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  • Tasaduq Hussain Wani added an answer in cDNA:
    Whole cDNA is required or just ORF is sufficient to overexpress proteins?

    I want to overexpress a protein in different cell lines of human. I know that we can use cDNA for it. But, I wonder is it possible to use just ORF (cDNA without UTR regions) for cloning in a vector and generation of proteins. Or I have to use whole cDNA.

    Tasaduq Hussain Wani · Shiv Nadar University

    Hey,

    You can use ORF for protein synthesis. If you are making your protein for antibody generation (polyclonal) then you need not to amplify ORF either. Just look for peptides with a good score to generate antibody. You can use any free online tool for that purpose. And please check with your vector system, whether you have to include stop codon or not.

    Cheers.

  • Phaniraj C added an answer in CNC:
    Is inconel 718 machining possible by HSS tool material?

    on cnc lathe.I want to work on this for my research work

    Phaniraj C · Indira Gandhi Centre for Atomic Research

    Please see the paper: may be useful:

    "Machinability of nickel-base super alloys: a general review", Journal of Materials Processing Technology 77 (1998) 278–284, by I.A. Choudhury, M.A. El-Baradie.

  • How to solve patchField entry problem in running solver of openFOAM?

    Dear all!

    As I get advised to use k-omega-SST turbulence model instead of K-epsilon model to get expected separation in near wall region. I have set 0/omega files as attached. After executing blockMesh command in terminal when I try to sun simpleFoam command in the terminal following errors found:

    Create time

    Create mesh for time = 0

    Reading field p

    Reading field U

    Reading/calculating face flux field phi

    Selecting incompressible transport model Newtonian
    Selecting RAS turbulence model kOmegaSST


    --> FOAM FATAL IO ERROR:
    Cannot find patchField entry for outlet

    file: /home/mukut/OpenFOAM/mukut-2.3.1/run/tutorials/incompressible/simpleFoam/pitzDaily/0/omega.boundaryField from line 26 to line 49.

    From function GeometricField<Type, PatchField, GeoMesh>::GeometricBoundaryField::readField(const DimensionedField<Type, GeoMesh>&, const dictionary&)
    in file /home/openfoam/OpenFOAM/OpenFOAM-2.3.1/src/OpenFOAM/lnInclude/GeometricBoundaryField.C at line 209.

    FOAM exiting

    ______________________________________________________

    I have found several post in cfd forum [I also posted there regarding my problem, but no one answer till now: http://www.cfd-online.com/Forums/openfoam-solving/147780-turbulence-model-applicable-plain-diffuser-flow-simulation-openfoam.html#post529618] by goggling in this issue. I found that this issue generally occurred due to semicolon ( ; ) missing or letter-case mismatch in patch name. But in my case I have checked and found no letter case mismatch and no semicolon missing.

    How to solve this problem? Any suggestion?

    A.N.M. Mominul Islam Mukut · Dhaka University of Engineering & Technology

    checkMesh result:

    /*---------------------------------------------------------------------------*\
    | ========= | |
    | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
    | \\ / O peration | Version: 2.3.1 |
    | \\ / A nd | Web: www.OpenFOAM.org |
    | \\/ M anipulation | |
    \*---------------------------------------------------------------------------*/
    Build : 2.3.1-bcfaaa7b8660
    Exec : checkMesh
    Date : Jan 30 2015
    Time : 12:42:59
    Host : "mukut-Endeavor-MR3300"
    PID : 4501
    Case : /home/mukut/OpenFOAM/mukut-2.3.1/run/tutorials/incompressible/simpleFoam/pitzDaily
    nProcs : 1
    sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
    fileModificationChecking : Monitoring run-time modified files using timeStampMaster
    allowSystemOperations : Allowing user-supplied system call operations

    // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
    Create time

    Create polyMesh for time = 0

    Time = 0

    Mesh stats
    points: 121242
    internal points: 0
    faces: 240620
    internal faces: 119380
    cells: 60000
    faces per cell: 6
    boundary patches: 5
    point zones: 0
    face zones: 0
    cell zones: 0

    Overall number of cells of each type:
    hexahedra: 60000
    prisms: 0
    wedges: 0
    pyramids: 0
    tet wedges: 0
    tetrahedra: 0
    polyhedra: 0

    Checking topology...
    Boundary definition OK.
    Cell to face addressing OK.
    Point usage OK.
    Upper triangular ordering OK.
    Face vertices OK.
    Number of regions: 1 (OK).

    Checking patch topology for multiply connected surfaces...
    Patch Faces Points Surface topology
    inlet 120 242 ok (non-closed singly connected)
    outlet 120 242 ok (non-closed singly connected)
    upperWall 500 1002 ok (non-closed singly connected)
    lowerWall 500 1002 ok (non-closed singly connected)
    frontAndBack 120000 121242 ok (non-closed singly connected)

    Checking geometry...
    Overall domain bounding box (0 -0.28 -0.1) (1.4 0.2 0.1)
    Mesh (non-empty, non-wedge) directions (1 1 0)
    Mesh (non-empty) directions (1 1 0)
    All edges aligned with or perpendicular to non-empty directions.
    Boundary openness (2.20781e-17 -1.44129e-16 1.75543e-15) OK.
    Max cell openness = 3.19023e-16 OK.
    Max aspect ratio = 5.91927 OK.
    Minimum face area = 1.29092e-06. Maximum face area = 0.00131724. Face area magnitudes OK.
    Min volume = 2.58185e-07. Max volume = 5.56073e-06. Total volume = 0.07756. Cell volumes OK.
    Mesh non-orthogonality Max: 19.941 average: 10.2709
    Non-orthogonality check OK.
    Face pyramids OK.
    Max skewness = 0.698374 OK.
    Coupled point location match (average 0) OK.

    Mesh OK.

  • Mustafa Wajidi added an answer in Proteomics:
    Can the terms 'upstream' and 'downstream' also be applied in proteomics?

    Or is it only limitied to DNA/genomics?

    Mustafa Wajidi · University of Science Malaysia

    It is more common to refer to N-terminus and C-terminus for describing positions on a polypeptide which can then be related to the nucleotide sequence of the gene that encodes the protein.

  • Akira Kanda added an answer in Frustration:
    Contrary to views of "flatlanders", the lack of topological features can frustrate the economic development of a region?

    Is there a way to reconcile Starrett's impossibility theorem with von Thunen's ideas in his treatise, The Isolated State?

    Is the complication to a feature- free region (e.g. desert), mainly the difficulties in extracting von Thunen rent?

    Akira Kanda · University of Toronto

    Shian-Loong,

    I am a pure mathematician and I studied Von Neumann's game theory from mathematical point of view. It is based upon the assumption that at each stage, each players act rationally to maximize the gain. The problem with this applied to real economics is that

    1. Real economics is so complex that nobody can grasp the situation well enough to act rationally.

    2. The current money market traders, whom I called "thugs" have no intention of acting rationally at all. They are basically rotten criminals who tried to thrive at the cost of entire humanity.

    In the past, it was easier. Each economy had its national boundary and global activities are done only through controlled trading and controlled currency exchange. So, Mr Abe's policy should have worked perfectly if the situation is not as global as now. Now, it seems that nothing can be done as any attempt to recover the economy is immediately attacked by the international money traders for their filthy greed. 50 years ago what they are doing was a serious financial crime which would have sent them to prison for a long time.

  • Do we have data for China Stock Market Capitalization from 1980?

    Do we have data for China Stock Market Capitalization from 1980?

    Paul Louangrath · Bangkok University

    If you are using the World Bank data, it is probably about CAPITAL ACCUMULATION. Market capitalization would generally come from the stock market. What kind of "capital" data are you looking for? capital accumulation in the mainland China, or stock market capitalization in mainland China?

  • Kamal Hadad added an answer in Radiation:
    What is reliability of radiation survey meters?

    Is there any reference data available for reliability  and availability of GM based radiation survey meters which are used for routine survey purpose in industrial or medical institutions. 

    Kamal Hadad · Shiraz University

    Noor, O. M. (2013). DEVELOPMENT OF ENERGY COMPENSATED GEIGER MULLER DETECTOR (Doctoral dissertation, University of Ontario Institute of Technology).

    Cadwallader, L. C., Bruyere, S. A., & Denny, B. J. (2013). Radiation Protection Instrument Reliability and Maintainability Data.

    Prasanna, G., & Jayapandian, J. (2014). An embedded read-out for GM counter. International Journal of Instrumentation Technology, 1(3), 228-240.  

  • I. M. Abu-Reidah added an answer in Gallic Acid:
    How can we calculate Gallic acid equivalent(GAE) in case of total phenolic compounds measurement?

    Since gallic acid has 4 hydrogen to reduce, 1 gallic acid eqv. 4 phenol. Is it?

    I. M. Abu-Reidah · Biodiversity and Environmental Research Center

     The use of gallic acid is just a representative phenolic acid, so the number of hydroxide moieties do not enter in the quantification of total phenols content.

  • I want to prepare DNA for next Generation Sequencing (Illumina sequencing) from previously collected DNA. by tris-EDTA Method. Please suggest kit?

    Next Generation Sequencing, DNA purifying kit, illumina  sequencing.

    Xavier Caguiat · Philippine Rice Research Institute

    Qiagen DNAeasy kit is good.

  • Tausif Alam added an answer in Research Projects:
    Looking for measuring the acute phase insulin release in diabetes patients. Is there any normal range for the acute phase insulin release (AIR)?

    For a research project thinking of measuring the first phase or acute phase insulin release in diabetes patients. Wonder whether there is any normal range for this or is it 'comparatively' lesser in diabetics when compared to the normal individuals? Thank you

    Tausif Alam · University of Wisconsin–Madison

    "Its on type 2 diabetes to be exact. None of the literature clearly states on whether there exists a normal range, as the changes seem only to be relative."

    Why would you expect a "normal" range in a progressively deteriorating condition? Doesn't it seem obvious that the best one can do is to have a relative change with time?

    There really is a plethora of information that stretches back decades. I am not sure how much more clear it needs to be...

    Here are the results of my first search:

    http://www.ncbi.nlm.nih.gov/pubmed/22834840

    http://www.ncbi.nlm.nih.gov/pubmed/11424229

    http://diabetes.diabetesjournals.org/content/51/suppl_1/S117.full

    https://www.google.com/webhp?sourceid=chrome-instant&ion=1&espv=2&ie=UTF-8#q=first+phase+insulin+secretion+in+type+2+diabetes

  • Vishal Soodan asked a question in Purchasing:
    Can anyone suggest the how purchase intention and purchase consistency be measured?

    During purchases, consumers develop intentions to purchase a product but when it comes to actual purchase, they change their behaviour and purchase a different product.

  • Shalkar Nurmoldin added an answer in LC-MS:
    Is anyone familiar with MTX determination in RBC with ESI LC-MS?

    Hello, everybody!

    Can you help me with Agilent 1260 and 6224 mass-spec. I'm using the many methods for sample preparation for eluate the MTX from blood cells, but my tries don't give me results?

    I'm use the 1mM ammonium formiate+ 0,1% Formic acid (75) and ACN 25 to mobile phase, and prepare the samples with Perchloric acid 16%, QC with 100ng and 1000ng don't shown after sample prep.  What is the reason?

    Shalkar Nurmoldin · Kazakh National Medical University

    Hi, we don't have a fluorescent detection hplc, our HPLC system tandem with TOF MS

  • Prakasam Muthusamy added an answer in Shimadzu:
    How do you prepare soil samples to measure total organic carbon for Shimadzu TOC-V csn?

    Unforunatelt, we dont have a solid combustion unit, but I know that there should be some digestion protocols.

    Thank you in advance!

    Prakasam Muthusamy · Wadia Institute of Himalayan Geology

    We are also using SSM 5000A Instrument which is attached with TOC vcph, to get TC, IC and TOC % from solid samples. We have have taken ~1 grm. of pulverized (~50 C an hour duration) sample for this analysis. After pulverizing we takes 20 mg samples for each TC and IC analysis. We have used raw samples for TC analysis at 950 C, and IC analysis we have used 0.5 ml orthophosphoric (10%) with 20 mg. of sample for reaction at 200 C.

  • Abbas Rahdar asked a question in Stoichiometry:
    In Reactive Sputtering method stoichiometry is maintained?

    In Reactive Sputtering method stoichiometry is maintained?

  • Himen Salimizand added an answer in Contamination:
    What are the criteria for infection and colonization or contamination?

    Infections and colonization or contamination criteria?

    If you know a paper to review, I was wonder if you can introduce me.

    Himen Salimizand · Mashhad University of Medical Sciences

    Hi Ibrahim. You made a complete definitions on the words that was unclear to me. Thanks so much. I appreciate.

  • Nabil Mustafa asked a question in Agricultural Systems:
    Looking for partnership?

    Seeking for partner 

    Here Eu call Horizone 2020. Is there somebody interesting to apply with me to this call under title'

    " Integrated agriculture system to protect environment "


    The Deadline for submission for RISE is: 28 April 2015


    Also the following link will help you to get more information about the submission process:
    http://ec.europa.eu/research/participants/portal4/desktop/en/funding/index.html

  • Imre Horvath added an answer in Design Theory:
    What are these terms about ? design methods, design theory and design philosophy ?

    What is definition or difference of these words ?

    Imre Horvath · Delft University Of Technology

    Dear Dr. Nazidizaji,

    There was a paper published in Research in Engineering Design in 2004, in which I tried to clarify the ontological status, epistemological relationships, pragmatic objectives, and research standing of the domains of interest in design research that you mentioned, and many more. For your convenience, please find a digital copy included.

    Kind regards, I.H.

  • chee guan Wong asked a question in Silicon:
    How can i better remove silica ( both colloidal and dissolved) in wastewater containing 33wt%PEG?

    silica / silicon is an unwanted impurity in our recycling of PEG from exhausted slurry , how can we better remove silica / silicon without usage of chemicals?

  • What type of material can be used as insulator for microwave hybrid heating?

    This question pertains to microwave processing which is used nowadays for a number of applications such as cladding, brazing and joining of materials. The problem that I am facing is that in the literature it is very hard to find the appropriate material for insulation of bulk metal as microwaves get reflected from the surface of bulk metals due to very low skin depth. Insulation is required for selective heating of bulk metals.

    Vasile Surducan · National Institute for Research and Development of Isotopic and Molecular Technologies

    I think that standard refractory bricks (orange color) are not suitable for this purpose because of the iron oxide inside which absorb microwaves. Perhaps you can try some white refractory bricks with high content of alumina. However we didn't try those behavior in microwave field.

    http://www.morganthermalceramics.com/products/insulating-fire-bricks-ifb

  • Catalin Lazar added an answer in Bone:
    Does anyone have experience using Bertillon calipers for measuring bone thickness in mm ?

    I'm looking for a conversion table in mm from the cm scale on the Bertillon caliper.

    Catalin Lazar · Muzeul Naţional de Istorie a României


    You can use a measurement converter available online on different websites.

  • How to calculate edge length from sobel operator gradient dx,dy ?

    How to calculate edge length from sobel operator gradient dx,dy??

  • Hakim SAIBI added an answer in Remote Sensing:
    High Resolution Remote Sensing Images, source?

    Dear all, I am looking for good high resolution remote sensing images to study dolerite intrusions. Any help? both possibilities are welcome: free and not-free images.

    Hakim SAIBI · Kyushu University

    Thank you all for information.

    Dr. Ghosh: sorry, I could not access the links!!

  • Kai Wang added an answer in Fiber:
    Has anyone tested how signals hybridize using a labeled DNA onto your DNA fiber?

    I am wondering about the application of FISH on the DNA fiber prepared by your new method. Has anyone tested how signals hybridize using a labeled DNA onto your DNA fiber?

    Kai Wang · Fujian Agriculture and Forestry University

    Hi Robert,

    Thanks for your reply. We haven`t tested yet, Overstetch is acceptable if all the chromatin was stretched evenly. What we worry about is if the "Zeonex" will block probe passing through or cause high background.

  • How to check quality of Salmon sperm SS DNA?

    I was making the solution of SS DNA. During this I have to sonicate to make working solution. This solution is not working for yeast two hybrid. I have changed all the yeast strain, DNA and medium but still I didnt get the result this time with same protocol (That I used earlier). So can any body suggest me to check the quality of SS DNA, or any other remedies for this problem.

    Sonalika Mahajan · Indian Council of Agricultural Research

    Which system you are using for yeast two-hybrid...? I mean the bait and prey yeast strains, vectors...? for salmon sperm ss DNA, check the concentration of the DNA and use as mentioned in the protocol. before using the ss DNA, denature it at 95 degree C for % min and therefter keep at 4 degree. after transformation store the leftover ss DNA at -20 or-40. 

  • Kunal P. Deshmukh added an answer in Cryptochromes:
    Which cry gene has been least studied by other researchers?

    I am working with B. thuringiensis.

    I have isolated about 50 B. thuringensis cultures from different regions of Marathwada, India. Now I have to check the presence of a specific cry gene which has been least studied by other researchers. 

    Kunal P. Deshmukh · Swami Ramanand Teerth Marathwada University

    Thank you very much Daniel Sir for your valuable answer and guidance...

  • Dipak Kumar Das asked a question in Air:
    What are the basic criteria foWhat are the basic criteria for filter sterilization in fermenter?

    I am facing problem in filter integrity during sterilization with fermenter. Every time after sterilization, integrity test of filter has failed. I am using PTFE membrane filter which are polypropylene and hydrophobic and the pore size is 0.2 micron. Those are air filter using for sterile air in fermenter. During sterilization, the filter has reached 121 degree temp and 1.5 bar pressure.
    When I checked new filter without sterilization, it has passed. So there is no question about integrity machine and sterility of fermenter media has also passed. So there is also no question about sterilization process.
    What are the main reason for integrity fail?

    Thanks & Regards
    Dipak Das

  • Kang Yang asked a question in Parameterization:
    How to measure the similarity of two land-cover polygon sets?

    I have two land-cover polygon sets from different times. Polygons from an earlier time merge/split/shrink/expand and generate a later pattern. I would like to find a parameter to measure the similarity between these two polygon "patterns". Any suggestions? Thanks!

  • V.K. JEENAGER added an answer in Wire:
    How can I clean the lubricant after drawing wire?

    I tried to clean with HCl but not effective. Anybody have different idea?

    V.K. JEENAGER · JECRC University

    If length of wire is not a constraint than use ultrasonic bath (acetone or phosphoric acid followed by distilled water) or make a setup followed by your wire drawn set up. 

  • Akanksha Gupta added an answer in VMD:
    Analyzing gromacs trajectory in vmd?

    my production run generated 2000 frames but when i i load my md.gro and md.trr file in vmd, vmd shows only 252 frames. what might be the problem? why all the frames cannot be seen? also,  i want to report here that the md.gro file generated during my md run in gromacs shows that the protein has moved out of the water box.

    please guide me as to why vmd is showing less number of frames from the 2000 generated frames.

    Akanksha Gupta · Netaji Subhas Institute of Technology

    upon giving gmxcheck -f md.xtc

    it says: checkin file md.xtc

    reading frame 0 time 0.000

    #atoms 355397

    precision 0.001(nm)

    last frame 2000 time 4000.000

    ..........."

    upon giving gmxcheck -e md.edr

    it says: checking energy file md.edr

    opened md.edr as single precision energy file

    frame: 0 (index 0), t: 0.000

    last energy frame read 2000 time 4000.000

    found 2001 frmaes with a timestep of 2 ps"

    please help as to what went wrong. why are the frmaes not getting opened in vmd?

  • Onny Nurrahman Marwayana added an answer in Codon:
    What shall we do when we have more than one stop codons inside (in the middle) of our DNA sequence?

    I have DNA sequences from my sample. I want to construct their phylogenetic tree. However, I found more than one stop codon in the middle of the sequences after I translated them to amino acid based on 1st codon position, 2nd codon position, and 3rd codon position. I think it is not good condition because normally we will find the stop codon at the last position of our sequence. So, what shall I do to solve this problem? Please, give me your suggestion. Thank you in advance.

    Onny Nurrahman Marwayana · Indonesian Institute of Sciences

    Dear Mathew,

    Thank you for your opinion. I will consider it.