@article{822, abstract = {Polymicrobial infections constitute small ecosystems that accommodate several bacterial species. Commonly, these bacteria are investigated in isolation. However, it is unknown to what extent the isolates interact and whether their interactions alter bacterial growth and ecosystem resilience in the presence and absence of antibiotics. We quantified the complete ecological interaction network for 72 bacterial isolates collected from 23 individuals diagnosed with polymicrobial urinary tract infections and found that most interactions cluster based on evolutionary relatedness. Statistical network analysis revealed that competitive and cooperative reciprocal interactions are enriched in the global network, while cooperative interactions are depleted in the individual host community networks. A population dynamics model parameterized by our measurements suggests that interactions restrict community stability, explaining the observed species diversity of these communities. We further show that the clinical isolates frequently protect each other from clinically relevant antibiotics. Together, these results highlight that ecological interactions are crucial for the growth and survival of bacteria in polymicrobial infection communities and affect their assembly and resilience. }, author = {De Vos, Marjon and Zagórski, Marcin P and Mcnally, Alan and Bollenbach, Mark Tobias}, issn = {00278424}, journal = {PNAS}, number = {40}, pages = {10666 -- 10671}, publisher = {National Academy of Sciences}, title = {{Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections}}, doi = {10.1073/pnas.1713372114}, volume = {114}, year = {2017}, } @inproceedings{833, abstract = {We present an efficient algorithm to compute Euler characteristic curves of gray scale images of arbitrary dimension. In various applications the Euler characteristic curve is used as a descriptor of an image. Our algorithm is the first streaming algorithm for Euler characteristic curves. The usage of streaming removes the necessity to store the entire image in RAM. Experiments show that our implementation handles terabyte scale images on commodity hardware. Due to lock-free parallelism, it scales well with the number of processor cores. Additionally, we put the concept of the Euler characteristic curve in the wider context of computational topology. In particular, we explain the connection with persistence diagrams.}, author = {Heiss, Teresa and Wagner, Hubert}, editor = {Felsberg, Michael and Heyden, Anders and Krüger, Norbert}, issn = {03029743}, location = {Ystad, Sweden}, pages = {397 -- 409}, publisher = {Springer}, title = {{Streaming algorithm for Euler characteristic curves of multidimensional images}}, doi = {10.1007/978-3-319-64689-3_32}, volume = {10424}, year = {2017}, } @article{805, abstract = {During corticogenesis, distinct classes of neurons are born from progenitor cells located in the ventricular and subventricular zones, from where they migrate towards the pial surface to assemble into highly organized layer-specific circuits. However, the precise and coordinated transcriptional network activity defining neuronal identity is still not understood. Here, we show that genetic depletion of the basic helix-loop-helix (bHLH) transcription factor E2A splice variant E47 increased the number of Tbr1-positive deep layer and Satb2-positive upper layer neurons at E14.5, while depletion of the alternatively spliced E12 variant did not affect layer-specific neurogenesis. While ChIP-Seq identified a big overlap for E12- and E47-specific binding sites in embryonic NSCs, including sites at the cyclin-dependent kinase inhibitor (CDKI) Cdkn1c gene locus, RNA-Seq revealed a unique transcriptional regulation by each splice variant. E47 activated the expression of the CDKI Cdkn1c through binding to a distal enhancer. Finally, overexpression of E47 in embryonic NSCs in vitro impaired neurite outgrowth and E47 overexpression in vivo by in utero electroporation disturbed proper layer-specific neurogenesis and upregulated p57(KIP2) expression. Overall, this study identified E2A target genes in embryonic NSCs and demonstrates that E47 regulates neuronal differentiation via p57(KIP2).}, author = {Pfurr, Sabrina and Chu, Yu and Bohrer, Christian and Greulich, Franziska and Beattie, Robert J and Mammadzada, Könül and Hils, Miriam and Arnold, Sebastian and Taylor, Verdon and Schachtrup, Kristina and Uhlenhaut, N Henriette and Schachtrup, Christian}, journal = {Development}, pages = {3917 -- 3931}, publisher = {Company of Biologists}, title = {{The E2A splice variant E47 regulates the differentiation of projection neurons via p57(KIP2) during cortical development}}, doi = {10.1242/dev.145698}, volume = {144}, year = {2017}, } @article{834, abstract = {Thermal and many-body localized phases are separated by a dynamical phase transition of a new kind. We analyze the distribution of off-diagonal matrix elements of local operators across this transition in two different models of disordered spin chains. We show that the behavior of matrix elements can be used to characterize the breakdown of thermalization and to extract the many-body Thouless energy. We find that upon increasing the disorder strength the system enters a critical region around the many-body localization transition. The properties of the system in this region are: (i) the Thouless energy becomes smaller than the level spacing, (ii) the matrix elements show critical dependence on the energy difference, and (iii) the matrix elements, viewed as amplitudes of a fictitious wave function, exhibit strong multifractality. This critical region decreases with the system size, which we interpret as evidence for a diverging correlation length at the many-body localization transition. Our findings show that the correlation length becomes larger than the accessible system sizes in a broad range of disorder strength values and shed light on the critical behavior near the many-body localization transition.}, author = {Serbyn, Maksym and Zlatko, Papic and Abanin, Dmitry}, issn = {24699950}, journal = {Physical Review B - Condensed Matter and Materials Physics}, number = {10}, publisher = {American Physical Society}, title = {{Thouless energy and multifractality across the many-body localization transition}}, doi = {10.1103/PhysRevB.96.104201}, volume = {96}, year = {2017}, } @article{823, abstract = {The resolution of a linear system with positive integer variables is a basic yet difficult computational problem with many applications. We consider sparse uncorrelated random systems parametrised by the density c and the ratio α=N/M between number of variables N and number of constraints M. By means of ensemble calculations we show that the space of feasible solutions endows a Van-Der-Waals phase diagram in the plane (c, α). We give numerical evidence that the associated computational problems become more difficult across the critical point and in particular in the coexistence region.}, author = {Colabrese, Simona and De Martino, Daniele and Leuzzi, Luca and Marinari, Enzo}, issn = {17425468}, journal = { Journal of Statistical Mechanics: Theory and Experiment}, number = {9}, publisher = {IOPscience}, title = {{Phase transitions in integer linear problems}}, doi = {10.1088/1742-5468/aa85c3}, volume = {2017}, year = {2017}, }