--- _id: '8028' abstract: - lang: eng text: 'Transmission of signals within the brain is essential for cognitive function, but it is not clear how neural circuits support reliable and accurate signal propagation over a sufficiently large dynamic range. Two modes of propagation have been studied: synfire chains, in which synchronous activity travels through feedforward layers of a neuronal network, and the propagation of fluctuations in firing rate across these layers. In both cases, a sufficient amount of noise, which was added to previous models from an external source, had to be included to support stable propagation. Sparse, randomly connected networks of spiking model neurons can generate chaotic patterns of activity. We investigate whether this activity, which is a more realistic noise source, is sufficient to allow for signal transmission. We find that, for rate-coded signals but not for synfire chains, such networks support robust and accurate signal reproduction through up to six layers if appropriate adjustments are made in synaptic strengths. We investigate the factors affecting transmission and show that multiple signals can propagate simultaneously along different pathways. Using this feature, we show how different types of logic gates can arise within the architecture of the random network through the strengthening of specific synapses.' article_processing_charge: No article_type: original author: - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 - first_name: L. F. full_name: Abbott, L. F. last_name: Abbott citation: ama: Vogels TP, Abbott LF. Signal propagation and logic gating in networks of integrate-and-fire neurons. Journal of Neuroscience. 2005;25(46):10786-10795. doi:10.1523/jneurosci.3508-05.2005 apa: Vogels, T. P., & Abbott, L. F. (2005). Signal propagation and logic gating in networks of integrate-and-fire neurons. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/jneurosci.3508-05.2005 chicago: Vogels, Tim P, and L. F. Abbott. “Signal Propagation and Logic Gating in Networks of Integrate-and-Fire Neurons.” Journal of Neuroscience. Society for Neuroscience, 2005. https://doi.org/10.1523/jneurosci.3508-05.2005. ieee: T. P. Vogels and L. F. Abbott, “Signal propagation and logic gating in networks of integrate-and-fire neurons,” Journal of Neuroscience, vol. 25, no. 46. Society for Neuroscience, pp. 10786–10795, 2005. ista: Vogels TP, Abbott LF. 2005. Signal propagation and logic gating in networks of integrate-and-fire neurons. Journal of Neuroscience. 25(46), 10786–10795. mla: Vogels, Tim P., and L. F. Abbott. “Signal Propagation and Logic Gating in Networks of Integrate-and-Fire Neurons.” Journal of Neuroscience, vol. 25, no. 46, Society for Neuroscience, 2005, pp. 10786–95, doi:10.1523/jneurosci.3508-05.2005. short: T.P. Vogels, L.F. Abbott, Journal of Neuroscience 25 (2005) 10786–10795. date_created: 2020-06-25T13:12:33Z date_published: 2005-11-16T00:00:00Z date_updated: 2021-01-12T08:16:37Z day: '16' doi: 10.1523/jneurosci.3508-05.2005 extern: '1' external_id: pmid: - '16291952' intvolume: ' 25' issue: '46' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6725859/ month: '11' oa: 1 oa_version: Published Version page: 10786-10795 pmid: 1 publication: Journal of Neuroscience publication_identifier: issn: - 0270-6474 - 1529-2401 publication_status: published publisher: Society for Neuroscience quality_controlled: '1' status: public title: Signal propagation and logic gating in networks of integrate-and-fire neurons type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 25 year: '2005' ... --- _id: '8029' abstract: - lang: eng text: 'Neural network modeling is often concerned with stimulus-driven responses, but most of the activity in the brain is internally generated. Here, we review network models of internally generated activity, focusing on three types of network dynamics: (a) sustained responses to transient stimuli, which provide a model of working memory; (b) oscillatory network activity; and (c) chaotic activity, which models complex patterns of background spiking in cortical and other circuits. We also review propagation of stimulus-driven activity through spontaneously active networks. Exploring these aspects of neural network dynamics is critical for understanding how neural circuits produce cognitive function.' article_processing_charge: No article_type: review author: - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 - first_name: Kanaka full_name: Rajan, Kanaka last_name: Rajan - first_name: L.F. full_name: Abbott, L.F. last_name: Abbott citation: ama: Vogels TP, Rajan K, Abbott LF. Neural network dynamics. Annual Review of Neuroscience. 2005;28(1):357-376. doi:10.1146/annurev.neuro.28.061604.135637 apa: Vogels, T. P., Rajan, K., & Abbott, L. F. (2005). Neural network dynamics. Annual Review of Neuroscience. Annual Reviews. https://doi.org/10.1146/annurev.neuro.28.061604.135637 chicago: Vogels, Tim P, Kanaka Rajan, and L.F. Abbott. “Neural Network Dynamics.” Annual Review of Neuroscience. Annual Reviews, 2005. https://doi.org/10.1146/annurev.neuro.28.061604.135637. ieee: T. P. Vogels, K. Rajan, and L. F. Abbott, “Neural network dynamics,” Annual Review of Neuroscience, vol. 28, no. 1. Annual Reviews, pp. 357–376, 2005. ista: Vogels TP, Rajan K, Abbott LF. 2005. Neural network dynamics. Annual Review of Neuroscience. 28(1), 357–376. mla: Vogels, Tim P., et al. “Neural Network Dynamics.” Annual Review of Neuroscience, vol. 28, no. 1, Annual Reviews, 2005, pp. 357–76, doi:10.1146/annurev.neuro.28.061604.135637. short: T.P. Vogels, K. Rajan, L.F. Abbott, Annual Review of Neuroscience 28 (2005) 357–376. date_created: 2020-06-25T13:13:11Z date_published: 2005-07-21T00:00:00Z date_updated: 2021-01-12T08:16:37Z day: '21' doi: 10.1146/annurev.neuro.28.061604.135637 extern: '1' external_id: pmid: - '16022600' intvolume: ' 28' issue: '1' language: - iso: eng month: '07' oa_version: None page: 357-376 pmid: 1 publication: Annual Review of Neuroscience publication_identifier: issn: - 0147-006X - 1545-4126 publication_status: published publisher: Annual Reviews quality_controlled: '1' status: public title: Neural network dynamics type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 28 year: '2005' ... --- _id: '9491' abstract: - lang: eng text: Cytosine DNA methylation in vertebrates is widespread, but methylation in plants is found almost exclusively at transposable elements and repetitive DNA [1]. Within regions of methylation, methylcytosines are typically found in CG, CNG, and asymmetric contexts. CG sites are maintained by a plant homolog of mammalian Dnmt1 acting on hemi-methylated DNA after replication. Methylation of CNG and asymmetric sites appears to be maintained at each cell cycle by other mechanisms. We report a new type of DNA methylation in Arabidopsis, dense CG methylation clusters found at scattered sites throughout the genome. These clusters lack non-CG methylation and are preferentially found in genes, although they are relatively deficient toward the 5′ end. CG methylation clusters are present in lines derived from different accessions and in mutants that eliminate de novo methylation, indicating that CG methylation clusters are stably maintained at specific sites. Because 5-methylcytosine is mutagenic, the appearance of CG methylation clusters over evolutionary time predicts a genome-wide deficiency of CG dinucleotides and an excess of C(A/T)G trinucleotides within transcribed regions. This is exactly what we find, implying that CG methylation clusters have contributed profoundly to plant gene evolution. We suggest that CG methylation clusters silence cryptic promoters that arise sporadically within transcription units. article_processing_charge: No article_type: original author: - first_name: Robert K. full_name: Tran, Robert K. last_name: Tran - first_name: Jorja G. full_name: Henikoff, Jorja G. last_name: Henikoff - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 - first_name: Renata F. full_name: Ditt, Renata F. last_name: Ditt - first_name: Steven E. full_name: Jacobsen, Steven E. last_name: Jacobsen - first_name: Steven full_name: Henikoff, Steven last_name: Henikoff citation: ama: Tran RK, Henikoff JG, Zilberman D, Ditt RF, Jacobsen SE, Henikoff S. DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. Current Biology. 2005;15(2):154-159. doi:10.1016/j.cub.2005.01.008 apa: Tran, R. K., Henikoff, J. G., Zilberman, D., Ditt, R. F., Jacobsen, S. E., & Henikoff, S. (2005). DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2005.01.008 chicago: Tran, Robert K., Jorja G. Henikoff, Daniel Zilberman, Renata F. Ditt, Steven E. Jacobsen, and Steven Henikoff. “DNA Methylation Profiling Identifies CG Methylation Clusters in Arabidopsis Genes.” Current Biology. Elsevier, 2005. https://doi.org/10.1016/j.cub.2005.01.008. ieee: R. K. Tran, J. G. Henikoff, D. Zilberman, R. F. Ditt, S. E. Jacobsen, and S. Henikoff, “DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes,” Current Biology, vol. 15, no. 2. Elsevier, pp. 154–159, 2005. ista: Tran RK, Henikoff JG, Zilberman D, Ditt RF, Jacobsen SE, Henikoff S. 2005. DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. Current Biology. 15(2), 154–159. mla: Tran, Robert K., et al. “DNA Methylation Profiling Identifies CG Methylation Clusters in Arabidopsis Genes.” Current Biology, vol. 15, no. 2, Elsevier, 2005, pp. 154–59, doi:10.1016/j.cub.2005.01.008. short: R.K. Tran, J.G. Henikoff, D. Zilberman, R.F. Ditt, S.E. Jacobsen, S. Henikoff, Current Biology 15 (2005) 154–159. date_created: 2021-06-07T10:24:30Z date_published: 2005-01-26T00:00:00Z date_updated: 2021-12-14T09:12:26Z day: '26' department: - _id: DaZi doi: 10.1016/j.cub.2005.01.008 extern: '1' external_id: pmid: - '15668172 ' intvolume: ' 15' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.cub.2005.01.008 month: '01' oa: 1 oa_version: Published Version page: 154-159 pmid: 1 publication: Current Biology publication_identifier: eissn: - 1879-0445 issn: - 0960-9822 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 15 year: '2005' ... --- _id: '9514' abstract: - lang: eng text: "Background:\r\nDNA methylation occurs at preferred sites in eukaryotes. In Arabidopsis, DNA cytosine methylation is maintained by three subfamilies of methyltransferases with distinct substrate specificities and different modes of action. Targeting of cytosine methylation at selected loci has been found to sometimes involve histone H3 methylation and small interfering (si)RNAs. However, the relationship between different cytosine methylation pathways and their preferred targets is not known.\r\nResults:\r\nWe used a microarray-based profiling method to explore the involvement of Arabidopsis CMT3 and DRM DNA methyltransferases, a histone H3 lysine-9 methyltransferase (KYP) and an Argonaute-related siRNA silencing component (AGO4) in methylating target loci. We found that KYP targets are also CMT3 targets, suggesting that histone methylation maintains CNG methylation genome-wide. CMT3 and KYP targets show similar proximal distributions that correspond to the overall distribution of transposable elements of all types, whereas DRM targets are distributed more distally along the chromosome. We find an inverse relationship between element size and loss of methylation in ago4 and drm mutants.\r\nConclusion:\r\nWe conclude that the targets of both DNA methylation and histone H3K9 methylation pathways are transposable elements genome-wide, irrespective of element type and position. Our findings also suggest that RNA-directed DNA methylation is required to silence isolated elements that may be too small to be maintained in a silent state by a chromatin-based mechanism alone. Thus, parallel pathways would be needed to maintain silencing of transposable elements." article_number: R90 article_processing_charge: No article_type: original author: - first_name: Robert K. full_name: Tran, Robert K. last_name: Tran - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 - first_name: Cecilia full_name: de Bustos, Cecilia last_name: de Bustos - first_name: Renata F. full_name: Ditt, Renata F. last_name: Ditt - first_name: Jorja G. full_name: Henikoff, Jorja G. last_name: Henikoff - first_name: Anders M. full_name: Lindroth, Anders M. last_name: Lindroth - first_name: Jeffrey full_name: Delrow, Jeffrey last_name: Delrow - first_name: Tom full_name: Boyle, Tom last_name: Boyle - first_name: Samson full_name: Kwong, Samson last_name: Kwong - first_name: Terri D. full_name: Bryson, Terri D. last_name: Bryson - first_name: Steven E. full_name: Jacobsen, Steven E. last_name: Jacobsen - first_name: Steven full_name: Henikoff, Steven last_name: Henikoff citation: ama: Tran RK, Zilberman D, de Bustos C, et al. Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis. Genome Biology. 2005;6(11). doi:10.1186/gb-2005-6-11-r90 apa: Tran, R. K., Zilberman, D., de Bustos, C., Ditt, R. F., Henikoff, J. G., Lindroth, A. M., … Henikoff, S. (2005). Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis. Genome Biology. Springer Nature. https://doi.org/10.1186/gb-2005-6-11-r90 chicago: Tran, Robert K., Daniel Zilberman, Cecilia de Bustos, Renata F. Ditt, Jorja G. Henikoff, Anders M. Lindroth, Jeffrey Delrow, et al. “Chromatin and SiRNA Pathways Cooperate to Maintain DNA Methylation of Small Transposable Elements in Arabidopsis.” Genome Biology. Springer Nature, 2005. https://doi.org/10.1186/gb-2005-6-11-r90. ieee: R. K. Tran et al., “Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis,” Genome Biology, vol. 6, no. 11. Springer Nature, 2005. ista: Tran RK, Zilberman D, de Bustos C, Ditt RF, Henikoff JG, Lindroth AM, Delrow J, Boyle T, Kwong S, Bryson TD, Jacobsen SE, Henikoff S. 2005. Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis. Genome Biology. 6(11), R90. mla: Tran, Robert K., et al. “Chromatin and SiRNA Pathways Cooperate to Maintain DNA Methylation of Small Transposable Elements in Arabidopsis.” Genome Biology, vol. 6, no. 11, R90, Springer Nature, 2005, doi:10.1186/gb-2005-6-11-r90. short: R.K. Tran, D. Zilberman, C. de Bustos, R.F. Ditt, J.G. Henikoff, A.M. Lindroth, J. Delrow, T. Boyle, S. Kwong, T.D. Bryson, S.E. Jacobsen, S. Henikoff, Genome Biology 6 (2005). date_created: 2021-06-07T13:12:41Z date_published: 2005-10-19T00:00:00Z date_updated: 2021-12-14T09:09:41Z day: '19' department: - _id: DaZi doi: 10.1186/gb-2005-6-11-r90 extern: '1' external_id: pmid: - '16277745' intvolume: ' 6' issue: '11' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1186/gb-2005-6-11-r90 month: '10' oa: 1 oa_version: Published Version pmid: 1 publication: Genome Biology publication_identifier: eissn: - 1465-6906 issn: - 1474-760X publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 6 year: '2005' ... --- _id: '843' abstract: - lang: eng text: The impact of an amino acid replacement on the organism's fitness can vary from lethal to selectively neutral and even, in rare cases, beneficial. Substantial data are available on either pathogenic or acceptable replacements. However, the whole distribution of coefficients of selection against individual replacements is not known for any organism. To ascertain this distribution for human proteins, we combined data on pathogenic missense mutations, on human non-synonymous SNPs and on human-chimpanzee divergence of orthologous proteins. Fractions of amino acid replacements which reduce fitness by >10-2, 10-2-10-4, 10-4-10-5 and <10-5 are 25, 49, 14 and 12%, respectively. On average, the strength of selection against a replacement is substantially higher when chemically dissimilar amino acids are involved, and the Grantham's index of a replacement explains 35% of variance in the average logarithm of selection coefficients associated with different replacements. Still, the impact of a replacement depends on its context within the protein more than on its own nature. Reciprocal replacements are often associated with rather different selection coefficients, in particular, replacements of non-polar amino acids with polar ones are typically much more deleterious than replacements in the opposite direction. However, differences between evolutionary fluxes of reciprocal replacements are only weakly correlated with the differences between the corresponding selection coefficients. author: - first_name: Lev full_name: Yampolsky, Lev Y last_name: Yampolsky - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Alexey full_name: Kondrashov, Alexey S last_name: Kondrashov citation: ama: Yampolsky L, Kondrashov F, Kondrashov A. Distribution of the strength of selection against amino acid replacements in human proteins. Human Molecular Genetics. 2005;14(21):3191-3201. doi:10.1093/hmg/ddi350 apa: Yampolsky, L., Kondrashov, F., & Kondrashov, A. (2005). Distribution of the strength of selection against amino acid replacements in human proteins. Human Molecular Genetics. Oxford University Press. https://doi.org/10.1093/hmg/ddi350 chicago: Yampolsky, Lev, Fyodor Kondrashov, and Alexey Kondrashov. “Distribution of the Strength of Selection against Amino Acid Replacements in Human Proteins.” Human Molecular Genetics. Oxford University Press, 2005. https://doi.org/10.1093/hmg/ddi350. ieee: L. Yampolsky, F. Kondrashov, and A. Kondrashov, “Distribution of the strength of selection against amino acid replacements in human proteins,” Human Molecular Genetics, vol. 14, no. 21. Oxford University Press, pp. 3191–3201, 2005. ista: Yampolsky L, Kondrashov F, Kondrashov A. 2005. Distribution of the strength of selection against amino acid replacements in human proteins. Human Molecular Genetics. 14(21), 3191–3201. mla: Yampolsky, Lev, et al. “Distribution of the Strength of Selection against Amino Acid Replacements in Human Proteins.” Human Molecular Genetics, vol. 14, no. 21, Oxford University Press, 2005, pp. 3191–201, doi:10.1093/hmg/ddi350. short: L. Yampolsky, F. Kondrashov, A. Kondrashov, Human Molecular Genetics 14 (2005) 3191–3201. date_created: 2018-12-11T11:48:48Z date_published: 2005-11-01T00:00:00Z date_updated: 2021-01-12T08:19:13Z day: '01' doi: 10.1093/hmg/ddi350 extern: 1 intvolume: ' 14' issue: '21' month: '11' page: 3191 - 3201 publication: Human Molecular Genetics publication_status: published publisher: Oxford University Press publist_id: '6807' quality_controlled: 0 status: public title: Distribution of the strength of selection against amino acid replacements in human proteins type: journal_article volume: 14 year: '2005' ...