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  • Danilo Corrêa Silva added an answer in Plagiarism:
    What percentage of plagiarism is generally treated as acceptable?

    Since there is no consensus about the plagiarism percentage which can be treated as fair, hence acceptable. How and where to draw a line to accept or reject a document suffering with a certain percentage of plagiarism. 

    Danilo Corrêa Silva · São Paulo State University

    I think it is important to say, as everyone should know, that direct citations are not plagiarism (of course they must obey some distinct rules of presentation/format). The profusion of those citation type is inelegant and shows inability to write as expected in academic fields. I think it is a methodological problem, but it is not plagiarism.

  • Huong Ha added an answer in Hippocampal Neurons:
    Why are our hippocampal neurons that loaded well with some dyes not loading well when they have mcherry tag?

    Hi all,

    I am trying to image zinc in our hippocampal neurons around DIV 12 - 21. I tried both New Port Green and Fluozin-3 (from 1 - 5 uM, load 30 min - 1 hour at RT, wash for 30 min) and the neurons seem to be loaded really well. We applied several zinc solutions and imaged them live. However, when we tried to combine these dyes with neurons transfected with mcherry, it did not turn out really well. Most of the transfected neurons were not at all loaded with the dyes very nicely. Has anyone experienced this? Do you have any hints of how this should be improved? 

    Also, have any of you tried to fix these dyes instead of doing live imaging? 

    Thank you so much for your help!

    Huong

    Huong Ha · Stanford University

    Hi Micheal, I am not sure what you meant with before and after images? Do you want to see the neurons before loading and after loading? I only have images of them after loading with the dyes in green and red fluorescent channels. Would you like to see that? We just tried again yesterday and loaded them with FluoZin-3 2 uM for 1 hour at RT, this seems to help visualizing the fine processces! Previously we used FluoZin-3 at 1 uM for 30 min and that is not at all enough to see the dendrites or any finer process. :) Anyone has other trick?

  • How do I increase protein solubility after purification?

    I am purifying a DNA-binding protein for use in in vitro transcription assays. However, solubility has been a huge issue. I have made a C-terminal fusion to MBP, and get great expression and can purify it using amylose resin beautifully. This fusion construct does not bind DNA however, which is why I need to cleave the tag. I have a Xa cleavage site, and within 24 hours, cleavage is 100% efficient. This is where the problems begin.

    The pI of my protein is very high (9.5), while the pI of the cleavage factor and the tag are low (5-5.5). I've tried both cation and anion exchangers, and cannot get my protein to purify - and I've deduced that it crashes out of solution once I've cleaved the tag and attempt to dialyze in a purification buffer. I've tried many different buffer conditions (altering the pH, adding glycerol, adding NaCl up to 200mM, and 5mM DTT) but I am still unable to clean it up. I am worried about increasing the salt concentration too much, as then it may not effectively stick to the column. 

    ANY advice would be greatly appreciated, as I've been working to purify this protein for over a year now, and feel like I'm so close to being able to do it! 

    David A Horita · University of North Carolina at Chapel Hill

    Is your target protein soluble and capable of binding DNA after it has been cleaved from MBP but before you attempt to purify it?  If it precipitates after cleavage and before purification, you need to find a cleavage buffer where you can keep it soluble.  If it is soluble but doesn't bind DNA, it may not be folded properly.  If the problem is only with changing buffer for purification, you can take a different route and clone in a his tag on the MBP and dump the cleavage mixture over Ni resin.  For that matter, what happens if you do an on-column cleavage (fusion on amylose)?  Do you recover soluble, active protein?

  • Ahmed Arbab added an answer in Hepatoprotective:
    What is the role of hepatoprotective product in treatment/management of hepatitis B virus infection?

    What is the role of hepatoprotective products in treatment/management of hepatitis B virus infection?

    Ahmed Arbab · King Saud University

    THANKS  ALL, Can hepatoprotective agent promote hepaotcyte regeneration and assist  to overcome cell injury due to infection ??   

  • Do ALL hermitian operators have real eigenvalues?

    In the standard proof showing that hermitian operators have real eigenvalues we exploit the  symmetry of the operators to show that they only have real eigenvalues.Does this hold for ALL hermitian operators in general?

    Anton Zizi Caprì · University of Alberta

    The simple answer is , "No!" To have only real eigenvalues an operator must be self adjoint (see my book–– Nonrelativistic Quantum Mechanics for the difference) .

    An example of a hermitian, but NOT  self adjoint operator is

    p = -i d/dx defined on the interval (0, infinity). Here the function

    f(x) = exp(-x) is an eigenfunction with the imaginary eigenvalue i.

  • Anyone recomend book , article or review about Piezoelectricity

    I'm looking for a book , article or review about piezoelectricity . Especially the physics of pizo - phenomena  and the meaning of the D33 , D31 , D51 , D15 , or K33 or e33 .

    also explanation of the piezo - measurement

  • Which is the best Fungal DNA extraction Kit in your opinion?

    I need to extract DNA from spores from herbaria material. I've used the Phenol-Chloroform method with success, but I'm interested in a Kit.

    Jinxiang Zhang · Joint BioEnergy Institute

    Right, not from spores.

  • Dynamic light scattering measurements for dynamic aggregation of micron-size particle

    Typically, DLS is valid for particle size range from 1-4000 nm. But we want to get a general idea of micron- size particle aggregation. So particle size ranging from 5um to several tens of microns. Has anyone done DLS measurement in this region ? Any advice?

    Alexander Malm · The University of Manchester

    I haven't done anything like this myself but I know that Malvern Instruments produce a range of commercial DLS systems, some of which are quoted to being able to measure particle size in your range of interest, so it must be doable. 

  • Can anyone help with recording AMPAR mediated mini EPSC in dissociated hippocampal cultured?
    I just started doing electrophysiology since last year and now interest in learning about the zinc sensitivity of AMPAR mediated mini EPSC. For this goal, I am trying to record from dissociated cultured embryonic hippocampal neurons at DIV 14-17. We use Banker configuration to keep the neurons fairly healthy (co-cultured with rat astrocyte). My recording solutions are: tyrodes (hepes based buffer ~ 250 mOs) for the bath and cesium gluconate (~ 240 mOs) for the pipette. I also have PTX, TTX and APV in the bath to isolate AMPA mediated currents from the others.

    In doing so, I have several challenges below. It would be great to have your advice/ recommendation of how to overcome them. Or, just to hear that someone also experienced these difficulties and how they dealt with that.

    - Unstable baseline: I could record some decent EPSC traces from normal neurons, with no perfusion. However, when I tried to record on either transfected cells or to perfuse the ZnCl2 during recording, the baseline just looks really not so nice. The combination of the two (transfected + perfusing) is even worse. Do you have any strategy to keep the baseline stable, or to keep the transfected neurons healthy? I am using calcium phosphate to transfect neurons at DIV 9. The protocol is pretty much identical to the one in this paper.
    http://www.ncbi.nlm.nih.gov/pubmed/23100419

    - Distinguish between an increase in frequency versus amplitude: In my luckiest day, I got a few recording on the untransfected neurons with zinc perfusion and maybe saw more frequent events during zinc treatment. Please see the attached file for an example. I wanted to analyze whether the zinc affects frequency and amplitude of the AMPA EPSC. What softwares or codes would you recommend for this kind of analysis? I am thinking about mini analysis but it is kind of expensive. The clampfit did not work really well (or maybe I am not so good at using it). Also, how do you know if the drug actually increase the frequency or it just increases the amplitude of the events that were small?

    - Inconsistent response: Among the cells that I recorded from, some of them seemed to respond to zinc and some of them do not. I am wondering if this is a cell type dependent effect. Other than doing post-hoc staining, how would you try to narrow down the neuron population to patch on? I am trying to only patch on only pyramidal neurons, but there shape of the neurons are so diverse and there are not many typical pyramidal-looking ones.

    - Low density: last but not least, it looks like my culture is quite sparse. This is shown by the fact that there are only a few cells (usually less than 10) in an 40x field of view. We plated 900 000 cells on a 100 mm petri dishes that contain 6 of 22 mm coverslips. We later flip the coverslips into the 60 mm dishes coated with astrocytes. I also found that the frequency of the EPSC is quite low. Usually less than 1 event every second. I am a bit hesitant to increase the density since it could affect the transfection efficiency, and sometimes the denser neurons just require too frequent media change. What is the ideal density that one should aim for to have nice and active culture?
    Huong Ha · Stanford University

    Hi Ke, yes, it should be a straightforward assay to do. I was also working on our cell health and tried different media plus culturing conditions. The Banker configuration seems to give us the healthiest and most active neurons. Increasing bath temperature should also help with activity. I will try this! Is the patching at high temperature a bit more challenging than room temperature? Thank you!

  • To What Degree Should We Tolerate, Cherish, and even Encourage Imperfection in Art, Architecture, Science, Literature, Law, and Music?

    In his "Ethics," Benedict de Spinoza calls God perfect Being, whereas all other beings are imperfect.  If this is so, then the creatures of human beings are even less perfect. Some artists, architects, scientists, writers, jurists, and composers prioritize some of their creatures over others and leave these others unfinished. They are imperfections to the fourth degree. The cultural landscape is littered with incomplete works. Why do their authors save them?  Should we not get rid of them?  If not, why not? What value can they have?  Offer outstanding examples of incomplete works from world art, science, philosophy, architecture, letters, law, and music, or else from your own research and creative work of pieces that you did not bother to finish, yet kept in your desk or lab.  Explain why the retention of all those works.  When is it proper to get rid of any? 

    Nageswara Rao Posinasetti · University of Northern Iowa

    Dear Nelson
    Very interesting question.
    A creative work was left unfinished because the author either busy with other things that were more important at that time, lost the inspiration to complete the work or passed away at that instant. Here is an example of the unfinished portrait of FDR. “The Unfinished Portrait is a watercolor of Franklin Delano Roosevelt that was in progress at the time of his collapse and subsequent death”. Wikipedia

    Even though they were unfinished, these works do speak of the intention and state of the creator at that point and will be a very valuable resource for future generations. So from that standpoint they should be retained as the creator desired.

  • What is your experience/opinion/reference regarding code-switching in education?

    Code-switching (http://en.wikipedia.org/wiki/Code-switching) can be defined as the alternation between languages or dialects in speaking or writing in a grammatically overall consistent manner. It usually appears in 3 types, that is extrasentential, intrasentential or intraword.

    Although it was previously considered as a lower level use of language, lately it is scholarly regarded a normal, natural or even beneficial phenomenon in bilingual or multilingual environments and societies, especially in education and language teaching. There are also those who advocate that not only should it be used as a strategy (http://digitalcommons.iwu.edu/cgi/viewcontent.cgi?article=1002&context=hispstu_honproj) but also taught as a goal, for example a communicative skill or competence (http://uege5102-09m.blogspot.gr/2009/07/teaching-code-switching-in-classroom.html).

    Please share with us your experience with or opinion on or interesting references to the use of code-switching in education.

    Thank you.

    Bachir Bouhania · University of Adrar

    dear Rafael Ibarra, I alawys codeswitch from english to french to arabic, believe me my students enjoy it very much becuase they not only hear english but they ca also see it through their own mother-tongue cognates.

  • Does anyone have experience with Barcoding?

    Is it correct to use barcoding to evaluate the validity of a species? It seems a stupid question but....literature shows it is not. Thank you.

    Dominic Evangelista · Rutgers, The State University of New Jersey

    My opinion is that a barcode only approach can be used for species identification when the reference library is well developed. 

    However, when the goal is species delimitation or defining new species using only barcode data applied to a species concept is a very weak approach (in my opinion). I would say that barcode data is not inherently bad at this but that any single point of inference for determining species is weak. There are many examples in nature of morphology being weakly informative or even entirely misleading for species delimitation. A barcode gene is no different. I think the best approach would use multiple independent sources of data (e.g. COI + nuclear gene + genital morphology) to infer a biological pattern consistent with biological differentiation based on some criteria set beforehand in the form of a species concept.

    See attached papers for my work in applying barcode data for species identification and determining local species richness.

    Hope this contributes to the conversation!

  • Aieman Ahmad Al-Omari added an answer in Words:
    Can speechlessness/silence be a better, more pungent/effective form of language than the (written or spoken) word?

    In certain circumstances, silence proves to be more meaningful/powerful a language than the spoken or the written word! Do you think this is true?

    To Professor Nelson Orringer, friend and colleague, with much admiration, to make sure what we can do with and without words!

    Aieman Ahmad Al-Omari · Hashemite University

     SILENCE SPEAKS WHEN WORDS CAN'T

  • Any software packages suggestions for nanomaterials research?

    My dear  friends, I am planing to do  some  simulation work on nanowires/ nanomaterials growth aspects. Please suggest some soft wares (free and paid also). It is bit urgent for me.

    Natheer Basheer Mahmood · Al-Nahrain University

    Quantumwise nano lab

    accelarys material studio for material modeling

    accelarys discovery studio for drug design and modeling

    crystal studio

  • Masataka Watanabe added an answer in fMRI:
    Are high-level visual areas sufficient for conscious vision? How does subjective vision gain holistic access to spatially distributed neural codes?

    I have a thought experiment (video link: "Paradox of Subjective Bilateral Vision"16:00-28:00) that results in very strange situations if "high-level visual areas themselves are not sufficient for conscious vision, (or low/mid-level visual areas are necessary)", namely, that the neural mechanism of conscious vision, its verbal report and solving of perceptual visual tasks (e.g. bilateral symmetry detection) violates physics that we know of today. I would like to know if there is any experimental/theoretical evidence on this issue. Thanks in advance!

    Thanks to the two contributors, the above question has developed into a discussion on how subjective vision gain simultaneous holistic access to spatially distributed neural codes. There have been claims that 'holistic access' should be considered as a serious constraint on the neural mechanism of subjective experience. In case of vision, the seamless and the unified nature of our bilateral percept can be thought as an indicator of our consciousness mechanism having holistic access to wide-spread neural representation.

    Unlike many popular theories of consciousness, some scientists believe that holistic access should be solved by actual physical processes in the realm of established science. In other words, there should be some single 'entity' that has causal physical access with consequences, to all subjectively experienced information. Although, there are surprising small number of models on consciousness that actually implement such a mechanism.

    I explain my "Chaotic Spatiotemporal Fluctuation" hypothesis in the linked video (40:00 - 50:00), where holistic access is implemented by deterministic chaos components in neural fluctuation. Here, I define holistic access as 'every local change in the distributed neural code evoking global system-level changes in neural fluctuation', which relies on the so-called 'butterfly effect' of deterministic chaos. For the sake of clarification, the link between 'holistic access' and 'subjective experience' goes beyond physics that we know of today.

    I would very much appreciate comments on the first question too.    

    Masataka Watanabe · The University of Tokyo

    Arnold

    An example of a widely-accepted interpretation of a psychophysical experiment would be something like

    Color after images and static motion aftereffects show very small ocular-transfer

    ->  There exists an independent adaptation mechanism for the two eyes

  • Hassan Mohammadpour added an answer in MATLAB:
    What is the refrence frame orientation on DFIG's control on MATLAB demos?

    The basis of vector control is to refer the rotor currents in a synchronous reference
    frame, oriented so that its d axis is aligned with the stator flux. In this way we can independently control the active and reactive power of DFIG by I-dr and I-qr, respectively. In this situation, in normal operation of DFIG, the reference value of I-dr and I-qr must be almost 0 p.u and 1 p.u respectively. But this values in matlab demo ( DFIG detailed model) are 0.8 p.u and -0.25 p.u respectively.

    If the control is base on flux oriented, at least one of the current references should be zero. 

    How can we explaining this values? 


    Hassan Mohammadpour · University of Tabriz

    Dear Vitalii

    Thanks a lot for your answer. It was so helpful.

    In normal operation, when Q-ref=0, what is the value of qr_ref? To obtain Q-ref value, Should not be equal to zero?

    Best Regards

  • Anjeet Verma added an answer in Spartan:
    Can i implement pmsm resolver using fpga and Matlab simulation?

    I am working on spartan 3e fpga board.can i implement resolver in pmsm using matlab simulation +fpga?

    Anjeet Verma · Indian Institute of Technology (Banaras Hindu University) Varanasi

    thanks

    but the native simulink blocks are not available for xilinx system generator.

    if it is? can you please tell me how to  do that?

  • How do you differentiate between acute and chronic HCV infection other than the duration of the infection?

    Do you any specific seromarkers, biomarkers or immunological tests that help in distinguishing acute form chronic HCV?

    Claudio Ucciferri · Università degli Studi del Molise

    You can help With western blot test. 

  • Dominic Evangelista added an answer in Fermentation:
    What is the effect of fermentation on DNA preservation?

    For example, if a dead tissue (e.g. metazoan) was left in an actively fermenting medium (e.g. beer), how would this affect the quality of the DNA one could extract or amplify from this tissue?

    Personal experiences or papers about this?

    Dominic Evangelista · Rutgers, The State University of New Jersey

    Please see the edited description again if it clarifies the question. Thank you.

  • William Mayor added an answer in Genesis:
    When were the Creation accounts in Genesis 1 & 2 composed, and who by?

    I am reading Mark Smith's "The Priestly Vision of Genesis 1" (2010) and finding it very frustrating.  He is so convinced that P wrote the account in the 6th century he doesn't bother to tell us why he is so sure.  I am not much disposed to believe in P, J  JE, RJE etc etc considering the fiasco that is the story of Q.  What is the evidence?  Note that I say "composed",  not "written"?  One issue is the canonical text and its editor.  Another issue is the set of sources the editor used.  A third issue of great importance is how the editor used his sources,  and what creative freedom he allowed himself.

    Chris, my "assertions" are my opinions, not hard fact.   I tried to convey that in my response. 

    Now as for chapter and verse citations, I will have to review the accounts.  I do recall having noted in one paper I did some years ago that the wandering Israelites appeared on both sides of a region that they could not get into and that should not have been possible to go around.   I noted this as a reason to suspect that there were at least two groups that merged in the "Promised land".  Likewise there is a covenant renewal ceremony recorded as being held in the Promised land, but in an area that is never listed as being conquered.  The numbers departing Egypt in the exodus are far too large to be believable as sustainable in one group. 

    Now all of these objections can be overcome if the accounts are a "we were there" type of story for a generation or two after moving into the "Promised land".  Relatively few were actually involved in the experiences, and the accounts might be a compilation of multiple groups experiences, but "we were all involved".

  • Boqiang Tu asked a question in Bioinformatics:
    Graduate programs in computational / systems biology

    I am looking for best graduate programs in computational / systems biology in US. Do you have any suggestions? Thanks a lot.

  • F. Leyvraz added an answer in Electron:
    Why don't electrons emit radiations in stationary orbits while revolving around the nucleus?

    As we know that, accelerated charged particle radiates energy while moving. why is this not so in the case of electron revolving in the stationary ortbit?

    F. Leyvraz · Universidad Nacional Autónoma de México

    The formulae of classical electrodynamics which you have in mind refer to a moving point charge. It is not appropriate to view the psi function of an electron as being the description of an underlying classical electron moving around. In quantum mechanics, if you go through the same steps which you went through in the classical case, you would find that radiation processes involve a change in the quantum state of the electron accompanied by the emission of a photon. It is not possible to have this if the atom is initially in the ground state.

  • Is RIN important when analysing microRNA?

    I've collected some clinical cytology samples from the upper respiratory tract for miRNA analysis. Unfortunately there is quite a lot of RNA degradation in the samples. We have RIN values between 1 and 9. In addition, there is some organic compound contamination, and 260/230 ratios are poor - below 1 for many of the samples. Would you trust miRNA expression results obtained from these samples?

    When I compare miRNA expression to RIN or 260/230 values, there is absolutely no correlation. The attached pdf image shows a plot of miRNA expression for each sample, plotted against RIN or 260/230 ratio. Thick dotted lines are the line of best fit. There are similar results when considering each miRNA individually.

    In the first attached publication (Jung et.al.), experimental heat-induced RNA degradation did not affect miRNA expression in several tissue types.

    In the second publication (Hall et.al.), miRNA were stably expressed in older formalin fixated cancer specimens, despite significant mRNA degradation.

    I am therefore not convinced that RIN is indicative of miRNA integrity.

    With regards to 260/230 ratio, contamination with organic compounds could reduce the efficiency of RT-qPCR, thereby reducing the measured miRNA expression and increasing standard deviation within each group. Normalisation may correct for some of this difference. 260/230 ratios are equally distributed between patient groups, so I expect that increasing the sample size and therefore statistical power will take care of this problem.

    Any thoughts? Would appreciate some input before taking on peer-reviewers :)

  • Truman P Young added an answer in Invasive Species:
    Do you know if invasive species are replacing another?

    I am interested in examples where one invasive species was replaced by a second invasive species. I am working with invasive parasites of the genus Anguillicola. To our knowledge A. novaezelandiae was replaced by A. crassus from a Lake in Italy. Do you have examples of other species?

    Thanks!

    Truman P Young · University of California, Davis

    There have been 'waves' of invasive annual plants that have invaded California, each reducing the numbers of the previous invaders.

  • Andréa Alves Araújo added an answer in Ammonia:
    Can you offer suggestions for the mechanical design of double rectifier and dephelegmator?

    I am interested in design of a compact ammonia - water absorbtion refrigeration cum milk pasteurization system for use in rural areas based on solar energy. The system can use small amount of gas/wood as a fuel. The capacity of equipment would be 2000/5000 liters per day in two shifts. I need support in mechanical design of double rectifier and dephelegmator. Any advice, reference, serious publication would be gratefully acknowledged.

    Andréa Alves Araújo · Federal University of Rio de Janeiro

    Punjrath:

    As a suggestion, I suggest you read the book:

    Refrigeration and Air Conditioning
    by Arora Ramesh Chandra

  • In your opinion to remove alien species can be considered an ecological restoration?

    In the sense of the Aichi biodiversity target n°14

    Truman P Young · University of California, Davis

    Yes.

  • Zoe E Taylor asked a question in Chaos:
    CHAOS scale in Spanish?

    I am looking for the Confusion, Hubbub, and Order Scale (CHAOS; Matheny, Wachs, Ludwig, & Phillips, 1995) in Spanish. If anyone has used this scale with Spanish speaking populations please could you contact me or send me the translated version. Best, Zoe

  • Are differential equations the proper tool to describe reality?
    Newton introduced differential equations to physics, some 200 years ago. Later Maxwell added his own set. We also have Navier-Stokes equation, and of course - Schroedinger equation. All they were big steps in science, no doubts. But I feel uneasy, when I see, for example in thermodynamics,
    differentiation with respect to the (discrete!) number of particles. That's clear abuse of a beautiful and well established mathematical concept - yet nobody complains or even raises this question. Our world seems discrete (look at STM images if you don't like XIX-th century Dalton's law), so perhaps we need some other mathematical tool(s) to describe it correctly? Maybe graph theory?
    Mostafa Gadal-Haqq. M. Mostafa · Ain Shams University

    @LGardi,

    Regarding a TOE, I don't think we could arrive to (or near) it . Simply because we are not only failed to interpret what we see (by our senses) but also our senses lack to detect Everything (at least now)!

    Thanks for the paper, it's very interesting.

  • Monosodium glutamate (MSG) and its relation to obesity
    What is the association of monosodium glutamate (also called exitotoxin) to the obesity epidemic?

    Hi Satyaprasad

    well you might be interested in the sites.

    Best regards

  • F. Leyvraz added an answer in Schrodinger:
    What is significance of Schrödinger equation in quantum mechanics?

    I am confused for the time dependent and time independent Schrodinger equation.  

    F. Leyvraz · Universidad Nacional Autónoma de México

    Physically, the difference is much like statics and dynamics in classical mechanics. In statics, you determine in which positions you must put the objects of  a system so that they do not move. In other words, you determine which states of the system do not depend on time. The equations involve setting sums of forces equal to zero, and do not involve time. In dynamics, you use Newton's equations, which do involve time and tell you about motion.

    In quantum mechanics it is similar: the time independent Schroedinger equation tells you which states are time independent. The equation, as in statics, does not involve time. On the other hand, the time-dependent Schroedinger equation tells you how a general state moves. The consistency of both view points is  maybe not quite obvious: if you have a solution psi of the time-independent Schroedinger equation, H psi = E psi, then the function psi exp(i E t) is a solution of the time-dependent equation. This does not look like an equilibrium. It is, however, because, in quantum mechanics, states are only defined up to a multiplicative phase factor.