@article{543, abstract = {A central goal in theoretical neuroscience is to predict the response properties of sensory neurons from first principles. To this end, “efficient coding” posits that sensory neurons encode maximal information about their inputs given internal constraints. There exist, however, many variants of efficient coding (e.g., redundancy reduction, different formulations of predictive coding, robust coding, sparse coding, etc.), differing in their regimes of applicability, in the relevance of signals to be encoded, and in the choice of constraints. It is unclear how these types of efficient coding relate or what is expected when different coding objectives are combined. Here we present a unified framework that encompasses previously proposed efficient coding models and extends to unique regimes. We show that optimizing neural responses to encode predictive information can lead them to either correlate or decorrelate their inputs, depending on the stimulus statistics; in contrast, at low noise, efficiently encoding the past always predicts decorrelation. Later, we investigate coding of naturalistic movies and show that qualitatively different types of visual motion tuning and levels of response sparsity are predicted, depending on whether the objective is to recover the past or predict the future. Our approach promises a way to explain the observed diversity of sensory neural responses, as due to multiple functional goals and constraints fulfilled by different cell types and/or circuits.}, author = {Chalk, Matthew J and Marre, Olivier and Tkacik, Gasper}, journal = {PNAS}, number = {1}, pages = {186 -- 191}, publisher = {National Academy of Sciences}, title = {{Toward a unified theory of efficient, predictive, and sparse coding}}, doi = {10.1073/pnas.1711114115}, volume = {115}, year = {2018}, } @article{544, abstract = {Drosophila melanogaster plasmatocytes, the phagocytic cells among hemocytes, are essential for immune responses, but also play key roles from early development to death through their interactions with other cell types. They regulate homeostasis and signaling during development, stem cell proliferation, metabolism, cancer, wound responses and aging, displaying intriguing molecular and functional conservation with vertebrate macrophages. Given the relative ease of genetics in Drosophila compared to vertebrates, tools permitting visualization and genetic manipulation of plasmatocytes and surrounding tissues independently at all stages would greatly aid in fully understanding these processes, but are lacking. Here we describe a comprehensive set of transgenic lines that allow this. These include extremely brightly fluorescing mCherry-based lines that allow GAL4-independent visualization of plasmatocyte nuclei, cytoplasm or actin cytoskeleton from embryonic Stage 8 through adulthood in both live and fixed samples even as heterozygotes, greatly facilitating screening. These lines allow live visualization and tracking of embryonic plasmatocytes, as well as larval plasmatocytes residing at the body wall or flowing with the surrounding hemolymph. With confocal imaging, interactions of plasmatocytes and inner tissues can be seen in live or fixed embryos, larvae and adults. They permit efficient GAL4-independent FACS analysis/sorting of plasmatocytes throughout life. To facilitate genetic analysis of reciprocal signaling, we have also made a plasmatocyte-expressing QF2 line that in combination with extant GAL4 drivers allows independent genetic manipulation of both plasmatocytes and surrounding tissues, and a GAL80 line that blocks GAL4 drivers from affecting plasmatocytes, both of which function from the early embryo to the adult.}, author = {György, Attila and Roblek, Marko and Ratheesh, Aparna and Valosková, Katarina and Belyaeva, Vera and Wachner, Stephanie and Matsubayashi, Yutaka and Sanchez Sanchez, Besaiz and Stramer, Brian and Siekhaus, Daria E}, journal = {G3: Genes, Genomes, Genetics}, number = {3}, pages = {845 -- 857}, publisher = {Genetics Society of America}, title = {{Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues}}, doi = {10.1534/g3.117.300452}, volume = {8}, year = {2018}, } @article{546, abstract = {The precise control of neural stem cell (NSC) proliferation and differentiation is crucial for the development and function of the human brain. Here, we review the emerging links between the alteration of embryonic and adult neurogenesis and the etiology of neuropsychiatric disorders (NPDs) such as autism spectrum disorders (ASDs) and schizophrenia (SCZ), as well as the advances in stem cell-based modeling and the novel therapeutic targets derived from these studies.}, author = {Sacco, Roberto and Cacci, Emanuele and Novarino, Gaia}, journal = {Current Opinion in Neurobiology}, number = {2}, pages = {131 -- 138}, publisher = {Elsevier}, title = {{Neural stem cells in neuropsychiatric disorders}}, doi = {10.1016/j.conb.2017.12.005}, volume = {48}, year = {2018}, } @article{55, abstract = {Many animals use antimicrobials to prevent or cure disease [1,2]. For example, some animals will ingest plants with medicinal properties, both prophylactically to prevent infection and therapeutically to self-medicate when sick. Antimicrobial substances are also used as topical disinfectants, to prevent infection, protect offspring and to sanitise their surroundings [1,2]. Social insects (ants, bees, wasps and termites) build nests in environments with a high abundance and diversity of pathogenic microorganisms — such as soil and rotting wood — and colonies are often densely crowded, creating conditions that favour disease outbreaks. Consequently, social insects have evolved collective disease defences to protect their colonies from epidemics. These traits can be seen as functionally analogous to the immune system of individual organisms [3,4]. This ‘social immunity’ utilises antimicrobials to prevent and eradicate infections, and to keep the brood and nest clean. However, these antimicrobial compounds can be harmful to the insects themselves, and it is unknown how colonies prevent collateral damage when using them. Here, we demonstrate that antimicrobial acids, produced by workers to disinfect the colony, are harmful to the delicate pupal brood stage, but that the pupae are protected from the acids by the presence of a silk cocoon. Garden ants spray their nests with an antimicrobial poison to sanitize contaminated nestmates and brood. Here, Pull et al show that they also prophylactically sanitise their colonies, and that the silk cocoon serves as a barrier to protect developing pupae, thus preventing collateral damage during nest sanitation.}, author = {Pull, Christopher and Metzler, Sina and Naderlinger, Elisabeth and Cremer, Sylvia}, journal = {Current Biology}, number = {19}, pages = {R1139 -- R1140}, publisher = {Cell Press}, title = {{Protection against the lethal side effects of social immunity in ants}}, doi = {10.1016/j.cub.2018.08.063}, volume = {28}, year = {2018}, } @article{554, abstract = {We analyse the canonical Bogoliubov free energy functional in three dimensions at low temperatures in the dilute limit. We prove existence of a first-order phase transition and, in the limit (Formula presented.), we determine the critical temperature to be (Formula presented.) to leading order. Here, (Formula presented.) is the critical temperature of the free Bose gas, ρ is the density of the gas and a is the scattering length of the pair-interaction potential V. We also prove asymptotic expansions for the free energy. In particular, we recover the Lee–Huang–Yang formula in the limit (Formula presented.).}, author = {Napiórkowski, Marcin M and Reuvers, Robin and Solovej, Jan}, issn = {00103616}, journal = {Communications in Mathematical Physics}, number = {1}, pages = {347--403}, publisher = {Springer}, title = {{The Bogoliubov free energy functional II: The dilute Limit}}, doi = {10.1007/s00220-017-3064-x}, volume = {360}, year = {2018}, } @article{555, abstract = {Conventional wisdom has it that proteins fold and assemble into definite structures, and that this defines their function. Glycosaminoglycans (GAGs) are different. In most cases the structures they form have a low degree of order, even when interacting with proteins. Here, we discuss how physical features common to all GAGs — hydrophilicity, charge, linearity and semi-flexibility — underpin the overall properties of GAG-rich matrices. By integrating soft matter physics concepts (e.g. polymer brushes and phase separation) with our molecular understanding of GAG–protein interactions, we can better comprehend how GAG-rich matrices assemble, what their properties are, and how they function. Taking perineuronal nets (PNNs) — a GAG-rich matrix enveloping neurons — as a relevant example, we propose that microphase separation determines the holey PNN anatomy that is pivotal to PNN functions.}, author = {Richter, Ralf and Baranova, Natalia and Day, Anthony and Kwok, Jessica}, journal = {Current Opinion in Structural Biology}, pages = {65 -- 74}, publisher = {Elsevier}, title = {{Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets?}}, doi = {10.1016/j.sbi.2017.12.002}, volume = {50}, year = {2018}, } @article{556, abstract = {We investigate the free boundary Schur process, a variant of the Schur process introduced by Okounkov and Reshetikhin, where we allow the first and the last partitions to be arbitrary (instead of empty in the original setting). The pfaffian Schur process, previously studied by several authors, is recovered when just one of the boundary partitions is left free. We compute the correlation functions of the process in all generality via the free fermion formalism, which we extend with the thorough treatment of “free boundary states.” For the case of one free boundary, our approach yields a new proof that the process is pfaffian. For the case of two free boundaries, we find that the process is not pfaffian, but a closely related process is. We also study three different applications of the Schur process with one free boundary: fluctuations of symmetrized last passage percolation models, limit shapes and processes for symmetric plane partitions and for plane overpartitions.}, author = {Betea, Dan and Bouttier, Jeremie and Nejjar, Peter and Vuletic, Mirjana}, issn = {1424-0637}, journal = {Annales Henri Poincare}, number = {12}, pages = {3663--3742}, publisher = {Springer Nature}, title = {{The free boundary Schur process and applications I}}, doi = {10.1007/s00023-018-0723-1}, volume = {19}, year = {2018}, } @misc{5569, abstract = {Nela Nikolic, Tobias Bergmiller, Alexandra Vandervelde, Tanino G. Albanese, Lendert Gelens, and Isabella Moll (2018) “Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations” Nucleic Acids Research, doi: 10.15479/AT:ISTA:74; microscopy experiments by Tobias Bergmiller; image and data analysis by Nela Nikolic.}, author = {Bergmiller, Tobias and Nikolic, Nela}, keywords = {microscopy, microfluidics}, publisher = {Institute of Science and Technology Austria}, title = {{Time-lapse microscopy data}}, doi = {10.15479/AT:ISTA:74}, year = {2018}, } @misc{5573, abstract = {Graph matching problems for large displacement optical flow of RGB-D images.}, author = {Alhaija, Hassan and Sellent, Anita and Kondermann, Daniel and Rother, Carsten}, keywords = {graph matching, quadratic assignment problem<}, publisher = {Institute of Science and Technology Austria}, title = {{Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow}}, doi = {10.15479/AT:ISTA:82}, year = {2018}, } @misc{5574, abstract = {Comparison of Scopus' and publisher's data on Austrian publication output at IOP. }, author = {Villányi, Márton}, keywords = {Publication analysis, Bibliography, Open Access}, publisher = {Institute of Science and Technology Austria}, title = {{Data Check IOP Scopus vs. Publisher}}, doi = {10.15479/AT:ISTA:86}, year = {2018}, } @misc{5575, abstract = {Comparison of Scopus' and FWF's data on Austrian publication output at RSC. }, author = {Villányi, Márton}, keywords = {Publication analysis, Bibliography, Open Access}, publisher = {Institute of Science and Technology Austria}, title = {{Data Check RSC Scopus vs. FWF}}, doi = {10.15479/AT:ISTA:87}, year = {2018}, } @misc{5576, abstract = {Comparison of Scopus' and FWF's data on Austrian publication output at T&F.}, author = {Villányi, Márton}, keywords = {Publication analysis, Bibliography, Open Access}, publisher = {Institute of Science and Technology Austria}, title = {{Data Check T&F Scopus vs. FWF}}, doi = {10.15479/AT:ISTA:88}, year = {2018}, } @misc{5577, abstract = {Data on Austrian open access publication output at Emerald from 2013-2017 including data analysis.}, author = {Villányi, Márton}, keywords = {Publication analysis, Bibliography, Open Access}, publisher = {Institute of Science and Technology Austria}, title = {{Emerald Austrian Publications 2013-2017}}, doi = {10.15479/AT:ISTA:89}, year = {2018}, } @misc{5578, abstract = {Data on Austrian open access publication output at IOP from 2012-2015 including data analysis.}, author = {Villányi, Márton}, keywords = {Publication analysis, Bibliography, Open Access}, publisher = {Institute of Science and Technology Austria}, title = {{IOP Austrian Publications 2012-2015}}, doi = {10.15479/AT:ISTA:90}, year = {2018}, } @misc{5579, abstract = {Data on Austrian open access publication output at RSC from 2013-2017 including data analysis.}, author = {Villányi, Márton}, keywords = {Publication analysis, Bibliography, Open Access}, publisher = {Institute of Science and Technology Austria}, title = {{RSC Austrian Publications 2013-2017}}, doi = {10.15479/AT:ISTA:91}, year = {2018}, } @misc{5580, abstract = {Data on Austrian open access publication output at SAGE from 2013-2017 including data analysis.}, author = {Villányi, Márton}, keywords = {Publication analysis, Bibliography, Open Access}, publisher = {Institute of Science and Technology Austria}, title = {{SAGE Austrian Publications 2013-2017}}, doi = {10.15479/AT:ISTA:92}, year = {2018}, } @misc{5581, abstract = {Data on Austrian open access publication output at Springer from 2013-2016 including data analysis.}, author = {Villányi, Márton}, keywords = {Publication analysis, Bibliography, Open Access}, publisher = {Institute of Science and Technology Austria}, title = {{Springer Austrian Publications 2013-2016}}, doi = {10.15479/AT:ISTA:93}, year = {2018}, } @misc{5582, abstract = {Data on Austrian open access publication output at Taylor&Francis from 2013-2017 including data analysis.}, author = {Villányi, Márton}, keywords = {Publication analysis, Bibliography, Open Access}, publisher = {Institute of Science and Technology Austria}, title = {{Taylor&Francis Austrian Publications 2013-2017}}, doi = {10.15479/AT:ISTA:94}, year = {2018}, } @misc{5583, abstract = {Data and scripts are provided in support of the manuscript "Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering", and the associated Python package FAPS, available from www.github.com/ellisztamas/faps. Simulation scripts cover: 1. Performance under different mating scenarios. 2. Comparison with Colony2. 3. Effect of changing the number of Monte Carlo draws The final script covers the analysis of half-sib arrays from wild-pollinated seed in an Antirrhinum majus hybrid zone.}, author = {Ellis, Thomas}, publisher = {Institute of Science and Technology Austria}, title = {{Data and Python scripts supporting Python package FAPS}}, doi = {10.15479/AT:ISTA:95}, year = {2018}, } @misc{5584, abstract = {This package contains data for the publication "Nonlinear decoding of a complex movie from the mammalian retina" by Deny S. et al, PLOS Comput Biol (2018). The data consists of (i) 91 spike sorted, isolated rat retinal ganglion cells that pass stability and quality criteria, recorded on the multi-electrode array, in response to the presentation of the complex movie with many randomly moving dark discs. The responses are represented as 648000 x 91 binary matrix, where the first index indicates the timebin of duration 12.5 ms, and the second index the neural identity. The matrix entry is 0/1 if the neuron didn't/did spike in the particular time bin. (ii) README file and a graphical illustration of the structure of the experiment, specifying how the 648000 timebins are split into epochs where 1, 2, 4, or 10 discs were displayed, and which stimulus segments are exact repeats or unique ball trajectories. (iii) a 648000 x 400 matrix of luminance traces for each of the 20 x 20 positions ("sites") in the movie frame, with time that is locked to the recorded raster. The luminance traces are produced as described in the manuscript by filtering the raw disc movie with a small gaussian spatial kernel. }, author = {Deny, Stephane and Marre, Olivier and Botella-Soler, Vicente and Martius, Georg S and Tkacik, Gasper}, keywords = {retina, decoding, regression, neural networks, complex stimulus}, publisher = {Institute of Science and Technology Austria}, title = {{Nonlinear decoding of a complex movie from the mammalian retina}}, doi = {10.15479/AT:ISTA:98}, year = {2018}, }