From nfournier from sasktel.net Mon Sep 1 00:15:12 2008 From: nfournier from sasktel.net (NMF) Date: Mon Sep 1 10:31:53 2008 Subject: [Neuroscience] Peristaltic Pump for rat perfusion/flash freezing Message-ID: Dear Colleagues, I am wondering if anyone can share with me there experiences using a peristaltic pump for perfusions (e.g., what specific equipment, tubing size, flow rate settings). Currently, I am using a Masterflex L/S economy drive pump for our perfusions and have noticed some inconsistent results from time to time which I believe might be related to our setup for perfusion. Any help would be appreciated. Lastly, does anyone have experience flash freezing tissue using liquid N2 cooled isopentane? If so, could you share with me your specific setup. I have explored some alternatives (e.g., dry ice, isopentante/dry ice slurries) and my experience suggests that liquid N2/isopentante produces the best results (but not as perfect as I would like), so I would like to get a little more detail of what most people are using. I have far more experience sectioning on a vibrating microtome and I am not use to seeing freeze fracture artifacts (i.e., swiss chesse effect), so I tend to--maybe unrealistically--have a fairly high standard for tissue quality. Thanks in advance, Neil From zhangw from stanford.edu Fri Sep 5 23:40:26 2008 From: zhangw from stanford.edu (Wei Zhang) Date: Sat Sep 6 13:21:33 2008 Subject: [Neuroscience] variance-mean analysis Message-ID: Hi, I tried to use the variance-mean analysis to describe n,p,q of hippocampal synapses. Is there anybody who have had experience on this and would be willing to help me work it out? Your help will be appreciated (like jamba juice or starbucks gift card). Wei From connelly.bill from gmail.com Mon Sep 8 17:49:17 2008 From: connelly.bill from gmail.com (Bill) Date: Mon Sep 8 18:57:01 2008 Subject: [Neuroscience] Re: variance-mean analysis References: Message-ID: <55b74684-1993-46f2-9cf5-73f6b2a7a1fc@t1g2000pra.googlegroups.com> Hi Wei, I'm certainly no expert on the subject, and I have never done it, but I did have quite a long talk about it with John Clements who invented the technique. If no one more qualified comes forward, potentially if we put our heads together we can solve your problems. Certainly, if you've got the data already it shouldn't be a problem (though I hope you filled your cell with Cs, and QX-314, so no pesky active channels mess with things, though with such a mix electrotonically distant and close synapses, I'm not sure how good results like this can be). On Sep 6, 4:40?pm, "Wei Zhang" wrote: > Hi, > ?I tried to use the variance-mean analysis to describe n,p,q of hippocampal > synapses. Is there anybody who have had experience on this and would be > willing to help me work it out? Your help will be appreciated (like jamba > juice or starbucks gift card). > Wei From connelly.bill from gmail.com Mon Sep 8 18:02:10 2008 From: connelly.bill from gmail.com (Bill) Date: Mon Sep 8 18:57:06 2008 Subject: [Neuroscience] Re: CURRENT CLAMP IN epc7 PLUS References: Message-ID: <8ef65648-53e0-43f8-8fb7-1a86a77de8e6@a2g2000prm.googlegroups.com> The EPC7 is one of those voltage clamp amplifiers like the Axopatch 200, which only has a psuedo current clamp mode. But those things usually have a response time of like 50 microseconds or less, so isn't that like a 3kHz filter, so it shouldn't mess with your signals too bad. Or am I completely off? On Aug 23, 10:50?am, "Claudio Elgueta Zu?iga" wrote: > Hey guys: > > ? ? ? ? ? ? I?m wondering if it?s possible to do decent current clamping > with this amplifier (HRKA EPC7 plus). I?m patching retinal ganglion cells > and when aplying a square current pulse, the spikes are incredibly > filtered. > > ???? > > Regards... > > -- > > Claudio Elgueta From rosanna from gionnethics.com Tue Sep 9 12:24:15 2008 From: rosanna from gionnethics.com (Rosanna Tarsiero) Date: Tue Sep 9 16:30:25 2008 Subject: [Neuroscience] Cognitive Neuroscience Textbook In-Reply-To: <200809091704.m89H4oV20905@net.bio.net> Message-ID: <21948.7366.qm@web1003.biz.mail.sp1.yahoo.com> Hello, my name is Rosanna Tarsiero. I'm searching a suggestion for a book on cognitive neuroscience for a person with a computer science background. Thanks Rosanna Tarsiero University of Pisa Italy From t.lewis from unsw.edu.au Tue Sep 9 21:22:04 2008 From: t.lewis from unsw.edu.au (Trevor Lewis) Date: Wed Sep 10 08:34:20 2008 Subject: [Neuroscience] Re: variance-mean analysis In-Reply-To: <200809091704.m89H4dV20866@net.bio.net> References: <200809091704.m89H4dV20866@net.bio.net> Message-ID: <200809100222.m8A2M4xB020446@smtp.unsw.edu.au> Dear Wei, John Clements and Angus Silver have written a couple of good methods papers on the variance-mean analysis. Here are two that will give you both the background and practical advice on the technique: J.D. Clements Variance?mean analysis: a simple and reliable approach for investigating synaptic transmission and modulation Journal of Neuroscience Methods Volume 130, Issue 2, 15 December 2003, Pages 115-125. J.D. Clements and R.A. Silver Unveiling synaptic plasticity: a new graphical and analytical approach Trends in Neuroscience Volume 23, Issue 3, 2000, pp. 105?113. John has certainly made the use of this technique easier to apply to your data by incorporating it into the AxoGraph software. It is also available in pClamp v.9 (I guess it is also available in v.10?). Hopefully this will get you started. Trevor >Date: Mon, 8 Sep 2008 15:49:17 -0700 (PDT) >From: Bill >Subject: [Neuroscience] Re: variance-mean analysis >To: neur-sci@net.bio.net > >Hi Wei, > >I'm certainly no expert on the subject, and I have never done it, but >I did have quite a long talk about it with John Clements who invented >the technique. If no one more qualified comes forward, potentially if >we put our heads together we can solve your problems. Certainly, if >you've got the data already it shouldn't be a problem (though I hope >you filled your cell with Cs, and QX-314, so no pesky active channels >mess with things, though with such a mix electrotonically distant and >close synapses, I'm not sure how good results like this can be). > >On Sep 6, 4:40 pm, "Wei Zhang" wrote: > > Hi, > > I tried to use the variance-mean analysis to describe n,p,q of hippocampal > > synapses. Is there anybody who have had experience on this and would be > > willing to help me work it out? Your help will be appreciated (like jamba > > juice or starbucks gift card). > > Wei From gyovaig from szentes.hu Wed Sep 10 13:20:19 2008 From: gyovaig from szentes.hu (Dr. Gyovai Gabriella) Date: Thu Sep 11 16:39:11 2008 Subject: [Neuroscience] Cognitive Neuroscience Textbook In-Reply-To: <21948.7366.qm@web1003.biz.mail.sp1.yahoo.com> Message-ID: <200809101820.m8AIKaV18708@net.bio.net> Dear Rossana, What kind of book are you searching for? Would you learn about cognitive tests with computer assistance or would you like something systematically composed book about cognitive neuroscience and the effect of the cognitive therapy on the brain or the relationship between behaviour and brain images. I hope with more information we can help you, Gabriella -----Original Message----- From: neur-sci-bounces@oat.bio.indiana.edu [mailto:neur-sci-bounces@oat.bio.indiana.edu] On Behalf Of Rosanna Tarsiero Sent: Tuesday, September 09, 2008 7:24 PM To: neur-sci@oat.bio.indiana.edu Subject: [Neuroscience] Cognitive Neuroscience Textbook Hello, my name is Rosanna Tarsiero. I'm searching a suggestion for a book on cognitive neuroscience for a person with a computer science background. Thanks Rosanna Tarsiero University of Pisa Italy _______________________________________________ Neur-sci mailing list Neur-sci@net.bio.net http://www.bio.net/biomail/listinfo/neur-sci From connelly.bill from gmail.com Wed Sep 10 23:21:48 2008 From: connelly.bill from gmail.com (Bill) Date: Thu Sep 11 16:39:24 2008 Subject: [Neuroscience] Re: variance-mean analysis References: <200809091704.m89H4dV20866@net.bio.net> Message-ID: <10968b96-3e9b-4c4b-88f9-9e79c2bbaa32@a18g2000pra.googlegroups.com> On Sep 10, 2:22?pm, Trevor Lewis wrote: > John has certainly made the use of this technique > easier to apply to your data by incorporating it > into the AxoGraph software. It is also available > in pClamp v.9 (I guess it is also available in v.10?). > Hopefully this will get you started. > Axograph has lots of helpful things like that in it, but it is easy enough to do with any curve fitting program and a pen and paper. From pranavpeshwe from gmail.com Tue Sep 16 02:59:14 2008 From: pranavpeshwe from gmail.com (Pranav Peshwe) Date: Tue Sep 16 09:12:41 2008 Subject: [Neuroscience] Re: Cognitive Neuroscience Textbook References: Message-ID: On Sep 9, 10:24?pm, Rosanna Tarsiero wrote: > Hello, > ? my name is Rosanna Tarsiero. I'm searching a suggestion for a book on cognitive neuroscience for a person with a computer science background. > Hi, Am not aware of any book on neurocognition written specifically for CS people but, Robert Solso's 'Cognitive Psychology' is a good read for anyone. HTH. Best regards, Pranav pranavsbrain.peshwe.com From ms.puja.parekh from gmail.com Tue Sep 16 19:33:08 2008 From: ms.puja.parekh from gmail.com (Puja Parekh) Date: Wed Sep 17 12:32:47 2008 Subject: [Neuroscience] Re: Cognitive Neuroscience Textbook In-Reply-To: References: Message-ID: <26fdbc5c0809161733v520488a0x7a3dc9305c59f71b@mail.gmail.com> One really good text is Gordon Shepherd's "The Synaptic Organization of the Brain." There is a lot in this book that draws from information theory, techniques in modeling, neurophysiology etc. It is comprehensive and very detailed. I highly recommend this text. Puja Parekh The College of William and Mary '09 On Tue, Sep 16, 2008 at 3:59 AM, Pranav Peshwe wrote: > On Sep 9, 10:24 pm, Rosanna Tarsiero wrote: > > Hello, > > my name is Rosanna Tarsiero. I'm searching a suggestion for a book on > cognitive neuroscience for a person with a computer science background. > > > > Hi, > Am not aware of any book on neurocognition written specifically > for CS people but, Robert Solso's 'Cognitive Psychology' is a good > read for anyone. > HTH. > > Best regards, > Pranav > pranavsbrain.peshwe.com > _______________________________________________ > Neur-sci mailing list > Neur-sci@net.bio.net > http://www.bio.net/biomail/listinfo/neur-sci > From robert.schleicher from tu-berlin.de Wed Sep 17 05:04:50 2008 From: robert.schleicher from tu-berlin.de (Robert Schleicher) Date: Wed Sep 17 12:33:10 2008 Subject: [Neuroscience] PhD-position: Brain-based Usability Evaluation (T-Labs TU Berlin) Message-ID: <40183.212.201.104.11.1221645890.squirrel@mailbox.tu-berlin.de> Deutsche Telekom Laboratories (T-Labs) is a joint scientific research institute of Deutsche Telekom AG and Berlin Institute of Technology (TU Berlin). We carry out pioneering research into innovative information and telecommunication technologies, addressing in particular human interaction, networking and security issues, see www.qu.tlabs.tu-berlin.de. The Quality and Usability Lab (Q&U Lab) of T-Labs is participating in the Bernstein Focus: Neurotechnology project sponsored by the German Federal Ministry of Education and Research (BMBF) together with other research groups from Berlin. In the frame of this project, new quality and usability evaluation methods will be developed which are based on neurophysiological measurements. Q&U Lab will lead the sub-project "Neuro-Usability" where various physiological signals will be integrated in usability evaluation and prediction. This project will open possibilities for several PhD projects, one of which will be directly connected to brain-based usability evaluation and prediction. The applicant's tasks include setting up a corresponding test site and running experiments with exemplary telecommunication applications that focus on video and audio quality. The findings should be integrated in a model on human quality perception and judgment on the one hand, whereas the empirical knowledge should lead to a novel usability evaluation test protocol that can be a scientific contribution of the thesis, and be transferred to standardization bodies on the other hand. Requirements: - PhD candidates must hold a Master Degree or equivalent - Strong background in either experimental psychophysiology / neuroscience (EEG, EDA, EMG, eye movements) and statistics (SPSS) or signal processing and machine learning - Some programming experience (C, C++, Matlab) - Good command of English Highly desirable - Interest in applied research and human-computer-interaction - Ability to work in a multidisciplinary team The position is available for 2.5 years and an optional extension for another 2.5 years, with immediate start. The salary is according to BAT 2a (full time). Interested candidates are asked to submit their application including a CV, copies of the most important certificates, contact information of at least one reference person, and a short statement describing their research interests to Irene Hube-Achter, Irene.hube [at] telekom.de, preferentially in one pdf file. Berlin Institute of Technology seeks to increase the percentage of female employees and par-ticularly encourages female candidates to apply. In case of equal qualifications, female candidates will be preferred. Handicapped candidates will be preferred in case of equal qualifications. ---------------------------------------------- Robert Schleicher Quality & Usability Lab Deutsche Telekom Laboratories TU Berlin Ernst-Reuter-Platz 7 10587 Berlin Tel: +49 (0)30 8353 58359 http://www.qu.tlabs.tu-berlin.de From jopower from yahoo.com Wed Sep 17 09:35:56 2008 From: jopower from yahoo.com (polly jo) Date: Wed Sep 17 12:33:18 2008 Subject: [Neuroscience] Re: Cognitive Neuroscience Textbook In-Reply-To: Message-ID: <932579.18625.qm@web65711.mail.ac4.yahoo.com> > > Hello, > > my name is Rosanna Tarsiero. I'm searching a > suggestion for a book on cognitive neuroscience for a person > with a computer science background. ... you could try Gazzaniga's tome on cognitive neurosciences. It is perhaps not completely useful for CS folks, however, it is very comprehensive and may list other CS articles. best Pow > > > > Hi, > Am not aware of any book on neurocognition written > specifically > for CS people but, Robert Solso's 'Cognitive > Psychology' is a good > read for anyone. > HTH. > > Best regards, > Pranav > pranavsbrain.peshwe.com > _______________________________________________ > Neur-sci mailing list > Neur-sci@net.bio.net > http://www.bio.net/biomail/listinfo/neur-sci From fredo from hotmail.com Mon Sep 29 09:57:28 2008 From: fredo from hotmail.com (Fredo) Date: Mon Sep 29 11:19:13 2008 Subject: [Neuroscience] Izhikevich's Large Scale Mammalian Thalamocrotical model Message-ID: I'm trying to implement something like Eugene Izhikevich's model described in "A Large-Scale Model of Mammalian Thalamocortical Systems", but I've run into an issue I can't quite figure out. >From the Supporting Information: http://vesicle.nsi.edu/users/izhikevich/publications/large-scale_model_of_human_brain_support.pdf On page 8, he describes the current used in the equation on page 7 as: I(t) = -Idendr - Isyn Then below, he provides the equation for calculating Idendr per compartment. He says in the text that the somatic and terminal dendritic compartments all have a value of 0 of Idendr. So my question is, in I(t) = -Idendr - Isyn What is Idendr? Is it the sum of Idendr for the compartments attached to the somatic compartment? The sum of all Idendr for all compartments? or something else? Does anyone know? Thanks