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  • What do you think about using normalized phenotypic data for performing an association mapping analysis?

    I have measured the sugar content of some potato landraces, These data are not normally distributed, I think this is mainly because I have some few individuals with extreme phenotypes. I have read in association mapping articles that many authors use normalized phenotypic data to perform association analysis. For me it is not clear the fundamentals of using transformed data into these analysis. I would be very grateful to hear your opinion into this matter. 

  • J. C. Zang added an answer in Emission:
    What is the second or third order wavelength of a radical's spectral line?

    In a paper about optical emission spectrum of a pulsed discharge in water, the author said that: The peaks at about 620 and 927 nm are the double and triple wavelengths of the OH radical line at 309 nm, respectively, because they disappeared when a UV filter was inserted to block the 309 nm emission line.
    Some authors also reported the occurrence of the 2nd order CN radical line. What's the meaning of second order? How does it happens?

    J. C. Zang · Beijing University of Technology

    先把波长变波数。927nm=10787cm-1,618nm(620nm)=16181cm-1,分别乘3, 乘2得32361cm-1和32362cm-1.再换成波长309nm.

  • Henry Withers added an answer in Illumina:
    Can anybody help with analysis of Illumina Bead Array using R?

    Dear all, 

    I am trying to do a differential expression analysis of Illumina Beadarray using R. I am new to both R and Illumina Microarray. I have summary files generated through beadstudio and I imported it in R. Now I am confused about how to go ahead with the normalization and differential expression analysis. If you have experience with this type of problem, please help!!! 

    Yogesh 

    Henry Withers · Roswell Park Cancer Institute

    I would second Han's recommendation and look into the lumiR package.  I am currently having similar problems but the lumiR package helped me through the normalization process.  My next step is to attempt to look at differential expression using the limma package from bioconductor.  This thread is almost a month old and so I would be curious if you could update us on your progress and if you found a nice solution.

  • Is it effective RNA isolation from 1-day whole blood at room temperature WITHOUT stabilization solution?

    Hi everyone, I will run a microarray assay using total RNA from 1-day whole blood (in EDTA) at room temperature but without stabilization solutions...Is it effective for microarray assays?? The array is customized for ~1000 genes. Thanks in advance,

    Carlos Córdova-Fletes · Autonomous University of Nuevo León

    Thank you Carl. The main trouble is that we are going to receive those samples and need to know how we should treat them before arriving here. I have read some papers but they show contradictory views and most of them suggest white blood cells separation before adding RNAlater (for example). For this particular case, people who is sending the samples, cannot separate white cells and RNAlater requires small volumes of blood to correctly operate. We are going to do a test with control samples here, I hope this helps. Greetings. 

  • Rahul Jamdade added an answer in Python:
    How do you find the K-mer size of a nucleotide sequence?

    The size of K-mers is between 1 and 8, for nucleotide sequence it is recommended from 4 to 7. The programs found were all in Python, Pearl, Linux or C language which are not userfriendly. Please suggest any executable userfriendly software or online server to find K-mers from nucleotide sequence.

    (I found, "K-mer counter.exe" (Deorowicz et al., 2013; http://www.biomedcentral.com/1471-2105/14/160)(downloaded from: http://sun.aei.polsl.pl/kmc) but not found any tutorial in this regard) Please suggest..... Thank's in advance

    Rahul Jamdade · Dr. Babasaheb Ambedkar Marathwada University

    Thank you, Kyungtaek Lim, following your instructions of KMC and will be back...

  • How to compare PL spectra that have different baseline level?

    I would like to qualitatively compare PL spectra that were taken in the same PL setup, but in different days. The baseline of the spectra shows differences as a function of the day. Should I multiply by the relationship or just adding a constant in order to obtain the same baseline? Why?

    Thank you

    Lock-in amplifier will cutoff any constant background in your measurement.

    Doing on different days should not change things. Unless some thing else also is changing. May be this is because of the detector. Because dark current, noise  in the detector can change.

    If that is so, does doing on the same day help?

  • Aram Mohammed Ahmed asked a question in Methane:
    I need some information why is methane measured after 24 hours in in-vitro?

    I am not sure for my question, I would be grateful if you could 

  • How can I measure flow rate using ANSYS in 2D or 3D?

    My assignment is to measure the flow rate using ANSYS where small channels are attached to main header line. Can you please guide me. 

    Ricardo Vicente de Paula Rezende · Federal University of Santa Catarina

    In CFD-post there are some macro calculation and native function that deal with these kind or demand. Mass flow rate,  Averages on areas or volumes are some of tools  available to do those calculations. 

    Once in this tab, select the function ( area, area average, mass flow rate,etc) , the region ( inlet, outlet, entire domain...) and if necessary, a variable to  perform a average, for example. 

    There is no coding, is a native feature in the post-processing tool. 

  • Can we analysis data without a respondent but instead using a official report, statistics, newspaper article or interview by a newspaper?

    I try to get a respondent but non of them replying or response to my calls and email. My research design was qualitative. It is possible or reliable just analyse a data using a data from a newspapers, official report and statistics? I possible how to analyse those data in qualitative?

    One more, can I using a software for analyse this data or manually coding?

    Please assist me.

  • Nelson Orringer added an answer in Literary Theory:
    Can anyone suggest any material on archetypal literary theory?

    The aim is to assist in writing a dissertation

    Nelson Orringer · University of Connecticut

    Arthur Symons's The Symbolist Movement in Literature is clear and straightforward. The symbols of the French Symbolists are archetypes.  Actually, archetypes go back to the Greeks. The Platonic Ideas were archetypes.

    I have advised many students in writing Ph.D. theses.  My suggestion is to narrow the focus of the dissertation so that the research and composition can be completed in a year.  In other words, if the student wants to write a thesis on archetypes, let him concentrate on a single author's use of them.

  • Nishanth Dikkala added an answer in HMM:
    What is known about learning of continuous state-space hidden Markov models with continuous observation processes?

    For example, consider a Gaussian variable which is linearly transformed in each time step and the observed value is a noisy version of this at each time step. Such HMMs are used as the underlying model, for example, in Kalman filters. I was looking for work which does HMM learning in such cases beyond EM-based approaches. The learning goal could either be to estimate the parameters of the process or accurately predict the observation sequence given a set of past observations.

    Nishanth Dikkala · Massachusetts Institute of Technology

    Thanks to everyone for the answers. The original question had some ambiguities as pointed by some of you and I've edited it to make it more detailed now. 

  • Edward Alain Pajarillo asked a question in Heating:
    Concentrating DNA using SpeedVac?

    Has anyone tried using SpeedVac to concentrate DNA samples?

    What is the optimum condition/setting for the SpeedVac so that the DNA won't be damaged? I tried using these parameters:

    Heating time = 30 min

    Running time = 45 min

    Temperature = 65 C

    Vacuum Pressure = default

    Please let me know your thoughts?

  • Evan Chiswick added an answer in Buffer:
    Are the Luminex Bead:Antibody Coupling Instructions Correct?

    Luminex, and several publications, report that carboxylated polystyrene beads should be activated with EDC:Sulfo-NHS in pH 6.2 phosphate buffer, and then coupled with antibody in pH 5.0 MES buffer. Shouldn't this be the other way around? Isn't amide bond (antibody amine to sulfo-NHS) formation favored in basic conditions? Would following Luminex' protocol simply result in passive adsorption instead of covalent attachment??

    Evan Chiswick · Boston University

    I wouldn't go that far. The new and old protocol should result mainly in adsorption of antibody to the beads, rather than covalent bonding, but that doesn't mean the assays would not work satisfactorily. ELISAs use adsorption to attach capture antibody to the plates. I have had good agreement of results between our standard ELISAs and the cytometric bead arrays that I've developed using Luminex' protocol. I imagine stability might become a problem, but only time will tell. I'm in the process of comparing coupling (adsorption) at ph 6.2 to coupling (covalent) at pH 8.

  • Why do I get textures in BaCeO3-BaZrO3 ceramic materials?

    We have recently synthesized the BaCe0.5Zr0.3Ln0.2O3 materials (Ln = Y, Yb, Gd, Sm, Nd and La).

    It is found that all the samples investigated possess a particular grain orientation in the ceramics surface, whereas the volume of the same materials is characterized by normally oriented (random) grains. (see attached file). The traditional method of ceramic sample formation was used, including synthesis of powders, pressing into the pellets and sintering. 

    What are the reasons of texturation in this systems, if

    1. The degree of texturation is a function of Ln.

    2. The literature data show no textured ceramics with the same compositions.

    Thanks & regards

    Dmitry

    Dmitry Medvedev · Institute of High Temprature Electrochemistry

    Dear Guilhem,

    thank you very much.

    Any explanation is useful for me. 

    However, recently we have not seen this phenomenon for other materials prepared by such traditional method. By the way, as i wrote... texture development (its degree) increases with increasing Ln3+ ionic radius. If the method features affect the surface of ceramics, why Ln  also plays  an important role?

  • Ankur Sharma added an answer in Likert Scale:
    Can anyone suggest better alternatives to the Likert type scale?

    Likert scale gives a fixed numerical value to a varied quality of perceptions that the participants usually tend to group under the same number/value. Is there any other scale that overcomes this shortcoming?

    Ankur Sharma · Manav Rachna International University

    Thanks Andrew, your answer gave me a lot of clarity on the matter... and some new avenues for a better methodology while preparing my questionnaire and study design..

  • Is there is any deep physical interpretation for the Lagrange's Multipliers?

    As is well known, Lagrange's Multiplier/s is an automatic mechanism of incorporating constraints to functions optimization. In some sort this mechanism expresses an orthogonality relationship between the Lagrange's Multipliers and the constraints. I wonder if there is any deeper physical interpretation for these multipliers?

    Morton E. O'Kelly · The Ohio State University

    Terrific question.

    I have always tried to understand LM in related physical terms. For example as a geographer, they can have meaning in terms of shadow prices for resources at locations. As indicated in the first answer, they tell us about the work the model needs to do in terms of bringing the (unconstrained) values into alignment with some fixed resources or endowment. (Related to concepts of shadow prices or dual prices in linear programs.)

    One way I have found to be extremely useful on these interpretations, is to compute the sensitivity of the LMs [not necessarily in a linear model] to some exogenous change ,,, then they can (at least in my work) line up with concepts such as rents and wages. Although you would have to slog through some preamble to get to the point, the idea is explained in this paper: (see below)

    In case you prefer a more physical approach there is a very nice connection between KKT conditions and forces on springs. I will add the reference in an update to this note.

  • R. C. Mittal added an answer in LS-DYNA:
    What is the advantage of using DEM rather than FEM element in LS-DYNA?

    FEM is long considered as an efficient tool. Not many finite element software have the DEM element for analysis. So, what is the basic difference that could make DEM as a strong tool for analysis?

    R. C. Mittal · Indian Institute of Technology Roorkee

    By DEM  if you mean Discrete Element Method, then it is a tool to show motion in fluid etc. DEM is always combined with FEM or a mesh free method.DEM is effective when your solution methodology is good.

  • Dinesh Saini asked a question in Rietveld Refinement:
    Can someone describe how to do Rietveld refinement of alloys?

    Please write the steps of Rietveld refinement in fullproof software.

  • My DNA dialysis against MilliQ results in lower purity and concentration (ng). Can you help me with this problem?

    Hi, 

    I have been doing DNA plasmid PhiX 174 RF I DNA dialysis against milliq water and purity after dialysis is 1.6. Before Dialysis i have checked and it was 1.92. For my further experiment I needed 1.92 purity (better if I get greater than 1.92). I am doing dialysis  to desalt (Tris EDTA ) / i want to remove TE buffer from DNA stock. 

    1} Milliq water that i used was sterilized, cellulose membrane was pre-treated with 2% sodium bicarbonate and1mM EDTA .

    2} Time duration for dialysis 6hrs and every 2hrs i changed milliq.

    3} sterile Ultra pure Milliq ph 6.3

    Dialysis clamp , forceps to hold the cellulose membrane or handling were all sterile.

    4} Dialysis done in 4 degree C.

    Thupten Tsering · Tata Institute of Fundamental Research

    in the pdf it has mentioned that ph does effect the reading of nano drop and when i sample blank on nano drop, i use milliq water. Thanks again adam.

  • Dago Ali asked a question in Documentation:
    How to collect, anayse and document false friends (false cognates)

    I seek your guidance on the methodology that i should use to collect, analyse and document false friends. My research topic is: Towards an investigation of false friends in Lusoga and Luganda

  • Pui Shing Ho added an answer in DNA Interactions:
    Is it true that octamer DNA sequences always crystallize as A-DNA ?

    Dear All,

    Recently I received a comment that octamer DNA sequence always crystallizes as A-DNA because end part of one DNA interacts with a major groove of the adjacent one. 

    But some references like Basham's A-DNA triplet code (http://www.pnas.org/content/92/14/6464 )and Dickerson's "... Tyranny of the Lattice ..." paper suggest this is not always true.

    Please give me your valuable comments to understand this observation. 

    Pui Shing Ho · Colorado State University

    There are always exceptions to every "rule." However, for the most part, if the DNA is not perturbed by a drug or other molecule, it is generally accepted that octadeoxynucleotide duplexes will crystallize as A-form DNA, driven primarily by crystal packing forces, as you had described.

  • How can I quantify bacterial DNA genome level from a single insect?

    Hi, I have to measure a bacterial DNA level in single insect level. Do you have any idea about how to quantify them? By insect weight or instar stage?    

    Carl Angelo Medriano · Korea University

    I agree... real time PCR. Should you have a specific target bacteria, you can use specific primers and normalize it with the 16s quantification to get relative quantification of that specific bacterial DNA.

  • Lianfeng Zhang added an answer in Benzene:
    Why does the color of benzene change when interface with uv lamp and what can I do to prevent of this?

    I am working on advanced oxidation processes.

  • Shian-Loong Bernard Lew added an answer in FDI:
    Has anyone used the concept of "attractors" to map out FDI flows for a nation?

    Attractors are probably what comes closest to an "equilibrium" for a dynamical system. While the trajectory of the system may vary, its stability may still be captured through an attractor classification. It would be interesting to note certain attractor properties in connection to FDI, and the set of assumptions need to allow for such a scrutiny.

    So far aware of one paper that uses the term "strange attractor" in connection to FDI figuratively. And not in its strictly chaos definition(s).

    Shian-Loong Bernard Lew · Taylor's University

    Hi Pahlaj,

    Thanks for your interest and vote of confidence!

  • Shian-Loong Bernard Lew added an answer in Topology:
    Do fish markets rely mainly on topological or geographic advantage for global dominance?

    Metric for dominance: tonnes/year.

    Topological:layout/floor plan (intra-organizational)

    Geographical:location relative to sea or urban centres (supra-organizational)

    Cases-in-point:Tsukiji (Tokyo) & La Nueva Viva (Mexico City): ranked 1st & 2nd in the world, respectively.

    Shian-Loong Bernard Lew · Taylor's University

    Hi Akira,

    Yes that is deliberate because I am trying to see where New Economic Geography (NEG), will take me with this question. Given that PEG has covered a lot of the messy, social, cultural issues. In essence whether idealism/theoretical explanations are possible (more akin to "laws of causation" than "issues of contention"). The two camps and their views are discussed in great detail in the linked resource.

  • Joseph R Moore asked a question in Allelopathy:
    Does anyone have a good publication examining dual direction allelopathy? ie both species interfere with each other?

    I want to examine the allelopathy (through root exudation) of two species to determine and compare the relative allelopathic potential of both species. 

  • A power series summation a_n z^n such that a_n tends 0 as n goes infinity. How can we show it does not have pole on unit circle?

    A power series summation a_n zn such that a_n tends 0 as n goes infinity. How can we show it does not have pole on unit circle?

    Suhail Gulzar · University of Kashmir

    @Peter;  The singularity of ln(1-z) is not an isolated singularity at z=1, so the usual classification into, pole, essential, or removable does not apply. It is the typical example of a branch point.

  • Melissa Morabito added an answer in Sexual Assault:
    Can anyone advise me about up-to-date campus security issues, particularly relating to sexual assaults?
    I am doing a paper on campus security and it covers such a large area that it is too difficult to cover in great detail. I am therefore trying to build it around the many recent news articles relating to campus assaults, and how the institutions handle these situations, particularly in relation to any discipline imposed if the attacker was a student.
    Melissa Morabito · University of Massachusetts Lowell

    Clearly, universities have not done a great job addressing sexual assault.  

    http://www.ed.gov/news/press-releases/us-department-education-releases-list-higher-education-institutions-open-title-ix-sexual-violence-investigations

    Keep in mind however, that victims can report anonymously to a counseling center. The Campus Police would only find out that a sexual assault had occurred but would not be able to investigate.  When reported to the campus police, they would investigate the crime but do not mete out the punishment. These decisions are separate from the criminal justice system. 

  • Is it possible to ensure the preservation of heritage through tourism proposals and make it profitable in times of crisis?
    This project aims to promote the dissemination of heritage interventions already performed related to local development as a long term strategy for the preservation of heritage.
  • How can I do Spatial Multicriteria Evaluation/Anaysis in ArcMap?

    I would like to identify suitable damping sites for our Municipality and I would like to use ArcMap. Is it possible? If so, how can I go about it? I also need to do network analysis for shortest routes from collection points to the damping sites. Anyone who can help me?

    Morton E. O'Kelly · The Ohio State University

    Generally, dumps and waste disposal sites are "noxious" facilities. While there is no easy analytical answer, a heuristic solution will often be to place this facility far away, i.e. on the edge of a jurisdiction -- away from as many people as possible. So, you might make two layers -- the cost of reaching all the cells in the region from each potential location (smaller is better) and the isolation or inaccessibility from affected populations (larger is better). A very simple multi-criterion analysis would show points with some weighted combination of these two scores, and possible identify local minima. Other environmental suitability / unsuitability scores can also be factored in.