1. 28 October 2014Ganesha Associates CC BY 3.01 Identifying reasons for success in biomedical research and publishing Department of Genetics and Evolutionary Biology, University of São Paulo 14 November 2014

2. CV 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 Consultant, European Bioinformatics Institute ELIXIR impact project 2015 28 October 2014Ganesha Associates CC BY 3.02

3. 28 October 2014Ganesha Associates CC BY 3.03 The growing importance of metrics

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6. Assessment of [ind/dept/inst] performance 28 October 2014Ganesha Associates CC BY 3.06

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8. 28 October 2014Ganesha Associates CC BY 3.0 Why do some papers not get cited? 8

9. Lost in translation? The regular assessment of Brazilian scientific output means that individual university departments need to constantly improve the quantity and quality of their scientific output. A significant proportion of this output involves the work of Master's and Doctoral students but getting these manuscripts published in a suitable journal can often prove to be a challenge. Although students' lack of fluency in English is a contributing factor, many of the problems observed have an early origin in the formulation of the research problem and connecting its relevance to current research trends in the international literature. 28 October 2014Ganesha Associates CC BY 3.09

10. 28 October 2014Ganesha Associates CC BY 3.0 www.ganesha-associates.com david@ganesha-associates.com 10

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12. Project proposal Experiment, results, analysis Write article Submit to journal Rejection/ acceptance Re-submit From idea to publication 28 October 2014Ganesha Associates CC BY 3.012

13. Preparation Journal Selection WritingSubmission Peer Review Publication 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 Publication ethics writing in English formatting to guidelines Publishing: an essential research skill that isn’t taught 5 August 2014Ganesha Associates CC BY 3.013

14. Reasons for failure - 2014 Badly written, bad English, bad Portuguese Failure to state a hypothesis: title, abstract, introduction Lack of originality, novelty, relevance or significance - in other words a weak hypothesis Flaws in study design, inappropriate control, poor experimental design, e.g. sample size to small Mismatch with journal aims and scope, ms submitted to the wrong journal Failure to follow journal’s instructions to authors 28 October 2014Ganesha Associates CC BY 3.014

15. Structure 28 October 2014Ganesha Associates CC BY 3.015 Article Sections Paragraphs Sentences Phrases Words Title Abstract Introductio n Methods Results Discussion

16. Structure “Similar levels were observed by Velázquez et al. (2009), who obtained average values ​​of NDFap 61.3 and 59.6%, respectively, for the grasses Tifton 85, cut to 15cm and Tanzania cut 30cm from ground level, both at 28 days of age, the similarity of the results, as well as the managements of age and height of cut, proving that even in intense levels of shading (48%), the levels of NDFap of buffel grass remain the same levels as other tropical forages studied without light restriction.” 28 October 2014Ganesha Associates CC BY 3.016

17. 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 among these individuals. REGIONAL LUNG VENTILATION DISTRIBUTION AMONG INDIVIDUALS WITH CHRONIC HEART FAILURE AFTER AN INSPIRATORY MUSCLE TRAINING PROGRAME: A RANDOMIZED CONTROLLED CLINICAL TRIAL 18/10/2013Ganesha Associates

18. 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 physio-pathological 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 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. REGIONAL LUNG VENTILATION DISTRIBUTION AMONG INDIVIDUALS WITH CHRONIC HEART FAILURE AFTER AN INSPIRATORY MUSCLE TRAINING PROGRAME: A RANDOMIZED CONTROLLED CLINICAL TRIAL 18/10/2013Ganesha Associates

19. 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. INSPIRATORY MUSCLE TRAINING IMPROVES REGIONAL LUNG VENTILATION DISTRIBUTION IN CHRONIC HEART FAILURE PATIENTS 18/10/2013Ganesha Associates

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24. 28 October 2014Ganesha Associates CC BY 3.024 Case study: Hummingbird territorial behaviour

25. 28 October 2014Ganesha Associates CC BY 3.025 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 ? H 0 : Hummingbirds are randomly distributed in space and time. Hummingbird territorial behaviour

26. 28 October 2014Ganesha Associates CC BY 3.026 Hummingbird territorial behaviour H 1 If territory = F(energy), then behavior not species-dependent If territory = F(mating), then behavior should be species and sex dependent If…

27. 28 October 2014Ganesha Associates CC BY 3.027 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.

28. 28 October 2014Ganesha Associates CC BY 3.028 Hummingbird territoriality since Digestive physiology is a determinant of foraging bout frequency in hummingbirds. Nature. 1986 Mar 6- 12;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.

29. Project titles – origin of the 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 28 October 2014Ganesha Associates CC BY 3.029

30. Reduction in perceived stress is a migraine trigger 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. 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. Neurology.Neurology. 2014 Apr 22;82(16):1395-401. Impact Factor 8.25 28 October 2014Ganesha Associates CC BY 3.030

31. 9 September 2013Ganesha Associates CC BY 3.031 Hypothesis examples 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 children with stutter.

32. 9 September 2013Ganesha Associates CC BY 3.032 Hypothesis 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

33. 9 September 2013Ganesha Associates CC BY 3.033 Hypothesis 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

34. Standing on the shoulders of giants The metaphor of dwarfs standing on the shoulders of giants expresses the meaning of "discovering truth by building on previous discoveries". But where are the giants and how do you climb on their shoulders? 28 October 2014Ganesha Associates CC BY 3.034

35. Learn to search effectively

36. Because… 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

37. The question behind the query Search engines think in terms of words, but users think in terms of sentences, specific problems! – 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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40. 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 28 October 2014Ganesha Associates CC BY 3.040

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42. Editorial review process Submit article Screening Peer review Rejection 80% Rejection 17% Revision Acceptance 3% 28 October 2014Ganesha Associates CC BY 3.042

43. 28 October 2014Ganesha Associates CC BY 3.043 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?

44. 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. 28 October 2014Ganesha Associates CC BY 3.044

45. 28 October 2014Ganesha Associates CC BY 3.0 Use eTBLAST to find similar articles 45

46. 28 October 2014Ganesha Associates CC BY 3.0 Use eTBLAST to find similar articles 46

47. 28 October 2014Ganesha Associates CC BY 3.0 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 47

48. 28 October 2014Ganesha Associates CC BY 3.0 EDANZ Journal Selector 48

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52. Reasons for failure - 2014 Badly written, bad English, bad Portuguese Failure to state a hypothesis: title, abstract, introduction Lack of originality, novelty, relevance or significance - in other words a weak hypothesis Flaws in study design, inappropriate control, poor experimental design, e.g. sample size to small Mismatch with journal aims and scope, ms submitted to the wrong journal Failure to follow journal’s instructions to authors 28 October 2014Ganesha Associates CC BY 3.052

53. Project proposal Experiment, results, analysis Write article Submit to journal Rejection/ acceptance Re-submit ? Success builds from the beginning! 28 October 2014Ganesha Associates CC BY 3.053

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 2014Ganesha Associates CC BY 3.054

55. 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 2014Ganesha Associates CC BY 3.055

56. UFxx – 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 2014Ganesha Associates CC BY 3.056

57. UFxx – 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 2014Ganesha Associates CC BY 3.057

58. UFxx – 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 2014Ganesha Associates CC BY 3.058

59. Good luck! 5 August 2014Ganesha Associates CC BY 3.059