14.4: Administering Inhaled Medications
By the end of this section, you will be able to:
- Describe the different forms of inhaled medications
- Understand the categories of inhaled medications
- Verbalize procedural steps for administering inhaled medications
Medications administered through inhalation are dispersed via an aerosol spray, mist, or powder that patients inhale into their airways. Although the primary effect of inhaled medications is respiratory, there are likely to be systemic effects as well. Inhaled medications are absorbed easily by the lungs because of the large surface area of the lungs with high blood flow. Therefore, inhaled medications work faster than oral medications. Medications may be inhaled into the respiratory tract to reduce inflammation in the airways, open the lungs, and treat a variety of respiratory illnesses.
Forms of Inhaled Medications
Inhaled medications may be administered by nebulizers or hand atomizer s. Although both forms of inhaled medications are used to deliver medications into the lungs to treat respiratory conditions, the selected form may depend on several factors. Hand atomizers tend to be smaller and more portable than nebulizers; however, nebulizers may be the preferred option for patients who experience difficulty in coordinating and controlling their breaths.
Nebulizer
A nebulizer is a small electric or battery-powered machine that delivers a fine mist of liquid medications (Figure 14.17). Oxygen or compressed air is used to transfer the medication from the nebulizer and into the lungs via a face mask or mouthpiece. The oxygen or compressed air moves the particles, so the patient may be instructed to breathe normally during nebulized medication administration. To reduce the risk of bacteria, nebulizers should be cleaned after each use, disinfected at least once per week, and left out to air-dry after cleaning. Medications, such as bronchodilators (medication that relaxes the muscles in the lungs and widens the airway) and antibiotics , may be administered via a nebulizer. Steroids cannot be administered via a nebulizer and require an inhaler . When administering medications via nebulizers, monitor the patient’s heart rate throughout the treatment because these medications may cause tachycardia or other cardiac effects, such as palpitations or irregular heart rhythms.
See the competency checklist for Administering a Nebulizer Treatment. You can find the checklists on the Student resources tab of your book page on openstax.org.
Nebulizers are often recommended for administering inhalation medications to children and older adults because nebulizers do not require coordination of breathing and administration efforts. Although typically a mouthpiece is more efficient for delivering nebulized medications, a face mask should be used with young children and older adults. Face masks are easier to use with these populations because these patients often have difficulty keeping nebulizer mouthpieces in their mouths. It is important to ensure the patient keeps the mask on for the duration of the treatment. Giving the patient something to do, such as reading a book, playing with a toy, or reading the newspaper, can be very beneficial for keeping children and older adults occupied and helping them remain still throughout the nebulizer treatment.
Though nebulizers take time to set up, they can be more effective to use during asthma attacks because the medication is pressurized into the lungs versus requiring a deep breath to inhale the medication into the lungs. Nebulizers may also be easier to use with young children because instructions for teaching the child how to breathe during the medication administration are not required. Another benefit of nebulizers is that multiple medications may be delivered simultaneously. Although nebulizers can be very beneficial, they are not as easy as an inhaler to transport, often require a power source, and take longer to administer the medication than when administered through an inhaler.
Nurse: Good morning. My name is Nurse Sarah and I’m here to help you with your nebulizer treatment today. What’s your name?
Child: Hi, Nurse Sarah. I’m Emily.
Nurse: It is nice to meet you, Emily. How are you feeling today?

Nurse: I’m sorry to hear that. It’s great that you’re here so we can help you feel better. Do you know what a nebulizer is, Emily?
Child: Yeah, my mom told me it’s a machine that will help me breathe better.
Nurse: That’s right! It’s like magic mist that helps open up your airways. It’s a bit noisy, but it’s not scary. Now, let’s get everything ready. I am going to turn on the machine and it will turn the medicine into a mist that you’ll breathe in through this mask.
Child: Okay, but will it taste bad?
Nurse: It might have a slightly funny taste, but it’s not too bad. You can think of it as a special potion that will help you breathe better. Plus, you can drink some water afterward if you like.
Child: Okay, I can do that.
 You can watch your favorite show, read a book, or even close your eyes and imagine a fun adventure.
Child : Can I pretend I’m a dragon breathing fire?
Nurse: Absolutely! That sounds like a fantastic adventure. You can be a dragon while you take your treatment.
Scenario follow-up: Emily puts on the mask, and Nurse Sarah starts the nebulizer machine. Emily continues her nebulizer treatment, imagining herself as a dragon, while Nurse Sarah keeps an eye on her and offers reassurance throughout the process.
Hand Atomizer
A hand atomizer ( inhaler ) is a pocket-sized device that delivers medications into the lungs without the use of electricity. There are three main types of hand atomizers: metered-dose inhaler s, dry powdered inhalers, and soft-mist inhaler s. To prevent bacterial growth, inhalers should be cleaned frequently. Most inhalers track the number of doses administered, allowing for medication refills to be obtained before running out of the medication.
Metered-Dose Inhaler (MDI)
A metered-dose inhaler (MDI) creates an aerosolized mist of medication that is inhaled through the mouth and into the lungs (Figure 14.18). The canister is attached to a mouthpiece and the medication is administered into the lungs by pressing on the canister while coordinating breathing efforts. Medication waste is common with MDIs because mist particles stick to the tongue or aerosolize in the air. MDIs may be used for steroids , bronchodilators , and combination medications. Examples of MDIs include albuterol inhalation (ProAir HFA) and fluticasone inhalation (Flovent).
A spacer may be used to prevent waste of medication and allow for the full dose to be administered (Figure 14.19). A spacer is a clear tube that fits between the inhaler and the mouthpiece. After the medication is released from the inhaler, it moves into the spacer, which allows the patient to inhale the medication more slowly and with control. The spacer must be cleaned frequently to prevent bacterial growth.
Dry Powder Inhalers (DPI)
A dry powder inhaler (DPI) provides dry powder medications that are inhaled through a device in the mouth and into the lungs (Figure 14.20). Unlike MDIs, DPIs use an inward breath to move the medications into the lungs instead of a propellant . After the dose is activated, a quick inhale activates the medication and moves it into the lungs. Typically, DPIs are easy to use, do not require a spacer, and do not require the same coordinated efforts in breathing and operating the device as MDIs. Unlike MDIs, DPIs require more forceful breaths, are more difficult to receive an exact dose of medication, and can be affected by humidity. Examples of DPI mediations include budesonide inhalation suspension (Pulmicort) and fluticasone-salmeterol inhalation powder (Advair Diskus). Patients should be instructed to rinse their mouth, spitting out the rinse, after use of a DPI to reduce the risk of oral thrush (fungal infection), local side effects (such as throat irritation, dry mouth, and hoarseness), and to prevent unintentional swallowing of the medication particles.
Soft-Mist Inhaler
A soft-mist inhaler is a handheld device that turns liquid medications into a mist cloud that can then be inhaled without a propellant. The medication contains more particles and leaves the inhaler more slowly than with MDIs or DPIs; therefore, more of the medication enters the lungs and a lower dose of the medication may be used. This type of inhaler does not require coordinated breathing efforts or a spacer. An example of soft-mist inhaler medication is tiotropium/olodaterol (Stiolto Respimat).
Categories of Inhaled Medications
There are several categories of inhaled medications, including bronchodilators , steroids , antibiotics , and dornase alfa, an inhaled medication made of synthetic proteins used to treat cystic fibrosis (CF). The category of inhaled medication prescribed is dependent on factors such as the patient’s condition, severity of symptoms, and potential side effects. It is important for the nurse to understand the various categories of inhaled medications, their indications, how they work, and potential side effects.
Bronchodilators
A bronchodilator is a medication that relaxes the muscles in the lungs and widens the airways. Bronchodilators are used to treat long-term conditions (e.g., asthma , chronic obstructive pulmonary disease [COPD]) in which the airways become narrower and more inflamed. Bronchodilators may be short-acting (i.e., unexpected attacks of breathlessness) or long-acting (i.e., to help control breathlessness) in asthma and COPD. Potential side effects of bronchodilators include trembling in the hands, headaches, dry mouth, heart palpitations, muscle cramps, cough, diarrhea, or nausea and vomiting.
The most widely used bronchodilators for inhalation are beta-2 agonists and anticholinergic s. Beta-2 agonists stimulate beta-2 receptors in the muscles that line the airways, causing them to relax and dilate. These medications should be used with caution for patients that have hyperthyroidism , cardiovascular disease, arrhythmias, hypertension , or diabetes , as the symptoms of these conditions may worsen. For example, bronchodilators can stimulate the sympathetic nervous system , which may lead to increased heart rate, increased blood pressure, chest pain, and an irregular heart rate. They can also stimulate the liver to release glucose , which increases the blood glucose levels. Examples of beta-2 agonists include salbutamol (Ventolin) and vilanterol (Breo Ellipta). Anticholinergics dilate the airways by blocking the cholinergic nerves. These medications should be used with caution for patients who have benign prostatic hyperplasia (BPH), bladder obstruction, or glaucoma . For example, anticholinergics can worsen the symptoms of BPH and bladder obstruction by relaxing the bladder muscles, causing urinary retention . These medications can also cause the pupil to dilate, thereby increasing intraocular pressure and worsening glaucoma. Examples of anticholinergics include ipratropium inhalation (Atrovent) and glycopyrronium (Qbrexza).
Steroids
A steroid is an anti-inflammatory medication. A corticosteroid is a medicine that reduces inflammation and prevents flare-ups of respiratory conditions. Corticosteroids are the gold standard treatment for asthma and may be taken in combination with bronchodilators to help keep the airways open and enhance the effectiveness of the corticosteroids. People taking inhaled steroid medications should be instructed to brush their teeth or rinse their mouth with water after administering the medication to decrease the risk of fungal infections. It is important they do not swallow the rinse water because doing so may cause a fungal infection in the throat. Examples of steroid inhalation medications include beclomethasone inhalation (Beclovent) and fluticasone inhalation (Flovent). Potential side effects of steroid inhalers include a sore mouth or throat, hoarse voice, cough, or oral thrush .
Antibiotics
Antibiotics may be warranted for patients with chronic respiratory diseases, such as CF, non-CF bronchiectasis (a chronic condition where the lung walls are thickened due to inflammation and infection), and ventilator-associated pneumonia . Inhaled antibiotics have the potential to deliver higher concentrations of medications without the systemic effects of oral or parenteral administration. Examples of inhaled antibiotics include aztreonam (Azactam) and tobramycin inhalation powder (Tobi Podhaler). Potential side effects of inhaled antibiotics include new or worsening breathing problems, ringing in the ears, hoarse voice, dizziness or balance problems, muscle weakness, or kidney problems.
Dornase alfa
An inhaled medication consisting of a synthetic protein that breaks down excess DNA in the pulmonary secretions of people with CF is known as dornase alfa (Pulmozyme). They help to improve the lung function and lower the risk of infection by thinning the mucus in the airways. Dornase alfa is inhaled via a nebulizing device that creates a mist from the liquid medication. It must be kept in the refrigerator, protected from sunlight, and discarded after it is opened. This medication is stored in foil pouches to protect it from sunlight and should not be left at room temperature for longer than twenty-four hours. No other medications should be mixed with dornase alfa during the nebulizing treatment. Potential side effects of dornase alfa include loss of voice, throat discomfort, red or watery eyes, rash, runny nose, shortness of breath, fever, chest pain, indigestion, or diminished lung function.
Procedural Steps for Administering Inhaled Medications
Regardless of the type of inhaled medication, the nurse should perform hand hygiene, apply gloves, and perform the same rights of medication administration as is completed with other types of medications. Perform and document a respiratory assessment, including respiratory rate, oxygen saturation level, heart rate, lung sounds, and respiratory effort.
To administer nebulizers, pour the liquid medication into the medication cup of the nebulizer . Sit the patient in high Fowler’s position with the head of the bed elevated between 60 and 90 degrees, if possible. Attach the nebulizer to an oxygen set with a flow rate of 6 to 10 L/min, based on the manufacturer’s guidelines. Check for misting to ensure the equipment is working properly. Attach the top end of the tubing to the nebulizer mask. Instruct the patient to take slow, deep breaths through their mouth, pausing for two to three seconds before each exhale. If the patient is dyspneic, encourage them to hold their breath every fourth or fifth breath for five to ten seconds. Instruct the patient to continue the breathing pattern until the medication has been fully administered, as evidenced by no visible misting. Nebulized medications typically take ten to fifteen minutes to administer. After the treatment is completed, turn off the oxygen flowmeter , unless the patient is receiving oxygen therapy, and disconnect the nebulizer. After administration, encourage the patient to cough and breathe deeply and perform oral care. The nurse should then re-evaluate the patient’s respiratory system to include respiratory effort. Perform hand hygiene and document administration of the medication as well as the patient’s tolerance of the medication and procedure.
To administer an MDI, shake the inhaler and attach the spacer , if applicable. Have the patient place the mouthpiece of the inhaler or spacer between their lips, while tightly closing their lips around it. If a spacer is not used, the inhaler may be held 1 to 2 in (2.5 to 5 cm) from the mouth. Instruct the patient to breathe out and then press the inhaler down at the same time the patient is breathing in. Instruct the patient to keep breathing in, slowly, for three to five seconds and then hold their breath for five to ten seconds to get the medication into the airways. A slow inhale is required to prevent the medication from hitting the back of the throat instead of moving into the lungs. Slowly breathe out and repeat if more than one puff is required. When administering corticosteroids, instruct the patient to rinse their mouth to prevent fungal infections. Instruct the patient not to swallow the rinse water to prevent fungal infections in the back of the throat. Perform hand hygiene and document administration of the medication as well as the patient’s tolerance of the medication and procedure.
Watch this demonstrational video about metered-dose inhaler medications to learn how to administer them.
The nurse is caring for an older patient who is taking a metered-dose inhaler. The patient will be discharged with the inhaler, so the nurse allows the patient to self-administer the medication under nurse supervision. The nurse notices the patient pressing down on the canister and then pausing before inhaling. The nurse recognizes the cues that the patient is using an incorrect technique. The nurse analyzes the cues , understanding that the patient should begin breathing in while simultaneously pressing down on the medication canister. The nurse prioritizes the hypotheses that the delay in breathing is resulting in medication waste and the patient is not receiving the full dose of the medication. The nurse generates a solution by recognizing that the patient may benefit from using a spacer and takes action by contacting the respiratory department to obtain a spacer that can be used with the next administration of the medication.
To administer dry-powder inhalers, remove or rotate the cap of the inhaler. Load the medication, if applicable, and press down on the lever per manufacturer’s guidelines to activate the medication. Instruct the patient to turn their head away from the device and breath all the way out. Place the mouthpiece into the mouth and close their lips around it. Breathe in deeply for a few seconds. Take the device out of the mouth and instruct the patient to hold their breath for up to ten seconds before slowly breathing out. Instruct the patient to rinse their mouth with water or brush their teeth, ensuring they do not swallow the rinse water. Perform hand hygiene and document administration of the medication as well as the patient’s tolerance of the medication and procedure.
To administer soft-mist inhaler s, prepare the device according to the manufacturer’s instructions, open the cap, and instruct the patient to breathe out slowly and fully. The nurse instructs the patient to place the mouthpiece in the mouth, using caution not to cover the air vents on the sides of the device. Press the dose release button while the patient slowly inhales the mist. Instruct the patient to hold their breath for ten seconds and repeat, as prescribed. Perform hand hygiene and document administration of the medication as well as the patient’s tolerance of the medication and procedure.
Order of Inhaled Medications
When administering multiple inhaled medications, the order of administration matters. If the patient is ordered a bronchodilator, the bronchodilator should be administered before any other inhaled medication, which relaxes and opens the airway and allows the other medications to work more effectively. Next, administer dornase alfa , if ordered, which breaks up and thins the mucus. After encouraging the patient to cough and breathe deeply to clear the mucus, the antibiotic is the next medication to be inhaled, which kills the bacteria in the lungs. Steroids are administered last, when the lungs are the most cleared, which reduces the swelling that may have been caused by the mucus and infection.


4.7: Activity-based costing for a service business to estimate factory overhead
Service businesses may also use activity-based costing to allocate general overhead costs to clients, patients, and guests, also by estimating costs of activities based on their use of resources, and assigning costs to customers based on their use of activities.
A hospital, for example, might identify the following activities whose general costs must be shared among patients. Each activity rate is estimated based on the activity’s budgeted overhead cost for the year divided by the number of occurrences expected during the year. For each patient stay, the number of times each activity occurs is multiplied by the overhead rate for that activity. The sum of all the activity costs is the amount of overhead applied to the cost of servicing the patient.
ABC costing for a patient’s six-day stay in a hospital is summarized in the following table.
|
Activity |
Activity Rate (estimated) |
Patient usage |
Patient Costs |
|
Admissions |
$70 per admission |
1 admission |
$70 x 1 = $70 |
|
Operating room use |
$900 per hour |
4 hours |
$900 x 4 = 3,600 |
|
Dispensing medications |
$25 per administration |
3 times per day / 6 days |
$25 x 3 x 6 = 450 |
|
Radiology testing |
$290 per image |
2 images |
$290 x 2 = 580 |
|
Diagnostic lab |
$150 test |
6 tests |
$150 x 6 = 900 = 900 |
|
Medical assistance |
$20 per visit |
6 visits per day / 6 days |
$20 x 6 x 6 = 720 |
|
Cleaning and laundry |
$80 per day |
6 days |
$80 x 6 = 480 |
|
Discharge |
$100 per discharge |
1 discharge |
$100 x 1 = 100 |
|
TOTAL = $6,900 |
A total of $6,900 of overhead costs is associated with this patient’s hospital stay.
ABC increases the accuracy of allocating overhead by budgeting multiple targeted activities that can be estimated more precisely than relying on one general overhead rate that applies to all overhead in a business This more granular approach also gives companies better insight into ways to control the cost of a product, such as reducing the time it takes to perform an activity or decreasing the number of times an activity occurs.
ABC helps managers, who already view costs by activity, and accountants communicate more effectively. “An activity-based system aligns organizational information with the business mission and operations rather than financial transactions. It tears down the barriers that segregate financial information from other information.” 1


1.10: Female Reproductive System
- Identify the anatomy of the female reproductive system
- Describe the main functions of the female reproductive system
- Spell the medical terms of the female reproductive system and use correct abbreviations
- Identify the medical specialties associated with the female reproductive system
- Explore common diseases, disorders, and procedures related to the female reproductive system
Female Reproductive System Word Parts
Click on prefixes, combining forms, and suffixes to reveal a list of word parts to memorize for the female reproductive system.
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Introduction to the Female Reproductive System
The female reproductive system produces gametes and reproductive hormones. In addition, the female reproductive system supports the developing fetus and delivers it to the outside world. The female reproductive system is located primarily inside the pelvic cavity. The female gonads are called ovaries and the gamete they produce is called an oocyte.
Watch this video:
Media 10.1. Reproductive System, Part 1 – Female Reproductive System: Crash Course A&P #40 [Online video]. Copyright 2015 by CrashCourse .
Female Reproductive System Medical Terms
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Anatomy (Structures) of the Female Reproductive System
External Female Genitals
The external female reproductive structures are referred to collectively as the vulva and they include:
- The mons pubis is a pad of fat that is located at the anterior, over the pubic bone. After puberty, it becomes covered in pubic hair.
- The labia majora (labia = “lips”; majora = “larger”) are folds of hair-covered skin that begin just posterior to the mons pubis.
-
The
labia minora
(labia = “lips”; minora = “smaller”) is thinner and more pigmented and extends medially to the labia majora.
- Although they naturally vary in shape and size from woman to woman, the labia minora serve to protect the female urethra and the entrance to the female reproductive tract.
- The superior, anterior portions of the labia minora come together to encircle the clitoris (or glans clitoris), an organ that originates from the same cells as the glans penis and has abundant nerves that make it important in sexual sensation and orgasm. The hymen is a thin membrane that sometimes partially covers the entrance to the vagina .
- The vaginal opening is located between the opening of the urethra and the anus. It is flanked by outlets to the Bartholin’s glands .
 It also serves as the exit from the uterus during menses and childbirth. The outer walls of the anterior and posterior vagina are columns with ridges. The superior fornix meets the uterine cervix. The cervix is the opening to the uterus .
The walls of the vagina are lined with:
- An outer, fibrous adventitia
- A middle layer of smooth muscle
- An inner mucous membrane with transverse folds called rugae .
Together, the middle and inner layers allow the expansion of the vagina to accommodate intercourse and childbirth. The thin, perforated hymen can partially surround the opening to the vaginal orifice. The Bartholin’s glands and the lesser vestibular glands (located near the clitoris) secrete mucus, which keeps the vestibular area moist .
The vagina has a normal population of microorganisms that help to protect against infection. There is both pathogenic bacteria, and yeast in the vagina. In a healthy woman, the most predominant type of vaginal bacteria is from the genus Lactobacillus, which s ecretes lactic acid. the lactic acid protects the vagina by maintaining an acidic pH (below 4.5) .
Lactic acid, in combination with other vaginal secretions, makes the vagina a self-cleansing organ. However, douching can disrupt the normal balance of healthy microorganisms, and increase a woman’s risk for infections and irritation. It is recommend that women do not douche and that they allow the vagina to maintain its normal healthy population of protective microbial flora .
Ovaries
The ovaries are the female gonads. There are two, one at each entrance to the fallopian tube. They are each about 2 to 3 cm in length, about the size of an almond. The ovaries are located within the pelvic cavity. The ovary itself is attached to the uterus via the ovarian ligament. The ovarian stroma forms the bulk of the adult ovary. Oocytes develop within the outer layer of this stroma, each surrounded by supporting cells. This grouping of an oocyte and its supporting cells is called a follicle.
The Fallopian Tubes
Fallopian tubes are not connected to the ovaries. Instead fimbriae catch the oocyte like a baseball in a glove.The fallopian tubes are the conduit of the oocyte from the ovary to the uterus. Each of the two fallopian tubes is close to, but not directly connected to, the ovary.
- The isthmus is the narrow medial end of each uterine tube that is connected to the uterus.
- The wide distal infundibulum flares out with slender, finger-like projections called fimbriae .
- The middle region of the tube, called the ampulla , is where fertilization often occurs.
The fallopian tubes have three layers:
- An outer serosa
- A middle smooth muscle layer
-
An inner mucosal layer
- In addition to its mucus-secreting cells, the inner mucosa contains ciliated cells that beat in the direction of the uterus, producing a current that will be critical to moving the oocyte .
The Uterus and Cervix
The uterus is the muscular organ that nourishes and supports the growing embryo. Its average size is approximately 5 cm wide by 7 cm long and it has three sections.
- The portion of the uterus superior to the opening of the uterine tubes is called the fundus .
- The middle section of the uterus is called the body of uterus (or corpus).
-
The
cervix
is the narrow
inferior
portion of the uterus that projects into the vagina.
- The cervix produces mucus secretions that become thin and stringy under the influence of high systemic plasma estrogen concentrations, and these secretions can facilitate sperm movement through the reproductive tract.
The wall of the uterus is made up of three layers:
- Perimetrium: the most superficial layer and serous membrane.
- Myometrium: a thick layer of smooth muscle responsible for uterine contractions.
- Endometrium: the innermost layer containing a connective tissue lining covered by epithelial tissue that lines the lumen. It provides the site of implantation for a fertilized egg, and sheds during menstruation if no egg is fertilized.
- Write or draw out the components of the pathway that an oocyte takes from beginning to end.
- Why do you think the fallopian tubes are not connected to the ovaries ?
Physiology (Function) of the Female Reproductive System-Ovulation
Following ovulation, the Fallopian tube receives the oocyte. Oocytes lack flagella, and therefore cannot move on their own.
- High concentrations of estrogen that occur around the time of ovulation induce contractions of the smooth muscle along the length of the Fallopian tube.
- These contractions occur every 4 to 8 seconds, causing the oocyte to flow towards the uterus, through the coordinated beating of the cilia that line the outside and lumen of the length of the Fallopian tube which pulls the oocyte into the interior of the tube.
- Once inside, the muscular contractions and beating cilia move the oocyte slowly toward the uterus.
- When fertilization does occur, sperm typically meet the egg while it is still moving through the ampulla.
Watch this video:
Watch this video on ovulation from MedLine Plus to observe ovulation and its initiation in response to the release of FSH and LH from the pituitary gland.Media 10.2. Ovulation. From Betts, et al., 2013. Licensed under CC BY 4.0 .
The Menstrual Cycle
The three phases of the menstrual cycle are:
- The menses phase of the menstrual cycle is the phase during which reproductive hormone levels are low, the woman menstruates, and the lining is shed. The menses phase lasts between 2 – 7 days with an average of 5 days.
- The proliferative phase is when menstrual flow ceases and the endometrium begins to proliferate . During this phase reproductive hormones are working in homeostasis to trigger ovulation on approximately day 14 of a typical 28-day menstrual cycle. Ovulation marks the end of the proliferative phase.
- The secretory phase the endometrial lining prepares for implantation of a fertilized egg. If no pregnancy occurs within approximately 10- 12 days the endometrium will grow thinner and shed starting the first day of the next cycle.
Anatomy Labeling Activity
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Female Reproductive System Terms not Easily Broken into Word Parts
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Female Reproductive System Medical Abbreviations
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Diseases and Disorders of the Female Reproductive System
Cancer
Breast Cancer
Breast cancer starts in the cells that line the ducts or the lobule of the breast. Some warning signs include a new lump in the breast or axilla , thickening or swelling, irritation or dimpling of the breast skin, redness or flaky skin, pain, discharge, all in the breast or nipple area, and change in breast size. Risk factors include family history, obesity, hormonal treatment and changes in breast cancer-related genes (BRCA1 or BRCA2) (Centers for Disease Control and Prevention, n.d.; Cancer Care Ontario, n.d.).
Treatment options include chemotherapy, radiation and surgical interventions such as mastectomy , biopsy, incision and drainage and mammoplasty (Centers for Disease Control and Prevention, n.d.; Cancer Care Ontario, n.d.). To learn more about breast cancer, view the Cancer Care Ontario: Breast Cancer web page .
Cervical Cancer
Cervical cancer is typically slow-growing cancer and is highly curable when found and treated early.  It is diagnosed during a Papanicolaou test (or Pap smear) which looks for precancers, cell changes, on the cervix. The Pap test can find cervical cancer early, when treatment is most effective. The Pap test only screens for cervical cancer (Centers for Disease Control and Prevention, 2019).
The HPV (Human papillomavirus) test looks for HPV strains which is the virus that can cause precancerous cell changes. Almost all cervical cancers are caused by HPV. HPV is a common virus that is passed from one person to another during sexual contact. In Canada, there is the HPV vaccine. The age of administration varies between the provinces and territories. See below under HPV for more information about the HPV vaccine (York Region Health Connect, n.d.). To learn more about cervical cancer please visit the Centers for Disease Control and Prevention’s cervical cancer factsheet (PDF file) .
Endometriosis
Endometriosis is an abnormal condition of the endometrium . Endometriosis occurs when this tissue grows and implants outside the uterus. The female hormone estrogen causes these implants to grow, bleed, and break down. They are implanted outside the uterus have no way to leave the body. They become painful, inflamed, and swollen. The inflammation causes scar tissue around nearby organs which can interfere with their normal functioning and cause pain (Canadian Women’s Health Network, 2012).
Endometriosis generally appears between the ages of 15 and 50. Signs and symptoms may include dysmenorrhea , lumbago , dyspareunia , menstrual irregularity and infertility. One-third of women diagnosed with endometriosis have no symptoms at all.Diagnosis may include laparoscopy and endometrial biopsy. Treatment may include medication, surgical interventions such as hysterectomy and oophorectomy . The cause of endometriosis is unknown (Canadian Women’s Health Network, 2012). To learn more about endometriosis visit the Endometriosis FAQ article on Canadian Women’s Health Network.
PCOS
Polycystic Ovary Syndrome (PCOS) has no known etiology but researchers have linked it to excessive insulin production. Excessive insulin in the body can release extra male hormones in women. Since the ovaries produce high levels of androgens this causes the eggs to develop into cysts and instead of releasing during ovulation, the cysts build up and enlarge. The most common symptoms of PCOS include oligomenorrhea , amenorrhea , polymenorrhea , enlarged ovaries with multiple small painless cysts or follicles that form in the ovary, acrochordons , acanthosis nigricans , hirsuitism , thinning hair, acne, weight gain, anxiety, depression, hyperglycemia, and infertility (Canadian Women’s Health Network, 2012a).
Treatments like medications such as birth control pills or antiandrogens can help balance the hormones in your body and relieve some of the symptoms (Canadian Women’s Health Network, 2012a).. To learn more about PCOS visit the PCOS article on the Canadian Women’s Health Network .
Sexually Transmitted Infections (STIs)
The terms for Sexually Transmitted Infections (STI) and Sexuality Transmitted Diseases (STD) are often used interchangeably. Sexuality Transmitted Diseases (STD) implies the disease was acquired through sexual transmission. A disease is a disorder of structure or function in a human, which produces specific signs or symptoms. A disease must be managed, as with the case of Human Immunodeficiency Virus (which can also be acquired to through the transmission of other bodily fluids; thus not solely sexual transmission). The treatment may include antiretrovirals or anti-virals (Urology Care Foundation, 2019).
Chlamydia (CT)
Chlamydia is one of the most common sexually transmitted infections (STIs) caused by bacteria that infect the cervix, urethra and other reproductive organs. Chlamydia is easy to treat and can be cured. Many people with chlamydia do not have any symptoms and unknowingly pass the infection to their sexual partner(s). If symptoms develop, they usually appear two to six weeks after sexual contact with an infected person. While females are most often asymptomatic they may experience cervicitis . Left untreated, chlamydia in females can lead to Pelvic Inflammatory Disease (PID) which can cause permanent damage to the reproductive organs and subsequent infertility (Sexually Transmitted Infections (STIs) Chlamydia, 2018) (Chlamydia and Gonorrhea, n.d.).
 Chlamydia can be spread to the eyes via the hands with direct contact of infected fluids. Until a patient finishes their treatment, they continue to have the infection and can continue to pass it to others . Chlamydia is treated with antibiotic pills. If the patient has epididymitis , they may need to be hospitalized and be treated with intravenous (IV) antibiotics. All sexual partners within the past 60 days should be examined, treated, and informed that having no symptoms does not mean there is no infection ( Ontario Agency for Health Protection and Promotion , 2019; Region of Peel, 2007).
Gonorrhea (Gonococcus) – (GC)
Gonorrhea is a sexually transmitted infection (STI) caused by bacteria that infects the cervix, urethra and other reproductive organs. Infections can also infect the throat and anus. Gonorrhea can be treated and cured. Many people infected with Gonorrhea have no symptoms and can unknowingly pass the infection on to their sexual partner(s). If symptoms develop, they may appear two to seven days after sexual contact with an infected person. Symptoms vary depending on which part of the body is infected. Females may experience abnormal vaginal bleeding, discharge, or dysuria . Left untreated, Gonorrhea in females may lead to pelvic inflammatory disease and fertility complications such as ectopic pregnancy. Gonorrhea infection from oral sex may lead to sore throat and swollen glands.   Until the patient finishes their treatment, they continue to have the infection and can pass it to others ( Ontario Agency for Health Protection and Promotion, 2019a; Region of Peel, 2007 ).
Gonorrhea is treated with oral antibiotics in combination with an intramuscular (IM) injection. It is important that one completes the treatment and abstain from unprotected sexual activity for at least seven days following treatment. All sexual partners within the past 60 days should be examined, treated and informed that having no symptoms does not mean there is no infection ( Ontario Agency for Health Protection and Promotion, 2019a; Region of Peel, 2007 ).
Reportable Diseases
Both chlamydia and gonorrhea are reportable diseases to the Ministry of Health and Long Term Care. Therefore, the local health department will be calling the doctors office or patient to ensure correct treatment was received and sexual partners have been followed up with testing and treatment ( Ontario Agency for Health Protection and Promotion, 2019a; Region of Peel, 2007 ). To learn more about STIs and STDs such as chlamydia and gonorrhea please go to the Public Health Ontario web page on sexually transmitted infections.
Human Papillomavirus- HPV
HPV is a common sexually transmitted infection (STI). Both males and females can be infected with HPV. Almost three quarters of sexually active individuals have been exposed to HPV during their lifetime. There are over 100 strains of HPV and some strains of HPV can cause visible genital warts. The warts are usually painless but may be itchy, uncomfortable and hard to treat. Some strains of HPV cause genital, anal, throat and cervical cancers . HPV spreads through sexual activity and skin-to-skin contact in the genital area with an infected person.  Treatments are available for genital warts but there is no cure for HPV (York Region Health Connect, n.d.).. To learn more about HPV symptoms, treatments, and prognosis visit the York Region Fact Sheet on HPV (PDF file).
HPV Vaccine
A vaccine called Gardasil® 9 is available for 9 HPV strains. This vaccine assists the immune system in protecting the body against infections and diseases caused by HPV (York Region Health Connect, n.d.). To learn more about Gardasil® 9 treatments, please visit the Gardasil® 9 website.
Herpes Simplex Virus (HSV)
Genital herpes is a sexually transmitted infection (STI) that is caused by a virus called herpes simplex virus (HSV). There are two types of herpes simplex viruses:
- Type 1- oral herpes or cold sores (HSV-1)
- Type 2- genital herpes (HSV-2).
These viruses are very similar and either type can cause genital herpes or cold sores. Symptoms might include dysuria , enlarged glands, myalgia , arthralgia and fever. Once a patient is infected with HSV, the virus remains in their body even after the symptoms are gone and can cause recurring outbreaks. Between the outbreaks, the virus stays in their body. When the virus becomes active again, the symptoms return but are usually less painful and heal faster. Recurring outbreaks vary from person-to-person, however they can be triggered by emotional or physical stress, exposure to sunlight, hormonal changes, poor nutrition, sexual intercourse, lack of sleep or a low immune system (Ontario Ministry of Health and Long-Term Care, 2015).
Herpes is spread through direct contact with the sores or blisters of an infected person. Contact (and transfer of the virus) can occur from genitals-to-genitals, mouth-to-genitals or mouth-to-mouth. Herpes can also be passed to the anal area. Herpes spreads easily during sexual contact while symptoms are present, or just before an outbreak of symptoms. An infected person may spread herpes even when they have no symptoms; this is called asymptomatic shedding. One can spread the herpes virus to other parts of their body after touching the sores; autoinoculation . The fingers, eyes and other body areas can accidentally become infected in this way. Hand washing after touching sores and blisters is recommended to prevent spreading the virus (Ontario Ministry of Health and Long-Term Care, 2015).
There is no cure for herpes. Antiviral pills help to reduce symptoms and speed the healing of blisters or sores and are prescribed by a doctor. Treatment of symptoms may be managed with medication for pain, bath salts, cold compresses and urinating in water may help to relieve discomfort. Keep the infected area clean and dry, wear cotton underwear and loose clothing to reduce discomfort. All sexual partner(s) should be informed. The only way to reduce the risk of transmission of herpes is to avoid direct contact with the sores and to use condoms. Condoms will reduce but not eliminate risk as the virus can be present and shed from the skin in the genital area (Ontario Ministry of Health and Long-Term Care, 2015).
To learn more about the symptoms, complications, treatments and prognosis of HSV please visit the Ontario Ministry of Health and Long-Term Care’s Sexually Transmitted Diseases : Genital Herpes website or Public Health Ontario’s Testing Index.
Female Reproductive System Medical Abbreviations
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Medical Terms in Context
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Medical Specialties and Procedures related to the Female Reproductive System
Gynecology
A gynecologist is a specialist in the area of gynecology focusing on the diagnosis, treatment, management and prevention of diseases and disorders of the female reproductive system. Obstetrics is a specialty that provides care through pregnancy, labour, and puerperium . Further subspecialties in women’s health include contraception, reproductive endocrinology , infertility, adolescent gynecology, endoscopy and gynecological oncology (Canadian Medical Association, 2018). To learn more about obstetrics or gynecology please follow visit the Canadian Medical Association’s Obstetrics/Gynecology Profile page (PDF file).
Hysterectomy
A hysterectomy is done to stage or treat female reproductive cancers, treat precancerous conditions of the cervix and some non-cancerous conditions that have not responded to other forms of treatment. There are three types of hysterectomy:
- A total hysterectomy removes both the uterus and the cervix.
- A subtotal hysterectomy removes the uterus only.
- A radical hysterectomy removes uterus, cervix, part of the vagina, and ligaments.
Sometimes the ovaries and fallopian tubes are removed at the same time that a hysterectomy is done. A bilateral salpino-oophorectomy (BSO) removes both ovaries and fallopian tubes. A unilateral salpingo-oophorectomy removes one ovary and one Fallopian tube (Canadian Cancer Society, 2020). To learn more about hysterectomy please follow visit the Canadian Cancer Society’s page on hysterectomies.
Female Reproductive System Vocabulary
Acanthosis Nigricans
A disorder that causes darkening and thickening of the skin on the neck, groin, underarms or skin folds.
Acrochordons
Skin tags, teardrop-sized pieces of skin that can be as large as raisins and are typically found in the armpits or neck area.
Amenorrhea
Absence of periods.
Androgens
Male hormones.
Antiandrogens
A group of medications that counteract the effects of male hormones.
Antibiotics
Medications that stop bacterial infections.
Antiretrovirals
Treatment that works against the virus replication.
Anti-virals
Treatments that work effectively against a virus.
Asymptomatic
Pertaining to without symptoms.
Autoinoculation
Self inoculation.
Axilla
The armpit.
Bartholin’s glands
Also known as greater vestibular glands they are responsible to secrete mucus to keep the vestibular area moist.
Bilateral
Pertaining to both sides.
Douching
Washing the vagina with fluid.
Dysmenorrhea
Painful periods.
Dyspareunia
Painful intercourse.
Dysuria
Painful urination.
Endocrinology
The study of the endocrine glands and hormones.
Endometrium
The innermost layer containing a connective tissue lining covered by epithelial tissue that lines the lumen. Provides the site of implantation for a fertilized egg. Sheds during menstruation if no egg is fertilized.
Endoscopy
Process of viewing internally.
Fornix
Superior portion of the vagina.
Gametes
Haploid reproductive cells that contribute genetic material to form an offspring.
Gynecologist
Specialist in the study and treatment of the female reproductive system.
Gynecology
The study of the female reproductive system
Hirsuitism
Excess hair all over the body.
Homeostasis
Biological process that results in stable equilibrium.
Hysterectomy
Surgical removal of the uterus.
Inferior
Pertaining to below.
Intramuscular
Pertaining to within the muscle.
Laparoscopy
Process of viewing internal organs.
Lumbago
Lower back pain.
Mammoplasty
Surgical repair of the breast particularly after a mastectomy.
Mastectomy
Excision of breast(s) and or breast tissue.
Oligomenorrhea
Infrequent or irregular periods.
Oocyte
Female gamete.
Oophorectomy
Surgical removal of the fallopian/uterine tubes.
Polymenorrhea
Excessive bleeding during one’s period.
Polyuria
Frequent urination.
Proliferate
Reproduce rapidly.
Puerperium
Time directly after childbirth.
Superior
Pertaining to above.
Unilateral
Pertaining to one side.
Urethritis
Inflammation of the urethra.
Test Yourself
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References
Canadian Medical Association. (2018, August). Obstetrics/gynecology profile . Canadian Medical Association Specialty Proflies. https://www.cma.ca/sites/default/files/2019-01/obgyn-e.pdf
Canadian Women’s Health Network. (2012). Endometriosis . http://www.cwhn.ca/en/node/40779
Canadian Women’s Health Network. (2012a). Polycystic ovary syndrome (PCOS) . http://www.cwhn.ca/en/node/44804
Cancer Care Ontario. (n.d.). Breast cancer . Ontario Health. https://www.cancercareontario.ca/en/types-of-cancer/breast-cancer
Centers for Disease Control and Prevention. (n.d.). Breast cancer: What you need to know . CDC: Cancer. https://www.cdc.gov/cancer/breast/pdf/breastcancerfactsheet.pdf
Centers for Disease Control and Prevention. (2019, January). Cervical cancer: Inside knowledge about gynecolocic cancer . CDC: Cancer. https://www.cdc.gov/cancer/cervical/pdf/cervical_facts.pdf?src=SocialMediaToolkits
[CrashCourse]. (2015, October 2015). Reproductive system, part 1 – female reproductive system: Crash course A&P #40 [Video]. YouTube. https://www.youtube.com/watch?v=RFDatCchpus
Ontario Agency for Health Protection and Promotion. (2019). Chlamydia . Public Health Ontario. https://www.publichealthontario.ca/en/diseases-and-conditions/infectious-diseases/sexually-transmitted-infections/chlamydia
Ontario Ministry of Health and Long-Term Care. (2015). Sexually transmitted diseases: Genital herpes (hur-peez) . Publications. http://www.health.gov.on.ca/en/public/publications/std/herpes.aspx
Ontario Agency for Health Protection and Promotion. (2019a). Gonorrhea . Public Health Ontario. https://www.publichealthontario.ca/en/diseases-and-conditions/infectious-diseases/sexually-transmitted-infections/gonorrhea
Region of Peel. (2007). Chlamydia and Gonorrhea . https://www.peelregion.ca/health/talk-to-me/download/lesson-plans/lesson6-pdf/lesson6i.pdf
Urology Care Foundation. (2019). What are sexually transmitted infections (STIs) or diseases (STDs) . Urology Care Foundation: Urologic Conditions. https://www.urologyhealth.org/urologic-conditions/sexually-transmitted-infections#Acquired_Immune_Deficiency_Syndrome_(AIDS)
York Region Health Connection. (n.d.). Human papillomavirus . https://www.york.ca/wps/wcm/connect/yorkpublic/b5158069-a667-4f43-bb25-e0449ba22caa/6052+Human+Papilloma+Virus+Fact+Sheet.pdf?MOD=AJPERES&CACHEID=b5158069-a667-4f43-bb25-e0449ba22caa
Image Descriptions
Figure 10.1 image description: This figure shows the structure and the different organs in the female reproductive system. The top panel shows the lateral view with labels (clockwise from top): utuerus, ovary, formix of uterus, cervix, rectum, vagina, anus, labium majora, labium minora, clitoris, urethra, mons pubis, pybic symphysis, bladder; and the bottom panel shows the anterior view with labels (clockwise from top): ovary, ovarian ligament, broad ligament, labia minora, labia majora, vagina, cervix, uterine tube, usterus, fimbriae. [Return to Figure 10.1].
Figure 10.2 image description: This figure shows the parts of the vulva. The right panel shows the external anterior view and the left panel shows the internal anteriolateral view. The major parts are labeled (from top): prepuce, glans clitoris, labia minora, corpus cavernosum, bulb of vestibule, urethral opening, labia majora, vaginal opening, opening of right Bartholin’s gland, Bartholin’s glands, anus. [Return to Figure 10.2].
Unless otherwise indicated, this chapter contains material adapted from Anatomy and Physiology (on OpenStax ), by Betts, et al. and is used under a a CC BY 4.0 international license . Download and access this book for free at https://openstax.org/books/anatomy-and-physiology/pages/1-introduction .


12: Thermodynamics
Among the many capabilities of chemistry is its ability to predict if a process will occur under specified conditions. Thermodynamics, the study of relationships between the energy and work associated with chemical and physical processes, provides this predictive ability. Previous chapters in this text have described various applications of thermochemistry, an important aspect of thermodynamics concerned with the heat flow accompanying chemical reactions and phase transitions. This chapter will introduce additional thermodynamic concepts, including those that enable the prediction of any chemical or physical changes under a given set of conditions.
Contributors and Attributions
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Paul Flowers (University of North Carolina - Pembroke), Klaus Theopold (University of Delaware) and Richard Langley (Stephen F. Austin State University) with contributing authors. Textbook content produced by OpenStax College is licensed under a Creative Commons Attribution License 4.0 license. Download for free at<EMAIL_ADDRESS>).


4.1: The Gut Microbiome and its Impact on the Brain
Previously it was believed that micro-organisms were solely responsible for the production of disease/pathology. However, more recently many different researchers and scientists have begun to re-evaluate this concept that microbes were only present or only useful in studying diseases.
Scientists have known for a very long period of time that there are a number of microbiota which consists of all of the bacteria, viruses and eukaryotes (i.e. fungi) that either grow in and or on the body (1014 bacteria internally; 1010 bacteria on skin; and an estimate quadrillion viruses). Since the microbiota are present on humans throughout almost our entire lifetime, current theories now highlight the possibility that the microbiota might also play a role in health, not only in disease. Conceptually, the genes encoded by all of the microbiota are known collectively as the microbiome . As the number of bacteria within the gut far exceeds all of the other microbiota, most research has started to investigate the role that the gut microbiome might have in health and disease, and more importantly in brain health and disease.
Specifically, within all fields of biology there is an emerging theme that an organ (such as skin) can be colonized by different types of microbes and this colonization does not have to be homogeneous across a particular organ. Although many of these gut bacteria can be treated pharmacologically in order for them to be eliminated, this may not be always be the best treatment. From a research perspective then, one key question that dominates, can controlling our gut microbiome produce changes in our biology, physiology and even behaviour?
What factors affect the gut microbiome?
Many factors have now been identified to affect the gut microbiome. As shown in Figure \(\PageIndex{1}\), an individual’s genetics, the types of drugs or antibiotics they are taking, hygiene, physical activity and other factors, all play a role in either mainintaining or, if changed, altering the gut microbiome.
Figure \(\PageIndex{1}\)
The “Normal” Gut Microbiome
As the intestine is an anaerobic environment, the majority of the gut bacteria species have been found to be anaerobic. Between 500-1000 different bacterial species have been identified in the gut through genetic sequencing, although these species belong to a very small number of phyla. In most healthy adult individuals, the most abundant phyla include Bacteriodetes (Gram(-) rods) and Firmicutes (Gram(+)) although other phyla such as Proteobacteria , Verrumicrobia , and Actinobacteria have also been identified.
Figure \(\PageIndex{2}\).
Microbial density in the gut. Overall, there are 10
14
microorganisms residing in the human gut, with over 500 unique species. In the stomach, the majority are the Lactobacilli, making up about 10
2
to 10
3
. In the Duodenum, there are Streptococci and Lactobacilli, with a concentration of 10
4
or 10
5
. As we descend past the jejunum and into the ileum, the concentration of bacteria increase dramatically – up to ten million bacteria reside here. Bacteria such as Enterobacteria, Enterococcus, Faecalis, Bacteroides, Bifidobacteria, Peptococcus, Peptosteptococc, Ruminococcus, Clostridia, and Lactobacilli. These bacteria are also common in the colon and appendix, but the microorganism concentrations increase yet again, to 10
9
to 10
12
. There is a general trend that complexity and concentration of bacteria increases as we descend the GI tract.
Frequently, researchers not only measure the typical bacteria living in various parts of the gastrointestinal (GI) tract but also measure the microbial density within various regions of the gut. As shown in Figure \(\PageIndex{2}\)., the types of resident or commensal bacteria found in the lumen of the gut regions as well as the density of bacteria (numbers on the right) show the density. Not surprisingly, the numbers as well as the complexity of bacteria increases distally down the length of the GI tract. This complexity started at birth and continues throughout development into adulthood.
But what types of bacteria dominate?
The gut microbiota is dominated by bacteria of which the major divisions of bacteria consist primarily of Bacteriodetes and Firmicutes . As mentioned previously there seems to be variation in bacteria between individuals although there is a suggestion that individuals normally have gut microbiota that dominate (the dominating bacterial fingerprint of each individual is referred to as an enterotype ). The dominating bacterial enterotypes in a healthy individual typically consists of the genera of Bacteroides , Prevotella or Ruminococcus (everyone has all 3 bacteria genera but the ratios between each individual will differ from having more or less of each genera).
Changes to the gut microbiota and the gut microbiome
Interestingly, although everyone has a common “core” group of bacteria as outlined in the previous section, lifestyle effects on microbiota (i.e. changes in diet and physiological status) seem to have the ability to quickly modify the types and numbers of bacteria living in the gut. This offers both a therapeutic opportunity by introducing new bacteria that may be beneficial through probiotics that contain bacteria capable of colonizing the gut.
From the earliest developmental age, our but show large changes in the bacterial genera and their numbers 2 during development, changes again depending on lifestyle changes and ageing. The stability of the gut microbiota and the changes in the types of bacteria is emerging as an important factor that has increasingly been implicated in impacting our health status and may be contributing to neurodegenerative processes (and other changes to the brain) as shown in Chapter 2.
Figure \(\PageIndex{3}\). Developmental
Changes.
An
illustration of the typical developmental colonization of the gut by bacteria. The initial colonies of bacteria that settle depend on the delivery method. In the first week of life, TLR is reduced, which may allow for the formation of stable bacterial colonies in the gut. During the first 6 months, as children are subjected to solid foods, the diversity of microbiota increases. The immune system is able to differentiate the difference between pathogenic and helpful bacteria. Disease appears to correlate with bacteria concentration and composition.
As shown in Figure \(\PageIndex{3}\). above, early bacterial gut colonizers such as Lactobacilli etc. are aerobic and most likely come from maternal sources – these are almost entirely unique and different by the first year of life. Bacteroides and Enterobacteria are anaerobic bacteria and tend to dominate later between 1-6 months of age. One of the most interesting aspects of gut colonization is that the source of bacteria is dependent on the environment as babies born via C-section tend to have colonization by Staphylococcus , Corynebacterium , Propionibacterium spp etc. which are normally found on the skin. This differs from the bacteria found in the gut of babies born through vaginal delivery as Lactobacilli , Prevotella and Sneathia dominate early on. Note that regardless of origin and initial colonization, that stability within the gut is reached around 1-2 years of age and is maintained into adulthood – where a unique balance between Bacterioidetes and Firmicutes exist while an individual stays healthy but can be altered by allergies, obesity, drugs and others to change this balance as shown in Figure \(\PageIndex{3}\).
Dysbiosis: The Basics
Dysbiosis represents an imbalance in the normal microbial community within your body. Experiments show that in adults, the bacteria, viruses and eukaryotes populations stay relatively stable. However, this stability occurs only in healthy individuals and these populations can change with diet, disease, treatment and environmental effects. For example, gut viromes (an extension of viral genomes) have been shown to have >95% stability in their sequences over the course of a year in healthy individuals – however this changes with alterations in an individual’s diet.
- In mice models – shifting diet from low-fat, plant-polysaccharide rich to high-fat, high sugar (Westernized) diet able to change the bacterial content within a day (Turnbaugh et al., 2009 Science Translational Medicine)
- In human studies – similar changes in gut microbiota observed within 24 hours (Wu et al, 2011 Science).
- This study showed that diet correlates with changing bacteria – high fat diet Bacteroides dominate, carbohydrate rich diet Prevotella dominate
In diet induced animal models of obesity there is a shift in dominant gut phyla with a decrease in Bacteroidetes and increase in Firmicutes . Similar results have been shown in human twin studies with decrease in Bacteroidetes but increase in Actinobacteria . The shift between these two phyla results in increased capacity for increasing energy from food but also results in inflammatory responses. By altering the gut microbiota in animal models, this seems to be sufficient to induce obesity as a phenotype (Turnbaugh et al., 2006 and 2008). These data suggest that the gut microbiota is capable of not only responding to changes in diet but can also induce phenotypes such as obesity.


2.4: Measures of the Center of the Data
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- Last updated
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The "center" of a data set is also a way of describing location. The two most widely used measures of the "center" of the data are the mean (average) and the median . To calculate the mean weight of 50 people, add the 50 weights together and divide by 50. Technically this is the arithmetic mean. We will discuss the geometric mean later. To find the median weight of the 50 people, order the data and find the number that splits the data into two equal parts meaning an equal number of observations on each side. The weight of 25 people are below this weight and 25 people are heavier than this weight. The median is generally a better measure of the center when there are extreme values or outliers because it is not affected by the precise numerical values of the outliers. The mean is the most common measure of the center.
NOTE
The words “mean” and “average” are often used interchangeably. The substitution of one word for the other is common practice. The technical term is “arithmetic mean” and “average” is technically a center location. Formally, the arithmetic mean is called the first moment of the distribution by mathematicians. However, in practice among non-statisticians, “average" is commonly accepted for “arithmetic mean.”
When each value in the data set is not unique, the mean can be calculated by multiplying each distinct value by its frequency and then dividing the sum by the total number of data values. The letter used to represent the sample mean is an x with a bar over it (pronounced “\(x\) bar”): \(\overline x\).
To see that both ways of calculating the mean are the same, consider the sample:
1; 1; 1; 2; 2; 3; 4; 4; 4; 4; 4
\[\overline{x}=\frac{1+1+1+2+2+3+4+4+4+4+4}{11}=2.7\nonumber\]
\[\overline{x}=\frac{3(1)+2(2)+1(3)+5(4)}{11}=2.7\nonumber\]
In the second calculation, the frequencies are 3, 2, 1, and 5.
The Greek letter \(\mu\) (pronounced "mew") represents the population mean . One of the requirements for the sample mean to be a good estimate of the population mean is for the sample taken to be truly random.
You can quickly find the location of the median by using the expression \(\frac{n+1}{2}\).
The letter \(n\) is the total number of data values in the sample. If \(n\) is an odd number, the median is the middle value of the ordered data (ordered smallest to largest). If \(n\) is an even number, the median is equal to the two middle values added together and divided by two after the data has been ordered. For example, if the total number of data values is 97, then \(\frac{n+1}{2}=\frac{97+1}{2}=49\). The median is the 49 th value in the ordered data. If the total number of data values is 100, then \(\frac{n+1}{2}=\frac{100+1}{2}=50.5\). The median occurs midway between the 50 th and 51 st values. The location of the median and the value of the median are not the same. The upper case letter \(M\) is often used to represent the median. The next example illustrates the location of the median and the value of the median.
Example \(\PageIndex{1}\)
AIDS data indicating the number of months a patient with AIDS lives after taking a new antibody drug are as follows (smallest to largest):
3; 4; 8; 8; 10; 11; 12; 13; 14; 15; 15; 16; 16; 17; 17; 18; 21; 22; 22; 24; 24; 25; 26; 26; 27; 27; 29; 29; 31; 32; 33; 33; 34; 34; 35; 37; 40; 44; 44; 47;
Calculate the mean and the median.
- Answer
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The calculation for the mean is:
\(\overline{x}=\frac{[3+4+(8)(2)+10+11+12+13+14+(15)(2)+\ldots+35+37+40+(44)(2)+47]}{40}=23.6\)
To find the median, \(M\), first use the formula for the location. The location is:
\(\frac{n+1}{2}=\frac{40+1}{2}=20.5\)
Starting at the smallest value, the median is located between the 20 th and 21 st values (the two 24s):
\(3; 4; 8; 8; 10; 11; 12; 13; 14; 15; 15; 16; 16; 17; 17; 18; 21; 22; 22; 24; 24; 25; 26; 26; 27; 27; 29; 29; 31; 32; 33; 33; 34; 34; 35; 37; 40; 44; 44; 47;\)\(M=\frac{24+24}{2}=24\)
Example \(\PageIndex{2}\)
Suppose that in a small town of 50 people, one person earns $5,000,000 per year and the other 49 each earn $30,000. Which is the better measure of the "center": the mean or the median?
- Answer
-
\(\overline{x}=\frac{5,000,000+49(30,000)}{50}=129,400\)
\(M = 30,000\)
(There are 49 people who earn $30,000 and one person who earns $5,000,000.)
The median is a better measure of the "center" than the mean because 49 of the values are 30,000 and one is 5,000,000. The 5,000,000 is an outlier. The 30,000 gives us a better sense of the middle of the data.
Another measure of the center is the mode. The mode is the most frequent value. There can be more than one mode in a data set as long as those values have the same frequency and that frequency is the highest. A data set with two modes is called bimodal.
Example \(\PageIndex{3}\)
Statistics exam scores for 20 students are as follows:
50; 53; 59; 59; 63; 63; 72; 72; 72; 72; 72; 76; 78; 81; 83; 84; 84; 84; 90; 93
Find the mode.
- Answer
-
The most frequent score is 72, which occurs five times. Mode = 72.
Example \(\PageIndex{4}\)
Five real estate exam scores are 430, 430, 480, 480, 495. The data set is bimodal because the scores 430 and 480 each occur twice.
When is the mode the best measure of the "center"? Consider a weight loss program that advertises a mean weight loss of six pounds the first week of the program. The mode might indicate that most people lose two pounds the first week, making the program less appealing.
NOTE
The mode can be calculated for qualitative data as well as for quantitative data. For example, if the data set is: red, red, red, green, green, yellow, purple, black, blue, the mode is red.
Calculating the Arithmetic Mean of Grouped Frequency Tables
When only grouped data is available, you do not know the individual data values (we only know intervals and interval frequencies); therefore, you cannot compute an exact mean for the data set. What we must do is estimate the actual mean by calculating the mean of a frequency table. A frequency table is a data representation in which grouped data is displayed along with the corresponding frequencies. To calculate the mean from a grouped frequency table we can apply the basic definition of mean: mean = \(\frac{\text { data sum }}{\text { number of data values }}\) We simply need to modify the definition to fit within the restrictions of a frequency table.
Since we do not know the individual data values we can instead find the midpoint of each interval. The midpoint is \(\frac{\text { lower boundary+upper boundary}}{2}\). We can now modify the mean definition to be \(\textbf{Mean of Frequency Table}=\frac{\sum f m}{\sum f}\) where f = the frequency of the interval and m = the midpoint of the interval.
Example \(\PageIndex{5}\)
A frequency table displaying professor Blount’s last statistic test is shown. Find the best estimate of the class mean.
| Grade interval | Number of students |
|---|---|
| 50–56.4 | 1 |
| 56.5–62.4 | 0 |
| 62.5–68.4 | 4 |
| 68.5–74.4 | 4 |
| 74.5–80.4 | 2 |
| 80.5–86.4 | 3 |
| 86.5–92.4 | 4 |
| 92.5–98.4 | 1 |
- Answer
-
Find the midpoints for all intervals
Grade interval Midpoint 50–56.4 53.25 56.5–62.4 59.5 62.5–68.4 65.5 68.5–74.4 71.5 74.5–80.4 77.5 80.5–86.4 83.5 86.5–92.4 89.5 92.5–98.4 95.5 Table 2.25 - Calculate the sum of the product of each interval frequency and midpoint. \(\sum f m\) \(53.25(1)+59.5(0)+65.5(4)+71.5(4)+77.5(2)+83.5(3)+89.5(4)+95.5(1)=1460.25\)
- \(\mu=\frac{\sum f m}{\sum f}=\frac{1460.25}{19}=76.86\)
Exercise \(\PageIndex{1}\)
Maris conducted a study on the effect that playing video games has on memory recall. As part of her study, she compiled the following data:
| Hours teenagers spend on video games | Number of teenagers |
|---|---|
| 0–3.4 | 3 |
| 3.5–7.4 | 7 |
| 7.5–11.4 | 12 |
| 11.5–15.4 | 7 |
| 15.5–19.4 | 9 |
What is the best estimate for the mean number of hours spent playing video games?


4.2: 1-Dimensional Plots
Our firm has just seven workers. How to analyze the bigger data? Let us first imagine that our hypothetical company prospers and hired one thousand new workers! We add them to our seven data points, with their salaries drawn randomly from interquartile range of the original sample (Figure \(\PageIndex{1}\)):
Code \(\PageIndex{1}\) (R): Boxplots
In a code above we also see an example of data generation. Function sample() draws values randomly from a distribution or interval. Here we used replace=TRUE , since we needed to pick a lot of values from a much smaller sample. (The argument replace=FALSE might be needed for imitation of a card game, where each card may only be drawn from a deck once.) Please keep in mind that sampling is random and therefore each iteration will give slightly different results.
Let us look at the plot. This is the boxplot (“box-and-whiskers” plot). Kathryn’s salary is the highest dot. It is so high, in fact, that we had to add the parameter log="y" to better visualize the rest of the values. The box (main rectangle) itself is bound by second and fourth quartiles, so that its height equals IQR. Thick line in the middle is a median. By default, the “whiskers” extend to the most extreme data point which is no more than 1.5 times the interquartile range from the box. Values that lay farther away are drawn as separate points and are considered outliers . The scheme (Figure \(\PageIndex{2}\)) might help in understanding boxplots.
Numbers which make the boxplot might be returned with fivenum() command. Boxplot representation was created by a famous American mathematician John W. Tukey as a quick, powerful and consistent way of reflecting main distribution-independent characteristics of the sample. In R , boxplot() is vectorized so we can draw several boxplots at once (Figure \(\PageIndex{3}\)):
Code \(\PageIndex{2}\) (R): Boxplots
(Parameters of trees were measured in different units, therefore we scale() ’d them.)
Histogram is another graphical representation of the sample where range is divided into intervals (bins), and consecutive bars are drawn with their height proportional to the count of values in each bin (Figure \(\PageIndex{4}\)):
Code \(\PageIndex{3}\) (R): Histograms
(By default, the command hist() would have divided the range into 10 bins, but here we needed 20 and therefore set them manually. Histogram is sometimes a rather cryptic way to display the data. Commands Histp() and Histr() from the asmisc.r will plot histograms together with percentages on the top of each bar, or overlaid with normal curve (or density—see below), respectively. Please try them yourself.)
A numerical analog of a histogram is the function cut() :
Code \(\PageIndex{4}\) (R):
There are other graphical functions, conceptually similar to histograms. The first is stem-and-leaf plot. stem() is a kind of pseudograph , text histogram. Let us see how it treats the original vector salary :
Code \(\PageIndex{5}\) (R): stem-and-leaf plot
The bar | symbol is a “stem” of the graph. The numbers in front of it are leading digits of the raw values. As you remember, our original data ranged from 11 to 102—therefore we got leading digits from 1 to 10. Each number to the left comes from the next digit of a datum. When we have several values with identical leading digit, like 11 and 19, we place their last digits in a sequence, as “leafs”, to the left of the “stem”. As you see, there are two values between 10 and 20, five values between 20 and 30, etc . Aside from a histogram-like appearance, this function performs an efficient ordering.
Another univariate instrument requires more sophisticated calculations. It is a graph of distribution density, density plot (Figure \(\PageIndex{5}\)):
CodeBox (R) \(\PageIndex{6}\): Density Plots
Code \(\PageIndex{6}\) (R): Density Plots
(We used an additional graphic function rug() which supplies an existing plot with a “ruler” which marks areas of highest data density.)
Here the histogram is smoothed , turned into a continuous function. The degree to which it is “rounded” depends on the parameter adjust . Aside from boxplots and a variety of histograms and alike, R and external packages provide many more instruments for univariate plotting.
One of simplest is the stripchart. To make stripchart more interesting, we complicated it below using its ability to show individual data points:
Code \(\PageIndex{7}\) (R): stripchart
(By default, stripchart is horizontal. We used method="jitter" to avoid overplotting, and also scaled all characters to make their distributions comparable. One of stripchart features is that col argument colorizes columns whereas bg argument (which works only for pch from 21 to 25) colorizes rows. We split trees into 3 classes of thickness, and applied these classes as dots background. Note that if data points are shown with multiple colors and/or multiple point types, the legend is always necessary.‘)
Beeswarm plot requires the external package. It is similar to stripchart but has several advanced methods to disperse points, plus an ability to control the type of individual points (Figure \(\PageIndex{7}\)):
Code \(\PageIndex{8}\) (R): Beeswarm plots
(Here with bxplot() command we added boxplot lines to a beehive graph in order to visualize quartiles and medians. To overlay, we used an argument add=TRUE .)
And one more useful 1-dimensional plot. It is a similar to both boxplot and density plot (Figure \(\PageIndex{8}\)):
Code \(\PageIndex{1}\) (R): Bean plots


25: RNA interference
Summary
RNA interference uses short RNA sequences complementary to a transcript of interest to decrease gene expression through transcriptional or translational silencing.
Also known as
RNAi, knockdown (different from knock-out); shRNA (“hairpins”) or siRNA
Samples needed
Cells to be treated
Method
siRNAs (small interfering RNAs) are short, ~19-21 basepair pieces of double-stranded RNA. They are processed by endogenous machinery in many cells, resulting in a temporary decreased expression of the target gene, usually on the scale of a few hours to a few days. siRNAs are transfected into cells, and once they degrade, expression of the gene of interest reverts to normal levels.
shRNAs (short hairpin RNAs) are longer than siRNAs and have a tight, hairpin turn on one end. When shRNAs are present in many cells, endogenous cell machinery processes them into siRNAs. shRNAs have the advantage of being delivered on a plasmid or viral vector. If the plasmid or vector contains a resistance gene, cells can be selected so that only those with genomic integration of the plasmid or vector remain. shRNAs can also be conditionally expressed, so that the gene of interest is only targeted upon administration of a certain compound, such as doxycycline. This allows for transient knock-down of genes whose complete knock-down would be lethal to the cells.
Controls
Usually qPCR or western blot are used to assess expression of gene of interest. Frequently, knockdown does not completely eliminate expression of the target gene. Furthermore, sh or siRNAs with different sequences will silences gene expression to different extents. Therefore, an analysis of the degree of silencing is a critical control and should always be shown.
Furthermore, in order to assess baseline levels of expression, a negative control si or shRNA should be used. Often, researchers will use an RNA that targets GFP, which is not normally present in cells outside of certain marine organisms, like the jellyfish from which GFP was first isolated. Sometimes an empty vector is used.
Lastly, when designing sh or siRNAs, researchers should always check that the target sequence does not appear in the genome anywhere besides the gene of interest. Otherwise, there can be unintended effects due to silencing of multiple genes.
Interpretation
In Figure 1 above, the authors show that loss of expression of either Nf1 or Rasal 2 results in three times as many colonies in a soft agar colony formation assay. Importantly, they verify that Nf1 and Rasal 2 ebxpression is actually decreased by performing a Western blot (right). The reader can see that expression of the Nf1 protein is decreased by the Nf1 shRNA but not the Rasal2 shRNAs or the empty vector control. Rasal 2 shRNAs only decrease Rasal2 protein expression, and Rasal2 shRNA1 is more effective than Rasal2 shRNA2. (These two shRNAs are complementary to different parts of the Rasal2 sequence.) Finally, the empty vector control has no discernible effect on Nf1 or Rasal2 protein levels.
Image Descriptions
Figure 1 image description:
A bar graph and Western blot. The bar graph shows relative number of colonies. Nf1 shRNA, Rasal2 shRNA1, and Rasal2 shRNA2 all have three times as many colonies as vector control. The Western blot shows loss of Nf1 expression only with Nf1 shRNA. Rasal2 shRNA1 shows nearly complete loss of Rasal2 expression; Rasal2 shRNA2 shows loss of most Rasal2 expression. p120 loading control is consistent in all samples. ↵
Thumbnail
"201412 RNAi blue.png" ↗ by DataBase Center for Life Science (DBCLS) is licensed under CC BY 4.0 ↗.
Description: Schematic of mRNA being cleaved when bound to the RISC complex.
Author
Katherine Mattaini, Tufts University
- McLaughlin, S. K., S. N. Olsen, B. Dake, T. De Raedt, E. Lim, R. T. Bronson, R. Beroukhim, K. Polyak, M. Brown, C. Kuperwasser, and K. Cichowski. 2013. The RasGAP gene, RASAL2, is a tumor and metastasis suppressor. Cancer Cell 24:365-378. ↵


3.2: Integrals as Antiderivatives
Since the value of a definite integral depends on the values of the upper and lower bounds, we can ask what happens to the value of the definite integral when either bound is varied. Using the defintion of the derivative from the previous chapter, we can show that \[\begin{align} \frac{d}{db} \left[\int_a^b dx\; f(x)\right] &= f(b), \\ \frac{d}{da} \left[\int_a^b dx\; f(x)\right] &= -f(a).\end{align}\] To prove the first equation, observe that increasing the upper bound from \(b\) to \(b + \delta b\) increases the area under the curve by \(f(b) \delta b\) (to lowest order in \(\delta b\) ). Hence, the definite integral’s rate of change with \(b\) is \(f(b)\) . Likewise, increasing the lower bound from \(a\) to \(\delta a\) decreases the area under the curve, leading to a rate of change of \(-f(a)\) .
From the above result, we define the concept of an indefinite integral , or antiderivative , as the inverse of a derivative operation: \[\int^x dx' f(x') \equiv F(x) \;\;\mathrm{such}\;\mathrm{that}\;\; \frac{d}{dx}F(x) = f(x).\] Since derivatives are not one-to-one (i.e., two different functions can have the same derivative), an antiderivative does not have a unique, well-specified value. Rather, its value is only defined up to an additive constant, called an integration constant . A definite integral, by contrast, always has a well-defined value.
Finding antiderivatives is much harder than differentiation. Once you know how to differentiate a few special functions, differentiating some combination of those functions usually involves a straightforward (if tedious) application of composition rules. By contrast, there is no general systematic procedure for symbolic integration. Integration often requires creative steps, like guessing a solution and checking if its derivative yields the desired integrand.
Some common techniques are summarized in the following sections; others will be introduced later in this course.