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  • Ashmit Singh added an answer in Genomics
    How to assign name to protein products of genome reannotation?
    I have around 15,000 protein sequences which are product of newly re-annotated genome. The sequences looks like >PRT1T1 MNNEPELELLEE........ >PRT1T2 MMMIIELPTTTTWEEEW........ >PRT2T2 MKKKPAVAVLKLKPLTR.. I want to assign "name" to all these proteins. Simple blast search will lead to mus-annotation. Please suggest some reliable tools/software.
    @Gustavo Costa - its nice one. I set-up all the db required for autofact. Do you/someone has kegg fasta and pathways file? It will help me a lot.
  • What are things make you really happy?
    Success, writing a research, travelling...
  • Is someone interested in a database of over 360 published papers addressing indoor microbiome and environmental characteristics?
    It is in MS Access format, enabling searches for any organism or environmental factor or substrate (air, dust, floors, walls, woods, gypsum board, etc.). We hope you find it useful and if you have suggestions of additional publications, you will send us the citation. Developed with support from the Alfred P. Sloan Foundation under a grant to the microBEnet project at University of California, Davis. Jonathan Eisen, PI.
    Lee Stanish · University of Colorado at Boulder
    This is great! I'll use it to compare to tap water microbiology. Thanks for sharing...
  • How to use Genetic Algorithm in MATLAB for system of nonlinear equations?
    I have a system of equations as given following: z=[3 7 10 27 30 42]; p=[10.2 8.7 7.1 6.4 3.2 2]; PROBLEM: ((x1*x2)+x2-(x3*x4)+z)/((x1-x2)*z+(x3*x4))=p; As I have 4 unknowns (x1,x2,x3,x4), z and p is a vectors, I need at least 4 equations to solve this problem. I have length(z)=length(p)=6, It means I have 6 equation and 4 unknown to solve. How can I use a genetic algorithm to solve this problem? As I saw in MATLAB help, a command is given like that: [x,fval,exitflag,output] = ga(fitnessfcn,nvars,A,b,Aeq,beq,LB,UB,nonlcon,options), How should I use this to solve my problem. OR How to solve a system of nonlinear equations in MATLAB using genetic algorithm? Thanks in advance.
    Felipe Scott · Pontificia Universidad Católica de Valparaíso
    @Behrouz I agree with you, sum of squares would be a better choice for objective function
  • Artur Burzynski added an answer in Cognitive
    How did intelligence evolve? In fact why did it evolve?
    An probable explanation can be organisms needed to survive but I think that alone can't be a reason for intelligence to evolve. Something other than survival might have motivated for the evolution of intelligence.
  • DNA degradation insects
    Hello, We are studying DNA degradation in drosophila after killing the flies ini different conditions When you kill an insect, the process that they undergo is it necrosis right? For sure not apoptosis. How can we prove it? Do you know any research similar to this one? Thank you
  • Marc Tessera added an answer:
    Is mathematics a human contrivance or is it innate to nature?
    Do we invent mathematical forms as we need them and then merely discover their emergent properties later? Or are those mathematical forms innate to nature, and are hence discovered rather than invented? Does it really matter to science, which way around we view this? Is it just philosophy or could there be real consequences? https://www.researchgate.net/publication/256838918 http://www.huffingtonpost.com/derek-abbott/is-mathematics-invented-o_b_3895622.html
    Arnold, The lowest level of awareness described by Irene Pepperberg and Spencer Lynn is "the ability to follow a simple rule involving perception of a specific item and its avoidance while the animal needs not necessarily be aware of devising or following the rule". Do you consider that the above ability is comparable to the ability of an engine to start when a key is turned on?
  • Is anyone working on Nymphaea lotus or other Water Lily species?
    I am working on the androgenic and aphrodisiac properties of the aqueous extract of the flowers of N. lotus, but I know that this plant is a widely spread plant, so I don't understand why no one has conducted studies (except for anti-bacterial properties) on this plant. Maybe I'm not good at searching for actualities on the web.
    Abiola Femi-Adepoju · Kwara State University
    Well, to the best of knowledge, i think generally aquatic plants do not as much attention as terrestrial plants maybe that is why it seems scanty literature is found on aquatic plants. It is high time we begin to do more research on aquatic plants as well. If you do not get enough information on the web about a material then it should be an eye opener that you too can build information on such material through your research so that others can refer to it
  • Does anyone have experience with treatment of severe compensatory hyperhidrosis after thoracoscopic sympathectomy for primary hyperhidrosis?
    see above
    Ahmet Bayram · Uludag University
    We removed clips in four patients. Two patients pleased and two patients neither bad nor Good. We made intercostal nerve indentation to one patient and he was very pleased
  • Pat Bailey asked a question in Applied Ethics
    Would growing the current global population be of any benefit?
    Given that we now have approximately seven billion people on our planet, and all of the problems that follow, is there any benefit to continue growing our numbers?
  • Can anyone help with OpenBabel and atom labelling?
    I have a molecule in cif format and am trying to generate the unit cell using command babel -i cif mol.cif -o pdb out.pdb --unitcell fillUC. I am getting proper output, but the atom label is gone missing. In fact the atom label in the pdb file format is replaced by atom type. For example, CA is replaced by C only. Any suggestion for getting the proper atom label?
    Thiruvalluvar Aravazhiamalan · Rajah Serfoji Government College (Autonomous)
    You use Mercury 3.3 from http://www.ccdc.cam.ac.uk/mercury/. Open your .CIF file using Mercury 3.3 and check for atom labels. Then save the .CIF file as .pdb file. Then open the .pdb file using Mercury 3.3 and check for atom labels. I hope this method will work nicely.
  • Is quantum mechanics subordinate to classical mechanics?
    I am giving some initial issues: 1) A certain field that QM cannot show is the concept of 'quantum chaos'. This is due to its linear form, so with linearity you can not explain the 'hard nonlinearity'... Although many attempts have been done there is not such a term in modern Physics. 2) Another issue is that of the curve fitting property of QM, especially in its QED representation. The level of accuracy is due to a procedure that, despite the efforts of Feynman et al, cannot be represented in a physical way: Since every function can be expanded with an infinite set of basis it is not reasonable to accept that every basis has a physical interpretation. This simple principle is violated in QM due to the Fourier basis preference. So, if we classify the theories by the range of applicability and by the clarity of their physical quantities, then we can certainly argue that QM is subordinate of CM. What do you think about?
    Manuel Morales · Institute of Prephysical Research
    Eugene, that question has been addressed: https://www.researchgate.net/publication/259293014_IN_SEARCH_OF_FIRST_CAUSE_How_art_football_fans_and_the_Super_Bowl_led_to_First_Cause_and_the_Theory_of_Everything?ev=prf_pub "(Page 3): So you might be thinking that the empirical evidence of first cause obtained by the TD experiment validates the God theory since such a deity is based on the principle of first cause [3]. However, since there are two first cause variables, the question is which selection is good and which one is evil? Then there is the problem of such a deity being all powerful, i.e., omnipotent, which would mean that God is both good and evil. The notion of morality being associated with first cause is clearly a paradox and appears to have nothing to do with the mechanisms of selection."
  • Electroporation protocol for FISH hybridization?
    Does any one has protocol for FISH hybridization using Electroporator, I want to do FISH hybridisation for environmental sample (water). I would like to try electrophoration to permeailize my probe into the cells. please help me out.
  • How can I do a Monte Carlo analysis with life cycle emissions analysis?
    The Monte Carlo method of data validation requires large data sets (random numbers) for starter.
    Alessio Boldrin · Technical University of Denmark
    My colleague has provided a structured procedure for systematic sensitivity/uncertainty analysis in waste LCA. We now follow it in most of our LCA studies. I think it is applicable in other types of LCA as well. http://www.sciencedirect.com/science/article/pii/S0956053X1200308X
  • Kenneth Towe added an answer in TEM Image Analysis
    How do I prepare the sample used in transmission electron microscopy (TEM) from powder?
    For testing brittle material the sample is prepared in grits. Please explain the way to prepare the sample, so to obtain the desired result?
  • Sarah Alshahrani added an answer in Insect
    Can anyone help me with 16S rRNA I can use in identifying insect species?
    With any insect (sandfly , tsetse fly, etc.).
    Sarah Alshahrani · King Khalid University
    Dear Dr Tsam, Thank you very much :) Good Evening
  • Gauge boson and fermion masses are proportional to VEVs of Higgs field: How is this phenomenon interpreted in terms of vacuum energy of scalars?
    Vacuum expectation value (VEV) of the Higgs scalar is responsible for fermion masses and also masses of the W+ W- and Z gauge bosons. Does it mean that the Higgs particle can extract energy out of vacuum and convert it to a new form in which gauge bosons and fermions are massive ? For quarks one can also have QCD correction to masses which are unrelated to Higgs VEV
    Orlando Peres · University of Campinas
    The source of masses of leptons is the interaction of scalars with fermions. What we call mass is proprotional to the Yukawa coupling of scalar and fermion. This is the reason that when you put the vaccuum expecation value to zero you get massless particles.
  • B.R. Vishvakarma added an answer in Antenna Design
    Can anyone help with a microstrip patch antenna?
    I have designed a microstrip patch antenna that works in 2.4 Ghz , but its bandwidth is 30 Mhz, I want to improve the BW, how can I do it?
    B.R. Vishvakarma · Banaras Hindu University
    You can design multi resonant antenna which can covet several usable freqiencies like GPS,WLAN,Wi max etc but you have to wotk hard.
  • Alan Holden added an answer in Obesity Epidemic
    Is sugar over consumption the underlying cause of the obesity epidemic?
    The current obesity paradigm is basically behavioural; overeating and under exercising as the cause of obesity. Both true but neither has explanatory power unless people deliberately set out to become obese. A single underlying cause is the over consumption of sugars. It fits the descriptive epidemiology: pandemic, both genders, all ages, increasing since the 80's, high prevalence. It fits the biochemistry as causing insulin resistance via glucose consumption stimulates appetite and reduces exercise. It fits the epidemic of Non Alcoholic Fatty liver Disease through fructose. This model supports both individual and public health responses: low sugars diets and low sugars food availability. It also supports recent observational studies and meta-analyses that fats are part of the solution, not part of the problem. Until the paradigm shifts back to the pre-50's diets, we will continue to do the ineffective, calorie restricted diets and increasing exercise, instead of decreasing sugars intake both as individual interventions and public health policy.
    Alan Holden · University of Texas Health Science Center at San Antonio
    In part, yes. One has to delve into the issue a little more - sugars exist in multiple forms and have different effects on the body. Perhaps we begin with the larger taxa e.g. "sweeteners".
  • If someone asked you to give him an advice for RG, what would you say?
    Share, losing time, fruitful, knowledge...
    Shafig Al-Haddad · Applied Science Private University
    Don't miss RG.
  • Can anyone help me understand the mechanism of the conversion of dialdehyde to dihydroxyquinone in the presence of KCN?
    The mechanism of reaction of conversion of the compound is 7 to 22 in the attached file. It is called Venuti's method.
    Divya Andy · University of Toledo
    thank you very much Adel Amer
  • Hassan Sedaghat added an answer in Dark Energy
    Do dark matter and dark energy constitute valid evidence of large spatial dimensions higher than 3?
    There are speculations that the gravitational effects of matter in 4 or greater LARGE spatial dimensions might account for the substantial discrepancy that exists between measured gravitational effects on normal baryonic matter and the amount of that matter that exists according to measurements. Could we be measuring the gravitational effects of "normal" matter in higher dimensions? And can large higher dimensions also explain the huge amount of dark energy that seems to be around?
    Hassan Sedaghat · Virginia Commonwealth University
    Point taken, James. I can only hope, with regard to preexisting knowledge, that we do not keep looking in the wrong places for answers to profound questions (as in "not seeing the forest for the trees").
  • Can anyone help me understand what went worng in my qPCR experiment?
    I did an real time experiment and I am having some trouble trying to analyze the results. Something definitely went wrong, but I don't know what the main problem is. Is it my cDNA (amplification plot very weird)? Is it contamination (got NTC amplification)? The cDNA are dilutted to 20 ng/ul, and I was careful with the pipetting. I appreciate any thoughts on this problem.
    Luiz Henrique Vargas · Universidade Federal de Lavras (UFLA)
    Jack Gallup, first of all thank you for your time. I´ll provide you the details you asked for help you help me: - The 20 ng/ul is the concentration measured after de RT-PCR and before the qPCR; - Yes, I´ve tried baseline corretcion and it give me no signifcant difference; - Yes, my primers are exactly specific for my targets. It was comproved by conventional PCR and eletrophoresis; - One target is housekeeping, while the another one it´s not. Thus, one of them can be present in the lab air; - I´ve drawn the threshold and my Cq´s values were from 31 to 35; - Thermocycling parameters: 95ºC-10´; 40 cycles of 95ºC-15" and 60ºC-60"; Melt curve. Master Mix parameters: same as the Sybr GreenER Protocol (standard); - No, I did not use an endogeneous reference dye; - In fact, I was not performing a dilution series, as I use only one cDNA concentration. I was trying to perform a comparative experiment for diferencial expression, thus I used a housekeeping gene and an unknown gene (suposed to express only in leaf); to do that, I use two samples (cDNA from leaves and cDNA form root); - I am using Sybr Green-based qCPR. Ahmed Atia, I will perform another run today using a dilution series of my cDNAs (1:100, 1:50 and 1:25) to see if the problem is really the cDNA concetration. I´ll post my results from the new experiment in about 8 hours. Hope I hear more insightful question and opinions later. Thank you two very much.
  • Alan Holden added an answer in Child Health
    Obesity as a disease: what impact will labeling it a disease have on primary prevention of childhood obesity?
    The American Medical Association has now joined other organizations in deeming obesity a disease (not just a condition or syndrome). There is hand-wringing about proliferation of pharmaceuticals, surgery, and other medical treatments. What about prevention, and specifically, primary prevention for children? Is there applicable evidence for other diseases to inform us what to expect for prevention and public health efforts around childhood obesity?
    Alan Holden · University of Texas Health Science Center at San Antonio
    Hello Richard, just an opinion of course but I suspect labeling obesity as a disease will have little or no impact on primary prevention efforts. Reason is, those efforts have been ongoing for a while now - at least 20 years - where obesity has been treated as a disease by many, including pharma etc. "Official" labeling may increase some of this of course and lend credibility to calls for more primary prevention, more drugs to prevent this disease, etc. - but take a look at the literature and you can see that the new, official label is kind of a belated attempt to legitimize what's been going on for some time already.
  • Giovanna Sclafani asked a question in Governance
    Do you know that OTIE is organizing a very intersting conference of one day on 5th August in Gozo (Malta) ?
    Daytime Meeting on Festivals and events impacts is a session open to researchers that want to present studies on events and their impacts. Only 10 abstracts will be accepted and the papers presented at the daytime meeting will be considered for publication in European Journal of Tourism Research – EJTR. The abstracts submission was extended to 30th April 2014. All information on http://www.otiesummerschool.com/daytime-meeting.html
  • Paweł Weichbroth added an answer in Web Mining
    Is there any free tool to perform preprocessing of a server log file?
    I am working on web log mining processes. I need a tool which performs pre-processing (data cleaning, user identification, sesion identification) of server log file.
    Paweł Weichbroth · University of Economics in Katowice
    Which variables do you have in your log file? Please paste a sample in your post. I think I can help you. I've got a few tools for such a task.
  • Is modern research becoming more and more “publication oriented”?
    The main aim of research should be either to gain knowledge or to solve a problem and to work for healthy development of mankind and nature. Nowadays researches are planning their work, so as to get it published in good journals. Journals are an excellent medium to communicate our findings to researchers worldwide, but in doing so are we parting away from our primary objective.
    Joseph Dubrovkin · Western Galilee College
    Dear S. Tan! "Comparison of numerical IF values between journals from different fields of study is meaningless" You can found the appropriate tools to do this in the mathematical methods of Big Data treatment. Data mining is a good example.
  • Javid Ziaei added an answer in Probability
    How can I derive probability density function for logistic map analytically?
    Example: x(n+1)=4*x(n)*(1-x(n)) ---> P(x)=1/[pi*(x*(1-x))^0.5]
    Javid Ziaei · Urmia University of Technology
    Dear Milad You can see the book of "Ott" entitled "chaos in dynamical systems" page 32 and "Probabilistic properties of deterministic systems" by "ANDRZEJ LASOTA & MICHAEL C. MACKEY" which provide a detail discussion about the probability density of maps.
  • Thomas I. Seidman added an answer in Heat Transfer
    If you have a time-dependent parabolic equation what is the best method to solve it other than finite difference method?
    The equation is u_t=a(t)u_xx+b(t)u_x+c(t)u+f(x,t) with initial condition and Direichet boundary conditions as follows: u(x,0)=u_0(x) and u(0,t)=u_1(t), u(1,t)=u_2(t).
    Thomas Seidman · University of Maryland, Baltimore County
    I haven't seen any consideration of what I would consider a most important aspect: where (physically) the time-variation comes from. In particular: how rapidly are the coefficients varying and are they doing so in some coordinated way (in which case an analytic change of the time variable may remove the problem)?