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  • Harold Gomez asked a question in Procedures:
    Is CFU-f a suitable procedure to confirm presence of MSC?

    Can anyone comment in whether CFU-f is a suitable procedure to confirm the isolation of MSC? I am using several surface markers, CD45, CD14, CD34 and CD90 to negatively and positively select for porcine MSC. I want to know whether CFU-f is suitable for confirming the isolation or whether another technique is recommended.

  • Can anyone help me find a method to semi-automate the analysis of mitochondrial morphology with electron microscopy images?

    We are currently measuring mitochondrial length, width, area, etc within electron microscopy images. Since this is performed by manually drawing around each mitochondrion in a given image, it is terribly time consuming. We are looking for a semi-automated method. Unfortunately these mitochondria are not labelled in any way.  Since the EM images are inherently noisy, we are not sure how to effectively detect mitochondria. Any suggestions?

    C. Lopez-Molina · Universidad Pública de Navarra

    my advise in here might look very different from what the others said, and that's mainly because my field of expertise is image processing (IP), not really biology. However, I am (co-) affiliated to a department of Bioengineering, what gives me some expertise on how these problems/collaborations can be carried out.

    I do recommend you to find an expert on IP,  and to give him/her original images + hand-made solutions (half a dozen of them might be enough). I'd be good if he/she's an expert you can talk to in a fluent and quick manner for him/her to be sure what you need, and also the degree of precision you need. There's probably someone around your research center with a career on IP, and he/she will now how to customize some simplistic technique. By playing out with some usual  techniques (bilateral filter, anisotropic diffusion,..) and some segmentation  technique, bioengineering imagery problems are usually solvable. If having the chance of going semi-supervised, I'd bet you get it done extremely soon. That's  usually what an IP guy does in those collaborations: not really research, just  assistance and support to bioengineers.

    Packaged software is usually hard to start with, then includes many parameters which you don't usually get to understand. And the results might or might not fit your needs. Plus, not understanding the tools you use in your research is to be avoided, if possible.

    So, from my experience, find someone nearby who researches on IP. You'll benefit from mutual collaboration and for us (IP researchers) doing something "real"  is usually challenging and fun. If you have no one with that profile around, I'm sorry that my comment was useless...


  • Filippo Salustri added an answer in Philosophy:
    Can ethics be measured objectively?
    Ethics, ethical committee, ethical approval and other ethical related words are extensively used on Researchgate and other places. How to define and measure ethics in objective bases?
  • Why are my DNA samples smearing?
    I am getting smearing as you can see in the pics attached. Please tell me where the problem could lie.
    Gary Laco · The Roskamp Institute

    RNA contamination, ran gel too fast (MW markers are smiling), samples are partially degraded due to age/storage conditions or were not denatured fast enough at a low temperature and so allowed DNAse to partially degrade the samples.

  • How do you make VCF files from excel files?

    Hey I am doing data analysis and I used Variant Studio tool for annotation and visualization. The Problem with this tool is that I only get Excel files ot TSV files but no VCF files. But I need them as VCF files for other tools. How can I change them into VCF? Is there an easy tool?

    Tank you !

    Khandker S. Ishtiaq · Florida International University

    plz follow the link

  • Does someone know of references for a sociology of error?

    I am looking for good references to a sociology of error (if there is such a thing), preferably in the area of science. By that I do not mean it in the sense denounced by David Bloor (as a self restriction sociology of knowledge puts on itself). What I am thinking of is an analysis of how the concept of "error" is ascribed to various situations, how it is used as resource, types of error ascription, etc.

    I am without formal training in sociology, and so, I am not sure whether this is a trivial question, or an interesting one.

    Thanks in advance!


    Patrick Watson · University of Waterloo

    Dianne Vaughan's work is important in terms of the complexity of using post hoc circumstances to evaluate in situ decision-making and 'error'.  You would be well served to consider her work before setting forth any hypotheses about error and spotting errors... 

  • Mahesh K. Varpe added an answer in FLUENT:
    How can I estimate uncertainty in the predicted result of CFD?.

     I have done a steady simulation of an optimized case using K-Omega SST turbulence model .I have an optimized model for a low speed application and the operating condition is fixed.The benefit, as predicted by Ansys FLUENT, is encouraging but how can I compute the uncertainty?

    Mahesh K. Varpe · Indian Institute of Technology Bombay

    Thank you Casanova and Abimael for valuable inputs.

  • Albino Bacolla added an answer in Mind:
    Are there any resources available to map SNPs and other genetic variations to the pathways?

    And what would be the probable criteria that one should keep in mind for doing the same?

    Albino Bacolla · University of Texas at Austin

    Would it be useful to start looking at the set of variants in the Human Gene Mutation Database and see if any of these coincide with your set?

  • What's the best statistical method of comparing two plant surveys of the same study area?

    The same random sites were used within  the study area for quadrat sampling 35 years apart. The species richness and diversity has changed over time so I'm wondering what is the most statistically sound method of comparing these two results.

    Keron Campbell · Institute of Jamaica

    Thanks much Luiz, Nestor and Vanessa! I'll look into the suggestions made. 

  • Chandani Chandra Neupane asked a question in Masonry:
    Which Finite Element software is best suitable to capture the failure mechanism of brick masonry infilled reinforced concrete building?

    I am doing thesis in effect of masonry infill walls on the failure mechanisms of low rise reinforced concrete frame building under seismic loading. It is possible to model whole building or not ? and how about opening in the infill panel. Is it possible to capture failure mechanism by using performed 3D or not? Which Finite Element software is best suitable to capture the failure mechanism of brick masonry infilled reinforced concrete building (with and without opening)?

  • Adem Ozcelik added an answer in Micromixing:
    Smaller channel = larger viscous effect = hard to be mixed, then why are we using micromixers?

    According to reynold no, the smaller the pipe diameter the larger viscous effect.

    How could this help making perfect mixing in microreactors?

    Adem Ozcelik · Pennsylvania State University

    Microfluidic devices are used for their advantages such as small sample consumption, precision and ease of operation. However mixing becomes an issue due to low Re's numbers so there is a need for micromixers. 

  • How to avoid protein foaming during sonication?

    Protein foaming during sonication is a sign of protein degradation. I tried my best to avoid it by using low amplitude (up to 60%) sonication but still i find foaming in the protein sample which makes lysis inefficient. My lysis buffer contains 10mM imidazole, 300mM NaCl and 10mM TrisCl pH 8.0. Can any body suggest some antifoaming agents which can improve my sonication?

    Gaurav Kumar Singh · IIT Kharagpur

    Thanks to both of you for suggestions. Does the size of sonication probe affect foaming? Well, I guess it does.  

  • Cesar Ortiz Ledon asked a question in Nanoparticles:
    How can I calculate accuretely the concentration of Pt nanoparticles I synthesized size is 4 nm?

    My calculation tells me I supposed to have 1 micronolar but I dont I have try it several times and same problem I get about 40 nm of Pt nanoparticles

  • Matts Roos added an answer in Photon Science:
    How can we explain the gravitational blueshift according to the relationship between photon energy and its frequency?
    The Einstein field equation or Einstein equation is a dynamical equation that describes how matter and energy change the geometry of space-time, this curved geometry being interpreted as the gravitational field of the matter source.Einstein tried to propound geometrical structures of space by mathematical equations. So, he used non-Euclidian geometry. There are three considerable notes on Einstein’s equations;1- Einstein Field Equations do not come from the equivalence principle directly. These equations are simply equations that are suitable for general relativity.2- There is a physical explanation for the path of light in a gravitational field. Although explaining the frames of reference is a physical conception, there is not any explain of how gravitational field affects photons.3- Space-time is a continuously quantity in general relativity. But the changing of photon frequency and production of energy is quantized. That gravitational blueshift (or redshift) is a special case of gravitational field affecting the photon.My question is therefore: how can we explain the gravitational blueshift according to the relationship between photon energy and its frequency?
    Matts Roos · University of Helsinki

    V. Fulcoli

    Your statement a photon never travels but it is already everywhere in its path is wrong. Photons emitted from distant stars, say supernovae, will be observed in a distant future because they travel over real distances with the velocity c.

    Yes you are able to give a location to the photon, those from a supernova explosion travel as a light front until they are observed.

  • Ahmed Bahloul added an answer in Supercapacitors:
    If i prepare a new (unknown) composite material as supercapacitor/pseudocapacitor, then what should be its potential range for CV curve?

    As per my knowledge it should be  +-0.5 V with respect to the open circuit potential. but in practice it is not true. please advice.

    Ahmed Bahloul · Laboratoire d'electrochimie et des matériaux, Setif

    It depends with electrolyte that you use, for an aqueous electrolyte you can go until 1V.

  • Buenaflor Jimenez added an answer in Trout:
    What is your diagnosis for this recent mortality in Rainbow Trout Fish?

    New mortality was observed in Rainbow trout fish farm lethargy and anorexia, unilateral exophthalmia, hemorrhage in eye orbit, septicemia in moribund fish were most important clinical signs. The highest prevalence and incidence of the mentioned bacterial disease were observed more in end of spring and summer seasons. In fact, disease was disappeared in low temperature of water supply.

    What do you think about causative agent of mortality?

    Buenaflor Jimenez · Mindanao State University - Iligan Institute of Technology

    Your description of the recent mortality of your rainbow trout is a characteristic manifestation of Pseudomonas and Aeromonas infections. We encountered similar manifestation in Oreochromis:  darker pigmentation, hemorrhagic and eroded scales and body surface, exopthalmia and mass mortality. 

  • Ibrahim Al Nasr added an answer in Toxoplasma:
    Has anyone cryopreserved Toxoplasma and Leishmania?

    Has anyone cryopreserved Toxoplasma (tachyzoites) and Leishmania(promastigotes) in -80. Is it suitable for long term preservation? 

    Ibrahim Al Nasr · Qassim University

    thanks dear edmundo

  • How can we prepare TEM samples without affecting the microstructure?

    I am planing on doing some TEM measurement on aluminum alloy. I would like to know the best practice in sample preparation without microstructure alteration?

    Thank you.

    Patitapabana Parida · National Institute of Technology Rourkela

    use of dichloromethane as solvent to disperse the particles without interrupt the micro structure of composite

  • Samir Ghosh asked a question in E.G:
    What techniques can be used to extract Indium Sulfide flakes?

    Hi, I am doing a research on deposition of Indium Sulfide on various substrates(e.g Silicon, glass). I was curious to know how to extract the flakes of Indium Sulfide from the substrates surface.

    It would be really helpful if anyone could suggest me with any techniques to extract Indium Sulfide flakes.

  • Is t-BuOK a suitable base to esterify an acid chloride (using phenol)?
    Esterification is one of the easy reactions in synthesis. I think, t-BuOK is a selective and suitable reagent to esterify an acid chloride using Ph-OH. And it wouldn't affect the other groups.
    Aaron Bloomfield · Yale University

    It depends what the acid chloride is. I might worry about the butoxide attacking to form the t-butyl ester. Tertiary amine bases like triethylamine, diisopropylethylamine (Hunig's base), and N-methylmorpholine are basic enough to deprotonate phenol, and won't irreversibly react with the acid chloride.

  • Does anybody have experience with heavy metal determination by AAS?

    Dear all,

    I've collected the tannery effluent and treated it with my purified enzyme. When I checked the heavy metals in atomic absorption spectroscopy, the concentration of copper in tannery effluent was 1.05 mg/L and, when treated with my enzyme, the concentration should be decreased down to 0.34.

    What does this mean? Is the enzyme (protein) capable of adsorption?


    Thank u nadwiga and ahamad for your contribution. is there detoxification?

  • Harold Gomez asked a question in Protocols:
    Protocol for Adipocyte differentiation studies in porcine MSC

    Can anyone suggest a suitable protocol for studying adipogenic differentiation with porcine bone marrow derived mesenchymal stem cells (BM-MSC) - primary culture? I have found many articles but each article details different cultivation procedures.

  • What is a set of general criteria used for introducing health technology?
    I am looking for comprehensive elaborations, presenting a set of criteria for introducing / adopting / market approval of drugs and medical devices. Could you recommend some reading?
    Donna Rindress · The LA-SER Group

    Anna's recommendations are good. You could also look at the recent literature on healthcare decision criteria, especially the use of MCDA (multicriteria decision analysis) to support healthcare decisionmaking. The EVIDEM framework (open source public domain research collaboration) aligns well with the EUneHTA framework and is being adapted by several HTA agencies for reimbursement value assessment as well as other priority setting purposes in healthcare.

  • Madison Ngafeeson added an answer in Healthcare:
    Can patient data be simulated and used for in research?

    Patient clinical data is private and acquiring it for research especially by researchers outside the affiliation to healthcare organisations can be close to impossible. Even when such data is anonymised.

    Can patient data be simulated? Will it then be considered applicable for use in a research?

    Are there any samples of simulated data which can be tested?

    Madison Ngafeeson · Northern Michigan University

    Very interesting question. I do agree with Emmanuel Lazaridis, that it is particularly difficult but possible to have simulated data. One of the hopes of Health Information Exchange (HIE) networks is to make this possible. It is evident that without the possibility of the use of "real" patient data in research, even our best predictions will still be erroneous. We hope that the current progress in HIEs will help address this problem. But, I most admit, this is unlikely to be achieved in the very near future.

  • Gaurav Kumar Singh added an answer in SDS-PAGE:
    Why the protein forms precipitate before loading in SDS-PAGE?

    I have observed recently, My protein forms a solid mass after heat denaturing with loading dye. It gets precipitated!! Why is it so? 

    Gaurav Kumar Singh · IIT Kharagpur

    I heat the sample for 5 mins at 37 degree Celsius with closed tubes. I do lysis by sonication in lysis buffer containing 10mM imidazole, 300mM NaCl and 10mM TrisCl. I am using 4x loading buffer which contains Beta-Mercaptoethanol, EDTA, Bromophenol blue, Glycerol, TrisCl and SDS.     

  • Ke Chung Kim added an answer in Climate Change:
    How could local communities help in the conservation of species engendered due to climate change???

    Sustainability of conservation project usually depends on the involvement of locals. but i don't see any relevance of locals involvement if the problem is not started at their level...

    opinions are requested...

    Ke Chung Kim · Pennsylvania State University: Frost Entomological Museum/Center for Biodiversity Research, PSIEE

    Yes, it certainly should. That, however, requires more research and support from the government and scientific community. Our approach should be focus on not only on anthropogenic interests but also the sustainability of backyard biodiversity and ecosystems.

  • Does it make sense to assess uncertainty in climate change impact projections?
    It is now widely admitted that climate change impacts on water resources are occurring and are expected to amplify in the future. However, these impacts are highly uncertain and usually scientist and decision makers prefer to have a quantitative assessment of these associated uncertainties. How can we assess future uncertainty related to climate change in the absence of observations? Then, how can decision makers consider these uncertainties in their future plan management of water resources for instance?
    John W. Kern · Kern Statistical Services, Inc., University of Wyoming, Montana State University

    @roger-- I agree with your points strongly.  Often the parameters being simulated are strongly correlated, whereas most canned routines for generating distributions allow them to vary independently. This nearly always results in gross overstatement of the output uncertainties.  Useful models for uncertainty distributions including reasonable dependencies among model inputs are difficult to develop, but highly useful when achieved.

  • Kyobi Skutt-Kakaria asked a question in Drosophila:
    Extracting RNA from Drosophila heads

    Hello, I am looking for the best strategy for extracting RNA from Drosophila heads. Can anyone recommend a homogenization procedure?

  • Clifford Kaumba added an answer in Church:
    How can ecclesial communion be strengthened Parishes?

    I would like to know how the Church is communion and how concretely this communion can be lived in communities.

    Clifford Kaumba · St. Mary's Seminary and University

    Communion can be expressed in individual families, Small Christian communities and Parish at large.

  • Can anyone suggest a simple protocol of esterification/transesterification of a glyceride using n-butanol as the solvent, as well as the catalyst?
    For a high yield of an ester, a catalyst that will give an optimum yield is needed in the esterification reaction.
    Aaron Bloomfield · Yale University

    Acids like H2SO4 or acidic resins like sulfonated polymers (Dowex, Nafion etc.) can catalyze trans-esterification. So can alkaline salts like NaOH, Ca(OH)2 and KOH... It depends what the substrates are, and what sort of other limitations there are on the reaction...