imone/ARB huggingface dataset:
Question: Osteomyelitis is a bone infection often caused by the bacterium Staphylococcus aureus, which spreads through the blood to the bones. The infection is quite common after surgeries when soft tissues become infected and the infection moves to the adjacent bones. The long bones of children are particularly susceptible as they have excellent circulation to them during the growth period. In adults, the best circulation is to the vertebrae, and these are the bones that are most likely to develop osteomyelitis.
Osteomyelitis is treated with various antibiotics, but some patients have chronic infections that are not eradicated by antibiotic therapy due to a unique feature of S. aureus. S. aureus can be internalized by osteoblasts where the bacteria can continue to survive in the intracellular environment. Inside the osteoblasts, bacteria can induce apoptosis, killing their host cell. Surgical debridement is often required to remove the damaged and dead bone tissue created by the infection.
A major research question deals with how an S. aureus infection induces apoptosis in the host osteoblasts. In order for apoptosis to initiate in osteoblasts, the enzyme capsase-8 must be activated. This enzyme serves as a protease that cleaves critical proteins in the cell, causing cell death. Capsase-8 is only expressed under certain circumstances. In the case of osteomyelitis, the S. aureus bacteria cause the induction of tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) in the osteoblasts. Then TRAIL activates capsase-8, which triggers a series of events leading to apoptosis and death of osteoblasts.
Osteoblasts are unusual in that they actively engulf $S$. aureus, which survives in the osteoblast and eventually triggers apoptosis. In engulfing the bacteria, the osteoblasts resemble the normal activities of which type of leukocyte?

Options:
A. basophils
B. lymphocytes
C. eosinophils
D. macrophages
Answer: The leukocytes that engulf microbes such as bacteria are macrophages. This process is termed phagocytosis. Basophils secrete histamine, which is involved in the initiation of the inflammatory response. Lymphocytes are involved in specific immune system defenses. Eosinophils are involved in the defense response to antigens from unique sources such as parasites. The correct answer is D.
Question: Passage $\mathrm{V}$
For many years, researchers have been interested in developing edible vaccines that would provide protection against various bacterial and viral diseases. An edible vaccine is a genetically modified organism (GMO) that is created when genes from the bacteria or virus being vaccinated against are inserted into plant cells. As the plants grow, they produce proteins from the bacteria or virus that the researchers are attempting to vaccinate against. When a person eats the plant, the viral or bacteria proteins serve as antigens, which initiates a primary immune response.
Some of the plants that are of interest in edible vaccine development are bananas, potatoes, tomatoes, corn, rice, tobacco, and soybeans. While early research focused on growing crops that produced edible products such as bananas, the most recent research is focused on extracting material from the leaves and seeds of the plants, dehydrating it, and putting it into capsules that can be swallowed. This allows for a more predictable dosage of the vaccine and eliminates concerns that the crops containing the vaccine would be accidentally eaten by individuals who are not in need of the vaccine. The term edible vaccine has now been replaced with the term plantderived oral vaccine.
The development of plant-derived oral vaccines solves many problems associated with injectable vaccines. Because plant-derived oral vaccines are grown in crops, there is no problem with storage or refrigeration that is required of most traditional vaccines. These plant-derived vaccines also require no special training to administer. Additionally, when a vaccine is taken orally, it provides mucosal immunity due to the production of IgA antibodies by the immune system-in addition to systemic immunity. Since 90 percent of diseases enter the body through a mucus membrane, a vaccine that coerces mucosal immunity is of great benefit in the prevention of many diseases.
A traditional vaccine that is administered either intramuscularly or subcutaneously would be expected to cause the formation of which type of antibodies initially following administration?

Options:
A. $\operatorname{IgE}$
B. IgG
C. IgM
D. IgA
Answer: IgM antibodies are produced first in response to exposure to a new antigen. Later, IgG antibodies will be produced. The correct answer is C.
Question: A certain type of cell makes antibodies that are secreted from the cell. It is possible to track the path of these as they leave the cell by labeling them with radioactive isotopes. Which of the following might be the path of antibodies from where they are made to the cell membrane?

Options:
A. Golgi complex to lysosomes to cell membrane
B. rough endoplasmic reticulum to Golgi complex to cell membrane
C. nucleus to Golgi complex to cell membrane
D. smooth endoplasmic reticulum to lysosomes to cell membrane
Answer: Antibodies are proteins that are secreted from the cell. Proteins would be produced and labeled by the rough endoplasmic reticulum. From there, they would be sorted by the Golgi complex and finally directed to the cell membrane for secretion. The correct answer is B.
Question: Passage $\mathrm{V}$
For many years, researchers have been interested in developing edible vaccines that would provide protection against various bacterial and viral diseases. An edible vaccine is a genetically modified organism (GMO) that is created when genes from the bacteria or virus being vaccinated against are inserted into plant cells. As the plants grow, they produce proteins from the bacteria or virus that the researchers are attempting to vaccinate against. When a person eats the plant, the viral or bacteria proteins serve as antigens, which initiates a primary immune response.
Some of the plants that are of interest in edible vaccine development are bananas, potatoes, tomatoes, corn, rice, tobacco, and soybeans. While early research focused on growing crops that produced edible products such as bananas, the most recent research is focused on extracting material from the leaves and seeds of the plants, dehydrating it, and putting it into capsules that can be swallowed. This allows for a more predictable dosage of the vaccine and eliminates concerns that the crops containing the vaccine would be accidentally eaten by individuals who are not in need of the vaccine. The term edible vaccine has now been replaced with the term plantderived oral vaccine.
The development of plant-derived oral vaccines solves many problems associated with injectable vaccines. Because plant-derived oral vaccines are grown in crops, there is no problem with storage or refrigeration that is required of most traditional vaccines. These plant-derived vaccines also require no special training to administer. Additionally, when a vaccine is taken orally, it provides mucosal immunity due to the production of IgA antibodies by the immune system-in addition to systemic immunity. Since 90 percent of diseases enter the body through a mucus membrane, a vaccine that coerces mucosal immunity is of great benefit in the prevention of many diseases.
The goal of any type of vaccination is to induce active immunity without people getting ill from the disease that they are being vaccinated against. In order to have long-term effectiveness, the vaccine must cause the development of which type of cells in the immune system?

Options:
A. cytotoxic T cells
B. helper T cells
C. plasma cells
D. memory cells
Answer: Once activated, most cells in the immune system do not live long. Activated cytotoxic T cells and plasma cells are inactivated once the antigen that they have been designed to fight has been eliminated. The basis of long-term immune system protection is the development of memory T and memory B cells (choice D). These memory cells are produced upon primary exposure to a specific antigen and have the ability to survive for years within the body. Should the same antigen return, memory cells quickly proliferate into cytotoxic T cells and plasma cells to fight the antigen. The correct answer is D.
Question: Leukemia is a term that describes a wide variety of blood cell cancers. Most leukemia cases involve elevated leukocyte counts. In acute cases of leukemia, immature leukocytes proliferate quickly, which leads to many abnormal immature cells in the bone marrow. This inhibits the ability of the bone marrow to produce healthy new leukocytes. This form of the cancer progresses rapidly, and the cells metastasize easily as they move into the bloodstream from the bone marrow. It can be fatal within weeks or months if not treated promptly. In contrast, chronic cases of leukemia typically involve the proliferation of abnormal mature leukocytes. This form of the disease progresses more slowly, and treatment need not always be immediate.
Once classified as acute or chronic, leukemia can be further subdivided into lymphocytic or myelogenous. This distinction depends on which type of leukocyte is abnormal in the patient. In lymphocytic leukemia, the lymphoid cells, such as the lymphocytes, are abnormal. In the myelogenous form, the myeloid cells, such as basophils, neutrophils, and eosinophils, are affected.
Chemotherapy drugs are often used in the management of leukemia cases. There are numerous categories of these drugs, and they have varied mechanisms of action. In treatment, several drugs are used in combination because some of the drugs are cell-cycle specific while others are not. Alkylating agents are capable of disrupting the function of DNA. Tubulin-binding agents are designed to interfere with microtubule formation. Other drugs are designed to interfere with DNA polymerase, DNA repair mechanisms, or protein synthesis, or to act as purine analogs. Many of these drugs cannot enter into the brain when injected or ingested, so if the cancer has spread to
this area, special methods must be used to introduce the drugs to the brain.
What would be the BEST explanation as to why people with chronic forms of leukemia can live longer untreated than those with acute cases of leukemia?

Options:
A. Chronic cases involve types of leukocytes that have less important functions in the body.
B. Chronic cases of leukemia involve abnormal cell division of mature cells, so there are still some immature cells that can proliferate into normal mature cells.
C. The immune system is less likely to recognize and destroy abnormal immature leukocytes than it would be to recognize and destroy abnormal mature leukocytes.
D. all of the above
Answer: The passage explains that in acute cases of leukemia, Passage I immature leukocytes are involved. This implies that these immature cells are abnormal and may not proliferate into normal mature leukocytes. The passage also indicates that in chronic cases of leukemia, mature leukocytes are affected so that it is possible that some unaffected immature cells may proliferate into functional mature cells. If there are some functional leukocytes, the person would be likely to survive longer without treatment. The correct answer is B.
Question: The process of quorum sensing is observed in a variety of species. It involves a system of communication between organisms that is dependent on population density. Bacteria are notorious for using quorum sensing (QS) via the secretion of secreted signaling molecules, called autoinducers (AI), to coordinate their gene expression once a threshold density of population is reached. Not only can bacteria communicate via QS within their species, but they can also cross-talk through QS between different species. In order to participate in quorum sensing, bacteria require a way to produce an autoinducer and a way to respond to autoinducers via binding to specific receptors.
One example of how bacteria use quorum sensing to their advantage is to regulate the gene expression of virulence factors. During infection, if a small number of bacteria were to express their virulence factors, this would largely have no impact on the host. Instead, bacteria wait until a quorum is reached in terms of population size, indicating that the population is large enough to express virulence factors. These virulence factors relate to such abilities as escaping the immune response, invasion, and spreading within the host.
We know that we are facing a current healthcare crisis related to the loss of effectiveness of many traditional types of antibiotics based on bacterial resistance. This provides a major impetus for identifying novel ways to target bacterial pathogens that avoid the use of antibiotics. Several chemical compounds and molecules have been identified as facilitators of quorum sensing inhibition. Typically, these factors can serve as signal-targeting enzymes or small-molecule inhibitors of signal synthases and receptors.
Targets of traditional antibiotics include all of the following EXCEPT:

Options:
A. ribosomes
B. metabolic processes
C. the cell wall
D. the nucleus
Answer: Antibiotics must target structures that are unique to prokaryotic cells. Of the choices listed, the nucleus is a structure lacking in prokaryotic cells and therefore could not serve as a target for antibiotics. The correct answer is D.
Question: The process of quorum sensing is observed in a variety of species. It involves a system of communication between organisms that is dependent on population density. Bacteria are notorious for using quorum sensing (QS) via the secretion of secreted signaling molecules, called autoinducers (AI), to coordinate their gene expression once a threshold density of population is reached. Not only can bacteria communicate via QS within their species, but they can also cross-talk through QS between different species. In order to participate in quorum sensing, bacteria require a way to produce an autoinducer and a way to respond to autoinducers via binding to specific receptors.
One example of how bacteria use quorum sensing to their advantage is to regulate the gene expression of virulence factors. During infection, if a small number of bacteria were to express their virulence factors, this would largely have no impact on the host. Instead, bacteria wait until a quorum is reached in terms of population size, indicating that the population is large enough to express virulence factors. These virulence factors relate to such abilities as escaping the immune response, invasion, and spreading within the host.
We know that we are facing a current healthcare crisis related to the loss of effectiveness of many traditional types of antibiotics based on bacterial resistance. This provides a major impetus for identifying novel ways to target bacterial pathogens that avoid the use of antibiotics. Several chemical compounds and molecules have been identified as facilitators of quorum sensing inhibition. Typically, these factors can serve as signal-targeting enzymes or small-molecule inhibitors of signal synthases and receptors.
N-Acyl homoserine lactones (N-AHLs) are one type of autoinducer produced by certain species of bacteria. Different types of bacteria can produce N-AHLs with unique molecular structures by making minor changes to the core structure of the molecule. Given the structure of the molecule, what would be the MOST likely way they could do this?

Options:
A. by altering the $\mathrm{R}$ group side chains
B. by altering fatty acid chains
C. by glycosylating the core structure
D. by methylating the core structure
Answer: This question relies on your knowledge of the structure of organic molecules. The N-AHLs in this question should be recognized as some derivative of an amino acid. Given that information, the most likely way to alter them would be by altering their R group side chains. The correct answer is A.
Question: Genetically modified (GM) foods contain DNA from more than one source. The goal of creating GM foods is to modify the organisms to express new and useful traits. A few examples involve engineering crops to be resistant to bacterial or viral infections, to be resistant to herbicides, to ripen more slowly, to survive extreme temperature changes, to contain vaccines, or to create crops that are more nutritious.
One GM food that has received media attention over the years is golden rice. This GM product was first introduced in 2000 and was engineered to provide carotene that is a precursor to vitamin $\mathrm{A}$. The carotene in the rice provides the golden color. Vitamin A deficiency is a major problem in underdeveloped parts of the world, killing more than one million people a year, most of whom are children. This vitamin is critical for the development and maintenance of epithelial tissues, for vision, and for growth.
Rice plants normally produce carotene in the inedible parts of the plant. To be able to access and use the carotene, it was necessary to engineer the rice to produce it in the edible grains. In order to achieve this goal, two genes from daffodil plants, psy and $l y c$, and a bacterial gene called $c r t 1$ were added to the rice genome. These genes engineered a pathway that produces lycopene, which is eventually converted to carotene. Each of these genes was placed under the control of a grain-specific promoter so that the products were produced in the rice grains.
While golden rice was produced to provide carotene, which the human body can convert into the essential vitamin A, the rice provided much less carotene than was anticipated. Golden rice 2, a modified version released in 2005, contains a much larger amount of carotene and, as such, is a better source of the vitamin. Field tests were conducted in 2009, and human consumption trials were completed in 2012. However, neither version has been grown in large-scale quantities at this time.
Genetically modified organisms, typically plants, are being developed as a means of administering vaccines. If these transgenic plants are to be successful as vaccines, they will need to:

Options:
A. stimulate inflammation in the recipient
B. express antigens to stimulate adaptive defenses in the recipient
C. contain antibodies to the organism being vaccinated against
D. contain memory cells against the organism being vaccinated against
Answer: Vaccines are designed to work by stimulating the primary immune response of the recipient. This requires the immune system to recognize an antigen and to mount a specific immune response. Ultimately, this leads to the production of memory cells that can survive for long periods of time. When the system is challenged by the actual antigen, different types of memory cells can quickly proliferate into plasma cells and cytotoxic $\mathrm{T}$ cells in order to destroy the antigen. The correct answer is B.
Question: According to the bystander effect, which is MOST likely to be true in an emergency?

Options:
A. the greater the number of people present, the slower the response because of increased diffusion of responsibility
B. the greater the number of people present, the slower the response because of decreased diffusion of responsibility
C. the greater the number of people present, the faster the response because of increased diffusion of responsibility
D. the greater the number of people present, the faster the response because of decreased diffusion of responsibility
Answer: The bystander effect is characterized by slowness in response due to diffusion of responsibility. The more people who are present, the less an individual is likely to feel responsible to respond to the emergency because of the collective presence of other individuals. The correct answer is A.
Question: Which of the following statements BEST explains why your body prefers to perform aerobic respiration as opposed to anaerobic respiration?

Options:
A. Anaerobic respiration does not allow for NADH to be recycled to NAD+.
B. Aerobic respiration requires less of an adenosine triphosphate (ATP) investment than anaerobic respiration does.
C. Aerobic respiration produces far more ATP than anaerobic respiration.
D. Aerobic respiration is easier for cells to perform than anaerobic respiration.
Answer: The primary difference between aerobic and anaerobic No Passage cellular respiration is the amount of ATP generated. Anaerobic respiration generates far less ATP per glucose molecule than does aerobic respiration. The correct answer is C.
Question: Prokaryotic and eukaryotic cells generally have which of the following structures in common?

Options:
A. a membrane-bound nucleus
B. a cell wall made of cellulose
C. ribosomes
D. linear chromosomes made of DNA
Answer: Prokaryotic cells lack membrane-bound organelles including a nucleus. Their DNA is circular and does not exist as linear chromosomes. Prokaryotic cells can have a cell wall, but it is typically made of peptidoglycan. The only item on this list that is common between prokaryotic and eukaryotic cells is that they both contain ribosomes needed for protein synthesis within the cell. The correct answer is C.
Question: When two solutions that differ in solute concentration are placed on either side of a semipermeable membrane and osmosis is allowed to occur, which of the following will be observed?

Options:
A. Water will move from an area of low solute concentration to an area of high solute concentration.
B. The solute will move from an area of high concentration to an area of low concentration.
C. There will be no net movement of water.
D. Water will move from an area of high solute concentration to an area of low solute concentration.
Answer: Osmosis is a specialized form of diffusion, or passive transport. During osmosis, water always moves from the side of the membrane that has more water to the side of the membrane that has less water. The only thing that moves by osmosis is water. This means that choice B can be eliminated because solutes are not moving by osmosis. If there is a concentration difference across the membrane, there will be water movement, which eliminates choice $\mathrm{C}$. When osmosis occurs, water moves from the side of the membrane that has more water to the side that has less water. This means that the side of the membrane with more water has less solute (and is therefore less concentrated) than the side of the membrane with less water and more solute (being more concentrated). Based on the choices provided, choice A is the most appropriate. The correct answer is A.
Question: Questions 18-20 are based on the following data.
The generalized events in DNA replication can be depicted by the following flowchart:
Double helix $\rightarrow$ Nicking of a strand $\rightarrow$ Unwinding $\rightarrow$ Destabilization and relief of pressure $\rightarrow$ Initiation $\rightarrow$ Elongation $\rightarrow$ Closing of nicks
Between which two steps would the enzyme DNA ligase be used?

Options:
A. Double helix $\rightarrow$ Nicking of a strand
B. Nicking of a strand $\rightarrow$ Unwinding
C. Initiation $\rightarrow$ Elongation
D. Elongation $\rightarrow$ Closing of nicks
Answer: Abutting segments of unjoined DNA can be annealed by ligases. Thus the enzyme acting between Elongation $\rightarrow$ Closing of nicks is $D N A$ ligase. The correct answer is D.