Infection

context:  Among the vast varieties of microorganisms, relatively few cause disease in otherwise healthy individuals. Infectious disease results from the interplay between those few pathogens and the defenses of the hosts they infect. The appearance and severity of disease resulting from any pathogen, depends upon the ability of that pathogen to damage the host as well as the ability of the host to resist the pathogen. However a host's immune system can also cause damage to the host itself in an attempt to control the infection. Clinicians therefore classify infectious microorganisms or microbes according to the status of host defenses - either as primary pathogens or as opportunistic pathogens:
qas: answers: text: relatively few
question: Of the huge amount of microorganisms, how many cause disease in otherwise healthy individuals?

answers: text: Infectious disease
question: Interplay between pathogens and defenses of hosts results in what?

answers: text: ability of that pathogen to damage the host
question: What does the severity of a disease resulting from a pathogen depend on?

answers: text: cause damage
question: What can a host's immune system do to a host?

answers: text: host defenses
question: What do clinicians classify infectious microorganisms according to the status of?

context: One way of proving that a given disease is "infectious", is to satisfy Koch's postulates (first proposed by Robert Koch), which demands that the infectious agent be identified only in patients and not in healthy controls, and that patients who contract the agent also develop the disease. These postulates were first used in the discovery that Mycobacteria species cause tuberculosis. Koch's postulates can not be applied ethically for many human diseases because they require experimental infection of a healthy individual with a pathogen produced as a pure culture. Often, even clearly infectious diseases do not meet the infectious criteria. For example, Treponema pallidum, the causative spirochete of syphilis, cannot be cultured in vitro - however the organism can be cultured in rabbit testes. It is less clear that a pure culture comes from an animal source serving as host than it is when derived from microbes derived from plate culture. Epidemiology is another important tool used to study disease in a population. For infectious diseases it helps to determine if a disease outbreak is sporadic (occasional occurrence), endemic (regular cases often occurring in a region), epidemic (an unusually high number of cases in a region), or pandemic (a global epidemic).
qas: answers: text: satisfy Koch's postulates
question: What is one way of proving that a given disease is infectious?

answers: text: patients and not in healthy controls
question: What must an infectious agent only be identified in to satisfy the first of Koch's postulates?

answers: text: patients who contract the agent also develop the disease
question: What is Koch's second postulate?

answers: text: because they require experimental infection of a healthy individual
question: Why can't Koch's postulates be applied ethically for many human diseases?

answers: text: Treponema pallidum
question: What is the causative spirochete of syphilis? 

context: Infectious diseases are sometimes called contagious disease when they are easily transmitted by contact with an ill person or their secretions (e.g., influenza). Thus, a contagious disease is a subset of infectious disease that is especially infective or easily transmitted. Other types of infectious/transmissible/communicable diseases with more specialized routes of infection, such as vector transmission or sexual transmission, are usually not regarded as "contagious", and often do not require medical isolation (sometimes loosely called quarantine) of victims. However, this specialized connotation of the word "contagious" and "contagious disease" (easy transmissibility) is not always respected in popular use.
qas: answers: text: when they are easily transmitted by contact with an ill person
question: When are infectious diseases called contagious diseases? 

answers: text: infectious disease
question: What is a contagious disease a subset of?

answers: text: especially infective or easily transmitted
question: What sets a contagious disease after from a standard infectious disease?

answers: text: medical
question: Diseases with vector transmission or sexual transmission don't often require what type of isolation?

answers: text: specialized connotation of the word "contagious"
question: What is not always respected in popular use?

context: Infection begins when an organism successfully enters the body, grows and multiplies. This is referred to as colonization. Most humans are not easily infected. Those who are weak, sick, malnourished, have cancer or are diabetic have increased susceptibility to chronic or persistent infections. Individuals who have a suppressed immune system are particularly susceptible to opportunistic infections. Entrance to the host at host-pathogen interface, generally occurs through the mucosa in orifices like the oral cavity, nose, eyes, genitalia, anus, or the microbe can enter through open wounds. While a few organisms can grow at the initial site of entry, many migrate and cause systemic infection in different organs. Some pathogens grow within the host cells (intracellular) whereas others grow freely in bodily fluids.
qas: answers: text: when an organism successfully enters the body, grows and multiplies.
question: When does infection begin?

answers: text: humans
question: What group is not easily infected?

answers: text: weak, sick, malnourished, have cancer or are diabetic
question: What group of humans have increased susceptibility to chronic or persistent infections?

answers: text: Individuals who have a suppressed immune system
question: What individuals are particularly susceptible to opportunistic infections?

answers: text: intracellular
question: What is it called when a pathogen grows within the host cells?

context: Wound colonization refers to nonreplicating microorganisms within the wound, while in infected wounds, replicating organisms exist and tissue is injured. All multicellular organisms are colonized to some degree by extrinsic organisms, and the vast majority of these exist in either a mutualistic or commensal relationship with the host. An example of the former is the anaerobic bacteria species, which colonizes the mammalian colon, and an example of the latter is various species of staphylococcus that exist on human skin. Neither of these colonizations are considered infections. The difference between an infection and a colonization is often only a matter of circumstance. Non-pathogenic organisms can become pathogenic given specific conditions, and even the most virulent organism requires certain circumstances to cause a compromising infection. Some colonizing bacteria, such as Corynebacteria sp. and viridans streptococci, prevent the adhesion and colonization of pathogenic bacteria and thus have a symbiotic relationship with the host, preventing infection and speeding wound healing.
qas: answers: text: nonreplicating microorganisms within the wound
question: What does wound colonization refer to?

answers: text: replicating
question: What type of organisms exist and injure tissue in infected wounds?

answers: text: extrinsic organisms
question: What are all multcellular organisms colonized to some degree by?

answers: text: only a matter of circumstance
question: What's the difference between an infection and a colonization?

answers: text: anaerobic bacteria
question: What species colonizes the mammalian colon?

context: Because it is normal to have bacterial colonization, it is difficult to know which chronic wounds are infected. Despite the huge number of wounds seen in clinical practice, there are limited quality data for evaluated symptoms and signs. A review of chronic wounds in the Journal of the American Medical Association's "Rational Clinical Examination Series" quantified the importance of increased pain as an indicator of infection. The review showed that the most useful finding is an increase in the level of pain [likelihood ratio (LR) range, 11-20] makes infection much more likely, but the absence of pain (negative likelihood ratio range, 0.64-0.88) does not rule out infection (summary LR 0.64-0.88).
qas: answers: text: Because it is normal to have bacterial colonization
question: Why is it difficult to now which chronic wounds are infected?

answers: text: symptoms and signs
question: What is there limited quality data for evaluating despite the huge number of wounds seen in a clinical practice?

answers: text: infection
question: What is increased pain an indicator of?

answers: text: absence of pain
question: What does not rule out infection?

context: Disease can arise if the host's protective immune mechanisms are compromised and the organism inflicts damage on the host. Microorganisms can cause tissue damage by releasing a variety of toxins or destructive enzymes. For example, Clostridium tetani releases a toxin that paralyzes muscles, and staphylococcus releases toxins that produce shock and sepsis. Not all infectious agents cause disease in all hosts. For example, less than 5% of individuals infected with polio develop disease. On the other hand, some infectious agents are highly virulent. The prion causing mad cow disease and Creutzfeldt–Jakob disease invariably kills all animals and people that are infected.
qas: answers: text: damage
question: Disease can arise when an organism inflicts what on the host?

answers: text: toxins
question: What can a microorganism cause tissue damage by releasing a variety of?

answers: text: paralyzes muscles
question: What does the of toxin Clostridium tetani releases do?

answers: text: staphylococcus
question: What releases toxins which product shock and sepsis?

answers: text: less than 5%
question: What percentage of people infected with polio develop disease?

context: Persistent infections occur because the body is unable to clear the organism after the initial infection. Persistent infections are characterized by the continual presence of the infectious organism, often as latent infection with occasional recurrent relapses of active infection. There are some viruses that can maintain a persistent infection by infecting different cells of the body. Some viruses once acquired never leave the body. A typical example is the herpes virus, which tends to hide in nerves and become reactivated when specific circumstances arise.
qas: answers: text: body is unable to clear the organism after the initial infection
question: Why do persistent infections occur?

answers: text: the infectious organism
question: What are persistent infections characterized by the continual presence of?

answers: text: by infecting different cells of the body
question: How can some viruses main a persistent infection?

answers: text: Some viruses
question: What never leave the body when acquired?

answers: text: in nerves
question: Where does the herpes virus hide?

context: Diagnosis of infectious disease sometimes involves identifying an infectious agent either directly or indirectly. In practice most minor infectious diseases such as warts, cutaneous abscesses, respiratory system infections and diarrheal diseases are diagnosed by their clinical presentation and treated without knowledge of the specific causative agent. Conclusions about the cause of the disease are based upon the likelihood that a patient came in contact with a particular agent, the presence of a microbe in a community, and other epidemiological considerations. Given sufficient effort, all known infectious agents can be specifically identified. The benefits of identification, however, are often greatly outweighed by the cost, as often there is no specific treatment, the cause is obvious, or the outcome of an infection is benign.
qas: answers: text: an infectious agent either directly or indirectly
question: What does diagnosis of an infectious sometimes involve identifying? 

answers: text: clinical
question: Many minor infectious diseases are diagnosed by what type of presentation?

answers: text: without knowledge of the specific causative agent
question: How are minor infectious diseases treated?

answers: text: all known infectious agents
question: What can be identified given sufficient effort?

answers: text: greatly outweighed by the cost
question: Why is it often not worth bothering to identify an infectious agent?

context: Diagnosis of infectious disease is nearly always initiated by medical history and physical examination. More detailed identification techniques involve the culture of infectious agents isolated from a patient. Culture allows identification of infectious organisms by examining their microscopic features, by detecting the presence of substances produced by pathogens, and by directly identifying an organism by its genotype. Other techniques (such as X-rays, CAT scans, PET scans or NMR) are used to produce images of internal abnormalities resulting from the growth of an infectious agent. The images are useful in detection of, for example, a bone abscess or a spongiform encephalopathy produced by a prion.
qas: answers: text: by medical history and physical examination
question: How is diagnosis of infectious disease almost always initiated?

answers: text: detailed identification
question: What does taking a culture of an infectious agent isolated from a patient allow?

answers: text: microscopic features
question: What features of an infectious organism does a culture allow examining?

answers: text: its genotype
question: What can organisms be directly identified by?

answers: text: X-rays, CAT scans, PET scans or NMR
question: What technique can be used to produce images of internal abnormalities?

context: Microbiological culture is a principal tool used to diagnose infectious disease. In a microbial culture, a growth medium is provided for a specific agent. A sample taken from potentially diseased tissue or fluid is then tested for the presence of an infectious agent able to grow within that medium. Most pathogenic bacteria are easily grown on nutrient agar, a form of solid medium that supplies carbohydrates and proteins necessary for growth of a bacterium, along with copious amounts of water. A single bacterium will grow into a visible mound on the surface of the plate called a colony, which may be separated from other colonies or melded together into a "lawn". The size, color, shape and form of a colony is characteristic of the bacterial species, its specific genetic makeup (its strain), and the environment that supports its growth. Other ingredients are often added to the plate to aid in identification. Plates may contain substances that permit the growth of some bacteria and not others, or that change color in response to certain bacteria and not others. Bacteriological plates such as these are commonly used in the clinical identification of infectious bacterium. Microbial culture may also be used in the identification of viruses: the medium in this case being cells grown in culture that the virus can infect, and then alter or kill. In the case of viral identification, a region of dead cells results from viral growth, and is called a "plaque". Eukaryotic parasites may also be grown in culture as a means of identifying a particular agent.
qas: answers: text: Microbiological
question: What type of culture is a principal tool used to diagnose infectious disease?

answers: text: growth
question: What type of medium is provided for a specific agent in a microbial culture?

answers: text: nutrient agar
question: What are most pathogenic bacteria easily grown on?

answers: text: a colony
question: What is it called when a visible mound forms on the surface of a plate?

answers: text: a "plaque"
question: What is a region of dead cells resulting from viral growth called?

context: In the absence of suitable plate culture techniques, some microbes require culture within live animals. Bacteria such as Mycobacterium leprae and Treponema pallidum can be grown in animals, although serological and microscopic techniques make the use of live animals unnecessary. Viruses are also usually identified using alternatives to growth in culture or animals. Some viruses may be grown in embryonated eggs. Another useful identification method is Xenodiagnosis, or the use of a vector to support the growth of an infectious agent. Chagas disease is the most significant example, because it is difficult to directly demonstrate the presence of the causative agent, Trypanosoma cruzi in a patient, which therefore makes it difficult to definitively make a diagnosis. In this case, xenodiagnosis involves the use of the vector of the Chagas agent T. cruzi, an uninfected triatomine bug, which takes a blood meal from a person suspected of having been infected. The bug is later inspected for growth of T. cruzi within its gut.
qas: answers: text: some microbes
question: What are live animals required by?

answers: text: animals
question: What can Mycobacterium leprae and Treponema pallidum be grown in?

answers: text: embryonated
question: What type of eggs may some viruses be grown in?

answers: text: use of a vector to support the growth of an infectious agent
question: What is Xenodiagnosis?

answers: text: the causative agent
question: What is it difficult to demonstrate the presence of in Chagas disease?

context: Another principal tool in the diagnosis of infectious disease is microscopy. Virtually all of the culture techniques discussed above rely, at some point, on microscopic examination for definitive identification of the infectious agent. Microscopy may be carried out with simple instruments, such as the compound light microscope, or with instruments as complex as an electron microscope. Samples obtained from patients may be viewed directly under the light microscope, and can often rapidly lead to identification. Microscopy is often also used in conjunction with biochemical staining techniques, and can be made exquisitely specific when used in combination with antibody based techniques. For example, the use of antibodies made artificially fluorescent (fluorescently labeled antibodies) can be directed to bind to and identify a specific antigens present on a pathogen. A fluorescence microscope is then used to detect fluorescently labeled antibodies bound to internalized antigens within clinical samples or cultured cells. This technique is especially useful in the diagnosis of viral diseases, where the light microscope is incapable of identifying a virus directly.
qas: answers: text: diagnosis of infectious disease
question: What is microscopy used for?

answers: text: microscopic examination
question: What do virtually all culture techniques rely on at some point?

answers: text: light microscope
question: What can samples obtained from patients viewed directly under?

answers: text: when used in combination with antibody based techniques.
question: When is microscopy exquisitely specific?

answers: text: bind to and identify a specific antigens present on a pathogen
question: What can antibodies with artificial fluorescence be directed to do? 

context: Other microscopic procedures may also aid in identifying infectious agents. Almost all cells readily stain with a number of basic dyes due to the electrostatic attraction between negatively charged cellular molecules and the positive charge on the dye. A cell is normally transparent under a microscope, and using a stain increases the contrast of a cell with its background. Staining a cell with a dye such as Giemsa stain or crystal violet allows a microscopist to describe its size, shape, internal and external components and its associations with other cells. The response of bacteria to different staining procedures is used in the taxonomic classification of microbes as well. Two methods, the Gram stain and the acid-fast stain, are the standard approaches used to classify bacteria and to diagnosis of disease. The Gram stain identifies the bacterial groups Firmicutes and Actinobacteria, both of which contain many significant human pathogens. The acid-fast staining procedure identifies the Actinobacterial genera Mycobacterium and Nocardia.
qas: answers: text: a number of basic dyes
question: What do almost all cells readily stain with?

answers: text: electrostatic attraction
question: Why do cells easily stain with dyes?

answers: text: negatively charged
question: What electronic charge do cellular molecules have?

answers: text: a dye
question: What is Geimsa stain?

answers: text: Two
question: How many methods comprise standard approaches used to classify bacteria and diagnose disease?

context: The isolation of enzymes from infected tissue can also provide the basis of a biochemical diagnosis of an infectious disease. For example, humans can make neither RNA replicases nor reverse transcriptase, and the presence of these enzymes are characteristic of specific types of viral infections. The ability of the viral protein hemagglutinin to bind red blood cells together into a detectable matrix may also be characterized as a biochemical test for viral infection, although strictly speaking hemagglutinin is not an enzyme and has no metabolic function.
qas: answers: text: enzymes
question: What needs to be isolated from infected tissue to provide a biochemical diagnosis of an infectious disease?

answers: text: RNA replicases
question: What enzyme's presence is characteristic of specific types of viral infections?

answers: text: red blood cells
question: What does the protein hemagglutinin bind together?

answers: text: humans can make neither RNA replicases nor reverse transcriptase
question: Why are the presence of certain enymzes a tell tale sign of a virus?

context: Serological methods are highly sensitive, specific and often extremely rapid tests used to identify microorganisms. These tests are based upon the ability of an antibody to bind specifically to an antigen. The antigen, usually a protein or carbohydrate made by an infectious agent, is bound by the antibody. This binding then sets off a chain of events that can be visibly obvious in various ways, dependent upon the test. For example, "Strep throat" is often diagnosed within minutes, and is based on the appearance of antigens made by the causative agent, S. pyogenes, that is retrieved from a patients throat with a cotton swab. Serological tests, if available, are usually the preferred route of identification, however the tests are costly to develop and the reagents used in the test often require refrigeration. Some serological methods are extremely costly, although when commonly used, such as with the "strep test", they can be inexpensive.
qas: answers: text: Serological
question: What methods are highly sensitive, specifc and rapid tests used to identify microorganisms?

answers: text: bind specifically to an antigen
question: What are serological tests based upon the ability of an antibody to do?

answers: text: a protein or carbohydrate made by an infectious agent
question: What is the antigen bound to by the antibody usually?

answers: text: a chain of events
question: What does the binding set off that will result in something visibly obvious in various ways?

answers: text: S. pyogenes
question: What is the causative agent of "strep throat"?

context: Complex serological techniques have been developed into what are known as Immunoassays. Immunoassays can use the basic antibody – antigen binding as the basis to produce an electro - magnetic or particle radiation signal, which can be detected by some form of instrumentation. Signal of unknowns can be compared to that of standards allowing quantitation of the target antigen. To aid in the diagnosis of infectious diseases, immunoassays can detect or measure antigens from either infectious agents or proteins generated by an infected organism in response to a foreign agent. For example, immunoassay A may detect the presence of a surface protein from a virus particle. Immunoassay B on the other hand may detect or measure antibodies produced by an organism's immune system that are made to neutralize and allow the destruction of the virus.
qas: answers: text: Complex serological techniques
question: What are immunoassays?

answers: text: electro - magnetic or particle radiation
question: What type of signal do immunoassays produce?

answers: text: unknowns can be compared to that of standards
question: What allows quantitation of the target antigen?

answers: text: generated by an infected organism in response to a foreign agent
question: Immunoassays are able to detect what type of proteins?

context: Technologies based upon the polymerase chain reaction (PCR) method will become nearly ubiquitous gold standards of diagnostics of the near future, for several reasons. First, the catalog of infectious agents has grown to the point that virtually all of the significant infectious agents of the human population have been identified. Second, an infectious agent must grow within the human body to cause disease; essentially it must amplify its own nucleic acids in order to cause a disease. This amplification of nucleic acid in infected tissue offers an opportunity to detect the infectious agent by using PCR. Third, the essential tools for directing PCR, primers, are derived from the genomes of infectious agents, and with time those genomes will be known, if they are not already.
qas: answers: text: polymerase chain reaction
question: What does the acronym PCR expand to?

answers: text: PCR
question: What will be the ubiquitous gold standards of diagnostics in the near future?

answers: text: virtually all of the significant infectious agents of the human population have been identified
question: What has the catalog of infectious agents grown to the point of?

answers: text: grow within the human body
question: What must an infectious agent do to cause disease?

answers: text: infectious agents
question: What are primers derived from the genomes of?

context: Thus, the technological ability to detect any infectious agent rapidly and specifically are currently available. The only remaining blockades to the use of PCR as a standard tool of diagnosis are in its cost and application, neither of which is insurmountable. The diagnosis of a few diseases will not benefit from the development of PCR methods, such as some of the clostridial diseases (tetanus and botulism). These diseases are fundamentally biological poisonings by relatively small numbers of infectious bacteria that produce extremely potent neurotoxins. A significant proliferation of the infectious agent does not occur, this limits the ability of PCR to detect the presence of any bacteria.
qas: answers: text: ability to detect any infectious agent
question: What technological ability with regards to detection is currently available? 

answers: text: cost and application
question: What are the remaining blockades to the use or PCR as a standard tool of diagnosis?

answers: text: clostridial diseases
question: What are some diseases which won't benefit from PCR methods?

answers: text: significant proliferation of the infectious agent
question: PCR can't detect the presence of any bacteria when what doesn't occur?

context: There is usually an indication for a specific identification of an infectious agent only when such identification can aid in the treatment or prevention of the disease, or to advance knowledge of the course of an illness prior to the development of effective therapeutic or preventative measures. For example, in the early 1980s, prior to the appearance of AZT for the treatment of AIDS, the course of the disease was closely followed by monitoring the composition of patient blood samples, even though the outcome would not offer the patient any further treatment options. In part, these studies on the appearance of HIV in specific communities permitted the advancement of hypotheses as to the route of transmission of the virus. By understanding how the disease was transmitted, resources could be targeted to the communities at greatest risk in campaigns aimed at reducing the number of new infections. The specific serological diagnostic identification, and later genotypic or molecular identification, of HIV also enabled the development of hypotheses as to the temporal and geographical origins of the virus, as well as a myriad of other hypothesis. The development of molecular diagnostic tools have enabled physicians and researchers to monitor the efficacy of treatment with anti-retroviral drugs. Molecular diagnostics are now commonly used to identify HIV in healthy people long before the onset of illness and have been used to demonstrate the existence of people who are genetically resistant to HIV infection. Thus, while there still is no cure for AIDS, there is great therapeutic and predictive benefit to identifying the virus and monitoring the virus levels within the blood of infected individuals, both for the patient and for the community at large.
qas: answers: text: AZT
question: What is used in the treatment of AIDS?

answers: text: monitoring the composition of patient blood samples
question: How was the course of AIDS followed?

answers: text: resources could be targeted to the communities at greatest risk
question: What could be done by understanding how the disease was transmitted?

answers: text: geographical origins of the virus
question: What did the genotypic identification of HIV later enable?

answers: text: Molecular diagnostics
question: What is now commonly used to identify HIV in healthy people before the onset of the illnes?

context: Techniques like hand washing, wearing gowns, and wearing face masks can help prevent infections from being passed from one person to another. Frequent hand washing remains the most important defense against the spread of unwanted organisms. There are other forms of prevention such as avoiding the use of illicit drugs, using a condom, and having a healthy lifestyle with a balanced diet and regular exercise. Cooking foods well and avoiding foods that have been left outside for a long time is also important.
qas: answers: text: infections from being passed from one person to another
question: What can wearing gowns and face masks help prevent?

answers: text: Frequent hand washing
question: What is the most important defense against the spread of unwanted organisms?

answers: text: prevention
question: Avoiding drugs and using condoms are other forms of what?

answers: text: prevention
question: Why is it important to cook foods well?

answers: text: avoiding
question: What should one do with foods that have been left outside for a long time?

context: One of the ways to prevent or slow down the transmission of infectious diseases is to recognize the different characteristics of various diseases. Some critical disease characteristics that should be evaluated include virulence, distance traveled by victims, and level of contagiousness. The human strains of Ebola virus, for example, incapacitate their victims extremely quickly and kill them soon after. As a result, the victims of this disease do not have the opportunity to travel very far from the initial infection zone. Also, this virus must spread through skin lesions or permeable membranes such as the eye. Thus, the initial stage of Ebola is not very contagious since its victims experience only internal hemorrhaging. As a result of the above features, the spread of Ebola is very rapid and usually stays within a relatively confined geographical area. In contrast, the Human Immunodeficiency Virus (HIV) kills its victims very slowly by attacking their immune system. As a result, many of its victims transmit the virus to other individuals before even realizing that they are carrying the disease. Also, the relatively low virulence allows its victims to travel long distances, increasing the likelihood of an epidemic.
qas: answers: text: prevent or slow down the transmission of infectious diseases
question: Recognizing the different characteristics of various diseases is one way to do what?

answers: text: virulence, distance traveled by victims, and level of contagiousness
question: What are some critical disease characteristics that should be evaluated?

answers: text: Ebola
question: What virus' strains incapacitate their victims extremely quickly before killing them?

answers: text: victims experience only internal hemorrhaging
question: Why is the initial stage of Ebola not very contagious?

answers: text: travel long distances
question: What does the low virulence of HIV allow victims to do?

context: Another effective way to decrease the transmission rate of infectious diseases is to recognize the effects of small-world networks. In epidemics, there are often extensive interactions within hubs or groups of infected individuals and other interactions within discrete hubs of susceptible individuals. Despite the low interaction between discrete hubs, the disease can jump to and spread in a susceptible hub via a single or few interactions with an infected hub. Thus, infection rates in small-world networks can be reduced somewhat if interactions between individuals within infected hubs are eliminated (Figure 1). However, infection rates can be drastically reduced if the main focus is on the prevention of transmission jumps between hubs. The use of needle exchange programs in areas with a high density of drug users with HIV is an example of the successful implementation of this treatment method.  Another example is the use of ring culling or vaccination of potentially susceptible livestock in adjacent farms to prevent the spread of the foot-and-mouth virus in 2001.
qas: answers: text: transmission rate of infectious diseases
question: Recognizing the effects of small-world networks allows one to decrease what?

answers: text: extensive interactions
question: What type of interactions happen within groups of infected individuals in epidemics?

answers: text: focus is on the prevention of transmission jumps
question: What is a way of drastically reducing infection rates?

answers: text: needle exchange programs in areas with a high density of drug users
question: What is an example of a success implementation of preventing transmission jumps?

answers: text: 2001
question: When was vaccination used to prevent the spread of the foot-and-mouth virus?

context: Resistance to infection (immunity) may be acquired following a disease, by asymptomatic carriage of the pathogen, by harboring an organism with a similar structure (crossreacting), or by vaccination. Knowledge of the protective antigens and specific acquired host immune factors is more complete for primary pathogens than for opportunistic pathogens. There is also the phenomenon of herd immunity which offers a measure of protection to those otherwise vulnerable people when a large enough proportion of the population has acquired immunity from certain infections.
qas: answers: text: immunity
question: What is resistance to infection known technically as?

answers: text: following a disease
question: When may immunity be acquired?

answers: text: primary pathogens
question: What is knowledge of protective antigens more complete for?

answers: text: a measure of protection
question: What does herd immunity offer to vulnerable people when a large enough proportion of the population has acquired immunity?

answers: text: immunity
question: Vaccination is a way in which what may be acquired?

context: The clearance of the pathogens, either treatment-induced or spontaneous, it can be influenced by the genetic variants carried by the individual patients. For instance, for genotype 1 hepatitis C treated with Pegylated interferon-alpha-2a or Pegylated interferon-alpha-2b (brand names Pegasys or PEG-Intron) combined with ribavirin, it has been shown that genetic polymorphisms near the human IL28B gene, encoding interferon lambda 3, are associated with significant differences in the treatment-induced clearance of the virus. This finding, originally reported in Nature, showed that genotype 1 hepatitis C patients carrying certain genetic variant alleles near the IL28B gene are more possibly to achieve sustained virological response after the treatment than others. Later report from Nature demonstrated that the same genetic variants are also associated with the natural clearance of the genotype 1 hepatitis C virus.
qas: answers: text: genetic variants
question: What can the clearance of pathogens be influenced by in an individual?

answers: text: Pegylated interferon-alpha-2b
question: What is the brand name Pegasys for?

answers: text: sustained virological response
question: What are patients carrying certain genetic variant alleles near the IL28B gene more likely to achieve?

context: When infection attacks the body, anti-infective drugs can suppress the infection. Several broad types of anti-infective drugs exist, depending on the type of organism targeted; they include antibacterial (antibiotic; including antitubercular), antiviral, antifungal and antiparasitic (including antiprotozoal and antihelminthic) agents. Depending on the severity and the type of infection, the antibiotic may be given by mouth or by injection, or may be applied topically. Severe infections of the brain are usually treated with intravenous antibiotics. Sometimes, multiple antibiotics are used in case there is resistance to one antibiotic. Antibiotics only work for bacteria and do not affect viruses. Antibiotics work by slowing down the multiplication of bacteria or killing the bacteria. The most common classes of antibiotics used in medicine include penicillin, cephalosporins, aminoglycosides, macrolides, quinolones and tetracyclines.[citation needed]
qas: answers: text: anti-infective
question: What type of drugs can suppress an infection when it attacks the body?

answers: text: Several
question: How many broad types of anti-infective drugs exist?

answers: text: severity and the type of infection
question: What depends on the method an antibiotic is given?

answers: text: with intravenous antibiotics
question: How are severe infections of the brain usually treated?

answers: text: slowing down the multiplication of bacteria or killing the bacteria
question: How do antibiotics work?

context: The top three single agent/disease killers are HIV/AIDS, TB and malaria. While the number of deaths due to nearly every disease have decreased, deaths due to HIV/AIDS have increased fourfold. Childhood diseases include pertussis, poliomyelitis, diphtheria, measles and tetanus. Children also make up a large percentage of lower respiratory and diarrheal deaths. In 2012, approximately 3.1 million people have died due to lower respiratory infections, making it the number 4 leading cause of death in the world.
qas: answers: text: HIV/AIDS, TB and malaria
question: What are the top three killer diseases?

answers: text: fourfold
question: How much have deaths due to HIV/AIDS increased?

answers: text: pertussis, poliomyelitis, diphtheria, measles and tetanus
question: What are some popular childhood diseases?

answers: text: Children
question: Who makes up a large percentage of diarrheal deaths?

answers: text: lower respiratory infections
question: What is the number 4 leading cause of death in the world?

context: The medical treatment of infectious diseases falls into the medical field of Infectious Disease and in some cases the study of propagation pertains to the field of Epidemiology. Generally, infections are initially diagnosed by primary care physicians or internal medicine specialists. For example, an "uncomplicated" pneumonia will generally be treated by the internist or the pulmonologist (lung physician). The work of the infectious diseases specialist therefore entails working with both patients and general practitioners, as well as laboratory scientists, immunologists, bacteriologists and other specialists.
qas: answers: text: field of Infectious Disease
question: What medical field does the treatment of infectious diseases fall into?

answers: text: Epidemiology
question: Disease propagation can fall under the purview of what field of study?

answers: text: primary care physicians or internal medicine specialists
question: Who tends to initially diagnose an infection?

answers: text: lung physician
question: What is the non-medical mumbo jumbo term for pulmonologist?

answers: text: infectious diseases specialist
question: Who works with both patients and general practitioners to identify a disease?

context: A number of studies have reported associations between pathogen load in an area and human behavior. Higher pathogen load is associated with decreased size of ethnic and religious groups in an area. This may be due high pathogen load favoring avoidance of other groups, which may reduce pathogen transmission, or a high pathogen load preventing the creation of large settlements and armies that enforce a common culture. Higher pathogen load is also associated with more restricted sexual behavior, which may reduce pathogen transmission. It also associated with higher preferences for health and attractiveness in mates. Higher fertility rates and shorter or less parental care per child is another association that may be a compensation for the higher mortality rate. There is also an association with polygyny which may be due to higher pathogen load, making selecting males with a high genetic resistance increasingly important. Higher pathogen load is also associated with more collectivism and less individualism, which may limit contacts with outside groups and infections. There are alternative explanations for at least some of the associations although some of these explanations may in turn ultimately be due to pathogen load. Thus, polygny may also be due to a lower male:female ratio in these areas but this may ultimately be due to male infants having increased mortality from infectious diseases. Another example is that poor socioeconomic factors may ultimately in part be due to high pathogen load preventing economic development.
qas: answers: text: pathogen load in an area and human behavior
question: What have a number of studies found a correlation between?

answers: text: decreased size of ethnic and religious groups in an area
question: What is higher pathogen load associated with?

answers: text: pathogen transmission
question: What does avoidance of other groups reduce?

answers: text: Higher pathogen load
question: What does more restricted sexual behavior result in?

answers: text: high pathogen load preventing economic development.
question: What may poor socioeconomic factors ultimately in part be due to?

context: Evidence of infection in fossil remains is a subject of interest for paleopathologists, scientists who study occurrences of injuries and illness in extinct life forms. Signs of infection have been discovered in the bones of carnivorous dinosaurs. When present, however, these infections seem to tend to be confined to only small regions of the body. A skull attributed to the early carnivorous dinosaur Herrerasaurus ischigualastensis exhibits pit-like wounds surrounded by swollen and porous bone. The unusual texture of the bone around the wounds suggests they were afflicted by a short-lived, non-lethal infection. Scientists who studied the skull speculated that the bite marks were received in a fight with another Herrerasaurus. Other carnivorous dinosaurs with documented evidence of infection include Acrocanthosaurus, Allosaurus, Tyrannosaurus and a tyrannosaur from the Kirtland Formation. The infections from both tyrannosaurs were received by being bitten during a fight, like the Herrerasaurus specimen.
qas: answers: text: paleopathologists
question: What profession finds evidence of infection in fossil remains to be interesting?

answers: text: occurrences of injuries and illness in extinct life forms
question: What do paleopathologists study?

answers: text: Signs of infection
question: What has been discovered in the bones of carnivorous dinosaurs?

answers: text: Herrerasaurus ischigualastensis
question: What dinosaur's skull had pit-like wounds surrounded by swollen and porous bone?

answers: text: being bitten during a fight
question: How did tyrannosaurs become infected?