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  • Manika Sehgal added an answer in Mind:
    Are there any resources available to map SNPs and other genetic variations to the pathways?

    And what would be the probable criteria that one should keep in mind for doing the same?

    Manika Sehgal · Jaypee University of Information Technology

    Hi abhinav.. thanks for ur suggestions but I am not interested in mapping genes as such onto the pathway rather want to map SNPs specific to genes in disease specific pathways. Mapping genes is not that difficult task but I am facing a huge difficulty in understanding as to how to map SNPs.. Regards

  • Peter Vogel added an answer in RNA Probes:
    Does anybody have experience in using ACD Bio in situ hybridisation kits?

    I am planning to do some in situ hybridisation for mRNA in the paraffin-embeded liver tissues. I came across a company called ACD- Advanced Cell Diagnostics, INC who makes RNA probes and sells kits for in situ hybridisation.  Has anybody used them before? If yes, can you recommend it? 

    Peter Vogel · St. Jude Children's Research Hospital

    We have been using their probes for about 6 months now and have had great success.  So far it has worked well every time for over 20 different targets.

  • Why are peaks in XRD patterns of nano-size materials wider and less intense?

    In comparison to micro meter size materials, nano-size materials exhibit wider and also less intense peaks.

    Cristóbal Verdugo-Escamilla · Spanish National Research Council

    Completely agree with the answers before. In the crystalline domain is too small, there are less "diffracting material" available and then the intensity is less. We can say that as soon as the domain size become lower the material become more and more close to a amorphous material.

  • Dason E Evans added an answer in Lectures:
    Flip Lectures - how to get students to do the prior learning?

    Hi all, A quick question triggered by the stanford video https://www.youtube.com/watch?v=cHPvW-pLJqE forwarded to me on here by Janet Thurston (thank you!)

    Flip lectures are currently very trendy, but nothing new. A colleague Maggie Nicol was using it as a routine educational method more than 20 years ago in the City University School of Nursing, and developed some brilliant learning materials.

    She struggled with ensuring that her nursing students did the preparatory work, and in those olden days ended up running "timetabled Self Directed Learning Sessions" where the students were sat in front of a video with workbooks to make sure that they looked at the material.

    With medical students we have a similar issue. I currently ask them to look at specific material before a clinical skills session, and they have timetabled SDL time ("free time" they call it), but very few look at this material beforehand. This is despite them knowing that they will not be spoon fed in the session.

    I'm curious what strategies are in use to ensure/encourage students to prepare BEFORE a teaching session, I'm particularly curious about how to do this whilst encouraging independent learning...

    Dason E Evans · Queen Mary, University of London

    Fantastic, I'm glad I'm not alone in this! will look forward to hearing more

  • Semiconductor laser flashes but there is no continuous wave radiation. What's going on?

    I have worked with quite a few laser diodes, but this one is proving rather mysterious. It is a non-coated LD. There is no lasing at the specified threshold current or operating current, just fluorescence.  However, there is a flash of, what looks to be, laser light when the current cable is simply connected to the diode with the expected mode shape (but not when using the on/off switch of the current supply).  There seems to be a momentary surge of current that creates the laser flash — nothing new, but it does suggest that the diode is not completely dead. The obvious thing to do is just keep ramping up the current until  there is complete failure (or lasing), which I will most likely do. I am curious to know if anyone has seen this kind of behaviour before. Maybe something is happening in the chip that prevents a stable cavity. The spec sheets weren't dated, so I don't know how old the chips are (the light is red, but this is likely to be inconsequential). 

    Gintaras Tamosauskas · Vilnius University

    It may be that LD is damaged by static discharge. In that case surface (end mirror or clean semiconductor surface) is damaged by high intensity light. Surfaces has few times lower damage level as bulk material. As result there is scattering spot where should be mirror-like surface and cavity quality goes down. So, you cannot get normal LD operation any more. But by over-pumping (due to some static or other way) you still can get generation with bad cavity quality.

    This is why special precautions should be taken working with LD - very easy to damage them by intense light due to strong static discharge current. And surge currents of power supplies at On Off kills LDs.

  • In Plant Systematics, particularly the Campanulaceae; which characters for generic circumscription have proven resilience, compatibility & stability?

    Campanulaceae work has showed that there are no characters by which distinctly could enable generic circumscription. Some have, argued for instance that in the Nothern Hemisphere, North American studies, characters (pollen and seedcoat sculpturing) used for family or subfamily circumscription,could be used for generic circumscription.

    Is it possible to do that for the Southern Hemisphere bellflowers? In South Africa as well, much work has been done on the family but mostly is outdated in terms of generic circumscriptions and needs urgent revision.

    I am currrently busy with the revision of the subgenus afrotrachelium. My intentions are to find new set of characters that will determine the fate of the subgenus; My question is does Prismatocarpus subgenus afrotrachelium deserve a genus status?

    The characters thus discovered in this subgenus could be used to for generic circumscription. I have  no intentions of using molecular phylogenetics since according to Cupido et al. (2011) and Cupido (2009) there is incongruency with the molecular phylogenetic trees with the trees for morphological characters, together with the primary character of capsule dehiscence.

    Thamsanqa Michael Makade · South African National Biodiversity Institute

    Thanks Mats,

    The issue with Campanulaceae as indicated from the studies done by Cupido (2009) is the incongruity between the trees (phylogenetic) for morphological characters and the molecular phylogenetic trees. Also the characters seem to be fine at the family level but at the generic level but do not hold taxonomic importance. Now I need to find out new characters that have never been explored, however, even them will not be enough until I compare with the molecular data.

    I just wanted to find out if there has been some other characters explored below family and generic levels, such as  tribe, subtribe or subgenera within the Campanulaceae family. I hope my question is clear?

  • Can anyone help me in writing a code in MATLAB between reproduction number and infectives or give me an example of a code?
    How are figures 1,2, and 3 plotted in the attached paper?
    Sudipa Sinha · Amity University

    Thanks for the reply. Can you please send me the algorithm or the paper  so that I may know where I am making mistake.

  • Do you use QUIS in your research?
    QUIS (Questionnaire for User Interface Satisfaction)
    Mikael Fernström · University of Limerick

    I use a modified QUIS, when appropriate.

  • Simon Salad asked a question in Finite Difference:
    NSE well posedness

    Hi guys,

    Whats the best way to solve the NSE well posedness problem ? FEM or finite difference ?  Thanks all, Si

  • Chitta Behera added an answer in Regression Trees:
    How do you build a CART (Classification and regression trees) model in R?

    I have data set Y(output)=40*1  and X(input)=40*1000

    Chitta Behera · Indian Institute of Technology Gandhinagar

    Thanks all. My worries is how can i write output= input1+input2+... in my case as i have input of order 1000. let say for example 

    fit <- rpart(Mileage~Price + Country + Reliability + Type,method="anova", data=cu.summary). so here for a bike   mileage= price+country+reliability+type.  What should be the formulation in my case.

  • Srinivasan Kesavan asked a question in Recovery:
    Any one can derive reverse recovery diode Qrr equation?

    Any one can derive reverse recovery diode Qrr equation?

  • Simon Albright added an answer in MCNP:
    Has anybody used the Particle Track card in MCNP input code?

    I need a help in explaining the output variables of the P-Track output file. There is no adequate explanation for tracing the particles in the user's guide! Please refer me to any relative information that may help me in that.

    Kind regards  

    Simon Albright · University of Huddersfield

    I'm not sure what the differences are but can you not set the position and direction for a source in 4C?

  • Judith S. Neulander added an answer in Identity:
    Is anyone working on distinguishing the self and an identity?
    Identity and self are often used interchangeable. However, the two terms appear through various meanings within psychological literature. Are there any proper (perhaps reputable) and useful definitions of identity and self that can illuminate substantial differences and clarify how the terms are best conceptualized in relation to multiple/unity, conflicting/harmonies etc? And how does the self relate to i.e. cultural identity?
    Judith S. Neulander · Case Western Reserve University

    There are a couple of golden oldies that might be helpful to you:  

    Ethnic Identity: Strategies of Diversity by anthropologist Anya Peterson Royce, IU Press 1982.

    Folklorist Richard Bauman has done important work on what he calls the "performance of identity."

  • What is the best indicator of Arsenic contamination in natural water bodies?
    How we can verify that a particular water resource has been contaminated with Arsenic?
    Manohar Sehgal · DAV College Jalandhar

    May God bless Kashmirees.
    Most of the current field TEST KITS are based on the Gutzeit method which involves the reduction of As(III) and As(V) by zinc to give arsine gas which is then used to produce a stain on mercuric bromide paper.
    There have been many studies of the sensitivity and reliability of these kits, particularly in India and Bangladesh. These kits are usually good at detecting high-As waters (say greater than 100 µg /litre) especially in Bangadesh and in some parts of India.

    In water, there are present both arsenic acid[H3AsO4] as well as arseneous acid [ H3AsO3] which are , in fact arsenic(V) oxides and arsenic(III) oxides in water. In acidic condions[ because there is always the possibility of presence of Cl(-), SO4(-2) or NO3(-)ions in ground water/ any sample of water], it is mainly H3AsO3 or As2O3 which reacts with zinc as follows and ultimately give a black stain as shown by reacions :
    As2O3+6Zn+ 12HNO3---- 2AsH3+ 6Zn(NO3)2+ 3H2O
    As2O3+6Zn+ 12HCl---- 2AsH3+ 6ZnCl2+ 3H2O
    As2O3+3Zn+ 6H2SO4---- 2AsH3+ 3ZnSO4+ 3H2O

    3HgBr2 +AsH3---- As(HgBr)3[ black*; causes stain] +3HBr(g)

    * In fact color changes from yellow to brown and finally black.

  • Hüseyin Polat added an answer in R&D Systems:
    Can someone comment on the variation in IL-6 elisa kit assays and why a kit from one company would be very different from another?

    I have used two different types of elisa kits (R&D systems and Elisakit) for my blood analysis and have found very large variation in the concentration of IL-6 that is determined between them.  For instance, in R&D systems high sensitivity kit, IL-6 at rest is usually was between 1-3pg/ml.  In the Elisakit kit, it is between 10-20pg/ml.  Can anyone comment on why this would be?  I understand that R&D was a high sensitivity kit, but why are the concentrations so much lower? Also, is one more justified to use than the other?  

    Hüseyin Polat · Aksaray Üniversitesi

    The variation in the sensitivity of ELISA there is always.  Sometimes, different lots numbers of the same company are seen. This usually, ELISA kits are related to the materials used in the construction. By firms is determined in trial tests.

    If your work requires you too sensitive, I would suggest the structure in RIA analysis.

  • Chengjie Chen added an answer in KEGG:
    Can you suggest a hypergeometric test for kegg enrichment pathway for a non model organism?


    I would like to run hypergeometric testing on KEGG terms for non-model organism. When it comes to Goterm for example, I always use Gostats.

    However, when it comes to Kegg pathways, I tried to use go stats again but it's based on the kegg.db which is outdated and thus does not work.

    Does anyone have any recommendations for Kegg enrichment analysis for non-model organism (as most of the Kegg softwares are specific to model organisms)?


    Chengjie Chen · South China Agricultural University

    Fisher exact test?

  • Kiran Naik asked a question in Measurement Error:
    Does measurement error only implies the error incurred by the measuring equipment ?

    Measurement error implies to a measuring equipment

  • David M Zuckerman added an answer in CST:
    Is antibody of IP grade good enough for ChIP?

    The antibody I have now is good for IP (from CST), but CST also has a specific tag for 'ChIP' and my antibody is not tagged for that one. Just wondering if I should buy one that's labelled exactly as 'ChIP grade'? Thanks!!!!

    P.S. Santa Cruz doesn't really seem to care about the difference between IP and ChIP, so I'm not sure if I can buy antibodies from them and use for ChIP.

    David M Zuckerman · Johns Hopkins Bloomberg School of Public Health

    When a company labels antibodies for specific uses (IB, IF, IP) it means that they've been tested and found to be of use for these protocols. Certain antibodies do better with denatured proteins (so good for immunoblotting), and others do well with folded proteins (good for IP). So the labeling is not necessarily a "grade," the way chemicals are graded for purity, but the assays that the company have found to work for that antibody.

    My guess is that if an antibody is good for IP, it should be good for ChIP as well. This is more likely to be true for a polyclonal antibody (since the epitope for a monoclonal antibody may be blocked by an interaction). If it's not labeled as good for ChIP, then it's either not a distinction the company makes (as you noted for Santa Cruz), or it hasn't been specifically tested. Another way to check is to search the literature to see if anyone else has used this antibody for ChIP before - usually the company's website will have links to papers that have used their antibody on that antibody's page.

  • Goran Jacobsson added an answer in Bonobo:
    Are there any conceptual metaphors used among chimps or bonobos?

    Do chimps or bonobos use some kind of simple conceptual metaphors in their communication and/or thinking?

    Goran Jacobsson · Lund University

    Thanks for interesting links. I refer to conceptual metaphors as elaborated by Lakoff and Johnson and others. Chimps and bonobos surely use  gestures for mainly indexical  reference in their communication, but sofar there is no evidence of use of symbols or displacement (temporal or spatial) referential gestures. Conceptual metaphors (among us Homo Sapiens normally manifested in linguistic metaphors) might be an interesting  greyzone between online and offline thinking and communication.

  • Taratisio Ndwiga added an answer in Water Pollution:
    Is anyone interested in co-authoring an article on the theme of water pollution and influence of human activities on water quality.

    I am looking for someone who is interested in water pollution, environmental problems, water quality, impact of human activities on water, importance of water for the people. I have made an article about the influence of human activities on water quality in Romania and now I am searching for some interested people which want to colaborate on the paper.
    If you're interested, please contact me and we can see if we can make a great job !

    Taratisio Ndwiga · Moi University

    Am interested. Just email me your contacts. let me have the sections which you want me to put the inputs. I will be gland to help.

  • Robert Urwiler added an answer in Web Services:
    Is there a specific tool for identifying Cloud Traffic ?

    Can someone suggest a tool that can identify Cloud Traffic or can differentiate Cloud services from other web services...

    If you are trying to determine what cloud-based services are running through your network, try using Skyhigh Networks.    They analyze traffic and provide a nice set of analysis regarding services accessed, by whom, and the relative security threat. http://www.skyhighnetworks.com 

  • Joaquin Menacho added an answer in Plating:
    How to calculate a pressure drop across the perforated plate?

    The diameter of the plate is 140mm, while the diameter of the perforation is 3mm. I want to calculate the pressure drop for various flow rates.

    Joaquin Menacho · Universitat Ramon Llull

    There is a good information in Malavasi et al., "On the pressure losses through perforated plates", Flow Measurement and Instrumentation 28 (2012), DOI: 10.1016/j.flowmeasinst.2012.07.006

    May be there is interesting information at this handbook: tp://www.qualityperf.com/media/ipa.pdf

    I found the link below, that is an online calculator (I cannot guarantee that it runs ok!)

  • Sujoy Bepari added an answer in XRD Analysis:
    How do I prepare a powder sample to calculate the lattice parameters by XRD analysis exactly?

    Lattice parameters calculated by XRD analysis.

    For example, how to eliminate the effect of sample position or powder density on the calculation results?

    Sujoy Bepari · IIT Kharagpur

    Dear Tao,

                   I think you have to prepare powder and homogeneous sample. Another one thing is that the sample is to be well dried before XRD analysis. After analysis,you have to find the d-spacing from JCPDS database. After that, you can estimate the lattice parameters (a,b,c) using d-spacing and miller indices (h k l). I like to attach one paper with my discussion. I think this paper will help you to find the lattice parameters. 

  • How can I completely remove DNA in my RNA sample?

    I am isolating a total RNA from bacterial sample for real time PCR studies. But i am facing a problem with the DNA contamination. I treated the final RNA sample with DNases enzyme. I had done a PCR with the DNase treated samples, i am getting amplification. Should i increase the incubation period of DNase treatment? 

    Ganga Viswanath · M S Swamininathan Research Foundation

    Thanks all  for your valuable information. Finally sort out the problem. Had  problem with the enzyme. I had changed the enzyme and now its working ...

  • Is it compulsory to exclude all Cq/Ct values more than 30?

    Does error (difference of less than 3 degree Celsius) in annealing temperature have any role in getting a higher Cq/Ct?

    Jens Koopmann · www.biomarker-discovery.com

    Hi Charles,

    I am not too much of an hands on expert, but we had a similar question in out lab and you could put your amplification product on a gel. If you can find a band you have product if you get a smear it is more likely to be background.

    Similarly you can run a dilution experiment as suggested already. You take sample that works well and dilute it down that should give you some indication about your lab settings, sample handling, quality of enzymes .......



  • Does anyone know about environmental risk assessment of polyacrylamides?

    More specifically, the desired assessment should target the use of these compounds as flocculants and coagulants to limit erosion (i.e. export of suspended solids) from construction sites/activities nearby water bodies.

    Taratisio Ndwiga · Moi University

    I have some results for acrylamide, i hope it will help you.

    Upon single exposure, acrylamide is toxic or harmful by all routes of administration. The principal effects prior to death relate to neurotoxicity, although severe effects on spermatid development were also noted. Acrylamide is a skin irritant, with skin peeling being a particular problem. Data are limited, but suggest that it should be considered as an eye irritant. There is clear evidence for skin sensitisation potential, but no data available regarding respiratory sensitisation. The principal effect observed as a result of repeated exposure, by all routes, is peripheral neuropathy including effects such as loss of use
    of limbs, tremor, loss of balance and loss of axons and ganglion cells, as well as other degenerative changes in peripheral and optic nerves, and degeneration of the lateral geniculate nucleus. However, the dose-response information from humans is inadequate and the clearest information available is from rodent studies. Histopathology has indicated peripheral nerve lesions at 2 mg/kg/day, and no effects at 0.5 mg/kg/dayina2-yearrat study. Additionally, degeneration of spermatids and spermatocytes was observed amongst animals receiving approximately 36 mg/kg/day for 8 weeks, although this study was not designed to identify a NOAEL.

  • P S S Chandrasekhar added an answer in MWCNT:
    Can anyone help me to make a counter electrode for dye sensitised solar cell using MWCNT by doctor blading technique.

    Is it possible to paste MWCNT without binder materials like terpinol and ethyl cellulose. Would be grateful if any refrence paper is attached. 

    P S S Chandrasekhar · Indian Institute of Technology Delhi

    If you  have MWCNT powder, first disperse in ethanol for 1 h, followed by taken it in to motor pestel and wait until half the amount evaporates, then add 20 or 40wt% PEG solution dropwise while grinding.

    Grinding should be continued till get paste. The attained paste you can use for doctor blade coating on FTO.



  • How would you decide how big your corpus should be for quantitative analysis?

    Besides common methodological limitations (e.g. limited historical data, chronological gaps, lack of annotated data), we still need to justify our choice, ex. 500/1000+  tokens per text, or century, or genre etc. Thank you in advance for you valuable input.

    David Lorenz · University of Freiburg

    I just came across this discussion and might have just two cents to add to the $100 of useful things that have been said …

    Regarding amounts of data for logistic regression models, Baayen cites a "rule of thumb" that "there should be at least fifteen times more observations than coefficients" (2008: 195); though this says nothing yet about how evenly the observations should be distributed across the levels of the dependent variable (I don't know if there's a "rule of thumb" for that, too, but it should certainly be considered).

    As for how to treat the time variable, I'd say that in principle continuous is better that categorial (on the rationale that one should not needlessly lower the level of measurement). If it seems more reasonable to use time periods (i.e. categories), I would suggest to treat them as ordered categories, i.e. an ordinal variable (such that, e.g., "Old" < "Middle" < "Late").

    And a third cent, in response to Gard's answer: If I understand mixed-effects models correctly, by using the time variable as a random effect, you factor out the different baselines in the different time periods, so what you get in the fixed effects is the effects of the other variables irrespective of the time period. If you're interested in change, that would be not what you want. Another option could be to treat the time variable as a moderator variable, that is to include its interaction with each of the other factors in the model. Interaction with time = change. (But I realize we're digressing from your original question..)

    [Baayen, R.H. 2008. Analyzing Linguistic Data. Cambridge University Press.]

  • Rakesh singh Gosain asked a question in Couples:
    What is Seismic coupling and how it is different from interseismic coupling?

    Please suggest me the relevant papers or methodology if possible.