@article{1019, abstract = {As a consequence of its difference in copy number between males and females, the X chromosome is subject to unique evolutionary forces and gene regulatory mechanisms. Previous studies of Drosophila melanogaster have shown that the expression of X-linked, testis-specific reporter genes is suppressed in the male germline. However, it is not known whether this phenomenon is restricted to testis-expressed genes or if it is a more general property of genes with tissue-specific expression, which are also underrepresented on the X chromosome. To test this, we compared the expression of three tissue-specific reporter genes (ovary, accessory gland and Malpighian tubule) inserted at various autosomal and X-chromosomal locations. In contrast to testis-specific reporter genes, we found no reduction of X-linked expression in any of the other tissues. In accessory gland and Malpighian tubule, we detected higher expression of the X-linked reporter genes, which suggests that they are at least partially dosage compensated. We found no difference in the tissue-specificity of X-linked and autosomal reporter genes. These findings indicate that, in general, the X chromosome is not a detrimental environment for tissue-specific gene expression and that the suppression of X-linked expression is limited to the male germline.}, author = {Argyridou, Eliza and Huylmans, Ann K and Königer, Annabella and Parsch, John}, issn = {0018067X}, journal = {Heredity}, number = {1}, pages = {27 -- 34}, publisher = {Nature Publishing Group}, title = {{X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster}}, doi = {10.1038/hdy.2017.12}, volume = {119}, year = {2017}, } @misc{9861, abstract = {As a consequence of its difference in copy number between males and females, the X chromosome is subject to unique evolutionary forces and gene regulatory mechanisms. Previous studies of Drosophila melanogaster have shown that the expression of X-linked, testis-specific reporter genes is suppressed in the male germline. However, it is not known whether this phenomenon is restricted to testis-expressed genes or if it is a more general property of genes with tissue-specific expression, which are also underrepresented on the X chromosome. To test this, we compared the expression of three tissue-specific reporter genes (ovary, accessory gland and Malpighian tubule) inserted at various autosomal and X-chromosomal locations. In contrast to testis-specific reporter genes, we found no reduction of X-linked expression in any of the other tissues. In accessory gland and Malpighian tubule, we detected higher expression of the X-linked reporter genes, which suggests that they are at least partially dosage compensated. We found no difference in the tissue-specificity of X-linked and autosomal reporter genes. These findings indicate that, in general, the X chromosome is not a detrimental environment for tissue-specific gene expression and that the suppression of X-linked expression is limited to the male germline.}, author = {Argyridou, Eliza and Huylmans, Ann K and Königer, Annabella and Parsch, John}, publisher = {Dryad}, title = {{Data from: X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster}}, doi = {10.5061/dryad.02f6r}, year = {2017}, } @article{1006, abstract = {Background: The phenomenon of immune priming, i.e. enhanced protection following a secondary exposure to a pathogen, has now been demonstrated in a wide range of invertebrate species. Despite accumulating phenotypic evidence, knowledge of its mechanistic underpinnings is currently very limited. Here we used the system of the red flour beetle, Tribolium castaneum and the insect pathogen Bacillus thuringiensis (Bt) to further our molecular understanding of the oral immune priming phenomenon. We addressed how ingestion of bacterial cues (derived from spore supernatants) of an orally pathogenic and non-pathogenic Bt strain affects gene expression upon later challenge exposure, using a whole-transcriptome sequencing approach. Results: Whereas gene expression of individuals primed with the orally non-pathogenic strain showed minor changes to controls, we found that priming with the pathogenic strain induced regulation of a large set of distinct genes, many of which are known immune candidates. Intriguingly, the immune repertoire activated upon priming and subsequent challenge qualitatively differed from the one mounted upon infection with Bt without previous priming. Moreover, a large subset of priming-specific genes showed an inverse regulation compared to their regulation upon challenge only. Conclusions: Our data demonstrate that gene expression upon infection is strongly affected by previous immune priming. We hypothesise that this shift in gene expression indicates activation of a more targeted and efficient response towards a previously encountered pathogen, in anticipation of potential secondary encounter.}, author = {Greenwood, Jenny and Milutinovic, Barbara and Peuß, Robert and Behrens, Sarah and Essar, Daniela and Rosenstiel, Philip and Schulenburg, Hinrich and Kurtz, Joachim}, issn = {14712164}, journal = {BMC Genomics}, number = {1}, pages = {329}, publisher = {BioMed Central}, title = {{Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae}}, doi = {10.1186/s12864-017-3705-7}, volume = {18}, year = {2017}, } @inproceedings{1011, abstract = {Pushdown systems (PDSs) and recursive state machines (RSMs), which are linearly equivalent, are standard models for interprocedural analysis. Yet RSMs are more convenient as they (a) explicitly model function calls and returns, and (b) specify many natural parameters for algorithmic analysis, e.g., the number of entries and exits. We consider a general framework where RSM transitions are labeled from a semiring and path properties are algebraic with semiring operations, which can model, e.g., interprocedural reachability and dataflow analysis problems. Our main contributions are new algorithms for several fundamental problems. As compared to a direct translation of RSMs to PDSs and the best-known existing bounds of PDSs, our analysis algorithm improves the complexity for finite-height semirings (that subsumes reachability and standard dataflow properties). We further consider the problem of extracting distance values from the representation structures computed by our algorithm, and give efficient algorithms that distinguish the complexity of a one-time preprocessing from the complexity of each individual query. Another advantage of our algorithm is that our improvements carry over to the concurrent setting, where we improve the bestknown complexity for the context-bounded analysis of concurrent RSMs. Finally, we provide a prototype implementation that gives a significant speed-up on several benchmarks from the SLAM/SDV project.}, author = {Chatterjee, Krishnendu and Kragl, Bernhard and Mishra, Samarth and Pavlogiannis, Andreas}, editor = {Yang, Hongseok}, issn = {03029743}, location = {Uppsala, Sweden}, pages = {287 -- 313}, publisher = {Springer}, title = {{Faster algorithms for weighted recursive state machines}}, doi = {10.1007/978-3-662-54434-1_11}, volume = {10201}, year = {2017}, } @article{1004, abstract = {The fundamental tasks of the root system are, besides anchoring, mediating interactions between plant and soil and providing the plant with water and nutrients. The architecture of the root system is controlled by endogenous mechanisms that constantly integrate environmental signals, such as availability of nutrients and water. Extremely important for efficient soil exploitation and survival under less favorable conditions is the developmental flexibility of the root system that is largely determined by its postembryonic branching capacity. Modulation of initiation and outgrowth of lateral roots provides roots with an exceptional plasticity, allows optimal adjustment to underground heterogeneity, and enables effective soil exploitation and use of resources. Here we discuss recent advances in understanding the molecular mechanisms that shape the plant root system and integrate external cues to adapt to the changing environment.}, author = {Ötvös, Krisztina and Benková, Eva}, issn = {0959437X}, journal = {Current Opinion in Genetics & Development}, pages = {82 -- 89}, publisher = {Elsevier}, title = {{Spatiotemporal mechanisms of root branching}}, doi = {10.1016/j.gde.2017.03.010}, volume = {45}, year = {2017}, } @article{1010, abstract = {We prove a local law in the bulk of the spectrum for random Gram matrices XX∗, a generalization of sample covariance matrices, where X is a large matrix with independent, centered entries with arbitrary variances. The limiting eigenvalue density that generalizes the Marchenko-Pastur law is determined by solving a system of nonlinear equations. Our entrywise and averaged local laws are on the optimal scale with the optimal error bounds. They hold both in the square case (hard edge) and in the properly rectangular case (soft edge). In the latter case we also establish a macroscopic gap away from zero in the spectrum of XX∗. }, author = {Alt, Johannes and Erdös, László and Krüger, Torben H}, issn = {10836489}, journal = {Electronic Journal of Probability}, publisher = {Institute of Mathematical Statistics}, title = {{Local law for random Gram matrices}}, doi = {10.1214/17-EJP42}, volume = {22}, year = {2017}, } @inproceedings{1009, abstract = {A standard objective in partially-observable Markov decision processes (POMDPs) is to find a policy that maximizes the expected discounted-sum payoff. However, such policies may still permit unlikely but highly undesirable outcomes, which is problematic especially in safety-critical applications. Recently, there has been a surge of interest in POMDPs where the goal is to maximize the probability to ensure that the payoff is at least a given threshold, but these approaches do not consider any optimization beyond satisfying this threshold constraint. In this work we go beyond both the “expectation” and “threshold” approaches and consider a “guaranteed payoff optimization (GPO)” problem for POMDPs, where we are given a threshold t and the objective is to find a policy σ such that a) each possible outcome of σ yields a discounted-sum payoff of at least t, and b) the expected discounted-sum payoff of σ is optimal (or near-optimal) among all policies satisfying a). We present a practical approach to tackle the GPO problem and evaluate it on standard POMDP benchmarks.}, author = {Chatterjee, Krishnendu and Novotny, Petr and Pérez, Guillermo and Raskin, Jean and Zikelic, Djordje}, booktitle = {Proceedings of the 31st AAAI Conference on Artificial Intelligence}, location = {San Francisco, CA, United States}, pages = {3725 -- 3732}, publisher = {AAAI Press}, title = {{Optimizing expectation with guarantees in POMDPs}}, volume = {5}, year = {2017}, } @misc{9859, abstract = {Lists of all differentially expressed genes in the different priming-challenge treatments (compared to the fully naïve control; xlsx file). Relevant columns include the following: sample_1 and sample_2 – treatment groups being compared; Normalised FPKM sample_1 and sample_2 – FPKM of samples being compared; log2(fold_change) – log2(FPKM sample 2/FPKM sample 1), i.e. negative means sample 1 upregulated compared with sample 2, positive means sample 2 upregulated compared with sample 1; cuffdiff test_statistic – test statistic of differential expression test; p_value – p-value of differential expression test; q_value (FDR correction) – adjusted P-value of differential expression test. (XLSX 598 kb)}, author = {Greenwood, Jenny and Milutinovic, Barbara and Peuß, Robert and Behrens, Sarah and Essar, Daniela and Rosenstiel, Philip and Schulenburg, Hinrich and Kurtz, Joachim}, publisher = {Springer Nature}, title = {{Additional file 1: Table S1. of Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae}}, doi = {10.6084/m9.figshare.c.3756974_d1.v1}, year = {2017}, } @misc{9860, author = {Greenwood, Jenny and Milutinovic, Barbara and Peuß, Robert and Behrens, Sarah and Essar, Daniela and Rosenstiel, Philip and Schulenburg, Hinrich and Kurtz, Joachim}, publisher = {Springer Nature}, title = {{Additional file 5: Table S3. of Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae}}, doi = {10.6084/m9.figshare.c.3756974_d5.v1}, year = {2017}, } @inproceedings{1002, abstract = { We present an interactive design system to create functional mechanical objects. Our computational approach allows novice users to retarget an existing mechanical template to a user-specified input shape. Our proposed representation for a mechanical template encodes a parameterized mechanism, mechanical constraints that ensure a physically valid configuration, spatial relationships of mechanical parts to the user-provided shape, and functional constraints that specify an intended functionality. We provide an intuitive interface and optimization-in-the-loop approach for finding a valid configuration of the mechanism and the shape to ensure that higher-level functional goals are met. Our algorithm interactively optimizes the mechanism while the user manipulates the placement of mechanical components and the shape. Our system allows users to efficiently explore various design choices and to synthesize customized mechanical objects that can be fabricated with rapid prototyping technologies. We demonstrate the efficacy of our approach by retargeting various mechanical templates to different shapes and fabricating the resulting functional mechanical objects. }, author = {Zhang, Ran and Auzinger, Thomas and Ceylan, Duygu and Li, Wilmot and Bickel, Bernd}, issn = {07300301}, location = {Los Angeles, CA, United States }, number = {4}, publisher = {ACM}, title = {{Functionality-aware retargeting of mechanisms to 3D shapes}}, doi = {10.1145/3072959.3073710}, volume = {36}, year = {2017}, }