Showing papers by "University of Bremen published in 2017"

Self-assembling peptide and protein amyloids: from structure to tailored function in nanotechnology

Abstract: Self-assembled peptide and protein amyloid nanostructures have traditionally been considered only as pathological aggregates implicated in human neurodegenerative diseases. In more recent times, these nanostructures have found interesting applications as advanced materials in biomedicine, tissue engineering, renewable energy, environmental science, nanotechnology and material science, to name only a few fields. In all these applications, the final function depends on: (i) the specific mechanisms of protein aggregation, (ii) the hierarchical structure of the protein and peptide amyloids from the atomistic to mesoscopic length scales and (iii) the physical properties of the amyloids in the context of their surrounding environment (biological or artificial). In this review, we will discuss recent progress made in the field of functional and artificial amyloids and highlight connections between protein/peptide folding, unfolding and aggregation mechanisms, with the resulting amyloid structure and functionality. We also highlight current advances in the design and synthesis of amyloid-based biological and functional materials and identify new potential fields in which amyloid-based structures promise new breakthroughs.

On Detecting Adversarial Perturbations

Abstract: Machine learning and deep learning in particular has advanced tremendously on perceptual tasks in recent years. However, it remains vulnerable against adversarial perturbations of the input that have been crafted specifically to fool the system while being quasi-imperceptible to a human. In this work, we propose to augment deep neural networks with a small "detector" subnetwork which is trained on the binary classification task of distinguishing genuine data from data containing adversarial perturbations. Our method is orthogonal to prior work on addressing adversarial perturbations, which has mostly focused on making the classification network itself more robust. We show empirically that adversarial perturbations can be detected surprisingly well even though they are quasi-imperceptible to humans. Moreover, while the detectors have been trained to detect only a specific adversary, they generalize to similar and weaker adversaries. In addition, we propose an adversarial attack that fools both the classifier and the detector and a novel training procedure for the detector that counteracts this attack.

Making sense of complexity in context and implementation: the Context and Implementation of Complex Interventions (CICI) framework

Abstract: The effectiveness of complex interventions, as well as their success in reaching relevant populations, is critically influenced by their implementation in a given context. Current conceptual frameworks often fail to address context and implementation in an integrated way and, where addressed, they tend to focus on organisational context and are mostly concerned with specific health fields. Our objective was to develop a framework to facilitate the structured and comprehensive conceptualisation and assessment of context and implementation of complex interventions. The Context and Implementation of Complex Interventions (CICI) framework was developed in an iterative manner and underwent extensive application. An initial framework based on a scoping review was tested in rapid assessments, revealing inconsistencies with respect to the underlying concepts. Thus, pragmatic utility concept analysis was undertaken to advance the concepts of context and implementation. Based on these findings, the framework was revised and applied in several systematic reviews, one health technology assessment (HTA) and one applicability assessment of very different complex interventions. Lessons learnt from these applications and from peer review were incorporated, resulting in the CICI framework. The CICI framework comprises three dimensions—context, implementation and setting—which interact with one another and with the intervention dimension. Context comprises seven domains (i.e., geographical, epidemiological, socio-cultural, socio-economic, ethical, legal, political); implementation consists of five domains (i.e., implementation theory, process, strategies, agents and outcomes); setting refers to the specific physical location, in which the intervention is put into practise. The intervention and the way it is implemented in a given setting and context can occur on a micro, meso and macro level. Tools to operationalise the framework comprise a checklist, data extraction tools for qualitative and quantitative reviews and a consultation guide for applicability assessments. The CICI framework addresses and graphically presents context, implementation and setting in an integrated way. It aims at simplifying and structuring complexity in order to advance our understanding of whether and how interventions work. The framework can be applied in systematic reviews and HTA as well as primary research and facilitate communication among teams of researchers and with various stakeholders.

Greater role for Atlantic inflows on sea-ice loss in the Eurasian Basin of the Arctic Ocean

Abstract: Arctic sea-ice loss is a leading indicator of climate change and can be attributed, in large part, to atmospheric forcing. Here, we show that recent ice reductions, weakening of the halocline, and shoaling of the intermediate-depth Atlantic Water layer in the eastern Eurasian Basin have increased winter ventilation in the ocean interior, making this region structurally similar to that of the western Eurasian Basin. The associated enhanced release of oceanic heat has reduced winter sea-ice formation at a rate now comparable to losses from atmospheric thermodynamic forcing, thus explaining the recent reduction in sea-ice cover in the eastern Eurasian Basin. This encroaching "atlantification" of the Eurasian Basin represents an essential step toward a new Arctic climate state, with a substantially greater role for Atlantic inflows.

Formal Verification of Piece-Wise Linear Feed-Forward Neural Networks

Abstract: We present an approach for the verification of feed-forward neural networks in which all nodes have a piece-wise linear activation function. Such networks are often used in deep learning and have been shown to be hard to verify for modern satisfiability modulo theory (SMT) and integer linear programming (ILP) solvers.

Internet-of-Things-Based Smart Cities: Recent Advances and Challenges

Abstract: The Internet of Things is a novel cutting edge technology that proffers to connect a plethora of digital devices endowed with several sensing, actuation, and computing capabilities with the Internet, thus offering manifold new services in the context of a smart city. The appealing IoT services and big data analytics are enabling smart city initiatives all over the world. These services are transforming cities by improving infrastructure and transportation systems, reducing traffic congestion, providing waste management, and improving the quality of human life. In this article, we devise a taxonomy to best bring forth a generic overview of the IoT paradigm for smart cities, integrated ICT, network types, possible opportunities and major requirements. Moreover, an overview of the up-to-date efforts from standard bodies is presented. Later, we give an overview of existing open source IoT platforms for realizing smart city applications followed by several exemplary case studies. In addition, we summarize the latest synergies and initiatives worldwide taken to promote IoT in the context of smart cities. Finally, we highlight several challenges in order to give future research directions.

MICROSCOPE Mission: First Results of a Space Test of the Equivalence Principle.

Abstract: According to the weak equivalence principle, all bodies should fall at the same rate in a gravitational field. The MICROSCOPE satellite, launched in April 2016, aims to test its validity at the 10−15 precision level, by measuring the force required to maintain two test masses (of titanium and platinum alloys) exactly in the same orbit. A nonvanishing result would correspond to a violation of the equivalence principle, or to the discovery of a new long-range force. Analysis of the first data gives δ(Ti; Pt)=[-1+/-9(stat)+/-9(syst)] × 10−15 (1σ statistical uncertainty) for the titanium-platinum Eotvos parameter characterizing the relative difference in their free-fall accelerations.

Safe Reinforcement Learning via Shielding

Abstract: Reinforcement learning algorithms discover policies that maximize reward, but do not necessarily guarantee safety during learning or execution phases. We introduce a new approach to learn optimal policies while enforcing properties expressed in temporal logic. To this end, given the temporal logic specification that is to be obeyed by the learning system, we propose to synthesize a reactive system called a shield. The shield is introduced in the traditional learning process in two alternative ways, depending on the location at which the shield is implemented. In the first one, the shield acts each time the learning agent is about to make a decision and provides a list of safe actions. In the second way, the shield is introduced after the learning agent. The shield monitors the actions from the learner and corrects them only if the chosen action causes a violation of the specification. We discuss which requirements a shield must meet to preserve the convergence guarantees of the learner. Finally, we demonstrate the versatility of our approach on several challenging reinforcement learning scenarios.

Long-Lived Direct and Indirect Interlayer Excitons in van der Waals Heterostructures

Abstract: We report the observation of a doublet structure in the low-temperature photoluminescence of interlayer excitons in heterostructures consisting of monolayer MoSe2 and WSe2. Both peaks exhibit long photoluminescence lifetimes of several tens of nanoseconds up to 100 ns verifying the interlayer nature of the excitons. The energy and line width of both peaks show unusual temperature and power dependences. While the low-energy peak dominates the spectra at low power and low temperatures, the high-energy peak dominates for high power and temperature. We explain the findings by two kinds of interlayer excitons being either indirect or quasi-direct in reciprocal space. Our results provide fundamental insights into long-lived interlayer states in van der Waals heterostructures with possible bosonic many-body interactions.

Surgical data science for next-generation interventions.

Abstract: Interventional healthcare will evolve from an artisanal craft based on the individual experiences, preferences and traditions of physicians into a discipline that relies on objective decision-making on the basis of large-scale data from heterogeneous sources.

FDR-controlled metabolite annotation for high-resolution imaging mass spectrometry

Abstract: High-mass-resolution imaging mass spectrometry promises to localize hundreds of metabolites in tissues, cell cultures, and agar plates with cellular resolution, but it is hampered by the lack of bioinformatics tools for automated metabolite identification. We report pySM, a framework for false discovery rate (FDR)-controlled metabolite annotation at the level of the molecular sum formula, for high-mass-resolution imaging mass spectrometry (https://github.com/alexandrovteam/pySM). We introduce a metabolite-signal match score and a target-decoy FDR estimate for spatial metabolomics.

Very large release of mostly volcanic carbon during the Palaeocene–Eocene Thermal Maximum

Abstract: The Palaeocene–Eocene Thermal Maximum1,2 (PETM) was a global warming event that occurred about 56 million years ago, and is commonly thought to have been driven primarily by the destabilization of carbon from surface sedimentary reservoirs such as methane hydrates3. However, it remains controversial whether such reservoirs were indeed the source of the carbon that drove the warming1,3,4,5. Resolving this issue is key to understanding the proximal cause of the warming, and to quantifying the roles of triggers versus feedbacks. Here we present boron isotope data—a proxy for seawater pH—that show that the ocean surface pH was persistently low during the PETM. We combine our pH data with a paired carbon isotope record in an Earth system model in order to reconstruct the unfolding carbon-cycle dynamics during the event6,7. We find strong evidence for a much larger (more than 10,000 petagrams)—and, on average, isotopically heavier—carbon source than considered previously8,9. This leads us to identify volcanism associated with the North Atlantic Igneous Province10,11, rather than carbon from a surface reservoir, as the main driver of the PETM. This finding implies that climate-driven amplification of organic carbon feedbacks probably played only a minor part in driving the event. However, we find that enhanced burial of organic matter seems to have been important in eventually sequestering the released carbon and accelerating the recovery of the Earth system12.

Leads in Arctic pack ice enable early phytoplankton blooms below snow-covered sea ice

Abstract: The Arctic icescape is rapidly transforming from a thicker multiyear ice cover to a thinner and largely seasonal first-year ice cover with significant consequences for Arctic primary production. One critical challenge is to understand how productivity will change within the next decades. Recent studies have reported extensive phytoplankton blooms beneath ponded sea ice during summer, indicating that satellite-based Arctic annual primary production estimates may be significantly underestimated. Here we present a unique time-series of a phytoplankton spring bloom observed beneath snow-covered Arctic pack ice. The bloom, dominated by the haptophyte algae Phaeocystis pouchetii, caused near depletion of the surface nitrate inventory and a decline in dissolved inorganic carbon by 16 ± 6 g C m−2. Ocean circulation characteristics in the area indicated that the bloom developed in situ despite the snow-covered sea ice. Leads in the dynamic ice cover provided added sunlight necessary to initiate and sustain the bloom. Phytoplankton blooms beneath snow-covered ice might become more common and widespread in the future Arctic Ocean with frequent lead formation due to thinner and more dynamic sea ice despite projected increases in high-Arctic snowfall. This could alter productivity, marine food webs and carbon sequestration in the Arctic Ocean.

Colloidal capsules: nano- and microcapsules with colloidal particle shells

Abstract: Utilizing colloidal particles for the assembly of the shell of nano- and microcapsules holds great promise for the tailor-made design of new functional materials. Increasing research efforts are devoted to the synthesis of such colloidal capsules, by which the integration of modular building blocks with distinct physical, chemical, or morphological characteristics in a capsule's shell can result in novel properties, not present in previous encapsulation structures. This review will provide a comprehensive overview of the synthesis strategies and the progress made so far of bringing nano- and microcapsules with shells of densely packed colloidal particles closer to application in fields such as chemical engineering, materials science, or pharmaceutical and life science. The synthesis routes are categorized into the four major themes for colloidal capsule formation, i.e. the Pickering-emulsion based formation of colloidal capsules, the colloidal particle deposition on (sacrificial) templates, the amphiphilicity driven self-assembly of nanoparticle vesicles from polymer-grafted colloids, and the closely related field of nanoparticle membrane-loading of liposomes and polymersomes. The varying fields of colloidal capsule research are then further categorized and discussed for micro- and nano-scaled structures. Finally, a special section is dedicated to colloidal capsules for biological applications, as a diverse range of reports from this field aim at pharmaceutical agent encapsulation, targeted drug-delivery, and theranostics.

Recurring and triggered slow-slip events near the trench at the Nankai Trough subduction megathrust

Abstract: The discovery of slow earthquakes has revolutionized the field of earthquake seismology. Defining the locations of these events and the conditions that favor their occurrence provides important insights into the slip behavior of tectonic faults. We report on a family of recurring slow-slip events (SSEs) on the plate interface immediately seaward of repeated historical moment magnitude (Mw) 8 earthquake rupture areas offshore of Japan. The SSEs continue for days to several weeks, include both spontaneous and triggered slip, recur every 8 to 15 months, and are accompanied by swarms of low-frequency tremors. We can explain the SSEs with 1 to 4 centimeters of slip along the megathrust, centered 25 to 35 kilometers (km) from the trench (4 to 10 km depth). The SSEs accommodate 30 to 55% of the plate motion, indicating frequent release of accumulated strain near the trench.

BlackHoleCam: Fundamental physics of the galactic center

Abstract: Einstein’s General theory of relativity (GR) successfully describes gravity. Although GR has been accurately tested in weak gravitational fields, it remains largely untested in the general strong field cases. One of the most fundamental predictions of GR is the existence of black holes (BHs). After the recent direct detection of gravitational waves by LIGO, there is now near conclusive evidence for the existence of stellar-mass BHs. In spite of this exciting discovery, there is not yet direct evidence of the existence of BHs using astronomical observations in the electromagnetic spectrum. Are BHs observable astrophysical objects? Does GR hold in its most extreme limit or are alternatives needed? The prime target to address these fundamental questions is in the center of our own Milky Way, which hosts the closest and best-constrained supermassive BH candidate in the universe, Sagittarius A* (Sgr A*). Three different types of experiments hold the promise to test GR in a strong-field regime using observations of Sgr A* with new-generation instruments. The first experiment consists of making a standard astronomical image of the synchrotron emission from the relativistic plasma accreting onto Sgr A*. This emission forms a “shadow” around the event horizon cast against the background, whose predicted size (∼50μas) can now be resolved by upcoming very long baseline radio interferometry experiments at mm-waves such as the event horizon telescope (EHT). The second experiment aims to monitor stars orbiting Sgr A* with the next-generation near-infrared (NIR) interferometer GRAVITY at the very large telescope (VLT). The third experiment aims to detect and study a radio pulsar in tight orbit about Sgr A* using radio telescopes (including the Atacama large millimeter array or ALMA). The BlackHoleCam project exploits the synergy between these three different techniques and contributes directly to them at different levels. These efforts will eventually enable us to measure fundamental BH parameters (mass, spin, and quadrupole moment) with sufficiently high precision to provide fundamental tests of GR (e.g. testing the no-hair theorem) and probe the spacetime around a BH in any metric theory of gravity. Here, we review our current knowledge of the physical properties of Sgr A* as well as the current status of such experimental efforts towards imaging the event horizon, measuring stellar orbits, and timing pulsars around Sgr A*. We conclude that the Galactic center provides a unique fundamental-physics laboratory for experimental tests of BH accretion and theories of gravity in their most extreme limits.

Mapping coral reefs using consumer-grade drones and structure from motion photogrammetry techniques

Abstract: We propose a novel technique to measure the small-scale three-dimensional features of a shallow-water coral reef using a small drone equipped with a consumer-grade camera, a handheld GPS and structure from motion (SfM) algorithms. We used a GoPro HERO4 with a modified lens mounted on a DJI Phantom 2 drone (maximum total take-off weight <2 kg) to perform a 10 min flight and collect 306 aerial images with an overlap equal or greater than 90%. We mapped an area of 8380 m2, obtaining as output an ortho-rectified aerial photomosaic and a bathymetric digital elevation model (DEM) with a resolution of 0.78 and 1.56 cm pixel−1, respectively. Through comparison with airborne LiDAR data for the same area, we verified that the location of the ortho-rectified aerial photomosaic is accurate within ~1.4 m. The bathymetric difference between our DEM and the LiDAR dataset is −0.016 ± 0.45 m (1σ). Our results show that it is possible, in conditions of calm waters, low winds and minimal sun glint, to deploy consumer-grade drones as a relatively low-cost and rapid survey technique to produce multispectral and bathymetric data on shallow-water coral reefs. We discuss the utility of such data to monitor temporal changes in topographic complexity of reefs and associated biological processes.

Choosing the correct hybrid for defect calculations: A case study on intrinsic carrier trapping in β − G a 2 O 3

Abstract: Due to its wide band gap and availability as a single crystal, $\ensuremath{\beta}\ensuremath{-}\mathrm{G}{\mathrm{a}}_{2}{\mathrm{O}}_{3}$ has potential for applications in many areas of micro/optoelectronics and photovoltaics. Still, little is as yet known about its intrinsic defects, which may influence carrier concentrations and act as recombination centers. From a theoretical point of view, the problem is that standard (semi)local approximations of density functional theory usually cannot handle wide band-gap oxides, while results of tuned hybrid functional calculations so far have shown little quantitative coincidence with experimental data on $\ensuremath{\beta}\ensuremath{-}\mathrm{G}{\mathrm{a}}_{2}{\mathrm{O}}_{3}$. Here, we show a method for selecting the optimal hybrid, which reproduces not only the band gap, but also satisfies the generalized Koopmans' theorem. Unless the screening is strongly orbital/direction dependent in the given material, such an optimal hybrid can reproduce the whole $GW$ band structure quite accurately. With the optimized functional, and introducing a modification into the charge correction process, we are able to give a consistent description of observed carrier trapping by intrinsic defects in $\ensuremath{\beta}\ensuremath{-}\mathrm{G}{\mathrm{a}}_{2}{\mathrm{O}}_{3}$. With the exception of gallium interstitials, which can act as shallow donors, all other intrinsic defects are deep. Gallium vacancies are the main compensating acceptors in $n$-type samples, while both oxygen interstitials and vacancies act as hole traps, in addition to small hole polarons. Considering the limitations imposed by a medium-sized (160-atom) supercell in an ionic solid, the calculated adiabatic and vertical transitions are in good agreement with available experimental data.

Standardized Nanomechanical Atomic Force Microscopy Procedure (SNAP) for Measuring Soft and Biological Samples.

Abstract: We present a procedure that allows a reliable determination of the elastic (Young's) modulus of soft samples, including living cells, by atomic force microscopy (AFM). The standardized nanomechanical AFM procedure (SNAP) ensures the precise adjustment of the AFM optical lever system, a prerequisite for all kinds of force spectroscopy methods, to obtain reliable values independent of the instrument, laboratory and operator. Measurements of soft hydrogel samples with a well-defined elastic modulus using different AFMs revealed that the uncertainties in the determination of the deflection sensitivity and subsequently cantilever's spring constant were the main sources of error. SNAP eliminates those errors by calculating the correct deflection sensitivity based on spring constants determined with a vibrometer. The procedure was validated within a large network of European laboratories by measuring the elastic properties of gels and living cells, showing that its application reduces the variability in elastic moduli of hydrogels down to 1%, and increased the consistency of living cells elasticity measurements by a factor of two. The high reproducibility of elasticity measurements provided by SNAP could improve significantly the applicability of cell mechanics as a quantitative marker to discriminate between cell types and conditions.

Market Mechanisms and Funding Dynamics in Equity Crowdfunding

Abstract: We use hand-collected data from four German crowdinvesting portals to analyze what determines individual investment decisions in crowdinvesting. In contrast with the crowdfunding campaigns on Kickstarter where the typical pattern of project support is U-shaped, we find crowdinvesting dynamics to be L-shaped under a first-come, first-serve mechanism and only U-shaped under a sealed-bid second-price auction. The evidence further shows that investors base their decisions on information provided by the entrepreneur in form of updates during the campaign and by the investment behavior and comments of other crowd investors. We also find evidence for herding behavior. As legislators around the world increasingly regulate crowdinvesting activities, knowing how crowd investors behave under no formal information disclosure provides important insights for issuers, portals, and lawmakers.

Advances and future directions of biochar characterization methods and applications

Abstract: Biochar is a carbon-rich by-product of the thermal conversion of organic feedstocks and is primarily used as a soil amendment. Identification and quantification of biochar properties are important to ensure optimal outcomes for agricultural or environmental applications. Advanced spectroscopic techniques have recently been adopted in biochar characterization. However, biochar characterization approaches rely entirely on the user's choice and accessibility to the new technology. The selection of proper methods is vital to accurately and consistently assess biochar properties. This review critically evaluates current biochar characterization methods of proximate, ultimate, physicochemical, surface and structural analyses, and important biochar properties for various applications.

Exciton fission in monolayer transition metal dichalcogenide semiconductors

Abstract: When electron-hole pairs are excited in a semiconductor, it is a priori not clear if they form a plasma of unbound fermionic particles or a gas of composite bosons called excitons. Usually, the exciton phase is associated with low temperatures. In atomically thin transition metal dichalcogenide semiconductors, excitons are particularly important even at room temperature due to strong Coulomb interaction and a large exciton density of states. Using state-of-the-art many-body theory, we show that the thermodynamic fission–fusion balance of excitons and electron-hole plasma can be efficiently tuned via the dielectric environment as well as charge carrier doping. We propose the observation of these effects by studying exciton satellites in photoemission and tunneling spectroscopy, which present direct solid-state counterparts of high-energy collider experiments on the induced fission of composite particles. Owing to their atomically thin nature, 2D transition metal dichalcogenides host room temperature, strongly bound excitons. Here, the authors show that the thermodynamical balance between fission and fusion of excitons can be tuned by the dielectric environment and charge carrier doping and observed by photoemission spectroscopy.

Causes of ice age intensification across the Mid-Pleistocene Transition

Abstract: During the Mid-Pleistocene Transition (MPT; 1,200–800 kya), Earth’s orbitally paced ice age cycles intensified, lengthened from ∼40,000 (∼40 ky) to ∼100 ky, and became distinctly asymmetrical. Testing hypotheses that implicate changing atmospheric CO2 levels as a driver of the MPT has proven difficult with available observations. Here, we use orbitally resolved, boron isotope CO2 data to show that the glacial to interglacial CO2 difference increased from ∼43 to ∼75 μatm across the MPT, mainly because of lower glacial CO2 levels. Through carbon cycle modeling, we attribute this decline primarily to the initiation of substantive dust-borne iron fertilization of the Southern Ocean during peak glacial stages. We also observe a twofold steepening of the relationship between sea level and CO2-related climate forcing that is suggestive of a change in the dynamics that govern ice sheet stability, such as that expected from the removal of subglacial regolith or interhemispheric ice sheet phase-locking. We argue that neither ice sheet dynamics nor CO2 change in isolation can explain the MPT. Instead, we infer that the MPT was initiated by a change in ice sheet dynamics and that longer and deeper post-MPT ice ages were sustained by carbon cycle feedbacks related to dust fertilization of the Southern Ocean as a consequence of larger ice sheets.

Detecting recovery of the stratospheric ozone layer

Abstract: As a result of the 1987 Montreal Protocol and its amendments, the atmospheric loading of anthropogenic ozone-depleting substances is decreasing. Accordingly, the stratospheric ozone layer is expected to recover. However, short data records and atmospheric variability confound the search for early signs of recovery, and climate change is masking ozone recovery from ozone-depleting substances in some regions and will increasingly affect the extent of recovery. Here we discuss the nature and timescales of ozone recovery, and explore the extent to which it can be currently detected in different atmospheric regions.