Prepared for : LPPM-UNSOED

1. Prepared for : LPPM-UNSOED PUBLISH OR PERISH ! WELL-WRITTEN SCIENTIFIC PAPER Low performance, it is not a duplication …….. Supreme performance, a Nobel-winning publication Presented by : Dr. Agung Dhamar SYAKTI CENTER FOR MARITIME BIOSCIENCE STUDIES INSTITUTE FOR RESEARCH AND COMMUNITY EMPOWERMENT JENDERAL SOEDIRMAN UNIVERSITY 2016

2. Dr. Agung Dhamar Syakti Singakerta, 27 Oktober 1975 HIGHLIGHTED CURRICULUM VITAE • Educational Backgound • 2004 – Dr. (AnalyticalChemistry) – Aix Marseille University (France) • 2000 – DEA. (Bioscience Marine) - Aix Marseille University (France) • 1998 – S.Pi.(Marine Science) – Univesity of Riau • 23 International publications Rank-A • Environmental Research (4.4; 2004, 2005) • Journal of Lipid Research (4.4; 2004) • Science of the Total Environment (4.1, 2014) • Organic Geochemistry (3.1; 2006) • Marine Pollution Bulletin (3.0; 2013) • Environental Science and Pollution Research (2.8; 2012a,b) • Journal of Chromatography B (2.7; 2005) • Marine Chemistry (2.7; 2007) • Research in Microbiology (2.7; 2006) • Etc… • 20 national/regional publications • 30 Scientific communications • 2 Handbooks h-index: 9 • Current assignments • Head – CMBS-Unsoed • Editor-in-Chief OmniAkuatika • Lecturer – FMSF-Unsoed • Senior Scientist –CCMRS-IPB

3. Reviewing Task Experiences • International • Environ. Pollut. (Elsevier) • Bioremed. J. (Taylor and Francis) • Environ. Sci. Pollut. Res.(Springer) • Chem. Eng. Technol. (Willey VCH Verlag) • RSC Adv. (Royal Society of Chemistry) • etc… • National • DIKTI’s National Reviewer for competitive grant schemes • DEPIK (Unsyiah) • JurnalTeknologiIndustriPertanian (IPB) • BIOTROPIA (Seamo-Biotrop), etc… Editorial Task Experiences International Guest Editor : Regional Science in Marine Science (Elsevier) National Editor-in-Chief : Omni-Akuatika (Accedited by Ristekdikti) • Others : • J. Environ. Biotech. (Bioremediation Forum) • Jurnal Perikanan dan Kelautan (UR) • Marisphere (CCMRS-IPB)

4. University Papers (February) Papers (August) Papers (September) UNSOED 207 241 250 UIN 157 217 222 UNDIP 915 1179 1264 IPB 1988 2303 2508 UGM 2825 3637 3931 UI 4297 4830 5029 ITB 5245 6185 6388 Via SCOPUS platform (2016) • Data reliabilities • References materials and Dbase • Editing service

5. OUTLINES HOW JOURNALS WORK OBJECTIVES : SKILL IMPROVEMENT PRIOR TO PUBLICATION OF THEIR RESEARCH FINDING PRE-WRITTING CONSIDERATIONS 1- Style 2- Tips SCIENTIFIC PAPER Composition 1- Title 2- Abstract 3- Introduction 4- Methods 5- Results 6- Discussion 7- Refs and Acknowledgment REVISING A MANUSCRIPT ETHICS CONCLUDING REMARKS AND PERSPECTIVES

6. HOW JOURNALS WORK

7. Here we go….. Publisher Editor-in-Chief Reviewer #1 Reviewer #2 Handling Editor Editorial officer Author(s) Editorial officer Editor-in-Chief Author Handling Editor Reviewer Publisher

8. Publishing Process START PaperSubmission Author(s) proof Final Editing Publication DataBase input + RefNumber Corrected Proofs FINISH Handling Editor assignment Accepted N Revising Peer review assignment Rejection Notification Author(s) Editorial officer N Referee report Accepted Major/Minor revision suggestion Editor-in-Chief Handling Editor Reviewer Publisher

9. 1. Evaluation form for reviews, e.g. • original • contribute to body of knowledge in the journal • coherent/logic argument • new data and new findings can be generalized • quality of empirical analysis • 2. Decision: Accept, Minor Revisions, Major Revisions, Reject • 3. Course time: 2-3 months per review round, acceptance can be 3 month to 2 years from initial submission.

10. PRE-WRITING CONSIDERATIONS

11. Style Be clear and brief • Prepare, write, re-write • Readers go straight to your results • Use the minimum number of words (BRIEF) • Many phase can be replaced by a single word “Everything should be made as simple as possible, but not simpler” (Albert Einstein) • Avoid giving too much introductory materials • Refs should be directly relevance to your results Be objective and accurate • Unbiased and honest • Consider opposing points of view • Minimize the use of personal pronouns

12. The results should include all relevance data you obtained • State any problems with the data (stat + conclusion) • Everything must be consistent (Table + Figure + text) • Avoid the use of casual and imprecise language AvoidBetter nowadays presently, currently despite the fact that although goes under the name of is called on the contrary in contrast (up) until now to date be that as it may however USA : We clearly demonstrated that activation led to cell death EU : The results demonstrated that activation led to cell death USA : We detect the 40-kD protein…. EU : The 40-kD protein was detected

13. Tips Ready to publish • The key findings • The supporting evidence • Organize the result : progression of argument • Thesis statement : question you addressed, the key findings, the most important points • Free resource : Colleagues Selecting of journal • Scope of the journal • Audience you will write for • Length of your paper, etc… • Impact Factor • PREDATORY !!! Copy the ‘House Style’ of the journal • Double-spaced, font size, margin sizes etc. • Headings style • Referencing style • Footnotes or Endnotes • Spelling style • Word limit • Figures and Tables style (usually at the end of the article)

14. Consistency enhances retrieval Authors should use the same variation of their name consistently throughout their academic careers. If the name is a common name, consider adding your full middle name to distinguish it from other authors.  Use a standardized institutional affiliation and address, using no abbreviations. Chose what we want ! University Eng Ind UNSOED 40 14 UNHAS 366 48 UNDIP 607 139 IPB 1551 127 UGM 1197 362 ITB 1720/1990 803 Via Sciencedirect platform

15. Total football principes : • Build relationships and networks, ideas travel through on. • Active before, during and soon after the research project . • Develop expertise in your field and be a trustworthy source of evidence. • Address areas of policy interest. • Join relevant committees and insert your findings into decision making. • Don’t wait for publication. Disseminate early. • Be opportunistic. • Present, Present, Present.

16. SCIENTIFIC PAPER

17. Composition Keep this in mind as you write. SECTION Quantity Unit Order Introduction 1 page 3 Materials and Methods 2-3 page Warming-up Results 4 page 1 Discussion 3-4 page 2 References 20-30 refs 4 Abstract 150-250 words Last

18. TITLE PURPOSE • To attract readers • To aid retrieval and indexing CONTENT • Concise • Specific and Clear • Accurately describe the main part of the paper Avoid unnecessary phrases such as: A Report of a Case of... The Treatment of... A Study of... The Effects of... RUNNING TITLE • A title or abbreviated title that is repeated at the head or foot of each page or leaf. Title : Hazard Identification and Dose-Response of Ingested Nickel Soluble Salt Running Title : Assessment of Nickel Soluble Salts – Oral exposure

19. ABSTRACT SHORTENED VERSION OF THE PAPER INTERESTING PAPERS (FULL-LENGTH) Key words ABSTRACTS • What the objectives of the study were • How the study was done • What results were obtained • Significance of the results • Write this section last • Keywords  Title  abstract content • Reiterate keywords but do not overdo it

20. abstract example-1Syakti et al. (2006). Research in Microbiology 157, 476-486 This in vitro study was conducted in order to determine the effects of hydrocarbons and growth phase on the phospholipid ester-linked fatty acid composition of two marine sedimentary hydrocarbon-degrading bacteria. These two strains, namely Corynebacterium sp. and Sphingomonas sp. 2MPII, were cultivated on either a simple soluble substrate (ammonium acetate) or a hydrocarbon (respectively n-eicosane and phenanthrene). The incubations were stopped at different times corresponding to point of lag (2 days), exponential (7 days) and stationary phases (21 and 56 days). The effects of growth phase and hydrophobic substrates were successfully demonstrated by a simple index, given as the sum of saturated fatty acids divided by the sum of unsaturated fatty acids (SFA/MUFA), ranging from 1.4 to 3, 0.3 to 0.6, and 0.5 to 1.0 for Corynebacterium sp., Sphingomonas sp. 2MPII, and mixed cultures, respectively. This result was validated by a principal component analysis. In pure cultures, the phospholipid fatty acid (PLFA) composition was strongly influenced by both the carbon source and the growth phase. Nevertheless, the two strains showed different “behaviors”. For 2MPII, the main PLFA composition changes were observed at 2 days while they were progressive as a function of time for Corynebacterium sp.These differences could explain the evolution of PLFAs of mixed cultures.

21. abstract example-2

22. abstract example-3Long et al. (2007). Nature 450, 376-382 Voltage-dependent K+ (Kv) channels repolarize the action potential in neurons and muscle. This type of channel is gated directly by membrane voltage through protein domains known as voltage sensors, which are molecular voltmeters that read the membrane voltage and regulate the pore. Here we describe the structure of a chimaeric voltage-dependent K+ channel, which we call the 'paddle-chimaera channel', in which the voltage-sensor paddle has been transferred from Kv2.1 to Kv1.2. Crystallized in complex with lipids, the complete structure at 2.4 ångström resolution reveals the pore and voltage sensors embedded in a membrane-like arrangement of lipid molecules. The detailed structure, which can be compared directly to a large body of functional data, explains charge stabilization within the membrane and suggests a mechanism for voltage-sensor movements and pore gating.

23. abstract example-4

24. Do not include any general discussion • Omit all references to the literature. • Do not refer to tables or figures. • Do not repeat the title in the abstract. • Omit P values. • Avoid abbreviations.

25. INTRODUCTION SCIENTIFIC INTEREST AND OBJECTIVES • Discusses the previously published studies • General to specific information • Background : summarized succinctly, not be itemized • Emphasized your specific contribution to the topic • Stating your objectives and hypothesis For example, you might write the following: "Our objective was to determine if the relationship between legumes and nitrogen-fixing bacteria is species-specific. We hypothesized that legumes would grow best when infected by the same Rhizobium species that it occurs with in the field." • Introduction after the Results and the Discussion sections • To state the fact clearly, use present tense • If the results require further investigation (support vs opposite), use the past tense. • If you make any mention of your own results in the introduction, you must use the past tense. • O and H should be placed at the last sentences of the introduction • Number the citation (rival/colleague/netral : 7/3/10)

26. INTRODUCTION HOW TO CITE • Make sure you give a full citation in the Literature Cited section for all sources mentioned in the text. • See Instruction for authors • Suggestion : use ref manager e.g. EndNote, Mendeley For example, you might write the following: "Smith (1983) found that N-fixing plants could be infected by several different species of Rhizobium." "Walnut trees are known to be allelopathic (Smith 1949, Bond et al. 1955, Jones and Green 1963)." "Although the presence of Rhizobium normally increases the growth of legumes (Nguyen 1987), the opposite effect has been observed (Washington 1999)."

27. METHODS • Clear and detailed enough (repeat the experiments and reproduce the result ) • Previously described protocols may be referenced but you must clearly outline any changes made to the previous approach • Only provide full details of a technique if your methods are new (unpublished). • Written in the past tense, and in the passive voice. • Do not quote or cite your laboratory manual! • example: • "We poured N-free fertilizer solution into a graduated cylinder until the bottom of the meniscus was at the 30 ml line. We poured the fertilizer onto the top of the soil in a pot and then repeated this procedure 24 times.“ • "We added 30 ml of N-free fertilizer to each of 24 pots."

28. METHODS • The statistical methods should include: • Statements regarding sample size choice based on statistical power calculations. • Delineation of dependent and independent variables, covariates, and subgroups of key interest. • Steps taken to prevent study biases. • Statistical methods used for the analysis of different variables. • Confidence intervals and their derivation. • Be sure not to include extraneous information, though, as scientists know all about null hypotheses and when to reject them • An important part of writing a scientific paper is deciding what bits of information needs to be given in detail

29. METHODS Examples : avoid To detect RAS RNA expression, total RNA was run on a 1% agarose gel containing formamide, transferred to a membrane, and the membrane was hybridised with a RAS-specific RNA probe overnight, followed by 3 washes in 2-SSC... better RAS expression was determined by northern blotting with a RAS-specific probe avoid PCR products were loaded and separated on a 1% agarose gel, stained with ethidium bromide, and photographed under UV illumination. better PCR products were fractionated through a 1% agarose gel and visualized by UV fluorescence.

30. RESULTS • Write it first • Organize all of your data into tables and figures (in logical order, not chronological order) • Spread these out on a table, and describe the important results in each figure/table in point form. • The results section must clearly outline the rationale or design of the experiments, and the experimental aims. • The details of the methods should not be repeated in the Results section. • It is not necessary to describe every step of your statistical analyses. Scientists understand all about null hypotheses, rejection rules, and so forth and do not need to be reminded of them. • Finish with a sentence giving your conclusions. This should not include any discussion. • The past tense is always used for the Results section, because this is not established knowledge. You may use the passive or active voice, but if you are confident of the results use the active voice.

31. RESULTS Figure and Table • A table is better if exact values should be given, and figures are more appropriate for trends, relationships and effects. • Figures and tables should be easy to understand without the reader having to refer to the text. • Use the figure legends or table footnotes to describe the experiment, and sometimes the key result. • The text and figure legends should complement, not overlap, each other. You must reach a careful balance between the presentation of data in a figure or table and the description of data in the text. • The text should emphasize or summarize the important results; it should not comprehensively describe every result. common mistake • The figures, tables and text must be accurately integrated. Figures and tables should be numbered in the order in which they are cited in the text, and all figures and tables must be cited.

32. RESULTS Examples • "Nitrogen fertilizer significantly increased soy bean total biomass (p=0.05) regardless of the presence or absence of Rhizobium (Table 1)." • The sentence above is well written because: • stated concisely, • Bits of information • the scientific name Rhizobium is italicized, and • the reader is referred to a table where the data to support the statement can be found. Note that the measurement (total biomass, in this case) is mentioned. • avoid • As shown in Fig.2, antisense treatment blocked all expression of the target gene. • better • Fig. 2 shows that antisense treatment blocked all expression of the target gene. • avoid • Treatment of cells with inhibitor was observed to block cell cycle progression. • better • Treatment of cells with inhibitor blocked cell cycle progression.

33. DISCUSSION • Be free to explain what the results mean or why they differ from what other workers have found. • Interpret your results in light of other results, by adding additional information as well as by introducing new sources. • Relate your discussion back to the O and H you raised in the Introduction section. Make statements that synthesize all the evidence (including previous work and the current work). • Do not make statements that are too broad. • Limit your conclusions to those that your data can actually support, but you can then proceed to speculate on why this occurred and whether you expected this to occur, based on other workers' findings. • Suggest future directions for research, new methods, explanations for deviations from previously published results, etc. • If necessary, note problems with the methods and explain anomalies in the data. Do not simply list the problems but provide thoughtful discussion about the implications of the errors in terms of your conclusions.

34. DISCUSSION Example • Western style : • present your conclusions, and then to argue their validity. • brief conclusions given at the end of the results; • then explain why they are valid conclusions. • Japanese style : • providing all of the evidence and interpretations • building their case to finally finish with the major conclusions. • Note : • Your current results are presented in the past tense. • The results of previous studies that are well known and confirmed, are given in the present tense. • Results from other studies that are preliminary or cast into doubt by your studies may be referred to in the past tense. • The interpretation of your results is in the present tense.

35. DISCUSSION Example • Consider the following example discussion: • "The neuroprotective mechanism of riluzole is not fully understood. Riluzole inhibits glutamate release from presynaptic nerve terminals (Martine et al., 1993). In the present study, riluzole inhibited sodium channels; sodium channels mediate a number of functions within the CNS, including apoptosis. This may be consistent with the recent finding that riluzole inhibited apoptosis in the CNS of a transgenic mouse model of ALS (Garney et al., 1999)" • "Riluzole inhibits glutamate release from presynaptic nerve terminals (Martine et al., 1993)." • These effects are well known or were clearly proven, and are therefore in the present tense. • " In the present study, riluzole inhibited sodium channels" • As these results are still unsure (not published), the past tense is used. • "This may be consistent with the recent finding that riluzole inhibited apoptosis.." • By putting this in the past tense, it suggests that these recent findings are not yet well established.

36. REFERENCES AND ACKNOWLEDGEMENT • References : • - different journals use different styles for Literature Cited sections. • Acknowledgements • Financial support or provision of supplies used in the study • Acknowledge other forms of assistance (eg for technical assistance, discussion of the manuscript, preparation of the paper or statistical review). • If the study was done by a large group of people, the names of all of the participants may be given in this section • Example : • This work was supported by grants from CNRS and Elf Aquitaine as a part of GDR ‘‘HYCAR’’1123 (Origin, Effects and Fate of Petroleum Hydrocarbons in Marine Environment). The authors thank the Foreign Ministryof France for the studentship Mr. A.D. Syakti. We also thank the anonymous reviewers for their constructive comments.

37. 12 WATCH-OUTS TO AVOID MS REJECTION Source : ASK Scientific Technicalterm usage (https://www.askscientific.com/translator/) Technicalterm format Genes and proteins format (http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0135305) Measurement system consistency Consistency of terms Defineabbreviationswhenthey first appear Refer to all Figures and Tables in the body Chechyourreferences Concicesupplementarymaterials Format to journal requirements Write a catchycoverletter (https://www.askscientific.com/other-services/cover-letter-journal/) 12. Language (Editing Service)

38. Revising a Manuscript • If you get a revise and resubmit • do everything every reviewer asks you to do (do not argue!) • write a letter to the editor summarising your revisions • attach a memo, where you explain in great detail how your revised paper has addressed the suggestions of each reviewer (e.g. 1-2 pages per reviewer, and start each reviewer on a separate page). • If you get a rejection • do not simply send the paper unrevised to another journal !! • spend time addressing as many of the original reviewers’ comments as possible

39. Ethics • Unique Submission • do not submit a paper to more than one journal at the same time • you will get ‘blackballed’ • Only submit highly polished papers, which have been through several revisions before initial submission • Reviewers as free ‘PhD supervisors’ ! • Do not challenge the decision of the editor • Be prepared to make your data publicly-available • If a journal accepts one of your papers for publication, be prepared to review papers for that journal • Otherwise, editors will tell each other not to accept any of your papers ever again

40. CONCLUDING REMARKS AND PERSPECTIVES LOW SCIENTIFIC PRODUCTION • Data reliabilities • Reference materials and Dbase • Editing service ONE STAR PROGRAM AT FACULTY OR UNIVERSITY LEVEL • One paper for each researcher during one institutional period • Need institutional support for recent publications bibliography • Use editing service provided by established publishers • Encouraging Ph.D fellows : Plan at least 2 journal articles from your PhD • Start early (e.g. in the first year of your PhD !!), as getting something published takes a long time • International collaboration

41. Now You Are Ready to Write-Down Your Scientific Paper T R E A T E D W A S T E W A T E R

43. BACK TO

44. BACK TO Impact Factors From the ISI Journal Citation Reports web page: “a measure of the frequency with which the "average article" in a journal has been cited in a particular year”. Cited in 2007 and 2008 papers Impact Factor 2009 = Papers published in 2007 or 2008 Implications of Impact Factor • Tell us how frequently has the average article in a journal been cited in a particular year. • The impact factor will help you evaluate a journal’s relative importance, especially when you compare it to others in the same field. • Impact factor > 1 implied a journal is frequently cited • Higher citations rate means your article has higher chances of getting cited or read by researchers. • Tells us NOTHING concrete about any specific paper and specific author. • Granting agencies and grant "assessors" may use the impact factor of journals in which you publish as an indicator of the quality of your work (i.e they may form an opinion of the value of your work without actually reading it).

45. BACK TO H-Index (Hirsch, G.E, 2005) From wikipedia: “The h-index is an author-level metric that attempts to measure both the productivity and citation impact of the publications of a scientist or scholar.”. h-index (f) = • f(A)=10, f(B)=8, f(C)=5, f(D)=4, f(E)=3　→ h-index=4 • f(A)=25, f(B)=8, f(C)=5, f(D)=3, f(E)=3　→ h-index=3 • f(A)=2, f(B)=1, f(C)=1, f(D)=0, f(E)=0　→ h-index=1 Implications of h-index • Enables the evaluation of authors and groups of authors within a specific subject area • Allows the filtering of researchers who are not prolific or rarely cited • Helps journal publishers and editors to find qualified reviewer. • Suitable for DIKTI/University/Ristek“reviewers" and Ph.D“promotor”

46. NATIONAL • Accreditated (RISTEKDIKTI) • BIKKK (FK-Unair) • Paediatrica Indonesiana (BPIKAI) • Jurnal Kardiologi Indonesia (PKI) • Makara Journal of Health Research (UI) • etc… • Not Accreditated • Journal Mandala of Health (FK-Unsoed) • Jurnal Keperawatan Soedirman (FK-Unsoed) • Medical Journal of Indonesia • Jurnal Kesehatan Masyarakat • etc.. INDEXED SCOPUS (22) Journal of the Indonesian Society of Critical Care Medicine. Health Science : 1863 Life Science : 1170 PhysicalSci and Eng. : 1225 Soc. Sci and Humanity : 757 Sciencedirect platform

47. Number of predatory publishers, 2011-2016 Number of predatory, standalone journals, 2013-2016 Predatory Publishers Predatory standalone journals Misleading metrics companies Hijacked journals http://scholarlyoa.com/2016/01/05/bealls-list-of-predatory-publishers-2016/