@article{924, abstract = {This paper presents a numerical study of a Capillary Pumped Loop evaporator. A two-dimensional unsteady mathematical model of a flat evaporator is developed to simulate heat and mass transfer in unsaturated porous wick with phase change. The liquid-vapor phase change inside the porous wick is described by Langmuir's law. The governing equations are solved by the Finite Element Method. The results are presented then for a sintered nickel wick and methanol as a working fluid. The heat flux required to the transition from the all-liquid wick to the vapor-liquid wick is calculated. The dynamic and thermodynamic behavior of the working fluid in the capillary structure are discussed in this paper.}, author = {Boubaker, Riadh and Platel, Vincent and Bergès, Alexis and Bancelin, Mathieu and Hannezo, Edouard B}, journal = {Applied Thermal Engineering}, pages = {1 -- 8}, publisher = {Elsevier}, title = {{Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop}}, doi = {10.1016/j.applthermaleng.2014.10.009}, volume = {76}, year = {2015}, } @article{929, abstract = {An essential question of morphogenesis is how patterns arise without preexisting positional information, as inspired by Turing. In the past few years, cytoskeletal flows in the cell cortex have been identified as a key mechanism of molecular patterning at the subcellular level. Theoretical and in vitro studies have suggested that biological polymers such as actomyosin gels have the property to self-organize, but the applicability of this concept in an in vivo setting remains unclear. Here, we report that the regular spacing pattern of supracellular actin rings in the Drosophila tracheal tubule is governed by a self-organizing principle. We propose a simple biophysical model where pattern formation arises from the interplay of myosin contractility and actin turnover. We validate the hypotheses of the model using photobleaching experiments and report that the formation of actin rings is contractility dependent. Moreover, genetic and pharmacological perturbations of the physical properties of the actomyosin gel modify the spacing of the pattern, as the model predicted. In addition, our model posited a role of cortical friction in stabilizing the spacing pattern of actin rings. Consistently, genetic depletion of apical extracellular matrix caused strikingly dynamic movements of actin rings, mirroring our model prediction of a transition from steady to chaotic actin patterns at low cortical friction. Our results therefore demonstrate quantitatively that a hydrodynamical instability of the actin cortex can trigger regular pattern formation and drive morphogenesis in an in vivo setting. }, author = {Hannezo, Edouard B and Dong, Bo and Recho, Pierre and Joanny, Jean and Hayashi, Shigeo}, journal = {PNAS}, number = {28}, pages = {8620 -- 8625}, publisher = {National Academy of Sciences}, title = {{Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes}}, doi = {10.1073/pnas.1504762112}, volume = {112}, year = {2015}, } @article{933, abstract = {Although collective cell motion plays an important role, for example during wound healing, embryogenesis, or cancer progression, the fundamental rules governing this motion are still not well understood, in particular at high cell density. We study here the motion of human bronchial epithelial cells within a monolayer, over long times. We observe that, as the monolayer ages, the cells slow down monotonously, while the velocity correlation length first increases as the cells slow down but eventually decreases at the slowest motions. By comparing experiments, analytic model, and detailed particle-based simulations, we shed light on this biological amorphous solidification process, demonstrating that the observed dynamics can be explained as a consequence of the combined maturation and strengthening of cell-cell and cell-substrate adhesions. Surprisingly, the increase of cell surface density due to proliferation is only secondary in this process. This analysis is confirmed with two other cell types. The very general relations between the mean cell velocity and velocity correlation lengths, which apply for aggregates of self-propelled particles, as well as motile cells, can possibly be used to discriminate between various parameter changes in vivo, from noninvasive microscopy data.}, author = {García, Simón and Hannezo, Edouard B and Elgeti, Jens and Joanny, Jean and Silberzan, Pascal and Gov, Nir}, journal = {PNAS}, number = {50}, pages = {15314 -- 15319}, publisher = {National Academy of Sciences}, title = {{Physics of active jamming during collective cellular motion in a monolayer}}, doi = {10.1073/pnas.1510973112}, volume = {112}, year = {2015}, } @article{9532, abstract = {Genomic imprinting, an inherently epigenetic phenomenon defined by parent of origin-dependent gene expression, is observed in mammals and flowering plants. Genome-scale surveys of imprinted expression and the underlying differential epigenetic marks have led to the discovery of hundreds of imprinted plant genes and confirmed DNA and histone methylation as key regulators of plant imprinting. However, the biological roles of the vast majority of imprinted plant genes are unknown, and the evolutionary forces shaping plant imprinting remain rather opaque. Here, we review the mechanisms of plant genomic imprinting and discuss theories of imprinting evolution and biological significance in light of recent findings.}, author = {Rodrigues, Jessica A. and Zilberman, Daniel}, issn = {1549-5477}, journal = {Genes and Development}, number = {24}, pages = {2517–2531}, publisher = {Cold Spring Harbor Laboratory Press}, title = {{Evolution and function of genomic imprinting in plants}}, doi = {10.1101/gad.269902.115}, volume = {29}, year = {2015}, } @article{9684, abstract = {The size dependence of the strength of nano- and micron-sized crystals is studied using a new simulation approach in which the dynamics of the density functions of dislocations are modeled. Since any quantity of dislocations can be represented by a density, this approach can handle large systems containing large quantities of dislocations, which may handicap discrete dislocation dynamics schemes due to the excessive computation time involved. For this reason, pillar sizes spanning a large range, from the sub-micron to micron regimes, can be simulated. The simulation results reveal the power-law relationship between strength and specimen size up to a certain size, beyond which the strength varies much more slowly with size. For specimens smaller than ~4000b, their strength is found to be controlled by the dislocation depletion condition, in which the total dislocation density remains almost constant throughout the loading process. In specimens larger than ~4000b, the initial dislocation distribution is of critical importance since the presence of dislocation entanglements is found to obstruct deformation in the neighboring regions within a distance of ~2000b. This length scale suggests that the effects of dense dislocation clusters are greater in intermediate-sized specimens (e.g. 4000b and 8000b) than in larger specimens (e.g. 16 000b), according to the weakest-link concept.}, author = {Leung, P S S and Leung, H S and Cheng, Bingqing and Ngan, A H W}, issn = {1361-651X}, journal = {Modelling and Simulation in Materials Science and Engineering}, number = {3}, publisher = {IOP Publishing}, title = {{Size dependence of yield strength simulated by a dislocation-density function dynamics approach}}, doi = {10.1088/0965-0393/23/3/035001}, volume = {23}, year = {2015}, } @article{1566, abstract = {Deposits of misfolded proteins in the human brain are associated with the development of many neurodegenerative diseases. Recent studies show that these proteins have common traits even at the monomer level. Among them, a polyglutamine region that is present in huntingtin is known to exhibit a correlation between the length of the chain and the severity as well as the earliness of the onset of Huntington disease. Here, we apply bias exchange molecular dynamics to generate structures of polyglutamine expansions of several lengths and characterize the resulting independent conformations. We compare the properties of these conformations to those of the standard proteins, as well as to other homopolymeric tracts. We find that, similar to the previously studied polyvaline chains, the set of possible transient folds is much broader than the set of known-to-date folds, although the conformations have different structures. We show that the mechanical stability is not related to any simple geometrical characteristics of the structures. We demonstrate that long polyglutamine expansions result in higher mechanical stability than the shorter ones. They also have a longer life span and are substantially more prone to form knotted structures. The knotted region has an average length of 35 residues, similar to the typical threshold for most polyglutamine-related diseases. Similarly, changes in shape and mechanical stability appear once the total length of the peptide exceeds this threshold of 35 glutamine residues. We suggest that knotted conformers may also harm the cellular machinery and thus lead to disease.}, author = {Gómez Sicilia, Àngel and Sikora, Mateusz K and Cieplak, Marek and Carrión Vázquez, Mariano}, journal = {PLoS Computational Biology}, number = {10}, publisher = {Public Library of Science}, title = {{An exploration of the universe of polyglutamine structures}}, doi = {10.1371/journal.pcbi.1004541}, volume = {11}, year = {2015}, } @misc{9712, author = {Tugrul, Murat and Paixao, Tiago and Barton, Nicholas H and Tkačik, Gašper}, publisher = {Public Library of Science}, title = {{Other fitness models for comparison & for interacting TFBSs}}, doi = {10.1371/journal.pgen.1005639.s001}, year = {2015}, } @misc{9714, author = {Gómez Sicilia, Àngel and Sikora, Mateusz K and Cieplak, Marek and Carrión Vázquez, Mariano}, publisher = {Public Library of Science }, title = {{An exploration of the universe of polyglutamine structures - submission to PLOS journals}}, doi = {10.1371/journal.pcbi.1004541.s001}, year = {2015}, } @misc{9715, author = {Trubenova, Barbora and Novak, Sebastian and Hager, Reinmar}, publisher = {Public Library of Science}, title = {{Mathematical inference of the results}}, doi = {10.1371/journal.pone.0126907.s001}, 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}, } @misc{9742, abstract = {Repeated pathogen exposure is a common threat in colonies of social insects, posing selection pressures on colony members to respond with improved disease-defense performance. We here tested whether experience gained by repeated tending of low-level fungus-exposed (Metarhizium robertsii) larvae may alter the performance of sanitary brood care in the clonal ant, Platythyrea punctata. We trained ants individually over nine consecutive trials to either sham-treated or fungus-exposed larvae. We then compared the larval grooming behavior of naive and trained ants and measured how effectively they removed infectious fungal conidiospores from the fungus-exposed larvae. We found that the ants changed the duration of larval grooming in response to both, larval treatment and their level of experience: (1) sham-treated larvae received longer grooming than the fungus-exposed larvae and (2) trained ants performed less self-grooming but longer larval grooming than naive ants, which was true for both, ants trained to fungus-exposed and also to sham-treated larvae. Ants that groomed the fungus-exposed larvae for longer periods removed a higher number of fungal conidiospores from the surface of the fungus-exposed larvae. As experienced ants performed longer larval grooming, they were more effective in fungal removal, thus making them better caretakers under pathogen attack of the colony. By studying this clonal ant, we can thus conclude that even in the absence of genetic variation between colony members, differences in experience levels of brood care may affect performance of sanitary brood care in social insects.}, author = {Westhus, Claudia and Ugelvig, Line V and Tourdot, Edouard and Heinze, Jürgen and Doums, Claudie and Cremer, Sylvia}, publisher = {Dryad}, title = {{Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant}}, doi = {10.5061/dryad.7kc79}, year = {2015}, } @misc{9765, author = {Chevereau, Guillaume and Lukacisinova, Marta and Batur, Tugce and Guvenek, Aysegul and Ayhan, Dilay Hazal and Toprak, Erdal and Bollenbach, Mark Tobias}, publisher = {Public Library of Science}, title = {{Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs}}, doi = {10.1371/journal.pbio.1002299.s008}, 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{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{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}, } @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{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{1618, abstract = {CCL19 and CCL21 are chemokines involved in the trafficking of immune cells, particularly within the lymphatic system, through activation of CCR7. Concurrent expression of PSGL-1 and CCR7 in naive T-cells enhances recruitment of these cells to secondary lymphoid organs by CCL19 and CCL21. Here the solution structure of CCL19 is reported. It contains a canonical chemokine domain. Chemical shift mapping shows the N-termini of PSGL-1 and CCR7 have overlapping binding sites for CCL19 and binding is competitive. Implications for the mechanism of PSGL-1's enhancement of resting T-cell recruitment are discussed.}, author = {Veldkamp, Christopher and Kiermaier, Eva and Gabel Eissens, Skylar and Gillitzer, Miranda and Lippner, David and Disilvio, Frank and Mueller, Casey and Wantuch, Paeton and Chaffee, Gary and Famiglietti, Michael and Zgoba, Danielle and Bailey, Asha and Bah, Yaya and Engebretson, Samantha and Graupner, David and Lackner, Emily and Larosa, Vincent and Medeiros, Tysha and Olson, Michael and Phillips, Andrew and Pyles, Harley and Richard, Amanda and Schoeller, Scott and Touzeau, Boris and Williams, Larry and Sixt, Michael K and Peterson, Francis}, journal = {Biochemistry}, number = {27}, pages = {4163 -- 4166}, publisher = {American Chemical Society}, title = {{Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites}}, doi = {10.1021/acs.biochem.5b00560}, volume = {54}, 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}, }