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  • Daniel Becker added an answer in Meta-Analysis:
    What is the number of species needed for a PGLS analysis?

    Hi all,

    I'm looking to do a phylogenetic generalized least squares analysis of a dataset I have on mammals, their average infection status between two habitat types, and various host traits. This dataset is derived from a systematic meta-analysis with quite specific conditions, so the phylogenetic dataset is for only 10 mammal species, where the outcome (infection difference between two habitats) is based on anywhere between 5 to 20 lines of data per species.

    I'd like to ask which (if any) host traits predict this difference in infection after controlling for phylogenetic distance, but am concerned that n of 10 really limits any power. As an optimistic point though, the exploratory analysis I've done so far has found very strong effects with very small p values for 3-4 covariates in the PGLS model. So my question is if my sample is simply too small and model overdispersed or if there is any precedent for PGLS with a smaller sample size being deemed acceptable, given the multiple lines of data that went into the outcome for each species (these are included in the PGLS model as weights).

    Thanks very much for your time

    Daniel Becker · University of Georgia

    Great reference, thank you!

  • Oscar Arrieta added an answer in Tumors:
    What is the most fatal type of cancer?

    some tumors are considered more aggressive than others and not resopnding to chemotherapy, according to the international statistics: which is the most agressive type of tumor with lowest expectancy of life? 

    Oscar Arrieta · Instituto Nacional de Cancerología - Mexico

    I would add, besides of pancreatic cancer and glioblastoma, the anaplastic thyroid cancer, although it is a rare tumor is extremely aggressive and with a poor prognosis

  • Genxing Pan added an answer in Biochar:
    What is the relationship between soil pH and biochar addition?

    I am trying to figure out the relationship between biochar addition and soil pH. Can any one direct me to a good analysis of this? e.g. do we know enough to say how much biochar (of a given pH) you need to add to soil type X or Y or Z to raise pH by one unit? I understand that the answer depends on the pH of the soil, i.e. is it 4 or 6, say. Maybe its too complicated to put the answer into a simple formulation for non-soil scientists like me?! Thanks for your help.

    Genxing Pan · Nanjing Agricultural University

    Dear Simon,

    It varies with the initial soil pH.. The increase in soil pH with alkaline biochar will be higher in acid soils than in originally high soil soils. However, some of biochar, if not with crop styraw or undr high temperature, could even have low pH (acid biochar). So it is hard to say biochar could convincingly incraese soil h nnor a linear response o soil pH to biochar added. You need carefully l;ook at your soil and biochr. 

  • Jose Paolo Orata Bantang added an answer in Ions:
    Can I use FTO conducting glass as electrodes for a symmetrical cell set-up for ionic conductivity determination of thin films?

    Most literature uses stainless steel or any metal electrodes for the determination of the ionic conductivity of a thin film with ion conductors such as Li ions. Is it advisable to use FTO conducting glass as an alternative electrode to these metal electrodes for ionic conductivity determination using impedance?

    Jose Paolo Orata Bantang · De La Salle University

    Thank you for your helpful answers.

  • Miguel Belbut Gaspar added an answer in Callbacks:
    Why is my event-loop in matlab non-gui executable not working?

    I am developing an application that should run in the command-line (console application), without gui. I want to reduce the memory footprint and load time. My application will be controlled trough a network connection. In Matlab I can have the callbacks persist after the script/function exits. In the compiled version,  I have included a pause(), to prevent the application from terminating. But when I run the compiled version it doesn't seem to respond to the callbacks. As there is no wait() for tcpip objects, I don't know how to keep the app. from exiting. Am I doing anything wrong? Is what I want possible, or do I need a Windows executable to have the event loop for the callbacks?

    Miguel Belbut Gaspar · Instituto Politécnico de Leiria


    Thanks for your comments. They made me think a bit more about how to formulate questions, the multiple diverse audiences a question might have, and what purpose they serve (only for the original poster, or for other people?). Still, I think your answer is polluting this thread with many questions unrelated to the original post.

    I realize the code above might be difficult to decode for those who are not familiar with Matlab. My question is pretty much specific to Matlab. I don't need help with what I want my code to do, it already does exactly what I want. The question is about a feature or internal working of Matlab Compiler Runtime.

    Still, although it is getting a bit off-topic, I will try to explain the code in previous comment, and make it a bit more understandable for those who might not be familiar with Matlab.

    You are right in your comments about tcp versus udp. That is precisely why I am using tcp for some communications and udp for other (and also because the tcp listening in Matlab is blocking, i.e., it doesn't return control until a connection is opened remotely).

    My workflow is as follows:

    I have three image processing tasks that need to grab frames from three cameras. They should run indefinitely, waiting for frames being acquired, processing them, and producing a result. This result is sent to an PLC that controls some equipment according to the result for each frame. This is time critical, so I want to avoid having to initialize the video input object repeatedly. So, I initialize three workers, possibly on different processor cores, each one attached to a camera. This is event-driven, in that there is a callback routine that is called when a camera has a frame available. After processing, a result is sent via tcp using modbus protocol.

    Those workers are console applications, with no gui, so that I don't need to load a java virtual machine. So I want to be able to control them using simple udp messages (no need to have guaranteed delivery, and also don't want to block waiting for a connection - I want it to be event-driven).

    Normaly, when running code under Matlab workspace (with or without the Matlab IDE ), there is a base workspace that isn't destroyed even after your code has returned, and keeps your callbacks running. So, your app just sets the proper callbacks, and exits, but the objects that use your callbacks, and in fact all their context, is still available until you terminate Matlab environment. That is somewhat like a closure.

    But when you compile your app into an executable, it starts a Matlab environment via Matlab Compiler Runtime (MCR), which only lives until the main app exits. Of course I don't want to do busy waiting, so I tried to use pause to prevent the main function from exiting. But that pauses also the callback processing, because it seems there is only a thread (whereas in normal Matlab usage there will be a main ui thread).

    // Pseudo-code:

    function worker(number)

    // create a udp object, equivalent to nc -u localhost <SOME_PORT> -p <THE_PORT>


    // set an event handler (@handleCommand is a reference to a function, not depicted here) to respond to external commands sent via udp.



    The code above would work as intended under Matlab environment; if I start netcat with

    system('nc -u localhost <THE_PORT>')

    I will be able to send commands to my 'zombie' application, which will invoke the handleCommand callback I defined.

    If it is compiled, no luck.

    There is one solution I didn't try yet, that consists of using wait(vid), which blocks the current context until the object vid is stopped (vid being a videoInput object).

    This is getting too long, I will try some solutions and will report the results later.

    P.S. I removed the topic Code Development becaus I think it is too broad a scope for this question.

  • Zhilian hu added an answer in cDNA Synthesis:
    For how long can I store cDNA at -80C?

    In Order to undergo qRT-PCR, after RNA extraction and cDNA synthesis, if I would like to collect the samples to be conducted through the same run.

    Zhilian hu · University of Michigan

    you can keep it for long time. Be careful minimum freeze-thaw cycle. 

  • Raid Amin added an answer in Statistical Analysis:
    How do I relate the mean ranks to the actual ranks In the output of the Kruskal_Wallis test?

    I had ranked data showing preferences from 1 to 7 where 1 was the most preferred and 7 the least, but on the Kruskal-Wallis I get mean ranks of 368, 168, and 155 etc.

    How do I relate this to my actual ranks?

    Raid Amin · University of West Florida

    Add to the Kruskal Wallis Test  a summary of statistics based on ranks. You will be able to see side by side box plots based on the ranks, ... etc.

  • Miranda Yeoh added an answer in Economic Modeling:
    Why are people (dis)honest?

    "Rooted in the philosophies of Thomas Hobbes, Adam Smith, and the standard economic model of rational and selfish human behavior (i.e., homo economicus) is the belief that people carry out dishonest acts consciously and deliberatively by trading off the expected external benefits and costs of the dishonest act (Allingham and Sandmo 1972; Becker 1968). According to this perspective, people reach a decision that maximizes their interests and are honest or dishonest only to the extent that the planned trade-off favors a particular action (Hechter 1990; Lewicki 1984).

    From the "The Dishonesty of Honest People" one of the most cited article (see)


    I am interested to know your opinion about

    Miranda Yeoh · Kolej Matrikulasi Selangor, MALAYSIA (Selangor Matriculation College)

    Good question, congratulations.  Friends, to be honest and ethical in a materialistic (and often dishonest) society shows a living being swimming against the tide, not to do unethical things that many people are doing.  (@Wong KH, those students are not fit to become medical doctors. They have nothing to give to support patients.  Perhaps they only want the job they consider to be respected and glamorous.)

    But honest people are not perfect people.  Being an honest person, I know my own weaknesses more than that of others.

  • Zhilian hu added an answer in PCR:
    How can we optimaise q pcr?


    Zhilian hu · University of Michigan

    Could you please show us more information? The we can figure out it.

  • Kamran Ahmad added an answer in Aircraft Structure:
    Which is the best element choice for muliti layered FRP material in ANSYS ?

    I have to conduct FE analysis of aircraft structure of GFRP material which is of multi layered kindly suggest me how to do modelling of multi layered elements with different material properties in either ANSYS Apdl or ANSYS Work bench

    Kamran Ahmad · Beijing University of Aeronautics and Astronautics (Beihang University)

    Vishesh Kar is right, one can use SHELL 281, however, SOLID 46 can also be used when the thickness is appreciable

  • Erik Rakovský added an answer in X-Ray:
    Which is the best (and user friendly) Single-crystal X-ray diffractometer on the market now?

    We are a research group in an academic institution and looking into buying a diffractometer for single-crystal X-ray studies of small molecules. We want an instrument combining excellent capabilities with a user-friendly interface and great customer support. Any suggestions on this? Thanks! 

    Erik Rakovský · Comenius University in Bratislava

    My opinion is that Agilent and Bruker are on par when considering interface, with Stoe and Rigaku software being somewhat outdated. Although Rigaku hardware is good, their software is horrible. This is somewhat applicable to Stoe: they have excellent mechanic, but somewhat strange software.
    As for hardware, I would buy Agilent (or Stoe) gonio with Incoatec sources (or Rigaku dual-target microfocused RAG) and Pilatus detector driven by Agilent's CrysAlis :D but back to reality, I cannot see much difference between Bruker and Agilent.
    I think that benchtops are history - several months ago, I had a proposal with approx. 50 % discount from Bruker and looking at Bruker and Rigaku websites, they are discontinued (Bruker) and I am strongly pessimistic about XtaLab Mini also (Rapid II based machine is much more flexible and with low maintenance costs - IP is serviceable in the field; even power consumption of microsources is 10x lower than of 600 W fine-focus tube in Mini, not talking about limited possibility of using cooling device with Mini).

  • Raid Amin added an answer in Statistical Programs:
    What is the best statistical program can be used for multivariate analysis?

    There are many statistical programs produced by software companies, enough to one should decide which software program is more fit to present and analyze the data. If we have data on ages of trees, size, growth rate, vitality, and seeds production. What is the best statistical program can be used for multivariate analysis for these parameters?

    Raid Amin · University of West Florida

    We are honored by your presence here, Dr. Shinmura. You have played an important rolerole in the development and dissemination of statistical software packages. 

  • João Conde added an answer in Nanotechnology:
    Which is the best method for conjugation of antibodies with nanomaterials (especially metallic nanoparticles)?
    Can the antibodies be directly attached or some other polymeric/protein based materials must be used on the surface of metallic nanoparticles.
    João Conde · Massachusetts Institute of Technology

    Check this paper....

  • João Conde added an answer in Nanobiotechnology:
    Which method may I used to capped Nanoparticles with polysaccharides or carbohydrates?
    I need some article on the methods.
    Thanks for your help.
    João Conde · Massachusetts Institute of Technology

    Check this paper....

  • João Conde added an answer in Nano Biomedicine :
    Nanotechnology applications in medicine: what are the updates?
    Nanotechnology is promising to introduce solutions in various fields of medicine. I would like to know the current status. Any comments are appreciated.
    João Conde · Massachusetts Institute of Technology

    Check this paper....

  • How to explain the difference between EDC-NHS coupling based and EDC-based mechanism?
    N-hydroxysuccinimide (NHS)
    1-Ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDC)
    João Conde · Massachusetts Institute of Technology

    Can also check this paper...

  • João Conde added an answer in DNA:
    What are the procedures for Gold nanaparticles/DNA Functionalisation?

    I´m trying to functionalize Gold nanoparticles(Citrate Stabilised, 10nm from Sigma) with Thiol Labelled DNA. I have tried couple of protocols, but so far nothing has worked out.  (Replacing Citrate with BSPP, Salt Aging, And Rapid Functionalizing with Citrate Buffer pH 3). 

    One of the common problem which I have noted is that there is irreversible aggregation of AuNP after Centrifugation (10000RPM, 40mins). Does this mean DNA is not at all attached to Gold nanoparticles.  (I have tried reducing thiols with TCEP and DTT). 

    Can anyone correct me above protocols or is there something which I have missed? Any suggestions are welcomed. 

    João Conde · Massachusetts Institute of Technology

    Check this paper....

  • Asma Alam added an answer in Literature:
    Is there any use of mytheme in Macbeth?
    I have failed to find it out.
    Asma Alam · Daffodil International University

    Thank you Harith for your help. Of course, I will read it and enjoy it.

  • Muhammed Malayan added an answer in Hematocrit:
    Can microhematocrit be measured without a microhematocrit centrifuge?

    I want to measure hematocrit on small samples, but don't have a microhematocrit centrifuge.

     Is there a special insert that can be used in a normal centrifuge, or just another method that may be used altogether?

    Muhammed Malayan · DM Wayanad Institute of Medical Sciences

    Dear Lisa,

    Would you make it clear whether you want to measure the microhematocrit or the % hemolysis ( as in the case of osmotic fragility of RBCs)? Because for both measurements different ways of measurements can be utilized.

  • Andrew Jonkers added an answer in Time Series:
    What are the different ways to extract dominate frequency component from a non stationary time series?

    Non stationary time series  is one whose mean and variance changes with time.

    Sample of non stationary times series are : exponentially decaying or increasing,   U shape ,mixed of decaying and increasing etc.

    So how to handle these type of problem??

    Andrew Jonkers · Independent Researcher

    It depends on what you want to use the analysis for - standard techniques like FFT and its moving window sub-types, or wavelets MIGHT give you what you need if your needs are very modest and the signal is non-stationary in a 'simple" way; but note your signal is breaking the assumptions underlying these techniques and artefacts of varying degrees are inevitable. If the signal is known to be a simple combination from different  sources, techniques like principle component analysis and independent component analysis might be of some use.

    I know of no general technique that can analyse a non-stationary non-simple signal about which nothing, other than the signal itself is known. My long experience with attempting such analysis has been that you will find many different  models that can completely explain the data, and yet have no predictability of future data whatsoever.

    I would suggest if it is a specific type of signal you are interested in (one about which you know something about its origin as compared to having just the signal itself), then you are best to come up with some differential equation that describes the physics of how the signal is produced, and solve that instead. This constrains the models available to just a subset of those capable of fitting the data well - and hopefully the predictive capability of such physical models is better, if you have done the physics right.

    Finally for complex signals, you must be extremely careful about how you test generic models for predictive power. You ask for trouble to fit several models and then choose the one with the best predictive power - all you will end up with is a model that predicts the fitted data, and the predictive dataset - but which may well have no predictive power on any further "new" data. Meta analysis of groups of Climate Change models routinely fall into this trap - not out of ignorance but out of necessity (there not being multiple sets of actual data available). In their case though, it is the use of physics behind the models which gives them some validity according to the scientific method.

  • Will we get the same linear and non-linear responses for a structure subjected to both normal and synthetic ground motion?

    We have a ground motion records for a site. Also, generated ground motions for the same site using analytical methods. The characteristics of both ground motions are similar. Will we get the same linear and non-linear responses for a structure subjected to both normal and synthetic ground motion?

    Pradeep Kumar Ramancharla · International Institute of Information Technology, Hyderabad

    No. Because the amplitudes corresponding to different frequencies do not match.

  • Iman Soltani asked a question in Polymerization:
    What is the best polymeric film in the market to hot press your polymeric samples in between (no adhesion, no contamination, high thermal stability) ?

    I know that one choice might be Teflon (PTFE or PFA) , but they have severe delamination that contaminates your sample.

  • Alejandro R. Giraudo added an answer in Endemism:
    What's the best method and software to identify areas of endemism?

    Thanks in advance.

    Alejandro R. Giraudo · Instituto Nacional de Limnología (INALI)

    I agree that NDM and VNDM are usually the best software, but requires well distributional data in the space.  The PAE may be used to detected or compared localities or areas with different surfaces.

  • Stephen Cheung added an answer in Eating Disorders:
    Do you or anybody you know run a support group for eating disorders in a rural or remote setting?

    I am currently exploring the capacity in setting up a support network in regional victoria, Australia for people with eating disorders, issues with body image and body dysmorphia. There are very few support groups which stand alone in the rural/remote setting and those which are available are based in metropolitan settings with outreach services in the country. Therefore, is anybody aware of any services available in the rural/remote setting (it does not need to be Australian specific). Regards

    Stephen Cheung · Azusa Pacific University

    Hi Catiray,

    Thanks for your question. For decades, I've found the effectiveness of integrating psychoeducation with group processes. For individuals contending with binge eating, I'd recommend Christopher Fairburn's (2013) Overcoming binge eating, a self-help book, for the psychoeducational component of the group followed by supportive group processes. In the weekly group session of 75-90 minutes, the psychoeducation would take about 20-30 minutes with the rest of the group time devoted to mutual support and work on the self.

  • How are jobs in Health Promotion classified in other jurisdictions?

    In the Canadian province of Nova Scotia, the job classification of Health Promotion is being downgraded from health care worker to clerical - see http://www.nsgeu.ca/filemanager/pdf/HANSClassificationList.pdf.

    I am looking for evidence to refute this re-classification. Are there any examples of how health promotion is classified elsewhere? Thanks!

    Leah C Stevenson · James Cook University

    Sara, unfortunately majority of health promotion staff were made redundant; a couple hundred.   I am not sure if they have started using the new classification.

    Genevieve, I agree with you that the title for health promotion officers/ specialists is problematic.  Health promotion specialist haven't ever attempted the hold this space as only their own, they don't try to be the keepers of information or try to take complete ownerships of the knowledge compared to other health professions. This profession historically was run by other health professional roles. But I think this skill set has progressed to be recognized as its own title (like any profession).  So I don't think it is straight forward.

    I think we will be comfortable with a title when the profession is recognized for its important work.

  • Alejandro R. Giraudo added an answer in Idrisi:
    What are the most important parameters to be considered when a distribution model is constructed for species groups considered “complex”?

    In the present study a distribution model through Mahalanobis-typicality algorithm in IDRISI Taiga was developed and validated using the area under the curve (AUC). The model showed that the taxa of the complex were associated with the Mexican Plateau´s vegetation, classified as Chihuahuan desert. Mainly xeric scrub and grasslands composed the vegetation, suggesting a factor that limits their distribution in northern and central Mexico, as it happens similar to other groups of reptiles.

    Alejandro R. Giraudo · Instituto Nacional de Limnología (INALI)

    This is a very good question. I think so Aspidocelis is a species complex, and I am modeling the distribution for the entire complex, I am implicitly assuming that the species complex Aspidocelis gularis shows niche conservatism. If there is the possibility that exist within the complex populations/subspecies/ or species that speciation processes or intra-interspecific competition have modified their niches for some,  the results of the models would be biasing the distribution of those populations/subespecies/species that have evolutionarily modified its niche. Therefore it is important to resolve the systematic taxonomists group (if we had more taxonomists studying we would not have so many problems of Linnaean shortfall or lack of data disitribución). It is important to model the best possible taxonomy to avoid what is called in conservation Darwinian shortfall (see Diniz-Filho, JAF, Loyola, RD, Raia, P., Mooers, AO, & Bini, LM (2013). Darwinian shortfalls in biodiversity conservation. Trends in Ecology & Evolution, 28 (12), 689-695).

  • Mengcheng Wang asked a question in Alabama:
    Does anyone can give me some advice regarding psychopathic traits longitudinal investigation?

    Hello everyone, I want to make a longitudinal investigation in a sample of 7-11 years old Chinese children about Psychopathic Traits and Callous-Unemotional Traits and their contextual factor, for example parental behavior. Children’ parents and teachers will be surveyed. I plan use “The Child Problematic Traits Inventory”, a new measure to assess psychopathic personality in children. Meanwhile, Alabama Parenting Questionnaire also will be used. Because I have limited experience in Psychopathic Traits, so I want relevant expert give me some suggestions. If you are interested in this project, maybe we can collaborate in some kind.
    Thanks in advance!

  • Alexander Chepick added an answer in Cosmos:
    What is the resolution of the black hole information paradox?

    -According to quantum theory, information -- whether it describes the velocity of a particle or the precise manner in which ink marks or pixels are arranged on a document -- cannot disappear from the universe. But the physicists Kip Thorne, John Preskill and Stephen Hawking have a standing bet: what would happen if you dropped a copy of the Encyclopaedia Britannica down a black hole? It does not matter whether there are other identical copies elsewhere in the cosmos. As defined in physics, information is not the same as meaning, but simply refers to the binary digits, or some other code, used to precisely describe an object or pattern. So it seems that the information in those particular books would be swallowed up and gone forever. And that is supposed to be impossible. Dr. Hawking and Dr. Thorne believe the information would indeed disappear and that quantum mechanics will just have to deal with it. Dr. Preskill speculates that the information doesn't really vanish: it may be displayed somehow on the surface of the black hole, as on a cosmic movie screen.  (taken from http://www.oglethorpe.edu/faculty/~m_rulison/top10.htm)

    Dear Peter Ouyang,
    No! I don’t think about gauge/gravity duality, about black hole evaporation, about Hawking's original argument.
    I know that Einstein's field equations are not applicable to the Universe.
    R.Hatch tried to show it in his work «Those Scandalous Clocks». He considered quasar signals accepted in opposite points of equator of the Earth in system VLBI. He has come to a conclusion that the signals will be fixed not simultaneously (the delay will make 4.09 microseconds) because of synchronization of clocks according to GR on the twirled Earth. But if this synchronization to make in the Solar frame of reference then moments of arrival of such signals will be equal. Measurings on GPS- satellites do not reveal such effect, hence the Solar frame of reference is not equivalent to the Ground frame of reference. Therefore Hatch has come to a conclusion that the equivalence principle is strictly observed not in local area, and in infinitesimal area. In the such conclusion he is solidary with deductions of such physicists as Michael Friedman [5, p. 202,] in “the Foundations of space-time theories : relativistic physics and philosophy of science”, and Ciufolini, Wheeler [6] in “Gravitation and inertia”.
    But (long before these authors) presence of one more basic restriction of a GR scope was proved by Landau, Lifshits in "Field theories", § 89.
    If we start from some accuracy it appear that in GR it is impossible to synchronise all the clocks on a twirling round (GPS developers later have faced this effect). Hence, the clocks cannot be synchronised on any curved paths, that is, GR is not applicable principally to any curvilinear motions.
    Hence, the more the viewed area or a bend of curvilinear motion of a matter, the larger an error of GR will be in exposition of happening processes. The greatest error will be in the maximal viewed space. These are unshakable theoretical and observational arguments. They demonstrate in limits of GR that Einstein's field equations are not applicable to the all Universe.
    Therefore in the Nature also there are no such consequences from these equations as Black holes and the Universe Expansion.

  • Tausif Alam added an answer in Insulin:
    Which method identification do you prefer to normalize insulin secretion?

    Q1 When comparing islet or INS-1 insulin secretion capacity, it is usually calculated on a per islet basis or normalized to DNA or total protein. What's the difference between them? And which one is preferred?

    Q2 As for GSIS or KSIS, will the released insulin affect the total insulin content?

    Tausif Alam · University of Wisconsin–Madison

    At cellular level, every seemingly simple and obvious event is quite complex. Active processes like regulated secretion involves considerable cytoskeletal action. The question is what is it that you wish to study! 

    The choice of technique depends on what questions do you wish to address. If you are interested in overall performance of insulin secreting cells at macroscopic level (in bulk), doing a sub cellular level analysis will give you the final numbers by summation of all measurements but it will be an unnecessary overkill.

    To illustrate the point, let's assume you goal is to weigh 10gm of NaCl accurately. You can weigh the amount quite accurately in one attempt by adding all the needed crystals or you can weigh one crystal at a time on a microbalance, keep adding them to a vessel until you have reached to the sum of 10gm.

    Some times one cal lose the forest for the trees!  Chose the best method that will answer your question in the simplest and most reliable way. 

  • Adesina Arikawe asked a question in ImageJ:
    Who has specific references on the origin and distribution of beta endorphin fibres in the rats central nervous system?

    I have been trying to analyze beta endorphin fibre density using imageJ in brain sections of locus coureleus and having some technical difficulties.