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  • How do I prove functional role of a new regulatory element using bioinformatics?

    I believe I might have found a common regulatory element for a dozen E coli genes/loci, however I need to find further evidence, preferably using bioinformatics. Can anyone help show me how can I prove these genes are co-expressed or not? Is there any database for expression of e.coli genes? or any other means to provide further evidence that my element is real.

    Osman Doluca · RTA Laboratories

    to Muhammad: Any names or links of databases that I can access online?

  • Shiv Prakash added an answer in Algorithms:
    Multiple objective shortest path algorithm ?

    Algorithms to solve multiple objective shortest path problem.

    articles or publications on multiple objective shortest path problem.

    non dominant algorithm for multiple objective shortest path problem.

    Shiv Prakash · Indian Institute of Technology Delhi

    Multiple objective shortest path algorithm is like TSP problem with more than one constrains. you can apply NSGA II , NSGA III. You can also look to this link http://citeseerx.ist.psu.edu/viewdoc/download?doi=

  • Piotr Zadora asked a question in Lysis Buffer:
    Do i need to use some specific infibitors (expcept proteas) in my lysis buffer for global acetylome enrichment??

    Hi everyone,

    Currently I mixed equal amounts of cell from SILAC experiment and freeze in -80. I'm planning to follow general protocol with double digestion (LysC+trypsin) and IP with anti-acetyllyssine antobodies. However I'm confused about inhibitors. In my global phosphoproteome I used protease and phosphatases inhibitors but for acetylome I don;t see any standardize procedure.

    Could you please share some experience with me if I should use some cocktail of NIC and TSA or sth.

    Thank you in advance.


  • Laura Ziukaite asked a question in Tooth Extraction:
    Are there any differences in a long term regarding buccal profile (around implant) if soft tissue augment.was performed at different time points?

    To be more precise:

    In the case of a single implant placement in anterior maxilla, what are the differences if soft tissue augmentation (for buccal profile) is performed at the time of tooth extraction, at the time of implant placement or at the time of abutment surgery?

  • What is the best method to measure habits of mind for pre-service science teachers?

    I mean Habits of Mind is knowing how to behave intelligently when you DON'T know the answer. It means having a disposition toward behaving intelligently when confronted with problems, the answers to which are not immediately known: dichotomies, dilemmas, enigmas and uncertainties.

    The 16 Habits of Mind identified by Costa and Kallick include:

    2.Thinking and communicating with clarity and precision
    3.Managing impulsivity
    4.Gathering data through all senses
    5.Listening with understanding and empathy
    6.Creating, imagining, innovating
    7.Thinking flexibly
    8.Responding with wonderment and awe
    9.Thinking about thinking (metacognition)
    10.Taking responsible risks
    11.Striving for accuracy
    12.Finding humor
    13.Questioning and posing problems
    14.Thinking interdependently
    15.Applying past knowledge to new situations
    16.Remaining open to continuous learning

    omda mohamed

    Fran Martin · University of Exeter

    George Kelly's personal construct theory provides many ways of measuring dispositions and habits of mind using repertory grid. It has been applied many ways in education - see the work of Pam Denicolo and Maureen Pope.

  • Dirk Pelt added an answer in Linear Regression:
    Which model to interpret when using polynomial regression?


    I am using polynomial regression to study the effects of person-job fit on job satisfaction (as outlined by Edwards).

    I am having difficulty with what model I should interpret. This is the full model:

    Job satisfaction = b0 + b1*X + b2*Y + b3*X^2 + b4*XY + b5*Y^2

    It is often the case that in the full model, for example only b1, b2, and b5 are significant. However, when I look at F-tests, sequentially adding the interaction (b4) is significant, and then adding the quadratic terms (b3 and b5) is significant: meaning that the full model is best.

    This leaves me to wonder what model (i.e. what response surface) is should look at when predicting job satisfaction by X and Y.

    Help would be very much appreciated!


    Dirk Pelt

    Dirk Pelt · Erasmus Universiteit Rotterdam

    Thank you all for your responses! They really helped to give me a better understanding of the whole subject.

    I am currently working in R already and using the siRSM package, I can really recommend it. It provides almost all parameters one is interested in when using polynomial regression to test person-job fit (slope along the X=Y axis, slope along X=-Y axis, slopes among principal axes), and significance tests by means of bootstrapping.

    And as some of you pointed out (and I discovered when reading a bit more): the most important criterium is (change in) R^2, and I need to use some sort of Bonferroni test because I test a lot of relationships. 

    The comment about the categorical dependent variable are very true, I will have to look into it.

  • Mercy Okoh added an answer in Halitosis:
    What could the cause of halitosis be when no obvious local or systemic causes could be found?

    some patient suffering from bad mouth odour and they have been warned by their surroundings, however, they have a good oral hygiene, and no any other systemic problems, what are the possible causes for their condition?

    Mercy Okoh · University of Benin

    If all the necessary investigations have be carried out and there's still no obvious cause for the halitosis, then it can be concluded that the patient is suffering from psychogenic halitosis (halitophobia).

  • Jyotir Moy added an answer in Cloud Computing:
    Are you familiar with privacy preservation in cloud computing?

    Can anyone tell me about what are the current research trends in privacy preservation in cloud computing?

    Jyotir Moy · KIIT University

    Thanks for your valuable responses!!

  • Jassy Lazarte asked a question in Immune Response:
    Is it possible to get data on different immune response genes (ex. IFN-1, Mx and IRF3) in antigen-stimulated cells?

    I want to determine if introducing an antigen into a fish cell line will create an immune response and thus will trigger the transcription of immune response genes such as IFN-1, Mx and IRF3.

    I am wondering if I could get pertinent data much the way as I could get if I did it in vivo. 


  • Stefano Salvatori added an answer in Alkaloids:
    Does anyone know a method for gravimetric alkaloids determination in fertilizers?

    see above.

    Stefano Salvatori · Environmental lab

    Thank you Ahmed

  • What is the incidence of acalculus cholecystitis?


    what is the incidence of acalculus cholecystitis?

    Abdullah Muhayl Alotaibi · National Guard Health Affairs

    Thank you very much Dr. Gautam Ray.

    that was a valuable information.

  • Ana Domínguez added an answer in GenAlEx:
    How can I generate a dendrogram with bootstraps numbers from micro satellite data?

    I am trying to get a dendrogram from microsatellite data. I am comparing among individuals, not populations. I got a dendrogram from MEGA, by using a genetic distance matriz generated in GENALEX but i am wondering if si possible to get a dendrogram with boostrap numbers.  Thanks in advance!

    Ana Domínguez · University of Oviedo

    You can use MSA to do the bootstraping. http://i122server.vu-wien.ac.at/MSA/MSA_download.html

  • How much strain occur in the Achilles tendon during running?

    According to strain-stress diagram of the Achilles tendon, one can consider one linear and one nonlinear part before rupture. It is important to see which of these two area should be considered in vibration analysis. 

    Is there any study (book, paper, etc) reporting that how much strain (what percent) occurs during running? 

    Thank you in advance

    Arash Khassetarash · University of Tabriz

    @ Gregory,

    Thank you very much for your suggestions.

    I read them, however, I couldn't quite understand that repetitive exposure to load and unload (fatiguing exercise) affects muscle contractile characteristics first and then it causes tendon over-elongation or the other way around?

    This seems pretty important when it comes to creating a vibration model.

    Repetitive exposure to load might affect the tendon in the same way as it occurs to engineering materials such as steel. However other factors like loss of collagen fibers might accelerate the fatigue process. I've read some papers on muscle force changes with fatigue. But I don't know if there is any research regarding the AT's stain-stress diagram during a fatiguing exercise?

  • Could anyone help me find an application of Poisson distribution in blasting or any other mining areas?

    I'd like to find a practical application not a theoritical one.

    Anahita Farsaee · University of Economic Sciences

    Dear Pedro Correia,

    Thank you so much for your respond. your answer helped me a lot.

  • Alexandre Mathieu added an answer in Laser Welding:
    Micro laser welding, is there a crack in the picture attached?

    Hi guys,

    My name is Rogelio H. Aguirre, a grad student at the University of Waterloo working on MEMS sensors. Currently, I am working with micro laser welding suppliers to fabricate the packaging of a pressure and a temperature sensor. I have some experience with welding, but not in micro laser one. I am welding a TO Header Substrate made of KOVAR with a Steel case. The device should resist a high pressure of 600 psi; however, I have some leak issues on the assembly at 300 psi approx. I am not sure if the leak is on the welding line, for me, looks like is in the center of the device. To check this, I check the sample using a microscope with an MPlan APO 20 lens, here is where I need your expertise guys. I am attaching a file with 4 pictures, two are under the microscope, do the images attached shows a fracture or crack on the welding line? According to my knowledge is not a crack, but I want to check with you guys.

    Thanks a lot


    Alexandre Mathieu · University of Burgundy

    As for me, it seems to be cracks, 

    on the second photo, bottom, some irisation is observable, meaning that  liquid reflues from the cracks, do you make any preparation of your sample? 

    maybe, try to test with penetrant to be sure.

    this kind of weld is very difficult to achieve due to dissimilarity of the materials, and circular welding.

    Best regards

  • Which type of testing technique covers all coverage like code, path, statement etc., in a better way?

    There are many type of testing techniques available, whether all techniques covers code, boundary, statement coverage?

    Stefan Kugele · Technische Universität München

    When using FShell and the FQL (query language), you can generate a test suite fitting different coverage criteria. It is very flexible.

    For more information, please have a look at the attached link. 

  • Roman Hackl added an answer in Anaerobic Digestion:
    How to optimize anaerobic digestion of sludge in Wwtp to enhance biogaz production?

    Dear researcher,

    i'm looking for phd topic that combine renewable energy and anerobic digestion of sludge in wastewater treatement to ensure energy autonomy. 

    Thank you for your support.

    Roman Hackl · IVL Swedish Environmental Research Institute


    there are several technologies to improve the biogas yield in anaerobic digestion of sewage sludge. You may want to have a look at the following:


    The sludge is heated and pressurized followed by rapid expansion prior to the digester. This improves among others the biogas yield and the sludge dewatering properties.

  • Alessandro Trentini added an answer in Zymography:
    Do we need to separate the gelatinases of the medium to perform zymography?

    We are trying to do a zymography to detect presence of gelatinases A and B in supernatant medium  of cell culture. We are using the medium RPMI and we couldn't make the samples run. The control (saliva) normally runs. We believe it is because of the medium,  very rich in amino acids. Do we need to separate the gelatinases of the medium for perform zymography?what is the most efficient method?

    Alessandro Trentini · Universita degli studi di Ferrara

    I ran zymography with RPMI-1640 conditioned medium from neutrophils as sample and I did not have any problem so far. The point is that if you have low levels of gelatinses you might not be able to see the bands, so as suggested before you have to concentrate your samples by ultrafiltration. I think that there is not need to do any pre-purification or dialysis. Be aware that if you use complete medium, the FBS should have functionally active (and visible) gelatinases (no matter the treatment at 56°C), so you should at least see the bands from the serum.

    Finally, did you check if your cells express gelatinases (probably this is the most important point...)?

  • Paras Dubey asked a question in Starch:
    What change will we observe at end point in iodometric titration with starch indicator of NiO( to obtain oxygen percentage )?

    Precipitates are obtained but will there be any change in colour of solution

  • Wim Van Averbeke added an answer in Agribusiness:
    Is there a proven method or measurement tool to measure the entrepreneurial competencies of farmers?

    Want to measure entrepreneurial characteristics/competencies of farmers that are reliable to illustrate their abilities to be entrepreneurial in a ever changing agricultural sector.

    Wim Van Averbeke · Tshwane University of Technology

    Dear Janus,

    I think you need to take a step back, and reflect on whether farmers are primarily 'managers' or 'entrepreneurs'. I have the impression that it easier to find valid and reliable instruments  to measure 'managerial competencies' than 'entrepreneurial competencies', one of the reasons being that there is still lack of agreement on what exactly these competencies are.  

  • Sanjay Kumar Chitrakar added an answer in Software:
    What are the most common software used by quantity surveyor?

    Especially during the preparation of Bill of Quantities

    Sanjay Kumar Chitrakar · AKS University, Satna

    Check this :


  • Laurence Stuart Hall added an answer in cDNA:
    What is the difference in cDNA and RNA in gene expression assays?

    I know that cDNA is more sensitive than RNA, but what exactly does that mean? I compared the same set of samples using both RNA and cDNA. The relative gene expression using RNA was higher than the cDNA. Is this what is expected? 

    Laurence Stuart Hall · University of Nottingham

    Now I completely undertsand the question: Like Jack I have used one step and 2 step qRT PCR both successfully; I cannot add anymore to Jacks excellent answer other than to say like Jack I have had success with both methodologies

  • Andrew Wutke added an answer in Special Relativity:
    Is relative simultaneity a misinterpretation of Special Relativity?

    I really need a lot of feedback on this particular issue.

    I think that relative simultaneity is a computational effect of no consequences to real temporal relations. This is based on my analysis of simultaneous trajectories.

    My claim of apparent nature of relative simultaneity is based on the assertion that relative lengths of rigid objects or points moving at a constant relative distance to each other in a stationary system are not conserved (in general ) in the moving system after Lorentz transformation when expressing multiple points trajectories in terms of common time of the moving system.

    More details in the linked document and relevant draft article available from my RG profile

    Andrew Wutke · Thales Group


    Thank you for the document. I thought you have forgotten. It looks really neat and I will digest it as soon as I can. I like when discussions enter this stage where we can make verifiable statements.

  • Susana Velasco added an answer in Fatty Acids:
    Which solvent is best for dissolving long chain fatty acids?

    we have a viscosity modifier (fatty acid) want to dissolve. which solvent will be best? 

    Susana Velasco · Complutense University of Madrid

    I use choroform and methanol, but for storage n-hexane is better.

  • Darshan Panda asked a question in Chlorophyll:
    What is the correlation between chlorophyll content and total N content in plants?

    What is the correlation between chlorophyll content and total N content in plants? 

  • Rupsingh Mathwale added an answer in Server:
    How can I handle this exception (packet transmission error)?

    The last packet sent successfully to the server was 0 milliseconds ago. The driver has not received any packets from the server. null null

    I read many blogs and tried everything like

    checking server name port number

    changing my.ini file

    changing timeouts

    but nothing is working .

    Rupsingh Mathwale · Shri Guru Gobind Singhji Institute of Engineering and Technology

    OS:Windows 8

    Database :mysql

    I am connecting to mysql by :

    String dburl = "jdbc:mysql://,&autoReconnect=true&failOverReadOnly=false&maxReconnects=10:3306/project";
    String driver = "com.mysql.jdbc.Driver";
    String sUser = "root";
    String sPwd = "root";

    these parameters.

  • Eiman Kanjo asked a question in Sensing:
    Here is our latest paper on pervasive affective sensing

    For those who are looking for the latest work in this area.

  • Dr. Susmita Roy added an answer in Lipid Extraction:
    What is the best way to assay diacylglycerol (DAG)?

    What may be the best way to assay diacylglycerol (DAG) extracted from rat liver? Some references say about ELISA kit and some says about the conventional assay for DAG is lipid extraction DAG separation by LC and then MS. Any suggestion is greatly appreciated.

    Dr. Susmita Roy · University of Calcutta

    The best way to assay DAG is to perform TLC, then scoop the silica portion containing DAG and then perform GC.

  • Annabeth Aagaard asked a question in CSR:
    CSR integration in SME's - any great contributions I should know of?

    I am working on a scientific article on CSR integration in SME's, but find very little research - any great contributions I should know of?