Q&A

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  • Joseph michael Cantor added an answer in Chemokines:
    Can Anybody provide suggestion for plasma murine lymphocyte markers for Th1 and Th2 immunoresponce?

    I'm looking for some reliable CD on murine  lymphocytes that can prove the shift Th1 or Th2 to be detected by flow cytometry. I can't do the cytoplasmic chemokines becouse I do not have access to spleen or other organs. I have to detect the responce on blood

    Joseph michael Cantor · University of California, San Diego

    Agreed, and don't forget to add PMA/Ionomycin to stimulate cytokine production.

  • Louis Brassard added an answer in Ideas:
    What is the relationship between basic concepts and mathematics in physical theory?

    Doing some background reading in Einstein, I came across the following quotation which inspired this question:

    Fundamental ideas play the most essential role in forming a physical theory. Books on physics are full of complicated mathematical formulae. But thought and ideas, not formulae, are the beginning of every physical theory. The ideas must later take the mathematical form of quantitative theory, to make possible the comparison with experiment. --Einstein and Infield, 1938, The Evolution of Physics, p. 277. 

    Are "thought and ideas" central and essential and the mathematics secondary and more important for experimental results? 

    The following paper:

    Leibniz's place in the history of physics by Joseph Agassi.

    http://www.tau.ac.il/~agass/joseph-papers/Leibniz.pdf

    is very interesting. It is an historical account of the debate debate between Leibniz and Newton and the later influence the Lebiztian relational conception of space and time on later philosphers , geometers and scientist up to Einstein.  We can see in this historical account the long ancestry of ideas on space and time that lead the the type of physics that Einstein developed.  

  • For assessment of cytotoxic activity of T cells against an antigen in Mice which way is the easiest?

    I want to asses the cellular immunity against an AG in Mice. Chromium release assays that use for cytotoxic activity of CTLs  is difficult for me. So, I want to know if there are any easier ways?  

    Joseph michael Cantor · University of California, San Diego

    Two convenient, modern, and accepted methods for CD8+ CTL assays are usually done in tandem:  (1) LAMP-1 (CD107a) exposure.  LAMP-1 is exposed on the surface of the CTL when cytotoxic granules are released.  antibody must be incubated with the culture during the last 2h or so.  Double-stain for the killer with CD8, NK, etc.  (2) Differentially labeled (CFSEhi or CFSElo) targets co-cultured together with killers.  One contains antigen, one doesn't.  Mix the targets 50-50 before culturing with killers overnight.  Measure the change in the % of Ag+ target.   Both of these are cheap and quite easy if you have access to a flow cytometer.

  • Yurii V Geletii added an answer in PEAKS:
    What is the meaning of broad peak and sharp peak in Cyclic Voltameter (CV)?

    I am working on electrochemical Oxidation of primary alcohols. For different catalyst the onset potential is same but the oxidation peak sharpness varies. I want to know what that means ?

    Yurii V Geletii · Emory University

    Cyrille Costentin , Samuel Drouet , Marc Robert , and Jean-Michel Savéant *

    Turnover Numbers, Turnover Frequencies, and Overpotential in Molecular Catalysis of Electrochemical Reactions. Cyclic Voltammetry and Preparative-Scale Electrolysis

    J. Am. Chem. Soc., 2012, 134 (27), pp 11235–11242

  • Omer Ucar added an answer in Fertility:
    Considering different genders (male/female), which one is the most effective on the fertility outcome and why?

    gender, fertility, offspring

    Omer Ucar · Ataturk University

    Drear Dr. Fiaveh,

    Thanks so much for your kind reply and provision of some related papers in Africa (Ghana). Regards.

  • How can we compare the genome size in cM (centimorgan) with bp (basepare)?
    I am in need for details on how to compare the genome size obtained in cM to comapre with Mbp or Kbp.
    Patrick Obia Ongom · Purdue University

    Based on your comments, my next project will now be designed with the objective of translating genetic maps into physical maps for a number of important species, allowing people to easily work back and forth  between cM  and  Bp. 

  • Xiaofeng Li added an answer in Building Performance:
    Which building element plays the most important role in saving energy, when applied in extreme weathers?

    For an instance, which building element should be prioritised during design stage?

    Xiaofeng Li · Macquarie University

    I believe the energy saving in buildings is not an issue of building design itself, but also significantly depends on the building service system design, including and especially on the heating, ventilation and air conditioning (HVAC) systems. 

    With the fact that we spend more and more time indoors and the pursuit of higher living standard, the energy consumption caused by HVAC systems is increasing dramatically. The energy demand of HVAC systems has broken through 50% of the overall building energy consumption. 

  • Any suggestion best DETERGENTS to isolate outer membrane proteins from intracellular bacteria?

    I have a short sample and cannot waste it testing different detergents.

    Marcel Martinez-Porchas · Research Center for Food and Development A.C.

    Thank you Drs. Papiz and Muench. We will strongly consider these suggestions.

  • Is it possible to derive Maxwell's equations from Dirac's equation or vice versa?

    Owing to particle-wave duality  particles have wave nature, and waves have particle nature. Does that mean we can derive their underlining equations from each other, i.e. Maxwell from Dirac and Dirac from Maxwell?

    Mohamed El Naschie · Alexandria University Alexanderia Egypt

    may be i shouid have mentioned that an ordinary diffusion equation is automaticaly converted into a schroedinger equation via ANALITICAL continuation. this means replacing time  t by it where i is square root of minus one.

  • Hayman Kakakhan Awla added an answer in rice fields:
    How can I do characterization for actinomycetes ?

    Isolated from soil rice field. I want use for control rice blast disease 

    Hayman Kakakhan Awla · Putra University, Malaysia

    many thanks, dear mubasher 

  • Lingli Li added an answer in Tamoxifen:
    Which way to dissolve Tamoxifen is better?

    Try to use tamoxifen to inject into mice. I used to dissolve Tamoxifen in Ethanol then dilute out for use, the new lab do dissolve in Peanut oil, it takes long time at room temperature to dissolve, some times we have to heat up for an hour or two at 37 degree. I can not find any reasons of which way is better, bu t my feeling is that it should be initially quick disolve in Ethanol, can anyone help me with some evidence?

    Lingli Li · St vincent research institute

    Dear Stefania,

    Thank you for your Kind info. I am wondering if tamoxifen would be completely dissolved in corn or peanut oil? Do you use it fresh each time or can it be frozen and thaw?

    Lingli

  • What kind of Ionic Liquid can you recommend me for hydrogen generation through water splitting?

    I am looking for a new Ionic Liquid generation to improve water splitting process

    Yurii V Geletii · Emory University

    The best solvent to split water is water. Water splitting means 2H2O -> O2 + 2H2 and includes water oxidation. Ionic liquids (organic materials) are much easier to oxidize than water. 

  • Xiaofeng Li added an answer in Microalgae:
    About renewable energy?

    I want to offer a mechanism for renewable energy production of Structures in sea with maximum 50m depth.that The structure is self-sufficient in energy supply.What strategy do you recommend to me؟

    someone have information about the use of Microalgae for renewable energy.that In relation to the conditions mentioned . can I use  Microalgae in this case ?

    thank u

    Xiaofeng Li · Macquarie University

    How about collecting the kinetic energy from ocean waves? You probably would like to have a search on Piezoelectric Energy Harvesting. 

    You might be interested in this article: Murray, R., and J. Rastegar. "Novel two-stage piezoelectric-based ocean wave energy harvesters for moored or unmoored buoys." SPIE Smart Structures and Materials+ Nondestructive Evaluation and Health Monitoring. International Society for Optics and Photonics, 2009.

    Cheers,

  • Dr A. Kumar added an answer in Optical Properties:
    What is the relation between skin depth and optical properties of semiconducting materials?

    What is the skin effect and what is it meaning for  semiconducting materials?

    Dr A. Kumar · Harcourt Butler Technological Institute

    My dear Ahmed

    Skin effect has been studied in semiconductors also at microwave frequencies.You can make Google research on skin effect in semiconductors then there are many research papers which relate skin effect to electrical conductivity. Since conductivity in semiconductors depends strongly on temperature and optical band gap, one can find a correlation with optical properties but it will be an indirect relation as skin effect is related to the electrical transport in metals and semiconductors.

  • What is the Integrated Pest Management (IPM) or Integrated Pest Control (IPC), what is its role in protecting our Environment?

    I would to ask on IPM and how benefits us in protecting the environment?

    Sheku Kanteh · Njala University

    IPM or Integrated Pest Management is the judicious combination of two or more management strategies for effective pest control. Ensure that management strategies to be combined are compatible ( with no harm to each other). For example, chemical control cannot be combined or immediately followed by biological control (use of animals). Combining cultural practices with biological or chemical may be okay.  When chemicals are included, it is important that they are judiciously use, to avoid damage to environment, microorganisms and health of man and other animals (livestock, fish, etc) . Misuse can be hazardous and associated with risks.

    Using fire (uncontrolled) can be hazardous to the environment, due to emission of pollutants, damage to microorganisms and destruction of organic matter. Based on these examples, IPM can be useful in protecting our environment only when the principles are adhered to. Every crop protection programme utilizing IPM approach must aimed at producing safe food for consumption, and in the process should be mindful not   .     

  • Sutomo Sutomo added an answer in Apocynaceae:
    Dose anybody know, how I can get accessions of Apocynaceae species from around the world for laboratory research?

    I need accessions (seed or leaf) of Apocynaceae taxa for DNA extraction. Does anybody know, how I can get them? Please give me addresses or links. I am ready for exchange my accessions (from Iran) to another countries.

    Sutomo Sutomo · Edith Cowan University

    you could send an email to bali botanical garden in Indonesia, there is apocynaceae family the Alstonia scholaris as well as other species

  • Thierry Beths added an answer in Medetomidine:
    What is the mechanism behind the increase in heart rate after injection of Lidocaine (around 2 mg/kg IV) we can observed in patient with bradycardia?

    In Veterinary medicine, in healthy dogs, for  our premedication prior to general anaesthesia we tend to use an alpha-2 adrenoceptor agonist such as medetomidine or its active enantiomer, dexmedetomidine. The resulting bradycardia, although being a normal response, can be disconcerting for some practitioners who then tend to reverse the alpha-2 and lose, with the sedation, its analgesic effect. Others, although discouraged by different papers in the literature, give an anticholinergic which then results in hypertension. Following the advice of a more experience anaesthetist, I tend nowadays to give 2 mg/kg IV of lido to increase the HR in those patients. The effect is usually a mild increase and of short duration. The experimented anaesthetist referred to a technique or info from the 70"s. I have asked around me since, and can not get the explanation for the mechanism. Naturally, I would have expected an injection of lido to result in a decrease of the HR as we observed when we treat ventricular rhythm disturbances such as V-Tach. Even when I look at data sheets, slower HR (bradycardia) is a side-effect, not faster heart rate. Does anyone have any idea?

    Cheers

    Thierry Beths · University of Melbourne

    Hi Geoffrey,

    usually the heart rate increases by about 10-20% at best. Blood pressure follows, but usually no hypertension per se. No arrhythmias observed so far, but N is low...about 20-30 dogs. Haven't tried in cats yet...

  • Raghvendra Pratap Singh added an answer in Gromacs:
    How to include the residues N-acetyl Glucosamine (NAG) and 2-amino 3-oxopropionic acid (ALS) in gromacs 4.6.5 version's topology ?

    My protein has 4 NAG and 1 ALS residue in its sequence. When I tried to simulate the protein using gromos96 53 a6 force field , it's showing a fatal error as: residue 'ALS' not found in residue topology database.

    How can I troubleshoot this problem? Can you  tell me the steps to overcome this problem? 

    P.S-  I have already gone through this website and tried to include the new residue in "residuetypes.dat" file, but the file was not saving the modified residue.

    Raghvendra Pratap Singh · Université des Sciences et Technologies de Lille 1

    it is basically the common point of Dr. Chaurasi and Dr. Lemkul's answers. Create a new topoly using PRODRG for gromacs and Add it to your local copy of amino acid topology file with the desired name with all the parameters required by gromacs.

  • Do you have any research that has been published recently on Occupational safety and health ondeveloping countries manufacturing industries?

    Do you have any research that has been published recently on Occupational safety and health on developing countries manufacturing industries? Is there any idea that argues  work place safety in developing countries is getting  difficult to optimize hazards?

    Roland Iosif Moraru · University of Petrosani

    Dear Kassu

    I attach some articles. Maybe they will be useful for your work. Please confirm.

  • I want to begin studying Machine Learning. Could anyone advise me on where I could start so that I'll can efficiently cover the basics?
    If possible suggest a good book or resource.
    Thank you!
    Senaka Amarakeerthi · Sabaragamuwa University of Sri Lanka

    Following YouTube playlist has an undergraduate machine learning course which is easy to understand compared to Prof. Andrew's lessons.

  • Robin Harger added an answer in Diversity Index:
    Can the Shannon-Weiner species diversity index be a good monitoring tool for assessment of health of any type of ecosystem?

    Diversity indicates the condition of an ecosystem.

    Robin Harger · Highspan International Environmental Consultants

    In New Zealand the use of “indicator species” seems to have taken over completely. For freshwater fish this approach is represented by something called “The Fish Index of Biotic Integrity (Fish IBI) Joy and Henderson 2004. This index can certainly generate a useful metric since it is widely applied but it has several drawbacks the chief of which is formed by an apparent disbelief” in the existence of highly diverse native fish communities ie the discarded 5% (see later).
    However, that may be it is also not a “clean” index in that introduced rainbow and brown trout have somehow acceded to the same level of “ecological desirability” as have native species ie brown and rainbow trout are counted-in with native species. However, the truth of the matter is that brown and rainbow trout are rather like clean-living, predatory, but edible forms of Pinus radiatea (a tree species imported from the Monterrey Peninsula and grown in New Zealand for its timber value) now widely considered a “pest” species.
    The argument concerning the valuation of the index (fish IBI) is based on a reference to a (selected) sample-base which is further truncated by dismissing the most diverse records of native fish populations (top 5%) and then creating a mysterious biased weighting-factor dependant on equally apportioned 1/3 intervals of the remainder. Furthermore, all other exotic species that turn up in various samples are then “struck from the register”.
    First the exclusion of the top 5% of the samples in respect of their diversity automatically tones-the index down – it caps maximal native ecological expression. Second the use of established samples as the sounding-board for the detection of change, being inherently circular, will not be at all sensitive at the limit and will eventually “wind-down” as time progresses. The introduced species are already saying something about the state of the aquatic environment; in truth they tell the whole story by themselves.
    If introduced species succeed because they are able to better partition available trophic levels than native species what is the incurred ecological measurement penalty? The same sun continues to shine over the New Zealand lake and river systems therefore the same ecological carrying capacity exists now as in pre-colonial times. So, counting both native and exotic fish production per unit area/volume, this is surely much the same as it was in the pre-colonial era (excluding artificial injections of nutrients ie farm effluent).
    What was happening prior to the invasion of European settlers that differs from now is that there were undoubtedly more native species in a given habitat, or, very much less likely about the same numbers of native species per location but maintaining higher standing populations. This latter scenario is highly unlikely but either way productivity would be much the same then as now. So a more informative index is simply to count the number of native species and form this into a ratio with respect to introduced species.
    All introduced species poach energy from native species and that includes both rainbow and brown trout. We may here also use three versions of H'’: that can be calculated on the whole fish population, on native species alone and then on introduced species. Each time this is done there is also an Hmax so that Hmax-H'’ gives a measure of “organisation. Where organisation is high the population is in pretty good shape and where low the reverse is the case.

  • Louis Brassard added an answer in Biology Theory:
    What are space and time?


    Space and time are widely used concepts or categories. They play a major role and are critically discussed in physics, natural science in general and in philosophy. A quote of Kant is: "Space and time are the framework within which the mind is constrained to construct its experience of reality.”. But in Einsteins approach space-time is an attitude of the reality. In cosmology space and time began after the big bang. But for MacTggert time was unreal.
    There is no doubt that space and time are basic concepts especially in modern scientific theories. Theories and sciences like cosmology, geology, theory of evolution and phylogenetics as well as developmental theories in biology or psychology, culture theory and especially history are unthinkable without space and time.
    What do you think?

    The following paper:

    Leibniz's place in the history of physics by Joseph Agassi.

    http://www.tau.ac.il/~agass/joseph-papers/Leibniz.pdf

    is very interesting.  It is an historical account of the debate debate between Leibniz and Newton and the later influence the Lebiztian relational conception of space and time on later philosphers , geometers and scientist up to Einstein.

  • Bernd Sing added an answer in PRIME:
    Given a prime p, is there any explicite formula to find a generator of cyclic group Zp*?

    Zp* = { 1, 2, ...... ..... ... p-1}, multiplication modulo p

  • Geng Ouyang added an answer in Infinity:
    What is 0 (zero), different roles, different positions?

    People believe that 0 (zero) has played different rolls as a kind of special form of number (substantiality) in our science, such as:
    (1) A kind of reference ------- generator, middle, neutral, beginner, origin, placeholder, marker,…,
    (2) Absolutely non-existent ------- without numerical value meaning, the negation of being, objectively nothingness,
    (3) Relatively non-existent ------- with numerical value meaning, subjectively nothingness, the approximate nothingness, the result of infinitesimal limit , ….


    Following three questions are important for us to understand what 0 (zero) is:
    1, How does 0 (zero) exist as mathematical language with or without numerical value meaning itself?
    2, What position dose 0 (zero) locate in the categorical spectrums of numbers?
    3, Do we need a negation of 0?

    Geng Ouyang · MinNan Normal University

    One thing has been troubling many people for long: at the time when 0 was born as a kind of number in our science, must it be proved scientifically and mathematically or just came out staying there without proof?

  • Which is the best free gene expression analysis software available?

    I need to perform analysis on microarray data for gene expression and signalling pathway identification. I am working on mac and I am looking for a free/open source good software to use that does not need programmation skills or complexe set-up. Do you have any idea?

    Nathan Salomonis · Cincinnati Children's Hospital Medical Center

    AltAnalyze actually supports a large number of statistical methods inclusibeg LIMMA based empirical moderated t-test and Benjamini-Hochberg adjustment. Besides being the easiest to use free application that I am aware of, it includes dozens of automated computational methods such as customizable heatmap visualization, comprehensive splicing and isoform function analyses, supports RNA-Seq, conventional and splicing arrays, PCA, identifier translation, file merging, Venn diagrams, QC plots, Wikipathway visualization and pathway/geneset/TF/miR/ontology enrichment analyses, network analysis and visualization, splicing graph visualization, marker identification, sample classification and accurate cell-type prediction analyses. One feature that is particularly useful is the advanced clustering and heatmap visualization options, which include the option to filter large datasets, use hopach clustering, perform correlation based queries, filter on many different ontologies and gene sets and selectively view specific genes of interest. We have recently added novel methods for single-cell seq analysis. There is extensive documentation, active development and a large user community. Many of these methods are still being improved so please provide feedback.

  • James F Peters added an answer in Mesh Generation:
    What is the good method for the 3D non-convex mesh generation?

    Can anyone guide me to a method which will support and be good for the 3D triangulation of non-convex surfaces, mesh generation of non-convex of 3D objects?

    James F Peters · University of Manitoba

    This is a good question with many possible answers.

    3D meshes with non-convex boundaries are considered in

    S.J. Gortler, C. Gotsman, D. Thorston, Discrete one-forms on meshes and applications to 3D mesh parameterization, Harvard University:

    http://www.cs.harvard.edu/~sjg/papers/tutte.pdf

    See, for example, Fig. 7,  page 19.   For the 2D case, see Fig. 4, page 14.

    More to the point, consider

    R. Fuchs, V. Weler, J. Hornegger, Non-convex polyhedral volume selection of interest selection, Computerized medical imaging and graphics 952, 2009:
    http://www.scivis.ethz.ch/publications/pdf/2010/polyVOI.pdf

    See Section 3, starting on page  2, on non-convex volume-of-interest (VOI) selection.   The contention is that non-convex VOIs are helpful in analyzing scientific data such as the surface of a bone (see Fig. 5, page 6).

  • Is it better to purchase graphene nano powder or synthesise using hummer/ modified hummer's method for modified electrode sensing?

    Lab synthesis using Marcano.et.al. 2010 has yielded a highly capacitive material. Looking for alternatives. 

    Khosro Zangeneh Kamali · University of Malaya

    If you want to synthesize a nanocomposite, it is better to prepare Graphene oxide (GO). I have to add that graphene layers agglomerate due to van der waals and  Pi to Pi interaction. GO does not suffer from agglomeration. Therefore if you use GO, you may have single layer graphene (or few layer graphene) in your final product.
    Other than that existence of functional groups on GO increase the chance of better attachment of particles on graphene sheets. 

  • Will different force-fields effect the structure and function of homology model and docking of ligands with that model?

    I am using MOE for homology modelling of an enzyme but the model contain too many outliers. So I applied different force-fields which minimized outliers. My question is on whether applying different force-fields on a homology model will effect the structure and function of that enzyme and also whether it will further effect the docking of ligands/drugs?

    Raghvendra Pratap Singh · Université des Sciences et Technologies de Lille 1

    Dear Sohaid, 

    First of all, you must run a long enough MD simulation to check weather your Homology Model is stable in terms of structure and energy..and then and only then you go for docking or any further steps you want to perform.

    Secondly, YES, of course different force field provide significant alterations in results. In different force-fields ...parameters such as bond length and partial charges are different which in theory force a molecule to behave differently. so primarily, before performing MD simulation of a homology model you must research and read about force-fields to chose wisely the one which fits you molecule type and depending upon the MD-engine you are about to use. MD-engines like GROMACS provides a wide variety of force-field parameters available to a researcher such as Amber, OPLS, Gromos and CHARMM and many community added ones too. so review carefully and then choose depending upon molecule type and the literature based information.

    Good Luck

    cheers : Raghav 

  • Maryam Ghorbani asked a question in Gas Sensors:
    What does it mean "utility factor"?

    In Book "Semiconductor gas
    sensors", Raivo Jaaniso and
    Ooi Kiang Tan had defined as:

    "The ratio of the actual gas
    response to the ideal (free of attenuation) is known as the ‘utility factor’
    (U)."