Input: Claim: Biohacking methods can fully reverse aging and extend lifespan indefinitely. [SEP] Text: with. is the publisher of Aging: www. impactjournals. com. is a member of the List of Compliant Publishers. is a member of the Society for Scholarly Publishing. Learn about our FREE Post-4 pp 315—327 Overexpression of Sir2 in the adult fat body is sufficient to extend lifespan of male and female Hoffmann1, Renja Romey1,2, Christine Fink1, Li Yong1, Thomas Roeder1, 1 University of Kiel, Dept. of Zoophysiology II, 24098 Kiel, Germany 2 and 20146 Hamburg, Germany Received: April 16, 2013 Accepted: April 27, 2013 Published: April 29, 2013 How to this 10. 18632/aging. 100553 Copy or Download citation: Select the format you require from the list below Plain text to copy this citation from the text box above or download the citation: Citation | Citation & Abstract Copyright: © 2013 Hoffmann et al. This is an open-access 2. 1 extends lifespan of worms by up to 50 % [2]. In Drosophila, ubiquitous, constitutive overexpression as well as panneuronal overexpression only in the adult animal was shown to extend lifespan [3, 4]. Studies in mice have demonstrated that the Sir2 homolog Sirt1 does not increase life expectancy but promotes a longer health span by prevention of age associated diseases [5-7]. Due to the apparent evolutionarily conserved effect of Sir2/Sirt1 on health and ageing, the physiological functions and protein targets of the enzyme have been intensively studied in mammals in order to cure age-related diseases. SIRT1 was shown to increase insulin sensitivity and regulate energy expenditure through stimulation of oxidative metabolism like fatty acid oxidation and oxidative phosphorylation in mice [5, 8-10]. This predestines the enzyme as a novel target for the treatment of diabetes [11]. In addition, it has been implicated in the etiology and/or cure of cancer, Alzheimer's and other age-related diseases [12-14]. In contrast to mammals, in Drosophila only few studies tried to elucidate physiological functions of Sir2 and the molecular mechanisms, which may mediate its effect on life span. A screen for obesity-inducing genes in Drosophila larvae pointed to a role for Sir2 in regulating fat metabolism and response to amino-acid starvation [15].

Output: contrast


Input: Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: The length of the inter-node between the third and fourth nodes (red lines) was determined (n=5). ** indicates a significant difference at the 0. 01 level. Fig. S3 GO enrichment analysis of DEGs identified from the comparisons MZ-vs-QQ (a), MZ-vs-LYQQ (b), and QQ-vs-LYQQ (c). Fig. S4 KEGG enrichment analysis of DEGs identified from the comparisons MZ-vs-LYQQ_MZ-vs-QQ _QQ-vs-LYQQ (a), MZ-vs-LYQQ (b), MZ-vs-QQ (c) and QQ-vs-LYQQ (d). Fig. S5. Differential metabolites identified from MZ-vs-QQ, MZ-vs-LYQQ, and QQ-vs-LYQQ. Additional file 2: Table S1 Summary of the RNA-Seq data derived from MZ, QQ, and LYQQ. Table S2 Statistics of the number of detected genes in each cultivar Additional file 3: Table S3 Seventy-six key DEGs identified to be involved in zigzag-shaped stem formation in tea plants Additional file 4: Table S4 DEGs and primers used for qRT-PCR validation of the transcriptomeSupplementary FilesAdditionalfile1Fig. S1. tifAdditionalfile1Fig. S3. tifAdditionalfile1Fig. S2. tifAdditionalfile1Fig. S4. tifAdditionalfile4TableS4. docxAdditionalfile3TableS3. docxAdditionalfile2TableS1. docxAdditionalfile2TableS2. docxAdditionalfile1Fig. S5. tif:Published04 Mar, 2020Read the published version in BMC →Version 3posted Submission checks completed at journal25 Feb, 2020Editorial decision: Accept25 Feb, 2020You are reading this latest preprint versionShow more versionslets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Company, we’re committed to making research communication faster, fairer, and more useful.

Output: pass


Input: Claim: Exposure therapy is a common psychological treatment for anxiety and phobias, and it works by gradually increasing exposure to the fear-inducing stimulus. [SEP] Text: It was determined that there was a significant interaction to the parietal region at 10-13 Hz for alpha right and left [(t (14)=3. 111, P<0. 05] (Table V) This indicates a change in EEG asymmetry asymmetry (please also see the aforementioned data; Fig. 3). These findings demonstrated that the therapeutic application affected the EEG asymmetry changes at the cortical level. Table VThe changes in the right and left frontal and parietal lobe alpha frequencies (10-13 Hz) between the pre-test and post-test. Table VThe changes in the right and left frontal and parietal lobe alpha frequencies (10-13 Hz) between the pre-test and post-test. Group10-13 HzMeannStd. deviationdftP-valueExperimental groupFrontal lobePre-test right2. 0000150. 00000141. 3440. 05 Post-test left6. 0000150. 81650 Parietal lobePre-test right2. 5000150. 29099143. 1110. 05 Post-test left6. 7500151. 50000 the present study, when the data obtained from the analyses were examined, the effectiveness of the gradually increasing levels of exposure therapy and cognitive behavioral therapy for maladaptive behavior and anxiety was examined. To date, to the best of our knowledge, there are no studies available in Turkey on the application of such methods, namely a brain-based psychological intervention program for anxiety. Therefore, the study is the first of its kind in Turkey. Herein, it was found that the methods used for maladaptive behavior and anxiety were effective and reduced the levels of anxiety in the study participants. This finding can be interpreted as an effective application method for anxiety. According to the follow-up evaluations at the end of the therapy, it was stated by all clients that they benefited greatly from the therapeutic application and that their quality of life increased compared to that before the therapy. A previous study on cognitive behavioral therapy demonstrated that the participants experienced a significant shift in their resting forebrain activity from greater relative right to greater relative left after receiving treatment (13). That study also found that individuals with higher levels of left frontal brain activity before treatment had larger reductions in anxiety symptoms after treatment and lower levels of anxiety post-treatment (11). These associations were specifically related to the frontal alpha EEG asymmetry metric.

Output: corroborate


Input: Claim: Biohacking methods can fully reverse aging and extend lifespan indefinitely. [SEP] Text: Moreover, Sir2 apparently regulates expression of genes involved in fat metabolism and the lack of Sir2 increases fat deposition under normal conditions and consequently impairs starvation survival of flies [16]. It has been hypothesized that Sir2 mediates the effects of dietary restriction (DR) on fly lifespan because decreased activity of the histone deacetylase RPD3, which is down-regulated in DR, increases SIR2 activity [3]. This hypothesis is corroborated by the recent results that revealed a diet-dependent effect of Sir2 on lifespan of Drosophila [17]. In addition, P53 is discussed as a downstream target of RPD3 and SIR2 in mediating longevity [4]. Strong doubts over the lifespan prolonging effect of Sir2 overexpression have recently been expressed [18]. As different genetic backgrounds of control and experimental animals can be a confounder in lifespan experiments, Burnett et al. [19] aimed to validate results for C. elegans and Drosophila with genetically matched controls and could not confirm the positive effect on lifespan. However, a very recent study has supported the initial observation by showing that genetic manipulation of Sir2 in the fly's fat body elongates lifespan in Drosophila [17]. Thus, an urgent need to either confirm or rebut these effects of Sir2 expression levels on lifespan exists. We used the inducible GeneSwitch Gal4/UAS system [20] to drive Sir2 overexpression in the fat body only, which offers two major advantages: first, it is possible to restrict overexpression to the adult animals without affecting development and second, Sir2 overexpressing flies and control flies have the same genetic background since overexpression is induced by treatment with mifepristone (RU486). We found that Sir2 overexpression in the fat body only can promote longevity in both sexes. Furthermore, a detailed analysis of the fat tissue revealed no overt structural changes. However transcriptional profiles of fat bodies after DR or Sir2 overexpression suggest that the interventions promote longevity through independent mechanisms. Overexpression of Sir2 in the of avoid differences in genotypes between control and experimental animals, we used the inducible Gene[20] to overexpress Sir2 in the fat body of adult flies.

Output: contrast


Input: Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: -19 PreprintsProtocolsVideosJournalsTools & a 10. 21203/rs. 3. rs-3111723/v1This work is licensed under a CC BY 4. 0 LicenseStatus:Published16 May, 2024Read the published version in →Version 1posted You are reading this latest preprint versionAbstractMany organisms, particularly plants, can reproduce both sexually and asexually but with varying frequencies. Because variations in the reproductive system profoundly affect fitness and genomic diversity, natural selection should act on changes between sexual and asexual types of propagation. However, the genomic evidence of natural selection driving switches between reproductive systems remains scarce, and the evolutionary consequences of such switches on the genomic and epigenomic diversity remain controversial. Here, by analyzing population genomes and epigenomes of Spirodela polyrhiza (L. ) Schleid. , a facultatively asexual angiosperm, we show that while the genomic diversity and DNA methylation levels are very low, they vary among populations. These variations are associated with both the demographic history and the frequency of sexual reproduction in each population. A genome-wide scan revealed that multiple genes involved in flowering and embryogenesis were under positive selection, consistent with the hypothesis that natural selection drove the evolution of asexuality in this plant. Together, these results provide new insights into the evolution of plant reproductive systems and suggest that natural selection can drive the evolutionary changes of asexuality, which in turn alters the levels of genomic and epigenomic diversity. Biological sciences/Evolution/Population geneticsBiological sciences/Genetics/EpigenomicsBiological sciences/Evolution/Evolutionary geneticsBiological sciences/Genetics/Evolutionary biologyBiological sciences/Plant sciences/Plant reproductionFiguresFigure 1Figure 2Figure 3Figure 4IntroductionUnderstanding the evolution of sexual reproduction has long been at the centre of evolutionary biology. Theories suggest that asexual reproduction is beneficial for the short term but costly for the long term, mainly due to accumulations of deleterious mutations and low effective population size1–5. Facultative asexuality, where organisms can reproduce both sexually and asexually depending on environmental conditions, should be optimal for one individual’s lifespan6,7.

Output: pass


Input: Claim: The placebo effect, where a patient experiences real improvements due to believing they're receiving treatment, is observed in many clinical trials. [SEP] Text: While you’re on the trial you get a lot more attention, people want to know how you’re going and you do get a bit of extra TLC, which is probably very egocentric but everyone on the trial experiences it and I think that is therapeutic in a way. (F, 70–79, C3) Stage 3: Coming off a clinical drug trialThis theme described the experiences of a considerable proportion of participants in both samples (21% and 25%, respectively) that had previously transitioned off a clinical drug trial (Table 1). In particular, participants reflected on the negative or challenging aspects of transitioning back to usual care and the worries and concerns which accompanied a trial drug not being successful in treating their cancer. Transition back to standard careComing off trial was described as a significant change. Transitions from highly attentive on-trial care to standard care that leaves a lot to be desired (M, 70–79, C3) were difficult for some participants. I suppose you tend to get rather spoiled by your trial nurse because, as I said, nothing was too much trouble, whereas being off the trial, well, yeah, that leaves a lot to be desired… like being part of the general population again… it makes life a bit more difficult. (M, 70–79, C3). For other participants, the possibility that they could go off the trial, and the conditions and decision-making to take them off, was poorly communicated. This meant it was a bit of a shock when they were transitioned off trial with little notice (M, 30–39, C1). They probably mentioned it in all the documents they’ve given me but there’s a lot to read and you don’t always retain everything either, like, I’m not in the medical profession. But maybe if they could just say, ‘If things go this way you won’t continue on the trial’… it would have been good maybe if they could just explain that a bit more that you’ll be on the trial until something like this happens and then you’ll be off. (M, 30–39, C1). One facet of coming off trial was a sense of worry about wasting time while being on an experimental drug that proved to be ineffective (M, 30–39, C1).

Output: corroborate


Input: Claim: Biohacking methods can fully reverse aging and extend lifespan indefinitely. [SEP] Text: Here, tissue-specific overexpression of Sir2 is achieved by administration of mifepristone (RU486) to the F1 generation of a cross of UAS-Sir2 with the driver line S1106-Gal4 while genetically and developmentally identical controls feed on normal medium supplemented with the same dose of the diluent ethanol. We first examined the expression level of Sir2 under the experimental conditions. UAS-Sir2>S1106-Gal4 flies were fed 400 μM RU486 or diluent only for 24 h. Fat bodies were dissected and qPCR for Sir2 mRNA was performed. We detected an approx. 3. 5 fold and 2. 5 fold up-regulation of Sir2 gene expression in the fat bodies of females and males, respectively (Fig. S1). This system induces a moderate increase of Sir2 expression, which is presumably in the physiological range of expression changes. Until recently, studies that aimed to investigate the effect of Sir2 on lifespan mainly manipulated its gene expression in whole animals or the nervous system. We decided to study the effect of overexpressing Sir2 in the fat body as it is strongly expressed in this tissue [3]. Moreover, the fat body integrates the response to both immune and metabolic stimuli, which are both important modulators of the aging process [21, 22]. To do so, we determined lifespan of mated UAS-Sir2>S1106-Gal4 flies fed on medium with or without RU486 throughout adult life. Survival curves of females (Fig. 1A) and males (Fig. 1C) overexpressing Sir2 are significantly shifted to the right. As shown in Table 1, median lifespan of females and males treated with RU486 is increased by 12 % and 13 % compared to controls, respectively. These data show that even the relatively weak overexpression of Sir2 induced by the S1106-Gal4 line in the adult fat body promotes longevity in flies, largely by delaying the onset of cohort aging. To rule out the possibility that the GAL4 activator RU486 itself may elongate lifespan of Drosophila, we performed lifespan experiments with flies from a crossing of the w1118 strain and the driver line S1106-Gal4. Flies were treated as described above and no significant shift in survival curves was observed for either females (Fig. 1B) or males (Fig.

Output: contrast


Input: Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: While rather few animals such as aphids (aphidoidea)8, water fleas (cladocerans)9, and rotifers10 reproduce facultatively asexually, up to ~ 80% of the flowering plants, including important crops and keystone species, can reproduce both sexually and asexually11. Asexual reproduction in plants involves different types of vegetative reproduction (e. g. runners, tubers, bulbs, corms, suckers, plantlets), as well as apomixis, the formation of seeds without fertilization12. Because changes between sexual and asexual reproduction profoundly affect fitness, natural selection might act on the genetic controls of sexual and asexual reproduction in facultative asexual organisms, which in turn can alter the levels of genomic diversity, heterozygosity and effectiveness of selection in the population2,5,13−15. However, direct evidence supporting this prediction remains scarce, mainly due to the lack of a suitable facultative asexually reproducing system in which the signature of selection can be detected at genomic levels. Evolutionary changes in sexual and asexual reproduction might also affect the maintenance and dynamics of epigenetic markers, i. e. , DNA methylations. In plants, cytosine methylation can occur in three sequence contexts: CpG, CHG, and CHH (H = A, T, or C), which are controlled by different mechanisms and have different dynamics during reproduction16. Typically, CpG and CHG methylation are maintained by methyltransferases1 (MET1) and 3 (CMT3), whereas CHH methylation is mostly maintained by CMT2 or the RNA-directed DNA methylation (RdDM) pathway17. However, CMT3 was found to also play a role in the maintenance of CHH methylation, as well as de novo methylation18. During sexual reproduction, DNA methylations are highly dynamic19. In both male and female gametogenesis, the megaspore mother cell and its male analogue experience dramatic chromatin changes during cell specification, such as heterochromatin decondensation and an enlarged nuclear21. During male gametogenesis, sperm DNA is highly methylated in the CpG and CHG context but has low CHH methylation in retrotransposons19,22,23. During female gametogenesis, CpG and CHH methylation remains largely steady24.

Output: pass


Input: Claim: The placebo effect, where a patient experiences real improvements due to believing they're receiving treatment, is observed in many clinical trials. [SEP] Text: AbstractMethodological aspects of study design affect therapeutic outcome. We tested the hypothesis that treatment effect of an active drug in studies on acute therapy of migraine is lower in placebo-controlled studies than in those not using a placebo-controlled design. From 522 eligible studies on acute therapy of migraine cited in Pubmed database which were published between 1964 and 1997 we randomly selected 100 studies for evaluation. We excluded five studies because they did not include a quantitative measurement of pain intensity. Of the 95 studies included in the analysis, 61 used placebo control. Response to active drug was significantly lower (P < 0. 05) in placebo-controlled studies (61% [lower and upper quartiles 44% and 75%] vs. 71% [56% and 75%]). We did not find any significant effect of quality of study design on net effect of verum. This observation should be taken into account for future planning of controlled clinical studies in acute migraine. IntroductionThe standard design for evaluation of treatment effects is a placebo-controlled trial. This design allows a separation of the active pharmacological effects of a drug from its placebo effect (1). Placebos have been reported to improve subjective and objective outcomes in pain therapy in about 30–40% of patients with a wide range of responses (2). Explanations for the mechanism of action of placebo in pain research include natural history and regression to the mean as well as non-specific influences. These non-specific influences include physician attention, the sense of interest and concern provided by a healing setting, as well as patient and physician expectations of treatment effects (3). Recent studies have focused on the impact of non-specific influences of placebo in pain therapy (2, 4). The extent to which the patient or clinician believes in the effectiveness of a therapy may influence the power of non-specific effects (5). When using placebo control in studies on pain therapy expectations of success of therapy by both clinicians and patients anticipating a potentially powerless placebo may be diminished. Therefore we tested the hypothesis that the total drug effect is lower in those studies using a placebo when compared with those trials designed without placebo control in studies on acute therapy of migraine. MethodsLiterature search and selection of studiesWe searched in the Pubmed database for trials published between 1964 and 1997. The search was performed using the keywords placebo, acute therapy, and migraine.

Output: corroborate


Input: Claim: Biohacking methods can fully reverse aging and extend lifespan indefinitely. [SEP] Text: 1D) compared to controls. Figure 1. Increased expression of Sir2 in the fat body extended lifespan of male and female flies. Mated female (A) or male (C) UAS-Sir2>S1106-Gal4 flies were fed 400 μM RU486 or diluent (ethanol) throughout adult life and lifespan was determined. As a control for a potential lifespan extending effect of RU486, the driver line was crossed to w1118 and female (B) or male control flies (D) of the F1 generation were treated as the experimental flies. For p-values of log rank test see Table 1, n = 100 for each group. Table 1. Elevated expression levels of Sir2 increased life expectancy of flies GenotypeSexRU486Median lifespan (d)Median lifespan extension (% of control)Maximum lifespan (d)χ2p-valueUAS-Sir2>S1106-Gal4♀−4912. 3598. 7960. 003UAS-Sir2>S1106-Gal4♀+5562UAS-Sir2>S1106-Gal4♂−5512. 76813. 150. 0003UAS-Sir2>S1106-Gal4♂+6271w1118>S1106-Gal4♀−456. 7630. 352nsw1118>S1106-Gal4♀+4863w1118>S1106-Gal4♂−573. 4700. 015nsw1118>S1106-Gal4♂+5976 Data derived from log rank analysis of the survival curves shown in Fig. 1. The maximum lifespan is the median of 10 % survival. Log rank test was performed using Graph6. 00. ns, not significant. Experiments shown are representatives of two independent experiments. by Sir2 Overexpression and Do not finding that fat body Sir2 can promote a long life led us to examine which candidate mechanisms may play a role in conferring Sir2-dependent longevity. As several studies suggest that Sir2 mediates at least parts of the response to dietary restriction (DR)[3, 17] we aimed to elucidate how these two interventions alter gene expression patterns of the fat body and to what extent transcriptional responses match.

Output: contrast


Input: Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: After fertilization, CHH methylation increases during embryogenesis and can approach 100% at individual cytosines, which then decreases likely through a passive mechanism after germination25–27. In contrast, during vegetative reproduction, DNA methylation is likely steady since meiosis and embryogenesis are lacking28–30. Although a recent study comparing DNA methylations among 34 angiosperm species suggested that clonally propagated species often have low CHH methylation31, the extent to which asexual reproduction affects genome-wide methylation levels remains unclear. Here, we investigated the population genome and epigenome of a facultatively asexual flowering plant, Spirodela polyrhiza (the giant duckweed; Lemnaceae), which has a global distribution. This species, like other duckweeds from the genera Spirodela, Landoltia and Lemna, is characterized by leaf-like fronds derived from fused stems32 and, with multiple roots on each frond33 and with a highly reduced vascular system34. Spirodela polyrhiza reproduces vegetatively via budding under normal conditions but rarely switches to sexual reproduction under unfavourable conditions35,36. Recent studies showed that despite its global distribution in diverse habitats, the genomic diversity, spontaneous mutation rates and DNA methylation levels in S. polyrhiza are very low37–42, which might be associated with its overall low frequency of sexual reproduction. DNA methylation profiling of two genotypes suggests that DNA methylation in S. polyrhiza, which is substantially lower than in other plants, likely due to the loss of the RdDM pathway, varied between genotypes41. Further insights into the evolutionary origin and consequences of asexuality on genomic and epigenomic variations in S. polyrhiza are required to understand the demographic history and to identify the footprint of selection on the genome. ResultsLow genomic variations in S. polyrhiza We sequenced the genomes of 131 globally distributed S. polyrhiza genotypes with an average of ~ 25 X coverage. Together with previously published samples1,2, we analysed the genomic diversity of 228 S. polyrhiza individuals across five continents (1). We identified 1,241,981 high-quality biallelic single-nucleotide polymorphisms (SNPs) and 166,075 short insertions and deletions (INDELs, less than 50 bp of length). Based on an updated genome annotation of S.

Output: pass


Input: Claim: The placebo effect, where a patient experiences real improvements due to believing they're receiving treatment, is observed in many clinical trials. [SEP] Text: From 522 eligible studies on acute therapy of migraine cited we excluded studies performed on children, adolescents, or with subjects suffering from menstrual migraine, and randomly selected 100 studies for evaluation. From that pool we excluded five studies which did not include quantitative assessment of pain intensity. Therefore, 95 studies were included in this prospective analysis. Sixty-one studies used a placebo, defined as an intervention labelled as such in the report of a clinical trial (2), while 34 did not. Extraction and synthesis of dataThe main outcome criterion of our study was the response to active treatment, defined as the decrease of pain intensity (percent of control). If more than one drug was tested in a study of acute migraine therapy, we only analysed the response to the first drug applied for comparison. Data are presented as median [quartiles]. The appropriate two-sided statistical null and alternative hypotheses were:H01: P11 = P12H11: P11 ≠ P12where P11 is the proportion for the effect of active drug in studies using placebo and P12 is the proportion for the effect of active drug in studies without a placebo-controlled design. The global level of significance in a two-sided hypothesis was α= 5%. According to the protocol, the hypothesis was to be proven with the non-parametric Mann–Whitney U-test. Furthermore, statistical measures and exploratory P-values were used to investigate the influence of the quality of the study design on the verum response rate. We used the following criteria which we considered critical to the quality of the study design, and assigned 0s and 1s as points: not-randomized (=0) vs. randomized (=1) study, not blinded (=0) vs. blinded (=1), unicentre (=0) vs. multicentre (=1) design, and the number of patients included (n < 50 = 0, n ≥ 50 = 1). From these data we built a quality score with 0 indicating the worst quality, and 4 indicating the best quality observed. We used the χ2 test for comparison of the dichotomous variables blinding and placebo control and we used the non-parametric Mann–Whitney U-test to compare with the verum response rate the dichotomous determinants of quality of study design. Finally, we tested the relationship between the quality score and the verum response rate by means of non-parametric correlation (Pearson).

Output: corroborate


Input: Claim: Biohacking methods can fully reverse aging and extend lifespan indefinitely. [SEP] Text: We performed microarray analysis with RNA isolated from fat bodies of mated, age-matched females either subjected to DR for 7 d or with fat body specific Sir2 overexpression after 24 h induction by RU486. The control and DR food was prepared according to recommendations by Ja et al. [23] to prevent desiccation, which robustly resulted in prolonged lifespan of male and female w1118 flies (Fig. S2). Surprisingly, when comparing gene expression profiles we noticed that only roughly 10 % of up- (p value 0. 355) or down-regulated genes (p value 0. 383) overlap between both samples (Fig 2A, B). This is a surprising small overlap, indicative for almost completely independent processes, especially when taking into account that fat tissue of age- and gender-matched flies was used for both analyses. Figure 2. Fat body Sir2 does not play a major role in the DR response. Transcriptional profiles of fat bodies from either w1118 females after a 7 d DR period or UAS-Sir2>S1106-Gal4 females after 24 h of Sir2 overexpression were compared. The scaled Venn diagrams depict the actual relationship of the numbers of up-regulated (A) and down-regulated genes (B) of both samples and the number of overlapping genes. Only roughly 10 % of differentially expressed genes are overlapping between DR samples and Sir2 overexpression. Statistical analyses were performed with Fisher's exact test. Genes, which were up-or downregulated > 1. 5 fold in at least 2 of 3 microarrays were included in the diagrams shown. Hierarchical clustering of DR and Sir2 Arrays reveals that transcriptional patterns elicited by DR and Sir2 overexpression in the fat body do not show substantial similarities. (D) mRNA levels of Sir2 in female w1118 whole animals and in their fat bodies were unchanged after DR. Shown are mean values of 3 replicates + SEM. Furthermore, hierarchical clustering of the microarray data shows substantial differences in gene expression patterns induced by both interventions (Fig 2C). Especially genes down-regulated in DR sets are up-regulated in Sir2 gene sets. Additionally, we did not detect an increase of Sir2 transcription in response to DR as reported by other groups, neither in whole animals nor in their fat tissues (Fig. 2D).

Output: contrast


Input: Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: polyrhiza (see Section 1. 1 of the Supplementary Information), we found that most of the SNPs (70. 3%) are in the intergenic regions (Supplementary Fig. 1). Of all the SNPs located in the protein-coding regions, 61,039 were identified as nonsynonymous and 44,287 as synonymous (2). Consistent with our previous study, the genome-wide nucleotide diversity at neutral sites is 0. 0013 (1), the lowest among multicellular eukaryotes. The species-wide efficacy of selection (πN/πS ratio) is 0. 39, the highest among studied organisms43, indicating relatively weak purifying selection in S. polyrhiza, despite its large effective population size1,2. In addition to SNPs and small INDELs, we also characterize the genome-wide structural variations (SVs, ≥ 50 bp in length) in S. polyrhiza (see Section 1. 2 of the Supplementary Information). We identified 3,205 high-quality SVs, including 2,089 deletions, 291 duplications, and 825 insertions. The abundance of the SVs is substantially lower than all reported multicellular organisms44,45. Among all identified SVs, 155 duplications and 169 deletions affected protein-coding genes (2). Interestingly, in comparison to the genome-wide average, the MADS-box genes (see Section 1. 3 of the Supplementary Information) showed a higher tendency to overlap with SVs (permutation tests; P = 0. 063). In addition, we also observed a significant overrepresentation of small INDELs in the MADS-box genes (permutation tests; P = 0. 008). These results indicate that MADS-box genes might be under positive or relaxed purifying selection in S. polyrhiza. Population structure and demographic history of S. polyrhiza Because S. polyrhiza is facultatively asexual, genotypes collected from the geographic proximity can be derived from the same clonal family. Using a previously established grouping threshold that was developed in S. polyrhiza2, we identified 159 likely clonal families (3). Population structure and principal component analyses revealed four populations in S. polyrhiza (Fig. 1a and 1b).

Output: pass


Input: Claim: The placebo effect, where a patient experiences real improvements due to believing they're receiving treatment, is observed in many clinical trials. [SEP] Text: ResultsResponse with active treatment was significantly lower (P < 0. 05) in placebo-controlled studies of acute migraine therapy compared with those studies not using placebo control (61. 5 [quartiles 45 and 73. 5]% vs. 71 [56 and 82. 25]%, respectively; Fig. 1). Figure 1 Plots of quartiles (boxes), median (line within box), 10th, and 90th percentiles (error bars, outliers given as open circles). Median of verum response is significantly (P = 0. 022) lower in studies using placebo control (61 [45, 73. 5]% compared with those studies not using a placebo 71. 5 [quartiles 56, 82. 25]%). Quality scores were significantly higher (P < 0. 01) in studies using placebo control (median of 3 vs. 1, respectively), but the quality did not correlate with the response rate. Comparing response rates of active drug with the single variables determining the quality of study design Table 1), only the effect of blinding approached but failed to reach statistical significance (P = 0. 068). Response rates with active drug in double-blind studies were 62. 5%[47. 1 and 75] compared with 72%[54 and 82] in those studies which did not blind to the test drug applied. Table 1 Quality of study design and success rate of verum All studies includedBlindingRandomizationFifty patients includedMulticentre design952075 98632636233Response rate verum (median, quartiles)65726268646366. 56370[49, 75][54, 82][47, 74][50, 85][48, 75][47, 63][50, 76][45, 74][56, 75]P-value 0. 0680. 40. 30. 11Distribution of the determinants of quality of study design and response rate reported. We compared with the verum response rate each dichotomous variable ((not) blinded, (not) randomized, (not) > 50 patients included, (no) multicentre study). Response rate of verum did not significantly depend on the variables determining the quality of the study design. The variables blinding and placebo control were significantly related (P < 0. 01). Therefore our data did not allow study of the effect of placebo control on verum response independently from the effect of blinding.

Output: corroborate


Input: Claim: Biohacking methods can fully reverse aging and extend lifespan indefinitely. [SEP] Text: Taken together, these results imply that fat body Sir2 evokes other cellular processes than those elicited by DR. Sir2 in a Gender-specific on the transcriptome studies performed with isolated fat tissue from Sir2 overexpressing males and females, we focused on those genes that are relevant for fat tissues. Within this tissue lipid droplets are of central importance to regulate fat utilization [24]. Thus, we hypothesized that fat body Sir2 modulates the composition of the lipid droplet proteome and compared the gene expression data from fat bodies overexpressing Sir2 with a list of Gene IDs corresponding to the lipid droplet proteome as defined by Beller et al. [25]. Corresponding genes of 39 out of 254 lipid droplet associated proteins were found to be differentially regulated in fat bodies overexpressing Sir2 which corresponds to 15 % of the lipid droplet proteome (Fig. 3A; p value 0. 007). The (putative) functions of these genes are very diverse and range from lipid storage and fatty acid metabolism, stress response and energy metabolism, to chromatin assembly (Table 2). Figure 3. Gene expression profiles of fat bodies overexpressing Sir2 show notable intersections with the lipid droplet proteome. (A) Differentially regulated genes (up-and down-regulated) found in Sir2 overexpressing males and females were compared with the lipid droplet proteome as defined by Beller et al. [25]. diagram shows considerable intersections between these different sample types (statistical analyses were performed with Fisher's exact test; see Table 2 for a list of intersecting genes). (B) To view gender-specific effects, the transcriptional profiles of fat bodies from UAS-Sir2>S1106-Gal4 males and females after 24 h of Sir2 overexpression were compared. The scaled Venn diagrams depict the actual relationship of the numbers of up- and down-regulated genes of both samples and the number of overlapping genes. Genes which were up- or down-regulated > 1. 5 fold in at least 2 of 3 microarrays were included in the diagrams shown in (A) and (B). Table 2.

Output: contrast


Input: Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: Consistent with our previous study, the four populations are largely concordant with their geographic origins, namely America, Asia (SE-Asia), Europe, and India (Supplementary Fig. 2), with a few exceptions that can be due to recent migration events or artefacts during long-term duckweed maintenance. We inferred the population history with a (ML) phylogeny combined with Computation (ABC). esculenta (from the Araceae family) as an outgroup, the maximum likelihood phylogeny of all 228 genotypes indicated an early split of the American population from the other populations and subsequent splits of the Indian and European populations from SE-Asia (Fig. 1c). population constitutes the most recent split (Fig. 1c-d). Here, genotypes collected from the transcontinental region (e. g. Russia) showed intermediate features of SE-Asian and European populations, suggesting this as a likely migration route. Furthermore, the Indian population possibly originated via Thailand and Vietnam, as genotypes from these countries show intermediate features between Indian and SE-Asian populations. We modelled the demographic history using an ABC modelling approach to further validate the evolutionary history of the four populations in S. polyrhiza. Three plausible demographic scenarios were simulated, allowing for either the SE-Asian, American or an additional putative population to function as the ancestral population (Supplementary Fig. 3). We found that the scenario, in which the American population and Asian population were derived from an additional putative ancestral population, constituted the most supported model (Fig. 1d). While the American population was separated from other populations around 1 million generations ago, the European population was derived from the SE-Asian population only 12,000 generations ago (see Section 1. 4 of the Supplementary Information). Determinants of genomic diversity among populations Among the four populations, nucleotide diversity (π) and the efficacy of selection (πN/πS ratio) varied among populations (Fig. 2b). While the SE-Asian population has the highest π and lowest πN/πS ratio, the American population has the lowest π and highest πN/πS ratio. Interestingly, while the European population has a much smaller π compared to the SE-Asian population, the πN/πS ratio of the European population remains similar to the latter, likely due to its recent split from the SE-Asian population.

Output: pass


Input: Claim: The placebo effect, where a patient experiences real improvements due to believing they're receiving treatment, is observed in many clinical trials. [SEP] Text: DiscussionThe main finding of this analysis is that placebo control reduces response rates of the active drug in controlled clinical studies on acute migraine therapy. Critique of methodsA high placebo effect in a study population may be useful to detect a significant influence of placebo control on the response to the active drug. In a recent meta-analysis the placebo effect was most distinct in studies on the treatment of pain (2). Other studies indicate that high patient compliance is also associated with a high placebo response (3). The compliance of patients to drug therapy is markedly higher during an acute migraine attack compared with migraine prophylaxis (6). Therefore, we speculated that studies on acute migraine therapy may be best to test our hypothesis. From the whole sample of 522 studies on acute migraine therapy available, we randomly selected 100 studies reflecting a representative sample for analysis. Using this technique, no selection bias was expected and the power was sufficiently high to detect a difference in response to active drug between studies using a placebo and those which did not. Methodological aspects of study design may affect therapeutic outcome (2, 7, 8). Therefore, we analysed the variables considered relevant to the quality of study design (2, 7) and their influence on the efficacy of the active drug. Since no scoring system for headache trials is established, we constructed a score without previous validation and also investigated the influence of each single determinant on response to the active drug. We found no relationship between the quality score and the response to active drug. The correlation between blinding and efficacy almost achieved significance (P = 0. 068). As the variables placebo control and blinding were significantly related (P < 0. 01), our data did not allow study of the influence of placebo control on active drug response independently from the effect of blinding. Interpretation of resultsA placebo effect is a change in a patient's illness attributable to a symbolic import to a treatment rather than a specific pharmacological or physiological effect (9). A placebo effect is expected in any therapeutic intervention and does not require a placebo tablet (3). There are two general reasons why the placebo effect may induce clinical improvement in a patient's condition: natural history, and regression to the mean. In addition, there are non-specific reasons including various psychological and social influences. In pain treatment it is well documented that the placebo effect exceeds natural history and regression to the mean (2), as measurable changes of biological variables are reported after placebo.

Output: corroborate


Input: Claim: Biohacking methods can fully reverse aging and extend lifespan indefinitely. [SEP] Text: Mated female (A) or male (B) UAS-Sir2>S1106-Gal4 flies fed on 1 % agar containing 400 μM RU486 or diluent (ethanol) and dead flies were scored 1-3 times a day. (C) Median lifespan of females was 217 ± 6 h and 215 ± 1 h in control and experimental flies, respectively. For males median lifespans were 172 ± 4 h and 185 ± 7 h for control and Sir2 overexpressing flies, respectively. Data are represented as means + SEM. Log rank analysis was performed using Graph6. 00, n = 50. of Sir2 on Sir2 overexpression in the fat body did not only extend lifespan of the flies but also influenced the relative abundance of lipid droplet proteome associated genes and starvation resistance in a gender-specific manner we wanted to elucidate the role of fat body Sir2 on fat storage and morphology of the fat cells. We tested if Sir2 overexpression affects relative body fat content, body weight, the morphology of the fat cells and the size of the fat droplets in males and females. Mated UAS-Sir2>S1106-Gal4 males or females were fed on medium containing RU486 or ethanol for 7 d before they were weighed and relative body fat content was quantified by a coupled colorimetric assay according to Hildebrandt et al. [27]. Neither sex showed fat body Sir2 - dependent effects on fat storage (Fig. 5A) and body weight (Fig. 5B). To analyze changes in the morphology of the fat body we performed Bodipy staining with L3 larvae (Fig. 5 D, G), adult females (Fig. 5 E, H) and males (Fig. 5 F, I). Although fat cell size and filling levels of fat stores obviously varied substantially between all sample types, no effect of Sir2 overexpression (Fig. 5 D-I, bottom row) was observed on these parameters compared to controls (Fig. 4 D-I, top row). We randomly selected 14 pictures comprising 7 biological replicates and measured diameters of fat droplets of the larval samples (Fig. 5C) to confirm the results of the qualitative analysis of the tissues. Altogether, these results do not reveal an obvious phenotype in fat body cells following Sir2 over-expression, regardless of developmental stage or sex.

Output: contrast


Input: Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: Using genome-wide SNPs, we found that linkage disequilibrium (LD) is comparable to Arabidopsis thaliana46, suggesting considerable historical sexual reproduction in S. polyrhiza. However, the extent of LD decay varied substantially among populations (Fig. 2b and Supplementary Fig. 4). While the Asian population showed the most rapid LD decay (about 12 kb at r2 = 0. 2), the European population had very long LD blocks (> 100 kb). and American populations had intermediate LD decay. This pattern is further supported by the recombination rates calculated for all four populations, where the Asian population had the highest recombination rate compared to the other three (Fig. 2b). Different LDs and recombination rates found among populations indicate that the frequencies of sexual reproduction varied among populations. In addition, we found that the variations of heterozygosity in S. polyrhiza showed a similar pattern with the genomic diversity and recombination rate among four populations (Fig. 2 and Supplementary Fig. 5). Interestingly, the changes in genomic diversity and levels of heterozygosity are associated with two SVs involving MADS-box genes that are involved in sexual reproduction. One SV is an 84 bp insertion at the last coding sequence (CDS) of gene SpGA2022_005278, a homolog of AGL62 from the Mα subclade of MADS-box genes (Supplementary Fig. 6). In A. thaliana, AGL62 is a transcription factor that suppresses endosperm cellularization by activating the expression of a putative invertase inhibitor, InvINH1, in the micropylar region of the endosperm47,48 (Supplementary Fig. 7). The insertion likely disrupted the function of the AGL62-like gene, thus reducing the suppression of endosperm development, which is likely required for sexual reproduction (Fig. 2a). Consistently, we found the insertion was at a higher abundance in the SE-Asian population (87. 5%) than in other populations (Fig. 2c and 2d). In addition, the insertion positively correlates with heterozygosity within the European population (3 and Supplementary Fig. 8). Another SV is a 69 bp deletion at 1. 8 kb upstream of SOC1 (SpGA2022_007306, Supplementary Fig. 5), the ortholog of which is a positive regulator of the flowering process in A.

Output: pass


Input: Claim: The placebo effect, where a patient experiences real improvements due to believing they're receiving treatment, is observed in many clinical trials. [SEP] Text: In fact, endogenous opioids have been associated with the analgesic placebo response (10, 11). Moreover, recent findings indicate that effective placebo treatment induces changes in brain function that are different from those associated with drug medication (12). These measurable effects may be modulated by various psychological and social phenomena such as patient–doctor relationship, classic conditioning and learned behaviour, the expectation of relief, and the will and belief of both patient and physician (13). Our data suggest that the placebo effect is less pronounced if the patient and the clinician anticipate a possible placebo treatment, which they may expect to be a less powerful treatment. Thus, placebo effect may be higher in those studies not using any placebo. Due to ethical considerations, it is suggested that the use of placebo in studies on pain therapy is justifiable only in high-quality trials (14). Our data support this statement, since therapeutically outcome of verum is reduced in studies using placebo control. Therefore, when pointing out the specific risks of participation in a placebo-controlled study on migraine therapy, these observations should be taken into account. AcknowledgementsWe are grateful to W. Laughey and M. Eikermann for their useful comments and criticism. 1. Beecher HK. The powerful placebo. JAMA 1955; 159: 1602–6. CrossrefPubMedWeb of Science2. Hrobjartsson A, Gotzsche PC. Is the placebo powerless? New Engl J Med 2001; 344: 1594–602. CrossrefPubMedWeb of Science3. The importance of placebo effects in pain treatment and research. JAMA 1994; 271: 1609–14. CrossrefPubMedWeb of Science4. de de Gans J, Kleijnen J. Placebo effect in the acute treatment of migraine: subcutaneous placebos are better than oral placebos. J Neurol 2000; 247: 183–8. CrossrefPubMedWeb of Science5. Clinician's expectations influence placebo analgesia. Lancet 1985; 1: 43. CrossrefPubMedWeb of Science6. If migraine prophylaxis does not work, think about compliance. Cephalalgia 1994; 14: 463–4. CrossrefPubMedWeb of Science7. Klejinen J, de Craen AJM, van Everdingen J, Krol L. Placebo effects in double blind clinical trials: a review of interactions with medications.

Output: corroborate


Input: Claim: Biohacking methods can fully reverse aging and extend lifespan indefinitely. [SEP] Text: Figure 5. Sir2 overexpression in the fat body did not affect fat storage and fat cell morphology. Relative body fat content as quantified by coupled colorimetric assay (A) and body weight (B) of male and female UAS-Sir2>S1106-Gal4 flies feeding on medium with or without 400 μM RU486 showed no significant differences. Diameters of fat droplets were measured in fat bodies of UAS-Sir2>S1106-Gal4 L3 larvae after Bodipy staining (C) and no differences were observed. Bodipy staining furthermore reveals no differences in size and structure of fat cells as well as droplet size in L3 larvae (D, G), adult females (E, H) or males (F, I) after feeding on ethanol (top row) or RU486 (bottom row). A-C, Data are represented as means + SEM. Mann-Whitney-U-Test was performed using Graph6. 00, n = 4 for coupled colorimetric assay and body weight, n = 7 for fat droplet diameter measurements. D-I, scale bar represents 50 μm. aim of this study was to test whether tissue-specific overexpression of Sir2 in the fat body of adult flies can elongate lifespan and to elucidate the mechanisms by which fat body Sir2 promotes longevity. We showed that moderate (roughly 3-fold) Sir2 overexpression in the fat body can extend median lifespan of both male and female Drosophila melanogaster by about 13 %. With this study, we provide additional independent evidence for the concept of Sir2 as a longevity gene in Drosophila as suggested by earlier studies [3, 4, 16, 17]. The UAS-line used in our study has not been employed for lifespan experiments so far and does not show increased expression of dnaJ-H, which has been shown to affect apoptosis control of Sir2 and may also interfere with Sir2 functions with regards to longevity [28]. Importantly, we used the inducible GeneSwitch Gal4 System; this removes the use of different genetic backgrounds in control and Sir2 overexpressing flies, a potentially severe confounder in lifespan studies. Geneswitch also allows overexpression during adulthood only, thus removing any developmental testing potential gerontogenes from a therapeutic perspective.

Output: contrast


Input: Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: thaliana49 (Fig. 2a). The deletion was exclusively found in the Indian population with the alternate allele frequency of 73% (Fig. 2c). It is plausible that the deletion, due to its disruption potential at the cis-regulatory region, reduces the ability of the SOC1-like gene to respond to the upstream floral activators (e. g. CO) in S. polyrhiza, thus reducing the frequency of sexual reproduction in the Indian population (Fig. 2d). Consistently, this deletion negatively correlates with heterozygosity in the Indian population (3, Supplementary Fig. 9). Population epigenomic diversity in S. polyrhiza As changes in sexual reproduction can also alter epigenomic dynamics, we further investigated the patterns of population epigenomic diversity in S. polyrhiza. We selected five individuals from each population and quantified their shoot DNA methylation levels at single-base resolution using whole genome bisulphite sequencing. Similar to a recent study40, we found that only 1. 5% of cytosines are methylated in S. polyrhiza (7. 2% of CpG, 2. 2% of CHG, and 0. 1% of CHH; see 4), and the average species-wide methylation levels are much lower than all other investigated angiosperm species (Supplementary Fig. 10)31,50. The hierarchical clustering of 20 methylomes in CpG, CHG, and CHH contexts show high consistency with their genetic similarity (Supplementary Fig. 11–13). Few discrepancies were mostly found within the same population or between the recently diverged SE-Asian and European populations, which indicates that population demography can strongly affect epigenomic variations in S. polyrhiza. We then compared the genome-wide weighted methylation level (wML) among populations. For CpG methylation, the four populations did not differ at genome-wide levels (Fig. 3a). However, CpG methylation level in gene bodies (but not in TEs) was higher in the American population than the other three populations (Fig. 3d, g). For CHG, the Indian population had the lowest genome-wide methylation level among all four populations (Fig. 3b, 3e and 3h). Interestingly, for CHH, the American population had the lowest genome-wide methylation level (P < 0.

Output: pass


Input: Claim: The placebo effect, where a patient experiences real improvements due to believing they're receiving treatment, is observed in many clinical trials. [SEP] Text: Scales were filled in twice daily; dots represent respective daily means prior to dosing (-d4 to -d1), during dosing (d1 to d11) and after cessation of dosage (d + 1 to d + 5)Full size imageFollow-up and outcomes: Already during the afternoon of the first dosing day, another inpatient asked the index case why her mood had improved noticeably. Family members also reported an improved mood early during the dosing period. The patient remarked an undefined happiness. The BDI-II score dropped from 29 one day prior to dosing to 12 at dosing day 8. EDI-2 total scores dropped from the 95th (d-1) to 85th (d10) centile (Table 1). Table 1 Inventory-II (BDI-II) and Inventory-2 (EDI-2) scores one day prior to dosing (d-1), during dosing (d8, d10) and 10 days after cessation of dosing (d + 10)Full size tableThe VAS revealed reductions of ≥ 30% for fear of weight gain, feeling fat, feeling full, preoccupation with food, urge to vomit, and mental narrowing (Fig. 1 a-f) and drive for activity (data not shown). Depressed mood and inner tension were initially ranked at 6 and dropped to mostly 4; during the first days of the dosing period an improved mood was primarily reported during the afternoon and evening. At the end of treatment mood was also perceived as better during the morning. Suicidal thoughts (ranked as absent throughout the observation span), tiredness (average score throughout the observation period: 3. 6), exhaustion (2. 4), hunger (3. 6), sleep quality (3. 4), urge to binge (1. 1), appetite (2. 3), nausea (1. 4), and interest in social interaction (6. 5) remained largely unchanged (data not shown). During and after the dosing period the patient did not vomit, which contrasted with its occurrence during initial inpatient treatment. She reported that respective urges only occurred once daily in contrast to 2–3 times prior to dosing. The strength of urges was reduced; she was better able to distract herself to overcome the urge.

Output: corroborate


Input: Claim: Biohacking methods can fully reverse aging and extend lifespan indefinitely. [SEP] Text: However, our results contradict the study from Burnett et al. [19] who did not observe an effect of ubiquitous overexpression of Sir2 on Drosophila lifespan. This may be due to antagonistic effects on lifespan caused by Sir2 overexpression during development, and/or due to the site of overexpression; by restricting overexpression of Sir2 to the fat body, possibly harmful effects caused by overexpression in other tissues may be excluded. In this context it is notable that overexpression of Sir2 in the nervous system prolonged lifespan of flies [3]. These results are in line with the observation that only these two tissues express SIR2 protein at high levels [3]. We also aimed to test different hypotheses of how fat body Sir2 may confer longevity. Our first working hypothesis was to presume that Sir2 overexpression mimics dietary restriction, which has been proposed by other studies [3, 17, 29]. This led us to compare microarray data generated from fat bodies overexpressing Sir2 with those obtained from fat bodies of animals subjected to DR. As the induced transcriptional changes of both interventions were different our data did not confirm this hypothesis. Instead they support the alternative hypothesis that DR and Sir2 overexpression are indendent processes. Furthermore, dietary restriction had no effect on Sir2 mRNA levels in fat tissue. Our results join a canon of studies presenting conflicting results regarding this topic. Previous findings in yeast [30-33], flies [3, 17, 19] and rodents [34, 35] are inconsistent, which may be due to application of different dietarycaloric restriction regimes, different sites of ectopic expression or knockout of Sir2 and/or genetic backgrounds. We used the food preparations recommended by Ja et al. [23] to circumvent adverse side effects caused by desiccation of the flies, which robustly produced a DR response in both sexes and the food used in the Sir2 experiments was identical except for addition of RU486 dissolved in ethanol or ethanol alone. However, the data presented here suggest that fat body Sir2 does not mediate the effects of DR on lifespan of Drosophila. It has also been proposed that Sir2 in the fat body plays a role in regulating fat storage and mobilization as Sir2 Sirt1 has been implicated in regulation of fat metabolism in flies and mammals.

Output: contrast


Input: Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: To further understand the selection that drove the evolution within individual populations, we identified the signature of positive selection in a three-population tree using patterns of linked allele frequency differentiation and calculating the corresponding composite-likelihood ratio (CLR, see Methods). In total, we found 1,883 genes on the SE-Asian branch, 593 genes on the Indian branch and 401 genes on the European branch (Fig. 4a; see Section 1. 5 of the Supplementary Information) which showed strong signatures of selection (top 1% of CLR values). We found that genes under positive selection in the European branch are enriched with reproduction and development-related GO terms (Supplementary Fig. 15). Among these, SpGA2022_013448, in chromosome 9, is an ortholog of (FLK) that delays flowering by up-regulating FLC family members in A. thaliana76. This gene showed a strong signature of selection in the European branch but not in other branches (Fig. 4c and d). Similarly, SpGA2022_006111, on chromosome 3, is an ortholog of the A. thaliana (BB) that negatively regulates floral organ size and is also under selection in Europe77 (Fig. 4c). In the SE-Asian population, we found that gene SpGA2022_051517, a 3 (CMT3) homolog in A. thaliana, is involved in maintaining CpG, particularly CHG methylation17. This is consistent with the higher CpG and CHG methylation levels observed in the SE-Asian population when compared to the European and Indian populations (Fig. 3a and 3b). Within the Indian population, we found that five MADS-box genes have been under selection exclusively along this branch. Given that there are 43 MADS-box genes in the genome, the fact that five of them have been targeted by selection, constitutes a significant enrichment of such genes under selection (P = 0. 0075, Fisher’s Exact test). For example, SpGA2022_013078 is an ortholog of -LIKE6 (AGL6), which is involved in flower and meristem identity specification in rice78; SpGA2022_052274, a homolog of 3 (AP3), is involved in the petal and stamen specification in A.

Output: pass


Input: Claim: The placebo effect, where a patient experiences real improvements due to believing they're receiving treatment, is observed in many clinical trials. [SEP] Text: She stated perceiving her evening hunger as normalized in contrast to a reduced hunger prior to treatment (VAS for hunger in the evening averaged two prior to dosing and four after initiation of dosing). Preoccupation with food was estimated at 80% and 20–30% before and after the dosing period. In the evening, she no longer needed to reflect on what she had eaten during the day. Whereas she had had an extreme fear of weight gain, she was much better able to accept weight gain at the end of dosing. She reported thoughts of the importance of a sufficient amount of energy. Prior to dosing, she had also known of this importance, but had been unable to act upon it. At the end of the dosing period, she experienced weight gains as positive and weight loss as negative. Eating became easier during dosing. At the end of dosing, the patient stated that she slept very well; she perceived a feeling of tiredness in the evening as positive and as an indicator of a fulfilled day. Her ability to concentrate had improved. Whereas looking after her horse had been perceived as an obligation for many months, she again enjoyed this activity. Both parents had observed an improved mood and a more normal eating behavior (e. g. , patient voluntarily ate a slice of cake at home, which she had not been able to for a long time). They perceived their daughter as much more open during social exchanges, she would again chime in during discussions at home. The quantity of her speech had increased. At the horse stable, she for the first time spoke to people she did not like. The parents too reported that her care for her horse had increased and was perceived as fulfilling. At the end of the dosing period the patient experienced stress due to the fact that the necessity of an outpatient treatment might not allow the family to undertake their vacation trip. She was nevertheless able to maintain course; intermittent downswings of her mood were not accompanied by deterioration of her eating behavior. Body weight remained stable during the dosing period (60. 9 kg one day prior to dosing; 60. 4 kg last day of dosing; range for the initial 10 post-dosing days: 61. 4–62. 0 kg). She entered an intensive home treatment program; during the vacation in a foreign country, she relapsed and lost 3 kgs of body weight. She was able to regain weight after her return and weighed 63.

Output: corroborate


Input: Claim: Biohacking methods can fully reverse aging and extend lifespan indefinitely. [SEP] Text: Firstly, we compared the part of the fat body's transcriptome that is altered by Sir2 overexpression with those genes coding for the lipid droplet proteome as these organelles are known to be central players for the control of fat storage and mobilization [36-39]. A considerable overlap between these data sets suggested a role for fat body Sir2 in modulating the composition of the lipid droplet proteome, a hypothesis that is supported by the statistical data. Nevertheless, as lipid droplets have been shown to regulate aging processes [40] our data provide a good starting point to unravel the putative role of Sir2 in lipid droplet biology. The overlap with genes coding for lipid droplet proteins was highly sex specific, a feature that was also seen for starvation resistance and the Sir2 induced transcriptional changes in fat tissues. Our findings that fat storage, body weight and lipid droplet size were not changed after Sir2 overexpression, contrast with other recent studies which demonstrated an impact of RNAi-mediated knockout of Sir2 in the fat body or constitutive whole body knockout, respectively, on fat metabolism [16]. Furthermore, data from mouse studies indicate a role for Sir2 in the regulation of lipid metabolism [8, 10]. These divergences may result from the different expression system used in our study. We aimed to overexpress Sir2 only moderately in the fat body and nowhere else, and only during adulthood. This strategy should have only minimal confounding effects on e. g. fat storage caused by complete silencing of Sir2 in either the fat body/liver or the whole animal. Overall, we conclusively showed that Sir2 is a longevity gene in Drosophila. With this study we provide additional independent evidence for its ability to extend lifespan of male and female flies when moderately overexpressed in the adult fat body. We also obtained transcriptional profiles elicited by this overexpression and propose a role for Sir2 in lipid droplet biology especially under conditions of starvation. However, the precise conditions under which Sir2 affects fat utilization and the molecular mechanisms involved in this function remain to be elucidated. Furthermore, our transcriptional data do not support the idea of Sir2 mediating the response to dietary restriction. This study again highlights the relevance of Sir2 for aging processes and its potential as a pharmacological target to cure age-related diseases.

Output: contrast


Input: Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: thaliana79; and SpGA2022_006905 belongs to the (SVP-group) which controls the time of flowering and meristem identity80. We found 77 genes under positive selection (top 1% CLR values) in both the European and Indian populations (Fig. 4b), significantly more genes than expected by chance (P < 2. 2e-16, Fisher’s Exact Test). Among these, gene SpGA2022_055195, a homolog to CYP78A9 of cytochrome P450 monooxygenases in A. thaliana, belongs to a highly conserved gene family CYP78A. Previous studies in A. thaliana and other species found that CYP78A9 plays a critical role in promoting cell proliferation during flower development and further impacts seed size81–83. Overall, these data consistently suggest that genes involved in reproduction and development were under selection in Indian and European populations, which might have led to reduced sexual reproduction in these two populations. DiscussionsHere, we characterized the genomic and epigenomic diversity, as well as the demographic history of a facultative asexual flowering plant, S. polyrhiza. We found that among populations of S. polyrhiza, demographic history and reproductive system jointly determine the population’s genomic and epigenomic diversity. Analyses on the footprint of selection suggest that natural selection drove the reduced vascular system and increased asexuality in S. polyrhiza. Theory predicts that asexual reproduction reduces genomic diversity and the efficiency of purifying selection84. Consistent with this prediction, at the species level, we found that S. polyrhiza has very low genomic diversity and reduced purifying selection (seen as an increased πN/πS ratio), when compared to a wide range of spermatophyte plants43. Within species, the SE-Asian population, which has the highest frequency of sexual reproduction based on the estimated recombination rate, has the highest genomic diversity, the lowest πN/πS ratio and the highest heterozygosity (Fig. 2b), supporting the theoretical prediction2,5,13−15. The low πN/πS ratio found in the European population, which has the lowest sexual reproduction and genomic diversity, is most likely due to its migration history. The demographic model suggested that the European population derived from the SE-Asian population very recently (Fig.

Output: pass


Input: Claim: The placebo effect, where a patient experiences real improvements due to believing they're receiving treatment, is observed in many clinical trials. [SEP] Text: Baseline migraine days per month, length of the double-blind, randomized treatment period and the year of the study were not found to be confounders or covariates; therefore, they were not included in the regression model (data not shown). Route (i. e. oral or injection) and sample size of randomized subjects were found to be covariates and were included in the model. Sample size was represented categorically as large and small sample sized based on the median split of number of randomized subjects (n = 216). Two studies were identified as outliers, falling outside the 95% prediction limits in the linear regression, and were therefore removed from the main analysis. Once these outliers were removed, 25 30. 4% ± 16. 3% for the placebo group, 42. 7% ± 14. 4% for the active group, and the placebo-subtracted response rate at 11. 9% ± 8. 4% (see Table 1). Table 1. Mean proportion of responders across all studies. placebo responders2830. 4%16. 3%0%67%Proportion active responders2842. 7%14. 4%22%77%Placebo-subtracted response rate2811. 9%8. 4%−6%25%Note: Responder defined as a patient with ≥ 50% reduction in migraines/month. N: number of studies; SD: standard deviation. After adjusting for the route of administration and sample size, there was a statistically significant association between the proportion of patients who were considered placebo responders and the placebo-subtracted response rate (b = −0. 27, p = 0. 022) (Figure 2). Further, 35% of the placebo-subtracted response rate is explained by the proportion of placebo responders. Based on the linear model for small sample sizes (n < 216), reducing the proportion of placebo responders from 50% to 20% would be predicted to almost double the placebo-subtracted response rate for injection treatments and would triple it for oral treatments. Figure 2. Difference in placebo-subtracted response rate by proportion of placebo responders. The placebo-subtracted response rate decreases with increasing proportions of placebo responders. Responder defined as a patient with ≥50% reduction in migraine days/month.

Output: corroborate


Input: Claim: Biohacking methods can fully reverse aging and extend lifespan indefinitely. [SEP] Text: Briefly, after mating and feeding on medium containing RU486 or ethanol for 7 d, for one biological replicate 8 males or 5 females were weighed on a digital accuracy balance and homogenized in 1 ml 0. 05 % Tween-20 with 3 zirconium beads (2,8 mm) for 2 min at 3. 25 m/s in a 24 (Omni International). Lysates were heat-inactivated for 5 min at 70 °C, centrifuged and supernatant was incubated with the for 30 min at 37 °C. Absorbance was measured at 562 nm and glyceryl trioleate served as a standard. and Determination of Diameters of After feeding on RU486 or control medium for 24 h L3 larvae or adults generated by crossing UAS-Sir2 flies to the driver line S1106-Gal4 were dissected, fixed and fat bodies were stained with a solution containing 1 μg/ml (Invitrogen) and 5 μg/ml Hoechst (Sigma) for 30 min at room temperature. Slides were mounted in Mowiol/DABCO (Roth) and photographed with a imager 7. 1 microscope equipped with a MRM camera within the next two days. 14 photographs taken from 7 biological replicates were analyzed per group with AxioVision 4. 1 (Zeiss). To measure fat droplet diameters a line was drawn across each picture and only droplets intersecting with the line were measured using a measurement tool implemented in the program. Mated Sir2>S1106-Gal4 flies were kept on 1 % agar containing either 400 μM RU486 or ethanol and vials were changed every 2-3 days. Dead flies were scored 1-3 times a day. Statistics and statistics were performed using Graphversion 6. 00 for www. graphpad. com. Lifespan and starvation survival data were analyzed by log rank test and data from qPCR, body fat quantification, body weight and diameters of lipid droplets by Mann-Whitney-U Test. Statistical analyses of Venn-diagram data were performed with Fisher's exact test. : dietary restriction; ns: not significant. 1. . The SIR2/3/4 complex and SIR2 alone promote longevity in Saccharomyces cerevisiae by two different mechanisms. Genes Dev.

Output: contrast


Input: Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: 1d). It is likely that the πN/πS ratio in the European population remained the same as its ancestral population and has not reached an equilibrium level yet. While there are fewer genome-wide SVs in S. polyrhiza compared to other species44,45, we found these variants and small INDELs are in tendency enriched in MADS-box genes. This indicates that the loss-of-function of MADS-box genes, many of them involved in flower development and sexual reproduction, is under natural selection. The results are consistent with the observation that the number of functional MADS-box genes was dramatically reduced in S. polyrhiza85. Single-base resolution methylomes of 20 individuals showed that the overall CpG, CHG and CHH methylation levels in S. polyrhiza shoots are very low, consistent with previous studies40,86. The low levels of DNA methylation might be associated with reduced sexual reproduction: while CpG and CHG methylations in plants are important for controlling cross-overs during meiosis87 and are increased during male gametogenesis, CHH methylation is highly accumulated during embryogenesis19,25−27. In facultative asexual plants, due to reduced sexual reproduction and meiosis, the selection of genetic mechanisms maintaining or increasing the CpG, CHG and CHH methylation is reduced or absent, which might have led to the reduced CpG, CHG and CHH methylation levels. Consistently, a recent study suggests that S. polyrhiza has lost several genes in the RdDM pathway86. Interestingly, within species, the methylation profile of the 20 individuals correlates with their genetic distance (Supplementary Fig. 11–13), indicating a gradual evolution of DNA methylomes in S. polyrhiza. For example, the Indian and European populations, which diverged from SE-Asian populations around 51,000 and 12,000 generations ago, gradually decreased their DNA methylations (Fig. 3a-c). At the species level, using a genome-wide scan approach, we found a strong signature of natural selection on genes involved in flower and seed development. indicating that the evolution of reproduction, likely, an increased clonal propagation in S. polyrhiza, was driven by natural selection. This is consistent with the pattern that many aquatic organisms reproduce clonally88.

Output: pass


Input: Claim: The placebo effect, where a patient experiences real improvements due to believing they're receiving treatment, is observed in many clinical trials. [SEP] Text: Variable xa is the proportion of placebo responders; variable xb is route where oral = 0 and injection = 1; variable xc is sample size where small = 0 and large = 1. indicates studies with large sample sizes. indicates studies with small sample sizes. In the exploratory analysis, a total of 11 (42. 3%) of the included trials failed to meet statistical significance of the primary endpoint, whereas 15 (57. 7%) of trials were successful (results were statistically significant). There was a statistically significant difference in proportion of successful trials between studies with ≤20% placebo responders (100%), 21–30% placebo responders (50%), and >30% placebo responders (40%; p = 0. 048). This statistically significant difference was driven by the 60% difference in trial success rate between studies with ≤20% placebo responders and studies with >30% placebo responders (p = 0. 034). However, there was a strong relationship between successful trials and baseline migraine days. Therefore, the relationship between the proportion of successful trials and proportion of placebo responders was stratified by high and low baseline migraine days based on the median split (8. 24 migraine days a month) – this stratification also led to some cells having less than three studies to represent that category. In the high baseline migraine group, there was not a statistically significant difference in proportion of successful trials between studies with ≤20% placebo responders (100%), 21–30% placebo responders (80%), and >30% placebo responders (75%; p = 1. 0). In the low baseline migraine group, there was not a statistically significant difference in proportion of successful trials between studies with ≤20% placebo responders (100%), 21–30% placebo responders (20%), and >30% placebo responders (17%; p = 0. 38) (Figure 3). Figure 3. Proportion of studies that met their primary endpoint by placebo response and baseline migraine frequency. A trial is considered successful if it meets statistical significance of its primary endpoint; see Methods. Numbers on the top of each bar indicate the number of studies. High baseline migraine frequency was considered ≥8. 24 migraines per month. Low baseline migraine frequency was considered <8. 24 migraines per month. Sample size estimates were calculated at an alpha level of 0. 05 and 80% power for oral and injection treatments using the regression model in Figure 2 for small sample sizes (n < 216).

Output: corroborate


Input: Claim: Biohacking methods can fully reverse aging and extend lifespan indefinitely. [SEP] Text: past decade has seen the identification of numerous conserved genes that extend lifespan in diverse species, yet the number of compounds that extend lifespan is relatively small. A class of compounds called STACs, which were identified as activators of Sir2/SIRT1 NAD+-dependent deacetylases, extend the lifespans of multiple species in a Sir2-dependent manner and can delay the onset of age-related diseases such as cancer, diabetes and neurodegeneration in model organisms. Plant-derived STACs such as fisetin and resveratrol have several liabilities, including poor stability and relatively low potency as SIRT1 activators. To develop improved STACs, stilbene derivatives with modifications at the 4’ position of the B ring were synthesized using a Horner-Emmons-based synthetic route or by hydrolyzing deoxyrhapontin. Here, we describe synthetic STACs with lower toxicity toward human cells, and higher potency with respect to SIRT1 activation and lifespan extension in Saccharomyces cerevisiae. These studies show that it is possible to improve upon naturally occurring STACs based on a number of criteria including lifespan extension. restriction (DR) delays aging and extends the maximum lifespan of a wide range of organisms (Koubova & Guarente, 2003). In mammals, DR delays numerous age-associated diseases including cancer, neurodegeneration, atherosclerosis and type II diabetes (Weindruch, 1996; Lane et al. , 2001; Roth et al. , 2001). The search for small molecule mimetics that can deliver the health benefits of DR is an active area of research, but no safe and effective DR mimetic has been found (Ingram et al. , 2004). An approach we have taken to finding DR mimetics has been to screen libraries for compounds that modulate the activity of longevity regulatory proteins, and to test these for their ability to extend lifespan in relatively simple organisms such as baker's yeast and the nematode Caenorhabditis elegans before moving on to mammals (Wood et al. , 2004). There are a number of reasons for taking this approach. First, DR works on almost all organisms that have been tested. Therefore, we expect bona fide DR mimetics to extend the lifespans of species as different as yeast, worms, flies and mice.

Output: contrast


Input: Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: In addition, several genes related to vascularity, root development and DNA damage repair were also under strong selection, suggesting the reduced root and vascular development and low mutation rate in S. polyrhiza were likely also driven by natural selection. Among populations, we found strong positive selection on genes involved in sexual reproduction and development in Indian and European populations, two recently evolved populations that showed reduced genomic recombination. These results suggest that natural selection favours clonal reproduction in S. polyrhiza during the recent colonization process, a pattern was frequently found in many invasive species89,90. However, despite strong selection favouring clonal reproduction, substantial recombination in the S. polyrhiza genome, mostly in the SE-Asian population, remained, reflecting that sexual reproduction is essential to overcome the costs involved in clonal reproduction in long term. Taken together, population genomes and epigenomes of S. polyrhiza suggest that natural selection acting on the mating system and organ development can shape genome-wide genomic and epigenomic variations. Methods DNA sample preparation and sequencing We sequenced 131 genotypes that were primarily collected from Asia and Europe (1). These samples were cultivated in N-medium91 until DNA isolation using a CTAB method. Library preparations were carried out following the protocol described in Xu et al. (2019)37. All libraries were sequenced either on Illumina HiTen or 4000 platforms for paired-end sequencing with a read size of 150 bp. Low-quality reads and adapter sequences were trimmed with AdapterRemoval (v2. 033)92. On average, 33. 8 million reads per genotype were obtained. The clean reads were aligned to the S. polyrhiza reference genome93,94 using BWA-MEM ( with default parameters. Reads without alignment hits or with multiple alignment positions were removed. SAMtools “rmdup” function was used to remove PCR duplicates95. Single nucleotide variant calling We filtered SNPs using GATK96 (v4. 1. 4. 1, Java 11) with options: "QD < 2. 0 | QUAL < 30. 0 | SOR > 3. 0 | FS > 60. 0 | MQ < 40. 0 | MQRankSum < -12. 5 | ReadPosRankSum < -8. 0". Then, VCFtools (v0. 1.

Output: pass


Input: Claim: The placebo effect, where a patient experiences real improvements due to believing they're receiving treatment, is observed in many clinical trials. [SEP] Text: A study with a placebo response rate of 40% would need approximately 830 subjects for oral treatments and 221 for injection treatments to meet statistical significance; however, a study with a placebo response rate of 20% would need only 197 subjects for oral treatments and 91 for injection treatments to reach statistical significance (Figure 4). Figure 4. Sample size estimates by proportion of placebo responders. Sample size requirements increase as proportion of placebo responders increase. Responder defined as a patient with ≥50% reduction in migraines/month. DiscussionWe found that in clinical trials of preventative treatments for migraine, the greater the placebo response, the smaller the placebo-subtracted response rate and the higher the sample size requirements. These results are consistent with other meta-analyses on the association between placebo response rates and the success of chronic pain trials, such as neuropathic pain (4,13). Other studies have also found an increasing placebo response over time (4,13). Our study, however, found no significant relation with year of study and placebo response when study year was added to the regression model. We did find route of treatment administration and sample size to be covariates in this model. Studies with an oral treatment had slightly lower levels of mean proportion of placebo responders than studies with an injection treatment. Other studies have also found an association between route of administration and placebo response, suggesting that the more invasive the treatment, the higher the placebo response (7). One study found baseline severity of depression to be associated with differences between drug and placebo (14); however, we did not find a similar trend in our analysis. We did find baseline migraine to be associated with success of meeting the primary endpoint in the exploratory analysis on the relationship between trial success and proportion of placebo responders. As many factors influence the ability to meet the primary endpoint – difference between arms, variability, and sample size – further research is warranted to determine which factors, or combination of factors, baseline migraine may influence. This analysis had several limitations. First, only published 1. Evidence-based clinical trial design for chronic pain pharmacotherapy: A blueprint for. Pain 2011; 152: S107–S115. CrossrefPubMed2. . Increasing uncertainty in CNS clinical trials: The role of placebo, nocebo, and Hawthorne effects. 2016; 15: 736–747. CrossrefPubMed3. A deeper look at pain variability and its relationship with the placebo response.

Output: corroborate


Input: Claim: Biohacking methods can fully reverse aging and extend lifespan indefinitely. [SEP] Text: Second, simple organisms are far more amenable to genetic manipulation and their lifespans are relatively short – less than 10 days in the case of actively dividing yeast – therefore, the pathways through which lifespan-extending compounds are working can be identified more readily. Third, the pathways that control the DR response are far better defined in these organisms than in mammals. Finally, small molecules can have effects that are more complex than simple activation or inhibition, such as altering substrate specificity, and understanding how they extend lifespan may reveal additional longevity pathways (Viswanathan et al. , 2005). cerevisiae, C. elegans, and Drosophila melanogaster, increased copy number or expression of the SIR2 gene extends lifespan 30–50% (Kaeberlein et al. , 1999; Tissenbaum & Guarente, 2001; Rogina & Helfand, 2004). With regards to S. cerevisiae, this refers to replicative lifespan, which is the number of daughter cells produced by a single mother before senescence, rather than the more recently defined chronological lifespan, which measures survival time in the absence of nutrients (Bitterman et al. , 2003). In wild-type S. cerevisiae and Drosophila, lifespan extension by DR requires SIR2, implying that the gene is intimately involved in mediating its effects. In the absence of the FOB1 gene, which suppresses the rDNA hyper-recombination defect of a sir2 mutant, glucose restriction can extend the lifespan of some sir2 strains (Kaeberlein et al. , 2004; Lin & Guarente, 2006) revealing that there is redundancy in the DR pathway, which we have shown is mediated, at least in part, by the Sir2 homolog Hst2 (Lamming et al. , 2005). Although it is not known whether the closest mammalian Sir2 homolog, SIRT1, extends lifespan in mammals, this gene is known to modulate several distinct physiologies known to be important for lifespan including cell survival, energy metabolism, and resistance to stresses (Luo et al. , 2001; Vaziri et al. , 2001; Araki et al. , 2004; Brunet et al. , 2004; Cohen et al. , 2004; Yeung et al. , 2004; Moynihan et al. , 2005; Bordone et al. , 2006).

Output: contrast


Input: Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: 13)97 was used to remove SNPs that have the following features: 1) non-biallelic; 2) minor allele frequency (MAF) less than 0. 01; 3) mean sequencing depth greater than eight or less than 41; 4) missing genotypes greater than 20%; 5) located in small SNP clusters (more than two SNPs in a ten base-pair window). SnpEff (version 5. 0c)98 was used to annotate SNPs and INDELs. We estimated genome-wide nucleotide diversity and genome-wide πN/πS ratios using SNPgenie (v2019. 10. 31)99. The genome-wide heterozygosity for each individual was calculated using VCFtools (v0. 1. 13)97. We estimated the genetic associations between heterozygosity and the SVs of AGL62 and SOC1 using 100 with single variant Wald test. Population structure and linkage disequilibrium (LD) We grouped genetically similar genotypes by defining clonal genotype pairs that have no more than 0. 01% different homozygous sites and no more than 2% different heterozygous sites. These thresholds were previously adopted by Ho et al. (2019)38. Prior to the population structure analysis, we removed SNPs that 1) deviated from Hardy-(Fisher exact test, P < 0. 01) or 2) linked loci (each pair of SNP have correlation coefficient r2 > 0. 33 in a sliding window with a size of 50 SNPs and step of 5 SNPs), using VCFtools (v0. 1. 13)97 and Plink (v1. 9)101. Principal component analysis (PCA) and population structure analysis were carried out using Plink (v1. 9)101 and fastStructure (v1. 0)102, respectively. The simple mode (as default) from fastStructure was used for the population structure analysis. value was estimated using a heuristic function in fastStructure. For each of the 159 clonal families, we selected the least missingness genotype (i. e. the genotype with the highest sequencing coverage of that clonal family) as the representative genotype. SNP information from all 159 representative genotypes was used to estimate the linkage disequilibrium decay for each of the four populations. PopLDdecay (v3.

Output: pass


Input: Claim: The placebo effect, where a patient experiences real improvements due to believing they're receiving treatment, is observed in many clinical trials. [SEP] Text: IntroductionCough is one of the most common and distressing of symptoms, yet at present, there is little to offer patients to relieve cough apart from cough syrups which are effective because of a powerful placebo effect [1, 2]. Codeine was once deemed a powerful antitussive for all types of cough because of its presumed depressant effect on cough control at the level of the brainstem but doubts have been raised on its efficacy and it is no longer considered a ‘gold standard’ antitussive [3]. Much progress is being made on the peripheral mechanism of cough at the level of sensory nerves in the airway but clinical trials on some of the best candidates for a new cough medicine are proving difficult because of side effects [4]. The placebo effect in cough therapy is both a gift and a problem to those working on treatments for cough. It is a gift because cough is so susceptible to a placebo effect with one review reporting that up to 85% of the efficacy of cough medicines is due to a placebo effect [5]. It is also a problem to researchers as with such a large placebo effect it is difficult to demonstrate that any new cough medicine is superior to placebo treatment in cough clinical trials. The magnitude of the placebo effect in the treatment of cough with inhaled steroids has recently been highlighted and the authors conclude that clinicians should be cautious about attributing the response of patients on inhaled steroids to anything more than a placebo effect [6]. This review will discuss the significance of the placebo effect in the development of new cough treatments and its importance in cough clinical trials. What is a Placebo and a Placebo Effect? The term ‘placebo’ originates as a Latin term and means ‘I shall please’ [7]. Before the introduction of codeine as a therapy for cough in the nineteenth century [8], all cough medicines could be considered as placebo treatments that were meant to please patients even though physicians and patients may have believed that they had active properties above that of a placebo treatment. An early edition of the Merck’s manual [9] lists 61 treatments for cough, including carbolic acid, alcohol, cannabis, indica, creosote, morphine, potassium bromide, sandalwood oil, and zinc sulfate, and describes cod-liver oil as the most useful of all remedies in cough.

Output: corroborate


Input: Claim: Biohacking methods can fully reverse aging and extend lifespan indefinitely. [SEP] Text: We recently reported the design, synthesis and characterization of SIRT1 inhibitors that are derivatives of splitomycin (Bedalov et al. , 2001; Mai et al. , 2005). Although SIRT1 inhibitors may be useful reagents in laboratory settings and possibly in the treatment of diseases such as cancer (Lim, 2006), we have placed most of our effort on identifying and optimizing molecules that activate Sir2/SIRT1, based on the hypothesis that they should extend lifespan and possibly mimic the health benefits of DR. To this end we performed in vitro screens for small molecules that could modulate human SIRT1 and identified 18 SIRT1-activating compounds or STACs, which were of three structural classes: chalcones, flavones and stilbenes (Howitz et al. , 2003). The most potent of these was 3,5,4′-hydroxystilbene (resveratrol). Resveratrol stimulated SIRT1 activity ∼tenfold by lowering the Km for both NAD+ and the peptide substrate. Resveratrol also provided the largest yeast lifespan extension, ∼60%, and this was entirely dependent on the SIR2 gene (Howitz et al. , 2003), as was the lifespan extension in C. elegans and D. melanogaster (Wood et al. , 2004), although we do not discount the possibility that the beneficial effects of resveratrol in mammals are mediated through a potentially large number of cellular factors in addition to SIRT1 (Baur & Sinclair, 2006). Keijer and colleagues recently identified three additional STACs from plants, but none of them was more potent than resveratrol (de Boer et al. , 2006). Interestingly, resveratrol has been shown to provide protection from numerous diseases in rodent models including cancer and diabetes, but the pathways through which it exerts these effects are not known (Bhat & Pezzuto, 2002; Aggarwal et al. , 2004; Su et al. , 2006). Activation of SIRT1 by STACs is detectable in a variety of in vitro assays including a fluorescent peptide-based assay (Howitz et al. , 2003), a high performance liquid chromatography (HPLC)-based assay (de Boer et al. , 2006) and a radiolabelled peptide assay (A. Suave & U.

Output: contrast


Input: Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: 41)103 was used to measure LD decay. For each population, we used the following filters: SNP of missing allele > 20% and MAF < 0. 05. The allele frequency correlation (denoted as r2) of pairwise SNPs within 100 kb physical distance was calculated. Phylogenetic tree reconstruction We used BLAST + version 2. 9. 0104 to identify orthologous fragments between the genomes of S. polyrhiza and Colocasia esculenta (Araceae). For each SNP from the core set, the reference allele and its flanking 300 bp (upstream 150 bp and downstream 150 bp, respectively) sequences were extracted from the S. polyrhiza genome and then aligned to the C. esculenta reference genome105. The hit thresholds were set as 1) alignment identity > 70%; 2) e-value > 1e − 6; 3) minimum aligned sequence length ≥ 50 (the aligned sequence must cover SNP position); 4) keep the best hit; and 5) ignore short deletions from C. esculenta. The orthologous alleles from C. esculenta were used as the outgroup genotype. We identified only 13,120 SNPs that have orthologous fragments in the C. esculenta genome. Those data were further used to infer the maximum-likelihood (ML) phylogenetic tree using RAxML-ng (v1. 0. 1)106. The best hit model was estimated to be ‘TVM + G4’ using Modeltest-ng (0. 1. 6)107,108. The bootstrapping converged after 700 iterations of the ML tree search. ITOL v5109 and the Python package ETE2110 were used for tree visualization. Selection analysis Genome-wide scans of selection were performed on all 20 chromosomes of all sampled populations. Selective sweeps were inferred by three programmes: RAiSD52, SweeD53 and LASSI54. RAiSD uses the µ statistic, which provides information on the SFS, LD, and genomic diversity to evaluate the presence of positive selection52. SweeD calculates the traditional composite likelihood ratio (CLR) to infer loci under selection53. LASSI employs the T statistic, which uses a likelihood model based on the haplotype frequency spectrum to detect hard and soft sweeps54.

Output: pass


Input: Claim: The placebo effect, where a patient experiences real improvements due to believing they're receiving treatment, is observed in many clinical trials. [SEP] Text: All of these cough medicines are likely to have had some beneficial placebo effect and reduced the severity of cough, and that is why they were regularly prescribed by physicians and regularly pleased patients. When patients are given any cough medicine, they usually feel better and the severity of their cough is reduced but it is difficult to separate out any pharmacological effect of the medicine from any placebo effect unless the treatment is compared with a placebo treatment in a double-blind randomized clinical trial. Perceived and EffectsThe efficacy of any cough medicine depends on two factors: firstly the efficacy of the pharmacologically active medicine such as codeine or dextromethorphan and secondly the placebo effect of the treatment. When discussing the placebo effect, it is important to separate the ‘perceived placebo effect’ from the ‘true placebo effect’. This distinction was first put forward by Ernst in 1995 [10] and was later extended to explain the placebo effect of cough medicines [5, 11]. The perceived placebo effect is the total response to placebo treatment seen in a clinical trial, and the perceived placebo effect is made up of three components as illustrated in Fig. 1. The ‘physiological effect’ of a cough treatment is the effect due to the taste of the medicine and is related to stimulation of salivation and mucus secretions that soothe and lubricate the airway, and may also be related to a specific effect of sweet taste as discussed below. The physiological effect of a cough medicine is utilized in cough syrups as a major component of their efficacy, and this physiological effect is not present or minimal in cough medicines formulated as a tablet or capsule. The ‘non-specific’ components of any treatment are related to factors such as natural recovery of the patient, and regression to a mean value of cough severity, as patients are generally recruited into a clinical trial with severe symptoms and these measures can only regress towards a mean value. The true placebo effect can be considered as the psychological effects of the treatment that lead to a reduction in cough severity. The true placebo effect was first of interest in clinical trials but interest in this phenomenon has evolved into a psychosocial model which incorporates a general interaction of the patient to their environment and how they respond to psychological mechanisms such as conditioning, expectation, reward, and anxiety reduction, and how these can be modulated by desire, motivation, and memory [12]. Fig.

Output: corroborate