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  • Soma Ghosh added an answer in Gradient PCR:
    9
    Why could I not get amplification for all my colony pcr?

    I did a butch of colonies pcr, but I only got 25% of my colonies amplified. I did gradient pcr to choose the best annealing temperature, it doesn't matter my target products are 4 kb or 2 kb, they just not all amplified!  Does any one have any suggestions?

    Thank you so much!

    Soma Ghosh

    Thanks Yuan,

    I also think it is a problem with using larger quantity of bacteria. Will let you know if i face  any other problem. 

    Soma

  • Abbas Akbari asked a question in High School:
    New
    Does anyone have a good scale to measure the informal reasoning?

    i want to research about the informal reasoning in high school students

  • Belel M D added an answer in Sustainable Agriculture:
    16
    Do you think conservation agriculture in developing countries generates private benefits to farmers?
    Conservation agriculture includes any practice that reduces, changes or eliminates soil tillage and avoids the burning of residue in order to maintain adequate surface cover throughout the year.

    We would expect lower production from low input technologies. For example, no-till technology is essential for sustaining soil productivity because crop residues are allowed to remain on the ground with the accompanying benefits of improving the soil's physical, chemical, and biological properties, but farmers may not gain financially because of low productivity.

    On the other hand, farmers may save on input costs (labor use should be lower). What would be the net effect? What are other benefits and costs?
  • Ann Christina Foldenauer added an answer in Multilevel Modeling:
    2
    What to do when residuals in multilevel model are not normal distributed?

    Hej,

    Im working with multilevel (hierarchical) data (Value < level 1 < level 2). When modeling this, using the lmer-function in R, the residuals are by far not normally distributed. 

    What could be my next steps to analyze this dataset? 

    Thank you 

    Ann Christina Foldenauer

    You could try to logarithmize your data. If this doesn't work, you should consider generalized linear mixed models respectively non-linear mixed models. In SAS you could try this using proc genmod or lnmixed.

  • The Nguyen Duc asked a question in Coral:
    New
    How to select bacterial colonies from spread on MA plates?

    Hello every body, Please help me!

    I want to study in bacterial communities of composition species from the coral tissue samples.

  • Fabrice Fekam Boyom added an answer in mycobacterium ulcerans:
    1
    Good morning all of you. So I would like to know how to conserve Mycobacterium ulcerans?

    In fact i would like to conserve Mycobacterium ulcerans. So I need to know the medium and if it is possible at -20 degree celcium

    Fabrice Fekam Boyom

    Rodrigue,

    Read the enclosed instructions from ATCC

  • Mary Nakafeero asked a question in Variability Modelling:
    New
    Has anyone used "exact logistic regression" for a small sample size and with multi-level predictor variables?

    Hello Team,

    I am having a challenge. I am trying to run exact logistic regression in STATA 13 which is recommended for rare events or small sample. In my case, it is a small sample.

    I have seen "exact logistic regression" applied but with dichotomous predictor variables. In my case, the categorical predictor variables have more than two levels. If I use "i.variable" in the model for the indicator variables, I get the error "factor variables and time-series operators not allowed".  

    If I leave out the 'i' before the categorical predictor variable, is that model applicable, how do i interpret the results from such a model?

  • Kamal Alogla added an answer in ANSYS Workbench:
    1
    When to use solid65 for concrete in ANSYS Workbench (for which type of loading) and why there are many convergence problems associated with it?

    I am modeling the debonding between concrete and CFRP subjected to tangential loading using ANSYS Workbench, I used (CZM/VCCT)  techniques to model the debonding. as you know with workbench you can't choose the element type directly. you have to insert commands for Solid65. or use the default solid186.

    1.  For pure tangential force applied on the plate. is it suitable to use solid65 element for concrete in this case. bearing in mind that in some failure modes in experimental there is a lump concrete attached to the plate after separation (Failure). and in others the concrete is intact (just debonding failure). 
    2. I tried different element types, but when I use the SOLID 65 command, my model lose convergence too early. If I remove cracking and crushing capability (Suppress the command), the solution runs fine without any convergence problems. (is this  due to cracking feature associated with solid65). how can I get the model to converge.
    3. in meshing,If the mid-side nodes are set to "dropped" for the default solid186 (20 nodes), will I get similar behavior as solid65 (8 nodes) (3 DOF/node for both). 

    I already tried the following to get my model to converge for solid65 in workbench:
    1- Refining the mesh.
    2- Reducing the normal stiffness of the contact region
    3- Use newton Raphson residuals.
    4- Playing with steps and sub-steps (applying displacement in small intervals).

    Any help or suggestions will be highly appreciated.
    Thanks in advance.

    Kamal Alogla

    I think you need to add a contact elements to represent the adhesive material ( such as epoxy) Or you can use nonlinear element such as (COMBIN39). These elements are available in ANSYS APDL. I am not sure if they are available in ANSYS workbench.

  • Scott Frendo-Cumbo asked a question in siRNA:
    New
    What is a good method/transfection reagent for knockdown in fully differentiated C2C12 myoTUBES?

    Hello all,

    I have been trying to knockdown various genes in fully differentiated C2C12 myotubes using Lipofectamine RNAiMAX reagent. In doing so I have tried various concentrations (50-200nM siRNA), time points (6h, 24h or 48h with siRNA, cells taken 24-48h following the transfection) and media (Optimem or DMEM, with or without serum during the transfection period). The maximal knockdown I have achieved is ~45% while some of the protocols seem to effect myotube morphology and RNAiMAX treatment activates my pathway of interest. 

    I have recently looked into adenovirus for siRNA delivery, but it is very expensive and I want to make sure this is a proven method prior to spending the money.

    Thanks for your help!

  • Ehsan Rasoulinezhad added an answer in Time Series Modeling:
    2
    How can I develop a time series model where some variables are monthly and districts wise and others are mothly at national level not district wise?

    W = f( p, q,  R ) where, w and p means monthly wages and food prices which are available from 2000 to 2015 from 20 districts (places).

    But others like production quantity of rice (q) are seasonal and  remittance (R) are in monthly at national level.

    How can I develop a time series model on such varied frequency variables.

    Ehsan Rasoulinezhad

    You can easily use various autoregressive models. I suggest you take a look on econometric books.

    Yours,

    Ehsan

  • Michael Greenhalgh added an answer in Stem Cell Differentiation:
    10
    How to generate neurons from human induced pluripotent stem cells?
    I am planning to generate neurons using human induced pluripotent cells (hiPSc). Could someone please share, if they have any protocols on generating neurons from hiPSc. And also how to maintain these cultures? Thanks in advance.
    Michael Greenhalgh

    Does anyone have an opinion or sources  on NSI-566 for ALS, or any other SC treatment for the disease ?

     I'm attempting to clarify ambiguities in  the clinical trials results and look for alternatives as well since the trials are proceeding slowly. 

  • Feilong Wang added an answer in IL-4:
    3
    How long should I wait after BMDM replated?

    Hi Guys,

    I am trying to stimulate BMDM with lps/ifn-gamma or IL-4 to induce m1 and m2 macrophages. After 7 days stimulating with M-CSF, I harvested BMDM from dishes and replated them in the plate. Does anyone knows that when can I start stimulating them? overnight or just when they attached?

    Thank you  so much!

    Feilong Wang

    Thank you very much for your answer! It really makes sense!

  • Alexander Yurkin added an answer in Physical Modeling:
    1
    Is there any physical model to interpret the forward scattering from a rigid complicated structure in Bessel beams?

    I want to give some reasonable explanation of my calculated results on the zeroth-order acoustical Bessel beam scattering from the forward half-space for rigid spheroids and finite cylinders. There is an obvious difference between the ordinary plane waves and Bessel beams. Could you suggest some appropriate physical models which may help to describe the results? Thank you very much.

    Alexander Yurkin

    Dear Zhixiong Gong,

    However, I up to the end can't understand your.

    The matter is that this winter on my site the white hare ran and ate bark from trees (growth from a half of dog). In the summer I have again met a hare on my site, but he was twice less than a winter hare and was brown on color and badly ran and jumped. All my friends have told that it is not a hare but a rabbit who has escaped from a cage from the owners, and now lives on my site together with hedgehogs. It is a shame to me that I live in the biological center of Russia, in the city of Pushchino and I have mixed a hare with a rabbit, but I feed up him.

    Sincerely, Alexander

  • Ann Christina Foldenauer added an answer in ANOVA:
    3
    Statistical analysis of change in Variable 'Y' over time within a session for a group?

    I want to see if there is an increase in my dependent variable 'Y' within a session for a group A (10 participants).

    My research question: IS there a significant increase in 'Y' within-session for group A?

    For every second, dependent variable 'Y' and sensor noise 'X' were sampled. 'Y' will be eliminated if the 'X' = YES. The session time varies for each participant (between 20 to 50 seconds). There are 10 participants. Every participant have around 20 sessions.

    I have attached the data format that was collected for every session for 10 participants (as image)

    My questions are:

    Q1: What statistical method should I use to show if the variable 'Y' significantly increased or decreased or no pattern observed within session for the group? I am aware of basic methods such as ANOVA.

    Q2: I was thinking about the following method: (1) treat each second as repeated measures and perform ANOVA with time as IV, and Y as DV for all 10 participants? In this case, the varying session time becomes a problem. How to handle this?

    Q3: is there any time-series statistical method that I can use to analyse the change in 'Y' within a session for the sessions numbers 1, 10 and 20 (individually) for all 10 participants?

    Thank you

    Ann Christina Foldenauer

    Dear Srilekha,

    you should try making a second dummy time variable (copy of your time), then you can include time as fixed (continuous) and random effect. The participants and sessions could be modelled as a fixed effect. If this doesn't work (estimation problems), try to model the sessions as random effect. The following paper might help on how to do it in SAS (especially page 14):

    http://www2.sas.com/proceedings/sugi29/188-29.pdf

    The comparison between session 1,10 and 20 could then be collected using linear contrasts (if you model them as fixed effects).

    Another issue for you might be the first few measurements of Y (also depending on the variation in Y). If the 'Base'-measurement differs a lot between the participants, you might want to consider including it as a fixed effect into your model to account for this difference.

    I hope this helps.

  • Manh Tin Ho added an answer in Actin:
    1
    Suggestions for western blots on H2O2 treated lysates?

    I have mock treated lysates and treated lysates. First problem comes with the BCA assay which is not compatible with H202 (nor is Bradford). Any suggestions how to get around this...should I just do loads of washes prior to my lysis? Second problem comes with the actual western blot on these lysates. My mock treated samples show actin and other protein just fine, while the treated samples look like there isn't even any protein there, including actin. It's not a lack of cells or cell death issue, I had plenty of cells upon collection of lysates. But not sure what the H2O2 is doing to cause this. Any advice would be greatly appreciated! Thanks!

    Manh Tin Ho

    Hi Monica,

    I don't know what problem you had with BCA on H2O2 treated samples but on my case BCA kit (and Bradford, either) has not ever worked wrongly with H2O2 treated protein. Depends on which origines (cell, tissues, etc.) you collected, they could affect on BCA (maybe on how the Cu ion binds to protein in kit) but not H2O2 itself. And about the protein quality on treated samples (which you said it was nothing, even actin), you can simply run commasive gel staining in parallel with WB gel, or before WB. Comassive stain (or even better with Silver staining) will give you the idea about how good quality of total protein you have, and then think about how you did not gain it on WB membrance, which could be hundreds of reason such as transfer, false antibody, etc.You also can run BSA scale down concentrations in commasive gel as a home-made ladder to identify the concentration of how much proteins you have if you cannot get rid of BCA problem.

    In addition, H2O2 may catalyze or support for some reactions (with some enzymes) to degrade almost your proteins before running WB (incase commasive gel shows nothing).

    Hope it helps! Good luck with your experiments :)

  • Shanmugam Govindan asked a question in Oxidative Stress:
    New
    Which is the suitable molarity for performing juglone induced oxidative stress in C.elegans?

    C.elegans research community,

  • Micol Pizzolati added an answer in Catholicism:
    1
    What is the "Day of the roses" [Le jour des roses] in France?

    For the French and Italian colleagues, or the experts  of French and Italian traditional culture.

    An italian colleague of mine is analysing some iconografic documents to complete a chapter of a book (on the representation of food). He is currently working on " Le jour des roses sur le toit [The Day of the roses on the roof]" of Martial Raysse. He asked me if "The Day of the Roses" is Italian "Easter of the Roses", that is to say the day of Pentecost.

    Is anybody able to answer to his question? I didn’t find any information on the web concerning this “Day of the roses”…

    Thank you!

    Cheers!

    Sandro

    Micol Pizzolati

    La Pentecoste in Italia è detta Pasqua Rosa o Pasqua delle Rose http://www.treccani.it/vocabolario/pentecoste/ così come in Francia http://www.france-pittoresque.com/spip.php?article12637

  • Cybel Mehawej asked a question in Nigericin:
    New
    What is the optimal stimulation for IL-1b secretion by BMDMs?

    I would like to assess IL-1b production in murine monocytes.

    For this purpose, I cultured BM in DMEM containing 20 % L-929 conditionned media (M-CSF). At day 4, cells were ` 80% CD115+ F4/80 int/+ CD11b int/+.

    Day-4 BMDMs were primed for 4h with LPS (1 ug/mL) in DMEM (without M-CSF) then stimulated for 30 minutes with 20 uM of Nigericin. IL-1b ELISA on supernatants from these cells showed undetectable levels of IL-1b.

    1) Can somebody help in optimizing this assay?

    2) Is there any way to obtain a higher % of CD11b int cells (monocytes) rather than macrophages?

    Thanks

  • Ricardo Frausto added an answer in RIPA Buffer:
    4
    How to thaw RIPA lysis buffer?

    I have the big brown bottle of RIPA and it takes ages to thaw. How to thaw safely? I know I have to aliquote but concerned to put in eppendorf as it light sensitive. 

    Ricardo Frausto

    Heba, you may need to warm to >30C. I imagine the SDS is what is causing the apparent slow "thaw," so warming above room temp to thaw should be fine. This will allow the SDS to go back into solution.

    As Nicolas has stated we also store the entire 500mL bottle at 4C with no issues. We use it for lysing cells to prepare them for Western blotting. Don't know if the original application requires different handling conditions.

  • Adam Cieplinski added an answer in Rotifers:
    3
    What is the best way to reduce the motility of Rotifer?

    I need to collect Raman measurements of Rotifer, Brachionus plicatilis, which are microscopic size (100 micro meter), however,  the motility of such organism is the biggest issues even with using POLY-L-L-YSINE (PLL) , since the adhesive is not strong enough resulting in  limited numbers of organism attached to the surface making the collection of the measurements is very difficult.

    I need to freeze the movement of the organism and in same time keep it alive.  Researchers usually use  anesthetic or formalin especially in the case of  imaging techniques such as scanning electron microscopy (SEM), however, these chemicals may affect the spectra of the organisms

    Are there other suggestions to overcome this problem?  

    Adam Cieplinski

    I work with Keratella cochlearis and I had the same problem while taking measurements. You can use very slowly added alcohol. However, it may result in retracting corona by rotifers (especially soft bodied rotifers or when the alcohol is added to fast). Yo can use bupivacaine. If added slowly it relaxes the animal. You have to test for dose though. You can also do the easiest thing and use a very minute amount of water so that they are immobilized in a small droplet. However, it is difficult to retrieve them if for example you want to use them for genetics. 

    Good luck

  • M.Reza Khoshi added an answer in CO2 Reduction:
    5
    Can anybody suggest me some organic solvent immiscible in water that I might use for electrochemical CO2 reduction?

    I want to reduce CO2 in 100% non aqueous medium. Non aqueous solvent that must be insoluble in water for suppressing Hydrogen evolution reaction. So can anybody suggest me or help me with that?

    M.Reza Khoshi

    Dear Kamrul 

    There have been some studies on adding acetonitrile in water, in order to achieve a desired CO2 reduction products. 

    Hope you find this helpful.

  • Paul Eisenberg added an answer in Audit:
    14
    Can anyone please tell me, what is the practical implication of audit fee research?

    Can any please tell me, what is the practical implication of audit fee research? For example, if we find that voluntary disclosures increase audit fee. Now, I want to know what is the contribution of this finding. How we can interpret this finding and show the practical implication of this findings.

    Paul Eisenberg

    Dear Babar,

    In addition to the issues mentioned by the scholars above, I would like to stress the importance of tracing back the findings on auditor independence and audit quality to observations in practice which go beyond audit fee increase or decrease. 

    For example, auditor independence can be regarded as a function of professional ethics. Independence can be threatened not only if audit fees grows, but also if auditor firms are increasingly governed by non-auditor personnel, say consultants, who are not subject to auditor professonal ethics. This was the case in the 1980s and 1990s in the US with the then Big Eight.   

    Also, audit quality can be threatened by either incresing audit fees (as a bribe) or by decreasing audit fees (in order to cut costs). However, poor audit quality can be a consequence of an anything-goes mentality as was the case in the 1970s in the USA. It can also be a consequence of poor auditor training. Please refer to "The Gatekeepers: The Role of the Professions and Corporate Governance" by John C. Coffee for more insight into these topics.

    The pracitcal implication of such a research would be well-informed decisions about audit fee regulations.

    Paul  

  • Maximiliano Marzetti added an answer in Contracts:
    6
    China is now making the draft of her Civil Code. Should the Franchising Contract be one of normal Contracts of it?

    China is making her new Civil Code, though she has already several single laws such as Contract Law, Torts Law and Property Law (Sachenrechts) . The Author is taking part in the draft of Contract of the Code. Should Franchising Contract be regulated as a new normal contract in the Code? DCFR seems to suggest other countries to take this path.

    Besides, how about making a new and independent law, Distribution Channels law, including Franchising, Commercial Agency and Commission etc.  This Law will be a positive response to Economy and Economics, probably. 

    Maximiliano Marzetti

    @Huanmin Lin, I'll let you know if I find an English translation of the new Argentine code. At least you can cite it as a contemporary antecedent. Regards. 

  • Terrence Patrick Mcgarty added an answer in Hypothesis Testing:
    2
    Is There a Closed form Expression for the Number of Bacteria as a Function of Time and Growth Rate?

    Bacteria growth are defined by a growth rate, say r. If one looks at a time sequence of growth, say d sec, d being quite small, then a bacteria can remain constant or double. The probability of doubling is say rd. Now does anyone know of a result for the probability density for the number of such cells as a function of r and time. Also can one construct a hypothesis test to examine the growth in two different media and ascertain if one has a higher or lower growth rate than the other and is there a way to calculate a p value?

    Terrence Patrick Mcgarty

    Thanks, my problem is to measure growth rates on a petri dish with several treatments. One is just a bactericidal and the others with various bacteriostatic nano treatments. I can measure grow per observed cell, many of standard measurements are not available since I cannot disturb the surface. Thus I can model growth rates and determine reasonable estimates via standard means, then the issue is how reliable is the estimate compared to the N substrates. I am writing this up in a white paper and appreciate comments. Again many thanks.

  • Ariel Villacorta asked a question in Calibration curve:
    New
    Is it possible to have a negative A595/A465?

    I'm currently trying to generate a calibration curve using BSA. The problem is that when I subtract some of the absorbance values (for both 595nm and 465nm), I get negative values. Thus, when I take the ratio of the two absorbances, I sometimes get negative or positive value. What should I do?

  • Raiyyan Masumdar asked a question in Pipeline:
    New
    How to calculate the design frequency ?

    I am trying to design a pipelined floating point Mac unit and my aim is to enhance the speed of the design, by adding multiple stages of pipelines. But, I am finding difficulty in knowing the frequency of design. Timing reports after Place and Route will generate the maximum period, but i learned recently from somewhere that it is not the actual frequency. So, how to know the exact frequency?

    One possible way would be to know, what logic is being inferred corresponding the verilog code, by the tool. But, even for this, I am facing difficulties. I don't exactly know what the tool will infer and how much delay to consider for the logic it is inferring. Any help would be appreciated. Thank You    

  • Sayan Mukhopadhaya added an answer in R Statistical Package:
    3
    How to work with Sentinel-2 .jp2 files in R?

    Hello,

    Does anyone knows how to work with the sentinel-2 .jp2 files in R?

    The earthexplorer has .jp2 files for sentinel-2 and I'm having some trouble in simply open it in R (I'm using R Studio in Windows)

    Thank you!

    Sayan Mukhopadhaya

    you can follow this link

  • Dyana Sari added an answer in Agriculture:
    6
    Is there hope for African agriculture?
    African farmers hitherto cultivated their crops and reared their livestock/animals without chemicals. Then, they were introduced to the so called improved farming methods with emphasis on heavy reliance on agro-chemicals, particularly inorganic fertilizers. Years after, they are asked to go back to the traditional farming methods they abandoned, this time with new names such as "organic farming", "conservation agriculture", etc. The African farmer is now in dilemma. The future of African agriculture is bleak unless this dilemma is resolved. The question is, how can the dilemma be resolved? Better still, what is the way forward for African agriculture?
    Dyana Sari

    Dear Mamudu, same questions come up from farmers in Indonesia and all answers are true.Now our turn to transfer the answers

  • Mousumi Bhattacharya added an answer in Trading:
    3
    Is there any Benchmark for trading strategy for the FX Market?

    Hi,

    as part of my PhD research, i have developed 2 trading strategies: TSFDC and BA. i applied them to 3 currency pairs from the FX markets: EUR/CHF, GBP/CHF, and EUR/USD.

    as for evaluation metrics, i used: total profit, profit factor, profitability percent, Max draw-dawn. beside, i measure the Sortino ratio. (i don't really like Sharpe ratio)

    in order to provide credit to my proposed trading strategies, i would like to know if there is a specific benchmark for the FX market?? 

    Mousumi Bhattacharya

    You can go through  a peer reviewed  article written  by K Lien