Showing papers by "ETH Zurich published in 2014"

Review of Particle Physics

Abstract: The Review summarizes much of particle physics and cosmology. Using data from previous editions, plus 3,283 new measurements from 899 Japers, we list, evaluate, and average measured properties of gauge bosons and the recently discovered Higgs boson, leptons, quarks, mesons, and baryons. We summarize searches for hypothetical particles such as heavy neutrinos, supersymmetric and technicolor particles, axions, dark photons, etc. All the particle properties and search limits are listed in Summary Tables. We also give numerous tables, figures, formulae, and reviews of topics such as Supersymmetry, Extra Dimensions, Particle Detectors, Probability, and Statistics. Among the 112 reviews are many that are new or heavily revised including those on: Dark Energy, Higgs Boson Physics, Electroweak Model, Neutrino Cross Section Measurements, Monte Carlo Neutrino Generators, Top Quark, Dark Matter, Dynamical Electroweak Symmetry Breaking, Accelerator Physics of Colliders, High-Energy Collider Parameters, Big Bang Nucleosynthesis, Astrophysical Constants and Cosmological Parameters.

cp2k: atomistic simulations of condensed matter systems

Abstract: cp2k has become a versatile open-source tool for the simulation of complex systems on the nanometer scale. It allows for sampling and exploring potential energy surfaces that can be computed using a variety of empirical and first principles models. Excellent performance for electronic structure calculations is achieved using novel algorithms implemented for modern and massively parallel hardware. This review briefly summarizes the main capabilities and illustrates with recent applications the science cp2k has enabled in the field of atomistic simulation.

Experimental realization of the topological Haldane model with ultracold fermions

Abstract: The Haldane model on a honeycomb lattice is a paradigmatic example of a Hamiltonian featuring topologically distinct phases of matter. It describes a mechanism through which a quantum Hall effect can appear as an intrinsic property of a band structure, rather than being caused by an external magnetic field. Although physical implementation has been considered unlikely, the Haldane model has provided the conceptual basis for theoretical and experimental research exploring topological insulators and superconductors. Here we report the experimental realization of the Haldane model and the characterization of its topological band structure, using ultracold fermionic atoms in a periodically modulated optical honeycomb lattice. The Haldane model is based on breaking both time-reversal symmetry and inversion symmetry. To break time-reversal symmetry, we introduce complex next-nearest-neighbour tunnelling terms, which we induce through circular modulation of the lattice position. To break inversion symmetry, we create an energy offset between neighbouring sites. Breaking either of these symmetries opens a gap in the band structure, which we probe using momentum-resolved interband transitions. We explore the resulting Berry curvatures, which characterize the topology of the lowest band, by applying a constant force to the atoms and find orthogonal drifts analogous to a Hall current. The competition between the two broken symmetries gives rise to a transition between topologically distinct regimes. By identifying the vanishing gap at a single Dirac point, we map out this transition line experimentally and quantitatively compare it to calculations using Floquet theory without free parameters. We verify that our approach, which allows us to tune the topological properties dynamically, is suitable even for interacting fermionic systems. Furthermore, we propose a direct extension to realize spin-dependent topological Hamiltonians.

A promoter-level mammalian expression atlas

Abstract: Regulated transcription controls the diversity, developmental pathways and spatial organization of the hundreds of cell types that make up a mammal Using single-molecule cDNA sequencing, we mapped transcription start sites (TSSs) and their usage in human and mouse primary cells, cell lines and tissues to produce a comprehensive overview of mammalian gene expression across the human body We find that few genes are truly 'housekeeping', whereas many mammalian promoters are composite entities composed of several closely separated TSSs, with independent cell-type-specific expression profiles TSSs specific to different cell types evolve at different rates, whereas promoters of broadly expressed genes are the most conserved Promoter-based expression analysis reveals key transcription factors defining cell states and links them to binding-site motifs The functions of identified novel transcripts can be predicted by coexpression and sample ontology enrichment analyses The functional annotation of the mammalian genome 5 (FANTOM5) project provides comprehensive expression profiles and functional annotation of mammalian cell-type-specific transcriptomes with wide applications in biomedical research

Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens

Abstract: The immune system influences the fate of developing cancers by not only functioning as a tumour promoter that facilitates cellular transformation, promotes tumour growth and sculpts tumour cell immunogenicity, but also as an extrinsic tumour suppressor that either destroys developing tumours or restrains their expansion. Yet, clinically apparent cancers still arise in immunocompetent individuals in part as a consequence of cancer-induced immunosuppression. In many individuals, immunosuppression is mediated by cytotoxic T-lymphocyte associated antigen-4 (CTLA-4) and programmed death-1 (PD-1), two immunomodulatory receptors expressed on T cells. Monoclonal-antibody-based therapies targeting CTLA-4 and/or PD-1 (checkpoint blockade) have yielded significant clinical benefits-including durable responses--to patients with different malignancies. However, little is known about the identity of the tumour antigens that function as the targets of T cells activated by checkpoint blockade immunotherapy and whether these antigens can be used to generate vaccines that are highly tumour-specific. Here we use genomics and bioinformatics approaches to identify tumour-specific mutant proteins as a major class of T-cell rejection antigens following anti-PD-1 and/or anti-CTLA-4 therapy of mice bearing progressively growing sarcomas, and we show that therapeutic synthetic long-peptide vaccines incorporating these mutant epitopes induce tumour rejection comparably to checkpoint blockade immunotherapy. Although mutant tumour-antigen-specific T cells are present in progressively growing tumours, they are reactivated following treatment with anti-PD-1 and/or anti-CTLA-4 and display some overlapping but mostly treatment-specific transcriptional profiles, rendering them capable of mediating tumour rejection. These results reveal that tumour-specific mutant antigens are not only important targets of checkpoint blockade therapy, but they can also be used to develop personalized cancer-specific vaccines and to probe the mechanistic underpinnings of different checkpoint blockade treatments.

EURO-CORDEX : new high-resolution climate change projections for European impact research

Abstract: A new high-resolution regional climate change ensemble has been established for Europe within the World Climate Research Program Coordinated Regional Downscaling Experiment (EURO-CORDEX) initiative. The first set of simulations with a horizontal resolution of 12.5 km was completed for the new emission scenarios RCP4.5 and RCP8.5 with more simulations expected to follow. The aim of this paper is to present this data set to the different communities active in regional climate modelling, impact assessment and adaptation. The EURO-CORDEX ensemble results have been compared to the SRES A1B simulation results achieved within the ENSEMBLES project. The large-scale patterns of changes in mean temperature and precipitation are similar in all three scenarios, but they differ in regional details, which can partly be related to the higher resolution in EURO-CORDEX. The results strengthen those obtained in ENSEMBLES, but need further investigations. The analysis of impact indices shows that for RCP8.5, there is a substantially larger change projected for temperature-based indices than for RCP4.5. The difference is less pronounced for precipitation-based indices. Two effects of the increased resolution can be regarded as an added value of regional climate simulations. Regional climate model simulations provide higher daily precipitation intensities, which are completely missing in the global climate model simulations, and they provide a significantly different climate change of daily precipitation intensities resulting in a smoother shift from weak to moderate and high intensities.

A+: Adjusted Anchored Neighborhood Regression for Fast Super-Resolution

Abstract: We address the problem of image upscaling in the form of single image super-resolution based on a dictionary of low- and high-resolution exemplars. Two recently proposed methods, Anchored Neighborhood Regression (ANR) and Simple Functions (SF), provide state-of-the-art quality performance. Moreover, ANR is among the fastest known super-resolution methods. ANR learns sparse dictionaries and regressors anchored to the dictionary atoms. SF relies on clusters and corresponding learned functions. We propose A+, an improved variant of ANR, which combines the best qualities of ANR and SF. A+ builds on the features and anchored regressors from ANR but instead of learning the regressors on the dictionary it uses the full training material, similar to SF. We validate our method on standard images and compare with state-of-the-art methods. We obtain improved quality (i.e. 0.2–0.7 dB PSNR better than ANR) and excellent time complexity, rendering A+ the most efficient dictionary-based super-resolution method to date.

Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry

Abstract: Mass cytometry enables high-dimensional, single-cell analysis of cell type and state. In mass cytometry, rare earth metals are used as reporters on antibodies. Analysis of metal abundances using the mass cytometer allows determination of marker expression in individual cells. Mass cytometry has previously been applied only to cell suspensions. To gain spatial information, we have coupled immunohistochemical and immunocytochemical methods with high-resolution laser ablation to CyTOF mass cytometry. This approach enables the simultaneous imaging of 32 proteins and protein modifications at subcellular resolution; with the availability of additional isotopes, measurement of over 100 markers will be possible. We applied imaging mass cytometry to human breast cancer samples, allowing delineation of cell subpopulations and cell-cell interactions and highlighting tumor heterogeneity. Imaging mass cytometry complements existing imaging approaches. It will enable basic studies of tissue heterogeneity and function and support the transition of medicine toward individualized molecularly targeted diagnosis and therapies.

Nitrogen-Vacancy Centers in Diamond: Nanoscale Sensors for Physics and Biology

Abstract: Crystal defects in diamond have emerged as unique objects for a variety of applications, both because they are very stable and because they have interesting optical properties. Embedded in nanocrystals, they can serve, for example, as robust single-photon sources or as fluorescent biomarkers of unlimited photostability and low cytotoxicity. The most fascinating aspect, however, is the ability of some crystal defects, most prominently the nitrogen-vacancy (NV) center, to locally detect and measure a number of physical quantities, such as magnetic and electric fields. This metrology capacity is based on the quantum mechanical interactions of the defect's spin state. In this review, we introduce the new and rapidly evolving field of nanoscale sensing based on single NV centers in diamond. We give a concise overview of the basic properties of diamond, from synthesis to electronic and magnetic properties of embedded NV centers. We describe in detail how single NV centers can be harnessed for nanoscale sensing,...

Food-101 – Mining Discriminative Components with Random Forests

Abstract: In this paper we address the problem of automatically recognizing pictured dishes. To this end, we introduce a novel method to mine discriminative parts using Random Forests (rf), which allows us to mine for parts simultaneously for all classes and to share knowledge among them. To improve efficiency of mining and classification, we only consider patches that are aligned with image superpixels, which we call components. To measure the performance of our rf component mining for food recognition, we introduce a novel and challenging dataset of 101 food categories, with 101’000 images. With an average accuracy of 50.76%, our model outperforms alternative classification methods except for cnn, including svm classification on Improved Fisher Vectors and existing discriminative part-mining algorithms by 11.88% and 8.13%, respectively. On the challenging mit-Indoor dataset, our method compares nicely to other s-o-a component-based classification methods.

The Dalton quantum chemistry program system

Abstract: Dalton is a powerful general-purpose program system for the study of molecular electronic structure at the Hartree-Fock, Kohn-Sham, multiconfigurational self-consistent-field, MOller-Plesset, confi ...

Review on iron and its importance for human health.

Abstract: It is well-known that deficiency or over exposure to various elements has noticeable effects on human health. The effect of an element is determined by several characteristics, including absorption, metabolism, and degree of interaction with physiological processes. Iron is an essential element for almost all living organisms as it participates in a wide variety of metabolic processes, including oxygen transport, deoxyribonucleic acid (DNA) synthesis, and electron transport. However, as iron can form free radicals, its concentration in body tissues must be tightly regulated because in excessive amounts, it can lead to tissue damage. Disorders of iron metabolism are among the most common diseases of humans and encompass a broad spectrum of diseases with diverse clinical manifestations, ranging from anemia to iron overload, and possibly to neurodegenerative diseases. In this review, we discuss the latest progress in studies of iron metabolism and bioavailability, and our current understanding of human iron requirement and consequences and causes of iron deficiency. Finally, we discuss strategies for prevention of iron deficiency.

Flood risk and climate change: global and regional perspectives

Abstract: A holistic perspective on changing rainfall-driven flood risk is provided for the late 20th and early 21st centuries. Economic losses from floods have greatly increased, principally driven by the expanding exposure of assets at risk. It has not been possible to attribute rain-generated peak streamflow trends to anthropogenic climate change over the past several decades. Projected increases in the frequency and intensity of heavy rainfall, based on climate models, should contribute to increases in precipitation-generated local flooding (e.g. flash flooding and urban flooding). This article assesses the literature included in the IPCC SREX report and new literature published since, and includes an assessment of changes in flood risk in seven of the regions considered in the recent IPCC SREX report—Africa, Asia, Central and South America, Europe, North America, Oceania and Polar regions. Also considering newer publications, this article is consistent with the recent IPCC SREX assessment finding that ...

Implication of sperm RNAs in transgenerational inheritance of the effects of early trauma in mice

Abstract: Small non-coding RNAs (sncRNAs) are potential vectors at the interface between genes and environment. We found that traumatic stress in early life altered mouse microRNA (miRNA) expression, and behavioral and metabolic responses in the progeny. Injection of sperm RNAs from traumatized males into fertilized wild-type oocytes reproduced the behavioral and metabolic alterations in the resulting offspring.

Migrations and dynamics of the intertropical convergence zone

Abstract: Rainfall on Earth is most intense in the intertropical convergence zone (ITCZ), a narrow belt of clouds centred on average around six degrees north of the Equator. The mean position of the ITCZ north of the Equator arises primarily because the Atlantic Ocean transports energy northward across the Equator, rendering the Northern Hemisphere warmer than the Southern Hemisphere. On seasonal and longer timescales, the ITCZ migrates, typically towards a warming hemisphere but with exceptions, such as during El Nino events. An emerging framework links the ITCZ to the atmospheric energy balance and may account for ITCZ variations on timescales from years to geological epochs.

Uncertainties in CMIP5 Climate Projections due to Carbon Cycle Feedbacks

Abstract: In the context of phase 5 of the Coupled Model Intercomparison Project, most climate simulations use prescribed atmospheric CO2 concentration and therefore do not interactively include the effect of carbon cycle feedbacks. However, the representative concentration pathway 8.5 (RCP8.5) scenario has additionally been run by earth system models with prescribed CO2 emissions. This paper analyzes the climate projections of 11 earth system models (ESMs) that performed both emission-driven and concentration-driven RCP8.5 simulations. When forced by RCP8.5 CO2 emissions, models simulate a large spread in atmospheric CO2; the simulated 2100 concentrations range between 795 and 1145 ppm. Seven out of the 11 ESMs simulate a larger CO2 (on average by 44 ppm, 985 ± 97 ppm by 2100) and hence higher radiative forcing (by 0.25 W m−2) when driven by CO2 emissions than for the concentration-driven scenarios (941 ppm). However, most of these models already overestimate the present-day CO2, with the present-day biase...

Genomics and the origin of species

Abstract: Speciation is a fundamental evolutionary process, the knowledge of which is crucial for understanding the origins of biodiversity. Genomic approaches are an increasingly important aspect of this research field. We review current understanding of genome-wide effects of accumulating reproductive isolation and of genomic properties that influence the process of speciation. Building on this work, we identify emergent trends and gaps in our understanding, propose new approaches to more fully integrate genomics into speciation research, translate speciation theory into hypotheses that are testable using genomic tools and provide an integrative definition of the field of speciation genomics.

Evidence for quantum annealing with more than one hundred qubits

Abstract: Quantum annealing is expected to solve certain optimization problems more efficiently, but there are still open questions regarding the functioning of devices such as D-Wave One. A numerical and experimental investigation of its performance shows evidence for quantum annealing with 108 qubits.

Regional climate modeling on European scales: a joint standard evaluation of the EURO-CORDEX RCM ensemble

Abstract: . EURO-CORDEX is an international climate downscaling initiative that aims to provide high-resolution climate scenarios for Europe. Here an evaluation of the ERA-Interim-driven EURO-CORDEX regional climate model (RCM) ensemble is presented. The study documents the performance of the individual models in representing the basic spatiotemporal patterns of the European climate for the period 1989–2008. Model evaluation focuses on near-surface air temperature and precipitation, and uses the E-OBS data set as observational reference. The ensemble consists of 17 simulations carried out by seven different models at grid resolutions of 12 km (nine experiments) and 50 km (eight experiments). Several performance metrics computed from monthly and seasonal mean values are used to assess model performance over eight subdomains of the European continent. Results are compared to those for the ERA40-driven ENSEMBLES simulations. The analysis confirms the ability of RCMs to capture the basic features of the European climate, including its variability in space and time. But it also identifies nonnegligible deficiencies of the simulations for selected metrics, regions and seasons. Seasonally and regionally averaged temperature biases are mostly smaller than 1.5 °C, while precipitation biases are typically located in the ±40% range. Some bias characteristics, such as a predominant cold and wet bias in most seasons and over most parts of Europe and a warm and dry summer bias over southern and southeastern Europe reflect common model biases. For seasonal mean quantities averaged over large European subdomains, no clear benefit of an increased spatial resolution (12 vs. 50 km) can be identified. The bias ranges of the EURO-CORDEX ensemble mostly correspond to those of the ENSEMBLES simulations, but some improvements in model performance can be identified (e.g., a less pronounced southern European warm summer bias). The temperature bias spread across different configurations of one individual model can be of a similar magnitude as the spread across different models, demonstrating a strong influence of the specific choices in physical parameterizations and experimental setup on model performance. Based on a number of simply reproducible metrics, the present study quantifies the currently achievable accuracy of RCMs used for regional climate simulations over Europe and provides a quality standard for future model developments.

Enzo: an adaptive mesh refinement code for astrophysics

Abstract: This paper describes the open-source code Enzo, which uses block-structured adaptive mesh refinement to provide high spatial and temporal resolution for modeling astrophysical fluid flows. The code is Cartesian, can be run in one, two, and three dimensions, and supports a wide variety of physics including hydrodynamics, ideal and non-ideal magnetohydrodynamics, N-body dynamics (and, more broadly, self-gravity of fluids and particles), primordial gas chemistry, optically thin radiative cooling of primordial and metal-enriched plasmas (as well as some optically-thick cooling models), radiation transport, cosmological expansion, and models for star formation and feedback in a cosmological context. In addition to explaining the algorithms implemented, we present solutions for a wide range of test problems, demonstrate the code's parallel performance, and discuss the Enzo collaboration's code development methodology.

Ultimate permeation across atomically thin porous graphene.

Abstract: A two-dimensional (2D) porous layer can make an ideal membrane for separation of chemical mixtures because its infinitesimal thickness promises ultimate permeation. Graphene—with great mechanical strength, chemical stability, and inherent impermeability—offers a unique 2D system with which to realize this membrane and study the mass transport, if perforated precisely. We report highly efficient mass transfer across physically perforated double-layer graphene, having up to a few million pores with narrowly distributed diameters between less than 10 nanometers and 1 micrometer. The measured transport rates are in agreement with predictions of 2D transport theories. Attributed to its atomic thicknesses, these porous graphene membranes show permeances of gas, liquid, and water vapor far in excess of those shown by finite-thickness membranes, highlighting the ultimate permeation these 2D membranes can provide.

OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data

Abstract: Hannes L Rost, 2, ∗ George Rosenberger, 2, ∗ Pedro Navarro, Ludovic Gillet, Sasa M Miladinovic, 3 Olga T Schubert, 2 Witold Wolski, Ben C Collins, Johan Malmstrom, Lars Malmstrom, and Ruedi Aebersold 6, 7, † Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, CH-8093 Zurich, Switzerland PhD Program in Systems Biology, University of Zurich and ETH Zurich, CH-8057 Zurich, Switzerland Biognosys AG, CH-8952 Schlieren, Switzerland SyBIT project of SystemsXch, ETH Zurich, CH-8092 Zurich, Switzerland Department of Immunotechnology, Lund University, S-22100 Lund, Sweden Competence Center for Systems Physiology and Metabolic Diseases, CH-8093 Zurich, Switzerland Faculty of Science, University of Zurich, CH-8057 Zurich, Switzerland (Dated: October 19, 2015)

Genomic analyses provide insights into the history of tomato breeding

Abstract: The histories of crop domestication and breeding are recorded in genomes. Although tomato is a model species for plant biology and breeding, the nature of human selection that altered its genome remains largely unknown. Here we report a comprehensive analysis of tomato evolution based on the genome sequences of 360 accessions. We provide evidence that domestication and improvement focused on two independent sets of quantitative trait loci (QTLs), resulting in modern tomato fruit ∼100 times larger than its ancestor. Furthermore, we discovered a major genomic signature for modern processing tomatoes, identified the causative variants that confer pink fruit color and precisely visualized the linkage drag associated with wild introgressions. This study outlines the accomplishments as well as the costs of historical selection and provides molecular insights toward further improvement.

The green valley is a red herring: Galaxy Zoo reveals two evolutionary pathways towards quenching of star formation in early-and late-type galaxies

Abstract: We use SDSS+GALEX+Galaxy Zoo data to study the quenching of star formation in low-redshift galaxies. We show that the green valley between the blue cloud of star-forming galaxies and the red sequence of quiescent galaxies in the colour-mass diagram is not a single transitional state through which most blue galaxies evolve into red galaxies. Rather, an analysis that takes morphology into account makes clear that only a small population of blue early-type galaxies move rapidly across the green valley after the morphologies are transformed from disc to spheroid and star formation is quenched rapidly. In contrast, the majority of blue star-forming galaxies have significant discs, and they retain their late-type morphologies as their star formation rates decline very slowly. We summarize a range of observations that lead to these conclusions, including UV-optical colours and halo masses, which both show a striking dependence on morphological type. We interpret these results in terms of the evolution of cosmic gas supply and gas reservoirs. We conclude that late-type galaxies are consistent with a scenario where the cosmic supply of gas is shut off, perhaps at a critical halo mass, followed by a slow exhaustion of the remaining gas over several Gyr, driven by secular and/or environmental processes. In contrast, early-type galaxies require a scenario where the gas supply and gas reservoir are destroyed virtually instantaneously, with rapid quenching accompanied by a morphological transformation from disc to spheroid. This gas reservoir destruction could be the consequence of a major merger, which in most cases transforms galaxies from disc to elliptical morphology, and mergers could play a role in inducing black hole accretion and possibly active galactic nuclei feedback.

Global assessment of trends in wetting and drying over land

Abstract: Past continental dryness trends are difficult to assess. A comprehensive analysis of hundreds of combinations of data sets suggests that only 24.6% of the global land area have been exposed to robust dryness changes since 1948.