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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  • Sabino Maggi added an answer in Gromacs:
    Which OS is best for GROMACS Molecular Dynamics package?

    I need to know which OS is best for GROMACS. gentoo  or Ubuntu?

    Sabino Maggi · National Research Council

    Not at all. Debian is well-known for being very stable and reliable. Dependencies may occasionally break in the development distribution only, aptly named 'unstable' (or sid), which is updated continuously.

    The main 'stable' branch, and to a lesser extent the intermediate 'testing' branch, is remarkably solid. In my opinion, the best compromise between stability and being up-to-date is the testing distribution.

  • Ling Johnson asked a question in Plating:
    What is the substance with much high oxygen component which is attached to the steel electrode by dielectric barrier dishcarge?

    The steel is mild steel, Carbon is ~7 wt% and iron (Fe) is 93 wt%. and firstly I used 96 % sulphuric acid to oxidise the  mild steel plate, during High voltage gas discharge process, ozone and oxygen atom produced will oxidise the surface of steel plate. after 30 mins gas discharge process, some places at the steel surface has clusters which has high concentration of oxygen element. Before the discharge process, the  atomic percentage is C:19.11%, O24.47%, Fe 55.87%. (fig 1), according to atmoic percentage, the iron oxidation process is not completed, so many of Fe is still pure metal. after discharge, surface has some clusters(fig 2), to analyse one of clusters, I find the white part has much higher oxygen component,   atomic percentage:C:13.98%, O 64.64%, Fe 21.23%. even C as CO2, Fe as Fe2O3, O is still left, what kind of formation it is to keep it on the surface? is it like a CuSO4 -5H2O, to form something like Fe2O3-5O2?

  • Kevin Marron added an answer in T Cell Activation:
    What are the main markers of T-cell activation?

    Hello, I'm trying to evaluate markers to establish change in T-cell status from naive to activated after I have stimulated them with a specific protein. Can anyone guide me on how to assess this?
    Thank you

    Kevin Marron · Sims IVF

    Hi Mabel.  The CD69 may only be expressed by the NK-T cells (CD4 or CD8 or both) so not sure it is a good general T-Cell activation marker

  • Surendra Singh added an answer in Chlorella:
    Why can microalgae grow in all pH level like 7,9 and 11? What is the mechanism that algae grows at all pH?

    I cultured chlorella sp (just found by microscopic analysis) and grew it at all mentioned pH. What mechanism affects the growth in all pH?

    Surendra Singh · Banaras Hindu University

    I agree with the opinion of Dr. Jay Hodson. Whatever the extracellular pH may be, the cytoplasmic pH always remains near neutral. This is basically  due to pH honeostasis which is maintained by proton efflux and influx mechanism. In addition to that microalgae release some extracellular metabolites which are acidic in nature and in turn netralize the high alkaline pH. This is one the strategies to protect the microalgal cells from high pH damage.

  • Can human platelet lysate be used to replace FCS for murine MSCs?

    Human platelet lysate (hPL) has been shown to be an efficient FCS replacement for human mesenchymal stem cells. Does anybody know of it is equally usefull for murine MSCs?

    thanks for every hint,

    Michael

    Sandra Mjoll Jonsdottir-Buch · University of Iceland

    It has been used for mouse MSC at least: http://www.ncbi.nlm.nih.gov/pubmed/24720766

    I've personally used hPL for MC3T3 cells (mouse osteoblasts) without any problems.

  • Xinghua Liu asked a question in Gene:
    Would you please pass me the paper "Analysis and expression of the class III peroxidase large gene family in Arabidopsis thaliana" in Gene?

    Tognolli, M., Penel, C., Greppin, H., and Simon, P. (2002). Analysis and expression of the class III peroxidase large gene family in Arabidopsis thaliana. Gene 288: 129–138.

  • How can I submit my paper in an international journal?

    I wrote some articles, but I couldn't find any valid international journal with ISI index and good Impact Factor (IF), could anyone suggest some journals or help me to find some?
    My paper is about "Electronic Supply Chain Management in E-Businesses" and other one "Evaluating Students Performance in E-learning system".

    Luis Fonseca · Polytechnic Institute of Porto

    Dear Mohsen,

    I think you already got some valuable inputs, so I would not go over these again.

    Since this is for me a very interesting topic (I started working in industry and only after several years decided to try and publish as an academic and researcher in scientific journals) I would add the following insights:

    - There are journals that are more quantitative while others are more qualitative. The same with filed scope and breath. Within the same field, there are journals that will not publish unless I apply SEM (Structural equation Modelling) while on the very same field, there are other journals (also SCOPUS indexed) where the reviewers advise me not to present a paper with a  simple correlation analysis since most readers would not understand it.

    - The time you are willing to wait is also another issue to consider. I had papers waiting for 2 years while others for 2 months. Many journals have a 1 year waiting time. So I suggest you try to find out the acceptance rate and the flow time of your target  journals .

    - Be careful with English language and formatting, many times this one of the main reason for not acceptance.

    - Last but not least you might think to have another more experienced researcher as coauthor that could advise you and increase the chances of the papers acceptance.

    All the Best.

    Luis Fonseca

  • Spring is slowly starting. What thoughts come to your mind with the idea of cycling and rebirth ?

    What are your scientific approasches to this, in terms of Phylosophy, Mathematics, Physics, Phisiology, Arts , or any of your own personal way?

    (I personally believe in the eternal power of natural cycling, and devote much of my works to the observation of the magical images of Human Angiogenesis and apoptosis.) 

    Marwan M. Obeidat · Hashemite University

    One central idea comes to my mind, dear Maria: that of regeneration!

  • G. C. Nayak added an answer in Permittivity:
    How can I calculate permitting and permeability of a material from its S parameters?

    Please suggest a matla or any other program to calculate permitting and Permeability of materials from its S parameters. 

    G. C. Nayak · Indian School of Mines

    Yes. 

  • What does ultraspherical polynomial mean ?

    Jacobi polynomials 

  • What precautions should be kept in our mind, if using chiral column in HPLC?

    I have a racemic mixture, which shows a spot on TLC slight lower than the mid position when using 60%EtOAc/hexane. I would like to know the appropriate mobile phase (eluent), and column specification.

    Paul Finn · Temple University

    Chiral columns are expensive. Be sure to look at column specs. Some solvents will ruin the column (eg chlorinated solvents). Make sure you are free of those solvents. 

  • Which kind of topologies in WSN are most efficient?

    Topologies are decided on basis of application area. But in general what kind of topologies are most efficient in terms of power consumption.

    Arjav Bavarva · RK University

    mesh topology

  • Jan Velterop asked a question in Diptera:
    Who can identify Rhagio rolandi and Rhagio perrisi, Diptera Rhagionidae?

    I did not find a key for identification. Enschede, 03-03-2015.

  • Veeresh Kumar added an answer in Graphene Oxide:
    Can anyone suggest a method to prepare graphene oxide stable solution in some organic solvent?

    Is there any simple method to prepare graphene oxide film?

    Veeresh Kumar · Indian Institute of Technology Delhi

    If it is not making stable disperson in water, please check your synthesis procedure of GO. In water it shows stable solution for very long period.

  • Faraz Khan added an answer in Trizol:
    Is there any way to extract RNA from old sample?

    No pellet using trizol protocol for RNA extraction. My leaf tissue samples are more than 2 years old. 

    Faraz Khan · University of Nottingham

    Hi Chris,

    I need to extract the total RNA for qPCR analysis.

    Thanks Jack. It was helpful. 

  • Panagiotis Tsakanikas added an answer in Gestures:
    How to get rid of the face when using skin detection algorithm for air gesture?

    when using a skin detection algorithm, i need to take the hand as an object, but this algorithm detects the face too, so i need a heuristic more powerful than taking the biggest contour so i need your suggestions please.

    Panagiotis Tsakanikas · Agricultural University of Athens

    You can try to use the ratio of contour to objects area, since the hand (as an more complicated object) should have a largest number than in the case of face. I believe this should be a more robust indicator...

  • Affar Shahid Karimullah added an answer in Comsol:
    What is the difference between power in or power deposited the electromagnetic ports section in COMSOL?

    Hi,
    I don't quite understand the difference between power input and power deposited in the Electromagnetic ports section. I am interested in simulating the laser irradiation of plasmonic arrays, hence I use a periodic boundary but with user defined ports. Now I assume that the power input should be the amount of power for that particular region, hence the laser power density is considered to calculate the power on just that 700nm region. Am I using this correctly? If so, what difference does P deposited make then?

    Affar Shahid Karimullah · University of Glasgow

    Thanks Lukas.

  • Michael Pfitzner added an answer in ANSYS CFX:
    Can anyone help me with combustion modeling in ANSYS CFX?

    I am working in combustion modeling of hybrid rocket using CFX. I am not able to initiate the combustion process. If anyone has a reference for combustion modeling do share it with me.

    Michael Pfitzner · Universität der Bundeswehr München

    combustion modeling in general is a complex issue. To get advice you first need to specify your problem more clearly and the combustion models you have been using in CFX.

  • Chayan Halder added an answer in Computer Vision:
    What are known domain specific languages or formal specifications of computer vision tasks?

    Can you tell me or point me to publications about domain specific languages to specify computer vision tasks or other ways of formally describing a sequence of image processing steps?

    Chayan Halder · West Bengal State University

    Any computer vision area needs image processing works so you can use Matlab, Opencv tool with c++ or java for computer vision tasks.

    Hope this will be helpful.

  • Khalid Mahrose added an answer in Ultrasonication:
    Detoxification of spice extract using Ultrasonication?

    Can we detoxify or remove aflatoxin B1,B2,G1,G2 by using ultrasonication?

    Khalid Mahrose · Zagazig University

    Dear Harish,

    Hope this website be useful for you: http://en.wikipedia.org/wiki/Sonication#cite_note-:0-1

    So, I do agree with Kan

  • Chandra Singh added an answer in Google Scholar:
    Does anybody know how we can add the missing citations to our profile in Google Scholar?
    There are several articles and textbooks that cite my articles but are not included as citations in my Google Scholar profile. Google Scholar says that the publishers of the corresponding journals should change their settings and there is nothing I can do. However, I was wondering whether anybody knows how we can add these missing citations to our profile in Google Scholar?
  • Marek Hoehse added an answer in Raman Spectroscopy:
    Any suggestions on the detection of diamond particles?

    I have a little emulsion of diamond particles. what is the best way for detect diamond?

    I want to ensure that there are diamond particle. i know that Raman spectroscopy is useful but I have to dry it. I don't want to dry.

    Marek Hoehse · Sartorius Stedim Biotech S.A.

    Dear Elmira,

    one more remark: You don´t have to dry the samples for Raman. Raman spectroscopy also works  in slurrys or liquids - water is not hampering the acquisition. If other solvents are used, you might check for overlapping bands (however despite the broader D band of carbon I cannot think of other vibrations that might overlap). Additionally the very narrow band width in combination with the high intensity of the diamond line make the detection easy, despite (broader) underlying bands. I was able to detect intense signatures of diamond in most of my ore samples, just because they were cut with a diamond saw blade despite strong underlying fluorescence.

    Regards

    Marek

  • Tasleem Arif added an answer in Acne:
    Which is the single best questionnaire to study the quality of life in acne patients?

    I want to study the quality of life in acne patients by a single questionnaire to make the study procedure and statistical part less cumbersome.

    Tasleem Arif · Government Medical College Srinagar

    Basically i have gone through a good number of questionnaires to asses quality of life in dermatological patients like SF-36, Skindex, DLQI, WHOQOL, NHP, SIP, etc. But in order to study quality of life completely and comprehensively, most of the times two or more questionnaires are needed to assess all the components. This makes the survey a bit cumbersome and very complex statistics which becomes difficult for both researcher as well as reader. Not only this many journals will ask for more comprehensive assessment of quality of life by combining two or more questionnaires. Every questionnaire has some deficiencies when applying it to the different diseases which makes it difficult to study comprehensively a disease by a single questionnaire. From a critical review published in J of Investigative dermatology by Both Hilde et al, they concluded that a combination of  SF-36 and Skindex-29 as the instruments of choice in dermatology.

    You can access this review below

    http://www.nature.com/jid/journal/v127/n12/full/5701142a.html

  • Andre Lindner added an answer in Forest Modeling:
    In the primary forest is forest biomass will be back to initial value after the disturbance (logging, fire)?

    I'm trying to develop biomass growth model of forest. Does anybody know that forest biomass will be back to initial value after the disturbance (logging, fire)?what the reference related with this?thanks

    Andre Lindner · Technische Universität Dresden

    This is a tough question ... first of all, the forest type is an important aspect to consider! Another one is, not only the absolute value of biomass, but also how stable it is during further succession. For south-east Atlantic Rainforest stands I can say, that secondary growth can recover in terms of biomass pretty fast - but this is not necessarily stable: e.g. fast growing species might increase biomass fast, but after species-turnover to mid-term/late successional species this might temporarily decrease again. Also the type of disturbance might be crucial: we found in one study that regrowth after complete cut-down recovered faster in terms of biomass than selectivily logged forest ... it's challenging to develop models for this, especially general ones - good luck!

  • Why does the color of Cd(1-x)ZnxS thin film deposited using CBD does not change to yellow as expected?

    I deposited the film using CBD ,but it's color does not change to yellow as expected.I changed the ratio of the chemicals but i got only white color not as supposed to be white to yellow color?

    Adam A Bahishti · Majmaah University

    I agree with Gowrish Rao sir, its better to go for composition analysis of prepared sample and then decide for further analysis or re-synthesis.

  • Leszek Flis added an answer in ANSYS:
    I have to do pushover analysis in ansys apdl ... plz help me how can i do pushover in Ansys?? what are the commands used in that?and how the substeps?

    i have to do pushover analysis in ansys apdl ... plz help me how can i do pushover in Ansys?? what are the commands used in that?and how the substeps?

    Leszek Flis · Polish Naval Academy

    APDL in native language of ANSYS and it is no common for most FEM users.

    Using APDL requires long time trainning or commercial help TECS from ANSYS developers. I don't think it is good chose. You probably want to focus FEM problem. Using APDL in ANSYS you focus on programing problem not engineering  problem. HypewWorks or LSDYNA should be beeter solution.

  • Fyza Sidek added an answer in CTAB:
    What is the best method to clean ~30ul of DNA?

    After extracting DNA from very dirty water samples doing a double PCI extraction (with CTAB) - pellets were brown. Rehydrated samples in 30ul of TE buffer but they have a light brown tinge to it - I want to clean these samples up but not sure on the volumes of ethanol to use.

    Was going to try the following:

    Dilute sample up to 200ul (adding 170ul ddH20), add 200ul cold 100% EtOH and 0.2V 3M sodium acetate (so 20ul). Let it sit for an hour at -20oC then spin it at max speed for 15 minutes. Remove the EtOH and do a second wash with 70% EtOH using 200ul. Spin it, let it dry and elute in 30ul of TE buffer again.

    Seen a lot of protocols out there, I don't want to mess my samples up (very precious samples!).

    Any advice would be much appreciated!

    Fyza Sidek · University Malaysia Sarawak

    Did u try spin column purification step? brownish colour in DNA samples usually caused by humic acid or phenolic compound contaminate, & sometimes it binds to the DNA. I used to have the same problem, but now I'm using spin column to purify my DNA samples. From my experience, EtOH alone couldn't help enough to remove the phenolic compound. 

  • Is it better to isolate rough endoplasmic reticulum first from virus infected plant to study viral replicase complexes?

    Bromovirus infection to plant

    Xinghua Liu · Jiangsu Academy of Agricultural Sciences

    sorry!

  • Burkhard Koehler added an answer in Polyaniline:
    Is there a single solvent in which both Polyaniline(EB) and poly carbonate are soluble?

    For making a blend.

    Burkhard Koehler · RWTH Aachen University

    Solvents for the emeraldine base (EB) are DMF, DMAc, NMP and DMSO. In all these solvents PC is also soluble. Another question is the stability of PC in presence of emeraldine base, because PC is sensitve to hydrolysis in presence of a base.

  • What is the main Difference between Raman and Infrared Spectroscopy?

    Open discussion

    Main Difference between Raman and Infrared Spectroscopy

    Johannes Kiefer · Universität Bremen

    Raman is inelastic scattering of light while IR is an absorption process. the selection rules are different, too (i.e. a vibration may be Raman active but not IR active and vice versa)