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Competências Básicas de Investigação Científica e de Publicação Lecture 3: Reading and writing skills August 2014.

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Presentation on theme: "Competências Básicas de Investigação Científica e de Publicação Lecture 3: Reading and writing skills August 2014."— Presentation transcript:

1 Competências Básicas de Investigação Científica e de Publicação Lecture 3: Reading and writing skills August 2014

2 24 August 2012Ganesha Associates2 Problem definition Grant proposal Experiments Seminar Conference proceedings More experiments Writing-up Publication The scientific research process [Greatly simplified!] Key: Experiments Reading and writing Verbal communication

3 5 July 2012Ganesha Associates3 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

4 The importance of regular reading

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.

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7 9 September 2013Ganesha Associates CC BY 3.07

8 24 August 2012Ganesha Associates8 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

9 Nature News and Views format

10 Current Opinion review style

11 Systematic reviews

12 Search for reviews as a specific document type

13 24 August 2012Ganesha Associates13 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!

14 12 August 2013Ganesha Associates14 Styles of communication – Conversation – Meeting minutes – Chemical patent – Legal document, e.g. a contract, a will – Car owner manual – Yellow pages – Computer software – Newspaper article – Which styles are similar to those of a scientific journal article ?

15 Scientific writing is linear Scientific writing must be unambiguous and logical Since logic tends to be linear, learn to express yourself that way

16 Scientific writing has structure Title Summary Introduction Discussion Conclusions Document Sections Paragraphs Sentences Phrases

17 Phrases are the basic building blocks [Noun phrase][Verb phrase][Noun phrase] Breathing exercises improve functional exercise capacity in people with COPD. There are no consistent effects on dyspnoea or health- related quality of life. Outcomes were similar across all the breathing exercises examined. Treatment effects for patient-reported outcomes may have been overestimated owing to lack of blinding. Breathing exercises may be useful to improve exercise tolerance in selected individuals with COPD. However, these data do not suggest a widespread role for breathing exercises in the comprehensive management of people with COPD.

18 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: Treatment effects for un-blinded patient-reported outcomes may have been overestimated Lack of blinding may have led to an overestimate in the treatment outcomes reported by patients. Patients report better treatment outcomes due to lack of blinding Often writers will chain sentences using the item stressed in the preceding sentence as the context for the next.

19 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 bacteria- induced pain in mice. Instead, mechanical and thermal hyperalgesia in mice is correlated with live bacteria load rather than tissue swelling or immune activation.

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21 12 August 2013Ganesha Associates21 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

22 12 August 2013Ganesha Associates22 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. Structure tips – sentence order (edit)

23 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…

24 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 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

25 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. 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

26 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 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. 18/10/2013Ganesha Associates INSPIRATORY MUSCLE TRAINING IMPROVES REGIONAL LUNG VENTILATION DISTRIBUTION IN CHRONIC HEART FAILURE PATIENTS: A RANDOMIZED CONTROLLED CLINICAL TRIAL

27 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: A RANDOMIZED CONTROLLED CLINICAL TRIAL 18/10/2013Ganesha Associates

28 12 August 2013Ganesha Associates28 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

29 Break

30 12 August 2013Ganesha Associates30 Types of scientific writing – Grant application – Mestrado or Doutorado proposal – Published scientific article Abstract Brief communication Primary research article Review Methods/Techniques Supplementary content – Book chapter – Monograph – Patent – Conference proceedings

31 12 August 2013Ganesha Associates31 Scientific papers have a structure A scientific paper is a written report describing original research results whose format has been defined by centuries of developing tradition, editorial practice, scientific ethics and the interplay with printing and digital publishing services. The result of this process is that virtually every scientific paper has a title, abstract, introduction, materials and methods, results and discussion – the so-called IMRD structure. Even so, most publications have their own rules about a paper's format: So read the Journal ’ s Instructions for Authors first!

32 Instructions to authors General Information Types of Articles Submission Fee Publication Fee Policies Contact Information Preparing a Manuscript Regular Manuscripts Brief Communications Journal Clubs Letters to the Editor Invited Articles Submitting a Manuscript Review Process Requirements for Submission Submission Fee Revising/Finalizing a Manuscript Revisions Proofs Publication Fee Embargo Policy Cover Art NIH Public Access Policy Correcting Errors in Published Articles Corrections Retractions 12 August 2013Ganesha Associates32

33 Other guides for authors CONSORT, which stands for Consolidated Standards of Reporting Trials, encompasses various initiatives developed by the CONSORT Group to alleviate the problems arising from inadequate reporting of randomized controlled trials (RCTs). Nature has also produced a checklist is used to ensure good reporting standards and to improve the reproducibility of published results 12 August 2013Ganesha Associates33

34 12 August 2013Ganesha Associates34 Summary of an article’s main components Title Author details Keywords Abstract/Summary Introduction Materials and Methods Results Tables Figures Discussion References/Citations

35 12 August 2013Ganesha Associates35 More on simple rules Research proposals (and research articles) tell a story Slides by Susan Ruff Spring 2007 Each section has a specific purpose

36 12 August 2013Ganesha Associates36 Title A title should be the fewest possible words that accurately describe the content of the paper. Omit all waste words such as "A study of...", "Investigations of...", "Observations on...", etc. Remember, the title appears in the search results – so make it explicit And, indexing and abstracting services depend on the accuracy of the title, extracting from it keywords used for cross-referencing and computer searching. So, a badly-titled paper may never reach the audience for which it was intended!

37 12 August 2013Ganesha Associates37 Titles – some good examples Cognitive-behavioral strategies improve dyspnea and related distress in COPD. Reversal of Histone Lysine Trimethylation by the JMJD2 Family of Histone Demethylases Similar Frontal and Distinct Posterior Cortical Regions Mediate Visual and Auditory Perceptual Awareness. Breathing exercises for adults with asthma. Wntless is a Conserved Membrane Protein Dedicated to the Secretion of Wnt Proteins from Signaling Cells

38 12 August 2013Ganesha Associates38 Titles – some not so good examples Cloning and nucleotide sequencing of three heat shock protein genes (hsp90, hsc70, and hsp19.5) from the diamondback moth, Plutella xylostella (L.) and their expression in relation to developmental stage and temperature. (Result ?, length, abbreviations) Effect of docosahexaenoic acid-rich fish oil supplementation on human leukocyte function. (Result ?) Organization and methodology of early rehabilitation of the patients with cardioembolic stroke complicated by cardiac insufficiency. (Length)

39 12 August 2013Ganesha Associates39 Titles – some not so good examples improved Diamondback moth heat shock genes are expressed differentially according to developmental stage and temperature Docosahexaenoic acid-rich fish oil supplementation has a positive effect on human leukocyte function. Early rehabilitation of patients with cardioembolic stroke and cardiac insufficiency].

40 12 August 2013Ganesha Associates40 Names: How many do you have?

41 12 August 2013Ganesha Associates41 Choose, and stick with, a unique author name. Register with ORCID André Luiz Cabral Monteiro de Azevedo Santiago Clarissa Daisy Costa Albuquerque Eliane Maria Soares-Ventura Neide Santos Bethânia de Araújo Silva Amaral Maria Tereza Cartaxo Muniz Flávio José da Costa Ramos Cecília S.C. Melo Raquel dos Santos Vera Cruz Vera Lúcia Lins de Morais Terezinha de Jesus Marques–Salles Maria Auxiliadora de Queiroz Cavalcanti Galba Maria de Campos Takaki

42 12 August 2013Ganesha Associates42 Keywords The author keyword list provides the opportunity to add alternative indexing terms, in addition to those already present in the title. Judicious use of keywords may increase the ease with which interested readers can locate your article in a database such as SciELO or ScienceDirect.

43 Keywords Title – Keywords BK Channels in Cardiovascular Diseases and Aging – Calcium-activated potassium channels, BK, vascular smooth muscle cells, endothelium, aging, cardiovascular diseases Qualitative changes in fetal trabecular meshwork fibers at the human iridocorneal angle – Trabecular meshwork, Schlemm's canal, collagen, silver staining 12 August 2013Ganesha Associates43

44 12 August 2013Ganesha Associates44 Abstract The abstract should summarize the results and principal conclusions. A well-prepared abstract enables the reader to identify the basic content of a document quickly and accurately, and thus to decide whether to read the document in its entirety. Do not include details of the methods used unless the study is methodological, i.e. primarily concerned with methods.

45 12 August 2013Ganesha Associates45 Abstract The abstract, together with the title, must be self- explanatory as they are published separately from the paper in abstracting/indexing services Omit all references to the literature and to tables or figures Omit obscure abbreviations and acronyms even though they may be defined in main body of the paper.

46 12 August 2013Ganesha Associates46 A good abstract always has a well-defined structure It is known that white adipose tissue (WAT) serves as the primary energy depot in the body by storing fat. During development, fat cell precursors (i.e., preadipocytes) undergo a hypertrophic response as they mature into lipid-laden adipocytes. However, the mechanisms that regulate adipocyte size and mass remain undefined. Herein, we demonstrate that the membrane anchored metalloproteinase, MT1-MMP, coordinates adipocyte differentiation in vivo. In the absence of the protease, WAT development is aborted, leaving tissues populated by mini-adipocytes which render null mice lipodystrophic. Hence, MT1- MMP acts as a 3-D-specific adipogenic factor that directs the dynamic adipocyte- ECM interactions critical to WAT development.

47 12 August 2013Ganesha Associates47 A good abstract always has a well-defined structure It is known that white adipose tissue (WAT) serves as the primary energy depot in the body by storing fat. During development, fat cell precursors (i.e., preadipocytes) undergo a hypertrophic response as they mature into lipid-laden adipocytes. However, the mechanisms that regulate adipocyte size and mass remain undefined. Herein, we demonstrate that the membrane anchored metalloproteinase, MT1-MMP, coordinates adipocyte differentiation in vivo. In the absence of the protease, WAT development is aborted, leaving tissues populated by mini-adipocytes which render null mice lipodystrophic. Hence, MT1- MMP acts as a 3-D-specific adipogenic factor that directs the dynamic adipocyte- ECM interactions critical to WAT development.

48 12 August 2013Ganesha Associates48 Different Abstract styles – Background: Markers of inflammation such as high sensitivity C-reactive protein (CRP) were shown to be elevated in patients with hypertension. Small trials using statin therapy showed blood- pressure (BP) reductions, but it is unknown whether this association extends to larger populations. The objective of this study was to determine whether statin use was associated with better blood- pressure control in adults with hypertension and whether inflammation levels mediated this relationship. – Methods: This was a cross-sectional study of 2584 hypertensive adults aged _40 years with no known cardiovascular disease from the National Health and Nutrition Examination Survey 1999– Logistic regression models were calculated to determine whether there was an association between statin use and blood-pressure control. C-reactive protein was added to the full model to determine its impact on the association. – Results: Compared with people not using statin medication, significantly more statin users had their blood pressure under control (52.2% v 38.0%). After adjustment for demographic factors, statin users were two times (95% confidence interval [CI], 1.46 to 2.72) more likely to have their blood pressure under control (_140/90 mm Hg) than nonusers. After further adjustment for body mass index, diabetes, smoking, exercise, low-salt diet, and antihypertensive medications, the likelihood of having blood pressure under control remained more likely among statin users (odds ratio, 1.46; 95% CI, 1.05 to 2.05). The association between statin use and lower BP was most evident among participants who used antihypertensive medication as well as statins and was unchanged with the addition of CRP to the model. – Conclusions: Statin use was associated with a BP level _140/90 mm Hg in a representative sample of US adults with hypertension. Levels of CRP did not attenuate the association. Further studies are needed to explore the effects of statin use on blood pressure and to determine how best to apply this knowledge in clinical care. – From the American Journal of Hypertension

49 12 August 2013Ganesha Associates49 Resource value affects territorial defense by Broad- tailed and Rufous hummingbirds Territorial behavior of Broad-tailed (Selasphorous platycercus) and Rufous (Selasphorous rufus) hummingbirds in Colorado was measured at sites with feeders containing 10%, 20%, and 30% sucrose solutions, respectively. The presence or absence of territory holders, number of intruders, and intensity of defense were measured at the three levels of energy availability. Migrating Rufous Hummingbirds displaced Broad-tailed Hummingbirds from territories they had defended during the breeding season; Broad- tailed Hummingbirds then defended only lower quality sites. Both Broad-tailed and Rufous hummingbirds employed more energetically expensive behaviors when defending high quality sites, with longer chases more often supplemented with chip calls and hovering. Other investigators have suggested that chip calls and hovering are precursors to a chase. However, I found that chasing was the default response to the presence of an intruder. Chip calls and hovering were added to intensify a chase. In the few cases where chip calls were uttered or hovering occurred without a chase, Rufous Hummingbirds were more likely to exhibit this behavior than Broad-tailed Hummingbirds. ©2006 Journal of Field Ornithology.

50 12 August 2013Ganesha Associates50 Introduction The Introduction establishes why there was a need to conduct the study by placing your objectives within the context of the current literature. Thus the need for the new work should clearly flow from that carried out previously. Each logical step should be fully supported by appropriate references. At the end of the Introduction you should state clearly the specific scope and objectives of the new research.

51 12 August 2013Ganesha Associates51

52 12 August 2013Ganesha Associates52 An example of a problem Ectomycorrhizal fungi (EMF) have a fundamental role in nutrient absorption of many plant species. Tree species of ecological and economic relevance in reforestation programs depend on ectomycorrhizal symbiosis, especially in soils contaminated by mining activities. The ability of EMF to reduce the toxicity of heavy metal ions (e.g. copper) in their host plants is accompanied by the decrease of metal concentrations in the aerial part of the plant. Due to increased absorption of these metals by the EM roots and the accumulation in the extra radical mycelium, greater tolerance to such elements is achieved by the host. Research has been conducted to determine the sensitivity of EMF to a variety of potentially toxic metals to understand the diverse mechanisms through which the fungi may tolerate heavy metals. Enzymatic activity is important for the mobilization and transference of soil nutrients through EM fungi towards the host plant. In this study we investigate the effects of copper and phosphorus concentrations on mycelial growth and enzymatic activities of the EM fungi Pisolithus microcarpus, Chondrogaster angustisporus and Suillus sp. in two growth experiments.

53 12 August 2013Ganesha Associates53 Materials and Methods The main purpose of the 'Materials and Methods' section is to provide enough detail for a competent worker to repeat your study and reproduce the results. Equipment and materials available off the shelf should be described briefly (e.g. Licor underwater quantum sensor, Model LI 192SB) and sources of materials should be given if there is there is likely to be a variation in quality between suppliers. Modifications to equipment or equipment constructed specifically for the study should be carefully described in detail. The methods used to prepare unusual reagents, fixatives, and stains should also be described in detail.

54 12 August 2013Ganesha Associates54 Materials and Methods Be precise in describing measurements and include the confidence intervals associated with your measurements. Ordinary statistical methods should be used without comment; advanced or unusual methods may require a literature citation. So there is a pattern emerging. Standard techniques can be dealt with quickly, but modified or new techniques should be described with a view to enabling replication Show your materials and methods section to a colleague. Ask them if they think they would have difficulty in repeating your study

55 12 August 2013Ganesha Associates55 Results Write this section first! Display items (figures and tables) are central in this section. Get them prepared and complete all of your statistical analysis before you start writing Present your results in the order that makes the overall significance of your work clearest. Note that this may not necessarily match the order in which the experiments were performed.

56 12 August 2013Ganesha Associates56 Results Many readers will start reading your paper by looking at the figures and tables. The conclusions to be drawn from individual figures and tables should be clear from the titles and captions used, i.e. they should be designed as self-contained units of information. The main text should read logically and be understandable without the reader initially having to refer back and forth repeatedly to the figures and tables So don’t say ”The relationship between bird species richness and habitat complexity is clearly evident from Fig. 1". Say instead "Bird species richness increased with habitat complexity (Fig. 1)".

57 12 August 2013Ganesha Associates57 Table design example Form/% NaCl 0%2%4%6%8% Globose 8.38 (±1.15)8.49 (±0,90)9.67 (±1.29)10,72 (±2,88)- Subglobose 9.38 (±1.44) x 8.44 (±1.18) 9.93 (±1.40) x 8.94(±2.8) 10.2 (±2.42) x 9.19 (±0.97) (±0.9) x 9.93 (±1.41) (±1.13) x 10.3 (±0.93) Subglobose to ellipsoidal 11.4 (±1.5) x 9.60 (±1,.2) (±0.64) x 9.30 (±1.15) (±1.0) x (±0.10) (±1.28) x (±0.82) (±1.92) x (±1.12) Ellipsoidal (±0.43) x 9.9 (±2.66) (±3.60) x 10.5 (±1.54) (±1.51) x 9.12 (±1.14) (±1.72) x 9.75 (±1.22) (±1.66) x (±1.23) Caption - Average size (μm) of C. elegans sporangioles in Hesseltine & Anderson culture media with 0, 2, 4, 6 and 8% NaCl at 20ºC. Why is this a bad example?

58 12 August 2013Ganesha Associates58

59 Discussion - structure Don’t repeat the results section Answer the research question(s) posed Emphasize the major finding(s) first What is your major conclusion, based on the results you have presented? Interpret your results … Compare with other studies Same or different? Possible reasons why? Unexpected results Briefly describe any limitations Sample sizes How could experiments be improved? Restate major conclusion(s) Possible applications and implications Suggest future work 12 August 2013Ganesha Associates59

60 12 August 2013Ganesha Associates60 References - purpose By placing references at strategic points in the text, the reader is able to retrieve the evidence being used to support a particular argument or statement In this way the reader is able to recreate the logical train of thought that led the author to a particular conclusion Any mistakes in reference use could result in rejection of your article

61 References - format References [1] Kotsis V, Stabouli S, Karafillis I, Nilsson P. Early vascular aging and the role of central blood pressure. J Hypertens. 2011;29(10):1847–53. [PubMed]PubMed [2] Barodka VM, Joshi BL, Berkowitz DE, Hogue CW, Jr, Nyhan D. Review article: implications of vascular aging. Anesth Analg. 2011;112(5):1048–60. [PMC free article] [PubMed]PMC free articlePubMed [3] Toro L, Marijic J, Nishimaru K, Tanaka Y, Song M, Stefani E. Aging, ion channel expression, and vascular function. Vascul Pharmacol. 2002;38(1):73–80. [PubMed]PubMed [4] Panza F, D’Introno A, Colacicco AM, Capurso C, Parigi AD, Capurso SA, Caselli RJ, Pilotto A, Scafato E, Capurso A, Solfrizzi V. Cognitive frailty: Predementia syndrome and vascular risk factors. Neurobiol Aging. 2006;27(7):933–40. [PubMed]PubMed [5] Jackson WFn. Ion channels and vascular tone. Hypertension. 2000;35(1 Pt 2):173–8. [PMC free article] [PubMed]PMC free articlePubMed 12 August 2013Ganesha Associates61

62 12 August 2013Ganesha Associates62 Plagiary and ‘language re-use’ If you use somebody else’s words, make this clear by using quotation marks and a reference The act of plagiarizing or appropriating the ideas, writings, or inventions of another without due acknowledgment; specifically the stealing of passages either for word or in substance, from the writings of another and publishing them as one's own It is now easy for publishers to detect plagiarism

63 Covering letter format Address to the editor personally State your manuscript title and publication type Give a brief background, rationale and description of your results Explain the importance of your findings and why they would be of interest to the journal’s target audience Supply details of possible reviewers

64 The “write” order 12 August 2013Ganesha Associates64

65 12 August 2013Ganesha Associates65 Common manuscript problems Failure to state the purpose of the study in the title, abstract, introduction… Failure to keep function of sections clear and distinct, e.g. merge results and discussion Including non-essential data Treating the Introduction and/or Discussion as an opportunity to review the entire field Not following Instructions to Authors

66 A letter of rejection Dear Author, We have received the reports from our advisors on your manuscript XYZ-D “Title********************************". With regret, I must inform you that, based on the advice received, I have decided that your manuscript cannot be accepted for publication in the Journal of Imaginary Microbiology. Below, please find the comments for your perusal. You are kindly requested to also check the website for possible reviewer attachment(s). I would like to thank you very much for forwarding your manuscript to us for consideration and wish you every success in finding an alternative place of publication. With kind regards, Editor

67 What to do next Unconditional rejection – Editor offers no opportunity for appeal – Show comments to colleagues – Revise as though the rejection was conditional – Submit to a different journal Conditional rejection – Regard this as an opportunity to improve your paper – Show comments to colleagues – Respond to all comments and record your actions in a covering letter – Consider submitting to a better journal!

68 Reviewer comments - example The paper needs to be formatted properly for the journal. This reviewer was only able to find information for papers submitted with Introduction, materials and methods, results and discussion sections while much of this is in the paper the format appears to be incorrect even for a short communication. It was difficult to find the number of samples taken or to understand the experimental set-up as written; changing the style to a more traditional journal format as suggested above would help with this. In addition the most important reference Brown et al 2013 is missing!

69 17 June 2013Ganesha Associates69 This paper describes clinical and cytogenetic finding in a child with retinoblastoma who had an aggressive fatal course. The authors postulate that this may be related to changes in chromosome 6. However, it is difficult to see how the findings here either promote or negate that hypothesis. In addition several other problems should be addressed: a.Abstract, line 9: could (not should) b.Abstract: define IO c.Staging details at the time of initial diagnosis are inadequate. Were scans done of the head? chest? abdomen? pelvis? bone? d.One assumes that the right eye was normal at initial diagnosis but this is not stated. Reviewer comments - example

70 Referee’s comments can be confusing

71 Referee response letter Respond to all of the reviewers’ comments Describe all of the changes you have made in the letter Also describe the reasons why you have not made suggested changes Make it easy to see the changes have made in the manuscript itself – Refer to line and page numbers – Different color font – Highlight the text

72 Referee response letter If you disagree with the reviewer with the reviewer be clear why: – Reviewer Comment: In your analysis of the data you have chosen to use a somewhat obscure fitting function (regression). In my opinion, a simple Gaussian function would have sufficed. Moreover, the results would be more instructive and easier to compare to previous results. – Author response: We agree with the reviewer that a simple Gaussian fit would facilitate comparison with the results of other studies. However, our tailored function allows for the analysis of the data in terms of the Smith model [Smith et al, 1998]. We have added two sentences to the paper (page 3 paragraph 2) to explain the use of this function and Smith’s model.

73 Journal of Voice Voice problems of future speech-language pathologists. The impact of phonation mode and vocal technique on vocal fold closure in young females with normal voice quality Acoustic voice analysis of prelingually deaf adults before and after cochlear implantation. Quantifying component parts of indirect and direct voice therapy related to different voice disorders. Acoustic and electroglottographic analyses of nonpathological, nonmodal phonation. The effect of experience on classification of voice quality. The vocal clarity of female speech-language pathology students: an exploratory study. Obstacles to communication in children with cri du chat syndrome. Current and emerging concepts in muscle tension dysphonia: a 30-month review.

74 Journal of Applied Oral Science 2.1 Illustrations and Tables The illustrations (photographs, graphs, drawings, charts, etc.), regarded as figures, should be limited to the least amount possible and should be uploaded in separate files, consecutively numbered with Arabic numbers according to the order they appear in the text Photographs should be sent in original colors and digitized in.jpg or tif formats with at least 10 cm width and at least 300 dpi. These illustrations should be provided in supplementary files and not inserted in the Word document The corresponding legends for figures should be clear, concise and typed at the end of the manuscript as a separate list preceded by the corresponding number The tables should be logically arranged, consecutively numbered with Arabic numbers. The legend shall be placed on the top of the tables. Tables should be open in the right and left laterals Footnotes should be indicated by asterisks and restricted to the least amount possible.

75 Results section A total of 60 direct speech sessions were completed during the 3 phases of the program. The assessment procedures described above were performed before and after the intensive speech therapy and bulb reduction program. As presented and described in Figure 7 all speech alterations present before the interventions were absent after the program (Figure 7).Figure 7

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77 Journal of Voice Legends to figures should be brief, specific, and explanatory. They should not unduly repeat information already given in the text

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79 PLoS Medicine Figure Legends The aim of the figure legend should be to describe the key messages of the figure, but the figure should also be discussed in the text. An enlarged version of the figure and its full legend will often be viewed in a separate window online, and it should be possible for a reader to understand the figure without switching back and forth between this window and the relevant parts of the text. Each legend should have a concise title of no more than 15 words. The legend itself should be succinct, while still explaining all symbols and abbreviations. Avoid lengthy descriptions of methods.

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81 Alternatives: PLOS ONE PLOS ONE is a journal that publishes reports of original research from all disciplines within science and medicine. PLOS ONE will rigorously peer-review manuscripts and will publish all papers that are technically sound. Judgments about the importance of any particular paper are made after publication by the readership, I,e, citations, article downloads. 17 June 2013Ganesha Associates81

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