Q&A

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  • Ganesh Prasad Mishra added an answer in Autodock:
    How do you find the error and repair my ligand? Is there any software?

    When I open my ligand in SPDBV, I get the following error

    "At least one HETATM group lacked proper CONNECT informations. Connection will be generated between atoms that are closer than 2.000A, which can generate false bonds. Nb of HETATM groups in this case:1

    When I use this ligand to dock in autodock, the energy poses stops abruptly.

    How to rectify the CONNECT error.?

  • Which is the 2nd moment of a truncated inverse Rayleigh distribution?

    Hi folks,

    Any idea about how to calculate analytically the second moment of a two-sided (or one sided) truncated inverse Rayleigh random variable?

    In my application this random variable appears when a Rayleigh fading channel gain is pre-compensated at the transmitter and the result is clipped to avoid high peaks in the signal to be amplified before transmission. Since the transmitted signal is antipodal, this generates a two-sided pdf.

    Just a comment: I am not quite sure about the correctness of the term "truncated" here, because the resultant pdf not simply exists from 0 to C, where C is the clipping value. There is a high "impulse" in the truncated pdf at the point C because values exceeding C in the original random variable are set to C in the truncated random variable.

    Thanks. Dayan

    Hossein Soleimani · Isfahan University of Technology

    pdf of tow sided truncated (restricted to [C1 C2]) inverse Raylein distribution is:

    f(x)=(2*K / x^3)* exp(-K / x^2) /(exp(-K/ (C2) ^2) - exp(-K/ (C1) ^2) );  C1 < x < C2

    therefore, second moment of that is:

    integral(x^2  * f(x) ),   C1 < x < C2

  • How do I extract RNA without using liquid nitrogen?

    Now am tried the RNA extraction by using the TRIzol reagent and i homogenize the tissue using polytron homogenizer at room temperature for 30secs is this correct?

    Mohamed Awaad ABOU-ATTIA · Northwest A & F University

    Please homogenize the tissue in ice

  • Do you think that we could prevent type 1 diabetes?

    Type 1 diabetes is increasing in industralized nations and developing countries as well.Trials to prevent type 1 diabetes are still in infancy stages.Using different approaches to combat autoimmune processes through ant-CD3 anti-GAD antibodies or biodegradable nanoparticles may have potential future immunoregulatory benefits.However,advanced soiphisaticated multidisplinary fusion technologies such as bionanotechnologies may help success in finding out effective biointerventional agents in the future.

    Hassan Shora · Ismailia general Hospital

    Alam

    I meant  more intensive research efforts to innovate future potential preventive bioagents.There are ongoing trials using anti-idiotypic anti-GAD65 antibodies in NOD mice with success in preventing type 1 diabetes.However, we need to fuse proteomics, transcriptomics and metabolomics altogether to find out effective preventive biointerventuonal strategiesfor combating major devestating side effects such as how to prevent massive lymphocyte reaction uponm injecting the antigen are these right or not?

  • Akira Kanda added an answer in Space Time:
    Do objects move in relation to space-time in GR?

    Generally sympathetic to Carlo Rovelli's pronounced "relationalism" regarding space and time, I still find some of what he says about this puzzling. This question seeks clarification. He argues, in his paper "Localization in QFT," (in Cao ed. Conceptual Foundations of Quantum Field Theory, 1999, p. 215, that "General relativity describes the relative motion of dynamical entities (fields, fluids, particles, planets, stars, galaxies) in relation to one another." This seems true enough. But this is supported by the idea that space-time itself in GR is a "dynamical object," which curves or changes by relation to mass and energy present. But that does not seem a reason to hold that objects do not move in relation to space-time in GR. Instead, it seems that the gravitation field (which determines space- time) is one of the things in relation to which objects move, and consequently that objects move in relation to space-time in GR. In spite of that, Rovelli can be found to say, on the same page, that "Objects do not move in respect to space-time, nor with respect to anything external: they move in relation to one another." Is it inconsistent to think that if objects move in relation to one another, then they move in relation to the encompassing space-time?   

    Akira Kanda · University of Toronto

    Mr. Low

    > As I told you there are infinitely many ways to increase the momentum of m from 0 to mv. This means mv2/2 is not the only work needed to achieve this acceleration. So, by choosing mv2/2, Newton violated the conservation of energy to begin with.
    15 hours ago

    By above, I told you that what your community has been upholding are all pure nonsense. I showed that Newton's definition of kinetic energy is in violation of his own conservation of energy. This makes the entire physics collapse as the energy is the most fundamental entity in today's physics. I wonder how physicists think if they do at all. They have been shown the most devastating argument against their practice. They have no concept of energy. Do you understand what I am saying?

    This kind of problem will not go away by trying to ignore it. You have written lengthy communication with Mihai on the issue I brought up and somehow avoiding to communicate with me. I repeat that you have been shown that you guys have no concept of energy. So, the entire physics is complete nonsense. Think about it.

    It is this kind of failed reasoning which made physics an absolute embarrassment to the community of science. The filthy tactics of name calling, intimidation now notorious among decent scientists is becoming the target of further condemnation.

  • Vishnu Sharma added an answer in Dermatophytes:
    What is a suitable method to use essential oils as antideramtophytic agent?

    MIC Method for dermatophytes 

    Vishnu Sharma · JECRC University

    Respected B.R. Rajeswara Rao

    Sir, I also requested that both paper have been checked on web but the download is unavailable. it is heartiest request that if you have content copy please attached here and send me. 

  • Is there any tissue spared from artificial chimerism after bone marrow transplant? Will it affect DNA based forensic sex determination?

    The level of artificial chimerism is considered to  be an assessment factor for success of bone marrow transplants. But a forensic sample from the recipient might give ambiguous result in DNA based sex determination tests if he received the transplant tissue from opposite sex. Studies showed that the chimeric cells can migrate to other organs too. So the question is, are there any tissues in the body spared from artificial chimerism in such situations??

    Jaime González-Gómez · University of Veracruz

    Hi Sir. It seems that it would be advisable a highly discriminating procedures such as multiplex Y chromosome STR typing.
    This study can guide the subject.

    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3684380/

  • Parth Sarathi Nayak added an answer in Fibrosarcoma:
    How do fibrosarcoma HT1080 cells looks like in confocal DIC image?

    I had performed nanoparticles cytotoxicity on these cell lines. I want to know if these cells are dead then how do they look like. Answers will be appreciable.

    Parth Sarathi Nayak · National Institute of Technology Rourkela

    Hey Amirali

    the first image was control and the next two are treated with Nanoparticle

  • Badrul Haidar asked a question in Media:
    Why some bacteria grow in TSA (solid) media but not in TSB (Liquid) media?

    We have grown some plant endophytic bacteria in TSB medium. Now we are trying to grow them in liquid medium (TSA) for genomic DNA isolation ,some are growing and some are not ,what can be the reason?

  • Amirmohammad Pasdar added an answer in ACO:
    Urgent help about heuristics code?

    Need a code of some heuristics algorithms like PSO, GA, ACO, DEA as resource allocation at the cloudlet level that allocate cloudlet to different VMS in datacenterbroker. Please I would like to know how I can implement this algorithm in java code if you have any code of these algorithms please send to me to implement a new one like it thanks in advance.

    Amirmohammad Pasdar · Ferdowsi University Of Mashhad

    Dear Elhossiny,


    In order to implement your code, you should write your own classes which are related to your heuristics algorithm and use CloudSim libraries/classes to build up your approach. Suppose you want to implement your algorithm in Java environment. CloudSim only provides the libraries/classes you may need for coding. As an example if you want to implement GA, the following scheme might help you: Create a class and define the structure of a genome/chromosome based on your requirements. Then you should build another class/classes to use genome/chromosome structure for your desired approach and implement all methods you may need such as mutation, crossover, fitness function and etc. These methods use CloudSim classes/libraries to complement your approach.


    Regards,
    Amirmohammad

  • Reza Hedayati added an answer in FEA Tools:
    Considering a deformed plate, how do I measure the angle of deformation?
    Ansys shows deformation DMX but not the angular rotation.
    Reza Hedayati · Amirkabir University of Technology

    You can obtain the angle of rotation by measuring the change in the angle between nodes. For that purpose, you can use the code:

    *GET, Par, NODE, N, Item1, IT1NUM, Item2, IT2NUM

    with Item1=ORBT and IT1NUM=PSI, PHI where the angles PSI and PHI re mesured in degrees. 

  • Sanjeev Sareen added an answer in Likert Scale:
    Which DEA software package accepts imprecise data for computation ?

    I am carrying out a performance analysis of some companies using DEA. This involves precise and ordinal  from likert scale) input factors to be computed using DEA. Please suggest an available DEA package that can do this, preferably one that is free.

    Sanjeev Sareen · Birla Institute of Management Technology

    Thank you for your interest. DEA stands for Data Envelopment Analysis..

  • George Emil Sakr added an answer in Tamil:
    Offline Tamil Handwritten character database ?

    Dear Friends 

    Are there any publicly available/ licensed Offline Tamil Handwritten character database ? 

    If so, please provide links or names of the database. 

    Many thanks

    George Emil Sakr · American University of Beirut

    here it is 

    http://lipitk.sourceforge.net/hpl-datasets.htm

    hope this helps

  • Dennis Soku added an answer in Linguistics:
    Can any grammarian or linguist explain to me the nature of the word, Nigerian in the sentence, ‘‘I am a Nigerian’’?

    A survey carried out among 60 students of nine nationalities in three Ghanaian universities revealed that 95% of them, when indicating their nationality either orally or in writing, place before their nationality an indefinite article as in the example above. Is Nigerian in the sentence an adjective or a noun? If it is an adjective, why is it written with a capital letter? Languages are said to be dynamic so I hesitate to pass a comment on the sentence. I want views from experts on acceptability or otherwise of the above sentence. Will it make any difference if one says, ‘‘I am Nigerian’’ and another one says ‘‘I am a Nigerian’’. I welcome your views.

    Dennis Soku · Wisconsin International University College, Ghana

    I am grateful to all those who contributed to the discussion of the question posed. The question focused on three issues:
    a. The nature of ‘‘a Nigerian’’ and ‘‘Nigerian’’ in the two sentences
    b. Reason(s) for the determiner ‘‘a’’ preceding ‘‘Nigerian’’
    c. Acceptability of the sentence, ‘‘I am a Nigerian’’ (with explanation)
    Concerning issue (a) and (b) the explanations from the contributors have been superb. Regarding (c), when Naom Chomsky’s principles of ‘‘Grammaticality’’ and ‘‘Acceptability’’ are applied, make both sentences acceptable and meaningful. But looking at it from the semantic level both sentences bring about different emphases. I may be wrong, but it appears to me that when one wants to tell his/ her nationality, the use the predicative adjective (i.e. Nigerian) becomes more acceptable and meaningful. The predicative normative, ‘‘a Nigerian’’ becomes more acceptable and meaningful:
    1. when painting a cultural behaviour / or
    Example:
    - Boy, why are you wearing an earring to class?
    - Oh, I am a Nigerian.

    2. When correcting one’s identity that has been misrepresented by another person.
    Example:
    - All along I have thought you were Gambian.
    - No, I am a Nigerian.

  • Akshit Patel asked a question in Polyvinylpyrrolidone:
    How monovalent and divalent ions in brine will affect the stability of silica nanoparticle solution?

    I want to understand the phenomena how Na+ and Mg+2/Ca+2 will affect particle dispersion. Which stabilizing agents are used for in it? 

    I have came across some literature and I found that Polyvinylpyrrolidone (PVP) can stabilize the solution upto 220 hours and after that particles will start to settle down.

    Can anyone make me understand how PVP will help in this regard? And please suggest if any alternate chemical I can use.

  • Is there some research regarding strategies for development of communicative competence of engineering students?

    What strategies may be used to develop communicative competence of engineering students? Can ESP (English for Specific Purpose) serve as a tool to develop communicative competence in engineering students?

    Nandini Borah · Royal Group of Institutions

    that was of immense help Martina..

    And thank you Pushpanathan

  • George Emil Sakr added an answer in Weka:
    How can I determine which attributes to use by applying SVM-RFE?

    I have some questions on classification using Support Vector Mahine Recursive Feature Extraction using WEKA. RFE gives a final ranking for the attributes however one need a method to decide which featuers to select from the final ranking. i am dealing with binary classification and have a set of features to discriminate between patients and healthy individuals but my dataset is unbalanced (have a few samples from patients) and need some help regarding these questions:

    - Should i normilize the data or not? when and why we normilize the data?

    - using SVM-RFE what is the best method to decide which features should be condidered to build the classifier and which not (sensitivity, accuracy, kappa statistic,....) considering that i am dealing with unbalanced data

    George Emil Sakr · American University of Beirut

    For feature selection, get the variance of all features and select the top ones. Features with low variance have less information. 

    As for normalization, look at your features, if you see a feature that has very large values compared to the others, then you need to normalize. Otherwise you don't.

  • Hari Prasad asked a question in Microbials:
    Does anybody know how to store microbial cell at -80?

    Hi, i started microbial work recently i need to store collected sample for long time can any suggest the protocol of preservation at -80 or -20  

  • Can anyone suggest suitable liquid medium to culture freshwater Dinoflagellates?

    I need to isolate and culture Gonyaulax apiculata and Gymnodinium palustre (from lake) in laboratory condition. I used soil extract but, it does not work well. Can I use DY3 media?

    Kaladharan Edavilakathil Ponnan · Central Marine Fisheries Research Institute

    Here is  a reference  for  using   extracts of aquatic weeds:

    Kaladharan, P. & R.Gireesh. 2003.  Laboratory culture of Gracilaria spp.and Ulva lactuca in seawater enriched media.. Seaweed Res. Utiln.,25 (1&2):139-142.

  • Douglas R. Daugherty added an answer in OHSAS 18001:
    How do you define nonconformity?

    Every safety management system needs a process for dealing with OH&S non-conformities and for taking corrective action, but how do you define ‘nonconformity’ in your system?  “The non-fulfillment of a requirement”, as nonconformity is defined OHSAS18001, seems extremely broad and liable to over-burden the best of processes.

    BS OHSAS 18001:2007 says: 3.11 nonconformity = non-fulfilment of a requirement  [ISO 9000:2005, 3.6.2; ISO 14001, 3.15]
    NOTE A nonconformity can be any deviation from:
    • relevant work standards, practices, procedures, legal
    requirements, etc.

    Douglas R. Daugherty · University of New Mexico

    Dear Roland,

    In defining nonconformity I find myself in a  very subjective contemplation. It seems to me I am in a mindset like attempting to answer if this or that group is a terrorist group or a freedom fighter, which is best for society collectivism or individualism, is the true nature of humanity good or as Nietzche argues a quest for power, ect.?

    So I define nonconformity as "a deliberate act of protest by an individual or group(s)  of a social norm, institutional rule(s), judicial law, or governmental policy, in protest and in defiance of dress, set of behaviors, of beliefs,by any and all social actors within its building, jurisdiction, or borders".  

    Douglas

  • Amir Hajirassouliha added an answer in Gaussian:
    Is it possible to reduce the noise in an image without losing high-frequency intensity data?

    Hi,

    I want to apply a noise-reduction algorithm on images before finding the sub-pixel shift between them. Therefore, I cannot use ordinary image filtering approaches since by applying most of them the high-frequency intensity information will be lost and as the consequence the sub-pixel shift estimation accuracy will decrease. Does anyone have a suggestion about the methods which I can use?
    I have the cameras that I want to use for the imaging and I think modeling the camera Gaussian+Poisson noise would be a solution. What do you think about that?

    Thank you.

    Amir Hajirassouliha · University of Auckland

    Dear All,

    Thank you very much for your suggestions. To keep you updated, I checked BM3D, deblurring filters and wiener filter for the images I have. They make images look smoother but also caused considerable decrease in the accuracy of the next step of my algorithm for finding the sub-pixel shift between two images.

    It means that both of these algorithms have removed part of the intensity information (especially high-frequency components) which I have used for sub-pixel measurements. I suspect that wavelet filters may cause the same issue.

    I will keep you updated.

    Thank you

  • Khalid Mahrose added an answer in Quasi-Experiment:
    Can anyone suggest the most appropriate analysis method for food consumption data?

    I have conducted a quasi-experiment in examining the food consumption pattern of the school children of a control and an intervention schools. The study involved four different time frames, i.e. at pre- and 3-post-interventions where at each time frame, the data were collected for 5 consecutive days. I am not sure which statistical analysis to use should I want to analyse using the SPSS. Really appreciate if any of you can assist me in solving this problem. Thank you.

    Khalid Mahrose · Zagazig University

    You can use one way ANOVA to get your results

  • Ashraf Islam added an answer in Drug Formulation:
    Can anyone suggest me the criterias for selecting pressure sensitive adhesive polymer for formulating pressure sensitive transdermal patch?
    Pressure sensitive transdermal patch.
    Ashraf Islam · The University of Asia Pacific

    criteria for selecting pressure sensitive adhesive polymer.

    Compatibilities between the adhesive system and other formulation excipients
    Compatibility with skin,
    Physical/chemical stability of the total formulation and components
    Skin adhesion performance (initial and long-term adhesion)
    Residue after removal should be minimum amount.
    Non sensitive to skin
    Silicones, acrylates, or polyisobutylenes are generally used as adhesive.

  • Khalid Mahrose added an answer in Manuscripts:
    Basic tips before submission of a manuscript to a journal, how to write / compile a manuscript, improve its presentation and acceptance rate?

    Let the experienced researchers / writers share some basic and useful tips regarding writing skills required for preparing / compiling a manuscript to be submitted in a journal, which could altogether improve its presentation and improve chances of acceptance, the discussion may be very useful for beginners / young researchers. 

    Khalid Mahrose · Zagazig University

    We would like to know your expertise as you are an Editor -in-chief.

  • Ashwani Kumar Gupta asked a question in Renal:
    How many and which renal progenitor markers should a cell express for it to be called a renal progenitor cell?

    I want to characterize renal progenitor population derived from human amniotic fluid, for this I want to know about minimum requirement of renal progenitor markers for the inclusion of a cell in renal progenitor population. 

    Thank you,

  • Abeyou Wale Worqlul added an answer in MODIS:
    Where can we find an annotated MODIS or LANDSAT open dataset for classification benchmarking?

    We developed several machine learning techniques for growth stages classification based on MODIS (or later incorporating LANDSAT). Currently, we obtained results on our own annotated dataset based on field survey. Are there some open annotated dataset that we can compare our algorithms to this data?

    Abeyou Wale Worqlul · Bahir Dar University

    You can check the following site for MODIS and Landsat: 

    http://earthexplorer.usgs.gov/

    http://ladsweb.nascom.nasa.gov/data/search.html

    http://daac.ornl.gov/cgi-bin/MODIS/GLBVIZ_1_Glb/modis_subset_order_global_col5.pl

    https://mrtweb.cr.usgs.gov/

  • Rajinder Gupta added an answer in Oryza sativa:
    Which is the best non coding RNA database for plants?

    I am looking for non coding RNA databases for plants in particular Wheat (Triticum aestivum) and Rice (Oryza sativa).

    EDIT: I need list of ncRNA with their sequences

    Rajinder Gupta · National Agri-Food Biotechnology Institute

    Thanks @Sahar

    Good resources

  • Shantanu Bandyopadhyay asked a question in PLGA:
    What is the criteria for the selection of a PLGA/PLA polymeric nanoparticles?

    Of late, polymeric nanoparticles employing PLA/PLGA have been developed for various types of targeting. However, there are various grades in these polymers which differ not only in their substitution (acid or ether) but also in the values of inherent viscosity. Additionally, they are also available in different ratios and hence, what shall be the criteria to select them for targeting a specific organ.

  • Akira Kanda added an answer in Galileo:
    When and by whom the Relativity Principle was first stated?

    By looking at the original publications, rather than only at the articles and books talking of them, one finds

    Galileo Galilei (1564-1642).
    Dialogo sopra i due massimi sistemi del mondo, Tolemaico e Copernicano (1632)
    Galilei states the relativity principle, without using the term, as a consequence of the experimental evidence, by stating that all possible experiments, with bodies interacting in any possible ways, performed inside a ship cannot show whether the ship is moving or not, provided the motion is uniform. The principle is stated to be valid for all the phenomena.
    After having performed a number of experiments inside a ship standing in the harbour,
    “... have the ship moving with whatever velocity, then (provided that the motion be uniform and not fluctuating in one or the other direction) you will not recognise any variation in any of the just mentioned effects, neither you will be able to recognise from any of them whether the ship is moving or standing.”

    Jules Henri Poincaré (1854-1912)
    L’état actuel et l’avenir de la Physique Mathématique (1904)
    For the first time the term “Relativity Principle” is introduced and stated, on the basis of all the experiments performed at the time, including Michelson Morley, as
    “According to the “Relativity Principle” the laws of the physical phenomena must be the same for a standing observer and for one in uniform translation motion; so that we have no means, neither we can have any, to chose whether we are or not transported in such a motion”


    Albert Einstein (1879-1955)
    Ist die Trägheit eines Körpers von seinen Energiehalt abhänging?, Ann. d. Phys, 18 (1905), 639
    Principle of Relativity: “The laws by which the states of physical systems undergo change are not affected, whether these changes of state be referred to the one or the other of two systems of co-ordinates in uniform translatory motion.”

    Hendrik Antoon Lorentz (1853-1928)
    Deux mémoires de Henri Poincaré dans la physique mathématique, Acta mathematica 38 (1921), 293-308 (written in 1914)
    “It was not me to establish the Relativity Principle as rigorously and universally valid. Poincaré on the contrary obtained the perfect invariance of the electrodynamic equations and formulated the “Relativity Principle”, a term that was first to use.”

    Does anybody understand why usually only the last one, Einstein, is quoted, and the other forgotten?

    Akira Kanda · University of Toronto

    Johan,

    As we agreed, communicating science with those who have no background is waste of time. Scientific discussion is give and take. You are not getting anything out of these fruitless communications. What do historians know about science?

    Focus on the issues which matter. Do you remember the question about the conflict between field theory and the third law, which has a lot to do with why aether theory got into trouble?

  • How to measure the Net Profit and Total Shareholders' Equity of Life Insurance Companies?

    Examining the relationship between corporate governance and performance of Insurance companies in Bangladesh

    Rashid Zaman · Bahria University

    Your will find both of them in annual reports of the said companies.