bluuebunny/crossref_metadata_2025_split huggingface dataset:
High‐Frequency (>2 Hz) Ambient Seismic Noise on High‐Melt Glaciers: Green's Function Estimation and Source Characterization
Authors: Preiswerk Lukas E. , Walter Fabian 
Published: June 2018

Using ambient noise to characterize subsurface structures has revolutionized solid earth seismology. In glacial applications, this technique could provide valuable information about ice thickness and bed properties, which to date are deduced from laborious and/or expensive active source geophysics or deep drilling. Despite challenging conditions such as minimal scattering and changing sources, we show that stacks of cross‐correlation functions of several hours of ambient seismic noise can converge towards Green's functions under favorable conditions. These contain the sought‐after information about subsurface seismic velocities and ice thickness. Applying this technique to two Alpine glaciers in Switzerland, we calculate signal‐to‐noise ratios of noise correlation functions. Faster Green's functions convergence during elevated ambient noise levels suggests that increased surface melt promotes spatially homogeneous excitation of noise sources. With the help of Green's functions amplitude asymmetry as well as standard beamforming, we locate dominant noise sources. In combination with spectrograms, glacier surface velocities from GPS and proglacial water discharge measurements, we find glacier noise in the range from 2 to 8 Hz to be a combination of tremor induced by flowing water, icequakes, and anthropogenic sources. We finally calculate dispersion curves from the cross‐correlation functions to arrive at an estimate of the ice thickness. In combination with H/V spectral ratios, the method shown here allows sampling the depth and the properties of the glacier bed by deploying only two seismometers for several hours. Ambient noise correlations could therefore be a valuable ingredient for studies of glacier and ice sheet beds.
Engineering polymer MEMS using combined microfluidic pervaporation and micro-molding
Authors: Thuau Damien , Laval Cédric , Dufour Isabelle , Poulin Philippe , Ayela Cédric , Salmon Jean-Baptiste 
Published: June 2018

AbstractIn view of the extensive increase of flexible devices and wearable electronics, the development of polymer micro-electro-mechanical systems (MEMS) is becoming more and more important since their potential to meet the multiple needs for sensing applications in flexible electronics is now clearly established. Nevertheless, polymer micromachining for MEMS applications is not yet as mature as its silicon counterpart, and innovative microfabrication techniques are still expected. We show in the present work an emerging and versatile microfabrication method to produce arbitrary organic, spatially resolved multilayer micro-structures, starting from dilute inks, and with possibly a large choice of materials. This approach consists in extending classical microfluidic pervaporation combined with MIcro-Molding In Capillaries. To illustrate the potential of this technique, bilayer polymer double-clamped resonators with integrated piezoresistive readout have been fabricated, characterized, and applied to humidity sensing. The present work opens new opportunities for the conception and integration of polymers in MEMS.
Footprints of parasitism in the genome of the parasitic flowering plant Cuscuta campestris
Authors: Vogel Alexander , Schwacke Rainer , Denton Alisandra K. , Usadel Björn , Hollmann Julien , Fischer Karsten , Bolger Anthony , Schmidt Maximilian H.-W. , Bolger Marie E. , Gundlach Heidrun , Mayer Klaus F. X. , Weiss-Schneeweiss Hanna , Temsch Eva M. , Krause Kirsten 
Published: June 2018

AbstractA parasitic lifestyle, where plants procure some or all of their nutrients from other living plants, has evolved independently in many dicotyledonous plant families and is a major threat for agriculture globally. Nevertheless, no genome sequence of a parasitic plant has been reported to date. Here we describe the genome sequence of the parasitic field dodder, Cuscuta campestris. The genome contains signatures of a fairly recent whole-genome duplication and lacks genes for pathways superfluous to a parasitic lifestyle. Specifically, genes needed for high photosynthetic activity are lost, explaining the low photosynthesis rates displayed by the parasite. Moreover, several genes involved in nutrient uptake processes from the soil are lost. On the other hand, evidence for horizontal gene transfer by way of genomic DNA integration from the parasite’s hosts is found. We conclude that the parasitic lifestyle has left characteristic footprints in the C. campestris genome.
FRET-enhanced photostability allows improved single-molecule tracking of proteins and protein complexes in live mammalian cells
Authors: Basu Srinjan , Needham Lisa-Maria , Lando David , Taylor Edward J. R. , Wohlfahrt Kai J. , Shah Devina , Boucher Wayne , Tan Yi Lei , Bates Lawrence E. , Tkachenko Olga , Cramard Julie , Lagerholm B. Christoffer , Eggeling Christian , Hendrich Brian , Klenerman Dave , Lee Steven F. , Laue Ernest D. 
Published: June 2018

AbstractA major challenge in single-molecule imaging is tracking the dynamics of proteins or complexes for long periods of time in the dense environments found in living cells. Here, we introduce the concept of using FRET to enhance the photophysical properties of photo-modulatable (PM) fluorophores commonly used in such studies. By developing novel single-molecule FRET pairs, consisting of a PM donor fluorophore (either mEos3.2 or PA-JF549) next to a photostable acceptor dye JF646, we demonstrate that FRET competes with normal photobleaching kinetic pathways to increase the photostability of both donor fluorophores. This effect was further enhanced using a triplet-state quencher. Our approach allows us to significantly improve single-molecule tracking of chromatin-binding proteins in live mammalian cells. In addition, it provides a novel way to track the localization and dynamics of protein complexes by labeling one protein with the PM donor and its interaction partner with the acceptor dye.
A model for super El Niños
Authors: Hameed Saji N. , Jin Dachao , Thilakan Vishnu 
Published: June 2018

AbstractSuper El Niños, the strongest and most powerful of El Niños, impact economies, societies, and ecosystems disproportionately. Despite their importance, we do not fully understand how super El Niños develop their intensity and unique characteristics. Here, combining observational analyses with simple numerical simulations, we suggest that eastern Pacific intensified super El Niños result from the interaction of an El Niño and a positive Indian Ocean Dipole. Further, we identify a self-limiting behavior inherent to El Niño Southern Oscillation (ENSO) dynamics. This behavior—a consequence of the atmospheric Kelvin wave response that develops to the east of ENSO's convective anomalies—dampens sea surface temperature (SST) variations in the eastern Pacific, thereby preventing super El Niños from developing through tropical Pacific dynamics alone. Our model explains the features of the large 1972, 1982, and 1997 El Niños; the large SST anomalies during the 2015 El Niño, however, were likely enhanced by strong decadal variability.
Efficient solar hydrogen generation in microgravity environment
Authors: Brinkert Katharina , Richter Matthias H. , Akay Ömer , Liedtke Janine , Giersig Michael , Fountaine Katherine T. , Lewerenz Hans-Joachim 
Published: June 2018

AbstractLong-term space missions require extra-terrestrial production of storable, renewable energy. Hydrogen is ascribed a crucial role for transportation, electrical power and oxygen generation. We demonstrate in a series of drop tower experiments that efficient direct hydrogen production can be realized photoelectrochemically in microgravity environment, providing an alternative route to existing life support technologies for space travel. The photoelectrochemical cell consists of an integrated catalyst-functionalized semiconductor system that generates hydrogen with current densities >15 mA/cm2 in the absence of buoyancy. Conditions are described adverting the resulting formation of ion transport blocking froth layers on the photoelectrodes. The current limiting factors were overcome by controlling the micro- and nanotopography of the Rh electrocatalyst using shadow nanosphere lithography. The behaviour of the applied system in terrestrial and microgravity environment is simulated using a kinetic transport model. Differences observed for varied catalyst topography are elucidated, enabling future photoelectrode designs for use in reduced gravity environments.
The origin and remolding of genomic islands of differentiation in the European sea bass
Authors: Duranton Maud , Allal François , Fraïsse Christelle , Bierne Nicolas , Bonhomme François , Gagnaire Pierre-Alexandre 
Published: June 2018

AbstractSpeciation is a complex process that leads to the progressive establishment of reproductive isolation barriers between diverging populations. Genome-wide comparisons between closely related species have revealed the existence of heterogeneous divergence patterns, dominated by genomic islands of increased divergence supposed to contain reproductive isolation loci. However, this divergence landscape only provides a static picture of the dynamic process of speciation, during which confounding mechanisms unrelated to speciation can interfere. Here we use haplotype-resolved whole-genome sequences to identify the mechanisms responsible for the formation of genomic islands between Atlantic and Mediterranean sea bass lineages. Local ancestry patterns show that genomic islands first emerged in allopatry through linked selection acting on a heterogeneous recombination landscape. Then, upon secondary contact, preexisting islands were strongly remolded by differential introgression, revealing variable fitness effects among regions involved in reproductive isolation. Interestingly, we find that divergent regions containing ancient polymorphisms conferred the strongest resistance to introgression.
Glutamic acid–valine–citrulline linkers ensure stability and efficacy of antibody–drug conjugates in mice
Authors: Anami Yasuaki , Yamazaki Chisato M. , Xiong Wei , Gui Xun , Zhang Ningyan , An Zhiqiang , Tsuchikama Kyoji 
Published: June 2018

AbstractValine–citrulline linkers are commonly used as enzymatically cleavable linkers for antibody–drug conjugates. While stable in human plasma, these linkers are unstable in mouse plasma due to susceptibility to an extracellular carboxylesterase. This instability often triggers premature release of drugs in mouse circulation, presenting a molecular design challenge. Here, we report that an antibody–drug conjugate with glutamic acid–valine–citrulline linkers is responsive to enzymatic drug release but undergoes almost no premature cleavage in mice. We demonstrate that this construct exhibits greater treatment efficacy in mouse tumor models than does a valine–citrulline-based variant. Notably, our antibody–drug conjugate contains long spacers facilitating the protease access to the linker moiety, indicating that our linker assures high in vivo stability despite a high degree of exposure. This technology could add flexibility to antibody–drug conjugate design and help minimize failure rates in pre-clinical studies caused by linker instability.
Mapping mesoscopic phase evolution during E-beam induced transformations via deep learning of atomically resolved images
Authors: Vasudevan Rama K. , Laanait Nouamane , Ferragut Erik M. , Wang Kai , Geohegan David B. , Xiao Kai , Ziatdinov Maxim , Jesse Stephen , Dyck Ondrej , Kalinin Sergei V. 
Published: June 2018

AbstractUnderstanding transformations under electron beam irradiation requires mapping the structural phases and their evolution in real time. To date, this has mostly been a manual endeavor comprising difficult frame-by-frame analysis that is simultaneously tedious and prone to error. Here, we turn toward the use of deep convolutional neural networks (DCNN) to automatically determine the Bravais lattice symmetry present in atomically resolved images. A DCNN is trained to identify the Bravais lattice class given a 2D fast Fourier transform of the input image. Monte-Carlo dropout is used for determining the prediction probability, and results are shown for both simulated and real atomically resolved images from scanning tunneling microscopy and scanning transmission electron microscopy. A reduced representation of the final layer output allows to visualize the separation of classes in the DCNN and agrees with physical intuition. We then apply the trained network to electron beam-induced transformations in WS2, which allows tracking and determination of growth rate of voids. We highlight two key aspects of these results: (1) it shows that DCNNs can be trained to recognize diffraction patterns, which is markedly different from the typical “real image” cases and (2) it provides a method with in-built uncertainty quantification, allowing the real-time analysis of phases present in atomically resolved images.
Learning hard quantum distributions with variational autoencoders
Authors: Rocchetto Andrea , Grant Edward , Strelchuk Sergii , Carleo Giuseppe , Severini Simone 
Published: June 2018

AbstractThe exact description of many-body quantum systems represents one of the major challenges in modern physics, because it requires an amount of computational resources that scales exponentially with the size of the system. Simulating the evolution of a state, or even storing its description, rapidly becomes intractable for exact classical algorithms. Recently, machine learning techniques, in the form of restricted Boltzmann machines, have been proposed as a way to efficiently represent certain quantum states with applications in state tomography and ground state estimation. Here, we introduce a practically usable deep architecture for representing and sampling from probability distributions of quantum states. Our representation is based on variational auto-encoders, a type of generative model in the form of a neural network. We show that this model is able to learn efficient representations of states that are easy to simulate classically and can compress states that are not classically tractable. Specifically, we consider the learnability of a class of quantum states introduced by Fefferman and Umans. Such states are provably hard to sample for classical computers, but not for quantum ones, under plausible computational complexity assumptions. The good level of compression achieved for hard states suggests these methods can be suitable for characterizing states of the size expected in first generation quantum hardware.
Co-protoporphyrin IX and Sn-protoporphyrin IX inactivate Zika, Chikungunya and other arboviruses by targeting the viral envelope
Authors: Neris Romulo L. S. , Figueiredo Camila M. , Higa Luiza M. , Araujo Daniel F. , Carvalho Carlos A. M. , Verçoza Brunno R. F. , Silva Mariana O. L. , Carneiro Fabiana A. , Tanuri Amilcar , Gomes Andre M. O. , Bozza Marcelo T. , Da Poian Andrea T. , Cruz-Oliveira Christine , Assunção-Miranda Iranaia 
Published: June 2018

AbstractThe global situation of diseases transmitted by arthropod-borne viruses such as Dengue (DENV), Yellow Fever (YFV), Chikungunya (CHIKV) and Zika (ZIKV) viruses is alarming and treatment of human infection by these arboviruses faces several challenges. The discovery of broad-spectrum antiviral molecules, able to inactivate different groups of viruses, is an interesting approach. The viral envelope is a common structure among arboviruses, being a potential target for antivirals. Porphyrins are amphipathic molecules able to interact with membranes and absorb light, being widely used in photodynamic therapy. Previously, we showed that heme, Co-protoporphyrin IX (CoPPIX) and Sn-protoporphyrin IX (SnPPIX) directly inactivate DENV and YFV infectious particles. Here we demonstrate that the antiviral activity of these porphyrins can be broadened to CHIKV, ZIKV, Mayaro virus, Sindbis virus and Vesicular Stomatitis virus. Porphyrin treatment causes viral envelope protein loss, affecting viral morphology, adsorption and entry into target cells. Also, light-stimulation enhanced the SnPPIX activity against all tested arboviruses. In summary, CoPPIX and SnPPIX were shown to be efficient broad-spectrum compounds to inactivate medically and veterinary important viruses.
Instability of personal human metabotype is linked to all-cause mortality
Authors: Lacruz M. E. , Kluttig A. , Tiller D. , Medenwald D. , Giegling I. , Rujescu D. , Prehn C. , Adamski J. , Greiser K. H. , Kastenmüller G. 
Published: June 2018

AbstractDisruption of metabolic homeostasis is an important factor in many diseases. Various metabolites have been linked to higher risk of morbidity and all-cause mortality using metabolomics in large population-based cohorts. In these studies, baseline metabolite levels were compared across subjects to identify associations with health outcomes, implying the existence of ‘healthy’ concentration ranges that are equally applicable to all individuals. Here, we focused on intra-individual changes in metabolite levels over time and their link to mortality, potentially allowing more personalized risk assessment. We analysed targeted metabolomics data for 134 blood metabolites from 1409 participants in the population-based CARLA cohort at baseline and after four years. Metabotypes of the majority of participants (59%) were extremely stable over time indicated by high correlation between the subjects’ metabolite profiles at the two time points. Metabotype instability and, in particular, decrease of valine were associated with higher risk of all-cause mortality in 7.9 years of follow-up (hazard ratio (HR) = 1.5(95%CI = 1.0–2.3) and 0.2(95%CI = 0.1–0.3)) after multifactorial adjustment. Excluding deaths that occurred in the first year after metabolite profiling showed similar results (HR = 1.8(95%CI = 1.1–2.8)). Lower metabotype stability was also associated with incident cardiovascular disease (OR = 1.2(95%CI = 1.0–1.3)). Therefore, changes in the personal metabotype might be a valuable indicator of pre-clinical disease.
SFTA3 – a novel surfactant protein of the ocular surface and its role in corneal wound healing and tear film surface tension
Authors: Schicht Martin , Garreis Fabian , Hartjen Nadine , Beileke Stephanie , Jacobi Christina , Sahin Afsun , Holland Detlef , Schröder Henrik , Hammer Christian M. , Paulsen Friedrich , Bräuer Lars 
Published: June 2018

AbstractThe study aimed to characterize the expression and function of SFTA3 at the ocular surface and in tears. Ocular tissues, conjunctival (HCjE) and human corneal (HCE) epithelial cell lines as well as tearfilm of patients suffering from different forms of dry eye disease (DED) were analyzed by means of RT-PCR, western blot, immunohistochemistry, and ELISA. A possible role of recombinant SFTA3 in corneal wound healing was investigated performing in vitro scratch assays. Tear film regulatory properties were analyzed with the spinning drop method and the regulation of SFTA3 transcripts was studied in HCE and HCjE after incubation with proinflammatory cytokines as well as typical ocular pathogens by real-time RT-PCR and ELISA. The results reveal that human ocular tissue as well as tears of healthy volunteers express SFTA3 whereas tears from patients with DED showed significantly increased SFTA3 levels. In vitro wounding of HCE cell cultures that had been treated with recombinant SFTA3 demonstrated a significantly increased wound closure rate and rSFTA3 reduced the surface tension of tear fluid. The results indicate that SFTA3 at the ocular surface seemed to be involved in wound healing and the reduction of surface tension.
Increased food supply mitigates ocean acidification effects on calcification but exacerbates effects on growth
Authors: Brown Norah E. M. , Bernhardt Joey R. , Anderson Kathryn M. , Harley Christopher D. G. 
Published: June 2018

AbstractBecause many of the negative effects of ocean acidification on marine life may result from underlying energetic short-falls associated with increased metabolic demands, several studies have hypothesized that negative responses to high CO2 could be reduced by energy input. Although this hypothesis was supported by a recent meta-analysis, we believe that the meta-analytic calculation used was not appropriate to test the stated hypothesis. Here, we first clarify the hypothesis put forward, the crux being that the effects of increased food supply and CO2 interact statistically. We then test this hypothesis by examining the available data in a more appropriate analytical framework. Using factorial meta-analysis, we confirm that food addition has a positive effect and CO2 has a negative effect on both growth and calcification. For calcification, food addition did indeed reduce CO2 impacts. Surprisingly, however, we found that food addition actually exacerbated the effects of acidification on growth, perhaps due to increased scope upon which CO2 effects can act in food-replete situations. These interactive effects were undetectable using a multilevel meta-analytic approach. Ongoing changes in food supply and carbonate chemistry, coupled with under-described, poorly understood, and potentially surprising interactive outcomes for these two variables, suggest that the role of food should remain a priority in ocean acidification research.Arising from: L. Ramajo et al., Sci. Rep. 6: 19374 (2016).
GTP-binding facilitates EB1 recruitment onto microtubules by relieving its auto-inhibition
Authors: Gireesh K. K. , Shine A. , Lakshmi R. Bhagya , Vijayan Vinesh , Manna Tapas K. 
Published: June 2018

AbstractMicrotubule plus end-binding protein, EB1 is a key regulator of microtubule dynamics. Auto-inhibitory interaction in EB1 has previously been shown to inhibit its ability to bind to microtubules and regulate microtubule dynamics. However, the factors that promote its microtubule regulatory activity by over-coming the auto-inhibition are less known. Here, we show that GTP plays a critical role in promoting the microtubule-targeting activity of EB1 by suppressing its auto-inhibition. Our biophysical data demonstrate that GTP binds to EB1 at a distinct site in its conserved N-terminal domain. Detailed analyses reveal that GTP-binding suppresses the intra-molecular inhibitory interaction between the globular N-terminus and the C-terminal coiled-coil domain. We further show that mutation of the GTP-binding site residues in N-terminus weakens the affinity for GTP, but also for the C-terminus, indicating overlapping binding sites. Confocal imaging and biochemical analysis reveal that EB1 localization on the microtubules is significantly increased upon mutations of the GTP-binding site residues. The results demonstrate a unique role of GTP in facilitating EB1 interaction with the microtubules by relieving its intra-molecular inhibition. They also implicate that GTP-binding may regulate the functions of EB1 on the cellular microtubules.