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  • Jason Cook added an answer in Gold Nanoparticles:
    Is it possible that after gold nanoparticle uptake, the cell pellet looks red?

    I treated ovarian cancer cells with as prepared gold nanoparticles and peg modified for 24 hours. Then I collected the cell pellet by trypsinisation and centrifugation. Pellet with as prepared gold nanoparticle was looking red, and with peg it was looking white mass as normal.

    Jason Cook · University of Texas at Austin

    Your nanoparticles will appear red if the plasmon resonance is not lost. If your PEG density is very high, then their organization will be like a brush. Generally this will prevent surface plasmon coupling giving your cells a red appearance. If you use lower densities of PEG, then the will organize like a mushroom on the surface of the nanoparticle. These nanoparticles can still be stable in PBS, but when internalized in cells they will appear gold (due to loss of surface plasmon resonance).

  • Does anyone have experience using the Shannon Wiener Diversity Index Score?

     I just completed the shannon Wiener diversity index and calculated a score of (H)=2.154890613. The values range from 0 to 5, with common ranges usually between 1.5 to 3.5. Can I really say that the population is diverse? What other index should I use when getting a score like this? Thanks

    Pedro M. Alcolado · Instituto de Oceanología

    To decide wether a diversity index in low, medium or high, is a relative issue. It depends of the biological group you are dealing with, the regional climate (tropical, temperate, cold) and the natural range of variation of the index in the involved taxonomical group in different ecosystems (seagrasses, coral reefs, muddy bottoms, estuaries...). A diversity index could be high for a taxonomic groug (e.g. sponges) for a seagrass bed but not for a coral reef ecosystem where environment can be more constant and predictable. To decide about that, look in the existing information the observed range of variation of your studied group considering the different inhabited biotopes and the relevant regional climate.

    Pedro

  • Jose Gros added an answer in DNA Damage:
    How can I impair DNA repair to mimic the effect of tobacco carcinogens ?
    I'd like to engineer an existing mouse model which normally develops relatively few spontaneous mutations. By delivering an shRNA or a dominant negative enzyme I'd like to make this model more prone to the development of point mutations. Ideally, like tobacco carcinogens do. What should I target ? NER components ? ATM/ATR? Could you point me to some references ? thanks.
    Jose Gros · Sociedad Española de Oncología Médica

    I was told by a patient about a relative developing a Lung Cancer shortly after leaving tobacco habit, she asked me if this may happen her if she abstained from smoking, a more than 20 pack-years history of it, and what would be better, continue smoking, and having all risks involved, or giving up, and having the risk of a Lung cancer as her relative. I told her I don't know, but the continued tobacco use has many added negative consequences besides Lung cancer. She gave up smoking, and she died in the term of three years from a NSCLC.

    After this, I found a publication indicating that an effect of continued smoking exists in reducing the growth of transformed Bronchial cells, as Lung Cancer is a bronchogenic disease.

    The effect of ceasing the smoking habit in increasing the tumor cells growth, I don't know if this is related to any special genetic background, can be reverted by the use of Nicotine Replacement Therapy, Nicotine seems effectively reducing this 'flare', or 'rebound' effect of giving up smoking in easing growth of Lung Cancer.

    Thanks. Salud †

  • Raoufi Mustapha added an answer in Switches:
    Where do you use a 2 quadrant switch converter and where 4 quadrant one?

    Where do you use a 2 quadrant switch converter and where 4 quadrant one? What is the criteria to choose one of the two types of converters?

    Raoufi Mustapha · Cadi Ayyad University

    Converter is used to manage the energy between the source and the load. In all cases the load is either in series with a coil or in parallel with a capacitor or the load itself may be inductive or capacitive. Therefore the combination load-coil or load-capacitor can act as a source of energy. In some cases one wants to recover the energy stored in the coil or in the capacitor and returning it to storage in the energy source. The structure of the converter must enable this energy recovery. This is why the switches must be bidirectional in current or voltage or both.
    Example:
    Suppose we feed a DC motor with a battery and a DC-DC converter and the motor must rotate in one direction with braking. When the motor rotates in one direction, power flows from the battery to the motor. When one wants to brake the motor, current direction is reversed in order to recover the stored energy of the rotor. Converter switches must be bidirectional in current. Thus we move from one quadrant to another. The power can flow from or to the battery.
    In the case of a four-quadrant converter the example is a DC motor to be rotated in one direction or the other with the brake possibility in both cases. 4 quadrants power are thus used.

  • Adam Hermawan added an answer in Hesperidin:
    Hesperidin is getting precipitated - How can I solve this problem?

    I need hesperidin conc of 100,200,300,400 microM.
    I am doing following -

    Made 100 mM hesperidin in DMSO.

    Then took 1 micro L (100mM hesperidin) + 1000 micro L media i.e 100 microM.
    2microL(100mM hesperidin) + 1000 micro L media i.e 200 microM
    3microL(100mM hesperidin) + 1000 micro L media i.e 300 microM
    and so on........(working conc.)

    The problem I am facing is - hesperidin gets precipitated when I put 100 microL of working conc. in a 96 well plate. How can I solve this precipitation problem?

    Adam Hermawan · Ludwig-Maximilian-University of Munich

    Hi Chandra,, I made 10 mM solution in DMSO, then I took 50 µL and add 950 µL BSA to make 500 µM of hesperidin solution, and made serial concentration from it.

  • Ehab El-Nahas added an answer in Influenza:
    Is someone familiar with propagation of influenza H5N2 in embryonated chicken eggs?

    I was trying to grow H5N2 virus through allantoic inoculation. I have tried several dilutions based on HA titer of the inoculum I have. I harvest the eggs 48 hours after inoculation and I never get a good titer of that inoculum (either HA titer or EID 50). The strain I have is mice adapted that I can not grow more than once in eggs to be good for my experiment. Any suggestion on what can solve my problem?

    Ehab El-Nahas · Benha University

    Hi Ahmed, i totally agree with Mutien and Trushar but another advice is to try to activate the strain firstly on mice before egg adaptation if the strain stored for long period. if there is no increase in the titre, you will try three successive passages on egg as virus is mouse adapted and you will obtain high titre.

    regards 

  • Ajeet Singh added an answer in Imidazoles:
    A very general query: What is the normal voltage condition for SDS-PAGE containing Ni-NTA eluted protein samples?

    I applied 140, 120. and 100 volts and I have obseved a very random migration of protein sample. It may be due to presence of salts (imidazole, NaCl, TisCl) in the sample. Sometimes the sample gets heated. Any suggestions?? 

    Ajeet Singh · I.I.T Guwahati

    Dear Gaurav,

    Many times, I have seen your question related to SDS-PAGE only. you can do one  more thing, you make fresh  & correctly all SDS PAGE chemicals and run @ 90-110 voltage. I have used voltage till 160 volt while working in IISc and worked fine. so better to make all things fresh and correctly and do the experiment again. I also faced same kind of problem and struggled a lot. so I changed all SDS PAGE chemicals and problem was rectified.

    I hope it will work fine with you.

    Good luck dear.

  • Jethro Betcke added an answer in Flying:
    What's your opinion about the impact on ecosystem from large scale renewable energy farm?

    We have heard about most common bird fatalities due to collisions with wind turbines. Over the last couple of years, there have been a number of reports detailing the impact wind farms have on bird populations. One report published in the Wildlife Society Bulletin said that 573,000 birds and 888,000 bats were being killed each year by wind turbines. 

    Recently, USFWS published a study of three solar farms in Southern California and found that some 231 birds from 71 species were killed over the two-year period. The cause of death ranged from exposure to high temperatures of up to 800 degrees (by flying through flux fields comprised of the rays of the sun directed off the solar panels), to blunt force trauma, to predators (due to birds losing the ability to fly because their wings have been singed by passing through a flux field).

    Some of these numbers are alarming and asking for more studies. I was wondering if there are more studies reported which I have missed. 

    Jethro Betcke · Carl von Ossietzky Universität Oldenburg

    It makes no sense to look at bird deaths of wind energy in isolation. You have to make a  comparison with other power sources. Sovocaal (2012) finds that nuclear power plants cause 2.2, and fossil power plants 9.4 times as much bird deaths per GWh. So wind energy actually reduces bird deaths.

    http://papers.ssrn.com/sol3/papers.cfm?abstract_id=2198024

  • How can I decrease the voltage drift coming from an array of 2 x High Tech HTI-90-U hydrophones (-154.5 dB re 1V/uPa), both powered by 9V batteries?
    Drift and noise with hydrophone preamplifier.
    Krzysztof Herman · Wroclaw University of Technology

    Dear Lucille,

    if You use digital signal acquisition You can consider some DSP methods (avraging, DC component removing, filtering, denoising etc. ). You can also other preamplifier with high input  impedance and low drift.

            Regards

             Chris

  • Is someone familiar with metabolite identification?

    I need help for metabolites identification from a ion trap GCMS. Can anybody help me out? I have done untarget metabolic profiling. The result look very good. Now I "just" need to identify the metabolites. It is from seminal plasma. Eradat

    David E Volk · University of Texas Health Science Center at Houston

    Look up the mass spec metabolite work of Arun Sreekumar at Baylor Medical School.

  • Ashish Gautam added an answer in ZnO Nanorods:
    Does anyone know the inside pressure (value) of autoclave during synthesizing ZnO nanorod at 130 C?

    Could you tell me the inside pressure (value) of autoclave during synthesizing ZnO nanorod at 130 C or suggest to me the relevant research article?

    Ashish Gautam · University of Rajasthan

    hey .. please go thru these papers ...u wl get an idea ..

    1] T. Al-Harbi, “Hydrothermal synthesis and optical properties of Ni doped ZnO hexagonal nanodiscs,” Journal of Alloys and Compounds, vol. 509, no. 2, pp. 387–390, 2011. 
    2] J. Wang and L. Gao, “Wet chemical synthesis of ultralong and straight single-crystalline ZnO nanowires and their excellent UV emission properties,” Journal of Materials Chemistry, vol. 13, no. 10, pp. 2551–2554, 2003. 
    3] L. Gong, X. Wu, H. Chen, F. Qu, and M. An, “Synthesis of vertically aligned dense ZnO nanowires,” Journal of Nanomaterials, vol. 2011, Article ID 428172, 5 pages, 2011. 
    4] H. Hu, X. Huang, C. Deng, X. Chen, and Y. Qian, “Hydrothermal synthesis of ZnO nanowires and nanobelts on a large scale,” Materials Chemistry and Physics, vol. 106, no. 1, pp. 58–62, 2007. 

    Thank You!

  • Richard A. Park added an answer in Eutrophication:
    Why do eutrophic rivers shift from extreme phytoplankton blooms to massive macrophyte developments?

    In the Loire River (France), the river was highly eutrophic during the 1990s with extreme phytoplankton developments (summer average > 0.15 mg Chl a/L). It was reduced to 0.05mg/L now, but it seems that a lot more macrophytes can develop. Have you observed such phenomena in the river you are studying?

    Richard A. Park · Eco Modeling

    As several correspondents have discussed above, light limitation places phytoplankton and macrophytes in direct competition in shallow river, lake, and estuarine ecosystems. The phenomenon can be represented and analyzed by models such as AQUATOX. Zamor's link to Dent et al. 2002 seems to be broken. However, the paper by Beisner, B. E., D. T. Haydon, and K. Cuddington. 2003. Alternative stable states in ecology. Frontiers in Ecology and the Environment 1:376-382, is available on-line and provides a review of key papers, including ones by Scheffer and Dent.

  • Can you suggest good references for learning Chaos in Partial Differential Equations?

    While there are many papers and good books about chaos in ordinary differential equations, I like to know if there are some good books and survey papers about chaos in partial differential equations. Your suggestions are highly appreciated.

    Best wishes

    Toufic El Arwadi · Beirut Arab University

    http://www.ams.org/journals/proc/2012-140-06/S0002-9939-2011-11069-4/

    This is an example about Chaos for PDE

  • Gopal kumar Rai asked a question in Bromides:
    Can any one suggest the best way for the N-propargylation of Aromatic amines?

    want to react the propargyl bromide with aromatic amines to prerform N-propargylation of such amines.
    please suggest, if you can.

  • Marcelle G. S. Pegurier added an answer in SDS-PAGE:
    Why the protein moves Zig Zag way in the SDS-PAGE?

    I have loaded protein sample eluted from Ni-NTA column with different concentration of imidazole. I have found that the migration of of protein sample in 12% SDS-PAGE is not smooth or in a straight line. It is running in zig zag direction! why is it so? Is it because of excess charge present in the sample due to presence of imidazole and salts during purification process? How should I avoid it?

    Marcelle G. S. Pegurier · National Institute of Metrology, Quality and Technology (Inmetro)

    Check your Solutions. 

    Acril-bisAcril Solutions, PSA and TEMED as well. Seems to me it's a polymerization problem. PSA must be fresh and dont add more than 5% of TEMED. And check you lab temperatura also. Polymerization  doesnt like cold rooms. ;)

    Hope it's help!

    Marcelle Pegurier

  • Tobias A Beyer added an answer in ChIP-Sequencing:
    What is the best and most accepted way to normalize NGS of ChIP material ("spiked" normalization vs input vs IgG)?

    We are planning to realize massive sequencing of ChIP derived DNA fragment. Due to the big number of sammples to sequence, we can not afford to run in parallel all the "normalizators" available. So I would like to know if some expert in the field could give some hints of which one is the most use by routine and if someone has already tested the "spiked" normalization.

    Tobias A Beyer · ETH Zurich

    Sequencing input DNA is for sure a good idea. As well as making sure, that you have as little duplicate reads as possible.

    However, I would, if possible, include another negative control:  We recently performed ChIP-seq using SMAD2. As a control we included cells treated with a specific inhibitor to TGFb signaling and precipitated with SMAD2 antibodies. It was amazing to see that reads in the negative control were randomly distributed and we could not see any enrichment in know SMAD2 targets. Looking at the read distribution in the SMAD2 precipitation with active TGFb signaling, we could see nice peaks. Therefore, if possible, I would include a negative control were your protein of interest is not present or not bound to the DNA.

    cheers

    Tobi

  • Mardelle Atkins added an answer in Transformation:
    What is maximum limit of gene size to clone into Drosophila?

    I want to clone a gene of 413kb size into drosophila system. Can anyone suggest the success rate of transformation of such sizes of genes and also what is the gene size limit for transformation in a model system like Drosophila?

    Mardelle Atkins · University of Leuven

    I agree with the others that you will need to go for a phiC-31 approach, but even with that you can expect low efficiency at that construct size.  I would definitely recommend talking to the authors that developed many of the tools for the techniques, and check out their website for resources and protocols:

    http://www.pacmanfly.org/index.html . Good luck!

  • How are the ploidy levels determined through analysis of flow cytometry peaks?

    See above

    Sameer Jagannathrao Salunkhe · Advanced Centre for Treatment, Research and Education in Cancer

    Run a PBMC sample and note the channel number( X)  for G0/G1 which is equivalent to 2n population. Keeping the same acquisition settings now run the sample for which you want ploidy level. Note the channel number for G0/G1 (Y). Now do Y/X. will give you ploidy number.

  • Jason Cook added an answer in Conjugation:
    Why am I having problems with my silver nanoparticle-antibody conjugation for immunoassay?

    I'm trying to conjugate an antibody to silver nanoparticles (20 nm diameter, citrate capped AgNPs).  The conjugation protocol essentially involves centrifuging AgNP stock, resuspending at the same volume and adding 10 ug/mL antibody, incubating while mixing, then centrifuging, resuspending, and centrifuging a last time to wash away unbound antibody.  Finally the pellet is resuspended.  Using the resuspended pellet, I can get great data performing ELISAs with an anti-species, secondary antibody-HRP conjugate.  However, whenever I try to detect the silver directly, I don't see anything.  

    My current hypotheses are: 1. Remaining unbound antibody is out-competing the conjugate and 2. The AgNP severely reduces antibody affinity for target.  

    Are there ways I can test my hypotheses, or in general find out why I can't detect silver in the assay?  Thanks.

    Jason Cook · University of Texas at Austin

    One possibility is that your bioconjugation protocol is not directional. If the antigen binding sites of the antibody is bound to the nanoparticle, then you bioconjugated nanoparticles are not immunospecific. I would suggest using a directional conjugation protocol such as the one written by Kumar, Aaron, and Sokolov (Nature Protocols 2009) if your antibodies are monoclonal.

    If your bioconjugated magnetic bead uses a secondary antibody then these typically bind to the light chain (base of the antibody), thus confirming loss of specificity.

  • How can i implement gysel power divider and which software can i use to implement it

    i have read many papers on power dividers but still i m not understanding how to proceed and simulate

  • Barry Turner added an answer in Patient Rights:
    Who owns patients' health information?

    According to the Freedom of Information Act, American patients can access their health information upon their request. I wonder if there is a global consensus over this issue? Do other countries have a similar legislation?

    In my country, doctors can refuse to show the patients their own information. They believe and say that the doctor and not the patient owns the patient's information. Is it legal? Is it ethical?

    ps. By "owning the health information" I mean "the right to read, copy, or keep a copy of everything written in the patient's record".

    Barry Turner · University of Lincoln

    Ownership does not ned to be interpreted as a form of possession, such as owning real estate.  What 'ownership' means in relation to medical records is a right to them.  Patients are entitled to autonomy (with certain legislative exceptions) and as such must be given access, even control over their records. No one can be autonomous with information to make choices.  Autonomy is a fundamental principalist medical ethic.  It is likely unethical practice to keep information from patients. 

  • Would you please give me hypothalamic 4B cells?

    The cost of primary cultures is a limiting factor because large quantities of hypothalamic tissue are needed to perform the nessary experiments. So, I sincerely hope you can give me some hypothalamic 4B cells. thank you!

    Deivasigamani Balaraman · Annamalai University

    we don't have that kinds of cells right know......

  • Galitskiy Sergey added an answer in Atoms:
    Can anyone help with D4d symmetry in GAMESS?

    I`m trying to apply D4d symmetry to my molecule, but the number of atoms is doubled.
    It should be square antiprism in the end with 8 atoms.

    Could you help me to solve this question.

    Here is input file:

    $CONTRL SCFTYP=UHF MULT=1 ICHARG=0 UNITS=BOHR $END
    $BASIS GBASIS=TZV $END
    $DATA
    Li8 D4d
    Dnd 4

    Lithium 3.0 0.000 3.000 4.000
    $END

    Galitskiy Sergey · Universität Kassel

    ATOM ATOMIC COORDINATES (BOHR)
    CHARGE X Y Z
    LITHIUM 3.0 4.0080000000 -4.0080000000 1.8890000000
    LITHIUM 3.0 4.0080000000 4.0080000000 1.8890000000
    LITHIUM 3.0 -4.0080000000 4.0080000000 1.8890000000
    LITHIUM 3.0 -4.0080000000 -4.0080000000 1.8890000000
    LITHIUM 3.0 0.0000000000 5.6690000000 -1.8890000000
    LITHIUM 3.0 -5.6690000000 0.0000000000 -1.8890000000
    LITHIUM 3.0 0.0000000000 -5.6690000000 -1.8890000000
    LITHIUM 3.0 5.6690000000 0.0000000000 -1.8890000000

  • Deivasigamani Balaraman added an answer in CSE:
    Can anyone suggest the method of activity measurement for Cystathione-beta synathase (CBS) and Cystathione gama-lyase (CSE) activity in mouse brain?

    I wanted to know it can be measure in stored tissue or fresh tissue. Which method will be  good spectrophotometric or ELISA if it is commercially available. Please give you opinion.

    Deivasigamani Balaraman · Annamalai University

    I think fresh tissue is better one then a week it is not good.....spectrophotometric is ok.....

  • Jarad Schiffer added an answer in Chickens:
    Does anyone know how to avoid variation in the negative control samples used in indirect ELISA ?

    I am doing ELISA to test the immune response in chicken after vaccination with recombinant vaccine.There is quite variation in OD between negative control sera used in each plate and across plates.I need to minimize these variations in order to calculate the cut off value?

    Jarad Schiffer · Centers for Disease Control and Prevention

    Other things that can affect your negative control: plate type (high-binding vs. medium binding plates), plate coating (well-to-well variation in the amount of target protein coated on the plate), blocking solution, and detergent concentration. I have seen cases where high-binding plates have high background signal that goes away when using medium-binding plates without losing signal in the positive samples. I have also seen cases where increasing the detergent concentration or adding a blocking step before addition of sample reduces the background. We use 0.2% tween in our ELISA sample buffer, then drop to 0.1% for subsequent steps. Some assays work well with BSA as a blocking agent, some better with milk powder. You may need to play with the concentration of the blocking agent as well.

  • Gustavo Mello asked a question in Trials:
    Spike Cross-correlogram Parameters

    I generated a corrected cross correlogram. To do so, I got a 1ms bin size raw cross-correlogram and subtracted an averaged jittered cross correlation from it. This average was generated from a pool of 1000 signals, where the every spike was jittered randomly 50 ms around its original position in both spike trains.

    Than in every time bin of the corrected cross correlogram I asked the probability of that value happens by chance. I assume that the value in that bin has a poisson distribution with the mean equals the value in the same bin in the jittered cross-correlogram. 

    If I accept the level of significance of 0.01, in a 4 seconds window (4000 milliseconds) I should get by chance 40 data points as significantly different just by chance.

    Here are my questions:

    1- P of 0.01 sound a little bit week as criteria of significance, given that in 4000 bins I should expect 40 to be significantly different by chance. I read that I should look for sequences of significantly different bins. My question is: What features this sequence must have? Length? Frequency?


    2- What is a good policy for picking bin sizes, and bin sizes for shuffling?


    3- Is there a good metric to distinguishing common input and synaptic coupling?

    4- I did not use Shift predictors (shifting the whole spike train by one trial) because it assumes that the spike train is stationary across trials. But do you think I should try it anyway? What information could it give me that the jitter shift predictor cannot give me?

  • Marcella Bini added an answer in JCPDS:
    How can I get the crystallographic card of Cloisite 93 A ( a modified Montmorillonite nanoclay) & epoxy/cloisite nanocomposites?

    Crystallographic card (PDF) JCPDS indexes

    Marcella Bini · University of Pavia

    In my crystallographic database I don't have any pdf card of cloisite. Have you got the molecular formula of this mineral?

  • Whats the best way to solve the NSE well posedness problem?

    FEM or finite difference ?  Thanks all, Si

    Toufic El Arwadi · Beirut Arab University

    Do you mean the Navier-Stokes equation?

  • Minh Thao asked a question in Spreadsheets:
    Scherrer Equation

    1) If I need to calculate the crystallite size in Scherrer Equation, how I can choose peak in its? 

    2) In Scherrer Equation d = (k * lamda) / (FWHM * cos (2theta) ) , the FWHM value is Full Width at Half Maximum, but in file Excel spreadsheet containing the Scherrer's Equation ( Link ), they calculate d with replace FWHM by [ FWHM (structural) = FWHM (observed ) - FWHM (standard) ], please explain clear about this replacement ! and I also don't know how way to find the REF VALUE NEEDED of FWHM (standard) ??

    Please help me ! Thanks in advance !!!

  • Ljubomir Jacić added an answer in IT services:
    Is it high time to include Information Literacy programme in Higher Education ? I

    Dear Sir,

    Information literacy (IL) plays a prominent role in the knowledge based society, especially in the effective use of IT based services and collaborative learning of various levels of the educational system. Information literacy is an integrated set of skills and knowledge of tools and resources. Is it now essential to be incorporated in the curricula of Educational system.?
    Dr. Shanmugasuandram P

    Ljubomir Jacić · Technical College Požarevac

    Dear @Palani, Information Literacy Programme is included in Higher Education of Serbia for many years. Information literacy should be in the focus of ethics within the course Techniques of academic writing. "one of the possible ways in which ethical issues can be addressed, such as: plagiarism, information and data protection and research ethics, would be to fully develop students' critical thinking in relation to the appropriate usage of sources and information"!