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- How can I plot/determine ROC/AUC for SVM?
ROC: Receiver Operator Curve
AUC: Area Under Curve.
You can look in the Matlab LSSVM toolbox how they doFollowing
- Transcription factor binding affinity. Method to asses binding affinity changes due to a TF interactor?
I have an interaction between a soluble protein and a Transcription Factor.
Using Yeast 1 Hybrid I observed that the interacting protein of my TF can change the activity of the TF. Using 2 different promoter regions (2 different gene promoters), the interacting protein either activated transcription driven by my TF or repressed it.
I'd like to have a different method to validate those results. I think EMSA won't work because I have 2 proteins. If I don't put the interactor, I'll have only one DNA shift (control lane), but if I put both proteins I'll have 2 DNA shifts (the unbound TF fraction and the complex of both proteins), since no interaction is 100% effective and I expect a small fraction of both proteins unbound. That will mess up any band intensity comparison.
In other words, I don't want to asses the TF affinity for a specific DNA region, but a CHANGE in the affinity due to a protein interaction (most likely due to a conformational change of the TF upon binding).
SPR is a good choice but if you have never done SPR then it might take a while to optimize it. If you have done EMSA then it might be worth trying it. In EMSA you will be detecting the DNA (free or bound). The free proteins most likely will not enter the gel. It would depend on their pKa. Normally DNA binding proteins are positively charged.
If the TF affinity for the promoter site is weak (in microM range), then ITC might be another good method to try.Following
- Could anybody tell me the appropriate cell concentration to run CHEF- DRIII
The concentration of the protoplast that will give good bound when running CHEF electrophoresisFollowing
- Do you agree with Stephen Hawking's recent conclusion that black holes don't exist? Black holes don't exist. I published this many years ago. Cantor's Universe doesn't allow the concept.
Stephen Hawking now came up with the same conclusion. Read: http://www.spektrum.de/news/es-gibt-keine-schwarzen-loecher/1222059
In my opinion he is right this time. What is your opinion? Was he right then or is he correct now?
Special relativity tells us that the mass of a particle increases with velocity. Therefore, prior to reaching the speed of light, all massive particles will have a mass exceeding the Planck mass. One might argue that, at such speeds, particles actually become miniature black holes. Because even light cannot escape from the event horizon, it is possible (and to my mind, likely) that the collision of a particle with a black hole is indistinguishable from the collision of two black holes. Since we know that many particles have properties that cannot be represented by black holes complying with the "no-hair" theorem, this may be another argument why general relativity is incomplete.Following
- Dr. Ertmer, what is the date of this study? Is this the one published elsewhere in 2006?
Thanks for clarifying and Happy Labor Day!Following
- Does anyone have experience describing long-term changes in stream habitat based on multiple sample protocols?
I'm interesting in linking several fish habitat sample protocols over a long time period to describe nearly a century of change. Bureau of Fisheries reports from the 1930s, Aquatic Habitat Inventories from the 1990s, and the Columbia Habitat Program at the present. The general problem is one of describing change in a consistent manner although protocols have changed drastically and there may be no or little crosswalk between the methodologies. Any suggestions for methods or relevant research would be helpful. Thanks.
Some kind of 'reference condition approach' could maybe work. This is usually used for fish or invert assemblages, where you set a reference condition based on undisturbed streams and then calibrate your metric based on that reference condition. You will always get a score between 0 and 1, which can then be compared to a a different measurement system. There's a few papers on this flying around, including one I was involved in where we modeled pre-european habitat conditions in Australia,
- Does anybody working on the concept of "Free Will" , if so then what are there few simple experiments to check the existence of "Free Will" ?
Hello everyone , I would like to assess the concept of "Free Will" for humans by experiments similar to "Ants in the Box" for insects and observe their behaviour based on artificially created situation. Already I am working on assigning this concept to electronic circuitry by to modes , 1. Requirement mode and 2. Free will mode. Can anybody give suggestions on simple experiments to be carried by humans?
It will generate the wrong type of interest if you apply it too quickly to a specific population. The subject alone will attract attack.Following
- What are the current innovations in better understanding of the role of organisms in regulation of water quality?
What quality is a key issue in water sustainability.
Thank you Steve for your answer and voting up. I am looking forward to hearing your opinion.Following
- Which are the main factors for the increasing of hurricane activity due to the possible climate change?
Observed records of Atlantic hurricane activity (e.g. Emanuel 2007.) show a strong correlation, on multi-year time-scales, between local tropical Atlantic sea surface temperatures (SSTs) and the Power Dissipation Index (PDI). PDI is an aggregate measure of Atlantic hurricane activity, combining frequency, intensity, and duration of hurricanes in a single index. Both Atlantic SSTs and PDI have risen sharply since the 1970s, and there is some evidence that PDI levels in recent years are higher than in the previous active Atlantic hurricane era in the 1950s and 60s. (Source: http://www.gfdl.noaa.gov/global-warming-and-hurricanes)Following
- Protein concentration
What is the proper way to concentrate a protein with 5 kDa from cell culture medium ?Following
- Functional annotation of proteins identifed through MS/MS analysis
does anybody have an experience with a software or any online source to perform functional annotation of proteins identified through MS/MS analysis. I found some publications used the Gene Ontology (GO) tool but I can't find the actual software or how to use. Any suggestions for this is highly appreciated. ThanksFollowing
- Can you predict whether or not shear banding will occur in a given material?
There is lots of discussion on shear banding in the literature but for different materials and systems. Clearly the same mechanisms can't explain banding in colloidal suspensions and also in polymer solutions.
Just looking for some thoughts.
Although I'm not expert in shear banding I can give a few hints: 1.wide gaps 2. increased packing or concentration 3. unsheared material. All these parameters either in solid/liquid systems, or in gels (certain polymers and/or biopolymers) are crucial to observe shear banding (at least, based on my experience)
- Do you know that the Constitution of the Republic of Argentina? Promotes Immigration everyone who wants to dwell on Argentine soil?
Every day, we see the entry of persons to various countries without guaranteed health and education for all residents is difficult.
Do you know that in Argentina primary, secondary and university level is free for all people and citizens?
Is it also about the public health system?
What other countries encourage the entry of new citizens?Following
- What production methods of industrial foods or drinks enriched with spirulina platensis without fishy odor for diabetic patients are there?
I want to produce foods or drinks enriched with spirulina platensis (without fishy odor) for diabetic patients. antioxidants and phycocyanins are reduced by sterilization and processing procedures.
I would recommend fermenting the spirulina which removes the fishy odours and taste and boosts the availability of the amino acids and enriches the vitamins.Following
- Using publicly available online data for health and sport science research.
I'm looking at the feasibility of using publicly available data downloaded from websites such as http://connect.garmin.com. http://strava.com for research. I've found one paper - Haney Jr, T. A., & Mercer, J. A. (2011). A description of variability of pacing in marathon distance running - that accessed 300 marathon profiles, but can't find any others. Anyone know of any others?Following
- Which database focus on the relationship of miRNA and pathway?
I want to see if one miRNA target on a pathway or not. Several database was used, include
However, each of database has the different answer. Could anyone tell the reason, AND which one is reliability？
Yes, these databases are shiny, nice, well-maintained and provide a lot of false positive target genes. I would not even put too much trust in databases using "validated" target genes. This is a messy issue and although this is a scientific issue, it is still driven by relatively huge amounts of gut feeling. If you want to know whether your microRNA of interest is involved in the regulation of a specific pathway, you already rely on other "databases" that define this pathway. So all is based on pretty shaky compilations of data, predictions of targets, validated target genes based on the individual preferences of scientists, and very few global, in depth analyses of real and comprehensive target genes.
My advice: you have to generate such data yourself or become a victim of the fallacy of database mania. Don't get me wrong: there is a lot of very good data but there are all a lot of microRNAs. The chances that you find a comprehensive dataset for your microRNAs is slim. Start manipulating your microRNA of interest and you will find the answers you are looking for.Following
- Are precise meteo data for the recent past available in some data-bank?
In our research on bird distribution & ecology, we have often important amounts of data with spatial localization and date, lacking information about weather conditions. These conditions influence bird detectability, so taking them into account could improve the performance, say, of habitat models. If it is available some sort of global meteorological database, giving weather data for every day, at a precise spatial scale, we could take into account weather data also for the (recent) past. Do someone know if this database exist, and the method to obtain the data?
You can download global weather station data, updated daily, from NCDC:
- Is there any free, open source software for optical component design? I am looking for open source or free software to design and simulate VCSEL cavities and other photonic / optical devices.
Windows or Linux based would be preferred.
Is this OpenEMS you speak of or CAMFR? Actually, I use CAMFR on WINE on Ubuntu 14.04. I strongly recommend CAMFR - so long as you're not simulating metals. It seemed that CAMFR had some stability problems when simulations included metals. While it's 2D only (with some other restrictions) CAMFR could be useful because it's considerably faster than FDTD for 2D.
For FDTD, I recommend first running your simulations as quasi 2D, whereby you take advantage of perfect magnetic or electric conductor boundary conditions to exploit symmetries. Anything you can do to reduce the number of cells will improve performance, which is key to optimization.
Please let me know if you have any questions,
- Access to markets
An important factor in the success of tropical species is their shelf life and saleability in southern markets.
Existing antimicrobials and antifungal chemicals are generally noxious with floriculturalists suffering from contact dermatitis and allergies from these toxic compounds.
One approach is to use a 1% solution of a natural antimicrobial made from culinary herbs and spices called Herbal-Active. It won an Australian Food Industry Innovation Award last year and trials with roses shower a dramatic shelf life extension as grey mould (Botrytis spp) was eliminated from the open buds on stem with an instantaneous dip and drain.
A comment from the florist conducting the research was that a test bucket full of dipped roses that were 15 days old were the preferred selection by a customer over roses just in from the market that day.
This provides a way that floriculturalists can gain better access to markets with naturally long life cut flowers.Following
- Which case study research on co-creation in product development projects you find very useful?
There are many cases of co-creation projects. However, each of them is specific in its own way and it is difficult to approach them in unique manner. Therefore, I would be thankful for some examples and experience in this kind of research.Following
- All phenomena are unique in perceived physical expression: what are the potential consequences for the definition of 'replicated' science practice? Philosophers or scientists aim to define unifying theories to explain as much as possible numerous phenomena based on a few principles. Philosophers might for instance state that two phenomena separated in time or space always differ in at least one scale of analysis or perception. Individual particles, like bosons or fermions, might be unique immeasurable physical expression because of Heisenberg principles. Physical expression combining these particles at higher levels of organisation should therefore also be unique in physical expression. Thus, two grains of sand on a beach or two oxygen atoms might never be structurally exactly the same at all scales of analysis. In addition, because phenomena will probably be perceived differently by organisms with different biology, philosophers might state that for at least one scale of analysis two phenomena will never be perceived exactly the same by different observers. Because phenomena might be material, objects or living beings all these philosophical statements would cover any spatiotemporal scale in distinct science disciplines, including Physics, Chemistry or Biology.
This would imply that physical, chemical or biological structures are physically always 'un-replicable' or perceived as 'un-replicable. Are 'replicable' phenomena as defined in science practice not more than human mental products disconnected from the true nature of nature? Scientists might for example accept 'imprecisions' when they define classes or groups of phenomena with common characteristics to make them 'replicable'. Do scientists invent artificial rules to make science practice workable from an empirical or mathematic point of view?
Replication, which is a necessary principle in investigating and studying things that are obscured or similar in some sense, should indeed be in terms of an existence of some mapping(s) between two physical or abstract things. In mathematics for instance we can differentiate two topological manifolds (or spaces ) as similar or topologically invariant, if one is continuously deformed to the other or simply if there is a homeomorphism between the two topological spaces. In mathematical discourse therefore, the mathematics we do in one manifold or space is equivalently valid in a topologically isomorphic or homeomorphic space as well, which is not the case in non-homeomorphic spaces. Therefore to count different- ness, it is non-homeomorphic spaces what are called different and distinct.
For instance the mathematics performed in doughnut like spaces is exactly valid in a coffee mug like spaces.Following
- Viable microbes from the salt to the food? Does anyone have experience with growth in foods of microbes/ spores carried by the salt used in the preparation?
Thank you, very much!Following
- What causes high CEC in biochars?
Biochars are thought to be a very stable form of carbon, yet normal CEC measurement (e.g., Neutral 1 M ammonium acetate) would yield very high CEC values (ranging from 15 - 40 cmolc/kg). Where are the sources of this CEC? Some people suggest that the surface, oxidized carboxylate and phenolate groups are the probable source, but I am not quite convinced!
I suspect that common CEC determination methods that are used for soils may not be appropriate for biochar or biochar-amended soils. That is because biochars, especially those derived from wood, have many micro/nanopores that can tightly trap ions (e.g., NH4+) and water or alcohol cannot flush them out. This is a physical adsorption as opposed to electrostatic attraction or chemi-sortion.Following
- How do you report the results of an independent samples t-test if the variances are unequal?
Can anyone direct me to an APA style publication which reports that the unequal variances figures for an independent samples t-test were used? (I'm doing this using SPSS, with n = 35 and 36, for the two groups).
Thanks, Bruce - that too is very useful. You're right - the signficances are actually identical as, although the varainces are signficantly different, in real terms it's not by much..Following
- Can we correct the spectrum of FTIR if too much sample is mixed with KBr ?
Sometime the sample dosage is too much put in KBr; the spectrum is too weak and not quite clear. Moreover, the transmittance may exceed 10 % than that of appropriate sample dosage.
Unadvisable. Use less sampleFollowing
- How can I remove organic acid smell from Lactobacillus extract?
As we know that LAB has lactic acid and acetic acid smell. Here I prepared ethanolic extract of my lactobacillus but I have some acetic smell in this please suggest how it can be reduced from the extract.
you might need to remove ehanol (Rotavapo),If you have a dry matter, you can remove this kind of smells in an exicator, using NaoOH or KOH pellets or do an lyophilisation in high vacuum alternatively.Following
- Do you have a data sheet or catalog for hybrid circuit breakers (AC)?
No, i don't have.Following
- Which one is the best and user friendlily simulation software for modelling and simulation of FACTS controllers?
Thanks, but can i make model of STATCOM in ETAP software?Following
- What is the importance of social media in political communication? Do you think social media has become more important than traditional media in political communication? I think it´s 50/50 more or less nowadays.
I'm not sure of the answer. Obviously, social media are important in political communication. but the real issue is how do social media change political communication not only in what is related with interactivity and participation, but in what about the quality of participation . And when we come to this point I have lots of doubts that I tried to present in the following textFollowing