Input: 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.

Output: contrast


Input: 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.

Output: pass


Input: 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).

Output: corroborate


Input: 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.

Output: contrast


Input: 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.

Output: pass


Input: 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.

Output: corroborate


Input: 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?

Output: contrast


Input: 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.

Output: pass


Input: 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.

Output: corroborate


Input: 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.

Output: contrast


Input: 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. . .

Output: pass


Input: 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.

Output: corroborate


Input: 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.

Output: contrast


Input: 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.

Output: pass


Input: 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.

Output: corroborate


Input: 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.

Output: contrast


Input: 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.

Output: pass


Input: 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.

Output: corroborate


Input: 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.

Output: contrast


Input: 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).

Output: pass


Input: 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.

Output: corroborate


Input: 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.

Output: contrast


Input: 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.

Output: pass


Input: 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.

Output: corroborate


Input: 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.

Output: contrast


Input: 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.

Output: pass


Input: 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.

Output: corroborate


Input: 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).

Output: contrast


Input: 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.

Output: pass


Input: 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.

Output: corroborate


Input: 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.

Output: contrast


Input: Claim: Some insects can undergo complete metamorphosis, transitioning through larval stages. [SEP] Text: In that work, the authors clearly state that in vivo cortisol treatment had no synergistic effect with TH in inducing metamorphosis. Moreover, in Senegalensis, the sole pre-otic CRH neuron number decreases during metamorphosis, further arguing that, at least in flatfish, cortisol is not involved in flatfish metamorphosis (PMID: 25575457). We will do our best to improve the clarity of the revised manuscript to avoid any misunderstanding about our claims. However, we would like to point out the semantic shift in the reviewer first sentence: Indeed “being involved” is not the same as “cortisol alone does not induce”. In ref 20 the authors explicitly wrote that “Cortisol further enhanced the effects of both T4 and T3, but was ineffective in the absence of thyroid hormones” and in our view this indeed corresponds to ”being involved in metamorphosis”. We are not claiming that cortisol alone is involved in metamorphosis as the reviewer suggests, but simply that there is a possible involvement of cortisol together with TH in metamorphosis. We stand on this claim as we indeed observed an activation of corticoid pathway genes around D32, which is sufficient to say it is involved. We do agree that functional experiments will be needed to properly demonstrate the involvement of corticoids in grouper metamorphosis, but this was not possible in the current study as it would imply to set up a full grouper life cycle in lab conditions which is impossible for the scope of this manuscript. We also mentioned in the discussion that the role of corticoids in fish larval development is still debated, and we agree that this remains a contentious issue. We have clarified the Discussion on this point (lines 375-376, lines 439-464). We wrote that “There is contrasting evidence of communication between these two pathways during teleost fish larval development with some data suggesting a synergic and other an antagonistic relationship. In terms of synergy, an increase in cortisol level concomitantly with an increase in TH levels has been observed in flatfish [26], golden sea bream [64] and silver sea bream [65]. Cortisol was also shown to enhance in vitro the action of TH on fin ray resorption (phenomenon occurring during flatfish metamorphosis) in flounder[27].

Output: pass


Input: Claim: Disruption of circadian rhythms can lead to health issues. [SEP] Text: to stroke, we implanted Wistar rats (n = 14) with pineal microdialysis probes and determined baseline melatonin secretion patterns. Since this is an outbred population, we observed a range of MT-on and melatonin offset (MT-off) times (Figure 1), defined by the interval between time of dark onset and time when the melatonin rhythm reached 20% of its nightly maximum. The variation of MT-on and MT-off within the cohort has been described previously [19]. Melatonin duration was calculated as the time difference between MT-on and MT-off. Although there was variation within the cohort of circadian profiles, individual rats prior to stroke showed virtually no day-to-day variation in MT-on, MT-off, or melatonin duration over more than three days of baseline observation, as described previously (14). Figure 1 Baseline melatonin profiles for rats prior to MCAo. Melatonin profiles were obtained for all animals prior to MCAo to determine baseline timing. Measurements were made for up to six days, and, in all cases, the daily melatonin timing was stable. Therefore, only a single day's tracing of each individual is shown in this composite illustration. Animals exhibit a wide range of timing profiles. There is a broader range of MT-on times compared to MT-off times. The melatonin duration is defined as the time between the MT-on and MT-off. The MT-on is defined as the time when melatonin rises to 20% of the daily maximum (set to 100%). The MT-off is defined as the time when the melatonin level falls to 20% of the daily maximum. The gray shaded area represents time of lights off. MCAo surgery was then performed on these animals. All surgeries were initiated between 12:15 h and 14:34 h during the day. Rats were then placed back on microdialysis to measure post-surgical circadian melatonin profiles. We could not record melatonin secretion from one animal, and it was excluded from analysis. Two animals did not show changes in melatonin secretion after MCAo. Eleven of the remaining 13 rats exhibited temporal shifts in melatonin secretion, beginning with the first night after MCAo (Day 0); a representative rat is shown in Figure 2A. These rats demonstrated clear brain infarctions of the cortex and basal ganglia, demonstrated by TTC staining (Figure 2A).

Output: corroborate


Input: Claim: Stem cells can regenerate any type of tissue instantly, curing all injuries. [SEP] Text: In addition, no human C-peptides were detected in the supernatant of dgHPSCs-ERRγ and dgHPSCs-Insulin, respectively. To our knowledge, this is the first time to discover that human pluripotent stem cells overexpression ERRγ can efficiently synthesize and secrete human insulin at the pluripotent stem cell state, and do not need to differentiate into β-like cells. Transplantation of dgHPSCs-ERRγ can replace exogenous insulin administration, efficiently reduce the blood glucose levels and increase C-peptide secretion The tested results were showed in Table 3, and the patient did twice tests at January 19th of 2018 before receiving stem cell transplantation and at March 7th of 2018 after five times transplantations, respectively. The patient stopped daily insulin injection at January 19th of 2018, and went to the of to test his fasting blood glucose, glycosylated haemoglobin, fasting insulin, and fasting C-peptide. The results showed that, without the exogenous insulin administration, the patient’s fasting blood glucose gradually increased from around 7mmol/L (with daily insulin injection) up to 9. 46mmol/L in the morning of January 19th of 2018 (at January 18th of 2018, the patient injected insulin twice, morning and night, 12U, respectively). With daily injection of insulin, his glycosylated hemoglubin value was 6. 0%, and the fasting insulin and C-peptide were 59. 88pmol/L and 0. 584nmol/L, respectively (Table 2). After receiving dgHPSCs-ERRγ cell transplantations, the patient could totally give up exogenous insulin administration, and maintained his fasting glucose level around 11. 23mmol/L (compared with his fasting glucose levels above 13mmol/L in 2013 before treatment with insulin administration), and his glycosylated hemoglubin value about 8. 3%, respectively. Surprisingly, his fasting C-peptide levels increased from 0. 584nmol/L up to 0. 890nmol/L, which is the hallmark for the repairing of the functions of pancreatic β cells.

Output: contrast


Input: Claim: Some insects can undergo complete metamorphosis, transitioning through larval stages. [SEP] Text: It has also been shown that cortisol regulates local T3 bioavailability in the juvenile sole via regulation of deiodinase 2 in an organ-specific manner [66]. On the antagonistic side, it has been shown that experimentally induced hyperthyroidism in common carp decreases cortisol levels[67], whereas cortisol exposure decreases TH levels in European eel [68]. Given this scattered evidence, the existence of a crosstalk active during teleost larval development and metamorphosis has never been formally demonstrated. The results we obtained in grouper are clearly indicating that HPI axis is activated during both early development and metamorphosis and that cortisol synthesis is activated during early development. 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 [25], but functional experiments need to be conducted to confirm this hypothesis. ” In the revised manuscript, we have also added the interesting case of the Senegal sole mentioned by the reviewer. In the last revision, we had also added that our results “brought a first insight into the potential role of corticoids in the metamorphosis of E. malabaricus and call for functional experiments directly testing a possible synergy” meaning that we clearly acknowledge that we are only revealing a hypothesis that remains to be tested. We later follow up with a discussion about the most novel observation and focus of our study, the increase in THs and cortisol during early development, which was unexpected and very intriguing. Again, these results suggest that there might be a link between the two, as has been shown in amphibians. This is typically the kind of results that should encourage more investigations into other fish species. Indeed, this has been pointed out by other authors and in particular by (probably the foremost expert on this topic) in Crespi and Denver 2012: “Elevation in HPA/I axis activity has been described prior to Metamorphosis in amphibians and fish, birth in mammals (reviewed in Crespi & Denver 2005a; Wada 2008)”. B. Denver also adds that: “Experiments in which GCs were elevated prior to metamorphosis or prior to hatching or birth (e. g. Weiss, Johnston & Moore 2007) or inhibited by treatments with GC synthesis blockers (e. g. metyrapone) or receptor antagonists (e. g.

Output: pass


Input: Claim: Disruption of circadian rhythms can lead to health issues. [SEP] Text: Figure 2 Effect of MCAo on rhythmic secretion of melatonin. Melatonin secretion was measured in animals before and after surgery. Representative animals undergoing MCAo (A) and sham surgery (B) are shown. Tracings represent daily melatonin profiles superimposed upon the time of the day, with the gray shaded area representing lights off. Each day is demonstrated in a different color. D-2 and D-1 are two and one day before surgery. D0 is the day of the surgery, which was performed in the daytime. Days one to four (D1 to D4) are post-operative days. MCAo caused an advance of MT-on that persisted through four days of monitoring (A). MCAo slightly delayed the MT-off. Due to technical reasons, the data for the third postoperative day was lost (D3*). TTC stained brain sections are displayed to demonstrate that MCAo induces cortical and subcortical infarction. Sham surgery (B) did not affect MT-on or MT-off timing and did not cause brain infarction. We also performed sham MCAo (control) surgery on six rats that were analyzed by pineal microdialysis. These rats had pre-surgical melatonin profiles that were similar to the rats with MCAo. All six rats exhibited identical timing of melatonin secretion before and after control surgery; a representative animal is shown in Figure 2B; as expected, TTC staining of control brains showed no infarction. We examined the entire cohort of animals that exhibited melatonin shifts to attempt to identify trends in circadian behavior. Figure 3 shows the MT-on and MT-off profiles for this set of rats. Surprisingly, the pattern of circadian phase shifts in melatonin secretion showed a heterogenous amplitude and direction of change. In general, however, the MT-on shifts were more pronounced than MT-off shifts. The duration of melatonin secretion also exhibited significant differences after stroke in these animals (Figure 4). The changes in melatonin duration varied in direction and amplitude. When daily shifts of MT-on were averaged following stroke surgery (a measure of deviation from baseline – see methods), we observed a significant difference (p < 0. 02) between sham and MCAo treated animals (Figure 5).

Output: corroborate


Input: Claim: Stem cells can regenerate any type of tissue instantly, curing all injuries. [SEP] Text: In addition, the daily monitoring of fingertip capillary blood glucose revealed that the effect of decreasing blood glucose by dgHPSCs-ERRγ cell transplantation could maintained at least for one and half months (Table 3). The exact duration of the effects of stem cell transplantations still needs to be determined further because the patient will take the second course of treatment using stem cell transplantation afterwards. The glucose challenge tests before and after stem cell transplantations did not show significant improvements both for insulin and C-peptide secretions (Table 2). These data demonstrated that transplantations of dgHPSCs-ERRγ cells could potentially replace exogenous insulin administration and restore the functions of the patient’s pancreatic β cells. The follow-up visit of the patient The patient reported that he had a transient fever after the transplantations of about 1x108 cells, and the body temperature reached up to 37°C. The fever faded away next day. 26 of 2018, about 50 days after the last transplantation, the patient described that he felt stronger physically, and his knees felt much better, he could exercise much longer than before and did not feel tired. His gross amount of food per meal did not change, but his body weight decreased slightly. In a word, his overall physical conditions were improved obviously. 2 diabetes is an increasing threat to human health span, and diabetes incidence and prevalence increase with the age. Approximately 25. 9% of Americans of 65 years or older have diabetes, whereas, 9. 3% of those in the general population. 3 In addition, diabetes is a major risk factor for premature onset of multiple age-related conditions, including renal dysfunction, cardiovascular disease, stroke, impaired wound healing, infection, depression, and cognitive decline. 25–27 Although, almost one hundred years ago, Banting et al. ,1 confirmed that administration of exogenous insulin can decrease blood glucose levels and improve the symptoms of diabetes, the administration of exogenous insulin cannot maintain blood glucose levels within the narrow physiological range and further protect from development of various diabetic complications, because normal pancreatic β cells adjust insulin secretion continually in response to varying blood glucose levels. 2 Therefore, to develop novel strategies for diabetes treatment to restore the normal functions of pancreatic β cells is critical to finally cure diabetes and protect from diabetic complications development.

Output: contrast


Input: Claim: Some insects can undergo complete metamorphosis, transitioning through larval stages. [SEP] Text: RU486, Glennemeir & Denver 2002) demonstrate that GCs play a causal role in precipitating these life-history transitions (also reviewed in Crespi & Denver 2005a; Wada 2008). ” We believe the reviewer will be convinced by these elements coming from a colleague unanimously respected in the field. Furthermore, the authors need to recognise that the transcriptomic analysis is whole-body and that HPA axis genes are upregulated, which does not mean they are involved in regulating the HPT axis. The authors do not show that in thyrotrophs, any CRH receptor is expressed or in any other HPT axis-relevant cells and that changes in these genes correlate with changes in TSH expression. An in-situ hybridisation experiment showing co-expression on thyrotrophs of HPA genes and TSH could be a good start. However, the best scenario would be conducting cortisol treatment experiments to see if this hormone affects grouper metamorphosis. We agree that functional experiments are needed to validate our hypothesis. As the early peaks of expression levels observed for many genes were very intriguing for us, we did carry out thyroid hormones and goitrogenic treatment on young grouper larvae to test their effect on the morphological changes. Unfortunately, such experiments, already tricky on metamorphosing larvae, are even more risky on such tiny individuals just after hatching and we encountered high mortality rates. We must add that because we cannot establish a full grouper life cycle under lab conditions, we have done these experiments in the context of a commercial husbandry system in Japan, which while excellent limits the scope of possible experiments. We were thus not able to provide functional validation of our hypothesis. Such experiments will be a full project in itself, requiring setting up a rearing system suitable for both larval survival and economical constraints related to drug treatments. We were further limited by the spawning times of the grouper in the operational aquaculture farm, which are limited to a short time during each year. So even if we strongly agree with the necessity of conducting such experiments, we think that this is not in the scope of the present paper, but something future research can explore. High TSH and Tg levels usually parallel whole-body TH levels during teleost metamorphosis.

Output: pass


Input: Claim: Disruption of circadian rhythms can lead to health issues. [SEP] Text: However, in animals for which we had daily data for extended periods, the MT-on and melatonin duration demonstrate highly dynamic day-to-day changes after stroke (Figures 8A and 8B); the change in MT-on and melatonin duration from day-to-day exhibited an alternating pattern, seeming to oscillate after stroke, albeit with progressively decreasing amplitude. The waning of day-to-day changes suggests that over time, the melatonin onset and duration are reaching equilibrium at a new set point. As on the first day after MCAo, MT-on and melatonin duration changes over the course of a few days correlate well with each other, indicating that the main determinant of melatonin duration changes after stroke is the MT-on shift (Figure 8C). Figure 8 Day to day changes in MT parameters after stroke. The day-to-day changes in MT-on and melatonin duration were defined as the change in melatonin timing compared to the time on the previous day. As expected, on Day -1, there is no shift since the melatonin rhythm is stable. However, on Day 0 (the day of the stroke) there is a change in the melatonin timing compared to before stroke. Only five animals, represented by different colors, were used for this analysis. Other animals in the study could not be used because of gaps in data. (A) MT-on changes markedly in most animals from day-to-day. In all animals, there is a remarkable oscillation of the daily changes in melatonin timing. In general, the amplitude of the oscillation decreases over time. (B) A similar trend is seen with the daily change in melatonin duration. (C) There is a strong relationship between the daily shift in MT-on and melatonin duration among most animals. The r2 coefficients (for each animal) were: 0. 85 (ID2658), 0. 56 (ID2833), 0. 15 (ID2839), 0. 92 (ID2892), and 0. 99 (ID2900). To determine whether circadian melatonin shifts were related to the degree of infarction, we computed the area of brain infarction using established morphometric methods. The range in infarction volume was typical of stroke studies (30% +/-15%).

Output: corroborate


Input: Claim: Stem cells can regenerate any type of tissue instantly, curing all injuries. [SEP] Text: To date, different protocols are reported for in vitro differentiation and production of pancreatic β cells from hESCs and hiPSCs. Transplantations of these β cells produced can decrease the blood glucose levels of the animal models, and elongate their life spans. Although these results are encouraging and promising, these protocols are complicated and time consuming. 4–16 Worth of particular note, to our knowledge, there are no successful reports for clinically treatment of human diabetes patients using in vitro differentiated pancreatic β cells thus far. ERRγ is a master regulator of β cell maturation in vivo, and in vitro overexpression of ERRγ in human iPSC-derived β-like cells can give rise to functional and transplantable glucose-responsive cells capable of restoring glucose hemeostasis in type 1 diabetic mouse models. More importantly, these transplanted β-like cells can control blood glucose levels in recipient mice chronically up to 56 days. 16 Surprisingly, we found that our transduced dgHPSCs-ERRγ cells could secrete insulin into cell culture supernatant, and the concentration of secreted insulin in the supernatant was 30. 84µIU/ml. Since our transduction format was performed in 50ml volume, in theory, our transduced cells could continually secrete about 1,542µIU insulin into the recipient blood after intravenous transplantation. Furthermore, we found that the patient’s fasting blood C-peptide is 0. 890nmol/L after stem cell transplantations, much higher than 0. 584nmol/L before those transplantations. Consequently, the fasting blood insulin concentration is 53. 06pmol/L after transplantations, which is slightly lower than 59. 88pmol/L before transplantations, with the exogenous insulin injection of 24IU daily before the test. These data demonstrated that the transplantation of dgHPSCs-ERRγ cells not only can decrease the blood glucose levels, but also increase the secretion of C-peptide by the pancreatic β cells, which is the hallmark for the improvement of the β cells functions. Therefore, we believe that the transplanted dgHPSCs-ERRγ cells can potentially differentiate into functional pancreatic β cells and further restore the injured patient’s pancreatic β cell’s normal functions.

Output: contrast


Input: Claim: Some insects can undergo complete metamorphosis, transitioning through larval stages. [SEP] Text: However, in this study, high Tg expression levels are only achieved at the juvenile stage, whereas high TSH is achieved at D32, and at the juvenile stage, they are already at their lowest levels. This is exactly our point. We observe two peaks in TSH expression, one at D3 and one at D32. The peak at D3 coincides with high thyroid hormone levels on the same day, and while we have not measured TH at D32, existing literature shows that there is a peak in TH during that time (e. g. , de Jesus et al. , 1998). Similarly, there is a small peak of Tg at D3. Our manuscript focused more on the upregulation of these genes at D3, which has not been reported before in the literature and raised the question of the role of TH so early in the larval development, outside of the metamorphosis period. Regarding the respective levels of TSH and Tg, we first would like to add that their respective order of appearance before metamorphosis (TSH at D32, Tg after) is consistent with what we would expect. We agree however that the strong increase of Tg and TPO expression is later than expected. Therefore, we have added the following sentence in lines 212 to 216: “The respective order of appearance of TSH and Tg (TSH at D32, Tg after) is consistent with what we would expect but a bit later than expected given the morphologicl transformation. It would be interesting to revisit this in a future series of experiments, with tighter temporal sampling to study how gene expression and morphological transformation aligned. “. It is very difficult to conclude anything with the TH and cortisol levels measurements. The authors only measured up until D10, whereas they argue that metamorphosis occurs at D32. In this way, these measurements could be more helpful if they focus on the correct developmental time. The data is irrelevant to their hypothesis.

Output: pass


Input: Claim: Disruption of circadian rhythms can lead to health issues. [SEP] Text: We could not identify a correlation between the degree of damage and either the direction or the amplitude of initial changes in MT-on, MT-off, and melatonin duration (Figure 9). Figure 9 Infarct volume and its relationship to shift in MT timing. Infarct volumes for all animals undergoing MCAo were computed. Each rat's infarct volume was plotted against the Day 0 shift in MT-on, melatonin duration, or MT-off relative to the baseline time before stroke. There was no linear relationship between infarct volume and any of the quantitative measures of circadian changes. The r2 values are shown; no relationship was found. Melatonin production in the pineal gland is controlled by a number of brain structures that include the SCN, paraventricular nucleus of the hypothalamus (PVN), and intermediolateral nucleus of the spinal cord (IML). In addition, the thalamic intergeniculate leaflet (IGL) [20] modulates SCN activity, which may affect melatonin output. Additionally, structures such as caudate putaman (CPu) and parietal cortex are involved in locomotor rhythm generation that can be dissociated from the SCN signals [21], and may be affected in animals after stroke. To determine whether specific regions affected by MCAo were responsible for melatonin rhythm disruption, we examined lesion sites of MCAo-treated animals. Of the animals that exhibited shifts in melatonin rhythms, only one showed injury near the SCN and only three animals showed infarctions of the IGL. None of the animals had injury to the PVN or IML. This indicates that injury to these structures cannot account for the change in melatonin timing after stroke. On the other hand, all animals had significant injury to the CPu, and all but two animals had cortical injury. Thus, CPu stroke is sufficient by itself to disrupt normal melatonin rhythms. is the first study to our knowledge that demonstrates an effect of stroke on diurnal melatonin secretion in experimental animals. Our experiments unequivocally demonstrate that ischemic strokes in rats disrupt the timing of melatonin onset and/or offset, which are the most consistent and direct markers of circadian timing. We also demonstrate that pineal microdialysis is a highly sensitive method for the study of modulation of the circadian pacemaker by disease states.

Output: corroborate


Input: Claim: Stem cells can regenerate any type of tissue instantly, curing all injuries. [SEP] Text: Although the patient’s blood glucose, C-peptide and glycosylated haemoglobin levels are still higher than normal physiological range, with continued transplantation of these stem cells, it is very promising to totally restore the normal functions of pancreatic β cells, and effectively cure type 2 diabetes and possibly prevent and reverse diabetic complications. There are two milestone works in differentiating hESCs/hiPSCs into functional pancreatic β cells in vitro by using 11 different factors or overexpressing ERRγ, respectively. 4,16 The produced functional adult pancreatic β-like cells share the common characteristics with bona fide pancreatic β cells, which include: 1) expressing markers found in mature β cells; 2) fluxing Ca2+ in response to glucose; 3) packaging insulin into secretory granules; 4) secreting quantities of insulin comparable to adult β cells in response to multiple sequential glucose challenges in vitro; 5) secreting human insulin into the serum of mice shortly after transplantation in a glucose-regulated manner; 6) transplantation of these cells ameliorates the hyperglucemia in diabetic mice. 4,16 Compared with these two important works, our strategy reported here have the following advantages. Firstly, our method can directly produce and secrete human insulin into the patient blood without the use of the complicated and time-consuming in vitro differentiation procedure. Secondly, our method can reduce the patient’s blood glucose levels and stop exogenous insulin administration immediately after transplantation. In addition, our method can improve the patient’s symptoms physically and mentally, not only by decreasing the glucose levels and improving glucose metabolism, but, more importantly, also by repairing the damaged tissues and organs, and further preventing the development of diabetic complications and even reversing the existed complications potentially. Furthermore, in our strategy, we use directly generated human pluripotent stem cells derived hADSCs without any genetic modifications, therefore, our stem cells are much safer than other reports. 4–16 Finally, we directly use our strategy to treat volunteered type 2 diabetes patient, and to our knowledge, this is the first report to directly use human pluripotent stem cells overexpressing ERRγ to treat human diabetes. As for the physical and mental improvements of the patient after stem cell transplantations, it is beyond the words to describe the overall beneficial effects, including the strengthened muscles and the knees, and the vitality of the patient.

Output: contrast