Week 5. Comprehensive Study Notes on Academic Integrity, Citation Standards, Biomedical Writing, and Database Search Methodologies

Academic Integrity, Plagiarism Definitions, and Institutional Policies

• Definition of Plagiarism: Plagiarism is defined as utilizing another individual's work, ideas, data, or exact words without providing proper acknowledgment or credit, thereby pretending that the work is one's own.
• Etymological Origin: The word plagiarism originates from a Latin root meaning "to kidnap" or "to abduct".
• Academic and Professional Codes of Conduct: These codes—also referred to as academic integrity or honesty policies—are the formal, documented rules governing ethical behavior in academic and professional settings.
• Institutional Sanctions: Violating academic integrity policies through plagiarism constitutes a severe ethical breach. Penalties range from receiving a zero or failing grade on an individual assignment or course to official academic suspension or complete expulsion from an educational institution or program. At Duval University, these policies are explicitly outlined within every course syllabus.

Classifications and Types of Plagiarism

• Direct / Verbatim Plagiarism: Copying another author's exact words word-for-word without using quotation marks and without providing a proper citation.
• Paraphrasing Plagiarism: Rewording, restructuring, or presenting another author's ideas, concepts, or arguments without proper attribution or credit to the original creator.
• Self-Plagiarism: Reusing one's own previously submitted or published work in a new context without proper citation. This occurs frequently in scientific literature when published authors fail to cite their own prior research.
• Patchwork / Mosaic Plagiarism: Combining unattributed snippets, phrases, or sentences from multiple different sources together into a single passage without using quotation marks or citations.
• Accidental Plagiarism: Unintentionally failing to cite sources, misquoting source material, or improperly paraphrasing due to negligence, lack of knowledge, or poor note-taking practices.

Ethical, Legal, and Professional Consequences of Plagiarism

• Ethical Implications: Plagiarism represents the theft of intellectual property and undermines intellectual honesty, institutional trust, and creative integrity.
• Academic and Career Consequences:
  • Failing marks on specific assignments or exams.
  • Failing an entire academic course.
  • Academic probation, suspension, or permanent expulsion.
  • Loss of academic scholarships and financial support.
  • Permanent damage to personal, academic, and professional reputation.
  • Loss of professional credibility and destruction of peer relationships.
  • Termination of employment or loss of future career opportunities.
  • The severity of consequences depends upon institutional guidelines, the student's educational level, prior offense history, and the overall scope of the offense.
• Legal Risks and Copyright Infringement: Although academic plagiarism itself is not a direct federal crime in the United States, it frequently involves copyright infringement, which is illegal. Legal liabilities include civil lawsuits, financial penalties, and court-ordered damages paid to copyright holders. Intentional commercial plagiarism that violates copyright law can escalate to a criminal offense resulting in substantial monetary fines and imprisonment.
• Reputational Erosion: Plagiarism signals a fundamental lack of effort and moral integrity, causing individuals and affiliated organizations to appear untrustworthy, uncredentialed, and unethical.

Rules and Rationale for Utilizing External Resources

• Purposes of Incorporating External Sources:
  • Substantiating claims, hypotheses, and clinical arguments.
  • Providing evidence, background context, and credibility to research papers and review articles.
  • Inspiring creative concepts and synthesizing current knowledge.
  • Fulfilling ethical, legal, and educational standards in scientific research.
• Mandatory Scenarios Requiring Source Citation: Sources must be cited whenever using:
  • Words or text written by someone else.
  • Ideas, theories, or concepts belonging to another person.
  • Data, statistics, or empirical results generated by external entities.
  • Information that had to be actively looked up in external references.
  • Topics or fields in which the author is not a recognized expert.
• The Two Essential Attribution Components:
  1. In-text Citations: Short embedded markers located within the body text directly following a quote or paraphrase that point the reader to the complete reference details in the bibliography.
  2. Bibliography / Reference List: A comprehensive, detailed list of all sources consulted or referenced, appearing at the very end of the document.
• Functions of Dual Attribution: Prevents accusations of academic dishonesty, enables readers to locate original source material for further research, and allows verification of fact accuracy.

American Medical Association (AMA) Citation Style Guidelines

• Biomedical Citation Frameworks:
  • AMA (American Medical Association): Highly prevalent in medical journals, clinical research, and pharmacy assignments.
  • APA (American Psychological Association): Primarily used in social sciences and education.
  • Vancouver (National Library of Medicine): Broadly utilized across general scientific and medical journals.
• AMA In-Text Citation Formatting:
  • In-text references are indicated using superscript Arabic numerals that correspond to a numbered reference list at the end of the paper.
  • Placement relative to punctuation: Superscript numbers are placed immediately after cited information outside of periods and commas (e.g., $\text{text.}^1$ or $\text{text,}^2$), but inside of colons and semicolons (e.g., $\text{text}^3:$ or $\text{text}^4;$).
  • Sequential order: References must be numbered consecutively in the order in which they are first mentioned in the text, beginning with $1$.
  • Multiple citations at a single point: Non-consecutive numbers are separated using commas without spaces (e.g., $1, 3$); continuous ranges of consecutive numbers use hyphens (e.g., $1-5$).
• AMA Reference List Rules:
  • References are listed in the order of their initial appearance in the document text.
  • Author Names: Format as Surname Initials without periods between initials (e.g., Smith AB). Do not include professional degrees or titles.
  • Author Count Standards: In updated standard AMA style, list all authors if $6$ or fewer; if $7$ or more, list the first $6$ followed by "et al.". For specific coursework assignments, if $6$ or fewer authors exist, list all; if $7$ or more exist, list the first $3$ followed by "et al.".
  • Article Titles: Use sentence case (capitalize only the first word of the title, proper nouns, and standard acronyms).
  • Journal Abbreviations: Abbreviate journal titles according to NLM/PubMed standards (e.g., Am J Health Syst Pharm). Use Google or PubMed to identify official abbreviations.
  • Standard Journal Citation Structure: Author(s). Title of article. Abbreviated Journal Name. Year;Volume(Issue):Page numbers. (Exclude month and day of publication).
  • Supplements: Include the abbreviation "suppl" or "SUPP" in parentheses with the issue number (e.g., 2021;12(suppl 1):S1-S8).
  • Epub Ahead of Print: Include "epub ahead of print" prior to print details if published on the journal's website before print issue release.
  • Digital Object Identifiers (DOI): May be included in place of volume, issue, and page numbers when unavailable; DOIs are strongly recommended whenever accessible.
  • Letters, Editorials, and Abstracts: Append document category designator at the end (e.g., [letter]).
  • Book Chapters: Author(s). Chapter title. In: Editor(s), eds. Book Title. Edition ed. Publisher; Year:Page numbers. (Example: Goodman and Gilman's Pharmacological Basis of Therapeutics).
  • Government Publications: State the publishing agency name first (e.g., National Institute on Alcohol Abuse and Alcoholism), report title, publication location, publisher, and year.
  • Package Inserts: Brand Name (generic name) [package insert]. City, State: Manufacturer Name; Publication/Update Year.
  • Meeting Presentations: Author(s). Title of paper. Paper presented at: Name of Meeting; Date; Location (e.g., ASHP Annual Meeting).
  • Electronic / Website Sources: Author/Organization. Page title. Website Name. URL. Published date. Updated date. Accessed [Date]. (Example: National Cancer Institute).

Technical Execution of Quoting, Paraphrasing, and Summarizing

• Direct Quoting:
  • Definition: Precise, word-for-word duplication of source text enclosed in quotation marks and cited.
  • Execution: Select the exact phrase/sentence, enclose in double quotes, place the superscript citation number after the ending period and closing quotation mark.
  • Constraints: Direct quotes must match original text verbatim, be strictly limited in scope, and never copy full paragraphs. Quotes must always carry an in-text citation; omitting citations despite quotation marks constitutes plagiarism.
• Paraphrasing:
  • Definition: Expressing another source's ideas in entirely original vocabulary and sentence structures while maintaining original meaning and attribution.
  • Execution: Rewrite the selected concept using different vocabulary and a altered sentence structure. Append the superscript citation number after the period.
  • Application: Applied to short passages, discrete sentences, or specific phrases as an alternative to direct quotes.
• Summarizing:
  • Definition: Condensing substantial portions of source text into a brief overview of main points.
  • Execution: Synthesize essential ideas into original words while eliminating non-essential details. Requires proper in-text citations and reference list entries.

Biomedical Writing Standards and Research Software Tools

• Best Practices for Biomedical Writing:
  • Word Economy: Avoid wordiness and jargon. Use single, concise verbs (e.g., replace "learn about" with "determine").
  • Redundancy: Eliminate repetitive phrasing to maximize readability.
  • Proofreading: Run automated spell-checkers to eliminate grammatical and spelling errors.
  • Sentence Structure: Avoid run-on sentences; correctly utilize commas and semicolons to preserve clarity and eliminate ambiguity.
  • Verb Tense: Maintain consistent verb tenses throughout; prefer the present tense in medical scientific writing.
  • Drug Naming Conventions: Always refer to medications using lowercase generic names (e.g., "metronidazole", "amlodipine"). Capitalized brand names are avoided in professional writing unless specifically evaluating a distinct proprietary product.
• Reference and Evaluation Tools:
  • Citation Generators: Online software (Zotero, Mendeley, EndNote) that automatically converts source data into bibliographic references. Academic Rule: Pharmacy students are prohibited from using citation generators during pharmacy school to enforce manual citation proficiency; post-graduation usage requires manual double-checking.
  • Plagiarism Checkers: Software (Turnitin, Grammarly) that scans documents against databases of published literature and web pages to generate similarity reports and percentage scores. Turnitin in Canvas evaluates submissions for duplicated content and AI-generated text.
  • Research Note-Taking: Maintain tracking logs (e.g., Excel spreadsheets) during literature reviews to record source origins for every idea and detail gathered.

Drug Information Question (DIQ) Assignment Instructions and Milestones

• Assignment Overview: A team-based project involving the creation, literature search, synthesis, and answer formulation of a clinical drug information question using the PICO framework.
• Resources Location: DIQ template, sample documents, citation guides, and pharmacy library database links are located in Canvas under Module 5. Submissions occur in progressive modular sections due on Sundays by $11:59\,\text{PM EST}$.
• PICO Question Architecture:
  • P (Patient / Population): Specific clinical demographic (e.g., a 43-year-old female or a 12-year-old male).
  • I (Intervention): Assigned drug intervention (e.g., an antihypertensive or antidiabetic medication).
  • C (Comparator): Comparative agent in the same or different drug class, or placebo.
  • O (Outcome): Objective clinical parameter (e.g., blood pressure lowering in mmHg or HbA1c reduction percentage).
• Submission Deadlines and Schedule:
  • Module 5 / 6: Conduct initial background research on the assigned drug using tertiary compendia (Lexicomp, Micromedex) and guidelines. Formulate the PICO question and post it to the Discussion Board by the end of Module 6 (Sunday, $11:59\,\text{PM EST}$).
  • Module 8: Submit the "Tertiary Resources and Guidelines Review". Requires using at least $2$ distinct tertiary databases (e.g., Lexicomp, Micromedex, Clinical Pharmacology, specialized pediatric/toxicology compendia) and relevant clinical practice guidelines (e.g., AHA or CHEST guidelines). If guidelines are outdated, report historical recommendations paired with recent primary literature.
  • Module 10: Submit the "Primary Resources Section". Search at least $2$ secondary databases (PubMed, Embase, Ovid Medline, EBSCO, Cochrane). Include $2$ to $3$ primary studies (preferably randomized controlled trials [RCTs] or meta-analyses; retrospective analyses or case reports permitted if RCTs are unethical/unavailable). Report complete search strategies: exact keywords, MeSH terms, limits, and retrieved result counts.
  • Module 12: Submit the Final Draft DIQ. Document length must be $3$ to $4$ pages. Professional literature only (no Wikipedia or class notes). Follow AMA citation guidelines consecutively.
• DIQ Document Section Breakdown:
  1. Title Block: Full names of team members and Team Number.
  2. Question Classification: Select category (Availability, Drug Interaction, Drug Therapy, or Other specified type).
  3. PICO Question: Formatted clinical question as posted on discussion boards.
  4. Search Strategy Details: List of tertiary resources, secondary databases, exact keywords, MeSH terms, applied limits, and result numbers.
  5. Evidence Section: Drafted prior to the recommendation. Includes background disease overview, tertiary data summaries, and primary literature analyses for at least $2$ articles (stating study objectives, patient populations, drug regimens, primary outcomes, statistical results, and author conclusions).
  6. Recommendation / Summarized Response: Drafted after completing evidence; provides a concise synthesis of findings and actionable clinical advice.
  7. References: Numbered consecutively matching superscript in-text citations in AMA format.

Secondary Database Search Strategies (PubMed, Ovid, EBSCO, FAERS)

• PubMed Search Mechanics:
  • Maintained by the National Library of Medicine (NLM); indexing over $30,000,000$ citations. Incorporates full MEDLINE records plus non-indexed material.
  • Automatic Query Logic: Unquoted keywords entered together automatically insert implicit AND/OR Boolean logic across multiple field tags.
  • Phrase Search: Enclose multi-word terms in double quotation marks (e.g., "adverse events", "whooping cough", "opioid abuse") to force exact phrase matching.
  • Boolean Operators: Must be capitalized (AND, OR, NOT). AND combines terms; OR expands search; NOT excludes trailing terms (risking exclusion of relevant papers).
  • Nesting: Using parentheses to define operational hierarchy (e.g., metronidazole AND ("adverse events" OR "adverse effects")).
  • Field Tags: Restrict queries to fields using tags such as [ti] or TI for Title, and [tiab] or TIAB for Title/Abstract.
  • Truncation: Place an asterisk * at the word root to capture all trailing variations (e.g., child* captures child, children, childhood).
  • Filters: Filter by publication date (1 year, 5 years, custom dates), text availability (free full text, full text), publication type (systematic review, meta-analysis, RCT, clinical guideline), species, sex, age, and MEDLINE indexing.
  • Advanced Search History: Track search details, combine previous query numbers, and evaluate mapping translations.
• Medical Subject Headings (MeSH) in PubMed:
  • Controlled vocabulary used to index MEDLINE journals, updated annually.
  • Maps variable synonyms (e.g., "breast cancer", "breast carcinoma", "mammary neoplasm") to standardized canonical terms like Breast Neoplasms.
  • Subheadings: Narrow scope to specific domains, such as drug therapy or administration & dosage.
  • Major Topic Restriction: Limits output to articles where the MeSH heading is the primary study focus.
  • Explosion: PubMed automatically explodes MeSH terms to include all lower narrow terms in the tree hierarchy. To prevent explosion, check "Do not include MeSH terms found below this term in the MeSH hierarchy".
  • New Drug Search Precaution: Newly approved drugs may lack assigned MeSH terms; always execute parallel searches using both MeSH terms and raw keyword text strings.
• Ovid MEDLINE Search Execution:
  • Map Term to Subject Heading: Check box to route queries through MeSH trees.
  • Scope Notes: Select scope icon to review definition, date of entry history, and linked mapped synonyms.
  • Explode vs. Focus: Manually check "Explode" to include narrower sub-terms; check "Focus" to restrict results to major topic status.
  • Syntax Details: exp indicates an exploded query; * before a term indicates major topic status; /dt suffix denotes the drug therapy subheading.
  • Combining Sets: Select query set numbers and combine using Boolean buttons or manual line syntax (e.g., 3 NOT 4).
• EBSCO Search Mechanics:
  • Provides multi-field drop-down interfaces for Boolean selection.
  • Quotation marks restrict exact phrase matches (e.g., "heparin induced thrombocytopenia" reduces broad result noise).
• FDA Adverse Event Reporting System (FAERS) Database:
  • Public post-marketing surveillance database collecting adverse event reports submitted by clinicians, consumers, and pharmaceutical manufacturers.
  • Tracked Data Parameters: Total case counts, serious outcomes, death reports, and annual case distributions (e.g., levothyroxine historical data spanning from 1987 to 2024).
  • Data Categories: Events classified by reaction type (e.g., drug ineffective, fatigue, headache, alopecia), patient age, reporter type, gender, seriousness (death, disability, hospitalization, life-threatening), and organ system class (e.g., skin and subcutaneous tissue disorders, blood and lymphatic system disorders).
  • Clinical Application: Identifying rare, un-labeled, or off-label adverse drug reactions. Case detail logs provide exact product names, active ingredients, clinical indications, event dates, age, weight, concomitant drugs, and reporting country.