Practical steps to better science

1. Practical steps to better science David Bousfield 22 October 2013

2. Me… • BSc Physics 1971, PhD Neuroscience 1976, post doc 1975-1979 • Editor, Publisher, Director at Elsevier Science 1979 – 2005 • Systems Expert, NCBI, NIH 2006-2007 • STM analyst, Outsell Inc, 2009-2011 • Visiting Professor UFPe, 1978-79, 1984, 2006, 2007, 2008, 2012, 2013 • david@ganesha-associates.com • http://www.ganesha-associates.com Ganesha Associates 2013

3. Publishing is an essential research skill determining likelihood of acceptance navigating a submission system in a second language assessing relevance to research topic comparing journals Peer Review Journal Selection Publication Success Writing Submission Preparation decision to re-submit, or try a different journal writing an outline understanding comments writing in English formatting to guidelines citation management long decision timelines Publication ethics Ganesha Associates 2013

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5. You… • How can we improve our research outputs? • Quantity • Quality • How can we avoid rejection? • How can we increase citation rates? • How can we publish in quality journals?

6. Main reasons for rejection – Brasil 2008 • Submitted to the wrong journal • Purpose of the work unclear • Work does not relate to current areas of research interest • Too long • Poor English Ganesha Associates 2013

7. Rejection: Company of Biologists • “…we editorially reject ~50% submitted papers…” • ~15% ‘insufficient advance’; 15% ‘insufficient interest’ to the journal readership or would be better in specialist journal; and remaining 70% ‘insufficient mechanistic insight’ i.e. based on the aims and scope. • Once papers have passed that test and get into peer review reasons for rejection are more specific to the content of the paper [such as] data not sound. • Some journals gets lots of papers that are just out of scope and often in really obvious ways e.g. cover plants when the journal doesn’t. Ganesha Associates 2013

8. Main opportunities for success - 2013 • 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 Ganesha Associates 2013

9. The research process Project proposal Experiment, results, analysis Write article • ? Submit to journal Rejection/ acceptance Re-submit

10. Project titles – the problem starts here • 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

11. Titles are easily improved – focus on outcomes rather than methods • DIAPHRAGM RELEASE MANUAL TECHNIQUE EFFECTS ON DIAPHRAGMATIC MOBILITY, RESPIRATORY MUSCLE STRENGTH AND EXERCISE PERFORMANCE IN COPD PATIENTS: A RANDOMIZED CONTROLLED TRIAL. • MANUAL DIAPHRAGM RELEASE TECHNIQUE INCREASES TIDAL VOLUME IN ELDERLY COPD PATIENTS

12. 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 evaluate and compare differences in the frequency , anatomical location and sensory threshold pressure of the trigger points of the trapezius ( descending fibers ) , masseter , sternocleidomastoid , in women with and without migraine .

13. Hypotheses – mechanism not measurement • Patients with migraine have a higher amount of myofascial trigger points in the temporalis, masseter, sternocleidomastoid and descending trapezius muscles. • Patients with migraine have a low threshold for pain sensation in these points. • Cutaneous mechanical cephalic and extra-cephalic allodynia vary within one month

16. Top ten journals in this field 1. Headache Total score: 1.46 2. Pain Total score: 1.24 3. Current pain and headache reports Total score: 0.91 4. Cephalalgia : an international journal of headache Total score: 0.71 5. The journal of pain : official journal of the American Pain Soc Total score: 0.51 6. European journal of neurology : the official journal of the Eur Total score: 0.47 7. Medical hypotheses Total score: 0.41 8. Brain : a journal of neurology Total score: 0.41 9. Chinese medicine Total score: 0.39 10. Neurology Total score: 0.39

20. Hypotheses - 2 • Women with migraine and tension-type headache have a smaller cross-sectional area of the flexor neck and greater activation and fatigue of the sternocleidomastoid muscle, than women without migraine. • Ten references, eight before 2010

24. Conclusions • Make sure your hypothesis is firmly routed in the current literature • Identify at least one journal that is publishing work based on similar hypotheses • I f your reference list does not contain many recently published articles, you have a problem

25. Measuring performance 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

27. Why do papers not get cited? Ganesha Associates 2013

28. 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. Ganesha Associates 2013

29. 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. Ganesha Associates 2013

30. 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. Ganesha Associates 2013

31. Use eTBLAST to identify similar articles Ganesha Associates 2013

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34. Family health program: Proposal for identification of risk factors for neuropsychomotor development • Objectives: To investigate the occurrence of delayed neuropsychological and motor development in a community assisted through the Family Health Program and to evaluate its association with possible biological, environmental and socioeconomic risk factors • Conclusions: The FHP was not only a valuable setting for developing studies of this nature but also an appropriate setting for child development follow-up Ganesha Associates 2013

35. Identification of risk factors for neuropsychomotordevelopment: a study within Brazil’s Family Health Program • Objectives: To investigate the occurrence of delayed neuropsychological and motor development and to evaluate their association with possible biological, environmental and socioeconomic risk factors • Conclusions:The statistical associations described suggest that less mother-child time, non-attendance of day care centersand father-child contact time were factors related to motor development delays. Ganesha Associates 2013

36. Hunt the hypothesis Ganesha Associates 2013

37. Do malnutrition and fluoxetine neonatal treatment program alterations in heart morphology? Abstract: Growth and development events are observed in all organisms and can be modified by exogenous factors such as nutritional changes. Drastic morphological and functional alterations may occur during a vulnerable stage of development. The aim of this study was to investigate if malnutrition and/or fluoxetine neonatal treatment program alterations in heart morphology during the postnatal period. The sample consisted of 48 albino Wistar male rats. The rats were divided into two groups: nourished and malnourished. Pharmacologic manipulation was performed during the suckling period. The animals of each group were divided into two subgroups: saline-nourished and saline-malnourished, treated with sodium chloride solution, and fluoxetine-nourished and fluoxetine-malnourished, treated with fluoxetine. Half of the individuals in each subgroup were weighed and sacrificed on day 30 and the other half on day 71. Myocardial perfusion was performed and the heart subsequently weighed. The ventricles were cross-sectioned into two parts, which were fixed, dehydrated and sectioned. There were differences in body weight, heart weight, cross-sectional area and perimeter of the heart and in the cross-sectional area and perimeter of the cardiac cells among the groups at the different ages. Malnutrition appears to program alterations in heart morphology. However, malnourished animals that had undergone drug treatment did not exhibit the same changes Ganesha Associates 2013

38. Introduction Long-term consequences in adult life dependent on environmental stimuli during critical periods of development (fetal, neonatal or infancy) have been evidenced by epidemiological and animal studies (Hales and Barker, 1992, Ozanne et al., 1998 and Lopes de Souza et al., 2008). The mechanism associated with these effects is called “programming”, whereby environmental aggression during a critical period of development would have permanent effects on the structure and function of the organs (Lucas, 1991). Nutritional status during the critical period of development has been considered an important inducer of programming in both animals and humans. A growth rate deficit, increased oxidative damage and changes in glucose/insulin metabolism have been observed in rats submitted early in life to either a maternal dietary-protein restriction (40–50% of normal intake) or to low-protein diet throughout gestation and lactation (Desai et al., 1996, Ozanne et al., 1998 and Toscano et al., 2008). In humans, a number of epidemiological studies have provided support to the association between low birth weight and metabolic diseases in adult life (Hales and Barker, 1992 and Ravelli et al., 1998). The effects of early malnutrition on cardiac development have been investigated. Malnutrition prevents growth and causes an overall deterioration of tissue, especially a severe loss of muscular tissue, including cardiac muscle (Bergman et al., 1988, Almeida and Mandarim-de-Lacerda, 2005 and Toscano et al., 2008). During its development, the heart is damaged by the adverse effects of malnutrition (Fioretto et al., 2002). Animal studies show that malnutrition reduces heart cell mass proportionally to weight loss (Alden et al., 1987, Pissaia et al., 1980, Vandewoude and Buyssens, 1992 and Webb et al., 1986). The interference in the growth and development processes caused by malnutrition is also seen in the balance of neurotransmitter systems. Regarding the serotonergic system, malnutrition in early life in rats reduces serotonergic fibers and serotonin (5-HT) reuptake sites in the hippocampus (Blatt et al., 1994). Even after short periods of food restriction, metabolic 5-HT changes and also changes in the levels of other substances, such as dopamine, were noted in rat pups (Ishida et al. 1997). It is well known that protein malnutrition early in life promotes an increase of 5-HT and norepinephrine levels in rat brain (Sobotka et al., 1974, Stern et al., 1975 and Resnick et al., 1979). There is also evidence that norepinephrine is increased in the heart of malnourished rats (Pissaia et al., 1980). Besides its action as a neurotransmitter, 5-HT plays a role in regulating the growth of neural and non-neural tissues (Buznicov et al., 2001). Serotonin is believed to act as a morphogenetic signal in rat embryos, possibly regulating the action or expression of other growth regulatory molecules (Yavarone et al., 1993). Manipulation of the serotonergic system may affect cardiovascular morphogenesis (Negibil et al., 2001) as well as regulating heart cell growth (Yavarone et al., 1993). According to these hypotheses, optimal serotonin levels may be mitogenic, although high concentrations of this amine seem to be inhibitory (Yavarone et al., 1993). The use of 5-HT reuptake inhibitors (SSRI) during development of the embryo decreased the cell proliferation in the myocardium, cardiac mesenchyma and endothelium growth (Yavarone et al., 1993). Fetal and early infancy environmental exposure can impair cardiovascular health and functioning (Mone et al., 2004). Among the cardiovascular problems that may be caused by environmental exposure is abnormal anatomic development (Mone et al., 2004). Therefore there is increasing evidence that the cardiovascular system is susceptible to external influences throughout gestation and after birth (Mone et al., 2004). Considering the nutritional and the neurotransmitters influences on body and heart development it would be very opportune to compare the consequences of the early malnutrition and 5-HT pharmacological manipulations on body and heart growth. The aim of this study was therefore to investigate if malnutrition and/or fluoxetine neonatal treatment program alterations in heart morphology. Ganesha Associates 2013

39. Introduction Besides its action as a neurotransmitter, 5-HT plays a role in regulating the growth of neural and non-neural tissues (Buznicov et al., 2001). Serotonin is believed to act as a morphogenetic signal in rat embryos, possibly regulating the action or expression of other growth regulatory molecules (Yavarone et al., 1993). Manipulation of the serotonergic system may affect cardiovascular morphogenesis (Negibil et al., 2001) as well as regulating heart cell growth (Yavarone et al., 1993). According to these hypotheses, optimal serotonin levels may be mitogenic, although high concentrations of this amine seem to be inhibitory (Yavarone et al., 1993). The use of 5-HT reuptake inhibitors (SSRI) during development of the embryo decreased the cell proliferation in the myocardium, cardiac mesenchyma and endothelium growth (Yavarone et al., 1993). Fetal and early infancy environmental exposure can impair cardiovascular health and functioning (Mone et al., 2004). Among the cardiovascular problems that may be caused by environmental exposure is abnormal anatomic development (Mone et al., 2004). Therefore there is increasing evidence that the cardiovascular system is susceptible to external influences throughout gestation and after birth (Mone et al., 2004). Considering the nutritional and the neurotransmitters influences on body and heart development it would be very opportune to compare the consequences of the early malnutrition and 5-HT pharmacological manipulations on body and heart growth. The aim of this study was therefore to investigate if malnutrition and/or fluoxetine neonatal treatment program alterations in heart morphology. Ganesha Associates 2013

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41. Choosing the right journal Ganesha Associates 2013

42. Impact factor statistics – PLoS Biology Ganesha Associates 2013

43. Communities of arbuscularmycorrhizal fungi in dry tropical forests of Northeast Brazil The arbuscularmycorrhizal 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 arbuscularmycorrhizal 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. Ganesha Associates 2013

44. Using eTBLAST to find similar articles Ganesha Associates 2013

45. Other titles included Oecologia, New Phytologist… Ganesha Associates 2013

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50. Arbuscularmycorrhizal fungi in a semiarid copper mining area in Brazil There are >160 species of arbuscularmycorrhizal 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 Trufem1983; Trufem1988, 1990; Trufem et al. 1994; Gomes and Trufem1998) and Santa Catarina (Stürmer and Bellei1994). In cultivated areas there are records for the States of São Paulo (Trufem and Bononi1985; Trufem et al. 1989, 1990; Grandi and Trufem1991; Carrenho et al. 2001) and Pernambuco (Maia and Trufem1990; 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 (Nogueira1996). An excess of Zn and Cu inhibits spore germination (Hepper1979), 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. Ganesha Associates 2013