@inbook{18734, abstract = {In this Introduction, we outline expectations for when and how the hydrogen and helium atoms in the universe turned from neutral to ionized, focusing on the earliest, least well understood stages, and emphasize the most important open questions. We include a historical summary, and highlight the role of reionization as one of the few milestones in the evolution of the universe since the Big Bang, and its status as a unique probe of the beginning stages of structure formation.}, author = {Haiman, Zoltán}, booktitle = {Understanding the Epoch of Cosmic Reionization}, editor = {Mesinger, Andrei}, isbn = {9783319219561}, issn = {2214-7985}, pages = {1--22}, publisher = {Springer Nature}, title = {{Cosmic Reionization and the First Nonlinear Structures in the Universe}}, doi = {10.1007/978-3-319-21957-8_1}, year = {2015}, } @article{12626, abstract = {Ice cliffs have been identified as a reason for higher ablation rates on debris-covered glaciers than are implied by the insulation effects of the debris. This study aims to improve our understanding of cliff backwasting, and the role of radiative fluxes in particular. An energy-balance model is forced with new data gathered in May and October 2013 on Lirung Glacier, Nepalese Himalaya. Observations show substantial variability in melt between cliffs, between locations on any cliff and between seasons. Using a high-resolution digital elevation model we calculate longwave fluxes incident to the cliff from surrounding terrain and include the effect of local shading on shortwave radiation. This is an advance over previous studies, that made simplified assumptions on cliff geometry and radiative fluxes. Measured melt rates varied between 3.25 and 8.6 cm d−1 in May and 0.18 and 1.34 cm d−1 in October. Model results reproduce the strong variability in space and time, suggesting considerable differences in radiative fluxes over one cliff. In October the model fails to reproduce stake readings, probably due to the lack of a refreezing component. Disregarding local topography can lead to overestimation of melt at the point scale by up to ∼9%.}, author = {Steiner, Jakob F. and Pellicciotti, Francesca and Buri, Pascal and Miles, Evan S. and Immerzeel, Walter W. and Reid, Tim D.}, issn = {1727-5652}, journal = {Journal of Glaciology}, number = {229}, pages = {889--907}, publisher = {International Glaciological Society}, title = {{Modelling ice-cliff backwasting on a debris-covered glacier in the Nepalese Himalaya}}, doi = {10.3189/2015jog14j194}, volume = {61}, year = {2015}, } @article{12627, abstract = {Spatial evolution of supraglacial debris cover on mountain glaciers is a largely unmonitored and poorly understood phenomenon that directly affects glacier melt. Supraglacial debris cover for 93 glaciers in the Karakoram, northern Pakistan, was mapped from Landsat imagery acquired in 1977, 1998, 2009 and 2014. Surge-type glaciers occupy 41% of the study area and were considered separately. The time series of debris-covered surface area change shows a mean value of zero or near-zero change for both surging and non-surging glaciers. An increase in debris-covered area is often associated with negative regional mass balances. We extend this logic to suggest that the stable regional mass balances in the Karakoram explain the zero or near-zero change in debris-covered area. This coupling of trends combined with our 37 year time series of data suggests the Karakoram anomaly extends further back in time than previously known.}, author = {Herreid, Sam and Pellicciotti, Francesca and Ayala, Alvaro and Chesnokova, Anna and Kienholz, Christian and Shea, Joseph and Shrestha, Arun}, issn = {1727-5652}, journal = {Journal of Glaciology}, number = {227}, pages = {524--536}, publisher = {International Glaciological Society}, title = {{Satellite observations show no net change in the percentage of supraglacial debris-covered area in northern Pakistan from 1977 to 2014}}, doi = {10.3189/2015jog14j227}, volume = {61}, year = {2015}, } @article{12628, abstract = {Thick debris cover on glaciers can significantly reduce ice melt. However, several studies have suggested that debris-covered glaciers in the Himalaya might have lost mass at a rate similar to debris-free glaciers. We reconstruct elevation and mass changes for the debris-covered glaciers of the upper Langtang valley, Nepalese Himalaya, using a digital elevation model (DEM) from 1974 stereo Hexagon satellite data and the 2000 SRTM (Shuttle Radar Topography Mission) DEM. Uncertainties are high in the accumulation areas, due to data gaps in the SRTM and difficulties with delineation of the glacier borders. Even with these uncertainties, we obtain thinning rates comparable to those of several other studies in the Himalaya. In particular, we obtain a total mass balance for the investigated debris-covered glaciers of the basin of –0.32 ± 0.18 m w.e. a−1. However, there are major spatial differences both between glaciers and within any single glacier, exhibiting a very distinct nonlinear mass-balance profile with elevation. Through analysis of surface velocities derived from Landsat ETM+ imagery, we show that thinning occurs in areas of low velocity and low slope. These areas are prone to a general, dynamic decay of surface features and to the development of supraglacial lakes and ice cliffs, which may be responsible for a considerable increase in overall glacier ablation.}, author = {Pellicciotti, Francesca and Stephan, Christa and Miles, Evan and Herreid, Sam and Immerzeel, Walter W. and Bolch, Tobias}, issn = {1727-5652}, journal = {Journal of Glaciology}, keywords = {Earth-Surface Processes}, number = {226}, pages = {373--386}, publisher = {International Glaciological Society}, title = {{Mass-balance changes of the debris-covered glaciers in the Langtang Himal, Nepal, from 1974 to 1999}}, doi = {10.3189/2015jog13j237}, volume = {61}, year = {2015}, } @article{12629, abstract = {Meteorological studies in high-mountain environments form the basis of our understanding of catchment hydrology and glacier accumulation and melt processes, yet high-altitude (>4000 m above sea level, asl) observatories are rare. This research presents meteorological data recorded between December 2012 and November 2013 at seven stations in Nepal, ranging in elevation from 3860 to 5360 m asl. Seasonal and diurnal cycles in air temperature, vapour pressure, incoming short-wave and long-wave radiation, atmospheric transmissivity, wind speed, and precipitation are compared between sites. Solar radiation strongly affects diurnal temperature and vapour pressure cycles, but local topography and valley-scale circulations alter wind speed and precipitation cycles. The observed diurnal variability in vertical temperature gradients in all seasons highlights the importance of in situ measurements for melt modelling. The monsoon signal (progressive onset and sharp end) is visible in all data-sets, and the passage of the remnants of Typhoon Phailin in mid-October 2013 provides an interesting case study on the possible effects of such storms on glaciers in the region.}, author = {Shea, J.M. and Wagnon, P. and Immerzeel, W.W. and Biron, R. and Brun, F. and Pellicciotti, Francesca}, issn = {1360-0648}, journal = {International Journal of Water Resources Development}, keywords = {Water Science and Technology, Development}, number = {2}, pages = {174--200}, publisher = {Taylor & Francis}, title = {{A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya}}, doi = {10.1080/07900627.2015.1020417}, volume = {31}, year = {2015}, } @article{12630, abstract = {The hydrology of high-elevation watersheds of the Hindu Kush-Himalaya region (HKH) is poorly known. The correct representation of internal states and process dynamics in glacio-hydrological models can often not be verified due to missing in situ measurements. We use a new set of detailed ground data from the upper Langtang valley in Nepal to systematically guide a state-of-the art glacio-hydrological model through a parameter assigning process with the aim to understand the hydrology of the catchment and contribution of snow and ice processes to runoff. 14 parameters are directly calculated on the basis of local data, and 13 parameters are calibrated against 5 different datasets of in situ or remote sensing data. Spatial fields of debris thickness are reconstructed through a novel approach that employs data from an Unmanned Aerial Vehicle (UAV), energy balance modeling and statistical techniques. The model is validated against measured catchment runoff (Nash–Sutcliffe efficiency 0.87) and modeled snow cover is compared to Landsat snow cover. The advanced representation of processes allowed assessing the role played by avalanching for runoff for the first time for a Himalayan catchment (5% of annual water inputs to the hydrological system are due to snow redistribution) and to quantify the hydrological significance of sub-debris ice melt (9% of annual water inputs). Snowmelt is the most important contributor to total runoff during the hydrological year 2012/2013 (representing 40% of all sources), followed by rainfall (34%) and ice melt (26%). A sensitivity analysis is used to assess the efficiency of the monitoring network and identify the timing and location of field measurements that constrain model uncertainty. The methodology to set up a glacio-hydrological model in high-elevation regions presented in this study can be regarded as a benchmark for modelers in the HKH seeking to evaluate their calibration approach, their experimental setup and thus to reduce the predictive model uncertainty. }, author = {Ragettli, S. and Pellicciotti, Francesca and Immerzeel, W.W. and Miles, E.S. and Petersen, L. and Heynen, M. and Shea, J.M. and Stumm, D. and Joshi, S. and Shrestha, A.}, issn = {0309-1708}, journal = {Advances in Water Resources}, keywords = {Water Science and Technology}, number = {4}, pages = {94--111}, publisher = {Elsevier}, title = {{Unraveling the hydrology of a Himalayan catchment through integration of high resolution in situ data and remote sensing with an advanced simulation model}}, doi = {10.1016/j.advwatres.2015.01.013}, volume = {78}, year = {2015}, } @article{12631, abstract = {Air temperature is one of the most relevant input variables for snow and ice melt calculations. However, local meteorological conditions, complex topography, and logistical concerns in glacierized regions make the measuring and modeling of air temperature a difficult task. In this study, we investigate the spatial distribution of 2 m air temperature over mountain glaciers and propose a modification to an existing model to improve its representation. Spatially distributed meteorological data from Haut Glacier d'Arolla (Switzerland), Place (Canada), and Juncal Norte (Chile) Glaciers are used to examine approximate flow line temperatures during their respective ablation seasons. During warm conditions (off-glacier temperatures well above 0°C), observed air temperatures in the upper reaches of Place Glacier and Haut Glacier d'Arolla decrease down glacier along the approximate flow line. At Juncal Norte and Haut Glacier d'Arolla, an increase in air temperature is observed over the glacier tongue. While the temperature behavior over the upper part can be explained by the cooling effect of the glacier surface, the temperature increase over the glacier tongue may be caused by several processes induced by the surrounding warm atmosphere. In order to capture the latter effect, we add an additional term to the Greuell and Böhm (GB) thermodynamic glacier wind model. For high off-glacier temperatures, the modified GB model reduces root-mean-square error up to 32% and provides a new approach for distributing air temperature over mountain glaciers as a function of off-glacier temperatures and approximate glacier flow lines.}, author = {Ayala, A. and Pellicciotti, Francesca and Shea, J. M.}, issn = {2169-8996}, journal = {Journal of Geophysical Research: Atmospheres}, keywords = {Space and Planetary Science, Earth and Planetary Sciences (miscellaneous), Atmospheric Science, Geophysics}, number = {8}, pages = {3139--3157}, publisher = {American Geophysical Union}, title = {{Modeling 2 m air temperatures over mountain glaciers: Exploring the influence of katabatic cooling and external warming}}, doi = {10.1002/2015jd023137}, volume = {120}, year = {2015}, } @inproceedings{12881, author = {Martius, Georg S and Olbrich, Eckehard}, booktitle = {Proceedings of the 13th European Conference on Artificial Life}, isbn = {9780262330275}, location = {York, United Kingdom}, pages = {78}, publisher = {MIT Press}, title = {{Quantifying self-organizing behavior of autonomous robots}}, doi = {10.7551/978-0-262-33027-5-ch018}, year = {2015}, } @article{1311, abstract = {In this paper, we develop an energy method to study finite speed of propagation and waiting time phenomena for the stochastic porous media equation with linear multiplicative noise in up to three spatial dimensions. Based on a novel iteration technique and on stochastic counterparts of weighted integral estimates used in the deterministic setting, we formulate a sufficient criterion on the growth of initial data which locally guarantees a waiting time phenomenon to occur almost surely. Up to a logarithmic factor, this criterion coincides with the optimal criterion known from the deterministic setting. Our technique can be modified to prove finite speed of propagation as well.}, author = {Julian Fischer and Grün, Günther}, journal = {SIAM Journal on Mathematical Analysis}, number = {1}, pages = {825 -- 854}, publisher = {Society for Industrial and Applied Mathematics }, title = {{Finite speed of propagation and waiting times for the stochastic porous medium equation: A unifying approach}}, doi = {10.1137/140960578}, volume = {47}, year = {2015}, } @article{1313, abstract = {We present an algorithm for the derivation of lower bounds on support propagation for a certain class of nonlinear parabolic equations. We proceed by combining the ideas in some recent papers by the author with the algorithmic construction of entropies due to Jüngel and Matthes, reducing the problem to a quantifier elimination problem. Due to its complexity, the quantifier elimination problem cannot be solved by present exact algorithms. However, by tackling the quantifier elimination problem numerically, in the case of the thin-film equation we are able to improve recent results by the author in the regime of strong slippage n ∈ (1, 2). For certain second-order doubly nonlinear parabolic equations, we are able to extend the known lower bounds on free boundary propagation to the case of irregular oscillatory initial data. Finally, we apply our method to a sixth-order quantum drift-diffusion equation, resulting in an upper bound on the time which it takes for the support to reach every point in the domain.}, author = {Julian Fischer}, journal = {Interfaces and Free Boundaries}, number = {1}, pages = {1 -- 20}, publisher = {European Mathematical Society Publishing House}, title = {{Estimates on front propagation for nonlinear higher-order parabolic equations: An algorithmic approach}}, doi = {10.4171/IFB/331}, volume = {17}, year = {2015}, } @article{1314, abstract = {We derive a posteriori estimates for the modeling error caused by the assumption of perfect incompressibility in the incompressible Navier-Stokes equation: Real fluids are never perfectly incompressible but always feature at least some low amount of compressibility. Thus, their behavior is described by the compressible Navier-Stokes equation, the pressure being a steep function of the density. We rigorously estimate the difference between an approximate solution to the incompressible Navier-Stokes equation and any weak solution to the compressible Navier-Stokes equation in the sense of Lions (without assuming any additional regularity of solutions). Heuristics and numerical results suggest that our error estimates are of optimal order in the case of "well-behaved" flows and divergence-free approximations of the velocity field. Thus, we expect our estimates to justify the idealization of fluids as perfectly incompressible also in practical situations.}, author = {Fischer, Julian L}, journal = {SIAM Journal on Numerical Analysis}, number = {5}, pages = {2178 -- 2205}, publisher = {Society for Industrial and Applied Mathematics }, title = {{A posteriori modeling error estimates for the assumption of perfect incompressibility in the Navier-Stokes equation}}, doi = {10.1137/140966654}, volume = {53}, year = {2015}, } @article{19805, abstract = {Understanding the role of electron correlations in strong spin-orbit transition-metal oxides is key to the realization of numerous exotic phases including spin-orbit–assisted Mott insulators, correlated topological solids, and prospective new high-temperature superconductors. To date, most attention has been focused on the 5d iridium-based oxides. We instead consider the Pt-based delafossite oxide PtCoO2. Our transport measurements, performed on single-crystal samples etched to well-defined geometries using focused ion beam techniques, yield a room temperature resistivity of only 2.1 microhm·cm (μΩ-cm), establishing PtCoO2 as the most conductive oxide known. From angle-resolved photoemission and density functional theory, we show that the underlying Fermi surface is a single cylinder of nearly hexagonal cross-section, with very weak dispersion along kz. Despite being predominantly composed of d-orbital character, the conduction band is remarkably steep, with an average effective mass of only 1.14me. Moreover, the sharp spectral features observed in photoemission remain well defined with little additional broadening for more than 500 meV below EF, pointing to suppressed electron-electron scattering. Together, our findings establish PtCoO2 as a model nearly-free–electron system in a 5d delafossite transition-metal oxide.}, author = {Kushwaha, Pallavi and Sunko, Veronika and Moll, Philip J. W. and Bawden, Lewis and Riley, Jonathon M. and Nandi, Nabhanila and Rosner, Helge and Schmidt, Marcus P. and Arnold, Frank and Hassinger, Elena and Kim, Timur K. and Hoesch, Moritz and Mackenzie, Andrew P. and King, Phil D. C.}, issn = {2375-2548}, journal = {Science Advances}, number = {9}, publisher = {American Association for the Advancement of Science}, title = {{Nearly free electrons in a 5d delafossite oxide metal}}, doi = {10.1126/sciadv.1500692}, volume = {1}, year = {2015}, } @article{1981, abstract = {Variation in mitochondrial DNA is often assumed to be neutral and is used to construct the genealogical relationships among populations and species. However, if extant variation is the result of episodes of positive selection, these genealogies may be incorrect, although this information itself may pro-vide biologically and evolutionary meaningful information. In fact, positive Darwinian selection has been detected in the mitochondrial-encoded subunits that comprise complex I from diverse taxa with seemingly dissimilar bioenergetic life histories, but the functional implications of the selected sites are unknown. Complex I produces roughly 40% of the proton flux that is used to synthesize ATP from ADP, and a functional model based on the high-resolution structure of complex I described a unique biomechanical apparatus for proton translocation. We reported positive selection at sites in this apparatus during the evolution of Pacific salmon, and it appeared this was also the case in published reports from other taxa, but a comparison among studies was difficult because different statistical tests were used to detect selection and oftentimes, specific sites were not reported. Here we review the literature of positive selection in mitochondrial genomes, the statistical tests used to detect selection, and the structural and functional models that are currently available to study the physiological implications of selection. We then search for signatures of positive selection among the coding mitochondrial genomes of 237 species with a common set of tests and verify that the ND5 subunit of complex I is a repeated target of positive Darwinian selection in diverse taxa. We propose a novel hypothesis to explain the results based on their bioenergetic life histories and provide a guide for laboratory and field studies to test this hypothesis.}, author = {Garvin, Michael and Bielawski, Joseph and Sazanov, Leonid A and Gharrett, Anthony}, journal = {Journal of Zoological Systematics and Evolutionary Research}, number = {1}, pages = {1 -- 17}, publisher = {Wiley}, title = {{Review and meta-analysis of natural selection in mitochondrial complex I in metazoans}}, doi = {10.1111/jzs.12079}, volume = {53}, year = {2015}, } @inproceedings{1992, abstract = {We present a method and a tool for generating succinct representations of sets of concurrent traces. We focus on trace sets that contain all correct or all incorrect permutations of events from a given trace. We represent trace sets as HB-Formulas that are Boolean combinations of happens-before constraints between events. To generate a representation of incorrect interleavings, our method iteratively explores interleavings that violate the specification and gathers generalizations of the discovered interleavings into an HB-Formula; its complement yields a representation of correct interleavings. We claim that our trace set representations can drive diverse verification, fault localization, repair, and synthesis techniques for concurrent programs. We demonstrate this by using our tool in three case studies involving synchronization synthesis, bug summarization, and abstraction refinement based verification. In each case study, our initial experimental results have been promising. In the first case study, we present an algorithm for inferring missing synchronization from an HB-Formula representing correct interleavings of a given trace. The algorithm applies rules to rewrite specific patterns in the HB-Formula into locks, barriers, and wait-notify constructs. In the second case study, we use an HB-Formula representing incorrect interleavings for bug summarization. While the HB-Formula itself is a concise counterexample summary, we present additional inference rules to help identify specific concurrency bugs such as data races, define-use order violations, and two-stage access bugs. In the final case study, we present a novel predicate learning procedure that uses HB-Formulas representing abstract counterexamples to accelerate counterexample-guided abstraction refinement (CEGAR). In each iteration of the CEGAR loop, the procedure refines the abstraction to eliminate multiple spurious abstract counterexamples drawn from the HB-Formula.}, author = {Gupta, Ashutosh and Henzinger, Thomas A and Radhakrishna, Arjun and Samanta, Roopsha and Tarrach, Thorsten}, isbn = {978-1-4503-3300-9}, location = {Mumbai, India}, pages = {433 -- 444}, publisher = {ACM}, title = {{Succinct representation of concurrent trace sets}}, doi = {10.1145/2676726.2677008}, year = {2015}, } @article{1993, abstract = {The fitness effects of symbionts on their hosts can be context-dependent, with usually benign symbionts causing detrimental effects when their hosts are stressed, or typically parasitic symbionts providing protection towards their hosts (e.g. against pathogen infection). Here, we studied the novel association between the invasive garden ant Lasius neglectus and its fungal ectosymbiont Laboulbenia formicarum for potential costs and benefits. We tested ants with different Laboulbenia levels for their survival and immunity under resource limitation and exposure to the obligate killing entomopathogen Metarhizium brunneum. While survival of L. neglectus workers under starvation was significantly decreased with increasing Laboulbenia levels, host survival under Metarhizium exposure increased with higher levels of the ectosymbiont, suggesting a symbiont-mediated anti-pathogen protection, which seems to be driven mechanistically by both improved sanitary behaviours and an upregulated immune system. Ants with high Laboulbenia levels showed significantly longer self-grooming and elevated expression of immune genes relevant for wound repair and antifungal responses (β-1,3-glucan binding protein, Prophenoloxidase), compared with ants carrying low Laboulbenia levels. This suggests that the ectosymbiont Laboulbenia formicarum weakens its ant host by either direct resource exploitation or the costs of an upregulated behavioural and immunological response, which, however, provides a prophylactic protection upon later exposure to pathogens. }, author = {Konrad, Matthias and Grasse, Anna V and Tragust, Simon and Cremer, Sylvia}, issn = {1471-2954}, journal = {Proceedings of the Royal Society of London Series B Biological Sciences}, number = {1799}, publisher = {The Royal Society}, title = {{Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host}}, doi = {10.1098/rspb.2014.1976}, volume = {282}, year = {2015}, } @article{1997, abstract = {We prove that the three-state toric homogeneous Markov chain model has Markov degree two. In algebraic terminology this means, that a certain class of toric ideals is generated by quadratic binomials. This was conjectured by Haws, Martin del Campo, Takemura and Yoshida, who proved that they are generated by degree six binomials.}, author = {Noren, Patrik}, journal = {Journal of Symbolic Computation}, number = {May-June}, pages = {285 -- 296}, publisher = {Elsevier}, title = {{The three-state toric homogeneous Markov chain model has Markov degree two}}, doi = {10.1016/j.jsc.2014.09.014}, volume = {68/Part 2}, year = {2015}, } @article{2006, abstract = {The monotone secant conjecture posits a rich class of polynomial systems, all of whose solutions are real. These systems come from the Schubert calculus on flag manifolds, and the monotone secant conjecture is a compelling generalization of the Shapiro conjecture for Grassmannians (Theorem of Mukhin, Tarasov, and Varchenko). We present some theoretical evidence for this conjecture, as well as computational evidence obtained by 1.9 teraHertz-years of computing, and we discuss some of the phenomena we observed in our data. }, author = {Hein, Nicolas and Hillar, Christopher and Martin Del Campo Sanchez, Abraham and Sottile, Frank and Teitler, Zach}, journal = {Experimental Mathematics}, number = {3}, pages = {261 -- 269}, publisher = {Taylor & Francis}, title = {{The monotone secant conjecture in the real Schubert calculus}}, doi = {10.1080/10586458.2014.980044}, volume = {24}, year = {2015}, } @article{2008, abstract = {The paper describes a generalized iterative proportional fitting procedure that can be used for maximum likelihood estimation in a special class of the general log-linear model. The models in this class, called relational, apply to multivariate discrete sample spaces that do not necessarily have a Cartesian product structure and may not contain an overall effect. When applied to the cell probabilities, the models without the overall effect are curved exponential families and the values of the sufficient statistics are reproduced by the MLE only up to a constant of proportionality. The paper shows that Iterative Proportional Fitting, Generalized Iterative Scaling, and Improved Iterative Scaling fail to work for such models. The algorithm proposed here is based on iterated Bregman projections. As a by-product, estimates of the multiplicative parameters are also obtained. An implementation of the algorithm is available as an R-package.}, author = {Klimova, Anna and Rudas, Tamás}, journal = {Scandinavian Journal of Statistics}, number = {3}, pages = {832 -- 847}, publisher = {Wiley}, title = {{Iterative scaling in curved exponential families}}, doi = {10.1111/sjos.12139}, volume = {42}, year = {2015}, } @article{2014, abstract = {The concepts of faithfulness and strong-faithfulness are important for statistical learning of graphical models. Graphs are not sufficient for describing the association structure of a discrete distribution. Hypergraphs representing hierarchical log-linear models are considered instead, and the concept of parametric (strong-) faithfulness with respect to a hypergraph is introduced. Strong-faithfulness ensures the existence of uniformly consistent parameter estimators and enables building uniformly consistent procedures for a hypergraph search. The strength of association in a discrete distribution can be quantified with various measures, leading to different concepts of strong-faithfulness. Lower and upper bounds for the proportions of distributions that do not satisfy strong-faithfulness are computed for different parameterizations and measures of association.}, author = {Klimova, Anna and Uhler, Caroline and Rudas, Tamás}, journal = {Computational Statistics & Data Analysis}, number = {7}, pages = {57 -- 72}, publisher = {Elsevier}, title = {{Faithfulness and learning hypergraphs from discrete distributions}}, doi = {10.1016/j.csda.2015.01.017}, volume = {87}, year = {2015}, } @article{2025, abstract = {Small GTP-binding proteins of the Ras superfamily play diverse roles in intracellular trafficking. Among them, the Rab, Arf, and Rho families function in successive steps of vesicle transport, in forming vesicles from donor membranes, directing vesicle trafficking toward target membranes and docking vesicles onto target membranes. These proteins act as molecular switches that are controlled by a cycle of GTP binding and hydrolysis regulated by guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs). In this study we explored the role of GAPs in the regulation of the endocytic pathway using fluorescently labeled yeast mating pheromone α-factor. Among 25 non-essential GAP mutants, we found that deletion of the GLO3 gene, encoding Arf-GAP protein, caused defective internalization of fluorescently labeled α-factor. Quantitative analysis revealed that glo3Δ cells show defective α-factor binding to the cell surface. Interestingly, Ste2p, the α-factor receptor, was mis-localized from the plasma membrane to the vacuole in glo3Δ cells. Domain deletion mutants of Glo3p revealed that a GAP-independent function, as well as the GAP activity, of Glo3p is important for both α-factor binding and Ste2p localization at the cell surface. Additionally, we found that deletion of the GLO3 gene affects the size and number of Arf1p-residing Golgi compartments and causes a defect in transport from the TGN to the plasma membrane. Furthermore, we demonstrated that glo3Δ cells were defective in the late endosome-to-TGN transport pathway, but not in the early endosome-to-TGN transport pathway. These findings suggest novel roles for Arf-GAP Glo3p in endocytic recycling of cell surface proteins.}, author = {Kawada, Daiki and Kobayashi, Hiromu and Tomita, Tsuyoshi and Nakata, Eisuke and Nagano, Makoto and Siekhaus, Daria E and Toshima, Junko and Toshimaa, Jiro}, journal = {Biochimica et Biophysica Acta - Molecular Cell Research}, number = {1}, pages = {144 -- 156}, publisher = {Elsevier}, title = {{The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins}}, doi = {10.1016/j.bbamcr.2014.10.009}, volume = {1853}, year = {2015}, }