For more information on using tentative language, classifying, listing and reporting results, visit the Manchester academic phrasebank .
Download the guide to writing lab and field reports (PDF) for further examples of the characteristics of scientific writing.
When you are asked to write a report on investigations you carry out in labs or when you go on fieldwork, it is important to recognise that these reports are structured differently from other types of research reports and essays.
Lab or fieldwork reports are based on detailed observations of the aims, methods and procedures of your experiments or fieldwork investigations, so it is important to keep very precise and detailed notes when you are out in the field or working in the lab.
Download the Guide to writing lab and field reports (PDF, 91.0KB) on this page for an overview of the structure of reports, as well as some language tips for each section of the report.
Note: Always follow the assessment instructions provided in your unit. This guide provides general advice only.
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This document originally came from the Journal of Mammalogy courtesy of Dr. Ronald Barry, a former editor of the journal.
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.”
***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.
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We hypothesized that reared in warm water will have a greater sexual mating response. (The dependent variable “sexual response” has not been defined enough to be able to make this hypothesis testable or falsifiable. In addition, no comparison has been specified— greater sexual mating response as compared to what?) | We hypothesized that ) reared in warm water temperatures ranging from 25-28 °C ( ) would produce greater ( ) numbers of male offspring and females carrying haploid egg sacs ( ) than reared in cooler water temperatures of 18-22°C. |
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.
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We hypothesize that the frequency and extent of algal blooms in Lake Mendota over the last 10 years causes fish kills and imposes a human health risk. (The variables “frequency and extent of algal blooms,” “fish kills” and “human health risk” have not been defined enough to be able to make this hypothesis testable or falsifiable. How do you measure algal blooms? Although implied, hypothesis should express predicted direction of expected results [ , higher frequency associated with greater kills]. Note that cause and effect cannot be implied without a controlled, manipulative experiment.) | We hypothesize that increasing ( ) cell densities of algae ( ) in Lake Mendota over the last 10 years is correlated with 1. increased numbers of dead fish ( ) washed up on Madison beaches and 2. increased numbers of reported hospital/clinical visits ( .) following full-body exposure to lake water. |
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
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.
from an Intro Ecology Lab: Researchers studying global warming predict an increase in average global temperature of 1.3°C in the next 10 years (Seetwo 2003). are small zooplankton that live in freshwater inland lakes. They are filter-feeding crustaceans with a transparent exoskeleton that allows easy observation of heart rate and digestive function. Thomas et al (2001) found that heart rate increases significantly in higher water temperatures are also thought to switch their mode of reproduction from asexual to sexual in response to extreme temperatures. Gender is not mediated by genetics, but by the environment. Therefore, reproduction may be sensitive to increased temperatures resulting from global warming (maybe a question?) and may serve as a good environmental indicator for global climate change. In this experiment we hypothesized that reared in warm water will switch from an asexual to a sexual mode of reproduction. In order to prove this hypothesis correct we observed grown in warm and cold water and counted the number of males observed after 10 days. Comments: Background information · Good to recognize as a model organism from which some general conclusions can be made about the quality of the environment; however no attempt is made to connect increased lake temperatures and gender. Link early on to increase focus. · Connection to global warming is too far-reaching. First sentence gives impression that Global Warming is topic for this paper. Changes associated with global warming are not well known and therefore little can be concluded about use of as indicator species. · Information about heart rate is unnecessary because heart rate in not being tested in this experiment. Rationale · Rationale is missing; how is this study related to what we know about D. magna survivorship and reproduction as related to water temperature, and how will this experiment contribute to our knowledge of the system? · Think about the ecosystem in which this organism lives and the context. Under what conditions would D. magna be in a body of water with elevated temperatures? Hypothesis · Not falsifiable; variables need to be better defined (state temperatures or range tested rather than “warm” or “cold”) and predict direction and magnitude of change in number of males after 10 days. · It is unclear what comparison will be made or what the control is · What dependent variable will be measured to determine “switch” in mode of reproduction (what criteria are definitive for switch?) Approach · Hypotheses cannot be “proven” correct. They are either supported or rejected. | Introduction are small zooplankton found in freshwater inland lakes and are thought to switch their mode of reproduction from asexual to sexual in response to extreme temperatures (Mitchell 1999). Lakes containing have an average summer surface temperature of 20°C (Harper 1995) but may increase by more than 15% when expose to warm water effluent from power plants, paper mills, and chemical industry (Baker et al. 2000). Could an increase in lake temperature caused by industrial thermal pollution affect the survivorship and reproduction of ? The sex of is mediated by the environment rather than genetics. Under optimal environmental conditions, populations consist of asexually reproducing females. When the environment shifts may be queued to reproduce sexually resulting in the production of male offspring and females carrying haploid eggs in sacs called ephippia (Mitchell 1999). The purpose of this laboratory study is to examine the effects of increased water temperature on survivorship and reproduction. This study will help us characterize the magnitude of environmental change required to induce the onset of the sexual life cycle in . Because are known to be a sensitive environmental indicator species (Baker et al. 2000) and share similar structural and physiological features with many aquatic species, they serve as a good model for examining the effects of increasing water temperature on reproduction in a variety of aquatic invertebrates. We hypothesized that populations reared in water temperatures ranging from 24-26 °C would have lower survivorship, higher male/female ratio among the offspring, and more female offspring carrying ephippia as compared with grown in water temperatures of 20-22°C. To test this hypothesis we reared populations in tanks containing water at either 24 +/- 2°C or 20 +/- 2°C. Over 10 days, we monitored survivorship, determined the sex of the offspring, and counted the number of female offspring containing ephippia. Comments: Background information · Opening paragraph provides good focus immediately. The study organism, gender switching response, and temperature influence are mentioned in the first sentence. Although it does a good job documenting average lake water temperature and changes due to industrial run-off, it fails to make an argument that the 15% increase in lake temperature could be considered “extreme” temperature change. · The study question is nicely embedded within relevant, well-cited background information. Alternatively, it could be stated as the first sentence in the introduction, or after all background information has been discussed before the hypothesis. Rationale · Good. Well-defined purpose for study; to examine the degree of environmental change necessary to induce the Daphnia sexual life |
How will introductions be evaluated? The following is part of the rubric we will be using to evaluate your papers.
0 = inadequate (C, D or F) | 1 = adequate (BC) | 2 = good (B) | 3 = very good (AB) | 4 = excellent (A) | |
Introduction BIG PICTURE: Did the Intro convey why experiment was performed and what it was designed to test?
| Introduction provides little to no relevant information. (This often results in a hypothesis that “comes out of nowhere.”) | Many key components are very weak or missing; those stated are unclear and/or are not stated concisely. Weak/missing components make it difficult to follow the rest of the paper. e.g., background information is not focused on a specific question and minimal biological rationale is presented such that hypothesis isn’t entirely logical
| Covers most key components but could be done much more logically, clearly, and/or concisely. e.g., biological rationale not fully developed but still supports hypothesis. Remaining components are done reasonably well, though there is still room for improvement. | Concisely & clearly covers all but one key component (w/ exception of rationale; see left) clearly covers all key components but could be a little more concise and/or clear. e.g., has done a reasonably nice job with the Intro but fails to state the approach OR has done a nice job with Intro but has also included some irrelevant background information
| Clearly, concisely, & logically presents all key components: relevant & correctly cited background information, question, biological rationale, hypothesis, approach. |
Teaching Resources & Guides > How to Teach Science Tips > Writing a Science Report
With science fair season coming up as well as many end of the year projects, students are often required to write a research paper or a report on their project. Use this guide to help you in the process from finding a topic to revising and editing your final paper.
Sometimes one of the largest barriers to writing a research paper is trying to figure out what to write about. Many times the topic is supplied by the teacher, or the curriculum tells what the student should research and write about. However, this is not always the case. Sometimes the student is given a very broad concept to write a research paper on, for example, water. Within the category of water, there are many topics and subtopics that would be appropriate. Topics about water can include anything from the three states of water, different water sources, minerals found in water, how water is used by living organisms, the water cycle, or how to find water in the desert. The point is that “water” is a very large topic and would be too broad to be adequately covered in a typical 3-5 page research paper.
When given a broad category to write about, it is important to narrow it down to a topic that is much more manageable. Sometimes research needs to be done in order to find the best topic to write about. (Look for searching tips in “Finding and Gathering Information.”) Listed below are some tips and guidelines for picking a suitable research topic:
There are numerous resources out there to help you find information on the topic selected for your research paper. One of the first places to begin research is at your local library. Use the Dewey Decimal System or ask the librarian to help you find books related to your topic. There are also a variety of reference materials, such as encyclopedias, available at the library.
A relatively new reference resource has become available with the power of technology – the Internet. While the Internet allows the user to access a wealth of information that is often more up-to-date than printed materials such as books and encyclopedias, there are certainly drawbacks to using it. It can be hard to tell whether or not a site contains factual information or just someone’s opinion. A site can also be dangerous or inappropriate for students to use.
You may find that certain science concepts and science terminology are not easy to find in regular dictionaries and encyclopedias. A science dictionary or science encyclopedia can help you find more in-depth and relevant information for your science report. If your topic is very technical or specific, reference materials such as medical dictionaries and chemistry encyclopedias may also be good resources to use.
If you are writing a report for your science fair project, not only will you be finding information from published sources, you will also be generating your own data, results, and conclusions. Keep a journal that tracks and records your experiments and results. When writing your report, you can either write out your findings from your experiments or display them using graphs or charts .
*As you are gathering information, keep a working bibliography of where you found your sources. Look under “Citing Sources” for more information. This will save you a lot of time in the long run!
Most people find it hard to just take all the information they have gathered from their research and write it out in paper form. It is hard to get a starting point and go from the beginning to the end. You probably have several ideas you know you want to put in your paper, but you may be having trouble deciding where these ideas should go. Organizing your information in a way where new thoughts can be added to a subtopic at any time is a great way to organize the information you have about your topic. Here are two of the more popular ways to organize information so it can be used in a research paper:
Depending on your topic and your writing preference, the layout of your paper can greatly enhance how well the information on your topic is displayed.
1. Process . This method is used to explain how something is done or how it works by listing the steps of the process. For most science fair projects and science experiments, this is the best format. Reports for science fairs need the entire project written out from start to finish. Your report should include a title page, statement of purpose, hypothesis, materials and procedures, results and conclusions, discussion, and credits and bibliography. If applicable, graphs, tables, or charts should be included with the results portion of your report.
2. Cause and effect . This is another common science experiment research paper format. The basic premise is that because event X happened, event Y happened.
3. Specific to general . This method works best when trying to draw conclusions about how little topics and details are connected to support one main topic or idea.
4. Climatic order . Similar to the “specific to general” category, here details are listed in order from least important to most important.
5. General to specific . Works in a similar fashion as the method for organizing your information. The main topic or subtopic is stated first, followed by supporting details that give more information about the topic.
6. Compare and contrast . This method works best when you wish to show the similarities and/or differences between two or more topics. A block pattern is used when you first write about one topic and all its details and then write about the second topic and all its details. An alternating pattern can be used to describe a detail about the first topic and then compare that to the related detail of the second topic. The block pattern and alternating pattern can also be combined to make a format that better fits your research paper.
When writing a research paper, you must cite your sources! Otherwise you are plagiarizing (claiming someone else’s ideas as your own) which can cause severe penalties from failing your research paper assignment in primary and secondary grades to failing the entire course (most colleges and universities have this policy). To help you avoid plagiarism, follow these simple steps:
Revising your paper basically means you are fixing grammatical errors or changing the meaning of what you wrote. After you have written the rough draft of your paper, read through it again to make sure the ideas in your paper flow and are cohesive. You may need to add in information, delete extra information, use a thesaurus to find a better word to better express a concept, reword a sentence, or just make sure your ideas are stated in a logical and progressive order.
After revising your paper, go back and edit it, correcting the capitalization, punctuation, and spelling errors – the mechanics of writing. If you are not 100% positive a word is spelled correctly, look it up in a dictionary. Ask a parent or teacher for help on the proper usage of commas, hyphens, capitalization, and numbers. You may also be able to find the answers to these questions by doing an Internet search on writing mechanics or by checking you local library for a book on writing mechanics.
It is also always a good idea to have someone else read your paper. Because this person did not write the paper and is not familiar with the topic, he or she is more likely to catch mistakes or ideas that do not quite make sense. This person can also give you insights or suggestions on how to reword or format your paper to make it flow better or convey your ideas better.
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Published on October 30, 2022 by Shona McCombes . Revised on October 19, 2023.
The research question is one of the most important parts of your research paper , thesis or dissertation . It’s important to spend some time assessing and refining your question before you get started.
The exact form of your question will depend on a few things, such as the length of your project, the type of research you’re conducting, the topic , and the research problem . However, all research questions should be focused, specific, and relevant to a timely social or scholarly issue.
Once you’ve read our guide on how to write a research question , you can use these examples to craft your own.
Research question | Explanation |
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The first question is not enough. The second question is more , using . | |
Starting with “why” often means that your question is not enough: there are too many possible answers. By targeting just one aspect of the problem, the second question offers a clear path for research. | |
The first question is too broad and subjective: there’s no clear criteria for what counts as “better.” The second question is much more . It uses clearly defined terms and narrows its focus to a specific population. | |
It is generally not for academic research to answer broad normative questions. The second question is more specific, aiming to gain an understanding of possible solutions in order to make informed recommendations. | |
The first question is too simple: it can be answered with a simple yes or no. The second question is , requiring in-depth investigation and the development of an original argument. | |
The first question is too broad and not very . The second question identifies an underexplored aspect of the topic that requires investigation of various to answer. | |
The first question is not enough: it tries to address two different (the quality of sexual health services and LGBT support services). Even though the two issues are related, it’s not clear how the research will bring them together. The second integrates the two problems into one focused, specific question. | |
The first question is too simple, asking for a straightforward fact that can be easily found online. The second is a more question that requires and detailed discussion to answer. | |
? dealt with the theme of racism through casting, staging, and allusion to contemporary events? | The first question is not — it would be very difficult to contribute anything new. The second question takes a specific angle to make an original argument, and has more relevance to current social concerns and debates. |
The first question asks for a ready-made solution, and is not . The second question is a clearer comparative question, but note that it may not be practically . For a smaller research project or thesis, it could be narrowed down further to focus on the effectiveness of drunk driving laws in just one or two countries. |
Note that the design of your research question can depend on what method you are pursuing. Here are a few options for qualitative, quantitative, and statistical research questions.
Type of research | Example question |
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Qualitative research question | |
Quantitative research question | |
Statistical research question |
If you want to know more about the research process , methodology , research bias , or statistics , make sure to check out some of our other articles with explanations and examples.
Methodology
Statistics
Research bias
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McCombes, S. (2023, October 19). 10 Research Question Examples to Guide your Research Project. Scribbr. Retrieved July 1, 2024, from https://www.scribbr.com/research-process/research-question-examples/
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Writing a scientific paper.
Figures and Captions in Lab Reports
Additional tips for results sections.
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.
A short article by Dr. Brett Couch and Dr. Deena Wassenberg, Biology Program, University of Minnesota
From: https://writingcenter.gmu.edu/guides/imrad-results-discussion
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Writing a good conclusion for your science lab report can be the difference between a good grade and a great one. It's your last chance to show you understand the experiment and why it matters. This article will help you learn how to write a lab conclusion that sums up your work and shows your teacher that you understood what you did.
A good lab report conclusion wraps up your lab work in a neat package. When you're thinking about how to write a conclusion for a lab report, focus on four main things. First, remind everyone in a sentence or two of your experiment objectives. Then, quickly mention how you did the experiment and what you found out, but don't introduce new ideas.
Next, talk about the most important things you learned from your experiment. Show how what you found out connects to what you initially tried to do. Lastly, think briefly about what your work means or any limitations you faced during the process. You may include suggestions for further investigation but refrain from proposing solutions.
To write a good lab conclusion, follow these steps:
Important: Keep your conclusion short and easy to understand. A lab conclusion should be about 200-300 words or one paragraph. But if your experiment was really complex, you might need up to 500 words.
Remember, your lab conclusion is part of a bigger report. Always make sure your whole report is well-organized, with a title, introduction, how you did things, what you found, what it means, conclusion, and a list of where you got your information. If you have a lot of numbers or calculations, put them at the end in a separate section to make your report easier to read.
Here's an example of how to write a scientific conclusion for a plant experiment:
The experiment examined how various light wavelengths impact tomato seedling growth. Our findings revealed that blue light (450-495 nm) significantly enhanced stem elongation and leaf surface area in tomato seedlings compared to red (620-750 nm) or full-spectrum white light. Throughout the 4-week study, seedlings exposed to blue light achieved an average height of 15.3 cm, surpassing those exposed to red (10.7 cm) and white light (12.1 cm). These results align with our hypothesis that blue light promotes more vigorous vegetative growth in tomato seedlings, potentially due to its activation of phototropins and cryptochromes. While these outcomes provide valuable insights into early-stage tomato plant development, additional research is necessary to determine the long-term effects on fruit production and quality. This study contributes to our understanding of optimizing light conditions for improved seedling growth in controlled agricultural environments.
This example shows the important parts of a good lab conclusion: it reminds us what the experiment was for, tells how it was done, shares the results, and explains what it all means.
To make your conclusion lab report better, try these tips:
When writing a discussion lab report, focus on clarity and sticking to what's important. Don't add new information or discuss things that aren't part of your experiment.
Writing a great lab report conclusion doesn't have to be hard. With the tips we've discussed on writing a scientific conclusion, you can now write good summaries of your science work. Remember, when writing your discussion lab report, stay focused on your experiment and what you found out. Don't talk about things that aren't related or say things you can't prove. Instead, explain your results, their meaning, and why they matter in science.
Need a little extra help polishing your scientific writing? Aithor might be just what you're looking for. This nifty AI writing tool will streamline your essay and report writing processes. It keeps your original ideas intact while giving your work a professional shine. Whether tackling a tricky lab report or a complex essay, this tool can help you craft well-structured, engaging content in no time.
Give Aithor a try and see the difference it can make in your academic work.
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FILE -This China National Space Administration (CNSA) handout image released by Xinhua News Agency, shows the lander-ascender combination of Chang’e-6 probe taken by a mini rover after it landed on the moon surface, June 4, 2024. China’s Chang’e 6 probe returned on Earth on Tuesday with rock and soil samples from the little-explored far side of the moon in a global first. The probe landed in northern China on Tuesday afternoon in the Inner Mongolian region. (CNSA/Xinhua via AP, File)
FILE -In this photo provided by China’s Xinhua News Agency, a Long March-5 rocket, carrying the Chang’e-6 spacecraft, blasts off from its launchpad at the Wenchang Space Launch Site in Wenchang, south China’s Hainan Province, May 3, 2024. China’s Chang’e 6 probe returned on Earth on Tuesday with rock and soil samples from the little-explored far side of the moon in a global first.The probe landed in northern China on Tuesday afternoon in the Inner Mongolian region. (Guo Cheng/Xinhua via AP, File)
BANGKOK (AP) — China’s Chang’e 6 probe returned on Earth with rock and soil samples from the little-explored far side of the moon in a global first.
The probe landed in the Inner Mongolian region in northern China on Tuesday afternoon.
“I now declare that the Chang’e 6 Lunar Exploration Mission achieved complete success,” Zhang Kejian, Director of the China National Space Administration, said in a televised news conference after the landing.
Chinese scientists anticipate the returned samples will include 2.5 million-year-old volcanic rock and other material that scientists hope will answer questions about geographic differences on the moon’s two sides.
The near side is what is seen from Earth, and the far side faces outer space. The far side is also known to have mountains and impact craters, contrasting with the relatively flat expanses visible on the near side.
The probe had landed in the moon’s South Pole-Aitken Basin, an impact crater created more than 4 billion years ago. The samples scientists are expecting will likely come from different layers of the basin, which will bear traces of the different geological events across its long chronology, such as when the moon was younger and had an active inside that could produce volcanic rock.
While past U.S. and Soviet missions have collected samples from the moon’s near side, the Chinese mission was the first that has collected samples from the far side.
“This is a global first in the sense that it’s the first time anyone has been able to take off from the far side of the moon and bring back samples,” said Richard de Grijs, a professor of astrophysics at Macquarie University in Australia.
The moon program is part of a growing rivalry with the U.S. — still the leader in space exploration — and others, including Japan and India. China has put its own space station in orbit and regularly sends crews there.
China’s leader Xi Jinping sent a message of congratulations to the Chang’e team, saying that it was a “landmark achievement in our country’s efforts at becoming a space and technological power.”
The probe left earth on May 3, and its journey lasted 53 days . The probe has drilled into the core and scooped rocks from the surface.
The samples “are expected to answer one of the most fundamental scientific questions in lunar science research: what geologic activity is responsible for the differences between the two sides?” said Zongyu Yue, a geologist at the Chinese Academy of Sciences, in a statement issued in the Innovation Monday, a journal published in partnership with the Chinese Academy of Sciences.
China in recent years has launched multiple successful missions to the moon, collecting samples from the moon’s near side with the Chang’e 5 probe previously.
They are also hoping that the probe will return with material that bear traces of meteorite strikes from the moon’s past. That material could shed light on the solar system’s early days. There’s a theory that the moon acted as a vaccum cleaner of sorts, attracting all the meteorites and debris in the system’s earlier era so that they didn’t hit Earth, said de Grijs, who is also executive director at the International Space Science Institute — Beijing.
China has said it plans to share the samples with international scientists, although it did not say exactly in which countries.
AP video producer Olivia Zhang contributed to this report.
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Scientific Reports volume 14 , Article number: 15009 ( 2024 ) Cite this article
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Ulcerative colitis (UC) is a chronic inflammatory bowel disease with intricate pathogenesis and varied presentation. Accurate diagnostic tools are imperative to detect and manage UC. This study sought to construct a robust diagnostic model using gene expression profiles and to identify key genes that differentiate UC patients from healthy controls. Gene expression profiles from eight cohorts, encompassing a total of 335 UC patients and 129 healthy controls, were analyzed. A total of 7530 gene sets were computed using the GSEA method. Subsequent batch correction, PCA plots, and intersection analysis identified crucial pathways and genes. Machine learning, incorporating 101 algorithm combinations, was employed to develop diagnostic models. Verification was done using four external cohorts, adding depth to the sample repertoire. Evaluation of immune cell infiltration was undertaken through single-sample GSEA. All statistical analyses were conducted using R (Version: 4.2.2), with significance set at a P value below 0.05. Employing the GSEA method, 7530 gene sets were computed. From this, 19 intersecting pathways were discerned to be consistently upregulated across all cohorts, which pertained to cell adhesion, development, metabolism, immune response, and protein regulation. This corresponded to 83 unique genes. Machine learning insights culminated in the LASSO regression model, which outperformed others with an average AUC of 0.942. This model's efficacy was further ratified across four external cohorts, with AUC values ranging from 0.694 to 0.873 and significant Kappa statistics indicating its predictive accuracy. The LASSO logistic regression model highlighted 13 genes, with LCN2, ASS1, and IRAK3 emerging as pivotal. Notably, LCN2 showcased significantly heightened expression in active UC patients compared to both non-active patients and healthy controls (P < 0.05). Investigations into the correlation between these genes and immune cell infiltration in UC highlighted activated dendritic cells, with statistically significant positive correlations noted for LCN2 and IRAK3 across multiple datasets. Through comprehensive gene expression analysis and machine learning, a potent LASSO-based diagnostic model for UC was developed. Genes such as LCN2, ASS1, and IRAK3 hold potential as both diagnostic markers and therapeutic targets, offering a promising direction for future UC research and clinical application.
Introduction.
Ulcerative colitis (UC) is indeed an inflammatory bowel disease (IBD) that predominantly impacts the mucosal and submucosal layers of the colon and rectum, manifesting as a chronic condition characterized by inflammation and the formation of ulcers in the lining of the colon and rectum. Simultaneously, prolonged UC results in structural damage, amplifying the susceptibility to conditions such as colon cancer and extraintestinal malignancies 1 , 2 . However, the pathogenesis of UC remains a complex and not fully elucidated process. It is currently understood that UC predominantly affects individuals with genetic susceptibility, while factors such as epithelial barrier defects, dysbiosis, and dysregulated immune responses play significant roles in its pathogenesis 3 , 4 , 5 . Epidemiologically, the incidence and prevalence of UC have been a dramatic rise in recent years. Globally, the highest incidence and prevalence are in Northern Europe, 505 per 100,000 in Norway, followed by North America, 286 per 100,000 in the USA 6 . The annual incidence of UC in Europe has surged to 24.3 cases per 100,000 individuals, and there is a clear upward trajectory in both the prevalence and incidence of UC over time 7 . It’s worth noting that in many emerging industrialized countries in South America, Asia, and Africa, although the prevalence is still low, the number of new UC diagnoses is increasing, and the prevalence is expected to rise in the future 8 . This presents a substantial challenge for healthcare systems on a global scale.
A potential pathogenesis of UC could be immune system dysfunction. When the immune system works hard to resist invading viruses or bacteria, an abnormal immune response can cause the immune system to also attack cells in the digestive tract, leading to chronic intestinal inflammation or mucosal damage. Genetics also play a role as UC is more common in people with family members who have the disease 9 . In the past, UC was commonly managed with 5-aminosalicylates, steroids, and thiopurines. However, despite these treatment options, UC continues to significantly affect patients' quality of life and is associated with a high morbidity rate 10 . Procedures such as ileo-pouch-anal anastomosis and colectomy come with the potential risks of infertility, compromised pouch function, and the development of capsulitis 11 . In recent years, targeted therapeutic agents like tumor necrosis factor (TNF) inhibitors and interleukin inhibitors have garnered increased attention in clinical practice. With ongoing advancements in drug development, there has been a substantial decrease in UC-related mortality, enhancing the overall prognosis for patients with UC 12 . Nonetheless, there is undeniably substantial room for enhancement in the management of UC, as indicated by existing studies that report remission rates (Based on clinical improvements in stool frequency, rectal bleeding, and mucosal appearance on endoscopy, Mayo score) typically falling below 20–30% 12 .
The diagnosis of UC primarily rests on a combination of clinical symptoms, endoscopic findings, histological examination, and exclusion of other causes of colitis, such as infections 13 , 14 . Serological markers and fecal calprotectin can assist in differentiating UC from other gastrointestinal disorders, but they are not definitive. Looking ahead, there is growing interest in the realm of genetics for diagnostic insights. Recent advancements in genome-wide association studies (GWAS) have identified numerous genetic loci associated with UC susceptibility 15 , 16 . The clinical symptoms might also correlate with genetic alterations, gene expression profiles in symptomatic controls, from whom inflammatory bowel disease (IBD) had been excluded, resembled those of IBD patients and diverged from healthy controls. The gene expression signatures of these IBD-excluded samples were related to their symptomatic status 17 . Crooke et al. detected the transcript levels of a total of 45 genes in blood by quantitative real-time polymerase chain reaction, and then used ratio score and support vector machine methods to distinguish UC from several types of gastro-intestinal diseases 18 . Recent years, next-generation sequencing is widely applied in disease diagnostic and precision treatment 19 , 20 . As our understanding of the genetic architecture of UC deepens, it is anticipated that genetic markers could serve as adjunct diagnostic tools, offering more precise disease categorization and personalized therapeutic strategies. This burgeoning area of research holds the promise of reshaping the diagnostic landscape of UC in the future.
The objective of current study is to explore the potential of gene expression profiles in enhancing the accuracy and early detection of UC, particularly in cases where traditional diagnostic methods may be inconclusive. While traditional diagnostics are indeed effective and cost-efficient, gene expression profiling offers several distinct advantages. These include the ability to identify molecular changes at an early stage, which may precede clinical symptoms, thus enabling earlier intervention and potentially improving patient outcomes. In this study, we incorporated soft tissue sequencing data from a cohort of 259 UC patients and 60 individuals without the condition. From this dataset, we identified six key genes and developed a predictive model with a high degree of accuracy for UC diagnosis.
We collected a total of eight cohorts contains both health controls and UC patients for the current study. The training datasets derived from mucosal tissue samples included GSE87466 with 21 normal and 87 UC patients, GSE59071 with 11 normal and 97 UC patients, GSE47908 with 15 normal and 45 UC patients, and GSE38713 with 13 normal and 30 UC patients. For validation, the mucosal tissue cohorts comprised GSE53306, which had 12 normal controls, 16 patients in the active UC category and 12 in the inactive UC category. Similarly, GSE13367 had 8 inflamed and 9 non-inflamed UC patients, compared with 10 controls. GSE48958 also from mucosal tissue had 7 active UC and 6 inactive UC patients, accompany with 8 controls. Finally, the GSE126124 dataset, derived from peripheral whole blood, included 39 normal and 18 UC patients (Table 1 ).
Batch effects represent the non-biological discrepancies observed across multiple datasets. To ensure analytical consistency and mitigate biases introduced by such effects, we employed the ComBat algorithms from the "sva" package. This methodology was instrumental in harmonizing the transcriptional profiles of the training cohorts (GSE87466, GSE59071, GSE47908, GSE38713), thus effectively offsetting the intrinsic batch differences among them. For the validation cohort, we abstained from this procedure, as our intent was to further authenticate the diagnostic across diverse platforms.
Gene Set Enrichment Analysis (GSEA) is a computational approach ascertaining whether a designated gene set exhibits statistically significant deviations between two groups. We implemented GSEA to initially contrast the various activated signaling pathways between UC patients and healthy controls. The backdrop file of molecular signature gene sets was procured from MSigDB, C5: Biological Process, comprising a total of 7530 gene sets 21 , 22 .
To craft a unified model possessing robust accuracy and stability in distinguishing between UC patients and healthy individuals, we amalgamated 10 machine learning algorithms, yielding 101 algorithmic combinations. The ensemble of algorithms comprised Elastic Net (Enet), Lasso, Ridge, Stepglm[both], Stepglm[backward], glmBoost, Latent Dirichlet Allocation (LDA), NaiveBayes, plsRglm, Random Forest (RF), and Support Vector Machine (SVM). The signature derivation protocol entailed: (1) Isolating the most prominently activated pathways in UC patients across the four GEO cohorts; (2) Subsequently, the 101 algorithmic combinations were executed on the genes curated from these prominently activated pathways; (3) All models underwent training within the GSE55235 dataset and validation in the remaining three cohorts, which remained untouched during pathway filtration; (4) For every model, the AUC metric was ascertained across all participating cohorts.
Through single-sample gene set enrichment analysis (ssGSEA), the infiltration of immune cells was discerned and evaluated using transcriptional data. The gene collections representing 28 immune cell types were sourced from the research undertaken by Charoentong et al 23 .
Tatistical analyses were conducted using R (Version: 4.2.2). For continuous variables, the Student's t-test and the two-sample Mann–Whitney test were employed for comparisons between two groups if data exhibited a normal distribution, whereas the Wilson rank test was invoked otherwise. A Pearson correlation analysis was employed for continuous datasets. Pertinent pathways were delineated using a heatmap, facilitated by the R package "pheatmap". The Kappa Statistic serves as a metric for contrasting predictive versus actual subtypes. For comparisons across more than two groups, the Kruskal–Wallis test was utilized, and for pairwise assessments, the Wilcoxon test was applied 24 . A two-tailed P value below 0.05 was considered to indicate statistical significance.
In this study, transcriptomic data from four cohorts, encompassing Ulcerative Colitis (UC) patients and healthy controls, were evaluated to identify key signaling pathways associated with UC. The gene expression profiles underwent batch correction to ensure uniformity and mitigate batch effects. Using Gene Set Enrichment Analysis (GSEA), over 7500 gene sets were computed, each representing a unique cellular signaling pathway. Machine learning techniques were then employed, with the LASSO regression model emerging as the most efficient diagnostic tool with an average AUC value of 0.942. The robustness of this model was validated using external cohorts. From the diagnostic model, 13 characteristic genes were identified and assessed for their expression differences. Three of these genes, LCN2, ASS1, and IRAK3, were particularly noteworthy as they exhibited elevated expression in UC patients. The study further examined the relationship between these genes and immune cell infiltration, establishing their correlation with activated dendritic cells. These findings reinforce the role of immune system dysregulation in UC and introduce potential biomarkers for diagnostic and therapeutic applications. The flowchart of the current study is displayed in Fig. 1 .
Flowchart illustrating the step-by-step methodology of the current study. Starting from transcriptomic data acquisition from four cohorts, through data preprocessing, gene set enrichment analysis, machine learning diagnostics, and concluding with the identification of characteristic genes and their association with immune cell infiltration.
As delineated in the methods section, our study incorporated samples from four cohorts, encompassing both UC patients and healthy controls. To ensure uniformity of the transcriptomic data before further analysis, we initially subjected the gene expression profiles from all four cohorts to batch correction. Prior to this correction, the PCA plot exhibited pronounced disparities among the four cohorts (Fig. 2 A). However, post-correction, batch effect variations in gene expression distribution across all cohorts were effectively nullified (Fig. 2 B). Subsequently, employing the GSEA method, we computed 7530 gene sets, each reflecting the activation status of distinct cellular signaling pathways; each sample included in the analysis garnered a score across these 7530 pathways. The distribution of scores for these pathways across samples in the different cohorts is illustrated in Fig. 2 C.
Batch correction and gene set enrichment analysis outcomes. ( A ) Principal component analysis (PCA) plot showing gene expression disparities among the four cohorts prior to batch correction. ( B ) PCA plot post batch correction showcasing uniform gene expression distribution across all cohorts. ( C ) Distribution of scores across 7530 signaling pathways, based on Gene Set Enrichment Analysis (GSEA), for samples in the different cohorts.
Subsequent to this, within each cohort, we discerned signaling pathways that were differentially activated between UC patients and healthy controls (Fig. 3 A). In the GSE38713 cohort, 79 pathways were upregulated in UC patients; in the GSE47908 cohort, 428 pathways were upregulated; in the GSE59071 cohort, 107 pathways were upregulated, and in the GSE87466 cohort, 3,609 pathways saw upregulation in UC patients. By extracting the intersecting upregulated pathways across the four cohorts, a total of 19 pathways were finalized (Fig. 3 B). These 19 pathways pertained to cell adhesion and development, cell respiration and metabolism, immune response and signaling, as well as regulation of protein activity and secretion (Fig. 3 C). Excluding the redundant genes within these pathways, a total of 83 unique genes remained.
Differentially activated signaling pathways in Ulcerative Colitis (UC) patients versus healthy controls for each cohort. ( A ) Visualization of pathways upregulated in UC patients across the four cohorts. ( B ) Venn diagram illustrating the 19 common upregulated pathways identified across all cohorts. ( C ) List of the names of the 19 upregulated pathways.
The predictors used as input for the ML models are the gene expression levels of the 83 identified genes. These variables are continuous, representing the expression levels of each gene. Through the iterative analysis of the selected 83 genes across 101 algorithm combinations, 40 combination models were successfully generated. These models displayed their predictive capabilities across different cohorts using AUC values, with the average AUC value across four cohorts also being computed (Fig. 4 A). Ultimately, the LASSO regression model demonstrated superior diagnostic capabilities (Average AUC = 0.942). The prediction score can be calculated with the formula: Score = 0.03328012 × SYK + 0.51625614 × CALR − 0.14331840 × GATA5 + 1.29808010 × FLRT2 + 0.80143919 × IRAK3 − 0.59448664 × DUSP26 + 0.85254969 × SPINK5 + 0.25364614 × PTPN6 + 0.44029637 × LCN2 + 0.70178103 × ASS1 + 0.20803807 × BAK1 + 0.70268334 × VCP + 0.27895531 × ACTN3.
Machine learning-based diagnostic model evaluation. ( A ) AUC values of the 40 types of machine learning model across the four cohorts. ( B – E ) Kappa statistics for GSE38713 ( B ), GSE47908 ( C ), GSE59071 ( D ), and GSE87466 ( E ) comparing predicted outcomes with actual UC statuses.
Based on the LASSO model, the AUC values for the GSE87466, GSE38713, GSE59071, and GSE47908 cohorts were 1, 0.903, 0.963, and 0.902, respectively. Further, the Kappa statistic was employed to evaluate the heterogeneity between predicted and actual outcomes, revealing that the novel diagnostic model exhibited robust predictive power across all four cohorts (GSE87466: Kappa = 1, P < 0.001; GSE38713: Kappa = 0.652, P < 0.001; GSE59071: Kappa = 0.544, P < 0.001; GSE47908: Kappa = 0.623, P < 0.001; Fig. 4 B–E).
To further ascertain the diagnostic capabilities of the model, we included four external cohorts: GSE53306, GSE13367, GSE48958, and GSE126124. The samples from the first three cohorts were derived from intestinal mucosal tissue, while the GSE126124 cohort utilized peripheral blood samples from patients and healthy controls. Using the same methodology, we computed the predictive results of the four external cohorts across the 40 models. Ultimately, the LASSO-based diagnostic model consistently showcased commendable diagnostic prowess (Fig. 5 A) with the following results: GSE53306 (AUC = 0.798, Kappa = 0.360, P = 0.024, Fig. 5 B), GSE13367 (AUC = 0.782, Kappa = 0.340, P = 0.006, Fig. 5 C), GSE48958 (AUC = 0.873, Kappa = 0.529, P = 0.007, Fig. 5 D). For the GSE126124 cohort, although the AUC value was only 0.694, considering that these samples were derived from peripheral blood, its predictive capability near 0.7 remains a valuable asset for clinical diagnosis (Kappa = 0.272, P = 0.003, Fig. 5 E).
Assessing of the LASSO-based diagnostic model on external cohorts. ( A ) Overall diagnostic performance across the four external cohorts. ( B – E ) Detailed diagnostic metrics including AUC, Kappa, and P-values for external cohort, GSE53306 ( B ), GSE13367 ( C ), GSE48958 ( D ), and GSE126124 ( E ).
The LASSO logistic regression analysis incorporated 13 genes into the model, namely SYK, CALR, GATA5, FLRT2, IRAK3, DUSP26, SPINK5, PTPN6, LCN2, ASS1, BAK1, VCP, and ACTN3. To elucidate the conditions of these 13 genes, their expression differences between UC patients and healthy controls in a training cohort amalgamated from four cohorts were initially assessed. Notably, 11 out of these 13 genes exhibited significantly heightened expression in UC patients, while DUSP26 manifested diminished expression and ACTN3 showcased no significant difference (Fig. 6 A). We selected three significantly upregulated genes in UC, namely LCN2, ASS1, and IRAK3, for further validation in external cohorts. In the GSE13367 dataset, the expression of three genes was notably elevated in UC patients compared to healthy controls. Although these genes exhibited higher expression in inflamed UC patients, there was no statistically significant difference when compared to non-inflamed patients (Fig. 6 B). In the GSE48958 dataset, the expression trends of these genes mirrored the previously described patterns, with LCN2 showing the highest expression in active UC patients (Fig. 6 C). In the GSE53360 dataset, we observed that LCN2 also had the highest expression in active UC patients, with significant differences when compared both to non-active patients (P < 0.05) and to healthy controls (P < 0.05) (Fig. 6 D). These findings indicate that LCN2, ASS1, and IRAK3 are crucial markers distinguishing between healthy controls and UC patients.
Expression profiles of the 13 characteristic genes. ( A ) Expression differences between UC patients and healthy controls for the identified genes in a merged training cohort. ( B – D ) Validation of expression patterns of LCN2, ASS1, and IRAK3 in three external datasets, GSE13367 ( B ), GSE48958 ( C ), and GSE53360 ( D ).
A plethora of research concurs that immune system dysregulation is a critical factor precipitating the onset of UC. Consequently, a comparison was made between all included normal controls and UC patients to discern differences in immune cell distribution. It was discerned that the majority of immune cells exhibited pronounced expression elevation in UC patients, most notably myeloid-derived suppressor cell (MDSC), Neutrophil, and central memory CD4 T cells (Fig. 7 A). Subsequent investigations evaluated the relationship between LCN2, ASS1, IRAK3, and immune cell infiltration in all UC patients. All three genes exhibited positive correlations with the majority of immune cells, with the strongest associations found with activated dendritic cells, neutrophils, and immature dendritic cells (Fig. 7 B–D). Additionally, correlations were established between LCN2 and Effector memory CD8 T cells as well as Gamma delta T cells (Fig. 7 B); ASS1 and Type 17T helper cells (Fig. 7 C); and IRAK3 with Type 1T helper cells and Gamma delta T cells (Fig. 7 D).
Analysis of immune cell infiltration in UC and its relationship with LCN2, ASS1, and IRAK3. ( A ) Differences in immune cell distribution between UC patients and normal controls. ( B – D ) Correlation plots showcasing associations between LCN2 ( B ), ASS1 ( C ), and IRAK3 ( D ) and various immune cells.
It was observed that all three genes had a pronounced positive correlation with activated dendritic cells. Therefore, further analysis delved into the relationship between these genes and different UC disease statuses. In the GSE13367 cohort, the strongest correlations in active UC patients with activated dendritic cells were noted (LCN2: R = 0.72, P = 0.0024; ASS1: R = 0.61, P = 0.014; IRAK3: R = 0.71, P = 0.0029; Fig. 8 A). In the GSE48958 cohort, only IRAK3 exhibited a positive correlation with activated dendritic cells in active UC patients (R = 0.82, P = 0.034, Fig. 8 B).
Correlation of LCN2, ASS1, and IRAK3 with activated dendritic cells across different UC disease statuses. ( A ) Correlations in the GSE13367 cohort for three genes and UC patients. ( B ) Correlation in the GSE48958 cohort for three genes and UC patients.
UC remains a focal point in gastroenterological research due to its multifaceted etiological profile and the intricacies associated with its management 25 , 26 . Developing a robust diagnostic model that can accurately differentiate between UC patients and healthy individuals could offer a paradigm shift in the management of this condition. The application of machine learning in biomedical research has surged exponentially in recent years, with its prowess in data handling and pattern recognition being especially transformative for complex datasets 27 , 28 , 29 . The present study exemplifies this paradigm shift by utilizing machine learning to sift through intricate gene expression profiles, leading to the elucidation of a diagnostic model for UC.
In the current study, four training cohorts were utilized to identify key pathways and genes, leading to the construction of the prediction model in GSE87466, followed by internal validation and subsequent external validation. GSE87466, comprising the largest sample size, was selected for model construction. We did not amalgamate all four training cohorts into a single extensive dataset due to the potential substantial batch effects within the cohorts. For the external validation cohort, GSE126124 comprises samples from peripheral whole blood, whereas the training cohort GSE87466 includes samples from mucosa. In summary, this study encompasses training, internal validation, external validation, and further validation with peripheral whole blood samples to ensure the diagnostic model's robustness and credibility. Central to our findings is the delineation of specific cellular pathways and genes that are distinctly altered in UC patients. Notably, the pathways identified in our study encompass a broad spectrum of cellular processes, ranging from cell adhesion to immune signaling, reinforcing the notion of UC as a systemic ailment with widespread cellular repercussions 30 , 31 . In subsequently study, the iterative analysis of 83 genes across 101 algorithm combinations is testament to this capability. It is noteworthy that out of these numerous combinations, a set of 40 viable diagnostic models emerged, showcasing the flexibility and rigor of machine learning in generating a suite of models tailored to the data's nuances. The Average AUC value of 0.942 achieved by the LASSO model, and its robust predictive power across all four cohorts, underscore its efficacy. In addition, the model demonstrating remarkable diagnostic precision across multiple external validation cohorts. The strength of the model, as evidenced by its high average AUC value, suggests that gene expression profiling can serve as a formidable tool in the diagnostic arsenal against UC. Furthermore, the robustness of this model, even when applied to peripheral blood samples, underscores its potential versatility and broad applicability in clinical settings.
The incorporation of machine learning also allowed for the identification of 13 key genes, which upon further validation, revealed LCN2, ASS1, and IRAK3 as pivotal markers distinguishing between healthy individuals and UC patients. It is well-established that UC is characterized by chronic inflammation of the colon, predominantly driven by an aberrant immune response 32 . In this study, the robust correlation observed between the expression levels of LCN2, ASS1, and IRAK3 and specific immune cell populations, particularly activated dendritic cells, highlights the intertwined relationship between these genes and immune cell activity in UC 33 . Dendritic cells are known to play a pivotal role in antigen presentation and initiation of adaptive immune responses, their activation could subsequently lead to the recruitment and activation of other immune cells, perpetuating the inflammatory cascade observed in UC 34 , 35 . Notably, LCN2 has been previously documented to play a role in innate immunity, being associated with neutrophil function and acting as a bacteriostatic agent by sequestering iron, which in turn limits bacterial growth 36 , 37 , 38 . Although we observed that IRAK3 is correlated with the infiltration of activated dendritic cell, however, it can not distinguish the disease status of UC, the potential reason is that in the UC cases, inflammation and tissue remodeling of uninflamed (inactive) regions similar to inflamed (active) regions, they all have the increased expression of TGF -β, vimentin, and α-SMA 39 .
Combining various methods in a multi-faceted research setup presents a range of benefits and drawbacks. One significant advantage is the increased robustness and reliability of the results. By integrating different techniques, such as machine learning algorithms and gene expression analyses, researchers can cross-validate findings, reducing the likelihood of false positives and enhancing the overall confidence in the results. Additionally, the flexibility in combining methods can facilitate the discovery of novel biomarkers and therapeutic targets, providing a holistic view of disease mechanisms and potential intervention points. However, there are inherent drawbacks to this approach. The complexity of managing and integrating diverse datasets and methodologies can be challenging, requiring advanced computational skills and substantial computational resources. The risk of overfitting increases with the use of multiple machine learning models, where a model may perform exceptionally well on training data but poorly on unseen data, thus limiting its generalizability. Furthermore, while combining methods can highlight potential biomarkers or pathways, it often does not provide mechanistic insights into their roles, necessitating further functional studies to elucidate their contributions to disease pathogenesis. Therefore, while the integration of multiple methods can significantly advance our understanding and management of diseases like UC, it requires careful consideration of these potential limitations.
While the advantages of machine learning are manifold, it is vital to approach its results with a measure of caution, and there are several limitations for the current study. First, this study utilized a relatively small cohort of patients. Larger and more varied cohorts are necessary to validate the diagnostic model across different demographic groups. Second, the external validation cohorts primarily consisted of mucosal tissue samples, with only one cohort (GSE126124) derived from peripheral blood. The diagnostic model's performance in blood samples was lower (AUC = 0.694) compared to mucosal samples, indicating the need for further refinement and validation in non-invasive sample types like blood. Third, while the study identified several key genes and pathways associated with UC, it did not provide detailed mechanistic insights into how these genes contribute to the disease's pathogenesis. Functional studies are necessary to elucidate the biological roles of these genes and their potential as therapeutic targets.
In conclusion, our research epitomizes the transformative potential of machine learning in the realm of UC research, offering hope for more accurate and early diagnosis. As we stand on the cusp of a new era in personalized medicine, integrating machine learning insights with traditional biomedical research could pave the way for novel therapeutic avenues and improved patient outcomes. Future studies should prioritize external validation of these models in diverse populations and delve deeper into the functional roles of identified biomarkers.
All the datasets presented in this study can be obtained from the GEO ( http://www.ncbi.nlm.nih.gov/geo ) database, and details listed in Table 1 . Data is provided within the manuscript or supplementary information files and it is available upon request from the corresponding author.
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The authors acknowledge support from 2023 Wan-nan Medical College Scientific Research Project (No. WK2023ZQNZ52), the Key Research Project of Wan-nan Medical College (No. WK2022ZF03) and Wuhu City Science and Technology Project (No. 2021cg36). Thanks to ChatGPT for polishing the language and grammar of the article.
These authors contributed equally: Lin Li and Pingbo Chen.
Department of Gastroenterology, The First Affiliated Hospital of Wan-Nan Medical College, Wuhu, 241001, China
Jing Wang, Lin Li, Chiyi He & Xiaoping Niu
Department of Joint-Orthopedics, The First Affiliated Hospital of Wan-Nan Medical College, Wuhu, 241001, China
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Jing Wang: Conceptualization, methodology, formal analysis, writing—original draft preparation; Lin Li: Data curation, software, validation, visualization; Pingbo Chen: Supervision, funding acquisition, project administration, writing—reviewing and editing; Chiyi He: Supervision, writing—reviewing and editing; Xiaoping Niu: Supervision, funding acquisition, writing—reviewing and editing. All authors read and approved the final manuscript.
Correspondence to Xiaoping Niu .
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To identify the research trends in studies related to STEM Clubs, 56 publications that met the inclusion and extraction criteria were identified from the online databases ERIC and WoS in this study. These studies were analysed by using the descriptive content analysis research method based on the Paper Classification Form (PCF), which includes publishing years, keywords, research methods, sample levels and sizes, data collection tools, data analysis methods, durations, purposes, and findings. The findings showed that, the keywords in the studies were used under six different categories: disciplines, technological concepts, academic community, learning experiences, core elements of education, and psychosocial factors (variables). Case studies were frequently employed, with middle school students serving as the main participants in sample groups ranging from 11–15, 16–20, and 201–250. Surveys, questionnaires, and observations were the primary methods of data collection, and descriptive analysis was commonly used for data analysis. STEM Clubs had sessions ranging from 2 to 16 weeks, with each session commonly lasting 60 to 120 min. The study purposes mainly focused on four themes: the impact of participation on various aspects such as attitudes towards STEM disciplines, career paths, STEM major selection, and academic achievement; the development and implementation of a sample STEM Club program, including challenges and limitations; the examination of students' experiences, perceptions, and factors influencing their involvement and choice of STEM majors; the identification of some aspects such as attitudinal effects and non-academic skills; and the comparison of STEM experiences between in-school and out-of-school settings. The study results mainly focused on three themes: the increase in various aspects such as academic achievement, STEM major choice, engagement in STEM clubs, identity, interest in STEM, collaboration-communication skills; the design of STEM Clubs, including sample implementations, design principles, challenges, and factors affecting their success and sustainability; and the identification of factors influencing participation, motivation, and barriers. Overall, this study provides a comprehensive understanding of STEM Clubs, leading the way for more targeted and informed future research endeavours.
The use of cronbach’s alpha when developing and reporting research instruments in science education.
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Worldwide, STEM education, which integrates the disciplines of science, technology, engineering, and math, is gaining popularity in K-12 settings due to its capacity to enhance 21st-century skills such as adaptability, problem-solving, and creative thinking (National Research Council [NRC], 2015 ). In STEM lessons, students are frequently guided by the engineering design process, which involves identifying problems or technical challenges and creating and developing solutions. Furthermore, higher achievement in STEM education has been linked to increased enrolment in post-secondary STEM fields, offering students greater opportunities to pursue careers in these domains (Merrill & Daugherty, 2010 ). However, STEM activities require dedicated time and the restructuring of integrated curricula, necessitating careful organization of lessons. Recognizing the complexity of developing 21st-century STEM proficiency, schools are not expected to tackle this challenge alone. In addition to regular STEM classes, there exists a diverse range of extended education programs, activities, and out-of-school learning environments (Baran et al., 2016 ; Kalkan & Eroglu, 2017 ; Schweingruber et al., 2014 ). In this paper, out-of-school learning environments, informal learning environments, extended education, and afterschool programs were used synonymously. It is worth noting that the literature lacks a universally accepted definition for out-of-school learning environments, leading to the use of various interchangeable terms (Donnelly et al., 2019 ). Some of these terms include informal learning environments, extended education, afterschool programs, all-day school, extracurricular activities, out-of-school time learning, extended schools, expanded learning, and leisure-time activities. These terms refer to optional programs and clubs offered by schools that exist outside of the standard academic curriculum (Baran et al., 2016 ; Cooper, 2011 ; Kalkan & Eroglu, 2017 ; Schweingruber et al., 2014 ).
Out-of-school learning, in contrast to traditional in-school learning, offers greater flexibility in terms of time and space, as it is not bound by the constraints of the school schedule, national or state standards, and standardized tests (Cooper, 2011 ). Out-of-school learning experiences typically involve collaborative engagement, the use of tools, and immersion in authentic environments, while school environments often emphasize individual performance, independent thinking, symbolic representations, and the acquisition of generalized skills and knowledge (Resnick, 1987 ). They encompass everyday activities such as family discussions, pursuing hobbies, and engaging in daily conversations, as well as designed environments like museums, science centres, and afterschool programs (Civil, 2007 ; Hein, 2009 ). On the other hand, extended education refers to intentionally structured learning and development programs and activities that are not part of regular classes. These programs are typically offered before and after school, as well as at locations outside the school (Bae, 2018 ). As a result, out-of-school learning environments encompass a wide range of experiences, including social, cultural, and technical excursions around the school, field studies at museums, zoos, nature centres, aquariums, and planetariums, project-based learning, sports activities, nature training, and club activities (Civil, 2007 ; Donnelly et al., 2019 ; Hein, 2009 ). At this point, STEM clubs are a specialized type of extracurricular activity that engage students in hands-on projects, experiments, and learning experiences related to scientific, technological, engineering, and mathematical disciplines. STEM Clubs, described as flexible learning environments unconstrained by time or location, offer an effective approach to conducting STEM studies outside of school (Blanchard et al., 2017 ; Cooper, 2011 ; Dabney et al., 2012 ).
Out-of-school learning environments, extended education or afterschool programs, hold tremendous potential for enhancing student learning and providing them with a diverse and enriching educational experience (Robelen, 2011 ). Extensive research supports the notion that these alternative educational programs not only contribute to students' academic growth but also foster their social, emotional, and intellectual development (NRC, 2015 ). Studies have consistently shown that after-school programs play a vital role in boosting students' achievement levels (Casing & Casing, 2024 ; Pastchal-Temple, 2012 ; Shernoff & Vandell, 2007 ), and contributing to positive emotional development, including improved self-esteem, positive attitudes, and enhanced social behaviour (Afterschool Alliance, 2015 ; Durlak & Weissberg, 2007 ; Lauer et al., 2006 ; Little et al., 2008 ). Moreover, engaging in various activities within these programs allows students to develop meaningful connections, expand their social networks, enhance leadership skills (Lipscomb et al., 2017 ), and cultivate cooperation, effective communication, and innovative problem-solving abilities (Mahoney et al., 2007 ).
Implementing STEM activities in out-of-school learning environments not only supports students in making career choices and fostering meaningful learning and interest in science, but also facilitates deep learning experiences (Bybee, 2001 ; Dabney et al., 2012 ; Sahin et al., 2018 ). Furthermore, STEM Clubs enhance students' emotional skills, such as a sense of belonging and peer-to-peer communication, while also fostering 21st-century skills, facilitating the acquisition of current content, and promoting career awareness and interest in STEM professions (Blanchard et al., 2017 ). In summary, engaging in STEM activities through social club activities not only addresses time constraints but also complements formal education and contributes to students' overall development. Hence, STEM Clubs, which are part of extended education, can be defined as dynamic and flexible learning environments that provide an effective approach to conducting STEM studies beyond traditional classroom settings. These clubs offer flexibility in terms of time and location, with intentionally structured programs and activities that take place outside of regular classes. They provide students with unique opportunities to explore and deepen their understanding of STEM subjects through collaborative engagement, hands-on use of tools, and immersive experiences in authentic environments (Bae, 2018 ; Blanchard, et al., 2017 ; Bybee, 2001 ; Cooper, 2011 ; Dabney et al., 2012 ). STEM Clubs have gained immense popularity worldwide, providing students with invaluable opportunities to explore and cultivate their interests and knowledge in these crucial fields (Adams et al., 2014 ; Bell et al., 2009 ). According to America After 3PM, nearly 75% of afterschool program participants, around 5,740,836 children, have access to STEM learning opportunities (Afterschool Alliance, 2015 ).
STEM Clubs as after-school programs come in various forms and provide diverse tutoring and instructional opportunities. For instance, the Boys and Girls Club of America (BGCA) operates in numerous cities across the United States, annually serving 4.73 million students (Boys and Girls Club of America, 2019 ). This program offers students the chance to engage in activities like sports, art, dance, field trips, and addresses the underrepresentation of African Americans in STEM. Another example is the Science Club for Girls (SCFG), established by concerned parents in Cambridge to address gender inequity in math, science, and technology courses and careers. SCFG brings together girls from grades K–7 through free after-school or weekend clubs, science explorations during vacations, and community science fairs, with approximately 800 to 1,000 students participating each year. The primary goal of these clubs is to increase STEM literacy and self-confidence among K–12 girls from underrepresented groups in these fields. More examples can be found in the literature, such as the St. Jude STEM Club (SJSC), where students conducted a 10-week paediatric cancer research project using accurate data (Ayers et al., 2020 ), and After School Matters, based in Chicago, offers project-based learning that enhances students' soft skills and culminates in producing a final project based on their activities (Hirsch, 2011 ).
The literature on STEM Clubs indicates a diverse range of such clubs located worldwide, catering to different student groups, operating on varying schedules, implementing diverse activities, and employing various strategies, methodologies, experiments, and assessments (Ayers et al., 2020 ; Blanchard et al., 2017 ; Boys and Girls Club of America, 2019 ; Hirsch, 2011 ; Sahin et al., 2018 ). However, it was previously unknown which specific sample groups were most commonly studied, which analytical methods were used frequently, and which results were primarily reported, even though the overall topic of STEM Clubs has gained significant attention. Therefore, organizing and categorizing this expansive body of literature is necessary to gain deeper insights into the current state of knowledge and practices in STEM Clubs. By systematically reviewing and synthesizing the diverse range of studies on this topic, we can develop a clearer understanding of the focus areas, methodologies, and key findings that have emerged from the existing research (Fraenkel et al., 2012 ). At this point, using a content analysis method is appropriate for this purpose because this method is particularly useful for examining trends and patterns in documents (Stemler, 2000 ). Similarly, some previous research on STEM education has conducted content analyses to examine existing studies and construct holistic patterns to understand trends (Bozkurt et al., 2019 ; Chomphuphra et al., 2019 ; Irwanto et al., 2022 ; Li et al., 2020 ; Lin et al., 2019 ; Martín-Páez et al., 2019 ; Noris et al., 2023 ). However, there is a lack of content analysis specifically focused on studies of STEM Clubs in the literature and showing the trends in this topic. Analysing research trends in STEM Clubs can help build upon existing knowledge, identify gaps, explore emerging topics, and highlight successful methodologies and strategies (Fraenkel et al., 2012 ; Noris et al., 2023 ; Stemler, 2000 ). This information can be valuable for researchers, educators, and policymakers to stay up-to-date and make informed decisions regarding curriculum design (Bozkurt et al., 2019 ; Chomphuphra et al., 2019 ; Irwanto et al., 2022 ; Li et al., 2020 ; Lin et al., 2019 ; Martín-Páez et al., 2019 ; Noris et al., 2023 ), the development of effective STEM Club programs, resource allocation, and policy formulation (Blanchard et al., 2017 ; Cooper, 2011 ; Dabney et al., 2012 ). Therefore, the identification of research trends in STEM Clubs was the aim of this study.
To identify research trends, studies commonly analysed documents by considering the dimensions of articles such as keywords, publishing years, research designs, purposes, sample levels, sample sizes, data collection tools, data analysis methods, and findings (Bozkurt et al., 2019 ; Chomphuphra et al., 2019 ; Irwanto et al., 2022 ; Li et al., 2020 ; Sozbilir et al., 2012 ). Using these dimensions as a framework is a useful and common approach in content analysis because this framework allows researchers to systematically examine the key aspects of existing studies and uncover patterns, relationships, and trends within the research data (Sozbilir et al., 2012 ). Hence, since the aim of this study is to identify and analyse research trends in STEM Clubs, it focused on publishing years, keywords, research designs, purposes, sample levels, sample sizes, data collection tools, data analysis methods, and findings of the studies on STEM Clubs.
As a conclusion, the main problem of this study is “What are the characteristics of the studies on STEM Clubs?”. The following sub-questions are addressed in this study:
What is the distribution of studies on STEM Clubs by year?
What are the frequently used keywords in studies on STEM Clubs?
What are the commonly employed research designs in studies on STEM Clubs?
What are the typical purposes explored in studies on STEM Clubs?
What are the commonly observed sample levels in studies on STEM Clubs?
What are the commonly observed sample sizes in studies on STEM Clubs?
What are the commonly utilized data collection tools in studies on STEM Clubs?
What are the commonly utilized data analysis methods in studies on STEM Clubs?
What are the typical durations reported in studies on STEM Clubs?
What are the commonly reported findings in studies on STEM Clubs?
In this study, the descriptive content analysis research method was employed, which allows for a systematic and objective examination of the content within articles, and description of the general trends and research results in a particular subject matter (Lin et al., 2014 ; Suri & Clarke, 2009 ; Sozbilir et al., 2012 ; Stemler, 2000 ). Given the aim of examining research trends in STEM Clubs, the utilization of this method was appropriate, as it provides a structured approach to identify patterns and trends (Gay et al., 2012 ). To implement the content analysis method, this study followed the three main phases proposed by Elo and Kyngäs ( 2008 ): preparation, organizing, and reporting. In the preparation phase, the unit of analysis, such as a word or theme, is selected as the starting point. So, in this study, the topic of STEM Clubs was carefully selected. During the organizing process, the researcher strives to make sense of the data and to learn "what is going on" and obtain a sense of the whole. So, in this study, during the analysis process, the content analysis framework (sample levels, sample sizes, data collection tools, research designs, etc.) was used to question the collected studies. Finally, in the reporting phase, the analyses are presented in a meaningful and coherent manner. So, the analyses were presented meaningfully with visual representations such as tables, graphs, etc. By adopting the content analysis research method and following the suggested phases, this study aimed to gain insights into research trends in STEM Clubs, identify recurring themes, and provide a comprehensive analysis of the collected data.
The online databases ERIC and Web of Science were searched using keywords derived from a database thesaurus. These databases were chosen because of their widespread recognition and respect in the fields of education and academic research, and they offer a substantial amount of high-quality, peer-reviewed literature. The search process involved several steps. Firstly, titles, abstracts, and keywords were searched using Boolean operators for the keywords "STEM Clubs," "STEAM Clubs," "science-technology-engineering-mathematics clubs," "after school STEM program" and "extracurricular STEM activities" in the databases (criterion-1). Secondly, studies were collected beginning from November to the end of December 2023. So, the studies published until the end of December 2023 were included in the search, without a specific starting date restriction (criterion-2). Thirdly, the search was limited to scientific journal articles, book chapters, proceedings, and theses, excluding publications such as practices, letters to editors, corrections, and (guest) editorials (criterion-3). Fourthly, studies published in languages other than English were excluded, focusing exclusively on English language publications (criterion-4). Fifthly, duplicate articles found in both databases were identified and removed. Next, the author read the contents of all the studies, including those without full articles, with a particular focus on the abstract sections. After that, studies related to after school program and extracurricular activities that did not specifically involve the terms STEM or clubs were excluded, even though “extracurricular STEM activities” and “after school STEM program” were used in the search process, and there were studies related to after school program or extracurricular activities but not STEM (criterion-5). Additionally, studies conducted in formal and informal settings within STEM clubs were included, while studies conducted in settings such as museums or trips were excluded (criterion-6). Because STEM Clubs are a subset of informal STEM education settings, which also include museums and field trips, the main focus of this study is to show the trends specifically related to STEM Clubs. Moreover, studies focusing solely on technology without incorporating other STEM components were also excluded (criterion-7). Finally, 56 publications that met the inclusion and extraction criteria were identified. These publications comprised two dissertations, seven proceedings, and 47 articles from 36 different journals. By applying these criteria, the search process aimed to ensure the inclusion of relevant studies while excluding those that did not meet the specified criteria as shown in Fig. 1 .
Flowchart of article process selection
Two different approaches were followed in the content analysis process of this study. In the first part, deductive content analysis was used, and a priori coding was conducted as the categories were established prior to the analysis. The categorization matrix was created based on the Paper Classification Form (PCF) developed by Sozbilir et al. ( 2012 ). The coding scheme devised consisted of eight classification groups for the sections of publication years, keywords, research designs, sample levels, sample sizes, data collection tools, data analysis methods, and durations, with sub-categories for each section. For example, under the research designs section, the sub-categories included qualitative and quantitative methods, case study, design-case study, comparative-case study, ethnographic study, phenomenological study, survey study, experimental study, mixed and longitudinal study, and literature review study. These sub-categories were identified prior to the analysis. Coding was then applied to the data using spreadsheets in the Excel program, based on the categorization matrix. Frequencies for the codes and categories created were calculated and presented in the findings section with tables. Line charts were used for the publication years section, while word clouds, which visually represent word frequency, were used for the keywords section. Word clouds display the most frequently used words in different sizes and colours based on their frequencies (DePaolo & Wilkinson, 2014 ). So, in this part, the analysis was certain since the studies mostly provided related information in their contents.
In the second part, open coding and the creation of categories and abstraction phases were followed for the purposes and findings sections. Firstly, the stated purposes and findings of the studies were written as text. The written text was then carefully reviewed, and any necessary terms were written down in the margins to describe all aspects of the content. Following this open coding, the lists of categories were grouped under higher order headings, taking into consideration their similarities or dissimilarities. Each category was named using content-characteristic words. The abstraction process was repeated to the extent that was reasonable and possible. In this coding process, two individuals independently reviewed ten studies, considering the coding scheme for the first part and conducting open coding for the second part. They then compared their notes and resolved any differences that emerged during their initial checklists. Inter-rater reliability was calculated as 0.84 using Cohen's kappa analysis. Once coding reliability was ensured, the remaining articles were independently coded by the author. After completing the coding process, consensus was reached through discussions regarding any disagreements among the researchers regarding the codes, as well as the codes and categories constructed for the purpose and findings sections. At this point, there were mostly agreements in the coding process since the studies had already clearly stated their key characteristics, such as research design, sample size, sample level, and data collection tools. Additionally, when coding the studies' stated purposes and results, the researchers closely referred to the original sentences in the studies, which led to a high level of consistency in the coded content between the two raters.
Studies related to the STEM Clubs were initially conducted in 2009 (Fig. 2 ). The noticeable increase in the number of studies conducted each year is remarkable. It can be seen that the majority of the 47 articles that were examined (56 articles) were published after 2015, despite a decrease in the year 2018. Additionally, it was observed that the articles were most frequently published (8) in the years 2019 and 2022, least frequently (1) in the years 2009, 2010, and 2014, and there were no publications in 2012.
Number of articles by years
Word clouds were utilized to present the most frequently used keywords in the articles, as shown in Fig. 3 . However, due to the lack of reported keywords in the ERIC database, only 30 articles were included for these analyses. The keywords that exist in these studies were represented in a word cloud in Fig. 3 . The most frequently appearing keywords, such as "STEM," "education" and "learning" were identified. Additionally, by using a content analysis method, these keywords were categorized into six different groups: disciplines, technological concepts, academic community, learning experiences, core elements of education, and psychosocial factors (variables) in Table 1 .
Word cloud of the keywords used in articles
The purposes of the identified studies identified were classified into six main themes: “effects of participation in STEM Clubs on” (25), “evolution of a sample program for STEM Clubs and its implementation” (25), “examination of” (11), “identification of” (3), “comparison of in-school and out-school STEM experiences” (2) and “others” (6). Table 2 presents the distribution of the articles’ purposes based on the classification regarding these themes. Therefore, it can be seen that purposes of “effects of participation in STEM Clubs on,” and “evolution of a sample program for STEM Clubs and its implementation” were given the highest and equal consideration, while the purposes related to "identification of" (3) and "comparison of in-school and out-of-school STEM experiences" (2) were given the least consideration among them.
Within the theme of "effects of participation in STEM Clubs on" there are 11 categories. The aims of the studies in this section are to examine the effect of participation in STEM Clubs on various aspects such as attitudes towards STEM disciplines or career paths, STEM major choice/career aspiration, achievement in math, science, STEM disciplines, or content knowledge, perception of scientists, strategies used, value of clubs, STEM career paths, enjoyment of physics, use of complex and scientific language, interest in STEM, creativity, critical thinking about STEM texts, images of mathematics, or climate-change beliefs/literacy. It is evident that the majority of research in this section focuses on the effects of participation in STEM Clubs on STEM major choice/career aspiration (5), achievement (4), perception of something (4), and interest in STEM (3).
Within the theme of "evolution of a sample program for STEM Clubs and its implementation" there are three categories: development of program/curriculum/activity (14), identification of program's challenges and limitations (3), and implementation of program/activity (8). The studies in this section aim to develop a sample program for STEM Clubs and describe its implementation. It can be seen that the most preferred purpose among them is the development of program/curriculum/activity (14), while the least preferred purpose is the identification of program's challenges and limitations (3). In addition, studies that focus on the development of the program, curriculum, or activity were classified under the "general" category (10). Sub-categories were created for studies specifically expressing the development of the program with a focus on a particular area, such as the maker movement or Arduino-assisted robotics and coding. Similarly, studies that explicitly mentioned the development of the program based on presented ideas and experiences formed another sub-category. Furthermore, the category related to the implementation of program/activity was divided into eight sub-categories, each indicating the specific centre of implementation, such as problem-based learning-centred and representation of blacks-centred.
The theme of "examination of" refers to studies that aim to examine certain aspects, such as the experiences and perceptions of students (7) and the factors influencing specific subjects (4). Studies focusing on examining the experiences and perceptions of students were labelled as "general" (4), while studies exploring their experiences and perceptions regarding specific content, such as influences and challenges to participation in STEM clubs (2) and assessment (1), were labelled accordingly. Additionally, studies that focused on examining factors affecting the choice of STEM majors (2), participation in STEM clubs (1), and motivation to develop interest in STEM (1) were categorized in line with their respective focuses. As shown in Table 2 , it is evident that studies focusing on examining the experiences and perceptions of students (7) were more frequently conducted compared to studies focusing on examining the factors affecting specific subjects (4).
The theme of "identification of" refers to studies that aim to identify certain aspects, such as the types of attitudinal effects (1), types of changes in affect toward engineering (1), and non-academic skills (1). Additionally, the theme of "comparison of in-school and out-of-school STEM experiences" (2) refers to studies that aim to compare STEM experiences within school and outside of school. Lastly, studies that did not fit into the aforementioned categories were included in the "others" theme (6) as no clear connection could be identified among them.
The research designs employed in the examined articles were identified as follows: qualitative methods (36), including case study (20), design-case study (6), comparative-case study (4), ethnographic study (2), phenomenological study (2), and survey study (2); quantitative methods (7), including survey study (4) and experimental study (3); mixed methods and longitudinal studies (10); and literature review (3), as illustrated in Table 3 . It can be observed that among these methods, case study was the most commonly utilized. Furthermore, it is evident that quantitative methods (7) and literature reviews (3) were employed less frequently compared to qualitative (36) and mixed methods (10). Additionally, survey studies were utilized in both quantitative and qualitative studies.
The frequencies and percentages of sample levels in the examined articles are presented in Table 4 . The studies involved participants at different educational levels, including elementary school (8), middle school (23), high school (14), pre-service teachers or undergraduate students (6), teachers (4), parents (3), and others (1). It is apparent that middle school students (23) were the most commonly utilized sample among them, while high school students (14) were more frequently chosen compared to elementary school students (8). It should be noted that while grade levels were specified for both elementary and middle school students, separate grade levels were not identified for high school students in these studies. Additionally, studies that involved mixed groups were labelled as 3-5th and 6-8th grades. However, when the mixed groups included participants from different educational levels such as elementary, middle, or high school, teachers, parents, etc., they were counted as separate levels. Furthermore, the studies conducted with participants such as pre-service teachers, undergraduates, teachers, and parents were less frequently employed compared to K-12 students.
The frequencies of sample sizes in the examined articles are presented in Table 5 . It was observed that in 15 studies, the number of sample sizes was not provided. The intervals for the sample size were not equally separated; instead, they were arranged with intervals of 5, 10, 50, and 100. This choice was made to allow for a more detailed analysis of smaller samples, as smaller intervals can provide a more granular examination of data instead of cumulative amounts. The analysis reveals that the studies primarily prioritized sample groups with 11–15 (f:8) participants, followed by groups of 16–20 (f:4) and 201–250 (f:4). Additionally, it is evident that sample sizes of 6–10, 21–25, 41–50, 50–100, and more than 2000 (f:1) were the least commonly studied.
The frequencies and percentages of data collection tools in the examined articles are presented in Table 6 . The analysis reveals that the studies primarily employed survey or questionnaires (31.6%) and observations (30.5%) as data collection methods, followed by interviews (15.8%), documents (13.7%), tests (4.2%), and field notes (4.2%). Regarding survey/questionnaires, Likert-type scales (f:23) were more commonly employed compared to open-ended questions (f:7). Tests were predominantly used as achievement tests (f:2) and assessments (f:2), representing the least preferred data collection tools. Furthermore, the table illustrates that multiple data collection tools were frequently employed, as the total number of tools (95) is nearly twice the number of studies (56).
The frequencies and percentages of data analysing methods in the examined articles are presented in Table 7 . The table reveals that the studies predominantly employed descriptive analysis (f:33, 41.25%), followed by inferential statistics (f:16, 20%), descriptive statistics (f:15, 18.75%), content analysis (f:14, 17.5%), and the constant-comparative method (f:2, 2.5%). It is notable that qualitative methods (f:49, 61.25%) were preferred more frequently than quantitative methods (f:31, 38.75%) in the examined studies related to STEM Clubs. Within the qualitative methods, descriptive analysis (f:33) was utilized nearly twice as often as content analysis (f:14), while within the quantitative methods, descriptive statistics (f:15) and inferential statistics (f:16), including t-tests, ANOVA, regression, and other methods, were used with comparable frequency.
The durations of STEM Clubs in the examined studies are presented in Table 8 . Based on the analysis, there are more studies (f:37) that do not state the duration of STEM Clubs than studies (f:19) that do provide information on the durations. Additionally, among the studies that do state the durations, there is no common period of time for STEM Clubs, as they were implemented for varying numbers of weeks and sessions, with session durations ranging from several minutes. Therefore, it can be observed that STEM Clubs were conducted over the course of 3 semesters (academic year and summer), 5 months, 2 to 16 weeks, with session durations ranging from 60 to 120 min. Furthermore, the durations of "3 semesters," "10 weeks with 90-min sessions per week," and "unknown weeks with 60-min sessions per week" were used more than once in the studies.
The content analysis of the findings of the identified examined articles are presented by their frequencies in Table 9 . Although the studies cover a diverse range of topics, the analysis indicates that the results can be broadly classified into three themes, namely, the "development of or increase in certain aspects" (f:68), "design of STEM Clubs" (f:17), and "identification of various aspects" (f:16). Based on the analysis, the findings in the studies are associated with the development of certain aspects such as skills or the increase in specific outcomes like academic achievement. Furthermore, the studies explore the design of STEM Clubs through the description of specific cases, such as sample implementations and challenges. Additionally, the studies focus on the identification of various aspects, such as factors and perceptions.
It is evident from the findings that the studies predominantly yield results related to the development of or increase in certain aspects (f:68). Within this theme, the most commonly observed result is the development of STEM or academic achievement or STEM competency (f:11). This is followed by an increase in STEM major choice or career aspiration (f:9), an increase in engagement or participation in STEM clubs (f:5), the development of identity including STEM, science, engineering, under-representative groups (f:5), the development of interest in STEM (f:4), an increase in enjoyment (f:4), and the development of collaboration, leadership, or communication skills (f:4). Furthermore, it can be observed that there are some results, such as the development of critical thinking, perseverance and the teachers’ profession, that were yielded less frequently (f:1). The results of 16 studies were found with a frequency of 1.
Within the design of STEM Clubs, the sample implementation or design model for different purposes such as the usage of robotic program or students with disabilities (f:7), design principles or ideas for STEM clubs, activities or curriculum (f:4), challenges or factors effecting STEM Clubs success and sustainability (f:3) were presented as a result. Additionally, the comparison was made between in-school and out-of-school learning environments (f:3), highlighting the contradictions of STEM clubs and science classes, as well as the differences in STEM activities and continues-discontinues learning experiences in mathematics. Within the identification of various aspects, the most commonly gathered result was the identification of factors affecting participation or motivation to STEM clubs (f:5). This was followed by the identification of barriers to participation (f:2). The identification of other aspects, such as parents' roles and perspectives on STEM, was comparatively less frequent.
Considering the wide variety of STEM Clubs found in different regions around the world, this study aimed to investigate the current state of research on STEM Clubs. It is not surprising to observe an increase in the number of studies conducted on STEM Clubs over the years. This can be attributed to the overall growth in research on STEM education (Zhan et al., 2022 ), as STEM education often includes activities and after-school programs as integral components (Blanchard et al., 2017 ). Identifying relevant keywords and incorporating them into a search strategy is crucial for conducting a comprehensive and rigorous systematic review (Corrin et al., 2022 ). To gain a broader understanding of keyword usage in the context of STEM Clubs, a word cloud analysis was performed (McNaught & Lam, 2010 ). Additionally, based on the content analysis method, six different categories for keywords were immerged: disciplines, technological concepts, academic community, learning experiences, core elements of education, and psychosocial factors (variables). The analysis revealed that the keyword "STEM" was used most frequently in the studies examined. This may be because authors want their studies to be easily found and widely searchable by others, so they use "STEM" as a general term for their studies (Corrin et al., 2022 ). Similarly, the frequent use of keywords like "education" and "learning" from the "core elements of education" category could be attributed to authors' desire to use broad, searchable terms to make their studies more discoverable (Corrin et al., 2022 ). Additionally, it was observed that from the STEM components, only "science" and "engineering" were used as keywords, while "mathematics" and "technology" were not present. This finding aligns with claims in the literature that mathematics is often underemphasized in STEM integration (Fitzallen, 2015 ; Maass et al., 2019 ; Stohlmann, 2018 ). Although the specific term "technology" did not appear in the word cloud, technology-related keywords such as "arduino," "robots," "coding," and "innovative" were present. Furthermore, the analysis revealed that authors preferred to use keywords related to their sample populations, such as "middle (school students)," "elementary (students)," "high school students," or "teachers." Additionally, keywords describing learning experiences, such as "extracurricular," "informal," "afterschool," "out-of-school," "social," "clubs," and "practice" were commonly used. This preference may stem from the fact that STEM clubs are often part of informal learning environments, out-of-school programs, or afterschool activities, and these concepts are closely related to each other (Baran et al., 2016 ; Cooper, 2011 ; Kalkan & Eroglu, 2017 ; Schweingruber et al., 2014 ). Moreover, the analysis showed that keywords related to psychosocial factors (variables), such as "disabilities," "skills," "interest," "attainment," "enactment," "expectancy-value," "self-efficacy," "engagement," "motivation," "career," "gender," "cognitive," and "identity" were also prevalent. This suggests that the articles investigated the effects of STEM club practices on these psychosocial variables. To sum up, by using these keywords, researchers can gain valuable insights and effectively search for relevant articles related to STEM clubs, enabling them to locate appropriate resources for their research (Corrin et al., 2022 ).
The popularity of case studies as a research design, based on the analysis, can be attributed to the fact that studies on STEM Clubs were conducted in diverse learning environments, highlighting sample implementation designs (Adams et al., 2014 ; Bell et al., 2009 ; Robelen, 2011 ). At this point, case studies offer the opportunity to present practical applications and real-world examples (Hamilton & Corbett-Whittier, 2012 ), which is highly valuable in the context of STEM Clubs. Additionally, the observation that quantitative methods were not as commonly utilized as qualitative methods in studies related to STEM Clubs contrasts with the predominant reliance on quantitative methods in STEM education research (Aslam et al., 2022 ; Irwanto et al., 2022 ; Lin et al., 2019 ). This suggests a lack of quantitative studies specifically focused on STEM Clubs, indicating a need for more research in this area employing quantitative approaches. Therefore, it is important to prioritize and conduct additional quantitative studies to further enhance our understanding of STEM Clubs and their impact. In studies on STEM Club, there is a higher frequency of research involving K-12 students, particularly middle school students, parallel to some studies on literature (Aslam et al., 2022 ), compared to other groups such as pre-service teachers, undergraduate students, teachers, and parents. This can be attributed to the fact that STEM Clubs are designed for K-12 students, and middle school is a crucial period for introducing them to STEM concepts and careers. Middle school students are developmentally ready for hands-on and inquiry-based learning, commonly used in STEM education. Additionally, time constraints, especially for high school students preparing for university, may limit their involvement in extensive STEM activities. Furthermore, STEM Clubs were primarily employed with sample groups ranging from 11–15, 16–20, and 201–250 participants. The preference for 11–20 participants, rather than less than 10, may be attributed to the collaborative nature of STEM activities, which often require a larger team for effective teamwork and group dynamics (Magaji et al., 2022 ). Utilizing small groups as samples can result in the case study research design being the most frequently employed approach due to its compatibility with smaller sample sizes. On the other hand, the inclusion of larger groups (201–250) is suitable for survey studies, as this number can represent the total student population attending STEM Clubs throughout a semester with multiple sessions (Boys & Girls Club of America, 2019 ).
According to studies on STEM Clubs, surveys or questionnaires and observations were predominantly used as data collection methods. This preference can be attributed to the fact that surveys or questionnaires allow researchers to gather data on diverse aspects, including students' attitudes, perceptions, and experiences related to STEM Clubs, facilitating generalization and comparison (McLafferty, 2016 ). Furthermore, observations were frequently employed because they can offer a deeper understanding of the lived experiences and actual practices within STEM Clubs (Baker, 2006 ). Along with data collection tools, descriptive analysis was predominantly utilized in studies on STEM Clubs, with quantitative methods including descriptive statistics and inferential statistics being used to a similar extent. The preference for descriptive analysis may arise from its effectiveness in describing activities, experiences, and practices within STEM Clubs. Given the predominance of case study research in the analysed studies, it is not surprising to observe a high frequency of descriptive statistics in the findings. On the other hand, the extensive use of quantitative analysing methods can be attributed to the need for statistical analysis of surveys and questionnaires (Young, 2015 ). Consequently, future studies on STEM Clubs could benefit from considering the use of tests and field notes as additional data collection tools, along with surveys, observations and interviews. Additionally, the development of tests specifically designed to assess aspects related to STEM could provide valuable insights (Capraro & Corlu, 2013 ; Grangeat et al., 2021 ). Moreover, increasing the utilization of content analysis and constant comparative analysis methods could further enhance the depth and richness of data analysis in STEM Club research (White & Marsh, 2006 ). In the studies on STEM Clubs, the duration and scheduling of the clubs varied considerably. While there was no common period of time for STEM Clubs, they were implemented for different numbers of weeks and sessions, with session durations ranging from several minutes to 60 to 120 min. However, it was observed that STEM Clubs were predominantly conducted over the course of three semesters, including the academic year and summer, or for durations of 2 to 16 weeks. This scheduling pattern can be attributed to the fact that STEM Clubs were often implemented as after-school programs, and they were designed to align with the academic semesters and summer school periods to effectively reach students. Additionally, the number of weeks in these studies may have been arranged according to the duration of academic semesters, although some studies were conducted for less than a semester (Gutierrez, 2016 ). The most common use of multiple sessions with a time range of 60 to 120 min can be attributed to the nature of the activities involved in STEM Clubs. These activities often require more time than regular class hours, and splitting them into separate sessions allows students to effectively concentrate on their work and engage in more in-depth learning experiences (Vennix et al., 2017 ).
The purposes of the studies on STEM Clubs were mostly related to effects of participation in STEM Clubs on various aspects such as attitudes towards STEM disciplines or career paths, STEM major choice/career aspiration, achievement etc., evolution of a sample program for STEM Clubs and its implementation including the development of program/activity, identification of program's challenges and limitations, and implementation of it, followed by the examination of certain aspects such as the experiences and perceptions of students and the factors influencing specific subjects, identification of such as the types of attitudinal effects and non-academic skills, and comparison of in-school and out-school STEM experiences. Therefore, the results of the studies parallel to the purposes were mostly related to development of or increase in certain aspects such as STEM or academic achievement or STEM competency STEM major choice or career aspiration engagement or participation in STEM Clubs, identity, interest in STEM, enjoyment, collaboration, communication skills, critical thinking, the design of STEM Clubs including the sample implementation or design model for different purposes such as the usage of robotic program or students with disabilities, design principles or ideas for STEM clubs or activities, challenges or factors effecting STEM Clubs success and sustainability, and the comparison between in-school and out-of-school learning environments. Also, they are related to the identification of various aspects such as factors affecting participation or motivation to STEM clubs, barriers to participation. At this point, it is evident that these identified categories align with the findings of studies in the literature. These studies claim that after-school programs, such as STEM Clubs, have positive impacts on students' achievement levels (NRC, 2015 ; Kazu & Kurtoglu Yalcin, 2021 ; Shernoff & Vandell, 2007 ), communication, and innovative problem-solving abilities (Mahoney et al., 2007 ), leadership skills (Lipscomb et al., 2017 ), career decision-making (Bybee, 2001 ; Dabney et al., 2012 ; Sahin et al., 2018 ; Tai et al., 2006 ), creativity (Wan et al., 2023 ), 21st-century skills (Hirsch, 2011 ; Zeng et al., 2018 ), interest in STEM professions (Blanchard et al., 2017 ; Chittum et al., 2017 ; Wang et al., 2011 ), and knowledge in STEM fields (Adams et al., 2014 ; Bell et al., 2009 ). Furthermore, it can be inferred that the studies on STEM Clubs paid significant attention to the design descriptions of programs or activities (Nation et al., 2019 ). This may be because there is a need for studies that focus on designing program models for different cases (Calabrese Barton & Tan, 2018 ; Estrada et al., 2016 ). These studies can serve as examples and provide guidance for the development of STEM clubs in various settings. By creating sample models, researchers can contribute to the improvement and expansion of STEM clubs across different environments (Cakir & Guven, 2019 ; Estrada et al., 2016 ).
In conclusion, as the studies on the trends in STEM education (Bozkurt et al., 2019 ; Chomphuphra et al., 2019 ; Irwanto et al., 2022 ; Li et al., 2020 ; Lin et al., 2019 ; Martín-Páez et al., 2019 ; Noris et al., 2023 ), the analysis of prevailing research trends specifically in STEM Clubs, which are implemented in diverse environments with varying methods and purposes, can provide a comprehensive understanding of these clubs as a whole.
It can also serve as a valuable resource for guiding future investigations in this field. By identifying common approaches and identifying gaps in methods and results, a holistic perspective on STEM Clubs can be achieved, leading to a more informed and targeted direction for future research endeavours.
Future research on STEM Clubs should consider the trends identified in the study and address methodological gaps. For instance, there is a lack of research in this area that employs quantitative approaches. Therefore, it is important for future studies to incorporate quantitative methods to enhance the understanding of STEM Clubs and their impact. This includes exploring underrepresented populations, investigating the long-term impacts of STEM Clubs, and examining the effectiveness of specific pedagogical approaches or interventions within these clubs. Researchers should conduct an analysis to identify common approaches used in STEM Clubs across different settings. This analysis can help uncover effective strategies, best practices, and successful models that can be replicated or adapted in various contexts. By undertaking these efforts, researchers can contribute to a more comprehensive understanding of STEM Clubs, leading to advancements in the field of STEM education.
It is important to consider the limitations of the study when interpreting its findings. The study's findings are based on the literature selected from two databases, which may introduce biases and limitations. Additionally, the study's findings are constrained by the timeframe of the literature review, and new studies may have emerged since the cut-off date, potentially impacting the representation and generalizability of the research trends identified. Another limitation lies in the construction of categories during the coding process. The coding scheme used may not have fully captured or represented all relevant terms or concepts. Some relevant terms may have been inadequately represented or identified using different words or phrases, potentially introducing limitations to the analysis. While efforts were made to ensure validity and reliability, there is still a possibility of unintended biases or inconsistencies in the categorization process.
The datasets (documents, excel analysis) utilized in this article are available upon request from the corresponding author.
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Öndeş, R.N. Research Trends in STEM Clubs: A Content Analysis. Int J of Sci and Math Educ (2024). https://doi.org/10.1007/s10763-024-10477-z
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Thinking of your research report as based on the scientific method, but elaborated in the ways described above, may help you to meet your audience's expectations successfully. ... These examples might explain the distinction between active and passive voice: Active: We heated the solution to 80°C. (The subject, "we," performs the action ...
In this post, we'll guide you step-by-step through how to write a scientific report and provide you with an example.
An experimental report documents the results of a scientific experiment, including the hypothesis, methods, results, and conclusions. Experimental reports are often used in biology, chemistry, and other sciences to communicate the results of laboratory experiments. ... For example, a research report on the effectiveness of a new drug could ...
This section describes an organizational structure commonly used to report experimental research in many scientific disciplines, the IMRAD format: Introduction, Methods, Results, And Discussion. Although the main headings are standard for many scientific fields, details may vary; check with your instructor, or, if submitting an article to a journal, refer to the instructions to authors.…
In the experiment section of the report, there is one crucial thing that several students fail to understand. A report is different from a manual for the experiment. While the manual is the complete how-to guide to perform the experiment, the report mainly emphasizes on analyzing results and deducing conclusions.
The guide breaks down the scientific writing process into easily digestible pieces, providing concrete examples that students can refer to when preparing a scientific manuscript or laboratory report. By increasing undergraduate exposure to the scientific writing process, we hope to better prepare undergraduates for graduate school and ...
Scientific and technical research reports generally follow a conventional format that includes a title, an abstract, a reference (or Literature Cited) section and the components of the IMRAD structure: ... Sample Writing Process. Prewriting: Make notes, scribble ideas: start generating text, drawing figures, sketching out presentation ideas.
Step 1: Find a topic and review the literature. As we mentioned earlier, in a research paper, you, as the researcher, will try to answer a question.More specifically, that's called a research question, and it sets the direction of your entire paper. What's important to understand though is that you'll need to answer that research question with the help of high-quality sources - for ...
A scientific paper is the formal lasting record of a research process. It is meant to document research protocols, methods, results and conclusions derived from an initial working hypothesis. ... As an example, the number of reports and reviews on obesity and diabetes has increased from 400 to close to 4000/year and 50 to 600/year respectively ...
This is the average for scientific articles. Make every word count. Abstract The abstract summarises your report's content in a restricted word limit. It might be read separately from your full report, so it should contain a micro-report, without references or personalisation. Usual elements you can include: Some background to the research area.
and relevant pieces of information for your report. This list gives some examples but is not exhaustive. 1. Your own lecture notes and lecture handouts. 2. Scientific Information search engines, e.g. PubMed. 3. Your own survey/experiment/research carried out. 4. Journals. 5. Books.
Here are some examples from recent issues of the Journal Psychological Science. ... Sample APA-Style Research Report. Figures 11.2, 11.3, 11.4, and 11.5 show some sample pages from an APA-style empirical research report originally written by undergraduate student Tomoe Suyama at California State University, Fresno. The main purpose of these ...
Author, A. A., Author, B. B., & Author, C. C. (year). Article title. Journal Title, volume number (issue number), page numbers. A simple way to write your reference section is to use Google scholar. Just type the name and date of the psychologist in the search box and click on the "cite" link. Next, copy and paste the APA reference into the ...
Scientific reports often adopt the IMRaD format: Introduction, Methods, Results, and Discussion. The summary below outlines the standard components of a scientific report: Abstract; The abstract is a short summary of your project. Here, you should state your research questions and aims and provide a brief description of your methodology.
In this video, a language and learning adviser provides some useful language tips for writing a scientific paper. In summary, these tips are: Be clear about the purpose of the paper. Use precise language. Be aware of your use of verb tense (past tense is often used, as you are reporting on past events in the lab/field).
A lab report conveys the aim, methods, results, and conclusions of a scientific experiment. The main purpose of a lab report is to demonstrate your understanding of the scientific method by performing and evaluating a hands-on lab experiment. This type of assignment is usually shorter than a research paper.
List the main results, with means, odds ratios, p -values, etc for each group. List the result of the primary endpoint first, followed by secondary outcomes Ensure that you have given a result for every method you mentioned in the methods section There should be enough detail to back up your conclusion. Conclusion.
The guide addresses four major aspects of writing journal-style scientific papers: (1) Fundamental style considerations; (2) a suggested strategy for efficiently writing up research results; (3) the nuts and bolts of format and content of each section of a paper (part of learning to
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.
Your report should include a title page, statement of purpose, hypothesis, materials and procedures, results and conclusions, discussion, and credits and bibliography. If applicable, graphs, tables, or charts should be included with the results portion of your report. 2. Cause and effect. This is another common science experiment research paper ...
The first question asks for a ready-made solution, and is not focused or researchable. The second question is a clearer comparative question, but note that it may not be practically feasible. For a smaller research project or thesis, it could be narrowed down further to focus on the effectiveness of drunk driving laws in just one or two countries.
Chris A. Mack. SPIE. 2018. 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 ...
Making Your Scientific Conclusion Clear and Impactful. Writing a great lab report conclusion doesn't have to be hard. With the tips we've discussed on writing a scientific conclusion, you can now write good summaries of your science work. Remember, when writing your discussion lab report, stay focused on your experiment and what you found out.
The World Economic Forum's Top 10 Emerging Technologies of 2024 report lists this year's most impactful emerging technologies. The list includes ways artificial intelligence is accelerating scientific research with a focus on applications in health, communication, infrastructure and sustainability.
The samples "are expected to answer one of the most fundamental scientific questions in lunar science research: what geologic activity is responsible for the differences between the two sides?" said Zongyu Yue, a geologist at the Chinese Academy of Sciences, in a statement issued in the Innovation Monday, a journal published in partnership ...
The Research and Development arm of the Forest Service, a component of the U.S. Department of Agriculture, works at the forefront of science to improve the health and use of our Nation's forests and grasslands. Research has been part of the Forest Service mission since the agency's inception in 1905. Read more
NASA's Earth Science Division's DEVELOP Program builds capacity in individuals and partner organizations to research the feasibility of using Earth observations for informed environmental decision making. Employing an internship-like model, DEVELOP conducts 10-week long feasibility studies that are focused on decision-making organizations' environmental concerns.
Ulcerative colitis (UC) is a chronic inflammatory bowel disease with intricate pathogenesis and varied presentation. Accurate diagnostic tools are imperative to detect and manage UC. This study ...
To identify the research trends in studies related to STEM Clubs, 56 publications that met the inclusion and extraction criteria were identified from the online databases ERIC and WoS in this study. These studies were analysed by using the descriptive content analysis research method based on the Paper Classification Form (PCF), which includes publishing years, keywords, research methods ...
This handout provides a general guide to writing reports about scientific research you've performed. In addition to describing the conventional rules about the format and content of a lab report, we'll also attempt to convey why these rules exist, so you'll get a clearer, more dependable idea of how to approach this writing situation.