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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• Would more comprehensive/scientifically valid nutrient monitoring for CO Reg. 85 benefit the point source dischargers performing the monitoring?
I am questioning the adequacy of CO Reg. 85 monitoring requirements. The regulation specifies that data collection must extend beyon the domain of the regulation for the success of a comprehensive nutrient control strategy. It is up to the point source dischargers who are being regulated to go above and beyond the requirements of the regulation. I am trying to determine what reasons they would have to do so. This information would be used for the support of the notion to develop and implement more comprehensive and adequate nutrient monitoring of Colorado surface waters. I am drafting a governmental "white paper" for this notion for the City of Greely Water and Sewer Department.
How can you test the wound healing capacity of thymol-loaded bacterial cellulose impregnated with silver nanoparticles using simple lab procedures?
I'm planning to test the wound healing capacity of thymol loaded bacterial cellulose impregnated with silver nanoparticles however I can't seem to find the proper procedure/protocol to apply in our laboratory. Our laboratory is limited so I'm looking for something that is simple and uses minimal resources (complicated instruments are out of the question). I'm not so sure yet what parameter to test as well. I've read tests which monitor cell migration, however, they use microscopes which are not readily available in the laboratory.
Aldo Medeiros · Universidade Federal do Rio Grande do Norte
Dear Anna, I do not have experience with this technique. Your, Aldo Medeiros
• Can someone help with understanding the Actor-Critic reinforcement algorithm?
To implement it using matlab.
Thanks for your help i will check it
• Does anyone have a protocol for recovering genomic DNA solubulized in 8mM NaOH?
I isolated genomic DNA from cells and dissolved the isolate in 8 mM NaOH. I wish to reprecipitate out the gDNA from the alkaline solution. Is there a very effective way to do this? Anyone know a good protocol or a method that will allow high recovery yields? Thanks.
Christian Rückert · Bielefeld University
Hi! Usually, just adding cold (-20°C) isopropanol in a large enough ratio (> 3:1 volumes) should already do the trick. If you want to be on the safe side: Add 3M sodium acetate solution (pH 4.8) to a final concentration of 0.3M beforehand. If necessary, wash 1-2 times with 70% ethanol.
• Is there any neurophysiologic test to differentiate in real time an evoked dorsal root ganglion potential from a dorsal nerve root one?
I am working on the possibility to evoke a direct response by stimulating dorsal root ganglion during radiofrequency procedures. An issue would be to have the neurophysiologic certainty of stimulating the dorsal ganglion rather than the root.
Benjamin Keeler · University of Miami Miller School of Medicine
Wow...that's a tough one. I assume you are doing this in vivo and using radiowaves for stimulation. Depending on your model system (and the size) it may be difficult to stimulate one and not the other. DRG's are small and often encased in the spinal column. I work with mice (but have also used rats) and the largest DRGs are millimeters across, meaning that if your system is focused enough to only stimulate one or the other of the DRG or root, then I would imagine it would be nearly impossible to find one. If however, you are doing this ex vivo, then would it be possible to shield the root? However, I have a question as to why the DRG and not the root? Stimulation of either would still result in an action potential, right? And if you stimulate the root, you can differentiate the type of stimulated fiber by the caliber (and threshold) of the axons you stimulate.
• Smear crescent electrophoresis
I work on candida yeasts and In their electrophoretic see smear crescent electrophoresis. What is a crescent smear due to their electrophoretic؟
Does anybody know of a open-source FEM code for EM simulation?
Most of the time these are FDTD. I want to combine it to some fluid modeling. Alternatively, is there an easy way to couple FDTD and FEM?
Sébastien Poncet · Aix-Marseille Université
One free cfd software for fem is freefem
What are successful ways to start CFD based work ?
Most of all would agree that start creating valid CFD model some times could be harder than it looks at first time. When your speciality are not CFD and you only need this for design validation or other purposes it looks like, that software does lots of things and gets colorfull pictures most of the every time - but how to know when results are good enough to show for others? My thoughts about "must do" things on this : 1.Have valid (experimental) data to compare numerical results 2.Know the limitations on used calculation model (be a little bit familar with mathematics under the software) 3.Start from simple problems and add more complexity after getting correct results for simple problems 4.Use appropriate meshing What is more ? Share your knowledge and experience about how to start on CFD modeling. Hope that propagation of this topic would help newbies like me...
• Gaurav Shrivastava asked a question in SDS-PAGE
Problem in SDS gel Heating and hampering in running the protein.
When I run my 12 % SDS gel, after 1 hr the gel and the buffer gets too hot and the gel start coming out yellow in the colour from the bottom of seperating gel. This yellow lane come up and then finally restrict the way of protein. Please suggest me what is the reason behind this problem and how it could be rectified??
• Can anyone help with purification of native thyroglobulin from thyroid tissues?
I’m trying to extract and purify native thyroglobulin from thyroid tissues. I have no background in tissue extraction and would appreciate any guidance on extraction and purification strategies? Ideally, I am aiming for a final purity of >90%.
Tom Hopp · Tom Hopp Consultant
Marcia's reference is a good one. Get some chitosan. I've never used it but the patent is very sensible. An up-to-date gel filtration (molecular sieve) method that I recommend is chromatography on Sephacryl S-200. That will remove almost all the contaminating proteins, which, according to the authors of the patent are under 200,000 MW.
• Are these feature selection methods the state of the art?
There is no widely-recommended technique for feature selection. Commonly used techniques applicable for image processing purposes are PCA, correlation-based, GA and sensitivity analysis. This is debatable. Are these feature selection methods the state of the art? Are there any other feature selection methods more commonly used are left out?
David Winkler · The Commonwealth Scientific and Industrial Research Organisation
Yes sparse methods are often very useful especially with data sets with thousands or tens of thousands of independent variables. We use multiple linear regression with an expectatation maximisation algorithm using a Laplacian prior. A related approach can be used with neural networks regularized by a sparse prior to effect nonlinear feature selection. We adapted these from Mario Figuieredo's work. See Le et al. Chem Rev 2012
Exponential speedup of prime sieving
It is surprisingly easy to show that when n equals a primorial (product of successive primes) the inner spacing between co-prime members of Z_n forms a palindrome whose length is one less than the size of the set. Since you can construct the set for the next primorial boundary from your current boundary by expanding the residuals you can double the speed of each new set's construction by taking advantage of this internal symmetry. Meaning at each step you only need to identify half of each new sets co-prime members, the rest is solved by taking advantage of the palindrome. Please read the paper in the link, I have a lot more equally cool and surprising proofs.
Patrick Solé · Institut Mines-Télécom
@Piotr: what about Cramer model of primes? Its prediction on prime gaps can NOT be proved by RH...
Does anyone have a good KEY for STIPA species?
I am working on Balkan Stipa species and the key in Flora Europaea seems to be a little bit out of date.
Krzysztof Piątek · Independent Researcher
You may try to contact Marcin Nobis (http://www.ib.uj.edu.pl/instytut/strony-indywidualne/marcin-nobis). He is a specialist in Stipa and I think he could help.
• Is there a *general physical* (not mathematical) reason behind the conjugacy of a pair of variables in quantum mechanics?
In other words: Why (from the *physical* point of view) some pairs of variables---e.g. energy and time---are "conjugate"? Does the phrase "conjugate variables" creates a false impression of its physical meaningfulness? The main reason for the question is that I have a sneaky suspicion, possibly unfair, that "conjugacy" is closer to a necessary technical 'trick' rather than to a *physical* insight into the interrelationship between the corresponding physical variables. Of course, the big question is: What is a physical insight? What complicates the situation is that none of our "variables" exist in Nature. ;--)
Dear Professor Spiros Koutandos Very nice, yes I read you many article and very much interesting. Thanks a lot.
Helicobacter pylori prophage induction?
I tried the induction of a prophage of H. pylori using UV, but the result is very similar to the control (without UV). This appears to be spontaneous phages being release in low number. After induction I allowed to a 24h incubation period and then check for phages. Do you have any suggestions of what could be used to induce H. pylori prophages? I read that Campylobacter prophages are not induced by UV, but are by bile salts.
Hosni Hassan · North Carolina State University
I agree with Ognjen and Catherine. You need to try different stress conditions, i.e., mitomycin C, grow at temperatures slightly above the optimum, salts including biles, redox cycling compounds to induce oxidative stress... etc
Could I get this SEM image with an AFM?
I use SEM to image gold nanoparticles on glass surfaces. I've attached a high res image at 30000X mag. Based on the scale bar, you can see I'm sampling an area of about 15um X 10um. In my post below, I attached a zoomed region that of 1um X 1um to show the type of resolution I get out of these images. My question is, with a modern AFM, would I be able to get this type of resolution at the same magnification? I know that AFM gives great resolution at high magnification, but would one be able to give similar resolution and depth of field at 30000X? If so, how long would you think it would take to acquire such an image (ie scan time)? I don't have any AFM experience. This image was taken on a fairly new Zeiss SEM; how would it compare to the standard commercially available AFM's?
Adam Hughes · George Washington University
What are the most interesting and challenging phenomena to model?
I'm putting together a list of ongoing modeling works (from different research areas) which try to understand and predict the behavior of an interesting phenomenon. Just a few examples to kick off the discussion: - In environmental systems, global climate change modeling seems to be a perpetual challenge. Making climate change models accurate enough for quantitative prediction has been bedeviling such models. - In obesity and nutrition, the current literature provides over 100 statistical equations to estimate basal metabolic rate (BMR) as a function of different attributes (e.g. age, weight, height, etc.), yet understanding how BMR is precisely modeled based on those attributes is an interesting area of research. There seem to be tons of examples in biology, psychology, economics, engineering, etc, but what are the 'publicly interesting' challenges that you would like to add here?
Romina Martin · Stockholm University
In the context of environmental science it is of relevance to understand human behavior on multiple scales. Why do people act against better knowledge? When and why do people cooperate to share resources? Which organisations are adaptive enough to respond in time to gradual change or external shocks? Challenging in this kind of models is that people constantly develop new tools and behavior. It is hard to say whether we are doomed by an ever growing population or whether we have enough head/heart skills to find a sustainable way of living. So, what are we goint to do about it?
What methods have you found to be effective for helping students improve critical thinking skills?
In my experience, most undergraduate students tend to be naive and accept information without much critical analysis. I have been experimenting with methods for teaching the basic skills of critical thinking, and I would like to read about other educators' experiences in this area.
Tolga Soyata · University of Rochester
Nelson, well said, but, I think I will keep "arsonist" out of my CV for now :) I might have issues in research funding :) :) :)
• How can i prepare cracking buffer for bacterial cell sonication for protein extraction?
I am going to prepare cracking buffer pH 7.5 can i replace Dithiotheritol (DTT) with SDS for availability?
Christian Rückert · Bielefeld University
Hi! The DTT is used as reducing agent for disulfide bonds of proteins while SDS is a detergent, thus SDS is not replacement for DTT. And depending on what you want to do with your proteins afterwards, adding a detergent might be a really bad idea.
• Can anyone help with 3'UTR for sequencing?
I've got a problem with planning my project. I would like to use miSeq for sequencing only 3'UTR of selected genes. On Illumina website I found Nextera Rapid Capture Expanded Exome Kit for preparing needed library, but I don't know it will be proper for my research.. Could you help me, please? Maybe somebody has more experience with NGS and miSeq?
Salvatore Piscuoglio · Memorial Sloan-Kettering Cancer Center
You can use the custom panel from ROCHE Nimblegen SeqCap EZ Choice Library can capture up to 7Mb custom regions with a single design. you need to create a panel with the genomic position of your 3'UTR and the do the capure!!! It will work 100%
Osteoporosis and renal stones.
Renal stone is a prevalent disease with loud symptoms, and osteoporosis a prevalent and silent disease. I read about their relation and the role of IL6, but I would like to hear details about your clinical experience. As a GP or specialist, do you ask for a bone mineral density (BMD) for renal stone patients or at least for some of them? Or even think about the probability of low BMD in them? Do you have any experience of pathological fracture and patients with renal stone?
Eva Kovacs · Cancer Immunology Research
Dear Enzo Parathormone (PTH) is secreted by the cells of the parathyroid glands; It increases the concentration of calcium in the blood. It enhances the release of calcium from the large reservoir contained in the bones. Bone resorption is indirectly stimulated by PTH. (1) It binds to osteoblasts leading to increased expression of RANKL and to reduced expression of Osteoprotegerin. (2) It enhances the absorption of calcium in the intestine. (3) It enhances active reabsorption of calcium from the distal tubules of kidney. with kind regards Eva
Imagine the service includes automatic conversion of file formats for using different codes together, convenient visualization of field and particle data in a common format, and a GUI for generating input files, managing the workflow, etc. Imagine one gets all the standard perks of cloud-based software: 24/7/365 access through a modern browser-based UI, convenient access through tablets and smart phones, back up and optional sharing of all data files, etc. If the service worked really well, would you pay a monthly subscription fee, even though the codes being used were all open source or otherwise freely accessible? Thanks in advance!
• How to compare Hydrological Model Results?
I have simulated daily and observed stream flow values for 13 years of period from two different hydrological models. I calculated RMSE, R^2, NSE, PVE, PBIAS, r, NSEsqrt for Daily, Monthly, Annually etc to compare my results. It is really difficult for me to explain my results using these statistical formula. I wonder if there is a specific method to compare the hydrological model results in the engineering field?
Alain Francés · Universiteit Twente
Sorry, I will add another paper! It is synthetic, show the formulas, explain advantages and disadvantages of the several criteria and finally show some examples. Moriasi, D.N. et al., 2007. Model evaluation guidelines for systematic quantification of accuracy in watershed simulations. Transactions of the ASABE, 50: 15. available at http://swat.tamu.edu/media/1312/moriasimodeleval.pdf
SDS GEL
For what temperature suitable for SDS gel METHOD
Gaurav Shrivastava · Center for Research and Advanced Studies of the National Polytechnic Institute( CINVESTAV)
When i run the sds gel at 100v , after 1 hrs gel gets too hot and the gel start getting yellow from bottom side and due to this, protein is not able to run in complete system and stuck in the lower region of seperating gel. Pls tell me how to get rid from this problem.
• Does the responsibility of researchers end with the scientific publication of their findings?
Or should he or she also ensure that these findings find a way to a) non-scientific public and b) the implementing authorities / institutions (a practical reference provided)? I have made it my habit to any scientific contribution to compose another layman's contribution and to publish in order to create the possibility of practical implementation. All non-academic partners are extremely grateful for it. Without access to databases they would probably know nothing about these results and findings. Other ways to make research applicable?
Max Chartrand · Northcentral University
Madelaine and Boris, good insights. The lion's share of my own work has been in publications not listed in PubMed, but which reach both a scientific and lay audience. For many years I served the media in codifying and digesting scientific discoveries in ways that could reach the policy makers and to the lay public who are the ones to benefit the most. Of course, at that level, politics and vested financial interests are out in full force, but over-all many good changes have come about, though not all that we would like. Key words: Persisence, consistance.
• Focusing Nonlinear Schrodinger Eq. integrability with a non-absolutely convergent input profile (e.g. sin(x)/x)?
I am considering the ordinary focusing integrable 1+1 NLSE, in particular doing with the direct scattering problem on the infinite line trying to identify the scattering data (continuous nonlinear spectrum and discrete solitonic eigenvalues) associated with some specific input profiles. In my case one of the input profiles has the form sin(x)/x, and it is not an absolutely integrable function though the integral $\int_{-\infty}^x dt sin(t)/t$ itself exists. From the book of Ablowitz etc. I see that the condition of absolute integrability is required for the validity of ordinary IST on the infinite line (actually this condition is required for the analyticity of scattering coefficient in upper half-plane of the spectral parameter). Can I actually apply it in my case, or what has been done in general for the IST method when the input profile is non-absolutely integrable although the improper integral of the profile exists?
Yaroslav Prylepskiy · Aston University
No, it's impossible here as in numerics I always have a finite extent for the NLSe input - it is not the case here as I would loose the very sense of the problem - the finite input will automatically give a 'normal' answer, it virtually has 'zero' wings as by using a finite extent in numerics we simply cut these off.. But I have already found an interesting reference describing the issue: For such an input the inverse scattering problem does not produce a UNIQUE solution
• How would one go about analyzing urine and plasma samples for 15N urea?
I am looking for details on the equipment and materials needed and the actual analysis process for measuring whole body protein turnover with 15N glycine using15N urea as end product.
• How can behavioral and health scientists participate in healthcare reform in an effort to reduce the chasm between science and practice?
Since 2001 when the Institutes of Medicine published "Crossing the Quality Chasm: A New Health System for the 21st Century", there has been little political pressure from the behavioral or health science community, academic institutions, or the NIH to get involved in healthcare reform. Rather, our academic institutions send health professionals into the clinical world where health insurance status rather than science dictates the care a child, adult, or senior adult receives. It has been over a decade since the IOM publication. Another decade will pass if those of us who generate knowledge in human growth, development, recovery, and aging do not get involved in the real-life translation of research evidence to practice. The changes needed must occur in reform in the health service delivery and payment system so that people receive healthcare and education that is accurate, timely, and effective. There must be bridges built between public health and health science, between basic science and behavioral science, between logistical engineers and health administrators, between those who make policies that interfere with the delivery of value-based health services and the practitioners that are trying against all odds to provide life saving care. There must be bridges built between medical professionals such as physicians, nurses, and rehabilitation therapists, oral health professionals such as dentists and dental hygienists, and behavioral health professionals such as psychologists, marriage family therapists, and social workers if we are going to create evidence-based, family-centered care. How can we participate in creating a 21st century health system that improves health outcomes despite social status? Something is terribly wrong if research evidence demonstrates that the best predictor of health status is the zip code where a US child or adult lives.
Max Chartrand · Northcentral University
David, on the button. Health is indeed a separate entity and nearly always has more to do with development or resolution of chronic conditions--which are essentially long-term collections of health habits and influences. Health psychologists can play a role in this way by fostering mind-body and body-mind concepts, behavioral medicine consultants by designing models for disease processes and their reversal, all mental health professionals and medical professionals by searching for and addressing underlying causes instead of fluffing over the distractions of symptomatic behaviors. The body and mind are one and not separate entities as we tend to regard them today. Specialization, while good for division and development of expertise, has tended to obscure the holistic framework of health, and we must somehow bring the larger open systems approach to health back. We are what we eat, sleep, think, and experience; in the long term, how far off these entities are from the needs of our mind and body bring us either health or illness. The correction of health, then, becomes a correction of course--the direction in all pertinent aspects that affect it. Thank you for your most cogent insights.