WorldWideScience

Sample records for clocked boehm trees

  1. Gerrard Winstanley and Jacob Boehme

    Directory of Open Access Journals (Sweden)

    Hessayon, Ariel

    2014-02-01

    Full Text Available Given, firstly, justifiable claims made by the editors of the complete works of the Digger leader Gerrard Winstanley, that he was not just the ‘foremost radical of the English Revolution’ but also one of the ‘finest writers’ of a ‘glorious age of English non-fictional prose’, and secondly, the important suggestion that Winstanley was a forerunner of Quakerism, indeed that his writings shaped the formation of Quaker thought, Winstanley’s potential reading of the German Lutheran mystic Jacob Boehme deserves close attention. For more than a century scholars encompassing a range of backgrounds and ideological commitments have, with varying degrees of caution, drawn a number of rarely convincing and, unfortunately, usually ill-informed parallels between Boehme and Winstanley. As I will show, it seems certain that Winstanley did not consult any of Boehme’s works while writing his own. It also appears very probable that he never read Boehme. The disparities between them are far too great. Indeed, there is no analogue in the relevant texts by Boehme for a number of Winstanley’s doctrines and exhortations. Furthermore, Winstanley never quotes, paraphrases or alludes to Boehme. His prose style differs from the way in which Boehme’s translators rendered him into English. Nor does Winstanley adopt any of the neologisms introduced by these translators. Consequently I will suggest that since Winstanley most likely possessed only a handful of printed works or else a modest library, greater consideration needs to be given to how ideas were transmitted – not textually but orally, because it is probable that some of the seeds that germinated into Winstanley’s mature philosophy were sown in this manner.

  2. Simultaneous Buffer-sizing and Wire-sizing for Clock Trees Based on Lagrangian Relaxation

    Directory of Open Access Journals (Sweden)

    Yu-Min Lee

    2002-01-01

    Full Text Available Delay, power, skew, area and sensitivity are the most important concerns in current clock-tree design. We present in this paper an algorithm for simultaneously optimizing the above objectives by sizing wires and buffers in clock trees. Our algorithm, based on Lagrangian relaxation method, can optimally minimize delay, power and area simultaneously with very low skew and sensitivity. With linear storage overall and linear runtime per iteration, our algorithm is extremely economical, fast and accurate; for example, our algorithm can solve a 6201-wire-segment clock-tree problem using about 1-minute runtime and 1.3-MB memory and still achieve pico-second precision on an IBM RS/6000 workstation.

  3. Evaluation of modified boehm titration methods for use with biochars.

    Science.gov (United States)

    Fidel, Rivka B; Laird, David A; Thompson, Michael L

    2013-11-01

    The Boehm titration, originally developed to quantify organic functional groups of carbon blacks and activated carbons in discrete pK ranges, has received growing attention for analyzing biochar. However, properties that distinguish biochar from carbon black and activated carbon, including greater carbon solubility and higher ash content, may render the original Boehm titration method unreliable for use with biochars. Here we use seven biochars and one reference carbon black to evaluate three Boehm titration methods that use (i) acidification followed by sparging (sparge method), (ii) centrifugation after treatment with BaCl (barium method), and (iii) a solid-phase extraction cartridge followed by acidification and sparging (cartridge method) to remove carbonates and dissolved organic compounds (DOC) from the Boehm extracts before titration. Our results for the various combinations of Boehm reactants and methods indicate that no one method was free of bias for all three Boehm reactants and that the cartridge method showed evidence of bias for all pK ranges. By process of elimination, we found that a combination of the sparge method for quantifying functional groups in the lowest pK range (∼5 to 6.4), and the barium method for quantifying functional groups in the higher pK ranges (∼6.4 to 10.3 and ∼10.3 to 13) to be free of evidence for bias. We caution, however, that further testing is needed and that all Boehm titration results for biochars should be considered suspect unless efforts were undertaken to remove ash and prevent interference from DOC. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

  4. Innovations of Theobald Boehm to the Flute Construction

    Directory of Open Access Journals (Sweden)

    Burcin Barut dikicigiller

    2014-11-01

    Full Text Available Theobald Boehm who had a long life full of creativity, tried to maintain his creativity and performing activities concurrently for almost sixty years in order to bring perfection to the construction of the flute. Two generation flutes that the German master invented in 1832 and 1847 had been one of the most important achievements in the development of the construction of the instrument until that date and those reforms had brought Boehm the reputation which he deserved. Beside from the reforms he made regarding the construction of the flute, Theobald Boehm also stands outs with the musical pieces that he wrote for this instrument. In this study, formation process of the Boehm system flute which is still being used and the evolution of the flute during this process has been analyzed and it has been aimed to relay the importance of Theobald Boehm, who has made a great contribution for the flute to become a solo instrument instead of orchestral instrument and obtain status, in the history of the flute to today’s flautists.

  5. Non-robust Phase Transitions in the Generalized Clock Model on Trees

    Science.gov (United States)

    Külske, C.; Schriever, P.

    2018-01-01

    Pemantle and Steif provided a sharp threshold for the existence of a robust phase transition (RPT) for the continuous rotator model and the Potts model in terms of the branching number and the second eigenvalue of the transfer matrix whose kernel describes the nearest neighbor interaction along the edges of the tree. Here a RPT is said to occur if an arbitrarily weak coupling with symmetry-breaking boundary conditions suffices to induce symmetry breaking in the bulk. They further showed that for the Potts model RPT occurs at a different threshold than PT (phase transition in the sense of multiple Gibbs measures), and conjectured that RPT and PT should occur at the same threshold in the continuous rotator model. We consider the class of four- and five-state rotation-invariant spin models with reflection symmetry on general trees which contains the Potts model and the clock model with scalarproduct-interaction as limiting cases. The clock model can be viewed as a particular discretization which is obtained from the classical rotator model with state space S^1. We analyze the transition between PT=RPT and PT≠ RPT, in terms of the eigenvalues of the transfer matrix of the model at the critical threshold value for the existence of RPT. The transition between the two regimes depends sensitively on the third largest eigenvalue.

  6. Non-robust Phase Transitions in the Generalized Clock Model on Trees

    Science.gov (United States)

    Külske, C.; Schriever, P.

    2017-11-01

    Pemantle and Steif provided a sharp threshold for the existence of a robust phase transition (RPT) for the continuous rotator model and the Potts model in terms of the branching number and the second eigenvalue of the transfer matrix whose kernel describes the nearest neighbor interaction along the edges of the tree. Here a RPT is said to occur if an arbitrarily weak coupling with symmetry-breaking boundary conditions suffices to induce symmetry breaking in the bulk. They further showed that for the Potts model RPT occurs at a different threshold than PT (phase transition in the sense of multiple Gibbs measures), and conjectured that RPT and PT should occur at the same threshold in the continuous rotator model. We consider the class of four- and five-state rotation-invariant spin models with reflection symmetry on general trees which contains the Potts model and the clock model with scalarproduct-interaction as limiting cases. The clock model can be viewed as a particular discretization which is obtained from the classical rotator model with state space S^1 . We analyze the transition between PT=RPT and PT≠RPT , in terms of the eigenvalues of the transfer matrix of the model at the critical threshold value for the existence of RPT. The transition between the two regimes depends sensitively on the third largest eigenvalue.

  7. Boehm, Mitchell e una storia ancora da scrivere

    Directory of Open Access Journals (Sweden)

    Luca Vargiu

    2012-12-01

    Full Text Available Following the correspondence between Boehm and Mitchell, the paper discusses some focal points related to the so-called iconic, or pictorial turn: the difficulty in writing a history of the Bildwissenschaft, the role of the medieval studies, affinities and differences between the European and the American approach to image (and between Boehm’s and Mitchell’s approach, the Italian and French reception, the meaning to attribute to the word ‘turn’, and the relationship among the iconic or pictorial turn, the visual studies and more traditional disciplines such as aesthetics and art history.

  8. PBCB: A Norming of the Spanish Translation of the Boehm Test of Basic Concepts.

    Science.gov (United States)

    Preddy, David; And Others

    1984-01-01

    Prueba Boehm de Conceptos Basicos (PBCB), a Spanish translation of the Boehm Test of Basic Concepts, was administered to 1,292 children in Puerto Rico. Normative information, reported by type of school, by grade, and by time of year tested is presented. The reliability of PBCB was established. (BH)

  9. [Prehn, Ulrich. Max Hildebert Boehm. Radikales Ordnungsdenken vom Ersten Weltkrieg bis in die Bundesrepublik] / Karsten Brüggemann

    Index Scriptorium Estoniae

    Brüggemann, Karsten, 1965-

    2015-01-01

    Arvustus: Prehn, Ulrich. Max Hildebert Boehm. Radikales Ordnungsdenken vom Ersten Weltkrieg bis in die Bundesrepublik (Hamburger Beiträge zur Sozizl- und Zeitgeschichte, 51). Wallstein Verlag. Göttingen 2013

  10. Determination of surface functional groups on mechanochemically activated carbon cloth by Boehm method

    Directory of Open Access Journals (Sweden)

    Đukić Anđelka B.

    2014-01-01

    Full Text Available In order to improve sorption properties of activated carbon cloth that can be used for wastewater purification, mechanochemical activation was performed in both inert and air atmosphere. Boehm method was used to follow the changes in the number and types of surface groups induced by mechanical milling. The number of the base groups of 0,2493 mmol/g is significantly smaller than the total amount of acidic functional groups, 2,5093 mmol/g. Among the acidic groups present on the surface, the most represented are phenolic groups (2.3846 mmol/g , ie . > 95 % , the carboxylic groups are present far less (0.1173 mmol /g, ie. 4.5 %, while the presence of the lactone group on the surface of ACC is negligible (0.0074 mmol/g ie. under 0.3 %. Mechanochemical activation lead to an increase in the number of acidic and basic groups on the surface of the ACC. The milling in inert atmosphere has dominant effect with respect to the changes in the total number of basic functional groups (compared to milling in an air atmosphere: the number of basic groups of the ACC was 0.8153 mmol/g milled under argon, 0.7933 mmol/g in the air; the number of acidic groups is 2.9807 mmol/g for a sample milled under argon and 3.5313 mmol/g for one milled in the air.

  11. Estimación en proyectos de software integrando los métodos de Boehm y Humphrey

    OpenAIRE

    Yadira Ruíz Constanten; Dasiel Cordero Morales

    2013-01-01

    En este documento se da una visión general del proceso de estimación del software. Se indican algunos fundamentos y se le ubica dentro de la gestión de proyectos de software. Se divide la estimación, en predicción del tamaño, del esfuerzo y del tiempo empleado para realizar el proyecto. Se hace especial énfasis, en los modelos propuestos por Barry Boehm y Watts Humphrey para estimar la duración de proyectos de software tratando de buscar puntos en común para una posible integración entre ello...

  12. Trees

    Science.gov (United States)

    Al-Khaja, Nawal

    2007-01-01

    This is a thematic lesson plan for young learners about palm trees and the importance of taking care of them. The two part lesson teaches listening, reading and speaking skills. The lesson includes parts of a tree; the modal auxiliary, can; dialogues and a role play activity.

  13. Tectonic blocks and molecular clocks

    OpenAIRE

    De Baets, Kenneth; Antonelli, Alex; Donoghue, Philip

    2016-01-01

    Evolutionary timescales have mainly used fossils for calibrating molecular clocks, though fossils only really provide minimum clade age constraints. In their place, phylogenetic trees can be calibrated by precisely dated geological events that have shaped biogeography. However, tectonic episodes are protracted, their role in vicariance is rarely justified, the biogeography of living clades and their antecedents may differ, and the impact of such events is contingent on ecology. Biogeographic ...

  14. Trees

    Directory of Open Access Journals (Sweden)

    Henri Epstein

    2016-11-01

    Full Text Available An algebraic formalism, developed with V. Glaser and R. Stora for the study of the generalized retarded functions of quantum field theory, is used to prove a factorization theorem which provides a complete description of the generalized retarded functions associated with any tree graph. Integrating over the variables associated to internal vertices to obtain the perturbative generalized retarded functions for interacting fields arising from such graphs is shown to be possible for a large category of space–times.

  15. Lego clocks : building a clock from parts

    NARCIS (Netherlands)

    Brunner, Michael; Simons, Mirre J. P.; Merrow, Martha

    2008-01-01

    A new finding opens up speculation that the molecular mechanism of circadian clocks in Synechococcus elongatus is composed of multiple oscillator systems (Kitayama and colleagues, this issue, pp. 1513-1521), as has been described in many eukaryotic clock model systems. However, an alternative

  16. GPS Composite Clock Analysis

    OpenAIRE

    Wright, James R.

    2008-01-01

    The GPS composite clock defines GPS time, the timescale used today in GPS operations. GPS time is illuminated by examination of its role in the complete estimation and control problem relative to UTC/TAI. The phase of each GPS clock is unobservable from GPS pseudorange measurements, and the mean phase of the GPS clock ensemble (GPS time) is unobservable. A new and useful observability definition is presented, together with new observability theorems, to demonstrate explicitly that GPS time is...

  17. Precision Clock Evaluation Facility

    Data.gov (United States)

    Federal Laboratory Consortium — FUNCTION: Tests and evaluates high-precision atomic clocks for spacecraft, ground, and mobile applications. Supports performance evaluation, environmental testing,...

  18. Clocked combustor can array

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Won-Wook; McMahan, Kevin Weston; Srinivasan, Shiva Kumar

    2017-01-17

    The present application provides a clocked combustor can array for coherence reduction in a gas turbine engine. The clocked combustor can array may include a number of combustor cans positioned in a circumferential array. A first set of the combustor cans may have a first orientation and a second set of the combustor cans may have a second orientation.

  19. Biological Clocks & Circadian Rhythms

    Science.gov (United States)

    Robertson, Laura; Jones, M. Gail

    2009-01-01

    The study of biological clocks and circadian rhythms is an excellent way to address the inquiry strand in the National Science Education Standards (NSES) (NRC 1996). Students can study these everyday phenomena by designing experiments, gathering and analyzing data, and generating new experiments. As students explore biological clocks and circadian…

  20. Optical Clocks in Space

    NARCIS (Netherlands)

    Schiller, S.; Görlitz, A.; Nevsky, A.; Koelemeij, J. C J; Wicht, A.; Gill, K.P.; Klein, H. A.; Margolis, H. S.; Mileti, G.; Sterr, U.; Riehle, F.; Peik, E.; Tamm, Chr; Ertmer, W.; Rasel, E.; van der Klein, M; Salomon, C.; Tino, G. M.; Lemonde, P.; Holzwarth, R.; Hänsch, T. W.

    The performance of optical clocks has strongly progressed in recent years, and accuracies and instabilities of 1 part in 1018 are expected in the near future. The operation of optical clocks in space provides new scientific and technological opportunities. In particular, an earth-orbiting satellite

  1. PARP Around the Clock

    OpenAIRE

    Kumar, Vivek; Takahashi, Joseph S.

    2010-01-01

    Cells possess internal ~24-hour or circadian clocks that synchronize physiological processes with daily cycles of light and nutrient availability. In this issue, Asher et al. (2010) find that PARP-1 (Poly(ADP-ribose) polymerase-1) modifies components of the clock machinery in response to feeding, providing a mechanism for how metabolic rhythms coordinate with circadian rhythms.

  2. Egyptian "Star Clocks"

    Science.gov (United States)

    Symons, Sarah

    Diagonal, transit, and Ramesside star clocks are tables of astronomical information occasionally found in ancient Egyptian temples, tombs, and papyri. The tables represent the motions of selected stars (decans and hour stars) throughout the Egyptian civil year. Analysis of star clocks leads to greater understanding of ancient Egyptian constellations, ritual astronomical activities, observational practices, and pharaonic chronology.

  3. Circadian clocks: Not your grandfather's clock.

    Science.gov (United States)

    Turek, Fred W

    2016-11-25

    The last 20 years have seen the rapid evolution of our understanding of the molecular genes and networks that enable almost all forms of life to generate 24-hour-or circadian-rhythms. One finding has been particularly exciting: that the molecular circadian clock resides in almost all of the cells of the body and that the clock regulates the timing of many cellular and signaling pathways associated with multiple disease states. Such advances represent a new frontier for medicine: circadian medicine. Copyright © 2016, American Association for the Advancement of Science.

  4. Optical clocks and relativity.

    Science.gov (United States)

    Chou, C W; Hume, D B; Rosenband, T; Wineland, D J

    2010-09-24

    Observers in relative motion or at different gravitational potentials measure disparate clock rates. These predictions of relativity have previously been observed with atomic clocks at high velocities and with large changes in elevation. We observed time dilation from relative speeds of less than 10 meters per second by comparing two optical atomic clocks connected by a 75-meter length of optical fiber. We can now also detect time dilation due to a change in height near Earth's surface of less than 1 meter. This technique may be extended to the field of geodesy, with applications in geophysics and hydrology as well as in space-based tests of fundamental physics.

  5. Tectonic blocks and molecular clocks

    Science.gov (United States)

    2016-01-01

    Evolutionary timescales have mainly used fossils for calibrating molecular clocks, though fossils only really provide minimum clade age constraints. In their place, phylogenetic trees can be calibrated by precisely dated geological events that have shaped biogeography. However, tectonic episodes are protracted, their role in vicariance is rarely justified, the biogeography of living clades and their antecedents may differ, and the impact of such events is contingent on ecology. Biogeographic calibrations are no panacea for the shortcomings of fossil calibrations, but their associated uncertainties can be accommodated. We provide examples of how biogeographic calibrations based on geological data can be established for the fragmentation of the Pangaean supercontinent: (i) for the uplift of the Isthmus of Panama, (ii) the separation of New Zealand from Gondwana, and (iii) for the opening of the Atlantic Ocean. Biogeographic and fossil calibrations are complementary, not competing, approaches to constraining molecular clock analyses, providing alternative constraints on the age of clades that are vital to avoiding circularity in investigating the role of biogeographic mechanisms in shaping modern biodiversity. This article is part of the themed issue ‘Dating species divergences using rocks and clocks’. PMID:27325840

  6. The modern molecular clock.

    Science.gov (United States)

    Bromham, Lindell; Penny, David

    2003-03-01

    The discovery of the molecular clock--a relatively constant rate of molecular evolution--provided an insight into the mechanisms of molecular evolution, and created one of the most useful new tools in biology. The unexpected constancy of rate was explained by assuming that most changes to genes are effectively neutral. Theory predicts several sources of variation in the rate of molecular evolution. However, even an approximate clock allows time estimates of events in evolutionary history, which provides a method for testing a wide range of biological hypotheses ranging from the origins of the animal kingdom to the emergence of new viral epidemics.

  7. Cryptochromes and Biological Clocks

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 7; Issue 9. Cryptochromes and Biological Clocks. V R Bhagwat. General Article Volume 7 Issue 9 September 2002 pp 36-48. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/reso/007/09/0036-0048. Keywords.

  8. Decamp Clock Board Firmware

    Energy Technology Data Exchange (ETDEWEB)

    Vicente, J. de; Castilla, J.; Martinez, G.

    2007-09-27

    Decamp (Dark Energy Survey Camera) is a new instrument designed to explore the universe aiming to reveal the nature of Dark Energy. The camera consists of 72 CCDs and 520 Mpixels. The readout electronics of DECam is based on the Monsoon system. Monsoon is a new image acquisition system developed by the NOAO (National Optical Astronomical Observatory) for the new generation of astronomical cameras. The Monsoon system uses three types of boards inserted in a Eurocard format based crate: master control board, acquisition board and clock board. The direct use of the Monsoon system for DECam readout electronics requires nine crates mainly due to the high number of clock boards needed. Unfortunately, the available space for DECam electronics is constrained to four crates at maximum. The major drawback to achieve such desired compaction degree resides in the clock board signal density. This document describes the changes performed at CIEMAT on the programmable logic of the Monsoon clock board aiming to meet such restricted space constraints. (Author) 5 refs.

  9. Evolution of the CLOCK and BMAL1 genes in a subterranean rodent species (Lasiopodomys mandarinus).

    Science.gov (United States)

    Sun, Hong; Zhang, Yifeng; Shi, Yuhua; Li, Yangwei; Li, Wei; Wang, Zhenlong

    2017-11-12

    Lasiopodomys mandarinus, a subterranean rodent, spends its entire life underground. To test whether the CLOCK and BMAL1 genes of L. mandarinus have undergone adaptive evolution to underground darkness, we cloned and analyzed their complete cDNA sequences, using Lasiopodomys brandtii as a control. The phylogenetic trees of the CLOCK and BMAL1 genes were similar to the trees of the conserved Cyt b gene,further, L. mandarinus clustered with L. brandtii and Microtus ochrogaster in the phylogenetic tree. The Q-rich region of the CLOCK gene in L. mandarinus was different from that of other subterranean rodents. Using phylogenetic analysis maximum likelihood (PAML), the ω value (ωimportant functionality of the TAD, which is putatively of functional relevance to CLOCK protein activity. The present findings provide novel insights into adaptation to underground darkness, at the gene level, in subterranean rodents. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. [Clocks, Behavior, and Cognition].

    Science.gov (United States)

    Futamura, Akinori; Shiromaru, Azusa; Kuroda, Takeshi; Honma, Motoyasu; Kinno, Ryuta; Ono, Kenjiro; Kawamura, Mitsuru

    2017-06-01

    The nerve center responsible for controlling our circadian rhythm is located in a cluster of cells known as the suprachiasmatic nucleus in the hypothalamus. Various physiological functions such as sleep, arousal, blood pressure, body temperature, and hormone secretion are regulated in a 24-hour rhythm by this circuit. Somatic cells of other organs have a peripheral clock gene and by synchronizing the rhythm of the central and peripheral clocks, it is possible to live a healthy life. Due to aging and degenerative disease, circadian rhythm gradually collapses. Factors that can contribute to this include reduced expression of the time gene associated with photo stimulation, a reduction in neurotransmitter levels, and reduced melatonin production. Biological clocks play an important role in our emotions, cognitive function, and behavior. Sleep disorders and metabolic disease related to the circadian rhythm affect metabolic and endocrine activities via the autonomic nervous system and the intestinal bacterial flora. Shift work disorder is associated with insomnia and excessive drowsiness as individuals often work during their sleeping hours. Now time management is placed at the center of our society, and it is important to evaluate the medical risk of engaging in shift work. In frontotemporal dementia (FTD), the stereotypical behaviors may be associated with time. In some patients, multiple timed behaviors occupy a considerable part of the patient's daily life. Stereotypical behaviors in FTD are often considered in contrast to obsessive-compulsive disease (OCD). Studies of OCD have found a close correlation between clinical symptoms, cognitive function, and brain function.

  11. A Light Clock Satisfying the Clock Hypothesis of Special Relativity

    Science.gov (United States)

    West, Joseph

    2007-01-01

    The design of the FMEL, a floor-mirrored Einstein-Langevin "light clock", is introduced. The clock provides a physically intuitive manner to calculate and visualize the time dilation effects for a spatially extended set of observers (an accelerated "frame") undergoing unidirectional acceleration or observers on a rotating cylinder of constant…

  12. Clock polymorphism in Pacific salmon: evidence for variable selection along a latitudinal gradient.

    Science.gov (United States)

    O'Malley, Kathleen G; Ford, Michael J; Hard, Jeffrey J

    2010-12-22

    Seasonal timing of life-history events is often under strong natural selection. The Clock gene is a central component of an endogenous circadian clock that senses changes in photoperiod (day length) and mediates seasonal behaviours. Among Pacific salmonids (Oncorhynchus spp.), seasonal timing of migration and breeding is influenced by photoperiod. To expand a study of 42 North American Chinook salmon (Oncorhynchus tshawytscha) populations, we tested whether duplicated Clock genes contribute to population differences in reproductive timing. Specifically, we examined geographical variation along a similar latitudinal gradient in the polyglutamine domain (PolyQ) of OtsClock1a and OtsClock1b among 53 populations of three species: chum (Oncorhynchus keta), coho (Oncorhynchus kisutch) and pink salmon (Oncorhynchus gorbuscha). We found evidence for variable selection on OtsClock1b that corresponds to latitudinal variation in reproductive timing among these species. We evaluated the contribution of day length and a freshwater migration index to OtsClock1b PolyQ domain variation using regression trees and found that day length at spawning explains much of the variation in OtsClock1b allele frequency among chum and Chinook, but not coho and pink salmon populations. Our findings suggest that OtsClock1b mediates seasonal adaptation and influences geographical variation in reproductive timing in some of these highly migratory species.

  13. Analysis list: CLOCK [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available CLOCK Blood,Digestive tract + hg19 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/target/CLOCK....1.tsv http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/target/CLOCK.5.tsv http://dbarchive.biosc...iencedbc.jp/kyushu-u/hg19/target/CLOCK.10.tsv http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/colo/CLOCK.Blo...od.tsv,http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/colo/CLOCK.Digestive_tract

  14. Physiological links of circadian clock and biological clock of aging

    Directory of Open Access Journals (Sweden)

    Fang Liu

    2017-01-01

    Full Text Available ABSTRACT Circadian rhythms orchestrate biochemical and physiological processes in living organisms to respond the day/night cycle. In mammals, nearly all cells hold self-sustained circadian clocks meanwhile couple the intrinsic rhythms to systemic changes in a hierarchical manner. The suprachiasmatic nucleus (SCN of the hypothalamus functions as the master pacemaker to initiate daily synchronization according to the photoperiod, in turn determines the phase of peripheral cellular clocks through a variety of signaling relays, including endocrine rhythms and metabolic cycles. With aging, circadian desynchrony occurs at the expense of peripheral metabolic pathologies and central neurodegenerative disorders with sleep symptoms, and genetic ablation of circadian genes in model organisms resembled the aging-related features. Notably, a number of studies have linked longevity nutrient sensing pathways in modulating circadian clocks. Therapeutic strategies that bridge the nutrient sensing pathways and circadian clock might be rational designs to defy aging.

  15. Acceleration effects on atomic clocks

    CERN Document Server

    Dahia, F

    2014-01-01

    We consider a free massive particle inside a box which is dragged by Rindler observers. Admitting that the particle obeys the Klein-Gordon equation, we find the frequencies of the stationary states of this system. Transitions between the stationary states are employed to set a standard frequency for a toy atomic clock. Comparing the energy spectrum of the accelerated system with the energy spectrum of an identical system in an inertial frame, we determine the influence of the instantaneous acceleration on the rate of atomic clocks. We argue that our result does not violate the clock hypothesis.

  16. Brain clocks for morning and evening behaviour

    Indian Academy of Sciences (India)

    Unknown

    228 taneously synthesized transcripts of a clock gene, mPer1, in one of the two lobes, and transcripts of another clock gene,. Bmal1, in the other, suggesting antiphasic nature of the two bilaterally symmetric SCN lobes. Further, it was ... resolution of clock cell targeting. The authors developed. Figure 1. Clock neurons in the ...

  17. Simulating Future GPS Clock Scenarios with Two Composite Clock Algorithms

    Science.gov (United States)

    2010-11-01

    Alexandria, Virginia), pp. 223-242. [8] C. A. Greenhall, 2007, “A Kalman filter clock ensemble algorithm that admits measurement noise,” Metrologia ...43, S311-S321. [9] J. A. Davis, C. A. Greenhall, and P. W. Stacey, 2005, “A Kalman filter clock algorithm for use in the presence of flicker frequency modulation noise,” Metrologia , 42, 1-10.

  18. Einstein's Clocks and Langevin's Twins

    CERN Document Server

    Weinstein, Galina

    2012-01-01

    In 1905 Einstein presented the Clock Paradox and in 1911 Paul Langevin expanded Einstein's result to human observers, the "Twin Paradox." I will explain the crucial difference between Einstein and Langevin. Einstein did not present the so-called "Twin Paradox." Later Einstein continued to speak about the clock paradox. Einstein might not have been interested in the question: what happens to the observers themselves. The reason for this could be the following; Einstein dealt with measurement procedures, clocks and measuring rods. Einstein's observers were measuring time with these clocks and measuring rods. Einstein might not have been interested in so-called biology of the observers, whether these observers were getting older, younger, or whether they have gone any other changes; these changes appeared to be out of the scope of his "Principle of relativity" or kinematics. The processes and changes occurring within observers seemed to be good for philosophical discussions. Later writers criticized Einstein's c...

  19. Biological clocks in theory and experiments

    OpenAIRE

    Millar Andrew J

    2005-01-01

    Eukaryotes and some prokaryotes have adapted to the 24 h day/night cycle by evolving circadian clocks. The circadian clock now controls 24-hour rhythms in very many aspects of metabolism, physiology and behaviour. Day-length (photoperiod) measurement depends on the circadian clock, so the 24 h clock mechanism also governs seasonal rhythms, such as reproduction. In the model plant species, Arabidopsis thaliana, the clock controls the expression of about 10% of genes, and this proportion is sim...

  20. Analysis list: Clock [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Clock Liver + mm9 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/target/Clock.1.tsv... http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/target/Clock.5.tsv http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/target/Clock....10.tsv http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/colo/Clock.Liver.tsv http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/colo/Liver.gml ...

  1. Stochastic models for atomic clocks

    Science.gov (United States)

    Barnes, J. A.; Jones, R. H.; Tryon, P. V.; Allan, D. W.

    1983-01-01

    For the atomic clocks used in the National Bureau of Standards Time Scales, an adequate model is the superposition of white FM, random walk FM, and linear frequency drift for times longer than about one minute. The model was tested on several clocks using maximum likelihood techniques for parameter estimation and the residuals were acceptably random. Conventional diagnostics indicate that additional model elements contribute no significant improvement to the model even at the expense of the added model complexity.

  2. Fossil butterflies, calibration points and the molecular clock (Lepidoptera: Papilionoidea).

    Science.gov (United States)

    Jong, Rienk DE

    2017-05-25

    Fossil butterflies are extremely rare. Yet, they are the only direct evidence of the first appearance of particular characters and as such, they are crucial for calibrating a molecular clock, from which divergence ages are estimated. In turn, these estimates, in combination with paleogeographic information, are most important in paleobiogeographic considerations. The key issue here is the correct allocation of fossils on the phylogenetic tree from which the molecular clock is calibrated.The allocation of a fossil on a tree should be based on an apomorphic character found in a tree based on extant species, similar to the allocation of a new extant species. In practice, the latter is not done, at least not explicitly, on the basis of apomorphy, but rather on overall similarity or on a phylogenetic analysis, which is not possible for most butterfly fossils since they usually are very fragmentary. Characters most often preserved are in the venation of the wings. Therefore, special attention is given to possible apomorphies in venational characters in extant butterflies. For estimation of divergence times, not only the correct allocation of the fossil on the tree is important, but also the tree itself influences the outcome as well as the correct determination of the age of the fossil. These three aspects are discussed.        All known butterfly fossils, consisting of 49 taxa, are critically reviewed and their relationship to extant taxa is discussed as an aid for correctly calibrating a molecular clock for papilionoid Lepidoptera. In this context some aspects of age estimation and biogeographic conclusions are briefly mentioned in review. Specific information has been summarized in four appendices.

  3. Atomic clock ensemble in space

    Science.gov (United States)

    Cacciapuoti, L.; Salomon, C.

    2011-12-01

    Atomic Clock Ensemble in Space (ACES) is a mission using high-performance clocks and links to test fundamental laws of physics in space. Operated in the microgravity environment of the International Space Station, the ACES clocks, PHARAO and SHM, will generate a frequency reference reaching instability and inaccuracy at the 1 · 10-16 level. A link in the microwave domain (MWL) and an optical link (ELT) will make the ACES clock signal available to ground laboratories equipped with atomic clocks. Space-to-ground and ground-to-ground comparisons of atomic frequency standards will be used to test Einstein's theory of general relativity including a precision measurement of the gravitational red-shift, a search for time variations of fundamental constants, and Lorentz Invariance tests. Applications in geodesy, optical time transfer, and ranging will also be supported. ACES has now reached an advanced technology maturity, with engineering models completed and successfully tested and flight hardware under development. This paper presents the ACES mission concept and the status of its main instruments.

  4. Circadian clocks, epigenetics, and cancer

    KAUST Repository

    Masri, Selma

    2015-01-01

    The interplay between circadian rhythm and cancer has been suggested for more than a decade based on the observations that shift work and cancer incidence are linked. Accumulating evidence implicates the circadian clock in cancer survival and proliferation pathways. At the molecular level, multiple control mechanisms have been proposed to link circadian transcription and cell-cycle control to tumorigenesis.The circadian gating of the cell cycle and subsequent control of cell proliferation is an area of active investigation. Moreover, the circadian clock is a transcriptional system that is intricately regulated at the epigenetic level. Interestingly, the epigenetic landscape at the level of histone modifications, DNA methylation, and small regulatory RNAs are differentially controlled in cancer cells. This concept raises the possibility that epigenetic control is a common thread linking the clock with cancer, though little scientific evidence is known to date.This review focuses on the link between circadian clock and cancer, and speculates on the possible connections at the epigenetic level that could further link the circadian clock to tumor initiation or progression.

  5. Sound Clocks and Sonic Relativity

    Science.gov (United States)

    Todd, Scott L.; Menicucci, Nicolas C.

    2017-10-01

    Sound propagation within certain non-relativistic condensed matter models obeys a relativistic wave equation despite such systems admitting entirely non-relativistic descriptions. A natural question that arises upon consideration of this is, "do devices exist that will experience the relativity in these systems?" We describe a thought experiment in which `acoustic observers' possess devices called sound clocks that can be connected to form chains. Careful investigation shows that appropriately constructed chains of stationary and moving sound clocks are perceived by observers on the other chain as undergoing the relativistic phenomena of length contraction and time dilation by the Lorentz factor, γ , with c the speed of sound. Sound clocks within moving chains actually tick less frequently than stationary ones and must be separated by a shorter distance than when stationary to satisfy simultaneity conditions. Stationary sound clocks appear to be length contracted and time dilated to moving observers due to their misunderstanding of their own state of motion with respect to the laboratory. Observers restricted to using sound clocks describe a universe kinematically consistent with the theory of special relativity, despite the preferred frame of their universe in the laboratory. Such devices show promise in further probing analogue relativity models, for example in investigating phenomena that require careful consideration of the proper time elapsed for observers.

  6. Clock, Circadian Rhythms, and Breast Cancer

    National Research Council Canada - National Science Library

    Hill, Steven M

    2004-01-01

    .... Work involving circadian clock genes and cell cycle components suggests not only an association between the two time-keeping systems, but also regulation of the cell cycle by the circadian clock...

  7. Light and the human circadian clock

    NARCIS (Netherlands)

    Roenneberg, Till; Kantermann, Thomas; Juda, Myriam; Vetter, Céline; Allebrandt, Karla V

    2013-01-01

    The circadian clock can only reliably fulfil its function if it is stably entrained. Most clocks use the light-dark cycle as environmental signal (zeitgeber) for this active synchronisation. How we think about clock function and entrainment has been strongly influenced by the early concepts of the

  8. Rate variation and estimation of divergence times using strict and relaxed clocks

    Directory of Open Access Journals (Sweden)

    Yang Ziheng

    2011-09-01

    datasets with higher σ2 for one or more partitions, supporting the simulation results. Conclusions The strict clock can be superior for trees with shallow roots because of low levels of rate variation between branches. The LRT allows robust assessment of suitability of the clock model as does examination of posteriors on σ2.

  9. Biological clocks: riding the tides.

    Science.gov (United States)

    de la Iglesia, Horacio O; Johnson, Carl Hirschie

    2013-10-21

    Animals with habitats in the intertidal zone often display biological rhythms that coordinate with both the tidal and the daily environmental cycles. Two recent studies show that the molecular components of the biological clocks mediating tidal rhythms are likely different from the phylogenetically conserved components that mediate circadian (daily) rhythms. Copyright © 2013 Elsevier Ltd. All rights reserved.

  10. <=ryptochromes and Biological Clocks -36 ...

    Indian Academy of Sciences (India)

    eyes (reptiles), pineal gland and deep brain photoreceptors. In mammals, all existing evidence indicates that photoreceptors. Figure 1. The anatomy of for both vision and the circadian clock are located in the eye. vision. A. Section through eye showing the location of light sensitive layer, the retina. B. The histological.

  11. Phylogenetic footprint of the plant clock system in angiosperms: evolutionary processes of Pseudo-Response Regulators

    Directory of Open Access Journals (Sweden)

    Saito Shigeru

    2010-05-01

    Full Text Available Abstract Background Plant circadian clocks regulate many photoperiodic and diurnal responses that are conserved among plant species. The plant circadian clock system has been uncovered in the model plant, Arabidopsis thaliana, using genetics and systems biology approaches. However, it is still not clear how the clock system had been organized in the evolutionary history of plants. We recently revealed the molecular phylogeny of LHY/CCA1 genes, one of the essential components of the clock system. The aims of this study are to reconstruct the phylogenetic relationships of angiosperm clock-associated PRR genes, the partner of the LHY/CCA1 genes, and to clarify the evolutionary history of the plant clock system in angiosperm lineages. Results In the present study, to investigate the molecular phylogeny of PRR genes, we performed two approaches: reconstruction of phylogenetic trees and examination of syntenic relationships. Phylogenetic analyses revealed that PRR genes had diverged into three clades prior to the speciation of monocots and eudicots. Furthermore, copy numbers of PRR genes have been independently increased in monocots and eudicots as a result of ancient chromosomal duplication events. Conclusions Based on the molecular phylogenies of both PRR genes and LHY/CCA1 genes, we inferred the evolutionary process of the plant clock system in angiosperms. This scenario provides evolutionary information that a common ancestor of monocots and eudicots had retained the basic components required for reconstructing a clock system and that the plant circadian clock may have become a more elaborate mechanism after the speciation of monocots and eudicots because of the gene expansion that resulted from polyploidy events.

  12. Circadian clock, cell cycle and cancer

    Directory of Open Access Journals (Sweden)

    Cansu Özbayer

    2011-12-01

    Full Text Available There are a few rhythms of our daily lives that we are under the influence. One of them is characterized by predictable changes over a 24-hour timescale called circadian clock. This cellular clock is coordinated by the suprachiasmatic nucleus in the anterior hypothalamus. The clock consist of an autoregulatory transcription-translation feedback loop compose of four genes/proteins; BMAL1, Clock, Cyrptochrome, and Period. BMAL 1 and Clock are transcriptional factors and Period and Cyrptochrome are their targets. Period and Cyrptochrome dimerize in the cytoplasm to enter the nucleus where they inhibit Clock/BMAL activity.It has been demonstrate that circadian clock plays an important role cellular proliferation, DNA damage and repair mechanisms, checkpoints, apoptosis and cancer.

  13. Automatic control of clock duty cycle

    Science.gov (United States)

    Feng, Xiaoxin (Inventor); Roper, Weston (Inventor); Seefeldt, James D. (Inventor)

    2010-01-01

    In general, this disclosure is directed to a duty cycle correction (DCC) circuit that adjusts a falling edge of a clock signal to achieve a desired duty cycle. In some examples, the DCC circuit may generate a pulse in response to a falling edge of an input clock signal, delay the pulse based on a control voltage, adjust the falling edge of the input clock signal based on the delayed pulse to produce an output clock signal, and adjust the control voltage based on the difference between a duty cycle of the output clock signal and a desired duty cycle. Since the DCC circuit adjusts the falling edge of the clock cycle to achieve a desired duty cycle, the DCC may be incorporated into existing PLL control loops that adjust the rising edge of a clock signal without interfering with the operation of such PLL control loops.

  14. Inertial Frames and Clock Rates

    CERN Document Server

    Kak, Subhash

    2012-01-01

    This article revisits the historiography of the problem of inertial frames. Specifically, the case of the twins in the clock paradox is considered to see that some resolutions implicitly assume inertiality for the non-accelerating twin. If inertial frames are explicitly identified by motion with respect to the large scale structure of the universe, it makes it possible to consider the relative inertiality of different frames.

  15. Entanglement of quantum clocks through gravity.

    Science.gov (United States)

    Castro Ruiz, Esteban; Giacomini, Flaminia; Brukner, Časlav

    2017-03-21

    In general relativity, the picture of space-time assigns an ideal clock to each world line. Being ideal, gravitational effects due to these clocks are ignored and the flow of time according to one clock is not affected by the presence of clocks along nearby world lines. However, if time is defined operationally, as a pointer position of a physical clock that obeys the principles of general relativity and quantum mechanics, such a picture is, at most, a convenient fiction. Specifically, we show that the general relativistic mass-energy equivalence implies gravitational interaction between the clocks, whereas the quantum mechanical superposition of energy eigenstates leads to a nonfixed metric background. Based only on the assumption that both principles hold in this situation, we show that the clocks necessarily get entangled through time dilation effect, which eventually leads to a loss of coherence of a single clock. Hence, the time as measured by a single clock is not well defined. However, the general relativistic notion of time is recovered in the classical limit of clocks.

  16. Hanle Detection for Optical Clocks

    Directory of Open Access Journals (Sweden)

    Xiaogang Zhang

    2015-01-01

    Full Text Available Considering the strong inhomogeneous spatial polarization and intensity distribution of spontaneous decay fluorescence due to the Hanle effect, we propose and demonstrate a universe Hanle detection configuration of electron-shelving method for optical clocks. Experimental results from Ca atomic beam optical frequency standard with electron-shelving method show that a designed Hanle detection geometry with optimized magnetic field direction, detection laser beam propagation and polarization direction, and detector position can improve the fluorescence collection rate by more than one order of magnitude comparing with that of inefficient geometry. With the fixed 423 nm fluorescence, the improved 657 nm optical frequency standard signal intensity is presented. The potential application of the Hanle detection geometry designed for facilitating the fluorescence collection for optical lattice clock with a limited solid angle of the fluorescence collection has been discussed. The Hanle detection geometry is also effective for ion detection in ion optical clock and quantum information experiments. Besides, a cylinder fluorescence collection structure is designed to increase the solid angle of the fluorescence collection in Ca atomic beam optical frequency standard.

  17. Explaining the imperfection of the molecular clock of hominid mitochondria.

    Directory of Open Access Journals (Sweden)

    Eva-Liis Loogväli

    Full Text Available The molecular clock of mitochondrial DNA has been extensively used to date various genetic events. However, its substitution rate among humans appears to be higher than rates inferred from human-chimpanzee comparisons, limiting the potential of interspecies clock calibrations for intraspecific dating. It is not well understood how and why the substitution rate accelerates. We have analyzed a phylogenetic tree of 3057 publicly available human mitochondrial DNA coding region sequences for changes in the ratios of mutations belonging to different functional classes. The proportion of non-synonymous and RNA genes substitutions has reduced over hundreds of thousands of years. The highest mutation ratios corresponding to fast acceleration in the apparent substitution rate of the coding sequence have occurred after the end of the Last Ice Age. We recalibrate the molecular clock of human mtDNA as 7990 years per synonymous mutation over the mitochondrial genome. However, the distribution of substitutions at synonymous sites in human data significantly departs from a model assuming a single rate parameter and implies at least 3 different subclasses of sites. Neutral model with 3 synonymous substitution rates can explain most, if not all, of the apparent molecular clock difference between the intra- and interspecies levels. Our findings imply the sluggishness of purifying selection in removing the slightly deleterious mutations from the human as well as the Neandertal and chimpanzee populations. However, for humans, the weakness of purifying selection has been further exacerbated by the population expansions associated with the out-of Africa migration and the end of the Last Ice Age.

  18. Circadian clock components in the rat neocortex

    DEFF Research Database (Denmark)

    Rath, Martin Fredensborg; Rohde, Kristian; Fahrenkrug, Jan

    2013-01-01

    The circadian master clock of the mammalian brain resides in the suprachiasmatic nucleus (SCN) of the hypothalamus. At the molecular level, the clock of the SCN is driven by a transcriptional/posttranslational autoregulatory network with clock gene products as core elements. Recent investigations...... in the rat neocortex. Among these, Per1, Per2, Per3, Cry1, Bmal1, Nr1d1 and Dbp were found to exhibit daily rhythms. The amplitude of circadian oscillation in neocortical clock gene expression was damped and the peak delayed as compared with the SCN. Lesions of the SCN revealed that rhythmic clock gene...... expression in the neocortex is dependent on the SCN. In situ hybridization and immunohistochemistry showed that products of the canonical clock gene Per2 are located in perikarya throughout all areas of the neocortex. These findings show that local circadian oscillators driven by the SCN reside within...

  19. Genetically Blocking the Zebrafish Pineal Clock Affects Circadian Behavior

    National Research Council Canada - National Science Library

    Ben-Moshe Livne, Zohar; Alon, Shahar; Vallone, Daniela; Bayleyen, Yared; Tovin, Adi; Shainer, Inbal; Nisembaum, Laura G; Aviram, Idit; Smadja-Storz, Sima; Fuentes, Michael; Falcón, Jack; Eisenberg, Eli; Klein, David C; Burgess, Harold A; Foulkes, Nicholas S; Gothilf, Yoav

    2016-01-01

    ... its synchronization with the solar day [2]. At the heart of the molecular clock in vertebrates are daily oscillations in the expression and function of evolutionarily conserved clock genes and their protein products, including CLOCK and BMAL, which form heterodimers that activate the transcription of clock and clock-controlled genes (CCGs) via E-box enhan...

  20. The Square Light Clock and Special Relativity

    Science.gov (United States)

    Galli, J. Ronald; Amiri, Farhang

    2012-01-01

    A thought experiment that includes a square light clock is similar to the traditional vertical light beam and mirror clock, except it is made up of four mirrors placed at a 45[degree] angle at each corner of a square of length L[subscript 0], shown in Fig. 1. Here we have shown the events as measured in the rest frame of the square light clock. By…

  1. Circadian clock genes, ovarian development and diapause

    Directory of Open Access Journals (Sweden)

    Bradshaw William E

    2010-09-01

    Full Text Available Abstract Insects, like most organisms, have an internal circadian clock that oscillates with a daily rhythmicity, and a timing mechanism that mediates seasonal events, including diapause. In research published in BMC Biology, Ikeno et al. show that downregulation of the circadian clock genes period and cycle affects expression of ovarian diapause in the insect Riptortus pedestris. They interpret these important results as support for Erwin Bünning's (1936 hypothesis that the circadian clock constitutes the basis of photoperiodism. However, their observations could also be the result of pleiotropic effects of the individual clock genes. See research article http://www.biomedcentral.com/1741-7007/8/116

  2. Transcriptional architecture of the mammalian circadian clock.

    Science.gov (United States)

    Takahashi, Joseph S

    2017-03-01

    Circadian clocks are endogenous oscillators that control 24-hour physiological and behavioural processes in organisms. These cell-autonomous clocks are composed of a transcription-translation-based autoregulatory feedback loop. With the development of next-generation sequencing approaches, biochemical and genomic insights into circadian function have recently come into focus. Genome-wide analyses of the clock transcriptional feedback loop have revealed a global circadian regulation of processes such as transcription factor occupancy, RNA polymerase II recruitment and initiation, nascent transcription, and chromatin remodelling. The genomic targets of circadian clocks are pervasive and are intimately linked to the regulation of metabolism, cell growth and physiology.

  3. High Performance Clocks and Gravity Field Determination

    Science.gov (United States)

    Müller, J.; Dirkx, D.; Kopeikin, S. M.; Lion, G.; Panet, I.; Petit, G.; Visser, P. N. A. M.

    2018-02-01

    Time measured by an ideal clock crucially depends on the gravitational potential and velocity of the clock according to general relativity. Technological advances in manufacturing high-precision atomic clocks have rapidly improved their accuracy and stability over the last decade that approached the level of 10^{-18}. This notable achievement along with the direct sensitivity of clocks to the strength of the gravitational field make them practically important for various geodetic applications that are addressed in the present paper. Based on a fully relativistic description of the background gravitational physics, we discuss the impact of those highly-precise clocks on the realization of reference frames and time scales used in geodesy. We discuss the current definitions of basic geodetic concepts and come to the conclusion that the advances in clocks and other metrological technologies will soon require the re-definition of time scales or, at least, clarification to ensure their continuity and consistent use in practice. The relative frequency shift between two clocks is directly related to the difference in the values of the gravity potential at the points of clock's localization. According to general relativity the relative accuracy of clocks in 10^{-18} is equivalent to measuring the gravitational red shift effect between two clocks with the height difference amounting to 1 cm. This makes the clocks an indispensable tool in high-precision geodesy in addition to laser ranging and space geodetic techniques. We show how clock measurements can provide geopotential numbers for the realization of gravity-field-related height systems and can resolve discrepancies in classically-determined height systems as well as between national height systems. Another application of clocks is the direct use of observed potential differences for the improved recovery of regional gravity field solutions. Finally, clock measurements for space-borne gravimetry are analyzed along with

  4. Gigabit Ethernet Asynchronous Clock Compensation FIFO

    Science.gov (United States)

    Duhachek, Jeff

    2012-01-01

    Clock compensation for Gigabit Ethernet is necessary because the clock recovered from the 1.25 Gb/s serial data stream has the potential to be 200 ppm slower or faster than the system clock. The serial data is converted to 10-bit parallel data at a 125 MHz rate on a clock recovered from the serial data stream. This recovered data needs to be processed by a system clock that is also running at a nominal rate of 125 MHz, but not synchronous to the recovered clock. To cross clock domains, an asynchronous FIFO (first-in-first-out) is used, with the write pointer (wprt) in the recovered clock domain and the read pointer (rptr) in the system clock domain. Because the clocks are generated from separate sources, there is potential for FIFO overflow or underflow. Clock compensation in Gigabit Ethernet is possible by taking advantage of the protocol data stream features. There are two distinct data streams that occur in Gigabit Ethernet where identical data is transmitted for a period of time. The first is configuration, which happens during auto-negotiation. The second is idle, which occurs at the end of auto-negotiation and between every packet. The identical data in the FIFO can be repeated by decrementing the read pointer, thus compensating for a FIFO that is draining too fast. The identical data in the FIFO can also be skipped by incrementing the read pointer, which compensates for a FIFO draining too slowly. The unique and novel features of this FIFO are that it works in both the idle stream and the configuration streams. The increment or decrement of the read pointer is different in the idle and compensation streams to preserve disparity. Another unique feature is that the read pointer to write pointer difference range changes between compensation and idle to minimize FIFO latency during packet transmission.

  5. Differential expression of circadian clock genes in two strains of beetles reveals candidates related to photoperiodic induction of summer diapause.

    Science.gov (United States)

    Zhu, Li; Liu, Wen; Tan, Qian-Qian; Lei, Chao-Liang; Wang, Xiao-Ping

    2017-03-01

    Diapause (also known as dormancy) is a state of arrested development induced by photoperiod or temperature that allows insects to survive adverse environmental conditions. By regulating diapause induction, the circadian clock is involved in short-day-induced winter diapause but whether this is also the case in long-day (LD)-induced summer diapause remains unknown. The cabbage beetle Colaphellus bowringi could enter summer diapause under LD conditions. However, a non-photoperiodic-diapause (NPD) strain of this species, which was developed in our laboratory by artificial selection, could not enter diapause under LD photoperiod. Therefore, we identified circadian clock genes in this species and measured differences in their expression between a high diapause (HD) strain and the NPD strain to investigate the potential relationship between circadian clock genes and summer diapause induction in C. bowringi. We successfully cloned eight circadian clock genes and obtained intact ORFs of four; cryptochrome2, double-time, shaggy and vrille. Phylogenetic trees and sequence alignment analyses indicated that these circadian clock genes were conserved across insect taxa. The quantitative real-time PCR indicated that clock, cycle, period, timeless, cryptochrome2, and vrille were differentially expressed between HD and NPD strains reared under LD photoperiod during the diapause induction phase. These findings suggest the potential relationship between circadian clock genes and LD-regulated summer diapause induction in C. bowringi. Copyright © 2016 Elsevier B.V. All rights reserved.

  6. Inferring rooted species trees from unrooted gene trees using approximate Bayesian computation.

    Science.gov (United States)

    Alanzi, Ayed R A; Degnan, James H

    2017-11-01

    Methods for inferring species trees from gene trees motivated by incomplete lineage sorting typically use either rooted gene trees to infer a rooted species tree, or use unrooted gene trees to infer an unrooted species tree, which is then typically rooted using one or more outgroups. Theoretically, however, it has been known since 2011 that it is possible to consistently infer the root of the species tree directly from unrooted gene trees without assuming an outgroup. Here, we use approximate Bayesian computation to infer the root of the species tree from unrooted gene trees assuming the multispecies coalescent model. It is hoped that this approach will be useful in cases where an appropriate outgroup is difficult to find and gene trees do not follow a molecular clock. We use approximate Bayesian computation to infer the root of the species tree from unrooted gene trees. This approach could also be useful when there is prior information that makes a small number of root locations plausible in an unrooted species tree. Copyright © 2017 Elsevier Inc. All rights reserved.

  7. Arabidopsis circadian clock and photoperiodism: time to think about location

    OpenAIRE

    Imaizumi, Takato

    2009-01-01

    Plants possess a circadian clock that enables them to coordinate internal biological events with external daily changes. Recent studies in Arabidopsis revealed that tissue specific clock components exist and that the clock network architecture also varies within different organs. These findings indicate that the makeup of circadian clock(s) within a plant is quite variable. Plants utilize the circadian clock to measure day-length changes for regulating seasonal responses, such as flowering. T...

  8. A clock synchronization skeleton based on RTAI

    NARCIS (Netherlands)

    Huang, Y.; Visser, P.M.; Broenink, Johannes F.

    2006-01-01

    This paper presents a clock synchronization skeleton based on RTAI (Real Time Application Interface). The skeleton is a thin layer that provides unified but extendible interfaces to the underlying operating system, the synchronization algorithms and the upper level applications in need of clock

  9. Internal Clock Drift Estimation in Computer Clusters

    Directory of Open Access Journals (Sweden)

    Hicham Marouani

    2008-01-01

    Full Text Available Most computers have several high-resolution timing sources, from the programmable interrupt timer to the cycle counter. Yet, even at a precision of one cycle in ten millions, clocks may drift significantly in a single second at a clock frequency of several GHz. When tracing the low-level system events in computer clusters, such as packet sending or reception, each computer system records its own events using an internal clock. In order to properly understand the global system behavior and performance, as reported by the events recorded on each computer, it is important to estimate precisely the clock differences and drift between the different computers in the system. This article studies the clock precision and stability of several computer systems, with different architectures. It also studies the typical network delay characteristics, since time synchronization algorithms rely on the exchange of network packets and are dependent on the symmetry of the delays. A very precise clock, based on the atomic time provided by the GPS satellite network, was used as a reference to measure clock drifts and network delays. The results obtained are of immediate use to all applications which depend on computer clocks or network time synchronization accuracy.

  10. Could Atomic clocks be affected by neutrinos?

    CERN Document Server

    Hanafi, Hanaa

    2016-01-01

    An atomic clock is a clock device that uses an electronic transition frequency of the electromagnetic spectrum of atoms as a frequency standard in order to derive a time standard since time is the reciprocal of frequency. If the electronic transition frequencies are in an "optical region", we are talking in this case about optical atomic clocks. If they are in an "microwave region" these atomic clocks are made of the metallic element cesium so they are called Cesium atomic clocks. Atomic clocks are the most accurate time and frequency standards known despite the different perturbations that can affect them, a lot of researches were made in this domain to show how the transitions can be different for different type of perturbations..Since atomic clocks are very sensitive devices, based on coherent states (A coherent state tends to loose coherence after interacting). One question can arise (from a lot of questions) which is why cosmic neutrinos are not affecting these clocks? The answer to this question requir...

  11. Global synchronization of parallel processors using clock pulse width modulation

    Science.gov (United States)

    Chen, Dong; Ellavsky, Matthew R.; Franke, Ross L.; Gara, Alan; Gooding, Thomas M.; Haring, Rudolf A.; Jeanson, Mark J.; Kopcsay, Gerard V.; Liebsch, Thomas A.; Littrell, Daniel; Ohmacht, Martin; Reed, Don D.; Schenck, Brandon E.; Swetz, Richard A.

    2013-04-02

    A circuit generates a global clock signal with a pulse width modification to synchronize processors in a parallel computing system. The circuit may include a hardware module and a clock splitter. The hardware module may generate a clock signal and performs a pulse width modification on the clock signal. The pulse width modification changes a pulse width within a clock period in the clock signal. The clock splitter may distribute the pulse width modified clock signal to a plurality of processors in the parallel computing system.

  12. Laser controlled atom source for optical clocks

    Science.gov (United States)

    Kock, Ole; He, Wei; Świerad, Dariusz; Smith, Lyndsie; Hughes, Joshua; Bongs, Kai; Singh, Yeshpal

    2016-11-01

    Precision timekeeping has been a driving force in innovation, from defining agricultural seasons to atomic clocks enabling satellite navigation, broadband communication and high-speed trading. We are on the verge of a revolution in atomic timekeeping, where optical clocks promise an over thousand-fold improvement in stability and accuracy. However, complex setups and sensitivity to thermal radiation pose limitations to progress. Here we report on an atom source for a strontium optical lattice clock which circumvents these limitations. We demonstrate fast (sub 100 ms), cold and controlled emission of strontium atomic vapours from bulk strontium oxide irradiated by a simple low power diode laser. Our results demonstrate that millions of strontium atoms from the vapour can be captured in a magneto-optical trap (MOT). Our method enables over an order of magnitude reduction in scale of the apparatus. Future applications range from satellite clocks testing general relativity to portable clocks for inertial navigation systems and relativistic geodesy.

  13. The ozone-iodine-chlorate clock reaction.

    Directory of Open Access Journals (Sweden)

    Rafaela T P Sant'Anna

    Full Text Available This work presents a new clock reaction based on ozone, iodine, and chlorate that differs from the known chlorate-iodine clock reaction because it does not require UV light. The induction period for this new clock reaction depends inversely on the initial concentrations of ozone, chlorate, and perchloric acid but is independent of the initial iodine concentration. The proposed mechanism considers the reaction of ozone and iodide to form HOI, which is a key species for producing non-linear autocatalytic behavior. The novelty of this system lies in the presence of ozone, whose participation has never been observed in complex systems such as clock or oscillating reactions. Thus, the autocatalysis demonstrated in this new clock reaction should open the possibility for a new family of oscillating reactions.

  14. Cost and Precision of Brownian Clocks

    CERN Document Server

    Barato, Andre C

    2016-01-01

    Brownian clocks are biomolecular networks that can count time. A paradigmatic example are proteins that go through a cycle thus regulating some oscillatory behaviour in a living system. Typically, such a cycle requires free energy often provided by ATP hydrolysis. We investigate the relation between the precision of such a clock and its thermodynamic costs. For clocks driven by a constant thermodynamic force, a given precision requires a minimal cost that diverges as the uncertainty of the clock vanishes. In marked contrast, we show that a clock driven by a periodic variation of an external protocol can achieve arbitrary precision at arbitrarily low cost. This result constitutes a fundamental difference between processes driven by a fixed thermodynamic force and those driven periodically. As a main technical tool, we map a periodically driven system with a deterministic protocol to one subject to an external protocol that changes in stochastic time intervals, which simplifies calculations significantly. In th...

  15. Flowering Trees

    Indian Academy of Sciences (India)

    Flowering Trees. Dolichandrone atrovirens (Roth) K. Schum. (Spathe Trumpet Tree) of Bignoniaceae is a medium-sized handsome tree with a straight bole that branches at the top. Leaves are once pinnate, with two to three pairs of leaflets. Young parts of the tree are velvety. Inflorescence is a branched raceme borne at the ...

  16. Circadian clocks are designed optimally

    CERN Document Server

    Hasegawa, Yoshihiko

    2014-01-01

    Circadian rhythms are acquired through evolution to increase the chances for survival by synchronizing to the daylight cycle. Reliable synchronization is realized through two trade-off properties: regularity to keep time precisely, and entrainability to synchronize the internal time with daylight. Since both properties have been tuned through natural selection, their adaptation can be formalized in the framework of mathematical optimization. By using a succinct model, we found that simultaneous optimization of regularity and entrainability entails inherent features of the circadian mechanism irrespective of model details. At the behavioral level we discovered the existence of a dead zone, a time during which light pulses neither advance nor delay the clock. At the molecular level we demonstrate the role-sharing of two light inputs, phase advance and delay, as is well observed in mammals. We also reproduce the results of phase-controlling experiments and predict molecular elements responsible for the clockwork...

  17. The circadian clock regulates inflammatory arthritis.

    Science.gov (United States)

    Hand, Laura E; Hopwood, Thomas W; Dickson, Suzanna H; Walker, Amy L; Loudon, Andrew S I; Ray, David W; Bechtold, David A; Gibbs, Julie E

    2016-11-01

    There is strong diurnal variation in the symptoms and severity of chronic inflammatory diseases, such as rheumatoid arthritis. In addition, disruption of the circadian clock is an aggravating factor associated with a range of human inflammatory diseases. To investigate mechanistic links between the biological clock and pathways underlying inflammatory arthritis, mice were administered collagen (or saline as a control) to induce arthritis. The treatment provoked an inflammatory response within the limbs, which showed robust daily variation in paw swelling and inflammatory cytokine expression. Inflammatory markers were significantly repressed during the dark phase. Further work demonstrated an active molecular clock within the inflamed limbs and highlighted the resident inflammatory cells, fibroblast-like synoviocytes (FLSs), as a potential source of the rhythmic inflammatory signal. Exposure of mice to constant light disrupted the clock in peripheral tissues, causing loss of the nighttime repression of local inflammation. Finally, the results show that the core clock proteins cryptochrome (CRY) 1 and 2 repressed inflammation within the FLSs, and provide novel evidence that a CRY activator has anti-inflammatory properties in human cells. We conclude that under chronic inflammatory conditions, the clock actively represses inflammatory pathways during the dark phase. This interaction has exciting potential as a therapeutic avenue for treatment of inflammatory disease.-Hand, L. E., Hopwood, T. W., Dickson, S. H., Walker, A. L., Loudon, A. S. I., Ray, D. W., Bechtold, D. A., Gibbs, J. E. The circadian clock regulates inflammatory arthritis. © The Author(s).

  18. Time clock requirements for hospital physicians.

    Science.gov (United States)

    Shapira, Chen; Vilnai-Yavetz, Iris; Rafaeli, Anat; Zemel, Moran

    2016-06-01

    An agreement negotiated following a doctors' strike in 2011 introduced a requirement that physicians in Israel's public hospitals clock in and out when starting and leaving work. The press reported strong negative reactions to this policy and predicted doctors deserting hospitals en masse. This study examines physicians' reactions toward the clock-in/clock-out policy 6 months after its implementation, and assesses the relationship between these reactions and aspects of their employment context. 676 physicians in 42 hospitals responded to a survey assessing doctor's reactions toward the clock, hospital policy makers, and aspects of their work. Reactions to the clock were generally negative. Sense of calling correlated positively with negative reactions to the clock, and the latter correlated positively with quit intentions. However, overall, respondents reported a high sense of calling and low quit intentions. We suggest that sense of calling buffers and protects physicians from quit intentions. Differences in reactions to the clock were associated with different employment characteristics, but sense of calling did not vary by hospital size or type or by physicians' specialty. The findings offer insights into how physicians' working environment affects their reactions to regulatory interventions, and highlight medical professionalism as buffering reactions to unpopular regulatory policies. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  19. Molecular Architecture of the Mammalian Circadian Clock

    Science.gov (United States)

    Partch, Carrie L.; Green, Carla B.; Takahashi, Joseph S.

    2013-01-01

    Circadian clocks coordinate physiology and behavior with the 24-hour solar day to provide temporal homeostasis with the external environment. The molecular clocks that drive these intrinsic rhythmic changes are based on interlocked transcription/translation feedback loops that integrate with diverse environmental and metabolic stimuli to generate internal 24-hour timing. In this review we highlight recent advances in our understanding of the core molecular clock and how it utilizes diverse transcriptional and post-transcriptional mechanisms to impart temporal control onto mammalian physiology. Understanding the way in which biological rhythms are generated throughout the body may provide avenues for temporally-directed therapeutics to improve health and prevent disease. PMID:23916625

  20. Transcripts from the Circadian Clock: Telling Time and Season

    NARCIS (Netherlands)

    K. Brand (Karl)

    2011-01-01

    textabstractWe all know it when we wake mere moments before an alarm clock is scheduled to wake us: our body clock made the alarm clock redundant. This phenomenon is driven by an endogenous timer known as the biological, or circadian clock. Each revolution of the Earth about its own axis produces

  1. Sundials: Ancestors of Our Clocks

    Indian Academy of Sciences (India)

    The earliest of the sundials dates back to 5000 BC. But it is reasonable to assume that our ancestors used 'something like a sundial' for timekeeping even before. Cavemen, who noticed the way in which the shadows of tall trees varied with the daily movement of the Sun, would have been tempted to use it as a time keeper.

  2. Clock Drawing in Spatial Neglect: A Comprehensive Analysis of Clock Perimeter, Placement, and Accuracy

    Science.gov (United States)

    Chen, Peii; Goedert, Kelly M.

    2012-01-01

    Clock drawings produced by right-brain-damaged (RBD) individuals with spatial neglect often contain an abundance of empty space on the left while numbers and hands are placed on the right. However, the clock perimeter is rarely compromised in neglect patients’ drawings. By analyzing clock drawings produced by 71 RBD and 40 healthy adults, this study investigated whether the geometric characteristics of the clock perimeter reveal novel insights to understanding spatial neglect. Neglect participants drew smaller clocks than either healthy or non-neglect RBD participants. While healthy participants’ clock perimeter was close to circular, RBD participants drew radially extended ellipses. The mechanisms for these phenomena were investigated by examining the relation between clock-drawing characteristics and performance on six subtests of the Behavioral Inattention Test (BIT). The findings indicated that the clock shape was independent of any BIT subtest or the drawing placement on the test sheet and that the clock size was significantly predicted by one BIT subtest: the poorer the figure and shape copying, the smaller the clock perimeter. Further analyses revealed that in all participants, clocks decreased in size as they were placed farther from the center of the paper. However, even when neglect participants placed their clocks towards the center of the page, they were smaller than those produced by healthy or non-neglect RBD participants. These results suggest a neglect-specific reduction in the subjectively available workspace for graphic production from memory, consistent with the hypothesis that neglect patients are impaired in the ability to enlarge the attentional aperture. PMID:22390278

  3. The Mechanics of Mechanical Watches and Clocks

    CERN Document Server

    Du, Ruxu

    2013-01-01

    "The Mechanics of Mechanical Watches and Clocks" presents historical views and mathematical models of mechanical watches and clocks. Although now over six hundred years old, mechanical watches and clocks are still popular luxury items that fascinate many people around the world. However few have examined the theory of how they work as presented in this book. The illustrations and computer animations are unique and have never been published before. It will be of significant interest to researchers in mechanical engineering, watchmakers and clockmakers, as well as people who have an engineering background and are interested in mechanical watches and clocks. It will also inspire people in other fields of science and technology, such as mechanical engineering and electronics engineering, to advance their designs. Professor Ruxu Du works at the Chinese University of Hong Kong, China. Assistant Professor Longhan Xie works at the South China University of Technology, China.

  4. CDDIS_GNSS_products_clocks_final

    Data.gov (United States)

    National Aeronautics and Space Administration — Satellite and receiver clock products derived from analysis of Global Navigation Satellite System (GNSS) data. These products are the generated by analysis centers...

  5. CDDIS_GNSS_products_clocks_rapid

    Data.gov (United States)

    National Aeronautics and Space Administration — Satellite and receiver clock products derived from analysis of Global Navigation Satellite System (GNSS) data. These products are the generated by analysis centers...

  6. Mini Review: Circadian Clocks, Stress and Immunity

    Directory of Open Access Journals (Sweden)

    Rebecca eDumbell

    2016-05-01

    Full Text Available In mammals, molecular circadian clocks are present in most cells of the body, and this circadian network plays an important role in synchronizing physiological processes and behaviors to the appropriate time of day. The hypothalamic-pituitary-adrenal endocrine axis regulates the response to acute and chronic stress, acting through its final effectors – glucocorticoids – released from the adrenal cortex. Glucocorticoid secretion, characterized by its circadian rhythm, has an important role in synchronizing peripheral clocks and rhythms downstream of the master circadian pacemaker in the suprachiasmatic nucleus. Finally, glucocorticoids are powerfully anti-inflammatory, and recent work has implicated the circadian clock in various aspects and cells of the immune system, suggesting a tight interplay of stress and circadian systems in the regulation of immunity. This mini-review summarizes our current understanding of the role of the circadian clock network in both, the HPA axis and the immune system, and discusses their interactions.

  7. Cellular Reprogramming–Turning the Clock Back

    Indian Academy of Sciences (India)

    Cellular Reprogramming - Turning the Clock Back - Nobel Prize in Physiology or Medicine, 2012. Deepa Subramanyam ... Keywords. Embryonic stem cells; pluripotency; reprogramming; differentiation; Nobel Prize 2012. ... National Centre for Cell Science University of Pune Campus Ganeshkhind Pune 411 007, India.

  8. Draper Clock-Synchronization Protocol in SAL

    Data.gov (United States)

    National Aeronautics and Space Administration — In 1973, Daly, Hpokins, and McKenna (from Draper Lab.) presented a fault-tolerant digital clocking system at the FTCS conference. This is probably one of the first...

  9. Programmable Clock Waveform Generation for CCD Readout

    Energy Technology Data Exchange (ETDEWEB)

    Vicente, J. de; Castilla, J.; Martinez, G.; Marin, J.

    2006-07-01

    Charge transfer efficiency in CCDs is closely related to the clock waveform. In this paper, an experimental framework to explore different FPGA based clock waveform generator designs is described. Two alternative design approaches for controlling the rise/fall edge times and pulse width of the CCD clock signal have been implemented: level-control and time-control. Both approaches provide similar characteristics regarding the edge linearity and noise. Nevertheless, dissimilarities have been found with respect to the area and frequency range of application. Thus, while the time-control approach consumes less area, the level control approach provides a wider range of clock frequencies since it does not suffer capacitor discharge effect. (Author) 8 refs.

  10. Cell-permeable Circadian Clock Proteins

    National Research Council Canada - National Science Library

    Johnson, Carl

    2002-01-01

    .... These 'biological clocks' are important to human physiology. For example, psychiatric and medical studies have shown that circadian rhythmicity is involved in some forms of depressive illness, 'jet lag', drug tolerance/efficacy, memory, and insomnia...

  11. Entrainment of the Neurospora circadian clock

    NARCIS (Netherlands)

    Merrow, M; Boesl, C; Ricken, J; Messerschmitt, M; Goedel, M; Roenneberg, T

    2006-01-01

    Neurospora crassa has been systematically investigated for circadian entrainment behavior. Many aspects of synchronization can be investigated in this simple, cellular system, ranging from systematic entrainment and drivenness to masking. Clock gene expression during entrainment and entrainment

  12. Photoemission delay: The White Rabbit's clock

    Science.gov (United States)

    Calegari, Francesca

    2017-03-01

    Without a very precise timer one can never catch up with the electron released in photoemission. Attosecond streaking spectroscopy allows such a chronometer clock to be set to zero and reveals the role of electron correlations.

  13. Avian Circadian Organization: A Chorus of Clocks

    Science.gov (United States)

    Cassone, Vincent M

    2013-01-01

    In birds, biological clock function pervades all aspects of biology, controlling daily changes in sleep: wake, visual function, song, migratory patterns and orientation, as well as seasonal patterns of reproduction, song and migration. The molecular bases for circadian clocks are highly conserved, and it is likely the avian molecular mechanisms are similar to those expressed in mammals, including humans. The central pacemakers in the avian pineal gland, retinae and SCN dynamically interact to maintain stable phase relationships and then influence downstream rhythms through entrainment of peripheral oscillators in the brain controlling behavior and peripheral tissues. Birds represent an excellent model for the role played by biological clocks in human neurobiology; unlike most rodent models, they are diurnal, they exhibit cognitively complex social interactions, and their circadian clocks are more sensitive to the hormone melatonin than are those of nocturnal rodents. PMID:24157655

  14. Flowering Trees

    Indian Academy of Sciences (India)

    Flowering Trees. Brachichiton acerifolius F. Muell., commonly called as the Illawara flame tree is a member of Malvaceae family and is native to sub-tropical parts of Australia. Due to its spectacular flowers and tolerance to wide range of climates, it's now cultivated all over the world for its beauty. The tree produces flowers ...

  15. Flowering Trees

    Indian Academy of Sciences (India)

    IAS Admin

    Flowering Trees. Ailanthus excelsa Roxb. (INDIAN TREE OF. HEAVEN) of Simaroubaceae is a lofty tree with large pinnately compound alternate leaves, which are crowded at the branch ends; leaflets 8–14 pairs, very variable in shape and with irregularly toothed margin. Flowers are small and appear in large, lax, often ...

  16. Flowering Trees

    Indian Academy of Sciences (India)

    Srimath

    Flowering Trees. Grevillea robusta A. Cunn. ex R. Br. (Sil- ver Oak) of Proteaceae is a daintily lacy ornamental tree while young and growing into a mighty tree (45 m). Young shoots are silvery grey and the leaves are fern- like. Flowers are golden-yellow in one- sided racemes (10 cm). Fruit is a boat- shaped, woody follicle.

  17. Flowering Trees

    Indian Academy of Sciences (India)

    Flowering Trees. Boswellia serrata Roxb. ex Colebr. (Indian Frankincense tree) of Burseraceae is a large-sized deciduous tree that is native to India. Bark is thin, greenish-ash-coloured that exfoliates into smooth papery flakes. Stem exudes pinkish resin when cut. Leaves are once compound and are crowded at the branch ...

  18. Flowering Trees

    Indian Academy of Sciences (India)

    Srimath

    Flowering Trees. Couroupita guianensis Abul (Cannonball tree) of Lecythidaceae is a large semi-evergreen tree with a straight bole and spreading crown. Leaves are simple and clustered at the end of short branches. Flowers are large, showy, strongly scented with six fleshy perianth lobes. They are borne on long woody ...

  19. Biological clocks and the practice of psychiatry

    OpenAIRE

    Schulz, Pierre

    2007-01-01

    Endogenous biological clocks enable living species to acquire some independence in relation to time. They improve the efficiency of biological systems, by allowing them to anticipate future constraints on major physyological systems and cell energy metabolism. The temporal organization of a giwen biological function can be impaired in its coordination with astronomical time or with other biological function. There are also external conditions that influence biological clocks. This temporal or...

  20. Cesium Atomic Fountain Clocks at NMIJ

    Science.gov (United States)

    2010-11-01

    Wynands and S. Weyers, 2005, “Atomic fountain clocks,” Metrologia , 42, S64-S79. [2] M. Takamoto, F. L. Hong, R. Higashi, et al., 2005, “An optical...beam of laser-cooled cesium atoms,” Physical Review, A 60, R4241-R4244. [13] V. Gerginov, N. Nemitz, S. Weyers, et al., 2010, “Uncertainty evaluation of the caesium fountain clock PTB-CSF2,” Metrologia , 47, 65-79.

  1. Reduced Kalman Filters for Clock Ensembles

    Science.gov (United States)

    Greenhall, Charles A.

    2011-01-01

    This paper summarizes the author's work ontimescales based on Kalman filters that act upon the clock comparisons. The natural Kalman timescale algorithm tends to optimize long-term timescale stability at the expense of short-term stability. By subjecting each post-measurement error covariance matrix to a non-transparent reduction operation, one obtains corrected clocks with improved short-term stability and little sacrifice of long-term stability.

  2. Clock gene variation in Tachycineta swallows

    Science.gov (United States)

    Dor, Roi; Cooper, Caren B; Lovette, Irby J; Massoni, Viviana; Bulit, Flor; Liljesthrom, Marcela; Winkler, David W

    2012-01-01

    Many animals use photoperiod cues to synchronize reproduction with environmental conditions and thereby improve their reproductive success. The circadian clock, which creates endogenous behavioral and physiological rhythms typically entrained to photoperiod, is well characterized at the molecular level. Recent work provided evidence for an association between Clock poly-Q length polymorphism and latitude and, within a population, an association with the date of laying and the length of the incubation period. Despite relatively high overall breeding synchrony, the timing of clutch initiation has a large impact on the fitness of swallows in the genus Tachycineta. We compared length polymorphism in the Clock poly-Q region among five populations from five different Tachycineta species that breed across a hemisphere-wide latitudinal gradient (Fig. 1). Clock poly-Q variation was not associated with latitude; however, there was an association between Clock poly-Q allele diversity and the degree of clutch size decline within breeding seasons. We did not find evidence for an association between Clock poly-Q variation and date of clutch initiation in for any of the five Tachycineta species, nor did we found a relationship between incubation duration and Clock genotype. Thus, there is no general association between latitude, breeding phenology, and Clock polymorphism in this clade of closely related birds. Figure 1 Photos of Tachycineta swallows that were used in this study: A) T. bicolor from Ithaca, New York, B) T. leucorrhoa from Chascomús, Argentina, C) T. albilinea from Hill Bank, Belize, D) T. meyeni from Puerto Varas, Chile, and E) T. thalassina from Mono Lake, California, Photographers: B: Valentina Ferretti; A, C-E: David Winkler. PMID:22408729

  3. Direct Laser Cooling Al{}^{+} Ion Optical Clocks

    Science.gov (United States)

    Zhang, Jie; Deng, Ke; Luo, Jun; Lu, Ze-Huang

    2017-05-01

    The Al {}+ ion optical clock is a very promising optical frequency standard candidate due to its extremely small black-body radiation shift. It has been successfully demonstrated with the indirect cooled, quantum-logic-based spectroscopy technique. Its accuracy is limited by second-order Doppler shift, and its stability is limited by the number of ions that can be probed in quantum logic processing. We propose a direct laser cooling scheme of Al {}+ ion optical clocks where both the stability and accuracy of the clocks are greatly improved. In the proposed scheme, two Al {}+ traps are utilized. The first trap is used to trap a large number of Al {}+ ions to improve the stability of the clock laser, while the second trap is used to trap a single Al {}+ ion to provide the ultimate accuracy. Both traps are cooled with a continuous wave 167 nm laser. The expected clock laser stability can reach 9.0× {10}-17/\\sqrt{τ }. For the second trap, in addition to 167 nm laser Doppler cooling, a second stage pulsed 234 nm two-photon cooling laser is utilized to further improve the accuracy of the clock laser. The total systematic uncertainty can be reduced to about 1× {10}-18. The proposed Al {}+ ion optical clock has the potential to become the most accurate and stable optical clock. Supported by the National Basic Research Program of China under Grant No 2012CB821300, the National Natural Science Foundation of China under Grant Nos 91336213, 11304109, 91536116 and 11174095, and the Program for New Century Excellent Talents by the Ministry of Education under Grant No NCET-11-0176.

  4. Clock Genes Control Cortical Critical Period Timing

    OpenAIRE

    Kobayashi, Yohei; Ye, Zhanlei; Hensch, Takao K.

    2015-01-01

    Circadian rhythms control a variety of physiological processes, but whether they may also time brain development remains largely unknown. Here, we show that circadian clock genes control the onset of critical period plasticity in the neocortex. Within visual cortex of Clock-deficient mice, the emergence of circadian gene expression was dampened, and the maturation of inhibitory parvalbumin (PV)-cell networks slowed. Loss of visual acuity in response to brief monocular deprivation was concomit...

  5. Do Caucasian and Asian clocks tick differently?

    Directory of Open Access Journals (Sweden)

    A.A. Barbosa

    Full Text Available The Period 3 and Clock genes are important components of the mammalian molecular circadian system. Studies have shown association between polymorphisms in these clock genes and circadian phenotypes in different populations. Nevertheless, differences in the pattern of allele frequency and genotyping distribution are systematically observed in studies with different ethnic groups. To investigate and compare the pattern of distribution in a sample of Asian and Caucasian populations living in Brazil, we evaluated two well-studied polymorphisms in the clock genes: a variable number of tandem repeats (VNTR in PER3 and a single nucleotide polymorphism (SNP in CLOCK. The aim of this investigation was to search for clues about human evolutionary processes related to circadian rhythms. We selected 109 Asian and 135 Caucasian descendants. The frequencies of the shorter allele (4 repeats in the PER3 gene and the T allele in the CLOCK gene among Asians (0.86 and 0.84, respectively were significantly higher than among Caucasians (0.69 and 0.71, respectively. Our results directly confirmed the different distribution of these polymorphisms between the Asian and Caucasian ethnic groups. Given the genetic differences found between groups, two points became evident: first, ethnic variations may have implications for the interpretation of results in circadian rhythm association studies, and second, the question may be raised about which evolutionary conditions shaped these genetic clock variations.

  6. Do Caucasian and Asian clocks tick differently?

    Science.gov (United States)

    Barbosa, A A; Pedrazzoli, M; Koike, B D V; Tufik, S

    2010-01-01

    The Period 3 and Clock genes are important components of the mammalian molecular circadian system. Studies have shown association between polymorphisms in these clock genes and circadian phenotypes in different populations. Nevertheless, differences in the pattern of allele frequency and genotyping distribution are systematically observed in studies with different ethnic groups. To investigate and compare the pattern of distribution in a sample of Asian and Caucasian populations living in Brazil, we evaluated two well-studied polymorphisms in the clock genes: a variable number of tandem repeats (VNTR) in PER3 and a single nucleotide polymorphism (SNP) in CLOCK. The aim of this investigation was to search for clues about human evolutionary processes related to circadian rhythms. We selected 109 Asian and 135 Caucasian descendants. The frequencies of the shorter allele (4 repeats) in the PER3 gene and the T allele in the CLOCK gene among Asians (0.86 and 0.84, respectively) were significantly higher than among Caucasians (0.69 and 0.71, respectively). Our results directly confirmed the different distribution of these polymorphisms between the Asian and Caucasian ethnic groups. Given the genetic differences found between groups, two points became evident: first, ethnic variations may have implications for the interpretation of results in circadian rhythm association studies, and second, the question may be raised about which evolutionary conditions shaped these genetic clock variations.

  7. Cost and Precision of Brownian Clocks

    Directory of Open Access Journals (Sweden)

    Andre C. Barato

    2016-12-01

    Full Text Available Brownian clocks are biomolecular networks that can count time. A paradigmatic example are proteins that go through a cycle, thus regulating some oscillatory behavior in a living system. Typically, such a cycle requires free energy often provided by ATP hydrolysis. We investigate the relation between the precision of such a clock and its thermodynamic costs. For clocks driven by a constant thermodynamic force, a given precision requires a minimal cost that diverges as the uncertainty of the clock vanishes. In marked contrast, we show that a clock driven by a periodic variation of an external protocol can achieve arbitrary precision at arbitrarily low cost. This result constitutes a fundamental difference between processes driven by a fixed thermodynamic force and those driven periodically. As a main technical tool, we map a periodically driven system with a deterministic protocol to one subject to an external protocol that changes in stochastic time intervals, which simplifies calculations significantly. In the nonequilibrium steady state of the resulting bipartite Markov process, the uncertainty of the clock can be deduced from the calculable dispersion of a corresponding current.

  8. Cost and Precision of Brownian Clocks

    Science.gov (United States)

    Barato, Andre C.; Seifert, Udo

    2016-10-01

    Brownian clocks are biomolecular networks that can count time. A paradigmatic example are proteins that go through a cycle, thus regulating some oscillatory behavior in a living system. Typically, such a cycle requires free energy often provided by ATP hydrolysis. We investigate the relation between the precision of such a clock and its thermodynamic costs. For clocks driven by a constant thermodynamic force, a given precision requires a minimal cost that diverges as the uncertainty of the clock vanishes. In marked contrast, we show that a clock driven by a periodic variation of an external protocol can achieve arbitrary precision at arbitrarily low cost. This result constitutes a fundamental difference between processes driven by a fixed thermodynamic force and those driven periodically. As a main technical tool, we map a periodically driven system with a deterministic protocol to one subject to an external protocol that changes in stochastic time intervals, which simplifies calculations significantly. In the nonequilibrium steady state of the resulting bipartite Markov process, the uncertainty of the clock can be deduced from the calculable dispersion of a corresponding current.

  9. Network features of the mammalian circadian clock.

    Directory of Open Access Journals (Sweden)

    Julie E Baggs

    2009-03-01

    Full Text Available The mammalian circadian clock is a cell-autonomous system that drives oscillations in behavior and physiology in anticipation of daily environmental change. To assess the robustness of a human molecular clock, we systematically depleted known clock components and observed that circadian oscillations are maintained over a wide range of disruptions. We developed a novel strategy termed Gene Dosage Network Analysis (GDNA in which small interfering RNA (siRNA-induced dose-dependent changes in gene expression were used to build gene association networks consistent with known biochemical constraints. The use of multiple doses powered the analysis to uncover several novel network features of the circadian clock, including proportional responses and signal propagation through interacting genetic modules. We also observed several examples where a gene is up-regulated following knockdown of its paralog, suggesting the clock network utilizes active compensatory mechanisms rather than simple redundancy to confer robustness and maintain function. We propose that these network features act in concert as a genetic buffering system to maintain clock function in the face of genetic and environmental perturbation.

  10. Do Caucasian and Asian clocks tick differently?

    Directory of Open Access Journals (Sweden)

    A.A. Barbosa

    2010-01-01

    Full Text Available The Period 3 and Clock genes are important components of the mammalian molecular circadian system. Studies have shown association between polymorphisms in these clock genes and circadian phenotypes in different populations. Nevertheless, differences in the pattern of allele frequency and genotyping distribution are systematically observed in studies with different ethnic groups. To investigate and compare the pattern of distribution in a sample of Asian and Caucasian populations living in Brazil, we evaluated two well-studied polymorphisms in the clock genes: a variable number of tandem repeats (VNTR in PER3 and a single nucleotide polymorphism (SNP in CLOCK. The aim of this investigation was to search for clues about human evolutionary processes related to circadian rhythms. We selected 109 Asian and 135 Caucasian descendants. The frequencies of the shorter allele (4 repeats in the PER3 gene and the T allele in the CLOCK gene among Asians (0.86 and 0.84, respectively were significantly higher than among Caucasians (0.69 and 0.71, respectively. Our results directly confirmed the different distribution of these polymorphisms between the Asian and Caucasian ethnic groups. Given the genetic differences found between groups, two points became evident: first, ethnic variations may have implications for the interpretation of results in circadian rhythm association studies, and second, the question may be raised about which evolutionary conditions shaped these genetic clock variations.

  11. Clock genes control cortical critical period timing.

    Science.gov (United States)

    Kobayashi, Yohei; Ye, Zhanlei; Hensch, Takao K

    2015-04-08

    Circadian rhythms control a variety of physiological processes, but whether they may also time brain development remains largely unknown. Here, we show that circadian clock genes control the onset of critical period plasticity in the neocortex. Within visual cortex of Clock-deficient mice, the emergence of circadian gene expression was dampened, and the maturation of inhibitory parvalbumin (PV) cell networks slowed. Loss of visual acuity in response to brief monocular deprivation was concomitantly delayed and rescued by direct enhancement of GABAergic transmission. Conditional deletion of Clock or Bmal1 only within PV cells recapitulated the results of total Clock-deficient mice. Unique downstream gene sets controlling synaptic events and cellular homeostasis for proper maturation and maintenance were found to be mis-regulated by Clock deletion specifically within PV cells. These data demonstrate a developmental role for circadian clock genes outside the suprachiasmatic nucleus, which may contribute mis-timed brain plasticity in associated mental disorders. Copyright © 2015 Elsevier Inc. All rights reserved.

  12. Modeling the mammalian circadian clock

    Science.gov (United States)

    Jolley, Craig; Ueda, Hiroki

    2012-02-01

    In biology, important processes often depend on a temporal schedule. The 24-hour periodicity of solar illumination caused by the earth's rotation has consequences for environmental factors such as temperature and humidity as well as ecological factors such as the presence of food, predators, or potential mates. As a result, many organisms have evolved to develop a circadian clock that allows them to anticipate these environmental changes in the absence of direct temporal cues. In recent years, extensive efforts have been made to deconstruct the biological clockwork from various organisms, develop mathematical models of circadian function, and construct synthetic analogues to test our understanding. My present work has two major foci. First, we have used regulatory principles revealed by recent experimental work to construct a model of the core genetic oscillator of the mammalian circadian system that captures key system-level behaviors. Second, we are exploring the possibility of a post-translational phosphorylation-based oscillator that is coupled to the core oscillator, conferring enhanced robustness and stability on the complete system. A simple model of this post-translational oscillator reveals key design constraints that must be satisfied by any such oscillator.

  13. The clock in the cell : Entrainment of the circadian clock in Neurospora crassa

    NARCIS (Netherlands)

    Madeti Jyothi-Boesl, Cornelia

    2008-01-01

    Since reports of daily leaf movements 2000 years ago, a so-called circadian clock (‘circa diem’ meaning ‘about a day’) has been described in organisms from almost all phyla. The work presented in this thesis gives special emphasis on the circadian clock in the fungus Neurospora crassa, a rather

  14. The Circadian Clock Mutation Promotes Intestinal Dysbiosis.

    Science.gov (United States)

    Voigt, Robin M; Summa, Keith C; Forsyth, Christopher B; Green, Stefan J; Engen, Phillip; Naqib, Ankur; Vitaterna, Martha H; Turek, Fred W; Keshavarzian, Ali

    2016-02-01

    Circadian rhythm disruption is a prevalent feature of modern day society that is associated with an increase in pro-inflammatory diseases, and there is a clear need for a better understanding of the mechanism(s) underlying this phenomenon. We have previously demonstrated that both environmental and genetic circadian rhythm disruption causes intestinal hyperpermeability and exacerbates alcohol-induced intestinal hyperpermeability and liver pathology. The intestinal microbiota can influence intestinal barrier integrity and impact immune system function; thus, in this study, we sought to determine whether genetic alteration of the core circadian clock gene, Clock, altered the intestinal microbiota community. Male Clock(Δ19) -mutant mice (mice homozygous for a dominant-negative-mutant allele) or littermate wild-type mice were fed 1 of 3 experimental diets: (i) a standard chow diet, (ii) an alcohol-containing diet, or (iii) an alcohol-control diet in which the alcohol calories were replaced with dextrose. Stool microbiota was assessed with 16S ribosomal RNA gene amplicon sequencing. The fecal microbial community of Clock-mutant mice had lower taxonomic diversity, relative to wild-type mice, and the Clock(Δ19) mutation was associated with intestinal dysbiosis when mice were fed either the alcohol-containing or the control diet. We found that alcohol consumption significantly altered the intestinal microbiota in both wild-type and Clock-mutant mice. Our data support a model by which circadian rhythm disruption by the Clock(Δ19) mutation perturbs normal intestinal microbial communities, and this trend was exacerbated in the context of a secondary dietary intestinal stressor. Copyright © 2016 by the Research Society on Alcoholism.

  15. Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution.

    Science.gov (United States)

    Warnock, Rachel C M; Yang, Ziheng; Donoghue, Philip C J

    2017-06-28

    Molecular sequence data provide information about relative times only, and fossil-based age constraints are the ultimate source of information about absolute times in molecular clock dating analyses. Thus, fossil calibrations are critical to molecular clock dating, but competing methods are difficult to evaluate empirically because the true evolutionary time scale is never known. Here, we combine mechanistic models of fossil preservation and sequence evolution in simulations to evaluate different approaches to constructing fossil calibrations and their impact on Bayesian molecular clock dating, and the relative impact of fossil versus molecular sampling. We show that divergence time estimation is impacted by the model of fossil preservation, sampling intensity and tree shape. The addition of sequence data may improve molecular clock estimates, but accuracy and precision is dominated by the quality of the fossil calibrations. Posterior means and medians are poor representatives of true divergence times; posterior intervals provide a much more accurate estimate of divergence times, though they may be wide and often do not have high coverage probability. Our results highlight the importance of increased fossil sampling and improved statistical approaches to generating calibrations, which should incorporate the non-uniform nature of ecological and temporal fossil species distributions. © 2017 The Authors.

  16. Clock drawing: analysis in a retirement community.

    Science.gov (United States)

    Paganini-Hill, A; Clark, L J; Henderson, V W; Birge, S J

    2001-07-01

    To test the hypothesis that performance on a clock-drawing test in a mailed survey to an older cohort is associated with known and potential risk and protective factors for Alzheimer's disease. The Leisure World Cohort Study is an ongoing study, begun in 1981, of nearly 14,000 older adults. In November 1992, the 8,406 living cohort members were mailed a follow-up questionnaire. Leisure World Laguna Hills, a southern California retirement community. The study population is a predominantly white, well-educated, upper-middle-class community; approximately two-thirds are women. Data from 4,843 cohort members (mean age 80 years; range 52-101) were analyzed. The questionnaire included a clock-drawing task: a predrawn circle 3 1/4 inches (8.3 cm) in diameter was provided with instructions "In the circle below, draw in the numbers as on a clock face. Make no erasures." Clocks were scored on 7 items: all numbers 1-12 present without adding extra or omitting numbers, sequencing of numbers, position of numbers, orientation of numbers to circle, consistent number style (either Arabic or Roman), tilt of numbers, and superfluous marks. A total clock score was calculated by summing the number of correct individual items (0-7). We also classified individuals as cognitively impaired by a previously suggested method: individuals were affected if they did not have three numbers drawn in the upper left quadrant of the clock face. Ninety percent or more of the participants across all ages placed the numbers 1 to 12 on their clocks without omissions or additions; 35% completed the clock drawing without error. The mean total clock scores decreased with each successive 5-year age group in both men and women. Regression analysis indicated a significant effect for age (b = -0.15, P education (b = 0.05, P =.0001), smoking (b = 0.13, P =.03), and female gender (b = -0.05, P =.05) and a marginally significant effect of nonrheumatoid arthritis (b = 0.05, P =.07) on total clock score. No other

  17. Circadian clock genes in Drosophila: recent developments.

    Science.gov (United States)

    Subramanian, P; Balamurugan, E; Suthakar, G

    2003-08-01

    Circadian rhythms provide a temporal framework to living organisms and are established in a majority of eukaryotes and in a few prokaryotes. The molecular mechanisms of circadian clock is constantly being investigated in Drosophila melanogaster. The core of the clock mechanism was described by a transcription-translation feedback loop model involving period (per), timeless (tim), dclock and cycle genes. However, recent research has identified multiple feedback loops controlling rhythm generation and expression. Novel mutations of timeless throw more light on the functions of per and tim products. Analysis of pdf neuropeptide gene (expressed in circadian pacemaker cells in Drosophila), indicate that PDF acts as the principal circadian transmitter and is involved in output pathways. The product of cryptochrome is known to function as a circadian photoreceptor as well as component of the circadian clock. This review focuses on the recent progress in the field of molecular rhythm research in the fruit fly. The gene(s) and the gene product(s) that are involved in the transmission of environmental information to the clock, as well as the timing signals from the clock outward to cellular functions are remain to be determined.

  18. Feasibility of an optical fiber clock

    Science.gov (United States)

    Ilinova, Ekaterina; Babb, James F.; Derevianko, Andrei

    2017-09-01

    We explore the feasibility of a fiber clock, i.e., a compact, high-precision, optical lattice atomic clock based on atoms trapped inside a hollow-core optical fiber. Such a setup offers an intriguing potential both for a substantially increased number of interrogated atoms (and thereby an improved clock stability) and for miniaturization. We evaluate the sensitivity of the 1S0-3P0 clock transition in Hg and other divalent atoms to the fiber inner core surface at nonzero temperatures. The Casimir-Polder interaction induced 1S0-3P0 transition frequency shift is calculated for the atom inside the hollow capillary as a function of atomic position, capillary material, and geometric parameters. For Hg atoms on the axis of a silica capillary with inner radius ≥15 μ m and optimally chosen thickness d ˜1 μ m , the atom-surface interaction induced 1S0-3P0 clock transition frequency shift can be kept on the level δ ν /νHg˜10-19 . We also estimate the atom loss and heating due to collisions with the buffer gas, lattice intensity noise induced heating, spontaneous photon scattering heating, and residual birefringence induced frequency shifts.

  19. Dating phylogenies with hybrid local molecular clocks.

    Directory of Open Access Journals (Sweden)

    Stéphane Aris-Brosou

    Full Text Available BACKGROUND: Because rates of evolution and species divergence times cannot be estimated directly from molecular data, all current dating methods require that specific assumptions be made before inferring any divergence time. These assumptions typically bear either on rates of molecular evolution (molecular clock hypothesis, local clocks models or on both rates and times (penalized likelihood, Bayesian methods. However, most of these assumptions can affect estimated dates, oftentimes because they underestimate large amounts of rate change. PRINCIPAL FINDINGS: A significant modification to a recently proposed ad hoc rate-smoothing algorithm is described, in which local molecular clocks are automatically placed on a phylogeny. This modification makes use of hybrid approaches that borrow from recent theoretical developments in microarray data analysis. An ad hoc integration of phylogenetic uncertainty under these local clock models is also described. The performance and accuracy of the new methods are evaluated by reanalyzing three published data sets. CONCLUSIONS: It is shown that the new maximum likelihood hybrid methods can perform better than penalized likelihood and almost as well as uncorrelated Bayesian models. However, the new methods still tend to underestimate the actual amount of rate change. This work demonstrates the difficulty of estimating divergence times using local molecular clocks.

  20. Evolutionary links between circadian clocks and photoperiodic diapause in insects.

    Science.gov (United States)

    Meuti, Megan E; Denlinger, David L

    2013-07-01

    In this article, we explore links between circadian clocks and the clock involved in photoperiodic regulation of diapause in insects. Classical resonance (Nanda-Hamner) and night interruption (Bünsow) experiments suggest a circadian basis for the diapause response in nearly all insects that have been studied. Neuroanatomical studies reveal physical connections between circadian clock cells and centers controlling the photoperiodic diapause response, and both mutations and knockdown of clock genes with RNA interference (RNAi) point to a connection between the clock genes and photoperiodic induction of diapause. We discuss the challenges of determining whether the clock, as a functioning module, or individual clock genes acting pleiotropically are responsible for the photoperiodic regulation of diapause, and how a stable, central circadian clock could be linked to plastic photoperiodic responses without compromising the clock's essential functions. Although we still lack an understanding of the exact mechanisms whereby insects measure day/night length, continued classical and neuroanatomical approaches, as well as forward and reverse genetic experiments, are highly complementary and should enable us to decipher the diverse ways in which circadian clocks have been involved in the evolution of photoperiodic induction of diapause in insects. The components of circadian clocks vary among insect species, and diapause appears to have evolved independently numerous times, thus, we anticipate that not all photoperiodic clocks of insects will interact with circadian clocks in the same fashion.

  1. Sugars, the clock and transition to flowering

    Directory of Open Access Journals (Sweden)

    Mohammad Reza eBolouri Moghaddam

    2013-02-01

    Full Text Available Sugars do not only act as source of energy, but they also act as signals in plants. This mini review summarizes the emerging links between sucrose-mediated signaling and the cellular networks involved in flowering time control and defense. Cross-talks with gibberellin (GA and jasmonate (JA signaling pathways are highlighted. The circadian clock fulfills a crucial role at the heart of cellular networks and the bilateral relation between sugar signaling and the clock is discussed. It is proposed that important factors controlling plant growth (DELLAs, PIFs, invertases and trehalose- 6-phosphate or T6P might fulfill central roles in the transition to flowering as well. The emerging concept of ‘sweet immunity’, modulated by the clock, might at least partly rely on a sucrose-specific signaling pathway that needs further exploration.

  2. Susceptibility of Redundant Versus Singular Clock Domains Implemented in SRAM-Based FPGA TMR Designs

    Science.gov (United States)

    Berg, Melanie D.; LaBel, Kenneth A.; Pellish, Jonathan

    2016-01-01

    We present the challenges that arise when using redundant clock domains due to their clock-skew. Radiation data show that a singular clock domain (DTMR) provides an improved TMR methodology for SRAM-based FPGAs over redundant clocks.

  3. DLRS: gene tree evolution in light of a species tree.

    Science.gov (United States)

    Sjöstrand, Joel; Sennblad, Bengt; Arvestad, Lars; Lagergren, Jens

    2012-11-15

    PrIME-DLRS (or colloquially: 'Delirious') is a phylogenetic software tool to simultaneously infer and reconcile a gene tree given a species tree. It accounts for duplication and loss events, a relaxed molecular clock and is intended for the study of homologous gene families, for example in a comparative genomics setting involving multiple species. PrIME-DLRS uses a Bayesian MCMC framework, where the input is a known species tree with divergence times and a multiple sequence alignment, and the output is a posterior distribution over gene trees and model parameters. PrIME-DLRS is available for Java SE 6+ under the New BSD License, and JAR files and source code can be downloaded from http://code.google.com/p/jprime/. There is also a slightly older C++ version available as a binary package for Ubuntu, with download instructions at http://prime.sbc.su.se. The C++ source code is available upon request. joel.sjostrand@scilifelab.se or jens.lagergren@scilifelab.se. PrIME-DLRS is based on a sound probabilistic model (Åkerborg et al., 2009) and has been thoroughly validated on synthetic and biological datasets (Supplementary Material online).

  4. Sample-Clock Phase-Control Feedback

    Science.gov (United States)

    Quirk, Kevin J.; Gin, Jonathan W.; Nguyen, Danh H.; Nguyen, Huy

    2012-01-01

    To demodulate a communication signal, a receiver must recover and synchronize to the symbol timing of a received waveform. In a system that utilizes digital sampling, the fidelity of synchronization is limited by the time between the symbol boundary and closest sample time location. To reduce this error, one typically uses a sample clock in excess of the symbol rate in order to provide multiple samples per symbol, thereby lowering the error limit to a fraction of a symbol time. For systems with a large modulation bandwidth, the required sample clock rate is prohibitive due to current technological barriers and processing complexity. With precise control of the phase of the sample clock, one can sample the received signal at times arbitrarily close to the symbol boundary, thus obviating the need, from a synchronization perspective, for multiple samples per symbol. Sample-clock phase-control feedback was developed for use in the demodulation of an optical communication signal, where multi-GHz modulation bandwidths would require prohibitively large sample clock frequencies for rates in excess of the symbol rate. A custom mixedsignal (RF/digital) offset phase-locked loop circuit was developed to control the phase of the 6.4-GHz clock that samples the photon-counting detector output. The offset phase-locked loop is driven by a feedback mechanism that continuously corrects for variation in the symbol time due to motion between the transmitter and receiver as well as oscillator instability. This innovation will allow significant improvements in receiver throughput; for example, the throughput of a pulse-position modulation (PPM) with 16 slots can increase from 188 Mb/s to 1.5 Gb/s.

  5. Overall alteration of circadian clock gene expression in the chestnut cold response.

    Directory of Open Access Journals (Sweden)

    Cristian Ibañez

    Full Text Available Cold acclimation in woody plants may have special features compared to similar processes in herbaceous plants. Recent studies have shown that circadian clock behavior in the chestnut tree (Castanea sativa is disrupted by cold temperatures and that the primary oscillator feedback loop is not functional at 4 degrees C or in winter. In these conditions, CsTOC1 and CsLHY genes are constantly expressed. Here, we show that this alteration also affects CsPRR5, CsPRR7 and CsPRR9. These genes are homologous to the corresponding Arabidopsis PSEUDO-RESPONSE REGULATOR genes, which are also components of the circadian oscillator feedback network. The practically constant presence of mRNAs of the 5 chestnut genes at low temperature reveals an unknown aspect of clock regulation and suggests a mechanism regulating the transcription of oscillator genes as a whole.

  6. Flowering Trees

    Indian Academy of Sciences (India)

    Srimath

    (Indian Coral Tree;Hindi:Pangra)of Leguminosae is a small, quick-growing deciduous tree with a small crown. Branches are covered with dark conical prickles, which fall off after some time. The leaves are compound with three leaflets. Bright red or scarlet flowers which appear following leaf fall are in clusters at branch ends.

  7. Talking Trees

    Science.gov (United States)

    Tolman, Marvin

    2005-01-01

    Students love outdoor activities and will love them even more when they build confidence in their tree identification and measurement skills. Through these activities, students will learn to identify the major characteristics of trees and discover how the pace--a nonstandard measuring unit--can be used to estimate not only distances but also the…

  8. Flowering Trees

    Indian Academy of Sciences (India)

    Gyrocarpus americanus Jacq. (Helicopter Tree) of Hernandiaceae is a moderate size deciduous tree that grows to about 12 m in height with a smooth, shining, greenish-white bark. The leaves are ovate, rarely irregularly lobed, dark green above and pale grey underneath. They are 3-nerved from the base and often ...

  9. Flowering Trees

    Indian Academy of Sciences (India)

    Cassia siamia Lamk. (Siamese tree senna) of Caesalpiniaceae is a small or medium size handsome tree. Leaves are alternate, pinnately compound and glandular, upto 18 cm long with 8–12 pairs of leaflets. Inflorescence is axillary or terminal and branched. Flowering lasts for a long period from March to February.

  10. Flowering Trees

    Indian Academy of Sciences (India)

    Srimath

    Flowering Trees. Diospyros montana Roxb. (Mountain Ebony) of. Ebenaceae is a medium size deciduous tree with slim, straight trunk and narrow open crown. Leaves are simple, elliptic and leathery. Young leaves are covered with dense velvety growth of hairs. Flow- ers are small, unisexual, males in groups of four or.

  11. Flowering Trees

    Indian Academy of Sciences (India)

    Flowering Trees. Acrocarpus fraxinifolius Wight & Arn. (PINK CEDAR, AUSTRALIAN ASH) of. Caesalpiniaceae is a lofty unarmed deciduous native tree that attains a height of 30–60m with buttresses. Bark is thin and light grey. Leaves are compound and bright red when young. Flowers in dense, erect, axillary racemes.

  12. Flowering Trees

    Indian Academy of Sciences (India)

    IAS Admin

    Flowering Trees. Alangium salviifolium (L.f.) Wangerin ssp. salviifolium (SAGE-. LEAVED ALANGIUM) of Alangiaceae is a small deciduous tree, sometimes straggling and sometimes spinous. Leaves are alternate, variable, narrowly oblong or ovate-lanceolate. Flowers are in axillary fascicles. They are 1.5–2 cms long, white ...

  13. Flowering Trees

    Indian Academy of Sciences (India)

    Flowering Trees. Diospyros peregrina (Gaertn.) Guercke Syn. Diospyros embryopteris Pers., Diospyros malabarica Desr. (PALE MOON EBONY, RIBER EBONY) of Ebenaceae is a small or mid-sized slow-growing evergreen tree with spreading branches that form a dense crown. The bark is smooth, thick, dark and flakes off ...

  14. Flowering Trees

    Indian Academy of Sciences (India)

    Baccaurea courtallensis Muell.-Arg. of Euphorbiaceae is an evergreen tree that is very attractive when in flower. Leaves are alternate. Male and female flowers are borne on separate trees. Inflorescences bearing several flowers arise in tufts on tubercles on the stem. Fruits are crimson red in colour. Seeds are covered.

  15. :Flowering 'Trees

    Indian Academy of Sciences (India)

    :Flowering 'Trees. Prima Vera of Mexico (botanical name: Cybistex donell-smithii) The tree planted in 1973 in the RRllawn at the spot where Prof Raman s body was cremated on 21. November 1970 flowered with a magnificient golden crown on the concluding day of the Golden Jubilee of the Institute. 4th February 1999.

  16. Clock frequency estimation under spontaneous emission

    Science.gov (United States)

    Qin, Xi-Zhou; Huang, Jia-Hao; Zhong, Hong-Hua; Lee, Chaohong

    2018-02-01

    We investigate the quantum dynamics of a driven two-level system under spontaneous emission and its application in clock frequency estimation. By using the Lindblad equation to describe the system, we analytically obtain its exact solutions, which show three different regimes: Rabi oscillation, damped oscillation, and overdamped decay. From the analytical solutions, we explore how the spontaneous emission affects the clock frequency estimation. We find that under a moderate spontaneous emission rate, the transition frequency can still be inferred from the Rabi oscillation. Our results enable potential practical applications in frequency measurement and quantum control under decoherence.

  17. Clocking Scheme for Switched-Capacitor Circuits

    DEFF Research Database (Denmark)

    Steensgaard-Madsen, Jesper

    1998-01-01

    A novel clocking scheme for switched-capacitor (SC) circuits is presented. It can enhance the understanding of SC circuits and the errors caused by MOSFET (MOS) switches. Charge errors, and techniques to make SC circuits less sensitive to them are discussed.......A novel clocking scheme for switched-capacitor (SC) circuits is presented. It can enhance the understanding of SC circuits and the errors caused by MOSFET (MOS) switches. Charge errors, and techniques to make SC circuits less sensitive to them are discussed....

  18. A transportable optical clock for chronometric levelling

    Science.gov (United States)

    Lisdat, C.; Koller, S. B.; Grotti, J.; Vogt, S.; Al-Masoudi, A.; Dörscher, S.; Herbers, S.; Häfner, S.; Sterr, U.

    2016-12-01

    With their supreme accuracy and precision, optical clocks in combination with new methods of long-distance frequency transfer can be used to determine height differences by measuring the gravitational red shift between two clocks without accumulation of measurement errors, as in classical levelling. We are developing transportable optical clocks for this purpose that will also serve for the technology development regarding optical clocks in Space and for international comparisons between optical clocks that cannot be linked with sufficient accuracy otherwise.In this talk we will focus on the transportable strontium lattice clock that we are developing and its first evaluation. Presently, we achieve a fractional frequency instability of 3×10-17 after 1000 s averaging time, which is equivalent to a height resolution of 30 cm. The first uncertainty evaluation of the system yielded 7×10-17. We expect rapid improvements to an uncertainty of a few parts in 1017.The clock then placed within a car trailer, which requires compact and rugged lasers systems and physics package. Special care has been taken in the design of the ultra-frequency stable interrogation laser that has to achieve fractional frequency instabilities of considerably below 10-15. Typical laboratory constructions of the reference resonator system used to pre-stabilize the laser frequency are not compatible with the requirement of transportability.In an actual levelling campaign, this clock will be connected e.g. via a stabilized optical fibre link with another, stationary frequency standard. The measured gravitational red shift can be compared to the ones calculated from potential differences derived with state of the art geodetic data and models. A first campaign has been completed in cooperation with colleagues from the Italian and UK metrology institutes INRIM and NPL, respectively, and the Institut für Erdmessung (IfE), Leibniz University Hannover. We will discuss the status of the evaluation and

  19. Synthesizing genetic sequential logic circuit with clock pulse generator

    National Research Council Canada - National Science Library

    Chuang, Chia-Hua; Lin, Chun-Liang

    2014-01-01

    .... This paper presents a genetic sequential logic circuit with a clock pulse generator based on a synthesized genetic oscillator, which generates a consecutive clock signal whose frequency is an inverse...

  20. Modulation of circadian clocks by nutrients and food factors.

    Science.gov (United States)

    Oike, Hideaki

    2017-05-01

    Daily activity rhythms that are dominated by internal clocks are called circadian rhythms. A central clock is located in the suprachiasmatic nucleus of the hypothalamus, and peripheral clocks are located in most mammalian peripheral cells. The central clock is entrained by light/dark cycles, whereas peripheral clocks are entrained by feeding cycles. The effects of nutrients on the central and peripheral clocks have been investigated during the past decade and much interaction between them has come to light. For example, a high-fat diet prolongs the period of circadian behavior, a ketogenic diet advances the onset of locomotor activity rhythms, and a high-salt diet advances the phase of peripheral molecular clocks. Moreover, some food factors such as caffeine, nobiletin, and resveratrol, alter molecular and/or behavioral circadian rhythms. Here, we review nutrients and food factors that modulate mammalian circadian clocks from the cellular to the behavioral level.

  1. Breast cancer risk, nightwork, and circadian clock gene polymorphisms

    National Research Council Canada - National Science Library

    Truong, Thérèse; Liquet, Benoît; Menegaux, Florence; Plancoulaine, Sabine; Laurent-Puig, Pierre; Mulot, Claire; Cordina-Duverger, Emilie; Sanchez, Marie; Arveux, Patrick; Kerbrat, Pierre; Richardson, Sylvia; Guénel, Pascal

    2014-01-01

    ...) in 23 circadian clock genes. We also used a gene- and pathway-based approach to investigate the overall effect on breast cancer of circadian clock gene variants that might not be detected in analyses based on individual SNPs...

  2. Novel transcriptional networks regulated by CLOCK in human neurons.

    Science.gov (United States)

    Fontenot, Miles R; Berto, Stefano; Liu, Yuxiang; Werthmann, Gordon; Douglas, Connor; Usui, Noriyoshi; Gleason, Kelly; Tamminga, Carol A; Takahashi, Joseph S; Konopka, Genevieve

    2017-11-01

    The molecular mechanisms underlying human brain evolution are not fully understood; however, previous work suggested that expression of the transcription factor CLOCK in the human cortex might be relevant to human cognition and disease. In this study, we investigated this novel transcriptional role for CLOCK in human neurons by performing chromatin immunoprecipitation sequencing for endogenous CLOCK in adult neocortices and RNA sequencing following CLOCK knockdown in differentiated human neurons in vitro. These data suggested that CLOCK regulates the expression of genes involved in neuronal migration, and a functional assay showed that CLOCK knockdown increased neuronal migratory distance. Furthermore, dysregulation of CLOCK disrupts coexpressed networks of genes implicated in neuropsychiatric disorders, and the expression of these networks is driven by hub genes with human-specific patterns of expression. These data support a role for CLOCK-regulated transcriptional cascades involved in human brain evolution and function. © 2017 Fontenot et al.; Published by Cold Spring Harbor Laboratory Press.

  3. Pulsed optically pumped atomic clock with zero-dead-time

    Science.gov (United States)

    Lin, Haixiao; Lin, Jinda; Deng, Jianliao; Zhang, Song; Wang, Yuzhu

    2017-12-01

    By alternatively operating two pulsed optically pumped (POP) atomic clocks, the dead time in a single clock can be eliminated, and the local oscillator can be discriminated continuously. A POP atomic clock with a zero-dead-time (ZDT) method is then insensitive to the microwave phase noise. From τ = 0.01 to 1 s, the Allan deviation of the ZDT-POP clock is reduced as nearly τ-1, which is significantly faster than τ-1/2 of a conventional clock. During 1-40 s, the Allan deviation returns to τ-1/2. Moreover, the frequency stability of the ZDT-POP clock is improved by one order of magnitude compared with that of the conventional POP clock. We also analyze the main factors that limit the short-term frequency stability of the POP atomic clock.

  4. It's time to swim! Zebrafish and the circadian clock

    National Research Council Canada - National Science Library

    Vatine, Gad; Vallone, Daniela; Gothilf, Yoav; Foulkes, Nicholas S

    2011-01-01

    .... In addition to this dedicated clock and photoreceptor organ, and unlike the situation in mammals, the clocks in zebrafish peripheral tissues and even cell lines are entrainable by direct exposure...

  5. Ancient dates or accelerated rates? Morphological clocks and the antiquity of placental mammals.

    Science.gov (United States)

    Beck, Robin M D; Lee, Michael S Y

    2014-10-22

    Analyses of a comprehensive morphological character matrix of mammals using 'relaxed' clock models (which simultaneously estimate topology, divergence dates and evolutionary rates), either alone or in combination with an 8.5 kb nuclear sequence dataset, retrieve implausibly ancient, Late Jurassic-Early Cretaceous estimates for the initial diversification of Placentalia (crown-group Eutheria). These dates are much older than all recent molecular and palaeontological estimates. They are recovered using two very different clock models, and regardless of whether the tree topology is freely estimated or constrained using scaffolds to match the current consensus placental phylogeny. This raises the possibility that divergence dates have been overestimated in previous analyses that have applied such clock models to morphological and total evidence datasets. Enforcing additional age constraints on selected internal divergences results in only a slight reduction of the age of Placentalia. Constraining Placentalia to less than 93.8 Ma, congruent with recent molecular estimates, does not require major changes in morphological or molecular evolutionary rates. Even constraining Placentalia to less than 66 Ma to match the 'explosive' palaeontological model results in only a 10- to 20-fold increase in maximum evolutionary rate for morphology, and fivefold for molecules. The large discrepancies between clock- and fossil-based estimates for divergence dates might therefore be attributable to relatively small changes in evolutionary rates through time, although other explanations (such as overly simplistic models of morphological evolution) need to be investigated. Conversely, dates inferred using relaxed clock models (especially with discrete morphological data and MrBayes) should be treated cautiously, as relatively minor deviations in rate patterns can generate large effects on estimated divergence dates. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  6. Improvement of an Atomic Clock using Squeezed Vacuum

    DEFF Research Database (Denmark)

    Kruse, I.; Lange, K; Peise, Jan

    2016-01-01

    .75 atoms to improve the clock sensitivity of 10000 atoms by 2.05+0.34−0.37  dB. The SQL poses a significant limitation for today’s microwave fountain clocks, which serve as the main time reference. We evaluate the major technical limitations and challenges for devising a next generation of fountain clocks...

  7. A practical clock synchronization algorithm for UWB positioning systems

    NARCIS (Netherlands)

    Xie, Y.; Janssen, G.J.M.; van der Veen, A.J.; Dong, Min; Zheng, Thomas Fang

    2016-01-01

    A clock synchronization scheme is crucial for obtaining accuracy in time-based positioning systems. Existing clock synchronization schemes are mostly based on a simplified linear clock model, which unfortunately have a poor long-term synchronization accuracy. Assuming a two-way time transfer

  8. On synchronization of clocks in general space-times

    Directory of Open Access Journals (Sweden)

    M. R. H Khajehpour

    2005-09-01

    Full Text Available   Einstein and transport synchronizations of infinitesimally spaced and distant clocks are considered in a general Riemannian space-time. It is shown that infinitesimally spaced clocks can always be synchronized. In general one can not find observers for whom distant clock are Einstein synchronized but transport synchronized observers do always exit. Whenever both procedures are possible, they are equivalent.

  9. Internal clock formulation of quantum mechanics

    Science.gov (United States)

    Małkiewicz, Przemysław; Miroszewski, Artur

    2017-08-01

    The basic tenet of the present work is the assumption of the lack of external and fixed time in the Universe. This assumption is best embodied by general relativity, which replaces the fixed space-time structure with the gravitational field, which is subject to dynamics. The lack of time does not imply the lack of evolution but rather brings to the forefront the role of internal clocks which are some largely arbitrary internal degrees of freedom with respect to which the evolution of timeless systems can be described. We take this idea seriously and try to understand what it implies for quantum mechanics when the fixed external time is replaced by an arbitrary internal clock. We put the issue in a solid, mathematically rigorous framework. We find that the dynamical interpretation of a quantum state of a timeless system depends on the employed internal clock. In particular, we find that the continuous spectra of well-known dynamical observables like the position of a free particle on the real line may turn discrete if measured in unusual clocks. We discuss the meaning of our result for attempts at quantization of global gravitational degrees of freedom.

  10. Rheumatoid arthritis and the biological clock.

    Science.gov (United States)

    De Cata, Angelo; D'Agruma, Leonardo; Tarquini, Roberto; Mazzoccoli, Gianluigi

    2014-05-01

    Rheumatoid arthritis (RA) is an autoimmune disease of unknown cause and a chronic and progressive inflammatory disorder ensuing in genetically predisposed subjects, characterized by synovitis causing joint destruction, as well as inflammation in body organ systems, leading to anatomical alteration and functional disability. Immune competent cells, deregulated synoviocytes and cytokines play a key role in the pathophysiological mechanisms. The immune system function shows time-related variations related to the influence of the neuroendocrine system and driven by the circadian clock circuitry. Immune processes and symptom intensity in RA are characterized by oscillations during the day following a pattern of circadian rhythmicity. A cross-talk between inflammatory and circadian pathways is involved in RA pathogenesis and underlies the mutual actions of disruption of the circadian clock circuitry on immune system function as well as of inflammation on the function of the biological clock. Modulation of molecular processes and humoral factors mediating in RA the interplay between the biological clock and the immune response and underlying the rhythmic fluctuations of pathogenic processes and symptomatology could represent a promising therapeutic strategy in the future.

  11. Clock Synchronization for Multihop Wireless Sensor Networks

    Science.gov (United States)

    Solis Robles, Roberto

    2009-01-01

    In wireless sensor networks, more so generally than in other types of distributed systems, clock synchronization is crucial since by having this service available, several applications such as media access protocols, object tracking, or data fusion, would improve their performance. In this dissertation, we propose a set of algorithms to achieve…

  12. Tick Tock, a Vitamin C Clock.

    Science.gov (United States)

    Wright, Stephen W.

    2002-01-01

    Presents an activity that uses supermarket chemicals to perform a clock reaction in which the endpoint is signaled by an abrupt change in the appearance from colorless to blue-black. This activity can be used to explore reaction kinetics and the effect of reactant concentrations on the apparent rate of reaction. (DDR)

  13. Analytic clock frequency selection for global DVFS

    NARCIS (Netherlands)

    Gerards, Marco Egbertus Theodorus; Hurink, Johann L.; Holzenspies, P.K.F.; Kuper, Jan; Smit, Gerardus Johannes Maria

    2014-01-01

    Computers can reduce their power consumption by decreasing their speed using Dynamic Voltage and Frequency Scaling (DVFS). A form of DVFS for multicore processors is global DVFS, where the voltage and clock frequency is shared among all processor cores. Because global DVFS is efficient and cheap to

  14. Crosstalk between xenobiotics metabolism and circadian clock

    NARCIS (Netherlands)

    Claudel, Thierry; Cretenet, Gaspard; Saumet, Anne; Gachon, Frederic

    2007-01-01

    Many aspects of physiology and behavior in organisms from bacteria to man are subjected to circadian regulation. Indeed, the major function of the circadian clock consists in the adaptation of physiology to daily environmental change and the accompanying stresses such as exposition to UV-light and

  15. Radium single-ion optical clock

    NARCIS (Netherlands)

    Versolato, O. O.; Wansbeek, L. W.; Jungmann, K.; Timmermans, R. G. E.; Willmann, L.; Wilschut, H. W.

    2011-01-01

    We explore the potential of the electric quadrupole transitions $7s\\,^2S_{1/2}$ - $6d\\,^2D_{3/2}$, $6d\\,^2D_{5/2}$ in radium isotopes as single-ion optical frequency standards. The frequency shifts of the clock transitions due to external fields and the corresponding uncertainties are calculated.

  16. The skeletal muscle circadian clock: current insights

    Directory of Open Access Journals (Sweden)

    Nakao R

    2017-11-01

    Full Text Available Reiko Nakao,1 Takeshi Nikawa,2 Katsutaka Oishi1,3,4 1Biological Clock Research Group, Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST, Tsukuba, 2Department of Nutritional Physiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, 3Department of Applied Biological Science, Graduate School of Science and Technology, Tokyo University of Science, Noda, 4Department of Computational and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Japan Abstract: Skeletal muscle functions in locomotion, postural support, and energy metabolism. The loss of skeletal muscle mass and function leads to diseases such as sarcopenia and metabolic disorders. Inactivity (lack of exercise and an imbalanced diet (increased fat or decreased protein intake are thought to be involved in the prevalence of such pathologies. On the other hand, recent epidemiological studies of humans have suggested that circadian disruption caused by shift work, jet lag, and sleep disorders is associated with obesity and metabolic syndrome. Experimental studies of mice deficient in clock genes have also identified skeletal muscle defects, suggesting a molecular link between circadian clock machinery and skeletal muscle physiology. Furthermore, accumulating evidence about chronotherapy, including chronopharmacology, chrononutrition, and chronoexercise, has indicated that timing is important to optimize medical intervention for various diseases. The present review addresses current understanding of the functional roles of the molecular clock with respect to skeletal muscle and the potential of chronotherapy for diseases associated with skeletal muscle. Keywords: biological rhythm, metabolic syndrome, physical activity, neural signal, chronotherapy

  17. Entrainment of the human circadian clock

    NARCIS (Netherlands)

    Roenneberg, T.; Merrow, M.

    2007-01-01

    Humans are an excellent model system for studying entrainment of the circadian clock in the real world. Unlike the situation in laboratory experiments, entrainment under natural conditions is achieved by different external signals as well as by internal signals generated by multiple feedbacks within

  18. Pineal clock gene oscillation is disturbed in Alzheimer's disease, due to functional disconnection from the "master clock"

    NARCIS (Netherlands)

    Wu, Ying-Hui; Fischer, David F.; Kalsbeek, Andries; Garidou-Boof, Marie-Laure; van der Vliet, Jan; van Heijningen, Caroline; Liu, Rong-Yu; Zhou, Jiang-Ning; Swaab, Dick F.

    2006-01-01

    The suprachiasmatic nucleus (SCN) is the "master clock" of the mammalian brain. It coordinates the peripheral clocks in the body, including the pineal clock that receives SCN input via a multisynaptic noradrenergic pathway. Rhythmic pineal melatonin production is disrupted in Alzheimer's disease

  19. Pineal clock gene oscillation is disturbed in Alzheimer's disease, due to functional disconnection from the "master clock".

    NARCIS (Netherlands)

    Wu, Y.-H.; Fischer, D.F.; Kalsbeek, A.; Garidou-Boof, M.-L.; Vliet, J. van der; Heijningen, C. van; Liu, R.-Y.; Zhou, J.-N.; Swaab, D.F.

    2006-01-01

    The suprachiasmatic nucleus (SCN) is the "master clock" of the mammalian brain. It coordinates the peripheral clocks in the body, including the pineal clock that receives SCN input via a multisynaptic noradrenergic pathway. Rhythmic pineal melatonin production is disrupted in Alzheimer's disease

  20. Clock measurements to improve the geopotential determination

    Science.gov (United States)

    Lion, Guillaume; Panet, Isabelle; Delva, Pacôme; Wolf, Peter; Bize, Sébastien; Guerlin, Christine

    2017-04-01

    Comparisons between optical clocks with an accuracy and stability approaching the 10-18 in term of relative frequency shift are opening new perspectives for the direct determination of geopotential at a centimeter-level accuracy in geoid height. However, so far detailed quantitative estimates of the possible improvement in geoid determination when adding such clock measurements to existing data are lacking. In this context, the present work aims at evaluating the contribution of this new kind of direct measurements in determining the geopotential at high spatial resolution (10 km). We consider the Massif Central area, marked by smooth, moderate altitude mountains and volcanic plateaus leading to variations of the gravitational field over a range of spatial scales. In such type of region, the scarcity of gravity data is an important limitation in deriving accurate high resolution geopotential models. We summarize our methodology to assess the contribution of clock data in the geopotential recovery, in combination with ground gravity measurements. We sample synthetic gravity and disturbing potential data from a spherical harmonics geopotential model, and a topography model, up to 10 km resolution; we also build a potential control grid. From the synthetic data, we estimate the disturbing potential by least-squares collocation. Finally, we assess the quality of the reconstructed potential by comparing it to that of the control grid. We show that adding only a few clock data reduces the reconstruction bias significantly and improves the standard deviation by a factor 3. We discuss the role of different parameters, such as the effect of the data coverage and data quality on these results, the trade-off between the measurement noise level and the number of data, and the optimization of the clock data network.

  1. Electron Tree

    DEFF Research Database (Denmark)

    Appelt, Ane L; Rønde, Heidi S

    2013-01-01

    The photo shows a close-up of a Lichtenberg figure – popularly called an “electron tree” – produced in a cylinder of polymethyl methacrylate (PMMA). Electron trees are created by irradiating a suitable insulating material, in this case PMMA, with an intense high energy electron beam. Upon discharge......, during dielectric breakdown in the material, the electrons generate branching chains of fractures on leaving the PMMA, producing the tree pattern seen. To be able to create electron trees with a clinical linear accelerator, one needs to access the primary electron beam used for photon treatments. We...... appropriated a linac that was being decommissioned in our department and dismantled the head to circumvent the target and ion chambers. This is one of 24 electron trees produced before we had to stop the fun and allow the rest of the accelerator to be disassembled....

  2. Tree compression with top trees

    DEFF Research Database (Denmark)

    Bille, Philip; Gørtz, Inge Li; Landau, Gad M.

    2015-01-01

    We introduce a new compression scheme for labeled trees based on top trees. Our compression scheme is the first to simultaneously take advantage of internal repeats in the tree (as opposed to the classical DAG compression that only exploits rooted subtree repeats) while also supporting fast...... navigational queries directly on the compressed representation. We show that the new compression scheme achieves close to optimal worst-case compression, can compress exponentially better than DAG compression, is never much worse than DAG compression, and supports navigational queries in logarithmic time....

  3. Tree compression with top trees

    DEFF Research Database (Denmark)

    Bille, Philip; Gørtz, Inge Li; Landau, Gad M.

    2013-01-01

    We introduce a new compression scheme for labeled trees based on top trees [3]. Our compression scheme is the first to simultaneously take advantage of internal repeats in the tree (as opposed to the classical DAG compression that only exploits rooted subtree repeats) while also supporting fast...... navigational queries directly on the compressed representation. We show that the new compression scheme achieves close to optimal worst-case compression, can compress exponentially better than DAG compression, is never much worse than DAG compression, and supports navigational queries in logarithmic time....

  4. The sympathy of two pendulum clocks: beyond Huygens’ observations

    Science.gov (United States)

    Peña Ramirez, Jonatan; Olvera, Luis Alberto; Nijmeijer, Henk; Alvarez, Joaquin

    2016-01-01

    This paper introduces a modern version of the classical Huygens’ experiment on synchronization of pendulum clocks. The version presented here consists of two monumental pendulum clocks—ad hoc designed and fabricated—which are coupled through a wooden structure. It is demonstrated that the coupled clocks exhibit ‘sympathetic’ motion, i.e. the pendula of the clocks oscillate in consonance and in the same direction. Interestingly, when the clocks are synchronized, the common oscillation frequency decreases, i.e. the clocks become slow and inaccurate. In order to rigorously explain these findings, a mathematical model for the coupled clocks is obtained by using well-established physical and mechanical laws and likewise, a theoretical analysis is conducted. Ultimately, the sympathy of two monumental pendulum clocks, interacting via a flexible coupling structure, is experimentally, numerically, and analytically demonstrated. PMID:27020903

  5. Optimal Implementations for Reliable Circadian Clocks

    Science.gov (United States)

    Hasegawa, Yoshihiko; Arita, Masanori

    2014-09-01

    Circadian rhythms are acquired through evolution to increase the chances for survival through synchronizing with the daylight cycle. Reliable synchronization is realized through two trade-off properties: regularity to keep time precisely, and entrainability to synchronize the internal time with daylight. We find by using a phase model with multiple inputs that achieving the maximal limit of regularity and entrainability entails many inherent features of the circadian mechanism. At the molecular level, we demonstrate the role sharing of two light inputs, phase advance and delay, as is well observed in mammals. At the behavioral level, the optimal phase-response curve inevitably contains a dead zone, a time during which light pulses neither advance nor delay the clock. We reproduce the results of phase-controlling experiments entrained by two types of periodic light pulses. Our results indicate that circadian clocks are designed optimally for reliable clockwork through evolution.

  6. Mechanisms linking circadian clocks, sleep, and neurodegeneration.

    Science.gov (United States)

    Musiek, Erik S; Holtzman, David M

    2016-11-25

    Disruptions of normal circadian rhythms and sleep cycles are consequences of aging and can profoundly affect health. Accumulating evidence indicates that circadian and sleep disturbances, which have long been considered symptoms of many neurodegenerative conditions, may actually drive pathogenesis early in the course of these diseases. In this Review, we explore potential cellular and molecular mechanisms linking circadian dysfunction and sleep loss to neurodegenerative diseases, with a focus on Alzheimer's disease. We examine the interplay between central and peripheral circadian rhythms, circadian clock gene function, and sleep in maintaining brain homeostasis, and discuss therapeutic implications. The circadian clock and sleep can influence a number of key processes involved in neurodegeneration, suggesting that these systems might be manipulated to promote healthy brain aging. Copyright © 2016, American Association for the Advancement of Science.

  7. Circadian clocks, feeding time and metabolic homeostasis

    Directory of Open Access Journals (Sweden)

    Georgios ePaschos

    2015-05-01

    Full Text Available Metabolic processes exhibit diurnal variation from cyanobacteria to humans. The circadian clock is thought to have evolved as a time keeping system for the cell to optimize the timing of metabolic events according to physiological needs and environmental conditions. Circadian rhythms temporally separate incompatible cellular processes and optimize cellular and organismal fitness. A modern 24 hour lifestyle can run at odds with the circadian rhythm dictated by our molecular clocks and create desynchrony between internal and external timing. It has been suggested that this desynchrony compromises metabolic homeostasis and may promote the development of obesity (Morris et al., 2012. Here we review the evidence supporting the association between circadian misalignment and metabolic homeostasis and discuss the role of feeding time.

  8. Supporting Family Awareness with the Whereabouts Clock

    Science.gov (United States)

    Sellen, Abigail; Taylor, Alex S.; Kaye, Joseph ‘Jofish'; Brown, Barry; Izadi, Shahram

    We report the results of a field trial of a situated awareness device for families called the “Whereabouts Clock”. The Clock displays the location of family members using cellphone data as one of four privacy-preserving, deliberately coarse-grained categories ( HOME, WORK, SCHOOL or ELSEWHERE). The results show that awareness of others through the Clock supports not only family communication and coordination but also more emotive aspects of family life such as reassurance, connectedness, identity and social touch. We discuss how the term “awareness” means many things in practice and highlight the importance of designing not just for family activities, but in order to support the emotional, social and even moral aspects of family life.

  9. Light and the human circadian clock.

    Science.gov (United States)

    Roenneberg, Till; Kantermann, Thomas; Juda, Myriam; Vetter, Céline; Allebrandt, Karla V

    2013-01-01

    The circadian clock can only reliably fulfil its function if it is stably entrained. Most clocks use the light-dark cycle as environmental signal (zeitgeber) for this active synchronisation. How we think about clock function and entrainment has been strongly influenced by the early concepts of the field's pioneers, and the astonishing finding that circadian rhythms continue a self-sustained oscillation in constant conditions has become central to our understanding of entrainment.Here, we argue that we have to rethink these initial circadian dogmas to fully understand the circadian programme and how it entrains. Light is also the prominent zeitgeber for the human clock, as has been shown experimentally in the laboratory and in large-scale epidemiological studies in real life, and we hypothesise that social zeitgebers act through light entrainment via behavioural feedback loops (zeitnehmer). We show that human entrainment can be investigated in detail outside of the laboratory, by using the many 'experimental' conditions provided by the real world, such as daylight savings time, the 'forced synchrony' imposed by the introduction of time zones, or the fact that humans increasingly create their own light environment. The conditions of human entrainment have changed drastically over the past 100 years and have led to an increasing discrepancy between biological and social time (social jetlag). The increasing evidence that social jetlag has detrimental consequences for health suggests that shift-work is only an extreme form of circadian misalignment, and that the majority of the population in the industrialised world suffers from a similarly 'forced synchrony'.

  10. The circadian clock, reward and memory

    Directory of Open Access Journals (Sweden)

    Urs eAlbrecht

    2011-11-01

    Full Text Available During our daily activities, we experience variations in our cognitive performance, which is often accompanied by cravings for small rewards, such as consuming coffee or chocolate. This indicates that the time of day, cognitive performance and reward may be related to one another. This review will summarize data that describes the influence of the circadian clock on addiction and mood-related behavior and put the data into perspective in relation to memory processes.

  11. The circadian clock, reward, and memory.

    Science.gov (United States)

    Albrecht, Urs

    2011-01-01

    During our daily activities, we experience variations in our cognitive performance, which is often accompanied by cravings for small rewards, such as consuming coffee or chocolate. This indicates that the time of day, cognitive performance, and reward may be related to one another. This review will summarize data that describe the influence of the circadian clock on addiction and mood-related behavior and put the data into perspective in relation to memory processes.

  12. Effects of mass defect in atomic clocks

    Science.gov (United States)

    Taichenachev, A. V.; Yudin, V. I.

    2018-01-01

    We consider some implications of the mass defect on the frequency of atomic transitions. We have found that some well-known frequency shifts (such as gravitational and quadratic Doppler shifts) can be interpreted as consequences of the mass defect, i.e., without the need for the concept of time dilation used in special and general relativity theories. Moreover, we show that the inclusion of the mass defect leads to previously unknown shifts for clocks based on trapped ions..

  13. Molecular clock in neutral protein evolution

    Directory of Open Access Journals (Sweden)

    Wilke Claus O

    2004-08-01

    Full Text Available Abstract Background A frequent observation in molecular evolution is that amino-acid substitution rates show an index of dispersion (that is, ratio of variance to mean substantially larger than one. This observation has been termed the overdispersed molecular clock. On the basis of in silico protein-evolution experiments, Bastolla and coworkers recently proposed an explanation for this observation: Proteins drift in neutral space, and can temporarily get trapped in regions of substantially reduced neutrality. In these regions, substitution rates are suppressed, which results in an overall substitution process that is not Poissonian. However, the simulation method of Bastolla et al. is representative only for cases in which the product of mutation rate μ and population size Ne is small. How the substitution process behaves when μNe is large is not known. Results Here, I study the behavior of the molecular clock in in silico protein evolution as a function of mutation rate and population size. I find that the index of dispersion decays with increasing μNe, and approaches 1 for large μNe . This observation can be explained with the selective pressure for mutational robustness, which is effective when μNe is large. This pressure keeps the population out of low-neutrality traps, and thus steadies the ticking of the molecular clock. Conclusions The molecular clock in neutral protein evolution can fall into two distinct regimes, a strongly overdispersed one for small μNe, and a mostly Poissonian one for large μNe. The former is relevant for the majority of organisms in the plant and animal kingdom, and the latter may be relevant for RNA viruses.

  14. Clock drawing in children with perinatal stroke.

    Science.gov (United States)

    Yousefian, Omid; Ballantyne, Angela O; Doo, Alex; Trauner, Doris A

    2015-06-01

    Children with perinatal stroke may show evidence of contralateral spatial neglect. The goal of this study was to determine whether the Clock Drawing Test commonly used in adults to identify neglect would be effective in detecting neglect in children with perinatal stroke. Thirty-eight individuals (age range 6-21 years) with left hemisphere or right hemisphere perinatal onset unilateral lesions and 179 age-matched controls were given a free-drawn Clock Drawing Test in a cross-sectional design. An adapted scoring system that evaluated right- and left-sided errors separately was developed as part of the investigation. Children with right hemisphere lesions made a greater number of errors on both the right and left sides of the clock drawings in all age subgroups (6-8 years, 9-14 years, and 15-21 years) compared with controls. Children with right hemisphere lesions showed greater left and right errors in the younger groups compared with controls, with significantly poorer performance on the left at 6-8 years, suggestive of contralateral neglect. However, by ages 15-21 years, the right hemisphere lesion subjects no longer differed from controls. Clock drawing can identify spatial neglect in children with early hemispheric damage. However, brain development is a dynamic process, and as children age, spatial neglect may no longer be evident. These findings demonstrate the limitations of predicting long-term outcome after perinatal stroke from early neurocognitive data. Children with perinatal stroke may require different neural pathways to accomplish specific skills or to overcome deficits, but ultimately they may have "typical" outcomes. Copyright © 2015 Elsevier Inc. All rights reserved.

  15. Regulated DNA Methylation and the Circadian Clock: Implications in Cancer

    Directory of Open Access Journals (Sweden)

    Tammy M. Joska

    2014-09-01

    Full Text Available Since the cloning and discovery of DNA methyltransferases (DNMT, there has been a growing interest in DNA methylation, its role as an epigenetic modification, how it is established and removed, along with the implications in development and disease. In recent years, it has become evident that dynamic DNA methylation accompanies the circadian clock and is found at clock genes in Neurospora, mice and cancer cells. The relationship among the circadian clock, cancer and DNA methylation at clock genes suggests a correlative indication that improper DNA methylation may influence clock gene expression, contributing to the etiology of cancer. The molecular mechanism underlying DNA methylation at clock loci is best studied in the filamentous fungi, Neurospora crassa, and recent data indicate a mechanism analogous to the RNA-dependent DNA methylation (RdDM or RNAi-mediated facultative heterochromatin. Although it is still unclear, DNA methylation at clock genes may function as a terminal modification that serves to prevent the regulated removal of histone modifications. In this capacity, aberrant DNA methylation may serve as a readout of misregulated clock genes and not as the causative agent. This review explores the implications of DNA methylation at clock loci and describes what is currently known regarding the molecular mechanism underlying DNA methylation at circadian clock genes.

  16. Photoperiodic plasticity in circadian clock neurons in insects

    Directory of Open Access Journals (Sweden)

    Sakiko eShiga

    2013-08-01

    Full Text Available Since Bünning’s observation of circadian rhythms and photoperiodism in the runner bean Phaseolus multiflorus in 1936, many studies have shown that photoperiodism is based on the circadian clock system. In insects, involvement of circadian clock genes or neurons has been recently shown in the photoperiodic control of developmental arrests, diapause. Based on molecular and neuronal studies in Drosophila melanogaster, photoperiodic changes have been reported for expression patterns of the circadian clock genes, subcellular distribution of clock proteins, fiber distribution, or the number of plausible clock neurons in different species. Photoperiod sets peaks of per or tim mRNA abundance at lights-off in Sarcophaga crassipalpis, Chymomyza costata and Protophormia terraenovae. Abundance of per and Clock mRNA changes by photoperiod in Pyrrhocoris apterus. Subcellular Per distribution in circadian clock neurons changes with photoperiod in P. terraenovae. Although photoperiodism is not known in Leucophaea maderae, under longer day length, more stomata and longer commissural fibers of circadian clock neurons have been found. These plastic changes in the circadian clock neurons could be an important constituent for photoperiodic clock mechanisms to integrate repetitive photoperiodic information and produce different outputs based on day length.

  17. Radium single-ion optical clock

    CERN Document Server

    Versolato, O O; Jungmann, K; Timmermans, R G E; Willmann, L; Wilschut, H W

    2011-01-01

    We explore the potential of the electric quadrupole transitions $7s\\,^2S_{1/2}$ - $6d\\,^2D_{3/2}$, $6d\\,^2D_{5/2}$ in radium isotopes as single-ion optical frequency standards. The frequency shifts of the clock transitions due to external fields and the corresponding uncertainties are calculated. Several competitive $^A$Ra$^+$ candidates with $A=$ 223 - 229 are identified. In particular, we show that the transition $7s\\,^2S_{1/2}\\,(F=2,m_F=0)$ - $6d\\,^2D_{3/2}\\,(F=0,m_F=0)$ at 828 nm in $^{223}$Ra$^+$, with no linear Zeeman and electric quadrupole shifts, stands out as a relatively simple case, which could be exploited as a compact, robust, and low-cost atomic clock operating at a fractional frequency uncertainty of $10^{-17}$. With more experimental effort, the $^{223,225,226}$Ra$^+$ clocks could be pushed to a projected performance reaching the $10^{-18}$ level.

  18. Tuning genetic clocks employing DNA binding sites.

    Directory of Open Access Journals (Sweden)

    Shridhar Jayanthi

    Full Text Available Periodic oscillations play a key role in cell physiology from the cell cycle to circadian clocks. The interplay of positive and negative feedback loops among genes and proteins is ubiquitous in these networks. Often, delays in a negative feedback loop and/or degradation rates are a crucial mechanism to obtain sustained oscillations. How does nature control delays and kinetic rates in feedback networks? Known mechanisms include proper selection of the number of steps composing a feedback loop and alteration of protease activity, respectively. Here, we show that a remarkably simple means to control both delays and effective kinetic rates is the employment of DNA binding sites. We illustrate this design principle on a widely studied activator-repressor clock motif, which is ubiquitous in natural systems. By suitably employing DNA target sites for the activator and/or the repressor, one can switch the clock "on" and "off" and precisely tune its period to a desired value. Our study reveals a design principle to engineer dynamic behavior in biomolecular networks, which may be largely exploited by natural systems and employed for the rational design of synthetic circuits.

  19. Three-Dimensional Phylogeny Explorer: Distinguishing paralogs, lateral transfer, and violation of "molecular clock" assumption with 3D visualization

    Directory of Open Access Journals (Sweden)

    Lee Christopher

    2007-06-01

    Full Text Available Abstract Background Construction and interpretation of phylogenetic trees has been a major research topic for understanding the evolution of genes. Increases in sequence data and complexity are creating a need for more powerful and insightful tree visualization tools. Results We have developed 3D Phylogeny Explorer (3DPE, a novel phylogeny tree viewer that maps trees onto three spatial axes (species on the X-axis; paralogs on Z; evolutionary distance on Y, enabling one to distinguish at a glance evolutionary features such as speciation; gene duplication and paralog evolution; lateral gene transfer; and violation of the "molecular clock" assumption. Users can input any tree on the online 3DPE, then rotate, scroll, rescale, and explore it interactively as "live" 3D views. All objects in 3DPE are clickable to display subtrees, connectivity path highlighting, sequence alignments, and gene summary views, and etc. To illustrate the value of this visualization approach for microbial genomes, we also generated 3D phylogeny analyses for all clusters from the public COG database. We constructed tree views using well-established methods and graph algorithms. We used Scientific Python to generate VRML2 3D views viewable in any web browser. Conclusion 3DPE provides a novel phylogenetic tree projection method into 3D space and its web-based implementation with live 3D features for reconstruction of phylogenetic trees of COG database.

  20. Flowering Trees

    Indian Academy of Sciences (India)

    Cerbera manghasL. (SEA MANGO) of Apocynaceae is a medium-sized evergreen coastal tree with milky latex. The bark is grey-brown, thick and rough. Leaves are leathery, long-veined, alternate and usually crowded at the end of branches. Flowers are in terminal compact clusters and are mildly scented, large (3–.

  1. Flowering Trees

    Indian Academy of Sciences (India)

    Andira inermis (wright) DC. , Dog Almond of Fabaceae is a handsome lofty evergreen tree. Leaves are alternate and pinnately compound with 4–7 pairs of leaflets. Flowers are fragrant and are borne on compact branched inflorescences. Fruit is ellipsoidal one-seeded drupe that is peculiar to members of this family.

  2. Flowering Trees

    Indian Academy of Sciences (India)

    IAS Admin

    handsome tree reaching a height of 15–20 feet. Leaves are alternate, pinnately compound (11–35 pairs of leaflets) and clustered at the branch ends. Flowers are small, fragrant and are borne on branched inflorescence directly from the trunk. Fruits are bright-green, oblong and lobed. They taste sour and are pickled.

  3. Flowering Trees

    Indian Academy of Sciences (India)

    narrow towards base. Flowers are large and attrac- tive, but emit unpleasant foetid smell. They appear in small numbers on erect terminal clusters and open at night. Stamens are numerous, pink or white. Style is slender and long, terminating in a small stigma. Fruit is green, ovoid and indistinctly lobed. Flowering Trees.

  4. Flowering Trees

    Indian Academy of Sciences (India)

    IAS Admin

    Caesalpinia coriaria (Jacq.) Willd. (THE AMERICAN SUMACH, DIVI-DIVI) of. Caesalpiniaceae is a small unarmed tree reaching up to 10 m in height with a spreading crown. Leaves are alternate and twice compound. The flowers are small, about 0.6 cm (enlarged 5 times here), greenish-yellow, fragrant and appear in dense ...

  5. Flowering Trees

    Indian Academy of Sciences (India)

    IAS Admin

    Benth. of Meliaceae is a small-sized evergreen tree of both moist and dry deciduous forests. The leaves are alternate and pinnately compound, terminating in a single leaflet. Leaflets are more or less elliptic with entire margin. Flowers are small on branched inflorescence. Fruit is a globose berry (1.5 to 2 cm across) with one ...

  6. Flowering Trees

    Indian Academy of Sciences (India)

    Celtis tetrandra Roxb. of Ulmaceae is a moderately large handsome deciduous tree with green branchlets and grayish-brown bark. Leaves are simple with three to four secondary veins running parallel to the mid vein. Flowers are solitary, male, female and bisexual and inconspicuous. Fruit is berry-like, small and globose ...

  7. Flowering Trees

    Indian Academy of Sciences (India)

    sriranga

    Haldina cordifolia (Roxb.) Ridsd. Syn. Adina cordifolia (Roxb.) Hook.f. ex Brandis (Yellow. Cadamba) of Rubiaceae is a large and handsome deciduous tree. Leaves are simple, large, orbicular, and drawn abruptly at the apex. Flowers are small, yellowish and aggregate into small spherical heads. The corolla is ...

  8. ~{owering 'Trees

    Indian Academy of Sciences (India)

    ... green but yellow when ripe, quite smooth at first but wrinkled in drying, remaining long on the tree ajier ripening. The species is widely natural but occasionally cultivated for firewood as it grows very fast. The bark is very bitter and is used as an anthelmintic. Heartwood is reddish brown and takes good polish and hence.

  9. Tree Mortality

    Science.gov (United States)

    Mark J. Ambrose

    2012-01-01

    Tree mortality is a natural process in all forest ecosystems. However, extremely high mortality also can be an indicator of forest health issues. On a regional scale, high mortality levels may indicate widespread insect or disease problems. High mortality may also occur if a large proportion of the forest in a particular region is made up of older, senescent stands....

  10. Flowering Trees

    Indian Academy of Sciences (India)

    user

    Gliricidia sepium(Jacq.) Kunta ex Walp. (Quickstick) of Fabaceae is a small deciduous tree with. Pinnately compound leaves. Flower are prroduced in large number in early summer on terminal racemes. They are attractive, pinkish-white and typically like bean flowers. Fruit is a few-seeded flat pod. G. sepium is a native of ...

  11. Flowering Trees

    Indian Academy of Sciences (India)

    deciduous tropical tree with often multiple stems and handsome foliage. Leaves are 8–10 cm long, dull green, the two thin leathery halves of the lamina fusing or the cleft between them extending beyond the middle. Flowers are gorgeous, axillary with ...

  12. Flowering Trees

    Indian Academy of Sciences (India)

    Trincomali Wood of Tiliaceae is a tall evergreen tree with straight trunk, smooth brownish-grey bark and simple broad leaves. Inflorescence is much branched with white flowers. Stamens are many with golden yellow anthers. Fruit is a capsule with six spreading wings. Seeds bear short stiff hairs that cause skin irritation.

  13. Flowering Trees

    Indian Academy of Sciences (India)

    Muntingia calabura L. (Singapore cherry) of. Elaeocarpaceae is a medium size handsome ever- green tree. Leaves are simple and alternate with sticky hairs. Flowers are bisexual, bear numerous stamens, white in colour and arise in the leaf axils. Fruit is a berry, edible with several small seeds embedded in a fleshy pulp ...

  14. Flowering Trees

    Indian Academy of Sciences (India)

    knobbly, rough and twisted medium-sized ev- ergreen tree with mottled bark. The wood is very hard and resinous. Leaves are compound. The leaflets are smooth, leathery, ovate-ellipti- cal and appear in two pairs. Flowers (about 1.5 cm across) are clustered in leaf axils and are bisexual. Fruit is yellow, fleshy, two-valved.

  15. Flowering Trees

    Indian Academy of Sciences (India)

    Srimath

    . (6-10m high) evergreen tree with a straight trunk and broad open crown. Leaves are clustered at the end of twigs. They are dark green, broadest near the rounded apex and tapering towards the base with a short stalk. Flowers are greenish or ...

  16. :Ffowering 'Trees-

    Indian Academy of Sciences (India)

    The tree is a host of lac insects which secrete a resinous substance that yields shellac or lac. A ruby-coloured gum known as Bengal Kino is collected from the incisions made in the bark. The wood, resistant to water, is used in water-well work. The seeds are used as anthelmintic and as an antidote for snake-bite.

  17. Flowering Trees

    Indian Academy of Sciences (India)

    Sterculia foetida L. (INDIAN ALMOND,. JAVA OLIVE) of Sterculiaceae is a tall deciduous tree reaching a height of 20 m with faintly ridged grey bark. The bole reaches up to 2m in girth. Branches are reddish, usually horizontal. Leaves are large, palmately compound (5–7 leaflets) and clustered at the branch ends. Flowers ...

  18. Synthetic Spin-Orbit Coupling in an Optical Lattice Clock

    Science.gov (United States)

    Wall, Michael L.; Koller, Andrew P.; Li, Shuming; Zhang, Xibo; Cooper, Nigel R.; Ye, Jun; Rey, Ana Maria

    2016-01-01

    We propose the use of optical lattice clocks operated with fermionic alkaline-earth atoms to study spin-orbit coupling (SOC) in interacting many-body systems. The SOC emerges naturally during the clock interrogation, when atoms are allowed to tunnel and accumulate a phase set by the ratio of the "magic" lattice wavelength to the clock transition wavelength. We demonstrate how standard protocols such as Rabi and Ramsey spectroscopy that take advantage of the sub-Hertz resolution of state-of-the-art clock lasers can perform momentum-resolved band tomography and determine SOC-induced s -wave collisions in nuclear-spin-polarized fermions. With the use of a second counterpropagating clock beam, we propose a method for engineering controlled atomic transport and study how it is modified by p - and s -wave interactions. The proposed spectroscopic probes provide clean and well-resolved signatures at current clock operating temperatures.

  19. Synthetic Spin-Orbit Coupling in an Optical Lattice Clock.

    Science.gov (United States)

    Wall, Michael L; Koller, Andrew P; Li, Shuming; Zhang, Xibo; Cooper, Nigel R; Ye, Jun; Rey, Ana Maria

    2016-01-22

    We propose the use of optical lattice clocks operated with fermionic alkaline-earth atoms to study spin-orbit coupling (SOC) in interacting many-body systems. The SOC emerges naturally during the clock interrogation, when atoms are allowed to tunnel and accumulate a phase set by the ratio of the "magic" lattice wavelength to the clock transition wavelength. We demonstrate how standard protocols such as Rabi and Ramsey spectroscopy that take advantage of the sub-Hertz resolution of state-of-the-art clock lasers can perform momentum-resolved band tomography and determine SOC-induced s-wave collisions in nuclear-spin-polarized fermions. With the use of a second counterpropagating clock beam, we propose a method for engineering controlled atomic transport and study how it is modified by p- and s-wave interactions. The proposed spectroscopic probes provide clean and well-resolved signatures at current clock operating temperatures.

  20. A clock network for geodesy and fundamental science

    CERN Document Server

    Lisdat, C; Quintin, N; Shi, C; Raupach, S M F; Grebing, C; Nicolodi, D; Stefani, F; Al-Masoudi, A; Dörscher, S; Häfner, S; Robyr, J -L; Chiodo, N; Bilicki, S; Bookjans, E; Koczwara, A; Koke, S; Kuhl, A; Wiotte, F; Meynadier, F; Camisard, E; Abgrall, M; Lours, M; Legero, T; Schnatz, H; Sterr, U; Denker, H; Chardonnet, C; Coq, Y Le; Santarelli, G; Amy-Klein, A; Targat, R Le; Lodewyck, J; Lopez, O; Pottie, P -E

    2015-01-01

    Leveraging the unrivaled performance of optical clocks in applications in fundamental physics beyond the standard model, in geo-sciences, and in astronomy requires comparing the frequency of distant optical clocks truthfully. Meeting this requirement, we report on the first comparison and agreement of fully independent optical clocks separated by 700 km being only limited by the uncertainties of the clocks themselves. This is achieved by a phase-coherent optical frequency transfer via a 1415 km long telecom fiber link that enables substantially better precision than classical means of frequency transfer. The fractional precision in comparing the optical clocks of three parts in $10^{17}$ was reached after only 1000 s averaging time, which is already 10 times better and more than four orders of magnitude faster than with any other existing frequency transfer method. The capability of performing high resolution international clock comparisons paves the way for a redefinition of the unit of time and an all-optic...

  1. Intercellular Coupling Regulates the Period of the Segmentation Clock

    OpenAIRE

    Herrgen, Leah; Ares, Saúl; Morelli, Luis G.; Schröter, Christian; Jülicher, Frank; Andrew C. Oates

    2010-01-01

    Coupled biological oscillators can tick with the same period. How this collective period is established is a key question in understanding biological clocks. We explore this question in the segmentation clock, a population of coupled cellular oscillators in the vertebrate embryo that sets the rhythm of somitogenesis, the morphological segmentation of the body axis. The oscillating cells of the zebrafish segmentation clock are thought to possess noisy autonomous periods, which are synchronized...

  2. [Physiological and pathophysiological role of the circadian clock system].

    Science.gov (United States)

    Halmos, Tamás; Suba, Ilona

    2012-09-02

    It has been well known for ages that in living organisms the rhythmicity of biological processes is linked to the ~ 24-hour light-dark cycle. However, the exact function of the circadian clock system has been explored only in the past decades. It came to light that the photosensitive primary "master clock" is situated in the suprachiasmatic photosensitive nuclei of the special hypothalamic region, and that it is working according to ~24-hour changes of light and darkness. The master clock sends its messages to the peripheral "slave clocks". In many organs, like pancreatic β-cells, the slave clocks have autonomic functions as well. Two essential components of the clock system are proteins encoded by the CLOCK and BMAL1 genes. CLOCK genes are in interaction with endonuclear receptors such as peroxisoma-proliferator activated receptors and Rev-erb-α, as well as with the hypothalamic-pituitary-adrenal axis, regulating the adaptation to stressors, energy supply, metabolic processes and cardiovascular system. Melatonin, the product of corpus pineale has a significant role in the functions of the clock system. The detailed discovery of the clock system has changed our previous knowledge about the development of many diseases. The most explored fields are hypertension, cardiovascular diseases, metabolic processes, mental disorders, cancers, sleep apnoe and joint disorders. CLOCK genes influence ageing as well. The recognition of the periodicity of biological processes makes the optimal dosing of certain drugs feasible. The more detailed discovery of the interaction of the clock system might further improve treatment and prevention of many disorders.

  3. FAD regulates CRYPTOCHROME protein stability and circadian clock in mice

    OpenAIRE

    Arisa Hirano; Daniel Braas; Ying-Hui Fu; Ptáček, Louis J.

    2017-01-01

    The circadian clock generates biological rhythms of metabolic and physiological processes, including the sleep-wake cycle. We previously identified a missense mutation in the flavin adenine dinucleotide (FAD) binding pocket of CRYPTOCHROME2 (CRY2), a clock protein that causes human advanced sleep phase. This prompted us to examine the role of FAD as a mediator of the clock and metabolism. FAD stabilized CRY proteins, leading to increased protein levels. In contrast, knockdown of Riboflavin ki...

  4. Relativity theory and time perception: single or multiple clocks?

    Science.gov (United States)

    Buhusi, Catalin V; Meck, Warren H

    2009-07-22

    Current theories of interval timing assume that humans and other animals time as if using a single, absolute stopwatch that can be stopped or reset on command. Here we evaluate the alternative view that psychological time is represented by multiple clocks, and that these clocks create separate temporal contexts by which duration is judged in a relative manner. Two predictions of the multiple-clock hypothesis were tested. First, that the multiple clocks can be manipulated (stopped and/or reset) independently. Second, that an event of a given physical duration would be perceived as having different durations in different temporal contexts, i.e., would be judged differently by each clock. Rats were trained to time three durations (e.g., 10, 30, and 90 s). When timing was interrupted by an unexpected gap in the signal, rats reset the clock used to time the "short" duration, stopped the "medium" duration clock, and continued to run the "long" duration clock. When the duration of the gap was manipulated, the rats reset these clocks in a hierarchical order, first the "short", then the "medium", and finally the "long" clock. Quantitative modeling assuming re-allocation of cognitive resources in proportion to the relative duration of the gap to the multiple, simultaneously timed event durations was used to account for the results. These results indicate that the three event durations were effectively timed by separate clocks operated independently, and that the same gap duration was judged relative to these three temporal contexts. Results suggest that the brain processes the duration of an event in a manner similar to Einstein's special relativity theory: A given time interval is registered differently by independent clocks dependent upon the context.

  5. Low Power GALS Interface Implementation with Stretchable Clocking Scheme

    OpenAIRE

    Anju C; Kirti S Pande

    2012-01-01

    Complex SoC imply the seamless integration of numerous IPs performing different functions and operating at different clock frequencies. The integration of several heterogeneous components into a single system gives rise to new challenges. Major issue includes controlling the clock frequencies of the different modules. As chips become faster and larger, designers face significant challenges including global clock distribution and power dissipation. In-order to achieve global synchronization wi...

  6. System-wide power management control via clock distribution network

    Science.gov (United States)

    Coteus, Paul W.; Gara, Alan; Gooding, Thomas M.; Haring, Rudolf A.; Kopcsay, Gerard V.; Liebsch, Thomas A.; Reed, Don D.

    2015-05-19

    An apparatus, method and computer program product for automatically controlling power dissipation of a parallel computing system that includes a plurality of processors. A computing device issues a command to the parallel computing system. A clock pulse-width modulator encodes the command in a system clock signal to be distributed to the plurality of processors. The plurality of processors in the parallel computing system receive the system clock signal including the encoded command, and adjusts power dissipation according to the encoded command.

  7. Glucocorticoids entrain molecular clock components in human peripheral cells.

    Science.gov (United States)

    Cuesta, Marc; Cermakian, Nicolas; Boivin, Diane B

    2015-04-01

    In humans, shift work induces a desynchronization between the circadian system and the outside world, which contributes to shift work-associated medical disorders. Using a simulated night shift experiment, we previously showed that 3 d of bright light at night fully synchronize the central clock to the inverted sleep schedule, whereas the peripheral clocks located in peripheral blood mononuclear cells (PBMCs) took longer to reset. This underlines the need for testing the effects of synchronizers on both the central and peripheral clocks. Glucocorticoids display circadian rhythms controlled by the central clock and are thought to act as synchronizers of rodent peripheral clocks. In the present study, we tested whether the human central and peripheral clocks were sensitive to exogenous glucocorticoids (Cortef) administered in the late afternoon. We showed that 20 mg Cortef taken orally acutely increased PER1 expression in PBMC peripheral clocks. After 6 d of Cortef administration, the phases of central markers were not affected, whereas those of PER2-3 and BMAL1 expression in PBMCs were shifted by ∼ 9.5-11.5 h. These results demonstrate, for the first time, that human peripheral clocks are entrained by glucocorticoids. Importantly, they suggest innovative interventions for shift workers and jet-lag travelers, combining synchronizing agents for the central and peripheral clocks. © FASEB.

  8. Clock genes show circadian rhythms in salivary glands.

    Science.gov (United States)

    Zheng, L; Seon, Y J; McHugh, J; Papagerakis, S; Papagerakis, P

    2012-08-01

    Circadian rhythms are endogenous self-sustained oscillations with 24-hour periods that regulate diverse physiological and metabolic processes through complex gene regulation by "clock" transcription factors. The oral cavity is bathed by saliva, and its amount and content are modified within regular daily intervals. The clock mechanisms that control salivary production remain unclear. Our objective was to evaluate the expression and periodicity of clock genes in salivary glands. Real-time quantitative RT-PCR, in situ hybridization, and immunohistochemistry were performed to show circadian mRNA and protein expression and localization of key clock genes (Bmal1, Clock, Per1, and Per2), ion and aqua channel genes (Ae2a, Car2, and Aqp5), and salivary gland markers. Clock gene mRNAs and clock proteins were found differentially expressed in the serous acini and duct cells of all major salivary glands. The expression levels of clock genes and Aqp5 showed regular oscillatory patterns under both light/dark and complete-dark conditions. Bmla1 overexpression resulted in increased Aqp5 expression levels. Analysis of our data suggests that salivary glands have a peripheral clock mechanism that functions both in normal light/dark conditions and in the absence of light. This finding may increase our understanding of the control mechanisms of salivary content and flow.

  9. The role of the mechanical clock in medieval science.

    Science.gov (United States)

    Álvarez, Víctor Pérez

    2015-03-01

    The invention and spread of the mechanical clock is a complex and multifaceted historical phenomenon. Some of these facets, such as its social impact, have been widely studied, but their scientific dimensions have often been dismissed. The mechanical clock was probably born as a scientific instrument for driving a model of the universe, and not only natural philosophers but also kings, nobles and other members of the social elites showed an interest in clocks as scientific instruments. Public clocks later spread a new way of telling time based on equal hours, laying the foundations for changes in time consciousness that would accelerate scientific thinking. Copyright © 2015 Elsevier Ltd. All rights reserved.

  10. Clock Genes: Critical Modulators of Breast Cancer Risk

    National Research Council Canada - National Science Library

    Kennaway, David J; Butler, Lisa M; Tilley, Wayne D

    2005-01-01

    .... Circadian rhythms are regulated by a panel of specific transcription factors, called clock genes, and our current understanding of endogenous cellular rhythmicity is that both positive and negative...

  11. Real-time geopotentiometry with synchronously linked optical lattice clocks

    CERN Document Server

    Takano, Tetsushi; Ushijima, Ichiro; Ohmae, Noriaki; Akatsuka, Tomoya; Yamaguchi, Atsushi; Kuroishi, Yuki; Munekane, Hiroshi; Miyahara, Basara; Katori, Hidetoshi

    2016-01-01

    According to the Einstein's theory of relativity, the passage of time changes in a gravitational field. On earth, raising a clock by one centimetre increases its tick rate by 1.1 parts in 10$^{18}$, enabling optical clocks to perform precision geodesy. Here, we demonstrate geopotentiometry by determining the height difference of master and slave clocks separated by 15 km with uncertainty of 5 cm. The subharmonic of the master clock is delivered through a telecom fibre to phase-lock and synchronously interrogate the slave clock. This protocol rejects laser noise in the comparison of two clocks, which improves the stability of measuring the gravitational red shift. Such phase-coherently operated clocks facilitate proposals for linking clocks and interferometers. Over half a year, 11 measurements determine the fractional frequency difference between the two clocks to be $1,652.9(5.9)\\times 10^{-18}$, or a height difference of 1,516(5) cm, consistent with an independent measurement by levelling and gravimetry. Ou...

  12. Unimodular trees versus Einstein trees

    Energy Technology Data Exchange (ETDEWEB)

    Alvarez, Enrique; Gonzalez-Martin, Sergio [Universidad Autonoma, Instituto de Fisica Teorica, IFT-UAM/CSIC, Madrid (Spain); Universidad Autonoma de Madrid, Departamento de Fisica Teorica, Madrid (Spain); Martin, Carmelo P. [Universidad Complutense de Madrid (UCM), Departamento de Fisica Teorica I Facultad de Ciencias Fisicas, Madrid (Spain)

    2016-10-15

    The maximally helicity violating tree-level scattering amplitudes involving three, four or five gravitons are worked out in Unimodular Gravity. They are found to coincide with the corresponding amplitudes in General Relativity. This a remarkable result, insofar as both the propagators and the vertices are quite different in the two theories. (orig.)

  13. Clocks underneath: the role of peripheral clocks in the timing of female reproductive physiology

    Directory of Open Access Journals (Sweden)

    Michael T Sellix

    2013-07-01

    Full Text Available The central circadian pacemaker in the suprachiasmatic nucleus (SCN is a critical component of the neuroendocrine circuit controlling gonadotropin secretion from the pituitary gland. The SCN conveys photic information to hypothalamic targets including the gonadotropin releasing hormone (GnRH neurons. Many of these target cells are also cell autonomous clocks. It has been suggested that, rather then being singularly driven by the SCN, the timing of gonadotropin secretion depends on the activity of multiple hypothalamic oscillators. While this view provides a novel twist to an old story, it does little to diminish the central role of rhythmic hypothalamic output in this system. It is now clear that the pituitary, ovary, uterus and oviduct have functional molecular clocks. Evidence supports the notion that the clocks in these tissues contribute to the timing of events in reproductive physiology. The goal of this review is to highlight the current evidence for molecular clock function in the peripheral components of the female hypothalamo-pituitary-gonadal (HPG axis as it relates to the timing of gonadotropin secretion, ovulation and parturition.

  14. Circadian expression of clock genes and clock-controlled genes in the rat retina

    NARCIS (Netherlands)

    Kamphuis, Willem; Cailotto, Cathy; Dijk, Frederike; Bergen, Arthur; Buijs, Ruud M.

    2005-01-01

    The circadian expression patterns of genes encoding for proteins that make up the core of the circadian clock were measured in rat retina using real-time quantitative PCR (qPCR). Transcript levels of several genes previously used for normalization of qPCR assays were determined and the effect of

  15. Technical Tree Climbing.

    Science.gov (United States)

    Jenkins, Peter

    Tree climbing offers a safe, inexpensive adventure sport that can be performed almost anywhere. Using standard procedures practiced in tree surgery or rock climbing, almost any tree can be climbed. Tree climbing provides challenge and adventure as well as a vigorous upper-body workout. Tree Climbers International classifies trees using a system…

  16. The circadian clock modulates enamel development.

    Science.gov (United States)

    Lacruz, Rodrigo S; Hacia, Joseph G; Bromage, Timothy G; Boyde, Alan; Lei, Yaping; Xu, Yucheng; Miller, Joseph D; Paine, Michael L; Snead, Malcolm L

    2012-06-01

    Fully mature enamel is about 98% mineral by weight. While mineral crystals appear very early during its formative phase, the newly secreted enamel is a soft gel-like matrix containing several enamel matrix proteins of which the most abundant is amelogenin (Amelx). Histological analysis of mineralized dental enamel reveals markings called cross-striations associated with daily increments of enamel formation, as evidenced by injections of labeling dyes at known time intervals. The daily incremental growth of enamel has led to the hypothesis that the circadian clock might be involved in the regulation of enamel development. To identify daily rhythms of clock genes and Amelx, we subjected murine ameloblast cells to serum synchronization to analyze the expression of the circadian transcription factors Per2 and Bmal1 by real-time PCR. Results indicate that these key genetic regulators of the circadian clock are expressed in synchronized murine ameloblast cell cultures and that their expression profile follows a circadian pattern with acrophase and bathyphase for both gene transcripts in antiphase. Immunohistological analysis confirms the protein expression of Bmal and Cry in enamel cells. Amelx expression in 2-day postnatal mouse molars dissected every 4 hours for a duration of 48 hours oscillated with an approximately 24-hour period, with a significant approximately 2-fold decrease in expression during the dark period compared to the light period. The expression of genes involved in bicarbonate production (Car2) and transport (Slc4a4), as well as in enamel matrix endocytosis (Lamp1), was greater during the dark period, indicating that ameloblasts express these proteins when Amelx expression is at the nadir. The human and mouse Amelx genes each contain a single nonconserved E-box element within 10 kb upstream of their respective transcription start sites. We also found that within 2 kb of the transcription start site of the human NFYA gene, which encodes a positive

  17. Food at work around the clock

    DEFF Research Database (Denmark)

    Dahl Lassen, Anne; Beck, Anne Marie; Thorsen, Anne Vibeke

    This report brings together 12 invited presentations and outcomes of a workshop on food and meals for employees working irregular hours “around the clock”. The workshop, “Food at work around the clock – The Nordic Model”, was hosted by the National Food Institute at the Technical University...... of Denmark on November 4, 2016, in Lyngby, near Copenhagen, Denmark. This was a culmination of the collaboration started in 2015 between researchers from the hosts institute, Gävle University and Kristianstad University in Sweden, and the School of Applied Educational Sciences and Teacher Education...

  18. Sumoylation Contributes to Timekeeping and Temperature Compensation of the Plant Circadian Clock

    NARCIS (Netherlands)

    Hansen, L.L; van den Burg, H.A.; van Ooijen, G.

    2017-01-01

    The transcriptional circadian clock network is tuned into a 24-h oscillator by numerous posttranslational modifications on the proteins encoded by clock genes, differentially influencing their subcellular localization or activity. Clock proteins in any circadian organism are subject to

  19. Clock genes of Mammalian cells: practical implications in tissue culture.

    Science.gov (United States)

    Kaeffer, Bertrand; Pardini, Lissia

    2005-01-01

    The clock genes family is expressed by all the somatic cells driving central and peripheral circadian rhythms through transcription/translation feedback loops. The circadian clock provides a local time for a cell and a way to integrate the normal environmental changes to smoothly adapt the cellular machinery to new conditions. The central circadian rhythm is retained in primary cultures by neurons of the suprachiasmatic nuclei. The peripheral circadian rhythms of the other somatic cells are progressively dampened down up to loss unless neuronal signals of the central clock are provided for re-entrainment. Under typical culture conditions (obscurity, 37 +/- 1 degrees C, 5-7% CO(2)), freshly explanted peripheral cells harbor chaotic expression of clock genes for 12-14 h and loose, coordinated oscillating patterns of clock components. Cells of normal or cancerous phenotypes established in culture harbor low levels of clock genes idling up to the re-occurrence of new synchronizer signals. Synchronizers are physicochemical cues (like thermic oscillations, short-term exposure to high concentrations of serum or single medium exchange) able to re-induce molecular oscillations of clock genes. The environmental synchronizers are integrated by response elements located in the promoter region of period genes that drive the central oscillator complex (CLOCK:BMAL1 and NPAS2:BMAL1 heterodimers). Only a few cell lines from different species and lineages have been tested for the existence or the functioning of a circadian clockwork. The best characterized cell lines are the immortalized SCN2.2 neurons of rat suprachiasmatic nuclei for the central clock and the Rat-1 fibroblasts or the NIH/3T3 cells for peripheral clocks. Isolation methods of fragile cell phenotypes may benefit from research on the biological clocks to design improved tissue culture media and new bioassays to diagnose pernicious consequences for health of circadian rhythm alterations.

  20. The Renaissance or the cuckoo clock.

    Science.gov (United States)

    Pines, Jonathon; Hagan, Iain

    2011-12-27

    '…in Italy, for thirty years under the Borgias, they had warfare, terror, murder and bloodshed, but they produced Michelangelo, Leonardo da Vinci and the Renaissance. In Switzerland, they had brotherly love, they had five hundred years of democracy and peace-and what did that produce? The cuckoo clock'. Orson Welles as Harry Lime: The Third Man. Orson Welles might have been a little unfair on the Swiss, after all cuckoo clocks were developed in the Schwartzwald, but, more importantly, Swiss democracy gives remarkably stable government with considerable decision-making at the local level. The alternative is the battling city-states of Renaissance Italy: culturally rich but chaotic at a higher level of organization. As our understanding of the cell cycle improves, it appears that the cell is organized more along the lines of Switzerland than Renaissance Italy, and one major challenge is to determine how local decisions are made and coordinated to produce the robust cell cycle mechanisms that we observe in the cell as a whole.

  1. Animal clocks: when science meets nature.

    Science.gov (United States)

    Kronfeld-Schor, Noga; Bloch, Guy; Schwartz, William J

    2013-08-22

    Daily rhythms of physiology and behaviour are governed by an endogenous timekeeping mechanism (a circadian 'clock'), with the alternation of environmental light and darkness synchronizing (entraining) these rhythms to the natural day-night cycle. Our knowledge of the circadian system of animals at the molecular, cellular, tissue and organismal levels is remarkable, and we are beginning to understand how each of these levels contributes to the emergent properties and increased complexity of the system as a whole. For the most part, these analyses have been carried out using model organisms in standard laboratory housing, but to begin to understand the adaptive significance of the clock, we must expand our scope to study diverse animal species from different taxonomic groups, showing diverse activity patterns, in their natural environments. The seven papers in this Special Feature of Proceedings of the Royal Society B take on this challenge, reviewing the influences of moonlight, latitudinal clines, evolutionary history, social interactions, specialized temporal niches, annual variation and recently appreciated post-transcriptional molecular mechanisms. The papers emphasize that the complexity and diversity of the natural world represent a powerful experimental resource.

  2. Synthetic clock transitions via continuous dynamical decoupling

    Science.gov (United States)

    Trypogeorgos, D.; Valdés-Curiel, A.; Lundblad, N.; Spielman, I. B.

    2018-01-01

    Decoherence of quantum systems due to uncontrolled fluctuations of the environment presents fundamental obstacles in quantum science. Clock transitions which are insensitive to such fluctuations are used to improve coherence, however, they are not present in all systems or for arbitrary system parameters. Here we create a trio of synthetic clock transitions using continuous dynamical decoupling in a spin-1 Bose-Einstein condensate in which we observe a reduction of sensitivity to magnetic-field noise of up to four orders of magnitude; this work complements the parallel work by Anderson et al. [R. P. Anderson et al., following paper, Phys. Rev. A 97, 013408 (2018), 10.1103/PhysRevA.97.013408]. In addition, using a concatenated scheme, we demonstrate suppression of sensitivity to fluctuations in our control fields. These field-insensitive states represent an ideal foundation for the next generation of cold-atom experiments focused on fragile many-body phases relevant to quantum magnetism, artificial gauge fields, and topological matter.

  3. Temperature-Compensated Clock Skew Adjustment

    Directory of Open Access Journals (Sweden)

    Joaquín Olivares

    2013-08-01

    Full Text Available This work analyzes several drift compensation mechanisms in wireless sensor networks (WSN. Temperature is an environmental factor that greatly affects oscillators shipped in every WSN mote. This behavior creates the need of improving drift compensation mechanisms in synchronization protocols. Using the Flooding Time Synchronization Protocol (FTSP, this work demonstrates that crystal oscillators are affected by temperature variations. Thus, the influence of temperature provokes a low performance of FTSP in changing conditions of temperature. This article proposes an innovative correction factor that minimizes the impact of temperature in the clock skew. By means of this factor, two new mechanisms are proposed in this paper: the Adjusted Temperature (AT and the Advanced Adjusted Temperature (A2T. These mechanisms have been combined with FTSP to produce AT-FTSP and A2T-FTSP. Both have been tested in a network of TelosB motes running TinyOS. Results show that both AT-FTSP and A2T-FTSP improve the average synchronization errors compared to FTSP and other temperature-compensated protocols (Environment-Aware Clock Skew Estimation and Synchronization for WSN (EACS and Temperature Compensated Time Synchronization (TCTS.

  4. The Circadian Clock and Human Health.

    Science.gov (United States)

    Roenneberg, Till; Merrow, Martha

    2016-05-23

    Epidemiological studies provided the first evidence suggesting a connection between the circadian clock and human health. Mutant mice convincingly demonstrate the principle that dysregulation of the circadian system leads to a multitude of pathologies. Chrono-medicine is one of the most important upcoming themes in the field of circadian biology. Although treatments counteracting circadian dysregulation are already being applied (e.g., prescribing strong and regular zeitgebers), we need to comprehend entrainment throughout the body's entire circadian network before understanding the mechanisms that tie circadian dysregulation to pathology. Here, we attempt to provide a systematic approach to understanding the connection between the circadian clock and health. This taxonomy of (mis)alignments on one hand exposes how little we know about entrainment within any organism and which 'eigen-zeitgeber' signals are used for entrainment by the different cells and tissues. On the other hand, it provides focus for experimental approaches and tools that will logically map out how circadian systems contribute to disease as well as how we can treat and prevent them. Copyright © 2016 Elsevier Ltd. All rights reserved.

  5. ClockWork: a Real-Time Feasibility Analysis Tool

    NARCIS (Netherlands)

    Jansen, P.G.; Hanssen, F.T.Y.; Mullender, Sape J.

    ClockWork shows that we can improve the flexibility and efficiency of real-time kernels. We do this by proposing methods for scheduling based on so-called Real-Time Transactions. ClockWork uses Real-Time Transactions which allow scheduling decisions to be taken by the system. A programmer does not

  6. A Novel Method of Clock Synchronization in Distributed Systems

    Science.gov (United States)

    Li, Gun; Niu, Meng-jie; Chai, Yang-shun; Chen, Xin; Ren, Yan-qiu

    2017-04-01

    Time synchronization plays an important role in the spacecraft formation flight and constellation autonomous navigation, etc. For the application of clock synchronization in a network system, it is not always true that all the observed nodes in the network are interconnected, therefore, it is difficult to achieve the high-precision time synchronization of a network system in the condition that a certain node can only obtain the measurement information of clock from a single neighboring node, but cannot obtain it from other nodes. Aiming at this problem, a novel method of high-precision time synchronization in a network system is proposed. In this paper, each clock is regarded as a node in the network system, and based on the definition of different topological structures of a distributed system, the three control algorithms of time synchronization under the following three cases are designed: without a master clock (reference clock), with a master clock (reference clock), and with a fixed communication delay in the network system. And the validity of the designed clock synchronization protocol is proved by both stability analysis and numerical simulation.

  7. Circadian clock regulation of skeletal muscle growth and repair.

    Science.gov (United States)

    Chatterjee, Somik; Ma, Ke

    2016-01-01

    Accumulating evidence indicates that the circadian clock, a transcriptional/translational feedback circuit that generates ~24-hour oscillations in behavior and physiology, is a key temporal regulatory mechanism involved in many important aspects of muscle physiology. Given the clock as an evolutionarily-conserved time-keeping mechanism that synchronizes internal physiology to environmental cues, locomotor activities initiated by skeletal muscle enable entrainment to the light-dark cycles on earth, thus ensuring organismal survival and fitness. Despite the current understanding of the role of molecular clock in preventing age-related sarcopenia, investigations into the underlying molecular pathways that transmit clock signals to the maintenance of skeletal muscle growth and function are only emerging. In the current review, the importance of the muscle clock in maintaining muscle mass during development, repair and aging, together with its contribution to muscle metabolism, will be discussed. Based on our current understandings of how tissue-intrinsic muscle clock functions in the key aspects muscle physiology, interventions targeting the myogenic-modulatory activities of the clock circuit may offer new avenues for prevention and treatment of muscular diseases. Studies of mechanisms underlying circadian clock function and regulation in skeletal muscle warrant continued efforts.

  8. The circadian clock in oral health and diseases.

    Science.gov (United States)

    Papagerakis, S; Zheng, L; Schnell, S; Sartor, M A; Somers, E; Marder, W; McAlpin, B; Kim, D; McHugh, J; Papagerakis, P

    2014-01-01

    Most physiological processes in mammals display circadian rhythms that are driven by the endogenous circadian clock. This clock is comprised of a central component located in the hypothalamic suprachiasmatic nucleus and subordinate clocks in peripheral tissues. Circadian rhythms sustain 24-hour oscillations of a large number of master genes controlling the correct timing and synchronization of diverse physiological and metabolic processes within our bodies. This complex regulatory network provides an important communication link between our brain and several peripheral organs and tissues. At the molecular level, circadian oscillations of gene expression are regulated by a family of transcription factors called "clock genes". Dysregulation of clock gene expression results in diverse human pathological conditions, including autoimmune diseases and cancer. There is increasing evidence that the circadian clock affects tooth development, salivary gland and oral epithelium homeostasis, and saliva production. This review summarizes current knowledge of the roles of clock genes in the formation and maintenance of oral tissues, and discusses potential links between "oral clocks" and diseases such as head and neck cancer and Sjögren's syndrome.

  9. Assignment of circadian function for the Neurospora clock gene frequency

    NARCIS (Netherlands)

    Merrow, Martha; Brunner, Michael; Roenneberg, Till

    1999-01-01

    Circadian clocks consist of three elements: entrainment pathways (inputs), the mechanism generating the rhythmicity (oscillator), and the output pathways that control the circadian rhythms. It is difficult to assign molecular clock components to any one of these elements. Experiments show that

  10. The role of biological clock in glucose homeostasis 

    Directory of Open Access Journals (Sweden)

    Piotr Chrościcki

    2013-06-01

    Full Text Available The mechanism of the biological clock is based on a rhythmic expression of clock genes and clock-controlled genes. As a result of their transcripto-translational associations, endogenous rhythms in the synthesis of key proteins of various physiological and metabolic processes are created. The major timekeeping mechanism for these rhythms exists in the central nervous system. The master circadian clock, localized in suprachiasmatic nucleus (SCN, regulates multiple metabolic pathways, while feeding behavior and metabolite availability can in turn regulate the circadian clock. It is also suggested that in the brain there is a food entrainable oscillator (FEO or oscillators, resulting in activation of both food anticipatory activity and hormone secretion that control digestion processes. Moreover, most cells and tissues express autonomous clocks. Maintenance of the glucose homeostasis is particularly important for the proper function of the body, as this sugar is the main source of energy for the brain, retina, erythrocytes and skeletal muscles. Thus, glucose production and utilization are synchronized in time. The hypothalamic excited orexin neurons control energy balance of organism and modulate the glucose production and utilization. Deficiency of orexin action results in narcolepsy and weight gain, whereas glucose and amino acids can affect activity of the orexin cells. Large-scale genetic studies in rodents and humans provide evidence for the involvement of disrupted clock gene expression rhythms in the pathogenesis of obesity and type 2 diabetes. In general, the current lifestyle of the developed modern societies disturbs the action of biological clock

  11. Design and implementation of a digital thermometer with clock ...

    African Journals Online (AJOL)

    Design and implementation of a digital thermometer with clock. ... Global Journal of Engineering Research ... The design was achieved using ATMEGA 328P PU Microcontroller Unit, MLX90614 Infrared Sensor for achieving contactless measurement (wireless) and the DS1307 Real Time Clock (RTC) for accurate time ...

  12. Characterization of the uncertainty of divergence time estimation under relaxed molecular clock models using multiple loci.

    Science.gov (United States)

    Zhu, Tianqi; Dos Reis, Mario; Yang, Ziheng

    2015-03-01

    Genetic sequence data provide information about the distances between species or branch lengths in a phylogeny, but not about the absolute divergence times or the evolutionary rates directly. Bayesian methods for dating species divergences estimate times and rates by assigning priors on them. In particular, the prior on times (node ages on the phylogeny) incorporates information in the fossil record to calibrate the molecular tree. Because times and rates are confounded, our posterior time estimates will not approach point values even if an infinite amount of sequence data are used in the analysis. In a previous study we developed a finite-sites theory to characterize the uncertainty in Bayesian divergence time estimation in analysis of large but finite sequence data sets under a strict molecular clock. As most modern clock dating analyses use more than one locus and are conducted under relaxed clock models, here we extend the theory to the case of relaxed clock analysis of data from multiple loci (site partitions). Uncertainty in posterior time estimates is partitioned into three sources: Sampling errors in the estimates of branch lengths in the tree for each locus due to limited sequence length, variation of substitution rates among lineages and among loci, and uncertainty in fossil calibrations. Using a simple but analogous estimation problem involving the multivariate normal distribution, we predict that as the number of loci ([Formula: see text]) goes to infinity, the variance in posterior time estimates decreases and approaches the infinite-data limit at the rate of 1/[Formula: see text], and the limit is independent of the number of sites in the sequence alignment. We then confirmed the predictions by using computer simulation on phylogenies of two or three species, and by analyzing a real genomic data set for six primate species. Our results suggest that with the fossil calibrations fixed, analyzing multiple loci or site partitions is the most effective way

  13. The quantum beat principles and applications of atomic clocks

    CERN Document Server

    Major, F

    2007-01-01

    This work attempts to convey a broad understanding of the physical principles underlying the workings of these quantum-based atomic clocks, with introductory chapters placing them in context with the early development of mechanical clocks and the introduction of electronic time-keeping as embodied in the quartz-controlled clocks. While the book makes no pretense at being a history of atomic clocks, it nevertheless takes a historical perspective in its treatment of the subject. Intended for nonspecialists with some knowledge of physics or engineering, The Quantum Beat covers a wide range of salient topics relevant to atomic clocks, treated in a broad intuitive manner with a minimum of mathematical formalism. Detailed descriptions are given of the design principles of the rubidium, cesium, hydrogen maser, and mercury ion standards; the revolutionary changes that the advent of the laser has made possible, such as laser cooling, optical pumping, the formation of "optical molasses," and the cesium "fountain" stand...

  14. Optical clocks and their contribution to gravity modeling

    Science.gov (United States)

    Naeimi, Mohammad; Mohamadhosseini, Babak; Hatami, Mohsen

    2016-04-01

    Optical clocks, as one of the latest achievements in atomic and molecular physics, have applications more than timing, due to their accuracy and stability. In general relativity, gravitational potential differences in space and time, cause frequency difference in optical clocks. Hence, ultra precise optical clocks can be used as a tool to observe potential differences and consequently as a new gravimetry technique. In this contribution, we investigate the latest optical clocks based on atomic transition in Al+ and derive a simple equation for frequency change related to geo-potential differences. Moreover, we consider the capability of optical clocks for gravity modeling in combination with other gravity observations. Finally, the possibility to detect potential changes in geo-dynamically active zones, such as East-Asia and the requirements for such studies are discussed.

  15. Standard Clock in primordial density perturbations and cosmic microwave background

    Directory of Open Access Journals (Sweden)

    Xingang Chen

    2014-12-01

    Full Text Available Standard Clocks in the primordial epoch leave a special type of features in the primordial perturbations, which can be used to directly measure the scale factor of the primordial universe as a function of time a(t, thus discriminating between inflation and alternatives. We have started to search for such signals in the Planck 2013 data using the key predictions of the Standard Clock. In this Letter, we summarize the key predictions of the Standard Clock and present an interesting candidate example in Planck 2013 data. Motivated by this candidate, we construct and compute full Standard Clock models and use the more complete prediction to make more extensive comparison with data. Although this candidate is not yet statistically significant, we use it to illustrate how Standard Clocks appear in Cosmic Microwave Background (CMB and how they can be further tested by future data. We also use it to motivate more detailed theoretical model building.

  16. Parcs:. a Laser-Cooled Atomic Clock in Space

    Science.gov (United States)

    Heavner, T. P.; Hollberg, L. W.; Jefferts, S. R.; Robinson, H. G.; Sullivan, D. B.; Walls, F. L.; Ashby, N.; Klipstein, W. M.; Maleki, L.; Seidel, D. J.; Thompson, R. J.; Wu, S.; Young, L.; Mattison, E. M.; Vessot, R. F. C.; Demarchi, A.

    2002-04-01

    This paper describes progress toward the development of a Primary Atomic Reference Clock in Space (PARCS) and reviews the scientific and technical objectives of the PARCS mission. PARCS is a collaborative effort involving the National Institute of Standards and Technology (NIST), the University of Colorado, the Jet Propulsion Laboratory (JPL), the Harvard Smithsonian Center for Astrophysics (SAO) and the Politecnico di Torino. Space systems for this experiment include a laser-cooled cesium atomic clock and a GPS frequency-comparison and orbit determination system, along with a hydrogen maser that serves as both a local oscillator for the cesium clock and a reference against which certain tests of gravitational theory can be made. In the microgravity environment of the International Space Station (ISS), cesium atoms can be launched more slowly through the clock's microwave cavity, thus significantly reducing a number of troubling effects (including several critical systematic effects), so clock performance can be substantially improved beyond that achieved on earth.

  17. Molecular Mechanisms Regulating Temperature Compensation of the Circadian Clock

    Directory of Open Access Journals (Sweden)

    David M. Virshup

    2017-04-01

    Full Text Available An approximately 24-h biological timekeeping mechanism called the circadian clock is present in virtually all light-sensitive organisms from cyanobacteria to humans. The clock system regulates our sleep–wake cycle, feeding–fasting, hormonal secretion, body temperature, and many other physiological functions. Signals from the master circadian oscillator entrain peripheral clocks using a variety of neural and hormonal signals. Even centrally controlled internal temperature fluctuations can entrain the peripheral circadian clocks. But, unlike other chemical reactions, the output of the clock system remains nearly constant with fluctuations in ambient temperature, a phenomenon known as temperature compensation. In this brief review, we focus on recent advances in our understanding of the posttranslational modifications, especially a phosphoswitch mechanism controlling the stability of PER2 and its implications for the regulation of temperature compensation.

  18. Trees are good, but…

    Science.gov (United States)

    E.G. McPherson; F. Ferrini

    2010-01-01

    We know that “trees are good,” and most people believe this to be true. But if this is so, why are so many trees neglected, and so many tree wells empty? An individual’s attitude toward trees may result from their firsthand encounters with specific trees. Understanding how attitudes about trees are shaped, particularly aversion to trees, is critical to the business of...

  19. Circadian clock genes as modulators of sensitivity to genotoxic stress.

    Science.gov (United States)

    Antoch, Marina P; Kondratov, Roman V; Takahashi, Joseph S

    2005-07-01

    A broad variety of organisms display circadian rhythms (i.e., oscillations with 24-hr periodicities) in many aspects of their behavior, physiology and metabolism. These rhythms are under genetic control and are generated endogenously at the cellular level. In mammals, the core molecular mechanism of the oscillator consists of two transcriptional activators, CLOCK and BMAL1, and their transcriptional targets, CRYPTOCHROMES (CRYS) and PERIODS (PERS). The CRY and PER proteins function as negative regulators of CLOCK/BMAL1 activity, thus forming the major circadian autoregulatory feedback loop. It is believed that the circadian clock system regulates daily variations in output physiology and metabolism through periodic activation/repression of the set of clock-controlled genes that are involved in various metabolic pathways. Importantly, circadian-controlled pathways include those that determine in vivo responses to genotoxic stress. By using circadian mutant mice deficient in different components of the molecular clock system, we have established genetic models that correlate with the two opposite extremes of circadian cycle as reflected by the activity of the CLOCK/BMAL1 transactivation complex. Comparison of the in vivo responses of these mutants to the chemotherapeutic drug, cyclophosphamide (CY), has established a direct correlation between drug toxicity and the functional status of the CLOCK/BMAL1 transcriptional complex. We have also demonstrated that CLOCK/BMAL1 modulates sensitivity to drug-induced toxicity by controlling B cell responses to active CY metabolites. These results suggest that the sensitivity of cells to genotoxic stress induced by anticancer therapy may be modulated by CLOCK/BMAL1 transcriptional activity. Further elucidation of the molecular mechanisms of circadian control as well as identification of specific pharmacological modulators of CLOCK/BMAL1 activity are likely to lead to the development of new anti-cancer treatment schedules with

  20. Math Clock: Perangkat Penunjuk Waktu Kreatif untuk Olahraga Otak

    Directory of Open Access Journals (Sweden)

    Galuh Boy Hertantyo

    2014-11-01

    Full Text Available Brain is one of the most vital parts for humans, with the number of brain function that is needed for the body, the brain becomes a very important part of the human body. If there is damage to the brain will certainly cause the performance of the human body will not run properly. Because of that, it’s very important to maintain brain health. There is a way to maintain brain health, for example is by doing brain exercise. Examples of brain exercise is to do simple math calculations or doing brain games like sudoku. Because of that, created a tool that can help the brain to maintain brain exercise. The tool is called math clock. Making math clock tool consists of hardware and software. The hardware consists of RTC as real time data input, ATmega328 as microcontroller and dot matrix 32x16 as a tool to display the output that has been processed by the microcontroller. The software is built using C with Arduino IDE. Math clock will process the data from RTC then processed it, in microcontroller so when output displayed on dot matrix, output will be simple mathematical operation with real time clock data on it. Test results show that, math clock is capable of displaying a simple mathematical calculation operations such as addition, subtraction, multiplication and division. The mathematical operation that display on math clock, appears to be random, so it’s not triggered by same mathematical operation. In math clock the display will change every 20 second, so in 1 minute there are 3 different kinds of mathematical operations. The results of questionnaires of 10 different students, showed 9 out of 10 students said math clock is a tool that easy to use as a clock. Math clock will be alternative for doing brain exercise every day.

  1. Circadian Clock Involvement in Zooplankton Diel Vertical Migration.

    Science.gov (United States)

    Häfker, N Sören; Meyer, Bettina; Last, Kim S; Pond, David W; Hüppe, Lukas; Teschke, Mathias

    2017-07-24

    Biological clocks are a ubiquitous ancient and adaptive mechanism enabling organisms to anticipate environmental cycles and to regulate behavioral and physiological processes accordingly [1]. Although terrestrial circadian clocks are well understood, knowledge of clocks in marine organisms is still very limited [2-5]. This is particularly true for abundant species displaying large-scale rhythms like diel vertical migration (DVM) that contribute significantly to shaping their respective ecosystems [6]. Here we describe exogenous cycles and endogenous rhythms associated with DVM of the ecologically important and highly abundant planktic copepod Calanus finmarchicus. In the laboratory, C. finmarchicus shows circadian rhythms of DVM, metabolism, and most core circadian clock genes (clock, period1, period2, timeless, cryptochrome2, and clockwork orange). Most of these genes also cycle in animals assessed in the wild, though expression is less rhythmic at depth (50-140 m) relative to shallow-caught animals (0-50 m). Further, peak expressions of clock genes generally occurred at either sunset or sunrise, coinciding with peak migration times. Including one of the first field investigations of clock genes in a marine species [5, 7], this study couples clock gene measurements with laboratory and field data on DVM. While the mechanistic connection remains elusive, our results imply a high degree of causality between clock gene expression and one of the planet's largest daily migrations of biomass. We thus suggest that circadian clocks increase zooplankton fitness by optimizing the temporal trade-off between feeding and predator avoidance, especially when environmental drivers are weak or absent [8]. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  2. The genetic basis of the circadian clock : identification of frq and FRQ as clock components in Neurospora

    NARCIS (Netherlands)

    Dunlap, Jay C.; Loros, Jennifer J.; Aronson, Benjamin D.; Merrow, Martha; Crosthwaite, Susan; Bell-Pedersen, Deborah; Johnson, Keith; Lindgren, Kristin; Garceau, Norman Y.

    1995-01-01

    Genetic approaches to the identification of clock components have succeeded in two model systems, Neurospora and Drosophila. In each organism, genes identified through screens for clock-affecting mutations (frq in Neurospora, per in Drosophila) have subsequently been shown to have characteristics of

  3. An Overview of Monthly Rhythms and Clocks

    Directory of Open Access Journals (Sweden)

    Florian Raible

    2017-05-01

    Full Text Available Organisms have evolved to cope with geophysical cycles of different period lengths. In this review, we focus on the adaptations of animals to the lunar cycle, specifically, on the occurrence of biological rhythms with monthly (circalunar or semi-monthly (circasemilunar period lengths. Systematic experimental investigation, starting in the early twentieth century, has allowed scientists to distinguish between mythological belief and scientific facts concerning the influence of the lunar cycle on animals. These studies revealed that marine animals of various taxa exhibit circalunar or circasemilunar reproductive rhythms. Some of these rely on endogenous oscillators (circalunar or circasemilunar clocks, whereas others are directly driven by external cues, such as the changes in nocturnal illuminance. We review current insight in the molecular and cellular mechanisms involved in circalunar rhythms, focusing on recent work in corals, annelid worms, midges, and fishes. In several of these model systems, the transcript levels of some core circadian clock genes are affected by both light and endogenous circalunar oscillations. How these and other molecular changes relate to the changes in physiology or behavior over the lunar cycle remains to be determined. We further review the possible relevance of circalunar rhythms for terrestrial species, with a particular focus on mammalian reproduction. Studies on circalunar rhythms of conception or birth rates extend to humans, where the lunar cycle was suggested to also affect sleep and mental health. While these reports remain controversial, factors like the increase in “light pollution” by artificial light might contribute to discrepancies between studies. We finally discuss the existence of circalunar oscillations in mammalian physiology. We speculate that these oscillations could be the remnant of ancient circalunar oscillators that were secondarily uncoupled from a natural entrainment mechanism, but

  4. Cryptochrome mediates light-dependent magnetosensitivity of Drosophila's circadian clock.

    Directory of Open Access Journals (Sweden)

    Taishi Yoshii

    2009-04-01

    Full Text Available Since 1960, magnetic fields have been discussed as Zeitgebers for circadian clocks, but the mechanism by which clocks perceive and process magnetic information has remained unknown. Recently, the radical-pair model involving light-activated photoreceptors as magnetic field sensors has gained considerable support, and the blue-light photoreceptor cryptochrome (CRY has been proposed as a suitable molecule to mediate such magnetosensitivity. Since CRY is expressed in the circadian clock neurons and acts as a critical photoreceptor of Drosophila's clock, we aimed to test the role of CRY in magnetosensitivity of the circadian clock. In response to light, CRY causes slowing of the clock, ultimately leading to arrhythmic behavior. We expected that in the presence of applied magnetic fields, the impact of CRY on clock rhythmicity should be altered. Furthermore, according to the radical-pair hypothesis this response should be dependent on wavelength and on the field strength applied. We tested the effect of applied static magnetic fields on the circadian clock and found that flies exposed to these fields indeed showed enhanced slowing of clock rhythms. This effect was maximal at 300 muT, and reduced at both higher and lower field strengths. Clock response to magnetic fields was present in blue light, but absent under red-light illumination, which does not activate CRY. Furthermore, cry(b and cry(OUT mutants did not show any response, and flies overexpressing CRY in the clock neurons exhibited an enhanced response to the field. We conclude that Drosophila's circadian clock is sensitive to magnetic fields and that this sensitivity depends on light activation of CRY and on the applied field strength, consistent with the radical pair mechanism. CRY is widespread throughout biological systems and has been suggested as receptor for magnetic compass orientation in migratory birds. The present data establish the circadian clock of Drosophila as a model system

  5. Transcriptional oscillation of canonical clock genes in mouse peripheral tissues

    Directory of Open Access Journals (Sweden)

    Nakahata Yasukazu

    2004-10-01

    Full Text Available Abstract Background The circadian rhythm of about 24 hours is a fundamental physiological function observed in almost all organisms from prokaryotes to humans. Identification of clock genes has allowed us to study the molecular bases for circadian behaviors and temporal physiological processes such as hormonal secretion, and has prompted the idea that molecular clocks reside not only in a central pacemaker, the suprachiasmatic nuclei (SCN of hypothalamus in mammals, but also in peripheral tissues, even in immortalized cells. Furthermore, previous molecular dissection revealed that the mechanism of circadian oscillation at a molecular level is based on transcriptional regulation of clock and clock-controlled genes. Results We systematically analyzed the mRNA expression of clock and clock-controlled genes in mouse peripheral tissues. Eight genes (mBmal1, mNpas2, mRev-erbα, mDbp, mRev-erbβ, mPer3, mPer1 and mPer2; given in the temporal order of the rhythm peak showed robust circadian expressions of mRNAs in all tissues except testis, suggesting that these genes are core molecules of the molecular biological clock. The bioinformatics analysis revealed that these genes have one or a combination of 3 transcriptional elements (RORE, DBPE, and E-box, which are conserved among human, mouse, and rat genome sequences, and indicated that these 3 elements may be responsible for the biological timing of expression of canonical clock genes. Conclusions The observation of oscillatory profiles of canonical clock genes is not only useful for physiological and pathological examination of the circadian clock in various organs but also important for systematic understanding of transcriptional regulation on a genome-wide basis. Our finding of the oscillatory expression of canonical clock genes with a temporal order provides us an interesting hypothesis, that cyclic timing of all clock and clock-controlled genes may be dependent on several transcriptional elements

  6. Simple street tree sampling

    Science.gov (United States)

    David J. Nowak; Jeffrey T. Walton; James Baldwin; Jerry. Bond

    2015-01-01

    Information on street trees is critical for management of this important resource. Sampling of street tree populations provides an efficient means to obtain street tree population information. Long-term repeat measures of street tree samples supply additional information on street tree changes and can be used to report damages from catastrophic events. Analyses of...

  7. Modular tree automata

    DEFF Research Database (Denmark)

    Bahr, Patrick

    2012-01-01

    Tree automata are traditionally used to study properties of tree languages and tree transformations. In this paper, we consider tree automata as the basis for modular and extensible recursion schemes. We show, using well-known techniques, how to derive from standard tree automata highly modular r...

  8. Programming macro tree transducers

    DEFF Research Database (Denmark)

    Bahr, Patrick; Day, Laurence E.

    2013-01-01

    A tree transducer is a set of mutually recursive functions transforming an input tree into an output tree. Macro tree transducers extend this recursion scheme by allowing each function to be defined in terms of an arbitrary number of accumulation parameters. In this paper, we show how macro tree ...

  9. Integration of biological clocks and rhythms.

    Science.gov (United States)

    Refinetti, Roberto

    2012-04-01

    Animals, plants, and microorganisms exhibit numerous biological rhythms that are generated by numerous biological clocks. This article summarizes experimental data pertinent to the often-ignored issue of integration of multiple rhythms. Five contexts of integration are discussed: (i) integration of circadian rhythms of multiple processes within an individual organism, (ii) integration of biological rhythms operating in different time scales (such as tidal, daily, and seasonal), (iii) integration of rhythms across multiple species, (iv) integration of rhythms of different members of a species, and (v) integration of rhythmicity and physiological homeostasis. Understanding of these multiple rhythmic interactions is an important first step in the eventual thorough understanding of how organisms arrange their vital functions temporally within and without their bodies. © 2012 American Physiological Society. Compr Physiol 2:1213-1239, 2012.

  10. Energy efficient lighting for the biological clock

    Science.gov (United States)

    Lang, Dieter

    2011-03-01

    Unexpectedly the existence of a formerly unknown type of photoreceptor in the human eye has been proven about 10 years ago. Primarily sensitive in the blue spectral range it is responsible for transducing light signals directly into the brain, controlling essential biological functions like setting of the circadian clock or daytime activation. Recent scientific research has enabled beneficial applications. The paradigms for good lighting design are shifting and standardization activities have been started to build up a sound base for description and application of biologically effective lighting. Latest improvements of LED technology are now allowing realizeation of advanced lighting solutions based on SSL. Optimization of biological effects is possible while demands on good vision are maintained. As biologically effective lighting is addressing a second system besides vision in the human body a measure beyond lumen per watt is required for a proper description of energy efficiency.

  11. A strontium lattice clock with reduced blackbody radiation shift

    Energy Technology Data Exchange (ETDEWEB)

    Al-Masoudi, Ali Khalas Anfoos

    2016-09-30

    Optical clocks have been quickly moving to the forefront of the frequency standards field due to their high spectral resolution, and therefore the potential high stability and accuracy. The accuracy and stability of the optical clocks are nowadays two orders of magnitude better than microwave Cs clocks, which realize the SI second. Envisioned applications of highly accurate optical clocks are to perform tests of fundamental physics, for example, searching for temporal drifts of the fine structure constant α, violations of the Local Position Invariance (LPI), dark matter and dark energy, or to performance relativistic geodesy. In this work, the uncertainty of a strontium lattice clock, based on the {sup 1}S{sub 0}-{sup 3}P{sub 0} transition in {sup 87}Sr, due to the blackbody radiation (BBR) shift has been reduced to less than 1 x 10{sup -18} by more than one order of magnitude compared to the previous evaluation of the BBR shift uncertainty in this clock. The BBR shift has been reduced by interrogating the atoms in a cryogenic environment. The systematic uncertainty of the cryogenic lattice clock is evaluated to be 1.3 x 10{sup -17} which is dominated by the uncertainty of the AC Stark shift of the lattice laser and the uncertainty contribution of the BBR shift is negligible. Concerning the instability of the clock, the detection noise of the clock has been measured, and a model linking noise and clock instability has been developed. This noise model shows that, in our lattice clock, quantum projection noise is reached if more than 130 atoms are interrogated. By combining the noise model with the degradation due to the Dick effect reflecting the frequency noise of the interrogation laser, the instability of the clock is estimated to be 1.6 x 10{sup -16}/√(τ/s) in regular operation. During this work, several high-accuracy comparisons to other atomic clocks have been performed, including several absolute frequency measurements. The Sr clock transition frequency

  12. PARCS-Primary Atomic Reference Clock in Space

    Science.gov (United States)

    Ashby, Neil

    2000-04-01

    The purpose of the PARCS project is to place an advanced Cesium clock on the International Space Station (ISS). The project has been approved by NASA at the level of Science Concept Review. Groups at the National Institute of Standards and Technology, Jet Propulsion Laboratory, University of Colorado, and Harvard-Smithsonian Astrophysical Observatory, University of Torino are collaborating on clock design and construction. The microgravity space environment allows laser-cooled Cs atoms to spend longer times in the beam, resulting in improved clock performance. Clock stabilities of 3 × 10-14 at one second and accuracies of 1 × 10-16 are projected. With improved clock performance, significant improvements in several fundamental special and general relativity experiments are expected. For an ISS orbit at 400 km altitude and eccentricity 0.02, the gravitational frequency shift should be measureable about 35 times better than the previous best, Gravity Probe A. Improvements in testing Local Position Invariance and in a Kennedy-Thorndike experiment are expected. Areas of technology such as world-wide timing and time transfer and navigation will also directly benefit from such a high-performance clock in space. This paper will briefly describe the PARCS clock. The principal limitations on performance of relativity experiments, scientific objectives and benefits, and projected outcomes, will be discussed.

  13. Diurnal oscillations of soybean circadian clock and drought responsive genes.

    Directory of Open Access Journals (Sweden)

    Juliana Marcolino-Gomes

    Full Text Available Rhythms produced by the endogenous circadian clock play a critical role in allowing plants to respond and adapt to the environment. While there is a well-established regulatory link between the circadian clock and responses to abiotic stress in model plants, little is known of the circadian system in crop species like soybean. This study examines how drought impacts diurnal oscillation of both drought responsive and circadian clock genes in soybean. Drought stress induced marked changes in gene expression of several circadian clock-like components, such as LCL1-, GmELF4- and PRR-like genes, which had reduced expression in stressed plants. The same conditions produced a phase advance of expression for the GmTOC1-like, GmLUX-like and GmPRR7-like genes. Similarly, the rhythmic expression pattern of the soybean drought-responsive genes DREB-, bZIP-, GOLS-, RAB18- and Remorin-like changed significantly after plant exposure to drought. In silico analysis of promoter regions of these genes revealed the presence of cis-elements associated both with stress and circadian clock regulation. Furthermore, some soybean genes with upstream ABRE elements were responsive to abscisic acid treatment. Our results indicate that some connection between the drought response and the circadian clock may exist in soybean since (i drought stress affects gene expression of circadian clock components and (ii several stress responsive genes display diurnal oscillation in soybeans.

  14. GNSS Clock Error Impacts on Radio Occultation Retrievals

    Science.gov (United States)

    Weiss, Jan; Sokolovskiy, Sergey; Schreiner, Bill; Yoon, Yoke

    2017-04-01

    We assess the impacts of GPS and GLONASS clock errors on radio occultation retrieval of bending angle, refractivity, and temperature from low Earth orbit. The major contributing factor is the interpretation of GNSS clock offsets sampled at 30 sec or longer intervals. Using 1 Hz GNSS clock estimates as truth we apply several interpolation and fitting schemes to evaluate how they affect the accuracy of atmospheric retrieval products. The results are organized by GPS and GLONASS space vehicle and the GNSS clock interpolation/fitting scheme. We find that bending angle error is roughly similar for all current GPS transmitters (about 0.7 mcrad) but note some differences related to the type of atomic oscillator onboard the transmitter satellite. GLONASS bending angle errors show more variation over the constellation and are approximately two times larger than GPS. An investigation of the transmitter clock spectra reveals this is due to more power in periods between 2-10 sec. Retrieved refractivity and temperature products show clear differences between GNSS satellite generations, and indicate that GNSS clocks sampled at intervals smaller than 5 sec significantly improve accuracy, particularly for GLONASS. We conclude by summarizing the tested GNSS clock estimation and application strategies in the context of current and future radio occultation missions.

  15. Enhancing circadian clock function in cancer cells inhibits tumor growth.

    Science.gov (United States)

    Kiessling, Silke; Beaulieu-Laroche, Lou; Blum, Ian D; Landgraf, Dominic; Welsh, David K; Storch, Kai-Florian; Labrecque, Nathalie; Cermakian, Nicolas

    2017-02-14

    Circadian clocks control cell cycle factors, and circadian disruption promotes cancer. To address whether enhancing circadian rhythmicity in tumor cells affects cell cycle progression and reduces proliferation, we compared growth and cell cycle events of B16 melanoma cells and tumors with either a functional or dysfunctional clock. We found that clock genes were suppressed in B16 cells and tumors, but treatments inducing circadian rhythmicity, such as dexamethasone, forskolin and heat shock, triggered rhythmic clock and cell cycle gene expression, which resulted in fewer cells in S phase and more in G1 phase. Accordingly, B16 proliferation in vitro and tumor growth in vivo was slowed down. Similar effects were observed in human colon carcinoma HCT-116 cells. Notably, the effects of dexamethasone were not due to an increase in apoptosis nor to an enhancement of immune cell recruitment to the tumor. Knocking down the essential clock gene Bmal1 in B16 tumors prevented the effects of dexamethasone on tumor growth and cell cycle events. Here we demonstrated that the effects of dexamethasone on cell cycle and tumor growth are mediated by the tumor-intrinsic circadian clock. Thus, our work reveals that enhancing circadian clock function might represent a novel strategy to control cancer progression.

  16. Circadian clock-mediated regulation of blood pressure.

    Science.gov (United States)

    Douma, Lauren G; Gumz, Michelle L

    2017-12-02

    Most bodily functions vary over the course of a 24h day. Circadian rhythms in body temperature, sleep-wake cycles, metabolism, and blood pressure (BP) are just a few examples. These circadian rhythms are controlled by the central clock in the suprachiasmatic nucleus (SCN) of the hypothalamus and peripheral clocks located throughout the body. Light and food cues entrain these clocks to the time of day and this synchronicity contributes to the regulation of a variety of physiological processes with effects on overall health. The kidney, brain, nervous system, vasculature, and heart have been identified through the use of mouse models and clinical trials as peripheral clock regulators of BP. The dysregulation of this circadian pattern of BP, with or without hypertension, is associated with increased risk for cardiovascular disease. The mechanism of this dysregulation is unknown and is a growing area of research. In this review, we highlight research of human and mouse circadian models that has provided insight into the roles of these molecular clocks and their effects on physiological functions. Additional tissue-specific studies of the molecular clock mechanism are needed, as well as clinical studies including more diverse populations (different races, female patients, etc.), which will be critical to fully understand the mechanism of circadian regulation of BP. Understanding how these molecular clocks regulate the circadian rhythm of BP is critical in the treatment of circadian BP dysregulation and hypertension. Copyright © 2017 Elsevier Inc. All rights reserved.

  17. The Circadian Clock in Cancer Development and Therapy

    Science.gov (United States)

    Fu, Loning; Kettner, Nicole M.

    2014-01-01

    Most aspects of mammalian function display circadian rhythms driven by an endogenous clock. The circadian clock is operated by genes and comprises a central clock in the brain that responds to environmental cues and controls subordinate clocks in peripheral tissues via circadian output pathways. The central and peripheral clocks coordinately generate rhythmic gene expression in a tissue-specific manner in vivo to couple diverse physiological and behavioral processes to periodic changes in the environment. However, as the world industrialized, activities that disrupt endogenous homeostasis with external circadian cues have increased. This change in lifestyle has been linked to increased risk of diseases in all aspects of human health, including cancer. Studies in humans and animal models have revealed that cancer development in vivo is closely associated with the loss of circadian homeostasis in energy balance, immune function and aging that are supported by cellular functions important for tumor suppression including cell proliferation, senescence, metabolism and DNA damage response. The clock controls these cellular functions both locally in cells of peripheral tissues and at the organismal level via extracellular signaling. Thus, the hierarchical mammalian circadian clock provides a unique system to study carcinogenesis as a deregulated physiological process in vivo. The asynchrony between host and malignant tissues in cell proliferation and metabolism also provides new and exciting options for novel anti-cancer therapies. PMID:23899600

  18. Circadian clock characteristics are altered in human thyroid malignant nodules.

    Science.gov (United States)

    Mannic, Tiphaine; Meyer, Patrick; Triponez, Frederic; Pusztaszeri, Marc; Le Martelot, Gwendal; Mariani, Olivia; Schmitter, Daniel; Sage, Daniel; Philippe, Jacques; Dibner, Charna

    2013-11-01

    The circadian clock represents the body's molecular time-keeping system. Recent findings revealed strong changes of clock gene expression in various types of human cancers. Due to emerging evidence on the connection between the circadian oscillator, cell cycle, and oncogenic transformation, we aimed to characterize the circadian clockwork in human benign and malignant thyroid nodules. Clock transcript levels were assessed by quantitative RT-PCR in thyroid tissues. To provide molecular characteristics of human thyroid clockwork, primary thyrocytes established from normal or nodular thyroid tissue biopsies were subjected to in vitro synchronization with subsequent clock gene expression analysis by circadian bioluminescence reporter assay and by quantitative RT-PCR. The expression levels of the Bmal1 were up-regulated in tissue samples of follicular thyroid carcinoma (FTC), and in papillary thyroid carcinoma (PTC), as compared with normal thyroid and benign nodules, whereas Cry2 was down-regulated in FTC and PTC. Human thyrocytes derived from normal thyroid tissue exhibited high-amplitude circadian oscillations of Bmal1-luciferase reporter expression and endogenous clock transcripts. Thyrocytes established from FTC and PTC exhibited clock transcript oscillations similar to those of normal thyroid tissue and benign nodules (except for Per2 altered in PTC), whereas cells derived from poorly differentiated thyroid carcinoma exhibited altered circadian oscillations. This is the first study demonstrating a molecular makeup of the human thyroid circadian clock. Characterization of the thyroid clock machinery alterations upon thyroid nodule malignant transformation contributes to understanding the connections between circadian clocks and oncogenic transformation. Moreover, it might help in improving the thyroid nodule preoperative diagnostics.

  19. The Bird of Time: Cognition and the Avian Biological Clock

    Directory of Open Access Journals (Sweden)

    Vincent Michael Cassone

    2012-03-01

    Full Text Available Avian behavior and physiology are embedded in time at many levels of biological organization. Biological clock function in birds is critical for sleep/wake cycles, but may also regulate the acquisition of place memory, learning of song from tutors, social integration and time-compensated navigation. This relationship has two major implications. First, mechanisms of the circadian clock should be linked in some way to the mechanisms of all these behaviors. How is not yet clear, and evidence that the central clock has effects is piecemeal. Second, selection acting on characters that are linked to the circadian clock should influence aspects of the clock mechanism itself. Little evidence exists for this in birds, but there have been few attempts to assess this idea. At its core, the avian circadian clock is a multi-oscillator system comprising the pineal gland, the retinae and the avian homologues of the suprachiasmatic nuclei, whose mutual interactions ensure coordinated physiological functions, which are in turn synchronized to ambient light cycles via encephalic, pineal and retinal photoreceptors. At the molecular level, avian biological clocks comprise a genetic network of positive elements clock and bmal1 whose interactions with the negative elements period2, period3 and the cryptochromes form an oscillatory feedback loop that circumnavigates the 24 hrs of the day. We assess the possibilities for dual integration of the clock with time-dependent cognitive processes. Closer examination of the molecular, physiological, and behavioral elements of the circadian system would place birds at a very interesting fulcrum in the neurobiology of time in learning, memory and navigation. 

  20. Molecular Clock of Neutral Mutations in a Fitness-Increasing Evolutionary Process

    Science.gov (United States)

    Iijima, Leo; Suzuki, Shingo; Hashimoto, Tomomi; Oyake, Ayana; Kobayashi, Hisaka; Someya, Yuki; Narisawa, Dai; Yomo, Tetsuya

    2015-01-01

    The molecular clock of neutral mutations, which represents linear mutation fixation over generations, is theoretically explained by genetic drift in fitness-steady evolution or hitchhiking in adaptive evolution. The present study is the first experimental demonstration for the molecular clock of neutral mutations in a fitness-increasing evolutionary process. The dynamics of genome mutation fixation in the thermal adaptive evolution of Escherichia coli were evaluated in a prolonged evolution experiment in duplicated lineages. The cells from the continuously fitness-increasing evolutionary process were subjected to genome sequencing and analyzed at both the population and single-colony levels. Although the dynamics of genome mutation fixation were complicated by the combination of the stochastic appearance of adaptive mutations and clonal interference, the mutation fixation in the population was simply linear over generations. Each genome in the population accumulated 1.6 synonymous and 3.1 non-synonymous neutral mutations, on average, by the spontaneous mutation accumulation rate, while only a single genome in the population occasionally acquired an adaptive mutation. The neutral mutations that preexisted on the single genome hitchhiked on the domination of the adaptive mutation. The successive fixation processes of the 128 mutations demonstrated that hitchhiking and not genetic drift were responsible for the coincidence of the spontaneous mutation accumulation rate in the genome with the fixation rate of neutral mutations in the population. The molecular clock of neutral mutations to the fitness-increasing evolution suggests that the numerous neutral mutations observed in molecular phylogenetic trees may not always have been fixed in fitness-steady evolution but in adaptive evolution. PMID:26177190

  1. Additive Similarity Trees

    Science.gov (United States)

    Sattath, Shmuel; Tversky, Amos

    1977-01-01

    Tree representations of similarity data are investigated. Hierarchical clustering is critically examined, and a more general procedure, called the additive tree, is presented. The additive tree representation is then compared to multidimensional scaling. (Author/JKS)

  2. City of Pittsburgh Trees

    Data.gov (United States)

    Allegheny County / City of Pittsburgh / Western PA Regional Data Center — Trees cared for and managed by the City of Pittsburgh Department of Public Works Forestry Division. Tree Benefits are calculated using the National Tree Benefit...

  3. Detection of weak frequency jumps for GNSS onboard clocks.

    Science.gov (United States)

    Huang, Xinming; Gong, Hang; Ou, Gang

    2014-05-01

    In this paper, a weak frequency jump detection method is developed for onboard clocks in global navigation satellite systems (GNSS). A Kalman filter is employed to facilitate the onboard real-time processing of atomic clock measurements, whose N-step prediction residuals are used to construct the weak frequency jump detector. Numerical simulations show that the method can successfully detect weak frequency jumps. The detection method proposed in this paper is helpful for autonomous integrity monitoring of GNSS satellite clocks, and can also be applied to other frequency anomalies with an appropriately modified detector.

  4. An atomic clock with 10(-18) instability.

    Science.gov (United States)

    Hinkley, N; Sherman, J A; Phillips, N B; Schioppo, M; Lemke, N D; Beloy, K; Pizzocaro, M; Oates, C W; Ludlow, A D

    2013-09-13

    Atomic clocks have been instrumental in science and technology, leading to innovations such as global positioning, advanced communications, and tests of fundamental constant variation. Timekeeping precision at 1 part in 10(18) enables new timing applications in relativistic geodesy, enhanced Earth- and space-based navigation and telescopy, and new tests of physics beyond the standard model. Here, we describe the development and operation of two optical lattice clocks, both using spin-polarized, ultracold atomic ytterbium. A measurement comparing these systems demonstrates an unprecedented atomic clock instability of 1.6 × 10(-18) after only 7 hours of averaging.

  5. High-precision multi-node clock network distribution

    Science.gov (United States)

    Chen, Xing; Cui, Yifan; Lu, Xing; Ci, Cheng; Zhang, Xuesong; Liu, Bo; Wu, Hong; Tang, Tingsong; Shi, Kebin; Zhang, Zhigang

    2017-10-01

    A high precision multi-node clock network for multiple users was built following the precise frequency transmission and time synchronization of 120 km fiber. The network topology adopts a simple star-shaped network structure. The clock signal of a hydrogen maser (synchronized with UTC) was recovered from a 120 km telecommunication fiber link and then was distributed to 4 sub-stations. The fractional frequency instability of all substations is in the level of 10-15 in a second and the clock offset instability is in sub-ps in root-mean-square average.

  6. The chlorate-iodine-nitrous acid clock reaction.

    Directory of Open Access Journals (Sweden)

    Rafaela T P Sant'Anna

    Full Text Available A new clock reaction based on chlorate, iodine and nitrous acid is presented. The induction period of this new clock reaction decreases when the initial concentrations of chlorate, nitrous acid and perchloric acid increase, but it is independent on the initial iodine concentration. The proposed mechanism is based on the LLKE autocatalytic mechanism for the chlorite-iodide reaction and the initial reaction between chlorate and nitrous acid to produce nitrate and chlorite. This new clock reaction opens the possibility for a new family of oscillating reactions containing chlorate or nitrous acid, which in both cases has not been observed until now.

  7. The clock-drawing test: time for a change?

    Science.gov (United States)

    Chan, Amy; Remington, Ruth; Paskavitz, James; Shea, Thomas B

    2008-01-01

    Clock-drawing tests are simple and rapid screening devices for dementia. It was observed that individuals digital prompt (" . . .make the clock read 12:45") or an analog prompt (" . . .quarter to 1"), whereas individuals >70 years of age showed improved performance with an analog prompt. The digital prompt has routinely been used to force participants to recode the prompt via conceptualization. Differential scoring across a range of ages has likely derived from the advent and increase of digital clocks with the younger segment of the population. This implies the need for as-yet undetermined alteration in the nature of prompts to force recoding as the current younger population ages.

  8. Plant circadian clocks increase photosynthesis, growth, survival, and competitive advantage.

    Science.gov (United States)

    Dodd, Antony N; Salathia, Neeraj; Hall, Anthony; Kévei, Eva; Tóth, Réka; Nagy, Ferenc; Hibberd, Julian M; Millar, Andrew J; Webb, Alex A R

    2005-07-22

    Circadian clocks are believed to confer an advantage to plants, but the nature of that advantage has been unknown. We show that a substantial photosynthetic advantage is conferred by correct matching of the circadian clock period with that of the external light-dark cycle. In wild type and in long- and short-circadian period mutants of Arabidopsis thaliana, plants with a clock period matched to the environment contain more chlorophyll, fix more carbon, grow faster, and survive better than plants with circadian periods differing from their environment. This explains why plants gain advantage from circadian control.

  9. A Low-jitter 2.5-to-10 GHz Clock Multiplier Unit in CMOS

    NARCIS (Netherlands)

    van de Beek, R.C.H.; Vaucher, C.S.; Leenaerts, D.M.W.; Klumperink, Eric A.M.; Nauta, Bram

    Abstract— This paper demonstrates a low-jitter clock multiplier unit [1] that generates a 10 GHz output clock from a 2.5 GHz reference clock. An integrated 10 GHz LCoscillator is locked to the input clock, using a simple and fast phase detector circuit. This phase detector overcomes the speed

  10. Is There a Clock in This Sabbatical?

    Science.gov (United States)

    Frederickson, Kathy

    2003-01-01

    Considers how a community-college professor's long-awaited sabbatical not only stimulates new thinking about projects and goals but also offers a foray into that forest of self that lies behind the trees. Discusses the author's experience with the time she spent on her sabbatical. (SG)

  11. Regulation of behavioral circadian rhythms and clock protein PER1 by the deubiquitinating enzyme USP2

    DEFF Research Database (Denmark)

    Yang, Yaoming; Duguay, David; Bédard, Nathalie

    2012-01-01

    Endogenous 24-hour rhythms are generated by circadian clocks located in most tissues. The molecular clock mechanism is based on feedback loops involving clock genes and their protein products. Post-translational modifications, including ubiquitination, are important for regulating the clock...... of the circadian clock, both at the level of the core pacemaker and its response to external cues....... feedback mechanism. Previous work has focused on the role of ubiquitin ligases in the clock mechanism. Here we show a role for the rhythmically-expressed deubiquitinating enzyme ubiquitin specific peptidase 2 (USP2) in clock function. Mice with a deletion of the Usp2 gene (Usp2 KO) display a longer free...

  12. An evolutionary tree for invertebrate globin sequences.

    Science.gov (United States)

    Goodman, M; Pedwaydon, J; Czelusniak, J; Suzuki, T; Gotoh, T; Moens, L; Shishikura, F; Walz, D; Vinogradov, S

    1988-01-01

    A phylogenetic tree was constructed from 245 globin amino acid sequences. Of the six plant globins, five represented the Leguminosae and one the Ulmaceae. Among the invertebrate sequences, 7 represented the phylum Annelida, 13 represented Insecta and Crustacea of the phylum Arthropoda, and 6 represented the phylum Mollusca. Of the vertebrate globins, 4 represented the Agnatha and 209 represented the Gnathostomata. A common alignment was achieved for the 245 sequences using the parsimony principle, and a matrix of minimum mutational distances was constructed. The most parsimonious phylogenetic tree, i.e., the one having the lowest number of nucleotide substitutions that cause amino acid replacements, was obtained employing clustering and branch-swapping algorithms. Based on the available fossil record, the earliest split in the ancestral metazoan lineage was placed at 680 million years before present (Myr BP), the origin of vertebrates was placed at 510 Myr BP, and the separation of the Chondrichthyes and the Osteichthyes was placed at 425 Myr BP. Local "molecular clock" calculations were used to date the branch points on the descending branches of the various lineages within the plant and invertebrate portions of the tree. The tree divided the 245 sequences into five distinct clades that corresponded exactly to the five groups plants, annelids, arthropods, molluscs, and vertebrates. Furthermore, the maximum parsimony tree, in contrast to the unweighted pair group and distance Wagner trees, was consistent with the available fossil record and supported the hypotheses that the primitive hemoglobin of metazoans was monomeric and that the multisubunit extracellular hemoglobins found among the Annelida and the Arthropoda represent independently derived states.

  13. A Fermi-degenerate three-dimensional optical lattice clock

    Science.gov (United States)

    Campbell, S. L.; Hutson, R. B.; Marti, G. E.; Goban, A.; Darkwah Oppong, N.; McNally, R. L.; Sonderhouse, L.; Robinson, J. M.; Zhang, W.; Bloom, B. J.; Ye, J.

    2017-10-01

    Strontium optical lattice clocks have the potential to simultaneously interrogate millions of atoms with a high spectroscopic quality factor of 4 × 1017. Previously, atomic interactions have forced a compromise between clock stability, which benefits from a large number of atoms, and accuracy, which suffers from density-dependent frequency shifts. Here we demonstrate a scalable solution that takes advantage of the high, correlated density of a degenerate Fermi gas in a three-dimensional (3D) optical lattice to guard against on-site interaction shifts. We show that contact interactions are resolved so that their contribution to clock shifts is orders of magnitude lower than in previous experiments. A synchronous clock comparison between two regions of the 3D lattice yields a measurement precision of 5 × 10-19 in 1 hour of averaging time.

  14. Circadian Clock, Cell Division, and Cancer: From Molecules to Organism

    Science.gov (United States)

    Shostak, Anton

    2017-01-01

    As a response to environmental changes driven by the Earth’s axial rotation, most organisms evolved an internal biological timer—the so called circadian clock—which regulates physiology and behavior in a rhythmic fashion. Emerging evidence suggests an intimate interplay between the circadian clock and another fundamental rhythmic process, the cell cycle. However, the precise mechanisms of this connection are not fully understood. Disruption of circadian rhythms has a profound impact on cell division and cancer development and, vice versa, malignant transformation causes disturbances of the circadian clock. Conventional knowledge attributes tumor suppressor properties to the circadian clock. However, this implication might be context-dependent, since, under certain conditions, the clock can also promote tumorigenesis. Therefore, a better understanding of the molecular links regulating the physiological balance between the two cycles will have potential significance for the treatment of cancer and associated disorders. PMID:28425940

  15. The circadian clock system in the mammalian retina.

    Science.gov (United States)

    Tosini, Gianluca; Pozdeyev, Nikita; Sakamoto, Katsuhiko; Iuvone, P Michael

    2008-07-01

    Daily rhythms are a ubiquitous feature of living systems. Generally, these rhythms are not just passive consequences of cyclic fluctuations in the environment, but instead originate within the organism. In mammals, including humans, the master pacemaker controlling 24-hour rhythms is localized in the suprachiasmatic nuclei of the hypothalamus. This circadian clock is responsible for the temporal organization of a wide variety of functions, ranging from sleep and food intake, to physiological measures such as body temperature, heart rate and hormone release. The retinal circadian clock was the first extra-SCN circadian oscillator to be discovered in mammals and several studies have now demonstrated that many of the physiological, cellular and molecular rhythms that are present within the retina are under the control of a retinal circadian clock, or more likely a network of hierarchically organized circadian clocks that are present within this tissue. BioEssays 30:624-633, 2008. (c) 2008 Wiley Periodicals, Inc.

  16. The circadian clock and pathology of the ageing brain.

    Science.gov (United States)

    Kondratova, Anna A; Kondratov, Roman V

    2012-03-07

    Ageing leads to a functional deterioration of many brain systems, including the circadian clock--an internal time-keeping system that generates ∼24-hour rhythms in physiology and behaviour. Numerous clinical studies have established a direct correlation between abnormal circadian clock functions and the severity of neurodegenerative and sleep disorders. Latest data from experiments in model organisms, gene expression studies and clinical trials imply that dysfunctions of the circadian clock contribute to ageing and age-associated pathologies, thereby suggesting a functional link between the circadian clock and age-associated decline of brain functions. Potential molecular mechanisms underlying this link include the circadian control of physiological processes such as brain metabolism, reactive oxygen species homeostasis, hormone secretion, autophagy and stem cell proliferation.

  17. Superradiance on the millihertz linewidth strontium clock transition

    Science.gov (United States)

    Norcia, Matthew A.; Winchester, Matthew N.; Cline, Julia R. K.; Thompson, James K.

    2016-01-01

    Laser frequency noise contributes a significant limitation to today’s best atomic clocks. A proposed solution to this problem is to create a superradiant laser using an optical clock transition as its gain medium. This laser would act as an active atomic clock and would be highly immune to the fluctuations in reference cavity length that limit today’s best lasers. We demonstrate and characterize superradiant emission from the millihertz linewidth clock transition in an ensemble of laser-cooled 87Sr atoms trapped within a high-finesse optical cavity. We measure a collective enhancement of the emission rate into the cavity mode by a factor of more than 10,000 compared to independently radiating atoms. We also demonstrate a method for seeding superradiant emission and observe interference between two independent transitions lasing simultaneously. We use this interference to characterize the relative spectral properties of the two lasing subensembles. PMID:27757423

  18. Quantum Atomic Clock Synchronization: An Entangled Concept of Nonlocal Simultaneity

    Science.gov (United States)

    Abrams, D.; Dowling, J.; Williams, C.; Jozsa, R.

    2000-01-01

    We demonstrate that two spatially separated parties (Alice and Bob) can utilize shared prior quantum entanglement, as well as a classical information channel, to establish a synchronized pair of atomic clocks.

  19. PHARAO space atomic clock: new developments on the laser source

    Science.gov (United States)

    Saccoccio, Muriel; Loesel, Jacques; Coatantiec, Claude; Simon, Eric; Laurent, Philippe; Lemonde, Pierre; Maksimovic, I.; Abgrall, M.

    2017-11-01

    The PHARAO project purpose is to open the way for a new atomic clock generation in space, where laser cooling techniques and microgravity allow high frequency stability and accuracy. The French space agency, CNES is funding and managing the clock construction. The French SYRTE and LKB laboratories are scientific and technical advisers for the clock requirements and the follow-up of subsystem development in industrial companies. EADS SODERN is developing two main subsystems of the PHARAO clock: the Laser Source and the Cesium Tube where atoms are cooled, launched, selected and detected by laser beams. The Laser Source includes an optical bench and electronic devices to generate the laser beams required. This paper describes PHARAO and the role laser beams play in its principle of operation. Then we present the Laser Source design, the technologies involved, and the status of development. Lastly, we focus of a key equipment to reach the performances expected, which is the Extended Cavity Laser Diode.

  20. Cellular Clocks : Coupled Circadian Dispatch and Cell Division Cycles

    NARCIS (Netherlands)

    Merrow, Martha; Roenneberg, Till

    2004-01-01

    Gating of cell division by the circadian clock is well known, yet its mechanism is little understood. Genetically tractable model systems have led to new hypotheses and questions concerning the coupling of these two cellular cycles.

  1. Liter Sized Ion Clock with 10 (exp -15) Stability

    National Research Council Canada - National Science Library

    Prestage, J. D; Chang, S; Le, T; Lim, L; Maleki, L

    2005-01-01

    .... This development shows that Hmaser quality stabilities can be produced in a small clock package, comparable in size to an ultra-stable quartz oscillator required for holding 1-2x10-13 at 1 second...

  2. Deficiency of circadian protein CLOCK reduces lifespan and increases age-related cataract development in mice

    OpenAIRE

    Dubrovsky, Yuliya V.; Samsa, William E.; Kondratov, Roman V.

    2010-01-01

    Circadian clock is implicated in the regulation of aging. The transcription factor CLOCK, a core component of the circadian system, operates in complex with another circadian clock protein BMAL1. Recently it was demonstrated that BMAL1 deficiency results in premature aging in mice. Here we investigate the aging of mice deficient for CLOCK protein. Deficiency of the CLOCK protein significantly affects longevity: the average lifespan of Clock−/− mice is reduced by 15% compared with wild type mi...

  3. Intra-panel interface with clock-embedded differential signalling for large size digital television

    Science.gov (United States)

    Choi, Dong-Ho; Yoo, Changsik

    2014-01-01

    For large size digital television, an intra-panel interface scheme with clock-embedded differential signalling is developed which connects a timing controller and column data driver at 2.0 Gbps. A two-wire differential data channel has tri-level and clock information is embedded in it. Embedded clocking eliminates the skew between data channel and clock, which makes the clock-data recovery very simple. A prototype chip has been implemented in a standard 45-nm CMOS technology.

  4. Clock Technology Development in the Laser Cooling and Atomic Physics (LCAP) Program

    Science.gov (United States)

    Seidel, Dave; Thompson, R. J.; Klipstein, W. M.; Kohel, J.; Maleki, L.

    2000-01-01

    This paper presents the Laser Cooling and Atomic Physics (LCAP) program. It focuses on clock technology development. The topics include: 1) Overview of LCAP Flight Projects; 2) Space Clock 101; 3) Physics with Clocks in microgravity; 4) Space Clock Challenges; 5) LCAP Timeline; 6) International Space Station (ISS) Science Platforms; 7) ISS Express Rack; 8) Space Qualification of Components; 9) Laser Configuration; 10) Clock Rate Comparisons: GPS Carrier Phase Frequency Transfer; and 11) ISS Model Views. This paper is presented in viewgraph form.

  5. The mammalian circadian clock and its entrainment by stress and exercise

    OpenAIRE

    Tahara, Yu; Aoyama, Shinya; Shibata, Shigenobu

    2016-01-01

    The mammalian circadian clock regulates day?night fluctuations in various physiological processes. The circadian clock consists of the central clock in the suprachiasmatic nucleus of the hypothalamus and peripheral clocks in peripheral tissues. External environmental cues, including light/dark cycles, food intake, stress, and exercise, provide important information for adjusting clock phases. This review focuses on stress and exercise as potent entrainment signals for both central and periphe...

  6. CSAC Characterization and Its Impact on GNSS Clock Augmentation Performance.

    Science.gov (United States)

    Fernández, Enric; Calero, David; Parés, M Eulàlia

    2017-02-14

    Chip Scale Atomic Clocks (CSAC) are recently-developed electronic instruments that, when used together with a Global Navigation Satellite Systems (GNSS) receiver, help improve the performance of GNSS navigation solutions in certain conditions (i.e., low satellite visibility). Current GNSS receivers include a Temperature Compensated Cristal Oscillator (TCXO) clock characterized by a short-term stability (τ = 1 s) of 10-9 s that leads to an error of 0.3 m in pseudorange measurements. The CSAC can achieve a short-term stability of 2.5 × 10-12 s, which implies a range error of 0.075 m, making for an 87.5% improvement over TCXO. Replacing the internal TCXO clock of GNSS receivers with a higher frequency stability clock such as a CSAC oscillator improves the navigation solution in terms of low satellite visibility positioning accuracy, solution availability, signal recovery (holdover), multipath and jamming mitigation and spoofing attack detection. However, CSAC suffers from internal systematic instabilities and errors that should be minimized if optimal performance is desired. Hence, for operating CSAC at its best, the deterministic errors from the CSAC need to be properly modelled. Currently, this modelling is done by determining and predicting the clock frequency stability (i.e., clock bias and bias rate) within the positioning estimation process. The research presented in this paper aims to go a step further, analysing the correlation between temperature and clock stability noise and the impact of its proper modelling in the holdover recovery time and in the positioning performance. Moreover, it shows the potential of fine clock coasting modelling. With the proposed model, an improvement in vertical positioning precision of around 50% with only three satellites can be achieved. Moreover, an increase in the navigation solution availability is also observed, a reduction of holdover recovery time from dozens of seconds to only a few can be achieved.

  7. Clocks, computers, black holes, spacetime foam, and holographic principle

    OpenAIRE

    Ng, Y. Jack

    2000-01-01

    What do simple clocks, simple computers, black holes, space-time foam, and holographic principle have in common? I will show that the physics behind them is inter-related, linking together our concepts of information, gravity, and quantum uncertainty. Thus, the physics that sets the limits to computation and clock precision also yields Hawking radiation of black holes and the holographic principle. Moreover, the latter two strongly imply that space-time undergoes much larger quantum fluctuati...

  8. CSAC Characterization and Its Impact on GNSS Clock Augmentation Performance

    Directory of Open Access Journals (Sweden)

    Enric Fernández

    2017-02-01

    Full Text Available Chip Scale Atomic Clocks (CSAC are recently-developed electronic instruments that, when used together with a Global Navigation Satellite Systems (GNSS receiver, help improve the performance of GNSS navigation solutions in certain conditions (i.e., low satellite visibility. Current GNSS receivers include a Temperature Compensated Cristal Oscillator (TCXO clock characterized by a short-term stability (τ = 1 s of 10−9 s that leads to an error of 0.3 m in pseudorange measurements. The CSAC can achieve a short-term stability of 2.5 × 10−12 s, which implies a range error of 0.075 m, making for an 87.5% improvement over TCXO. Replacing the internal TCXO clock of GNSS receivers with a higher frequency stability clock such as a CSAC oscillator improves the navigation solution in terms of low satellite visibility positioning accuracy, solution availability, signal recovery (holdover, multipath and jamming mitigation and spoofing attack detection. However, CSAC suffers from internal systematic instabilities and errors that should be minimized if optimal performance is desired. Hence, for operating CSAC at its best, the deterministic errors from the CSAC need to be properly modelled. Currently, this modelling is done by determining and predicting the clock frequency stability (i.e., clock bias and bias rate within the positioning estimation process. The research presented in this paper aims to go a step further, analysing the correlation between temperature and clock stability noise and the impact of its proper modelling in the holdover recovery time and in the positioning performance. Moreover, it shows the potential of fine clock coasting modelling. With the proposed model, an improvement in vertical positioning precision of around 50% with only three satellites can be achieved. Moreover, an increase in the navigation solution availability is also observed, a reduction of holdover recovery time from dozens of seconds to only a few can be achieved.

  9. Clocks in Space for Tests of Fundamental Physics

    Science.gov (United States)

    Delva, Pacôme; Hees, Aurélien; Wolf, Peter

    2017-11-01

    In this paper we describe some of the past, present and near future experiments that take advantage of clocks in space for tests of fundamental physics, together with some of the theoretical background. It is impossible to describe all missions and projects in the field, and we will only mention some of the most important ones. Nonetheless, we hope that the reader will learn from the past, appreciate the present and look forward to the future of space clocks in fundamental physics.

  10. Clock face drawing test performance in children with ADHD.

    Science.gov (United States)

    Ghanizadeh, Ahmad; Safavi, Salar; Berk, Michael

    2013-01-01

    The utility and discriminatory pattern of the clock face drawing test in ADHD is unclear. This study therefore compared Clock Face Drawing test performance in children with ADHD and controls. 95 school children with ADHD and 191 other children were matched for gender ratio and age. ADHD symptoms severities were assessed using DSM-IV ADHD checklist and their intellectual functioning was assessed. The participants completed three clock-drawing tasks, and the following four functions were assessed: Contour score, Numbers score, Hands setting score, and Center score. All the subscales scores of the three clock drawing tests of the ADHD group were lower than that of the control group. In ADHD children, inattention and hyperactivity/ impulsivity scores were not related to free drawn clock test scores. When pre-drawn contour test was performed, inattentiveness score was statistically associated with Number score while none of the other variables of age, gender, intellectual functioning, and hand use preference were associated with that kind of score. In pre-drawn clock, no association of ADHD symptoms with any CDT subscales found significant. In addition, more errors are observed with free drawn clock and Pre-drawn contour than pre-drawn clock. Putting Numbers and Hands setting are more sensitive measures to screen ADHD than Contour and Center drawing. Test performance, except Hands setting, may have already reached a developmental plateau. It is probable that Hand setting deficit in children with ADHD may not decrease from age 8 to 14 years. Performance of children with ADHD is associated with complexity of CDT.

  11. Tissue-intrinsic dysfunction of circadian clock confers transplant arteriosclerosis.

    Science.gov (United States)

    Cheng, Bo; Anea, Ciprian B; Yao, Lin; Chen, Feng; Patel, Vijay; Merloiu, Ana; Pati, Paramita; Caldwell, R William; Fulton, David J; Rudic, R Daniel

    2011-10-11

    The suprachiasmatic nucleus of the brain is the circadian center, relaying rhythmic environmental and behavioral information to peripheral tissues to control circadian physiology. As such, central clock dysfunction can alter systemic homeostasis to consequently impair peripheral physiology in a manner that is secondary to circadian malfunction. To determine the impact of circadian clock function in organ transplantation and dissect the influence of intrinsic tissue clocks versus extrinsic clocks, we implemented a blood vessel grafting approach to surgically assemble a chimeric mouse that was part wild-type (WT) and part circadian clock mutant. Arterial isografts from donor WT mice that had been anastamosed to common carotid arteries of recipient WT mice (WT:WT) exhibited no pathology in this syngeneic transplant strategy. Similarly, when WT grafts were anastamosed to mice with disrupted circadian clocks, the structural features of the WT grafts immersed in the milieu of circadian malfunction were normal and absent of lesions, comparable to WT:WT grafts. In contrast, aortic grafts from Bmal1 knockout (KO) or Period-2,3 double-KO mice transplanted into littermate control WT mice developed robust arteriosclerotic disease. These lesions observed in donor grafts of Bmal1-KO were associated with up-regulation in T-cell receptors, macrophages, and infiltrating cells in the vascular grafts, but were independent of hemodynamics and B and T cell-mediated immunity. These data demonstrate the significance of intrinsic tissue clocks as an autonomous influence in experimental models of arteriosclerotic disease, which may have implications with regard to the influence of circadian clock function in organ transplantation.

  12. Clocking In Turbines: Remarks On Physical Nature And Geometric Requirements

    Directory of Open Access Journals (Sweden)

    Swirydczuk Jerzy

    2015-04-01

    Full Text Available The article discusses two issues relating to the clocking phenomenon in turbines, which are the physical course of stator wake deformation in rotor passages and its further interaction with downstream stator blades, and turbine geometry parameters which are believed to be most favourable for clocking. In both cases, the results presented in the article have made it possible to verify and reformulate the previously accepted opinions.

  13. Oscillation of Clock and Clock Controlled Genes Induced by Serum Shock in Human Breast Epithelial and Breast Cancer Cells: Regulation by Melatonin

    Science.gov (United States)

    Xiang, S.; Mao, L.; Duplessis, T.; Yuan, L.; Dauchy, R.; Dauchy, E.; Blask, D.E.; Frasch, T.; Hill, S.M.

    2012-01-01

    This study investigates differences in expression of clock and clock-controlled genes (CCGs) between human breast epithelial and breast cancer cells and breast tumor xenografts in circadian intact rats and examines if the pineal hormone melatonin influences clock gene and CCG expression. Oscillation of clock gene expression was not observed under standard growth conditions in vitro, however, serum shock (50% horse serum for 2 h) induced oscillation of clock gene and CCG expression in MCF-10A cells, which was repressed or disrupted in MCF-7 cells. Melatonin administration following serum shock differentially suppressed or induced clock gene (Bmal1 and Per2) and CCG expression in MCF10A and MCF-7 cells. These studies demonstrate the lack of rhythmic expression of clock genes and CCGs of cells in vitro and that transplantation of breast cancer cells as xenografts into circadian competent hosts re-establishes a circadian rhythm in the peripheral clock genes of tumor cells. PMID:23012497

  14. The quantum beat the physical principles of atomic clocks

    CERN Document Server

    Major, F G

    1998-01-01

    One of the indicators of the level of technological development of a society has been, throughout history, the precision of clocks it was able to build. This book examines the physical principles underlying the workings of clocks--from the earliest mechanical clocks to the present-day sophisticated clocks based on the properties of individual atoms. Intended for non-specialists with some knowledge of physics or engineering,the book treats the material in a broad intuitive manner, with a minimum of mathematical formalism. The presentation covers a broad range of salient topics relevant to the measurement of frequency and time intervals. The main focus is on electronic time-keeping: clocks based on quartz crystal oscillators and, at greater length, atomic clocks based on quantum resonance in rubidium, cesium, and hydrogen atoms, and, more recently, mercury ions. The book treats the revolutionary changes that the optical laser has wrought on atomic standards through laser cooling and optical pumping, and it disc...

  15. Deregulated expression of the clock genes in gliomas.

    Science.gov (United States)

    Chen, Z; Liu, P; Li, C; Luo, Y; Chen, I; Liang, W; Chen, X; Feng, Y; Xia, H; Wang, F

    2013-02-01

    Growing evidence shows that the deregulation of the circadian clock plays an important role in the development of malignant tumors, including gliomas. However, the molecular mechanisms of genes controlling circadian rhythm in glioma cells have not been explored. Using reverse transcription polymerase chain reaction and immunohistochemistry techniques, we examined the expression of the most important clock genes, clock, in 67 gliomas.Our results revealed that asynchronized expression of the clock gene was found in cancerous tissues in comparison with paired non-cancerous tissues. The expression levels of clock mRNA in grade III or IV glioma was significantly different from the surrounding non-tumor tissues (P  0.05). The intensity of immunoactivity for Clock in highgrade gliomas was significantly higher than that of low-grade gliomas (r = -0.403, P 5 0.012 ,  0.05). The expression of PCNA (Proliferating Cell Nuclear Antigen) protein in highgrade gliomas was significantly higher than that of low-grade gliomas (P control of normal circadian rhythm, thus benefiting the survival of glioma cells and promoting carcinogenesis.

  16. A clock network for geodesy and fundamental science.

    Science.gov (United States)

    Lisdat, C; Grosche, G; Quintin, N; Shi, C; Raupach, S M F; Grebing, C; Nicolodi, D; Stefani, F; Al-Masoudi, A; Dörscher, S; Häfner, S; Robyr, J-L; Chiodo, N; Bilicki, S; Bookjans, E; Koczwara, A; Koke, S; Kuhl, A; Wiotte, F; Meynadier, F; Camisard, E; Abgrall, M; Lours, M; Legero, T; Schnatz, H; Sterr, U; Denker, H; Chardonnet, C; Le Coq, Y; Santarelli, G; Amy-Klein, A; Le Targat, R; Lodewyck, J; Lopez, O; Pottie, P-E

    2016-08-09

    Leveraging the unrivalled performance of optical clocks as key tools for geo-science, for astronomy and for fundamental physics beyond the standard model requires comparing the frequency of distant optical clocks faithfully. Here, we report on the comparison and agreement of two strontium optical clocks at an uncertainty of 5 × 10(-17) via a newly established phase-coherent frequency link connecting Paris and Braunschweig using 1,415 km of telecom fibre. The remote comparison is limited only by the instability and uncertainty of the strontium lattice clocks themselves, with negligible contributions from the optical frequency transfer. A fractional precision of 3 × 10(-17) is reached after only 1,000 s averaging time, which is already 10 times better and more than four orders of magnitude faster than any previous long-distance clock comparison. The capability of performing high resolution international clock comparisons paves the way for a redefinition of the unit of time and an all-optical dissemination of the SI-second.

  17. Circadian rhythms and clocks in adipose tissues: current insights

    Directory of Open Access Journals (Sweden)

    Kiehn JT

    2017-04-01

    Full Text Available Jana-Thabea Kiehn,* Christiane E Koch,* Marina Walter, Alexandra Brod, Henrik Oster Chronophysiology Group, Medical Department I, University of Lübeck, Lübeck, Germany *These authors contributed equally to this work Abstract: Endogenous circadian timekeepers are found in most cells and organs of the body, including the different types of adipose tissues. This clock network orchestrates 24-hour rhythms of physiology and behavior to adapt the organism to daily recurring changes in the environment. Energy intake and expenditure as well as adipose physiology are under circadian control and, therefore, energy homeostasis and circadian clock function are closely linked. In this review, we summarize the current knowledge about the regulation and targets of adipocyte circadian clocks and how circadian rhythm disruption affects energy homeostasis and adipose tissue function. We provide a more detailed overview of metabolic phenotypes of different mouse models of circadian clock dysfunction and discuss the implications of (adipose clock disruption on adipocyte–brain cross talk and metabolic homeostasis. Keywords: food intake, metaflammation, clock genes, adipocyte–brain cross talk, adipokines

  18. The Molecular Circadian Clock and Alcohol-Induced Liver Injury

    Directory of Open Access Journals (Sweden)

    Uduak S. Udoh

    2015-10-01

    Full Text Available Emerging evidence from both experimental animal studies and clinical human investigations demonstrates strong connections among circadian processes, alcohol use, and alcohol-induced tissue injury. Components of the circadian clock have been shown to influence the pathophysiological effects of alcohol. Conversely, alcohol may alter the expression of circadian clock genes and the rhythmic behavioral and metabolic processes they regulate. Therefore, we propose that alcohol-mediated disruption in circadian rhythms likely underpins many adverse health effects of alcohol that cut across multiple organ systems. In this review, we provide an overview of the circadian clock mechanism and showcase results from new studies in the alcohol field implicating the circadian clock as a key target of alcohol action and toxicity in the liver. We discuss various molecular events through which alcohol may work to negatively impact circadian clock-mediated processes in the liver, and contribute to tissue pathology. Illuminating the mechanistic connections between the circadian clock and alcohol will be critical to the development of new preventative and pharmacological treatments for alcohol use disorders and alcohol-mediated organ diseases.

  19. The central clock neurons regulate lipid storage in Drosophila.

    Directory of Open Access Journals (Sweden)

    Justin R DiAngelo

    Full Text Available A proper balance of lipid breakdown and synthesis is essential for achieving energy homeostasis as alterations in either of these processes can lead to pathological states such as obesity. The regulation of lipid metabolism is quite complex with multiple signals integrated to control overall triglyceride levels in metabolic tissues. Based upon studies demonstrating effects of the circadian clock on metabolism, we sought to determine if the central clock cells in the Drosophila brain contribute to lipid levels in the fat body, the main nutrient storage organ of the fly. Here, we show that altering the function of the Drosophila central clock neurons leads to an increase in fat body triglycerides. We also show that although triglyceride levels are not affected by age, they are increased by expression of the amyloid-beta protein in central clock neurons. The effect on lipid storage seems to be independent of circadian clock output as changes in triglycerides are not always observed in genetic manipulations that result in altered locomotor rhythms. These data demonstrate that the activity of the central clock neurons is necessary for proper lipid storage.

  20. Influence of relativistic effects on satellite-based clock synchronization

    Science.gov (United States)

    Wang, Jieci; Tian, Zehua; Jing, Jiliang; Fan, Heng

    2016-03-01

    Clock synchronization between the ground and satellites is a fundamental issue in future quantum telecommunication, navigation, and global positioning systems. Here, we propose a scheme of near-Earth orbit satellite-based quantum clock synchronization with atmospheric dispersion cancellation by taking into account the spacetime background of the Earth. Two frequency entangled pulses are employed to synchronize two clocks, one at a ground station and the other at a satellite. The time discrepancy of the two clocks is introduced into the pulses by moving mirrors and is extracted by measuring the coincidence rate of the pulses in the interferometer. We find that the pulses are distorted due to effects of gravity when they propagate between the Earth and the satellite, resulting in remarkably affected coincidence rates. We also find that the precision of the clock synchronization is sensitive to the source parameters and the altitude of the satellite. The scheme provides a solution for satellite-based quantum clock synchronization with high precision, which can be realized, in principle, with current technology.

  1. Genetically Blocking the Zebrafish Pineal Clock Affects Circadian Behavior

    Science.gov (United States)

    Alon, Shahar; Vallone, Daniela; Tovin, Adi; Shainer, Inbal; Nisembaum, Laura G.; Aviram, Idit; Smadja-Storz, Sima; Fuentes, Michael; Falcón, Jack; Eisenberg, Eli; Klein, David C.; Burgess, Harold A.; Foulkes, Nicholas S.; Gothilf, Yoav

    2016-01-01

    The master circadian clock in fish has been considered to reside in the pineal gland. This dogma is challenged, however, by the finding that most zebrafish tissues contain molecular clocks that are directly reset by light. To further examine the role of the pineal gland oscillator in the zebrafish circadian system, we generated a transgenic line in which the molecular clock is selectively blocked in the melatonin-producing cells of the pineal gland by a dominant-negative strategy. As a result, clock-controlled rhythms of melatonin production in the adult pineal gland were disrupted. Moreover, transcriptome analysis revealed that the circadian expression pattern of the majority of clock-controlled genes in the adult pineal gland is abolished. Importantly, circadian rhythms of behavior in zebrafish larvae were affected: rhythms of place preference under constant darkness were eliminated, and rhythms of locomotor activity under constant dark and constant dim light conditions were markedly attenuated. On the other hand, global peripheral molecular oscillators, as measured in whole larvae, were unaffected in this model. In conclusion, characterization of this novel transgenic model provides evidence that the molecular clock in the melatonin-producing cells of the pineal gland plays a key role, possibly as part of a multiple pacemaker system, in modulating circadian rhythms of behavior. PMID:27870848

  2. Extracting dark matter signatures from atomic clock stability measurements

    Science.gov (United States)

    Kalaydzhyan, Tigran; Yu, Nan

    2017-10-01

    We analyze possible effects of the dark matter environment on the atomic clock stability measurements. The dark matter is assumed to exist in the form of waves of ultralight scalar fields or in the form of topological defects (monopoles and strings). We identify dark matter signal signatures in clock Allan deviation plots that can be used to constrain the dark matter coupling to the Standard Model fields. The existing data on the Al+/Hg+ clock comparison are used to put new limits on the dilaton dark matter in the region of masses mϕ>10-15 eV . We also estimate the sensitivities of future atomic clock experiments in space, including the cesium microwave and strontium optical clocks aboard the International Space Station, as well as a potential nuclear clock. These experiments are expected to put new limits on the topological dark matter in the range of masses 10-10 eV

  3. Atomic clocks and the continuous-time random-walk

    Science.gov (United States)

    Formichella, Valerio; Camparo, James; Tavella, Patrizia

    2017-11-01

    Atomic clocks play a fundamental role in many fields, most notably they generate Universal Coordinated Time and are at the heart of all global navigation satellite systems. Notwithstanding their excellent timekeeping performance, their output frequency does vary: it can display deterministic frequency drift; diverse continuous noise processes result in nonstationary clock noise (e.g., random-walk frequency noise, modelled as a Wiener process), and the clock frequency may display sudden changes (i.e., "jumps"). Typically, the clock's frequency instability is evaluated by the Allan or Hadamard variances, whose functional forms can identify the different operative noise processes. Here, we show that the Allan and Hadamard variances of a particular continuous-time random-walk, the compound Poisson process, have the same functional form as for a Wiener process with drift. The compound Poisson process, introduced as a model for observed frequency jumps, is an alternative to the Wiener process for modelling random walk frequency noise. This alternate model fits well the behavior of the rubidium clocks flying on GPS Block-IIR satellites. Further, starting from jump statistics, the model can be improved by considering a more general form of continuous-time random-walk, and this could bring new insights into the physics of atomic clocks.

  4. Cancer/testis antigen PASD1 silences the circadian clock

    Science.gov (United States)

    Michael, Alicia K.; Harvey, Stacy L.; Sammons, Patrick J.; Anderson, Amanda P.; Kopalle, Hema M.; Banham, Alison H.; Partch, Carrie L.

    2015-01-01

    SUMMARY The circadian clock orchestrates global changes in transcriptional regulation on a daily basis via the bHLH-PAS transcription factor CLOCK:BMAL1. Pathways driven by other bHLH-PAS transcription factors have a homologous repressor that modulates activity on a tissue-specific basis, but none have been identified for CLOCK:BMAL1. We show here that the cancer/testis antigen PASD1 fulfills this role to suppress circadian rhythms. PASD1 is evolutionarily related to CLOCK and interacts with the CLOCK:BMAL1 complex to repress transcriptional activation. Expression of PASD1 is restricted to germline tissues in healthy individuals, but can be induced in cells of somatic origin upon oncogenic transformation. Reducing PASD1 in human cancer cells significantly increases the amplitude of transcriptional oscillations to generate more robust circadian rhythms. Our results describe a function for a germline-specific protein in regulation of the circadian clock and provide a molecular link from oncogenic transformation to suppression of circadian rhythms. PMID:25936801

  5. Genetically Blocking the Zebrafish Pineal Clock Affects Circadian Behavior.

    Directory of Open Access Journals (Sweden)

    Zohar Ben-Moshe Livne

    2016-11-01

    Full Text Available The master circadian clock in fish has been considered to reside in the pineal gland. This dogma is challenged, however, by the finding that most zebrafish tissues contain molecular clocks that are directly reset by light. To further examine the role of the pineal gland oscillator in the zebrafish circadian system, we generated a transgenic line in which the molecular clock is selectively blocked in the melatonin-producing cells of the pineal gland by a dominant-negative strategy. As a result, clock-controlled rhythms of melatonin production in the adult pineal gland were disrupted. Moreover, transcriptome analysis revealed that the circadian expression pattern of the majority of clock-controlled genes in the adult pineal gland is abolished. Importantly, circadian rhythms of behavior in zebrafish larvae were affected: rhythms of place preference under constant darkness were eliminated, and rhythms of locomotor activity under constant dark and constant dim light conditions were markedly attenuated. On the other hand, global peripheral molecular oscillators, as measured in whole larvae, were unaffected in this model. In conclusion, characterization of this novel transgenic model provides evidence that the molecular clock in the melatonin-producing cells of the pineal gland plays a key role, possibly as part of a multiple pacemaker system, in modulating circadian rhythms of behavior.

  6. Mitochondrial Aging: Is There a Mitochondrial Clock?

    Science.gov (United States)

    Zorov, Dmitry B; Popkov, Vasily A; Zorova, Ljubava D; Vorobjev, Ivan A; Pevzner, Irina B; Silachev, Denis N; Zorov, Savva D; Jankauskas, Stanislovas S; Babenko, Valentina A; Plotnikov, Egor Y

    2017-09-01

    Fragmentation (fission) of mitochondria, occurring in response to oxidative challenge, leads to heterogeneity in the mitochondrial population. It is assumed that fission provides a way to segregate mitochondrial content between the "young" and "old" phenotype, with the formation of mitochondrial "garbage," which later will be disposed. Fidelity of this process is the basis of mitochondrial homeostasis, which is disrupted in pathological conditions and aging. The asymmetry of the mitochondrial fission is similar to that of their evolutionary ancestors, bacteria, which also undergo an aging process. It is assumed that mitochondrial markers of aging are recognized by the mitochondrial quality control system, preventing the accumulation of dysfunctional mitochondria, which normally are subjected to disposal. Possibly, oncocytoma, with its abnormal proliferation of mitochondria occupying the entire cytoplasm, represents the case when segregation of damaged mitochondria is impaired during mitochondrial division. It is plausible that mitochondria contain a "clock" which counts the degree of mitochondrial senescence as the extent of flagging (by ubiquitination) of damaged mitochondria. Mitochondrial aging captures the essence of the systemic aging which must be analyzed. We assume that the mitochondrial aging mechanism is similar to the mechanism of aging of the immune system which we discuss in detail. © The Author 2016. Published by Oxford University Press on behalf of The Gerontological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  7. Laser Technology in Commercial Atomic Clocks

    Science.gov (United States)

    Lutwak, R.

    2006-05-01

    Commercial atomic frequency standards (AFS) are deployed in diverse civilian, military, and aerospace applications, ranging from high-precision measurement and calibration to navigation, communications and, of course, timekeeping. Currently, commercially available AFS include magnetically-selected cesium beam frequency standards and hydrogen masers and lamp-pumped rubidium oscillators. Despite the revolution in atomic physics and laboratory-scale AFS brought about by the advent of the tunable laser in the early 1970s, commercial AFS invariably rely on more conventional atomic physics technology developed in the 1950s. The reason for this lack of advancement of commercial AFS technology is the relatively poor reliability and environmental sensitivity of narrow-linewidth single-mode laser sources at atomic resonance wavelengths. Over the past 8 years, Symmetricom, in collaboration with laser manufacturers, has developed specialized laser sources for commercial AFS applications. These laser devices, optimized for high spectral purity and long-term reliability, will enable a new generation of commercial AFS. This talk will briefly describe two laser-based atomic frequency standard development programs at Symmetricom. The Chip-Scale Atomic Clock, two orders of magnitude smaller and lower power than any commercial AFS, will enable atomic timing accuracy in portable battery-powered applications. The Optically-Pumped Cesium Beam Frequency Standard, under development for deployment onboard the GPS-III satellite constellation, will provide enhanced short-term stability and longer lifetime compared to magnetically-selected cesium beam AFS.

  8. Maternal feeding controls fetal biological clock.

    Directory of Open Access Journals (Sweden)

    Hidenobu Ohta

    Full Text Available BACKGROUND: It is widely accepted that circadian physiological rhythms of the fetus are affected by oscillators in the maternal brain that are coupled to the environmental light-dark (LD cycle. METHODOLOGY/PRINCIPAL FINDINGS: To study the link between fetal and maternal biological clocks, we investigated the effects of cycles of maternal food availability on the rhythms of Per1 gene expression in the fetal suprachiasmatic nucleus (SCN and liver using a transgenic rat model whose tissues express luciferase in vitro. Although the maternal SCN remained phase-locked to the LD cycle, maternal restricted feeding phase-advanced the fetal SCN and liver by 5 and 7 hours respectively within the 22-day pregnancy. CONCLUSIONS/SIGNIFICANCE: Our results demonstrate that maternal feeding entrains the fetal SCN and liver independently of both the maternal SCN and the LD cycle. This indicates that maternal-feeding signals can be more influential for the fetal SCN and particular organ oscillators than hormonal signals controlled by the maternal SCN, suggesting the importance of a regular maternal feeding schedule for appropriate fetal molecular clockwork during pregnancy.

  9. Biological clocks and rhythms in intertidal crustaceans.

    Science.gov (United States)

    de la Iglesia, Horacio O; Hsu, Yun-Wei A

    2010-06-01

    Animals with habitats within the intertidal zone are exposed to environmental cycles that include the ebb and flow of tidal waters, changes in tidal levels associated with the lunar month, the light-dark cycle and the alternation of seasons. This intricate temporal environment results in the selection of biological timing systems with endogenous clocks that can oscillate with this wide range of periodicities. Whereas great progress has been made in our understanding of the molecular and neural bases of circadian rhythms, that is, endogenous rhythms synchronized to the solar day, there is little understanding on how circatidal rhythms, namely endogenous rhythms synchronized to tides, are generated. Intertidal crustaceans have been a pivotal group for the demonstration of the endogenous nature of circatidal rhythms and their mechanisms of entrainment. We review here some of the classic work using intertidal crustaceans to unmask basic properties of circatidal systems, as well as work from our laboratory that aims to identify putative chemical signals that could be involved in the circatidal systems of decapod crustaceans.

  10. Reduced Voltage Scaling in Clock Distribution Networks

    Directory of Open Access Journals (Sweden)

    Khader Mohammad

    2009-01-01

    Full Text Available We propose a novel circuit technique to generate a reduced voltage swing (RVS signals for active power reduction on main buses and clocks. This is achieved without performance degradation, without extra power supply requirement, and with minimum area overhead. The technique stops the discharge path on the net that is swinging low at a certain voltage value. It reduces active power on the target net by as much as 33% compared to traditional full swing signaling. The logic 0 voltage value is programmable through control bits. If desired, the reduced-swing mode can also be disabled. The approach assumes that the logic 0 voltage value is always less than the threshold voltage of the nMOS receivers, which eliminate the need of the low to high voltage translation. The reduced noise margin and the increased leakage on the receiver transistors using this approach have been addressed through the selective usage of multithreshold voltage (MTV devices and the programmability of the low voltage value.

  11. The clock of a quantum computer

    CERN Document Server

    Apolloni, B

    2002-01-01

    If the physical agent (the 'pointer', or 'cursor', or 'clocking mechanism') that sequentially scans the T lines of a long computer program is a microscopic system, two quantum phenomena become relevant: spreading of the probability distribution of the pointer along the program lines, and scattering of the probability amplitude at the two endpoints of the physical space allowed for its motion. We show that the first effect determines an upper bound O(T sup - sup 2 sup / sup 3) on the probability of finding the pointer exactly at the END line. By adding an adequate number delta of further empty lines ('telomers'), one can store the result of the computation up to the moment in which the pointer is scattered back into the active region. This leads to a less severe upper bound O(sq root delta/T) on the probability of finding the pointer either at the END line or within the additional empty lines. Our analysis is performed in the context of Feynman's model of quantum computation, the only model, to our knowledge, ...

  12. The canary tree

    OpenAIRE

    Mekler, Alan H.; Shelah, Saharon

    1993-01-01

    A canary tree is a tree of cardinality the continuum which has no uncountable branch, but gains a branch whenever a stationary set is destroyed (without adding reals). Canary trees are important in infinitary model theory. The existence of a canary tree is independent of ZFC + GCH.

  13. Urban tree growth modeling

    Science.gov (United States)

    E. Gregory McPherson; Paula J. Peper

    2012-01-01

    This paper describes three long-term tree growth studies conducted to evaluate tree performance because repeated measurements of the same trees produce critical data for growth model calibration and validation. Several empirical and process-based approaches to modeling tree growth are reviewed. Modeling is more advanced in the fields of forestry and...

  14. Clock gene expression in the murine gastrointestinal tract: endogenous rhythmicity and effects of a feeding regimen.

    Science.gov (United States)

    Hoogerwerf, Willemijntje A; Hellmich, Helen L; Cornélissen, Germaine; Halberg, Franz; Shahinian, Vahakn B; Bostwick, Jonathon; Savidge, Tor C; Cassone, Vincent M

    2007-10-01

    Based on observations that the gastrointestinal tract is subject to various 24-hour rhythmic processes, it is conceivable that some of these rhythms are under circadian clock gene control. We hypothesized that clock genes are present in the gastrointestinal tract and that they are part of a functional molecular clock that coordinates rhythmic physiologic functions. The effects of timed feeding and vagotomy on temporal clock gene expression (clock, bmal1, per1-3, cry1-2) in the gastrointestinal tract and suprachiasmatic nucleus (bmal, per2) of C57BL/6J mice were examined using real-time polymerase chain reaction and Western blotting (BMAL, PER2). Colonic clock gene localization was examined using immunohistochemistry (BMAL, PER1-2). Clock immunoreactivity was observed in the myenteric plexus and epithelial crypt cells. Clock genes were expressed rhythmically throughout the gastrointestinal tract. Timed feeding shifted clock gene expression at the RNA and protein level but did not shift clock gene expression in the central clock. Vagotomy did not alter gastric clock gene expression compared with sham-treated controls. The murine gastrointestinal tract contains functional clock genes, which are molecular core components of the circadian clock. Daytime feeding in nocturnal rodents is a strong synchronizer of gastrointestinal clock genes. This synchronization occurs independently of the central clock. Gastric clock gene expression is not mediated through the vagal nerve. The presence of clock genes in the myenteric plexus and epithelial cells suggests a role for clock genes in circadian coordination of gastrointestinal functions such as motility, cell proliferation, and migration.

  15. Multiphase clock generators with controlled clock impulse width for programmable high order rotator SC FIR filters realized in 0.35 μm CMOS technology

    Science.gov (United States)

    Dlugosz, Rafal; Pawlowski, Pawel; Dabrowski, Adam

    2005-06-01

    Complexity of clock generator is one of the most important parameters in the design and optimization of switched-capacitor (SC) finite impulse response (FIR) filters. There are different SC FIR filter architectures. Some of them need a simple clock generator but the others require a quite complicated multiphase clock system. In the latter case an external clock system (i.e., outside the integrated circuit) is unrealistic because of a great number of the required external pins. We have implemented various SC FIR filter architectures together with complex internal clock generators in the CMOS 0.8 μm and 0.35 μm technologies. One of the most important problems in the design process was the optimization of waveforms and widths of the clock impulses. SC FIR filters are very sensitive to parameters of clock systems. Thus the clock generators must be designed very precisely. We demonstrate results of the design of the 64-phase clock generator for a programmable rotator SC FIR filter. In our approach the width of the clock impulses is controlled by two external signals. This is a very convenient solution, because optimization of the clock impulses, which was difficult in other approaches, is currently much easier. The internal clock generator area is ca. 0.15 mm2 in the CMOS 0.35 μm technology, i.e., only 7 % of the entire SC FIR filter chip area.

  16. The retinal clock in mammals: role in health and disease

    Directory of Open Access Journals (Sweden)

    Felder-Schmittbuhl MP

    2017-05-01

    Full Text Available Marie-Paule Felder-Schmittbuhl,1,* Hugo Calligaro,2 Ouria Dkhissi-Benyahya2,* 1Institute of Cellular and Integratives Neurosciences, UPR3212, CNRS, Université de Strasbourg, Strasbourg, 2University of Lyon, Stem Cell and Brain Research Institute, INSERM U1208, Bron, France *These authors contributed equally to this work Abstract: The mammalian retina contains an extraordinary diversity of cell types that are highly organized into precise circuits to perceive and process visual information in a dynamic manner and transmit it to the brain. Above this builds up another level of complex dynamic, orchestrated by a circadian clock located within the retina, which allows retinal physiology, and hence visual function, to adapt to daily changes in light intensity. The mammalian retina is a remarkable model of circadian clock because it harbors photoreception, self-sustained oscillator function, and physiological outputs within the same tissue. However, the location of the retinal clock in mammals has been a matter of long debate. Current data have shown that clock properties are widely distributed among retinal cells and that the retina is composed of a network of circadian clocks located within distinct cellular layers. Nevertheless, the identity of the major pacemaker, if any, still warrants identification. In addition, the retina coordinates rhythmic behavior by providing visual input to the master hypothalamic circadian clock in the suprachiasmatic nuclei (SCN. This light entrainment of the SCN to the light/dark cycle involves a network of retinal photoreceptor cells: rods, cones, and intrinsically photosensitive retinal ganglion cells (ipRGCs. Although it was considered that these photoreceptors synchronized both retinal and SCN clocks, new data challenge this view, suggesting that none of these photoreceptors is involved in photic entrainment of the retinal clock. Because circadian organization is a ubiquitous feature of the retina and controls

  17. Development of a strontium optical lattice clock for space applications

    Science.gov (United States)

    Singh, Yeshpal

    2016-07-01

    With timekeeping being of paramount importance for modern life, much research and major scientific advances have been undertaken in the field of frequency metrology, particularly over the last few years. New Nobel-prize winning technologies have enabled a new era of atomic clocks; namely the optical clock. These have been shown to perform significantly better than the best microwave clocks reaching an inaccuracy of 1.6x10-18 [1]. With such results being found in large lab based apparatus, the focus now has shifted to portability - to enable the accuracy of various ground based clocks to be measured, and compact autonomous performance - to enable such technologies to be tested in space. This could lead to a master clock in space, improving not only the accuracy of technologies on which modern life has come to require such as GPS and communication networks. But also more fundamentally, this could lead to the redefinition of the second and tests of fundamental physics including applications in the fields of ground based and satellite geodesy, metrology, positioning, navigation, transport and logistics etc. Within the European collaboration, Space Optical Clocks (SOC2) [2-3] consisting of various institutes and industry partners across Europe we have tried to tackle this problem of miniaturisation whilst maintaining stability, accuracy (5x10-17) and robustness whilst keeping power consumption to a minimum - necessary for space applications. We will present the most recent results of the Sr optical clock in SOC2 and also the novel compact design features, new methods employed and outlook. References [1] B. J. Bloom, T. L. Nicholson, J. R. Williams, S. L. Campbell, M. Bishof, X. Zhang, W. Zhang, S. L. Bromley, and J. Ye, "An optical lattice clock with accuracy and stability at the 10-18 level," Nature 506, 71-75 (2014). [2] S. Schiller et al. "Towards Neutral-atom Space Optical Clocks (SOC2): Development of high-performance transportable and breadboard optical clocks and

  18. Classification and regression trees

    CERN Document Server

    Breiman, Leo; Olshen, Richard A; Stone, Charles J

    1984-01-01

    The methodology used to construct tree structured rules is the focus of this monograph. Unlike many other statistical procedures, which moved from pencil and paper to calculators, this text's use of trees was unthinkable before computers. Both the practical and theoretical sides have been developed in the authors' study of tree methods. Classification and Regression Trees reflects these two sides, covering the use of trees as a data analysis method, and in a more mathematical framework, proving some of their fundamental properties.

  19. Inflation of Molecular Clock Rates and Dates: Molecular Phylogenetics, Biogeography, and Diversification of a Global Cicada Radiation from Australasia (Hemiptera: Cicadidae: Cicadettini).

    Science.gov (United States)

    Marshall, David C; Hill, Kathy B R; Moulds, Max; Vanderpool, Dan; Cooley, John R; Mohagan, Alma B; Simon, Chris

    2016-01-01

    Dated phylogenetic trees are important for studying mechanisms of diversification, and molecular clocks are important tools for studies of organisms lacking good fossil records. However, studies have begun to identify problems in molecular clock dates caused by uncertainty of the modeled molecular substitution process. Here we explore Bayesian relaxed-clock molecular dating while studying the biogeography of ca. 200 species from the global cicada tribe Cicadettini. Because the available fossils are few and uninformative, we calibrate our trees in part with a cytochrome oxidase I (COI) clock prior encompassing a range of literature estimates for arthropods. We show that tribe-level analyses calibrated solely with the COI clock recover extremely old dates that conflict with published estimates for two well-studied New Zealand subclades within Cicadettini. Additional subclade analyses suggest that COI relaxed-clock rates and maximum-likelihood branch lengths become inflated relative to EF-1[Formula: see text] intron and exon rates and branch lengths as clade age increases. We present corrected estimates derived from: (i) an extrapolated EF-1[Formula: see text] exon clock derived from COI-calibrated analysis within the largest New Zealand subclade; (ii) post hoc scaling of the tribe-level chronogram using results from subclade analyses; and (iii) exploitation of a geological calibration point associated with New Caledonia. We caution that considerable uncertainty is generated due to dependence of substitution estimates on both the taxon sample and the choice of model, including gamma category number and the choice of empirical versus estimated base frequencies. Our results suggest that diversification of the tribe Cicadettini commenced in the early- to mid-Cenozoic and continued with the development of open, arid habitats in Australia and worldwide. We find that Cicadettini is a rare example of a global terrestrial animal group with an Australasian origin, with all non

  20. British domestic synchronous clocks 1930-1980 the rise and fall of a technology

    CERN Document Server

    Pook, Leslie Philip

    2015-01-01

    This book complements available one-make books on domestic synchronous clocks. It is also a history of science book that sets British domestic synchronous clocks, their manufacturers and technology in their social context. Part I covers the historical background, British domestic synchronous clock manufacturers and brands, how synchronous clocks work, domestic synchronous clock cases, practical advice on the servicing of domestic synchronous clocks, and analysis of the marketing and reliability of British domestic synchronous clocks. This analysis provides an explanation of the rise and eventual fall of their technology. Part II contains galleries of a selection of British domestic synchronous clocks, and of the movements with which they are fitted. There is a front and back view of each clock, together with a brief description. Views of each movement include views with the movement partly dismantled, together with a brief technical description of the movement. This profusely illustrated book is primarily fo...

  1. Functional Implications of the CLOCK 3111T/C Single-Nucleotide Polymorphism.

    Science.gov (United States)

    Ozburn, Angela R; Purohit, Kush; Parekh, Puja K; Kaplan, Gabrielle N; Falcon, Edgardo; Mukherjee, Shibani; Cates, Hannah M; McClung, Colleen A

    2016-01-01

    Circadian rhythm disruptions are prominently associated with bipolar disorder (BD). Circadian rhythms are regulated by the molecular clock, a family of proteins that function together in a transcriptional-translational feedback loop. The CLOCK protein is a key transcription factor of this feedback loop, and previous studies have found that manipulations of the Clock gene are sufficient to produce manic-like behavior in mice (1). The CLOCK 3111T/C single-nucleotide polymorphism (SNP; rs1801260) is a genetic variation of the human CLOCK gene that is significantly associated with increased frequency of manic episodes in BD patients (2). The 3111T/C SNP is located in the 3'-untranslated region of the CLOCK gene. In this study, we sought to examine the functional implications of the human CLOCK 3111T/C SNP by transfecting a mammalian cell line (mouse embryonic fibroblasts isolated from Clock(-/-) knockout mice) with pcDNA plasmids containing the human CLOCK gene with either the T or C SNP at position 3111. We then measured circadian gene expression over a 24-h time period. We found that the CLOCK3111C SNP resulted in higher mRNA levels than the CLOCK 3111T SNP. Furthermore, we found that Per2, a transcriptional target of CLOCK, was also more highly expressed with CLOCK 3111C expression, indicating that the 3'-UTR SNP affects the expression, function, and stability of CLOCK mRNA.

  2. FUNCTIONAL IMPLICATIONS OF THE CLOCK 3111T/C SINGLE-NUCLEOTIDE POLYMORPHISM

    Directory of Open Access Journals (Sweden)

    Angela Renee Ozburn

    2016-04-01

    Full Text Available Circadian rhythm disruptions are prominently associated with Bipolar Disorder (BD. Circadian rhythms are regulated by the molecular clock, a family of proteins that function together in a transcriptional-translational feedback loop. The CLOCK protein is a key transcription factor of this feedback loop, and previous studies have found that manipulations of the Clock gene are sufficient to produce manic-like behavior in mice (Roybal et al., 2007. The Clock 3111T/C single-nucleotide polymorphism (SNP; rs1801260 is a genetic variation of the human Clock gene that is significantly associated with increased frequency of manic episodes in BD patients (Benedetti et al., 2003. The 3111T/C SNP is located in the 3’ untranslated region of the Clock gene. In this study, we sought to examine the functional implications of the human Clock 3111T/C SNP by transfecting a mammalian cell line (mouse embryonic fibroblasts isolated from Clock -/- knockout mice with pcDNA plasmids containing the human Clock gene with either the T or C SNP at position 3111. We then measured circadian gene expression over a 24 hour time period. We found that the Clock3111C SNP resulted in higher mRNA levels than the Clock 3111T SNP. Further, we found that Per2, a transcriptional target of CLOCK, was also more highly expressed with Clock 3111C expression, indicating the 3’UTR SNP affects the expression, function and stability of Clock mRNA.

  3. There's Life in Hazard Trees

    Science.gov (United States)

    Mary Torsello; Toni McLellan

    The goals of hazard tree management programs are to maximize public safety and maintain a healthy sustainable tree resource. Although hazard tree management frequently targets removal of trees or parts of trees that attract wildlife, it can take into account a diversity of tree values. With just a little extra planning, hazard tree management can be highly beneficial...

  4. Atomic clocks as a tool to monitor vertical surface motion

    CERN Document Server

    Bondarescu, Ruxandra; Lundgren, Andrew; Hetényi, György; Houlié, Nicolas; Jetzer, Philippe; Bondarescu, Mihai

    2015-01-01

    Atomic clock technology is advancing rapidly, now reaching stabilities of $\\Delta f/f \\sim 10^{-18}$, which corresponds to resolving $1$ cm in equivalent geoid height over an integration timescale of about 7 hours. At this level of performance, ground-based atomic clock networks emerge as a tool for monitoring a variety of geophysical processes by directly measuring changes in the gravitational potential. Vertical changes of the clock's position due to magmatic, volcanic, post-seismic or tidal deformations can result in measurable variations in the clock tick rate. As an example, we discuss the geopotential change arising due to an inflating point source (Mogi model), and apply it to the Etna volcano. Its effect on an observer on the Earth's surface can be divided into two different terms: one purely due to uplift and one due to the redistribution of matter. Thus, with the centimetre-level precision of current clocks it is already possible to monitor volcanoes. The matter redistribution term is estimated to b...

  5. FAD Regulates CRYPTOCHROME Protein Stability and Circadian Clock in Mice.

    Science.gov (United States)

    Hirano, Arisa; Braas, Daniel; Fu, Ying-Hui; Ptáček, Louis J

    2017-04-11

    The circadian clock generates biological rhythms of metabolic and physiological processes, including the sleep-wake cycle. We previously identified a missense mutation in the flavin adenine dinucleotide (FAD) binding pocket of CRYPTOCHROME2 (CRY2), a clock protein that causes human advanced sleep phase. This prompted us to examine the role of FAD as a mediator of the clock and metabolism. FAD stabilized CRY proteins, leading to increased protein levels. In contrast, knockdown of Riboflavin kinase (Rfk), an FAD biosynthetic enzyme, enhanced CRY degradation. RFK protein levels and FAD concentrations oscillate in the nucleus, suggesting that they are subject to circadian control. Knockdown of Rfk combined with a riboflavin-deficient diet altered the CRY levels in mouse liver and the expression profiles of clock and clock-controlled genes (especially those related to metabolism including glucose homeostasis). We conclude that light-independent mechanisms of FAD regulate CRY and contribute to proper circadian oscillation of metabolic genes in mammals. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  6. The Circadian Clock-controlled Transcriptome of Developing Soybean Seeds

    Directory of Open Access Journals (Sweden)

    Karen A. Hudson

    2010-07-01

    Full Text Available A number of metabolic and physiological processes in plants are controlled by the circadian clock, which enables a plant to anticipate daily changes in the environment. Relatively little is known about circadian rhythms in developing seeds, which may be important for determining the extent and timing of nutrient storage in grain. Microarray expression profiling was used to identify genes expressed in developing soybean ( seeds that are controlled by the circadian clock. Genes with predicted functions in protein synthesis, fatty acid metabolism, and photosynthesis totaling 1.8% of the mRNAs detected in seed were found to be expressed in a circadian rhythm. Known circadian and light-controlled promoter elements were identified as over-represented in the promoters of clock-controlled seed genes, with the over-represented elements varying according to the phase of circadian expression. A subset of circadian-regulated genes were found to be expressed in different phases in developing seeds with respect to leaves from the same plants, many of which have roles in photosynthesis and carbon metabolism. These results help to characterize the genes and processes in seeds that may be regulated by the circadian clock, and provide some insight into organ-specific phasing of clock controlled gene expression.

  7. Photosynthetic entrainment of the Arabidopsis thaliana circadian clock.

    Science.gov (United States)

    Haydon, Michael J; Mielczarek, Olga; Robertson, Fiona C; Hubbard, Katharine E; Webb, Alex A R

    2013-10-31

    Circadian clocks provide a competitive advantage in an environment that is heavily influenced by the rotation of the Earth, by driving daily rhythms in behaviour, physiology and metabolism in bacteria, fungi, plants and animals. Circadian clocks comprise transcription-translation feedback loops, which are entrained by environmental signals such as light and temperature to adjust the phase of rhythms to match the local environment. The production of sugars by photosynthesis is a key metabolic output of the circadian clock in plants. Here we show that these rhythmic, endogenous sugar signals can entrain circadian rhythms in Arabidopsis thaliana by regulating the gene expression of circadian clock components early in the photoperiod, thus defining a 'metabolic dawn'. By inhibiting photosynthesis, we demonstrate that endogenous oscillations in sugar levels provide metabolic feedback to the circadian oscillator through the morning-expressed gene PSEUDO-RESPONSE REGULATOR 7 (PRR7), and we identify that prr7 mutants are insensitive to the effects of sucrose on the circadian period. Thus, photosynthesis has a marked effect on the entrainment and maintenance of robust circadian rhythms in A. thaliana, demonstrating that metabolism has a crucial role in regulation of the circadian clock.

  8. FAD Regulates CRYPTOCHROME Protein Stability and Circadian Clock in Mice

    Directory of Open Access Journals (Sweden)

    Arisa Hirano

    2017-04-01

    Full Text Available The circadian clock generates biological rhythms of metabolic and physiological processes, including the sleep-wake cycle. We previously identified a missense mutation in the flavin adenine dinucleotide (FAD binding pocket of CRYPTOCHROME2 (CRY2, a clock protein that causes human advanced sleep phase. This prompted us to examine the role of FAD as a mediator of the clock and metabolism. FAD stabilized CRY proteins, leading to increased protein levels. In contrast, knockdown of Riboflavin kinase (Rfk, an FAD biosynthetic enzyme, enhanced CRY degradation. RFK protein levels and FAD concentrations oscillate in the nucleus, suggesting that they are subject to circadian control. Knockdown of Rfk combined with a riboflavin-deficient diet altered the CRY levels in mouse liver and the expression profiles of clock and clock-controlled genes (especially those related to metabolism including glucose homeostasis. We conclude that light-independent mechanisms of FAD regulate CRY and contribute to proper circadian oscillation of metabolic genes in mammals.

  9. Covering tree with stars

    DEFF Research Database (Denmark)

    Baumbach, Jan; Guo, Jian-Ying; Ibragimov, Rashid

    2013-01-01

    We study the tree edit distance problem with edge deletions and edge insertions as edit operations. We reformulate a special case of this problem as Covering Tree with Stars (CTS): given a tree T and a set of stars, can we connect the stars in by adding edges between them such that the resulting...... tree is isomorphic to T? We prove that in the general setting, CST is NP-complete, which implies that the tree edit distance considered here is also NP-hard, even when both input trees having diameters bounded by 10. We also show that, when the number of distinct stars is bounded by a constant k, CTS...

  10. Covering tree with stars

    DEFF Research Database (Denmark)

    Baumbach, Jan; Guo, Jiong; Ibragimov, Rashid

    2015-01-01

    We study the tree edit distance problem with edge deletions and edge insertions as edit operations. We reformulate a special case of this problem as Covering Tree with Stars (CTS): given a tree T and a set of stars, can we connect the stars in by adding edges between them such that the resulting...... tree is isomorphic to T? We prove that in the general setting, CST is NP-complete, which implies that the tree edit distance considered here is also NP-hard, even when both input trees having diameters bounded by 10. We also show that, when the number of distinct stars is bounded by a constant k, CTS...

  11. To Tree or Not to Tree

    NARCIS (Netherlands)

    Holmgren, Milena; Scheffer, Marten

    2017-01-01

    Few things are more defining in a landscape compared to the absence or presence of trees, both in aesthetic and in functional terms. At the same time, tree cover has been profoundly affected by humans since ancient times. It is therefore not surprising that opinions about deforestation and

  12. Searching for dark matter with optical atomic clocks

    CERN Document Server

    Wcislo, Piotr; Bober, Marcin; Cygan, Agata; Lisak, Daniel; Ciurylo, Roman; Zawada, Michal

    2016-01-01

    One of the most fundamental questions of modern physics is the existence of yet unknown forms of matter and interactions. The total mass density of the Universe appears to be dominated by some hypothetical dark matter (DM). However, beyond its gravitational interaction at galactic scale, little is known about the DM nature and properties. One possibility is that it has a form of stable topological defects built from light scalar fields which, for nonzero DM-SM coupling, would result in transient variations of fundamental constants. Optical atomic clocks, highly sensitive to variations of the fine-structure constant, seem to be natural candidates for such searches. Here we demonstrate the first experimental constraint on the strength of transient DM-SM coupling determined with optical atomic clocks. Instead of measuring the phase difference between two distant clocks we determine a common component of their readouts. We show that our constraint, even for one-day measurement, greatly exceeds previous laboratory...

  13. A comparative view of insect circadian clock systems.

    Science.gov (United States)

    Tomioka, Kenji; Matsumoto, Akira

    2010-05-01

    Recent studies revealed that the neuronal network controlling overt rhythms shows striking similarity in various insect orders. The pigment-dispersing factor seems commonly involved in regulating locomotor activity. However, there are considerable variations in the molecular oscillatory mechanism, and input and output pathways among insects. In Drosophila, autoregulatory negative feedback loops that consist of clock genes, such as period and timeless are believed to create 24-h rhythmicity. Although similar clock genes have been found in some insects, the behavior of their product proteins shows considerable differences from that of Drosophila. In other insects, mammalian-type cryptochrome (cry2) seems to work as a transcriptional repressor in the feedback loop. For photic entrainment, Drosophila type cryptochrome (cry1) plays the major role in Drosophila while the compound eyes are the major photoreceptor in others. Further comparative study will be necessary to understand how this variety of clock mechanisms derived from an ancestral one.

  14. Revisiting a Classic Study of the Molecular Clock.

    Science.gov (United States)

    Robinson, Lauren M; Boland, Joseph R; Braverman, John M

    2016-03-01

    A constant rate of molecular evolution among homologous proteins and across lineages is known as the molecular clock. This concept has been useful for estimating divergence times. Here, we revisit a study by Richard Dickerson (J Mol Evol 1:26-45, 1971), wherein he provided striking visual evidence for a constant rate of amino acid changes among various evolutionary branch points. Dickerson's study is commonly cited as support of the molecular clock and a figure from it is often reproduced in textbooks. Since its publication, however, there have been updates made to dates of common ancestors based on the fossil record that should be considered. Additionally, collecting the accession numbers and carefully outlining Dickerson's methods serves as a resource to students of the molecular clock hypothesis.

  15. Circadian clocks optimally adapt to sunlight for reliable synchronization

    CERN Document Server

    Hasegawa, Yoshihiko

    2014-01-01

    Circadian oscillation provides selection advantages through synchronization to the daylight cycle. However, a reliable clock must be designed through two conflicting properties: entrainability to properly respond to external stimuli such as sunlight, and regularity to oscillate with a precise period. These two aspects do not easily coexist because better entrainability favors higher sensitivity, which may sacrifice the regularity. To investigate conditions for satisfying the two properties, we analytically calculated the optimal phase-response curve with a variational method. Our result indicates an existence of a dead zone, i.e., a time during which external stimuli neither advance nor delay the clock. This result is independent of model details and a dead zone appears only when the input stimuli obey the time course of actual insolation. Our calculation demonstrates that every circadian clock with a dead zone is optimally adapted to the daylight cycle. Our result also explains the lack of a dead zone in osc...

  16. Heisenberg-limited atom clocks based on entangled qubits.

    Science.gov (United States)

    Kessler, E M; Kómár, P; Bishof, M; Jiang, L; Sørensen, A S; Ye, J; Lukin, M D

    2014-05-16

    We present a quantum-enhanced atomic clock protocol based on groups of sequentially larger Greenberger-Horne-Zeilinger (GHZ) states that achieves the best clock stability allowed by quantum theory up to a logarithmic correction. Importantly the protocol is designed to work under realistic conditions where the drift of the phase of the laser interrogating the atoms is the main source of decoherence. The simultaneous interrogation of the laser phase with a cascade of GHZ states realizes an incoherent version of the phase estimation algorithm that enables Heisenberg-limited operation while extending the coherent interrogation time beyond the laser noise limit. We compare and merge the new protocol with existing state of the art interrogation schemes, and identify the precise conditions under which entanglement provides an advantage for clock stabilization: it allows a significant gain in the stability for short averaging time.

  17. Spanning Tree Problem

    Directory of Open Access Journals (Sweden)

    Yen Hung Chen

    2012-01-01

    minimum cost spanning tree T in G such that the total weight in T is at most a given bound B. In this paper, we present two polynomial time approximation schemes (PTASs for the constrained minimum spanning tree problem.

  18. Ras-mediated deregulation of the circadian clock in cancer.

    Directory of Open Access Journals (Sweden)

    Angela Relógio

    Full Text Available Circadian rhythms are essential to the temporal regulation of molecular processes in living systems and as such to life itself. Deregulation of these rhythms leads to failures in biological processes and eventually to the manifestation of pathological phenotypes including cancer. To address the questions as to what are the elicitors of a disrupted clock in cancer, we applied a systems biology approach to correlate experimental, bioinformatics and modelling data from several cell line models for colorectal and skin cancer. We found strong and weak circadian oscillators within the same type of cancer and identified a set of genes, which allows the discrimination between the two oscillator-types. Among those genes are IFNGR2, PITX2, RFWD2, PPARγ, LOXL2, Rab6 and SPARC, all involved in cancer-related pathways. Using a bioinformatics approach, we extended the core-clock network and present its interconnection to the discriminative set of genes. Interestingly, such gene signatures link the clock to oncogenic pathways like the RAS/MAPK pathway. To investigate the potential impact of the RAS/MAPK pathway - a major driver of colorectal carcinogenesis - on the circadian clock, we used a computational model which predicted that perturbation of BMAL1-mediated transcription can generate the circadian phenotypes similar to those observed in metastatic cell lines. Using an inducible RAS expression system, we show that overexpression of RAS disrupts the circadian clock and leads to an increase of the circadian period while RAS inhibition causes a shortening of period length, as predicted by our mathematical simulations. Together, our data demonstrate that perturbations induced by a single oncogene are sufficient to deregulate the mammalian circadian clock.

  19. Conservation of Arabidopsis thaliana circadian clock genes in Chrysanthemum lavandulifolium.

    Science.gov (United States)

    Fu, Jianxin; Yang, Liwen; Dai, Silan

    2014-07-01

    In Arabidopsis, circadian clock genes play important roles in photoperiod pathway by regulating the daytime expression of CONSTANS (CO), but related reports for chrysanthemum are notably limited. In this study, we isolated eleven circadian clock genes, which lie in the three interconnected negative and positive feedback loops in a wild diploid chrysanthemum, Chrysanthemum lavandulifolium. With the exception of ClELF3, ClPRR1 and ClPRR73, most of the circadian clock genes are expressed more highly in leaves than in other tested tissues. The diurnal rhythms of these circadian clock genes are similar to those of their homologs in Arabidopsis. ClELF3 and ClZTL are constitutively expressed at all time points in both assessed photoperiods. The expression succession from morning to night of the PSEUDO RESPONSE REGULATOR (PRR) gene family occurs in the order ClPRR73/ClPRR37, ClPRR5, and then ClPRR1. ClLHY is expressed during the dawn period, and ClGIs is expressed during the dusk period. The peak expression levels of ClFKF1 and ClGIs are synchronous in the inductive photoperiod. However, in the non-inductive night break (NB) condition or non-24 h photoperiod, the peak expression level of ClFKF1 is significantly changed, indicating that ClFKF1 itself or the synchronous expression of ClFKF1 and ClGIs might be essential to initiate the flowering of C. lavandulifolium. This study provides the first extensive evaluation of circadian clock genes, and it presents a useful foundation for dissecting the functions of circadian clock genes in C. lavandulifolium. Copyright © 2014. Published by Elsevier Masson SAS.

  20. Breast cancer risk, nightwork, and circadian clock gene polymorphisms.

    Science.gov (United States)

    Truong, Thérèse; Liquet, Benoît; Menegaux, Florence; Plancoulaine, Sabine; Laurent-Puig, Pierre; Mulot, Claire; Cordina-Duverger, Emilie; Sanchez, Marie; Arveux, Patrick; Kerbrat, Pierre; Richardson, Sylvia; Guénel, Pascal

    2014-08-01

    Night shift work has been associated with an increased risk of breast cancer pointing to a role of circadian disruption. We investigated the role of circadian clock gene polymorphisms and their interaction with nightwork in breast cancer risk in a population-based case-control study in France including 1126 breast cancer cases and 1174 controls. We estimated breast cancer risk associated with each of the 577 single nucleotide polymorphisms (SNPs) in 23 circadian clock genes. We also used a gene- and pathway-based approach to investigate the overall effect on breast cancer of circadian clock gene variants that might not be detected in analyses based on individual SNPs. Interactions with nightwork were tested at the SNP, gene, and pathway levels. We found that two SNPs in RORA (rs1482057 and rs12914272) were associated with breast cancer in the whole sample and among postmenopausal women. In this subpopulation, we also reported an association with rs11932595 in CLOCK, and with CLOCK, RORA, and NPAS2 in the analyses at the gene level. Breast cancer risk in postmenopausal women was also associated with overall genetic variation in the circadian gene pathway (P=0.04), but this association was not detected in premenopausal women. There was some evidence of an interaction between PER1 and nightwork in breast cancer in the whole sample (P=0.024), although the effect was not statistically significant after correcting for multiple testing (P=0.452). Our results support the hypothesis that circadian clock gene variants modulate breast cancer risk. © 2014 Society for Endocrinology.

  1. Ras-Mediated Deregulation of the Circadian Clock in Cancer

    Science.gov (United States)

    Relógio, Angela; Thomas, Philippe; Medina-Pérez, Paula; Reischl, Silke; Bervoets, Sander; Gloc, Ewa; Riemer, Pamela; Mang-Fatehi, Shila; Maier, Bert; Schäfer, Reinhold; Leser, Ulf; Herzel, Hanspeter; Kramer, Achim; Sers, Christine

    2014-01-01

    Circadian rhythms are essential to the temporal regulation of molecular processes in living systems and as such to life itself. Deregulation of these rhythms leads to failures in biological processes and eventually to the manifestation of pathological phenotypes including cancer. To address the questions as to what are the elicitors of a disrupted clock in cancer, we applied a systems biology approach to correlate experimental, bioinformatics and modelling data from several cell line models for colorectal and skin cancer. We found strong and weak circadian oscillators within the same type of cancer and identified a set of genes, which allows the discrimination between the two oscillator-types. Among those genes are IFNGR2, PITX2, RFWD2, PPARγ, LOXL2, Rab6 and SPARC, all involved in cancer-related pathways. Using a bioinformatics approach, we extended the core-clock network and present its interconnection to the discriminative set of genes. Interestingly, such gene signatures link the clock to oncogenic pathways like the RAS/MAPK pathway. To investigate the potential impact of the RAS/MAPK pathway - a major driver of colorectal carcinogenesis - on the circadian clock, we used a computational model which predicted that perturbation of BMAL1-mediated transcription can generate the circadian phenotypes similar to those observed in metastatic cell lines. Using an inducible RAS expression system, we show that overexpression of RAS disrupts the circadian clock and leads to an increase of the circadian period while RAS inhibition causes a shortening of period length, as predicted by our mathematical simulations. Together, our data demonstrate that perturbations induced by a single oncogene are sufficient to deregulate the mammalian circadian clock. PMID:24875049

  2. Atomic clock ensemble in space (ACES) data analysis

    Science.gov (United States)

    Meynadier, F.; Delva, P.; le Poncin-Lafitte, C.; Guerlin, C.; Wolf, P.

    2018-02-01

    The Atomic Clocks Ensemble in Space (ACES/PHARAO mission, ESA & CNES) will be installed on board the International Space Station (ISS) next year. A crucial part of this experiment is its two-way microwave link (MWL), which will compare the timescale generated on board with those provided by several ground stations disseminated on the Earth. A dedicated data analysis center is being implemented at SYRTE—Observatoire de Paris, where our team currently develops theoretical modelling, numerical simulations and the data analysis software itself. In this paper, we present some key aspects of the MWL measurement method and the associated algorithms for simulations and data analysis. We show the results of tests using simulated data with fully realistic effects such as fundamental measurement noise, Doppler, atmospheric delays, or cycle ambiguities. We demonstrate satisfactory performance of the software with respect to the specifications of the ACES mission. The main scientific product of our analysis is the clock desynchronisation between ground and space clocks, i.e. the difference of proper times between the space clocks and ground clocks at participating institutes. While in flight, this measurement will allow for tests of general relativity and Lorentz invariance at unprecedented levels, e.g. measurement of the gravitational redshift at the 3×10-6 level. As a specific example, we use real ISS orbit data with estimated errors at the 10 m level to study the effect of such errors on the clock desynchronisation obtained from MWL data. We demonstrate that the resulting effects are totally negligible.

  3. Complementary approaches to understanding the plant circadian clock

    Directory of Open Access Journals (Sweden)

    Ozgur E. Akman

    2010-02-01

    Full Text Available Circadian clocks are oscillatory genetic networks that help organisms adapt to the 24-hour day/night cycle. The clock of the green alga Ostreococcus tauri is the simplest plant clock discovered so far. Its many advantages as an experimental system facilitate the testing of computational predictions. We present a model of the Ostreococcus clock in the stochastic process algebra Bio-PEPA and exploit its mapping to different analysis techniques, such as ordinary differential equations, stochastic simulation algorithms and model-checking. The small number of molecules reported for this system tests the limits of the continuous approximation underlying differential equations. We investigate the difference between continuous-deterministic and discrete-stochastic approaches. Stochastic simulation and model-checking allow us to formulate new hypotheses on the system behaviour, such as the presence of self-sustained oscillations in single cells under constant light conditions. We investigate how to model the timing of dawn and dusk in the context of model-checking, which we use to compute how the probability distributions of key biochemical species change over time. These show that the relative variation in expression level is smallest at the time of peak expression, making peak time an optimal experimental phase marker. Building on these analyses, we use approaches from evolutionary systems biology to investigate how changes in the rate of mRNA degradation impacts the phase of a key protein likely to affect fitness. We explore how robust this circadian clock is towards such potential mutational changes in its underlying biochemistry. Our work shows that multiple approaches lead to a more complete understanding of the clock.

  4. Coded Splitting Tree Protocols

    DEFF Research Database (Denmark)

    Sørensen, Jesper Hemming; Stefanovic, Cedomir; Popovski, Petar

    2013-01-01

    This paper presents a novel approach to multiple access control called coded splitting tree protocol. The approach builds on the known tree splitting protocols, code structure and successive interference cancellation (SIC). Several instances of the tree splitting protocol are initiated, each...... as possible. Evaluations show that the proposed protocol provides considerable gains over the standard tree splitting protocol applying SIC. The improvement comes at the expense of an increased feedback and receiver complexity....

  5. Decision-Tree Program

    Science.gov (United States)

    Buntine, Wray

    1994-01-01

    IND computer program introduces Bayesian and Markov/maximum-likelihood (MML) methods and more-sophisticated methods of searching in growing trees. Produces more-accurate class-probability estimates important in applications like diagnosis. Provides range of features and styles with convenience for casual user, fine-tuning for advanced user or for those interested in research. Consists of four basic kinds of routines: data-manipulation, tree-generation, tree-testing, and tree-display. Written in C language.

  6. Fibrations of Tree Automata

    OpenAIRE

    Riba, Colin

    2015-01-01

    International audience; We propose a notion of morphisms between tree automata based on game semantics. Morphisms are winning strategies on a synchronous restriction of the linear implication between acceptance games. This leads to split indexed categories, with substitution based on a suitable notion of synchronous tree function. By restricting to tree functions issued from maps on alphabets, this gives a fibration of tree automata. We then discuss the (fibrewise) monoidal structure issued f...

  7. Latent tree models

    OpenAIRE

    Zwiernik, Piotr

    2017-01-01

    Latent tree models are graphical models defined on trees, in which only a subset of variables is observed. They were first discussed by Judea Pearl as tree-decomposable distributions to generalise star-decomposable distributions such as the latent class model. Latent tree models, or their submodels, are widely used in: phylogenetic analysis, network tomography, computer vision, causal modeling, and data clustering. They also contain other well-known classes of models like hidden Markov models...

  8. Twin paradox with macroscopic clocks in superconducting circuits

    Science.gov (United States)

    Lindkvist, Joel; Sabín, Carlos; Fuentes, Ivette; Dragan, Andrzej; Svensson, Ida-Maria; Delsing, Per; Johansson, Göran

    2014-11-01

    We propose an implementation of a twin-paradox scenario in superconducting circuits, with velocities as large as a few percent of the speed of light. Ultrafast modulation of the boundary conditions for the electromagnetic field in a microwave cavity simulates a clock moving at relativistic speeds. Since our cavity has a finite length, the setup allows us to investigate the role of clock size as well as interesting quantum effects on time dilation. In particular, our theoretical results show that the time dilation increases for larger cavity lengths and is shifted due to quantum particle creation.

  9. Recent results of the pulsed optically pumped rubidium clock

    Science.gov (United States)

    Levi, F.; Micalizio, S.; Godone, A.; Calosso, C.; Bertacco, E.

    2017-11-01

    A laboratory prototype of a pulsed optically pumped (POP) clock based on a rubidium cell with buffer gas is described. This clock has shown very interesting physical and metrological features, such as negligible light-shift, strongly reduced cavity-pulling and very good frequency stability. In this regard, an Allan deviation of σy(τ) = 1.2 τ-1/2 for measurement times up to τ = 105 s has been measured. These results confirm the interesting perspectives of such a frequency standard and make it very attractive for several technological applications, such as radionavigation.

  10. Timing Jitter Analysis for Clock recovery Circuits Based on an Optoelectronic Phase-Locked Loop (OPLL)

    DEFF Research Database (Denmark)

    Zibar, Darko; Mørk, Jesper; Oxenløwe, Leif Katsuo

    2005-01-01

    Timing jitter of an OPLL based clock recovery is investigated. We demonstrate how loop gain, input and VCO signal jitter, loop filter bandwidth and a loop time delay influence jitter of the extracted clock signal...

  11. The E3 ubiquitin ligase CTRIP controls CLOCK levels and PERIOD oscillations in Drosophila.

    Science.gov (United States)

    Lamaze, Angélique; Lamouroux, Annie; Vias, Carine; Hung, Hsiu-Cheng; Weber, Frank; Rouyer, François

    2011-06-01

    In the Drosophila circadian clock, the CLOCK/CYCLE complex activates the period and timeless genes that negatively feedback on CLOCK/CYCLE activity. The 24-h pace of this cycle depends on the stability of the clock proteins. RING-domain E3 ubiquitin ligases have been shown to destabilize PERIOD or TIMELESS. Here we identify a clock function for the circadian trip (ctrip) gene, which encodes a HECT-domain E3 ubiquitin ligase. ctrip expression in the brain is mostly restricted to clock neurons and its downregulation leads to long-period activity rhythms in constant darkness. This altered behaviour is associated with high CLOCK levels and persistence of phosphorylated PERIOD during the subjective day. The control of CLOCK protein levels does not require PERIOD. Thus, CTRIP seems to regulate the pace of the oscillator by controlling the stability of both the activator and the repressor of the feedback loop.

  12. Generating clock signals for a cycle accurate, cycle reproducible FPGA based hardware accelerator

    Science.gov (United States)

    Asaad, Sameth W.; Kapur, Mohit

    2016-01-05

    A method, system and computer program product are disclosed for generating clock signals for a cycle accurate FPGA based hardware accelerator used to simulate operations of a device-under-test (DUT). In one embodiment, the DUT includes multiple device clocks generating multiple device clock signals at multiple frequencies and at a defined frequency ratio; and the FPG hardware accelerator includes multiple accelerator clocks generating multiple accelerator clock signals to operate the FPGA hardware accelerator to simulate the operations of the DUT. In one embodiment, operations of the DUT are mapped to the FPGA hardware accelerator, and the accelerator clock signals are generated at multiple frequencies and at the defined frequency ratio of the frequencies of the multiple device clocks, to maintain cycle accuracy between the DUT and the FPGA hardware accelerator. In an embodiment, the FPGA hardware accelerator may be used to control the frequencies of the multiple device clocks.

  13. The mammalian circadian clock and its entrainment by stress and exercise.

    Science.gov (United States)

    Tahara, Yu; Aoyama, Shinya; Shibata, Shigenobu

    2017-01-01

    The mammalian circadian clock regulates day-night fluctuations in various physiological processes. The circadian clock consists of the central clock in the suprachiasmatic nucleus of the hypothalamus and peripheral clocks in peripheral tissues. External environmental cues, including light/dark cycles, food intake, stress, and exercise, provide important information for adjusting clock phases. This review focuses on stress and exercise as potent entrainment signals for both central and peripheral clocks, especially in regard to the timing of stimuli, types of stressors/exercises, and differences in the responses of rodents and humans. We suggest that the common signaling pathways of clock entrainment by stress and exercise involve sympathetic nervous activation and glucocorticoid release. Furthermore, we demonstrate that physiological responses to stress and exercise depend on time of day. Therefore, using exercise to maintain the circadian clock at an appropriate phase and amplitude might be effective for preventing obesity, diabetes, and cardiovascular disease.

  14. Macro tree transducers

    NARCIS (Netherlands)

    Engelfriet, Joost; Vogler, Heiko

    1985-01-01

    Macro tree transducers are a combination of top-down tree transducers and macro grammars. They serve as a model for syntax-directed semantics in which context information can be handled. In this paper the formal model of macro tree transducers is studied by investigating typical automata theoretical

  15. Total well dominated trees

    DEFF Research Database (Denmark)

    Finbow, Arthur; Frendrup, Allan; Vestergaard, Preben D.

    cardinality then G is a total well dominated graph. In this paper we study composition and decomposition of total well dominated trees. By a reversible process we prove that any total well dominated tree can both be reduced to and constructed from a family of three small trees....

  16. Winter Birch Trees

    Science.gov (United States)

    Sweeney, Debra; Rounds, Judy

    2011-01-01

    Trees are great inspiration for artists. Many art teachers find themselves inspired and maybe somewhat obsessed with the natural beauty and elegance of the lofty tree, and how it changes through the seasons. One such tree that grows in several regions and always looks magnificent, regardless of the time of year, is the birch. In this article, the…

  17. Flowering T Flowering Trees

    Indian Academy of Sciences (India)

    Flowering T. Flowering Trees. Adansonia digitata L. ( The Baobab Tree) of Bombacaceae is a tree with swollen trunk that attains a dia. of 10m. Leaves are digitately compound with leaflets up to 18cm. long. Flowers are large, solitary, waxy white, and open at dusk. They open in 30 seconds and are bat pollinated. Stamens ...

  18. D2-tree

    DEFF Research Database (Denmark)

    Brodal, Gerth Stølting; Sioutas, Spyros; Pantazos, Kostas

    2015-01-01

    We present a new overlay, called the Deterministic Decentralized tree (D2-tree). The D2-tree compares favorably to other overlays for the following reasons: (a) it provides matching and better complexities, which are deterministic for the supported operations; (b) the management of nodes (peers...

  19. Circadian Clock genes Per2 and clock regulate steroid production, cell proliferation, and luteinizing hormone receptor transcription in ovarian granulosa cells

    Energy Technology Data Exchange (ETDEWEB)

    Shimizu, Takashi, E-mail: shimizut@obihiro.ac.jp [Graduate School of Animal and Food Hygiene, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555 (Japan); Hirai, Yuko; Murayama, Chiaki; Miyamoto, Akio [Graduate School of Animal and Food Hygiene, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555 (Japan); Miyazaki, Hitoshi [Gene Research Center, University of Tsukuba, Tsukuba, Ibaraki 305-8572 (Japan); Miyazaki, Koyomi [Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) Central 6, 1-1-1, Higashi, Tsukuba, Ibaraki 305-8566 (Japan)

    2011-08-19

    Highlights: {yields} Treatment with Per2 and Clock siRNAs decreased the number of granulosa cells and LHr expression. {yields}Per2 siRNA treatment did not stimulate the production of estradiol and expression of P450arom. {yields} Clock siRNA treatment inhibited the production of estradiol and expression of P450arom mRNA. {yields}Per2 and Clock siRNA treatment increased and unchanged, respectively, progesterone production in FSH-treated granulosa cells. {yields} The expression of StAR mRNA was increased by Per2 siRNA and unchanged by Clock siRNA. -- Abstract: Circadian Clock genes are associated with the estrous cycle in female animals. Treatment with Per2 and Clock siRNAs decreased the number of granulosa cells and LHr expression in follicle-stimulating hormone FSH-treated granulosa cells. Per2 siRNA treatment did not stimulate the production of estradiol and expression of P450arom, whereas Clock siRNA treatment inhibited the production of estradiol and expression of P450arom mRNA. Per2 and Clock siRNA treatment increased and unchanged, respectively, progesterone production in FSH-treated granulosa cells. Similarly, expression of StAR mRNA was increased by Per2 siRNA and unchanged by Clock siRNA. Our data provide a new insight that Per2 and Clock have different action on ovarian granulosa cell functions.

  20. Performance Evaluation of Clock Recovery for Coherent Mode Division Multiplexed Systems

    DEFF Research Database (Denmark)

    Medeiros Diniz, Júlio César; Piels, Molly; Zibar, Darko

    2017-01-01

    The impact of mode mixing and group delay spread on clock tone quality of a 6-mode 32 GBd NRZ-QPSK MDM system is investigated. Even for low group delay spread, strong coupling causes clock tone disappearance.......The impact of mode mixing and group delay spread on clock tone quality of a 6-mode 32 GBd NRZ-QPSK MDM system is investigated. Even for low group delay spread, strong coupling causes clock tone disappearance....

  1. System and method for clock synchronization and position determination using entangled photon pairs

    Science.gov (United States)

    Shih, Yanhua (Inventor)

    2010-01-01

    A system and method for clock synchronization and position determination using entangled photon pairs is provided. The present invention relies on the measurement of the second order correlation function of entangled states. Photons from an entangled photon source travel one-way to the clocks to be synchronized. By analyzing photon registration time histories generated at each clock location, the entangled states allow for high accuracy clock synchronization as well as high accuracy position determination.

  2. Functional Implications of the CLOCK 3111T/C Single-Nucleotide Polymorphism

    OpenAIRE

    Ozburn, Angela R.; Purohit, Kush; Parekh, Puja K.; Kaplan, Gabrielle N.; Falcon, Edgardo; Mukherjee, Shibani; Cates, Hannah M.; Colleen A McClung

    2016-01-01

    Circadian rhythm disruptions are prominently associated with bipolar disorder (BD). Circadian rhythms are regulated by the molecular clock, a family of proteins that function together in a transcriptional–translational feedback loop. The CLOCK protein is a key transcription factor of this feedback loop, and previous studies have found that manipulations of the Clock gene are sufficient to produce manic-like behavior in mice (1). The CLOCK 3111T/C single-nucleotide polymorphism (SNP; rs1801260...

  3. FUNCTIONAL IMPLICATIONS OF THE CLOCK 3111T/C SINGLE-NUCLEOTIDE POLYMORPHISM

    OpenAIRE

    Angela Renee Ozburn; Kush ePurohit; Parekh, Puja K.; Kaplan, Gabrielle N.; Edgardo eFalcon; Shibani eMukherjee; Cates, Hannah M.; Colleen A McClung

    2016-01-01

    Circadian rhythm disruptions are prominently associated with Bipolar Disorder (BD). Circadian rhythms are regulated by the molecular clock, a family of proteins that function together in a transcriptional-translational feedback loop. The CLOCK protein is a key transcription factor of this feedback loop, and previous studies have found that manipulations of the Clock gene are sufficient to produce manic-like behavior in mice (Roybal et al., 2007). The Clock 3111T/C single-nucleotide polymorphi...

  4. Differential Phasing between Circadian Clocks in the Brain and Peripheral Organs in Humans

    OpenAIRE

    Hughey, Jacob J; Butte, Atul J

    2016-01-01

    The daily timing of mammalian physiology is coordinated by circadian clocks throughout the body. Although measurements of clock gene expression indicate that these clocks in mice are normally in phase with each other, the situation in humans remains unclear. We used publicly available data from five studies, comprising over 1000 samples, to compare the phasing of circadian gene expression in human brain and human blood. Surprisingly, after controlling for age, clock gene expression in brain w...

  5. Altered expression pattern of clock genes in a rat model of depression

    DEFF Research Database (Denmark)

    Christiansen, Sofie; Bouzinova, Elena; Fahrenkrug, Jan

    2016-01-01

    of clock gene expression in depressive patients many studies have reported single-nucleotide polymorphisms in clock genes in these patients. METHODS: In the present study we investigated whether a depression-like state in rats associates with alternations of the diurnal expression of clock genes......: The present results suggest that altered expression of investigated clock genes are likely to associate with the induction of a depression-like state in the CMS model...

  6. Oscillating perceptions: the ups and downs of the CLOCK protein in ...

    Indian Academy of Sciences (India)

    2008-12-31

    Dec 31, 2008 ... A functional mouse CLOCK protein has long been thought to be essential for mammalian circadian clockwork function, based mainly on studies of mice bearing a dominant negative, antimorphic mutation in the Clock gene. However, new discoveries using recently developed Clock-null mutant mice have ...

  7. The absolute frequency of the 87Sr optical clock transition

    DEFF Research Database (Denmark)

    Campbell, Gretchen K.; Ludlow, Andrew D.; Blatt, Sebastian

    2008-01-01

    a detailed study of systematic effects, which reduced the total systematic uncertainty of the Sr lattice clock to 1.5 × 10-16, the clock frequency is measured against a hydrogen maser which is simultaneously calibrated to the US primary frequency standard, the NIST Cs fountain clock, NIST-F1. The comparison...

  8. Regulation of behavioral circadian rhythms and clock protein PER1 by the deubiquitinating enzyme USP2

    Directory of Open Access Journals (Sweden)

    Yaoming Yang

    2012-06-01

    Endogenous 24-hour rhythms are generated by circadian clocks located in most tissues. The molecular clock mechanism is based on feedback loops involving clock genes and their protein products. Post-translational modifications, including ubiquitination, are important for regulating the clock feedback mechanism. Previous work has focused on the role of ubiquitin ligases in the clock mechanism. Here we show a role for the rhythmically-expressed deubiquitinating enzyme ubiquitin specific peptidase 2 (USP2 in clock function. Mice with a deletion of the Usp2 gene (Usp2 KO display a longer free-running period of locomotor activity rhythms and altered responses of the clock to light. This was associated with altered expression of clock genes in synchronized Usp2 KO mouse embryonic fibroblasts and increased levels of clock protein PERIOD1 (PER1. USP2 can be coimmunoprecipitated with several clock proteins but directly interacts specifically with PER1 and deubiquitinates it. Interestingly, this deubiquitination does not alter PER1 stability. Taken together, our results identify USP2 as a new core component of the clock machinery and demonstrate a role for deubiquitination in the regulation of the circadian clock, both at the level of the core pacemaker and its response to external cues.

  9. Regulation of behavioral circadian rhythms and clock protein PER1 by the deubiquitinating enzyme USP2.

    Science.gov (United States)

    Yang, Yaoming; Duguay, David; Bédard, Nathalie; Rachalski, Adeline; Baquiran, Gerardo; Na, Chan Hyun; Fahrenkrug, Jan; Storch, Kai-Florian; Peng, Junmin; Wing, Simon S; Cermakian, Nicolas

    2012-08-15

    Endogenous 24-hour rhythms are generated by circadian clocks located in most tissues. The molecular clock mechanism is based on feedback loops involving clock genes and their protein products. Post-translational modifications, including ubiquitination, are important for regulating the clock feedback mechanism. Previous work has focused on the role of ubiquitin ligases in the clock mechanism. Here we show a role for the rhythmically-expressed deubiquitinating enzyme ubiquitin specific peptidase 2 (USP2) in clock function. Mice with a deletion of the Usp2 gene (Usp2 KO) display a longer free-running period of locomotor activity rhythms and altered responses of the clock to light. This was associated with altered expression of clock genes in synchronized Usp2 KO mouse embryonic fibroblasts and increased levels of clock protein PERIOD1 (PER1). USP2 can be coimmunoprecipitated with several clock proteins but directly interacts specifically with PER1 and deubiquitinates it. Interestingly, this deubiquitination does not alter PER1 stability. Taken together, our results identify USP2 as a new core component of the clock machinery and demonstrate a role for deubiquitination in the regulation of the circadian clock, both at the level of the core pacemaker and its response to external cues.

  10. File list: Oth.Bld.50.CLOCK.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.Bld.50.CLOCK.AllCell hg19 TFs and others CLOCK Blood SRX1091039,SRX1091022,SRX1...091036,SRX1091025,SRX1091030 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Oth.Bld.50.CLOCK.AllCell.bed ...

  11. File list: Oth.Bld.05.CLOCK.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.Bld.05.CLOCK.AllCell hg19 TFs and others CLOCK Blood SRX1091036,SRX1091039,SRX1...091022,SRX1091025,SRX1091030 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Oth.Bld.05.CLOCK.AllCell.bed ...

  12. File list: Oth.ALL.10.CLOCK.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.ALL.10.CLOCK.AllCell hg19 TFs and others CLOCK All cell types SRX1091039,SRX109...1022,SRX1091036,SRX359928,SRX1091025,SRX1091030 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Oth.ALL.10.CLOCK.AllCell.bed ...

  13. File list: Oth.ALL.20.CLOCK.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.ALL.20.CLOCK.AllCell hg19 TFs and others CLOCK All cell types SRX1091039,SRX109...1022,SRX1091036,SRX1091025,SRX1091030,SRX359928 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Oth.ALL.20.CLOCK.AllCell.bed ...

  14. File list: Oth.ALL.05.CLOCK.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.ALL.05.CLOCK.AllCell hg19 TFs and others CLOCK All cell types SRX1091036,SRX109...1039,SRX1091022,SRX359928,SRX1091025,SRX1091030 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Oth.ALL.05.CLOCK.AllCell.bed ...

  15. File list: Oth.Bld.20.CLOCK.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.Bld.20.CLOCK.AllCell hg19 TFs and others CLOCK Blood SRX1091039,SRX1091022,SRX1...091036,SRX1091025,SRX1091030 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Oth.Bld.20.CLOCK.AllCell.bed ...

  16. File list: Oth.Bld.10.CLOCK.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.Bld.10.CLOCK.AllCell hg19 TFs and others CLOCK Blood SRX1091039,SRX1091022,SRX1...091036,SRX1091025,SRX1091030 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Oth.Bld.10.CLOCK.AllCell.bed ...

  17. File list: Oth.ALL.50.CLOCK.AllCell [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.ALL.50.CLOCK.AllCell hg19 TFs and others CLOCK All cell types SRX1091039,SRX109...1022,SRX1091036,SRX1091025,SRX1091030,SRX359928 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/Oth.ALL.50.CLOCK.AllCell.bed ...

  18. Using Integer Clocks to Verify the Timing-Sync Sensor Network Protocol

    Science.gov (United States)

    Huang, Xiaowan; Singh, Anu; Smolka, Scott A.

    2010-01-01

    We use the UPPAAL model checker for Timed Automata to verify the Timing-Sync time-synchronization protocol for sensor networks (TPSN). The TPSN protocol seeks to provide network-wide synchronization of the distributed clocks in a sensor network. Clock-synchronization algorithms for sensor networks such as TPSN must be able to perform arithmetic on clock values to calculate clock drift and network propagation delays. They must be able to read the value of a local clock and assign it to another local clock. Such operations are not directly supported by the theory of Timed Automata. To overcome this formal-modeling obstacle, we augment the UPPAAL specification language with the integer clock derived type. Integer clocks, which are essentially integer variables that are periodically incremented by a global pulse generator, greatly facilitate the encoding of the operations required to synchronize clocks as in the TPSN protocol. With this integer-clock-based model of TPSN in hand, we use UPPAAL to verify that the protocol achieves network-wide time synchronization and is devoid of deadlock. We also use the UPPAAL Tracer tool to illustrate how integer clocks can be used to capture clock drift and resynchronization during protocol execution

  19. Photic and non-photic modulation of the mammalian circadian clock

    NARCIS (Netherlands)

    Oosterhout, Floortje Francisca Theodora Odilia van

    2012-01-01

    Throughout the animal kingdom, species have evolved an internal time-keeping system, referred to as a 'biological clock'. This internal clock allows anticipation to profound, but largely predictable, environmental day-night changes on earth. The biological clock drives 24h-rhythms in physiology and

  20. Telling time from analog and digital clocks: A multiple-route account

    NARCIS (Netherlands)

    Korvorst, M.H.W.; Roelofs, A.P.A.; Levelt, W.J.M.

    2007-01-01

    Does the naming of clocks always require conceptual preparation? To examine this question, speakers were presented with analog and digital clocks that had to be named in Dutch using either a relative (e.g., "quarter to four") or an absolute (e.g., "three forty-five") clock time expression format.

  1. Oscillating perceptions: the ups and downs of the CLOCK protein in ...

    Indian Academy of Sciences (India)

    A functional mouse CLOCK protein has long been thought to be essential for mammalian circadian clockwork function, based mainly on studies of mice bearing a dominant negative, antimorphic mutation in the Clock gene. However, new discoveries using recently developed Clock-null mutant mice have shaken up this ...

  2. Distributed Contour Trees

    Energy Technology Data Exchange (ETDEWEB)

    Morozov, Dmitriy; Weber, Gunther H.

    2014-03-31

    Topological techniques provide robust tools for data analysis. They are used, for example, for feature extraction, for data de-noising, and for comparison of data sets. This chapter concerns contour trees, a topological descriptor that records the connectivity of the isosurfaces of scalar functions. These trees are fundamental to analysis and visualization of physical phenomena modeled by real-valued measurements. We study the parallel analysis of contour trees. After describing a particular representation of a contour tree, called local{global representation, we illustrate how di erent problems that rely on contour trees can be solved in parallel with minimal communication.

  3. Turning Back the Clock: Inferring the History of the Eight O'clock Arc

    Science.gov (United States)

    Finkelstein, Steven L.; Papovich, Casey; Rudnick, Gregory; Egami, Eiichi; Le Floc'h, Emeric; Rieke, Marcia J.; Rigby, Jane R.; Willmer, Christopher N. A.

    2009-07-01

    We present the results from an optical and near-infrared (NIR) spectroscopic study of the ultraviolet-luminous z = 2.73 galaxy, the 8 o'clock arc. Due to gravitational lensing, this galaxy is magnified by a factor of μ > 10, allowing in-depth measurements which are usually unfeasible at such redshifts. In the optical spectra, we measured the systemic redshift of the galaxy, z = 2.7322± 0.0012, using stellar photospheric lines. This differs from the redshift of absorption lines in the interstellar medium, z = 2.7302 ± 0.0006, implying gas outflows on the order of 160 km s-1. With H- and K-band NIR spectra, we have measured nebular emission lines of Hα, Hβ, Hγ, [N II], and [O III], which have a redshift z = 2.7333 ± 0.0001, consistent with the derived systemic redshift. From the Balmer decrement, we measured the dust extinction in this galaxy to be A 5500 = 1.17 ± 36 mag. Correcting the Hα line flux for dust extinction as well as the assumed lensing factor, we measure a star formation rate (SFR) of ~270 M sun yr-1, which is higher than ~85% of star-forming galaxies at z ~ 2-3. Using combinations of all detected emission lines, we find that the 8 o'clock arc has a gas-phase metallicity of ~0.8 Z sun, showing that enrichment at high redshift is not rare, even in blue, star-forming galaxies. Studying spectra from two of the arc components separately, we find that one component dominates both the dust extinction and SFR, although the metallicities between the two components are similar. We derive the mass via stellar population modeling, and find that the arc has a total stellar mass of ~4.2 × 1011 M sun, which falls on the mass-metallicity relation at z ~ 2. Finally, we estimate the total gas mass, and find it to be only ~12% of the stellar mass, implying that the 8 o'clock arc is likely nearing the end of a starburst. Based partly on observations obtained at the Gemini Observatory, which is operated by the Association of Universities for Research in Astronomy

  4. The segmentation clock: inherited trait or universal design principle?

    Science.gov (United States)

    Richmond, David L; Oates, Andrew C

    2012-12-01

    Metamerism is a widespread feature of multicellular body plans; however, our understanding of the underlying mechanisms that generate these patterns is currently based on only a few model organisms. In particular, vertebrate embryos use a segmentation clock to rhythmically and sequentially add segments in concert with posterior elongation of their body. Recent evidence of a segmentation clock acting in arthropods indicates that this mechanism may be a widely used strategy for generating serial anatomy in animals. Whether this is due to homology or convergence is not yet known, but the recent discovery of an oscillatory process associated with the production of sequential root primordia in plants suggests that a segmentation clock is a fundamental patterning principle in growing tissues, independent of ancestry. In this review, we consider the principles of the segmentation clock that may be conserved across the animal and plant kingdoms, and discuss opportunities for cross-fertilization between these active fields of research. Copyright © 2012 Elsevier Ltd. All rights reserved.

  5. One-Way Speed of Light Measurements without Clock Synchronisation

    Directory of Open Access Journals (Sweden)

    Cahill R. T.

    2012-07-01

    Full Text Available The 1991 DeWitte double one-way 1st order in v= c experiment successfully measured the anisotropy of the speed of light using clocks at each end of the RF coaxial cables. However Spavieri et al. , Physics Letters A (2012, have reported that (i clock effects caused by clock transport should be included, and (ii that this additional effect cancels the one-way light speed timing effect, implying that one-way light speed experiments “do not actually lead to the measurement of the one-way speed of light or determination of the absolute velocity of the preferred frame”. Here we explain that the Spavieri et al. derivation makes an assumption that is not always valid: that the propagation is subject to the usual Fresnel drag effect, which is not the case for RF coaxial cables. As well DeWitte did take account of the clock transport effect. The Spavieri et al. paper has prompted a clarification of these issues.

  6. Ytterbium optical lattice clock with 10-18 level characterization

    Science.gov (United States)

    Phillips, Nathaniel; Sherman, Jeff; Beloy, Kyle; Hinkley, Nathan; Schioppo, Marco; Oates, Chris; Ludlow, Andrew

    2014-05-01

    A recent comparison of two ytterbium-based optical lattice clocks at NIST demonstrated record stability of 1 . 6 parts in 1018 after 25,000s averaging. We report on measurements of the two primary systematic effects that shift the ultra-narrow clock transition, towards a reduction of the clock uncertainty to the 10-18 level. Uncertainty stemming from the blackbody radiation (BBR) shift is largely due to imprecise knowledge of the thermal environment surrounding the atoms. We detail the construction and operation of an in-vacuum, thermally-regulated radiation shield, which permits laser cooling and trapping while enabling an absolute temperature measurement with mK precision. Additionally, while operation of the optical lattice at the magic wavelength (λm) cancels the scalar Stark shift (since both clock states shift equally), higher-order vector and two-photon hyperpolarizability shifts remain. To evaluate these effects, as well as the polarizability away from λm, we implement a lattice buildup cavity around the atoms. The resulting twenty-fold enhancement of the lattice intensity provides a significant lever arm for precise measurement of these effects.

  7. Integration of metabolic and cardiovascular diurnal rhythms by circadian clock.

    Science.gov (United States)

    Kohsaka, Akira; Waki, Hidefumi; Cui, He; Gouraud, Sabine S; Maeda, Masanobu

    2012-01-01

    Understanding how the 24-hour blood-pressure rhythm is programmed has been one of the most challenging questions in cardiovascular research. The 24-hour blood-pressure rhythm is primarily driven by the circadian clock system, in which the master circadian pacemaker within the suprachiasmatic nuclei of the hypothalamus is first entrained to the light/dark cycle and then transmits synchronizing signals to the peripheral clocks common to most tissues, including the heart and blood vessels. However, the circadian system is more complex than this basic hierarchical structure, as indicated by the discovery that peripheral clocks are either influenced to some degree or fully driven by temporal changes in energy homeostasis, independent of the light entrainment pathway. Through various comparative genomic approaches and through studies exploiting mouse genetics and transgenics, we now appreciate that cardiovascular tissues possess a large number of metabolic genes whose expression cycle and reciprocally affect the transcriptional control of major circadian clock genes. These findings indicate that metabolic cycles can directly or indirectly affect the diurnal rhythm of cardiovascular function. Here, we discuss a framework for understanding how the 24-hour blood-pressure rhythm is driven by the circadian system that integrates cardiovascular and metabolic function.

  8. Circadian clocks are seeing the systems biology light

    OpenAIRE

    Hayes, Kevin R.; Baggs, Julie E.; Hogenesch, John B

    2005-01-01

    Circadian rhythms are those biological rhythms that have a periodicity of around 24 hours. Recently, the generation of a circadian transcriptional network - compiled from RNA-expression and promoter-element analysis and phase information - has led to a better understanding of the gene-expression patterns that regulate the precise 24-hour clock.

  9. Light Reception : Discovering the Clock-Eye in Mammals

    NARCIS (Netherlands)

    Roenneberg, Till; Merrow, Martha

    2002-01-01

    Light is the most reliable environmental signal for adjusting biological clocks to the 24-hour day. Mammals receive this signal exclusively through the eyes, but not just via rods and cones. New evidence has been uncovered for a novel photoreceptor that may be responsible for more than just

  10. Deregulated expression of circadian clock genes in gastric cancer.

    Science.gov (United States)

    Hu, Ming-Luen; Yeh, Kun-Tu; Lin, Pai-Mei; Hsu, Cheng-Ming; Hsiao, Hui-Hua; Liu, Yi-Chang; Lin, Hugo You-Hsien; Lin, Sheng-Fung; Yang, Ming-Yu

    2014-04-06

    Gastric cancer (GC), an aggressive malignant tumor of the alimentary tract, is a leading cause of cancer-related death. Circadian rhythm exhibits a 24-hour variation in physiological processes and behavior, such as hormone levels, metabolism, gene expression, sleep and wakefulness, and appetite. Disruption of circadian rhythm has been associated with various cancers, including chronic myeloid leukemia, head and neck squamous cell carcinoma, hepatocellular carcinoma, endometrial carcinoma, and breast cancer. However, the expression of circadian clock genes in GC remains unexplored. In this study, the expression profiles of eight circadian clock genes (PER1, PER2, PER3, CRY1, CRY2, CKIϵ, CLOCK, and BMAL1) of cancerous and noncancerous tissues from 29 GC patients were investigated using real-time quantitative reverse-transcriptase polymerase chain reaction and validated through immunohistochemical analysis. We found that PER2 was significantly up-regulated in cancer tissues (p clock genes exist in GC and circadian rhythm disturbance may be associated with the development of GC.

  11. No more moody mornings : Alarm clock anticipates sleepers' emotions

    NARCIS (Netherlands)

    Wensveen, S.; Overbeeke, K.; Van Kasteren, J.

    2002-01-01

    More eloquent alternatives to the harsh tones of the oldfashioned alarm-clock bells abound, including a newsreaders voice summing up last nights disasters, or a tape of your favourite early morning music. Still, getting out of bed has its difficult moments. All this could well change in the near

  12. The Rock Island Clock Tower, From Ordnance to Engineers

    Science.gov (United States)

    1977-05-01

    name can be given to the ex- terior architecture.൛ A local art historian at Augustana College has suggested that the original plans are an example of...11.) The Clock Tower shows no influence of two other architectural styles which were rapidly becoming popular in 1863: the Victor ian and gothic

  13. Essen and the National Physical Laboratory's atomic clock

    Science.gov (United States)

    Henderson, Dale

    2005-06-01

    To commemorate the fiftieth anniversary of the development of the first atomic frequency standard, we present some notes about the work of Louis Essen at the National Physical Laboratory. In addition, we publish below some personal recollections of Essen on his work, which have previously been available only on the Internet (http://www.btinternet.com/~time.lord/TheAtomicClock.htm).

  14. Genetic polymorphism at the CLOCK gene locus and major depression.

    Science.gov (United States)

    Desan, P H; Oren, D A; Malison, R; Price, L H; Rosenbaum, J; Smoller, J; Charney, D S; Gelernter, J

    2000-06-12

    Genetic analysis in both mouse and Drosophila has indicated that the product of the CLOCK gene is an essential component of a circadian rhythm timing system. A single nucleotide polymorphism (SNP), T3111C, in the 3' flanking region of the human CLOCK gene has been identified. Homozygotes or heterozygotes for the 3111C allele have been reported to have higher mean scores on a measure of evening preference for activity (vs. morning preference) than subjects homozygous for the 3111T allele. Since major depression is hypothesized to be closely linked to circadian rhythms, we explored whether this polymorphism might be related to susceptibility to major depression. We also ascertained allele frequency in an African-American control population, to begin to evaluate population variation at this locus. CLOCK T3111C allele frequencies were determined in 280 European American (EA) subjects, 143 with a history of major depression and 137 screened controls, and in 58 African American (AA) screened control subjects, using a polymerase chain reaction (PCR) - restriction fragment length polymorphism (RFLP) method. There was no significant difference between EA depressed and control subjects in allele frequency. There was a significant difference in allele frequency between EA and AA subjects, demonstrating a potential for population stratification. In none of these groups were significant deviations from Hardy-Weinberg equilibrium found. The present data do not support an association between CLOCK gene alleles at the T3111C locus and major depression.

  15. Optimal Infinite Runs in One-Clock Priced Timed Automata

    DEFF Research Database (Denmark)

    David, Alexandre; Ejsing-Duun, Daniel; Fontani, Lisa

    We address the problem of finding an infinite run with the optimal cost-time ratio in a one-clock priced timed automaton and pro- vide an algorithmic solution. Through refinements of the quotient graph obtained by strong time-abstracting bisimulation partitioning, we con- struct a graph with time...

  16. Peripheral circadian clocks are diversely affected by adrenalectomy

    Czech Academy of Sciences Publication Activity Database

    Soták, Matúš; Bryndová, Jana; Ergang, Peter; Vagnerová, Karla; Kvapilová, Pavlína; Vodička, Martin; Pácha, Jiří; Sumová, Alena

    2016-01-01

    Roč. 33, č. 5 (2016), s. 520-529 ISSN 0742-0528 R&D Projects: GA ČR(CZ) GA13-08304S Institutional support: RVO:67985823 Keywords : adrenalectomy * circadian rhythms * corticosterone * peripheral clock Subject RIV: ED - Physiology Impact factor: 2.562, year: 2016

  17. High-performance coherent population trapping clock with polarization modulation

    CERN Document Server

    Yun, Peter; Calosso, Claudio Eligio; Micalizio, Salvatore; François, Bruno; Boudot, Rodolphe; Guérandel, Stéphane; de Clercq, Emeric

    2016-01-01

    We demonstrate a vapor cell atomic clock prototype based on continuous-wave (CW) interrogation and double-modulation coherent population trapping (DM-CPT) technique. The DM-CPT technique uses a synchronous modulation of polarization and relative phase of a bi-chromatic laser beam in order to increase the number of atoms trapped in a dark state, i.e. a non-absorbing state. The narrow resonance, observed in transmission of a Cs vapor cell, is used as a narrow frequency discriminator in an atomic clock. A detailed characterization of the CPT resonance versus numerous parameters is reported. A short-term frequency stability of $3.2 \\times 10^{-13} \\tau^{-1/2}$ up to 100 s averaging time is measured. These performances are more than one order of magnitude better than industrial Rb clocks and comparable to those of best laboratory-prototype vapor cell clocks. The noise budget analysis shows that the short and mid-term frequency stability is mainly limited by the power fluctuations of the microwave used to generate ...

  18. Self-clocked sequential circuits: - a design example | Aghdasi ...

    African Journals Online (AJOL)

    This paper uses a design methodology for the State variable toggling through data driven clocks to implement a Direct Memory Access Controller (DMAC) as a design example. The design is simulated on software and also implemented using discrete hardware components. The methodology can be extended to parallel ...

  19. Topology and dynamics of the zebrafish segmentation clock core circuit.

    Directory of Open Access Journals (Sweden)

    Christian Schröter

    Full Text Available During vertebrate embryogenesis, the rhythmic and sequential segmentation of the body axis is regulated by an oscillating genetic network termed the segmentation clock. We describe a new dynamic model for the core pace-making circuit of the zebrafish segmentation clock based on a systematic biochemical investigation of the network's topology and precise measurements of somitogenesis dynamics in novel genetic mutants. We show that the core pace-making circuit consists of two distinct negative feedback loops, one with Her1 homodimers and the other with Her7:Hes6 heterodimers, operating in parallel. To explain the observed single and double mutant phenotypes of her1, her7, and hes6 mutant embryos in our dynamic model, we postulate that the availability and effective stability of the dimers with DNA binding activity is controlled in a "dimer cloud" that contains all possible dimeric combinations between the three factors. This feature of our model predicts that Hes6 protein levels should oscillate despite constant hes6 mRNA production, which we confirm experimentally using novel Hes6 antibodies. The control of the circuit's dynamics by a population of dimers with and without DNA binding activity is a new principle for the segmentation clock and may be relevant to other biological clocks and transcriptional regulatory networks.

  20. A Medieval Clock Made out of Simple Materials

    Science.gov (United States)

    Danese, B.; Oss, S.

    2008-01-01

    A cheap replica of the verge-and-foliot clock has been built from simple materials. It is a didactic tool of great power for physics teaching at every stage of schooling, in particular at university level. An account is given of its construction and its working principles, together with motivated examples of a few activities. (Contains 3 tables…

  1. On the genetic basis of temperature compensation of circadian clocks

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 83; Issue 1. On the genetic basis of temperature compensation of circadian clocks. Vijay Kumar Sharma. Hypothesis Volume 83 Issue 1 April 2004 pp 9-11. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/jgen/083/01/0009-0011 ...

  2. The Cell Cycle & Circadian Clock: a tale of two cycles

    NARCIS (Netherlands)

    E. Destici (Eugin)

    2010-01-01

    textabstractMost organisms have evolved an internal timekeeper to anticipate and coordinate internal processes with the external 24-h environment imposed upon all living creatures due to rotation of the Earth around its axis. At the cellular level, the circadian clock is generated by a genetic

  3. Phase resetting of the mammalian circadian clock by DNA damage

    NARCIS (Netherlands)

    Oklejewicz, Malgorzata; Destici, Eugin; Tamanini, Filippo; Hut, Roelof A.; Janssens, Roel; van der Horst, Gijsbertus T. J.

    2008-01-01

    To anticipate the momentum of the day, most organisms have developed an internal clock that drives circadian rhythms in metabolism, physiology, and behavior [1]. Recent studies indicate that cell-cycle progression and DNA-damage-response pathways are under circadian control [2-4]. Because circadian

  4. Special Relativity in Week One: 2) All Clocks Run Slow

    Science.gov (United States)

    Huggins, Elisha

    2011-01-01

    In our initial article on teaching special relativity in the first week of an introductory physics course, we used the principle of relativity and Maxwell's theory of light to derive Einstein's second postulate (that the speed of light is the same to all observers). In this paper we study thought experiments involving a light pulse clock moving…

  5. Analysis of the performance of hydrogen maser clocks at the ...

    African Journals Online (AJOL)

    Cilence

    Hydrogen maser frequency standards are commonly utilised in various space geodetic techniques such as Very Long Baseline Interferometry (VLBI) as local reference clocks. The. Hartebeesthoek Radio Astronomy Observatory in South Africa is currently operating two maser frequency standards i.e., an EFOS28 and an ...

  6. Analysis of the performance of hydrogen maser clocks at the ...

    African Journals Online (AJOL)

    Hydrogen maser frequency standards are commonly utilised in various space geodetic techniques such as Very Long Baseline Interferometry (VLBI) as local reference clocks. The Hartebeesthoek Radio Astronomy Observatory in South Africa is currently operating two maser frequency standards i.e., an EFOS28 and an ...

  7. The hypothalamic clock and its control of glucose homeostasis

    NARCIS (Netherlands)

    Kalsbeek, Andries; Yi, Chun-Xia; la Fleur, Susanne E.; Fliers, Eric

    2010-01-01

    The everyday life of mammals, including humans, exhibits many behavioral, physiological and endocrine oscillations. The major timekeeping mechanism for these rhythms is contained in the central nervous system (CNS). The output of the CNS clock not only controls daily rhythms in sleep/wake (or

  8. Circadian neurons in the lateral habenula: Clocking motivated behaviors.

    Science.gov (United States)

    Mendoza, Jorge

    2017-11-01

    The main circadian clock in mammals is located in the hypothalamic suprachiasmatic nucleus (SCN), however, central timing mechanisms are also present in other brain structures beyond the SCN. The lateral habenula (LHb), known for its important role in the regulation of the monoaminergic system, contains such a circadian clock whose molecular and cellular mechanisms as well as functional role are not well known. However, since monoaminergic systems show circadian activity, it is possible that the LHb-clock's role is to modulate the rhythmic activity of the dopamine, serotonin and norephinephrine systems, and associated behaviors. Moreover, the LHb is involved in different pathological states such as depression, addiction and schizophrenia, states in which sleep and circadian alterations have been reported. Thus, perturbations of circadian activity in the LHb might, in part, be a cause of these rhythmic alterations in psychiatric ailments. In this review the current state of the LHb clock and its possible implications in the control of monoaminergic systems rhythms, motivated behaviors (e.g., feeding, drug intake) and depression (with circadian disruptions and altered motivation) will be discussed. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. Food-reward signalling in the suprachiasmatic clock.

    Science.gov (United States)

    Mendoza, Jorge; Clesse, Daniel; Pévet, Paul; Challet, Etienne

    2010-03-01

    Under special restricted feeding conditions the mammalian circadian clock, contained in the hypothalamic suprachiasmatic nucleus (SCN), can be entrained by food. During food restriction, hungry animals are very motivated to obtain food. This motivational state could be a key component in altering the SCN timing by feeding. In order to comprehend how hedonic signals of food affect the SCN clock, we evaluated the effects of a daily palatable snack on the behavioural rhythm of mice fed ad libitum with regular food, and housed under constant darkness conditions. As light synchronization of the SCN is modulated by feeding/metabolic cues, the effects of a palatable meal coupled to a light pulse were tested on behavioural and molecular rhythms. A daily palatable snack entrained behavioural rhythms of mice in constant darkness conditions. Furthermore, palatable meal access at the activity onset reduced light-induced behavioural phase-delays and Period genes expression in the SCN. In addition, an increase in the dopamine content and Period genes expression in the forebrain of mice was observed, concomitant with a c-FOS activation in dopaminergic and orexinergic neurons, suggesting that the effects of a palatable snack on the SCN clock are mediated by the reward/arousal central systems. In conclusion, this study establishes an underlying sensitivity of the master circadian clock to changes in motivational states related to palatable food intake.

  10. Why Do Clocks Move Clockwise? The Dynamics of Collective ...

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 3; Issue 1. Why Do Clocks Move Clockwise? The Dynamics of Collective Learning. Vivek S Borkar. General Article Volume 3 Issue 1 January 1998 pp 27-35. Fulltext. Click here to view fulltext PDF. Permanent link:

  11. Phenotypic effects of genetic variability in human clock genes on ...

    Indian Academy of Sciences (India)

    Several mouse models of clock gene null alleles have been demonstrated to have affected sleep homeostasis. Recent findings have shown that the variable number tandem polymorphism in PER3, previously linked to diurnal preference, has profound effects on sleep homeostasis and cognitive performance following sleep ...

  12. Divergence time estimates of mammals from molecular clocks and ...

    Indian Academy of Sciences (India)

    2009-10-30

    Oct 30, 2009 ... This paper presents a brief review of recent advances in the classification of mammals at higher levels using fossils and molecular clocks. It also discusses latest fossil discoveries from the Cretaceous – Eocene (66–55 m.y.) rocks of India and their relevance to our current understanding of placental ...

  13. Sampling phase lock loop (PLL) with low power clock buffer

    NARCIS (Netherlands)

    Gao, X.; Bahai, A.; Bohsali, M.; Djabbari, A.; Klumperink, Eric A.M.; Nauta, Bram; Socci, G.

    2012-01-01

    A sampling phase locked loop (PLL) circuit includes a pull-up/down buffer configured to convert an oscillator reference clock into a square wave sampling control signal input to a sampling phase detector. The buffer circuit is configured to reduce power by controlling the switching of the pull-up

  14. Sampling phase lock loop (PLL) with low power clock buffer

    NARCIS (Netherlands)

    Gao, X.; Bahai, A.; Bohsali, M.; Djabbari, A.; Klumperink, Eric A.M.; Nauta, Bram; Socci, G.

    2013-01-01

    A sampling phase locked loop (PLL) circuit includes a pull-up/down buffer configured to convert an oscillator reference clock into a square wave sampling control signal input to a sampling phase detector. The buffer circuit is configured to reduce power by controlling the switching of the pull-up

  15. Adaptive Significance of Circadian Rhythms-Biological Clocks and ...

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 4; Issue 1. Adaptive Significance of Circadian Rhythms - Biological Clocks and Darwinian Fitness in Cyanobacteria. V Sheeba Vijay Kumar Sharma Amitabh Joshi. Research News Volume 4 Issue 1 January 1999 pp 73-75 ...

  16. Disruption of clock gene expression in human colorectal liver metastases

    NARCIS (Netherlands)

    S.A. Huisman (Sander); K.R. Ahmadi (Kourosh); J.N.M. IJzermans (Jan); C. Verhoef (Kees); G.T.J. van der Horst (Gijsbertus); R.W.F. de Bruin (Ron)

    2016-01-01

    textabstractThe circadian timing system controls about 40 % of the transcriptome and is important in the regulation of a wide variety of biological processes including metabolic and proliferative functions. Disruption of the circadian clock could have significant effect on human health and has an

  17. Living by the clock: the circadian pacemaker in older people

    NARCIS (Netherlands)

    Hofman, Michel A.; Swaab, Dick F.

    2006-01-01

    The suprachiasmatic nucleus (SCN) of the hypothalamus is considered to be a critical component of a neural oscillator system implicated in the timing of a wide variety of biological processes. The circadian cycles established by this biological clock occur throughout nature and have a period of

  18. Erratic overdispersion of three molecular clocks: GPDH, SOD, and XDH.

    Science.gov (United States)

    Rodríguez-Trelles, F; Tarrío, R; Ayala, F J

    2001-09-25

    The neutrality theory predicts that the rate of neutral molecular evolution is constant over time, and thus that there is a molecular clock for timing evolutionary events. It has been observed that the variance of the rate of evolution is generally larger than expected according to the neutrality theory, which has raised the question of how reliable the molecular clock is or, indeed, whether there is a molecular clock at all. We have carried out an extensive investigation of three proteins, glycerol-3-phosphate dehydrogenase (GPDH), superoxide dismutase (SOD), and xanthine dehydrogenase (XDH). We have observed that (i) the three proteins evolve erratically through time and across lineages and (ii) the erratic patterns of acceleration and deceleration differ from locus to locus, so that one locus may evolve faster in one than another lineage, whereas the opposite may be the case for another locus. The observations are inconsistent with the predictions made by various subsidiary hypotheses proposed to account for the overdispersion of the molecular clock.

  19. Digital clocks: simple Boolean models can quantitatively describe circadian systems

    Science.gov (United States)

    Akman, Ozgur E.; Watterson, Steven; Parton, Andrew; Binns, Nigel; Millar, Andrew J.; Ghazal, Peter

    2012-01-01

    The gene networks that comprise the circadian clock modulate biological function across a range of scales, from gene expression to performance and adaptive behaviour. The clock functions by generating endogenous rhythms that can be entrained to the external 24-h day–night cycle, enabling organisms to optimally time biochemical processes relative to dawn and dusk. In recent years, computational models based on differential equations have become useful tools for dissecting and quantifying the complex regulatory relationships underlying the clock's oscillatory dynamics. However, optimizing the large parameter sets characteristic of these models places intense demands on both computational and experimental resources, limiting the scope of in silico studies. Here, we develop an approach based on Boolean logic that dramatically reduces the parametrization, making the state and parameter spaces finite and tractable. We introduce efficient methods for fitting Boolean models to molecular data, successfully demonstrating their application to synthetic time courses generated by a number of established clock models, as well as experimental expression levels measured using luciferase imaging. Our results indicate that despite their relative simplicity, logic models can (i) simulate circadian oscillations with the correct, experimentally observed phase relationships among genes and (ii) flexibly entrain to light stimuli, reproducing the complex responses to variations in daylength generated by more detailed differential equation formulations. Our work also demonstrates that logic models have sufficient predictive power to identify optimal regulatory structures from experimental data. By presenting the first Boolean models of circadian circuits together with general techniques for their optimization, we hope to establish a new framework for the systematic modelling of more complex clocks, as well as other circuits with different qualitative dynamics. In particular, we

  20. CULLIN-3 controls TIMELESS oscillations in the Drosophila circadian clock.

    Directory of Open Access Journals (Sweden)

    Brigitte Grima

    Full Text Available Eukaryotic circadian clocks rely on transcriptional feedback loops. In Drosophila, the PERIOD (PER and TIMELESS (TIM proteins accumulate during the night, inhibit the activity of the CLOCK (CLK/CYCLE (CYC transcriptional complex, and are degraded in the early morning. The control of PER and TIM oscillations largely depends on post-translational mechanisms. They involve both light-dependent and light-independent pathways that rely on the phosphorylation, ubiquitination, and proteasomal degradation of the clock proteins. SLMB, which is part of a CULLIN-1-based E3 ubiquitin ligase complex, is required for the circadian degradation of phosphorylated PER. We show here that CULLIN-3 (CUL-3 is required for the circadian control of PER and TIM oscillations. Expression of either Cul-3 RNAi or dominant negative forms of CUL-3 in the clock neurons alters locomotor behavior and dampens PER and TIM oscillations in light-dark cycles. In constant conditions, CUL-3 deregulation induces behavioral arrhythmicity and rapidly abolishes TIM cycling, with slower effects on PER. CUL-3 affects TIM accumulation more strongly in the absence of PER and forms protein complexes with hypo-phosphorylated TIM. In contrast, SLMB affects TIM more strongly in the presence of PER and preferentially associates with phosphorylated TIM. CUL-3 and SLMB show additive effects on TIM and PER, suggesting different roles for the two ubiquitination complexes on PER and TIM cycling. This work thus shows that CUL-3 is a new component of the Drosophila clock, which plays an important role in the control of TIM oscillations.

  1. Spin Resonance Clock Transition of the Endohedral Fullerene 15N @ C60

    Science.gov (United States)

    Harding, R. T.; Zhou, S.; Zhou, J.; Lindvall, T.; Myers, W. K.; Ardavan, A.; Briggs, G. A. D.; Porfyrakis, K.; Laird, E. A.

    2017-10-01

    The endohedral fullerene 15N @ C60 has narrow electron paramagnetic resonance lines which have been proposed as the basis for a condensed-matter portable atomic clock. We measure the low-frequency spectrum of this molecule, identifying and characterizing a clock transition at which the frequency becomes insensitive to magnetic field. We infer a linewidth at the clock field of 100 kHz. Using experimental data, we are able to place a bound on the clock's projected frequency stability. We discuss ways to improve the frequency stability to be competitive with existing miniature clocks.

  2. Byzantine-fault tolerant self-stabilizing protocol for distributed clock synchronization systems

    Science.gov (United States)

    Malekpour, Mahyar R. (Inventor)

    2010-01-01

    A rapid Byzantine self-stabilizing clock synchronization protocol that self-stabilizes from any state, tolerates bursts of transient failures, and deterministically converges within a linear convergence time with respect to the self-stabilization period. Upon self-stabilization, all good clocks proceed synchronously. The Byzantine self-stabilizing clock synchronization protocol does not rely on any assumptions about the initial state of the clocks. Furthermore, there is neither a central clock nor an externally generated pulse system. The protocol converges deterministically, is scalable, and self-stabilizes in a short amount of time. The convergence time is linear with respect to the self-stabilization period.

  3. BEAST: Bayesian evolutionary analysis by sampling trees.

    Science.gov (United States)

    Drummond, Alexei J; Rambaut, Andrew

    2007-11-08

    The evolutionary analysis of molecular sequence variation is a statistical enterprise. This is reflected in the increased use of probabilistic models for phylogenetic inference, multiple sequence alignment, and molecular population genetics. Here we present BEAST: a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree. A large number of popular stochastic models of sequence evolution are provided and tree-based models suitable for both within- and between-species sequence data are implemented. BEAST version 1.4.6 consists of 81000 lines of Java source code, 779 classes and 81 packages. It provides models for DNA and protein sequence evolution, highly parametric coalescent analysis, relaxed clock phylogenetics, non-contemporaneous sequence data, statistical alignment and a wide range of options for prior distributions. BEAST source code is object-oriented, modular in design and freely available at http://beast-mcmc.googlecode.com/ under the GNU LGPL license. BEAST is a powerful and flexible evolutionary analysis package for molecular sequence variation. It also provides a resource for the further development of new models and statistical methods of evolutionary analysis.

  4. BEAST: Bayesian evolutionary analysis by sampling trees

    Directory of Open Access Journals (Sweden)

    Drummond Alexei J

    2007-11-01

    Full Text Available Abstract Background The evolutionary analysis of molecular sequence variation is a statistical enterprise. This is reflected in the increased use of probabilistic models for phylogenetic inference, multiple sequence alignment, and molecular population genetics. Here we present BEAST: a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree. A large number of popular stochastic models of sequence evolution are provided and tree-based models suitable for both within- and between-species sequence data are implemented. Results BEAST version 1.4.6 consists of 81000 lines of Java source code, 779 classes and 81 packages. It provides models for DNA and protein sequence evolution, highly parametric coalescent analysis, relaxed clock phylogenetics, non-contemporaneous sequence data, statistical alignment and a wide range of options for prior distributions. BEAST source code is object-oriented, modular in design and freely available at http://beast-mcmc.googlecode.com/ under the GNU LGPL license. Conclusion BEAST is a powerful and flexible evolutionary analysis package for molecular sequence variation. It also provides a resource for the further development of new models and statistical methods of evolutionary analysis.

  5. NPAS2 Compensates for Loss of CLOCK in Peripheral Circadian Oscillators.

    Directory of Open Access Journals (Sweden)

    Dominic Landgraf

    2016-02-01

    Full Text Available Heterodimers of CLOCK and BMAL1 are the major transcriptional activators of the mammalian circadian clock. Because the paralog NPAS2 can substitute for CLOCK in the suprachiasmatic nucleus (SCN, the master circadian pacemaker, CLOCK-deficient mice maintain circadian rhythms in behavior and in tissues in vivo. However, when isolated from the SCN, CLOCK-deficient peripheral tissues are reportedly arrhythmic, suggesting a fundamental difference in circadian clock function between SCN and peripheral tissues. Surprisingly, however, using luminometry and single-cell bioluminescence imaging of PER2 expression, we now find that CLOCK-deficient dispersed SCN neurons and peripheral cells exhibit similarly stable, autonomous circadian rhythms in vitro. In CLOCK-deficient fibroblasts, knockdown of Npas2 leads to arrhythmicity, suggesting that NPAS2 can compensate for loss of CLOCK in peripheral cells as well as in SCN. Our data overturn the notion of an SCN-specific role for NPAS2 in the molecular circadian clock, and instead indicate that, at the cellular level, the core loops of SCN neuron and peripheral cell circadian clocks are fundamentally similar.

  6. Frequency ratios of Sr, Yb and Hg based optical lattice clocks and their applications

    CERN Document Server

    Takamoto, Masao; Das, Manoj; Nemitz, Nils; Ohkubo, Takuya; Yamanaka, Kazuhiro; Ohmae, Noriaki; Takano, Tetsushi; Akatsuka, Tomoya; Yamaguchi, Atsushi; Katori, Hidetoshi

    2015-01-01

    This article describes the recent progress of optical lattice clocks with neutral strontium ($^{87}$Sr), ytterbium ($^{171}$Yb) and mercury ($^{199}$Hg) atoms. In particular, we present frequency comparison between the clocks locally via an optical frequency comb and between two Sr clocks at remote sites using a phase-stabilized fibre link. We first review cryogenic Sr optical lattice clocks that reduce the room-temperature blackbody radiation shift by two orders of magnitude and serve as a reference in the following clock comparisons. Similar physical properties of Sr and Yb atoms, such as transition wavelengths and vapour pressure, have allowed our development of a compatible clock for both species. A cryogenic Yb clock is evaluated by referencing a Sr clock. We also report on a Hg clock, which shows one order of magnitude less sensitivity to blackbody radiation, while its large nuclear charge makes the clock sensitive to the variation of fine-structure constant. Connecting all three types of clocks by an o...

  7. Fault-Tolerant Self-Stabilizing Distributed Clock Synchronization Protocol for Arbitrary Digraphs

    Science.gov (United States)

    Malekpour, Mahyar R. (Inventor)

    2014-01-01

    A self-stabilizing network in the form of an arbitrary, non-partitioned digraph includes K nodes having a synchronizer executing a protocol. K-1 monitors of each node may receive a Sync message transmitted from a directly connected node. When the Sync message is received, the logical clock value for the receiving node is set to between 0 and a communication latency value (gamma) if the clock value is less than a minimum event-response delay (D). A new Sync message is also transmitted to any directly connected nodes if the clock value is greater than or equal to both D and a graph threshold (T(sub S)). When the Sync message is not received the synchronizer increments the clock value if the clock value is less than a resynchronization period (P), and resets the clock value and transmits a new Sync message to all directly connected nodes when the clock value equals or exceeds P.

  8. The valuative tree

    CERN Document Server

    Favre, Charles

    2004-01-01

    This volume is devoted to a beautiful object, called the valuative tree and designed as a powerful tool for the study of singularities in two complex dimensions. Its intricate yet manageable structure can be analyzed by both algebraic and geometric means. Many types of singularities, including those of curves, ideals, and plurisubharmonic functions, can be encoded in terms of positive measures on the valuative tree. The construction of these measures uses a natural tree Laplace operator of independent interest.

  9. Maximal buttonings of trees

    Directory of Open Access Journals (Sweden)

    Short Ian

    2014-05-01

    Full Text Available A buttoning of a tree that has vertices v1, v2, . . . , vn is a closed walk that starts at v1 and travels along the shortest path in the tree to v2, and then along the shortest path to v3, and so forth, finishing with the shortest path from vn to v1. Inspired by a problem about buttoning a shirt inefficiently, we determine the maximum length of buttonings of trees

  10. A theory of game trees, based on solution trees

    NARCIS (Netherlands)

    W.H.L.M. Pijls (Wim); A. de Bruin (Arie); A. Plaat (Aske)

    1996-01-01

    textabstractIn this paper a complete theory of game tree algorithms is presented, entirely based upon the notion of a solution tree. Two types of solution trees are distinguished: max and min solution trees respectively. We show that most game tree algorithms construct a superposition of a max and a

  11. A parallel buffer tree

    DEFF Research Database (Denmark)

    Sitchinava, Nodar; Zeh, Norbert

    2012-01-01

    We present the parallel buffer tree, a parallel external memory (PEM) data structure for batched search problems. This data structure is a non-trivial extension of Arge's sequential buffer tree to a private-cache multiprocessor environment and reduces the number of I/O operations by the number...... of available processor cores compared to its sequential counterpart, thereby taking full advantage of multicore parallelism. The parallel buffer tree is a search tree data structure that supports the batched parallel processing of a sequence of N insertions, deletions, membership queries, and range queries...

  12. Morocco - Fruit Tree Productivity

    Data.gov (United States)

    Millennium Challenge Corporation — Date Tree Irrigation Project: The specific objectives of this evaluation are threefold: - Performance evaluation of project activities, like the mid-term evaluation,...

  13. Transgenic Forest Trees

    Directory of Open Access Journals (Sweden)

    Ertuğrul Filiz

    2011-11-01

    Full Text Available Biotechnological methods are used in many areas nowadays and one of these areas is applications of biotechnology in forest trees. Biotechnological methods are used frequently on vital issues such as gaining resistance against diseases and herbicide of forest trees, increasing tree growth rates and development of resistance against environmental stresses (drought, salinity, climate change etc.. Also, for improving the quality of wood that reducing lignin content and increasing the amount of cellulose draws attention. This together with applications, positive and negative effects of transgenic trees to the environment is discussed and it was tried to be provided on the auditing legal regulations concerned with these studies.

  14. Are trees long-lived?

    Science.gov (United States)

    Kevin T. Smith

    2009-01-01

    Trees and tree care can capture the best of people's motivations and intentions. Trees are living memorials that help communities heal at sites of national tragedy, such as Oklahoma City and the World Trade Center. We mark the places of important historical events by the trees that grew nearby even if the original tree, such as the Charter Oak in Connecticut or...

  15. Formal verification of a fault tolerant clock synchronization algorithm

    Science.gov (United States)

    Rushby, John; Vonhenke, Frieder

    1989-01-01

    A formal specification and mechanically assisted verification of the interactive convergence clock synchronization algorithm of Lamport and Melliar-Smith is described. Several technical flaws in the analysis given by Lamport and Melliar-Smith were discovered, even though their presentation is unusally precise and detailed. It seems that these flaws were not detected by informal peer scrutiny. The flaws are discussed and a revised presentation of the analysis is given that not only corrects the flaws but is also more precise and easier to follow. Some of the corrections to the flaws require slight modifications to the original assumptions underlying the algorithm and to the constraints on its parameters, and thus change the external specifications of the algorithm. The formal analysis of the interactive convergence clock synchronization algorithm was performed using the Enhanced Hierarchical Development Methodology (EHDM) formal specification and verification environment. This application of EHDM provides a demonstration of some of the capabilities of the system.

  16. Gravitational wave detection with optical lattice atomic clocks

    CERN Document Server

    Kolkowitz, Shimon; Langellier, Nicholas; Lukin, Mikhail D; Walsworth, Ronald L; Ye, Jun

    2016-01-01

    We propose a space-based gravitational wave detector consisting of two spatially separated, drag-free satellites sharing ultra-stable optical laser light over a single baseline. Each satellite contains an optical lattice atomic clock, which serves as a sensitive, narrowband detector of the local frequency of the shared laser light. A synchronized two-clock comparison between the satellites will be sensitive to the effective Doppler shifts induced by incident gravitational waves (GWs) at a level competitive with other proposed space-based GW detectors, while providing complementary features. The detected signal is a differential frequency shift of the shared laser light due to the relative velocity of the satellites, rather than a phase shift arising from the relative satellite positions, and the detection window can be tuned through the control sequence applied to the atoms' internal states. This scheme enables the detection of GWs from continuous, spectrally narrow sources, such as compact binary inspirals, ...

  17. Synchronization of Distant Optical Clocks at the Femtosecond Level

    Directory of Open Access Journals (Sweden)

    Jean-Daniel Deschênes

    2016-05-01

    Full Text Available The use of optical clocks or oscillators in future ultraprecise navigation, gravitational sensing, coherent arrays, and relativity experiments will require time comparison and synchronization over terrestrial or satellite free-space links. Here, we demonstrate full unambiguous synchronization of two optical time scales across a free-space link. The time deviation between synchronized time scales is below 1 fs over durations from 0.1 to 6500 s, despite atmospheric turbulence and kilometer-scale path length variations. Over 2 days, the time wander is 40 fs peak to peak. Our approach relies on the two-way reciprocity of a single-spatial-mode optical link, valid to below 225 attoseconds across a turbulent 4-km path. This femtosecond level of time-frequency transfer should enable optical networks using state-of-the-art optical clocks or oscillators.

  18. Circadian clock NAD+ cycle drives mitochondrial oxidative metabolism in mice.

    Science.gov (United States)

    Peek, Clara Bien; Affinati, Alison H; Ramsey, Kathryn Moynihan; Kuo, Hsin-Yu; Yu, Wei; Sena, Laura A; Ilkayeva, Olga; Marcheva, Biliana; Kobayashi, Yumiko; Omura, Chiaki; Levine, Daniel C; Bacsik, David J; Gius, David; Newgard, Christopher B; Goetzman, Eric; Chandel, Navdeep S; Denu, John M; Mrksich, Milan; Bass, Joseph

    2013-11-01

    Circadian clocks are self-sustained cellular oscillators that synchronize oxidative and reductive cycles in anticipation of the solar cycle. We found that the clock transcription feedback loop produces cycles of nicotinamide adenine dinucleotide (NAD(+)) biosynthesis, adenosine triphosphate production, and mitochondrial respiration through modulation of mitochondrial protein acetylation to synchronize oxidative metabolic pathways with the 24-hour fasting and feeding cycle. Circadian control of the activity of the NAD(+)-dependent deacetylase sirtuin 3 (SIRT3) generated rhythms in the acetylation and activity of oxidative enzymes and respiration in isolated mitochondria, and NAD(+) supplementation restored protein deacetylation and enhanced oxygen consumption in circadian mutant mice. Thus, circadian control of NAD(+) bioavailability modulates mitochondrial oxidative function and organismal metabolism across the daily cycles of fasting and feeding.

  19. Covariance and Quantum Cosmology: A Comparison of Two Matter Clocks

    Science.gov (United States)

    Halnon, Theodore; Bojowald, Martin

    2017-01-01

    In relativity, time is relative between reference frames. However, quantum mechanics requires a specific time coordinate in order to write an evolution equation for wave functions. This difference between the two theories leads to the problem of time in quantum gravity. One method to study quantum relativity is to interpret the dynamics of a matter field as a clock. In order to test the relationship between different reference frames, an isotropic cosmological model with two matter ingredients is introduced. One is given by a scalar field and one by vacuum energy or a cosmological constant. There are two matter fields, and thus two different Hamiltonians are derived from the respective clock rates. Semi-classical solutions are found for these equations and a comparison is made of the physical predictions that they imply. Partial funding from the Ronald E. McNair Postbaccalaureate Achievement Program.

  20. Elemental technetium and promethium as cosmic-ray clocks

    Science.gov (United States)

    Drach, J.; Salamon, M. H.

    1987-01-01

    The possibility of using elemental Tc (Z = 43) and Pm (Z = 61) as clocks to measure the mean cosmic-ray confinement time in the Galaxy, tau(epsilon) is considered. For this purpose it is necessary to estimate the unknown beta(+) decay half-lives of several Tc and Pm isotopes; these estimates are obtained using beta-decay systematics. In the case of Tc it is possible to estimate the half-lives sufficiently well and show that this element can indeed be used as a cosmic-ray clock; in the case of Pm the half-lives are too uncertain to permit any conclusion. In order to make meaningful measurement of tau(epsilon) using elemental Tc, a comsic-ray detector must have a charge resolution less than about 0.25e in the region around Tc, and enough collecting power to detect a few hundred Tc nuclei.

  1. Phase Locking a Clock Oscillator to a Coherent Atomic Ensemble

    Directory of Open Access Journals (Sweden)

    R. Kohlhaas

    2015-04-01

    Full Text Available The sensitivity of an atomic interferometer increases when the phase evolution of its quantum superposition state is measured over a longer interrogation interval. In practice, a limit is set by the measurement process, which returns not the phase but its projection in terms of population difference on two energetic levels. The phase interval over which the relation can be inverted is thus limited to the interval [-π/2,π/2]; going beyond it introduces an ambiguity in the readout, hence a sensitivity loss. Here, we extend the unambiguous interval to probe the phase evolution of an atomic ensemble using coherence-preserving measurements and phase corrections, and demonstrate the phase lock of the clock oscillator to an atomic superposition state. We propose a protocol based on the phase lock to improve atomic clocks limited by local oscillator noise, and foresee the application to other atomic interferometers such as inertial sensors.

  2. Pyrethroid residue dynamics in insects depends on the circadian clock.

    Science.gov (United States)

    Maliszewska, Justyna; Piechowicz, Bartosz; Maciąga, Gabriela; Zaręba, Lech; Marcinkowska, Sonia

    2018-02-27

    Many factors may affect pesticide effectiveness against pests. One of the factors that should be considered is circadian rhythmicity. In this study, we evaluated daily variations in pyrethroid susceptibility in the house cricket, Acheta domesticus L. Crickets were exposed to a standard dose of ß-cyfluthrin at different times of a day, and pesticide residue levels were evaluated using gas chromatography. Results demonstrate that the time of pyrethroid disappearance is correlated with the circadian clock, with the highest decomposition rate at night. Furthermore, crickets also showed the highest resistance to the insecticide at night, expressed as a high survival rate. Moreover, ß-cyfluthrin induced significant changes in thermal preferences of intoxicated crickets. This is the first report showing that pyrethroid residue levels in the crickets' body depend on its circadian clock.

  3. Open Core Protocol (OCP) Clock Domain Crossing Interfaces

    DEFF Research Database (Denmark)

    Herlev, Mathias; Poulsen, Christian Keis; Sparsø, Jens

    2014-01-01

    The open core protocol (OCP) is an openly licensed configurable and scalable interface protocol for on-chip subsystem communications. The protocol defines read and write transactions from a master towards a slave across a point-to-point connection and the protocol assumes a single common clock...... these control signals are passed across the clock-domain boundary and synchronized it may add significant latency to the duration of a transaction. Our interface designs avoid this and synchronize only a single signal transition in each direction during a read or a write transaction. While the problem...... of synchronizing a simple streaming interface is well described in the literature and often solved using bi-synchronous FIFOs we found surprisingly little published material addressing synchronization of bus-style read-write transaction interfaces....

  4. Integration of Bayesian molecular clock methods and fossil-based soft bounds reveals early Cenozoic origin of African lacertid lizards

    Directory of Open Access Journals (Sweden)

    Metzler Dirk

    2009-07-01

    Full Text Available Abstract Background Although current molecular clock methods offer greater flexibility in modelling evolutionary events, calibration of the clock with dates from the fossil record is still problematic for many groups. Here we implement several new approaches in molecular dating to estimate the evolutionary ages of Lacertidae, an Old World family of lizards with a poor fossil record and uncertain phylogeny. Four different models of rate variation are tested in a new program for Bayesian phylogenetic analysis called TreeTime, based on a combination of mitochondrial and nuclear gene sequences. We incorporate paleontological uncertainty into divergence estimates by expressing multiple calibration dates as a range of probabilistic distributions. We also test the reliability of our proposed calibrations by exploring effects of individual priors on posterior estimates. Results According to the most reliable model, as indicated by Bayes factor comparison, modern lacertids arose shortly after the K/T transition and entered Africa about 45 million years ago, with the majority of their African radiation occurring in the Eocene and Oligocene. Our findings indicate much earlier origins for these clades than previously reported, and we discuss our results in light of paleogeographic trends during the Cenozoic. Conclusion This study represents the first attempt to estimate evolutionary ages of a specific group of reptiles exhibiting uncertain phylogenetic relationships, molecular rate variation and a poor fossil record. Our results emphasize the sensitivity of molecular divergence dates to fossil calibrations, and support the use of combined molecular data sets and multiple, well-spaced dates from the fossil record as minimum node constraints. The bioinformatics program used here, TreeTime, is publicly available, and we recommend its use for molecular dating of taxa faced with similar challenges.

  5. TreeCmp: Comparison of Trees in Polynomial Time

    Science.gov (United States)

    Bogdanowicz, Damian; Giaro, Krzysztof; Wróbel, Borys

    2012-01-01

    When a phylogenetic reconstruction does not result in one tree but in several, tree metrics permit finding out how far the reconstructed trees are from one another. They also permit to assess the accuracy of a reconstruction if a true tree is known. TreeCmp implements eight metrics that can be calculated in polynomial time for arbitrary (not only bifurcating) trees: four for unrooted (Matching Split metric, which we have recently proposed, Robinson-Foulds, Path Difference, Quartet) and four for rooted trees (Matching Cluster, Robinson-Foulds cluster, Nodal Splitted and Triple). TreeCmp is the first implementation of Matching Split/Cluster metrics and the first efficient and convenient implementation of Nodal Splitted. It allows to compare relatively large trees. We provide an example of the application of TreeCmp to compare the accuracy of ten approaches to phylogenetic reconstruction with trees up to 5000 external nodes, using a measure of accuracy based on normalized similarity between trees.

  6. Coordination of the maize transcriptome by a conserved circadian clock.

    Science.gov (United States)

    Khan, Sadaf; Rowe, Scott C; Harmon, Frank G

    2010-06-24

    The plant circadian clock orchestrates 24-hour rhythms in internal physiological processes to coordinate these activities with daily and seasonal changes in the environment. The circadian clock has a profound impact on many aspects of plant growth and development, including biomass accumulation and flowering time. Despite recent advances in understanding the circadian system of the model plant Arabidopsis thaliana, the contribution of the circadian oscillator to important agronomic traits in Zea mays and other cereals remains poorly defined. To address this deficit, this study investigated the transcriptional landscape of the maize circadian system. Since transcriptional regulation is a fundamental aspect of circadian systems, genes exhibiting circadian expression were identified in the sequenced maize inbred B73. Of the over 13,000 transcripts examined, approximately 10 percent displayed circadian expression patterns. The majority of cycling genes had peak expression at subjective dawn and dusk, similar to other plant circadian systems. The maize circadian clock organized co-regulation of genes participating in fundamental physiological processes, including photosynthesis, carbohydrate metabolism, cell wall biogenesis, and phytohormone biosynthesis pathways. Circadian regulation of the maize genome was widespread and key genes in several major metabolic pathways had circadian expression waveforms. The maize circadian clock coordinated transcription to be coincident with oncoming day or night, which was consistent with the circadian oscillator acting to prepare the plant for these major recurring environmental changes. These findings highlighted the multiple processes in maize plants under circadian regulation and, as a result, provided insight into the important contribution this regulatory system makes to agronomic traits in maize and potentially other C4 plant species.

  7. Coordination of the maize transcriptome by a conserved circadian clock

    Directory of Open Access Journals (Sweden)

    Harmon Frank G

    2010-06-01

    Full Text Available Abstract Background The plant circadian clock orchestrates 24-hour rhythms in internal physiological processes to coordinate these activities with daily and seasonal changes in the environment. The circadian clock has a profound impact on many aspects of plant growth and development, including biomass accumulation and flowering time. Despite recent advances in understanding the circadian system of the model plant Arabidopsis thaliana, the contribution of the circadian oscillator to important agronomic traits in Zea mays and other cereals remains poorly defined. To address this deficit, this study investigated the transcriptional landscape of the maize circadian system. Results Since transcriptional regulation is a fundamental aspect of circadian systems, genes exhibiting circadian expression were identified in the sequenced maize inbred B73. Of the over 13,000 transcripts examined, approximately 10 percent displayed circadian expression patterns. The majority of cycling genes had peak expression at subjective dawn and dusk, similar to other plant circadian systems. The maize circadian clock organized co-regulation of genes participating in fundamental physiological processes, including photosynthesis, carbohydrate metabolism, cell wall biogenesis, and phytohormone biosynthesis pathways. Conclusions Circadian regulation of the maize genome was widespread and key genes in several major metabolic pathways had circadian expression waveforms. The maize circadian clock coordinated transcription to be coincident with oncoming day or night, which was consistent with the circadian oscillator acting to prepare the plant for these major recurring environmental changes. These findings highlighted the multiple processes in maize plants under circadian regulation and, as a result, provided insight into the important contribution this regulatory system makes to agronomic traits in maize and potentially other C4 plant species.

  8. Clock-modulation based watermark for protection of embedded processors

    OpenAIRE

    Kufel, Jedrzej; Wilson, Peter; Hill, Stephen; Al-Hashimi, Bashir; Whatmough, Paul N.; Myers, James

    2014-01-01

    This paper presents a novel watermark generation technique for the protection of embedded processors. In previous work, a load circuit is used to generate detectable watermark patterns in the ASIC power supply. This approach leads to hardware area overheads. We propose removing the dedicated load circuit entirely, instead to compensate the reduced power consumption the watermark power pattern is emulated by reusing existing clock gated sequential logic as a zero-overhead load circuit and modu...

  9. Ultra-stable clock laser system development towards space applications.

    Science.gov (United States)

    Świerad, Dariusz; Häfner, Sebastian; Vogt, Stefan; Venon, Bertrand; Holleville, David; Bize, Sébastien; Kulosa, André; Bode, Sebastian; Singh, Yeshpal; Bongs, Kai; Rasel, Ernst Maria; Lodewyck, Jérôme; Le Targat, Rodolphe; Lisdat, Christian; Sterr, Uwe

    2016-09-26

    The increasing performance of optical lattice clocks has made them attractive for scientific applications in space and thus has pushed the development of their components including the interrogation lasers of the clock transitions towards being suitable for space, which amongst others requires making them more power efficient, radiation hardened, smaller, lighter as well as more mechanically stable. Here we present the development towards a space-compatible interrogation laser system for a strontium lattice clock constructed within the Space Optical Clock (SOC2) project where we have concentrated on mechanical rigidity and size. The laser reaches a fractional frequency instability of 7.9 × 10-16 at 300 ms averaging time. The laser system uses a single extended cavity diode laser that gives enough power for interrogating the atoms, frequency comparison by a frequency comb and diagnostics. It includes fibre link stabilisation to the atomic package and to the comb. The optics module containing the laser has dimensions 60 × 45 × 8 cm3; and the ultra-stable reference cavity used for frequency stabilisation with its vacuum system takes 30 × 30 × 30 cm3. The acceleration sensitivities in three orthogonal directions of the cavity are 3.6 × 10-10/g, 5.8 × 10-10/g and 3.1 × 10-10/g, where g ≈ 9.8 m/s2 is the standard gravitational acceleration.

  10. An Optical Lattice Clock with Spin 1/2 Atoms

    Science.gov (United States)

    2012-01-01

    one piece, albeit an important one. There are several reasons to search for such variations, ranging from tests of new cosmological and unification...that the outcome of a non- gravitational measurement does not depend on the value of the local gravitational potential. Space-born optical clocks could...Alternatively, the ratio could be monitored as the satellite traverses a highly eccentric orbit, thus modulating the gravitational potential in time. In this

  11. Clock upregulates intercellular adhesion molecule-1 expression and promotes mononuclear cells adhesion to endothelial cells.

    Science.gov (United States)

    Gao, Yinghua; Meng, Dan; Sun, Ning; Zhu, Zhu; Zhao, Ran; Lu, Chao; Chen, Sifeng; Hua, Luchun; Qian, Ruizhe

    2014-01-10

    Clock is a basic helix-loop-helix (bHLH) transcription factor that plays important role in circadian rhythms of various physiological functions. Previous study showed that the expression of intercellular adhesion molecule-1 (ICAM-1) was reduced in the liver tissues of Clock mutant mice. However, how Clock regulates ICAM-1 expression and whether Clock affects cell adhesion function remain unknown. In the present study, we found that exogenous expression of Clock upregulated the gene expressions of ICAM-1 and other adhesion-related genes including VCAM1 and CCL-2, and increased the transcriptional activity of ICAM-1 in mouse brain microvascular endothelial cell lines. In contrast, loss of Clock decreased these gene expressions and ICAM-1 transcriptional activity. Chromatin immunoprecipitation (ChIP) assay revealed that Clock binds to the E-box-like enhancer of ICAM-1 gene. ICAM-1 gene showed rhythmic expression in endothelial cells after serum shock in vitro, suggesting ICAM-1 may be a Clock-controlled gene. Clock regulates the adhesion of mononuclear cells to endothelial cells via ICAM-1. Together, our findings show that Clock is a positive regulator of ICAM-1, and promotes the adhesion of mononuclear cells to endothelial cells. Copyright © 2013 Elsevier Inc. All rights reserved.

  12. Protein phosphatase 1 (PP1 is a post-translational regulator of the mammalian circadian clock.

    Directory of Open Access Journals (Sweden)

    Isabelle Schmutz

    Full Text Available Circadian clocks coordinate the timing of important biological processes. Interconnected transcriptional and post-translational feedback loops based on a set of clock genes generate and maintain these rhythms with a period of about 24 hours. Many clock proteins undergo circadian cycles of post-translational modifications. Among these modifications, protein phosphorylation plays an important role in regulating activity, stability and intracellular localization of clock components. Several protein kinases were characterized as regulators of the circadian clock. However, the function of protein phosphatases, which balance phosphorylation events, in the mammalian clock mechanism is less well understood. Here, we identify protein phosphatase 1 (PP1 as regulator of period and light-induced resetting of the mammalian circadian clock. Down-regulation of PP1 activity in cells by RNA interference and in vivo by expression of a specific inhibitor in the brain of mice tended to lengthen circadian period. Moreover, reduction of PP1 activity in the brain altered light-mediated clock resetting behavior in mice, enhancing the phase shifts in either direction. At the molecular level, diminished PP1 activity increased nuclear accumulation of the clock component PER2 in neurons. Hence, PP1, may reduce PER2 phosphorylation thereby influencing nuclear localization of this protein. This may at least partially influence period and phase shifting properties of the mammalian circadian clock.

  13. Individual tree control

    Science.gov (United States)

    Harvey A. Holt

    1989-01-01

    Controlling individual unwanted trees in forest stands is a readily accepted method for improving the value of future harvests. The practice is especially important in mixed hardwood forests where species differ considerably in value and within species individual trees differ in quality. Individual stem control is a mechanical or chemical weeding operation that...

  14. Tree biology and dendrochemistry

    Science.gov (United States)

    Kevin T. Smith; Walter C. Shortle

    1996-01-01

    Dendrochemistry, the interpretation of elemental analysis of dated tree rings, can provide a temporal record of environmental change. Using the dendrochemical record requires an understanding of tree biology. In this review, we pose four questions concerning assumptions that underlie recent dendrochemical research: 1) Does the chemical composition of the wood directly...

  15. Trees Are Terrific!

    Science.gov (United States)

    Braus, Judy, Ed.

    1992-01-01

    Ranger Rick's NatureScope is a creative education series dedicated to inspiring in children an understanding and appreciation of the natural world while developing the skills they will need to make responsible decisions about the environment. Contents are organized into the following sections: (1) "What Makes a Tree a Tree?," including…

  16. Structural Equation Model Trees

    Science.gov (United States)

    Brandmaier, Andreas M.; von Oertzen, Timo; McArdle, John J.; Lindenberger, Ulman

    2013-01-01

    In the behavioral and social sciences, structural equation models (SEMs) have become widely accepted as a modeling tool for the relation between latent and observed variables. SEMs can be seen as a unification of several multivariate analysis techniques. SEM Trees combine the strengths of SEMs and the decision tree paradigm by building tree…

  17. Matching Subsequences in Trees

    DEFF Research Database (Denmark)

    Bille, Philip; Gørtz, Inge Li

    2009-01-01

    Given two rooted, labeled trees P and T the tree path subsequence problem is to determine which paths in P are subsequences of which paths in T. Here a path begins at the root and ends at a leaf. In this paper we propose this problem as a useful query primitive for XML data, and provide new...

  18. Uncovering dynamic fault trees

    NARCIS (Netherlands)

    Junges, Sebastian; Guck, Dennis; Katoen, Joost P.; Stoelinga, Mariëlle Ida Antoinette

    Fault tree analysis is a widespread industry standard for assessing system reliability. Standard (static) fault trees model the failure behaviour of systems in dependence of their component failures. To overcome their limited expressive power, common dependability patterns, such as spare management,

  19. Grading hardwood trees

    Science.gov (United States)

    Robert L. Brisbin

    1989-01-01

    Tree grading provides a way to evaluate the quality characteristics and value of standing hardwood trees. This is important because the differences in price between high-quality and low-quality end products can be very large. Since hardwood timber varies greatly in quality and value among species, within species, and even within specific geographic areas, timber...

  20. CSI for Trees

    Science.gov (United States)

    Rubino, Darrin L.; Hanson, Deborah

    2009-01-01

    The circles and patterns in a tree's stem tell a story, but that story can be a mystery. Interpreting the story of tree rings provides a way to heighten the natural curiosity of students and help them gain insight into the interaction of elements in the environment. It also represents a wonderful opportunity to incorporate the nature of science.…

  1. Relative clock verifies endogenous bursts of human dynamics

    Science.gov (United States)

    Zhou, Tao; Zhao, Zhi-Dan; Yang, Zimo; Zhou, Changsong

    2012-01-01

    Temporal bursts are widely observed in many human-activated systems, which may result from both endogenous mechanisms like the highest-priority-first protocol and exogenous factors like the seasonality of activities. To distinguish the effects from different mechanisms is thus of theoretical significance. This letter reports a new timing method by using a relative clock, namely the time length between two consecutive events of an agent is counted as the number of other agents' events appeared during this interval. We propose a model, in which agents act either in a constant rate or with a power-law inter-event time distribution, and the global activity either keeps unchanged or varies periodically vs. time. Our analysis shows that the bursts caused by the heterogeneity of global activity can be eliminated by setting the relative clock, yet the bursts from real individual behaviors still exist. We perform extensive experiments on four large-scale systems, the search engine by AOL, a social bookmarking system —Delicious, a short-message communication network, and a microblogging system —Twitter. Seasonality of global activity is observed, yet the bursts cannot be eliminated by using the relative clock.

  2. Analysis of the Precision of Pulsar Time Clock Model

    Science.gov (United States)

    Zhao, C. S.; Tong, M. L.; Gao, Y. P.; Yang, T. G.

    2017-05-01

    Millisecond pulsars have high rotation stability, which can be applied to many research fields, such as the establishment of the pulsar time standard, detection of gravitational wave, spacecraft navigation by using X-ray pulsars and so on. In this paper, we employ two millisecond pulsars PSR J0437-4715 and J1713+0743 which are observed by International Pulsar Timing Array (IPTA), to analyze the precision of pulsar clock parameter and the prediction accuracy of pulse time of arrival (TOA). It is found that the uncertainty of spin frequency is 10-15 Hz, the uncertainty of the first derivative of spin frequency is 10-23 s-2, and the precision of measured rotational parameters increases by one order of magnitude with the accumulated observational data every 4-5 years. In addition, the errors of 4.8 yr TOAs which are predicted by the clock model established by the 10 yr data of J0437-4715 are less than 1 μs. Therefore, one can use the pulsar time standard to calibrate the atomic clock, which can make atomic time deviate from TT (Terrestrial Time) less than 1 μs within 4.8 yr.

  3. Circadian clocks and neurodegenerative diseases: time to aggregate?

    Science.gov (United States)

    Hastings, Michael H; Goedert, Michel

    2013-10-01

    The major neurodegenerative diseases are characterised by a disabling loss of the daily pattern of sleep and wakefulness, which may be reflective of a compromise to the underlying circadian clock that times the sleep cycle. At a molecular level, the canonical property of neurodegenerative diseases is aberrant aggregation of otherwise soluble neuronal proteins. They can thus be viewed as disturbances of proteostasis, raising the question whether the two features - altered daily rhythms and molecular aggregation - are related. Recent discoveries have highlighted the fundamental contribution of circadian clocks to the correct ordering of daily cellular metabolic cycles, imposing on peripheral organs such as the liver a strict programme that alternates between anabolic and catabolic states. The discovery that circadian mechanisms are active in local brain regions suggests that they may impinge upon physiological and pathological elements that influence pro-neurodegenerative aggregation. This review explores how introducing the dimension of circadian time and the circadian clock might refine the analysis of aberrant aggregation, thus expanding our perspective on the cell biology common to neurodegenerative diseases. Copyright © 2013 The Authors. Published by Elsevier Ltd.. All rights reserved.

  4. The Importance of the Circadian Clock in Regulating Plant Metabolism

    Directory of Open Access Journals (Sweden)

    Jin A Kim

    2017-12-01

    Full Text Available Carbohydrates are the primary energy source for plant development. Plants synthesize sucrose in source organs and transport them to sink organs during plant growth. This metabolism is sensitive to environmental changes in light quantity, quality, and photoperiod. In the daytime, the synthesis of sucrose and starch accumulates, and starch is degraded at nighttime. The circadian clock genes provide plants with information on the daily environmental changes and directly control many developmental processes, which are related to the path of primary metabolites throughout the life cycle. The circadian clock mechanism and processes of metabolism controlled by the circadian rhythm were studied in the model plant Arabidopsis and in the crops potato and rice. However, the translation of molecular mechanisms obtained from studies of model plants to crop plants is still difficult. Crop plants have specific organs such as edible seed and tuber that increase the size or accumulate valuable metabolites by harvestable metabolic components. Human consumers are interested in the regulation and promotion of these agriculturally significant crops. Circadian clock manipulation may suggest various strategies for the increased productivity of food crops through using environmental signal or overcoming environmental stress.

  5. Compact atomic clock prototype based on coherent population trapping

    Directory of Open Access Journals (Sweden)

    Danet Jean-Marie

    2014-01-01

    Full Text Available Toward the next generations of compact atomic clocks, clocks based on coherent population trapping (CPT offer a very interesting alternative. Thanks to CPT, a quantum interfering process, this technology has made a decisive step in the miniaturization direction. Fractional frequency stability of 1.5x10-10 at 1 s has been demonstrated in commercial devices of a few cm3. The laboratory prototype presented here intends to explore what could be the ultimate stability of a CPT based device. To do so, an original double-Λ optical scheme and a pulsed interrogation have been implemented in order to get a good compromise between contrast and linewidth. A study of two main sources of noise, the relative intensity and the local oscillator (LO noise, has been performed. By designing simple solutions, it led to a new fractional frequency limitation lower than 4x10-13 at 1 s integration. Such a performance proves that such a technology could rival with classical ones as double resonance clocks.

  6. Biological Clocks and Rhythms of Anger and Aggression.

    Science.gov (United States)

    Hood, Suzanne; Amir, Shimon

    2018-01-01

    The body's internal timekeeping system is an under-recognized but highly influential force in behaviors and emotions including anger and reactive aggression. Predictable cycles or rhythms in behavior are expressed on several different time scales such as circadian ( circa diem , or approximately 24-h rhythms) and infradian (exceeding 24 h, such as monthly or seasonal cycles). The circadian timekeeping system underlying rhythmic behaviors in mammals is constituted by a network of clocks distributed throughout the brain and body, the activity of which synchronizes to a central pacemaker, or master clock. Our daily experiences with the external environment including social activity strongly influence the exact timing of this network. In the present review, we examine evidence from a number of species and propose that anger and reactive aggression interact in multiple ways with circadian clocks. Specifically, we argue that: (i) there are predictable rhythms in the expression of aggression and anger; (ii) disruptions of the normal functioning of the circadian system increase the likelihood of aggressive behaviors; and (iii) conversely, chronic expression of anger can disrupt normal rhythmic cycles of physiological activities and create conditions for pathologies such as cardiovascular disease to develop. Taken together, these observations suggest that a comprehensive perspective on anger and reactive aggression must incorporate an understanding of the role of the circadian timing system in these intense affective states.

  7. Circadian intraocular pressure rhythm is generated by clock genes.

    Science.gov (United States)

    Maeda, Ari; Tsujiya, Sosuke; Higashide, Tomomi; Toida, Kazunori; Todo, Takeshi; Ueyama, Tomoko; Okamura, Hitoshi; Sugiyama, Kazuhisa

    2006-09-01

    The present study in a mouse model was undertaken to reveal the role of the circadian clock genes Cry1 and Cry2 in generation of 24-hour intraocular pressure (IOP) rhythm. IOP was measured at eight time points daily (circadian time [CT] 0, 3, 6, 9, 12, 15, 18, and 21 hours), using a microneedle method in four groups of C57BL/6J mice (groups 1 and 3, wild-type; groups 2 and 4, Cry-deficient [Cry1-/-Cry2-/-]). During the IOP measurements, mice in groups 1 and 2 were maintained in a 12-hour light-dark cycle (LD), whereas mice in groups 3 and 4 were kept in a constant darkness (DD) that started 24 to 48 hours before the measurements. Circadian IOP variations in each group were evaluated by one-way analysis of variance (ANOVA) and Scheffé tests. In wild-type mice living in LD conditions, pressures measured in the light phase were significantly lower than those in the dark phase. This daily rhythm was maintained under DD conditions with low pressure in the subjective day and high pressure in the subjective night. In contrast, Cry-deficient mice did not show significant circadian changes in IOP, regardless of environmental light conditions. These findings demonstrate that clock oscillatory mechanisms requiring the activity of core clock genes are essential for the generation of a circadian rhythm of intraocular pressure.

  8. Clock-cancer connection in non-Hodgkin's lymphoma.

    Science.gov (United States)

    Zhu, Yong; Zheng, Tongzhang

    2008-01-01

    The universal 24-hour circadian clock has a profound impact on many daily biological processes. Disturbance of circadian rhythms has been implicated in the etiologies of many chronic illnesses, including cancer; with correlations most profoundly found among hormone-related breast and prostate cancers. Given the fact that circadian disruption can cause immune deregulation, which is so far the only established risk factor for non-Hodgkin's lymphoma (NHL), we hypothesize that altered circadian rhythms due to environmental factors and/or genetic variations in genes responsible for maintaining circadian rhythms may result in the deregulation of clock-associated biological processes such as immune responses and activities, and consequently influence an individual's risk of developing NHL. Our recent findings provided the first molecular epidemiological evidence linking a major circadian gene to NHL and warrant further investigation. Confirmation of this hypothesis will further add to our understanding of the role of the circadian clock in lymphomagenesis and facilitate the development of novel risk and prognostic biomarkers for NHL.

  9. Causes and consequences of hyperexcitation in central clock neurons.

    Science.gov (United States)

    Diekman, Casey O; Belle, Mino D C; Irwin, Robert P; Allen, Charles N; Piggins, Hugh D; Forger, Daniel B

    2013-01-01

    Hyperexcited states, including depolarization block and depolarized low amplitude membrane oscillations (DLAMOs), have been observed in neurons of the suprachiasmatic nuclei (SCN), the site of the central mammalian circadian (~24-hour) clock. The causes and consequences of this hyperexcitation have not yet been determined. Here, we explore how individual ionic currents contribute to these hyperexcited states, and how hyperexcitation can then influence molecular circadian timekeeping within SCN neurons. We developed a mathematical model of the electrical activity of SCN neurons, and experimentally verified its prediction that DLAMOs depend on post-synaptic L-type calcium current. The model predicts that hyperexcited states cause high intracellular calcium concentrations, which could trigger transcription of clock genes. The model also predicts that circadian control of certain ionic currents can induce hyperexcited states. Putting it all together into an integrative model, we show how membrane potential and calcium concentration provide a fast feedback that can enhance rhythmicity of the intracellular circadian clock. This work puts forward a novel role for electrical activity in circadian timekeeping, and suggests that hyperexcited states provide a general mechanism for linking membrane electrical dynamics to transcription activation in the nucleus.

  10. Positive temporal dependence of the biological clock implies hyperbolic discounting

    Directory of Open Access Journals (Sweden)

    Debajyoti eRay

    2011-01-01

    Full Text Available Temporal preferences of animals and humans often exhibit inconsistencies, whereby an earlier, smaller reward may be preferred when it occurs immediately but not when it is delayed. Such choices reflect hyperbolic discounting of future rewards, rather than the exponential discounting required for temporal consistency. Simultaneously, however, evidence has emerged that suggests that animals and humans have an internal representation of time that often differs from the calendar time used in detection of temporal inconsistencies. Here, we prove that temporal inconsistencies emerge if fixed durations in calendar time are experienced as positively related (positive quadrant dependent. Hence, what are time-consistent choices within the time framework of the decision maker appear as time-inconsistent to an outsider who analyzes choices in calendar time. As the biological clock becomes more variable, the fit of the hyperbolic discounting model improves. A recent alternative explanation for temporal choice inconsistencies builds on persistent under-estimation of the length of distant time intervals. By increasing the expected speed of our stochastic biological clock for time farther into the future, we can emulate this explanation. Ours is therefore an encompassing theoretical framework that predicts context-dependent degrees of intertemporal choice inconsistencies, to the extent that context can generate changes in autocorrelation, variability, and expected speed of the biological clock. Our finding should lead to novel experiments that will clarify the role of time perception in impulsivity, with critical implications for, among others, our understanding of aging, drug abuse and pathological gambling.

  11. Colour As a Signal for Entraining the Mammalian Circadian Clock

    Science.gov (United States)

    Walmsley, Lauren; Hanna, Lydia; Mouland, Josh; Martial, Franck; West, Alexander; Smedley, Andrew R.; Bechtold, David A.; Webb, Ann R.; Lucas, Robert J.; Brown, Timothy M.

    2015-01-01

    Twilight is characterised by changes in both quantity (“irradiance”) and quality (“colour”) of light. Animals use the variation in irradiance to adjust their internal circadian clocks, aligning their behaviour and physiology with the solar cycle. However, it is currently unknown whether changes in colour also contribute to this entrainment process. Using environmental measurements, we show here that mammalian blue–yellow colour discrimination provides a more reliable method of tracking twilight progression than simply measuring irradiance. We next use electrophysiological recordings to demonstrate that neurons in the mouse suprachiasmatic circadian clock display the cone-dependent spectral opponency required to make use of this information. Thus, our data show that some clock neurons are highly sensitive to changes in spectral composition occurring over twilight and that this input dictates their response to changes in irradiance. Finally, using mice housed under photoperiods with simulated dawn/dusk transitions, we confirm that spectral changes occurring during twilight are required for appropriate circadian alignment under natural conditions. Together, these data reveal a new sensory mechanism for telling time of day that would be available to any mammalian species capable of chromatic vision. PMID:25884537

  12. Elemental technetium as a cosmic-ray clock

    Science.gov (United States)

    Drach, J.; Salamon, M. H.

    1985-01-01

    Several radioactive isotopes have been proposed as clocks for the study of the mean cosmic ray confinement time, T sub e. Measurements of Be-10 and Al-26 give a value for T sub e of about 10 Myr when one uses a leaky box cosmic ray propagation model. It is important to obtain additional measurements of T sub e from other radioactive isotopes in order to check whether the confinement is the same throughout the periodic table. The possible use of Tc (Z = 43) as a cosmic clock is investigated. Since all isotopes of Tc are radioactive, one might be able to group these isotopes and use the elemental abundance as a whole. The results of the calculations are somewhat inconclusive for two reasons. First, the beta + decay half lives of two of the Tc isotopes relevant to our calculation are not known. Second, the dependence of the Tc abundance on the mean confinement time is rather weak when one considers the number of events expected in 4 trays of plastic track detectors. However, a future, finite measurement of the Beta + half lives and the possible use of the entire collecting area of the HNC to detect Tc nuclei could make the use of Tc as a cosmic ray clock more attractive.

  13. Temporal Regulation of Cytokines by the Circadian Clock

    Directory of Open Access Journals (Sweden)

    Atsuhito Nakao

    2014-01-01

    Full Text Available Several parameters of the immune system exhibit oscillations with a period of approximately 24 hours that refers to “circadian rhythms.” Such daily variations in host immune system status might evolve to maximize immune reactions at times when encounters with pathogens are most likely to occur. However, the mechanisms behind circadian immunity have not been fully understood. Recent studies reveal that the internal time keeping system “circadian clock” plays a key role in driving the daily rhythms evident in the immune system. Importantly, several studies unveil molecular mechanisms of how certain clock proteins (e.g., BMAL1 and CLOCK temporally regulate expression of cytokines. Since cytokines are crucial mediators for shaping immune responses, this review mainly summarizes the new knowledge that highlights an emerging role of the circadian clock as a novel regulator of cytokines. A greater understanding of circadian regulation of cytokines will be important to exploit new strategies to protect host against infection by efficient cytokine induction or to treat autoimmunity and allergy by ameliorating excessive activity of cytokines.

  14. Causes and consequences of hyperexcitation in central clock neurons.

    Directory of Open Access Journals (Sweden)

    Casey O Diekman

    Full Text Available Hyperexcited states, including depolarization block and depolarized low amplitude membrane oscillations (DLAMOs, have been observed in neurons of the suprachiasmatic nuclei (SCN, the site of the central mammalian circadian (~24-hour clock. The causes and consequences of this hyperexcitation have not yet been determined. Here, we explore how individual ionic currents contribute to these hyperexcited states, and how hyperexcitation can then influence molecular circadian timekeeping within SCN neurons. We developed a mathematical model of the electrical activity of SCN neurons, and experimentally verified its prediction that DLAMOs depend on post-synaptic L-type calcium current. The model predicts that hyperexcited states cause high intracellular calcium concentrations, which could trigger transcription of clock genes. The model also predicts that circadian control of certain ionic currents can induce hyperexcited states. Putting it all together into an integrative model, we show how membrane potential and calcium concentration provide a fast feedback that can enhance rhythmicity of the intracellular circadian clock. This work puts forward a novel role for electrical activity in circadian timekeeping, and suggests that hyperexcited states provide a general mechanism for linking membrane electrical dynamics to transcription activation in the nucleus.

  15. CODE's multi-GNSS orbit and clock solution

    Science.gov (United States)

    Prange, Lars; Orliac, Etienne; Dach, Rolf; Arnold, Daniel; Beutler, Gerhard; Schaer, Stefan; Jäggi, Adrian

    2015-04-01

    The Center for Orbit Determination in Europe (CODE) is contributing as a global analysis center to the International GNSS Service (IGS). Since 2012 CODE participates in the "Multi-GNSS EXperiment" (MGEX), launched by the IGS as a testbed for the incorporation of new GNSS and their signals into the existing IGS processing chains and software packages. We present CODE's latest MGEX solution - a fully integrated 5-system (GPS, GLONASS, Galileo, BeiDou, QZSS) GNSS orbit and clock solution, based on data starting from January 2014. The impact of radiation pressure modeling and orbital arc length on the solution quality will be discussed. The results will be validated with satellite laser ranging (SLR), assessment of satellite clock performance, and precise point positioning (PPP). The CODE MGEX orbit and clock products are publicly available in the IGS MGEX products directory at the CDDIS data center: ftp://cddis.gsfc.nasa.gov/gnss/products/mgex (the solution ID "com" stands for CODE-MGEX). The CODE MGEX products have been generated occasionally so far. Beginning in early 2015 they are provided in a more operational way with a delay of about two weeks.

  16. Magnetization dynamics, Bennett clocking and associated energy dissipation in multiferroic logic

    Science.gov (United States)

    Salehi Fashami, Mohammad; Roy, Kuntal; Atulasimha, Jayasimha; Bandyopadhyay, Supriyo

    2011-04-01

    It has been recently shown that the magnetization of a multiferroic nanomagnet, consisting of a magnetostrictive layer elastically coupled to a piezoelectric layer, can be rotated by a large angle if a tiny voltage of a few tens of millivolts is applied to the piezoelectric layer. The potential generates stress in the magnetostrictive layer and rotates its magnetization by ~ 90° to implement Bennett clocking in nanomagnetic logic chains. Because of the small voltage needed, this clocking method is far more energy efficient than those that would employ spin transfer torque or magnetic fields to rotate the magnetization. In order to assess if such a clocking scheme can also be reasonably fast, we have studied the magnetization dynamics of a multiferroic logic chain with nearest-neighbor dipole coupling using the Landau-Lifshitz-Gilbert (LLG) equation. We find that clock rates of 2.5 GHz are feasible while still maintaining the exceptionally high energy efficiency. For this clock rate, the energy dissipated per clock cycle per bit flip is ~ 52 000 kT at room temperature in the clocking circuit for properly designed nanomagnets. Had we used spin transfer torque to clock at the same rate, the energy dissipated per clock cycle per bit flip would have been ~ 4 × 108 kT, while with current transistor technology we would have expended ~ 106 kT. For slower clock rates of 1 GHz, stress-based clocking will dissipate only ~ 200 kT of energy per clock cycle per bit flip, while spin transfer torque would dissipate about 108 kT. This shows that multiferroic nanomagnetic logic, clocked with voltage-generated stress, can emerge as a very attractive technique for computing and signal processing since it can be several orders of magnitude more energy efficient than current technologies.

  17. Magnetization dynamics, Bennett clocking and associated energy dissipation in multiferroic logic

    Energy Technology Data Exchange (ETDEWEB)

    Fashami, Mohammad Salehi; Atulasimha, Jayasimha [Department of Mechanical and Nuclear Engineering, Virginia Commonwealth University, Richmond, VA 23284 (United States); Roy, Kuntal; Bandyopadhyay, Supriyo, E-mail: jatulasimha@vcu.edu [Department of Electrical and Computer Engineering, Virginia Commonwealth University, Richmond, VA 23284 (United States)

    2011-04-15

    It has been recently shown that the magnetization of a multiferroic nanomagnet, consisting of a magnetostrictive layer elastically coupled to a piezoelectric layer, can be rotated by a large angle if a tiny voltage of a few tens of millivolts is applied to the piezoelectric layer. The potential generates stress in the magnetostrictive layer and rotates its magnetization by {approx} 90{sup 0} to implement Bennett clocking in nanomagnetic logic chains. Because of the small voltage needed, this clocking method is far more energy efficient than those that would employ spin transfer torque or magnetic fields to rotate the magnetization. In order to assess if such a clocking scheme can also be reasonably fast, we have studied the magnetization dynamics of a multiferroic logic chain with nearest-neighbor dipole coupling using the Landau-Lifshitz-Gilbert (LLG) equation. We find that clock rates of 2.5 GHz are feasible while still maintaining the exceptionally high energy efficiency. For this clock rate, the energy dissipated per clock cycle per bit flip is {approx} 52 000 kT at room temperature in the clocking circuit for properly designed nanomagnets. Had we used spin transfer torque to clock at the same rate, the energy dissipated per clock cycle per bit flip would have been {approx} 4 x 10{sup 8} kT, while with current transistor technology we would have expended {approx} 10{sup 6} kT. For slower clock rates of 1 GHz, stress-based clocking will dissipate only {approx} 200 kT of energy per clock cycle per bit flip, while spin transfer torque would dissipate about 10{sup 8} kT. This shows that multiferroic nanomagnetic logic, clocked with voltage-generated stress, can emerge as a very attractive technique for computing and signal processing since it can be several orders of magnitude more energy efficient than current technologies.

  18. Investigations of the CLOCK and BMAL1 Proteins Binding to DNA: A Molecular Dynamics Simulation Study.

    Science.gov (United States)

    Xue, Tuo; Song, Chunnian; Wang, Qing; Wang, Yan; Chen, Guangju

    2016-01-01

    The circadian locomotor output cycles kaput (CLOCK), and brain and muscle ARNT-like 1 (BMAL1) proteins are important transcriptional factors of the endogenous circadian clock. The CLOCK and BMAL1 proteins can regulate the transcription-translation activities of the clock-related genes through the DNA binding. The hetero-/homo-dimerization and DNA combination of the CLOCK and BMAL1 proteins play a key role in the positive and negative transcriptional feedback processes. In the present work, we constructed a series of binary and ternary models for the bHLH/bHLH-PAS domains of the CLOCK and BMAL1 proteins, and the DNA molecule, and carried out molecular dynamics simulations, free energy calculations and conformational analysis to explore the interaction properties of the CLOCK and BMAL1 proteins with DNA. The results show that the bHLH domains of CLOCK and BMAL1 can favorably form the heterodimer of the bHLH domains of CLOCK and BMAL1 and the homodimer of the bHLH domains of BMAL1. And both dimers could respectively bind to DNA at its H1-H1 interface. The DNA bindings of the H1 helices in the hetero- and homo-bHLH dimers present the rectangular and diagonal binding modes, respectively. Due to the function of the α-helical forceps in these dimers, the tight gripping of the H1 helices to the major groove of DNA would cause the decrease of interactions at the H1-H2 interfaces in the CLOCK and BMAL1 proteins. The additional PAS domains in the CLOCK and BMAL1 proteins affect insignificantly the interactions of the CLOCK and BMAL1 proteins with the DNA molecule due to the flexible and long loop linkers located at the middle of the PAS and bHLH domains. The present work theoretically explains the interaction mechanisms of the bHLH domains of the CLOCK and BMAL1 proteins with DNA.

  19. The TS-Tree

    DEFF Research Database (Denmark)

    Assent, Ira; Krieger, Ralph; Afschari, Farzad

    2008-01-01

    Continuous growth in sensor data and other temporal data increases the importance of retrieval and similarity search in time series data. Efficient time series query processing is crucial for interactive applications. Existing multidimensional indexes like the R-tree provide efficient querying......, the efficiency benefits of indexing are lost. In this paper, we propose the TS-tree (time series tree), an index structure for efficient time series retrieval and similarity search. Exploiting inherent properties of time series quantization and dimensionality reduction, the TS-tree indexes high-dimensional data...... in an overlap-free manner. During query processing, powerful pruning via quantized separator and meta data information greatly reduces the number of pages which have to be accessed, resulting in substantial speed-up. In thorough experiments on synthetic and real world time series data we demonstrate that our TS-tree...

  20. Tree damage and mycotrophy

    Energy Technology Data Exchange (ETDEWEB)

    Heyser, W.; Iken, J.; Meyer, F.H.

    1988-10-22

    Tree species that are particularly endangered in our forests are characterized by the fact that they live in an obligatory symbiosis with ectomycorrhiza fungii. In verifying which tree species appear to be more damaged or less severely damaged, a conspicuous phenomenon noted was that the tree species exhibiting slight symptoms of damage or none at all included such ones as form mycorrhizas facultatively or dispense with mycorrhizas, e.g. Acer, Aesculus, Fraxinus, Populus, Salix. Given that trees in municipal gardens reflect the development and extent of damage in a way similar to forests, and given also that much greater numbers of tree species are often cultured in parks of this type, the latter were considered particularly suited to examine the question of whether a relationship exists between mycotrophy and the severity of damage.

  1. Random Walks and Trees

    Directory of Open Access Journals (Sweden)

    Shi Zhan

    2011-03-01

    Full Text Available These notes provide an elementary and self-contained introduction to branching random walks. Section 1 gives a brief overview of Galton–Watson trees, whereas Section 2 presents the classical law of large numbers for branching random walks. These two short sections are not exactly indispensable, but they introduce the idea of using size-biased trees, thus giving motivations and an avant-goût to the main part, Section 3, where branching random walks are studied from a deeper point of view, and are connected to the model of directed polymers on a tree. Tree-related random processes form a rich and exciting research subject. These notes cover only special topics. For a general account, we refer to the St-Flour lecture notes of Peres [47] and to the forthcoming book of Lyons and Peres [42], as well as to Duquesne and Le Gall [23] and Le Gall [37] for continuous random trees.

  2. From Family Trees to Decision Trees.

    Science.gov (United States)

    Trobian, Helen R.

    This paper is a preliminary inquiry by a non-mathematician into graphic methods of sequential planning and ways in which hierarchical analysis and tree structures can be helpful in developing interest in the use of mathematical modeling in the search for creative solutions to real-life problems. Highlights include a discussion of hierarchical…

  3. Estradiol differently affects melanin synthesis of malignant and normal melanocytes: a relationship with clock and clock-controlled genes.

    Science.gov (United States)

    Poletini, Maristela Oliveira; de Assis, Leonardo Vinicius Monteiro; Moraes, Maria Nathalia; Castrucci, Ana Maria de Lauro

    2016-10-01

    Melanin production within melanocytes is regulated, among others, by estradiol, whose effects on melanogenesis are still not completely elucidated. Here we show that although 10(-7) M 17β-estradiol (E2) increased tyrosinase mRNA levels in B16-F10 malignant melanocytes, there was a transient decrease and abolishment of the temporal variation of melanin content. Both parameters were much higher in the malignant than in normal Melan-a cells. Considering that silencing clock machinery in human melanocytes increases melanogenesis, we investigated clock gene expression in those cell lines. Except for Melan-a Bmal1 and B16-F10 Per2 expression of control cells, Per1, Per2, and Bmal1 expression increased independently of cell type or E2 treatment after 24 h. However, melanoma cells showed a marked increase in Per1 and Bma11 expression in response to E2 at the same time points, what may rule out E2 as a synchronizer agent since the expression of those genes were not in antiphase. Next, we investigated the expression of Xpa, a clock-controlled gene, which in Melan-a cells, peaked at 18 h, and E2 treatment shifted this peak to 24 h, whereas B16-F10 Xpa expression peaked at 24 h in both control and E2 group, and it was higher compared to Melan-a cells in both groups. Therefore, malignant and normal melanocytes display profound differences on core elements of the local clock, and how they respond to E2, what is most probably determinant of the differences seen on melanin synthesis and Tyrosinase and Xpa expression. Understanding these processes at the molecular level could bring new strategies to treat melanoma.

  4. Regulation of clock-controlled genes in mammals.

    Directory of Open Access Journals (Sweden)

    Katarzyna Bozek

    Full Text Available The complexity of tissue- and day time-specific regulation of thousands of clock-controlled genes (CCGs suggests that many regulatory mechanisms contribute to the transcriptional output of the circadian clock. We aim to predict these mechanisms using a large scale promoter analysis of CCGs.Our study is based on a meta-analysis of DNA-array data from rodent tissues. We searched in the promoter regions of 2065 CCGs for highly overrepresented transcription factor binding sites. In order to compensate the relatively high GC-content of CCG promoters, a novel background model to avoid a bias towards GC-rich motifs was employed. We found that many of the transcription factors with overrepresented binding sites in CCG promoters exhibit themselves circadian rhythms. Among the predicted factors are known regulators such as CLOCKratioBMAL1, DBP, HLF, E4BP4, CREB, RORalpha and the recently described regulators HSF1, STAT3, SP1 and HNF-4alpha. As additional promising candidates of circadian transcriptional regulators PAX-4, C/EBP, EVI-1, IRF, E2F, AP-1, HIF-1 and NF-Y were identified. Moreover, GC-rich motifs (SP1, EGR, ZF5, AP-2, WT1, NRF-1 and AT-rich motifs (MEF-2, HMGIY, HNF-1, OCT-1 are significantly overrepresented in promoter regions of CCGs. Putative tissue-specific binding sites such as HNF-3 for liver, NKX2.5 for heart or Myogenin for skeletal muscle were found. The regulation of the erythropoietin (Epo gene was analysed, which exhibits many binding sites for circadian regulators. We provide experimental evidence for its circadian regulated expression in the adult murine kidney. Basing on a comprehensive literature search we integrate our predictions into a regulatory network of core clock and clock-controlled genes. Our large scale analysis of the CCG promoters reveals the complexity and extensiveness of the circadian regulation in mammals. Results of this study point to connections of the circadian clock to other functional systems including

  5. Regulation of Clock-Controlled Genes in Mammals

    Science.gov (United States)

    Kielbasa, Szymon M.; Heine, Markus; Dame, Christof; Kramer, Achim; Herzel, Hanspeter

    2009-01-01

    The complexity of tissue- and day time-specific regulation of thousands of clock-controlled genes (CCGs) suggests that many regulatory mechanisms contribute to the transcriptional output of the circadian clock. We aim to predict these mechanisms using a large scale promoter analysis of CCGs. Our study is based on a meta-analysis of DNA-array data from rodent tissues. We searched in the promoter regions of 2065 CCGs for highly overrepresented transcription factor binding sites. In order to compensate the relatively high GC-content of CCG promoters, a novel background model to avoid a bias towards GC-rich motifs was employed. We found that many of the transcription factors with overrepresented binding sites in CCG promoters exhibit themselves circadian rhythms. Among the predicted factors are known regulators such as CLOCK∶BMAL1, DBP, HLF, E4BP4, CREB, RORα and the recently described regulators HSF1, STAT3, SP1 and HNF-4α. As additional promising candidates of circadian transcriptional regulators PAX-4, C/EBP, EVI-1, IRF, E2F, AP-1, HIF-1 and NF-Y were identified. Moreover, GC-rich motifs (SP1, EGR, ZF5, AP-2, WT1, NRF-1) and AT-rich motifs (MEF-2, HMGIY, HNF-1, OCT-1) are significantly overrepresented in promoter regions of CCGs. Putative tissue-specific binding sites such as HNF-3 for liver, NKX2.5 for heart or Myogenin for skeletal muscle were found. The regulation of the erythropoietin (Epo) gene was analysed, which exhibits many binding sites for circadian regulators. We provide experimental evidence for its circadian regulated expression in the adult murine kidney. Basing on a comprehensive literature search we integrate our predictions into a regulatory network of core clock and clock-controlled genes. Our large scale analysis of the CCG promoters reveals the complexity and extensiveness of the circadian regulation in mammals. Results of this study point to connections of the circadian clock to other functional systems including metabolism, endocrine

  6. Modelling the widespread effects of TOC1 signalling on the plant circadian clock and its outputs.

    Science.gov (United States)

    Pokhilko, Alexandra; Mas, Paloma; Millar, Andrew J

    2013-03-19

    24-hour biological clocks are intimately connected to the cellular signalling network, which complicates the analysis of clock mechanisms. The transcriptional regulator TOC1 (TIMING OF CAB EXPRESSION 1) is a founding component of the gene circuit in the plant circadian clock. Recent results show that TOC1 suppresses transcription of multiple target genes within the clock circuit, far beyond its previously-described regulation of the morning transcription factors LHY (LATE ELONGATED HYPOCOTYL) and CCA1 (CIRCADIAN CLOCK ASSOCIATED 1). It is unclear how this pervasive effect of TOC1 affects the dynamics of the clock and its outputs. TOC1 also appears to function in a nested feedback loop that includes signalling by the plant hormone Abscisic Acid (ABA), which is upregulated by abiotic stresses, such as drought. ABA treatments both alter TOC1 levels and affect the clock's timing behaviour. Conversely, the clock rhythmically modulates physiological processes induced by ABA, such as the closing of stomata in the leaf epidermis. In order to understand the dynamics of the clock and its outputs under changing environmental conditions, the reciprocal interactions between the clock and other signalling pathways must be integrated. We extended the mathematical model of the plant clock gene circuit by incorporating the repression of multiple clock genes by TOC1, observed experimentally. The revised model more accurately matches the data on the clock's molecular profiles and timing behaviour, explaining the clock's responses in TOC1 over-expression and toc1 mutant plants. A simplified representation of ABA signalling allowed us to investigate the interactions of ABA and circadian pathways. Increased ABA levels lengthen the free-running period of the clock, consistent with the experimental data. Adding stomatal closure to the model, as a key ABA- and clock-regulated downstream process allowed to describe TOC1 effects on the rhythmic gating of stomatal closure. The integrated

  7. A recursive algorithm for trees and forests

    OpenAIRE

    Guo, Song; Guo, Victor J. W.

    2017-01-01

    Trees or rooted trees have been generously studied in the literature. A forest is a set of trees or rooted trees. Here we give recurrence relations between the number of some kind of rooted forest with $k$ roots and that with $k+1$ roots on $\\{1,2,\\ldots,n\\}$. Classical formulas for counting various trees such as rooted trees, bipartite trees, tripartite trees, plane trees, $k$-ary plane trees, $k$-edge colored trees follow immediately from our recursive relations.

  8. Maximum-Likelihood Estimator of Clock Offset between Nanomachines in Bionanosensor Networks

    Directory of Open Access Journals (Sweden)

    Lin Lin

    2015-12-01

    Full Text Available Recent advances in nanotechnology, electronic technology and biology have enabled the development of bio-inspired nanoscale sensors. The cooperation among the bionanosensors in a network is envisioned to perform complex tasks. Clock synchronization is essential to establish diffusion-based distributed cooperation in the bionanosensor networks. This paper proposes a maximum-likelihood estimator of the clock offset for the clock synchronization among molecular bionanosensors. The unique properties of diffusion-based molecular communication are described. Based on the inverse Gaussian distribution of the molecular propagation delay, a two-way message exchange mechanism for clock synchronization is proposed. The maximum-likelihood estimator of the clock offset is derived. The convergence and the bias of the estimator are analyzed. The simulation results show that the proposed estimator is effective for the offset compensation required for clock synchronization. This work paves the way for the cooperation of nanomachines in diffusion-based bionanosensor networks.

  9. Time Synchronization and Performance of BeiDou Satellite Clocks in Orbit

    Directory of Open Access Journals (Sweden)

    Han Chunhao

    2013-01-01

    Full Text Available The time model of Beidou satellite clocks is analyzed. The general relations of satellite clocks with the system time are studied. The error sources of two-way radio time transfer between satellites and uplink stations are analyzed. The uncertainty of type A is about 0.3 ns in Beidou system. All the satellite clocks in orbit of Beidou satellite navigation system are evaluated by the clock offsets observed by the two-way radio time transfer. The frequency stabilities at a sample time of 10000 s and 1 day for all the satellite clocks are better than . It means that the performance of Beidou satellite clocks in orbit is consistent with the ground test, and the results in orbit are a little better than those in ground vacuum.

  10. MTL-Model Checking of One-Clock Parametric Timed Automata is Undecidable

    Directory of Open Access Journals (Sweden)

    Karin Quaas

    2014-03-01

    Full Text Available Parametric timed automata extend timed automata (Alur and Dill, 1991 in that they allow the specification of parametric bounds on the clock values. Since their introduction in 1993 by Alur, Henzinger, and Vardi, it is known that the emptiness problem for parametric timed automata with one clock is decidable, whereas it is undecidable if the automaton uses three or more parametric clocks. The problem is open for parametric timed automata with two parametric clocks. Metric temporal logic, MTL for short, is a widely used specification language for real-time systems. MTL-model checking of timed automata is decidable, no matter how many clocks are used in the timed automaton. In this paper, we prove that MTL-model checking for parametric timed automata is undecidable, even if the automaton uses only one clock and one parameter and is deterministic.

  11. Skewed Binary Search Trees

    DEFF Research Database (Denmark)

    Brodal, Gerth Stølting; Moruz, Gabriel

    2006-01-01

    It is well-known that to minimize the number of comparisons a binary search tree should be perfectly balanced. Previous work has shown that a dominating factor over the running time for a search is the number of cache faults performed, and that an appropriate memory layout of a binary search tree...... can reduce the number of cache faults by several hundred percent. Motivated by the fact that during a search branching to the left or right at a node does not necessarily have the same cost, e.g. because of branch prediction schemes, we in this paper study the class of skewed binary search trees....... For all nodes in a skewed binary search tree the ratio between the size of the left subtree and the size of the tree is a fixed constant (a ratio of 1/2 gives perfect balanced trees). In this paper we present an experimental study of various memory layouts of static skewed binary search trees, where each...

  12. Phylogenetic trees in bioinformatics

    Energy Technology Data Exchange (ETDEWEB)

    Burr, Tom L [Los Alamos National Laboratory

    2008-01-01

    Genetic data is often used to infer evolutionary relationships among a collection of viruses, bacteria, animal or plant species, or other operational taxonomic units (OTU). A phylogenetic tree depicts such relationships and provides a visual representation of the estimated branching order of the OTUs. Tree estimation is unique for several reasons, including: the types of data used to represent each OTU; the use ofprobabilistic nucleotide substitution models; the inference goals involving both tree topology and branch length, and the huge number of possible trees for a given sample of a very modest number of OTUs, which implies that fmding the best tree(s) to describe the genetic data for each OTU is computationally demanding. Bioinformatics is too large a field to review here. We focus on that aspect of bioinformatics that includes study of similarities in genetic data from multiple OTUs. Although research questions are diverse, a common underlying challenge is to estimate the evolutionary history of the OTUs. Therefore, this paper reviews the role of phylogenetic tree estimation in bioinformatics, available methods and software, and identifies areas for additional research and development.

  13. Fragmentation trees reloaded.

    Science.gov (United States)

    Böcker, Sebastian; Dührkop, Kai

    2016-01-01

    Untargeted metabolomics commonly uses liquid chromatography mass spectrometry to measure abundances of metabolites; subsequent tandem mass spectrometry is used to derive information about individual compounds. One of the bottlenecks in this experimental setup is the interpretation of fragmentation spectra to accurately and efficiently identify compounds. Fragmentation trees have become a powerful tool for the interpretation of tandem mass spectrometry data of small molecules. These trees are determined from the data using combinatorial optimization, and aim at explaining the experimental data via fragmentation cascades. Fragmentation tree computation does not require spectral or structural databases. To obtain biochemically meaningful trees, one needs an elaborate optimization function (scoring). We present a new scoring for computing fragmentation trees, transforming the combinatorial optimization into a Maximum A Posteriori estimator. We demonstrate the superiority of the new scoring for two tasks: both for the de novo identification of molecular formulas of unknown compounds, and for searching a database for structurally similar compounds, our method SIRIUS 3, performs significantly better than the previous version of our method, as well as other methods for this task. SIRIUS 3 can be a part of an untargeted metabolomics workflow, allowing researchers to investigate unknowns using automated computational methods.Graphical abstractWe present a new scoring for computing fragmentation trees from tandem mass spectrometry data based on Bayesian statistics. The best scoring fragmentation tree most likely explains the molecular formula of the measured parent ion.

  14. Association between Circadian Clock Genes and Diapause Incidence in Drosophila triauraria

    OpenAIRE

    Yamada, Hirokazu; Yamamoto, Masa-Toshi

    2011-01-01

    Diapause is an adaptive response triggered by seasonal photoperiodicity to overcome unfavorable seasons. The photoperiodic clock is a system that controls seasonal physiological processes, but our knowledge about its physiological mechanisms and genetic architecture remains incomplete. The circadian clock is another system that controls daily rhythmic physiological phenomena. It has been argued that there is a connection between the two clocks. To examine the genetic connection between them, ...

  15. One-liter Hg ion clock for space and ground applications

    Science.gov (United States)

    Prestage, John D.; Chung, Sang; Le, Thanh; Beach, Maggie; Maleki, Lute; Tjoelker, Robert L.

    2003-01-01

    We describe the development of a small Hg ion clock suitable for space use. A small clock occupying 1-2 liters volume and producing stability of 10 to the power negative twelve, divided by square root pi would significantly advance the state of space-qualified atomic clocks. Based on recent measurements, this technology should produce long-term stability as good as 10 to the power negative fifteen.

  16. Brain-specific rescue of Clock reveals system-driven transcriptional rhythms in peripheral tissue.

    Science.gov (United States)

    Hughes, Michael E; Hong, Hee-Kyung; Chong, Jason L; Indacochea, Alejandra A; Lee, Samuel S; Han, Michael; Takahashi, Joseph S; Hogenesch, John B

    2012-01-01

    The circadian regulatory network is organized in a hierarchical fashion, with a central oscillator in the suprachiasmatic nuclei (SCN) orchestrating circadian oscillations in peripheral tissues. The nature of the relationship between central and peripheral oscillators, however, is poorly understood. We used the tetOFF expression system to specifically restore Clock function in the brains of Clock(Δ19) mice, which have compromised circadian clocks. Rescued mice showed normal locomotor rhythms in constant darkness, with activity period lengths approximating wildtype controls. We used microarray analysis to assess whether brain-specific rescue of circadian rhythmicity was sufficient to restore circadian transcriptional output in the liver. Compared to Clock mutants, Clock-rescue mice showed significantly larger numbers of cycling transcripts with appropriate phase and period lengths, including many components of the core circadian oscillator. This indicates that the SCN oscillator overcomes local circadian defects and signals directly to the molecular clock. Interestingly, the vast majority of core clock genes in liver were responsive to Clock expression in the SCN, suggesting that core clock genes in peripheral tissues are intrinsically sensitive to SCN cues. Nevertheless, most circadian output in the liver was absent or severely low-amplitude in Clock-rescue animals, demonstrating that the majority of peripheral transcriptional rhythms depend on a fully functional local circadian oscillator. We identified several new system-driven rhythmic genes in the liver, including Alas1 and Mfsd2. Finally, we show that 12-hour transcriptional rhythms (i.e., circadian "harmonics") are disrupted by Clock loss-of-function. Brain-specific rescue of Clock converted 12-hour rhythms into 24-hour rhythms, suggesting that signaling via the central circadian oscillator is required to generate one of the two daily peaks of expression. Based on these data, we conclude that 12-hour rhythms

  17. Brain-specific rescue of Clock reveals system-driven transcriptional rhythms in peripheral tissue.

    Directory of Open Access Journals (Sweden)

    Michael E Hughes

    Full Text Available The circadian regulatory network is organized in a hierarchical fashion, with a central oscillator in the suprachiasmatic nuclei (SCN orchestrating circadian oscillations in peripheral tissues. The nature of the relationship between central and peripheral oscillators, however, is poorly understood. We used the tetOFF expression system to specifically restore Clock function in the brains of Clock(Δ19 mice, which have compromised circadian clocks. Rescued mice showed normal locomotor rhythms in constant darkness, with activity period lengths approximating wildtype controls. We used microarray analysis to assess whether brain-specific rescue of circadian rhythmicity was sufficient to restore circadian transcriptional output in the liver. Compared to Clock mutants, Clock-rescue mice showed significantly larger numbers of cycling transcripts with appropriate phase and period lengths, including many components of the core circadian oscillator. This indicates that the SCN oscillator overcomes local circadian defects and signals directly to the molecular clock. Interestingly, the vast majority of core clock genes in liver were responsive to Clock expression in the SCN, suggesting that core clock genes in peripheral tissues are intrinsically sensitive to SCN cues. Nevertheless, most circadian output in the liver was absent or severely low-amplitude in Clock-rescue animals, demonstrating that the majority of peripheral transcriptional rhythms depend on a fully functional local circadian oscillator. We identified several new system-driven rhythmic genes in the liver, including Alas1 and Mfsd2. Finally, we show that 12-hour transcriptional rhythms (i.e., circadian "harmonics" are disrupted by Clock loss-of-function. Brain-specific rescue of Clock converted 12-hour rhythms into 24-hour rhythms, suggesting that signaling via the central circadian oscillator is required to generate one of the two daily peaks of expression. Based on these data, we conclude

  18. Ultracold Molecules in Optical Lattices: Efficient Production and Application to Molecular Clocks

    Science.gov (United States)

    2015-05-03

    Martin, M. M. Boyd, and J. Ye. Rabi spectroscopy and excitation inhomogeneity in a one-dimensional optical lattice clock. Phys. Rev. A, 80:052703, 2009...can fully control the molecules’ internal and external quantum states, as in state-of-the-art atomic lattice clocks. Using the quantized molecular...spectra in an optical lattice , we devised a new lattice thermometry method that is advantageous for many lattice experiments, including clocks and

  19. The expression of melanopsin and clock genes in Xenopus laevis melanophores and their modulation by melatonin

    Energy Technology Data Exchange (ETDEWEB)

    Bluhm, A.P.C.; Obeid, N.N.; Castrucci, A.M.L.; Visconti, M.A. [Departamento de Fisiologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP (Brazil)

    2012-05-25

    Vertebrates have a central clock and also several peripheral clocks. Light responses might result from the integration of light signals by these clocks. The dermal melanophores of Xenopus laevis have a photoreceptor molecule denominated melanopsin (OPN4x). The mechanisms of the circadian clock involve positive and negative feedback. We hypothesize that these dermal melanophores also present peripheral clock characteristics. Using quantitative PCR, we analyzed the pattern of temporal expression of Opn4x and the clock genes Per1, Per2, Bmal1, and Clock in these cells subjected to a 14-h light:10-h dark (14L:10D) regime or constant darkness (DD). Also, in view of the physiological role of melatonin in the dermal melanophores of X. laevis, we determined whether melatonin modulates the expression of these clock genes. These genes show a time-dependent expression pattern when these cells are exposed to 14L:10D, which differs from the pattern observed under DD. Cells kept in DD for 5 days exhibited overall increased mRNA expression for Opn4x and Clock, and a lower expression for Per1, Per2, and Bmal1. When the cells were kept in DD for 5 days and treated with melatonin for 1 h, 24 h before extraction, the mRNA levels tended to decrease for Opn4x and Clock, did not change for Bmal1, and increased for Per1 and Per2 at different Zeitgeber times (ZT). Although these data are limited to one-day data collection, and therefore preliminary, we suggest that the dermal melanophores of X. laevis might have some characteristics of a peripheral clock, and that melatonin modulates, to a certain extent, melanopsin and clock gene expression.

  20. Analysis of Characteristics of QZSS Satellite Orbit and Clock Products during Yaw Attitude Model Switching

    OpenAIRE

    ZHOU Peiyuan; Du, Lan; FANG Shanchuan; Lu, Yu; Zhang, Zhongkai; Li, Fupeng

    2016-01-01

    Yaw attitude model switching of navigation satellites have great impact on its orbit and clock products derived from precise orbit determination. Firstly, the yaw attitude and solar radiation model of QZSS is given briefly. Then, using QZSS precise orbit and clock products provided by IGS MGEX analysis center, precision of orbit and clock is analyzed by satellite laser ranging residuals and polynomial fit residuals respectively. Finally, spectral analysis and modified Allan variance is carrie...