romikgosai/squad_modified huggingface dataset:
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.

Questions and answers:
['
Q: Why do persistent infections occur?
A: body is unable to clear the organism after the initial infection', '
Q: What are persistent infections characterized by the continual presence of?
A: the infectious organism', '
Q: How can some viruses main a persistent infection?
A: by infecting different cells of the body', '
Q: What never leave the body when acquired?
A: Some viruses', '
Q: Where does the herpes virus hide?
A: in nerves']
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.

Questions and answers:
['
Q: What does diagnosis of an infectious sometimes involve identifying? 
A: an infectious agent either directly or indirectly', '
Q: Many minor infectious diseases are diagnosed by what type of presentation?
A: clinical', '
Q: How are minor infectious diseases treated?
A: without knowledge of the specific causative agent', '
Q: What can be identified given sufficient effort?
A: all known infectious agents', '
Q: Why is it often not worth bothering to identify an infectious agent?
A: greatly outweighed by the cost']
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.

Questions and answers:
['
Q: How is diagnosis of infectious disease almost always initiated?
A: by medical history and physical examination', '
Q: What does taking a culture of an infectious agent isolated from a patient allow?
A: detailed identification', '
Q: What features of an infectious organism does a culture allow examining?
A: microscopic features', '
Q: What can organisms be directly identified by?
A: its genotype', '
Q: What technique can be used to produce images of internal abnormalities?
A: X-rays, CAT scans, PET scans or NMR']
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.

Questions and answers:
['
Q: What type of culture is a principal tool used to diagnose infectious disease?
A: Microbiological', '
Q: What type of medium is provided for a specific agent in a microbial culture?
A: growth', '
Q: What are most pathogenic bacteria easily grown on?
A: nutrient agar', '
Q: What is it called when a visible mound forms on the surface of a plate?
A: a colony', '
Q: What is a region of dead cells resulting from viral growth called?
A: a "plaque"']
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.

Questions and answers:
['
Q: What are live animals required by?
A: some microbes', '
Q: What can Mycobacterium leprae and Treponema pallidum be grown in?
A: animals', '
Q: What type of eggs may some viruses be grown in?
A: embryonated', '
Q: What is Xenodiagnosis?
A: use of a vector to support the growth of an infectious agent', '
Q: What is it difficult to demonstrate the presence of in Chagas disease?
A: the causative agent']
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.

Questions and answers:
['
Q: What is microscopy used for?
A: diagnosis of infectious disease', '
Q: What do virtually all culture techniques rely on at some point?
A: microscopic examination', '
Q: What can samples obtained from patients viewed directly under?
A: light microscope', '
Q: When is microscopy exquisitely specific?
A: when used in combination with antibody based techniques.', '
Q: What can antibodies with artificial fluorescence be directed to do? 
A: bind to and identify a specific antigens present on a pathogen']
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.

Questions and answers:
['
Q: What do almost all cells readily stain with?
A: a number of basic dyes', '
Q: Why do cells easily stain with dyes?
A: electrostatic attraction', '
Q: What electronic charge do cellular molecules have?
A: negatively charged', '
Q: What is Geimsa stain?
A: a dye', '
Q: How many methods comprise standard approaches used to classify bacteria and diagnose disease?
A: Two']
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.

Questions and answers:
['
Q: What needs to be isolated from infected tissue to provide a biochemical diagnosis of an infectious disease?
A: enzymes', "
Q: What enzyme's presence is characteristic of specific types of viral infections?
A: RNA replicases", '
Q: What does the protein hemagglutinin bind together?
A: red blood cells', '
Q: Why are the presence of certain enymzes a tell tale sign of a virus?
A: humans can make neither RNA replicases nor reverse transcriptase']
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.

Questions and answers:
['
Q: What methods are highly sensitive, specifc and rapid tests used to identify microorganisms?
A: Serological', '
Q: What are serological tests based upon the ability of an antibody to do?
A: bind specifically to an antigen', '
Q: What is the antigen bound to by the antibody usually?
A: a protein or carbohydrate made by an infectious agent', '
Q: What does the binding set off that will result in something visibly obvious in various ways?
A: a chain of events', '
Q: What is the causative agent of "strep throat"?
A: S. pyogenes']
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.

Questions and answers:
['
Q: What are immunoassays?
A: Complex serological techniques', '
Q: What type of signal do immunoassays produce?
A: electro - magnetic or particle radiation', '
Q: What allows quantitation of the target antigen?
A: unknowns can be compared to that of standards', '
Q: Immunoassays are able to detect what type of proteins?
A: generated by an infected organism in response to a foreign agent']
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.

Questions and answers:
['
Q: What does the acronym PCR expand to?
A: polymerase chain reaction', '
Q: What will be the ubiquitous gold standards of diagnostics in the near future?
A: PCR', '
Q: What has the catalog of infectious agents grown to the point of?
A: virtually all of the significant infectious agents of the human population have been identified', '
Q: What must an infectious agent do to cause disease?
A: grow within the human body', '
Q: What are primers derived from the genomes of?
A: infectious agents']
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.

Questions and answers:
['
Q: What technological ability with regards to detection is currently available? 
A: ability to detect any infectious agent', '
Q: What are the remaining blockades to the use or PCR as a standard tool of diagnosis?
A: cost and application', "
Q: What are some diseases which won't benefit from PCR methods?
A: clostridial diseases", "
Q: PCR can't detect the presence of any bacteria when what doesn't occur?
A: significant proliferation of the infectious agent"]
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.

Questions and answers:
['
Q: What is used in the treatment of AIDS?
A: AZT', '
Q: How was the course of AIDS followed?
A: monitoring the composition of patient blood samples', '
Q: What could be done by understanding how the disease was transmitted?
A: resources could be targeted to the communities at greatest risk', '
Q: What did the genotypic identification of HIV later enable?
A: geographical origins of the virus', '
Q: What is now commonly used to identify HIV in healthy people before the onset of the illnes?
A: Molecular diagnostics']
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.

Questions and answers:
['
Q: What can wearing gowns and face masks help prevent?
A: infections from being passed from one person to another', '
Q: What is the most important defense against the spread of unwanted organisms?
A: Frequent hand washing', '
Q: Avoiding drugs and using condoms are other forms of what?
A: prevention', '
Q: Why is it important to cook foods well?
A: prevention', '
Q: What should one do with foods that have been left outside for a long time?
A: avoiding']
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.

Questions and answers:
['
Q: Recognizing the different characteristics of various diseases is one way to do what?
A: prevent or slow down the transmission of infectious diseases', '
Q: What are some critical disease characteristics that should be evaluated?
A: virulence, distance traveled by victims, and level of contagiousness', "
Q: What virus' strains incapacitate their victims extremely quickly before killing them?
A: Ebola", '
Q: Why is the initial stage of Ebola not very contagious?
A: victims experience only internal hemorrhaging', '
Q: What does the low virulence of HIV allow victims to do?
A: travel long distances']
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.

Questions and answers:
['
Q: Recognizing the effects of small-world networks allows one to decrease what?
A: transmission rate of infectious diseases', '
Q: What type of interactions happen within groups of infected individuals in epidemics?
A: extensive interactions', '
Q: What is a way of drastically reducing infection rates?
A: focus is on the prevention of transmission jumps', '
Q: What is an example of a success implementation of preventing transmission jumps?
A: needle exchange programs in areas with a high density of drug users', '
Q: When was vaccination used to prevent the spread of the foot-and-mouth virus?
A: 2001']