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  • Liya Liang asked a question in Saccharomyces cerevisiae:
    Who can tell me the detailed method for the plasmid in Saccharomyces cerevisiae that can be removed by counter selection of URA3?

    I transformed a URA-selection plasmid into Saccharomyces cerevisiae and then I want to remove the plasmid for further research and I saw some papers suggest it can be removed  by counter selection of URA3. Who did this before or is there anyone have the detailed mothod? Thank you very much.

  • Nathan Rice added an answer in Spatial Autocorrelation:
    Does anyone know about autocorrelation in spatial modeling by logistic regression?

    I am wondering if anyone here has ever dealt with spatial autocorrelation using Logistic Regression in GIS.

    In the literature I have read so far, sometimes the issue is not even addressed. In other instances, the authors used the geographic coordinates as covariates. For example, quoting from Hu, Z., & Lo, C. P. (2007). Modeling urban growth in Atlanta using logistic regression. Computers, Environment and Urban Systems, 31, 667–688: "The second step was including spatial coordinates of data points into the list of independent variables. Spatial autocorrelation can be alleviated to some extent by attempting to introduce location into the link function to remove any such effects present (Bailey & Gatrell, 1995). For example, spatial coordinates of observations might be introduced as additional covariates, or to classify regions in terms of their broad location and treat this classification as an extra categorical explanatory factor in the model."

    At the best of my understanding, the latter approach is termed "autocovariate" modeling by: F. Dormann, C., M. McPherson, J., B. Araújo, M., Bivand, R., Bolliger, J., Carl, G., … Wilson, R. (2007). Methods to account for spatial autocorrelation in the analysis of species distributional data: A review. Ecography, 30(5), 609–628. http://doi.org/10.1111/j.2007.0906-7590.05171.x

    I would like to know your opinion on the issue, and what approach you happened to use.

    Nathan Rice

    Hi Gianmarco, 

    Thanks for starting this thread. I am working on a similar problem. Did you find a good solution?

    I am trying to figure out how to calculate a Join Count statistic for my model and then incorporate the correlation structure into my logistic regression. Have you tried this approach? 



  • Lilliana Ramos-Collado added an answer in Philosophy of Social Science:
    Praxis versus academic noises?

    Karl Marx states in "Theses on Feuerbach" that "The philosophers have only interpreted the world in various ways; the point, however, is to change it." (Thesis Eleven) I must admit that I'm all the more persuaded by that statement as time goes by. When was the last time you heard voices of conviction and righteousness oozed out from academia and how often do you see an academician get his/her hands dirty?

    If you want to get you hands dirty, here's a link:


    Hm, I guess this post so far has not been qualified as a question. So let me ask this: what do you think of Marx's Thesis Eleven in "Theses on Feuerbach"?

    Lilliana Ramos-Collado

    Dear dear dear, very dear Louis, going back to the feminine/masculine polarization sounds to me rather weird in this day and age. I cannot identify with it. I do not think there is a feminine side or a masculine side of a person because that is part of culture, not a genetic thing. I enjoy Pascal, but evidently some of his theories are rather dated, like this one. We are talking about Marx's pertinence today. I do not think Marx would predicate world change based on going back to Pascal's ideas of the feminine, frankly. Marx was talking about assuming responsibility of changing the world and, probably, the first thing that needs changing are those categories that define women with those feminine traits invented by culture, and which are not "natural". The very division of feminine and masculine is patriarchal, Louis!

  • Yik Hei Ng asked a question in Fetal Bovine Serum:
    Should heat-inactivated fatal bovine serum be used in murine islet cell culture?

    I am culturing primary murine islet cells, however, I am not sure about whether I should place a heat-inactivated fetal bovine serum in the media or not?

  • Gholamreza Mohammadi asked a question in Mechanobiology:
    What is the best issue in vascular biomechanics/ biomaterials?

    Hello everyone 

    I want to propose a subject for my master degree in vascular filed. I can perform simulation in abaqus or comsol moreover I can use some Lab device such as electrospining and bioreactor and maybe AFM. My prefer is to choice an issue that involve two methods. A primary simulation and validation experimental. 

    now please help me to choice the best.

    vascular tissue engineering, mechanical property or mechanobiology? which of these you offer to me?

  • Roumen Nedev added an answer in Optimization:
    How to tell if an excited state frequency calculation is converging (Gaussian09)?

    I am performing excited state optimizations, and I would like to do frequency calculations on these structures. When performing any optimization, I am able to see Max/RMS of the force/displacement and predicted change in energy in the output .log file updated over the course of the calculation. However, when I perform a excited state frequency calculation, I can only see these numbers and if they meet the convergence criteria at the very end of the entire calculation.

    My question is: how do you monitor excited state frequency calculations while they are running to see if they are in fact converging? 

    Roumen Nedev

    This transformation computes the second derivatives of the energy with respect to a Cartesian coordinates. It is valid only for a stationary point. 

  • Arturo Rivera added an answer in E-Learning:
    E-learning as revolution or evolution?

    Based on the current literature, is e-learning a overgrown fad or, natural evolution in human learning?

    Arturo Rivera

    EStimado Sebastian considero que e learning es mas que una moda ya que  existe un marco teórico abundante de teorías que sustentan la educación a traves de elearning en muchas universidades que dan testimonio del avance de la rigurosidad académica en sus procesos  didácticos y en el aprendizaje autónomo e independiente.

  • António Maximiano Fernandes added an answer in Eukaryotic Cells:
    How can I take out eukaryotic cells from solution when organic substances are sticking to filter?

    I have a solution of methanol with solvated extracellar components made by a yeast I'm growing. I'm trying to take out any stray cells that may have made their way into my solution . I just tried using a .45 nm pore filter but my solution can't even make it through other than a ml or 2.

    I am assuming this is because the solutes I am trying to isolate are sticking to the filter or each other.

    Thank you for your help. 

    António Maximiano Fernandes

    Can you dilute the extracellular components after extraction?

    0,45 nm is very small, I face this problem when filter plant extract though the pore. Sometimes we use filter applying pressure using seringue. If not, after dilution, you should filter under vaccun negative pressure

    Good Job

  • Lilliana Ramos-Collado added an answer in Visual Culture:
    Is public art "public"? Is it art? Who's its owner/its public? What does it mean? We need it? Who will preserve it? Can any such artwork be universal?

    With respect to “public art,” an examination of the state of the question points to at least two ways in which that concept may be defined, two “circles” within which it may fall: It may be related either to the space the art object is to occupy (which might be called a “public space”) or to the art object itself (which might then be called “public art”). Here, we might pose several questions that seem either to make it easier to understand the public art/ public space duality, or to make such an understanding impossible. We might, for example, ask questions about:

    Legitimacy (Is the work an art object?)  

    The constitution of the cultural imaginary with respect to what a “public space” is and what “public art” is (Does the work reflect my identity?)

    Ownership of the space and the work (Who owns what?)

    Authorship (Is the work created by an individual with personal title to it, or is it created on behalf of a collectivity?)

    Decency and decorum (Is the art appropriate to the space it occupies or will occupy, and is it suitable for being seen by men, women, and children?)

    Preservation and conservation (Who shall assume the ownership of the patrimonial work and be responsible for its explanation and esteem, defense, custody, maintenance, restoration, and permanence?)

    Each of these issues raises a debate, implicit in the very existence of the public-art object, and each debate may be different. And each potential controversy suggests its own “public,” in the sense of audience or interest group, each with its own defining expectations. Below a polemical article I wrote about a country-wide public art project:


    What is left of the project's website: http://www.artepublicopr.com/html_espanol/ambitos/1492_1898/portacoeli/fase3.htm#

    Lilliana Ramos-Collado

    Dear Barbara! Please explain why exactly you mention the copyright. Just to be sure I understand. :-)

  • Prakash S Bisen added an answer in Lead:
    How to make 50 mg/ kg lead concentration from lead nitrate in soil

    How to make 50 mg/kg lead concentration from lead nitrate in soil.

    Prakash S Bisen

    Please calculate the lead present in lead nitrate and make the mathmatical calculation as mg/Kg.

  • Janaka J. Kumara added an answer in Dam Engineering:
    What will be the initial condition or prior questions before select internal erosion test?

    In case of evaluating the susceptibility of internal erosion phenomenon in dam material (Core, filter and transitions), what will be the initial conditions to consider or prior questions before select the test I must have to do (Continue Erosion Filter test, Hole Erosion Test, No Erosion Filter).


    Janaka J. Kumara

    Maybe I didn't understand the question well, but I guess you have to consider the material type itself (so the strength parameters), compaction level, water level, how the structures are constructed, etc. 

  • Yogesh Kanna Sathyamoorthy added an answer in Cryopreservation:
    Has anyone used Fluoro-Jade stain in PFA perfused brains?


    I want to detect neuronal degeneration through the use of Fluoro-Jade C (Chemicon International).

    I have rat brains perfused with PFA, preserved 2 days in PBS(0.01M)-sucrose 30% for cryopreservation. Finally, the brains were cut in 20 um sections and conserved in PBS 0.01M.

    I used the protocol of the datasheet. After mounting the sections on a gelatinized slides, and leave them dry 30 min at 50ºC, I made the steps in the protocol.

    -5 min in 1%NaOH in 80% EtOH

    -2 min in 70% EtOH

    -2 min in distilled water...

    During the distilled water step, the sections started to swell, increasing their volume and making wrinkles in the tissue.

    I have try it with another sections and the result was the same.

    Anyone has some idea of what is happening?

    Than you in advance.

    Yogesh Kanna Sathyamoorthy

    One other tricky way to escape folding and floating is that you could do the staining procedure using pasteur pippette( dropping method). There by you add jus the right amount and control swelling and folding.

  • Roumen Nedev added an answer in Multiobjective Optimization:
    How to find the value of Epsilon where using Epsilon constraints method?

    Using Epsilon constraints method to solve multi-objectives problems How to find the value of Epsilon? Any easy method?

    Roumen Nedev

    In a multi-objective problems any different objective function has a different optimal solution. There is no optimal solution for all objective functions, but some solutions are better, than others. First you should decide if the epsilon will be predefined, or computed interactively during the optimization process. 

  • U. Dreher added an answer in Circuits:
    Who knows the properties and the working principle of this circuit?

    Recently I came across with the shown circuit.

    It has some interesting properties. Is there anybody who has used such a circuit already? Both opamps are assumed to be ideal.

    U. Dreher

    I asked my 'friend' once again:

    NO - all voltages are perfectly symmetrical with respect to ground. (Symmetry cause by the single resistor to ground in the 2nd stage.)

    The only 'odd' thing: If you split the voltage source into two, you will find the 'center point' traveling with the output frequency - with a reasonable amplitude :)

    Real fun!

  • Mirella Ejiugwo added an answer in DPPH:
    Is there a detailed protocol for measuring the antioxidant activity of orange juice and orange using DPPH method?

    Hello All,

    I am presently doing a short period undergraduate project based on assessing the antioxidant activity of orange and orange juice using the DPPH method.However, upon incubating my positive control (different known concentrations of ascorbic acid, ranging from 1 to 10 nanograms per ml) with DPPH reagent, my spectroscopic readings are so inconsistent: they actually make no sensesense and, thus, cannot yield a useful standard curve. Could there be a detailed protocol to execute this assay successfully please? Thanks in advance.

    Mirella Ejiugwo

    Another concern,reading though the protocol, is the use of eppendorfs. Won't it be better using cuvettes straightaway?



  • António Maximiano Fernandes added an answer in PCR Primer Design:
    I am doing PCR with GJB2 Gene for human hearing loss. When i dilute the primer for the first time, it work only for 2 days, after it does not work?

    I am doing PCR with GJB2 primer regarding hearing loss. When i dilute the primer for the first time from the stock, it works only for 2 days. After it it does not work even i dilute it again from the stock. Can anyone help me what is the main cause of it?

    António Maximiano Fernandes

    We use to face this problem when thawing the primers several times. As Paul said should check the solution the primers is diluted in. If the problem persist should consider the quality of your primers. 

    Good Job

  • Tom A Campbell added an answer in Digital Natives:
    What is the attention span of today's student [digital native] in an acaedmic setting?

    Brain Rules by John Medina suggests that attention span of a person/student [presumably in an academic setting] is about 10 minutes.  However, after I dug around I could not find any current  research to support this.  Certainly we are told and assume that attention span is relatively short for today's digital native, however, I cannot find much research supporting this claim.  The issue seems a tad important considering, many teachers use lectures to teach. 

    Tom A Campbell

    Potentially of interest: 


  • Md Junaid asked a question in Ligand:
    How do I validate results in Ligplot+?

    I have obtained the results of my ligand interacting with my protein using LigPlot+.How do I validate results in Ligplot+?

  • Jorge A. Quirós-Rodríguez added an answer in Seagrass:
    Is there a relationship between the type of seagrass species and the abundance of macroinvertebrates?

    hi. I just read an article recently regarding structural complexity of seagrass, which may lead to an explanation to its relationship with the invertebrate macrofauna. Also, I would like to know if a certain seagrass species can affect the population of the macroinvertebrates. Thanks much!

    Jorge A. Quirós-Rodríguez

    Here is another paper about the relationship between moluscs and Sargassum


  • Bahram Shirmohammadi asked a question in Geosynthetics:
    Can anyone help me find information about '' influence of foundation stiffness on dynamic behavior of geosynthetic retaining walls''?

    I want to investigate '' influence of soft foundation on dynamic behavior of geosynthetic retaining walls''. I wonder if anyone help me to obtain information about influence of foundation stiffness on dynamic behavior of geosynthetic retaining walls.

  • Morton E. O'Kelly added an answer in Urbanization:
    Is there are a relationship Between Transport Systems and Urbanization?

    What is a relationships between transportation and Urbanization?

    Morton E. O'Kelly

    Google this:

    "world bank transport and urbanization"

  • Abdul Ghafoor asked a question in Seeds:
    What plant is this?

    The plant is a small tree with imparipinnate compound, glabrous leaves. The bark is grey. Fruits are 4-loculed or by abortion of 2 ovules/seeds they produce 2 seeds. The plant is growing in Australia. 

    + 3 more attachments

  • Hugo Asselin added an answer in Indigenous People:
    What are the effects of colonialism, capitalism on indigenous people?


    People relations 


    Please give ideas and post journal articles

    Hugo Asselin

    You can take a look at the UN report "State of the World's Indigenous Peoples" (see attached link).

  • Mohamed ahmed Sebak asked a question in Natural Product Isolation:
    What is the best method for isolation of Actinomycetes microorganisms when they are contaminated with gram negative bacteria?

    I have faced a great problem that my Actinomycetes isolates get contamination by gram negative bacteria many times. To face this problem I made isolation of them many times on ISP 4 agar containing rifampicin as antibacterial to get red of these gram negative contamination. I got pure colonies of Actinomycetes and reisolated them on new plates of ISP 4 agar. However after subculture of these isolates for production of antimicrobial activity, I found that contamination reappeared in some isolates. I need a trusted method to get red of gram negative contamination as many of them are difficult to be removed from mixed cultures and can grow even in presence of antibacterial agents in the media.

    Please help me with solving this problem as it's a great challenge for me now to get pure Actinomycetes isolates without contamination.

    Best regards 

    Thanks in advance 

  • Yoshinobu Tanaka added an answer in Ion Exchange:
    How can I experimentally measure surface charge density of ion-exchange membrane?

    I wish to know the surface charge density of some commercially available ion-exchange membranes by means of a practical method in lab.

    Thank you in advance

    Yoshinobu Tanaka

    I measured electric potential on the membrabe surface.

    See "ISBN 978-0-444-63319-4, Section 7.7.5 Electric potential in an ion exchange membrane"

  • Sigit Sutikno added an answer in Peat:
    How to map peat soil / peat dome?

    Can anyone give me suggestion on how to map peat soil / peat dome quickly and accurately in a wide area. The map also includes the thickness of the peat layer. Thank you.


    Sigit Sutikno

    Hi Csaba, Thank you for your response..