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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  • How do I solve this twinning problem in my protein crystal?

    Dear All,

    I am working with a 20 kDa highly glycosylated protein, I got few protein crystals and diffraction shows its a protein crystals, but spots are merging with each other due to twinnig in crystal. How can I reduce or completely eliminate twinning in my protein crystal? What are the parameter I should change while setting up the crystallization trials? The buffer conditions which gave the protein crystal contains PEG 8K and Ammonium sulfate.

    Chanakya Nugoor · Strides Arcolab

    there is a compilation of lot of crystallographic software called Autorickshaw which know a lot about data handling. there are ways to clean the diffractiondata if there is twinging and if the twin is systematic and got symmentry, it can be easily solved  in xtallography. 

  • Miranda Yeoh added an answer in Peer Review:
    When does a rejection of a scientific paper become beneficial to the author? Have you experienced a rejection that worked out for your good?
    All of us go through this experience. We love our research, we work very hard at it. We want to share it with the scientific community and the lay people. But, sometimes our paper is not accepted. Two of 3 reviewers came back with some comments that may not be called for.
    When does a rejection work out for your good? What were the circumstances? Please share for the mutual benefit/s of our RG community.
    Miranda Yeoh · Kolej Matrikulasi Selangor, MALAYSIA (Selangor Matriculation College)

    Thanks for your posts, my dear friends.  This abstract from Prof Ljubomir is highly encouraging: 

    'The study of science-making is a growing discipline that builds largely on online publication and citation databases, while pre-publication processes remain hidden. Here, we report on results from a large-scale survey of the submission process, covering 923 scientific journals from the biological sciences in years 2006 to 2008. Manuscript flows among journals revealed a modular submission network, with high-impact journals preferentially attracting submissions. However, about 75% of published articles were submitted first to the journal that would publish them, and high-impact journals published proportionally more articles that had been resubmitted from another journal. Submission history affected post-publication impact: Resubmissions from other journals received significantly more citations than first-intent submissions, and resubmissions between different journal communities received significantly fewer citations.'

  • Mojtaba Akhtari added an answer in Splenomegaly:
    Is there any role for a splenectomy before allogeneic hematopoietic stem cell transplantation in patients with chronic myelomonocytic leukemia (CMML)?

    Is there any role for elective splenectomy before allogeneic hematopoietic stem cell transplantation in patients with CMML who have massive splenomegaly?

    Mojtaba Akhtari · University of Southern California

    Some hematologists believe that the risk of relapse can be reduced by performing splenectomy before allogeneic hematopoietic stem cell transplantation in patients with CMML, and it is considered to help with reducing the leukemic burden; however, I am not sure about this argument. That is why I have asked this question.

  • Muhammad Yaseen added an answer in Crop Physiology:
    Does salicylic acid, hydrogen peroxide, potassium or zinc boron help to reduce ethylene production?

    Thanks in advance for your replies.

    Muhammad Yaseen · University of Agriculture Faisalabad

    SA is better option to reduce the production as well as to overcome the ill effects of over production of ethylene.

  • Jayan V added an answer in Research Ethics:
    Should we mention the name of data in our thesis which we evaluated?

    My friend is working on evaluating the theses with respect to their Reliability and Validity Methods. Is it is necessary to attach the name of theses which he evaluated or not at the end. What about research ethics in this matter? 

    Jayan V · NTPC Limited

    I think university might have given enough thought about the ethics involved in this case before approving the research topic. When it is approved as a research topic, data sources/references are required to be cited. Otherwise credibility of the current research work will not be appreciated by the scientific community.

  • Is it necessary to clean-up PCR products of ddRAD-Seq samples prior to Illumina sequencing?

    I follow Peterson et. al 2012's procedure for ddRAD-Seq. I ran PCR products-only and SPRI cleaned PCR products on a fragment analyzer, and seems like my PCR products are pretty clean and they are at the desired fragment range. 

    My problem is losing too much DNA when I clean-up PCR products with SPRI. 

    Do you think I can directly send my PCR products to Illumina sequencing?


    Chanakya Nugoor · Strides Arcolab

    normally it is required  to clean the products that you eliminate anything which can interfere in sequencing.  One can actually send the pCR product directly also. 

  • How do you culture lymphocytes for a proliferation assay using alamar blue?

    I am trying to do a lymphocyte proliferation assay but the cells are attaching to the plate. Do I have macrophage contamination?

    Hemavathi Dhandapani · Cancer Institute (WIA)

    Hi

    Currently I do not have experience in Con A stimulated cells, but I have tried using PMA and PHA this also causes the proliferation of lymphocytes. In response to that mitogenic stimuli most of the cells will attach.

    Try using U bottom 96 well plate to prevent attachment of cells or you can also use Dyna beads (see Life tech) to stimulate the Lymphocyte proliferation, I  got good results by using that beads. 

    Good luck

  • Has anyone come across occult cleft in a adult population? and is there an indication for surgery?

    A 24 year lady has presented with an occult cleft? How does one treat it?

    Kiran Nakarmi · Kathmandu Model Hospital

    Occult cleft of lip (forme fruste) can be treated depending on the deficiency. Muscle defect may or may no be there. Your treatment choice depends on that. vermillion notch can be treated by simple z-plasty or white roll mismatch can be treated sometimes just by taking out a diamond and suturing as a straightline. I do

  • Is it possible to generalized estimating equation for both Univariate and multivariate analysses?

    adherence data repetitively measured at month 03, 06, 09, and 12 once patients initiated on treatment. I what to use generalized estimating equation for analysis of my data. I have grouped patients as adherent (=1) and non adherent (=0), which is may dependent variable. I have number predictors measured at baseline. 

  • On which basis you do set your priorities?

    You set priorities to determine which tasks, from a set of alternatives, will be done first. You have a long list of things to do. For example, conduct a research, write a textbook, prepare a conference paper, prepare for lecture, and score examinations. You may determine priority based on importance, value of money, urgency, etc.  What is your opinion?

    Prabhakar Purushothaman · UCAM Pvt Ltd, Bangalore, India

    In my Profession Priorities are not set by me it is by need and requirements of company I will be doing some work suddenly from my boss I will be instructed to do other work. Initially I was feeling bad and I used to argue with my boss later I understood something which is key for my success I can say it as a quote" ** Eight hour is duty and extra is OT (over time)** " it helped me a lot so now a days whenever I was directed to change my priorities without any hesitation immediately I change my priorities therefore  I can say I am successful in my profession everyone is happy but the last thing either I do this or that I used to do with proper care

  • Tomasz Jaroń added an answer in XPS:
    How much powder sample is required for XPS analysis?

    I am  going to characterize

    powder sample by using XPS

    Tomasz Jaroń · University of Warsaw

    It depends on the geometry of the beam you use.

    I use 50 - 200 mg, but less could work as well.

  • Leonard Goeirmanto asked a question in Server:
    How to speed up starting time of Apache Tomcat?

    apache tomcat is a well known java web server but starting time always slower than other web server, maybe there are some configurations, tips or script to make it faster.

  • Can anyone help me with anodic stripping voltammetry of arsenic?

    I want to detect arsenic with anodic stripping voltammetry but finding some problems. I am attaching my results herewith. Could somebody help us in what error we are doing ?

    For ASV analysis:

    1) We prepared 1 mM NaAsO2 (sodium arsenite) solution in 1 M HCl.
    2) We measured CV first and attaching the result herewith
    3) Then we clicked on stripping mode and used following parameters:
    deposition potential = - 0.4 V
    depsoition time = 80 sec
    4) The we performed Square Wave Voltammetry with following parameters:
    intial E = -0.2
    Final E =0.8
    amplitude = 0.025V
    Frequency = 40 hertz
    Potential Increment = 0.004V

    But Current voltage curve is not giving desired result. Also many times there is overflow of current. IV graph instead of showing Gaussian curve is showing Z like curve.

    I am attaching herewith result of CV, ASV and also paper we are following.
    Kindly look into them and let us know what is the problem....

    Isaiah Owusu Gyan · University of Idaho

    My best bet is a mistake with the experimental design. You have As 3+ as your initial analyte however, your CV shows that your initial E = -1 V which means that your scan direction was towards positive potentials (from -1 V to 1 V). Are you trying to oxidize As further? My guess is that you were using the CV to locate the reduction potential and add an overpotential to be applied in the deposition step in the ASV. If the lower line of the CV is considered, then you almost have a current of zero at -0.4 V and -0.2 V, which are the potentials you used in the ASV and SWV respectively.

    My advice is that (1) Use CV to locate the reduction potential of As. To do this, take a background scan first (in 1 M HCl) and then analyte scan (As + HCl). Start at a potential where there is zero current and sweep towards negative (reduction) potentials. The background scan will let you know what the H2 evolution potential on your WE is. (2) Once you find the potential where you suspect As to be reduced, add a few mV (overpotential), still within your solvent breakdown limit and use this potential as the deposition potential in the ASV.

    Also, consider your working electrode (WE) and make sure it is stable within the potential window you are working in. Note that chloride oxidation is possible together with oxygen evolution on the positive side.

  • Can anyone suggest me the name of researchers, those are working on invitro haploid plant development ?

    I am interested in working on invitro double haploid plant development in Maize, Brassica juncea, Rice, etc.

  • S. G. Tan added an answer in Academic Writing:
    How far are scientists willing to go to publish their rejected articles or scientific reviews?
    I am wondering how many papers are sleeping in a computer file because they were rejected or not completed.
    One would say very few, since a paper "has to be published".
    Asking 9 university-based physicians, 5/9 reported to have 1 to 3 papers into their personal files...that will never be re-submitted!

    Would be glad to hear from a "larger size", do you have unpublished papers?
    S. G. Tan · Putra University, Malaysia

    This article on journal choice which appeared in Sci Dev Net on 23/12/14 may be helpful in finding the right journal for your paper. Do feel free to disseminate this information to your friends and colleagues as its Open Access.

  • Kymbra Clayton asked a question in SPSS:
    How to analyse / reduce very skewed survey data of 93 items. to then check if differences in rural versus city. Is PCA best method?

    I am attempting to analyse data in SPSS version 17. I have 93 items dealing with ethical dilemmas faced and wish to work out if there are differences for those in rural versus city. Principal Components was suggested, and I have run this many times but I am concerned that the 'variables produced through this end up with residuals >3 and removal of these individuals, then rerunning the PCA means components change and there are 'new residuals'...

    any help would be appreciated. 

  • Vladimir Joukov added an answer in Centrosome:
    What does this statement really mean: Although the centrosome has a key role in efficient mitosis in animal cells, it is not essential?
    There is a statement which says something like this: "Although the centrosome has a key role in efficient mitosis in animal cells, it is not essential."

    How can something which has got a key role in a process, its absence does't really affect the process?
    Vladimir Joukov · Harvard Medical School

    Hi Rajesh. I guess, the statement you mention is not absolutely accurate or, rather is incomplete. It probably should have ended with “for mitosis per se” or “for cell division per se” (exactly as Jens pointed out). One could spice up Rustem’s example. Like most mammals, which have four limbs, can still move, although slower, when one or even several limbs are down, the spindle apparatus, which is build from several microtubule-organizing centers (the major of which is the centrosome), can still form and function, albeit less efficiently/accurately, when one (or even two) of the centers is absent/deficient.

  • Md Wasim Khan added an answer in Dynabeads:
    Can anyone propose an IP protocol for Ago2?

    Hello,

    I am planning to IP and Ago2 protein from Jurkat cells, but unfortunately I haven't been doing an IP before. I am planning to use dynabeads protein G for my  purposes and I have browsed through many online protocols though I may need some "starting conditions". How many total lysate is recommended, how many Abs etc. Can I use JUST BEADS as a negative control (without adding whole IgG, for example)?

    Maybe there's some standard procedures that one must start from and ajust depending on the results?

    Well, thanks to anyone who can help!

    P.S. And, merry christmas just in case! ;)

    Md Wasim Khan · Indian Institute of Chemical Biology

    oh yes....everything in a cold room...end over end incubation.....and RT is good but try the conventional way....

  • James R Knaub added an answer in Traffic:
    How can I compare crash characteristics between two locations?

    I have to compare the crash characteristics two roads at two different geographical conditions, A and B. A have their own segments A1,A2,A3 and A4. B also have their own segments B1,B2,B3,B4 and B5. Every segments have their own crashes, length and average annual daily traffic(AADT). Should I compare the total of crashes (by consider total length and AADT) for both roads or doing separately by segments and after that compare the average?

    James R Knaub · Energy Information Administration

    Sounds good. Hope you find some interesting, useful information. 

  • Plant or microbe, secondary metabolites ?

    This time i would like to ask a general question from your experience, which source of natural products is more favored, herbs or microorganisms as a source of new compounds ?

    Biswapriya Biswavas Misra · University of Florida

    Microbes are more dynamic and inducible to yield new compounds than plants- as per bookish knowledge that I have !

  • Do you think whether it is proper to connect gravity exclusively with the speed of light?

    Since the beginning of the twentieth century the speed of light is thought to be fundamental to gravitation and its transmission effectiveness. Mathematical physics seeks whether this idea is sufficient for explanation of all phenomena related to mass attraction. Is a change of position needed? What is your opinion?

    Manuel Morales · Institute of Prephysical Research

    Actually George, the new way completes the old way. It takes into consideration everything both existence and nonexistence, and in so doing, shows us how we get something from nothing.

    The argument you speak of stems from ignorance of cause. We assume existence is self causal. In essence, the findings show we have a fundamental perception problem when it comes to reality. The perception that the existence of something begets the existence of something else says nothing about how such existence came to be in the first place. Yet, something from nothing is what each and everyone of us does throughout our entire existence until we can no longer select.

    What the findings show is that nonexistence gives rise to the cause of the existence of its effects.

  • Paresh Gujarati asked a question in Iterative Methods:
    Which are the stable iterative numerical methods?

    Currently I am using Gauss Siedel Iterative method to solve CFD equations. I am facing instability problem i.e. iterations keep on increasing without change in rms value for a given variable such as temperature. 

    I want to know which are some stable iterative methods so that one can implement to get rid of diagonal dominance criteria to be satisfied?

  • Can we define an order topology on an ordered vector spaces which makes it into an ordered topological vector space?

    We know that there is an order topology on a totally ordered set. How about an order topology on a poset?

    George Stoica · University of New Brunswick

    Dear Omid,

    There is an old result by R. DeMarr (Order convergence in linear topological spaces, Pacific J. Math. 14 1964 17–20) that partially answers your question: a locally convex linear topological space X admits a partial ordering so that the convergence of an arbitrary net to 0 is equivalent to the order convergence of the net to 0 if and only if X is normable. Related to this paper, in the 1970`s, Vulih and Danilenko provided a method of partial ordering of a normed space.  

    Sincerely,

    George

  • Nimesh Madushanka asked a question in Cell Count:
    Is there anyone who knows how to practice a testicle cell count ?

    I'm hoping to conduct a study on testicle histology of Rats. Can any one please answer the question that I've asked ?

    A proper protocol or anything would help or any helpful references. Million Thanks

  • Songlin Yu asked a question in Lentivirus:
    Lentivirus expressing non-fluorescent gene linked by Puro with 2A sequence, can I titrate the lentivirus using puromycin screening-based TCID50?

    I use Hela for this titration, in which viruses are 10-fold serial diluted and inoculated into 96-well plated Hela. 48 hrs later,  the medium is changed with DF-10 plus 2ug/mL puromycin, after 10 to 12-day screening, cells infected with higher dilution of virus will get fewer viable clones. A well containting at least one visible single cell clone is defined as positive "plaque".  Can this method equal to traditional Plaque Forming Unit based TCID50? 

  • Aysha Bey added an answer in Government Regulation:
    How would government regulations impact the intrinsic motivation of a teacher?

    As a progressive move, the Malaysian government has made the implementation of Outcome Based Education (OBE) compulsory in the country’s Higher Education Institutions thus requiring a major shift in the teaching paradigm. 

    Aysha Bey · University of Alabama at Birmingham

    Although I can speak only for the U.S. government, I can imagine that most governmental interventions create nothing but disasters for the teachers in classrooms.  When the NCLB foolishness began with all the high-stakes testing, the departure of teachers was huge, as Douglas points out.  But the impact of NCLB continues into college core curriculum with freshmen and sophomores.  Far too often, principals "pass" weak students just to keep the federal figures looking good; too often these students wind up failing even in small junior colleges.  Some students, who manage to score the "magic 20" on the ACT, get into four-year universities, where they are totally unprepared.  The ACT organization tells us that a 20 represents a 50/50 possibility that a student may survive the freshman year.  Most do not survive and our university alone loses $2 million per year on dropouts. Now even our universities are beginning to dictate what percentage of students can be failed (or withdraw) per semester. This is a different form of intervention--the university directly rather than the government itself. 

    Outcome-Based Education has been in place in different states across the U.S. for several decades.  It is not any more effective than any other direct, intervention by the government, whether federal, state, or local. The presence of intrinsic motivation may help teachers remain in place--but even the best motivated teacher grows weary of being told she/he must teach EXACTLY this or that guidelines, sub-paragraph 2(a), ad infinitum. Right now many of our K-12 educators are trying to figure out how to teach with this Common Core Curriculum, supposedly designed to prepare our students for a globalized world.  Well, I can pretty much guarantee from what we are seeing so far that the kids I see may be prepared--so long as they don't have to calculate anything.  They may be able to reason out a fun game to play about ratio and proportion, but don't ask them to set up a proportion and figure out how to calculate it.  "Word problems" confound them and most high-stakes testing from high school through graduate school involves word problems, reasoning, and calculating based on the underlying math principles, which our kids don't recognize because nobody bothered "to connect the dots."  I personally know teachers close to retirement who are leaving as early as possible because they hate this curriculum and are already seeing poor testing consequences from students who have been taught this new core for several years already. Kids are failing chemistry frequently because they can't perform the math needed to balance chemical equations.

    Their reading and reasoning skills are generally terrible and that includes reading social/behavioral sciences, arts and humanities--just about anything except social media and celebrity gossip.  Even the best pre-med students score significantly lower on the Verbal Reasoning portion of the MCAT admission exam.  And the new test for this spring is significantly more difficult, longer, and involves more complex reasoning in the verbal reasoning section plus an entirely new section of social/behavioral sciences, chiefly principles and theories. This new test comes at just the time that arts & humanities are being cut, reduced, or funded at low levels both in K-12 and in colleges.  Usually the first cuts made to K-12 involve art, music, not football or basketball (and I love football!). But we know that children involved in the arts tend to have higher grades in class work, testing, and GPA scores as well.

    Good educators are intrinsically motivated, or many would not put up with even decent (not necessarily good)  school systems, but helping students to gain that intrinsic motivation is another matter entirely.  All too often, even at college level, we still are forced to resort to extrinsic motivation for many of our freshmen and sophomores, who are unaccustomed to the rigors of academia without the "extra credit" or "bonus points" or "excuses" for late papers, missed tests, etc.

    I'm not sure what is running this "high-stakes" testing idea.  I know a lot of people and organizations are making millions from this push.  But it can't improve student performance because these tests are not designed for such results.  Most of these tests (ACT, GRE, GMAT, etc) are predictor exams, not knowledge exams that test specific items like teacher-made tests usually do. A 20 on the ACT for one student doesn't mean he/she won't pass the first year; a 27 doesn't mean a student will pass the first year either.  These tests can't measure motivation, drive, study habits, family and university support (mentoring, tutoring).  Using these tests so extensively when they tell us so little seems rather a waste of time and money.

  • Ning Chuang added an answer in LMI:
    What is the good method for design feedforward controller using LMI?

    I want to design a feedforward controller using LMI. Can you recommend me a good method to design this type of controller using for example Hinf approche or publication on this subject?

    Regards

    Ning Chuang · University of New South Wales

    Yes, Hinf control method is the best approach, because it is very very robust indeed. You may like to look at my research papers using the robust Hinf control method. I'm sure you would like it. - Ning

  • In teaching English as a Foreign Language, how much of the class should be about culture?

    Most teachers agree that teaching the culture of nature speaking countries is valuable, but how MUCH should this be done?  Do you have a percentage in mind or other way of saying how much of the course should be about culture?

    Michael W. Marek · Wayne State College

    John F. Wilhite -- I meant "native speaking."  But maybe I was making an assumption.  As Brian Poole alludes to, there is no single culture of native English speakers. 

    I see culture as important in two areas -- 1) in understanding idioms and cultural references, and 2) in stimulating motivation.  How we handle these two things may be very different.

  • Is there a database enlisting signature metabolites in particular plant species?

    I want to enlist all the characterized secondary metabolites in a certain plant, what database/method I should adopt. So I can say with confidence, for example, that up till now 178 secondary metabolites have been identified from Rosa indica with their molecular weights and chemical formulas.

    (This step is crucial for metabolome based phytochemical characterization)

    Huma Qureshi · University

    After getting name of metabolite from any publication, can we use databases (PubChem, ChemSpider, HMDB etc.) as authentic source for further information like molecular weight, chemical formula and structure etc.?

  • Parviz Parvin added an answer in AES:
    How can we calculate the small-signal gain of a laser amplifier?

    there is a formula in koechner that go=Ep/ηl

    Ep= pumping energy

    l=cavity length

    η = ηtηaηSηQηBηStηASE/AES

    but in this formula there isn't any coefficient for dopant density Nd:YAG.

    Parviz Parvin · Amirkabir University of Technology

    The stimulated emission cross-section varies with spectral broadening due to temperature ( Inhom broadeninig) or pressure (hom broadening) in gases and temperature (hom broadening) and dislocations (inhom broadening) in crystals:

    St. cross-section = (A21lambda2/8pi.n2)g(w)

    where g(w) is the lineshape that could be Lorentzian (homogeneous broadening) or Gaussian(inhomogeneous broadeninig).