Transcript Document

Identifying reasons for success in
biomedical research and publishing
UFRN
7 August 2014
5 August 2014
Ganesha Associates CC BY 3.0
1
Me…
• BSc Physics 1971, PhD Neuroscience 1976, post
doc Epidemiology 1975-1979
• Visiting Researcher, UFPe 1978-79, 1984
• Editor, Publisher, Director at Elsevier Science,
1979 – 2005
• Pubmed systems expert, NCBI, NIH 2006-2007
• STM business analyst, Outsell Inc, 2009-2011
• Visiting Professor UFPe, 2006-2008, 2012-2014
• Independent consultant Ganesha Associates
2006-2014
5 August 2014
Ganesha Associates CC BY 3.0
2
5 August 2014
Ganesha Associates CC BY 3.0
3
5 August 2014
Ganesha Associates CC BY 3.0
4
Assessment of [ind/dept/inst] performance
5 August 2014
Ganesha Associates CC BY 3.0
5
Impact factors and research assessment
• Publishers LOVE impact factors!
– “Nature remains #1 in the Multidisciplinary
Sciences, with an Impact Factor of 38.597, and is
the most cited science journal in the world with
554,745 citations in 2012.”
• Researchers and funding agencies HATE them!
• But citations do prove that your work is being
integrated into the consensus view for your
discipline
Source: Nature press release July 2013
5 August 2014
Ganesha Associates CC BY 3.0
6
Your goals as researchers
•
•
•
•
Get your paper published
At first/second attempt
In a Qualis A journal
And receive lots of citations…
5 August 2014
Ganesha Associates CC BY 3.0
7
Publishing: an essential research
skill that isn’t taught
assessing
relevance to
research topic
Preparation
citation
management
determining
likelihood of
acceptance
Journal
Selection
writing
an outline
navigating a
submission system in a
second language
comparing
journals
Writing
writing in
English
Submission
understanding
comments
formatting to
guidelines
Publication
ethics
5 August 2014
Peer
Review
Ganesha Associates CC BY 3.0
Publication
Success
decision to
re-submit, or try a
different journal
long decision
timelines
8
Reasons for failure - 2009
1. Many manuscripts made no clear attempt to define the
purpose, or, better still, the main conclusion of the study.
2. Over two-thirds of the manuscripts given to me in 2006
contained few or no references to work done after 2001!
3. It was quite common for articles to have been rejected
because they had been sent to the wrong journal.
4. Little thought had been given to experimental design
until after the experiments have been performed.
5. And, yes, the English is often poor, but these problems
stem from the logical structure of what is being said,
which is not really a translation issue!
5 August 2014
Ganesha Associates CC BY 3.0
9
5 August 2014
Ganesha Associates CC BY 3.0
10
Let’s see where failure occurs
Project
proposal
Experiment,
results,
analysis
Write article
?
Submit to
journal
Rejection/
acceptance
Re-submit
5 August 2014
Ganesha Associates CC BY 3.0
11
Reasons for failure - 2014
• Badly written, bad English [bad Portuguese]
• Mismatch with journal aims and scope [submit to
wrong journal]
• Failure to follow journal’s instructions to authors
• Lack of originality, novelty, relevance or significance
[weak hypothesis]
• Flaws in study design, poor control [poor experimental
design]
• Some of these problems are avoidable if you spot them
early!
5 August 2014
Ganesha Associates CC BY 3.0
12
Let’s see where failure occurs
?
Project
proposal
Experiment,
results,
analysis
Write article
Submit to
journal
Rejection/
acceptance
Re-submit
5 August 2014
Ganesha Associates CC BY 3.0
13
Your priorities…
• Learn to search and read the primary literature
regularly.
• Formulate and maintain strong, up-to-date hypotheses
• Identify journals that ‘fit’ your hypothesis. Be realistic
about your chances of publishing in them.
• Study the structure of scientific English and learn to
write like that in Portuguese
5 August 2014
Ganesha Associates CC BY 3.0
14
www.ganesha-associates.com
[email protected]
5 August 2014
Ganesha Associates CC BY 3.0
15
There are many sources of content and
each one is different
• Free
– Google, Google Scholar, Pubmed Central
• Subscription
– Scopus, ScienceDirect, Ovid
• Abstracts and citations only
– PubMed, Web of Science
• Full text, single publisher
– SpringerLink, Wiley Online Library
• Full text, many publishers
– Pubmed Central, SwetsWise Online Content
5 August 2014
Ganesha Associates CC BY 3.0
16
Does anybody know how to search?
5 August 2014
Ganesha Associates CC BY 3.0
17
Does anybody know how to search?
5 August 2014
Ganesha Associates CC BY 3.0
18
5 August 2014
Ganesha Associates CC BY 3.0
19
5 August 2014
Ganesha Associates CC BY 3.0
20
5 August 2014
Ganesha Associates CC BY 3.0
21
Project titles – what is your problem?
• Análise dos limiares de sensibilidade à pressão e
à corrente elétrica em acupontos em indivíduos
com e sem migrânea
• Frequência, localização anatômica e limiar de
percepção dolorosa em pontos gatilhos
miofasciais na cabeça e pescoço em mulheres
com migrânea.
• Ultrassonografia e eletromiografia de superfície
dos músculos flexores cervicais em mulheres com
migrânea e cefaleia do tipo tensional
5 August 2014
Ganesha Associates CC BY 3.0
22
Abstracts – what is your problem?
Frequência, localização anatômica e limiar de percepção
dolorosa em pontos gatilhos miofasciais na cabeça e pescoço em
mulheres com migrânea.
Context: Migraine is a very common pain syndrome and the mechanisms that
can cause or aggravate the pain and the consequences of its chronicity are
still not completely understood. Studies have shown that migraine is
associated with a central sensitization phenomena in which noxious stimuli
cause changes in the central nervous system , sensitizing cranial nociceptors
and reducing their activation threshold . In this context , the constant
peripheral nociceptive input due to myofascial trigger points in the muscles
of the head and neck may be associated with the onset of the migraine
attack. The elucidation of the role of trigger points in migraine is essential in
order to establish and direct physical therapy through tools useful for patients
with myofascial disorders associated with migrainous framework .
Objective: To measure differences in the frequency , anatomical location and
sensory threshold pressure of the trigger points of the trapezius (descending
fibers), masseter and sternocleidomastoid muscles in women with and
without migraine .
5 August 2014
Ganesha Associates CC BY 3.0
23
Reduction in perceived stress as a migraine trigger: the
"let-down headache" hypothesis.
OBJECTIVE:
To test whether level of perceived stress and reductions in levels of perceived stress (i.e., "let-down")
are associated with the onset of migraine attacks in persons with migraine.
METHODS:
Patients with migraine from a tertiary headache center were invited to participate in a 3-month
electronic diary study. Participants entered data daily regarding migraine attack experience, subjective
stress ratings, and other data. Stress was assessed using 2 measures: the Perceived Stress Scale and
the Self-Reported Stress Scale. Logit-normal, random-effects models were used to estimate the odds
ratio for migraine occurrence as a function of level of stress over several time frames.
RESULTS:
Of 22 enrolled participants, 17 (median age 43.8 years) completed >30 days of diaries, yielding 2,011
diary entries including 110 eligible migraine attacks (median 5 attacks per person). Level of stress was
not generally associated with migraine occurrence. However, decline in stress from one evening diary
to the next was associated with increased migraine onset over the subsequent 6, 12, and 18 hours,
with odds ratios ranging from 1.5 to 1.9 (all p values < 0.05) for the Perceived Stress Scale. Decline in
stress was associated with migraine onset after controlling for level of stress for all time points.
Findings were similar using the Self-Reported Stress Scale.
CONCLUSIONS:
Reduction in stress from one day to the next is associated with migraine onset the next day. Decline in
stress may be a marker for an impending migraine attack and may create opportunities for
preemptive pharmacologic or behavioral interventions.
5 August 2014
Neurology. 2014 Apr 22;82(16):1395-401. Impact Factor 8.25
Ganesha Associates CC BY 3.0
24
O efeito do Neuropeptídeo S na resposta
comportamental ao predador e a sua ativação neuronal
RESUMO: O neuropeptídeo S (NPS) é um peptídeo composto por 20 aminoácidos
altamente conservado entre as espécies. NPS é expresso em diversos tecidos e na
parte central do sistema nervoso de rato ele tem sua expressão restrita a região periceruleus no tronco encefálico. No entanto, o receptor de NPS (NPSR) tem uma ampla
distribuição no encéfalo de rato, sendo o hipotálamo, amígdala e córtex motor as
áreas de maior expressão. Estudos funcionais tem demonstrado que NPS está
envolvido principalmente com aumento de vigília, comportamento hiperlocomotor e
redução de ansiedade, fazendo do NPS um neuropeptídeo de função particular, um
ansiolítico excitatório. Até o momento, o efeito ansiolítico do NPS foi avaliado em
diversos modelos de ansiedade, como caixa claro-escuro, labirinto em cruz elevado,
teste de esconder bolinhas, teste da hipertermia induzida por estresse e o teste do
“defensive burying behavior”, que apesar de válidos, são paradigmas que apresentam
perigos artificiais. A relação presa-predador é especial por suas características
peculiares, como a apresentação de um perigo tão real e forte para a presa, que gera
um condicionamento quase que instantâneo. Neste projeto pretendemos trabalhar
com o paradigma presa-predador para estudar o efeito do NPS diante de um perigo
real (avaliando comportamentos relacionados ao medo), bem como investigar o papel
do NPS na modulação da memória aversiva (em situações de re-exposição dos
camundongos ao ambiente sem a presença do predador). Além disso, pretendemos
fazer um mapeamento da ativação neuronal causado pela injeção
intracerebroventricular de NPS em camundongos, através da expressão de Fos.
5 August 2014
Ganesha Associates CC BY 3.0
25
Edited version
Neuropeptide S (NPS) is highly conserved among species and is expressed in many tissues.
In the central nervous system of the rat expression is restricted to peri-coeruleus region of the brain stem.
Paradoxically (=However) the NPS receptor has a broad distribution in the rat brain with particularly high levels
of expression occurring in the hypothalamus, amygdala and motor cortex.
Functional studies have shown that NPS could act as an excitatory anxiolytic since it has been shown to be
involved primarily in promoting increased wakefulness, hyper-locomotor behavior and anxiety reduction.
The anxiolytic effect of NPS has been evaluated in several models of anxiety, such as light-dark box, elevated
plus maze, hide dot test, the stress-induced hyperthermia and the test of "defensive burying behavior", which
though valid, are artificial paradigms that have hazards.[These two sentences should be combined and the link
with predator-prey relationships made clear]
The predator-prey relationship is special because of its peculiar characteristics, such as presentation of a danger
as real and strong to prey, which generates an almost instant conditioning.[???]
In this project we intend to work with the predator-prey paradigm [???] to study the effect of NPS facing a real
danger (assessing behaviors related to fear), as well as investigating the role of the NPS in the modulation of
aversive memory (in case of re-exposure of mice to the environment without the presence of predator).[???]
Moreover, we want to map the neuronal activation caused by intracerebroventricular injection of NPS in mice
on the expression of Fos.[!!!]
5 August 2014
Ganesha Associates CC BY 3.0
26
Case study: Hummingbird territorial
behaviour
9 September 2013
Ganesha Associates CC BY 3.0
27
Hummingbird territorial behaviour
Most hummingbird species demonstrate strong territorial behavior
If a bluffing charge attack does not work, the resident
may engage the trespasser in a brief but intense physical battle
So why do hummingbirds defend territories ?
H0: Hummingbirds are randomly distributed in space and time.
9 September 2013
Ganesha Associates CC BY 3.0
28
Hummingbird territorial behaviour
H1
If territory = F(energy), then behavior not species-dependent
If territory = F(mating), then behavior should be species and sex dependent
If…
If…
9 September 2013
Ganesha Associates CC BY 3.0
29
Territorial behaviour in 1971
• Time, Energy, and Territoriality of the Anna Hummingbird
(Calypte anna) Science 173 (1971) 818-821.
• When territory quality decreases defenders may
switch to less expensive forms of defense because
the energy savings outweigh the loss of resources
• Augmented territorial defense during the breeding
season is made possible by increased feeding
efficiency due to the availability at this time of very
nectar-rich flowers.
• Individuals with large territories are more successful
reproductively.
9 September 2013
Ganesha Associates CC BY 3.0
30
Hummingbird territoriality since
• Digestive physiology is a determinant of foraging bout
frequency in hummingbirds. Nature. 1986 Mar 612;320(6057):62-3.
• Mitochondrial respiration in hummingbird flight
muscles. Proc Natl Acad Sci U S A. 1991 Jun 1;88(11):4870-3.
• Cloning and analysis of the gene encoding hummingbird
proinsulin. Gen Comp Endocrinol. 1993 Jul;91(1):25-30.
• Flight and size constraints: hovering performance of
large hummingbirds under maximal loading. J Exp Biol.
1997 Nov;200(Pt 21):2757-63.
9 September 2013
Ganesha Associates CC BY 3.0
31
Humming bird relevance
• I think that there will be an association (+ or -) between mutations
in gene x and susceptibility to disease y
– No causal basis for a relationship given
• I predict that mutations in gene x will increase susceptibility to
disease y because patients with disease y often have low levels of
gene product x.
– Built-in control, patients with normal levels of the gene product should not
have the disease.
• I predict that chemically non-neutral mutations in gene x will
increase susceptibility to disease y in patients with low levels of
gene product x.
– Second level of control – neutral mutations should be asymptomatic
5 August 2014
Ganesha Associates CC BY 3.0
32
Hypotheses – moral of the story
• With a strong hypothesis, you:
– Avoid following leads which go nowhere – false
positives, fail early
– Avoid ignoring unexpected observations that are
of high interest – false negatives
– May need to do less work !
– Will get published in better journals !
– And get cited more!!
5 August 2014
Ganesha Associates CC BY 3.0
33
What is the Editor looking for ?
• Will the article get cited (and boost the IF?)?
• Is the subject of the article relevant to any of
the main stories currently being published in
the journal?
• Are the findings novel, interesting to the
readership?
• Is the purpose of the research clearly stated in
the title, abstract?
• Is the experimental design appropriate?
5 August 2014
Ganesha Associates CC BY 3.0
34
Your journal selection criteria
• Your hypothesis – where have other recent
papers on this subject been published?
• Are the aims and scope of journal
appropriate?
• The Impact Factor and Qualis ranking
• Speed and ease of publication
• Publisher’s statistics on circulation, downloads
5 August 2014
Ganesha Associates CC BY 3.0
35
Screening: Royal Society for Chemistry
• “Articles submitted to our journals are screened
so the editor that is handling the article decides
that the article is either out of the journal scope
or that the article is clearly below the quality
level of the journal.
• The screening rates of our journals varies a lot.
Our high quality journals have a pre screen rate
of about 80%.”
• So only 20% of articles ever get to the peer
review stage (and 85% of them are rejected!)
5 August 2014
Ganesha Associates CC BY 3.0
36
Editorial review process
Submit article
Screening
5 August 2014
Rejection 80%
Peer review
Rejection 17%
Revision
Acceptance 3%
Ganesha Associates CC BY 3.0
37
Example: Communities of arbuscular mycorrhizal
fungi in dry tropical forests of Northeast Brazil
The arbuscular mycorrhizal association is one of the important
strategies used by plants in arid and semiarid regions to support water
scarcity and soil nutrient deficiency. In this study the diversity and
activity of arbuscular mycorrhizal fungi (AMF) were investigated in two
types of dry tropical forest. Soil and roots samples were collected in
areas of thorny dry woody savanna (TDWS) and in areas of mixed
savanna and montane deciduous shrub (SMDS) in Pernambuco State,
Brazil. Twenty seven species from 10 genera of Glomeromycota were
identified, and Acaulospora was the most representative. An average
of 50 spores per 100 g of soil was recovered from the two areas. The
infection potential of the AMF was determined using colonized root
fragments and extraradical mycelium and demonstrated the
importance of these propagules for the colonization of roots. Under the
same semiarid conditions, the two tropical dry forests studied harbored
distinct AMF communities indicating that the soil and vegetation type
are the key influencers of the composition and activity of these fungi in
the studied areas.
5 August 2014
Ganesha Associates CC BY 3.0
38
Use eTBLAST to find similar articles
5 August 2014
Ganesha Associates CC BY 3.0
39
Use eTBLAST to find similar articles
5 August 2014
Ganesha Associates CC BY 3.0
40
Top 10 Journals in this area of research
1. Mycorrhiza Total score: 8.23
2. Oecologia Total score: 1.40
3. The New phytologist Total score: 1.31
4. Mycologia Total score: 0.81
5. Molecular ecology Total score: 0.75
6. Ying yong sheng tai xue bao = The journal of applied ecology
Total score: 0.67
7. Applied and environmental microbiology Total score: 0.65
8. Environmental microbiology Total score: 0.62
9. Revista de biología tropical Total score: 0.46
10. Journal of plant physiology Total score: 0.44
5 August 2014
Ganesha Associates CC BY 3.0
41
EDANZ Journal Selector
5 August 2014
Ganesha Associates CC BY 3.0
42
5 August 2014
Ganesha Associates CC BY 3.0
43
5 August 2014
Ganesha Associates CC BY 3.0
45
5 August 2014
Ganesha Associates CC BY 3.0
47
The importance of being cited
The h-index is an index that attempts to
measure both the productivity and impact of
the published work of a scientist or scholar.
The index is based on the set of the scientist's
most cited papers and the number of citations
that they have received in other publications
H index = 2
5 August 2014
Ganesha Associates CC BY 3.0
48
Departmental performance
8
7
6
H-index
5
4
3
2
1
0
0
5
10
15
20
25
Article output 2008-2013
5 August 2014
Ganesha Associates CC BY 3.0
49
Why do some papers not get cited?
5 August 2014
Ganesha Associates CC BY 3.0
50
Echocardiography evaluations for
asymptomatic patients with severe obesity
Abstract
Objective: To study the systolic and diastolic function of asymptomatic patients with
severe obesity using a Doppler echocardiography. Methods: Thirty candidates for
bariatric surgery, with an average BMI of 49.2 ± 8.8 Kg/m2 and no previous history of
heart disease were evaluated through transthoracic echocardiography. Results:
Enlarged left chambers were observed in 42.9% of the sample, diastolic dysfunction in
54.6% and left ventricular hypertrophy in 82.1%, of which 50% of the cases presented
the geometric pattern of eccentric hypertrophy. Indexation of left ventricular mass to
height resulted in a significantly higher number of diagnoses for hypertrophy than
indexation to body surface area (p = 0.0053), demonstrating that this index is more
appropriate to determine ventricular hypertrophy in obese people. Correlations
between left ventricular hypertrophy with obesity duration and pressure levels were
positive as well as correlations between body mass index and diastolic dysfunction
indicators. Conclusion: This study demonstrated that echocardiograms performed on
asymptomatic severely obese patients can detect alterations in the cardiac structure
that are common in cases of obesity cardiomyopathy and can be associated with the
development of heart failure, arrhythmias and sudden death, enabling the
identification of patients with greater cardiovascular risk.
5 August 2014
Ganesha Associates CC BY 3.0
51
Before: Echocardiography evaluations for
asymptomatic patients with severe obesity
• Objective: To study the systolic and diastolic function of
asymptomatic patients with severe obesity using a
Doppler echocardiography.
• Conclusion: This study demonstrated that
echocardiograms performed on asymptomatic severely
obese patients can detect alterations in the cardiac
structure that are common in cases of obesity
cardiomyopathy and can be associated with the
development of heart failure, arrhythmias and sudden
death, enabling the identification of patients with
greater cardiovascular risk.
5 August 2014
Ganesha Associates CC BY 3.0
52
After: Echocardiography identifies obese
patients at risk of cardiovascular complications
• Objective: Can echocardiograms be used to
identify patients at risk of cardiovascular
complications?
• Conclusion: Echocardiograms detect common
alterations in the cardiac structure in
asymptomatic severely obese patients. These
changes are associated with the development of
heart failure, arrhythmias and sudden death.
Thus, echocardiograms can be used to identify
patients at risk of cardiovascular complications.
5 August 2014
Ganesha Associates CC BY 3.0
53
Lost in translation
• “Poor English” often used as a euphemism for
“badly written”
• Poor Portuguese translates into poor English
• Structured Portuguese translates into
structured English
• If the science is clear (title, abstract, intro,
results) the chances of early rejection are
reduced
5 August 2014
Ganesha Associates CC BY 3.0
54
Conclusions
• Make sure your hypothesis is firmly rooted in
the current literature
• Make sure you express your problem and its
solution clearly in the title and abstract
• Make sure that the hypothesis and its basis in
the current literature are clearly expressed in
the Introduction
• Identify at least one journal that is publishing
work based on similar hypotheses
5 August 2014
Ganesha Associates CC BY 3.0
55
Main opportunities for success - 2014
• Start with a well-defined hypothesis that has
its foundations firmly rooted in the
international literature.
• Have a clear message
• Develop a well-structured writing style
• Understand the publishing process
• Choose the right journal at the beginning of
the project
5 August 2014
Ganesha Associates CC BY 3.0
56
Future of the course
• Embed in departmental publishing strategy
• Integrate with creation of student project
proposals
• Project document needs to provide a
framework for critical thinking later
• “Talk and chalk” can largely be replaced by
Moodle-based course work and Skype
sessions
5 August 2014
Ganesha Associates CC BY 3.0
57
UFRN – stage 1
Identify literature hot spots (story clusters) for
projects before students arrive.
Focus on a few technologies that are robust
Teach students to search, summarize and debate
literature hot spots
Understand the ecology of journals associated
with each hot spot
Choose journal
5 August 2014
Ganesha Associates CC BY 3.0
58
UFRN – stage 2
Teach students structured writing techniques
(can be Portuguese or English)
Teach experimental design on an as-needs basis
Encourage students to visualise and analyse data
as it is being produced
Carry out essential maintenance on hypotheses
5 August 2014
Ganesha Associates CC BY 3.0
59
UFRN – stage 3
Start writing as soon as main figures and tables
are completed and the story clear
Check journal choice, read instructions to
authors
Write article, show to peers
Submit and prepare for rejection!
Take the comments seriously
Reconsider journal choice
5 August 2014
Ganesha Associates CC BY 3.0
60
Good luck!
5 August 2014
Ganesha Associates CC BY 3.0
61