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  • James F Peters added an answer in Mereology
    Thank you
    Thank you for the invitation--Judith Miller
    James F Peters · University of Manitoba

    Judith,

    Here is a paper on mereology from a philosophical perspective:

    G. Hellman, Mereology in philosophy of mathematics:

    http://www.tc.umn.edu/~hellm001/Publications/MereologyandPhilMath.pdf

    Here is another paper that might interest you:

    C.M. Keet, Introduction to part-whole relations: mereology, conceptual modelling and mathematical aspects, 2006:

    http://www.inf.unibz.it/krdb/pub/TR/KRDB06-3.pdf

     

    What aspects of mereology do you find interesting?

     

  • How to prevent protein aggregation during purification?
    I am purifying a protein having molecular weight around 65KDa. I want to use it at a concentration of 5mg/ml but at this concentration it gets aggregated. What should I do to prevent its aggregation?
    Bhupesh Taneja · Institute of Genomics and Integrative Biology

    What's tangential filtration? 

  • Kyle Kovary added an answer in Phosphorylation
    Can anyone help with quantitative mass spectrometry of proteins?

    I don't have an idea about mass specs of proteins but am curious to know if it is possible to have a relative abundance of phosphorylated/unphosphorylated protein from mass spec data? 

    Kyle Kovary · Stanford University

    If you don't know what phospho sites you want to quantify before hand, this is a good method:

    "A large-scale method to measure absolute protein phosphorylation stoichiometries." 

    http://www.nature.com/nmeth/journal/v8/n8/abs/nmeth.1636.html

     

    If you do know the phospho sites/states you can use SRM-MS. Here is a paper that came out of my lab a few months ago using SRM-MS: 

    "Gli protein activity is controlled by multisite phosphorylation in vertebrate Hedgehog signaling."

    http://www.sciencedirect.com/science/article/pii/S221112471300733X

     

    Let me know if this answers your question or if you have any more questions.

    + 1 more attachment

  • How do banking bail-outs and other corporate welfare undermine the state's moral authority?or citizens to get money?

    Considerable discussion & opining occurs on various blogs concerning government spending, debt and allocation of funds to respective persons and causes, but often neglect how money is created and conveyed to institutions at the top of the economic food-chain, or how those institutions benefit, often at the direct cost of those farther down. In the case of banks and their investment mistakes, bailing them out reflects directly upon the debt side of the public's balance sheet (taxpayers), at the expense of public benefits & services (not enough money, and printing more dilutes the value of dollars already in circulation). Since the notion of capitalism promotes self-reliance & responsibility on the part of all players, how do bail-outs in general (and the laws surrounding banking in particular) undermine the moral authority of governments to enforce work norms when high-level players seem to be exempt, even while enjoying obscene benefits obtained by ostensibly legal business practices that amount to gaming the system?

  • Hossein Soleimani added an answer in X-ray CT
    How do I find the threshold value for soil-water-air system?

    My image contains soil-water and air. How should I segment this picture and find threshold value.

    Hossein Soleimani · Isfahan University of Technology

    I could not find that slices you have attached!!!!!

  • Panayot Tanchev asked a question in Hip Arthroplasty
    Does anyone have experience with bilateral Girdlestone hips after removal of infected THR ?

    In the past the Girdlestone procedure has been practiced for severe OA of the hip. In cases of bilateral Girdlestone very poor results have been reported in the 1950's and 60's as far as walking ability, daily activities, pain, etc. In the era of THA similar cases seem to be very rare. Nevertheless, there are some patients who refuse re-arthroplasty or cannot be subjected to it for different reasons. I wonder if somebody has experience with the outcome results in such cases.

  • Jorge Leao added an answer in Physics
    Can we mathematically model consciousness?
    We have seen that AI, which was supposed to be a failure, is coming back with gusto on the back of multi sensor robotics and possibly androids with quantum computers. There is some mysterious counter intuitive behaviour in the sub atomic world which seems to suggest inanimate objects do sense the external world. It would be nice to know the views of experts from different fields, such as math, science, psychology, sociology, cosmology on this intriguing subject. One possibility that comes to mind is if probability is actually such a model, as it does incorporate randomness.
    Jorge Leao · Federal University of Rio de Janeiro

    Dear all,
    I am an engineer doing very practical developments in AI (expert systems), nothing near research about consciousness.
    Of course I am very interested in this subject for even a small progress in this field may help me make better systems.
    I was thinking about the difficulty an arthropod (say a centipede, a predator like us), after their first 130 million years of evolution (we primates have no more than 30 million years of evolution, depending how you count them), would have to understand the level of consciousness and the cognitive powers a human, a species that would exist some 300 million years in their future would have. I am supposing we, primates and arthropods, are two points in an evolutionary tree and that we have much in common, like a nervous system ;) .
    Maybe many people are not bothered at all when someone says it would possible to model the consciousness of a centipede by a Turing machine. But then why would one be bothered if someone says it would be possible to model human consciousness alike.
    In fact, I do have doubts if humans like the ones of the present will ever be able to have a complete understanding of what we call physics (dark matter and energy and what cames after). Maybe another species, superior to humans in this aspect, will be able to understand a little more. And then again…

  • Which method will be better for the vibrational properties simulation, GGA or B3LYP?

    I am calculating the vibrational properties such as IR and Raman for Conducting polymers at DFT, so which functional will be appropriate for my system and why?

    T. Karthick · KSR Institute for Engineering and Technology

    Dear Habib Ullah

    Actually B3LYP with the higher level basis set 6-311++G(d,p) gives better results when compared to GGA. you may find the usage of B3LYP with 6-311++G(d,p) in many literatures. 

     

  • Wenfeng Cai added an answer in Senescence
    Can anyone give advice on heart tissue senescence detection?

    I want to detect the heart tissue senescence by Senescence β-Galactosidase Staining Kit purchase from CST company.The aged mouse (17 months) has been used in my experiment, but I can't get the positive result according to the protocol. I wonder if someone can analyze the reason for me? Thank you for your help.

    Wenfeng Cai · University of Cincinnati

    To detect telemere lengh may be another choice.

  • What is the ideal management span of control within an organization?

    Span of control is most used in Business Management and Human Resources Management. The bigger the number of the subordinates a manager controls, the broader is her/his span of control.

    Reginald L. Bell · Prairie View A&M University

    I say the perfect number is 10 people should be reporting directly to one person in a functional organization. In a matrix organization or a more modern hybrid organizational structure, there should not be more direct reports than a manager can communicate with in a timely manner; a manner that does not clog-up decision making and hampers the feedback and feed-forward process. 

     

    When a manager cannot communicate effectively with direct reports because there are too many the span of control must be reduced.

  • Emilie Lacaze added an answer in Comet Assay
    What is the best way to degrease glass slides for the Comet Assay?

    I have tried ethanol and methanol, and the agarose still ends up at the center of the slides before it is completely dried or it does not cover the periphery of the slides. Any suggestions? I am having a hard time with this one. Thanks.

    Emilie Lacaze · Institut national de la recherche scientifique

    Dear Karen,

    to avoid the gels falling off the slides during electrophoresis, you can try to play with 2 parameters : temperature and electrophoresis time. Prepare your electrophoresis buffer at least 1 hour before and keep it at 4°C. You can also put ice packs around your electrophoresis chamber to keep the temperature low. You could also increase the ratio V/cm (generally between 0.6 to 0.8 V/cm) while decreasing time duration of electrophoresis (it is the voltage gradient across the agarose gel coupled with duration time of electrophoresis that determines the migration of DNA).

    Hope it can help you.

  • Leona M. Ungerer added an answer in E-Commerce
    What factors will affect online shopping behavior of consumers?
    What enters the mind of consumers before making an online purchase? Doubt, excitement, convenience, risk, etc.
    Leona M. Ungerer · University of South Africa

    The link that I referred to.

  • Doreen Saidpace added an answer in Anatomy
    (How) do you include Bloom's Taxonomy in your anatomy course?

    Bloom's Taxonomy (originally developed by Benjamin Bloom) is a classification method used to assess the different student learning outcomes set by instructors. This tool categorizes questions into six levels of cognition; Knowledge (remember), comprehension (understand), application (apply), analysis (analyze), synthesis (create), evaluation (evaluate). While knowledge and comprehension are considered low order cognitive skills, application, analysis, synthesis, and evaluation represent high order cognitive skills.

     

    Generally, anatomy is regarded primarily as a memorization-centered discipline, or a low order cognitive skill course. However, there are many possible ways to design exam questions to promote higher order thinking, thus, I propose the following question:

     

    Do you design questions for your anatomy course with Bloom's Taxonomy in mind?

    How do you implement these questions for each level of the tool (ie. multiple choice, short answer, etc.)?

    What designs have proven to be the most effective to promote student learning?

     

    Resource:
    http://fitnyc.edu/files/pdfs/CET_TL_BloomsTaxonomy.pdf

    Doreen Saidpace · The University of Sheffield

    For any lesson or lecture, there has to be at least 4 to 6 open ended pre-planned questions, based on Blooms to ensure opportunities to think at a higher order level. These have to be pre-planned as higher order questions are not easy to formulate. Also, you can use posters for each level of thinking so even your students can formulate their questions using question starters on the stems of each flower. These posters can be found on tes.co.uk.

    I am attaching a slightly modified version. Hope that you will find them useful.

    + 5 more attachments

  • Can serum amyloid A (SAA) be used as an indicator of health status in reptiles?

    During a health assessment is necessary to identify healthy individuals, but reptiles are considered stoic, able to avoid showing obvious signs of inflammatory diseases.

    Acute phase-response proteins, such as haptoglobin and serum amyloid A, have proven to be sensitive measures of inflammation/infection in domestic large animal species. 

    Caliendo et al. (2013) investigate the possible use of SAA as a health indicator in falcons. (See attached)

    Harr et al. (2006) assessed diagnosis of generalized inflammatory disease by Serum amyloid A, measured by ELISA, followed by albumin:globulin ratio, measured by plasma gel electrophoresis in manatees. (See attached)

    Under what conditions might be useful to determine this acute phase-protein (SAA) as an indicator of an inflammatory process during a health assessment in reptiles? 

    Payam Hatami · University of Tehran

    Usually increase in diabetic patients because of to dialysis

  • Daniel Lajeunesse added an answer in Osteoblasts
    Can anyone share a good method for quantifying alizarin red staining in osteoblasts?

    I need to quantify the intensity of alizarin red staining / mineralized nodule formation in osteoblasts derived from differentiated MSCs. Can anyone recommend a good method?

    Daniel Lajeunesse · Université de Montréal

    Mineralization

    of cell cultures was measured by quantification of alizarin

    red staining (ARS) with the procedure of Gregory et al. [54]. Briefly,

    cells were fixed in 10% formaldehyde, incubated with 40 mM alizarin

    red at pH 4.1, washed and air-dried. Cells are then extracted with 10%

    acetic acid for 30 min, scraped from the Petri dishes, heated at 85 °C

    for 10 min and then transferred on ice. An aliquot of the cell extract is

    incubated with 10% ammonium hydroxide and the color product read

    at 550 nm against a standard curve.

  • Fabian Benz added an answer in Gastroenterology
    Does anyone have any experience with Adrenomedullin and Pancreatic Cancer?
    Adrenomedullin (AM) seems to be linked to pancreatic adenocarcinoma (ADC) and new-onset diabetes (NOD). Does anyone have any experience in this field? We are trying to test serum AM levels and immunohistochemical AM staining in patients with pancreatic ADC. We need to share our experience.
  • Which is the most accurate technique for solving MHD equations ?
    I want to know which technique gives more accurate result for solving MHD equations ?
    Sergey Victorovich Shchepetov · Russian Academy of Sciences

    Sorry, but you need to clarify the question. MHD equations have no general solution idependent on model, boundary conditions, geometry etc. Variety of problems can be solved analytically within simplified equations. Numerical tools also work within simplified models, say reduced MHD. .

  • How can you take a Blood Pressure measurement using PPG signal from a fingertip only?
    I am working on the measurement of blood pressure using a PPG signal only detected from a fingertip. I want to measure both systolic and diastolic levels based on PPG signal only (without ECG). Can anyone suggest anything in this regard?
    Paulo R Benchimol-Barbosa · Hospital Universitario Pedro Ernesto

    As PPG measures vascular volume changes, PPG is very sensitive to maneuvers that causes either vasodilation or vasoconstriction locally . Therefore, a continuous calibration of the PPG curve seems to be a key point for an accurate pressure measurements.

    Although PPG waveform is quite similar to pulse pressure waveform, a transfer function may be suitable to more accurately assess and display the pressure waveform.

    Peace and blessings.

  • Agus Triawan added an answer in Mycology
    Please help me to identify these mushrooms

    please help me to identify these mushrooms

    Agus Triawan · Airlangga University

    hi Christian, thanks for the answer!

  • Martin Kang'ethe added an answer in Traceability
    Connect food safety and environmental performances of food supply chains - any thoughts or suggestions?
    For three years I deal with environmental sustainability, particularly of voluntary instruments such as Environmental Management Systems and Environmental Labels. I’d like to find a link between environmental sustainability and traceability of food supply chains. I did a research but I could not find much on the subject (if you do not respect the chain Coop in Italy and Unilever at the international level), especially regarding scientific publications. In particular, I’m looking for examples regarding disciplinary in the food chain that connect food security and the reduction of environmental impacts.
    Martin Kang'ethe · Riara University

    Dear Michele,

    You can as well refer to the concept done by Normansyah Syahruddin in 2011 on Towards Traceability of Cocoa- Chocolate Supply Chain. He highlights on issues of sustainability and traceability. See the following link.

    http://mpra.ub.uni-muenchen.de/31247/

    Regards,

    Martin Kang'ethe

  • Which is the best kit for BAC DNA isolation?

    I received some RP23 and RP24 BAC clones form CHORI BACPAC resource center. I am trying to isolate the BAC DNAs in high quality (free of chromosomal DNA and RNA). I tried the QIAGEN large construct kit but the final yield is extremely low. For 500 ml E. coli culture, only about 1 ug BAC DNA was isolated. If not using the exonuclease that was included in the kit to remove the E. coli chromosomal DNA, I have higher yield but 90% are E. coli chromosomal DNA, 10% are BAC DNAs (confirmed by qPCR). I have noticed that some researcher uses different kits for BAC isolation. Two kits seem to be mentioned.
    1) MACHEREY-NAGEL NucleoBond® Xtra BAC kit
    2) Epicenter BACMAX™ DNA Purification Kit
    Which kit is the best one for BAC DNA isolation? Did anyone use one of the kits and get a high yield of BAC DNAs free of chromosomal DNA and RNA? I've never worked with BACs and neither has anyone else in my lab. Any advice would be appreciated. Many thanks.

    Rajendra K Gangalum · University of California, Los Angeles

    One of the best kits i used to get intact BAC with simple protocol is

    BAC MAX BACDNA isolation kit from Epicenter Technologies.

    Pls see the article we published in Biotechniques

    http://www.biotechniques.com/BiotechniquesJournal/2011/November/Purification-of-BAC-DNA-for-high-efficiency-transgenesis/biotechniques-323254.html

    Hope this help you.

    RKG

     

  • Debi S. Saini added an answer in Curriculum Design
    How do academics act as central agents for curriculum change in higher education? How would you act as one in your context?
    Curriculum change in higher education involves a broad range of behaviors between (1) accepting or allowing what happens or what others do without active response or resistance to (2) creating or controlling actively a situation rather than just reacting to it after the change has started; actions of academics lies at the various points along “the continuum between passivity and pro-activity”(Louvel, 2013, p. 669). THIS QUESTION SEEKS TO IDENTIFY AT WHAT POINT YOUR ACTIONS ARE IN THE CONTINUUM, YOUR BEHAVIORS, AND YOUR STRATEGY TO THE CURRICULUM CHANGE. Reference: Louvel, S. (2013). Understanding change in higher education as bricolage: how academics engage in curriculum change. Higher Education, 66(6), 669-691.
    Debi S. Saini · Management Development Institute Gurgaon

    I know, academics in India in universities have not done well in the area of  curriculum change. In many departments, the old syllabus goes on for more than two decades. Teachers do not want to update themselves as that would involve more work on their part. Fortunately, my institute is outside the university system, and we have our own autonomy.

    I partly change my course contents almost every year at least in case of one of the three subjects that I teach, by adding and subtracting new readings and cases. In case of labour law, the syllabi can not be changed unless a law is repealed or replaced or amended, which does not happen too often.

  • Bettina Braun added an answer in Linear Regression
    How can I interpret regression when an insignificant interaction term makes significant predictors insignificant?

    I have two predictors in linear regression: A (gender coded as 0-1) and B (continuous, centered). A and B are significant predictors. When I further introduce the interaction term (A x B), the interaction term is insignificant, yet, it also makes B insignificant.

    How to interpret and handle this situation? Should I retain the interaction term in the equation? Does it mean that B is insignificant after all?

    Theory-wise, the effects of A and B are hypothesized, yet I introduce the interaction to claim that these effects are independent from gender differences.

    Thank you RG community for your support!

     

    Bettina Braun · Universität Konstanz

    Dear Jochen, thanks for the very detailed outline, with which I fully agree. It reminded me of a recent paper by Cumming (2014) in Psychological Science. However, practically speaking, it is very difficult to get research published if you do not provide p-values (I just mention the efforts of various authors to estimate p-values for linear-mixed-effects regression models). 

    Regarding Lukasz' question, I would have thought that a reasonable next step would be to compare the linear regression model with the interaction term to one with only the main effects (for instance using the R-function anova(mod1.lmer,mod2.lmer, see suggestions in Cunnings 2012). Or do you see problems with that procedure, Jochen?

     

    References

    Cumming, Geoff. 2014. The new statistics: Why and How. Psychological Science 25(2). 7-29.

    Cunnings, Ian. 2012. An overview of mixed-effects statistical models for second language researchers. Second Language Research 28(3). 369-382.

  • Protein-Peptide docking

    I am facing problems while running the peptide docking. First I tried using the peptide docking panel provided by the BioLuminate module since there is a provision in providing the peptides in the form of text. I exercised that option and I run the job though the job got completed successfully there were no ligands found. Then I tried following the normal Glide XP docking for that I need the peptides to be prepared using LigPrep but the job died due the exceed in the no.of atoms. The peptide length is of 13 and 12 residues respectively and I am unable to proceed. Please suggest what should be done? Is there a way the no.of atoms count can be increased so that the Ligprep job is done? Even though the no.of atoms are within the range 300 but the no.of rotatable bonds are many and the docking job dies.
    From the manual, the peptide docking can be done provided the peptide length range is within 16. In my case it falls within that range am unable to complete the job. Please suggest what exactly I must do.

    Vijayinder Saini · Central University of Punjab

    Hi Richard,

    The problem that i have found with you is self explainable by the line you have said 'no.of rotatable bonds are many and the docking job dies' . So try the docking by restrict the rotatable bonds as minimum as possible. May this will help....have a good time

  • What is the best introductory book on medical statistics for beginners?
    A text that explains the concepts without much math and formulae? Beginners in medical research in clinical trials/epidemiology often need a basic book on medical statistics that is appropriate for self study.
    Sean P Madden · Infraredx, Inc.

    All good suggestions above.  I think Bernard Rosner's, Fundamentals of Biostatistics is an excellent and reasonably-priced choice as well. 

    It is the reference used for the highly useful page for contingency table analysis: http://statpages.org/ctab2x2.html.  I find this page to be more accurate than a couple of expensive software packages, and it includes confidence intervals for many quantities that the others don't.

    In my own work however, I find it a bit frustrating that there is sort of a different gold standard text or publication for a wide variety of commonly used methods.  And equally frustrating that you can spend a lot of time getting a computation exactly right by the literature only to have a nit-picky journal reviewer still disagree with some subtlety (or even just be dead-wrong).  And acquiescing rather than arguing is usually the better path to publication.

    All that being said, I find that a good software package, its help files, and the function reference therein to be more useful than any single textbook.  i.e. Matlab, SAS, PASS,...etc.  They will usually have a programmed method and example for something you are interested in, there will be a succinct and effective explanation, and there is a reference for you to use in the paper.  PASS even goes a step further in frequently generating the proper statistical jargon for you to use as well.

  • Digital communication

    Why and which type between discrete scalar channel and vector discrete channel is advantageous ?

  • Why would the amygdala be more active during a congruent Stroop trial, compared to an incongruent?

    I have conducted an fMRI study comparing recovered anorexia nervosa patients to healthy controls on an emotional stroop task. The task consists of fearful and happy faces, overlaid with either the word 'fear' or 'happy'. Thus, a given trial can either be congruent (face and word match) or incongruent (face and word mismatch). The task was to designate if the face was happy or fearful, ignoring the word. Reaction time data showed that it takes longer to respond to incongruent trials compared to congruent trials, which we expected.

    However, the fMRI analysis shows that, for the control group, participants had more bilateral amygdala activation during congruent compared to incongruent trials (as shown by the extracted beta weights from left and right amygdala). I expected more amygdala activation for incongruent trials (thinking that an emotional conflict conveys more saliency). I am struggling to understand our observation. 

    Does anyone have any comments regarding this finding? All comments are highly appreciated!

    Steve Thomas Beukema · The University of Western Ontario

    Perhaps it has something to do with an emotional memory contribution? According to http://www.sciencedirect.com/science/article/pii/S000632230600583X 

    "Following sad mood induction, bilateral amygdala response during encoding of valenced words predicted increased recall of negative self-referent words..."

  • What are the reasons to consider humans as a resource in modern business?

    I am Md. Mizanur Rahman. Now i am working as a Senior Lecturer, Department of Business Administration, Metropolitan University, Sylhet, Bangladesh. My research interest areas are Management, HRM Issues. 

    Reginald L. Bell · Prairie View A&M University

    ...By the way, read Peter F. Drucker's (1954) The Practice of Management where he answers your question nearly perfectly.

  • What is the best way to teach qualitative research?
    My students find it difficult to apply theory to practice.
    Doreen Saidpace · The University of Sheffield

    Hi!

    I concur with the above answers that to learn about something is to either engage in it or else read papers who have engaged with it and learn from their experience.