Showing papers by "Free University of Berlin published in 2018"

Microplastics as an emerging threat to terrestrial ecosystems

Abstract: Microplastics (plastics < 5 mm, including nanoplastics which are < 0.1 μm) originate from the fragmentation of large plastic litter or from direct environmental emission. Their potential impacts in terrestrial ecosystems remain largely unexplored despite numerous reported effects on marine organisms. Most plastics arriving in the oceans were produced, used, and often disposed on land. Hence, it is within terrestrial systems that microplastics might first interact with biota eliciting ecologically relevant impacts. This article introduces the pervasive microplastic contamination as a potential agent of global change in terrestrial systems, highlights the physical and chemical nature of the respective observed effects, and discusses the broad toxicity of nanoplastics derived from plastic breakdown. Making relevant links to the fate of microplastics in aquatic continental systems, we here present new insights into the mechanisms of impacts on terrestrial geochemistry, the biophysical environment, and ecotoxicology. Broad changes in continental environments are possible even in particle-rich habitats such as soils. Furthermore, there is a growing body of evidence indicating that microplastics interact with terrestrial organisms that mediate essential ecosystem services and functions, such as soil dwelling invertebrates, terrestrial fungi, and plant-pollinators. Therefore, research is needed to clarify the terrestrial fate and effects of microplastics. We suggest that due to the widespread presence, environmental persistence, and various interactions with continental biota, microplastic pollution might represent an emerging global change threat to terrestrial ecosystems.

The landscape of genomic alterations across childhood cancers

Abstract: Pan-cancer analyses that examine commonalities and differences among various cancer types have emerged as a powerful way to obtain novel insights into cancer biology. Here we present a comprehensive analysis of genetic alterations in a pan-cancer cohort including 961 tumours from children, adolescents, and young adults, comprising 24 distinct molecular types of cancer. Using a standardized workflow, we identified marked differences in terms of mutation frequency and significantly mutated genes in comparison to previously analysed adult cancers. Genetic alterations in 149 putative cancer driver genes separate the tumours into two classes: small mutation and structural/copy-number variant (correlating with germline variants). Structural variants, hyperdiploidy, and chromothripsis are linked to TP53 mutation status and mutational signatures. Our data suggest that 7-8% of the children in this cohort carry an unambiguous predisposing germline variant and that nearly 50% of paediatric neoplasms harbour a potentially druggable event, which is highly relevant for the design of future clinical trials.

Effect of friction on oxidative graphite intercalation and high-quality graphene formation

Abstract: Oxidative wet-chemical delamination of graphene from graphite is expected to become a scalable production method. However, the formation process of the intermediate stage-1 graphite sulfate by sulfuric acid intercalation and its subsequent oxidation are poorly understood and lattice defect formation must be avoided. Here, we demonstrate film formation of micrometer-sized graphene flakes with lattice defects down to 0.02% and visualize the carbon lattice by transmission electron microscopy at atomic resolution. Interestingly, we find that only well-ordered, highly crystalline graphite delaminates into oxo-functionalized graphene, whereas other graphite grades do not form a proper stage-1 intercalate and revert back to graphite upon hydrolysis. Ab initio molecular dynamics simulations show that ideal stacking and electronic oxidation of the graphite layers significantly reduce the friction of the moving sulfuric acid molecules, thereby facilitating intercalation. Furthermore, the evaluation of the stability of oxo-species in graphite sulfate supports an oxidation mechanism that obviates intercalation of the oxidant. Scalable graphene production from graphite via an intercalation-oxidation-reduction process is still hampered by low reproducibility and many lattice defects. Here, the authors show that reducing molecular friction by using highly crystalline graphite and mild oxidizing conditions is the key to high quality graphene.

ProTox-II: a webserver for the prediction of toxicity of chemicals.

Abstract: Advancement in the field of computational research has made it possible for the in silico methods to offer significant benefits to both regulatory needs and requirements for risk assessments, and pharmaceutical industry to assess the safety profile of a chemical. Here, we present ProTox-II that incorporates molecular similarity, pharmacophores, fragment propensities and machine-learning models for the prediction of various toxicity endpoints; such as acute toxicity, hepatotoxicity, cytotoxicity, carcinogenicity, mutagenicity, immunotoxicity, adverse outcomes pathways (Tox21) and toxicity targets. The predictive models are built on data from both in vitro assays (e.g. Tox21 assays, Ames bacterial mutation assays, hepG2 cytotoxicity assays, Immunotoxicity assays) and in vivo cases (e.g. carcinogenicity, hepatotoxicity). The models have been validated on independent external sets and have shown strong performance. ProTox-II provides a freely available webserver for in silico toxicity prediction for toxicologists, regulatory agencies, computational and medicinal chemists, and all users without login at http://tox.charite.de/protox_II. The webserver takes a two-dimensional chemical structure as an input and reports the possible toxicity profile of the chemical for 33 models with confidence scores, and an overall toxicity radar chart along with three most similar compounds with known acute toxicity.

Impacts of Microplastics on the Soil Biophysical Environment

Abstract: Soils are essential components of terrestrial ecosystems that experience strong pollution pressure. Microplastic contamination of soils is being increasingly documented, with potential consequences for soil biodiversity and function. Notwithstanding, data on effects of such contaminants on fundamental properties potentially impacting soil biota are lacking. The present study explores the potential of microplastics to disturb vital relationships between soil and water, as well as its consequences for soil structure and microbial function. During a 5-weeks garden experiment we exposed a loamy sand soil to environmentally relevant nominal concentrations (up to 2%) of four common microplastic types (polyacrylic fibers, polyamide beads, polyester fibers, and polyethylene fragments). Then, we measured bulk density, water holding capacity, hydraulic conductivity, soil aggregation, and microbial activity. Microplastics affected the bulk density, water holding capacity, and the functional relationship between the microbial activity and water stable aggregates. The effects are underestimated if idiosyncrasies of particle type and concentrations are neglected, suggesting that purely qualitative environmental microplastic data might be of limited value for the assessment of effects in soil. If extended to other soils and plastic types, the processes unravelled here suggest that microplastics are relevant long-term anthropogenic stressors and drivers of global change in terrestrial ecosystems.

Magic Angle Spectroscopy

Abstract: The electronic properties of heterostructures of atomically-thin van der Waals (vdW) crystals can be modified substantially by Moire superlattice potentials arising from an interlayer twist between crystals. Moire-tuning of the band structure has led to the recent discovery of superconductivity and correlated insulating phases in twisted bilayer graphene (TBLG) near the so-called "magic angle" of $\sim$1.1°, with a phase diagram reminiscent of high T$_c$ superconductors. However, lack of detailed understanding of the electronic spectrum and the atomic-scale influence of the Moire pattern has so far precluded a coherent theoretical understanding of the correlated states. Here, we directly map the atomic-scale structural and electronic properties of TBLG near the magic angle using scanning tunneling microscopy and spectroscopy (STM/STS). We observe two distinct van Hove singularities (vHs) in the LDOS which decrease in separation monotonically through 1.1° with the bandwidth (t) of each vHs minimized near the magic angle. When doped near half Moire band filling, the conduction vHs shifts to the Fermi level and an additional correlation-induced gap splits the vHs with a maximum size of 7.5 meV. We also find that three-fold (C$_3$) rotational symmetry of the LDOS is broken in doped TBLG with a maximum symmetry breaking observed for states near the Fermi level, suggestive of nematic electronic interactions. The main features of our doping and angle dependent spectroscopy are captured by a tight-binding model with on-site (U) and nearest neighbor Coulomb interactions. We find that the ratio U/t is of order unity, indicating that electron correlations are significant in magic angle TBLG. Rather than a simple maximization of the DOS, superconductivity arises in TBLG at angles where the ratio U/t is largest, suggesting a pairing mechanism based on electron-electron interactions.

VAMPnets for deep learning of molecular kinetics.

Abstract: There is an increasing demand for computing the relevant structures, equilibria, and long-timescale kinetics of biomolecular processes, such as protein-drug binding, from high-throughput molecular dynamics simulations. Current methods employ transformation of simulated coordinates into structural features, dimension reduction, clustering the dimension-reduced data, and estimation of a Markov state model or related model of the interconversion rates between molecular structures. This handcrafted approach demands a substantial amount of modeling expertise, as poor decisions at any step will lead to large modeling errors. Here we employ the variational approach for Markov processes (VAMP) to develop a deep learning framework for molecular kinetics using neural networks, dubbed VAMPnets. A VAMPnet encodes the entire mapping from molecular coordinates to Markov states, thus combining the whole data processing pipeline in a single end-to-end framework. Our method performs equally or better than state-of-the-art Markov modeling methods and provides easily interpretable few-state kinetic models.

The quantum technologies roadmap: a European community view

Abstract: Within the last two decades, quantum technologies (QT) have made tremendous progress, moving from Nobel Prize award-winning experiments on quantum physics (1997: Chu, Cohen-Tanoudji, Phillips; 2001: Cornell, Ketterle, Wieman; 2005: Hall, Hansch-, Glauber; 2012: Haroche, Wineland) into a cross-disciplinary field of applied research. Technologies are being developed now that explicitly address individual quantum states and make use of the 'strange' quantum properties, such as superposition and entanglement. The field comprises four domains: quantum communication, where individual or entangled photons are used to transmit data in a provably secure way; quantum simulation, where well-controlled quantum systems are used to reproduce the behaviour of other, less accessible quantum systems; quantum computation, which employs quantum effects to dramatically speed up certain calculations, such as number factoring; and quantum sensing and metrology, where the high sensitivity of coherent quantum systems to external perturbations is exploited to enhance the performance of measurements of physical quantities. In Europe, the QT community has profited from several EC funded coordination projects, which, among other things, have coordinated the creation of a 150-page QT Roadmap (http://qurope.eu/h2020/qtflagship/roadmap2016). This article presents an updated summary of this roadmap.

Toward a Definition of Complexity for Quantum Field Theory States

Abstract: We investigate notions of complexity of states in continuous many-body quantum systems. We focus on Gaussian states which include ground states of free quantum field theories and their approximations encountered in the context of the continuous version of the multiscale entanglement renormalization ansatz. Our proposal for quantifying state complexity is based on the Fubini-Study metric. It leads to counting the number of applications of each gate (infinitesimal generator) in the transformation, subject to a state-dependent metric. We minimize the defined complexity with respect to momentum-preserving quadratic generators which form su(1,1) algebras. On the manifold of Gaussian states generated by these operations, the Fubini-Study metric factorizes into hyperbolic planes with minimal complexity circuits reducing to known geodesics. Despite working with quantum field theories far outside the regime where Einstein gravity duals exist, we find striking similarities between our results and those of holographic complexity proposals.

Global rise in emerging alien species results from increased accessibility of new source pools.

Abstract: Our ability to predict the identity of future invasive alien species is largely based upon knowledge of prior invasion history Emerging alien species—those never encountered as aliens before—therefore pose a significant challenge to biosecurity interventions worldwide Understanding their temporal trends, origins, and the drivers of their spread is pivotal to improving prevention and risk assessment tools Here, we use a database of 45,984 first records of 16,019 established alien species to investigate the temporal dynamics of occurrences of emerging alien species worldwide Even after many centuries of invasions the rate of emergence of new alien species is still high: One-quarter of first records during 2000–2005 were of species that had not been previously recorded anywhere as alien, though with large variation across taxa Model results show that the high proportion of emerging alien species cannot be solely explained by increases in well-known drivers such as the amount of imported commodities from historically important source regions Instead, these dynamics reflect the incorporation of new regions into the pool of potential alien species, likely as a consequence of expanding trade networks and environmental change This process compensates for the depletion of the historically important source species pool through successive invasions We estimate that 1–16% of all species on Earth, depending on the taxonomic group, qualify as potential alien species These results suggest that there remains a high proportion of emerging alien species we have yet to encounter, with future impacts that are difficult to predict

Advances and current challenges in calcium signaling

Abstract: Content Summary 414 I. Introduction 415 II. Ca2+ importer and exporter in plants 415 III. The Ca2+ decoding toolkit in plants 415 IV. Mechanisms of Ca2+ signal decoding 417 V. Immediate Ca2+ signaling in the regulation of ion transport 418 VI. Ca2+ signal integration into long-term ABA responses 419 VII Integration of Ca2+ and hormone signaling through dynamic complex modulation of the CCaMK/CYCLOPS complex 420 VIII Ca2+ signaling in mitochondria and chloroplasts 422 IX A view beyond recent advances in Ca2+ imaging 423 X Modeling approaches in Ca2+ signaling 424 XI Conclusions: Ca2+ signaling a still young blooming field of plant research 424 Acknowledgements 425 ORCID 425 References 425 SUMMARY: Temporally and spatially defined changes in Ca2+ concentration in distinct compartments of cells represent a universal information code in plants. Recently, it has become evident that Ca2+ signals not only govern intracellular regulation but also appear to contribute to long distance or even organismic signal propagation and physiological response regulation. Ca2+ signals are shaped by an intimate interplay of channels and transporters, and during past years important contributing individual components have been identified and characterized. Ca2+ signals are translated by an elaborate toolkit of Ca2+ -binding proteins, many of which function as Ca2+ sensors, into defined downstream responses. Intriguing progress has been achieved in identifying specific modules that interconnect Ca2+ decoding proteins and protein kinases with downstream target effectors, and in characterizing molecular details of these processes. In this review, we reflect on recent major advances in our understanding of Ca2+ signaling and cover emerging concepts and existing open questions that should be informative also for scientists that are currently entering this field of ever-increasing breath and impact.

Applying LDA Topic Modeling in Communication Research: Toward a Valid and Reliable Methodology

Abstract: Latent Dirichlet allocation (LDA) topic models are increasingly being used in communication research. Yet, questions regarding reliability and validity of the approach have received little attentio...

Second-order topological insulators and superconductors with an order-two crystalline symmetry

Abstract: While topological insulators have a gapped bulk band structure, they have gapless surface states. Recently, it was shown that the presence of additional crystalline symmetries can lead to topological phases that combine a gapped bulk spectrum with gapless states on edges or corners of the crystal. Such topological phases have been called ``higher-order topological phases''. This article presents a complete classification of second-order topological insulators and superconductors with mirror, twofold-rotation, or inversion symmetry. The authors show that crystals with a mirror symmetry and a nontrivial bulk band structure either have gapless surfaces or gapless edges. On the other hand, there are crystals with twofold rotation or inversion symmetry with a nontrivial bulk topology but without surface or edge states.

Antimicrobial resistance in Escherichia coli.

Abstract: Multidrug resistance in Escherichia coli has become a worrying issue that is increasingly observed in human but also in veterinary medicine worldwide. E. coli is intrinsically susceptible to almost all clinically relevant antimicrobial agents, but this bacterial species has a great capacity to accumulate resistance genes, mostly through horizontal gene transfer. The most problematic mechanisms in E. coli correspond to the acquisition of genes coding for extended-spectrum β-lactamases (conferring resistance to broad-spectrum cephalosporins), carbapenemases (conferring resistance to carbapenems), 16S rRNA methylases (conferring pan-resistance to aminoglycosides), plasmid-mediated quinolone resistance (PMQR) genes (conferring resistance to [fluoro]quinolones), and mcr genes (conferring resistance to polymyxins). Although the spread of carbapenemase genes has been mainly recognized in the human sector but poorly recognized in animals, colistin resistance in E. coli seems rather to be related to the use of colistin in veterinary medicine on a global scale. For the other resistance traits, their cross-transfer between the human and animal sectors still remains controversial even though genomic investigations indicate that extended-spectrum β-lactamase producers encountered in animals are distinct from those affecting humans. In addition, E. coli of animal origin often also show resistances to other-mostly older-antimicrobial agents, including tetracyclines, phenicols, sulfonamides, trimethoprim, and fosfomycin. Plasmids, especially multiresistance plasmids, but also other mobile genetic elements, such as transposons and gene cassettes in class 1 and class 2 integrons, seem to play a major role in the dissemination of resistance genes. Of note, coselection and persistence of resistances to critically important antimicrobial agents in human medicine also occurs through the massive use of antimicrobial agents in veterinary medicine, such as tetracyclines or sulfonamides, as long as all those determinants are located on the same genetic elements.

Unified structural motifs of the catalytically active state of Co(oxyhydr)oxides during the electrochemical oxygen evolution reaction

Abstract: Efficient catalysts for the anodic oxygen evolution reaction (OER) are critical for electrochemical H2 production. Their design requires structural knowledge of their catalytically active sites and state. Here, we track the atomic-scale structural evolution of well-defined CoOx(OH)y compounds into their catalytically active state during electrocatalytic operation through operando and surface-sensitive X-ray spectroscopy and surface voltammetry, supported by theoretical calculations. We find clear voltammetric evidence that electrochemically reducible near-surface Co3+–O sites play an organizing role for high OER activity. These sites invariably emerge independent of initial metal valency and coordination under catalytic OER conditions. Combining experiments and theory reveals the unified chemical structure motif as µ2-OH-bridged Co2+/3+ ion clusters formed on all three-dimensional cross-linked and layered CoOx(OH)y precursors and present in an oxidized form during the OER, as shown by operando X-ray spectroscopy. Together, the spectroscopic and electrochemical fingerprints offer a unified picture of our molecular understanding of the structure of catalytically active metal oxide OER sites. Knowledge of the active sites in catalysts—including the sites that form under working conditions—is vital for future design and development. Here, the authors track the atomic-scale changes in a series of well-defined cobalt-based oxide electrocatalysts, showing that the structurally distinct catalysts develop a similar structural motif as they transform into the catalytically active state.

Antiferromagnetic opto-spintronics

Abstract: Control and detection of spin order in ferromagnetic materials is the main principle enabling magnetic information to be stored and read in current technologies. Antiferromagnetic materials, on the other hand, are far less utilized, despite having some appealing features. For instance, the absence of net magnetization and stray fields eliminates crosstalk between neighbouring devices, and the absence of a primary macroscopic magnetization makes spin manipulation in antiferromagnets inherently faster than in ferromagnets. However, control of spins in antiferromagnets requires exceedingly high magnetic fields, and antiferromagnetic order cannot be detected with conventional magnetometry. Here we provide an overview and illustrative examples of how electromagnetic radiation can be used for probing and modification of the magnetic order in antiferromagnets. We also discuss possible research directions that are anticipated to be among the main topics defining the future of this rapidly developing field. An overview of how electromagnetic radiation can be used for probing and modification of the magnetic order in antiferromagnets, and possible future research directions.

Production and integration of the ATLAS Insertable B-Layer

Abstract: During the shutdown of the CERN Large Hadron Collider in 2013-2014, an additional pixel layer was installed between the existing Pixel detector of the ATLAS experiment and a new, smaller radius beam pipe. The motivation for this new pixel layer, the Insertable B-Layer (IBL), was to maintain or improve the robustness and performance of the ATLAS tracking system, given the higher instantaneous and integrated luminosities realised following the shutdown. Because of the extreme radiation and collision rate environment, several new radiation-tolerant sensor and electronic technologies were utilised for this layer. This paper reports on the IBL construction and integration prior to its operation in the ATLAS detector.

Active Salt/Silica-Templated 2D Mesoporous FeCo-Nx -Carbon as Bifunctional Oxygen Electrodes for Zinc-Air Batteries.

Abstract: Two types of templates, an active metal salt and silica nanoparticles, are used concurrently to achieve the facile synthesis of hierarchical meso/microporous FeCo-Nx -carbon nanosheets (meso/micro-FeCo-Nx -CN) with highly dispersed metal sites. The resulting meso/micro-FeCo-Nx -CN shows high and reversible oxygen electrocatalytic performances for both ORR and OER, thus having potential for applications in rechargeable Zn-air battery. Our approach creates a new pathway to fabricate 2D meso/microporous structured carbon architectures for bifunctional oxygen electrodes in rechargeable Zn-air battery as well as opens avenues to the scale-up production of rationally designed heteroatom-doped catalytic materials for a broad range of applications.

Fake News: A Definition

Abstract: Despite being a new term, ‘fake news’ has evolved rapidly. This paper argues that it should be reserved for cases of deliberate presentation of (typically) false or misleading claims as news, where these are misleading by design. The phrase ‘by design’ here refers to systemic features of the design of the sources and channels by which fake news propagates and, thereby, manipulates the audience’s cognitive processes. This prospective definition is then tested: first, by contrasting fake news with other forms of public disinformation; second, by considering whether it helps pinpoint conditions for the (recent) proliferation of fake news.

Time-lagged autoencoders: Deep learning of slow collective variables for molecular kinetics.

Abstract: Inspired by the success of deep learning techniques in the physical and chemical sciences, we apply a modification of an autoencoder type deep neural network to the task of dimension reduction of molecular dynamics data. We can show that our time-lagged autoencoder reliably finds low-dimensional embeddings for high-dimensional feature spaces which capture the slow dynamics of the underlying stochastic processes—beyond the capabilities of linear dimension reduction techniques.

Improved Cycling Stability of Li[Ni0.90Co0.05Mn0.05]O2 Through Microstructure Modification by Boron Doping for Li-Ion Batteries

Abstract: This work was supported by National Research Foundation of Korea (NRF) grant funded by the Korea government Ministry of Education and Science Technology (NRF-2018R1A2B3008794) and supported by a Human Resources Development program (No. 20154010200840) of a Korea Institute of Energy Technology Evaluation and Planning grant funded by the Ministry of Trade, Industry and Energy of the Korean government. K.-J.P. and H.-G.J. contributed equally to this work.

Past and future global transformation of terrestrial ecosystems under climate change

Abstract: Impacts of global climate change on terrestrial ecosystems are imperfectly constrained by ecosystem models and direct observations. Pervasive ecosystem transformations occurred in response to warming and associated climatic changes during the last glacial-to-interglacial transition, which was comparable in magnitude to warming projected for the next century under high-emission scenarios. We reviewed 594 published paleoecological records to examine compositional and structural changes in terrestrial vegetation since the last glacial period and to project the magnitudes of ecosystem transformations under alternative future emission scenarios. Our results indicate that terrestrial ecosystems are highly sensitive to temperature change and suggest that, without major reductions in greenhouse gas emissions to the atmosphere, terrestrial ecosystems worldwide are at risk of major transformation, with accompanying disruption of ecosystem services and impacts on biodiversity.

From the euro to the Schengen crises: European integration theories, politicization, and identity politics

Abstract: This contribution argues that the three dominant approaches to European integration cannot fully explain why the two most recent crises of the European Union (EU) resulted in very different outcome...

Engineering oxygen-containing and amino groups into two-dimensional atomically-thin porous polymeric carbon nitrogen for enhanced photocatalytic hydrogen production

Abstract: Polymeric carbon nitride (PCN) is a promising earth-abundant photocatalyst for solar energy conversion. However, the photocatalytic activities of PCN-based materials remain moderate because of their poor dispersion in water and their fast electron–hole recombination. Here, a facile two-step continuous thermal treatment strategy is presented to endow the bulk PCN nanosheets with an atomically-thin structure, strong hydrophilicity and Lewis basicity to dramatically enhance the photocatalytic hydrogen (H2) generation performance. The formation of the oxygen-containing and amino groups in the atomically-thin PCN sheets improves the charge separation and provides rich active sites for the surface reaction. Such synergistic effects lead to a superior visible-light-driven photocatalytic activity and its H2 evolution rate (1233.5 μmol h−1 g−1) is more than 11 times higher than the bulk PCN using Ni as a cocatalyst. Additionally, the H2 evolution rate can reach 20948.6 μmol h−1 g−1 using Pt as a cocatalyst under AM1.5G solar irradiation.