ResearchGate Q&A lets scientists and researchers exchange questions and answers relating to their research expertise, including areas such as techniques and methodologies.
Browse by research topic to find out what others in your field are discussing.
- What is meant by the term "fitness' in the context of Transposon sequencing?
I am very new to the topic of Transposon sequencing. Can anyone suggest a good book for beginners? My question at this moment is :
I come across the term Fitness very often when reading articles on Transposon-sequencing. For example: Tn-seq, a robust and sensitive method for the discovery of quantitative genetic interactions in microorganisms through massively parallel sequencing. The approach
does not depend on a pre-existing array of mutants but is instead based on the assembly of a saturated transposon insertion library. After growth of the library under a test condition, the change in frequency of each insertion mutant is determined by sequencing the transposon flanking regions en masse. The change in frequency reflects the effect of the insertion on
fitness. Fitness of every insertion in a genome can be determined in this way and is a quantitative measure of the growth rate.
The fitness is just how well an insertion mutant grows relative to the "wildtype" (parent). i.e if the growth rate was halved, the insertion mutant would have a fitness of 0.5. If it grew 10% faster, it would have a fitness of 1.1.Following
- Can you suggest me about the different applications of DFT theory?
Basically, in theoretical condensed matter area , what are the different properties those can be studied by DFT.
Can you please mention the name of that review paper.Following
- Do people pay more attention to distinguish the person or to his downfall (failure)?
When the tree falls everyone hear the sound of the crash. While growing a full hearing of the jungle does not have any noise. Does this apply to the dealing with the humans?
Dear Qasim, YOU ARE ASKING, " Does this apply to the dealing with the humans?"
WHAT I LEARN IS THAT I SHOULD BE HUMBLE AND THANKFUL FOR EACH DAY THAT I AM NOT ACCUSED OF FAILURE, KNOWING THE PROPENSITY TO ERROR THAT IS IN ME AND ALL HUMANS.
I BELIEVE THAT IT'S PRIDE THAT MAKES PEOPLE REJOICE IN THE FALL OF OTHERS. WHY SHOULD I WASTE TIME ON THIS? I SHOULD BE WORKING HARD TO PREVENT MY OWN MISTAKES. THANKS.Following
- What are the pros and cons of KUMU versus NetDraw for simple SNA analysis?
I have been using NetDraw for SNA visualisation, loading data from excel. I am thinking about moving my current project over to KUMU. Having just recently commenced playing with it I have not yet explored all its nuances. Can anyone provide commentary on pro's and con's of using KUMU for (relatively simple) SNA analysis versus NetDraw?
Thanks for your input. YOur insights are much appreciated. In a previous round of SNA software investigations i tried out gephi before settling on ucinet/netdraw for a few minor display reasons. I have not yet played with R but it sounds like i should as plotting a network over the top of a background image would be perfect for my project.
For note, in NetDraw you can 'save diagram as' / 'metafile' - this not only gives a vectorised graphic, but if you open it in an office program, say powerpoint, it can be converted to a microsoft office drawing object with all nodes, edges, arrow heads, text etc becoming editable objects and text boxes. Infinitely editable and zoomable. Also, as it becomes a drawing object made of a group of shapes and text boxes without a 'background' it is easy to place an image or background behind such a network, again using powerpoint is easiest and later PDFable..
The challenges i am having in deciding between KUMU and Ucinet/netdraw at this stage are metrics based. I wonder if anyone has any experience of using the metrics available in KUMU, in particular networks with directed ties.
- What's the difference between control schemes,control methods,control logic,control algorithm and other control terms in canal control?
In paper, we can see the author use control methods,control schemes, control algorithm, control logic or other terms to describe how they make control of the canal system, so what's the difference between these terms in canal control?Following
- How long can we store competent Agrobacterium cells?
I'm facing problem in transformation of Agrobacterium cells via electroporation, the electrocompetent cells are about 15 months older, stored at -80 degree C. Anybody face the same problem?
Thank you so much for your answers, I didn't use positive control, i will try to use it as well,Following
- Is anyone aware of any validated questionnaire for 'Critical Thinking Skills', other than the California Critical Thinking Skills Test form B?
Any one who is working in the field of TEFL, please inform me since I need it desperately for my thesis.
Dear Ms Saedpanah ,
My articles on critical thinking on Researchgate can provide you with the information you need.
good luck with your thesis .Following
- I want to measure antioxidant capacity of my samples by ABTS assay. How can I measure Vitamin C Equivalent Antioxidant Capacity(VCEAC)per g of sample?
I will be thankful if anybody answer my question and send me a clear protocol to measure ABTS Radical scavenging activity of protein samples.
In case of ABTS assay you can express activity either as % scavenging or mg equi of trolox / g wt of sample. Insted of trolox you can also use vit C ie. Ascorbic acid.
For that you need a calibration curve for assay using ascorbic acid as a standard ie. % scavenging vs conc of ascorbic acid. Then apply the same method to samples and from calibration curve you will get an antioxidant activity of your sample in mg equi of ascorbic acid / g wt of sample.
You can also go through the article attached.
- Where can I get "Optifilter" to Intrusion Detection?
I'm very interested in the Optifilter (a tool to transform raw packets in connection vectors).
This tool was used in some works, like this: http://ieeexplore.ieee.org/xpl/login.jsp?tp=&arnumber=6785478&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D6785478
Can someone tell me how can I get it?
- Do citations for an edited book automatically count for all chapters in that book?
I recently saw several cases on Google Scholar that many colleagues add an edited book and its citations to their own Google scholar portfolio even though they are not one of the book editors but they do have a chapter in that book. Have you seen any cases too? What do you think: is that correct to count the citations of an edited book for yourself even though the citations are for the book in general and not for your specific chapter?Following
- What competencies should have faculty members in the international interactions from your point of view?
Faculty members play important role in the universities.Nowadays the globalization and subsequently internationalization growing in the all country. Therefore universities and particularly faculty members should have the competencies to international interactions.
So, what competencies should have faculty members in the international interactions from your point of view?
What areas? How do you define competencies?Following
- What are 2 main conditions for controlling drill-ability of rocks and how can I monitor these parameters while drilling?
I am trying to find ways to monitor rock drill ability using rotary tools. what are the parameters that can be easily monitored and if there are any ranges for these parameters for different rock types that are already defined, it would be lot more helpful. Thanks in advance
Dear Mr. Pavlovic,
Thanks for the response!.
Rock compressive strength can be measured for a rock sample in labs. However, while drilling the rock what is it that can be measured to decide rock drillability.
For example, If I am drilling in granite rock and there are some deposits of clay in between. How do I measure drillability during the drilling process. My ability to measure here would help me to control drilling technical parameters accordingly.
- Please can anyone suggest me how to redue the noise in chronoamperometry?
I am doing chronoamperometry studies of GCE modified electrodes, but recently i am getting huge noise while i was stirring the electrolyte solution at 120 rpm. i am facing the same problem with the bare electrode. Any suggestions to reduce the noise??Following
- Have you encountered racism in textbooks? How should we cope with this issue? What are the consequences of such an ideological dissemination?
Racism and discrimination in curricula and textbooks. Causes and consequences.
Thank you very much Artur , for the profound analysis of the issue.Following
- Which are the most important contributions of Martin Buber's philosophy to existential psychotherapy?
Buber's "I-Thou relationship" is one of the most cited contributions of this author to the field of existential psychotherapy. In your opinion, is there any other aspect of Buber's thinking that could be considered as a major contribution?Following
- What is the best way for growing sp2/0 cell line?
I am growing cells in DMEM+FBS10% , but most of cells died after passaging.
can someone help me?
Dear Atefeh Hemati,
Sp2/0 is a suspension cell line. It is quite robust and easy to maintain. I used to grow it up in a DMEM+FBS 10%, 1%p/s medium. I strongly recommend checking your cells for a mycoplasma contamination since it might affect cells growth.
I hope it could help.
- What is the relationship between Maxwell equations and an emitted photon?
This is not something you can find clearly stated.
If photon is a particle then it should be not applicable, but in the double slit experiment a photon interferes with itself. But if this is the case it must be propagating in all directions but it clearly doesn't.
There may be some misunderstanding here. A photon behaves as a particle or a wave according to how it is detected. If by an interference experiment, it acts as a wave. If by, say, the photoelectric effect, it acts as a particle. These are just the ways photons appear to us as a result of our measurements. In the theory of the quantization of the electromagnetic field, the factors of the harmonic components of the Fourier expansion of the electromagnetic potential are replaced by (creation and annihilation) operators. This introduces the idea of quasiparticles of the EM field (photons). (See "Advanced Quantum Mechanics" by Sakurai.) This is the theoretical relationship between Maxwell's theory and quantum theory. Whether or not this is a fruitful approach can only be answered by experiment.Following
- What is the difference in their characteristics of stainless steel material grades 316 and 316L?
I want the difference in their characteristics of AISI 316 and AISI 316L stainless steel materials in turning operations.
The main and most important difference between Grade 316 and Grade 316L stainless steel is the lower carbon content of the latter. The maximum carbon content for 316 stainless steel is 0.08%, whereas for 316L, it is 0.03%.
The lower carbon stainless steel 316L is an alternative to 316 stainless steel to overcome the risk of corrosion (also called weld decay). This type of corrosion occurs near the grain boundaries and can occur in austenitic stainless steels such as Grade 316 and Grade 304 in the heat affected zones of welds made in them or if the steels is encounter thermal histories in the temperature range 450 to 850°C for even short periods.
The main reason for the corrosion is the formation of chromium carbides (Cr23C6) at the grain boundaries when the steels undergo the thermal history mentioned above. The formation of chromium carbides at the grain boundaries causes depletion of the chromium concentration of the grain matrix near the grain boundaries ( (because chromium moves from the matrix towards the grain boundaries to form the carbides) , thus reducing the corrosion resistance.
If the carbon content of the stainless steel is kept at or below 0.03% (as in Grades 304L and 316L), grain boundary formation of chromium carbides following exposure to the temperatures is inhibited. Consequently result, there is no chromium depletion of the grain matrix and the risk of corrosion is reduced.Following
- How can i calculate lacks activity by using ABTS?
100 ul ABTS 2mM
250 ul sample
and add Na-acetate buffer 1M pH 4.5 to total volume 2000 ul
mesure at 436 nM , Epsilon = 29,300 M-1cm-1(Rodríguez Coutor, 2009)
If i have change in extinction of light in one minutes around 0.5 min-1
How can i calculate this data to u/L or U/ml?
- Is Chalmers' so-called "hard problem" in consciousness real?
In his 2014 book "Consciousness and the Brain: Deciphering How the Brain Codes Our Thoughts" Stanislas Dehaene wrote "Chalmers, a philosopher of the University of Arizona, is famous for introducing a distinction between the easy and the hard problems. The easy problem of consciousness, he argues, consists in explaining the many functions of the brain: how do we recognize a face, a word, or a landscape? How do we extract information form the senses and use it to guide our behavior? How do we generate sentences to describe what we feel?
“Although all these questions are associated with consciousness,” Chalmers argues, “they all concern the objective mechanisms of the cognitive system, and consequently, we have every reason to expect that continued work in cognitive psychology and neuroscience will answer them. By contrast the hard problem is the “question of how physical processes in the brain give rise to subjective experience … the way things feel for the subject. When we see for example, we experience visual sensations, such as that of vivid blue. Or think of the ineffable sound of a distant oboe, the agony of an intense pain, the sparkle of happiness or the meditative quality of a moment lost in thought … It is these phenomena that poses the real mystery of the mind”."
Stanislas Dehaene's opinion is "that Chalmers swapped the labels: it is the “easy” problem that is hard, while the “hard” problem just seems hard because it engages ill-defined intuitions. Once our intuition is educated by cognitive neuroscience and computer simulations, Chalmers’ “hard problem” will evaporate".
Personally, I agree with Stanislas Dehaene's opinion.
Graeme, For me the best way to figure out the workings of the mind is to observe it during meditation , breathing deeply and questioning all I experience and see. So based on these observations painstakingly over last 10 years ,the theory of 3 D default intra-personal space for external world has been proposed.
At this point no other theory explains how our minds reflect the internal space or what hub is the center that integrates sensory , motor and cognitive input . It may not be a popular theory at present , but it has already answered the etiologies of various disorders that have been clinical puzzles .Following
- Can democracy function without a free market economy, and vice versa? A free market economy requires less state intervention. Concurrently, it often requires a degree of democratisation of its institutions which- to a certain extent- facilitates economic activity. This is at least partially true as far as a significant number of countries in Africa, the Middle East and Asia are concerned. Thus, it seems that a democratic climate seems to favour a free market economy. At the same time, a free market economy appears to be reliant on democracy for its functioning. This reciprocal relationship presents an interesting research ground that has probably been explored in insufficient depth. What are your kind responses to this empirical observation?
None of the developed country in the west and in the east have a population problem and absolutly no public policy were put in place to convince people to reduce the number of children. In Quebec, the average family of my generation is 1.2 children, of the generation of my parent 4, of my grand parent 10 and of my grand grand parent 15. My wife's grand mother had 24 pregnancies. At no point there was a campaing to tell people how they should behave. The level of education of my grand parent was grade 3 on average, of my parent grade 6 , of my generation grade 12 and now we have no religion and the modern method of fertility control. Why trying another recepy. What these countries need is : 1. education, 2. development and jobs and opportunities exactly as my society got.
I found the justification of european colonianism of the african as an attempt to save them from their despot and slavery very unrealistic. This is the typical justification of any evasion: We will save the Irakis from their despot, a few years later the saved Irakis are fledding to Europe.Following
- Who can help me to construct the perovskite of CH3NH3PbI3?
I want to calculate the property of CH3NH3PbI3,but i meet some problem when i construct the perovskite of CH3NH3PbI3. I use the cell unit parameters of Katsuhiko published in JPSJan in 2002. I use the Material Studio to construct the structure of CH3NH3PbI3.
Hi Elisban Sacari
Thank you very much for your help. I try to search the structure following your suggestion. However, I still have a problem that if I don't know the COD ID and I just konw the molecular formular,I should search the cif file?Following
- How to quantify root hair in Rapeseed?
Root hair is a very interesting/important trait for plant to uptake nutrients and water, but it is very difficult to quantify them.
Attached is the root hair of rapeseed seedlings, can anybody share me the way/idea to quantify them? Thanks
Thanks David for your kindly and useful help. I think your second suggestion is just what I needed.
Due to my background, I don't know too much on programming. Also this is my first time to hear OpenCV. However, I have some limited experience on ImageJ. I'd like to start with ImageJ to see how it works with you idea. Would you please get me some further suggestion on it?
- How can we treat missing data during survival data analysis?
I am conducting a survival data analysis regarding HIV treatment outcomes. Do I need to treat the missing data while applying my survival data analysis? How?
- Are there any known rocks with negligible radioactivity?
Which chemogenic or clastic deposits (type and locality) would have the most negligible -practically zero-radioactivity? I would expect halite and gypsum to have very low radioactivity, if they are pure (no clay or detrital minerals). With the same restriction, sandstones (quartzite) should do it too? Are there any known deposits with almost zero radioactivity?
Unlikely that Thoron (Rn 220) would migrate far underground, except with a significant air flow, as its half life is only 54 seconds. Radon (222) has a half of 3.8 days, so could be transported underground for some distance.Following
- Leadership styles and which is most effective?
Leadership styles and which is most effective?Following
- How to measure the concentration of starch? What are the various possible methods for measuring the concentration of starch in mol/L?
starch is a complex, so you can not get concentration of starch in Mol/LFollowing
- How to induce cardiomyocyte hypertrophy with angiotensin II in vitro
I want to induce hypertrophy of neonatal rat cardiomyocytes with Ang II. Can anyone provide me a detailed protocol? What's culture condition? the concentration of Ang II and its storage? and how long of the treatment?Following
- What is suspension gelatinisation procedure of Starch?
Is it requires continuous stirring / no stirring to starch sol. during heating at 95 Deg C in water Bath
Starch will deposited without stirringFollowing
- Comments on "The Pagerank-Index: Going beyond Citation Counts in Quantifying Scientific Impact of Researchers" ?
I'm using this question to instigate a discussion on our recent paper in PLoS ONE. It's essentially a new way of quantifying the impact of publications/scientists as opposed to h-index. It addresses a some well-known drawbacks of h-index and demonstrates the fairness of the new index using a simulated data set as well as two real-world citation networks.
We started this work to address the common drawbacks we've seen in h-index and have since improved its resilience to various sorts of manipulations that are possible in h-index. We would like to know your comments/suggestions about the work we've carried out. All constructive criticism is welcome.
Thanks in advance.Following