Q&A

ResearchGate Q&A lets scientists and researchers exchange questions and answers relating to their research expertise, including areas such as techniques and methodologies.

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  • Jake Kennard added an answer in Spectrophotometry:
    Is it possible to quantify Alizarin red stains with spectrophotometry?

    Does anyone have a protocol they can recommend? Is this possible at all? I'll be trying to quantify mineralisation after obtaining cell culture images. 

    Jake Kennard · University Campus Suffolk

    Dear Gerhard,

    Both very sound pieces of advice, though I think the latter may have been intended for someone else's question. I see now that not only is smoking bad for my health but a distraction for champions of scientific research such as yourself.

    I shall cease immediately!

    Warmest regards,

    Jake 

  • Muhammad Shoaib added an answer in Grounded Theory:
    Does Grounded Theroy always have to develop a 'new' theory?

    I have been exploring grounded theory and have read somewhere that GT does not have to develop a 'new theory' but can build on existing theories. My reading suggests that there are only 'so many' theories that can be developed.  Advice please.

    Muhammad Shoaib · University of Gujrat

    Please check the article, if it works. Thanks, Shoaib

    http://www.qualitative-research.net/index.php/fqs/article/view/1412/2902

  • Riza Arief Putranto added an answer in VectorNTI:
    Best software/server for bacterial genome annotation and primer design?

    I am looking for software or a server that will allow me to easily and rapidly annotate regions of interest and design primers against a Pseudomonas genome. I currently use Vector NTI, but find the primer design process to be frustratingly slow. I am particularly interested in servers linked to high-performance computing clusters that would allow me to save or upload a copy of the genome that I have already annotated so I don't have to re-do my work each session.

    Thanks,
    Anna

    Riza Arief Putranto · Balai Penelitian Bioteknologi Perkebunan Indonesia

    Hello Anna. Maybe I can interest you to use Geneious software where you can work on and offline. Please check the following link http://www.geneious.com/. I used this software to annotate a superfamily of genes related to abiotic stress in rubber tree and it worked great. Hope this will get you more insights. Cheers.

  • Esra'a Alkafaween added an answer in Optimal Design:
    What is the difference between multimodal optimization and optimal solution?

    I know that multimodal optimization designed for multi-solutions, and we are our goal that we get in the end the best solution. 

     but I am now confused, since we can get the best solution alone, why use a multi-optimizations and I finally will get the result equal ? Is this related to exploration and exploitation?

    Esra'a Alkafaween · Mu’tah University

    Thank you Antonio

  • Steve Wang added an answer in Virtual Museum:
    Virtual museum collections of skeletal material?

    Hi folks

    I wonder if any of you have experience working with Virtual museum collections of skeletal material?I'm familiar with Digimorph and I use it for teaching.  Are there others that you use, and particularly are there any working at the population level with multiple examples of each species?

    Thanks everyone.

    Declan

    Steve Wang · CUNY Graduate Center

    Another U Texas Austin product:

    http://www.eskeletons.org/

    this is entirely for those in primatology and anthropology -- it's comparative primate morphology.

    scroll all the way down the home page. on the lower right-hand corner, you will see add'l links titled:

    • 3D PRINTING
    • eFOSSILS (hominin fossil record)
    • eLUCY (Lucy, you know, the famed Lucy!)
    • eFORENSICS (coming Fall 2015)

    ENJOY! :-)

  • Shashi Vardhan Naidu asked a question in MODIS:
    How to choose, the peak value in the calculation of PSNR where the pixel values range from -1.0 to 1.0 for MODIS images?

    In most internet sources , it is not clearly mentioned as to consider the peak value or the range. In my case peak becomes 1 and range is 2 , so what should i go with ?

  • Naga Raja Paidimarri asked a question in Aspen Plus:
    Is it possible to simulate an electrolysis system in ASPEN Plus, if possible are there any specific modules available?

    For my project on electrolysis it would better if i simulate it , So is it possible to simulate electrolysis in ASPEN. I am aware of a ASPEN module regarding the electrolyte systems but nothing regarding electrolysis

  • Ben Bachmair added an answer in Education Research:
    What is your opinion about the advantages and disadvantages of the use of Vygotsky's cultural historical approach in educational research?
    Today many pedagogical research using this theory.
    Ben Bachmair · University of London

    I see Vygotsky in the historical epistemological line of learning as appropriation which is an outcome of the social and political turbulences at the end of the 18th century. The key name is Wilhelm von Humboldt (not: Alexander) and the theory of Bildung/ appropriation. Humboldt's idea was to see learning as a dialect and mediated process of the formation of subjectivity by appropriation of cultural objects. This was a counter-reaction to Rousseau's idea of learning as unfolding of already existing capacities. Piaget is the 20th century version of Rousseau's 'unfolding' theory of learning. Vygotsky in the turmoil of the Russian Revolution tried to reconsider as psychologist the development of subjectivity and personality inclusive learning mediated in and by social contexts. Therefore Vygotsky was in a severe debate with Piaget's 'unfolding' theory of learning. In contrast Vygotsky tried to understand the socio-cultural contextualization of learning as a dialectic process. I am rather sure that the mantra-like debate about Vygotsky's idea of 'zone of proximal development' and its scholastic version of 'scaffolding' subdues Vygotsky's endeavour under the hospices of Piaget's 'unfolding' concept. Leontyev, one of the younger discussants of Vygotzky made the appropriation model more visible despite the Marxist rhetoric of Leontyev does not makes it easy to distillate the basic ideas.

    For me it seems really helpful to look for another authors of the same time and with the same socio-cultural framing of the development of subjectivity who works on the basis of an appropriation model: Norbert Elias. 1939. The Civilizing Process. Both together, Vygotsky and Elias, their dialectic theory of the development of subjectivity and personality in processes of appropriation, have still the capacity to contribute to the actual socio-cultural context if we identify the interdependence of structuration (Giddens) of our recent cultural turmoil.

  • Suresh Rewar asked a question in Heart:
    How oxidizing a heart 'brake' causes heart damage?

    Oxidative stress has been long known to fuel disease, but how exactly it damages

  • Riza Arief Putranto added an answer in rel Genes:
    Which gene is best suited to serve as reference gene for relative gene expression studies in rubber tree?

    In rubber tree, which gene is best suited to serve as reference gene for relative gene expression?

    Riza Arief Putranto · Balai Penelitian Bioteknologi Perkebunan Indonesia

    Hi Dejun Li, I worked also with rubber tree and did all transcriptomic and gene expression. Hannah was right. For each experiment, you should have a package set of reference genes like mentioned in Heping Li's paper. The better way to ensure the right reference gene(s) is to check your cDNA used for the eperiment to all reference genes you've had. In my experiment, I found several ribosomal housekeeping genes which are stable. 

  • Philip Bromiley added an answer in Equity:
    Can anyone tell me how does the financial profitability be calculated for firms with negative equity?

    I know that is a bankrupt situation but I need to give a value for do principal components factor analysis and the formula "net profit / equity" not seems to works

    Philip Bromiley · University of California, Irvine

    I'm surprised that you have that many negative equity companies.  I'm wondering if your negative equity doesn't mean something different in your sample than it does in US companies.  

    If there really are that many negative equity companies, then they're not really odd.  Likewise, you probably don't want to treat 40% of your sample as moderate outliers.

    As I said, I'd skip the entire issue by moving to ROA, but whether that is acceptable depends on your discipline.

  • What is the relationship between spatial autocorrelation in SDM and environmental data selection?

    One of the steps in the preparation of a model for the exploitation of species distribution (in current or future conditions) is the statistical analysis of spatial autocorellation between enviromental raster data.

    How much autocorellated data influence a model ?

    if i use all (let say the 19 Bioclim data) and then remove the high (> 0.7) correlated variables, i don;t see any improvement on my results (or drop in the accuracy - spatial extend).

    Any advice on how to handle them ?

    There is a lot of literature around based on case studies so any on hands experience could be more helpfull.

    Dimitris Poursanidis · Foundation for Research and Technology - Hellas

    Thanks Robby and Maurizio. PCA is what i will use for the WORLDCLIM dataset.

    For the autocorellation of the presence data, what i do is an occurence thinner / remove duplicate records from same pixels.

    All data (18000 records) are from literature georeferenced locations.

  • Prabhat Chandra Mondal added an answer in Gynecology:
    Is female sterilization using Pomeroy's Technique justified in all cases?

    As per rule/law, at least in India, we have to perform female sterilization with Pomeroys technique. But over the years, I came across several cases, where I feel this technique should not be used in some cases. For example
    Previous 3/4 cesarean section
    Previous rupture uterus and scar dehiscence this time
    Scar dehiscence without labour in previous one scar
    If we perform pomeroy's technque in these cases, there is a little chance of spontaneous recanalization, and surgical recanalization is never intended or advised in such cases.

    Prabhat Chandra Mondal · Bankura Sammilani Medical College

    I think Dr. you are making it a game. 

    You said, "We dont have option of any technique in India. I suggest fimbriectomy should be done after discussing with patient and husband, in these situations."

    Later you said,"Cauterization or crushing the tubes is not allowed."

  • How to remove the attachment of a publication?

    I want remove the full text of me publiction

  • Nagarjun Kasaraneni added an answer in Vitronectin:
    Is there a way to confirm an assumed protein coating of a plastic well?

    We coat "tissue treated plastic" with different proteins and would like to confirm that the amount we add to the wells also remains as coated proteins after one night of incubation. Is there an assay to measure protein content in the wells? The proteins we are using is collagen type I, osteopontin and vitronectin.

    Regards from Amsterdam,

    Sara

    Nagarjun Kasaraneni · Texas A&M University

    The simple experiment to do is plate the concentration gradient protein and after overnight incubation carry out a Bradford assay on the plate by adding Bradford agent directly onto the plate.  Compare the amount of concentration you obtained to the actual plated concentration. This assay will help you with confirmation of the plating and if any protein is denatured during overnight incubation. 

  • Maniram Kumar added an answer in Spirituality:
    Is there a "philosophy" approach to define spirituality?

    I have a student interested in comparing different fields' definitions of spirituality and/or approaches to defining spirituality. She's hoping to incorporate a "philosophy" perspective. Broad topic, obviously, but any suggestions for a representative article?

    Maniram Kumar · Dr. Sivanthi Aditanar College Of Engineering

    Kindly read this paper on Kundalini Gnanam: the mystical way of South Indian Siddhars. Hope this will be useful

    - Maniram 

  • Does anyone know about C, C++ or Matlab implementations of "direct plug-in" method for bandwidth selection in kernel density estimation problem?

    I need to add to a Matlab function of mine the capability to perform (univariate) kernel density estimation. Unlike R's "KernSmooth" package, Matlab does not support direct plug-in method (dpi) for bandwidth selection as  suggested by Wand (1995, Data-Based Choice of Histogram Bin Width), but I need just that. Anyone knows about free-of-charge code implementing dpi?

    Francesco Sigona · Università del Salento

    Hi Giorgio, many thanks for your reply. Meanwhile I have "translated" to Matlab some mixed R/Fortran functions from source package KernSmooth that do the job: dpik, bkfe, linbin. Calling R from Matlab was not an option for my in this particular case (I did it in other applications, calling Rscript by the matlab system command).

    See ya.

  • Zeynep Orhan added an answer in Ethanol:
    How can I eliminate ethanol contamination from phage DNA samples?

    I isolated M13 phage DNA from bacteria cells with NaI and ethanol steps (for sequencing of phage DNA), but I got very low values of 260/230 as 0,2. I think I have ethanol contamination in my samples. Could anyone help me how I can eliminate ethanol contamination from my DNA samples?

    Zeynep Orhan · Bilkent University

    thank you very much

  • E. Fiona Bailey asked a question in Wills:
    I would like to perform CO2 rebreathing to determine CO. Would anyone be willing to share the details of their experimental protocol?

    I have the  references of Heigenhauser and Jone among others but would really benefit from more detailed instructions regarding the experimental set up and procedure.

    Thank you.

  • Heino Martin Heyman asked a question in HTTP:
    Want to download this article?

    Downloadable for free until the 2nd of June 2015 via the following link:

    http://authors.elsevier.com/a/1QsPL,8MXwU0Cx

  • Prem Rajak added an answer in Catalase:
    How do I prepare the standard curve for H202(800micromoles) and use it to calculate catalase activity using sinha's method?

    I want to apply the method by Sinha 1972?

    Prem Rajak · University of Burdwan

    Sir, Mehdi Hedayati, i am getting the concentration of 30% H2O2 soln (w/w, Merck) as 9.76M/L using d=1.11. By this method,  1uL is needed to in 9999ul of ddH2O to make a soln of 1mM. [9.76V=0.001*10]. kindly make a correction in it,if it is wrong.

  • Bruce Weaver added an answer in Multicollinearity:
    How can I calculate VIF (Variance Inflation Factor) in Cox regression using R software?

    Hi, I am currently investigating the impact of D-dimer level on prognosis in patients with metastatic gastric cancer.

    Because the variable of interest was significantly associated with several covariates in Chi-square test, I think that the multicollinearity among these variables should be taken into consideration before Cox regression analysis.

    Is it possible to calculate VIF in Cox regression (R or SPSS software)?

    Bruce Weaver · Lakehead University Thunder Bay Campus

    No worries, Olivier!  ;-)

  • Thierry Chopin added an answer in Seagrass:
    Can any one provide litrature on marine plant and associated animals?

    We are currently working on epiphytic infestations in commercial seaweed farming. It would be nice, if some one could share literature on interaction studies between host (algae) and epiphytic organisms also chemical and molecular signalling. The references pertaining to other marine plants such as seagrass also would be welcome addition.  

    Thierry Chopin · University of New Brunswick

    I would recommend the book by Chuck Amsler:
    Amsler CD, Ed., Algal Chemical Ecology (Springer-Verlag, 2008). Paperback edition in 2009.
    and other publications by Chuck.

  • What are the methods for estimation of light induced defects in chalcogenide glasses?

    Explain and give suitable explanation. 

    Anjani Kumar · Harcourt Butler Technological Institute

    Thanks Prof Roughani for your nice discussion kindly tell any more methods also. 

  • Gerald Mcclain asked a question in Feet:
    How can you use the constant temperature of the ground 5-400 feet deep to heat and cool your home or business?

    Rather than use the amibuent temperature which varies from -15 degrees to 110 degrees F outside air.  How do you transmit the stored energy from the earth to a heating/cooling system?

  • What does Loschmidt's paradox tell us about the second law of thermodynamics?

    Also known as the reversibility paradox, this is an objection to the effect that it should not be possible to derive an irreversible process from time-symmetric dynamics, or that there is an apparently conflict between the temporally symmetric character of fundamental physics and the temporal asymmetry of the second law.

    It has sometimes been held in response to the problem that the second law is somehow "subjective" (L. Maccone) or that entropy has an "anthropomorphic" character. I quote from an older paper by E.T. Jaynes,

    http://bayes.wustl.edu/etj/articles/gibbs.vs.boltzmann.pdf

    "After the above insistence that any demonstration of the second law must involve the entropy as measured experimentally, it may come as a shock to realize that, nevertheless, thermodynamics knows no such notion as the "entropy of a physical system." Thermodynamics does have the notion of the entropy of a thermodynamic system; but a given physical system corresponds to many thermodynamic systems" (p. 397). 

    The idea here is that there is no way to take account of every possible degree of freedom of a physical system within thermodynamics, and that measures of entropy depend on the relevancy of particular degrees of freedom in particular studies or projects. 

    Does Loschmidt's paradox tell us something of importance about the second law? What is the crucial difference between a "physical system" and a "thermodynamic system?" Does this distinction cast light on the relationship between thermodynamics and measurements of quantum systems?  

    Sofia D. Wechsler · Technion - Israel Institute of Technology

    Dear H.G., Dr. Alfredo, and the other users interested in the Loschmidt paradox,

    I apologize for my question, but, who of you read indeed Loschmidt's original article? Some people discuss this paradox, first describing it by some variant that they imagined. It's not correct. People should refer to the actual work, not do modifications as they like.

    It seems that the work of Loschmidt was never translated in English. I am not sure of that, and if somebody knows such a translation, PLEASE TELL US.

    I am trying to do such a translation, and as far as I advanced with it, Loschmidt seems NOT to have worked with an ideal gas, i.e. NOT with point-like molecules, but with spherically symmetrical balls. Let me tell you that for such objects, the evolution of the gas is DETERMINISTIC. The probabilistic treatment is necessary ONLY because of our limited computing probability.

    Now, if the evolution is deterministic and if leads to an increase of entropy, how can one return to low entropy? And how can one obtain reversibility?

  • Saleheh Shahmoradi asked a question in Electrospinning:
    Does time delay between two stages of electrospininng have effect on nanofibers on foil?

    I wanna use electrospinning to fabricate PCL scaffold. but I have to use time delay. does it affect on nanofibers?

  • Emile Alghoul asked a question in Culturing:
    Hello, does someone have the protocol for culturing endometrial cells from a biopsy?

    I want to culture endometrial cells to confluence into culture dishes. I want to know if someone has a good protocol with the mention of the need of coated dishes or other special equipments. Thanks in advance.