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  • Kamal Kumar added an answer in Y2H:
    Why can't I transform MaV203 yeast cells to test the bait?

    I recently have problems in yeast transformation.  Our lab uses the Proquest Y2H system from invitrogen.  I followed the transformation protocol from the kit to transform my bait plasmid with pDEST22 empty plasmid to test the bait.  However, no colonies formed on fresch SC-Leu-Trp plates after 4 days.  The bait plasmid was freshly made.  The yeast cells and pDEST22 were from -80 and -20, respectively.  These reagents have been around the lab for about 5 years.  I put the yeast out on YPAD plate and the cells grew just fine. 

    Is there any potential problem or trick in the transformation protocol?  Why did this simple transformation not work?  Help~

    Kamal Kumar · National Institute of Plant Genome Research

    I use the small scale protocol of this manual & lot of colonies appear

  • Shaikat Debnath asked a question in Atoms:
    Doesn't a 13-atoms 13-electrons icosahedron system incorporate with jelium model?

    Lets say if we dope a monovalent atom into a 13 atom Ag cluster to make a 13-electrons system with icosahedron symmetry, will it actually fit in the jellium model?

  • Jephias Gwamuri added an answer in Platinum:
    Which is the Area we should use for calculating the resistivity, in a four probe conductivity measurement,?

    I am measuring the resistivity of the sample using the four probe measurement. My electrodes are rectangular (1mm*5mm )shaped platinum (50nm thickness) deposited on top of the sample separated by 1mm width . Considering the penetration depth of the sample, Which area should i choose as the Area for the resistivity calculations. Should i use the entire base area of the sample (could have shorter current penetration depth), Or should i use the Area of the current electrode ( considering the current Penetration depth ) for accurate calculation !!!

    Jephias Gwamuri · Michigan Technological University

    I agree with Prateek. Resistivity  is sheet resistance multiplied by the film thickness and its expressed as ohm.cm. You only require area when you want to determine resistance which is simple the resistivity x length of electrode all divided by the electrode cross-sectional area.

    I would advice you to characterize your electrodes first by depositing them on glass substrate or Si with oxide spacer layer of 25 nm or greater.,otherwise your sheet resistance values will be inaccurate if your electrodes are on a conducting material .

  • Are you aware of combined studies on probabilistic risk assessment of hazardous objects and air pollution modelling?

    Could you please help me with finding references regarding combination of probabilistic risk assessment studies with air pollution modelling?

    For instance, probabilistic safety assessment conducted for ammonia pipeline combined with the results of dispersion modelling can be used to assess annual costs of losses caused by accident. I met such works regarding groundwater pollution (http://www.sciencedirect.com/science/article/pii/S0304389413008005), however not so much regarding air pollution, or maybe I am wrong?

    Thank you in advance.

    Ivan Kovalets · Institute of Mathematical Machines and Systems Problems, National Academy of Sciences of Ukraine

    Thank you, James,

    I found your paper and will study it.

  • Should OST be offered to non-injectors?
    PWID programs
    John Anthony · Independent Researcher

    Thanks All. In Kenya we are starting OST program and we are using the following as an inclusion criteria:

    All female injectors and non injectors

    All HIV positive drug users

    Only male injecting drug users

    This is for now given the resources. 

  • Yoav Raz asked a question in Algorithms:
    Do you know of any other publication (see the two below) that uses the very fast solution by Sort to that special case of Linear Programming?

    One article article (origin 2007)

    "An adaptive special purpose algorithm for a class of two - stage single constrained linear fractional programming problem"
    by Prapapan Ketsarapong, Peerayuth Charnsethikul, Suwitchaporn Witchakul


    The other article from 1983:

    "linear programming problems with bounded variables and a single linear combination constraint " by Yoav Raz



    The solution for linear programming problems with bounded variables and a single linear combination constraint is given. Necessary and sufficient conditions for the existence of a feasible solution and for a bounded optimum are derived. This solution is used for constructing a simple 0(n) space and 0(n log n) time algorithm where n is the number of variables. The algorithm has been implemented successfully on a personal computer for problems with thousands of variables.

    It looks as if the solution in the first article above relates to the same basic LP special case as in the second, and uses the same solution technique (Sort) to get an extremely faster solution than those known for general LP (see an analysis in the second paper).

    Yoav Raz

  • John F. Wilhite asked a question in Teacher Education:
    What's your opinion of cameras in classrooms at all levels of education, elementary through university?

    Cameras in classrooms are becoming more common.  Often two cameras are used, one in the back to show the teacher and one in the front to show the students.  One of the primary rationales behind this use is safety concerns due to numerous school shootings.  Monitoring student behavior is another reason for their use.

    There are other potential uses.  For teacher evaluation, rather than disrupting a class with a personal visit an evaluator could observe the camera feed.  Students of teacher education could observe a number of teachers more conveniently with the camera feeds. 

    What are other positive uses?  What are the negatives?

  • N. K. Naik added an answer in Fatigue:
    What is the measurement of the fatigue in any structures which are undergoing the cyclic loading?

    What is the measurement of the fatigue in any structures which are under going the cyclic loading?

    N. K. Naik · Indian Institute of Technology Bombay

    Question is not clear. Generally, fatigue studies include determination of residual stiffness, residual strength, life and remaining life of the structure. 

  • Rajat Pradhan added an answer in General Relativity:
    What physically changes when a particle is elevated and gains gravitational potential energy?

    We frequently speak of an object having gained gravitational potential energy when work is done in lifting a mass from a lower elevation to a higher elevation. However, what exactly has physically changed? Where is this gravitational potential energy stored? When a photon propagates from a lower elevation to a higher elevation, we say that it has undergone a gravitational redshift. However, this is entirely due to the gravitational change in the rate of time. Local clocks at the two elevations are running at different rates of time giving the perception of a lower frequency at the higher elevation. The photon appears to have lost energy but there is no change in frequency if adjustments are made for the different clock rates. If an electron is perceived as a point particle with no internal structure, then it is impossible to assign any change in the internal energy of an electron at two different elevations. Therefore, where is gravitational potential energy stored when an electron or other particle is elevated?

    Rajat Pradhan · Utkal University

    Hi everyone,

    I do not know if it has already been written in these answers by others. The object does not gain or store Grav. Pot. energy. The pot. energy always resides in the space between the objects, in the field, and not in the objects. So nothing changes for the objects themselves. It is only a loose manner of speaking that such and such object has gained/stored pot. energy.



  • Vadim Khlestkin added an answer in Viscosity:
    What methods are known to introduce and evenly distribute an additive in micro amounts (say, 0.01%) in viscous fluid?

    The problem is real, for example, in polymer industry. Micro and nano sized additives tend to aggregate. Their even distribution is always a challenge, especially in a viscous fluid. Which techniques are the best,  and how to prove even distribution in low concentrations (0.01 - 0.001%)?

    Vadim Khlestkin · Novosibirsk State University

    Hi Alex, thank you for the interesting example. ESR is certainly advantageous method in case you deal with paramagnetic species. I will have a look at the paper to find a method for even distribution Gd3+ in viscose glass melt, and also to see if the distribution was really even.

  • Does thinking itch?

    Is it just a social habit to scratch our head as we concentrate? Or is there a scientific explanation for this fact?

    - Is it simply not natural for mammals to think?

    Or is there an unusual concentration of neurotransmissers in the blood vessels of the head, as serotonin levels, that cause itching?

    Maria Bettencourt Pires · New University of Lisbon

    (I was absolutely right, when I added the topic «Humor in science» to this debate)

  • Peter Smetacek added an answer in Insect Ecology:
    Those insects in light-polluted environments (urban) living what changes will come in the life cycle?
    Insects as well as plants respond to artificial light. Photoperiod on growth and ecology of insects that live in seasonal climates affect.
    Peter Smetacek · Butterfly Research Center, Bhimtal

    I was brought up in a rural area that is suburban today. We have monitored moth populations since 1973. The biggest challenge of light pollution seems to be that moths and other nocturnal insects tend to be attracted to street lights and other all-night lights, so that species tend to fade out of the area, perhaps because of not mating and ovipositing on time. This is followed by an erosion of plant species that are not pollinated by nocturnal insects. So there is a cascade effect. There is a strong case for the 'night sky' movement, which questions the need for continuous lighting in many areas.
    Having said that, one might add that not enough is known about the life history of most nocturnal insects to judge whether artificial light affects their circadian rhythms and, if so, in what way this is expressed.

  • Timothy A Ebert added an answer in Sharks:
    Does anyone know how to randomly allocate observation 'slots' for a sample (3), while considering the day of the week and time of day?

    I'll be observing grey reef sharks (3) within an aquarium and trying to find a way to randomly allocate time slots for each shark for a focal sample. Observations will take place over several months for 2/3 days per week. Each observation day is then split into 3 time periods AM, NOON, PM (1 slot for each shark). This leads me onto...

    Is there a method which takes all the observation days into consideration so that at the end- each shark would equally cover ever day of the week and all three time periods for each day?

    Thanks for reading, I hope I've explained it ok?

    Timothy A Ebert · University of Florida

    The random number sampler might get you into trouble. To avoid problems try a stratified random number generation. Choose the first shark randomly. Then choose the next shark randomly from the remaining two. In the next cycle choose the first shark randomly from the two sharks that were not chosen first before. Then choose the next shark randomly from the remaining two. The third cycle starts with the shark that wasn't chosen first previously. In the fourth cycle, start by choosing the first shark randomly as you did in the first cycle.

    Another approach: Make everything random to start. Towards the end of the experiment favor treatments that have been chosen less often. Make sure that you keep running treatments where you have plenty of data but at lower frequency. If there is a systematic change (for example a seasonal component), this approach could bias your data.

    I would probably favor this approach: Work on the treatments in a orderly fashion making sure that all permutations of the data are used. You have three sharks, you have three time slots. It is very important that you go through all the possible combinations before starting over. If you like, you can select the first combination at random.

    A truly random design could have an outcome where you focus on shark 1 at all time slots in the first week. Then focus on shark 2 in the second week, then shark 3 in the third week. Unlikely though it would be, this is still one possibility using a random sampling approach. No one would like this outcome, so you rerun the random number generator until you get an outcome that we like. Is that really random? 

    The last suggestion distributes all "shark X time" treatments evenly through the study period. It also makes sure that there are equal numbers of all observations, and you have an equal number of times where you observe shark 1 first then shark 3 versus observing shark 3 first and then shark 1.

    You should keep track of Julian day. However, note that cyclical patterns due to season or day complicate the analysis. The nuts-and-bolts of how to do these analyses using the statistical analysis programs that you have available are more efficiently taken care of by consulting a statistician at your university.

    Keep track of all standard weather variables, and miscellaneous events like feeding, when the water in the tank is changed (or is there continuous sea water exchange), moon phase if the tank is outside, and anything else that you can think of that could influence shark behavior. If the tank is outside and it rains, then there will be a layer of fresh water that is a different temperature. This could influence behavior.

  • How to perform docking with a library of compounds?
    I wish to dock a group of phenolic compounds (plant/soil origin) with a protein of my interest, to see if any of them can act as a ligand (substrate/inhibitor). After docking, I will proceed with biochemical kinetics studies with the selected candidates. I have a few questions regarding the work, since I'm new to modeling and docking.
    1) Where is it possible to obtain a collection of such compounds (plant phenolics and related compounds)?
    2) Is it easy to do docking of a chemical library without advanced software?
    3) In a few papers, I encountered the use of a 'non-substrate' as a negative control. What does a non-substrate signify?
    Danish Jasnaik · Dr. D. Y. Patil Biotechnology & Bioinformatics Institute

    If you want to dock multiple ligands to a single receptor that iGemDock would be good. Hope this helps.


  • How I can extract DNA from fungi without liquid nitrogen?

    I would like to extract DNA from soil fungi, but we haven't got liquid nitrogen, are there alternative techniques? Preferably without kit

    Thank you. ;)

    Maria del Carmen Casado Muñoz · Universidad de Jaén

    thank you all, you are very kind I'll be telling !!

  • Danish Jasnaik added an answer in Docking Studies:
    Can anybody suggest how long it generally takes to finish one docking study for protien ligand interactions for 10 runs?
    Danish Jasnaik · Dr. D. Y. Patil Biotechnology & Bioinformatics Institute

    It depends on which software you are using and what kind of docking you are performing

  • Sarika Rohatgi asked a question in Macro:
    Macros for trichrome stain and IHC analysis by image J?

    I am looking for some macros that I can modify to help me analyze my slides faster. each of my slides are huge ~20 MB and breaking the Tiff files down to 40x, 256 mb sized manageable images has created several smaller images which though easier and more accurate to analyze but is taking extremely long to do.

    I would appreciate if anybody can suggest on how to make the macro for my desired functions?

  • Arabidopsis mutants, how to germinate and growth?

    Sometimes I have problems with germination and post-germination growth of some Arabidopsis mutants. Can anybody give me any general advice about cultivation strategies for Arabidopsis mutants, independently of the type of mutation?

  • Bonnie Mcbryde added an answer in Primary Education:
    Do boys and girls learn differently?
    Are teachers aware of these differences? When planning lessons, are these differences acknowledged?
    Bonnie Mcbryde · Carson-Newman College

    I agree with most of these answers. However, I do have one thing to add. As a pre-service teacher, I have noticed that the boys I have taught over my 9 practicums seem in general to respond more to kinetic and visual activities, while many of the girls don't have a preference. The girls that do seem to be more visual. I'm not sure that this is generalizable to all students, but it is something I have noticed.

  • Does any one have fuzzy filter which using in filtration of 2D resisitivity imaging data. I need it because i have noisy 2D resisirivity data?

    I read some articles where this filter software was used to enhance the 2D imaging data therefore i need to get this filter to make my data better before inversion

  • Mohammad Noori added an answer in Vibration:
    Can someone suggest a random vibration book?


    Can anyone introduce a good random vibration book?


    Mohammad Noori · California Polytechnic State University, San Luis Obispo

    Two  books that I highly recommend:

    - Random vibrations,  by Stephen Crandall

    - Probabilistic Structural Dynamics, by Y.K. Lin

    these two are two of the oldest books in this area, Crandall's book is very simple and fundamental, YK Lin's is very comprehensive and excellent for those who want to do research in the filed.

    I also suggest Random Vibrations by Newland.


  • Siddhartha Chattopadhyay added an answer in Cesium:
    What is the experimental and calculated value of the Lamb shift for 6S1/2, 6P1/2 and 6P3/2 levels of cesium?

    Please also send me the relevant paper for lamb shift in alkalis as a whole, if available. Thanks.

    Siddhartha Chattopadhyay · Aarhus University


     Apart from the above references, may be you can go through one of the recent works by V. M. Shabaev et al. (http://journals.aps.org/pra/abstract/10.1103/PhysRevA.88.012513). It estimates the Lamb shift of ns_1/2 state of the alkali metals in Table VII.  In one of the previous work by W. R. Johnson et al (http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.87.233001) the vacuum polarization correction (a component  of Lamb shift) of Cesium is calculated. Hope it will help you.

  • Paul C D Hawkins added an answer in Binding Energy:
    It is possible to calculate the IC50 value of a ligand-receptor complex with any of the opensource softwares?

    I wonder that there should be a relationship between binding energies, and IC50 values. Is there any open-source program to estimate it, or any technique to estimate it using binding energy values ??

    Will be grateful to receive suggestions...

    Thanks in advance

    Paul C D Hawkins · OpenEye Scientific Software

    Binding energy or binding affinity and IC50 have no defined relationship. Binding energy can be used to calculate binding affinity or Kd, because Kd has a defined thermodynamic relationship with binding energy. However docking cannot calculate absolute binding energy because docking does not know about the unbound state of the protein and the ligand, which is required to estimate binding affinity.

  • Chiranjeev Sharma asked a question in Oxygen:
    How to obtain the electron density of any organic compound experimentally & determine the O-O coupling constants between two O atoms?

    We have crystallized some bioactive organic molecules. On the basis of van der Waals radius of oxygen we found them to possess remarkably short intramolecular oxygen...oxygen interaction. Is IR and Raman spectroscopy helpful in finding the oxygen-oxygen coupling constants between the non-bonded oxygen interactions? Also how can one calculate the electron density of a molecule experimentally, without using any computational methods?

  • Rajat Pradhan asked a question in Theoretical Physics:
    Does Rayleigh Scattering really explain blueness of sky?

    This question may sound a little funny to most of us, since it is presumed that the 1/(lambda)4 formula for Raleigh scattering does really explain the blueness of sky.

    However, there must be additional factors responsible for the "Perceived" blueness, since the lowest wavelength is violet, and not blue, in the visible spectrum. To answer this puzzle, it is sometimes stated that the human eye is more sensitive to blue than to violet, and thus we perceive the blue and not the violet. But, we could have perceived INDIGO even! Why not?

    If the eye were most sensitive to Green or Yellow could we have seen Green or Yellow skies?

    Next, what are the particles that scatter the blue wave lengths predominantly? Are they nitrogen molecules which form more than 75% of all constituents of air?

    Can anyone give quantitative details on these issues?

  • Brian A Rothbart asked a question in Metatarsus:
    Your thoughts on the Ontogeny - Phylogeny Evolution Model?

    I believe that the adage - ontogeny recapitulates phylogeny - embodies the 'smoking gun' (e.g., in determining the ancestrally lineage of homo sapiens).

    The etiology of the two abnormal foot structures that I have written about (PreClinical Clubfoot Deformity and Primus Metatarsus Supinatus foot structure) can be easily understood when one studies the normal embryological development of the human foot.

    During embryogenesis, first the fetal foot bud emerges, then it develops into the the Clubfoot Structure, then as it continues to develop, it becomes a PreClinical Clubfoot Structure, then a Primus Metatarsus Supinatus Foot Structure, and finally the Plantargrade Foot.

    Using this same methodology (e.g., the Ontogeny - Phylogeny Evolution Model), I believe we can trace back our homo sapien prototypes. That is, our earliest ancestors (who were bipedal obligates) would have the PreClinical Clubfoot Structure (twisted calcaneus and talar head). This would rule out A. afarensis. The A. sebida fossil's do have the twisted calcaneus.

    The PreClinical Clubfoot Structure/deformity forces the foot to hyperpronate. If the Laetoli footprints indicate that foot did not hyperpronate, following the above methodology, that upright walker would not be in our direct prototype, but rather a divergent line.

    I believe this line of reasoning will help uncomplicate our understanding of hominine taxonomy; which is consistent with my own research. That is, the closer you get to the truth, the easier it becomes to understand.

  • Kai Hahn asked a question in Fructokinases:
    Is there a potential problem with SGLT2 Inhibitors and tubular injury?

    Has anyone got information of a possible problem with SGLT2 Inhibitors creating a hyperosmolar urine that might upregulate or express fructokinase in tubular cells under certain circumstances e.g. ischemia or acidosis. If this could happen, then the urinary glucose could be converted to fructose via the polyol pathway and then will be metabolized to uric acid. This would cause tubular injury and mybe AKI.

  • Ulrich Deiters added an answer in Binary Mixture:
    Is it possible to predict vapor liquid equilibrium of binary mixtures with known excess enthalpy information ?

    In our lab, we are doing experiments about the excess enthalpy of refrigerant and organic absorbent mixtures. With obtained excess enthalpy data at different temperatures, would it be possible to predict  the vapor-liquid equilibrium behavior of the mixtures and how ?


    Ulrich Deiters · University of Cologne

    If your pure fluids can be described by equations of state, it is possible to determine the binary interaction parameters from HE. You can probably do this with the ThermoC software via your browser (http://thermoc.uni-koeln.de/index.html).

    But do not expect miracles: The excess enthalpy captures only a part of the nonidealities in a mixture.