Zucolotto - Como Escrever Artigos Científicos

Organização: Pró-Reitoria de Pesquisa - USP
Workshop de Capacitação em
Escrita Científica
Módulo 1
Prof. Dr. Valtencir Zucolotto

Laboratório de Nanomedicina e Nanotoxicologia
Instituto de Física de São Carlos, USP
USP, 2012
www.nanomedicina.com.br zuco@ifsc.usp.br
Workshop Outline
Modulo 1: O Gênero Literário
Seções de Um Artigo Científico
Módulo 2: Estrutura 1: Abstract
Módulo 3: Estrutura 2: Introduction
Módulo 4: Estrutura 3: Results and Discussion, Conclusion
Módulo 5: Estilo
Linguagem 1: Especificidade, Complexidade e Ambiguidade
Módulo 6: Linguagem 2: Redundâncias, Ação no Verbo, Fluidez de
Texto, Ritmo de Escrita
Módulo 7: Linguagem 3: Plain English, Escrever em Inglês, Preposições
Módulo 8: Linguagem 4: Topic Sentences, Cover Letters, Final Remarks

Módulo 1
O Gênero Literário
Estrutura 1

Why?, What?, When?....

Why to Publish??
Publication is one of the most important steps

of the scientist’s work
If nobody knows, or can benefit from your work,
Why being at work ??

What do we Publish?
Scientists Publish Ideas !!

When to Publish?
When the initial
question/problem/hypothesis
had been answered/solved/tested !!!!!!

When to Publish?
Scientific Method /
Hypothesis testing

When to Publish?
-Distinct time scales for distinct areas;
-Depends on the type of research:
Breakthroughs and Innovative research.
Advances on a specific, systematic

investigation area.

Publishing Ideas
Ideas
Implementation of the Research
Results
Ideas
New Ideas?
Output
(Papers, Thesis, etc.)

1.
General Considerations

Lesson Zero
Scientific writing as a “new” Literary

Genre

A bit of History…
In the very beginning….
 Informal Letters exchanged by scientists.
1665: Creation of the first scientific periodical: The

Philosophical Transactions of the Royal Society.
This new arena for discussion led to the development of

a new genre:
The Scientific Report

Audience
Who will read your paper?
Highly technical journal vs. less specific ones.

Clarity and Concision
Report your results clearly
Use as few words as necessary
Save words!!

References
All information or ideas must be referenced!

Including your own work

2.
Sections of a Regular Paper

Types of Scientific Publications
Thesis Reviews
Research Regular
Papers
Articles
Short
Books Communication
s/Letters
Encyclopedias
Organization of a paper
Title, Authors and Affiliations
Abstract
General
Introduction
Methodology
Specific
Results
Discussion
Conclusions
General
References
Adapted from: Hill et al., Teaching ESL students to read and write
experimental papers, TESOL Quarterly, 16: 333, 1982:
A good Title describes the contents of the

paper
Function: to attract reader’s attention
Use specific words strongly associated with

the outcome of the paper: Keywords

Example 1: A paper reporting on the influence of the

molecular weight on the mechanical properties of Polyaniline
thin films:
Title 1: Mechanical properties of Polyaniline films
Poor, too general!

Title 2: The influence of the MW on the Mechanical

properties of polyaniline spin-coated films
Expresses the main idea of the work, the kind of film and its
fabrication technique.
Keywords Included: mechanical properties, polyaniline,

spin coated

Emphasize your key findings whenever possible
Title:
Metal-Polymer nanocomplexes induce spontaneous
regression of lung tumors
OK!! The author describes the most important result

shortly and concisely

Who are the authors of a paper?

Guidelines to define authorship:
All authors must be able to present/discuss/defend

the paper.

Authors Names Sequence:
First Name
The researcher who did the work, junior researcher.
Middle names
Anyone who intellectually contributed to the work
Last Name
The responsible for the research: supervisor/ group
head/ senior scientist

Affiliations usually include the following information:
Group
Department, Center
Institution, University
City, Zip code, PO Box
Country

Abstract

A Model
Contextualization
Gap
Purpose
Methodology
Results
Conclusions
Aluísio, S.M. (1995). Ferramentas para Auxiliar a Escrita de Artigos Científicos em Inglês como
Língua Estrangeira. Tese de Doutorado, IFSC-USP, 228 p.
Abstract
Self-assembly of components larger than molecules into ordered arrays is an

efficient way of preparing microstructured materials with interesting mechanical and
optical properties. Although crystallization of identical particles or particles of different
sizes or shapes can be readily achieved, the repertoire of methods to assemble binary
lattices of particles of the same sizes but with different properties is very limited. This
paper describes electrostatic self-assembly of two types of macroscopic components of
identical dimensions using interactions that are generated by contact electrification. The
systems we have examined comprise two kinds of objects (usually spheres) made of
different polymeric materials that charge with opposite electrical polarities when agitated
on flat, metallic surfaces. The interplay of repulsive interactions between like-charged
objects and attractive interactions between unlike-charged ones results in the self-
assembly of these objects into highly ordered, closed arrays. Remarkably, some of the
assemblies that form are not electroneutral—that is, they possess a net charge. We
suggest that the stability of these unusual structures can be explained by accounting for
the interactions between electric dipoles that the particles in the aggregates induce in
their neighbors.
Grzybowski et al., Nature Materials 2, 241–245 (2003)

Abstract
1) Context: Self-assembly of components larger than molecules into ordered arrays is an

optical properties.
2) GAP: Although crystallization of identical particles or particles of different sizes or
shapes can be readily achieved, the repertoire of methods to assemble binary lattices of
particles of the same sizes but with different properties is very limited.
3) Purpose: This paper describes electrostatic self-assembly of two types of macroscopic
components of identical dimensions using interactions that are generated by contact
electrification.
4) Methodology: The systems we have examined comprise two kinds of objects (usually
spheres) made of different polymeric materials that charge with opposite electrical
polarities when agitated on flat, metallic surfaces.
5) Results: The interplay of repulsive interactions between like-charged objects and
attractive interactions between unlike-charged ones results in the self-assembly of these
objects into highly ordered, closed arrays. Remarkably, some of the assemblies that form
are not electroneutral—that is, they possess a net charge.
6) Conclusions: We suggest that the stability of these unusual structures can be
explained by accounting for the interactions between electric dipoles that the particles in
the aggregates induce in their neighbors.

Introduction

Introduction
General Contextualization Your Field
Sumarizing Previous
Research
Purpose
Specific Your work

Methodology

Methodology
Materials
What materials were employed?
Where did the materials come from?
Methods/Procedures
Reference to any well established methods and
analyses
Details concerning the procedure adopted
Justifying the procedures adopted
Equipment
Equipment employed
Data analyses
Methods used for data processing and analyses

Results and Discussion

Results
Introduction
(purpose)

(Key Results)

Conclusion

Conclusion
In contrast to the Introduction, the

conclusions section starts the Specific–to–
General Movement.

Conclusion
Specific
Key findings
Interpretation of main Results
Contribution to the field

General

References
All information or ideas must be referenced!

Including your own work
There are a number of different formats/styles you may

use to cite other’s work in the text, or arrange the
references list:
Always consult the Journal’s Guide for Authors

References
1. The citation-sequence system

References are numbered in the order they appear in the text.
Examples
―….However, recent reports have been made on the fabrication of
ultrathin films of metallic phthalocyanines and polyelectrolytes
via the electrostatic layer-by-layer technique (LBL).10
(10) Lutt, M.; Fitzsimmons, M. R.; Li, D. Q. J. Phys. Chem. B 1998,

102, 400.

References
2. The name-year system
References are listed alphabetically, using the first author´s last name.
Examples
―….The layer-by-layer (LbL) technique has been largely employed in
the immobilization of proteins and other biomolecules following
the pioneering work of Lvov et al. [Lvov et al., 1993; Lvov et al.,
1995]….‖
Lvov, Y., Ariga, K., Ichinose, I., Kunitake, T., 1995. Assembly of multicomponent
protein films by means of electrostatic layer-by-layer adsorption. J. Am. Chem.
Soc.117, 6117- 6123.
Lvov, Y., Decher, G., Sukhorukov, G. 1993. Assembly of Thin Films by Means of
Successive Deposition of Alternate Layers of DNA andv Poly(allylamine).
Macromolecules 26, 5396-5399.
A Suggested Sequence….
Results and Discussions
Conclusions
Introduction
Experimental
Abstract
Title
Translations ??
Begin writing in English
Take your notes in English
Final version of a paper translated into

English

Plagiarism
You may cite others’ words, data, etc. using

your own words;
Do not paraphrase other author´s text
Do not paraphrase your early papers.

Plagiarism
http://www.fapesp.br/boaspraticas/codigo_fapesp0911.pdf

Plagiarism

Sources
-Introduction to Journal-Style Scientific Writing:

http://abacus.bates.edu/~ganderso/biology/resources/writing/HTW
general.html
-http://www.inter-biotec.com/biowc/style.html
-Scientific Writing, Easy When ou Know How, Peat, J., Elliot, E., Baur, L.,
Keena, V., BMJ Books, 2009
-Hill et al., Teaching ESL students to read and write experimental papers,
TESOL Quarterly, 16: 333, 1982:
-Int. Committee of Medical J. Editors, Ann. Intern. Med., 1997, 126, 36.

Muito Obrigado
Valtencir Zucolotto
zuco@ifsc.usp.br
www.nanomedicina.com.br
www.lnn.ifsc.usp.br
www.twitter.com/Nanomedicina
Instituto de Física de São Carlos - USP
www.twitter.com/escreverartigos
www.twitter.com/writingpapers

Escrita Científica
Módulo 2

USP, 2012
Workshop Outline
Módulo 5: Estilo

Módulo 2
Estrutura 1: Abstract

Organization of a paper
Abstract
General
Introduction
Methodology
Specific
Results
Discussion
Conclusions
General
References
Abstract

Abstract
An abstract summarizes the major aspects of the

paper
The abstract contains only text

Abstract
Informative Descriptive
Contains all the X Describes only the
relevant information of nature/purpose of the
the paper study
Michael Alley The Craft of Scientific Writing, 3rd edition (Springer-Verlag, 1996).

Abstract
Style
- Past Tense (whenever possible);
- Active voice preferred;
- Concise, complete sentences.

Abstract
Contextualization
Gap
Purpose
Methodology
Results
Conclusions
Aluísio, S.M. (1995). Ferramentas para Auxiliar a Escrita de Artigos Científicos em Inglês como
Língua Estrangeira. Tese de Doutorado, IFSC-USP, 228 p.

Abstract
J Pharm Pharmaceut Sci 8(2):162-178, 2005

Examples from the Literature

Abstract
Case 1 M2P1 Nature Mat
Self-assembly of components larger than molecules into ordered arrays
is an efficient way of preparing microstructured materials with interesting
mechanical and optical properties. Although crystallization of identical particles or
particles of different sizes or shapes can be readily achieved, the repertoire of
methods to assemble binary lattices of particles of the same sizes but with
different properties is very limited. This paper describes electrostatic self-
assembly of two types of macroscopic components of identical dimensions using
interactions that are generated by contact electrification. The systems we have
examined comprise two kinds of objects (usually spheres) made of different
polymeric materials that charge with opposite electrical polarities when agitated
on flat, metallic surfaces. The interplay of repulsive interactions between like-
charged objects and attractive interactions between unlike-charged ones results
in the self-assembly of these objects into highly ordered, closed arrays.
Remarkably, some of the assemblies that form are not electroneutral—that is,
they possess a net charge. We suggest that the stability of these unusual
structures can be explained by accounting for the interactions between electric
dipoles that the particles in the aggregates induce in their neighbors.

Abstract
1) Context: Self-assembly of components larger than molecules into ordered arrays is an

optical properties.
2) GAP: Although crystallization of identical particles or particles of different sizes or
shapes can be readily achieved, the repertoire of methods to assemble binary lattices of
particles of the same sizes but with different properties is very limited.
3) Purpose: This paper describes electrostatic self-assembly of two types of macroscopic
components of identical dimensions using interactions that are generated by contact
electrification.
4) Methodology: The systems we have examined comprise two kinds of objects (usually
spheres) made of different polymeric materials that charge with opposite electrical
polarities when agitated on flat, metallic surfaces.
5) Results: The interplay of repulsive interactions between like-charged objects and
attractive interactions between unlike-charged ones results in the self-assembly of these
objects into highly ordered, closed arrays. Remarkably, some of the assemblies that form
are not electroneutral—that is, they possess a net charge.
6) Discussion/Conclusions: We suggest that the stability of these unusual structures
can be explained by accounting for the interactions between electric dipoles that the
particles in the aggregates induce in their neighbors.

Abstract
Case 2
M2P2 Nature Mat
Bioinert polyelectrolyte multilayers comprised of poly(acrylic acid)

and polyacrylamide were deposited on colloidal particles (1.7 m diameter)
at low pH conditions by layer-by-layer assembly using hydrogen-bonding
interactions. The multilayer films were coated uniformly on the colloidal
particles without causing any flocculation of the colloids, and the deposited
films were subsequently cross-linked by a single treatment of a
carbodiimide aqueous solution. The lightly cross-linked multilayer films
show excellent stability at physiological conditions (pH 7.4, phosphate-
buffered saline), whereas untreated multilayer films dissolved. The
multilayer-coated surfaces, both on flat substrates and on colloidal
particles, exhibit excellent resistance toward mammalian cell adhesion.
With this new solution-based cross-linking method, bioinert H-bonded
multilayer coatings offer potential for biomedical applications.
Yang et al, Langmuir; 2004; 20; 5978

Abstract
Context??
Gap??
Purpose?: Bioinert polyelectrolyte multilayers comprised of poly(acrylic
acid) and polyacrylamide were deposited on colloidal particles (1.7 m
diameter) at low pH conditions by layer-by-layer assembly using hydrogen-
bonding interactions.
Methodology: The multilayer films were coated uniformly on the colloidal
particles without causing any flocculation of the colloids, and the deposited
films were subsequently cross-linked by a single treatment of a carbodiimide
aqueous solution.
Results: The lightly cross-linked multilayer films show excellent stability at
physiological conditions (pH 7.4, phosphate-buffered saline), whereas
untreated multilayer films dissolved. The multilayer-coated surfaces, both on
flat substrates and on colloidal particles, exhibit excellent resistance toward
mammalian cell adhesion.
Conclusions: With this new solution-based cross-linking method, bioinert H-
bonded multilayer coatings offer potential for biomedical applications.

Abstract
Case 3
M2P3 Nature Biotech
Dendrimers are branched, synthetic polymers with layered architectures

that show promise in several biomedical applications. By regulating
dendrimer synthesis, it is possible to precisely manipulate both their
molecular weight and chemical composition, thereby allowing predictable
tuning of their biocompatibility and pharmacokinetics. Advances in our
understanding of the role of molecular weight and architecture on the in
vivo behavior of dendrimers, together with recent progress in the design
of biodegradable chemistries, has enabled the application of these
branched polymers as anti-viral drugs, tissue repair scaffolds, targeted
carriers of chemotherapeutics and optical oxygen sensors. Before such
products can reach the market, however, the field must not only address
the cost of manufacture and quality control of pharmaceutical-grade
materials, but also assess the long-term human and environmental health
consequences of dendrimer exposure in vivo.
Lee et al., Nature Biotechnology 23, 1517, 2005 (Review)

Abstract
Context: Dendrimers are branched, synthetic polymers with layered
architectures that show promise in several biomedical applications. By
regulating dendrimer synthesis, it is possible to precisely manipulate
both their molecular weight and chemical composition, thereby allowing
predictable tuning of their biocompatibility and pharmacokinetics.
Advances in our understanding of the role of molecular weight and
architecture on the in vivo behavior of dendrimers, together with recent
progress in the design of biodegradable chemistries, has enabled the
application of these branched polymers as anti-viral drugs, tissue repair
scaffolds, targeted carriers of chemotherapeutics and optical oxygen
sensors.
Gap: Before such products can reach the market, however, the field
must not only address the cost of manufacture and quality control of
pharmaceutical-grade materials, but also assess the long-term human
and environmental health consequences of dendrimer exposure in vivo.
Descriptive or Informative ??

Prática 1
M2P4
Metallophthalocyanines (MPcs) are conjugated macrocyclic compounds that have been

widely investigated in different scientific and technological fields. However, one of the
limitations of the use of MPcs in technological devices is the limited solubility of these
molecules, which makes difficult the deposition as thin films. This paper describes the use of
the layer-by-layer technique to obtain thin films of cobalt tetrasulfonated phthalocyanine
(CoTsPc) and the polyelectrolytes poly(allylamine hydrochloride) (PAH) and poly(amido
amine) generation 4 (PAMAM G4). In addition to the structural investigations that revealed
the nanoscale organization of the films, the possibility of using these platforms as humidity
sensors has also been exploredA comprehensive SPR investigation on film growth
reproduced dynamically the deposition process and provided an estimation of the layers’
thicknesses. The electrical conductivity of the films deposited on interdigitated electrodes
was found to be very sensitive to water vapor. This sensitivity is caused by the positioning of
the Pc rings along the multilayers, which is a consequence of the self-assembly method.
These results point to the development of a phthalocyanine-based humidity sensor obtained
from a simple thin film deposition technique, whose outstanding ability to tailor molecular
organization was crucial to achieve such high sensitivity.
Centurion et al., J. Nanosc. Nanotech, 2012 in press

Prática 2
M2P9 Nat Chem
Vibrational energy flow into reactants, and out of products, plays a key
role in chemical reactivity, so understanding the microscopic detail of the
pathways and rates associated with this phenomenon is of considerable
interest. Here, we use molecular dynamics simulations to model the
vibrational relaxation that occurs during the reaction CN1c-C6H12 HCN1
c-C6H11 in CH2Cl2, which produces vibrationally hot HCN. The
calculations reproduce the observed energy distribution, and show that
HCN relaxation follows multiple timescales. Initial rapid decay occurs
through energy transfer to the cyclohexyl co-product within the solvent
cage, and slower relaxation follows once the products diffuse apart. Re-
analysis of the ultrafast experimental data also provides evidence for the
dual timescales. These results, which represent a formal violation of
conventional linear response theory, provide a detailed picture of the
interplay between fluctuations in organic solvent structure and thermal
solution-phase chemistry.
Glowacki et al., Nature Chem., 3, 850, 2011

Prática 3
M2P10 ACS Nano
Polymer nanoparticles are widely used as a highly generalizable tool to entrap a

range of different drugs for controlled or site-specific release. However, despite
numerous studies examining the kinetics of controlled release, the biological
behavior of such nanoparticles remains poorly understood, particularly with
respect to endocytosis and intracellular trafficking. We synthesized
polyethyleniminedecorated polymer nanospheres (ca. 100 250 nm) of the type
commonly used for drug release and used correlated electron microscopy,
fluorescence spectroscopy and microscopy, and relaxometry to track endocytosis
in neural cells. These capabilities provide insight into how polyethylenimine
mediates the entry of nanoparticles into neural cells and show that polymer
nanosphere uptake involves three distinct steps, namely, plasma membrane
attachment, fluid-phase as well as clathrin- and caveolinindependent endocytosis,
and progressive accumulation in membrane-bound intracellular vesicles. These
findings provide detailed insight into how the intracellular delivery of nanoparticles
is mediated by polyethylenimine, which is presently the most commonly used
nonviral gene transfer agent. This fundamental knowledge may also assist in the
preparation of next-generation nonviral vectors.
Evans et al., ACS Nano, In Press

Prática 4
M2P11 Anal Chem
Currently, mass spectrometry-based protein bioanalysis is primarily achieved through

monitoring the representative peptide(s) resulting from analyte protein digestion. However,
this approach is often incapable of differentiating the measurement of protein analyte from
its post-translational modifications (PTMs) and/or potential biotransformation (BTX)
products. This disadvantage can be overcome by direct measurement of the intact protein
analytes. Selected reaction monitoring (SRM) on triple quadrupole mass spectrometers has
been used for the direct measurement of intact protein. However, the fragmentation
efficiency though the SRM process could be limited in many cases, especially for high
molecular weight proteins. In this study, we present a new strategy of intact protein
bioanalysis by high-resolution (HR) full scan mass spectrometry using human lysozyme as a
model protein. An HR linear ion-trap/ Orbitrap mass spectrometer was used for detection. A
composite of isotopic peaks from one or multiple charge states can be isolated from the
background and used to improve the signal-to-noise ratio. The acquired data were
processed by summing extracted ion chromatograms (EIC) of the 10 most intense isotopic
ions of octuply protonated lysozyme. Quantitation of the plasma lysozyme was conducted
by utilizing high resolving power and an EIC window fitting to the protein molecular weight.
An assay with a linear dynamic range from 0.5 to 500 μg/mL was developed with good
accuracy and precision. The assay was successfully employed for monitoring the level of
endogenous lysozyme and a potential PTM in human plasma. The current instrumentation
limitations and potential advantages of this approach for the bioanalysis of large proteins
are discussed.
Juan et al., Analytical Chem, In Press
Prática 5
M2P12 JACS
Hoover et al., J. Am. Chem. Soc. 133, 16901, 2011

Prática 6
M2P5 IEEE Sig Proc
Accurate and low-cost sensor localization is a critical requirement for the deployment of
wireless sensor networks in a wide variety of applications. Low-power wireless sensors may
be many hops away from any other sensors with a priori location information. In cooperative
localization, sensors work together in a peer-to-peer manner to make measurements and
then form a map of the network. Various application requirements (such as scalability,
energy efficiency, and accuracy) will influence the design of sensor localization systems. In
this article, we describe measurement-based statistical models useful to describe time-of-
arrival (TOA), angle-of-arrival (AOA), and received-signal-strength (RSS) measurements in
wireless sensor networks. Wideband and ultra-wideband (UWB) measurements, and RF
and acoustic media are also discussed. Using the models, we show how to calculate a
Cramér-Rao bound (CRB) on the location estimation precision possible for a given set of
measurements. This is a useful tool to help system designers and researchers select
measurement technologies and evaluate localization algorithms. We also briefly survey a
large and growing body of sensor localization algorithms. This article is intended to
emphasize the basic statistical signal processing background necessary to understand the
state-of-the-art and to make progress in the new and largely open areas of sensor network
localization research.
IEEE Signal Processing Magazine, 2005, p 55

Prática 7
M2P6 Int J Plast
Commercial canmaking processes include drawing, redrawing and several ironing operations.
It is experimentally observed that during the drawing and redrawing processes earing
develops, but during the ironing processes earing is reduced. It is essential to understand the
earing mechanism during drawing and ironing for an advanced material modeling. A new
analytical approach that relates the earing profile to r-value and yield stress directionalities is
presented in this work. The analytical formula is based on the exact integration of the
logarithmic strain. The derivation is for a cylindrical cup under the plane stress condition
based on rigid perfect plasticity while force equilibrium is not considered. The earing profile is
obtained solely from anisotropic plastic properties in simple tension. The earing mechanism is
explained from the present theory with explicit formulae. It has been proved that earing is the
combination of the contributions from r-value and yield stress directionalities. From a
directionality (y-axis) vs. angle from the rolling (x-axis) plot, the earing profile is generated to
be a scaled mirror image of the r-value directionality with respect to 90 (x = 90) and also a
scaled mirror image of the yield stress directionality with respect to the reference yield stress
(y = 1). Three different materials (Al–5% Mg alloy, AA 2090-T3 and AA 3104 RPDT control
coil) are considered for verification purposes. This approach provides a fundamental basis for
understanding the earing mechanism. In practice, the present theory is also very useful for the
prediction of the earing profile of a drawn and iron cup and its related convolute cut-edge
design for an earless cup.
International Journal of Plasticity 27 (2011) 1165

Prática 8
M2P7 Int J electron
Network-on-chip (NoC) is considered the next generation of

communication infrastructure, which will be omnipresent in different
environments. In the platform-based design methodology, an application
is implemented by a set of collaborating intellectual property (IP) blocks.
The selection of the most suited set of IPs as well as their physical
mapping onto the NoC to efficiently implement the application at hand
are two hard combinatorial problems. In this article, we propose an
innovative power-aware multi-objective evolutionary algorithm to perform
the assignment and mapping stages of a platform-based NoC design
synthesis tool. Our algorithm uses the well-known multi-objective
evolutionary algorithms NSGA-II and microGA as kernels. The
optimisation is driven by the required area and the imposed execution
time, considering that the decision maker’s restriction is the power
consumption of the implementation.
International Journal of Electronics, 97, 2010, 1163

Prática 9
M2P13 IEEE T.E.C.
Design optimization problems in chemical engineering and in many other engineering domains
are characterized by the presence of a large number of discrete and continuous decision
variables, complex nonlinear models that restrict the search space, nonlinear cost functions,
and the presence of many local optima. The classical approach to such problems are mixed
integer nonlinear program solvers that work on a superstructure formulation which explicitly
represents all design alternatives. The structural decisions lead to a large number of discrete
variables and an exponential increase in the computational effort. The mathematical
programming (MP) methods which are usually employed to solve the continuous subproblems
that arise by fixing the discrete variables provide only one local optimum which depends
strongly on the initialization. Thus standard methods may not find the global optimum despite
long computation times. In this contribution we introduce a memetic algorithm (MA) for the
global optimization of a computational demanding real-world design problem from the chemical
engineering domain. The MA overcomes the problem of getting stuck in local optima by the use
of an evolution strategy (ES) which addresses the global optimization of the design decisions,
whereas a robust MP solver is used to handle complex nonlinear constraints as well as to
improve the individuals of the ES by performing a local search in continuous sub-spaces in an
integrated fashion. The MA is discussed in detail, the novel decomposition of the problem class
at hand is analyzed and the MA is tested for the example of the optimal design of a reactive
distillation column with several thousand decision variables. The MA is the only algorithm that
finds the global solution in reasonable computation times. The introduction of structural
decisions and additional constraints and discontinuous penalty terms lead only to a moderate
increase in the computational effort which demonstrates the potential of this class of memetic
algorithms in real-world design optimization problems.
Urselmann, et al., IEEE Transactions on Evolutionary Computation, 15, 2011, 659

Prática 10
M2P14 Int J Inf
The problem of predicting the next request during a user’s navigation session
has been extensively studied. In this context, higher-order Markov models have
been widely used to model navigation sessions and to predict the next
navigation step, while prediction accuracy has been mainly evaluated with the hit
and miss score.We claim that this score, although useful, is not sufficient for
evaluating next link prediction models with the aim of finding a sufficient order of
the model, the size of a recommendation set, and assessing the impact of
unexpected events on the prediction accuracy. Herein, we make use of a
variable length Markov model to compare the usefulness of three alternatives to
the hit and miss score: the Mean Absolute Error, the Ignorance Score, and the
Brier score. We present an extensive evaluation of the methods on real data
sets and a comprehensive comparison of the scoring methods.
Borges et al., International Journal of Information Technology & Decision Making, 9, 2010, 547.

Prática 11
M2P15 Human Comp Int
Educative sensemaking focuses on the needs of self-directed learners, a nonexpert

population of thinkers who must locate relevant information sources, evaluate the
applicability and accuracy of digital resources for learning, and determine how and when to
use these resources to complete educational tasks. Self-directed learners face a
sensemaking paradox: They must employ deep-level thinking skills to process information
sources meaningfully, but they often lack the requisite domain knowledge needed to
deeply analyze information sources and to successfully integrate incoming information with
their own existing knowledge. In this article, we focus on the needs of college-aged
students engaged in learning about natural sciences using web-based learning resources.
We explored the impact of cognitive personalization technologies on students’
sensemaking processes using a controlled study in which students’ cognitive and
metacognitive processes were analyzed as they completed a common educational task:
writing an essay.We coded students’ observable on-screen behaviors, selfreported
processes, final essays, and responses to domain assessments to assess benefits of
personalization technologies on students’ educative sensemaking. Results show that
personalization supported students’ analysis of knowledge representations, helped
students work with their representations in meaningful ways, and supported effective
encoding of new knowledge. We discuss implications for new technologies to help
students overcome the educative sensemaking paradox.
Butcher et al., Human–Computer Interaction, 26, 2011,123.

Prática 12
Reordene as frases da maneira correta, categorizando-as:
M2P8 Nature Mat
Here we report that dentin matrix protein 1 (DMP1), an acidic protein, can nucleate the
formation of hydroxyapatite in vitro in a multistep process that begins by DMP1 binding
calcium ions and initiating mineral deposition.
Bones and teeth are biocomposites that require controlled mineral deposition during their
self-assembly to form tissues with unique mechanical properties.
Acidic extracellular matrix proteins play a pivotal role during biomineral formation.
The nucleated amorphous calcium phosphate precipitates ripen and nanocrystals form.
Subsequently, these expand and coalesce into microscale crystals elongated in the c-
axis direction.
Protein-mediated initiation of nanocrystals, as discussed here, might provide a new
methodology for constructing nanoscale composites by self-assembly of polypeptides
with tailor-made peptide sequences.
However, the mechanisms of protein-mediated mineral initiation are far from understood.
Characterization of the functional domains in DMP1 demonstrated that intermolecular
assembly of acidic clusters into a -sheet template was essential for the observed mineral
nucleation.
Nature Materials 2, 552–558, 2003

Sources
Source: Michael Alley The Craft of Scientific Writing, 3rd edition (Springer-Verlag, 1996).
Hill et al., Teaching ESL students to read and write experimental papers, TESOL Quarterly, 16: 333, 1982:
Aluísio, S.M. (1995). Ferramentas para Auxiliar a Escrita de Artigos Científicos em Inglês como Língua Estrangeira. Tese
de Doutorado, IFSC-USP, 228 p.
Yang et al, Langmuir; 2004; 20; 5978
Lee et al., Nature Biotechnology 23, 1517, 2005 (Review)
Centurion et al., J. Nanosc. Nanotech, 2011 in press
Glowacki et al., Nature Chem., 3, 850, 2011
IEEE Signal Processing Magazine, 2005, p 55
International Journal of Plasticity 27 (2011) 1165

International Journal of Electronics, 97, 2010, 1163
Nature Materials 2, 552–558, 2003

Muito Obrigado
Valtencir Zucolotto
zuco@ifsc.usp.br
www.lnn.ifsc.usp.br

Escrita Científica
Módulo 3

USP, 2012
Workshop Outline
Módulo 5: Estilo

Módulo 3
Estrutura 2:
Introduction

Sections of a Paper
Abstract
Introduction
Methodology
Results
Discussion
Conclusions
References
Introduction

Introduction
3-D Architecture

Introduction
1. Information

Introduction
1. Contextualization
Present the research field and show the importance of the main area,
Make terms and processes familiar.
M3P1 Lang
“The ability to pattern mammalian cells in specific areas on a surface has

become a very important topic of research because of its applications in tissue
engineering, cell arrays, and biosensors. [….]. Early work to confine cells to
micron-size areas was performed by Carter, where fibroblasts were patterned
on islands of alladium [1]. Later, the Whitesides group utilized self-assembled
monolayers (SAMs) to present microcontact printed adhesive islands against an
inert ethylene glycol (EG) background to geometrically control cell adhesion.[2]”
Rubner et al., Langmuir 2004, 20, 1362.

Introduction
M3P8 Anal Chem
“Concentration determination of analytes such as biomarker molecules and drug

substances and their related compounds in biological matrixes, termed as
“bioanalysis”, is a critical part of drug discovery and development. Although
ligand-binding assays are still the main platform for the bioanalysis of protein
and peptide analytes, liquid chromatography mass spectrometry (LC MS)
assays play increasingly more important roles as a complementary platform.

Introduction
M3P10 Int J Inf
Web usage mining is a discipline within the field of web mining that concentrates
on developing data mining techniques to model and study user web navigation
behavior.1,2 In the context of web site personalization, web usage mining
techniques have been utilized to take advantage of the data collected from
users‟ interactions with a web site to study users‟ navigation behavior.
Understanding user behavior is invaluable in order to deliver tailored content to
the user,3 to support the creation of web agents aimed at guiding users within
web site,4 or to improve the strategic requirements analysis for web sites.5.

Introduction
2. State the Gap
Open Questions, Restrictions and Limitations
M3P2 IEEE Sig Proc

“To make these applications viable with possibly vast numbers of sensors,
device costs will need to be low (from a few dollars to a few cents depending on
the application), sensors will need to last for years or even decades without
battery replacement, and the network will need to organize without significant
human moderation. Traditional localization techniques are not well suited for
these requirements. Including a global positioning system (GPS) receiver on
each device is cost and energy prohibitive for many applications, not sufficiently
robust to jamming for military applications, and limited to outdoor applications.
Local positioning systems (LPS) [6] rely on high-capability base
stations being deployed in each coverage area, an expensive burden for most
low-configuration wireless sensor networks.
Patwari N. et al, IEEE Signal Processing Magazine, 2005, p 54

Introduction
2. State the Gap
M3P9 JACS
“Molecular oxygen is an ideal oxidant, and significant progress has been made
in the development of catalytic methods for aerobic alcohol oxidation.9
Nevertheless, key challenges must be addressed in order for such reactions to
find widespread use in the synthesis of complex molecules. Large-scale
applications of aerobic alcohol oxidation are constrained by safety concerns
associated with the combination of O2 and organic solvents and reagents,8a,b
as well as the frequent use of halogenated solvents.

Introduction
2. State the Gap
M3P8 Anal Chem
“One common drawback of the full scan MS approach is the lower selectivity
caused by higher background or interferences as compared to that seen in the
SRM approach. Recently, there have been significant advances in the
capabilities of high-resolution mass spectrometry (HR-MS) instrumentation
[11,12]. HR-MS can provide additional advantages in resolving each isotopic ion
from the background so that higher selectivity can be achieved.

Introduction
2. State the Gap
M3P11 SIAM J Comput
The complexity of terrain guarding has been an open problem of interest

since 1995, when an NP-completeness proof was proposed but never
completed by Chen, Estivill-Castro, and Urrutia [2]. They described
vertex and clause gadgets and suggested that they could be put
together along the lines of Lee and Lin‟s reduction for guarding
polygons [13].
King et al., SIAM J. Comput. 40, 1316, 2011

Introduction
3. Show the State-of-the-Art
Evidencing recent research and findings
M3P8 Anal Chem
“One common drawback of the full scan MS approach is the lower selectivity
caused by higher background or interferences as compared to that seen in the
SRM approach. Recently, there have been significant advances in the
capabilities of high-resolution mass spectrometry (HR-MS) instrumentation
[11,12]. HR-MS can provide additional advantages in resolving each isotopic ion
from the background so that higher selectivity can be achieved.

Introduction
M3P3 Int J Plast
“Recently, there have been developed many advanced approaches to describe plastic
anisotropy. The strain rate potential is another concept that can describe plastic anisotropy
(Barlat et al., 1993; Yoon et al., 1995; Chung et al., 1996; Kim et al., 2008a,b; Rabahallah
et al., 2009; Van Houtte et al., 2009; Cazacu et al., 2010). Non-associated flow plasticity
was also implemented to the finite element method to predict plastic anisotropy (Civitanic
et al., 2008; Taherizadeh et al., 2009). Experimentally it was shown that the yield surface
shape can evolve in complex ways (Kuroda and Tvergaard, 2001; Kuwabara, 2007). For
the corresponding modeling, it has been acknowledged that more advanced models
should capture the distortion of the yield surface (Wu et al., 2005; Holmedal et al., 2008;
Aretz, 2008; Korkolis and Kyriakides, 2008; Stoughton and Yoon, 2009). Yield criteria to
describe plastic anisotropy for complex hcp materials were proposed by Cazacu et al.
(2006) and Plunkett et al. (2008). Anisotropic hardening behaviors for the hcp materials
were also investigated (Plunkett et al., 2007; Nixon et al., 2009). [….].
Recently, an analytical approach considering the r-value directionality as a main
contributor to the earing profile was derived by Yoon et al. (2006). The method provides a
simple tool for the prediction of the earing profile using, as input, basic information
including the r-value directionality, the initial blank size and the cup radius.
Yoon et al., International Journal of Plasticity 27 (2011) 1165
Introduction
4. State the importance of your study

Evidencing Implications and/or Applications
M3P4 Nano Lett
“ [….] This is a simple way to produce fundamentally and practically

interesting multilayer structures with unique mechanical properties
and precise control over film composition and thickness. More
importantly, this technique offers a possibility of multifunctional
composites in which the strength will be only one of the factors
determining its applications. Additionally, deposition of nanotubes in
the form of individual layers opens the way to oriented
nanocomposites,[43] taking advantage of the sheer force as in spun
fibers [44,45,47] or magnetic fields.[46]”
Olek et al., Nano Lett., Vol. 4, 1889, (2004)

Introduction

M3P12 IEEE T.E.C.
“The proposed memetic algorithm that combines search by an ES [44]

on the upper level and nonlinear local optimizations to handle
complex nonlinear equality constraints and to realize a Lamarckian
learning principle is a promising concept for general design
optimization problems in which a large number of nonlinear model
equations and constraints as well as discrete design decisions and
possibly discontinuous value functions are present, well beyond the
domain of chemical engineering.”

Introduction
5. State the purpose of the paper
M3P5 Lang
“In this paper, detailed characteristics of the hydrated (LPEI/PAA)OEGDA
composite are investigated and the reason for its relatively high ionic
conductivity is discussed. Morphological effects due to the presence of
OEGDA oligomer on the phase transition will also be described.”
Lowman et al., Langmuir 2004, 20, 9791-9795
M3P6 Lang
“In the work reported here, a polyelectrolyte multilayer platform capped by
a polyanionic surface was created through layer-by-layer assembly [21] and
stamped with a polycationic pattern using POPS, to form docking sites for the
negatively charged magnetic beads.”
Lyles et al., Langmuir 2004, 20, 3028-3031

Introduction
M3P9 JACS
Here, we report a new, highly active (bpy)CuI/TEMPOcatalyst system that

effects selective aerobic oxidation of a broad range of primary alcohols,
including allylic, benzylic, and aliphatic derivatives, to the corresponding
aldehydes. The reactions proceed in high yield, exhibit broad functional-
group compatibility, and achieve chemoselective formation of aldehydes with
negligible overoxidation to the carboxylic acids. Furthermore, the reactions
exhibit exquisite selectivity for 1 over 2 alcohols, enabling selective
oxidation of diols, without requiring the use of protecting groups. The use of a
traditional organic solvent (acetonitrile), and the ability to carry out most of
the reactions at room temperature with ambient air as the oxidant greatly
enhances the practicality of these methods. Overall, the utility of these
methods rivals or surpasses that of traditional laboratory-scale alcohol
oxidation reactions. The development, scope, and limitations of these
methods are elaborated below.

Introduction
M3P13 Human Comp Int
In this article, we explore the ways in which cognitive personalization technologies can
support effective sensemaking with web-based educational resources. First, we
describe several use cases to illustrate how learners in a variety of settings might
interact with and benefit from cognitive personalization tools. We then discuss a
theoretical model of educative sensemaking. Next, we describe a prototype cognitive
personalization service, the Customized Learning Service for Concept Knowledge:
CLICK. Its personalization capabilities are realized through a combination of natural
language processing algorithms and graph analytic techniques. We use the term
„„service‟‟ as CLICK has been designed and implemented as a web service application
programming interface, enabling cognitive personalization capabilities to be flexibly
embedded in a rich variety of tools, portals, and learning environments. We then
describe a learning environment implemented with CLICK and discuss empirical
findings from a controlled, mixed-method study that explored its impact on learners‟
sensemaking processes. Finally, we discuss implications of our work and future
challenges for promoting personalized sensemaking with digital educational resources.

Introduction
Usually for Computer Science-related areas
Introduction may be followed by additional Sections on:
- Problem Formulation
- Related Work
- Case Studies
-Relevant, Specific Topics

Introduction
Present the research field and show the importance of the main area
2. State the Gap




Introduction
2. Flow

Introduction
Structure
Information in the text flows from General

to Specific, arriving at purpose.

Introduction
General Contextualization Your Field
Sumarizing Previous
Research
Purpose
Specific Your work

Introduction
“Afunilando” o fluxo de idéias….
M3P7 Nano Lett
While a vast majority of LBL systems undergo linear growth (l-LBL),

there are also some quite special combinations of polyelectrolytes
which exhibit so-called “exponential growth” (e-LBL). Recently, a
different modification of the technique which does not require rinsing
and is based on dewetting phenomena, so-called dewetting LBL or
d-LBL, was also introduced by our group.44 The l-LBL method has
been studied and applied most extensively and thus covers most of
LBL publications. A substantially smaller and more recent subset of
LBL literature is related to e-LBL films. Historically, e-LBL was
observed for the first time in 1999 by Elbert et al.45 for poly(L-
lysine) (PLL) and alginate (AG) polyelectrolytes pair. The authors
observed......
Podsiadlo et al., Nano Letters, 2008 , 8, 1762

Introduction
3. Citation

Introduction
The citation process:
Authors cite to indicate where the ideas came

from
Authors DO NOT cite to show where the text

came from!!!

Introduction
Selecting references to cite
Seminal Papers
Contextualization / Gap
Most Recent Papers

State of the Art / Gap
Most Important Papers

Relevance / Motivation / Importance

Introduction
Style
-Contextualization and Gap: Past, present-perfect

(continuous) generally used.
-Purpose: Present or past tense are preferable.
-Use the active voice as much as possible.
-Third Person with some use of first person.

Sources
John M. Swales, Genre Analysis: English in Academics and Research

Settings, Cambridge University Press, 1990.
Rubner et al., Langmuir 2004, 20, 1362.
Borges et al., International Journal of Information Technology & Decision
Making, 9, 2010, 547.
Urselmann, et al., IEEE Transactions on Evolutionary Computation, 15,
2011, 659
Olek et al., Nano Lett., Vol. 4, 1889, (2004)
Yoon et al., International Journal of Plasticity 27 (2011) 1165
Podsiadlo et al., Nano Letters, 2008 , 8, 1762
King et al., SIAM J. Comput. 40, 1316, 2011

Muito Obrigado
Valtencir Zucolotto
zuco@ifsc.usp.br
www.lnn.ifsc.usp.br

Escrita Científica
Módulo 4

USP, 2012
Workshop Outline
Módulo 5: Estilo

Módulo 4
Estrutura 3:
Results and Discussion, Conclusion

Sections of a Paper
Abstract
Introduction
Methodology
Results
Discussion
Conclusions
References

Possible Structures
Results – Discussion – Conclusion
Results – Discussion
Results and Discussion – Conclusion
Results – Discussion and Conclusion
Source: Science Research Writing for Non-Native Speakers of

English, Hilary Glasman-Deal, Imperial College Press, 2009

The most important section of a paper
The section where you prove your initial question,

hypothesis, idea, etc.
Illustrative Materials (figures, tables, graphs, images),

Outcome of Calculations, and TEXT.
Importance of figure Quality, Data Analyses and

Statistics
The way you write your achievements makes the whole

difference

An Interesting Example…
M4P1 Nature
“It has not escaped our notice that the specific

pairing we have postulated immediately suggests
a possible copying mechanism for the genetic
material”
Watson, JD, Crick, FHC, Nature, 171, 737, 1953.

Remember !!!!!!

You (and maybe your advisor) know every detail

about your investigation.
Readers know nothing about your work (yet).

Introduction
(purpose)

(Key Results)

Model/Structure for Results

and Discussion
????????

A Tentative Model:
- Background / Importance
-Describe the outcomes of your research

(figure, tables, graph, image, calculations, algorithm tests, etc)
* In computer Science-related areas this section is usually divided in a number
of specific subtopics .
- Interpretation
- Comparison

Example 1
M4P2 Nano Lett
Figure 4. Cycling performance of hybrid nanostructured electrodes. (a)

Comparison of cycling performance for three hybrid systems showing
capacitance retention of ∼93%, ∼96%, and ∼95% after 3000 cycles of
charging and discharging at current density of 1 mA/cm2 for GM, GMC, and
GMP, respectively. (b, c) SEM images of GMC- and GMP-based textiles
after 3000 cycles showing that the MnO2 nanoflowers were still wrapped
with conductive layers and the whole structural integrity of active electrode
materials was well maintained. Scale bars: 1 μm.
Yu et al., Nano Lett. 2011, 11,
4438 Prof. Dr. Valtencir Zucolotto
Example 1 M4P2 Nano Lett
- Cycling performance is another key factor in determining the

supercapacitor electrodes for many practical applications. Excellent
cycling stability is crucial for real supercapacitor operations. The cycling
tests for all three different electrode systems were carried out using the
same current density of 1 mA/cm2. Figure 4a compares the cycling
stability of three systems and shows that ∼93%, ∼96%, and ∼95%
capacitance was retained over 3000 cycles of charging and discharging
for GM-, GMC-, and GMP-based electrodes, respectively. All three
electrode systems demonstrate much better cycling performance
compared to those reported in previous work (typically 7585% retention
over 1000 cycles),13,21,22 thanks to hierarchical structures of
graphene/MnO2 textiles.
Yu et al., Nano Lett. 2011, 11, 4438

M4P6 JACS
Example 3

M4P6 JACS
Example 3
- As shown in the time course plot, the new catalyst system enables
complete conversion of this aliphatic alcohol within approximately 1 h at
room temperature. A 10-15 min induction period is observed at the start
of the reaction, the mechanistic origin of which is currently under
investigation. Sheldon and Koskinen have noted the beneficial effect of
noncoordinating anions with CuII-based catalyst systems;24b,25c
however, we observe that the initial oxidation state of the copper catalyst
has the most significant impact on the reaction efficiency (Figure 2). Cu I
salts exhibit much higher reactivity than Cu II salts. It is reasonable to
expect that Cu cycles between +1 and +2 oxidation states during the
catalytic mechanism, so the origin of the dramatic difference in rates
using CuI vs CuII precursors is not clear. Ongoing mechanistic studies
are focused on elucidating the origin of this unusual effect.

Style
- Past tense;
- Third Person, preferably;
- Use active voice whenever possible.
-Subheadings may improve organization and

comprehension

The right place for captions
Tables: above, left justified.
Figures: below, left justified
Always consult the Journal’s Guide for Authors

Reach a balance between description of data in the

text and in the figure/table legend
Any reader must understand a Figure/Table without

reading the results section.

Tips

Do you really need a figure?
“ The thickness of the film was estimated at 10 nm per bilayer,

using AFM….”
“Seed production was higher for plants in the full-sun treatment

(52.3 +/-6.8 seeds) than for those receiving filtered light (14.7+/-
3.2 seeds)….”
Note: Always use a space between the value and the unit:
“The estimated length was 10 m", or, "the optimum time was
100 min."

Conclusions

Conclusions
Function: To state the importance of the paper to

the development of the field.

Conclusions
Ideas flowing from Specific to General.

Conclusions
Pyramidal Structure
Specific
Key findings
Interpretation of main Results
Contribution to the field

General

Conclusions
A Suggested Model
1. State main findings

Emphasize your main results.
2.Interpretation of the main findings

Take a few sentences to re-state the interpretation
of the key results.

Conclusions
3. Contributions/Progress to the field

Describe the implications of your achievements
to the field.
4. Further Work (optional)

Be careful: To much future work may suggest
that your paper is not complete

Conclusions
Style
- Past and Present tense;
- Third Person, preferably;

Conclusions
Categorize the sentences in the following

conclusions sections:

Conclusions
Example 1 M4P1 Nano Lett
In summary, by 3D conductive wrapping of graphene/MnO2 nanostructured

electrodes with CNTs or conducting polymer, we can optimize the
electrochemical utilization of highly insulating MnO2 materials and greatly
enhance their supercapacitor performance. The rationally designed composite
electrodes exhibit high specific capacitance, excellent rate capability, and
exceptional cycling stability. Such a 3D conductive wrapping approach
represents an effective and convenient technique to improve the specific
capacitance and rate capability of oxidebased supercapacitors and can be
applicable to a wide range of insulating energy storage electrode materials
such as sulfur, LiMnPO4, and silicon in lithium-ion batteries. For example,
conductive polymer can be used for wrapping sulfur cathode materials to
enhance electrode conductivity and contain polysulfide intermediates, therefore
minimizing polysulfide dissolution and improving the performance of LiS
batteries.
Yu et al., Nano Lett. 2011, 11, 4438

Conclusions
Example 2 M4P4 Mechatronics
For the purpose of increasing generated power in harvesting energy, according to Eq.
(14) that has been derived in this paper, the elastic base can indeed lower the resonant
frequency of the miniature generator to approach ambient vibration frequency. The
resonant frequency reduction percentage depends on mass and stiffness of the proposed
elastic base. Based on Eq. (14) and Table 1, the resonant frequency reduction
percentage can reach 70% when r = 1 and a = 10. If the miniature generator is attached
to the rigid base, the maximum power is 1.08 nW. By contrast, if the miniature generator
is attached to an elastic base with a point mass, the maximum value of the power 0.92
lW is obtained with the mass ratio a = 10 and stiffness ratio r = 6. The power of different
cases on elastic base with point mass is shown in Table 4. In this study, the arm swing
frequency is designated as 15 Hz, and the theoretical resonant frequency of the
miniature generator of piezoelectric bender shown in Eq. (22) is about 81.2 Hz. According
to Table 1, when the stiffness ratio r is fixed if the mass ratio a
increases, the resonant frequency decreases and is close to 15 Hz, the arm swing
frequency. Therefore, the bender vibration amplitude becomes larger. The more the
bender deforms, the more…….
W. Li et al., Mechatronics 21 (2011) 1183

Conclusions
M4P5 Nature Nanotech
Example 3
In this study, we demonstrated cancer immunotherapy using DCs pulsed with
multifunctional core–shell nanoparticles consisting of a superparamagnetic
Fe3O4 core covered with a photonic ZnO shell. The nanoparticles provided
simple and consistent outcomes for the ex vivo antigen loading of DCs, for in
vivo tracking and induction of strong anti-CEA immune responses, even in an
immune-tolerant host. The ability of the nanoparticles to be efficiently loaded
into DCs in a short incubation period (1 h) without surface modifications or
transfection agents may expedite clinical trials. It might be possible to bypass
the complex chemical modifications of the Fe3O4 surface that are generally
performed in an organic environment to conjugate tumour antigens, a step that
has the potential to alter their antigenicity. When combined with a tumour-
associated antigen, nanoparticle- loaded DCs did not show changes in viability
and phenotype. Taken together, the core–shell nanoparticle could be applied in
diverse DC-based immunotherapies that need to monitor antigen loading in
vitro and track DCs in vivo to ensure consistent clinical efficacy.
Cho et al., Nature Nanotechnology, 6, 2011, 675

Conclusions
M4P7 ACS Nano
Example 4
The nanospheres used in the present study represent a novel combination of

features including direct visualization by electron and fluorescence microscopy,
as well as the ability to examine compartmentalization after endocytosis by
relaxometry. The magnetic properties also enabled removal of excess PEI,
enabling examination of PEI-mediated endocytosis without the confounder of
toxicity of free PEI. Endocytosis involved a clear sequence of events:
interaction of nanoparticles with the cell membrane induced membrane ruffling
and tubular invagination, characteristic respectively of unregulated/unselective
macropinocytosis and clathrin- and caveolin-independent endocytosis, followed
by time-dependent intracellular clusteringwithin lamellar envelopes. The
nanosphere architecture thus offers a broad scope for delivery of a wide range
of agents to intracellular compartments. The findings we have presented will
assist in the design and synthesis of nextgeneration nanoparticles for site-
specific drug delivery.

Conclusions
M4P8 Human Comp Int
Example 5
For novice learners, educative sensemaking is a daunting task. Students must identify relevant
information, analyze its relevance to the task at hand, make connections with prior knowledge,
diagnose the adequacy and accuracy of their current representations, integrate new information into
their current representations, and reanalyze emerging representations. The results presented here
demonstrate consistent, positive impact of personalization on students‟ metacognitive processes, the
depth of their sensemaking behaviors, and the integration of new and prior knowledge. Although our
results were gathered using a prototype instantiation of the CLICK service, there are a wide variety of
tasks that could be supported by CLICK‟s personalization technologies. Our work advances the
capabilities of sensemaking tools and stimulates future potential research by providing a flexible set of
cognitive personalization algorithms that can be embedded in a wide variety of learning technologies
for a large range of educational tasks. Future technologies could support the use cases we have
gathered from educators (e.g., concept map development and presentation building), or could embed
the algorithms into new tasks such as developing scientific experiments (e.g., collecting and analyzing
relevant prior findings) or analyzing visual representations. As we move forward, we are especially
interested in studying how we can support multimedia forms of student sensemaking. We see great
potential in increasing the richness of students‟ instantiated representations, for example, by using a
combination of visual, audio, and textual information. By not tying our algorithms to a stand-alone
prototype, we hope to facilitate the development of new sensemaking tools and to set the stage for
future technologies that will push the envelope of educative sensemaking support and discover robust
solutions to the sensemaking paradox in self-directed learning.

Example 6
Conclusions
M4P9 Int J Inf
In this work, we tackle the problem of predicting the next web page request of users‟ when
navigating the web. Most previous research in the field has exclusively made use of the Hit and Miss
score (HM) for evaluating prediction accuracy. We argue that the HM score has limitations in terms of
evaluating the accuracy and therefore complementary scoring methods are necessary.
To alleviate this problem we have investigated three additional useful scoring metrics: the
Mean Absolute Error (MAE), the Ignorance Score (IS) and the Brier Score (BS). As we have discussed
the scoring metrics have different interpretations [….]
This work makes use of the VLMC model as our prediction mechanism, however, we
believe the study can be generalized to other prediction mechanisms that provides a set of predictions
ranked by their probabilities. One such example is the use of hybrid Markov models that assemble
models of various orders.47 Such models could benefit [….]
Our experiments show that the additional scores and the concept of unexpected events
provide valuable insight when setting up a model for predicting the next link choice of a user based on
other users navigation preferences. The detection of unexpected events can also provide the means
to assess the adequacy of recommendations that are provided based on historical data. [….] In
addition, the experimental results confirm that the prediction accuracy increases with the order of the
model, and also increases when unexpected events (or unpredictable), controlled by a parameter, α,
are being detected rather than being predicted. The experiments also show that the accuracy of
prediction varies for different data sets.
Future work involves a better understanding of what makes a prediction algorithm such as
maximum likelihood perform better on different data sets. A preliminary investigation taking into
account concept drift 45 when building the variable length Markov model over a long period was
conducted and the results reported in Ref. 50. Finally, we also wish to apply the prediction algorithm to
data sets from different applications areas such as patrolling the web.

Conclusions
Example 7 M4P10 IEEE T.E.C.
“Conclusion and Outlook”
[.................] *
In future work, initialization procedures based on statistically-rigorous
methods such as latin hypercube design or orthogonal arrays will be
implemented within the memetic algorithm introduced in this contribution. The
MA will be applied to an extended model of the reactive distillation column with
an optional external side reactor and also to different design optimization
problems from the domain of chemical engineering to further test the potential
and the limitations of the proposed solution approach. This will also provide
additional insight into the performance of the different mechanisms for mutation
and recombination used in the MA.

Sources
John M. Swales, Genre Analysis: English in Academics and Research
Settings, Cambridge University Press, 1990.
Science Research Writing for Non-Native Speakers of English, Hilary

Glasman-Deal, Imperial College Press, 2009
Watson, JD, Crick, FHC, Nature, 171, 737, 1953.
Yu et al., Nano Lett. 2011, 11, 4438

Brawand et al., Nature, 2011, 478, 343
W. Li et al. / Mechatronics 21 (2011) 1183
Cho et al., Nature Nanotechnology, 6, 2011, 675
Urselmann, et al., IEEE Transactions on Evolutionary Computation, 15,
2011, 659
Borges et al., International Journal of Information Technology & Decision
Making, 9, 2010, 547.

Muito Obrigado
Valtencir Zucolotto
zuco@ifsc.usp.br
www.lnn.ifsc.usp.br

Escrita Científica
Módulo 5

USP, 2012
Workshop Outline
Módulo 5: Estilo

Módulo 5
- Estilo
- Linguagem 1:
Especificidade, Complexidade e Ambiguidade

Scientific Writing Style

Abbreviations
Define the abbreviation in parentheses the

first time you use it:
Green Fluorescent Protein (GFP)

Abbreviations
Use Abbreviations / acronyms with discretion
Ex: Use of combined 5-PAS and BTR3 increased the

OP toxicity for MD14+ cells
??????

Abbreviations
Words “day’, “week”, “month” and “year” are not

abbreviated.
Except in the case of footnotes, tables and captions, spell out

all months with or without a specific day :
Ex: Data were collected in January, 2000.

Abbreviations
U.S. citizens;
U.K. football team
(Adjectives)
or
“The citizens from United States….”

“The football team of United Kingdom….”
(nouns)

Abbreviations
Units of measure are abbreviated : 2 mm.; 10 min.
In a non-measurable context: "we measured length in

millimeters"
OBS: Never add an "s" to the measure unit.

Abbreviations
Latin abbreviations:
- i.e., id est (that is),

- e.g., exempli gratia (for example),
- etc. (so on),
- vs (versus),
- et al., et alli, and others,
- via (road),
- in situ (in a place)

Abbreviations
Controversy: Some authors agree that a period is used

only if the last letter of the abbreviation is not the last
letter of the word:
Ex.: Prof. , Vol. 1, p. 23-25 , 2nd ed. , et al. , etc.

Dr , Mr , Ms , vs

Numerals
A good reference material may be found at:
The ACS Style Guide, Dodd, J. S., Ed;

American Chemical Society, Washington, DC, 2006

Numerals
Use a space between the number and the unit:
6 min, 0.3 g, 80 mL, etc.
Exception: %, $ and °
50%, $400, 180° (Obs: 90 °C, 180 °F).

What Tense to use?
Use past tense for sentences concerning your findings.
Ex: This study was aimed at investigating.. (The study)

What Tense to use?
Present forms preferable in
Conclusion Section
Present and even Future Tenses may be used!!

Active / Passive Voices
Passive voice almost always requires more words than

Active voice:
ACTIVE: “the melting processing consumed

polymeric material at a higher rate..” (10 words)
PASSIVE: “Polymeric material was consumed by the
melting process at a higher rate..” (12 words)
Mathews, JR and and Mathews RW, Successful Scientific Writing, Cambridge University
Press; 3 edition 2007)
Dodd, J. S., Ed. The ACS Style Guide; American Chemical Society: Washington,
DC, 1986.).

First vs Third Person
Sometimes first person may be used to

emphasize important information
Our research group has investigated….
We have demonstrated that….
Avoid: “we believe”, “we feel”, “we can see”

Formal Language
Avoid Better
nowadays presently, currently
on the contrary in contrast
(up) until now to date

Language I

Lets face it, English is a stupid language.
There is no egg in the eggplant.
No ham in the hamburger.
And neither pine nor apple in the pineapple.
English muffins were not invented in England.
French fries were not invented in France.
http://www.gray-area.org/Research/Ambig/#HEAD

Specificity
The efficient writing is specific
“Novel strategies have been proposed to overcome the

limitations regarding diseases diagnosis.”
What were the strategies?

Too general!! What are the limitations?
What are the diseases?

Specificity
The use of carbon nanotubes-based biosensors

has been proposed to overcome the poor selectivity
exhibited by conventional systems used for cancer
detection.
Better !!

Specificity
Carbon nanotubes-based biosensors exhibit high

selectivity for cancer detection.
Efficient Scientific Writing!!

The right emphasis on details
Possible ways of emphasizing details:
Repetition, wording, illustration and placement
Source: Michael Alley The Craft of Scientific Writing, 3rd edition

(Springer-Verlag, 1996).

The right emphasis on Details
1. Repetition
Title, abstract, discussion and conclusions ??

2. Wording
Stress the most important details in a sentence!!
Ex: High levels of the protein were found in the blood

samples from patients with hemorrhagic infections.
What is the most important detail?
The protein, the levels or the infection?

Unexpected high levels of a protein were found in the

blood samples from patients with hemorrhagic infections.
High levels of a very specific S100 family protein were

found in the blood samples from patients with
hemorrhagic infections.
High levels of a specific protein were found in the blood

samples from examined patients. This may be the cause
of the hemorrhagic infection.

Complexity: Sentences
A huge problem: Long Sentences
The mechanical analyses had been carried out using

stress-strain measurements and indicated that the
copper-based alloys are more resistant than the silver-
based ones, which may be due to the fabrication process
used for each composite material, since the copper
alloys had been produced via casting, whereas the silver
composites had been fabricated via reactive extrusion
under high pressures, controlled atmosphere, and at
temperatures ranging from 300 – 400 °C.
????????
Too long!, Too wordy!
Too many ideas in a single sentence!!
Streamlining it:
First half of the sentence:

The mechanical analyses had been carried out
using…..
Second half :
.............................................................................

M5P2 IEEE T.E.C.
The proposed memetic algorithm that combines search by an ES [44] on

the upper level and nonlinear local optimizations to handle complex
nonlinear equality constraints and to realize a Lamarckian learning
principle is a promising concept for general design optimization problems
in which a large number of nonlinear model equations and constraints as
well as discrete design decisions and possibly discontinuous value
functions are present, well beyond the domain of chemical engineering.
While the selection of the representation as well as of the mutation and
recombination operators is of course problem specific and has to be
modified for different applications, and the use of other local solvers may
also require small changes to the algorithm, the general principle can be
transferred to any similar problem, and significant gains in computational
performance and robustness (probability of finding the best as well as most
of the local optima) can be expected.

Stacking of Passive Voice
A new methodology for protein purification

is presented. Isolation techniques using
HPLC are discussed. The amount of
protein purified in each cycle is revealed.

Stacking of Passive Voice
This study describes a new methodology for

protein purification using novel techniques based
on HPLC experiments. Each purification cycle
provided a total amount of 1.2 mg of protein.
Better!!
Active voice is straightforward

Ambiguity
Words/phrases with more than one

meaning
Chickens are ready to eat
????

Ambiguity
Word Choice:
Be careful with:
as, only

Ambiguity
Word Choice:
“Tissue temperature increased as the

particles released the phytotherapics”
????
The word “as” may be interpreted as “because” or “while”

Ambiguity
“Tissue temperature increased because the

particles released the phytotherapics”
Better

Ambiguity
Only I tested the device yesterday

I only tested the device yesterday
I tested only the device yesterday

Ambiguity
“ In low water temperatures and high toxicity levels of

oil, we tested how well the microorganisms survived”
Better: “We tested how well the microorganisms

survived in low water temperatures and high toxicity
levels of oil”
Extracted from: Michael Alley The Craft of Scientific Writing,

3rd edition (Springer-Verlag, 1996).

Ambiguity
“The train left the station crowded and dirty.”
Better: “The train was crowded and dirty when it left the station”
www.1-language.com/eslquizzes/ambiguoussentences.htm

Ambiguity
Unclear Pronoun
Since the platform has a support system

connected to the equipment, it was mounted
inside the lab.
What was mounted inside the lab????
It = The platform or the support system??

Ambiguity
Exercises at:
http://www.writing.engr.psu.edu/handbo
ok/exercises/exercise4.html

Sources
-Michael Alley. The Craft of Scientific Writing, 3rd edition (Springer-

Verlag, 1996).
Mathews, JR and and Mathews RW, Successful Scientific Writing, Cambridge

University Press; 3 edition 2007)
Dodd, J. S., Ed. The ACS Style Guide; American Chemical Society:
Washington, DC, 1986.).
Brawand et al., Nature, 2011, 478, 343

Muito Obrigado
Valtencir Zucolotto
zuco@ifsc.usp.br
www.nanomedicinna.com.br
www.lnn.ifsc.usp.br

Escrita Científica
Módulo 6

USP, 2012
Workshop Outline
Módulo 5: Estilo

Módulo 6
Linguagem 2:
Redundâncias, Ação no Verbo, Fluidez da
Escrita, Ritmo de Escrita

Language II

Redundancies
During the data collection phase of the study, all

experimental measurements were performed in a
period of time of 3 months. All the obtained results
were further analyzed and possible errors were
completely eliminated.
Adapted from Michael Alley. The Craft of Scientific Writing, 3rd edition
Redundancies
Better:
During the data collection, all measurements were

performed in 3 months. The results were further
analyzed and possible errors were eliminated.

Redundancies
Best:
All measurements were performed in 3 months.

Redundancies
Efficient Scientific Writing:

Redundancies
Common redundancies from Non-Native Speakers
Alternative choices Period of time Obtained Results

Basic fundamentals Separate entities Definitely proved
Completely eliminate Still persists Exactly true
Currently underway Quite unique First of all
Empty space Very similar
Introduced a new Join together
Mix together Completely full
Never before
Strong Nouns
Strong nouns provide a “visual image” to the reader.
A short list of abstract nouns:
Ability, approach, capability, concept, environment,

factor, nature, parameter,….
Action in the verb
Não-Nativos tendem a “Substantivar”

os Verbos

Strong Verbs
Replace verb phrases by the correspondent strong verb
Weak verb phrase Strong Verb
Made the arrangement for Arranged

Made the decision Decided
Made the measurement of Measured
Performed the development of Developed

Action in the verb
“A continuous improvement in patient´s condition

was observed”
Better:
“Patient´s condition improved”

Action in the verb
Administration of dopamine produced a decrease

in the frequency of convulsions
Better:
Administration of dopamine decreased convulsions

frequency

Action in the verb
The new phytotherapics exert their action by

blocking the cells communications.
Better:
The new phytotherapics block cells

communications.

Flow
A Clear and Effective Writing is made of Smooth

Transitions between Ideas, Sentences, Paragraphs
Problem: Complementary ideas disconnected and/or

placed far way from each other.

Flow
The level of the proteins found in the blood samples

is similar to that observed by other researchers. Due to its
ability to form complexes with DNA and RNA, such proteins
had been extensively investigated by a number of research
groups, including the group from Harvard, which estimated
that the normal level of the protein in blood should be
around 1 mg/dL.
????

Flow
Better:
The level of the proteins found in the blood
samples was 1 mg/dL, which is similar to that
observed by Harvard´s group.
The word which brings the ideas closer to

each other!

Flow
Transitional words within a sentence
1) Reason:
Because, since, due to,….
Example: The size of the nanoparticles was ca. 5 nm

because of the synthetic route employed.

Flow
2) Consequence:
therefore, as a consequence,….
Example: The enzymes showed a high specificity to

pesticides, therefore allowing its use in biosensors.

Flow
3) Concession:
Although, even though, ….
Example: Although individual residues in the repeated-

sequence blocks in the core have diverged, the
patterns of amino acids are identical.

Flow
Smooth Transition between sentences
1) Continuation: Movement of ideas in the same

direction:
Examples:
Also;
Moreover;
first, second…;
In addition;
……..

Flow
2) Pause:
Examples:
For example;
In other words;
…….

Flow
3) Reversal: Movement of ideas reverses direction.
Examples:
However;
In contrast;
On the other hand;
Conversely;
Contrarily;

Flow
4) Conclusion:
Examples:
In summary
Concluding
…….

Rhythm

Flow
Sentence Openers: Rhythm
DNA sensing has been considered a powerful tool to diagnose cancer. Cancer
diagnosis is usually not straightforward due to a large number of pathologies
variations as well as to the very low amount of DNA molecules expressed in the
beginning of disease. Sensors capable of detecting specific types of tumoral
cells may represent a breakthrough in medicine. This paper describes the
development of special sensors for cancer detection. The sensors comprise
immobilized antibodies that recognizes specific types of proteins produced by
cancer cell. The sensor systems were produced using different immobilization
strategies. The results show that different types of cancer cells can be detected
at very low limits of detection. The experiments were carried out in triplicate.
The systems we developed will be evaluated in clinical trials in a few months.
Many medicine areas will benefit from our new technologies.
????
Flow
Vary sentence openers
Topic of Sentence Subject

Time of action Prepositional Phrase
Location of action Prepositional Phrase
Manner of action Adverb
Subordinate action Dependent Clause
Reason for action Infinitive Phrase
Source: Michael Alley. The Craft of Scientific Writing, 3rd edition

Flow
adverb Recently, DNA sensors….
dependent clause Although cancer diagnosis is not

straightforward ,….
infinitive phrase To optimize the systems….
subject-verb The results show that….
prepositional phrase In a few months, the systems will

be….

Flow
Recently, DNA sensing has been considered a powerful tool to diagnose cancer.
Although cancer diagnosis is not straightforward, due to a large number of
pathologies variations, this strategy may be very efficient for some cancer
types. Sensors capable of detecting specific types of tumoral cells may
represent a breakthrough in medicine. In this paper we describe the
development of special sensors for cancer detection. The sensors comprise
immobilized antibodies that recognizes specific types of proteins produced by
cancer cell. To optimize the systems, the sensor were produced using different
immobilization strategies. The results show that different types of cancer cells
can be detected at very low limits of detection. The experiments were carried
out in triplicate. In a few months, the systems will be evaluated in clinical
trials in a few months. Since highly sensitivity and specificity were achieved by
the sensors, clinical areas may benefit from our new technologies.
Rhythm !!!!
Flow
Rewrite the following Abstract improving rhytm
The development of new antimicrobial peptides (AMPs) has arisen as a novel,

promising strategy to overcome the effects of antibiotic resistance developed
by several pathogens. The efficient design and development of such
biomolecules, however, requires an understanding of the mechanisms of
interactions between the peptides and cell membrane. In this study we
examined the interactions of the cationic antimicrobial peptide dermaseptin 01
with three membrane systems. The membrane systems had been
investigated in the form of Langmuir monolayers. The degree of interaction of
DS 01with the different biomembrane models was quantified from equilibrium
and dynamic liquid-air interface parameters, such as: minimum molecular
area and dilatational elasticity modulus. The interaction between DS 01 and
the zwitterionic phospholipid, as well as with the LRE-La monolayers were
very weak at low peptide concentrations, whereas with negatively charged
phospholipids the interactions were stronger. The latter is in agreement with
previous literature for vesicles and planar lipid bilayers, and with the greater
activity of AMPs against bacterial membranes, as compared to mammalian
cell membranes.

Sources
-Michael Alley. The Craft of Scientific Writing, 3rd edition


Mathews, JR and and Mathews RW, Successful Scientific Writing,

Cambridge University Press; 3 edition 2007)

Muito Obrigado
Valtencir Zucolotto
zuco@ifsc.usp.br
www.lnn.ifsc.usp.br

Escrita Científica
Módulo 7

USP, 2012
Workshop Outline
Módulo 5: Estilo

Módulo 7
Linguagem 3:
Plain English, Escrever em Inglês, Preposições

Language III

The concept of Plain English
Writing Nothing
It is significant to note the fact that…
It is relevant to mention here that the results…
The findings reported here demonstrated that…

The concept of Plain English
Needlessly Complex words:
Avoid Use
Utilization Use
Facilitate Cause*
Finalize End
Utilize Use
Firstly, Secondly First, Second
Commencement Beginning

Plain English
The word “Fact”

Replace “This fact” by:
This effect,
This hypothesis,
This observation,
This value,
This phenomenon,
This finding, etc.
The same applies to “Case”

Complex Words
Oooops: The word “work”
M7P1 Lang
“In this paper, detailed characteristics of the hydrated (LPEI/PAA)OEGDA composite

are investigated and the reason for its relatively high ionic conductivity is discussed.
Morphological effects due to the presence of OEGDA oligomer on the phase transition
will also be described.”
M7P2 Lang
“In the work reported here, a polyelectrolyte multilayer platform capped by a
polyanionic surface was created through layer-by-layer assembly [21] and stamped
with a polycationic pattern using POPS, to form docking sites for the negatively
charged magnetic beads.”
Lyles et al., Langmuir 2004, 20, 3028-3031

Plain English + Common Sense
Preliminary
Careful
Obtained
Novel
Successfully
Are these words relevant in SW??

Write in English
Brazilian´s problems with articles
The determination of the mechanical properties of

alloys containing manganese was carried out using
the stress-strain tests

Write in English
Better ??
Mechanical properties of alloys containing manganese

were evaluated using the stress-strain tests

Write in English
In Scientific Writing:
Mechanical properties of Mn-containing alloys

were evaluated via stress-strain analyses

Write in English
Lack of a subject
Acid rain is now a worldwide concern. Observed

initially in Europe as a form of an acidic rain, also
is now observed in the Americas.

Write in English
Acid rain is now a worldwide concern. Observed

initially in Europe as a form of acidic rain, it is
now also observed in the Americas.
Remember:
It rained a lot yesterday….

One may observe that....

Write in English
Thus,
In this context,
So,

Practice
Go to:
http://corpus.byu.edu/coca/
And check about the use of prepositions in
the following cases:

Verbs + Prepositions
VERBS FOLLOWED BY PREPOSITIONS
account decide estimate

agree decrease exceed
allow determine fit
answer develop hinder
balance differ identify
change disagree originate
compare discern prepare
connect discriminate qualify
convert distinguish range
correlate divide
correspond elaborate

Words + Prepositions
WORDS FOLLOWED BY PREPOSITIONS
abundance control enthusiasm necessary

abundant convenient equality necessity
affinity correct equivalent need
akin decrease evidence opportunity
applicable deficient familiar parallel
appropriate demand focus proficiency
available dependent fundamental proficient
basis difference identical search
capability different improvement sufficient
capacity disagreement independent suitable
cause discussion influence suited
close disparity inherent superiority
common distinct intended test
concern distinction level valuable
consistent enhanced method variation

Commonly Misused Words

Misused Words
To Administer or to administrate?
To administrate: to manage.
A drug is administered.
Ulcers were induced by administrating 20% acetic acid.
Ulcers were induced by administering 20% acetic acid.

http://www.inter-biotec.com/biowc/style.html

Misused Words
Common or popular?
Common: widespread
Popular: especially liked or preferred.
Cancer is the most common cause of death in….

Cancer is the most popular cause of death in….
Soccer is a popular sport in Brazil

Soccer is a common sport in Brazil

Misused Words
To Describe or to report?
Cases are reported

Patients are described
We describe/report a patient with malaria.

We report/describe a case of malaria.

Misused Words
Analysis or Analyses?
Analysis = Singular
Analyses = Plural
Thermal analyses were carried out using DSC ….

The infrared spectroscopic analysis was performed….

Misused Words
Reproductive or reproducible?
Reproductive: related to reproduction
Reproducible: can be repeated, reproduced.
Results were reproducible or reproductive in all three

experiments.

Misused Words
Eminent, Immanent or Imminent ?
Eminent: Famous
Immanent: Inherent or intrinsic
Imminent: Ready to take place
An eminent peak….
A combination of immanent properties….
An Imminent event will happen soon….

Misused Words
Through, Thorough or Though?
Through: by means of;

Thorough: careful, complete
Though: however; nevertheless
-Calculations were made through computational simulations
-The substrates were thoroughly washed with pure water
- Results agreed with previous papers, though few discrepancies

appeared

Misused Words
Hard or Hardly?
Hard: Performed with energy:

A project that required years of hard work.
Hardly: Barely; almost not:

I could hardly hear the speaker.
Work hard or work hardly??

Misused Words
Compose or Comprise?
Water is composed of hydrogen and oxygen
Training comprised theoretical and practical classes

Misused Words
Ability and capacity
Ability: Skill
Ex: Hemoglobin has the ability to combine with oxygen.
Capacity: Total amount that something can hold, contain

or receive
Ex: The beaker used in distillation had a capacity of 50

mL.

Misused Words
Increase, Enhance and Improve
Increase: To become grater or larger in size, number, degree…
Enhance: To add value or worthy to something already attractive
Improve: To raise to a better quality or condition.
The number of transgenic species increased in the last years.

Computer software enhanced with the advent of Internet.
The treatment improved patient's condition.

Misused Words
Data: A plural, like phenomena and strata.

William Strunk and E. B. White, The Elements of Style
Data: In its current use, data occurs in two constructions: as a

plural noun (like earnings) taking a plural verb…and as
an abstract mass noun (like information) taking a singular
verb…
Merriam-Webster Dictionary of English Usage

Sources
Essentials of Writing Biomedical Research Papers by Mimi Zeiger,

Mcgraw-Hill Professional, 2nd Ed, 2000.
http://www.infoplease.com/ipa/A0200807.html

Muito Obrigado
Valtencir Zucolotto
zuco@ifsc.usp.br
www.lnn.ifsc.usp.br

Escrita Científica
Módulo 8

USP, 2012
Workshop Outline
Módulo 5: Estilo

Módulo 8
Linguagem 4:
Topic Sentences, Cover Letters, Final Remarks

Language IV

Topic Sentences
A topic sentence is the most important sentence in the

paragraph.
T. Sentences are strongly correlated with:

-Topic (keyword) and
-Message of the paragraph (verb/subject structure).

Topic Sentences
To assess the distribution, size, and shape of ganglion cell bodies

in the tracheal neural plexus, we examined individual cell bodies in their
entirety at 100-400 x with a compound microscope. For the assessment of
distribution, first ganglion….
There are three different theories put forward for the very slow
relaxation of catch muscles in molluscs. One theory holds that….
Pulmonary nerve endings were relatively insensitive to diguanides,

as seen in table 1). Of 25 pulmonary nerve ending tested, only 10 were
stimulated….
Essentials of Writing Biomedical Research Papers by

Mimi Zeiger, Mcgraw-Hill Professional, 2nd Ed, 2000.

Topic Sentences
Garlic (Allium sativum L.) has been used for centuries for medicinal
purposes.
[….]. Its use for healing purposes can be traced back as far as
1550BC when documentations of its therapeutic use first appear in
Egypt (Hassan, 2003; Rivlin, 2001). In modern times belief in the
beneficial effects of garlic on health has led to it being used for a
number of conditions. Garlic has been shown to reduce the risk of
cardiovascular disease (Aboul-Enein and Aboul-Enein, 2005), and
possess anti-microbial (Sivam, 2001) and antioxidant properties
(Imai et al., 1994). This essay will explore research into garlic's
potential roles in reducing cancer risk and in treating cancer.
http://www.monash.edu.au/lls/llonline/writing/science/paragraphs/1.2.xml

Topic Sentences
Student success at university is the result of a number of inter-

related factors.
[….]. The most important factor is a student's past experience of

study. If a student has already developed good study habits, study
at university should not be difficult. Good study habits need to be
complemented by interest and motivation, factors which are
important when competition gets tough. We should however not
underestimate the distracting effects of financial and personal
difficulties. All students have to grapple with these at some stage
of their university life. Beyond the personal factors it has to be said
that there is also a certain element of luck involved in success:
this includes finding excellent teachers and the subject matter that
inspires one to give one's best.
http://www.victoria.ac.nz/llc/academic-writing/index.html
X
:)
Topic Sentences
Find the appropriate Topic sentence:
__________________________________ (topic sentence).

Arriving in the land below the Rio Grande River, the Spanish
conquistador Hernando Cortez was surprised to see the local inhabitants
raising crops that included avocados, corn, garlic and nuts. Onions,
tomatoes, chilli peppers and pumpkins were also grown in the rich soil.
Irrigation systems were employed in some of the drier regions. The Aztec
farmers also were skilful in creating terraced gardens to make the most
of the rainfall and to minimise soil erosion. Evidence shows that they
employed crop rotation as well as natural fertilisers to enhance the
production of their farm products.
Options:
1. The Aztecs of Mexico were a nation of accomplished farmers.
2. Hernando Cortez discovered farming in Mexico.
3. Mexico is blessed with rich farmland and an abundance of food products.
http://www.victoria.ac.nz/llc/academic-writing/index.html
Topic Sentences
M8P1 Nature Mat
When the materials from which the spheres were made charged at different rates,
structures of different morphologies could form during the course of charging.
Figure 3 illustrates the assembly of 40 Teflon and 80 PP spheres agitated at ω ~ 9
Hz and A ~ 10 mm. The Teflon spheres charged more rapidly than the PP ones
(Fig. 3a). When, after approximately 30 seconds from the start of agitation, the
ratio of charges QTef/QPP was close to –2, the spheres organized into a
hexagonal structure (Fig. 3b, left). PTMC simulations predicted this structure to be
a global energy minimum of the system. As the agitation continued, the
magnitudes of charges on the Teflon and PP spheres equalized. The hexagonal
arrangement became energetically unstable. After ∼15 minutes, approximately
half of the PP spheres were expelled towards the walls of the container, and the
morphology of the aggregate changed to square (Fig. 3b,right)……

Topic Sentences
M8P2 IEEE Sig Proc
Other articles in this issue also discuss statistical models for location
measurements. Compared to Gustafsson and Gunnarsson [87], who
present models for RSS, TOA, and AOA measurements useful for cellular
mobile system (MS) location and tracking, our focus is on the shorter-
range, low-antenna, sensor network environment. Gezici et al. investigate
UWB measurement models for both RSS and TOA in much greater detail
than in this article, in which UWB is just one of multiple measurement
modalities [89].

Topic Sentences
Cystic fibrosis (CF) is one of the most common genetic disorders.
[….] CF is inherited as an autosomal recessive trait and a

defective gene causes the body to produce an abnormal amount
of very thick, sticky mucus which clogs the lungs and pancreas,
interfering with breathing and digestion. This mucus builds up in
the breathing passages in the lungs and the pancreas and
respiratory complications develop from the blockage of the
bronchial passages. Eventually, the cilia which are responsible
for clearing the mucus are destroyed. In addition, the mucus
traps bacteria which cause infections and permanent damage to
the lungs, and may also block the ducts of the pancreas which
contains enzymes necessary for the digestion of food.
http://www.monash.edu.au/lls/llonline/writing/science/paragraphs/1.2.xml

Final Remarks

Practice
Transform the text into a Scientific Abstract
In this work we describe the experimental development of special sensors

for diagnosis of diseases. Experimentally, the sensors comprise antibodies
that recognize specific kinds of human proteins produced by a persons
immunological system fighting against mammalian cancer cells in a very
short period of time. In this context, a new methodology for protein detection
was developed and the efficiency improvement is presented. Protein
isolation techniques are discussed. The amount of protein detected by the
sensors was evaluated. The preliminary results were analyzed using
appropriate statistical methods. To optimize the systems, the sensor were
experimentally produced using different immobilization strategies and all the
collected data obtained from preliminary results show that different types of
cancer cells lines can be detected at very low limits of detection. The
obtained results corroborated previous results found in published papers.
The systems will be evaluated in clinical trials in a period of few months.
Since highly sensitivity and specificity were achieved by the sensors, clinical
areas may benefit from our new technologies.

The Paper is ready.
What happens now??

The cover Letter
The cover letter is the document that introduce the

manuscript to the editor.
A good cover letter makes clear the importance of

the paper and the reasons it deverves to be
published.

The cover Letter
Remember:
Editors must reject 70 – 90% of submitted manuscripts

The cover Letter
Example 2:
Dear Editor:
Please find attached the manuscript entitled: A new strategy to investigate the
toxicity of nanomaterials using Langmuir monolayers as membrane
models, which we submit for publication in Nanotoxicology. The reasons why we
believe it deserves to be published stem from the following features:
i) To our knowledge, this manuscript is the first report of a novel strategy to
investigate the types of interaction that may occur between a nanomaterial, viz.,
carbon nanotubes and phospholipid membranes, in a way that experimental
parameters can be controlled at the molecular level.
ii) The methodology is reported here for a specific carbon nanotube/dendrimer
complex, which had been applied as drug-delivery systems. However, this new
methodology may be of interest to a wider audience investigating the toxicity of
nanomaterials, either in vitro or in vivo, since the same strategy can be applied to
different nanocomplexes, nanoparticles, etc.
Sincerely

The Manuscript
JPCC Manuscript

Responding to the Editor
JPCC manuscript corrected version
JPCC response letter
BB response letter

After Acceptance
JPCC Proofs
JPCC Editorial revision

How to skim a paper?????

Skimming a paper
1. Read the Title

2. Check the Authors and Date
3. Read the Abstract
4. Read the 1st Paragraph
5. Read the First Sentence of each Paragraph
6. Look quickly at each Figure/Table and Captions
7. Read the Conclusion
Adapted from: Science Research Writing for Non-Native Speakers of

English, Hilary Glasman-Deal, Imperial College Press, 2009

Sources
Scientific Writing, Easy When ou Know How, Peat, J., Elliot, E., Baur,
L., Keena, V., BMJ Books, 2009
Essentials of Writing Biomedical Research Papers by Mimi Zeiger,

Mcgraw-Hill Professional, 2nd Ed, 2000.

http://www.uottawa.ca/academic/arts/writcent/hypergrammar/partopi
c.html

Muito Obrigado
Valtencir Zucolotto
zuco@ifsc.usp.br
www.lnn.ifsc.usp.br


Zucolotto - Como Escrever Artigos Científicos

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Zucolotto - Como Escrever Artigos Científicos

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Organização: Pró-Reitoria de Pesquisa - USP

Prof. Dr. Valtencir Zucolotto

Prof. Dr. Valtencir Zucolotto

Prof. Dr. Valtencir Zucolotto

Prof. Dr. Valtencir Zucolotto

Publication is one of the most important steps

If nobody knows, or can benefit from your work,

Why being at work ??

Prof. Dr. Valtencir Zucolotto

Scientists Publish Ideas !!

Prof. Dr. Valtencir Zucolotto

When the initial

had been answered/solved/tested !!!!!!

Prof. Dr. Valtencir Zucolotto

Prof. Dr. Valtencir Zucolotto

-Distinct time scales for distinct areas;

-Depends on the type of research:

Breakthroughs and Innovative research.

Advances on a specific, systematic

Prof. Dr. Valtencir Zucolotto

Implementation of the Research

Prof. Dr. Valtencir Zucolotto

Prof. Dr. Valtencir Zucolotto

Scientific writing as a “new” Literary

Prof. Dr. Valtencir Zucolotto

In the very beginning….

 Informal Letters exchanged by scientists.

1665: Creation of the first scientific periodical: The

This new arena for discussion led to the development of

Prof. Dr. Valtencir Zucolotto

Who will read your paper?

Highly technical journal vs. less specific ones.

Prof. Dr. Valtencir Zucolotto

Report your results clearly

Use as few words as necessary

Prof. Dr. Valtencir Zucolotto

All information or ideas must be referenced!

Prof. Dr. Valtencir Zucolotto

Prof. Dr. Valtencir Zucolotto

Title, Authors and Affiliations

A good Title describes the contents of the

Use specific words strongly associated with

Prof. Dr. Valtencir Zucolotto

Example 1: A paper reporting on the influence of the

Title 1: Mechanical properties of Polyaniline films

Poor, too general!

Prof. Dr. Valtencir Zucolotto

Title 2: The influence of the MW on the Mechanical

Keywords Included: mechanical properties, polyaniline,

Prof. Dr. Valtencir Zucolotto

Emphasize your key findings whenever possible

OK!! The author describes the most important result

Prof. Dr. Valtencir Zucolotto

Who are the authors of a paper?

Prof. Dr. Valtencir Zucolotto

Guidelines to define authorship:

All authors must be able to present/discuss/defend

Prof. Dr. Valtencir Zucolotto

Prof. Dr. Valtencir Zucolotto

Affiliations usually include the following information:

City, Zip code, PO Box

Prof. Dr. Valtencir Zucolotto

Prof. Dr. Valtencir Zucolotto