in the text  Return revised manuscript and response letter within the requested time period
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Summary Checklist for acceptance
        Appropriate study design Compliance with ethics guidelines Appropriate statistical tests Novel and interesting results Clear, concise, accurate writing Compliance with the Guide for Authors Significance of findings explained Appropriate choice of journal
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