@article{410, abstract = {Lesion verification and quantification is traditionally done via histological examination of sectioned brains, a time-consuming process that relies heavily on manual estimation. Such methods are particularly problematic in posterior cortical regions (e.g. visual cortex), where sectioning leads to significant damage and distortion of tissue. Even more challenging is the post hoc localization of micro-electrodes, which relies on the same techniques, suffers from similar drawbacks and requires even higher precision. Here, we propose a new, simple method for quantitative lesion characterization and electrode localization that is less labor-intensive and yields more detailed results than conventional methods. We leverage staining techniques standard in electron microscopy with the use of commodity micro-CT imaging. We stain whole rat and zebra finch brains in osmium tetroxide, embed these in resin and scan entire brains in a micro-CT machine. The scans result in 3D reconstructions of the brains with section thickness dependent on sample size (12–15 and 5–6 microns for rat and zebra finch respectively) that can be segmented manually or automatically. Because the method captures the entire intact brain volume, comparisons within and across studies are more tractable, and the extent of lesions and electrodes may be studied with higher accuracy than with current methods.}, author = {Masís, Javier and Mankus, David and Wolff, Steffen and Guitchounts, Grigori and Jösch, Maximilian A and Cox, David}, journal = {Scientific Reports}, number = {1}, publisher = {Nature Publishing Group}, title = {{A micro-CT-based method for quantitative brain lesion characterization and electrode localization}}, doi = {10.1038/s41598-018-23247-z}, volume = {8}, year = {2018}, } @article{277, abstract = {Arabidopsis and human ARM protein interact with telomerase. Deregulated mRNA levels of DNA repair and ribosomal protein genes in an Arabidopsis arm mutant suggest non-telomeric ARM function. The human homolog ARMC6 interacts with hTRF2. Abstract: Telomerase maintains telomeres and has proposed non-telomeric functions. We previously identified interaction of the C-terminal domain of Arabidopsis telomerase reverse transcriptase (AtTERT) with an armadillo/β-catenin-like repeat (ARM) containing protein. Here we explore protein–protein interactions of the ARM protein, AtTERT domains, POT1a, TRF-like family and SMH family proteins, and the chromatin remodeling protein CHR19 using bimolecular fluorescence complementation (BiFC), yeast two-hybrid (Y2H) analysis, and co-immunoprecipitation. The ARM protein interacts with both the N- and C-terminal domains of AtTERT in different cellular compartments. ARM interacts with CHR19 and TRF-like I family proteins that also bind AtTERT directly or through interaction with POT1a. The putative human ARM homolog co-precipitates telomerase activity and interacts with hTRF2 protein in vitro. Analysis of Arabidopsis arm mutants shows no obvious changes in telomere length or telomerase activity, suggesting that ARM is not essential for telomere maintenance. The observed interactions with telomerase and Myb-like domain proteins (TRF-like family I) may therefore reflect possible non-telomeric functions. Transcript levels of several DNA repair and ribosomal genes are affected in arm mutants, and ARM, likely in association with other proteins, suppressed expression of XRCC3 and RPSAA promoter constructs in luciferase reporter assays. In conclusion, ARM can participate in non-telomeric functions of telomerase, and can also perform its own telomerase-independent functions.}, author = {Dokládal, Ladislav and Benková, Eva and Honys, David and Dupláková, Nikoleta and Lee, Lan and Gelvin, Stanton and Sýkorová, Eva}, journal = {Plant Molecular Biology}, number = {5}, pages = {407 -- 420}, publisher = {Springer}, title = {{An armadillo-domain protein participates in a telomerase interaction network}}, doi = {10.1007/s11103-018-0747-4}, volume = {97}, year = {2018}, } @inproceedings{299, abstract = {We introduce in this paper AMT 2.0 , a tool for qualitative and quantitative analysis of hybrid continuous and Boolean signals that combine numerical values and discrete events. The evaluation of the signals is based on rich temporal specifications expressed in extended Signal Temporal Logic (xSTL), which integrates Timed Regular Expressions (TRE) within Signal Temporal Logic (STL). The tool features qualitative monitoring (property satisfaction checking), trace diagnostics for explaining and justifying property violations and specification-driven measurement of quantitative features of the signal.}, author = {Nickovic, Dejan and Lebeltel, Olivier and Maler, Oded and Ferrere, Thomas and Ulus, Dogan}, editor = {Beyer, Dirk and Huisman, Marieke}, location = {Thessaloniki, Greece}, pages = {303 -- 319}, publisher = {Springer}, title = {{AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic}}, doi = {10.1007/978-3-319-89963-3_18}, volume = {10806}, year = {2018}, } @article{413, abstract = {Being cared for when sick is a benefit of sociality that can reduce disease and improve survival of group members. However, individuals providing care risk contracting infectious diseases themselves. If they contract a low pathogen dose, they may develop low-level infections that do not cause disease but still affect host immunity by either decreasing or increasing the host’s vulnerability to subsequent infections. Caring for contagious individuals can thus significantly alter the future disease susceptibility of caregivers. Using ants and their fungal pathogens as a model system, we tested if the altered disease susceptibility of experienced caregivers, in turn, affects their expression of sanitary care behavior. We found that low-level infections contracted during sanitary care had protective or neutral effects on secondary exposure to the same (homologous) pathogen but consistently caused high mortality on superinfection with a different (heterologous) pathogen. In response to this risk, the ants selectively adjusted the expression of their sanitary care. Specifically, the ants performed less grooming and more antimicrobial disinfection when caring for nestmates contaminated with heterologous pathogens compared with homologous ones. By modulating the components of sanitary care in this way the ants acquired less infectious particles of the heterologous pathogens, resulting in reduced superinfection. The performance of risk-adjusted sanitary care reveals the remarkable capacity of ants to react to changes in their disease susceptibility, according to their own infection history and to flexibly adjust collective care to individual risk.}, author = {Konrad, Matthias and Pull, Christopher and Metzler, Sina and Seif, Katharina and Naderlinger, Elisabeth and Grasse, Anna V and Cremer, Sylvia}, journal = {PNAS}, number = {11}, pages = {2782 -- 2787}, publisher = {National Academy of Sciences}, title = {{Ants avoid superinfections by performing risk-adjusted sanitary care}}, doi = {10.1073/pnas.1713501115}, volume = {115}, year = {2018}, } @article{195, abstract = {We demonstrate that identical impurities immersed in a two-dimensional many-particle bath can be viewed as flux-tube-charged-particle composites described by fractional statistics. In particular, we find that the bath manifests itself as an external magnetic flux tube with respect to the impurities, and hence the time-reversal symmetry is broken for the effective Hamiltonian describing the impurities. The emerging flux tube acts as a statistical gauge field after a certain critical coupling. This critical coupling corresponds to the intersection point between the quasiparticle state and the phonon wing, where the angular momentum is transferred from the impurity to the bath. This amounts to a novel configuration with emerging anyons. The proposed setup paves the way to realizing anyons using electrons interacting with superfluid helium or lattice phonons, as well as using atomic impurities in ultracold gases.}, author = {Yakaboylu, Enderalp and Lemeshko, Mikhail}, journal = {Physical Review B - Condensed Matter and Materials Physics}, number = {4}, publisher = {American Physical Society}, title = {{Anyonic statistics of quantum impurities in two dimensions}}, doi = {10.1103/PhysRevB.98.045402}, volume = {98}, year = {2018}, } @inproceedings{144, abstract = {The task of a monitor is to watch, at run-time, the execution of a reactive system, and signal the occurrence of a safety violation in the observed sequence of events. While finite-state monitors have been studied extensively, in practice, monitoring software also makes use of unbounded memory. We define a model of automata equipped with integer-valued registers which can execute only a bounded number of instructions between consecutive events, and thus can form the theoretical basis for the study of infinite-state monitors. We classify these register monitors according to the number k of available registers, and the type of register instructions. In stark contrast to the theory of computability for register machines, we prove that for every k 1, monitors with k + 1 counters (with instruction set 〈+1, =〉) are strictly more expressive than monitors with k counters. We also show that adder monitors (with instruction set 〈1, +, =〉) are strictly more expressive than counter monitors, but are complete for monitoring all computable safety -languages for k = 6. Real-time monitors are further required to signal the occurrence of a safety violation as soon as it occurs. The expressiveness hierarchy for counter monitors carries over to real-time monitors. We then show that 2 adders cannot simulate 3 counters in real-time. Finally, we show that real-time adder monitors with inequalities are as expressive as real-time Turing machines.}, author = {Ferrere, Thomas and Henzinger, Thomas A and Saraç, Ege}, location = {Oxford, UK}, pages = {394 -- 403}, publisher = {IEEE}, title = {{A theory of register monitors}}, doi = {10.1145/3209108.3209194}, volume = {Part F138033}, year = {2018}, } @article{203, abstract = {Asymmetric auxin distribution is instrumental for the differential growth that causes organ bending on tropic stimuli and curvatures during plant development. Local differences in auxin concentrations are achieved mainly by polarized cellular distribution of PIN auxin transporters, but whether other mechanisms involving auxin homeostasis are also relevant for the formation of auxin gradients is not clear. Here we show that auxin methylation is required for asymmetric auxin distribution across the hypocotyl, particularly during its response to gravity. We found that loss-of-function mutants in Arabidopsis IAA CARBOXYL METHYLTRANSFERASE1 (IAMT1) prematurely unfold the apical hook, and that their hypocotyls are impaired in gravitropic reorientation. This defect is linked to an auxin-dependent increase in PIN gene expression, leading to an increased polar auxin transport and lack of asymmetric distribution of PIN3 in the iamt1 mutant. Gravitropic reorientation in the iamt1 mutant could be restored with either endodermis-specific expression of IAMT1 or partial inhibition of polar auxin transport, which also results in normal PIN gene expression levels. We propose that IAA methylation is necessary in gravity-sensing cells to restrict polar auxin transport within the range of auxin levels that allow for differential responses.}, author = {Abbas, Mohamad and Hernández, García J and Pollmann, Stephan and Samodelov, Sophia L and Kolb, Martina and Friml, Jirí and Hammes, Ulrich Z and Zurbriggen, Matias D and Blázquez, Miguel and Alabadí, David}, journal = {PNAS}, number = {26}, pages = {6864--6869}, publisher = {National Academy of Sciences}, title = {{Auxin methylation is required for differential growth in Arabidopsis}}, doi = {10.1073/pnas.1806565115}, volume = {115}, year = {2018}, } @article{399, abstract = {Following an earlier calculation in 3D, we calculate the 2D critical temperature of a dilute, translation-invariant Bose gas using a variational formulation of the Bogoliubov approximation introduced by Critchley and Solomon in 1976. This provides the first analytical calculation of the Kosterlitz-Thouless transition temperature that includes the constant in the logarithm.}, author = {Napiórkowski, Marcin M and Reuvers, Robin and Solovej, Jan}, journal = {EPL}, number = {1}, publisher = {IOP Publishing Ltd.}, title = {{Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation}}, doi = {10.1209/0295-5075/121/10007}, volume = {121}, year = {2018}, } @article{5830, abstract = {CLE peptides have been implicated in various developmental processes of plants and mediate their responses to environmental stimuli. However, the biological relevance of most CLE genes remains to be functionally characterized. Here, we report that CLE9, which is expressed in stomata, acts as an essential regulator in the induction of stomatal closure. Exogenous application of CLE9 peptides or overexpression of CLE9 effectively led to stomatal closure and enhanced drought tolerance, whereas CLE9 loss-of-function mutants were sensitivity to drought stress. CLE9-induced stomatal closure was impaired in abscisic acid (ABA)-deficient mutants, indicating that ABA is required for CLE9-medaited guard cell signalling. We further deciphered that two guard cell ABA-signalling components, OST1 and SLAC1, were responsible for CLE9-induced stomatal closure. MPK3 and MPK6 were activated by the CLE9 peptide, and CLE9 peptides failed to close stomata in mpk3 and mpk6 mutants. In addition, CLE9 peptides stimulated the induction of hydrogen peroxide (H2O2) and nitric oxide (NO) synthesis associated with stomatal closure, which was abolished in the NADPH oxidase-deficient mutants or nitric reductase mutants, respectively. Collectively, our results reveal a novel ABA-dependent function of CLE9 in the regulation of stomatal apertures, thereby suggesting a potential role of CLE9 in the stress acclimatization of plants.}, author = {Zhang, Luosha and Shi, Xiong and Zhang, Yutao and Wang, Jiajing and Yang, Jingwei and Ishida, Takashi and Jiang, Wenqian and Han, Xiangyu and Kang, Jingke and Wang, Xuening and Pan, Lixia and Lv, Shuo and Cao, Bing and Zhang, Yonghong and Wu, Jinbin and Han, Huibin and Hu, Zhubing and Cui, Langjun and Sawa, Shinichiro and He, Junmin and Wang, Guodong}, issn = {01407791}, journal = {Plant Cell and Environment}, publisher = {Wiley}, title = {{CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana}}, doi = {10.1111/pce.13475}, year = {2018}, } @article{288, abstract = {Recent lineage tracing studies have revealed that mammary gland homeostasis relies on unipotent stem cells. However, whether and when lineage restriction occurs during embryonic mammary development, and which signals orchestrate cell fate specification, remain unknown. Using a combination of in vivo clonal analysis with whole mount immunofluorescence and mathematical modelling of clonal dynamics, we found that embryonic multipotent mammary cells become lineage-restricted surprisingly early in development, with evidence for unipotency as early as E12.5 and no statistically discernable bipotency after E15.5. To gain insights into the mechanisms governing the switch from multipotency to unipotency, we used gain-of-function Notch1 mice and demonstrated that Notch activation cell autonomously dictates luminal cell fate specification to both embryonic and basally committed mammary cells. These functional studies have important implications for understanding the signals underlying cell plasticity and serve to clarify how reactivation of embryonic programs in adult cells can lead to cancer.}, author = {Lilja, Anna and Rodilla, Veronica and Huyghe, Mathilde and Hannezo, Edouard B and Landragin, Camille and Renaud, Olivier and Leroy, Olivier and Rulands, Steffen and Simons, Benjamin and Fré, Silvia}, journal = {Nature Cell Biology}, number = {6}, pages = {677 -- 687}, publisher = {Nature Publishing Group}, title = {{Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland}}, doi = {10.1038/s41556-018-0108-1}, volume = {20}, year = {2018}, } @article{304, abstract = {Additive manufacturing has recently seen drastic improvements in resolution, making it now possible to fabricate features at scales of hundreds or even dozens of nanometers, which previously required very expensive lithographic methods. As a result, additive manufacturing now seems poised for optical applications, including those relevant to computer graphics, such as material design, as well as display and imaging applications. In this work, we explore the use of additive manufacturing for generating structural colors, where the structures are designed using a fabrication-aware optimization process. This requires a combination of full-wave simulation, a feasible parameterization of the design space, and a tailored optimization procedure. Many of these components should be re-usable for the design of other optical structures at this scale. We show initial results of material samples fabricated based on our designs. While these suffer from the prototype character of state-of-the-art fabrication hardware, we believe they clearly demonstrate the potential of additive nanofabrication for structural colors and other graphics applications.}, author = {Auzinger, Thomas and Heidrich, Wolfgang and Bickel, Bernd}, journal = {ACM Transactions on Graphics}, number = {4}, publisher = {ACM}, title = {{Computational design of nanostructural color for additive manufacturing}}, doi = {10.1145/3197517.3201376}, volume = {37}, year = {2018}, } @article{12, abstract = {Molding is a popular mass production method, in which the initial expenses for the mold are offset by the low per-unit production cost. However, the physical fabrication constraints of the molding technique commonly restrict the shape of moldable objects. For a complex shape, a decomposition of the object into moldable parts is a common strategy to address these constraints, with plastic model kits being a popular and illustrative example. However, conducting such a decomposition requires considerable expertise, and it depends on the technical aspects of the fabrication technique, as well as aesthetic considerations. We present an interactive technique to create such decompositions for two-piece molding, in which each part of the object is cast between two rigid mold pieces. Given the surface description of an object, we decompose its thin-shell equivalent into moldable parts by first performing a coarse decomposition and then utilizing an active contour model for the boundaries between individual parts. Formulated as an optimization problem, the movement of the contours is guided by an energy reflecting fabrication constraints to ensure the moldability of each part. Simultaneously, the user is provided with editing capabilities to enforce aesthetic guidelines. Our interactive interface provides control of the contour positions by allowing, for example, the alignment of part boundaries with object features. Our technique enables a novel workflow, as it empowers novice users to explore the design space, and it generates fabrication-ready two-piece molds that can be used either for casting or industrial injection molding of free-form objects.}, author = {Nakashima, Kazutaka and Auzinger, Thomas and Iarussi, Emmanuel and Zhang, Ran and Igarashi, Takeo and Bickel, Bernd}, journal = {ACM Transaction on Graphics}, number = {4}, publisher = {ACM}, title = {{CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds}}, doi = {10.1145/3197517.3201341}, volume = {37}, year = {2018}, } @article{454, abstract = {Direct reciprocity is a mechanism for cooperation among humans. Many of our daily interactions are repeated. We interact repeatedly with our family, friends, colleagues, members of the local and even global community. In the theory of repeated games, it is a tacit assumption that the various games that a person plays simultaneously have no effect on each other. Here we introduce a general framework that allows us to analyze “crosstalk” between a player’s concurrent games. In the presence of crosstalk, the action a person experiences in one game can alter the person’s decision in another. We find that crosstalk impedes the maintenance of cooperation and requires stronger levels of forgiveness. The magnitude of the effect depends on the population structure. In more densely connected social groups, crosstalk has a stronger effect. A harsh retaliator, such as Tit-for-Tat, is unable to counteract crosstalk. The crosstalk framework provides a unified interpretation of direct and upstream reciprocity in the context of repeated games.}, author = {Reiter, Johannes and Hilbe, Christian and Rand, David and Chatterjee, Krishnendu and Nowak, Martin}, journal = {Nature Communications}, number = {1}, publisher = {Nature Publishing Group}, title = {{Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness}}, doi = {10.1038/s41467-017-02721-8}, volume = {9}, year = {2018}, } @article{320, abstract = {Fast-spiking, parvalbumin-expressing GABAergic interneurons (PV+-BCs) express a complex machinery of rapid signaling mechanisms, including specialized voltage-gated ion channels to generate brief action potentials (APs). However, short APs are associated with overlapping Na+ and K+ fluxes and are therefore energetically expensive. How the potentially vicious combination of high AP frequency and inefficient spike generation can be reconciled with limited energy supply is presently unclear. To address this question, we performed direct recordings from the PV+-BC axon, the subcellular structure where active conductances for AP initiation and propagation are located. Surprisingly, the energy required for the AP was, on average, only ∼1.6 times the theoretical minimum. High energy efficiency emerged from the combination of fast inactivation of Na+ channels and delayed activation of Kv3-type K+ channels, which minimized ion flux overlap during APs. Thus, the complementary tuning of axonal Na+ and K+ channel gating optimizes both fast signaling properties and metabolic efficiency. Hu et al. demonstrate that action potentials in parvalbumin-expressing GABAergic interneuron axons are energetically efficient, which is highly unexpected given their brief duration. High energy efficiency emerges from the combination of fast inactivation of voltage-gated Na+ channels and delayed activation of Kv3 channels in the axon. }, author = {Hu, Hua and Roth, Fabian and Vandael, David H and Jonas, Peter M}, journal = {Neuron}, number = {1}, pages = {156 -- 165}, publisher = {Elsevier}, title = {{Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons}}, doi = {10.1016/j.neuron.2018.02.024}, volume = {98}, year = {2018}, } @article{423, abstract = {Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity.}, author = {Payne, Pavel and Geyrhofer, Lukas and Barton, Nicholas H and Bollback, Jonathan P}, journal = {eLife}, publisher = {eLife Sciences Publications}, title = {{CRISPR-based herd immunity can limit phage epidemics in bacterial populations}}, doi = {10.7554/eLife.32035}, volume = {7}, year = {2018}, } @inproceedings{5791, abstract = {Due to data compression or low resolution, nearby vertices and edges of a graph drawing may be bundled to a common node or arc. We model such a “compromised” drawing by a piecewise linear map φ:G → ℝ. We wish to perturb φ by an arbitrarily small ε>0 into a proper drawing (in which the vertices are distinct points, any two edges intersect in finitely many points, and no three edges have a common interior point) that minimizes the number of crossings. An ε-perturbation, for every ε>0, is given by a piecewise linear map (Formula Presented), where with ||·|| is the uniform norm (i.e., sup norm). We present a polynomial-time solution for this optimization problem when G is a cycle and the map φ has no spurs (i.e., no two adjacent edges are mapped to overlapping arcs). We also show that the problem becomes NP-complete (i) when G is an arbitrary graph and φ has no spurs, and (ii) when φ may have spurs and G is a cycle or a union of disjoint paths.}, author = {Fulek, Radoslav and Tóth, Csaba D.}, isbn = {9783030044138}, location = {Barcelona, Spain}, pages = {229--241}, publisher = {Springer}, title = {{Crossing minimization in perturbed drawings}}, doi = {10.1007/978-3-030-04414-5_16}, volume = {11282 }, year = {2018}, } @article{291, abstract = {Over the past decade, the edge of chaos has proven to be a fruitful starting point for investigations of shear flows when the laminar base flow is linearly stable. Numerous computational studies of shear flows demonstrated the existence of states that separate laminar and turbulent regions of the state space. In addition, some studies determined invariant solutions that reside on this edge. In this paper, we study the unstable manifold of one such solution with the aid of continuous symmetry reduction, which we formulate here for the simultaneous quotiening of axial and azimuthal symmetries. Upon our investigation of the unstable manifold, we discover a previously unknown traveling-wave solution on the laminar-turbulent boundary with a relatively complex structure. By means of low-dimensional projections, we visualize different dynamical paths that connect these solutions to the turbulence. Our numerical experiments demonstrate that the laminar-turbulent boundary exhibits qualitatively different regions whose properties are influenced by the nearby invariant solutions.}, author = {Budanur, Nazmi B and Hof, Björn}, journal = {Physical Review Fluids}, number = {5}, publisher = {American Physical Society}, title = {{Complexity of the laminar-turbulent boundary in pipe flow}}, doi = {10.1103/PhysRevFluids.3.054401}, volume = {3}, year = {2018}, } @article{58, abstract = {Inside a two-dimensional region (``cake""), there are m nonoverlapping tiles of a certain kind (``toppings""). We want to expand the toppings while keeping them nonoverlapping, and possibly add some blank pieces of the same ``certain kind,"" such that the entire cake is covered. How many blanks must we add? We study this question in several cases: (1) The cake and toppings are general polygons. (2) The cake and toppings are convex figures. (3) The cake and toppings are axis-parallel rectangles. (4) The cake is an axis-parallel rectilinear polygon and the toppings are axis-parallel rectangles. In all four cases, we provide tight bounds on the number of blanks.}, author = {Akopyan, Arseniy and Segal Halevi, Erel}, journal = {SIAM Journal on Discrete Mathematics}, number = {3}, pages = {2242 -- 2257}, publisher = {Society for Industrial and Applied Mathematics }, title = {{Counting blanks in polygonal arrangements}}, doi = {10.1137/16M110407X}, volume = {32}, year = {2018}, } @misc{9840, abstract = {Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity.}, author = {Payne, Pavel and Geyrhofer, Lukas and Barton, Nicholas H and Bollback, Jonathan P}, publisher = {Dryad}, title = {{Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations}}, doi = {10.5061/dryad.42n44}, year = {2018}, } @article{616, abstract = {Social insects protect their colonies from infectious disease through collective defences that result in social immunity. In ants, workers first try to prevent infection of colony members. Here, we show that if this fails and a pathogen establishes an infection, ants employ an efficient multicomponent behaviour − "destructive disinfection" − to prevent further spread of disease through the colony. Ants specifically target infected pupae during the pathogen's non-contagious incubation period, relying on chemical 'sickness cues' emitted by pupae. They then remove the pupal cocoon, perforate its cuticle and administer antimicrobial poison, which enters the body and prevents pathogen replication from the inside out. Like the immune system of a body that specifically targets and eliminates infected cells, this social immunity measure sacrifices infected brood to stop the pathogen completing its lifecycle, thus protecting the rest of the colony. Hence, the same principles of disease defence apply at different levels of biological organisation.}, author = {Pull, Christopher and Ugelvig, Line V and Wiesenhofer, Florian and Grasse, Anna V and Tragust, Simon and Schmitt, Thomas and Brown, Mark and Cremer, Sylvia}, journal = {eLife}, publisher = {eLife Sciences Publications}, title = {{Destructive disinfection of infected brood prevents systemic disease spread in ant colonies}}, doi = {10.7554/eLife.32073}, volume = {7}, year = {2018}, }