IOS, CAS Webinar 2 - Focus On Scientific Writing II - Watermarked

Masterclass in Scientific Writing
and Publishing
Webinar 2: Focus on Scientific Writing II
State Key Laboratory Superlattices & Microstructure,

Institution
Institute of Semiconductors, CAS
dates
23 March 2021
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Institute of Semiconductors, CAS, 23 March 2021

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Workshop materials
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● Participant Guide
● Resources booklet
● Webinar slides
Participant guide page 8
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Trainer: Webinar 1, 2 & Abstract Review
Christiana Varnava
Senior Editor, Nature Electronics
• PhD from University of Cambridge, UK
• Research focused on entangled light-
emitting diodes based on quantum dots
and on optical quantum information
applications

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This makes the workshop more
engaging and interactive!

Objectives for this workshop
• Increase confidence in writing papers
• Make the most of the writing process to improve accessibility
and increase impact
• Understand editorial processes and how to work with them

Webinar 1: Webinar 2: Webinar 3: Webinar 4:
Focus on Scientific Focus on Scientific Abstract Review Focus on Scientific Focus on Scientific
Writing I Writing II Publishing I Publishing II
What Makes a Great From Introduction to Abstract Consultation Submitting Your Journal Decisions
Paper? Conclusion • How to structure and Paper • Journal decisions and
• What researchers and improve your how they affect your
• How to structure each scientific writing • Journal submission
editors look for in a manuscript
great paper part of your paper to procedures • How to assess and
• Characteristics of facilitate clear writing • How to structure and respond to journal
excellent primary write a good cover decisions
research papers and letter to the Editor
review articles Figure Presentation Plagiarism and Other
• An interactive module An individual 8-minute
session with a Nature The Editorial Process Ethical Issues
Titles and Abstracts on designing clear and
• How to write a informative figures and Research journal editor and Peer Review • Why research
compelling title tables to discuss your pre- • The editorial process misconduct happens,
• Structuring a well- submitted abstract and the value of peer what it looks like and
balanced abstract + Interactive activities review
what to do about it
and Q&A sessions • The importance of
+ Interactive activities referee reports
+ Interactive activities
and Q&A sessions
+ Interactive activities and Q&A sessions
and Q&A sessions

From Introduction to Conclusion

Elements of a paper
Broad Introduction
Methods
Detailed Results
Discussion
Broad Conclusion

The Introduction
What information do you think readers are looking for in
the introduction?
Share your suggestions!

Hands raised
Chat box

The Introduction
GENERAL SPECIFIC
Context: Focus:
Findings:
why your key studies,
a preview
study is rationale,
(optional)
useful objectives
• Mention papers • Start leading readers • Reminder before

with similar towards the objective the detailed
conclusions methods and
• “Why should I care?”
results
• Be specific about
• Stick to the point
what we don’t know
The Introduction: an example
• Context The immediate impact and far reaching
implications of a nuclear clock become clear
when considering current applications of existing
atomic-clock technology. […] This has motivated
significant experimental effort aimed at further
• Focus validation of the isomer’s existence and direct
detection of the isomeric de-excitation. For a
detailed overview, we refer the reader to a
recent review and references therein. Despite
• Findings decade-long efforts, none of these previous
attempts has conclusively reported the isomer’s
direct detection. Here we report the direct
observation of this elusive isomeric decay.
Nature 533, 47–51 (2016).

Golden rules for the Introduction
• Give credit where credit is due
• Cite papers selectively, not exhaustively
• Be concise: it’s an Introduction, not a thesis

References and citation
Include:
• Findings, case studies, theories, predictions and opinions
• Materials, methods, unconventional statistics and data
Avoid:
• Too many self-citations and over-referencing
• Citing unrelated papers in the same journal to try to
influence the editor!

Managing your reference list
• Several different systems in use for referencing:
alphabetical (Harvard style); numerical (Vancouver style)
• Follow the journal’s style
• Use dedicated software to manage your reference library,
such as:
– Endnote, Refworks or Ref Manager (paid)
– Readcube and Mendeley (free)

The Results
What do you think is the main purpose of the results section?
• Describing figures
• Highlighting important data
• Evaluating findings and their implications
• Providing context for your data
• Explaining methods used
Vote in the poll!

The Results
• For highlighting the most important features of your data
• Use a narrative; don’t just ‘dump’ your data
• Order your data logically (not necessarily chronologically)
• Cite all figures, in the correct order
• Deeper evaluation of the results, their implications and the
literature comes in the Discussion

The Results: an example
• Aim or link to To assess the conductivity of strongly
coupled organic semiconductors, we
previous paragraph
recording current–voltage (I–V) curves for
thin films of the semiconductors between
• Method two electrodes. First, a 100-nm-thick layer
of Al or Ag was evaporated on a glass
substrate through a shadow mask to yield a
long 80-μm-wide strip... We found that
• Finding width of these gaps had a strong effect on…
– a distance larger than the decay of the
evanescent field of the surface plasmon
resulted in the current flowing through an
area where the material would not be
• Conclusion hybridized. This suggests that…
Nature Materials 14, 1123–1129 (2015).
.
Verbs and tenses
“Following a decrease in X…”
• “…Y might increase.”
– Modal verb: a hypothesis or tentative statement
• “…Y increased.”
– Past simple: your observations – usually appropriate for
the Results section
• “…Y increases.”
– Present simple: a permanent truth or fact

Verbs and tenses
Examples:
● Hypothesis
- “a small increase in MIC might decrease the efficacy of
vancomycin in clearing a S. aureus infection”
● Observation
- “experimental warming increased soil CO2 emissions by
55%”
● Fact
- “treatment with EGCG also decreases tau
phosphorylation”
Sci Rep 10, 13121 (2020) Nature 584, 234–237 (2020).. Sci Rep 10, 12827 (2020).

Supplementary Information
• For results of peripheral Supplementary Information to [paper title]
importance to your
argument Table of contents
• Check the journal’s 1. Expanded experimental methods
guide to authors 2. Extended deductions of mathematical
formulae
3. Raw data (e.g. crystallographic)
See attached files for:
• Raw data
• Video files and 3D rendering
of molecules

Data deposition
• Best practice is to make all data available
– A requirement of many journals (including Nature)
• Any restrictions on data availability should be disclosed on
submission
• Usually, a community-endorsed public repository is most
appropriate, with the accession number cited

The Discussion
Why should I trust

your data?
Why should I
care?

The Discussion: an example
• Link to previous ideas We expect the fundamental limit on the speed
of modulation to be significantly faster than this
initial demonstration. In our experiment, the
• Deeper investigation speed of switching was mainly limited by the AOM
used to modulate the 1,064 nm control laser. In
theory, dynamic modulation of emission through
tuning the LDOS is only limited by retardation
effects (that is, the time needed for light to
propagate from the emitter to the reflecting layer
and back). Therefore, […]
• Limitations and caveats Although our device has a very simple geometry,
this enabled us to… In future, …
We envisage that our device could form the basis
• Short-term for a unit that can easily be integrated on a variety
implications and of structures including cavities, waveguides and
light-emitting devices. These structures could
applications, future perhaps enable....
Natureresearch
Communications 6, 8636 (2015).
Combined Results and Discussion
• Link to previous Some structures made of long-lived microtubules in
sensory organelles, such as sensory cilia or axons,
paragraph maintain their mechanical properties despite being
continuously subjected to external constraints. This raises
• Aim the possibility that mechanisms may protect long-lived
microtubules from material fatigue or allow them to
recover from the effect of injurious bending. We tested
• Method this hypothesis by letting microtubules recover for long
periods of time between the bending cycles. Microtubules
• Key features were assembled at 20 μM of free tubulin. As the duration
of the rest period increased from 10 to 100 s, the
proportion of microtubules affected by fatigue was
progressively reduced. Remarkably, when microtubules
remained at rest for 100 s between the bending cycles,
• Conclusion microtubule stiffness was unchanged from one cycle to
another […] These findings demonstrate that damaged
• Wider discussion microtubules have the ability to recover their stiffness
Nature Materials 14, 1156–1163 (2015). through self-repair.
Importance of conclusions
• Your last chance to convince the reader
• Only if necessary, give a brief summary of the key
finding
• Assume readers have read at least the title and abstract
• Where could these results lead (in the near future)?
• Perspective is good, hype is bad!

Improving conclusions
Abstract
Soft particle glasses form a broad family of materials made of deformable particles, as diverse as
microgels1, emulsion droplets2, star polymers3, block copolymer micelles and proteins4, which
are jammed at volume fractions where they are in contact and interact via soft elastic
repulsions. Despite a great variety of particle elasticity, soft glasses have many generic features
in common. They behave like weak elastic solids at rest but flow very much like liquids above the
yield stress. This unique feature is exploited to process high-performance coatings, solid inks,
ceramic pastes, textured food and personal care products. Much of the understanding of these
materials at volume fractions relevant in applications is empirical, and a theory connecting
macroscopic flow behaviour to microstructure and particle properties remains a formidable
challenge. Here we propose a micromechanical three-dimensional model that quantitatively
predicts the nonlinear rheology of soft particle glasses. The shear stress and the normal stress
differences depend on both the dynamic pair distribution function and the solvent-mediated
EHD interactions among the deformed particles. The predictions, which have no adjustable
parameters, are successfully validated with experiments on concentrated emulsions and
polyelectrolyte microgel pastes, highlighting the universality of the flow properties of soft
glasses. These results provide a framework for designing new soft additives with a desired
rheological response.
The authors have supplied the following conclusion:
In conclusion, this report shows novel tools for manufacturing and
processing, which provide various insights about particle properties.
Can you suggest ways to improve this conclusion?

Hands raised
Chat box

A better conclusion
The theory and the experimental data we have presented are not very
sensitive to the exact form of the interacting potential, so the generic
properties reported here will be found in many other systems. Our results
open new strategies to estimate particle properties from macroscopic
rheology and conversely provide rational tools for manufacturing and
processing soft materials in industrial applications
Wider relevance Future applications

Summary
NARRATIVE THREAD
Introduction: Discussion:
Results:
topic, key self-reflection,
strong
studies, key studies,
evidence
objectives what next?
• “Why should I care?” • Don’t just ‘dump’ • “Why should I

your data believe you?”
• Mention papers with
similar conclusions • Write in a narrative • “Why should I
care?”
• Lead to the objective
Q&A
Ask the Editor!

Participant guide page ??
Exercise 1
Pitching Your Research

??

You are the author of Abstract 5. At an upcoming conference, you hope to
catch the attention of an editor at the journal where you wish to publish
your paper.
Present a 3-sentence pitch to the editor that describes your work!
Hints:
• Describe what you did and how you did it
• Explain how your findings advance the field
• Say why they will be of interest to the journal’s readers

??

Abstract 5: Simultaneous voltage and current density imaging of flowing electrons in two
dimensions
A variety of physical phenomena associated with nanoscale electron transport often results in
non-trivial spatial voltage and current patterns, particularly in nonlocal transport regimes. While
numerous techniques have been devised to image electron flows, the need remains for a
nanoscale probe capable of simultaneously imaging current and voltage distributions with high
sensitivity and minimal invasiveness, in a magnetic field, across a broad range of temperatures
and beneath an insulating surface. Here we present a technique for spatially mapping electron
flows based on a nanotube single-electron transistor, which achieves high sensitivity for both
voltage and current imaging. In a series of experiments using high-mobility graphene devices, we
demonstrate the ability of our technique to visualize local aspects of intrinsically nonlocal
transport, as in ballistic flows, which are not easily resolvable via existing methods. This technique
should aid in understanding the physics of two-dimensional electronic devices and enable new
classes of experiments that image electron flow through buried nanostructures in the quantum
and interaction-dominated regimes.
Use your own research instead of Abstract 5 if you’re feeling brave!

??

Facilitator Pitch
Listen to an example pitch by the Facilitator
Present a 3-sentence pitch to the editor that describes

your work!

??

Facilitator Pitch
You are an Editor at a Nature Research journal.
Would you consider the author’s work for your
journal?
• Yes
• No
• Need more information to decide
Vote in the poll!

??

Facilitator Pitch — Trainer feedback
We demonstrate a highly sensitive and minimally invasive nanoscale

imaging technique for voltage and current distributions in 2D. Unlike
existing methods, our technique is able to image non-local transport
phenomena such as ballistic voltage distribution. This technique opens
up avenues for imaging and characterising electron flow in 2D materials
and devices that wouldn’t be possible using conventional methods.

??

Participant Pitches
Present a 3-sentence pitch to the Editor that describes

your work!
Pitch to the group!

Hands raised

??

Participant Pitches
You are an Editor at a Nature Research journal.
Would you consider the author’s work for your

journal, and why?

Hands raised
Chat box

??

Participant Pitches — Trainer feedback

??

Participant Pitches — Final discussion
Share any further comments on the participant pitches you’ve heard
today!
Share your comments!

Hands raised
Chat box

Break

Figure Presentation

Before digital graphics
• Figures and tables were
difficult to print
• Watson and Crick’s famous
1953 paper
Nature 171, 737–738 (1953).

From data to figures
Figures are the backbone of the paper.
They serve to:

• Structure the logical progression of the article
• Help readers understand complex data and ideas quickly
• Show readers how authors have reached the main
conclusions
Figures need to function as standalone display items with their

legends.

Figure guidelines
• Decide what message you want to convey
– Clarity trumps beauty
• Make the most important features of the data obvious
• Include statistics wherever possible
• Ensure that images submitted with the manuscript are
minimally processed
• Make your legends informative
• Use colour considerately

Visual clarity
‘Chartjunk’ is defined as redundant and distracting information
on graphics.
The top three types of chartjunk are:

1. Patterned fill on bar charts and pie charts
2. Unnecessary grid lines
3. Unnecessary design features
Nature Methods 10, 371 (2013).

Visual clarity
What would you change in
these graphics?

Hands up
Chat box

Visual clarity

Visual clarity
Figure 1 | Bacterial expression of three fibrillizing peptides tagged with GFP,

over time (minutes).

Visual clarity
What would you improve in the figure?
• Axes labelling and origin

• Unnecessary grid lines
• Colours and background
• Statistics
• Key
Figure 1 | Bacterial expression of three

Vote in the poll! fibrillizing peptides tagged with GFP, over time
(minutes).

Visual clarity
Improved graph
Figure 1 | Bacterial expression of three fibrillizing peptides tagged with GFP,

over time (minutes).

Figure legend guidelines
• Self-contained
– Readers should not need to consult the main text to
understand the data
• Descriptive title
• Incorporate crucial information about methods to
enable interpretation
• Define scale bars, error bars and other statistics
• Define colours and annotations
• Cite third-party material

Figure legends
How could this legend be
improved?

Figure 1 | Bacterial expression of three Hands raised
fibrillizing peptides tagged with GFP, over time
(minutes). Chat box

Figure legends
Original legend
Figure 1 | Bacterial expression of three fibrillizing peptides tagged with GFP, over time (minutes).
Improved legend
Figure 1 | Temporal variation in protein expression of the three GFP-

tagged peptides, Pep 1–3, in BL21(DE3) cells. The x axis shows timing
relative to induction with IPTG. Means (± S.E.) of n=6 independent
experiments.

Statistics
Make sure that you specify where relevant:
• Exact sample size (n)
• Indication of how the measurements were taken on the
sample
• Statistical tests and assumptions
• Estimates of effect sizes
• Clearly defined error bars
Resource
Nature Research’s reporting summary
www.nature.com/documents/nr-reporting-summary-flat.pdf
Representing your data
Guidelines for choosing an appropriate graph type:
• 1–4 data points

– Plot only individual points
– Plot individual points with or without a mean or median bar
– Error bars optional
– Box plots
• >50 data points
– Violin, bean or related plots
Bar charts versus box plots
• Box plots
should be used
to represent
the
characteristics
of a distribution

Choosing a representative image
• A representative image should reflect the dataset
– A typical image, not the most beautiful
• Best avoided unless really valuable
– Numerical data often more effective
• Avoid showing a representative image when there is
high variability in the data
• Best practice: make all images available to reviewers
– Preferably also to readers

Use of colour
• Avoid red–green colour Natural colour vision Colour-blind vision
combination (top)
• For good contrast, replace red
with magenta (middle) or green
with turquoise (bottom).
• To simulate colour-blind vision
and correct scientific graphics,
use: vischeck.com
• A good resource for sequential,
diverging or qualitative colours:
colorbrewer2.org

Schematics
• Guide readers
through the
experiment or
data
• Be logical and
clear
Nature 538, 222–225 (2016).

Insets
• Used to show greater detail
• Add scale bars for photos

and microscopy images
• Add clear labels
Nature 538, 222–225 (2016).

Tables Nature Reviews Drug Discovery 6, 357–372 (2007).
Nature Reviews Drug Discovery 7, 358–368 (2008).
Useful for:
• Displaying raw or
moderately complex
data
• Lists that would make
the text cumbersome
• Summarising findings
across many studies
• Comparisons of
approaches or models
Summary
• Be mindful of figure clarity
• Figure legends should be self-contained
• Carefully consider which graph type is most appropriate

for your data
• Use other display items to help your narrative flow

– Tables and conceptual figures

Q&A
Ask the Editor!

Participant guide page ??
Exercise 2
Improving Figures

??
Improving Figures
Examine Figure 1 and its legend in the Participant Guide.
Which aspect of Figure 1 do you think needs most improvement?
Hints:
• Is the figure legend self-contained?
• Is colour being used appropriately?
• Does the figure clearly convey the data?

??
Improving Figures
Figure 1
Spin-density wave transition temperature TSDW and Korringa rate b as a function of transition
metal substitution M when the ESR spin probe is a) out of the Fe-As plane and, b) in the Fe-As
plane. Scientific Reports 4, 6543 (2015).

??
Improving Figures
Which aspect of Figure 1 do
you think most needs
improvement? (Select one)
• Panel labels
• Use of colour
• Use of arrows
• Graph type
• y-axes Spin-density wave transition temperature TSDW and
Korringa rate b as a function of transition metal
substitution M when the ESR spin probe is a) out of
Vote in the poll! the Fe-As plane and, b) in the Fe-As plane.
Scientific Reports 4, 6543 (2015).
??
Improving Figures
Potential issues
• Panel labels
– Obscuring the data
– Should be moved elsewhere
• Use of colour
– Colour unnecessary for x-axis
labels, right-hand y-axis and
data points
• Use of arrows Spin-density wave transition temperature TSDW
– Undefined in legend and Korringa rate b as a function of transition
metal substitution M when the ESR spin probe is
– Reconsider use of colour a) out of the Fe-As plane and, b) in the Fe-As
??
Improving Figures
Potential issues
• Graph type
– Inappropriate
representation of data
– Consider presenting TSDW
and Korringa state b data
as separate panels
• y-axes
– Left-hand y-axis units Spin-density wave transition temperature TSDW
missing and Korringa rate b as a function of transition
– Formatting of y-axes labels a) out of the Fe-As plane and, b) in the Fe-As
??
Improving Figures
Are there any other improvements you would suggest for

Figure 1?

Hands raised
Chat box

??
Improving Figures
Other issues
• Data points
– Make filled or open
– Make smaller and avoid
overlapping
• Figure legend
– Figure title missing
– Does not describe how
data were obtained Spin-density wave transition temperature TSDW
and Korringa rate b as a function of transition
– Should describe the panels metal substitution M when the ESR spin probe is
separately a) out of the Fe-As plane and, b) in the Fe-As
??
Improving Figures
Write an improved legend
for Figure 1.

Hands raised
Spin-density wave transition temperature TSDW Chat box
and Korringa rate b as a function of transition
a) out of the Fe-As plane and, b) in the Fe-As Scientific Reports 4, 6543 (2015).
plane.
Q&A
Ask the Editor!

Webinar 1: Webinar 2: Webinar 3: Webinar 4:
Focus on Scientific Focus on Scientific Abstract Review Focus on Scientific Focus on Scientific
Writing I Writing II Publishing I Publishing II
What Makes a Great From Introduction to Abstract Consultation Submitting Your Journal Decisions
Paper? Conclusion • How to structure and Paper • Journal decisions and
• What researchers and improve your how they affect your
• How to structure each scientific writing • Journal submission
editors look for in a manuscript
great paper part of your paper to procedures • How to assess and
• Characteristics of facilitate clear writing • How to structure and respond to journal
excellent primary write a good cover decisions
research papers and letter to the Editor
review articles Figure Presentation Plagiarism and Other
• An interactive module An individual 8-minute
session with a Nature The Editorial Process Ethical Issues
Titles and Abstracts on designing clear and
• How to write a informative figures and Research journal editor and Peer Review • Why research
compelling title tables to discuss your pre- • The editorial process misconduct happens,
• Structuring a well- submitted abstract and the value of peer what it looks like and
balanced abstract + Interactive activities review
what to do about it
and Q&A sessions • The importance of
+ Interactive activities referee reports
+ Interactive activities
and Q&A sessions
+ Interactive activities and Q&A sessions
and Q&A sessions

Still to come
Abstract Review
Wednesday 24 March, 16:00 -18:30 CST
You should have received an e-mail with your time slot for the Abstract Review session. If you
haven’t, or if you have any questions, please get in touch by e-mailing:
trainingwebinars_china@springernature.com
Webinar 3: Focus on Scientific Publishing I

Thursday 25 March, 16:00 -18:30 CST
Webinar 4: Focus on Scientific Publishing II

Friday 26 March, 16:00 -18:30 CST

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Masterclass in Scientific Writing

Webinar 2: Focus on Scientific Writing II

State Key Laboratory Superlattices & Microstructure,

Please message the Organizer if

Institute of Semiconductors, CAS, 23 March 2021

Vote in the poll

Institute of Semiconductors, CAS, 23 March 2021

This is the hand raising

Alternatively, share your comments and

Here you can download:

Show of hands: Have you completed the pre-

Institute of Semiconductors, CAS, 23 March 2021

Institute of Semiconductors, CAS, 23 March 2021

Institute of Semiconductors, CAS, 23 March 2021

Institute of Semiconductors, CAS, 23 March 2021

Institute of Semiconductors, CAS, 23 March 2021

From Introduction to Conclusion

Institute of Semiconductors, CAS, 23 March 2021

Institute of Semiconductors, CAS, 23 March 2021

Share your suggestions!

Institute of Semiconductors, CAS, 23 March 2021

• Mention papers • Start leading readers • Reminder before

Nature 533, 47–51 (2016).

Institute of Semiconductors, CAS, 23 March 2021

Institute of Semiconductors, CAS, 23 March 2021

Institute of Semiconductors, CAS, 23 March 2021

Institute of Semiconductors, CAS, 23 March 2021

Vote in the poll!

Institute of Semiconductors, CAS, 23 March 2021

Institute of Semiconductors, CAS, 23 March 2021

Institute of Semiconductors, CAS, 23 March 2021

Institute of Semiconductors, CAS, 23 March 2021

Institute of Semiconductors, CAS, 23 March 2021

Institute of Semiconductors, CAS, 23 March 2021

Why should I trust

Institute of Semiconductors, CAS, 23 March 2021

Institute of Semiconductors, CAS, 23 March 2021

Can you suggest ways to improve this conclusion?

Share your suggestions!

Institute of Semiconductors, CAS, 23 March 2021

Wider relevance Future applications

Nature Materials 10, 838–843 (2011).

Institute of Semiconductors, CAS, 23 March 2021

• “Why should I care?” • Don’t just ‘dump’ • “Why should I

Ask the Editor!

Institute of Semiconductors, CAS, 23 March 2021

Pitching Your Research

Institute of Semiconductors, CAS, 23 March 2021

Pitching Your Research

Present a 3-sentence pitch to the editor that describes your work!

Institute of Semiconductors, CAS, 23 March 2021

Pitching Your Research

Use your own research instead of Abstract 5 if you’re feeling brave!

Pitching Your Research

Listen to an example pitch by the Facilitator

Present a 3-sentence pitch to the editor that describes

Institute of Semiconductors, CAS, 23 March 2021

Pitching Your Research

Vote in the poll!

Pitching Your Research

We demonstrate a highly sensitive and minimally invasive nanoscale

Institute of Semiconductors, CAS, 23 March 2021

Pitching Your Research