many changes

thesis/citations.bib

@@ -0,0 +1,206 @@
+@article{bastian1981electrolocation,
+  title={Electrolocation},
+  author={Bastian, Joseph},
+  journal={Journal of comparative physiology},
+  volume={144},
+  number={4},
+  pages={465--479},
+  year={1981},
+  publisher={Springer}
+}
+
+@article{benda2003universal,
+  title={A universal model for spike-frequency adaptation},
+  author={Benda, Jan and Herz, Andreas VM},
+  journal={Neural computation},
+  volume={15},
+  number={11},
+  pages={2523--2564},
+  year={2003},
+  publisher={MIT Press}
+}
+
+@article{benda2005spike,
+  title={Spike-frequency adaptation separates transient communication signals from background oscillations},
+  author={Benda, Jan and Longtin, Andr{\'e} and Maler, Len},
+  journal={Journal of Neuroscience},
+  volume={25},
+  number={9},
+  pages={2312--2321},
+  year={2005},
+  publisher={Soc Neuroscience}
+}
+
+@article{benda2010linear,
+  title={Linear versus nonlinear signal transmission in neuron models with adaptation currents or dynamic thresholds},
+  author={Benda, Jan and Maler, Leonard and Longtin, Andr{\'e}},
+  journal={Journal of Neurophysiology},
+  volume={104},
+  number={5},
+  pages={2806--2820},
+  year={2010},
+  publisher={American Physiological Society Bethesda, MD}
+}
+
+@article{todd1999identification,
+  title={The identification of peaks in physiological signals},
+  author={Todd, Bryan S and Andrews, David C},
+  journal={Computers and biomedical research},
+  volume={32},
+  number={4},
+  pages={322--335},
+  year={1999},
+  publisher={Elsevier}
+}
+
+@article{chacron2001simple,
+  title={Simple models of bursting and non-bursting P-type electroreceptors},
+  author={Chacron, Maurice J and Longtin, Andr{\'e} and Maler, Leonard},
+  journal={Neurocomputing},
+  volume={38},
+  pages={129--139},
+  year={2001},
+  publisher={Elsevier}
+}
+
+@article{chacron2005delayed,
+  title={Delayed excitatory and inhibitory feedback shape neural information transmission},
+  author={Chacron, Maurice J and Longtin, Andr{\'e} and Maler, Leonard},
+  journal={Physical Review E},
+  volume={72},
+  number={5},
+  pages={051917},
+  year={2005},
+  publisher={APS}
+}
+
+@article{chacron2005electroreceptor,
+  title={Electroreceptor neuron dynamics shape information transmission},
+  author={Chacron, Maurice J and Maler, Leonard and Bastian, Joseph},
+  journal={Nature neuroscience},
+  volume={8},
+  number={5},
+  pages={673--678},
+  year={2005},
+  publisher={Nature Publishing Group}
+}
+
+@article{chacron2001negative,
+  title={Negative interspike interval correlations increase the neuronal capacity for encoding time-dependent stimuli},
+  author={Chacron, Maurice J and Longtin, Andre and Maler, Leonard},
+  journal={Journal of Neuroscience},
+  volume={21},
+  number={14},
+  pages={5328--5343},
+  year={2001},
+  publisher={Soc Neuroscience}
+}
+
+@article{gussin2007limits,
+  title={Limits of linear rate coding of dynamic stimuli by electroreceptor afferents},
+  author={Gussin, Daniel and Benda, Jan and Maler, Leonard},
+  journal={Journal of neurophysiology},
+  volume={97},
+  number={4},
+  pages={2917--2929},
+  year={2007},
+  publisher={American Physiological Society}
+}
+
+@phdthesis{walz2013Phd,
+  author  = {Henriette Walz},
+  title   = {Encoding of Communication Signals in Heterogeneous Populations ofElectroreceptors},
+  school  = {Eberhard-Karls-Universität Tübingen},
+  year    = {2013}
+}
+
+@article{walz2014static,
+  title={Static frequency tuning accounts for changes in neural synchrony evoked by transient communication signals},
+  author={Walz, Henriette and Grewe, Jan and Benda, Jan},
+  journal={Journal of Neurophysiology},
+  volume={112},
+  number={4},
+  pages={752--765},
+  year={2014},
+  publisher={American Physiological Society Bethesda, MD}
+}
+
+@article{kashimori1996model,
+  title={Model of P-and T-electroreceptors of weakly electric fish},
+  author={Kashimori, Yoshiki and Goto, Mituyuki and Kambara, Takeshi},
+  journal={Biophysical journal},
+  volume={70},
+  number={6},
+  pages={2513--2526},
+  year={1996},
+  publisher={Elsevier}
+}
+
+@article{nelson1997characterization,
+  title={Characterization and modeling of P-type electrosensory afferent responses to amplitude modulations in a wave-type electric fish},
+  author={Nelson, ME and Xu, Z and Payne, JR},
+  journal={Journal of Comparative Physiology A},
+  volume={181},
+  number={5},
+  pages={532--544},
+  year={1997},
+  publisher={Springer}
+}
+
+@article{ratnam2000nonrenewal,
+  title={Nonrenewal statistics of electrosensory afferent spike trains: implications for the detection of weak sensory signals},
+  author={Ratnam, Rama and Nelson, Mark E},
+  journal={Journal of Neuroscience},
+  volume={20},
+  number={17},
+  pages={6672--6683},
+  year={2000},
+  publisher={Soc Neuroscience}
+}
+
+@article{xu1996logarithmic,
+  title={Logarithmic time course of sensory adaptation in electrosensory afferent nerve fibers in a weakly electric fish},
+  author={Xu, Zhian and Payne, Jeremy R and Nelson, Mark E},
+  journal={Journal of neurophysiology},
+  volume={76},
+  number={3},
+  pages={2020--2032},
+  year={1996},
+  publisher={American Physiological Society Bethesda, MD}
+}
+
+@article{burkitt2006review,
+  title={A review of the integrate-and-fire neuron model: I. Homogeneous synaptic input},
+  author={Burkitt, Anthony N},
+  journal={Biological cybernetics},
+  volume={95},
+  number={1},
+  pages={1--19},
+  year={2006},
+  publisher={Springer}
+}
+
+@article{wark2007sensory,
+  title={Sensory adaptation},
+  author={Wark, Barry and Lundstrom, Brian Nils and Fairhall, Adrienne},
+  journal={Current opinion in neurobiology},
+  volume={17},
+  number={4},
+  pages={423--429},
+  year={2007},
+  publisher={Elsevier}
+}
+
+@article{herz2006modeling,
+  title={Modeling single-neuron dynamics and computations: a balance of detail and abstraction},
+  author={Herz, Andreas VM and Gollisch, Tim and Machens, Christian K and Jaeger, Dieter},
+  journal={science},
+  volume={314},
+  number={5796},
+  pages={80--85},
+  year={2006},
+  publisher={American Association for the Advancement of Science}
+}
+
+
+

thesis/sources/notes/notes.bbl

@@ -0,0 +1,8 @@
+\begin{thebibliography}{}
+
+\bibitem[Benda and Herz, 2003]{benda2003universal}
+Benda, J. and Herz, A.~V. (2003).
+\newblock A universal model for spike-frequency adaptation.
+\newblock {\em Neural computation}, 15(11):2523--2564.
+
+\end{thebibliography}

thesis/sources/notes/notes.blg

@@ -0,0 +1,46 @@
+This is BibTeX, Version 0.99d (TeX Live 2015/Debian)
+Capacity: max_strings=35307, hash_size=35307, hash_prime=30011
+The top-level auxiliary file: notes.aux
+The style file: apalike.bst
+Database file #1: ../../citations.bib
+You've used 1 entry,
+            1935 wiz_defined-function locations,
+            480 strings with 3819 characters,
+and the built_in function-call counts, 443 in all, are:
+= -- 44
+> -- 13
+< -- 1
++ -- 6
+- -- 4
+* -- 39
+:= -- 77
+add.period$ -- 3
+call.type$ -- 1
+change.case$ -- 7
+chr.to.int$ -- 1
+cite$ -- 1
+duplicate$ -- 14
+empty$ -- 33
+format.name$ -- 7
+if$ -- 84
+int.to.chr$ -- 1
+int.to.str$ -- 0
+missing$ -- 1
+newline$ -- 8
+num.names$ -- 3
+pop$ -- 4
+preamble$ -- 1
+purify$ -- 7
+quote$ -- 0
+skip$ -- 12
+stack$ -- 0
+substring$ -- 45
+swap$ -- 1
+text.length$ -- 0
+text.prefix$ -- 0
+top$ -- 0
+type$ -- 6
+warning$ -- 0
+while$ -- 4
+width$ -- 0
+write$ -- 15

thesis/sources/notes/notes.tex

@@ -26,27 +26,29 @@
 \section{To-read}
 
 \begin{itemize}
-\item other models of P-units:
+\item other models/papers to P-units:
 
 Bastian 1981a Electrolocation I. How the electroreceptors of Apteronotus albifrons code for moving objects and other electrical stimuli
 
-Benda abd Herz 2003
 
-Benda et al. 2005
+%Benda and Herz 2003 
+\cite{benda2003universal}
 
-Chacron et al 2001, 2005
+%Benda et al. 2005, 2006
 
-Kreiman et al. 2000 
+%Chacron et al 2001, 2005a
 
-Ludtke and Nelson 2006
+%Kreiman et al. 2000 
 
-Nelson et al. 1997
+%Ludtke and Nelson 2006
 
-Ratman and Nelson 2000
+%Nelson et al. 1997
 
-Wessel et al 1996
+%Ratman and Nelson 2000
 
-Xu et al 1996
+%Wessel et al 1996
+
+%Xu et al 1996
 
 
 \end{itemize}
@@ -59,12 +61,16 @@ Xu et al 1996
 
 \item to mention: size range, tank conditions, 
 
-\item continuous sinusoidal electric organ discharge EOD with near constant amplitude and frequency (Moortgat et al. 1998) 
+\item continuous sinusoidal electric organ discharge EOD with near constant amplitude and frequency (Moortgat et al. 1998)
+
+\item EOD carrier signal for AMs caused by nearby objects like prey or other electric fish
 \end{itemize}
 
 \subsection{general P-unit notes}
 \begin{itemize}
 
+\item consist of 25-40 receptor cells and a nerve fiber that makes synaptic contact to at least 16 active neurotransmitter release sites per receptor cell. (M.V.L. Bennett, C. Sandri, K. Akert, Fine Structure of the tuberous electroreceptor of the high-frequency electric "sh Sternachus albifrons (gymnotiformes), J. Neurocytol. 18 (1989) 265.)
+
 \item most abundant tuberous receptor 
 
 \item spikes in probabilistic manner to upward phase of eod
@@ -75,6 +81,8 @@ Xu et al 1996
 
 \item can predict up to 80\% of the AM using reverse correlation and coherence but no obvious decoding mechanism  
 
+\item linear coders of intensity, additive noise models are suitable Gussin et al. 2007
+
 \end{itemize}
 
 \subsection{Coding}
@@ -84,9 +92,17 @@ Xu et al 1996
 
 \begin{itemize}
 
-\item sample descriptions in: Hernriettes phd, Gussin 2007, 
+\item sample descriptions in: Hernriettes phd, Gussin et al. 2007, Benda et al. 2005
 \end{itemize}
 
+\section{Mat\&Met}
+
+\subsection{model construction}
+\begin{itemize}
+
+
+\item explain why adaption current and not a dynamic threshold: chosen AC other possibilities(dyn. thresh. voltage hyperpol.) why AC is better.
+\end{itemize}
 
 \section{Paper}
 
@@ -109,7 +125,21 @@ then more sophisticated methods like spike-triggered stimulus averages (STA) are
 \end{itemize}
 
 
+\subsection{Simple models of bursting and non-bursting P-type electroreceptors}
+Maurice J. Chacron, Andre H Longtin , Leonard Maler, 2001
+
+\begin{itemize}
+
+\item simple math. model of P-units for just the baseline behavior.
+
+\item uses dynamic threshold, abs refractory period, for bursty cells added a delayed depolarization current
+
+\item wasn't "fitted" to data just compared, chosen and fixed(?) parameters 
+
+\end{itemize}
 
 
+\bibliography{../../citations} 
+\bibliographystyle{apalike}
 
 \end{document}