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  • Essam Kotb added an answer in Enzyme Purification:
    Is a column for gel filtration chromatography (120 cm*1cm) for protein purification an appropriate method?

    We have a column for gel filtration chromatography (120 cm*1cm) that we will use for enzyme purification. We want to load it by Sephadex G-75. What height (cm) of column packed with sephadex is needed? Is this an appropriate method?

    Essam Kotb · Zagazig University

    I agreed with all comments in that your column longer and thinner than usual. I dont agree with Bahman Momen in stopping of valve after sample application. Elution must not disturbed by closing and opening of valve.

  • Yordan Muhovski added an answer in Contamination:
    Fungal genomic DNA isolation issue? I am seeing low MW bands of contanination in my gels... ANY IDEA?


    My DNA isolation protocol seems to be working ok but I am seeing some low MW bands around 75-300 bps. Attached you will see my most recent gel. Gels (1% agarose) run for 30 minutes @ 130mV. Any idea what the low bands could be? I am looking for clean high MW DNA for sequencing this organism. 

    To give more background on my gDNA isolation protocol, I am running a phenol:chloroform extraction with both a RNase A and proteinase K digest. I am able to reproduce these results but everytime I isolate DNA I am seeing these smaller bands present in my DNA samples. I am working with a fungal cell whose cell wall is very difficult to disrupt. I am using a freeze-dry approach and mashing up cells into a fine powder. In my final steps, I am using a isopropanol and then an ethanol precipitation of DNA.

    When running nano-drop analysis, I am seeing a  OD (260/280) of around                  1.98-2.0. so I can assume there is some sort of contaminant. I know I should be seeing a reading closer to ~ 1.8. I have been told everything from "I have RNA contamination, to even having protein contamination." I am not sure what it is, but does anyone have any easy ways to clean these contaminants out?   

    Thanks for input!

    Dan Roettger

    Yordan Muhovski · Walloon Agricultural Research Centre CRA-W

    For me this is  RNA contamination (not well digested by RNAse A RNA). Try to clean up by column as proposed Ivan. Good luck!

  • James F Peters added an answer in Medieval History:
    How did Greek arithmetic give rise to Liber Abaci arithmetic?
    See above.
    James F Peters · University of Manitoba

    As a followup to the observations by @Milo, consider first a detailed account of liber abaci from an ancient Arab mathematician's perspective is given in

    J.D. Rey, Algebraic operations in an early sixteenth-century Catalan manuscript, 2008: 


    And in an effort to get closer to an answer to the question for this thread, consider

    J. Hoyrup, Proportions in Liber Abaci, 2008:


    See, especially, the comments about Fibonacci on the 10 non-arithmetical means between two numbers studied in ancient Greek mathematics (p. 9) and the Table (p. 10) that compares various ratios relative to Pappos, Nicomachus and Liber Abaci.

  • Jack M. Gallup added an answer in RNA:
    Oligo-dT vs. random Primer cDNA synthesis of RNA from FFPET

    I'm currently working on my bachelor thesis, where I use to extract RNA form FFPET.

    Therefor I've compared different kits for their quality of extracting RNA from 10ym tissue samples simultaneousely. The quality of the recovered RNA was assessed by 260/280nm ratio and by synthesising cDNA using both, oligo-dT- as well as random-primer. The synthesised cDNA was further used in a PCR with a self-made cDNA-ladder, which amplifies products between 100 and 600bp.

    However, the cDNA synthesised by usage of oligo-dT only resulted in amplification of maximum 200bp-products, whereas cDNA synthesised by usage of random-primers showed products with a size up to 600bp.

    I'm grateful for every explanation!

    Jack M. Gallup · Iowa State University

    There have been publications a while back that have discussed the idea that many mRNAs isolated from FFPE sections lack their poly A tails due to fixation and adduction. of adenine by methylol bridging interferes with 3'-oligo d[T]n binding as well.
    One such reference:
    RNA expression analysis from formalin fixed paraffin embedded tissues
    Susan M. Farragher · Austin Tanney · Richard D. Kennedy · D. Paul Harkin
    Accepted: 5 July 2008 © Springer-Verlag 2008

  • Kirk Flippo added an answer in Projection:
    What is shape of our universe?

    Its been told that we are all projection of holographic plate , can anybody let me know what is shape of our universe?

    Kirk Flippo · Los Alamos National Laboratory

    Latest  from the WMAP data (Jan 2014) confirms that it is flat to within 0.4 percent..



    More on geometry..


    but, I think this all assumes "normal" inflation is correct...which the holographic theory may have a different interpretation(1), as the 4-D event horizon is 3D which would shield this universe from the initial singularity (the big bang).  This of course all assumes stars in a 4D universe implode into black holes. :-)  We will find out maybe soon if Fermilab's Holometer (E-990) experiment works and let us know if we are living in a hologram!

    (1) http://www.pbs.org/wgbh/nova/next/physics/collapsing-4-d-star-could-have-spawned-universe/





  • Donald Myers added an answer in Kalman Filtering:
    Can Kalman filter apply in pixel value to interpolate pixel?

    I want to reconstruct images using a Kalman filter. The pixel has three value R, G, B so I don't know how to deal with Kalman filter equations.

    Donald Myers · The University of Arizona

    In general a Kalman filter only works with numerical data. One solution is to replace the RGB pixel values with numeric ones, e.g.  R =1, G =2, B =3 but this assignment is arbitrary and your predicted values will not necessarily be integers. A better choice would be to use the wavelengths corresponding to RGB  but again the predicted values would not necessarily be limited to the wavelengths corresponding to RGB.

    You probably need to look at the literature on Bayesian image reconstruction, this is similar but not quite the same as suggested by Acharya. They appear to be suggesting a Markov chain approach, one problem is that the image is presumably 2D unlike time which is 1 D and has a clear notion of before and after.

    One possibility is to use Indicator Kriging, you still have to transform to numeric values (see the literature on geostatistics).

    It would help if you could clarify whether you have a fixed image with some pixel values missing and you want to predict the missing values vs an image that is changing and you want to predict future images from past images (the latter is closer to a Kalman filter problem, even there you will want to also look at either Markov chain or Bayesian methods)

  • Petr Neruda added an answer in Iron Age:
    Do you know prehistoric graves of which the season of burial is known?

    I am looking for graves for which the season of burial is known. I am particularly interested in Neolithic, Bronze and Iron Age Europe, but will follow up any hints! Season should be documented by botanical remains, pollen, or other scientific evidence.

    Many thanks!

    Petr Neruda · Moravské zemské muzeum

    Dear Katharina,

    for Palaeolithic period it is interesting the grave of a man in Dolní Věstonice II where the season was analysed on the base of fauna seasonality analysis. See e.g. https://www.researchgate.net/publication/251636471_Seasonality_of_Gravettian_sites_in_the_Middle_Danube_Region_and_adjoining_areas_of_Central_Europe

    It is DV II, skeleton 16.


  • Where is the intelligence in AI?

    Like many others, I am very enthusiastic about artificial intelligence, but the more I studied the AI, the less intelligence I found in it. What I found was classification, pattern recognition, and regression. Is there any hope for real AI to be developed in the future? Is it still correct to call AI AI?

    Taiwo Oyedare · Tennessee State University

    Artificial Intelligence is a very interesting field with a lot of mathematical concepts embedded. I believe that it is better than programmable machines because it learns from its environment and the makes a decision based on the input to its environment.

  • How do I conduct a focus groups interview (FGI)?

    Focus groups interview (FGI) is  one of the method for data gathering in qualitative research. what are the criteria for conducing an appropriate FGI or how to conduct a focus groups interview (FGI)? 

    Fatma Osman Ibnouf · University of Khartoum

    Focus group is a form of group interview that places particular importance on interaction between participants. Focus groups interview is ‘focused’ which means that it is used for a specific purpose and that a fair amount of advance planning/preparing is required. The group discussion must be guided by a moderator using a carefully designed interview guide - meaning the moderator is required to determine what should be asked. The questioning process needs to be structured in a particular way – start by opening questions after the moderator introduces him/herself, explains the goals of the research, and thanks the participants for their time and involvement in the study. The first question is a general inquiry into the topic, and should be followed by specific questions relevant to the study. After the group of participants reflects on these opening questions, the moderator should ask more in-depth questions for clarification or validation purposes. Interesting issues that have been emerged during focus group discussions should be further examined by the moderator by asking relevant questions. The formulation of questions thus depends largely on the extent to which the moderator feels a need for the clarification of issues, to validate certain information that have been gathered during the discussions. During the session, the moderator should not losing control of the discussion to participants who deviate from the topic, probe when interesting ideas emerge, and ensure that everyone has an equal chance to participate and each question is answered during the session.

    Conducting accurate focus groups depends on the skills of the moderator, appropriate note taking, the accurate transcription of the discussions and well organized focus groups. In addition the location of the focus groups should be well thought out. For best results, a group of 6 to 8 participants is highly recommended. The interviews should be recorded or an assistant moderator should assign to record key notes of the discussions.

  • Omid Paknia added an answer in DIVA GIS:
    How to refine MaxEnt model by removing variables that are highly correlated?
    I have 30 non-overlapping presence records of a species collected during 2011-2013 across 1000 sq. km. landscape. I tried MaxEnt modelling using 19 bioclimatic variables obtained from worldclim and altitude, but I am not sure about how to choose appropriate variables and how to refine the model step-by-step. I tried doing a correlation analysis on the 20 variables which I extracted from DIVA GIS in the form of text files, and found that there is high correlation between lots of them. I also want to add vegetation data to the model, how should I go about it?
    Omid Paknia · University of Veterinary Medicine Hannover

    I was following this interesting discussion! But  so far could figure out how do PCA on WORLDCLIM variables! From the technical perspective and after extracting 2-3 axes how model the potential distribution on that?! Any packages exist for these steps? Thanks in advance for your help!    

  • How can one make explicit a focus group's interaction while analyzing and reporting data?

    In an ongoing analyze and writing process according to a focus group study I have to be aware of how the interaction produced a depth of data. Further I have to find a way reporting this in the manuscript. What is your experiences and ways of dealing with this issue?

  • Yordan Muhovski added an answer in Blood Cells:
    How can I extract mRNA directly from whole bird blood?

    I want to isolate mRNA from bird blood (nucleated blood cells), but haven't found a protocol that does that directly.  Most of the protocols I've seen for blood entail a two step process: isolating total RNA, and then enriching for mRNA.  On the other hand, there are non-blood protocols that can isolate mRNA directly.  Does anyone know of a one-step protocol for getting mRNA from whole blood?

    Yordan Muhovski · Walloon Agricultural Research Centre CRA-W

    Hi, I do not think that such a kit exists. Why don't you extract total RNA and afterwards mRNA, it will take you not so long.Good luck!I

  • Tapasya Babu added an answer in Soil Analysis:
    Could somebody tell me a standard procedure to determine iron, aluminium oxides and hydroxides in soil samples?
    Determination of the iron oxide and aluminium oxide fractions in soils
    Tapasya Babu · Louisiana State University

    Thank you very much Dr Kenneth Towe. 

  • Salam Alrekabi added an answer in Sonication:
    Do the defects on the sidewall of CNTs, caused by intense sonication condition, lead to influence the interfacial bonding between CNTs and the matrix?

    It's obvious that the intense sonication conditions lead to increase the dispersion level of CNTs and in the same time shortening the CNTs length and making defect on the side wall of the tubes. would you please advice me with appropriate way to make the dispersions and avoiding these issues.

    Salam Alrekabi · University of Brighton

    Dear Noa,

    Thanks a lot for your answer, am using powder CNTs ( as recieved).

  • Christopher R. Lee added an answer in 3D Printing:
    What is the future of liquid chromatography?

    LC is/has been traditionally associated with mm-scale inner diameter columns, packed with 3-5 um particles. But today, we have access to e.g. UHPLC columns, monolithic columns, in all shapes and sizes. Some groups are in the trenches working on e.g. pilar array structures, open tubular columns, and 3D-printed columns.

    But what would you say is the future of LC? Or to be a bit provocative, does it have a future at all?

    Christopher R. Lee · Retired

    Returning to my earlier comment about the absence of a universal detector, it may be worth remarking that the particle beam LC/MS interface of a quarter century ago did perform that role --- sometimes. Electron and chemical ionisation are, together, nearly universal, but (according to the theory) the momentum separator was effective only when the amount and properties of the analyte permitted the formation of discrete particles. I don't know if the technique could be revived, perhaps by exploiting more recent developments in ion mobility separation methods.

  • Jack M. Gallup added an answer in RNA Yield:
    What do you think is the best and the most sensitive Reverse Transcription Kit?

    I want to synthesize cDNA, but my RNA yield is so low (around 10-50 ng/ul). It will need more than just an ordinary Reverse Transcription Kit. What do you think is the best for this case? Thanks before! :)

    Jack M. Gallup · Iowa State University

    Hi Ariananda -- The VILO cDNA synthesis kit (Invitrogen) claims to be good at this - and you may also want to look at a TATAA Biocenter product as well (Mikael Kubista is the founder there):


  • We are not detecting any absorption dip for any gas! Light is passing through the mirrors and mirrors are 99.999% reflective! Reasons??

    Laser spectroscopy, Optics and Photonics, Spectroscopy

    Serge Grabtchak · University of Prince Edward Island


    Can you clarify the statement that  "Light is passing through the mirrors and mirrors are 99.999% reflective!" One excludes the other. Which one are you certain in? Have you measured transmission and reflection?


  • Kerry Altman added an answer in Psychiatry:
    What are some practical ideas for providing trauma-informed services?

    I teach a variety of continuing education seminars to practitioners who provide public behavioral health care services in Pennsylvania. I am always looking for practical and accessible information for these courses that, broadly speaking, address trauma, PTSD and complex PTSD in various populations across the lifespan, including children, adolescents, veterans, adults with Serious Mental Illness, including Personality Disorders, and  co-occurring disorders, etc. SAMHSA's publication of TIP 57 (Trauma-informed Care in Behavioral Health Services) is an excellent reference. I was wondering if there are individuals who have experience with developing or providing a training series to staff about the actual implementation, e.g., the "what" and the "how's" of practices that are trauma-informed. Thank you.

    Kerry Altman · Strategic Interactions, Fairfax, VA, United States

    Yes, of course-  John Briere's work is a perfect example of applied psychodynamic/attachment theory in the field of trauma recovery

  • How to estimate the mineralogical composition (C3S, C2S etc.) of cement?

    How to estimate the mineralogical composition (C3S, C2S, C3A, C4AF etc.) of cement? Is there any analytical instrument or we can estimate it from oxide composition?


    Matteo Leoni · Università degli Studi di Trento

    try using X-ray diffraction. Identification is almost unequivocal and if you are lucky you can even quantify them

  • James J Coyle added an answer in Server:
    Are we going to see inheritance IT infrastructure and its setting vanish within the next 5 years?

    Eliminating the need of having servers, meanwhile the new software would be ready to run on cloud available online, not to mention the expansion in applications and increase in complexity and scalability. All of these changes I suggest would mean the vanishing of IT infrastructure as we know it.

    James J Coyle · Iowa State University

      If you look at the US electrical grid as a model for this, then one could say that most people use centralized services rather than have their own generators.

      However, big data centers use UPS power to bridge to generator power for their most critical services,  likely computing would be the same.  On site (backup) computing power for critical infrastructure for when network interruptions occur, with automated switchover.  Hybrid private public clouds already exist for this kind of situation.

      Individual even have backup generation capabilities. (Backup gasoline generators or automated natural gas whole house backup generators.)

      Prices for cloud services will have to come down.  We already have heavy users who tried EC2 and have come back to campus for cheaper service.  Light users, or users of free services of course keep using those.  (Free advertizing supported email, etc.)

  • EL AJJOURI Mohssine added an answer in Omnet++:
    Intrusion detection with NETA and Omnet++

    I would like to implement my new architecture of intrusion detection with omnet ++ and NETA framework, can someone advise me some technical articles in order to evaluate and validate my approach :

    1. Identify modules: Simple modules and parameters.
    2. Set network topology via the NED language.
    3. Add behaviors C ++, every single module requires a class C ++
    4. Write code: for each simple module, write a derived class cSimpleModule
    5. Write the configuration file, INI file.
    6. Building project.
    7. Perform simulation
    EL AJJOURI Mohssine · Ecole Nationale Supérieure d'Electricité et de Mécanique de Casablanca

    Thank you Peng for your answer.

    Other suggestions ?

  • How do you analyse Raman spectra data with the Raman peak, area, width, intensity? Is there a program which could help me analyze these data easily?
    I have a set of multiple Raman map scannings which consist of various data points on the map. I am trying to study the formation of the MoS2 tribofilms on the surface and hence would like to understand its phenomenon according to the Raman data analyzed. However, the software which I am using is the Renishaw Wire 4.0, and is not really helpful in analyzing batch processes. I was wondering if there is a program which can help me do this analysis more easily and also to understand the phenomenon according to the various Raman characteristics I can obtain.
    Vinay Veerachary · Technische Universität Chemnitz

    LabSpec has been very useful for me.

  • Justin Snyder added an answer in Psychotraumatology:
    Does anyone know about guidelines for diagnostics of PTSD in refugees/asylum-seekers?

    It is a dilemma how to screen asylum-seekers for PTSD, if this diagnosis can enhance the likelihood that the person can stay in the host country. Are there any standards, guidelines, or best-practice-experiences on how to ensure the quality of the diagnostical process in such cases?

    Justin Snyder · Saint Francis University, USA


    Now that I better understand your question, I think the Fassin and Rechtman citation would be very useful to you.  I would agree with Dragana that this is a country by country issue, including the ultimate relevance of a PTSD diagnosis in granting asylum.

    I think the fundamental question regarding "best-practices" is whether the PTSD diagnosis is useful for validating the story of torture, genocide, etc., especially since only a minority of victims will typically suffer it.   Furthermore, if these refugees are being persecuted for religious or political reasons, their religious and political convictions can make them resilient to PTSD.  Finally, why is a medical diagnosis being used to judge the veracity of a story, as if the truth lies in the symptoms rather than the person's own words?  (This is in no way to disparage the work people like Dragana do in helping potential refugees.  I think it is quite commendable!!!)


  • Could somebody recommend a good working selective growing medium for Glomus intraradices and Trichoderma harzianum?

    Could somebody recommend a good working selective growing medium for Glomus intraradices and Trichoderma harzianum?

    Wolfgang Schweigkofler · Dominican University of California

    Hi Ivan,

    there are a number of semi-selective growing media for Trichoderma listed on the net; most of them using rose bengal. I'm attaching an example (Elad et al. 1981):


  • How do you choose the optimal laglength in a time series?

    There are several criterion for choosing the optimal laglength in a time serie: AIC : Akaike information criterion ; BIC : Schwartcz information criterion ; HQ : Hannan-Quinn criterion ; RMSE : Root Mean Square Error ; MAE : Mean Absolute Error; BP : Bias proportion ; LIK : Log-Likelihood. The discrimination function differs from one to another criterion.

     We can therefore obtain conflicting results.  How to choose the optimal laglength? Are there tests that compare the criteria between them?

    Hamed Shakouri G. · University of British Columbia - Vancouver

    In my opinion, each individual criterion is insufficient to judge about model, e.g. a time series model. I prefer combining several criteria, especially significance of the parameters (using say t-student) is important, as well as the statistics on the residuals behavior, e.g. being white and normality.

    See: A Systematic Fuzzy Decision-Making Process to Choose the Best Model Among a
    Set of Competing Models

    by Hamed Shakouri G. and Mohammad B. Menhaj


  • Cesar Valencia added an answer in Fuzzy Clustering:
    Is there example of FCM and ANFIS working collaboratively in practice?

    Anyone have a clear practical example of how those two algorithms work together ? 

    Cesar Valencia · Pontifícia Universidade Católica do Rio de Janeiro

    Hi, have another paper here:


  • Francine Vachon added an answer in Failure:
    How can I get data showing project failure for an extended period for an IT project?

    I need help getting data showing project failure for an extended period to determine if there is some trend to be seen. Because of the interdisciplinary nature of IT Management, I would need a cross-sectional view to look at a minimum of two variables i.e. project management failure and IT governance failure or any other combination with project management being the focal point i.e. project management failures and IT service management failures or project management failures and enterprise architecture failures.

    This will help me to cover one of the sections within my literature review to be able to quantitatively scrutinise possible correlation between these variables in the context of IT Management.

    The extended period should, at the very minimum, be five years - preferably a minimum of 10 years - so I can work on producing graphs and analyse these as part of my literature review.

    Thank you in advance for your help - any guidance is welcome. All I need is data showing percentage failures in years between 1990 and 2000 - or something mirroring this view.


    Francine Vachon · Brock University

    Unfortunate, organizations actively avoid making data about failures public.  It may be difficult for you to obtain this data (but I hope you do). 

    Roy and Aubert studied systems failure with qualitative case studies with face to face interviews with employees.  The employees and company names were kept confidential.  See this reference:

    Roy, Vital, and Benoit A. Aubert. "A Dream Project Turns Nightmare: How Flawless Software Never Got Implemented." Cahier du GReSI no 2 (2002): 05.


    This paper was published as book chapter:

    You may be able to obtain data about the "Canadian Firearms Information Systems" which was a spectacular failure in terms of cost over runs, and project management and implementation problems.  Since it is a government project, a great deal of data should be obtainable.


  • Please, I need powerpoint presentation of seminar in inorganic chemistry, in synthesis of inorganic complexes, please help me???????

    please, I need powerpoint presentation of seminar in inorganic chemistry, in synthesis of inorganic complexes, please help me???????

    I want to write my seminar, but I don't know how

  • David A. Reilly asked a question in Rage:
    What musical artist has the best lyrics and songs about social justice?

    Bob Dylan, Rage Against the Machine, Dead Kennedys, Billy Bragg, Cake... who else?  I'm particularly interested in anti-globalization music...