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What Is the Appendix? A Vestigial Organ, or One With a Purpose?
The role of the appendix has long been something of a mystery, but some experts now believe they've finally discovered its function.
The role of the appendix has long been something of a mystery, but some experts now believe they've discovered its function.
The appendix is a thin, roughly four-inch-long tube that's part of your gastrointestinal (GI) tract. (1)
The GI tract is a complex group of organs, each of which helps your body digest and absorb food.
Your upper GI tract includes your esophagus, stomach, and the first section of your small intestine, called the duodenum.
The lower GI tract is made up of most of your small intestine and all of your large intestine, which includes your colon, rectum, and anal canal. (2)
The presentation of acute appendicitis includes abdominal pain, nausea, vomiting, and fever. As the appendix becomes more swollen and inflamed, it begins to irritate the adjoining abdominal wall. This leads to the localization of the pain to the right lower quadrant. This classic migration of pain may not be seen in children under three years. This pain can be elicited through signs and can be severe. Symptoms include localized findings in the right iliac fossa. The abdominal wall becomes very sensitive to gentle pressure (palpation). There is severe pain in the sudden release of deep tension in the lower abdomen (Blumberg sign). If the appendix is retrocecal (localized behind the cecum), even deep pressure in the right lower quadrant may fail to elicit tenderness (silent appendix). This is because the cecum, distended with gas, protects the inflamed appendix from pressure. Similarly, if the appendix lies entirely within the pelvis, there is typically a complete absence of abdominal rigidity. In such cases, a digital rectal examination elicits tenderness in the rectovesical pouch. Coughing causes point tenderness in this area (McBurney's point), historically called Dunphy's sign.
Acute appendicitis seems to be the result of a primary obstruction of the appendix.   Once this obstruction occurs, the appendix becomes filled with mucus and swells. This continued production of mucus leads to increased pressures within the lumen and the walls of the appendix. The increased pressure results in thrombosis and occlusion of the small vessels, and stasis of lymphatic flow. At this point, spontaneous recovery rarely occurs. As the occlusion of blood vessels progresses, the appendix becomes ischemic and then necrotic. As bacteria begin to leak out through the dying walls, pus forms within and around the appendix (suppuration). The end result is appendiceal rupture (a 'burst appendix') causing peritonitis, which may lead to sepsis and eventually death. These events are responsible for the slowly evolving abdominal pain and other commonly associated symptoms. 
The causative agents include bezoars, foreign bodies, trauma, intestinal worms, lymphadenitis and, most commonly, calcified fecal deposits that are known as appendicoliths or fecaliths.   The occurrence of obstructing fecaliths has attracted attention since their presence in people with appendicitis is higher in developed than in developing countries.  In addition an appendiceal fecalith is commonly associated with complicated appendicitis.  Fecal stasis and arrest may play a role, as demonstrated by people with acute appendicitis having fewer bowel movements per week compared with healthy controls.  
The occurrence of a fecalith in the appendix was thought to be attributed to a right-sided fecal retention reservoir in the colon and a prolonged transit time. However, a prolonged transit time was not observed in subsequent studies.  Diverticular disease and adenomatous polyps was historically unknown and colon cancer was exceedingly rare in communities where appendicitis itself was rare or absent, such as various African communities. Studies have implicated a transition to a Western diet lower in fibre in rising frequencies of appendicitis as well as the other aforementioned colonic diseases in these communities.   And acute appendicitis has been shown to occur antecedent to cancer in the colon and rectum.  Several studies offer evidence that a low fiber intake is involved in the pathogenesis of appendicitis.    This low intake of dietary fiber is in accordance with the occurrence of a right-sided fecal reservoir and the fact that dietary fiber reduces transit time. 
Diagnosis is based on a medical history (symptoms) and physical examination, which can be supported by an elevation of neutrophilic white blood cells and imaging studies if needed. Histories fall into two categories, typical and atypical.
Typical appendicitis includes several hours of generalized abdominal pain that begins in the region of the umbilicus with associated anorexia, nausea, or vomiting. The pain then "localizes" into the right lower quadrant where the tenderness increases in intensity. It is possible the pain could localize to the left lower quadrant in people with situs inversus totalis. The combination of pain, anorexia, leukocytosis, and fever is classic.
Atypical histories lack this typical progression and may include pain in the right lower quadrant as an initial symptom. Irritation of the peritoneum (inside lining of the abdominal wall) can lead to increased pain on movement, or jolting, for example going over speed bumps.  Atypical histories often require imaging with ultrasound or CT scanning. 
- : Increased pain on palpation with finger in right Petit triangle (can be a positive Shchetkin-Bloomberg's).  : Increased pain on palpation at the right iliac region as the person being examined lies on their left side compared to when they lie on their back.  : Increased pain in the right lower quadrant with coughing.  : The patient refuses to eat (anorexia is 80% sensitive for appendicitis) 
- Kocher's (Kosher's) sign: From the person's medical history, the start of pain in the umbilical region with a subsequent shift to the right iliac region.  : Developed in and popular in southwest England, the examiner performs a firm swish with his or her index and middle finger across the abdomen from the xiphoid process to the left and the right iliac fossa. A positive Massouh sign is a grimace of the person being examined upon a right sided (and not left) sweep.  : The person being evaluated lies on her or his back with the hip and knee both flexed at ninety degrees. The examiner holds the person's ankle with one hand and knee with the other hand. The examiner rotates the hip by moving the person's ankle away from his or her body while allowing the knee to move only inward. A positive test is pain with internal rotation of the hip.  , also known as "Obraztsova's sign", is right lower-quadrant pain that is produced with either the passive extension of the right hip or by the active flexion of the person's right hip while supine. The pain that is elicited is due to inflammation of the peritoneum overlying the iliopsoas muscles and inflammation of the psoas muscles themselves. Straightening out the leg causes pain because it stretches these muscles, while flexing the hip activates the iliopsoas and causes pain.  : Pain in the lower right abdominal quadrant with continuous deep palpation starting from the left iliac fossa upwards (counterclockwise along the colon). The thought is there will be increased pressure around the appendix by pushing bowel contents and air toward the ileocaecal valve provoking right-sided abdominal pain.  : Increased pain in the right iliac region as the person is being examined lies on their left side. 
- Perman´s sign: In acute appendicitis palpation in the left iliac fossa may produce pain in the right iliac fossa.Emil Samuel Perman 1856-1946 "About the indications for surgery in appendicitis and an account of cases of Sabbatsberg Hospital in Hygiea 1904
Blood and urine test Edit
While there is no laboratory test specific for appendicitis, a complete blood count (CBC) is done to check for signs of infection. Although 70–90 percent of people with appendicitis may have an elevated white blood cell (WBC) count, there are many other abdominal and pelvic conditions that can cause the WBC count to be elevated.  Due to its low sensitivity and specificity, on its own, WBC is not seen as a good indicator of appendicitis. 
A urinalysis generally does not show infection, but it is important for determining pregnancy status, especially the possibility of an ectopic pregnancy in women of childbearing age. The urinalysis is also important for ruling out a urinary tract infection as the cause of abdominal pain. The presence of more than 20 WBC per high-power field in the urine is more suggestive of a urinary tract disorder. 
In children the clinical examination is important to determine which children with abdominal pain should receive immediate surgical consultation and which should receive diagnostic imaging.  Because of the health risks of exposing children to radiation, ultrasound is the preferred first choice with CT scan being a legitimate follow-up if the ultrasound is inconclusive.    CT scan is more accurate than ultrasound for the diagnosis of appendicitis in adults and adolescents. CT scan has a sensitivity of 94%, specificity of 95%. Ultrasonography had an overall sensitivity of 86%, a specificity of 81%. 
Abdominal ultrasonography, preferably with doppler sonography, is useful to detect appendicitis, especially in children. Ultrasound can show the free fluid collection in the right iliac fossa, along with a visible appendix with increased blood flow when using color Doppler, and noncompressibility of the appendix, as it is essentially walled-off abscess. Other secondary sonographic signs of acute appendicitis include the presence of echogenic mesenteric fat surrounding the appendix and the acoustic shadowing of an appendicolith.  In some cases (approximately 5%),  ultrasonography of the iliac fossa does not reveal any abnormalities despite the presence of appendicitis. This false-negative finding is especially true of early appendicitis before the appendix has become significantly distended. Also, false-negative findings are more common in adults where larger amounts of fat and bowel gas make visualizing the appendix technically difficult. Despite these limitations, sonographic imaging with experienced hands can often distinguish between appendicitis and other diseases with similar symptoms. Some of these conditions include inflammation of lymph nodes near the appendix or pain originating from other pelvic organs such as the ovaries or Fallopian tubes. Ultrasounds may be either done by the radiology department or by the emergency physician. 
Ultrasound showing appendicitis and an appendicolith 
Ultrasound showing appendicitis and an appendicolith 
Ultrasound of a normal appendix for comparison
A normal appendix without and with compression. Absence of compressibility indicates appendicitis. 
Computed tomography Edit
Where it is readily available, computed tomography (CT) has become frequently used, especially in people whose diagnosis is not obvious on history and physical examination. Although some concerns about interpretation are identified, a 2019 Cochrane review found that sensitivity and specificity of CT for the diagnosis of acute appendicitis in adults was high.  Concerns about radiation tend to limit use of CT in pregnant women and children, especially with the increasingly widespread usage of MRI.  
The accurate diagnosis of appendicitis is multi-tiered, with the size of the appendix having the strongest positive predictive value, while indirect features can either increase or decrease sensitivity and specificity. A size of over 6 mm is both 95% sensitive and specific for appendicitis. 
However, because the appendix can be filled with fecal material, causing intraluminal distention, this criterion has shown limited utility in more recent meta-analyses.  This is as opposed to ultrasound, in which the wall of the appendix can be more easily distinguished from intraluminal feces. In such scenarios, ancillary features such as increased wall enhancement as compared to adjacent bowel and inflammation of the surrounding fat, or fat stranding, can be supportive of the diagnosis. However, their absence does not preclude it. In severe cases with perforation, an adjacent phlegmon or abscess can be seen. Dense fluid layering in the pelvis can also result, related to either pus or enteric spillage. When patients are thin or younger, the relative absence of fat can make the appendix and surrounding fat stranding difficult to see. 
Magnetic resonance imaging Edit
Magnetic resonance imaging (MRI) use has become increasingly common for diagnosis of appendicitis in children and pregnant patients due to the radiation dosage that, while of nearly negligible risk in healthy adults, can be harmful to children or the developing baby. In pregnancy, it is more useful during the second and third trimester, particularly as the enlargening uterus displaces the appendix, making it difficult to find by ultrasound. The periappendiceal stranding that is reflected on CT by fat stranding on MRI appears as an increased fluid signal on T2 weighted sequences. First trimester pregnancies are usually not candidates for MRI, as the fetus is still undergoing organogenesis, and there are no long-term studies to date regarding its potential risks or side effects. 
In general, plain abdominal radiography (PAR) is not useful in making the diagnosis of appendicitis and should not be routinely obtained from a person being evaluated for appendicitis.   Plain abdominal films may be useful for the detection of ureteral calculi, small bowel obstruction, or perforated ulcer, but these conditions are rarely confused with appendicitis.  An opaque fecalith can be identified in the right lower quadrant in fewer than 5% of people being evaluated for appendicitis.  A barium enema has proven to be a poor diagnostic tool for appendicitis. While failure of the appendix to fill during a barium enema has been associated with appendicitis, up to 20% of normal appendices do not fill. 
Scoring systems Edit
Several scoring systems have been developed to try to identify people who are likely to have appendicitis. The performance of scores such as the Alvarado score and the Pediatric Appendicitis Score, however, are variable. 
The Alvarado score is the most known scoring system. A score below 5 suggests against a diagnosis of appendicitis, whereas a score of 7 or more is predictive of acute appendicitis. In a person with an equivocal score of 5 or 6, a CT scan or ultrasound exam may be used to reduce the rate of negative appendectomy.
|Migratory right iliac fossa pain||1 point|
|Nausea and vomiting||1 point|
|Right iliac fossa tenderness||2 points|
|Rebound abdominal tenderness||1 point|
|High white blood cell count (leukocytosis)||2 points|
|Shift to left (segmented neutrophils)||1 point|
|Total score||10 points|
Even for clinically certain appendicitis, routine histopathology examination of appendectomy specimens is of value for identifying unsuspected pathologies requiring further postoperative management.  Notably, appendix cancer is found incidentally in about 1% of appendectomy specimens. 
Pathology diagnosis of appendicitis can be made by detecting a neutrophilic infiltrate of the muscularis propria.
Periappendicitis, inflammation of tissues around the appendix, is often found in conjunction with other abdominal pathology. 
Micrograph of appendicitis and periappendicitis. H&E stain.
Micrograph of appendicitis showing neutrophils in the muscularis propria. H&E stain.
Acute suppurative appendicitis with perforation (at right). H&E stain.
- Only neutrophils in lumen
- No ulceration or transmural inflammation
- Neutrophils within mucosa, and possibly in submucosa
- Mucosal ulceration
- Dull mucosa
- Congested surface vessels
- Fibropurulent serosal exudate in late cases
- Dilated appendix
- Neutrophils in mucosa, submucosa and muscularis propria, potentially transmural.
- Extensive inflammation
- Commonly intramural abscesses
- Possibly vascular thrombosis
- Friable wall
- Purple, green or black color
- Transmural inflammation
- Necrotic areas
- Extensive mucosal ulceration
- Serosa may be congested, dull and exudative
- Serosal and subserosal inflammation, no further than outer muscularis propria to be called isolated
- >10 eosinophils/mm 2 in muscularis propria.
- No changes conforming to other types of appendicitis
Differential diagnosis Edit
Children: Gastroenteritis, mesenteric adenitis, Meckel's diverticulitis, intussusception, Henoch–Schönlein purpura, lobar pneumonia, urinary tract infection (abdominal pain in the absence of other symptoms can occur in children with UTI), new-onset Crohn's disease or ulcerative colitis, pancreatitis, and abdominal trauma from child abuse distal intestinal obstruction syndrome in children with cystic fibrosis typhlitis in children with leukemia.
Women: A pregnancy test is important for all women of childbearing age since an ectopic pregnancy can have signs and symptoms similar to those of appendicitis. Other obstetrical/ gynecological causes of similar abdominal pain in women include pelvic inflammatory disease, ovarian torsion, menarche, dysmenorrhea, endometriosis, and Mittelschmerz (the passing of an egg in the ovaries approximately two weeks before menstruation). 
The term " pseudoappendicitis " is used to describe a condition mimicking appendicitis.  It can be associated with Yersinia enterocolitica. 
Acute appendicitis  is typically managed by surgery. While antibiotics are safe and effective for treating uncomplicated appendicitis,   26% of people had a recurrence within a year and required an eventual appendectomy.  Antibiotics are less effective if an appendicolith is present.  Surgery is the standard management approach for acute appendicitis, however, the 2011 Cochrane review comparing appendectomy with antibiotics treatments has not been updated and has been withdrawn.  The cost effectiveness of surgery versus antibiotics is unclear. 
Using antibiotics to prevent potential postoperative complications in emergency appendectomy procedures is recommended, and the antibiotics are effective when given to a person before, during, or after surgery. 
Pain medications (such as morphine) do not appear to affect the accuracy of the clinical diagnosis of appendicitis and therefore should be given early in the patient's care.  Historically there were concerns among some general surgeons that analgesics would affect the clinical exam in children, and some recommended that they not be given until the surgeon was able to examine the person. 
The surgical procedure for the removal of the appendix is called an appendectomy. Appendectomy can be performed through open or laparoscopic surgery. Laparoscopic appendectomy has several advantages over open appendectomy as an intervention for acute appendicitis. 
Open appendectomy Edit
For over a century, laparotomy (open appendectomy) was the standard treatment for acute appendicitis.  This procedure consists of the removal of the infected appendix through a single large incision in the lower right area of the abdomen.  The incision in a laparotomy is usually 2 to 3 inches (51 to 76 mm) long.
During an open appendectomy, the person with suspected appendicitis is placed under general anesthesia to keep the muscles completely relaxed and to keep the person unconscious. The incision is two to three inches (76 mm) long, and it is made in the right lower abdomen, several inches above the hip bone. Once the incision opens the abdomen cavity, and the appendix is identified, the surgeon removes the infected tissue and cuts the appendix from the surrounding tissue. After careful and close inspection of the infected area, and ensuring there are no signs that surrounding tissues are damaged or infected. In case of complicated appendicitis managed by an emergency open appendectomy, abdominal drainage (a temporary tube from the abdomen to the outside to avoid abscess formation) may be inserted, but this may increase the hospital stay.  The surgeon will start closing the incision. This means sewing the muscles and using surgical staples or stitches to close the skin up. To prevent infections, the incision is covered with a sterile bandage or surgical adhesive.
Laparoscopic appendectomy Edit
Laparoscopic appendectomy was introduced in 1983 and has become an increasingly prevalent intervention for acute appendicitis.  This surgical procedure consists of making three to four incisions in the abdomen, each 0.25 to 0.5 inches (6.4 to 12.7 mm) long. This type of appendectomy is made by inserting a special surgical tool called a laparoscope into one of the incisions. The laparoscope is connected to a monitor outside the person's body, and it is designed to help the surgeon to inspect the infected area in the abdomen. The other two incisions are made for the specific removal of the appendix by using surgical instruments. Laparoscopic surgery requires general anesthesia, and it can last up to two hours. Laparoscopic appendectomy has several advantages over open appendectomy, including a shorter post-operative recovery, less post-operative pain, and lower superficial surgical site infection rate. However, the occurrence of an intra-abdominal abscess is almost three times more prevalent in laparoscopic appendectomy than open appendectomy. 
The treatment begins by keeping the person who will be having surgery from eating or drinking for a given period, usually overnight. An intravenous drip is used to hydrate the person who will be having surgery. Antibiotics given intravenously such as cefuroxime and metronidazole may be administered early to help kill bacteria and thus reduce the spread of infection in the abdomen and postoperative complications in the abdomen or wound. Equivocal cases may become more difficult to assess with antibiotic treatment and benefit from serial examinations. If the stomach is empty (no food in the past six hours), general anaesthesia is usually used. Otherwise, spinal anaesthesia may be used.
Once the decision to perform an appendectomy has been made, the preparation procedure takes approximately one to two hours. Meanwhile, the surgeon will explain the surgery procedure and will present the risks that must be considered when performing an appendectomy. (With all surgeries there are risks that must be evaluated before performing the procedures.) The risks are different depending on the state of the appendix. If the appendix has not ruptured, the complication rate is only about 3% but if the appendix has ruptured, the complication rate rises to almost 59%.  The most usual complications that can occur are pneumonia, hernia of the incision, thrombophlebitis, bleeding and adhesions. Evidence indicates that a delay in obtaining surgery after admission results in no measurable difference in outcomes to the person with appendicitis.  
The surgeon will explain how long the recovery process should take. Abdomen hair is usually removed to avoid complications that may appear regarding the incision.
In most cases, patients going in for surgery experience nausea and vomiting that require medication before surgery. Antibiotics, along with pain medication, may be administrated before appendectomies.
After surgery Edit
Hospital lengths of stay typically range from a few hours to a few days but can be a few weeks if complications occur. The recovery process may vary depending on the severity of the condition: if the appendix had ruptured or not before surgery. Appendix surgery recovery is generally a lot faster if the appendix did not rupture.  It is important that people undergoing surgery respect their doctor's advice and limit their physical activity so the tissues can heal faster. Recovery after an appendectomy may not require diet changes or a lifestyle change.
The length of hospital stays for appendicitis varies on the severity of the condition. A study from the United States found that in 2010, the average appendicitis hospital stay was 1.8 days. For stays where the person's appendix had ruptured, the average length of stay was 5.2 days. 
After surgery, the patient will be transferred to a postanesthesia care unit, so his or her vital signs can be closely monitored to detect anesthesia- or surgery-related complications. Pain medication may be administered if necessary. After patients are completely awake, they are moved to a hospital room to recover. Most individuals will be offered clear liquids the day after the surgery, then progress to a regular diet when the intestines start to function correctly. Patients are recommended to sit upon the edge of the bed and walk short distances several times a day. Moving is mandatory, and pain medication may be given if necessary. Full recovery from appendectomies takes about four to six weeks but can be prolonged to up to eight weeks if the appendix had ruptured.
Most people with appendicitis recover quickly after surgical treatment, but complications can occur if treatment is delayed and if peritonitis occurs. Recovery time depends on age, condition, complications, and other circumstances, including the amount of alcohol consumption, but usually is between 10 and 28 days. For young children (around ten years old), the recovery takes three weeks.
The possibility of peritonitis is the reason why acute appendicitis warrants rapid evaluation and treatment. People with suspected appendicitis may have to undergo a medical evacuation. Appendectomies have occasionally been performed in emergency conditions (i.e., not in a proper hospital) when a timely medical evacuation was impossible.
Typical acute appendicitis responds quickly to appendectomy and occasionally will resolve spontaneously. If appendicitis resolves spontaneously, it remains controversial whether an elective interval appendectomy should be performed to prevent a recurrent episode of appendicitis. Atypical appendicitis (associated with suppurative appendicitis) is more challenging to diagnose and is more apt to be complicated even when operated early. In either condition, prompt diagnosis and appendectomy yield the best results with full recovery in two to four weeks usually. Mortality and severe complications are unusual but do occur, especially if peritonitis persists and is untreated.
Another entity known as the appendicular lump is talked about. It happens when the appendix is not removed early during infection, and omentum and intestine adhere to it, forming a palpable lump. During this period, surgery is risky unless there is pus formation evident by fever and toxicity or by USG. Medical management treats the condition.
An unusual complication of an appendectomy is "stump appendicitis": inflammation occurs in the remnant appendiceal stump left after a prior incomplete appendectomy.  Stump appendicitis can occur months to years after initial appendectomy and can be identified with imaging modalities like ultrasound. 
Appendicitis is most common between the ages of 5 and 40.  In 2013, it resulted in 72,000 deaths globally, down from 88,000 in 1990. 
In the United States, there were nearly 293,000 hospitalizations involving appendicitis in 2010.  Appendicitis is one of the most frequent diagnoses for emergency department visits resulting in hospitalization among children ages 5–17 years in the United States. 
Structure and Writing Style
I. General Points to Consider
When considering whether to include content in an appendix, keep in mind the following:
- It is usually good practice to include your raw data in an appendix, laying it out in a clear format so the reader can re-check your results. Another option if you have a large amount of raw data is to consider placing it online and note that this is the appendix to your research paper.
- Any tables and figures included in the appendix should be numbered as a separate sequence from the main paper. Remember that appendices contain non-essential information that, if removed, would not diminish a reader's ability to understand the research problem being investigated. This is why non-textual elements should not carry over the sequential numbering of non-textual elements in the body of your paper.
- If you have more than three appendices, consider listing them on a separate page at the beginning of your paper. This will help the reader know what information is included in the appendices [always list the appendix or appendices in a table of contents].
- The appendix can be a good place to put maps, photographs, diagrams, and other images, if you feel that it will help the reader to understand the content of your paper, while keeping in mind the study should be understood without them.
- An appendix should be streamlined and not loaded with a lot information. If you have a very long and complex appendix, it is a good idea to break it down into separate appendices, allowing the reader to find relevant information quickly as the information is covered in the body of the paper.
Never include an appendix that isn&rsquot referred to in the text. All appendices should be summarized in your paper where it is relevant to the content. Appendices should also be arranged sequentially by the order they were first referenced in the text [i.e., Appendix 1 should not refer to text on page eight of your paper and Appendix 2 relate to text on page six].
There are very few rules regarding what type of material can be included in an appendix, but here are some common examples:
- Correspondence -- if your research included collaborations with others or outreach to others, then correspondence in the form of letters, memorandums, or copies of emails from those you interacted with could be included.
- Interview Transcripts -- in qualitative research, interviewing respondents is often used to gather information. The full transcript from an interview is important so the reader can read the entire dialog between researcher and respondent. The interview protocol [list of questions] should also be included.
- Non-textual elements -- as noted above, if there are a lot of non-textual items, such as, figures, tables, maps, charts, photographs, drawings, or graphs, think about highlighting examples in the text of the paper but include the remainder in an appendix.
- Questionnaires or surveys -- this is a common form of data gathering. Always include the survey instrument or questionnaires in an appendix so the reader understands not only the questions asked but the sequence in which they were asked. Include all variations of the instruments as well if different items were sent to different groups [e.g., those given to teachers and those given to administrators] .
- Raw statistical data &ndash this can include any numerical data that is too lengthy to include in charts or tables in its entirety within the text. This is important because the entire source of data should be included even if you are referring to only certain parts of a chart or table in the text of your paper.
- Research instruments -- if you used a camera, or a recorder, or some other device to gather information and it is important for the reader to understand how, when, and/or where that device was used.
- Sample calculations &ndash this can include quantitative research formulas or detailed descriptions of how calculations were used to determine relationships and significance.
NOTE: Appendices should not be a dumping ground for information. Do not include vague or irrelevant information in an appendix this additional information will not help the reader&rsquos overall understanding and interpretation of your research and may only distract the reader from understanding the significance of your overall study.
ANOTHER NOTE : Appendices are intended to provide supplementary information that you have gathered or created it is not intended to replicate or provide a copy of the work of others. For example, if you need to contrast the techniques of analysis used by other authors with your own method of analysis, summarize that information, and cite to the original work. In this case, a citation to the original work is sufficient enough to lead the reader to where you got the information. You do not need to provide a copy of this in an appendix.
Here are some general guideline on how to format appendices. If needed, consult the writing style guide [e.g., APA, MLS, Chicago] your professor wants you to use for more detail:
- Appendices may precede or follow your list of references.
- Each appendix begins on a new page.
- The order they are presented is dictated by the order they are mentioned in the text of your research paper.
- The heading should be "Appendix," followed by a letter or number [e.g., "Appendix A" or "Appendix 1"], centered and written in bold type.
- If there is a table of contents, the appendices must be listed.
- The page number(s) of the appendix/appendices will continue on with the numbering from the last page of the text.
Appendices. The Structure, Format, Content, and Style of a Journal-Style Scientific Paper. Department of Biology. Bates College Appendices. Academic Skills Office, University of New England Appendices. Writing Center, Walden University Chapter 12, "Use of Appendices." In Guide to Effective Grant Writing: How to Write a Successful NIH Grant. Otto O. Yang. (New York: Kluwer Academic, 2005), pp. 55-57 Tables, Appendices, Footnotes and Endnotes. The Writing Lab and The OWL. Purdue University Lunsford, Andrea A. and Robert Connors. The St. Martin's Handbook. New York: St. Martin's Press, 1989 What To Know About The Purpose And Format Of A Research Paper Appendix. LoyolaCollegeCulion.com.
Biology 2e is optional and free. Read Biology2e online and download (PDF, Kindle). (Book URL: https://openstax.org/details/books/biology-2e)
Clark, M.A., Douglas, M., & Choi, J. (2018) (2019). Biology 2e. Houston, Texas: OpenStax. Creative Commons Attribution License 4.0
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Plan of Research:
In this thesis, I will compare the cranial anatomy of A. cacatuoides to that of “Cichlasoma” (Archocentrus) nigrofasciatum, a commonly bred fish reared by aquarists known as the Convict Cichlid, a “typical” medium-sized cichlid also of South American origin. The Convicts will be examined at various stages in development, from juvenile to adult, and will be compared to A.cacatuoides.
The first part of this project will involve whole mount preparation of A. cacatuoides, utilizing the staining and clearing procedures described by Taylor and Van Dyke, 1985. This procedure involves the use of Alizarin Red and Alcian Blue to stain bone and cartilage, and takes into account the adaptations and recommendations Proposed in an earlier paper (Hanken and Wassersug 1981). The Taylor and Van Dyke procedure is specifically for the staining and clearing of small fish and other vertebrates. I tested the procedure during last semester¹s Independent Study and made a few minor adjustments to the protocol.
First, the specimens will be placed serially into an absolute ethyl alcohol solution and stained with Alcian Blue. The fish will then be neutralized in a saturated borax solution, transferred to a 20% hydrogen peroxide solution in potassium hydroxide, and then bleached under a fluorescent light. The unwanted soft tissues will then be cleared using trypsin powder, and then stained in KOH again with alizarin red. The final preparation of the fish involves rinsing the fish, and placing them serially into 40%, 70%, and finally 100% glycerin.
Following the above preparation of the specimens, the crania of the A. cacatuoides specimens will be examined for morphological variation and compared to the cranial anatomy of the Convict cichlid as a progenitor reference point examined at various developmental stages to see if paedomorphosis in indeed the mechanism of miniaturization in A. cacatuoides.
The longtime justice, appointed by President Clinton, added a lengthy appendix of evidence he found relevant to his dissent.
Things go well until Oscar the Grouch is diagnosed with a burst appendix and Romney discovers he is uninsured.
That appendix is taken more seriously because it is between the covers of a holy book.
Comes with the funniest footnotes and appendix (no kidding) ever written.
The procedure is now the most common surgery performed in the U.S.—more common than getting your tonsils or appendix removed.
I shall then give an account of my various excursions in an Appendix, and afterwards resume the thread of my journal.
The geological character of this rock is more fully treated upon in the Appendix by my friend Dr. Fitton.
See Appendix I for the exact facts which were not known to me until long afterwards.
Mr. Brae, in the Appendix to his edition of Chaucer's Astrolabe (p. 101), has a long note on the present passage.
Implementing the New Biology: Decadal Challenges Linking Food, Energy, and the Environment: Summary of a Workshop, June 3-4, 2010 (2010)
Keith Yamamoto, Ph.D. (NAS/IOM), chair, is professor of cellular and molecular pharmacology and executive vice dean of the School of Medicine at the University of California, San Francisco (UCSF). He has been a member of the UCSF faculty since 1976, serving as director of the Program in Biomedical Science&rsquos (PIBS) Graduate Program in Biochemistry and Molecular Biology (1988-2003), vice chair of the Department of Biochemistry and Biophysics (1985-1994), chair of the Department of Cellular and Molecular Pharmacology (1994-2003), and vice dean for research, School of Medicine (2002-2003). Dr. Yamamoto&rsquos research is focused on signaling and transcriptional regulation by intracellular receptors, which mediate the actions of several classes of essential hormones and cellular signals he uses both mechanistic and systems approaches to pursue these problems in pure molecules, cells, and whole organisms. Dr. Yamamoto was a founding editor of Molecular Biology of the Cell and serves on numerous editorial boards, scientific advisory boards, and national committees focused on public and scientific policy, public understanding and support of biological research, and science education he has served on the Coalition for the Life Sciences (formerly the Joint Steering Committee for Public Policy) since 1996. For the National Academy of Sciences, he chairs the Board on Life Sciences. Dr. Yamamoto has long been involved in the process of peer review and the policies that govern it at the National Institutes of Health (NIH), serving as chair of the Molecular Biology Study Section, member of the NIH Director&rsquos Working Group on the Division of Research Grants, chair of the Advisory Committee to the NIH Center
for Scientific Review (CSR), member of the NIH Director&rsquos Peer Review Oversight Group, member of the CSR Panel on Scientific Boundaries for Review, member of the Advisory Committee to the NIH Director, co-chair of the Working Group to Enhance NIH Peer Review, and co-chair of the Review Committee for the Transformational R01 Award. Dr. Yamamoto was elected as a member of the American Academy of Arts and Sciences in 1988, the National Academy of Sciences in 1989, the Institute of Medicine in 2003, and a fellow of the American Association for the Advancement of Sciences in 2002.
Vicki L. Chandler, Ph.D. (NAS) is the chief program officer for science at the Gordon & Betty Moore Foundation in Palo Alto, California. She also maintains an active research program at the University of Arizona-Tucson, where she is a Regents&rsquo Professor in the Departments of Plant Sciences and Molecular and Cellular Biology and a member of the BIO5 Institute. She holds the Carl E. and Patricia Weiler Endowed Chair for Excellence in Agriculture and Life Sciences. Dr. Chandler received her B.A. from the University of California, Berkeley, and her Ph.D. from the University of California, San Francisco. She has conducted pioneering research on the control of gene expression in plants and animals. She has received numerous honors and awards including a Presidential Young Investigator Award, Searle Scholar Award, the National Science Foundation (NSF) Faculty Award for Women Scientists and Engineers, and the NIH Director&rsquos Pioneer Award. She was elected to the National Academy of Sciences in 2002. She has served extensively on national advisory boards and panels for NSF, the Department of Energy (DOE), NIH, and the Howard Hughes Medical Institute (HHMI). She served on the NSF Biological Directorate Advisory Committee from 2001to 2004 and served on the National Research Council (NRC) Committee on Defining and Advancing the Conceptual Basis of Biological Science. She has chaired or co-chaired national conferences for Keystone, the Federation of American Societies for Experimental Biology (FASEB), and the Gordon Research Conference (GRC), serving on the GRC board of trustees, and in 2001 as chair of the board. Dr. Chandler was elected to the International Society of Plant Molecular Biology Board of Directors 1999-2003 and elected president of the American Society of Plant Biologists for 2002. In 2007 she was elected to the Council of the National Academy of Sciences.
Christopher B. Field, Ph.D. (NAS) is the founding director of the Carnegie Institution&rsquos Department of Global Ecology, professor of biological sciences at Stanford University, and faculty director of Stanford&rsquos Jasper Ridge Biological Preserve. For most of the last two decades, Dr. Field has fostered the emergence of global ecology. His research emphasizes
ecological contributions across the range of earth science disciplines. Dr. Field and his colleagues have developed diverse approaches to quantifying large-scale ecosystem processes, using satellites, atmospheric data, models, and census data. They have explored local- and global-scale patterns of climate change impacts, vegetation-climate feedbacks, carbon cycle dynamics, primary production, forest management, and fire. At the ecosystem scale, Dr. Field has, for more than a decade, led major experiments on grassland responses to global change, experiments that integrate approaches from molecular biology to remote sensing. His activities in building the culture of global ecology include service on many national and international committees, including committees of the National Research Council, the International Geosphere-Biosphere Programme, and the Earth System Science Partnership. Dr. Field was a coordinating lead author for the fourth assessment report of the Intergovernmental Panel on Climate Change. He is a fellow of the Ecological Society of America&rsquos Aldo Leopold Leadership Program and a member of the U.S. National Academy of Sciences. He has served on the editorial boards of Ecology, Ecological Applications, Ecosystems, Global Change Biology, and Proceedings of the National Academy of Sciences (PNAS). Dr. Field received his Ph.D. from Stanford in 1981 and has been at the Carnegie Institution since 1984. His recent priorities include high-performance &ldquogreen&rdquo laboratories, integrity in the use of science by governments, local efforts to reduce carbon emissions, ecological impacts of biofuels, and the future of scientific publishing.
Jeffrey I. Gordon, M.D. (NAS/IOM), is the Dr. Robert J. Glaser Distinguished University Professor and Director of the Center for Genome Sciences at Washington University School of Medicine. He received his A.B. in biology from Oberlin College and his M.D. from the University of Chicago. Dr. Gordon joined the faculty of Washington University in 1981, after completing his clinical training in internal medicine and gastroenterology. He has remained at Washington University for his entire professional career. From 1991 to 2004, he was head of the Department of Molecular Biology and Pharmacology. In 2004 he resigned as department head to become the first director of the newly founded Center for Genome Sciences. This new center represents an interdepartmental, interdisciplinary, and multigenerational intentional community of faculty, postdocs, and students who are geneticists, population biologists and biostatisticians, computational biologists and computer scientists, systems biologists and engineers, and microbiologists and ecologists. The focus of the center is on comparative genomics and biodiversity, plus systems biology (an emerging area that seeks to describe how complex networks of interacting genes, proteins, and metabolites function to maintain normal cells
and how these networks adapt to perturbations, including those brought about by various disease states). Dr. Gordon&rsquos lab studies the genomic and metabolic foundations of mutually beneficial host-microbial relationships in the human gut with an emphasis on the interrelationships between the gut microbiome, diet, and nutritional status. He has published more than 400 scientific papers and is named as inventor or co-inventor on 23 U.S. patents. He has received a number of honors in recognition of his scientific contributions, including election to the National Academy of Sciences, the Institute of Medicine, and the American Academy of Arts and Sciences.
Pedro A. Sanchez, Ph.D., is director of tropical agriculture and senior research scholar at the Earth Institute of Columbia University in New York City. He serves as co-chair of the Hunger Task Force of the Millennium Project, an advisory body to the United Nations. Sanchez served as director general of the World Agroforestry Center (ICRAF) headquartered in Nairobi, Kenya, from 1991 to 2001. He is also professor emeritus of soil science and forestry at North Carolina State University and was a visiting professor at the University of California, Berkeley. He was named a MacArthur Foundation fellow in 2003 and received the World Food Prize in 2002. His professional career has been dedicated to improving the management of tropical soils through integrated natural resource management approaches to achieve food security and reduce rural poverty while protecting and enhancing the environment. Sanchez is author of Properties and Management of Soils of the Tropics (John Wiley and Sons 1976 rated among the top 10 best-selling books in soil science worldwide), and author of more than 200 scientific publications. He is a fellow of the American Society of Agronomy and the Soil Science Society of America. He has received decorations from the governments of Colombia and Peru and was awarded the International Soil Science Award and the International Service in Agronomy Award. In 2001, the Catholic University of Leuven, Belgium, awarded him a doctor honoris causa degree for his work on tropical soils in Africa and he was anointed as elder by the Luo community of Western Kenya, in recognition for his assistance in eliminating hunger from many villages in the region. A native of Cuba, he received his Ph.D. degree from Cornell University.
Christopher R. Somerville, Ph.D. (NAS), is the director of the Energy BioSciences Institute in Berkeley, California. He oversees all activities at the institute, including research, communication, education, and outreach. He also chairs the institute&rsquos Executive Committee. Dr. Somerville is a professor in the Department of Plant and Microbial Biology at the University of California, Berkeley, and a visiting scientist at the Lawrence
Berkeley National Laboratory. His research focuses on the characterization of proteins implicated in plant cell-wall synthesis and modification. He has published more than 200 scientific papers in plant and microbial genetics, genomics, biochemistry, and biotechnology. Dr. Somerville has served on the scientific advisory boards of many corporations, academic institutions, and private foundations in Europe and North America. He is a member of the National Academy of Sciences, the Royal Society of London, and the Royal Society of Canada.
Honors in the Biological Sciences
More than 30 percent of concentrators in the Biological Sciences earn honors each year. To be eligible for honors, students must meet three requirements:
1) Completion of an original research thesis that is recommended for honors by both the Thesis Advisor and Second Reader.
2) Formal and public presentation of the thesis (oral seminar or by poster presentation).
3) Demonstration of quality grades in the concentration.
The senior honors thesis is typically developed through a minimum of two, but more often three, semesters of research. Students intending to pursue a thesis in Biology often have a Brown faculty mentor and project secured in the summer prior to the senior year. Many students use UTRAs to help support research, though this is not the only mechanism of support. Often faculty members provide student support from their own grants. Students may also register for BIOL 1950/1960 independent study courses to support honors theses research, though this is not required. Please note that the Honors application process is separate from the independent study BIOL 1950/1960 registration project proposal. The application for Honors is below.
Students who have earned a majority of "A" grades in courses required for the concentration and who are are in good academic standing are eligible to apply for honors at the start of their penultimate (typically 7th) semester at Brown. Classes taken S/NC will count as qualifying towards that majority if they are marked "S* with distinction" indicating that had the student taken the course for a grade, the grade would have been an "A". Courses with a grade of S may be counted when a Course Performance Report indicates a grade of A. Students just shy of meeting the grade requirement for honors are encouraged to apply. Grades earned in penultimate semester concentration courses will be accounted for in the determination of quality grades made in the final semester.
Deadlines, and guidelines listed below apply to students in the following concentrations:
Health & Human Biology AB
Students concentrating in Biology AB, ScB, or Health & Human Biology are all eligible for Honors and the process is the same for each of those concentrations.
Concentrators in Biochemistry apply via Biochemistry advisors Applied Math-Biology students apply via Applied Mathematics Computational Biology students apply via CCMB Biomedical Engineering concentrators proceed via Engineering.
As per University policy, students may not use the same thesis to gain honors in more than one concentration. If pursuing honors in two concentrations, the theses must be fully distinct in content.
Thesis Advisor & Second Reader
The Thesis Advisor and Second Reader will evaluate and recommend the thesis for honors based on the criteria outlined below.
The Thesis Advisor is the primary investigator who will mentor the project, and who will be available to the student in developing the thesis aims, designing methods, analyzing data, interpreting outcomes and casting the work in the context of the scholarly field(s) of relevance. The Thesis Advisor is also expected to guide the student in developing and delivering a polished final presentation of the thesis. The Thesis Advisor should be a Brown faculty member, usually but not always, from the Division of Biology and Medicine.
The Second Reader will be a faculty member or associated scientist who is identified by the student, in consult with the Thesis Advisor, as appropriate to review the work. The Second Reader will evaluate the thesis, and provide an evaluation of the work. Second Readers should be acquainted with the field of research described by the project, and be willing and able to provide input and critique that will challenge and strengthen the thesis. The Second Reader should be at the doctoral level and ideally not from the same laboratory or research group where the project originates.
Application for Honors
Students should complete the Honors Proposal Application in collaboration with the Thesis Advisor and Second Reader. Both advisor signatures are due at the application proposal deadline (below). Please save your completed application as a pdf and email your Thesis Advisor and Second Reader for their electronic signatures. Please submit your completed and signed application and deliver to the BUE office or send via email to [email protected] . If you're unable to secure electronic signatures please have your advisors email their intent to act as your advisor and/or reader to Michelle Leiber at the email listed above.
Presentation of the thesis can be fulfilled by participation in the Annual Biology Senior Research, Capstone, and Declaration Day or an arranged oral seminar. If the oral seminar format is chosen the student will make scheduling arrangements with guidance from the Thesis Advisor. The oral presentation should be scheduled early to mid-March in order to meet the Thesis Advisor and Second Reader Final Evaluation Deadline.
While formal presentation of the thesis is required, there is not a specific set of criteria for evaluation. Advisors have the opportunity to comment on the presentation in the formal evaluation. Advisors should develop a mentoring plan to teach students about the various approaches to presenting scientific research. Opportunities for students to practice the presentation, receive, and incorporate feedback is especially helpful and encouraged.
Biology honors applicants are required to present their thesis research and senior capstone students are encouraged to do the same (though this is not a requirement). The Program in Biology will host the Annual Biology Senior Research, Capstone, and Declaration Day event in April 2022. Please check back here or email [email protected] for the upcoming date.
Final Thesis Submission
BUE submission instructions:
1. Email a copy of the final thesis to [email protected] as a single pdf document. The format of the thesis is determined by the faculty advisor and student. The pdf file name should be the student’s first name initial(s) in all caps, followed by the last name (no spaces). For example, Dean Smith’s thesis file name would read KFSmith.pdf. The BUE Office will maintain a copy of the thesis for programming purposes. The thesis will not be shared or made public without the student’s permission.
2. The email subject heading should read: Honors thesis for BUE filing only.
Thesis Evaluation for Honors
The Thesis Advisor and Second Reader will evaluate and recommend the thesis for honors based on the criteria outlined below. An electronic honors evaluation form will be provided directly, via email, to the Thesis Advisor and Second Reader by the Office of Biology Undergraduate Education. This form will be sent well in advance of the final evaluation due date (below). It is up to the student and Thesis Advisors to develop internal project deadlines for submitting drafts and final copies of the thesis so there is time for revisions, as well as formal presentation of your honors thesis (poster/oral) so that the final evaluation can be submitted. The entire thesis presentation should be delivered prior to the final evaluation deadline. Please adhere to the BUE internal deadlines below.
Students graduating in May:
First Monday in October
October 4, 2021
Fourth Friday in March
April 22, 2022
Students graduating in December*:
- Honors Application Due Date
Thesis Advisor and Second Reader approval signature required
First Friday in March
March 5, 2021
First Friday in December
December 3, 2021
Thesis Guidelines & Expectations
A senior honors thesis in Biology is a substantial body of original scholarly research. Successful theses can be grounded in a number of methodological approaches including bench or field research, clinical study, mathematical models, computer simulations, meta-analyses that test hypotheses or yield new synthesis in a scholarly context. Regardless of the approach, successful theses will be inquiry-based and demonstrate contextual understanding of the work, formal assessment of scientific information, critical thinking, clear communication and a high level of independence.
Faculty Advisors recommend the thesis for honors based on the following criteria:
1) The writing, format, and presentation of the thesis are appropriate for the intended audience.
2) The introduction of the thesis offers a formal review of the literature that presents the state of the field to date, and in doing so sets up a clear argument for the value of the work presented.
3) The introduction of the thesis offers a clearly articulated goal, aim, question, and /or hypothesis to be tested.
4) The methods and analyses selected are clearly justified.
5) Results are interpreted appropriately and based on the analyses presented in the methods.
6) The discussion section offers a compelling consideration of a) unexpected findings or challenges during the research process that may have influenced the results, b) implications of overall findings and their impact on the relevant field(s), c) future directions / next steps.
Thesis Form and Format
A thesis in Biology, Health & Human Biology, and Biophysics make take a variety of forms and formats. It is up to the honors candidate and Thesis Advisors to determine the specific expectations for the final thesis form and format. Elements of a thesis in Biology vary greatly depending on the nature of the project, the specific sub-field, and the student's learning goals. Communication about these expectations should be clearly articulated and agreed upon early in the research process. A common choice is for students to prepare the thesis as if they were to submit the work to a peer-reviewed journal. This approach offers the opportunity for students to experience the first step of the publication process. Another option is to prepare the thesis manuscript following the dissertation guidelines set forth by Brown's Graduate School. Previous students have found this useful in preparing for doctoral or master's research programs. Students and Advisors may also look to Brown University's Digital Repository of Undergraduate Theses in Biology for examples of formatting previously followed. Regardless of format, a thesis in Biology, Health & Human Biology, and Biophysics will exhibit the highest quality writing, novel content, context of findings, and documentation of sources expected at the undergraduate level. STEM theses generally include an abstract, robust introduction, complete methods, results, full discussion & conclusion, a complete list of references that illustrate the state of the field of relevance, clear figures and tables with appropriate captions, and necessary appendices. Regardless of format, a thesis in Biology, Health & Human Biology, and Biophysics will exhibit the highest quality writing, clear articulation of the state of the field relevant to the work, novel content, context of findings, and documentation of sources expected at the undergraduate level.
“There is no such thing as a failed experiment, only experiments with unexpected outcomes (Richard Buckminster Fuller).”
Science does not always go as planned. Methodological hurdles and insignificant results are common experiences of researchers at every stage. Regular communication with the Thesis Advisors is essential for navigating hurdles that arise during the research process. Students with an approved application to the honors program are encouraged to submit the thesis even when challenges occur along the way. When outcomes are not as planned the student and Advisors are encouraged to work together to develop a new plan for presenting the work in the form of a formal thesis. Indeed, there is great value in presenting work completed and formally discussing challenges, unexpected outcomes, and insignificant findings. Dean Smith is available to assist with planning during this process and to discuss alternative means of evaluation as necessary.