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  • How to visualize vectors obtained in matlab ... processing image?

    I have been using the function vision.Localmaxfinder and it has given me the vectors in a data table... what function would be useful to visualize it within the image?

    Mohammad Karim Hardani Asl · Islamic Azad University

    Dear Piero,

    You are using function that returns X and Y as a single points! I'm attaching a link for the function. The LocalMaximaFinder object finds local maxima in matrices. describe your needs my friend, why you want to use a function? what for?

    if you are going to recognize patterns or object, you should use something else.

  • Are gravity scientists willing to abandon General Relativity when another theory shows much more success in explaining phenomenas?

    This is an open question about the willingness of scientists to abandon GR, based upon a possible successful competing theory. As an example, we take a gravity theory that has shown an important number of successes, as explained in the power-point presentation below.
    My assumption is that General Relativity scientists are not willing to abandon it, whatever the reasons or successes of other theories are, and no matter the disproves that are found about GR issues. They prefer to further develop GR.
    I suspect that the reason is that most of the General Relativity scientists live within a profit structure that they are not able to abandon, by a lack of time to study the competing theory and by the impossibility to cover or overcome the missing wages when they would quit the General Relativity theory. This causes a vicious circle that they cannot abandon.

  • Jamal Hussen added an answer in Cell Culture:
    My monocyte does not adhere to plastic - can anyone help?
    I am isolating monocytes from bovine peripheral blood, either by CD14+ MACS positive selection or by plating the whole PBMCs. The problem is that my monocytes don't adhere to the plastic plates. I try also to generate DCs from monocytes and the cells don't look like DCs under microscope. So can any body help me to find the reason why my monocytes don't adhere to plastic?
    Jamal Hussen · University of Veterinary Medicine Hannover

    The FCS charge used seems to play a role.

  • Yavuz Abut asked a question in Factorial Design:
    How can I Choose the Best Regression Model/Equation?

    Attached is a regression model by full factorial design which has 4 factors and 144 runs..But the final equation too long and adjusted-R is not feasible.

    How can I find the best equation and fitted model in Matlab?

  • Is UV light of laminar having any effect on murashige and skoog media?

    I turned on UV light while my bottles with MS media was in laminar. Is there any effect of UV on nutritional quality of media.

    Saeid Abu-Romman · Al-Balqa' Applied University

    I don't think that UV light affect the nutritional quality of the media. Good luck

  • Is it possible to take EBSD for the compressive stress induced specimen ?

    compressive residual stress induced surface specimen is possible to take Electron Back Scattering Diffraction or not.

    Tarik Ömer Oğurtani · Middle East Technical University

    Sorry! You have an awkward question. No ordinary person can get anything out of that.  If I guess properly.  You wish to known that whether  EBSD associated with the  strained surfaces can be used to evaluate residual stresses etc.  My answer would be yes!!!

  • Massimiliano Grassi added an answer in Resampling:
    Is it possible to calculate p-value with Bias-Corrected and Accelerated Bootstrapped CI of a Regression Coefficient?

    Hi everyone,

    I'm running a regression model (multiple predictors) with bootstrap resampling. 
    I asked for Bias-Corrected and Accelerated confidence interval (as usually preferred to a percentile based one).

    However, in one of the coefficient the BCa 99% CI contains the 0, while the p-value is inferior to the significance level (p<0.01).  I find out that the hypothesis testing is calculated considering percentiles and not the application of BCa.

    I wonder if is there a way (e.g. in R) to calculate the p-value associated to the BCa CI. I understand that the sole CI would be enough to decide in accept (contains 0) or refuse (does not contains 0) the null-hypotesis, but I would like to have also the explicit p-value. This mainly for make it more easy to understand to readers.

    Thank you,

    Massimiliano

    Massimiliano Grassi · Villa San Benedetto Hospital

    Quite analytically consuming but such a brilliant solution!

    You can even test the interpolated value and eventually fine-tune it to the desired decimal with some more runs!

  • Specificity and sensitivity differs in each article, How to decide which one to follow?

    Hi as many students early in their period of evidence based practice we face lots of problem while searching for the best evidence. One of major difficulties is the reliability of the test or a tool. There are at least 10 published article when we search for a particular test with different range of sensitivity and specificity, even few systematic reviews with pooled Sn and Sp.How do we decide which article to follow? what are the few key strategies followed, what do you look in the methodology of these studies apart from the journal quality and search methods.

    Charles Qishi Zheng · Singapore Clinical Research Institute

    Upon you question, the topic seems quite hot since there are a few SRs published already. That is a good news and may save you a lot of time. : )

    I would propose to follow the several steps:

    1. Run a systematic literature search to find all the available SRs;

    2. Find out two or three SRs that are most up to date or mostly cited;

    3. Read and appraise the selected SRs first. The appraisal should focus on

        1). Directness: whether the patients, test/tool for diagnosis and outcomes in these SRs are same or similar with your question;

        2). Quality: what are the type of included studies (RCTs or observational studies)?; how are quality of those included studies (risk of bias assessment)?;

        3) Methods and results: whether they used appropriate method to analyse the data; whether they report results comprehensively (e.g. any sensitivity analysis or/and subgroup analysis) to enable you to understand the results well

    4. If you fortunately find suitable SR for answering your question, then that's it!

    5. However, if the SRs are 1) not fits in your question (e.g. different population, different tools etc.); 2) not good enough in terms of quality; 3) not up-to-date at all, I will suggest to do a meta-analysis by yourself to gain a more reliable Se and Sp and contribute updated evidence to the area! : )

    Above are just very rough steps for your reference. You may refer to some other existing papers which explain how they extracted Se and Sp for their studies, and also some systematic review handbooks and literature appraisals methods.

    Good luck!

  • How Stacking fault energy is a function of material?

    Cu and Al have same FCC crystal structure but differ in SFE (stacking fault energy). Why is this so? On what parameters SFE is dependent and how it is calculated?

    Tapan Chatterji · Institut Laue-Langevin

    Tarik has pointed out that the calculation of stacking fault energy has difficulties. This is true but I must also point out that the experimental determination of stacking fault energies is alsp not easy and the different methods to determine the stacking fault energy gives different results. For fcc alloys a number of techniques have een used to evluate the the stacking fault energy viz. x-ray method, plastic deformation of single crystals, electron mcroscopy of thin films (nodes and tetrahedra), density of annealing twins etc.These mehods have shown that a pronounced increase in stacking fault density, or lowering of sttacking fault energy, usually occurs with increasing solute concentration in the alloys based on Cu, Ag and Au, although there are considerable discrepencies between individual methods.

    The stacking faults are onserved often in connection with the splitting of dislocations into partials. In this process the energy cost of forming the fault oppoes the energy gain ed by moving the partials apart, eading to an equilibrium distance of dissociation of the partials. The precise determination of the stacking fault energies is difficult, especially with the materials with large stacking fault energies, because the separation between partials is inversly proportionl to the fault energy. Therefore the experimental determinied values have errors of unknown magnitude.

       From theoretical point of view, the twin and stacking fault in closed packed metals represent well defined planar defects, and the determination of the energy of formation is an appropriate starting point. In addition comprehensive theoretical studies of stacking faults may serve to establish simple trends in the energies which of course be confirmed by experiments.

  • Ranjith garigipati Kumar added an answer in Abaqus:
    How can I write Abaqus 's results to a text file via an Umat subroutine ?

    Dear all, 

    Actually, I am wondering how can I write specific data to a text file via Umat as        I need this data for further purposes?

    Many thanks for your help

    Ranjith garigipati Kumar · Masdar Institute of Science and Technology

    Dear Ali Nassr,

    You can write the data to text file using the following commands:

    *************************************************************

    open(105,file='D:\Ranjith\My_work\tt.txt',position='append')
    WRITE(105,*)Z, E1
    close(105)

    *************************************************************

    The above lines are self explanatory :-) I'm writing two variable Z and E1 to the text file tt.txt. 

    Thanks & Regards,

    Ranjith.

  • Frank Höger added an answer in Shrimp:
    How to analyse free amino acid in Fermented Fish and Shrimp?

    I had a problem to find simple protocol to analyze total free amino acid in fermented fish and shrimp. any suggestion? 

    Regards

    Frank Höger · BASF SE

    Hi Heru

    To make it really quick you can measure a protein content with a standard Proteinassay,

    Bradford, BCA and/or E280 to fix the total amount of protein. Maybe you do this already, than you can analyze the samples with ninhydrin-assay, this stains only amino acids and short peptides. This will give you a good overview about the distribution of Amino Acids and Proteins and you can correlate them

    To get a better qualitative proof you can run a quick TLC with a system to separate Amino Acid, TLC can be principally measured and quantified too....

  • Can anyone give me information on any sociological inquiry about how (natural) science functions and progresses?

    I am interested NOT in research in the area of the philosophy of science (e.g. Kuhn, Popper, Feyerabend, etc), but, specifically, in the sociology of science with a particular focus on scientists' use of and reliance on non-epistemic values  (e.g. social, moral, aesthetic, etc.) and social practices. Thank you.

    Stephen Linstead · The University of York

    I guess the first entry into this area was Latour's Laboratory Life, but ANT generally since then has been less directly concerned with the issues you are speaking of although you'd find some useful sources (if the approach is not too offputting - not everyone writes as well as Latour!).Steve Woolgar's work might also be a resource. However, the work of John Law on the relation between ANT and STS could be more helpful - try his paper On Sociology and STS in Sociological Review 56.4 2008 to get you started, Donna Haraway and Susan Leigh Star also come to mind, although they have a more technological interest. I personally love Allucquere Rosanne Stone's "On the War of Desire and Technology at the Close of the Mechanical Age" (1996) as a great read - a sort of avant-garde sociological classic. I've also found the journal "Science as Culture" very useful for crossover studies. Chris Grey has a recent book on the  organization of Alan Turing's group and the relationof secrecy and organization that might be relevant Decoding Organization : Bletchley Park, Codebreaking and Organization Studies. / Grey, Christopher.Cambridge : Cambridge University Press, 2012. 340 p. Hope some of this is useful!

  • What type of statistical test would give significance or p-vlaue for protein-protein interactions indentified between two gene sets?

    Hi, anyone has answer to this question? I have two gene sets. Geneset-1 has 50 genes and Geneset-2 has 300 genes. When I input all these 350 genes into protein interaction database, I found protein interactions between 57 genes. This 57 genes include: 17 genes from Geneset-1 and 40 genes from Geneset-2. Now, I would like to know signifcance (p-value) of protein interactions between Geneset-1 and Geneset-2. What kind of test I should use to find-out the significance (p-value). Thank you.

    Prashanth Suravajhala · University of Copenhagen

    Dear Nsr

    You could as well apply Betweenness and Closeness centralities as a measure.  They are wonderful measures as the latter is an indicative of computing the average shortest path length between the nodes to infer significance.

    Hope this helps

    Prash 

  • A. Lincy added an answer in Orbit:
    A coordination complex has one unpaired electron in t2g orbital and two unpaired electron in eg orbital. will it show antiferromagnetism?

    when M-H room temperature study was done, a small curve was obtained. the metal in the complex is cobalt and the ligand is malonate.

    A. Lincy · Mahatma Gandhi University

    sir can you give some supporting theory? thanks for the response.

  • Is there software available to calculate the Tm of complementary DNA/primer strands with multiple adjacent mismatches?

    The software available is limited to one base pair mismatches.  

    Paolo Scarpelli · Università degli Studi di Perugia

    This is an example of Snapgene application for your own purposes


  • Prerna Joshi asked a question in Soil Quality:
    Which seasons need to be accounted for while analysing soil health in the semi arid regions around delhi?

    In a tropical country like India heavily influenced by S-W monsoon, while analysing soil characteristics (physical, chemical and biological) of a semi arid region near Delhi, what seasons should be considered for seasonal sampling of soils? keeping in mind, the objectives are to determine soil quality based on these physico- chemical and biological parameters....

  • How can DFT calculation from gaussian contribute to my research about doping TiO2?

    Can DFT calculation from gaussian predict or explain the result of doping from TiO2 with metals?

    Bartosz Trzaskowski · University of Warsaw

    The very general answer is yes. One thing that DFT can give you is the band structure of the pristine and doped TiO2, which allows you to evaluate the band gap and all the features connected to it.

  • Mukut Gohain added an answer in Publications:
    Can solvent attain higher temperature than its boiling point?

    I have seen in many publications that solvent is heated to higher temperature than its boiling. Is it correct?

    Mukut Gohain · University of the Free State

    Boiling-point elevation describes the phenomenon that the boiling point of a solvent will be higher when another compound is added, i.e., a solution has a higher boiling point than a pure solvent. This happens whenever a non-volatile soluteis added to a pure solvent.

  • Prashanth Suravajhala added an answer in Plink:
    Do you know a software to identify gene-environment associations that supports NGS data?

    I have been using Sambada but with my quantity of loci (arround 1700) together with the fact that the software applies Bonferoni correction, I am only able to find associations when I drop my loci number to 15....

    Do you know other programs where I can look for Genotype - Environmental variable associations?

    I'm thinking of trying PLINK and treating the environmental variables as phenotypic variables, what do you think of this approach?

    Prashanth Suravajhala · University of Copenhagen

    Dear Telma

    Apart from the wonderful suggestions above, PLATO could be a wonderful alternative for PLINK, especially when you pose problems with TPED input files:  http://plato.stanford.edu/entries/eugenics/

    Best

    Prash

  • Leo Vleugels added an answer in Microemulsions:
    When stop considering micelles and start considering microemulsions?

    At what percentage of ”internal phase” (either water or oil, depending which is the phase added progressively to the system) can we stop considering the existence of micelles and start considering the formation of true droplets? For example, adding 2.5% water to a [Surfactant mixture+Oil] system generates a clear, transparent, single phase. Can this be a microemulsion? Is there such a threshold that differentiates between micelles and microemulsions? Do you know any paper on this topic? What is your opinion on this subject? Thank you.

    Leo Vleugels · Royal DSM

    Micellar systems can absorb apolar substances which will swell the micelles, thus bringing their size in the same region as microemulsions. So it is in fact hard to say based on size what is present. In our experience it is not size of the system but interfacial tension that can be used to distinguish between micelles and microemulsions. Micellar solutions never get as low as microemulsions do. The interfacial tension in microemulsions is far below 1 mN/m and only techniques like spinning drop tensiometers are suitable for the exact measurement of these systems. 

  • Anuraag Guleria asked a question in Lung Compliance:
    Can you direct me to any studies/data on neonatal physiology that I can use to answer some clinical research questions?

    I specifically need data on Cardiovascular parameters eg Blood pressure, cardiac output. blood volumes,Hb concentration, HbF fraction

    Respiratory: lung volumes,alveolar ventilation oxygen consumption tidal volume, FRC, lung compliance,  etc

  • How to analyze the between-group difference in a mixed binary-continuous data?

    Hello there! I really need help trying to figure out what statistical tests are at my disposal to find the difference (especially, if it is significant) between two test groups.

    I gave my participants an exam. Half of the participants belonged to the group where IV was present and half to the group where IV was absent (so, IV is categorical and has two levels of abs/pres). The test asked 11 questions, of which 4 asked for continuous data and 7 binary data. The test is a mix of your common multiple-choice exam, where the answer is either right or wrong, and fill-in questions, where it is more about how accurate the answer is (for instance, 0-100% or points). The test resembles many exams often handed out to students for the assessment.

    My question is, how do I analyze such data and how can I find the difference in the scores between the two groups? I need the analysis for each question as well as for the overall test. 

    If you need further information, please, let me know.

    Thank you!

    Billy the Poet · Webster University

    Dear Ijeoma, I understand that SPSS is a very effective and powerful tool with a wide range of both parametric and non-parametric tests as well as models that can be utilized to derive insights. However, before jumping into the software and playing with its toys, I have to be aware of the type of the data I have at my disposal and the things that I can actually do to get any idea of what is going on, 

  • Lucie Knabe asked a question in Rabbit:
    Why does p16/ink4 labeling work alone in IF whereas it doesn't when used with another antibody?

    we work on human epithelial bronchial cells. When using p16/ink4 alone (abcam, monoclonal mouse anti-h, 1:200), we obtain great labeling...but when we do co-labeling (p16/ink4 AND ccsp (biovendor, polyclonal rabbit anti-h, 1:1000)) it doesn't work at all >> we can see CCSP labeling but not p16/ink4 anymore...do you have any idea why we obtain this result? can you propose something to help us?

  • Is end product of social constructionism vs. interpretative phenomenological analysis different?

    Can anybody tell me how the finish product from a thematic analysis of some qualitative interviews from a social constructionist perspective would differ from that performed from an interpretative phenomenological perspective?  That is, how would the general nature of the themes derived be different?

    And no, I am not referring to the Interpretative Phenomenological Analysis specifically or for that matter, to a constructivist grounded theory approach.  Instead I am assuming Braun & Clarke’s idea that a thematic analysis is a flexible method which may be applied within any ontological or epistemological perspective, provided it is made explicit.

    I do understand that phenomenology is based upon experience as the basis of some core reality, and social constructivism is based upon the idea that reality is negotiated within the context of social interaction. 

    The problem is that when I compare studies in my area (that is, recovery from addiction) done under the guise of each of these two positions the nature of their results seem very similar, most often reflecting the experience of participants (e.g., uncertainty, ambivalence).

    And of course, if you happen to have a couple of studies in mind that might clear this up for me it would be GREATLY appreciated!!!

    Jacob Y. Stein · Bar Ilan University

    Dear all,

    The question at and is an interesting and timely one. Anchored in Social Constructionism (SC) myself, I would like to add my two cents. 

    First, I think interpretative phenomenological analysis (IPA) and thematic analysis (TA) are first and foremost analytical methods while SC is a theory of knowledge. Thus these should not be conflated. Although IPA is rooted in a certain epistemology (i.e., interpretative), TA, as David showed, claims to be free of epistemological obligations (although Braun & Clark are not doubt interpretavists). That said, not al interpretavists are also constructionists! 

    Methodically, IPA incorporates TA but goes far deeper than TA and employs also other methods of inquiry (e.g., metaphor interpretation, embodiment guided interpretation etc.). While both IPA and TA may be employed from a SC stance, they are not obligated to it. Moreover, hermeneutic phenomenology (e.g., van Manen, 1990/1997. 2014) is certainly not constructionistic as is Giorgi's (2009) phenomenology. The crux of the distinction for the case at hand is not in the methodical work (i.e., how meanings are obtained), but rather in the meaning of the findings (e.g., correspondence to 'reality' vs. construction). 

    It is quite confusing because SC draws extensively from phenomenology and pragmatism, and shares many attributes with these philosophical traditions, while at the same time veering from other assumptions they hold. Moreover, both phenomenology and pragmatism are themselves social constructions, as is SC itself. As such, we must recognize that different scholars use these words differently. Gadamer's phenomenology rests on Husserl's yet differs from it considerably. Likewise, Rorty's pragmatism draws on Dewey's or James' yet is not identical to them.

    There is much more to be said, but I think for now this may guide you in your work.

    Good luck.

    Jacob.

  • Tom Kurian asked a question in Coding:
    How to create a new table within each node in ns2?

    How can I create an instance of a table at each node, and also be able to call the add and update functions when certain packets enters the node accordingly.

    I have attached the code which has a new table structure and and the functions required for adding and updating entries into the table.

  • Yasser Refaey added an answer in Soil Analysis:
    Anyone can explain the data in the attached file?

    I received the result of measuring specific surface area (SSA) for a clay fraction soil sample. This sample (size < 2 micron m) contain about 85 % smectite, 10% kaolinite, and 5 % illite. The CO2 gas was used in this measurement. Although the sample is rich in smectite the measured SSA was about 46 m2/g. Is this SSA value reasonable? and is this value resemble the external, internal, or total surface area?

    Yasser Refaey · University of Amsterdam

    Thank you so much Behzad,

    Actually I have only the results shown in the previous attached file where the P/P0 have been measured till 0.04 as well as I haven't not experienced in this topic.

    Regards,

  • Gift Mehlana added an answer in Polytopes:
    When analysing the topology of a MOF built from polytopic ligands do you think it appropriate to represent this ligand by two or more nodes?

    For example: a 4-c ligand could be represented by two 3-c nodes if this describes the structure better.

    Gift Mehlana · University of Cape Town

    In my opinion, I think a 4-connected ligand should be represented by 4-c nodes. Using  3-c nodes to represent a 4-connected ligand will result in loss of structural information. Such simplification is not useful in other applications were the knowledge of topology is applied especially in reticular synthesis as suggested by O’Keeffe and Yaghi.