Transcript Document

Competências Básicas de Investigação
Científica e de Publicação
Lecture 4: Basic reading and writing skills
The scientific research process
[Greatly simplified!]
Experiments
Problem definition
Grant proposal
More
experiments
Seminar
Conference proceedings
Writing-up
Publication
Key:
Experiments
Reading and writing
Verbal communication
24 August 2012
Ganesha Associates
2
The importance of reading and writing
• Good science begins and ends in the literature
• Good experimental design requires an awareness of the latest
research trends and findings in your area together with a clear
definition of the problem you are trying to solve
• Acceptance of your work for publication requires clear logical
presentation of your results together with a clear explanation
of how they advance our understanding
• Analysis of the literature is a constant component of a good
researcher’s daily routine
5 July 2012
Ganesha Associates
3
The importance of regular reading
The importance of regular reading
Engineers ~ 72 articles per year
Physicists ~ 204 articles per year
Chemists ~ 276 articles per year
University medical faculty ~ 322 articles per year
Source: Carol Tenopir, University of Tennessee, USA
5 July 2012
Ganesha Associates
5
A strategy for reading
• Search Scopus, WoS, PubMed, etc regularly for new
articles, or look at articles citing landmark papers
• The worst way is to read from title to references,
digesting every word along the way without any
reflection or criticism, so…
–
–
–
–
Read often
Skim the articles and identify their structure.
Distinguish the main points, starting with the results.
Generate questions and be aware of where your
understanding begins and ends
– Draw inferences – where are the gaps?
– Take notes as you read.
Building reading into writing
•
•
•
•
•
Notes made while reading
Summaries of areas of research activity
Writing a literature review
Preparing for a seminar
Writing research paper
Literature review structure
• Can range from one to several pages in length
• Concise analyses of recent published research in
rapidly progressing or emerging areas.
• No original research
• Set the background and then concentrate on setting
the most recent findings in context.
• Balanced view of developments, even in fields that are
controversial.
• Can contain some speculation and debate, but it
should be made clear where opinions are being
presented.
• End with a clear assessment of the major unanswered
questions in the field
9 September 2013
Ganesha Associates CC BY 3.0
10
Finding a place to start
• Understanding the background
– Review journals
• Trends in…, Current Opinions in…, Annual Reviews in…, Nature
Reviews in…
– Use ‘cited by’ functionality in Scopus and WoS
– Use ‘related article’ functionality in PubMed
• Finding the frontier
–
–
–
–
Scientific weeklies, Nature, Science
Top international journals in your field
Conference reports
Talk to a leader in the field
24 August 2012
Ganesha Associates
11
Nature News and Views format
Current Opinion review style
Systematic reviews
Search for reviews as a specific document type
Beware of choosing a topic because “little
is known about it”
• This means either the area is of little interest,
or you haven’t done your literature search
effectively
• Use a comparative or inductive approach and
look for examples in similar systems - this
technique is particularly useful in any field
with a molecular component
• But it also works for the caatinga!
24 August 2012
Ganesha Associates
17
Literature review structure
Title
Document
Summary
Sections
Introduction
Paragraphs
Discussion
Sentences
Conclusions
Phrases
Scientific writing is linear
• Scientific writing must be unambiguous and
logical
• Since logic tends to be linear, learn to express
yourself that way
Phrases are the basic building blocks
Some examples of phrases are underlined in the sentences below. The
head noun appears in bold.
• The election year politics are annoying for many people.
• Almost every sentence contains at least one noun phrase.
• Current economic weakness may be a result of high energy prices.
Noun phrases can be identified by the possibility of pronoun substitution,
as is illustrated in the examples below.
• This sentence contains two noun phrases.
• It contains them.
• The subject noun phrase that is present in this sentence is long.
• It is long.
• Noun phrases can be embedded in other noun phrases.
• They can be embedded in them.
A string of words that can be replaced by a single pronoun without
rendering the sentence grammatically unacceptable is a noun phrase
Phrase order and stress
Readers expect context first, with the take-home message
in the stress position at the end of the sentence.
For example:
The dog sat when her mistress offered a treat.
The dog sat when a treat was offered by her mistress.
When the mistress offered her a treat, the dog sat.
Often writers will chain sentences using the item stressed
in the preceding sentence as the context for the next.
Phrase order and stress
• Por 37 votos a favor e 11 abstenções (deputados ausentes), foi
aprovado, ontem, na Assembléia Legislativa, a 2a versão do
Projeto de Lei Antinepotismo que prevê a proibição de
contratação de parentes até terceiro grau no Poder Executivo.
• A 2a versão do Projeto de Lei Antinepotismo, que prevê a
proibição de contratação de parentes até terceiro grau no Poder
Executivo, foi aprovado ontem na Assembléia Legislativa por 37
votos a favor e 11 abstenções (deputados ausentes)
• Source: Diario de Pernambuco 20 Set 2007
12 August 2013
Ganesha Associates
22
Example of chaining sentences
• Nociceptor sensory neurons are specialized to detect potentially
damaging stimuli
• These stimuli initiate the sensation of pain.
• However, bacterial infections produce pain by unknown molecular
mechanisms.
• These mechanisms are presumed to be secondary to immune
activation.
• Here we demonstrate that bacteria directly activate nociceptors.
• So the immune response mediated through TLR2, MyD88, T cells, B
cells., neutrophils and monocytes is not necessary for Staphylococcus
aureus-induced pain in mice.
• Instead, mechanical and thermal hyperalgesia in mice is correlated
with live bacterial load rather than tissue swelling or immune
activation.
Structure tips – sentence order
• The smallest of the URF's* (URFA6L), a 207-nucleotide (nt) reading frame
overlapping out of phase the NH2-terminal portion of the
adenosinetriphosphatase (ATPase) subunit 6 gene has been identified as the
animal equivalent of the recently discovered yeast H+-ATPase subunit 8 gene.
• The functional significance of the other URF's has been, on the contrary,
elusive.
• Recently, however, immunoprecipitation experiments with antibodies to
purified, rotenone-sensitive NADH-ubiquinone oxido-reductase [hereafter
referred to as respiratory chain NADH dehydrogenase or complex I] from
bovine heart, as well as enzyme fractionation studies, have indicated that six
human URF's (that is, URF1, URF2, URF3, URF4, URF4L, and URF5, hereafter
referred to as ND1, ND2, ND3, ND4, ND4L, and ND5) encode subunits of
complex I.
• This is a large complex that also contains many subunits synthesized in the
cytoplasm.
* URF = uncharacterized open reading frame
12 August 2013
Ganesha Associates
24
Structure tips – sentence order (edit)
• The smallest of the URF's, URFA6L, has been identified as the animal functional
equivalent of the recently discovered yeast H+-ATPase subunit 8 gene.
• However, the functional significance of other URF's has been more elusive.
• Recently, several human URF's have been shown to encode subunits of
rotenone-sensitive NADH-ubiquinone oxido-reductase.
• This is a large complex that also contains many subunits synthesized in the
cytoplasm - it will be referred to hereafter as respiratory chain NADH
dehydrogenase or Complex I.
• Six subunits of Complex I were shown by enzyme fractionation studies and
immunoprecipitation experiments to be encoded by six human URF's (URF1,
URF2, URF3, URF4, URF4L, and URF5)
• These URF's will be referred to subsequently as ND1, ND2, ND3, ND4, ND4L and
ND5.
12 August 2013
Ganesha Associates
25
Role of DMSP biosynthesis in coral
thermal stress response
Globally, reef-building corals are the most prolific producers of
dimethylsulphoniopropionate (DMSP)1, 2, a central molecule in the marine
sulphur cycle and precursor of the climate-active gas dimethylsulphide3, 4. At
present, DMSP production by corals is attributed entirely to their algal
endosymbiont, Symbiodinium2. However, by combining chemical, genomic
and molecular approaches, we show that coral juveniles produce DMSP in the
absence of algal symbionts. DMSP levels increased up to 54% over time in
newly settled coral juveniles lacking algal endosymbionts, and further
increases, up to 76%, were recorded when juveniles were subjected to
thermal stress. We uncovered coral orthologues of two algal genes recently
identified in DMSP biosynthesis, strongly indicating that corals possess the
enzymatic machinery necessary for DMSP production. Our results overturn
the paradigm that photosynthetic organisms are the sole biological source of
DMSP. They highlight the double jeopardy represented by worldwide
declining coral cover, as the potential to alleviate thermal stress through
coral-produced DMSP declines correspondingly.
Structure - paragraphs
• Start with generalities and then move towards
more specific ideas.
• There should be an obvious logical connection
between paragraphs.
• There should be one main or theme point per
paragraph; if the paragraph contains too many
themes, create a new paragraph or
paragraphs.
• Now some examples…
Arbuscular mycorrhizal fungi in a semiarid
copper mining area in Brazil
There are >160 species of arbuscular mycorrhizal fungi (AMF), whose taxonomic history is recent. Based on their symbiotic
habit and morphology, Morton and Benny (1990) included all of the AMF in the order Glomales, with three families
(Acaulosporaceae, Gigasporaceae and Glomaceae) and six genera ( Acaulospora, Entrophospora , Gigaspora , Glomus ,
Sclerocystis and Scutellospora). However, Redecker et al. (2000), using phylogenetic information obtained from morphological
and molecular data, transferred the species of Sclerocystis to Glomus, reinforcing the proposal of Almeida and Schenck (1990).
Morton and Redecker (2001) created two new families, Archaeosporaceae and Paraglomaceae, respectively, typified by the
genera Archaeospora and Paraglomus, and currently the AMF are included in a new phylum: Glomeromycota (Schüssler et al.
2001).
The distribution of AMF in natural Brazilian ecosystems has not been well studied: Trufem (1996) mentioned some species in
the Amazon and Atlantic provinces, as well as in cerrado areas, without records for other important areas (caatinga in the
northeast and pampas in the south). Taxonomic inventories of AMF in undisturbed areas were done in São Paulo (Bononi and
Trufem 1983; Trufem 1988, 1990; Trufem et al. 1994; Gomes and Trufem 1998) and Santa Catarina (Stürmer and Bellei 1994).
In cultivated areas there are records for the States of São Paulo (Trufem and Bononi 1985; Trufem et al. 1989, 1990; Grandi and
Trufem 1991; Carrenho et al. 2001) and Pernambuco (Maia and Trufem 1990; Melo et al. 1997).
The excess of heavy metals in soils has a direct toxic effect on plants, being deleterious to the AMF and having an impact on
plant and microbial communities (Valsecchi et al. 1995). Various heavy metals are fungitoxic, reducing spore germination,
mycelial growth and, consequently, mycorrhizal colonization (Nogueira 1996). An excess of Zn and Cu inhibits spore
germination (Hepper 1979), while colonization can be reduced in the presence of high levels of Zn, Cu, Ni, and Cd (Gildon and
Tinker 1983).
There are apparently no papers that mention species of AMF in areas in Brazil that have been degraded by mining. However,
taxonomic surveys in these areas are important to provide information regarding environmental impact and also about the
AMF species that are adapted to this stress condition, and would be useful for revegetation programs.
This paper deals with the identification of AMF species that occur in areas affected by copper mining, relating the presence of
such species to the levels of environmental impact found in the areas and comparing the occurrence of these fungi with the
local
plant diversity.
02/10/2013
Ganesha Associates 2013
Arbuscular mycorrhizal fungi in a
semiarid copper mining area in Brazil
There are >160 species of arbuscular mycorrhizal fungi (AMF), whose
taxonomic history is recent.
The distribution of AMF in natural Brazilian ecosystems has not been well
studied:
The excess of heavy metals in soils has a direct toxic effect on plants, being
deleterious to the AMF and having an impact on plant and microbial
communities (Valsecchi et al. 1995).
There are apparently no papers that mention species of AMF in areas in Brazil
that have been degraded by mining
This paper deals with the identification of AMF species that occur in areas
affected by copper mining, relating the presence of such species to the levels
of environmental impact found in the areas and comparing the occurrence of
these fungi with the local plant diversity.
02/10/2013
Ganesha Associates 2013
REGIONAL LUNG VENTILATION DISTRIBUTION AMONG INDIVIDUALS WITH
CHRONIC HEART FAILURE AFTER AN INSPIRATORY MUSCLE TRAINING
PROGRAME: A RANDOMIZED CONTROLLED CLINICAL TRIAL
Introduction: Chronic heart failure (CHF) is a complex syndrome caused by functional or structural cardiac abnormalities, leading to defects in
ventricular filling/ejection. As a result, the heart is unable to adequately supply the blood demand of tissues.1,2
The main symptoms of CHF are dyspnea and fatigue,3,4 caused by a physiopathological interaction beyond the hemodynamic disorder itself.3-6
Research shows that the lungs, with the exception of possible pulmonary function damage, are not responsible for reduced functional capacity in
patients with chronic heart failure (CHF).4 Since hemodynamic and pulmonary limitations do not sufficiently explain the appearance of fatigue and
dyspnea in CHF sufferers, several studies suggest that skeletal muscle abnormalities may contribute to these symptoms among subjects with CHF.6,7
Fatigue and dyspnea hamper performance in activities of daily living and exercise among patients with CHF.8 These symptoms are caused by skeletal
muscle atrophy, lower percentages of type I fibers in relation to type II, a decline in oxidative enzymes with rapid depletion of glycolytic mechanisms,
as well as a decrease in the size and number of mitochondria.9 In addition, respiratory muscle weakness may be involved in increased breathing
effort during hyperpnea required to perform activities with greater energy expenditure.10
Inspiratory muscle dysfunction is characterized by a reduction in their ability to generate pressure and force. This decreased strength is the result of
histological and biochemical changes. Based on diaphragm biopsies of individuals with CHF, histological studies recorded an increase in type I fibers,
suggesting a compensatory mechanism for the ventilation overload of these muscles. 11 Moreover, weakness in these muscles can also be explained
by the reduced diameter of muscular fibers, causing mechanical alterations.12 Clinically, this dysfunction may lead to limited exercise ability and
diminished quality of life, as well as a less favorable prognosis among individuals affected.10
In an attempt to reduce respiratory muscle dysfunction in CHF sufferers, several investigations have demonstrated the effects of Inspiratory Muscle
Training (IMT). 8,10,13 Inspiratory muscles, particularly the diaphragm, exhibit plasticity and are therefore susceptible to the principles of training.14 In
accordance with the specificity of training, IMT improves respiratory function in daily activities with regard to the type of muscle recruitment pattern
required during exercise or activities of daily living of patients. 15
A recent study by Chiappa et al 13, recorded a 72% increase in MIP among individuals who underwent IMT and suffered from CHF related to
inspiratory muscle weakness, compared to patients not submitted to training. Using ultrasound testing, the investigation also found that IMT
provoked notable diaphragmatic hypertrophy.
Another clinically significant aspect in CHF sufferers is the presence of cardiomegaly in some patients. In this condition expansion of the chest wall is
limited and extrapulmonary restriction, caused by competition between the lungs and heart for space inside the chest, may occur. As the disease
advances and worsens, in association with cardiomegaly, episodes of dyspnea become more frequent and severe with minimal effort and muscle
fatigue sets in progressively sooner.14-15
Thus, the present study aims to assess regional lung ventilation distribution in patients with CHF after completing an inspiratory muscle training
program
and correlate it with functional capacity and quality of life
amongAssociates
these individuals.
18/10/2013
Ganesha
REGIONAL LUNG VENTILATION DISTRIBUTION AMONG INDIVIDUALS WITH
CHRONIC HEART FAILURE AFTER AN INSPIRATORY MUSCLE TRAINING
PROGRAME: A RANDOMIZED CONTROLLED CLINICAL TRIAL
Introduction: Chronic heart failure (CHF) is a complex syndrome caused by functional or structural cardiac
abnormalities, leading to defects in ventricular filling/ejection.
The main symptoms of CHF are dyspnea and fatigue,3,4 caused by a physiopathological interaction beyond the
hemodynamic disorder itself.3-
Fatigue and dyspnea hamper performance in activities of daily living and exercise among patients with CHF.8
Inspiratory muscle dysfunction is characterized by a reduction in their ability to generate pressure and force.
In an attempt to reduce respiratory muscle dysfunction in CHF sufferers, several investigations have demonstrated
the effects of Inspiratory Muscle Training (IMT). 8,10,13
A recent study by Chiappa et al 13, recorded a 72% increase in MIP among individuals who underwent IMT and
suffered from CHF related to inspiratory muscle weakness, compared to patients not submitted to training. Using
ultrasound testing, the investigation also found that IMT provoked notable diaphragmatic hypertrophy.
Another clinically significant aspect in CHF sufferers is the presence of cardiomegaly in some patients.
Thus, the present study aims to assess regional lung ventilation distribution in patients with CHF after completing an
inspiratory muscle training program and correlate it with functional capacity and quality of life among these
individuals.
18/10/2013
Ganesha Associates
REGIONAL LUNG VENTILATION DISTRIBUTION AMONG INDIVIDUALS WITH
CHRONIC HEART FAILURE AFTER AN INSPIRATORY MUSCLE TRAINING
PROGRAME: A RANDOMIZED CONTROLLED CLINICAL TRIAL
18/10/2013
Ganesha Associates
REGIONAL LUNG VENTILATION DISTRIBUTION AMONG INDIVIDUALS WITH
CHRONIC HEART FAILURE AFTER AN INSPIRATORY MUSCLE TRAINING
PROGRAME: A RANDOMIZED CONTROLLED CLINICAL TRIAL
Introduction: The main symptoms of chronic heart failure (CHF) are dyspnea and fatigue,3,4 Several
studies suggest that skeletal muscle abnormalities may contribute to these symptoms. 6,7 Diaphragm
biopsies of individuals with CHF show an increase in type I fibers, suggesting a compensatory
mechanism for the ventilation overload of these muscles. 11 Moreover, weakness in these muscles can
also be explained by the reduced diameter of muscular fibers, causing mechanical alterations. 12
Clinically, this dysfunction may lead to limited exercise ability and diminished quality of life, as well as a
less favorable prognosis among individuals affected.10 Some CHF patients have cardiomegaly. Expansion
of the chest wall is limited and extra-pulmonary restriction, caused by competition between the lungs
and heart for space inside the chest, may occur. As the disease advances episodes of dyspnea become
more frequent and muscle fatigue sets in progressively sooner.14-15
In an attempt to increase respiratory muscle function in CHF sufferers, several investigations have
demonstrated the positive effects of Inspiratory Muscle Training (IMT). 8,10,13 IMT improves respiratory
function in daily activities with regard to the type of muscle recruitment pattern required during
exercise or activities of daily living of patients. 15 For example, a recent study by Chiappa et al 13,
recorded a 72% increase in MIP in CHF patients who underwent IMT. Using ultrasound testing, the
investigation also found that IMT provoked notable diaphragmatic hypertrophy.
Here we show that IMT improved muscle strength, functional capacity and quality of life in CHS
patients. We also analyzed the distribution behavior of lung volumes for the thoracoabdominal system
in this population and found that larger abdominal rib cage and abdomen volumes may result in more
effective diaphragmatic contraction.
18/10/2013
Ganesha Associates
INSPIRATORY MUSCLE TRAINING IMPROVES REGIONAL LUNG VENTILATION
DISTRIBUTION IN CHRONIC HEART FAILURE PATIENTS: A RANDOMIZED
CONTROLLED CLINICAL TRIAL
Introduction: The main symptoms of chronic heart failure
(CHF) are dyspnea and fatigue.
Clinically, this dysfunction may lead to limited exercise ability
and diminished quality of life, as well as a less favourable
prognosis among individuals affected.
In an attempt to increase respiratory muscle function in CHF
sufferers, several investigations have demonstrated the
positive effects of Inspiratory Muscle Training (IMT).
Here we show that IMT improved muscle strength, functional
capacity and quality of life in CHS patients.
18/10/2013
Ganesha Associates
Nature News and Views article structure
Nature News and Views storyline
• Coral reefs owe their success to a symbiosis between the animal host (the
coral polyp) and intracellular photosynthetic algae of the genus
Symbiodinium which supply up to 95% of the host's energy requirements.
• Reef-building corals, such as Acropora species, are prolific producers of
DMSP and DMS.
• Raina et al.5 use chemical, genomic and molecular approaches to reveal
that coral polyps also produce DMSP, in the absence of their algal
symbionts.
• The authors found two genes encoding enzymes known to be involved in
DMSP synthesis in diatoms — NADPH reductase and AdoMet-dependent
methyltransferase — have clear orthologues in both Acropora and
Symbiodinium.
• When seawater temperatures and light levels are high, the symbiosis
between a coral polyp and its algae can break down, such that the algae
are expelled.
• These findings not only help us to understand how corals may respond to
changing ocean temperatures, but may also contribute to our
understanding of climate-feedback cycles.
Learning points
• Read critically, make notes
• Analyse the structure of articles
• Because each paragraph has a specific function they
should appear in a logical order
• Ditto each sentence within the paragraph.
• Within each sentence, try to move from the general
to the particular
• Punctuation can alter meaning, so use it sparingly
– Example: The panda eats shoots and leaves vs. The panda
eats, shoots and leaves
12 August 2013
Ganesha Associates
37
Break
Keeping track of what you have seen and read
GOOGLE search
Search results
24 August 2012
GOOGLE search
AbstractPlus
AbstractPlus
Full Text
Search results
BLAST results
Ganesha Associates
AbstractPlus
Full Text
NCBI full_report
Full Text
39
Keeping track of what you have seen and read
?
Scielo
CAPES
Portal
Web of
Science
Scopus
National
Literature
OA: BMC
Or PLoS
Science
Direct
Springer
Link
24 August 2012
Ganesha Associates
PubMed
Google
Other
HighWire Databases,
e.g. NCBI
40
Documenting your search behaviour
Managing the results of your literature
research
• Download PDF/HTML versions of important
documents
• Give the files concise explanatory titles so you
will remember what they are about
• Ditto folder names
• Download Google Desktop Search, a utility
that indexes all the files on your PC and
displays results in a Google search page
• Or use Spotlight if you have a Mac
• Or use citation management software
24 August 2012
Ganesha Associates
42
Why use citation management software?
• Organize your references by research project in your own searchable
database.
• Import references from online databases, library catalogs, and journal
indexes, full-text databases such as ScienceDirect and from Web sites.
• Eliminate the need to type references into your research paper.
• The programs will automatically format your references in any style you
choose, such as MLA, APA or the style of a particular journal.
• …and more, e.g. share information within groups.
• Examples of uses:
– collect and organize references from many different resources into your own
personal, searchable database
– create formatted bibliographies and reading lists
– develop lists of cited papers as footnotes or as endnotes at the conclusion of
scholarly papers
Endnote
•
EndNote automates the creation of bibliographies. Writers can save hours of
typing and interpreting journal and other style requirements by simply selecting
the publication or style by name and generating a perfectly formatted document.
The EndNote support site includes new and updated import filters and output
styles to download.
•
Offers sophisticated, flexible tools for organizing references and PDFs and for
creating bibliographies
Offers most comprehensive array of citation output styles
Link EndNote records to PDFs and other types of documents saved on your hard
drive
In EndNote version X2 and higher: download article PDFs automatically
EndNote software must be purchased and installed onto your computer
EndNote is not very intuitive, but is not difficult with training
Best option for large research projects
Current version of EndNote Web is not recommended
•
•
•
•
•
•
•
Mendeley
• Mendeley is a free online service that allows you to index and organize
your PDF documents, collaborate with fellow researchers and share
information via shared and public collections, and discover new research
through the Mendeley research network. In addition, you can create
reference lists and bibliographies in Word (Windows only) or OpenOffice
(all platforms).
• Free software/web hybrid for PC, Mac, Linux
• Organizes and manages the pdfs that are already on your computer
• Introduces social networking tools to collaborate with fellow researchers,
including sharing lists of references and collaborative tagging of
documents
• Sync PDFs to your web account for access to them anywhere you are
online
• Annotate PDFs
• Search within the text of all of your PDFs
• Good way to capture citations from the PDFs on your computer and export
them into EndNote
Optional practical: Using Mendeley
• Create an account with Mendeley
• Experiment with the basic functionality by
adding documents from your own library.
• Join the group “UFPE 2013”
• Add your project proposal to the group
Document library