Competências Básicas de Investigação Científica e de Publicação

Ganesha Associates

Competências Básicas de Investigação Científica e de Publicação

Lecture 1: Hypotheses and SearchPhonoaudiology November 2013

13/08/2013

Preparation Journal Selection Writing Submission Peer

ReviewPublication

Success

determining likelihood of acceptance

citation management

navigating a submission system in a

second language

writing an outline

comparing journals

assessing relevance to

research topic

understanding comments

long decision timelines

decision to re-submit, or try a different journal

Publicationethics

writing in English formatting to

guidelines

Publishing is an essential research skill

13/08/2013 Ganesha Associates

www.ganesha-associates.com

Ganesha Associates

Me…

• BSc Physics 1971, PhD Neuroscience 1976, post doc 1975-1979

• Visiting Professor, UFPe 1978-79• 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, 2007, 2008, 2012,

2013

13/08/2013

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The scientific process involves making models of how things work

• These evolving models are described in the scientific literature

• Sometimes the models are wrong, often they are incomplete

• Scientific progress is driven by the communication and publication of the results of new research, and the reinterpretation of older work

• The tool which makes all of this possible is the hypothesis

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Neural correlates of mapping from phonology to orthography in children performing an auditory spelling task

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Experimental and observational types of research

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Experimental vs. Observational studies

No modification of experimental variablesUseful to discover trends and associationsCannot directly be used to infer causality

Compare responses different treatmentsDesigned to avoid misleading results

e.g. randomisationCan be used to infer cause and effect9 September 2013

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Main learning points

• Student projects fall into three categories– No hypothesis, i.e. observational– Weak hypothesis– Strong hypothesis

• The work will be published in a – National journal– Low impact factor journal– High impact factor journal

• Starting with strong hypothesis improves your chances of getting published in a good journal



What is a strong hypothesis ?

• A strong hypothesis is based on a series of premises – things that are already known with some certainty

• Each premise must be supported by references back to the (international) primary literature

• So a strong hypothesis will be backed by references to recent papers in high quality journals



Coin-tossing - an example• I wonder how many heads or tails I will get if I toss

this coin 100 times– No model

• The frequency distribution of heads and tails will be approximated by a binomial distribution with n=100 and p=0.5– Simple model, based on symmetry

• A detailed analysis of the dynamics reveals that the probability of a head is 0.51– Complex model, based on asymmetry, aerodynamics, etc


Coin-tossing – impact on CV1. None, or possibly negative

2. R. A. Fisher and others did perform this experiment in the early days of biological statistics, before the advent of computers, as a proof that the binomial distribution tended towards a normal one at high levels of n.

Interestingly they all found that the probability of a head p was usually slightly higher than 0.5, but this difference was ignored.

3. Persi Diacusis, Susan Holmes and Richard Montgomery (Stanford, 2004) publish a paper on the ‘Dynamical bias in the coin toss’ proving that the lack of total symmetry in a coin means that the probability of a head will always be slightly greater than 0.5.


Coin tossing - relevance• Children with unilateral hearing loss (UHL) have been found to have lower language scores,

and increased rate of speech therapy, grade failures, or needing Individualized Education Plans . The objective of this study was to determine whether language skills and educational performance improved or worsened over time in a cohort of children with UHL.

• To determine factors associated with physical therapy or occupational therapy evaluation and speech or swallow therapy evaluation in hospitalized children with traumatic brain injury; to describe when during the hospital stay the initial therapy evaluations typically occur; and to quantify any between-hospital variation in therapy evaluation.

• Articulation disorders in young children are due to defects occurring at a certain stage in sensory and motor development. Some children with functional articulation disorders may also have sensory integration dysfunction (SID). We hypothesized that speech therapy would be less efficacious in children with SID than in those without SID

• The present study provides data that support the hypothesis that children who stutter and typically developing children differ on both composite temperament factors and temperament scales. The findings were interpreted within existing frameworks of temperament development, as well as with regard to previous studies of temperament in CWS.


Case study: Hummingbird territorial behaviour


Most hummingbird species demonstrate strong territorial behavior

If a bluffing charge attack does not work, the residentmay 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.

Hummingbird territorial behaviour


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…


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.


Hummingbird territoriality since

• Hovering performance of hummingbirds in hyperoxic gas mixtures. J Exp Biol. 2001 Jun;204(Pt 11):2021-7.

• Adipose energy stores, physical work, and the metabolic syndrome: lessons from hummingbirds. Nutr J. 2005 Dec 13;4:36.

• Neural specialization for hovering in hummingbirds: hypertrophy of the pretectal nucleus Lentiformis mesencephali. J Comp Neurol. 2007 Jan 10;500(2):211-21.

• Three-dimensional kinematics of hummingbird flight. J Exp Biol. 2007 Jul;210(Pt 13):2368-82.


Hypothesis lecture learning points

• Good hypotheses build directly onto previous work

• So they need to become technically more sophisticated over time moving from the general to the particular

• A given problem can be associated with a number of very different hypotheses – your experiments should include tests to exclude these alternative explanations


Hypothesis lecture learning points

• Hypotheses can be weak (observational) or strong (mechanism-based)

• For example, a hypothesis which predicts that a tossed coin will end up ‘heads’ 50% of the time is much weaker than one that can predict the exact sequence of ‘heads’ and ‘tails’

• So hypothesis ‘quality’ is important

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Search

13/08/2013

Some sources of scientific content• Google• PubMed/Medline (NLM)• Scopus (Elsevier)• Web of Science (Thomson Reuters) • Google Scholar• PubMed Central, PubMed Central Europe• SciELO, Biblioteca Virtual em Saude• Science Direct, Ovid, SpringerLink, Wiley Online Library,

BiomedCentral, Public Library of Science, SWETSwise…• CAPES Portal de Periódicos

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Each source is different

• Free– Google, Google Scholar, Pubmed Central

• Subscription– Scopus, ScienceDirect

• Abstracts and citations only– PubMed, Web of Science

• Full text, single publisher– SpringerLink

• Full text, many publishers– Pubmed Central, SwetsWise Online Content

Classify sources of content

Abstract only

Full text

Free access Subscription


You can get access if…

• The journal is subscribed to by CAPES• You have a personal subscription• The journal is of the ‘Open Access’ type

– Note: some journals only make their content ‘Open Access’ after 6 or longer months. Some journals contain a mixture of OA and non-OA articles. See http://europepmc.org/journalList for more info.

• Journals in the ‘red’ categories are available anywhere.• Most journals subscribed to by CAPES will be available from

more than one source.• CAPES journals are only available from computers within the

University network unless you have remote access privileges.


So which sources should I use ?

• No single source contains all of the articles relevant to your research

• Google has the broadest coverage, but not all of the documents you find will be peer-reviewed articles

• Scopus, WoS and PubMed give you the best balance between quality and quantity, and, in theory, should link to all the content subscribed to by CAPES, plus OA content.

Components of a bibliographic database

• Content such as abstracts and full-text articles [or a pointer to where these may be found]

• Metadata [data about data]• Index• Search engine• Ranking/relevance algorithm• Plus many additional features



Content (Basic PDF)


Content (HTML)

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The basis of search: Indexing• The purpose of an index is to optimize speed and performance

in finding relevant documents for a search query.

• Without an index, the search engine would have to scan every document in the corpus, which would require considerable time and computing power.

• Metadata helps the indexing algorithm to select different classes of terminology from which to make an index, so a search can be carried out on just the authors names, for example

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Search: how the result list is ranked

• Date of publication• Relevance– Frequency with which search terms occur in the

document– Proximity of search terms

• Google’s PageRank algorithm uses "link popularity”- a document is ranked higher if there are more links to it


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The question behind the query

• Search engines think in terms of words, but users think in terms of sentences!– How do you spell Bousfield?– What do we know about BRCA1?– Given these symptoms, what is the most likely

diagnosis?– What are the side effects of aspirin?– Has this chemical structure been synthesized before?

• “Cancer causes X” vs. “Y causes cancer”

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What real queries look like - Google

• pharmacogenomics and disorders• bacteria growth casein media effect• waal pseudomonas• TRPM2 PCR mouse• Chitinases in carnivorous plants• glycerophosphoinositol 4-phosphate• Dai N, Gubler C, Hengstler P, Meyenberger C,

Bauerfeind P. Improved capsule endoscopy after bowel preparation. Gastrointest Endosc 2005;61(1) 28-31.

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Query changes people actually make

• Query series 1– latrunculin– latrunculin fm3a cell arrest– latrunculin fm3a arrest– latrunculin fm3a – latrunculin FM3A

• Query series 2– cytokinin signalling in arabidopsis– "cytokinin signalling in arabidopsis"– cytokinin delta– spindly arabidopsis

• Results– Remember to look beyond the first page. Compare the results of

Query 1 in PubMed and Google (add the term PubMed)

Ganesha Associates13/08/2013

Improving search accuracy

• Wild card characters– "a * saved is a * earned"

• Operators– jaguar speed -car– Pandas -site:wikipedia.org– “ribosome”

• Synonyms– MeSH terms

• Boolean terms– AND, OR, NOT

• Faceted search– GO terms

Anatomy of a query - Pubmed

• invasive fungal infections in young children• invasive[All Fields] AND ("mycoses"[MeSH

Terms] OR "mycoses"[All Fields] OR ("fungal"[All Fields] AND "infections"[All Fields]) OR "fungal infections"[All Fields]) AND ("Young Child"[Journal] OR ("young"[All Fields] AND "children"[All Fields]) OR "young children"[All Fields])


So…

• Using the same search terms will produce different results in different databases because:– Content different– Preparation of search terms will be different, e.g.

only Pubmed uses MeSH terms– Indexing process, implementation of stemming,

removal of stop words will be different– Ranking algorithms will be different

Quick tour

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Learning points

13/08/2013

• Google, Pubmed, Scopus and WoS are good places to start• Learn to use several information resources• Modify your search terms during the

course of a search session• Understand how the results are ranked

and don’t just look on the first page

Competências Básicas de Investigação Científica e de Publicação

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