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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Should I centrifuge the cells after thawing them in order to remove the DMSO from the medium?

All we know, centrifuging the cell is harmful right after thawing the cell. But in the other hand, remaining the DMSO in the medium can hit the cells, too. So shall I remove the DMSO or it's better to avoid the centrifuge?

Asif Amin · University of Kashmir

I recommend the view point of Mr. Ajay Kumar

• Is there a specific reference or guideline that we can refer to for the theory/methodology behind setting significance levels other than 0.05?

Generally, the significance level used to detect statistical significance is set at 0.05. However, for investigations involving much larger samples, a very small difference can yield significance levels that mislead us to think that these values are statistically significant. Therefore, some studies set a much more strict (conservative) significance levels for their analysis.

1. Is there a specific reference or guideline that we can refer to for the theory/methodology behind these strict, conservative significance levels?

2. Can this new, strict significance level be applied to all statistical analyses in a given study or would we have to re-designate a significance level for each analytic method used?

Marco Biffino · Azienda Sanitaria di Firenze

To my knowledge, any guidelines for statistical significance thresholds (alpha) are misleading in the framework of frequentist inference.

No statistical testing would tell you the truth.

A data analyst should also keep in mind that typically he wouldn't like to reject some test (e.g. Bartlet o Levene test for homogeneity of variances), while he strongly would like to reject the null hypothesis of other test (e.g. an ANOVA or two sample T- test). The "preferred" decision depends both on the research question and on the statistical techniques used, which determine the null and alternative hypothesis. So, sometimes we wish very small p-values, and we are happier as they get smaller; other times we wish large p-values.

After rejecting a null hypothesis, one should assess the practical relevance (e.g. clinical relevance) of his result. Many tests are statistically significant but practically irrelevant. Only many independent (different samples at different places at different time) tests on the same research question can contribute to a corpus of evidence that could be studied via meta-analysis.

Moreover, when setting a significance level, one should consider how many test he is going to perform, if these test are dependent and so on. Some contribution from Alessio Farcomeni could help in this discussion:
1. A review of modern multiple hypothesis testing, with particular attention to the false discovery proportion. Scandinavian Journal of Statistics 34 (2), 275-297
2. Some results on the control of the false discovery rate under dependence. Scandinavian Journal of Statistics 34 (2)

Anyway smaller thresholds are usefull to control the false discovery rate and when reporting p-values we should use a scientific notation: if p=0.0000056, we should report p=5.6E-06.

• How does Bose-Einstein condensation manifest itself in real (configuration) space?

BEC represents order in momentum space, which is fictitious.  It occurs at k = 0 (or, more precisely, at the lowest momentum state, depending on the observer's reference frame).  This corresponds to the infinite- (or large-) r limit in configuration space.  How exactly?  How does no (the condenate fraction) appear in this space (which is related to  momentum space through, of course, a Fourier transform)?

L. I. Plimak · Max Born Institute for Nonlinear Optics and Short Pulse Spectroscopy

A quick - and utterly incomplete - answer is that one should look at correlation functions. The two-point amplitude-amplitude correlations contain in particular the phase correlation length. The latter becoming macroscopic is the characteristic property of the real condensate (as opposed to the ideal one where all particles are in the same state, but this ideal is inaccessible in practice). In experiment, macroscopic coherence manifests itself in emergence of an interference pattern were the condensate coherently split in two and then recombined.

Why the parity need to be violated?

There is parity violation in the weak interaction especially. But the actual cause is still hidden.

Mohamed El Naschie · Alexandria University

GOD does not play dice said Einstein but he should not be telling God what He should or should not said Bohr

How can I rotate a solid component in CST Design Studio?

Thanks.

Fabrice Auzanneau · Atomic Energy and Alternative Energies Commission

Zelimkhan is right; keep 0 or 90 degrees orientation and use angled wiring connections to build your circuit

Why does the rate at which VFAs disappear from the rumen increases with the length of the hyrocarbone chain?

butyrate>propionate>acetate

Coral Kent-Dennis · University of Saskatchewan

Below is an excellent review on rumen fermentation. For specific information about SCFA absorption mechanisms, see the section on proton removal starting on pg 1098. Butyrate is probably absorbed at higher rate because the rumen epithelial cells utilize butyrate (by converting it to BHBA) as an energy source. But there are a number of factors that influence the rate of absorption of SCFA, such as rumen pH.

Aschenbach et al., 2011, J ANIM SCI 89:1092-1107.

• Does the speed of the vortex depend on the amount and viscosity the bacterial culture?

whether the speed and time of vortex depends on amount and viscosity of sample ( bacterial culture) or not. If depend, then  for 5000 and 500 microliter of sample ( bacterial culture in juice )how long and how much speed I can use for my experiment. Could you please give me the idea about that if anybody know?

Yinkuse o Osu · Fort Hare University

Just as Juan said all that is important is proper mixing.  In addition to vortexing, pipet for mixing before taking out the required volume for analysis.

• What are the methods for obtain the depth of an object?

We would like methods that have low cost and high performance.

Please if you know special reference, introduce to us.

Alireza Rahmani · Arak University

We would like use stereo vision (multiple cameras) method, Please if you have information about it, explain to us.

Can reinvestment of profits be a solution to business growth?

Growth has been a major concern in recent years, especially in the context of the current crisis. Yet diverse solutions and recommendations have been tried. Reinvestment is rarely discussed as a viable solution to companies growth, though is had yielded significant growth in some developing countries. What are your kind opinions and views on this issue?

Arturo Geigel · Polytechnic University of Puerto Rico

I am not an expert on the field, but I would say that it depends. It depends on the rate of expenditures vs profits of the company. In a deflationary environment where the profits remain steady and expenditures are low, it might be good to invest in growth(it would also be a matter of timing). as inflation takes hold, the growth prospects becomes a tough decision that I would weigh against overall profits, the expectation of additional market share, among other factors.

Just an opinion

• Hans Georg Schaathun asked a question in Sqlite:
Software suggestions for qualitative research (CAQDAS)?

Yeah, I know that's very generic.  I am after software to manage coding and categorisation of text in general and focusgroup transcripts in particular. Having earned my spores in mathematics and computing, I am a newbie in qualitative research.

So far, I have tried RQDA, and I guess the pros and cons will illustrate what I am after.

Pro.

+ fairly easy to install on linux (unfortunately not really easy though)

+ fairly transparent data model, where the SQLite database can be accessed and comprehended using any SQLite tool.

+ simple and straight-forward GUI

+ open source

Con.

- crashes on Mac OS

- lacks hierarchical coding

- sparse documentation

- primitive GUI, where routine operations require many clicks, and with no obvious way to manage by keyboard

- little recent maintenance or development

Free software is nice, cost is not really an issue if I am confident that the software is going to serve me well. Availability on both linux and Mac OS is not a strict necessity, but some glorious benefits are needed to offset the hassle of not having access on both platforms :-)

Any recommendations?

TIA

Which tool is best to generate patterns for a LoC delay test?

We have a lot of commercial ATPG tools to generate patterns for specific faults like stuck-at, delay faults. But which tool will provide more reliable patterns which can be used for research purposes?

S. Sivanantham · VIT University

Do you have these tools

Hi, best solvent system for separation of plant pigments on TLC????

can any one suggest the best solvent system as mobile phase for the separation of pigments in thin layer paper chromatography

Luis Quirós · University of Costa Rica

The solvent system will depend of the pigments that you are looking for. For example if those pigments are chlrophylls, polyhenols, carotenoids, etc... An usual system consist in a mixture of dichloromethane and methane 9:1, just as a preview....

How should i design the 96 well plate of qPCR for 2 samples and i have 5 different apoptosis genes?

I have two cDNA samples

i need to compare the expression of 5 different genes ?

How should i do this?

Shahinaz Mahmood Shams · Georgia Regents University

Thanks so much Celestina

you are great teacher and scientist!!

i appreciate expending your time helping me

All respect and Best wishes

Are goals encoded in genetic code?
Wikipedia defines a goal as "a goal is a desired result a person or a system envisions, plans and commits to achieve...". Where do goals come from? Do living beings have goals as individuals or as whole populations? Is it encoded somehow or it is coming from "nowhere"?
Leonard Greenfield · Temple University

Dear Vitaly;

"Thus, goals are encoded as neural currents in the nervous system." which is a consequence/product of genetic code. Isn't it?

Goals are represented by neural currents but they should not be considered products of the genetic code. In short-term learning, which can include the creation of new goals, the resulting learned behaviors are solely the products of neural currents passing through new combinations of neurons. The passing of neural current through synapses, by itself, sensitizes all of the neurons in these new negative feedback loops.

Repeated passage of neural current continues to augment the sensitivity of the many participating synapses operationally nested within these loops. When one re-members the participants in these loops, in a fraction of a second, the memory is maintained or strengthened. When one does not use these combinations, the synapse sensitivity weakens and one forgets (unable to re-member). Thus, short term learning and re-membering occur very rapidly, excluding the possibility that genes are involved, and can be explained as products of neural currents.

The neurons participating in short term learning, their selection out of the vast web of neuronal connections, their re-membering into the thoughts learned, and their synaptic connections already existed prior to the learning and no protein synthesis occurred.

As I noted previously, long-term learning does occur over a time scale that can and does include protein synthesis because new synapses are created during the process and building their structures includes protein synthesis. When short term learning, with the neuronal web already in existence, has not led to "understanding", neurons are triggered into creating something new . The mechanism creating these new synapses is a blind one. The nervous system does not "know" what will work so it blindly creates an enormous number of new synapses for potential use among neurons likely to be "on topic".

In some cases, a single neuron might create up to 10,000 new synapses in one night (presumably this allows a single neuron to be nested operationally in an even greater number of feedback processes (the economy of anatomy I mentioned in a previous response)).

These most likely will be built among the best potential neuronal candidates for operational nesting in the new loops of negative feedback processes that need constructing and through which neural current will be sent. The DNA of these cells goes through a transposition process (generating jumping genes) that randomly places these jumping genes among loci involved in synapse formation. As much as 10 % of the entire genome of a neuron can be transposed (but, presumably not all at once) in these events. Random placement guarantees that each newly transposed location will be unique and different from all of the ones already present that failed to allow neural current to sensitize  the negative feedback loops of synapses needed to reach the goal of "understanding."

These transpositions, epigenetically created mutations, but not inherited genes, participate in the construction of a wide variety of new synapses. Presumably, only a small fraction of these new synapses will be sensitized as components of negative feedback loops that will be composed of new combinations of synapses that provide understanding. These loops of synapses are sensitized so that they can be re-membered, when necessary. But, sensitization of combinations chosen, will be accomplished by neural current alone.

With this perspective, inherited genes and their epigenetically altered mutated forms have a necessary participatory role in all of these processes but they should only be considered as cogs in much larger processes whose emergent products are the thoughts and behaviors that will be operationally nested, using only neural currents as the means of selection, within successful negative feedback processes one of whose properties will be optimal points or "goals."

In a side note, you might be interested to know that US government granting agencies like NIH and NSF spent (wasted) $60,000,000 in the 1970's on finding out whether RNA was the "memory" molecule. Needless to say, they came up empty-handed. lol Happy Holidays, Leonard • Natalia-Meropi Antypa added an answer in Rhodiola: Does anyone have experience with Rhodiola rosea vegetative propagation? I am interested in vegetatively propagating approximately 6-month-old open-pollinated Rhodiola rosea plants, and I was wondering if anyone knows of an effective way to do so with relatively fast results. In addition, I would love to hear any suggestions about achieving uniform plants size-wise, as this would also be very desirable for my project! Suggestions about any other method of obtaining clonal Rhodiola rosea plants fast would be much appreciated. Thank you! Natalia-Meropi Antypa · University of Copenhagen No but we might give it a shot, thank you! • Yinkuse o Osu added an answer in Agarose Gel: What is a suitable gel to detect small (below 250bp) DNA fragment ? I'm doing a DNA digestion and I'm using a 3% agarose gel in my experiment. Failed to get any band. Do you have any suggestion or recommendation of what type of gel best use to detect small DNA fragment? Thank you very much. Yinkuse o Osu · Fort Hare University Follow Mohammad's guideline • Why do I only see the first 50 curves in the s-paramters (CST) results window, even though I ran the parameter sweep for about 2000 simulations? I ran a parameter sweep in CST microwave studio for about 2000 simulations. But in the S-parameters results window i can only see the first 50 curves. I have tried copying the results to a new folder but only 50 results are copied. How can I see the rest of them? Btw I am using CST 2014. Fabrice Auzanneau · Atomic Energy and Alternative Energies Commission click on your picture to select the S parameters (S11 forexample) you want to save, the hit Ctrl+C, then open a file editor able to handle big files, and finally hit Ctrl+V to copy the values in the file. Save your file. Do this again for the other parameters. This saves the values of the parameters in columns such as freq, real part, imaginary part, with some information about the case. But this information is sometimes very short, and correspondance with the sweep is not evident. You should also save the log file of your sweep to make this correspondance easier. • Aparna Srivastava asked a question in LC-MS: How to isolate a purified compound from plants extract ? I have isolated the active fraction from plant extract. I have done a TLC of the active fraction isoated the spot showing activity. I did the LC-MS of the spot. found to contain many compounds. Now i want to isolate a compound of specific mass from that spot. how do i proceed now? • James O'Rourke added an answer in Social Media: If I want to qualitatively describe and analyse social media debates that happened in the past: is this observation? I plan to do a close reading of past debates on social media about a certain public case, as a part of an ethnographic study. This will include note-taking and description about the nature of the content, the general atmosphere of the debate and any other notes (timing, activity, popularity..etc.). I feel confused about the appropriate academic name for such method. could it be considered observation even if it depends on saved data from the past that is still available on social media- sort of archival observation. Or is it enough just to call it ethnographic reading? James O'Rourke · University of Notre Dame Prof. Alhuzami: I see a number of good observations here, notably the idea that this is mostly about an appropriate label for your work. Observational anthropology, later relabeled as systematic ethnography is only partially appropriate, I think. You are, in fact, talking about textual content analysis and have any number of sources to consult. You might begin with Webb, Campbell, Schwartz and Sechrest, Unobtrusive Measures. They define much of the field and offer time-tested, systematic approaches. Krippendorf has produced a very helpful paperback on Content Analysis: An Introduction to Its Methodology that may prove helpful. Margrit Schreier's text on Content Analysis will tell you just about all you need to know. Base your methodologies on time-tested (and peer reviewed) approaches and you'll find much wider acceptance for your work. Best wishes, J. S. O'Rourke, IV • Precedence Case: Language requirements for EU-students studying in other Member States - high or low? In many member states of the EU (and specifically in Germany) each University is able to set its own standards of language requirements (some recommendations exist from the HRK, but neither regulation nor law). Generally speaking a university can follow two tracks for education: 1) 'Elitism' and trying to attract the best (for professors, students, research, ...) which (can) lead to effect that entry language criteria are very high so no language student support has to be given or hinders academic understanding 2) 'Place of Learning' meaning that in a mobile EU for most languages students which not have acquired a academic level of the language and students must be given the chance to enter other Member States with medium language levels and continue learning the language at the host university/state The highest administrative court in Bavaria has now recognized the discrepancy between European standards and unusually high demands of universities and in the Case of Fuentes given protection (http://www.discrimination.guru/?p=52) What do you think? PS: for mobile workers (doctors, lawyers, pharmacists, ...) it is already decided. Language levels must be uniform and low to avoid discrimination (full academic research here: https://www.researchgate.net/publication/262638113_EU_Student_Language_Discrimination_English_Version?ev=prf_pub) Jakub Kociubiński · University of Wroclaw Hello, I'm course coordinator for Bachelor studies in Law at the Faculty of Law & Administration and Economics, University of Wroclaw. We decided to set the bar for entry at B2 level of the CEFR system (or its equivalent). But it turned out that the actual language proficiency level of our students varies greatly despite the fact that at least in theory (from purely formal perspective) their language certificates shows comparable skills. Therefore in my opinion there is potential risk here. In cases where proficiency assessments are based on "external" certificates, candidates from countries where it easiest to obtain required proof of language skills are being favored. Therefore recruitment procedures will fail to ensure desired language level anyways. The solution would be of course in-house language pre-entry evaluations, but it goes without saying that it would add costs. Additionally such test may be practically unrealistic for foreign students (online is not feasible). In conclusion, I would say that there are in fact two inherently interlinked problems: the required level in itself and the evaluation procedures during recruitment. Assuming that proper pre-study evaluation could be done, I'd say for English bachelor course, aforementioned level of B2 is adequate. Kind Regards, dr Jakub Kociubinski • Antonia Cuff asked a question in Ames Test: What would cause a protein to lose activity after 1 or 2 freeze-thaw cycles from-80 freezer? I am testing the proposed antiviral activity of a protein in an in vitro culture of HeLa cells together with a virus. I recorded good activity from my first two attempts however, the response failed to reproduce a third time when tested alongside a mutant form of the protein. The mutant is not expected to work, as observed. The first two attempts were completed in triplicate. I attempted to dilute my protein in protein-rich media which had already underwent 1 freeze-thaw cycle. Do you have in your experience an idea of what could be the underlying factors at work here. Thanks in advance for your insight. • What is the innovations in traffic data collection and analysis? As all of us know that data is a very important while dealing with traffic engineering What is the innovations in traffic data collection and analysis? Brian Portugais · Boise State University Bluetooth has gained popularity, although from my experience, the percentage matching is much lower than reported in most literature. Apple and Samsungs new phones are scrambling MAC addresses. Although, this is newer technology, it will catch ground especially in the US. V-Box is both impressive and expensive! wavetronix radar works great for freeway applications when speed and volume are of interest. arterial collection methods are hybrid measurements and traffic models such as in adaptive signal systems. Look into various systems and how they are collecting data. Controllers now store and transmit through ethernet or wireless to a TMC and soon to vehicles through I2V communications and new 5.9 GHz • Mohammad Shirdel added an answer in Martensite: What is the specification of Martensite (displacive) transformation in ceramics comparing to the metals? I just know about Martensite transformation in metals. For example, these transformations are thermal and diffusionless. Also, the kinetic and morphology are dominant by strain energy. Mohammad Shirdel · University of Tehran Hi, There are many articles on your mentioned topic. However, I direct your attention toward the following article: http://www.sciencedirect.com/science/article/pii/S0079642500000050 • Why do we use ACT, instead of INR, to guide heparin use during cardiopulmonary bypass? INR is commonly used to guide heparin use in many clinical situations. I just want to know the reason why ACT is chosen during CPB. Why not INR? Fabrizio Sansone · Azienda Ospedaliera Ospedali Riuniti Papardo Piemonte ACT is easier and faster to be calculated than aptt-inr. Moreover, mechanisms of action of heparin and warfarin are different and this requird different • Michael A Rice added an answer in Gastropoda: Can anyone help me to identify this gastropod? I was trying to identify this gastropod, but not able to identify it clearly, so please can anyone help me to identify this gastropod. This may belong to slipper limpet i guess. The photos of the gastropods was attached too. Michael A Rice · University of Rhode Island The photo is not too clear, but I agree with Roger that it is Nerita of some sort. There does not appear to be strong teeth on the shelf & the shell sculpture is pretty weak. My best guess is Nerita polita based on this & the fact that shell coloration is variable and it is likely found in Tamil Nadu, but it's best you double check with some bona fide reference sources. • Is z[i] the Ring of Gaussian integers a principal ideal domain? I saw a note on my notebook that in z[i] is prime if a is irreducible .But while I was checking the conditions of prime elements in z[i], I was confused. Wiwat Wanicharpichat · Naresuan University Nitin Bisht given a correct answer. We will give some detail, as follows: Every Euclidean domain is a PID. Proof: Let$R$be an Euclidean domain. Take a non-zero ideal$I$of$R.$Pick$0 \ne a \in I$with$d(a)$minimal. We claim simply that$I = < a>.$Indeed, take any other$0 \ne b \in I.$Write$b = qa + r$with$r = 0$or$d(r) < d(a).$Then,$r = b - qa \in I.$The minimality of the choice of$a$implies that in fact$r = 0.$Hence,$b = qa$so$b \in <a>\$.

Does writing quality in a first language corellates with writing quality in a second language?

I am just wondering if ESL learners who write well in their first language will be able to write in the same quality in a second language. Are there any relationships between the writing quality in both languages?

M. Laura Angelini · Catholic University of Valencia "San Vicente Martir"

Hi Yahya,

I believe that if a learner learns a foreign language and cares about register, levels of formality, language expressions and active in practising it in the written form, the benefits are also seen in the speaking and the other way about. Eventually, I may sustain that the more you study a foreign language, the more you know about your first language, its rules, its linguistic shifts, etc.

See it it helps:

Fullana, N. (2006). The development of English (FL) perception and production skills: Starting age and exposure effects. Age and the rate of foreign language learning, 41-64.
ISO 690

Is anyone interested in investigating the kinesthetic and somesthetic sense through proprioceptive control?

Until now we have investigated the arm proprioceptive control in volleyball players - female, but we intend to develop our researches in enrolled patients in rehabilitation programs ( i.e. post stroke ).

Nicolae Neagu · University of Medicine and Pharmacy of Târgu Mures

Hello Elisabeth (may I ?),

It is already done in prototype phase. The movement sensor (for instant only for arms/hands - staying or sitting as basic position) is coupled through a NI transducer to the computer. As I said, I will be back after the winter holidays. Yours, Nicolae

Hello Giovanna (also, may I ?),

Thank you, for your references. Yours, Nicolae