Writing scientific papers in English successfully: A complete roadmap

1. Writing scientific papers in English successfully: A complete roadmap Osvaldo N. OliveiraJr. chu@ifsc.usp.br Universityof São Paulo NILC: nilc.icmc.usp.br

2. amazon.com/dp/8588533979 Gráfica Compacta compactg@terra.com.br +16 33711404

3. “Interesting and Unpublished is equivalent to non-existent” George M. Whitesides, Adv. Mat., 16, 1375, 2004 AcademicvsScientificWriting ScientificWriting & ScientificMethod Getting the message across • What are the contributions of your work? • Why are these contributions important? Organizing ideas and results • What are your key findings? • What is the importance of your key findings to the field? • Are your findings complete? If not, what is missing? • What is the supporting evidence? • Do they provide a basis for publication? Scientists publish ideas and concepts, NOT results!

4. Publishing Ideas Ideas Implementation of the Research Results Ideas New Ideas? Output (Papers, Thesis, etc.)

5. Corpus Linguistics “Corpus linguistics is the study of language as expressed in samples (corpora) of "real world" text. This method represents a digestive approach to deriving a set of abstract rules by which a natural language is governed or else relates to another language”. (Wikipedia) Based on the assumption that language is probabilistic, that is, that certain combinations of words have a higher probability of occurring than others, although these other ones may be perfectly grammatical (Tagnin, 2014). A Corpus is a large and structured set of texts (written or spoken). Machine learning for NLP is always based on corpus

6. Using the COCA corpus 1 2 3 4

7. The structure of a paper Title, Authors and Affiliations Abstract Introduction General Materials and Methods Specific Results Discussion General Conclusions References Hill et al.,, TESOL Quarterly, 16: 333, 1982:

8. The Abstract • Setting/Background • Purpose • Methodology • Main Results • Conclusion Informative Contains all the relevant information of the paper X Descriptive Describes only the nature/purpose of the study

9. The Introduction

10. The Introduction C4: Purpose S1 Indicating the main purpose S1A Solving a conflict among authors S1B Presenting a novel approach, or methodology, or technique S1C Presenting an improvement in a research topic S1D Presenting an extension of an author's previous work S1E Proposing an alternative approach S1F Presenting a comparative work S2 Specifying the purpose S3 Introducing more purposes C5: Methodology S1 Listing criteria or conditions S2 Describing methods and materials S3 Justifying choices for methods and materials C6: Main Results S1 Presenting/emphasizing results S2 Commenting on the results C7: Value of the Research S1 Stating the value of the work C8: Layout of the article S1A Outlining the parts of the article S1B Listing issues to be addressed Model for Writing Tools Aluísio and Oliveira, 1995 C1: Setting S1 Introducing the research topic within the research area S2 Familiarizing terms, objects, or processes S3 Arguing about the topic prominence C2: Review S1 Historical review S2 Current trends S3 General-to-specific ordering for citations S4 Progress in the area S5 Requirements for the progress in the area S6 State-of-the-art S7 Compounding reviews of the literature and their gaps S8 Citations grouped by approaches C3: Types of Gap S1 Unresolved conflict or problem among previous studies S2 Limitations of previous work S3 Raising questions

11. The AMADEUS strategy Aluísio & Oliveira, 1995 (www.nilc.icmc.usp.br) Learning by doing What is conventionality in language? Contrary to common belief, a very large part of language is not compositional, which means it is not created on the spur of the moment. Rather, it is made up of prefabricated chunks, that is, fixed or semi-fixed combinations of words. Mastering these chunks and using them appropriately is what makes a language sound natural and fluent (Tagnin, 2014).

12. Exploiting Corpus Linguistics Why are textual patterns of special interest? The recurrent use of textual patterns is said to be closely associated with fluent linguistic production Do novice and expert writers use similar patterns? Scholars haveshownthatthelanguageproducedbystudentsandnovicewritersisdifferentfromthatof experts, irrespectiveofwhethernovices are nativeor non-native speakers ofEnglish. Carmen Dayrell - 2014

13. Results from Corpus Linguistics Stating the purpose of the study: Abstracts from Life and Health Sciences(Dayrell et al 2014)

14. Learning by Doing AMADEUS strategy learning by example through critical analysis of scientific discourse (corpus linguistics) It takes only a few minutes to say how to do it BUT It may take years to learn how to do it

15. Learning by Example Observe how others do it Imitate Note the structure of the language Do not copy “as is” Factual information is your own

16. Plagiarism You may cite others’ words, data Using your own words Do not copy verbatim Other authors’ text From your earlier papers

17. Step 1 Select texts from reliable sources Are theywell-written? Produced by native speakers? Read material critically, annotate expressions that convey important messages for your work

18. Step 2 Compile expressions and sentences Mark distinct messages This procedure should be part of your learning life Never stop doing it!

19. Step 3 Classify materials according to schemata of a scientific paper

20. Classification: Strategy 1 Assign expressions to pre-defined schemes, e.g. Where does it fit? Introduction? Methods? Results? Advantage: easier and quicker Disadvantage: lack of practice reshuffling material

21. G.M. Whitesides et al.,Electrostatic self-assembly of macroscopic crystals using contact electrification,Nature Materials2, 241–245 (2003) Self-assembly of components larger than molecules into ordered arrays is an efficient way of preparing microstructured materials with interesting mechanical and optical properties. Although crystallization of identical particles or particles of different sizes or shapes can be readily achieved, the repertoire of methods to assemble binary lattices of particles of the same sizes but with different properties is very limited. This paper describes electrostatic self-assembly of two types of macroscopic components of identical dimensions using interactions that are generated by contact electrification. The systems we have examined comprise two kinds of objects (usually spheres) made of different polymeric materials that charge with opposite electrical polarities when agitated on flat, metallic surfaces. The interplay of repulsive interactions between like-charged objects and attractive interactions between unlike-charged ones results in the self-assembly of these objects into highly ordered, closed arrays. Remarkably, some of the assemblies that form are not electroneutral—that is, they possess a net charge. We suggest that the stability of these unusual structures can be explained by accounting for the interactions between electric dipoles that the particles in the aggregates induce in their neighbors.

22. 1) Context:Self-assembly of components larger than molecules into ordered arrays is an efficient way of preparing microstructured materials with interesting mechanical and optical properties. 2) GAP:Although crystallization of identical particles or particles of different sizes or shapes can be readily achieved, the repertoire of methods to assemble binary lattices of particles of the same sizes but with different properties is very limited. 3) Purpose:This paper describes electrostatic self-assembly of two types of macroscopic components of identical dimensions using interactions that are generated by contact electrification. 4) Methodology:The systems we have examined comprise two kinds of objects (usually spheres) made of different polymeric materials that charge with opposite electrical polarities when agitated on flat, metallic surfaces. 5) Results:The interplay of repulsive interactions between like-charged objects and attractive interactions between unlike-charged ones results in the self-assembly of these objects into highly ordered, closed arrays. Remarkably, some of the assemblies that form are not electroneutral—that is, they possess a net charge. 6) Conclusions:We suggest that the stability of these unusual structures can be explained by accounting for the interactions between electric dipoles that the particles in the aggregates induce in their neighbors. Abstract

23. Classification: Strategy 2 Select a large number of expressions (hundreds!) Classify them later Advantage: more efficient Disadvantage: more time-consuming

24. Step 4 Practice Identify distinct ways of conveying rhetorical messages Example This ……. …….. the ….… paperaddressesproblem letteranalyzescase

25. Extract from original corpus a) Importance of the field, general interests, etc. There has been substantial interest in the fabrication of ... b) Previous reports on related work. Several papers have reported measurements aimed at obtaining evidence for, and insight into, ... processes in ... c) What is lacking in the field. Although significant advances have been made in the understanding of how ... (something) influences ... (another), very little further attention appears to have been given to the ... d) What the present work does. The purpose of the work reported here was to study the influence of ... on the ... f) Layout or Outline of the paper The organisation (outline) of the (this) paper is as follows. In Section II we describe ... The ... is presented in section III. In Sec. II we solve the ... equation giving expressions for ... This is necessary for the work of Sec. III, in which the extended ... equation is derived. Numerical results of the theory are given in Sec. IV, together with a comparison with ... and... calculations. Setting Review of Literature Gap Purpose Structure See also: Academic Phrasebank – by John Morley

26. Step 5 Fill in the content with your own material Continue to enrichthe options by selecting additional expressions (step 2) Identify additional helpful messages (step 4)

27. Repeat process with the selected expressions Classify them according to rhetorical message Example describe, contrast, confirm, define, compare, introduce Step 6

28. Step 6 Explained Goal: collect expressions to (1) retrieve as needed and (2) help you analyze specific contents Continue selecting expressions and identifying their messages

29. Step 7 Work on full text segments instead of individual sentences Repeat procedures in step 5 (fill-in) Connect sentences for coherence Compile a list including terms: however, in contrast, indeed, on the other hand, furthermore, nevertheless, since, because

30. Step 8 Time to produce a complete section of a paper Select subcomponents Implement them using material from previous steps Check use of connectives and coherence

31. Step 9: Edit text Check spelling and grammar Eliminate unnecessary words Check consistency of subcomponents and their inter-relationship Analyze contents for Completeness and accuracy

32. Keep in Mind From the very beginning, you must provide the reader with Your most important Findings Contributions

33. Preparing your own corpus • Select papers and books • Select expressions and mark them • Paste them on a file with the structure of a paper • Classify the expressions according to rhetorical messages (summarize, describe, exemplify, oppose, explain, justify, compare, contrast, etc.

34. The Introduction C4: Purpose S1 Indicating the main purpose S1A Solving a conflict among authors S1B Presenting a novel approach, or methodology, or technique S1C Presenting an improvement in a research topic S1D Presenting an extension of an author's previous work S1E Proposing an alternative approach S1F Presenting a comparative work S2 Specifying the purpose S3 Introducing more purposes C5: Methodology S1 Listing criteria or conditions S2 Describing methods and materials S3 Justifying choices for methods and materials C6: Main Results S1 Presenting/emphasizing results S2 Commenting on the results C7: Value of the Research S1 Stating the value of the work C8: Layout of the article S1A Outlining the parts of the article S1B Listing issues to be addressed Model for Writing Tools Aluísio and Oliveira, 1995 C1: Setting S1 Introducing the research topic within the research area S2 Familiarizing terms, objects, or processes S3 Arguing about the topic prominence C2: Review S1 Historical review S2 Current trends S3 General-to-specific ordering for citations S4 Progress in the area S5 Requirements for the progress in the area S6 State-of-the-art S7 Compounding reviews of the literature and their gaps S8 Citations grouped by approaches C3: Types of Gap S1 Unresolved conflict or problem among previous studies S2 Limitations of previous work S3 Raising questions

35. Resources & Tools in AMADEUS Authoring Writing Learning Assessing Processes Reference Tool Support Tool Critiquing Tool CAPTEAP Module Control Tools Standard expressions and chunks of texts Schematic structures Strategies to write paragraphs Critiques based on criteria for submission Question items Resources By Sandra Aluísio and her team

36. Scipo-Farmácia Web-based tool based on AMADEUS Support Tool with • Knowledge base of selected, published English papers in the field of Pharmaceutical Sciences V.D. Feltrim et al, ArgumentativeZoningAppliedtoCritiquingNovices’ Scientific Abstracts. Springer (2005)

37. Details of Scipo-Farmácia • Each sentence classified according to main components of scientific discourse • Abstract: • Background, Gap, Purpose, Methodology, Main Results, and Conclusion • Components further classified in strategies • Arguing about the topic prominence • Familiarizing terms or objects or processes • Listing criteria or conditions • Indicating/Describing materials or methods

38. Scipo-Farmácia Interface

39. What kind of papers get rejected in pre-refereeing? • Incremental papers – a very small advance on earlier work. This is not enough for many quality journals • Papers that are outside the journal’s scope • Papers that do not have enough content or new data for the journal - the expected quality level may vary between journals • Papers that reproduce earlier work – including text and including the author’s own previous work

40. Top 10 tips for getting published

41. Do… • Check the literature for work in your field to check for similar results • Use appropriate references that show context of your work and why it is new and significant • Consider who you are writing for – specialist or non-specialist • Decide which journal will be most appropriate and check the author guidelines; also check other articles in the journal for style • Write a clear title and abstract – this will be what most people will see first.

42. Do… • Avoid speculation or anecdotes – keep to the facts • Keep it concise – even when there are no limits as it makes it easier to read your article. Clearly state your conclusions • Allow time for rewriting • Include a cover letter outlining the main achievements of the work and why it is a good fit for your journal of choice • Get a colleague to read your article before submitting it to the journal

43. Problema Escrever um Abstract para um trabalho de biossensores, em que: Background: Doenças ou processos difíceis de detectar. Purpose: Produzir biossensor com alta sensibilidade e seletividade. Results: Filmes nanoestruturados fornecem arquitetura adequada para os sensores, com alta sensibilidade. Também é usada microfluídica. Conclusion: Há implicações para outras áreas.

44. Carnall JMA et al. (SCIENCE, 2010)    Abstract: Self-replicating moleculesare likely to have played an important role in the origin of life, and a small number of fully synthetic self-replicators have already been described. Yet it remains an open question which factors most effectively bias the replication toward the far-from-equilibrium distributions characterizing even simple organisms. (Background and gap) We report here two self-replicating peptide-derived macrocycles that emerge from a small dynamic combinatorial library and compete for a common feedstock. Replication is driven by nanostructure formation, resulting from the assembly of the peptides into fibers held together by beta sheets. Which of the two replicators becomes dominant is influenced by whether the sample is shaken or stirred. These results establish that mechanical forces can act as a selection pressure in the competition between replicators and can determine the outcome of a covalent synthesis.

45. Eid, John et al, SCIENCE 2009   Abstract: We present single- molecule, real- time sequencing data obtained from a DNA polymerase performing uninterrupted template- directed synthesis using four distinguishable fluorescently labeled deoxyribonucleoside triphosphates (dNTPs). We detected the temporal order of their enzymatic incorporation into a growing DNA strand with zero- mode waveguide nanostructure arrays, which provide optical observation volume confinement and enable parallel, simultaneous detection of thousands of single- molecule sequencing reactions. (Results) Conjugation of fluorophores to the terminal phosphate moiety of the dNTPs allows continuous observation of DNA synthesis over thousands of bases without steric hindrance. The data report directly on polymerase dynamics, revealing distinct polymerization states and pause sites corresponding to DNA secondary structure. Sequence data were aligned with the known reference sequence to assay biophysical parameters of polymerization for each template position. Consensus sequences were generated from the single- molecule reads at 15- fold coverage, showing a median accuracy of 99.3%, with no systematic error beyond fluorophore- dependent error rates.

46. Molecular Confinement Accelerates Deformation of Entangled Polymers During Squeeze Flow Rowland HD, SCIENCE 2008 Abstract: The squeezing of polymers in narrow gaps is important for the dynamics of nanostructure fabrication by nanoimprint embossing and the operation of polymer boundary lubricants. (Methodology) We measured stress versus strain behavior while squeezing entangled polystyrene films to large strains. In confined conditions where films were prepared to a thickness less than the size of the bulk macromolecule, resistance to deformation was markedly reduced for both solid- glass forging and liquid- melt molding. For melt flow, we further observed a complete inversion of conventional polymer viscosity scaling with molecular weight. Our results show that squeeze flow is accelerated at small scales by an unexpected influence of film thickness in polymer materials.

47. Yeung T et al. SCIENCE (2008) Abstract: Electrostatic interactions with negatively charged membranes contribute to the subcellular targeting of proteins with polybasic clusters or cationic domains. Although the anionic phospholipid phosphatidylserine is comparatively abundant, its contribution to the surface charge of individual cellular membranes is unknown, partly because of the lack of reagents to analyze its distribution in intact cells. We developed a biosensor to study the subcellular distribution of phosphatidylserine and found that it binds the cytosolic leaflets of the plasma membrane, as well as endosomes and lysosomes. (Methodology + Results) The negative charge associated with the presence of phosphatidylserine directed proteins with moderately positive charge to the endocytic pathway. More strongly cationic proteins, normally associated with the plasma membrane, relocalized to endocytic compartments when the plasma membrane surface charge decreased on calcium influx.

48. Bornhop et al, SCIENCE (2007)   Abstract: Free-solution, label-free molecular interactions were investigated with back-scattering interferometry in a simple optical train composed of a helium-neon laser, a microfluidic channel, and a position sensor. Molecular binding interactions between proteins, ions and protein, and small molecules and protein, were determined with high dynamic range dissociation constants (K-d spanning six decades) and unmatched sensitivity (picomolar K-d's and detection limits of 10,000s of molecules). With this technique, equilibrium dissociation constants were quantified for protein A and immunoglobulin G, interleukin-2 with its monoclonal antibody, and calmodulin with calcium ion Ca2+, a small molecule inhibitor, the protein calcineurin, and the M13 peptide. The high sensitivity of back-scattering interferometry and small volumes of microfluidics allowed the entire calmodulin assay to be performed with 200 picomoles of solute. (Results + Conclusion)

49. Schroder L, SCIENCE (2006)  Abstract: A magnetic resonance approach is presented that enables high-sensitivity, high-contrast molecular imaging by exploiting xenon biosensors. These sensors link xenon atoms to specific biomolecular targets, coupling the high sensitivity of hyperpolarized nuclei with the specificity of biochemical interactions. We demonstrated spatial resolution of a specific target protein in vitro at micromolar concentration, with a readout scheme that reduces the required acquisition time by >3300-fold relative to direct detection. This technique uses the signal of free hyperpolarized xenon to dramatically amplify the sensor signal via chemical exchange saturation transfer (CEST). Because it is similar to 10,000 times more sensitive than previous CEST methods and other molecular magnetic resonance imaging techniques, it marks a critical step toward the application of xenon biosensors as selective contrast agents in biomedical applications. (Conclusion).

50. Self-replicating moleculesare likely to have played an important role in the origin of life, and a small number of fully synthetic self-replicators have already been described. Yet it remains an open question which factors most effectively bias the replication toward the far-from-equilibrium distributions characterizing even simple organisms. (Background and gap) Chagas’ disease is likely to have been one of the most important neglected diseases, and a small number of methods have already been developed to detect it. Yet it remains an open question which factors most affect the detection. We detected the temporal order of their enzymatic incorporation into a growing DNA strand with zero- mode waveguide nanostructure arrays, which provide optical observation volume confinement and enable parallel, simultaneous detection of thousands of single- molecule sequencing reactions. (Results) We detected the presence of antibodies against T. Cruzi with nanostructured films, which provide molecular recognition processes and enable parallel, simultaneous detection of Chagas’ disease and Leishmaniasis. The squeezing of polymers in narrow gaps is important for the dynamics of nanostructure fabrication by nanoimprint embossing and the operation of polymer boundary lubricants. (Methodology) The organization of polymeric nanostructured films has been exploited in the fabrication of sensing units by the layer-by-layer technique.