yz2022/T2P-DownstreamNLP huggingface dataset:
Circadian_rhythm

The central oscillator generates a self-sustaining rhythm and is driven by two interacting feedback loops that are active at different times of day. The morning loop consists of CCA1 (Circadian and Clock-Associated 1) and LHY (Late Elongated Hypocotyl), which encode closely related MYB transcription factors that regulate circadian rhythms in Arabidopsis, as well as PRR 7 and 9 (Pseudo-Response Regulators.) The evening loop consists of GI (Gigantea) and ELF4, both involved in regulation of flowering time genes. When CCA1 and LHY are overexpressed (under constant light or dark conditions), plants become arrhythmic, and mRNA signals reduce, contributing to a negative feedback loop. Gene expression of CCA1 and LHY oscillates and peaks in the early morning, whereas TOC1 gene expression oscillates and peaks in the early evening. While it was previously hypothesised that these three genes model a negative feedback loop in which over-expressed CCA1 and LHY repress TOC1 and over-expressed TOC1 is a positive regulator of CCA1 and LHY, it was shown in 2012 by Andrew Millar and others that TOC1 in fact serves as a repressor not only of CCA1, LHY, and PRR7 and 9 in the morning loop but also of GI and ELF4 in the evening loop. This finding and further computational modeling of TOC1 gene functions and interactions suggest a reframing of the plant circadian clock as a triple negative-component repressilator model rather than the positive/negative-element feedback loop characterizing the clock in mammals.

Question: What produces a self-sustaining rhythm?
Answer: central oscillator

Question: What researcher showed that the gene  feedback loop serves as a repressor?
Answer: Andrew Millar

Question: Which loop that consists of GI and ELF4 functions?
Answer: evening

Question: What was the previous belief of feedback in the gene loop?
Answer: negative feedback loop
Circadian_rhythm

The simplest known circadian clock is that of the prokaryotic cyanobacteria. Recent research has demonstrated that the circadian clock of Synechococcus elongatus can be reconstituted in vitro with just the three proteins (KaiA, KaiB, KaiC) of their central oscillator. This clock has been shown to sustain a 22-hour rhythm over several days upon the addition of ATP. Previous explanations of the prokaryotic circadian timekeeper were dependent upon a DNA transcription/translation feedback mechanism.[citation needed]

Question: How long a rhythm were researchers able to sustain in the in vitro experiment?
Answer: 22-hour

Question: What type of feedback mechanism was previously thought to be needed to sustain the clock?
Answer: DNA

Question: What were the only proteins necessary to the circadian timekeeper experiment?
Answer: KaiA, KaiB, KaiC
Circadian_rhythm

The earliest recorded account of a circadian process dates from the 4th century B.C.E., when Androsthenes, a ship captain serving under Alexander the Great, described diurnal leaf movements of the tamarind tree. The observation of a circadian or diurnal process in humans is mentioned in Chinese medical texts dated to around the 13th century, including the Noon and Midnight Manual and the Mnemonic Rhyme to Aid in the Selection of Acu-points According to the Diurnal Cycle, the Day of the Month and the Season of the Year.

Question: When did the Chinese use diurnal rhythms to remember Acu-points?
Answer: 13th century

Question: What is the earliest recorded instance of circadian rhythm?
Answer: 4th century B.C.E

Question: What type of Chinese texts mention circadian process in humans?
Answer: medical
Circadian_rhythm

The simplest known circadian clock is that of the prokaryotic cyanobacteria. Recent research has demonstrated that the circadian clock of Synechococcus elongatus can be reconstituted in vitro with just the three proteins (KaiA, KaiB, KaiC) of their central oscillator. This clock has been shown to sustain a 22-hour rhythm over several days upon the addition of ATP. Previous explanations of the prokaryotic circadian timekeeper were dependent upon a DNA transcription/translation feedback mechanism.[citation needed]

Question: With how many proteins can the circadian clock of Synechococcus elongatus are needed to reproduce its effect?
Answer: three proteins
Circadian_rhythm

For temperature studies, subjects must remain awake but calm and semi-reclined in near darkness while their rectal temperatures are taken continuously. Though variation is great among normal chronotypes, the average human adult's temperature reaches its minimum at about 05:00 (5 a.m.), about two hours before habitual wake time. Baehr et al. found that, in young adults, the daily body temperature minimum occurred at about 04:00 (4 a.m.) for morning types but at about 06:00 (6 a.m.) for evening types. This minimum occurred at approximately the middle of the eight hour sleep period for morning types, but closer to waking in evening types.

Question: How long before wake time is the lowest temperature reached?
Answer: two hours

Question: When does the temperature of morning type young adults reach its lowest?
Answer: 04:00
Circadian_rhythm

Light is the signal by which plants synchronize their internal clocks to their environment and is sensed by a wide variety of photoreceptors. Red and blue light are absorbed through several phytochromes and cryptochromes. One phytochrome, phyA, is the main phytochrome in seedlings grown in the dark but rapidly degrades in light to produce Cry1. Phytochromes B–E are more stable with phyB, the main phytochrome in seedlings grown in the light. The cryptochrome (cry) gene is also a light-sensitive component of the circadian clock and is thought to be involved both as a photoreceptor and as part of the clock's endogenous pacemaker mechanism. Cryptochromes 1–2 (involved in blue–UVA) help to maintain the period length in the clock through a whole range of light conditions.

Question: What signals plants to synchronize their internal clocks?
Answer: Light
Circadian_rhythm

For temperature studies, subjects must remain awake but calm and semi-reclined in near darkness while their rectal temperatures are taken continuously. Though variation is great among normal chronotypes, the average human adult's temperature reaches its minimum at about 05:00 (5 a.m.), about two hours before habitual wake time. Baehr et al. found that, in young adults, the daily body temperature minimum occurred at about 04:00 (4 a.m.) for morning types but at about 06:00 (6 a.m.) for evening types. This minimum occurred at approximately the middle of the eight hour sleep period for morning types, but closer to waking in evening types.

Question: What is the time of lowest temperature for evening type young adults?
Answer: 06:00
Circadian_rhythm

Light is the signal by which plants synchronize their internal clocks to their environment and is sensed by a wide variety of photoreceptors. Red and blue light are absorbed through several phytochromes and cryptochromes. One phytochrome, phyA, is the main phytochrome in seedlings grown in the dark but rapidly degrades in light to produce Cry1. Phytochromes B–E are more stable with phyB, the main phytochrome in seedlings grown in the light. The cryptochrome (cry) gene is also a light-sensitive component of the circadian clock and is thought to be involved both as a photoreceptor and as part of the clock's endogenous pacemaker mechanism. Cryptochromes 1–2 (involved in blue–UVA) help to maintain the period length in the clock through a whole range of light conditions.

Question: What do plants use to sense light?
Answer: photoreceptors
Circadian_rhythm

The earliest recorded account of a circadian process dates from the 4th century B.C.E., when Androsthenes, a ship captain serving under Alexander the Great, described diurnal leaf movements of the tamarind tree. The observation of a circadian or diurnal process in humans is mentioned in Chinese medical texts dated to around the 13th century, including the Noon and Midnight Manual and the Mnemonic Rhyme to Aid in the Selection of Acu-points According to the Diurnal Cycle, the Day of the Month and the Season of the Year.

Question: What ship captain described daily leaf movements?
Answer: Androsthenes
Circadian_rhythm

What drove circadian rhythms to evolve has been an enigmatic question. Previous hypotheses emphasized that photosensitive proteins and circadian rhythms may have originated together in the earliest cells, with the purpose of protecting replicating DNA from high levels of damaging ultraviolet radiation during the daytime. As a result, replication was relegated to the dark. However, evidence for this is lacking, since the simplest organisms with a circadian rhythm, the cyanobacteria, do the opposite of this - they divide more in the daytime. Recent studies instead highlight the importance of co-evolution of redox proteins with circadian oscillators in all three kingdoms of life following the Great Oxidation Event approximately 2.3 billion years ago. The current view is that circadian changes in environmental oxygen levels and the production of reactive oxygen species (ROS) in the presence of daylight are likely to have driven a need to evolve circadian rhythms to preempt, and therefore counteract, damaging redox reactions on a daily basis.

Question: What is thought that circadian rhythm evolved to protect?
Answer: replicating DNA

Question: What is theorized to have evolved with circadian rhythms?
Answer: photosensitive proteins

Question: One possible reason for the development of the circadian system is the need to counteract what ?
Answer: redox reactions

Question: From what did  DNA need to be protected in the earliest cells? 
Answer: ultraviolet radiation
Circadian_rhythm

Light is the signal by which plants synchronize their internal clocks to their environment and is sensed by a wide variety of photoreceptors. Red and blue light are absorbed through several phytochromes and cryptochromes. One phytochrome, phyA, is the main phytochrome in seedlings grown in the dark but rapidly degrades in light to produce Cry1. Phytochromes B–E are more stable with phyB, the main phytochrome in seedlings grown in the light. The cryptochrome (cry) gene is also a light-sensitive component of the circadian clock and is thought to be involved both as a photoreceptor and as part of the clock's endogenous pacemaker mechanism. Cryptochromes 1–2 (involved in blue–UVA) help to maintain the period length in the clock through a whole range of light conditions.

Question: What receptors absorb red and blue light in plants?
Answer: phytochromes and cryptochromes
Circadian_rhythm

What drove circadian rhythms to evolve has been an enigmatic question. Previous hypotheses emphasized that photosensitive proteins and circadian rhythms may have originated together in the earliest cells, with the purpose of protecting replicating DNA from high levels of damaging ultraviolet radiation during the daytime. As a result, replication was relegated to the dark. However, evidence for this is lacking, since the simplest organisms with a circadian rhythm, the cyanobacteria, do the opposite of this - they divide more in the daytime. Recent studies instead highlight the importance of co-evolution of redox proteins with circadian oscillators in all three kingdoms of life following the Great Oxidation Event approximately 2.3 billion years ago. The current view is that circadian changes in environmental oxygen levels and the production of reactive oxygen species (ROS) in the presence of daylight are likely to have driven a need to evolve circadian rhythms to preempt, and therefore counteract, damaging redox reactions on a daily basis.

Question: What environmental event occurred 2.3 million years ago?
Answer: Great Oxidation Event
Circadian_rhythm

Light is the signal by which plants synchronize their internal clocks to their environment and is sensed by a wide variety of photoreceptors. Red and blue light are absorbed through several phytochromes and cryptochromes. One phytochrome, phyA, is the main phytochrome in seedlings grown in the dark but rapidly degrades in light to produce Cry1. Phytochromes B–E are more stable with phyB, the main phytochrome in seedlings grown in the light. The cryptochrome (cry) gene is also a light-sensitive component of the circadian clock and is thought to be involved both as a photoreceptor and as part of the clock's endogenous pacemaker mechanism. Cryptochromes 1–2 (involved in blue–UVA) help to maintain the period length in the clock through a whole range of light conditions.

Question: Which phytochrome found in seedlings deteriorates with light and growth?
Answer: phyA
Circadian_rhythm

For temperature studies, subjects must remain awake but calm and semi-reclined in near darkness while their rectal temperatures are taken continuously. Though variation is great among normal chronotypes, the average human adult's temperature reaches its minimum at about 05:00 (5 a.m.), about two hours before habitual wake time. Baehr et al. found that, in young adults, the daily body temperature minimum occurred at about 04:00 (4 a.m.) for morning types but at about 06:00 (6 a.m.) for evening types. This minimum occurred at approximately the middle of the eight hour sleep period for morning types, but closer to waking in evening types.

Question: What physical factor must be continuously monitored during temperature studies> 
Answer: temperatures

Question: At what time does the average adult human reach his lowest temperature?
Answer: 05:00
Circadian_rhythm

Light is the signal by which plants synchronize their internal clocks to their environment and is sensed by a wide variety of photoreceptors. Red and blue light are absorbed through several phytochromes and cryptochromes. One phytochrome, phyA, is the main phytochrome in seedlings grown in the dark but rapidly degrades in light to produce Cry1. Phytochromes B–E are more stable with phyB, the main phytochrome in seedlings grown in the light. The cryptochrome (cry) gene is also a light-sensitive component of the circadian clock and is thought to be involved both as a photoreceptor and as part of the clock's endogenous pacemaker mechanism. Cryptochromes 1–2 (involved in blue–UVA) help to maintain the period length in the clock through a whole range of light conditions.

Question: What is the main phytochrome found in seedling grown in light?
Answer: phyB
Circadian_rhythm

The earliest recorded account of a circadian process dates from the 4th century B.C.E., when Androsthenes, a ship captain serving under Alexander the Great, described diurnal leaf movements of the tamarind tree. The observation of a circadian or diurnal process in humans is mentioned in Chinese medical texts dated to around the 13th century, including the Noon and Midnight Manual and the Mnemonic Rhyme to Aid in the Selection of Acu-points According to the Diurnal Cycle, the Day of the Month and the Season of the Year.

Question: What tree leaves did Androsthenes describe?
Answer: tamarind
Circadian_rhythm

Early research into circadian rhythms suggested that most people preferred a day closer to 25 hours when isolated from external stimuli like daylight and timekeeping. However, this research was faulty because it failed to shield the participants from artificial light. Although subjects were shielded from time cues (like clocks) and daylight, the researchers were not aware of the phase-delaying effects of indoor electric lights.[dubious – discuss] The subjects were allowed to turn on light when they were awake and to turn it off when they wanted to sleep. Electric light in the evening delayed their circadian phase.[citation needed] A more stringent study conducted in 1999 by Harvard University estimated the natural human rhythm to be closer to 24 hours, 11 minutes: much closer to the solar day but still not perfectly in sync.

Question: What did early research show people preferred as a day length?
Answer: 25 hours

Question: What was the fault not considered in the early theories of day length?
Answer: artificial light
Circadian_rhythm

It is now known that the molecular circadian clock can function within a single cell; i.e., it is cell-autonomous. This was shown by Gene Block in isolated mollusk BRNs.[clarification needed] At the same time, different cells may communicate with each other resulting in a synchronised output of electrical signaling. These may interface with endocrine glands of the brain to result in periodic release of hormones. The receptors for these hormones may be located far across the body and synchronise the peripheral clocks of various organs. Thus, the information of the time of the day as relayed by the eyes travels to the clock in the brain, and, through that, clocks in the rest of the body may be synchronised. This is how the timing of, for example, sleep/wake, body temperature, thirst, and appetite are coordinately controlled by the biological clock.[citation needed]

Question: Inside of what can the molecular circadian clock operate?
Answer: single cell
Circadian_rhythm

Early research into circadian rhythms suggested that most people preferred a day closer to 25 hours when isolated from external stimuli like daylight and timekeeping. However, this research was faulty because it failed to shield the participants from artificial light. Although subjects were shielded from time cues (like clocks) and daylight, the researchers were not aware of the phase-delaying effects of indoor electric lights.[dubious – discuss] The subjects were allowed to turn on light when they were awake and to turn it off when they wanted to sleep. Electric light in the evening delayed their circadian phase.[citation needed] A more stringent study conducted in 1999 by Harvard University estimated the natural human rhythm to be closer to 24 hours, 11 minutes: much closer to the solar day but still not perfectly in sync.

Question: What did electric lighting in the evening do to the test subjects circadian phase?
Answer: delayed

Question: To what is the 24 hours, 11 minutes day outcome of research closest ?
Answer: solar day

Question: When did more stringent testing determine that humans preferred a 24 hour day? 
Answer: 1999
Circadian_rhythm

Studies by Nathaniel Kleitman in 1938 and by Derk-Jan Dijk and Charles Czeisler in the 1990s put human subjects on enforced 28-hour sleep–wake cycles, in constant dim light and with other time cues suppressed, for over a month. Because normal people cannot entrain to a 28-hour day in dim light if at all,[citation needed] this is referred to as a forced desynchrony protocol. Sleep and wake episodes are uncoupled from the endogenous circadian period of about 24.18 hours and researchers are allowed to assess the effects of circadian phase on aspects of sleep and wakefulness including sleep latency and other functions.[page needed]

Question: What time cycle did studies in 1938 and 1990s use on humans?
Answer: 28-hour

Question: What conditions were suppressed in the 28 hour wake-sleep cycle studies ?
Answer: time cues

Question: How long did the suppression of time clues study last?
Answer: month

Question: What is this forced type of study called?
Answer: forced desynchrony
Circadian_rhythm

The primary circadian "clock" in mammals is located in the suprachiasmatic nucleus (or nuclei) (SCN), a pair of distinct groups of cells located in the hypothalamus. Destruction of the SCN results in the complete absence of a regular sleep–wake rhythm. The SCN receives information about illumination through the eyes. The retina of the eye contains "classical" photoreceptors ("rods" and "cones"), which are used for conventional vision. But the retina also contains specialized ganglion cells that are directly photosensitive, and project directly to the SCN, where they help in the entrainment (synchronization) of this master circadian clock.

Question: Where is the primary circadian gene located in humans?
Answer: suprachiasmatic nucleus

Question: Where are these cell groups found in humans?
Answer: hypothalamus

Question: What provides information to the SCN?
Answer: eyes

Question: What special cells in the eyes communicate directly to the SCN cells?
Answer: ganglion

Question: What would the loss of the SCN cells cause in the sleep-wake rhythm?
Answer: complete absence
Circadian_rhythm

Studies by Nathaniel Kleitman in 1938 and by Derk-Jan Dijk and Charles Czeisler in the 1990s put human subjects on enforced 28-hour sleep–wake cycles, in constant dim light and with other time cues suppressed, for over a month. Because normal people cannot entrain to a 28-hour day in dim light if at all,[citation needed] this is referred to as a forced desynchrony protocol. Sleep and wake episodes are uncoupled from the endogenous circadian period of about 24.18 hours and researchers are allowed to assess the effects of circadian phase on aspects of sleep and wakefulness including sleep latency and other functions.[page needed]

Question: When in the cycle do wake-sleep cycles break off from the circadian period?
Answer: 24.18 hours
Circadian_rhythm

Shift-work or chronic jet-lag have profound consequences on circadian and metabolic events in the body. Animals that are forced to eat during their resting period show increased body mass and altered expression of clock and metabolic genes.[medical citation needed] In humans, shift-work that favors irregular eating times is associated with altered insulin sensitivity and higher body mass. Shift-work also leads to increased metabolic risks for cardio-metabolic syndrome, hypertension, inflammation.

Question: How does irregular eating during shift-work effect insulin?
Answer: insulin sensitivity
Circadian_rhythm

It is now known that the molecular circadian clock can function within a single cell; i.e., it is cell-autonomous. This was shown by Gene Block in isolated mollusk BRNs.[clarification needed] At the same time, different cells may communicate with each other resulting in a synchronised output of electrical signaling. These may interface with endocrine glands of the brain to result in periodic release of hormones. The receptors for these hormones may be located far across the body and synchronise the peripheral clocks of various organs. Thus, the information of the time of the day as relayed by the eyes travels to the clock in the brain, and, through that, clocks in the rest of the body may be synchronised. This is how the timing of, for example, sleep/wake, body temperature, thirst, and appetite are coordinately controlled by the biological clock.[citation needed]

Question: By functioning within a single, what is the system?
Answer: cell-autonomous
Circadian_rhythm

Shift-work or chronic jet-lag have profound consequences on circadian and metabolic events in the body. Animals that are forced to eat during their resting period show increased body mass and altered expression of clock and metabolic genes.[medical citation needed] In humans, shift-work that favors irregular eating times is associated with altered insulin sensitivity and higher body mass. Shift-work also leads to increased metabolic risks for cardio-metabolic syndrome, hypertension, inflammation.

Question: Besides insulin sensitivity, what other effect does shift-work have on the body?
Answer: higher body mass
Circadian_rhythm

It is now known that the molecular circadian clock can function within a single cell; i.e., it is cell-autonomous. This was shown by Gene Block in isolated mollusk BRNs.[clarification needed] At the same time, different cells may communicate with each other resulting in a synchronised output of electrical signaling. These may interface with endocrine glands of the brain to result in periodic release of hormones. The receptors for these hormones may be located far across the body and synchronise the peripheral clocks of various organs. Thus, the information of the time of the day as relayed by the eyes travels to the clock in the brain, and, through that, clocks in the rest of the body may be synchronised. This is how the timing of, for example, sleep/wake, body temperature, thirst, and appetite are coordinately controlled by the biological clock.[citation needed]

Question: What section of the brain periodically releases hormones?
Answer: endocrine glands