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- 2PCR based genotyping amplifying either mutant or wild type mice but not heterozygous ones?
Hi, I have heterogygous mice with 450 bp deletion to genotype, I am doing PCR and for some mice I am getting only mutant amplicon and for the rest only wild type amplicon, how can I solve this problem. Primers are designed outside of the deletion, so if I have wt mice I get full size amplicon, if I have mutant mice I get smaller size amplicon, I mated my mutant mouse with wild type mice and so I definitely have htz mice, However, PCR giving me only one band, either wt or mutant band. Can anyone help me to understand what is wrong. Thank you
if your mouse had a polymorphism just under the 3' end of one primer then the pcr pair would act like an ARMS pcr and one allele would not amplify so if you started with mice with deletions on both types of chromosome then perhaps you are getting selective non amplification of one chromosomeFollowing
- 19Educational smartphone & tablets apps for teaching Physics & Math. Which ones would you suggest?
On the internet, we find several options of smartphones & tablets apps for playing games with physics and mathematical concepts. Which ones have you already used and would recommend for the use in the basic & high schools?
Some researchers on 'Science Education' have been studying their use already and have made public some of their presentations about these works. Would you have some recommendation of researchers to be contacted that have been working on this topic?
Thanks in advance!
You're welcome. If you want to know more about usage of this app in educational research please contact me via email.Following
- 10How to measure delay time for ultrasonic flow meter?
I use a microcontroller to turn on the transmitter and detect received signal so I can measure the time from turning on the transmitter to detecting signal after receiver. this time includes sound traveling time (between two sensors) plus circuit propagation delay time. I want to know how I can measure the sound traveling time (T1_2 and T2_1) which is my goal to be able to measure the flow with equation below. These times show the time from sensor 1 to 2 and sensor 2 to 1.
flow = (D/sin(2a))*((T1_2 - T2_1)/(T1_2*T2_1))
To measure circuit propagation delay use conditions with substance flow equal to zero.
What substance flow do You measure? Liquid or gas?
May be syncronous phase detector is more suitable for Your's task? It is more sensitive.Following
- 4Odds ratio per standard deviation increase/decrease?
How would one acquire an Odds ratio per standard deviation (OR per SD) increase/decrease of an explanatory variable?
The link from the IBM website below explains that one may use OR per SD if the value of exp(B) is too close to 1 to be meaningful, by "simply [standardizing] the variable, so that a unit change is one standard deviation."
I am confused how this might be implemented in SPSS. Let's say I have an explanatory variable (money) in a regression model with an outcome variable (happiness) for example. If I were to follow the definition of OR per SD above, that would mean a dollar change would be a change in SD.
But what if my money variable had a standard deviation value of, say, 200. How wold I use this value as the SD in a regression model?
Jerry, excellent point about the distinction between the SD computed from the sample data and some external (e.g., national) SD. I agree that it is often preferable to standardize to some such external standard if one is available. (I often make the same kind of argument about centering variables on some convenient value that can be used across studies rather than centering on the mean, or some other value, computed for each sample separately.)
Re the final point, using the Z-score variable has not changed anything in that regard. If you include a continuous variable in the model (with no polynomial terms etc.), the odds ratio for that variable is for a one-unit increase at any point along the scale. (By using a z-score variable, all you do is change one unit from the original units to SD units.) If this is not a reasonable assumption, then one has to do something else (e.g., introduce appropriate polynomial terms, splines, etc.)
- 2How do I remove an uploaded publication ?
I uploaded the wrong version
Thanks for your response.
I don't want to remove the listing.
I only want to remove the document version that I uploaded.
Any other ideas, please?
- 7Picogreen assay quantification of samples ?
My query is regarding the amount of DNA in my sample using Picogreen assay kit.
I normally use a total reaction volume of 100 microlitre out of which 50 microlitre is 1:200 fold diluted Picogreen (as per manufacturer recommendation) and 50 microlitre is standard DNA or my sample.
For the standard, the final concentration expressed in ng/ml is as per the manufacturer after diluting with TE buffer.
I use a 5 microlitre of a sample (which has been pre-diluted already 10 times before being used) and obtain a DNA concentration of
e.g 800 ng/ml, the actual concentration of my sample would be
= (800 ng/1000 ml)*20*10 = 160 ng/ ml (5 microlitre of sample in 100 microlitre of reaction volume and 10 fold prior dilution of sample).
Please suggest as I got faint band for normal tissues following agarose (1.5%) gel electrophoresis using TBE buffer.
You're right, it all depends on if you factored this into the standard curve values. If you don't use the 1:2 dilution for the standards then you don't need to for the samples.Following
- 3What is the difference between BER Calculation for a binary chaos based CDMA system and conventional CDMA system?
hi dear all, Assume that we intend to calculate BER performance of a chaos based CDMA with binary spreading sequence compared with a conventional CDMA system. where is the difference between this two calculations? if your answer is cross correlation function, how we can express this difference?
I thin there is no difference in the method of calculating the bit error rate in both cases.
The difference only is that one substitute the spreading sequence by a chaotic sequence. In both cases one get the spread signal which is binary phase keyed and sent across white additive Guassian noise channel.
So in this case the chips may be detected in errors because of the additive noise.
Then one correlates the received spreading signal with the the spreading sequence irrespective of its type. After despreading one gets the an estimate of the input data sequence. When compared to the input sequence one gets the bits in error and the bit error rate.
In summary one uses the same same signal processes to get the bit error rate.
wish you successFollowing
- 43What do you think about scientific accuracy in movies? And does it affect public’s science literacy?
Scientific accuracy in films is an issue intensely discussed. If fantasy and artistic licenses are part of a good story, some scientists think that many scenes violate natural laws to such a degree that they may produce in the public false perceptions of reality and incorrect scientific views.
When the film “2012” depicted the end of the world, taking advantage of public worries about the event supposedly predicted by the Mayans (whose calendar ends on December 21, 2012), NASA had to create a special website because of the many questions from terrified people that the agency received (1). Less shocking but recurrent inaccuracies may be misleading in other ways. Spaceships roar in outer space, where sound cannot propagate. People jump from high speeding cars and land safely, infringing all laws of physics.
Other problem lies in the stereotyping of scientists. They are often portrayed as closed-minded individuals, who create troubles but cannot solve them. Some scholars think that this helps to create an anti-science environment (2).
There are films, however, that contain good science. Ridley Scott’s "The Martian" has been considered “the first genuine Mars movie” due to its realistic nature. But it also has a number of technical mistakes (see The Guardian link). For example, the violent storm that forced the crew to hurriedly abandon Mars –leaving the main character on the planet- would be an absolute impossibility, since the Martian atmosphere is just 1% as thick as Earth’s. On the contrary, it is plausible that the Matt Damon character could have survived when his rocket was launched from Mars without windows.
As for "Interstellar" (link below), an astrophysicist finds very accurate the visual appearance of the supermassive black hole, which is based in real physics simulations. It seems that money allows Hollywood’s special effects companies to do physics visualizations much more quickly than universities. The time dilation effect that the crew experiences on the planet that orbits very close to the black hole would be also a precise representation of real physics, assuming that the black hole is rapidly spinning. However, the commentator says that it is highly unlikely that such a planet could exist so close to the black hole without being destroyed.
Many films depict an infectious disease outbreak that quickly spreads, often around the world. This kind of movies also presents realistic and not so realistic features (link below). It seems, for example, that contagion inside an airplane would be much less likely than it is usually represented, because the ventilation systems in planes are highly efficient.
In 2008, Hollywood and the National Academy of Sciences launched the Science and Entertainment Exchange. This partnership, whose main goal is to improve scientific accuracy in cinema, includes an advisory board of scientists, producers, directors and actors.
What is your opinion about the scientific accuracy in movies?
Have you noted inaccuracies related to your field of work?
Do you think that unrealistic scenes can affect public’s scientific knowledge and views?
(1) Nastasi, A.: “NASA Names Most Realistic and Unrealistic Sci-Fi Films of All Time. Moviefone.com. January 3, 2011.
(2) LaFee, S.: “Scientific accuracy in movies? It’s neither universal nor paramount”. The San Diego Union-Tribune. July 20, 2009.
Scientific accuracy in films is a way to increase scientific literacy. The films are for instance the science fiction films.Following
- 7What are some good Islamic Sources on Environmentalism from Islam's Golden Age (750-1258CE)?
I have been asked to write a book chapter on Islam and the environment. I plan on offering a 2 brief qualitative brief case studies; 1) on the 2006 Somalia Islamic Courts Union (if I can find enough sources) and 2) the participation and role of the OIC-member states in the 2015 Paris COP21 conference (which I am sure I will be able to find enough sources for).
I would welcome a couple good short references to Islamic sources on the environment during Islam's 'Golden Age' Period (approx. 750- until the sack of Baghdad in 1258 CE). I would like to write perhaps 1 or 2 minor paragraphs on this for my introductory section-- a couple nice zinger quotes from someone like Al-Farabi or Ibn Rushd (or someone a bit more obscure) would be welcomed.
It may be worth looking at Pathfinders - The Golden Age of Arabic Science, Jim Al-Khalili, (2010) Allen Lane, London. There's a reference to Al-Jahith on page 76. He was, as you're probably aware, an influential figure in Arabic literature/fiction. He also, however, had an interest in biology. In his Book of Animals, he speculated on the influence of the environment on animals.
Hope this is of some useFollowing
- 4Which refrigerants do we use commercially in which applications as of now (in India)? And which refrigerants will we use after phase-out?
Eg. which ones in supermarkets, which ones in domestic A/Cs or refrigerators, which ones in ice/brine production in industries, etc. segments
We will be phasing out some refrigerants. So, which technologies are ready with us as of now? Whats the issue with other refrigerant use? How are we dealing with this?
Ammonia is in use in some industrial and commercial applications like ice making because of its high refrigeration effect but it has to be handled with great care due to its toxic behavior.Following
- 1Does anyone know any literature on Amblypygi , Opiliones , Solifugae and Thelyphonida of Indian subcontinent?
I am looking for any publication, website or any other source on Amblypygi , Opiliones , Solifugae and Thelyphonida of Indian subcontinent other than "The Fauna of British India, including Ceylon and Burma". Even in there I can't find anything about Opiliones.
Thanks in advance.Please contact Dr Suresh Benjamin at National Institution of Fundamental Studies KandyFollowing
- 4What is a good alternative for the BioRAPTR from Beckman Coulter?
I would like to buy a good liquid handler which can handle at least 96 and 384 well plates. It should be possible to attach multiple liquids and to discriminate between all wells. I had good experience with the Beckman Coulter BioRAPTR but they don't sell that anymore.
Does anyone know an different supplier for this machine or a good alternative?
There are several players in this field, and it really depends on how you were using your BioRaptr as to which is best for you.
The Certus Flex is the microdispenser we use with our customers, since it is as flexible and compatible as a BioRaptr, and more robust. 8 different fluid channels, dispense into anywhere from 96 to 1536 wellplates and beyond, dispense volumes of <35nL to >35uL. You can learn more at the link provided.
Other players include the Tecan D300 (used to be the HP), the mantis, and even a combi nL if you're just looking for higher volume backfills.
Feel free to reach out if you want to know more.Following
- 23Can you please recommend me a source that is about qualitative content analysis?
We are working on a project about innovation strategies. We followed a qulitative process in gathering data (semi-structured interview), and used Venkatraman's 6 dimensions of strategic orientation as a coding manual. Also utilized quotes from participants in supporting our findings. Can you recommend me a basic source that used smilar steps?
Thank you Dr. Rejno. I have reviewed Hsieh & Shannon' paper. It is very useful. İ Will also check Elo & Kyngäs'.Following
- 3How can i perform Time to progression using SPSS ?
How can i perform TTP using SPSS, i know how to perform survival tables and KM curves for survival analysis.
Is it one minus survival?
Your Kaplan-Meier curve can be either stepping down from left to right (survival), or stepping up (1 - survival), depending on how you want to present your data. But they are totally the same graph showing the same data, just flipped. It's all a matter of the visual impact you want to produce; you could for example have one of your axes labeled 'Time to Progression', or alternatively, 'Progression-free Survival.' But it's the same curve, just mirror images.
To determine significance between two (or more) groups in your survival curves, use the log-rank test. SPSS has three variants of the log-rank test, which weight more heavily for early survival, late survival, or overall. You can also indicate median survival by drawing a horizontal (or vertical) line at the 50% point of survival, and then dropping a perpendicular line to the other axis from where that line hits the survival curve (so you could say for example that "median survival was 43 months"). (and of course compare the medians with a medians test in SPSS!).Following
- 7How can I measure Carbon sequestration rate of a site over a year period of sampling?
I am going to measure above ground, below ground and soil carbon concentration of a site and I am wondering if I can have its sequestration rate !!
Considering short time period of sampling ( monthly period for one year)
Very informative are tagged websites, Mr. XiaoguangFollowing
- 2Cancer expression and co-expression
I am looking for a tool-database that will allow me to determine in which cancer or cancer cell-line a set of genes is up or down regulated at the expression level. With all the cancer databases and tools available I assume that such a database visualization should be possible but having hard time finding it.
- 1What is your idea about the modelling arms race between countries?
Hi to everyone
I'm working on the modelling of arms race between countries. In this line, I have selected Richarson model, but, since I'm focused on four countries, I had to extend it to a n-adic one. Fortunately, I found a paper that did this extension. and now I want to run an experimental test and estimate the coefficients of the model, but I don't Know how to choose a more appropriate model. Would you please help me to select a econometric model for this?
The attached is the underlying paper, and my intended model is the first one that is presented in the paper.
Every help is appreciated.
You can go through the article written by JP Dunne in 2000?Following
- 9What is the best method to remove soft tissues from a dissected rat's long bone?
I have tried scraping the soft tissues off using a scalpel but the whole procedure was a lengthy one. So I was wondering if anyone could tell me any other quicker way of removing the soft tissues without compromising on its structural integrity? I am planning to use it for histology and micro CT.
You have received good suggestions already. I suspect just soaking in water ( for x time) and then very gently picking off tissue with forceps would work. No quick fix!Following
- 1How far should the distance in between two accessions be while collecting accessions for reaserch?
the crop I need to collect seed accessions is not indigenous, and the research is about to study acession variations:molecular, physiological and phenotypecal variation
There is no hard and fast rule for collection of accessions and distance in between. Moreover, the crop is not indigenous, it might have been introduced in the region through cultivation of varieties mostly developed by other nations or regions to whom it belongs or variability is maintained in different collections for breeding purpose. While collection of accessions, you are not sure that plant population of an accession has same source or variety. If the crop, you are going to collect germplasm is self pollinated, chances of variability will be very less, if crop is often cross pollinated or highly cross pollinated, chances of getting variability will be more. because the population gets chances of random mating and variability is generated at its own. Even in the segregated population, lot of variability can be collected and stabilized. Therefore it is difficult to answer about the distance for collection of accessions.Following
- 4Has anyone use MaxQuant and Perseus to analyze pulse-chased SILAC data?
How to analyze pulse-chased SILAC data using MaxQuant and Perseus (or any other tools, preferably open source)? Also, how to calculate protein synthesis/degradation rate? I used heavy Arg and Lys until they were fully incorporated into the cells and then switched to light media for 24 and 48 hours.
Thank you very much for the feedback and tips. You're a lifesaver!
Because this is a pulse-chase setup, do you use min ratio for quantification of 2 in MaxQuant? Do you impute your data when there were Nan values?
The R scripts are very helpful indeed. Could you please send me the scripts? My email is email@example.com
- 1Forest values analysis: free listing and ranking. Is it possible to analyze them together?
I am trying to determine an "order" of collected information about forest values from informants of different ethnic groups:
1) Using the free-listing method I collected the first ideas related to forest values.
Due to the diversity of collected items, each one was classified into a specific value category. That is to say, from the ~460 collected value items, I could aggregated them into 9 value categories. Ex: Item 1: "food"; Item 2: "shelter"; Item 3: "medicine" belong to "Life support", and so on for the other 8 categories.
2) After that, I asked the participants to rank how important each value category was. The scale had five level possibilities (5: very important; 4: important; 3: more or less; 2: little important; 1: not important at all). Each participant ranked forest in relation to its "Life support" value.
Now, for each value category I have in fact: 1) magnitude (frequency) and 2) a respective ranking.
Ex: Case x ---> Life support: 6 (frequency); and 5 (very important)
Is there a method that analyses both and allows to build a hierarchy (system) of those 9 value categories grouped by ethnic group, so interethnic differences in valuing forest can be recognized?
It is possible by using cluster analysis or applying some sort of cluster algorithm,
Below is a link to a chapter that would help you to understand how to proceed in your endeavour.
- 6Does anyone knows which size needs each sample to have when we conduct a cross-cultural study and analyse these differences using SEM?
Could you please advice me about the size of the samples when we conduct a cross-cultural study for comparing behaviours between two cultures? Does the sample size has to be similar? For instance, if I have a sample with 532 participants and the other sample has 699 participants, do you think that these number should be fine if we want to analyse the differences between sample using SEM?
Many thanks in advance for your help
I don't have experience with Mplus, I prefer SAS and SPSS for statistical analysis, this software effective and widely used.
- 6Any suggestion for human mesenchymal stem cell markers ?
I would like to identify mesenchymal stem cells in human formalin fixed paraffin embedded tissue with heterotopic ossification. The samples are from a variety of tissues like large blood vessels, bladder, prostate, adrenal, kidney and skeletal muscle. Which mesenchymal stem cell marker(s) is/are the best choice ? It can be a nuclear, cytoplasmic or membranous protein.
Thank you all for your input, I appreciate.Following
- 19Can anyone suggest some free remote sensing data?What is the available multispectral and hyperspectral data that we can download for free? I know the earth explorer and glovis, however, if there is any other websites that offer good resolution images or if there is any commercial images offered for free for specific places I would like to have images in London or Baghdad. I am interesred in studying urban materials and surface temperature(urban heat island) by remote sensingthere are many free remote sensing data.: MODIS, Sentinel 1, 2,.....Following
- 2Normality of censored data?
Can anyone point me to a way to test for the normality of censored data in R? I have heard of the Crame'r-von Mises statistic but the paper is behind a paywall.
I have already made graphs and they appear to be reasonable fits. I am evaluating the distribution of rodent longevities from multiple studies.
Also, I show that package has been removed from R.Following
- 1How to plot Impulsive Mathematical model ?
Friends, I am working on mathematical models with impulse effect, i am facing difficulty to plot them.
There is not enough information in your question in order to help you. Please would you state what the model is. Is it a problem you are having with software. Is it a problem with the maths. ThanksFollowing
- 99+The gravitational redshift is a phenomenon based on gravitational time dilation, don't we want to exclude definitely any loss of energy of photons?
The gravitational Redshift is a phenomenon which is directly related to the time dilation of the atomic clocks in a gravitational potential. Somebody still gives the interpretation of an energy loss of photons in a gravitational potential.
If the interpretation is due the exchange of net amount of energy with the gravitational field while crossing different gravitational potentials, treating the radiation as being massive while travelling, such hypothesys has to be excluded. The results of the PRS experiments verify (1+gh/c2) as being the frequency shift ratio, and since in both cases (lossive and clock hypothesys) the same shift is predicted, one of the two interpretation has to be discarded.
Lev Okun invited to perform such a sharp distinction more than 15 years ago, discarding forever the gain or loss of energy of the photons as measured always in the same RF.
The two interpretations cannot be considered alternative views of the same phenomenon and the net electromagnetic energy exchange with the gravitational field during the transit has to be discarded and is not certainly supported by the GRT.
The Clock hypothesys is verified also in the experiment of Vessot and Levine by testing the Schwartschild solution . It is also verified that when clocks are in sync in a gravitational potential, due to the compensation of the kinetics, there is not redshift at all, In other words, although there is a different gravitational potential between the emitter and the observer, there is a specific point along the ballistic motion where no redshift is observed or present, and no time dilation between the emitter and observer is present according to GRT.
GD: "The experimental physics I pointed out is the Ives-Stilwell experiment. Again I have repeated this many times, the scientific facts aren't going to go away just because you can't cope with them."
AKA: Hahahahaha!!! Why do you like the reality to be observer independent in nature????
Based on that idiotic comment, I can only conclude that you either have no idea what Ives and Stilwell did in their experiment or you have no idea what the phrase "observer dependent" means, perhaps both. Whichever it is, you need to go and look up both before you make any more of a fool of yourself.
AKA: As Hermann Minkowski announced that,
HM: "The views of space and time which I wish to lay before you have sprung from the soil of experimental physics, and therein lies their strength. They are radical. henceforth, space by itself, and time by itself, are doomed to fade away into mere shadows, and only a kind of union of the two will preserve an independent reality."
Exactly, and my HTML page on the Twins illustrates precisely what he was saying, but you couldn't even recognise that. You've got a long way to go.Following
- 1Does climate change impact the effectiveness of plant protection products and to what extent?
Will there be a positive, negative or neutral effect of climate change on the efficacy of plant protection products?
The quick answer is: results may vary. To the extent that temperature regime changes in a given location, and the product in question is tempertaure regime sensitive (most are not very), then yes. There may be more of an effect from changes in precipitation, with areas experiencing increased ppt seeing some minor impact.
The larger impact will be on the pest and diseases themselves - a changed climate in a goven area will mean better or worse conditions for the suite of pests and diseases already rpesetn there, and for possible invaders. So it is not so much that the plant proteciton products will become more or less effective, as it is that the pests and diseases they are used to protect against will become more or less agressive and may change.
This is a location-dependant perspective; on a broader non-locational perspective, there should be no hnage in the effectiveness of the products, but there may be a change in which products need to be deployed where.Following