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  • Nata Kuzlo added an answer in Framework Analysis:
    What is the framework for analysis texts with images?

    I have got the samples of some civil engineering projects ( some floor plans, elevations). I consider them to be texts with professional civil engineering images. I have defined some typical grammar structures and words typical for notes. How can I analyze them from another viewpoint?

    Nata Kuzlo · National university of water management and nature resources use, Ukraine, Rivne

    thanks for answers

  • Darko Pavlović asked a question in Comics:
    What are the fictional characters (people) from the literature, legends, comic books, movies ... that had an important place in your life ?

    Let's go back for a moment in a childhood, adolescence and peek in our memories ...

  • What's the true meaning of a negative weight in a connection from input to hidden node in ANNs?

    Imagine that you have several emotions as predictors (input layers) of a certain output (lets say... wellbeing). You create an ANN and the best architecture contains 5 hidden nodes.

    To determine the contribution of the individual emotions, apart from sensitivity analysis, can we also measure the value of the weights of the connections between them and the hidden nodes?

    And if the contribution of a given emotion to the most important hidden nodes is inhibitory, can we assume that the relation of that emotion and the outcome is negative?

    TIA

  • Sezer Okay added an answer in SEC:
    Is my gene amplifying?

    I have a gene(wild type) cloned in pBAD18 Kanamycin resistant plasmid. The gene is 2185 bp. And the plasmid is 5437 bp. I wanted to insert a 6X His tag at the C-terminal end of the protein of this gene. I found that the last codon codes itself for a His. So I followed the general method for designing a primer i.e.: Last codon(CAT)-6X His codon (CAT or CAC)- Stop codon-XbaI recognition sequence. The primer length is 30 bp with a Tm of 62 degrees approx and the forward primer I used was 28 bp and has a EcoRI recognition site with Tm 59 degrees approx.
    I have tried amplifying my gene using a gradient PCR vaying the annealing temperature (see gel image). I expect to get the product in between 2Kb and 3Kb(2203 bp). But I have a range of variation in amplification above 10 Kb. What is getting amplified is my question? Is my gene at all getting amplified? I dont think so. What is going wrong.

    I am using Pfu polymerase with 30 steps amplification. I have done gradient PCR with variation in annealing please see gel image attached. PCR program:
    Initial denaturation: 95 degree- 3 min

    Loop:30X

    denaturation: 95 degree- 30 sec

    annealing: gradient- 55- 64 degree- 30 sec

    extension: 72 degree- 3 min 30 sec

    Final extension: 8 min

    Store: 4 degree.
    Notice the amplified product that I am getting is above 10 Kb.- DNA Ladder used is 1Kb NEB ladder.
    please suggest ways I can get my gene amplified for cloning. I want my insert to have a 5'-EcoRI and 3'-6X His-XbaI.

  • Austin Peasley added an answer in Plasmids:
    Are there any known issues with protein function for fusion proteins that have a protein of interest bound to the 3' end of GFP?

    We're testing protein localization using plasmids that place our gene of interest both 5' and 3' of the GFP, and while the plasmid with the protein of interest 5' of the GFP has clear and specific fluorescence, the plasmid with the protein 3' of the GFP has absolutely no fluorescence, not even the nonspecific fluorescence we see with just the plasmid with GFP but no protein of interest.

    I've sequenced the 3' plasmid, and everything is in-frame and in order, so at this point my suspicion is that the protein of interest is interfering with the GFP folding, but I'm curious if anyone else has had this problem or has any advice? So far the only relevant publication I've found is one focusing on reverse transfection (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447460/), which indicated that they had a high failure rate for fusion proteins that bound the protein of interest to the N-terminal of the GFP as compared to when bound to the C-terminal.

    Austin Peasley · Washington State University

    Thanks Nick,

    Yes, these are over-expressing lines. The protein of interest is a bacterial ankyrin, and as far as I am aware (I am new to the lab, so I'm not previously familiar with ankyrin proteins) the primary functionality is distant from the C and N terminals. Right now we're seeing localization of the ankyrin-GFP to, we believe, the Golgi, which is in line with our predictions, and the control GFP without ankyrin is showing nonspecific cytoplasmic fluorescence. It's just our GFP-ankyrin fusion protein that's showing no expression whatsoever, even compared to just the nonspecific GFP.

    Given that the GFP is upstream of the ankyrin, even if the inserted ankyrin was out of frame (Which it's not, as best as we can tell with sequencing) the GFP should still (in theory) be folding correctly and at least displaying nonlocalized cytoplasmic fluorescence. The reason I suspect that the issue may be due to folding is that the ankyrin we're working with is over 3.5 kilobases compared to the 700bp for GFP; My thought is that if the protein begins folding in a 5' to 3' manner, for our Ankyrin-GFP fusion protein the larger ankyrin would fold first, and the GFP would be relatively insignificant compared to the rest of the length for folding, while the GFP-Ankyrin protein might encounter issued with the GFP barrel structure formation due to steric hindrance from the longer ankyrin peptide tail. However, this is the first time I've worked with translation-level fusion proteins, as before I've only done work with binding markers to proteins, so I'm not sure what issues to keep a watchful eye out for when working with fusion proteins.

  • The difference in the productivity and selectivity of phyochemical extraction in laboratory scale compared to the same in industrial scale?

    We have optimized the extraction some phytochemicals in laboratory scale.How can I contend that our optimization should work at a larger scale?

    What are the factors or aspects influence the difference in the productivity and selectivity of phyochemical extraction in laboratory scale compared to the same in industrial scale?

    Mahesha Manjunatha Poojary · University of Camerino

    Dear Dr. Ravi and Dr. Juliana, thanks for your valuable suggestions.

    @ Dr. Juliana, I am extraction carotenoids from vegetables. 

  • Paola Saccomandi asked a question in MATLAB:
    Any suggestions about the implementation of Inverse Monte Carlo for estimation of tissue optical properties?

    Hallo everyone! Have you any experience about the implementation of inverse Monte Carlo algorithm for the simulation of photon transport through biological tissues and th estimation of optical properties (absorption, scattering and anisotropy coefficients)?

    I implemented the algorithm on Matlab, it works, but I have some doubts.

    Thank you in advance for you kind attention,

    Paola

  • Gabrielle Cauvi added an answer in Magnetic Beads:
    Any suggestion on the identification of memory Tregs?

    Dear all,

    I'll stimulate full PBMC with PMA-Iono TGF-beta and IL-2 (without the use of magnetic beads) to check Treg proportions before and after a vitamin stimulus.
    Do you have any idea of how to discriminate Treg cells that were stimulated in vitro from those who were already regulatory in my PBMC?
    Do you think a memory marker would be suitable?

    Cells will be FACs sorted without any stimulation too so I'll have basal Treg numbers from each patient.

    Thank you,

    Gabrielle Cauvi · Kyowa Hakko Kirin California, Inc.

    Hi Maria,

    you might want to look at this discussion here on research Gate.

    https://www.researchgate.net/post/Is_CD45RO_CD45RA_or_both_better_for_differentiation_of_naive_memory_and_activated_Treg

    good luck!

    Gabrielle

  • Christopher Wilson asked a question in Reading:
    What's the most personally influential scientific paper you've read?

    What's the most personally influential scientific paper you've read?

  • Walaa El-Henawy added an answer in Teaching Skills:
    What techniques can be used to train pre-service teachers on the mastery over different teaching skills?

    Command over different teaching skills is an important work for pre-service teachers. I am interested to know the different training tasks/techniques for which we can train pre-service teachers in various teaching skills. 

  • Where can I find the ATC 20 or other reference material for post earthquake damage assessment?

    Need the Post Earthquake Rapid Damage Assessment Documents. Any thought, where I would find the ATC 20 or other reference materials?

  • When it comes to simultaneity is Einstein correct or is Dingle correct?

    Albert Einstein claimed in 1905 that a single event can occur simultaneously at different times within two inertial reference frames moving relative to one another. In 1950 Herbert Dingle argued that different times cannot be simultaneous. I have analysed this conflict by deriving the Lorentz equations using both points of view. According to this analysis Dingle must be correct. See youtube presentation of this analysis at  https://youtu.be/4XLYzhHQ64Y

    Johan Frans Prins · Sage Wise 66 (Pty) Ltd

    Charlie Dimwit the troll,

    "No, Johan, that is all woolly headedness and evasion. I am assuming nothing. ""

    YOU ARE assuming that two events at different positions cannot be simultaneous unless there is a man-made clock at each position; which is absurd. YOU are also assuming that when a SINGLE event occurs at a position in space two synchronized clocks at this same position records different times for this SINGLE event. This is just as moronically absurd.

    "It is you who has to provide a real meaning for your assumption. Shouting about the SAME instant is no good if you cannot say what that instant is

    So according to you the concept of "same instant has no meaning"? Well then define to me what your asinine assumption is. How can two events be simultaneous if they do not occur at the SAME instant and how can two coinciding clocks have different time at the same instant?

  • Muhit Rana added an answer in Nanoparticles:
    How can I calculate the ratio of DNA and nanoparticle?

    I am looking at a protocol of binding AuNPs with thiolated DNA. It says AUNPs that were lyophilized with thiol-functionalized DNA (AuNP/DNA 1: 160 for high coverage, 1: 80 for low coverage). How can I calculate this ratio?

    Muhit Rana · University at Albany, The State University of New York

    Hi, to find the gold nanoparticles concentration, you can use extinction coefficient of AuNP is 2.7 x 10^8 M^-1 S^-1 at 520 nm wavelength. Let's see if, you find your gold nano particles absorbance A is 3.4 at 520 nm, then 3.4 divided by extinction coefficient 2.7 x 10^8 M^-1 S^-1, so you will get 0.000000013 M or 13 nM. This 13 nM is your gold nano particles concentration.

    I hope this will help to understand.

  • Is it a routine in your intensive care unit to perform ultrasound-guided central venous catheterization?

    Is it a routine in your intensive care unit to perform ultrasound-guided central venous catheterization?

    Seth Manoach · Weill Cornell Medical College

    Tomaste, thanks for the reply. My axillary arterial lines are US guided and the vein looks like a decent sized vessel,  but hard to do in the US without data.  I'm guessing someone will look at this,  as double lumen piccs are threaded from the arm into the central circulation. 

  • Andreas Stürmer added an answer in Stop Codon:
    Can there be stop codons in 5'UTR in mammalian cells?

    Good day.

    I was wondering whether it is allowed to have stop codons in the 5' leader sequence... On the one hand, the eukaryotic ribosome falls off as soon as it hits a stop codon. Well, it scans along the mRNA from the 5' cap until it meets a kozak-ATG where it starts translating...

    My 5'UTR would have this sequence agatcTAAgccaccATG...Is that a problem?

    pFlag-cmv10 has  GCTCGTTTAGTGAACCGTCAGAATTAaccATG as the leader sequence so a frame-shifted taa seems to be ok... Maybe also the position of taa is important?

    Thanks a lot!

    Andreas Stürmer · Fachhochschule Oberösterreich

    Thanks for all the answers!

    http://en.wikipedia.org/wiki/Eukaryotic_translation#/media/File:Eukaryotic_Translation_Initiation.png

    For what I understand from this picture is that only the small subunit scans along the mRNA and when finding the ATG, the large subunit assembles on it. The ribosome disassembles at stop codons, but it can't disassemble when it isn't assembled yet. Right?

  • Stephen Joy added an answer in Academic Psychology:
    Ravens Progressive Matrices Cut Off?

    Dear All,

    I have administered the full version of the Ravens Progressive Matrices to a sample of 95 University Students. I am trying to decide what criteria to use for the cut off score. The scores range from 20-52, I definitely have, what I consider to be, a few outliers. I am several papers that appear to use different cut off scores i.e. 3 SD below the mean. 

    Does anyone have any suggestions or advice for proceeding? Intelligence is the variable under investigation per se, more of a control measure.

    Cheers and thanks in advance.

    Stephen Joy · Albertus Magnus College

    I see two ways of proceeding. Traditionally, if you are going to "trim" a sample to get rid of outliers, you would do so from both ends. That's just being fair and balanced. (Of course, if you are running correlations the resulting loss of variance will attenuate the correlation coefficients.) But your concern may not be with outliers as such, but with the possibility that some of your participants "blew you off" and just answered randomly, or started to do so part-way through the procedure. In that case, you want a way of determining who (if anyone) did this. Well, there are 60 test items and each has 6 response options. So a random respondent would (on average) get about 10 correct. You could make a case that anyone with a raw score near that level (say, below 15) was essentially random. But your lowest score was 20, right? That's going to be tricky. In theory, you could see whether they "went random" on the last 30 or 40 items. But there's the problem that the items do grow progressively more difficult, so a less intelligent person might show exactly that pattern.

    Are there any other components of the study (other measures) that could also be looked at as well? Perhaps you could look for multivariate outliers? Just a thought...

  • Saleh Alresheed added an answer in Attitudes:
    Any references on teacher beliefs, attitudes and their relationship on the classroom practice?

    I am interested to explore the effects of the first pair on the third.

    Saleh Alresheed · University of Bedfordshire

    Hi

    check my page I have a paper in the same topic.

  • What the relationship between body shape and structure genetic in invasive species ?

    Are their any relationships between the body shape and genetic structure in the invasive species ?
    How organisms adapts in new ecosystem ?
    Is their any ecosystem modeling regarding these to understand clearly

    Thank you ...

    Abdulghani Abdulghani · University of Salford

    Hi Jose

    my question bout the invasive species ( fish ). 

  • Maik Bieleke added an answer in Prosocial Behavior:
    Are there any studies which find that different self control tasks correlate with each other and/or prosocial behavior?

    I'm doing research for my internship at the university, and we're interested in former or recent studies, which examines, if different self control tasks or questionnaires (e.g. Affective Go/No Go Task, Visual Dot Probe Task,Temporal Discount of Money,BIS,BIS&BAS,Rosenbaum Self Control Schedule,...)correlate with each other and/or with prosocial behavior? For example shown in an ultimatum or dictator game.Thank you in advance!

    Maik Bieleke · Universität Konstanz

    These authors examine the relationship between prosociality (dictator game), self-control (Rosenbaum scale), and  detection of a self-control conflict:

    http://journal.sjdm.org/11/111202/jdm111202.html

  • Jatin Tulsulkar added an answer in Neurogenesis:
    Which is the best way to track down neurogenesis spatiotemporally in my samples?

    i would like to know the best way to track down neurogenesis spatiotemporally in my samples, please suggest the best method? which is the best method?

    Jatin Tulsulkar · University of Toledo school of pharmacy

    Yogesh: For Brdu protocol you need to inject your animals initially with Brdu and continue dosing until u sacrifice. If you already got the tissues the only thing I can suggest is use of PCNA or Ki67 along with NeuN antibody.

  • Jesus Romero added an answer in Integrated Circuits:
    Which is the best Integrated circuit for thermocouple type R signal amplification?

    Hello everyone, I'm going to make some experimental validations of a welding simulation and when it comes to the thermal field, i've found several signal amplifiers and junction compensation IC's on the literature. I would like to know your experience filtering the noise and acquiring accurate data.

    additional information:

    GMAW process, AISI 304 material. Thermocouple type R.

    thanks in advance.

    Jesus Romero · Center for Engineering and Industrial Development

    Basically, thermocouples type R have low sensitivity (10 µV/°C) and a typical exposed junction thermocouple with 32 AWG wire (0.25 mm diameter) will have a resistance of about 15 ohms / meter.

    I’ve found an amplifier (LTK001A) and a cold junction compensator (LT1025) that supports thermocouple type R.

    Based on their datasheets, I have a circuit proposal that you will find attached.

    Your comments suggestions would be greatly appreciated.

  • Bhukya Bhima asked a question in Probiotics:
    Any body working on Bacillus spores as probiotics?

    If any body working on Bacillus as probiotics, please give some references

  • Rich Mcdonnell added an answer in Profit:
    Is there any knowledge of the performance of cooperative firms?

    Cooperative firms are owned and run by their employees, who receive a fair share of the profit. I'm looking at any existing literature on the performance of such firms. Any suggestions? Thank you. 

    Rich Mcdonnell · Parker Hannifin Corporation

    Thomas,

    With regard to the US, you may want to investigate ESOP (Employee Stock Ownership Programs). In the late 80's early 90's they were the rage with Owner/Managers of industrial distribution whom sought to transition out of their businesses - the perception within the market / employees as buyers - ESOPs provided substantial operational control and tax benefits to the Owner/s, while obtaining a significant premium for the business.

    The Industrial Distribution program at Texas A&M would be an excellent resource to engage on this.

    Cheers,

    Rich 

  • What is the maximum volume of DNA you can concentrate using the NaOAc method?

    I need to concentrate 10 mL of DNA down to 100 uL as I need a very high DNA concentration for an NGS application. Has anyone used the NaOAc/EtOH precipitation method to concentrate from such a large volume? I have only used this method for smalls volumes <100 uL. My method:

    For 20 uL of DNA, add:

    - 2 uL of 3 M NaOAc pH 5.2

    - 50 uL 96% EtOH

    - vortex and leave at ambient for 10'

    - cen. max. speed for 15'

    - remove supernatant and add 200 uL of 70% EthOH

    - remove supernatant and dry under flame

    - resuspend in desired volume of MG H2O or buffer of choice

    Concentrating DNA results in a loss of 10 - 20% DNA.

    Has anyone attempted this (or this type of), method for initial volumes of 10 mL?

    Thanks, 

    Natalie

    Richard A Lease · The Ohio State University

    Hi, Natalie. Isopropanol (IPrOH) will work, but I am not sure of the correct volume ratio. Your salts ratio is correct. IPrOH may also bring down a lot of salt, and there may be increased risk of losing the pellet during subsequent 70% EtOH washes. I don't know what you mean by drying under flame, but if too dry, the DNA will not properly rehydrate in water. Let it dry at room temp or briefly speedvac but don't overdry. I would resuspend in 10 mM tris pH 8 (no EDTA for subsequent enzyme operations) but talk to your NGS service about buffer pH/compatibility - they are probably also concerned about EDTA. Maybe resuspend DNA in something compatible with their first enzyme operation, such as their buffer? Or resuspend in Tris and then desalt with spin column. Very pure water is pH ~5.5 due to dissolved CO2 as carbonate. You can elute DNA off of a silica column in water but resuspending a pellet is different. Cheers & good luck.

  • Van Dung Pham added an answer in Plasmids:
    Does anyone know a suitable software to draw plasmids?

    I have some issues with plasmid drawing for publishing. It is very grateful if anyone can suggest a suitable software for creating the plasmid map? Thank you in advance.

    Van Dung Pham · University of Ulsan

    Thanks Christian. I have tried already!

  • Angélica Nascimento Martins asked a question in ELISA:
    Any good pair of antibodies for mouse and human IFNb ELISA?

    I'm trying to avoid expensive kits and coat my own plates. We do this a lot with other cytokines, but now I need to get a good pair of Ab for IFNb ELISA (mouse and human). Please let me know what you tried!

  • Daryn Dyer added an answer in Research Topics:
    Does anyone have idea how to or from where to get the questionnaires for the topic of Blue Ocean Strategy ?

    It it my final year dissertation topic further more can we test this theory ? i want to do research on this topic but what i shall research still blur .. help and comments are needed and welcomed :) 

    Daryn Dyer · York University

    These are not questionnaires but they are indicators based on survey research:

    Parvinen, P., Aspara, J., Hietanen, J., & Kajalo, S. (2011). Awareness, action and context-specificity of blue ocean practices in sales management. Management Decision, 49(8), 1218-1234.

    Koo, L. C., Koo, H., & Luk, L. (2008). A pragmatic and holistic approach to strategic formulation through adopting balanced scorecard, SWOT analysis and blue ocean strategy–a case study of a consumer product manufacturer in China. International Journal of Managerial and Financial Accounting, 1(2), 127-146.

  • Navneet Ammal Kaidery added an answer in SH-SY5Y:
    What is the best in-vitro parkinson's disease model?

    Im trying to conduct a neuroprotective assay with SH-SY5Y cells differentiated with RA and TPA to dopaminergic neurons. 

    There seem to be multiple cell lines capable of similar feats, and some that seem to be used more without differentiation.

    Is there any reason to go through the trouble of dual differentiation? or would it be easier and more reliable/reproducible to work with N2A/CATHa/PC12 cell lines, as they seem to be the standard in neuroprotective research. 

    I understand that SH-SY5Y cells are of human origin, but even still, they dont seem to be heavily used when compared to mouse line.

    Navneet Ammal Kaidery · Georgia Regents University

    Hi Kelly,

    I have worked with SHSY5Y, N27, N2A and PC12 cells. SHSY5Y differentiation using RA always resulted in a mixed population with rather low efficiency, and I wonder whether that would affect the outcome of your experimental results. N2A cells and PC12s give rather uniform differentiation and both are Dopaminergic. PC12 are more troublesome to work with forming clusters in the plate when not differentiated.