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  • Zakia Sultana added an answer in Autophagosomes:
    How should one interpret LC3 puncta in immunofluorescence?

    Hi all,

    I am trying to detect autophagy in primary blood neutrophils using LC3 puncta as markers.

    I have attached 2 figures with different morphology of LC3 distribution (green color).

    I speculated that: In the Ctrl figure, LC3 is accumulated which indicated fewer autophagosome. In treated cells, LC3 puncta distributed in the cytosol indicating a higher level of autophagosome.

    Am I right? Could you please let me know your opinion to interpret those figures?

    Thank you very much for your help.

    Zakia Sultana · Hunter Medical Research Institute

    I am also new in the field of autophagy research. I also observed similar phenomena on my tissue samples. By immunohistochemistry analysis using antibody against LC3, I found that the number of autophagosomal vacuoles increases on serum starved samples. But I am not sure whether this autophagosome accumulation is related to induction of autophagy or not. I am very interested to see the level of LC3I and LC3II by western blotting.
    Literature suggests that the amount of LC3-II correlates well with the number of autophagosomes or the amount of autophagic membrane labelled with LC3-II. Starvation induces the conversion of cytosolic LC3-I to membrane bound LC3-II. However, when lysosomes are fused with autophagosomes, autophagy is activated and LC3-II in autolysosome is selectively degraded by lysosomal hydrolases. Lysosomal inhibitors (e.g., chloroquine, or Bafilomycin) inhibit acidification inside the lysosome or inhibit autophagosome-lysosome fusion and can block the degradation of LC3-II, leading to the accumulation of LC3-II even under non-starved conditions.

    You could find this article helpful
    “Mizushima, N., T. Yoshimori, and B. Levine, Methods in Mammalian Autophagy Research. Cell. 140(3): p. 313-326”



  • Can anyone suggest some literature on Biomimics?
    I am new to the topic (Biomimics). Kindly suggest me some good literature on this topic such as books, websites and relevant stuff.
    Maibritt Pedersen Zari · Victoria University of Wellington

    I am coming a bit late to this discussion but if you are still looking into biomimicry I have published quite a few articles about biomimicry and architectural and urban design that might be of interest. One of the key things with biomimicry is to understand if you want to look into biomimicry that is solely for the purpose of creating new technologies for the sake of innovation or if you are interested in biommicry as a means to work towards better sustainability outcomes. Not all biomimicry has the same motivations and therefore outcomes in terms of sustainability and different researchers emphasise different aspects of biomimicry. My work is about biomimicry for sustainability. Michael Pawlyn has an easy to read book about biomimicry and architecture as well that might be of interest also.

  • Sir A. Quark asked a question:
    About DC offset?

    I think that DC offset rarely causes a problem in practice, should I?

  • What (recent) accounts on language evolution would you identify as 'alternatives' outside of the nativist-v-emergentist dichotomy—if any?

    The pervasive polarization over the emergence and evolution of language—cf. nativism vs. emergentism—persists because it reflects a very relevant distinction at the core of language. So, this is hard question I'm asking but, if we were to identify alternative accounts falling a bit further from the large dichotomy—with a novel theory or method—, could you think of any? 

    Thank you

    Pablo C Bernabéu · Tilburg University

    Hi Liljana,

    In light of the method, the results make quite a turn of events indeed. Such a closer look at syntax, in combination with recent evolutionary advances, seems a timely addition to the state of affairs of this topic. Looking forward to reading more!

  • Sofiya Lazarova asked a question in Sugar Phosphates:
    Does extraction of plant non-structural carbohydrates with Methanol:Chloroform:Water also extract sugar phosphates?

    After extracting non-structural carbohydrates (soluble sugars) from Arabidopsis stems and leaves I quantified Gluc, Suc, and Fruc. Can I use the same extract (in water) to quantify sugar phosphates on HPLC? Are they present in my sample? If yes, what are some standard HPLC methods for quantification of sugar phosphates (Gluc-6-P, Fruc-6-P, Gluc-1-P)?

  • Is there a Java code for using processor cores as multiple CPUs in parallel programming?

    Java parallel programming code.

    Khalid Hasanov · University College Dublin

    If you are going to parallelize some operations based on some sequence of elements, I would suggest have a look to the Java 8 Stream API. By using that you can benefit from all the available cores without writing any single line of multi-threaded code. The API itself is based on some functional programming ideas, such as lambdas and monads.

  • What is the best simulation tool to implement bandwidth-aware VM placement algorithms?

    My thesis work on bandwidth guarantee in cloud computing.

    Arnaud R Legrand · University Joseph Fourier - Grenoble 1


    If network simulation is important, you should definitely consider the SimGrid toolkit (http://simgrid.gforge.inria.fr) that relies on fluid network models whose validity has been thoroughly evaluated (see for example http://hal.inria.fr/hal-00872476) and whose implementaion is often orders of magnitude faster than classical packet-level based simulators (http://hal.inria.fr/hal-01017319).

    The Simgrid toolkit ( http://simgrid.gforge.inria.fr ) has been extended to address virtualization and cloud computing challenges. Additional information regarding some examples are available on http://simgrid.gforge.inria.fr/contrib/clouds-sg-doc.html

    There has recently been work on using simgrid for cloud computing simulation (see for example http://dl.acm.org/citation.cfm?id=2568524). I was not involved in this work but simgrid seemed flexible enough to model non-trivial performance phenomenon of  VM migrations. 

    Knowing little about your phd subject, I cannot tell whether SimGrid is perfectly fitted for you but you should definitely look into it...

  • Joseph L Alvarez added an answer in Back:
    Can the reviewer request new additions or amendments to the article before publication?

    After doing all the amendments requested by reviewer, and after sending the article back to the editor. Does the reviewer have the right to request new amendments to the article?

    Joseph L Alvarez · Alpha Beta Gamut

    As Hanno stated, the author has an expectation to be treated fairly. It should be obvious if the reviewer is helpful or obstructive. An author should embrace helpful comments and requirements that will strengthen the final publication. An author should reject a review that obviously is delaying publication without an increase in quality.

  • Could someone suggest a technique to deactivate commercial Alkaline Phosphatase?
    I am doing chromogenic staining on embryonic tissue sections using alkaline phosphatase and peroxidase IHC. I already used HRP and AP markers but I would need to use another marker again with AP. To do so, I would thus need to deactivate the previous AP to not get the old and new signal when I develop it with an AP substrate. I was thinking of inactivating the first AP, but I think techniques such as levamisol or acetic acid do not work on commercial AP (ex ABC AP vector kit) but only on endogenous Alkaline phosphatase (which are different). Any suggestions?
    Ghislaine Lioux · Paris Diderot University

    Thank you!!!!!

  • Do you think that digital technologies can stimulate an increased interest in reading and writing and or increase the level of literacy within a society?
    In some developed countries, functional illiteracy continues to be a very serious problem, partly due to their crisis in education.. Do you think digital technologies might influence an increase in the level of literacy - particularly among children. In countries where illiteracy has historically been a persistent problem, Book publishers have been making efforts to give their books away to poorer children who have access to the internet because they believe that by introducing children to online stories these children will eventually be encouraged to read 'classical' books.

    I have been doing this sort of thing since the 1980s..

    I've worked with a number of different databases that I ran on mainframes..as well as the usual database applications that are found on personal computers. I have dealt with both relational data structures and object oriented data structures. as well as images,  statisitcal and qualitative (full text) data..  I have taught people courses on these subjects and worked in research projects with a wide range of people and institutions.

  • How to make cellulose nanocrystal films?
    What are the important parameters in the process of CNC film formation and how stable are those types of films?
    Akwasi Asamoah · University of Exeter

    When you have decided on an appropriate matrix within which to infuse or mix, the cast method in petri dishes and the like could be used. CNC could be aligned by electromagnetism before setting or curing of matrix.   

  • Does anyone know the growth rate of the amoeba Naegleria Fowleri?

    Is anyone familiar with this amoeba? 

  • Is my Network performance analysis well presented?

    my output is as in attach file

    Ranjana Pathak · University of Queensland

    Give more detail regarding the experiments and the basis of this analysis.

  • Which are the economic and social development perspectives for Africa within the Millennium Development Goals?

    Donors; Tied Aid

    John Mukum Mbaku · Weber State University

    Hello F. Saitote: It is true that many African leaders are opportunistic and engage primarily in public policies that promote their own personal interests, which include what economists call primitive accumulation. Foreign aid provides an opportunity for them to accumulate extra-legal wealth. Nevertheless, such corrupt leaders can be pushed out (as occurred in Egypt, Tunisia, and Burkina Faso) and the country's institutions reformed and restructured to provide institutional arrangements that adequately constrain those who serve in government. The process is gradual but many Africans are realizing that they do not have to continue to submit to opportunistic and despotic leaders anymore. Unfortunately, once these leaders are chased out of government, the necessary state reconstruction to produce institutional arrangements that guarantee the rule of law is not being undertaken. As a consequence, the new leaders are able to act with impunity, the same way that their predecessors did. All is not lost, especially when you consider the fact that after apartheid was dethroned in South Africa, the new government, headed by Nelson Mandela, was able to lead South Africans in their successful efforts to reconstruct and reconstitute the state and today, the country has one of the most progressive constitutions in the world. Other African countries are making progress--consider Ghana, Rwanda, and Cape Verde. I am optimistic.

  • Martha Hyde added an answer in Logical Thinking:
    Does thinking itch?

    Is it just a social habit to scratch our head as we concentrate? Or is there a scientific explanation for this fact?

    - Is it simply not natural for mammals to think?

    Or is there an unusual concentration of neurotransmissers in the blood vessels of the head, as serotonin levels, that cause itching?

    Joseph what a great explanation. It was truly worthwhile reading, along with some more serious answers given to this question.

  • Srivani Manchala added an answer in Green Roof:
    Are green roofs the only solution to make the existing cities "healthier"?

    To reduce the temperature in the city, urban heat island effect, what can be the possible solutions?

    Srivani Manchala · Deakin University

    I asked this question coz it has become very common now a days to have green roofs n make the city healthier. For example Geelong, Australia has adopted that technique to make the city green. So I was wondering if that's the best solution to make an existing city healthier. 

  • Trevor Moffiet added an answer in TASSEL:
    Why do we need Tasseled Cap when we already have indices like NDVI and EVI?

    Tasseled Cap is an orthogonal index based on Brightness, Greenness, and wetness.

    If we develop correlation between tasseled cap greenness index and EVI, we will get 99% correlation, then why do we need an orthogonal index like tasseled cap when we can map and assess vegetation by using EVI?

    Trevor Moffiet · University of Newcastle

    Dear Muhammad

    I include here some of my thoughts on indices.

    There are problems with the blind use of indices whether they be Tasseled Cap Greenness or NDVI or any of the other myriad of spectral indices. All spectral variation has to map somewhere onto any index scale. If you have a requirement to map vegetation amount  then you require an index where variation in vegetation amount maps as unique variation on the vegetation index scale. All variations associated with other landscape/atmospheric dimensions should ideally map to fixed points (not necessarily zero) on that vegetation index scale. For example the effects of shade and brightness should not map as variation on the vegetation index scale. Variation in brightness should be orthogonal to the index scale. Similarly, variation in soil dampness should not project as variation on the  vegetation index scale. There are fundamental problems with the design of Tasseled cap indices. The indices might have been designed to be orthogonal by using an orthogonal principal component transformation process but that process did not properly account for the ratio-scaled nature of the spectral data. The orthogonality of the chosen method (principal components/ factor rotation) has not resulted in the indices being truly orthogonal indices for brightness greenness and wetness.

    With uni-dimensional spectral indices such as NDVI and EVI there are no other-dimensional, companion indices like brightness or wetness to assist with understanding how the other landscape variations map onto a reduced spectral space. Some uni-dimensional indices perform better at high levels of cover, some at low levels of cover. Most are sensitive to brightness variation, smoke haze, cloud shadow, terrain shadow and background soil variation.

    When developing vegetation change maps using a vegetation index like TC Greenness one needs those detected changes over time to be vegetation changes, not some other change like soil moisture changes . In other words you don't want soil moisture variation to appear as though it is vegetation variation. (This example might only apply to some special landscapes)

    If you were mapping change in vegetation over a rainforest you would want the vegetation index scale to be sensitive to small changes in vegetation at high levels of vegetation cover but insensitive to changes in brightness and shade. I suspect, in general, that indices are used by researchers without checking whether they have the desired properties for the application at hand.

  • Akwasi Asamoah added an answer in Nanocomposites:
    Does preparation procedure of Fe3O4 nps affect XRD studies?
    It have been very difficult for me to get proper XRD peaks for the Fe3O4 nps. It might be due to too much impurity in my sample during preparation. I am using standardized sol gel method.
    Akwasi Asamoah · University of Exeter

    There is something to take from all the above. Crystal lattice/structure, degrees and proportions of amorphous and orientation influence XRD patterns.  

  • How can I mathematically model the behaviour of the humans?

    Any suggestion/resources are appreciated.

    Dejenie A. Lakew · John Tyler Community College

    As we humans are complex, our behaviors in most cases are intent and hidden goal driven. But fuzzy mathematics (a  multivalued logical structure )  can at least help to start an incomplete study of few of our behaviors that are less involved in our thoughtful decision process.

    As James put it eloquently these few  behaviors of humans  can be studied via stimuli-response mechanism in fuzzy logic setting, but the problem in this mechanism is that the responses might not be the actual or real reactions conceived by the person from the stimuli but an a priori intent driven response ( in most cases a thoughtful decision ) for a posteriori purpose. 

    Such study that bases on stimuli-response processes on human behaviors might not be therefore a real mathematical study but purely an entertainment. For instance a school principal wants to know how many kids feel happy today and those who do not happy will receive some unknown gifts so that they will be happy for the whole day.

    As happiness is a feeling that can not be measured or detected by some happy-o-meter but an information gained from direct responses of individuals,  the answer for this question may be true or may not be true. Some kids will simply say, they are not happy today (although they might actually are as happy as ever), because they want to know what the unknown gift will be and want to get one. Therefore in this case the study fails in principle to get a real response of a stimuli.

    Although I brought school kids as an example but true to almost all humans who habitually make decisions based on thinking and presumed a posteriori results or intents on any stimuli they encountered.   

  • Can anyone recommend good articles on ongoing training of elementary school teachers?

    Articles based on qualitative research methods such as in-depth interviews.

  • Luisiana Cundin added an answer in Photodetectors:
    How is the performance of an optical detector independent of temperature?

    (Of course other than the method of, "using a polymer layer with an opposite temperature coefficient .")

    I want to decrease the effect of temperature non-linearity on a refractive index and so on, of some properties of ring resonator based photodetectors, such as " Quantum Efficiency", " Responsivity", " Dark Current", "BEP" and so on.

    The use of polymer cladding layers with opposite temperature coefficients, has been studied in previous works.

    Luisiana Cundin · Die Wand : leben heißt kampf

    It has been sometime since I have thought about electro-optics, but the field - from a precursory, contemporaneous overview in the existing literature - proves similar to "my time". The Devil is in the details, but I will tell you this much: the trick is to increase the antenna size, that is, the electrodes must be increased in height in order to improve the SNR. 

  • Abdur Rab added an answer in Water Balance:
    Which soil water balance estimation would you employ to calculate the soil water change [balance] in the field?

    Data generated at the field through field-based monitoring and assessment include climate data: temperature (C), relative humidity (%), wind speed (mph) and direction, dew point, precipitation (mm), [Evapotranspiration (ETc), and we also have Evaporation measured from an evaporation pan (ETp)], Daily soil moisture (%), Adjusted Irrigation Rate; that is, if P < ETc and the average daily soil moisture was significantly lower relative to soil temperature. Given this information, which model of soil water balance would you use to compute the water balance?

    In its simplest form:

    Change in Soil Water  = Inputs of Water - Losses of Water

    If we break these two components further, we get:

    Water inputs is a function of = Precipitation + Irrigation + Groundwater charge 

    Water Outputs = Evapotranspiration + Deep Drainage + Surface Runoff

    Thus leading us to:

    Change in Soil water = (P + I + C) - (ET + D + RO)

    Some of these parameters are unknown, but can be computed, since we know others. We assumed surface Runoff (RO) to be zero due to drainage at the experimental unit, which means that RO wasn't an issue.

    Change in Soil Water:

    Inputs [P = Precipitation, I = irrigation rate [adj recharge + Cal Recharge], C = Groundwater Charge]

    Outputs [ET = evapotranspiration, DD = Deep Drainage, RO = Surface Runoff]

    Others would used the Water Balance Calculation (This is more of the general calculation of water balance and might not necessarily be applicable here.)

    Change in Volume (V) = [P + R + Bf] - [I + E + Et + O]

    Where:     P = Precipitation

                     R = Runoff

                     Bf = Baseflow

                     I = Infiltration

                     E = Evaporation

                     Et = Evapotranspiration

                     O = Overflow (this is usually not considered or considered to be 0)

    Soil Water Surplus was calculated using:

         S = P + I -ETc (SMa / t)

    Where S = Surplus, P = Precipitation, I = Irrigation, ETc is evapotranspiration, SMa = Averaged Soil Moisture and t = Time.

    Any ideas?

    Abdur Rab · Department of Environment and Primary Industries

    Yes, you are using correct method, I was going to suggest that ET calculated using 0.95 of E (pan evaporation). If you have time, climatic data you could esality calculate ETpenmann using Penmann-Monteith equation then calculate ETspinach using 0.95 x ETpenmann and compare with your method.

  • Raana Ramouz added an answer in Antibodies:
    Could anyone tell me what I should dilute my antibody in during using of sure beads in a IP test?

    Hi, I am using new sure beads for a IP test but I am not sure if I should dilute my antibody in PBS or PBS tween ? (the protocol is not detailed at all) On the other hand I tested them in parallel with protein A beads but I see the bands in my control of IP in sure beads case! Also I have a background noise, are there any suggestions for reducing this background noise? and I want to also know if sure beads are better than the others.

    Thanks a lot

    Raana Ramouz · Cancer Research Center of Lyon

    Thank you all so much. i started to dilute my antibodies with RIPA and it worked :)

  • Cristina Leonte asked a question in Risk:
    RISK PREMIUM CAPM: which risk premium do you use for evaluate a company starting from the next year, 2015?

    Ignoring that it has a lot of shortcomings, which source do you use for this parameter? and what number do you use? please if you answer, tell also the industry of the company you are talking about.

  • Jenny Lawrence added an answer in Dialysis:
    Is there anyone who knows where to find a dialysis membrane in a polysulfone or in any other material but cellulose?

    Non-cellulose dialysis membranes?

    Jenny Lawrence · St. Vincent's Hospital Sydney

    Fresenius is the company you need to contact. All their dialysis membranes are made of polysulphone.

  • Can anyone recommend good articles on ongoing training of elementary school teachers?

    Articles based on qualitative research methods such as in-depth interviews.

  • Do you think that the Von Neumann Architecture will be diminished within the next few years? and what is the next computer architecture as you see?
    There are new discovered devices which are nonvolatile. They motivate us to think about brain modeling. Is it possible? Are there any other newly coming architectures?
    William H Ett · MITRE

    Look into quantum computing.

  • Steingrimur Stefansson added an answer in Proteases:
    Is there any shortcut method for extracellular protease activity?

    Except from the conventional method by folin reagent.

    Steingrimur Stefansson · HeMemics Biotechnologies Inc

    Hi Atanu, the descriptor "alkaline proteinase" is mostly used for bacterial and fungal proteinases that work under alkaline conditions.

    It does not describe their substrate specificity, nor to which class of proteinases they belong.

    So, is your alkaline proteinase a serine, cysteine, metallo, or a aspartic proteinase? Do you know its substrate specificity?

  • What is a standardised psychological test for measuring Peer relations?

    For measuring Peer relation is there a standardised psychological test?

    Béatrice Marianne Ewalds-Kvist · Stockholm University

    Dear Sasmita,

    I have found drawing a sociogram in a classroom  very useful. A sociogram is a charting of the inter-relationships within a group; the basic "network" of friendship patterns and sub-group organization is revealed. The relations of any one child to the group can be seen e.g. if a child is completely isolated.  This gives potential for developing greater understanding of group behavior to operate more wisely in group . SOCIOMETRY IN THE CLASSROOM , how to do it

    is found here: http://www.users.miamioh.edu/shermalw/sociometryfiles/socio_are.htmlx