Input: Task: pass the claim using the given text. Claim: Some insects can undergo complete metamorphosis, transitioning through larval stages. [SEP] Text: Normalization was done in DESeq2, while the following parameters were used for coseq: model = ‘Normal,’ transformation = ‘arcsin,’ seed = 1234, iter = 10,000. Specific genes belonging to clusters where D03 and/or Day 32 showed upregulation and were then re-clustered with the same parameter for visualization. A complete representation of all initial clusters found in this study can be found in Figure 2—figure supplement 1. Pairwise analysis of differentially expressed genes between two-time points was done using the Wald test in DESeq2 (design = ~dph, adjusted p-value threshold: 0. 01, log2FoldChange ≥ ±0. 58). Figures were plotted using ggplot2 (V3. 4. 1) (Wickham, 2009), and the analysis made general use of the tidyverse package (V1. 3. 2) (Wickham et al. , 2019). Lastly, expression levels shown in Figures 3—6 are normalized gene counts produced by DESeq2. Materials and correspondence Request a detailed protocol Correspondence and material requests should be addressed to at either roger. huerlimann@oist. jp or roger. huerlimann@gmail. com. Add a comment + Open annotations. The current annotation count on this page is being calculated. 3. The homogenate sample was denatured with acetonitrile and then, equilibrated for 30 min at room temperature on dark After equilibration, the sample was centrifuged at 3000 rpm for 3 min, and then the supernatant was decanted into a new PP tube which was added to distilled water. The sample was applied to an Oasis MCX cartridge which had been successively conditioned in methanol, distilled water, and 1% acetic acid solution. After the cartridge was washed with distilled water followed by methanol, the thyroid hormones were eluted with methanol/distilled water/ammonia solution (70:30:1,v/v/v). After the sample was evaporated to dryness, the residue was dissolved with methanol/distilled water pyridine solution (40:60:1, v/v/v). [SEP] Justify:

Output: The text is irrelevant to the claim about insects undergoing complete metamorphosis. Instead, it discusses technical details of a scientific study involving data normalization and gene expression analysis, which has no connection to insect biology or metamorphosis.


Input: Task: corroborate the claim using the given text. Claim: Disruption of circadian rhythms can lead to health issues. [SEP] Text: , 2009): in many animal models, inflammatory responses to bacterial lipopolysaccharide (LPS) are greater during the interval approaching the onset of the active phase and reduced near the beginning of the rest phase (Curtis et al. , 2014). Conversely, innate immune activation affects circadian timekeeping. LPS elicits SCN c-fos expression and shifts the circadian pacemaker (Marpegan et al. , 2005). Convergent evidence suggests that LPS-induced phase shifts are mediated by proinflammatory cytokines (Marpegan et al. , 2005; Paladino et al. , 2010; Leone et al. , 2012). Thus, time-of-day information derived from the circadian pacemaker modulates responsiveness of the immune system, and conversely, immune mediators modulate clock function. Whereas circadian rhythms provide circa-24-h temporal order, ultradian rhythms (URs) impose essential temporal structure on subcircadian timescales (periods <8 h; Veldhuis, 2008; Yates and Yates, 2008). URs affect diverse aspects of physiology and behavior, including sleep (Mueller et al. , 2012), hormones (Knobil, 1999; Choe et al. , 2013; Lloyd et al. , 2008), food intake (Warner et al. , 2010), and body temperature (Heldmaier et al. , 1989), traits that undergo striking changes during the acute response to infection (Hart, 1988). Despite the ubiquity of physiological and behavioral URs, it is unknown whether the temporal structure of URs, like circadian rhythm (CRs), is affected by immune activation. Induced circadian arrhythmia has been widely used to assess circadian regulation of organismal physiology. Insights regarding circadian influences on immune responses have been gleaned from models of circadian arrhythmia induced by clock gene knockouts (Gibbs et al. , 2012), constant illumination (LL; Deprés-Brummer et al. , 1997), and ablation of the SCN (SCNx; Filipski et al. , 2003; Guerrero-Vargas et al. , 2014), but each of these models has limitations. Clock genes are present in all tissues, and resulting immunophenotypes may reflect either arrhythmia or interference with cellular metabolic processes; LL can elevate immunosuppressive glucocorticoids (Welberg et al. [SEP] Justify:

Output: The text corroborates the claim by discussing how circadian rhythms are involved in various physiological and behavioral processes, particularly in relation to immune responses. It notes that immune activation can affect circadian timekeeping, indicating a bidirectional relationship between circadian rhythms and health outcomes, especially under stress or infection conditions. This supports the assertion that disruption of these rhythms could lead to health issues.


Input: Task: contrast the claim using the given text. Claim: Biotechnology allows people to live forever by continually replacing damaged tissues. [SEP] Text: Living cells operate constantly under threat of disruption, and the germ line is not immune. The reason that the germ line does not die out in a catastrophe of errors has to do, on the one hand, with its highly sophisticated mechanisms for cellular self-maintenance and repair and, on the other hand, with its ability to get rid of its more serious mistakes through continual rounds of competition. Sperm are produced in vast excess; usually only a good one can fertilize the egg. Egg-forming cells are produced in much greater numbers than can ovulate; stringent quality control eliminates the ones that fail to make the grade. And finally, if errors slip past all these checks, natural selection provides the final arbiter of which individuals are the fittest to transmit their germ line to future generations. After the seemingly miraculous feat of growing a complex body from a single cell—the fertilized egg—it should be relatively straightforward merely to keep a body going indefinitely—as American evolutionist has pointed out. Indeed, for some multicelled organisms, an absence of aging appears to be the rule. The freshwater hydra, for example, shows an extraordinary power of survival. Not only does the hydra apparently not age, in the sense that as it gets older it shows no increase in death rate or decline in fertility, it also appears capable of regrowing a whole new body from even a tiny fragment, if by chance it is cut into pieces. The secret of the hydra's eternal youth: quite simply, germ cells permeate its body. If the immortal germ line is everywhere, it actually comes as no surprise that an individual hydra can survive without any foreseeable end, presuming it does not succumb to injury or predators. In most multicelled animals, however, the germ line is found only in the tissue of the gonads, where the sperm and eggs form. This arrangement provides great advantages. During the long history of evolution, it freed other cell types to become specialists—nerve, muscle and liver cells, among others, that are required for the development of any complex organism, whether a Triceratops or a human. This division of labor had far-reaching consequences for how organisms age and how long they can live. As soon as the specialist cells surrendered the role of continuing the species, they also abandoned any need for immortality; they could die after the body had passed on its genetic legacy through the germ line to the next generation. [SEP] Justify:

Output: The text contrasts the claim by discussing the limitations of cellular immortality in complex multicellular organisms. It explains that while certain organisms like hydras exhibit properties that allow them to not age and have regenerative capabilities, most multicellular animals, including humans, have specialized cells that do not retain immortality. The text states, 'As soon as the specialist cells surrendered the role of continuing the species, they also abandoned any need for immortality; they could die after the body had passed on its genetic legacy through the germ line to the next generation.' This indicates that even while biotechnology may aim to repair or replace tissues, it does not guarantee immortality, as not all cells are designed to live indefinitely.


Input: Task: pass the claim using the given text. Claim: Some insects can undergo complete metamorphosis, transitioning through larval stages. [SEP] Text: The sample was subjected to an LC-MS/MS system for determination of T4, T3, and rT3. The SRM transitions were m/z 777. 8/731. 6 for T4, 651. 9/605. 8 for T3 and 651. 9/507. 7 for rT3. The measurement ranges were 4–4000 pg/tube for T4 and 0. 5–500 pg/tube for both T3 and rT3. The limits of quantification were 4 pg/tube for T4 and 0. 5 pg/tube for both T3 and rT3. 4. F was extracted with 4 mL of methyl tert-butyl ether. After the organic layer was evaporated to dryness, the extract was dissolved in 0. 5 mL of methanol and diluted with 1 mL of distilled water. The sample was applied to an cartridge which had been successively conditioned with 3 mL of methanol and 3 mL of distilled water. After the cartridge was washed with 1 mL of distilled water, 1 mL of methanol/distilled water/acetic acid (45:55:1,v/v/v), and 1 mL of 1% pyridine solution, the F was eluted with 1 mL of methanol/pyridine (100:1,v/v). After evaporation, the residue was reacted with 50 μL of mixed solution (80 mg of 2-methyl-6-nitrobenzoic anhydride, 20 mg of 4-dimethylaminopyridine, 40 mg of picolinic acid and 10 μL of triethylamine in 1 mL of acetonitrile) for 30 min. at room temperature. After the reaction, the sample was dissolved in 0. 5 mL of ethyl acetate/hexane/acetic acid (15:35:1, v/v) and the mixture was applied to a HyperSep SI cartridge which had been successively conditioned with 3 mL of acetone and 3 mL of hexane. The cartridge was washed with 1 mL of hexane, and 2 mL of ethyl acetate/hexane (3:7, v/v). Steroids was eluted with 2. 5 mL of acetone/hexane (7:3, v/v). After evaporation, the residue was dissolved in 0. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses a scientific method for measuring hormones and steroids using LC-MS/MS analysis. There is no information or mention of insects or metamorphosis in the provided text.


Input: Task: corroborate the claim using the given text. Claim: Disruption of circadian rhythms can lead to health issues. [SEP] Text: , 2006) and SCN lesions damage adjacent hypothalamic tissue, increase stress hormones (Buijs et al. , 1993; Kalsbeek et al. , 2012), and generate glial scars and neuroinflammation that persist for months after the insult (Logan et al. , 1992; Silver and Miller, 2004). A general theme emerging from these and other studies is that the circadian system inhibits inflammatory responses and may provide a circadian temporal gating of inflammatory responses (Gibbs et al. , 2012); other reports, however, indicate attenuated inflammatory responses in circadian-disrupted animals (Wachulec et al. , 1997; Liu et al. , 2006; Spengler et al. , 2012). Here we used a noninvasive model of circadian arrhythmia: the disruptive phase-shifted (DPS) hamster, which avoids the aforementioned complications, to examine the consequences of circadian disruption on innate inflammatory responses. DPS hamsters are well suited for translational analyses because, as in humans, dysrhythmia is manifested by genetically and neurologically intact individuals that remain exposed to circadian light-dark cycles. In DPS hamsters, CRs in locomotor activity (LMA), Tb, sleep, hormone secretion, and SCN clock gene expression are eliminated by light treatments administered over the course of 2 days (Ruby et al. , 2004; Fernandez et al. , 2014). The present experiment was conducted on female Siberian hamsters; females are understudied in neuroscience research (Beery and Zucker, 2011; Prendergast et al. , 2014), an impediment to establishing brain-behavior relations applicable to both sexes. Materials and MethodsAnimalshamsters (Phodopus sungorus) were derived from a breeding colony maintained in a long-day, 15L:9D photoperiod (LD) at the University of Chicago. Hamsters were housed in polypropylene cages, with food (Teklad; Harlan; Madison, WI) and filtered tap water provided ad libitum; cotton nesting material was available in the cages. Ambient temperature and relative humidity were held constant at 19 ± 2°C and 53% ± 10%, respectively. All procedures conformed with principles and guidelines in the Guide for the Care and Use of and were approved by the Care and of the University of Chicago. [SEP] Justify:

Output: The text corroborates the claim by discussing how circadian disruption, as evidenced by the use of the DPS hamster model, affects various physiological processes such as locomotor activity, hormone secretion, and inflammatory responses. It highlights that the circadian system plays a critical role in managing inflammatory responses and implies that disruptions to these rhythms can lead to health complications. Specifically, it mentions that studies indicate both increases in stress hormones and neuroinflammation associated with circadian disruption, thereby supporting the claim that such disruptions can lead to health issues.


Input: Task: contrast the claim using the given text. Claim: Biotechnology allows people to live forever by continually replacing damaged tissues. [SEP] Text: Ultimate trade-offsSo how long can those specialist cells survive? In other words, how long can we and other complex organisms live? The answer for any given species has a lot to do with the environmental threats its ancestors faced as they evolved and with the energy costs of maintaining the body in good operating order. By far the majority of natural organisms die at relatively young ages because of accidents, predation, infection or starvation. Wild mice, for example, are at the mercy of a very dangerous environment. They are killed rather quickly—it is rare for a wild mouse to see its first birthday. Bats, on the other hand, are safer because they can fly. Meanwhile maintenance of the body is expensive, and resources are usually limited. Out of the daily intake of energy, some might go to growth, some to physical work and movement, some to reproduction. Some energy, instead, might be stored as fat to protect against famine, but much gets burned just to fix the innumerable faults that arise every second the organism is alive. Another increment of these scarce resources goes to proofread the genetic code involved in the continual synthesis of new proteins and other essential molecules. And still another allocation powers the energy-hungry garbage disposal mechanisms that clear molecular debris out of the way. Here is where the disposable soma theory comes in. The theory posits that, like the human manufacturer of an everyday product—a car or a coat, for example—evolving species have to make trade-offs. It does not pay to invest in allowing indefinite survival if the environment is likely to bring death within a fairly predictable time frame. For the species to survive, a genome basically needs to keep an organism in good shape and enable it to reproduce successfully within that time span. At all stages of life, even to its very end, the body does its utmost to stay alive—in other words, it is programmed not for aging and death but for survival. But under the intense pressure of natural selection, species end up placing higher priority on investing in growth and reproduction—in the perpetuation of the species—than on building a body that might last forever. So aging is driven by the gradual lifelong accumulation of diverse forms of unrepaired molecular and cellular damage. No biological software program, then, dictates precisely when it is time to die, but growing evidence suggests that certain genes can nonetheless influence how long we live. [SEP] Justify:

Output: The text contrasts the claim by discussing the limitations on organism lifespan imposed by environmental factors, energy costs, and evolutionary trade-offs. It highlights that aging is influenced by the accumulation of unrepaired cellular damage and suggests that species prioritize reproduction over indefinite survival. It also notes that there is no biological mechanism ensuring immortality, thus undermining the idea that biotechnology could allow for eternal life through tissue replacement.


Input: Task: pass the claim using the given text. Claim: Some insects can undergo complete metamorphosis, transitioning through larval stages. [SEP] Text: 1 mL of acetonitrile/distilled water (2:3, v/v), and the solution was subjected to an LC-MS/MS. The SRM transitions was m/z 468. 2/309. 2 for F and 472. 2/454. 3 for F-d4. The measurement range was 10–100000 pg/tube. The limit of quantification of F was 10 pg/tube. 4. 0 Kit, which is a commercially available version of the Hi-C protocol (Lieberman-Aiden et al. , 2009). Following the manufacturer’s instructions for the kit, intact cells from two samples were crosslinked using a formaldehyde solution, digested using the DPNII restriction enzyme, and proximity ligated with biotinylated nucleotides to create chimeric molecules composed of fragments from different regions of the genome that were physically proximal in vivo, but not necessarily genomically proximal. Continuing with the manufacturer’s protocol, molecules were pulled down with streptavidin beads and processed into an Illumina-compatible sequencing library. Sequencing was performed on an Illumina HiSeq 4000, generating a total of 159,606,973 read pairs. Reads were aligned to the draft assembly also following the manufacturer’s recommendations (Phase Genomics, 2024). Briefly, reads were aligned using BWA-MEM (Li and Durbin, 2010) with the –5SP and -t 8 options specified, and all other options default. (Faust and Hall, 2014) was used to flag PCR duplicates, of which were later excluded from the analysis. Alignments were then filtered with samtools (Li et al. , 2009) using the -F 2304 filtering flag to remove non-primary and secondary alignments. -Phase (Kronenberg et al. , 2018) was used to correct likely phase switching errors in the primary contigs and alternate haplotigs from -Unzip and output its results in pseudohap format, creating one complete set of contigs for each phase. Phase Genomics' Proximo Hi-C genome scaffolding platform was used to create chromosome-scale scaffolds from -Phase’s phase 0 assembly, following the same single-phase scaffolding procedure described in Bickhart et al. , 2017. As in the method (Burton et al. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses methodologies involving acetonitrile, LC-MS/MS, sequencing libraries, and genome scaffolding without any reference to insects or metamorphosis. There are no keywords or contexts that relate to the claim about insect life cycles.


Input: Task: corroborate the claim using the given text. Claim: Disruption of circadian rhythms can lead to health issues. [SEP] Text: Hamsters were subjected to the circadian DPS procedure at 2 to 8 months of age, and LPS treatments were administered between 8 and 15 months of age, after stable behavioral phenotypes had emerged. Because the DPS procedure induces circadian arrhythmia in a subset of hamsters (see below), middle-aged hamsters 8 to 15 months of age received the DPS treatment at one time point. In some reports, Siberian hamsters are regarded as “aged” at 17 to 24 months (Horton and Yellon, 2001; McKeon et al. , 2011) and in others at 24 to 28 months (Reuss and Bürger, 1994; Reuss et al. , 2000). manipulation that destabilizes the hamster circadian pacemaker employs phase-resetting light stimuli that render a substantial proportion of hamsters permanently behaviorally circadian arrhythmic (“ARR”; Ruby et al. , 2004) and disrupts SCN clock gene expression (Grone et al. , 2011). Hamsters were housed for 4 weeks in a 16L:8D photoperiod, and then on a single night, a 2-h light pulse was administered during the fifth through seventh hours of the dark phase. The next day, the 16L:8D photocycle was phase-delayed by 3 h, by extending the light phase. Ninety-three hamsters were subjected to the DPS protocol, which typically renders >50% of hamsters permanently circadian arrhythmic (Ruby et al. , 2004). treatment, home-cage LMA was assessed using passive infrared motion detectors positioned outside the cage (22 cm above the cage floor). Motion detectors registered activity when 3 of 27 zones were crossed. Activity triggered closure of an electronic relay recorded by a computer running ClockLab software (Actimetrics, Evanston, IL). Cumulative activity counts were collected at 1-min intervals. Activity data were collected in consecutive 10-day blocks, over an interval spanning 2 to 3 months after the DPS treatment (cf. Ruby et al. , 1998). Circadian PhenotypingCriteria for assessing the presence/absence of CRs were comparable to those in prior reports of DPS-induced CR disruption (Ruby et al. , 2004; Ruby et al. , 1998). [SEP] Justify:

Output: The text corroborates the claim by describing the effects of the DPS procedure on hamsters, which induces circadian arrhythmia and disrupts SCN clock gene expression. The reference to a substantial proportion of hamsters becoming permanently behaviorally circadian arrhythmic supports the assertion that the disruption of circadian rhythms can indeed have significant health implications.


Input: Task: contrast the claim using the given text. Claim: Biotechnology allows people to live forever by continually replacing damaged tissues. [SEP] Text: , working with tiny nematode worms, discovered a gene with such an effect on longevity in the 1980s. Mutation of a gene that the researchers aptly named age-1 produced a 40 percent increase in average life span. Since then, investigators in many laboratories have found numerous other genes capable of increasing nematode life span, and similar mutations have turned up in other animals, from fruit flies to mice. The genes that extend life span mostly alter an organism's metabolism, the way it uses energy for bodily functions. Often investigators find these genes play a role in the insulin-signaling pathway, pivotal in metabolic regulation. The cascades of molecular interactions constituting this pathway shift the overall level of activity of literally hundreds of other genes responsible for controlling all the intricate processes that carry out cellular maintenance and repair. In effect, it seems that lengthening life span requires changing exactly those processes we know protect the body against buildup of damage. The amount of food available also ratchets metabolism up or down. As long ago as the 1930s, researchers discovered, rather surprisingly, that underfeeding lab rodents extends their lives. Once again, modulating metabolism seems to have an effect on the rate of damage accumulation because mice subjected to dietary restriction increase the activity of a range of maintenance and repair systems. At first glance, it might seem strange that an animal short of food should spend more, not less, energy on bodily maintenance. A period of famine is, however, a bad time to reproduce, and some evidence suggests that during famines certain animals will do better to switch off their fertility, thereby diverting a large fraction of their remaining energy budget to cell maintenance. Of mice and menThis notion of caloric restriction—and its purported ability to extend longevity—has captured the attention of people who wish to live longer. Humans who go hungry in the hope of a longer life should take note, though, that such a mechanism is much less likely to work for members of our species because our slow-paced metabolism differs greatly from that of organisms in which this strategy has already been tested. Dramatic extension of life span has indeed been achieved in worms, flies and mice. These animals, with their short-lived, fast-burn biology, have an urgent need to manage their metabolism in a way that adapts rapidly to changing circumstances. [SEP] Justify:

Output: The text contrasts the claim by discussing the limitations of applying findings from experiments on organisms like nematode worms, fruit flies, and mice to humans. While it describes how mutations can significantly extend the lifespan of these organisms through metabolic alterations and maintenance processes, it also emphasizes that the same mechanisms may be ineffective in humans due to our different metabolism. The statement explicitly notes that dramatic longevity improvements have been demonstrated only in organisms with 'short-lived, fast-burn biology,' indicating that the notion of biotechnology leading to human immortality is not supported.


Input: Task: pass the claim using the given text. Claim: Some insects can undergo complete metamorphosis, transitioning through larval stages. [SEP] Text: , 2013), this process computes a contact frequency matrix from the aligned Hi-C read pairs, normalized by the number of DPNII restriction sites (GATC) on each contig, and constructs scaffolds in such a way as to optimize expected contact frequency and other statistical patterns in Hi-C data. Juicebox (Durand et al. , 2016; Rao et al. , 2014) was then used to correct scaffolding errors, and -Phase was run a second time to detect and correct phase switching errors that were not detectable at the contig level, but which were detectable at the chromosome-scaffold level. Metadata generated by -Phase about scaffold phasing was used to generate matching. assembly files (a file format used by Juicebox) and subsequently used to produce a diploid, fully-phased, chromosome-scale set of scaffolds using a purpose-built script (Sullivan, 2021). In these final scaffolds, phase 0 included 24 scaffolds spanning 1,027,591,625 bp (92. 82% of input) with a scaffold N50 of 43,313,630 bp, and phase 1 included 24 scaffolds spanning 1,019,278,383 bp (91. 98% of input) with a scaffold N50 of 43,164,609 bp. Data availability Code used in genome assembly and annotation, as well as in developmental transcriptome analysis can be found under the following DOI: All raw and assembled data used in this study has been deposited on GenBank under umbrella 798702, with the principal phased assembly in 798188, the alternate phased assembly in 798189, and the raw data in 794870. BioSamples can be found under SAMN24662200 (genome sequencing), SAMN24664212 (ISO-seq), and SAMN24664213 - SAMN24664234 SAMN32359227 - SAMN32359229 (RNA-seq). PacBio and Illumina raw data can be found under SRR17639994 - SRR17640023 SRR22859365 - SRR22859367. The final scaffolded assembly can be found under accession 000000000 and the alternative phase under accession 000000000. The genome and functional annotation are deposited on figshare under. The raw gene expression count data can be found in 1. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses genome assembly and data management in a scientific context, without mentioning insects or metamorphosis. Therefore, it does not provide any support, contradiction, or relation to the claim about the metamorphic process in insects.


Input: Task: corroborate the claim using the given text. Claim: Disruption of circadian rhythms can lead to health issues. [SEP] Text: The χ2 periodogram analyses (ClockLab; Actimetrics) were performed on 10-day blocks of activity data (cf. Ruby et al. , 1998). Hamsters were designated ARR absent clear and significant (p < 0. 001) peaks in the periodogram in the circadian range, with LMA distributed throughout the light-dark cycle, and daily discrete activity onsets and offsets not evident on visual inspection of the periodogram; hamsters with significant circadian activity peaks in the χ2 periodogram and clear daily activity onsets and offsets were considered entrained/rhythmic (RHYTH) (Ruby et al. , 1998). and 16 ARR hamsters were randomly assigned to receive LPS and saline treatments. LMA records of representative RHYTH and ARR hamsters are illustrated in Figure 1. Figure 1. Disruptive phase shifts render hamsters behaviorally arrhythmic. Representative double-plotted activity records of circadian entrained hamsters (RHYTH; A and C) and of hamsters rendered circadian arrhythmic (ARR; B and D) by disruptive phase shift (DPS) light treatments (see “DPS Procedure” for details). Records depict 10 consecutive days of home-cage locomotor activity collected >1 month after the DPS procedure was applied; corresponding χ2 periodogram analyses are depicted below each activity record. Values above the ascending line in the periodogram analysis indicate a significant (p < 0. 001) period. Time is indicated on the horizontal axis at the top of each actogram, along with light (white) and dark (black) phases of the 16L:8D photocycle. Shaded area indicates the dark phase. Surgical ProceduresUpon completion of circadian phenotyping, hamsters were anesthetized with isoflurane vapors (3% in medical O2) and received precalibrated radio-telemetric transmitters intraperitoneally (i. p. ) (Mini-Mitter ER-4000, E-mitters; Murrysville, PA). Postoperatively, subcutaneous (s. c. ) buprenorphine analgesic was administered at 12-h intervals for 48 h. E-mitters transmitted mean body temperature (Tb) and cumulative LMA at 6-min intervals to receiver boards placed under the cages. [SEP] Justify:

Output: The text corroborates the claim by describing how disruptive phase shifts can render hamsters behaviorally arrhythmic. It indicates that hamsters designated as 'ARR' displayed a lack of clear and significant peaks in the periodogram analysis, which implies disruption of their circadian rhythms. This condition is explicitly connected to a lack of rhythmicity in their behavior, supporting the assertion that disturbances in circadian functions can lead to health issues.


Input: Task: contrast the claim using the given text. Claim: Biotechnology allows people to live forever by continually replacing damaged tissues. [SEP] Text: In nematode worms, for example, most of the more spectacular effects on life span result from mutations that evolved to allow the worms to switch their development to a stress-resistant form whenever they find themselves in a bad environment and potentially required to make a long trek to find better living conditions. We humans, in any case, may not have the same flexibility in altering our own metabolic control. Immediate metabolic effects, of course, occur in humans who undergo voluntary dietary restriction, but only time—and many hungry years—will tell if these have any beneficial impact on the aging process and, in particular, on longevity. The goal of gerontology research in humans, however, is always improving health at the end of life, rather than achieving Methuselean life spans. One other thing is also very clear: the longer-lived worms, flies and mice still undergo the aging process. Aging happens because damage still accumulates and in time leads to the breakdown of healthy functions of the body. Therefore, if we want our end to be actually better, we need to look elsewhere. In particular, we need to focus on figuring out how to safely limit or reverse the buildup of damage that leads eventually to age-related frailty, disability and disease. This goal represents a huge challenge and calls for some of the most demanding of today's interdisciplinary research. No simple answersAging is complicated. It affects the body at all levels, from molecules to cells to organs. It also involves multiple kinds of molecular and cellular damage. And although it is true that, in general, this damage accumulates with age and occurs slower in some cell types than in others (depending on the efficiency of the repair systems), injury to any given cell occurs randomly, and the extent can differ even in two cells of the same type in an individual. Thus, all individuals age and die, but the process varies considerably—more confirmation that aging does not stem from a genetic program that specifies how quickly we become frail and die. To understand aging in enough detail to intervene in a suitably targeted fashion that stops or slows the death of selected kinds of cells, we need to know the nature of the molecular defects that drive the aging process at the cellular level. How many of these flaws must accrue before the cell can no longer function? How many defective cells need to accumulate in a given organ before it shows signs of disease? [SEP] Justify:

Output: The text contrasts the claim by discussing the complexities of aging and the limitations of current scientific knowledge in extending life indefinitely. It emphasizes that aging involves the accumulation of damage and that while research aims to improve health at the end of life, the goal is not achieving immortality. Furthermore, it mentions that even longer-lived organisms still undergo aging, directly opposing the idea that biotechnology can prevent death by simply replacing damaged tissues.


Input: Task: pass the claim using the given text. Claim: Some insects can undergo complete metamorphosis, transitioning through larval stages. [SEP] Text: The following data sets were generated (2024) 798702. Chromosome level assembly of the malabar grouper (Epinephelus malabaricus genome) genome. (2024) 794870. Epinephelus malabaricus (Malabar grouper). (2024) figshare Malabar grouper (Epinephelus malabaricus) genome resources. 410. PubMed 0416. 1692. PubMed 650. PubMed 3016. PubMed 026. PubMed 108. PubMed 60. PubMed 1125. PubMed 2267. PubMed 3024. 749. PubMed 489. 1498. 2558. PubMed 465. PubMed 428. PubMed 206. PubMed 173. PubMed 376. PubMed 16. 818. PubMed 31. PubMed 0301. PubMed 914. PubMed 21. PubMed 101. PubMed 2505. PubMed 9457. 1582. PubMed 1469. PubMed 452. PubMed 65. 2638. PubMed 3435. 70. 1771. PubMed 656. PubMed 6152. PubMed 769. PubMed 10. 1007/978-1-4939-9173-0_5 7595. PubMed 2122. 350. 161. PubMed 1251. 1769. 4. PubMed 181. 316. 10. 1101/327064 737. PubMed 1249. 2079. PubMed 595. 293. PubMed 6506. PubMed 119. PubMed 550. PubMed 350. 4654. PubMed 10. 27. 611. 165. PubMed 1361. PubMed 419. PubMed 131. 382. PubMed 468. PubMed 156. 1595. PubMed 122. PubMed 2024. Prévot‐D’Rostaing‐Leung‐(2008) Grouper aquaculture: Asian success and Mediterranean trials 18:297–308. 185. 1680. 128. 413. PubMed 5543. 87. 460. PubMed 2661. PubMed 074. PubMed 287. PubMed 136. 4118. 5181. PubMed 257. 194. PubMed 124. PubMed 11. PubMed 644. PubMed 2. PubMed 192. [SEP] Justify:

Output: The text is irrelevant to the claim as it does not mention insects or metamorphosis. Instead, it consists mainly of references to genome resources and various PubMed articles related to the malabar grouper, which has no connection to insect development.


Input: Task: corroborate the claim using the given text. Claim: Disruption of circadian rhythms can lead to health issues. [SEP] Text: 46, p = 0. 0013; chronotype × injection: F119,1428 = 1. 73, p ≤ 0. 001; Fig. 2). hamsters, LPS tended to decrease LMA during the first and second light phases postinjection (F1,14 = 4. 31, p = 0. 057, Fig. 2F) but not thereafter. LPS also inhibited activity during the first dark phase after treatment (F1,14 = 18. 3, p = 0. 0008), and nocturnal hypoactivity persisted for the next 3 nights (F1,14 > 6. 4, p ≤ 0. 04, all comparisons; Fig. 2F). In ARR hamsters, inhibitory effects of ZT1 LPS were not apparent during the light phase on any day after injection (Fig. 2H). In common with ZT16 injections, ZT1 LPS treatment decreased activity during the first dark phase postinjection (F1,14 = 10. 7, p = 0. 0056) but not during subsequent dark phases (Fig. 2H). AnorexiaLPS reduced food intake (F6,336 = 36. 2, p ≤ 0. 0001; Fig. 3), which depended on treatment ZT (injection × ZT: F6,336 = 2. 81, p = 0. 011). Anorexic responses were reduced in hamsters injected with LPS at ZT1 relative to ZT16 (F6,336 = 14. 3, p ≤ 0. 0001). LPS-induced anorexia at ZT16 was comparable in RHYTH and ARR hamsters (Fig. 3A, F6,168 = 0. 89, p = 0. 51). Food intake was lower in LPS-treated hamsters on posttreatment days 1 to 3 (p ≤ 0. 013, Fig. 3A), but not thereafter. Figure 3. Lipopolysaccharide (LPS)–induced anorexia. Mean ± SEM change in food intake (A and B) of circadian entrained (RHYTH; squares) and circadian arrhythmic (ARR; circles) female Siberian hamsters injected intraperitoneally (i. p. [SEP] Justify:

Output: The text discusses the effects of lipopolysaccharide (LPS) injections on hamsters' activity and food intake in relation to circadian time (ZT1 and ZT16). It specifically notes that LPS treatment decreases activity during the first dark phase after injection and that these effects vary based on the time of day, indicating a disruption in normal circadian rhythms, which is linked to health issues such as anorexia in the hamsters. This supports the claim that disruption of circadian rhythms can lead to health issues.


Input: Task: contrast the claim using the given text. Claim: Biotechnology allows people to live forever by continually replacing damaged tissues. [SEP] Text: And if we agree that some organs are more important to target than others, how do we deliver the necessary precision? It may be possible to combat aging by altering important mechanisms that cells use to counteract the buildup of damage. One way that a cell responds to too much wear and tear is simply to kill itself. At one time, scientists viewed this cellular suicide process, technically called apoptosis, as evidence that aging adheres to a genetic program. In aged tissues the frequency of cells killing themselves increases, and this process does indeed contribute to aging. But we now know that apoptosis acts chiefly as a survival mechanism that protects the larger body from injured cells that could potentially cause trouble, notably ones that have become malignant. Apoptosis happens more in old organs because their cells have suffered more insults. Remember, though, that in nature animals rarely live long enough to grow old. Apoptosis evolved to deal with damaged cells in younger organs, when many fewer would need to be eliminated. If too many cells die, an organ fails or becomes debilitated. So apoptosis is good and bad—good when it deletes potentially dangerous cells, bad when it deletes too many. Nature cares more about survival of the young than managing decline in old age, so not all apoptosis might be strictly necessary in our later years. In some diseases, such as stroke, researchers hope that by suppressing apoptosis in the less damaged tissue, the resulting loss of cells may be reduced, thereby aiding recovery. Instead of dying, hurt cells that are normally able to reproduce may take a less extreme course and simply stop dividing, a fate known as replicative senescence. More than 50 years ago Leonard Hayflick, now at the University of California, San Francisco, discovered that cells tend to divide a set number of times—now called the Hayflick limit—and then stop. Later work showed that they often stop dividing when the caps, or telomeres, that protect the ends of chromosomes erode too much. But other details of how cell senescence sets in remained obscure. A few years ago, though, my colleagues and I made an exciting discovery. We found that each cell has highly sophisticated molecular circuitry that monitors the level of damage both in its DNA and in its energy-forming units known as mitochondria. When the amount of damage passes some threshold, the cell locks itself into a state where it can still perform useful functions in the body but can never divide again. [SEP] Justify:

Output: The text contrasts the claim by discussing the complexities of cellular processes such as apoptosis and replicative senescence, which highlight the challenges associated with cellular damage and aging. It indicates that while apoptosis helps eliminate damaged cells and protects the body, it can also lead to organ failure if too many cells die. This suggests that biotechnology's potential to extend life is not straightforward and is limited by natural processes of cell death and senescence, which contradicts the claim of achieving everlasting life through tissue replacement.


Input: Task: pass the claim using the given text. Claim: Some insects can undergo complete metamorphosis, transitioning through larval stages. [SEP] Text: Peer review processEditorsReviewer #1Author ResponsePeer review processRevised: Preprint has been revised by the authors in response to the previous round of peer review; the eLife assessment and the public reviews have been updated where necessary by the editors and peer reviewers. Read more about eLife’s peer review process. de la újoUniversity of Barcelona, Barcelona, SpainReviewer #1 (Public Review): Summary and strength: The authors undertook to assemble and annotate the genome sequence of the Malabar grouper fish, with the aim to provide molecular resources for fundamental and applied research. Even though this is more mainstream, the task is still daunting and labor intensive. Currently, high quality and fully annotated genome sequences are of strategic importance in modern biology. The authors make use of the resource to address the endocrine control of an ecologically and developmentally relevant life cycle transition, metamorphosis. As opposed to amphibian and flat fish where body plan changes, fish metamorphosis is anatomically more subtle and much less known, although it is clear that thyroid hormone (TH) signaling is a key player. The authors thus provide a repertoire of TH-relevant gene expression changes during development and across post-embryonic transitions and correlate developmental stages with changes of gene expression. Overall, this work represents a significant advance in the field. Fish 'metamorphosis' is well known because it is not as spectacular as amphibians. This work clearly provides technical and theoretical resources to address in a more systematic manner the molecular changes occurring during development and post-embryonic transitions. Heterochrony is a major source of functional and life cycle diversity in fish, which blurs our anatomy-based understanding of fish biology, and has a direct impact on the protocols and rearing procedures used to produce live stocks. This work illustrates how, by using genomics coupled to simple experimental endocrinology, one directly addresses these challenges. response: The following is the authors’ response to the original reviews. Responses to recommendations Reviewer #1 (The Authors): Describe more precisely how gene expression graphs are built (tissues, reads counts). For example, how were read counts normalized? Were they from DESeq2 data, which only works by comparing two samples? If so, all samples should be independently compared to a reference and the normalized expression value of the reference will change from sample to sample. . . [SEP] Justify:

Output: The text does not address the claim regarding insects undergoing complete metamorphosis. Instead, it discusses the genome sequence of the Malabar grouper fish and its metamorphosis, which is not related to the claim about insects. Thus, the text is irrelevant.


Input: Task: corroborate the claim using the given text. Claim: Disruption of circadian rhythms can lead to health issues. [SEP] Text: ZT1—CR powerLocomotor activityLPS decreased circadian power (F6,36 = 3. 68, p = 0. 0059; Fig. 6C) during the first 4 posttreatment days (p < 0. 05, all comparisons) with a greater reduction in ZT1 than ZT16 hamsters on days 3 to 7 posttreatment (p < 0. 05, all comparisons; Fig. 6A,C). In contrast, LPS at ZT1 did not affect power in the Tb circadian rhythm (Fig. 6D). DiscussionLPS-induced activation of the hamster innate immune system induced fever and sickness behaviors. Novel findings in the present report include evidence that power in locomotor activity (LMA) and Tb URs was enduringly altered, UR period was transiently lengthened, and CR power was chronically attenuated by LPS. Many of these responses were influenced by the timing of the immune challenge and/or the integrity of the circadian pacemaker. These data add to an emerging literature on effects of circadian organization and timing of immune challenges on multiple aspects of the acute-phase response to infection. Despite unavoidable limitations in clock gene knockout, LL, and SCNx models of circadian arrhythmia, results from the DPS hamster model used here (which is genetically and neurologically intact) underscore a theme that has emerged from these other models, namely, that the circadian clock has important influences on the immune system. That these different approaches converge in establishing a strong circadian-immune connection suggests that effects observed after gene knockouts or SCN ablation may indeed reflect loss of timing information per se rather than pleiotropic effects or nonspecific lesion confounds. Time of on LMA vs. TbThe severity of the response to LPS varied over circadian time in a trait-specific manner. hamsters, LPS at ZT16 elicited more enduring febrile responses than at ZT1, whereas LMA responses were more persistent at ZT1 than at ZT16. These data add to work in rodents (Liu et al. , 2006; Marpegan et al. , 2009; Keller et al. , 2009; Weil et al. , 2009; Spengler et al. , 2012) and humans (Petrovsky et al. , 1998) documenting circadian variation in responses to LPS and other inflammatory challenges. [SEP] Justify:

Output: The text corroborates the claim by describing how LPS-induced activation of the hamster innate immune system affects circadian rhythms. It highlights that 'power in locomotor activity (LMA) and Tb URs was enduringly altered' due to the timing of immune challenges, indicating that disruptions in the circadian clock can have significant implications for health, particularly in regards to immune responses. This supports the notion that disturbances in circadian rhythms may lead to health complications.


Input: Task: contrast the claim using the given text. Claim: Biotechnology allows people to live forever by continually replacing damaged tissues. [SEP] Text: As with apoptosis, nature's bias toward the survival of the young probably means that not all these lockdowns are strictly necessary. But if we are to unpick the locks and so restore some division capacity to aged cells, without unleashing the threat of cancer, we need to understand very thoroughly just how cell senescence works. The demanding science needed to make this discovery required a multidisciplinary team, including molecular biologists, biochemists, mathematicians and computer scientists, as well as state-of-the-art instruments for imaging the damage in living cells. Where such discoveries might lead we do not yet know, but it is through studies of this kind that we can hope to identify novel drugs able to combat age-related diseases in completely new ways and thereby shorten the period of chronic illness experienced at the end of life. The difficulty of this type of basic research means that many years, perhaps decades, may pass before these drugs come to market. Using the science of aging to improve the end of life represents a challenge, perhaps the greatest yet to face medical science. Solutions will not come easily, despite the claims made by the merchants of immortality who assert that caloric restriction or dietary supplements, such as resveratrol, may allow us to live longer. The greatest human ingenuity will be needed to meet this challenge. I believe we can and will develop treatments targeted at easing our final years. But when the end arrives, each of us—alone—will need to come to terms with our own mortality. All the more reason then to focus on living—on making the most of the time of our lives, because no magic elixir will save us. Rights & and Age. Leonard Hayflick. Ballantine Books, 1994. Understanding Ageing. Robin Holliday. Press, 1995. Age: about the Body's Journey through Life. Steven N. Austad. and Sons, 1999. from an Evolutionary Perspective. T. B. Kirkwood in Journal of Internal Medicine, Vol. 263, No. 2, pages 117–127; February 2008. of Age. Thomas Kirkwood. BBC Reith Lectures. www. bbc. co. uk/radio4/reith2001More by Thomas KirkwoodThis 10. 1038/scientificamericansecrets0315-12with ScienceLearn and share the most exciting discoveries, innovations and ideas shaping our world today. [SEP] Justify:

Output: The text contrasts the claim by stating that the notion of living forever through biotechnology is an oversimplification. It discusses the challenges of understanding cell senescence and emphasizes that the research needed to develop effective treatments for age-related diseases is demanding and may take decades. Furthermore, the text asserts that there's no 'magic elixir' for immortality, focusing instead on the inevitability of mortality and the need to make the most of our lives. This directly contradicts the claim that biotechnology can allow people to live forever.


Input: Task: pass the claim using the given text. Claim: Some insects can undergo complete metamorphosis, transitioning through larval stages. [SEP] Text: thus introducing a pure technical artifact. We have added additional information about the normalisation method to the Material and Methods section (Lines 597-598: “Lastly, expression levels shown in figures 2-5 are normalised gene counts produced by DESeq2. ”) and figure legends (lines 247, 286, 372, 404: “Gene expression data was generated from whole fish. Expression levels were derived from DESeq2 normalised gene counts. ”) to address this recommendation. DESeq2 provides a reference independent normalisation through a median of ratios method (a good explanation can be found here: tml). The normalised expression values are independent of any reference, and therefore will not change from sample and sample as suggested in this comment. In contrast, the pairwise comparisons are done when analysing significantly differentially expressed genes between two treatments using a Wald test, which is done against a reference and generates log2 fold change information and p-values. ; however, this is different to the normalisation we described above. Provide bioinformatics workflows and, if possible, the set of parameters used, the computing resources, etc. Were some assembly finishing steps carried out (by long-range PCR? ) and experimental validations (especially for allelespecific transcripts, by conventional RT-PCR based on diagnostic mutations)? We have added additional information on the bioinformatics workflows where required, including parameters used (Lines 530, 536, 549-551, and 574-583. ). No finishing steps other than HiC scaffolding were performed. No allele-specific analysis was done as part of this manuscript. To further improve transparency, we have also uploaded all the scripts used for this study to and the gene models and functional annotation to annotation/199909. This information has been added to the manuscript in lines 600601 and 609-611. Reviewer #3 (The Authors): General author response: All the recommendations of this reviewer are very relevant and would certainly provide a lot of information, but they are constituting a full project in themselves as they would imply establishing this grouper species as an experimental model in our lab. Currently we only have access to the larval and juvenile stages via a collaboration with the Center, which is an hour drive from our lab, and is limited to the grouper spawning season. [SEP] Justify:

Output: The text does not address the claim regarding the metamorphic process of insects. Instead, it discusses technical details related to bioinformatics methods and research procedures, making it irrelevant to the claim about insect metamorphosis.


Input: Task: corroborate the claim using the given text. Claim: Disruption of circadian rhythms can lead to health issues. [SEP] Text: The time of peak responsiveness to inflammogens depends on species, type of inflammatory challenge, and outcome measure. A minority of responses to LPS in ARR hamsters varied as a function of injection ZT (e. g. , anorexia). This may be attributable to masking effects of ZT treatment. There is precedent for circadian arrhythmic animals to exhibit trait-specific masking responses in a full L:D cycle: 42% of Syrian hamsters with large SCN lesions, behaviorally arrhythmic in running wheels in LL, synchronized locomotor activity, and ingestive behavior in the presence of a light-dark cycle (Rusak 1977). Synchronization of wheel-running behavior by the light-dark cycle also is evident in multiple gene knockout mice (e. g. , Bae et al. , 2001; Izumo et al. , 2014) that are circadian arrhythmic in constant darkness. Although LMA and Tb are arrhythmic in DPS hamsters exposed to a full light-dark cycle, a complete inventory of traits that exhibit masking responses to light (or darkness) in this model does not yet exist. to LPSCompared to their respective saline-injected controls, Tb responses to LPS at ZT16 were attenuated in ARR compared to RHYTH hamsters, as was true of diminished LMA in response to LPS at ZT1. LPS has been reported to attenuate (Wachulec et al. , 1997) or exacerbate (Guerrero-Vargas et al. , 2014) Tb responses to LPS in SCNx rats. The dose of LPS and route of administration may account for these divergent results. Species and sex differences (Wachulec et al. , 1997; Guerrero-Vargas et al. , 2014) and the procedures employed to induce circadian arrhythmia also may affect responses to LPS. For example, the effects of circadian arrhythmia on memory processing differ categorically depending on whether arrhythmia is induced via SCNx or DPS (Fernandez et al. , 2014). The direction and magnitude of effects of circadian arrhythmia on the inflammatory response to LPS may similarly depend on the methods employed to render animals arrhythmic. [SEP] Justify:

Output: The text corroborates the claim by discussing the effects of circadian arrhythmia on health-related responses, particularly in the context of inflammatory challenges. It references how circadian arrhythmia influenced responses to LPS (lipopolysaccharide), noting that the 'effects of circadian arrhythmia on memory processing differ categorically' and that 'the direction and magnitude of effects of circadian arrhythmia on the inflammatory response to LPS may similarly depend on the methods employed to render animals arrhythmic.' This suggests a clear link between disruption of circadian rhythms and health issues related to inflammation and memory processing.


Input: Task: contrast the claim using the given text. Claim: Stem cells can regenerate any type of tissue instantly, curing all injuries. [SEP] Text: of human pluripotent stem cells overexpressing errgamma can efficiently improve the symptoms of type 2 diabetes patient Submit manuscript. . . Advances in eISSN: 2572-8490 & Regenerative Medicine: Transplantation of human pluripotent stem cells overexpressing ERRγ can efficiently improve the symptoms of type 2 diabetes patient Taihua Wang,1-3 × Regret for the inconvenience: we are taking measures to prevent fraudulent form submissions by extractors and page crawlers. Please type the correct Captcha word to see email ID. Xin Wang,1-3 Bailing Zhang,1-3 Meidai Fan,1-3 Xiaohui Cui,1-4 Lina Zhao,1-3 Xin Chen,3 Zhenzhen Yang,1,2 Xinyi Shi,1,2 Rongrong Li,1,2 Qingchang Fang,1,2 Xiaojuan Diao,1,2 Limin Zhang,1,2 Guoke Yang,4 Ying Meng,4 Guiwen Yang1-4 1of 2Institute of Shandong Province, China3Co. , Guangdong Province, China4School of : Taihua Wang, of of Room 509, 5th Floor, 2766 Yingxiu Road, Jinan, Shandong Province, 250101, China Received: May 27, 2018 | Published: June 12, 2018 Citation: Transplantation of human pluripotent stem cells overexpressing ERR? can efficiently improve the symptoms of type 2 diabetes patient. . 2018;4(3):457–462. DOI: 10. 15406/atroa. 2018. 04. 00078 the discovery that insulin can reduce blood glucose levels in 1922, exogenous insulin administration becomes the standard method to treat human diabetes patients. Yet, this method cannot efficiently prevent the development of diabetes complications. Here, we report a combinatorial strategy that combines human pluripotent stem cells and overexpression of estrogen-related receptor γ (ERRγ) together, which, in theory, not only can repair the damaged tissues and restore the function of human pancreatic β cells, but also can synthesize and secrete human insulin, so that to reduce the blood glucose levels of the diabetic patients after transplantation. [SEP] Justify:

Output: The text contrasts the claim by discussing the specific application of human pluripotent stem cells in treating type 2 diabetes, and while it mentions tissue repair, it does not support the notion that stem cells can regenerate any type of tissue instantly or cure all injuries. Instead, it implies a targeted therapeutic effect rather than an instantaneous or universal healing capability.


Input: Task: pass the claim using the given text. Claim: Some insects can undergo complete metamorphosis, transitioning through larval stages. [SEP] Text: If we want to do all what is suggested, we need to have a regular and easy access to the fishes. This would require establishing this model in our marine station, which is not possible due to space and time issues. These groupers grow to a very large size (1-2 m in length, and up to 150 kg in weight) and only mature into males after > 6 years. First and foremost, I would advise the authors to extend their TH and cortisol levels measurements to the entire developmental time considered in their analysis. For the reasons stated above we could not perform these experiments. We must emphasize that the data regarding TH are available for a closely related species (e. g. , Epinephelus coioides, de Jesus et al. 1998) and there is no reason to think that the situation will be drastically different in E. malabaricus. In addition, given that we have now studied several coral reef fish species in the same context (clownfish, surgeonfish, damselfish, gobies) we observed that the transcriptomic data are more robust, more sensitive, and more precise than hormone measurements. Consider carrying out in situ hybridisation of TSH with putative CRH receptors to determine if thyrotrophin could be competent to respond to HPA axis signals. We agree studying the interplay between corticoids and thyroid hormones at the neuroendocrine level would be desirable and we fully agree with the experiment suggested by the reviewer, but this is impossible in our current situation. We are not working with an establish animal model like zebrafish or Xenopus, but with a large, long-lived marine fish that reproduces in spawning aggregations and whose husbandry is notoriously difficult. Consider conducting cortisol treatment experiments to functionally determine if indeed cortisol is involved in grouper metamorphosis. We tried to do TH and cortisol treatments specifically on the early larval stages corresponding to the early TH peak to see how this would impact the development of the fin spines, but our trials were unsuccessful. The larvae at that stage are extremely fragile and even putting them into small volumes of treatment drugs induced massive mortalities. Again, this would mean establishing this grouper species as a model organism and would require a massive effort to improve larval rearing as discussed above. We feel that our data stands on its own in the meantime and adds valuable information to the existing literature by studying a rarely investigated species. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses research related to marine fish, their hormonal measurements, and challenges faced during larval development. It does not mention insects or metamorphosis, thus failing to support or contradict the claim.


Input: Task: corroborate the claim using the given text. Claim: Disruption of circadian rhythms can lead to health issues. [SEP] Text: Inflammatory responses in rodents with CR disruption induced by clock gene mutations likewise suggest that the method by which CRs are disrupted can affect the immunophenotype. Some circadian clock genes appear to enhance inflammatory responses to LPS: Clock-deficient mice exhibit reduced tumor necrosis factor α (TNFα)–mediated NF-κB activation (Spengler et al. , 2012), and per2 mutant mice are resistant to LPS-induced sepsis (Liu et al. , 2006). On the other hand, macrophages rendered arrhythmic via bmal1–/– failed to exhibit CRs in LPS-induced interleukin (IL)–6 production, an effect also evident in macrophages from mice deficient in rev-erbα; macrophages of rev-erbα–/– mice exhibit enhanced IL-6 responses to LPS (Gibbs et al. , 2012). The macrophage clock likely inhibits cytokine production at certain circadian phases. Assessment of the proinflammatory cytokine responses to LPS in DPS-ARR hamsters would be instructive in ascertaining whether effects of chronotype reported here reflect ARR-induced decrements in peripheral production of inflammatory mediators. Ultimately, disentangling the effects of loss of temporal order per se from the direct (noncircadian) effects of interventions that induce temporal disorder (Gibbs et al. , 2012; Spengler et al. , 2012; Sato et al. , 2014) remains a challenge to understanding how the circadian timing system affects inflammatory responses and, more broadly, organismal-level immune function. Nevertheless, the present data, derived from neurologically and genetically “intact” hamsters, underscore the importance of the circadian system in the maintenance of normal immune responses. LPS-aspects of the circadian waveform changed after LPS treatment, which immediately decreased power of LMA activity CRs, regardless of injection ZT. Effects of LPS on power of CRs in Tb were only evident after ZT16 injections, however, and were delayed in appearance. LPS causes modest but stable shifts in the phase of the circadian pacemaker in the SCN (Marpegan et al. , 2005), effects mimicked by intracerebroventricular (i. c. v. [SEP] Justify:

Output: The text corroborates the claim by discussing how disruptions in circadian rhythms (CR) can lead to alterations in inflammatory responses and immune function. It highlights that certain circadian clock genes, when disrupted, affect the production of proinflammatory cytokines in response to stimuli like LPS, suggesting a link between circadian disruption and health issues, particularly in the context of immune responses.


Input: Task: contrast the claim using the given text. Claim: Stem cells can regenerate any type of tissue instantly, curing all injuries. [SEP] Text: Our preliminary investigation demonstrated that our method can efficiently secrete human insulin, increase the secretion of human C-peptide, and improve the patient’s health conditions physically and mentally, thus, with the potential to prevent and even to reverse human diabetic complications with more transplantations. Our reports laid an important foundation for treating human diabetes and eventually cure this disease. Keywords: directly generated human pluripotent stem cells, ERRγ, insulin secretion, C-peptide increase, human type 2 diabetes Abbreviations hESCs, human embryonic stem cells; hiPSCs, human induced pluripotent stem cells; ERRγ, estrogen-related receptor γ; hADSCs, human adipose-derived stem cells; dgHPSCs: directly generated human pluripotent stem cells 1922, Banting et al. ,1 first discovered that daily insulin injection could decrease the blood glucose levels and other associated symptoms of type I diabetes, and since then, insulin is generally used for treatment of diabetes with absolute insulin deficiency. 1,2 However, with the progressing of the symptoms, exogenous insulin administration need to be intensified with more and more dosages, and even worse, the only administration of insulin cannot maintain blood glucose levels within the narrow physiological range that protects from development of various diabetic complications. 2 In addition, currently available therapies for diabetes have limited effects in preventing the progression of diabetes complications and repairing existing tissue damages. 3 Therefore, more efficient strategies for diabetes treatment are urgently needed to develop. To generate insulin-producing pancreatic β cells from human embryonic stem cells (hESCs) and induced pluripotent stem cells (hiPSCs) in vitro provides an unlimited cell source for transplantation therapy in diabetes. 4,5 So far, a number of groups have generated immature or mature human insulin-producing pancreatic β cells from hESCs/hiPSCs. 4–16 After transplantation of these β cells, they can restore the glucose homeostasis in diabetic mice shortly after or after a period of in vivo maturation. 4,5,16 Although the protocols to generate pancreatic β cell-like cells are complicated and challenging, these achievements are encouraging and promising with the potential for better treatment for human type I and type 2 diabetes. Yet, very few reports for successful treatment of human diabetes patients are known with this strategy. [SEP] Justify:

Output: The text contrasts the claim by stating that while stem cells can potentially treat diabetes by generating insulin-producing pancreatic β cells, this process is complicated and challenging. It emphasizes that current therapies have limited effects and acknowledges that successful treatment of human diabetes patients using this strategy is very rare. This indicates that stem cells do not cure all injuries instantly as suggested by the claim.


Input: Task: pass the claim using the given text. Claim: Some insects can undergo complete metamorphosis, transitioning through larval stages. [SEP] Text: Responses to comments Reviewer #1 (Public Review): Weaknesses: The manuscript needs proper editing and is not complete. Some wordings lack precision and make it difficult to follow (e. g. line 98 "we assembled a chromosome-scale genome of. . . " should read instead "we assembled a chromsome-scla genome sequence of. . . ". Also, panel Figure 2E is missing. We made the suggested change of adding “sequence” in lines 32 and 121. Concerning additional changes, we have carefully edited our manuscript and looked for any incomplete sections. Unfortunately, it is difficult to see what other issues are being raised here without any further information. As for panel E of figure 2, it is not missing. The panel is located to the right, just below “Target Cells”. The shortcomings of the manuscripts are not limited to the writing style, and important technical and technological information is missing or not clear enough, thereby preventing a proper evaluation of the resolution of the genomic resources provided: Several RNASeq libraries from different tissues have been built to help annotate the genome and identify transcribed regions. This is fine. But all along the manuscript, gene expression changes are summarized into a single panel where it is not clear at all which tissue this comes from (whole embryo or a specific tissue), or whether it is a cumulative expression level computed across several tissues (and how it was computed) etc. This is essential information needed for data interpretation. No fertilised eggs or embryos have been sequenced. The individual tissues derived from juvenile fish were used for the genome annotation only, using ISOseq. The whole larval fish were used for the developmental analysis using RNAseq, as well as the genome annotation. We have added additional information in the figures and text that the results shown are from whole larvae, and added more detail to the material and methods section about which type of sample was analysed in which way. Specifically, we have added “Lastly, expression levels shown in figures 2-5 are normalised gene counts produced by DESeq2. ” to lines 597-598 in the Material and Methods section, “Gene expression data was generated from whole larvae. ” to line 191, and “Gene expression data was generated from whole fish. Expression levels were derived from DESeq2 normalised gene counts. ” to the figure legends in lines 247, 286, 372, 404). [SEP] Justify:

Output: The text does not provide information pertinent to the claim about insects undergoing complete metamorphosis. Instead, it discusses the weaknesses and editorial recommendations for a manuscript, focusing on technical details regarding genomic resources and gene expression analysis without mentioning metamorphosis or larval stages.


Input: Task: corroborate the claim using the given text. Claim: Disruption of circadian rhythms can lead to health issues. [SEP] Text: )treatments with IL-1β or TNFα, and blocked by inhibitors of TNFα signaling (Leone et al. , 2012), suggesting that TNFα plays a central role in LPS-induced phase shifts. Decreases in overall LMA levels by LPS or live bacterial infections have been reported in several rodent models (reviewed in Harrington, 2012), as has inhibition by the viral mimetic Poly I:C (Katafuchi et al. , 2005) and treatment with proinflammatory cytokines (e. g. , IL-1β; Anisman et al. , 2008). Initial global disruption of LMA, followed by a resumption of circadian activity patterns, is commonly reported (Harrington, 2012). Decreases in global LMA levels and decrements in the circadian waveform may reflect dampening of the underlying circadian pacemaker (Okada et al. , 2008) and may constitute an underrecognized symptom of the acute-phase response to infection. Changes in CRs during acute illness may constitute an adaptive component of the acute-phase response to infection, conserving energy by decreasing the amount or amplitude of LMA and peak Tb. Altered by Inflammatory ResponsesEffects of LPS on URs were evident in both RHYTH and ARR chronotypes, but there was a general pattern of diminished effects of LPS in ARR hamsters. females, the temporal structure (period) of URs was disrupted shortly after LPS treatment at ZT16. A ~1-h increase in the period of the LMA UR was evident during the first dark phase, immediately after injection. Normal UR periods were restored by the following night. Period-lengthening effects of LPS on LMA URs were not evident after ZT1 injections, and the periods of URs in Tb were unaffected by LPS. Thus, LPS has a potent, transitory period-lengthening effect on select URs and may be limited to inflammatory responses initiated around the time of activity onset. In contrast, effects of LPS on UR power were evident at both ZTs; in many instances, decreases in UR power persisted for several days depending on trait and chronotype. At ZT16, LPS inhibited dark-phase LMA and Tb UR power of RHYTH hamsters for 2 to 3 nights. [SEP] Justify:

Output: The text corroborates the claim by discussing how treatments and interventions such as LPS (lipopolysaccharide) lead to disruptions in locomotor activity (LMA) and circadian rhythms (CRs) in rodent models. It highlights that changes in circadian rhythms during acute illness are adaptive responses to infection, and alterations in circadian activity patterns and period-lengthening effects imply that disruptions of these rhythms can correlate with health complications related to inflammation and infection.


Input: Task: contrast the claim using the given text. Claim: Stem cells can regenerate any type of tissue instantly, curing all injuries. [SEP] Text: Estrogen-related receptor γ (ERRγ) is a master regulator of β cell maturation in vivo. Forced expression of ERRγ in hiPSC-derived β-like cells enables glucose-responsive secretion of human insulin in vitro, and can further restore the glucose homeostasis in type 1 diabetes mouse models after transplantation, without the need for kidney capsule maturation, to achieve functionality immediately. 16 Human adipose-derived stem cells (hADSCs) were first confirmed by Zuk et al. ,17 to have the potentials to differentiate toward the osteogenic, adipogenic, myogenic, chondrogenic, and putative neurogenic cells. Sun et al. 18 reported the successful induction of hiPSCs from hADSCs with lentivirus transduction containing human Oct4, Sox2, Klf4, and c-MYC. 18 Yet the use of oncogene c-MYC as one of the inducing factors still remained to be a potential concern for the clinical application of these hADSC-derived iPSCs. During the past years, we invented a novel protocol, which can directly generate human pluripotent stem cells from hADSCs without any genetic modification. We termed these cells as directly-generated human pluripotent stem cells (dgHPSCs). Then, we transduced human ERRγ gene into dgHPSCs (termed as dgHPSCs-ERRγ) via a lentivirus vector, and the forced expression of ERRγ conferred the dgHPSCs secrete human insulin immediately after transduction. When clinically delivered these dgHPSCs-ERRγ cells into type 2 diabetes patients, they can not only decrease the blood glucose levels, but also increase the secretion of C-peptide, which indicates the improvement of the functions of the pancreatic β-cells of the patient. Our data provided an efficient strategy for treatment of diabetes with the potential to repair the malfunctioned pancreatic β cells by human stem cell therapy. Materials and methods Statement of ethical approval The treatments for the patients and the use of human stem cells were approved by the of of (Shengjieyi 2003, No. 26) in compliance with Helsinki Declaration. Committee of of approved this clinical study and treatments. The participants provided their written confirmed consent to participate the clinical study and treatments. [SEP] Justify:

Output: The text contrasts the claim by detailing specific applications of stem cells in treating type 1 and type 2 diabetes, emphasizing that while stem cells can aid in repairing specific tissues, such as pancreatic beta cells in diabetes, they do not regenerate 'any type of tissue instantly' as the claim suggests. Furthermore, the text outlines the need for additional protocols, ethical approval, and the potential concerns regarding oncogene use, all indicating that stem cell therapy is not a universal or instantaneous cure for all injuries.


Input: Task: pass the claim using the given text. Claim: Some insects can undergo complete metamorphosis, transitioning through larval stages. [SEP] Text: Additionally, we have added clarifications in lines 489, 497, 530, and 536. The bioinformatic processing, especially of the assemble and annotation, is very poorly described. This is also a sensitive topic, as illustrated by the numerous "assemblathon" and "annotathon" initiatives to evaluate tools and workflows. Importantly, providing configuration files and in-depth description of workflows and parameter settings is highly recommended. This can be made available through data store services and documents even benefit from DOIs. This provides others with more information to evaluate the resolution of this work. No doubt that it is well done,but especially in the field of genome assembly and annotation, high resolution is VERY cost and time-intensive. Not surprisingly, most projects are conditioned by trade-offs between cost, time, and labor. The authors should provide others with the information needed to evaluate this. We have added additional information on parameters used in the genome assembly, annotation and transcriptome analysis in lines 549-551, 577, 579, 580, and 582. Additionally, we have uploaded all scripts to github as outlined in the Code and section (lines 599-614). The genome assembly did not use a specific workflow (e. g. , nextflow), but was done with a simple command and standard parameters in IPA. Scaffolding was carried out by using their standardised proprietary workflow, of which a detailed description provided by can be found in the supplementary material. Quantifications of T3 and T4 levels look fairly low and not so convincing. The work would clearly benefit from a discussion about why the signal is so low and what are the current technological limitations of these quantifications. This would really help (general) readers. The T3/T4 levels are consistent with other published work in fish. In the present manuscript for grouper we have a peak level of 1. 2 ng/g (1,200 pg/g) of T4 and 0. 06 ng/g (60 pg/g) of T3. This is a higher level of T4 and comparable level of T3 to what was found in convict tang (Holzer et al. 2017; Figure 2) with 30 pg/g of T4 and 100 pg/g of T3. Of course, there are also examples with higher levels, such as clownfish (Roux et al. [SEP] Justify:

Output: The text does not address the claim about insects undergoing complete metamorphosis. Instead, it focuses on discussing issues related to genome assembly, annotation, and quantifications of hormone levels in fish. Thus, it is irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Disruption of circadian rhythms can lead to health issues. [SEP] Text: ZT1 LPS likewise inhibited UR power in both chronotypes, with more enduring effects in RHYTH hamsters. To our knowledge, these are the first quantitative descriptions of changes in the UR waveform during the acute-phase response to simulated infection. Numerous reports describe effects of LPS on sleep (Krueger et al. , 1986; Exton et al. , 1995; Kapás et al. , 1998; Schiffelholz and Lancel, 2001; Jakubcakova et al. , 2011), a behavior with clear ultradian characteristics, but information on LPS-induced changes in the sleep ultradian waveform (period, power) is lacking. URs are ubiquitous in vertebrate physiology, evident during both the active (food intake, LMA, Tb) and inactive (sleep, rest) phases. An important functional role for URs may lie in higher-frequency temporal partitioning of activity during each phase of the circadian cycle, conserving energy by consolidating behavior into bouts of relative activity and inactivity (Aschoff and Gerkema, 1985). Disorganization of ultradian temporal order normally present in well individuals may reflect novel, energetically costly aspects of the acute-phase response to infection. Quantification of CNS cytokine or monoaminergic responses to LPS, although beyond the scope of the present study, could provide mechanistic insights into the chronobiological consequences of innate immune activation (cf. Blum et al. , 2014). SummaryIn a novel model of circadian arrhythmia, with relevance to human circadian disruption, we investigated the role of circadian phase and integrity on multiple components of the behavioral response to infection. We confirmed and extended existing reports of circadian phase-specific effects of inflammation on sickness responses. Circadian arrhythmia attenuated several sickness responses, suggesting that temporal disorganization of the internal milieu in the DPS model may interfere with the generation of robust behavioral and immune responses to infection. The DPS treatment does not involve surgical or genomic manipulations; nevertheless, DPS-ARR hamsters exhibited altered inflammatory responses to LPS. These data offer novel, convergent evidence toward the importance of the circadian system in maintaining normal immune responses and suggest that immunological changes observed in knockout and lesion models may indeed be consequences of the elimination of circadian time information. Novel inhibitory effects of LPS on the generation of CRs and URs in multiple traits also were documented. [SEP] Justify:

Output: The text corroborates the claim by discussing the effects of circadian arrhythmia and how it interferes with robust behavioral and immune responses to infection. It states, 'Circadian arrhythmia attenuated several sickness responses,' indicating that disruptions in circadian rhythms can negatively impact health. The mention of 'the importance of the circadian system in maintaining normal immune responses' further supports the claim that circadian disruptions can lead to health issues.


Input: Task: contrast the claim using the given text. Claim: Stem cells can regenerate any type of tissue instantly, curing all injuries. [SEP] Text: Committee of of approved this consent procedure. All the treatments for the patients and use of human stem cells were performed in accordance with the guidelines established in of approved by the Ethics Committee. After traditional daily insulin injection for about four years, the patient agreed to try the stem cell therapy with overexpression of ERRγ in our hospital to control his blood glucose levels and wanted to restore his physical conditions and potential complications of type 2 diabetes, including his pancreatic β cell functions. The stem cells used in these clinical treatments are dgHPS#1 stored at our Bank. All these stem cells were isolated and proliferated with the written confirmed consent of the participants and their parents. Patient case The patient (designed as patient #1, initials T. S. D. , male, born at 1958) was first diagnosed as type 2 diabetes with high blood glucose values in 2005, and the value was about 7. 0mmol/L. Subsequently, his blood glucose levels increased with the time going on, and the testing results were approximately above 7. 0mmol/L in 2006, above 9. 0mmol/L in 2007, about 12. 0mmol/L in 2012, and above 13. 0mmol/L in 2013, respectively. of 2014, he was diagnosed with coronary heart disease, and three cardiac stents were implanted at 11th of September. He began to inject insulin (Humalog Mix25, Italia S. P. A. , Italy) in October of 2014 twice a day, 10IU in the morning and 8IU at night, respectively, together with taking Repaglinide (NovoNorm, A/S, Denmark) orally to control his blood glucose levels for about a month. After stop taking Repaglinide, the insulin injected was increased to 12IU in the morning and 10IU at night daily. Beginning at 2016, the insulin injected was intensified as 12IU in the morning and 12IU at night daily. 19th of 2018 on, he gave up insulin injection and accepted stem cell therapy to treat his type 2 diabetes. Cell preparation We isolated processed lipoaspirate cells from one of the volunteered author (G. Z. ) and cultured the ADSCs according to the method described by Zuk et al. 17 Then, we directly generated dgHPSCs using our invented novel protocol without any genetic modifications. [SEP] Justify:

Output: The text contrasts the claim as it describes a specific case where stem cell therapy was used to treat type 2 diabetes, rather than asserting that stem cells can regenerate any type of tissue instantly or cure all injuries. The description includes the patient's medical history and the gradual effectiveness of treatments rather than an immediate or universal cure from stem cell application.


Input: Task: pass the claim using the given text. Claim: Some insects can undergo complete metamorphosis, transitioning through larval stages. [SEP] Text: 2023; Figure 1), with 10 ng/g (10,000 pg/g) of T4 and 2 ng/g (2,000 pg/g) of T3. The differences could be due to different structure of fish tissues and therefore different hormone extraction efficiency, different hormone measurement protocols, different fish physiology, different fish size (e. g. , the weighting of tiny grouper larvae is difficult and less precise than in convict tang). What is important is not the absolute level but the relative level, which shows the change within different larval stages of a species with identical extraction and measurement protocols. Which means our data is internally consistent and coherent with what the grouper literature says. Holzer, Guillaume, et al. "Fish larval recruitment to reefs is a thyroid hormonemediated metamorphosis sensitive to the pesticide chlorpyrifos. " Elife 6 (2017): e27595. Roux, Natacha, et al. "The multi-level regulation of clownfish metamorphosis by thyroid hormones. " 42. 7 (2023). Differential analysis highlights up to ~ 15,000 differentially expressed genes (DEG), out of a predicted 26k genes. This corresponds to more than half of all genes. ANOVA-based differential analysis relies on the simple fact that only a minority of genes are DEG. Having >50% DEG is well beyond the validity of the method. This should be addressed, or at least discussed. The large number of differentially expressed genes is due to the fact that this is coming from a larval developmental transcriptome going from one day old larva to fully metamorphosed juveniles at around day 60. While DESeq2 indeed works on an assumption that most genes are not differentially expressed, this affects normalization but not hypothesis testing (Wald-test, LRT tests or ANOVA). However, normalisation in DESeq2 is fairly robust to this assumption. According to the author of DESeq2, Micheal Love, DESeq2 is using the median ratio for normalisation, and as long as the number of up and down regulated genes is relatively even, DESeq2 will be able to handle the data. As part of our general quality control for this project we consulted the MA plots, which do not show any overrepresented up or down expression patterns. [SEP] Justify:

Output: The text does not provide information relevant to the claim about insects undergoing complete metamorphosis. Instead, it discusses thyroid hormone-mediated metamorphosis in fish larval development and the analysis of gene expression, which is unrelated to the metamorphosis of insects.


Input: Task: corroborate the claim using the given text. Claim: Disruption of circadian rhythms can lead to health issues. [SEP] Text: Journal of Circadian RhythmsStart SubmissionBecome a ReviewerReading: Ischemic stroke destabilizes circadian rhythmsDownloadXML (US English)PDF (US English)Alt. DisplayShareShareResearch 10. 1186/1740-3391-6-9Submitted on Sep 4, 2008Accepted on Oct 15, 2008Published on Oct 15, 20084. 0 is a leading cause of death and disability world-wide. While the immediate consequences of stroke include permanent cognitive deficits, paralysis, visual impairment, and sensory disturbances, stroke also results in long term dysregulation of sleep and mood, which may be equally disabling. The influence of ischemic stroke on circadian rhythm regulation, which is strongly linked to sleep and mood, may thus potentially influence long-term recovery in stroke patients. In humans, the daily expression of a multitude of physiological variables is suppressed by ischemic stroke [1 - 8], but limited work has been done to establish whether these effects reflect true disruption of the circadian timing system. To address the status of the central circadian pacemaker, other investigators have measured melatonin after stroke [9]. Beloosesky et al. [10] sampled urinary melatonin metabolites every four hours and found that rhythms persisted in all stroke patients, but the phase was delayed by about 4 hours during the first day in patients with extensive brain injury; the delay was not apparent 10 days after stroke. Fiorini et al. [11] measured urinary melatonin every 12 hours after stroke and demonstrated decreases in stroke patients that persisted for two weeks. The precise timing of melatonin secretion could not be determined in this study. Pang et al. [9] demonstrated that intracerebral hemorrhage in a variety of locations inhibits the production of melatonin measured by venipuncture. The lack of longitudinal data in human subjects makes it difficult to determine whether stroke induces changes in circadian timing. In addition, the interpretation of these studies is difficult, since standard medical care of acute stroke patients by necessity requires nocturnal disruption that may suppress melatonin and falsely imply changes in circadian timing. To overcome limitations of clinical studies, a small number of experimental systems have been used to study the effect of stroke on circadian regulation. Work in mice has shown that sleep [12] is inhibited by ischemic stroke. [SEP] Justify:

Output: The text corroborates the claim by discussing how ischemic stroke affects circadian rhythms, which in turn, influences sleep and mood regulation. It indicates that stroke leads to long-term dysregulation of these rhythms, highlighting the relationship between circadian disruption and potential health problems, particularly in the context of recovery from a stroke.


Input: Task: contrast the claim using the given text. Claim: Stem cells can regenerate any type of tissue instantly, curing all injuries. [SEP] Text: These cells are termed as dgHPS#1 and show TRA-1-60 positive, which is a pluripotent marker of human stem cells (Data not shown). 19 A detailed report of the method of the generation and identification of dgHPSCs will be published at an early date after finishing the patenting procedure. Lentivirus vector construction, production and infection A clinical level third generation of lentivirus vector pWPI/ERRγ was constructed according to the combinatorial strategy previously described20–23 from original vector pWPI/hPLKWT/Neo (Addgene plasmid #35385). 24 The pWPI/ERRγ lentivirus vector was produced, and infected into dgHPS#1 cells according to a previous report. 24 Briefly, one 15-cm dish of dgHPSCs was infected with 25ml lentiviruses, and two 15-cm dishes of dgHPSCs were infected with 50ml lentiviruses. dgHPSCs transplantation After clinical treatment of dgHPSCs-ERRγ cells, the cells were transplanted into the patient intravenously. Each time, approximately 8x107 to 1. 5x108 cells were transplanted into the patient, and the intervals between transplantations were around three to five days, respectively. Totally, five times of transplantation were performed (Table 1). Transplantation date Cell type Cell number 20-01-2018 dgHPSCs+pWPI/ERRγ 8. 1x107 24-01-2018 dgHPSCs+pWPI/ERRγ 1. 4x108 29-01-2018 dgHPSCs+pWPI/ERRγ 9. 36x107 02-02-2018 dgHPSCs+pWPI/ERRγ 1. 53x108 05-02-2018 dgHPSCs+pWPI/ERRγ 1. 12x108 Table 1 Time table of human stem cell transplantations Insulin secretion test The insulin secreted into cell culture supernatant was tested via electrochemiluminescence method performed by (Jinan, Shandong Province, China). Clinical responses and treatment efficacy assessment The venous blood C-peptide and insulin were tested by (Jinan, Shandong, China). [SEP] Justify:

Output: The text contrasts the claim as it describes a specific procedure involving human stem cells (dgHPS#1) but does not support the assertion that they can regenerate any type of tissue instantly or cure all injuries. Instead, it presents a detailed method of transplantation and monitoring of a particular type of stem cell treatment, which implies that the usage of stem cells is methodical and not instant.


Input: Task: pass the claim using the given text. Claim: Some insects can undergo complete metamorphosis, transitioning through larval stages. [SEP] Text: Additionally see comment on comparing different tissues, which is also applicable here when comparing vastly different larval stages ( “For experiments where all genes increase in expression across conditions, the median ratio method will not be able to capture this difference, but this is typically not the case for a tissue comparison, as there are many "housekeeping" genes with relatively similar expression pattern across tissues. ” Reviewer #3 (Public Review): Weaknesses: However, the authors make substantial considerations that are not proven by experimental or functional data. In fact, this is a descriptive study that does not provide any functional evidence to support the claims made. We agree with the reviewer that our paper lacks functional experiments but despite that, the transcriptomic data clearly show the activation of TH and corticoid pathways during two distinct periods: an early activation between D1 and D10, and a second one between D32 and juvenile stage. These data are interesting as they call for further examination of 1) the existence of an early larval developmental step also involving TH and corticosteroids and 2) the possible interaction of corticoids and TH during metamorphosis. This is a question that is certainly not settled yet in teleost fishes and which is of great interest. Especially 1) is of interest and importance, since this early activation (unique to our knowledge in any teleost fish studied so far) raises a lot of new questions and once again will certainly be scrutinised by other groups in the years to come, therefore ensuring a good citation impact of this study. We hope that the reviewer, while disagreeing with some our statements, will recognize that our study will be stimulating at that level and that this is what scientific studies should do. We acknowledge the descriptive nature of the data and the lack of functional experiments in the Discussion in lines 443 to 445: “This may suggest that in some aspect, cortisol synthesis could work in concert with TH, as has been shown in several different contexts in amphibians, but functional experiments need to be conducted to confirm this hypothesis. ” As stated above doing such functional experiment would require establishing the grouper as an experimental model in our husbandry, which currently is not possible due to the large size of the adult fish. The consideration that cortisol is involved in metamorphosis in teleosts has never been shown, and the only example cited by the authors (REF 20) clearly states that cortisol alone does not induce flatfish metamorphosis. [SEP] Justify:

Output: The text is irrelevant to the claim as it primarily discusses the lack of functional experimental data in a study about hormonal pathways in teleost fish and does not mention insects or metamorphosis in the context of the claim. The focus on corticoid pathways and TH suggests a biological process in fishes, which is outside the scope of insect metamorphosis.


Input: Task: corroborate the claim using the given text. Claim: Disruption of circadian rhythms can lead to health issues. [SEP] Text: Spontaneously hypertensive stroke prone rats, which spontaneously undergo both hemorrhagic and ischemic stroke, exhibit blunting of heart rate and blood pressure rhythms, but changes in circadian timing were not clear [13]. The circadian variables in these studies have limited time resolution and thus are insufficient to prospectively quantify circadian phase changes. Pineal microdialysis offers an exceptional technique for measuring quantitative changes in circadian melatonin secretion [14]. This method enables real time analysis of a single individual, and therefore can prospectively measure quantitative circadian responses to environmental changes, pharmaceuticals, and potentially disease states. In addition, the precise and sensitive measurement of pineal melatonin permits the quantitative determination of melatonin phase with up to 10-minute resolution. Pineal melatonin is the most accurate marker of the central circadian clock [15,16] and is not subject to pathological masking that could be affected by the neurological compromise (eg. suppression of motor activity secondary to hemiparesis, abulia, or ataxia after stroke). In this report, we applied pineal microdialysis to determine whether ischemic stroke in rats alters the circadian rhythm. All experiments were performed in accordance with NIH guidelines and approved by the University of on Use and Care of Animals. Adult male Wistar rats (300 g) (Harlan) were housed at 20 to 25°C under LD 12:12 h conditions, with ad libitum food and water. Illumination levels were 300–400 lux at cage level. Microdialysis probe implantation Surgical placement of microdialysis probes was performed as described [14]. Briefly, following deep anesthesia, the animal's head was shaved and positioned in a stereotaxic instrument with the head flat. Two small burr holes were created on both sides of the skull. A custom linear microdialysis probe was inserted carefully through the burr holes into the brain tissue containing the pineal gland and was connected with dialysis tubing at both ends. Following surgery, animals were housed individually and allowed to recover for 16–24 h before microdialysis. Sample collection and analysis Following recovery, animals were transferred to dialysis chambers where their pineal glands were continuously perfused with artificial cerebral spinal fluid at a low (2 ul/min) rate via inlet tubing connected at one end of the microdialysis probe. [SEP] Justify:

Output: The text supports the claim by discussing the effects of ischemic stroke on circadian rhythms in rats, noting that blunting of heart rate and blood pressure rhythms was observed. The investigation of circadian melatonin secretion through pineal microdialysis indicates that the circadian system is influenced by environmental and pathological states, which suggests that disruptions of such rhythms could indeed correlate with health issues.


Input: Task: contrast the claim using the given text. Claim: Stem cells can regenerate any type of tissue instantly, curing all injuries. [SEP] Text: 5 23-02-2018 10. 4 24-02-2018 8. 8 25-02-2018 9. 4 26-02-2018 8. 4 27-02-2018 8. 6 28-02-2018 9. 6 01-03-2018 9. 1 02-03-2018 7. 2 03-03-2018 10. 1 04-03-2018 10. 5 05-03-2018 9. 4 06-03-2018 9. 3 07-03-2018 10. 7 08-03-2018 10. 4 10-03-2018 10. 6 11-03-2018 10. 4 13-03-2018 10. 9 15-03-2018 10. 8 16-03-2018 10. 2 18-03-2018 10. 6 19-03-2018 10. 2 Table 3 Daily monitoring of fasting fingertip capillary blood glucose (FFT-CBG) levels Results dgHPSCs-ERRγ cells can secrete insulin immediately after transduction Yoshihara et al. ,16 reported that forced expression of ERRγ gene in human iPSC-derived β-like cells enabled glucose-responsive secretion of human insulin in vitro, and demonstrated that ERRγ is a master regulator of β cell maturation in vivo. At the same time, this function of ERRγ could be recapitulated in vitro. 16 Inspired by this finding, we reasoned that the overexpression of ERRγ might drive the synthesis and secretion of human insulin from human pluripotent stem cells without differentiating into β-like cells in vitro. To confirm this hypothesis, we used 50ml clinical level third generation of lentiviruses pWPI/ERRγ to infect approximately 1x108 dgHPSCs, 2 days post infection, the insulin in the cell culture supernatants were tested. To our surprise, we found that the concentration of insulin in the supernatant was 30. 84µIU/ml, whereas, the concentration of secreted insulin in the supernatant was 11. 61µIU/ml when dgHPSCs were infected with pWPI/Insulin lentivirus vectors (designated as dgHPSCs-Insulin) using the same method. [SEP] Justify:

Output: The text contrasts the claim by providing specific research results that highlight the capabilities of stem cells, particularly focusing on insulin secretion from human pluripotent stem cells. Instead of supporting the idea that stem cells can instantaneously regenerate all types of tissue, the findings indicate that specific functions, like insulin secretion, can be engineered, which suggests limitations. The results of insulin secretion by cell culture models do not support the claim of 'curing all injuries' or instant regeneration of tissue, highlighting the complexity and specificity of stem cell applications.