Input: Claim: The suprachiasmatic nucleus is the master regulator of circadian rhythms. [SEP] Text: Photomicrographs of coronal sections that contained grafted tissue with VIP immunoreactivity (arrows)in four of the hamsters from the study. Lesions of the host SCN can also be seen in A and D. Och, Optic chiasm;3V, third ventricle. The phases of activity onset on the day after the first set of injections are shown in Figure 4. The mean phase of activity onset of the hamsters in group 1 was 0030 hr (8. 5 hr before the time of melatonin injection at 0900 hr), and that of Group 2 was 0910 hr (11. 83 hr before the time of melatonin injection at 2100 hr), a difference of 8. 67 hr. The distribution of phases for each group was significantly clustered (group 1, r = 0. 67; group 2, r = 0. 89; p < 0. 01 in both groups, Rayleigh test). There was also a significant difference between the distributions of the two groups (p < 0. 01, Mardia–Watson–Wheeler test). Thus melatonin injections given at opposite times of day to hamsters bearing newly implanted SCN grafts were able to entrain the restored rhythms to different phases. Download figureOpen in new tabDownload powerpointFig. 4. Phases of activity onset on the day after the final injection for all animals plotted on a circle representing the 24 hr of that day. Open circles represent individual animals that received melatonin in the morning and vehicle in the evening (group 1), and closed circles represent animals that received vehicle in the morning and melatonin in the evening (group 2). The average phase for each group is shown by the arrows within the circle (open arrow, group 1;closed arrow, group 2), and the degree of synchrony within each group is represented by the length of thearrows and by the value of r. Arrows outside the circle indicate the times of the injections. In 10 of the 11 hosts tested, a second series of melatonin or vehicle injections delivered 6 weeks after transplantation failed to induce either phase shifts or entrainment to the injections (Figs. 1 and 2).

Output: pass


Input: Claim: Hydropower generation can disrupt aquatic ecosystems. [SEP] Text: Other solutions, using behavioral systems to guide fish, have been tested (Mueller and Simmons, 2008; Perry et al. , 2014; Tétard et al. , 2019) but no clear solution easily applicable to diverse locations has been determined (Williams et al. , 2012). Consequently, other active solutions, such as trap-and-transport or turbine modulation/shutdown during migration peaks, are sometimes considered to mitigate the impact of dams (Thorstad et al. , 2012; Stich et al. , 2015; Teichert et al. , 2020a). To be effective and acceptable for stakeholders, these mitigation measures need a precise forecast of migration timing, based on calendar dates or using environmental records, to limit the financial impact on hydropower generation (Teichert et al. , 2020b). In most cases, these measures are implemented in conjunction with biological monitoring (telemetry, capture, etc. ). Most smolts migrate to the ocean in spring (Otero et al. , 2014), but in some locations some individuals migrate outside of the peak season, especially in fall (Birnie‐Gauvin and Aarestrup, 2019). “Smoltification” is controlled by photoperiod and temperature, with migration onset triggered by temperature and sometimes by discharge (McCormick et al. , 1998; Thorstad et al. , 2012), especially when river flow peaks occur at the beginning of the migration season (Whalen et al. , 1999; Otero et al. , 2014; Teichert et al. , 2020a). Some studies modeling smolt migration with these environmental variables showed high predictive performance (Sykes et al. , 2009; Teichert et al. , 2020a), which can give credence to active solution approaches. Nevertheless, whatever the “passage” solution (active or passive), and no matter how effective it may be, some large reservoirs can cause substantial migratory delay of several days or even weeks in some locations (Venditti et al. , 2000; Schwinn et al. , 2017, 2019; Tétard et al. , 2019; Babin et al. , 2020). However, barriers, and especially hydropower regulations, typically focus only on passage efficiency and mortality (Marschall et al.

Output: corroborate


Input: Claim: Every genetic trait can be modified without affecting other genes. [SEP] Text: We also used the RNA-seq reads to identify segregating genetic variants in the Amboseli population. We considered only high confidence sites that were variable within the Amboseli population (‘Materials and methods’; Figure 1—figure supplement 3). As expected (Piskol et al. , 2013), these sites were highly enriched in annotated gene bodies (Figure 1; Figure 1—figure supplement 4). Based on parallel analyses applied to human RNA-seq data, we estimated approximately 97% of these sites to be true positives, and a median correlation between true genotypes and inferred genotypes of 98. 7% (‘Materials and methods’; Figure 1—figure supplements 5–6). To identify putative expression quantitative trait loci (eQTL), we focused on variants that passed quality control filters, within 200 kb of the gene of interest. Such variants represent likely cis-acting eQTL, which are more readily identifiable in small sample sizes than trans-eQTL. To identify cases of allele-specific expression, which provides independent but complementary evidence for functional cis-regulatory variation, we focused on genes for which multiple heterozygotes were identified for variants in the exonic regions of expressed genes. We also required a minimum total read depth at exonic heterozygous sites of 300 reads (which should provide high power to detect modest ASE: Fontanillas et al. , 2010), resulting in a total set of 2280 genes tested for ASE. Figure 1 with 14 supplements see all Download asset Open asset Baboon eQTLs are enriched in and near genes. The locations of all SNPs tested in the eQTL analysis are shown in gold relative to the 5′ most gene transcription start site (TSS) and the 3′ most gene transcription end site (TES) for all 10,409 genes. SNPs detected as eQTL are overplotted in blue, and are enriched, relative to all SNPs tested, near transcription start sites, transcription end sites, and within gene bodies. Gray shaded rectangle denotes the region bounded by the TSS and TES, with gene lengths divided into 20 bins for visibility (because the gene body is thus artificially enlarged, SNP density within genes cannot be directly compared with SNP density outside of genes). Note that SNPs that fall outside of one focal gene may fall within the boundaries of other genes.

Output: contrast


Input: Claim: The suprachiasmatic nucleus is the master regulator of circadian rhythms. [SEP] Text: The circadian times (CTs, with activity onset as CT 12) at which the first of the five injections occurred for the hamsters that received melatonin were 9, 17, 18, 22, 23, and 24, and for those that received vehicle were 6, 11, 12, 17, and 21. 5. The only hamster that showed a phase shift did so in response to vehicle injections at CT 11 (Fig. 2B). Thus melatonin did not entrain or phase shift the activity rhythms of hamsters with well-established SCN grafts. of melatonin to SCN-lesioned adult hamsters bearing newly implanted fetal SCN grafts entrained the restored circadian activity rhythms. In particular, significantly different average phases were established by injections given at different times of day. Melatonin must have caused the difference in average phase, because the hosts and the donor tissues were all treated identically in the two groups except for the timing of melatonin exposure; all hosts received injections twice a day, and all donor tissues came from fetuses of SCN-lesioned dams that were maintained under the same conditions. Entrainment of the restored rhythms with injections given immediately after transplantation indicates that circadian oscillations were being generated during this time, within 7 d of E14, the age of the tissue when transplanted. The results also suggest that the fetal and neonatal hypothalami are direct targets of melatonin. It seems unlikely that synaptic communication between potential melatonin targets within the host (Morgan et al. , 1994) and the graft would have been established within 7 d after transplantation. Furthermore, although the presence of melatonin receptors within grafts has not been examined, the presence of receptors in intact fetal and neonatal SCN (Duncan and Davis, 1993) suggests that receptors would be present in grafts. It cannot be excluded, however, that a humoral signal from the host to the graft mediates indirect effects of the injections. In addition, although the dose of melatonin used (25 μg) is commonly used in reproductive studies, such an injection produces serum levels three orders of magnitude above physiological levels (Maywood et al. , 1993). Thus it is not known whether the entrainment observed here is a physiological effect of melatonin. In contrast to the effects of injections given immediately after transplantation, a second set of injections given 6 weeks after transplantation had no measurable effect on the phase of the rhythms.

Output: pass


Input: Claim: Hydropower generation can disrupt aquatic ecosystems. [SEP] Text: , 2011) with most managers and developers overlooking the potential for sublethal costs induced by migratory delay (Silva et al. , 2018). Poutès dam is located in the River (France), the main tributary of the Loire River. Although this hydropower dam was equipped with fish passage solutions in the late 1980s, a number of problems remained when the Poutès-Monistrol hydropower complex was relicensed in 2011: migratory delay for upstream and downstream migration, and difficulty for fish in using the fishways (Bach et al. , 2000; Tétard et al. , 2019). After several years of concerted discussions between stakeholders, it was decided to reconfigure the Poutès dam to meet ecological connectivity requirements for sediment and fish. The project included new fishways and a much lower reservoir level. 1 As a first step, a scientific program helped to assess the initial impact of the Poutès dam on smolt migration before reconfiguration (Tétard et al. , 2019). The beginning of construction, which was to start in 2016, was postponed until summer 2019, and temporary measures during smolt migration were needed as early as 2017, pending the start of reconfiguration. These proposed measures were discussed with stakeholders and aimed to improve passage efficiency while minimizing residence time in the reservoir. They consisted in temporarily lowering the reservoir level to decrease migratory delay, building a temporary bypass, and modulating (in 2017) or stopping (in 2018) turbine operation. The present study aimed to provide feedback on the successes and failures encountered during the 2 years in which management rules were implemented, based on a telemetry experiment. The temporary measures were discussed with stakeholders and continuously improved during the experiment, through a structured iterative process of “learning by doing”. Comprehensive assessment of successive measures implemented at the Poutès dam thus provides feedback to guide management plans in other hydropower sites for solving issues of migratory delay and passage efficiency during smolt migration. 2 Materials and methods 2. 1 Study area River (Fig. 1) is 1012 km long and has a drainage area of 117,000 km2. It is the longest river system in Europe in which spawning migration of Atlantic salmon still occurs (Cuinat, 1988). River, its main tributary, is the main migration axis, with high-quality habitats for salmon reproduction (Baisez et al.

Output: corroborate


Input: Claim: Every genetic trait can be modified without affecting other genes. [SEP] Text: Inset: distribution of all SNPs tested relative to the location of genes, highlighting the concentration of SNPs in genes (the peak at the center of the plot). 1—figure supplements 1–14 for additional details on workflow, variant calling validation, location of all analyzed SNPs relative to genes, agreement between eQTL and ASE detection, and effects of local structure. Both analyses converged to reveal extensive segregating genetic variation affecting gene expression levels in the Amboseli population. At a 10% false discovery rate, we identified eQTL for 1787 (17. 2%) of the genes we analyzed, and evidence for ASE for 510 (23. 4%) of tested genes. Consistent with reports in humans (e. g. , Veyrieras et al. , 2008; Pickrell et al. , 2010a), eQTL were strongly enriched near gene transcription start sites and in gene bodies (Figure 1; controlling for the background distribution of sites tested, which were also enriched in and around genes). Within gene bodies, eQTL were particularly likely to be detected near transcription end sites; this potentially reflects enrichment in 3′ untranslated regions, which are poorly annotated in baboon. Also as expected, genes with eQTL were more likely to exhibit significant ASE and vice-versa (hypergeometric test: p < 10−25; Figure 1—figure supplement 7). The magnitude and direction of ASE and eQTL were significantly correlated when an ecould also be assessed for ASE (n = 123 genes; r = 0. 719, p < 10−20, Figure 1—figure supplement 7), and when were assessed as eQTL (n = 510 genes; r = 0. 575, p < 10−45, Figure 1—figure supplement 7). Detection of ASE was most strongly favored for highly expressed genes (i. e. , higher RPKM: Wilcoxon test: p < 10−208; Figure 1—figure supplement 8), whereas detection of eQTL was most strongly favored for genes with high local SNP density (p < 10−72; Figure 1—figure supplement 8).

Output: contrast


Input: Claim: The suprachiasmatic nucleus is the master regulator of circadian rhythms. [SEP] Text: Although it is possible that melatonin injections given over >5 d could at some phases cause entrainment, any such effect on established grafts would have to be much smaller than the effects on perinatal grafts. That is, it is likely that the melatonin injections given immediately after transplantation fell at a wide range of phases of the oscillations generated within the grafts; melatonin was given at two times of day, and the phases of oscillations within different grafts were likely to have been initially scattered, because they came from fetuses of SCN-lesioned dams (Davis and Gorski, 1988). Despite this wide range of initial phases, the groups became clustered after only 7 d of injections. Thus in at least some of the grafts large phase shifts must have been produced. In contrast, no phase shifts in response to five melatonin injections were observed when given 6 weeks after transplantation. The apparent loss in sensitivity to melatonin in grafts is consistent with a loss observed in hamster pups; entrainment of hamster pups can be achieved with injections on P1–P5 but not with injections on P6–P10 (Grosse et al. , 1996). It is possible that the normal loss in sensitivity to melatonin is part of a developmental program intrinsic to the SCN; the loss occurred in the grafts despite isolation from the rest of the developing animal. Plausible hypotheses for the loss of sensitivity in intact pups, such as synaptogenesis of retinal afferents or the onset of the pup’s own pineal melatonin rhythm, are less plausible, because neither of these would have occurred for the grafts. On the other hand, other afferents from the host are likely to innervate the grafts and could influence its development in ways similar to what might occur during normal development (Lehman et al. , 1987; Botchkina and Morin, 1993, 1995; Ueda et al. , 1995, 1996). The average phase of entrainment achieved by melatonin injections in this study differed from that seen after injections to neonatal hamsters (Grosse et al. , 1996). In neonates, the average phase of activity onset after weaning was almost coincident with the time at which the melatonin injections were given.

Output: pass


Input: Claim: Hydropower generation can disrupt aquatic ecosystems. [SEP] Text: , 2011). Located 861 km from the estuary, the Poutès dam is a crucial zone for the salmon population, as upstream areas account for about 60% of the potential juvenile production of the (Minster and Bomassi, 1999). Nevertheless, since the stop of restocking in 2008, it is estimated that only a few thousand of smolts are produced each year in upstream habitats (Bach et al. , 2015). This is due to a low transfer rate of adult salmon upstream of Poutès dam so far; this situation should be significantly improved soon with the dam reconfiguration under way. The dam, 18 m high and 85 m wide, bypasses a 10 km river stretch of the and engenders a reservoir of 2. 4 Mm3 that extends over 3. 5 km in normal conditions. The fish assemblage in the impoundment is dominated by roach (Rutilus rutilus). Common species like spirlin (Alburnoides bipunctatus), eurasian minnow (Phoxinus phoxinus), chub (Squalius cephalus), perch (Perca fluviatilis) and pike (Esox Lucius) are also found. The mean annual discharge of the is 16. 6 m3 s−1, and mean water residence time in the impoundment is 1. 67 days. The maximum flow diverted to the powerhouse is 28 m3 s−1. The powerhouse is equipped with three Francis turbines (#1/2: 16 m3 s−1; #3: 3 m3 s−1); Legal minimum flow in the bypass stretch downstream of the dam is 4 or 5 m3 s−1, depending on the season (Tétard et al. , 2019). Three spillways, each 14 m long, discharge floodwater. An intake protected by a rack (24 m wide, 5. 7 m high) is located on the left bank, between 7 and 13 m below the surface (in normal operating conditions), and has a gap-width of 3 cm (Fig. 2). A surface bypass, operating from March to June, is located on the right side of the rack. A gate automatically regulates the water level to ensure a continuous flow of 2 m3 s−1, representing 7. 1% of the maximum turbine flow.

Output: corroborate


Input: Claim: Every genetic trait can be modified without affecting other genes. [SEP] Text: First, we simulated the effect size of the eQTL, with possible effect sizes ranging from 0. 25 to 2. 5, in intervals of 0. 25 (effect sizes are relative to a standard normal distribution). The power to detect an eQTL of a given effect size is contingent on the relative representation of different genotype classes in a population, and hence MAF (larger MAFs produce a more balanced set of alternative genotypes, and thus more power). Second, we simulated the proportion of variance in gene expression levels (PVE) explained by the eQTL, with possible PVE values ranging from 5% to 50%, in intervals of 5%. In this case, power to detect an eQTL does not depend on MAF because simulating the PVE directly integrates across the combined impact of effect size and MAF (a simulated high PVE eQTL with low MAF implies a large effect size variant). Thus, the impact of the MAF spectrum on the power to detect eQTL is reflected in the differences in power between the baboon data set and the YRI data set in the effect size-based vs the PVE-based simulations. In all cases, we calculated power as the proportion of genes with simulated eQTL recovered at a 10% FDR. In PVE-based simulations, power to detect simulated eQTL was greater in the YRI data set (Figure 2A, dashed orange line vs dashed purple line), although this advantage disappeared when the YRI data set was subsampled to the same size as the baboon data set (Figure 2A, dashed gray line). However, the baboon data set provided more power to detect eQTL than the YRI data set (whether subsampled or not) when simulations were based on effect size, where power scales with MAF (Figure 2A, solid lines). Based on these differences, we estimate that the power to identify an eQTL of effect size equal to the mean estimated beta in baboons (0. 96), is increased in the Amboseli baboons by approximately 1. 34-fold (Figure 2A, solid purple line vs solid orange line) as a function of differences in the MAF spectrum alone. Differences in genetic diversity and linkage disequilibrium Because our RNA-seq-based approach does not identify variants outside of transcribed regions, causal SNPs were probably often not typed.

Output: contrast


Input: Claim: The suprachiasmatic nucleus is the master regulator of circadian rhythms. [SEP] Text: The age of the neonates in that study was P1–P5 during the injections, similar to the age of the grafts in the present study (approximately E15–P6). However, in the present study, the average phase (both groups combined) occurred 10 hr before the injection so that the melatonin was closer to being coincident with the end of activity rather than the onset of activity. The reason for this difference is unclear. The dose of melatonin used in the current study was the same per gram of body weight as that used by Grosse et al. (1996), and because melatonin distributes rapidly through tissues, it is unlikely that there would have been a lag of several hours before the melatonin reached the grafts. A better explanation may be that melatonin actually entrains the pacemaker in the same way in both situations, but that the phase relationship between the pacemaker within the SCN and the expressed activity is different. For example, if in one situation activity onset was linked to CT 12 (intact pups) but in the other to CT 0 (graft/host), then the expressed rhythms would have opposite phases. Rhythms restored by transplantation often show bimodal patterns in which it is ambiguous as to which of two opposite phases should be considered activity onset (Lehman et al. , 1987; Davis and Viswanathan, 1996). It is possible that abnormal communication between the grafted SCN and the host brain target tissues could affect the relationship between pacemaker output signals and the response of downstream systems. For example, the output of grafts may depend entirely on humoral signals (Silver et al. , 1996), whereas SCN output in intact hamsters might include specific synaptic connectivity. Interestingly, abnormal communication by grafts would not, in this hypothesis, simply introduce variability in phase or ambiguity between two possible choices but would have to be consistently different in some way so that similar phases among the restored rhythms of a particular treatment group are observed. Because in the present study activity onset of the restored rhythms was closer to coinciding with the time of the vehicle-only injections than with the time of the melatonin injections, it is tempting to suggest that the vehicle, not melatonin, caused the entrainment. This, however, cannot be.

Output: pass


Input: Claim: Hydropower generation can disrupt aquatic ecosystems. [SEP] Text: Turbine modulation was implemented from March 4th, when river flow was 20 m3 s−1, to March 16th, when the local monitoring committee decided to suspend temporary measures until more favorable environmental conditions were met (8 “modulation nights” left). (Fig. 4). 24th, a second flood quickly raised the river flow, which reached 108 m3 s−1 on March 25th, resulting in turbine operation modulation being stopped. After the flood, modulation was reiterated for 8 nights until April 7th: i. e. , 20 nights over the season (Fig. 4). During the first season, 54 smolts were tagged and released between March 9th and April 12th 2017 (Tab. 2). Only 10 wild smolts were caught and tagged on March 9th, 18th and 24th. The rotary screw traps were inoperable after this date because of the high river flow. Accordingly, hatchery smolts from the fish farm were used for tracking, because environmental conditions (flood, temperature between 6. 5° and 9°C) and smolt abundance in the trap on March 24th suggested the beginning of an important migration episode. A total of 44 hatchery smolts were thus tagged and released on April 2nd at low reservoir level (24 individuals) and on April 12th at high reservoir level (20 individuals). No significant differences between wild and hatchery smolts were reported, either in total length (Mann−Whitney, p = 0. 09) or in weight (t-test, p = 0. 2). Overall, the migration pattern differed between periods of low and high reservoir level (Fig. 4). When reservoir level was low, passage dynamics tended to be similar to that observed upstream of the temporary reservoir (station 1), suggesting that smolts rapidly crossed the dam to reach downstream reaches. Cumulative percentage of passages was usually higher than the percentage of detection in station 1, because of individuals undetected during the flood. After raising the reservoir level, cumulative detections in station 1 greatly increased (from 35% to 69% between April 8th and April 18th), but the percentage of passages remained much lower (Fig. 4). This observation suggests that smolts continued to enter the reservoir but did not manage to exit it. Fig.

Output: corroborate


Input: Claim: Every genetic trait can be modified without affecting other genes. [SEP] Text: 34× from the MAF, 1. 21× from SNP density effects, and 1. 43× from LD effects). Further, considering that the effect size estimates in baboons tended to be larger than in the YRI (mean of 0. 96 in baboons vs mean of 0. 80 in YRI), the actual fold increase estimated from simulations is approximately 6-fold (Figure 4—figure supplement 1: ratio of purple vs orange lines at these effect sizes). This estimate is remarkably consistent with empirical results from our comparison of the real baboon and YRI data, in which we identified 6. 16-fold the number of eQTL in the baboons. One possibility is that this difference arises from a history of known admixture in Amboseli between the dominant yellow baboon population and immigrant anubis baboons (Papio anubis: Alberts and Altmann, 2001; Tung et al. , 2008). Thus, it might reflect the difference between an admixed population and an unadmixed population rather than a difference between species. However, this explanation seems unlikely because evidence for ASE does not extend further from tested genes in baboons compared to YRI (Figure 1—figure supplement 10), and because adding controls for local (chromosome-specific) structure when testing for eQTL still results in a large excess of eQTL detected in the baboon data set (∼7× higher than in YRI: ‘Materials and methods’ and Figure 1—figure supplement 11) Mixed evidence for natural selection on gene expression levels Interestingly, we found that genes harboring eQTL in baboons were also more likely to have detectable eQTL in the YRI (hypergeometric test, p = 2. 39 × 10−7). Given the sample size limitations of the data sets we considered, this overlap suggests that large effect eQTL tend to be nonrandomly concentrated in specific gene orthologues. This pattern could arise if the regulation of some genes has been selectively constrained over long periods of evolutionary time, whereas others have been more permissible to genetic perturbation.

Output: contrast


Input: Claim: The suprachiasmatic nucleus is the master regulator of circadian rhythms. [SEP] Text: In the present study, the appropriate direct comparisons to address this question were not available, and the question of whether melatonin has an organizational effect on the developing SCN, in addition to entrainment, will require further studies. FootnotesThis work was supported by of HD18686 to F. C. D. Correspondence should be addressed to Fred C. Davis, Department of Biology, 414 02115. 91. ↵(1993) Development of the hamster serotoninergic system: cell groups and diencephalic projections. J 338:405–431. ↵(1995) Organization of permanent and transient neuropeptide Y-immunoreactive neuron groups and fiber systems in the developing hamster diencephalon. J 357:573–602. ↵(1988) Development of hamster circadian rhythms: role of the maternal suprachiasmatic nucleus. J [A] 162:601–610. ↵Davis FC, (1988) Entrainment of hamster pup circadian rhythms by prenatal melatonin injections to the mother. Physiol 255:R439–R448. OpenUrlPubMed↵Davis FC, (1996) The effect of transplanting one or two suprachiasmatic nuclei on the period of the restored rhythm. J 11:291–301. ↵(1988) Restoration of circadian locomotor activity in arrhythmic hamsters by fetal SCN transplants. 7:49–54. OpenUrl↵Drucker-Colin R, Aguilar-Roblero R, Garcia-Hernandez F, Fernandez-Cancino F, Rattoni FB (1984) Fetal suprachiasmatic nucleus transplants: diurnal rhythm recovery of lesioned rats. 311:353–357. ↵(1993) Developmental appearance and age related changes in specific 2-[125I]iodomelatonin binding sites in the suprachiasmatic nuclei of female Syrian hamsters. Res 73:205–212. OpenUrlPubMed↵(1989) Specificity of circadian function in transplants of the fetal suprachiasmatic nucleus. J Neurosci 9:2671–2677. OpenUrlAbstract/↵(1996) Entrainment of Syrian hamster circadian activity rhythms by neonatal melatonin injections. Physiol 270:R533–R540.

Output: pass


Input: Claim: Hydropower generation can disrupt aquatic ecosystems. [SEP] Text: The results are provided for all tagged fish (global) and depending on the local conditions (reservoir level and river flow) when smolts entered in the Poutès reservoir. Fig. 5Radial plots of passages times (UTC) at Poutès according to reservoir level in 2017 and 2018. Fig. 6Distribution of passage periods according to river flow at low reservoir level. 3. 3 Residence time and behavior in the reservoir 3. 3. 1 Residence time At low reservoir level, median residence time was 50. 8 min in 2017 and 2. 1 h in 2018 at high river flow, and slightly longer at low river flow (3. 6 h in 2017 and 4. 4 h in 2018; Fig. 7). At high reservoir level, the time spent by smolts in the reservoir was substantially longer, at a median 4 days in 2017 at low river flow (no smolts entered the reservoir at high river flow in 2017). In 2018, median residence times at high reservoir level were 19. 1 h and 4. 4 h at high and low river flow, respectively. Linear model on log-transformed data showed that reservoir level (= 64. 99, p < 0. 001) and flow conditions (= 11. 46, p < 0. 01) were the only variables that significantly influenced the residence time (Tab. 4). Fig. 7Residence time according to reservoir level and river flow during smolt entry in 2017 (left) and 2018 (right). LL and HL: low and high level, respectively. LF and HF: low and high flow, respectively. Note that the scale of y-axis differs between the 2 graphs. Table 4Analysis of variance table on log-transformed residence time. 3. 3. 2 Attempts to pass At low reservoir level, 93% and 87% of smolts passed the dam at the first attempt, in 2017 and 2018, respectively (Fig. 8). At high reservoir level, the median number of attempts per smolt was 3. 5 (range, 1−16) in 2017 and 3 (range, 1−6) in 2018. The difference in number of attempts between low and high levels was significant in both years (2017: W = 50. 5, p < 0. 01; 2018: W = 115, p < 0. 001).

Output: corroborate


Input: Claim: Every genetic trait can be modified without affecting other genes. [SEP] Text: Indeed, we found that the mean per-gene phyloP score calculated based on a 46-way primate comparison was significantly reduced (reflecting less conservation) for genes with detectable eQTL in both species, and greatest for genes in which eQTL were not detected in either case (p < 10−53; Figure 3A). We obtained similar results using phyloP scores based on a 100-way vertebrate comparison (p < 10−21; Figure 3—figure supplement 1). Figure 3 with 1 supplement see all Download asset Open asset Mixed evidence for negative selection on variants affecting gene expression level. (A) Genes that harbor detectable eQTL in baboons, the YRI, or both are more likely to be conserved across long stretches of evolutionary time, based on mean phyloP scores in a 46-way primate genome comparison (n = 7268; p < 10−53). (B) These genes are also more likely to be lineage-specific, based on Homologene annotations (n = 7065; p = 1. 78 × 10−8). (C) Although we detect a strong negative correlation between eQTL effect size and eQTL minor allele frequency, in support of pervasive selection against alleles with large effects on gene expression levels, this correlation also appears when simulating constant eQTL effect sizes, suggesting winner's curse effects. 3—figure supplement 1 for phyloP results based on a 100-way vertebrate genome comparison. eQTL were more likely to be identified for genes with higher genetic diversity (Figure 1—figure supplement 8), which may account for the relationship between phyloP score and eQTL across species: highly conserved genes are less likely to contain many variable sites. More conserved genes also tend to have slightly lower average minor allele frequencies (p = 0. 002), which might reduce the power to detect eQTL (although the effect size is small: r2 = 0. 001). However, genes with eQTL in both species were also less likely to have orthologues in deeply diverged species, based on conservation in Homologene (β = −0. 036, p = 1. 78 × 10−8; Figure 3B). Genetic diversity within the baboons is very weakly correlated with Homologene conservation (r2 = 0. 004) and uncorrelated with average minor allele frequency (p = 0.

Output: contrast


Input: Claim: The suprachiasmatic nucleus is the master regulator of circadian rhythms. [SEP] Text: ↵(1995) Role of neuropeptide Y projection on the development of serotonergic innervation in the suprachiasmatic nucleus of the rat, shown by triple intraocular grafts. 673:325–330. ↵Ueda S, Aikawa M, Ishizuya-(1996) Alteration of serotonergic innervation in the suprachiasmatic nucleus of the rat following removal of input fibers from retina and lateral geniculate nucleus. 211:97–100.

Output: pass


Input: Claim: Hydropower generation can disrupt aquatic ecosystems. [SEP] Text: In 2017, UD maps revealed that detection density peaked in the north-west corner of hydrophone array (Fig. 9). Despite the DOP filter, a few positions lay outside reservoir boundary. At low reservoir level, the probability distribution of smolt relocation was quite concentrated, forming a “channel” directed toward the bypass. The maximum probability density was located just upstream of the bypass, at approximately 11 to 29 meters from the bypass entrance. In contrast, relocations were distributed over the whole dam area at high reservoir level. Fig. 8Number of passage attempts per smolt according to reservoir level in 2017 (left) and 2018 (right). Note that the scale of y-axis differs between the 2 graphs. Fig. 9Probability density of smolt relocation (UD) according to reservoir level in 2017. 4 studies reported migration delay due to hydropower reservoirs and/or tested the efficiency of various fish passage solutions (Tomanova et al. , 2018; Schwinn et al. , 2019). To our knowledge, our study is the first to assess the impact of temporary measures aiming both to improve passage efficiency and reduce migration delay, with targeted turbine operations and reservoir level lowering. The study confirmed that lowering the reservoir level and reducing mean water residence time from 1. 67 days to 4 hours was a very effective means of reducing the migration delay caused by the reservoir. In 2017, when river flow was less than twice the mean annual flow, operating at low level reduced median residence time from 4 days to 3. 6 hours. In low-flow conditions, median residence time at high reservoir level as evaluated in 2015 was 9. 3 days (Tétard et al. , 2016a). River flow had an important impact whatever the reservoir level, and explained the great difference in residence time between 2017 (mean river flow = 9. 6 m3 s−1) and 2018 (mean river flow = 49. 4 m3 s−1). The causes of the substantial migration delay at high reservoir level were identified in 2015 as reluctance to enter the bypass and disorientation in the reservoir (Tétard et al. , 2016a). Accordingly, the median number of passage attempts in the dam zone before passing downstream was 12, and 64. 8% of smolts went back to the upstream end of the reservoir at least once after being detected in the dam area (Tétard et al. , 2016a).

Output: corroborate


Input: Claim: Every genetic trait can be modified without affecting other genes. [SEP] Text: 38). Thus, sequence-level conservation scores and depth of homology across species combine to suggest that eQTL—or at least those with relatively large effect sizes—are least likely to be detected for strongly conserved loci, and most likely to be detected for lineage-specific, rapidly evolving genes. Consistent with this idea, genes involved in basic cellular metabolic processes were under-enriched among the set of genes with eQTL in both species, and enriched among the set of genes for which no eQTL were detected in either species (Supplementary file 1B–C). The set of genes with eQTL in either or both species, on the other hand, were enriched for loci involved in antigen processing, catalytic activity, and interaction with the extracellular environment (e. g. , receptors, membrane-associated proteins). Widespread selective constraint on gene expression levels has been suggested in previous eQTL analyses in humans, with evidence supplied by a strong negative correlation between minor allele frequency and eQTL effect size (Battle et al. , 2014). This pattern could arise if selection acts against large genetic perturbations, such that variants of large effect would be present only at low frequencies. Consistent with this idea, plotting eQTL effect size vs MAF in the baboons results in a very strong, highly significant negative correlation (r = −0. 723, p < 10−280; Figure 3C), with no large effect eQTL detected at higher MAFs. However, such a relationship could also be a consequence of the so-called winner's curse (in which sampling variance leads to upwardly biased effect size estimates: Zöllner and Pritchard, 2007) because the degree of bias in effect size estimation is itself negatively correlated with MAF. Indeed, when we simulated sets of eQTL with constant small effect sizes (β = 0. 75, close to the mean effect size detected for SNPs with MAF ≥0. 4), we found that the relationship between estimated effect size and MAF among detected eQTL almost perfectly recapitulated the observed negative correlation. Hence, the correlation between estimated eQTL effect size and MAF in the baboons does not provide strong support for widespread negative selection on gene expression phenotypes within species.

Output: contrast


Input: Claim: The suprachiasmatic nucleus is the master regulator of circadian rhythms. [SEP] Text: Such dense connectivity means that many important features of SCN dynamics can be described by a mean-field model with all-to-all interaction (Dorogovtsev et al. , 2008). The SCN in the left and right hemispheres comprises 2 main groups of clock cells, namely, the core and shell. As we have noted in the Introduction, since clock cells in the SCN demonstrate self-sustained, nearly sinusoidal oscillations, one can model them as weakly nonlinear oscillators with a stable limit cycle (Liu et al. , 1997). The dynamics of this kind of oscillators is described by the Kuramoto model. Let us consider a generalized Kuramoto model where N heterogeneous phase oscillators are divided into M groups (or communities). Each oscillator i is characterized by a phase θi(m) and has its own natural angular frequency ωi(m), where m is the group index. Each group comprises Nm oscillators, coupled with strength Kmm within groups and strength Knm between groups. In a periodic external field with period T and angular frequency ωF=2π/T, the local field phase ωFt+ϕ(m) and strength F(m) can differ between groups. If interaction between the oscillators is absent, then the time evolution of individual Kuramoto oscillators isdθi(m)dt=ωi(m)+F(m)sin(ωFt+ϕ(m)−θi(m)). (1)In a system with interaction, the time evolution of the phase θi(m) of each Kuramoto oscillator isdθi(m)dt=ωi(m)+1Nn∑n∑j∈GnKnmsin(θj(n)−θi(m))+F(m)sin(ωFt+ϕ(m)−θi(m)). (2)The macroscopic state of each group is characterized by the synchronization index ρm and group phase ψm of the complex order parameterzm=ρmeiψm≡1Nm∑j∈Gmeiθj(m).

Output: pass


Input: Claim: Hydropower generation can disrupt aquatic ecosystems. [SEP] Text: In this configuration, focusing only on smolts that pass the dam by whichever route (bypass, spillways or intake), the proportion of smolts using the bypass at high reservoir level was calculated in a radiotracking study in 2004 as close to 90% (Bach et al. , 2004). At low reservoir level, almost all smolts detected at the dam passed it, indicating that a higher proportion was led into the intake and hydropower turbines. This seems obvious, as the intake is 7 m below the surface at normal reservoir level but only 1. 5 m at low level. Nevertheless, modulating turbine operations should have reduced the risk by reducing the attractiveness of the intake. Due to the high hydrological conditions during the two years of the study, spill ratio (Q spill/Q total) during passage at low reservoir level was substantial, at 20–74% in 2017. This shows that spilling water to divert smolts is not enough if the gap-width of the rack is not sufficiently repulsive, especially when the hydropower plant is approaching maximum capacity. Haraldstad et al. (2018) showed that river flow negatively affected fish guidance efficiency in plants with rack gap-width between 50 and 80 mm. High (>90%) fish guidance efficiency was obtained, but only with river flow ≤30% of maximum plant capacity. Moreover, the geometry of the intake and resulting approach flow patterns are undoubtedly of great importance: in the case of Poutès, they may guide smolts toward the intake. Smolts typically follow bulk flow (Coutant and Whitney, 2000) and, even with high spill, it may still guide them toward the intake. This result underlines the importance of (1) stopping fish, (2) guiding them toward bypasses and (3) safely transferring them downstream, and gives credence to design criteria developed for “fish-friendly” intakes (Courret and Larinier, 2008; Calles et al. , 2013; Nyqvist et al. , 2018; Tomanova et al. , 2018). As it was concluded that modulation did not improve passage efficiency (compared to that of 2015) after the 2017 experiment, it was decided, in coordination with local stakeholders, to stop the turbines entirely with the same 20-night quota.

Output: corroborate


Input: Claim: Every genetic trait can be modified without affecting other genes. [SEP] Text: 8%) than the cis component (median PVE = 2. 9%) (Figure 4). Unsurprisingly, we estimated a larger cis-acting component for genes in which functional cis-regulatory variation was detected in our previous analysis (median PVE = 10. 2% among eQTL genes and median PVE = 5. 0% among ASE genes). Figure 4 with 3 supplements see all Download asset Open asset Genetic contributions to variance in gene expression levels in wild baboons. Proportion of variance in gene expression levels estimated for all genes, genes without detectable eQTL, and genes with detectable eQTL. Additive genetic effects on gene expression variation, especially cis-acting effects, are larger for eQTL genes than for other genes. 4—figure supplements 1–3 for related results on percent variance explained by genetic, environmental, and demographic variables and results using an alternative set of SNPs for estimating ptrans. In contrast to the substantial genetic effects we detected, the median PVE explained by age and sex were 1. 89% and 0. 82%, respectively (Figure 4—figure supplements 1–2). The distribution of PVE explained by age was significantly greater than expected by chance (Kolmogorov–Smirnov test on binned PVEs, in comparison to permuted data: p < 10−11), whereas that explained by sex was not (p = 0. 100); large sex effects tended to be constrained to a small set of genes on the X chromosome (Figure 4—figure supplement 1). Of the early environmental variables we investigated, only maternal social connectedness to males explained more variance in gene expression levels than expected by chance (p = 4. 19 × 10−3), with a median PVE of 1. 9%. Notably, while social connectedness to males (i. e. , heterosexual bonds) and social connectedness to females (i. e. , same-sex bonds) are both known predictors of longevity in the Amboseli baboons, previous analyses suggest that their effects are largely independent (Archie et al. , 2014). Our result extends this observation to the early life effects of maternal social connectedness on variance in gene expression levels. Taken together, our data suggest that while almost all genes are influenced by genetic variation, the effects of demographic and environmental parameters are generally modest for any single aspect of the environment.

Output: contrast


Input: Claim: The suprachiasmatic nucleus is the master regulator of circadian rhythms. [SEP] Text: (3)The amplitude (synchronization index) ρm characterizes the extent of phase alignment between oscillators in group m and varies between 0 and 1. When ρm=0, oscillators within group m are in an asynchronous state, while ρm=1 corresponds to a completely synchronized state. The group phase ψm is the average phase or direction of the oscillators. Here, we restrict our attention to a 2-group version of equation (2), with which we will model the core-shell organization and dynamics of the SCN. As shown elsewhere, equation (2) can be reduced to explicit equations for the phase and amplitude of each group (Ott and Antonsen, 2008; Yoon et al. , 2021). Following this approach, the time dependence of the amplitude and phase in the core (υ) and shell (d) becomesdρυdt=−ρυΔυ+12ρυKυυ(1−ρυ2)+12F(1−ρυ2)cosψυ+12ρdKdυ(1−ρυ2)cos(ψd−ψυ),(4)dψυdt=−Ωυ−12F(1+ρυ2)ρυsinψυ+12ρdKdυ(1+ρv2)ρvsin(ψd−ψυ),(5)dρddt=−ρdΔd+12ρdKdd(1−ρd2)+12ρυKυd(1−ρd2)cos(ψυ−ψd),(6)dψddt=−Ωd+12ρυKυd(1+ρd2)ρdsin(ψυ−ψd),(7)in the frame rotating at the external field frequency ωF. The field phase is set to 0 since it provides a reference time for the external cue. Equations (4)-(7) describe the core-shell model schematically depicted in Figure 1, where the parameters characterizing the heterogeneity of dynamical properties among SCN oscillators are reduced to a set of parameters characterizing the mean properties of the core and shell.

Output: pass


Input: Claim: Hydropower generation can disrupt aquatic ecosystems. [SEP] Text: This strategy did not achieve the expected results on tagged smolts either, due to diurnal migration and turbine restarting during floods. To be effective, shutdown periods must take account of smolt presence in the vicinity of the dam, in terms both of daily time slots for shutdowns (if turbines are to be restarted) and of numbers of days of shutdown. At low reservoir level, passage times suggested that a time slot from 6pm to 6am UTC would have protected 84% of smolts with turbine shutdown every night of the migration period, and 91% with a 4pm-8am time slot. This measure would have resulted in 97% global survival (or 98. 5% with a 4pm-8am time slot) for 65% passage success (see results above) and 50% turbine mortality for smolts arriving outside the shutdown time slot (Larinier and Dartiguelongue, 1989). Accordingly, thanks to the predominantly nocturnal behavior of smolts in Poutès, shutdowns targeting twilight and nights should show good efficiency. However, an important consideration to be kept in mind is that the Poutès dam is located 861 km from the sea, and the smolt downstream migration period begins early and is mainly nocturnal (Tétard et al. , 2019). Presence of migrating smolts in the front of an obstacle and the duration of their period of migration depend on local context: e. g. , environmental conditions triggering and driving migration, location of juvenile habitats according to dam location, etc. However, 40% of the smolts of the first release in 2018 (10/25) migrated between 6am and 6pm. During the first flood peak, after river flow reached 30 m3 s−1, 38% of smolts migrated during daytime (8/21), with mean river flow 57 m3 s−1 (for 5 of them, ≥66 m3 s−1). These results indicated that a substantial proportion of smolts can migrate during daytime and twilight during floods, even in locations where smolts are supposedly mainly nocturnal.

Output: corroborate


Input: Claim: Every genetic trait can be modified without affecting other genes. [SEP] Text: However, in at least some cases, we find evidence that early environmental effects on gene expression levels appear to persist across the life course, as has previously been demonstrated in laboratory settings and in response to severe early adversity in humans (e. g. , Weaver et al. , 2004; Miller et al. , 2009; Cole et al. , 2012). of what we know about genetic contributions to variation in gene expression levels in primates (and vertebrates more generally) come from the extensive body of research on humans. However, increasing evidence indicates that humans are demographically unusual: compared to other primates, humans exhibit low levels of neutral genetic diversity and a low long-term effective population size (Chen and Li, 2001; Hernandez et al. , 2007; Perry et al. , 2012). Further, humans are distinguished from other primates by recent explosive population growth (Keinan and Clark, 2012; Tennessen et al. , 2012). While late Pleistocene population expansion has been suggested for some nonhuman primates, including chimpanzees and Chinese-origin rhesus macaques (Hernandez et al. , 2007; Wegmann and Excoffier, 2010), none have undergone the extreme levels of population increase that characterized humans. Indeed, evidence from microsatellite data suggests that the long-term effective population size of baboons actually may have contracted during this period (Storz et al. , 2002). These differences are not simply of historical interest, but also important for understanding the genetic architecture of traits measured in the present day. Differences in demographic history not only affect overall levels of genetic variation and the minor allele frequency spectrum, but also the mean effect size of sites that contribute to phenotypic variation (Lohmueller, 2014). Interestingly, demographic history does not impact overall trait heritability (Lohmueller, 2014; Simons et al. , 2014), perhaps explaining why we estimated mean additive genetic PVEs for gene expression levels in baboons that are similar to those estimated for humans. However, demographic history can influence the power to detect individual genetic contributions to phenotypic variation. Large-scale population expansion of the type that occurred in human history appears to reduce power to identify genotype-phenotype correlations for fitness-related traits (Lohmueller, 2014). This observation may account, in part, for our ability to identify many more functional regulatory variants in the baboons than we expected based on previous studies in humans.

Output: contrast


Input: Claim: The suprachiasmatic nucleus is the master regulator of circadian rhythms. [SEP] Text: These include the characteristic mean ω¯υ (cd) and half width at half maximum ∆υ (∆d) of the natural frequency distribution in the core (shell). At a given field frequency, the mean natural frequency determines the detuning Ωυ=ωF−ω¯υ in the core and Ωd=ωF−ω¯d in the shell. Note that a periodic external field is taken explicitly into account by equations (4)-(7), which allows to study nonlinear impacts of the external field on the SCN. At Kυd=Kdυ=0, these equations are reduced to the explicit equations for the forced Kuramoto model derived in Childs and Strogatz (2008). Figure 1. Schematic representation of the core-shell model consisting of 2 groups of oscillators, the core (ventral part υ) and shell (dorsal part d). and wF are the strength and frequency of an external light cue acting exclusively on the core. The core (shell) is characterized by a mean free-running frequency w¯u(d), the statistical spread of free-running frequencies ∆u(d) (Lorentzian half width at half maximum), and the intracoupling Kuu(dd) between oscillators within the core (shell). Coupling between core and shell oscillators is determined by intercouplings Kud (core on shell) and Kdu (shell on core). In exchange for the simplification of equation (2) into equations (4)-(7), the natural frequencies or free-running periods of SCN oscillators are assumed to follow a Cauchy-Lorentz distribution. Despite the restriction, the Cauchy-Lorentz distribution is unimodal and symmetric, like the Gaussian distribution, which has been used to model the distribution of free-running periods in the core and shell (Taylor et al. , 2017). From the physical point of view, the Kuramoto model demonstrates qualitatively similar behavior for both the Cauchy-Lorentz and Gaussian distributions of natural frequencies. The main difference is in their analytical properties. The Cauchy-Lorentz distribution has residuals in the complex plane.

Output: pass


Input: Claim: Hydropower generation can disrupt aquatic ecosystems. [SEP] Text: Consequently, negotiations to set the appropriate shutdown time slot should: (1) carefully consider the presence periods of smolts, either by analyzing biological data when available or with reference to similar contexts (time slots can focus on twilight and night at the beginning then extend over day later in the migration period) and (2) keep a flexible approach, possibly stopping turbines during the day at the beginning of the migration period when floods occur. The second important item of the negotiation is the shutdown quota to set appropriate measures. When available, phenological models can accurately predict the phenology of smolt migration (Teichert et al. , 2020a) and therefore be used to set shutdown quotas. Otherwise, the smolts' migration phenology in several similar contexts can be examined and the quota set in a conservative manner. Finally, the negotiation process will have to find a compromise according to the global survival target set by environmental authorities. The shutdown quota to reach this target will depend on the passage success rate outside of the shutdown period: the greater the success, the fewer shutdown days are needed. 1999. Movements of two strains of radio tagged Altlantic salmon, Salmo salar L. , smolts through a reservoir. Ecol 6: 97–107. [2020. An innovative bivariate approach to detect joint temporal trends in environmental conditions: Application to large French rivers and diadromous fish. Environ 141260. [PubMed] [2020. Migration of Atlantic salmon (Salmo salar) smolts in a large hydropower reservoir. Sci. [2000. Etude du franchissement (dévalaison − montaison) du complexe hydroélectrique de Poutès − Monistrol par les saumons en 1999. çain sur Sioule. [2004. Suivi de la dévalaison 2004 des saumoneaux au droit du barrage de Poutès. çain sur Sioule. [2015. Suivi de la dévalaison 2014 des saumoneaux au droit du barrage de Poutès. çain sur Sioule. [2011. Migration delays and mortality of adult Atlantic salmon Salmo salar en route to spawning grounds on the River Allier, France. Res 15: 265–270. [2019.

Output: corroborate


Input: Claim: Every genetic trait can be modified without affecting other genes. [SEP] Text: However, while our analysis extends previous observations that large effect eQTL are nonrandomly distributed, we found mixed evidence for widespread negative selection on gene expression levels. Specifically, within the baboons alone, we found that the negative relationship between eQTL effect size and minor allele frequency was explicable based on winner's curse effects alone. Thus, increased power to identify functional regulatory variants in the baboons is probably not due to pervasive associations between gene expression levels and fitness. In contrast, stronger evidence for selection on gene expression patterns stems from our cross species comparisons. In particular, we observed that genes with eQTL in baboons significantly overlapped with genes with eQTL in humans, and that these genes as a class also tended to be less constrained at the sequence-level (consistent with observations for analyses of cis-eQTL in humans alone: Popadin et al. , 2014). This result suggests that genes vary in their tolerance of functional regulatory genetic variation, and, intriguingly, that gene-specific robustness to genetic perturbation may be a conserved property across species. Because no comparable data are yet available for other large mammal populations, including for other baboons, it is unclear whether our results are typical or instead a consequence of the Amboseli population's own unique history. In particular, the population has experienced recent admixture between yellow baboons, the dominant taxon, and closely related anubis baboons (P. anubis) (Alberts and Altmann, 2001; Tung et al. , 2008). Admixture, which appears to be relatively common in natural populations (Mallet, 2005), can have important consequences for genetic diversity and LD patterns. While it appears to have had a modest impact on the relative ability to map gene expression phenotypes in baboons vs the YRI data set, comparison to a non-admixed baboon population could help resolve this question further. More generally, our results encourage further investigation of the relationship between demography and trait genetic architecture in other populations, as has been suggested for humans (Lohmueller, 2014) but could also be profitably extended to nonhuman model systems. Such comparisons would provide an empirical basis for testing predicted relationships between demographic history and the power to identify genotype-phenotype associations.

Output: contrast


Input: Claim: The suprachiasmatic nucleus is the master regulator of circadian rhythms. [SEP] Text: This fact simplifies analytical calculations and allows an explicit reduction of microscopic equation (2) to a set of equations (4)-(7) that describe the evolution of the macroscopic characteristics of the Kuramoto model. Note that stationary values of the synchronization indices ρυ and ρd can be found analytically by solving equations (4)-(7) at zero time derivatives on the left hand side. Unfortunately, the strong non-linearity of these equations makes it difficult to find a simple analytical expression, while numerical solutions can be readily computed. Recently, a model similar to our model in Figure 1 was considered by Hannay et al. (2020). Using the Ott-Antonsen ansatz, Hannay et al. (2020) derived equations similar to equations (4)-(7) to describe the evolution of the core and shell. et al. (2020) focused on seasonal day length, after-effects of light entrainment, and seasonal variations in light sensitivity in the mammalian circadian clock, in this 1. List of parameters (parameters) and a summary of the corresponding values reported by Taylor et al. (2017) (reference), the core-shell model (model) of equations (4)-(7). ParametersReferenceModelτυ25. 1 h25. 1 hτd23. 9 h23. 3 hσυ1. 3 h1. 3 hσd1. 9 h1. 9 hKυυ—5. 6Kdd—4. 0Kυd—1. 1Kdυ—0. 5F—1. 5ω¯υ—19. 3ω¯d—20. 8∆υ—1. 0∆d—1. 7Time-dimensional parameters include συ(d), the standard deviation of free-running periods reported by Taylor et al. (2017); τυ(d), the mean free-running period of the core (shell). Dimensionless parameters are obtained by multiplying time-dimensional parameters and dividing frequency-dimensional parameters by the frequency unit Δυ=πσυ/τυ2.

Output: pass


Input: Claim: Hydropower generation can disrupt aquatic ecosystems. [SEP] Text: Evidence of late migrant smolts of Atlantic salmon (Salmo salar) in the Loire-Allier System, France. Cybium 37: 5–14. [2015. The cold-water climate shield: delineating refugia for preserving salmonid fishes through the 21st century. Biol 21: 2540–2553. [1998. Survival of radiotagged Atlantic salmon (Salmo salar L. ) and trout (Salmo trutta L. ) smolts passing a reservoir during seaward migration. Hydrobiologia 371: 347. [2009. A review of the likely effects of climate change on anadromous Atlantic salmon Salmo salar and brown trout Salmo trutta, with particular reference to water temperature and flow. J 75: 2381–2447. [CrossRef] [PubMed] [2014. Time and size at seaward migration influence the sea survival of Salmo salar. J 84: 1457–1473. [PubMed] [2017. Indirect effect of temperature on fish population abundances through phenological changes. PLoS One 12: e0175735. [1989. La circulation des poissons migrateurs: le transit a travers les turbines des installations hydroélectriques. Pêche Piscic 312–313: 1–94. [2002. Downstream migration: problems and facilities. Pêche Piscic 364 supplément: 181–207. [CrossRef] [2020. Performance of a large partial-depth guide wall to divert downstream migrating Atlantic salmon smolts at Tuilières dam, Dordogne River. 15. [2009. Dramatic declines in diadromous fishes. BioScience 59: 955–965. [2001. Migration of Freshwater Fishes. [2011. Migration delays caused by anthropogenic barriers: modeling dams, temperature, and success of migrating salmon smolts. 21: 3014–3031. [1998. Movement, migration, and smolting of Atlantic salmon (Salmo salar). Sci 55: 77–92. [1999. Temperature-related loss of smolt characteristics in Atlantic salmon (Salmo salar) in the wild. Sci 56: 1649–1667. [1999.

Output: corroborate


Input: Claim: Every genetic trait can be modified without affecting other genes. [SEP] Text: For each gene, we considered all variants within 200 kb of the gene as candidate eQTLs. For each variant, we fitted the following linear mixed model: y=μ+xβ+u+ε, u∼MVN(0, σu2K), ε∼MVN(0, σe2I), and tested the null hypothesis H0: β = 0 vs the alternative H1: β ≠ 0. Here, y is the n by 1 vector of gene expression levels for the n individuals in the sample. Gene expression values were first corrected for hidden factors that could act as sources of global structure (e. g. , batch effects or ancestry- or environment-related trans effects) by regressing out the first 10 principal components of the gene expression data. Consistent with previous results (e. g. , Pickrell et al. , 2010a), this procedure greatly improves our ability to detect eQTL (Figure 1—figure supplement 12). In the model, μ is the intercept; x is the n by 1 vector of genotypes for the variant of interest; and β is the variant's effect size. The n by 1 vector of u is a random effects term to control for individual relatedness and other sources of population structure, where the n by n matrix K = XXT/p provides estimates of pairwise relatedness derived from the complete 63 × 64,432 genotype data set X. Residual errors are represented by ε, an n by 1 vector, and MVN denotes the multivariate normal distribution. We took the variant with the best evidence (i. e. , lowest p-value) for association with gene expression levels for each gene, and then calculated corrected gene-wise q-values (with a 10% false discovery rate threshold) via comparison to the same values obtained from permuted data (similar to Barreiro et al. , 2012; Pickrell et al. , 2010a). Possible confounds associated with eQTL mapping using RNA-seq data Request a detailed protocol We evaluated the potential for eQTL mapping based on RNA-seq data to introduce four possible confounds. First, for genes with large effect cis-eQTLs, reads from heterozygotes at eQTL-linked sites might be biased towards the allele associated with higher gene expression levels.

Output: contrast


Input: Claim: The suprachiasmatic nucleus is the master regulator of circadian rhythms. [SEP] Text: Frequency-dimensionless parameters include Kυυ(dd), the intracoupling in the core (shell); Kυd and Kdυ, the core-shell intercouplings; F, the strength of the light cue acting exclusively on the core. The dimensionless equivalents of the model parameters: ω¯υ(d)=2π/τυ(d), the mean free-running frequency of core (shell) oscillators; and ∆υ(d), the Lorentzian spread (half width at half maximum) of free-running frequencies in the core (shell). The choice of ω¯υ(d) and ∆υ(d) is based on a study of mice exposed to symmetric 12-h LD cycles by Taylor et al. (2017). In the present core-shell model, 12-h LD cycles correspond to sequential half cycles of the field with period T=24h. Based on experimental observations, Taylor et al. (2017) fitted the free-running periods of the core (υ) and shell (d) to Gaussian distributions with mean τυ=25. 1h and τd=23. 9h, respectively, and standard deviation συ=1. 3h and σd=1. 9h. The mean free-running periods can be directly converted to mean free-running frequencies ω¯υ(d)=2π/τυ(d). From the definition of standard deviation, and given τυ(d)≫συ(d), the standard deviation of the free-running frequencies is approximated as SDυ(d)≈2πσυ(d)/τυ(d)2. Although the present core-shell model is based on a Lorentzian distribution of free-running frequencies with half width at half maximum ∆υ(d), Gaussian and Lorentzian distributions both describe a system where most neurons have a free-running period approximately equal to the system average, and the number of neurons with larger or smaller than average free-running frequencies is symmetric and monotonically decreasing.

Output: pass


Input: Claim: Hydropower generation can disrupt aquatic ecosystems. [SEP] Text: Artificial lakes delay the migration of brown trout Salmo trutta smolts: a comparison of migratory behaviour in a stream and through an artificial lake. J 94: 745–751. [PubMed] [2018. The future of fish passage science, engineering, and practice. 19: 340–362. [2015. Catchment-wide survival of wild-and hatchery-reared Atlantic salmon smolts in a changing system. Sci 72: 1352–1365. [2009. Temperature and flow effects on migration timing of Chinook salmon smolts. 138: 1252–1265. [0212. [PubMed] [2015. EDF R&D. [2019. Behaviour of Atlantic salmon smolts approaching a bypass under light and dark conditions: Importance of fish development. 131: 39–52. [2008. Factors affecting the within-river spawning migration of Atlantic salmon, with emphasis on human impacts. 18: 345–371. [2012. A critical life stage of the Atlantic salmon Salmo salar: behaviour and survival during the smolt and initial post‐smolt migration. J 81: 500–542. [CrossRef] [PubMed] [2017. Survival and behaviour of Atlantic salmon smolts passing a run‐of‐river hydropower facility with a movable bulb turbine. Ecol 24: 199–207. [2017. Protecting fish from entering turbines: the efficiency of a low-sloping rack for downstream migration of Atlantic salmon smolts. Blanche 1: 11–13. [2018. Protecting efficiently sea-migrating salmon smolts from entering hydropower plant turbines with inclined or oriented low bar spacing racks. 122: 143–152. [2000. Migratory behavior and forebay delay of radio-tagged juvenile fall Chinook salmon in a lower impoundment. J 20: 41–52. [1999. Migration timing of Atlantic salmon smolts relative to environmental and physiological factors. 128: 289–301. [2012. Thinking like a fish: a key ingredient for development of effective fish passage facilities at river obstructions. Appl 28: 407–417. [1996. Advances in underwater biotelemetry. 2nd 555–590. [2021.

Output: corroborate


Input: Claim: Every genetic trait can be modified without affecting other genes. [SEP] Text: Further, systematic calling of false positive eQTLs due to biased read mapping would predict a bias towards negative effect sizes (i. e. , eQTL effects suggesting that the alternate allele is associated with lower expression levels). Our data are not consistent with such a pattern: 47% of eQTL betas are negative, whereas 53% are positive. Reference allele mapping biases are, however, more likely to affect ASE analysis, producing a pattern of greater expression in the reference allele. Indeed, we do observe a bias towards negative betas in the ASE analysis (67. 2% of n = 510 genes), although the overall magnitude and direction of ASE data agree well with eQTL evidence. Fourth, lower mean coverage in homozygotes of either type relative to heterozygotes could induce false positive eQTLs in which the major allele was associated with lower gene expression levels. To test this possibility, we recoded eQTL effects to reflect the effect of the major allele instead of the effect of the alternate allele (i. e. , a genotype of 0 = homozygous minor and a genotype of 2 = homozygous major). We observed a modest excess of eQTL for which the major allele was associated with lower gene expression levels (56%, binomial test p = 1. 15 × 10−7). This bias did not differ depending on whether the major allele was the reference allele or the alternate allele (Fisher's Exact Test, p = 0. 28), supporting minimal read mapping biases in our data. Instead, it appears to be primarily driven by SNPs with low minor allele frequencies (proportion of negative betas for the lowest quartile of MAFs = 62. 8%, p = 7. 49 × 10−8; highest quartile of MAFs = 48. 6%, p = 0. 602). At these sites, eQTL inference relies primarily on two genotype classes (the major allele homozygotes and heterozygotes) rather than three genotype classes. Because heterozygotes tend to have slightly higher coverage than homozygotes of both classes, spurious relationships between genotype and gene expression levels are much less likely to be observed when both types of homozygotes are well represented (i. e. , MAFs are larger).

Output: contrast


Input: Claim: The suprachiasmatic nucleus is the master regulator of circadian rhythms. [SEP] Text: In both cases, ∆υ(d) and SDυ(d) provide a measure of the statistical spread of free-running frequencies about the mean value, so we simply take ∆υ(d)=SDυ(d). The coupling mechanisms between SCN neurons are an ongoing topic of research (see, for example, Tokuda et al. , 2018; Hastings et al. , 2018; and 0. 9 in the entrained SCN. Considering a slightly smaller value of ρυ=0. 8 in the isolated core, the corresponding shell value is ρd=0. 4. In dimensionless units, equation (8) then yields Kυυ=5. 6 and Kdd=4. 0. The critical value of the core (shell) intracoupling Kcυυ=2∆v (Kcdd=2∆d) at which synchronization emerges follows directly from equation (8) in the limit where ρυ(d)=0. Thus, the chosen intracoupling is considerably closer to the critical value Kcdd=3. 4 in the shell, where (Kdd−Kcdd)/Kcdd=0. 18, than to the critical value Kcυυ=2. 0 in the core, where (Kυυ−Kcυυ)/Kcυυ=1. 8. “Near-critical” coupling in the shell is compatible with the idea that variability between species and/or individuals can result in coupling changes around the critical value and may explain why the isolated shell has been observed to synchronize in rats (Noguchi et al. , 2004) but not in mice (Yamaguchi et al. , 2003). Regarding the intercouplings Kυd and Kdυ, experimental evidence shows that there are far more contacts made by neurons expressing vasoactive intestinal polypeptide (VIP) in the core onto neurons expressing arginine vasopressin (AVP) in the shell than the converse (Varadarajan et al. , 2018). In addition, functional studies of resynchronization dynamics in the SCN have revealed that the core entrains the shell (Taylor et al. , 2017).

Output: pass


Input: Claim: Hydropower generation can disrupt aquatic ecosystems. [SEP] Text: Temporary turbine and reservoir level management to improve downstream migration of juvenile salmon through a hydropower complex. Knowl. Manag. Aquat. Ecosyst. , 422, 4. Table 1Turbine management rules during temporary measures period for the 2017 season. In the text Table 2Characteristic of tagged smolts in 2017 and 2018. The number, origin, length, and weight of fish are provided, as well as the reservoir level at the time of release. In the text Table 3Number of smolts and transfer rates between stations in 2017 and 2018. The results are provided for all tagged fish (global) and depending on the local conditions (reservoir level and river flow) when smolts entered in the Poutès reservoir. In the text Table 4Analysis of variance table on log-transformed residence time. In the text Fig. 1Geographical location of the study area (a, b) and description of the areas close to the Poutès dam (c). The crosses indicate hydrophone positions in the dam zone for the season 2017. In the text Fig. 2Aerial view of the Poutès dam (a), side view of the bypass entrance (b) and front view of the intake and bypass entrance (c). In the text Fig. 3Picture of upstream limit of the temporary Poutès reservoir (a). Top view of temporary bypass (b). Upstream view of intake, usual (non-functional) and temporary bypass entrances (c). In the text Fig. 4Changes in hourly river flow (blue), reservoir level (black) and captures at the Alleyras trap (x10, orange) during the study period in 2017 (a) and 2018 (b). The periods of turbine operation modulation are indicated (red rectangle). Cumulative percentages of smolts detected in Station 1 (thick dashed line) and passing the Poutès dam (dotted) are also indicated In the text Fig. 5Radial plots of passages times (UTC) at Poutès according to reservoir level in 2017 and 2018. In the text Fig. 6Distribution of passage periods according to river flow at low reservoir level. In the text Fig. 7Residence time according to reservoir level and river flow during smolt entry in 2017 (left) and 2018 (right). LL and HL: low and high level, respectively.

Output: corroborate


Input: Claim: Every genetic trait can be modified without affecting other genes. [SEP] Text: 266, p < 10−100); however, when sites were partitioned by total read depth (in deciles), sites with significant ASE were not more likely to harbor more heterozygotes in any decile (Wilcoxon test comparing number of heterozygotes in significant sites vs background; Figure 1—figure supplement 14). After these filtering steps, we retained 8154 SNPs associated with 2280 genes for ASE analysis. For ASE analysis, we did not take into account possible recombination between exonic SNPs and the (unknown) cis-regulatory variants whose effects they capture, as we did not have detailed data on recombination rates across the baboon genome. However, recombination between exonic SNPs and the true causal regulatory SNPs would decrease our power to detect ASE. For each variant, we considered a beta-binomial distribution (following Pickrell et al. , 2010a) to model the number of reads from the (+) haplotype (denoted as xi+) or the number of reads from the (−) haplotype (denoted as xi−), conditional on the number of total reads (denoted as yi = xi+ + xi−), for each individual i, or xi+|yi∼binomial(yi,θ), θ∼beta(α,β). We tested the null hypothesis H0: α = β vs the alternative H1: α ≠ β using a likelihood ratio test. For both the null model and the alternative model, beta distribution parameters (α and β) were estimated via a maximum likelihood approach, using the R function optim. Again, we took the variant with the lowest p-value for each gene, and then calculated corrected gene-wise q-values (using a 10% false discovery rate threshold) via comparison to the same values obtained from an empirical null distribution. To construct the empirical null distribution, we performed the same analysis after substituting the xi+ value for each variant of interest, for each heterozygous individual, with a randomly selected xi+ value from a heterozygous site elsewhere in the genome (contingent on that site having the same number of total reads, yi). Power simulations Request a detailed protocol To assess the relative power of eQTL mapping in baboons vs the YRI data set, we randomly selected 10% of the genes in each data set to harbor eQTL.

Output: contrast


Input: Claim: The suprachiasmatic nucleus is the master regulator of circadian rhythms. [SEP] Text: Viewed together, such findings support the hypothesis that signaling from the core to the shell is stronger than the reverse (Kυd>Kdυ). However, different contributions to coupling by different neurotransmitters and neuropeptides may affect the sign of the coupling, which impacts entrainment boundaries, the emergence of unstable states, and splitting of activity rhythms into 2 synchronized bouts cycling in antiphase (Daan and Berde, 1978; Oda and Friesen, 2002; Evans et al. , 2005; Evans and Gorman, 2016). For instance, the neurotransmitter gamma-aminobutyric acid (GABA) has been found to both inhibit and promote synchrony in the SCN network depending on the state of the SCN (Evans et al. , 2013). In an antiphase configuration (ψd=π+ψυ) following prolonged light exposure, GABA works with the neuropeptide VIP to promote synchrony. In the steady-state induced by symmetric LD conditions, GABA counters the synchronizing effect of the neuropeptide VIP. Since experimental observations demonstrate that the core entrains the shell under symmetric LD conditions (Taylor et al. , 2017), the inhibiting contribution of GABA signaling is assumed smaller than the synchronizing effect of VIP (Kυd>0). Reasonable bounds on the intercouplings can also be established through analysis of equations (4)-(7) under symmetric LD conditions, as discussed in the next section, and constant darkness, as discussed in the section on DD conditions. In particular, equation (11) shows that Kυd>ω¯d−ωF=0. 15, and equation (24) shows that Kυd+Kdυ>ω¯d−ω¯υ=0. 97. Starting from these bounds and intracouplings Kυυ=5. 6 and Kdd=4. 0 (chosen in the previous paragraph), parameters Kυd, Kdυ, F, and τd were adjusted to ensure agreement with experimental observations of the difference in peak activity time between the core and the shell tυ(p)−td(p).

Output: pass


Input: Claim: Geothermal energy is reliable and operates independently of weather conditions. [SEP] Text: Drilling of supercritical systems in IcelandA 2265-m-deep well (NJ-11) drilled at the Nesjavellir geothermal field on the NE flank of the Hengill volcano in 1988 unexpectedly encountered temperatures >380 °C with very high fluid pressures and inflow rates (Fournier 1991; Steingrimsson et al. 1990). Because of the threat of a blowout at greater than hydrostatic pressures, the lower portion of the well was filled with a gravel plug. However, this well led to the concept of deliberately seeking out supercritical temperatures as part of the initiative in Iceland in 2000, which later transformed into the Drilling project (IDDP) (Friðleifsson and Elders 2005; Friðleifsson et al. 2007). The primary objective of the Drilling project was to conduct deep drilling at selected sites with very high thermal gradients, to attempt to validate the concept that supercritical fluids with temperatures ranging from 450 to 600 °C could be encountered and produced from depths of 3. 5 to 5 km and be used for commercial power generation (Elders and Friðleifsson 2010; Friðleifsson and Elders 2005; Friðleifsson et al. 2007, 2014). Observed seismic activity indicates that brittle failure occurs at these depths in this region, suggesting that there are permeable zones even at these elevated temperatures. An initial attempt was made to deepen an exploratory well on the Reykjanes peninsula (RN-17). However, the 3. 1-km-deep well suffered a wellbore collapse during flow testing, and could not be deepened. The effort shifted then to the Krafla geothermal field, where the IDDP-1 well was spudded in 2008. The plan was to drill this well to a depth of 4. 5 km; however, rhyolitic magma was encountered at a depth of 2104 m, and the well was completed just above this point at 2072 m (Elders and Friðleifsson 2010; Elders et al. 2014a, c). Subsequent flow testing produced superheated steam at flow rates of 10–12 kg/s with wellhead temperatures reaching up to 450 °C, fluid enthalpies of 3200 kJ/kg, and wellhead pressures of up to 140 bar (Friðleifsson et al. 2014).

Output: corroborate


Input: Claim: Every genetic trait can be modified without affecting other genes. [SEP] Text: For each of these simulated eQTL genes, we then randomly chose a SNP among all the cis-SNPs tested (i. e. , all variable sites that passed quality control filters and fell within 200 kb of a gene of interest) and assigned it as a causal eQTL. The impact of the eQTL was simulated using either effect size, in which we simulated a constant effect size between 0. 25 and 2. 5 (in intervals of 0. 25) or PVE, in which we chose an effect size that explained a specific proportion of variance in gene expression levels (from 5% to 50%, in intervals of 5%). We then simulated gene expression levels by adding the effect of the simulated cis-eto residual errors drawn from a standard normal distribution. To calculate the FDR, we also simulated a set of genes with no eQTL. For each combination of effect sizes and population (baboon or YRI), and for each simulation scenario (e. g. , with the causal SNP masked or unmasked, with SNP density thinned in the baboons, or using PVE vs a constant effect size), we performed 10 replicates. For each replicate, we calculated the power to detect eQTL as the proportion of simulated eQTL genes recovered at a 10% empirical FDR. Testing the contribution of admixture to eQTL detection Request a detailed protocol To investigate whether admixture might drive our power to detect eQTL in the baboon data set, we performed three analyses. First, we asked whether evidence for ASE remained similar across longer distances (i. e. , between sites separated by more base pairs) in the baboons vs in the YRI. Such a pattern might be expected if long-distance, admixture-driven LD explained our other observations. However, the pattern of ASE similarity (the magnitude of the difference between ASE estimates) by distance between sites was highly congruent between the YRI and baboon data sets (Figure 1—figure supplement 10). Second, we investigated whether adding a control for local structure (i. e. , population structure in cis to a gene of interest, and based only on variants located on the same chromosome) asymmetrically reduced evidence for eQTL in the baboon data set relative to the YRI data set.

Output: contrast


Input: Claim: The suprachiasmatic nucleus is the master regulator of circadian rhythms. [SEP] Text: In this case, the phase difference Δψ=ψd−ψυ is positive since Kυd is also positive (Kυd=1. 1). The extent to which ψd leads ψυ is determined by the period of LD cycles T=π/ωF. As hinted by equation (9), the phase difference −π/2≤Δψ≤π/2 tends to decrease as T decreases below 24 h, toward the shell’s free-running period τd=23. 3h, and tends to increase as T increases above 24h. In general, the entrained phase difference is also dependent on how the synchronization indices ρυ and ρd vary with T. In the laboratory (non-rotating) frame, the real part of core (shell) order parameter zυ(d) in equation (3) oscillates with frequency ωF=2π/T. Symbolically, Re(zυ(d))=ρυ(d)cos(ωFt+ψυ(d)). This time-dependent observable acts as a proxy for SCN activity, encoding synchronization index and phase at a given cue frequency or period. Note that the peak in core activity is locked to the peak in the external cue because the photic cue in our core-shell model acts exclusively on the core. The observable Re(zυ(d)) is maximum in the core (shell) at time tυ(d)(p)=2πn/ωF−ψυ(d)/ωF, where n is an integer number. From here, it follows that the difference in peak activity time between the shell and the core istυ(p)−td(p)=T(ψd−ψυ)2π. (12)Thus, the peak time difference tυ(p)−td(p) is determined by the phase difference ψd−ψυ.

Output: pass


Input: Claim: Geothermal energy is reliable and operates independently of weather conditions. [SEP] Text: Its neighbor, Argentina, installed a binary ORC power plant of 0. 67 MW in capacity in 1988, in Copahue, Neuquén Province, near the border with Chile, which was stopped in 1996 (Gutiérrez-Negrín, 2022). Power plants in operation in Chile are in the geothermal field of Cerro Pabellón, located in the at 4500 m above sea level (masl), near the border with Bolivia. It is operated by Geotérmica del Norte, a joint venture between Power (85%) and the Chilean national oil company ENAP (15%) (Morata et al. 2023). There are currently three power units of binary ORC type and manufactured by Ormat, two of them of 24 MW in capacity, and the more recent of 33 MW, for a total of 81 MW. The first units started to operate in 2017 (see Fig. 5), and the latter was commissioned in 2021; thus, as shown in Table 2, Chile presents a net increment of 33 MW in the last 3 years, equivalent to 69%, in the geothermal installed capacity. Geothermal generation increased approximately 200 GWh, or 50%. Fig. 5(Credit: ThinkGeoEnergy, 2018; of the first power plant of Cerro Pabellón, ChileFull size imageCerro Pabellón is a field of hydrothermal, liquid dominant and high enthalpy type, and there were ~ 11 production wells operating in 2022, the deepest of which is 2500 m, according to the IGA reporting-tables filled by Morata et al. (2023). Considering the gross generation of 600 GWh (Table 2), the average production was 6. 3 MWh per production well. Another important parameter is the annual capacity factor, which results in 84. 6%. The main geothermal power parameters in Chile for 2021–2022 are as follows:- Geothermal fields in operation:1- Production wells:13- Capacity (MW)81- Generation (GWh)600- Capacity factor (%)84. 6- Average production per well (MWh):6. 3The geothermal–electric potential in the country is the largest in the region, due to its geologic context characterized by the continuous subduction of the Nazca and Antarctic plates beneath the plate (see Fig. 4), with active volcanism and seismicity along the subduction zone.

Output: corroborate


Input: Claim: Every genetic trait can be modified without affecting other genes. [SEP] Text: To investigate whether the correlation between minor allele frequency and eQTL effect size could be a result of winner's curse effects, we extracted the results from our simulations in which the causal variant was masked and the true effect size was fixed at a small value (beta = 0. 75). We then calculated the correlation between the estimated effect size (β) from these simulations against minor allele frequency, for detected eQTL only. Estimation of genetic contributions to gene expression Request a detailed protocol We used the Bayesian sparse linear mixed model (BSLMM) approach implemented in the GEMMA software package (Zhou and Stephens, 2012) to estimate the genetic contribution to gene expression variation. Specifically, for each gene, we fit the following model: y=μ+xcisβcis+xtransβtrans+ε, βcis,i∼πN(0, σa2)+(1−π)δ0, βtrans,i∼N(0, σb2), where y is the n by 1 vector of gene expression levels for n individuals; μ is the intercept; xcis is an n by pcis matrix of genotypes for pcis cis-SNPs and βcis are the corresponding effect sizes; xtrans is an n by ptrans matrix of genotypes for ptrans trans-SNPs and βtrans are the corresponding effect sizes; and ε is an n by 1 vector of i. i. d. residual errors. We used different priors for cis-acting effects and trans-acting effects to capture different properties for the two components. Specifically, the spike-slab prior on the cis effects βcis captures our prior belief that only a small proportion of local SNPs has cis effects and these effects are relatively large. The normal prior on the trans effects captures our prior knowledge that trans-acting SNPs tend to be relatively difficult to find and have relatively small effects. In addition, because pcis is small and ptrans approximately equals p, the number of total SNPs, we used p instead of ptrans to facilitate computation (i. e. , ptrans was based on all genotyped sites used in our analyses, n = 64,432). Results are qualitatively similar if ptrans is calculated based on sites that must act in trans (i. e.

Output: contrast


Input: Claim: The suprachiasmatic nucleus is the master regulator of circadian rhythms. [SEP] Text: Using equation (10), we find how far ahead in time is the shell activity with respect to the core activity in the dependence on the frequency of the endogenous cycles in the shell, ωd, and the coupling Kυd:td(p)=tυ(p)−T2πarcsin(ω¯d−ωFKυd). (13)As discussed in the preceding paragraph, ψd leads ψυ for positive Kυd, since τd<T and therefore ω¯d−ωF>0. From equation (12), it then follows that with increasing time, the core must peak after the shell, that is, tυ(p)>td(p) (see Figure 2b). At that time, the peak of the core activity is locked to the peak of the external cue. This result agrees with the experimental observation that peak Per2 expression in the shell precedes peak Per2 expression in the core by 2. 4±0. 9h (Taylor et al. , 2017). Figure 2. Results of numerical simulations of equations (4)-(7) with the parameters in Table 1. (a) Times tυ(p) (red circles) and td(p) (navy squares) at which the real part of complex order parameters zυ and zd peak in the core and shell, respectively, and the core-shell difference between peak times tυ(p)−td(p) (green diamonds) in the entrained state, as a function of the external light-dark period T. (b) Time dependence of the real part of the order parameter in the core (Re(zυ), red line) and shell (Re(zd), navy line) for light-dark cycles with period T=24h. The peak time in the shell precedes the peak time in the core by 2. 3h. Viewed together, the results presented in this section show that the core-shell organization of the SCN enables the shell to anticipate events by advancing its phase relative to the phase of the core and the external cue while entrained to a symmetric LD cycle of period T. This lead is determined by the core-shell phase difference.

Output: pass


Input: Claim: Geothermal energy is reliable and operates independently of weather conditions. [SEP] Text: At ≥ 2000 m depth, temperatures can exceed 100–120 °C, and provide favorable conditions for developing medium-enthalpy geothermal systems and CHP plants. In addition, EGS projects could be developed in deeply buried granitoid rocks with high in situ temperatures (≥ 200 °C), extensional regimes, and low levels of natural seismicity. A call to support drilling of geothermal wells for heating reducing geological risks of the first reinjection wells (at 1000–2500 m depth) was launched in 2023. The total budget is approximately US$18 million (Toth and Nádor 2023). No new geothermal power projects are planned, but some 20 MW are expected by 2028. However, “for the Hungarian geothermal industry to progress, it needs a well-considered energy policy together with a framework of supportive legal and financial conditions” (Toth and Nádor 2023). IcelandIceland is a geothermal country per excellence giving that 65% of its primary energy supply and 30% of its electric demand (Fig. 2) are provided by geothermal energy (Rágnarsson et al. 2023). Just one small binary ORC plant of 0. 3 MW has been commissioned in the country since WGC2020+1, and so the installed capacity is 755. 3 MW, although the oldest power plant in Iceland, originally commissioned in 1969 in Bjarnarflag, was replaced by a new backpressure unit in 2019. The electricity generation in 2022 was lower, with a total of 5788. 4 (Ragnarsson et al. 2023) (Table 2). This island state has a huge geothermal potential, due to its location on a hot spot on the Mid-Atlantic Ridge, the boundary between the and Eurasian plates (see Fig. 4), which are moving apart at a rate of ~ 2 cm/year and that is why the geological and tectonic processes in the country are quicker than in other parts, and more easily observed. Between 20 and 30 volcanic eruptions occur every century on average, and approximately 4. 5 km3 of magma equivalent is erupted every century on average. The Mid-outcrops along 400 km on the island, making it possible to observe on land a variety of tectonic and volcanic processes that only occur at the bottom of the sea in the rest of the oceanic ridge (Ragnarsson et al. 2023).

Output: corroborate


Input: Claim: Every genetic trait can be modified without affecting other genes. [SEP] Text: For each gene, we fit the following model: y=μ+xβ+u+ε, u∼MVN(0, σu2K), ε∼MVN(0, σe2I), where x is the n by 1 vector of values for the demographic or environmental predictor of interest and β is its coefficient. The n by 1 vector of u is a random effects term with K = XXT/p controlling for additive genetic effects. We calculated the PVE estimate as var(xβ)/var(y), where var denotes the sample variance. Add a comment + Open annotations. The current annotation count on this page is being calculated. Data availability The following data sets were generated (2015) Architecture of Levels in 63788. Publically available at the ( The following previously published data sets were used (2010) Understanding mechanisms underlying human gene expression variation with RNA sequencing ID GSE19480. Publically available at the ( 1073. 1465. 154. 501. 840. 1261. 79. 109. 1249. 1209. 24. 189. 0271. 1028. 348. 223. 3035. 305. 2040. 456. 0583. 2158. 548. 498. 142. 428. 343. 227. 461. 245. 680. 537. 1634. 150. 1144. 243. 790. 1320. 185. 1328. 725. 743. 132. 116. 1786. 511. 1760. 4379. 237. 1303. 373. 4721. 1105. 0888. 610. 772. 1236. 651. 121. 674. 1317. 144. 0345. 1234. 3104. 1361. 224. 536. 1990. 69. 40. 2011. 391. 0214. 854. 1435. 216. 437. 3264. 824. 615. 2. 0). experimentation: Samples and data used in this study were collected from wild baboons living in the Amboseli ecosystem of southern Kenya. All behavioral, environmental, and demographic data are gathered as part of noninvasive observational monitoring of known individuals within the study population.

Output: pass


Input: Claim: The suprachiasmatic nucleus is the master regulator of circadian rhythms. [SEP] Text: This section studies dissociation from the point of view of an observer in the laboratory frame. To this end, it is assumed that the observer measures the observable Re(zυ(d))=ρυ(d)cos(ωFt+ψυ(d)) or the corresponding distribution of frequency components Sυ(d)(ω) (spectral density), as a proxy for SCN activity under varying LD period T. Here, the core (shell) synchronization index ρυ(d) and phase ψυ(d) are determined by numerical solution of equations (4)-(7), using the parameters in Table 1. The main results concerning independent components of the spectral density Sυ(d)(ω) are presented in Figure 3. Figure 3. Results of numerical simulations of equations (4)-(7) with the parameters in Table 1. (a) of independent SCN activity components under external light-dark cycles of varying period T (in hours). The component at the field period T is indicated in red open circles within the entrainment range and in gray circles outside the entrainment range. Red stars indicate the period of SCN activity at a second (dissociated) rhythm Tsr. Black crosses are experimental data reported by Campuzano et al. (1998). The dashed horizontal line is the period of SCN oscillations τDD=24. 84h under dark-dark conditions (cue strength F=0), calculated from the mean value of equations (5) and (7) in the synchronized state. (b) Intensity of light-dark (F, hollow markers) and second rhythm (sr, solid makers) components of SCN activity, in the core (υ, circles) and shell (d, squares). Vertical lines indicate the lower and upper bounds of the entrainment range, LLE=23. 26h and ULE=25. 28h, respectively. For comparison, the mean free-running periods of the shell and the core are τd=23. 3h and τυ=25. 1h, respectively. (c) Dependence of the entrainment range (gray horizontal bars) on the difference between the free-running periods of core and shell, τυ−τd. Here, τυ is fixed as τυ=25.

Output: pass


Input: Claim: Geothermal energy is reliable and operates independently of weather conditions. [SEP] Text: There are numerous active volcanoes and hot springs in the country, as well as frequent earthquakes. The main volcanic zone, composed of more than 200 volcanoes, crosses the island from NE to SW; at least 30 of those volcanoes have erupted since the country was settled approximately 1150 years ago. As expected, there are numerous geothermal systems related to the volcanoes, whose fluids vary in composition from freshwater to saline and from warm to supercritical in temperature. At least 25 high-temperature areas have been identified within the volcanic zones with ≥ 200 °C at ≤ 1000 m depths, and some high-temperature fields are known (and more are expected) in ocean ridges southwest and north of Iceland. Moreover, there are ~ 250 separate low-temperature areas (≤ 150 °C at ≤ 1000 m depth) in the country, mostly located in the flanks of active volcanic zones, and over 600 hot spring areas with temperatures ≥ 20 °C have been located (Ragnarsson et al. 2023). Considering the mentioned tectonic and geological characteristics of Iceland, it is no surprise that the country started to use its vast geothermal resources for power generation in the late sixties, when the first power plant was commissioned at Bjarnarflag in 1969, as mentioned above. It was a single-flash, backpressure unit of 3. 2 MW in capacity, followed in 1978 by the smaller Unit 1 of 1 MW in Svarstengi and by the larger Unit 1 in Krafla with 30 MW, both still in operation. Currently, there are 35 individual geothermal power units in Iceland, distributed into eight geothermal fields, and fed by approximately 200 production wells that produce 5332 m3/hour of steam. Most of the power plants are of the single or double-flash type, with inlet temperatures varying from 122 to 210 °C and admission pressures from 1. 25 to 18 barg. The binary ORC plants are located at Svarstengi, Flúdir, and Reykholt, and work at lower temperatures and pressures, and there is one plant using dry steam in the Svarstengi field. There are also two backpressure units. The main features of the power units are presented in Table 9.

Output: corroborate