how to write a scientific paper example

This document originally came from the Journal of Mammalogy courtesy of Dr. Ronald Barry, a former editor of the journal.

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10 Simple Steps to Writing a Scientific Paper

At any given time, Andrea Armani ’s lab at the University of Southern California has up to 15 PhD students, a couple of postdocs, nine undergrads, and an occasional high school student, all busy developing new materials for diagnostic and telecommunications devices.

When conducting scientific research, Armani believes it’s important to test a hypothesis—not prove it. She recruits students who are willing to adopt that “testing” mentality, and are excited to explore the unknown. “I want them to push themselves a little bit, push the field a little bit, and not be afraid to fail,” she says. “And, know that even if they fail, they can still learn something from it.”

Armani often coaches students through the process of writing their first scientific paper. Her 10-step formula for writing a scientific paper could be useful to anyone who has concluded a study and feels the dread of the blank page looming.

1. Write a Vision Statement

What is the key message of your paper? Be able to articulate it in one sentence, because it's a sentence you'll come back to a few times throughout the paper. Think of your paper as a press release: what would the subhead be? If you can't articulate the key discovery or accomplishment in a single sentence, then you're not ready to write a paper.

The vision statement should guide your next important decision: where are you submitting? Every journal has a different style and ordering of sections. Making this decision before you write a single word will save you a lot of time later on. Once you choose a journal, check the website for requirements with regards to formatting, length limits, and figures.

2. Don't Start at the Beginning

Logically, it makes sense to start a paper with the abstract, or, at least, the introduction. Don't. You often end up telling a completely different story than the one you thought you were going to tell. If you start with the introduction, by the time everything else is written, you will likely have to rewrite both sections.

3. Storyboard the Figures

Figures are the best place to start, because they form the backbone of your paper. Unlike you, the reader hasn't been living this research for a year or more. So, the first figure should inspire them to want to learn about your discovery.

A classic organizational approach used by writers is "storyboarding" where all figures are laid out on boards. This can be done using software like PowerPoint, Prezi, or Keynote. One approach is to put the vision statement on the first slide, and all of your results on subsequent slides. To start, simply include all data, without concern for order or importance. Subsequent passes can evaluate consolidation of data sets (e.g., forming panel figures) and relative importance (e.g., main text vs. supplement). The figures should be arranged in a logical order to support your hypothesis statement. Notably, this order may or may not be the order in which you took the data. If you're missing data, it should become obvious at this point.

4. Write the Methods Section

Of all the sections, the methods section is simultaneously the easiest and the most important section to write accurately. Any results in your paper should be replicable based on the methods section, so if you've developed an entirely new experimental method, write it out in excruciating detail, including setup, controls, and protocols, also manufacturers and part numbers, if appropriate. If you're building on a previous study, there's no need to repeat all of those details; that's what references are for.

One common mistake when writing a methods section is the inclusion of results. The methods section is simply a record of what you did.

The methods section is one example of where knowing the journal is important. Some journals integrate the methods section in between the introduction and the results; other journals place the methods section at the end of the article. Depending on the location of the methods section, the contents of the results and discussion section may vary slightly.

5. Write the Results and Discussion Section

In a few journals, results and discussion are separate sections. However, the trend is to merge these two sections. This section should form the bulk of your paper-by storyboarding your figures, you already have an outline!

A good place to start is to write a few paragraphs about each figure, explaining: 1. the result (this should be void of interpretation), 2. the relevance of the result to your hypothesis statement (interpretation is beginning to appear), and 3. the relevance to the field (this is completely your opinion). Whenever possible, you should be quantitative and specific, especially when comparing to prior work. Additionally, any experimental errors should be calculated and error bars should be included on experimental results along with replicate analysis.

You can use this section to help readers understand how your research fits in the context of other ongoing work and explain how your study adds to the body of knowledge. This section should smoothly transition into the conclusion.

6. Write the Conclusion

In the conclusion, summarize everything you have already written. Emphasize the most important findings from your study and restate why they matter. State what you learned and end with the most important thing you want the reader to take away from the paper-again, your vision statement. From the conclusion, a reader should be able to understand the gist of your whole study, including your results and their significance.

7. Now Write the Introduction

The introduction sets the stage for your article. If it was a fictional story, the introduction would be the exposition, where the characters, setting, time period, and main conflict are introduced.

Scientific papers follow a similar formula. The introduction gives a view of your research from 30,000 feet: it defines the problem in the context of a larger field; it reviews what other research groups have done to move forward on the problem (the literature review); and it lays out your hypothesis, which may include your expectations about what the study will contribute to the body of knowledge. The majority of your references will be located in the introduction.

8. Assemble References

The first thing that any new writer should do is pick a good electronic reference manager. There are many free ones available, but often research groups (or PIs) have a favorite one. Editing will be easier if everyone is using the same manager.

References serve multiple roles in a manuscript:

1) To enable a reader to get more detailed information on a topic that has been previously published. For example: "The device was fabricated using a standard method." You need to reference that method. One common mistake is to reference a paper that doesn't contain the protocol, resulting in readers being sent down a virtual rabbit hole in search of the protocol.

2) To support statements that are not common knowledge or may be contentious. For example: "Previous work has shown that vanilla is better than chocolate." You need a reference here. Frequently, there are several papers that could be used, and it is up to you to choose.

3) To recognize others working in the field, such as those who came before you and laid the groundwork for your work as well as more recent discoveries. The selection of these papers is where you need to be particularly conscientious. Don't get in the habit of citing the same couple of papers from the same couple of groups. New papers are published every day-literally. You need to make sure that your references include both foundational papers as well as recent works.

9. Write the Abstract

The abstract is the elevator pitch for your article. Most abstracts are 150–300 words, which translates to approximately 10–20 sentences. Like any good pitch, it should describe the importance of the field, the challenge that your research addresses, how your research solves the challenge, and its potential future impact. It should include any key quantitative metrics. It is important to remember that abstracts are included in search engine results.

10. The Title Comes Last

The title should capture the essence of the paper. If someone was interested in your topic, what phrase or keywords would they type into a search engine? Make sure those words are included in your title.

Andrea Martin Armani is an SPIE Fellow and the Ray Irani Chair in Engineering and Materials Science and Professor of Chemical Engineering and Materials Science at the USC Viterbi School of Engineering.

Writing the Scientific Paper

When you write about scientific topics to specialists in a particular scientific field, we call that scientific writing. (When you write to non-specialists about scientific topics, we call that science writing.)

The scientific paper has developed over the past three centuries into a tool to communicate the results of scientific inquiry. The main audience for scientific papers is extremely specialized. The purpose of these papers is twofold: to present information so that it is easy to retrieve, and to present enough information that the reader can duplicate the scientific study. A standard format with six main part helps readers to find expected information and analysis:

• Title--subject and what aspect of the subject was studied.
• Abstract--summary of paper: The main reason for the study, the primary results, the main conclusions
• Introduction-- why the study was undertaken
• Methods and Materials-- how the study was undertaken
• Results-- what was found
• Discussion-- why these results could be significant (what the reasons might be for the patterns found or not found)

There are many ways to approach the writing of a scientific paper, and no one way is right. Many people, however, find that drafting chunks in this order works best: Results, Discussion, Introduction, Materials & Methods, Abstract, and, finally, Title.

The title should be very limited and specific. Really, it should be a pithy summary of the article's main focus.

• "Renal disease susceptibility and hypertension are under independent genetic control in the fawn hooded rat"
• "Territory size in Lincoln's Sparrows ( Melospiza lincolnii )"
• "Replacement of deciduous first premolars and dental eruption in archaeocete whales"
• "The Radio-Frequency Single-Electron Transistor (RF-SET): A Fast and Ultrasensitive Electrometer"

This is a summary of your article. Generally between 50-100 words, it should state the goals, results, and the main conclusions of your study. You should list the parameters of your study (when and where was it conducted, if applicable; your sample size; the specific species, proteins, genes, etc., studied). Think of the process of writing the abstract as taking one or two sentences from each of your sections (an introductory sentence, a sentence stating the specific question addressed, a sentence listing your main techniques or procedures, two or three sentences describing your results, and one sentence describing your main conclusion).

Example One

Hypertension, diabetes and hyperlipidemia are risk factors for life-threatening complications such as end-stage renal disease, coronary artery disease and stroke. Why some patients develop complications is unclear, but only susceptibility genes may be involved. To test this notion, we studied crosses involving the fawn-hooded rat, an animal model of hypertension that develops chronic renal failure. Here, we report the localization of two genes, Rf-1 and Rf-2 , responsible for about half of the genetic variation in key indices of renal impairment. In addition, we localize a gene, Bpfh-1 , responsible for about 26% of the genetic variation in blood pressure. Rf-1 strongly affects the risk of renal impairment, but has no significant effect on blood pressure. Our results show that susceptibility to a complication of hypertension is under at least partially independent genetic control from susceptibility to hypertension itself.

Brown, Donna M, A.P. Provoost, M.J. Daly, E.S. Lander, & H.J. Jacob. 1996. "Renal disease susceptibility and hypertension are under indpendent genetic control in the faun-hooded rat." Nature Genetics , 12(1):44-51.

Example Two

We studied survival of 220 calves of radiocollared moose ( Alces alces ) from parturition to the end of July in southcentral Alaska from 1994 to 1997. Prior studies established that predation by brown bears ( Ursus arctos ) was the primary cause of mortality of moose calves in the region. Our objectives were to characterize vulnerability of moose calves to predation as influenced by age, date, snow depths, and previous reproductive success of the mother. We also tested the hypothesis that survival of twin moose calves was independent and identical to that of single calves. Survival of moose calves from parturition through July was 0.27 ± 0.03 SE, and their daily rate of mortality declined at a near constant rate with age in that period. Mean annual survival was 0.22 ± 0.03 SE. Previous winter's snow depths or survival of the mother's previous calf was not related to neonatal survival. Selection for early parturition was evidenced in the 4 years of study by a 6.3% increase in the hazard of death with each daily increase in parturition date. Although there was no significant difference in survival of twin and single moose calves, most twins that died disappeared together during the first 15 days after birth and independently thereafter, suggesting that predators usually killed both when encountered up to that age.

Key words: Alaska, Alces alces , calf survival, moose, Nelchina, parturition synchrony, predation

Testa, J.W., E.F. Becker, & G.R. Lee. 2000. "Temporal patterns in the survival of twin and single moose ( alces alces ) calves in southcentral Alaska." Journal of Mammalogy , 81(1):162-168.

Example Three

We monitored breeding phenology and population levels of Rana yavapaiensis by use of repeated egg mass censuses and visual encounter surveys at Agua Caliente Canyon near Tucson, Arizona, from 1994 to 1996. Adult counts fluctuated erratically within each year of the study but annual means remained similar. Juvenile counts peaked during the fall recruitment season and fell to near zero by early spring. Rana yavapaiensis deposited eggs in two distinct annual episodes, one in spring (March-May) and a much smaller one in fall (September-October). Larvae from the spring deposition period completed metamorphosis in earlv summer. Over the two years of study, 96.6% of egg masses successfully produced larvae. Egg masses were deposited during periods of predictable, moderate stream flow, but not during seasonal periods when flash flooding or drought were likely to affect eggs or larvae. Breeding phenology of Rana yavapaiensis is particularly well suited for life in desert streams with natural flow regimes which include frequent flash flooding and drought at predictable times. The exotic predators of R. yavapaiensis are less able to cope with fluctuating conditions. Unaltered stream flow regimes that allow natural fluctuations in stream discharge may provide refugia for this declining ranid frog from exotic predators by excluding those exotic species that are unable to cope with brief flash flooding and habitat drying.

Sartorius, Shawn S., and Philip C. Rosen. 2000. "Breeding phenology of the lowland leopard frog ( Rana yavepaiensis )." Southwestern Naturalist , 45(3): 267-273.

Introduction

The introduction is where you sketch out the background of your study, including why you have investigated the question that you have and how it relates to earlier research that has been done in the field. It may help to think of an introduction as a telescoping focus, where you begin with the broader context and gradually narrow to the specific problem addressed by the report. A typical (and very useful) construction of an introduction proceeds as follows:

"Echimyid rodents of the genus Proechimys (spiny rats) often are the most abundant and widespread lowland forest rodents throughout much of their range in the Neotropics (Eisenberg 1989). Recent studies suggested that these rodents play an important role in forest dynamics through their activities as seed predators and dispersers of seeds (Adler and Kestrell 1998; Asquith et al 1997; Forget 1991; Hoch and Adler 1997)." (Lambert and Adler, p. 70)

"Our laboratory has been involved in the analysis of the HLA class II genes and their association with autoimmune disorders such as insulin-dependent diabetes mellitus. As part of this work, the laboratory handles a large number of blood samples. In an effort to minimize the expense and urgency of transportation of frozen or liquid blood samples, we have designed a protocol that will preserve the integrity of lymphocyte DNA and enable the transport and storage of samples at ambient temperatures." (Torrance, MacLeod & Hache, p. 64)

"Despite the ubiquity and abundance of P. semispinosus , only two previous studies have assessed habitat use, with both showing a generalized habitat use. [brief summary of these studies]." (Lambert and Adler, p. 70)

"Although very good results have been obtained using polymerase chain reaction (PCR) amplification of DNA extracted from dried blood spots on filter paper (1,4,5,8,9), this preservation method yields limited amounts of DNA and is susceptible to contamination." (Torrance, MacLeod & Hache, p. 64)

"No attempt has been made to quantitatively describe microhabitat characteristics with which this species may be associated. Thus, specific structural features of secondary forests that may promote abundance of spiny rats remains unknown. Such information is essential to understand the role of spiny rats in Neotropical forests, particularly with regard to forest regeneration via interactions with seeds." (Lambert and Adler, p. 71)

"As an alternative, we have been investigating the use of lyophilization ("freeze-drying") of whole blood as a method to preserve sufficient amounts of genomic DNA to perform PCR and Southern Blot analysis." (Torrance, MacLeod & Hache, p. 64)

"We present an analysis of microhabitat use by P. semispinosus in tropical moist forests in central Panama." (Lambert and Adler, p. 71)

"In this report, we summarize our analysis of genomic DNA extracted from lyophilized whole blood." (Torrance, MacLeod & Hache, p. 64)

Methods and Materials

In this section you describe how you performed your study. You need to provide enough information here for the reader to duplicate your experiment. However, be reasonable about who the reader is. Assume that he or she is someone familiar with the basic practices of your field.

It's helpful to both writer and reader to organize this section chronologically: that is, describe each procedure in the order it was performed. For example, DNA-extraction, purification, amplification, assay, detection. Or, study area, study population, sampling technique, variables studied, analysis method.

Include in this section:

• study design: procedures should be listed and described, or the reader should be referred to papers that have already described the used procedure
• particular techniques used and why, if relevant
• modifications of any techniques; be sure to describe the modification
• specialized equipment, including brand-names
• temporal, spatial, and historical description of study area and studied population
• assumptions underlying the study
• statistical methods, including software programs

Example description of activity

Chromosomal DNA was denatured for the first cycle by incubating the slides in 70% deionized formamide; 2x standard saline citrate (SSC) at 70ºC for 2 min, followed by 70% ethanol at -20ºC and then 90% and 100% ethanol at room temperature, followed by air drying. (Rouwendal et al ., p. 79)

Example description of assumptions

We considered seeds left in the petri dish to be unharvested and those scattered singly on the surface of a tile to be scattered and also unharvested. We considered seeds in cheek pouches to be harvested but not cached, those stored in the nestbox to be larderhoarded, and those buried in caching sites within the arena to be scatterhoarded. (Krupa and Geluso, p. 99)

Examples of use of specialized equipment

• Oligonucleotide primers were prepared using the Applied Biosystems Model 318A (Foster City, CA) DNA Synthesizer according to the manufacturers' instructions. (Rouwendal et al ., p.78)
• We first visually reviewed the complete song sample of an individual using spectrograms produced on a Princeton Applied Research Real Time Spectrum Analyzer (model 4512). (Peters et al ., p. 937)

Example of use of a certain technique

Frogs were monitored using visual encounter transects (Crump and Scott, 1994). (Sartorius and Rosen, p. 269)

Example description of statistical analysis

We used Wilcox rank-sum tests for all comparisons of pre-experimental scores and for all comparisons of hue, saturation, and brightness scores between various groups of birds ... All P -values are two-tailed unless otherwise noted. (Brawner et al ., p. 955)

This section presents the facts--what was found in the course of this investigation. Detailed data--measurements, counts, percentages, patterns--usually appear in tables, figures, and graphs, and the text of the section draws attention to the key data and relationships among data. Three rules of thumb will help you with this section:

• present results clearly and logically
• avoid excess verbiage
• consider providing a one-sentence summary at the beginning of each paragraph if you think it will help your reader understand your data

Remember to use table and figures effectively. But don't expect these to stand alone.

Some examples of well-organized and easy-to-follow results:

• Size of the aquatic habitat at Agua Caliente Canyon varied dramatically throughout the year. The site contained three rockbound tinajas (bedrock pools) that did not dry during this study. During periods of high stream discharge seven more seasonal pools and intermittent stretches of riffle became available. Perennial and seasonal pool levels remained stable from late February through early May. Between mid-May and mid-July seasonal pools dried until they disappeared. Perennial pools shrank in surface area from a range of 30-60 m² to 3-5- M². (Sartorius and Rosen, Sept. 2000: 269)

Notice how the second sample points out what is important in the accompanying figure. It makes us aware of relationships that we may not have noticed quickly otherwise and that will be important to the discussion.

A similar test result is obtained with a primer derived from the human ß-satellite... This primer (AGTGCAGAGATATGTCACAATG-CCCC: Oligo 435) labels 6 sites in the PRINS reaction: the chromosomes 1, one pair of acrocentrics and, more weakly, the chromosomes 9 (Fig. 2a). After 10 cycles of PCR-IS, the number of sites labeled has doubled (Fig. 2b); after 20 cycles, the number of sites labeled is the same but the signals are stronger (Fig. 2c) (Rouwendal et al ., July 93:80).

Related Information: Use Tables and Figures Effectively

Do not repeat all of the information in the text that appears in a table, but do summarize it. For example, if you present a table of temperature measurements taken at various times, describe the general pattern of temperature change and refer to the table.

"The temperature of the solution increased rapidly at first, going from 50º to 80º in the first three minutes (Table 1)."

You don't want to list every single measurement in the text ("After one minute, the temperature had risen to 55º. After two minutes, it had risen to 58º," etc.). There is no hard and fast rule about when to report all measurements in the text and when to put the measurements in a table and refer to them, but use your common sense. Remember that readers have all that data in the accompanying tables and figures, so your task in this section is to highlight key data, changes, or relationships.

In this section you discuss your results. What aspect you choose to focus on depends on your results and on the main questions addressed by them. For example, if you were testing a new technique, you will want to discuss how useful this technique is: how well did it work, what are the benefits and drawbacks, etc. If you are presenting data that appear to refute or support earlier research, you will want to analyze both your own data and the earlier data--what conditions are different? how much difference is due to a change in the study design, and how much to a new property in the study subject? You may discuss the implication of your research--particularly if it has a direct bearing on a practical issue, such as conservation or public health.

This section centers on speculation . However, this does not free you to present wild and haphazard guesses. Focus your discussion around a particular question or hypothesis. Use subheadings to organize your thoughts, if necessary.

This section depends on a logical organization so readers can see the connection between your study question and your results. One typical approach is to make a list of all the ideas that you will discuss and to work out the logical relationships between them--what idea is most important? or, what point is most clearly made by your data? what ideas are subordinate to the main idea? what are the connections between ideas?

Achieving the Scientific Voice

Eight tips will help you match your style for most scientific publications.

• Develop a precise vocabulary: read the literature to become fluent, or at least familiar with, the sort of language that is standard to describe what you're trying to describe.
• Once you've labeled an activity, a condition, or a period of time, use that label consistently throughout the paper. Consistency is more important than creativity.
• Define your terms and your assumptions.
• Include all the information the reader needs to interpret your data.
• Remember, the key to all scientific discourse is that it be reproducible . Have you presented enough information clearly enough that the reader could reproduce your experiment, your research, or your investigation?
• When describing an activity, break it down into elements that can be described and labeled, and then present them in the order they occurred.
• When you use numbers, use them effectively. Don't present them so that they cause more work for the reader.
• Include details before conclusions, but only include those details you have been able to observe by the methods you have described. Do not include your feelings, attitudes, impressions, or opinions.
• Research your format and citations: do these match what have been used in current relevant journals?
• Run a spellcheck and proofread carefully. Read your paper out loud, and/ or have a friend look over it for misspelled words, missing words, etc.

Applying the Principles, Example 1

The following example needs more precise information. Look at the original and revised paragraphs to see how revising with these guidelines in mind can make the text clearer and more informative:

Before: Each male sang a definite number of songs while singing. They start with a whistle and then go from there. Each new song is always different, but made up an overall repertoire that was completed before starting over again. In 16 cases (84%), no new songs were sung after the first 20, even though we counted about 44 songs for each bird.

After: Each male used a discrete number of song types in his singing. Each song began with an introductory whistle, followed by a distinctive, complex series of fluty warbles (Fig. 1). Successive songs were always different, and five of the 19 males presented their entire song repertoire before repeating any of their song types (i.e., the first IO recorded songs revealed the entire repertoire of 10 song types). Each song type recurred in long sequences of singing, so that we could be confident that we had recorded the entire repertoire of commonly used songs by each male. For 16 of the 19 males, no new song types were encountered after the first 20 songs, even though we analyzed and average of 44 songs/male (range 30-59).

Applying the Principles, Example 2

In this set of examples, even a few changes in wording result in a more precise second version. Look at the original and revised paragraphs to see how revising with these guidelines in mind can make the text clearer and more informative:

Before: The study area was on Mt. Cain and Maquilla Peak in British Columbia, Canada. The study area is about 12,000 ha of coastal montane forest. The area is both managed and unmanaged and ranges from 600-1650m. The most common trees present are mountain hemlock ( Tsuga mertensiana ), western hemlock ( Tsuga heterophylla ), yellow cedar ( Chamaecyparis nootkatensis ), and amabilis fir ( Abies amabilis ).

After: The study took place on Mt. Cain and Maquilla Peak (50'1 3'N, 126'1 8'W), Vancouver Island, British Columbia. The study area encompassed 11,800 ha of coastal montane forest. The landscape consisted of managed and unmanaged stands of coastal montane forest, 600-1650 m in elevation. The dominant tree species included mountain hemlock ( Tsuga mertensiana ), western hemlock ( Tsuga heterophylla ), yellow cedar ( Chamaecyparis nootkatensis ), and amabilis fir ( Abies amabilis ).

Two Tips for Sentence Clarity

Although you will want to consider more detailed stylistic revisions as you become more comfortable with scientific writing, two tips can get you started:

First, the verb should follow the subject as soon as possible.

Really Hard to Read : "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 gene."

Less Hard to Read : "The smallest of the UR-F's is URFA6L, a 207-nucleotide (nt) reading frame overlapping out of phase the NH2-terminal portion of the adenosinetriphosphatase (ATPase) subunit 6 gene; it has been identified as the animal equivalent of the recently discovered yeast H+-ATPase subunit 8 gene."

Second, place familiar information first in a clause, a sentence, or a paragraph, and put the new and unfamiliar information later.

More confusing : The epidermis, the dermis, and the subcutaneous layer are the three layers of the skin. A layer of dead skin cells makes up the epidermis, which forms the body's shield against the world. Blood vessels, carrying nourishment, and nerve endings, which relay information about the outside world, are found in the dermis. Sweat glands and fat cells make up the third layer, the subcutaneous layer.

Less confusing : The skin consists of three layers: the epidermis, the dermis, and the subcutaneous layer. The epidermis is made up of dead skin cells, and forms a protective shield between the body and the world. The dermis contains the blood vessels and nerve endings that nourish the skin and make it receptive to outside stimuli. The subcutaneous layer contains the sweat glands and fat cells which perform other functions of the skin.

Bibliography

• Scientific Writing for Graduate Students . F. P. Woodford. Bethesda, MD: Council of Biology Editors, 1968. [A manual on the teaching of writing to graduate students--very clear and direct.]
• Scientific Style and Format . Council of Biology Editors. Cambridge: Cambridge University Press, 1994.
• "The science of scientific writing." George Gopen and Judith Swann. The American Scientist , Vol. 78, Nov.-Dec. 1990. Pp 550-558.
• "What's right about scientific writing." Alan Gross and Joseph Harmon. The Scientist , Dec. 6 1999. Pp. 20-21.
• "A Quick Fix for Figure Legends and Table Headings." Donald Kroodsma. The Auk , 117 (4): 1081-1083, 2000.

Wortman-Wunder, Emily, & Kate Kiefer. (1998). Writing the Scientific Paper. Writing@CSU . Colorado State University. https://writing.colostate.edu/resources/writing/guides/.

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How to write your paper

On this page, writing for a nature journal, how to write a scientific paper.

Before writing a paper, authors are advised to visit the author information pages of the journal to which they wish to submit (see this link for a  full list of Nature Portfolio publications ). Each journal has slightly different format requirements depending on readership, space, style and so on. The journal's website will contain detailed information about format, length limits, figure preparation, and similar matters. If your questions are not answered on these pages or through our recommended guidelines below, we suggest you contact the journal’s editorial office for further guidance before submitting. Contact information for the editorial offices can be found on the journal websites.

We also strongly recommend that authors read a few issues of the journal to which they wish to submit, to obtain a sense of the level, length and readership of the journal. Looking at the print issue, or at PDFs in the online edition, is particularly useful for details such as presentation of figures or style of reference numbering. (All Nature Portfolio journals have a free online issue of the journal for those who do not subscribe or have site-licence access, which can be accessed via the journal's "about" web page.)

Nature journals are international, so in writing a paper, authors should consider those readers for whom English is a second language. The journals are read mainly by professional scientists, so authors can avoid unnecessary simplification or didactic definitions. However, many readers are outside the immediate discipline of the author(s), so clarity of expression is needed to achieve the goal of comprehensibility. (See the section below for links to some websites that provide writing help and advice.)

Nature journals prefer authors to write in the active voice ("we performed the experiment...") as experience has shown that readers find concepts and results to be conveyed more clearly if written directly. We have also found that use of several adjectives to qualify one noun in highly technical language can be confusing to readers. We encourage authors to "unpackage" concepts and to present their findings and conclusions in simply constructed sentences.

Many papers submitted for publication in a Nature journal contain unnecessary technical terminology, unreadable descriptions of the work that has been done, and convoluted figure legends. Our journal subeditors and copyeditors edit the manuscript so that it is grammatically correct, logical, clear and concise. They also ensure that manuscripts use consistent search terms and terminology that is consistent with what is used in previous articles published in the journal. Of course, this process is assisted greatly if the authors have written the manuscript in a simple and accessible style, as the author is the best person to convey the message of the paper and to persuade readers that it is important enough to spend time on.

We ask authors to avoid jargon and acronyms where possible. When essential, they should be defined at first use; after first use, the author should use pronouns when possible rather than using the abbreviation or acronym at every occurrence. The acronym is second-nature to the author but is not to the reader, who may have to refer to the original definition throughout the paper when an acronym is used.

Titles need to be comprehensible and enticing to a potential reader quickly scanning a table of contents or performing an online search, while at the same time not being so general or vague as to obscure what the paper is about. We ask authors to be aware of abstracting and indexing services when devising a title for the paper: providing one or two essential keywords within a title will be beneficial for web-search results.

Within the text of papers, Nature journals use a numbering (Vancouver) system for references, not the Harvard method whereby the authors and year of publication are included in the text in parentheses. We adopt this numbering style because we believe the text flows more smoothly, and hence is quicker for the reader to absorb.

Our experience has shown that a paper's impact is maximized if it is as short as is consistent with providing a focused message, with a few crucial figures or tables. Authors can place technical information (figures, protocols, methods, tables, additional data) necessary to support their conclusion into Supplementary Information (SI), which is published online-only to accompany the published print/online paper. SI is peer-reviewed, and we believe that its use means that the impact of the conclusions of the study is enhanced by being presented in concise and focused form in the print/online journal, emphasizing the key conclusions of the research and yet providing the full supporting details required by others in the field in online-only form. We encourage authors to use SI  in this way to enhance the impact of the print/online version, and hence to increase its readership. Authors are asked to provide short "signposts" at appropriate points in their paper to indicate that SI is present to expand on a particular point (for example "for more details, see figure x in SI) so that readers can navigate easily to the relevant information.  We also encourage authors who are describing methods and protocols to provide the full details as SI.

We all face the challenge of how to make the best use of our time in an era of information overload. Judicious use of SI to ensure that the printed version of a paper is clear, comprehensible and as short as is consistent with this goal, is very likely to increase the paper's readership, impact and the number of times others cite it.

Nature Physics: the Editorial  Elements of style  explains the importance of clear and accessible writing. The advice contained within this Editorial applies to all the Nature journals.

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A number of articles and websites provide detailed guidelines and advice about writing and submitting scientific papers. Some suggested sources are:

• SciDev.Net's  Practical guides section  (including  How to submit a paper to a scientific journal  and  How to write a scientific paper )
• The Human Frontier Science Program's report  Websites and Searching for Collaborations  also contains useful writing guidelines for non-native-English speakers, as well as other helpful advice related to scientific publishing
• The classic book Elements of Style by William J. Strunk, Jr (Humphrey, New York, 1918) is now published by Bartleby.com (New York, 1999) and is  freely available on the web  in searchable format.
• Advice about how to write a Nature journal paper is provided in the Nature Physics Editorial  Elements of style .
• Advice about how to write a summary paragraph (abstract) in Nature Letter format is available as a  one-page downloadable information sheet .
• An amusing but pertinent algorithm,  How to write a paper (one possible answer) is at Nature Network's New York blog.

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How to Format a Scientific Paper

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Written by  Joanna Kimmerly-Smith

You've done the research. You've carefully recorded your lab results and compiled a list of relevant sources. You've even written a draft of your scientific, technical, or medical paper, hoping to get published in a reputable journal. But how do you format your paper to ensure that every detail is correct? If you're a scientific researcher or co-author looking to get your research published, read on to find out how to format your paper.

While it's true that you'll eventually need to tailor your research for your target journal, which will provide specific author guidelines for formatting the paper (see, for example, author guidelines for publications by Elsevier , PLOS ONE , and  mBio ), there are some formatting rules that are useful to know for your initial draft. This article will explore some of the formatting rules that apply to all scientific writing, helping you to follow the correct order of sections ( IMRaD ), understand the requirements of each section, find resources for standard terminology and units of measurement, and prepare your scientific paper for publication.

Format Overview

The four main elements of a scientific paper can be represented by the acronym IMRaD: introduction, methods, results, and discussion. Other sections, along with a suggested length,* are listed in the table below.

* Length guidelines are taken from https://www.elsevier.com/connect/11-steps-to-structuring-a-science-paper-editors-will-take-seriously#step6 .

Now, let's go through the main sections you might have to prepare to format your paper.

On the first page of the paper, you must present the title of the paper along with the authors' names, institutional affiliations, and contact information. The corresponding author(s) (i.e., the one[s] who will be in contact with the reviewers) must be specified, usually with a footnote or an asterisk (*), and their full contact details (e.g., email address and phone number) must be provided. For example:

Dr. Clara A. Bell 1, * and Dr. Scott C. Smith 2

1 University of Areopagitica, Department of Biology, Sometown, Somecountry

2 Leviathan University, Department of Biochemistry and Biomedical Sciences, Sometown, Somecountry

*[email protected]

FORMATTING TIPS:

• If you are unsure of how to classify author roles (i.e., who did what), guidelines are available online. For example, American Geophysical Union (AGU) journals now recommend using Contributor Roles Taxonomy (CRediT), an online taxonomy for author contributions.

In this summary of your research, you must state your subject (i.e., what you did) and encapsulate the main findings and conclusions of your paper.

• Do not add citations in an abstract (the reader might not be able to access your reference list).
• Avoid using acronyms and abbreviations in the abstract, as the reader may not be familiar with them. Use full terms instead.

Below the abstract, include a list of key terms to help other researchers locate your study. Note that "keywords" is one word (with no space) and is followed by a colon:

Keywords : paper format, scientific writing.

• Check whether "Keywords" should be italicized and whether each term should be capitalized.
• Check the use of punctuation (e.g., commas versus semicolons, the use of the period at the end).
• Some journals (e.g., IEEE ) provide a taxonomy of keywords. This aids in the classification of your research.

Introduction

This is the reader's first impression of your paper, so it should be clear and concise. Include relevant background information on your topic, using in-text citations as necessary. Report new developments in the field, and state how your research fills gaps in the existing research. Focus on the specific problem you are addressing, along with its possible solutions, and outline the limitations of your study. You can also include a research question, hypothesis, and/or objectives at the end of this section.

• Organize your information from broad to narrow (general to particular). However, don't start too broad; keep the information relevant.
• You can use in-text citations in this section to situate your research within the body of literature.

This is the part of your paper that explains how the research was done. You should relate your research procedures in a clear, logical order (i.e., the order in which you conducted the research) so that other researchers can reproduce your results. Simply refer to the established methods you used, but describe any procedures that are original to your study in more detail.

• Identify the specific instruments you used in your research by including the manufacturer’s name and location in parentheses.
• Stay consistent with the order in which information is presented (e.g., quantity, temperature, stirring speed, refrigeration period).

Now that you've explained how you gathered your research, you've got to report what you actually found. In this section, outline the main findings of your research. You need not include too many details, particularly if you are using tables and figures. While writing this section, be consistent and use the smallest number of words necessary to convey your statistics.

• Use appendices or supplementary materials if you have too much data.
• Use headings to help the reader follow along, particularly if your data are repetitive (but check whether your style guide allows you to use them).

In this section, you interpret your findings for the reader in relation to previous research and the literature as a whole. Present your general conclusions, including an assessment of the strengths and weaknesses of the research and the implications of your findings. Resolve the hypothesis and/or research question you identified in the introduction.

• Use in-text citations to support your discussion.
• Do not repeat the information you presented in the results or the introduction unless it is necessary for a discussion of the overall implications of the research.

This section is sometimes included in the last paragraph of the discussion. Explain how your research fits within your field of study, and identify areas for future research.

• Keep this section short.

Acknowledgments

Write a brief paragraph giving credit to any institution responsible for funding the study (e.g., through a fellowship or grant) and any individual(s) who contributed to the manuscript (e.g., technical advisors or editors).

• Check whether your journal uses standard identifiers for funding agencies (e.g., Elsevier's Funder Registry ).

Conflicts of Interest/Originality Statement

Some journals require a statement attesting that your research is original and that you have no conflicts of interest (i.e., ulterior motives or ways in which you could benefit from the publication of your research). This section only needs to be a sentence or two long.

Here you list citation information for each source you used (i.e., author names, date of publication, title of paper/chapter, title of journal/book, and publisher name and location). The list of references can be in alphabetical order (author–date style of citation) or in the order in which the sources are presented in the paper (numbered citations). Follow your style guide; if no guidelines are provided, choose a citation format and be consistent .

• While doing your final proofread, ensure that the reference list entries are consistent with the in-text citations (i.e., no missing or conflicting information).
• Many citation styles use a hanging indent and may be alphabetized. Use the styles in Microsoft Word to aid you in citation format.
• Use EndNote , Mendeley , Zotero , RefWorks , or another similar reference manager to create, store, and utilize bibliographic information.

Appendix/Supplementary Information

In this optional section, you can present nonessential information that further clarifies a point without burdening the body of the paper. That is, if you have too much data to fit in a (relatively) short research paper, move anything that's not essential to this section.

• Note that this section is uncommon in published papers. Before submission, check whether your journal allows for supplementary data, and don't put any essential information in this section.

Beyond IMRaD: Formatting the Details

Aside from the overall format of your paper, there are still other details to watch out for. The sections below cover how to present your terminology, equations, tables and figures, measurements, and statistics consistently based on the conventions of scientific writing.

Terminology

Stay consistent with the terms you use. Generally, short forms can be used once the full term has been introduced:

• full terms versus acronyms (e.g., deoxyribonucleic acid versus DNA);
• English names versus Greek letters (e.g., alpha versus α); and
• species names versus short forms (e.g., Staphylococcus aureus versus S. aureus ).

One way to ensure consistency is to use standard scientific terminology. You can refer to the following resources, but if you're not sure which guidelines are preferred, check with your target journal.

• For gene classification, use GeneCards , The Mouse Genome Informatics Database , and/or genenames.org .
• For chemical nomenclature, refer to the International Union of Pure and Applied Chemistry (IUPAC) Compendium of Chemical Terminology (the Gold Book ) and the  IUPAC–IUB Combined Commission on Biochemical Nomenclature .
• For marine species names, use the World Register of Marine Species (WoRMS) or the European Register of Marine Species (ERMS) .

Italics must be used correctly for scientific terminology. Here are a couple of formatting tips:

• Species names, which are usually in Greek or Latin, are italicized (e.g., Staphylococcus aureus ).
• Genes are italicized, but proteins aren't.

Whether in mathematical, scientific, or technical papers, equations follow a conventional format. Here are some tips for formatting your calculations:

• Number each equation you present in the text, inserting the number in parentheses.

X + Y = 1                                                                                                                                               (1)

• Check whether your target journal requires you to capitalize the word "Equation" or use parentheses for the equation number when you refer to equations within the text.

In Equation 1, X represents . . .

In equation (1), X represents . . .

(Note also that you should use italics for variables.)

• Try using MathType or Equation Editor in Microsoft Word to type your equations, but use Unicode characters when typing single variables or mathematical operators (e.g., x, ≥, or ±) in running text. This makes it easier to edit your text and format your equations before publication.
• In line with the above tip, remember to save your math equations as editable text and not as images in case changes need to be made before publication.

Tables and Figures

Do you have any tables, graphs, or images in your research? If so, you should become familiar with the rules for referring to tables and figures in your scientific paper. Some examples are presented below.

• Capitalize the titles of specific tables and figures when you refer to them in the text (e.g., "see Table 3"; "in Figure 4").
• In tables, stay consistent with the use of title case (i.e., Capitalizing Each Word) and sentence case (i.e., Capitalizing the first word).
• In figure captions, stay consistent with the use of punctuation, italics, and capitalization. For example:

Figure 1. Classification of author roles.

Figure 2: taxonomy of paper keywords

Measurements

Although every journal has slightly different formatting guidelines, most agree that the gold standard for units of measurement is the International System of Units (SI) . Wherever possible, use the SI. Here are some other tips for formatting units of measurement:

• Add spaces before units of measurement. For example, 2.5 mL not 2.5mL.
• Be consistent with your units of measure (especially date and time). For example, 3 hours or 3 h.

When presenting statistical information, you must provide enough specific information to accurately describe the relationships among your data. Nothing is more frustrating to a reviewer than vague sentences about a variable being significant without any supporting details. The author guidelines for the journal Nature recommend that the following be included for statistical testing: the name of each statistical analysis, along with its n value; an explanation of why the test was used and what is being compared; and the specific alpha levels and P values for each test.

Angel Borja, writing for Elsevier publications, described the statistical rules for article formatting as follows:

• Indicate the statistical tests used with all relevant parameters.
• Use mean and standard deviation to report normally distributed data.
• Use median and interpercentile range to report skewed data.
• For numbers, use two significant digits unless more precision is necessary.
• Never use percentages for very small samples.

Remember, you must be prepared to justify your findings and conclusions, and one of the best ways to do this is through factual accuracy and the acknowledgment of opposing interpretations, data, and/or points of view.

Even though you may not look forward to the process of formatting your research paper, it's important to present your findings clearly, consistently, and professionally. With the right paper format, your chances of publication increase, and your research will be more likely to make an impact in your field. Don't underestimate the details. They are the backbone of scientific writing and research.

One last tip: Before you submit your research, consider using our academic editing service for expert help with paper formatting, editing, and proofreading. We can tailor your paper to specific journal guidelines at your request.

Image source: 85Fifteen/ Unsplash.com

Let Us Format Your Paper to Your Target Journal’s Guidelines

Hire an expert academic editor , or get a free sample, about the author.

Joanna's passion for English literature (proven by her M.A. thesis on Jane Austen) is matched by her passion to help others with their writing (shown by her role as an in-house editor with Scribendi). She enjoys lively discussions about plot, character, and nerdy TV shows with her husband, and she loves singing almost as much as she loves reading. Isn't music another language after all?

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Writing an Introduction for a Scientific Paper

Dr. michelle harris, dr. janet batzli, biocore.

This section provides guidelines on how to construct a solid introduction to a scientific paper including background information, study question , biological rationale, hypothesis , and general approach . If the Introduction is done well, there should be no question in the reader’s mind why and on what basis you have posed a specific hypothesis.

Broad Question : based on an initial observation (e.g., “I see a lot of guppies close to the shore. Do guppies like living in shallow water?”). This observation of the natural world may inspire you to investigate background literature or your observation could be based on previous research by others or your own pilot study. Broad questions are not always included in your written text, but are essential for establishing the direction of your research.

Background Information : key issues, concepts, terminology, and definitions needed to understand the biological rationale for the experiment. It often includes a summary of findings from previous, relevant studies. Remember to cite references, be concise, and only include relevant information given your audience and your experimental design. Concisely summarized background information leads to the identification of specific scientific knowledge gaps that still exist. (e.g., “No studies to date have examined whether guppies do indeed spend more time in shallow water.”)

Testable Question : these questions are much more focused than the initial broad question, are specific to the knowledge gap identified, and can be addressed with data. (e.g., “Do guppies spend different amounts of time in water <1 meter deep as compared to their time in water that is >1 meter deep?”)

Biological Rationale : describes the purpose of your experiment distilling what is known and what is not known that defines the knowledge gap that you are addressing. The “BR” provides the logic for your hypothesis and experimental approach, describing the biological mechanism and assumptions that explain why your hypothesis should be true.

The biological rationale is based on your interpretation of the scientific literature, your personal observations, and the underlying assumptions you are making about how you think the system works. If you have written your biological rationale, your reader should see your hypothesis in your introduction section and say to themselves, “Of course, this hypothesis seems very logical based on the rationale presented.”

• A thorough rationale defines your assumptions about the system that have not been revealed in scientific literature or from previous systematic observation. These assumptions drive the direction of your specific hypothesis or general predictions.
• Defining the rationale is probably the most critical task for a writer, as it tells your reader why your research is biologically meaningful. It may help to think about the rationale as an answer to the questions— how is this investigation related to what we know, what assumptions am I making about what we don’t yet know, AND how will this experiment add to our knowledge? *There may or may not be broader implications for your study; be careful not to overstate these (see note on social justifications below).
• Expect to spend time and mental effort on this. You may have to do considerable digging into the scientific literature to define how your experiment fits into what is already known and why it is relevant to pursue.
• Be open to the possibility that as you work with and think about your data, you may develop a deeper, more accurate understanding of the experimental system. You may find the original rationale needs to be revised to reflect your new, more sophisticated understanding.
• As you progress through Biocore and upper level biology courses, your rationale should become more focused and matched with the level of study e ., cellular, biochemical, or physiological mechanisms that underlie the rationale. Achieving this type of understanding takes effort, but it will lead to better communication of your science.

***Special note on avoiding social justifications: You should not overemphasize the relevance of your experiment and the possible connections to large-scale processes. Be realistic and logical —do not overgeneralize or state grand implications that are not sensible given the structure of your experimental system. Not all science is easily applied to improving the human condition. Performing an investigation just for the sake of adding to our scientific knowledge (“pure or basic science”) is just as important as applied science. In fact, basic science often provides the foundation for applied studies.

Hypothesis / Predictions : specific prediction(s) that you will test during your experiment. For manipulative experiments, the hypothesis should include the independent variable (what you manipulate), the dependent variable(s) (what you measure), the organism or system , the direction of your results, and comparison to be made.

If you are doing a systematic observation , your hypothesis presents a variable or set of variables that you predict are important for helping you characterize the system as a whole, or predict differences between components/areas of the system that help you explain how the system functions or changes over time.

Experimental Approach : Briefly gives the reader a general sense of the experiment, the type of data it will yield, and the kind of conclusions you expect to obtain from the data. Do not confuse the experimental approach with the experimental protocol . The experimental protocol consists of the detailed step-by-step procedures and techniques used during the experiment that are to be reported in the Methods and Materials section.

Some Final Tips on Writing an Introduction

• As you progress through the Biocore sequence, for instance, from organismal level of Biocore 301/302 to the cellular level in Biocore 303/304, we expect the contents of your “Introduction” paragraphs to reflect the level of your coursework and previous writing experience. For example, in Biocore 304 (Cell Biology Lab) biological rationale should draw upon assumptions we are making about cellular and biochemical processes.
• Be Concise yet Specific: Remember to be concise and only include relevant information given your audience and your experimental design. As you write, keep asking, “Is this necessary information or is this irrelevant detail?” For example, if you are writing a paper claiming that a certain compound is a competitive inhibitor to the enzyme alkaline phosphatase and acts by binding to the active site, you need to explain (briefly) Michaelis-Menton kinetics and the meaning and significance of Km and Vmax. This explanation is not necessary if you are reporting the dependence of enzyme activity on pH because you do not need to measure Km and Vmax to get an estimate of enzyme activity.
• Another example: if you are writing a paper reporting an increase in Daphnia magna heart rate upon exposure to caffeine you need not describe the reproductive cycle of magna unless it is germane to your results and discussion. Be specific and concrete, especially when making introductory or summary statements.

Where Do You Discuss Pilot Studies? Many times it is important to do pilot studies to help you get familiar with your experimental system or to improve your experimental design. If your pilot study influences your biological rationale or hypothesis, you need to describe it in your Introduction. If your pilot study simply informs the logistics or techniques, but does not influence your rationale, then the description of your pilot study belongs in the Materials and Methods section.  

How will introductions be evaluated? The following is part of the rubric we will be using to evaluate your papers.

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Scientific Writing: Sections of a Paper

• Sections of a Paper
• Common Grammar Mistakes Explained
• Citing Sources

Introduction

• Materials & Methods

Typically scientific journal articles have the following sections:

Materials & Methods

References used:

Kotsis, S.V. and Chung, K.C. (2010) A Guide for Writing in the Scientific Forum. Plastic and Reconstructive Surgery. 126(5):1763-71. PubMed ID:  21042135

Van Way, C.W. (2007) Writing a Scientific Paper. Nutrition in Clinical Practice. 22: 663-40. PubMed ID:  1804295

What to include:

• Background/Objectives: include the hypothesis
• Methods: Briefly explain the type of study, sample/population size and description, the design, and any particular techniques for data collection and analysis
• Results: Essential data, including statistically significant data (use # & %)
• Conclusions: Summarize interpretations of results and explain if hypothesis was supported or rejected
• Be concise!
• Emphasize the methods and results
• Do not copy the introduction
• Only include data that is included in the paper
• Write the abstract last
• Avoid jargon and ambiguity
• Should stand-alone

Additional resources: Fisher, W. E. (2005) Abstract Writing. Journal of Surgical Research. 128(2):162-4. PubMed ID:  16165161 Peh, W.C. and Ng, K.H. (2008) Abstract and keywords. Singapore Medical Journal. 49(9): 664-6. PubMed ID:  18830537

• How does your study fit into what has been done
• Explain evidence using limited # of references
• Why is it important
• How does it relate to previous research
• State hypothesis at the end
• Use present tense
• Be succinct
• Clearly state objectives
• Explain important work done

Additional resources: Annesley, T. M. (2010) "It was a cold and rainy night": set the scene with a good introduction. Clinical Chemistry. 56(5):708-13. PubMed ID:  20207764 Peh, W.C. and Ng, K.H. (2008) Writing the introduction. Singapore Medical Journal. 49(10):756-8. PubMed ID:  18946606  

• What was done
• Include characteristics
• Describe recruitment, participation, withdrawal, etc.
• Type of study (RCT, cohort, case-controlled, etc.)
• Equipment used
• Measurements made
• Usually the final paragraph
• Include enough details so others can duplicate study
• Use past tense
• Be direct and precise
• Include any preliminary results
• Ask for help from a statistician to write description of statistical analysis
• Be systematic

Additional resources: Lallet, R. H. (2004) How to write the methods section of a research paper. Respiratory Care. 49(10): 1229-32. PubMed ID:  15447808 Ng, K.H. and Peh, W.C. (2008) Writing the materials and methods. Singapore Medical Journal. 49(11): 856-9. PubMed ID:  19037549

• Describe study sample demographics
• Include statistical significance and the statistical test used
• Use tables and figures when appropriate
• Present in a logical sequence
• Facts only - no citations or interpretations
• Should stand alone (not need written descriptions to be understood)
• Include title, legend, and axes labels
• Include raw numbers with percentages
• General phrases (significance, show trend, etc. should be used with caution)
• Data is plural ("Our data are" is correct, "Our data is" is in-correct)

Additional resources: Ng, K.H and Peh, W.C. (2008) Writing the results. Singapore Medical Journal. 49(12):967-9. PubMed ID:  19122944 Streiner, D.L. (2007) A shortcut to rejection: how not to write the results section of a paper. Canadian Journal of Psychiatry. 52(6):385-9. PubMed ID:  17696025

• Did you reject your null hypothesis?
• Include a focused review of literature in relation to results
• Explain meaning of statistical findings
• Explain importance/relevance 
• Include all possible explanations
• Discuss possible limitations of study
• Suggest future work that could be done
• Use past tense to describe your study and present tense to describe established knowledge from literature
• Don't criticize other studies, contrast it with your work
• Don't make conclusions not supported by your results
• Stay focused and concise
• Include key, relevant references
• It is considered good manners to include an acknowledgements section

Additional resources: Annesley, T. M. (2010) The discussion section: your closing argument. Clinical Chemistry. 56(11):1671-4. PubMed ID:  20833779 Ng, K.H. and Peh, W.C. (2009) Writing the discussion. Singapore Medical Journal. 50(5):458-61. PubMed ID:  19495512

Tables & Figures: Durbin, C. G. (2004) Effective use of tables and figures in abstracts, presentations, and papers. Respiratory Care. 49(10): 1233-7. PubMed ID:  15447809 Ng, K. H. and Peh, W.C.G. (2009) Preparing effective tables. Singapore Medical Journal. (50)2: 117-9. PubMed ID:  19296024

Statistics: Ng, K. H. and Peh, W.C.G. (2009) Presenting the statistical results. Singapore Medical Journal. (50)1: 11-4. PubMed ID:  19224078

References: Peh, W.C.G. and Ng, K. H. (2009) Preparing the references. Singapore Medical Journal. (50)7: 11-4. PubMed ID:  19644619

Additional Resources

• More from Elsevier Elsevier's Research Academy is an online tutorial to help with writing books, journals, and grants. It also includes information on citing sources, peer reviewing, and ethics in publishing
• Research4Life Training Portal Research4Life provides downloadable instruction materials, including modules on authorship skills as well as other research related skills.
• Coursera: Science Writing Coursera provides a wide variety of online courses for continuing education. You can search around for various courses on scientific writing or academic writing, and they're available to audit for free.

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Research Paper Writing Guides

Scientific Research Paper

Last updated on: May 13, 2024

Scientific Research Paper: Types, Formats, Structure & Writing Process

By: Barbara P.

10 min read

Reviewed By:

Published on: May 4, 2024

Are you on the lookout for some guidance on scientific research papers? You have come to the right place. Research papers can be difficult to understand, whether they're about science or other topics. With so many subjects and formats, writing your own paper can be challenging.In this blog, we'll explore the different types of scientific research papers. We’ll guide you with formats, as well as the structure and the writing process involved. In the end, we have handpicked a number of interesting scientific research topics as well. Let’s get started!

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What is a Scientific Research Paper? 

A scientific research paper is a formal document that presents the results of scientific investigations or experiments conducted by researchers. These papers aim to communicate new findings, theories, methodologies, or interpretations of data to the scientific community.

Other than that, they seek to reach a broader audience that is interested in the subject matter.

Scientific research papers are typically published in academic journals after undergoing a rigorous peer-review process to ensure their quality, validity, and integrity.

Parts of a Scientific Research Paper 

Just like other types of research papers , the main parts of a scientific research paper typically include:

• Introduction: This section provides background information on the research topic, outlines the research question or hypothesis, and presents the objectives of the study.
• Methods: Here, researchers describe the experimental design, materials used, and procedures followed in the study. 
• Results: The results section presents the findings of the study, often through tables, figures, or textual descriptions. Researchers report their observations, data analyses, and any statistical outcomes.
• Discussion: In the discussion section , authors interpret the results in the context of existing literature and discuss the implications of their findings.
• Conclusion: The conclusion summarizes the main findings of the research and highlights their significance.

The Major Types of Scientific Research Papers 

Scientific research papers can be divided into subtypes. Here's a brief explanation of each major type of scientific research paper:

• Original Research Articles: These papers present new findings from research conducted by the authors. 
• Review Articles: Review articles summarize and analyze existing research on a topic, identifying trends and gaps in the literature.
• Meta-analyses and Systematic Reviews: These papers statistically analyze data from multiple studies to provide a comprehensive summary of findings or evaluate the effectiveness of interventions.
• Perspective or Opinion Articles: These papers express the author's viewpoint on a topic and offer insights or commentary based on personal experience.
• Case Studies: Case studies provide detailed examinations of specific cases, often focusing on rare or unusual phenomena.
• Short Communications: These are concise and brief papers reporting preliminary or concise findings that do not require a full-length research article.
• Editorials: Editorials are opinion pieces written by journal editors or invited experts, and they discuss recent developments or important issues in the field.
• Letters to the Editor: These are brief communications from readers offering additional insights or criticisms related to published articles.

What are Some Common Scientific Research Paper Citation Formats? 

Here are some popular and widely used scientific research paper formats: 

• APA Style (American Psychological Association)
• MLA Style (Modern Language Association)
• Chicago Style
• IEEE Style (Institute of Electrical and Electronics Engineers)
• AMA Style (American Medical Association)
• Harvard Style
• Vancouver Style

How to Structure Your Scientific Research Paper? 

The specific structure of your scientific research paper may vary depending on your field of study and the requirements of the target journal. Having said that, here's a general scientific research paper outline you can follow to structure your paper: 

Scientific Research Paper Writing Process

Let's break down the process step by step to help you understand how scientific research papers are crafted. 

Step 1. Choose a Research Topic 

Start by identifying areas of interest or gaps in existing knowledge. Ask yourself: What questions intrigue me? What issues do I want to address? Consider the relevance and significance of your chosen topic to both the scientific community and society at large.

Step 2. Conduct Literature Review

Before jumping to your own research, it's necessary to survey the existing literature. In the literature review , explore academic journals, books, and online databases to familiarize yourself with relevant studies and theories. 

Take notes, identify key findings, and pinpoint areas where your research can contribute new insights or perspectives.

Step 3. Formulate Your Hypotheses or Research Questions

Based on your literature review, formulate clear and testable hypotheses or research questions. These hypotheses or questions should serve as the guiding principles of your study, outlining the specific aims and objectives you aim to achieve. 

Make sure that they are precise, measurable, and aligned with the scope of your research.

Step 4. Designing and Conducting Experiments or Studies

With your hypotheses or research questions in hand, it's time to design your study or experiments. Consider the appropriate research methodology, sampling techniques, and data collection methods that best address your research objectives. 

Pay attention to experimental controls, ethical considerations, and potential confounding variables to verify the validity and reliability of your results.

Step 5. Data Analysis

Once you've collected your data, it's time to analyze it rigorously. Choose appropriate statistical methods or qualitative analysis techniques, depending on the nature of your data and research questions. 

Interpret your findings objectively by drawing meaningful conclusions that are supported by evidence. Remember to acknowledge any limitations or uncertainties in your data analysis.

Step 6. Writing and Drafting

Now comes the challenging yet rewarding task of translating your research findings into a coherent scientific research paper. Start by outlining your paper and organize your thoughts logically into sections such as Introduction, Methods, Results, and Discussion. 

Write with clarity, and precision, and stick to the style and formatting guidelines of your target journal.

Step 7. Peer Review and Revision

Before submitting your paper for publication, seek feedback from colleagues, mentors, or peer reviewers. Peer review is a significant step in the scientific writing process and provides valuable insights and constructive criticism to improve the quality of your manuscript. 

Be open to feedback, address any concerns or suggestions raised, and revise your paper accordingly.

Scientific Research Paper Examples

Here are some sample scientific research paper PDF examples for you to get inspired.

Scientific Research Paper Template

Sample Scientific Research Paper Introduction Example 

Interesting Scientific Research Paper Topics 

Below is a list of some great and trending scientific research paper ideas that you can get guidance from.

• The Role of Specific Gut Microbiota Strains in Modulating Immune Response in Inflammatory Bowel Disease Patients
• Predictive Modeling of Patient Outcomes using Machine Learning Algorithms in Cardiovascular Disease Management
• Additive Manufacturing of Bioactive Scaffolds for Tissue Engineering Applications
• Quantifying the Impact of Climate Change on Species Distribution and Habitat Loss in Tropical Rainforests
• Integrative Analysis of Multi-Omics Data for Biomarker Discovery in Complex Diseases
• Investigating Quantum Error Correction Schemes for Fault-Tolerant Quantum Computing Architectures
• CRISPR-Cas9 Editing of Disease-Associated Genetic Variants in Human Embryonic Stem Cells
• Design and Characterization of Targeted Nanoparticle Delivery Systems for Cancer Therapy
• Epigenetic Modifications in Histone Methylation Patterns and Cancer Risk Assessment

To sum it up, scientific research papers are extremely important for learning new things in a range of different research areas. This blog breaks down how research papers are structured, with a step-by-step approach to every section of the paper. 

We discussed how picking the right topic, reviewing past research, conducting careful experiments, and understanding your results can make your research paper valuable. Each step is vital because it helps you complete your research paper.

However, if you need assistance with your scientific research papers, SharkPapers.com should be your obvious choice. We are a paper writing service online that will write your research papers at the most affordable rates.

Get in touch with us to buy research paper , tell us about what you need, and our professional academic experts will handle the rest!

Barbara has a Ph.D. in public health from an Ivy League university and extensive experience working in the medical field. With her practical experience conducting research on various health issues, she is skilled in writing innovative papers on healthcare. Her many works have been published in multiple publications.

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Writing a scientific paper.

• Writing a lab report
• INTRODUCTION

Writing a "good" results section

Figures and Captions in Lab Reports

"Results Checklist" from: How to Write a Good Scientific Paper. Chris A. Mack. SPIE. 2018.

Additional tips for results sections.

• LITERATURE CITED
• Bibliography of guides to scientific writing and presenting
• Peer Review
• Presentations
• Lab Report Writing Guides on the Web

This is the core of the paper. Don't start the results sections with methods you left out of the Materials and Methods section. You need to give an overall description of the experiments and present the data you found.

• Factual statements supported by evidence. Short and sweet without excess words
• Present representative data rather than endlessly repetitive data
• Discuss variables only if they had an effect (positive or negative)
• Use meaningful statistics
• Avoid redundancy. If it is in the tables or captions you may not need to repeat it

A short article by Dr. Brett Couch and Dr. Deena Wassenberg, Biology Program, University of Minnesota

• Present the results of the paper, in logical order, using tables and graphs as necessary.
• Explain the results and show how they help to answer the research questions posed in the Introduction. Evidence does not explain itself; the results must be presented and then explained. 
• Avoid: presenting results that are never discussed;  presenting results in chronological order rather than logical order; ignoring results that do not support the conclusions; 
• Number tables and figures separately beginning with 1 (i.e. Table 1, Table 2, Figure 1, etc.).
• Do not attempt to evaluate the results in this section. Report only what you found; hold all discussion of the significance of the results for the Discussion 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. Just say something like, "Honeybees did not use the flowers in proportion to their availability (X2 = 7.9, p<0.05, d.f.= 4, chi-square test)." Likewise, cite tables and figures without describing in detail how the data were manipulated. Explanations of this sort should appear in a legend or caption written on the same page as the figure or table.
• You must refer in the text to each figure or table you include in your paper.
• Tables generally should report summary-level data, such as means ± standard deviations, rather than all your raw data.  A long list of all your individual observations will mean much less than a few concise, easy-to-read tables or figures that bring out the main findings of your study.  
• Only use a figure (graph) when the data lend themselves to a good visual representation.  Avoid using figures that show too many variables or trends at once, because they can be hard to understand.

From:  https://writingcenter.gmu.edu/guides/imrad-results-discussion

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How to Write a Research Paper 

• Smodin Editorial Team
• Updated: May 17, 2024

Most students hate writing research papers. The process can often feel long, tedious, and sometimes outright boring. Nevertheless, these assignments are vital to a student’s academic journey. Want to learn how to write a research paper that captures the depth of the subject and maintains the reader’s interest? If so, this guide is for you.

Today, we’ll show you how to assemble a well-organized research paper to help you make the grade. You can transform any topic into a compelling research paper with a thoughtful approach to your research and a persuasive argument.

In this guide, we’ll provide seven simple but practical tips to help demystify the process and guide you on your way. We’ll also explain how AI tools can expedite the research and writing process so you can focus on critical thinking.

By the end of this article, you’ll have a clear roadmap for tackling these essays. You will also learn how to tackle them quickly and efficiently. With time and dedication, you’ll soon master the art of research paper writing.

Ready to get started?

What Is a Research Paper?

A research paper is a comprehensive essay that gives a detailed analysis, interpretation, or argument based on your own independent research. In higher-level academic settings, it goes beyond a simple summarization and includes a deep inquiry into the topic or topics.

The term “research paper” is a broad term that can be applied to many different forms of academic writing. The goal is to combine your thoughts with the findings from peer-reviewed scholarly literature.

By the time your essay is done, you should have provided your reader with a new perspective or challenged existing findings. This demonstrates your mastery of the subject and contributes to ongoing scholarly debates.

7 Tips for Writing a Research Paper

Often, getting started is the most challenging part of a research paper. While the process can seem daunting, breaking it down into manageable steps can make it easier to manage. The following are seven tips for getting your ideas out of your head and onto the page.

1. Understand Your Assignment

It may sound simple, but the first step in writing a successful research paper is to read the assignment. Sit down, take a few moments of your time, and go through the instructions so you fully understand your assignment.

Misinterpreting the assignment can not only lead to a significant waste of time but also affect your grade. No matter how patient your teacher or professor may be, ignoring basic instructions is often inexcusable.

If you read the instructions and are still confused, ask for clarification before you start writing. If that’s impossible, you can use tools like Smodin’s AI chat to help. Smodin can help highlight critical requirements that you may overlook.

This initial investment ensures that all your future efforts will be focused and efficient. Remember, thinking is just as important as actually writing the essay, and it can also pave the wave for a smoother writing process.

2. Gather Research Materials

Now comes the fun part: doing the research. As you gather research materials, always use credible sources, such as academic journals or peer-reviewed papers. Only use search engines that filter for accredited sources and academic databases so you can ensure your information is reliable.

To optimize your time, you must learn to master the art of skimming. If a source seems relevant and valuable, save it and review it later. The last thing you want to do is waste time on material that won’t make it into the final paper.

To speed up the process even more, consider using Smodin’s AI summarizer . This tool can help summarize large texts, highlighting key information relevant to your topic. By systematically gathering and filing research materials early in the writing process, you build a strong foundation for your thesis.

3. Write Your Thesis

Creating a solid thesis statement is the most important thing you can do to bring structure and focus to your research paper. Your thesis should express the main point of your argument in one or two simple sentences. Remember, when you create your thesis, you’re setting the tone and direction for the entire paper.

Of course, you can’t just pull a winning thesis out of thin air. Start by brainstorming potential thesis ideas based on your preliminary research. And don’t overthink things; sometimes, the most straightforward ideas are often the best.

You want a thesis that is specific enough to be manageable within the scope of your paper but broad enough to allow for a unique discussion. Your thesis should challenge existing expectations and provide the reader with fresh insight into the topic. Use your thesis to hook the reader in the opening paragraph and keep them engaged until the very last word.

4. Write Your Outline

An outline is an often overlooked but essential tool for organizing your thoughts and structuring your paper. Many students skip the outline because it feels like doing double work, but a strong outline will save you work in the long run.

Here’s how to effectively structure your outline.

• Introduction: List your thesis statement and outline the main questions your essay will answer.
• Literature Review: Outline the key literature you plan to discuss and explain how it will relate to your thesis.
• Methodology: Explain the research methods you will use to gather and analyze the information.
• Discussion: Plan how you will interpret the results and their implications for your thesis.
• Conclusion: Summarize the content above to elucidate your thesis fully.

To further streamline this process, consider using Smodin’s Research Writer. This tool offers a feature that allows you to generate and tweak an outline to your liking based on the initial input you provide. You can adjust this outline to fit your research findings better and ensure that your paper remains well-organized and focused.

5. Write a Rough Draft

Once your outline is in place, you can begin the writing process. Remember, when you write a rough draft, it isn’t meant to be perfect. Instead, use it as a working document where you can experiment with and rearrange your arguments and evidence.

Don’t worry too much about grammar, style, or syntax as you write your rough draft. Focus on getting your ideas down on paper and flush out your thesis arguments. You can always refine and rearrange the content the next time around.

Follow the basic structure of your outline but with the freedom to explore different ways of expressing your thoughts. Smodin’s Essay Writer offers a powerful solution for those struggling with starting or structuring their drafts.

After you approve the outline, Smodin can generate an essay based on your initial inputs. This feature can help you quickly create a comprehensive draft, which you can then review and refine. You can even use the power of AI to create multiple rough drafts from which to choose.

6. Add or Subtract Supporting Evidence

Once you have a rough draft, but before you start the final revision, it’s time to do a little cleanup. In this phase, you need to review all your supporting evidence. You want to ensure that there is nothing redundant and that you haven’t overlooked any crucial details.

Many students struggle to make the required word count for an essay and resort to padding their writing with redundant statements. Instead of adding unnecessary content, focus on expanding your analysis to provide deeper insights.

A good essay, regardless of the topic or format, needs to be streamlined. It should convey clear, convincing, relevant information supporting your thesis. If you find some information doesn’t do that, consider tweaking your sources.

Include a variety of sources, including studies, data, and quotes from scholars or other experts. Remember, you’re not just strengthening your argument but demonstrating the depth of your research.

If you want comprehensive feedback on your essay without going to a writing center or pestering your professor, use Smodin. The AI Chat can look at your draft and offer suggestions for improvement.

7. Revise, Cite, and Submit

The final stages of crafting a research paper involve revision, citation, and final review. You must ensure your paper is polished, professionally presented, and plagiarism-free. Of course, integrating Smodin’s AI tools can significantly streamline this process and enhance the quality of your final submission.

Start by using Smodin’s Rewriter tool. This AI-powered feature can help rephrase and refine your draft to improve overall readability. If a specific section of your essay just “doesn’t sound right,” the AI can suggest alternative sentence structures and word choices.

Proper citation is a must for all academic papers. Thankfully, thanks to Smodin’s Research Paper app, this once tedious process is easier than ever. The AI ensures all sources are accurately cited according to the required style guide (APA, MLA, Chicago, etc.).

Plagiarism Checker:

All students need to realize that accidental plagiarism can happen. That’s why using a Plagiarism Checker to scan your essay before you submit it is always useful. Smodin’s Plagiarism Checker can highlight areas of concern so you can adjust accordingly.

Final Submission

After revising, rephrasing, and ensuring all citations are in order, use Smodin’s AI Content Detector to give your paper one last review. This tool can help you analyze your paper’s overall quality and readability so you can make any final tweaks or improvements.

Mastering Research Papers

Mastering the art of the research paper cannot be overstated, whether you’re in high school, college, or postgraduate studies. You can confidently prepare your research paper for submission by leveraging the AI tools listed above.

Research papers help refine your abilities to think critically and write persuasively. The skills you develop here will serve you well beyond the walls of the classroom. Communicating complex ideas clearly and effectively is one of the most powerful tools you can possess.

With the advancements of AI tools like Smodin , writing a research paper has become more accessible than ever before. These technologies streamline the process of organizing, writing, and revising your work. Write with confidence, knowing your best work is yet to come!

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How to write a materials and methods section of a scientific article?

In contrast to past centuries, scientific researchers have been currently conducted systematically in all countries as part of an education strategy. As a consequence, scientists have published thousands of reports. Writing an effective article is generally a significant problem for researchers. All parts of an article, specifically the abstract, material and methods, results, discussion and references sections should contain certain features that should always be considered before sending a manuscript to a journal for publication. It is generally known that the material and methods section is a relatively easy section of an article to write. Therefore, it is often a good idea to begin by writing the materials and methods section, which is also a crucial part of an article. Because “reproducible results” are very important in science, a detailed account of the study should be given in this section. If the authors provide sufficient detail, other scientists can repeat their experiments to verify their findings. It is generally recommended that the materials and methods should be written in the past tense, either in active or passive voice. In this section, ethical approval, study dates, number of subjects, groups, evaluation criteria, exclusion criteria and statistical methods should be described sequentially. It should be noted that a well-written materials and methods section markedly enhances the chances of an article being published.

How to Write a Materials and Methods Section of a Scientific Article?

Up to the 18 th Century scientific researches were performed on a voluntary basis by certain scientists. However from the second half of the 19 th century, scientific development has gained momentum with the contributions of numerous scientists including Edison, Fleming, and Koch. In parallel with these developments, apparently each scientific field, and even their branches made, and still making magnificent progressions from the end of the 18 th century. Secondary to these developments, scientific researches have been implemented systematically by universities, and various institutions in every part of the world as an integral component of national strategies. Naturally, the number of researchers who performed scientific investigations or sponsored by various institutions increased considerably. Also, as is known very well, all over the world scientists, and researchers move from one place to another to disseminate scientific knowledge. All of these scientific efforts, and activities reflect on clinical practice, and hundreds of thousands, and millions scientific articles which we can currently gain access into all of them online. As indicated by the investigator Gerard Piel, “Without publication, science is dead” which explains the importance of publication. In other words, if you don’t share your investigation and knowledge, they don’t mean anything by themselves. Although sharing the knowledge is essential for writing a scientific paper, nowadays writing a scientific article is mostly learnt as a master-apprentice relationship, and therefore certain standards have not been established. This phenomenon creates serious stress especially for young investigators in their early stage of writing scientific papers. Indeed investigators receiving their residency training confront this reality finally during writing of their dissertations. Though sharing knowledge is known as a fundamental principle in writing a scientific paper, it creates difficulties in the whole world. Relevant to this issue, in the whole world investigations have been performed, and books have been written on the subject of how to write a scientific paper. Accordingly, in our country mostly local meetings, and courses have been organized. These organizations, and investigations should be performed. Indeed, nowadays, in the first assessments, the rejection rate of the journals by internationally acknowledged scientific indexes as “Science Citation İndex (SCI)” and “Science Citation İndex Expanded (SCI-extended” which have certain scientific standards, increases to 62 percent. As a matter of fact only 25% of Class A journals have been included in the lists of SCI, and SCI-extended.

As we all know very well, scientific articles consist of sections of summary, introduction, material, and methods, discussion, and references. Among them, conventionally Materials and Methods section has been reported as the most easily written or will be written section. Although it is known as the most easily written section, nearly 30% of the reasons for rejection are related to this section per se. Therefore due care, and attention should be given to the writing of this section. In the writing process of the ‘Material and Methods’ section, all achievements performed throughout the study period should be dealt with in consideration of certain criteria in a specific sequence. Since as a globally anticipated viewpoint, ‘Materials and Methods’ section can be written quite easily, it has been indicated that if difficulties are encountered in writing a manuscript, then one should start writing from this section. In writing this section, study design describing the type of the article, study subjects to be investigated, methods, and procedures of measurements should be provided under four main headings. [ 1 , 2 ] Accordingly, in brief, we can emphasize the importance of providing clear-cut, adequate, and detailed information in the ‘Materials and Methods’ section to the scientists who will read this scientific article. Meeting these criteria carries great importance with respect to the evaluation of reliability of the investigation by the readers, and reviewers, and also informing them about procedural method, design, data collection, and assessment methods of the investigation, Priorly, as is the case in all scientific investigations, one should be reminded about the importance, and indispensability of compliance with certain standard writing rules. Accordingly, rules of grammar should be obeyed, and if possible passive voice of simple past tense should be used. Related to these rules, use of verbs ‘investigated’, ‘evaluated’ or ‘performed’ will be appropriate. Recently, expressions showing the ownership of the investigation as ‘we performed’, ‘we evaluated’, ‘we implemented’ have taken priority. Since the important point is communication of the message contained in the scientific study, the message should be clearly comprehensible. While ensuring clarity of the message, use of flourishing, and irrelevant sentences should be avoided. [ 1 , 3 ] According to another approach, since our article will be read by professionals of other disciplines, it is important to comply with certain rules of writing. To that end, standard units of measurements, and international abbreviations should be used. Abbreviations should be explained within parentheses at their first mention in the manuscript. For instance let’s analyze the following sentence” The patients were evaluated with detailed medical history, physical examination, complete urinalysis, PSA, and urinary system ultrasound” The abbreviation PSA is very well known by the urologist. However we shouldn’t forget that this article will be read by the professionals in other medical disciplines. Similarly this sentence should not be written as: “The patients were evaluated with detailed medical history, physical examination, complete urinalysis PSA (prostate-specific antigen), and urinary system ultrasound.” Indeed the abbreviation should follow the explanation of this abbreviation. Then the appropriate expression of the sentence should be. “The patients were evaluated with detailed medical history, physical examination, complete urinalysis, prostate-specific antigen (PSA), and urinary system ultrasound.”

In addition to the abovementioned information, in the beginning paragraphs of ‘Materials and Methods’ section of a clinical study the answers to the following questions should be absolutely provided:

• The beginning, and termination dates of the study period.
• Number of subjects/patients/experimental animals etc. enrolled in the study,
• Has the approval of the ethics committee been obtained?
• Study design (prospective, retrospective or other). [ 1 , 2 , 4 – 7 ]

Still additional features of the study design (cross-sectional) should be indicated. Apart from this, other types of study designs (randomized, double-blind, placebo-controlled or double-blind, parallel control etc.) should be revealed.

The heading of the section “Materials and Methods” can be changed to “Patients and the Method” in accordance with writing rules of the journal in question. Indication of starting, and termination dates of a clinical study will facilitate scientific interpretation of the article. Accordingly, outcomes obtained during development phase of a newly implemented method might be considered differently from those acquired during conventional use of this method. Besides, incidence of the diseases, and number of affected people might vary under the impact of social fluctuations, and environmental factors. Therefore with this justification study period should be specified. Number of cases included in the study should be absolutely indicated in the ‘Materials and Methods’ section. It will be appropriate to determine study population after consultation to a statistician-and if required-following “power analysis” Accordingly, the need for a control group will be indicated based on the study design. Nowadays, as a requirement of patient rights, obtainment of approval from ethics committee should be indicated with its registration number. In addition, acquirement of informed consent forms from patients should be indicated. Ethics Committee approval should be obtained in prospective studies performed with study drugs. Otherwise in case of occurrence of adverse effects, it should be acknowledged that in compliance with Article #90 of the Turkish Criminal Law, a 3-year prison sentence is given to the guilty parties. [ 8 ] Since issues related to the Ethics Committee are the subject of another manuscript, they won’t be handled herein.

The following paragraph exemplifies clearly the aforementioned arguments: “After approval of the local ethics committee (BADK-22), informed consent forms from the patients were obtained, and a total of 176 cases with lower urinary tract symptoms (LUTS) were retrospectively evaluated between January 2011, and December 2012.” In a prospectively designed study, methods used to communicate with the cases including face-to-face interviews, phone calls and/or e-mail should be indicated. [ 1 , 2 ] Each paragraph or subheading in the ‘Materials and Methods’ section should be in accordance with the related ones in the ‘Results’ section. In other words, the sequence of paragraphs, and subheadings in the ‘Results’ section should be the same in the ‘Materials and Methods’ section.

As a next step, names of the groups, and distribution of the cases in these groups should be indicated. For instance: the statement “Cases were divided into 3 groups based on their LUTS scores as. Groups 1 (0–9; n=91), 2 (10–18; n=66), and 3 (≥19; n=20)” clearly delineates the scope of the study at baseline.. In the ‘Materials and Methods’ section the number of study subjects should be absolutely documented. Herein, after assignment of names to groups, in the rest of the manuscript, these names should be used. For example instead of saying: “Mean ages of the cases with LUTS scores between 0–9, 10–18, and ≥19 were determined to be 63.2±2.1, 62.8±4.5, and 65.7±3.9 years, respectively” it will be more comprehensible to use the expression: “Mean ages of the Groups 1, 2, and 3 were specified as 63.2±2.1, 62.8±4.5, and 65.7±3.9 years.” (p=0.478). Expressions indicated in the ‘Materials and Methods’ section should not be repeated in the “Results” section. Thus, errors of repetition will be precluded. Following the abovementioned information, the evaluation method of the cases enrolled in the study should be indicated. Hence, results of medical history, physical examination, and if performed laboratory or radiological evaluations-in that order-should be indicated. The application of survey study-if any-should be investigated, and documented. Therefore, the following sentences encompass all the information stated above: “The cases were evaluated with detailed medical history, physical examination, measurements of serum follicle stimulating hormone (FSH), luteinizing hormone (LH), testosterone (T) levels, complete urinalysis, urinary flow rate, direct urinary system roentgenograms, urinary system ultrasound, and if required cyctoscopy. Lower urinary system complaints, and erectile dysfunction were evaluated using International Prostate Symptom Score (IPSS), and International Erectile Function Scale (IIEF), respectively.” Apparently, questionnaire forms were used in the above-cited study. However, methods used for the evaluation of questionnaire forms, and significance of the results obtained, and if possible, the first performer of this survey should be written with accompanying references. In relation to the abovementioned questionnaires the following statements constitute standard expressions for the ‘Materials and Methods’ section: “International Prostate Symptom Score (IPPS) was used in the determination of the severity of prostatic symptoms. IPSS used to determine the severity of the disease, evaluate treatment response, and ascertain the symptomatic progression, is the most optimal scoring system recommended by European Association of Urology (EAU) which classifies the severity of the disease based on IPSS scores as mild (0–7), moderate (8–19), and severe symptomatic (20–35) disease. In the evaluation of sexual function International Erectile Function Scale (IIEF) was used. IIEF is one of the most prevalently used form for the patients who consulted for the complaints of sexual dysfunction Based on IIEF scores, the severity of the disease was classified as severe (1–10), moderate (11–16), mild to moderate (17–21), mild (22–25), and no ED (26–30).”

Whether the institutions of the authors working for should be written in the ‘Materials and Methods’ section can be a subject of debate, generally viewpoints favour provision of this information. However, in compliance with their writing rules, some journals do not favour open-label studies where name of the study site is indicated, and this principle is communicated to the author during editorial evaluation Besides, in the ‘Materials and Methods’ section, the brand of the study object, and its country of origin should be indicated. (ie. if radiological methods are used, then the brand of radiological equipment, and its manufacturing country should be specified. In a study entitled ‘The Impact of Computed Tomography in the Prediction of Post-Radical Nephrectomy Stage in Renal Tumours’ since the main topic of the study is computed tomography, the specifications of the equipment used should be explicitely indicated. On the other hand, the details of the medical method which can effect the outcomes of the study should be also recorded. Accordingly, the methods applied for percutaneous nephrolithotomy, ureterorenoscopy, varicocelectomy, transurethral prostatectomy, radical prostatectomy (perineal, open, laparoscopic or robotic should be absolutely indicated. Then inclusion, and exclusion criteria, and if used control group, and its characteristics should be documented. Thus the following paragraph about exclusion criteria will be appropriate: Patients with a history of neurogenic bladder, prostatic or abdominal operation, and transrectal ultrasound guided prostate biopsy (within the previous 6 months), those aged <40 or >70 years, individuals with a peak urine flow rate below 10 ml/sec, and residual urine more than 150 cc were not included in the study.” [ 1 – 3 , 9 ]

Some diseases mentioned in the “Materials and Methods” section require special monitorization procedures. In these cases the procedure of monitorization should be documented for the sake of the validity of the study in question. Accordingly, in conditions such as “nephrectomy, prostatectomy, orchidectomy, pyeloplasty, varicocelectomy, drug therapies, penile prosthesis, and urethral stricture” clinical follow-up protocols should be provided.

The abovementioned rules, and recommendations are most frequently valid for a clinical study, and some points indicated in experimental studies should be also considered. Types, weights, gender, and number of the animals used in animal studies should be absolutely specified. Besides condition of evaluation of experimental animals should be noted. Then as is the case with clinical studies, approval of the ethics committee should be obtained, and documented. Accordingly, the beginning paragraphs of the ‘Materials and Methods’ can be expressed as follows:

“In the study, 40 Wistar-Albino 6-month-old rats each weighing 350–400 g were used. After approval of the ethics committee (HADYEK-41) the study was performed within the frame of rules specified by the National Institute for animal experiments. The rats were divided into 3 groups. Hence, Group 1 (n=7) was accepted as the control group. The rats subjected to partial ureteral obstruction with or without oral carvedilol therapy at daily doses of 2 mg/kg maintained for 7 days constituted Groups 3 (n=8), and 2 (n=8), respectively. Each group of 4 rats was housed in standard cages with an area of 40×60 cm. The animals were fed with standard 8 mm food pellets, and fresh daily tap water. The rats were kept in the cages under 12 hours of light, and 12 hours of dark. Ambient temperature, and humidity were set at 22±2°C, and 50±10%, respectively.”

Herein, the method, and agent of anesthesia used (local or general anesthesia) in surgical procedures, and then the experimental method applied should be clearly indicated. For example the following sentences explain our abovementioned arguments; “All surgical procedures were performed under xylazine-ketamine anesthesia. In all groups, ureters were approached through midline abdominal incision. In Group 1, ureters were manipulated without causing obstruction. Results of biochemical, and pathological evaluations performed in Group 1 were considered as baseline values.”

“Through a midline abdominal incision partial ureteral obstruction was achieved by embedding two-thirds of the distal part of the left ureter into psoas muscle using 4/0 silk sutures as described formerly by Wen et al. [ 10 ] ( Figure 1 ). [ 11 ] All rats were subjected to left nephrectomies at the end of the experimental study.” As formulated by the above paragraph, if the method used is not widely utilized, then the first researcher who describes the method should be indicated with relevant references. One or more than one figures with a good resolution, and easily comprehensible legends should be also included in the explanation of the experimental model. For very prevalently used experimental models as torsion models cited in the “Materials and Methods” section, there is no need to include figures in the manuscript.

Partial ureteral obstruction model [ 11 ]

Appropriate signs, and marks placed on the figure will facilitate comprehension of the legends ( Figure 2 ).

Ureteral segments (black arrows) seen in a rat partial ureteral obstruction model [ 11 ]

The signs used will also improve intelligibility of the target. The figures should be indicated within parentheses in their first mention in the “Materials and Methods” section. Headings and as a prevalent convention legends of the figures should be indicated at the end of the manuscript.

If a different method is used in the study, this should be explained in detail. For instance, in a study where the effect of smoking on testes was investigated, the method, and the applicator used to expose rats to cigarette smoke should be indicated in the ‘Methods’ section following classical description. Relevant to the study in question, the following paragraph explaining the study method should be written: “A glass chamber with dimensions of 75 × 50 × 50 cm was prepared, and divided into 4 compartments with wire fences. The rats in the 2., and 4. cages were placed in these compartments. Each compartment contained 4 rats. Cigarette smoke was produced using one cigarette per hour, and smoke coming from the tip, and the filter of the lighted cigarette was pumped into the gas chamber with a pneumatic motor. The rats were exposed to smoke of 6 cigarettes for 6 hours. The compartments of the rats were changed every day so as to achieve balanced exposure of the rats to cigarette smoke.” [ 12 ]

Meanwhile, chemical names, doses, and routes of administration of the substances used in experimental studies should be indicated. If the substance used is a solution or an antibody, then manufacturing firm, and its country should be indicated in parenthesis. This approach can be exemplified as “Animals used in experiments were randomized into 4 groups of 8 animals. Each group was housed in 2 cages each containing 4 animals. The first group did not undergo any additional procedure (Group 1). The second group was exposed to cigarette smoke (Group 2). The third (Group 3), and the fourth (Group 4) groups received daily intraperitoneal injectable doses of 10 mg/kg resveratrol (Sigma-Aldrich, St. Louis, MO, USA). The Group 4 was also exposed to cigarette smoke. [ 12 ]

After all of these procedures, method, and analytical procedure of histopathological examination used should be described-if possible-by a pathologist Similarly, biochemical method used should be referenced, and written by the department of clinical chemistry. It can be inferred that each division should describe its own method. In other words, histopathological, microbiological, and pharmacological method should be described in detail by respective divisions.

If we summarize all the information stated above, understandably sharing of the scientific knowledge is essential.. Since reproducibility of a study demonstrates the robustness of a study, with the detailed approaches indicated above, reproducibility of our study is provided, and the relevant questions of “How?”, and “How much?” are answered. Besides, since ‘Materials, and Methods’, and ‘Results’ sections will constitute a meaningful whole, explanations of all information related to the data mentioned in the ‘Results’ section should be provided. As an important point not to be forgotten, evaluation or measurement method used for each parameter indicated in the ‘Results’ section should be expounded in the “Materials and Methods” section. For example if you used an expression in the” Results” section like “median body mass index (BMI) of the patients was 27.42 kg/m 2 ”, then you should beforehand indicate that comparative evaluation of BMIs will be done in the “Materials and Methods” section. In addition, the description, and significance of the values expressed in the “Results” section should be indicated in the “Materials and Methods” section. In other words, it should be stated that the patients were evaluated based on their BMIs as normal (18–24.9 kg/m 2 ), overweight (25 kg/m 2 –40 kg/m 2 ), and morbid obesity (>40 kg/m 2 ). If you encounter difficulties in writing “Materials and Methods” section, also a valid approach for other sections, firstly simple headings can be written, then you can go into details. In brief, for every parameter, the reader should get clear-cut answers to the questions such as “How did they evaluate this parameter, and which criteria were used?”. [ 1 , 3 , 13 – 15 ]

The last paragraph of the ‘Materials, and Methods’ section should naturally involve statistical evaluations. This section should be written by statisticians. Accordingly, the preferred statistical method, and the justifications for this preference should be indicated. In conventional statistical evaluations, provision of details is not required. In information indicated above, the statement “For statistical analysis, ANOVA test, chi-square test, T test, Kruskal-Wallis test have been used.” is not required very much. Instead, more appropriate expression will be a statement indicating that recommendations of a knowledgeable, and an experienced statistician were taken into consideration or advanced statistical information was reflected on the statistical evaluations as follows: “Chi-square tests were used in intergroup comparisons of categorical variables, and categorical variables were expressed as numbers, and percentages. In comparisons between LUTS, and ED as for age, independent two samples t-test was used. In the evaluation of the factors effective on erectile dysfunction multivariate logistic regresssion test was used. P values lower than 0.05 were considered as statistically significant The calculations were performed using a statistical package program (PASW v18, SPSS Inc, Chicago, IL).” Herein, the type of statistical package used for statistical methods should be emphasized.