Scientific Writing Lectures 2024-2025 (Part 1) PDF

Features of a good research problem Significant to the field Societal Original impact Interesting Research Feasible problem...

Features of a good research problem Significant to the field Societal Original impact Interesting Research Feasible problem Current Ethical Researchable 1.Clear: Easy to understand. 2. Specific: Focused on a single problem or issue. 3. Researchable: using primary and/or secondary sources. 4. Feasible: to answer within the timeframe and practical constraints. 4. Complex: enough to develop the answer over the space of a paper or thesis. 5. Arguable: meaning that there are different perspectives or viewpoints on the topic. 6. Relevant: to your field of study. 7. Original: meaning that it contributes to the existing body of knowledge in your field of study.  Difference between research problem &research question Research Problem Research Question Definition: A research problem is a broad Definition: A research question is a specific, issue or gap in knowledge that you aim to focused inquiry that you seek to answer address through your research. It identifies through your research. It stems from the what is unknown or what needs further exploration. research problem and guides the direction of Characteristics: your study. Characteristics: Contextual: Often framed within a larger context or area of study. Narrowed Focus: It is more precise and Significance: Highlights the importance targeted than the research problem. of the issue and why it needs to be Investigative: Designed to be answered investigated. through data collection and analysis. General: It is usually more general and Clear and Concise: Formulated in a way that may encompass multiple research allows for clear methodology and outcomes. questions.  Examples on research problem & research question Example 1 Example 3 Research Problem: The high cost of monoclonal antibody production limits their Research Problem: Cancer treatment often leads to accessibility for therapeutic use. severe side effects due to non-specific targeting of Research Question: How can fermentation therapies. conditions be optimized to enhance the yield Research Question: How can targeted drug delivery and quality of monoclonal antibodies systems enhance the efficacy and reduce the side effects produced in bioreactors? of chemotherapy in breast cancer treatment? Example 2 Example 4 Research Problem: Traditional vaccine development is Research Problem: The increasing prevalence of antibiotic resistance in bacterial pathogens time-consuming and may not keep pace with emerging poses a significant public health threat. infectious diseases. Research Question: What are the Research Question: How can mRNA technology be mechanisms of resistance in E. coli to utilized to rapidly develop vaccines against newly commonly used antibiotics, and how can we emerging viral pathogens? inhibit these mechanisms?  Research objective Research Objective Definition: It outlines the purpose of the study and what you aim to achieve. It specifies the goals of the research and provides a framework for what will be done. Characteristics:  Examples on research problem, research question & objective Example 1: Genetic Engineering of Crops Example 2: Bioremediation of Contaminated Soils Research Problem: Despite advancements in Research Problem: Traditional methods of soil genetic engineering, the public remains skeptical remediation are often costly and time-consuming, about the safety and efficacy of genetically modified (GM) crops, leading to low adoption rates in some highlighting the need for more efficient bioremediation regions. techniques to address soil contamination. Research Question: What are the key factors Research Question: How effective are specific influencing consumer attitudes towards genetically microbial consortia in degrading polycyclic aromatic modified crops in urban populations? hydrocarbons (PAHs) in contaminated soils? Research Objective: To analyze consumer Research Objective: To evaluate the degradation rates perceptions and knowledge about genetically modified crops through surveys and focus groups, of PAHs using different microbial consortia in laboratory aiming to identify educational strategies that could settings, aiming to identify the most effective strains for enhance acceptance. bioremediation applications.  Examples on research problem, research question & objective Example 3: Development of mRNA Vaccines Example 4: CRISPR Technology Research Problem: While mRNA vaccines have Research Problem: Although CRISPR-Cas9 shown promise against infectious diseases, technology has revolutionized gene editing, off-target challenges remain in their stability and delivery effects pose significant challenges for its application in mechanisms, which can limit their effectiveness. therapeutic settings. Research Question: How do lipid nanoparticle formulations affect the stability and cellular Research Question: What are the most effective uptake of mRNA vaccines in different cell types? strategies for minimizing off-target effects in CRISPR- Cas9 gene editing in mammalian cells? Research Objective: To assess the impact of various lipid nanoparticle compositions on the Research Objective: To evaluate various guide RNA stability and efficacy of mRNA delivery to target design strategies and delivery methods for their impact on cells, with the goal of optimizing vaccine formulations. off-target effects in CRISPR-Cas9 gene editing, aiming to enhance the precision of this technology.  Steps to help you select a meaningful and engaging topic: Identify Your Interests: Start with areas you are passionate about. Reflect on your coursework, readings, or experiences that intrigued you. Review Existing Literature: Conduct a preliminary literature review to understand what has already been studied. Look for gaps, contradictions, or emerging trends. Consider Relevance: Think about the significance of your topic. How does it contribute to your field? Does it address a current issue or need? Consult with Advisors or Peers: Discuss your ideas with professors, mentors, or classmates. They can offer insights and suggest angles you might not have considered. Narrow Your Focus: Once you have a general idea, narrow it down to a specific question or hypothesis. Ensure it’s manageable within your timeframe and resources. Feasibility: Assess whether you have access to the necessary resources, data, and tools to conduct your research. Flexibility: Be open to adjusting your topic as you delve deeper into your research. Sometimes, your initial idea may evolve. Passion and Motivation: Choose a topic that you find compelling, as this will keep you motivated throughout the research process. Common mistakes encountered during research topic selection Common mistakes encountered during research topic selection Rushing the Process: Hurrying through the topic selection without adequate reflection can lead to poor choices. Take time to explore and refine your ideas Lack of Clarity: Not articulating your topic clearly can lead to confusion. Be specific about what you want to study Neglecting the Target Audience: Failing to consider who will benefit from your research can result in a topic that lacks relevance or significance. Overcomplicating the Topic: Choosing a topic that is too complex or ambitious can lead to overwhelming challenges. Aim for clarity and manageability Common mistakes encountered during research topic selection Avoiding Literature Review: Skipping an initial literature review may result in redundant research or missing critical insights. Understand what has already been explored Ignoring Methodological Constraints: Not considering the methods available for your research can lead to impractical topics. Ensure that you can effectively investigate your question Not Considering Ethical Implications: Ignoring ethical concerns can lead to serious issues later. Always evaluate the ethical dimensions of your topic Common mistakes encountered during research topic selection Underestimating Time and Resource Needs: Misjudging the time and resources required for your research can lead to incomplete work. Be realistic about what you can achieve. Lack of Engagement with Existing Research: Not engaging with the work of others in your field can result in isolation. Use existing research as a foundation for your topic. Forgetting Practical Applications: Neglecting to consider the practical implications of your research can limit its impact. Think about how your work can be applied in real-world contexts. Not Seeking Diverse Perspectives: Limiting discussions to a narrow circle can lead to a lack of ideas. Seek input from a variety of sources. Disregarding Personal Growth Opportunities: Choosing a topic that doesn’t challenge you may hinder your development. Select topics that push your boundaries and enhance your skills. How to read a scientific article?  Do I need to read every journal article on my topic? No, there is no need to read every single journal article on the topic. But, make sure that you have a comprehensive view of the current state of the literature (and of knowledge) in the area of research. Understand the current state of the literature. Focus on articles that are recent, relevant and well cited. Quality trumps quantity. (Golden role). How do I know if an article is well cited?  Do I need to read the full journal article when reviewing the literature? No, you don’t need to read every single word in each journal article. Why? You need to get a big picture view of what each journal article is saying (e.g. the key questions and findings). Achieved via reading a few key sections in each article. Once you’ve narrowed down your focus and have a core set of highly relevant articles, you can dive deeper into them, paying closer attention to the methodology, results and its interpretation.  Which sections of each journal article should I read? You need to have a clear idea of which kind of information you need to get in the first place. Then, focus on that aspect. How?? Let’s brainstorm  Passive vs active reading 2020 1. What is the question that the authors are trying to address? Why is it important? 2. If this were my work, what kind of experimental approach can I take in tackling the problem? 3. What kind of data would I need to generate in order to support the conclusions of this paper? 4. How would this conclusion fit into my previous understanding? How to read a research article How to read a research article Contents IMR&D structure How to structure your research article Formatting and style of your manuscript Paragraph and sentence building-word use Grammatical tips Common mistakes authors do in their manuscripts  Title It is the first impression that people will have of your research. It should be descriptive, concise, precise, focusing on the novelty of the information presented. The fewest possible words that adequately describe the content. Each word should be chosen with care.  Types of Titles 1. Descriptive Titles: Clearly convey the study's focus. "Advancements in Biopharmaceutical Production Using Recombinant DNA Technology" "Exploring the Potential of Plant-Based Vaccines in Disease Prevention“ 2. Interrogative Titles Pose a question related to the research. "Can Microbial Fuel Cells Provide a Sustainable Energy Source?" "What Are the Ethical Concerns Surrounding Gene Editing in Agriculture?“ 3. Comparative Titles: Highlight comparisons within biotechnological methods or products. "Comparative Analysis of Traditional Breeding and Genetic Modification in Crop Improvement" "Evaluating the Performance of Biodegradable Plastics vs. Conventional Plastics"  Types of Titles 4. Methodological Titles Emphasize the methods or techniques used in the research. "A Novel Method for Isolating High-Yield Antibiotic-Producing Microbes" "Optimizing CRISPR-Cas9 Delivery Systems for Gene Editing in Plants“ 5. Result-Focused Titles Highlight significant findings or outcomes. "Significant Increase in Insulin Production through Engineered Yeast Strains" "Evidence of Enhanced Nutritional Value in Biofortified Crops“ 6. Thematic Titles Focus on broader themes or implications within biotechnology. "The Intersection of Biotechnology and Environmental Sustainability" "Biotechnology in the Fight Against Infectious Diseases: Challenges and Opportunities"  Types of Titles 7. Action-Oriented Titles Suggest implications or future directions based on findings. "Transforming Waste into Resources: Biotechnological Innovations for Circular Economy" "Leveraging Biotechnology for Climate Resilience in Agriculture" 8. Acronym or Abbreviation Titles "GEM: Genomic Editing for Microbial Bioremediation Strategies" "ABCD: Advances in Biochemical Characterization of Drug Delivery Systems"  How to craft an effective title 1. Identify Key Elements Main Topic: Clearly define the subject of your research. Methodology: If your method is novel or significant, consider mentioning it. Findings/Results: If your research has a key finding, consider incorporating it into the title. Context or Relevance: Mention the broader implications or field of study. 2. Keep It Concise Aim for clarity and brevity; typically, titles should be around 10-15 words. Avoid unnecessary jargon or overly complex language. 3. Use Keywords Incorporate important keywords to enhance searchability and relevance in databases. Think about what terms researchers or practitioners might use to find your work.  How to craft an effective title 4. Choose the Right Type Decide on the type of title that best fits your research (e.g., descriptive, interrogative, thematic). Make sure the title reflects the nature of your study accurately. 5. Consider Your Audience Tailor the title to your target audience, whether they are academics, industry professionals, or the general public. 6. Review and Revise After drafting, review your title for clarity, accuracy, and impact. Get feedback from peers or mentors to ensure it resonates well.  Tips Be Clear and Specific Use precise language that accurately reflects your research focus. Incorporate Keywords Include relevant keywords for better searchability and discoverability. Keep It Concise Aim for a length of 10-15 words to maintain clarity and impact Use Active Voice Engage readers with dynamic phrasing. Highlight Methodology or Findings Mention innovative methods or key results if they are significant.  Tips Consider Your Audience Tailor the title to the knowledge level and interests of your target readership. Use Different Title Structures Experiment with descriptive, interrogative, and comparative formats. Iterate and Revise Draft multiple versions and refine them based on feedback. Check for Uniqueness Ensure your title isn’t too similar to existing literature.  Tips Avoid Vagueness Don’t use vague terms or phrases that don’t clearly convey your research. Don’t Overuse Jargon Avoid excessive technical language that may confuse readers outside your field. Refrain from Lengthy Titles Avoid overly long titles that dilute the message; stick to concise wording. Don’t Use Abbreviations or Acronyms (e.g: RFLP, FISH, SNP) Unless they are widely recognized, avoid abbreviations that might not be clear to readers. Avoid Passive Voice Steer clear of passive constructions that can make your title less engaging.  Tips Don’t Mislead Ensure the title accurately represents your research to avoid misleading readers. Refrain from Including Unnecessary Details Don’t clutter the title with excessive information; focus on the key elements. Don’t Ignore the Research Context Avoid titles that don’t situate your work within a broader research context. Neglecting Final Review Don’t skip the final evaluation of your title after completing your research.  Lets brainstorm "An Investigation into the Various Ways in Which Different Types of Microorganisms Can Be Utilized for a Range of Biotechnological Applications in Agriculture, Medicine, and Environmental Remediation" Overly lengthy and too broad; lacks focus. "A Comprehensive Study of the Effects of Genetic Modification Techniques on the Growth and Development of Various Plant Species Across Different Environmental Conditions" Wordy and not specific enough about which plants or conditions.  Lets brainstorm Exploring the Potential Benefits and Risks Associated with the Use of Advanced Gene Editing Technologies in Diverse Fields Such as Agriculture, Medicine, and Industrial Biotechnology" Unfocused and tries to cover too many areas without depth. "Analyzing the Impact of Synthetic Biology Innovations on the Future of Global Food Production, Climate Change Mitigation, and Sustainable Development Goals" Extremely broad and lacks a clear research question. "A Detailed Examination of the Role of Various Biotechnological Processes in the Production of Pharmaceuticals, Biofuels, and Biodegradable Plastics in the Modern Economy" Too many topics combined, making it hard to grasp the main focus.  Lets brainstorm Engineering Bacterial Strains for Enhanced Biodegradation of Environmental Pollutants" Clear focus on a specific application and organism. "Optimization of CRISPR-Cas9 Techniques for Targeted Gene Editing in Human Stem Cells" Specifies the method and its application in a particular context. "Harnessing Plant-Microbe Interactions to Improve Crop Resilience Against Climate Stress" Highlights the interaction and its practical implications in agriculture. "Development of Bioinformatics Tools for Predicting Protein-Protein Interactions in Synthetic Biology" Clearly outlines the purpose and area of research.  Lets brainstorm "Evaluating the Potential of Microalgae as Sustainable Feedstocks for Biofuel Production" Focuses on a specific organism and its sustainable application. "Development of a Biosensor for Real-Time Detection of Pathogenic Bacteria in Food Products" Specifies the technology and its application in food safety. "Application of Synthetic Biology in the Production of Anticancer Compounds from Engineered Yeast" Specific about the organism and its therapeutic application. "Impact of Genetic Engineering on the Nutritional Value of Staple Crops: A Case Study of Golden Rice" Focuses on a specific crop and its enhanced nutritional aspect.  Authors and their affiliations ❖ Department, Faculty/institute, University, City, Country  Abstract The abstract is a condensed version of the research article in its entirety. Reflect the structure and the novelty of the work. It allows readers to judge whether it is relevant to their own research interests therefore, worthwhile reading the research article itself. Be fully understandable on its own (stand alone). Length: 100-250 words as a single paragraph.  Abstract The basic approach and The conclusion methodology, usually in (briefly) and the broad one sentence implications of it WHY, HOW, WHAT, SO WHAT The reason behind the research being The main findings (results) in done very few sentences  Graphical Abstract Graphical abstracts are visual representations of the key findings or the concept of a research study. They serve to summarize the main points of a paper in a clear, concise manner, making it easier for readers to grasp the essence of the research at a glance. Key Features of Graphical Abstracts Simplicity: Focus on the main findings or concepts without overwhelming detail. Clarity: Use clear visuals and minimal text to convey the message. Visual Appeal: Utilize colors, shapes, and layouts that are aesthetically pleasing and easy to read. Relevance: Ensure that the visuals directly relate to the research question and findings. Example on graphical abstracts  Steps to Create a Graphical Abstract 1. Identify Key Messages: Determine the main findings or conclusions of your research. What do you want the audience to remember? 2. Choose a Format: Decide whether to use a flowchart, diagram, infographic, or another visual format that best represents your data. 3. Sketch a Layout: Plan the arrangement of elements (images, text, graphs) to ensure a logical flow of information. Consider using boxes, arrows, or lines to guide the viewer. 4. Select Visual Elements: Use icons, charts, or images that represent your findings. Make sure they are relevant and easy to understand.  Steps to Create a Graphical Abstract 5. Keep Text Minimal: Use short phrases or bullet points instead of long sentences. The graphical abstract should complement your paper, not replace it. 6. Use Colors Wisely: Choose a color scheme that is professional and enhances readability. Avoid overly bright or distracting colors. Design and Software Tools: Use graphic design software or online tools like Adobe Illustrator, Canva, or BioRender. These tools offer templates and features tailored for creating scientific graphics. Review and Revise: Get feedback from colleagues or mentors to ensure clarity and effectiveness. Revise the design based on their input. Finalize: Ensure the graphical abstract meets any specific guidelines set by the journal or platform where you intend to publish. Brainstorm whether this abstract is written well or bad?why? Brainstorm whether this abstract is written well or bad?why?  Tips DO DON’T (Avoid) Lengthy background information Keep it brief Citations Use short sentences with varied structure Details about routine laboratory procedures Use appropriate voice (active voice) Details about the statistical methods or software Use appropriate tense used Undefined abbreviations or acronyms Formal academic tone Results not discussed in the text Repetition and filler words Typo and punctuation errors Poor grammar  Keywords These keywords help potential readers find your paper during their own literature searches. 5-7 words  How to create a good keyword section in a journal article? Consider the point of view of the reader. What keywords would the reader search for that would help retrieve your article? Use multi-word ‘key phrases’ where possible. single word keywords are acceptable, but they may lead to many false matches. Focus on terms related to the main topic of your research. Test your keywords  How do I know that the keywords are good enough? How do I know if my keywords are good enough? Test your keywords and see how many results you get. If you get too many results, your keywords may be too broad or common. If you get too few results, your keywords may be too narrow or specific. You can also compare your keywords with those used by other articles in your field  Introduction What is known about the area of study?” or “What the current literature is telling about the research problem?” Aspects of what has not been answered about the broader area of the study until date. Identify the gaps in the current literature and answer “What gaps in the literature would be filled by the current study?” this part essentially identifies the shortcomings of the existing studies Explain the rationale and introduce the hypothesis of the study. Enlist specific objectives “Why this study is going to be important?” or “What is the purpose of this study?”. Funnel-down scheme followed while writing the introduction section of a manuscript, moving from broader to specific information.  Introduction Introduction is regarded as the start of the storyline of the manuscript, hence, the three Cs’ scheme is adopted: Context in terms of what has been published on the current research problem. Content in terms of what we are going to do about the problem in hand (rationale). Conclusion as to how it is going to be done (specific objective of the study). Objective(s)  Materials &Methods section The methods section is critical because the procedures adopted determines the reliability of the results obtained and the analyses of the findings made. It informs the readers how data collection was done since the methods used affects results. It clearly expresses the reasons for choosing a specific technique or procedure among other different methods that could be used to investigate a research problem. It illustrates the appropriateness of the procedures and methods in achieving the overall aims of the study. Materials &Methods section  Structure of the Materials &Methods section Key subsections include: 1. Study participants and data collection This subsection describes the participants involved in the research study: 1. Their number e.g: “This case-control study was conducted on 59 Hashimoto Thyroiditis (HT) patients as well as 50 matched healthy controls.” 2. Sample size calculation 3. From where did we get those patients? e.g: “ HT patients were selected from those who admitted the Endocrinology Unit, Faculty of Medicine, Alexandria University, during the period from August 2016 to October 2016.” 4. Inclusion and exclusion criteria 5. Data collection methods e.g: “ Data was collected from all patients using a well-structured questionnaire designed to cover the following aspects: (variable e.g: age, family history of breast cancer, medical history ) 6. Patient consent 7. Ethical approval  Tips for Writing the Materials & Methods section Use an academic tone. Borrow a leaf from others. Be descriptive but avoid unnecessary details. Assume the reader’s view. Cite published methods instead of writing them in full details. Provide a context for the methods section (justify the choices made in the methods by using language that show intents, purpose and aim).  Tips for Writing the Materials & Methods section Use subheadings to structure the methods section  Tips for Writing the Materials & Methods section Mention the ethical approval given by the ethics committee. Use the past tense. Use passive voice. Consider the choice of words.  Tips for Writing the Materials & Methods section Mention the statistical analyses used. Provide the source for the materials used. Proofread.