Clock Variation Research Articles

Searching for large dark matter clumps using the Galileo Constellation clock variations

This study presents bounds on transient variations of fundamental constants, with typical timescales ranging from minutes to months, using clocks in space. The underlying phenomenology describing such transient variations relies on models for Dark Matter (DM) which suggest possible encounters of macroscopic compact objects with the Earth, due to the motion of the solar system in the galactic halo. If such compact objects possess an effective feeble interaction with the ordinary matter beyond the gravitational one, it may result in effective transient variations of fundamental constants. Such variations leave signatures on clocks onboard GNSS satellites. In this paper, we introduce a phenomenological study dedicated to the search for such DM transient objects using the network of passive hydrogen masers (H-Masers) onboard Galileo satellites. We first model the signature of transient variations of fundamental constants as a frequency modulation in the difference between two satellite clocks, considering the satellite trajectories relative to the transient event. Then, we present first results based on a fast analysis method, the maximum reach analysis. The main result is a significant extension of the discovery range for DM transients, with a sensitivity never achieved before. We investigate indeed the range of transient sizes from 105 to 109 kilometres, which, apart from indirect and model-dependent non-transient effects, has never been explored previously.

Exercise training modifies skeletal muscle clock gene expression but not 24-hour rhythmicity in substrate metabolism of men with insulin resistance.

Twenty-four hour rhythmicity in whole-body substrate metabolism, skeletal muscle clock gene expression and mitochondrial respiration is compromised upon insulin resistance. With exercise training known to ameliorate insulin resistance, our objective was to test if exercise training can reinforce diurnal variation in whole-body and skeletal muscle metabolism in men with insulin resistance. In a single-arm longitudinal design, 10 overweight and obese men with insulin resistance performed 12weeks of high-intensity interval training recurrently in the afternoon (between 14.00 and 18.00h) and were tested pre- and post-exercise training, while staying in a metabolic research unit for 2days under free-living conditions with regular meals. On the seconddays, indirect calorimetry was performed at 08.00, 13.00, 18.00, 23.00 and 04.00h, muscle biopsies were taken from the vastus lateralis at 08.30, 13.30 and 23.30h, and blood was drawn at least bi-hourly over 24h. Participants did not lose body weight over 12weeks, but improved body composition and exercise capacity. Exercise training resulted in reduced 24-h plasma glucose levels, but did not modify free fatty acid and triacylglycerol levels. Diurnal variation of muscle clock gene expression was modified by exercise training with period genes showing an interaction (time × exercise) effect and reduced mRNA levels at 13.00h. Exercise training increased mitochondrial respiration without inducing diurnal variation. Twenty-four-hour substrate metabolism and energy expenditure remained unchanged. Future studies should investigate alternative exercise strategies or types of interventions (e.g. diet or drugs aiming at improving insulin sensitivity) for their capacity to reinforce diurnal variation in substrate metabolism and mitochondrial respiration. KEY POINTS: Insulin resistance is associated with blunted 24-h flexibility in whole-body substrate metabolism and skeletal muscle mitochondrial respiration, and disruptions in the skeletal muscle molecular circadian clock. We hypothesized that exercise training modifies 24-h rhythmicity in whole-body substrate metabolism and diurnal variation in skeletal muscle molecular clock and mitochondrial respiration in men with insulin resistance. We found that metabolic inflexibility over 24h persisted after exercise training, whereas mitochondrial respiration increased independent of time of day. Gene expression of Per1-3 and Rorα in skeletal muscle changed particularly close to the time of day at which exercise training was performed. These results provide the rationale to further investigate the differential metabolic impact of differently timed exercise to treat metabolic defects of insulin resistance that manifest at a particular time of day.

High-precision velocity determination using mass-market Android GNSS measurements in the case of anomalous clock variations

High-precision velocity determination using mass-market Android GNSS measurements in the case of anomalous clock variations

Mitigation of lamp oven and cavity oven temperature-induced frequency variation in rubidium atomic clock.

The long-term frequency stability of the rubidium atomic clock is primarily affected by temperature variations in the lamp oven and the cavity oven, which cause changes in light intensity, which are then converted into frequency variations. Therefore, we propose using light intensity variations to actively improve the cavity oven and lamp oven temperature sensitivity of the rubidium atomic clock. This is accomplished through research into the theory of the rubidium atomic frequency standard, specifically the effect of light intensity, lamp oven temperature, and cavity oven temperature on the frequency deviation. In previous work, we discovered the relationship between the light intensity and frequency deviation by combining this with our engineering expertise. Furthermore, some related experiments show that the method is feasible with the lamp oven and cavity oven temperature sensitivity of the rubidium atomic clock greatly improved, providing an effective way to improve the rubidium atomic clock's long-term frequency stability.

Heritability of the glycan clock of biological age.

Immunoglobulin G is posttranslationally modified by the addition of complex N-glycans affecting its function and mediating inflammation at multiple levels. IgG glycome composition changes with age and health in a predictive pattern, presumably due to inflammaging. As a result, a novel biological aging biomarker, glycan clock of age, was developed. Glycan clock of age is the first of biological aging clocks for which multiple studies showed a possibility of clock reversal even with simple lifestyle interventions. However, none of the previous studies determined to which extent the glycan clock can be turned, and how much is fixed by genetic predisposition. To determine the contribution of genetic and environmental factors to phenotypic variation of the glycan clock, we performed heritability analysis on two TwinsUK female cohorts. IgG glycans from monozygotic and dizygotic twin pairs were analyzed by UHPLC and glycan age was calculated using the glycan clock. In order to determine additive genetic, shared, and unique environmental contributions, a classical twin design was applied. Heritability of the glycan clock was calculated for participants of one cross-sectional and one longitudinal cohort with three time points to assess the reliability of measurements. Heritability estimate for the glycan clock was 39% on average, suggesting a moderate contribution of additive genetic factors (A) to glycan clock variation. Remarkably, heritability estimates remained approximately the same in all time points of the longitudinal study, even though IgG glycome composition changed substantially. Most environmental contributions came from shared environmental factors (C), with unique environmental factors (E) having a minor role. Interestingly, heritability estimates nearly doubled, to an average of 71%, when we included age as a covariant. This intervention also inflated the estimates of unique environmental factors contributing to glycan clock variation. A complex interplay between genetic and environmental factors defines alternative IgG glycosylation during aging and, consequently, dictates the glycan clock's ticking. Apparently, environmental factors (including lifestyle choices) have a strong impact on the biological age measured with the glycan clock, which additionally clarifies why this aging clock is one of the most potent biomarkers of biological aging.

Bright Light Decreases Peripheral Skin Temperature in Healthy Men: A Forced Desynchrony Study Under Dim and Bright Light (II).

Human thermoregulation is strictly regulated by the preoptic area of the hypothalamus, which is directly influenced by the suprachiasmatic nucleus (SCN). The main input pathway of the SCN is light. Here, thermoregulatory effects of light were assessed in humans in a forced desynchrony (FD) design. The FD experiment was performed in dim light (DL, 6 lux) and bright white light (BL, 1300 lux) in 8 men in a semi-randomized within-subject design. A 4 × 18 h FD protocol (5 h sleep, 13 h wake) was applied, with continuous core body temperature (CBT) and skin temperature measurements at the forehead, clavicles, navel, palms, foot soles and toes. Skin temperature parameters indicated sleep-wake modulations as well as internal clock variations. All distal skin temperature parameters increased during sleep, when CBT decreased. Light significantly affected temperature levels during the wake phase, with decreased temperature measured at the forehead and toes and increased navel and clavicular skin temperatures. These effects persisted when the lights were turned off for sleep. Circadian amplitude of CBT and all skin temperature parameters decreased significantly during BL exposure. Circadian proximal skin temperatures cycled in phase with CBT, while distal skin temperatures cycled in anti-phase, confirming the idea that distal skin regions reflect heat dissipation and proximal regions approximate CBT. In general, we find that increased light intensity exposure may have decreased heat loss in humans, especially at times when the circadian system promotes sleep.

Know Time to Die – Integrity Checking for Zero Trust Chiplet-based Systems Using Between-Die Delay PUFs

Industry trends are moving toward increasing use of chiplets as a replacement for monolithic fabrication in many modern chips. Each chiplet is a separately-produced silicon die, and a system-on-chip (SoC) is created by packaging the chiplets together on a silicon interposer or bridge. Chiplets enable IP reuse, heterogeneousintegration, and better ability to leverage cost-appropriate process nodes. Yet, creating systems from separately produced components also brings security risks to consider, such as the possibility of die swapping, or susceptibility to interposer probing or tampering. In a zero-trust security posture, a chiplet should not blindly assume it is operating in a friendly environment.In this paper we propose a delay-based PUF for chiplets to verify system integrity. Our technique allows a single chiplet to initiate a protocol with its neighbors to measure unique variations in the propagation delays of incoming signals as part of an integrity check. We prototype our design on Xilinx Ultrascale+ FPGAs, which are constructed as multi-die systems on a silicon interposer, and which also emulate the general features of other industrial chiplet interfaces. We perform experiments on, and compare data from, dozens of Ultrascale+ FPGAs by making use of Amazon’s Elastic Compute Cloud (EC2) F1 instances as a testing platform. The PUF cells are shown to reject clock and temperature variation as common mode, and each cell produces approximately 5 ps of unique delay variation. For a design with 144 PUF cells, we measure the mean within-class and between-class distances to be 68.3 ps and 847.7 ps, respectively. The smallest between-class distance of 686.0 ps exceeds the largest within-class distance of 124.0 ps by more than 5x under nominal conditions, and the PUF is shown to be resilient to environmental changes. Our findings indicate the PUF can be used for authentication, and is potentially sensitive enough to detect picosecond-scale timing changes due to tampering.

Circadian rhythm and depression: CLOCK variation interacts with stress but not chronotype in impacting depression

Circadian rhythm and depression: CLOCK variation interacts with stress but not chronotype in impacting depression

Selecting and averaging relaxed clock models in Bayesian tip dating of Mesozoic birds

AbstractRelaxed clock models are fundamental in Bayesian clock dating, but a single distribution characterizing the clock variation is typically selected. Hence, I developed a new reversible-jump Markov chain Monte Carlo (rjMCMC) algorithm for drawing posterior samples between the independent lognormal (ILN) and independent gamma rates (IGR) clock models. The ability of the rjMCMC algorithm to infer the true model was verified through simulations. I then applied the algorithm to the Mesozoic bird data previously analyzed under the white noise (WN) clock model. In comparison, averaging over the ILN and IGR models provided more reliable estimates of the divergence times and evolutionary rates. The ILN model showed slightly better fit than the IGR model and much better fit than the autocorrelated lognormal (ALN) clock model. When the data were partitioned, different partitions showed heterogeneous model fit for ILN and IGR clocks. The implementation provides a general framework for selecting and averaging relaxed clock models in Bayesian dating analyses.

Experimental scheme and noise analysis of weak-light phase locked loop for large-scale intersatellite laser interferometer.

In the current space gravitational wave (GW) detection, satellites are separated by millions of kilometers. As a result, watts of laser from one satellite is attenuated to the picowatt level at the other end due to the Gaussian beam divergence and the finite aperture of the telescope. Establishing an effective interferometry with such weak-light is a major challenge. The key is to enhance the weak-light while preserving its phase information, which carries the actual GW signal. This can be accomplished by employing an optical phase-locked loop (PLL) to lock the phase of a local oscillator (LO) laser to the weak-light and then sending the power-amplified LO back to the interferometer on the other satellite. Although shot-noise-limited performance of the picowatt level weak-light PLL has been achieved for high frequencies, it remains elusive for frequencies below 0.1Hz. Here, we propose a three-step experimental scheme to identify the main noise sources of the weak-light PLL, which turn out to be the low-frequency phase measurement noise, the weak-light shot noise, and the laser phase noise. In this paper, the first step experiment result shows that the out-loop phase noise can be suppressed to a level less than 6 × 10-6 rad/√Hz from 6 mHz to 1Hz by first using the special pilot-tone technique in the PLL to directly reduce the sampling time jitter noise in the digital phasemeter. The out-loop phase noise is mainly limited by the signal amplitude variation and differential time jitter noise of the reference clock.

Precision and Characteristics Analysis of Precise Satellite Clock Bias Data of BDS

High-precision satellite clock bias (SCB) data is a critical product for satellite navigation systems to realize accurate navigation, positioning and timing. Unlike other satellite navigation systems, the precise SCB data for the BeiDou Navigation Satellite System (BDS) are mainly determined by two methods, the Two-Way Time Transfer (TWTT) method and the Orbit Determination and Time Synchronization (ODTS) method. Awareness of the data variations obtained from different methods can be used to improve clock modeling performance, and be beneficial to higher-rate GNSS positioning and for predictions in real-time applications. We describe a comprehensive method to analyze the systematic and random characteristics of BDS SCB data obtained from TWTT and ODTS and discuss possible causes of observed variations. Some new conclusions are drawn: the data continuity of TWTT is highly related to satellite orbit types; affected by orbit error and other factors, the fitting residuals (RMS) of ODTS is 0.2 ns worse than that of TWTT on average, while the fitting precision of TWTT is 0.49 ns. There are up to 8ns periodic fluctuations in the mutual agreement between TWTT and ODTS data. The stability result shows a remarkable effect of flicker phase modulation (FLPM) noise can be seen in the period of 300-1000 s in TWTT data. All the BDS satellites display more complex, nonpower law behavior due to the effects of periodic clock variations.

Extensive tissue-specific expression variation and novel regulators underlying circadian behavior.

Natural genetic variation affects circadian rhythms across the evolutionary tree, but the underlying molecular mechanisms are poorly understood. We investigated population-level, molecular circadian clock variation by generating >700 tissue-specific transcriptomes of Drosophila melanogaster (w1118 ) and 141 Drosophila Genetic Reference Panel (DGRP) lines. This comprehensive circadian gene expression atlas contains >1700 cycling genes including previously unknown central circadian clock components and tissue-specific regulators. Furthermore, >30% of DGRP lines exhibited aberrant circadian gene expression, revealing abundant genetic variation-mediated, intertissue circadian expression desynchrony. Genetic analysis of one line with the strongest deviating circadian expression uncovered a novel cry mutation that, as shown by protein structural modeling and brain immunohistochemistry, disrupts the light-driven flavin adenine dinucleotide cofactor photoreduction, providing in vivo support for the importance of this conserved photoentrainment mechanism. Together, our study revealed pervasive tissue-specific circadian expression variation with genetic variants acting upon tissue-specific regulatory networks to generate local gene expression oscillations.

Populations Are Differentiated in Biological Rhythms without Explicit Elevational Clines in the Plant Mimulus laciniatus.

Environmental variation along an elevational gradient can yield phenotypic differentiation resulting from varying selection pressures on plant traits related to seasonal responses. Thus, genetic clines can evolve in a suite of traits, including the circadian clock, that drives daily cycling in varied traits and that shares its genetic background with adaptation to seasonality. We used populations of annual Mimulus laciniatus from different elevations in the Sierra Nevada in California to explore among-population differentiation in the circadian clock, flowering responses to photoperiod, and phenological traits (days to cotyledon emergence, days to flowering, and days to seed ripening) in controlled common-garden conditions. Further, we examined correlations of these traits with environmental variables related to temperature and precipitation. We observed that the circadian period in leaf movement was differentiated among populations sampled within about 100 km, with population means varying by 1.6 h. Significant local genetic variation occurred within 2 populations in which circadian period among families varied by up to 1.8 h. Replicated treatments with variable ecologically relevant photoperiods revealed marked population differentiation in critical day length for flowering that ranged from 11.0 to 14.1 h, corresponding to the time period between late February and mid-May in the wild. Flowering time varied among populations in a 14-h photoperiod. Regardless of this substantial population-level diversity, obvious linear clinality in trait variability across elevations could not be determined based on our genotypic sample; it is possible that more complex spatial patterns of variation arise in complex terrains such as those in the Sierra Nevada. Moreover, we did not find statistically significant bivariate correlations between population means of different traits. Our research contributes to the understanding of genetic variation in the circadian clock and in seasonal responses in natural populations, highlighting the need for more comprehensive investigations on the association between the clock and other adaptive traits in plants.

Habitat-Specific Clock Variation and Its Consequence on Reproductive Fitness.

The circadian clock controls daily activities at the cellular and organismic level, allowing an organism to anticipate incoming stresses and to use resources accordingly. The circadian clock has therefore been considered a fitness trait in multiple organisms. However, the mechanism of how circadian clock variation influences organismal reproductive fitness is still not well understood. Here we describe habitat-specific clock variation (HSCV) of asexual reproduction in Neurospora discreta, a species that is adapted to 2 different habitats, under or above tree bark. African (AF) N. discreta strains, whose habitat is above the tree bark in light-dark (LD) conditions, display a higher rhythmicity index compared with North American (NA) strains, whose habitat is under the tree bark in constant dark (DD). Although AF-type strains demonstrated an overall fitness advantage under LD and DD conditions, NA-type strains exhibit a habitat-specific fitness advantage in DD over the LD condition. In addition, we show that allelic variation of the clock-controlled gene, Ubiquinol cytochrome c oxidoreductase (NEUDI_158280), plays a role in HSCV by modulating cellular reactive oxygen species levels. Our results demonstrate a mechanism by which local adaptation involving circadian clock regulation influences reproductive fitness.

Question 1: Clock variation; Question 2: Recycling coffee pods: Solutions for Fermi Questions, December 2018

Question 1: Clock variation; Question 2: Recycling coffee pods: Solutions for Fermi Questions, December 2018

Question 1: Clock variation; Question 2: Recycling coffee pods

Question 1: Clock variation; Question 2: Recycling coffee pods

Synthesis and exploration of clock spines

This study addresses the problem of developing a synthesis algorithm for clock spine networks, which is able to systematically explore the clock resources and clock variation tolerance. The idea is to transform the problem of allocating and placing clock spines on a plane into a slicing floorplan optimisation (SFO) problem, in which every candidate of clock spine network structures is uniquely expressed into a postfix notation to enable a fast cost computation in the SFO. As a result, the authors proposed synthesis algorithm can explore the diverse structures of the clock spine network to find globally optimal ones within acceptable run time. Through experiments with benchmark circuits, it is shown that the proposed algorithm is able to synthesise the clock spine networks with 38% reduced clock skew over the clock tree structures, even 11% reduced clock power. In addition, in comparison with the clock mesh structures, the proposed clock spine networks have comparable tolerance to clock skew variation while using considerably less clock resources, reducing clock power by 36%.

Circadian rhythms are associated with variation in photosystem II function and photoprotective mechanisms.

The circadian clock regulates many aspects of leaf gas supply and biochemical demand for CO2 , and is hypothesized to improve plant performance. Yet the extent to which the clock may regulate the efficiency of photosystem II (PSII) and photoprotective mechanisms such as heat dissipation is less explored. Based on measurements of chlorophyll a fluorescence, we estimated the maximum efficiency of PSII in light (Fv'/Fm') and heat dissipation by nonphotochemical quenching (NPQ). We further dissected total NPQ into its main components, qE (pH-dependent quenching), qT (state-transition quenching), and qI (quenching related to photoinhibition), in clock mutant genotypes of Arabidopsis thaliana, the cognate wild-type genotypes, and a panel of recombinant inbred lines expressing quantitative variation in clock period. Compared with mutants with altered clock function, we observed that wild-type genotypes with clock period lengths of approximately 24hr had both higher levels of Fv'/Fm', indicative of improved PSII function, and reduced NPQ, suggestive of lower stress on PSII light harvesting complexes. In the recombinant inbred lines, genetic variances were significant for Fv'/Fm' and all 3 components of NPQ, with qE explaining the greatest proportion of NPQ. Bivariate tests of association and structural equation models of hierarchical trait relationships showed that quantitative clock variation was empirically associated with Fv'/Fm' and NPQ, with qE mediating the relationship with gas exchange. The results demonstrate significant segregating variation for all photoprotective components, and suggest the adaptive significance of the clock may partly derive from its regulation of the light reactions of photosynthesis and of photoprotective mechanisms.

Circadian rhythms are associated with shoot architecture in natural settings

Circadian rhythms are key regulators of diverse biological processes under controlled settings. Yet, the phenotypic and fitness consequences of quantitative variation in circadian rhythms remain largely unexplored in the field. As with other pathways, phenotypic characterization of circadian outputs in the field may reveal novel clock functions. Across consecutive growing seasons, we test for associations between clock variation and flowering phenology, plant size, shoot architecture, and fruit set in clock mutants and segregating progenies of Arabidopsis thaliana expressing quantitative variation in circadian rhythms. Using structural equationmodeling, we find that genotypic variation in circadian rhythms within a growing season is associated directly with branching, which in turn affects fruit production. Consistent with direct associations between the clock and branching in segregating progenies, cauline branch number is lower and rosette branch number higher in a short-period mutant relative to wild-type and long-period genotypes, independent of flowering time. Differences in branching arise from variation in meristem fate as well as leaf production rate before flowering and attendant increases in meristem number. Our results suggest that clock variation directly affects shoot architecture in the field, suggesting a novel clock function and means by which the clock affects performance.

Improved prediction of GPS satellite clock sub-daily variations based on daily repeat

High-precision estimates of GPS satellite clock errors reveal systematic sub-daily clock bias variations on the order of 1 ns. The low noise levels in the Rubidium Atomic Frequency Standards onboard GPS IIR, IIR-M, and IIF satellites provide visibility of these small, but systematic behaviors. Prior studies have reported on this phenomenon and sought to characterize the specific frequency components present and to identify potential causes of the observed periodic variations. Our research focuses on the repeatability of the clock variations and the potential for using observed variations directly to predict future clock behavior. Results are presented and compared to IGS Ultra-rapid and broadcast message predictions for all operating GPS satellite clocks for a 1-month period in July 2017. During this time, the accuracy of the proposed sub-daily variation prediction is better than 0.15 ns (RMS) for 8 out of 9 GPS Block IIF Rb clocks and under 0.3 ns (RMS) for most GPS IIR and IIR-M Rb clocks. This approach is complementary to existing techniques for estimating longer-term clock rates and drift and can be combined with them to improve the fidelity of predictive satellite clock models for real-time GPS position, navigation, and timing applications.