write a literature review paper


Question Description


Topic: Public health microbiology: recent (2015-2018) - Cases of pandemic outbreaks, how were they contained

Attached are the guidelines.

Attached are the approved references (11 references in total. I can only download 4 as of now, when accepted, I will send the rest of the references)

Students are expected to write a literature review paper on a topic relevant to microbiology. The chosen topic may not cover an event more than 5 years old. You are encouraged to start your research paper as early in the semester as you possibly can. Your choice of topic may reflect your personal interests, support your career goals or nurture your inherent intuition and curiosity. Have enough time to gather literature, write, revise, revise some more, and turn in a scholarly paper. Maximum page limit is 10 (MINIMUM 8 pages), double spaced, AMA (American Medical Association) format.

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FAIRLEIGH DICKINSON UNIVERSITY SCHOOL OF NATURAL SCIENCES BIOL 3225 General Microbiology  Literature review paper and presentation: 15% Students are expected to write a literature review paper on a topic relevant to microbiology. The chosen topic may not cover an event more than 5 years old. You are encouraged to start your research paper as early in the semester as you possibly can. Your choice of topic may reflect your personal interests, support your career goals or nurture your inherent intuition and curiosity. Have enough time to gather literature, write, revise, revise some more, and turn in a scholarly paper. Maximum page limit is 10, double spaced, AMA (American Medical Association) format. - Presentations should be 7-10 minutes long and should include all pertinent information as per their literature review. The Scientific Literature Review  OBJECTIVES/RATIONALE Background research is a vital component of the scientific research process. The students will be able to locate, identify and critique key elements of scientific literature to discover what is known and what remains to be learned about a topic. Books and articles are categorized as either primary or secondary sources. It is always more desirable to use primary sources whenever possible. Primary sources are first-hand accounts of events Secondary sources are second-hand accounts. The competent researcher never relies on secondary sources but always reviews the primary source as a check against possible errors. The researcher then makes records of the sources studied and summarizes the pertinent information found in each. The most common and useful method for recording bibliographical information is to write the complete information for each publication on a separate 3X5 card (or file). These cards are kept in alphabetical order in a file to be a ready source to cite relevant works in the body of the research paper. The researcher must develop an orderly and systematic approach to coding their index cards. It is important to summarize an article or book using the same format each time. This will enable quick comparisons. For an article, examine the author’s credentials, scan the hypothesis, and focus on the methods of research used (how the sample was selected and the data was analyzed). Read the conclusion and summary. Retain sound and pertinent articles. To summarize and record the information, note author, title, and year of publication. • Title of article • Authors name(s) - all authors MUST be recorded. • Full reference – year of publication, FULL name of the journal or book, # of issue or edition and page numbers. • Summary of information of interest NOTE: no everything may be of importance to your research, concentrate only on the issues that are pertinent to your work.  REVIEWS For the past three or four years you have learned how to review a scientific paper, now is time to learn how to use this information in a more productive form. Scientist must keep up with the advances on their area of interest by constantly reading new publications. This will give them an overview of what is being accomplished by the scientific community. Each individual paper you read will give you a piece of the puzzle. During this exercise, you will learn how to put all the pieces of the puzzle together as a BIG PICTURE – Scientific Literature Review. ELEMENTS OF SCIENTIFIC LITERATURE Title short, specific, clear Introduction WHY are you doing this research?- state the propose of what you are expecting to find (Present tense), review the individual literature and compile what information already exists on this subject (background information reported by the papers you read regarding your topic) Materials & Methods HOW was the research carried out? (Past tense) (design, target population, treatment, analytical methods ---- brief explanation on how the different authors conducted their experiments) – compare their methods), please NOTE that this may not be appropriated for your research. Results WHAT kind of results were reported by the papers you read (past tense) again, this may not apply to your research or it could be combine with your discussion and conclusion. Discussion/Conclusions WHAT do the results published by the different researchers mean to you? (present tense) References / Literature cited Paper Guidelines: The project will be based on new literature, at least seven original research articles from scientific journals (primary source). Beside the new scientific literature (primary sources), background references like books, popular science magazines or older articles from science journals should be used to complete your work; to create the BIG PICTURE. (Minimum 10-12 references) The steps required for the completion of the project are: 1. Sign-up for a topic provided by your instructor or if you have a particular topic or interest, you may clear it with your instructor. Due (in class) by the 2nd week of class. Please note that no two person will be allow to research the same topic. • When deciding on a topic, you should ask yourself the question….. What do you want to know about this subject? * Once you define your topic, you will not be allowed to change it. • Find primary references – at least 7 original research scientific articles from reputable scientific journals (use the library services!). – NOTE: scientific reviews and mini-reviews are considered as secondary source. -- Copies of the scientific papers PDF’s must be e-mailed to the instructor for approval no later than September 23, 2018. late delivers will be penalized • NOTE that I cannot open any link! You must download the paper into your computer as a PDF file and then forward the PDF as an email attachment. 2. Read the papers (followed guide provided in the beginning of this assignment) and look for additional scientific articles and background material (minimum 10 references should be included on your paper). • Prepare individual summary for each paper (like single pieces of a puzzle) write a two page “resume” in your own words for each reference. E-mail then to the instructor no later than October 6, 2018. – late delivers will be penalized 3. Compile all your information to give an overview of the studies done in a particular area of interest. “the entire puzzle” -4. Start writing your scientific literature review. First draft must be e-mailed to your instructor no later than 11:59pm October 27, 2018. • You may re-submit via e-mail working drafts until November 17. NO MORE DRAFTS WILL BE ACCEPTED AFTER THAT DAY. Make sure you have addressed all the recommendations and that your paper is free of grammatical errors and of good scientific quality as per the guide provided at the beginning of the assignment. • Points to remember: i. You are not to review each paper independently. DO NOT DESCRIBE INDIVIDUAL RESEARCHES, YOU MUST SUMMARIZE AND COMPARE ALL THE PAPERS. ii. You must compile all the information as a single unit iii. Don’t forget to cite in text what each author have to say. When citing in text use author(s) name(s) coma and year of publication. e.g. (Johnson, 2015) or (Johnson & Smith, 2016) or if more than two authors use (Willey et al., 2014) • It MUST include: o Title page -- (Title of your paper, your name and course number) o Introduction (background information reported by the papers you read regarding your topic) o Material & Methods if appropriate to your topic (brief explanation on how the different authors conducted their experiments) – compare their methods o Result / Discussion what do the results published by the different researchers mean to you. You may compare the data in tables, schemes or figures. BUT it has to be selfexplanatory and created by YOU. (do not copy them from the literature – that is considered plagiarism!) o Conclusion (what did you learn from your research) o Reference -- In text references and literature cited. In text references should be done by using the author(s) last name followed by a coma and the year of publication (ex. Johns, 2016; Johns & Willian, 2016; if more than three authors use the first authors name and et al. - Johns et al., 2016) End of the paper reference (literature cited) can be written as follow…Make sure to write the name of all authors here. -- do not use et al.! • Authors’ names (last name, Initial(s).and ; between the authors and before the last one)) Year of publication. Article title (capitalize only the first letter of the first word and proper nouns), Journal name (in italic), Volume number; full page numbers. o Li, B.; Li, W.; Chen, X.; Jiang, M.; and Dong, M. (2012). In vitro antibiofilm activity of the melanin from Auricularia auricula, an edible jelly mushroom. Annals of Microbiology, 62(4), 1523-1530. • Article in an online journal: Author(s) (same as above). Year Title. Journal Name; volume (issue NO.):inclusive pages. URL [provide the URL in this field; no need to use “URL:” preceding it]. Published [date]. Updated [date]. Accessed [date]. o Drake A.J., Smith A., and Betts P.R., (2002). Type 2 Diabetes in Obese White Children. Archives of Disease in Childhood 86(3), 207-208. http://vsearch.nlm.nih.gov/vivisimo/cgibin/query-meta?v:project=nlm-main-website&query=Archives+of+disease+in+childhood. Accessed April 5, 2016. o Langer, S., D. Schropp,, F. R. Bengelsdorf,, M. Othman, and M. Kazda. 2014. Dynamics of biofilm formation during anaerobic digestion of organic waste. Anaerobe 29 , p 44-51. http://dx.doi.org/10.1016/j.anaerobe.2013.11.013. Accessed April 5, 2016 • When citing data from a Web site, include the following elements, if available, in the order shown below: Author(s), if given (often, no authors are given). Title of the specific item cited (if none is given, use the name of the organization responsible for the site). Name of the Web site. URL [provide URL and verify that the link still works as close as possible to publication]. Published [date]. Updated [date]. Accessed [date]. o Living With Type 1 Diabetes. Diabetes.org. http://www.diabetes.org/living-withdiabetes/recently-diagnosed/living-with-type-1-diabetes.html. Published February 9, 2015. Accessed April 7, 2015. o Why Immunize? cdc.gov. http://www.cdc.gov/vaccines/vac-gen/why.htm. Updated September 23, 2014. Accessed April 7, 2015. o Yale University. Science Daily. http://www.sciencedaily.com/relesases/2015/01/1501733950. Published January 7, 2015. Accessed April 5, 2015. • When referring to an entire book, not pages or specific sections, use the following format: References should include the last name and first and middle initials of the author(s), italicized title case format for all titles (capitalize all words except prepositions such as of, between, through), articles (such as a, the, and an), and conjunctions (such as but, and, or; however, capitalize them if they begin the title or the subtitle) the city and state of publication, the publisher, and the year of publication/creation. o Silverstein A., Silverstein V.B., Nunn L.S. Cancer. Minneapolis, MN: Twenty-First Century Books; 2006. o Maul-Mellott, S.K. and Adams, J.N. Childhood Cancer: A Nursing Overview. Boston, MA: Jones and Bartlett; 1987. o Willey,J. M., L. M. Eherwood and C. J. Woolverton. Prescott’s MICROBIOLOGY 9th. Edition. McGraw-Hill. 2014. • Chapters from books should be capitalized in the same format as journal articles (sentence case format) and should not use quotation marks. Additionally, inclusive page numbers for the each chapter should be provided. The title of the book, however, should be title cased and italicized, following the print book format. A colon should follow the publication date and no space should be provided between the colon or the page number(s) and hypen. o Yagyu, S. and Iehara, T. MYCN nonamplified neuroblastoma: Detection of tumor-derived cellfree DNA in serum for predicting prognosis of neuroblastoma. In Hayat MA, ed. Pediatric Cancer Diagnosis, Therapy, and Prognosis. Dordrecht, NY: Springer; 2013:11-17. 5. You must prepare the material to be presented to your classmates. All Presentations (ppt, prezi, etc.. and an one page summary) regardless of your presentation date are due via e-mail to your instructor on November 25, 2018 NO EXCEPTIONS. Points will be deducted for late submissions  You will be presenting your topic during the class schedule time (based on the topic) and credit will be given for the presentation and for answered questions.  Presentations should be 7-10 min. long and should include all pertinent information as per their literature review.  A summary (one page) of your presentation should be prepared and e-mailed to your instructor before your presentation date for distribution to your classmates. All presentation materials will be included in your final examination. 6. Final paper is to be submitted via Safe-Assignment by 11:59PM DECEMBER 1, 2018- Once you submit it via Safe-assignment, you can no longer re-write it or fix it. EVALUATION OF THE PROJECT (15%) • • • • • Primary references delivered on time (1 pt each) Two page summary for each reference (2 pts each) First draft complete and delivered on time Final paper o Paper depth o Format o Spelling, paragraph and sentence structure, grammar and punctuation Oral presentation o One page summary o Presentation content o Timing + Question and answers Penalties: • Late submission(s) • No approved topic or literature • No drafts • No oral presentation 30pts 5pts 5pts 5pts 10pts 5pts - 50% of original pts. - 50 pts - 25 pts - 30 pts. 10pts 20pts 10pts 40pts 20pts SAMPLE LITERATURE REVIEW Prion propagation and their effect in humans Introduction Prions cause diseases like Creutzfeldt-Jakob disease (CJD), Gerstmann-Strässler-Scheinker syndrome (GSS), kuru, and fatal familial insomnia in humans (Barbisin et al. 2014). Diseases caused by prions in animals include bovine spongiform encephalopathy (BSE), also known as Mad Cow Disease, in cattle (Strom et al. 2014), scrapie in sheep, chronic wasting disease (CWD) in cervids (which includes deer), transmissible mink encephalopathy, and feline spongiform encephalopathy (Barbisin et al. 2014). Prion diseases are both fatal and currently incurable. These neurodegenerative diseases are collectively referred to as transmissible spongiform encephalopathies (TSEs). Prions cannot be seen by the naked eye and are naturally found in cells as normal, functional proteins. Their microbiological influence affects organisms on the cellular level, with neurons as the primary focus for most studies……………………….. Materials and Methods The researchers, Krejciova et al.(2014), simulated PrP conversion from the normal form to the abnormal form (that would normally occur in cells) in vitro using a technique called protein misfolding cyclic amplification (PMCA). PMCA works by incubating normally folded protein mixed with a small amount of misfolded protein. Then the conversion is sped up with a blast of ultrasound. The cycle is repeated until the desired end result is achieved (Zou & Pierluigi, 2012)……………….. Barbisin et al. (2014) were also concerned about humans becoming infected with prions. They had worked under certain assumptions. The primate Macaca fasicularis is known to be a good research subject for the understanding prion diseases inflicting humans………. Another group of scientists (Belay et al. 2015) found that prion studying from RNA studies had problems in maintaining RNA integrity, specifically from the heat produced using a rotating biopsy stamp when extracting cells…………………………………………………... Results/Discussion The findings of these studies indicate that prions continue to boggle the minds of researchers. These studies do, however, give more insight to the capabilities of TSE-related prions……………………………. Conclusion Researchers Krejciova et al. (2014) have concluded that prions from cattle infected with BSE can effectively afflict sheep of certain genotypes. However, the prion types found in these sheep have lost the capability to infect humans…………. Ultimately the ways prions propagate and influence cells and other microbes continues to elude researchers. The current level of knowledge surrounding prions highlights that there is little information on how to protect livestock and people from TSEs and other prion related neurodegenerative disorders………. Literature cited: Barbisin, M., Silvia Vanni, Ann-Christin Schmädicke, Judith Montag, Dirk Motzkus, Lennart Opitz, Gabriela Salinas-Riester, Giuseppe Legname (2014) Gene expression profiling of brains from bovine spongiform encephalopathy (BSE)infected cynomolgus macaques BMC Genomics. 2014; 15: 434. Published online 2014 Jun 5. doi: 10.1186/14712164-15-434 9/22/2018 World Health Organization Estimates of the Global and Regional Disease Burden of 22 Foodborne Bacterial, Protozoal, and Viral Diseas… World Health Organization Estimates of the Global and Regional Disease Burden of 22 Foodborne Bacterial, Protozoal, and Viral Diseases, 2010: A Data Synthesis Martyn D. Kirk , Sara M. Pires, Robert E. Black, Marisa Caipo, John A. Crump, Brecht Devleesschauwer, Dörte Döpfer, Aamir Fazil, Christa L. Fischer-Walker, Tine Hald, Aron J. Hall, Karen H. Keddy, Robin J. Lake, Claudio F. Lanata, Paul R. Torgerson, Arie H. Havelaar, Frederick J. Angulo Published: December 3, 2015 https://doi.org/10.1371/journal.pmed.1001921 Correction 23 Dec 2015: Kirk MD, Pires SM, Black RE, Caipo M, Crump JA, et al. (2015) Correction: World Health Organization Estimates of the Global and Regional Disease Burden of 22 Foodborne Bacterial, Protozoal, and Viral Diseases, 2010: A Data Synthesis. PLOS Medicine 12(12): e1001940. https://doi.org/10.1371/journal.pmed.1001940 | View correction Abstract Background Foodborne diseases are important worldwide, resulting in considerable morbidity and mortality. To our knowledge, we present the first global and regional estimates of the disease burden of the most important foodborne bacterial, protozoal, and viral diseases. Methods and Findings We synthesized data on the number of foodborne illnesses, sequelae, deaths, and Disability Adjusted Life Years (DALYs), for all diseases with sufficient data to support global and regional estimates, by age and region. The data sources included varied by pathogen and included systematic reviews, cohort studies, surveillance studies and other burden of disease assessments. We sought relevant data circa 2010, and included sources from 1990–2012. The number of studies per pathogen ranged from as few as 5 studies for bacterial intoxications through to 494 studies for diarrheal pathogens. To estimate mortality for Mycobacterium bovis infections and morbidity and mortality for invasive non-typhoidal Salmonella enterica infections, we excluded cases attributed to HIV infection. We excluded stillbirths in our estimates. We estimate that the 22 diseases included in our study resulted in two billion (95% uncertainty interval [UI] 1.5–2.9 billion) cases, over one million (95% UI 0.89–1.4 million) deaths, and 78.7 million (95% UI 65.0–97.7 million) DALYs in 2010. To estimate the burden due to contaminated food, we then applied proportions of infections that were estimated to be foodborne from a global expert elicitation. Waterborne transmission of disease was not included. We estimate that 29% (95% UI 23–36%) of cases caused by diseases in our study, or 582 million (95% UI 401–922 million), were transmitted by contaminated food, resulting in 25.2 million (95% UI 17.5–37.0 million) DALYs. Norovirus was the leading cause of foodborne illness causing 125 million (95% UI 70–251 million) cases, while Campylobacter spp. caused 96 million (95% UI 52–177 million) foodborne illnesses. Of all fo ...
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School: UT Austin


Cases of Pandemic Outbreaks and their Containment
Student’s Name

Background Information
Throughout history, epidemics and pandemics have ravaged the human existence and
societies. Cholera, HIV-AIDS chicken pox, and small pox have killed tens of thousands (Sands,
Mundaca-Shah, Dzau, 2016). Ebola has a case fatality rate 40-50%, human noroviruses have
caused 500-800 deaths a year, while avian influenza epidemic has resulted to millions perishing
(Cenciarelli et al., 2015). Advancements in the medical field have revolutionized the defenses
against infectious diseases. Diagnostics, hygiene, vaccines and antibiotics are the most preferred
prevention and response tools to outbreaks. Despite this, the severe acute respiratory syndrome
(SARS) and the Ebola outbreak in West Africa have proved that we are not complacent (Sands,
Mundaca-Shah, Dzau, 2016). Therefore, it is important to study the pandemics and epidemics,
their course, diagnosis and control to advocate for policies, mechanisms of coordination and
resources to respond to crises from infectious diseases. Infectious diseases leading to potential
epidemics and pandemics cause huge disruptions in the economy and loss of life.
Ebola Virus Disease (EVD)
Certainly, Ebola demonstrated the ill-preparedness of crises for such infectious disease. It
iss one of the most fatal (40-50%) and serious viral diseases (Cenciarelli et al., 2015). There are
no strategies either therapeutic or prophylactics that could deal with this disease, hence, a great
community threat. The epidemic became a real concern in 2014 when it hit urban areas. The
World Health Organization declared EVD outbreak in western Africa an emergency of the public
health. There five classes of Ebola including Ebola virus (EBOV), Reston virus (RESTV),
Bundibugyo virus (BDBV), Tai forest virus (TAFV) and Sudan Virus (SUDV) (2). All except
RESTV are pathogenic to humans.

Several studies have indicated filoviruses as zoonotic, that is, transmission to humans
from animals’ ongoing life cycles and fruit bats were identified as probable disease vectors and
virus reservoir. Transmission is through close contact with organs, blood, other body fluids or
secretions of infected animals. It can also be transmitted through personal contact with
individuals having broken skins and that of a healthy individual with the body fluids of an
infected person (saliva, urine, fasces or semen). Ebola’s incubation period is between two to
twenty-one days and individuals are only infectious in the symptomatic phase (Cenciarelli et al.,
2015). After, a febrile illness developed with characteristics such as joint pain, weakness,
headache and joint pain. A major form of clinical manifestation is the hemorrhagic manifestation
in the gastrointestinal tract and many others develop a rash that is maculopapular in association
with arrythmia.
Disease diagnosis is through specific laboratory tests for example electron microscopy,
isolation of virus by the cell’s nature, antibody -capture enzyme linked immunosorbent assay
(ELISA), serum neutralization test, reverse transcriptase polymerase chain reaction (RT-PCR)
and serum neutralization test).
Norovirus Diarrheal Disease
Across all age groups, human noroviruses are the leading causes of erratic and epidemic
gastroenteritis (Matsushima et al, 2015). Although it is a self-limiting disease, it has resulted in a
whopping 56,000-71,000 in-patients flooding the health facilities, approximately 500-800 deaths
in a year, about 400,000 visits that demand emergency services and 1.7 million to 1.9 million
visits by out-patients (Kirk et al., 2010). In the 1990’s it was a relatively unrecognized virus
among individuals of all ages. Most of the norovirus outbreaks take place in the health facility
the predominant transmission mode is from one person to another. The characteristics of

noroviruses project after an incubation period of 22 hours to 48 hours. They include nausea, low
grade fever, vomiting, abdominal cramps and nonblood diarrhea (Matsushima et al, 2015). In
vulnerable populations for example the elderly or the pediatrics, they are prone to a more

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