bluuebunny/crossref_metadata_2025_split huggingface dataset:
PI3KC2α-dependent and VPS34-independent generation of PI3P controls primary cilium-mediated autophagy in response to shear stress
Authors: Boukhalfa Asma , Nascimbeni Anna Chiara , Ramel Damien , Dupont Nicolas , Hirsch Emilio , Gayral Stephanie , Laffargue Muriel , Codogno Patrice , Morel Etienne 
Published: January 2020

AbstractCells subjected to stress situations mobilize specific membranes and proteins to initiate autophagy. Phosphatidylinositol-3-phosphate (PI3P), a crucial lipid in membrane dynamics, is known to be essential in this context. In addition to nutriments deprivation, autophagy is also triggered by fluid-flow induced shear stress in epithelial cells, and this specific autophagic response depends on primary cilium (PC) signaling and leads to cell size regulation. Here we report that PI3KC2α, required for ciliogenesis and PC functions, promotes the synthesis of a local pool of PI3P upon shear stress. We show that PI3KC2α depletion in cells subjected to shear stress abolishes ciliogenesis as well as the autophagy and related cell size regulation. We finally show that PI3KC2α and VPS34, the two main enzymes responsible for PI3P synthesis, have different roles during autophagy, depending on the type of cellular stress: while VPS34 is clearly required for starvation-induced autophagy, PI3KC2α participates only in shear stress-dependent autophagy.
Acquisition, transmission and strain diversity of human gut-colonizing crAss-like phages
Authors: Siranosian Benjamin A. , Tamburini Fiona B. , Sherlock Gavin , Bhatt Ami S. 
Published: January 2020

AbstractCrAss-like phages are double-stranded DNA viruses that are prevalent in human gut microbiomes. Here, we analyze gut metagenomic data from mother-infant pairs and patients undergoing fecal microbiota transplantation to evaluate the patterns of acquisition, transmission and strain diversity of crAss-like phages. We find that crAss-like phages are rarely detected at birth but are increasingly prevalent in the infant microbiome after one month of life. We observe nearly identical genomes in 50% of cases where the same crAss-like clade is detected in both the mother and the infant, suggesting vertical transmission. In cases of putative transmission of prototypical crAssphage (p-crAssphage), we find that a subset of strains present in the mother are detected in the infant, and that strain diversity in infants increases with time. Putative tail fiber proteins are enriched for nonsynonymous strain variation compared to other genes, suggesting a potential evolutionary benefit to maintaining strain diversity in specific genes. Finally, we show that p-crAssphage can be acquired through fecal microbiota transplantation.
Herpes simplex virus blocks host transcription termination via the bimodal activities of ICP27
Authors: Wang Xiuye , Hennig Thomas , Whisnant Adam W. , Erhard Florian , Prusty Bhupesh K. , Friedel Caroline C. , Forouzmand Elmira , Hu William , Erber Luke , Chen Yue , Sandri-Goldin Rozanne M. , Dölken Lars , Shi Yongsheng 
Published: January 2020

AbstractInfection by viruses, including herpes simplex virus-1 (HSV-1), and cellular stresses cause widespread disruption of transcription termination (DoTT) of RNA polymerase II (RNAPII) in host genes. However, the underlying mechanisms remain unclear. Here, we demonstrate that the HSV-1 immediate early protein ICP27 induces DoTT by directly binding to the essential mRNA 3’ processing factor CPSF. It thereby induces the assembly of a dead-end 3’ processing complex, blocking mRNA 3’ cleavage. Remarkably, ICP27 also acts as a sequence-dependent activator of mRNA 3’ processing for viral and a subset of host transcripts. Our results unravel a bimodal activity of ICP27 that plays a key role in HSV-1-induced host shutoff and identify CPSF as an important factor that mediates regulation of transcription termination. These findings have broad implications for understanding the regulation of transcription termination by other viruses, cellular stress and cancer.
Anti-BCMA chimeric antigen receptors with fully human heavy-chain-only antigen recognition domains
Authors: Lam Norris , Trinklein Nathan D. , Buelow Benjamin , Patterson George H. , Ojha Namrata , Kochenderfer James N. 
Published: January 2020

AbstractChimeric antigen receptor (CAR)-expressing T cells targeting B-cell maturation antigen (BCMA) have activity against multiple myeloma, but improvements in anti-BCMA CARs are needed. We demonstrated recipient anti-CAR T-cell responses against a murine single-chain variable fragment (scFv) used clinically in anti-BCMA CARs. To bypass potential anti-CAR immunogenicity and to reduce CAR binding domain size, here we designed CARs with antigen-recognition domains consisting of only a fully human heavy-chain variable domain without a light-chain domain. A CAR designated FHVH33-CD8BBZ contains a fully human heavy-chain variable domain (FHVH) plus 4-1BB and CD3ζ domains. T cells expressing FHVH33-CD8BBZ exhibit similar cytokine release, degranulation, and mouse tumor eradication as a CAR that is identical except for substitution of a scFv for FHVH33. Inclusion of 4-1BB is critical for reducing activation-induced cell death and promoting survival of T cells expressing FHVH33-containing CARs. Our results indicate that heavy-chain-only anti-BCMA CARs are suitable for evaluation in a clinical trial.
Tree species traits affect which natural enemies drive the Janzen-Connell effect in a temperate forest
Authors: Jia Shihong , Wang Xugao , Yuan Zuoqiang , Lin Fei , Ye Ji , Lin Guigang , Hao Zhanqing , Bagchi Robert 
Published: January 2020

AbstractA prominent tree species coexistence mechanism suggests host-specific natural enemies inhibit seedling recruitment at high conspecific density (negative conspecific density dependence). Natural-enemy-mediated conspecific density dependence affects numerous tree populations, but its strength varies substantially among species. Understanding how conspecific density dependence varies with species’ traits and influences the dynamics of whole communities remains a challenge. Using a three-year manipulative community-scale experiment in a temperate forest, we show that plant-associated fungi, and to a lesser extent insect herbivores, reduce seedling recruitment and survival at high adult conspecific density. Plant-associated fungi are primarily responsible for reducing seedling recruitment near conspecific adults in ectomycorrhizal and shade-tolerant species. Insects, in contrast, primarily inhibit seedling recruitment of shade-intolerant species near conspecific adults. Our results suggest that natural enemies drive conspecific density dependence in this temperate forest and that which natural enemies are responsible depends on the mycorrhizal association and shade tolerance of tree species.
Mechanical sensing protein PIEZO1 regulates bone homeostasis via osteoblast-osteoclast crosstalk
Authors: Wang Lijun , You Xiuling , Lotinun Sutada , Zhang Lingli , Wu Nan , Zou Weiguo 
Published: January 2020

AbstractWolff’s law and the Utah Paradigm of skeletal physiology state that bone architecture adapts to mechanical loads. These models predict the existence of a mechanostat that links strain induced by mechanical forces to skeletal remodeling. However, how the mechanostat influences bone remodeling remains elusive. Here, we find that Piezo1 deficiency in osteoblastic cells leads to loss of bone mass and spontaneous fractures with increased bone resorption. Furthermore, Piezo1-deficient mice are resistant to further bone loss and bone resorption induced by hind limb unloading, demonstrating that PIEZO1 can affect osteoblast-osteoclast crosstalk in response to mechanical forces. At the mechanistic level, in response to mechanical loads, PIEZO1 in osteoblastic cells controls the YAP-dependent expression of type II and IX collagens. In turn, these collagen isoforms regulate osteoclast differentiation. Taken together, our data identify PIEZO1 as the major skeletal mechanosensor that tunes bone homeostasis.
Strategy to control magnetic coercivity by elucidating crystallization pathway-dependent microstructural evolution of magnetite mesocrystals
Authors: Park Bum Chul , Cho Jiung , Kim Myeong Soo , Ko Min Jun , Pan Lijun , Na Jin Yeong , Kim Young Keun 
Published: January 2020

AbstractMesocrystals are assemblies of smaller crystallites and have attracted attention because of their nonclassical crystallization pathway and emerging collective functionalities. Understanding the mesocrystal crystallization mechanism in chemical routes is essential for precise control of size and microstructure, which influence the function of mesocrystals. However, microstructure evolution from the nucleus stage through various crystallization pathways remains unclear. We propose a unified model on the basis of the observation of two crystallization pathways, with different ferric (oxyhydr)oxide polymorphs appearing as intermediates, producing microstructures of magnetite mesocrystal via different mechanisms. An understanding of the crystallization mechanism enables independent chemical control of the mesocrystal diameter and crystallite size, as manifested by a series of magnetic coercivity measurements. We successfully implement an experimental model system that exhibits a universal crystallite size effect on the magnetic coercivity of mesocrystals. These findings provide a general approach to controlling the microstructure through crystallization pathway selection, thus providing a strategy for controlling magnetic coercivity in magnetite systems.
Nanoelectrode design from microminiaturized honeycomb monolith with ultrathin and stiff nanoscaffold for high-energy micro-supercapacitors
Authors: Lei Zhendong , Liu Long , Zhao Huaping , Liang Feng , Chang Shilei , Li Lei , Zhang Yong , Lin Zhan , Kröger Jörg , Lei Yong 
Published: January 2020

AbstractDownsizing the cell size of honeycomb monoliths to nanoscale would offer high freedom of nanostructure design beyond their capability for broad applications in different fields. However, the microminiaturization of honeycomb monoliths remains a challenge. Here, we report the fabrication of microminiaturized honeycomb monoliths—honeycomb alumina nanoscaffold—and thus as a robust nanostructuring platform to assemble active materials for micro-supercapacitors. The representative honeycomb alumina nanoscaffold with hexagonal cell arrangement and 400 nm inter-cell spacing has an ultrathin but stiff nanoscaffold with only 16 ± 2 nm cell-wall-thickness, resulting in a cell density of 4.65 × 109 cells per square inch, a surface area enhancement factor of 240, and a relative density of 0.0784. These features allow nanoelectrodes based on honeycomb alumina nanoscaffold synergizing both effective ion migration and ample electroactive surface area within limited footprint. A micro-supercapacitor is finally constructed and exhibits record high performance, suggesting the feasibility of the current design for energy storage devices.
Reference tool kinematics-kinetics and tissue surface strain data during fundamental surgical acts
Authors: Schimmoeller Tyler , Neumann Erica E. , Nagle Tara F. , Erdemir Ahmet 
Published: January 2020

AbstractHaptic based surgical simulations are popular training aids in medicine. Previously, surgical tool loads and motion were measured during cutting and needle insertion on non-human tissue and several haptic based simulations were developed to enhance surgical training. However, there was a lack of realistic foundational data regarding the mechanical responses of human tissue and tools during fundamental acts of surgery, i.e., cutting, suturing, retracting, pinching and indenting. This study used four recently developed surgical tools in a variety of procedures on a diverse set of cadaver leg specimens from human donors. The kinematics and kinetics of surgical tools were recorded along with topical three-dimensional strain during commonly performed surgical procedures. Full motion and load signatures of foundational surgical acts can also be used beyond the development of authentic visual and haptic simulations of surgery, i.e., they provide mechanical specifications for the development of autonomous surgical systems.
Brian2GeNN: accelerating spiking neural network simulations with graphics hardware
Authors: Stimberg Marcel , Goodman Dan F. M. , Nowotny Thomas 
Published: January 2020

Abstract“Brian” is a popular Python-based simulator for spiking neural networks, commonly used in computational neuroscience. GeNN is a C++-based meta-compiler for accelerating spiking neural network simulations using consumer or high performance grade graphics processing units (GPUs). Here we introduce a new software package, Brian2GeNN, that connects the two systems so that users can make use of GeNN GPU acceleration when developing their models in Brian, without requiring any technical knowledge about GPUs, C++ or GeNN. The new Brian2GeNN software uses a pipeline of code generation to translate Brian scripts into C++ code that can be used as input to GeNN, and subsequently can be run on suitable NVIDIA GPU accelerators. From the user’s perspective, the entire pipeline is invoked by adding two simple lines to their Brian scripts. We have shown that using Brian2GeNN, two non-trivial models from the literature can run tens to hundreds of times faster than on CPU.
Relativistic Surface Wave Oscillator in Y-Band with Large Oversized Structures Modulated by Dual Reflectors
Authors: Li Shuang , Wang Jianguo , Wang Dongyang 
Published: January 2020

AbstractTo increase the generation efficiency of the terahertz wave in the Y band, the idea of dual-reflector is introduced in the relativistic surface wave oscillator (SWO) with large oversized structures. The dual-reflector and the slow-wave structure (SWS) construct a resonator where the field strength of TM01 mode inside is intensively enhanced and then the efficiency is increased. The pre-modulation on electron beam caused by the reflector is also helpful in improving the output power. Meanwhile, the reflector can reduce the loss of negatively going electrons. Through the particle-in-cell (PIC) simulations, the optimized structure is tested to be stable and little power is transmitting back to the diode area. The output power reaches 138 MW in the perfectly electrical conductivity condition and the frequency is 337.7 GHz with a pure spectrum. The device’s efficiency is increased from 10.7% to 16.2%, compared with the device without any reflectors. The performance of device with lossy material is also focused on. In the situation of copper device, the output power is about 41 MW under the same input conditions and the corresponding efficiency is about 4.8%.
Hexagonal GaN nanorod-based photonic crystal slab as simultaneous yellow broadband reflector and blue emitter for phosphor-conversion white light emitting devices
Authors: Ko Suk-Min , Hur Joonseok , Lee Chulwon , Isnaeni  , Gong Su-Hyun , Kim MinKwan , Cho Yong-Hoon 
Published: January 2020

AbstractWe report a hexagonal GaN nanorod-based two-dimensional photonic crystal (PhC) slab for phosphor-conversion white light emitting devices analyzed by three-dimensional finite-difference time-domain simulation; this slab has a broad reflection band at yellow wavelength with low Fabry-Pérot background at normal incidence. For practical use as a wavelength-selective reflector, a buffer layer under the PhC slab is employed to sustain the nanorods in the PhC slab. However, we observed that the buffer layer placed below the slab destroys the broad reflection band due to evanescent coupling of electromagnetic field in the slab and the buffer layer. By introducing small-sized base pillars between the slab and the buffer layer, we could decouple the interaction between the slab and the buffer layer and maintain the broad reflection band without any unexpected dips. Since this GaN nanorod-based PhC slab is designed for practical light emitting devices by considering dielectric and transparent conducting layers, this structure is directly applicable for developing hybrid white light emitting devices having both an (active) blue-color-emitting nanorod emitters and a (passive) normal reflector of phosphor emission.
Removal of ammonium ion from aqueous solutions by using unmodified and H2O2-modified zeolitic waste
Authors: Vaičiukynienė Danutė , Mikelionienė Agnė , Baltušnikas Arūnas , Kantautas Aras , Radzevičius Algirdas 
Published: January 2020

AbstractIn the petroleum industry during a catalytic cracking process, the used zeolitic catalyst becomes waste. This article investigated the sorption capacities of ammonium ions from aqueous solutions onto the previously mentioned zeolitic waste by batch experiments. Three types of zeolitic waste were used: unmodified zeolitic waste with two different particle size distributions and H2O2-modified zeolitic waste. Several techniques, including X-ray diffraction (XRD) analysis, Fourier transform infrared spectroscopy (FT-IR), Brunauer-Emmett-Teller (BET) multilayer adsorption theory measurements, and X-ray fluorescence analysis (XRF) were used to demonstrate experimentally that the zeolitic waste could be used as a sorbent for the water decontamination of NH4+ ions. The morphology of zeolitic waste investigated by scanning electron microscopy (SEM) revealed particles with a spherical shape. The nitrogen adsorption–desorption isotherms showed an isotherm mixture of types I (pure microporous) and IV (mesoporous). This suggested that the investigated zeolitic materials were mesoporous (4.84 nm) and microporous (0.852 nm), as well as containing slit/cylindric pores, according to a quench solid density functional theory (QSDFT) adsorption branch model. Zeolitic waste from the oil industry showed good NH4+ sorption properties (removal efficiency of 72%), thus becoming a potential adsorbent to be used in the treatment of contaminated aqueous effluents polluted with ammonium ions. Simultaneous waste and water decontamination can be achieved, providing a new tool and enhanced capabilities for environmental remediation.
Current-induced shuttlecock-like movement of non-axisymmetric chiral skyrmions
Authors: Murooka Remi , Leonov Andrey O. , Inoue Katsuya , Ohe Jun-ichiro 
Published: January 2020

AbstractCurrent-induced motion of non-axisymmetric skyrmions within tilted ferromagnetic phases of polar helimagnets with the easy plane anisotropy is studied by micromagnetic simulations. Such non-axisymmetric skyrmions consist of a circular core and a crescent-shaped domain-wall region formed with respect to the tilted surrounding state. Current-driven motion of non-axisymmetric skyrmions exhibits two distinct time regimes: initially the skyrmions rotate towards the current flow direction and subsequently move along the current with the skyrmionic crescent first. According to the Thiele equation, the asymmetric distribution of the topological charge and the dissipative force tensor play an important role for giving the different velocities for the circular and the crescent-shaped constituent parts of the skyrmion what underlies such a shuttlecock-like movement. Moreover, the current-velocity relation depends on the angle of the tilted ferromagnetic phase what makes in particular the transverse velocity of skyrmions sensitive to their field-driven configurational transformation. We also argue the possibility of magnetic racetrack waveguides based on complex interplay of robust asymmetric skyrmions with multiple twisted edge states.
Role of non-linear data processing on speech recognition task in the framework of reservoir computing
Authors: Abreu Araujo Flavio , Riou Mathieu , Torrejon Jacob , Tsunegi Sumito , Querlioz Damien , Yakushiji Kay , Fukushima Akio , Kubota Hitoshi , Yuasa Shinji , Stiles Mark D. , Grollier Julie 
Published: January 2020

AbstractThe reservoir computing neural network architecture is widely used to test hardware systems for neuromorphic computing. One of the preferred tasks for bench-marking such devices is automatic speech recognition. This task requires acoustic transformations from sound waveforms with varying amplitudes to frequency domain maps that can be seen as feature extraction techniques. Depending on the conversion method, these transformations sometimes obscure the contribution of the neuromorphic hardware to the overall speech recognition performance. Here, we quantify and separate the contributions of the acoustic transformations and the neuromorphic hardware to the speech recognition success rate. We show that the non-linearity in the acoustic transformation plays a critical role in feature extraction. We compute the gain in word success rate provided by a reservoir computing device compared to the acoustic transformation only, and show that it is an appropriate bench-mark for comparing different hardware. Finally, we experimentally and numerically quantify the impact of the different acoustic transformations for neuromorphic hardware based on magnetic nano-oscillators.
Immediate early gene fingerprints of multi-component behaviour
Authors: Rook Noemi , Letzner Sara , Packheiser Julian , Güntürkün Onur , Beste Christian 
Published: January 2020

AbstractThe ability to execute different responses in an expedient temporal order is central for efficient goal-directed actions and often referred to as multi-component behaviour. However, the underlying neural mechanisms on a cellular level remain unclear. Here we establish a link between neural activity at the cellular level within functional neuroanatomical structures to this form of goal-directed behaviour by analyzing immediate early gene (IEG) expression in an animal model, the pigeon (Columba livia). We focus on the group of zif268 IEGs and ZENK in particular. We show that when birds have to cascade separate task goals, ZENK expression is increased in the avian equivalent of the mammalian prefrontal cortex, i.e. the nidopallium caudolaterale (NCL) as well as in the homologous striatum. The results provide the first link between cellular IEG expression and behavioural outcome in multitasking situations. Moreover, the data suggest that the function of the fronto-striatal circuitry is comparable across species indicating that there is limited flexibility in the implementation of complex cognition such as multi-component behaviour within functional neuroanatomical structures.
Carotenoids are used as regulators for membrane fluidity by Staphylococcus xylosus
Authors: Seel Waldemar , Baust Denise , Sons Dominik , Albers Maren , Etzbach Lara , Fuss Janina , Lipski André 
Published: January 2020

AbstractCarotenoids are associated with several important biological functions as antenna pigments in photosynthesis or protectives against oxidative stress. Occasionally they were also discussed as part of the cold adaptation mechanism of bacteria. For two Staphylococcus xylosus strains we demonstrated an increased content of staphyloxanthin and other carotenoids after growth at 10 °C but no detectable carotenoids after grow at 30 °C. By in vivo measurements of generalized polarization and anisotropy with two different probes Laurdan and TMA-DPH we detected a strong increase in membrane order with a simultaneous increase in membrane fluidity at low temperatures accompanied by a broadening of the phase transition. Increased carotenoid concentration was also correlated with an increased resistance of the cells against freeze-thaw stress. In addition, the fatty acid profile showed a moderate adaptation to low temperature by increasing the portion of anteiso-branched fatty acids. The suppression of carotenoid synthesis abolished the effects observed and thus confirmed the causative function of the carotenoids in the modulation of membrane parameters. A differential transcriptome analysis demonstrated the upregulation of genes involved in carotenoid syntheses under low temperature growth conditions. The presented data suggests that upregulated synthesis of carotenoids is a constitutive component in the cold adaptation strategy of Staphylococcus xylosus and combined with modifications of the fatty acid profile constitute the adaptation to grow under low temperature conditions.