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.

Browse by research topic to find out what others in your field are discussing.

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How do you isolate fibroblasts from mouse liver?

What is the best method to take liver samples for animals and isolate fibroblasts that will be placed on cell cultures to grow?

Milena Veskovic · University of Belgrade

Thank You.

• What is the best antibody to label diffuse amyloid plaques?

To differentiate between the core plaques and the diffuse plaques of beta- amyloid.

Max Stanley Chartrand · Northcentral University

Let me first say that the premise of removing amyloid plaques is, in my studied opinion, a fool's errand and built on an erroneous theory. The plaques are there priimarily because of inflammation and other underlying disease processes. They are a poor, but worthy substitute for the loss of myelin (astroglia, a type of floating myelin) that is supposed to protect the brain's neuron's from free radicals (unpaired molecules that make it past the blood brain barrier). Usually, it is pharmaceutical agents that send these off, either primarily or secondarily. In secondary cases, drugs like coumedin sent a flood of free radicals all over the body and brain every time the victim reaches into their purse or pocket and break blood vessels. The amyloid plauqes serve in a protective role, not an adversarial one, which is why the drugs that are designed to remove never bring back memory. They are too toxic to do much of anything, really. For that reason, we want instead to reduce offending medications and address underlying causes of disease (unaddressed subclinical infections of tooth and jaw are common, as are stenoses of the spine, chronic dehydration, nutrition deficiencies, food additives, heavy metals, uncorrected hearing loss, and lack of sleep). Take care of what is causing the plaques and we see brains rehydrate, neurons repair, astroglia (and other forms of myelin) restore, and memory comes back. I am attaching one of my monographs on this topic for some thoughts on this.

How to find any specific trend or any pattern in signal data stored in CSV format ??

I have some data set in CSV format i need to find some specific pattern or trend in those data, can any one please help me for implementing the same, does it requires some software or does some AI(artificial intelligence ) algo. has to be used?? please help in either case .

Eric Atwell · University of Leeds

You say you have signal data in cdv format. I guess this means you have a text file split into lines, where each line contains a set of data features from the signal at a point in time, and the lines are in time sequence.  If so, this may look like WEKA arff format - weka accepts input in a cdv-like format arff, basically cdv with added header to specify the features and range of values allowed for each feature. So, as Reisel suggested, you might try input to WEKA, try some classifiers or clsuterers to find patterns.

BUT ...

WEKA assumes each line represents an instance of data, in no particular order: the data set is a SET of instances, and order is NOT important.  So, if you have SIGNAL days, you probably want order to be taken ito account: you might expect the signal at time N to be influenced by or dependent on the signal values at time N-1, N-2, ... But WEKA cannot do this, UNLESS you artificially add extra features to each instance , to represent the features from instance N-1 etc.

The general point is: WEKA (and many other Data Mining toolkits) assume the input is an UNORDERED set of example data instances, and only find "patterns" linking features to the class. For patterns about the order of data, try  n-gram modelling tools, or NLP language-modelling tools.

• How can I block the oxidation of Fe2+ to Fe3+ in aqueous media? Do I add any chemical reagents to the solution?
See above
Louis Noodleman · The Scripps Research Institute

The suggestions above are excellent and practical. I just want to point out one

fundamental issue. Aside from chelation of Fe3+, which has good and bad points,

when Fe3+ encounters H2O, especially when one or more water molecules are

coordinated, Fe3+ tends to acidify one H2O, producing coordinated OH- ,

particularly in aqueous or polar environments. (Note that enzyme interiors can

be charged or polar or nonpolar or mixed.)

This is

why acidifying the solution works well, because (by Le Chatlier's principle), this

inhibits dissociation of the bound H2O-> OH- +H+ .This is why Fe3+ is quite insoluble

in pH normal solution, since Fe3+ forms hydrated Fe3+ OH- Fe3+ dimers, then on

to oligomers and precipitates. Conversely, by keeping the solution acid, the formation of oligomers is inhibited. This is why when free in solution Fe2+ dominates over

Fe3+, and why in an oxidizing environment, Fe3+ in solution is scarce, which leads biologically to the fight for Fe. The issue of H2O vs OH binding to either Fe3+ or Fe2+

is an important one for metalloenzyme active sites (see W.G. Han-Du and L. Noodleman, Inorg. Chem. 2013, 52, 14072-14088, and L. Noodleman , W.G. Han-Du, A.W Goetz, and R. C. Walker, Inorg. Chem. 2014, 53, 6458-6472) plus

ongoing work. For bio-geochemical cycles, some fundamental calculations and

analysis are reported in J. Li, C.L. Fisher, J.L. Chen, D. Bashford, L. Noodleman,

Inorg. Chem. 35, 4694-4702, 1996.

Which mouse tracking tools work best for in page analytics of user behaviour?
Are there any tools (preferably non commercial e.g. not Clicktale, but if they are the best please say so) you can recommend such as open web analytics or simple mouse tracker 2?
Tara Schnaible · The Nature Conservancy

Might be a lot late for your purposes, but Google Analytics has an in-page analytics feature that can track clicks within a page, although not hover-time or path.

How do you use syndromic surveillance data to indicate the beginning of the flu season?

Using ILI cumulative summation currently. Is there another method that has proven valuable?

Adrian Esterman · University of South Australia

Exponentially weighted moving averages (EWMA) has very similar properties to cusums, and is another method you might consider

Does anyone have any information about the mechanism of cyanotoxin production by cyanobacteria?

Does anyone have any information about mechanism of cyanotoxin production by cyanobacteria? Thanks

Mohammad Nik · Tarbiat Modares University

hi

i have a file and you can find your question in it . i hope it be useful for you

with the best

What are the effects of nanosilica on the thermal expansion of cement pastes?
The effect of nanosilica on the thermal expansion of cement.
S. Abd.El.Aleem · Fayoum University

Thermally induced cracks are formed among the main forms of deterioration of concrete if the structures are exposed to elevated temperature in a short period.The hardened cement paste and aggregates in concrete have different thermal expansion properties, which leads to different volumetric changes, if the concrete is rapidly heated or cooled. Internal stress is thus generated, causing cracking of concrete in the micro- or macro-scale. The internal stress of concrete caused by temperature changes could be reduced by choosing proper aggregates, whose thermal expansion coefficients (TEC) matches with that of hardened cement paste (HCP). But, considerations on the availability and cost of aggregates impede the choice of alternative aggregates in practice. Therefore, it would be more feasible to change the mix of the cement pastes or to choose appropriate supplementary materials as binders to adapt the TEC of HCP, so that the thermal stress caused by the difference in TEC of HCP and aggregates could be minimized. Replacing Portland cement with micro and NS reduce the total amount of CH through pozzolanic reaction and change the porosity of the paste.

As a nerve regeneration speed is 1 inch per month, and as the distance between the primary sensory neuron and the toes of the foot is about 20 inches, the usual rule is to consider that we can hope a nerve regeneration only until 20 months.

Through somatosensory rehabilitation method we are able to change the somaesthetic condition after years. Do anyone know article about  this border of 20 months ? We would like to publish a paper about our results to focus about the possibility to stimulate neuroplasticity mechanisms even after 20 months.

Sean Patterson · National University of Cuyo

Claude, I recently published a combined review/methodology on sciatic nerve injury as an experimental model. In section 1.3 there is an overview of questions related to regeneration, neuron survival and also recovery through neuroplasticity. It is not very complete - the information is spread out over many, many publications and I had to be selective in my citations - but there is additional information tabulated and referenced in the supplementary dataset.

It is clear that there is a great deal of variability in recovery, including paradoxical effects of too-rapid and inexplicably-slow recovery. Also inter- and intra-species differences can be substantial. In what system are you working, that the DRG-toe distance is 20 inches?

Where can I get vehicle information in traffic data?

I am working with VANETs and need to get some authenticated dataset. Please suggest the ways, I can get the dataset online or offline.

Mike Mcgurrin · Noblis, Inc.

The NGSIM data sets may help. They are actual vehicle trajectory data for multiple locations (although each is a pretty small area). I used a subset of one data set as input to an NS-2 model some years ago, and other researchers on VANETs have used the data sets. Unfortunately the site seems to be not working right at the moment. You need to go to http://ngsim-community.org/ and register, then in theory when you go to downloads and select data sets, you can download them, but at the moment, you just get a blank page. There are several emails in to those responsible for the site, so hopefully it will soon be resolved.

The NGSim program developed improved algorithms for traffic simulaton, and to validate the algorithms they captured video data from multiple roadway types and locatons and then used image processing to convert the video data into vehicle trajectories.

If you're interested and the site doesn't get fixed promptly, let me know, as I suspect one of my colleagues might have at least some of the data sets stored away somewhere.

What is the best methodology for debriefing in clinical simulations?

What is the best methodology for debriefing in clinical simulations?
Use some background?

Shokoh Varaei · Tehran University of Medical Sciences

i think it is better to hava a osce exam

• Does anyone have experience with the SEER12 GE Holter Recorder and data extraction?
Our research group is trying to conduct ECG studies and needs high frequency sampling (ideally >1000Hz). The SEER12 GE Holter samples at 1024Hz but cannot be accessed due to encryption. If the data is extracted using the GE software (MARs or CadrioDay) it is down-sampled to 128Hz or 256Hz and is useless for our research. Any experience or suggestions would be appreciated
Michael M Laks · University of California, Los Angeles

The best  Holter (ambulatory ECG System) that I have used is the Mortara 12 ECG that

records a 1,000 Hz. and can use it for research.

How can one find out the socioeconomic class of certain districts or neighborhood?

Community pharmacies are spread over wide area in each city. Each pharmacy serve the surrounding neighborhood which can have some distinctive characteristics regarding prevalence of diseases and socioeconomic factors affecting choice of medications. How can a pharmacist describe the socioeconomic class of his neighborhood?

Diane Prashad · The University of York

Census data is the best way to look at the socio economic status of a community. Look at employment/unemployment statistics. Looking at mean income per family usually helps to determine socioeconomic status. Additionally a good way to start is looking at what is socioeconomics and then that would inform a more precise discussion of what you're looking for. In general terms, socioeconomics would look at the level of poverty experienced in a certain neighbourhood, and the ability of those living in those neighbourhoods to access goods and services. I guess in this case it would start with an examination into census data. Key areas (poverty, unemployment, income).

• Klaus Schuricht asked a question in R:
Would you agree with me when I say phones are highly abstract abstractions?

When we say [r] and [R] in some languages are allophones we have to keep in mind that [r] and [R] aren’t realizations of sounds but abstractions, too. So /r/ vs [r], [R] symbolize only different levels of abstraction, but no individual sound. We have no possibility to WRITE a certain real-sound. The possible realizations are uncountable. So phonetics when using symbols like r, R, x or even compound symbols, with diacritics, like ø̞̈ (for the German ø) etc. is highly abstract. Like mathematics.

• Does otitis media causes fatal brain abscesses?

It has of course been known for a long time that there is a connection and correlation between brain abscess and otitis media (or sinusitis).  But is this a simple causal link?  Self-evidently so, according to modern medical opinion.   However, I think Hippocrates was correct in believing that the primary cause was cerebral, eg a traumatic fluid leak into the middle ear or mastoid, and that the ear infection was secondary.  So instead of the massive number of case reports of abscesses with unilateral or acute OM, which clearly support the Hippocratic theory, can we please have case report(s) where there is an obvious dose respone relation with OM, ie a symmetrical bilateral severe case of OM with uniform bone erosion and destruction, not dependent on any previous trauma or disease?

Max Stanley Chartrand · Northcentral University

The companion monograph that goes with the keratosis obturans topic (above) is attached here. This one is about how septic tooth and jaw problems cause otitis cases of the ear, both in the middle and outer ear. Overlooked 99% of the time, I would say.

Can anyone recommend an alternative to Click-it EdU labeling kit from Invitrogen?

I have had great results with the Click-it EdU labeling kit from Invitrogen, but it is too expensive for my budget.  Does anyone know of an alternative kit that works as well, but is cheaper?  Alternatively, any simple homemade protocols for EdU click labeling would be profoundly appreciated.

Thanks!

Sanket Rane · National Institute of Immunology

Yes, we use a "homemade" recipe do to click reactions. You can easily find out the composition of click it buffer and concentration of CuSo4 used. We do it and get wonderful results. I think its citrate buffer and 10M CuSO4 but not sure. I am traveling now so can't confirm. But if you want I can ask my colleague to post it here.

Could anyone help? What is the proper wavelength of the laser if one would like to make the photo-darkening in thin films?

I would like to study the photo-induced structural change in amorphous thin chalcogenide films (Cux[As2(S0.5Se0.5)3]100-x). Just, if anyone could explain on which parameter of the material depends the laser wavelength which is to be used.

Bojan Miljevic · University of Novi Sad

Thank you, Jan Gutwirth. Let me kindly ask whether you know something about the power of the laser and the exposure time.

Does anyone have any suggestions for good Paleolimnology papers (yours or otherwise) that would be good for teaching limnology concepts?

I am looking to use paleolimnology examples to sum up the learning objectives for a limnology class.  E.g. good clean, easy to understand examples of eutrophication, mixing, contamination, etc? thank you!

Martin Bohle · European Commission - RTD

Hello - if you can handle French language, then look for the papers / books of Alphonse Forel (http://en.wikipedia.org/wiki/François-Alphonse_Forel, http://fr.wikipedia.org/wiki/François-Alphonse_Forel). regards, Martin

Dose anyone know a tool to measure self-efficacy in clinical nursing field and/or nursing education?

Self-efficacy refers to the extent of an individual’s belief in his or her abilities. Because self-efficacy is based on feelings of self-confidence and control, it is a good predictor of motivation and behavior. This is particularly ingesting in nursing field, there are different questionnaire used to measure self efficacy, is there someone confident with some of the availed tools?

Shokoh Varaei · Tehran University of Medical Sciences

i used the self efficacy tools in mothers who had a breast feeding but i think it is better to look at bandura scale

How does one go about converting/translating IDL scripts to Matlab?

I have IDL scripts (".pro") which I would like to translate to Matlab (".m"). Any tips or guides would be greatly appreciated. Thanks in advance!

in my experience it is usually quicker and cleaner to reimplement the scripts.

"literal" translation may be problematic when you are heavily relying on very specific IDL capabilities.

Is it possible to compare cost and schedule overrruns for infrastructure projects between different countries?
Factors such as different cultures, procurement methods, governance, safety requirements, contracts all differ.
Massimo Florio · University of Milan

You may like to give a look to this. The first author has written extensively on this topic

Underestimating Costs in Public Works Projects Error or Lie? Bent Flyvbjerg, Mette Skamris Holm, and Søren Buhl

• Does anyone know any paper where the primer purity or supplier source has been compared in saturation mutagenesis experiments?

I need to know if desalted primers can be better than HPLC...

• Why is trizol lysis of Bacillus subtilis more efficient before freezing than after freezing?

I am prepping B. subtilis cultures for RNAseq, and have been comparing different storage and lysis methods.

I have prepped most of my samples using RNAprotect based on what I understood were well-established protocols from the literature and previous work with E. coli.  However, in pilot samples I happened to discover that when I skip the RNAprotect step and dispatch live cultures directly into Trizol-LS, and then store at -80C, I get much better total RNA yields (>20ug) compared to RNAprotect/-80C storage/Trizol treatment (~5 ug). These values are post-DNAse treatment, and DNAse eliminated about 30-35% of the measured pre-treatment nucleic acid in both cases.

The only downside is that I have to use a much larger volume of Trizol-LS since it's volume has to be proportional to the whole culture rather than the pelleted cells... and the fact that the samples I have already collected and stored at -80C were stored in RNAprotect, not Trizol.  But I am curious why trizol would be so much more effective at recovering nucleic acid from live cells versus dead-but-well-preserved cells, if anyone knows.

Margaret Kenyon Applebee · University of California, San Diego

So basically what this is suggesting is that my assumption that both Trizol and RNAprotect equally prevent RNA degradation is incorrect.  Thank you!

Is there a family of graphs with negative signed domination numbers?

Let f be a function from V(G) to \{-1,1\}. If for all vertices $v\in V(G)$,

\sum_{x \in N_G[v]}f(x) \geq 1,  f is a signed domination function.

The weight of f is equal to \sum_{x \in V(G)}f(x). Minimum weight among all signed domination functions is called signed domination number.

Dear A.N. Ghameshlou

Yes, of course. In the following paper,  we have proved that for each integer $k$ there exists a connected graph $G$ with signed domination number $k$.

D.A. Mojdeh, B. Samadi and S.M. Hosseini Moghaddam, Bounds on the signed distance-k-domination number of graphs, Iranian Journal of Science and Thechnology, (2012) A3 (Special issue-Mathematics), 367-370.

Regards

• Why high concentrations of pepsin interfere with the pepsin activity assay?

Hi everyone, I would really appreciate your help with this....

We got a new batch of pepsin, and we want to know its activity (U/mg). I've repeated the test with Haemoglobin based on Anson's method (Anson, 1932), and suggested by INFOGEST (Minekus, 2014). When working with low concentrations for pepsin (5-35 microgram/mL, as suggested by Minekus, et. al.), I get one result, but increasing pepsin concentrations to 50-200 microgram/mL will give me not only a different result, but LOWER activity of pepsin (like half of the obtained for lower concentrations of pepsin).
I would like to know if this result is logical, and what is the reason behind it... why the activity of pepsin seems to decrease when using higher concentrations of pepsin in the assay?

If someone has better experience working with pepsin, I would appreciate your answer very much! Thanks!! :)

Cynthia Qun Sun · Callaghan Innovation

you need to increase the substrate concentration accordingly when the enzyme amount in the assay is increased. I would go with the results tested in lower enzyme concentration.

Is a low Cronbach's alpha problematic for a composite scale?

I am using a published psychometric instrument with two scales, each with high internal consistency (Cronbach's alpha > .80). My hypothesis is that certain items from each of the two scales combine to form a new factor. This new factor is working as a predictor in a regression, but it has a low alpha (.59). Is this a problem given it is a composite scale, and can I justify it / use a different method to test reliability? Thanks.

Rosa Angela Fabio · Università degli Studi di Messina

Hi

Yes, .59 is a low internal consistency. Try to find  if in your new factor there are items that are unrelated with the others at all. If you subtract them, your Alpha can increase.

Can anybody help me identify non-roar underwater vocalizations of harbour seals?

I am currently conducting a study on harbour seal vocalizations in British Columbia, and I have summer recordings near a large haul-out. Strangely, I'm not getting a lot of roar vocalizations, which are typical during the breeding season. I do, however, have a number of low-frequency pulses, grunts and croaks that might be fish, but some look like Hanggi and Schusterman's (1994) non-roar underwater vocalizations of harbour seals.

Can anybody listen to these sound clips and confirm for me whether it's fish or pinniped in origin?

Thanks!

Thomas Götz · University of St Andrews

Hi Katrina,

I had a quick look at your recordings and I think it will be very difficult to determine whether these sounds are seals or fish. I personally believe that non-roar vocalisation in harbour seals are rare (at least here in Scotland) but I am aware of the paper by Hangi & Schusterman (1994) on the Pacific harbour seals. As for your 2nd and 3rd recording ('Seal Maybe' & 'Croak'), there is also a similar call in grey seals, the 'type 10' call which has been described in McCulloch (1999). This is just an unpublished PhD thesis (St Andrews Uni) but the 'Growl E' in Asselin & Hammill (1993, Can. J Zool.) may also be similar. The dilemma is that some gadoid 'drumming' sounds are also similar. As a side note, you will have probably noticed that many of the sounds you uploaded (e.g. some of the grunts, croaks & growls) are of a pulsed nature with the 'harmonic pattern' being merely a result of the high pulse repetition rate and chosen FFT size (in a spectrogram display). A close look at the waveform is revealing here. Some of the weak 'pulses' may be ambient noise but others may be fish (could be a gadoid) or even seals (see 'knocks' in Asselin & Hammill). I would generally recommend to obtain recordings with a better signal to noise ratio and use a passive acoustic localisation method (i.e. large aperture hydrophone array) to link visual and acoustic observations.

Best, Thomas

• Does anybody know of a method to further optimise the result of the greedy scheduling algorithm?

After a result using greedy schooling approach has been calculated I would like to further optimise it (if necessary). Any ideas?

Lukasz Wisniewski · Hochschule Ostwestfalen-Lippe

This is a great suggestion! Thank you very much!

Kind Regards Lukasz