romikgosai/squad_modified_2 huggingface dataset:
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:

Q1: Of the huge amount of microorganisms, how many cause disease in otherwise healthy individuals?
A1: relatively few
Q2: Interplay between pathogens and defenses of hosts results in what?
A2: Infectious disease
Q3: What does the severity of a disease resulting from a pathogen depend on?
A3: ability of that pathogen to damage the host
Q4: What can a host's immune system do to a host?
A4: cause damage
Q5: What do clinicians classify infectious microorganisms according to the status of?
A5: host defenses
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).

Q1: What is one way of proving that a given disease is infectious?
A1: satisfy Koch's postulates
Q2: What must an infectious agent only be identified in to satisfy the first of Koch's postulates?
A2: patients and not in healthy controls
Q3: What is Koch's second postulate?
A3: patients who contract the agent also develop the disease
Q4: Why can't Koch's postulates be applied ethically for many human diseases?
A4: because they require experimental infection of a healthy individual
Q5: What is the causative spirochete of syphilis?
A5: Treponema pallidum
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.

Q1: When are infectious diseases called contagious diseases?
A1: when they are easily transmitted by contact with an ill person
Q2: What is a contagious disease a subset of?
A2: infectious disease
Q3: What sets a contagious disease after from a standard infectious disease?
A3: especially infective or easily transmitted
Q4: Diseases with vector transmission or sexual transmission don't often require what type of isolation?
A4: medical
Q5: What is not always respected in popular use?
A5: specialized connotation of the word "contagious"
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.

Q1: When does infection begin?
A1: when an organism successfully enters the body, grows and multiplies.
Q2: What group is not easily infected?
A2: humans
Q3: What group of humans have increased susceptibility to chronic or persistent infections?
A3: weak, sick, malnourished, have cancer or are diabetic
Q4: What individuals are particularly susceptible to opportunistic infections?
A4: Individuals who have a suppressed immune system
Q5: What is it called when a pathogen grows within the host cells?
A5: intracellular
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.

Q1: What does wound colonization refer to?
A1: nonreplicating microorganisms within the wound
Q2: What type of organisms exist and injure tissue in infected wounds?
A2: replicating
Q3: What are all multcellular organisms colonized to some degree by?
A3: extrinsic organisms
Q4: What's the difference between an infection and a colonization?
A4: only a matter of circumstance
Q5: What species colonizes the mammalian colon?
A5: anaerobic bacteria
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).

Q1: Why is it difficult to now which chronic wounds are infected?
A1: Because it is normal to have bacterial colonization
Q2: What is there limited quality data for evaluating despite the huge number of wounds seen in a clinical practice?
A2: symptoms and signs
Q3: What is increased pain an indicator of?
A3: infection
Q4: What does not rule out infection?
A4: absence of pain
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.

Q1: Disease can arise when an organism inflicts what on the host?
A1: damage
Q2: What can a microorganism cause tissue damage by releasing a variety of?
A2: toxins
Q3: What does the of toxin Clostridium tetani releases do?
A3: paralyzes muscles
Q4: What releases toxins which product shock and sepsis?
A4: staphylococcus
Q5: What percentage of people infected with polio develop disease?
A5: less than 5%
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.

Q1: Why do persistent infections occur?
A1: body is unable to clear the organism after the initial infection
Q2: What are persistent infections characterized by the continual presence of?
A2: the infectious organism
Q3: How can some viruses main a persistent infection?
A3: by infecting different cells of the body
Q4: What never leave the body when acquired?
A4: Some viruses
Q5: Where does the herpes virus hide?
A5: 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.

Q1: What does diagnosis of an infectious sometimes involve identifying?
A1: an infectious agent either directly or indirectly
Q2: Many minor infectious diseases are diagnosed by what type of presentation?
A2: clinical
Q3: How are minor infectious diseases treated?
A3: without knowledge of the specific causative agent
Q4: What can be identified given sufficient effort?
A4: all known infectious agents
Q5: Why is it often not worth bothering to identify an infectious agent?
A5: 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.

Q1: How is diagnosis of infectious disease almost always initiated?
A1: by medical history and physical examination
Q2: What does taking a culture of an infectious agent isolated from a patient allow?
A2: detailed identification
Q3: What features of an infectious organism does a culture allow examining?
A3: microscopic features
Q4: What can organisms be directly identified by?
A4: its genotype
Q5: What technique can be used to produce images of internal abnormalities?
A5: 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.

Q1: What type of culture is a principal tool used to diagnose infectious disease?
A1: Microbiological
Q2: What type of medium is provided for a specific agent in a microbial culture?
A2: growth
Q3: What are most pathogenic bacteria easily grown on?
A3: nutrient agar
Q4: What is it called when a visible mound forms on the surface of a plate?
A4: a colony
Q5: What is a region of dead cells resulting from viral growth called?
A5: 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.

Q1: What are live animals required by?
A1: some microbes
Q2: What can Mycobacterium leprae and Treponema pallidum be grown in?
A2: animals
Q3: What type of eggs may some viruses be grown in?
A3: embryonated
Q4: What is Xenodiagnosis?
A4: use of a vector to support the growth of an infectious agent
Q5: What is it difficult to demonstrate the presence of in Chagas disease?
A5: 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.

Q1: What is microscopy used for?
A1: diagnosis of infectious disease
Q2: What do virtually all culture techniques rely on at some point?
A2: microscopic examination
Q3: What can samples obtained from patients viewed directly under?
A3: light microscope
Q4: When is microscopy exquisitely specific?
A4: when used in combination with antibody based techniques.
Q5: What can antibodies with artificial fluorescence be directed to do?
A5: 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.

Q1: What do almost all cells readily stain with?
A1: a number of basic dyes
Q2: Why do cells easily stain with dyes?
A2: electrostatic attraction
Q3: What electronic charge do cellular molecules have?
A3: negatively charged
Q4: What is Geimsa stain?
A4: a dye
Q5: How many methods comprise standard approaches used to classify bacteria and diagnose disease?
A5: 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.

Q1: What needs to be isolated from infected tissue to provide a biochemical diagnosis of an infectious disease?
A1: enzymes
Q2: What enzyme's presence is characteristic of specific types of viral infections?
A2: RNA replicases
Q3: What does the protein hemagglutinin bind together?
A3: red blood cells
Q4: Why are the presence of certain enymzes a tell tale sign of a virus?
A4: 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.

Q1: What methods are highly sensitive, specifc and rapid tests used to identify microorganisms?
A1: Serological
Q2: What are serological tests based upon the ability of an antibody to do?
A2: bind specifically to an antigen
Q3: What is the antigen bound to by the antibody usually?
A3: a protein or carbohydrate made by an infectious agent
Q4: What does the binding set off that will result in something visibly obvious in various ways?
A4: a chain of events
Q5: What is the causative agent of "strep throat"?
A5: 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.

Q1: What are immunoassays?
A1: Complex serological techniques
Q2: What type of signal do immunoassays produce?
A2: electro - magnetic or particle radiation
Q3: What allows quantitation of the target antigen?
A3: unknowns can be compared to that of standards
Q4: Immunoassays are able to detect what type of proteins?
A4: 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.

Q1: What does the acronym PCR expand to?
A1: polymerase chain reaction
Q2: What will be the ubiquitous gold standards of diagnostics in the near future?
A2: PCR
Q3: What has the catalog of infectious agents grown to the point of?
A3: virtually all of the significant infectious agents of the human population have been identified
Q4: What must an infectious agent do to cause disease?
A4: grow within the human body
Q5: What are primers derived from the genomes of?
A5: infectious agents