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  • Hellen Chaya Greenblatt added an answer in Thyroiditis:
    Why are autoimmune diseases more common in female than male ?

    It is said that autoimmune diseases are about 90% more common in female than male. E.g, female:male ratios in Autoimmune Diseases:  Hashimoto's thyroiditis 10:1, Systemic lupus erythematosus 9:1,Sjogren's syndrome 9:1, Antiphospholipid syndrome-secondary 9:1 etc. What is the actual reason behind it?

    Hellen Chaya Greenblatt

    I have always thought that the fact that the female must not reject the fetus (which is partly foreign) contributes significantly to  increased autoimmunity in females. Perhaps the factors that inhibit rejection, "encourage" pathways that permit autoimmune responses.

  • Ali Ahmadi Peyghan added an answer in Density Functional Theory:
    Any suggestion why in a geom opt DFT calc for a Cu(I)-complex the geom converges but the freq not, but when substituting phenyl with H freq converges?

    I am performing a geom freq DFT calculation with the G03 package on different heteroleptic Cu(I)-complexes with one Bis[(2-diphenylphosphino)phenyl] ether (DPEPhos) ligand and varying second ligand, phenathroline, pyridine and similar ligands. The geometry optimization always converges but the frequency calculation at the optimized geometry gives only convergence for the forces not the displacement. I get NO imaginary frequencies and running a geom opt with the calcall command on the structure of the previous opt freq calculation gives also no convergence for the frequency. However, when I substitute the four pheynl groups at the DPEPhos ligand with H atoms, I get convergence also in the frequency calculation (see attached structures). I don't understand what the problem with the phenyl groups is and what to do in order to achieve convergence in the freq calculation for the compounds?

    The input for the compounds is:

    #P B3LYP/LANL2DZ Opt Freq=NoRaman gfoldprint pop=full formcheck

    CuphenPOP LANL2DZ Molekel

    1 1

     I perform and opt freq calc and then at the optimized geometry using the checkpoint file from the opt freq calculation a calcall calculation:

    #P B3LYP/LANL2DZ Opt=CalcAll Freq=NoRaman Geom=AllCheck Guess=Read gfoldprint pop=full formcheck

    With the phenyl groups I get this output after the freq calculation:

    Low frequencies --- -6.0179 -2.2307 0.0005 0.0009 0.0010 3.7862
    Low frequencies --- 7.8641 11.7632 15.4691
    Diagonal vibrational polarizability:
    124.3077904 52.8075211 113.8823113
    Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
    activities (A**4/AMU), depolarization ratios for plane and unpolarized
    incident light, reduced masses (AMU), force constants (mDyne/A),
    and normal coordinates:
    1 2 3
    A A A
    Frequencies -- 7.3431 11.2067 15.3067
    Red. masses -- 5.9950 5.2088 6.0434
    Frc consts -- 0.0002 0.0004 0.0008
    IR Inten -- 0.1901 0.0183 0.4275

    Item Value Threshold Converged?
    Maximum Force 0.000361 0.000450 YES
    RMS Force 0.000057 0.000300 YES
    Maximum Displacement 0.316848 0.001800 NO
    RMS Displacement 0.060707 0.001200 NO
    Predicted change in Energy=-8.661564D-05

    and with phenyl substituted by H:

    Rotating derivatives to standard orientation.
    Dipole = 1.51776480D+00 1.56759125D-01 4.17815692D-01
    Polarizability= 4.02814584D+02-1.31586962D+01 3.68441420D+02
    8.69063669D+00-3.81612415D+01 2.36612166D+02
    Full mass-weighted force constant matrix:
    Low frequencies --- -6.8423 -0.6698 -0.0006 -0.0003 0.0004 2.6307
    Low frequencies --- 10.0913 18.0893 21.7442
    Diagonal vibrational polarizability:
    58.7865711 38.2904911 54.5692058
    Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
    activities (A**4/AMU), depolarization ratios for plane and unpolarized
    incident light, reduced masses (AMU), force constants (mDyne/A),
    and normal coordinates:

    Item Value Threshold Converged?
    Maximum Force 0.000001 0.000450 YES
    RMS Force 0.000000 0.000300 YES
    Maximum Displacement 0.000433 0.001800 YES
    RMS Displacement 0.000110 0.001200 YES
    Predicted change in Energy=-2.290532D-10
    Optimization completed.
    -- Stationary point found.

    I used also different basis sets:

    b) #P B3LYP/GEN PSEUDO=READ Opt Freq=NoRaman gfoldprint pop=full formcheck 

    P O N C H 0
    Cu 0

    Cu 0

    c) #P B3LYP/GEN PSEUDO=READ Opt Freq=NoRaman gfoldprint pop=full formcheck

    P O N C H 0
    Cu 0

    Cu 0

    and the same result, so I am assuming it is not a problem with the basis set.

    Any suggestions would be highly appreciated.

    Thank you!

    + 1 more attachment

    Ali Ahmadi Peyghan

    It seems that the origin of this error is your computer performance! replacing phenyl groups with H atoms makes the molecule smaller, therefore the freq calculation is converged.

  • Ahmed Guerine added an answer in Suspension Systems:
    How can I scale a dynamic system?

    Dear all,

    I have to do an experimental work which should contain a scale model for active suspension system. Is there any one can advise me about the sequence that I should follow in the experimental work to make the active suspension system scale model mimic the real active suspension which I have its dynamic response. Thanks in advance

    Ahmed Guerine


    I advice you to see these documents. You will find what you need.

    Best regards

    + 1 more attachment

  • Daniel M Cohen added an answer in Plasmid Cloning:
    Why does our diagnostic double digest of pGL4.27 plasmid yield bands that are longer than expected?

    We performed an overnight double digest of pGL4.27 plasmid using XhoI and BamHI in a 37oC water bath. After running the digest on a gel along with a 2log ladder, we observed two bands: one around 2400bp and another around 4100bp. The pGL4.27 is a 6010bp plasmid and the expected bands for this digest are 3855bp and 2155bp. What could be the reasons for this? Thank you.

    Daniel M Cohen

    Agree with Michael. Either it already has an insert in the MCS, or is misidentified.

  • Alastair Bain McDonald added an answer in Climate Variability:
    Where can I get climate variables for the Younger Dryas period (circa 14.000 years BP)?

    In my study I am trying to verify whether there have been climate refugia for a species. Unfortunately, publicly available databases only have data for the Last Glacial Maximum (circa 21kya), the Holocene (circa 6kya) present and future. Considering that the Younger Dryas were a period of forest (vegetation) contraction and this could influence the distribution of my targeted species, I think it would be important to include it in my study. Unfortunately, I can't find climate variables for this period. Can anyone provide any suggestion?

    Thanks in advance!

    Alastair Bain McDonald


    You are quite right. I had missed that. They prefer an alternative scenario. But the point I am making is that it was not the warm summers which caused the YD to end abruptly. The mini ice sheet in Scotland had disappeared 500 years before the end of the YD, and during those years presumably the warm summers continued.


    The following papers also argue for warm summers during the YD

    Björck S, et al. Anomalously mild Younger Dryas summer conditions in southern Greenland. Geology. 2002;30(5):427–430.

    Ballantyne CK. The Loch Lomond Readvance on the Isle of Mull, Scotland: Glacier reconstruction and palaeoclimatic implications. Jour. Quat. Sci. 2002;17(8):759–771

    Benn DI, Lukas S. Younger Dryas glacial landsystems in western Scotland: Possible modern analogues and palaeoclimatic implications. Quat Sci Rev. 2006;25(17-18):2390–2408.

  • Chris Turner added an answer in Grammar:
    Which broad areas of grammar or specific grammar points do you think are poorly described in grammar books?

    I'm thinking of both pedagogical grammar books such as "English Grammar in Use" and more academic, descriptive  grammars such as "The Longman Grammar of Written and Spoken English". I'm interested both in broad areas-such as spoken language or the noun phrase-and specific grammar points, such as the future continuous or the passive.

    Chris Turner

    Thank you for your answer. Originally, I was thnking more of specific grammar points rather than larger areas, but you are quite right to consider broader areas of grammar as well. I have changed my question accordingly.

  • Sheeraz Ali added an answer in Discourse Analysis:
    How do I teach text and critical discourse in an EFL academic context?

    Dear All,

    I have viewed articles, books, and research papers on crtical discourse analysis. This is an interesting area of language teaching but how to teach critical discourse is somewhat practical. Therefore, researchers are requested to send Teaching activities for the practice teaching critical discourse. 

    Sheeraz Ali

     Dear Arif Jawaid and Sajjad Kabgani'

    Thanks to you for making things more clear. Yes Sajjad, you are right and i agree with your point of view. There are countless research papers, and articles on the issue of Critical Discourse Analysis but the issue is after all addressed by a teacher in his classroom context.

  • Jan Holmgren added an answer in Cognitive Systems:
    Is Chalmers' so-called "hard problem" in consciousness real?

    In his 2014 book "Consciousness and the Brain: Deciphering How the Brain Codes Our Thoughts" Stanislas Dehaene wrote "Chalmers, a philosopher of the University of Arizona, is famous for introducing a distinction between the easy and the hard problems. The easy problem of consciousness, he argues, consists in explaining the many functions of the brain: how do we recognize a face, a word, or a landscape? How do we extract information form the senses and use it to guide our behavior? How do we generate sentences to describe what we feel?

    “Although all these questions are associated with consciousness,” Chalmers argues, “they all concern the objective mechanisms of the cognitive system, and consequently, we have every reason to expect that continued work in cognitive psychology and neuroscience will answer them. By contrast the hard problem is the “question of how physical processes in the brain give rise to subjective experience … the way things feel for the subject. When we see for example, we experience visual sensations, such as that of vivid blue. Or think of the ineffable sound of a distant oboe, the agony of an intense pain, the sparkle of happiness or the meditative quality of a moment lost in thought … It is these phenomena that poses the real mystery of the mind”."

    Stanislas Dehaene's opinion is "that Chalmers swapped the labels: it is the “easy” problem that is hard, while the “hard” problem just seems hard because it engages ill-defined intuitions. Once our intuition is educated by cognitive neuroscience and computer simulations, Chalmers’ “hard problem” will evaporate".

    Personally, I agree with Stanislas Dehaene's opinion.

    Jan Holmgren

    Bernd: “But in addition I see the fundamental property of the process of nature that whatever system we have constructed, even "commensurate with the laws of nature”, we always pass by the most fundamental law by which nature stultifies our audience, namely that a single step of its ‘time type processor’, as you call it, can violate the systems law, that is, it transcends the system altogether. Erkki, this is, where nature is realizing Kurt Gödel’s insight in a general way.”

    Jan: Agreed, for the reason that our insights are limited because natural evolution gave us instruments for survival and successful reproduction, not for a complete grasp of the continuous universe. Probably it is not nature that realizes, but we humans. In a paper on detectism (as I called my view in1999, attached) I referred to J.W. Carroll (1994) A new theory of the relationship of mind and matter. I wrote: “Thanks to Carroll's careful analysis, I now feel confident in suggesting the following statement: (I) Humans have access to just one kind of entities, conscious experiences, which are immediately given. / Since humans have a special construction, which in principle can change in unforeseeable ways in evolutionary time, this statement should not be considered a law of nature. The statement is an accidentally true proposition, but in effect we are at present restrained by it as if it was a law of nature.”

  • Juan Antonio Baeza added an answer in Microbial Biofilms:
    Would a biofilm on anode of a microbial fuel cell impede transfer of electrons from microbes in the anolyte?

    As the microbial biofilm develops, would it not block access of the anode to other microbes that are suspended in the anolyte?

    Juan Antonio Baeza

    Geobacter in bioelectrochemical systems grow mainly attached to the anode. Planktonic growth of Geobacter is usually orders of magnitude lower than as biofilm. Geobacter growing as suspended biomass in the anolyte does not have good conditions to release the electrons that could be accumulated due to the metabolism. If the biofilm is thicker, the conditions for releasing electrons would be worst, unless you consider that the biofilm is conductive due to the presence of nanowires.

  • Chithan C Kandaswami added an answer in Tea:
    Is there cellulose in tea?

    I have had a look at my tea this morning. Does anyone know if Tea (Rooibos for example) contains cellulose?

    Chithan C Kandaswami

    Dear Andile,

    Here is a link to an IARC monograph.


    Cellulose constitutes 7% of the dry weight in fresh tea lea (var. assamica).


  • Alexandre Ataide Da Silva added an answer in LC-MS:
    As can proceed to the analysis of pharmaceuticals submit NaOH, HCl and Fe +2 and H2O2 by LC-MS?

    As can proceed to the analysis of pharmaceuticals submit NaOH, HCl and Fe +2 and H2O2 by LC-MS? I need analize degradation products in pharmaceuticals by LC-MS. lc-ms it is compatible with these agents?

    Alexandre Ataide Da Silva

    Thank you Mr Khedr. Thank you Mr Khedr.
    Do you belive that de products generated by forced degradation are stable after neutralization?

    best regard

  • Charles Berg added an answer in Intercultural Communication:
    Are there any scholarly articles on the subject of international communication? Does anyone know some newest articles?

    international communication

    international connections

    or intercultural communication.

    thank you in advance

    Charles Berg

    Look into the writings of John Galtung.

  • Hira Usman added an answer in Soda Ash:
    How can CaCl2 be recovered from the waste stream of the Solvay process?

    With a number of uses of CaCl2, it's recovery from Solvay's process would be beneficial for the industry. Also, how feasible is this recovery?

    Hira Usman

  • Ahmed Guerine added an answer in Simulink:
    How can I properly simulate self-excited induction generator using MATLAB Simulink?

    I have tried using the induction machine model with capacitor connected parallel. I have changed the initial condition of the induction machine to have little current to act as residual magnetism so it can self excite. So far I can only use constant negative torque as input to make it operate. How do I make the input in rpm?
    Even I used negative torque, the voltage seems wrong as it can rise to over 1kV or 2kV. At no load, the voltage can rise to 3kV or more. A 400V induction generator shouldn't have that high voltage right?
    Should I specify the magnetic saturation?

    Ahmed Guerine


    I advice you to see these documents. You will find what you need.

    Best regards

    + 1 more attachment

  • Martin A Thomas added an answer in Bulk Density:
    Is it acceptable to measure the bulk density of a ceramic powder using D = m/v?

    Hi everyone,

    I need to calculate the Hausner Ratio of my samples. My limitation is such that I don't have much powder for each sample (approx 5cm3), I have been able to get a Tapped Density Tester with a cylinder of 5 ml but how can I measure the bulk density of the samples with such a small quantity?

    Would it work if I use a graduated cylinder and weigh the powder?

    Any suggestions will be greatly appraised.

    With thanks,


    Martin A Thomas

    To determine Hausner ratio you need to measure BULK density (from the volume of particles PLUS voids) in two conditions as Peter identified.  The first, the unsettled/loose volume (density) can be done in the small measuring cylinder... indeed no worse than the second condition... the settled/tapped volume(density) in the same small cylinder.  

    The greater uncertainty is always in the starting (untapped) volume since that volume will change relatively rapidly even with just a few taps. You can tap for hundreds/thousands /tens of thousands and the end point won't change. The starting volume is always user dependent and often poorly repeatable because of different "fluffed" starting state, roughness of handling the cylinder when filling and mounting on device.  

    It is for this reason many workers use a Scott volumeter to obtain the lowest practically achievable loose density. Easy enough to find details on the web, but with such small amount of material you would need to use a custom-fabricated receiving cup.

    You might also like to determine not just a single Hausner ratio from just two numbers (start and finish), but to measure tapped volume as a function of number of taps (use a geometric progression e.g. 1,2,5,10,20,50 etc) then apply the Kawakita equation. Let me know if you have trouble tracking it down.

  • Daniel William Hutchins added an answer in Culture Cells:
    Why do primary liver cells isolated from porcine not attaching to the plate?

    I isolated primary liver cells from porcine by two step collagenase method. I am using RPMI 1640 medium for culturing the cells on collagen coated plates (collagen coating is done by myself). The cells are not attaching even it is 10 to 14 days old, but they are viable and forming clusters. Please suggest me any method to have cell attachment

    Daniel William Hutchins

    Depending on what you want to do with the cells, you could try using Matrigel or a similar product. I found it to be very good for rat and human hepatocytes.

  • Ryan Trexler asked a question in Humic Acid:
    References citing adsorption of phospholipids or fatty acids to kerogen and/or humic acids?

    Does anyone know of any publications that have looked at the adsorption of phospholipids/fatty acids to either kerogen or humic acids?

  • Gerry A Quinn added an answer in Extracellular Polymeric Substances:
    Which procedure is effective in Extracellular Polymeric Substances extraction from marine biofilm forming bacteria?

    Dear Researchers.

    There are many procedures for Extracellular polymers extraction. Such as 2% EDTA, 3% NaCl, 0.5N HCl, 0.5N NaOH, Ultrasonication and Heating.

    Gerry A Quinn

    Comparison of extraction methods for quantifying extracellular polymers in biofilms

    Xiaoqi Zhang*, Paul L. Bishop*, Brian K. Kinkle**


  • Ahmed Guerine added an answer in Reservoir Operation:
    What is the method to find loss function in a hedging rule?

    I'm working on reservoir operation releasing policy by hedging rule and i'm unable to find loss function.please suggest me what is the procedure to find loss function

    Ahmed Guerine


    I advice you to see this document. You will find what you need.

    Best regards

  • Gerry A Quinn asked a question in FASTA:
    Recommenations please for pipelines/programes to build soil proteomic databases ?

    I am trying to identify proteins from soil using mass spectrometry with a soil protein database. Are there any good pipelines out there that can take protein fasta files, assemble/join them all together in one large file, remove duplicate sequences and then add a unique identifier to each protein sequence. I am also currently trying to write a code for this in python .

  • Robin Hartley added an answer in Image Processing:
    How can I match or correct World Geodetic System WGS 84 level and Mean Sea Level (MSL)?

    Any one who is working on image processing 

    Robin Hartley

    Follow up to my last reply. The British Ordinance survey group, http://www.ordnancesurvey.co.uk, use the Airy ellipsoid model to propagate MSL from the Newlyn Datum. They have their own transformation model (OSGN02) to transform between Airy & WSG84. This is only applicable to the Newlyn Datum. I assume other countries will have similar transforms for their datums

  • Stephanie Thomas added an answer in RNA Extraction:
    What is the best way to separate sperm for RNA extraction? Does anybody uses RNA later in the samples?

    Hi! I am testing different methods of semen purification, and I would like to know what the best method for isolating sperm cells for RNA extraction. Is it recommended adding RNA later in the samples? At what stage? Thanks!

    Stephanie Thomas

    I used Isolate (similar to percoll) to separate semen into mature and immature spermatozoa. However, if you need all spermatozoa independent of maturation status, you can centrifuge semen and then wash the pellet with cell culture medium to get rid of the seminal plasma. As the semen sample is not divided by its density, different cells (not only spermatozoa) will be located in the pellet.

    For RNA isolation use Trizol or TriFast according to the manufacturer. You can store the sperm pellet or the trizol lysed sample at -80 C for at least a month.

  • Stephen Opot asked a question in Anammox:
    Anyone with Fluorescence In Situ Hybridization (FISH) protocol for Anaerobic Ammonia Oxidizing (Anammox) culture?

    I need to ascertain anammox bacteria, in addition to monitoring the activities, in my reactor. From reported studies, FISH technique seems to be very popular.  

  • Saleh Alkarim added an answer in Embryos:
    Why is my Ciona in situ staining very slowly and how can I speed it up?

    I'm finding my Ciona embryos for in situ are staining very slowly; I am seeing obvious specific staining in the controls but the candidate genes stay too light. I have left for 3 days, then kept it overnight at 37 degrees to speed it up; slight improvement but still no background and no indication of pH change in the staining solution.

    I should really be seeing background by now and I believe the slow reaction is limiting my signal strength. How can I fix this?

    Saleh Alkarim


    Yes , try with new solutions may help you 

    look at some protocol here , hope help you 

    Good Luck 

    + 2 more attachments

  • Hamdan Zaki Hamdan added an answer in 3D:
    Is there any software that can predict the effect of the SNPs in the 3D of the protein?

    I would like to study certain SNPs which is coding and change the amnio acids, so I need to know whether this SNP affect the protein 3D or not

    Hamdan Zaki Hamdan

    Thank you Tobias for your help 

  • Ahmed Guerine added an answer in Sliding Mode Control:
    What is difference between matched and unmatched uncertainty in SMC ?

    Sliding Mode control

    Ahmed Guerine


    I advice you to see these documents. You will find what you need.

    Best regards

    + 1 more attachment

  • Josef Punčochář added an answer in Voltage Divider:
    How do I get Vgs equation for MOSFET small signal equivalent model ?

    In attachment, I have shown two Small Signal Equivalent Models of MOSFET for finding out Vgs.
    In First Small Signal Equivalent Model of MOSFET, I have found out Vgs = Vg= (Vin R1//R2)/(Rg+R1//R2), because R1//R2 parallel with the Vin and Rg. Using Voltage divider, I found Vgs=Vg=(Vin R1//R2)/(Rg+R1//R2).

    In Second Small Signal Equivalent Model of MOSFET shown in the attachment, I need to find out Vgs. In the Second Small Signal Equivalent Model of MOSFET shown in the attachment, I have removed the R1//R2 for my own circuit. What is the Vgs equation for the Second Small Signal Equivalent Model of MOSFET, when R1//R2 is not Parallel with the Vin and Rg (source generator resistance).

    Can you help me to find out Vgs equation for Second Small Equivalent Circuit shown in the attachment, when R1// R2 are not present in the SSM of MOSFET.

    Josef Punčochář

    And the next thing you have to yourself. Perhaps with the help of a  mathematician.


  • Sunday. Ndubueze Ukachukwu added an answer in Broilers:
    What could be the cause for sudden death for broilers?

    What are the possible causes for layer birds refuse eating and become paralysed and then die? What could be the possible poissoning agent ? If post mortem give no evedence for  symptoms of any known disease.  

    Sunday. Ndubueze Ukachukwu

    From personal experience, heat stress is a mostly likely cause especially when there is restricted air movement. this is especially true in the hot humid tropics.

  • Yusuke Tamura added an answer in Solvent Effect:
    How effective are the optimization (and sadpoint) searchs with solvent effects to give good results compared to the vacuum models?

    Hello there noble science people...

    i am doing equilibrium geometries and saddle point searchs in gaseous phases. but the experiments in which the mechanism were based, used polar solvent and the substances involved were charged particles (although closed shell species).

    does this mean i have to emulate these solvent effects for better elucidation and results ? or it'll just make calculation more expensive with little positive gain.

    if so,,, is the PCM compatible with geometry and sadsearch? or is there any other alternative approach?

    Thank you all. Live long and prosper. 

    Yusuke Tamura

    If you are using GAMESS current version of Dec 5, 2014, SMD is available in it. Refer the documents, INPUT.DOC (section2. Input Description) and REFS.DOC (section 4. Further Information on GAMESS document page).

    I'm not sure whether GAMESS works as same as G09. I'm afraid you have done TS search with PCM in only one shot. The example 'Fluorescence example' given in the page 'http://www.gaussian.com/g_tech/g_ur/k_scrf.htm' shows a multistep procedure.
    Let M(GS) and C(GS) be the energy of solute and the cavity energy, respectively. Geometry optimization for searching M(TS) starts, but C(GS) keeps unchanged. Then optimization of C(TS) is needed until SCF is achieved for both M(TS) and C(TS).?

  • Jonathan Edwards added an answer in Proteoglycans:
    Do the positive ions in cartilage have a negative effect on its compression load?

    We know that one of the effective things on compression load in cartilage is due to the repulsion of negative ions which are on the Proteoglycans, but on the other hand the cartilage is inactive due to the positive ions.

    Does the positive ions cause any disorders on this work of Proteoglycans? How?

    Jonathan Edwards

    Sorry, that should have been cations in the last line but one.