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  • Eric van der Graaff added an answer in DIP:
    What is effective in the transformation of Arabidopsis thaliana? can be a contamination in vector?

    i work in transformation of arabidopsis and i have a problem. i could not get a transgenic plant. time of floral dip? after dip? and concentration of antibiotic(kanamycin) in peti dishes?

    Eric van der Graaff

    There can be many reasons why you have a (very) low transformation frequency. I was used to the 1-2% Maya mentioned, but at the last two work placed barely reached 0.1%.Still when using enough plants for transformation it is possible to obtain enough transformants. Important is to use Silwet, other alternatives such as Tween20 don't work well. Also you need day/night conditions and temperatures 20-23 degrees.

  • Tim Jenkins added an answer in R:
    What type of diagram is this?

    What is this type of diagram called (similar to alluvial diagram) and does anyone know how I might create one (e.g. in R)? 

    Tim Jenkins

    That is a great graphic. Drawn by hand apparently (see link). It is indeed similar to an alluvial plot. Simpler in that there is little crossover. But more complex in the entries and exits.

    Yes it would be doable in R with "basic" plotting. Biggest challenge is an artful way of showing the entries and exits and making it all smooth. You could have a variable for each category and separate variables for completely new entries and complete exits for each category. And variables for switching between categories each way. The plotting could be conventional curves but the entries and exits using somewhat randomly assigned curves, mostly exponential in shape and ones from further out sigmoidal. To get such an organic looking graphic some randomness needs to be added to the entry and exit curves. Some policy decisions needed to on treatment of the entry and exit curves (e.g. is thickness maintained regardless of angle as on the example at the expense of representing a quantity accurately on the horizontal axis - and extent to which entries and exits add to the overall quantity on one side during that pathway in and out).

  • Tofigh Saadi asked a question in Downscaling:
    Can I study extreme precipitation changes detection and attribution to climate change for basin scale without downscaling the CMIP5?

    Also can I use the SDSM for downscaling the Control run and historical forcings of CMIP5 for study detection and attribution?  

  • Aleksandar M. Kovacevic added an answer in ISO 17025:
    Can any body help me to make validation of qualitative biological method to agree with ISO 17025 requirements?

    The method concerning with detect the presence or absence of organisms

    Aleksandar M. Kovacevic

    Dear Dr. Sabry,

    Looking back to ISO17025 (see

    NOTE 2 The techniques used for the determination of the performance of a method should be one of, or a combination of, the following:

    — calibration using reference standards or reference materials;

    — comparison of results achieved with other methods;

    — interlaboratory comparisons;

    — systematic assessment of the factors influencing the result;

    — assessment of the uncertainty of the results based on scientific understanding of the theoretical principles of the method and practical experience.

  • Hamid Reza Hassanzadeh added an answer in Scripting:
    Software to compute least cost path (LCP) in raster files?

    Hello every one.

    I need a stand alone tool so that I can call from my matlab script to compute the LCP distance between two points on the raster. Is such a tool available?


    Hamid Reza Hassanzadeh

     Thanks a lot Simon an Bash,

    I tried to use the costDistance function but the results do not make sense to me. My distances are friction and that's why I use transitionfunction 1/mean(x). I assume that should be enough.

    Here is my code, 

    original_tr<-transition(original_raster,transitionFunction=function(x) 1/mean(x), directions = 8)

    However, the resulting distance are around 80 which does not make sense because each cell friction is at least 100. What is wrong with the above code?

  • Chauhan Dipeshkumar added an answer in Penetration Testing:
    Which current age technology are used by indutries to detect crack in various mechanical structures?

    Specially technologies which are already adopted by industries...

    Not like magnetic particle test, penetration test etc...

    Chauhan Dipeshkumar

    Dr. Russell,

    Thanks for providing a information about Center for NDE at Lowa State University. It helps me to get some idea related to my question. I am also happy to see research going on at that center.

  • Mani A. added an answer in Geometry and Topology:
    Is there a model for ZF in which a pathwise connected Hausdorff space is not arcwise connected?

    Let us have a look at the following statement: every pathwise connected Hausdorff space is arcwise connected. It holds true in ZFC or even in ZF+an appropriate weaker form of AC. I wonder if someone knows whether there is a model for ZF in which a pathwise connected Hausdorff space can be not arcwise connected.  I would appreciate correct answers.

    Mani A.

    Eliza, you are asking at the wrong place. Only people interested in foundations of mathematics or reverse mathematics may be interested in the question. Post it in the FOM mailing list. 

  • Nigel Nunn added an answer in Foundations of Physics:
    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?
    Nigel Nunn

    Dear Matts - thank you for the clear statement about the current situation regarding abstract vs. actual centers of gravity.  You wrote:

    "Only a supermassive black hole can have this much mass in this volume of space. Call it something else if you like."

    Some of us are slowly coming to prefer the term "dark island".


  • Nilimesh Mridha asked a question in ERDAS Imagine:
    What may be the possible issues arise when converting shapefile to aoi in ERDAS imagine 2014?

    while trying to convert shapefile to aoi, everytime blank aoi is created without any dotted line. I am aware of the simple conversion steps, but in my PC i could not do it successfully. plz help me with your suggestions.  

  • Nazir Hussain added an answer in Soil Fertility:
    How can we proceed for decision on soil resource-based cropping sequence?

    Development of soil resource inventory of a given area , is considered highly imperative to take decisions on the options about the suitability of different crops in a farming system mode. At the same time, the information on edaphological requirements of different crops , is equally paramount , so that both are super-imposed in such a way, to delineate soil-crop analogues. This will pave the way for better land utilization efficiency. My further querries in this regard are as follows:

    * How should we develop a soil resource inventory ?. Shall we go for master soil pfofile stdies  or follow the grid- based soil sampling  coupled soil profiles to be later used for developing soil fertility variograms?. 

    * How shall we identify the soil fertility constraints of multiple nature from such soil resource inventory?.

    * What methodology , shall we adopt to identify   optimum soil requirement for different crops ?.

    * How should we identify the cropping sequence based on such soil resource inventory?.

    * Whether cropping sequence and land utilization efficiency are inter-related ?.If so , in what way?.

    I request my esteemed colleagues to share their experiences on these issues. Regards

    Nazir Hussain

    Thank you Dr. Subba Rao, You have mentioned some practical analyses that are deriving the farmers what to grow. Of course price is the deriving force above all. It is very difficult to teach the farmers and refrain them from immediate profits, though these may not be sustainable in the long run based upon land evaluation studies.

  • Christopher Robert Scotese asked a question in Externalities:
    XOJO. Are there any XOJO (RealBasic) programmer users out there?

    I would like to dialogue with someone familiar with programming in XOJO (formerly RealBasic).  I am an old VisualBasic programmer, and need some help with  code to read external files (common delimited variable lists) and write external files (also common delimited variable lists). Some sample code would be great! I've attached a program (zipped archive) that I've written to help with some paleomagnetic research. I need to write a batch version of this program.


  • Manuel Morales asked a question in Discovery:
    Will the 2015 Nobel Prize in physics be based on false-positive data?

    On April 30, 2011, at an American Physical Society meeting, I presented my initial findings that showed that Albert Einstein's notion of hidden variables, although not local, was indeed correct.

    In 2012, I applied my discovery of these hidden variables to the Higgs boson initial discovery and found it to be based on omitted-variable bias since the two origin variables that caused the predicted effects observed were not factored into the results (see "Assumed Higgs" link). Since the two origin variables are mutually exclusive yet can produce the same results, obtaining false-positive data from experiments based on omitted-variable bias is unavoidable (see "Tempt Destiny Experiment Results" link). In science, a discovery cannot be obtained based on false-positive data. Yet in 2013, physicists confirmed that they discovered the Higgs boson and then was awarded the same year the Noble Prize for their discovery. This all took place despite both parties being informed in 2012 of the discovery of Einstein's hidden variables which would negate the Higgs boson discovery since the Large Hadron Collider cannot detect which origin variable caused which particle collision effect which in turned caused the decay product used as evidence for their discovery.

    In the meantime, I have invited the general public to confirm if the Higgs boson discovery was or was not based on an omission error (see "How Grade School Children Can Confirm If Quantum Mechanics Is a Fundamental Theory - Class Assignment Search For First Cause" link).

    It is rumored that science self-corrects itself when a new discovery supersedes previous knowledge. If this is true then how long does it take for such a correction to take place and will the 2015 Nobel Prize in physics be given for yet another discovery based on false-positive data?

    + 2 more attachments

  • Mohit Kumar added an answer in Gels:
    No migration of protein during SDS page?

    No migration of protein during SDS page.

    separating gel - 12% and stacking gel - 5%,

    samples taking too long time to come out from the wells and they start migrating from the middle of the well. and after they reach in separating gel no dye front has been seen in the gel. most of the sample remain in the stacking gel. even protein marker also did not show any separation. please suggest what can be the possible factors.

    i am using Bio-rad assembly. i changed every buffer and twice and make it fresh every time. but still having same problem.

    i am using 4X laemmli buffer having composition:




    BPB dye - 0.02%

    Tris-cl buffer - 250mM

    please suggest something. 

    Mohit Kumar

    thanks Ke-Wei Zhao for ur suggestions. but i checked pH for the buffers. and used fresh running buffer for every time. there may be some problem with power supply. and i used 4x loading dye in vol half of the sample volume. 

  • James R Knaub added an answer in Sample Size:
    Is it possible to compute a covariance matrix with unequal sample sizes?

    I'm not sure if this question is correct, but is there a way to construct a covariance matrix for two vectors that have different lengths? If so, how?

    And would it have a size of (m+n)×(m+n) (assuming the two vectors are of length m and n)?

    (25* 5) * (5*25)

    James R Knaub

    Rasika -

    So you have one set of questions for customers and another set of questions for organizations, and likert scales.  I don't see anything pairing specific observations that would be appropriate for obtaining covariances.

    You wrote that "Now I want to calculate the relationship between market orientation and service quality..." but that seems to me to be a bit of a vague notion, not based on specifically paired, appropriate data for a covariance matrix. 

    It sounds like you need to match customer responses with the organizations, and that would not be a one-to-one match.  I'm not familiar with likert scale data, but perhaps there is some standard technique for looking into this, but as your data currently are configured, if I understand this question, covariance matrices would not be an option.

    Best wishes - Jim 

  • Chao-Dong Zhu asked a question in Ecological Genomics:
    Joining the Working Group and Collaborate to Study on Pollinator Insects in China?

    Special Committee on Pollinator Insects was established under the Chinese Entomological Society on Sept. 23rd, 2015. Currently, committee members include Chinese experts on systematics, diversity, pollination biology, apiculture, ecology, genome biology and climate change.

    We are going to set up a working group, which we would like to invite external members with expertise on pollinators. If you have any comments or interests, you are warmly welcome to contact me at zhucd@ioz.ac.cn.

  • Hasnahana Chetia added an answer in BioPerl:
    Perl/BioPerl or bash; which is better for handling large sets of genomic data?

    I want to analyze large sets of data with sizes around 30-70 GB. The type of analyses I want to run include contig filtering, assembly, annotation, etc.

    Which language will give me faster results on a tetra-core workstation with 12 GB RAM; Perl/Bioperl or Bash?

    Hasnahana Chetia

    How can I use the "awk" command for selectively removing a group of sequences from a large sequence file in Perl/Bioperl?


  • Arunaksharan Narayanankutty added an answer in MTT Assay:
    For MTT assay how to dissolve sample which is only soluble in 100% DMSO?

    I added 1%dmso and 99%PBS to my compound which made suspension rather than solution. Can I still use this for MTT assay? Even some of my compounds precipitate on PBS addition, what to do with that?

    Arunaksharan Narayanankutty

    You can try by increasing the concentration of DMSO, (better to use 100% DMSO as suggested by Nikola M Stojanovic). However, if the compound is getting precipitated upon addition of PBS, i think it wont be suitable for cell culture.

    The following discussion may be useful for you:


  • Elman Shahverdiev added an answer in Atoms:
    Dear Researchers , Is there any membrane allows the passage of electrons , but not for metal ions ?

    Electrons as we know are very small in size comparing to whole atoms and ions , so , i need a method could isolate electrons from its metal atoms by a special membrane...


    Elman Shahverdiev

    Any porous membranes with relevant size will block the passage of metal ions and will not interfere with the passage of electrons

  • Disella Keltem asked a question in Copper:
    Describe specifically Thiobacillius ferrooxidans and Beijerinckia lacticogenes ,their relationship that help purify copper from copper ore?

    Describe specifically Thiobacillius ferrooxidans and Beijerinckia lacticogenes ,their relationship that help purify copper from copper ore?

  • Dushyant Kumar Garg added an answer in Protein Folding:
    Protein Denaturation: Urea vs Guanidine Hydrochloride (GdnHCl)
    In equilibrium denaturation experiments, the concentration of urea at mid-point of denaturation is always higher than that of GdnHCl for any given protein. What is the reason for this? How are they related? If they are related, what is the correlation coefficient? If one value is known for any protein (say for example, that of Urea) is it possible to predict that of the other (say, that of GdnHCl)?
    Dushyant Kumar Garg

    As per my experience, there is no such specific correlation between denaturing ability of urea and GdnCl or any other denaturant. It depends on what kind of interactions are stabilizing your protein of interest and the nature of denaturant. If your protein is a membrane protein, than it would be difficult to be denatured by SDS, as membrane protein love the membrane like environment of SDS solution. I am working on one hyperthermophilic protein, and it exhibits no denaturation upto 8M Urea. However, it gets completely denatured at 3.25M GdnCl.  Here the ionic nature of GdnCl comes into play which destabilizes salt bridges of hyperthermophilic protein (which are more prominent). 

  • Neha Arora added an answer in DAPI:
    How do I stain microlagal cells with DAPI?

    I tried fixing the cells, treatment with 2 % SDS but the dye is not goin inside the cells.

    Neha Arora

    Thanks Alexei , I did stain overnight but the stain is getting accumulated on the periphery of the cells. Ill try using DMSO. 

  • Rajesh kumar R asked a question in Metal Oxides:
    In sonochemical method what is the use of urea and polyethylenglycol?

    In sonochemical method along with the precursors(metal oxide). what is the exact chemical reaction that is happening by adding urea and polyethylenglycol. And what should be the ratio of the chemical mixing with repect to the precursor solution. What will the difference if I use polyethylenglycol 2000 and 6000

  • Rohit Kumar Singh asked a question in Big Data:
    How big data differs from traditional Data?

    what does the term “big data” actually entail, and how will the insights it yields differ from what managers might generate from traditional analytics?

  • Sy Fe asked a question in Tinnitus:
    In our quest for the causation of tinnitus it is important to ask if tinnitus really fits the physicalist agenda? As scientists we think it does, but


    Unaided by external influences, entropy (or “disorder”) in a closed or isolated system (auditory, if this is valid?) tends to increase. To oppose this, work must be done and must be supplied from sources external to the system. Does this (work) contribute to tinnitus? This would of course have to supply energy, and this would be a measurable property of the system. Where can we measure this?


    As humans, in trying to understand  tinnitus, it is important to remember that the proper model of human cognition is not computational, for, if the essential nature of human thinking were computational, the limitations imposed by Gödel’s incompleteness theorem would be manifest. It is therefore non-algorithmic. So in fathoming tinnitus maybe we need more ideas to chase rather than brute laboratory computations?

  • Lahieb Mohammed Jawad added an answer in Network Security:
    How do you work with the NIST Statistical Test Suite for Random Numbers?
    How do you use it to test a random sequence for randomness?
    Lahieb Mohammed Jawad

    Thank you I will try it.

  • Seyed Aliakbar Mousavi asked a question in Mobile Phones:
    Study of immunohistochemistry and histopathology of effect of mobile phone on brain tissue in rat?


    I need the below article. Can u plz find and send it to me for free?

    Study of immunohistochemistry and histopathology of effect of mobile phone on brain tissue in rat

  • Satish kumar Talloj added an answer in Dicarboxylic Acids:
    How do I synthesize Chelidamic acid hydrate ?

    I wish to  synthesize Chelidamic acid hydrate from diethylpyridine-2,6-dicarboxylic acid?

    Satish kumar Talloj

    Dear Rakesh,

    from the statting you provided ,may not be good process , I suggest you to change the stating material if not it could be the lengthy synthesis.

  • Robert Zhu added an answer in Redox Proteomics:
    Western blot of low molecular weight proteins?
    I am trying to detect a 6kda (metallothionein) protein from mouse liver, brain and spleen. I am using 15 % gel and monoclonal antibody but I am getting a band at 50kda? Please help.
    Robert Zhu

    It is so kind of you. Thank you Mansi

  • Jorge Herbstein added an answer in Upper Limb:
    Head should be the first. Shouldn't be?

    According to international guidelines, we should start internal examination of the body with the opening of the skull and with the investigation of the intracranial content. At our department, we respect this rule. But what are meaningful reasons for such a strategy?

    Firstly, textbooks usually recommend dissection of the head prior to the rest of the body. And the advantage? A bloodless field within cervical organs, which is important in asphyxia-related deaths especially in stranglings.

    Secondly, it is quite logical to follow a process of dissection "a capite usque ad calcem". External inspection is, also, done from head till feet, sometimes in a counter-clockwise pattern (head - right upper limb - right part of the trunk - right lower limb - left lower limb - left part of the trunk - left upper limb).

    Thirdly, after the opening of the skull we may immediately smell the presence of volatile, poisonous substances (e.g., ethanol, cyanide, solvents, etc.) without competing odors from thoracic and abdominal cavity.

    How do you see it colleagues? Please advise... Let's share our knowledge.

    Jorge Herbstein

    As Dr.Henja and Dr. Asirdizer in most of the cases we routinely start opening the skull and then from head to heel, but in those cases where are involved injuries to the neck we always left it to the end. In this way the anatomic structure can drain not only to the head but also to the chest cavity, in our experience we have a better and "clean" neck dissection. So if head should be the first, why don´t let the neck to the end in asphyxia-related deaths?

    Best Regards