[{"abstract":[{"lang":"eng","text":"In retina and in cortical slice the collective response of spiking neural populations is well described by &quot;maximum-entropy&quot; models in which only pairs of neurons interact. We asked, how should such interactions be organized to maximize the amount of information represented in population responses? To this end, we extended the linear-nonlinear-Poisson model of single neural response to include pairwise interactions, yielding a stimulus-dependent, pairwise maximum-entropy model. We found that as we varied the noise level in single neurons and the distribution of network inputs, the optimal pairwise interactions smoothly interpolated to achieve network functions that are usually regarded as discrete–stimulus decorrelation, error correction, and independent encoding. These functions reflected a trade-off between efficient consumption of finite neural bandwidth and the use of redundancy to mitigate noise. Spontaneous activity in the optimal network reflected stimulus-induced activity patterns, and single-neuron response variability overestimated network noise. Our analysis suggests that rather than having a single coding principle hardwired in their architecture, networks in the brain should adapt their function to changing noise and stimulus correlations."}],"type":"journal_article","date_published":"2010-08-10T00:00:00Z","extern":1,"citation":{"mla":"Tkačik, Gašper, et al. “Optimal Population Coding by Noisy Spiking Neurons.” <i>PNAS</i>, vol. 107, no. 32, National Academy of Sciences, 2010, pp. 14419–24, doi:<a href=\"https://doi.org/10.1073/pnas.1004906107\">10.1073/pnas.1004906107</a>.","apa":"Tkačik, G., Prentice, J., Balasubramanian, V., &#38; Schneidman, E. (2010). Optimal population coding by noisy spiking neurons. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1004906107\">https://doi.org/10.1073/pnas.1004906107</a>","short":"G. Tkačik, J. Prentice, V. Balasubramanian, E. Schneidman, PNAS 107 (2010) 14419–14424.","ista":"Tkačik G, Prentice J, Balasubramanian V, Schneidman E. 2010. Optimal population coding by noisy spiking neurons. PNAS. 107(32), 14419–14424.","ieee":"G. Tkačik, J. Prentice, V. Balasubramanian, and E. Schneidman, “Optimal population coding by noisy spiking neurons,” <i>PNAS</i>, vol. 107, no. 32. National Academy of Sciences, pp. 14419–14424, 2010.","ama":"Tkačik G, Prentice J, Balasubramanian V, Schneidman E. Optimal population coding by noisy spiking neurons. <i>PNAS</i>. 2010;107(32):14419-14424. doi:<a href=\"https://doi.org/10.1073/pnas.1004906107\">10.1073/pnas.1004906107</a>","chicago":"Tkačik, Gašper, Jason Prentice, Vijay Balasubramanian, and Elad Schneidman. “Optimal Population Coding by Noisy Spiking Neurons.” <i>PNAS</i>. National Academy of Sciences, 2010. <a href=\"https://doi.org/10.1073/pnas.1004906107\">https://doi.org/10.1073/pnas.1004906107</a>."},"publisher":"National Academy of Sciences","author":[{"full_name":"Gasper Tkacik","orcid":"0000-0002-6699-1455","last_name":"Tkacik","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Prentice, Jason S","last_name":"Prentice","first_name":"Jason"},{"first_name":"Vijay","last_name":"Balasubramanian","full_name":"Balasubramanian, Vijay"},{"first_name":"Elad","full_name":"Schneidman, Elad","last_name":"Schneidman"}],"date_updated":"2021-01-12T07:51:50Z","day":"10","publication_status":"published","_id":"3736","intvolume":"       107","publist_id":"2492","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2922524/","open_access":"0"}],"year":"2010","acknowledgement":"R01 EY08124/EY/NEI NIH HHS/United States; T32-07035/PHS HHS/United States","month":"08","volume":107,"date_created":"2018-12-11T12:04:53Z","status":"public","page":"14419 - 14424","issue":"32","title":"Optimal population coding by noisy spiking neurons","doi":"10.1073/pnas.1004906107","quality_controlled":0,"publication":"PNAS"},{"month":"04","volume":81,"date_created":"2018-12-11T12:04:54Z","status":"public","issue":"4","doi":"10.1103/PhysRevE.81.041905","title":"Optimizing information flow in small genetic networks. II. Feed-forward interactions","publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","quality_controlled":0,"type":"journal_article","date_published":"2010-04-06T00:00:00Z","abstract":[{"text":"Central to the functioning of a living cell is its ability to control the readout or expression of information encoded in the genome. In many cases, a single transcription factor protein activates or represses the expression of many genes. As the concentration of the transcription factor varies, the target genes thus undergo correlated changes, and this redundancy limits the ability of the cell to transmit information about input signals. We explore how interactions among the target genes can reduce this redundancy and optimize information transmission. Our discussion builds on recent work [Tkacik, Phys. Rev. E 80, 031920 (2009)], and there are connections to much earlier work on the role of lateral inhibition in enhancing the efficiency of information transmission in neural circuits; for simplicity we consider here the case where the interactions have a feed forward structure, with no loops. Even with this limitation, the networks that optimize information transmission have a structure reminiscent of the networks found in real biological systems.","lang":"eng"}],"publisher":"American Institute of Physics","extern":1,"citation":{"apa":"Walczak, A., Tkačik, G., &#38; Bialek, W. (2010). Optimizing information flow in small genetic networks. II. Feed-forward interactions. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1103/PhysRevE.81.041905\">https://doi.org/10.1103/PhysRevE.81.041905</a>","mla":"Walczak, Aleksandra, et al. “Optimizing Information Flow in Small Genetic Networks. II. Feed-Forward Interactions.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 81, no. 4, American Institute of Physics, 2010, doi:<a href=\"https://doi.org/10.1103/PhysRevE.81.041905\">10.1103/PhysRevE.81.041905</a>.","ieee":"A. Walczak, G. Tkačik, and W. Bialek, “Optimizing information flow in small genetic networks. II. Feed-forward interactions,” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 81, no. 4. American Institute of Physics, 2010.","ama":"Walczak A, Tkačik G, Bialek W. Optimizing information flow in small genetic networks. II. Feed-forward interactions. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. 2010;81(4). doi:<a href=\"https://doi.org/10.1103/PhysRevE.81.041905\">10.1103/PhysRevE.81.041905</a>","chicago":"Walczak, Aleksandra, Gašper Tkačik, and William Bialek. “Optimizing Information Flow in Small Genetic Networks. II. Feed-Forward Interactions.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics, 2010. <a href=\"https://doi.org/10.1103/PhysRevE.81.041905\">https://doi.org/10.1103/PhysRevE.81.041905</a>.","ista":"Walczak A, Tkačik G, Bialek W. 2010. Optimizing information flow in small genetic networks. II. Feed-forward interactions. Physical Review E Statistical Nonlinear and Soft Matter Physics. 81(4).","short":"A. Walczak, G. Tkačik, W. Bialek, Physical Review E Statistical Nonlinear and Soft Matter Physics 81 (2010)."},"author":[{"full_name":"Walczak, Aleksandra M","last_name":"Walczak","first_name":"Aleksandra"},{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Gasper Tkacik","last_name":"Tkacik","orcid":"0000-0002-6699-1455"},{"full_name":"Bialek, William S","last_name":"Bialek","first_name":"William"}],"day":"06","date_updated":"2021-01-12T07:51:50Z","publication_status":"published","_id":"3738","intvolume":"        81","publist_id":"2494","main_file_link":[{"url":"http://arxiv.org/abs/0912.5500","open_access":"0"}],"year":"2010"},{"main_file_link":[{"url":"http://arxiv.org/abs/1006.4291v1","open_access":"1"}],"year":"2010","_id":"3743","publist_id":"2487","author":[{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Gasper Tkacik","orcid":"0000-0002-6699-1455","last_name":"Tkacik"}],"date_updated":"2021-01-12T07:51:53Z","day":"22","publication_status":"published","oa":1,"type":"preprint","abstract":[{"lang":"eng","text":"These are notes for a set of 7 two-hour lectures given at the 2010 Summer School on Quantitative Evolutionary and Comparative Genomics at OIST, Okinawa, Japan. The emphasis is on understanding how biological systems process information. We take a physicist's approach of looking for simple phenomenological descriptions that can address the questions of biological function without necessarily modeling all (mostly unknown) microscopic details; the example that is developed throughout the notes is transcriptional regulation in genetic regulatory networks. We present tools from information theory and statistical physics that can be used to analyze noisy nonlinear biological networks, and build generative and predictive models of regulatory processes."}],"date_published":"2010-06-22T00:00:00Z","citation":{"short":"G. Tkačik, ArXiv q-MN (2010) 1–52.","chicago":"Tkačik, Gašper. “From Statistical Mechanics to Information Theory: Understanding Biophysical Information-Processing Systems.” <i>ArXiv</i>. ArXiv, 2010.","ista":"Tkačik G. 2010. From statistical mechanics to information theory: understanding biophysical information-processing systems. ArXiv, q-MN, 1–52, .","ieee":"G. Tkačik, “From statistical mechanics to information theory: understanding biophysical information-processing systems,” <i>ArXiv</i>, vol. q-MN. ArXiv, pp. 1–52, 2010.","ama":"Tkačik G. From statistical mechanics to information theory: understanding biophysical information-processing systems. <i>ArXiv</i>. 2010;q-MN:1-52.","mla":"Tkačik, Gašper. “From Statistical Mechanics to Information Theory: Understanding Biophysical Information-Processing Systems.” <i>ArXiv</i>, vol. q-MN, ArXiv, 2010, pp. 1–52.","apa":"Tkačik, G. (2010). From statistical mechanics to information theory: understanding biophysical information-processing systems. <i>ArXiv</i>. ArXiv."},"publisher":"ArXiv","extern":1,"title":"From statistical mechanics to information theory: understanding biophysical information-processing systems","publication":"ArXiv","quality_controlled":0,"date_created":"2018-12-11T12:04:55Z","status":"public","page":"1 - 52","month":"06","volume":"q-bio.MN"},{"volume":468,"month":"12","publication":"Nature","quality_controlled":0,"doi":"10.1038/nature09551","title":"Interdependence of behavioural variability and response to small stimuli in bacteria","page":"819 - 823","status":"public","date_created":"2018-12-11T12:04:57Z","oa":1,"publication_status":"published","day":"09","date_updated":"2021-01-12T07:51:55Z","author":[{"full_name":"Park, Heungwon","last_name":"Park","first_name":"Heungwon"},{"last_name":"Pontius","full_name":"Pontius, William","first_name":"William"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet","full_name":"Calin Guet"},{"last_name":"Marko","full_name":"Marko, John F","first_name":"John"},{"first_name":"Thierry","full_name":"Emonet,Thierry","last_name":"Emonet"},{"first_name":"Philippe","full_name":"Cluzel,Philippe","last_name":"Cluzel"}],"extern":1,"publisher":"Nature Publishing Group","citation":{"short":"H. Park, W. Pontius, C.C. Guet, J. Marko, T. Emonet, P. Cluzel, Nature 468 (2010) 819–823.","ama":"Park H, Pontius W, Guet CC, Marko J, Emonet T, Cluzel P. Interdependence of behavioural variability and response to small stimuli in bacteria. <i>Nature</i>. 2010;468:819-823. doi:<a href=\"https://doi.org/10.1038/nature09551\">10.1038/nature09551</a>","ista":"Park H, Pontius W, Guet CC, Marko J, Emonet T, Cluzel P. 2010. Interdependence of behavioural variability and response to small stimuli in bacteria. Nature. 468, 819–823.","ieee":"H. Park, W. Pontius, C. C. Guet, J. Marko, T. Emonet, and P. Cluzel, “Interdependence of behavioural variability and response to small stimuli in bacteria,” <i>Nature</i>, vol. 468. Nature Publishing Group, pp. 819–823, 2010.","chicago":"Park, Heungwon, William Pontius, Calin C Guet, John Marko, Thierry Emonet, and Philippe Cluzel. “Interdependence of Behavioural Variability and Response to Small Stimuli in Bacteria.” <i>Nature</i>. Nature Publishing Group, 2010. <a href=\"https://doi.org/10.1038/nature09551\">https://doi.org/10.1038/nature09551</a>.","mla":"Park, Heungwon, et al. “Interdependence of Behavioural Variability and Response to Small Stimuli in Bacteria.” <i>Nature</i>, vol. 468, Nature Publishing Group, 2010, pp. 819–23, doi:<a href=\"https://doi.org/10.1038/nature09551\">10.1038/nature09551</a>.","apa":"Park, H., Pontius, W., Guet, C. C., Marko, J., Emonet, T., &#38; Cluzel, P. (2010). Interdependence of behavioural variability and response to small stimuli in bacteria. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature09551\">https://doi.org/10.1038/nature09551</a>"},"type":"journal_article","date_published":"2010-12-09T00:00:00Z","abstract":[{"lang":"eng","text":"The chemotaxis signalling network in Escherichia coli that controls the locomotion of bacteria is a classic model system for signal transduction1, 2. This pathway modulates the behaviour of flagellar motors to propel bacteria towards sources of chemical attractants. Although this system relaxes to a steady state in response to environmental changes, the signalling events within the chemotaxis network are noisy and cause large temporal variations of the motor behaviour even in the absence of stimulus3. That the same signalling network governs both behavioural variability and cellular response raises the question of whether these two traits are independent. Here, we experimentally establish a fluctuation–response relationship in the chemotaxis system of living bacteria. Using this relationship, we demonstrate the possibility of inferring the cellular response from the behavioural variability measured before stimulus. In monitoring the pre- and post-stimulus switching behaviour of individual bacterial motors, we found that variability scales linearly with the response time for different functioning states of the cell. This study highlights that the fundamental relationship between fluctuation and response is not constrained to physical systems at thermodynamic equilibrium4 but is extensible to living cells5. Such a relationship not only implies that behavioural variability and cellular response can be coupled traits, but it also provides a general framework within which we can examine how the selection of a network design shapes this interdependence"}],"year":"2010","main_file_link":[{"url":"http://europepmc.org/articles/pmc3230254","open_access":"1"}],"publist_id":"2480","intvolume":"       468","_id":"3748"},{"issue":"3","page":"764 - 769","status":"public","date_created":"2018-12-11T12:04:57Z","publication":"Current Microbiology","quality_controlled":0,"doi":"10.1007/s00284-010-9778-z","title":"Fine-tuning of chemotactic response in E. coli determined by high-throughput capillary assay","acknowledgement":"P50 GM081892-04/GM/NIGMS NIH HHS/United States\nR01 AI059195-01A1/AI/NIAID NIH HHS/United States\nR01 AI059195-02/AI/NIAID NIH HHS/United States\nR01 AI059195-03/AI/NIAID NIH HHS/United States\nR01AI059195-03/AI/NIAID NIH HHS/United States\n\n\nPMCID: PMC3230253 ","volume":62,"month":"10","publist_id":"2479","intvolume":"        62","_id":"3749","year":"2010","main_file_link":[{"open_access":"1","url":"http://europepmc.org/articles/pmc3230253"}],"citation":{"mla":"Park, Heungwon, et al. “Fine-Tuning of Chemotactic Response in E. Coli Determined by High-Throughput Capillary Assay.” <i>Current Microbiology</i>, vol. 62, no. 3, Springer, 2010, pp. 764–69, doi:<a href=\"https://doi.org/10.1007/s00284-010-9778-z\">10.1007/s00284-010-9778-z</a>.","apa":"Park, H., Guet, C. C., Emonet, T., &#38; Cluzel, P. (2010). Fine-tuning of chemotactic response in E. coli determined by high-throughput capillary assay. <i>Current Microbiology</i>. Springer. <a href=\"https://doi.org/10.1007/s00284-010-9778-z\">https://doi.org/10.1007/s00284-010-9778-z</a>","short":"H. Park, C.C. Guet, T. Emonet, P. Cluzel, Current Microbiology 62 (2010) 764–769.","ama":"Park H, Guet CC, Emonet T, Cluzel P. Fine-tuning of chemotactic response in E. coli determined by high-throughput capillary assay. <i>Current Microbiology</i>. 2010;62(3):764-769. doi:<a href=\"https://doi.org/10.1007/s00284-010-9778-z\">10.1007/s00284-010-9778-z</a>","ista":"Park H, Guet CC, Emonet T, Cluzel P. 2010. Fine-tuning of chemotactic response in E. coli determined by high-throughput capillary assay. Current Microbiology. 62(3), 764–769.","chicago":"Park, Heungwon, Calin C Guet, Thierry Emonet, and Philippe Cluzel. “Fine-Tuning of Chemotactic Response in E. Coli Determined by High-Throughput Capillary Assay.” <i>Current Microbiology</i>. Springer, 2010. <a href=\"https://doi.org/10.1007/s00284-010-9778-z\">https://doi.org/10.1007/s00284-010-9778-z</a>.","ieee":"H. Park, C. C. Guet, T. Emonet, and P. Cluzel, “Fine-tuning of chemotactic response in E. coli determined by high-throughput capillary assay,” <i>Current Microbiology</i>, vol. 62, no. 3. Springer, pp. 764–769, 2010."},"extern":1,"publisher":"Springer","type":"journal_article","date_published":"2010-10-23T00:00:00Z","abstract":[{"lang":"eng","text":"In E. coli, chemotactic behavior exhibits perfect adaptation that is robust to changes in the intracellular concentration of the chemotactic proteins, such as CheR and CheB. However, the robustness of the perfect adaptation does not explicitly imply a robust chemotactic response. Previous studies on the robustness of the chemotactic response relied on swarming assays, which can be confounded by processes besides chemotaxis, such as cellular growth and depletion of nutrients. Here, using a high-throughput capillary assay that eliminates the effects of growth, we experimentally studied how the chemotactic response depends on the relative concentration of the chemotactic proteins. We simultaneously measured both the chemotactic response of E. coli cells to L: -aspartate and the concentrations of YFP-CheR and CheB-CFP fusion proteins. We found that the chemotactic response is fine-tuned to a specific ratio of [CheR]/[CheB] with a maximum response comparable to the chemotactic response of wild-type behavior. In contrast to adaptation in chemotaxis, that is robust and exact, capillary assays revealed that the chemotactic response in swimming bacteria is fined-tuned to wild-type level of the [CheR]/[CheB] ratio."}],"oa":1,"publication_status":"published","date_updated":"2021-01-12T07:51:55Z","day":"23","author":[{"first_name":"Heungwon","last_name":"Park","full_name":"Park, Heungwon"},{"full_name":"Calin Guet","last_name":"Guet","orcid":"0000-0001-6220-2052","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thierry","full_name":"Emonet,Thierry","last_name":"Emonet"},{"full_name":"Cluzel,Philippe","last_name":"Cluzel","first_name":"Philippe"}]},{"author":[{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan"},{"last_name":"Thürey","full_name":"Thürey, Nils","first_name":"Nils"},{"first_name":"Markus","full_name":"Gross, Markus","last_name":"Gross"},{"first_name":"Greg","full_name":"Turk, Greg","last_name":"Turk"}],"date_updated":"2023-02-23T11:41:24Z","day":"01","publication_status":"published","date_published":"2010-01-01T00:00:00Z","type":"journal_article","abstract":[{"text":"We propose a mesh-based surface tracking method for fluid animation that both preserves fine surface details and robustly adjusts the topology of the surface in the presence of arbitrarily thin features like sheets and strands. We replace traditional re-sampling methods with a convex hull method for connecting surface features during topological changes. This technique permits arbitrarily thin fluid features with minimal re-sampling errors by reusing points from the original surface. We further reduce re-sampling artifacts with a subdivision-based mesh-stitching algorithm, and we use a higher order interpolating subdivision scheme to determine the location of any newly-created vertices. The resulting algorithm efficiently produces detailed fluid surfaces with arbitrarily thin features while maintaining a consistent topology with the underlying fluid simulation.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Wojtan, C., Thürey, N., Gross, M., &#38; Turk, G. (2010). Physics-inspired topology changes for thin fluid features. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/1778765.1778787\">https://doi.org/10.1145/1778765.1778787</a>","mla":"Wojtan, Chris, et al. “Physics-Inspired Topology Changes for Thin Fluid Features.” <i>ACM Transactions on Graphics</i>, vol. 29, no. 4, ACM, 2010, doi:<a href=\"https://doi.org/10.1145/1778765.1778787\">10.1145/1778765.1778787</a>.","ama":"Wojtan C, Thürey N, Gross M, Turk G. Physics-inspired topology changes for thin fluid features. <i>ACM Transactions on Graphics</i>. 2010;29(4). doi:<a href=\"https://doi.org/10.1145/1778765.1778787\">10.1145/1778765.1778787</a>","chicago":"Wojtan, Chris, Nils Thürey, Markus Gross, and Greg Turk. “Physics-Inspired Topology Changes for Thin Fluid Features.” <i>ACM Transactions on Graphics</i>. ACM, 2010. <a href=\"https://doi.org/10.1145/1778765.1778787\">https://doi.org/10.1145/1778765.1778787</a>.","ieee":"C. Wojtan, N. Thürey, M. Gross, and G. Turk, “Physics-inspired topology changes for thin fluid features,” <i>ACM Transactions on Graphics</i>, vol. 29, no. 4. ACM, 2010.","ista":"Wojtan C, Thürey N, Gross M, Turk G. 2010. Physics-inspired topology changes for thin fluid features. ACM Transactions on Graphics. 29(4).","short":"C. Wojtan, N. Thürey, M. Gross, G. Turk, ACM Transactions on Graphics 29 (2010)."},"extern":"1","publisher":"ACM","main_file_link":[{"url":"http://kucg.korea.ac.kr/seminar/2010/src/paper-2010-09-02.pdf"}],"year":"2010","_id":"3759","intvolume":"        29","publist_id":"2470","month":"01","volume":29,"language":[{"iso":"eng"}],"doi":"10.1145/1778765.1778787","title":"Physics-inspired topology changes for thin fluid features","oa_version":"None","publication":"ACM Transactions on Graphics","article_processing_charge":"No","date_created":"2018-12-11T12:05:00Z","status":"public","issue":"4"},{"language":[{"iso":"eng"}],"month":"01","volume":16,"status":"public","date_created":"2018-12-11T12:05:01Z","article_processing_charge":"No","issue":"1","page":"70 - 80","title":"Fluid simulation with articulated bodies","doi":"10.1109/TVCG.2009.66","publication":"IEEE Transactions on Visualization and Computer Graphics","oa_version":"None","citation":{"ista":"Kwatra N, Wojtan C, Carlson M, Essa I, Mucha P, Turk G. 2010. Fluid simulation with articulated bodies. IEEE Transactions on Visualization and Computer Graphics. 16(1), 70–80.","ama":"Kwatra N, Wojtan C, Carlson M, Essa I, Mucha P, Turk G. Fluid simulation with articulated bodies. <i>IEEE Transactions on Visualization and Computer Graphics</i>. 2010;16(1):70-80. doi:<a href=\"https://doi.org/10.1109/TVCG.2009.66\">10.1109/TVCG.2009.66</a>","ieee":"N. Kwatra, C. Wojtan, M. Carlson, I. Essa, P. Mucha, and G. Turk, “Fluid simulation with articulated bodies,” <i>IEEE Transactions on Visualization and Computer Graphics</i>, vol. 16, no. 1. IEEE, pp. 70–80, 2010.","chicago":"Kwatra, Nipun, Chris Wojtan, Mark Carlson, Irfan Essa, Peter Mucha, and Greg Turk. “Fluid Simulation with Articulated Bodies.” <i>IEEE Transactions on Visualization and Computer Graphics</i>. IEEE, 2010. <a href=\"https://doi.org/10.1109/TVCG.2009.66\">https://doi.org/10.1109/TVCG.2009.66</a>.","short":"N. Kwatra, C. Wojtan, M. Carlson, I. Essa, P. Mucha, G. Turk, IEEE Transactions on Visualization and Computer Graphics 16 (2010) 70–80.","apa":"Kwatra, N., Wojtan, C., Carlson, M., Essa, I., Mucha, P., &#38; Turk, G. (2010). Fluid simulation with articulated bodies. <i>IEEE Transactions on Visualization and Computer Graphics</i>. IEEE. <a href=\"https://doi.org/10.1109/TVCG.2009.66\">https://doi.org/10.1109/TVCG.2009.66</a>","mla":"Kwatra, Nipun, et al. “Fluid Simulation with Articulated Bodies.” <i>IEEE Transactions on Visualization and Computer Graphics</i>, vol. 16, no. 1, IEEE, 2010, pp. 70–80, doi:<a href=\"https://doi.org/10.1109/TVCG.2009.66\">10.1109/TVCG.2009.66</a>."},"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"IEEE","type":"journal_article","date_published":"2010-01-01T00:00:00Z","abstract":[{"text":"We present an algorithm for creating realistic animations of characters that are swimming through fluids. Our approach combines dynamic simulation with data-driven kinematic motions (motion capture data) to produce realistic animation in a fluid. The interaction of the articulated body with the fluid is performed by incorporating joint constraints with rigid animation and by extending a solid/fluid coupling method to handle articulated chains. Our solver takes as input the current state of the simulation and calculates the angular and linear accelerations of the connected bodies needed to match a particular motion sequence for the articulated body. These accelerations are used to estimate the forces and torques that are then applied to each joint. Based on this approach, we demonstrate simulated swimming results for a variety of different strokes, including crawl, backstroke, breaststroke, and butterfly. The ability to have articulated bodies interact with fluids also allows us to generate simulations of simple water creatures that are driven by simple controllers.","lang":"eng"}],"day":"01","date_updated":"2023-02-23T11:41:31Z","author":[{"first_name":"Nipun","last_name":"Kwatra","full_name":"Kwatra, Nipun"},{"full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Carlson, Mark","last_name":"Carlson","first_name":"Mark"},{"full_name":"Essa, Irfan","last_name":"Essa","first_name":"Irfan"},{"first_name":"Peter","full_name":"Mucha, Peter","last_name":"Mucha"},{"last_name":"Turk","full_name":"Turk, Greg","first_name":"Greg"}],"publication_status":"published","_id":"3761","publist_id":"2468","intvolume":"        16","year":"2010"},{"intvolume":"        29","publist_id":"2463","_id":"3766","year":"2010","type":"journal_article","date_published":"2010-07-01T00:00:00Z","abstract":[{"text":"We present an approach to simulate flows driven by surface tension based on triangle meshes. Our method consists of two simulation layers: the first layer is an Eulerian method for simulating surface tension forces that is free from typical strict time step constraints. The second simulation layer is a Lagrangian finite element method that simulates sub-grid scale wave details on the fluid surface. The surface wave simulation employs an unconditionally stable, symplectic time integration method that allows for a high propagation speed due to strong surface tension. Our approach can naturally separate the grid-and sub-grid scales based on a volumepreserving mean curvature flow. As our model for the sub-grid dynamics enforces a local conservation of mass, it leads to realistic pinch off and merging effects. In addition to this method for simulating dynamic surface tension effects, we also present an efficient non-oscillatory approximation for capturing damped surface tension behavior. These approaches allow us to efficiently simulate complex phenomena associated with strong surface tension, such as Rayleigh-Plateau instabilities and crown splashes, in a short amount of time.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Thürey, N., Wojtan, C., Gross, M., &#38; Turk, G. (2010). A multiscale approach to mesh-based surface tension flows. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/1778765.1778785\">https://doi.org/10.1145/1778765.1778785</a>","mla":"Thürey, Nils, et al. “A Multiscale Approach to Mesh-Based Surface Tension Flows.” <i>ACM Transactions on Graphics</i>, vol. 29, no. 4, ACM, 2010, doi:<a href=\"https://doi.org/10.1145/1778765.1778785\">10.1145/1778765.1778785</a>.","ama":"Thürey N, Wojtan C, Gross M, Turk G. A multiscale approach to mesh-based surface tension flows. <i>ACM Transactions on Graphics</i>. 2010;29(4). doi:<a href=\"https://doi.org/10.1145/1778765.1778785\">10.1145/1778765.1778785</a>","chicago":"Thürey, Nils, Chris Wojtan, Markus Gross, and Greg Turk. “A Multiscale Approach to Mesh-Based Surface Tension Flows.” <i>ACM Transactions on Graphics</i>. ACM, 2010. <a href=\"https://doi.org/10.1145/1778765.1778785\">https://doi.org/10.1145/1778765.1778785</a>.","ista":"Thürey N, Wojtan C, Gross M, Turk G. 2010. A multiscale approach to mesh-based surface tension flows. ACM Transactions on Graphics. 29(4).","ieee":"N. Thürey, C. Wojtan, M. Gross, and G. Turk, “A multiscale approach to mesh-based surface tension flows,” <i>ACM Transactions on Graphics</i>, vol. 29, no. 4. ACM, 2010.","short":"N. Thürey, C. Wojtan, M. Gross, G. Turk, ACM Transactions on Graphics 29 (2010)."},"publisher":"ACM","extern":"1","publication_status":"published","author":[{"last_name":"Thürey","full_name":"Thürey, Nils","first_name":"Nils"},{"full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gross","full_name":"Gross, Markus","first_name":"Markus"},{"full_name":"Turk, Greg","last_name":"Turk","first_name":"Greg"}],"day":"01","date_updated":"2023-02-23T11:41:44Z","issue":"4","article_processing_charge":"No","date_created":"2018-12-11T12:05:03Z","status":"public","oa_version":"None","publication":"ACM Transactions on Graphics","title":"A multiscale approach to mesh-based surface tension flows","doi":"10.1145/1778765.1778785","language":[{"iso":"eng"}],"volume":29,"month":"07"},{"external_id":{"isi":["000279805200002"]},"article_number":"e1000987","file":[{"content_type":"application/pdf","checksum":"5c14de2680ab483cb835096c99ee734d","date_updated":"2020-07-14T12:46:15Z","creator":"system","date_created":"2018-12-12T10:14:24Z","relation":"main_file","file_size":349965,"access_level":"open_access","file_id":"5075","file_name":"IST-2016-524-v1+1_journal.pgen.1000987.PDF"}],"author":[{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2020-07-14T12:46:15Z","oa":1,"publication_status":"published","department":[{"_id":"NiBa"}],"ddc":["570","576"],"publisher":"Public Library of Science","scopus_import":"1","date_published":"2010-06-17T00:00:00Z","type":"journal_article","title":"Understanding adaptation in large populations","publication":"PLoS Genetics","status":"public","article_processing_charge":"No","date_created":"2018-12-11T12:05:05Z","language":[{"iso":"eng"}],"corr_author":"1","year":"2010","_id":"3772","publist_id":"2454","intvolume":"         6","day":"17","date_updated":"2025-09-30T09:45:21Z","isi":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"citation":{"ama":"Barton NH. Understanding adaptation in large populations. <i>PLoS Genetics</i>. 2010;6(6). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1000987\">10.1371/journal.pgen.1000987</a>","ieee":"N. H. Barton, “Understanding adaptation in large populations,” <i>PLoS Genetics</i>, vol. 6, no. 6. Public Library of Science, 2010.","ista":"Barton NH. 2010. Understanding adaptation in large populations. PLoS Genetics. 6(6), e1000987.","chicago":"Barton, Nicholas H. “Understanding Adaptation in Large Populations.” <i>PLoS Genetics</i>. Public Library of Science, 2010. <a href=\"https://doi.org/10.1371/journal.pgen.1000987\">https://doi.org/10.1371/journal.pgen.1000987</a>.","short":"N.H. Barton, PLoS Genetics 6 (2010).","apa":"Barton, N. H. (2010). Understanding adaptation in large populations. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1000987\">https://doi.org/10.1371/journal.pgen.1000987</a>","mla":"Barton, Nicholas H. “Understanding Adaptation in Large Populations.” <i>PLoS Genetics</i>, vol. 6, no. 6, e1000987, Public Library of Science, 2010, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1000987\">10.1371/journal.pgen.1000987</a>."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1371/journal.pgen.1000987","quality_controlled":"1","oa_version":"Published Version","has_accepted_license":"1","issue":"6","month":"06","volume":6,"pubrep_id":"524"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"short":"N.H. Barton, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 365 (2010) 1825–1840.","chicago":"Barton, Nicholas H. “What Role Does Natural Selection Play in Speciation?” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society, 2010. <a href=\"https://doi.org/10.1098/rstb.2010.0001\">https://doi.org/10.1098/rstb.2010.0001</a>.","ama":"Barton NH. What role does natural selection play in speciation? <i>Philosophical Transactions of the Royal Society of London Series B, Biological Sciences</i>. 2010;365(1547):1825-1840. doi:<a href=\"https://doi.org/10.1098/rstb.2010.0001\">10.1098/rstb.2010.0001</a>","ista":"Barton NH. 2010. What role does natural selection play in speciation? Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 365(1547), 1825–1840.","ieee":"N. H. Barton, “What role does natural selection play in speciation?,” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 365, no. 1547. Royal Society, pp. 1825–1840, 2010.","mla":"Barton, Nicholas H. “What Role Does Natural Selection Play in Speciation?” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 365, no. 1547, Royal Society, 2010, pp. 1825–40, doi:<a href=\"https://doi.org/10.1098/rstb.2010.0001\">10.1098/rstb.2010.0001</a>.","apa":"Barton, N. H. (2010). What role does natural selection play in speciation? <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society. <a href=\"https://doi.org/10.1098/rstb.2010.0001\">https://doi.org/10.1098/rstb.2010.0001</a>"},"day":"12","date_updated":"2025-09-30T09:45:54Z","isi":1,"publist_id":"2455","intvolume":"       365","_id":"3773","year":"2010","acknowledgement":"The author thanks the Werner-Gren Foundation and the Royal Swedish Academy of Sciences for organizing the symposium on the ‘Origin of Species’. He also thanks Reinhard Bürger, and two anonymous referees, for their helpful comments.\r\n","volume":365,"month":"06","issue":"1547","quality_controlled":"1","oa_version":"Submitted Version","doi":"10.1098/rstb.2010.0001","scopus_import":"1","publisher":"Royal Society","abstract":[{"text":"If distinct biological species are to coexist in sympatry, they must be reproductively isolated and must exploit different limiting resources. A two-niche Levene model is analysed, in which habitat preference and survival depend on underlying additive traits. The population genetics of preference and viability are equivalent. However, there is a linear trade-off between the chances of settling in either niche, whereas viabilities may be constrained arbitrarily. With a convex trade-off, a sexual population evolves a single generalist genotype, whereas with a concave trade-off, disruptive selection favours maximal variance. A pure habitat preference evolves to global linkage equilibrium if mating occurs in a single pool, but remarkably, evolves to pairwise linkage equilibrium within niches if mating is within those niches--independent of the genetics. With a concave trade-off, the population shifts sharply between a unimodal distribution with high gene flow and a bimodal distribution with strong isolation, as the underlying genetic variance increases. However, these alternative states are only simultaneously stable for a narrow parameter range. A sharp threshold is only seen if survival in the 'wrong' niche is low; otherwise, strong isolation is impossible. Gene flow from divergent demes makes speciation much easier in parapatry than in sympatry.","lang":"eng"}],"type":"journal_article","date_published":"2010-06-12T00:00:00Z","oa":1,"publication_status":"published","department":[{"_id":"NiBa"}],"author":[{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H"}],"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pubmed/20439284","open_access":"1"}],"external_id":{"pmid":["20439284"],"isi":["000277208600009"]},"corr_author":"1","language":[{"iso":"eng"}],"page":"1825 - 1840","status":"public","pmid":1,"date_created":"2018-12-11T12:05:05Z","article_processing_charge":"No","publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","title":"What role does natural selection play in speciation?"},{"pmid":1,"status":"public","article_processing_charge":"No","date_created":"2018-12-11T12:05:06Z","page":"414 - 425","title":"Phenotypic correlates of hybridisation between red and sika deer (genus Cervus)","publication":"Journal of Animal Ecology","language":[{"iso":"eng"}],"external_id":{"isi":["000274321200014"],"pmid":["20002231"]},"scopus_import":"1","publisher":"Wiley-Blackwell","type":"journal_article","date_published":"2010-03-01T00:00:00Z","abstract":[{"lang":"eng","text":"1. Hybridisation with an invasive species has the potential to alter the phenotype and hence the ecology of a native counterpart. 2. Here data from populations of native red deer Cervus elaphus and invasive sika deer Cervus nippon in Scotland is used to assess the extent to which hybridisation between them is causing phenotypic change. This is done by regression of phenotypic traits against genetic hybrid scores. 3. Hybridisation is causing increases in the body weight of sika-like deer and decreases in the body weight of red-like females. Hybridisation is causing increases in jaw length and increases in incisor arcade breadth in sika-like females. Hybridisation is also causing decreases in incisor arcade breadth in red-like females. 4. There is currently no evidence that hybridisation is causing changes in the kidney fat weight or pregnancy rates of either population. 5. Increased phenotypic similarity between the two species is likely to lead to further hybridisation. The ecological consequences of this are difficult to predict."}],"author":[{"first_name":"Helen","full_name":"Senn, Helen","last_name":"Senn"},{"full_name":"Swanson, Graeme","last_name":"Swanson","first_name":"Graeme"},{"first_name":"Simon","full_name":"Goodman, Simon","last_name":"Goodman"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"full_name":"Pemberton, Josephine","last_name":"Pemberton","first_name":"Josephine"}],"department":[{"_id":"NiBa"}],"publication_status":"published","issue":"2","doi":"10.1111/j.1365-2656.2009.01633.x","quality_controlled":"1","oa_version":"None","acknowledgement":"This project was funded through a NERC studentship to HVS which was CASE partnered by the Macaulay Institute.\r\nWe thank the Forestry Commission Scotland rangers for all their help with providing the larder data for and samples from red and sika deer, Stephen Senn and Jarrod Hadfield for statistical advice and Steve Albon for helpful comments on the manuscript.","month":"03","volume":79,"_id":"3774","publist_id":"2453","intvolume":"        79","year":"2010","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"ista":"Senn H, Swanson G, Goodman S, Barton NH, Pemberton J. 2010. Phenotypic correlates of hybridisation between red and sika deer (genus Cervus). Journal of Animal Ecology. 79(2), 414–425.","chicago":"Senn, Helen, Graeme Swanson, Simon Goodman, Nicholas H Barton, and Josephine Pemberton. “Phenotypic Correlates of Hybridisation between Red and Sika Deer (Genus Cervus).” <i>Journal of Animal Ecology</i>. Wiley-Blackwell, 2010. <a href=\"https://doi.org/10.1111/j.1365-2656.2009.01633.x\">https://doi.org/10.1111/j.1365-2656.2009.01633.x</a>.","ama":"Senn H, Swanson G, Goodman S, Barton NH, Pemberton J. Phenotypic correlates of hybridisation between red and sika deer (genus Cervus). <i>Journal of Animal Ecology</i>. 2010;79(2):414-425. doi:<a href=\"https://doi.org/10.1111/j.1365-2656.2009.01633.x\">10.1111/j.1365-2656.2009.01633.x</a>","ieee":"H. Senn, G. Swanson, S. Goodman, N. H. Barton, and J. Pemberton, “Phenotypic correlates of hybridisation between red and sika deer (genus Cervus),” <i>Journal of Animal Ecology</i>, vol. 79, no. 2. Wiley-Blackwell, pp. 414–425, 2010.","short":"H. Senn, G. Swanson, S. Goodman, N.H. Barton, J. Pemberton, Journal of Animal Ecology 79 (2010) 414–425.","apa":"Senn, H., Swanson, G., Goodman, S., Barton, N. H., &#38; Pemberton, J. (2010). Phenotypic correlates of hybridisation between red and sika deer (genus Cervus). <i>Journal of Animal Ecology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1365-2656.2009.01633.x\">https://doi.org/10.1111/j.1365-2656.2009.01633.x</a>","mla":"Senn, Helen, et al. “Phenotypic Correlates of Hybridisation between Red and Sika Deer (Genus Cervus).” <i>Journal of Animal Ecology</i>, vol. 79, no. 2, Wiley-Blackwell, 2010, pp. 414–25, doi:<a href=\"https://doi.org/10.1111/j.1365-2656.2009.01633.x\">10.1111/j.1365-2656.2009.01633.x</a>."},"day":"01","date_updated":"2025-09-30T09:44:45Z","isi":1},{"publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","title":"Genetic linkage and natural selection","page":"2559 - 2569","status":"public","article_processing_charge":"No","date_created":"2018-12-11T12:05:06Z","language":[{"iso":"eng"}],"corr_author":"1","file":[{"content_type":"application/pdf","checksum":"4d8aade10db030124ab158b622e337e0","date_updated":"2020-07-14T12:46:15Z","creator":"system","date_created":"2018-12-12T10:14:40Z","relation":"main_file","file_name":"IST-2016-555-v1+1_RS2009_revised.pdf","file_id":"5093","file_size":250255,"access_level":"open_access"}],"external_id":{"isi":["000280097000016"]},"oa":1,"file_date_updated":"2020-07-14T12:46:15Z","publication_status":"published","department":[{"_id":"NiBa"}],"author":[{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"}],"publisher":"Royal Society","scopus_import":"1","abstract":[{"lang":"eng","text":"The prevalence of recombination in eukaryotes poses one of the most puzzling questions in biology. The most compelling general explanation is that recombination facilitates selection by breaking down the negative associations generated by random drift (i.e. Hill-Robertson interference, HRI). I classify the effects of HRI owing to: deleterious mutation, balancing selection and selective sweeps on: neutral diversity, rates of adaptation and the mutation load. These effects are mediated primarily by the density of deleterious mutations and of selective sweeps. Sequence polymorphism and divergence suggest that these rates may be high enough to cause significant interference even in genomic regions of high recombination. However, neither seems able to generate enough variance in fitness to select strongly for high rates of recombination. It is plausible that spatial and temporal fluctuations in selection generate much more fitness variance, and hence selection for recombination, than can be explained by uniformly deleterious mutations or species-wide selective sweeps."}],"type":"journal_article","date_published":"2010-08-27T00:00:00Z","ddc":["570"],"quality_controlled":"1","oa_version":"Submitted Version","doi":"10.1098/rstb.2010.0106","issue":"1552","has_accepted_license":"1","volume":365,"month":"08","pubrep_id":"555","acknowledgement":"Royal Society and Wolfson Foundation for their support\r\nWe would like to thank Brian Charlesworth and Sally Otto for their helpful comments.","year":"2010","publist_id":"2450","intvolume":"       365","_id":"3776","date_updated":"2025-09-30T09:43:27Z","day":"27","isi":1,"citation":{"ieee":"N. H. Barton, “Genetic linkage and natural selection,” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 365, no. 1552. Royal Society, pp. 2559–2569, 2010.","ama":"Barton NH. Genetic linkage and natural selection. <i>Philosophical Transactions of the Royal Society of London Series B, Biological Sciences</i>. 2010;365(1552):2559-2569. doi:<a href=\"https://doi.org/10.1098/rstb.2010.0106\">10.1098/rstb.2010.0106</a>","ista":"Barton NH. 2010. Genetic linkage and natural selection. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 365(1552), 2559–2569.","chicago":"Barton, Nicholas H. “Genetic Linkage and Natural Selection.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society, 2010. <a href=\"https://doi.org/10.1098/rstb.2010.0106\">https://doi.org/10.1098/rstb.2010.0106</a>.","short":"N.H. Barton, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 365 (2010) 2559–2569.","apa":"Barton, N. H. (2010). Genetic linkage and natural selection. <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society. <a href=\"https://doi.org/10.1098/rstb.2010.0106\">https://doi.org/10.1098/rstb.2010.0106</a>","mla":"Barton, Nicholas H. “Genetic Linkage and Natural Selection.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 365, no. 1552, Royal Society, 2010, pp. 2559–69, doi:<a href=\"https://doi.org/10.1098/rstb.2010.0106\">10.1098/rstb.2010.0106</a>."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"volume":365,"month":"04","acknowledgement":"I would like to thank W. G. Hill and L. Loewe for organizing this special issue, and the Royal Society and Wolfson Foundation for their support. Also, A. Kondrashov and L. Loewe gave very helpful comments that helped improve the manuscript.","oa_version":"Submitted Version","quality_controlled":"1","doi":"10.1098/rstb.2009.0320","issue":"1544","isi":1,"date_updated":"2025-09-30T09:44:03Z","day":"27","citation":{"apa":"Barton, N. H. (2010). Mutation and the evolution of recombination. <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society. <a href=\"https://doi.org/10.1098/rstb.2009.0320\">https://doi.org/10.1098/rstb.2009.0320</a>","mla":"Barton, Nicholas H. “Mutation and the Evolution of Recombination.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 365, no. 1544, Royal Society, 2010, pp. 1281–94, doi:<a href=\"https://doi.org/10.1098/rstb.2009.0320\">10.1098/rstb.2009.0320</a>.","chicago":"Barton, Nicholas H. “Mutation and the Evolution of Recombination.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society, 2010. <a href=\"https://doi.org/10.1098/rstb.2009.0320\">https://doi.org/10.1098/rstb.2009.0320</a>.","ama":"Barton NH. Mutation and the evolution of recombination. <i>Philosophical Transactions of the Royal Society of London Series B, Biological Sciences</i>. 2010;365(1544):1281-1294. doi:<a href=\"https://doi.org/10.1098/rstb.2009.0320\">10.1098/rstb.2009.0320</a>","ista":"Barton NH. 2010. Mutation and the evolution of recombination. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 365(1544), 1281–1294.","ieee":"N. H. Barton, “Mutation and the evolution of recombination,” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 365, no. 1544. Royal Society, pp. 1281–1294, 2010.","short":"N.H. Barton, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 365 (2010) 1281–1294."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2010","intvolume":"       365","publist_id":"2451","_id":"3777","corr_author":"1","language":[{"iso":"eng"}],"publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","title":"Mutation and the evolution of recombination","page":"1281 - 1294","date_created":"2018-12-11T12:05:07Z","article_processing_charge":"No","pmid":1,"status":"public","publication_status":"published","department":[{"_id":"NiBa"}],"oa":1,"author":[{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"type":"journal_article","abstract":[{"text":"Under the classical view, selection depends more or less directly on mutation: standing genetic variance is maintained by a balance between selection and mutation, and adaptation is fuelled by new favourable mutations. Recombination is favoured if it breaks negative associations among selected alleles, which interfere with adaptation. Such associations may be generated by negative epistasis, or by random drift (leading to the Hill-Robertson effect). Both deterministic and stochastic explanations depend primarily on the genomic mutation rate, U. This may be large enough to explain high recombination rates in some organisms, but seems unlikely to be so in general. Random drift is a more general source of negative linkage disequilibria, and can cause selection for recombination even in large populations, through the chance loss of new favourable mutations. The rate of species-wide substitutions is much too low to drive this mechanism, but local fluctuations in selection, combined with gene flow, may suffice. These arguments are illustrated by comparing the interaction between good and bad mutations at unlinked loci under the infinitesimal model.","lang":"eng"}],"date_published":"2010-04-27T00:00:00Z","scopus_import":"1","publisher":"Royal Society","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pubmed/20308104","open_access":"1"}],"external_id":{"pmid":["20308104"],"isi":["000275811000015"]}},{"has_accepted_license":"1","issue":"7","doi":"10.1371/journal.pbio.1000429","oa_version":"Published Version","quality_controlled":"1","acknowledgement":"This was supported by a Marie Curie grant for early stage training and the BBSRC-John Innes Centre PhD Rotation Program.\r\nWe would like to thank X. Feng and A. Hudson for assistance with introgressions and genotyping; A. Green, A. Bangham and J. Pateman for advice and assistance on shape model procedures; F. Alderson and S.Mitchell from JIC horticultural services; P.J. Wittkopp for protocols and advice on pyrosequencing; and R. Sablowski for discussions and comments.\r\n","pubrep_id":"366","month":"07","volume":8,"_id":"3779","intvolume":"         8","publist_id":"2448","year":"2010","citation":{"short":"U. Rosas, N.H. Barton, L. Copsey, P. Barbier De Reuille, E. Coen, PLoS Biology 8 (2010).","ama":"Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. Cryptic variation between species and the basis of hybrid performance. <i>PLoS Biology</i>. 2010;8(7). doi:<a href=\"https://doi.org/10.1371/journal.pbio.1000429\">10.1371/journal.pbio.1000429</a>","ista":"Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. 2010. Cryptic variation between species and the basis of hybrid performance. PLoS Biology. 8(7), e1000429.","chicago":"Rosas, Ulises, Nicholas H Barton, Lucy Copsey, Pierre Barbier De Reuille, and Enrico Coen. “Cryptic Variation between Species and the Basis of Hybrid Performance.” <i>PLoS Biology</i>. Public Library of Science, 2010. <a href=\"https://doi.org/10.1371/journal.pbio.1000429\">https://doi.org/10.1371/journal.pbio.1000429</a>.","ieee":"U. Rosas, N. H. Barton, L. Copsey, P. Barbier De Reuille, and E. Coen, “Cryptic variation between species and the basis of hybrid performance,” <i>PLoS Biology</i>, vol. 8, no. 7. Public Library of Science, 2010.","mla":"Rosas, Ulises, et al. “Cryptic Variation between Species and the Basis of Hybrid Performance.” <i>PLoS Biology</i>, vol. 8, no. 7, e1000429, Public Library of Science, 2010, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1000429\">10.1371/journal.pbio.1000429</a>.","apa":"Rosas, U., Barton, N. H., Copsey, L., Barbier De Reuille, P., &#38; Coen, E. (2010). Cryptic variation between species and the basis of hybrid performance. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1000429\">https://doi.org/10.1371/journal.pbio.1000429</a>"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"day":"20","date_updated":"2025-09-30T09:42:52Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"No","date_created":"2018-12-11T12:05:07Z","status":"public","title":"Cryptic variation between species and the basis of hybrid performance","publication":"PLoS Biology","language":[{"iso":"eng"}],"external_id":{"isi":["000280557100013"]},"article_number":"e1000429","file":[{"file_id":"5060","file_name":"IST-2015-366-v1+1_journal.pbio.1000429.pdf","file_size":1089530,"access_level":"open_access","date_created":"2018-12-12T10:14:11Z","relation":"main_file","date_updated":"2020-07-14T12:46:15Z","creator":"system","content_type":"application/pdf","checksum":"ee1ce2fb283a6b4127544ae532d0b4a1"}],"ddc":["576"],"type":"journal_article","date_published":"2010-07-20T00:00:00Z","abstract":[{"lang":"eng","text":"Crosses between closely related species give two contrasting results. One result is that species hybrids may be inferior to their parents, for example, being less fertile [1]. The other is that F1 hybrids may display superior performance (heterosis), for example with increased vigour [2]. Although various hypotheses have been proposed to account for these two aspects of hybridisation, their biological basis is still poorly understood [3]. To gain further insights into this issue, we analysed the role that variation in gene expression may play. We took a conserved trait, flower asymmetry in Antirrhinum, and determined the extent to which the underlying regulatory genes varied in expression among closely related species. We show that expression of both genes analysed, CYC and RAD, varies significantly between species because of cis-acting differences. By making a quantitative genotype-phenotype map, using a range of mutant alleles, we demonstrate that the species lie on a plateau in gene expression-morphology space, so that the variation has no detectable phenotypic effect. However, phenotypic differences can be revealed by shifting genotypes off the plateau through genetic crosses. Our results can be readily explained if genomes are free to evolve within an effectively neutral zone in gene expression space. The consequences of this drift will be negligible for individual loci, but when multiple loci across the genome are considered, we show that the variation may have significant effects on phenotype and fitness, causing a significant drift load. By considering these consequences for various gene-expression-fitness landscapes, we conclude that F1 hybrids might be expected to show increased performance with regard to conserved traits, such as basic physiology, but reduced performance with regard to others. Thus, our study provides a new way of explaining how various aspects of hybrid performance may arise through natural variation in gene activity."}],"scopus_import":"1","publisher":"Public Library of Science","author":[{"first_name":"Ulises","full_name":"Rosas, Ulises","last_name":"Rosas"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"first_name":"Lucy","full_name":"Copsey, Lucy","last_name":"Copsey"},{"last_name":"Barbier De Reuille","full_name":"Barbier De Reuille, Pierre","first_name":"Pierre"},{"full_name":"Coen, Enrico","last_name":"Coen","first_name":"Enrico"}],"department":[{"_id":"NiBa"}],"publication_status":"published","oa":1,"related_material":{"record":[{"status":"public","relation":"research_data","id":"9764"}]},"file_date_updated":"2020-07-14T12:46:15Z"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","citation":{"mla":"Chen, Chao, and Daniel Freedman. “Topology Noise Removal for Curve  and Surface Evolution.” <i> Conference Proceedings MCV 2010</i>, vol. 6533, Springer, 2010, pp. 31–42, doi:<a href=\"https://doi.org/10.1007/978-3-642-18421-5_4\">10.1007/978-3-642-18421-5_4</a>.","apa":"Chen, C., &#38; Freedman, D. (2010). Topology noise removal for curve  and surface evolution. In <i> Conference proceedings MCV 2010</i> (Vol. 6533, pp. 31–42). Beijing, China: Springer. <a href=\"https://doi.org/10.1007/978-3-642-18421-5_4\">https://doi.org/10.1007/978-3-642-18421-5_4</a>","short":"C. Chen, D. Freedman, in:,  Conference Proceedings MCV 2010, Springer, 2010, pp. 31–42.","ista":"Chen C, Freedman D. 2010. Topology noise removal for curve  and surface evolution.  Conference proceedings MCV 2010. MCV: Medical Computer Vision, LNCS, vol. 6533, 31–42.","chicago":"Chen, Chao, and Daniel Freedman. “Topology Noise Removal for Curve  and Surface Evolution.” In <i> Conference Proceedings MCV 2010</i>, 6533:31–42. Springer, 2010. <a href=\"https://doi.org/10.1007/978-3-642-18421-5_4\">https://doi.org/10.1007/978-3-642-18421-5_4</a>.","ama":"Chen C, Freedman D. Topology noise removal for curve  and surface evolution. In: <i> Conference Proceedings MCV 2010</i>. Vol 6533. Springer; 2010:31-42. doi:<a href=\"https://doi.org/10.1007/978-3-642-18421-5_4\">10.1007/978-3-642-18421-5_4</a>","ieee":"C. Chen and D. Freedman, “Topology noise removal for curve  and surface evolution,” in <i> Conference proceedings MCV 2010</i>, Beijing, China, 2010, vol. 6533, pp. 31–42."},"scopus_import":1,"date_published":"2010-12-31T00:00:00Z","abstract":[{"text":"In cortex surface segmentation, the extracted surface is required to have a particular topology, namely, a two-sphere. We present a new method for removing topology noise of a curve or surface within the level set framework, and thus produce a cortical surface with correct topology. We define a new energy term which quantifies topology noise. We then show how to minimize this term by computing its functional derivative with respect to the level set function. This method differs from existing methods in that it is inherently continuous and not digital; and in the way that our energy directly relates to the topology of the underlying curve or surface, versus existing knot-based measures which are related in a more indirect fashion. The proposed flow is validated empirically.","lang":"eng"}],"type":"conference","day":"31","date_updated":"2021-01-12T07:52:10Z","author":[{"id":"3E92416E-F248-11E8-B48F-1D18A9856A87","first_name":"Chao","last_name":"Chen","full_name":"Chen, Chao"},{"last_name":"Freedman","full_name":"Freedman, Daniel","first_name":"Daniel"}],"publication_status":"published","department":[{"_id":"HeEd"}],"_id":"3782","publist_id":"2445","intvolume":"      6533","year":"2010","conference":{"location":"Beijing, China","name":"MCV: Medical Computer Vision","end_date":"2010-09-20","start_date":"2010-09-20"},"acknowledgement":"Partially supported by the Austri an Science Fund unde r grant P20134-N13.\r\nWe thank Helena Molina-Abril for very helpful discussion. We thank anonymous reviewers for helpful comments.","language":[{"iso":"eng"}],"month":"12","volume":6533,"status":"public","date_created":"2018-12-11T12:05:08Z","page":"31 - 42","alternative_title":["LNCS"],"doi":"10.1007/978-3-642-18421-5_4","title":"Topology noise removal for curve  and surface evolution","publication":" Conference proceedings MCV 2010","quality_controlled":"1","oa_version":"None"},{"scopus_import":"1","publisher":"Oxford University Press","date_published":"2010-12-02T00:00:00Z","abstract":[{"lang":"eng","text":"MICROSATELIGHT is a Perl/Tk pipeline with a graphical user interface that facilitates several tasks when scoring microsatellites. It implements new subroutines in R and PERL and takes advantage of features provided by previously developed freeware. MICROSATELIGHT takes raw genotype data and automates the peak identification through PeakScanner. The PeakSelect subroutine assigns peaks to different microsatellite markers according to their multiplex group, fluorochrome type, and size range. After peak selection, binning of alleles can be carried out 1) automatically through AlleloBin or 2) by manual bin definition through Binator. In both cases, several features for quality checking and further binning improvement are provided. The genotype table can then be converted into input files for several population genetics programs through CREATE. Finally, Hardy–Weinberg equilibrium tests and confidence intervals for null allele frequency can be obtained through GENEPOP. MICROSATELIGHT is the only freely available public-domain software that facilitates full multiplex microsatellite scoring, from electropherogram files to user-defined text files to be used with population genetics software. MICROSATELIGHT has been created for the Windows XP operating system and has been successfully tested under Windows 7. It is available at http://sourceforge.net/projects/microsatelight/."}],"type":"journal_article","author":[{"full_name":"Palero, Ferran","last_name":"Palero","orcid":"0000-0002-0343-8329","id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87","first_name":"Ferran"},{"last_name":"González Candelas","full_name":"González Candelas, Fernando","first_name":"Fernando"},{"last_name":"Pascual","full_name":"Pascual, Marta","first_name":"Marta"}],"publication_status":"published","department":[{"_id":"NiBa"}],"external_id":{"isi":["000287496700012"]},"language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","date_created":"2018-12-11T12:05:09Z","page":"247 - 249","title":"Microsatelight – Pipeline to expedite microsatellite analysis","publication":"Journal of Heredity","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"ieee":"F. Palero, F. González Candelas, and M. Pascual, “Microsatelight – Pipeline to expedite microsatellite analysis,” <i>Journal of Heredity</i>, vol. 102, no. 2. Oxford University Press, pp. 247–249, 2010.","ista":"Palero F, González Candelas F, Pascual M. 2010. Microsatelight – Pipeline to expedite microsatellite analysis. Journal of Heredity. 102(2), 247–249.","ama":"Palero F, González Candelas F, Pascual M. Microsatelight – Pipeline to expedite microsatellite analysis. <i>Journal of Heredity</i>. 2010;102(2):247-249. doi:<a href=\"https://doi.org/10.1093/jhered/esq111\">10.1093/jhered/esq111</a>","chicago":"Palero, Ferran, Fernando González Candelas, and Marta Pascual. “Microsatelight – Pipeline to Expedite Microsatellite Analysis.” <i>Journal of Heredity</i>. Oxford University Press, 2010. <a href=\"https://doi.org/10.1093/jhered/esq111\">https://doi.org/10.1093/jhered/esq111</a>.","short":"F. Palero, F. González Candelas, M. Pascual, Journal of Heredity 102 (2010) 247–249.","apa":"Palero, F., González Candelas, F., &#38; Pascual, M. (2010). Microsatelight – Pipeline to expedite microsatellite analysis. <i>Journal of Heredity</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jhered/esq111\">https://doi.org/10.1093/jhered/esq111</a>","mla":"Palero, Ferran, et al. “Microsatelight – Pipeline to Expedite Microsatellite Analysis.” <i>Journal of Heredity</i>, vol. 102, no. 2, Oxford University Press, 2010, pp. 247–49, doi:<a href=\"https://doi.org/10.1093/jhered/esq111\">10.1093/jhered/esq111</a>."},"date_updated":"2025-09-30T09:42:17Z","day":"02","isi":1,"_id":"3783","publist_id":"2444","intvolume":"       102","year":"2010","acknowledgement":"Ministerio de Educación y Ciencia (CGL2006-13423, CTM2007-66635). M.P. and FP are part of the research group 2009SGR-636 of the Generalitat de Catalunya. F.P. acknowledges an EU-Synthesys grant (GB-TAF-4474).\r\n\r\nThanks to José Gabriel Segarra-Moragues (Centro de Investigaciones sobre Desertificación) for sending us pictures with several types of stuttering and Pedro Simões and Gemma Calàbria (Universitat de Barcelona) for testing this software. Finally, thanks are due to 2 anonymous referees for their valuable comments. These comments certainly helped to improve the manuscript.","month":"12","volume":102,"issue":"2","doi":"10.1093/jhered/esq111","quality_controlled":"1","oa_version":"None"},{"corr_author":"1","language":[{"iso":"eng"}],"publication":"Journal of Crustacean Biology","title":"Genetic diversity levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda: Achelata)","page":"658 - 663","status":"public","date_created":"2018-12-11T12:05:09Z","article_processing_charge":"No","department":[{"_id":"NiBa"}],"publication_identifier":{"eissn":["1937-240X"],"issn":["0278-0372"]},"publication_status":"published","author":[{"id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87","first_name":"Ferran","orcid":"0000-0002-0343-8329","last_name":"Palero","full_name":"Palero, Ferran"},{"first_name":"Pere","full_name":"Abello, Pere","last_name":"Abello"},{"full_name":"Macpherson, E.","last_name":"Macpherson","first_name":"E."},{"first_name":"C.","full_name":"Matthee, C.","last_name":"Matthee"},{"first_name":"Marta","full_name":"Pascual, Marta","last_name":"Pascual"}],"publisher":"Oxford University Press","scopus_import":"1","type":"journal_article","date_published":"2010-10-01T00:00:00Z","abstract":[{"lang":"eng","text":"Most fisheries involving spiny lobsters of the genus Palinurus have been over exploited during the last decades, so there is a raising concern about management decisions for these valuable resources. A total of 13 microsatellite DNA loci recently developed in Palinurus elephas were  assayed  in  order  to  assess  genetic  diversity  levels  in  every  known  species  of  the  genus.  Microsatellite  markers  gave amplifications  and  showed  polymorphism  in  all  species,  with  gene  diversity  values  varying  from  0.65060.077  SD  (Palinurus barbarae) to 0.79260.051 SD (Palinurus elephas). Most importantly, when depth distribution was taken into account, shallower waters pecies consistently showed larger historical effective population sizes than their deeper-water counterparts.  This could explain why deeper-water species are more sensitive to overfishing, and would indicate that overexploitation may have a larger impact on their long-term genetic diversity."}],"external_id":{"isi":["000284514100015"]},"volume":30,"month":"10","quality_controlled":"1","oa_version":"None","doi":"10.1651/09-3192.1","issue":"4","date_updated":"2025-09-30T09:41:44Z","day":"01","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"ieee":"F. Palero, P. Abello, E. Macpherson, C. Matthee, and M. Pascual, “Genetic diversity levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda: Achelata),” <i>Journal of Crustacean Biology</i>, vol. 30, no. 4. Oxford University Press, pp. 658–663, 2010.","ama":"Palero F, Abello P, Macpherson E, Matthee C, Pascual M. Genetic diversity levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda: Achelata). <i>Journal of Crustacean Biology</i>. 2010;30(4):658-663. doi:<a href=\"https://doi.org/10.1651/09-3192.1\">10.1651/09-3192.1</a>","chicago":"Palero, Ferran, Pere Abello, E. Macpherson, C. Matthee, and Marta Pascual. “Genetic Diversity Levels in Fishery-Exploited Spiny Lobsters of the Genus Palinurus (Decapoda: Achelata).” <i>Journal of Crustacean Biology</i>. Oxford University Press, 2010. <a href=\"https://doi.org/10.1651/09-3192.1\">https://doi.org/10.1651/09-3192.1</a>.","ista":"Palero F, Abello P, Macpherson E, Matthee C, Pascual M. 2010. Genetic diversity levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda: Achelata). Journal of Crustacean Biology. 30(4), 658–663.","short":"F. Palero, P. Abello, E. Macpherson, C. Matthee, M. Pascual, Journal of Crustacean Biology 30 (2010) 658–663.","apa":"Palero, F., Abello, P., Macpherson, E., Matthee, C., &#38; Pascual, M. (2010). Genetic diversity levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda: Achelata). <i>Journal of Crustacean Biology</i>. Oxford University Press. <a href=\"https://doi.org/10.1651/09-3192.1\">https://doi.org/10.1651/09-3192.1</a>","mla":"Palero, Ferran, et al. “Genetic Diversity Levels in Fishery-Exploited Spiny Lobsters of the Genus Palinurus (Decapoda: Achelata).” <i>Journal of Crustacean Biology</i>, vol. 30, no. 4, Oxford University Press, 2010, pp. 658–63, doi:<a href=\"https://doi.org/10.1651/09-3192.1\">10.1651/09-3192.1</a>."},"year":"2010","publist_id":"2442","intvolume":"        30","_id":"3785"},{"_id":"3786","publist_id":"2441","intvolume":"      2403","year":"2010","article_type":"original","publisher":"Magnolia Press","citation":{"mla":"Palero, Ferran, et al. “Final-Stage Phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The First Complete Description.” <i>Zootaxa</i>, vol. 2403, no. 1, Magnolia Press, 2010, pp. 42–58, doi:<a href=\"https://doi.org/10.11646/zootaxa.2403.1.4\">10.11646/zootaxa.2403.1.4</a>.","apa":"Palero, F., Guerao, G., Clark, P., &#38; Abello, P. (2010). Final-stage phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first complete description. <i>Zootaxa</i>. Magnolia Press. <a href=\"https://doi.org/10.11646/zootaxa.2403.1.4\">https://doi.org/10.11646/zootaxa.2403.1.4</a>","short":"F. Palero, G. Guerao, P. Clark, P. Abello, Zootaxa 2403 (2010) 42–58.","ieee":"F. Palero, G. Guerao, P. Clark, and P. Abello, “Final-stage phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first complete description,” <i>Zootaxa</i>, vol. 2403, no. 1. Magnolia Press, pp. 42–58, 2010.","ama":"Palero F, Guerao G, Clark P, Abello P. Final-stage phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first complete description. <i>Zootaxa</i>. 2010;2403(1):42-58. doi:<a href=\"https://doi.org/10.11646/zootaxa.2403.1.4\">10.11646/zootaxa.2403.1.4</a>","chicago":"Palero, Ferran, Guillermo Guerao, Paul Clark, and Pere Abello. “Final-Stage Phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The First Complete Description.” <i>Zootaxa</i>. Magnolia Press, 2010. <a href=\"https://doi.org/10.11646/zootaxa.2403.1.4\">https://doi.org/10.11646/zootaxa.2403.1.4</a>.","ista":"Palero F, Guerao G, Clark P, Abello P. 2010. Final-stage phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first complete description. Zootaxa. 2403(1), 42–58."},"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Four rare palinurid phyllosoma larvae, one mid-stage and three final stage, were found among the unclassified collections in the Crustacea Section, Natural History Museum, London. Detailed morphological analysis of the larvae indicated that they belong to several Palinustus species given the presence of incipient blunt-horns, length of antennula, length ratio of segments of antennular peduncle, distribution of pereiopod spines, and shape of uropods and telson. Moreover, the size of the final-stage larvae agrees with that expected given the size of the recently described puerulus stage of Palinustus mossambicus. This constitutes the first description of a complete phyllosoma assigned to Palinustus species. The phyllosoma described in the present study include the largest Palinuridae larva ever found."}],"date_published":"2010-03-19T00:00:00Z","type":"journal_article","date_updated":"2022-03-21T08:22:58Z","day":"19","author":[{"id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87","first_name":"Ferran","orcid":"0000-0002-0343-8329","last_name":"Palero","full_name":"Palero, Ferran"},{"first_name":"Guillermo","last_name":"Guerao","full_name":"Guerao, Guillermo"},{"first_name":"Paul","full_name":"Clark, Paul","last_name":"Clark"},{"last_name":"Abello","full_name":"Abello, Pere","first_name":"Pere"}],"department":[{"_id":"NiBa"}],"publication_status":"published","status":"public","article_processing_charge":"No","date_created":"2018-12-11T12:05:10Z","issue":"1","page":"42 - 58","title":"Final-stage phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first complete description","doi":"10.11646/zootaxa.2403.1.4","quality_controlled":"1","publication":"Zootaxa","oa_version":"None","language":[{"iso":"eng"}],"month":"03","volume":2403},{"title":"DNA extraction from formalin-fixed tissue: new light from the deep sea","publication":"Scientia Marina","status":"public","date_created":"2018-12-11T12:05:10Z","article_processing_charge":"No","page":"465 - 470","corr_author":"1","language":[{"iso":"eng"}],"external_id":{"isi":["000280917100005"]},"main_file_link":[{"url":"https://eprints.soton.ac.uk/68731/","open_access":"1"}],"author":[{"first_name":"Ferran","id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87","last_name":"Palero","orcid":"0000-0002-0343-8329","full_name":"Palero, Ferran"},{"last_name":"Hall","full_name":"Hall, Sally","first_name":"Sally"},{"last_name":"Clark","full_name":"Clark, Paul","first_name":"Paul"},{"first_name":"David","full_name":"Johnston, David","last_name":"Johnston"},{"last_name":"Mackenzie Dodds","full_name":"Mackenzie Dodds, Jackie","first_name":"Jackie"},{"last_name":"Thatje","full_name":"Thatje, Sven","first_name":"Sven"}],"oa":1,"department":[{"_id":"NiBa"}],"publication_status":"published","scopus_import":"1","publisher":"Consejo Superior de Investigaciones Científicas","date_published":"2010-09-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"DNA samples were extracted from ethanol and formalin-fixed decapod crustacean tissue using a new method based on Tetramethylsilane (TMS)-Chelex. It is shown that neither an indigestible matrix of cross-linked protein nor soluble PCR inhibitors impede PCR success when dealing with formalin-fixed material. Instead, amplification success from formalin-fixed tissue appears to depend on the presence of unmodified DNA in the extracted sample. A staining method that facilitates the targeting of samples with a high content of unmodified DNA is provided."}],"doi":"10.3989/scimar.2010.74n3465","quality_controlled":"1","oa_version":"Submitted Version","issue":"3","month":"09","volume":74,"acknowledgement":"The authors would like to thank two anonymous reviewers for their remarks, which helped to improve the manuscript. This project was supported by the Marine Biodiversity and Ecosystem Functioning Network of Excellence MarBEF (Contract no. GOCE-CT-2003-505446) of the 6th European Framework Programme(FP6), the Zoology Research Fund, Department of Zoology, NHM, London, a Research Grant from the Royal Society to S.T., and a pre-doctoral fellowship awarded by the Autonomous Government of Catalonia to F.P.(2006FIC-00082). This research received support from the SYNTHESYS Project http://www.synthesys. info/ which is financed by European Community Research Infrastructure Action under the FP6 “Structuring the European Research Area” Programme. Many thanks are due to J. Fortuño for suggesting TMS as an alternative to critical point drying, P.Crabb for helping with the UV-light photography setting and our colleagues/friends in the Whale Basement Molecular Laboratories, Department of Zoology NHM \r\n\r\n","year":"2010","_id":"3787","publist_id":"2440","intvolume":"        74","date_updated":"2025-09-30T09:41:18Z","day":"01","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"short":"F. Palero, S. Hall, P. Clark, D. Johnston, J. Mackenzie Dodds, S. Thatje, Scientia Marina 74 (2010) 465–470.","ieee":"F. Palero, S. Hall, P. Clark, D. Johnston, J. Mackenzie Dodds, and S. Thatje, “DNA extraction from formalin-fixed tissue: new light from the deep sea,” <i>Scientia Marina</i>, vol. 74, no. 3. Consejo Superior de Investigaciones Científicas, pp. 465–470, 2010.","ista":"Palero F, Hall S, Clark P, Johnston D, Mackenzie Dodds J, Thatje S. 2010. DNA extraction from formalin-fixed tissue: new light from the deep sea. Scientia Marina. 74(3), 465–470.","chicago":"Palero, Ferran, Sally Hall, Paul Clark, David Johnston, Jackie Mackenzie Dodds, and Sven Thatje. “DNA Extraction from Formalin-Fixed Tissue: New Light from the Deep Sea.” <i>Scientia Marina</i>. Consejo Superior de Investigaciones Científicas, 2010. <a href=\"https://doi.org/10.3989/scimar.2010.74n3465\">https://doi.org/10.3989/scimar.2010.74n3465</a>.","ama":"Palero F, Hall S, Clark P, Johnston D, Mackenzie Dodds J, Thatje S. DNA extraction from formalin-fixed tissue: new light from the deep sea. <i>Scientia Marina</i>. 2010;74(3):465-470. doi:<a href=\"https://doi.org/10.3989/scimar.2010.74n3465\">10.3989/scimar.2010.74n3465</a>","mla":"Palero, Ferran, et al. “DNA Extraction from Formalin-Fixed Tissue: New Light from the Deep Sea.” <i>Scientia Marina</i>, vol. 74, no. 3, Consejo Superior de Investigaciones Científicas, 2010, pp. 465–70, doi:<a href=\"https://doi.org/10.3989/scimar.2010.74n3465\">10.3989/scimar.2010.74n3465</a>.","apa":"Palero, F., Hall, S., Clark, P., Johnston, D., Mackenzie Dodds, J., &#38; Thatje, S. (2010). DNA extraction from formalin-fixed tissue: new light from the deep sea. <i>Scientia Marina</i>. Consejo Superior de Investigaciones Científicas. <a href=\"https://doi.org/10.3989/scimar.2010.74n3465\">https://doi.org/10.3989/scimar.2010.74n3465</a>"}},{"year":"2010","intvolume":"        33","publist_id":"2439","_id":"3788","isi":1,"date_updated":"2025-09-30T09:40:53Z","day":"18","citation":{"apa":"Klopper, A., Krens, G., Grill, S., &#38; Heisenberg, C.-P. J. (2010). Finite-size corrections to scaling behavior in sorted cell aggregates. <i>The European Physical Journal E: Soft Matter and Biological Physics</i>. Springer. <a href=\"https://doi.org/10.1140/epje/i2010-10642-y\">https://doi.org/10.1140/epje/i2010-10642-y</a>","mla":"Klopper, Abigail, et al. “Finite-Size Corrections to Scaling Behavior in Sorted Cell Aggregates.” <i>The European Physical Journal E: Soft Matter and Biological Physics</i>, vol. 33, no. 2, Springer, 2010, pp. 99–103, doi:<a href=\"https://doi.org/10.1140/epje/i2010-10642-y\">10.1140/epje/i2010-10642-y</a>.","ieee":"A. Klopper, G. Krens, S. Grill, and C.-P. J. Heisenberg, “Finite-size corrections to scaling behavior in sorted cell aggregates,” <i>The European Physical Journal E: Soft Matter and Biological Physics</i>, vol. 33, no. 2. Springer, pp. 99–103, 2010.","ama":"Klopper A, Krens G, Grill S, Heisenberg C-PJ. Finite-size corrections to scaling behavior in sorted cell aggregates. <i>The European Physical Journal E: Soft Matter and Biological Physics</i>. 2010;33(2):99-103. doi:<a href=\"https://doi.org/10.1140/epje/i2010-10642-y\">10.1140/epje/i2010-10642-y</a>","chicago":"Klopper, Abigail, Gabriel Krens, Stephan Grill, and Carl-Philipp J Heisenberg. “Finite-Size Corrections to Scaling Behavior in Sorted Cell Aggregates.” <i>The European Physical Journal E: Soft Matter and Biological Physics</i>. Springer, 2010. <a href=\"https://doi.org/10.1140/epje/i2010-10642-y\">https://doi.org/10.1140/epje/i2010-10642-y</a>.","ista":"Klopper A, Krens G, Grill S, Heisenberg C-PJ. 2010. Finite-size corrections to scaling behavior in sorted cell aggregates. The European Physical Journal E: Soft Matter and Biological Physics. 33(2), 99–103.","short":"A. Klopper, G. Krens, S. Grill, C.-P.J. Heisenberg, The European Physical Journal E: Soft Matter and Biological Physics 33 (2010) 99–103."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"None","doi":"10.1140/epje/i2010-10642-y","issue":"2","volume":33,"month":"09","external_id":{"isi":["000284841700002"]},"publication_status":"published","department":[{"_id":"CaHe"}],"author":[{"first_name":"Abigail","full_name":"Klopper, Abigail","last_name":"Klopper"},{"id":"2B819732-F248-11E8-B48F-1D18A9856A87","first_name":"Gabriel","orcid":"0000-0003-4761-5996","last_name":"Krens","full_name":"Krens, Gabriel"},{"last_name":"Grill","full_name":"Grill, Stephan","first_name":"Stephan"},{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"type":"journal_article","abstract":[{"text":"Cell sorting is a widespread phenomenon pivotal to the early development of multicellular organisms. In vitro cell sorting studies have been instrumental in revealing the cellular properties driving this process. However, these studies have as yet been limited to two-dimensional analysis of three-dimensional cell sorting events. Here we describe a method to record the sorting of primary zebrafish ectoderm and mesoderm germ layer progenitor cells in three dimensions over time, and quantitatively analyze their sorting behavior using an order parameter related to heterotypic interface length. We investigate the cell population size dependence of sorted aggregates and find that the germ layer progenitor cells engulfed in the final configuration display a relationship between total interfacial length and system size according to a simple geometrical argument, subject to a finite-size effect.","lang":"eng"}],"date_published":"2010-09-18T00:00:00Z","scopus_import":"1","publisher":"Springer","publication":"The European Physical Journal E: Soft Matter and Biological Physics","title":"Finite-size corrections to scaling behavior in sorted cell aggregates","page":"99 - 103","article_processing_charge":"No","date_created":"2018-12-11T12:05:10Z","status":"public","corr_author":"1","language":[{"iso":"eng"}]}]