Q&A

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  • Hongtian Yang added an answer in Hela Cells:
    Can anyone provide me Lentiviral transfer vector (2nd generation) for the expression of desired gene of interest?

    I want to over express my gene of interest in HeLa cell line, I will be highly grateful if some one can provide me Lentiviral transfer vectors (2nd generation with GFP/RFP).  I do have psPAX2 and pMD2.G for packaging and we are regular in the generating lentiviral particles to knockdown gene of interest.

    Hongtian Yang · Louisiana State University Health Sciences Center New Orleans

    I would also be interested to find out the overexpression vectors. What I used to do is to use pLL3.7 (also available from addgene) vector for both gene knockdown and rescue. I replaced gfp with gfp fusion protein containing gene of interest under CMV promoter, while shRNA is inserted after U6 promotor. I guess it would work for overexpression by only manipulating protein after CMV promotor without shRNA insertion.

  • Have I found a new way to the concept of DERIVATIVE?

    Given an algebraic system based on polarities on the sphere. A pair of opposite points and their equator constitute a basic element. (Add the equator to Riemann's unification of opposite points in elliptic geometry.) Two elements determine a resulting element of the same set. This is a partial binary operation with two axioms: ab = ba; (ab)(ac) = a. I call any set of this type a projective sphere. (Cf. Baer's finite projective planes and Devidé's plane pre-projective geometries.) From these axioms a number of important properties can be deduced. For example, if the set has at least two elements a and b, then xx cannot be properly defined for the whole set, because (ab)(ab)=a=(ba)(ba)=b contradiction. This means that in the general case xx must remain undefined, as with the case of division by zero in fields. However, if a smooth curve is given on the sphere, or an oval in a finite set, then the xx operation CAN partially be defined for the elements of the curve or of the oval as the tangent to the given point. Example: given the oval of the four reflexive (self-conjugated) elements in a 13-element finite sphere; the derivative consists of the same four elements. Another example: Given the basic elements on the sphere with homogeneous coordinates. Take the circle with center (1,0,0) and radius pi/4, given by elements (1,√(1-c^2 ),c); its derivative is the curve given by elements (-1,√(1-c^2 ),c). In this interpretation, the derivative does not represent the number indicating the slope of a straight line, but a set of the same type of geometric objects out of which the original curve is made. Also, this gives that every smooth curve evokes a geometry of its own, defined specifically for the given curve.

    István Lénárt · Eötvös Loránd University

    Dear Satyabrata, thank you very much - kind words are always welcome. I will do my best to publish something in this topic.

  • Juehui Shi added an answer in Phototherapy:
    Do you think that older people may benefit from phototherapy?

    Older people are often more exposed to artificial light because of mobility problems perhaps influencing mental states. For instance, lack of exposure to natural light might impact mental state.

    Do you think that older people may benefit from light treatment simulating expose to natural light conditions?

    Juehui Shi · University at Buffalo, The State University of New York

    We shall embrace the nature.

  • Does anyone know if the molecule Zsgreen can be detected with a GFP antibody? Have you ever worked with animal models?

    I am working with a vector named as "pLVX-IRES.Zsgreen. It contains a green tag called "Zsgreen" instead of GFP and I am using it in animal models, but I am not able to detect itself so I need to perform immunofluorescence within the tissues. 

    Stephen Lewis Beauparlant · Tufts Medical Center

    Although Green Fluorescent, GFP and zsGreen share NO homology, therefore GFP antibodies wont work. As far as antibodies on the market, I have tried clonetech 632474 RAb, and so far it BARELY works in tissue IF. I am currently working on protocols to maintain the fluorescent signal in fixed (4%paraformaldehyde) tissue. I work in the mammary gland, and using a fluorescent, dissection microscope I can see my zsGreen+ structures easily in whole mount.

  • Alex Russell added an answer in Hair:
    Is it true that bald researchers are better researchers?

    Samson's strength was in his hair. What happening with the researchers? Does the bald researchers are more effective researchers? How the presence or absence of hair affects the activity of scientific researchers?

  • What is the best alternative for the Support Vector Machine?

    Support Vector Machines (SVM) typically suffer from drawbacks concerning the choice of the kernel, low speed, high algorithmic complexity, and intense memory requirement. What is the best alternative for the SVM, which mitigates these problems?

    Mustafa Üstüner · Yildiz Technical University

    Import vector machines

    http://www.ipb.uni-bonn.de/ivm/?L=1

    SVM+

    http://www.ece.umn.edu/users/cherkass/predictive_learning/SOFTWARES.html

    http://en.wikipedia.org/wiki/Nelder%E2%80%93Mead_method

  • Kelvyn Jones added an answer in Likert Scale:
    How can I correlate ordinal variable (attitude Likert scale) with continuous ratio data (years of experience)?

    Currently I am working on my dissertation which explores learning organisation characteristics at HEIs. One of the predictor demographic variables is the indication of the years of experience. Respondents were asked to fill in the gap the number of years. Should I categorise the responses instead? as for example:

    1. from 1 to 4 years

    2. from 4 to 10

    and so on?

    or is there a better choice/analysis I could apply?

    Kelvyn Jones · University of Bristol

    Four options are

    1 treat as a nominal category as you suggest - and use dummy variable coding you need to make sensible cutoffs and the number of categories can grow and become problematic if you are interacting this variable  with other variables

    2 create an ordinal variable and use orthogonal polynomial coding that exploits this ordinality - this can be quite parsimonious

    3 Treat as a numerical variable and fit say linear, quadratic and cubic model - looking for the most parsimonious fit - this model can be rather inflexible

    4 Treat as a numerical variable and fit  underlying smooth relationship as in a General Additive Model which can be very flexible and parsimonious

    Much will depend on the nature of your data and your experience.

  • Md. Ashaduzzaman added an answer in Electrospinning:
    What is the most efficient method to prepare a stable sol of TTIP/PVP for electrospinning?

    For preparing TiO2 /PVP nanocomposite by electrospinning, I mixed a TTIP/2-propanol (20 wt%) + 2 mL glacial acetic acid + 2.5 mL PVP/2-propanol (10 wt% or 8 wt%). Upon dropwise adding TTIP/2-propanol (20 wt%) to acidic polymer solution the solution turned cloudy instead of remaining transparent (used PVP is 360,000 g/mol).

    Md. Ashaduzzaman · University of Dhaka

    Do you have low Mw of PVP? Then try to use and observe what happen?

  • Abdulaziz M. Ghaleb added an answer in MATLAB:
    Extracting image from avi video?

    I've used some Matlab codes for image extracting from geovision camera (.avi video) but I faced this error ("The file requires the following codec(s) to be installed on your system:GMP4"). I cannot solve this problem after installing GMP4 codec!!! I can play video with some players like windows media player. does any one know how can I do it.

    Abdulaziz M. Ghaleb · Qatar Mobility Innovations Center

    You can try video cutter and cut the portion you want and save it with different format.

    Hope this help

  • Volker Linss added an answer in XPS Peak:
    What is the relevance of C correction in XPS analysis?

    I have taken the XPS of Ti3SiC2 and after deconvoluting the peaks, it shows the following peaks without any correction.

    for C1s at B.E.  281.1eV ( very small),  288.3eV ( medium intensity ) and 293.4eV ( high intensity)

    for Ti2p at 462eV, 466eV (high intensity), 472eV

    fro O1S at 539 eV ( intense) and 535eV ( less intense and broad)

    What may be the reason for the peak shift?

    whether the C correction is mandatory in XPS analysis? while doing the Correction which peak in C1s spectrum have to be considered? The one which is more close to the reference value or the most intense peak?

    I will be happy and thankful if anyone can help me to solve these questions.

  • Basant Hamdy added an answer in Cancer Cell Line:
    How can I transport cell lines from one country to other?
    What is the best method to transport the cell line? What are the legal issues, courier problems, cargo issues in airports?
    Basant Hamdy · Tanta University

    In case of transportation in sealed culture flasks full of media, what is the recommended technique for distributing these cells among several culture dishes??
    should i centrifuge part or the whole medium-containing cells ???

  • Claire Chenu added an answer in Texture:
    Are there simple protocols to measure soil texture -plus other significant physical properties?

    What authors/references would you recommend? Are there modifications to Bouyucos for organic rich soils? THANKS!!

    Claire Chenu · AgroParisTech

    you can have a look at :

    http://www.soilquality.org.au/factsheets/soil-texture

    but if your soils are organic, this will very likely not apply as organic matter modifies soil mechanical properties

  • Mustafa Üstüner added an answer in SAR:
    Does anyone have experience with SAR image classification?

    Dear all, I am trying to classify a SAR image using machine learning algorithms. I am finding difficulty in choosing an appropriate approach. Also, once a technique is chosen (SVM or Random forests or any), how do I transform the SAR image training samples into the required format suitable for the classification approach? I am trying this in Python. Any help is highly appreciated. Thanks very much!

    Mustafa Üstüner · Yildiz Technical University

    Test "supervised wishart classification" which is available in Sentinel toolbox...Hope it helps you... I would suggest also SVM... 

    Moreover if the SVM or RF is not enough for you, you could work on ensemble learning or information fusion.....

  • Yuan-Yeu Yau added an answer in Gene:
    I want to get the positions of a gene or its regulatory elements in the given region. Can details regarding this be found anywhere in a websites/database?
    I want take out all the genes falling under a given start and stop position of all the genes deletion/duplication. Is it possible to get that ? If its possible, then please let me know.
    Yuan-Yeu Yau · Northeastern State University

    Depending on which plant species you are studying-- some genes and their regulatory regions are well studied in some species (such as model plants) and have been stored in databases, then you can get these info, otherwise you cannot.

  • Rob Catlett added an answer in Economic Policy:
    What kind of economic theoretical framework could we use to study the effect of independent monetary and fiscal policies on economic growth?
    In countries like Iran, the lack of independence between monetary and fiscal policies causes many economic problems such as price fluctuations, inequalities of AD and AS etc. This strong correlation between these two policies also influences the rate of economic growth. If we want to demonstrate the role of this problem in economic growth and solve the consequences, we need an economic theoretical framework.
    Rob Catlett · Emporia State University

    This is an interesting question, especially about the independence of monetary and fiscal policy. John Ryding's answer is helpful, especially in the observations he presents; the detail is impressive. Luca Deidda' suggestion is among my favorites; dynamic general equilibrium models seem to capture the best of macro models.

    I want to go in a different direction because the lack of independence of fiscal and monetary policy is especially challenging, especially in disentangling their respective impacts.  My suspicion is that countries where there is little or no independence of monetary and fiscal policy tend to be in disequilibrium longer and fluctuate more and recover slower than the opposite type of countries.  At least I would like to test these hypotheses.  Obviously, it would be important to control for several things (e.g., advanced economies,  political stability, and others).

    It seems to me that macro models each have advantages and limitations.  I am not sure if there is one model that fits all you are seeking; however, if any of my conjectures above are correct, then perhaps assessing fiscal and monetary measures as a composite might be interesting. Some of the rational expectations ideas might provide some insight.  

    I hope this helps. It is an interesting question.

  • Vladimir Morozov added an answer in SDS-PAGE:
    Running two SDS-PAGE in the same tank. One is running normally, the other is not. Any ideas?

    Both the gels have 5% stacking and 10% resolving. They are essentially copies of each other and they even have the samples. One of them is running while the other is not. I'm running them at 200V.

    Vladimir Morozov · Robert Koch Institut

    Hello Anand,

     There should not be the any difference during migration of two gels. Besides the residual tape that was  mentioned above by Phillip,  check for the air babbles "sticking" to the gel at the bottom.

  • Joseph F McDonald added an answer in Car:
    What is the deal with Liquefied Petroleum Gas car?

    A recent discussion on pollution affecting landmark buildings has inspired me to ask this question. In big cities in India, currently there is a move to switch to LPG-based vehicles like LPG-based auto-rickshaws (three-wheelers), LPG-based cars etc. The LPG-based cars have the advantages of very low pollution (compared to petrol or diesel based cars) and LPG-based cars are good for the environment. I have also read about some safety issues with LPG-based cars.

    What is the deal with LPG car? Your views are welcome! - Sundar

    Joseph F McDonald · United States Environmental Protection Agency

    Gasoline-fueled light-duty vehicles in the U.S. are among the lowest polluting vehicles in the world and are now nearing zero emissions of criteria pollutants.  There are numerous vehicles certified as LEV-II SULEV or Tier 2 Bin 2 that achieve combined NMOG+NOx emissions of less than 30 mg/mi and PM emissions of less than 1 mg/mi.  This is roughly equivalent to the lowest emitting natural gas fueled vehicles (Honda Civic GX) or better and is significantly lower than spark-ignition vehicles converted to LPG.  Instead of subsidizing a particular fuel, environmental goals may be better served by focusing on stringent standards for NOx, NMOG, PM and CO2 and by reducing sulfur levels in all fuels (gasoline, diesel, NG, LPG, including mercaptans added as odorants to gaseous fuels) to enable the use of very high efficiency catalytic emissions controls.

  • Is this model of power network theoretically correct ?

    Hi every body,

    I want to simulate a power network with two generators and transmission line and a R-L load in matlab. the figure illustrate this system:

    I write the one phase equations of this model as below

    But result of simulation is unstable!

    Is this model theoretically correct  ?

    Hamed Shakouri G. · University of British Columbia - Vancouver

    To answer Mina's question:

    It depends on the power factor of the load which is usually leading in phase (inductive). With a high pf (as for a residential area), the answer is yes. As we know the maximum power transmission occurs when the load impedance is conjugate of the Thevenin equivalent of the network at the load nodes. So the load should be lagging phase (negative inductance: compensated with capacitors), which means higher (positive) inductance for the Thevenin equivalent.

  • Is random forest better than support vector machines?
    I have some problems when comparing machine learning algorithms. Sometimes support vector machines gives better results than random forest. But not always. How do we compare these two algorithms?
    Jose A Fernandes · Plymouth Marine Laboratory
    It seems to me that the difference in accuracy in not so big. Is that difference statistically significant? What is the variance? Have you performed a paired t-test? I would recommed corrected paired t-test. You can also use repeated cross-validation to reduce your variance. Random forest is usually superior in a problem that is similar to yours: Automatic classification of Zooplankton. I dont know in your problem, but in the case of Zooplankton, there is many classes (30-50) and there are classes with hundreds or thousands of examples, but in others only a few (imbalance). Therefore you have to look further than only at the accuracy, since that can be due the one or two most abundant classes can be being well classified, whereas all the rare examples are misclassified. So, you need to look at other metrics such as true positive or area under roc curve. But, all this depends at the final objective of the classification for your specific problem. For Zooplankton classification, that difference you get would be insignificant for the biologists and they will care more about that certain classes have a minimum of performance. However, these classes could change depending on the biological problem that they want to answer. Maybe this paper can be relevant to you:
    https://www.researchgate.net/publication/228658125_Optimizing_the_number_of_classes_in_automated_zooplankton_classification?ev=prf_pub
  • M. Mozaffari added an answer in Co-precipitation:
    How can I Synthesize Sn doped Iron Oxide Nanostructures ?

    I want to Synthesize Sn doped Nanostrucutres with Iron and Sn Chlorides by Co-precipitation method... 

    M. Mozaffari · University of Isfahan

    Dear Artavazd;

    In hydrothermal process, heat treatment at 200°C is not a low temperature because of high pressure. Instead it is a relatively high temperature, may be equall to 1000°C in conventional process.

  • Can any one help me in carrying out the execution of weed classification using a SVM classifier?
    My topic is to classify the weeds from crops using texture classification. i am working on satellite images
    Mustafa Üstüner · Yildiz Technical University

    http://www.cs.waikato.ac.nz/ml/weka/

  • Chun-Sheng Ruan added an answer in Life Sciences:
    Does a short communication paper carry the same impact factor as the full length paper?
    Or simply what is the weightage difference (in terms of service for sciences) between the two?
    Chun-Sheng Ruan · University of South Australia

    It can not be simply distinguish which one is better. I think they serve for different functions. Assuming to use the same research topic for publication, you probably can only choose one type of them. It really depends on your information you want to deliver to the scientific field. Both types of publication carry new information.

    If you want to send an important and urgent signal, for example, you found a new type virus rapidly spreading in the world, or you found a clinical case which can not be explained by the current knowledge, choosing a short communication will be much much better than spending many years for a thoroughly detailed paper, a detailed investigation can be published further to support your findings.

    On the contrary, some of full papers may not be suitable to be published as a short communication, because the conclusion of the findings links with a serial of detailed experiments,  a simply short communication may be weak to spread your idea.

    FYI. All the best . 

  • Shaina Alysa Kelly added an answer in PECVD:
    What is a good RIE etching formula for generating smooth structures in SiO2?

    I am etching quartz substrates with a March Plasma RIE machine (but also have access to a PECVD Oxford PlasmaLab80 if necessary) and would like to produce 60-100nm deep trenches in the areas not covered by a copper mask. I also would like these trenches to be as smooth as possible with minimized sidewall tapering.  

    I know there are many RIE formulas out there, but was wondering if anyone had some they knew worked particularly well for these machines and the desired output? Thank you in advance!

    Shaina Alysa Kelly · University of Texas at Austin

    Mohamed,

    Thank you again for your reply. I am new to this sort of fabrication style and appreciate the help. 

    Yes, the Cu mask (thin film) is very thin; it is 20- 30 nm. Also, you are correct that the smallest dimensions are less than 1 um; some of the smallest trenches are 200 - 500 nm wide.

    In regard to your third point, yes, the smaller trenches are initially open after shadow mask deposition. I have inspected the samples with an SEM before etching procedures and confirmed this.

    So from what I gather from your responses, it appears that minimizing redeposition is the way to deal with properly etching the small CD features. As a review, to etch small CDs and help eliminate redeposition I should:

    1a.) try using a mask that achieves volatile byproducts (neither Cu or Al do this with flourine gases alone); OR 1b.) use an etching formula (like incorporating Argon) that does produce volatile byproducts.

    Are there any other techniques to minimize the predominance of redeposition over etching? Overall, would you still recommend Al over Cu? I will start to look more into the redeposition vs etching  issue in the literature...

    Thanks again,

    Shaina

  • In psychotherapy/counselling, some clients take time to build up trust with the therapist. How can trust be built quickly?
    Is this a process that can be managed, or does it simply take as long as it takes?
    John Christopher Muran · Adelphi University

    One way would be to address early dysfluencies in relatedness or ruptures in the therapeutic alliance.  Trust is an important component in the alliance.  See attached for definitions & strategies.

    Developing Therapist Abilities to Negotiate Alliance Ruptures
    Muran, J.C, Safran, J.D, C. Eubanks-Carter
    The Therapeutic Alliance: An Evidence-Based Guide to Practice, Edited by J.C. Muran, J.P. Barber, 08/2010: chapter Developing Therapist Abilities to Negotiate Alliance Ruptures: pages 320-340; Guilford Press, New York, NY., ISBN: 1606238736

  • Mohammed Alhaj added an answer in MTT Assay:
    Among DMSO and MTT dissolving solution (containing HCl, isopropanol and SDS), which is better in an MTT assay?

    Some studies have shown use of DMSO to dissolve the formazon crystals, while some have used MTT dissolving solution. DMSO is rapid and produces colour within seconds, while using MTT dissolving solution may need some time for getting proper OD readings 0.75-1.25. Which is reliable? Please suggest.

    Mohammed Alhaj · King Saud University

    both DMSO and isopropanol/HCl gave a color immediately after added to cell culture

     but before read the absorbance it is better to shake plate for 5 minutes 

  • Vladimir Farber asked a question in Imaging:
    Can somebody recommend references on the technique for imaging of the occluded objects?

    I am mainly interested in the understanding the techniques used for this and in algorithms for recovering the occluded objects from the acquired data. Can somebody recommend relevant references? Thank you in advance!

  • Gena Lasko added an answer in Fecal Sampling:
    Can anyone help me to identify the structure I found from bird droppings?

    I recently work on the diet analyses for woodland migrants. I found couple of spring-like and brown or pinkish structures from bird fecal samples. It feels like rock or iron when I try to break it. Does anybody know what they are? Thanks in advance!

    Gena Lasko · California Department of Fish and Wildlife

    They resemble some sort of pupae a little like #3. Cant really see the ends in the photo. Were you able to break them?

    http://ipm.ncsu.edu/AG369/keys.html

  • Deborah Jean Verran added an answer in Social Media:
    Are there any studies on the correlation between social media use and personality traits? or social media use in general?

    I plan to do my thesis on the correlation between social media use and narcisstic personality traits

    Deborah Jean Verran · Royal Prince Alfred Hospital

    Here is another reference-

    The relationship between personality traits and social media use

    http://www.sbp-journal.com/index.php/sbp/article/view/2793

    As use of social media is becming pervasive I would have thought it would be useful to also characterize what is currently felt to be an acceptable rate of use versus what is felt to be excessive. There is some literature on the benefits of social media and also some on the harms-eg trolling, abusive behaviour online.

    If your university has a good online library with the appropriate access to publications then I would set your search terms after some preliminary reading and then start delving into the literature a bit more.

  • Yuan-Yeu Yau added an answer in PCR:
    what the causes of faint PCR product ?

    I  optimized my PCR Reaction and it gave me very good result , after that some  PCR product samples start to appear very faint in comparison with the other samples and the product of the first reactions i did !!

    Does I have to change the PCR condition or it is a problem of the quality of DNA used  ??

    Yuan-Yeu Yau · Northeastern State University

    Hopefully, your template DNA has not digested away by contaminants:

    1. Did you use a commercial kit for your DNA extraction? This generally increase your DNA purity (avoid contaminants) compared to use home-made solution for isolation.

    2. Store your aliquot DNA in -20C, instead of 4C.

  • In teaching English as a Foreign Language, how much of the class should be about culture?

    Most teachers agree that teaching the culture of nature speaking countries is valuable, but how MUCH should this be done?  Do you have a percentage in mind or other way of saying how much of the course should be about culture?

    Dejenie A. Lakew · John Tyler Community College

    Language is a part of a culture of society and studying the culture enables one to easily know the basis of the social meanings and usages of words and narratives of the  language under study. But to study or learn it as a foreign language, it is not a necessity. As a matter of fact English as a foreign language is taught by local people of non-English speaking countries who have no cultural background of the English speaking people who themselves have different dialects and cultures today.

    The American English is different from the British and the British is different from people of other continents. In most cases the language is studied for academic purposes,  for reading English documents and communicating with the language to teach non-English subjects such as mathematics or physics which do not require any cultural flavor of the language. Teaching mathematics in English for instance requires less English, as it by itself  has its own language system of abstraction.