Q&A

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  • Sang-Im Lee added an answer in Spectrophotometer:
    What wavelength should I use to quantify carotenoids?

    More people rely on spectrophotometer, instead of HPLC, to quantify the amount of carotenoids in the plasma of birds. But different people measure absorbance at different wavelength; some used 470 nm, others used 450 nm etc. How do they determine which wavelength to measure? Any tip would be appreciated!

    Sang-Im Lee · Institute for Advanced Machinery and Design

    thanks Othman

    Why did you use 470 nm? is there any reason?

    I did some MS on my plasma samples and the types of carotenoids were different, with 2-3 types dominating. I guess I could use the wavelengths where these major carotenoids show peak absorbance. Is this how the researchers choose which wavelength to use? or they just do it blindly?

  • How can I create a pdb file of the standard RNA triplex?

    Hi all,

    I need a pdb file of an RNA triplex to do Molecular Dynamics Simulations. Do you know what software or method can be used to create structures of a (the) standard RNA triplex? Thanks a lot.

    Ya-Zhou Shi · Wuhan University

    To Amir Abbasi,

    Hi, Amir, thank you for your answer. Yes,  MMB (also known as RNAbuilder)  is powerful in RNA 3D structure prediction. However, as a homology-based method, I wonder if it can be used to predict RNA triplex, because the known information of triplex in PDB is still limited. Even so, I will try. Thank you very much. 

  • Abd ALMONEM Doolaanea added an answer in Acrylate:
    How to separate inorganic nanoparticles from the wide particles range?

    Do anybody suggests how to separate particles (<300nm size) from the mixture?

    I have hard inorganic oxide particles from ~50 nm to 900 nm range. But, I need to collect particles <300nm for biological applications? I used centrifuge separation or sedimentation but bigger particles contamination occurred.

    I am looking for the Syringe filters but there are varieties (220 nm & 450nm filters) . But I have no idea to select the type of filters like Nylon, Acrylic, cellulose etc for hard inorganic particles! or any other idea to separate?

    Abd ALMONEM Doolaanea · International Islamic University Malaysia

    you may try it. you can do primary centrifuge to remove the very large particles first then filter, dilute the nanoparticle suspension for easy filtering. 

  • Zhichao Lou added an answer in Spin Coating:
    What are the best solvant and surfactant to deposit gold nanoparticles on glass substrate using spin-coating?

    I would like to use spherical nanoparticles (diameter around 30 nm) and deposit them homogeneously on a glass substrate previously cleaned using the RCA method. I have a POLO150i spin-coater. Any advice about protocole or spin-coating recipes is welcome. Idealy, I would prefer to work with water as a solvant.

    Zhichao Lou · Nanjing University of Aeronautics & Astronautics

    How about APTES?

  • Hongyang Li added an answer in Water Turbines:
    Where can we get public data on water turbines including geometry of volute, guide vanes, blade and cone and the test data for academic use?

    Where can we get public data on water turbines including geometry of volute, guide vanes, blade and cone and the test data for academic use?

    Hongyang Li · Chinese Academy of Sciences

    can you tell me how can I get Kovalev's Guide of Water turbines? 

    I searched the internet and I found there is a book 'Hydroturbines: design and construction', but I cannot get the book.

  • Is there a difference in outcomes from Motivational Interviewing between Anorexia, Bulima, and Binge Eating Disorder?

    A meta analysis of Motivational Interviewing showed a negative effect for eating disorder treatment? Does anyone know of a study comparing outcomes of AN, BN, and Binge Eating Disorder?

  • Mao wei Liang added an answer in Ecosystems:
    Is Net Ecosystem Production Equal to Net Ecosystem Exchange minus Ecosystem Respiration?

    The NEE CO2 (Net Ecosystem CO2 Exchange/umol.m-2.s-1) and ER(Ecosystem Respiration/umol.m-2.s-1) were measured in growing season from 2012 to 2013, respectively. Recently, I'm frustrated when I have to calculate the Net Ecosystem Production (NEP/gCm-2.yr-1).
    Is NEP equal to NEE minus ER in numerically?
    Can I directly calculate the Ecosystem Carbon Accumulation in growing season (gCm-2.yr-1) using the NEP(umolCO2.m-2.s-1)?
    What is the equation from umol CO2.m-2.s-1 turn to g C.m-2.yr-1?
    I‘m not assure about it.
    Any help appreciated.
    Thank you much indeed!

    Mao wei Liang · Inner Mongolia University

    To Sara,

    It's very grateful for your help,you're very nice.

    Thank you very much.

  • Z.A. Muchlisin, Ph.D added an answer in Aquaculture:
    Is there any researcher here open to a corresponding cooperation in work on the breeding and status evaluation of freshwater decapods?

    I would like to start some research in Hungary which is aimed to develop captive breeding technology and evaluate status of the three autochthonous decapods of Hungary and Central-Europe (Astacus astacus, Astacus leptodactylus, Austropotamobius torrentium). For this project I'm looking for a corresponding advisor/consultant/cooperator. Details of the planned work and ideas would be shared via private message/ e-mail.

    Z.A. Muchlisin, Ph.D · Syiah Kuala University

    Hi Peter, I am Aceh Province Indonesia. I am ready to make collaborations with you, please send detail information to my email: muchlisinza@unsyiah.ac.id, thanks

  • Hong Yu added an answer in Graphite Oxide:
    Can anyone help me getting a method that can make graphene oxide bonded to the surface of the quartz crystal?

    I want to replace gold electrode with  graphene in QCM .Can anyone help me getting a method that can make graphite oxide bonded to the surface of the quartz crystal? Thanks!

    Hong Yu · Chinese Academy of Agricultural Sciences

    Ján Kozempel, Thank you for your help!

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

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

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

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

    Timothy A Ebert · University of Florida

    One could hypothesize a number of cases. The easiest is if the sharks are always fed on Tuesday. An alternative is that the real issue is seasonality, and week was just what the fingers typed first. However, I am just guessing here.

  • Does any one know how many time the abalone and freshwater angel fish eggs will hatch after incubation?

    Does any one know how many time the abalone and freshwater angel fish eggs will hatch after incubation?

    Z.A. Muchlisin, Ph.D · Syiah Kuala University

    thanks you Dr. Navid

  • Which is the best tool for analyzing the WSN?

    I am using Ns2 for WSN simulation. Can anyone help me for an alternative efficient tool for the same.

    Moshaddique Al Ameen · Kyung Hee University

    OMNet++ is a very good tool. good IDE. Its free has got great resources and community help docs.

    OPNET is also good but its not free.

  • Can anyone help with the storage of histopathological samples taken at an autopsy?
    I'm investigating the best way to store histopathological samples between autopsy and preparation of the samples. Normally, the samples are stored in formalin directly after sampling, but due to renewal of our section, we will have a delay of 1 - 5 hours from sampling to storage in formalin. Does storage of samples in an isotonic saline solution for 1 - 5 hours before storage in formalin lessen the quality of the sample? Any other possible solutions?
    Jorge Herbstein · University of Buenos Aires

    Pardon I have a question, how many autopsies do you perform per day ???

  • Miao Lee asked a question in Bacterial Infection:
    Could someone download this paper for me ?

    miR-15a/16 Regulates Macrophage Phagocytosis after Bacterial Infection. J.Immulology.2014

    Much thanks!!

  • Mikhail V Matz added an answer in Introgression:
    How do we use the RAD sequencing to detect loci under selection at both interspecific and intraspecific levels?

    Hello,

    I am writing a project about Hybridization and introgression in some succulent plant species. My project is based both on populations and species level. I will use the RAD sequencing, and then will use the data and the SNP markers. I want to know some details about the genetic analysis particularly to know how to use such data to detect loci under selection. Waiting for your kind views and reviews.

    Thanks with profound regards

    Khan Gulzar

    Mikhail V Matz · University of Texas at Austin

    Baysecan will definitely work as long as the divergence between the species in question is not too great - i.e., as long as the majority of polymorphisms are not nearing fixation in any of the species.

  • Brahm Pal Singh added an answer in Chimpanzee:
    What makes us human?

    Just looking at our DNA won't tell us – the human genome is 99% identical to a chimpanzee's and, for that matter, 50% to a banana's. We do, however, have bigger brains than most animals – not the biggest, but packed with three times as many neurons as a gorilla (86bn to be exact).

    A lot of the things we once thought distinguishing about us – language, tool-use, recognising yourself in the mirror – are seen in other animals.

    Brahm Pal Singh · Eco Solutions Company, Panasonic Corporation

    Dear Hanno Krieger,

    You are absolutely correct. Mother nature has taught us the humans a lot lessons through such beautiful examples as you have kindly mentioned, and as human nature, shared with others around us to understand that "United We Stand Devided We Fall" but with "Honesty As Our Best Policy". Thus, More We Share, More Rapidly We Progress; and it gives more peace to human heart.

    In short, it is the results of the sharing nature of human, that has made it possible to see such an  amazing rapid progress in mankind, which no other animals could/would do. Many thanks and best regards.

  • Can anybody tell how to measure absorption spectra of single and isolated CdSe quantum dots spread over a 200 nm thick silver film?

    Diameter of CdSe quantum dot is about 5 nm.

  • Can anyone help with body area networks?

    EL = (Pc+Pt)Tac+PtrTtr

    In connection with the above eqn how can we justify the validity of the following sentence extracted from the attached file? 

    "where Ptr is the circuit power consumption during the transient mode period. It is seen from eqn that the active mode duration Tac is an influential factor in energy  having, as EL is a monotonically decreasing function of Tac ."

    where EL is the total transmit and receive energy consumption during the active period.

    Moshaddique Al Ameen · Kyung Hee University

    You need to consider the parameter Pc, the total circuit power consumption during active time. The first term in RHS will have lower value as time pass by. This is due to the fact that although the node is active, the ratio between number of packet transmitted and received over large amount of time (ie large Tac) will become smaller. So if you draw a graph EL vs Time (Tac), the energy consumption will decrease as the time increases.

  • Nikolas Dietis added an answer in Autism:
    What’s the latest insight about pain and autism?
    As far as I know the controversy is or was between a higher pain threshold, so less pain experience on one hand or a different expression of the same pain felt by non-autistic people. Nader et al. (2004) and Tordjman et al. (2009) are in favor of the latter and have done empirical research to support this. Yet, from clinical practice the anecdotes about – especially autistic children – apparently being oblivious to pain, are abundant. The latter is reflected in the DSM-IV and DSM-IV-TR which mention “a high threshold for pain”.
    Nikolas Dietis · University of Tasmania

    Hi Flip, that's an interesting question and although I don't have a solid insight, my premature opinion is that a hight nociceptive threshold can certainly fit with the Opioid Excess theory in autism (quick link below), since an excess in endogenous opioids could in theory contribute to a form of "endgogenic analgesic tolerance", manifested as an increase in pain threshold. So, the biochemical data seem to fit with the theory, but not sure if this is (has been) backed up by electrophysiology. 

  • Hyde Chen added an answer in Gamma Irradiation:
    Does anyone know the price of a gamma irradiator for the lab and what company sell the most convenient ones?

    We need a gamma irradiator to prepare feeder cells.

    Hyde Chen · Zhejiang University

    The public platform uses Rad Source--RS2000 x-ray.

  • Agustin Luz Madrigal added an answer in Sucrose:
    Why are retina fixation procedures inconsistent?

    I have been using a procedure for mouse eye fixation in paraformaldehyde. We remove the mouse eye after sacrafice. We immediately put it in 4% pfa for 30 minutes. After that we punch a hole in the eye, we do not remove the cornea or lens. After fixing for 4 hours, we put it in 10% sucrose for an hour, 20% sucrose for an hour, then 30% sucrose overnight. We then put the fixed eye into a cryomold filled with OCT mixture without sucrose. We freeze the tissue on dry ice. Sometimes the retina is perfectly sectioned, other times, it is extremely detached and has cells missing or shrunken. Any advice would be helpful. Thanks

    Agustin Luz Madrigal · Miami University

    Hi Matthew,

    Take a look of the enclosed paper, I hope it helps!!

  • Which methodology is the best for bacterial capsule staining?

    Fundemantal Microbiology Laboratory

    Christopher Omelon · University of Texas at Austin

    Ruthenium red is a good EPS stain.

  • Can somebody explain influence of symmetries on the different order nonlinear susceptibilities?

    I met an explanation similar to what appears in "Nonlinear optics" of Boyd 2ed. But I do not understand physics behind the symmetries.

    Can somebody explain in the simple words the physics behind the symmetries, and how symmetries reduce the number of elements in the high order nonlinear susceptibility?

    Aleksandr Aleksandrovsky · Russian Academy of Sciences

    Nonlinearity of group of atoms (ions) is a sum of nonlinearities of each interatomic bond (with account for the phases of nonlinear polarization). Symmetry, e.g., of crystal unit cell, means certain order in the atoms' positions and, correspondingly, in the bonds. Zero components correspond to completely destructive interference of contributions from all bonds. Naturally, it is governed by the symmetry of unit cell.

  • Is it possible to come up with a vibrational model of nucleus?

    In a paper that I just found, Roger A. Rydin wrote about possibility to construct a classical electromagnetic model of nuclear reactions.

    His abstract goes as follows: "A comparison is made between the conventional way nuclear reactions were considered to take place circa 1960, and how they might take place using a new Classical electromagnetic model of the nucleus proposed by Charles Lucas. The old analysis used an analytic model of a compound nucleus and the linear Schrödinger wave equation to predict reaction cross sections by treating the wave solutions as quantum mechanical
    probabilities. Actual experimental data had to be inserted into the equation to get the response for each case."

    One interesting discussion in this paper that i do not found elsewhere is that Rydin proposes a vibration model of nucleus using matrix equation. But I find that his matrix model is too complicated. Some other questions:

    a. Can we simplify the matrix model to become 2x2 or 3x3 matrix?

    b. Can we explain the sub barrier fusion through Coulomb barrier?

    c. How to explain recent experimental data with quarks etc. using this matrix model?

    So what do you think? Is it possible to come up with a vibrational model of nucleus? Your comments are welcome.

  • Can anybody suggest a favourable way to calculate interaction energy due to a weak interaction in a dimer which contains intermolecuar H-bonding?

    For instance in the given acetic acid dimer( coordinates from X-ray) how can I calculate the interaction energy due to C-H...O in presence of strong O...H-O intermolecular H-Bonding?

    ya Wang · Nankai University

    You can use the Software called "Multiwfn‘.You can download the software from "http://Multiwfn.codeplex.com".This software can calculate weak interaction very well.

  • Tang Yicun asked a question in Heat & Mass Transfer:
    How to simulate the heat and mass transfer process of porous media when it is heated by hot air?

    My ways to investigate this problem mainly focus on solving the governing equations with the proper boundary conditions. However, there are so many parameters involved in the equation and they are often non-linearly distributed. The coefficient matrix is rather difficult to solve using some ordinary methods, like LU Seperation, QR Sepeartion, etc. When solved by iteration method, the iteration process is hard to reach convergence.

  • Yin Linzi added an answer in Feature Selection:
    How can I select optimal features from feature selection method?

    I used PCA and GA but I got only  ranking of features I was unable to find best features

    Yin Linzi · Central South University

    there are lots of algorithms to calculate optimal features. but unfortunately, it is a NP-hard problem. I have two simple heuristic algorithms to calculate one optimal feature and published in related chinese journals. they are wtried by chinese. 

  • Matthew Edward Thornton added an answer in mRNA:
    How to retain DNA, miRNA and mRNA from one sample for NGS?

    Hi,

    So I am interested in a way for generating DNA, smallRNA and mRNA from the same biological sample for NGS (ExomeSeq, smallRNAseq and RNAseq). Essentially I am looking for a protocol/kit that gives me 3 extracts for the desired nucleotide fractions.

    I read about http://www.qiagen.com/us/products/catalog/sample-technologies/rna-sample-technologies/dna-rna-protein/allprep-dnarnamirna-universal-kit/#productdetails and it sounds interesting, but it gives only one RNA fraction.

    Thanks,

    Matthew Edward Thornton · University of Southern California

    Hi

    This may be too elementary, but we use Trizol and Qiagen RNeasy kits. QIagen makes columns that are specific for micro RNA. You would take the 'aqueous fraction' above the phenol-chloroform and then add isopropanol and transfer into the column. We use RNeasy micro columns for total RNA  (probably loses some miRNA), but they work pretty well RIN usually above 9.5. I had planned on precipitation if we needed the miRNA, we have a speedvac and it is kind of hard to mess up. Good luck!!

  • R. C. Mittal added an answer in Fourier Series:
    Why there should be finite number of discontinuities for existence of Fourier Series?

    Why there should be finite number of discontinuities for existence of Fourier Series?

    R. C. Mittal · Indian Institute of Technology Roorkee

    @Peter - What I meant was bounded and periodic functions. Your example does not hold this property. Precisely Gibb's phenomenon is for discontinuous functions and piece-wise continuous means discontinuous functions having finite number of discontinuity.

  • Jeremy P Wrobel asked a question in Sputum:
    Is pseudomonas colonisation a contraindication for broncoschopic lung volume reduction with endobronchial valves?

    Is pseudomonas colonisation a contraindication for BLVR with EBV if there is minimal secretions / sputum production?