Q&A

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  • Ajay Kumar added an answer in Mesenchymal Stem Cell:
    What is the best clinically approved MSC media to be used for clinical trials?

    Hello everyone,

    I need details about mesenchymal stem cell (bone marrow stem cell) media which can be used for clinical trial studies and which is clinically approved.

    Our application can also involve the injection of this media into patient. I need media which is safe for human applications and properly approved clinically.

    Please add your suggestions.

    Ajay Kumar · Postgraduate Institute of Medical Education and Research

    Thanks Carolina.. I use alpha MEM from Sigma in powder form.. Which media are you talking about actually? Kindly tell company and cat. no. so that I can have a look on the same!

  • Hanno Krieger added an answer in Economic Modeling:
    Why are people (dis)honest?

    "Rooted in the philosophies of Thomas Hobbes, Adam Smith, and the standard economic model of rational and selfish human behavior (i.e., homo economicus) is the belief that people carry out dishonest acts consciously and deliberatively by trading off the expected external benefits and costs of the dishonest act (Allingham and Sandmo 1972; Becker 1968). According to this perspective, people reach a decision that maximizes their interests and are honest or dishonest only to the extent that the planned trade-off favors a particular action (Hechter 1990; Lewicki 1984).

    From the "The Dishonesty of Honest People" one of the most cited article (see)

    http://people.duke.edu/~dandan/Papers/PI/Dishonest_JMR.pdf

    I am interested to know your opinion about

    Hanno Krieger · retired from Justus-Liebig-Universität Gießen

    My prompt response, because they are normal people. To be honest needs a lot of education and thinking about rules and ethics.

  • Do you suggest any antigen as a possible cause of Dermatitis Herpeiformis?

    Dermatitis herpetiformis (DH) is an autoimmune blistering disorder of known antibody IgA and unknown antigen associated with a gluten-sensitive enteropathy (GSE), and is generally accepted as a cutaneous manifestation of celiac disease and is characterized by grouped excoriations; erythematous, urticarial plaques; and papules with vesicles.

    Adil H.H. Bashir · University of Khartoum

    Dear all I am so pleased to hear from you may I add a study we had done for possible antigen and hear from you.

    British Journal of Medicine & Medical Research
    1(3): 163-169, 2011
    SCIENCEDOMAIN international
    www.sciencedomain.org

  • Tausif Alam added an answer in Stethoscopes:
    How do I measure blood pressure in both arms at the same time?

    Hello,

    Can someone help me ? I need of a equipment to measurement of blood pressure in both arms at same time. It has two pieces and the stethoscope is interconnected with a piece in form T.
    Does anyone know?

    Tausif Alam · University of Wisconsin–Madison

    Rather than relying on a stethoscope modified to listen to two set of pulses simultaneously, wouldn't it be better to use two identical machines with built-in sensors; all you need to do is to hit the two switch to start (the two can be wired so a single "on" command can get both going.

  • Gerro Prinsloo added an answer in SCADA:
    What are up to date techniques of energy management within a Microgrids (for example using Multi-agent systems, SCADA..)?

    Dear All,

    I am looking for techniques and architectures of energy management within Microgrids that were and still studied in research project. I found the multi-agent systems, the conventional SCADA systems; I am still looking for other techniques in literature review. Please, if you have some guidelines I would be grateful.

    Thanks,

    Gerro Prinsloo · Stellenbosch University

    Fatima

    this is the link to Greenius http://freegreenius.dlr.de 

  • fa Tari asked a question in Dip Coating:
    How can I coat silica nanopowder on steel plates?

    I have silica nano powder and want to coat it on stainless steel plates. I tried slurry and dip coating, using silica powder+ water and silica powder+ silica sol sluries. but coated layers were so unstable and fall or removed from the surface. what can I do to make stronger coating?

  • Hitesh Inamdar added an answer in Running:
    HPLC: Do I need to change the timing of my buffer gradient with a longer column?

    We are changing the column that we are using on our HPLC from a 50mm column to a 250 mm column to get better peak resolution. I am wondering if I need to change the timing of my buffer gradient along with the increase in run time, or if I just need to increase the run time for each sample? 

    Hitesh Inamdar · Getz Pharma Research

    Dear Caitlin Powell

    When you will increase the column length, retention time will increase in the multiple of column length increase.

    There are many calculator present online, which will convert your gradient according to 250 mm column length.

    If you are unable to find it just ask me....

  • Jai Ghosh added an answer in Housekeeping Gene:
    Does anyone know what is the best housekeeping gene for rt -PCR assays with staphylococcus aureus?

    I've been doing some  rt-PCR assays, but neither of my housekeeping genes (chosen from literature) are working. I've already tried spa, gmk, glyA and hla genes. 

    Jai Ghosh · Shivaji University, Kolhapur

    I would recommend that spa or gly as house keeping gene.

  • Mark Hahn added an answer in Computer:
    What is the relation between throughput and power in computers?

    I am trying to come up with a mathematical model for different parameters used in computers for performance calculation. Can anyone help me understand the relationship between throughput and power?

    Mark Hahn · McMaster University

    I think this is a pretty reasonable question.  Basically, any given set of technology constraints will provide a sweet-spot for throughput, and another for speed (latency).  In a sense even fundamental techniques like pipelining are a way to improve throughput - somewhat at the expense of latency.  If you push above the sweet spot, because power scales superlinearly with frequency, you'll have to accept fewer cores.  You can try pushing "down" too (more cores at lower clock, for instance), but secondary factors may deprive you of throughput improvement (more cores means more synchronization, etc).

    On the other hand, I don't see that much value is gained from trying to model this: any single workload will respond to so many parameters of actual systems that it's more useful to just measure them.

  • What is the best statistical program can be used for multivariate analysis?

    There are many statistical programs produced by software companies, enough to one should decide which software program is more fit to present and analyze the data. If we have data on ages of trees, size, growth rate, vitality, and seeds production. What is the best statistical program can be used for multivariate analysis for these parameters?

    Paul R. Yarnold · Optimal Data Analysis LLC

    Warmest greetings from cold Chicago, Shuichi!

    Last we spoke Rob and I became aware of your heavy workload until next fall. I am grateful and honored that you have interest in and make time to follow our work.

    As you discuss, Rob and I found that although SAS/OR is an excellent system for small experimental test problems, it is unsuitable for large applications. When this became apparent we desired to obtain other optimization programs including LINGO, but we had insufficient resources: we had no institutional support for this aspect of our research, and we thus personally funded our laboratory. However, being forced in new directions has been intellectually rewarding, so I am happy about that.

    I am saddened but not surprised to learn that your proposal to integrate your optimal methods with JMP was rejected. Optimal statistical methods have nearly gone extinct in America. Herbert Simon won a Nobel Prize for his work in “satisfycing”, and that seems to be a prevalent theme today. Problems with legacy LDF and QDF models are generally not widely known, and/or aren’t perceived as being an important issue. However, I have been encouraged lately that the temperament may be changing in favor of exploring more accurate methods: RG has been very instrumental, hopefully for us both.

    It is incredible to me, in this context, how scientists from every corner of the world communicate using English. I am grateful for and humbled by the use of English to communicate. I hope your important works written in Japanese will soon be translated. This I believe may help the companies you mention to understand the importance and pursue the development of optimal methods. I will write to the Japanese scientists translating the book on legacy multivariate procedures and ask if they would be interested in translating Japanese work in optimal methods into English, and vice versa. I will report my findings to you when they materialize. I doubt that any decisions will be made rapidly.

    Yes, we were LINDO users briefly. I’m not surprised that the optimization software you mention is much faster after much time and many updates. It is slow to sell optimal software we have produced even for a nominal fee, because so few people understand these methods. This doesn’t deter us, we hope for a brighter tomorrow.

    As we discussed previously, I look forward to exploring ways to collaborate when your current projects are completed and opportunity arises. Until then I hope there is a strong and steady wind in your sails, and in ours.

    With optimal wishes…

  • Jai Ghosh added an answer in Yeast Biology:
    What is the correct way to adjust the OD of a yeast culture?

    I am growing several yeast strains in culture tubes on YPD (at 30°C with shaking) and when I mesure the absorbance after approx 12 h each one has reached a different optical density. Let's say that from a 1:10 dilution I read an OD of 0.35, meaning my stock culture has an initial OD of 3.5. I want 1 mL solution of OD 1. Can you tell me if this protocol is correct? Do you know a better one? And finally, can I use it even when the initial OD is < 1?

    initial Volume = ( final volume * final OD ) / initial OD

    x = ( 1 mL * 1 A ) / 3.5 = 0,285 mL

    • Take 285 uL of stock preculture to an 1.5 mL eppendorf
    • Centrifuge for 1 min
    • Rapidly take out the supernatant and resuspend the cell pellet in 1 mL of sterile 0.9% NaCl.
    • Centrifuge for 1 min
    • Take out supernatant and repeat the wash one more time.
    • You now have your 1 mL OD 1 solution.
    Jai Ghosh · Shivaji University, Kolhapur

    Your method is perfectly right. What you need is to adjust the OD by trial and error method.

  • Tausif Alam added an answer in Diabetes:
    How can I determine the Bio availability of anti diabetic tablets by Computational Method?

    I have formulated anti diabetic tablets from Plant active constituent. I want to check the bio availability of tablets with computational model, can anyone suggest me some software in this issue?

    Tausif Alam · University of Wisconsin–Madison

    If you know the structure of a compound, their dissolution profiles based on their ionization potential and hydrophobicity can be predicted and that pattern can be correlated with plausible bioavailability in vivo. Software such as STELLA allow one to run through various scenarios and may help you reduce the number of doses you may have to test in vivo, and thereby number of animals to be used.

    Good luck! 

  • Jai Ghosh added an answer in Chlamydomonas:
    How can I transform C.reinhardtii CC124 by glass bead?

    Hi, everybody!

    Now I am trying to transform wild type C.reinhardtii CC124 with 1302 vector by glass bead. I am not so familiar with Chlamydomonas strains. In research papers, it was reported that mating type (+) and (-) was mixed before transformation and they obtained mating type (+) and (-) from from stock center . I have only wild type C.reinahrdtii CC124. To transform by glass bead, how should I continue with this wild type strain? I am strongly expecting everybody's suggestion and will treasure any advice.

    Jai Ghosh · Shivaji University, Kolhapur

    Glass beads will not bring about any transformation. 

  • Adib Kabir Chowdhury added an answer in MATLAB:
    How can I find an expert in ANN in MATLAB?

    I want to check my program (ANN) in MATLAB. Is anybody interested?

    Adib Kabir Chowdhury · University College Technology Sarawak

    Can you please specify your problem?

  • Jai Ghosh added an answer in PCR:
    In the case of sequencing, is it normal for a chromatogram to show a shortened gene sequence when I'm actually expecting a full-length sequence?

    I amplified my gene of interest using a set of primers and PCR, then I had it sent to get sequenced (dye-terminator). Lo and behold, it was the gene that I was expecting. However, I could not find the forward primer's sequence and several base pairs downstream from it in the chromatogram. Although the reverse primer's sequence was there, it isn't exactly correct (some bases were different from the original sequence). Needless to say, the sequence I got from the chromatogram was shorter because of the loss of several bases from the 5' and 3' ends. Is this normal? The primers were designed to flank the whole gene.

    Also, I did the experiment again and got it sequenced again. This time around, the chromatogram showed an even shorter sequence (about 100+ bases in total were lost from the ends). Both the primers' sequence were absent this time. Could DNA purity be a factor?   

    Jai Ghosh · Shivaji University, Kolhapur

    What you are getting is normal. However, it is better. you still check your system ( I think there will be no difference). 

  • Is there any technique to find legal and illegal traffic over DNS?

    I want to identify when multiple queries arises from same IP address, then I want to analyze which one is legal /illegal that makes traffic over the DNS.

    Ashok Paranjothi · Veltech High Tech Dr.Rangarajan Dr.Sakunthala Engineering College

    Actually, a query like"www.google.in" reaches DNS to match with its IP
    address. When multiple queries from same IP address may leads to hang the
    server.

    yes, one can give more queries from same IP , but bots make use of
    this and increase illegal traffic over the DNS.

    Now my question is that hw to know/analysis these queries are legal or illegal...??

    I have decided to assign Time-to-Live (TTL) for each queries....is this possible??

    Please suggest any idea or technique to solve this problem

  • How can I solve this error in GROMACS while simulating the lipid protein pull?

    I am trying to pull the peptide through the lipid bilayer using GROMACS 4.5.6 double precision but getting the following error while carrying it out. 

    Program mdrun_d, VERSION 4.5.6
    Source code file: pull.c, line: 329

    Fatal error:
    Distance of pull group 1 (5.326382 nm) is larger than 0.49 times the box size (5.435044)

    What could be the probable reason for the same and how can i remove that?

    Kindly help.

    Regards,

    Tarun

    Selva Chemist (Bio) · GreyMatterResearch Foundation, India

    Dear Tarun Agarwa,

    This is some type of specific nature so you should need to set essential parameter to the instrument and also need to change the box size too,

    Whenever you try to do this you set the box as larger based on your peptide

    You just check the error

    Distance of pull group 1 (5.326382 nm) is larger than 0.49 times the box size (5.435044)

    So that you just increase box size means this error will minimize.

    The distance between pulled peptide and reference group also includes periodicity, and you should need to use some other different pull-geometry

    i thing now recently some improved auto programed version was introduced so you just try to update your software from GROMACS 4.5.6 to next version, because i have seen in latest version some automatic adjustment of box size and other parameter base on sample reading info., i forget the version but via your instrument ID you just put upgrade..,

    Good Luck & Regards

    R.Selva............

  • Stuti Patel asked a question in Endotoxins:
    Can anyone tell me the procedure for extraction and purification of endotoxin (Lipopolysaccharide) from the bacteria?

    Relevant references on the question or procedure on the subject.

  • As you konw aging of layered double hydroxide (LDH) is required for crystallinity enhancement. what are the experimental conditions for aging step?

    After co-precipitation step for LDH preparation,  there is a step called "aging" to increase crystallinity of LDH materials. what is the best condition for aging (e.g., rpm, temperature).

    Hong-Jie Peng · Tsinghua University

    Our group prepared MgAl-based LDH by urea-assisted co-precipitation method. The condition is 90-100 oC aging without stirring. Detailed information can be found in my Carbon paper. Hope this is helpful to you. 

    Best!

    Hongjie

  • Sindhu Govindan added an answer in Exons:
    I am getting DNA amplification with Ex-Ex primer, can anybody help on it?

     DNA contamination of RNA is checked with 25ng of RNA in Q-RT PCR with an exon specific primer and Exon -Exon primer , but I am getting DNA amplification in both. Quite surprising? My Negative controls are fine.

    Can anybody help to ressolve this issue

    Sindhu Govindan · Mazumdar Shaw Cancer Centre

    Thank you All for the valid suggestions,  I guess, the same amplicon size, that I am getting in my PCR with RNA samples using Intron spanning primers, is becuase of the pesudogene. Am I correct?? 

  • Stuti Patel added an answer in Botrytis cinerea:
    Does anyone have a protocol to measure plant defence-related enzyme activity (PAL,PPO & POD) as a response against Botrytis cinerea?

    I'd like to do Colorimetric assay to measure PAL, PPO and POD activities, does anyone knows/has a method or protocol to extract them from tomato leaf tissue?

    Thanks a lot!

    Stuti Patel · Gujarat University

    Thank you so much sir (B.A. Padder) evenI was also looking for the same procedure

  • How can I use electrochemical impedance spectroscopy to study batteries?

    I made a new battery.

    I did charge and discharge for this battery.

    Now I am going to study this battery by means of the electrochemical impedance epectroscopy method.

    But I do not know how I can use electrochemical impedance spectroscopy to study the battery.

    Manindra Kumar · Banaras Hindu University

    Dear Yousofian,

    "Impedance spectroscopy" by "J. R. Macdonald"  will provide you a broad view. You can see the book. 

  • Elavarasi S added an answer in Mathematical Models:
    Which are the most frequent complications caused by Diabetes?

    I am interested by mathematical modeling of the complications  caused by Diabetes.

    Elavarasi S · Nehru Memorial College

    Retinopathy (Retinal damage in eye), Neuropathy (nerve damage), Nephropathy (Kidney damage), heart disease, impotence and miscarriage are the main complications of diabetes.

  • what is the best ChIP-qPCR calculation method?

    Hi Guys,

    I've recently started doing ChIP-qPCR and have questions regarding analysis of data obtained from qPCR.

    My experimental design: I'm transfecting cells with a luciferase reporter plasmid containing a promoter that is stimulated by my transcription factor (TF) of interest. When I perform the luciferase assay I include a DNA-binding mutant of the TF that is unable to stimulate any luciferase expression. I need to show that the mutant version is indeed unable to to bind DNA resulting in no activation of luciferase expression. For this purpose we chose to do ChIP-qPCR. So when I setup for ChIP I've got one plate of cells with TF of interest + reporter and another plate of cells with mutant TF + reporter. 

    During ChIP I include a no-antibody (Mock) control to check specificity of antibody. ChIP-qPCR results are as below:

    Cells transfected with TF of interest:

    Ct input (10%) = 24.42246151
    Ct with antibody = 28.97134145
    Ct no antibody = 32.08292007

    Cells transfected with mutant TF:

    Ct input (10%) = 23.01083565
    Ct with antibody = 29.89976883
    Ct no antibody = 32.16822243


    I use the percent input method [100*2^(Adjusted input - Ct (IP)] to calculate enrichment (pardon me if this is not the correct term to use here). I got the formula from here: http://www.lifetechnologies.com/au/en/home/life-science/epigenetics-noncoding-rna-research/chromatin-remodeling/chromatin-immunoprecipitation-chip/chip-analysis.html

    With this method I get the following values:

    % input TF of interest (with antibody) = 0.42721913
    % input TF of interest (no antibody) = 0.049427904
    % input mutant TF (with antibody) = 0.084377077
    % input mutant TF (no antibody) = 0.017512651 

    My question is how to present this data?

    I also used primers for an unrelated region as everybody seems to 'normalize' their results to that. The values I got are below:

    Cells transfected with TF of interest:

    Ct input (10%) = 26.65428988
    Ct with antibody = 30.54074732
    Ct no antibody = 35.37199211

    Cells transfected with mutant TF:

    Ct input (10%) = 26.33532206
    Ct with antibody = 31.8692112
    Ct no antibody = 34.11607869

    % input TF of interest (with antibody) = 0.67617597
    % input TF of interest (no antibody) = 0.023752544
    % input mutant TF (with antibody) = 0.215840718 
    % input mutant TF (no antibody) = 0.045473551

    I was assuming that cells transfected with TF of interest and those with mutant TF will show similar % input for the unrelated region but that clearly is not the case and it seems like the TF of interest perhaps does bind to this region, although the Ct values are high (since they are in the 30s?)..

    So if I can get any help in analysing this data and some suggestion on how to present it that would be great. I need to find a way that'll convince the reader that the wildtype (TF of interest) does bind and the mutant TF has reduced capability.

    Thanks heaps!!

    Jerry

    Jehangir Ahmed · Australian National University

    That was surprising for me too. The unrelated region belongs to a gene whose expression should be unaffected by my TF of interest (in theory). I used it because somebody in my lab had already used this region for their RT-PCR analysis.

  • Selva Chemist (Bio) added an answer in PAHs:
    Why does Phosphate buffer increase the water solubility of PAHs?

    I am using 20mM phosphate buffer at pH = 7. It increased the solubility of dibenzothiophene and its alkylated homologeous. 

    Selva Chemist (Bio) · GreyMatterResearch Foundation, India

    Dear Parichehr Saranjampour,

    The Solubility of dibenzothiophene and its alkylated homologeous is directly depends on pH, So solubility difference persists, for conducting one reaction, the main parameter is the reactant activation in functional group, for this solubility of the reactant should be needed and same way pH.

    You are used 20mM phosphate buffer at pH = 7, so that the buffer will alter the pH towards H+ enhance so that the dibenzothiophene and its alkylated homologeous system solubility getting increased..,

    Hope you clear..,

    Good Luck & Regards

    R.Selva.........

  • Pushpa Al Bakri added an answer in Oral History:
    How do I apply discourse analysis in my work?

    I am not sure how to approach discourse analysis in my work? Can someone give me an advice? I plan to employ oral history, content analysis, survey and discourse analysis in my study of Malaysian war journalists.

    Pushpa Al Bakri · Monash University (Australia)

    Thanks David.

    My emphasis in the study of not so much studying the journalsts products but more of their routines and practices therefore what would you think if I were to conduct content analysis on their news reports and images and subsequently oral history to capture their practices. I am applying memory framework as my theoretical framework. Your precious comments please

  • Sayed Zaheen Alam added an answer in Academia:
    Do you have experience with caste employment at Universities in spite of the law?
    There are many examples of illegal employment of children of professors. It is an ethical issue. It is about nepotism. Rectors of the University of Novi Pazar, in Serbia, hired several members of their closest family, although there were better candidates for the academic places. Do you have experience with such phenomena?
    Sayed Zaheen Alam · University of Delhi

    Dear András 

    Thanks for your encouragement and support on an important issue happening in India.

    NOW  TODAY's National Daily  ( December 19, 2014 23:42 IST)

    ‘Higher education destroyed by academics, politicians’ (In India)

    http://www.thehindu.com/news/national/interview-with-devesh-kapur-higher-education-destroyed-by-academics-politicians/article6708898.ece

    Thanks

  • Animesh Patra added an answer in Photochemistry:
    What is the reason for fluorescence enhancement of any probe on addition of dna when excited at the formers abs wavelength?

    there is only negligible red shift in the emission maxima of the probe with fluorescent enhancement. My molecule is strongly fluorescent in water and hepes buffer in which experiments are performed

    Animesh Patra · S.N. Bose National Centre for Basic Sciences

    When a dye binds with a DNA the interaction is largely hydrophobic in nature which may leads to increase in fluorescence intensity. Now the dye binds to a large bio-molecule so its molecular motions slow down and non-radiative energy loss due to collision with solvent and other molecules decreases which also lead to increase in fluorescence intensity. (Also their are some examples where intercalation lead to quenching of fluorescence through electron transfer process between base pair and dye.) And the red shift of the fluorescence telling the binding process may be a minor groove binding as intercalation leads to non-negligible blue shift.

  • What type of element should be adopted in modeling shear banding in 3D?

    Dear all,

    As I am modeling shear banding phenomena in 3D, I am confused on what element type I should adopt, since there are many versions in literature. In 2D simulation, some author suggests using quadrilaterals consists of 4 cross-triangular elements, while some other use 9 node quadrilaterals. In 3D, some author use 20 node hexahedral while some other use 8 node hexahedral with 1 integration point.

    So in all I am very confused about this. And I wish there could be some paper recommended to address the element-type issue in modeling shear banding. Could anyone please help me with this?

    Thank you very much!

    Dr.O.P. Gupta · IIT Kharagpur

    As additional input I may suggest the use of large number of simple 4 node tetrahedron elements with single integration point. The size of the element should be smaller than the expected size of the band. If the number of elements becomes unmanageable due to memory restriction etc., adaptive meshing can be used where the elements are smaller only in the region where shear bands are expected. I believe large elements will result in somewhat smooth deformation preventing appearance of shear bands and if this is what is called  the problem of volumetric locking, it will possibly be overcome by use of very small elements. Of course, large deformation, large strain capability is  to be used. I hope this may be useful to you. Best of luck.