Q&A

ResearchGate Q&A lets scientists and researchers exchange questions and answers relating to their research expertise, including areas such as techniques and methodologies.

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  • Does anyone have published before and after data on the impact of the use of electronic system reporting of medication errors?

    I'm doing a systematic review on the impact of electronic databases for reporting M. E's amongst healthcare professionals. Finding it difficult to get primary research articles on this. Has anyone published?

    Florence Horsman Hogan · Royal College of Surgeons in Ireland

    Thanks Ulrich

  • Atheer Al-nuaimi asked a question in Traffic Accidents:
    How can I generate data if I do not have real data?

    I need data about the effect of multiple treatments to reduce traffic accidents but I do not have data after the implementation of these treatments. How can I generate data if I do not have real data?

  • Reza Khakvar added an answer in Bacterial DNA:
    How can I quantify bacterial DNA genome level from a single insect?

    Hi, I have to measure a bacterial DNA level in single insect level. Do you have any idea about how to quantify them? By insect weight or instar stage?    

    Reza Khakvar · University of Tabriz

    You can use realtime-PCR (qPCR); extract total DNA from you insect samples (control+ treatments) then use a 16s universal primer in a realtime PCR.

  • Aniket Patole asked a question in Quenching:
    Can CNT be used in oil base for quenching purpose?

    Need of advance quenchants in combination with CNT.

  • Tamara Pianos added an answer in Assessment:
    How do we as librarians assess and evaluate library services?
    For instance, when we offer a library workshop, how do we show adminstration that our work is valuable in aiding the goals and purposes of the community.
    Tamara Pianos · German National Library of Economics - Leibniz Information Centre for Economics, Kiel Germany

    The Technical Information Library in Hanover Germany did an evaluation on Return of Investment into Library Services some time ago. If you think this might be useful, you find the report here: http://www.wpp.com/wpp/marketing/consumerinsights/the-tib/#

  • Natallia Sianko added an answer in MANOVA:
    How to conduct a MANOVA with three continous independent variables in SPPS or a better choice?

    My problem is that in all places only talk about conducting a MANOVA with the independente variable being categorical in SPSS. But I need to do with continous independente variables.

    Hope you could help me and indicate the best away to do it.

    Thank you for your consideration.

    All the best,

    Maria João

    Natallia Sianko · Clemson University

    What is your research question? anovas are commonly used to compare groups (that's why categorical independent variables).

  • Ian Teo added an answer in Agarose Gel:
    Does no band on TBE agarose gel mean no RNA?

    Dear all
    Hi,
    I am facing the problem of no visible band of rna on TBE agarose gel. I have isolated PBMCs from blood using Histopaque , then dissolved these cells in TRIZOl and freezed it to -80 till the RNA extraction. Now I am performing Rna extraction through Rneasy mini kit as per given protocol. When I run the eluted sample on gel to see quality of RNA, I get no bands . Spectrophotometer reading is showing the quantity as 1 -2ug/ml of RNA. Does no band mean no RNA? And what is the effect of Guanidine Thiocynate / isothiocynate on RNA? My samples are being treated with two reagents having guanidine thiocynate. I am speculating that this reagent may affect my samples.
    I have to make cDNA from that RNA and will have to further proceed of RT2 profiler PCR Array.
    Any of the expert if can provide suggestion, will be appreciating.

    Ian Teo · Imperial College London

    1) GuCSN  is routinely used for RNA work. Not a problem

    2) are your gel tanks, buffers, agarose, gel loading tips RNAse free ? - have you treated the apparatus with RNase away or H2O2 to get rid of RNAse? Are you running a formaldehyde gel?

    3)How much RNA are you loading? Your concentration is very low and you may not be loading on enough to see it.

  • Chao Hsu-Wen added an answer in Neuron:
    What is the best model and origin to check the effect of some drugs on neuronal plasticity?

    mature neuron or neural stem cell/ NPC?

    cortex or hypocampus?

    Chao Hsu-Wen · Academia Sinica

    For my case, I always use mature hippocampal neurons for monitoring neuronal plasticity.  They are easy to handle, and the morphological change of dendritic spines is quite obvious.

  • Ephrem Guchi added an answer in Metabolic Pathways:
    What are the physiological effects of toxins from Pyricularia oryzae in rice?

    What organs or metabolic pathways are influenced by toxins by Pyricularia oryzae sintetisadas?

    Ephrem Guchi · Haramaya University

    Dear! It is acutely toxic, immunosuppressive, mutagenic, teratogenic and carcinogenic targeting mainly the liver for toxicity and carcinogenicity.

  • Fatima Salahdine asked a question in Bayesian Network:
    There are any other solution to leave uncertainty, except bayesian networks ???

    Bayesian networks are used to represent knowledge about an uncertain domain, i am looking for other solutions such as bayesian network.

  • Adam B Shapiro added an answer in Probes:
    What causes my sample spectral peak to change and appear so confused?

    Hello everyone ,currently I am doing one project about protein-peptide complex with a  low binding about 0.3mM by ITC.

       I prepare my protein with peptide at a ratio in 2:1 , and test sample stability
    in room temperature(22C). I overlap spectral (after3.5day ) with 1st spectral acquired in room probe. And I find sample after 3.5day can overlap all the signal with 1st day but appear additional 5 peak with a strong peak intensity. After 3.5day in room temperature.

       I didn't carry out NMR titration, because I find such sample have a dramatic conformation change after adding peptide against protein. I don't know where additional 6 peak come from. Thanks a lot!

    Adam B Shapiro · AstraZeneca

    Perhaps your peptide is becoming degraded by proteolytic activity present as a minor contaminant in your protein. Try analyzing the sample by mass spec to find out the masses of the new substances.

  • Ian Casci asked a question in Sonication:
    Does sonication damage RNA?

    I would like to extract RNA from Drosophila tissue.  We typically sonicate when analyzing protein in these samples, but I am not sure if sonication will damage the RNA.

  • Xin Wang asked a question in Bacterial Cells:
    Hi, Is there any method or solution could lyse human cells, while leave bacterial cells intact?

    Hi, here i want to ask if there is the method or solution could lyse human cells, while leave bacterial cells intact? since my samples contain both human cell and bacterial cell, and I want to collect the bacterial cell. If you know the components of this kind of solution, please send me a copy, because this is a problem for me! many thanks!

  • Renzo Bianchi added an answer in Depression:
    Which are the most commonly used cut-offs for these depression scales: GDS, HADS, MADRS, CORNELL?

    Dear all,

    Please, which are the most commonly used clinical cut-offs for considering depression in the following depression scales?

    GDS- 15 items version

    HADS- 7 items version (Depression sub-scale)

    MDRS- 10 items version

    Cornell

    thanks so much

  • Markus Stenemo added an answer in Meta-Analysis:
    Can any one suggest the best software to use for creating forest plots?

    We have carried out a systematic review of the prevalence of food allergies worldwide and although meta analysis was not appropriate due to the high heterogeneity of included studies we would like to present the data in forest plots. The data is currently in an excel spreadsheet. Many thanks in advance.

    Markus Stenemo · Uppsala University

    I am no expert, but here is my impression:

    If you want a decent looking forest plot quickly, you want to use GraphPad Prism. Example: http://www.graphpad.com/guides/prism/6/user-guide/index.htm?forest_plot.htm

    If you are willing to put in a lot of effort in order to get a beautiful forest plot you are better of with R. Example: http://www.matthewmaenner.com/blog/2012/08/26/lets-make-a-forest-plot/

    and 

    https://ecologyforacrowdedplanet.wordpress.com/2013/05/10/using-metafor-and-ggplot-togetherpart-1/

  • Bernabé Moreno added an answer in Dissolved Oxygen:
    According to the Draftsman-plot: How exactly do I know if I have to transform my environmental data (prior to normalization and PCA)?

    I've attached the Draftsman-plot that I've obtained.
    I'm using 04 variables: Temperature, Dissolved oxygen, Current speed and Depth ('Profundidad' in the attached figure).
    I see no necessity of transforming it, but I just want to be sure if I'm correct or not.
    Thanks and cheers 

    Bernabé Moreno · Universidad Científica del Sur

    Thank you very much Aimeric. Helpful indeed! Now I'm sure how to proceed.
    Cheers.

  • Marc P. Hayes added an answer in Frogs:
    Does anyone know of data indicating that the thermal properties of wood can reduce the likelihood of freezing in higher latitude stillwater habitats?

    Woody structures appear to increase the likelihood of overwinter survival in selected frogs overwintering in stillwater habitats and we are attempting to tie this to properties of wood that may reduce the likelihood of freezing in the water column.

    Marc P. Hayes · Washington Department of Fish & Wildlife

    Nancy, I mean frogs associated with those habitats, and Jay, you guessed it, I am talking RAPR overwintering because we are working with some data that suggest the likelihood of mortality with frogs either using wood overwintering structures or use wood overwintering structures for more of the overwintering period is less that with those that do not. Of course, I have always viewed the use of beaver dams as the near ideal overwintering habitat because of the triumvirate of adequate oxygenation, protection from freezing and protection from predators, so the freezing option is clearly not the only basis for using wood.  However, some of the overwintering wood structures we found used were not beaver dams, in fact, they were artificial structures placed for habitat enhancement (but not originally with the overwintering purpose in mind), so as frequently occurs, the issue is likely more complicated than we perceive.  And Jay, I am wondering if your log in the pool is really purely mechanical.  Anyway, I did some digging, probably not enough, into literature on the thermal properties of wood....as you can expect, a lot of stuff from the construction angle that is not very useful in the context I suggest here, but I have not been able to find anything linked with wood linked to water that might provide insights.

  • Thomas Klebel added an answer in R:
    How can one generate GAM and GAMM models without using R or within R?

    I have been trying to generate generalized additive models (GAM) in R. For some reason, my commands are not working. For instance, a command such as fit <- gam.fit(data[,-1], data[1]); does not run. What is correct way to generate GAM models in R? Can someone give an explicit example of a GAM model. And are there other softwares other than R that can generate GAM models.

    Thomas Klebel · Karl-Franzens-Universität Graz

    A well documented package for GAMs seems to be mgcv.

    typical use, taken from the introduction:

    ================= Code =================

    install.packages(mgcv) # install the package, if it is not already installed

    library(mgcv) # load the package
    set.seed(2) ## simulate some data...
    dat <- gamSim(1,n=400,dist="normal",scale=2)
    b <- gam(y~s(x0)+s(x1)+s(x2)+s(x3),data=dat)
    summary(b) # inspect the model
    plot(b,pages=1,residuals=TRUE) ## show partial residuals
    plot(b,pages=1,seWithMean=TRUE) ## `with intercept' CIs
    ## run some basic model checks, including checking
    ## smoothing basis dimensions...
    gam.check(b)

    # if you type '?gam' you will get a full documentation of the main function for GAMs, including examples.

    ============= End of Code =================

    I found some helpful slides by the author of the package here: http://people.bath.ac.uk/sw283/mgcv/tampere/mgcv.pdf

    For this procedure to work, your variables have to be stored in the columns of a data.frame. If that's not the case, take a look at the 'tidyr' package (very useful cheat sheet:  http://www.rstudio.com/wp-content/uploads/2015/02/data-wrangling-cheatsheet.pdf)

  • Can anyone advise where to download DEA frontier software from?
    My library has the book with which it comes but have misplaced the CD. So can anyone guide me to download from somewhere
    Mohammad Firoz Khan · Jamia Millia Islamia

    Free version as well as purchasable:
    http://www.deafrontier.net/software.html
    Open source:
    http://www.opensourcedea.org/index.php?title=Open_Source_DEA
    Free demonstration version
    http://www.banxia.com/frontier/

  • V. Sivakumar added an answer in Plant Extracts:
    How do I filter the plant extract?

    I have prepared Shikakai extract by digesting shikakai fruits in water using Pressure Cooking Technology, after digestion I am unable to filter it using Vaccum filtration. Is there any method to filter and seperate the particles in the extract please tell.

    V. Sivakumar · Adhiparasakthi College of Arts and Science

    Ananda, first filter extract with using muscling cotton clothe and use whaatmam filter paper and filter the filtrate 

  • Nicola Robinson added an answer in Positive Health:
    Is anyone aware of any research on the impact of parent-child communication about weight on child's behaviour/wellbeing (helpful or harmful)?

    Specifically:

    • Do changes in parent-child weight-related communication impact on children’s wellbeing and self-perceptions?
    • Do changes in parent-child weight-related communication impact on children’s eating or exercise behaviours and practices?
    • Are the effects of parent-child weight-related communication moderated by; child’s weight, age, gender, stimulus for weight talk, parenting style*
    • What are the specific strategies and techniques within interventions to improve adult-child weight-related communication associated with positive health or wellbeing outcomes?

    Nicola Robinson · London South Bank University

    I understand Paula Watson, from Liverpool John Moores University, has recently published a service evaluation of the first three years of implementing a family-based child weight management intervention (GOALS).  The article contains an insight into the processes of implementing a complex intervention and translating evidence to practice.  It might be of interest to CHAIN users in the areas of:

    -          Childhood obesity, nutrition and physical activity

    -          Intervention development and evaluation

    -          Translation of evidence to practice

    The article can be accessed here: http://bmjopen.bmj.com/content/5/2/e006519.full “

  • Guy Roemer added an answer in ArcMap:
    Open .XYZ files in ArcMap 10.1?

    Hello,

    Does any body know how can I open .XYZ files in Arcmap 10.1?

    I have tried the GridBatch Software to convert them to raster but it didn't work as I Guess the files are too heavy (100MB) and there is an error in the processing. 

    Appreciate in advance,

    Fatemeh

    Guy Roemer · Tetra Tech

    If your xyz file is just columns of data, you can rename the file to TXT or put commas in between the columns and rename it CSV and directly add the file into ArcMap.  Then, you can convert the file to a raster.

  • Types of images normalization models in digital image processing?

    in order to normalize some of satellite images capture the same area but in different time?

    Michael Porter · University of Dundee

    Dear Hayder

    With a rejection of histogram scaling it's difficult to know what you are looking to do with your images. Perhaps you could give us an example description of what you would like to achieve? What feature of your images are you trying to normalise?

  • Does anyone know of research into links between "crucial conversations" and "positive organizational psychology"?

    Crucial Conversations is a particular approach to having difficult discussions and fostering strong relationships in the process. I'd like to see if effective conversations using this technique contribute to generating positive organizational psychology (or behaviour).

  • What contemporary visual artists are applying principles from fields like neuroscience, neuroaesthetics, and visual perception?
    Scientific research has shed much light on how we see, and on how visual art resonates in our minds. I am interested in reading about contemporary visual artists who have applied this information in their creative processes.
    David Charles Wright-Carr · Universidad de Guanajuato

    You're right John; you've already published your research on line. It's the bibliophile in me that wants to see Jupe's work on the printed page. As it is, the virtual presentations are much more accessible to my students than a book would be.

  • Muhammad Radifar added an answer in Python:
    How can I create a cylinder with 2 point in space and diameter?

    I would like to create a cylinder with python. I have two defined points in the space (the center of the 2 circles) and the diameter. How can I write this code?

    Muhammad Radifar · Gadjah Mada University

    I love it how people quickly suggest a library when it comes to programming problem (especially with Python). I think it is clear that when people understand the basic of Python (data type, conditional, loop, OOP, etc.) they have to learn about several built-in module in Python (like time, sys, os, etc.). And then start to learn to find and use Python library that suit their specific need. In the Hacker culture, reinventing the wheel is a crime (http://www.catb.org/esr/faqs/hacker-howto.html) unless for the sake of polishing the skill. That's why people create and share libraries, so everybody won't need to deal with the same problem, and focusing with the unsolved one instead ;)

  • Chira Alexandru added an answer in Abaqus:
    Does anyone know if a custom element shape can be programmed in Abaqus?

    Hello

    I am using Abaqus for my numerical models. I want to create a user element with more nodes than the usual elements and in different place. I understand that following this i have to provide in the input file. the coordinates of the nodes and the connectivity of the elements. 

    I wonder if there is a way to program an CUSTOM ELEMENT SHAPE in order to create the abaqus the connectivity instead.

    Thank you

    Chira Alexandru · Universitatea Tehnica Cluj-Napoca

    I think you can use this  http://imechanica.org/files/Writing%20User%20Subroutines%20with%20ABAQUS_0.pdf

    You can find everything explaned in there!!!

  • Alexandre Albore added an answer in Graphical Model:
    Are there any studies concerning the usage of graphical models for operational tasks?

    I'am interested in literature / research, which deal (capabilities, advantages, disatvantages) with the use of graphical models for operational tasks, which are traditional are executed with charts and schedules. For instance workforce assignment via drag and drop in a graphic model instead of filling out a table.

    I would be very thankful, if you could share your knowledge in that issue-area, give some literature hints or name the right keywords to search. Thank you!

    Alexandre Albore · The French Aeropace Lab ONERA

    Hi, there are many applications of Graphical Models in Precision Agriculture.

    A couple of references from the French context, but I'm sure that you can find many more: 

    http://www.agrosupdijon.fr/research/umr-agroecologie/agricultural-machinery-research-team/staff/christelle-gee.html?L=1

    https://carlit.toulouse.inra.fr/wikiz/index.php/R%C3%A9gis_SABBADIN

  • At Sathe added an answer in Conventional PCR:
    How do we determine the concentration of the components of PCR reaction such as Mg++, dNTP etc before we do PCR reaction?

    Oh I want to do PCR amplification for certain gene. So, I try prepare the components to run the whole process but I'm quite clueless about how much concentration or volume needed to do in order to get a good result. Anyone can ask my question? Thanks. :)

    At Sathe · Central Institute for Cotton Research

    You have to work out the concentration of t each component out of the given ranges.

    MgCl2- 1.5 to 2.0 mM

    dNTPs- 40 to 200 uM of EACH of four dNTPs

    Primer- 0.1 to 1 uM of each primer

    Taq polymerase- 1 unit/25 ul reaction

    DNA template- 50-100 ng

    Don't forget to work out the Annealing temp for primers.

    Hope this will be helpful.

    Good luck!