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  • Qiang Zhang asked a question in Gene Prediction:
    How can I determine the number

    My investigation is focused on a gene from Arabidopsis thaliana. The gene is predicted to have four alternative splicing. Two of them are very similar, they are different with each other with one short intron. Now I want to clone the two similar alternative splicing. But I did only get the short one. Now I want to know how I can clone the longer one  and how I can confirm whether the longer one does exist in the Arabidopsis or not?

    Thank you!

  • Is it possible to present a PhD thesis without an advisor?
    I am about to start some independent work, without an academic advisor. The analysis I made so far seems positive. The contribution, should it work in practice, would be interesting but not astonishing.

    I am asking your counseling about how would I present the final work in order to get the PhD (or DEng, or whatever) degree.

    Are universities open to this kind of endeavour? Or would I be required to go through the complete process (credits, advisor, etc)?

    Another concern of mine is how and where I can publish the paper when I am not affiliated to a particular academic institution?

    Thank you very much in advance for any assistance.
    Tomasz J Kotarba · SYSTEM7

    @Michael:

    From my own observations and my conversations with friends (supplemented with countless articles and discussions one can find in the press and online), I do believe that the texts I quoted are very accurate in depicting what the academic system has become. I do understand that you may disagree with the Economist or me and I do respect your right to have your own opinion.

    I think it is always good to concentrate on facts and numbers. This is what the article in the Economist does. The number of new PhDs produces by the system in the past and now versus the number of professorships (or lectureships) is a fact. The emergence of the postdoc phenomenon and how it influenced career prospects of young academics (again, some numbers can be found there) is also a fact. The numbers describing career prospects and earnings of PhDs versus MA/Ss and others outside of academia are a fact too (and let us not even talk about the opportunity cost of one's doing a PhD instead of joining the workforce years earlier). These are not hyperboles.

    As for what you wrote about the Ponzi or pyramid scheme, well, the fact is that university PR departments (and many senior academics) do paint a rather rosy picture of one's career prospects and life after one earns a PhD and, as you yourself have said earlier, universities take on PhD candidates for just one reason - to make money (tuition fees, prestige, number of publications and how it all translates to money from research contracts and grants (the research mostly done by PhD candidates and underpaid postdocs (both categories often called 'apprentices' by senior academics))). Combine this with the hierarchical structure of the academic world and it all sounds just like a pyramid scheme (according to what you said in your last message).

    This is all OT. I am afraid we have hijacked this discussion. Apologies to all who have come here to find some information about what the OP asked about.

  • Nader Aghakhani added an answer in Stomach:
    Does lady's finger (Okra, Bamia, Abelmoschus esculentus) help in controlling diabetes?

    In one news paper I came across a news article regarding controlling diabetes by lady's finger. The methodology is described below. Cut a lady's finger vertically. Remove all inner materials seeds etc. and put all scrapped materials and outer layer in about 250 ml water. Store it overnight and use the filtered water in empty stomach. I myself practised it and got good result. Can anybody suggest how these inner materials react with body sugar? or is it a natural source which has similarity with insulin.

    Nader Aghakhani · Urmia University of Medical Sciences

    Dear Dr. Sahoo

    I sent a better address for the article.

    Volume : 3, Issue : 6, June - 2014 Effectiveness of Lady’s Finger Juice in the Control of Blood Sugar Among Type 2 Diabetes Mellitus Clients Aged 45–60 Years in Selected Areas of Mangalore Ms. Sarika Davis. , Mrs. Jennifer D Souza. - See more at: http://theglobaljournals.com/ijsr/articles.php?val=MzQ0MQ==&b1=497&k=125#sthash.Z2BzD3kI.dpuf

  • Where can I get prolog reference material?

    I am trying to develop a rule based machine translation system using prolog so I need prolog materials please help me.

    Nusra Jamaldeen · Rajarata University of Sri Lanka

    Tx madam

    i am translating from Tamil to Sinhala

  • What is the appropriate effect size calculation for Wilcoxon signed rank test (related samples)?

    I use nonparametric tests due to small groups and the absence of normal distribution. For Mann-Whitney U test I calculate the effect size by dividing U with the product of the two group sizes (as suggested by Ronán M. Conroy as well as others).

    How do I most appropriately calculate effect size for Wilcoxon signed rank test (related samples)? 

    I believe Cohen's d is not appropriate since it requires normal distribution and is based on means, hence the alternative effect size above for M-W U. Agree?

    Gloriam Guenzburger · State of California

    It has been a while since I worked with this, so I just relied on Google. This guy seems to have a good grasp of what is needed. I hope this helps.

    http://yatani.jp/teaching/doku.php?id=hcistats:wilcoxonsigned

  • Hu Pei asked a question in SSP:
    How to design the SSP primers of gene HLA-A*0201?

    I want to screen out the HLA-A*0201 petients through their peripheral blood by PCR-SSP,  however, I donot know how to design the primers, does anyone have some good suggstions?

  • How can I measure piezoelectric constant?

    I a higher constant always better?

    Dariush Montasserasadi · University of New Orleans

    Thanks every one

  • Ana Nora Alix Donaldson added an answer in SPSS:
    Is there any difference in formula when calculating Skewness manually and using SPSS software?

    When I calculate Skewness manually, i get that the value of Skewness is 1.26, but when I calculate in SPSS program, the value of Skewness is 0.000. What am i doing wrong in this calculation? Is there any correction in SPSS software for this value or is it something else?

    Mean = 6

    Median = 2

    Standard deviation = 3.16

    Hi Boban, thanks for your reply. The manual formula should be subtracting median instead of mode and also there should be a factor there. Look at this link, it will help: 

    http://growingknowing.com/GKStatsBookSkewness.php

  • What does a refugee need coming to a new country ( germany ) - concearning landscape architecture - the open space, ...

    it needs to provide security - over viewable, .... flexible, cheap......

  • Thu le asked a question in Garlic:
    Would you mind helping me with finding this full-text article " Characterization and effect of edible coatings on minimally processed garlic quality"?

    Hi everyone !, I am a new member of this page. I like garlic so much, so I am conducting some experiments on garlic. Would you mind helping me with finding this full-text article " Characterization and effect of edible coatings on minimally processed garlic quality" ?. Thank you so much !

  • Arnold Trehub added an answer in Cognitive Systems:
    Is Chalmers' so-called "hard problem" in consciousness real?

    In his 2014 book "Consciousness and the Brain: Deciphering How the Brain Codes Our Thoughts" Stanislas Dehaene wrote "Chalmers, a philosopher of the University of Arizona, is famous for introducing a distinction between the easy and the hard problems. The easy problem of consciousness, he argues, consists in explaining the many functions of the brain: how do we recognize a face, a word, or a landscape? How do we extract information form the senses and use it to guide our behavior? How do we generate sentences to describe what we feel?

    “Although all these questions are associated with consciousness,” Chalmers argues, “they all concern the objective mechanisms of the cognitive system, and consequently, we have every reason to expect that continued work in cognitive psychology and neuroscience will answer them. By contrast the hard problem is the “question of how physical processes in the brain give rise to subjective experience … the way things feel for the subject. When we see for example, we experience visual sensations, such as that of vivid blue. Or think of the ineffable sound of a distant oboe, the agony of an intense pain, the sparkle of happiness or the meditative quality of a moment lost in thought … It is these phenomena that poses the real mystery of the mind”."

    Stanislas Dehaene's opinion is "that Chalmers swapped the labels: it is the “easy” problem that is hard, while the “hard” problem just seems hard because it engages ill-defined intuitions. Once our intuition is educated by cognitive neuroscience and computer simulations, Chalmers’ “hard problem” will evaporate".

    Personally, I agree with Stanislas Dehaene's opinion.

    Arnold Trehub · University of Massachusetts Amherst

    Marc: Haven't you any comment on my reply to you: 'According to me a neural model should correspond to an identifiable neural network which should be shown by neuroimaging such as fMRI'?"

    My reply is that some of our most important scientific models are of physical entities that we are not able to observe directly but are, nevertheless, able to empirically validate by observing that their predicted effects actually occur.

  • Juan Marcos Sanz added an answer in MATLAB:
    Any suggestions about the implementation of Inverse Monte Carlo for estimation of tissue optical properties?

    Hallo everyone! Have you any experience about the implementation of inverse Monte Carlo algorithm for the simulation of photon transport through biological tissues and th estimation of optical properties (absorption, scattering and anisotropy coefficients)?

    I implemented the algorithm on Matlab, it works, but I have some doubts.

    Thank you in advance for you kind attention,

    Paola

    Juan Marcos Sanz · Textil Santanderina, S.A.

    Hi Paola,

    I'm not sure if this can help you:

    https://www.researchgate.net/publication/260996446_Development_of_a_Mueller_matrix_imaging_system_for_detecting_objects_embedded_in_turbid_media

    There are some recent studies in the bibliography section. Best wishes!

  • Shuvayan Brahmachary added an answer in JScript:
    How can I create a script to generate the meshing in Ansys?

    I want to create JScript macro for Ansys Meshing [Fluid Flow]. So, does anyone knows any meshing scripting guidline? I've already generated Workbench journal code to automatically carry out the process of fluid flow simulation with FLUENT. However, this journal coding in Workbench won't record the operations in geometry creation and mesh generation. So, I had to generate JScript code for the geometry and embedded into the journal code. So, if anybody have experience on this matter, please share it with us!

    Thank you very much for your help

    Shuvayan Brahmachary · Indian Institute of Technology Guwahati

    If you want to create mesh using ICEM-CFD then the scripting is very easy. Journal script in ANSYS Fluent is rather complex. It am not sure if it works while meshing as I couldn't do. It works for solver setting though, like you said. I suggest the use of ICEM-CFD for meshing as the scripting is very easy. Hope it helps.

  • What can be done to minimize the challenge of incessant radiology equipment breakdown in developing countries?

    The frequency of radiology equipment breakdown often with prolonged down-time in developing countries is quite worrisome, this in turn, adversely affects effective healthcare delivery to our patients in radiology. How best can this worrisome trend be reversed? Opinions needed from experts. Thank you 

    Jacqueline Gallet · University of Texas Southwestern Medical Center

    My first question to you is whether you are purchasing from a distributor, or from the manufacturer? Are you purchasing refurbished x-ray equipment or new? 

    X-ray equipment requires maintenance and a quality control program. Are you responsible for the maintenance, is there someone at your facility who was trained to maintain the equipment, or the vendor just installed and left with no discussion as to how to maintain should there be a problem. 

    First and foremost, there must be a quality control program, irrespective of the questions above. Two, you should only purchase from reputable vendors. Three, you should always insist on some form of training for the person designated as the service person for the medical institution. 

    If you could answer the questions above, there might be alternatives to the suggestions made.

    Jacqueline

  • Tom Robinson added an answer in Fluorophore:
    How do I interpret my time resolved decay data?

    I am using a Becker and Hickl Tau 130 TCSPC system to take some time resolved emission decays for CdSe quantum dots. I am using a 440 nm diode laser for excitation and I can operate at 3 rep rates (1MHz, 20MHz and 50 MHz). My quantum dots generally show an average lifetime of about 70ns  and therefore for capturing the whole decay profile (the signal to decay to the baseline), I chose my rep rate to be 1MHz (TAC range- 1000ns). 

    However, I am also interested in finding out about what is happening at earlier time scales, and therefore I tried to acquire the decay profiles at 20 and 50 MHz as well with the same number of time bins (4096) and I tried to superimpose the 3 decay profiles over each other(refer attached fig.) to make sure that they lie on each other, thus representing the same decay profile. However, I found out that they do not overlap over each other. Now, as far as my understanding goes, this could be due to 2 reasons:

    1. For higher rep rates, the signal is wrapping around and the photons with longer lifetimes than the TAC range+dead time are getting counted on the histogram and thus giving me a skewed decay profiles.

    2. As the rep rate increases, the time bin width decreases and therefore I am getting higher resolution with higher rep rate and thus overlap mismatch.

    I also tried the same experiment with Fluorescein dianion (lifetime--4.1ns) at 3 different rep rates (refer attached fig.) and I found out that the decay profiles very well overlap and thus I can rule out reason 2 mentioned above. I am thinking that in case of Fluorescein, most of the signal decays to the baseline in the first 40-50 ns after excitation (see fluorescein 20Mhz) and therefore there is no wrap around of signal, or in other words, there are almost no photons with lifetime greater than TAC+dead time to skew the decay profiles.

    Are my conclusions correct? 

    More importantly, is there a way to study the long living fluorophores at higher rep rates using TCSPC system? Thanks,

    Saurabh

    Tom Robinson · Max Planck Institute of Colloids and Interfaces

    Have you considered using the "Incomplete Multiexponentials" decay model in the options --> models in SPImage fitting software from B&H?

  • Rudolph E. Schild added an answer in Big Bang:
    How much does the Lithium problem affect our understanding of the Big bang theory?

    The observed Lithium abundance is in disagreement with the standard big bang model. What are the possible solutions to the problem?  How much the observations are reliable in this case? Is it possible to exist a method of destruction of Li that we don't considering or it is beyond standard model phenomenon?

    Rudolph E. Schild · Smithsonian Institution

    Not everybody thinks that the standard Lambda-CDM theory of cosmic structureformation is a good idea. Recent patches to the theory propose that the strongest signal in the COBE/WMAP/PLANCK background maps is baryonic accoustic oscillations, but nobody has the courage to ask, "If the baryons dominate structure formation scenario, what about turbulence in the baryons?" Indeed many find that the background overall obeys fractal mathematics and is turbulent in origin at z = 1100. See papers by Carl H. Gibson (UCSD), Sylos Labini (Rome), and Bershadskii (Tel Aviv).

    If that is true, and turbulence traces back to the era of atomic element formation, the standard assumption of a homogeneous Universe expanding in thermal equilibrium are in question, and in particular the Michael Turner and more recent calculations of thermal equilibrium elemant formation are questionable. For example, when the temperature of the hj-z universe was 10^7, local heating of a volume would produce atomic fusion with its very strong 10^12 temperature dependence. This would cause runaway fusion and solve the puzzle of the Spite minimum in atomic abundances, the fact that we do not find any Pop III stars at any redshift,  or anywhere in our Galaxy or Halo.

  • Walter Filho added an answer in Staining:
    Can anyone help me in the diagnosis of Cryptosporidiun parvum in the attached pictures?

    This parasite stain with acid fast stain

    Walter Filho · Federal Rural University of Rio de Janeiro

    Dear, Muhammed.

    Can not say that Cryptosporidium is, given the fact that the color does not allow such identification.

  • Franz-Josef Hambsch added an answer in Neutrons:
    Why resonance region occur at all?

    If we see the cross section curve of any nuclei with respect to the relative energy of neutron and nuclei, we find a resonance region in between thermal and fast region. My question is why such resonance region occur at all?

    Franz-Josef Hambsch · European Commission

    Please have a look at this link to a book of A. Michaudon.

    http://books.google.be/books?id=r7I3BQAAQBAJ&printsec=frontcover&source=gbs_ge_summary_r&cad=0#v=onepage&q&f=false

    It is about nuclear fission where resonances are observed in the fission cross section of isotopes.

    Concerning your additional question why we do not see in all energy band resonances is due to the resolution of our accelerators, which is nit sufficient to resolve resonances at higher incident neutron energies. The limit depends on the isotope (see also the link to the book).

  • Mohammed Nasser Alhajj added an answer in Teeth:
    With increasing the number of the abutment teeth, can we use Fixed PD rather than RPD in cross-arch long edentulous span?

    Kennedy Class IV.

    Mohammed Nasser Alhajj · Thamar university

    Thank you very much Dr. Regina Dorothea.

  • How can we analyze the property and structure of seed coat ?

    Physical structure of the seed coat is frequently associated with the dormancy of the seed. Although various physical and chemical scarification methods are there to break the physical seed dormancy, structural approach will help to understand the phenomena more clearly.  

    Josimara Nolasco Rondon · Universidade Católica Dom Bosco (UCDB)

    Hi, Gogoi.

    You need to use  SEM (scanning electron microscopy). Differences between lateral, dorsal and ventral surfaces and cell wall of seed coat is observed too. 

    Regards.

  • Sajjad Ahmad added an answer in Plant Extracts:
    After GC-MS, How Can we get the full chemical profile(with name identification) of a crude plant extract ?

    We are working on Diabetes , we are using some crude extracts for DPPIV inhibition. We need full chemical components of some plants so that we can perform Protein Docking with Schrodinger software tool.

    Sajjad Ahmad · University of Malakand

    one way is there i would like to suggest...  convert the sample into crystalline structure and then just do XRD that will be sufficient for the structure elucidation. no GCMS NMR etc will be required then.. the docking of crystaline structure is very easy to do..

    regards

  • Nicola Falco added an answer in Image Segmentation:
    Is it possible to extract a region based on its area?

    I am  working on segmentation,my segmented image contain 2 regions which have same intensity,so is it possible to extract the region of interest based on its area??

    Thank you

  • Paul A. Rubin added an answer in MIP:
    What types of problems are more suitable and preferable to be solved with Bender decomposition algorithm?

    As I know, most mixed integer programming problems with block diagonal structure are suitable to be solved with Dantzig-Wolfe decomposition and column generation. Analogously, which kinds of problems or which structures are preferable to be solved with Bender decomposition. Can Bender decomposition also be feasible for general MIP problem, and which one can get better performance for general MIP, Bender decomposition or Dantzig-Wolfe decomposition?

    Paul A. Rubin · Michigan State University

    Certain problem structures are particularly amenable to Benders decomposition. Consider a mixed integer program where binary variables are used to turn constraints on and off (constraint is enforced if binary variable = 1, not enforced if binary variable = 0). The typical formulation involves the product of a "big M" constant with the binary variable, but large values of M make the LP relaxation loose and can cause numerical instability. An alternative is to move those constraints into a subproblem and use "combinatorial Benders decomposition". (There's a nice paper from 2006 by Codato and Fischetti describing it.)

    Another example is the "implicit hitting set problem" (and its twin, the "implicit set covering problem"), in which not all constraints are known at the outset. Instead, potential incumbent solutions are passed to a subproblem (sometimes called an "oracle"), which either blesses them or generates constraints removing them (Benders feasibility cuts). A recent paper by Moreno-Centeno and Karp (2013) describes the implicit hitting set problem.

  • Boban Stanić added an answer in Interpretation:
    How to interpretate Wilcoxon Signed Ranks test test?

    How to interpretate positive and negative ranks?

    Boban Stanić · University of Novi Sad

    Reicelis,

    Thank you for your answer. However, i made a mistake in my question and i have correct that mistake. My question is about Wilcoxon Signed Ranks test and it's interpretation, but you answered me very nicely. 

  • Would you participate on an international study of laparoscopic vs. open left sided pancreatic resection?

    The evidence on laparoscopic vs. open left sided pancreatic resection is limited. Up to now no evidence from RCT can be used to evaluate the value of the laparoscopic technique.

    Given the fact that the incidence of left sided resections is low even in centers for pancreatic surgery we postulate that it is necessary to perform an international trail. Would you be willing to participate?

    Santiago Sánchez-Cabús · Hospital Clínic de Barcelona

    I think that certainly would be a very nice study. Although first we should agree on the details, probably we would be willing to participate. 

  • When it comes to simultaneity is Einstein correct or is Dingle correct?

    Albert Einstein claimed in 1905 that a single event can occur simultaneously at different times within two inertial reference frames moving relative to one another. In 1950 Herbert Dingle argued that different times cannot be simultaneous. I have analysed this conflict by deriving the Lorentz equations using both points of view. According to this analysis Dingle must be correct. See youtube presentation of this analysis at  https://youtu.be/4XLYzhHQ64Y

    Johan Frans Prins · Sage Wise 66 (Pty) Ltd

    Charles,

    " I do point out that it is a necessary prerequisite to being a scientist that one is not a devotee of the religious dogma of absolute space and time to which Valentin and Johan subscribe,"

    This is hilarious. YOU are the devotee of the religious dogma that time is relative. We are just pointing out that this concept is absurd and can therefore not be correct. Just like epicycles is absurd and cannot be correct. It is YOU who are a Cardinal of religious dogma: Not us!

    "and that one pays attention to empirical fact."

    Then why do you not adhere to this? It is an empirical fact that an instantaneous single event in space can ONLY be recorded at a SINGLE instant in time, not two, not three, not four not anything more than ONE single time 

    Anyone who subscribes to dogma, like Charles Francis the Cardinal cannot be a scientist, by definition. Correct!

  • Swapan Kumar Maity added an answer in Soil:
    Is there any research on how I can get full root system of the soil?

    Root system - Irrigation Methods 

    Swapan Kumar Maity · Visva Bharati University

    I have learned following the discussion. Thank you all.

  • Ugenthira Gunasekaran added an answer in Microalgae:
    How far light and dark cycle effects the production of secondary metabolites in microalgae cultivation?

    example production of astaxanthin by haematococcus pluvialis.

    Ugenthira Gunasekaran · Universiti Tunku Abdul Rahman

    Thanks Diana L. Reinecke.

  • Jennifer EMELDA asked a question in HL60:
    Can anyone share me the mtt and xtt assay protocol for handling suspension cells?

     suspension cells- molt 4 & hl60.

    Kindly suggest Which assay will b best to handle suspension cells.

  • Robert G. Maunder added an answer in LDPC:
    Why LDPC decoding has to decoded in the log likelyhood ratio manner. Are there any other methods for decoding it. ?

    Hi sir,

    Why LDPC decoding has to decoded in the log likelyhood ratio ( LLR ) manner. Are there any other methods for decoding it? 

    Thanking you. 

    Robert G. Maunder · University of Southampton

    You don't have to use LLRs. For example, the sum-product algorithm uses the sum and product of probabilities, rather than the min and sum of LLRs, as in the min-sum algorithm. However, LLRs have the advantage of having a low dynamic range, allowing them to be represented using fixed-point numbers, rather than the more complex floating-point number representation. Also, min and sum calculations are simpler to implement than sum and product calculations. These are the reasons why LLRs are used in the most popular ways of implementing LDPC decoders.