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Online Lab 3: How to read a Scientific Paper

INTRODUCTION:

Scientific papers are the heart of the science community; they are one of the major ways scientists communicate their results and ideas to one another. Reading a scientific paper is a completely different process than reading an article about science in a blog or newspaper. Not only do you read the sections in a different order than they’re presented, but you also have to take notes, read it multiple times, and probably go look up other papers for some of the details. Reading a single paper may take you a very long time at first. Be patient with yourself. The process will go much faster as you gain experience. Today we will look at strategies to use as you begin to read scientific papers.

Reasons to read a scientific paper:

Current research: textbooks can be outdated by the time they are published. New scientific papers tell you what is happening right now.

It can be replicated: A scientific paper should include methods for how the research was done that give enough information for others to do the same experiment.

It has actual data: Articles include actual data, uncertainties, conditions of the experiment, and much more. This can greatly increase the understanding and interpretation of the research.

You can evaluate the conclusions: Articles provide the authors’ explanation of their results and conclusions. You can see their assumptions and determine whether you agree with them or not

How to evaluate the credibility of a publication:

Fully evaluating the credibility of research can take years of training and special knowledge in a particular area of research. However, there are many clues that can help as you begin to evaluate scientific research.

Author Affiliation: When authors are from established universities, government agencies, or well-known research institutes, there is a much higher chance they are publishing credible data.

Has the information been peer-reviewed? The scientific community uses a system of peer-review to help check the quality of research. A reputable journal will send the article out to 2 or 3 researchers with no direct ties to the authors to evaluate the research before publication. You can check journal page and their instruction to authors to see their peer review requirements.

Journal Source: Large scientific publishing companies such as Elsevier, Springer, Wiley, JSTOR only publish peer reviewed papers. Additionally, research articles indexed in major scientific databases such as PubMed or Web of Science are more likely to be credible.

Citations: Has the research been published long enough that other authors are citing it in their work? As with the author affiliations of the article itself, the affiliations of the authors citing the researcher also provide strong clues to how credible the reach is.

Organization of a scientific paper:

Most research papers will be divided into the following main sections: Abstract, Introduction, Methods, Results, and Discussion/Conclusions.

Abstract. The abstract is a summary of the paper. It usually highlights the main question(s) the authors investigated, provides the key results of their experiments, and gives an overview of the authors' conclusions. Reading the abstract will help you decide if the article was what you were looking for, or not, without spending a long time reading the whole paper. Abstracts are usually accessible for free either online at journals' websites or in scientific literature databases. 2. Introduction. The introduction gives background information about the topic of the paper, and sets out the specific questions to be addressed by the authors. 3. Materials and Methods. The materials and methods section gives the technical details of how the experiments were carried out, including the types of controls used and where unusual resources were obtained. 4. Results. The results section contains all the data from the experiments. The figures contain the majority of the data. The accompanying text contains verbal descriptions of the data and the results of statistical analysis. 5. Discussion. The discussion section describes, analyzes, and interprets the research. Authors explain the significance of their results and tie everything back to the research question. The purpose of discussion sections in papers is to allow the exchange of ideas between scientists.

Activity 1

Video 1

Mini Series Part 3 - Reading a Scientific Article

You only need to watch the first ~14 minutes of this video (13:40). Stop at why do we read scientific papers.

Answer the multiple choice questions as you watch the video.

https://www.youtube.com/watch?v=QYRhfW5vvK8

ACTIVITY 1: Video

Types of Scientific Literature and Organization of a research Article

Answer the following questions as you view the video

What type of literature reports original findings that can be directly attributed to the scientist who did the research?
Primary Literature
Secondary Literature
Tertiary Literature
Gray Literature

2. What type of literature includes publications that use primary literature as a source of information to provide an overview of a scientific topic?

Primary Literature
Secondary Literature
Tertiary Literature
Gray Literature

What is one purpose of tertiary literature?
To present new research
To debate the merits of a particular scientific publication
Provide textbooks for students

The order that the authors’ names are listed can be important. If I was looking for the head of the laboratory or the principle investigator (the scientist who directed the study), where is the best place to look?
The first author
The second author
The last author
the editor

Which section of the scientific paper is like a mini-paper that usually contains a summary of information from the main sections of the scientific paper?
Discussion
Results
Methods
Introduction
Abstract

Video 2

How to Read a Journal Article in 10 Minutes or Less

Watch the entire video and answer the multiple choice questions.

https://www.youtube.com/watch?v=466X7ti1kcs

ACTIVITY 2: Video

How to read a journal article in 10 minutes or less

Answer the following questions as you view the video

What is one reason (according to the video) that scientific articles are hard to read?
They use a secret code to pass confidential information
They are of no use to anyone outside of that specialized field
The are a specialized form of writing that requires training

What is a good description of the title of a scientific article?
A description of the animal the research focuses on
A one sentence summary of the journal article
A description of the most important equipment used in the research.

Where is the hypothesis (and/ or research question) usually stated in a scientific article?
The first paragraph of the introduction
The last paragraph of the introduction
The first paragraph of the methods

Which sections of the research paper are aimed more for other scientists and specialists in the field, and not critical for students to study in depth?
Introduction and Conclusions (=Discussion)
Results and Conclusions (=Discussion)
Methods and Results

As a student, which parts of the scientific article should you focus on?
Title, Abstract and Conclusions (=Discussion)
Introduction and Conclusions (=Discussion)
Methods and Results

ACTIVITY 3. Analyzing Abstracts

The abstract of a scientific paper is like a mini-paper that summarizes each of the four main sections. Read the following abstracts and break them down into the 4 main components of a scientific paper:

1) Introduction (background).

2) Methods

3) Results

4) Discussion (conclusions, interpretation)

Read the title of the paper. Then read each abstract.. Did the title of the paper relate well to the information in the abstract? Read the abstract again and highlight the sentences related to each of the 4 sections listed above, with a different color for each section. Then provide a short summary of one interesting fact or insight of one thing that stood out to you in the abstract. Sometimes one sentence may overlap a couple of sections. You may mark that sentence with both colors.

For each abstract:

One sentence that relates to the introduction:

One sentence that relates to the methods:

One sentences that relates to the results:

One sentence that relates to the discussion:

One fact that you found interesting about the research summarized in the abstract

Article 1:

Title: Reading on a smartphone affects sigh generation, brain activity, and comprehension

Authors: Motoyasu Honma, Yuri Masaoka, Natsuko Iizuka, Sayaka Wada, Sawa Kamimura, Akira Yoshikawa, Rika Moriya, Shotaro Kamijo & Masahiko Izumizaki

Journal: Scientific Reports volume 12, Article number: 1589 (2022)

Abstract: Electronic devices have become an indispensable part of our daily lives, while their negative aspects have been reported. One disadvantage is that reading comprehension is reduced when reading from an electronic device; the cause of this deficit in performance is unclear. In this study, we investigated the cause for comprehension decline when reading on a smartphone by simultaneously measuring respiration and brain activity during reading in 34 healthy individuals. We found that, compared to reading on a paper medium, reading on a smartphone elicits fewer sighs, promotes brain overactivity in the prefrontal cortex, and results in reduced comprehension. Furthermore, reading on a smartphone affected sigh frequency but not normal breathing, suggesting that normal breathing and sigh generation are mediated by pathways differentially influenced by the visual environment. A path analysis suggests that the interactive relationship between sigh inhibition and overactivity in the prefrontal cortex causes comprehension decline. These findings provide new insight into the respiration-mediated mechanisms of cognitive function.

Article 2:

Title: The phylogenetic relationships of the extant pelicans inferred from DNA sequence data

Authors: Martyn Kennedy, Scott A. Taylor, Petr Nádvorník , Hamish G. Spencer

Journal: Molecular Phylogenetics and Evolution, Volume 66, Issue 1, January 2013, Pages 215-222

Abstract: The pelicans are a charismatic group of large water birds, whose evolutionary relationships have been long debated. Here we use DNA sequence data from both mitochondrial and nuclear genes to derive a robust phylogeny of all the extant species. Our data rejects the widespread notion that pelicans can be divided into white- and brown-plumaged groups. Instead, we find that, in contrast to all previous evolutionary hypotheses, the species fall into three well-supported clades: an Old World clade of the Dalmatian, Spot-billed, Pink-backed and Australian Pelicans, a New World clade of the American White, Brown and Peruvian Pelicans, and monospecific clade consisting solely of the Great White Pelican, weakly grouped with the Old World clade. We discuss possible evolutionary scenarios giving rise to this diversity.

Article 3:

Title: Evaluation of a rapid and reliable multiplex PCR assay for the detection of Salmonella Typhi in stool samples. Abdulridha, FM and Kudhair, BK. Gene Reports Volume 33, December 2023, 101812

Abstract: Salmonella Typhi causes typhoid fever and requires prompt and precise diagnosis to prevent the disease from spreading. However, traditional methods for diagnosing the disease are time-consuming. The objective of this research is to assess the speed and reliability of Salmonella Typhi detection through multiplex PCR (mPCR) assay. Initially, Vitek2 system was used to identify 43 Salmonella Typhi isolates from fecal samples. These isolates were then subjected to PCR and mPCR, targeting genes of 16S rRNA, ropE, hil (hilA, hilC, hilD), and sip (sipA, sipB, sipC, sipD). The assay was also tested on seven non-Salmonella gram-negative bacteria known to cause diarrhea to verify the assay's specificity. Subsequently, mPCR was directly conducted on total gDNA extracted from patients' fecal samples to verify its effectiveness. The mPCR technique accurately amplified the target genes to the expected size and effectively distinguished between Salmonella and non-Salmonella isolates. The mPCR assay proved to be a reliable and rapid method for detecting Salmonella, significantly reducing the time required for diagnosis compared to traditional methods, allowing for timely and appropriate treatment of patients.

Bonus assignment: 10 points

To be completed outside of lab: Due by March14

This assignment may be used to replace 1 missing quiz or 1 homework assignment, or to replace you lowest homework/quiz grade. Print assignment and turn in to instructor.

Choose one of the articles we used for online lab 3, and do a more in depth study of the scientific article. Links to a pdf for each paper can be found in canvas: modules: bonus online lab 3. In particular, you will be searching for some information in the Introduction and Discussion sections. Write a report on the article (1/2 page to 1 page). Report should be typed.

Include the following:

Read the last paragraph in the Introduction. What is the question that this research is addressing? Did they state a hypothesis, or a prediction? If so, what was it? Please type and turn in a print

Read the Discussion section.

Include information on the following questions in your report:

What were the authors’ main conclusions or interpretations of the data they collected and presented?
Did the authors describe any limitations of their experiments?
Did the authors describe any unanswered questions, or new questions that need further research?
Give an example of at least one comparison of results from this research with experiments done by other scientists.
How does this research help solve a problem or answer a scientific question?
What is one thing you found interesting in this study?