@article{12586, abstract = {Ice cliffs are common on debris-covered glaciers and have relatively high melt rates due to their direct exposure to incoming radiation. Previous studies have shown that their number and relative area can change considerably from year to year, but this variability has not been explored, in part because available cliff observations are irregular. Here, we systematically mapped and tracked ice cliffs across four debris-covered glaciers in High Mountain Asia for every late ablation season from 2009 to 2019 using high-resolution multi-spectral satellite imagery. We then quantified the processes occurring at the feature scale to train a stochastic birth-death model to represent the cliff population dynamics. Our results show that while the cliff relative area can change by up to 20% from year to year, the natural long-term variability is constrained, thus defining a glacier-specific cliff carrying capacity. In a subsequent step, the inclusion of external drivers related to climate, glacier dynamics, and hydrology highlights the influence of these variables on the cliff population dynamics, which is usually not a direct one due to the complexity and interdependence of the processes taking place at the glacier surface. In some extreme cases (here, a glacier surge), these external drivers may lead to a reorganization of the cliffs at the glacier surface and a change in the natural variability. These results have implications for the melt of debris-covered glaciers, in addition to showing the high rate of changes at their surface and highlighting some of the links between cliff population and glacier state.}, author = {Kneib, M. and Miles, E. S. and Buri, P. and Molnar, P. and McCarthy, M. and Fugger, S. and Pellicciotti, Francesca}, issn = {2169-9003}, journal = {Journal of Geophysical Research: Earth Surface}, keywords = {Earth-Surface Processes, Geophysics}, number = {10}, publisher = {American Geophysical Union}, title = {{Interannual dynamics of ice cliff populations on debris‐covered glaciers from remote sensing observations and stochastic modeling}}, doi = {10.1029/2021jf006179}, volume = {126}, year = {2021}, } @article{12587, abstract = {Surface energy-balance models are commonly used in conjunction with satellite thermal imagery to estimate supraglacial debris thickness. Removing the need for local meteorological data in the debris thickness estimation workflow could improve the versatility and spatiotemporal application of debris thickness estimation. We evaluate the use of regional reanalysis data to derive debris thickness for two mountain glaciers using a surface energy-balance model. Results forced using ERA-5 agree with AWS-derived estimates to within 0.01 ± 0.05 m for Miage Glacier, Italy, and 0.01 ± 0.02 m for Khumbu Glacier, Nepal. ERA-5 data were then used to estimate spatiotemporal changes in debris thickness over a ~20-year period for Miage Glacier, Khumbu Glacier and Haut Glacier d'Arolla, Switzerland. We observe significant increases in debris thickness at the terminus for Haut Glacier d'Arolla and at the margins of the expanding debris cover at all glaciers. While simulated debris thickness was underestimated compared to point measurements in areas of thick debris, our approach can reconstruct glacier-scale debris thickness distribution and its temporal evolution over multiple decades. We find significant changes in debris thickness over areas of thin debris, areas susceptible to high ablation rates, where current knowledge of debris evolution is limited.}, author = {Stewart, Rebecca L. and Westoby, Matthew and Pellicciotti, Francesca and Rowan, Ann and Swift, Darrel and Brock, Benjamin and Woodward, John}, issn = {1727-5652}, journal = {Journal of Glaciology}, number = {262}, pages = {366--384}, publisher = {Cambridge University Press}, title = {{Using climate reanalysis data in conjunction with multi-temporal satellite thermal imagery to derive supraglacial debris thickness changes from energy-balance modelling}}, doi = {10.1017/jog.2020.111}, volume = {67}, year = {2021}, } @article{12588, abstract = {The thinning patterns of debris-covered glaciers in High Mountain Asia are not well understood. Here we calculate the effect of supraglacial ice cliffs on the mass balance of all glaciers in a Himalayan catchment, using a process-based ice cliff melt model. We show that ice cliffs are responsible for higher than expected thinning rates of debris-covered glacier tongues, leading to an underestimation of their ice mass loss of 17% ± 4% in the catchment if not considered. We also show that cliffs do enhance melt where other processes would suppress it, that is, at high elevations, or where debris is thick, and that they contribute relatively more to glacier mass loss if oriented north. Our approach provides a key contribution to our understanding of the mass losses of debris-covered glaciers, and a new quantification of their catchment wide melt and mass balance.}, author = {Buri, Pascal and Miles, Evan S. and Steiner, Jakob F. and Ragettli, Silvan and Pellicciotti, Francesca}, issn = {1944-8007}, journal = {Geophysical Research Letters}, keywords = {General Earth and Planetary Sciences, Geophysics}, number = {6}, publisher = {American Geophysical Union}, title = {{Supraglacial ice cliffs can substantially increase the mass loss of debris‐covered glaciers}}, doi = {10.1029/2020gl092150}, volume = {48}, year = {2021}, } @article{12589, abstract = {Near-surface air temperature (Ta) is highly important for modelling glacier ablation, though its spatio-temporal variability over melting glaciers still remains largely unknown. We present a new dataset of distributed Ta for three glaciers of different size in the south-east Tibetan Plateau during two monsoon-dominated summer seasons. We compare on-glacier Ta to ambient Ta extrapolated from several local off-glacier stations. We parameterise the along-flowline sensitivity of Ta on these glaciers to changes in off-glacier temperatures (referred to as “temperature sensitivity”) and present the results in the context of available distributed on-glacier datasets around the world. Temperature sensitivity decreases rapidly up to 2000–3000 m along the down-glacier flowline distance. Beyond this distance, both the Ta on the Tibetan glaciers and global glacier datasets show little additional cooling relative to the off-glacier temperature. In general, Ta on small glaciers (with flowline distances <1000 m) is highly sensitive to temperature changes outside the glacier boundary layer. The climatology of a given region can influence the general magnitude of this temperature sensitivity, though no strong relationships are found between along-flowline temperature sensitivity and mean summer temperatures or precipitation. The terminus of some glaciers is affected by other warm-air processes that increase temperature sensitivity (such as divergent boundary layer flow, warm up-valley winds or debris/valley heating effects) which are evident only beyond ∼70 % of the total glacier flowline distance. Our results therefore suggest a strong role of local effects in modulating temperature sensitivity close to the glacier terminus, although further work is still required to explain the variability of these effects for different glaciers.}, author = {Shaw, Thomas E. and Yang, Wei and Ayala, Álvaro and Bravo, Claudio and Zhao, Chuanxi and Pellicciotti, Francesca}, issn = {1994-0424}, journal = {The Cryosphere}, keywords = {Earth-Surface Processes, Water Science and Technology}, number = {2}, pages = {595--614}, publisher = {Copernicus Publications}, title = {{Distributed summer air temperatures across mountain glaciers in the south-east Tibetan Plateau: Temperature sensitivity and comparison with existing glacier datasets}}, doi = {10.5194/tc-15-595-2021}, volume = {15}, year = {2021}, } @article{12590, abstract = {Ice cliffs play a key role in the mass balance of debris-covered glaciers, but assessing their importance is limited by a lack of datasets on their distribution and evolution at scales larger than an individual glacier. These datasets are often derived using operator-biased and time-consuming manual delineation approaches, despite the recent emergence of semi-automatic mapping methods. These methods have used elevation or multispectral data, but the varying slope and mixed spectral signal of these dynamic features makes the transferability of these approaches particularly challenging. We develop three semi-automated and objective new approaches, based on the Spectral Curvature and Linear Spectral Unmixing of multispectral images, to map these features at a glacier to regional scale. The transferability of each method is assessed by applying it to three sites in the Himalaya, where debris-covered glaciers are widespread, with varying lithologic, glaciological and climatic settings, and encompassing different periods of the melt season. We develop the new methods keeping in mind the wide range of remote sensing platforms currently in use, and focus in particular on two products: we apply the three approaches at each site to near-contemporaneous atmospherically-corrected Pléiades (2 m resolution) and Sentinel-2 (10 m resolution) images and assess the effects of spatial and spectral resolution on the results. We find that the Spectral Curvature method works best for the high spatial resolution, four band Pléaides images, while a modification of the Linear Spectral Unmixing using the scaling factor of the unmixing is best for the coarser spatial resolution, but additional spectral information of Sentinel-2 products. In both cases ice cliffs are mapped with a Dice coefficient higher than 0.48. Comparison of the Pléiades results with other existing methods shows that the Spectral Curvature approach performs better and is more robust than any other existing automated or semi-automated approaches. Both methods outline a high number of small, sometimes shallow-sloping and thinly debris-covered ice patches that differ from our traditional understanding of cliffs but may have non-negligible impact on the mass balance of debris-covered glaciers. Overall these results pave the way for large scale efforts of ice cliff mapping that can enable inclusion of these features in debris-covered glacier melt models, as well as allow the generation of multiple datasets to study processes of cliff formation, evolution and decline.}, author = {Kneib, M. and Miles, E.S. and Jola, S. and Buri, P. and Herreid, S. and Bhattacharya, A. and Watson, C.S. and Bolch, T. and Quincey, D. and Pellicciotti, Francesca}, issn = {0034-4257}, journal = {Remote Sensing of Environment}, keywords = {Computers in Earth Sciences, Geology, Soil Science}, number = {2}, publisher = {Elsevier}, title = {{Mapping ice cliffs on debris-covered glaciers using multispectral satellite images}}, doi = {10.1016/j.rse.2020.112201}, volume = {253}, year = {2021}, } @article{12591, abstract = {Glacier albedo determines the net shortwave radiation absorbed at the glacier surface and plays a crucial role in glacier energy and mass balance. Remote sensing techniques are efficient means to retrieve glacier surface albedo over large and inaccessible areas and to study its variability. However, corrections of anisotropic reflectance of glacier surface have been established for specific shortwave bands only, such as Landsat 5 Thematic Mapper (L5/TM) band 2 and band 4, which is a major limitation of current retrievals of glacier broadband albedo. In this study, we calibrated and evaluated four anisotropy correction models for glacier snow and ice, applicable to visible, near-infrared and shortwave-infrared wavelengths using airborne datasets of Bidirectional Reflectance Distribution Function (BRDF). We then tested the ability of the best-performing anisotropy correction model, referred to from here on as the ‘updated model’, to retrieve albedo from L5/TM, Landsat 8 Operational Land Imager (L8/OLI) and Moderate Resolution Imaging Spectroradiometer (MODIS) imagery, and evaluated these results with field measurements collected on eight glaciers around the world. Our results show that the updated model: (1) can accurately estimate anisotropic factors of reflectance for snow and ice surfaces; (2) generally performs better than prior approaches for L8/OLI albedo retrieval but is not appropriate for L5/TM; (3) generally retrieves MODIS albedo better than the MODIS standard albedo product (MCD43A3) in both absolute values and glacier albedo temporal evolution, i.e., exhibiting both fewer gaps and better agreement with field observations. As the updated model enables anisotropy correction of a maximum of 10 multispectral bands and is implemented in Google Earth Engine (GEE), it is promising for observing and analyzing glacier albedo at large spatial scales.}, author = {Ren, Shaoting and Miles, Evan S. and Jia, Li and Menenti, Massimo and Kneib, Marin and Buri, Pascal and McCarthy, Michael J. and Shaw, Thomas E. and Yang, Wei and Pellicciotti, Francesca}, issn = {2072-4292}, journal = {Remote Sensing}, number = {9}, publisher = {MDPI}, title = {{Anisotropy parameterization development and evaluation for glacier surface albedo retrieval from satellite observations}}, doi = {10.3390/rs13091714}, volume = {13}, year = {2021}, } @article{12667, abstract = {Unlike crystalline atomic and ionic solids, texture development due to crystallographically preferred growth in colloidal crystals is less studied. Here we investigate the underlying mechanisms of the texture evolution in an evaporation-induced colloidal assembly process through experiments, modeling, and theoretical analysis. In this widely used approach to obtain large-area colloidal crystals, the colloidal particles are driven to the meniscus via the evaporation of a solvent or matrix precursor solution where they close-pack to form a face-centered cubic colloidal assembly. Via two-dimensional large-area crystallographic mapping, we show that the initial crystal orientation is dominated by the interaction of particles with the meniscus, resulting in the expected coalignment of the close-packed direction with the local meniscus geometry. By combining with crystal structure analysis at a single-particle level, we further reveal that, at the later stage of self-assembly, however, the colloidal crystal undergoes a gradual rotation facilitated by geometrically necessary dislocations (GNDs) and achieves a large-area uniform crystallographic orientation with the close-packed direction perpendicular to the meniscus and parallel to the growth direction. Classical slip analysis, finite element-based mechanical simulation, computational colloidal assembly modeling, and continuum theory unequivocally show that these GNDs result from the tensile stress field along the meniscus direction due to the constrained shrinkage of the colloidal crystal during drying. The generation of GNDs with specific slip systems within individual grains leads to crystallographic rotation to accommodate the mechanical stress. The mechanistic understanding reported here can be utilized to control crystallographic features of colloidal assemblies, and may provide further insights into crystallographically preferred growth in synthetic, biological, and geological crystals.}, author = {Li, Ling and Goodrich, Carl Peter and Yang, Haizhao and Phillips, Katherine R. and Jia, Zian and Chen, Hongshun and Wang, Lifeng and Zhong, Jinjin and Liu, Anhua and Lu, Jianfeng and Shuai, Jianwei and Brenner, Michael P. and Spaepen, Frans and Aizenberg, Joanna}, issn = {1091-6490}, journal = {PNAS}, number = {32}, publisher = {Proceedings of the National Academy of Sciences}, title = {{Microscopic origins of the crystallographically preferred growth in evaporation-induced colloidal crystals}}, doi = {10.1073/pnas.2107588118}, volume = {118}, year = {2021}, } @inproceedings{12767, abstract = {Several problems in planning and reactive synthesis can be reduced to the analysis of two-player quantitative graph games. Optimization is one form of analysis. We argue that in many cases it may be better to replace the optimization problem with the satisficing problem, where instead of searching for optimal solutions, the goal is to search for solutions that adhere to a given threshold bound. This work defines and investigates the satisficing problem on a two-player graph game with the discounted-sum cost model. We show that while the satisficing problem can be solved using numerical methods just like the optimization problem, this approach does not render compelling benefits over optimization. When the discount factor is, however, an integer, we present another approach to satisficing, which is purely based on automata methods. We show that this approach is algorithmically more performant – both theoretically and empirically – and demonstrates the broader applicability of satisficing over optimization.}, author = {Bansal, Suguman and Chatterjee, Krishnendu and Vardi, Moshe Y.}, booktitle = {27th International Conference on Tools and Algorithms for the Construction and Analysis of Systems}, isbn = {9783030720155}, issn = {1611-3349}, location = {Luxembourg City, Luxembourg}, pages = {20--37}, publisher = {Springer Nature}, title = {{On satisficing in quantitative games}}, doi = {10.1007/978-3-030-72016-2}, volume = {12651}, year = {2021}, } @inproceedings{12909, author = {Schlögl, Alois and Elefante, Stefano and Hornoiu, Andrei and Stadlbauer, Stephan}, booktitle = {ASHPC21 – Austrian-Slovenian HPC Meeting 2021}, isbn = {978-961-6980-77-7}, location = {Virtual}, pages = {5}, publisher = {University of Ljubljana}, title = {{Managing software on a heterogenous HPC cluster}}, doi = {10.3359/2021hpc}, year = {2021}, } @misc{12987, abstract = {Chromosomal inversion polymorphisms, segments of chromosomes that are flipped in orientation and occur in reversed order in some individuals, have long been recognized to play an important role in local adaptation. They can reduce recombination in heterozygous individuals and thus help to maintain sets of locally adapted alleles. In a wide range of organisms, populations adapted to different habitats differ in frequency of inversion arrangements. However, getting a full understanding of the importance of inversions for adaptation requires confirmation of their influence on traits under divergent selection. Here, we studied a marine snail, Littorina saxatilis, that has evolved ecotypes adapted to wave exposure or crab predation. These two types occur in close proximity on different parts of the shore. Gene flow between them exists in contact zones. However, they exhibit strong phenotypic divergence in several traits under habitat-specific selection, including size, shape and behaviour. We used crosses between these ecotypes to identify genomic regions that explain variation in these traits by using QTL analysis and variance partitioning across linkage groups. We could show that previously detected inversion regions contribute to adaptive divergence. Some inversions influenced multiple traits suggesting that they contain sets of locally adaptive alleles. Our study also identified regions without known inversions that are important for phenotypic divergence. Thus, we provide a more complete overview of the importance of inversions in relation to the remaining genome.}, author = {Koch, Eva and Morales, Hernán E. and Larsson, Jenny and Westram, Anja M and Faria, Rui and Lemmon, Alan R. and Lemmon, E. Moriarty and Johannesson, Kerstin and Butlin, Roger K.}, publisher = {Dryad}, title = {{Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis}}, doi = {10.5061/DRYAD.ZGMSBCCB4}, year = {2021}, } @unpublished{9695, abstract = {Real-world data typically contain a large number of features that are often heterogeneous in nature, relevance, and also units of measure. When assessing the similarity between data points, one can build various distance measures using subsets of these features. Using the fewest features but still retaining sufficient information about the system is crucial in many statistical learning approaches, particularly when data are sparse. We introduce a statistical test that can assess the relative information retained when using two different distance measures, and determine if they are equivalent, independent, or if one is more informative than the other. This in turn allows finding the most informative distance measure out of a pool of candidates. The approach is applied to find the most relevant policy variables for controlling the Covid-19 epidemic and to find compact yet informative representations of atomic structures, but its potential applications are wide ranging in many branches of science.}, author = {Glielmo, Aldo and Zeni, Claudio and Cheng, Bingqing and Csanyi, Gabor and Laio, Alessandro}, booktitle = {arXiv}, title = {{Ranking the information content of distance measures}}, year = {2021}, } @unpublished{9696, abstract = {Most water in the universe may be superionic, and its thermodynamic and transport properties are crucial for planetary science but difficult to probe experimentally or theoretically. We use machine learning and free energy methods to overcome the limitations of quantum mechanical simulations, and characterize hydrogen diffusion, superionic transitions, and phase behaviors of water at extreme conditions. We predict that a close-packed superionic phase with mixed stacking is stable over a wide temperature and pressure range, while a body-centered cubic phase is only thermodynamically stable in a small window but is kinetically favored. Our phase boundaries, which are consistent with the existing-albeit scarce-experimental observations, help resolve the fractions of insulating ice, different superionic phases, and liquid water inside of ice giants.}, author = {Cheng, Bingqing and Bethkenhagen, Mandy and Pickard, Chris J. and Hamel, Sebastien}, booktitle = {arXiv}, title = {{Predicting the phase behaviors of superionic water at planetary conditions}}, year = {2021}, } @article{9698, abstract = {Machine learning models are poised to make a transformative impact on chemical sciences by dramatically accelerating computational algorithms and amplifying insights available from computational chemistry methods. However, achieving this requires a confluence and coaction of expertise in computer science and physical sciences. This review is written for new and experienced researchers working at the intersection of both fields. We first provide concise tutorials of computational chemistry and machine learning methods, showing how insights involving both can be achieved. We then follow with a critical review of noteworthy applications that demonstrate how computational chemistry and machine learning can be used together to provide insightful (and useful) predictions in molecular and materials modeling, retrosyntheses, catalysis, and drug design.}, author = {Keith, John A. and Valentin Vassilev-Galindo, Valentin and Cheng, Bingqing and Chmiela, Stefan and Gastegger, Michael and Müller, Klaus-Robert and Tkatchenko, Alexandre}, issn = {1520-6890}, journal = {Chemical Reviews}, number = {16}, pages = {9816--9872}, publisher = {American Chemical Society}, title = {{Combining machine learning and computational chemistry for predictive insights into chemical systems}}, doi = {10.1021/acs.chemrev.1c00107}, volume = {121}, year = {2021}, } @phdthesis{9728, abstract = {Most real-world flows are multiphase, yet we know little about them compared to their single-phase counterparts. Multiphase flows are more difficult to investigate as their dynamics occur in large parameter space and involve complex phenomena such as preferential concentration, turbulence modulation, non-Newtonian rheology, etc. Over the last few decades, experiments in particle-laden flows have taken a back seat in favour of ever-improving computational resources. However, computers are still not powerful enough to simulate a real-world fluid with millions of finite-size particles. Experiments are essential not only because they offer a reliable way to investigate real-world multiphase flows but also because they serve to validate numerical studies and steer the research in a relevant direction. In this work, we have experimentally investigated particle-laden flows in pipes, and in particular, examined the effect of particles on the laminar-turbulent transition and the drag scaling in turbulent flows. For particle-laden pipe flows, an earlier study [Matas et al., 2003] reported how the sub-critical (i.e., hysteretic) transition that occurs via localised turbulent structures called puffs is affected by the addition of particles. In this study, in addition to this known transition, we found a super-critical transition to a globally fluctuating state with increasing particle concentration. At the same time, the Newtonian-type transition via puffs is delayed to larger Reynolds numbers. At an even higher concentration, only the globally fluctuating state is found. The dynamics of particle-laden flows are hence determined by two competing instabilities that give rise to three flow regimes: Newtonian-type turbulence at low, a particle-induced globally fluctuating state at high, and a coexistence state at intermediate concentrations. The effect of particles on turbulent drag is ambiguous, with studies reporting drag reduction, no net change, and even drag increase. The ambiguity arises because, in addition to particle concentration, particle shape, size, and density also affect the net drag. Even similar particles might affect the flow dissimilarly in different Reynolds number and concentration ranges. In the present study, we explored a wide range of both Reynolds number and concentration, using spherical as well as cylindrical particles. We found that the spherical particles do not reduce drag while the cylindrical particles are drag-reducing within a specific Reynolds number interval. The interval strongly depends on the particle concentration and the relative size of the pipe and particles. Within this interval, the magnitude of drag reduction reaches a maximum. These drag reduction maxima appear to fall onto a distinct power-law curve irrespective of the pipe diameter and particle concentration, and this curve can be considered as the maximum drag reduction asymptote for a given fibre shape. Such an asymptote is well known for polymeric flows but had not been identified for particle-laden flows prior to this work.}, author = {Agrawal, Nishchal}, issn = {2663-337X}, keywords = {Drag Reduction, Transition to Turbulence, Multiphase Flows, particle Laden Flows, Complex Flows, Experiments, Fluid Dynamics}, pages = {118}, publisher = {Institute of Science and Technology Austria}, title = {{Transition to turbulence and drag reduction in particle-laden pipe flows}}, doi = {10.15479/at:ista:9728}, year = {2021}, } @phdthesis{9733, abstract = {This thesis is the result of the research carried out by the author during his PhD at IST Austria between 2017 and 2021. It mainly focuses on the Fröhlich polaron model, specifically to its regime of strong coupling. This model, which is rigorously introduced and discussed in the introduction, has been of great interest in condensed matter physics and field theory for more than eighty years. It is used to describe an electron interacting with the atoms of a solid material (the strength of this interaction is modeled by the presence of a coupling constant α in the Hamiltonian of the system). The particular regime examined here, which is mathematically described by considering the limit α →∞, displays many interesting features related to the emergence of classical behavior, which allows for a simplified effective description of the system under analysis. The properties, the range of validity and a quantitative analysis of the precision of such classical approximations are the main object of the present work. We specify our investigation to the study of the ground state energy of the system, its dynamics and its effective mass. For each of these problems, we provide in the introduction an overview of the previously known results and a detailed account of the original contributions by the author.}, author = {Feliciangeli, Dario}, issn = {2663-337X}, pages = {180}, publisher = {Institute of Science and Technology Austria}, title = {{The polaron at strong coupling}}, doi = {10.15479/at:ista:9733}, year = {2021}, } @article{9746, abstract = {Evolutionary adaptation is a major source of antibiotic resistance in bacterial pathogens. Evolution-informed therapy aims to constrain resistance by accounting for bacterial evolvability. Sequential treatments with antibiotics that target different bacterial processes were previously shown to limit adaptation through genetic resistance trade-offs and negative hysteresis. Treatment with homogeneous sets of antibiotics is generally viewed to be disadvantageous, as it should rapidly lead to cross-resistance. We here challenged this assumption by determining the evolutionary response of Pseudomonas aeruginosa to experimental sequential treatments involving both heterogenous and homogeneous antibiotic sets. To our surprise, we found that fast switching between only β-lactam antibiotics resulted in increased extinction of bacterial populations. We demonstrate that extinction is favored by low rates of spontaneous resistance emergence and low levels of spontaneous cross-resistance among the antibiotics in sequence. The uncovered principles may help to guide the optimized use of available antibiotics in highly potent, evolution-informed treatment designs.}, author = {Batra, Aditi and Römhild, Roderich and Rousseau, Emilie and Franzenburg, Sören and Niemann, Stefan and Schulenburg, Hinrich}, issn = {2050-084X}, journal = {eLife}, publisher = {eLife Sciences Publications}, title = {{High potency of sequential therapy with only beta-lactam antibiotics}}, doi = {10.7554/elife.68876}, volume = {10}, year = {2021}, } @inbook{9756, abstract = {High-resolution visualization and quantification of membrane proteins contribute to the understanding of their functions and the roles they play in physiological and pathological conditions. Sodium dodecyl sulfate-digested freeze-fracture replica labeling (SDS-FRL) is a powerful electron microscopy method to study quantitatively the two-dimensional distribution of transmembrane proteins and their tightly associated proteins. During treatment with SDS, intracellular organelles and proteins not anchored to the replica are dissolved, whereas integral membrane proteins captured and stabilized by carbon/platinum deposition remain on the replica. Their intra- and extracellular domains become exposed on the surface of the replica, facilitating the accessibility of antibodies and, therefore, providing higher labeling efficiency than those obtained with other immunoelectron microscopy techniques. In this chapter, we describe the protocols of SDS-FRL adapted for mammalian brain samples, and optimization of the SDS treatment to increase the labeling efficiency for quantification of Cav2.1, the alpha subunit of P/Q-type voltage-dependent calcium channels utilizing deep learning algorithms.}, author = {Kaufmann, Walter and Kleindienst, David and Harada, Harumi and Shigemoto, Ryuichi}, booktitle = { Receptor and Ion Channel Detection in the Brain}, isbn = {9781071615218}, keywords = {Freeze-fracture replica: Deep learning, Immunogold labeling, Integral membrane protein, Electron microscopy}, pages = {267--283}, publisher = {Humana}, title = {{High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL)}}, doi = {10.1007/978-1-0716-1522-5_19}, volume = {169}, year = {2021}, } @article{9759, author = {Bartlett, Michael John and Arslan, Feyza N and Bankston, Adriana and Sarabipour, Sarvenaz}, issn = {15537358}, journal = {PLoS Computational Biology}, number = {7}, publisher = {Public Library of Science}, title = {{Ten simple rules to improve academic work- life balance}}, doi = {10.1371/journal.pcbi.1009124}, volume = {17}, year = {2021}, } @article{9760, abstract = {The quantum approximate optimization algorithm (QAOA) is a prospective near-term quantum algorithm due to its modest circuit depth and promising benchmarks. However, an external parameter optimization required in the QAOA could become a performance bottleneck. This motivates studies of the optimization landscape and search for heuristic ways of parameter initialization. In this work we visualize the optimization landscape of the QAOA applied to the MaxCut problem on random graphs, demonstrating that random initialization of the QAOA is prone to converging to local minima with suboptimal performance. We introduce the initialization of QAOA parameters based on the Trotterized quantum annealing (TQA) protocol, parameterized by the Trotter time step. We find that the TQA initialization allows to circumvent the issue of false minima for a broad range of time steps, yielding the same performance as the best result out of an exponentially scaling number of random initializations. Moreover, we demonstrate that the optimal value of the time step coincides with the point of proliferation of Trotter errors in quantum annealing. Our results suggest practical ways of initializing QAOA protocols on near-term quantum devices and reveal new connections between QAOA and quantum annealing.}, author = {Sack, Stefan and Serbyn, Maksym}, issn = {2521-327X}, journal = {Quantum}, publisher = {Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften}, title = {{Quantum annealing initialization of the quantum approximate optimization algorithm}}, doi = {10.22331/Q-2021-07-01-491}, volume = {5}, year = {2021}, } @article{9761, abstract = {The important roles of mitochondrial function and dysfunction in the process of neurodegeneration are widely acknowledged. Retinal ganglion cells (RGCs) appear to be a highly vulnerable neuronal cell type in the central nervous system with respect to mitochondrial dysfunction but the actual reasons for this are still incompletely understood. These cells have a unique circumstance where unmyelinated axons must bend nearly 90° to exit the eye and then cross a translaminar pressure gradient before becoming myelinated in the optic nerve. This region, the optic nerve head, contains some of the highest density of mitochondria present in these cells. Glaucoma represents a perfect storm of events occurring at this location, with a combination of changes in the translaminar pressure gradient and reassignment of the metabolic support functions of supporting glia, which appears to apply increased metabolic stress to the RGC axons leading to a failure of axonal transport mechanisms. However, RGCs themselves are also extremely sensitive to genetic mutations, particularly in genes affecting mitochondrial dynamics and mitochondrial clearance. These mutations, which systemically affect the mitochondria in every cell, often lead to an optic neuropathy as the sole pathologic defect in affected patients. This review summarizes knowledge of mitochondrial structure and function, the known energy demands of neurons in general, and places these in the context of normal and pathological characteristics of mitochondria attributed to RGCs. }, author = {Muench, Nicole A. and Patel, Sonia and Maes, Margaret E and Donahue, Ryan J. and Ikeda, Akihiro and Nickells, Robert W.}, issn = {20734409}, journal = {Cells}, number = {7}, publisher = {MDPI}, title = {{The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease}}, doi = {10.3390/cells10071593}, volume = {10}, year = {2021}, }