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- 11Is the Topology of a phylogenetic tree same from different tools?
I am very new to bioinformatics. Here,i am trying to make a phylogeny reconstruction of protein sequences following methods like Maximum likelihood (MEGA 6.0 and GARLI) and Bayesian inference (Mr.bayes). At first, the corresponding protein sequences are collected and aligned using ClustalX. Later, i used gblocks to get a block for the further studies. For ML analysis tree, bootstrap of 1000 replicates was done and for Mr.Bayes, the tree was obtained after 1000000 generations with 2 parallel runs 4 chains (1cold and 3 heat). Indeed, both the methods did use the same substitution model (JTT) and rates (gamma; 6). But still, both the trees looks different and does not have the same topology to each other for the same set of proteins. I really cannot understand it. Please some could advise me to go forward in this work.
Bayesian trees are very often somewhat different fro ML because the search methods and the philosphy of what the final tree should represent is very different.
Bayesian analysis uses MCMC fro the search, which by the definition of Markov Chains mean that the next step in the search through tree space depends the present state. Hence there is necessarily a correlation running though the search and the likelihood scores of each tree that tends to bias upwards the posterior probabilities.
Furthermore the aim of a Maximum Likelihood search is to find the one maximum (highest) likelihood tree. The tree is integrated over tree space alone (conditioned on previously optimized model parameters). The aim of a Bayesian Analysis is to obtain a large sample of trees that maximizes both the model parameters and the tree. The resulting tree is a consensus tree of all of the trees sampled after the burnin. The topology sometimes is similar to the maximum likelihood tree but the Bayes tree is not a maximum likelihood tree. The credibility set usually includes the ML tree but need not include it.
A maximum likelihood tree optimizes the model parameters in a separate step and Bayes optimizes the parameters along with the tree so it is not surprising that both trees and parameter estimates differ.
For a statistician like me trained in maximum likelihood methods, I generally publish the maximum likelihood tree with ML branch lengths because Bayesian branch lengths tend to be quite inflated for various reasons. But I label the branches with the bootstrap and aLRTs (approximate Likelihood Ratio Test statistics) as well as the Bayesian posterior probabilities because the MCMC set of trees provides a genuine confidence statement on branches.
Bottom line do both types of analysis. Recognize that both trees are mere estimates (but generally very good) and that both analyses have their drawbacks and strengths.
Fro Bayesian analyses see recent Z.Yang and others from the last two years or so on choice of priors - very, very important for both topology and branch length estimation.Following
- 17Could anybody suggest how to induce spawning in bivalves?
I´m using thermal shocks but I would like to know if there are more effective options. Thank you.
I'm agree with Dawn. There are the difference about the mechanism of oocytic maturation on bivalve which is gonochorist (I studied with oyster Crassostre gigas) and those of hermaphrodites (as scallop, I studied by using Pecten maximus). So, which species that you work? It define the method that you must used. For gonochorist, temperature, usually works. But not for the hermaphodites (case of Pecten maximus).Please see the abstract of my old works as attached.
Hopely that could help you.
- NewIs it possible to increase the accuracy of low cost GPS with low cost INS?
In INS/GPS, GPS is refrence and goal is to model INS error to enhance stand-alone INS solution but I am looking for a solution to enhance low cost GPS positioning with INS/GPS integration (INS is low cost). is this possible?Following
- 3Has anyone tried to model a social network from a software repository?
I'm trying to model a social network from a software repository, but I haven't found any former investigation about it.
Look up this issue: http://pubsonline.informs.org/toc/mnsc/52/7, there are some interesting ideas in there.Following
- 2How can we define the motion of aircraft by using concept of matrix?
Application of matrix in aircraft maintenance engineering
- 4What is the best management for chondromalacia patella?
Can it cause swelling in the feet and ankles?
There is bilateral chondromalacia patella confirmed by MRI, with pain and inflammation in knees and there is also swelling in the feet and ankles too... since the knee pain started. Blood tests negative for RA and autoimmune disease.
How much does the cortisone injections help to relieve pain in Chondromalacia patella?
Thank you all for the answers. The patient has swelling in ankles and feet especially in the late hours of the day. What could be the reason for this in the absence of any other rheumatological diseases?Following
- 1What is the thermal stress in nanocomposites?
I understand the thermal stress in metals and ceramics, and I want to understand who is the thermal stress in nano composites?
Thermal stress in polymer composites depends on multiple factors. One of the most important is the interfacial adhesion to distribute thermal energy to the matrix with embedded particles or fibres being a conduit for thermal stress distributions.
Other important phase of thermal stress distribution is processing temeprature and cooling rate of the composites; depending on the chemical and physical characteristics of those polymers and fillers, thermal stress can be regulated to achieve the desired result.Following
- 16Any ideas on this material found in a Scottish lochan?
The material in the photos (natural size and enlarged) was found in a small lake. Any ideas on what it might be?
Marc, c'est vraiment proche! J'attends avec impatience l'occasion de vous rencontrer avec un mars bar.
- 1What's the difference between splenic (mouse) dendritic cells and macrophages?
Is there any distinct markers to differentiate macrophages and dendritic cells from mouse spleen?
Seems that most of the answers can be found in this open access article:
Most of the relevant info is in Supplementary Materials.Following
- 1Could anybody tell me how WRF treat clear-sky variables?
In the output of WRF model, clear-sky doesn't mean a clear sky day, which means may have some clouds in the sky. Then my question is how model treat the values at some cloudy grid points. Are the values will be zero. Could anybody give me an example, like SWDOWNC, SWUPTC and so on.
You might try contacting Dr. Keith Brewster, Associate Director of the Center for Analysis & Prediction of Storms (firstname.lastname@example.org). They are the folks who do the modeling for the U.S. National Weather Service. Explain that you were referred by a colleague, and you wonder if he could please direct you to a graduate student or post-doc who could answer your question. Just keep in mind that he is a very busy person, that you appreciate that, and that is why you're asking for a student to help you. Good luck with your modeling.Following
- 13In a 8 hour shift basis, what is the usual schedule? How the week is distributed between working and free days?
I`m a critical care nurse from Chile and we work on a basis of 12 hours shifts called "4ª turno" (fourth shift) which means a 4 day rotation starting with a day shift (8:00 am to 20:00 pm), second day night shift (20:00 pm to 08:00 am of the next day), third day and fourth day are free.
I would like how works the 8 hours shifts because some hospitals in my country are trying to change to this kind of work.
A normal eight hour shift schedule as I have worked them, work M-F work 7-3:30, 3:00-11:30; 11:00-7:30. There are 30 minute overlaps for shift reports. Saturday-Sunday off. The following week you work Monday-Thursday, get off Friday, work Sat-and Sunday, and get Monday off, then work Tuesday-Friday get the week end off etc. On night shift this is dismal because you only get one night off and then have to go back to work again:) Your shifts do not allow time to get acclimated to either days or nights! good luck:)Following
- 2Do you have recent article with literature on pesticide use in rice field in Asia?
The overall scenario of pesticide use in this region and negative consequences of those pesticides in soil, environment, human health and their profitability.
Loganathan, B.G. and Lam, PKS. 2012. Global Contamination Trends of Persistent Organic Chemicals. CRC Press Taylor and Francis Group. Chapters 6 to 12 deal with Persistent Organic Chemicals in the Asia-Pacific Region. All the best!!!Following
- NewHas Turkey a rightful place as EU state-member?
The EU-Turkey summit has just finished and finalized the announced agreement through which the European Union gives 3.2 billions in aid for Turkey to assist the 2.2 million Syrian refugees sheltered in the country and mainly compromises to stem the flow of migrants to Europe. However, much more important for the Turkey prime-minister, Ahmet Davutoglu, was the formal re-opening of the process of negotiations aiming to discuss Turkish full membership of the EU. Needless to say that the summit took place few days after the Turkish destruction of a Russian fighter jet that seems to have violated during 17 seconds Turkey airspace, although without making any remote hostile action. It is not also worth to stress that the European extreme right wing movements immediately started vibrant protests against the perspective of a future Turkish adhesion to the EU, arguing that the almost 80 million Turks are not really “European” and only want to wider the huge number of foreign emigrants living and working in Europe.Following
- 7Does anyone have online academic writing exercises such as quizzes and the like?
I need to provide some practice academic writing exercises for graduate students doing their final research papers. However, I thought I can save time by using what's available, so I am asking if you have such online resources that students can actually do online and receive automatic feedback (e.g., citing in APA, case study terms, etc.).
Thank you so much for sharing these valuable resources that would save me time in not having to create new academic writing exercises.
- NewWhat kind of correlation or regression model we can apply to an unbalanced panel (continuous data only) and no demographic variables?
- Data is inconsistent and lot of missing values. For instance, if I have to analyze 10 companies for certain variables for 10 years, foo some companies I might have data for 2 or 3 years only i.e. the unbalanced panel. Similarly, data is inconsistent in a way that I have data for company abc from year 1 - 3 and then 6-10, couple of years in between are missing.
- I proposed to carry out FEM keeping in view balanced panel, however, it was only during the data collection when I cam across above stated issues.
- There is no random/time variant/demographic variable in study under consideration.
- There is no qualitative variable in our study.
- This is a multivariate model (I hope that's obvious).
- 3How can I compare my experimental coupling efficiency between laser diode to optical fiber with other researchers?
For my experiments I use 405 nm wavelength, 3.6 µm core, NA value 0.12 single-mode fiber and 25 µm, NA value 0.1 multi-mode fiber. My coupling efficiency is 30-40%. But the other researchers use 980 -1550 nm, core diameter 9 µm to 50 µm. they claim their coupling efficiency 60-70 %.
Is it butt coupling? You mentioned a lot of details except what optics you use for coupling.Following
- 5Why is the susceptibility for real superconductors always less than -1?
For an ideal superconductors susceptibility is -1, however, for real superconductors it is always less then -1, why?
When one say Susceptibility=-1, does it mean (emu/cm3)/Oe? or do it need to be multiplied with 4*pi?
How do we determine the superconducting volume fraction? is it right for one to say that the superconducting volume fraction is 50% if for example, for the lowest temperature, FCsusceptibilty = -0.4 and ZFCsusceptibilty = -0.8.
With ceramics, the ac susceptibility can be large in very small fields when there are
screening currents between the superconducting grains (Josephson currents) . It becomes smaller when the applied field is larger, so that the screening is due to the currents of all the individual grains.
So, to evaluate the superconducting fraction of a ceramics sample, it is better to take an ac field as large as 1 gauss or more (not to see the screening through the contacts between grains)
Previous answers are right about demagnetizing factor, and reference to a (Pb, Sn..) spherical superconductor, for calibration.Following
- 3How can I prove that innovation network exist and evaluate it?
If I want to prove that innovation network is exist in Shenzhen High-tech Industry, how can I prove that? Is it possible to prove that without questionnaire survey? And how can I evaluate the strength of the network? Looking forward to your answer.
Look for industry forums/consortia, specialized databases, news announcements.Following
- 1Hello, how many days do T-cells need to be incubated with Ags before a flouresence assay could be carried out to quantify the level of stimulation ?
Just wondering on the optimum number of days advised to incubate T cells with Ags to test for their stimulating potentials before conducting a fluoresence assay to quantify T cell proliferation ?
Being depended on the antigen presenting cell and its activation status you can detect proliferation as early as 48 hours. For 10 min staining at room temp. with 5uM of final CFSE concentration in 0.1% BSA in PBS is optimal for viability of cells and can detect up to 7-8 cycles with that after 96h.Following
- 12How to measure fungal growth rate during growth on insoluble carbon/nitrogen sources?
What is/are the best method/s to measure fungal growth rate during growth on insoluble carbon or nitrogen sources, such as cellulose/straw, oil cakes etc. during submerged fermentation in shake flask or fermenter. I am interested in knowing the direct methods for growth/growth rate measurements.
I am lichenologist!Following
- 1Can anybody guide me how Laplace Transform becomes applicable to antenna analysis?Laplace Transform in Antenna Analysis.
Treating antenna as a circuit element gives us circuit a model of antenna. Then, what ideas we would get if we use Laplace transform for analysing it?
I think your solution in following book of chapter2.1 of rigid antenna model
Modeling and Control of Antennas and Telescopes
By Wodek GawronskiFollowing
- NewHow to calculate IC 50 value of extract and standard using DPPH assay?
HOW TO CALCULATE IC50 VALUEFollowing
- 7Student T-test versus Wilcoxon rank-sum?
I would like to compare the vessels density between to samples (control versus treatment, so 2 groups) of healed skin wounds, based on histological analysis. In each group I have 30 measurement data. At the beginning I was thinking about a simple Student t-test, but I have also found other papers using the Mann-Whitney (=Wilcoxon rank-sum test). Any idea about what is the most suitable?
All references said that the distribution of your data will determine the statistical procedure , so you must determine the distribution of your data ( normal distribution or others ) , in case of normal distribution T test effective test and I expect that 30 observations good number and may be normally distributed .
- 9What is the difference between scenario earthquake and characteristic earthquake for a given active fault?
I know the characteristic earthquake model and scenario earthquake model, but I am confused by their magnitude calculation. Some relationships, like Wells and Coppersmith (1994) and Hanks and Bakun (2008), are used to calculate the magnitude of future earthquake, e.g. scenario earthquake. For the fault or segment that have never occurred large earthquake, is the magnitude of scenario earthquake equal to that of characteristic earthquake?
A "characteristic" magnitude as used in a probabilistic seismic hazard analysis need not, even often should not, be explicitly defined by a single magnitude. A PSHA should include a consideration of the uncertainty of even a best estimate of the characteristic. For example, Wells and Coppersmith evaluations include a "sigma" that is one measure of that uncertainty. A more robust consideration whould be a Bayesian or Kijko approach to determine maximum magnitude distribution.
A "scenario" event may not even be associated with a characteristic magnitude, which is usually considered a measure of the largest event for a given fault source. Some smaller magnitude event may occur more frequently than the characteristic [See Youngs and Coppersmith (1985)]. There may be a near-term engineering reason [e.g., earthquake hazard during construction] that may suggest looking at the ground motion impact of, say, a magnitude 6 event, much smaller than a given source is capable, more more likely to occur in the near-term.
Finally, if your scenario event were intended to be your [best estimate, mean, etc.] characteristic event, then you may want to consider specific event characteristics that are not often considered in a PSHA. For example, if you are near to the active fault of interest, you may want to consider scenarios where the fault rupture is either toward or away from your site [directivity]. You may also want to consider in those cases the ground motions associated with fault parallel or fault normal. If there is any ambiguity with the rupture characteristics of your fault, your scenario could consider strike-slip, reverse, normal, or some oblique combination.Following
- 1Is it possible to have one species of mushroom grow on a spent substrate of another species?
For instance a Volvariella volvacea fruiting body growing on spent P. tuber -regium substrate without inoculating the spent substrate of P. tuber regium with V. volvacea.
It is possible! After discarding, spent substrate is usually piled up when the temperature in the pile raise to kill all mycelia of Pleurotus. Straw mushroom spores from the air drop at the compost accidently then germinate ... High temperature of the compost pile is also very suitable condition for the development of Volvariella volvaceaFollowing
- 5How has colonialism affected institutional development and its impacts on economic and political development?
Any literature suggestions,,,Thanking in advance
You would appreciate colonialism when you read Postcolonialism. There are a number of authors whom you can google. I recommend, Edward Said, Ranajit Guha and Gayatri Chakrovoethi.
- NewIs acidification of a sample absolutely nesserary to prevent adsorption of Na+ on polypropylene sample tubes before AAS analysis?
When I acidify my samples precipitates form (probably humic acids in one case and sodium alginate in the other case). I have been able to solubilize humic acids by dilution, but have not been able to do so for sodium alginate (so far). In the original experimental protocol there is no acidification step, but my laboratory technician suggested it might be important to acidifiy samples prior to analysis, in order to prevent adsorption of Na+ on sample tube. Is there a reference that states whether sample acidification is necessary and, if not, if there is a delay to respect for the analysis of non-acidified samples? thank youFollowing
- NewCan somebody tell about calculation of FRAP assay of plant extract......?
i have prepare linear curve of 2.5micrmolar FeSO4 to 20 micrmolar FeSO4...also i have taken absorance of standard Ascobric acid and my extract at different concentration ....Then how to calculate FRAP activity?Following
- 3How can I study the earth revolving around the sun computationally?
The electron revolves around the nucleus of an atom with an electrostatic force of attraction and the earth revolves around the sun with a gravitational force of attraction between the two. can the earth and the sun be simulated?? and how?
any advise please?
You could use a numerical approximation, such as a Runge Kutta method, to solve the equations of motion for the two-body system (sun and earth). But you don't really need to since Isaac Newton solved them analytically. See https://en.wikipedia.org/wiki/Gravitational_two-body_problem, for example.
If you want to include other planets in your simulation, things get much more interesting. I recently came upon this old paper on the n-body problem which gives a great summary: http://www.math.uvic.ca/faculty/diacu/diacuNbody.pdf.Following
- 2Do you prefer embolization than surgical removal or stenting than surgical removal for carotid body tumor?
Or do you have any other thecnique to share?
We do not utilise embolization for carotid body tumors even preoperatively. I excise the Cervical benign paragangliomas usually without using carotid shunts. High altitude areas ( e.g.Kasmir) have high incidence of paragangliomas, so we operate many CBT patients. In our experience only 10% pts. with large tumors engulfing the internal carotid artery need intraoperative shunts.
Malignant tumors if large usually need intra operative carotid shunts and may need sacrificing the ECA(safe) and internal carotid artery bypass grafting for radical excision of the tumor, as there is little role of radiotherapy or chemotherapy .Following