Q&A

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  • Florin Constantin Mihai asked a question in Metrics:
    Does ” publish or perish” policy favors a pathological disorder ?

    The paper below outlines several unethical practices of scientists (“ the falsification and manipulation of research and researchers' CVs “ ) who seems to be obsessed to publish more in a quantitative manner in order to increase their metrics (nr. of papers, citations, impact factor, h-index etc) which lead to a dangerous question… if researchers & publishers have forgot what is the purpose of science… to spread valuable knowledges or to hunt metrics ?

  • Chiara Giangrande added an answer in SDS-PAGE:
    Have you ever used Glu-C endoproteinase to perform in gel digestion?

    I'm wondering if someone has ever digested proteins after SDS-PAGE by using Glu-C. I can't find any publication on the subject because this enzyme is often used to perform in solution digestion.

    Chiara Giangrande · École Supérieure de Physique et de Chimie Industrielles

    Thank you very much! I tested it and it works...

  • Is logical independence of the square root of minus one a consequence of arithmetic's incompleteness?

    In a formal arithmetical system, axiomatised under the field axioms, the square root of minus one is logically independent of axioms.  This is proved using Soundness and Completeness Theorems together. This arithmetic is incomplete and is therefore subject to Gödel's Incompletenss Theorems. But can it be said that the logical independence of the square root of minus one, is a consequence of incompleteness?

    Peter T Breuer · Birmingham City University

    Yes, well it's hard to get out of the habit of understanding consequence as logical consequence.

    I don't think the poster means anything else, though. He's a little fuzzy on the steps involved, and probably is deliberately offering up the fog as an opportunity to shine a light for someone. Assuming he's not crankishly crazy [benefit given! I've had to decide many times in my life if a paper were written by a crank or a geniius - and I've got it right every time so far as I know], I suppose that he wants to point us at the problematic analogy between adding a square root of -1 because we can and yet not adding an axiom of consistency even though we know we can't disprove it (if it's true).

    And I'm fuzzy on why not too. Probably because we could only add the axiom for the existence of a number satisfying a certain predicate that says it is the Goedel encoding of a proof of consistency). Then the proof would exist, but it would be a proof about the system without the extra axiom in, so we'd have a hierarchy ...

  • How additives will play a major role in phase transition of a Polymorphic compound?

    Some researchers have reported the role of additives in the phase transformation of polymorphic compounds. Reports are telling that this additives are playing major role in the transformation of phase and are not getting in to the structure of the compound. Can anyone suggest me how this is happening?

    Dominik Kurzydłowski · University of Warsaw

    Dear Arul,

    It's hard to answer this question without knowing what specific polymorphic compounds and additives you have in mind. The influence of additives may be different for different systems.

    Generally I would expect that the pathway of a polymorphic transformation may be influenced by the interaction of the compound with the surface of the additive. For example one of the polymorphic forms of the compound may be preferentially stabilized on this surface.

  • Can anyone explain the relationship between total phenolic activity and total antioxidant activity?

    It is well known that phenolic compounds are mainly responsible for antioxidant activities and total antioxidant activity is a integrated parameter of antioxidants present in a complex. A correlation between these two activities could help in identifying the contributing factors for both the activities.

    Tunde Jurikova · University of Constantinus the Philosopher in Nitra - Univerzita Konstant’na Filozofa v Nitre

    I devote to polyphenols and their relation to antioxidant activity. I can claim that we measure a strong positive correlation in the samples of lesser known fruit species

  • Titus Sobisch added an answer in Polymer Science:
    Is it possible to use sodium lauryl sulfate (SLS) as a water in oil (W/O) emuslifier?

    Does anybody know why Prof. Peppas, an expert in polymer science, has used SLS as an emulsifier for water in oil emulsion in the following article?

    http://www.sciencedirect.com/science/article/pii/016836599390156Y

    seems to be impossible

    Titus Sobisch · LUM GmbH

    Stoyan,

    this is simply not true, only in terms, preferentially stabilizes an emulsion with the continuous phase where it is soluble. How well it stabilizes the emulsion is another question. Otherwise you say Prof. Peppas is lying or did not made his observations well. Only in a w/o emulsion he should be able to prepare the PVA particles.

  • Rekha Mittal added an answer in Origin (software):
    How do I calculate the tangent of a curve using the Origin software?

    I need this to effectively and correctly calculate the Band-gap of a thin film.

    Thanks!

    Rekha Mittal · Indian Institute of Technology Delhi

    Could you please explain it more by giving example.I did'nt got the tangent from the curve.

  • Dason E Evans added an answer in Teaching:
    Is peer observation of teaching work in your context?

    Peer observation of teaching (or POT) is where two or more colleagues
    collaborate in observing each other’s teaching and then provide feedback
    and suggestions for improvement. It can provide a number of benefits
    both to the teacher and the teaching institution.

    Dason E Evans · Queen Mary, University of London

    We find it useful but time consuming in current resource limited settings.

    I often feel a little guilty doing peer observation of teaching, as I feel I learn more by observing (in a structured way) than the person who is being observed!

    The most important aspect for me, is being clear on the purpose. An observation as an assessment for promotion is very very different than an observation as a colleague where you both feel that you are keen to grow and develop as teachers.

  • Tommaso Bolognesi asked a question in Reductionism:
    Shortest path length in percolation random graph

    Take all the naturals, and for each pair (i, j) with i<j create a directed edge i -> j with fixed probability p, thus obtaining an infinite DAG (directed acyclic graph) G.  Let T be the transitive reduction of G (which is unique).  How does the length of the shortest path *in T* from node h to node k (if any) grow with their 'numeric distance' (k - h)?

    (The *longest* path from h to k should grow linearly with their numeric distance.)

  • Ram Kishor Singh asked a question in High Power Lasers:
    How does one experimentally achieve an amplitude modulated laser beam, the frequency of which is in the THz range?

    When a high power amplitude modulated Gaussian laser beam propagates in a ripple density plasma then a transient transverse current is generated by transverse component of ponderomotive force exerted by laser beam on electrons that drives radiation at the modulation frequency. If the modulation frequency in the THz range then one get the high power radiation in the THz regime. If we have a seed signal in the THz regime and  can modulate with the high power laser beam then we can achieve the THz radiation generation at high power with this technique . But, how to optically modulate a weak signal (THz signal) with the high power laser beam (either CO2 laser or Nd-Yag laser) ?

  • Anuj Kumar Singh added an answer in Splines:
    Can we get the smoothed data after applying smoothing spline on given vector of data in matlab

    i have a vector of real values ranging from 1 to 100 randomly. i want to fit a smoothing spline curve on the vector. i also want the data after fit operation. fit operation in matlab only give the curve.

    Anuj Kumar Singh · PDPM Indian Institute of Information Technology, Design and Manufacturing Jabalpur

    Thanks for your solution ......this code works well using spline model ...but i need to use smoothing spline ....please tell how can we get data by smoothing spline in matlab.

  • Dr Balwinder Kumar added an answer in Phloem:
    Does anyone know studies on influence of nitrogen deposition on seed quality (chemical content)?

    As in the subject. I am looking for papers that look for the effects of nitrogen deposition on seeds/acorns chemial content/quality. I found a lot of papers on other tissues (like increase in N foliar concentration, phloem) but it seems like those on seeds are scare.

    Anyone?

    Dr Balwinder Kumar · Guru Angad Dev Veterinary and Animal Sciences University

    Dear Michal

    Its true application of N through foliar application increases N content and ten also improve protein content of seed. You can download my paper of Exogenous application of bioregulator improves seed yield and quality in  forage cowpea for detailed reasoning and discussion

    Regards

  • Is 16kb big in terms of plasmid construct?

    I've had some problems transforming my 16kb plasmid in competent bacteria using the heat shock/chemical method. Should I be using electroporation instead of heat shock?

    And if my plan is to then transfect the plasmid into a mammalian cell line to overexpress a particular protein of interest (Mw = 400kDa), are there any steps which I should be aware of in order to get maximum expression into conditioned media?

    Jonathan D Finn · Arthrogen

    Hello Jing,

    16 kb is a large plasmid, but not that big.  You should not have too much trouble transforming it.  Are you transforming a ligation, or the intact plasmid?  You could try using some competent cells that are optimized for larger plasmid, such as NEB 10-beta cells.  

    As for expression in mammalian cells, the transfection efficiency of a plasmid is directly related to its size.  That means your expression levels might not be great.  What cell line are you going to transfect into? If you need a lot of your protein (I assume it is secreted or you woudn't care about the secreted media), you can try using your plasmid to generate stable cell lines.  That way every cell will be expressing your protein.  You will need a selectable marker on your plasmid if you want to try doing this (such as Blasticidin). 

    Good luck

    J

  • Valery Pipin added an answer in Solar Activity:
    What are the origins of DeVries (~200 year) and Gleissberg (~83 year) solar cycles?
    I am trying to find information on DeVries (~200 year) and Gleissberg (~83 year) solar cycles. What is their origin? Are these manifestations of the 11 year sunspot cycle or some other mechanism? A pointer to any publications much appreciated.
    Valery Pipin · Russian Academy of Sciences

    There several  physical processes which can result to  the Gleissberg variations of the   sunspot cycle. One of  the first proposed mechanism  is related with the beating of two fundamental modes with close periods, see the recent paper by Feynmann & Ruzmaikin JGR 2014.  Another mechanism  is related with the nonlinear interaction of the differential rotation and the solar dynamo (Tobias, 1996,1997), Pipin (1999), Kueker Ruediger, Arlt (1999). Currently it is unclear how strong such interaction could be on the Sun.  The direct numerical simulation support the idea that both the Reynolds and the Maxwell stresses are essential to reproduce the solar angular velocity profile. The third possibility for the Gliessberg cycle variations is related with the stochastic excitation. In this case  the typical periods of the long-term variations are related to the typical times on the nonlinear re-establishment  of the basic state of the dynamo which is perturbed by stochastic fluctuations. Those stochastic fluctuations of the dynamo governing parameters are naturally appeared  in the the stellar convection zones (Pipin, Sokoloff, Usoskin 2012).

  • Is it compulsory to exclude all Cq/Ct values more than 30?

    Does error (difference of less than 3 degree Celsius) in annealing temperature have any role in getting a higher Cq/Ct?

    Pietro Pilo Boyl · University of Bonn

    Hi Charles, I see no one really answered your question about the 2-3 °C in PCR... not sure what you really mean, anyway, it is difficult to say yes or no in general, but if a PCR is not optimal, a 2-3 °C shift can change things radically.

    But you should run your product on gel and see how it looks: if it's clean but weak, you can decrease 2-3 °C the annealing and you might increase your yield... but you might also increase unspecific! If your amplification is already smeared, or with (multiple) unspecific bands, then you know why your specific band is weak. In this case raising the temperature might help, elongating the annealing time might help (thermodinamically a specific binding is normally more stable than an unspecific, but you also have to consider the kinetics of the binding, some primers bind slowly, while unspecific binding is almost always a quick on-off, therefore giving more time for the annealing builds up specific annealing vs. unspecific), but you might also need to simply change primer pair.

    By the way, actin mRNA is probably the most abundant mRNA in the cell. If you are not diluting your cDNA at least 10 times and using 0.5 ug of RNA for your RT the Ct is not particularly good... So, it would be ok if your gene would come out also in a similar range, but in your specific conditions it might want some improvements on the RNA and/or RT side...

    Good luck

  • Shanice Chiang added an answer in Rosetta:
    Anyone have experience in autoinduction?

    I have cloned lipase gene into pET28+ and express it in Rosetta(DE3)pLyss. I have tried to induce with IPTG but I cant spot any difference between the clone and the empty pET. I varied the temperature, IPTG concentration. I have tried whatever I could possibly think of. I happened to read Studier (2005) on the autoinducting medium. I carried it out at 20C O/N. The expected protein size should be around 23kDa but I am seeing a band at around 35kDa. Could someone enlight me please

    Shanice Chiang · UCSI University

    nope. but i the rare codon are well covered by Rosetta (DE3)plyss

  • Can anyone assist me with whether my data is paired or unpaired?

    Please could someone help me determine whether my data is paired or unpaired.

    I have done gene expression profiling on a cell line that was treated with three different concentrations of the same drug.  I also have an untreated control. I repeated the experiment a further two times but independently of one another (number of biological repeats=3).  Would my data be paired or unpaired?  

    Raid Amin · University of West Florida

    Whenever the modeling seems relatively complex, and the necessary statistical analysis is  advanced, consult with a statistics professor.  In fact, statistics professors consult with each other in order to get a second opinion in experiments  in which modeling and analysis are not straightforward.  

  • Hee Sun Kang added an answer in Vaccination:
    What are the reasons for under- performance of oral vaccines in low income countries?
    Literature lists out some factors:

    1. Prior exposure to the diseases
    2. Poverty
    3. Small Bowel Bacterial Overgrowth (SBBO)
    4. Intestinal Helminths
    5. Others

    What is your opinion?
    Hee Sun Kang · Chung-Ang University

    Check these articles

    Refusal of oral polio vaccine in northwestern Pakistan: a qualitative and quantitative study
    Listening to the rumours: What the northern Nigeria polio vaccine
    boycott can tell us ten years on

  • Mario Stipčević added an answer in Physics:
    Can we mathematically model consciousness?
    We have seen that AI, which was supposed to be a failure, is coming back with
    gusto on the back of multi sensor robotics and possibly androids with quantum computers. There is some mysterious counter intuitive behaviour in the sub atomic world which seems to suggest inanimate objects do sense the external world.
    It would be nice to know the views of experts from different fields, such as math, science, psychology, sociology, cosmology on this intriguing subject. One possibility
    that comes to mind is if probability is actually such a model, as it does incorporate
    randomness.
    Mario Stipčević · Ruđer Bošković Institute

    @Johnatan

    We seem to agree more and more that the question posed in this thread is very interesting but, unfortunately, the state of our understanding of matters is such that it is way premature.

  • Ankita Pagedar added an answer in Biofilms:
    Can I use glass to form biofilm instead stainless steel?

    I have to form biofilm onto stainless steel. Can I use glass (Glass slide for microscopic observation) instead ?

    Ankita Pagedar · A. D. Patel Institute of Technology

    glass and steel like surfaces are hydrophilic and may decrease the biofilm formation. You may prefer polystyrene plates or polypropylene surfaces. The plates can be directly stained and observed under microscope (with no concern of opacity). If you want to analyse only live cells under microscope then use any substratum to form biofilm but use MTT to stain (the formazan reading is in visible range and not fluorescent). if you want to estimate the biomass, then use crystal violet staining.

  • Justin Lemkul added an answer in CHARMM:
    QM/MM scheme of CHARMM

    Dear all, I would like to know which is the QM/MM scheme implemented in the program CHARMM.

    Justin Lemkul · University of Maryland, Baltimore

    Have you read http://www.charmm.org/documentation/c38b1/qmmm.html ?

  • Ilja Schmelzer added an answer in Space:
    Is there more than one theory of gravity that can demonstrate compatibility with the Einstein equivalence principle?

    I am looking for theories that give different observations, i.e. that are measurably different.

    • Observations must match Minkowski space in free space.  This is a theoretical question.  Not looking for radical theories that would violate Minkowski space.
    • Each theory must be able to demonstrate that observations in an accelerated elevator in free space are the same as in an elevator sitting on a planetary surface.
    • Please show how multiple elevators over an extent of space are integrated to give the different observations of each theory, i.e. how the same local observations integrate differently.
    Ilja Schmelzer · Independent Researcher

    Stefano: "Einstein affirmed that the contribution of radiation for the metric was negligible, so he didn't try to include it in his equations. "

    There is no need to try.  Once you write down a Lagrange formalism which includes the EM field, the action equals reaction principle manages automatically that this backreaction of EM radiation on gravity is incorporated. 

    The question of how the collapse of the wave function can be incorporated into the theory of gravity is a problem of quantization of gravity, it is the problem which suggests that the gravitational field has to be quantized too.  But it is not a problem of incorporation of the EM field. 

  • What is the fullform of YCD-1 in Gerbera (Floriculture)?

    Dear All,
        Myself Dr. Kiran Ranadive, Asst Prof of Botany in Waghire College Saswad. I am teaching FYBSC Paper II , in which Floriculture is one of the topic. Today i have taught the Gerbera cultivation, there are so many varieties of the same but i have't got any clue that why the variety YCD -1 , 2. What is the fullform of YCD?
         If anybody could send me the answer then it will be very much informative to my students during learning the same. If anybody could send me the floricultural PPTs then it will be great help for my student to start business in floriculture.
         I hope that you will send me the same at your earliest.Eagerly waiting for early reply.
    Thanking you

    yours sincerely

    Dr. Kiran Ramchandra Ranadive

    Dr. Kiran Ramchandra Ranadive · Waghire College Saswad

    Respected Dr.Gederts Ievinsh,

      Thanks a lot for your answer. 

    Thanking you 

    yours sincerely

    Dr. Kiran Ranadive

  • Shrawan Kumar asked a question in Plant Extracts:
    How to find minimum ihhibitory concentration

    i have a data showing antifungal activity of some plant extracts. i want to calculate minimum inhibitory concentration of these extracts. can anyone tell me how to do this.

  • I would like to know that KDD 99 CUP dataset can be used in hybrid intrusion detection system?

    Data mining

    Ahmed Fares · Egypt-Japan University of Science and Technology

    yes you can

  • Jörg Freiling added an answer in Entrepreneurship:
    Anyone interested in a workshop on transnational entrepreneurship?
    ZenTra Workshop on Migration and Diaspora Entrepreneurship.
    Jörg Freiling · Universität Bremen

    Dear all-- 

    Thanks for your interesting replies. 

    @Robert: After the next workshop in Bremen, Germany (11 November) and a follow-up event in Turku, Finland, we are now going to plan a workshop in the US. Participation will be waived for the Bremen workshop and rather low in case of the other two events. We'll keep you posted via RG!

    @Bastijan: At least entrepreneurship is getting more transnational year by year - in many aspects. Insofar, we see the topic still on the way up - with migration issues on the front seat. 

    @Marco: Thanks for the useful paper. I will attach a file with some thoughts on conceptualizing entrepreneurship in a way based on entrepreneurial functions. 

    Best regards for now,

    Jörg

  • Antonio Del Zoppo added an answer in Transmission:
    How can we derive the transmission probability of a charged particle in a parabolic barrier?
    How can we derive the transmission probability of a charged particle in a parabolic barrier?
    Antonio Del Zoppo · INFN - Istituto Nazionale di Fisica Nucleare

    The exact solution of the problem of quantum transmission through an inverted parabolic barrier is given by the formalism in Physical Review 89, 1102 (1953), the so-called Hill-Wheeler formula.

    Antonio Del Zoppo

  • Is any one familiar with Principal Components Analysis and Cronbach's alpha?

    I have wanted to explore the idea of identifying a latent variable through PCA in two questions about the timing and quantity of adherence to medication. The PCA comes out very well, including with split-sample validation, however the Cronbach alpha is very low (<0.45), which is almost to be expected as each of the two questions should act like a single-question 'sub-scale'. As this is not going to be used as a psychometric scale but just a 'composite variable', I'm wondering if I can just go ahead and use the resulting factor-variable/composite in analysis. Can any well-informed data-analysts guide me on this? Thank you. 

    Saeed Akbari-Zardkhaneh · Allameh Tabatabai University

    I think, there are few reverse items in your questionnaire. if you recode these items, your alpha will increase. alpha approximately is the average of between items correlations and reverse items produce negative correlations and finally reduce the average.

  • Who owns patients' health information?

    According to the Freedom of Information Act, American patients can access their health information upon their request. I wonder if there is a global consensus over this issue? Do other countries have a similar legislation?

    In my country, doctors can refuse to show the patients their own information. They believe and say that the doctor and not the patient owns the patient's information. Is it legal? Is it ethical?

    Poloko Kebaabetswe · University of Botswana

    I recently completed training on medical ethics for MMeds residents . The group was divided some strongly belief that  patients records belong to them and can look at them at any time  even if  they may not fully undestand what is written about them, Others feel patients records especially if a patient is admitted belongs to the hospital and patients should not even be allowed to read their charts. The practice in most health facilities in my country is more on the latter. I personally belief  patients records belong to them and should access them and read them any time they wish to