Q&A

ResearchGate Q&A lets scientists and researchers exchange questions and answers relating to their research expertise, including areas such as techniques and methodologies.

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  • Mark E Cleasby added an answer in Anti Obesity:
    Is there any human study on Irisin hormone?
    See above
    Mark E Cleasby · Royal Veterinary College

    The suspicion is that the kits being used to detect "irisin" in humans are probably detecting something else. In addition, the FNDC5 gene appears to have an atypical start codon in humans. Thus, there is little convincing evidence of a role for irisin in humans at present.

    See for example:

    http://www.ncbi.nlm.nih.gov/pubmed/24040023

  • James E Talmadge added an answer in Lung:
    Is it appropriate to use only GR-1 or F4/80 FITC labeled antibody( without cd45 or cd11b) to isolate mice lung neutrophils or macrophages?

    to find out role of Neutrophils and machrophages in lung inflammation after drug treatment isolated mice lung single cells and by the help of Percoll separate leukocytes..than stained with GR-1 and F4/80 separately because both are FITC labbeled for flowcytometry. But now confused which cells i have to select for Neutrophils and Machrophages stained with Gr-1 or F4/80. I donot understand how i gate or which cell collection represent neutrophils. please see attached file.either R2 or R1 represent neutrophils?or i should have to gate  differently.

    James E Talmadge · University of Nebraska Medical Center

    Charly provided a solid response.  A couple of clarifications to your protocol might be helpful.  First how are you obtaining single cells.  Presumably, collogenase/DN'ase but is this correct. Always be careful that you have no contaminating proteases in your enzyme mix as they will strip membrane markers.  Second, what Percoll gradient are you using?  Is it continuous or discontinuous?  Which bands are you calling the myeloid cells?  Having said this the lymphocytes, macrophages and granulocytes would be at different densities in a Percoll gradient.  Please see papers by myself and Bob Wiltrout some time ago on a 5 step gradient.  Having said this, a murine Ficoll Hypaque gradient will largely separate parenchymal from non- parenchymal cells.  Alternatively, as suggested doing the flow without gradient separation might also prove useful.  Lastly, consider removing doubles and apoptotic cells from analysis. 

    Depending on the drug used to treat the mice you might want to also consider the presence of MDSCs and myeloid progenitors in the lungs (add Sca-1 and Lin markers to panel).  When working with myeloid cells antibodies to CD115 and CD66b can also be useful.  Similar to what Charly is suggesting when doing studies of this nature we use at least 3 lasers and 8-10 colors. 

  • How can I simulate a tsunami in Indian ocean using MATLAB? Which algorithm helps better for simulation?
    The simulation should depicts the carrying of coral reefs or some oceanic material with tsunami waves.
    Julius Jara-Muñoz · Universität Potsdam

    http://www.mathworks.com/matlabcentral/fileexchange/17716-shallow-water-wave-cfd--tsunami-modelling-

    boundary conditions must be better adjusted, like coastline for instance

  • Reza Farrahi Moghaddam added an answer in LaTeX:
    Why is LaTeX not used as an end-to-end solution in the publishing industry?
    Many publishers ask authors to provide LaTeX source of their article or book. It is believed that this helps in easier handling of the publication tasks. However, it seems that publishers use some other "Photoshop-like" software at the end of the publication process for copy-editing and similar tasks. Does LaTeX lack a specific feature that forces publishers to use these labor-intensive software?
    Reza Farrahi Moghaddam · École de Technologie Supérieure

    I agree Guy that the case of publishing a book is more straightforward and manageable. However, when someone tries to publish an article in a journal, there is almost no control after submitting the accepted version.

    In terms of a good combination of tools for LaTeX, I would suggest Texstudio editor + Miktex + PDFLaTeX class. All are free and available. Using the PDFLatex and the graphicx package, you can directly include pictures in their original format (such as PNG) in your LaTeX file without converting them to postscript format..

  • When it comes to simultaneity is Einstein correct or is Dingle correct?

    Albert Einstein claimed in 1905 that a single event can occur simultaneously at different times within two inertial reference frames moving relative to one another. In 1950 Herbert Dingle argued that different times cannot be simultaneous. I have analysed this conflict by deriving the Lorentz equations using both points of view. According to this analysis Dingle must be correct. See youtube presentation of this analysis at  https://youtu.be/4XLYzhHQ64Y

    Charles Francis · Jesus College, Cambridge

    Andrew, I think I recognise the quote as Einstein c1923. I don't agree with it. I think Einstein's earlier ideas were better. I would have to say that as far as general relativity is concerned, it is an unresolved question as to whether there is a substantive spacetime. As far as quantum theory is concerned, I think there is irrefutable proof that there is no substantive space. Certainly, that cannot be dogma, because I am in a very small minority of people who think they understand such a proof. If there is any dogma, it is that one should not think about such questions.

  • Jeff Prystupa asked a question in Switches:
    What is the mitochondrial mechanism of control between aerobic and anaerobic respiration?

    Inflammation is the cell marker for stress of all kinds. Chronic inflammation is the pre-cursor to cancer and is implicated in 7 of the top 10 diseases. I am searching for the 'switch' that induces a certain type of cell, with a dual genome, to switch from its normal growth characteristics, i.e., aerobic respiration to anaerobic respiration. I ask those with experience to help illuminate this pathway, which appears to be mitochondrially-controlled.

  • Can Trivial Games solve Post Traumatic Stress Disorderliness?

    Can Trivial Games solve Post Traumatic Stress Disorderliness?

  • Pasquale Piombino added an answer in Cleft Lip:
    I am looking for a craniofacial or cleft specific quality of life instrument that has been validated in Spanish. Does anyone have such an instrument?

    I am doing research with adolescents in Mexico City who have cleft lip and/or cleft palate and want to measure quality of life related to the facial difference.  I need a measure that has been validated in Spanish, not just translated into Spanish.

    Thank you.

    Pasquale Piombino · Second University of Naples

    Hy... you could try my AdoCleftQoL, we published the results last year

  • Sezginer Tuncer added an answer in Species Invasion:
    Any advice on the Invasive species in the Mediterranean sea ?

    I'm studying the attitude of Lessepsian species and invasive species in the Mediterranean sea, I would like to work on Genetic invasive species where invasive species of Lessepsian species have become more abundant .
    Can anybody give me occurrence data of these invasive species I would like to receive published research, grey literature
    I’m working on species distribution models for exotic species Libya. I need records of presence (geographical coordinates) of the sites in other location in Mediterranean sea as well as new recorded invasive species . Thanks for your collaboration.

    Sezginer Tuncer · Çanakkale Onsekiz Mart Üniversitesi

    Dear Abdulghani,

    I understand very well, both of these species immigrant from Red sea , occurs in Turkish coasts..

    it will be very good..Ithink..

    I wish a good luck for you..

    Sezginer

  • Traci L Testerman added an answer in Chromophores:
    Can GFP be used to detect cell death?

    We want to evaluate a killing kinetic through GFP labeled bacteria in order to assess the bactericidal activity of plant compounds. Will GFP give us the detection of cellular death or chromophores will still be active after the bacterium has died?

    Is there a better methodology for this purpose?

  • Napoleon Ono Imaah asked a question in IT Architecture:
    Which parmeters while designing facilities and hotels for tourism in coastal areas ?

    Choosing the right architectural scales and proportions has been a bad in designing attractive architecture at coastal zones since coastal landscape, vary dramatically. Is there a methodology for designing architecture for tourist places?

  • Scott Russell 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?
    Scott Russell · University of Michigan-Flint

    One could argue that our ethics usually play the role of regulator of our desires. These are caused by biological needs at some basic level. However, a desire can even be injurious to one's health at times because desires are to a large extent symbolic. Even the desire to be ethical is a symbolic gesture, an expression of how one wishes to be known or perceived.

  • Yeghig Armoudjian added an answer in PEAKS:
    What are this peaks at 280 nm in my blood plasma samples?

    We developed a bioanalytical LC-MS/MS method and everything is OK, but to determine whether the run time and the organic percent is enough for plasma's effect on column we did a UV detection between 200 to 300 nm wavelength, and found unknown peaks in the bio samples at the 5th min. and 11th min. that not causing any carry over or any effect on the MS method and results, but its interesting to know what peaks those might be! we reduced the run time but the 11th min. peak had no effect on the later injections. Has anyone similar experience ?
    PS. extraction method : protein precipitation
    column : C18 100 x 2.1
    mobile phase 17.5 methanol , 82.5 (0.1%) FA

    Yeghig Armoudjian · Darmantest Laboratories LLC

    I could figure that Plasma's proteins containing tyrosine aid tryptophan side chains adsorbs at around 280 nm, but why they're not causing carry over in later UV injections ?
    In case we ignored it, will it effect the column or the results in the primary MS method ?

  • Any advice on MATLAB embedded function under simpowersystem environment?

    I am working on a simulink model built under simpowersystem environment. The model contains some matlab functions embedded in simulink blocks. When I'm trying to run the programme, there is always the following error message:'model_sfun.bat' indicating that this is not recognize as internal or external, executable program or files commanded. I have built a simulink model to replace some embedded matlab function and the model in which I have only simulink model and elctric components works. So I have a sad impression that the problems in my models are on the use of matlab embedded function  under simpowersystem environment. I wish to know how  I can solve this problem. In fact in many papers I have found in the literature on the use of simpower in the field of modeling and simulation of electric systems, many authors have used this kind of combination (matlab embedded function+simulink blokc+ electrics components on simpower). Pleased can any people help me to solve this urgent problem.

    Pisupati Sadasiva Subramanyam · Vignana Bharathi Institute of Technology

    The following References deal with Creating Components and Libraries in Aimpower Systems.It may be useful.

    1.    Features- Simpower Systems

    Link:   http://in.mathworks.com/products/simpower/features.html

    2.   SimPowerSystems Examples

    Simscape Components                         

    More Examples         ( Where Available) 

    Link: http://in.mathworks.com/help/physmod/sps/examples.html

    P.S.

  • Fadel Djamel asked a question in Literature and Music:
    What decade of the 20th century was the most prolific in events?

    The twentieth century has had its share of glory. He had effervescence in happy and unhappy events in all fields: political, scientific and cultural, health, movie, literature and music.

    Events

  • How a climate smart territory would look like?
    It is more and more clear that the solutions for a sustainable human development and also for a mitigation and adaptation to climate change have to follow a territorial strategy ( a territory as a landscape with people, thus a social process). The Millennium Ecosystem Approach in the proposed scenarios for 2050, shows that the adaptive mosaic development strategy, is the one that better supply the population with ecosystem services. In that sense a climate smart territory has to be managed in a way that contributes to sustainable human development and to climate change mitigation and adaptation.
    Peter Salonius · Natural Resources Canada, Retired

    Climate change mitigation? I hope you will become aware that almost all climate change is NATURAL and has been going on since the Earth cooled..... see: 


    One of many papers showing that CLIMATE WARMING CAUSES INCREASED ATMOSPHERIC CO2 CONCENTRATIONS suggests  that the IPCC thesis and the assumptions of Global Climate Models ----------- that that assume CLIMATE WARMING
    IS CAUSEDBY ATMOSPHERIC CO2 CONCENTRATIONS ----------------- are in serious error.... see: 
     
     
    http://www.clim-past.net/8/1213/2012/cp-8-1213-2012.html
     
    The IPCC thesis and the assumptions of Global Climate Models that that assume that
    CLIMATE WARMING IS CAUSED BY  INCREASED ATMOSPHERIC CO2 CONCENTRATIONS ..........has been the basis for taxpayer funded and enormously misguided government policies and regulations designed to curb human emissions of CO2.
     

     ----------------------------------------------


    QUOTING from the FULL TEXT of the paper (with somewhat 'iffy' English) concerning the dominance of the Sun's influence on the Earth's CYCLICAL warming and cooling ................. available at:

     http://www.doiserbia.nb.rs/Article.aspx?id=0354-98361500018A&AspxAutoDetectCookieSupport=1#.VRbMQPnF-ah
     
     
     
    "The start of the Grand Minimum of TSI is anticipated approximately in cycle 27±1 approximately in 2043±11 and the beginning of the phase of deep cooling of the 19th Little Ice Age (of the Maunder Minimum type) in the past 7,500 years approximately in 2060±11, with possible duration of 45-65 years "
     
    "The Sun is controlling and practically totally determining the mechanism of quasi-bicentennial cyclic alternations of climate changes from warming to Little Ice Age and set corresponding time-scales for practically all physical processes taking place in the Sun-Earth system. The current long practically stable levels of World Ocean and of temperature additionally reflects the current state of global warming during past 17 years, which are under the direct control of the quasi-bicentennial decrease of TSI. Approximately in the end of 2014 we begin the descent into 19th Little Ice Age in the past 7,500 years " 
     
    SECOND you asked if forests can provide biomass to produce the energy of the future in a sustainable way.
     
    Using the forests of Canada (a country with low population density) as an example --- IF the total annual allowable harvest was used to produce energy it might yield 2 EXAJOULES per year --- while Canada presently uses 10 EXAJOULES per year ... so there is no way that the forests of most countries could supply yhe energy required for modern civilization// sustainably or not.

    Peter Salonius

  • Alessandro Zanarini added an answer in Bearings:
    Rubbing between journal and bearing with oil film nonlinear force consideration, can any one help me?

    Hi all,

    I'm looking for papers or thesis about rubbing between journal and bearing with oil film nonlinear force consideration and its effect on dynamics of the rotor, can any one help me?

    Alessandro Zanarini · University of Bologna

    I personally work on the experimental side of rotor dynamics on fluid film bearing, you can see a paper from my list, which shows the orbit shape as function of speed and inherent dynamics.

    Best regards,

    Alessandro

  • Is there a model to analyze case studies or you just use other models like grounded theory?

    I have a student that is going to research a multi intervention in a family, how can she analyze the data? Is there a specific modelo for case studies or something like grounded theory would do? In case that there is a specific methodology for case studies, could you refer some information (like authors)? Thank you very much!

    Richard C. Mitchell · Brock University

    And here's a great little (5 minute) Youtube on Case Studies for beginners.

    https://www.youtube.com/watch?v=FuG8AzK9GVQ

  • Gerd Kloeck added an answer in Extreme Environments:
    Which algae can theoretically survive on Mars?

    I'm looking for algae that could survive in extreme environment conditions, such as:

    1. Low atmospheric pressure
    2. High level of perchlorates in soil
    3. Water boils at +10oC (because of low pressure)
    4. Rarefied atmosphere
    5. Low solar energy level
    6. High radiation level 

    Maybe someone knows any good publications or books about the algae that can survive in extreme conditions? 

    Gerd Kloeck · Hochschule Bremen

    Have a look at Dr. de Vera`s work: https://www.researchgate.net/publication/259773164_Results_on_the_survival_of_cryptobiotic_cyanobacteria_samples_after_exposure_to_Mars-like_environmental_conditions

  • Ricardo Matias added an answer in 3D Modeling:
    What are all the softwares that are used for converting 2D photos into 3D models for measuring purposes and so on.?

    Hi all,actually i am looking to find out the correct software for converting the 2D photos into 3D model which where taken from a CAM and by adding those photos to software i need to get it mesh up and convert into 3D model for having measurements without scanning or on by modelling. Please come know that what are all the softwares that are usefull for me.

    Ricardo Matias · Instituto Politécnico de Setúbal

    Hi Keelapattu,

    Please see if this 3D object manipulation project match your needs:

  • Is it important to measure the internal resistance of a MFC?

    Can any one explain the importance of measuring internal resistance of MFC and its effect in MFC performance? and how can one measure it practically?

  • Jan Azim Svanberg asked a question in Brain:
    How mutch force(N) do the brain create an use per day?

    Also if info, how mutch force every part of brain create and use per day?

  • Pavel Trávník added an answer in Vitamin D:
    Can you please suggest information on the evaluation of vitamin D in seminal plasma?

    I wonder which metabolites and at what concentrations I can expect.

    Pavel Trávník · Sanatorium REPROMEDA

    Dear Paweł,

    the role o the vitamin D in spermatogenesis and sperm function is well known (e.g. Blomberg 2014),  but in my opinion the concentration in seminal plasma, mostly composed of prostate gland and seminal vesicles secretions, may have in physiological conditions (relatively short time of the seminal plasma with the spermatozoa contact) negligible importance.  The concentration in oviduct fluid could be interesting.

    Best regards

    Pavel Travnik

  • Inbesat Khan added an answer in PDB:
    Best File of Ligands for Molecular Docking ?

    Which is the best file format for Ligand (SDF,PDB,MOL,MOL2 etc.) please provide answers why particular ligand file format is best for docking against protein in PDB format. I am using Scrodinger GLIDE for docking.

    Inbesat Khan · Rajiv Gandhi Proudyogiki Vishwavidyalaya

    Thanks A lot !!!

  • Ruiqiang Liu added an answer in Leaching:
    From US-EPA TCLP 1311 method, the hazard of the soil will be decided on basis of concentration in fluid (mg/L) or leached from soil (mg/kg)?

    I carried out US-EPA 1311 methods on soil which is 100 % solid, the hazardous nature of this soil will be estimated through concentration (mg/L) leached in extraction fluid or the amount leached per gram (ug/g) of soil ?

    Ruiqiang Liu · The Ohio State University

    the former concentration (mg/L) leached;

  • Björn Christians added an answer in Aggression:
    Is there any good tool that measures "aggressive responses" online?

    Hello there,

    This is a project on some environmental effects on aggressive responses. Previously, my team has reported some consistent effect on people's response in assigning unpleasant pictures for strangers' viewing. 

    The result is interesting, but the journal editor worries about the validity of the picture assignment measure, and suggests a replication of the experiment with a well-validated measure of aggressive response.

    As time is limited, we plan to replicate the experiment online. So my question is, is there any well-validated aggressive response measure that can be applied online? Below are what we have considered, and/or rejected:

    1) Noise blast paradigm -- We have used this already, and the effect size isn't very impressive (though results are sig). Probably will be much confounding effect for an online study.

    2) Aggressive word completion task -- Assess the implicit accessibility of aggressive thoughts. It will help generalise the previous findings to aggressive thoughts, but not "behavioural/ decisional response

    Would appreciate very much for your advice here!

    Henry

    Björn Christians · Universität Trier

    Hi Henry,

    the Point Subtraction Aggression Paradigm should be a possibility to measure aggressive responses. We used it in a couple of Experiments and got adequate effect sizes

    See:

    LCherek, Don R., et al. "Laboratory measures of aggressive responding in male parolees with violent and nonviolent histories." Aggressive Behaviour 22.1 (1996): 27-36.

    Golomb, B. A., Cortez-Perez, M., Jaworski, B. A., Mednick, S., & Dimsdale, J. (2007). Point Subtraction Aggression Paradigm: validity of a brief schedule of use. Violence and victims, 22(1), 95-103.

     Björn

  • Jiaur R Gayen added an answer in PC12 Cells:
    Why are PC12 cells not responding to Nicotine Induction?

    Hi All;

    I am growing PC12 cells and trying to do a secretion assay with Nicotine induction. I have done it couple of times already but not getting enough induction with nicotine. I have tried with different aliquots of cells and also used new Nicotine stock as well. Without nicotine induction I can not really go to the next step of my experiment, so I am kind of stuck. Any suggestion? Thanks in advance.

    Saiful.

    Jiaur R Gayen · Central Drug Research Institute

    may be your cell line modified after long passage (it commonly happens with carcinoma cell lines). it may contains very less nAChR (nicotic receptor). You may transfect your cell with nAChR Plasmid.

  • Mark E Cleasby added an answer in Insulin:
    Does a dose of insulin 20 minutes before sacrifice alter mitochondrial gene expression or mitochondrial protein levels in adipose tissue?
    I want to know if there is any evidence of changes in mitochondrial gene expression or protein levels in adipose tissue or liver due to a i.p. dose of insulin 20 min before the sacrifice of the rat. When I say mitochondrial gene expression, I'm referring to genes involved in biogenesis or mitochondrial dynamics like pgc1, tfam, nrf1, mfn1,2 fis1, or drp1.
    Mark E Cleasby · Royal Veterinary College

    Gene expression changes are unlikely to be detected at significant levels on this time-scale. Hours would be required. Post-translational modifications are the usual detectable changes that occur within minutes of an insulin treatment, eg. Phosphorylation of signalling intermediates.

  • Sergey Shityakov added an answer in Autodock:
    Any suggestions on docking of nanoparticle to protein?

    Hi

    I have tried docking a unit cell of a nanoparticle onto protein (rigid blind docking) using autodock. Is it reasonable enough to assume the docked site (only one site was observed with low energy and 100% population with 2A cutoff) to be the desired protein-nanoparticle interaction site? or the nanoparticle must be of proper dimensions?

    Also, is autodock an appropriate tool for such calculations (even if proper sizes are taken into account)?

    Sergey Shityakov · University of Wuerzburg

    We recently published our findings on the P-gp interaction with various nanoparticles (fullerenes and carbon nanotube) using different docking algorithms, such as gradient optimisation algorithm (ADVina), Lamarckian genetic algorithm (FastDock), and shape-based approach (PatchDock) to estimate the binding affinities between these structures. Please refer to our publication.