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**Bacterial meningitis** is one of the most serious forms of meningitis. Bacteria that cause meningitis often gain access to the CNS through the bloodstream after trauma or as a result of the action of bacterial toxins. Bacteria may also spread from structures in the upper respiratory tract, such as the oropharynx, nas... | {
"Header 1": "**26.2 Bacterial Diseases of the Nervous System**",
"Header 2": "**Bacterial Meningitis**",
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Meningococcal infections can be treated with antibiotic therapy, and third-generation cephalosporins are most often employed. However, because outcomes can be negative even with treatment, preventive vaccination is the best form of treatment. In 2010, countries in Africa's meningitis belt began using a new serogroup ... | {
"Header 1": "**26.2 Bacterial Diseases of the Nervous System**",
"Header 2": "**Bacterial Meningitis**",
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http://www.cdc.gov/meningococcal/surveillance/index.html.
#### **Neonatal Meningitis**
*S. agalactiae*, Group B streptococcus (GBS), is an encapsulated gram-positive bacterium that is the most common cause of **neonatal meningitis**, a term that refers to meningitis occurring in babies up to 3 months of age.[10] *S... | {
"Header 1": "**26.2 Bacterial Diseases of the Nervous System**",
"Header 2": "**Bacterial Meningitis**",
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Neonatal tetanus has a very poor prognosis with a mortality rate of 70%–100%.[12]
Treatment for patients with tetanus includes assisted breathing through the use of a ventilator, wound debridement, fluid balance, and antibiotic therapy with metronidazole or penicillin to halt the growth of *C. tetani*. In addition, p... | {
"Header 1": "**26.2 Bacterial Diseases of the Nervous System**",
"Header 2": "**Bacterial Meningitis**",
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monocytogenes* uses other proteins called listeriolysin O and ActA to facilitate intercellular movement, allowing the infection to spread from cell to cell (**[Figure 26.10](#page-1189-0)**).
*L. monocytogenes* is usually identified by cultivation of samples from a normally sterile site (e.g., blood or CSF). Recovery... | {
"Header 1": "**26.2 Bacterial Diseases of the Nervous System**",
"Header 2": "**Bacterial Meningitis**",
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**Hansen's disease** (also known as **leprosy**) is caused by a long, thin, filamentous rod-shaped bacterium *Mycobacterium leprae*, an obligate intracellular pathogen. *M. leprae* is classified as gram-positive bacteria, but it is best visualized microscopically with an acid-fast stain and is generally referred to as ... | {
"Header 1": "**26.2 Bacterial Diseases of the Nervous System**",
"Header 2": "**Hansen's Disease (Leprosy)**",
"token_count": 1929,
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Although it is much more common than bacterial meningitis, viral meningitis is typically less severe. Many different viruses can lead to meningitis as a sequela of the primary infection, including those that cause herpes, influenza, measles, and mumps. Most cases of viral meningitis spontaneously resolve, but severe ca... | {
"Header 1": "**26.3 Acellular Diseases of the Nervous System**",
"Header 2": "**Viral Meningitis**",
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- Why is it unlikely that arboviral encephalitis viruses will be eradicated in the future?
- Which is the most common form of viral encephalitis in the United States?
#### **Clinical Focus**
#### **Part 2**
Levofloxacin is a quinolone antibiotic that is often prescribed to treat bacterial infections of the resp... | {
"Header 1": "**26.3 Acellular Diseases of the Nervous System**",
"Header 2": "**Viral Meningitis**",
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We now know these histologic changes *cannot* be used to confirm a rabies diagnosis. There are no tests that can detect rabies virus in humans at the time of the bite or shortly thereafter. Once the virus has begun to replicate (but before clinical symptoms occur), the virus can be detected using an immunofluorescence ... | {
"Header 1": "**26.3 Acellular Diseases of the Nervous System**",
"Header 2": "**Viral Meningitis**",
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**Poliomyelitis (polio)**, caused by poliovirus, is a primarily intestinal disease that, in a small percentage of cases, proceeds to the nervous system, causing paralysis and, potentially, death. Poliovirus is highly contagious, with transmission occurring by the fecal-oral route or by aerosol or droplet transmission. ... | {
"Header 1": "**26.3 Acellular Diseases of the Nervous System**",
"Header 2": "**Poliomyelitis**",
"token_count": 2017,
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In addition, PrPSc can induce PrP<sup>C</sup> to become misfolded and produce more rogue protein (**[Figure 26.18](#page-1202-0)**).
As PrPSc accumulates, it aggregates and forms fibrils within nerve cells. These protein complexes ultimately cause the cells to die. As a consequence, brain tissues of infected individu... | {
"Header 1": "**26.3 Acellular Diseases of the Nervous System**",
"Header 2": "**Poliomyelitis**",
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*Cryptococcus neoformans* is a fungal pathogen that can cause meningitis. This yeast is commonly found in soils and is particularly associated with pigeon droppings. It has a thick capsule that serves as an important virulence factor, inhibiting clearance by phagocytosis. Most *C. neoformans* cases result in subclinica... | {
"Header 1": "**26.4 Fungal and Parasitic Diseases of the Nervous System**",
"Header 2": "**Cryptococcocal Meningitis**",
"token_count": 1052,
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#### **Resolution**
David's new prescription for two antifungal drugs, amphotericin B and flucytosine, proved effective, and his condition began to improve. Culture results from David's sputum, skin, and CSF samples confirmed a fungal infection. All were positive for *C. neoformans*. Serological tests of his tissues ... | {
"Header 1": "**26.4 Fungal and Parasitic Diseases of the Nervous System**",
"Header 2": "**Clinical Focus**",
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*Acanthamoeba* and *Balamuthia* species are free-living amoebae found in many bodies of fresh water. Human infections by these amoebae are rare. However, they can cause amoebic keratitis in contact lens wearers (see **[Protozoan and Helminthic Infections of the Eyes](#page-953-0)**), disseminated infections in immunoco... | {
"Header 1": "**26.4 Fungal and Parasitic Diseases of the Nervous System**",
"Header 2": "**Granulomatous Amoebic Encephalitis**",
"token_count": 2018,
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<sup>37.</sup> Uppal, Gulshan, "CNS Toxoplasmosis in HIV," 2015. Accessed June 30, 2016. http://emedicine.medscape.com/article/ 1167298-overview#a3.
<sup>38.</sup> Konradt, Christoph, Norikiyo Ueno, David A. Christian, Jonathan H. Delong, Gretchen Harms Pritchard, Jasmin Herz, David J. Bzik et al., "Endothelial Cel... | {
"Header 1": "**26.4 Fungal and Parasitic Diseases of the Nervous System**",
"Header 2": "**Granulomatous Amoebic Encephalitis**",
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#### **Parasitic Diseases of the Nervous System**
Parasites that successfully invade the nervous system can cause a wide range of neurological signs and symptoms. Often, they inflict lesions that can be visualized through radiologic imaging. A number of these infections are fatal, but some can be treated (with varyin... | {
"Header 1": "**26.4 Fungal and Parasitic Diseases of the Nervous System**",
"Header 2": "**Disease Profile**",
"token_count": 1945,
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Life is made up of matter. Matter occupies space and has mass. All matter is composed of **atoms**. All atoms contain **protons**, **electrons**, and **neutrons** (**[Figure A1](#page-1220-1)**). The only exception is hydrogen (H), which is made of one proton and one electron. A proton is a positively charged particle ... | {
"Header 1": "**Atomic Structure**",
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All matter is composed of atoms of **elements**. Elements have unique physical and chemical properties and are substances that cannot easily be transformed either physically or chemically into other substances. Each element has been given a name, usually derived from Latin or English. The elements also have one- or two... | {
"Header 1": "**Chemical Elements**",
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The strongest chemical bond between two or more atoms is a **covalent bond**. These bonds form when an electron is shared between two atoms, and these are the most common form of chemical bond in living organisms. Covalent bonds form between the atoms of elements that make up the biological molecules in our cells. An e... | {
"Header 1": "**Chemical Bonds**",
"Header 2": "**Covalent Bonds**",
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When an atom does not contain equal numbers of protons and electrons, it is called an **ion**. Because the number of electrons does not equal the number of protons, each ion has a net charge. Positive ions are formed by losing electrons and are called **cations**. Negative ions are formed by gaining electrons and are c... | {
"Header 1": "**Chemical Bonds**",
"Header 2": "**Ions and Ionic Bonds**",
"token_count": 805,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
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For molecules formed by covalent bonds, the molecular formula represents the number and types of elemental atoms that compose the molecule. As an example, consider a molecule of glucose, which has the molecular formula $C_6H_{12}O_6$ . This molecular formula indicates that a single molecule of glucose is formed from s... | {
"Header 1": "Molecular Formula, Molecular Mass, and the Mole",
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Thermodynamics refers to the study of energy and energy transfer involving physical matter.
Matter participating in a particular case of energy transfer is called a system, and everything outside of that matter is called the surroundings. There are two types of systems: open and closed. In an **open system**, energy ... | {
"Header 1": "Molecular Formula, Molecular Mass, and the Mole",
"Header 2": "Energy",
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"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
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**Chemical reactions** occur when two or more atoms bond together to form molecules or when bonded atoms are broken apart. The substances used in a chemical reaction are called the **reactants** (usually found on the left side of a chemical equation), and the substances produced by the reaction are known as the **produ... | {
"Header 1": "Molecular Formula, Molecular Mass, and the Mole",
"Header 2": "**Chemical Reactions**",
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The hydrogen and oxygen atoms within water molecules form polar covalent bonds. There is no overall charge to a water molecule, but there is one $\partial^+$ on each hydrogen atom and two $\partial^-$ on the oxygen atom. Each water molecule attracts other water molecules because of the positive and negative charges... | {
"Header 1": "Molecular Formula, Molecular Mass, and the Mole",
"Header 2": "**Properties of Water and Solutions**",
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The **pH** of a solution is a measure of hydrogen ion (H<sup>+</sup> ) and hydroxide ion (OH– ) concentrations and is described as acidity or alkalinity, respectively. Acidity and alkalinity (also referred to as basicity) can be measured and calculated. pH can be simply represented by the mathematic equation, $pH = -l... | {
"Header 1": "**Acids and Bases**",
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A percent is a way of expressing a fractional amount of something using a whole divided into 100 parts. A percent is a ratio whose denominator is 100. We use the percent symbol, %, to show percent. Thus, 25% means a ratio of $\frac{25}{100}$ ,
3% means a ratio of $\frac{3}{100}$ , and 100 % percent means $\frac{10... | {
"Header 1": "**Calculating Percents**",
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In many fields, especially in the sciences, it is common to multiply decimals by powers of 10. Let's see what happens when we multiply 1.9436 by some powers of 10.
> 1.9436(10) = 19.436 1.9436(100) = 194.36 1.9436(1000) = 1943.6
The number of places that the decimal point moves is the same as the number of zeros in... | {
"Header 1": "**Multiplying and Dividing by Tens**",
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Scientific notation is used to express very large and very small numbers as a product of two numbers. The first number of the product, the digit term, is usually a number not less than 1 and not greater than 10. The second number of the product, the exponential term, is written as 10 with an exponent. Some examples of ... | {
"Header 1": "**Scientific Notation**",
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The common logarithm (log) of a number is the power to which 10 must be raised to equal that number. For example, the common logarithm of 100 is 2, because 10 must be raised to the second power to equal 100. Additional examples are in **[Table B3](#page-1233-0)**.
| Number | Exponential Form | Common Logarithm |
|---... | {
"Header 1": "**Logarithms**",
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In reporting numerical data obtained via measurements, we use only as many significant figures as the accuracy of the measurement warrants. For example, suppose a microbiologist using an automated cell counter determines that there are 525,341 bacterial cells in a one-liter sample of river water. However, she records t... | {
"Header 1": "**Rounding and Significant Digits**",
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It is possible to write an equation to calculate the cell numbers at any time if the number of starting cells and doubling time are known, as long as the cells are dividing at a constant rate. We define *N*<sup>0</sup> as the starting number of bacteria, the number at time *t* = 0. *N<sup>i</sup>* is the number of bact... | {
"Header 1": "**Generation Time**",
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"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
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**Figure C5** In this transition reaction, a multi-enzyme complex converts pyruvate into one acetyl (2C) group plus one carbon dioxide (CO2). The acetyl group is attached to a Coenzyme A carrier that transports the acetyl group to the site of the Krebs cycle. In the process, one molecule... | {
"Header 1": "**TCA Cycle**",
"token_count": 263,
"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
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The following tables list the species, and some higher groups, of pathogenic Eubacteria mentioned in the text. The classification of Bacteria, one of the three domains of life, is in constant flux as relationships become clearer through sampling of genetic sequences. Many groups at all taxonomic levels still have an un... | {
"Header 1": "**Bacterial Pathogens**",
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"source_pdf": "datasets/websources/Med_v1/med_textbook/Microbiology-LR.pdf"
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There are several classification systems for viruses. The International Committee on Taxonomy of Viruses (ICTV) is the international scientific body responsible for the rules of viral classification. The ICTV system used here groups viruses based on genetic similarity and presumed monophyly. The viral classification sy... | {
"Header 1": "**Viral Pathogens**",
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The Fungi are one of the kingdoms of the domain Eukarya. Fungi are most closely related to the animals and a few other small groups and more distantly related to the plants and other groups that formerly were categorized as protist. At present, the Fungi are divided into seven phyla (or divisions, a hold over from when... | {
"Header 1": "**Fungal Pathogens**",
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The relationships among the organisms (and thus their taxonomy) previously grouped under the name Protists are better understood than they were two or three decades ago, but this is still a work in progress. In 2005, the Eukarya were divided into six supergroups.[5] The latest high-level classification combined two of ... | {
"Header 1": "**Protozoan Pathogens**",
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The taxonomy of parasitic worms, all of which belong to the kingdom Animalia still contains many uncertainties. The
pathogenic species are found in two phyla: the Nematoda, or roundworms, and the Platyhelminthes, or flat worms. The Nematoda is tentatively divided into two classes[7], one of which, Chromadorea, probab... | {
"Header 1": "**Parasitic Helminths**",
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difficile* is a particularly serious example
**antibody screen** test to make sure that a potential blood recipient has not produced antibodies to antigens other than the ABO and Rh antigens
**antibody** Y-shaped glycoprotein molecule produced by B cells that binds to specific epitopes on an antigen
**antibody-de... | {
"Header 1": "**Glossary**",
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and characterized by malaise, fatigue, fever, headache, myalgia, and joint pain
**bacillary dysentery** gastrointestinal illness caused by *Shigella* bacteria, also called shigellosis
**bacillus** (bacilli) rod-shaped prokaryotic cell
**bacitracin** group of structurally similar peptides that block the movement o... | {
"Header 1": "**Glossary**",
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Its interior is filled with ribulose-1,5-bisphosphate carboxylase/ oxygenase (RuBisCO) and carbonic anhydrase, which are both used for carbon metabolism
**carbuncle** abscess containing a large, deep, purulent skin lesion
**carcinogen** agent that causes cancer
**case-control study** a type of observational study... | {
"Header 1": "**Glossary**",
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perfringens*
**clusters of differentiation (CD)** cell-surface glycoproteins that serve to identify and distinguish white blood cells
**coagulase** enzyme that causes the activation of fibrinogen to form fibrin, promoting clotting of the blood
**coarse focusing knob** a knob on a microscope that produces relative... | {
"Header 1": "**Glossary**",
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hominis*
**culture density** the number of cells per volume of broth
**culture medium** combination of compounds in solution that supports growth
**cutaneous mycosis** any fungal infection that affects the surface of the skin, hair, or nails
**cyanobacteria** phototrophic, chlorophyll-containing bacteria that p... | {
"Header 1": "**Glossary**",
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and autoimmune disorders
**direct ELISA** enzyme-linked immunoabsorbent assay in which the antigens are immobilized in the well of a microtiter plate; only a single antibody is used in the test
**direct fluorescent antibody (DFA) test** FA technique in which the labeled antibody binds to the target antigen
**dire... | {
"Header 1": "**Glossary**",
"token_count": 1914,
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coli* **(EHEC)** *E. coli* bacteria that cause severe gastrointestinal illness with potential serious complications such as hemolytic uremic syndrome
**enteroinvasive** *E. coli* **(EIEC)** *E. coli* bacteria that cause relatively mild gastrointestinal illness
**enteropathogenic** *E. coli* **(EPEC)** *E. coli* bac... | {
"Header 1": "**Glossary**",
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**gastritis** inflammation of the lining of the stomach **gastroenteritis** inflammation of the lining of the stomach and intestine
**gene expression** production of proteins from the information contained in DNA through the processes of transcription and translation
**gene gun** an apparatus that shoots gold or ... | {
"Header 1": "**Glossary**",
"Header 2": "**G**",
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It is associated with virulence and stimulates a strong immune response
**macrolides** class of protein synthesis inhibitors containing a large, complex ring structure that binds to the 50S subunit, inhibiting peptide bond formation
**macromolecule** polymer assembled from of individual units, monomers, that bind t... | {
"Header 1": "**Glossary**",
"Header 2": "**G**",
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the structural component of the cytoskeleton, centrioles, flagella, and cilia
**miliary tuberculosis** hematogenous dissemination and spread of *Mycobacterium tuberculosis* from tubercles
**minimal bactericidal concentration (MBC)** lowest antibacterial drug concentration that kills ≥99.9% of a starting inoculum of... | {
"Header 1": "**Glossary**",
"Header 2": "**G**",
"token_count": 958,
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jirovecii*
**pneumonia** pulmonary inflammation that causes the lungs to fill with fluids
**pneumonic plague** rare form of plague that causes massive hemorrhages in the lungs and is communicable through aerosols
**point mutation** mutation, most commonly a base substitution, that affects a single base pair
**p... | {
"Header 1": "**Glossary**",
"Header 2": "**G**",
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**reverse transcriptase** enzyme found in retroviruses that can make a copy of ssDNA from ssRNA
**reverse transcriptase inhibitor** classes of antiviral drugs that involve nucleoside analog competitive inhibition and non-nucleoside noncompetitive inhibition of the HIV reverse transcriptase
**reverse transcriptase... | {
"Header 1": "**Glossary**",
"Header 2": "**R**",
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which typically has suckers and/or hooks for attachment to the host
**scrapie** form of transmissible spongiform encephalopathy that primarily affects sheep
**sebaceous gland** a gland located in hair follicles that secretes sebum
**sebum** lipid-rich substance secreted by the sebaceous glands of the skin
**sec... | {
"Header 1": "**Glossary**",
"Header 2": "**S**",
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albicans*
**TH2 cells** subtype of T cells that stimulate B cells and direct their differentiation; also involved in directing antibody class switching
**thallus** body of fleshy fungi (more generally, a body without a root, stem, or leaf) that commonly cooccurs with HIV infection; the microbes move to the lymphati... | {
"Header 1": "**Glossary**",
"Header 2": "**S**",
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and transmitted through contact with cysts in cat feces; infections in pregnant women may cause birth defects or miscarriage
**trace element** indispensable element present in cells in lower amounts than macronutrients; also called *micronutrient*
**trachea** also known as the windpipe, this is a stiffened tube of ... | {
"Header 1": "**Glossary**",
"Header 2": "**S**",
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**UHT pasteurization** method of pasteurization that exposes milk to ultra-high temperatures (near 140 °C) for a few seconds, effectively sterilizing it so that it can be sealed and stored for long periods without refrigeration
#### **ulcer** open sore
**ultramicrotome** a device that cuts thin sections for electro... | {
"Header 1": "**Glossary**",
"Header 2": "**U**",
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OpenIntro is an organization focused on developing free and affordable education materials. OpenIntro Statistics, our first project, is intended for introductory statistics courses at the high school through university levels.
We encourage anyone learning or teaching statistics to visit [openintro.org](http://www.ope... | {
"Header 1": "OpenIntro, online resources, and getting involved",
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"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
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Scientists seek to answer questions using rigorous methods and careful observations. These observations – collected from the likes of field notes, surveys, and experiments – form the backbone of a statistical investigation and are called data. Statistics is the study of how best to collect, analyze, and draw conclusion... | {
"Header 1": "Introduction to data",
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"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
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Section [1.1](#page-10-1) introduces a classic challenge in statistics: evaluating the efficacy of a medical treatment. Terms in this section, and indeed much of this chapter, will all be revisited later in the text. The plan for now is simply to get a sense of the role statistics can play in practice.
In this sectio... | {
"Header 1": "1.1 Case study: using stents to prevent strokes",
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"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
Table [1.3](#page-13-0) displays rows 1, 2, 3, and 50 of a data set concerning 50 emails received during early 2012. These observations will be referred to as the email50 data set, and they are a random sample from a larger data set that we will see in Section [1.7.](#page-44-0)
<sup>2</sup>The proportion of the 224 ... | {
"Header 1": "1.2.1 Observations, variables, and data matrices",
"token_count": 2023,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
Examine the fed spend, pop2010, state, and smoking ban variables in the county data set. Each of these variables is inherently different from the other three yet many of them share certain characteristics.
First consider fed spend, which is said to be a numerical variable since it can take a wide range of numerical v... | {
"Header 1": "1.2.2 Types of variables",
"token_count": 634,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
Many analyses are motivated by a researcher looking for a relationship between two or more variables. A social scientist may like to answer some of the following questions:
- (1) Is federal spending, on average, higher or lower in counties with high rates of poverty?
- (2) If homeownership is lower than the national ... | {
"Header 1": "1.2.3 Relationships between variables",
"token_count": 875,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
Consider the following three research questions:
- 1. What is the average mercury content in swordfish in the Atlantic Ocean?
- 2. Over the last 5 years, what is the average time to degree for Duke undergraduate students?
- 3. Does a new drug reduce the number of deaths in patients with severe heart disease?
Each r... | {
"Header 1": "1.3.1 Populations and samples",
"token_count": 224,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
Consider the following possible responses to the three research questions:
- 1. A man on the news got mercury poisoning from eating swordfish, so the average mercury concentration in swordfish must be dangerously high.
- 2. I met two students who took more than 7 years to graduate from Duke, so it must take longer to... | {
"Header 1": "1.3.2 Anecdotal evidence",
"token_count": 476,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
We might try to estimate the time to graduation for Duke undergraduates in the last 5 years by collecting a sample of students. All graduates in the last 5 years represent the population, and graduates who are selected for review are collectively called the sample. In general, we always seek to randomly select a sample... | {
"Header 1": "1.3.3 Sampling from a population",
"token_count": 835,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
Consider the following question from page [7](#page-16-0) for the county data set:
(1) Is federal spending, on average, higher or lower in counties with high rates of poverty?
If we suspect poverty might affect spending in a county, then poverty is the explanatory variable and federal spending is the response varia... | {
"Header 1": "1.3.4 Explanatory and response variables",
"token_count": 331,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
There are two primary types of data collection: observational studies and experiments.
Researchers perform an observational study when they collect data in a way that does not directly interfere with how the data arise. For instance, researchers may collect information via surveys, review medical or company records, ... | {
"Header 1": "1.3.5 Introducing observational studies and experiments",
"token_count": 332,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
Generally, data in observational studies are collected only by monitoring what occurs, while experiments require the primary explanatory variable in a study be assigned for each subject by the researchers.
Making causal conclusions based on experiments is often reasonable. However, making the same causal conclusions ... | {
"Header 1": "1.4.1 Observational studies",
"token_count": 647,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
Almost all statistical methods are based on the notion of implied randomness. If observational data are not collected in a random framework from a population, these statistical methods – the estimates and errors associated with the estimates – are not reliable. Here we consider three random sampling techniques: simple,... | {
"Header 1": "1.4.2 Three sampling methods (special topic)",
"token_count": 1095,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
Randomized experiments are generally built on four principles.
- Controlling. Researchers assign treatments to cases, and they do their best to control any other differences in the groups. For example, when patients take a drug in pill form, some patients take the pill with only a sip of water while others may have i... | {
"Header 1": "1.5.1 Principles of experimental design",
"token_count": 421,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
Randomized experiments are the gold standard for data collection, but they do not ensure an unbiased perspective into the cause and effect relationships in all cases. Human studies are perfect examples where bias can unintentionally arise. Here we reconsider a study where a new drug was used to treat heart attack patie... | {
"Header 1": "1.5.2 Reducing bias in human experiments",
"token_count": 752,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
In this section we will be introduced to techniques for exploring and summarizing numerical variables. The email50 and county data sets from Section [1.2](#page-12-0) provide rich opportunities for examples. Recall that outcomes of numerical variables are numbers on which it is reasonable to perform basic arithmetic op... | {
"Header 1": "1.6 Examining numerical data",
"token_count": 261,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
A scatterplot provides a case-by-case view of data for two numerical variables. In Figure 1.8 on page 7, a scatterplot was used to examine how federal spending and poverty were related in the county data set. Another scatterplot is shown in Figure 1.16, comparing the number of line breaks (line\_breaks) and number of c... | {
"Header 1": "1.6 Examining numerical data",
"Header 3": "1.6.1 Scatterplots for paired data",
"token_count": 1217,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
Sometimes two variables is one too many: only one variable may be of interest. In these cases, a dot plot provides the most basic of displays. A dot plot is a one-variable scatterplot; an example using the number of characters from 50 emails is shown in Figure [1.18.](#page-30-2) A stacked version of this dot plot is s... | {
"Header 1": "1.6.2 Dot plots and the mean",
"token_count": 1303,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
Dot plots show the exact value for each observation. This is useful for small data sets, but they can become hard to read with larger samples. Rather than showing the value of each observation, we prefer to think of the value as belonging to a bin. For example, in the email50 data set, we create a table of counts for t... | {
"Header 1": "1.6.3 Histograms and shape",
"token_count": 1379,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
The mean was introduced as a method to describe the center of a data set, but the variability in the data is also important. Here, we introduce two measures of variability: the variance and the standard deviation. Both of these are very useful in data analysis, even though their formulas are a bit tedious to calculate ... | {
"Header 1": "1.6.3 Histograms and shape",
"Header 3": "**1.6.4** Variance and standard deviation",
"token_count": 1633,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
A box plot summarizes a data set using five statistics while also plotting unusual observations. Figure [1.25](#page-37-1) provides a vertical dot plot alongside a box plot of the num char variable from the email50 data set.
Figure 1.25: A vertical dot plot next to a labeled box plot for... | {
"Header 1": "1.6.5 Box plots, quartiles, and the median",
"token_count": 1496,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
How are the sample statistics of the num char data set affected by the observation, 64,401? What would have happened if this email wasn't observed? What would happen to these summary statistics if the observation at 64,401 had been even larger, say 150,000? These scenarios are plotted alongside the original data in Fig... | {
"Header 1": "1.6.6 Robust statistics",
"token_count": 756,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
When data are very strongly skewed, we sometimes transform them so they are easier to model. Consider the histogram of salaries for Major League Baseball players' salaries from 2010, which is shown in Figure 1.28(a).
Figure 1.28: (a) Histogram of MLB player salaries for 2010, in millions... | {
"Header 1": "1.6.6 Robust statistics",
"Header 3": "**1.6.7** Transforming data (special topic)",
"token_count": 665,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
The county data set offers many numerical variables that we could plot using dot plots, scatterplots, or box plots, but these miss the true nature of the data. Rather, when we encounter geographic data, we should map it using an **intensity map**, where colors are used to show higher and lower values of a variable. Fig... | {
"Header 1": "**1.6.8** Mapping data (special topic)",
"token_count": 603,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
Table [1.32](#page-44-3) summarizes two variables: spam and number. Recall that number is a categorical variable that describes whether an email contains no numbers, only small numbers (values under 1 million), or at least one big number (a value of 1 million or more). A table that summarizes data for two categorical v... | {
"Header 1": "1.7.1 Contingency tables and bar plots",
"token_count": 639,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
Table [1.35](#page-45-2) shows the row proportions for Table [1.32.](#page-44-3) The row proportions are computed as the counts divided by their row totals. The value 149 at the intersection of spam and none is replaced by 149/367 = 0.416, i.e. 149 divided by its row total, 367. So what does 0.416 represent? It corresp... | {
"Header 1": "1.7.2 Row and column proportions",
"token_count": 1808,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
Contingency tables using row or column proportions are especially useful for examining how two categorical variables are related. Segmented bar and mosaic plots provide a way to visualize the information in these tables.
A segmented bar plot is a graphical display of contingency table information. For example, a segm... | {
"Header 1": "1.7.3 Segmented bar and mosaic plots",
"token_count": 959,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
Some of the more interesting investigations can be considered by examining numerical data across groups. The methods required here aren't really new. All that is required is to make a numerical plot for each group. Here two convenient methods are introduced: side-by-side box plots and hollow histograms.
We will take ... | {
"Header 1": "1.7.5 Comparing numerical data across groups",
"token_count": 1647,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
We consider a study investigating gender discrimination in the 1970s, which is set in the context of personnel decisions within a bank.<sup>48</sup> The research question we hope to answer is, "Are females unfairly discriminated against in promotion decisions made by male managers?"
The participants in this study are... | {
"Header 1": "1.8.1 Variability within data",
"token_count": 1479,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
Table [1.44](#page-52-1) shows that 35 bank supervisors recommended promotion and 13 did not. Now, suppose the banker's decisions were independent of gender. Then, if we conducted the experiment again with a different random arrangement of files, differences in promotion rates would be based only on random fluctuation.... | {
"Header 1": "1.8.2 Simulating the study",
"token_count": 1570,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
#### 1.9.1 Case study
1.1 Migraine and accupuncture. A migraine is a particularly painful type of headache, which patients sometimes wish to treat with acupuncture. To determine whether acupuncture relieves migraine pain, researchers conducted a randomized controlled study where 89 females diagnosed with migraine hea... | {
"Header 1": "**1.9** Exercises",
"token_count": 746,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
1.3 Identify study components, Part I. Identify (i) the cases, (ii) the variables and their types, and (iii) the main research question in the studies described below.
- (a) Researchers collected data to examine the relationship between pollutants and preterm births in Southern California. During the study air pollut... | {
"Header 1": "1.9.2 Data basics",
"token_count": 1850,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
1.11 Propose a sampling strategy. A large college class has 160 students. All 160 students attend the lectures together, but the students are divided into 4 groups, each of 40 students, for lab sections administered by different teaching assistants. The professor wants to conduct a survey about how satisfied the studen... | {
"Header 1": "1.9.4 Observational studies and sampling strategies",
"token_count": 1693,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
1.19 Vitamin supplements. In order to assess the effectiveness of taking large doses of vitamin C in reducing the duration of the common cold, researchers recruited 400 healthy volunteers from staff and students at a university. A quarter of the patients were assigned a placebo, and the rest were evenly divided between... | {
"Header 1": "1.9.5 Experiments",
"token_count": 977,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
1.51 Side effects of Avandia, Part I. Rosiglitazone is the active ingredient in the controversial type 2 diabetes medicine Avandia and has been linked to an increased risk of serious cardiovascular problems such as stroke, heart failure, and death. A common alternative treatment is pioglitazone, the active ingredient i... | {
"Header 1": "1.9.8 Case study: gender discrimination",
"token_count": 1831,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
Example 2.1 A "die", the singular of dice, is a cube with six faces numbered 1, 2, 3, 4, 5, and 6. What is the chance of getting 1 when rolling a die?
If the die is fair, then the chance of a 1 is as good as the chance of any other number. Since there are six outcomes, the chance must be 1-in-6 or, equivalently, 1/6.... | {
"Header 1": "2.1 Defining probability (special topic)",
"token_count": 570,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
We use probability to build tools to describe and understand apparent randomness. We often frame probability in terms of a random process giving rise to an outcome.
> Roll a die → 1, 2, 3, 4, 5, or 6 Flip a coin → H or T
Rolling a die or flipping a coin is a seemingly random process and each gives rise to an outcom... | {
"Header 1": "2.1.1 Probability",
"token_count": 641,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
Two outcomes are called disjoint or mutually exclusive if they cannot both happen. For instance, if we roll a die, the outcomes 1 and 2 are disjoint since they cannot both occur. On the other hand, the outcomes 1 and "rolling an odd number" are not disjoint since both occur if the outcome of the roll is a 1. The terms ... | {
"Header 1": "2.1.2 Disjoint or mutually exclusive outcomes",
"token_count": 1973,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
If you are unfamiliar with the cards in a regular deck, please see the footnote.<sup>7</sup>
• Exercise 2.13 (a) What is the probability that a randomly selected card is a diamond? (b) What is the probability that a randomly selected card is a face card?<sup>8</sup>
Venn diagrams are useful when outcomes can be cat... | {
"Header 1": "2.1.2 Disjoint or mutually exclusive outcomes",
"token_count": 1641,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
A probability distribution is a table of all disjoint outcomes and their associated probabilities. Table [2.5](#page-83-4) shows the probability distribution for the sum of two dice.
| Dice sum | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 |
|-------------|----|----|----|----|----|----|----|----|----|----... | {
"Header 1": "2.1.4 Probability distributions",
"token_count": 2047,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
Just as variables and observations can be independent, random processes can be independent, too. Two processes are independent if knowing the outcome of one provides no useful information about the outcome of the other. For instance, flipping a coin and rolling a die are two independent processes – knowing the coin was... | {
"Header 1": "2.1.6 Independence",
"token_count": 1998,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
Are students more likely to use marijuana when their parents used drugs? The drug use data set contains a sample of 445 cases with two variables, student and parents, and is summarized in Table [2.11.](#page-89-1) [23](#page-88-3) The student variable is either uses or not, where a student is labeled as uses if she has... | {
"Header 1": "2.2 Conditional probability (special topic)",
"token_count": 727,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
Table [2.13](#page-90-1) includes row and column totals for each variable separately in the drug use data set. These totals represent marginal probabilities for the sample, which are the probabilities based on a single variable without conditioning on any other variables. For instance, a probability based solely on the... | {
"Header 1": "2.2.1 Marginal and joint probabilities",
"token_count": 770,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
There is some connection between drug use of parents and of the student: drug use of one is associated with drug use of the other.[25](#page-90-4) In this section, we discuss how to use information about associations between two variables to improve probability estimation.
The probability that a random student from t... | {
"Header 1": "2.2.2 Defining conditional probability",
"token_count": 1928,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
$<sup>{}^{30}</sup>P(\texttt{result} = \texttt{died} \mid \texttt{inoculated} = \texttt{no}) = \frac{P(\texttt{result} = \texttt{died} \text{ and } \texttt{inoculated} = \texttt{no})}{P(\texttt{inoculated} = \texttt{no})} = \frac{0.1356}{0.9608} = 0.1411.$
| | | inocu | inoculated | | |
|-------... | {
"Header 1": "2.2.2 Defining conditional probability",
"token_count": 558,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
Section 2.1.6 introduced the Multiplication Rule for independent processes. Here we provide the **General Multiplication Rule** for events that might not be independent.
**General Multiplication Rule** If A and B represent two outcomes or events, then $P(A \text{ and } B) = P(A|B) \times P(B)$ It is useful to think ... | {
"Header 1": "2.2.4 General multiplication rule",
"token_count": 1146,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
Tree diagrams are a tool to organize outcomes and probabilities around the structure of the data. They are most useful when two or more processes occur in a sequence and each process is conditioned on its predecessors.
The smallpox data fit this description. We see the population as split by inoculation: yes and no. ... | {
"Header 1": "2.2.6 Tree diagrams",
"token_count": 1618,
"source_pdf": "datasets/websources/Med_v1/med_textbook/OpenIntroStatSecond.pdf"
} |
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