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I worked with Chronolab program, but this program is for Mac and it's old. Is there some similar program for PC or some latter version of Chronolab? Thanks
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The following publication discusses relative merits of different software packages available for rhythm assessment:
Cornelissen G. Applications of cosinor rhythmometry in pharmacology. Journal of Pharmacokinetics and Pharmacodynamics 2021; 48: 339–359. https://doi.org/10.1007/s10928-021-09748-x(0123456789().,-volV)(0123456789().,-volV)
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Biomechanics face grand challenges due to the intricacy of living things. We need multidiciplinary approach (mechanical, chemical, electrical, and thermal ) to unravel these intricacies. We need to integrate observations from multiple length scales - from organ level to, tissue level, cell level, molecular level, atomic level, and then to energy level) Over these intricacies, their dynamism, the complexity of their response makes it very difficult to correlate empirical data with theoretical models. Among these challenges, which is the most important challenge. If we solve the most important challenge, we could solve most of the other challenges easily.
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Biomechanics is both Art & Science because it does not follow Newton's Three Primary Laws predictably. I can stop rolling down a hill biomechanically at will. A bird can fly away when dropped from a tree as opposed to an apple or a piece of gold of the same mass.
The main problem that I have encountered in researching and practicing biomechanics clinically is that its researchers and clinicians are deterministically trying to study it quantitatively (Science) when n=1, there are too many variables to do so. The best that can currently be done is to study it stochastically (Art) or some hybrid of both (Art & Science).
When studying mankind biomechanically we need to seek disruptive biomechanical theories with new terminology and methods of research, diagnosis and treatment. Ones that consider the myofascial organ, the endocannabinoid system and the true actions and purpose of the CNS and neural strategy.
We need to abandon subtalar joint neutral, pronation and "normal" for words that lead us to a better understanding and control of human stance and movement efficiently and without injury or degeneration.
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The research that we are performing is using 2-times cortisol (8 AM - 10 PM) as circadian biomarker for acute sleep deprivation. The thing is, we ask them to avoid the ingestion of any caffeine-based substances (beverages or medications) the day before the test, but we want to know if the caffeine ingestion can anyhow "reset", or modify the cortisol curve after the first sample collected. Does anyone knows if there are any papers assessing the effects of caffeine over the cortisol circadian curve?
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Please go through the following PDF attachments.
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I want to localize the pinealocytes, using immunohistochemistry. Generally, the pineal organ of the catfish is very tiny and thread like appearance. Sectioning of the pineal organ is too difficult.Can you provide me any protocol to study the localization of the pinealocytes using confocal microscopy?
Thanks.
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Dear Saurav:
I think I might give you some general guidelines even though I have not a specific protocol for catfish pineal organ wholemount immunofluorescence, and it has been a while since I worked on fish pineal organs.
First, I found that antibodies against serotonin and S-antigen were the most reliable pinealocyte markers. They labeled the vast majority of pineal cells, all of which where clearly photoreceptor cells when checked at the ultrastructural level. And they labeled the entire cells. Any well-documented commercial antibody against serotonin should do well; as for S-antigen antibodies, you will have to consult recent literature (it’s more than 25 years since I did this!).
Second, it should certainly be possible to perform whole-mount immunofluorescence on catfish pineal organs. For this it is an advantage that they are so small, and if they are difficult to handle because of the small size you could try embedding them in low-temperature gel-point agarose before the immunoprotocol.
I attach a suggested protocol outline.
Best of luck – it’s good knowing someone is still interested in fish pineal organs!
Peter
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I noticed that most study on sleep (including sleep deprivation and rebound) use a photoperiod of LD 12:12. In this way, for sleep deprivation, they usually choose to deprive 6, 12, 24h. Is that like a convention we should follow?
For me I want to raise them under different photoperiod, like longday and shortday photoperiod (e.g. LD 11:13, 15:9..). I am not sure whether it is OK. Thanks for your kind and useful answer!
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If you systematically change the photoperiod from 12:12 to another photoperiod in certain small increments that can be a useful way to ascertain the impacts of gradual shifts in the day length. Just because certain photoperiods (e.g., 6:18, 24:0, etc.) have been used should not limit you from looking at others. Having said that, you may find it beneficial to include at least one photoperiod that has been included in other studies for comparison purposes. But ultimately, it depends upon your specific hypothesis you want to test.
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Besides the previously discovered circadian clock (the 24-hour timekeeper) is there another master regulator clock controlling aging and other time scheduled events of life, such as fetal development and puberty (and ultimately over-watching the whole cycle of aging) which are precisely time-dependent, by keeping the track of solar “years” passed?
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Hi Sina,
There is the "DNA methylation clock", named "epigenetic clock": the degree of methylation of few CpG loci reflects the biological age. It keeps track of the "solar years", except for many diseased tissues which appear "epigenetically older" than healthy tissues, and has a different pace in different tissues.
Two reviews about this question: PMID: 25913071; PMID: 25341512. There are many recent papers about the epigenetic clock but not that many reviews. One founding paper: PMID: 24138928.
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After a long bibliographic search I could not find any data with regard on the performance of Ewoks on the novel object recognition (NOR) test. Any information would be greatly appreciated.
These animals seem pretty hostile to novel stimuli (i.e. stormtroopers) so I wonder if longer habituation sessions would be needed to avoid their neo-phobia.
I also have concerns on the housing light conditions, and preferred stage of the light cycle for the test. I am unfamiliar with the light cycle hours in their natural environment. They also seem pretty active at night.
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You might need to consider their behavior in terms of aggressiveness rather than neo-phobia. Although they might appear hostile to a novel stimulus, the persistence of hostility probably means that it is not so much the novelty of the stimulus that matters. Have you looked at territoriality? Maybe putting them in a neutral environment (i.e. another planet) would decrease this aggressiveness. Also, I would suggest to present them with smaller stimuli. They might be confused by the size of stormtroopers and consider them as a threat.
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Hi all,
I have list of genes with their phase of expression. Frequency of phase distributions shows two distinct phase clusters. I would like to calculate the mean of each phase clusters (circular phase) What I understand is simple averaging is not right for this type of directional data.
It would be great if someone can help me to calculate the mean circular phase of phase clusters. what I have with me is phase of expression of each gene and frequency of each phase.
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Amit,
You can use circular statistics.  Search for a software package called Oriana or other stats software that can do this:
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Is there any type of circadian clock rhythmic expression happens due to different colors of light? Or different intensity of the light can affects? 
Kindly give me any suggestion.
Thanks 
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Hi, may I know which part of the gene region you are targeting to control the circadian rhythm? What is the model organism used?
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Not a single gene, not a Gene but several genes (Per, Tim, Clock, Cry .... ) working in a very complex way.
The SCN generates circadian rhythms by means of a transcriptional-translational
feedback loop. In short, the mechanism is formed by the basic helix-loop-helix (bHLH) Per-Arnt-Sim (PAS) domain containing transcription factors circadian locomotor output cycles kaput (CLOCK) and brain and muscle ARNT-like 1 (BMAL1), which activate the expressionof three Period (Per 1–3) and two Cryptochrome (Cry 1–2) genes by
binding to their E-box (5′-CACGTG-3′) promoter elements. The PERIOD
(PER 1–3) and CRYPTOCHROME (CRY1–2) proteins rhythmically accumulate,
heterodimerize, and translocate to the nucleus to suppress
their own transcription by interactionwith the CLOCK:BMAL1 complex.
CLOCK/BMAL1 also rhythmically control the expression of nuclear receptors,
such as REV-ERBα/β (reverse transcript of erythroblastosis
gene) and RORα/β/γ (retinoic acid related (RAR) orphan receptor),
which in turn repress and activate Bmal1 expression, respectively, conferring
amplitude and robustness to the oscillations in the molecular
clockwork. From a molecular point of view, light activates the expression
of several genes in SCN with different expression patterns
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I am curious from the point of view of those who may take sleep-aiding/soporific drugs to hasten adaptation to new time-zones?
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Thanks Tomás!
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Is it possible that the value of circadian amplitude higher than circadian MESOR? or depends upon the variable such as physiological (blood pressure) or biochemical (ex. melatonin)?
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Hi, Babita 
Yes, it is quite a usual thing. The amplitude of a rhythm can be a higher value then mesor. The mesor is usually an estimate of statics of a wave and derived from the average of all variable samples, whereas amplitude is specific to a acrophase of the curve. I would suggest reading this paper would give better insight. 
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Does anybody know works where two or more circadian genes were overexpressed multiplexly and lifespan of a model was observed? Probably somebody knows groups solving the problem of combined overexpression for life extension, I would be grateful to recieve any information.
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Dear Ilya,
I have not looked at double-over expression but I have looked at single-over expression of several core clock genes in whole body or specific tissues. Based on that, I would say that effect of double-over expression on lifespan could be tricky as the two genes-when taken individually have different effects on lifespan based on the tissues they are over expressed.  I also look at effects of diet on lifespan and that adds a new dimension on the lifespan measurements of the animals.  
Cheers,
Subhash
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I am hoping to find answers for an issue that I am facing when using LumiCycle from Actimetrics. I have been using U2OS cells with Per2-Luciferase in it, which has given me stable rhythmic outputs consistently. Over the last few months, I have encountered a strange problem when the signal dies off at the end of Day 3 after plating while previously it used to continue till day 7. This problem is erratic as it comes and goes. I have changed the batch of my cells, used fresh lumicycle media, luciferin, cell densities while plating etc. When the signal is lost, the cells still look healthy and there is definitely no contamination in the media, nor is there any loss in the volume of the media since they were set up. The problem is at times seen on all the channels or in some channels while the other channels are just fine.
 I was wondering if anyone experienced in working with this instrument has encountered any similar problem and would appreciate any assistance or direction to resolve this issue.
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Thank you so much Filipa. I have tried the greasing option. Am presently checking for mycoplasma. But, I haven't checked the first option. I will definitely give it a go. Thanks a lot.
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I'm looking for raw data of weight change over the course of a single day/night.  How does weight change hour-to-hour, minute-to-minute, over the course of a single day?  I know of one guy who has done an overnight weight loss study in Brazil but his work appears to be ignored by mainstream science at this point.
Keywords: Circadian biology, weight flux, weight loss, metabolism.
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Hi Aaron,
My research was about weight flutuctuation during sleep and awake rest. What I found was that the lowest weight in a 24 hour period is immediatly after o person wakes up. It decreases gradually during sleep, faster during the firs hour. During the day a person generally gains weight after meals, loses after urinating, sweating or defecting (that is quite obvious! But weight loss during sleep is not obvious).
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As already established that our performance rhythms in various cognitive domains are the outcome of two processes- homoeostasis and circadian timing system (CTS). Having said that, if we assess the influence of CTS in cognitive performance through time-of-day protocol method preferably over other two methods i.e. forced de-synchronization and constant routine, can we make sure that both the aforementioned processes are individually unmasked, if not completely, then even partially?
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1. I attached a couple papers that should help. In general people are using a 72hr protocol regardless of whether it is designed to also include forced desynchrony or not.
2. I actually couldn't quickly find something from the Boivin lab that did both ultradian and forced desynchrony so I attached a Kripke paper where they used 1 hour wake, 0.5 hour nap. As you can see, because the cycles do not harmonize with 24 hours it acts similarly to forced desynchrony so that a full day falls outside the range of human entrainment (28hrs). So this protocol is kinda of a best of both worlds. 
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medical physiology 
cronobiology 
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I don't think there's great human data. For mouse, though, we've collected this data in 14 organs. For the most part, the organs are synchronized. However, SCN and adrenal are advanced a few hours. 
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I am currently working with activity data on European badger (Meles meles). They are nocturnal, and begin their winter sleep (not true hibernation) approx. early November lasting to early March. Their activity in the winter is limited indirectly by low temperature (frost) and snow cover due to less access to food (e.g. digging after earthworms). 
This circannual rhythm of activity might be endogenously generated, although external cues such as photoperiod, temperature or snow cover can function to entrain a circannual rhythm.
I working with data from wild badgers and I will not be able to control for the different variables experimentally.
I am planning to test if the decrease in activity in the fall and increased activity in spring could be explained by the time of the year, photoperiod, temperature and snow cover.
However, I will not be able to separate photoperiod from time of the year, but temperature and snow cover do varies. I am seeking the most parsimonious model to explain what causes the badgers to go to winter sleep.
I wish to discuss and get advice on how I should treat the data.
Response variable:
Activity index (numbers of observations adjusted for monitoring effort).
Explanatory variables:
Temperature
Snow (depth)
Time of the year
Time of the year is the variable I find challenging and I want to hear your opinions. I am in particular interested in the fall vs winter and winter vs. spring. Could one solution be to split the data set into summer and winter solstice, i.e. June and December solstice (Northern Hemisphere)? Then I could use days until winter solstice and days since winter solstice as an explanatory variables respectively in addition to temperature and snow. 
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Hi Ronny, it sounds as though you are not only interested in factors that induce winter sleep, but also spring emergence. Since each of these falls, respectively into the fall equinox-winter solstice and winter solstice-spring equinox periods, it would make sense that you would split the analytical timeline (as you suggest) at the winter solstice to avoid the issue of similar daylengths on either side of the solstice boundary, but also because in the former case, you are analyzing co-variates potentially related to the induction of winter sleep, whereas in the latter, your interest is co-variates related to spring emergence. This becomes especially true if you are including day length or a John suggests, night length, as a focal co-variate. My suggestion for a boundary using the equinoxes is to allow enough of a timeline period before the engagement of the winter sleep or spring emergence, respectively, to enable a reasonably robust analysis.
Also, on using temperature as an explanatory variable, you should consider grabbing soil temperature as well as air temperature if the former is available.  Soil temperature tends to be uniformly highly predictable in its slow seasonal change and have a much more direct influence on the overwintering site of the animal than rapidly changing air temperature that is not only much less predictable, but has a much less direct influence on your animal.
Lastly, to confidently answer this question, it would seem that you would need temporal or spatial replication of some kind to develop a robust model. Since between-year variability is frequently high, a number of years of repeat data would be ideal.  You might be able to do this with spatial replication if your spatial replicates are different enough in context of the explanatory variables that you are measuring.  Some combination of both may also be possible. I would expect that replication via repeat years would likely give the best analytical results.
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Melatonin and Circadian Typology
What are the causes behind the late secretion (i.e. 2-3 hours) of melatonin hormone in owls as compared to that of larks?
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Hello Amrit,
The neural mechanisms regulating  circadian changes in melatonin secretion are well described. A number of studies suggested a role of the  clock genes  in the control of the phase, and therefore circadian rhythms in melatonin secretion. At the same time, the synthesis of melatonin is inhibited directly by light, and the duration of melatonin release is reported to be related to the length of the dark period. These evidences suggest that there likely multiple mechanisms which drive melatonin secretion in both owls and larks.
Best wishes, Tatyana 
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Clock genes are controlled by the temperature and photoperiod. But I wanted to know different temperatures like 15c,250 c,350 c so on.How to regulate the expression of clock genes of different temperatures? Kindly anyone tell me or send me any research article regarding this.
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Yes indeed, the clock is temperature compensated.
From my experience - I mean in vitro experiments using pike or white sucker pineal glands-  temperature cycles can synchronize the melatonin secretion rhythm under LD. Temperature cycles can also synchronize the rhythm under DD, i.e., it can synchronize the pineal clocks. However, a return to constant conditions (temperature & DD) results in an loss of the endogenous melatonin rhythm. This suggests to me that temperature cycles cannot entrain the pineal clocks. Another indication of this is that the melatonin rhythm  is of high amplitude providing the temperature applied during the night (or subjective night) is as closed as possible to the preferred fish temperature. Whether this applies to other clocks in the fish organism, I don't know. I can send you some refs later if you want to.
Melatonin is one output of the pineal clocks. How does temperature impact the clock genes ? I cannot tell. I suspect it may have to do with the fish thermal preferences and aerobic scope.
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What are the connections between the reticular nucleus of the thalamus and the reticular formation of the brain stem, the hypothalamus and the cerebral cortex? What role does GABA play?
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Hello Jennifer,
The thalamic reticular nucleus received its name because of its appearance (net-like). It considers to play an important role in consciousness (and WAKE state and REM sleep) and unconsciousness (and NREM sleep), being a “gatekeeper” of the thalamo-cortical circuits and their two fundamentally different states (sleep and wakefulness). All the thalamic RN neurons are GABAnergic, and therefore, they can inhibit the area of the thalamus from where the information came; this can block flow from thalamus to cortex ( i.e.,  negative modulation of  the excitatory projections between the thalamus and cortex).
Kind regards, Tatyana
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Hello, I like to ask for information about genetic markers of time perception, internal clock or duration representation or trials in rat model.
In the same way, ask for specific trials in rat model that can be linked with duration process or internal clocking. 
I really appreciate your help!
David 
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Dear David,
there is a relative simple model of molecular events that explains drive circadian rhythm in rats. It is focused on regulating internal clock based on the concentration of PER/TIM complex protein in hypothalamic cells. Some useful references: Yu et al., 2006; Lee et al., 1999.
Best regards,
Francisco.
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I am analyzing microarray data for circadian experiments (8 timepoints, 4-hour sampling resolution) and I would like to do a COSOPT analysis. I could not find the COSOPT code or the email of Dr. Straume. Do you have acess to that code in a programming language? I wonder if someone can share the algorithm source. I already analyzed the data using JTK_Cycle. Do you know any other program for analyzing periodic patterns in genome-scale data sets?
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Here is our published paper including source code of COSOPT. http://link.springer.com/article/10.1007/s10015-015-0237-6
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Abrupt changes from weekend to weekday and vice versa worsen circadian disruption as several days of a stable sleep schedule is required to shift the hormone rhythms completely?...and is the latter part correct or just an assumption? 
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You must keep in mind that important individual differences are found in the weekday/weekend changes, perhaps a general rule will turn out too general and therefore meaningless. Living organisms should not be considered as mechanical costructions, both species and individual histories (evolution and adaptation) are present in present behviour. I suggerst Nicholas Mrozovki's papers in that matter.
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Everywhere is clear that melatonin is produced mainly at nighttime, and its production decreases with age almost half from 25 to 50 years old. However the absolute amount of produced melatonin remains unclear for me. I would appreciate very much any information on that. Maximum concentrations in blood in young or old individuals would help also!
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All the answers are correct, but the body’s melatonin levels maybe different according the dietary, for instance, the people, who uses to eat rice, have a higher level of melatonin, because the tryptophan content is higher in this grain, the principal precursor of melatonin.
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I would like to create a mathematical model on the interaction between NOX and NADH to understand one aspect of circadian rhythms. The answer might help a little.
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I Guillermo, I find the aim of your study very interesting.
I'm not an expert of NOX proteins but I have a friend of mine that could probably answer to your question. Unforntunately, he has not an account. 
What isoform are you interested in? I'll try to ask him
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We found in our recent study (in prep.) an indication that the daylight's brightness suppresses activity of a nocturnal/crepuscular insect, not any other environmental factor. In other words, the period of inactivity matches exactly the peak of brightness, while peaks of temperature/humidity and wind speed don't match as nicely.
Are there any existing studies that we can cite to support this assertion? It's not central to our research question, but would be useful to elaborate. The only references I could find deal with seasonal patterns of activity entrained by daylight duration on longer time scales. But what about diel patterns of activity? Any pointer would be much appreciated.
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"Brightness" is not an identifiable measurable factor that can be studied. Thus the basis of much work of yesteryear. I know of no work per se.
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Does anyone know the profile of circadian change of PPAR-alpha in mRNA and protein level? Thank you!
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Fig 4, C and D.
I hope that helps.
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Hello Good People!
For my thesis purpose, I need to measure some LED lights (blue LED, and also others, except IR LED, UV LED). My main purpose to find out the non-visual effect of LED light on human circadian rhythm such like melanopic lux and so on. I need to compare LED spectrum with the light spectrum (D65). 
Now, my main need to measure the light both horizontal and vertical directions. Can anyone suggest the proper methods how can I measure the LED lights?
Thanking,
Bipul Mohanto 
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Do you want to measure spatial distribution of radiation from your LEDs and analyze it by spectra in each direction? If yes typical method to measure spatial distribution of light emmission from light sources is suitable. You have to replace luxmeter/irradiance meter with the spectroradiometer. Fiberoptic device would be very easy to use in this case. There are several possibilities how to construct this kind of stand. Finally, recently one of my students has investigated spectral distribution of LEDs in different directions as a part of his egineer project - in his case there were no differences, but he tested only few LEDs. I am curous your results. He used C-gamma  goniometric stand with the fiberoptic spectroradiometer.
I do not recommend camera based method. 
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I know about  LL and DD condition which can disturb normal circadian cycle of light. when we are talking about rat as a model, how much change is ok in light/dark cycle of animal ? I mean, is it possible to have below schedule time for D and L sequences in different groups?
12D/12L in one group, 6D/6L in other group or 48 D/48L?
Does any role exist in this model?
Thanks for your help
Farzaneh
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I guess it all depends on what you mean by "disturbance", the LD of 22 hours we use leads to internal desynchrony, which I consider a disturbance. 
LD that are longer or much shorter will not lead to entrainment, but this does not mean the rhythm is free-running, because light still stimulates the PRC, so you will not get the endogenous period of the animal but a different period emerges, and its calculation is more complex. So, in this case the rhythm is somehow "disturbed"
Finally, chronic jet lags as suggested above, will also disturb the system
H
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Dear All,
There is very little information on dormancy in woody species in tissue culture systems. I am more after bud dormancy and apical dominance. In nature, the axillary buds are often dormant and this is controlled by sucrose, water supply to the bud and more than anything hormonal balances. In tissue culture, we give the same photoperiod and temperature throughout the year and conditions are ideal for all the buds to grow, but still we find that apical dominance exists more often than not. Has anyone studied these aspects in detail - biochemistry, gene regulation etc.? I am asking because when we test the tolerance to vitrification solution, axillary buds tend to be more tolerant than the apical buds. Any clues?
Thanks in advance
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For you statement "In tissue culture, we give the same photoperiod and temperature throughout the year and conditions are ideal for all the buds to grow, but still we find that apical dominance'' - is also not true for plants in natural habitat - for a given time scale ll shoot parts get the same  environment, so why should apical dominance be different in vitro? After all, you have yourself pointed towards hormonal balances and it is widely known that auxins produced at shoot tip (apical) has a role in apical dominance, and considering how auxin moves in intact shoots, what amount of auxin you put to the media becomes immaterial for the whole plant (it has consequences on tissues though). That is why we maintain plants in vitro in 1/2MS and hormone free medium.  .
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I am working on the circadian rhythym of recovery after fatigue.  I have seen many researches in this area but still not satisfied with the work done.  Can somebody suggest something who have worked in this area?
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Look up the papers by Prof Sonia Ancoli-Israel, PhD.  She and her group conducted studies on fatigue, sleep and circadian rhythms in women undergoing adjuvant chemotherapy after surgery for  breast cancer.   She studied the women prior to chemo, during and then after through several cycles.  Most of the statistics were done by Lianqi Liu, MD, and by me, so look for us in the authorship lists.
One of the good papers, on the effectiveness of light treatment, was conducted by Prof. Lavinia Fiorention, PhD, so look for her name as well.
The attached paper is about one of the techniques that we used for measuring circadian rhythms, to assess disruption and then recovery following chemo.  The patients wore an actigraph, and sleep, rest, and activity were assessed by detailed analyses of the actigraphy records, beyond the fitting of the curve.
Matthew
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I am doing some experiments about clock gene in broiler. And I need some relative articles. Articles in relation to clock gene,cry gene,per gene and bmal gene are best. Thanks.
from : Lei Liu,China Agriculture University, BeiJing,China 
Private message me
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Modulation of metabolic and clock gene mRNA rhythms by pineal and retinal circadian oscillators
Stephen P. Karaganis, , , Paul A. Bartell, Vikram R. Shende, Ashli F. Moore, Vincent M. Cassone ,
doi: 10.1016/j.ygcen.2008.12.015.
Daily expression of six clock genes in central and peripheral tissues of a night-migratory songbird: evidence for tissue-specific circadian timing.
Singh D1, Rani S, Kumar V.
doi: 10.3109/07420528.2013.810632.
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Moon gravity influences plants, animal reproduction, human behavior, etc. It is time to demonstrate to the scientific world that the cosmic and lunar periodicities significantly affects, even in the field of biological clocks.
Since 2014 they are beginning to appear incredibly many studies about these topics before then were almost nonexistent since the nineties.
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If you use Newtonian Gravity where M1 is multiplied by m2 you will get a wrong
answer.  Each Planet exerts a gravitation force on the other planet that is
proportional to its own mass and inversely proportional to the distances
between the two planets.   The Barycenter is useful to ballance angular
momentums of two co-orbiting planets  that must remain Tri-linear 
across the two planets Barycenter.  In short M1*r1 = m2 * R2 or
it cn be expressed as M1 * v1 = m2 * V2 .     In the case of the Earth and the 
Moon, all the lower case letters are equal to one (1) , while all the Upper 
case letters are equal to a value just higher than 81.3.
in both equations 81.3 x 1 = 1 x 81.3.  The gravitational forces of each
one are ballanced by the centrifugal forces of co-orbital motions.
As planets grow larger, the larger planet accelerates the smaller 
planet to a higher orbit, and simultaneously decellerates itself to a 
lower orbit, both relatirve to the barycenter.  The Moon is thus moved away
from the Earth, and its orbital travel distance ( circumference ) becomes
greater with time.  That is 9 days becomes 27.3 Days over a 
protracted period of geologic and biologic time.
The plants and animals just record the light availability in their 
teeth and skeletons, and shells.
It is up to man to determine the method that caused these changes.
you do not get changes in the length of the day, or the length of the
Lunar month, unless something does " Work " on the system,
because the system is always in mass, and gravitationally induced
force ballance.  If the distances changed, and the  periods changed,
then the masses changed, and the mass ratios changed.   The bigger
planet always grows faster than the smaller planet, even if both growth
rates make snails look like rockets.  The change in the distance from
center to center is less than 44.86 mm per year between the Moon
and the Earth.  The measured amount from surface to surface
is only 38.2 mm ( net ).  Mc Donald Observatory, Fort Davis, Texas, to the 
correner array left by the apollo astronauts on the moons surface.
The measure amount in the distance between the Earth and Mars is also
increasing as time passes.  This would indicate that the Sun is 
gaining more mass from the Universe than it is loosing in the form
of energy sent out radially from the Sun.  So it would be moving all
of its planets to higher orbits.   Now wouldn't that be a fun load of 
simultaneous equations to solve?
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I have just started with analysing daily periodicity in animal behaviour and I'm a bit confused about the use of the term "Circadian rhythms. There seems to be two different definitions, see below.
I wonder if it is common to use circadian to describe observations of animals in their natural environment (no experiment controlling for light-dark cycles)? Or should I just use "diel" or " daily" activity when describing behaviour throughout a 24 h cycle?
“Circadian rhythms are by definition endogenous rhythms with a period of about 24 hours that persist even with the loss of external synchronizers, that is, under constant conditions (1). In the absence of such experimental evidence, characterizing the locomotor activity pattern of juvenile Alligator mississippiensis as circadian is premature.
PAUL KANCIRU” 
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It is common to incorrectly refer to daily patterns of behavior and physiology in field studies with the term "circadian rhythm". However, this inference can only be confirmed experimentally by maintaining the organism under study in constant environmental conditions, such as constant darkness (DD) or very dim light, and constant temperature to discount the real possibility that the organism's rhythmic pattern is due to response to the rhythmic signal or Zeitgeber. If the rhythm persists in constant environmental conditions, it would be considered a circadian rhythm. Typically, these rhythms are expressed with a period of approximately (circa) 24 hrs, and the organism's internal circadian clock is then synchronized or entrained to the Zeitgeber (usually the light:dark cycle.). In the specific case of alligator circadian rhythms, I believe there is a 1976 paper in Science by Lang and a 1980 paper in J. Comp. Physiol. by Kavaliers and Ralph showing free-running circadian rhythms in juvenile alligators that entrain to LD cycles. Therefore, it is reasonable to infer that field studies of the phenology of alligator behavior has as one of its underpinnings a circadian clock.
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We are designing a neuroimaging study to test hypothesised circadian moderation of reward function in humans. Seems like our hypothesis is best tested using resting state methods, ideally with the hypothalamic suprachiasmatic nucleus as a 'seed region' to investigate correlations with brain reward centres (particularly ventral striatum).
I understand that small, deep brain centres are difficult to image.
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Hi Greg,
Interesting idea. In theory, almost any brain region can be used as a seed region for resting-state functional connectivity studies. In practice, I think the SCN is going to be tricky. Maybe not impossible, but certainly difficult.
Your two main problems are going to be:
1. Localisation - getting an accurate SCN ROI for each of your subjects. I'm only aware of one paper which tried to localise the SCN in humans (http://onlinelibrary.wiley.com/doi/10.1111/j.1460-9568.2008.06582.x/abstract;jsessionid=1DDF475BBC25A93E627D75AD61392F59.f04t04?deniedAccessCustomisedMessage=&userIsAuthenticated=false) and they did it basically by anatomical means - using the optic chiasm as a landmark. Since the SCN is so small (about 2mm^3) they admitted in the paper that their ROI probably included bits of the surrounding structures i.e. the anterior hypothalamus. I would imagine that this is probably the only option for such a small structure. Functional localisation would be extremely difficult given that typical fMRI resolutions are 3mm^3 - you'd be looking at a single voxel. Possibly you could try a functional localiser (i.e. a visual stimulus) with some very small voxels (2mm or 1.5mm) and just a few slices in that region, but you'd be losing so much signal that you might have to scan your subjects for hours to get anything reliable. Which leads me on to...
2. Signal-to-noise. You're right in saying that small, deep structures like this are difficult to image. The SCN in particular is right on the bottom of the hypothalamus, next to a pocket of CSF - this means you're going to get some pretty nasty magnetic susceptibility artefacts and partial-voluming effects, which will essentially serve to reduce your signal and inflate the noise. Plus, it's a very small area, so even if you localise anatomically (and manage to do it accurately) you're probably only going to be looking at a handful (5-10?) of functional voxels that are forming your ROI - this will give you a noisy estimate of the time-course of that area, which means when you feed that in to a functional connectivity analysis, your power to detect results will be reduced.
One solution might be to go the other way around, and localise the reward areas to be used as the seed region in your FC analysis - this can be pretty easily accomplished either anatomically, or using a functional localiser like the MID task.
Hope that helps!
M.
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I have recently started analyzing animal circadian activity (24 hours). I started my analyzes with the use of GAM (or more precise GAMM, with random term (animal ID)). However, I'm now aware that some use cosine curve fitting when working with circadian data. What is the best approach?
My activity data is nest attendance in breeding birds. I have repeated measurements of several breeding pairs. And I look at nest visits per hour block (activity index). From this I would like to model the circadian activity throughout the day, and try to see if there are some peaks.
I have used the following script in R:
Cosine curve fitting#
M1 <- lme(Activity ~ I(cos(2*pi*Time/24))+I(sin(2*pi*Time/24))+
I(cos(2*2*pi*Time/24))+I(sin(2*2*pi*Time/24)),
random =~ 1 | ID,
data = observations, method = "REML")
Note: fixed at 2 harmonics gave the best fit.
GAMM#
M2 <- gamm(Activity ~ s(Time),
random = list(ID=~1),
data = observations, method = "REML")
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Dear Ronny,
JTK-cycle, COSOPT and CircWave are all aimed at gene expression data with relatively low sampling rates (~ 1 sample per hour or so). CircWave is an F-tested forward harmonic regression procedure and similar to you Rscript, except that CircWave automatically detects how many harmonics can be added by F-test criterion (step forward regression style), your Rscript is fixed at 2 harmonics. CircWave has not been used in over 50 publications, and circadian biologists seem to like for its simple logic and ease of use.
We have tested COSOPT against CircWave and found that COSOPT more conservative (less powerful) and very obscure (Oster et al JBR 2006). The parameter settings and threshold for detecting a rhythm seems quite arbitrary and is not documented (the publication is not clarifying it either). On top of that, COSOPT is far too conservative in detecting rhythmicity when compared to CircWave.
JTK cycle is different from CircWave and COSOPT in that it uses a non-parametric approach and therefore likely less powerfull to detect rhythmicity in normal distributed data, but more reliable when data not normally distributed.
But you asked about activity data. Such data are usually not sine shaped, so you would need a lot of harmonics to be added (certainly more than 2!) in order to describe the profile of your activity pattern. JTK cycle mightwork better, but I cannot recall that anybody ever published JTK cycle with activity data.
For activity data, people like Bill Schwartz have advocated to use Wavelet analysis for onset & offset determination, but this analysis depends greatly on the choice of Wavelet shape, which depends again on the shape of the activity profile and the species etc.
In my view (and I have ample experience in a behavioural chronobiology lab), the best option for analysing activity data still is the periodogram analyses (either Sokolof & Bushell or Lomb-Scargle with missing data) to test for significance of circadian rhythmicity and to find the circadian period. The big advantage of this method is that periodogram analysis is independent of the shape of the 24-h activity profile. Onsets and Offsets of activity can be simply determined by 24-h running average vs. 3-h running average based threshold crossing, as published by Kamiel Spoelstra (Speolstra et al - journal of biological rhythms 2004). Kamiel also wrote a freely available software package to do this, called ChronoShop.
Both ChronoShop and CircWave are downloadable from the Hut-lab website. If the site does not download (it had some problems recently), please contact me directly by email.
greetings,
Roelof Hut.
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It would be of great interest how the sleep wake cycle changes during the seasons in a population without artificial light.
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Thanks for the references.
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From what I understand there is approximately 2 hours in the sleep/wake cycle of the 'lark' and 'owl' but I am trying to find out how this affects the timing of other biological clocks. I am a design student - I hope I am not asking an obvious question.
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Hi Thomas - Thank you for your response. Of course I do not think that larks and owls have un-normal cycles. Actually, I think it's quite frustrating that what I have read on this subject thus far seems to refer to individuals who have schedules conducive to the majority of a population are called 'normal'. In my question here I did not know what other term to use. However, I do not think I phrased my question incorrectly. What I meant was if an 'owl' chronotype wakes at 11 a.m. and a 'normal' chronotype wakes at 9 a.m. is the schedule for the function of the other organisms in the body bumped 2 hours later in the 'owl' than in the 'normal' chronotype? The reason I was asking is because it seems there is confusion about these functions in the fields of writing outside of professional researchers and chronobiologists.
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Also antibodies for PACAP and calbindin. What are other neuronal phenotypes in the SCN?
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For Calbindin, I recommend the various antibodies (different species) from SWANT. Excellent quality, highly specific.
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I would like to investigate a possible relationship between the daily activity patterns of an animal and the timing and amount of daylight experiences by the animal. I do not have light-logger data per animal, so I am searching for a free data source. Ideally this data would be location specific (I'm working near Albany, New York, USA) and available per minute. Can any one suggest a data source? Perhaps something widely accepted within the circadian biology community?
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Costa/Lievore reported in (10.1080/00140138908966104): "Conversely, morningness appeared to be
unrelated to long-term tolerance, but did influence circadian adjustments and
sleep behaviour." in their abstract.
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We examined chronotype and shiftwork adaptation and found that indeed, night shift workers were more likely to consider themselves late types than early types. We also found that early types were very well adapted to day shift and poorly adapted to night shift while late types were not well adapted to either type of shift. We discussed these results in terms of social jet lag.
Also, regarding the comment above, one may assume that evening types may adapt better to night shift if they are permanent night shift but our research suggests this is not true, primarily due to the fact that in our sample, 97% of shift workers prefer to sleep at night on days off. This means that the worker is constantly jet lagged when working and on off days.
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We're interested in using WI-38 cells to establish an assay. We are interested in a human fibroblast cell line which is haploid and has been previously used in circadian experiments. The assay will require us to transfect or infect the cells and then to create clonal populations. Does anyone have experience with WI-38 cells and can speak to the ease/difficulty of working with WI-38 cells?
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Dear jacqueline, Transfecting Wi 38 is done with great precaaution, i am sending you paper containing process of transfection kindly chk it in attachment.
all d best.