@article{2919, abstract = {The distribution of the phytohormone auxin regulates many aspects of plant development including growth response to gravity. Gravitropic root curvature involves coordinated and asymmetric cell elongation between the lower and upper side of the root, mediated by differential cellular auxin levels. The asymmetry in the auxin distribution is established and maintained by a spatio-temporal regulation of the PIN-FORMED (PIN) auxin transporter activity. We provide novel insights into the complex regulation of PIN abundance and activity during root gravitropism. We show that PIN2 turnover is differentially regulated on the upper and lower side of gravistimulated roots by distinct but partially overlapping auxin feedback mechanisms. In addition to regulating transcription and clathrin-mediated internalization, auxin also controls PIN abundance at the plasma membrane by promoting their vacuolar targeting and degradation. This effect of elevated auxin levels requires the activity of SKP-Cullin-F-box TIR1/AFB (SCF TIR1/AFB)-dependent pathway. Importantly, also suboptimal auxin levels mediate PIN degradation utilizing the same signalling pathway. These feedback mechanisms are functionally important during gravitropic response and ensure fine-tuning of auxin fluxes for maintaining as well as terminating asymmetric growth.}, author = {Baster, Pawel and Robert, Stéphanie and Kleine Vehn, Jürgen and Vanneste, Steffen and Kania, Urszula and Grunewald, Wim and De Rybel, Bert and Beeckman, Tom and Friml, Jirí}, journal = {EMBO Journal}, number = {2}, pages = {260 -- 274}, publisher = {Wiley-Blackwell}, title = {{SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism}}, doi = {10.1038/emboj.2012.310}, volume = {32}, year = {2013}, } @article{2920, abstract = {Cell polarisation in development is a common and fundamental process underlying embryo patterning and morphogenesis, and has been extensively studied over the past years. Our current knowledge of cell polarisation in development is predominantly based on studies that have analysed polarisation of single cells, such as eggs, or cellular aggregates with a stable polarising interface, such as cultured epithelial cells (St Johnston and Ahringer, 2010). However, in embryonic development, particularly of vertebrates, cell polarisation processes often encompass large numbers of cells that are placed within moving and proliferating tissues, and undergo mesenchymal-to-epithelial transitions with a highly complex spatiotemporal choreography. How such intricate cell polarisation processes in embryonic development are achieved has only started to be analysed. By using live imaging of neurulation in the transparent zebrafish embryo, Buckley et al (2012) now describe a novel polarisation strategy by which cells assemble an apical domain in the part of their cell body that intersects with the midline of the forming neural rod. This mechanism, along with the previously described mirror-symmetric divisions (Tawk et al, 2007), is thought to trigger formation of both neural rod midline and lumen.}, author = {Compagnon, Julien and Heisenberg, Carl-Philipp J}, journal = {EMBO Journal}, number = {1}, pages = {1 -- 3}, publisher = {Wiley-Blackwell}, title = {{Neurulation coordinating cell polarisation and lumen formation}}, doi = {10.1038/emboj.2012.325}, volume = {32}, year = {2013}, } @inproceedings{2940, abstract = {A chain rule for an entropy notion H(.) states that the entropy H(X) of a variable X decreases by at most l if conditioned on an l-bit string A, i.e., H(X|A)>= H(X)-l. More generally, it satisfies a chain rule for conditional entropy if H(X|Y,A)>= H(X|Y)-l. All natural information theoretic entropy notions we are aware of (like Shannon or min-entropy) satisfy some kind of chain rule for conditional entropy. Moreover, many computational entropy notions (like Yao entropy, unpredictability entropy and several variants of HILL entropy) satisfy the chain rule for conditional entropy, though here not only the quantity decreases by l, but also the quality of the entropy decreases exponentially in l. However, for the standard notion of conditional HILL entropy (the computational equivalent of min-entropy) the existence of such a rule was unknown so far. In this paper, we prove that for conditional HILL entropy no meaningful chain rule exists, assuming the existence of one-way permutations: there exist distributions X,Y,A, where A is a distribution over a single bit, but $H(X|Y)>>H(X|Y,A)$, even if we simultaneously allow for a massive degradation in the quality of the entropy. The idea underlying our construction is based on a surprising connection between the chain rule for HILL entropy and deniable encryption. }, author = {Krenn, Stephan and Pietrzak, Krzysztof Z and Wadia, Akshay}, editor = {Sahai, Amit}, location = {Tokyo, Japan}, pages = {23 -- 39}, publisher = {Springer}, title = {{A counterexample to the chain rule for conditional HILL entropy, and what deniable encryption has to do with it}}, doi = {10.1007/978-3-642-36594-2_2}, volume = {7785}, year = {2013}, } @inproceedings{2948, abstract = {Many visual datasets are traditionally used to analyze the performance of different learning techniques. The evaluation is usually done within each dataset, therefore it is questionable if such results are a reliable indicator of true generalization ability. We propose here an algorithm to exploit the existing data resources when learning on a new multiclass problem. Our main idea is to identify an image representation that decomposes orthogonally into two subspaces: a part specific to each dataset, and a part generic to, and therefore shared between, all the considered source sets. This allows us to use the generic representation as un-biased reference knowledge for a novel classification task. By casting the method in the multi-view setting, we also make it possible to use different features for different databases. We call the algorithm MUST, Multitask Unaligned Shared knowledge Transfer. Through extensive experiments on five public datasets, we show that MUST consistently improves the cross-datasets generalization performance.}, author = {Tommasi, Tatiana and Quadrianto, Novi and Caputo, Barbara and Lampert, Christoph}, location = {Daejeon, Korea}, pages = {1 -- 15}, publisher = {Springer}, title = {{Beyond dataset bias: Multi-task unaligned shared knowledge transfer}}, doi = {10.1007/978-3-642-37331-2_1}, volume = {7724}, year = {2013}, } @inproceedings{2973, abstract = {Efficient zero-knowledge proofs of knowledge (ZK-PoK) are basic building blocks of many practical cryptographic applications such as identification schemes, group signatures, and secure multiparty computation. Currently, first applications that critically rely on ZK-PoKs are being deployed in the real world. The most prominent example is Direct Anonymous Attestation (DAA), which was adopted by the Trusted Computing Group (TCG) and implemented as one of the functionalities of the cryptographic Trusted Platform Module (TPM) chip. Implementing systems using ZK-PoK turns out to be challenging, since ZK-PoK are, loosely speaking, significantly more complex than standard crypto primitives, such as encryption and signature schemes. As a result, implementation cycles of ZK-PoK are time-consuming and error-prone, in particular for developers with minor or no cryptographic skills. In this paper we report on our ongoing and future research vision with the goal to bring ZK-PoK to practice by making them accessible to crypto and security engineers. To this end we are developing compilers and related tools that support and partially automate the design, implementation, verification and secure implementation of ZK-PoK protocols.}, author = {Bangerter, Endre and Barzan, Stefania and Stephan Krenn and Sadeghi, Ahmad-Reza and Schneider, Thomas and Tsay, Joe-Kai}, editor = {Christianson, Bruce and Malcolm, James A. and Matyas, Vashek and Roe, Michael}, pages = {51 -- 62}, publisher = {Springer}, title = {{Bringing Zero-Knowledge Proofs of Knowledge to Practice}}, doi = {10.1007/978-3-642-36213-2_9}, volume = {7028}, year = {2013}, } @article{3261, abstract = {Cells in a developing embryo have no direct way of "measuring" their physical position. Through a variety of processes, however, the expression levels of multiple genes come to be correlated with position, and these expression levels thus form a code for "positional information." We show how to measure this information, in bits, using the gap genes in the Drosophila embryo as an example. Individual genes carry nearly two bits of information, twice as much as expected if the expression patterns consisted only of on/off domains separated by sharp boundaries. Taken together, four gap genes carry enough information to define a cell's location with an error bar of ~1% along the anterior-posterior axis of the embryo. This precision is nearly enough for each cell to have a unique identity, which is the maximum information the system can use, and is nearly constant along the length of the embryo. We argue that this constancy is a signature of optimality in the transmission of information from primary morphogen inputs to the output of the gap gene network.}, author = {Dubuis, Julien and Tkacik, Gasper and Wieschaus, Eric and Gregor, Thomas and Bialek, William}, journal = {PNAS}, number = {41}, pages = {16301 -- 16308}, publisher = {National Academy of Sciences}, title = {{Positional information, in bits}}, doi = {10.1073/pnas.1315642110}, volume = {110}, year = {2013}, } @article{10895, abstract = {Due to their sessile lifestyles, plants need to deal with the limitations and stresses imposed by the changing environment. Plants cope with these by a remarkable developmental flexibility, which is embedded in their strategy to survive. Plants can adjust their size, shape and number of organs, bend according to gravity and light, and regenerate tissues that were damaged, utilizing a coordinating, intercellular signal, the plant hormone, auxin. Another versatile signal is the cation, Ca2+, which is a crucial second messenger for many rapid cellular processes during responses to a wide range of endogenous and environmental signals, such as hormones, light, drought stress and others. Auxin is a good candidate for one of these Ca2+-activating signals. However, the role of auxin-induced Ca2+ signaling is poorly understood. Here, we will provide an overview of possible developmental and physiological roles, as well as mechanisms underlying the interconnection of Ca2+ and auxin signaling. }, author = {Vanneste, Steffen and Friml, Jiří}, issn = {2223-7747}, journal = {Plants}, keywords = {Plant Science, Ecology, Ecology, Evolution, Behavior and Systematics}, number = {4}, pages = {650--675}, publisher = {MDPI}, title = {{Calcium: The missing link in auxin action}}, doi = {10.3390/plants2040650}, volume = {2}, year = {2013}, } @article{11085, abstract = {During mitotic exit, missegregated chromosomes can recruit their own nuclear envelope (NE) to form micronuclei (MN). MN have reduced functioning compared to primary nuclei in the same cell, although the two compartments appear to be structurally comparable. Here we show that over 60% of MN undergo an irreversible loss of compartmentalization during interphase due to NE collapse. This disruption of the MN, which is induced by defects in nuclear lamina assembly, drastically reduces nuclear functions and can trigger massive DNA damage. MN disruption is associated with chromatin compaction and invasion of endoplasmic reticulum (ER) tubules into the chromatin. We identified disrupted MN in both major subtypes of human non-small-cell lung cancer, suggesting that disrupted MN could be a useful objective biomarker for genomic instability in solid tumors. Our study shows that NE collapse is a key event underlying MN dysfunction and establishes a link between aberrant NE organization and aneuploidy.}, author = {Hatch, Emily M. and Fischer, Andrew H. and Deerinck, Thomas J. and HETZER, Martin W}, issn = {0092-8674}, journal = {Cell}, keywords = {General Biochemistry, Genetics and Molecular Biology}, number = {1}, pages = {47--60}, publisher = {Elsevier}, title = {{Catastrophic nuclear envelope collapse in cancer cell micronuclei}}, doi = {10.1016/j.cell.2013.06.007}, volume = {154}, year = {2013}, } @article{11086, abstract = {Faithful execution of developmental gene expression programs occurs at multiple levels and involves many different components such as transcription factors, histone-modification enzymes, and mRNA processing proteins. Recent evidence suggests that nucleoporins, well known components that control nucleo-cytoplasmic trafficking, have wide-ranging functions in developmental gene regulation that potentially extend beyond their role in nuclear transport. Whether the unexpected role of nuclear pore proteins in transcription regulation, which initially has been described in fungi and flies, also applies to human cells is unknown. Here we show at a genome-wide level that the nuclear pore protein NUP98 associates with developmentally regulated genes active during human embryonic stem cell differentiation. Overexpression of a dominant negative fragment of NUP98 levels decreases expression levels of NUP98-bound genes. In addition, we identify two modes of developmental gene regulation by NUP98 that are differentiated by the spatial localization of NUP98 target genes. Genes in the initial stage of developmental induction can associate with NUP98 that is embedded in the nuclear pores at the nuclear periphery. Alternatively, genes that are highly induced can interact with NUP98 in the nuclear interior, away from the nuclear pores. This work demonstrates for the first time that NUP98 dynamically associates with the human genome during differentiation, revealing a role of a nuclear pore protein in regulating developmental gene expression programs.}, author = {Liang, Yun and Franks, Tobias M. and Marchetto, Maria C. and Gage, Fred H. and HETZER, Martin W}, issn = {1553-7404}, journal = {PLoS Genetics}, keywords = {Cancer Research, Genetics (clinical), Genetics, Molecular Biology, Ecology, Evolution, Behavior and Systematics}, number = {2}, publisher = {Public Library of Science}, title = {{Dynamic association of NUP98 with the human genome}}, doi = {10.1371/journal.pgen.1003308}, volume = {9}, year = {2013}, } @article{11087, abstract = {Intracellular proteins with long lifespans have recently been linked to age-dependent defects, ranging from decreased fertility to the functional decline of neurons. Why long-lived proteins exist in metabolically active cellular environments and how they are maintained over time remains poorly understood. Here, we provide a system-wide identification of proteins with exceptional lifespans in the rat brain. These proteins are inefficiently replenished despite being translated robustly throughout adulthood. Using nucleoporins as a paradigm for long-term protein persistence, we found that nuclear pore complexes (NPCs) are maintained over a cell’s life through slow but finite exchange of even its most stable subcomplexes. This maintenance is limited, however, as some nucleoporin levels decrease during aging, providing a rationale for the previously observed age-dependent deterioration of NPC function. Our identification of a long-lived proteome reveals cellular components that are at increased risk for damage accumulation, linking long-term protein persistence to the cellular aging process.}, author = {Toyama, Brandon H. and Savas, Jeffrey N. and Park, Sung Kyu and Harris, Michael S. and Ingolia, Nicholas T. and Yates, John R. and HETZER, Martin W}, issn = {0092-8674}, journal = {Cell}, keywords = {General Biochemistry, Genetics and Molecular Biology}, number = {5}, pages = {971--982}, publisher = {Elsevier}, title = {{Identification of long-lived proteins reveals exceptional stability of essential cellular structures}}, doi = {10.1016/j.cell.2013.07.037}, volume = {154}, year = {2013}, } @article{11088, abstract = {The crowded intracellular environment poses a formidable challenge to experimental and theoretical analyses of intracellular transport mechanisms. Our measurements of single-particle trajectories in cytoplasm and their random-walk interpretations elucidate two of these mechanisms: molecular diffusion in crowded environments and cytoskeletal transport along microtubules. We employed acousto-optic deflector microscopy to map out the three-dimensional trajectories of microspheres migrating in the cytosolic fraction of a cellular extract. Classical Brownian motion (BM), continuous time random walk, and fractional BM were alternatively used to represent these trajectories. The comparison of the experimental and numerical data demonstrates that cytoskeletal transport along microtubules and diffusion in the cytosolic fraction exhibit anomalous (nonFickian) behavior and posses statistically distinct signatures. Among the three random-walk models used, continuous time random walk provides the best representation of diffusion, whereas microtubular transport is accurately modeled with fractional BM.}, author = {Regner, Benjamin M. and Vučinić, Dejan and Domnisoru, Cristina and Bartol, Thomas M. and HETZER, Martin W and Tartakovsky, Daniel M. and Sejnowski, Terrence J.}, issn = {0006-3495}, journal = {Biophysical Journal}, keywords = {Biophysics}, number = {8}, pages = {1652--1660}, publisher = {Elsevier}, title = {{Anomalous diffusion of single particles in cytoplasm}}, doi = {10.1016/j.bpj.2013.01.049}, volume = {104}, year = {2013}, } @article{11520, abstract = {We present the spatially resolved Hα dynamics of 16 star-forming galaxies at z ∼ 0.81 using the new KMOS multi-object integral field spectrograph on the ESO Very Large Telescope. These galaxies, selected using 1.18 μm narrowband imaging from the 10 deg2 CFHT-HiZELS survey of the SA 22 hr field, are found in a ∼4 Mpc overdensity of Hα emitters and likely reside in a group/intermediate environment, but not a cluster. We confirm and identify a rich group of star-forming galaxies at z = 0.813 ± 0.003, with 13 galaxies within 1000 km s−1 of each other, and seven within a diameter of 3 Mpc. All of our galaxies are “typical” star-forming galaxies at their redshift, 0.8 ± 0.4 SFR$^*_{z = 0.8}$, spanning a range of specific star formation rates (sSFRs) of 0.2–1.1 Gyr−1 and have a median metallicity very close to solar of 12 + log(O/H) = 8.62 ± 0.06. We measure the spatially resolved Hα dynamics of the galaxies in our sample and show that 13 out of 16 galaxies can be described by rotating disks and use the data to derive inclination corrected rotation speeds of 50–275 km s−1. The fraction of disks within our sample is 75% ± 8%, consistent with previous results based on Hubble Space Telescope morphologies of Hα-selected galaxies at z ∼ 1 and confirming that disks dominate the SFR density at z ∼ 1. Our Hα galaxies are well fitted by the z ∼ 1–2 Tully–Fisher (TF) relation, confirming the evolution seen in the zero point. Apart from having, on average, higher stellar masses and lower sSFRs, our group galaxies at z = 0.81 present the same mass–metallicity and TF relation as z ∼ 1 field galaxies and are all disk galaxies.}, author = {Sobral, D. and Swinbank, A. M. and Stott, J. P. and Matthee, Jorryt J and Bower, R. G. and Smail, Ian and Best, P. and Geach, J. E. and Sharples, R. M.}, issn = {1538-4357}, journal = {The Astrophysical Journal}, keywords = {Space and Planetary Science, Astronomy and Astrophysics, galaxies: evolution – galaxies, high-redshift – galaxies, starburst}, number = {2}, publisher = {IOP Publishing}, title = {{The dynamics of z=0.8 H-alpha-selected star-forming galaxies from KMOS/CF-HiZELS}}, doi = {10.1088/0004-637x/779/2/139}, volume = {779}, year = {2013}, } @article{11759, abstract = {Matching markets play a prominent role in economic theory. A prime example of such a market is the sponsored search market. Here, as in other markets of that kind, market equilibria correspond to feasible, envy free, and bidder optimal outcomes. For settings without budgets such an outcome always exists and can be computed in polynomial-time by the so-called Hungarian Method. Moreover, every mechanism that computes such an outcome is incentive compatible. We show that the Hungarian Method can be modified so that it finds a feasible, envy free, and bidder optimal outcome for settings with budgets. We also show that in settings with budgets no mechanism that computes such an outcome can be incentive compatible for all inputs. For inputs in general position, however, the presented mechanism—as any other mechanism that computes such an outcome for settings with budgets—is incentive compatible.}, author = {Dütting, Paul and Henzinger, Monika H and Weber, Ingmar}, issn = {0020-0190}, journal = {Information Processing Letters}, number = {3}, pages = {67--73}, publisher = {Elsevier}, title = {{Sponsored search, market equilibria, and the Hungarian Method}}, doi = {10.1016/j.ipl.2012.11.006}, volume = {113}, year = {2013}, } @inproceedings{11791, abstract = {The focus of classic mechanism design has been on truthful direct-revelation mechanisms. In the context of combinatorial auctions the truthful direct-revelation mechanism that maximizes social welfare is the VCG mechanism. For many valuation spaces computing the allocation and payments of the VCG mechanism, however, is a computationally hard problem. We thus study the performance of the VCG mechanism when bidders are forced to choose bids from a subspace of the valuation space for which the VCG outcome can be computed efficiently. We prove improved upper bounds on the welfare loss for restrictions to additive bids and upper and lower bounds for restrictions to non-additive bids. These bounds show that the welfare loss increases in expressiveness. All our bounds apply to equilibrium concepts that can be computed in polynomial time as well as to learning outcomes.}, author = {Dütting, Paul and Henzinger, Monika H and Starnberger, Martin}, booktitle = {9th International Conference on Web and Internet Economics}, isbn = {9783642450457}, issn = {1611-3349}, location = {Cambridge, MA, USA}, pages = {146–159}, publisher = {Springer Nature}, title = {{Valuation compressions in VCG-based combinatorial auctions}}, doi = {10.1007/978-3-642-45046-4_13}, volume = {8289}, year = {2013}, } @inproceedings{11792, abstract = {We study the problem of maximizing a monotone submodular function with viability constraints. This problem originates from computational biology, where we are given a phylogenetic tree over a set of species and a directed graph, the so-called food web, encoding viability constraints between these species. These food webs usually have constant depth. The goal is to select a subset of k species that satisfies the viability constraints and has maximal phylogenetic diversity. As this problem is known to be NP-hard, we investigate approximation algorithm. We present the first constant factor approximation algorithm if the depth is constant. Its approximation ratio is (1−1𝑒√). This algorithm not only applies to phylogenetic trees with viability constraints but for arbitrary monotone submodular set functions with viability constraints. Second, we show that there is no (1 − 1/e + ε)-approximation algorithm for our problem setting (even for additive functions) and that there is no approximation algorithm for a slight extension of this setting.}, author = {Dvořák, Wolfgang and Henzinger, Monika H and Williamson, David P.}, booktitle = {21st Annual European Symposium on Algorithms}, isbn = {9783642404498}, issn = {1611-3349}, location = {Sophia Antipolis, France}, pages = {409 -- 420}, publisher = {Springer Nature}, title = {{Maximizing a submodular function with viability constraints}}, doi = {10.1007/978-3-642-40450-4_35}, volume = {8125}, year = {2013}, } @inproceedings{11793, abstract = {We study the problem of maintaining a breadth-first spanning tree (BFS tree) in partially dynamic distributed networks modeling a sequence of either failures or additions of communication links (but not both). We show (1 + ε)-approximation algorithms whose amortized time (over some number of link changes) is sublinear in D, the maximum diameter of the network. This breaks the Θ(D) time bound of recomputing “from scratch”. Our technique also leads to a (1 + ε)-approximate incremental algorithm for single-source shortest paths (SSSP) in the sequential (usual RAM) model. Prior to our work, the state of the art was the classic exact algorithm of [9] that is optimal under some assumptions [27]. Our result is the first to show that, in the incremental setting, this bound can be beaten in certain cases if a small approximation is allowed.}, author = {Henzinger, Monika H and Krinninger, Sebastian and Nanongkai, Danupon}, booktitle = {40th International Colloquium on Automata, Languages, and Programming}, isbn = {9783642392115}, issn = {1611-3349}, location = {Riga, Latvia}, pages = {607–619}, publisher = {Springer Nature}, title = {{Sublinear-time maintenance of breadth-first spanning tree in partially dynamic networks}}, doi = {10.1007/978-3-642-39212-2_53}, volume = {7966}, year = {2013}, } @inproceedings{11856, abstract = {We study dynamic (1 + ϵ)-approximation algorithms for the all-pairs shortest paths problem in unweighted undirected n-node m-edge graphs under edge deletions. The fastest algorithm for this problem is a randomized algorithm with a total update time of Ȏ(mn) and constant query time by Roditty and Zwick (FOCS 2004). The fastest deterministic algorithm is from a 1981 paper by Even and Shiloach (JACM 1981); it has a total update time of O(mn 2 ) and constant query time. We improve these results as follows: (1) We present an algorithm with a total update time of Ȏ(n 5/2 ) and constant query time that has an additive error of two in addition to the 1 + ϵ multiplicative error. This beats the previous Ȏ(mn) time when m = Ω(n 3/2 ). Note that the additive error is unavoidable since, even in the static case, an O(n 3-δ )-time (a so-called truly sub cubic) combinatorial algorithm with 1 + ϵ multiplicative error cannot have an additive error less than 2 - ϵ, unless we make a major breakthrough for Boolean matrix multiplication (Dor, Halperin and Zwick FOCS 1996) and many other long-standing problems (Vassilevska Williams and Williams FOCS 2010). The algorithm can also be turned into a (2 + ϵ)-approximation algorithm (without an additive error) with the same time guarantees, improving the recent (3 + ϵ)-approximation algorithm with Ȏ(n 5/2+O(1√(log n)) ) running time of Bernstein and Roditty (SODA 2011) in terms of both approximation and time guarantees. (2) We present a deterministic algorithm with a total update time of Ȏ(mn) and a query time of O(log log n). The algorithm has a multiplicative error of 1 + ϵ and gives the first improved deterministic algorithm since 1981. It also answers an open question raised by Bernstein in his STOC 2013 paper. In order to achieve our results, we introduce two new techniques: (1) A lazy Even-Shiloach tree algorithm which maintains a bounded-distance shortest-paths tree on a certain type of emulator called locally persevering emulator. (2) A derandomization technique based on moving Even-Shiloach trees as a way to derandomize the standard random set argument. These techniques might be of independent interest.}, author = {Henzinger, Monika H and Krinninger, Sebastian and Nanongkai, Danupon}, booktitle = {54th Annual Symposium on Foundations of Computer Science}, issn = {0272-5428}, location = {Berkeley, CA, United States}, pages = {538--547}, publisher = {Institute of Electrical and Electronics Engineers}, title = {{Dynamic approximate all-pairs shortest paths: Breaking the O(mn) barrier and derandomization}}, doi = {10.1109/focs.2013.64}, year = {2013}, } @article{12198, abstract = {The Arabidopsis thaliana central cell, the companion cell of the egg, undergoes DNA demethylation before fertilization, but the targeting preferences, mechanism, and biological significance of this process remain unclear. Here, we show that active DNA demethylation mediated by the DEMETER DNA glycosylase accounts for all of the demethylation in the central cell and preferentially targets small, AT-rich, and nucleosome-depleted euchromatic transposable elements. The vegetative cell, the companion cell of sperm, also undergoes DEMETER-dependent demethylation of similar sequences, and lack of DEMETER in vegetative cells causes reduced small RNA–directed DNA methylation of transposons in sperm. Our results demonstrate that demethylation in companion cells reinforces transposon methylation in plant gametes and likely contributes to stable silencing of transposable elements across generations.}, author = {Ibarra, Christian A. and Feng, Xiaoqi and Schoft, Vera K. and Hsieh, Tzung-Fu and Uzawa, Rie and Rodrigues, Jessica A. and Zemach, Assaf and Chumak, Nina and Machlicova, Adriana and Nishimura, Toshiro and Rojas, Denisse and Fischer, Robert L. and Tamaru, Hisashi and Zilberman, Daniel}, issn = {1095-9203}, journal = {Science}, keywords = {Multidisciplinary}, number = {6100}, pages = {1360--1364}, publisher = {American Association for the Advancement of Science}, title = {{Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes}}, doi = {10.1126/science.1224839}, volume = {337}, year = {2012}, } @article{12644, abstract = {In the Dry Andes of central Chile, summer water resources originate mostly from snowmelt and ice melt. We use the physically based, spatially distributed hydrological model TOPKAPI to study the exchange between glaciers and climate in the upper Aconcagua River Basin during the summer season and identify the model parameters that are robust and transferable and those that are more dependent on calibration. TOPKAPI has recently been adapted to incorporate an enhanced temperature index approach for snow and ice melting. We suggest a calibration procedure that allows calibration of parameters in three steps by separating parameters governing distinct processes. We evaluate the parameters' transferability in time and in space by applying the model at two spatial scales. TOPKAPI's ability to simulate the relevant processes is tested against meteorological, ablation, and glacier runoff data measured on Juncal Norte Glacier during two glacier ablation seasons. The model was applied successfully to the climatic setting of the Dry Andes once its parameters were recalibrated. We found a clear distinction between parameters that are stable in time and those that need recalibration. The parameters of the melt model are transferable from one season to the other, while the parameters governing the extrapolation of meteorological input data and the routing of glacier meltwater need recalibration from one season to the other. Sensitivity analysis revealed that the model is most sensitive to the temperature lapse rate governing the extrapolation of air temperature from point measurements to the glacier scale and to the melt parameter that multiplies the shortwave radiation balance.}, author = {Ragettli, S. and Pellicciotti, Francesca}, issn = {0043-1397}, journal = {Water Resources Research}, number = {3}, publisher = {American Geophysical Union}, title = {{Calibration of a physically based, spatially distributed hydrological model in a glacierized basin: On the use of knowledge from glaciometeorological processes to constrain model parameters}}, doi = {10.1029/2011wr010559}, volume = {48}, year = {2012}, } @article{12646, abstract = {Assessment of water resources from remote mountainous catchments plays a crucial role for the development of rural areas in or in the vicinity of mountain ranges. The scarcity of data, however, prevents the application of standard approaches that are based on data-driven models. The Hindu Kush–Karakoram–Himalaya mountain range is a crucial area in terms of water resources, but our understanding of the response of its high-elevation catchments to a changing climate is hindered by lack of hydro-meteorological and cryospheric data. Hydrological modeling is challenging here because internal inconsistencies—such as an underestimation of precipitation input that can be compensated for by an overestimation of meltwater—might be hidden due to the complexity of feedback mechanisms that govern melt and runoff generation in such basins. Data scarcity adds to this difficulty by preventing the application of systematic calibration procedures that would allow identification of the parameter set that could guarantee internal consistency in the simulation of the single hydrological components. In this work, we use simulations from the Hunza River Basin in the Karakoram region obtained with the hydrological model TOPKAPI to quantify the predictive power of discharge and snow-cover data sets, as well as the combination of both. We also show that short-term measurements of meteorological variables such as radiative fluxes, wind speed, relative humidity, and air temperature from glacio-meteorological experiments are crucial for a correct parameterization of surface melt processes. They enable detailed simulations of the energy fluxes governing glacier–atmosphere interaction and the resulting ablation through energy-balance modeling. These simulations are used to derive calibrated parameters for the simplified snow and glacier routines in TOPKAPI. We demonstrate that such parameters are stable in space and time in similar climatic regions, thus reducing the number of parameters requiring calibration.}, author = {Pellicciotti, Francesca and Buergi, Cyrill and Immerzeel, Walter Willem and Konz, Markus and Shrestha, Arun B.}, issn = {1994-7151}, journal = {Mountain Research and Development}, number = {1}, pages = {39--50}, publisher = {International Mountain Society}, title = {{Challenges and uncertainties in hydrological modeling of remote Hindu Kush–Karakoram–Himalayan (HKH) basins: Suggestions for calibration strategies}}, doi = {10.1659/mrd-journal-d-11-00092.1}, volume = {32}, year = {2012}, }