Q&A

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  • Annemarie Honegger added an answer in PDB:
    Can multiple pdb files be merged for getting full query coverage for developing 3d protein homology model structures?

    I need to develop a 3d protein structure but i dont have any sitable full length crystalline structure in PDB. Can i use atomic coordinates to of the high sequence identity regions of the available templates and make a full length template file form homology modelling?

    Annemarie Honegger · University of Zurich

    Of course you can do that! Even if you have a full length template, superposition of multiple templates can help you to improve model quality, e.g. for divergent loop regions, for complex multi-domain proteins you frequently find higher-resolution templates for individual domains than for the whole molecule. I you have multiple, overlapping templates, you may be able to patch together a full-length model.

  • Selvakumar Manickam added an answer in Interdisciplinary Research:
    What are the main challenges for interdisciplinary research?

    I am wondering about peoples experience in interdisciplinary research and especially in the area computer science and medicine (but not limited).

    Selvakumar Manickam · University of Science Malaysia

    I have worked in the area of health informatics. The issues of such inter-disciplinary area are :

    1. Medical practitioners are not willing to accept too much computer science elements .

    2. Due to heavy privacy issue with medical data, it is very difficult to carry out research such as medical data analytics.

    3. Computer scientists on the other hand (due to lack of domain knowledge) will find miss out a lot on the tacit knowledge that exists in the medical field.

  • Laurence Eyres added an answer in Lipase:
    What is the use for analysis of positional distribution in TAG fatty acid?

    Positional distribution is used to identify the fatty acid present at Sn-2 position by using lipase. What is the use of identification of fatty acid present in TAG? Please give detailed applications of positional distribution of fatty acids?

    Laurence Eyres · University of Auckland

    Mainly for infant formula nutrition.the palmitic acid needs v to be be in the Sn 2 position

  • Vethaiya Balasubramanian added an answer in Biofertilizers:
    Is possible to create a livestock/agricultural farm coupled with biogas generator and microalgae culturing as biofertilizer?

    In ordet to close a full resource use cycle I wonder about the use of the digestate  as substrate for microalgae growth. With the biomass obtained, after the extraction of value added products (lipids, carotenoids), can be used as biofertilizer. So nutrients can be recycled "from cradle to grave". Please, I would also known your concerns regarding any possible contamination and health problems related to the use of microalgae from wastewater as fertilizer for food. 

    Thanks

    Vethaiya Balasubramanian · International Rice Research Institute

    Crop-livestock integration is highly complementary in terms of diverse products for home use and sale, family nutrition and cash flow, build-up of soil fertility and use of crop residues as fodder. Recycling of nutrients is enhanced. When you add biogas generator, you can use the cattle dung to generate gas (fuel) for domestic use without losing nutrients; the biogas slurry containing the nutrients can be used as rich manure in the field. I have no experience in using the biogas slurry to grow algae, another loop in the recycling of resources.

  • Srikanta Sannigrahi asked a question in Land Cover:
    How can I extract the required land use, land cover classes from MODIS land cover type data (MCD12Q1)?

    In default image, it shows only the DN value, how to convert this DN value to exact LULC classes? 

  • Selina Ewoenam Ahorsu asked a question in Word:
    Is the lexeme appropriate in our definition of the word?

    There has been several attempts to define the word. My burden is to find out whether the term 'lexeme' has been able to take care of all the discrepancies.

  • Stefano Polesello added an answer in Water Quality Analysis:
    How do I analyse quantitatively As(III) and As(V) species separately from a ground water system?

    How do I analyse quantitatively As(III) and As(V) species separately from a ground water system?

    Stefano Polesello · National Research Council

    it is possible to use Ion Chromatography but you need an electrochemical detector because the equivalent conductivities of the arsenic compounds are low. If you analyse groundwater, the key point is the handling of the sample, especially if anoxic. Sampling procedures for groudwaters  can alter the redox potential of the waters, causing the interconversion between arsenic species. The oxidation is catalysed by the presence of dissolved organic matter. See in my researchgate profile
    Article: Ion-chromatographic screening method for monitoring arsenate and other anionic pollutants in ground waters of Northern Italy
    S Polesello · S Valsecchi · S Cavalli · C Reschiotto
    [Show abstract]
    Journal of Chromatography A 07/2001; 920(1-2):231-8. 

  • Koos Fransen added an answer in Spatial Modeling:
    What are the latest methods of modelling spatial accessibility to facilities?

    In analyzing accessibility, many  methods such as nearest facility, service areas have been used. 

    In the current times, what are the methods/model that are suitable to model accessibility.

    Koos Fransen · Ghent University

    Dear Peter

    The (theoretically) most suited measure of accessibility strongly depends on the scale of analysis you wish to achieve and topic you want to examine. In addition to the previous posts, also take a look at the following literature review by Tijs Neutens (2015, Transportation Research Part A: Policy and Practice): "Accessibility, equity and health care: review and research directions for transport geographers". Whereas previous posts are based on accessibility analysis for larger geographical zones, the inidividual accessibility also plays an important role in this topic. Maybe it would be easier to provide an answer if you would add a specific case study you wish to examine.

    Kind regards,

    Koos

  • Chithan C Kandaswami added an answer in Lipoproteins:
    How can I perform lipoprotein isolation without an ultracentrifuge?

    We are interested to isolate crude lipoprotein preparation, which may consist of a mixture of VLDL/LDL/HDL, from patient and mouse serum. Further separation of VLDL/LDL/HDL is not necessary.

    Since we are not equipped with an ultracentrifuge, any protocol for crude lipoprotein isolation without ultracentrifugation technique is appreciated. 

    Thank you.

    Chithan C Kandaswami · University at Buffalo, The State University of New York

    Dear Chung-Wei,

    Size exclusion chromatography, could serve an alternate method to isolate lipoproteins from plasma.  During preparatory ultracentrifugation of lipoproteins damage to HDL particles has been demonstrated to begin at approximately 30,000 rpm, and the degree of loss increases in a rotor speed dependent fashion.

    Regards... 

  • Suparna Sengupta added an answer in Cell Count:
    Why do I always get a very low cell count when I count cancer cells using Haemocytometer?

    I have counted different cell lines like HeLa, LNCap.FGC, PC-3, CHO-b using a haemocytometer on T-25 and T-75 flasks. But even when the flasks are fully confluent, or 90% confluent, I get a very low cell count form flask. I usually trypsinize the flasks, pellet down the cells and add fresh 1-3ml of medium depending on cell density before counting. I make sure the flasks are always completely trypsinized with hardly any cells left behind after trypsinization. I also pipette and mix the cell pellet in the 1-3ml of medium thoroughly, so that there are no clumps. But I have got very low cell counts each and every time. Why is this so?

    Suparna Sengupta · Rajiv Gandhi Centre for Biotechnology

    There has to be some kind of mixing problem of the cell pellet. We need to dilute one step more (from initial 2-3 ml suspension) to avoid crowding of cells in the haemocytometer. Pl also check that cells are not broken as suggested by Anne.

  • Laith Najam added an answer in Irradiation:
    What is the difference in Neutron beam irradiation and Ion Beam irradiation?

    Can anyone please discuss the major difference between ION BEAM IRRADIATION ,NEUTRON BEAM IRRADIATION and GAMMA IRRADIATION? Among these irradiation treatments,which will be more beneficial for induction of stable cytoplasmic male sterile lines in any crop? 

    Please tell how to fix LD 50 for any physical or chemical mutagen for induction of mutagenesis in a new crop?

    Which chemical mutagens effectively induce mutations in cytoplasmic genes? 

    Thank You

    Laith Najam · University of Mosul

    always we used th e radioactive sources Co-60 and Cs-1237 for gamma radiation

    while the neutron beam we used(  Am-Be)  source with known value of neutron flux.

    For Ion/Proton beam we use Van De Graaff or charged particle accelerator

    so, you can select the experiment you  want to work

    Best regards

  • Ilya B. Gertsbakh added an answer in Server:
    Does changing service discipline in a queue has an effect on utilization of the server, and what about effect on queueing networks also?

    from example, changing service discipline from FCFS to SPT. I know that it affects average waiting time, but about the utilization of server. I think that it has no effect on single queue, but what about a queueing network?

    Ilya B. Gertsbakh · Ben-Gurion University of the Negev

    Service discipline is not a well-defined notion. You can always generalize this notion and to include in it some special rules (for example, transferring customers from long queue to a small one), so that  it ceratinly will affect  the server working parameters.

    Ilya Gertsbakh

  • Ian Westerman added an answer in Defense Industry:
    Can we say that the policy of militarization of Israeli is forced by its geopolitical situation?

    Israel is one of the most militarized country in the world. It is caused by experience and the fact that the country is surrounded on all sides by openly hostile countries that deny its right to exist. Israel explains that there is no other exit and policies of militarization and increase to the highest level the defense industry and defense capability is a condition for the survival of this country. That's why according to Global Peace Index Israel is one of the least peaceful country. Is Israel really has no other way out? Are the skeptics of the theory of the contract against Israel?

    Ian Westerman · Cranfield University

    Jessica, from the tone of your post you seem to be using the word 'militarised' almost as a term of abuse here, or certainly indicating that it is an undesireable situation which needs to be corrected - and I suspect that most people would agree take the same stance.  However, it is important to consider what you actually mean by it.  If a state has a strong military, with a close linkage between its military forces and its population, and perhaps its government bodies (retired or reservist military personnel in key government positions), is that necessarily a bad thing?  It is certainly not the western way of doing things, but is that the only norm against which we can make value judgements? I am not saying that you are wrong here, but I am questioning whether any state, not just Israel, must be criticized simply because it does not fit our western view of how its civil-military relations are organised. I would be interested in others' views. 

  • Marko Milojević added an answer in Accounting Education:
    Does anyone have any information about framework-based teaching in accounting?

    really need information about framework-based in accounting education. 

    any country have already implemented this method?

    Marko Milojević · Singidunum University

    As Ane said framework teaching in accounting is based on IFRS (Europe) and GAAP (in USA). In Europe, each country has an agency which deals with the harmonization and implementation of IFRS in the domestic market because many European countries have national laws in different ways interpret IFRS. Precisely this is the main difference between IFRS and GAAP. GAP are much more detailed and do not allow accounting assessment.

  • Catherine Viot added an answer in Marketing Communication:
    Can you all find me articles on application of BIG Five personality theory into Brand Evangelism & Customer Brand Relationship?

    I am developing my conceptual framework for the PhD , and need to have hypotheses ( being tested) to verify the mediating or moderating impact of BIG Five personality factors towards Brand Evangelism and Customer Brand Relationship. Anyone who is alert on Branding,Consumer Behavior, Marketing,Marketing Communication,Advertising  and Celebrity Endorsement may help me for this.

    Thank you

    Ravi from Sri Lanka. 

    Catherine Viot · Claude Bernard University Lyon 1

    This paper may help you.

  • Hao Wu added an answer in Mitochondria:
    Anyone familiar with an antibody against mitochondria fixed cells IF?

    Hi,

    I would like some advice to purchase an antibody against mitochondria for IF on fixed cells from people that have used an specific one and can tell me that it worked :-)

    I cannot use either Mitotracker red or green.

    Thanks you!

    Hao Wu · Institute of Zoology

    Cytochrome C (if there is no Cyto-c release or no cell death) , Tim23, Tom20 antibody from BD, or Hsp60 antibody from Cell Signaling Tech.

  • Amir Mehmood Shaheen added an answer in Routing Protocols:
    Does anyone have implemented a routing protocol for body area network in castalia simulator?

    Wireless Body area Network, Wireless sensor networks.

    Amir Mehmood Shaheen · Federal Urdu University of Arts, Science and Technology

    Thanks all of you for replying me. I want to implement my own routing protocol for WBAN scenario in castalia but there is no any routing protocol implementation found for WBAN. If any one implemented the routing protocol specially for BAN so please share it with me so I can have an idea how to implement my own protocol. 

  • Marialuisa Mongelli added an answer in SAP2000:
    How can I get the high-rise building capacity under seismic load?

    how can i get the capacity of high rise building using time history analysis in SAP2000 or i must use pushover analysis method

    Marialuisa Mongelli · ENEA

    Hi Ahmed, if you use SAP2000 looks at  the  D and E sections of the attached file. As getting started, you can also see the following video clicking on the following link at

    https://www.youtube.com/watch?v=CzqZVDse-eI

  • Marcel M. Lambrechts added an answer in Teacher Education:
    How can we measure teacher effectiveness?
    Teacher effectivness is the measure part of quality education. Efficient and effective teachers performance is different than normal. But the main problem lies in assessing their work.
    Marcel M. Lambrechts · Centre d'Ecologie Fonctionnelle et Evolutive, Montpellier, France

    Grades apparently do not reflect intelligence.

    Cheers

  • Uģis Lācis added an answer in Extinction Coefficient:
    Can someone kindly explain how I can use Excel to determine area under a curve especially wile plotting extinction coefficient against wavenumber?

    I want to calculate the area under a curve using Excel. Can someone please help?

    Uģis Lācis · KTH Royal Institute of Technology

    When I used Excel last time, I didn't see any functions for integration.

    However, it is very easy to numerically integrate the function manually. If you have your function sampled over some interval, then the integral between two points can be approximated using trapezoidal rule (see link). Then the total integral will be a sum over all of the segments.

  • Maciej Wawrzczak added an answer in Social Systems:
    How archaeologists justify the adequacy of their proxies?

    Archaeologists make propositions about properties of social systems of the past, because the past is in itself unobservable we have to use indicators that postulate a causal relation between the observable fact (the contemporary archaeological register and his properties) and the unobservable property (usually of the social systems) we are interested in studying. This jump to the past implies some epistemological problems, in the first place how we justify the causal relation we postulate and how we can reduce ambiguity of the indicator considering that many causes can have the same observable effect in the archaeological register?

    Maciej Wawrzczak · Museum of Spa, Poland, Szczawnica

    Hi Andone

    I recomend You to contact with Prof. Sławomir Kadrow. He is on ResearchGate. Maybe in his works there are some informations and answers to your question.

    Best Regards

    Maciej Wawrzczak

  • Riccardo Lenzi added an answer in Oral, Head and Neck Cancer:
    Is it reasonable to deal with neck surgically first when treating head and neck cancers characteristic with T- and N- discrepency?

    BUT,leave the primary tumor for conservation therapy considering a safe surgical resection might lead to an unfavorable funcitonal result. Of course, the patients we are mentioning are likely to have a planned neck disseciton.

     whats the pros and cons?

    Riccardo Lenzi · Azienda Unità Sanitaria Locale 1 Massa-Carrara

    I agree with dr. Granell, there is no need to perform neck dissection before an organ preservation strategy

  • Andrei I. Fischer added an answer in Inorganic Chemistry:
    How can I synthesise Co(OH)2 from solution without transformation to Co(OH)3 or other Co(III) hydroxide compounds?

    How can I synthesis Co(OH)2 from solution whitout transformation to Co(OH)3 or other Co(III) hyderoxide componds?

    Andrei I. Fischer · Saint Petersburg State Institute of Technology (Technical University)

    You can use the reagents (solutions of sodium or potassium hydroxides and a solution of cobalt(II) nitrate), which are blown by argon or nitrogen for total extraction of the oxygen.

  • Hussein Elasrag added an answer in Islamic Finance:
    Small and medium-sized enterprises (SMEs) and Islamic finance. what's next ?

    Experiences from across the Mena region indicate that a number of SMEs, estimated at about 20%-25% of the total, prefer sharia-compliant products . Thus, better risk management protocols would strengthen lenders’ confidence to create more sharia-compliant financing options. Risk management frameworks that protect lender's’ rights and address their concerns for transparent information could not only strengthen the evolution of Islamic finance with respect to SMEs, but allow traditional banks to develop more confidence in lending to SMEs, as well.

    Your opinion matters and will be gratefully appreciated.

    Hussein Elasrag · Ministry Of Industry And Foreign Trade

    Dear Dr.Maha Radwan

    Thank you very much for your helpful answer.

  • Smitha Gopinath added an answer in Shear Strength:
    Is it reliable if i propose a non-linear regression model to predict shear strength based on some controlling parameter?

    controlling parameter such as concrete tensile strength, depth, shear span-to-depth ratio etc

    Smitha Gopinath · CSIR Structural Engineering Research Centre

    Leon,

    It is also well possible that you can see some parameter missed out in the existing models, and incorporation of that either into existing or as a new form pave way for new mathematical predictions.

  • Peter T Breuer added an answer in Fixed Point Theory:
    Is there a fixed-point theorem related to functions defined in the integer numbers?

    I have a function f

    f: Z^2 -> Z^2

    such that

    (x', y') = f(x, y)

    and

    x'-y' <= x-y

    I need a reference paper or book that shows (perhaps using a more general statement) that iterative applications of f converge to a fixed point (x_0, y_0) IN A FINITE NUMBER OF ITERATIONS.

    Peter T Breuer · Birmingham City University

    Yes, but  I don't think the condition g((Gk)) <= Gk will work on its own, where Gk is the 2kx2k square about the origin.

    Try something like g(n,m)=(n+1,m) for n<k, and g(k,m)=(k-1,n). That is, step UP when not at the top edge of the square, and step DOWN when at the top edge. That'll keep the drunkard oscillating from the top edge to the level below and back.

  • A. Gravey added an answer in Omnet++:
    How can I include routing and wavelength assignment node within each router?

    GMPLS based Optical Network over Omnet++ tool

    I am building GMPLS based optical network over Omnet++ tool

    A. Gravey · Institut Mines-Télécom

    my answer is not related to Omnet++ but to the principle of including RWA in each router.

    I do not see why you would wish to implement RWA in each router. RWA is part of the control plane (you compute the paths within a domain or a network) and is typically done in a centralized manner (e.g. within  a Path Computing Element) . Implementing RWA in each router would correspond to perform this control plane issue in a distributed manner.

    Maybe I miss your point!

  • Young Jin Jeon added an answer in Navier-Stokes Equations:
    What is the appropriate B.C for the pressure poisson equation derived from Navier-Stokes Equations

    Hi everyone

    Suppose for the Navier-Stokes problem using FEM that the velocity field is known, and we want to solve the problem for the pressure field, what I'm doing is taking the divergence of the momentum equation so that I  get a Poisson equation on the pressure, in The weak form and after integration by parts, I get the boundary term which I can't deal with!

    my question is : what is the adequate B.C that I have to impose on the pressure for this problem ?

    Young Jin Jeon · Institut Pprime

    Bonjour,

    I am not sure that followings are what you would like to find...

    All the boundary points should be assigned as Dirichlet (pressure) or Neumann (pressure gradient) B.C., while at least one Dirichlet condition is required to avoid the singularity of Poisson equation.

    Laplacian of pressure, div ( grad p ), can be expressed in central differential scheme as, (assuming as 1D case for simplifying the equation...)

     Eq. 1   :   ( grad p(i+0.5) - grad p (i-0.5) ) / dx                 

    or

    Eq.   2  :    ( ( p(i+1) - p(i) ) / dx - ( p(i) - p(i-1) ) / dx ) / dx

    (here ( p(i+1) - p(i) ) / dx = grad p(i+0.5),  p(i) - p(i-1) ) / dx = grad p(i-0.5) )

    You can find here how you can apply Dirichlet (Eq. 2) or Neumann (Eq.1) boundary condition. For a general example, Neumann condition at the left side, the above equation can be expressed as

    div ( grad p ) = ( ( p(i+1) - p(i) ) / dx - [ pressure gradient at the left side] ) / dx 

    Best,

  • Naveen Nagiah added an answer in Electrospinning:
    How can I make core shell nanofiber?

    I am working on PCL based nanofiber. I have to make core shell nano fiber using electrospinning unit. Please suggest me the way and other polymer or material to make these core shell nanofiber?

    Naveen Nagiah · Nanomyp, Granada,Spain

    Please use this publication for ur reference. 

    Materials Science and Engineering C 33 (2013) 4444–4452

    the supporting info has the pic of the setup used.