bluuebunny/crossref_metadata_2025_split huggingface dataset:
Measurements of the Vorticity in the Bursty Bulk Flows
Authors: Zhang L.Q. , Baumjohann W. , Dai L. , Khotyaintsev Yu V. , Wang C. 
Published: September 2019

AbstractCurlometer analysis from 4‐point Magnetospheric Multiscale spacecraft measurements is applied to obtain the vorticity (ω) in the bursty bulk flow (BBF) from tail reconnection. Increases of the vorticity is associated with enhancements of the high‐energy ion flux (above 10 keV) and the flow speed during the BBF. Finger‐like structure, consisting of the lower‐energy ions below 10 keV, occurs mainly during intervals of small vorticity. The vorticity during BBF consistently shows a dominant −Z Geocentric solar magnetospheric (GSM) component, indicating clockwise vortexes in the flows. Combined with bipolar signals of Vy‐geocentric solar magnetic, the Magnetospheric Multiscale observations provide evidence for flow eddies in the BBF. Power spectral analysis suggests existence of kinetic Alfvénic wave emissions, in addition to the flow eddy, in the high‐frequency regime in the BBF turbulence.
An Objective and Efficient Method for Assessing the Impact of Reduced‐Precision Calculations On Solution Correctness
Authors: Zhang Shixuan , Wan Hui , Rasch Philip J. , Singh Balwinder , Larson Vincent E. , Woodward Carol S. 
Published: September 2019

AbstractRecent studies have shown that reducing the precision of floating‐point calculations in an atmospheric model can improve the model's computational performance without affecting model fidelity, but code changes are needed to accommodate lower precision or to prevent undue round‐off error. For complex and computationally expensive systems like the Energy Exascale Earth System Model, a method is needed to objectively and efficiently assess the quality of the lower‐precision simulations and to quickly identify problematic code pieces. This paper demonstrates that the accuracy of the computed solution can be evaluated through a simple and quantitative error metric based on time step convergence. The proposed test method can unambiguously detect the accumulation of precision error and objectively assess its impact on solution accuracy. Furthermore, since fast physical processes are known to affect key features of the multiyear mean climate in atmospheric models, we show that the convergence test applied to short simulations can provide useful information about the impact of reduced precision on a model's long‐term behavior. In contrast, the traditional method of climate model evaluation requires multiple years of simulations and involves inspecting many physical quantities for statistical significance in the presence of natural variability. The simplicity, computational efficiency, and objectivity of the proposed method makes it very attractive for high‐resolution model development. The method is also expected to be applicable to other models that numerically solve time evolution equations.
Emerging role of machine learning in light-matter interaction
Authors: Zhou Jiajia , Huang Bolong , Yan Zheng , Bünzli Jean-Claude G. 
Published: September 2019

AbstractMachine learning has provided a huge wave of innovation in multiple fields, including computer vision, medical diagnosis, life sciences, molecular design, and instrumental development. This perspective focuses on the implementation of machine learning in dealing with light-matter interaction, which governs those fields involving materials discovery, optical characterizations, and photonics technologies. We highlight the role of machine learning in accelerating technology development and boosting scientific innovation in the aforementioned aspects. We provide future directions for advanced computing techniques via multidisciplinary efforts that can help to transform optical materials into imaging probes, information carriers and photonics devices.
Deep learning in holography and coherent imaging
Authors: Rivenson Yair , Wu Yichen , Ozcan Aydogan 
Published: September 2019

AbstractRecent advances in deep learning have given rise to a new paradigm of holographic image reconstruction and phase recovery techniques with real-time performance. Through data-driven approaches, these emerging techniques have overcome some of the challenges associated with existing holographic image reconstruction methods while also minimizing the hardware requirements of holography. These recent advances open up a myriad of new opportunities for the use of coherent imaging systems in biomedical and engineering research and related applications.
ATF6 regulates the development of chronic pancreatitis by inducing p53-mediated apoptosis
Authors: Zhou Lei , Tan Jie-hui , Cao Rong-chang , Xu Jia , Chen Xue-mei , Qi Zhao-chang , Zhou Su-ying , Li Su-bing , Mo Qi-xin , Li Zhi-wei , Zhang Guo-wei 
Published: September 2019

AbstractChronic pancreatitis (CP) is a progressive, recurrent inflammatory disorder of the pancreas. Initiation and progression of CP can result from serine protease 1 (PRSS1) overaccumulation and the ensuing endoplasmic reticulum (ER) stress. However, how ER stress pathways regulate the development and progression of CP remains poorly understood. In the present study we aimed to elucidate the ER stress pathway involved in CP. We found high expression of the ER stress marker genes ATF6, XBP1, and CHOP in human clinical specimens. A humanized PRSS1 transgenic mouse was established and treated with caerulein to mimic the development of CP, as evidenced by pathogenic alterations, collagen deposition, and increased expression of the inflammatory factors IL-6, IL-1β, and TNF-α. ATF6, XBP1, and CHOP expression levels were also increased during CP development in this model. Acinar cell apoptosis was also significantly increased, accompanied by upregulated p53 expression. Inhibition of ATF6 or p53 suppressed the expression of inflammatory factors and progression of CP in the mouse model. Finally, we showed that p53 expression could be regulated by the ATF6/XBP1/CHOP axis to promote the development of CP. We therefore conclude that ATF6 signalling regulates CP progression by modulating pancreatic acinar cell apoptosis, which provides a target for ER stress-based diagnosis and treatment of CP.
Calcium-signaling proteins mediate the plant transcriptomic response during a well-established Xanthomonas campestris pv. campestris infection
Authors: Tortosa Maria , Cartea Maria E. , Velasco Pablo , Soengas Pilar , Rodriguez Victor M. 
Published: September 2019

Abstract
The plant immune system is divided into two branches; one branch is based on the recognition of pathogen-associated molecular patterns (PAMP-triggered immunity), and the other relies on pathogenic effector detection (effector-triggered immunity). Despite each branch being involved in different complex mechanisms, both lead to transcription reprogramming and, thus, changes in plant metabolism. To study the defense mechanisms involved in the Brassica oleracea–Xanthomonas campestris pv. campestris (Xcc) interaction, we analyzed the plant transcriptome dynamics at 3 and 12 days postinoculation (dpi) by using massive analysis of 3′-cDNA ends. We identified more induced than repressed transcripts at both 3 and 12 dpi, although the response was greater at 12 dpi. Changes in the expression of genes related to the early infection stages were only detected at 12 dpi, suggesting that the timing of triggered defenses is crucial to plant survival. qPCR analyses in susceptible and resistant plants allowed us to highlight the potential role of two calcium-signaling proteins, CBP60g and SARD1, in the resistance against Xcc. This role was subsequently confirmed using Arabidopsis knockout mutants.
Different brain networks mediate the effects of social and conditioned expectations on pain
Authors: Koban Leonie , Jepma Marieke , López-Solà Marina , Wager Tor D. 
Published: September 2019

AbstractInformation about others’ experiences can strongly influence our own feelings and decisions. But how does such social information affect the neural generation of affective experience, and are the brain mechanisms involved distinct from those that mediate other types of expectation effects? Here, we used fMRI to dissociate the brain mediators of social influence and associative learning effects on pain. Participants viewed symbolic depictions of other participants’ pain ratings (social information) and classically conditioned pain-predictive cues before experiencing painful heat. Social information and conditioned stimuli each had significant effects on pain ratings, and both effects were mediated by self-reported expectations. Yet, these effects were mediated by largely separable brain activity patterns, involving different large-scale functional networks. These results show that learned versus socially instructed expectations modulate pain via partially different mechanisms—a distinction that should be accounted for by theories of predictive coding and related top-down influences.
Gene-diet interactions associated with complex trait variation in an advanced intercross outbred mouse line
Authors: Vorobyev Artem , Gupta Yask , Sezin Tanya , Koga Hiroshi , Bartsch Yannic C. , Belheouane Meriem , Künzel Sven , Sina Christian , Schilf Paul , Körber-Ahrens Heiko , Beltsiou Foteini , Lara Ernst Anna , Khil’chenko Stanislav , Al-Aasam Hassanin , Manz Rudolf A. , Diehl Sandra , Steinhaus Moritz , Jascholt Joanna , Kouki Phillip , Boehncke Wolf-Henning , Mayadas Tanya N. , Zillikens Detlef , Sadik Christian D. , Nishi Hiroshi , Ehlers Marc , Möller Steffen , Bieber Katja , Baines John F. , Ibrahim Saleh M. , Ludwig Ralf J. 
Published: September 2019

AbstractPhenotypic variation of quantitative traits is orchestrated by a complex interplay between the environment (e.g. diet) and genetics. However, the impact of gene-environment interactions on phenotypic traits mostly remains elusive. To address this, we feed 1154 mice of an autoimmunity-prone intercross line (AIL) three different diets. We find that diet substantially contributes to the variability of complex traits and unmasks additional genetic susceptibility quantitative trait loci (QTL). By performing whole-genome sequencing of the AIL founder strains, we resolve these QTLs to few or single candidate genes. To address whether diet can also modulate genetic predisposition towards a given trait, we set NZM2410/J mice on similar dietary regimens as AIL mice. Our data suggest that diet modifies genetic susceptibility to lupus and shifts intestinal bacterial and fungal community composition, which precedes clinical disease manifestation. Collectively, our study underlines the importance of including environmental factors in genetic association studies.
The CONSTANS flowering complex controls the protective response of photosynthesis in the green alga Chlamydomonas
Authors: Tokutsu Ryutaro , Fujimura-Kamada Konomi , Matsuo Takuya , Yamasaki Tomohito , Minagawa Jun 
Published: September 2019

AbstractLight is essential for photosynthesis, but the amounts of light that exceed an organism’s assimilation capacity can result in oxidative stress and even cell death. Plants and microalgae have developed a photoprotective response mechanism, qE, that dissipates excess light energy as thermal energy. In the green alga Chlamydomonas reinhardtii, qE is regulated by light-inducible photoprotective proteins, but the pathway from light perception to qE is not fully understood. Here, we show that the transcription factors CONSTANS and Nuclear transcription Factor Ys (NF-Ys) form a complex that governs light-dependent photoprotective responses in C. reinhardtii. The qE responses do not occur in CONSTANS or NF-Y mutants. The signal from light perception to the CONSTANS/NF-Ys complex is directly inhibited by the SPA1/COP1-dependent E3 ubiquitin ligase. This negative regulation mediated by the E3 ubiquitin ligase and the CONSTANS/NF-Ys complex is common to photoprotective response in algal photosynthesis and flowering in plants.
A GABAergic and peptidergic sleep neuron as a locomotion stop neuron with compartmentalized Ca2+ dynamics
Authors: Steuer Costa Wagner , Van der Auwera Petrus , Glock Caspar , Liewald Jana F. , Bach Maximilian , Schüler Christina , Wabnig Sebastian , Oranth Alexandra , Masurat Florentin , Bringmann Henrik , Schoofs Liliane , Stelzer Ernst H. K. , Fischer Sabine C. , Gottschalk Alexander 
Published: September 2019

AbstractAnimals must slow or halt locomotion to integrate sensory inputs or to change direction. In Caenorhabditis elegans, the GABAergic and peptidergic neuron RIS mediates developmentally timed quiescence. Here, we show RIS functions additionally as a locomotion stop neuron. RIS optogenetic stimulation caused acute and persistent inhibition of locomotion and pharyngeal pumping, phenotypes requiring FLP-11 neuropeptides and GABA. RIS photoactivation allows the animal to maintain its body posture by sustaining muscle tone, yet inactivating motor neuron oscillatory activity. During locomotion, RIS axonal Ca2+ signals revealed functional compartmentalization: Activity in the nerve ring process correlated with locomotion stop, while activity in a branch correlated with induced reversals. GABA was required to induce, and FLP-11 neuropeptides were required to sustain locomotion stop. RIS attenuates neuronal activity and inhibits movement, possibly enabling sensory integration and decision making, and exemplifies dual use of one cell across development in a compact nervous system.
Broadband on-chip single-photon spectrometer
Authors: Cheng Risheng , Zou Chang-Ling , Guo Xiang , Wang Sihao , Han Xu , Tang Hong X. 
Published: September 2019

AbstractSingle-photon counters are single-pixel binary devices that click upon the absorption of a photon but obscure its spectral information, whereas resolving the color of detected photons has been in critical demand for frontier astronomical observation, spectroscopic imaging and wavelength division multiplexed quantum communications. Current implementations of single-photon spectrometers either consist of bulky wavelength-scanning components or have limited detection channels, preventing parallel detection of broadband single photons with high spectral resolutions. Here, we present the first broadband chip-scale single-photon spectrometer covering both visible and infrared wavebands spanning from 600 nm to 2000 nm. The spectrometer integrates an on-chip dispersive echelle grating with a single-element propagating superconducting nanowire detector of ultraslow-velocity for mapping the dispersed photons with high spatial resolutions. The demonstrated on-chip single-photon spectrometer features small device footprint, high robustness with no moving parts and meanwhile offers more than 200 equivalent wavelength detection channels with further scalability.
Biphoton shaping with cascaded entangled-photon sources
Authors: Riazi Arash , Chen Changjia , Zhu Eric Y. , Gladyshev Alexey V. , Kazansky Peter G. , Sipe J. E. , Qian Li 
Published: September 2019

AbstractQuantum entanglement is an integral part of quantum optics and has been exploited in areas such as computation, cryptography and metrology. The entanglement between photons can be present in various degrees of freedom (DOFs), and even the simplest bi-partite systems can occupy a large Hilbert space. Therefore, it is desirable to exploit this multi-dimensional space for various quantum applications by fully controlling the properties of the entangled photons in multiple DOFs. While current entangled-photon sources are capable of generating entanglement in one or more DOFs, there is currently a lack of practical techniques that can shape and control the entanglement properties in multiple DOFs. Here we show that cascading two or more entangled-photon sources with tunable linear media in between allows us to generate photon-pairs whose entanglement properties can be tailored and shaped in the frequency and polarisation domains. We first develop a quantum mechanical model to study the quantum state generated from the cascade structure with special considerations paid to the effects of pump temporal coherence, linear dispersion, and in-structure polarisation transformation applied between the entangled-photon sources. We then experimentally generate photon-pairs with tunable entanglement properties by manipulating the dispersion and birefringence properties of the linear medium placed in between two entangled-photon sources. This is done in an all-fibre, phase stable, and alignment-free configuration. Our results show that the cascade structure offers a great deal of flexibility in tuning the properties of entangled photons in multiple DOFs, opening up a new avenue in engineering quantum light sources.
Nodeless superconductivity and its evolution with pressure in the layered dirac semimetal 2M-WS2
Authors: Guguchia Zurab , Gawryluk Dariusz J. , Brzezinska Marta , Tsirkin Stepan S. , Khasanov Rustem , Pomjakushina Ekaterina , von Rohr Fabian O. , Verezhak Joel A. T. , Hasan M. Zahid , Neupert Titus , Luetkens Hubertus , Amato Alex 
Published: September 2019

AbstractRecently, the transition metal dichalcogenide (TMD) system 2M-WS2 has been identified as a Dirac semimetal exhibiting both superconductivity with the highest Tc ~ 8.5 K among all the TMD materials and topological surface states. Here we report on muon spin rotation (μSR) and density functional theory studies of microscopic SC properties and the electronic structure in 2M-WS2 at ambient and under hydrostatic pressures (pmax = 1.9 GPa). The SC order parameter in 2M-WS2 is determined to have single-gap s-wave symmetry. We further show a strong negative pressure effect on Tc and on the SC gap Δ. This may be partly caused by the pressure induced reduction of the size of the electron pocket around the Γ-point. We also find that the superfluid density ns is weakly affected by pressure. The absence of a strong pressure effect on ns and the absence of a correlation between ns and Tc in 2M-WS2, in contrast to the other SC TMDs Td-MoTe2 and 2H-NbSe2, is explained in terms of its location in the optimal (ambient pressure) and above the optimal (under pressure) superconducting regions of the phase diagram and its large distance to the other possible competing or cooperating orders.
Biological surface properties in extracellular vesicles and their effect on cargo proteins
Authors: Santucci Laura , Bruschi Maurizio , Del Zotto Genny , Antonini Francesca , Ghiggeri Gian Marco , Panfoli Isabella , Candiano Giovanni 
Published: September 2019

AbstractUltracentrifugationon sucrose density gradientappears to be the best purification protocol for extracellular vesicle (EVs) purification. After this step, to reduce disulfide bridges linking exogenous proteins to the vesicles, the collected samples are routinely washed and treated with dithiothreitol (DTT). Such incubations are performed at temperatures ranging from room temperature up to 95 °C, with either Tris or PBS as buffers. We re-investigated these steps on both exosomes and microvesicles purified from blood (serum) and urine by electrophoretic separation, silver staining and western blots analysis. Data confirm that an extra centrifugation on a sucrose cushion can effectively eliminate contaminants. Tris buffer (50 Mm) and β-mercaptoethanol as a reducing agent at room temperature dramatically improved either sample cleaning. By contrast, especially for exosomes PBS buffer and DTT, above 37 °C, caused massive protein aggregations, yielding blurred SDS-PAGE gels in both samples. Immuno-blot analyses demonstrated that in PBS-DTT contamination with albumin (in serum) or with uromodulin (in urine) occurs. DTT, likely due to its two–SH groups, might form scrambled SS-bonds promoting EVs interaction with environmental macromolecules via disulphide bridges. Therefore, to obtain maximum vesicle purity for biomarker investigations and to maximize both presence of EVs proteins and their accessibility, use of DTT is not recommended.
A Prediction Model with Lifestyle in Addition to Previously Known Risk Factors Improves Its Predictive Ability for Cardiovascular Death
Authors: Nishimoto Masatoshi , Tagawa Miho , Matsui Masaru , Eriguchi Masahiro , Samejima Ken-ichi , Iseki Kunitoshi , Iseki Chiho , Asahi Koichi , Yamagata Kunihiro , Konta Tsuneo , Fujimoto Shouichi , Narita Ichiei , Kasahara Masato , Shibagaki Yugo , Moriyama Toshiki , Kondo Masahide , Watanabe Tsuyoshi , Tsuruya Kazuhiko 
Published: September 2019

AbstractThis longitudinal cohort study aimed to create a novel prediction model for cardiovascular death with lifestyle factors. Subjects aged 40–74 years in the Japanese nationwide Specific Health Checkup Database in 2008 were included. Subjects were randomly assigned to the derivation and validation cohorts by a 2:1 ratio. Points for the prediction model were determined using regression coefficients that were derived from the Cox proportional hazards model in the derivation cohort. Models 1 and 2 were developed using known risk factors and known factors with lifestyle factors, respectively. The models were validated by comparing Kaplan-Meier curves between the derivation and validation cohorts, and by calibration plots in the validation cohort. Among 295,297 subjects, data for 120,823 were available. There were 310 cardiovascular deaths during a mean follow-up of 3.6 years. Model 1 included known risk factors. In model 2, weight gain, exercise habit, gait speed, and drinking alcohol were additionally included as protective factors. Kaplan-Meier curves matched better between the derivation and validation cohorts in model 2, and model 2 was better calibrated. In conclusion, our prediction model with lifestyle factors improved the predictive ability for cardiovascular death.
Localized microwave-heating (LMH) of basalt – Lava, dusty-plasma, and ball-lightning ejection by a “miniature volcano”
Authors: Jerby Eli , Shoshani Yoav 
Published: September 2019

AbstractThis paper presents various phenomena obtained by localized microwave-heating (LMH) of basalt, including effects of inner core melting, lava eruption and flow (from the molten core outside), plasma ejection from basalt (in forms of fire-column and ball-lightning), and effusion of dust (deposited as powder by the plasma). The experiments are conducted by irradiating a basalt stone (~30-cm3 volume, either naturally shaped or cut to a cubic brick) in a microwave cavity, fed by an adaptively-matched magnetron (~1 kW at 2.45 GHz). Effects of LMH and thermal-runaway instability in basalt are observed and compared to theory. Various in- and ex-situ diagnostics are used in order to characterize the dusty-plasma observed and its nanoparticle products. The resemblance of the experimental phenomena obtained in small laboratory scale to gigantic volcanic phenomena in nature is noticed, and its potential relevance to further volcanic studies is discussed. In particular, we show that LMH could be instrumental for laboratory demonstrations and simulations of miniature-volcano effects, such as lava flows, formation of volcanic glass (obsidian), eruption of dusty-plasma and volcanic ash, and ejection of ball lightning. These findings might be significant as well for various applications, such as drilling and mining, microwave-induced breakdown spectroscopy (MIBS), mineral extraction, and powder production directly from basalts.