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  • In Molecular dynamics, which ensemble is better to use: NVE or NVT?

    We use different ensembles in MD, which one is preferred to use?

    Ma'mon M Hatmal · Hashemite University

    Thanks All,

    but after finishing 11 nanoseconds of simulation using NVE, is there any problem to use the results of the simulation in further pharmacophore model building, (specially  that for using NVE we depended on the assumption that the temperature of the body is different from the temperature of experiment)?

  • Can we run a td dft calculation in gaussian09?

    or any other softwares like octopus useful?

    Aleksey E. Kuznetsov · Universidade Federal de São Carlos

    Yes, with Gaussian you can do it using the keyword 'td':


  • What is the ideal participation rate in observational studies? Is there any good references on this topic?

    Trial participation rate can give additional informations on patient representativeness. No consensus on this indicator have been published since it seems to have no ideal rate. However, some people says that by convention, a participation rate lower than 80% may increase the risk of selection bias.

    Sylvain L'Espérance · CHU de Québec

    Thanks for all your valuable answers. It will be very helpful for updating our own tool for evaluating observational study quality.

    Merci beaucoup Christophe pour votre réponse en français! C'est très apprécié.

  • S.I.s. Hassan added an answer in Probes:
    Why does current on outer surface of shorter coaxial line vary spatially?

    I am trying to measure current on outer surface of outer conductor of a 50ohms co-axial line of 1m in length. Line is fed from 50ohms line and terminated in 50ohms. In this arrangement current is expected to be uniform on outer surface also. But spatial variation is found. Current amplitude is maximum at source end, half at the middle and 1/3 at termination end. Measurement is carried out by current probe and spectrum analyzer.

    S.I.s. Hassan · Universiti Malaysia Perlis

    apart from that the attenuation of the cable, slightly matched and radiation make it lower

  • Do you know any masterpieces of art which are devoted to anti-war themes?

    One of the main tasks is to cultivate peacemakers. Anti-war arts (painting, sculpture, literature, music, photo) can be helpful in upbringing future generation. Cultivating a culture of peace through awareness of genius message (implicit and explicit) is important in schooling. We are going to research the sources, organize the conference and stage one of the creative works. We will be thankful for every contribution.    

    David Charles Wright-Carr · Universidad de Guanajuato

    The third image from the article mentioned in my last two posts is called On Psychological Operation in the Garden of Basra, Iraq, by Xavier Pick.

  • Joaquín Sarrión asked a question in EU Law:
    Searching for recent articles on conflicts between market freedoms and fundamental rights in ECJ case law. Any article?

    From 2009-2011 I developed my research thesis on conflicts between market freedoms and fundamental rights in ECJ case law (Schmidberger, Omega, Viking, Laval, etc.) And I would like to update my work and to cite recent works on this topic. 

    Many thanks. 

  • Inês Pita added an answer in Protein Fractionation:
    Is anyone familiar with a protein concentration method for western blotting?


    I'm using a new protocol for subcelular fractioning for rat striatum and frontal cortex. Unfortunately I'm obtaining little protein in fractions (nuclear, sinaptosomal and non-sinaptosomal), especially in the striatum. I already used a pool of the cerebral regions but it's not enough.

    Thank you

    Inês Pita

    Inês Pita · University of Coimbra

    Hi Jonas!

    In fact, I'm not using any protease inhibitor cocktail. I tryed a new protocol using sucrose gradient and it didn't mention that, Ok. I'll do it before use another method. And I'm gonna check if there is that equipment in my institute.

    Thank's a lot.

  • Is it possible that hydrogen peroxide can oxidize paper?

    Curious to know

    Elsayed Mohamed Elsayed Ahmed · Zagazig University

    here are the kinks of two papers


  • M.G. Chapman added an answer in ANOVA:
    In asymmetrical ANOVA, fixed and orthogonal, which term is the Control vs others tested over?

    I have an experiment with two fixed and orthogonal factors (dose and concentration) and one control. I thought I knew how to do it, but have found contrasting literature on how to carry out the asymmetrical anova and most papers do not declare the details of how the analyses were done. Also most of the papers refer to designs with random factors, such as those in Glasby and Underwood etc and mine are all fixed. I have carried out two separate anovas, (1) one way with all treatments including control and (2) two way with dose x concentration without control. When I construct the asymmetrical anova from the two analyses, I am not sure whether to test control vs others against the res from analysis (1) or from the combined residual from (1) and (2). Any suggestions?

    M.G. Chapman · University of Sydney

    Hi Danni,

    It is quite straightforward and you are on the right track.  Do the 1-way analysis using all treatments, then the balanced design omitting the controls.  Construct the asymmetrical design as you have described.  The Residual must come from the complete 1-factor design, it is the only one with all the data in it.  Calculate the MS for Controls vs Other Treatments, by subtraction of the relevant SS and df and test against that Residual.  As it is all fixed factors, everything gets tested against the Residual.

    The issue is that the fixed contrasts after the analysis uses Dunnetts test because that takes into account (1) the fact that the controls are used in all contrast (the relevant contrasts are the conrol against each of the other treatments) and the fact that if there are only significant main effects, the treatments will have a bigger n than the controls.  Tony deals with it in his book in quite detail.

    If you want to send me the analysis to look at, I will be happy to do so.

    Hope you are well.


  • Liming Wang added an answer in Reaction Kinetics:
    How do I determine rate of reaction or kinetics of reaction without taking into consideration the reactant concentration?

    can we find out rate of reaction only on product  concentration

    Liming Wang · South China University of Technology

    It is difficult to get rate from the product only unless we have the full information of the product branching ratios. For example, if a reaction have two parallel product channels as A --> B and A --> C, and assume both are 1st-order to A. Then the concentrations of B and C will increase, and we can fit the curve to [B](t) = B(t=infinite)*[1-exp(-(k1+k2)t)]. So what we have is the summation of k1 and k2, instead of individual k1 or k2.

    A lot of other things can spoil it further. Product B may undergo futher reaction, or different product channels may have different orders.

  • What is the most frequently used orthogonal polynomial over [-1,1]?
    [-1,1] is the classical finite interval on which ops are defined.
    Hugh Lachlan Kennedy · University of South Australia

    Yes the Legendre polynomial would be ideal. Do you need to use a polynomial? Could you also use complex sinusoids (i.e. frequency analysis)? 

  • Hugh Lachlan Kennedy added an answer in Geophysics:
    Fitting Laguerre polynomials to observed datasets?
    I'm trying to fit orthogonal polynomials to sets of geophysical data (x, t) ... ie. find a set of coefficients with which to describe t(x)... Given the Laguerre Polynomials are orthogonal over the function e^-x, just wondering whether in order to exploit the orthogonality I should fit the laguerre polynomials to t(e^-x), as opposed to t(x) ?
    Hugh Lachlan Kennedy · University of South Australia

    Hi Alan,

    I don't know if you are still looking at this, but here are my thoughts ...

    The (discrete) Laguerre polynomials are used in discounted least-squares regression. So exp() is used as a weighting function, to emphasise the data at a particular sample and de-emphasise more distant data. When you use the Laguerre polynomials, they are orthogonal with respect to this weighting function, so you don't have to worry about matrix inversion; furthermore, large data sets can be processed very efficiently using recursion.

    I think they would be an excellent choice in geophysical data processing because a particular polynomial representation would only be appropriate over a local area.


  • Did we obliged to re-test the reliability & validity of a previous questionnaire that has been tested before ?

        In other way, the use of a previous questionnaire as a measurement tool that has been taken the reliability & validity test; does not need to make a new test of that step again.

    Otherwise, you can check more about the use of a previous tool of measurement (questionnaire), see the article attached.

    See also:


    Chems Eddine TIDJANI · Université Kasdi Merbah Ouargla

    Dear Sethilvel, 

    Thank's for your interesting response, and i'm agree with you about remaking the reliability & validity test to enhance more the significance of my study. But depending to the some references that i have read on this issue, i think that we can gain more time wether we make also a pre-test questionnaire, then we remake the Rel & Valid tests again; and this is especialy where we have a previous questionnaire with a sample of 500 firms, that has been examined that tests rather than my small sample study (for 30 observ..).


  • What does the multifactor dimensionality reduction whole dataset statistics show?

    Dear colleagues, I see clear difference between the training and testing statistics in MDR, but I don't get (and could not find the answer in a bunch of publications - it is not even discussed mostly) the real meaning of the whole dataset statistics? I feel it like it's between training and testing statistics towards all my data. As 9/10 is in training and only 1/10 is in testing in each round of cross-validation, the whole dataset statistics is almost identical to the training statistsics. Yet, it reports the final results of the best-model statistical testing of my data. Thus it also feels like applying ROC-analysis to the whole dataset in order to report on the best-model properties. However, the training and testing statistics are only reported in most MDR-based publications. So what do we actually do with the whole dataset statistics? 

    Andrew Messing · Harvard University

    Dear Peter V. Zolotukhin:

    I didn't mean to imply you were at all a newbie and apologize for apparently doing so. I assumed the complete opposite, as I would for anybody who asks about statistics in terms of training (instead of the standard statistics that have been around since before computers (many of which were known to be inferior to alternative methods even then, but were to computationally demanding). I simply thought that there was a breakdown in communication due to different uses of terms or just different terms.

    It is not entirely true, though, that MDR either uses terms specific even to genetics nor that it is offered through only through MDR software. The latter I know to be true because I've loaded the R MDR package (for your convenience, I have attached the paper "An R package implementation of multifactor dimensionality reduction" from the open access journal BioData Mining). The former I know because even though I've rarely seen MDR used outside of genetics, bioinformatics, etc., I have frequently seen it in volumes from Springer's Lecture Notes in Computer Science volumes such as Artificial Intelligence: Theories and Applications (Lecture Notes in Computer Science Vol. 7297) and Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics (Lecture Notes in Computer Science 7833), not to mention a few IEEE articles (some of which had nothing to do with the life sciences, e.g. "The Multifactor Extension of Grassmann Manifolds for Face Recognition"). Also, regardless of the fields in which I've read about MDR, I've frequently seen it compared to PCA and other dimensionality reduction methods (not to mention artificial neural networks). 

    Finally, I've read a fair amount of papers on MDR for someone who hasn't yet found a good use for it, but I'm not sure "whole dataset statistics" is a technical term reserved just for MDR given that I've seen it in everything from a geophysics power-point presentations (see link) to a computer science research project (see 2nd link), to a paper on signal processing in geoscience (see attached paper). It just seems like the phrase isn't generally found anywhere, but where it is found it means exactly what it sounds like. After all, as you yourself state, your no beginner to statistics yet you are unsure of what the term means.

  • Troubleshoot transwell migration assay with A2780-cis cells?

    I have tried various cell concentrations and addition of collagen or fibronectin to the transwell before seeding cells however they still do not attach and migrate, rather stay floating in the top layer of media. Has anyone had experience with these cells?  

  • Sergei Esipov added an answer in Crop Yield:
    Which factors effect the forecasting of olive yield?

    Climate, biotic factors, pollen concentration, etc. 

  • Can't download this book, help ? Organic Geochemistry ?

    D.H. Welte
    M.A. Yükler
    M. Radke
    D. Leythaeuser

    The previous chapter of the mentioned book, or any kind of information related to organic geochemistry applied to petroleum exploration would be very useful as I have to prepare a presentation about the topic in 2 weeks. Thank you.

    Elsayed Mohamed Elsayed Ahmed · Zagazig University

    here download link to ur book


  • Ijaz S. Jamall added an answer in Risk Factors:
    Cancer a mere matter of luck? Or is there something under-appreciated?

    It has been all over in the news lately: The majority of cancer is obtained by bad luck, not by lifestyle or inheritance. See attached. 

    Really? The data appear solid and they make sense, but the conclusion seems a bit premature: the observations are based on established risk factors in the USA and I assume (let the experts please come forward!) that these risk factors are based on occurrence. This means we do not see all those cases where the patient's immune system adequately takes care of the anomaly. 

    How does occurrence of cancer relate to failure of the patient's immune system, and can we monitor this based on adequate biomarkers? How will the statistics and the conclusions change when this factor is included in the analysis?

    Ijaz S. Jamall · Risk-Based Decisions, Inc.


    You state: "But those growth factors are NOT SECRETED BY ALIVE CANCER CELLS! THEY ARE SECRETED BY 5-20% OF DYING CELLS (necroric metaphase death due to chomosome aberrations leading to unequal distribution of chromosomes in anaphase)."

    Are you suggesting that there may be a way to tip the balance such that instead of 5-20% of cancer cells, we might be able to increase the fraction that die (necrotic metaphase death)? Thank you. 

  • Drew Coe added an answer in Biomonitoring:
    Lots of food for thought! But the question remains: what sort of monitoring should we be doing?

    The article starts by saying that the biomonitoring lags behind the science, and ends by saying that the science is lagging behind the policy. Given that the policy / legislation (i.e. WFD) more or less dictates the biomonitoring, where does that leave us?

    The implications of the opening section is that a wide range of methods are available to regulatory agencies, but are underused. Although the article is a good critique of existing methods, it doesn't really explain what aspects of science should be incorporated into existing monitoring straight away. The authors admit that most new methods don't necessarily relate to existing known pressures and/or require further development. What new methods are cost-effective, better than existing tools, and could be deployed in a 3-5 year timetable after an initial piloting and testing phase?

    Drew Coe · CAL FIRE

    What are your objectives? 

  • Sai Mynampati asked a question in Protein Folding:
    Is the rate of protein synthesis faster or slower than protein folding ?

    Which process takes longer time protein synthesis or protein folding?

  • Attila Haris added an answer in Identification:
    Does anybody know good identification key for Arabian Gulf marine species?

    Does anybody know good identification key for Arabian Gulf marine species?

    Attila Haris · Somogy County Museum, Kaposvar

    This very extensive photogallery and identification guide of World Register of Marine Species helps you in identification of several groups of marine spec. of Arabian Gulf. as Bivalvia, Cephalophoda, gastropoda, Nudibranchia, Polyplachophora and Scaphopoda. 


    I hope, you find it useful. :)

  • How could determining the molecular weight of asphaltenes be important in the Hydrocarbons Industry?

    I just want to have an idea of how helpful it can be to determine the molecular weight of asphaltenes in a SARA analysis. Which kind of studies can we develop with that asphaltenes MW or if there are any imminent problems that need this variable to be properly measured. I appreciate all of your opinions!

    Miguelangel Ballestreros · South Colombian University

     Thanks for sharing your point of view Ashis. The origin of petroleum is an important issue and I didn't know the molecular weight analysis of asphaltenes could help this research. I'll search for the techniques you mentioned.

  • How can I design an experiment to measure the deformation of helical gear tooth?

    I am studying on gear dynamics, and I firstly want to get stiffness curve of gear tooth,so I intend to design an experiment.

    Claes Richard Fredö · Qring Technology Intl. AB


    The simplest way would likely be to set up a Finite Element modal and calculate the data you want.

    Testwise, I believe you may be able to work data from the Transmission Error (TE).

    RB Randall has worked the TE measurement problem, so take a look at his work. https://www.researchgate.net/publication/245391679_Gear_transmission_error_measurement_using_phase_demodulation



  • Why does dilution of homoeopathic medicines enhance their potency? Is this not against scientific phenomena?
    I have been told by homoeopathic practitioners that dilution and potency of homoeopathic medicines is inversely proportional. This means the higher the dilution the more potent the medicine will be and vice versa. I have doubts which may be due to my bias because personally I did not find any experience of homoeopathic medicine effective.
    Barry Turner · University of Lincoln

    Muhammed I like your question especially this part...

    I have been told by homoeopathic practitioners that dilution and potency of homoeopathic medicines is inversely proportional.

    Such a claim is absurd in extremis and I doubt anyone saying this understands what inversely proportional means.  While we can subscribe to the idea that people may adhere to their own beliefs we do not have to treat those beliefs in the way we treat serious scientific theory.  

    Homeopathy is a quaint idea that no doubt gives some people comfort and a lot of laughs to many others.  We should look on the bright side, I think it is absolutely hilarious that anyone thinks water has a 'memory' so even I get benefit from homeopathy.  I have often offered a deal to those who believe in homeopathy.  I will not deny them their belief if they promise not to bore me with it.  

  • Can anyone advise on how to categorize types and levels of work (occupations) ?

    For my masters in health research, I am exploring differences in factors seen as faciliators or barriers to return to work following acquired brain injury between professional/managerial and non professional/managerial jobs.

    I feel I have made a novices blunder, as I am struggling to find a reference on which to base my incl/exclu criteria for professional/managerial jobs as the taxonomies i have come accross are based more on industry than career level.

    I know that i want to compare careers that usually require higher level education and/ or where there is responsibility for managing others, but now Im questioning whether i should put these two catergories together.  My assumption  is that these jobs will have higher cognitive and interpersonal demands, but now I am questioning even that!  any thoughts/advice would be appreciated.

    Jacquelin Capell · University of Wollongong

    Hi Annette, try this address:


  • Mingkai Liu added an answer in THz:
    How can I efficiently remove the water vapor absorption peaks in THz measurement?

    Hello, as a newbie in THz measurement, I encountered something strange when I tried to remove the absorption peaks in the THz measurement by pumping nitrogen into the chamber.

    I found that most of the absorption peaks can be removed, such as the ones around 0.55, 0.75, 1 THz, 1.22 THz and 1.42 THz; however, the ones around 1.11 and 1.3 THz could not be removed clean even though other peaks were already unnoticeable and they just stayed there no matter how long the nitrogen pumping was. Does anyone have similar experience and how would you solve the problem? I was surprised since if these peaks are all from water vapor in the air, why they don't disappear simultaneously? 

    Mingkai Liu · Australian National University

    Thank you Joongmok! Unfortunately the designed resonance of our sample overlaps with the H2O absorption, so probably difficult to remove the absorption peak directly. 

  • When it comes to simultaneity is Einstein correct or is Dingle correct?

    Albert Einstein claimed in 1905 that a single event can occur simultaneously at different times within two inertial reference frames moving relative to one another. In 1950 Herbert Dingle argued that different times cannot be simultaneous. I have analysed this conflict by deriving the Lorentz equations using both points of view. According to this analysis Dingle must be correct. See youtube presentation of this analysis at  https://youtu.be/4XLYzhHQ64Y

    Valentin Danci · Science

    Eric wrote: "from the point of view of a stationary observer, the frequency of a moving oscillator is observed to be less than it would be if the oscillator were stationary − as predicted by the Lorentz transformation, properly interpreted."

    Congratulations Eric, you just contradicted the relativists who claim the GPS satellite clocks do suffer a frequency shift and they need to be adjusted because of that. They event proudly present relativistic calculations of the said adjustment.

    The point is, if the frequency shift is mutual then there is no adjustment needed at all!

    On a side note, your example of A and B in relative motion and emitting sound signals to each other happens in an absolute frame. Their motion is relative to the independent absolute frame in which the propagation of sound happens. Pretty much what happens with the propagation of light too. So I'm glad you finally reached the truth - even though you can't admit it.

  • How to make synthesis for Aminorhodanine ?


    I have reference inform about the method of synthesis but it is so sad that the paper now is offline so I cant get the paper please Scientists here who are expert in Organic Synthesis Please Suggest design to method of synthesis with the available reagents and solvents mentioned in the attached image of reaction.and please every one here tell about the amounts of reagents suggested and if one have experience with the same conditions for another reactions tell about ur experience.

    thanks in advance

  • Someone has already produced self-compacting concrete with rubber?

    I tried to produce but without success.

    Claes Richard Fredö · Qring Technology Intl. AB


    Not my topic, but here are some links





    That said, I do know that concrete mixed with latex produces a more flexible material with a higher structural damping loss factor. To exemplify, it can float on top of an elastic layer as is done for floating floors without cracking when mixed with latex.