Q&A

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  • Gelatin concentration in Zymography ?

    What would be the optimum con. of gelatin in gelatin zymography for observing clear MMP-9 activity. 

  • Omar Sabbagh added an answer in 3D Printing:
    What software/tools are you using/aware of to assist in the decision making for choosing how to manufacture (particularly metal) components?

    Component manufacturing route selection tools 

    What software or other tools are you using/aware of (commercially available or otherwise) to assist in the decision making for choosing how to manufacture (particularly metal) components ? I'd like to find a methodical way to identify the technically most appropriate but also most cost effective method (e.g. considering part size, tolerance specifications, material/performance requirements etc. etc.). I'd like to be able to consider more recent approaches such as :

    3D Metal Printing (Laser Sintering or Electron Beam melting)

    Metal Injection Moulding (MIM)

    Metal Die Casting / Investment Casting (potentially using 3D printing to create IC patterns to avoid high tooling cost)

    Traditional CNC Machining

    Sheet Metal fabrication

    Any thoughts ?

    Omar Sabbagh · National University of Malaysia

    I think , first you have to perform the experiments for all materials and augment the results , after that you can use Mini Tab statistical software in order to find the mean experimental value with lowest deviation comparing with the other results from other implemented methods

  • What is the basis for practical elimination of an accident sequence for nuclear power plants?

    Is it the frequency of occurrence, DiD implementation, provision of safety systems

    Roland Iosif Moraru · University of Petrosani

    Accidents can not be "eliminated" in real-world practice. There is no such thing as "zero risk". We only try to reduce the probability of occurrence.

    Various means (both technical and organizational) are employed to this purpose, but all of them are based on proper risk assessment.

  • Narasim Ramesh added an answer in Randomized:
    How to calculate P(Y < X), when X and Y are not independent random variables?

    Variables calculations.

    Narasim Ramesh · Sri Jagadguru Chandrasekaranathaswamiji Institute of Technology

    Please see if attached pdf  with a trivial example is useful.

    Cheers

  • Is there a way to extinguish or reduce the underground coal mine fires with the help of remote sensing or geological mapping?

    Underground coal mine fire is a major problem faced by many countries. Not only does it reduce the amount of fossil fuel but also adds on to the risk of land subsidence in the area. So, is there any measures that can be taken to reduce or extinguish the coal mine fires so that we can save coal for future uses?

    Roland Iosif Moraru · University of Petrosani

    Remote sensing is extremely useful for early detection of underground coal mine fires (spontaneous combustions). Detecting carbon monoxide and other combustion products one can determine fire indexes (Graham, Tricket-Jones, Willet etc) and based on adequate interpretation the heating processes can be mitigated in early stages.

  • Aline Villarrea asked a question in Zeolites:
    How do you perform zeolite steaming?

    I want to put a flow of high temperature steam through a zeolite, which can be the experimental process? 

  • Can anyone suggest a method for innovation in entrepreneurship?

    I read some innovation methods in technology, but in management, I think there are some also.

    Louis Augustin-jean · The Hong Kong Polytechnic University

    I feel I need to answer David Francis. First, I did not say that entrepreneurship and innovation are conjoint twins. Joseph Schumpeter did. Of course, it is possible to disagree with Schumpeter but then, it needs to know precisely what he was saying -- especially since he is still, 80 years after the publication of his book, the main reference for that topic. Here, the question of vocabulary and definition are crucial. And "innovation" should not be confused with "technological innovation" and with "invention".I explain.

    For Schumpeter, innovation is multiform and takes one or more of the five following components: (1) The introduction of a new good; (2) the introduction of a new method of production; (3) the opening of a new market; (4) the conquest of a new source of supply; and (5) the introduction of a new organization to any industry (I copy this sentence from my article in the Canadian Journal of Development Studies). Based on that, it is difficult to argue that Ms A, who bought stocks from bankrupt firms to sell them on the internet is not an innovator. To me, her business fits with at least the third characteristics of innovation, as stated by Schumpeter.

    Similarly, innovation and invention are different. Is Mr  B, who invented a new type of radar, an innovator? He is an inventor, for sure.. But it seems to me that he is not really an innovator, in the sense given by Schumpeter. An invention becomes an innovation when it finds its way in the market. If it fails to do that, it remains at the invention stage. In any case, the figures provided by David are just here to blur the issues, because you can be a successful entrepreneur (and make lots of money) or an unsuccessful one (and rent a flat), but in both cases, you are an entrepreneur. The issue here are more fundamental.

    Of course, what I presented is the vision of Schumpeter and it is quite possible to criticize it. Others (including myself) have done it. I would have no problem en engage in a debate on that topic -- hope you read my article first!

  • Why is UV solar radiation measured only as global radiation?

    I'm studing the correlations between solar radiation (global, direct and diffuse) and UV solar radiation.  

    Germán Salazar · INENCO (Argentina)

    Hello Sebastian Michael:

    even under clear-sky conditions?

  • Daniel J Levendowski added an answer in Laptop:
    Are there any PC or laptop based polysomnography kits for research purposes available in the market?

    I'm looking to undertake research in this area, any guidance is appreciated

    Daniel J Levendowski · Independent Researcher

    Anand:  I agree with Thorsten that Sensormedics is a good product if you need to diagnose sleep disordered breathing.  

    We have a number of hospitals in the UK using our Sleep Profiler device to monitor sleep in the ICU.

    Please go to www.advancedbrainmonitoring.com and click on Sleep Medicine.  We just posted a webinar conducted last week....

  • Stephany Corrêa added an answer in ChIP Assay:
    How does normalization occur in ChIP-qPCR if everything relies on fixed volume rather than fixed amount?

    I have a question regarding ChIP-qPCR normalization. I am very familiar with qPCR and gene expression analyses but very new to chromatin immunoprecipitation qPCR. When performing gene expression, the variation in RNA extraction from sample to sample is corrected by total RNA quantification to ensure an equal amount is loaded in each RT reaction, followed by normalization by the use of housekeeping genes at the qPCR level.
    For ChIP, I didn't find any details regarding correction of the input amount of DNA in the qPCR reaction. From the numerous protocol that I red, it seems like people don't care and perform their IP on a fixed volume of ChIP DNA (no matter what the total DNA quantity as judged by spectrophotometer) and/or use a fixed volume of purified DNA at the qPCR level. As the preferred method of analysis is to simply process the raw Ct value and expressed it as a % input followed by comparison across multiple experimental conditions, I am wondering how one can account for the variability from sample to sample in such a long protocol without virtually any normalization?
    Can anyone with strong hands-on experience with ChIP-qPCR comment on this please?

    Stephany Corrêa · Brazilian National Cancer Institute

     I also had the same result with - ptn - dna quantification along with %input method. I think the important step is to be sure about the amount of Dna (assuming an IP with the same quantification of starting material) in your Pcr.

  • Zhao Dongxing added an answer in Plasmonics:
    Why does the dark plasmons can be excited by a dipole source?

    I know that the dark plasmons cannot be excited by a plane wave, but to its nearly zero net dipole moment. But why can it be excited by a dipole emitter?

    Zhao Dongxing · Peking University

    Thank your for your answer. You mean that the excitation way of the modes is limited to its symmetry. I think it is quite resonable. Can we find some mathematical foundation for this explanation? 

  • James F Peters added an answer in 2D & 3D:
    What are applications of convex sets and the notion of convexity in mathematics and science?

    In a Euclidean space, an object S is convex, provided the line segment connecting each pair of points in S is also within S. Examples of convex objects in the attached image include convex polyhedra and tilings containing convex polygons.  Can other tilings containing convex shapes be found?

    Solid cubes (not hollow cubes or cubes with dents in them) are also examples of convex objects.   However, crescent shapes (a partial point-filled circular disk) are non-convex .   To test the non-convexity of a crescent, select a pair of points along the inner edge of a crescent and draw a line segment between the selected points.   Except for the end points, the remaining points in the line segment will not be within the crescent.  Except for the 3rd and 5th cubes, the cubes in the attached images are convex objects (all points bounded by walls of each cube are contained in the cube).

    http://en.wikipedia.org/wiki/Cube

    From left-to-right, the cresent shapes are shown in the attached image are non-convex: Nakhchivan, Azerbaijan dome, Taj Mahal, flags of Algeria, Tunisia, Turkey and Turkmenistan. For more examples of crescent objects, see

    http://en.wikipedia.org/wiki/Crescent

    Can you identify other crescent shapes in art or in architecture that are non-convex?  Going further, can you identify other non-convex objects in art or in architecture?

    The notion of convexity leads to many practical applications such as optimization

    http://www.lix.polytechnique.fr/~liberti/phdthesis.pdf

    image processing

    http://signal.ee.bilkent.edu.tr/Theses/kkoseThesis.pdf

    and antismatroids, useful in discrete event simulation, AI planning, and feasible states of learners:
    http://en.wikipedia.org/wiki/Antimatroid
    In science, convex sets provide a basis solving optimization and duality problems, e.g.,
    http://ocw.mit.edu/courses/electrical-engineering-and-computer-science/6-253-convex-analysis-and-optimization-spring-2012/Syllabus/MIT6_253S12_summary.pdf
    Convex sets also appear in solving force closure in robotic grasping, e.g.,

    https://www.researchgate.net/publication/221105156_Projection_on_Convex_Set_and_Its_Application_in_Testing_Force_Closure_Properties_of_Robotic_Grasping

    Recent work has been done on decomposing 2D and 3D models into their approximate convex components. See, for example, the attached decompositions from page 6 in
    J.-M. Lien, Approximate convex decomposition and its applications, Ph.D. thesis, Texas A&M University, 2006:

    http://cs.gmu.edu/~jmlien/research/app-cd/lien-dissertation.pdf

    There are many other applications of the notion of convexity in Science. Can you suggest any?

    James F Peters · University of Manitoba

    Dear @George and @Demetris,

    Yes, many thanks for the suggestions about mathematical finance and econometrics.    See, for example,

    E. Hazan, Efficient Algorithms for Online Convex Optimization and Their Applications, Ph.D. thesis, Princeton University, 2006:

    http://ie.technion.ac.il/~ehazan/papers/thesis.pdf

    See Chapter 3, starting on page 39, experiments with portfolio management.

  • Dipesh Rupakheti added an answer in Ozone:
    Do we need (at least) a year of Ozone data in order to calculate AOT40?

    Do we need (at least) a year of Ozone data in order to calculate AOT40?

    Dipesh Rupakheti · Chinese Academy of Sciences

    Thanks alot for the response Prof. Kim and A. Pelliccioni .

  • Rolando Garcia-Milian added an answer in NCBI:
    Can anyone inform me how to get the CDS from partial gene sequence?

    I have isolate the MtDNA from different Noctuidae moths. From the MtDNA i sequenced the COI gene (Cytochrome oxidase sub I). When i submit the sequence to NCBI,C they asked to submit the Coding region (CDS features). So i need to submit the CDS along with the sequence.

    Rolando Garcia-Milian · Yale University

    Dear Siva,

    You could start by entering your sequence into GENSCAN http://genes.mit.edu/GENSCAN.html - this is a great annotation tool.

    "GENSCAN is a general-purpose gene identification program which analyzes genomic DNA sequences from a variety of organisms including human, other vertebrates, invertebrates and plants"

    "For each sequence, the program determines the most likely "parse" (gene structure) under a probabilistic model of the gene structural and compositional properties of the genomic DNA for the given organism. This set of exons/genes is then printed to an output file (the text output) together with the corresponding predicted peptide sequences"

    Good luck!

  • After injecting 99mTc-MIBI how much activity (MBq/ml or mCi/ml) is absorbed by a typical myocardium at peak absorption?

    As far as I know, within several min after injection activity absorption would be in the highest value possible. What is "the" value in (Mbq/ml or mCi/ml) ?

    Farshid Salehzahi · ACT Health Directorate

    The values that you ae referring to are more likely to be investigated in a PET/CT study related to establishing SUV.  I would imagine that you may be able to generate the same in conventional Nuclear Medicine, using the same methodology, if of any use to you. 

    There is not a global set of values available, for SUV in a region of interest, because it depends on several patient related factors as well as the activity injected.  The answer to your specific question will then be similar to that of SUV given above, in my opinion.

    There are several guidelines in the EANM website which may be helpful for your inetrest.

  • Can we use heavy metal concentration ref. values like UCC for sediments of all the regions globally?

    During calculation of Heavy metal contamination levels of  a region through its sediments, can we take base line values like UCC for calculation? If it is so, we may have a chance to miss the assessment of real contamination level of a region. How will you clarify this issue?

    Benamar Mohammed El Amine · Saad Dahlab University

    You find an article that I published in 1999, you may be helpful:

    https://www.researchgate.net/publication/258848016_Assessment_of_the_state_of_pollution_by_heavy_metals_in_the_surficial_sediments_of_Algiers_Bay#share

  • Evangelina Sánchez added an answer in SYBR Green:
    Can an ABI 7300 Real Time PCR system do high resolution melting?

    My team and I want to do HRM (high resolution melting) for analyse change between uracile and citokine by construction of dissociation curve in ABI (Applied Biosystem) 7300 real time PCR system.

    Dissociation curve constructed by ABI 7300 system is the same quality like HRM dissociation curve constructed by a more new version of real time PCR system?

    Can I use with ABI 7300 system the LCG Sybr Green?

    Can I use ABI 7300 system the Master Mix LCG Sybr Green?

    Can I use with ABI 7300 system the software to analyse the HRM?

    Evangelina Sánchez · Venezuelan Institute for Scientific Research

    Thanks a lot for your answers (Banyar Than Naing and Sergio Espinola).

    I understand very well is not possible to do HRM in my ABI 7300 system, because do not use fluorophores and software for this test.

    Well may be in a future we buy an advanced RT-qPCR system like AB 7500 or Fast System.

    Evangelina

  • Are you use Statics Package for Social Sciences (SPSS) in your research?
    Today, there are so many challenges faced by the researcher when they are doing research. SPSS is a software for tabulation, graph and so many function you can do here. You just download this software from the net and it is very simple to run or function
    Han Ping Fung · Hewlett-Packard

    Hi both,

    Yes SPSS is a popular software for social science research especially for quantitative analysis albeit SPSS also include Text Analytics module which is meant for qualitative analysis.  However, many universities also teach beyond SPSS base module to include more advanced analysis module like AMOS  and Path Analysis / Partial Least Squares.

    If you want to know what quantitative & qualitative analysis tools  used in social science research, you can refer to this article of mine:

    https://www.researchgate.net/publication/256463237_Effects_of_Information_and_Communication_Technology_%28ICT%29_on_Social_Science_Research

    Agreed also doctorate candidates should expose to other quantitative, qualitative & mixed method research methods beyond their comfort zone e.g. only quantitative.  I find that knowing beyond one's core research method will help the person more prepare for the PhD proposal defense & viva defense (some examiners might purposely question the PhD student why s/he didn't consider other research methods & why the research objective set in such etc.).  Moreover, knowing other research methods also can help the PhD holder to provide a balanced view of what kind of research method to adopt in solving a particular issue and provide the right guidance to his / her students who are embarking on new research.  I also find some students' preference on which research method is influenced by his or her lecturer / supervisor who might only skilled in one research method.

  • Is a theorem in mathematics discovered or invented?
    For a Platonist, a theorem is a provable assertion about something that is external to us (written on the wall of a cave, as it were) and which is discovered by us. Otherwise, for a non-Platonist, a theorem is a provable assertion that is invented by us concerning one or more relationships that we have put together. The relationships themselves can either be as a result of our experience, observations of natural phenomena, experiments in attempting to corroborate some hypothesis, perception of external events such as the time of sunrise or sunset (a posteriori) or can be purely abstract as a result of our understanding of definitions such as descriptively near sets, relations such as a traditional proximity relation, axioms such as those from Efremovic or Leader or Naimpally (a priori).
    James F Peters · University of Manitoba

    @Geng Ouyang: ...a theorem is a compound integrated by concepts (maybe mathematical things) and their relationships (logics). 

    The late mathematician P. Erdős has often been associated with the observation that "a mathematician is a machine for converting coffee into theorems" (e.g., Hoffman 1998, p. 7). However, this characterization appears to be due to his friend, Alfred Rényi (MacTutor, Malkevitch). This thought was developed further by Erdős' friend and Hungarian mathematician Paul Turán, who suggested that weak coffee was suitable "only for lemmas" (MacTutor, Malkevitch).

    http://mathworld.wolfram.com/Theorem.html

    In simple terms, a theorem is a statement that requires proof.    And, yes, a theorem can be a statement that combines concepts and one or more relationships.    For example, let A be a subset of real linear space E, int A (interior of points of A), bdy A (boundary points of A), cl A (closure of A).    Then

    Theorem   Cl A not empty implies int A union bdy A not empty.

  • Alexander Cao asked a question in Extension:
    How to concentrate large volume of protein?

    I'm working on a protein that is 75kDa in size. My dialysate containing the protein is extensively diluted and the volume is fairly large. What's the best way to concentrate my protein besides from Amicon?

  • How much dispersion on Ct values can be tolerated for a housekeeping gene?

    I have values ranging from 19 to 22 among three experimental groups. Thanks.

    Stephany Corrêa · Brazilian National Cancer Institute

    Hello Augusto. I also agree that your range is too high for realtime Pcr. I would accept a maximum of 1 Ct in housekeeping gene, specially if your experimental group is a biological replicate. 1 Ct = 2^1=2 fold change (the minimum considered for real time). So, if you have this 1Ct range among housekepping I would just consider as differentially expressed a fold change higher than 2x. E.g 10x. 

  • Flow Cytometry on Fresh Samples

    Hello -- I'm looking to develop a flow panel for human PBMCs and PMNs that utilizes fresh samples. We fix first and then stain with antibodies. If my cells are fixed and sitting at 4*C, how many days could that be left before staining and flow? Just because the timing of clinical samples is so difficult.

    Bashir Alsiddig Yousef · China Pharmaceutical University

    Hello Meaghan,

    It is totally depend on what test u want to carry? As some tests are affected with time such as (ROS), while others not. And I agree with Salman, when I have fresh sample I have better result than that stored in 4C for long time.

    Good luck

  • James Garry added an answer in Cryogenics:
    Can someone suggest some name of commercial 50 ohm cryogenic, vacuum feedthrough company?

    I want a 50 ohm coaxial, vacuum feedthrough capable of operating at 4 K . It should be non- magnetic too if possible? Please suggest any company that provide it commercially....

    James Garry · Red Core Consulting ltd.

    If the feedthrough is to survive 4K then you might need advice - I'd be inclined to go for a gold seal, rather than a conf-flat flange. But frankly, I've never seen a demountable cryogenic flange that was also UHV rated.

    Try Kurt Lesker or MDC Caburn for detailed information.

    If I had to tackle this I would probably soft-solder the feed-through in place with Woods metal (stainless steel for the vessel presumably) to ensure a tight seal.

  • Diego Kietzmann added an answer in Paleontology:
    Can anybody help with identification of "mikroproblematium" from the K/T boundary?

    This "things" come from the K/T boundary interval in Poland. They are 0.2-0.8mm in size. All have brown color, are polished and usually have oval shape (second photo). Some of them are elongated (first and last photo). Additionally, they have a "nipple-like" structure at one side (compare right side of specimen on first and second photo).
    These things are quite common in the boundary interval and I simply don’t know what it is. Waiting for your suggestions. Thank you in advance.

    Diego Kietzmann · University of Buenos Aires

    Dear Mike,
    Do you have by chance a pdf copy of the paper you mention? I am interested in bibliography on coprolites.
    Best wishes.
    Diego.

  • Nagaraja Suryadevara added an answer in PCR:
    Can anyone help solve a problem I've been having with PCR?

    I used from High Fidelity PCR
    Enzyme Mix (thermo scientific:product number k0191) for PCR performing.
    My PCR product is 3131bp from HEK-293 cell line DNA.
    On the first day, I performed PCR test but reach to weak specific band. There are not exist eny extra band and not exist primer dimer.
    Cycling protocol for PCR product:
    Initial Denaturation: 95˚C for 3 min
    Denaturation: 95˚C -30 s
    Annealing: 55˚C for 30 s
    Extension 72 ˚C for 3.30 min.
    Final Extension 72 ˚C for12 min
    Number of cycle: 30
    Component of any reaction:
    10X High Fidelity PCR buffer with 15 mM MgCl2…….5ul
    dNTP Mix (10mM)……………………………….……..1 ul
    Forward primer (10pm)……………………..…….…...2.5 ul
    Revers primer (10pm)…………………………...……..2.5 ul
    Template DNA (46ngr/1ul)……………………………….3 ul (138 ngr/50ul reaction)
    High Fidelity PCR Enzyme Mix……………………..…0.6 ul
    Water, nuclease-free……………………………….….35.4 ul
    On the second day, I performed PCR with same cycling protocol but I used from 7ul (322 ngr/50ul reaction) of Template DNA in this reaction (insted of 3ul) for reach to stronger band. No Bands Observed.
    Can you help me?

    Nagaraja Suryadevara · Mahsa University College

    Have got solution ? if yes post it. Hope so optimization of Mgcl2 will give better result

  • Vasiliy Triandafilidi added an answer in Chaos:
    How can I calculate Maximal Lyapunov exponent in a molecular dynamics simulation?

    I want know how to calculate the Maximal Lyapunov Exponent of a Hamiltonian system numerically. Then, yes, I want calculate the Maximal Lyapunov exponent of particles trajectories.

    I'm using this paper as reference: http://chaos.utexas.edu/manuscripts/1085774778.pdf. The Maximal Lyapunov Exponent (MLE) is proportional to the logarithm of phase space separation. Then, for a chaotic system, we should have an straight line when plot the MLE vs time.

    I found something like a log curve with saturation at MLE ~0.2 and a little 'noise' (figure). I investigated the behavior of this system with Poincaré sections, which shows chaos.

    The behavior that I found in the figure, is due some computational problem, like finite size effects or time scale? How can I interpret this behavior?

    ps. I'm limiting the separation of the particles do 10^-4 and starting the test system (a copy, except for a particle with a shifted position by 10^-2) after reference system relaxation.

    Vasiliy Triandafilidi · University of British Columbia - Vancouver

    Here is the reference where you may find all the answers you need

  • What is the origin and how do we explain the growth of mathematical concepts?

    A.N. Whitehead contended that the science of pure mathematics is the most original creation of the human spirit (Science and the modern world. 1948).

    Number and Geometry appear to be earliest mathematical concepts (see the attached diagram, where N = number, G = geometry). The concept of number has had a huge influence in astronomy, commerce and religion as well as other disciplines.   Geometry has had an enormous influence on agriculture (layout of fields, design of buildings, land surveys, measure, metrics) and philosophy (view of space, dimensionality, permanence vs. impermanence of form, continuity, betweeness, boundedness). Such concepts gradually emerged from a number of cultures in the Middle East, Greece, and in Asia (especially, India and China).  In his history of geometrical methods, J.L. Coolidge, 1940, observed that many mathematicians believed that analytic geometry sprang from the head of Descartes as did Athene from that of Zeus (p. 5).   The attached chart showing the influence of number and geometry on other subjects is incomplete (e.g., physics, chemistry, genetics, engineering, architecture are missing from the chart).

     

    The concept of a curve has its origin in antiquity and continues to contribute to growth of mathematics.  The attached chart traces the history of the concept of a curve (from R.L. Wilder, AMS talk, 1953).   The story of curvature can be traced back written records in Greece (geometry, Archimedes and others) and in Persia (algebra—Al-Jabr—from treatise by Muhammed ibn Musa al-Khwarizmi, 820 A.D., which originally meant restoration and completion).   See, e.g.:

     

     http://en.wikipedia.org/wiki/History_of_algebra and https://www.khanacademy.org/math/algebra/introduction-to- algebra/overview_hist_alg/v/origins-of-algebra

     

     

    Geog Cantor is credited with introducing the continuous curve concept.  The attached chart is incomplete and needs many more notes to make it more representative of what has happened since the introduction of geometry and algebra more than 20 centuries ago.   See, e.g.:

     

    http://www3.villanova.edu/maple/misc/history_of_curvature/k.htm and

    http://www.eecs.berkeley.edu/Pubs/TechRpts/2008/EECS-2008-103.pdf

     

    James F Peters · University of Manitoba

    @Milo Gardner: Number theory seems to define the 'ab initio' aspect of great ancient cultures.

    Yes, to a large extent.   In addition, our culture is defined by our preoccupation with symbolic reasoning (consider the growth of algebra from its beginnings in the work of Omar Khayyam to its current stages, where we now have pure algebraic structures such as groupoids, rings and fields and its marriage with geometry in algebraic geometry).

    http://mathworld.wolfram.com/AlgebraicGeometry.html