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  • Alfredo Oliveira added an answer in Dark Energy:
    Is dark energy merely an illusion?

    According to a report by Carlo Iorio and Timothy Clifton, dark energy may be an illusion. And LTb model or variations of it can be promising candidates to get rid of it. What do you think?


    Physics of the XX century is a desperate attempt to obtain a consistent description of the universe in the reference frame of the observer, a possibility that the work of Lorentz, and Poincare, was putting in question. Einstein’s SR seemed to have established that possibility. No one noticed something that Einstein himself mentioned in on of his texts about SR: to obtain the equations of transformation (end of § 3), he had to find the value of a parameter fi(v), but he had no clue on it; so, he invoked what is now called the symmetry principle and made fi(v)=fi(-v). Without this assumption, he could not have finished his theory. In that text about SR, he asks: “what else could I have done?”. The problem is that the “symmetry principle” does not hold and that is the cause of SR paradoxes. The practical consequences are insignificant but the theoretical ones are relevant.

    I explain all this and deduct the “objective reality” that his behind SR equations and why it is almost possible to describe the universe in the reference frame of the observer here: http://arxiv.org/abs/physics/0205033

    Cosmic data was also analyzed in the same paradigm that the universe could be described in the reference frame of the observer. Once one questions the invariance of the observer, the solution is at the reach of a high school student. Available here: http://vixra.org/abs/1107.0016

    As Einstein said, “God is subtle”; the evanescence of matter, which is the cause of the apparent expansion of space, is such that the only law that is affected is the conservation of angular momentum; and the local consequences can only be detected in the longtime behavior of isolated systems, namely orbital motion. That is why GR is not affected by the evanescence of matter in what concerns interactions and short duration phenomena.

    There is a great confusion around GR because people fail to understand something that Einstein mentioned over and over: that the reference body depends on field and acceleration; he even called it “reference-mollusk”. Instead, people interpret GR as if the observer were invariant, mixing the real space curvature that corresponds to the field with the apparent one that results from the use of varying length and time units. I think that GR can be formulated in a much simpler way if one uses a different kind of units but I have not analyzed it (yet).

    So, the change of paradigm to be made is to drop the idea that we can obtain a consistent description of the universe in the reference-frame of the observer.

  • How might I make a quantitative analysis of the crystal shape by XRD?

    I want to compute shapes of crystals from X-ray Diffraction data, thank you.

    Lawrence Margulies · University of Guelph


  • V. T. Toth added an answer in Gravity:
    Is any one interested in a theory of gravity that assumes constancy of speed of light globally?

    I wonder is a theory of gravity that assumes constancy of speed of light globally will make any progress towards building a quantum theory of gravity?

    V. T. Toth · N/A

    If you take into account the bending of spacetime, that means that the global speed of light between two points is not constant anymore: it depends on the gravitational fields present between the two points. Locally, that is, measured in a small neighborhood of the passing light ray, the vacuum speed of light is constant in general relativity.

    I.e., given a ray of light between, say, a distant spacecraft and the Earth, if you could examine that ray of light at any point along its trajectory, you'd find that (ignoring media effects, such as charged particles from the Sun) it is propagating exactly at c (local measurement). However, if the light ray passes near the Sun, it takes longer to arrive at the Earth due to spacetime curvature (that is, the Shapiro effect), so its global speed is less than c and variable. This is standard relativity.

    In reviewing the question though, I wonder if perhaps you had something other than the standard meaning in mind when you used the word "global".

  • Kwamina Ewur Banson added an answer in Soil:
    What is the difference between "Soil Water Holding Capacity" and "Field Capacity"?

    Are those terms synonymous?

    Kwamina Ewur Banson · University of Adelaide

    Dearest J.D.,

                                they are not synonymous. Available water is the difference between field capacity which is the maximum amount of water the soil can hold and wilting point where the plant can no longer extract water from the soil.
    Water holding capacity is the total amount of water a soil can hold at field capacity.

    The field capacity is the amount of water remaining in the soil a few days after having been wetted and after free drainage has ceased.


    The soil water holding capacity is the portion of water that can be absorbed by plant roots. By definition it is the amount of water available, stored, or released between field capacity and the permanent wilting point water contents.

  • Matthew Hayden added an answer in IMAC:
    Why is most of my recombinant protein in the wash after His-tag IMAC?

    I recently did His-tag purification for a recombinant protein under denaturing conditions. I incubated the protein extract for 1 hour. I proceeded to wash 3x and elute 2x. After running an SDS-PAGE, it was apparent that the majority of the purified protein was in the second wash (not the first or third). Any recommendations or advice?

    Matthew Hayden · Columbia University

    Hi, Amien.  There are several reasonable explanations.  It would help troubleshoot if you provided more information about your protocol: composition of wash and elution buffers, bed volume, wash and elution volumes, and, perhaps, an image of the gel.

  • What are the new techniques used for storm water management?

    I want to know about new technologies to filter the storm water from different contents  in it? And What innovations can be done for storm water management for a commercial building?

    Mohammad Azmi · Monash University (Australia)

    Check this document, it gives you a great vision towards this issue.


  • Can anyone help me with my problems transforming Mycobacterium avium?

    I have been trying to transform this bug for a few months with little success. I am trying to get an allelic exchange mutant using a disrupted gene in a mycobacterial plasmid but I can't even seem to get the plasmid to go into the bacteria. I have tried optimizing conditions as best as I can using the attached paper from 2002 but still no luck. Does anyone else out there have experience with transforming this bacteria?

    Kathryn Sydney Doornbos · University of Alabama at Birmingham

    Try adding sterile 15% glycine to a final concentration of 1.5% O/N prior to preparing your competent cells. Glycine prevents lipid cross-linking in the outer membrane making transformation more efficient, but can result in an irreversible loss of PDIMs, so be mindful of what your final goal for these strains is.

    What are you transforming? Is it possible that it is toxic? If so, maybe try a tightly regulated inducible system (Tet)?

    What are the settings on your electroporater? How many millisecs is your 'charge' (22-25 seems optimum in our lab)? What is the method by which you are preparing competent cells? How much DNA are you using? Is the plasmid you are trying to transform episomal or integrative? How long is your outgrowth? What is your selective antibiotic and what concentration are you using it at? All these factors influence transformation efficiency.

  • Dejun Li added an answer in DNA Insert:
    Does anyone know about multiple cloning sites of YEp24 vector?

    I want to clone DNA insert into this vector but I am not able to find mcs of this vector.

    Dejun Li · Chinese Academy of Tropical Agricultural Sciences

    Hi, Sonam Sharma. You can find the answer with the following website (http://www.neb.com/~/media/nebus/page%20images/tools%20and%20resources/interactive%20tools/dna%20sequences%20and%20maps/yep24_map.pdf)

  • Alexei Chadyuk added an answer in Qualitative:
    Is it possible to set hypothesis for qualitative data?

    in the process of analysing data collected, it was discovered that all are qualitative and contemplation is on to state and possibly test hypothesis

    Alexei Chadyuk · National Technical University of Ukraine Kiev Polytechnic Institute

    In the Popperian epistemology, your research -- whether qualitative or not -- cannot prove any theory (however many black crows you see, you can never prove that all crows are black).  All you can do is find a likely hypothesis and show that it is wrong (i.e. falsify it).  Note that finding an unlikely hypothesis wrong is trivial (this is called strawman's fallacy).  

    This is a very brief summary of modus tollens hypothesis testing.

    Now, coming to your question, imagine that possible qualitative findings about your phenomenon of interest are data points on a nominal scale: A, B, C, etc.  If it is feasible to differentiate between them in your observations, you can postulate your null hypothesis as A (it must be a likely choice based on your prior knowledge of phenomenon, see above).  Then, if your observations point to B, you can claim that you falsified your null, and that is your original finding.  (In lieu of statistical significance test, you can claim that the likelihood of misclassifying A, B and C in your setting is less than 5%; this is almost nearly equivalent to the coveted p < 0.05.)

    Totally support the comment of Dr. Morgan above.  You cannot state your hypothesis based on your findings.  If is called 'begging the question', i.e. assuming your findings are right and then using them to show that they are right.

  • Kwamina Ewur Banson added an answer in Apple:
    Are you available to send a chapter for the Apple Academic Series on innovations- free to publish; response this week?

    Greetings , please forward to the groups. Abstract/title&/or outline
    this week,
    Best regards,

     Here is the new Apple Academic series invitational again vol 1-2
    priority now. https://lnkd.in/e25dufT
    Apple : ​cnourani@appleacademicpress.com

    Kwamina Ewur Banson · University of Adelaide

    Is it a new Journal?

  • How can the radial stiffness of a hollow cylinder be estimated based on thickness and Youngs Modulus?

    How can the radial stiffness of a hollow cylinder be estimated based on thickness and youngs modulus?

    Jacob Ohrvik-Stott · University of Melbourne

    I could have been more specific, apologies. I wish to design a cylinder to give a certain radial stiffness, with my design variable being the thickness. As the cylinder is a stent, it isnt subject to any internal pressure like a pipe, so i suppose the internal pressure could be taken as atmospheric. I know the material i wish to use and thus I have information such as the Young's modulus and intensive properties available to me 

  • Why is Tyloxapol preferred instead of tween 80 for mycobacteria?
    I want to grow Mtb for metabolic studies. In some stress conditions people had used Tyloxapol instead of tween 80. Kindly elaborate the main reason behind it and provide and cite a reference, if possible.
    Kathryn Sydney Doornbos · University of Alabama at Birmingham

    No one has yet noted that Mtb can use Tween-80 as a carbon source. This is obviously problematic in carbon-restricted/metabolomics experiments but can also modify the transcriptome of the bugs making modified growth phenotypes tricky to dissect. This is not a problem when using tyloxapol as the detergent.

  • Madhurima Saha added an answer in Gene Sequencing:
    How can I preserve DNA samples for long time at room temperature for shipment purpose?

    Dear colleagues,

    I would like send  DNA samples for sequencing to company outside my stay country for gene sequencing service. The company that will do the sequence service requested me to send the samples in room temperature; kindly supply me your experiences for preserving DNA samples in room temperature for minim one week interval.

    Your sincerely

  • What software is good in the FTIR and Raman spectra analysis ?

    I have FTIR  and Raman spectra and want to analyze these spectra and make peaks deconvolution.

    Christopher Bruce Riley · Massey University

    I agree GRAMS is a decent program, but you may also want to look at The Unscrambler by Camo. Depends on whether you are model building or straight identification of compounds. We do the former and do much of analysis using purpose written script in MatLab after using GRAMS to preprocess spectra.

  • Eric B. J. Harris added an answer in Polyesters:
    What would be the appropriate way to link the -COOH or -OH group to NH2 group?

    In our reaction we would like to attach an aromatic compound to the COOH or OH group of a polyester (PolyethyleneTerepathalate). Aromatic compound contains NH2 group and S=O group. What would be the most appropriate reaction to attach aromatic compound to the polyester?

    Eric B. J. Harris · Australian National University

    If you use thionyl chloride then you will have to add an additional base or use an excess of the amine. However as earlier mentioned it may exchange any free hydroxyl termini in the polymer to chlorides, potentially resulting in two modes of attachment that may complicate characterisation.

  • Chuka Emezue asked a question in Quantitative:
    Does anyone know of any standardized multiple-item instrument to assess exposure to police violence?

    Help needed finding a quantitative or preferably quantitative survey instrument, that has become acclaimed in assessing self-reported exposures in frequency, intensity and timing of any forms of police violence. Thank you!

  • Can you help me out with expression vector pET32a?

    I am trying to clone a gene in expression vector pET 32a but while doing so when I run a gel (0.8 agarose) with cut and uncut vector I got some weird result. The cut vector resulted in band of 4 kb approx instead of 5.9 kb. What could be the possible reason for this? I have use bam HI as restriction endonuclease since it have one one site in the vector, so ideally vector should give linear fragment of 6 kb aprox.

    Dejun Li · Chinese Academy of Tropical Agricultural Sciences

    Check it again. It is something wrong.

  • Matt Jans asked a question in Parental Consent:
    What are the major (and minor) surveys that interview teens?


    I'm survey methodologist for the California Health Interview Survey (CHIS) and I'm working on a research project on obtaining parental permission for our teen interview. As part of that project I'm trying to find surveys that interview teens, preferably on the phone, and preferably from RDD (random digit dial) samples.

    They can be large-scale or small-scale. They can be educational or health surveys, polls, etc. (topic isn't important). 

    Study qualities I'm seeking:

    1) Interview teens/adolescents of any age under 18

    2) Conducted by phone (at least partly). All things considered, surveys in other modes (e.g., web-based or paper-and-pencil) may be helpful, so don't hesitate to suggest. But since our survey is a phone survey (RDD), that's the design I'm most interested in. 

    3) Require parent permission before talking to the teen.

    The rates I'm looking for:

    1) Parental permission rate
    2) Teen response rate or interview completion rate given parental consent

    I don't expect you'll send me these rates (unless you have them handy), but just the names of the surveys would be great. 

    I did a quick search in the J. of Adol. Res. and J. of Adol., but didn't see any review articles on this topic.

    I'm happy to share our research progress in return as it develops, but you can learn more about CHIS in the mean time here.


    Thanks in advance for your suggestions. 

  • Andrew Messing added an answer in Ancient History:
    The Ancient Roman view of women being always/permanently connected to their family and the difference to Ancient Greek practice. How do they differ?

    The Ancient Roman view of women being always/permanently connected to their family and the difference to Ancient Greek practice. How do they differ? And why the Greeks seem not to have the same limits and constraints as do the Ancient Romans? And what is the best secondary literature that deals with this topic?

    Andrew Messing · Harvard University

    Totally forgot to include one of the books I got off of my shelves for recommendation:

    Grubbs' Women and the Law in the Roman Empire: A Sourcebook on Marriage, Divorce and Widowhood

  • Zelalem Mekonnen asked a question in HDF5:
    Is there any tool that can easily batch import latest HDF5 files and allow to conduct some level of analysis more than just visualization?

    Hi, I am looking for a tool to batch import HDF5 files from GPM and do zonal statistics and some mapping. Any suggestions ? The HDF5 is version 1.8.2 so is not recognized by the Version of IDL I have and many other tools I tried.

  • Abid Ali added an answer in AHP:
    Can any one help me to understand the Analytical Network Process as a multicriteria decision making method?

    I understand well AHP(Analytical Hierarchy Process) method, i know that the first of AHP is like ANP but i am confused in the last step to measure the weight of each attribute. I see researches but it didn't illustrate how the last result is reached. 
    Can any one help me to understand ANP(Analytical Network Process) steps as a multicriteria decision making method?

    Abid Ali · Northern University

    In AHP we use a hierarchical approach to model relative preference and in case of ANP we use Network approach to model the relative preference. In later case , the precision of relative preferences increases by checking each element with respect to other in network.

  • Which paradigm(s) is(are) the most suitable for assessing the economy-environment relationship?

    Given the existence of different schools of thought within social science-at times complementary and at times contradictory-the debate over the way in which this relationship should be conceptualized and analyzed is a hotly contested one.

    Nathan Weatherdon · Nathan Translates

    Since the debate on warming is heating up here, let's see what the rocket scientists have to say about the matter.

    "NASA, NOAA Find 2014 Warmest Year in Modern Record"


    I would take the work of the rocket scientists on the matter over just about anyone.

    As for arctic ice coverage, 2014 was the second lowest coverage on record, after 2012: http://www.arctic.noaa.gov/reportcard/sea_ice.html

    Not very consistent with the picture that things have been cooling since 1998.

    FYI, winters trending cooler in Europe is consistent with the fear of reduced salinity (from ice melting) leading to less mixing and a reduction in the Gulf Stream. It's a horror story scenario for Europe and I hope to hell they are wrong.

  • Mahmood Y Bilal added an answer in Competent Cells:
    How to Amplify a 15kb PCR product?

    I am trying to introduce two point mutations in a 15 kb lentiviral vector using Q5 site directed mutagenesis kit from NEB. I am using a amplification time of 10 min for 30 cycles. I performed the DpnI digestion to get rid of the template Sequence before transformation of PCR products into Stbl3 competent cells. Although good number of colonies were obtained but on screening of around 12 colonies, I could not get the desired mutation. Please share your experiences. 

    Mahmood Y Bilal · University of Iowa


    What is the bacterial source of your lentiviral vector? The template should not be purified from methylation deficient strains, otherwise you will get too much background colonies due to DpnI indigestion. If you are unsure, you may want to retransform your plasmid into DH5a (sublconing) strains, purify, then perform your mutagensis protocol. I've found that sometimes re-mutating DNA coming from XL-10 Gold gives too much background (perhaps low methylation?), and so sublconing back into DH5a-subcloning helps alot with getting rid of background.

    Hope this helps


  • Do all fluorescent molecules show some level of change with solvent polarity?


    I am currently studying some fluorophores and wanted to check that they don't show solvent dependency. When I change the solvent there is not a change in absorption/fluorescent spectrum by eye but there are changes picked up by spectroscopy.

    I have attached the spectra and the solvent details are on the plot.

    So my question is, would you consider this molecule's spectroscopy to be unaffected by solvent polarity or would you consider it to be polarity dependent?


    Ali Ameen Abd Ali · Monash University (Australia)

    The spectra look the same in all solvents. However, there is a "solvatochromic shift" which is happening if you change the solvent for the fluorescent dye. Sometimes you might see a 10nm difference in the wavelength (absorption lambda) and it is still normal. For further details please refer to one of the most wonderful book in this area:

    Principles of Fluorescence Spectroscopy  by Lakowicz. 

  • How can I design a standard curve for methylation detection by methylight real time PCR?

    I bought a 100% methylated human control DNA(bisulfite converted) 10 ng/μl & unmethylated human control DNA (bisulfite converted) 10 ng/μl  (EpiTect PCR Control DNA Set, QIAGEN). I don't know if i should use only the 100% methylated human control DNA in the standard curve or both of them.

    In standard curve design, should i use both primers& probes of the reference gene and the gene of interest or only of the reference gene? If i use the reference gene only, how can i get the  value of the gene of interest used in the formula:

    [(gene/ALU)sample/(gene/ALU) CpGenome universal methylated DNA]*100 

    Knowing  that i use probes labeled by different fluorescence dyes(FAM& VEC) for the reference and target genes respectively.

    Daniel J Weisenberger · University of Southern California

    Please read the attached PDF file. This should have a complete protocol. Please also let me know if you need anything else.


  • Andrew Rypel added an answer in Otolith:
    Is it imperative to back-calculate the age of fish even if you have sufficient samples?

    I'm working on age of snapper using otolith, as I came across some articles some workers back-calculate and others did not.

    Andrew Rypel · Wisconsin Department of Natural Resources and Center for Limnology, University of Wisconsin-Madison

    No, in fact I would suggest the simple length-at-observed age observations would be superior to back-calculations. One problem with back-calculations is that it over-emphasizes older fish because they will have more back-calculated lengths at ages. This can be handled statistically using mixed effects models, but these models are inherently more complex and harder to explain to non-statistical persons. Another problem with back-calcs relates to issues arising from Lee's and Reverse Lee's phenomenon (not fixed by using observed ages, but effect potentially lessened). So, bottom line is don't feel the need to back-calculate if you have a good sample size of observed lengths at age.

  • Drew Coe added an answer in Channels:
    Does anyone know about channel Sinuosity Index Measurement?

    What should be the minimum/ideal reach length for SI calculation of any sample basin? Rosgen (1996) suggested taking 20 to 40 time of bankfull width of the study reach; this may be too short to examine planform characteristics such as sinuosity.

    We can find the huge variation between reach scales SI as suggested by Rosgen and long reach scale SI calculation.

    Then, what should be followed for better result?

    Drew Coe · CAL FIRE

    You have some flexibility in how you define your reach or reaches.  See if there are systematic changes in sinuosity based on changes in valley slope or confinement, sediment supply, discharge, or riparian vegetation.  Have attached a couple of papers that might be helpful.

  • Philip Spear asked a question in Imaris:
    How can I flatten 3D image data?

    I'm trying to perform PIV analysis to examine cell migration. The problem is that the tissues (neural tube) is moving in 3D, preventing easy analysis.

    I want to look at how cells are moving in relation to each other rather than in 3D space.

    See the example movie: the neural tube is curling, pulling the outer cells with it. I want to see how those cells are moving on their own.

    I think the easiest way to do this might be to generate a 3D image of the embryo (see second movie) and then use this to flatten out the actual data (first movie), then perform PIV analysis on the resulting files using PIVlab.

    The issue is that I have no idea how to use the generated surface data (second movie) to flatten out the first data set.

    I'm using Imaris (7.4.2) and matlab (2013b). I haven't found a function in Image J or fiji that can accomplish this, though I haven't extensively looked.