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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• Negar Kamali asked a question in Abaqus:
System error code 1073740940 when using UEL ?

I'm trying to run an analysis with a simple UEL subroutine that I wrote and after compiling, linking, analyzing the input file and the subroutine suddenly it crashes with this error:

Abaqus Error: The executable standard.exe
aborted with system error code 1073740940.
Please check the .dat, .msg, and .sta files for error messages if the files
exist.

has anyone encountered this before? I can not find a bug in my code (I write out all the matrices and they're all correct) I also checked everything else that comes to my mind.

P.S: I can run other subroutines to the completed stage

How do I acquire a specific number of cells/events from a mixed population during flow cytometry?

I am new to flow cytometry and doing analysis of platelet activation markers (CD62P and PAC-1) in whole blood. Many authors recommend acquiring a certain number of platelets (usually 5,000 or 10,000 platelet events). How can I achieve this from the mixed population of whole blood?

Ijeoma Esiaba · Loma Linda University

Did anyone hear about consistent databases regarding accidents related to sports activities?

Most data regarding sports accidents emanate from hospitals and rescuers. In France, it is somewhat difficult to get precise information as to these accidents. I would be interested in international data in order to compare the situation in France and in other countries...

Joni Roh · California University of Pennsylvania

The NCAA collects data I believe yearly for collegiate sports.  It measures injuries across all NCAA sports, across disciplines, and according to exposure, including practices and game situations.  Not sure if this of interest, but thought I would post.

Any suggestions about the integration of sustainability indicators in energy systems optimisation models?

For energy modellers, first idea is using externalities (extra costs in the objective function) but what's the point for the LCA modellers? Evolutive environmental profiles?

Indicators can be these you say but also the LCA indicators. The problem is how to combine them and weigh them.

• Who rewrote General Relativity?

Einstein's General Theory of Relativity seems to have “crashed” as a scientific theory in about ~1960, and to have been "rebooted" some time in the early 1960s as "modern GR" with a different set of definitions and rules that differ from those laid out by Einstein.

I'd like to know who originally made those "redesign" decisions, how the community consensus was reached, and where the changes (and their justifications) are documented.

Background: Einstein had based his theory on the General Principle of Relativity: the idea that all motion was relative, and that even “absolute” motions such as rotations and accelerations could successfully be “relativised” if bodies showing those relative motions could be associated with suitable gravitational/distortional effects. This was an idea previously proposed by Ernst Mach, and Einstein described his general theory as being the theoretical embodiment of Mach's principle.

For derivational convenience, Einstein also initially assumed that the theory should reduce to the physics of special relativity over small regions.

However, the publication of the Harwell group's 1960 paper on centrifuge redshifts (Phys. Rev. Lett. 4, 165 (1960) ) apparently triggered a controversy within the community, and an appreciation that a literal application of the GPoR seemed to lead to results that were geometrically incompatible with special relativity – the consequence of the GPoR being treated as a “law” then seemed to be not only the loss of Einstein's 1905 "Special" theory, but also the loss of the 1916 "General" theory that had been partly built upon it (Schild, Am. J. Phys. 28, 778 (1960) ).

We were facing the unpalatable prospect of a major rewrite of theoretical physics, and although a rederivation of GR to avoid its dependency on SR had already been suggested by Einstein back in 1950 (SciAm 182, 4, 13-17), we found it easier to modify the rules of general relativity to allow the GPoR to be suspended in cases where it seemed to clash with other parts of the 1916 theory. In effect, we accepted that the original “SR+GPoR” structure was logically inconsistent, but maintained order by redefining SR's position in GR's definitional hierarchy to one in which GR could not disagree with SR “by definition”, and establishing a "failure etiquette" ("If the GPoR conflicts with SR, keep SR and suspend the GPoR").

This change seems to have happened with minimal recorded public comment or discussion. Although Schild's paper mentions discussions and "a certain lack of unanimity" in the community as to how to proceed (before he presents the "modern GR" position as unavoidable) Schild doesn't indicate who participated in those discussions.

I'd like to know who was on the committee, who voted for or against the change, and whether any of those concerned published anything on the nature of the 1960 crisis and the chosen response. Does anyone here remember it or have direct personal experience of what happened? Is there any historical record of the episode other than the rather skimpy Schild paper? Did anyone else publish the arguments for modifying Einstein's theory, or the contemporary arguments why GR1916 couldn't continue to be used in its pre-1960 form?

Any references to additional contemporary material would be very, very welcome.

Is an anti-depressive incompatible with EMDR?

Does anyone know - based on scientific research or clinical experience - whether EMDR is incompatible with an anti-depressive? An acquaintance, Mrs. C., is on 15 mg Mirtazapine (almost the minimum dosage) to keep her extreme generalized anxiety somewhat between limits. In the past she had suffered a brief psychotic episode. Her therapist (Mrs. C. is still on the waiting-list) claims that being medication-free is an absolute condition for EMDR to be effective. To me the risk seems too big.

David M Fresco · Kent State University

Two things:  First, no one uses systematic desensitization anymore.  Pairing relaxation with fear exposure adds nothing.  Second, I doubt that EMDR will ever be shown to be better or different than properly conducted exposure therapy.

• Which cardiovascular diseases have been diagnosed via Artificial Intelligence classifiers?

I would be grateful if you could list a few applications of neural network and machine learning classifiers in diagnosing cardiovascular diseases.

Thank you very much in advance.

Judocus Borm · Reinier de Graaf Groep

In the late nineties I have seen an interesting applcation of artificial intelligence techniques in a research laboratorium of a company building gamma-camera's for one of the big vendors in medical imaging.

The application was designed and trained to assess ejection fractions using the MUGA technique.

It worked fine and certainly outperformed human operators with respect to just about any parameter one could think of except:

when confronted with a novum, that is a fact . circumstance , or detail that was known to interfere. Without human guidance it could not learn to handle the exceptional cases.

At that time I was confronted with a patient with a monoventricular heart.

That AI program started of by defining / outlining the interventricular septum and started from there off.  People with monoventricular hearts are rare, very rare, but the AI algorithms had no way of properly dealing with such novum. Forcing such dataset in the learning set affected overall performance significantly.

One serious problem for any such AI software package is, that it cannot be trained for the extremily wide [in this case: anatomical] variation that actually will be found in routine clinical settings, whereas human experts can and [almost] routinely do.

To my knowledge that specific AI code was never marketed.

More on myocardial perfusion scintigraphy:

Some image processing tricks added to accomodate anatomical problems can cause problems in a small wel defined subset of patients for reasons obvious to anyone understanding the algorith used.

Let me give an example [that is not truely AI and more about advanced feature extraction] to show how good basic understanding of pathophysiology can make humans outperform otherwise excelent code.

My example is about the Germano approach towards defining the left ventricular wall in myocardial perfusion scintigraphy. The tracer accumulates in the myocardium but also in variable amounts in the liver. Germano had to introduce additional code because the combination of the motion of the diaphragm [breathing] interfered and because of the closeness of the myocardum and the left live lobe, without the additional code, his algorithm [based on the Hough transform] failed far too often to delineate the left vetricular wall, and instead was including part of the left liver lobe.

When working in an academic centre doing a lot of work up for liver transplant candidates, we discovered that in quite a few of them, the segmentation of the left ventricular wall failed because of very high uptake of the perfusion agent in the spleen an dnotin the left lobe of the liver. The Germano code did not deal with the high uptake inferolaterally [in the spleen] whereas a similar pattern on the inferoseptal side was easily accomodated.

So before  starting the Germano feature extraction, we manually rotated the heart about 65 degrees along the long axis of the left ventricle and then the Germano code could deal with this problem without problems.

I had never heard of that problem before at that time. So far I have never found it in literature. In general hospitals, this will be very rare pattern, so it is unlikely [without expert input when designing the algorithm and choosing candidates for the trainingset] that any AI algorithm will automaticaly come with such solutions.

At any time the expert must know and understand what the machine is doing [understand the training process and th eadditional image processing algorithms]and be able to assess the validity of the trainingset.

When judging/diagnosing/assessing routine patients I certainly believe AI techniques will result in much improved reproducebility, but in special / exceptional cases humans will outperform AI for a long time

Another example allong this  line: the perfusion agent used for myocardial perfusion scintigraphy is also taken up by most tumours. In the presence of a close by tumour, in at least some studies humans will outperform any AI based algorithm.

AI techniques are surely stronger than humans at discrminating between two specific entities in otherwise normal subjects, But when other mechanisms / pathology / rare anatomical variants interfere, I am not sure any more.

And when a lot of such examples / considerations must all be explicitely coded into algorithms and corresponding production rules, no AI system will likely become smarter than the smart person that selected the examples or mede the ruleet.

• How can I calculate Gold nanoparticle concentration in Molars and coverage?

I have some doubts.hope u guys can clear. I am attaching thioated dna with gold nanoparticle. I know my thiolated dna concentration in molars but I don`t know  how to calculate gold nanoparticle concentration in molars. my 2nd question is if i mix 2 different oligo then how to caculate gold oligo coverage.Also, i am going to use a dna sequence partial complementary to my dna linker attached to nanoparticle then how to calculate that coverage part.

David J. Lewis · The University of Manchester

Hi

Yes agree with Dr Murugesan use my method to calculate the NP conc from Lewis et al. Chem Comm 2006 support info

But then you could use ICP MS to get a Au:P ratio

Has anyone ever used ATLAS.ti for qualitative data analysis in applied linguistics?

I'm interested in finding research that has made used of this software.

Thanks.

http://atlasti.com

Pascual Pérez-Paredes · University of Murcia

It seems it is a widely used annotation tool for multiformat sources very popular, I understand, in the education field.

Nice to hear from you Prof. Bhatia.

Best,

Pascual

• Could anyone explain the relationship between firms' innovative capability and organizational agility?

i am interested for your response

Justin Gabriel · Rivers State University of Science and Technology

I think there is a positive association between organisational agility and innovation  capability. Agile organisation has higher tendency for innovation. Agility makes organisation flexible, proactive, creative and resilient.

• Raj Kumar asked a question in Sensing:
How to choose our materials is capable for sensing particular gas?

How can we get a knowledge about sensing nature of our own materials.

Who can explain why intermodal dispersion is zero for a graded-index fiber with a quadratic index profile?

The refractive index of the core in graded-index fibers is not constant but decreases
gradually from its maximum value n1 at the core center to its minimum value n2 at

Dr A. Kumar · Harcourt Butler Technological Institute

In case of graded index fiber, critical angle condition is satisfied at different distances from the axis of the core for different modes as refractive index is decreasing from the axis up to core cladding interface. The wave which is internally reflected near axis travel less distance but will also have low velocity due to  higher refractive index. On the other hand, wave reflected near the interface will travel more distance but with higher velocity due to smaller refractive index. Hence, the time to reach the other hand will be same for these waves which means no intermodal dispersion.

• Uggo Pinho asked a question in Fluorescent Dye:
How to measure 3D water surface elevation?

I need to measure water surface elevation [eta(x,y,z,t)] from image processing (video and photo). Would someone know techniques for either the image processing of water surface detection and to improve water surface detection (lightning/colouring)? Maybe by applying a fluorescent dye or colouring the water with a pigment. To be more specific, how to do that in a wave tank with 30m long and 20m wide, with an accuracy of 1 cm squared of the surface. Waves of typically 1 second of period and 5-15 cm of wave height.

Many thanks for any information.

Can anyone provide me the visual recordings or step by step guide to build the microfluidic culture chamber for the study of neuronal growth pattern?

A sample image of the culture system.

How can I demonstrate the existence of permafrost in the Picos de Europa (NW Spain)?

Current research suggests the possible existence of sporadic permafrost in relation to several buried ice patches of Picos de Europa, with mean annual temperatures close to 0ºC in the debris that cover these relict ice bodies. But so far it has not been demostrated to 100%.

Petru Urdea · West University of Timisoara

BTS  measuremets, ground temperatures monitoring at different depths at least 2 years, conducting geophysical investigations (Electrical Resistivity Tomography, GPR).

How can I avoid burning of the PMMA during CABIE or ICP-RIE for dry etching?

I want to pattern 100nm holes in SiO2 with PMMA mask for dry etching. While during SF6 RIE process, I found the there is some sputtered polyer left in the holes, which I suggest to be burned PMMA residuals. I am just wondering how to improve the selectivity of SiO2/PMMA and avoid the burning of PMMA?

Dingding Ren · Norwegian University of Science and Technology

Than you Benjamin. I want to use PMMA as a mask for dry etching first and then final wet etching step to form hole patterns of 100nm. My problem is that after dry etching, there may be some burned polymer left in the holes, which prevent further wet etching....How to remove the burned PMMA in the holes and facilitate further wet etching....Happy Easter:)

• Rongrong Fan asked a question in Deoxycholic Acid:
Does deoxycholic acid (DCA) normally appear in mice gallbladder? Is it functionally important?

I am recently analyzing the bile acid composition in our mice, and I observed about 2% deoxycholic acid there... I am not sure if deoxycholic acid composition change in the gallbladder (for example from 2% to 1%) actually lead to a major physiological change... I checked some literature, if I am correct, it seems DCA is a 'secondary bile acid' which should in theory only appear in the intestine, serum and hepatocyte? Why it appears in the gallbladder... Anyone has suggestions or explanations about this?

Sustainable Procurement : Is the practice to be avoided or appreciated by SMEs ?

All SMEs operate under various constraints and those are impacting their operations at the higher level. If the organization is refusing/constrained not to adopt the strategy in its procurement practices ? what would be the impact ? how do they mitigate them with an alternate strategy to sustain/ maintain their operations in the market ?

Would appreciate, if any one come across any articles related to Sustainable Procurement... Thanks

Chwen Sheu · Kansas State University

I don't think any companies, regardless of the size/type, can avoid this issue. See "Don't tweak your supply chain", HBR, October 2010 for good examples/discussion.

Do you who can supply us the Costa Rican coral snake venom?

Hello,

We are interested in Costa Rican coral snake venom and in Texas coral snake (Micrurus tener tener) venom. Could you produce them for us? What will be the quotation for those venom? Could you recommend us a snake farm that have that kind of snakes?

Thanks and Best Regards,

Laura Feldman

Russell Eyre · Acucela

A few decades ago, the Miami Serpentarium would have likely been able o help.  I'm not sure the status of the business now.

Can anyone provide effects of studies of planting on soil loss?

This research may be article, thesis, dissertation etc.Thanks in advance.

Rita Sousa · Universidade Federal de Santa Maria

There are two good books that speak about the influence of plants in soil loss:

COPPIN, N. J.; RICHARDS, I. G. (EDS.). Use of Vegetation in Civil Engineering. 2a. ed. London, UK: Construction Industry Research and Information Association (CIRIA), 2007.

MORGAN, R. P. C.; RICKSON, R. J. Slope stabilization and erosion control - A bioengineering approach. 1a. ed. London, UK: Chapman & Hall, 1995.

Which technology file/ transisitor to be used at RF frequency?

Hello Everyone,

I want to implement a CMOS inverter that can work at GSM band (850MHz/900MHz) in SPICE tool. I am using TSMC's 180nm model file. I am not getting exact output at this much high frequency. So, can anyone suggest which model file to be used for higher frequencies and from where can I get it?

Basavaraj Choukimath · K.L.E. College of Engineering & Technology

I hope this link may helps you

Is the minimum concentration of protein to be loaded in FPLC sephacryl s-200 column?

I get very small peaks if I load 0.3 microgram (total concentration)

Richard Jayaraj · University of Washington Seattle

Hi Liger. Thanks for your answer. My loop size is 100 microliter and the total amount of protein is 0.2µg.

Does anyone have the 5D-ASC questionnaire?
We found the OAV questionnaire (66 items) but would really like to use the 5D-ASC with 94 items for our clinical trial. Does anyone know how to get it? Possibly even in German?
Daryn Dyer · York University

Dittrich, A. (1998). The standardized psychometric assessment of altered states of consciousness (ASCs) in humans. Pharmacopsychiatry.

• Kevin Mcdaniel asked a question in Diaspora:
Has anyone studied the history of okra from Africa to South America?

I am trying to look at how the African diaspora brought African food items to the new world.

• Is there any correlation to predict capillary pressure in soil or other porous media?

I want to generate a code for simulating three phase (water, oil, gas) flow in soil and it needs to calculate capillary pressure between each two phase as a function of saturation, soil properties, and fluid surface tension

Ramanathan Sri Ranjan · University of Manitoba

There are empirical equations available to model capillary pressure as a function of saturation.  Brooks-Corey equation or van Genuchten equation are used in models. The curve fitting parameters in these equations are dependent on soil type and poresize distribution.

What is the range of Fourier transform from continuous space to discrete space?

Recently I read a paper where Fourier transformation is done from continuous k-space to discrete lattice space. The range is taken as ($-\pi$ to $\pi$).  Can you explain how  it can be done or any reference to that.

You are welcome Debajyoti.

How do I design or choose primers for porcine mesenchymal stem cell targets?

I'm trying to do a gene expression study for porcine mesenchymal stem cells which have been induced towards differentiation using different chemical agents.

At first, I tried to design my own primers by using "consensus sequences" I found in this database for the pig genome (http://pig.genomics.org.cn/transview.jsp?transcript=ENST00000230354&seq_type=all).  I would get the consensus sequence and use Primer 3 to design a primer pair for that sequence.  Then I used UCSC In-Silico PCR to check the specificity of the primers.  Before using UCSC In silico, I tried using Primer Blast but it confused me as even published primers did not seem to be specific when I used Primer Blast..sometimes even declaring there were no relevant matches or sometimes giving so many matches none of which contain the expected amplicon.  So anyway, using In-Silico and the pig's reference genome (2011) they have there, I made sure the primers I designed were specific to one product only.

The problem is when I ran my primers, I got a signal in my "no reverse transcriptase" controls that have the same peak at the melting curve as my expected amplicon.  I thought this was a contamination problem so I bought new primers and took care in diluting them and I also bought new primers from a published paper.  Interestingly, my fresh primer (which I have designed) still gave the similar peak for my "No RT" control, but the published primers didn't give a peak in their "No RT" control. I do not understand if this is an inherent problem in my primer design as it doesn't seem to be a primer dimer because the peak is the same as for my reaction tubes.  I am testing for housekeeping genes right now.  I am so tired already from designing and redesigning primers and doing standard calibration plates for so many times already that I have resigned to just using the published primers.  However what worries me is how do I then choose primers for the specific cardiac genes I want to study.  If I attempt to design them again similarly as to what I described earlier, then I might face the same issue in the signal in my no RT control.  I have ruled out the problem of contamination as my "water and primers only" control doesn't give any signal.  There are not much published primers for the porcine cardiac genes that I want.  There are a lot of studies however for human, mouse and rat.  Can I simply use these?

Michael Rosemann · Helmholtz Zentrum München

Dear Christine,  here are some suggestions:

1.) "The problem is when I ran my primers, I got a signal in my "no reverse transcriptase" controls that have the same peak at the melting curve as my expected amplicon."

Run the product from the NTC and from a positive control well on a high% agarose gel and check the size. If the size is below 50bp, most likely you see primer dimers (which are more or less normal in the NTC, but also appear if any of your samples have not template expressed to be amplified.  If the products are between 80 and 150 bp (as predicted from the target sequence), then you definitely have a contamination in the NTC. The contamination will come either from post-PCR products of the same gene, or in case you cloned the same sequence in plasmid and worked with it on the same bench using the same pipettes, racks etc etc.  This is a real nasty problem. Usually the only solution is to go to another lab (that has never "seen" an amplified PCR product or cloned fragment of your target gene). Contamination by genomic DNA, in contrast, is very unlikely.

2.) " ... it doesn't seem to be a primer dimer because the peak is the same as for my reaction tubes."  If your reaction tubes have no amplifiiable target (i.e. zero expression of the target gene), you will get the same type of primer dimers as in the NTC.

One thing that always makes problems are residual random- or oligo-dT primers from the reverse transcription. They are easily carried over toegther with the cDNA into the qRT-PCR tubes. They can make funny amplification curves with an early rise in the signal (at around 10 CTs) and a second rise (at the expected CT value, see the left curve in the picture below).  The funny thing is, that the first rise of the curve even happens WITHOUT any qRT-PCR primers, since it only uses the carried-over reverse transcription primers. If you have something like this, dilute the cDNA 1:5 instead of using the indeluted from the reverse transcription. Or purify the cDNA from all other reverse transcription components, using QIAgen spin columns.

3.) For qRT-PCR primer design I usually use an on-line program from GeneScript. Although it only has inbuildt mismatch tables for human, mouse, rat and "others", I guess if you use human for your pig-genes, it should work.

(https://www.genscript.com/ssl-bin/app/primer)