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  • Jan Rahnenführer added an answer in Real-Time PCR:
    How i can remove dimer primer,additive band and smear in real time pcr?

    i design primer exactly with allel id software and try different annealing tempreture.i work with transvription factor in rapeseed

    Jan Rahnenführer

    As already suggested, a good software like Primer3 to design primer is the first step to avoid dimers. Nevertheless, dimers may appear. Try different primer concentration (both, less or higher concentrated may help) to reduce additional bands or dimers. Also, higher annealing temperature increases the reaction specifity.

    Smeared products can be interpreted as incomplete PCR products - maybe increase your extension time.

    Best, Jan

  • Chen Gafni added an answer in Praat:
    How do I calculate the Breathiness Index?

    I am trying to calculate the Breathiness Index, suggested by Fukazawa et al. (1988), as a measure for breathy voice. The paper indicates a range of 8.3 to 75.7 for values of BRI, but my calculations yield values at an order of 1015.

    I refer to the definition of BRI as the ratio between the energy of the second derivative of a signal and the energy of the non-derived signal.

    I performed the analysis in Praat. The original sound was converted to a matrix, then I applied a formula ((self [col+1] - self [col]) / dx) twice, to obtain the second derivative, and cast the matrix to a sound. Energy was calculated using the Get energy command (which calculates the integral of the squared signal between two time points).

    Any idea what I am missing here?

    Alternatively, can anyone suggest another measure for spectral tilt that does not require an arbitrary cut-off frequency between low and high frequencies?

    Chen Gafni

    Well, increasing dx, definitely changes the result. But I'm not sure about dx=1. It seems to me that the matrix index is not an integer. The basic unit is total time divided by the number of columns in the matrix (which equals to the sampling frequency). Thus, if the sound duration is x=1 and sampling frequency is 10kHz, then the matrix has 10000 columns and dx = 10-4.

    You might be right that changing dx will solve my problem. I am less certain, though, that dx=1 is the best option.

    As to why I use matrices, here is what Paul Boersma wrote when asked about derivations in Praat:

    "But if you want to have the derivative as a time function, you convert the Pitch to a Matrix (unvoiced regions will be set to zero) and apply the following formula: (self [col+1] - self [col]) / dx"

    And that's what I did (but with sound object rather than pitch).

    Can you suggest a different approach?


  • K. Annapoorani asked a question in Emission:
    Why does the intensity of blue emission increases with increase in the concentration of Erbium while the intensity of green emission quenches?

    what makes to populate the 2H9/2 level of Erbium for a long time without any energy transfer...

  • Mihai Prunescu added an answer in Numbers:
    Do you know examples of first order sentences true in Q and C but false in R?

    I was looking for examples of first order sentences written in the language of fields, true in Q (field of rational numbers) and C (field of complex numbers) but false in R (field of real numbers). I found the following recipe to construct such sentences. Let a be a statement true in C but false in R and let b be a statement true in Q but false in R. Then the statement z = a \/ b is of course true in Q and C, but false in R. 

    Using this method, I found the following z:=

    (Ex x^2 = 2) ---> (Au Ev v^2 = u)

    which formulated in english sounds as "If 2 has a square-root in the field, then all elements of the field have square roots in the field." Of course, in Q the premise is false, so the implication is true. In C both premise and conclusion are true, so the implication is true. In R, the premise is true and the conclusion false, so the implication is false. Bingo.

    However, this example is just constructed and does not really contain too much mathematical enlightment. Do you know more interesting and more substantial (natural) examples? (from both logic and algebraic point of view)

    Mihai Prunescu

    Dear Paul, this is indeed a very interesting conjecture. I would like to see such a sentence S.

  • Mariya Radeva added an answer in Cloning:
    Which is the way to clone big inserts (9000 bp)?

    Hi there, I will appreciate if someone gives me an advice how to clone big inserts in range of 9000 bp...I tried with Gateway system- does not work!

    best wishes


    Mariya Radeva

    Thank you Mark, I could always try!

    I try to build up some experience now! 3000-4000 bp is not a problem, but the big once are more stubborn! How ever, I will not give up! Best wishes

  • Bassem Nabawy added an answer in Total Porosity:
    How do I estimate the porosity of fractured basement rocks?

    - Measuring porosity from the core Samples.

    - Estimating porosity form the satellite image analyses.

    - Estimating porosity form the field studies by measuring the fractures dimensions.

    Bassem Nabawy

    But, it is known that the saturation method is not accurate with basement rocks, in addition the fractures in basements can't retain the fluids during handling. I think there is another more accurate method

  • Marcel M. Lambrechts added an answer in Science Education:
    What ways have you found to be effective to deal with students' misconceptions in science?

    My students learn biology and other sciences in English. Recently they had the Mid-semester test. Two of my 90 students had an F grade. When I checked their answers I found they had many misconceptions. Even simple questions like formation of a dipeptide; simple structure of a nucleotide were wrongly answered. The students admitted that they studied at the last minute.

    Any suggestions how to help such students with their misconceptions/confusions? I I believe it is related to their lack of motivation.  They take life easy; so different from the time when I was a student.  All my class mates worked hard to achieve, for the sake of our families.  Besides that, we found that science was interesting, and this fueled our curiosity.

    Marcel M. Lambrechts

    Knowledge is accumulating fast. What students have to learn today largely exceeds the knowledge available several decades ago. How will future students handle all this, given that the basic brain structures of today do not truly differ from those a couple of thousand years ago?

    An evolutionary framework: the brain structures selected in environments in the evolutionary past  handled substantially less information in the evolutionary past? Were brains naturally selected to handle the huge amounts of information to which students are exposed today (besides some exceptions that do not reflect the human population)?

    Hard selection: If teachers/leaders or their behaviour would be the outcome of hard selection processes, how can they understand (e.g. via empathy) the feelings and capacities of students/citizens that resulted from other selection processes?

  • Ghosoun Al Hindi added an answer in Genetic Algorithm:
    Any ideas about SQLI Detection with Genetic algorithms?

    I Need ideas about the following :

    HOW we can apply genetic algorithm (GA) on web application vulnerabilities detection ? (what do you think about this ) 
    ideas about sql injection detection on web application..
    could we combine decision tree with genetic algorithm ? and how ?

    Ghosoun Al Hindi

    thanks for ur reply ,

    do you have an ideas about implementation of GA ON SQLI detection ?

  • Faris Alshubiri added an answer in Capital Structure:
    Which Capital Structure Theory is/are mostly followed in Asian countries' economic structure?

    Researcher from Commerce and Management discipline

    Faris Alshubiri

    Dear Pranesh Debnath

    Yes there are many  factors effect to choose or think  about capital structure theory and may be the theory is different based on economic conditions in Asian countries .

    Best Regards

  • Janos Polonyi added an answer in Quantum Field Theory:
    Are there Lorentz invariant quantum field theories?

    The provocative question is motivated by the lack of non-perturbative regulators in quantum field theory which preserve the Lorentz symmetry. Higher order derivatives regulate the time reversal invariant sector only. Do we have to return to the idea of H. B. Nielsen about the recovery of Lorentz invariance in low energy effective theories? One may even sharpen the question by asking whether there are boost invariant theories with either Galilean or Lorentz symmetry.

    Janos Polonyi

    Stam, you are right, the chiral symmetry breaking indeed prevents qed to reach the Landau pole. But the driving force of chiral symmetry breaking is the running of the coupling constant. The pole, though non accessible, is a good parametrization to understand the qualitative features of the accessible region. But these are words only and I think that we agree about the facts, namely that the renormalization of a non-asymptotically free theory is nonperturbative.

    I think that the other point you mention, parameterization of the possible breaking of the Lorentz invariance and its comparison with experiments is very important. The earlier works of Kostelecky and his collaborators were based on string theory. One may consider the string as a rather involved regularization which preserves the Lorentz invariance. It is used perturbatively and we can not draw conclusions about non-perturbative theories. But an enormous work has indeed been done to parameterize the Lorentz invariance breaking in quantum field theory models and the effects are below observational threshold as far as I know. The papers I know in this direction are based on perturbation expansion where the regulator was supposed to be Lorentz invariant. Do we have the same possibility of breaking Lorentz invariance when the regulator, rather than the vertices violates the symmetry? I suspect that the scaling laws will be different.

    Thank you for mentioning Kostelecky's name, he is strongly involved in the project of the checking of Lorentz invariance and his works are relevant. He and Long have a recent paper, http://journals.aps.org/prd/abstract/10.1103/PhysRev with an upper limit of some Lorentz invariance violation in gravity. This is interesting because quantum gravity, being the gauge group of the Lorentz group, can not tolerate a regulator which violates the Lorentz symmetry. Can the negative results, obtained in the search of Lorentz violation in gravity be considered as a hint towards either string theories or the classical nature of the gravitational forces?

    I agree completely, that the recovery of a global and a local symmetry are different. This is why the Lorenzt invariance of the regulator is obligatory in quantum gravity. In other words, in the absence of a nonperturbative, Lorenz invariant regulator there is no quantum gravity.

    Dear Vahtang, welcome back. Thank you for your explanation about the separation by the Picuard theorem, I start to understand your construction, it is quite unusual and interesting. About the Euclidean signature: You are right, the Osterwalder-Schrader decomposition theorem applies and there is no problem with Wick rotating renormalized Green functions. What I try to understand is a strange limitation of this strategy: it seems to apply to perturbatively renormalizable theories only. Because we are short of nonperturbative regulator which preserves Lorentz symmetry. Only asymptotically free theories can be renormalized by perturbation expansion hence the Yang-Mills theory is the only four dimensional realization of the Osterwalder-Schrader theorem(???).

    Jaykov, the point you have mentioned, strings, could be the solution of this problem! A short (open) string can serve as regulator when combined with point splitting. And this is used in loop gravity in four dimensional space-time. Therefore the proposition is to use point splitting in theories in flat space-time, too. But this still introduces a new class of dynamical variables, the strings. It would be useful to understand how do they avoid the infinities of the volume of regions in Minkownsi space-time which are bounded by invariant length and wether we can repeat this trick without them. Or if the strings form a non-dynamical, fixed set of lines then to prove that the renormalized theory is universal, namely it is independent of the choice of the set of strings, used as regulator. Do you know some results in this direction?

  • Yahya Farahani asked a question in Knee Injuries:
    Relationship between core muscle strength and other extremities injury?

    there are any relationship between core muscle strength and other extremities injury?

    for example knee injury or ankle and pelvic or shoulder injury

  • Biju Chandran asked a question in Agar:
    How to explain the colony count confidence limit in layman's terms?

    For eg.The precision of the test is dependent on the number colonies that form on the agar plate and may be indicated by quoting 95% confidence limits. These limits define the range within which, with a 95% probability, the true colony count lies.

  • Arshath Raja asked a question in Tamil:
    How to Cluster words for tamil language using mat file?

    Can any one help me in doing Perl scripts for doc2mat file for clustering Tamil word. Im finding it difficult to write the following code: doc2mat -nostem a.doc a.mat


  • Robin Thiers added an answer in Informal Economy:
    Any literature on entry in / access to labor markets in developing countries and/or informal economies?

    Labor sociology has criticized neoclassical ideas about labor markets as a game of supply and demand, instead emphasizing the importance of social institutions in structuring access to labor markets. Most of this literature deals with developed economies, and I am looking for similar literature that deals with developing countries.

    Robin Thiers

    Haven't got very much to add really beyond the authors you mention.

    Maybe you could take a look at the work of Alessandra Mezzadri and Guy De Neve, who focus on gender and labour in India in similar ways as Breman and Harriss-White. Beyond India, maybe Stephanie Barrientos, also taking a gender-focus?

  • Faris Alshubiri added an answer in Internal Audit:
    Please, advise, where can I find more statistical evidence on joint tax audits?

    In their joint fight against tax avoidance and tax evasion international governance developed different tools. One of these tools is the joint audit. The term “joint audit is used to express that two or more countries join together to form a single audit team to examine an issue(s)/transaction(s) of one or more related taxable persons with cross-border business activities.

    Taking into account that countries like Australia, the UK, Canada and the US are effectively engaging in joint tax audits, I would like to look into statistical evidence obtained in these countries (e.g. the time length, outcome achieved, resources employed between an internal audit and a joint audit).

    Faris Alshubiri

    Dear Diana Criclivaia 

    Really , it is very interesting and challenge for you to write in  tax audit  topic, based on my experience  work in banking sector in audit department i, it is some of difficult for this because the confidentially .

    Best Regrds

  • Farhan A. Larik added an answer in Simulink:
    How can I calculate the heat losses in the stator windings of SCIG (squirrel cage induction generator)?

    and how can i make a simulink model to calculate them?

    Farhan A. Larik

     can't understand the language of the file u have attached

  • Ulf Bergmann added an answer in Peptides:
    How to remove TFA from peptide?

    synthetic peptide(MW is 1KDa or 2KDa) from a company contains 0.1% TFA and I use 50mM Tris buffer(pH 8.0) to dissolve it. However, when i do enzyme activtiy measurement, I found that the high concentration peptide is very acid so that it affects the enzyme actvity. I try to apply C18 reversed-phase resin to solve it, but my tutor think that TFA binds peptide(containing Arg and lysine) so that it can not separate TFA from peptide well.Therefore, i want to remove the TFA by some effective methods with little sample loss . 

    If you have some ideas, please tell me as soon as possible.

    Thank you very much.

  • Stelios Ioannou added an answer in Capacitor:
    What are alternatives to batteries for power storage?

    Battaries are used to store power for onward use.Due to more storage losses and size of battaries this is not useful.What are the possibilities of capacitors for this purpose in this field ?

    Stelios Ioannou

    Actually I will have to disagree a little bit with Vimarsh.

    Advances in manufacturing and materials have enabled a lot of improvements in battery technology. Lithium Batteries nowadays can offer burst discharge currents up to 50 and 100C. Also, deep discharge lead acid batteries can have End Voltages as low as 1.35v/cell instead of 1.75v and still recover.

    So, batteries nowadays can also serve as "spontaneous" energy releasers with time constants in the range of 1-2 seconds which is enough for many applications. however when the required time constant is in the range of micro or milli-seconds then I agree that Supercapacitors can not be replaced. 

    It all depends on the application.

  • Mubashar Rehman added an answer in Liposomes:
    Can anyone provide me a protocol for the preparation of liposome by reversephase evaporisation method?

    provide a protocol by which i can entrap methotraxate drug into that 

    Mubashar Rehman

    Dear Vasu Patel, this paper may also help you about different variations of liposomes prepared by reverse phase evaporation method:


    • Source
      [Show abstract] [Hide abstract]
      ABSTRACT: Liposomes are lipid based vesicular systems that offer novel platform for versatile drug delivery to target cell. Liposomes were first reported by Bangham and his co-workers in 1964 (1). Since then, liposomes have undergone extensive research with the prime aim to optimize encapsulation, stability, circulation time and target specific drug delivery. Manipulation of a liposome's lipid bilayer and surface decoration with selective ligands has transformed conventional liposomes into adaptable and multifunctional liposomes. Development of liposomes with target specificity provide the prospect of safe and effective therapy for challenging clinical applications. Bioresponsive liposomes offer the opportunity to release payload in response to tissue specific microenvironment. Incorporation of novel natural and synthetic materials has extended their application from stable formulations to controlled release targeted drug delivery systems. Integration and optimization of multiple features into one system revolutionized research in the field of cancer, gene therapy, immunotherapy and infectious diseases. After 50 years since the first publication, this review is aimed to highlight next generation of liposomes, their preparation methods and progress in clinical applications. This article is open to POST-PUBLICATION REVIEW. Registered readers (see "For Readers") may comment by clicking on ABSTRACT on the issue's contents page.
  • Mariano Ruiz Espejo added an answer in Advanced Statistical Analysis:
    Can I include correlated residuals in the model when performing a bifactor analysis?

    The best model before the bifactor is one which have correlated residuals.

    Mariano Ruiz Espejo

    Dear Sergio, I think that correlated residuals is a consequence of multidimensional Normal hypothesis for the data analysis. A supposed statistical model can have these effects.

  • Amit Prabhakar added an answer in Saliva:
    Can anyone suggest a protocol for DNA isolation from dry blood and dry saliva on microscope slides?

    I am a bit new and I cannot find anything for DNA isolation for dried samples on glass slides. I only find DBS on filter papers. How do I dilute them? And then, when diluted , I continue normally with the kits I have?

    Thank you very much!

    Amit Prabhakar

    Hey Nef, there are various methods in practice and good in isolation of DNA from dry blood samples. This attaches article may somehow help you.


  • Ritika Rajpoot asked a question in Manganese:
    What are the specific areas which are contaminated with manganese in soil??

    Manganese soil toxicity

  • Majid Shahbabaei added an answer in Molecular Dynamics Simulation:
    What is the cause of having bidirectional water molecules motion while implementing a non-equilibrium MD simulation?

    Dear All,

    I am doing non-equilibrium MD simulation to analyze water transport properties through CNT. My model composed of a pool region filled by water molecules and CNT. I have applied an external force on water molecules inside the pool just in Z direction (pore axis). After simulation I expect that water molecules enter the pore from one end. But, via viz I see that water molecules enter both ends of the pore. Is it due to the periodic boundary condition?

    Could anybody let me know why?

    Thanks in advance

    Majid Shahbabaei

    Dear Hari,

    Thank you very much for your kind reply. The attached is the LAMMPS data file includes the coordinates for CNT (C atoms are frozen) and water (Oxygen and Hydrogen atoms). Please kindly find the attached file

    Thanks in advance

  • Mubashar Rehman added an answer in Microemulsions:
    What is effect of oil (continuous phase ) on the flouresence intensity in water-in-oil microemulsion?

    what is effect of oil (continuous phase ) on the flouresence intensity in water-in-oil microemulsion?

    Mubashar Rehman

    Dear Abbas Rahdar, I don't know if your oil gives flourescence itself. Mostly, we add fluorescent dyes that, depending upon its solubility, will be incorporated in continuous oil phase or dispersed aqueous phase. If you are using lipophilic dyes, the continuous phase will give fluorescence with dull or non-fluorescent aqueous droplet dispersed in it. This test is used to identify type of emulsion being o/e or w/o. 

  • Gaopeng Zhang asked a question in Isogeometric Analysis:
    How can I updat the coordinates of the internal control points in shape optimization based isogeometric analysis?

       I am now doing the shape optimization based on isogeometric analysis, I encountered a problem. How to efficiently carry out grid updates? That is, how to set up the internal control point coordinates according to the coordinates of the design variables and the coordinates of the fixed control points. I refer to some  literatures, using the method of linked control point, that is, the coordinates of the boundary control points, internal control points and fixed control point have proportional relationship.But for some complex geometric model, this method is not applicable.I would like to know if there exists a general using method of  grid updating .you can take 1/4 single hole plate as an example. Beg your answer!

  • Francis Steven Mickus added an answer in Art:
    Do we need any definition of Art?

    I´am wondering if we need any kind of definition of Art. In the last period of time, the Fine Art lack any boundaries, or rather should I say any bounderies that couldn´t be falsified. For example if some artist make sincerely a piece of Art and react on something, and some years later, somebody else make something simmilar but inspired only by succes of the first artist and we recognise him, is the second artist also real artist and maker of Fine Art? So I think, there should be some ground rules, and we couldn´t just agree with everything. What I am trying to say, is that despite the overcome normativity in art there should be some rules.

    Francis Steven Mickus

    I would say art is more a deconstruction of the social narratives then a resistance (although that deconstruction is vital to any resistance). art explains the workings of the world as well as opposes them, at times or reinforces them at others.

    Which is why I think art is much more than the creation of beautiful objects. I won't go into it here, but there is a distinction that must be made (and that I have made previously) between art and a work of art.

    Art is the creative process at the human level. Evryone is an artist, and as such an anarchist. This is why the artictic is quickly crushed in mass education and reserved for an élite of specialists.

    This also why art is so subversive. The artistic naturally goes against the grain of standardising social norms. A potter never tires of making a jug because each new jug is a challenge. Its creation has a beginning a middle and an end that the potter can see. Jugs become boring when their production is placed on an assembly line and broken down into discreet tasks, which taken separately are meaningless because without beginning or end.

    Here we have actually achieved what everybody says is impossible: we have established a working definition of what art is. Basic ground rules in discussing and appreciating art in a meaningful way.

  • Nikolay Raychev added an answer in Quantum Cryptography:
    Which is the best Quantum Cryptography protocol till date?

    Which is the best quantum cryptography protocol in any dimension till date? please provide some numerical values regarding the error rate of Bob and information gained by eve...

    Nikolay Raychev

    BB84-based quantum protocols are only secure when in communication used a single photon. 

    The multi-photon tolerant quantum cryptography protocols /multi-photon systems/ provides better error rate tolerance during the transmission in a noisy environment and better support on hardware equipment design. Also, the multi-photon tolerant quantum cryptography protocols can detect Eve’s siphoning by the change of the bit error rate, which increases the robustness of the system. 

  • Jisoo . Lee asked a question in Glutaral:
    What is this mutation abbreviation?

    It is a mutation in the ETFB gene which causes Glutaric Acidemia IIB

    ETFB, 1-EX DEL, IVSDS, +1, G-C

    Thank you!

  • Aminah Bibi Zahrah Nandoo added an answer in Data Presentation:
    What is the best program to draw a molecular biology experiment procedures or schematics?

    I would like to draw a figure to explain "transformation process" and "HPLC process". So, Is there any recommended program for that?