@article{SchmaelzlinMoralejoGersondeetal.2018, author = {Schm{\"a}lzlin, Elmar Gerd and Moralejo, Benito and Gersonde, Ingo and Schleusener, Johannes and Darvin, Maxim E. and Thiede, Gisela and Roth, Martin M.}, title = {Nonscanning large-area Raman imaging for ex vivo/in vivo skin cancer discrimination}, series = {Journal of biomedical optics}, volume = {23}, journal = {Journal of biomedical optics}, number = {10}, publisher = {SPIE}, address = {Bellingham}, issn = {1083-3668}, doi = {10.1117/1.JBO.23.10.105001}, pages = {11}, year = {2018}, abstract = {Imaging Raman spectroscopy can be used to identify cancerous tissue. Traditionally, a step-by-step scanning of the sample is applied to generate a Raman image, which, however, is too slow for routine examination of patients. By transferring the technique of integral field spectroscopy (IFS) from astronomy to Raman imaging, it becomes possible to record entire Raman images quickly within a single exposure, without the need for a tedious scanning procedure. An IFS-based Raman imaging setup is presented, which is capable of measuring skin ex vivo or in vivo. It is demonstrated how Raman images of healthy and cancerous skin biopsies were recorded and analyzed. (C) The Authors. Published by SPIE under a Creative Commons Attribution 3.0 Unported License.}, language = {en} } @article{MannRahmstorfKornhuberetal.2018, author = {Mann, Michael E. and Rahmstorf, Stefan and Kornhuber, Kai and Steinman, Byron A. and Miller, Sonya K. and Petri, Stefan and Coumou, Dim}, title = {Projected changes in persistent extreme summer weather events}, series = {Science Advances}, volume = {4}, journal = {Science Advances}, number = {10}, publisher = {American Assoc. for the Advancement of Science}, address = {Washington}, issn = {2375-2548}, doi = {10.1126/sciadv.aat3272}, pages = {9}, year = {2018}, abstract = {Persistent episodes of extreme weather in the Northern Hemisphere summer have been associated with high-amplitude quasi-stationary atmospheric Rossby waves, with zonal wave numbers 6 to 8 resulting from the phenomenon of quasi-resonant amplification (QRA). A fingerprint for the occurrence of QRA can be defined in terms of the zonally averaged surface temperature field. Examining state-of-the-art [Coupled Model Intercomparison Project Phase 5 (CMIP5)] climate model projections, we find that QRA events are likely to increase by similar to 50\% this century under business-as-usual carbon emissions, but there is considerable variation among climate models. Some predict a near tripling of QRA events by the end of the century, while others predict a potential decrease. Models with amplified Arctic warming yield the most pronounced increase in QRA events. The projections are strongly dependent on assumptions regarding the nature of changes in radiative forcing associated with anthropogenic aerosols over the next century. One implication of our findings is that a reduction in midlatitude aerosol loading could actually lead to Arctic de-amplification this century, ameliorating potential increases in persistent extreme weather events.}, language = {en} } @article{ThapaWyłomańskaSikoraetal.2021, author = {Thapa, Samudrajit and Wyłomańska, Agnieszka and Sikora, Grzegorz and Wagner, Caroline E. and Krapf, Diego and Kantz, Holger and Chechkin, Aleksei V. and Metzler, Ralf}, title = {Leveraging large-deviation statistics to decipher the stochastic properties of measured trajectories}, series = {New Journal of Physics}, volume = {23}, journal = {New Journal of Physics}, publisher = {Dt. Physikalische Ges. ; IOP}, address = {Bad Honnef ; London}, issn = {1367-2630}, doi = {10.1088/1367-2630/abd50e}, pages = {22}, year = {2021}, abstract = {Extensive time-series encoding the position of particles such as viruses, vesicles, or individualproteins are routinely garnered insingle-particle tracking experiments or supercomputing studies.They contain vital clues on how viruses spread or drugs may be delivered in biological cells.Similar time-series are being recorded of stock values in financial markets and of climate data.Such time-series are most typically evaluated in terms of time-averaged mean-squareddisplacements (TAMSDs), which remain random variables for finite measurement times. Theirstatistical properties are different for differentphysical stochastic processes, thus allowing us toextract valuable information on the stochastic process itself. To exploit the full potential of thestatistical information encoded in measured time-series we here propose an easy-to-implementand computationally inexpensive new methodology, based on deviations of the TAMSD from itsensemble average counterpart. Specifically, we use the upper bound of these deviations forBrownian motion (BM) to check the applicability of this approach to simulated and real data sets.By comparing the probability of deviations fordifferent data sets, we demonstrate how thetheoretical bound for BM reveals additional information about observed stochastic processes. Weapply the large-deviation method to data sets of tracer beads tracked in aqueous solution, tracerbeads measured in mucin hydrogels, and of geographic surface temperature anomalies. Ouranalysis shows how the large-deviation properties can be efficiently used as a simple yet effectiveroutine test to reject the BM hypothesis and unveil relevant information on statistical propertiessuch as ergodicity breaking and short-time correlations.}, language = {en} } @misc{RisbeyLewandowskyCowtanetal.2018, author = {Risbey, James S. and Lewandowsky, Stephan and Cowtan, Kevin and Oreskes, Naomi and Rahmstorf, Stefan and Jokim{\"a}ki, Ari and Foster, Grant}, title = {A fluctuation in surface temperature in historical context}, series = {Environmental research letters}, volume = {13}, journal = {Environmental research letters}, number = {12}, publisher = {IOP Publ. Ltd.}, address = {Bristol}, issn = {1748-9326}, doi = {10.1088/1748-9326/aaf342}, pages = {23}, year = {2018}, abstract = {This work reviews the literature on an alleged global warming 'pause' in global mean surface temperature (GMST) to determine how it has been defined, what time intervals are used to characterise it, what data are used to measure it, and what methods used to assess it. We test for 'pauses', both in the normally understood meaning of the term to mean no warming trend, as well as for a 'pause' defined as a substantially slower trend in GMST. The tests are carried out with the historical versions of GMST that existed for each pause-interval tested, and with current versions of each of the GMST datasets. The tests are conducted following the common (but questionable) practice of breaking the linear fit at the start of the trend interval ('broken' trends), and also with trends that are continuous with the data bordering the trend interval. We also compare results when appropriate allowance is made for the selection bias problem. The results show that there is little or no statistical evidence for a lack of trend or slower trend in GMST using either the historical data or the current data. The perception that there was a 'pause' in GMST was bolstered by earlier biases in the data in combination with incomplete statistical testing.}, language = {en} } @article{MardoukhiChechkinMetzler2020, author = {Mardoukhi, Yousof and Chechkin, Aleksei V. and Metzler, Ralf}, title = {Spurious ergodicity breaking in normal and fractional Ornstein-Uhlenbeck process}, series = {New Journal of Physics}, volume = {22}, journal = {New Journal of Physics}, publisher = {IOP}, address = {London}, issn = {1367-2630}, doi = {10.1088/1367-2630/ab950b}, pages = {18}, year = {2020}, abstract = {The Ornstein-Uhlenbeck process is a stationary and ergodic Gaussian process, that is fully determined by its covariance function and mean. We show here that the generic definitions of the ensemble- and time-averaged mean squared displacements fail to capture these properties consistently, leading to a spurious ergodicity breaking. We propose to remedy this failure by redefining the mean squared displacements such that they reflect unambiguously the statistical properties of any stochastic process. In particular we study the effect of the initial condition in the Ornstein-Uhlenbeck process and its fractional extension. For the fractional Ornstein-Uhlenbeck process representing typical experimental situations in crowded environments such as living biological cells, we show that the stationarity of the process delicately depends on the initial condition.}, language = {en} } @article{NivenAbelSchlegeletal.2019, author = {Niven, Robert K. and Abel, Markus and Schlegel, Michael and Waldrip, Steven H.}, title = {Maximum Entropy Analysis of Flow Networks: Theoretical Foundation and Applications}, series = {Entropy}, volume = {21}, journal = {Entropy}, number = {8}, publisher = {MDPI}, address = {Basel}, issn = {1099-4300}, doi = {10.3390/e21080776}, pages = {776}, year = {2019}, abstract = {The concept of a "flow network"-a set of nodes and links which carries one or more flows-unites many different disciplines, including pipe flow, fluid flow, electrical, chemical reaction, ecological, epidemiological, neurological, communications, transportation, financial, economic and human social networks. This Feature Paper presents a generalized maximum entropy framework to infer the state of a flow network, including its flow rates and other properties, in probabilistic form. In this method, the network uncertainty is represented by a joint probability function over its unknowns, subject to all that is known. This gives a relative entropy function which is maximized, subject to the constraints, to determine the most probable or most representative state of the network. The constraints can include "observable" constraints on various parameters, "physical" constraints such as conservation laws and frictional properties, and "graphical" constraints arising from uncertainty in the network structure itself. Since the method is probabilistic, it enables the prediction of network properties when there is insufficient information to obtain a deterministic solution. The derived framework can incorporate nonlinear constraints or nonlinear interdependencies between variables, at the cost of requiring numerical solution. The theoretical foundations of the method are first presented, followed by its application to a variety of flow networks.}, language = {en} } @article{CoduttiBenteFaivreetal.2019, author = {Codutti, Agnese and Bente, Klaas and Faivre, Damien and Klumpp, Stefan}, title = {Chemotaxis in external fields: Simulations for active magnetic biological matter}, series = {PLoS Computational Biology : a new community journal}, volume = {15}, journal = {PLoS Computational Biology : a new community journal}, number = {12}, publisher = {PLoS}, address = {San Fransisco}, issn = {1553-734X}, doi = {10.1371/journal.pcbi.1007548}, pages = {26}, year = {2019}, abstract = {The movement of microswimmers is often described by active Brownian particle models. Here we introduce a variant of these models with several internal states of the swimmer to describe stochastic strategies for directional swimming such as run and tumble or run and reverse that are used by microorganisms for chemotaxis. The model includes a mechanism to generate a directional bias for chemotaxis and interactions with external fields (e.g., gravity, magnetic field, fluid flow) that impose forces or torques on the swimmer. We show how this modified model can be applied to various scenarios: First, the run and tumble motion of E. coli is used to establish a paradigm for chemotaxis and investigate how it is affected by external forces. Then, we study magneto-aerotaxis in magnetotactic bacteria, which is biased not only by an oxygen gradient towards a preferred concentration, but also by magnetic fields, which exert a torque on an intracellular chain of magnets. We study the competition of magnetic alignment with active reorientation and show that the magnetic orientation can improve chemotaxis and thereby provide an advantage to the bacteria, even at rather large inclination angles of the magnetic field relative to the oxygen gradient, a case reminiscent of what is expected for the bacteria at or close to the equator. The highest gain in chemotactic velocity is obtained for run and tumble with a magnetic field parallel to the gradient, but in general a mechanism for reverse motion is necessary to swim against the magnetic field and a run and reverse strategy is more advantageous in the presence of a magnetic torque. This finding is consistent with observations that the dominant mode of directional changes in magnetotactic bacteria is reversal rather than tumbles. Moreover, it provides guidance for the design of future magnetic biohybrid swimmers. Author summary In this paper, we propose a modified Active Brownian particle model to describe bacterial swimming behavior under the influence of external forces and torques, in particular of a magnetic torque. This type of interaction is particularly important for magnetic biohybrids (i.e. motile bacteria coupled to a synthetic magnetic component) and for magnetotactic bacteria (i.e. bacteria with a natural intracellular magnetic chain), which perform chemotaxis to swim along chemical gradients, but are also directed by an external magnetic field. The model allows us to investigate the benefits and disadvantages of such coupling between two different directionality mechanisms. In particular we show that the magnetic torque can speed chemotaxis up in some conditions, while it can hinder it in other cases. In addition to an understanding of the swimming strategies of naturally magnetotactic organisms, the results may guide the design of future biomedical devices.}, language = {en} } @article{MeiKochovskiRoaetal.2019, author = {Mei, Shilin and Kochovski, Zdravko and Roa, Rafael and Gu, Sasa and Xu, Xiaohui and Yu, Hongtao and Dzubiella, Joachim and Ballauff, Matthias and Lu, Yan}, title = {Enhanced Catalytic Activity of Gold@Polydopamine Nanoreactors with Multi-compartment Structure Under NIR Irradiation}, series = {Nano-Micro Letters}, volume = {11}, journal = {Nano-Micro Letters}, number = {1}, publisher = {Shanghai JIAO TONG univ press}, address = {Shanghai}, issn = {2311-6706}, doi = {10.1007/s40820-019-0314-9}, pages = {16}, year = {2019}, abstract = {Photothermal conversion (PTC) nanostructures have great potential for applications in many fields, and therefore, they have attracted tremendous attention. However, the construction of a PTC nanoreactor with multi-compartment structure to achieve the combination of unique chemical properties and structural feature is still challenging due to the synthetic difficulties. Herein, we designed and synthesized a catalytically active, PTC gold (Au)@polydopamine (PDA) nanoreactor driven by infrared irradiation using assembled PS-b-P2VP nanosphere as soft template. The particles exhibit multi-compartment structure which is revealed by 3D electron tomography characterization technique. They feature permeable shells with tunable shell thickness. Full kinetics for the reduction reaction of 4-nitrophenol has been investigated using these particles as nanoreactors and compared with other reported systems. Notably, a remarkable acceleration of the catalytic reaction upon near-infrared irradiation is demonstrated, which reveals for the first time the importance of the synergistic effect of photothermal conversion and complex inner structure to the kinetics of the catalytic reduction. The ease of synthesis and fresh insights into catalysis will promote a new platform for novel nanoreactor studies.}, language = {en} } @article{SahaOwenOrretal.2019, author = {Saha, Sourav and Owen, Lewis A. and Orr, Elizabeth N. and Caffee, Marc W.}, title = {Cosmogenic Be-10 and equilibrium-line altitude dataset of Holocene glacier advances in the Himalayan-Tibetan orogen}, series = {Data in brief}, volume = {26}, journal = {Data in brief}, publisher = {Elsevier}, address = {Amsterdam}, issn = {2352-3409}, doi = {10.1016/j.dib.2019.104412}, pages = {13}, year = {2019}, abstract = {A comprehensive analysis of the variable temporal and spatial responses of tropical-subtropical high-altitude glaciers to climate change is critical for successful model predictions and environmental risk assessment in the Himalayan-Tibetan orogen. High-frequency Holocene glacier chronostratigraphies are therefore reconstructed in 79 glaciated valleys across the orogen using 519 published and 16 new terrestrial cosmogenic 10Be exposure age dataset. Published 10Be ages are compiled only for moraine boulders (excluding bedrock ages). These ages are recalculated using the latest ICE-D production rate calibration database and the scaling scheme models. Outliers for the individual moraine are detected using the Chauvenet's criterion. In addition, past equilibrium-line altitudes (ELAs) are determined using the area-altitude (AA), area accumulation ratio (AAR), and toe-headwall accumulation ratio (THAR) methods for each glacier advance. The modern maximum elevations of lateral moraines (MELM) are also used to estimate modern ELAs and as an independent check on mean ELAs derived using the above three methods. These data may serve as an essential archive for future studies focusing on the cryospheric and environmental changes in the Himalayan-Tibetan orogen. A more comprehensive analysis of the published and new 10Be ages and ELA results and a list of references are presented in Saha et al. (2019, High-frequency Holocene glacier fluctuations in the Himalayan-Tibetan orogen. Quaternary Science Reviews, 220, 372-400).}, language = {en} } @article{PalyulinBlackburnLomholtetal.2019, author = {Palyulin, Vladimir V. and Blackburn, George and Lomholt, Michael A. and Watkins, Nicholas W. and Metzler, Ralf and Klages, Rainer and Chechkin, Aleksei V.}, title = {First passage and first hitting times of Levy flights and Levy walks}, series = {New journal of physics : the open-access journal for physics}, volume = {21}, journal = {New journal of physics : the open-access journal for physics}, number = {10}, publisher = {IOP Publ. Ltd.}, address = {Bristol}, issn = {1367-2630}, doi = {10.1088/1367-2630/ab41bb}, pages = {23}, year = {2019}, abstract = {For both L{\´e}vy flight and L{\´e}vy walk search processes we analyse the full distribution of first-passage and first-hitting (or first-arrival) times. These are, respectively, the times when the particle moves across a point at some given distance from its initial position for the first time, or when it lands at a given point for the first time. For L{\´e}vy motions with their propensity for long relocation events and thus the possibility to jump across a given point in space without actually hitting it ('leapovers'), these two definitions lead to significantly different results. We study the first-passage and first-hitting time distributions as functions of the L{\´e}vy stable index, highlighting the different behaviour for the cases when the first absolute moment of the jump length distribution is finite or infinite. In particular we examine the limits of short and long times. Our results will find their application in the mathematical modelling of random search processes as well as computer algorithms.}, language = {en} }