Input: Task: corroborate the claim using the given text. Claim: Circadian rhythms are regulated by light-sensitive proteins. [SEP] Text: Humans may be an exception [16]. Much progress has been made in understanding the mechanisms of mammalian photoperiodism. The light stimulus is probably transmitted from retinal neurons containing the photopigment melanopsin and supplying the axons of the retino-hypothalamic tract [17 - 20], which synapse within the suprachiasmatic nucleus (SCN), releasing neurotransmitters PACAP, glutamate, and perhaps acetylcholine [21]. Accessory pathways to the SCN may be involved, including pathways from the serotonin-releasing cells of the midbrain and the intergeniculate leaflet cells releasing NPY and GABA. SCN cell-surface receptors regulate the transcription of circadian clock genes through complex pathways [20,22]. The SCN appears to be a crucial center of photoperiodic control [23]. The timing of dawn and dusk influences SCN functional circadian organization, apparently through differential entrainment effects on morning and evening circadian oscillator components [24 - 26]. It is possible that separate evening and morning components are represented in the molecular circadian clock, e. g. , by PER1, PER2, and the cryptochromes, the circadian phase relationships of which, somehow mediate photoperiodism [27 - 30]. Thus, the timing of light exposure may influence the dynamics of the SCN molecular circadian clock. An important output of the SCN controls the nocturnal release of melatonin from the pineal. The secretion of melatonin is longer in long nights (short days), but may be abbreviated by brief light exposures during the night [6]. There is much evidence that the pineal and melatonin are necessary for the inhibition of gonadal function produced by short days. It appears that melatonin effects on hypothalamic synthesis of active T3 and reverse T3 may mediate some of these responses [31,32]. Regulation of LH and FSH is responsive to the circadian timing of light, to the absolute photoperiod, and also to the history of change in photoperiod [4,33]. Pituitary release of LH is largely governed by the frequency of pulsatile releases of gonadotropin releasing hormone (GnRH) into the portal circulation [34]. Part of the response involves sensitivity to negative feedback of gonadal hormones (such as estrogen) upon GnRH cells [35]. There is considerable interspecies variation in the anatomy and connections of GnRH cells. [SEP] Justify:

Output: The text corroborates the claim by discussing how light influences the suprachiasmatic nucleus (SCN), which plays a crucial role in regulating circadian rhythms. It mentions that the light stimulus is transmitted through retinal neurons containing the photopigment melanopsin, indicating that light-sensitive proteins are involved in the circadian regulation mechanisms described.


Input: Task: pass the claim using the given text. Claim: Some scientists believe nanomedicine could eventually allow for treatments that reverse aging or repair the body from within, extending human lifespan. Nanomedicine will soon allow humans to cure all diseases by sending tiny robots into the body to repair cells and eliminate pathogens. [SEP] Text: Many details in the structure of the nucleus, mitochondria, ER, and Golgi are visible. Of particular interest is the large cup-shaped chloroplast and the associated light-sensing eyespot and the ‘pyrenoid,’ a Rubisco-rich structure involved in the first major step of carbon fixation. All these structures are clearly distinguishable; their overall organization and interplay, in various functional conditions and in light-sensitive mutants, would provide new light on mechanisms of photosynthesis. C. reinhardtii flagella have also been extensively studied to understand cell motility. Zooming into the flagellar base (see inset Figure 6b and Videos 6 and 7), the nine-fold doublet microtubule structure becomes clearly visible, and details of the mature basal body pair and two probasal bodies are revealed. The latter form during basal body replication, at a very early stage of cell division in C. reinhardtii. After cytokinesis, the daughter cell will contain one mature basal body and one newly-formed one from which the flagella pair will grow (Silflow and Lefebvre, 2001; Preble et al. , 2000). Our imaging of this stage illustrates how recording a large data set that includes a population of cells allows the researcher to capture a variety of details through the cell cycle, as well as being more statistically meaningful than a single tomogram of a thin section of a single cell could ever be. Video 6 Download asset This video cannot be played in place because your browser does support HTML5 video. You may still download the video for offline viewing. Download as MPEG-4 Download as WebM Download as Chlamydomonas reinhardtii. Video 7 Download asset This video cannot be played in place because your browser does support HTML5 video. You may still download the video for offline viewing. Download as MPEG-4 Download as WebM Download as structure of a Chlamydomonas reinhardtii. Video 8 Download asset This video cannot be played in place because your browser does support HTML5 video. You may still download the video for offline viewing. Download as MPEG-4 Download as WebM Download as of volume stitch test in Drosophila protocerebral bridge region between hot knife sections #26 and #27. The wealth of structural data yielded by this approach merits the application of data mining tools. [SEP] Justify:

Output: The text is irrelevant to the claim as it focuses on the structural analysis of cellular components in Chlamydomonas reinhardtii and cell motility, without mentioning nanomedicine, aging, or treatments for diseases. Therefore, it does not support or contrast the claim regarding nanomedicine and its potential effects on human lifespan.


Input: Task: pass the claim using the given text. Claim: Army ants are known for their aggressive foraging behavior and colony movement. [SEP] Text: The general linear model was used to determine whether replicate type (solvent control or dance compounds) and colony identity (colony 1 or colony 2) were significant factors with respect to the first two variables (Number of Visits and Number of Visitors). The differences used in the general linear model are expressed as percent changes in Figure 2a, b for ease of comparison. Because the data for the third variable (Number of per Bee) were self-paired, a repeated measures ANOVA was used to determine the effect of replicate type and colony identity. The repeated measures ANOVA used as subjects the 76 individual bees which visited during both solvent control and dance compound replicates. In cases where an individual bee participated in more than one replicate of either type, we calculated the average difference between visits before and after exposure and used this average in the T test. All three variables were normally distributed with equal variances between both factors. 3 Results3. 1 Experiment 1: number of bee departures from hiveThe average number of departures from the hive following substance exposure depended on whether waggle-dance compounds or solvent was introduced (Figure 1a). The time course of this effect can be divided into three distinct phases: before substance exposure (minutes 1–9), immediately following substance exposure (minutes 11–19), and the second half of the experiment (minutes 21–39). Before substance exposure, there was no difference in departures between waggle-dance compound and control exposures (two sample T test of average number of departures between minutes 1 and 9—T value = 1. 47, P value = 0. 153, df = 27). Immediately following substance exposure, there was a momentary decrease in the number of departures, which was more quickly recovered from during waggle-dance compound than control replicates (Figure 1a, minute 13), though the overall trend for this period of the experiment did not significantly favor waggle-dance over control exposures (two sample T test, minutes 13–19—T value = −1. 74, P value = 0. 094, df = 27; minute 11 removed from analysis to avoid artifacts of the disturbance resulting from introduction of the compounds into the hive). [SEP] Justify:

Output: The text is irrelevant to the claim regarding army ants, as it discusses a study related to bee behavior and experimental methods involving substances, without any reference or connection to army ants or their foraging behavior.


Input: Task: corroborate the claim using the given text. Claim: Circadian rhythms are regulated by light-sensitive proteins. [SEP] Text: In a small study of 11 healthy young men, our laboratory found that 1000 lux bright light from 0500-0600 in the morning for 5 mornings could increase daily LH production as much as 65% [54]. This dramatic augmentation of LH production by bright light needed replication. It also raised many additional questions: What would happen with light treatment at other times of day? What would happen with longer durations of daily treatment? What would happen after several weeks of treatment? Will similar responses occur in older men who may be more in need of LH-testosterone augmentation? Would similar responses occur in women, in whom there is preliminary evidence that light may augment LH, FSH, and ovulation [55]? Would the effect in women depend upon menstrual cycle phase or upon menopause? To seek data relevant to these questions, we assayed LH and FSH in samples from three human studies undertaken for other goals. 1, PRseries of experiments were performed to examine light circadian phase-response curves (PRCs), contrasting adult women and men of young and older ages [56]. Baseline circadian phase was assessed by monitoring subjects for 30-48 hours in the laboratory while they underwent an ultra-short 90-min sleep-wake cycle, consisting of a 30 min. lights-out-sleep period followed by a 60 min. lights-on-wake interval in 50 lux. Urine samples collected by the participants were frozen every 90 min. (2 ml) for later assays, to measure urinary aMT6s (6-sulfatoxymelatonin), the primary metabolite of melatonin. After aMT6s was assayed, the refrozen samples were subsequently rethawed for urinary LH assays. Using stratified randomization, subjects were assigned to receive 3000 lux light treatment for 3 hours on each of 3 consecutive days at one of 8 times of day, while continuing the 90-min ultra-short sleep-wake cycle. Because of variability in baseline circadian phase adjustment, light treatments were effectively administered randomly throughout the 360-degree circadian cycle. Then a 30-hour follow-up assessment was made with further urine collections every 90 minutes. LH was assayed in rethawed baseline and follow-up samples with the DSL-10-460 ActiveR LH Elisa, an enzymatically amplified "one-step" sandwich-type immunoassay (Laboratories, Inc. , Webster, TX. [SEP] Justify:

Output: The text supports the claim by discussing various experiments that assess the influence of light on hormonal production, particularly focusing on LH and FSH. It highlights how light exposure at specific times can alter daily hormone levels, indicating that light plays a significant role in regulating biological rhythms, which are part of the broader concept of circadian rhythms.


Input: Task: pass the claim using the given text. Claim: Some scientists believe nanomedicine could eventually allow for treatments that reverse aging or repair the body from within, extending human lifespan. Nanomedicine will soon allow humans to cure all diseases by sending tiny robots into the body to repair cells and eliminate pathogens. [SEP] Text: a detailed protocol Fault-tolerant protected facilities with layers of backups were implemented on all utilities to provide uninterrupted and stable power, cooling water, compressed air, room temperature, air handling, etc. These back-up utilities were further tuned so that any transition would not produce a damaging fluctuation. For example, switching from a failed main air handler to an auxiliary unit will produce a transient in room temperature of <0. 5°C. Although costly, these facility upgrades are the foundation of stable long-term operation. A second layer of protection is achieved by monitoring environmental parameters like room temperature, so that the system can be paused quickly in the event of an anomalous excursion. In-line image auto-optimization Request a detailed protocol During extended image acquisition, SEM focus, stigmation, and aperture alignment must be optimized periodically to correct drift of various components. Traditionally, these adjustments are performed manually off-line, causing interrupts to the continuous milling and imaging process. Besides increasing overhead, this approach introduces further errors by disturbing the steady state of milling and imaging cycles. The in-line optimization procedure described below effectively overcomes the deficiencies in conventional methods. Recognizing these problems, a functionally similar approach was previously described (Binding et al. , 2013). In our approach, a ‘focus index’ (FI) based on the strength of the highest spatial frequency components is calculated to assess the focus quality for each acquired image. FI=[∑i=0n−1(I∗S1−I∗S2)2]/n, where the original 2D image I is smoothed by 2D Gaussian functions of a shorter (S1) and a longer (S2) length scale that straddles the resolution limit. Typical standard deviation values for Gaussian distributions S1 and S2 are 1 and 4 pixels, respectively. The total root mean square pixel-to-pixel difference between those two smoothed images averaged over the total number of pixels (n) is assigned to the original image as a focus index, where i is the index of each pixel. A higher focus index indicates more high spatial frequency content, and therefore a better-focused image. The focus index value depends upon the highest spatial frequency features of the sample, the actual focus of the electron beam spot, and the signal intensity. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses protocols for maintaining stable operational facilities and optimizing imaging processes, with no mention of nanomedicine, aging, or medical treatments. Therefore, it does not support or contrast the claim in any way.


Input: Task: pass the claim using the given text. Claim: Army ants are known for their aggressive foraging behavior and colony movement. [SEP] Text: During the last half of the experiment, there was little change in the average number of departures, but there were significantly more departures during waggle-dance compound exposures than during control exposures (two sample T test, minutes 21–39—T value = −2. 11, P value = 0. 044, df = 27). Figure 1Mean normalized number of bee departures from the hive and arrivals at a feeder station for two treatments over the course of 29 40-min trials. At minute 10, either the waggle-dance compound mixture or the mixture’s solvent, ether, was introduced into the hive. Error bars indicate one standard error. a Bee departures from the hive. Counts for each replicate were normalized to the average number of bees departing between minutes 1 and 9. b Bee arrivals at feeder station. Counts for each replicate were normalized to the number of bees arriving at minute 9. Full size image 3. 2 Experiment 1: number of bee arrivals at feederThe average number of arrivals at the feeder following substance exposure depended greatly upon whether waggle-dance compounds or solvent was introduced (Figure 1b). The time course of this effect can be divided into the same three phases as above: before substance introduction (minutes 1–9), immediately following substance introduction (minutes 11–19), and the second half of the experiment (minutes 21–39). Before substance introduction, there was again no difference in arrivals between waggle-dance compound and control exposures (two sample T test of the average number of arrivals between minutes 1 and 9—T value = −0. 52, P value = 0. 610, df = 27). Immediately following substance introduction at minute 10, feeder arrivals remained unchanged (Figure 1b, minute 11), but then increased significantly more quickly during waggle-dance compound than during control exposures (two sample T test, minutes 11 to 19—T value = −3. 80, P value ≤ 0. 001, df = 27). During the last half of the experiment, feeder arrivals increased slowly for both types of substance introductions, but by this point arrivals during waggle-dance compound exposures outnumbered those during control exposures by nearly a factor of two (two sample T test, minutes 21 to 39—T value = −3. 61, P value ≤ 0. 001, df = 27). [SEP] Justify:

Output: The text is irrelevant to the claim about army ants as it specifically discusses the behaviors of bees in relation to the waggle dance and substance exposure. There is no mention or implication of army ants or their foraging behavior.


Input: Task: corroborate the claim using the given text. Claim: Circadian rhythms are regulated by light-sensitive proteins. [SEP] Text: In pilot studies, adult women with PMDD exhibited an abnormal phase shift to early morning light, suggesting some disorder of the circadian system. This study contrasted the phase-shifting responses to early-night and early-morning bright light in women with DSM-with the responses of normal controls. The age range was 20-45 years. First, the women underwent extensive diagnostic evaluations and preliminary Center admissions to determine their dim light melatonin onset (DLMO) in the follicular and luteal menstrual phases. DLMO is that time of evening when the onset of melatonin secretion occurs, an excellent circadian timing marker, which is used to insure that each subject can be exposed to bright light at standardized phases of the circadian rhythm, even though circadian rhythms differ in phase-timing from one subject to another. Then, in separate months, each woman underwent two Center admissions to test bright light responses, once in the follicular menstrual phase (8 ± 2 days after the onset of menses) and once in the luteal menstrual phase (2-4 days before the date of next expected menses, over a month later). Each of these Center admissions included a baseline urine-sampling night, a bright light treatment night, and an additional follow-up night for urine sampling to determine hormonal results of light treatment. Apart from the treatment, subjects were maintained in dim light or darkness. Fractional urine specimens were measured and sampled both during the baseline (6 PM to 11 AM) and during the follow-up (6 PM to 11 AM). Part of each group (PMDD and controls) received bright 6000 lux light for 3 hours early in the night, starting 3 hours after the DLMO (approximately 24:00-0300). Also, the other half of each group (PMDD and controls) received similar bright light early in the morning starting 8 hours after the DLMO (approximately 05:00-08:00). Blood and urine samples were assayed for melatonin, to determine the phase of the circadian system, which is indicated well by the nocturnal rise and morning fall of melatonin. The bright light administered starting 3 hours after the DLMO was expected to be phase-delaying. The bright light starting 8 hours after the DLMO was expected to be phase-advancing in controls, but possibly not among PMDD patients. Urinary LH and FSH data were analyzed in SPSS 12. [SEP] Justify:

Output: The text corroborates the claim by discussing how bright light affects circadian rhythms, as indicated by the phase-delaying and phase-advancing responses after exposure to light at different times relative to the dim light melatonin onset (DLMO). The connection between light treatment and hormonal results, such as melatonin levels, exemplifies the role of light-sensitive proteins in the regulation of circadian rhythms.


Input: Task: pass the claim using the given text. Claim: Some scientists believe nanomedicine could eventually allow for treatments that reverse aging or repair the body from within, extending human lifespan. Nanomedicine will soon allow humans to cure all diseases by sending tiny robots into the body to repair cells and eliminate pathogens. [SEP] Text: Effect of landing energy on signal and contrast Request a detailed protocol The dependence of the fraction of backscattered electrons on the energy of the primary beam is summarized in the table of Figure 15a for both modeled and measured values, for the three reference samples and for a modeled lipid-osmium sample. The parameter of interest is the staining contrast for a known percentage of highly scattering heavy metal. This is tabulated for contrast between epoxy to Pt[(C6H5)3P]4 for both modeled and measured values, and also between lipid membrane with 0 and 1 molarity of osmium stain. In all cases, the best contrast is at the highest energies of 1. 2 keV, and drops over a factor of 2 with lower landing energies of about 600 eV, reflecting the increased relative backscattering cross-section of carbon vs. osmium at low energies, Figure 15b. For typical samples with ~100 low Z (mainly hydrogen, carbon and oxygen) atoms for every high Z osmium atom, this explains why contrast vanishes below 600 eV, when the weighted contrast ratio falls to unity. Effect of landing energy on the point spread function Request a detailed protocol The landing energy determines the resolution, since higher energy electrons scatter further and explore larger volumes of the sample before they backscatter. This can be quantified by the model in Figure 17a,b, which shows such a distribution of scattering locations for primary electron energies of 0. 8 and 1. 2 keV in a sample not stained with osmium, and approximates the Function (PSF) for signal. The spatial distribution difference between stained and unstained samples is relatively small, Figure 17a,c. These figures of scattering location can be misleading in estimating the contribution to PSF arising from the distribution of scattering locations. Any differential contrast will also be heavily weighted by the higher energy scattering events, which are concentrated even more to the center in the red (highest energy backscattered electrons) region. Figure 17 Download asset Open asset Effect of landing energy on the point spread function based on simulations. (a,b,c). simulation of backscattered electrons at different landing energies. Lower landing energy generates smaller sampling volume (implying better resolution), but with reduced contrast and SNR, as discussed in (d,e). [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses the effects of landing energy on signal and contrast regarding backscattered electrons, focusing on technical details in a scientific context. There is no mention of nanomedicine, aging, lifespan, or disease treatment, thus failing to relate to the claim.


Input: Task: pass the claim using the given text. Claim: Army ants are known for their aggressive foraging behavior and colony movement. [SEP] Text: This difference between waggle-dance compounds and control exposures remained through to the end of the experiment, 30 min after substance introduction (Figure 1b, minute 39). 3. 3 Experiment 2: number of visits to feederThe number of visits to the empty feeder dish was significantly greater following exposure to the waggle-dance compounds compared to the solvent control (general linear model, F = 14. 69, P ≤ 0. 001, df = 1,19), while colony was not a significant factor affecting the number of visits (F = 0. 02, P = 0. 895, df = 1,19). Data from the two colonies are therefore pooled into one data set, and this is displayed as percentage changes in Figure 2a. Figure 2Comparison of changes in foraging behavior following exposure to waggle-dance compounds and a solvent control. Change is the difference between the bees’ behavior during the 30 min prior to substance introduction and the 30 min following substance introduction. Error bars indicate one standard error. a The number of total visits to the feeder station (n is the number of replicates of each type). b The number of marked unique individual bees visiting the feeder (n is the number of replicates of each type). c The number of feeder visits per marked unique individual bee (n is the number of unique individual bees that participated in at least one of each type of replicate). Full size image 3. 4 Experiment 2: number of visitors to feederThe number of unique visitors to the empty feeder was significantly greater following exposure to the waggle-dance compounds compared to the solvent control (general linear model, F = 6. 42, P = 0. 020, df = 1,19), while colony was not a significant factor affecting the number of visits (F = 0. 28, P = 0. 606, df = 1,19). Data from the two colonies are therefore pooled into one data set, and this is displayed as percentage changes in Figure 2b. 3. 5 Experiment 2: number of feeder visits per beeThe number of feeder visits per bee was significantly greater following exposure to the waggle-dance compounds compared to the solvent control (repeated measures = 14. 28, P = 0. 0003, df = 1,75) while colony was not a significant factor (F = 2. 58, P = 0. [SEP] Justify:

Output: The text is irrelevant to the claim about army ants and their behavior. It discusses the foraging behavior of bees in relation to waggle-dance compounds and provides statistical analysis of feeder visits, which does not relate to army ants' aggressive foraging or colony movement behaviors.


Input: Task: corroborate the claim using the given text. Claim: Circadian rhythms are regulated by light-sensitive proteins. [SEP] Text: Therefore, we cannot exclude that the increases in LH were due to various placebo and nonspecific experimental effects, as well as the passage of time. For example, suggestion and hope often produce positive placebo responses in a wide variety of trials. If a clinical trial commenced with subjects in a heightened state of anxiety or depression, spontaneous remission might lead to endocrine changes such as enhancements of LH and FSH production. In a separate study, our group demonstrated a significant increase in FSH after early morning stimulations with bright green light, as compared to dim light placebo, but this effect was not very robust [65]. We are left with tantalizingly suggestive evidence that bright light stimulates LH and FSH in human subjects, but there is a need for much more convincing evidence. These studies had a number of limitations. In the first study, the light stimuli were administered for only 3 days at a level of only 3000 lux, whereas, a longer duration of brighter stimulation might have produced a greater gonadotropic response. In the second study, though 10,000 lux bright light stimuli were randomized for 4 weeks, we were uncertain of the compliance of these very depressed and elderly study participants, particularly since there was only weak evidence for circadian phase-shifting effect in the experimental groups and no persuasive evidence of a favorable mood effect. Only data from the morning light treatments were analyzed because of lack of evidence that the evening treatments had any physiologic or mood effects. In the third study, the numbers of subjects were extremely small, and the light stimulation was given only on a single day, which may have been insufficient to produce a large effect. A light stimulus intended to produce a phase shift may not be optimal for stimulating LH and FSH. Though we were able to obtain data from these studies which had been organized for other goals, the numbers of participants yielding usable data was unexpectedly small in the second and third studies. There is also concern that the several years that the urine samples were frozen, and the freezing and thawing processes, might have introduced inaccuracy into the assays. studies organized specifically to measure bright light effects on gonadotropins may be needed to verify the potential of bright light regulation for the reproductive endocrine system. Longer durations of exposure should be tested. Competing interests The authors declare that they have no competing interests. Authors' contributions DFK participated in design, acquisition of data, interpretation and statistics, and manuscript preparation. [SEP] Justify:

Output: The text corroborates the claim by presenting evidence from studies that suggest bright light can stimulate hormonal changes, specifically LH and FSH production, which are influenced by circadian rhythms. The mention of 'bright light stimulates LH and FSH in human subjects' indicates a likely connection between light exposure, which is a component of circadian rhythms, and hormonal regulation.


Input: Task: pass the claim using the given text. Claim: Some scientists believe nanomedicine could eventually allow for treatments that reverse aging or repair the body from within, extending human lifespan. Nanomedicine will soon allow humans to cure all diseases by sending tiny robots into the body to repair cells and eliminate pathogens. [SEP] Text: A model for ribosome biogenesis that includes DNA replication, transcription, translation, and ribosome assembly in slow growing E. coli has already been developed (Earnest et al. , 2015; Earnest et al. , 2016). As its components have on average 50% sequence identity to those genetic information processing genes in JCVI-syn3A, this model is assumed to be applicable to JCVI-syn3A as well. Hence, the next important step in modeling JCVI-syn3A is the reconstruction of its metabolic network. The metabolic reconstruction presented here is based on the curated genome annotation, extensive experimental information from the literature on M. mycoides capri and other mycoplasma species, and accompanying transposon insertion and proteomics data. Our model features 338 reactions organized in nine subsystems (see Supplementary file 1B), involving 304 metabolites, catalyzed by gene products of 155 genes, thus covering a third of the genes of JCVI-syn3A. The reconstruction process enabled us to suggest several annotation refinements and updates, and yielded a metabolic network that is fairly complete. Together with the reconstructed biomass composition of JCVI-syn3A and estimates of its reaction flux constraints and energy expenses, the reconstructed metabolic network was cast into a flux-balance analysis (FBA) model (Orth et al. , 2010). FBA yields the set of steady-state reaction fluxes through a metabolic network that maximize a pre-defined objective function, for example production of cellular biomass. The solution space of possible fluxes is constrained not only by the steady-state assumption, but also by specific flux limits accounting for maximal uptake/secretion rates or cellular energy expenses. If these flux limits are not known, the network stochiometry predicts the biomass yield achieved by the cell, that is gram biomass produced/gram carbon source taken up (or equivalently biomass production rate/carbon substrate uptake rate). If flux constraints, in particular substrate uptake rates are known or can be assumed, the yield as growth rate per uptake rate can be converted to an absolute growth rate. While measurements to derive such flux constraints are not available yet for JCVI-syn3A, some measurements are available from other mycoplasmas and bacteria that have the same high-affinity glucose transporter (PtsG) found in JCVI-syn3A. Using the glucose uptake rate measured in M. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses the development of a model for ribosome biogenesis and metabolic network reconstruction in bacteria, specifically focusing on JCVI-syn3A. There is no mention of nanomedicine, aging, treatments, or any related concepts that would support or contrast the claim.


Input: Task: pass the claim using the given text. Claim: Army ants are known for their aggressive foraging behavior and colony movement. [SEP] Text: 1107, df = 1,75). The mean difference for all 76 bees (from both colonies) between the number of visits before and after substance introduction for solvent control exposures was −0. 75, and for dance-compound exposures was −0. 07. These means are displayed in Figure 2c. 3. 6 Experiment 2: number of bee departures from hiveThe results concerning the number of bee departures from the hive do not directly relate to the hypothesis under investigation in the second part of this study, so they are only summarized here. This summary is included to verify the effect of the dance compounds on hive departures observed in a single colony in Section 2. 1. Two approaches were taken to assess the effect of the dance compounds on the number of departures from the hive. First, the number of bee departures from ten replicates using colony 1 and 12 replicates using colony 2 were pooled. For each replicate, we tallied the number of departures for minutes 30–40 (i. e. , the 10 min following substance introduction) and the number of departures for minutes 41–60 (i. e. , through to the end of the experiment). The percent change was then calculated by comparing these two time intervals to the number of departures during minutes 0–29 (i. e. , before substance introduction). The mean percent changes for solvent control replicates was −43% and −22% for minutes 30–40 and minutes 41–60, respectively, while the mean percent changes for waggle-dance compound replicates were −30% and +12% for minutes 30–40 and minutes 41–60, respectively. Second, a general linear model using changes in departures and incorporating replicate type (waggle-dance compound or control), time interval (minutes 30–40 or minutes 41–60), and colony (1 or 2) showed both replicate type and time interval as highly significant factors while colony was not (F = 10. 54, P = 0. 002 for replicate type; F = 21. 7, P ≤ 0. 001 for time interval; and F = 0. 01, P = 0. 941 for colony; all df = 1,40). 4 DiscussionThe results from the two experiments presented here suggest two major conclusions. First, the hydrocarbons emitted by waggle-dancing bees affect the behavior of bees by stimulating foraging activity. [SEP] Justify:

Output: The text is irrelevant to the claim regarding army ants' foraging behavior and colony movement. Instead, it discusses bee behavior related to substance introduction and dance compounds, which does not relate to army ants or their known behaviors.


Input: Task: corroborate the claim using the given text. Claim: Circadian rhythms are regulated by light-sensitive proteins. [SEP] Text: DOI: [PubMed] Hattar, S; Liao, H-W; Takao, M; Berson, DM; Yau, K-WMelanopsin-containing retinal ganglion cells: Architecture, projections, and intrinsic photosensitivity Science 295: 1065–1070, DOI: [PubMed] Berson, DM; Dunn, FA; Takao, MPhototransduction by retinal ganglion cells that set the circadian clock Science 295: 1070–1074, DOI: [PubMed] Gillette, MU; Mitchell, JWSignaling in the suprachiasmatic nucleus: selectively responsive and integrative Res 309: 99–107, DOI: [PubMed] Reppert, SM; Weaver, DRCoordination of circadian timing in mammals Nature 418: 935–941, DOI: [PubMed] Schwartz, WJ; de la Iglesia, HO; Zlomanczuk, P; within the mammalian brain: Photoperiodic orchestration through the suprachiasmatic nucleus J 16: 302–311, DOI: [PubMed] Jagota, A; de la Iglesia, HO; Schwartz, WJMorning and evening circadian oscillations in the suprachiasmatic nucleus in vitro 3: 372–376, DOI: [PubMed] vanderLeest, HT; Houben, T; Michel, S; Deboer, T; Albus, H; Vansteensel, MJ; Block, GD; Meijer, JHSeasonal encoding by the circadian pacemaker of the SCN 17: 468–473, DOI: [PubMed] Naito, E; Watanabe, T; Tei, H; Yoshimura, T; Ebihara, SReorganization of the suprachiasmatic nucleus coding for day length J 23: 140–149, DOI: [PubMed] Daan, S; Albrecht, U; Horst, GTJ van der; Illnerova, H; Roenneberg, T; Wehr, TA; Schwartz, WJAssembling a clock for all seasons: Are there M and E oscillators in the genes? [SEP] Justify:

Output: The text corroborates the claim by discussing melanopsin-containing retinal ganglion cells and their role in phototransduction, which is directly related to how circadian rhythms are influenced by light-sensitive proteins. The references to studies about the architecture and projections of these cells suggest they are critical in regulating circadian rhythms through their intrinsic photosensitivity.


Input: Task: pass the claim using the given text. Claim: Some scientists believe nanomedicine could eventually allow for treatments that reverse aging or repair the body from within, extending human lifespan. Nanomedicine will soon allow humans to cure all diseases by sending tiny robots into the body to repair cells and eliminate pathogens. [SEP] Text: ACP carries a 4′-phosphopantetheine moiety in its holo form, and including the holoenzyme in the biomass equation enforces flux through the corresponding prosthetic group attachment reaction. dUTPase is included for technical reasons discussed in Section 'Nucleotide metabolism'. We use cellular abundances of 138 (ACP) and 10 (dUTPase), derived from the proteomics experiments. The resulting mass fractions are then subtracted from the total protein mass fraction. Lipids and capsule Based on the experimental lipid composition of M. mycoides capri serovar capri PG3 (Archer, 1975) and M. mycoides capri LC Y (Plackett, 1967a), the model includes the phospholipids phosphatidylglycerol and cardiolipin, the glycolipid monogalactosyl-diacylglycerol (Gal-DAG), cholesterol, diacylglycerol and free fatty acids. For fatty acids, palmitic acid (C16:0) and oleic acid (C18:1 cis-9) are considered to be the two most important representatives, and an average ‘fatty acid’ with a molecular weight averaged between palmitate and oleate is used in all lipid species. In addition, a galactan polysaccharide capsule is included in the biomass. M. mycoides capri LC GM12 (the strain from which JCVI-syn3A is derived) is known to produce a galactan polysaccharide (specifically, poly-β−1→6-galactofuranose) (Schieck et al. , 2016); while it is not yet experimentally known whether the minimal cell still produces this galactan, genetic features suggest it does. As other M. mycoides capri LC strains form a polysaccharide capsule but secrete negligible amounts of polysaccharide (Bertin et al. , 2015), the JCVI-syn3A galactan is assumed to form a capsule as well and is included as polygalactosyl-diacylglycerol (lipogalactan). [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses the technical details of lipids and polysaccharide capsules in specific bacteria, without any mention of nanomedicine, aging, or disease treatment. Therefore, it does not support, contrast, or provide insights regarding the claim about nanomedicine.


Input: Task: pass the claim using the given text. Claim: Army ants are known for their aggressive foraging behavior and colony movement. [SEP] Text: This was shown in the first experiment by the immediate rise and sustained high level of bee departures from the hive (Figure 1a) and bee arrivals at the feeder (Figure 1b) following exposure to a blend of three waggle-dance compounds. Some of this rise in foraging activity following exposure was no doubt due to natural waggle-dance recruitment to the sucrose solution available at the feeder, but comparison to control exposures shows that bee departures increased over control levels by as much as 46% and bee arrivals increased by as much as 106%. These increases in foraging activity over control levels must be due to the effect of the waggle-dance compounds. The difference in arrivals between dance compound and solvent control treatments was highly significant for the single colony tested in Section 2. 1. Similar results were obtained in Section 2. 2 for two additional colonies of a different subspecies during a different year (Figure 2a; shown are comparisons of before and after substance introduction, not the timescale of difference as in Figure 1). The observed responses of bees to the waggle-dance compounds are therefore not likely idiomatic, suggesting that the waggle-dance compounds play an important role in organizing foraging tasks within honey bee colonies. The second major conclusion to be drawn from the experiments described in this study is that the hydrocarbons emitted by waggle-dancing bees increase foraging activity at least partly by means of reactivation, i. e. , by stimulating foragers with knowledge of a food site to depart the hive and fly to the location of the food. Following exposure to the waggle-dance compounds, foragers visited an empty feeder in greater numbers (Figure 2b) and more often (Figure 2c) than following exposure to the solvent control. Because the feeder was empty, these increases over control levels cannot possibly be explained by enhanced recruitment to the feeder, but must be due to stimulation of foragers with experience foraging at the feeder. These experienced foragers are not only reactivated by the dance compounds but also stimulated to forage at a faster rate than the bees visiting the feeder during control replicates, which were either inspectors spontaneously checking known food sources or experienced foragers reactivated by a stimulus other than the introduced dance compounds. This increase in foraging rate (i. e. [SEP] Justify:

Output: The text is irrelevant to the claim about army ants' aggressive foraging behavior and colony movement, as it discusses honey bee foraging behavior and the effects of waggle-dance compounds. There is no mention or connection to army ants or their behavior in the provided text.


Input: Task: corroborate the claim using the given text. Claim: Circadian rhythms are regulated by light-sensitive proteins. [SEP] Text: Journal of Circadian RhythmsStart SubmissionBecome a ReviewerReading: Phase delaying the human circadian clock with a single light pulse and moderate delay of the sleep/dark episode: no influence of iris colorDownloadXML (US English)PDF (US English)Alt. DisplayShareShareResearch 1. 3 ± 0. 6 h, with a maximum delay of ~2 hours, and was similar for subjects with blue and brown irises. There were no significant correlations between any of the iris color variables and the magnitude of the phase delay. Conclusion: A single 2-hour bright light pulse combined with a moderate delay of the sleep/dark episode delayed the circadian clock an average of ~1. 5 hours. There was no evidence that iris color influenced the magnitude of the phase shift. Future studies are needed to replicate our findings that iris color does not impact the magnitude of light-induced circadian phase shifts, and that the previously reported differences may be due to race. Year: 2009Page/10. 1186/1740-3391-7-8Submitted on Jun 3, 2009Accepted on Jul 17, 2009Published on Jul 17, 20094. 0 exposure can shift the human circadian clock in a phase-dependent manner. Light exposure during the evening hours or early in the habitual sleep episode produces phase delays, while light exposure late in the habitual sleep episode or morning hours produces phase advances [1 - 4]. The crossover point at which the phase shift in response to light exposure changes from delays to advances is estimated to occur near the body temperature minimum (Tmin) [1]. The rate at which the circadian clock can be shifted with light exposure is dependent on the spectral composition of the light source [5 - 8], the light level [9,10], and the duration and pattern of the light pulse(s) [11 - 14]. As the converse of light exposure, the timing or duration of the sleep/dark episode can also phase shift the circadian clock [15 - 19]. Many studies have measured the phase delay produced by bright light exposure administered over successive days (e. g. [20 - 23]). Some studies have also administered phase delaying light pulses on a single day. Understanding how much a single pulse of light can delay the circadian clock is important because practical constraints in the real world may limit the ability of individuals to adhere to several consecutive days of light treatment. [SEP] Justify:

Output: The text corroborates the claim by discussing how light exposure can phase shift the human circadian clock, indicating that light plays a crucial role in regulating circadian rhythms. It highlights the effects of bright light pulses and notes the phase-dependent manner in which these exposures manage the timing of the circadian clock, supporting the idea that light-sensitive proteins are involved in this regulatory process.


Input: Task: pass the claim using the given text. Claim: Some scientists believe nanomedicine could eventually allow for treatments that reverse aging or repair the body from within, extending human lifespan.Nanomedicine will soon allow humans to cure all diseases by sending tiny robots into the body to repair cells and eliminate pathogens. [SEP] Text: The product DAG serves as the lipid moiety for the synthesis of lipogalactan (catalyzed by epsG/0113 and cps/0114, see Section 'Biomass composition and reaction') and Gal-DAG. Lacking further evidence, Gal-DAG is assumed to be formed by either of the two glycosyltransferases, cps/0114 and 0697. Possibly related to lipid metabolism, the existing annotation lists a putative choline/ethanolamine kinase (0906); however, as M. mycoides capri LC is experimentally known to not produce phosphatidylcholine (Plackett, 1967a), we assume that this kinase has some yet to be determined substrate and do not include it in the model. Macromolecules and amino acids Schematics of the macromolecular and amino acid reaction networks are provided in Figure 11 and Figure 12. The genome of JCVI-syn3A contains a putative oligopeptide ABC importer (Opp/Ami, oppB/0165 through oppA/0169). lactis, the Opp system has been found to import peptides of four to at least 35 amino acids with little dependence of uptake rates on peptide length or amino acid composition (Detmers et al. , 1998; Doeven et al. , 2004). For the sake of simplicity, peptides imported are assumed to be representative homotetrapeptides of all amino acids except cysteine, since cysteine contained in peptides cannot be easily utilized by mycoplasmas (Yus et al. , 2009). The model assumes that any of four peptidases (ietS/0133, 0305, 0444, and 0479) can split these peptides into individual amino acids. Figure 11 Download asset Open asset Macromolecule metabolism in JCVI-syn3A. Map components and labels as in Figure 5. The detailed (amino acid-specific) stoichiometry of the protein synthesis and degradation reactions can be found in Supplementary file 4. Protein synthesis reactions for the proteins explicitly included in the model (apo-ACP, dUTPase and PdhC) are analogous to the translation reaction shown and are therefore not included in the map. Figure 12 Download asset Open asset Amino acid metabolism in JCVI-syn3A. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses the synthesis of lipogalactan and details about peptides and amino acid metabolism in a specific strain of bacteria. It does not mention nanomedicine, aging, or treatments related to extending human lifespan, thus offering no corroboration or contrast to the claim.


Input: Task: pass the claim using the given text. Claim: Army ants are known for their aggressive foraging behavior and colony movement. [SEP] Text: , number of visits per bee over 30 min) was relative rather than absolute. The absolute change in foraging rate for 76 bees when exposed to the dance compounds was not different from zero (Figure 2c). However, when compared to the control treatment, which contained the same amount of the solvent, the waggle-dance compounds had a significant stimulating effect (P = 0. 001). The depressant effect of the solvent on foraging behavior, which is seen throughout the data presented here, appears to be working in opposition to the stimulating effect of the dance compounds. Temporary disruption of foraging is not a particularly surprising response to ether, but use of such a solvent was unavoidable given the nature of the waggle-dance compounds. The conclusions from the experiments described in this study imply that the hydrocarbons emitted by waggle-dancing bees are a semiochemical that functions in concert with the information contained in the waggle dance to speedily and efficiently direct foragers to exploit available food sources. While the waggle dance advertises profitable food locations, the compounds emitted by the dancers may advertise to a wider audience favorable foraging conditions. A close comparison might be drawn to the foraging pheromone of bumblebees, which is released by bumblebee foragers upon returning from a successful foraging trip (Dornhaus and Chittka 2001; Dornhaus et al. 2003; Granero et al. 2005) and appears to act as a general foraging activation signal, indicating favorable foraging conditions. This pheromone, a collection of terpenes (Granero et al. 2005), is not chemically related to the long-chain hydrocarbons produced by honey bee waggle dancers. Similarity in function may therefore indicate convergent evolution. Within a honey bee nest, foragers with current memories of profitable food sites would be an important task group receiving and responding to a signal indicating favorable foraging conditions. Stimulation of experienced foragers by the waggle-dance compounds might explain why previous studies have found that experienced foragers can become reactivated after following dances very briefly (<5 s) or not at all (Gil and Farina 2002; Biesmeijer and Seeley 2005). However, we do not yet know whether a forager needs to follow a dance to be stimulated by the waggle-dance compounds, so this connection remains tentative. [SEP] Justify:

Output: The text does not address the claim directly as it focuses on the foraging behavior of honey bees and their communication through waggle dances and semiochemicals. There are no mentions of army ants, their behaviors, or comparisons to other ant species, making it irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Circadian rhythms are regulated by light-sensitive proteins. [SEP] Text: Phase delays of up to one hour per day can be produced when a phase delaying light pulse is combined with awakening at the usual time the next morning [24 - 26]. However, holding wake time constant would likely constrain phase delays of the circadian clock because morning light exposure on the advance portion of the light PRC would oppose the delaying effect of the evening/nighttime light pulse. When a very long single light pulse is combined with 2 days of a large abrupt shift of the sleep episode, the circadian clock can be delayed as much as three hours [9,27,28]. Although these delays can be quite large, delaying the sleep episode that much is not practical for most individuals trying to phase shift their circadian rhythms at home. When a phase-delaying evening light pulse is used in the field, it may be most practical to combine it with a moderate delay of the sleep/dark episode (e. g. [29,30]). The first goal of this study was thus to measure the phase delay produced by a single 2-hour light pulse before bedtime combined with a moderate delay of the sleep episode. A number of studies have shown large individual differences in the magnitude of the phase shift produced within the same protocol (e. g. [8,12,24,31,32]). Factors that may contribute to these individual differences include light exposure history, iris color and/or race. Light history has been shown to influence light-induced melatonin suppression [33,34], and these findings have recently been extended to circadian phase shifting [32,35]. One study found that light-eyed subjects had earlier sleep times and more "morningness" on a chronotype questionnaire [36], which could suggest that light-eyed subjects are more sensitive to the phase-advancing effects of morning light exposure. Light-induced melatonin suppression has been reported to be greater for light-eyed Caucasian than dark-eyed Asian subjects [37]. In this latter study it could not be determined whether iris color, race, or both accounted for the group differences. Differences in intraocular straylight as a result of iris color could influence non-image-forming responses such as melatonin suppression and circadian phase shifts. Intraocular straylight (light scattering) is the name for the phenomenon in which the retina receives light at locations that do not optically correspond to the direction light is coming from, but that nonetheless could trigger phototransduction. [SEP] Justify:

Output: The text corroborates the claim by discussing how light exposure influences the circadian clock, specifically through mechanisms such as light-induced melatonin suppression and circadian phase shifts. It states that phase delays and shifts in circadian rhythms can be significantly affected by light pulses, indicating that light-sensitive proteins play a crucial role in regulating these rhythms.


Input: Task: pass the claim using the given text. Claim: Some scientists believe nanomedicine could eventually allow for treatments that reverse aging or repair the body from within, extending human lifespan. Nanomedicine will soon allow humans to cure all diseases by sending tiny robots into the body to repair cells and eliminate pathogens. [SEP] Text: An estimated 92,000 colonies were harvested from the plates in 20 ml of SP4 media (passage zero, P0) and a 45 µl sample was added to 45 ml SP4 media containing puromycin 2 µg/ml and grown for 24 hr (passage one, P1). A 45-µl sample of P1 culture was added to 45 ml of fresh SP4 media (P2) and grown for 48 hr. Two more passages (P3 and P4) were done. DNA preparations from each passage were done as described in Hutchison et al. (2016a), and DNA preparations were additionally purified by gel electrophoresis. library preparation kit was used for paired-end library construction (Illumina, San Diego, CA) by the manufacturer’s protocol with the following change. A forward primer 5′-designed by us and the reverse primer from the kit were used for the PCR amplification to achieve marker-specific sequencing (Wright et al. , 2017). To locate points of Tn5 insertion in the JCVI-syn3A genome, sequence reads were searched for the Tn5 19 bp terminus followed by an exact 30 bp match to genome sequence. The Tn5 to genome junction point identified the insertion location. ‘Duplicate insertions’ (i. e. insertions found in sequences repeated in the genome) were ignored in all further analyses since they could not be unequivocally assigned to a single gene. Tn5 insertions were displayed using CLC (). Classification of genes Request a detailed protocol To place genes into ‘essential’, ‘quasi-essential’, and ‘non-essential’ classifications, a simple statistical model of transposon insertion was used. It assumes that the positions of insertions within a gene are unbiased (Poisson distributed) and that the number of insertions in a particular gene is described by one of two possible distributions. The two distributions separate the genes into groups with few and many insertions. The probability to observe ni insertions for gene i, which has a sequence length of ℓi is (1) P(ni|ℓi)=ploekloℓi(kloℓi)nini! [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses methods related to DNA preparations and transposon insertions rather than any content related to nanomedicine, aging, or the use of tiny robots for healing. There is no information that supports, contrasts, or relates to the idea of nanomedicine's potential impact on lifespan or disease treatment.


Input: Task: pass the claim using the given text. Claim: Army ants are known for their aggressive foraging behavior and colony movement. [SEP] Text: Reception of the waggle-dance semiochemical may also explain why exposure of a non-foraging honey bee colony to the dance-floor odors of a foraging colony increases the number of foragers visiting an empty feeder (Thom and Dornhaus 2007), and why, in response to dancers indicating an unknown food source with an unfamiliar scent, most bees (82%) fly to previously visited food sites (Grüter et al. 2008). Floral food-source odors, which are known to reactivate experienced but inactive foragers in much the same way as the waggle-dance compounds (Reinhard et al. 2004), may be an alternative explanation for the former result (i. e. , Thom and Dornhaus 2007), but cannot explain the latter (i. e. , Grüter et al. 2008) because the food odor emanating from the dancer did not match the site with which the foragers were familiar. The discovery of the waggle-dance compounds’ role in the reactivation of nectar foragers also reinforces Grüter and Farina’s (2009) emphases regarding (a) the importance in honey bee foraging of private information about food sources, and (b) the clarification that the waggle-dance language is only one component of the multimodal, multicomponent waggle-dance signal and synonymous use of these terms should be avoided. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses the foraging behaviors of honey bees in relation to the waggle-dance and the effects of semiochemicals, without mentioning army ants or their behavior.


Input: Task: corroborate the claim using the given text. Claim: Circadian rhythms are regulated by light-sensitive proteins. [SEP] Text: Studies in which a single long duration bright light pulse (> 6 hours, up to ~10,000 lux) was paired with 2 days of a large delay (>8 hours) in the sleep/dark episode have reported phase delays of up to 3 hours [9,12,27,28]. Although a 3 hour phase delay from a single day of light treatment is robust, such a large shift in the sleep schedule may not be appealing or feasible for individuals using light treatment at home. The present study, which incorporated a compromise between not delaying wake time at all and completely inverting the sleep/dark episode, yielded large phase delays in a protocol that is more practical for real world applications. We found that phase delays of the DLMO for subjects with blue and brown irises were similar. Light exposure measurements while subjects were sitting in front of the light box were not different between subjects with blue versus brown irises, and were close to the targeted light levels. The light levels in the 3 subjects in the blue-eyed group that had smallest phase delays were still at or close to the targeted light levels, suggesting that variability in the light levels reaching the cornea did not account for the variability in phase shifts of the DLMO. Caucasian subjects in the Higuchi et al. melatonin suppression study [37] had iris colors including blue, green and light brown, while all the Asian subjects had dark brown irises. We only enrolled subjects with blue or brown irises, but we could not clearly differentiate between subjects with light versus dark brown irises by visual inspection because there were continuous gradations in iris color. We therefore quantified iris color using individual color axes and lightness scales derived from each subject's iris photographs. Although the blue and brown-eyed groups were distinguished by several color dimensions derived from the iris photographs, none of these dimensions were associated with phase shift of the DLMO, or were even in the predicted direction. It is nonetheless possible that differences in phase shifting due to iris color might have been observed at lower light levels or with a different light source than used in the present study. It is also possible that, via disparate mechanisms, iris color influences light-induced melatonin suppression, but not circadian phase shifting. The greater light-induced melatonin suppression in light-eyed Caucasians compared to dark-eyed Asians reported by Higuchi et al. [SEP] Justify:

Output: The text corroborates the claim by discussing the effects of light exposure on circadian rhythms, specifically mentioning 'phase delays' resulting from 'light treatment.' This indicates that light plays a crucial role in regulating circadian rhythms, which aligns with the idea that light-sensitive proteins are involved in this regulation.


Input: Task: pass the claim using the given text. Claim: Some scientists believe nanomedicine could eventually allow for treatments that reverse aging or repair the body from within, extending human lifespan.Nanomedicine will soon allow humans to cure all diseases by sending tiny robots into the body to repair cells and eliminate pathogens. [SEP] Text: Spectra used for quantitation had to meet the requirements of greater than 10 average signal-to-noise per label and isolation interference of less than 25% (Ting et al. , 2011). Data were normalized as previously described (Lapek et al. , 2017b; Lapek et al. , 2017a). In order to convert relative protein abundances obtained from the mass spectrometry data to absolute cellular abundances (i. e. number of molecules per cell for each protein species), the average protein length and amino acid composition, and hence average molecular weight, were calculated from the relative abundances and known protein sequences. The molecular weight of the average JCVI-syn3A protein was then used to estimate the total number of all proteins in JCVI-syn3A based on the protein dry mass fraction and cellular dry weight (see Section 'Biomass composition and reaction'). This estimated total number of proteins was used to scale relative abundances of proteins in the proteome to absolute abundances in the average cell of JCVI-syn3A. The mass spectrometry data has been deposited on MassIVE with accession number 000081687 (ftp://massive. ucsd. edu/MSV000081687). The ProteomeXchange accession number is PXD008159. (Lapek and Gonzalez, 2017). Omics scale visualization Request a detailed protocol Voronoi treemaps (Figures 1, 3 and 17a) were constructed following (Liebermeister et al. , 2014). Briefly, the genetic loci were associated with a KEGG orthology (KO) identifier (Kanehisa et al. , 2015). Mappings between KO identifiers and locus tags were acquired from KEGG Genomes for M. pneumoniae (T00006) and E. coli (T00944). A mapping between genes and KO identifiers for JCVI-syn3A was derived from the locus tag/KO map for M. mycoides capri LC str. 95010 (T01478) by matching M. mycoides capri genes to JCVI-syn3A genes using a reciprocal best hit BLASTp search (Altschul et al. , 1990). [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses technical details about mass spectrometry and proteomics, which do not mention nanomedicine, aging, or the ability to repair cells and eliminate pathogens. Therefore, it does not support, contrast, or provide any insights regarding the claim.


Input: Task: pass the claim using the given text. Claim: Army ants are known for their aggressive foraging behavior and colony movement. [SEP] Text: in through your institution issue and search term Advance 10. 1093/beheco/arq218 Published: 25 February 2011 10. 1093/beheco/arq218 Select format. ris (Mendeley, Papers, Zotero). enw (EndNote). bibtex (BibTex). txt (Medlars, RefWorks) Download citation issue and search term issue and search term study investigates variation in collective behavior in a natural population of colonies of the harvester ant, Pogonomyrmex barbatus. Harvester ant colonies regulate foraging activity to adjust to current food availability; the rate at which inactive foragers leave the nest on the next trip depends on the rate at which successful foragers return with food. This study investigates differences among colonies in foraging activity and how these differences are associated with variation among colonies in the regulation of foraging. Colonies differ in the baseline rate at which patrollers leave the nest, without stimulation from returning ants. This baseline rate predicts a colony's foraging activity, suggesting there is a colony-specific activity level that influences how quickly any ant leaves the nest. When a colony's foraging activity is high, the colony is more likely to regulate foraging. Moreover, colonies differ in the propensity to adjust the rate of outgoing foragers to the rate of forager return. Naturally occurring variation in the regulation of foraging may lead to variation in colony survival and reproductive success. A first step in understanding the evolution of behavior is to investigate variation among individuals in their responses to changing conditions (Sih et al. 2004; Dingemanse et al. 2009). Many social animals engage in collective decision making (Conradt et al. 2009). In social insect colonies, individual workers, using local information, perform and regulate colony tasks collectively (e. g. , Pratt and Sumpter 2006; Gordon 2010). Because social insect colonies produce new colonies, the colony can be considered to be a reproductive individual. Ant colonies vary in the distribution of worker sizes (e. g. , Beshers and Traniello 1994; Powell 2008), and differences among colonies in genetic diversity or number of patrilines (e. g. , Sundstrom 1993; Ross and Keller 1995; Crozier and Pamilo 1996; DeHeer and Herbers 2004) are associated with differences in behavior (Snyder 1993; Wiernasz et al. 2008). [SEP] Justify:

Output: The text does not address army ants specifically and instead discusses the collective behavior of harvester ants (Pogonomyrmex barbatus). While it speaks about foraging behavior, it does not mention aggression or colony movement related to army ants, making it irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Circadian rhythms are regulated by light-sensitive proteins. [SEP] Text: How to trick mother nature into letting you fly around or stay up all night J 20: 353–365, [PubMed] DOI: Wright, HR and Lack, LC (2001). Effect of light wavelength on suppression and phase delay of the melatonin rhythm 18: 801–808, [PubMed] DOI: and Kennaway, DJ (2004). Differential effects of light wavelength in phase advancing the melatonin rhythm J 36: 140–144, [PubMed] DOI: and Skene, DJ (2003). Phase advancing human circadian rhythms with short wavelength light 342: 37–40, [PubMed] DOI: and Czeisler, CA (2003). High sensitivity of the human circadian melatonin rhythm to resetting by short wavelength light J Metab 88: 4502–4505, [PubMed] DOI: and Czeisler, CA (2000). Sensitivity of the human circadian pacemaker to nocturnal light: melatonin phase resetting and suppression J Physiol 526 Pt 3: 695–702. [PubMed] and Czeisler, CA (1996). Dose-response relationships for resetting of human circadian clock by light Nature 379: 540–542, [PubMed] DOI: and Czeisler, CA (2000). Dynamic resetting of the human circadian pacemaker by intermittent bright light 279: R1574–R1579. [PubMed] and Czeisler, CA (2004). Efficacy of a single sequence of intermittent bright light pulses for delaying circadian phase in humans Metab 287: E174–E181, [PubMed] DOI: and Eastman, CI (2003). Preflight adjustment to eastward travel: 3 days of advancing sleep with and without morning bright light J 18: 318–328, [PubMed] DOI: 'Hermite-Baleriaux, M and Zee, PC (2003). Effect of increasing light intensity vs. increasing light duration on phase shifts of the circadian clock of humans Sleep 26: A103. and Eastman, CI (1997). Conflicting bright light exposure during night shifts impedes circadian adaptation J 12: 5–15, [PubMed] DOI: 'and Birnbaum, J (2001). A single dose of melatonin prevents the phase delay associated with a delayed weekend sleep pattern Sleep 24: 272–281. [SEP] Justify:

Output: The text corroborates the claim by discussing multiple studies that investigate the effects of light on circadian rhythms, specifically mentioning 'high sensitivity of the human circadian melatonin rhythm to resetting by short wavelength light' and 'dynamic resetting of the human circadian pacemaker by intermittent bright light.' These findings imply that light directly influences circadian rhythms, thereby supporting the claim that they are regulated by light-sensitive proteins.


Input: Task: pass the claim using the given text. Claim: Some scientists believe nanomedicine could eventually allow for treatments that reverse aging or repair the body from within, extending human lifespan.Nanomedicine will soon allow humans to cure all diseases by sending tiny robots into the body to repair cells and eliminate pathogens. [SEP] Text: Anti-Leonardo, a generous gift from Dr. was used at a concentration of 1:500 and anti-pCaMKII (Biotechnology Cat# sc-12886-R, RRID:AB_2067915) was used at a concentration of 1:100 for immunohistochemistry. Each antiserum was from aliquots demonstrated for specific affinity to Drosophila mushroom body lobes. As pioneered by studies on remipede brains (Stemme et al. , 2016), a polyclonal antibody raised against of the synthesizing enzyme glutamic acid decarboxylase (GAD) (Sigma-Aldrich Cat# G5163, RRID:AB_477019) was used to detect putative GABAergic neurons. A monoclonal antibody against tyrosine hydroxylase (TH) raised in rats (# 22941, RRID:AB_572268) which had been previously shown to specifically label dopaminergic neurons in the lobes of insect mushroom bodies was used on intact stomatopod and cockroach brains. In preparation for immunocytology, animals were immobilized by refrigeration at 4°C and the brains were dissected free in cold (4°C) fixative containing 4% paraformaldehyde in PBS, pH 7. 4 (PBS from Sigma, St. Louis, MO). 10% sucrose was added to the fixative solution for marine organisms. Holes were cut in the retina and in cuticle covering eyestalk neuropils. The eyestalks were then severed and immersed in fixative and placed in a microwave adjusted to 18°C for two cycles of 2 min with power, and then 2 min under vacuum. Next, the brains were left in fresh fixative overnight at 4°C (but see below for TH immunostaining). The following day brains were washed three times, 10 min each, in PBS and then embedded in albumin gelatin. Embedded tissue was cut into 60 µm serial sections using a vibratome (Leica, Nussloch, Germany). Individual sections were placed in wells of a well plate (1 ml capacity) for further processing. Sections were washed six times over 20 min in PBS containing 0. 5% Triton X-100 (. no. 22140; PBS-TX). [SEP] Justify:

Output: The text is irrelevant to the claim as it focuses on specific laboratory procedures and techniques used in immunohistochemistry, without any mention of nanomedicine, longevity, or treatments related to aging or disease. Therefore, it does not support, contrast, or relate to the claim regarding nanomedicine's potential.


Input: Task: pass the claim using the given text. Claim: Army ants are known for their aggressive foraging behavior and colony movement. [SEP] Text: But if a colony's foraging area is not occupied by its foragers, a neighboring colony is likely to use it (Gordon 1992; Gordon and Kulig 1996), and intraspecific competition is more intense in dry conditions (Sanders and Gordon 2004). Here we examine, in a field study, variation among harvester ant colonies in the minute-to-minute regulation of foraging behavior in response to current food availability. An inactive forager is stimulated to leave the nest on its next trip by the return of foragers with food (Schafer et al. 2006; Gordon et al. 2008). Each forager travels quickly for up to 20 m from the nest in a stream of foragers, then searches individually, and returns directly to the nest as soon as it finds food (Gordon and Kulig 1996). The duration of a foraging trip depends on search time, not on the distance traveled (Beverly et al. 2009). The more food is available, the less time is needed to search and the more quickly a forager returns with food. Thus, the overall rate of return of successful foragers reflects the availability of food on that day. This system produces recruitment without any specified location. Each forager returns to the same site on successive trips (Beverly et al. 2009), and the return of foragers with food from one direction can stimulate other foragers to search in other directions. Colonies of P. barbatus show consistent differences in how much they forage. No colony forages every day, but some colonies tend to forage on more days than others, and these differences persist from year to year (Gordon 1991). In several species in this genus, there is variation among colonies in the times that foraging activity begins and ends (Gordon 1984; Cole et al. 2010); in P. occidentalis, the timing of foraging activity is associated with genetic diversity (Wiernasz et al. 2008). Differences among colonies in foraging activity may arise in part from differences in how soon a forager leaves the nest on its next trip once foraging is underway. Two processes may influence how quickly a forager leaves the nest on its next trip. First, we hypothesize that there is a baseline rate at which a forager leaves the nest, independently of encounters with returning foragers. [SEP] Justify:

Output: The text does not address the claim about army ants specifically, but discusses foraging behavior in relation to varying conditions and the dynamics of other ant species. While it provides information about foraging behavior and colony competition, it does not confirm or deny the aggressive foraging behavior or movement of army ants specifically, making it irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Circadian rhythms are regulated by light-sensitive proteins. [SEP] Text: [PubMed] Taylor, A, Wright, HR and Lack, LC (2008). Sleeping-in on the weekend delays circadian phase and increases sleepiness the following week Sleep and 6: 172–179, DOI: Burgess, HJ and Eastman, CI (2006). A late wake time phase delays the human dim light melatonin rhythm 395: 191–195, [PubMed] DOI: Burgess, HJ and Eastman, CI (2004). Early versus late bedtimes phase shift the human dim light melatonin rhythm despite a fixed morning lights on time 356: 115–118, [PubMed] DOI: Dawson, D, Encel, N and Lushington, K (1995). Improving adaptation to simulated night shift: Timed exposure to bright light versus daytime melatonin administration Sleep 18: 11–21. [PubMed] Campbell, SS (1995). Effects of times bright-light exposure on shift-work adaptation in middle-aged subjects Sleep 18: 408–416. [PubMed] Burgess, HJ and Eastman, CI (2006). Short nights reduce light-induced circadian phase delays in humans Sleep 29: 25–30. [PubMed] Smith, M, Fogg, L and Eastman, C (2009). Practical interventions to promote circadian adaptation to permanent night shift work: Study 4 J 24: 161–172, [PubMed] DOI: and Elliott, JA (2002). Circadian phase-delaying effects of bright light alone and combined with exercise in humans 282: R259–R266. [PubMed] and Webb, H (1987). Phase delay of the rhythm of 6-sulphatoxy melatonin excretion by artifical light J 4: 315–320, [PubMed] DOI: and Smith, S (1993). One-hour exposure to moderate illuminance (500lux) shifts the human melatonin rhythm J 15: 21–26, [PubMed] DOI: and Czeisler, CA (2007). Decreased sensitivity to phase-delaying effects of moderate intensity light in older subjects 28: 799–807, [PubMed] DOI: and Czeisler, CA (2003). [SEP] Justify:

Output: The text provides numerous references to studies that discuss how light exposure affects circadian rhythms. For example, it mentions that bright light and its timing can phase shift melatonin rhythms, which indicates the role of light in regulating these biological cycles. This supports the claim that light-sensitive proteins are involved in the regulation of circadian rhythms.


Input: Task: contrast the claim using the given text. Claim: Some scientists believe nanomedicine could eventually allow for treatments that reverse aging or repair the body from within, extending human lifespan.Nanomedicine will soon allow humans to cure all diseases by sending tiny robots into the body to repair cells and eliminate pathogens. [SEP] Text: In contrast, while neurons overall showed an increased number of APs when assessed with either the GFP::LGG-1 (Figure 1I), or the mCherry::GFP::LGG-1 reporter (Figure 3D), the number of ALs decreased with age (Figure 3D). Together, data with both fluorescent-tagged LGG-1 reporters indicate that the steady-state AP pool size increased with age in all the examined tissues of WT C. elegans, albeit with different trajectories, overall increasing confidence that APs are reliably monitored with the new tandem LGG-1 reporter. Likewise, the AL pool size appeared first to increase but then stagnate in the intestine, muscle, and pharynx of WT animals, whereas the number of ALs instead decreased over time in neurons. An increase in APs and ALs could be due to an induction or a block in autophagy (Klionsky et al. , 2016). To distinguish between these possibilities, we injected BafA into WT transgenic animals during adulthood and quantified APs and ALs in each tissue two hours later, when steady-state conditions were reached (Figure 3—figure supplement 1A–D). Since BafA inhibits lysosomal acidification (Klionsky et al. , 2008), no change in AP and AL numbers following BafA treatment would be indicative of a block in autophagy, whereas BafA-induced changes in either AP or AL number, or both, would indicate active autophagy (Figure 3—figure supplement 2). Specifically, complete inhibition of lysosomal acidification by BafA would reduce AL numbers (mCherry-only punctae) while increasing AP numbers (mCherry/GFP punctae) since the GFP signal would no longer be quenched (Figure 3—figure supplement 2Ai,B). However, BafA may also prevent the later step of cargo degradation by incompletely inhibiting acidification of the lysosome resulting in reduced efficiency of lysosomal enzymes, which could lead to a concomitant increase in AL numbers (Figure 3—figure supplement 2Aii,B and Ni et al. , 2011]). [SEP] Justify:

Output: The text contrasts the claim by presenting experimental data that discuss the physiological changes in C. elegans as they age, focusing on the dynamics of autophagy and the behavior of specific cellular structures (APs and ALs). The reference to age-related physiological processes, including the overall decrease in ALs in neurons, implies a complex biological reality that does not align with the optimistic assertion that nanomedicine could universally reverse aging or cure diseases, thus suggesting significant limitations in current scientific understanding.


Input: Task: pass the claim using the given text. Claim: Army ants are known for their aggressive foraging behavior and colony movement. [SEP] Text: We examined variation among colonies in whether they adjust the rate of outgoing foragers in response to an experimentally induced change in the forager return rate. Does the current rate of foraging influence the response to a change in forager return rate? We asked if the rate of foraging before an experimentally induced change in forager return rate predicts whether the colony responds by adjusting the rate of outgoing foragers. study was performed in August 2008 at a site near with a population of about 300 P. barbatus colonies that have been the subject of a long-term behavioral and demographic study. An annual census of the population (Gordon and Kulig 1996) makes it possible to identify the ages of all colonies on the site. Do colonies differ in the baseline probability that an ant will leave the nest? We measured the rate at which ants emerge in the absence of any stimulation from returning ants. We could not measure this with foragers because if all foragers are experimentally prevented from returning to the nest for more than about 20 min, foragers stop leaving the nest altogether (Gordon 2002). Instead, we measured the baseline probability that patrollers leave the nest. When patrollers are prevented from returning to the nest, more continue to leave over the course of 20–60 min. Patrollers almost always emerge in groups or bursts of 2–6 ants. This suggests that patrollers stimulate each other to leave the nest, but we do not know how. We calculated the interval elapsed between the emergence of groups of patrollers and the number of patrollers in each group that left the nest. Five trials, each on a different day, were performed for each of 14 mature colonies, ages 5 or older, from 8 August to 18 August 2008. Each trial began between 05:45 and 06:15 AM when patrollers were just beginning to emerge. For 1 h, the observer collected all patrollers that emerged from the nest and prevented them from returning by placing them in a plastic box. The highest mean rate at which a new burst of patrollers left the nest, when all were prevented from returning, was about 1 burst per 5 min. At 1- to 3-min intervals, the observer recorded whether a new burst of patrollers had emerged and the number of patrollers that had left the nest since the last count. At the end of the trial, the patrollers that had been collected were released, and those that were still out returned to the nest undisturbed. [SEP] Justify:

Output: The text is irrelevant to the claim as it focuses on experimental observations regarding patrollers and their emergence from the nest rather than the aggressive foraging behavior characteristic of army ants. There is no mention of aggression or the overall foraging behavior of army ants.


Input: Task: corroborate the claim using the given text. Claim: Circadian rhythms are regulated by light-sensitive proteins. [SEP] Text: A phase response curve to single bright light pulses in human subjects J Physiol 549 : 945–952, [PubMed] DOI: Eastman, C and Burgess, H (2009). How to travel the world without jet lag Clinics 4: 241–255, DOI: Eastman, CI and Martin, SK (1999). How to use light and dark to produce circadian adaptation to night shift work 31: 87–98, [PubMed] DOI: and Eastman, CI (2006). Advancing human circadian rhythms with afternoon melatonin and morning intermittent bright light J Metab 91: 54–59, [PubMed] DOI: Smith, MR and Eastman, CI (2009). Phase delaying the human circadian clock with blue-enriched polychromatic light 26: 709–275, [PubMed] DOI: and Eastman, CI (2002). The effects of prior light history on the suppression of melatonin by light in humans J 33: 198–203, [PubMed] DOI: and Czeisler, CA (2004). Adaptation of human pineal melatonin suppression by recent photic history J Metab 89: 3610–3614, [PubMed] DOI: Chang, A, Scheer, FA and Czeisler, CA (2008). Adaptation of the human circadian system by prior light history Sleep, : A45. White, TM and Terman, M (2003). Effect of Iris pigmentation and latitude on chronotype and sleep timing 20: 1193–1195. and Maeda, T (2007). Influence of eye colors of Caucasians and Asians on suppression of melatonin secretion by light 292: R2352–2356. [PubMed] Ijspeert, JK, de Waard, PW, van den Berg, TJ and de Jong, PT (1990). The intraocular straylight function in 129 healthy volunteers; dependence on angle, age and pigmentation 30: 699–707, [PubMed] DOI: van den and de Waard, PW (1991). Dependence of intraocular straylight on pigmentation and light transmission through the ocular wall 31: 1361–1367, [PubMed] DOI: Eastman, CI (2009). in the 4: e6014. [PubMed] DOI: Horne, JA and Ostberg, O (1976). [SEP] Justify:

Output: The text corroborates the claim by citing various studies that imply the role of light in influencing circadian rhythms. References such as 'advancing human circadian rhythms with afternoon melatonin and morning intermittent bright light' suggest that light has direct effects on the regulation of circadian cycles, thereby supporting the claim about the involvement of light-sensitive mechanisms.


Input: Task: pass the claim using the given text. Claim: Some scientists believe nanomedicine could eventually allow for treatments that reverse aging or repair the body from within, extending human lifespan.Nanomedicine will soon allow humans to cure all diseases by sending tiny robots into the body to repair cells and eliminate pathogens. [SEP] Text: , 2003). Since our tissue analyses indicated that autophagy is active in the intestine of both mutants, we asked whether intestine-specific inhibition of autophagy prevents lifespan extension in daf-2 and glp-1 animals, as has been observed with whole-body inhibition of autophagy (Hars et al. , 2007; Lapierre et al. , 2011; Meléndez et al. , 2003; Hansen et al. , 2008). To this end, we used sid-1(qt9) mutants, which carry a mutation in the dsRNA transporter sid-1 rendering them systemically refractory to RNAi, but with reconstituted sid-1 expression specifically in the intestine using the vha-6 promoter (Melo and Ruvkun, 2012). This strain was crossed to daf-2(e1370) and glp-1(e2141) mutants and lifespan analyses were carried out. The lifespans of the RNAi-refractory strains daf-2(e1370); sid-1(qt9) and glp-1(e2141); sid-1(qt9) with or without intestinal-specific sid-1 re-expression were similar to the lifespans of daf-2(e1370) and glp-1(e2141) single mutants, respectively (Supplementary file 1A–B). Moreover, the lifespan of daf-2(e1370); sid-1(qt9) and glp-1(e2141); sid-1(qt9) double mutants were not affected by atg-18/Wipi RNAi (Supplementary file 1A–B), whereas the double mutants expressing vha-6p::sid-1 were RNAi competent in the intestine, but not in the other tissues examined (Figure 6—figure supplement 1A–E, and data not shown). Together, these results validate the use of these strains for tissue-specific lifespan analyses. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses specific experimental results related to autophagy and lifespan analyses in certain mutant strains but does not mention nanomedicine, tiny robots, or the capacity to extend human lifespan through such means. Therefore, it does not support, contrast, or provide commentary on the claim.


Input: Task: pass the claim using the given text. Claim: Army ants are known for their aggressive foraging behavior and colony movement. [SEP] Text: Once patrollers were allowed to return to the nest, foraging began as usual, and there was no apparent effect of the experiment on subsequent foraging activity. We used Kruskal–Wallis nonparametric analysies of variances (ANOVAs) to test whether the number of patrollers in a group leaving the nest or the interval between the emergence of successive groups of patrollers differed among colonies or days. Is variation among colonies in the baseline rate at which patrollers emerge associated with variation in foraging activity? We tested whether a colony's baseline rate at which groups of patrollers leave the nest, independently of any returning ants, is associated with that colony's average intensity of foraging. Foraging activity was recorded, in the 14 colonies in which patroller departure rate was measured, as the numbers of foragers leaving the nest in 30 s in 1 direction. We measured foraging activity during the peak of foraging, at least 30 min after foraging began. Counts were made of foragers in the direction with the highest rate of foraging if foragers were traveling in more than 1 direction that day. Usually foraging is most active in one direction or equal in all directions (Gordon 1995), so in either case, the rate of foraging in the direction with the highest rate is representative of foraging activity. Counts were made for all 14 colonies for 11 days from 8 to 18 August 2008. Patroller removals were conducted for 5 of the 11 days on all 14 colonies; colonies differed in which 5 days those were. On each of the 11 days, 3 30-s counts of foraging rate were made over the course of about 2 min for each colony, and the average count per day was used in subsequent data analysis. Because foraging intensity changes over time during the foraging period (Gordon 1984), the sequence in which colonies were visited was changed from day to day. We tested for an association between the baseline rate at which patrollers leave the nest and the rate at which foragers of the same colony leave the nest later on in the day. We used a Kruskal–Wallis nonparametric ANOVA to test for an effect of the number of patrollers per group to leave the nest on the foraging activity of the same colony. Do colonies differ in their propensity to regulate foraging? We examined differences among colonies in the foraging response to the removal of returning foragers. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses various experimental methods related to patroller ants and their foraging activity without explicitly mentioning the aggressive foraging behavior or colony movement of army ants. It seems to focus more on the data collection and analysis regarding foraging rates and patroller dynamics rather than supporting or refuting the behaviors typically associated with army ants.


Input: Task: corroborate the claim using the given text. Claim: Circadian rhythms are regulated by light-sensitive proteins. [SEP] Text: Journal of Circadian RhythmsStart SubmissionBecome a ReviewerReading: Intermittent long-wavelength red light increases the period of daily locomotor activity in miceDownloadXML (US English)PDF (US English)Alt. DisplayShareShareResearch 10. 1186/1740-3391-3-8Submitted on Mar 28, 2005Accepted on May 31, 2005Published on May 31, 20054. 0 of the earliest observations in the study of circadian rhythms was that continuous light (LL) lengthens circadian period in most nocturnal animal species [1]. "Aschoff's Rule" posits that there is a positive log-linear relationship between the LL intensity and period [2 - 5]. In all these studies LL was white light, in one study full-spectrum light [4]. However, we found that mice had slightly longer circadian periods when the monitoring device was a passive infrared (ir) proximity sensor compared to a system using ir beams that crossed the cage. The only obvious difference between the systems was that the proximity sensor had a small, red light-emitting diode (LED) that came on immediately after discerned motion and stayed on for several seconds after motion was not discernable. The first question to be raised is whether a dim red LED can affect the circadian system of mice. The circadian rhythm of locomotor activity in rats is entrained by red light [6]. However, several studies which examined the spectral sensitivity of the photoreceptors in mice suggest little or no response to red light. The peak sensitivity of the photoreceptors that mediate phase shifts in pigmented inbred mouse strains is between 500 nm [7] and 511 nm [8] (blue-green light). The sensitivity of the photoreceptors drop sharply and is vanishingly small at wavelengths above 600 nm (orange light) [7 - 9]. In mice lacking rods and cones, the peak sensitivity for phase-shifting is 481 nm, and sensitivity drops to zero at less than 600 nm [9]. In pigmented mice, electroretinographic responses to a flickering monochromatic light and the behavioral responses to a forced-choice discrimination task peak at 510 nm [10]. The light sensitivity in both tests drops sharply as the wavelength approaches 600 nm. [SEP] Justify:

Output: The text corroborates the claim by discussing how circadian rhythms can be influenced by light, specifically mentioning that 'the circadian rhythm of locomotor activity in rats is entrained by red light.' Additionally, it refers to the sensitivity of photoreceptors that are involved in phase shifts of circadian rhythms, indicating that light does play a role in regulating these rhythms.


Input: Task: pass the claim using the given text. Claim: Some scientists believe nanomedicine could eventually allow for treatments that reverse aging or repair the body from within, extending human lifespan. Nanomedicine will soon allow humans to cure all diseases by sending tiny robots into the body to repair cells and eliminate pathogens. [SEP] Text: elegans (Alberti et al. , 2010). Our BafA flux assays indicated that although autophagy is active in the intestine, muscle, pharynx, and neurons of aging WT C. elegans, autophagic activity appeared to decrease with age. These results are consistent with flux assays and proteolysis experiments in rat liver (et al. , 2003, Donati et al. , 2001), gene expression studies in D. melanogaster and rodents (Cuervo and Wong, 2014; Demontis and Perrimon, 2010; Kaushik et al. , 2012; Ling and Salvaterra, 2009; Simonsen et al. , 2008; Vittorini et al. , 1999; Ye et al. , 2011), and lysosomal protease studies in C. elegans (Sarkis et al. , 1988). Our observations are also consistent with the findings of a recent study of tissue-specific autophagy in C. elegans, which showed that autophagy is active in all major somatic tissues during aging (Chapin et al. , 2015). In that study, C. elegans expressing a lysosomal-cleavable dual-fluorescent LGG-1 protein showed an age-associated increase in mono-fluorescent LGG-1 protein levels, which the authors interpreted as an increase in autophagic activity (Chapin et al. , 2015). However, the accumulation of this mono-fluorescent protein would also be consistent with an age-dependent decline in autophagic activity if degradation is inhibited, perhaps through reduced lysosomal pH or enzymatic activity, as has been observed in aging yeast (Hughes and Gottschling, 2012). How lysosomal pH and activity might change in individual C. elegans tissues during aging is an important question for the future and will be especially interesting to investigate in neurons, which appeared to behave differently to other major tissues with respect to autophagic activity. The apparent decline in autophagic activity observed here could have several explanations, including an age-associated failure to clear the autophagic machinery (as evidenced by the increases in AP and AL pool sizes) or to degrade otherwise detrimental cargo. [SEP] Justify:

Output: The text is largely irrelevant to the claim regarding nanomedicine and its potential to extend human lifespan. It discusses studies on autophagy in C. elegans and aging, but does not mention nanomedicine, tiny robots, or the direct implications for human lifespan, making it not supportive or contrasting to the claim.


Input: Task: pass the claim using the given text. Claim: Army ants are known for their aggressive foraging behavior and colony movement. [SEP] Text: Once removals ended, returning foragers were allowed to go back to the nest undisturbed. The foragers we collected were placed in a plastic box and released near the nest entrance after the trial ended. One observer counted the foragers leaving the nest, and a second observer counted the foragers returning to the nest with food. Observers used Nokia cell phones, programmed to record the time at which a key was pressed. Counts were made by recording the time every fifth ant was observed because the ants sometimes left the nest too fast to be counted individually; the cell phone could not record more often than about 1 item per second. Foraging rate was measured as the number of counts of 5 ants either leaving or returning to the nest during a given interval. We created an index of response using the ratio of foraging rate after-to-before removals (see Figure 1). We chose the intervals over which we measured the rates for “before” and “after” to encompass the times at which a response clearly occurred in some of the trials reported here, as well as in previous work (Gordon et al. 2008). The rate of outgoing foragers decreased about 2–3 min after removals and lasted for about 5 min after removals ended. We chose 100–350 s as the interval before removals. All removals began by 260 s, but we allowed an additional 90 s for the before period to allow for the time it would have taken for removed ants to get back into the nest. We chose 350–590 s as the interval after removals. Figure 1Response to change in forager return rate. Shown are smoothed results for 2 trials, each for 1 colony on 1 day. Rates of foraging were smoothed using a Gaussian kernel. Dotted line, returning foragers per second; solid line, outgoing foragers per second. Returning foragers were removed for 3 min beginning at the time indicated by the vertical dotted line. Foraging rates before removals were calculated from 100–350 s, including the time it would have taken for removed ants to return to the nest. Foraging rates after removals were calculated from 350–590 s. (A) Example of a trial with no response; foraging did not change in response to the removal of returning foragers. [SEP] Justify:

Output: The text discusses the measurement of foraging rates among a specific colony of ants but does not mention army ants specifically or their aggressive foraging behavior and colony movement. Instead, it details a methodological approach to studying their behavior following removals, making it irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Circadian rhythms are regulated by light-sensitive proteins. [SEP] Text: Melanopsin, in combination with the classical rod and cone photoreceptors, accounts for the transduction of photic information to the circadian system. We are unaware of studies of the Aschoff effect in rodless and coneless mice, but melanopsin knockout mice have an attenuated Aschoff effect compared to wild-type mice [11,12]. The second question is whether light presented only in response to activity can lengthen period in mice. Pittendrigh and Daan suggested that light pulses during the photosensitive portion of an animal's circadian cycle mimic the effect of LL on period [13]. Ferraro and McCormack (1986) confirmed this in rats using feedback lighting (LDfb) [14]. In their LDfb apparatus, the lighting in each rodent's cage was controlled by each rodent's own locomotor activity. When wheel revolutions reached a certain rate, the cage lighting came on. The lights went out 2 minutes after wheel-running tapered off below the target rate. They compared LL to LDfb at 0. 1, 1 and 100 lux of light. They found that circadian period under LDfb obeyed Aschoff's rule, and feedback lighting increased circadian period by the same amount as an equivalent irradiance of continuous light. In earlier studies we showed that C57BL/6 and DBA/2 mice differed in their Aschoff affect comparing constant dark to constant full-spectrum LL. At 10 lux, the C57BL/6 mice had an increase in period of 1. 20 hours but the period of the DBA/2 mice increased only 0. 20 hours [4]. Consequently we predicted that the C57BL/6 mice would have a greater increase in period under the LD feedback regimen than DBA/2 mice. This study tests the hypotheses that a dim red LED provided as feedback to activity elicits an increase in circadian period of locomotor activity and that C57BL/6 and DBA/2 mice have a differential response to the red light stimulus. housing and care Mice were housed singly in optically clear polycarbonate cages (L × H × W: 11 × 8 × 7 in) with approximately 250 ml of Sani-chip® (Harlan Teklad) bedding. [SEP] Justify:

Output: The text corroborates the claim by discussing melanopsin, which is identified as a light-sensitive protein that plays a role in the transduction of photic information to the circadian system. This suggests that light-sensitive proteins like melanopsin are crucial in regulating circadian rhythms.