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Difference in reagents for dissection/growth of mouse vs rat cortical neurons?

Hello all,

I usually perform dissections and culture postnatal rat cortex (P0-P3) and am about to try out the same dissection in mouse. I use a modified version of the brainbits protocol for cell dissociation (papain, etc). I was wondering if anyone had come across reagents that work well for rat cortical dissections but not mouse? Or additional reagents/issues/anything relevant for mouse, that doesn't come up in rat? Thanks for your help in advance!

Molly Boutin · Brown University

Thank you very much Yuan Lee for your help. I have now performed a couple mouse dissections. I have very high cell viability immediately after dissection/dissociation (>95%) but my attached neurons look sad- slowly growing extensions, dead cell accumulation, etc. I was wondering if, because the cells are initially alive, this could be a medium issue? You did not make any modifications to your growth medium formulation or the way that you treated the cells in culture? Thanks so much!

• How can I improve the RNA extraction from a desert plant, using the RNeasy kit?

RNA extraction from ta desert plant using RNeasy kit is giving us a very low concentration -below the range-.

The main problem is that desert plant are really rich on polysaccharides, polyphenols and other various secondary metabolites such as alkaloids, flavonoids, terpenes and tannins which usually hamper the DNA and RNA isolation procedure.
How to improve the RNA isolation protocol of 'Rneasy kit' to over come this difficulty?

Any methods, tips or notes are appreciated in advance.

Nesreen Fayyad Al-Khuffash · University of Sharjah

Thank you all for your collaboration, really valuable notes are being posted.

Unfortunately, it isn't possible for us to switch from RNeasy to trizol or CTAB.

Anyways your notes will be taken in consideration in our future work :) Bless You All.

• Zeineb Mhamdi asked a question in Pymol:
Pymol Molecular systems ?

Hello

I need to use PyMOLM GHRAPHIC SYSTEMS, but I don’t know if there is a free version to use use!!!

Tanks

How do I calculate the annealing temperature of my PCR reaction?
Tm value of one of my primer is 52.8 (50mM NaCl) and another one is 54.5 (50mM NaCl) as given by the primer making company.

Primer Sequence is – i> 5' TGT GTA TCA TAG ATT GAT GCT TTT GA 3' and ii> 5' AAA TAA AGA TGT CAG ATA CCA CAG CA 3'. But when I calculate by manually or by online it shows different. What is the Exact Tm Value? Which one is correct?

What will be the annealing temperature of my PCR reaction? My PCR product size is 282 and GC% is 34.
Mohsen Sohrabi · Griffith University

it may help

http://www.lifetechnologies.com/au/en/home/brands/thermo-scientific/molecular-biology/molecular-biology-learning-center/molecular-biology-resource-library/thermo-scientific-web-tools/tm-calculator.html

But the best way to find it is running gradient PCR

• Ayman Ahmed asked a question in Hydrogeology:
Recent interests and challenges in the hydrogeologic research?

I am looking for statistics/information/literature of the top research topics in hydrogeology worldwide, I need to know what are the topics that scientists think and deal with for the last five or ten years, what are the most interesting topics, what are the major challenges and problems that scientists are trying to address through their publications in the international journals or conferences. Any help and suggestions are appreciated.

Which geophysical methods or combination of methods can be most appropriate for detecting fractures/fault in a rock formation?

Hi, I have a course work where I should suggest geophysical methods for the investigation for the construction of the rock tunnel. I know the location of the tectonic zone and I need to investigate soil conditions and bedrock quality.
Unfortunately I have no previous experience with geology. Hence, would like to get some suggestions, please.
Tunnel depth will be between 30 and 100 m below the ground. It is known that soil depth is 3 - 10 m and it mainly consists of till, sometimes covered by peat. Minor areas consist of sand and gravel. Gneiss is dominating rock type and it can be cut by amphibolite dykes.

Alexandre Ribó · Ministerio de Salud, El Salvador

As told Aleksey, first you should descrive the topography and also carry out a detalied geological surface cartography theand with this data you have to try geological profile of the tunnel. First you need a geologic model . If you have a relative flat topography you can carry out high resolution seismic reflectio, multichanel analysis of surface waves (MASW) or electric resistivity tomography (ERT). These methods are useful to identify anomalies in gneis (fractures, faults and amphibolite dykes).  If you have non flat terrain maybe magnetic methods could help you (by these methdos you can identify main faults and maybe amphibolite dykes.

Here is a question about two nucleon system. The question is why nn(neutron-neutron )bound state is not possible ?

For nn bound state the total wave function (i.e spatial * spin) has to be anti-symmetric. Now the nn is the iso-spin triplet state(both the neutron is of isospin 1/2: T3 = +1 )which is spatially symmetric. So the spin singlet state(when both spin are anti-parallel: S=0) which is spin anti-symmetric state can give rise to nn bound state. Inspite of this why this is not allowed ?

Kåre Olaussen · Norwegian University of Science and Technology

It is interesting (and humbling) to learn that a question I thought was clearly resolved 40+ years ago actually isn't. I don't think there is anything fundamental about the issue, since it is only a delicate dynamical question, but it is very interesting anyway. Nature has of course solved the problem long ago, but if experimenters are unable to read the solution we are equally ignorant.

I would not trust any theoretical computations based on phenomenological boson exchange models, due to their own uncertain limitations. I would rather wait for very accurate ab initio lattice calculations (if I could convince the ultimate authority to live long enough for that...).

• Miodrag Mateljević asked a question in Criticism:
Describe zero set of Jacobian of injective harmonic maps in space?

For example consider the following question:

1.Let $\mathbb{B}^m$ be hyperbolic space and let $f : \mathbb{B}^m \rightarrow \mathbb{B}^m$ be harmonic $K$-qc map.
Whether $f$ has critical points on $\mathbb{B}^m$ ?

2.  Whether  injective euclidan-harmonic map  has critical points?

• Which disturbances in the brain positioning system can explain autistic problems of orientation in space?

It is well known people on the spectrum experience difficulties in orientation in space. For general explanations of this, disturbances in proprioception and the vestibular system are usually mentioned.

Now that more is known about the way spatial orientation works in the brain (place cells, a sort of compass plus the discovery of a 'grid' for which the 2014 Nobel Prize in Physiology or Medicine was awarded to John O'Keefe, May-Britt Moser and Edvard I. Moser), one wonders if (additional) explanations can be found there.

One fool can ask more questions than a hundred savants can answer, but stil:

How does overconnectivity in the brain affect these different navigational mechanisms? And more specifically:

What disturbances in bottom-up sensory processing do affect these mechanisms?

To what extent are (top-down) templates in the brain affected by problems in central coherence?

So generally: is anyone applying knowledge about spatial orientation to such problems as experienced by people on the autism spectrum?

Jan Golembiewski · Queensland University of Technology

As I said- I don't know how well these apply to autism, so I won't go far to defend it until I've given the concept more thought. But don't imagine that I believe that schizophrenics have any great central coherence either - in fact, I suggest the opposite. What coherence schizophrenics have prior to the prodrome can be subject to atrophy and distortion very quickly due to the failure of the BUA feedback loop. Similarly my guess is that the somatogenic life-space of autistic people is likely subject to distortion and quick atrophy.

How do I estimate the coefficient of dependency of the states on central government ?

is there any formula to estimate the extent of dependency of the states on central government ? guide me in this.

and also i want to know the capacity ratio and priority ratio in states expenditure policy/pattern as a panel data analysis.

Paul Louangrath sir thanks for your reply. sir i am little confused about state budget (dependent variable). as independent variable i can take state own resources - tax,non tax etc along with central transfers.

or the state budget itself  tax, non tax revenue ? - i am confused sir.

i got priority concept

COD= 1- (B+C)/D, Where

A= Total revenue receipts excluding any grants & transfers;

B= Transfers = Grants from state governments

C= Net Borrowing of the states = - (A-D);

D = Expenditure of the states = Total Expenditure & Lending – Repayments.

sir do you have any article on this. or refer me any book or article sir. it will e useful for my research a lot in future.

• What is the recommended ratio of each Na acetate:absolute ethanol used to purify plant RNA from contaminating polysaccharides & phenols?

RNA extraction from a desert plant is giving us a low concentration below the range. The main problem is that desert plant are really rich on polysaccharides, polyphenols and other various secondary metabolites such as alkaloids, flavonoids, terpenes and tannins which usually hamper the DNA and RNA isolation procedure.

we are trying to over come this problem by adding Na acetate + absolute ethanol after the isolation step to re-precipitate the RNA and purify it as much as possible from the contaminating compounds.

what are the recommended concentrations of each Na acetate + absolute ethanol? Any tips or notes are appreciated.

Nesreen Fayyad Al-Khuffash · University of Sharjah

Thank you all for your collaboration, really valuable notes are being posted.

:) Bless You All.

How can I simulate a dynamic system like this in Matlab / Simulink?

I am trying to simulate this system im Matlab / Simulink with the block S-Function but it won't work. I do not know how many states, outputs and inputs I declare in the function and really how the system flag works and how to write the derivative equations. Is there another way? If yes, how could I do it? If no, how I write the derivative equations in my function and inputs, outputs, ... ?

Any suggestions about an article that linked Hofstede-Gray model (Culture Dimensions - Financial Standard) to IFRS?

Looking for article that linked Hofstede-Gray model (Culture Dimensions - Financial Standard) to IFRS. Any suggestions?

Mohammed Nadeem · National University (California)

Hi, Gati:

Hofstede's model for vendor selection! International vendor selection has been a lightly researched area of organizational buying behavior. The few studies in the field have examined differences in the importance of vendor selection criteria to purchasers across countries, but did not attempt to identify the potential cause of these differences. In a recent research study (Van Winter, & Liebrenz-Himes, 2015) surveyed purchasers in the United States and Germany and identified differences in the importance placed on vendor selection criteria factors.

The authors then took the additional step of examining to see if there was a relationship between these perceived differences and differences in the cultural dimensions of purchasers, a relationship which has been suggested but not tested by earlier studies. A relationship was found between Hofstede's cultural dimension of uncertainty avoidance and the vendor selection factors of quality, price, vendor reputation, firm characteristics and vendor attitude. In addition, a relationship was found between individualism and the quality, price and vendor attitude factors!

• Van Winter, J., & Liebrenz-Himes, M. (2015). THE RELATIONSHIP BETWEEN CULTURAL DIMENSIONS AND INTERNATIONAL VENDOR SELECTION CRITERIA. Review Of Business & Finance Studies, 6(1), 1-12.

Hope this helps!

• Napoleon Ono Imaah asked a question in Italian:
Who is the greater of the two iconic Italian titans: Michelangelo or Leonardo Da Vinci ?

What are your reasons for choosing either of them?

Do you know of any annotation for P. kudriavzevii M12 strain?

Is it possible to obtain the annotation generated for the publication as it isn't deposited in genbank despite a description of the features predicted in the article text.

Jason Stajich · University of California, Riverside

Solution - use SD108 strain instead http://www.ncbi.nlm.nih.gov/nuccore/695114318

• Ramón Bonfil asked a question in Marine Birds:
Do bobbies react to drones or other flying apparatusses?

Hi

I wonder if anyone has experience with marine birds in colonies and their reaction to flying devices such as drones, or remotely operated helicopters and airplanes. I am planning to film with a Phantom 2 Vision + drone around a rocky outcrop which has a huge brown bobbie colony. I am worried about possible aggresion from the birds to the drone and the potential injuries to the birds and demise of my drone. Any direct experience advice would be appreciated, not looking much for especulation. Thanks in advance.

• Is a potentiostat with output (10V, 650 mA) suitable for doing electrochemical tests of reinforced concrete specimens at laboratory?

Reinforced concrete specimens will be used to study the design of cathodic protection system at laboratory. The compressive strength will be about 45 MPa. Specimens will be subjected to the air. Surface area of steel embedded in concrete will be 0.35 m2.

Thank you

Hayder Oleiwi · University of Salford

Thank you Mr. Hongyan for you answer, 0.35 m2 will be the rebars area for a small column reinforced with 6 rebars , D=12 mm. the applied current is between 20 and 100 mA/m2. I am not worried about the current. i am concerned about the voltage that I require to apply the current. you may know the resistivity of air dried concrete is high and it may need to apply a high voltage which I dont not know how much .

Do you mean by the current amplifier a device which can be used to apply a constant current? Is it the same of transformer rectifier which is used in the field in the cathodic protection system.

• Tanmoy Das asked a question in ImageJ:
How to create Ground truth in Matlab to verify segmented image?

I am developing an algorithm to segment nanorods image. To understand the performance of my algorithm, I need to create, manually, ground truth by Matlab.

I tried Sefexa, but Sefexa does not give me enough information. I have tired ImageJ which gives me kinda satisfactory information like coordinate of each ROI. But, now I am looking for Linear Discriminate Analysis (LDA) through Matlab which I can apply to generate ground truth.

What is the best way for modeling epidemiological time series data?

Dear RG members. Epidemiological research sometimes deals with time series count data as the dependent variable. But, what is the best regression model for these data? ARIMA has been the classical approach taking into account the autoregressive nature of the data. Recently, other approaches have been proposed, such as the Poisson autoregressive regression models for count data. Any suggestion? Pros and cons of each method? Thank you.

Jeffrey P. Prestemon · USDA Forest Service, Southern Research Station

Dear Andres,

I like the ACP model of Heinen and Rengifo, and their model can incorporate any exogenous shock (an intervention) as an exogenous factor affecting the poisson autoregressive process. I have tried this and it works fine (examining the effect of preventive measures in human-ignited wildfire). Here's a citation of a paper you can examine:

Heinen A., RengifoE (2003) Multivariate modelling of time series count data: an autoregressive conditional poisson model. Center for Operations Research and Econometrics, Catholic University of Louvain, Louvainla-Neuve, Belgium. http://alfresco.uclouvain.be/alfresco/download/attach/workspace/SpacesStore/e8b81e6f-0b93-4fc1-9d1d-643579c8f578/coredp_2003_25.pdf

What is meant by "orientalism is a style of thought based on an ontological and epistemological distinction" made between the east and west?

Edward Said in his introduction to Orientalism (1978) says this....what colud be the ontological and epistemological distinction between east and west?

What is the best method to assess the knowledge of the health care professional regarding acetaminophen ,open or closed ended questions ?

what is the best method to assess the knowledge of the health care professional regarding acetaminophen ,open or closed ended questions ?

Correct Ariel. Iftikhar - at the end of the day which type of questions you want to use will depend entirely on what you want to find out.Closed questions will generally lead to using quantitative methodology and open questions often to a qualitative narrative methodology. There is then mixed method approaches whereby you could use both. Because your topic relates to a pharmacological intervention - then this would usually tend to lend itself more to a closed question approach to investigate effectiveness - unless you wanted to know about patients experiences of the intervention - then that would be more open

• How can I evaluate the quality of nutritional care in hospitals and the relationship with the state of nutritional knowledge in physicians?

I need to asociate the state of nutrional knowledges and the quality of nutrional cares

Joan Vaccaro · Florida International University

Yes, Ihsane, you make an excellent point concerning physician's knowledge. Surveys would have to take into account the hospital's guidelines, the physician's health beliefs and opinion of patient's needs, and the nutrition guidelines they are following. For example, in the USA the most widely accepted guidelines are MyPlate.gov for the general population, healthy children and healthy older adults. For patients with particular chronic diseases, guidelines are based on the recommendations of the particular organizations such as cancer and diabetes organizations. Healthy populations may also follow the Harvard public health nutrition guidelines, which emphasizes healthy oils (MUfA)..

• Maria Garces asked a question in Crayfish:
How to prepare dried DNA or lyophilized without using any sophisticated device?

I am working with fresh crayfish gill samples from the field and would like to run PCR to look for mitochondrial DNA gene 16s. I have to lyophilize the dna with out an expensive machine- just want a simple method that works correctly.

• How can we do analysis of the Likert Scale in SPSS?
I would be glad if you could suggest any way of analyzing the Likert scale in SPSS.

For Likert type data, it would be critical to do exploratory analysis to find validity and reliability of the instruments of interest to your study. Cronbach Alpha is a common test of ascertaining the reliability of Likert type instruments. Recent statistical developments sometimes call for the computation of ordinal alpha in place of Cronbach Alpha especially where data is not continuous to address bias.  Factor analysis and principle component analysis are equally an option for further analysis of Likert type data but certainly, an exact answer to your question would be to first know your objective/purpose of your study.

Do you know Open Access articles in peer-reviewed journals on the topic of health communication and health promotion?

Libraries of most American and European universities have subscriptions to peer-reviewed journals. However, scholars from many other countries around the world--or those currently not affiliated with universities--have to sift through a lot of citations to find high-quality papers. Yet, more and more papers appear in open access.

If you come across such papers on the topic of public engagement with science, please add citation and DOI link here.

Most 'generic' titles will have content within them that relates directly to health communication (you could throw in health literacy and mass media as well) i.e. Health Promotion International, Health Education Research, Global Health Promotion, Health Promotion Practice, Health Education, Preventative Health etc. If you check them out via a PubMed search - you will find many articles that are open access (or at least the abstracts are). Other good sources would be generic Public Health journals and journals related to marketing and communication

Can you provide any references that support the use of logic as a research methodology?

Goldratt's thinking processes have been used extensively in various industries globally to identify core problems, develop win-win solutions and structure implementation plans that reduce resistance. In business research, high powered statistical techniques and operations research techniques are required for publishing in quality academic journals.  In the hard sciences logic and gedanken exercises are frequently used to prove hypotheses.  Are there references for using logic in academic soft science research?  Are there other accepted forms of applied logic in the academic literature?

James R Knaub · N/A

Jim -

Two little statistical comments: 1) R2, like a p-value, is inconveniently susceptible to influences that can make it misleading. Sometimes you can't beat a graphical display, particularly scatterplots, for communicating what the data has to say. 2) Statistics can show correlations, but not causality. You assume a model, and check it out with data, but not vice versa.

Are you familiar with Deming's quality management work? If not, I have seen a survey done in Greece just after WWII that he and some other well-known statisticians did that might be of interest, if I can find that reference again ... if you are interested. After that, he got into quality management, and when US industrialists failed to listen, he went to Japan, and soon "made in Japan" was no longer a joke.

I'm rather certain you can find a number of articles by Deming, though nothing new actually by him (but maybe by others on his methods) as he died at least 20 years ago, I think. There is a special Deming
Lecture at the Joint Statistical Meetings each year (JSM is sponsored partly by ASA).

Another old source would be John Tukey, who started Exploratory Data Analysis (EDA), which is just a bunch of common sense.

Not sure that this is exactly what you are looking for, but hopefully related.

- Jim

PS - I think the author of your first reference is missing.

Where do Mitochondria-rich cells exist in fish?

For example they can be found in: Inner ear, gills, Skin, kidney, yolk sac.

I was wondering if you could mention more organs and if possible, please give an example (Article).

Mojtaba, most organisms have higher concentration of mitochondria in muscle cells. My bet for fish would be red muscle cells, and heart.

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.

Dorian: "

the cellular membrane is not a Faraday cage. The electric charges,all kind of ions can cross the cell membrane, and importantly do not forget "the brain bath" in case of a real brain."

Is Chalmers' so-called "hard problem" in consciousness real?. Available from: https://www.researchgate.net/post/Is_Chalmers_so-called_hard_problem_in_consciousness_real/401 [accessed Apr 19, 2015].

No, the cellular membrane is highly capacitative and attenuates electrical signals within a 16th of an inch, plus there are cells that have a damping role on signals that surround areas like the columns in the cortex, and isolate columns from each other.

I think that you are being somewhat disingenious to say that all kinds of ions can cross the cell membrane, there are distinct ion pumps and ion channels for the most electrically active ions.

"Brain Bath"? all you need is soap! and you can do brain washing. (Just kidding)

By the way, notice the new way that internal citations are being handled... Cool!

• Which one is more appropriate to analyze repeated measurements of longitudinal intervention study: Repeated ANOVA or Mixed effects analysis? Why?

I want to use the most valid and reliable analysis technique (Evidenced-based). That is why your inputs will be of paramount importance for me to decide!!

Luis A. Apiolaza · University of Canterbury