Q&A

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  • Yurii V Geletii added an answer in Metal Complexes:
    Which metal complex (Ni or Zn) shows better results in Cyclic voltmeter studies ?

    Which one is best for CV studies of metal complexes with same type of Aromatic ligand environment.

    Yurii V Geletii · Emory University

    Your question does not make much sense. First, try to find the answer yourself. If failed, learn how to ask professional questions.

  • Dejun Li added an answer in Taqman:
    Hi, I want to perform an expression assay using TaqMan probes, is there any cheap and effective reverse transcription kit that you recommend?

    I know Applied biosystems has a good reverse transcriptase, but I need something not so expensive. If there is any kind of one step RT-PCR that you also know feel free to recommend any....Thanks!

    Dejun Li · Chinese Academy of Tropical Agricultural Sciences

    We often use reverse transcriptase of Invitrogen, and it is cheap and good quality.

  • Yurii V Geletii added an answer in Catalyst:
    What is the critical parameter in the oxidation reaction by H2O2 with Na2WO4 2H2O and PTC catalyst?

     We are busy in oxidation of a long chain aliphatic alcohol to acid by H2O2 with catalytic quantity of   Na2WO4. 2H2O and PTC (Tricaprylmethylammonium chloride), but  we could not see exothermicity during addition of H2O2 for 2/3 reactions, and getting less yield compare to our  previous reactions. Does anyone have  experiences of catalyst inactivation during the course of this type of oxidation reaction?

    Yurii V Geletii · Emory University

    H2O2 reacts with Na2WO4 to produce "law molecular weight polyperoxotungstates," which are likely to be the reactive species. pH is a key parameter, which controls overall process. If you are running the reaction in organic solvent, then the solvent nature is important. If H2O2 solution in water and the solvent are not miscible, you have two phases reaction.  Thus, numerous parameters may control your reaction. 

  • Sal Lombardi added an answer in Frozen Sections:
    How do you store tissues before frozen sectioning?

    Fairly soon I will be finished decalcifying my tissues for frozen section preparation. Normally I would then pass the tissue along to my lab specialist to perform frozen sectioning. However, that specialist will be leaving soon, and I want to make sure my method for storage works until another cutting specialist arrives.

    I plan to wash the tissue with 1X PBS multiple times and cryopreserve the tissue in a 30% sucrose solution at 4 C overnight. The next day I will embed the tissues in OCT compound and store at -40 C in the deep freezer. Would this method work in preserving the tissues and their possible fluorescence? Thank you very much!

    Sal Lombardi · Rush University, United States, Chicago

    Thank you all for your answers.

    Jill, while I plan to use the blocks as soon as possible to avoid drying out, how soon does it take for them to dry out? A week? A few days? Thanks again!

  • Robert Wojciechowski added an answer in GWAS:
    Which is the best tool for meta-analysis of GWAS data?

    Dear all,

    I am performing a meta-analysis of multiple GWAS data and now, after an intensive QC, I have to choose a suitable software for doing it. From literature it seems that the most used tool is ´Metal´ but also ´GWAMA´ is widely used. From your experience, which one performs better? Is there any other software you can suggest me? Thanks in advance for all your answers.

    Robert Wojciechowski · Johns Hopkins Bloomberg School of Public Health

    Depends on what you want to do. If you're analyzing a half-dozen studies, just flip a coin to pick your software.

    METAL and GWAMA are both good programs. METAL does not do random-effects models as far as I know. GWAMA will spit out a lot of data errors and inconsistencies, which is great for QC. I haven't used R packages for meta-analyses mainly because of limited memory and sloooow load times. If you're doing trans-ethnic meta-analyses, MANTRA is excellent--if you have access to a lot of computing power and/or patience.

    I haven't used PLINK for metas, but it's worth a try since PLINK does everything well and, importantly, efficiently. PLINK2 (PLINK1.9) is a brilliant implementation of PLINK and amazingly incredibly fast. Plus, by far the best documentation in statistical genetics software, IMO. Thanks, Shaun Purcell. 

  • Markus Peter Auer added an answer in Stock Pricing:
    Can anyone recommend some research papers regarding the effect of earning declaration on stock prices?

    if you can provide me it by tomorrow it would be very helpful 

    Markus Peter Auer · University of Innsbruck

    The paper by Bernard & Thomas is pretty much the standard on the matter: 
    http://sites.fas.harvard.edu/~ec970lt/Readings/Post_Earnings_Announcement_Drift/Bernard%20and%20Thomas%201989.pdf

  • Gunawan Indrayanto added an answer in MS/MS:
    Can anyone advise me on GC mass spectrometry for metabolomics?

    MS or MS/MS?; single quad or triple quad?

    As a newbie, I find it puzzling with the many different configurations a GC-mass spectrometer can possess (for metabolites identification and profiling).

    I would appreciate it a lot if you could please enlighten me on a few questions below:

    1.      Is the same concept in LC-MS/MS proteomics transferrable to the field of GC-MS or GC-MS/MS based metabolomics? E.g., GC-MS/MS allows one to achieve additional structural confirmation, while triple quad allows one to perform targeted analysis of selected metabolites, etc.

    2.     Would you mind sharing with me the system you are using for routine metabolites identification and profiling, preferably with a “all-in-one functionality”?

    • (e.g. Would a triple quadrupole GC-MS/MS system the most applicable to process a much broader types of metabolites, and could fulfill the needs for most diverse scenarios of metabolomics experiments)? Just like the latest QTOF or Orbitrap mass spec which allows one to do protein/peptide quantification, quantitation; discovery, as well as certain level of targeted (MRM) analysis on the same instrument.

    If there is one such "comprehensive" GC mass spec, it would be a useful starting point for me to focus, consolidate, and read more on the literature related to its applications.

    Appreciate your advice. Thank you very much.

    Gunawan Indrayanto · Airlangga University

    Hi

    I have publications regarding metabolomic by GCMS (but it is not too new publications), maybe you have not yet those articles

  • Can I use the GPS locations of wolf scat for studying habitat selection?

    I would like to know if it is possible to use GPS locations of wolf's scats as a radiocollar fix. My doubts are that this datas violate the assumptions of statistical analysis (eg. indipendence of samples) such as multiple logistic regression.

    Darcy R. Visscher · The King's University, Canada, Edmonton

    I think occupancy is probably the way to go in this situation.  More often then not when you find one wolf scat you will find a number of other close by (at a kill site, rendezvous site...) and they certainly lack independence, even if you do the genetics to ID individuals.

  • Markus Peter Auer added an answer in Capital:
    Is a free cash flow to invested capital (FROIC) a superior indicator of shareholder value creation to return to invested capital (ROIC)?

    Building on the discussion concerning the subjectivity of accruals and all other kinds of critique on the accounting process, wouldn't a free cash flow measure of return (FROIC) be a more valuable performance metric than its earnings counterpart (ROIC)? ROIC currently is an important ratio of interest in many boardrooms and financial planning departments, but what is your though about this cash flow version of return?

    Markus Peter Auer · University of Innsbruck

    There is no easy clear-cut answer to this. The answer depends very much on what the purpose of the metric should be. If it is used in a investor relations context ROIC (or ROE for that matter) may very well be the metric of choice due to its simplicity and widespread use. Very often you will find that institutional investors demand certain performance metrics like ROIC as an input for their internal portfolio optimization models. Furthermore, just like ROE, ROIC can be easily analyzed using the DuPont decomposition. 

    You are right that free cash flows are not as prone to "creative accounting" as a simple profit measure. However, they are also more obscure and finding performance drivers might prove impossible. In the end, free cash flow is often consulted when traditional return metrics fail. The best example for this are venture capital or private companies with consistently negative operating results and concentrated stockholders.  

  • How could I analyze which variable is categorized as CSF?

    Im conducting a research titled "Critical Success Factor of Stakeholder Management in procurement phase in EPC projects"

    I collected 48 variables from various sources such as Journal and Thesis. I designed the research with questionnaire containing likert scale 1 (not important) to 5 (most important) and asked 30 respondents to give their views on those variables.

    What I want to ask is, how could I analyze which variable is categorized as CSF? Can I use its median? If so, what is the parameter of the median?

    Thx

    One easy way to analyse your  collected data is simply ranking your 48 variables summed up (each one will vary somehow between 30 and 150). For further analysis you need to pay attention because the Likert scale used is discrete, and has only 5 levels.

  • Someone are working with Fluent, modelling cavitating flows in orifices (e.g. Nurick 1976 case)?

    I trying to do that but with not so high pressures at the inlet (around 2e5 Pa, i.e., flow with incipient cavitation). By using the Singhal (or other, e.g. Zwart et al.) model and depending on the turbulence model used, the discharge coefficient obtained is quite reasonable but, pressures along the wall are overpredicted. All papers that I have seen, showed simulations with more high pressures (5e5Pa), with some quite good discharge coefficients results. Nobody modelled cases with less pressure at the inlet. At 5e5Pa there is no data concerning about pressures along the wall, only discharge coefficient is given.

    Hamed Sadeghi · University of Toronto

    Hi Miguel,

    See the attached paper!

    Hamed

  • Dejun Li added an answer in RNA-Seq:
    Is RNA-seq reads number related to the quality of RNA preparation?

    Dear all,

    I don't have much experience of RNA-seq. I noticed that the reads number of one treatment (3 individuals) was lower than the other treatment. Similarly, the signal intensity of samples from that treatment was lower than the others in DNA-array analysis. I wonder is there any relationship between reads number/signal intensity and RNA preparation or may be in the treatment, the gene expression are not very active? 

    Any idea is welcome.

    Cheers,

    Fang 

    Dejun Li · Chinese Academy of Tropical Agricultural Sciences

    Yes, the gene number you find is related to your sample. The samples from different times or tissues show different gene number.

  • William Fuller added an answer in Value Creation:
    Do I would like to use a paired or an unpaired t test on my results?

    I am investigating the value-relevance of two performance metrics. In order to test whether one metric is superior to the other in terms of indicating shareholder value creation, I ranked the total number of firms into buckets based on their performance on either one of the metrics and then ccalculated the average return in each bucket. To test the difference between these means I use a t test. The total dataset doesn't' change (also n per bucket is the same), but the buckets may differ in firm composition. What would you advice about using a paired or unpaired t test? And if I would use a paired t test, do I would like to take the correlation between both metrics over the whole data set or per bucket? Thanks in advance.

    William Fuller · Providence Health and Services

    I find that in many cases using the paired t-test results in a much smaller number of observations because one of the constructs has either changed its characteristics significantly or declines to be measured.  As a result I find myself performing both paired and unpaired examinations between the original and subsequent measurements.  If there are statistically significant differences I look for additional causative factors before rejecting the hypotheis.

  • What is the impact of the water-cement ratio and the consistency on the compressive strength of concrete?

    Additional; What are the possible effects of a plasticizer (Sika ViscoCrete 2520) on the electrical conductivity?

    Sayed Mohammadmehdi Jamal · Hormozgan University

    The impact of the water to cement ratio is dependent on the concrete mixture in most of the time. Although, generally, with increase in the water to cement ration the compressive strength decreases. In other words, they have inverse effect on each other. In addition, the more the water in the mixture, the faster the compressive strength changes. We have been working on a paper in the same area which will be published by the end of next month. You can have it for more information if you like. 

  • Pouyan Motamedi added an answer in ALD:
    How ALD GaN, AlN and IN thin films could be protected from outer environment?

    Good day to all who are interested!Here is the question.

    I have to make some ALD processes to get some GaN, AlN and InN thin films (atomic layers near angstroms and few nm). Then I have to make a transportation from ALD system to another system. But I know that these films can be damaged by outer environment, so I have to protect them starting from ALD system till the next process begins. 

    So I think it might be some automatical box, that can be used in ALD an then it might be closed right after the ALD inside ALD system directly, so that it can keep this environment in which the process was flown.

    Is there some boxes for such purpose? Or maybe there are some other ways to protect these films?

    Thank you for the answers!

    Pouyan Motamedi · University of Alberta

    Hello Petro,

    We did a comprehensive study on oxidation of AlN. It was published a few months ago. You can find it here:

    https://www.researchgate.net/publication/264742207_XPS_analysis_of_AlN_thin_films_deposited_by_plasma_enhanced_atomic_layer_deposition

    In short, we found that the top 2-4 nanometers of ALD AlN films are extremely susceptible to oxidation. As for cleaning them, I recommend this very useful article:

    http://scitation.aip.org/content/aip/journal/jap/84/9/10.1063/1.368814

    Good Luck,

    Pouyan

  • Xiaoxi Lin added an answer in Electroporation:
    Could anyone suggest a way to cleanup ligation reaction for electroporation?

    Is it better to use column or ethanol? and would tRNA help?

    Xiaoxi Lin · University of Alberta

    Thank you! 

  • Alexander Landa added an answer in Ab Initio:
    Does somebody know publications on ab initio study of Co-Cr alloys?

    Need a copy of publication or reference

    Alexander Landa · Lawrence Livermore National Laboratory

    Thank you very much: I downloaded this paper from arXiv.

  • Kenji Kayashima added an answer in Subjectivity:
    Do you use a diagnostic cutoff value of “a”?

    An imaginary researcher obtained a diagnostic cutoff value of “a” with sensitivity of 90% and specificity of 90% for diagnosis of rare illness. Data of 20 in 200 subjects exceeded “a”; however, all 20 subjects were diagnosed normal after close examination. Is it reasonable not to obtain any patients from 20 subjects? I expected 18 of 20 patients (90%) were diagnosed abnormal. Is it a bad expectation? Do you use the cutoff value of “a”?

    Kenji Kayashima · Japan Community Health care Orgnization (Previous name, Kyushu Kosei Nenkin Hospital)

    Thank you for the answer to my question, Mr. Robert E. Erard.  I try to understand what you mean taking a long time because it is complicated.   

     I was involved in an issue regarding statistics as attached file.

  • Why my ligation is not working?

    I am doing a ligation procedure, unfortunately, I am having some problems. My vector is a pET28b that was digested with NcoI (5')  and XhoI (3'). My insert contain same restriction sites (it was amplified, digested and gel purified). It seems that it would be a easy ligation, however I do not get any colony. I am currently working with the T4 DNA ligase from Invitrogen. According with its protocol, for cohesive ends 1 hour incubation at RT can be good enough for good ligations (using 0.1 unit of ligase). Also I have tried these: According with its protocol, you can use 1-2ul of ligation reaction and transform directly. Also you can dilute the ligation reaction >5 fold and use for transformation in E.coli. In addition, after the incubation I have done Ethanol precipitation (15ul of volume) and resuspended in 5ul (I used 2.5ul of this for transformation).

    Unfortunately, I am not able to obtain any colonies at all. I would like to receive some feedback to solve this ligation issue. I will really appreciate it.

    PD: My insert concentration is 31.76ng/ul; ratio 1.90 (A260/280), my vector concentration is 13.9ng/ul; ratio 1.87 (A260/280).

    Edgard Francisco Jauregui · Washington State University

    Finally I obtained colonies that were screened with PCR, and showed my insertion!. Thanks for your help. I really appreciate your help. Amanda and Lorraine, I ran an agarose gel with my ligation product and the mix without ligase. Devin, I will have in mind your advice (it seems a nice strategy).  

  • Daniel Ivanusic added an answer in Expression:
    Which MOI is optimal?

    I am using insect cell sf9 to express my protein Uba6, which is an enzyme to activate ubiqution .Using baculovirus to express, which MOI is optimal fot Uba6 expression?

  • Daniel Davis added an answer in Metaphysics:
    Is the Principle of Sufficient Reason (PSR) invalidated by QM uncertainty, Gödel incompleteness and objective randomness in Nature and mathematics?

    The PSR “is a powerful and controversial philosophical principle stipulating that everything must have a reason or cause.” (Stanford Encyclopedia of Philosophy)The PSR looks for explanations in terms of causation and logic. Though it is not clear that both are required. The principle has a long tradition in the history of philosophy. While there appears to be little support for PSR in the philosophical literature at least one philosopher, Alexander Pruss argues in support of PSR in his book “The Principle of Sufficient Reason: A Reassessment” (2006). There are consequences in metaphysical terms that flow from either acceptance or rejection of PSR. Is there a middle ground which allows a partial or modified form of the principle in our metaphysics? Does anyone know of other contemporary philosophers, scientists, mathematicians who argue in favor of the PSR?

    Daniel Davis · Strayer University

    Jonathon,

    "Consciousness is not hard to fit into a world where consciousness is the starting point of any theory."

    Well, yeah. But the hoops you have to jump though to constitute the natural world out of consciousness sends you right out of the empirical method into the world of rational causes.

    I also think you are incorrect to claim there is no efficient causation at the quantum level. The sculpture is just an analogy and it can apply equally well to the interactions of fermions and bosons as to chiseling stone. Efficient causation has come to mean having a law or set of standards that lets you predict experimental results or engineer physical structures and processes. 

    At least 80% of all philosophy has been consumed with trying to generate the natural world out of consciousness, intelligence, spirit, divinity, goodness and many other imaginable rational causes. All these attempts have failed, including Liebniz's Monadology.

    My alternative is to acknowledge that 80% of the progress in human cultural development has been due to empirical pursuits that do everything they can to eliminate all those subjective factors from consideration. Given this fact, I recommend doing ontology and metaphysics according to the empirical method I outlined in my previous post to you.

    This method relies on the way we can imagine things occurring  in nature, rather than how we can imagine reasons and motivations for doing things. It looks for arguments to the best naturalistic explanation of things; not the best rationalistic explanation.

    A necessary being really does not explain the world of becoming and contingency, with regular ways of changing, that characterizes what we find when we look.

    More later.

    DCD. 

  • Which Factorial model is more applicable for concrete prediction modeling?

    I am working on ultra high performance concrete, I would like to know which prediction model is more suitable for concrete in terms of compressive strength

    Sayed Mohammadmehdi Jamal · Hormozgan University

    It has been proved that the artificial neural network can predict the large numbers of concrete specimens compressive strength in a very strong way with the coefficient R^2 of more than 0.9. 

  • Adam B Shapiro added an answer in Extracts:
    Does anyone know if I can use serum sample directly to perform western blot or I have to isolate protein from serum first then run the western blot?

    i must perform western blot on a protein from rat serum sample. Do I have to extract proteins from serum first and then run that on SDS-PAGE as the first step of western blot? or I can run the serum directly on SDS-PAGE and perform western blot? 

    Adam B Shapiro · Entasis Therapeutics

    The problem with running serum on SDS-PAGE is that it contains an enormous amount of albumin compared with all the other proteins, making it difficult to detect the minor proteins on Western blot. There are resins available to remove the albumin from serum.

  • Akira Kanda added an answer in Triplets:
    Is it possible to come up with a Classical model of Neutrino?

    In his recent paper, Valerii Temnenko proposes a new classical model of neutrino. He wrote the abstract as follows: "The theory contains a number of wave states, both one-sector (singlet or triplet waves) and compound two-sector ones (singlet-triplet waves). Wave states differ in number of currents: zero-current waves (free singlet or free triplet waves), one current, two-current, three-current and four-current ones. Wave states also differ in character of four-dimensional wave vector (the waves with time-like and space-like wave vector). Some forms of waves may have negative density of energy. Some wave states can be treated as classical models of a neutrino. Neutrino states are classified in accordance with the character of the current which forms the state: singlet (maxwellian) neutrino, Yang-Mills triplet neutrino, Maxwell-Yang-Mills singlet-triplet neutrino."

    Do you think that such a Classical model of Neutrino is possible? What is your opinion? Thanks

    Akira Kanda · University of Toronto

    Victor, there is a serious discrepancy between the classical theory of light and quantum (thus relativistic) theory of light as per Einstein and de Broglie.

    1. According to the classical theory, the speed of light is dependent upon the frequency of light in vacuum with current. As according to the classical theory, there must be current to have em waves, the speed of light in vacuum is relative to the frequency of light. This is in contradiction to the CSL axiom of Einstein which says that the speed of light in vacuum is constant c regardless of its frequency.
    2. According to the STR, due to Compton effect, the reflected at mirror  light changes its frequency and so the speed of light incoming to the mirror and out going from the mirror are not the same. When we apply Maxwell's result, it mast be the case that the speed of light going towards the mirror and coming back from the mirror must be different then. The Einstein's interpretation of MM does not agree with Maxwell's interpretation of MM.
    3. I know that relativists would shout saying that I am a crank and so I do not understand that Maxwell's interpretation of MM is false. Well What about Einstein's result which claims that Maxwell's theory is relativistic as it is invariant under the LT.
    4. You see it is a very subtle issue which may be too much so for the believers of STR. I am saying that if Maxwell's theory is covariant under the LT and is indeed correct relativistic theory, it must be the case that the relativistic result of Compton effect will kill the relativist's interpretation of MM which assumes that the light going out and coming back must have the same speed.

    All of this nonsense is caused because the superior Theoretical Physicists think that logic is inferior and need not be taken seriously.  I study physics and question. They never study logic. They were told by their teachers that logic is nonsense. So, they do not see when they make this kind of fatal errors.

    I know their typical argument for this: They say CSL, MM and Compton Effect are all verified by experiments and so there is nothing wrong with STR and QM.?!

  • Napoleon Ono Imaah asked a question in Housing:
    Which extant traditional beliefs are observed in the process of building a specific type of building by your people?

    Please can you help in revealing observed traditional beliefs, rituals, ethics and native codes in: foundation-laying, ground-breaking, house warming, opening of house, house purification or house dedication births, deaths, cosmology ... etcetera ceremonies and your people's reasons for observing them?

  • Aurea Rosal added an answer in Professionalism:
    Do you think our professional school teach students enough about how to make a living with their professional skills?

    As professional graduate school curriculum have evolved to emphasis their course specific disciplines we find many graduates who are subject matter experts but do they have the street smarts to actually use their knowledge to earn a living in their field?

    Aurea Rosal · Polytechnic University of the Philippines

    In courses with licensing requirement, the effectiveness of the teachers with regards to the future profession is measured by the result of the licensing exam. For other fields of study, the school can probably do a tracer study of their students of what they are doing after graduating. This might help evaluate the effectivity of the teacher. However, this is not enough as the graduate may opt to the other things not related to their degree.

  • Why in some cases use DTT in elution buffer in purification protein ??

    why in some cases use DTT in elution buffer in purification protein ??

    Adam B Shapiro · Entasis Therapeutics

    Cytoplasmic proteins usually lack disulfide bonds. To keep the cysteine side chains in their normal reduced state, a reducing agent such as DTT is included in the purification. For proteins that have disulfide bonds as part of their native structure (such as antibodies), reducing agents may be avoided during purification to prevent disulfide reduction.

  • Claudio Vieira da Silva asked a question in HTTP:
    Crowdfuding Laboratório de Tripanosomatideos Could you take it foward, please???

    http://www.kickante.com.br/campanhas/pesquisa-em-doenca-de-chagas-e-cancer

    Could you take it foward, please???

  • Whats best method of Predicting compressive strength of the limestones?

    los angelos method is meant for shear resistance, I tried it already.

    the Brazilian methods does not account for water in rocks either.

    schmidts hammer

    Sayed Mohammadmehdi Jamal · Hormozgan University

    You can measure the ultrasonic pulse velocity of the specimens and then using the exponential formula you can predict the compressive strength of the concrete.

    Please pay attention that the constant parameters in this exponential formula depend on you mix design and they differ from one mix design to the other. 

  • How can I interpret compressive strength of concrete at 28 days?

    It is known that; many of specification stipulates that samples compressive strength of concrete must be at least "fck+delta (MPa)" at 28 days.
    But;
    1) In-situ construction of cure condition is different from the samples.
    2) Hydration improves strength continuously at very long period and It is possible that even if strength is low, it may reach value of 28 days in the long run.

    So, how can I interpret compressive strength of concrete at 28 days?

    Sayed Mohammadmehdi Jamal · Hormozgan University

    The 28 days compressive strength of concrete is the most popular one, because of the time economy. Although the compressive strength with more days than 28 days would be more reliable.  I hope I can have answered your question as your desired.