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  • Yves Lignereux added an answer in Mass Extinctions:
    Are we entering the sixth mass extinction?

    (This is in response to current article in Science journal published on 19 June 2015)

    Yves Lignereux · Institut National Polytechnique de Toulouse

    18,000 discovered in 2012 are not new species: they existed before their description.

    322 killed off since 1500 : many more may have disappeared without having been officially described or even only seen.

    How many dinosaur species disappeared in the KT crisis ? Not so much (only 800 dinosaur species are known for the entire Mesozoic !)… We can conjecture that much less than a hundred dinosaur species were killed off, plus some pterosaurs and mosasaurs, a few ammonites and foraminifer species. Not really a mass extinction, was it ?

    As for the impact of human caused extinctions on human well-being, only psychiatrists will be able to characterize it: a kind of schizophrenia between stupid triumph over savageness and profound sense of guilt.

  • Calli Tzani added an answer in SPSS:
    Is my variable scale or ordinal in SPSS?

    I conducted an experiment on polygraph to test its efficiency. Participants' scores were ranked as 2 for the highest score, as 1 for the second highest and as 0 for all the rest. In SPSS i set the values as 0 for low efficiency and as 1 for high efficiency. Is my variable scale or ordinal?

    Thank you

    Calli Tzani · University of Huddersfield

    thank you Steve,

    a lot researchers of the field use logistic regression, that is true, but here i want to compare the efficiency in each repetition of the tests' questions. in addition there are no other independent variables.

  • Virginia Claudio added an answer in Exosomes:
    Best kit for exosome isolation: Life Technologies, Exoquick or Exo-spin?
    I would like to isolate exosomes from a culture of macrophages (RAW) and 3 available exosome purification kits came up: the Exosome Isolation kit (Life Technologies), Exoquick (System Bioscience) and Exo-spin (Cell Guidance System). What is the most efficient kit? (I would like to analyse the protein content of those exosomes by western blot).

    Also, I have no idea about the size of the cell culture required to yield enough exosomes for analysis. Does anyone have an answer?
    Virginia Claudio · Chalmers University of Technology

    Check this out everybody! 

    http://www.ncbi.nlm.nih.gov/pubmed/25939587

    "Exosomes derived via Total Exosome Isolation Reagent (TEIR) as well as ultracentrifugation (UC) from the SKOV3 cell line were analyzed. Spectra of exosomes derived via TEIR are dominated by a signal characteristic for the TEIR kit that needs to be subtracted for all measurements."

    @Heather: getting single beautiful peaks is no sign of lack of artifacts due to the specific isolation method. You can still use a kit, but then one should be careful and honest about the biological claims and conclusions.

    @Wassim: One can quantify based on total protein extract and/or NTA. In my opinion protein is better.

  • Adil Abu shana added an answer in Shared Decision Making:
    Does anybody know of any research exploring the relationship between cancer follow up management and the governance model of cancer care networks?

    Does anybody know of any research exploring the relationship between cancer follow up management and the governance model of cancer care networks?

    Well, Thanks a lot!

    Adil Abu shana · University Of Kufa

    dear  angela

    answer for your letter

    i will try to design and implement  methodology for diagnosis breast cancer   using heath care management  and need for scholarship phd to doing it

  • Erlandio R Wobber asked a question in Transportation:
    Can anyone help me in finding real data set for capacitated directed transportation network?

    I am looking for a transportation network with directions and capacity for each link/edge.

  • Peter G Hains added an answer in LC-MS/MS:
    How do I analyze LC-MS/MS data for a with label free approach using progenesis QI software?

    I am searching for a reference article which uses  LC-MS/MS analysis to make Quantification with label free approach using Progenesis QI software. I have two set of protein profile with control and treated with a target compound, this results are obtain through LC-MS/MS analysis followed with label free approach using Progenesis QI software.

    if there any related research article to take as reference while writing a article ?

  • Tausif Alam added an answer in Cognitive Systems:
    Is Chalmers' so-called "hard problem" in consciousness real?

    In his 2014 book "Consciousness and the Brain: Deciphering How the Brain Codes Our Thoughts" Stanislas Dehaene wrote "Chalmers, a philosopher of the University of Arizona, is famous for introducing a distinction between the easy and the hard problems. The easy problem of consciousness, he argues, consists in explaining the many functions of the brain: how do we recognize a face, a word, or a landscape? How do we extract information form the senses and use it to guide our behavior? How do we generate sentences to describe what we feel?

    “Although all these questions are associated with consciousness,” Chalmers argues, “they all concern the objective mechanisms of the cognitive system, and consequently, we have every reason to expect that continued work in cognitive psychology and neuroscience will answer them. By contrast the hard problem is the “question of how physical processes in the brain give rise to subjective experience … the way things feel for the subject. When we see for example, we experience visual sensations, such as that of vivid blue. Or think of the ineffable sound of a distant oboe, the agony of an intense pain, the sparkle of happiness or the meditative quality of a moment lost in thought … It is these phenomena that poses the real mystery of the mind”."

    Stanislas Dehaene's opinion is "that Chalmers swapped the labels: it is the “easy” problem that is hard, while the “hard” problem just seems hard because it engages ill-defined intuitions. Once our intuition is educated by cognitive neuroscience and computer simulations, Chalmers’ “hard problem” will evaporate".

    Personally, I agree with Stanislas Dehaene's opinion.

    Tausif Alam · University of Wisconsin–Madison

    Arnold,

    Can your retinoid model also predict that I am hallucinating an image of Johnny Carson with a turban holding a card in his hand but the face is actually yours!  ;) 

  • Violeta Beleva Guthrie added an answer in Network Analysis:
    Random walk betweenness centrality algorithm for a directed weighted graph?

    I am interested in algorithms that do not use shortest paths to estimate node and edge centralities in directed weighted networks.

    I have considered the algorithm by M.E.J. Newman, which was derived from a current flow analogy, therefore it seems to me it would not apply to a directed network: http://arxiv.org/pdf/cond-mat/0309045.pdf 

    I am also trying out the algorithm by Alahakoon et. al., from  which I can get an approximation of the betweenness centralities for nodes, but the error terms and required run time have been derived for node and not edge betweenness:  http://www.csee.usf.edu/~tripathi/kpath-centrality.pdf

    Are there other (random-walk) algorithms can estimate both node and edge betweenness for my type of network?

    Violeta Beleva Guthrie · Johns Hopkins University

    Thank you very much, Henning: I am looking at the 'spanning edge' paper, and it does seem to provide an interesting alternative to current-flow-type centralities. My network is however not strongly connected, so there are quite a few node pairs with no directed paths connecting them.

    I also found a method that generalizes Newman's random-walk betweenness to directed graphs and allows for self-loops via the "counting betweenness":  http://journals.aps.org/pre/pdf/10.1103/PhysRevE.83.046127

    Still, I would be happy to learn about more methods that assess centrality without using optimal paths (shortest paths, maximum flow, etc).

  • Thomas Fungenzi asked a question in Farming:
    How to determine an optimal soil respiration (or microbial respiration)?

    It is commonly suggested that the higher the soil respiration (or the higher microbial respiration) the better for the soil.

    Is it true?

    Do you know if, instead of this approach "the more is better", scientist have determined that actually higher respiration in farm soils is not always needed.

    I have seen that some authors suggested that respiration reduces through the establishment of a living cover, meaning that a more stable status of the vegetation after disturbances is associated with lower respiration rates.

    My question concern mainly agricultural soils.

    I could summarise by asking: Do we want our farm soils to exhale as much as possible CO2?

  • Scheherazade Sadegh-Nasseri added an answer in T Cell Receptor:
    Can someone explain what the phrase "high affinity T cell receptor" means?

    I need it in lay language. I am reading a paper right now.

    My understanding right now is that T cells are usually low affinity for the MHC ligand. What is the importance of a high affinity T cell receptor for cancer research?

    Thanks!

    Scheherazade Sadegh-Nasseri · Johns Hopkins Medicine

    Low affinity T cell receptor bearing T cells bind poorly to their pMHC ligand. The idea to generate T cells with higher affinity has been around in Cancer treatment but making T cells with high affinity TCR is not trivial, and their more effective responsiveness is not granted. One can increase the affinity or rather avidity (longer overall binding) by increasing the ligand density (number of pMHC ligand). Alternatively, one can generate genetically altered multimeric TCR to increase binding affinity/avidity. The concept of CAR in cancer treatment is based on higher receptor affinity that may not even be specific for pMHC ligand but some other molecules of the cancer cells. These receptors are chimeric and send effective signals through the cell leading to killing.  Look up at some of Carl June publications. A link for some general information is attached.

  • Dol Nath Khanal added an answer in Python:
    I'm beginner in programming.Among two languages Matlab & Python which is more efficient for scientific computation?

    Scientific Computation

    Dol Nath Khanal · University of Wisconsin - Milwaukee

    Thank you very much for your insight. I am also considering Python but the libraries associated with Matlab is something to also consider. 

  • Mirosław Stygar added an answer in Materials Engineering:
    What is a suitable Etchant for Al 6061?
    I want to see the grain boundaries of Al 6061, so what is the proper etchant and what is the etching procedure? I tries Kellers reagent but it still doesn't work.
    Mirosław Stygar · AGH University of Science and Technology in Kraków

    Hello, I found this in "Metallography and Microstructures 2004 - Vol. 9 ASM Handbook".

    Please look at attached file.

    Best regards and also good luck :-)

  • Paul Walsh added an answer in Molecular Biology:
    Circular plasmid or linearized plasmid, which one is better for transformation?
    For transformation of foreign DNA, E. coli prefer circular plasmid while Bacillus subtilis get higher transformation efficiency with linearized plasmid. What is the reason for that?
    Paul Walsh · Massachusetts Institute of Technology

     @Partha you asked, "1.what about the endonucleases, isn't it cleaves circular DNA also?”..
    E coli and B subtilis inhere endonucleases and exonucleases.
    Endonucleases digest both linear and circular DNA.
    Exonucleases digest only at DNA ends. Circular DNA has no ends and, therefore, cannot be digested by exonucleases. That is a major reason why circular DNA is digested more slowly than linear DNA within bacterial cells. 

     
    You also asked, “2. linear DNA can also be religated by DNA ligase present in the host. Does it occurs?
    Ligase is present within cells at a much lower concentration than exonucleases and endonucleases.  
    Digestion by nucleases is ONE reason why circular DNA transforms E coli more efficiently than linear DNA. 

     
    Wikipedia has two entries which describe transformation. They include the following, "The chemical method, however, usually does not work well for linear DNA, such as fragments of chromosomal DNA, probably because the cell's native exonuclease enzymes rapidly degrade linear DNA. In contrast, cells that are naturally competent are usually transformed more efficiently with linear DNA than with plasmid DNA.”


    Transformation efficiency:  https://en.wikipedia.org/wiki/Transformation_efficiency


    Transformation (genetics):  https://en.wikipedia.org/wiki/Transformation_(genetics)


    Each includes links to source material in pier-reviewed journals including data on DNA deletions and rearrangements much greater for linear DNA than for circular DNA when transformation of E coli is attempted.

  • Natalia L Kononenko added an answer in Mouse Brain:
    What part of mouse brain should be analyzed for seizures?

    What part of mouse brain should be analyzed for seizures?

    Natalia L Kononenko · Charité Universitätsmedizin Berlin

    Entorhinal and perirhinal cortices!

  • Shaloam Dasari added an answer in GPx:
    What is the relatioship between lipid peroxidation and antioxidant enzymes in case of treated Vs normal cancer cells ?

    I know that there exists a direct relationship between lipid peroxidation and SOD, Cat, GPX etc., But there is lot of ambiguity when it comes to working with a particular cell line. Please post your inputs here. Thank you.

    Shaloam Dasari · Jackson State University

    Thank you. This is going to be very useful. I appreciate your valuable suggestion.

  • Peter Kobor added an answer in Miridae:
    Where can I find a good key on the Central-European members of familiy Nabidae and Miridae?

    I'm looking for key on the families written above, any kind of help is welcome!

    Thank you in advance,

    Peter

    Peter Kobor

    Thank you, Eduardo!

  • Hossein Dariush Fahimi added an answer in Autistic Disorder:
    Does any one have access to the electronic or print version of some new assessment tools in Autism?

    I need some newly assessment tools in autism including Autism Spectrum Disorder- Comorbid for Children (ASD-CC), Autism Spectrum Disorder- Diagnostic for Children (ASD-DC), Autism Spectrum Disorder- Problem Behavior for Children (ASD-PBC), and Profile of Toileting Issues (POTI).

    Hossein Dariush Fahimi · Universität Heidelberg

    Sorry this is not my field.

    Best of luck

  • Alain Celzard added an answer in Materials Research:
    Is PVC carcinogenic when exposed to sunlight?

    I am writing a paper regarding PVC and the effect of sunlight on the material. I am looking at it from a chemistry perspective in terms of human health.

    Alain Celzard · University of Lorraine

    PVC under sunlight produces elimination reactions, i.e., -CH2-CHCl-   -->   -CH=CH- + HCl, as the C-Cl bond is the weakest (at around 300 kJ/mol). HCl is obviously neither an inert nor harmless compound ...
    Alain

  • Carmine Taglialatela Scafati added an answer in Dental Implants:
    What is immediate dental implant protocol?

    What is immediate dental implant protocol?

    Carmine Taglialatela Scafati · Ospedale S.Maria delle Grazie - Pozzuoli
    1. 1) una buona quantità di osso disponibile, ancora meglio se di buona qualità: D1-D2 Misch
    2. inserire quanto più impianti è possibile: il carico immetiato su un solo elemento triturante o  di guida occlusale, ha ridotte possibilità di sopravvivenza, soprattutto in pazienti bruxisti.

    Per a mia esperienza, il problema è più semplice di quanto si possa immaginare.

  • Isbelia Mejia Cordero asked a question in Teaching:
    Are there research works about reflection as a way to improve teaching practices?

    Selfreflection

    teacher development

    Autoetnography

    Journals

  • Artur Pomadowski added an answer in Biopython:
    Does class DSSP of biopython gives the relative solvent accessibility value of amino acids?

    I would like to have relative solvent accessibilities of amino acids in a protein, thinking of using DSSP module of biopython. I am not sure if the output has rsa (relative solvent accessibility) or is it needed to be calculated?  

    Artur Pomadowski · Jagiellonian University

    According to the example in commentary line in DSSP class (attached link):
    """
    190 >>> p = PDBParser()
    191 >>> structure = p.get_structure("1MOT", "1MOT.pdb")
    192 >>> model = structure[0]
    193 >>> dssp = DSSP(model, "1MOT.pdb")
    194 >>> # DSSP data is accessed by a tuple (chain_id, res_id)
    195 >>> a_key = list(dssp)[2]
    196 >>> # residue object, secondary structure, solvent accessibility,
    197 >>> # relative accessiblity, phi, psi
    198 >>> dssp[a_key]
    199 (<Residue ALA het= resseq=251 icode= >,
    200 'H',
    201 72,
    202 0.67924528301886788,
    203 -61.200000000000003,
    204 -42.399999999999999)

    it looks like it gives you both, absolute (72) and relative (0.679...) values of solvent accessibility.

    also:
    300 # Relative accessibility
    301 resname = res.get_resname()
    302 try:
    303 rel_acc = acc/MAX_ACC[resname]

  • Faranack Nader Benz added an answer in Pastoralism:
    Does anyone know of studies that deal with the settlement of semi-nomadic community?

    I'm looking for research articles about the relationship between pastoralism and a sense of place, especially in the Middle East and East Africa.

    Faranack Nader Benz · Niagara University, New Yok, United States

    Historically, rivers, seas or oceans would be the origin of any primary civilisation because of the asistance of the water to any basic organism and live-cells to florish and survive; human-kind and its livestock was not exception is this regard. Of course, plants and vegitations came right after livestock; but suitable soil & climate, immobility of plants, and time conseming process of basic agriculture, were some of the issues that animals became the number one companion for mankind. The space related phenomena, especially in the dry and hot climate of Middle East caused that primary communities formed themsevies right around the fertile areas of water-sides, far from challenge with gravity and no water in higher elevations for most, unless it was cold enough to prevent evapurations from body. Seasons, altitudes, and longitutes' differences were other scope of problems, in which each culture developed its own style to use plants and animal-skins as textile to stay rested along with his or her companions; the rest would be a graduale process of development, in this vicinities.   

  • Jill Miotke added an answer in DAPI:
    How can I prevent auto florescence in a frozen section of human skin?

    Hi everyone, I need your help! The image below was stained with DAPI (blue), Phalloidin alexa flour 568 (grey), vancomycin bodipy® fl conjugate (Red) and CD163 alexa flour 647 . I get unspecific signal with very high intensity when i excite at  wave lengths 405 and 488 and 568 nm. How can i solve this problem? Thanks!

    Jill Miotke · University of California, Irvine

    Dear Rueben ,

    I can't tell from your image, but it it possible you are looking at collagen or elastin autofluorescence?  I see this some times in nerve sheaths (collagen) and blood vessels (elastin), and it is excitable with a couple of the wavelengths you mention.  I would think that both of these proteins would be present in skin samples.

    The link below is to the PDF containing common cures for autofluorescence from the Wright Cell Imaging Facility in Toronto.  It has more information about dealing with collagen and elastin autofluorescence, as well as a bit more detail on the techniques mentioned by Barae and Maria.   

    http://www.uhnres.utoronto.ca/facilities/wcif/PDF/Autofluorescence.pdf

    Also, thanks to Khalid for the information on TrueBlack treatment for lipofuscin autofluorescence! 

    Good luck,

    Jill

  • Neil Culff added an answer in Experiential Learning:
    Any advice on experiential learning cycle and organisations?

    Grateful for your assistance.  Does anyone know of any texts which discuss how organisations fit within the Experiential Learning Cycle?  Particularly, can undertaking an activity - in this case, an emergency exercise - provide an organisation the opportunity to go through the 'active experimentation' phase, or is this restricted to individuals and teams/groups?

    Many thanks,

    Neil

    Neil Culff · Coventry University

    Many thanks Laura, I shall take a look at those sites.

    Neil

  • Terry Moore added an answer in Measure Theory:
    Is there any use in constructing/defining integration over (some subset of) the rationals?

    I was working on 2 papers on statistics when I recalled a study I’d read some time ago: “On ‘Rethinking Rigor in Calculus...,’ or Why We Don't Do Calculus on the Rational Numbers’”. The answer is obviously trivial, and the paper was really in response to another suggesting that we eliminate certain theorems and their proofs from elementary collegiate calculus courses. But I started to wonder (initially just as a thought exercise) whether one could “do calculus” on the rationals and if so could the benefits outweigh the restrictions? Measure theory already allows us to construct countably infinite sample spaces. However, many researchers who regularly use statistics haven’t even taken undergraduate probability courses, let alone courses on or that include rigorous probability. Also, even students like engineers who take several calculus courses frequently don’t really understand the real number line because they’ve never taken a course in real analysis.

    The rationals are the only set we learn about early on that have so many of the properties the reals do, and in particular that of infinite density. So, for example, textbook examples of why integration isn’t appropriate for pdfs of countably infinite sets typically use examples like the binomial or Bernoulli distributions, but such examples are clearly discrete. Other objections to defining the rationals to be continuous include:
    1) The irrational numbers were discovered over 2,000 years ago and the attempts to make calculus rigorous since have (almost) always taken as desirable the inclusion of numbers like pi or sqrt(2). Yet we know from measure theory that the line between distinct and continuous can be fuzzy and that we can construct abstract probability spaces that handle both countable and uncountable sets.
    2) We already have a perfectly good way to deal with countably infinite sets using measure theory (not to mention both discrete calculus and discretized calculus). But the majority of those who regularly use statistics and therefore probability aren’t familiar with measure theory.

    The third and most important reason is actually the question I’m asking: nobody has bothered to rigorously define the rationals to be continuous to allow a more limited application of differential and integral calculi because there are so many applications which require the reals and (as noted) we already have superior ways for dealing with any arbitrary set.

    Yet most of the reasons we can’t e.g., integrate over the rationals in the interval [0,1] have to do with the intuitive notion that it contains “gaps” where we know irrational numbers exist even though the rationals are infinitely dense. It is, in fact, possible to construct functions that are continuous on the rationals and discontinuous on the reals. Moreover, we frequently use statistical methods that assume continuity even though the outcomes can’t ever be irrational-valued. Further, the Riemann integral is defined in elementary calculus and often elsewhere as an integer-valued and thus a countable set of summed "terms" (i.e., a function that is Riemann integrable over the interval [a,b]  is integrated by a summation from i=1 to infinity of f(x*I)Δx, but whatever values the function may take, by definition the terms/partitions are ordered by integer multiples of i). As for the gaps, work since Cantor in particular (e.g., the Cantor set) have demonstrated how the rationals “fill” the entire unit interval such that one can e.g., recursively remove infinitely many thirds from it equal to 1 yet be left with infinitely many remaining numbers. In addition to objections mostly from philosophers that even the reals are continuous, we know the real number line has "gaps" in some sense anyway; how many "gaps" depends on whether or not one thinks that in addition to sqrt(-1) the number line should include hyperreals or other extensions of R1. Finally, in practice (or at least application) we never deal with real numbers anyway (we can only approximate their values).
    Another potential use is educational: students who take calculus (including multivariable calculus and differential equations) never gain an appreciable understanding of the reals because they never take courses in which these are constructed. Initial use of derivatives and integrals defined on the rationals and then the reals would at least make clear that there are extremely nuanced, conceptually difficult properties of the reals even if these were never elucidated.

    However, I’ve been sick recently and my head has been in a perpetual fog from cold medicines, so the time I have available to answer my own question is temporarily too short. I start thinking about e.g., the relevance of the differences between uncountable and countable sets, compact spaces and topological considerations, or that were we to assume there are no “gaps” where real numbers would be we'd encounter issues with e.g., least upper bounds, but I can't think clearly and I get nowhere: the medication induced fog won't clear. So I am trying to take the lazy, cowardly way out and ask somebody else to do my thinking for me rather than wait until I am not taking cough suppressants and similar meds. 

    Terry Moore · Retired

    Neil, you don't lose this result with interval arithmetic.

  • Savannah Brookins asked a question in Tissue Sectioning:
    What is a good antibody for IHC to identify dendrites in mouse tissue sections?

    I know Map2 is most commonly used to identify dendrites, but it seems to only work in cultured neurons. Does anyone have a recommendation for a different marker for IHC use in tissue sections? Or a Map2 protocol that works with sections? 

  • Isbelia Mejia Cordero added an answer in Action Research:
    What are some good models for conducting action research in your classroom?

    Time to do research is sometimes challenging when you have a busy teaching schedule. Doing action research involving issues in your classroom is one way around the "research time" challenge, but what are some good models for conducting action research successfully (e.g. completing it in a reasonable time)?

    Isbelia Mejia Cordero · Universidad del Norte (Colombia)

    Hi, Debra

    Nowadays, is meaningful and better use the PAR because is a collaborative work that involves students, peer colleagues, parents, and administrator staff.  We can use the qualitative approach using different techniques to develop our research projects.

  • Kåre Olaussen added an answer in Electrostatics:
    Could the fundamental dimension of Electric Charge be Mass only?

        After solving dimensions of electrical equations, I found out that the fundamental dimension of Electric charge is mass only. This also leads to the derivation of dimensions of other Electrical units like Electric Current, Magnetic flux density etc in terms of Mass, Length and Time only. These are not cgs units.
         This discovery can help unify the force of gravitation that uses mass and the electrostatic force(Force between charges).This will help contribute to the theory of everything, also in better understanding of the electrical units and equations. e.g Work done=Charge times Voltage. Substituting the right handside with their dimensions of Charge=Mass and Voltage=L^2T^-2 proves that the equation is dimensionally consistent. Also other theories can be uncovered and better understood with this finding.
         I wish to be challenged if possible and I will show the steps of the derivation.

    Kåre Olaussen · Norwegian University of Science and Technology

    Max. I have rarely read such an amount of rubbish in a single paragraph in my life. Nevertheless, I must disappoint you with the verdict that it does not quite qualify as Toillprat!

  • Ryan M Boileau added an answer in S2 Cells:
    Any suggestions for a good inducible expression systems in S2 cells?

    I am looking for a non-leaky inducible systems in fly S2 cells.

    Found "copper sulfate" but not sure if there are better solutions.

    Ryan M Boileau · University of California, Berkeley

    My experience with S2's is that a pMT vector (CuSO4 induction) is the standard for inducible expression in S2. I have not observed any leaky expression in my experiments with this.