[{"month":"11","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Information processing in the sensory periphery is shaped by natural stimulus statistics. In the periphery, a transmission bottleneck constrains performance; thus efficient coding implies that natural signal components with a predictably wider range should be compressed. In a different regime—when sampling limitations constrain performance—efficient coding implies that more resources should be allocated to informative features that are more variable. We propose that this regime is relevant for sensory cortex when it extracts complex features from limited numbers of sensory samples. To test this prediction, we use central visual processing as a model: we show that visual sensitivity for local multi-point spatial correlations, described by dozens of independently-measured parameters, can be quantitatively predicted from the structure of natural images. This suggests that efficient coding applies centrally, where it extends to higher-order sensory features and operates in a regime in which sensitivity increases with feature variability."}],"license":"https://creativecommons.org/licenses/by/4.0/","issue":"November","language":[{"iso":"eng"}],"file":[{"creator":"system","file_size":5117086,"date_updated":"2020-07-14T12:45:20Z","file_name":"IST-2016-420-v1+1_e03722.full.pdf","date_created":"2018-12-12T10:12:04Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"766ac8999ac6e3364f10065a06024b8f","file_id":"4922"}],"publication_status":"published","pubrep_id":"420","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"1886","department":[{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:45:20Z","ddc":["570"],"date_updated":"2021-01-12T06:53:50Z","oa":1,"quality_controlled":"1","publisher":"eLife Sciences Publications","date_created":"2018-12-11T11:54:32Z","date_published":"2014-11-14T00:00:00Z","doi":"10.7554/eLife.03722","publication":"eLife","day":"14","year":"2014","has_accepted_license":"1","project":[{"grant_number":"P 25651-N26","name":"Sensitivity to higher-order statistics in natural scenes","call_identifier":"FWF","_id":"254D1A94-B435-11E9-9278-68D0E5697425"}],"article_number":"e03722","title":"Variance predicts salience in central sensory processing","publist_id":"5209","author":[{"first_name":"Ann","last_name":"Hermundstad","full_name":"Hermundstad, Ann"},{"first_name":"John","last_name":"Briguglio","full_name":"Briguglio, John"},{"first_name":"Mary","last_name":"Conte","full_name":"Conte, Mary"},{"full_name":"Victor, Jonathan","last_name":"Victor","first_name":"Jonathan"},{"first_name":"Vijay","full_name":"Balasubramanian, Vijay","last_name":"Balasubramanian"},{"full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"short":"A. Hermundstad, J. Briguglio, M. Conte, J. Victor, V. Balasubramanian, G. Tkačik, ELife (2014).","ieee":"A. Hermundstad, J. Briguglio, M. Conte, J. Victor, V. Balasubramanian, and G. Tkačik, “Variance predicts salience in central sensory processing,” eLife, no. November. eLife Sciences Publications, 2014.","ama":"Hermundstad A, Briguglio J, Conte M, Victor J, Balasubramanian V, Tkačik G. Variance predicts salience in central sensory processing. eLife. 2014;(November). doi:10.7554/eLife.03722","apa":"Hermundstad, A., Briguglio, J., Conte, M., Victor, J., Balasubramanian, V., & Tkačik, G. (2014). Variance predicts salience in central sensory processing. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.03722","mla":"Hermundstad, Ann, et al. “Variance Predicts Salience in Central Sensory Processing.” ELife, no. November, e03722, eLife Sciences Publications, 2014, doi:10.7554/eLife.03722.","ista":"Hermundstad A, Briguglio J, Conte M, Victor J, Balasubramanian V, Tkačik G. 2014. Variance predicts salience in central sensory processing. eLife. (November), e03722.","chicago":"Hermundstad, Ann, John Briguglio, Mary Conte, Jonathan Victor, Vijay Balasubramanian, and Gašper Tkačik. “Variance Predicts Salience in Central Sensory Processing.” ELife. eLife Sciences Publications, 2014. https://doi.org/10.7554/eLife.03722."}},{"acknowledgement":"The work was supported by the VEGA Grant No. 1/0459/13 (R.K. and K.B.).","oa":1,"publisher":"American Institute of Physics","publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","day":"04","year":"2014","date_created":"2018-12-11T11:54:35Z","date_published":"2014-03-04T00:00:00Z","doi":"10.1103/PhysRevE.89.032701","article_number":"032701","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Kollár, Richard, et al. “Mathematical Model of Alternative Mechanism of Telomere Length Maintenance.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 89, no. 3, 032701, American Institute of Physics, 2014, doi:10.1103/PhysRevE.89.032701.","ama":"Kollár R, Bodova K, Nosek J, Tomáška Ľ. Mathematical model of alternative mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2014;89(3). doi:10.1103/PhysRevE.89.032701","apa":"Kollár, R., Bodova, K., Nosek, J., & Tomáška, Ľ. (2014). Mathematical model of alternative mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.89.032701","short":"R. Kollár, K. Bodova, J. Nosek, Ľ. Tomáška, Physical Review E Statistical Nonlinear and Soft Matter Physics 89 (2014).","ieee":"R. Kollár, K. Bodova, J. Nosek, and Ľ. Tomáška, “Mathematical model of alternative mechanism of telomere length maintenance,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 89, no. 3. American Institute of Physics, 2014.","chicago":"Kollár, Richard, Katarina Bodova, Jozef Nosek, and Ľubomír Tomáška. “Mathematical Model of Alternative Mechanism of Telomere Length Maintenance.” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2014. https://doi.org/10.1103/PhysRevE.89.032701.","ista":"Kollár R, Bodova K, Nosek J, Tomáška Ľ. 2014. Mathematical model of alternative mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear and Soft Matter Physics. 89(3), 032701."},"title":"Mathematical model of alternative mechanism of telomere length maintenance","article_processing_charge":"No","publist_id":"5198","author":[{"last_name":"Kollár","full_name":"Kollár, Richard","first_name":"Richard"},{"id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","first_name":"Katarína","orcid":"0000-0002-7214-0171","full_name":"Bod'ová, Katarína","last_name":"Bod'ová"},{"first_name":"Jozef","full_name":"Nosek, Jozef","last_name":"Nosek"},{"first_name":"Ľubomír","full_name":"Tomáška, Ľubomír","last_name":"Tomáška"}],"oa_version":"Submitted Version","abstract":[{"text":"Biopolymer length regulation is a complex process that involves a large number of biological, chemical, and physical subprocesses acting simultaneously across multiple spatial and temporal scales. An illustrative example important for genomic stability is the length regulation of telomeres - nucleoprotein structures at the ends of linear chromosomes consisting of tandemly repeated DNA sequences and a specialized set of proteins. Maintenance of telomeres is often facilitated by the enzyme telomerase but, particularly in telomerase-free systems, the maintenance of chromosomal termini depends on alternative lengthening of telomeres (ALT) mechanisms mediated by recombination. Various linear and circular DNA structures were identified to participate in ALT, however, dynamics of the whole process is still poorly understood. We propose a chemical kinetics model of ALT with kinetic rates systematically derived from the biophysics of DNA diffusion and looping. The reaction system is reduced to a coagulation-fragmentation system by quasi-steady-state approximation. The detailed treatment of kinetic rates yields explicit formulas for expected size distributions of telomeres that demonstrate the key role played by the J factor, a quantitative measure of bending of polymers. The results are in agreement with experimental data and point out interesting phenomena: an appearance of very long telomeric circles if the total telomere density exceeds a critical value (excess mass) and a nonlinear response of the telomere size distributions to the amount of telomeric DNA in the system. The results can be of general importance for understanding dynamics of telomeres in telomerase-independent systems as this mode of telomere maintenance is similar to the situation in tumor cells lacking telomerase activity. Furthermore, due to its universality, the model may also serve as a prototype of an interaction between linear and circular DNA structures in various settings.","lang":"eng"}],"intvolume":" 89","month":"03","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1402.0430"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","volume":89,"issue":"3","_id":"1896","status":"public","type":"journal_article","date_updated":"2022-08-01T10:50:10Z","department":[{"_id":"NiBa"},{"_id":"GaTk"}]},{"volume":28,"issue":"3","file":[{"file_id":"5167","checksum":"3cbe8623174709a8ceec2103246f8fe0","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2016-419-v1+1_Ezard_et_al-2014-Functional_Ecology.pdf","date_created":"2018-12-12T10:15:45Z","file_size":536154,"date_updated":"2020-07-14T12:45:20Z","creator":"system"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"06","intvolume":" 28","scopus_import":1,"oa_version":"Published Version","abstract":[{"text":"Summary: Phenotypes are often environmentally dependent, which requires organisms to track environmental change. The challenge for organisms is to construct phenotypes using the most accurate environmental cue. Here, we use a quantitative genetic model of adaptation by additive genetic variance, within- and transgenerational plasticity via linear reaction norms and indirect genetic effects respectively. We show how the relative influence on the eventual phenotype of these components depends on the predictability of environmental change (fast or slow, sinusoidal or stochastic) and the developmental lag τ between when the environment is perceived and when selection acts. We then decompose expected mean fitness into three components (variance load, adaptation and fluctuation load) to study the fitness costs of within- and transgenerational plasticity. A strongly negative maternal effect coefficient m minimizes the variance load, but a strongly positive m minimises the fluctuation load. The adaptation term is maximized closer to zero, with positive or negative m preferred under different environmental scenarios. Phenotypic plasticity is higher when τ is shorter and when the environment changes frequently between seasonal extremes. Expected mean population fitness is highest away from highest observed levels of phenotypic plasticity. Within- and transgenerational plasticity act in concert to deliver well-adapted phenotypes, which emphasizes the need to study both simultaneously when investigating phenotypic evolution.","lang":"eng"}],"department":[{"_id":"NiBa"},{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:45:20Z","ddc":["570"],"date_updated":"2021-01-12T06:54:00Z","status":"public","pubrep_id":"419","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"1909","date_published":"2014-06-01T00:00:00Z","doi":"10.1111/1365-2435.12207","date_created":"2018-12-11T11:54:40Z","page":"693 - 701","day":"01","publication":"Functional Ecology","has_accepted_license":"1","year":"2014","publisher":"Wiley-Blackwell","oa":1,"acknowledgement":"Engineering and Physical Sciences Research Council. Grant Number: EP/H031928/1","title":"The fitness costs of adaptation via phenotypic plasticity and maternal effects","publist_id":"5186","author":[{"full_name":"Ezard, Thomas","last_name":"Ezard","first_name":"Thomas"},{"last_name":"Prizak","full_name":"Prizak, Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87","first_name":"Roshan"},{"last_name":"Hoyle","full_name":"Hoyle, Rebecca","first_name":"Rebecca"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Ezard T, Prizak R, Hoyle R. The fitness costs of adaptation via phenotypic plasticity and maternal effects. Functional Ecology. 2014;28(3):693-701. doi:10.1111/1365-2435.12207","apa":"Ezard, T., Prizak, R., & Hoyle, R. (2014). The fitness costs of adaptation via phenotypic plasticity and maternal effects. Functional Ecology. Wiley-Blackwell. https://doi.org/10.1111/1365-2435.12207","ieee":"T. Ezard, R. Prizak, and R. Hoyle, “The fitness costs of adaptation via phenotypic plasticity and maternal effects,” Functional Ecology, vol. 28, no. 3. Wiley-Blackwell, pp. 693–701, 2014.","short":"T. Ezard, R. Prizak, R. Hoyle, Functional Ecology 28 (2014) 693–701.","mla":"Ezard, Thomas, et al. “The Fitness Costs of Adaptation via Phenotypic Plasticity and Maternal Effects.” Functional Ecology, vol. 28, no. 3, Wiley-Blackwell, 2014, pp. 693–701, doi:10.1111/1365-2435.12207.","ista":"Ezard T, Prizak R, Hoyle R. 2014. The fitness costs of adaptation via phenotypic plasticity and maternal effects. Functional Ecology. 28(3), 693–701.","chicago":"Ezard, Thomas, Roshan Prizak, and Rebecca Hoyle. “The Fitness Costs of Adaptation via Phenotypic Plasticity and Maternal Effects.” Functional Ecology. Wiley-Blackwell, 2014. https://doi.org/10.1111/1365-2435.12207."}},{"intvolume":" 360","month":"11","publisher":"Elsevier","scopus_import":1,"acknowledgement":"J.H. received support from the Zdenek Bakala Foundation and the Mobility Fund of Charles University in Prague.","oa_version":"None","abstract":[{"text":"In infectious disease epidemiology the basic reproductive ratio, R0, is defined as the average number of new infections caused by a single infected individual in a fully susceptible population. Many models describing competition for hosts between non-interacting pathogen strains in an infinite population lead to the conclusion that selection favors invasion of new strains if and only if they have higher R0 values than the resident. Here we demonstrate that this picture fails in finite populations. Using a simple stochastic SIS model, we show that in general there is no analogous optimization principle. We find that successive invasions may in some cases lead to strains that infect a smaller fraction of the host population, and that mutually invasible pathogen strains exist. In the limit of weak selection we demonstrate that an optimization principle does exist, although it differs from R0 maximization. For strains with very large R0, we derive an expression for this local fitness function and use it to establish a lower bound for the error caused by neglecting stochastic effects. Furthermore, we apply this weak selection limit to investigate the selection dynamics in the presence of a trade-off between the virulence and the transmission rate of a pathogen.","lang":"eng"}],"date_created":"2018-12-11T11:54:46Z","volume":360,"date_published":"2014-11-07T00:00:00Z","doi":"10.1016/j.jtbi.2014.06.039","page":"149 - 162","publication":"Journal of Theoretical Biology","language":[{"iso":"eng"}],"day":"07","publication_status":"published","year":"2014","status":"public","type":"journal_article","_id":"1928","title":"Evolutionary dynamics of infectious diseases in finite populations","department":[{"_id":"GaTk"}],"publist_id":"5166","author":[{"first_name":"Jan","id":"2E9627A8-F248-11E8-B48F-1D18A9856A87","last_name":"Humplik","full_name":"Humplik, Jan"},{"full_name":"Hill, Alison","last_name":"Hill","first_name":"Alison"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:54:08Z","citation":{"mla":"Humplik, Jan, et al. “Evolutionary Dynamics of Infectious Diseases in Finite Populations.” Journal of Theoretical Biology, vol. 360, Elsevier, 2014, pp. 149–62, doi:10.1016/j.jtbi.2014.06.039.","short":"J. Humplik, A. Hill, M. Nowak, Journal of Theoretical Biology 360 (2014) 149–162.","ieee":"J. Humplik, A. Hill, and M. Nowak, “Evolutionary dynamics of infectious diseases in finite populations,” Journal of Theoretical Biology, vol. 360. Elsevier, pp. 149–162, 2014.","apa":"Humplik, J., Hill, A., & Nowak, M. (2014). Evolutionary dynamics of infectious diseases in finite populations. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2014.06.039","ama":"Humplik J, Hill A, Nowak M. Evolutionary dynamics of infectious diseases in finite populations. Journal of Theoretical Biology. 2014;360:149-162. doi:10.1016/j.jtbi.2014.06.039","chicago":"Humplik, Jan, Alison Hill, and Martin Nowak. “Evolutionary Dynamics of Infectious Diseases in Finite Populations.” Journal of Theoretical Biology. Elsevier, 2014. https://doi.org/10.1016/j.jtbi.2014.06.039.","ista":"Humplik J, Hill A, Nowak M. 2014. Evolutionary dynamics of infectious diseases in finite populations. Journal of Theoretical Biology. 360, 149–162."}},{"volume":8,"issue":"MAY","publication_status":"published","language":[{"iso":"eng"}],"scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4035833/"}],"month":"05","intvolume":" 8","abstract":[{"text":"A wealth of experimental evidence suggests that working memory circuits preferentially represent information that is behaviorally relevant. Still, we are missing a mechanistic account of how these representations come about. Here we provide a simple explanation for a range of experimental findings, in light of prefrontal circuits adapting to task constraints by reward-dependent learning. In particular, we model a neural network shaped by reward-modulated spike-timing dependent plasticity (r-STDP) and homeostatic plasticity (intrinsic excitability and synaptic scaling). We show that the experimentally-observed neural representations naturally emerge in an initially unstructured circuit as it learns to solve several working memory tasks. These results point to a critical, and previously unappreciated, role for reward-dependent learning in shaping prefrontal cortex activity.","lang":"eng"}],"oa_version":"Submitted Version","department":[{"_id":"GaTk"}],"date_updated":"2021-01-12T06:54:09Z","type":"journal_article","status":"public","_id":"1931","doi":"10.3389/fncom.2014.00057","date_published":"2014-05-28T00:00:00Z","date_created":"2018-12-11T11:54:46Z","year":"2014","day":"28","publication":"Frontiers in Computational Neuroscience","publisher":"Frontiers Research Foundation","quality_controlled":"1","oa":1,"acknowledgement":"Supported in part by EC MEXT project PLICON and the LOEWE-Program “Neuronal Coordination Research Focus Frankfurt” (NeFF). Jochen Triesch was supported by the Quandt foundation.","author":[{"id":"3933349E-F248-11E8-B48F-1D18A9856A87","first_name":"Cristina","last_name":"Savin","full_name":"Savin, Cristina"},{"first_name":"Jochen","last_name":"Triesch","full_name":"Triesch, Jochen"}],"publist_id":"5163","title":"Emergence of task-dependent representations in working memory circuits","citation":{"mla":"Savin, Cristina, and Jochen Triesch. “Emergence of Task-Dependent Representations in Working Memory Circuits.” Frontiers in Computational Neuroscience, vol. 8, no. MAY, 57, Frontiers Research Foundation, 2014, doi:10.3389/fncom.2014.00057.","ama":"Savin C, Triesch J. Emergence of task-dependent representations in working memory circuits. Frontiers in Computational Neuroscience. 2014;8(MAY). doi:10.3389/fncom.2014.00057","apa":"Savin, C., & Triesch, J. (2014). Emergence of task-dependent representations in working memory circuits. Frontiers in Computational Neuroscience. Frontiers Research Foundation. https://doi.org/10.3389/fncom.2014.00057","short":"C. Savin, J. Triesch, Frontiers in Computational Neuroscience 8 (2014).","ieee":"C. Savin and J. Triesch, “Emergence of task-dependent representations in working memory circuits,” Frontiers in Computational Neuroscience, vol. 8, no. MAY. Frontiers Research Foundation, 2014.","chicago":"Savin, Cristina, and Jochen Triesch. “Emergence of Task-Dependent Representations in Working Memory Circuits.” Frontiers in Computational Neuroscience. Frontiers Research Foundation, 2014. https://doi.org/10.3389/fncom.2014.00057.","ista":"Savin C, Triesch J. 2014. Emergence of task-dependent representations in working memory circuits. Frontiers in Computational Neuroscience. 8(MAY), 57."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","article_number":"57"}]