Q&A

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  • What are the best conceptual model simulation tools based on your experience?

    Is it an open source tool?

    What modeling language/method/diagrams does it use?

    What type of simulation is that, e.g. symbolic animation, prototyping, ...?

    Research methodologies/publications behind?

  • What are the Zone Diameter breakpoints of Colistin (25 microgram) for Pseudomonas aeruginosa?
    According to CLSI guideline Zone Diameter breakpoints of Colistin (10 microgram) for Pseudomonas aeruginosa are ≥ 11 mm for sensitive and ≤ 10 mm for resistance but if we use Colistin (25 microgram) what will be the new breakpoints range?
    Saroj Chandra Lohani · Tribhuvan University

    Actually I am looking articles for the polymixins group of Antibiotics but any articles related to the topic will be a valuable assets.  If it could be shared I would definitely like to have it. 
    Thank you Patrick Druggan

  • Ishag Adam added an answer in Antimalarial Drug:
    In reference to antimalarial drugs what is the difference between Gametocidal and Gametocytocidal ?

    Q.In reference to antimalarial drug what is difference b/w Gametocidal and Gametocytocidal ??

    Ishag Adam · University of Khartoum

    Dear  पूजा मीणा we honestly  heard only  about Gametocidal

  • Ruhul Amin added an answer in microRNA:
    Can a miRNA exhibit opposite effects on it's targets in normal and cancer cells of the same cell type?

    upon transfection of the miRNA in Cancerous cells of patients , it showed downregulation of it's targets, however transfection of the same miRNA in Healthy cells (of the same cell type), showed upregulation of the same targets. Could the same microRNA show different effects on the same target upon transfection, of the same cell types of patients versus controls ?

    Thank you in advance   

    Ruhul Amin · Tohoku University

    I guess Maria is talking about this Science paper (http://www.ncbi.nlm.nih.gov/pubmed/18048652). Same miRNA is upregulating or downregulating its target depending on the  proliferative status of cells. In proliferating cells certain miRNAs suppress its target but in nonproliferating state, same miRNA can upregulate its target.

  • Ajay Kumar added an answer in Endosomes:
    Is Gelatin or BSA best for blocking in immunofluorescence?

    In my immunofluorescence protocol, I normally use 2% BSA in blocking solution and also in Ab dilutions.

    In a new protocol than I want to try for staining endosome markers, it's recommend to use 0,02% gelatin instead.

    Since I do not have gelatin, I'm planning to use BSA like usual. Do you think will it be ok? Or can anyone explain the differences between gelatin and BSA? 

    Ajay Kumar · Postgraduate Institute of Medical Education and Research

    Hello Nazli,

    I am completely agree with you. One can get best results if blocking is done overnight. In case your samples are crucial and antibody is costly, I will recommend you to stick to the protocol only. And wheather you can use BSA instead of gelatin is to try it. But BSA concentration for blocking is generally 2-5% for blocking and 0.1% for antibody dilutions. 

    Hope it helps.

  • Sunbeam Rahman added an answer in Landsat:
    How do you remove cloud from Landsat Images?

    I just want to know if there is any algorithms developed for this purpose. i will be glad to know that please.

    Sunbeam Rahman · Bangladesh Centre for Advanced Studies

    Removing cloud is not easy. Atmospheric haze of any sort influences or blocks radiation signal. You can use any one of these, 

    • use modules from commercial (in Erdas Imagine you have ATCOR, ENVI has ACM) or non-commercial (fmask) softwares to mask out the cloud
    • try spectral mixing/ ratioing to optimize shadow effects over other features
    • try secondary sources for those areas. 
  • Muthamil Iniyan added an answer in Endophytes:
    How can we isolate antibacterial compounds from endophytic bacteria using organic solvents?

    How to isolate antibacterial compounds from endophytic baceteria using organic solvents, what is the best procedure to do so and which organic solvents can be use in successive extraction method?

    Muthamil Iniyan · Manonmaniam Sundaranar University

    Prepare a broth of your bacteria in a suitable media and get a cell free supernatant by centrifuging the culture broth. The supernatant can be extracted using equal volume of increasing polarity of solvents like hexane, chloroform, ethyl acetate, acetone, methanol by series of one by one each in the same supernatant. Do this in a separation funnel for about 2 to 3 hours each and evaporate the solvent phase. Then go for antibacterial assay using disc diffusion method to check which extract having  antibacterial activity. Hope this will be useful.

  • Celestina Mazzotta added an answer in cDNA:
    How should i design the 96 well plate of qPCR for 2 samples and i have 5 different apoptosis genes?

    I have two cDNA samples

    i need to compare the expression of 5 different genes ?

    How should i do this?

    Celestina Mazzotta · University of Florence

    Sorry: my mistake.

    The protocol is:

    qPCR absolute and comparative quantification volume 20 microliters.
    10 µl master mix (2X)
    1 µl of probe (20X) if probes contain F and R primers or 1 µl of probe (20X) without primers, so add primers 0,6µl  F and 0,6µ R
    1µl cDNA (35nanogrammi)
    H2O to 20µl final volume

    all the best

  • Roger Jelliffe added an answer in Warfarin:
    Will warfarin be a historical drug after introduction of many new anticoagulants?

    Any comparative studies between warfarin and the new anticoagulants

    Roger Jelliffe · University of Southern California

    Good for you, Mohammed. I think the problem is that these are really good drugs, but the way they are dosed is the problem - the one size fits all, plus the really strange behavior of the marketers that THEY SAY monitoring is not needed, and because of this, the FDA and the almost the entire medical community thinks this is so. Look at the paper by Migliorini et al in Am. J. Cardiol. 2013;112:1843-1848, and especially in Figure 2 of it. The antiplatelet effect with both Prasugrel and Clopidogrel ranges from 70% residual platelet activity all the way down to zero, for BOTH drugs. The most frequent effect is about 30% for Prasugrel and 45% for Clopidogrel in the actual distributions AT THE DOSES GIVEN (never mentioned in the discussion!), not the assumed normal curve they erect around each set of data. This  extremely great variability in response is the problem. This is why these drugs NEED to be MONITORED with antiplatelet effect and the dosage individualized. Again, the authors MUST have the data, from the figure and their published responses, and be able to  know WHICH patients clot and which ones bleed. But they do not show it! Look at their reply to my letter to the editor of the Am. J. Cardiol. in Am. J. Cardiol 2014;113: 2086-2090. It also reveals the depth of their lack of knowledge of the problem, I believe.

         I was put on clopidogrel after my stents were put in, and if I would take 75 mg/day on top of my aspirin 650- mg.day for my arthritis, I would bleed all over the place. I take the clopidogrel 75 on Mondays, Wednesdays, and Fridays. My assay system is my nuisance bleeding which is not too bad, and the fact that my dermatologist has significantly more trouble taking my basal cell carcinomas off my face when I forget to stop it, and a much better time of it when I do remember to stop it. That is the way I have to monitor my antiplatelet effect. I bet a whole bunch of other patients do something similar, and may not even tell their docs..

         The lawyers see both ends of the spectrum of response and say to call 1-800-BAD-DRUG. They are laughing all the way to the bank, and so is Big Pharma. What is wrong with the medical schools that their education is so bad in this regard? It is because the medical community never kept up with the quantitative advances of pharmacokinetics in the last 50 years, including those in the FDA, which has not ketp up either! So tragic! There are lots of good modelers in the FDA and in Big Bad Pharma, but the marketers hold sway and all you can do today is to call 1-800-BAD-DRUG, worse luck. WHERE IS THE FDA?? waiting for jobs in big pharma?

         These are actually good drugs. It is the way they are marketed and given that is so tragic and evil, in my opinion. One size fits all is NOT the way to give such  meds. Individualized approaches are the way to go. You might look at Jelliffe et al: Human Genetic Variation, Population Pharmacokinetic/Dynamic Models, Bayesian Feedback Control, and Maximally Precise Individualize Drug Dosage Regimens, in Current Pharmacogenomics and Personalized Medicine, 2009, 7: 249-267. I think any clinician who can give coumadin can, in exactly the same way, but probably less frequently, adequately monitor the antiplatelet effect with an assay for it, and simply empirically adjust the dose. Better that than what BIG BAD PHARMA tells us to do now. 

  • How many different angles between lattice planes {hkl} exist?

    Is the number of possible angles between symmetry-equivalent lattice planes {hkl} predictable, or do I have to generate them all and calculate the angles for each pair? I assume it is a property of the metric tensor (and the implemented lattice symmetry).

    Tarik Ömer Oğurtani · Middle East Technical University

    Take  Z[001)}  there  3  four fold axis. [100],[010],[001].  each zone axis has 4 {100} planes but only the six out of twelve planes are distinct as one expects. That number appears as multiplicity as reported previously.  Here one has following distinct angles for each zone axis. {90,180,270,360}  the angle between two planes belonging two different  zones is either equal to zero or ninety  degrees. This is due to the fact every zone shares its two members with another zone.

    Z{011}= There 3 four fold axis [100],[010],[001]. each zone axis has  4 planes  {1+-1+-0}, {1+-01+-},{01+-1+-} all these planes are distinct and multiplicity is 12. The angles between planes  in same zone is  90o and distinct angles are  {90,180,270,360}.  The angles between planes belonging different zone are

    {60, 120, 240,300} where  cos (teta) = +-1/2.

  • Ajay Kumar added an answer in Seeding Density:
    How is a grooving curve made for determining cell seeding density?

    I am new to cell culture. I have been trying to standardize my MTT assay for two cell lines, but the seeding density is not clear and this affects reproducibility. Please advise.

    Ajay Kumar · Postgraduate Institute of Medical Education and Research

    Dear Deepjyoti,

    Most universal approach in case of maximum cell lines is seeding 5,000 cells/well of a 96-well plate. Add your drug of interest next day and culture for required incubation time.

    Best way to cunt cells is hemocytometer or use an automated cell counter whichever is available..

    Hope it helps!

  • How can one compare organic and conventional farms having different cropping pattern?

    Conventional farms are in general are monocropping based whereas organic agriculture is suppose to have a more diverse cropping system and these two systems may have a different cropping cycles. Most studies compare them on basis of single crop which seems unfair to the organic systems. I want to design an experiment to systematically compare  the yields and soil parameters in these systems. Can anyone suggest studies that are present or any ideas to compare these in common unit(besides money, I don't want to use money either as they do not reflect the true value).

    Reto J Strasser · Nanjing Agricultural University

    What pet is better for your pleasure? a cat or a dog?.......

    If you do not know, trye both and make your mind.

    Organic or conventional farming is a similar question.

    The advantage in Science is (so as well in Agronomy): you are allowed to do what you like to do......but you have to say WHAT you do and HOW you did it.

    If you have the will and the time, then you should compare both growing methods after having optimised both ways relatively to some critical growth parameters (density of plants, treatments,.....any thing you think is important). 

    Finally you rank the results according to your criteria: e.g. crop yield, labor, total costs, etc and finally you choose what fitts your needs most.

    In some cases low yield, but less work and lower costs may be preferable (for you, and your situation, but not for enyone).

    Consider, what I'm calling: "Creative INEFFICIENCY". good luck

    Reto.Strasser@unige.ch 

  • I'm looking for partners for the ERANETMED International project. Are you interested?

    Concerning the ERANETMED project (http://www.eranetmed.eu/​): I am looking for 3 partners from any of the following countries to participate as PIs working on groundwater hydrogeology and climate change:

    Italy - France - Germany - Greece - Portugal - Malta

    If you are interested, please send me an email with your CV or list of publications to start discussing the details.

    Best regards

    Dr. Ayman A. Ahmed

    Associate Professor of Hydrogeology

    Faculty of Science

    Sohag, Egypt

    email: ayman@sohag.edu.eg

    Nora Tabouche Bouchahm · Centre for Scientific and Technical Research on Arid Regions

    I am interested to colaborate in this call of project please consult my profil in research hate

  • After importing .dxf or .gbr file in ADS, how to simulate mimo antennas in ADS software?

    Actually I have designed mimo antenna in cst microwave studio. After importing .dxf file in ADS software it contains only one single layer so how to make layout of this antenna. Please explain with some procedure.

    Mauro Ferrari · University of Rome Tor Vergata

    Hello,

    i suggest this link to learn about substrate and metallic layer in ADS

    http://www.uwaverf.altervista.org/forum/viewtopic.php?f=19&t=27

    Mauro

  • Ajay Kumar added an answer in EpCAM:
    How people are isolating stem-like cells from established human cancer cell line, which are grown many year in serum containing medium?

    After sorting based on surface makers (like CD44+, CD24+, EpCAM etc.,) cells were maintained in serum free medium

    Ajay Kumar · Postgraduate Institute of Medical Education and Research

    Dear Saravanakumar,

    the best two methods which are most reliable to isolate CSCs from established cancer cell lines are SP (side population) analysis and staining with ALDEFLUOR (Aldehyde dehydrogenase). SPis a hoechst-33342 based assay which relies on pumping out of hoechst by CSC through ABCG2 channels and thus this population comes in FACS as a side low fluorescent population. You can refer to literature for that.

    Secondly a more costly affair is ALDEFLUOR assay, in which ALDH positive cells are CSCs. but this kit is costly, say around 78,000 for 100 rxns.

    In both the cases, selected cells can be sorted and you can obtain a pure population of CSCs..

    Cheers!

  • Leonard Scott added an answer in Biblical Studies:
    How did Rabbis Akiva and Ismael understand the nature of God?
    Their discussion has informed the understanding of the "Image of God."

    Thomas, You can find the answer to your question in Gershom Scholem's book On The Mystical Shape of the Godhead on pages 21,24, 32,35,148, 149, and 316. Leonard C. Scott

  • The spin of a fermion is s=1/2 (hbar=1). What is the experimental evidence for s^2=s(s+1)?

    In QM/QED we say that the spin component sz is 1/2 and this component is measurable. Are there any (more or less) direct measurements of s^2,

    i.e. is there experimental evidence for s^2=s(s+1)?

    Walter Smilga · Retired

    The operator s2 is the Casimir operator of the Lie algebra of the rotation group. As such it commutes with all generators of the rotation group. In consequence, it has the same value for all states of a given irreducible representation of the rotation group, where it can be replaced by a constant. Therefore, once you have determined the value of s2, you can measure sz of different states (within the same representation) without effecting the value of s2. This can be verified theoretically and experimentally.

  • Archit Garg added an answer in SWISS-model:
    I'm looking for a server to validate the 3D-structure modeling of my protein. Do you have any suggestions?

    My protein sequence has been modeled by swiss-model server. How can I validate the result?

    Archit Garg · Institute of Molecular Biology

    Dear Bakr,

    You may validate it through SAVES server. There are 4-5 servers in it like Errat, Verify3D, Ramachandran plot etc. You may run all of those to validate the structure. Also in addition, you may validate it through ProSA web server which analyze the protein structure and matches with X-Ray and NMR calculated structures. Also, you may also analyze your structure through TM-align. I hope this helps you.

    Best Regards,

  • Srinath Rao added an answer in Plant Tissue Culture:
    Musa paradisiaca responds low in Tissue culture in Multiplication Stage. Any suggestion on growth regulators and its combination?

    Plant Tissue Culture

    Srinath Rao · Gulbarga University

    It is in response to combination of A & B genome

  • Kunal . asked a question in Taguchi Method:
    How can one learn about RSM and Taguchi method?

    How can one learn about RSM and Taguchi method? How can one employ it in research? Any manual or link if available, Please provide.

    Thanks.

  • Ajay Kumar added an answer in Cell Culture:
    Should I centrifuge the cells after thawing them in order to remove the DMSO from the medium?

    All we know, centrifuging the cell is harmful right after thawing the cell. But in the other hand, remaining the DMSO in the medium can hit the cells, too. So shall I remove the DMSO or it's better to avoid the centrifuge?

    Ajay Kumar · Postgraduate Institute of Medical Education and Research

    Dear Aref, A stright answer to your question is 100% YES !

    It is always recommended to centrifuge the cells after thawing to remove DMSO. But befor that, you can thaw your cells containg DMSO and add it to 4ml of culture media in a 15ml falcon and then you can centrifuge it. To avoid damage to cells you can go for low rpm or g values, say 2,000rpm or 800g for 2 minutes only. Then you can discard the supernatant and resuspend the cells in complete culture medium. Don't ever risk to keep the cells in DMSO for one day in culture media as that is more apoptotic cells and in case of centrifugation at the mentioned settings, you will hardly encounter any cell death. 

  • Girish Deokar added an answer in Vicia:
    How long a plant extract can be stored at 4 degrees?

    I want to extract vicia shoot and root and perform several enzymatic assays on it so how long the extract can be stored without loosing its activity 

    Girish Deokar · North Maharashtra University

    Hi

    When considering storage, it's better to dehydrate sample and store @RT for long time. If not possible so please do assays in a week. Till store the extract @4 oC. 

  • Srinath Rao added an answer in Botany:
    Can anyone help me identifying this plant?

    this is a climber.

    Srinath Rao · Gulbarga University

    Ctenolepis garcinii 80% sure

  • Does anyone have a protocol for cell viability assay in which no absorbance measuring is needed?

    I need to measure cell viability in 48/24 well plates. However, since the cells are under treatment of an organic material which has some absorbance itself, I can't use/ trust the optical density of the culture. I would be appreciated if you suggest a method (not trypan blue) by which I can measure the cell viability in well plates.

    Achilleas Mitrakas · Democritus University of Thrace

    You can use Alamar Blue assay (http://www.ncbi.nlm.nih.gov/pubmed/24910583). You could use our protocol.
    You could also use CyQuant assay (based on DNA content).

  • Matts Roos added an answer in Special Relativity:
    Is Loretnz symmetry conserved for all velocity ranges?

    I want to know whether Lorentz symmetry is conserved for all the velocity ranges or not?

    Is the Lorentz invariance completely related to Lorentz symmetry; i.e. if Lorentz symmetry conserved then Lorentz invariance is also conserved or there are certain conditions where the Lorentz invariance conserved while Lorentz symmetry is not? what are they if there are such conditions.

    Matts Roos · University of Helsinki

    I would prefer decent conversation, so since Johan's contributions include frequent use of the word "bullshit" I I politely ask him to leave this thread.

  • Sarwar Muhamad asked a question in Thalidomide:
    What is the SAR of lenalidomide ( REvlimide ) ?

    What is the Stracture Activity Relationship of lenalidomide ( REvlimide ) ?

    Lenalidomide and pomalidomide are synthetic compounds derived by modifying the chemical structure of thalidomide .In particular lenalidomide has been synthesized from the structural bone of thalidomide molecule. Lenalidomide has been developed by adding an amino group (NH2–) at 4th position of phthaloyl ring and by removing the carbonyl group (C=O) of the 4-amino-substituted phthaloyl ring. This drug is the result of the pressing need to develop molecules with enhanced immunomodulatory and antitumor activity in comparison to thalidomide. Lenalidomide, which possesses pleiotropic properties, belongs to the second generation of immunomodulatory drugs (IMiDs).

  • Dmitri Kudryashov added an answer in Gelsolin:
    What is the possible mechanism of plasma gelsolin in Analgesic activity?

    See above

    Dmitri Kudryashov · The Ohio State University

    Hello, Ashu.

    I was not aware of gelsolin having analgesic activity. Could you please provide a reference?

    Thanks,

    Dmitri

  • Samuel Kyei added an answer in Wildlife:
    Do you know any wildlife studies that looked at age-related vision capacities?

    In humans, it is well known that vision changes with age in humans or that vision varies across individuals within populations. But what about inter-individual variation in vision characteristics and age-related change with age in vertebrate wildlife?

    Samuel Kyei · University of Cape Coast

    @Marcel M. Lambrechts: This is getting more interesting, some of these are predominantly nocturnal other than diurnal; some depend heavily on acuity vision ( the eagle)  while other may require moderate visual acuity; those requiring moderate visual acuity may have other well developed senses to compensate for their visual deficit. If all the natural principles of use, disuse and excessive use apply, it only logic that "exaggerated" use should lead to vision expression of senescence and could vary among wildlife. Research is still need to concertize these assertions (hypothesis).