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  • Jack M Gallup added an answer in RNA Extraction:
    5
    How to remove RNaprotect from lysited cells before RNA extraction?

    my samples are disrupted cells in RNAprotect + PBS. I have tryed to perform RNA extraction using Trizol but i get litle RNA concentration and pourly clean. Any suggestions about removing the RNA protect? Thank you

    Jack M Gallup

    The expected RNA yield from 5000 cells (if mammalian/human) is actually about 7.5 ng/uL (when diluting the final RNA pellet in the 20 uL that you add back at the end and assuming 100% recovery at the rate of 30 pg total RNA/cell).  So you are actually getting readings (50-80 ng/uL) that exceed by ~10X what would be expected from this small number of cells.  You should try to increase the number of cells you are isolating to ~5 million.

    NanoDrop readings in your current range could be a little shaky - so perhaps that is where your 'random' concentration values are coming from with these relatively low RNA concentrations. Where you are getting the 10-fold higher RNA than expected is curious...

  • Pavla Stojkova asked a question in Bacterial Transcription:
    New
    Has anyone experience with ChIP and bacterial transcriptional factors?

    I am going to try applied this method for prokaryotic cells - gram negative bacteria. I want to define regulon of DNA-binding protein. My protein is non specific binding to dsDNA. Is it problem?

  • Vincenzo Fiorentini added an answer in VASP:
    7
    Whether there is dielectric constants for metal? How to calculate the dielectric function for metal with the standard DFT based on VASP?

    I want to study the optical properties of metal based on VASP. However, some arguments say there may be no dielectric constants for metal. Furthermore, using LOPTICS=T bases on the formula which requires wave functions of the conduction and valence band. Thus it may be not appropriate to use LOPTICS.

    Vincenzo Fiorentini

    compare the two in the same diel func values window (say, -1 to 5). I suspect they will be similar around the plasma frequency.

  • Shuichi Shinmura added an answer in Data Science:
    4
    Is Big Data handling/analytics really a big challenge?

    Now these days 'Big Data' is being considered a vital field of research ( rather I should say it is a buzzword in today's data science research community). This question, I want to float to discuss some real challenges pertaining to Big Data handling for various purposes. So many researchers are viewing this filed merely as extended field of distributed processing by simply dividing the task into small pieces and then agglomerating the results to handle scalability issue( i.e. simple design of map and reduce procedures).

    I request respondents to provide references of vital resources, which are posing challenges( theoretical as well as practical aspects) to understand Big Data environment in true sense and to understand difference between distributed environment and big data environment.

    Shuichi Shinmura

    Over ten years, many researchers analyzed the microarray data and could not conclude clear results. I proposed the Matroska feature selection method for microarray data that consists several small linear separable gene sub-spaces and other high-dimension gene spaces that is not linear separable. Therefore, we can easily analyze these small genes sets. Download my papers from RG. 

  • Marta Vila Cejudo added an answer in alpha-Fetoproteins:
    3
    Can anyone reccomend me a good antibody against alpha fetoprotein?

    I have been using for long time AFP from Dako, but from several months I am not able to obtain a good signal and I observe spots and precipitates, and there is no apparent reason for having trouble, since other antibodies work as usually. 
    So that, I would kindly appreciate your references from other AFP-antibodies that give you no trouble.

    Thank you in advanced!

    Marta Vila Cejudo

    Dear Amilcar,
    I've realized that I haven't specified the tecnique nor the specie of my research. I am interested in an antibody against AFP for Immunofluorescence in mouse samples. Do you think that your antibody fits these conditions?

    Thank you very much!

  • Emanuel Xavier added an answer in Microalgae:
    6
    What are the wavelengths that we should read for calculating chlorophyll a, b and carotenoids in microalgae by spectrophotometry?

    The literature varies widely with respect to these values.

    Emanuel Xavier

    Many thanks to all, your help was critical.

  • Matteo Paganoni added an answer in Fluid:
    3
    How can we distinguish between real morphology and artefact within a fluid-escape pipe in 3d seismic (sometimes called chimneys)?

    ...''Fluid escape pipes as defined here as highly localized vertical to sub-vertical pathways of focused fluid venting from some underlying source region and are recognizable on seismic data as columnar zones of disrupted reflection continuity, commonly associated with amplitude and velocity anomalies, and scattering, attenuation and transmission artifacts (from Cartwright and Santamarina, 2015)...''

    Matteo Paganoni

    Thanks everyone!

  • Xavier Le Polozec added an answer in Instrumentation:
    6
    What is the fundamental limit on thickness of microwave absorbers?

    Like there is chu and harrington limit on the size of electrically small antennas, I would like to know whether any such limit exists in absorbers? If not, then how would we define some absorber as electrically small absorbers?

    Xavier Le Polozec

    Hi

    The following paper could be usefull as well

    http://www.microwavejournal.com/articles/25704-basic-rules-for-anechoic-chamber-design-part-one-rf-absorber-approximations

    Best Regards

  • Klaus-Holger Knorr added an answer in Biogeochemistry:
    2
    Does anyone have protocols for carbonate removal from freeze-dried dissolved organic matter?

    The aim is to eliminate inorganic carbon for isotopic analysis (13C an 14C) of organic C. DOM  has been concentrated by reverse osmosis from river water samples.

    Klaus-Holger Knorr

    If you analyze it as freeze dried material, you can follow protocols to remove inorganic carbon from soils and sediments, keeping in mind that you might have much less carbonates in your solids and therefore reducing the amount of acid to minimize negative effects on the elemental analyzer. Some people prefer adding acid into tin or silver capsules, other fumigate their capsules in HCl vapor. It depends probably on which method is established in your lab.

    On the other hand we use a TOC analyzer coupled to a Picarro CO2 isotope analyzer. In this case you keep using a liquid sample, the DOC or TOC is digested and the resulting CO2 is analyzed. An acidification step prior to analysis removed DIC, as in a normal TOC/DOC analyzer.

  • Samira Lalaoua asked a question in Lanthanum:
    New
    What is the lanthanum oxide structure?

    I did the mechanical grinding of lanthanum oxide but I had an obstacle to determine the probable structure of this oxydeau beginning I found at least three ifferent structure.

    more after grinding I found only the phase of the oxide of hexagonal structure?

  • Rajinder Singh Brar added an answer in Poultry Health:
    7
    What are vaccination programs for broilers, layers and breeders in Brazil?

    I would be very pleased if someone can tell me where I can find recommended vaccination programs for broilers, layers and breeders in Brazil.

    Rajinder Singh Brar

    Follow Merck Veterinary Manual keeping in view the diseases prevalent in area

  • Christina Vogelaar asked a question in Recombinant Proteins:
    New
    Does anyone know a specific Cre antibody for immunohistochemistry?

    Some neurons in glial Cre mouse express the transgene. How can I find out whether this is aberrant recombination or protein transfer? The Cre Ab in our lab is not working well on tissue. Does anyone know a good antibody, that they have used for IHC? I'm not interested in cell culture or Western blotting.

    Thank you very much in advance

  • Raymond J Ritchie added an answer in Microalgae:
    3
    How is the economic feasibility of using microalgae biofuel as renewable energy?

    I've been read some journals about microalgae biofuel. I think it seems to be feasible in engineering view because microalgae have high content of lipids and carbohydrate. Beside that, microalgae also have high growth rate. But, I doubt its feasibility in economic view because the first investment is very high. How do you think about this? Can you give the other sources of biofuel which more economic feasible than microalgae?

    Thanks anyway

    Raymond J Ritchie

    This is a pipe dream.  A reasonable 2nd year undergraduate student should be able to work out that it cannot work.  I have been telling people that for years.  The response has been interesting.  Some have said "Yes - I do know but my funding depends on it" but most have simply not understood what I was trying to tell them.

    It has got nothing to do with refining the oil.  You can make biofuel out of almost anything. It is simply that sunlight is a dilute energy source and the land area of shallow ponds required that makes the whole proposition comical.  See some of my papers (Ritchie 2010, Ritchie and Larkum 2013, Ritchie 2013).  All are on Research Gate.

  • Saeed Qureshi added an answer in Pharmaceutics and Pharmaceutical Technology:
    35
    Dissolution testing of tablets- Which is the most accepted method for the purpose?
    All the pharmacopoeias have given the standard procedures for performing this test. Which is the most accurate and acceptable as far as the pharmaceutical industry is concerned? Or do they have their own in-house methods for these purposes?
    Saeed Qureshi

    Upcoming Webinar  (BioRelevant Drug Dissolution Testing)

    (http://www.drug-dissolution-testing.com/?p=2204)

  • Steven J. Wright added an answer in Open Channel Hydraulics:
    22
    Is manning equation the best method to determine the discharges in open channels?

    Is manning equations the best method to determine the discharges in open channels?

    Steven J. Wright

    I think a better answer and neglected by most of the discussion is no. Using a uniform flow equation, regardless of the one selected, will never be "the best method" to determine discharge simply because too many things are uncertain.  For example, the conventional application of Manning equation is to use bed slope in the analysis but it should be the energy slope that should be applied for gradually varied flows, which most open channel flows would better be approximated as.  So you need to use the right slope first of all.  Then there is the problem of roughness coefficient.  Manning equation effectively was developed under conditions that would best be approximated as high Reynolds number flows, so would need to conform to that.    Assuming that this condition is satisfied, there is some difficulty in estimating n value.  Even if we have some well-characterized channel lining such as concrete, for example, Sturm's Open Channel Hydraulics book has a detailed table providing Manning n values that range from 0.01 to 0.02 for concrete.  This implies that even for concrete lined channels, there could be tremendous uncertainty in the discharge and the problenm only gets worse in natural channels.   Having some sort of control such as gate or weir is a far better method to determine the discharge

  • Matthew Mcgrath added an answer in AES:
    1
    I need a compound that give a colorful product in reaction with 4-hydroxybenzaldehyde?

    4-hydroxybenzaldehyde separated as a byproduct in some reaction and determined by spectroscopy method, If some derivatives of this compound have a color in Visible area, detection of this compound became more easily.

    phenyhydrazine may be helpful? 

    Matthew Mcgrath

    A 2,4-dinitrophenylhydrazone derivative (made with 2,4-dintirophenylhydrazine) might be coloured.

  • Arnold Trehub added an answer in Cognitive Systems:
    99+
    Is Chalmers' so-called "hard problem" in consciousness real?

    In his 2014 book "Consciousness and the Brain: Deciphering How the Brain Codes Our Thoughts" Stanislas Dehaene wrote "Chalmers, a philosopher of the University of Arizona, is famous for introducing a distinction between the easy and the hard problems. The easy problem of consciousness, he argues, consists in explaining the many functions of the brain: how do we recognize a face, a word, or a landscape? How do we extract information form the senses and use it to guide our behavior? How do we generate sentences to describe what we feel?

    “Although all these questions are associated with consciousness,” Chalmers argues, “they all concern the objective mechanisms of the cognitive system, and consequently, we have every reason to expect that continued work in cognitive psychology and neuroscience will answer them. By contrast the hard problem is the “question of how physical processes in the brain give rise to subjective experience … the way things feel for the subject. When we see for example, we experience visual sensations, such as that of vivid blue. Or think of the ineffable sound of a distant oboe, the agony of an intense pain, the sparkle of happiness or the meditative quality of a moment lost in thought … It is these phenomena that poses the real mystery of the mind”."

    Stanislas Dehaene's opinion is "that Chalmers swapped the labels: it is the “easy” problem that is hard, while the “hard” problem just seems hard because it engages ill-defined intuitions. Once our intuition is educated by cognitive neuroscience and computer simulations, Chalmers’ “hard problem” will evaporate".

    Personally, I agree with Stanislas Dehaene's opinion.

    Arnold Trehub

    Alftrdo: "The astrocyte network integrates the patterns instantiated by a large distributed population of (neuron) dendrites, resulting in the feeling of the episode (for instance, scoring a goal is composed of several patterns, including the ball, the field, the other players, the referee, the audience, etc. etc.)"

    The large population of autaptic neurons in retinoid space already has integrated all the features/patterns that you mention, and does so by organizing each feature in proper spatio-temporal register (feature binding) within a global space with a locus of perspectival origin (the core self, I!). I don't see how the astrocyte network can conserve the egocentric spatiotemporal organization -- the distinctive subjectively organized  combination of sensory patterns that give each feeling its special quality -- of the conscious experience, and even if it were able to do so, I don't see what it would add to the experience. Notice that I am not claiming that astrocytic networks are not necessary for the proper function of the retinoid system.

  • Lakshmi durga Maddukuri asked a question in Nutrients:
    New
    Even though, STCR based SSNM studies has been thoroughly done in Agricultural crops, Why research is so scanty in Horticulture using STCR approach??

    In the era of sustainability, soil test based fertilizer approach is one of the viable option to follow for the dynamic adjustment of nutrients based on soil nutrient status. Even though STCR based SSNM concept emerged in the early 1960's and a lot of research has been done on food grains and cereal crops, why that kind of research has not implemented in flower crops till now. How far it is worthful if we follow in flower crops too???

  • Victoria E. Palau added an answer in Drug Synthesis:
    4
    What cell density to use for MCF-7 and MDA-MB-231 MTT/MTS assay after treatment with common cancer chemo agents?

    I am screening for drug synergy but can't quite seem to get some of the chemotherapeutics library working in a 96 wells MTS assay. I have read somewhere that some drugs work well in high and low cell density/proliferation rates and some drugs work only on rapidly dividing cells. What is the optimal cell density for MCF-7 and MDA-MB-231 cells? 

    Victoria E. Palau

    I agree with Robert, cells should be between 70-80%. You might have to wait 48  hours to see the effect of the chemotherapeutic agent (5-fluorouracil for example). But if there is a synergistic effect the treated cells will not be able to recover. Dose your cells with the drugs and plan to run the MTT 48 hours after dosing.

    Good luck

  • Kristian Spilling added an answer in Marine Virus:
    3
    What is the carbon content of marine virus?

    I am looking for the carbon content of individual virus (e.g. fg C virus-1) and its variability. 

    Kristian Spilling

    Thanks for the paper Sigitas, an approximate value of 0.055 fg C virus-1 is just what I was looking for :-)

    Another paper I found was Steward et al 2007. Deep Sea Res I: 54:1744-1757

  • Giuseppe Cotellessa asked a question in Hepatitis E virus:
    New
    Could Shells of Hepatitis E Virus Deliver Drugs to Kill Cancer and Treat Other Diseases?

    The viral shell could be  selected because the Hepatitis E virus is able to travel through the digestive system without being destroyed,

  • Sujoy Sarkar added an answer in Cyclic Voltammetry:
    3
    Can any one help me how to calculate specific capciatance from cyclic voltammetry graph?
    Sujoy Sarkar

    Dear Amol,

    You can message me in RG.

  • Lilliana Ramos-Collado added an answer in Drama:
    73
    Why is writing drama on the decline?

    Novel has considerably replaced drama. Some amount of drama is found only in a different genre - film. I think Television, Video and Film restrain people from going to the theatres. Theatre gives enormous scope to dramatic literature which other media cannot. I would like to know and be connected with modern English playwrights in Britain and USA. Some experiments are made in India, but they are not worth the salt.

    Lilliana Ramos-Collado

    There are other thoughts in my mind, Sibaprasad. Greek tragedy was a three-part unit, and we only one we have complete tragedy: The Orestia, by Aeschylus. Aeschylus is the oldest  of the authors, and it is evident that Sofocles and Euripides were very different from him, so we do not exactly know how was the three-part tragedy of Oedipus by Sofocles or the three-part tragedy of Medea by Euripides, for example. All three-part tragedies were rounded up in the end by a "satyr play", a sort of antidote to catharsis. We are judging what a tragedy is on the basis of extant single-parts of what were very complex three-part plays. 

    It bears noting that Greek tragedy used mythical situations that were never contemporary with the audience, the only exception being Aeschylus' The Persians, for which he was fined by the city because the present time should never be staged on the theater. We should ask why was that: maybe because they thought the audience needed distance in space and time in order to be able to examine clearly the political issues at hand.

    Then, in France in the last 20 years or so, there has been a sort of" revolution" of classical philologists who claim that the Greek "dictionary", literally "created" by the Germans in the 18th century, is very confuse and lacking in correct definitions and examples, and they have taken to renewing that dictionary in view of current philological discoveries. A case in point is Nicole Loraux's very eloquent book Tragic ways to kill a woman, where she  explores the meaning of only two words —neck and fly/float— which have a great importance in tragedies where women might be the protagonists. Loraux discovered that current dictionaries of Greek (including classic Greek) do not include the evident meaning of these two key words in their tragic context. If that happens with just two words, can you imagine, Sibaprasad, how many ancient literary words are not being correctly understood by us because we lack their full semantic import?

    My guess is that the the meaning we give to tragedy, and our current interpretation of this Athenian phenomenon, are off the mark, and that we have taken away from ancient tragedy what was more important: it's metaphorical import and its intense political intent. Maybe that is one of the reasons why tragic theater is not quite working since Shakespeare and we should ask why Shakespeare has been really the only successful tragedy author after the Greeks.

    My best, as always, Lilliana

  • Robert Kiss added an answer in Chemoprevention:
    7
    How does a chemo-preventive compound inhibits the cancer growth in mice model?

    Dear All,

    I'm using DMBA/TPA to induce the skin cancer in Balb/C mice, I would like to know how does my compound of interest in inhibiting the growth of tumors. What are the mechanisms that are involved in the inhibition of the cancer in the skin of Mice.

    Please help me to get a clear concept of this phenomenon.

    Thank You

       
    Robert Kiss

    Dear Vladimir,

    In an ideal World, what would be your choice of language for the world scientific community ... ? ...

    Robert

  • Marcelo Guimarães Silva added an answer in Joint Prosthesis:
    1
    Are there other calculations which can be used to determine the thickness of the knee femoral component?

    Hi,

    In my research I am designing a femoral knee component. I found a simple calculation in the paper entitled: "Custom Design of Knee Joint Prosthesis by Using Computerized Tomography (CT) Images and 3D Modelling," in which the authors calculated the required thickness using a cantilever beam. This is shown in page 4 and 5, on the journal paper attached.

    Can anyone tell me if there are other methods to determining the minimum thickness of the femoral component? An FEA model will be later used, but first I want to determine the thickness of the femoral component based on a calculation.

    Thanks.

    Robert

    Marcelo Guimarães Silva

    Hi Robert,

    There is an algorithm has been developped by Schnurr et al. (2011) in which tey developped a type of calculation to find to resection depth of tibia. I don't know if this study will can help you, but maybe it will clarify your ideas. In any way, I found some others papers which can deal with this subject.

    Sincerely yours,

    + 2 more attachments

  • Xavier Sans added an answer in Mixed Models:
    2
    Do you think that high school students would be mature enough to deal with a blended-learning model of learning?

    May be this facator  precisely the great handicap for a mixed model?

    Xavier Sans

    Thank you so much. I'm sure it will be very interesting.

    Thanks again

  • Emmanuel Buganga asked a question in God:
    New
    One God or Two Different Gods (Christian and Islamic)?

    In Feb. 7, 2015 it was posted at [http://www.npr.org/sections/thetwo-way/2016/02/07/465916095/professor-who-said-christians-muslims-share-a-god-is-leaving-christian-college] an article about a professor Larycia Hawkins from Wheaton College, an evangelical one who declared that Christians and Muslims share one God. The result was for her being chased out of her career.

    With sincere mind and understanding, can we contribute our perception on this matter? Objective proofs will stand as facts of the discussion. Are Christians and Muslims share one God? What about other gods of other religions?

  • Eric Lord added an answer in Gravitational Field:
    99+
    Is the clock rate of free falling clocks the same?

    In a gravitational field of a homogeneous spherical mass M, a sufficiently small mass B, compared to M,  is left free in the gravitational field of M at a certain distance H from the center of mass, outside his surface. B gains speed, relative to the center of mass M, because of gravitational attraction. Many small objects like B free fall from different heights or from the same height at different instants.

    Every object has an atomic clock on board. Would these clocks have the same clock-rates during the free fall?

    A reference, master clock has to be adopted, otherwise the problem is ill posed. Clock-rates are refererred to an atomic clock on the surface of M for example (negligible M  rotation speed).

    The time elapsed for each body to go from the same starting and ending point counted by the atomic clocks on board is certainly the same (UFF).

    Their clock rate should be different, in general, unless they start from the same position and instant. Not because  light takes less time to reach the closest, since they are in different positions, but  because there exists a  relation between the very small object and the massive object.

    I would like your opinion regarding this problem.

    Eric Lord

    Stephano ~

    yes I agree so where is the kinematics? They belong to different world lines, that is basically what make them different, but they don't go for different paths. So there is a intrinsic difference, the only thing is to properly characterize a worldline, not as abstract math but something which has a physical meaning.”

    Kinematics deals with how things move; it’s exclusively about about positions and times. Once one considers also masses, energy, momentum, and forces, then it is Dynamics. None of those concepts enter into the solution of this problem. That’s why I it’s a kinematics problem. (Keeping the clocks at fixed positions does admittedly require supporting forces that prevent the clocks from falling, but that’s a consideration that lies outside the scope of the problem. And gravity is not a “force” in the context of  GR…)

     The clocks are “not moving”. But motion is relative, not absolute. We have to ask “not moving relative to what?” They are obviously moving, for example, with respect to any inertial observer - ie., a freely falling observer.

     I can’t understand you when you say “the only thing is to properly characterize a worldline, not as abstract math but something which has a physical meaning.” To my mind a “worldline” is not  “abstract maths” it’s a very real physical thing. The “trajectory” of an object is a description of the way it is observed to move relative to some  reference system (eg, a set of observers).  That is a “mathematical abstraction”. The object’s “worldline” is the reality that underlies all the possible descriptions of the object’s motion. It is independent of the reference system.