Q&A

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  • What are the best choices for the cell culture to study Alzheimer's disease?

    I plan to investigate the implications of a compound in Alzheimer's disease and conduct some pharmacological tests.
    What is the cell line(s) you suggest me to use?

    Sandra Antonieta Acosta · University of South Florida

    I agree with Kai Lun Chang.

    thanks

  • Imre Tóth added an answer in Kinetic Modeling
    What does the kinetic model for the oxidation of atmospheric so2 entail?

    what is

    the kinetic model for the oxidation of atmospheric so2 ?

    Imre Tóth · University of Pannonia, Veszprém

    You haven't specified which catalyst system (and what oxidant) you are interested in. For the commercially used vanadium catalysts with air as oxidant see for example DOI: 10.1021/i260044a020 or http://eportfolio.lib.ksu.edu.tw/~T093000207/repository/fetch/(6)Oxidation%20of%20sulfur%20dioxide%20to%20sulfur%20trioxide%20over%20supported%20vanadium%20catalyst.pdf. A lot more information is available on the net for this and for another systems.

  • Tomek Stępniewski added an answer in Docking
    Protein preparation for Docking purpose: Do I need to remove all non standard residues from protein structure?

    I want to dock protein with chemical and I am using Auto Dock Vina. I am confused, do I need to remove all non standard residues like ligand, phosphate group, sulphate group, etc.

    Tomek Stępniewski · Nencki Institute of Experimental Biology

    You have to remove the ligand, and sulphate groups, in some docking systems it's better to leave the water and phosphate groups (they may be involved in binding)

  • When should we reopen a patient after cardiac surgery in ICU?

    the indication is cardiac arrest usually or tamponade which is not giving us time enough to shift the patient back to theater. but when exactly should we say lets re-open the patient and stop defibrillating etc any more.? 

  • Lingaraj Behera asked a question in Coastal Sciences
    Is any one work on Coastal Science and Human Habitat on Coastal Zone Management in India.

    I try to assess the Socio-economic relationship with coastal sciences for better prediction and management of coastal zone. 

  • How to break the cells of mixed microalgae for protein, lipid and carbohydrate analysis?

    I have to analyse protein (Bradford method), lipid (Chloroform: Methanol method) and carbohydrate in freeze dried mixed microalgae sample. As I know the microwave digestion is the best method to breakdown the microalgal cells. But, we don't have this facility in our lab. Can anyone suggest the suitable method to break the cells?..

    Jorge Varejao · Instituto Politécnico de Coimbra

    You may try a an ultrasound bath to disrupt cell walls. But add 1-2% of wash detergent to the bath and try to visualize ultrasound power in the bath with aluminium kitchen foil, in two ortogonal directions. Use also glass vessel to contain yours cells when in the bath.

  • In Postgraduate studies full time VS part time any difference in the outcome and quality?

    does part time studies produce less quality

    András Bozsik · University of Debrecen

    Dear All,


    According to my experiences, generally when the studying opportunities (teaching hours, assignments etc.) are decreased the quality of the future degree holders decreases. However, it is a complicated question because studying moral of students generally decreased heavily compared with the situation say 20 years ago. There are too big differences among the abilities, diligence and possibilities of students. Unfortunately, for many students not the knowledge but the paper (the degree) matters. Some teaching institutions do not make efforts to increase the standard even on the contrary.

  • Extraction of RNA from Agarose Gel Electrophoresis

    Can anyone suggest me a standard procedure for the extraction of RNA from Agarose Gel Electrophoresis.

    Khaled Said Ali · Aden University

    Hi, dear

    cut your RNA bands from agarose gel and put it into sterile tube, then keep it in freeze (- 20 degree ) for 3-4 hours. After that destroying the cutting bands by pipette at room temperature. put the fluid phase into another sterile tube and centrifuge it. 

  • Yuelin Wu asked a question in Anodization
    Why do we have to make the cathode area and anode area equal when measuring galvanic current using ZRA

    Why do we have to make the cathode area and anode area equal when measuring galvanic current using zero resistance ammeter?  We can still measure the current density of the cathode and anode by dividing the current by area.

  • Rosa Serra added an answer in Western Blot
    Which is the best and more sensitive western blot imaging system?
    Our institute is planning to buy a documentation system, and I would like to ask for some advice about that. We are mainly interested in a system that provides the best sensitivity (at least same as film) and reliability. I am not sure whether we should choose chemiluminescence, multifluorescence or both. So, here are some options that we are considering (please, let me know if you have something better):

    1. odissey CLX (from Licor)
    2. Typhoon 7000 (GE)
    3. Amershan 600 RGB (GE)
    4. Fluorchem M (protein simple)
    5. Chemidoc MP (BioRad)

    Any suggestion, pros, cons?

    Thanks in advance for your help.
    Rosa Serra · University of Alabama at Birmingham

    We use both LiCOr and the BIorad system. I think the Biorad system is more versatile and I haven't noticed any difference in sensitivity between it and the LiCor. IF I could only have one I would take the Biorad Chemidoc.

  • Stephen P Holly added an answer in Imines
    Can anyone suggest the most effective protocol for SiRNA transfection?

    I would like to know the optimum confluency of cells at the time of transfection. I have seen some protocols that suggest 30-50%  and some 50-80%. So, I am confused about the confluency to start the experiment. I am using SKOV3 cell line.

    Please correct me if I am wrong, if I am increasing the concentration of siRNA  accordingly I should also increase the concentration of my transfection reagent. But the transfection reagents are so expensive, so I am planning to try using Polyethylene imine as transfection reagent. Has anyone used PEI for transfecting siRNA?

    Stephen P Holly · University of North Carolina at Chapel Hill

    I have used Dharmafect I successfully in megakaryocytic cells. I highly recommend it for use with naked siRNA. To keep costs down, you can use the same concentration of Dharmafect for a narrow range of siRNA. For example, I used 5 microliters for both 50 and 100 nM siRNA. Good luck, Steve

  • What is the fastest way to hash (md5) large files?

    Cryptographic hashing is used in many areas regarding computer forensics. The increase of disk sizes makes hashing a lot of files take a longer time. Using recursive tools like md5deep makes the process simpler but faster?

    Timur Kaan Gunduz · Council of Forensic Medicine (ATK)

    I had to use encrypted disks because of security concerns. I chose truecrypt (although it is deprecated) because it' supported on linux and windows platforms. I used AES encryption which was the simplest one i could choose.

    I'm not sure if truecrypt keeps the hashes. I didn't see any hash values anywhere in the disk.

  • How can you define the past, the present and the future of the welfare state?

    Many believe that the welfare state is the phenomena of the past history in the West and that globalization and liberalism during the last 30 years have tremendously changed the world. This is one of the reasons why developing countries are cautious about wide and deep implementation of such welfare elements as state social security measures. What is your view about the present and future of the welfare state? 

    Kuriakose Mathew · Indian Institute of Technology Bombay

    If you think outside the West, this may perhaps for the first time in history, millions of the poorest people on the planet experienced something like the welfare state. The general upliftment, that is now happening in India, China, Brazil and so on, is on an unprecedented scale; however limited it may be. Behind the rhetoric of neoliberalism, it is a matter of fact that these states continue to pursue large scale welfare measures for good.

  • An ISI journal in the field of data center network architectures and topologies

    Hi all,

    As you know, there is a lot of ISI journals in the field of data center and interconnection network architectures and topologies. Which one do you suggest me to submit our research papers? Our paper is about "introducing a new topology (architecture) for data center and interconnection networks".

    I found several journals, but I want to have your suggestions, too.

    Thank you so much in advance.

  • Does anyone have a reference for the metabolic engineering of a plant species used in the treatment of Chagas disease?

    I'm looking for novel ways to explore treatments for Chagas disease-- particularly through in vitro cultivation and/or genetic manipulation of plants.

    Michael Timko · University of Virginia

    What do you want to engineer or express. We have expressed humanized monoclonal antibodies in plants as well as other biochemicals. What is your end point? an edible vaccine, an extract, an industrial grade proteins?

    Let uus know and we can work something out.

  • Mazdak Hashempour added an answer in Catalysis
    What is the role of oxidized states of Pt catalyst in its electrocatalytic activity for PEM and DMFCs?

    It is known that through different synthesis methods used to decorate the carbon support with the Pt catalyst, there is most often a fraction of synthesized platinum in oxidized states, namely Pt 2+ and Pt 4+. Do these oxidized parts of the catalyst also contribute in the electrocatalytic activity for hydrogen oxidation, oxygen reduction and methanol oxidation in different types of fuel cells?
    A lax answer could be NO, and that is the condition in many works published every day using the XPS to determine the contributions of Pt 0, Pt 2+ and Pt 4+ in the total Pt present, and taking the Pt 0 only as responsible for the electrocatalytic activity. But I would like to know if there has been any detailed work on probable contributions of Pt 2+ and Pt 4+. The tougher question in case they have any contribution can be: “what is the extent of the contribution of each chemical state in the total electrocatalytic current measured?”

    Mazdak Hashempour · Politecnico di Milano

    Hi Gustav and Sourov,
    Thanks for your answers and comments.

    Gustav, thanks also for the paper you mentioned. I checked it and there were useful information there, further enlightening your viewpoint and the answer you gave.

    I think your answer has implicitly a part of the reality, especially where saying “Pt oxide, and ORR/HOR are not occurring in the same potential region”. But before going further on, let me say few words about some points. Disregarding the type of the catalyst and its chemical state, there is most often an activation polarization that is controlled by the reaction sequence at the metal-electrolyte interface. This activation polarization is not exclusively determined by the quality of catalyst surface (other parameters like: activation energy of the redox event or the electron transfer contribution, chemical reactions that precede electron transfer, reaction byproducts and their effect on both surface and the engaged analyst and so on). So, the fact you pointed out about the less activity of Pt at high potentials (low overpotentials), is a phenomenological description of the activation polarization (in a wide sense) and is not exclusively caused by the Pt oxidation, though it is a part of that.

    Now, let’s get back to the question and imagine that we are at high enough overpotentials (to avoid the abovementioned issue) guaranteeing a good electrocatalyric current. How can we ensure that 100% of this current is coming from 100% metallic Pt? Do we have any “in-situ spectroscopic evidence” for that?

    Let’s look at this question from another angle and here is where Sourov’s comment arrives.

    Imagine that you prepare some Pt nanoparticles supported on a carbon material. Then, you check it with XPS and you figure out that there are 40% of Pt oxides and 60% of Pt 0. Now you put your catalyst-support system on a GCE and immerse it in 0.1 M HClO4 and do the ORR. Of course you’ll read a current. But how do you know if the current is coming only from the 60% of Pt 0 or also that 40% of Pt oxides have “reduced” and are producing current. Moreover, even if that 40% of Pt oxides have not been reduced by any reason, how can we confirm that their contribution in the measured current is zero?

    In the final reading, based on what you told and wrote in your paper, since only at high enough overpotentials “the stability of the oxygen bond decreases and the ORR may proceed”, regardless of the origin of the oxygen (you have mentioned indifferently whether water dissociation or oxygen molecules, and I would add, other sources such preexisting surface oxides from the synthesis procedure), one can expect that if such high enough overpotential is applied to your partially oxidized catalyst, the stability of the oxygen bonds will decrease and the ORR may proceed. This will in turn mean that one should consider all the 100% Pt content (both metallic and and oxidized) in his calculations as responsible for the electrocatalytic activity and all other electrochemical parameters he is trying to figure out.

  • Can someone provide details on Surface Acoustic Wave Filter Simulators?
    .
    Hany A. Atallah · South Valley University

    you can see this file about

    Simulation of Surface
    Acoustic Wave Devices
    Current Status and Future Prospects
    Ken-ya Hashimoto
    Chiba University

    link

    http://www.google.com.eg/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&ved=0CDIQFjAA&url=http%3A%2F%2Fwww.te.chiba-u.jp%2F~ken%2FUFFC_IDL%2FSAW_Simulation.pdf&ei=JwP1U_vhAcHmyQOd14KADQ&usg=AFQjCNHvgwJtPmO63qhqU8Bn_EEgICMdqw&bvm=bv.73231344,d.bGQ

  • What are the most important recent reforms in terms of strenghtening or renewal of local democracy?

    Since mid-1990s approximately 80 % of all countries have implemented some form of decentralization (Crook and Manor, 2000). In addition, thanks to "pressure" from the side of various international/transnational organizations, good governance principles have become fashion and many countries have implemented them on both national and sub-national levels. The implemented reforms vary a lot in terms of their goals, outcomes as well as impacts. From this perspective I am wondering whether one could consider some of those reforms more important in terms of strenghtening or renewal of local democracy.

  • What is the most effective way to enhance Building design toward energy efficient?
    In Colombia, Builders and Architects believe that using the energy efficient solutions and strategies in their design will increase its cost. Based on your experiences, how we can increase the awareness of builders and architects toward the energy used in buildings?
    Lennart Bertram Poehls · Universidade Federal do Rio Grande do Sul

    I have little to add to the very good answer of my before-speaker.

    Indeed, I think that looking at the original question - which is about energy efficiency -  we have to answer one thing (as done by the first answers), when talking about sustainability - which includes energy efficiency as part of resource efficiency - we have to answer in another manner.

    Briefly I would like to do both: as to efficiently optimize energy efficiency (and I talk about costs in time and money) it is surely the orientation and the openings that have to be thought about. As they are normally decisions taken in an early design stage, their effect is automatically more efficient than - later taken - detail or technical decisions.

    As for efficient sustainable construction results, it is very difficult to answer without defining the weights attributed to the different pillars and criteria. Therefore, I personally try not to give generalised answers.

    Best regards,

    Lennart

  • Robert Tinkler added an answer in Pollen
    Can you recommend a microscope preferebly with digital imaging for pollen identification?

    I would like to upgrade my pollen sampling station and buy a new microscope on which I can also make good digital  images of pollen and fungal spores. I'd appreciate a brand and serial no, if possible.

    Moreover I've seen voice recognition systems used in pollen identification. Do you have any info about that?

    Your help is very much appreciated.

    Robert Tinkler · Ministry for Primary Industries

    Classifynder is a digital microscope and software system that has been specifically developed as an aid to Palynology. The system enables slides to be scanned and the entire contents to be located, measured and the resulting digital images to be archived and then classified automatically.  http://www.classifynder.com/

  • Supratip Ghose added an answer in Optimal Control
    What measures exist for characterising and classifying segments of data acquired over a period of time?

    I have measurements from a system over a long period of time. During this time, the system has been in different states (for example, different controller tuning configurations). Now, looking at the data alone (the time series), how can I identify the portion that corresponds to a certain (normal) state of the system (for example, optimal controller tuning)? OR: How to identify normal data from abnormal data in a time series?

    You can research with google a bit with the subject Outlier detection of time-series data!!

  • Jorge Varejao added an answer in Xylitol
    Is there any method for detection of Glu, Xylose and Xylitol by HPLC

    Hello Every one,

    Please let me know that, if there is any single or different methods available for detection of glucose, xylose and xylitol by HPLC equiped with C18 column and UV detector. If not please let me know the best methods for detection of the above with HPLC  in detail (conditions like run time, mobile phase, columnan and its conditions and detector or suggest an alternative columns for HPX 87H. 

    Thank you

    Jorge Varejao · Instituto Politécnico de Coimbra

    With your equipment the best I can see is trying to separate xylose from glucose with only distilled water as mobile phase at 1ml/min or less with UV detection at 190nm.

    Using a NH2 phase column and a RI detetor  will be a more convenient, or onther carbohydrate coolumn.

  • Is contemporary stabilization of surface air T an indication that anthropogenic forcing is probably not the main driver of climate variability?
    Despite the continuous rise of CO2 density, the surface air T stops rising since the beginning of the 21-st century. The attribution of this global warming slow-down to the sudden intensification of trade winds seems quite unconvincing, because the reason of this intensification remains unknown (for more details, see Nature Geo-science, Editorial from March, 2014)
    Harry ten Brink · Energy Research Centre of the Netherlands

    There is another question in this topic

    Difference between climate (natural) variability and (anthropogenic) change.

    I notice that in the title of this question the term variability is used or should it be "change"?

    Like to remind that climate change can only be assessed over periods in which the variability is averaged out; this depends on the amplitude of the differences per year/decade/NAOpattern etc

  • Robert Shuler added an answer in Gravitation
    Why has the length contraction in GR not been proven experimentally until now?

    A spacecraft of length L0 moves in negligible speed between two observers A and B at different gravitational potential. If A is at the region of higher gravitational potential, will B measure a different length than L0 ignoring special relativity effects?
    I want to know why length contraction in GR is not proven experimentally until now?
    What' the difficulties (experimental and theoretical) in front of such proving?
    Why the above experiment wouldn't be done?

    Robert Shuler · NASA

    Thanks Matts, and Guoliang.  : )

    What I was trying to get at with the wavelength comment is just that atomic and molecular bond dimensions are determined by waves.  Maybe "wavelength" is too simple, but if something affects wavelength and affects everything globally in the same way, it should change the lengths of those bonds.  de Broglie frequency is the clock that drives quantum waves (though Schrodinger uses a different zero energy reference point, the wavelengths don't change).  If the relation of de Broglie frequency to the speed of light changes, then lengths change.  In "natural" coordinates these always change together.  But in extensions of observer coordinates, the de Broglie frequency of particles (their energy) changes as 1/Γ, but the coordinate velocity of light is c/Γ2.  I will look at Guoliang's paper to see how he explains this.

  • Are the staining procedures in biopsies to underline mineral deposits accurate?

    Standardized staining procedures for histopathology are the gold standard to reveal ectopic calcifications. Typically, tissue samples are taken from patients and stained for examination by pathologists. Several publications have underlined the limitations of this procedure. Bonnewald et al [ Bonewald L F, Harris S E, Rosser J, Dallas M R, Dallas S L, Camacho N P, Boyan B and Boskey A 2003 Calcif. Tissue Int. 72 537–47] demonstrated that staining procédures such as von Kossa staining alone is not appropriate for identifying and quantifying apatite. Identification can be completed by other techniques routinely used in some cases: Fourier transform infrared (FTIR)61 and Raman spectroscopy.

    In fact, crystals are found in kidney biopsies performed in order to understand the mechanism of the loss of renal function. However, only few histochemical tests are available to attempt an identification of the crystals. Moreover, in some cases, common crystals such as calcium oxalate monohydrate may be present as a consequence of renal failure, but they are not involved in the kidney loss. For these reasons, it is of clinical importance to accurately identify crystals found in the tissue as they can help to early characterization of a disease,

    In a recent investigation, new crystalline phases were described such as amorphous silica, sodium hydrogen urate, methyl-1 uric acid and three different Ca2+ phosphates namely whitlockite, OCP and ACCP. Moreover, for the first time, we underline the chemical heterogeneity of intratissular calcifications.

    Note that Dihydroxyadenine crystals were found in four patients (five biopsies in Table 1). Such crystals deposits in parenchyma are pathognomonic of a rare disease, adenine phosphoribosyltransferase deficiency, an inherited disease able to induce recurrent kidney stones and/or kidney failure. Dihydroxyadenine is often too late identified in patients who have developedrenal insufficiency and sometimes after the crystal-induced destruction of a kidney transplant.

  • Konrad Matyja asked a question in Chlorella
    Have you ever use dry algae (Chlorella bought in Apoteke) to feed Daphnia? Should I use it or not? And why...?

    Trying to make culturing more easier and wondering about advantages and disadvantages of dry algae as a food for Daphnia magna

  • How does one decide relationship between points and polygon?

    Hello, Everyone! I have some coordinates and anyone who knows how to plot polygon using these points through R software, and then, I want to know the relationships between some other points and polygon. For example, I like to know which points are in the polygon and which points are out of the polygon. Anyone who can write such R code for me, or tell me which package in R can achieve my purpose. Thanks a lot!

    Richard Anthony Champion Jr · City College of San Francisco

    I solved this problem in the early 1980's with an algorithm written in Fortran. The application involved GIS. I may have complete documentation. I'll try to locate it, if you request it.

    Otherwise, the answers above are all correct.

    Goggalize : "point in polygon" and "r point in polygon".

    The web sites that I got are:

    http://en.wikipedia.org/wiki/Point_in_polygon

    http://de.wikipedia.org/wiki/Punkt-in-Polygon-Test_nach_Jordan
    http://alienryderflex.com/polygon/
    http://www.rforge.net/doc/packages/SDMTools/pnt.in.poly.html

    Luckily for you, some R programmer has already implemented the code.

  • Can anyone suggest some Cereal-based infant formulas?

     Cereal-based infant formulas

    Ass.Prof. Ashraf Mahdy Sharoba · Benha University

    thanks for all Researchers

  • How do Dopamine Transporter (DAT) and Serotonin Transporter (SERT) interact?

    Is there any interaction between the DAT and SERT? Dopamine and Serotonin, both found to be involved in same psychological disorders, such as depression. Do the transporters (DAT and SERT) of these major neurotransmitters interact and work together to maintain the normal function of the brain or operate in two independent parallel pathways?

    Béatrice Ewalds-Kvist · Stockholm University

    Dear Sunil,

    Various kinases have been linked to DAT regulation including PKA, PKC, PI-3K, ERK, ERK, Akt, CaMKII, CDK, and MAPK.

    Regulation of SERT has been linked to acute depletion of intracellular Ca Na 2+, calmodulin inhibition, CaMKII, Src, p38 MAP kinase, PKC, and activation of NOS/cGMP

    Perhaps Gavin can explain this.