Q&A

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  • Jean Paul Bourgault added an answer in Antibodies:
    What dose (mg) of 17β-ESTRADIOL pellet (60 day release) should I use to grow MCF-7 induced tumors in SCID-SHO mice from charles river?

    We are growing these tumors for a passive antibody transfer experiment to study effect on tumor growth 

    Jean Paul Bourgault · University of Toledo

    thanks Saku, will keep this in mind for next time

  • Adam Hughes added an answer in matplotlib:
    What is the best framework or package support for DSP / Fiber Optics Communication GUI interface?

    I am developing a DSP / Fiber Optics Communication simulation suite in Python using Numpy & SciPy. Currently I am using Matplotlib to plot graphs and render various output.

    However I want to make the interface more interactive - user can select params, enter data, see animations, click button to start etc.

    Which is the best GUI platform to make use with backend being in Python? I know a couple of Python GUI tools - like Tkinter / wxPython / JPython / LAMP (Linux,Apache,MySQL,Python) / Django? Which of them are fine to be used or anything else is available that I can make use for ease of GUI interface development?

    Adam Hughes · George Washington University

    You might want to try Enaml or TraitsUI from the Enthought Tool Suite.  They will speed up your dev time substantially, and are bulit over QT/WX so you don't need to be so far down in the weeds so-to-speak.

  • Is there any study on the impact of the absence of media convergence for in the distance?

    In his book Convergence Culture, Henry Jenkins addresses the contemporary setting of communication from three pillars: collective intelligence, participatory culture and media convergence, also called the convergence of communications media. Emphasizes that the Collective Intelligence (CI) is related to consumption, in which discourses are constructed and reconstructed collaboratively.

  • Barbara Rezende asked a question in LaTeX:
    Is it possible to remove SDS from latex sample through dyalisis?

    I'm trying to determine the stability of a latex by quantifying how much SDS  migrates to the aqueous phase during dyalisis process.  Does this molecule pass through the membrane? Is it possible to quantiy it by UV-vis?

    Thank you!

    Regards

  • Can anyone recommend some tools for HARDI DTI data analysis and tractography?

    For my project, we will acquire HARDI DTI data of brain tumor patients and healthy controls in order to construct structural connectivity matrices (based on tractography results) for graph theory analysis.

    Can anyone recommend any program, preferably script-based?

    I heard of the Diffusion Toolkit/TrackVis, MRtrix, and Camino, but I don't know which one would be best for my purpose.

    Angelique Van Ombergen · University of Antwerp

    MRTrix is good for HARDI data and user-friendly! 

  • How can we utilize the knowledge of marine microbiology in the development of fisheries resources?

    How can we utilize the knowledge of marine microbiology in the development of fisheries resources (e.g. Utilization of various Marine microbes e.g. bacteria, yeast, fungi, probiotics, peribiotics and their application in mariculture, aquaculture, fish feed nutrition etc.). 

    Would you any Scientists can share ideas, provide suggestions, or information or article regarding recent research on Marine Microbiology concerning incorporation with fisheries?

  • Standard of the permissible limits of toxic heavy metals and arsenic in fish and sea water and sediment?

    I hope you help me find a Standard of the permissible limits of toxic heavy metals and arsenic in fish and sea water and sediment

    John Ν. Hahladakis · Technical University of Crete

    The World Health Organization, WHO, has established as safety metal quantity limits from eating fishes a weekly maximum dosage, commonly known as Provisional Table Weekly Intake (PTWI), per kg of body weight. Taking an average human body weight of approximately 70kg, we can calculate the quantity per person/per week. Therefore, these limits are given in μg/person/week and are the following:

    Hg: 5 μg/kgb.w.  = 350 μg/person/week = 0.35 mg/person/week
    Cd: 7 μg/kgb.w. = 490 μg/person/week / = 0.49 mg/person/week
    Pb: 25 μg/kgb.w. = 1750 μg/person/week = 1.75 mg/person/week
    Cu: 3500 μg/kgb.w. = 245000 μg/person/week = 245 mg/person/week
    Zn: 7000 μg/kgb.w. =  490000 μg/person/week = 490 mg/person/week
    Ni: 35 μg/kgb.w. = 2450 μg/person/week = 2.45 mg/person/week
    Fe: 5600 μg/kgb.w. = 392000 μg/person/week = 392 mg/person/week
    Mn: 980 μg/kgb.w. =68600 μg/person/week = 68.6 mg/person/week

    Furthermore the EU Regulation1881/2006/ΕU has established the following maximum concentration limits in fish tissues for Hg, Cd, Pb and these are 0.5 mg/kg, 0.05 mg/kg, 0.30 mg/kg, respectively.   

    Kind regards!

  • What are the recent research progress concerning Marine Microbiology (particular focus to fisheries resources)?

    I am very much interested to know about recent research progress in the field of Marine microbiology to incorporate in with sustainable development of fisheries.   

    Would you any Scientists can provide suggestions, ideas, information or article regarding recent research on Marine Microbiology (Particular focus to fisheries)?

  • Matt Jans asked a question in OneNote:
    Who has a good workflow for reviewing articles and note taking on Android devices?

    I've worked out a great workflow for taking summary notes on articles on my PCs, but am having trouble transferring it to Android due to the lack of good screen capture options within PDFs. Here's what I do on a PC.

    1) Open PDF and start reading

    2) Open OneNote document and start taking notes there. I take text notes unless I find a key table or quote, and then I take a screen cap and paste it into OneNote. Sometimes I'll do some highlighting before the screen cap. 

    3) Rinse and repeat

    I realize I could also annotate the PDFs directly (I used to do that), but then my notes would just be sitting in the PDF and harder to extract when needed. This method brings out the notes and take-home messages better in my experience. 

    I've tried several PDF readers including Adobe, Foxit, Google Drive Reader, Skitch, etc., but haven't found anything. I've also tried Screenshot Easy as a general screen cap program, but no luck.

    Has anyone worked out such a workflow within Android?

    One work-around I've done is to zoom in on the section of the PDF page I want and do a full screen cap, but that's a little clunky. I'd love to find a program that lets me draw and capture a focus square just like on a PC. 

    Thanks in advance. 

  • Daniel Pereira asked a question in HOMO-LUMO:
    What are the HOMO and LUMO levels of Coumarin-500?

    I'm a graduate student researcher currently working on OLED processing using a host:guest system and I'm trying to understand which process takes place in my structure when I add coumarin-500 as a dye in my matrix. The problem is I can't find the currect energy levels of this material. Does anybody know where I can find this information?

  • Munya Kabba asked a question in Africa:
    Can the books, "The Invention of Africa" and the "Idea of Africa" provide insight that enable African overcome its crisis-ridden conditions?

    The Invention of Africa, and the Idea of Africa are books by Mudimbe, an African scholar that is becoming popular.  On learning that his work takes the postmodern perspective of Michel Foucault, a great French scholar, I have felt the need to ask if a work inform by such perspective can provide the much needed insights to resolve Africa's crisis conditions in the realm of political, social and economic development.

  • Ariel Linden added an answer in Municipality:
    How can I improve audit outcomes and achieve clean audits in South African municipalities?

    For sometime now that South African municipalities have been struggling to achieve desirable audit outcomes. Then the question is "what is actually supposed to be done to ensure that these public institutions achieve as expected"?

    Ariel Linden · University of Michigan

    It seems that there are limited option available. Is it possibly to implement financial penalties on the municipalities for not meeting the Auditor General criteria? Also, perhaps the introduction of random audits or investigations outside of the usual reporting periods by the Auditor General's office may force the municipalities to consider their actions on a regular basis

  • Are there previous studies where Transcranial Magnetic Stimulation been used in animals, specifically dogs ?

    To reduce epileptic seizures in dogs with epilepsy focal measuring EEG experiment results .

    Grateful link to publications on the subject . :)

    Angelique Van Ombergen · University of Antwerp

    Hi Cecilia, 

    possibly also interesting to you: 
    - J.R. Ives, A. Rotenberg, R. Pomma, G. Thut & A. Pascual-Leone: Electroencephalographic recording during transcranial magnetic stimulation in humans and animals. Clin Neurophysiol. 2006;117(8):1870-5. 

    I haven't found much on TMS and epilepsy in dogs, most of the papers I found were on the use of TMS in spinal cord abnormalities in dogs: 


    - De Decker S, Gielen IM, Duchateau L, Oevermann A, Polis I, Van Soens I, van Bree HJ, Van Ham LM: Evolution of clinical signs and predictors of outcome after conservative medical treatment for disk-associated cervical spondylomyelopathy in dogs. J Am Vet Med Assoc. 2012 Apr 1;240(7):848-57. doi: 10.2460/javma.240.7.848.

    - De Decker S, Van Soens I, Duchateau L, Gielen IM, van Bree HJ, Binst DH, Waelbers T, Van Ham LM: Transcranial magnetic stimulation in Doberman Pinschers with clinically relevant and clinically irrelevant spinal cord compression on magnetic resonance imaging. J Am Vet Med Assoc. 2011 Jan 1;238(1):81-8. doi: 10.2460/javma.238.1.81.

    - Poma R, Parent JM, Holmberg DL, Partlow GD, Monteith G, Sylvestre AM: Correlation between severity of clinical signs and motor evoked potentials after transcranial magnetic stimulation in large-breed dogs with cervical spinal cord disease. J Am Vet Med Assoc. 2002 Jul 1;221(1):60-4.

    Good luck!
    Best wishes,
    Angelique

  • Narendra Kumar added an answer in Hindi:
    Can someone provide me with a list of Psych verbs (Experiencer verbs) of Hindi/ English ?

    The list of experiencer verbs with its classification in Subject experiencer and Object experiencer verbs will be appreciated and I'll be thankful ever for this kind support.

    Narendra Kumar · Indian Institute of Technology Ropar

    Dear Amy,

    Thanks a lot. It really seems very useful for my research. 

    Regards,

    Narendra

  • Besides publishing in journals and writing books, what ways help promote ideas that have been researched?

    I have just gotten published a book on transpersonal experiences surrounding death.  These include near-death visits, near-death experiences, out-of-body experiences, death bed communication, after death communication and other related phenomena.  The books that prepare health professionals to assist patients and family members close to death who have these experiences are woefully lacking in discussing these phenomena.  Millions of people have these experiences but those helping them often are confused or conflicted about how to respond. 

  • Nadir Alloui added an answer in Avian Pathology:
    Can we meet Newcastle disease outbreaks in a region where the vaccination program was conducted? Is what we are dealing with a new biotype?
    An outbreak of Newcastle disease made its appearance in late May, the disease has a strong lead very mortality in livestock farming of chickens and laying hens, despite vaccination of animals against ND.
    Nadir Alloui · The University of Batna

    Thank you for your opinion. I would like to collaborate with your Institute.
    Currently we are working on infectious bronchitis in poultry. Can we determine the IB virus strains by PCR-RPT in your lab

    Best regards

  • What are proper housekeeping genes in the plasma membrane fraction for western blotting?

    I studied the regulation of Caveolin-1. I used coomassie staining of PVDF membrane as loading control for western blotting of membrane fraction (isolated by differentiational centrifugation). But reviewer is not convinced. He asked me to use proper housekeeping gene control because according to him it is not a reliable method. 
    Can you please suggest me whether beta-Actin be used in membrane fraction loading control? Some feel assertive, whereas some feel that  actin is a contamination in membrane fraction.For this ambiguity, I did not use it as a housekeeping gene in membrane fraction. I failed to find a exact answer in the literature resolving the issue of cytoskeleton proteins in plasma membrane fractionation.Can you suggest me any reference?

     Except cadherin, Na,/K-Atpase, what housekeeping gene can be used, since they are not housekeeping for my experiment? 

    Hoping your response.

    Regards,

    Amar Bahadur Singh · VA Palo Alto Health Care System

    Transferrin receptor is a good control for transmembrane protein.

    good luck!

  • Vanessa Meloni Massara added an answer in AHP:
    Does consistency index in ahp test depend on the number of used parameters? Does this method accept more than 30 parameters simultaneously?

    In comparison "pairwise" in AHP method, the consistency index should be less than 1. When placing various parameters seems that the index approaches the inconsistency (> 1).

    Does this method accept more than 30 parameters simultaneously? or no relationship : "number of parameters vs. index "?

    Thank You very much!

    Vanessa Meloni Massara · University of São Paulo

    Dear Manuel,

    Thank You very much. You all are experts in multi-criteria and I only can thank you for sharing your knowledge with me.

    I am crawling but learning from all the explanations.

    Best wishes,
    Vanessa

  • Arijit Ghosh added an answer in Robetta:
    How can I join the fragments output by Robetta online structure prediction server?

    I am using Robetta online structure prediction server. But it gives me the structure in 4 domains (all in different PDB files). I am wondering if there is a process by which I can generate the whole structure. Please help ASAP.

    Arijit Ghosh · The National Institute of Science Education and Research

    Thanks Priyanka for the valuable suggestion, I will try it and let you know.

  • Has anyone tried to investigate the topography of land segmentation through graph theory?

    If a graph depicts connectivity, what does it tell us about the space it segments?

    Shian-Loong Bernard Lew · Taylor's University

    Dear  Thomas,

    Though I'm aware of the four color theorem, the genus aspects that you brought up really helped in my thinking of what kinds of graphs may be suitable for the kind of problem I am facing.

    I am trying to get to the inverse of graph-based solutions. What I mean by "inverse" is akin to veins in leaves (I take this to be graphs in this analogy but perhaps they are more "tree-structures"). The question is how to investigate what is left if I were to take out all the veins in a tree leaf? The remaining spaces of chlorophyll is what I am interested in. Which I think is a kind of segmentation- therefore am not sure whether this is a graph-related problem or should be another mathematical domain altogether. 

    Thanks,

    Bernard

  • What is the availability of principal component analysis for time series of groundwater chemistry data?

    I am looking at the availability of Principal Component Analysis for hydrogeochemical data sets displayed as time series and I would like to know your opinions .

    Paul R. Yarnold · Optimal Data Analysis LLC

    Dear Can,

    In the article I cited, Rob and I used goal-programming to identify the unconfounded factors (see pages 74-79). This is a situation-specific manual iterative analysis, so there is no software suite that accomplishes this analysis generically. In the project that I cited we described our goals: "The application of our algorithm involved searching for homogeneous spatial areas within which geopotential height measurements are highly related. Constraints included that independent application of PCA to the S, NS and C samples yields comparable, excellent macro performance (strong eigenvalues) and internal measurement properties across samples, and that mode constituents are physically contiguous" (p. 74).

  • Mahesha Manjunatha Poojary asked a question in STD:
    How to identify triglycerides in HPLC chromatogram?

    Hi, I am separating triglycerides from oils using HPLC. I have run a standard solution containing 5 standard triglycerides. I found that retention time was based on their carbon no. 

    Later I separated triglycerides of oil samples. I found multiple peaks. Now I am confused to which group do they belong (LLL, LOP, MOP, LnLO etc etc etc). The literature says that use effective carbon no. method. ECN = CN-2DB, where DB= no. of double bonds. 

    Now to identify triglycerides in my sample should I plot a graph of Retention Time of Std triglycerides Vs their ECN and based on the should I check the ECN of sample triglycerides, thereby identifying the triglyceride composition? 

    attached is the standard protcol. 

  • Vijay Kumar added an answer in Pectinase:
    I'm not getting results on pectinase zymography but getting bands on SDS-PAGE. What may be the reason?

    I performed the SDS-PAGE and zymographic analysis of Pectinase (polygalacturonase) enzyme from B. subtilis after ammonium sulphate precipitation and dialysis. I am getting bands on SDS-PAGE but no clear zone on the zymographic analysis (I checked both overlay method and pectin incorporation in gel) but I'm getting no result. What might be the reason?

    Vijay Kumar · Sri Venkateswara University

    Try to concentrate ur protein with PEGin 1:1 ration,and u have to do zymography in native page electrophoresis.....avoid heating and lastly u have to maintain same PH in all conditions....

  • Swapna Simon Ph.D asked a question in SPSS:
    Is SPSS an easily available software for statistical analysis?

    Need more informations regarding SPSS  software for statistical analysis?

  • Hung Phan added an answer in Thin Film Transistor:
    Why does my bottom contact organic thin film transistor have large leakage current?

    As a reference, I have made devices without active layer- pentacene and it showed low gate leakage current. However the otft device I made have large gate current and the current is always one order smaller than drain current. It seems that the gate current form the drain current.

    Hung Phan · University of California, Santa Barbara

    I agree with Leszek. If you still get high leakage, you can just attach an I-V curve with both Ig and Id here so I'll see if I can help. Sometimes it's just the wiring around your probe contacts.

  • Singgih Afifa Putra added an answer in Coral:
    Any idea about this coral-killing sponge-like?

    We found this during my colleague research survey on Seribu Islands, Indonesia. We found this only living on lagoon systems. We was thought this is kind of sponges, but we still not find the relevant publications. Can anyone help us for recommended publications or links? Many thanks, 

    Singgih Afifa Putra · Operation Wallacea, Indonesia

    Hi Dr. Risk,

    That is really surprised me. That's why I feet something horror on that station. :D

    So, This probably as you said, because for now Pari Island hasn't only as a research islands anymore, some tourism activities and resorts was build at there in the recent years. But still, if you also found this sponge like what we also found, it was not really changes since you visit this islands. Perhaps, the organic matter already accumulated in the lagoons and backreefs for many years.

    So, may be we can write an article about this sponge correlated with the water quality as bioindicator.

    Cheers, ***

  • Lucie Grodecká added an answer in RNA Splicing:
    Can you suggest any splicing factor binding motif search tools?
    I'm looking for a reliable and easy-to-use online programs to search for enrichment of splicing factor binding sites within sequences surrounding alternative exons. I know both the binding site and the alternative exon sequences, plus 500nt upstream and 500nt downstream of the exon. Can anyone give suggestions?
    Lucie Grodecká · Masaryk University

    Hi, Simona,

    if you want to search for factors binding to your sequence/sites, SpliceAid makes some suggestions: http://193.206.120.249/splicing_tissue.html

    If you search for the regulatory sequences (with or without known binding proteins), you can try also Sroogle engine, similarly to human splicing finder it shows predictions based on several individual programs. http://sroogle.tau.ac.il/

    Hope it helps. Lucie

  • Do Fisher test in Ingenuity highlight only enriched terms?

    Dear everybody,

    I have a very basic question regarding Ingenuity results.

    When IPA provides biological terms enriched with a significant p.values, are these term always enriched in elements or they could be as well depaupered?

    Sorin Draghici · Wayne State University

    Unfortunately, yes, the p-values are calculated for enrichment alone. In fact, most tools that perform GO and pathway analysis only provide p-values for over-enrichment. In fact, the approach is known as Over-Representation Analysis or ORA. This is very unfortunate since under-representation can be equally important. Here is s fragment from Section 24.5 Common mistakes in functional profiling from this book: http://www.amazon.com/Statistics-Microarrays-Bioconductor-Mathematical-Computational/dp/1439809755.

    "In addition, many current tools only measure enrichment and ignore depleted GO terms, which could lead to partial answers to the biological problem at hand. For instance, in a cancer data set, the apoptosis pathway will probably have many differentially expressed genes, more so than expected by chance. This is because cancer usually disables the normal apoptotic program of a cell, and the cells proliferate in an uncontrolled manner. This is the justification behind the hunt for enrichment. However, a GO term that is represented significantly less than expected by chance can also have an important biological meaning. A strong under-representation of a biological process in a condition could mean that the normal functioning of that process may be necessary for that particular phenotype. The same reasoning is used when judging the importance of a piece of DNA that is conserved across many species. In essence, that DNA is exhibiting much fewer mutations than expected by chance and therefore, the classical argument goes, it must be important in some way. Many genes for instance, have sequences that are well conserved across related species. A similar argument can be made here. This is not merely an academic argument. If we knew that the homeostasis of a given pathway is crucial for tumor development in a particular type of cancer, and if we could temporarily disturb that pathway without killing the patient, we could, in principle, destroy the tumor. Hence, in principle, the functional profiling should be done for both over- and under-representation. By performing only enrichment, one gives up the ability to ever discover if any GO terms (e.g., biological processes) are essential to the phenotype."

    Read the whole chapter if you are interested in other egregious mistakes. The chapter should be available for free on Amazon.