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  • Marcel Bucher added an answer in Cleome:
    How can I find the genome sequence of Cleome spinosa or Cleome gynandra?

    Can anyone please tell me how to find the genome sequence of Cleome spinosa or Cleome gynandra ?

    I know Cleome spinosa is fully sequenced and that the assembly is available. I cannot seem to locate it.

    Thank you very much.

    Marcel Bucher · University of Cologne

    The persons to ask are Professor Andreas Weber or Dr. Andrea Bräutigamm from University of Düsseldorf. 

  • Niloy Kumar Das added an answer in Competent Cells:
    Hi, I have two enzymes - EcoR1 and Kpn1. Both the enzyme expirations dates in 2010. Can I use these two enzymes for cloning?

    Hi, I have two enzymes - EcoR1 and Kpn1. Both the enzyme expirations dates in 2010. Can I use these two enzymes for cloning? Will it work and, if yes, will there be proper restriction overhangs? Because my insert is just 700 base long and I find it very difficult to get it cloned. After double digestion, vector gives desired single band. but I doubt if the overhangs are maintained.The PCR product is good. my competent cells and transformation protocol is fine. and i use new vial of T4 DNA ligase. 

    Thanks in advance ...

    Niloy Kumar Das · Shahjalal University of Science and Technology

    It depends. Better if you done a small experiment  whether it provides you desired result or not. All the best

  • Dominique Liger added an answer in Taq Polymerase:
    I am using Genei Taq polymerase which amplifies the target gene in a plasmid but it does not amplifies a particular cDNA from RACE protocol. helpme !

    10X Taq buffer and MgCl2 were provided separately and i am using these at 1X concentration. Positive control and Water controls are working good but the target cDNA has not yet been amplified.

    Dominique Liger · Université Paris-Sud 11

    Hi there,

    Are you using exactly the same set of primers for both experiments on plasmid and mRNAs? If yes there might be a problem with the mRNA template you are using.

  • Which software tool can be used for optimization over integer variables?
    I tried to do two-objective non-linear optimization over three decision variables: one real and two integers. MATLAB optimization toolbox did not help. Does anybody have experience with Cplex?
    R. Russell Rhinehart · Oklahoma State University - Stillwater

    Nuno Ricardo Costa.  Thanks for the question.  Yes, I think the optimizer algorithm, objective function, and convergence criterion need to be appropriately chosen.  Leapfrogging is a general multivariable optimizer, that only uses function values (not gradients).  It is a multi-player approach that observes multiple trial solutions simultaneously.  Although the optimizer treats decision variables (DVs) as continuous, they can be truncated to integer values for the calculation of the objective function OF).  When this happens small changes in the continuum DV version may not make changes in the integer version, so from the optimizer perspective, the OF has flat spots.  In this case the convergence criterion should be appropriately chosen.  One approach for multi-player optimizers is to claim convergence when the cluster of players is small, when the DV range of all players is small.  This works when continuum variables are converted to integers.  However, if all players are giving the same integer versions of the DV, then the OF will  be the same for allplayers. So, for integer applications, I prefer to claim convergence and stop the leap-overs when all the player OF values are the same.     

  • Okan Akar asked a question in Endosomes:
    Cationic and anionic liposomes and cells' effect on transfection help?

    Hello, i want to learn that when doing transfection, does cell membrane's kationic and anionic faces affect to endosome for my reagent? I mean if my cells' membrane's outer face is kationic and my reagent outer face is anionic that means transfection is gonne fail. Is this true and if it', where can i learn cell lines potantiel?

  • András Bozsik added an answer in Health Research:
    What are the diet practices of researchers; are they based on health research?

    At a time when viruses are mutating, and vaccines are still being tested, and new diseases causing deaths; what are the diet practices of researchers and scientists. Are our practices in line with our knowledge, and current health research?

    András Bozsik · University of Debrecen

    Dear All,

    According to research on diets, the most efficient opportunity for remaining healthy is the very good – hereditary – constitution. You can do what you want without good constitution the best diet, continuous exercises, sporty life are good for nothing. However, nobody can be aware of his/her constitution thus, each of us should give up smoking, drink few alcohol, and eat moderately preferring fruits, vegetables, whole grains, plant oils, nuts, and fish, avoid salt, fats, pastries, sugared sodas and highly processed food items. Daily multivitamin and extra vitamin D intake may be useful.

  • Abdenour Achour asked a question in Desiccation:
    How do you dry Co(NO3)2*6H2O and La(NO3)3*6H2O salts?

    I am looking for to dry those two salts. I am trying to process two ways the first way is using a desiccator under a vacuum. The other way, which I am waiting due to the toxicity level of Co(NO3)2, is to try them under an oven at 45C due to the melting point.

    Thanks

  • Adam B Shapiro added an answer in Viral Proteins:
    Is viral protein expression important for peptide vaccine?

    I would like to know if proteins expressed in higher quantities, such as DNA polymerase, would be better vaccine candidates for a T-cell based vaccine.

    Thanks, Bernardo

    Adam B Shapiro · AstraZeneca

    It's not my area of expertise, but I would think that a viral protein found on the outside of the virus would be a better antigen for a vaccine than one found on the inside, like polymerase.

  • Dan Gwinn added an answer in Binomial Distribution:
    Should I care about the goodness of fit for a subset of GLM models selected in MuMin Package (R software), after i tested this on the global model?

    Hi everyone

    I'm just create a model selection table with MuMin Package in R for a GLM. To do this, I specify the global model which includes all independent variables (X) and the response variable (Y), and tested the goodness of fit using Chi square test (pchisq in R). To my first global model, I used a Poisson distribution, but the Chi square test rejected the null hypothesis (Overdispersion). So, I decide to use negative binomial distribution, and for this GLM, the test accept the null hypothesis.

    After this, I use MuMIn to create a table model selection which create a subset of models derived of the global model, and testing each independent variable like in stepwise process. But for this package, i can´t calculate the Chi square for the models subset. Should I still care about the goodness of fit of my subset of model after knowing that for my global model it fits?

    Dan Gwinn · Biometric Research, LLC

    It's perfectly acceptable in the literature to only test the goodness of fit for the global model and report the AIC (or other criterion) for your multi-model comparisons. I think it would be very unlikely that the reviewers will have a problem with this. 

  • Presentation of Data - What do you show on boxplots?

    Hi,

    I am writing my thesis results section and wanted some advice on presentation of data.

    Would it be appropriate to use IQR (25-75) as the box, 1.5*95% CI (outliers) as the whiskers, with both mean and median lines, to highlight the lack of normality in some continuous data sets? In the text, I give mean/95%CI for normally distributed data, and median/IQR for non-normal/non-continuous data.

    I have plotted each data set as I have reported (i.e. only showing mean or median line), but am wondering whether what I outlined above would also be an appropriate approach.

    Help much appreciated!

    Clement Oluseye Ogunkunle · University of Ilorin

    @Jochen, Is it mandatory in the Boxplot to indicate the mean etc which were not displayed automatically by the program. For instance, SPSS will not indicate the mean value in the boxplot but the median value. Is it necessary to indicate it alongside the median value etc.

    Is boxplot useful for parametric distribution? I read somewhere that boxplot is only used to describe non-parametric data. How true is that?

  • Dragan Pavlovic added an answer in Aristotle:
    Which links exist between the logic in De Interpretatione and the ethic of Nicomac, between truth and good for Aristotle?

    Would you say that there is an implicit logic in the Ethic or that the purpose of good in a way means truth? 

    Dragan Pavlovic · Dalhousie University, Halifax, Canada; European University, Belgrade, Serbia.

    "nous" (Baywater, Cardwell, Wilkinson).

    Latin: intelligentia (Wilkinson)

    Roger Crisp uses "intelect" too. German "Geist" (O. Gigon), so...

  • What are some possible causes of unusually high Km Value?

    I am performing a very straightforward continuous assay where I basically follow a decrease in absorbance which corresponds to the conversion of my substrate to its product. However, I am getting a Km value about much higher than reported in the literature. The assay conditions and substrate are identical. Many times when I run the assay, the Vi does not seem to even approach Vmax even at substrate concentrations far in excess of the Km. Does anyone know any common mistakes (technical or data processing) which may cause this? 

    Adam B Shapiro · AstraZeneca

    Without more details, it's difficult to provide advice, but I'll try anyway. If you are using a coupled enzyme assay (for example, I have often used pyruvate kinase and lactic dehydrogenase with phosphoenolpyruvate and NADH to measure ADP production by some other enzyme, using the 340 nm absorbance decrease when NADH is converted to NAD), make sure that your enzyme reaction of interest is rate-limiting, not the coupler reaction. Two things should be true: (1) Increasing the amount of coupler enzyme(s) has no effect on the rate. (2) The initial rate is directly proportional to the concentration of the enzyme of interest in the range at which you are working.

    Also, make sure that the rate you are measuring is actually due to the enzyme of interest, not to background activity of the coupler. For example, if you are measuring ATP hydrolysis by the above-mentioned coupler, but the ATP you are using has a substantial contamination with ADP, increasing the ATP concentration in the assay will proportionately increase the ADP concentration, which gives a background signal. You should always subtract the rate from a background control in which you leave out the enzyme of interest but keep everything else the same.

    Make sure the enzyme of interest does not have the same activity as the coupler to any significant extent by leaving out the coupling enzyme but keeping everything else the same.

    Finally, check that your substrate stock solution has the concentration you think it has, by whatever means is available. As an example, you can check the concentration of an ATP solution by measuring its absorbance at 259 nm in a spectrophotometer with a quartz cuvette, using the Beer-Lambert law and the published extinction coefficient to calculate the concentration.

  • Sirajus Salehin asked a question in XRD Analysis:
    What are crystallite height and diameter values in XRD analysis?

    I have performed XRD analysis for my oil fly ash samples. I have the results and I want to make a tabular representation of these data such as inter-layer spacing (d), crystallite height (Lc), crystallite diameter (La) values to compare with natural graphite. 

    But I don't see any thing mentioned as Lc or La in my result sheets. I've got the 'd' values and there is a term 'Crystallite size' with values around 13-14 angstrom. 

    I don't understand, which value is this? Is it Lc or La? Plus I would appreciate if you can show me some different analysis with XRD results for my thesis. 

    Thank you very much for your time!!

  • Volker Lohweg added an answer in Image Processing:
    Why gray level image are the most preferred image format ?

    why gray level image are the most preferred image format

    whats the main reason

    Volker Lohweg · Hochschule Ostwestfalen-Lippe

    Dear Rakesh,

    A "Gray-level"-, "grayscale"- or "grayvalue"-image is not a format. It is, as we call it, an image representation. A format would be "tiff", "jpg" or "RAW", etc.This has to be commented for clarification.

    Now to you question: The answer is quite simple. However, there are several reasons. Any multi-channel image (RGB, YCMK, Multi-spectral, etc) contains N grayscale images, in general.

    Historically digital image processing was first applied on - of course - grayscale images because of computational power at that time in the early '80s (I assume here image processing on the first PCs; of course image processing was executed on mainframe computers at NASA, etc. earlier).

    In the today's world this is of course no argument anymore. But: In industrial imasge processing usually resource-efficient embedded systems are in use. And therefore, many simple applications are executed on grayscale images.

    As a matter of course today we apply colour image processing were necessary!

  • Geleta Dugassa Barka asked a question in Plasmids:
    What is the conc. (and purity of PCR product at 260/280nm) that could be used for sequencing?

    What is the conc. (and purity of PCR products at 260/280nm) that could be used for sequencing. I have DNA samples amplified by PCR and thinking to use directly for sequencing than using the extracted plasmid with insert as it is less concentrated to be used for sequencing. I am wondering about the purity of my PCR products as it could have some primer and dNTP remainants that could compromise sequencing. The con. of my PCR products are 200-350ng/microlitre with 1.8-2.03 at 260/280nm. Is this ok to be used for sequencing? Anyone who can help me please?

  • Is there really a connection between the celebration of the new year and Saint Sylvester?
    Many people in Israel believe it
    Cecile Furstenberg · Pontifical Catholic University of Chile

    For those who are called Sylvestre: Yes!!!... subjectives percepcion interesting...

    http://fr.wikipedia.org/wiki/R%C3%A9veillon_de_la_Saint-Sylvestre

    and in some countries it's the same...but historical and cultural differences influencies exists ... 

  • Felix Clemens Richter added an answer in FACS:
    Which is better method to measure the amount/level of antibodies - ELISA or FACS???

    I am working with Indirect ELISA to measure the level of  IgG and IgM in CSF of MS patients.I have 2 dilutions in triplicates.

    Regards,

    Pooja

    Felix Clemens Richter · Karolinska Institutet

    Hey Pooja,
    from my personal experiences, you can already get pretty good results using ELISA as default measure for antibody titers. And personally I would suggest you to keep on working with ELISA as it is in literature still the most commonly used measurement for antibodies. In my opinion, FACS is always a bit time consuming, although (what Ben Roediger already mentioned) it provides maybe sligtly more sensitive results. But as a control experiment to verify your ELISA or FACS results, I would suggest you another technique which is a turbidimetric assay (giving antiserum to you serum and look for the change in turbidity cause of precipitations). I hope that could help you a bit and good success with your experiments.

  • Ashish Sharma asked a question in Transcriptomics:
    Best Database to access Transcriptomics/microarray data ?

    Although there are various databases for micro array experiments. Some of then are restricted to particular university and some are not updated and some do not provide enough utilities for data analysis. While there are other databases which actually collects micro array data from different websites, well updated and provide decent features for cross platform and data analysis tools.

    I am looking for the best database to access maximum number of microarray experiments (which had been done till date). Along with integrated tools for data analysis.

    My organism of interest is Escherichia coli.

  • Yordan Muhovski added an answer in Primer Sequences:
    Which primer is preferable for sequencing: M13 (-21) or another one?

    I have a question in choosing primers for sequencing. Which one is preferable: using only M13 (-21) or sp6 and T7 forward and reverse primers, respectively? As I don't know the orientation of my insert, I'm likely to amplify the complementary to my insert than the insert itself if I use only M13 (-21) which could result in taking complementary sequence for annotation. How can I solve this limitations in using single (only forward) primer (M13-21)? I think I have to use sp6 and T7 as either of the two surely amplify my insert as the amplification occurs in both orientations. My vector was pGEM-T easy.

    Yordan Muhovski · Walloon Agricultural Research Centre CRA-W

    Hi, Geleta!For the sequencing I am using 3.2pmol either T7 or sp6 primers in 20µl reaction and also I use CEQ DTCS Quick start kit from beckman coulter. the annealing T for the reaction is 50 deg. The protocol is according to the kit. I don't know if you are going to do the sequencing by yourself or not but if you need anything just tell me.

  • Dan Gwinn added an answer in Biomass:
    Does anyone know the law of growth in fish breeding for production prediction?

    In microbiology, knowing the biomass (Xt) that we want to achieve in culture at time (t) and the specific growth rate (μ) of the studied specie, it is possible to estimate the initial biomass (Xt0) with which one must start its culture at time (t0), using the law of microbial growth which is written :
    Xt = xt0 *exp (μ * t).
    Does anyone know the law of growth in fish, which would allow me to determine the initial biomass (Xo) of fish with which I have to start my breeding to achieve a final biomass (X20) after 20 months? My final biomass is imposed to me by the amount of food I can produce for my fish breeding.

    Dan Gwinn · Biometric Research, LLC

    Certainly depends on the species and the conditions.  My recommendation would be to look to the literature on your species.  I'm sure this information is out there for common lab species such as zebrafish or guppies.  And it will be out there for common hatchery-reared fish such as rainbow trout.

    Also fishbase may have some useful  information (http://www.fishbase.org/search.php). The life history tool provides the intrinsic growth rate (μ), life span, generation time, age-at-maturation, etc. 

    Good luck!

  • Cecile Furstenberg asked a question in Husserl:
    Can empathy (einfühlung) as Husserl describe it in his phenomenologie research be applied and really usefull for relationcare?

    Empathie in care seems to be quite different than the empahie (einfühlung) ? What can phenomenologie intersubjectivity comprehension offer for better understanding of relation care?

  • How do I plot a graph of concentration effect curve?

    This is a pharmacology subject where we collect some data analysis and we plot them on a graph to see the dose response curve. There is a file attachment where we add results

    There this image which my lecturer explained to draw with the data we obtained

    Dragan Pavlovic · Dalhousie University, Halifax, Canada; European University, Belgrade, Serbia.

    In short :
    For each concentration, produce the responces as means and s.e.m., express the concentrations on a p scale (as –log10M) on the abscissa (x axis), and the absolute values of the response (y axis) (and in another table and graph as the percents of maximum responses). You will use the percents to calculate EC50 and pA2. Anyway, you cannot learn it just from the books - or who knows, may be you can…

  • Mehdi ABDEDDAIM added an answer in Simulation:
    Simulation time too slow for a magneto-rheological damper

    Hello;

    I am using SIMULINK for modeling and simulation of the behivor of a magneto-rheological damper MR damper, i am using an equation proposed by Spencer et al, when i finished the modeling of the damper i had a problem, when I put it in a structure and a submit the system to a seismic excitation for 25 seconds the time of simulation is running sooooooo slowly 0.001 second as a step it take 4 hours to move frome 3 s to 4 s, the preoblem disappear when i put a [Abs] (absolute) value bloc befor the damper subsystem, the simulation is finished quickly

    if any one can help me about that ? i will be thankful

    as attached file you will find the paper i ma using
    and MRDAMPER file, the parameter file of the damper, the structure model and the data of the structure and the [t g] files for time and ground acceleration

    thank you

    Mehdi ABDEDDAIM · Université de Biskra

    Dear Monica

    it did not work the time simulation is tooooo slow ! any help will be useful

  • Bradley Ridder added an answer in MATLAB:
    Can anyone help with the iteration of converged solution using Matlab?

    I have a nonlinear algebraic equation representing the relationship between the stress strain of concrete. I need to calculate the modulus of concrete at every point on the curve. How can I get iteration of converged solution using Matlab to get the real value of concrete modulus.

    Bradley Ridder · Purdue University

    Matlab's fsolve function is meant specifically for solving nonlinear algebraic equations. However, it requires initial guess. Is there any reason to suspect that this system of equations has more than one solution? If so, you'll need to provide a reasonably accurate initial guess. A good choice for x0 is a simplified version of your original problem (especially a simplified linear problem of the form Ax = b for which exact solution is possible.)

    The stability of fsolve can be significantly improved by providing an analytic  expression for the Jacobian matrix and using the trust-region-reflective algorithm. You'll have to decide if this problem justifies the extra labor of writing the Jacobian (though the symbolic math toolbox is quite helpful for this). Read further on that here: http://www.mathworks.com/help/optim/ug/nonlinear-equations-with-jacobian.html?refresh=true

  • Andrew R Garcia asked a question in Attachment:
    Suppose there is a propeller inside a stationary cylinder submerged in water. Can you elucidate the velocity profile of the moving propeller?

    [See attached figure]

    There is a significant gap between the propellers and the cylinder (figure 2) and we want to elucidate the velocity profile at this gap and the bottom of the cylinder. Is it possible to assume the moving propeller would have the same velocity profile than a moving cylinder inside stationary cylinder (figure 3)? If so, what would be the criteria for making this assumption (e.g. certain speed of propeller) [You may assume a Couette flow or a variation of such may be used as an approximation for the moving cylinder's velocity profile]

  • Darko Pavlović asked a question in Geopolitics:
    Are gas and oil, and in the future drinking water blessing or a curse of modern geopolitical expansion of globalism?

    The development of civilization shows that for economic growth and technological development needs more and more energy ....

    In this context it should be noted that the main geopolitical disputes and conflicts are related to the richest and the most profitable reserves of future world oil production and natural gas, and that conflicts in the guise of a clash of civilizations are in fact conflicts over energy resources and in the future over drinking water...

  • Yordan Muhovski added an answer in Pipetting:
    Does anyone run 10uL qPCR reactions?

    I use Bio-Rad's SYBR Green Master Mix for my qPCR work which, according to the manufacturer's instructions calls for a 50uL reaction volume. I use 20uL on a regular basis without any problems. As I am running a lot of qPCR in the future and looking for ways to save some money, I was wondering if it's realistically possible to use a 10uL reaction volume and achieve the same results in terms of well-to-well variability. My main concern is the inevitable increase in pipet ting error as the reaction volume decreases. 

    So, does anyone use 10uL qPCR reaction volumes? Have you ever had any issues?

    Yordan Muhovski · Walloon Agricultural Research Centre CRA-W

    Hi, I am doing 10µl qRTPCR reactions using Promega qRTPCR kit which is also suitable for fast PCR and it is working very well.

  • Tools for analyzing regulatory FBA i.e integration of transcriptomics with FBA ?

    Is there a online or standalone tool for analyzing flux balance analysis of E.coli gene knockouts which also considers the regulatory controls ex. RFBA, SRFBA, PROM etc.

  • What is the role of Thermogravimetric analysis in concrete?

    Please, can anyone tell me what the role of TGA/DTA in the analysis of concrete is? What does it depict? Why do we TGA analysis on concrete?

    Thanks.

    S. Abd.El.Aleem · Fayoum University

    Yes, TGA helps is identifying various phases present in the concrete, like portlandite, calcite, C-A-H, C-A-S-H etc. Most often CH content is measured to check the hydration reaction i.e. if CH content has reduced that means it has been used up in the hydration reaction. These various phases break down at different  temperatures to release chemically bound water in case of hydration products and CO2 in case of calcite. This release of chemically bound water and CO2 helps in identifying the various phases present. But to start the experiment, make sure that your sample is free from physically bound water, that is present in pores as it hasn't reacted to form any hydration product. There are various ways to remove physically bound water and to stop further hydration. You can quantify the proportions of the various phases present in your hardened cement paste with the help of derivative curves. Attached is a list of some common phases present in cement paste along with the references, they will be quite handy for phase identification.