bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Deep Learning Model for the Thermospheric Nitric Oxide Emission
Authors: Chen Xuetao , Lei Jiuhou , Ren Dexin , Wang Wenbin 
Published: March 2021

AbstractNitric oxide (NO) infrared radiation is an essential cooling source for the thermosphere, especially during and after geomagnetic storms. An accurate representation of the three‐dimension (3‐D) morphology of NO emission in models is critical for predicting the thermosphere state. Recently, the deep‐learning neural network has been widely used in space weather prediction and forecast. Given that the 3‐D image of NO emission from the Sounding of the Atmosphere using Broadband Emission Radiometry (SABER) onboard the Thermosphere Ionosphere Energetics and Dynamics satellite contains a large amount of missing data which is unobserved, a context loss function is applied to extract the features from the incomplete SABER NO emission images. A 3‐D NO emission model (referred to as NOE3D) that is based on the convolutional neural network with a context loss function is developed to estimate the 3‐D distribution of NO emission. NOE3D can effectively extract features from incomplete SABER 3‐D images. Additionally, NOE3D has excellent performance not only for the training datasets but also for the test datasets. The NO emission climate variations associated with solar activities have been well reproduced by NOE3D. The comparison results suggest that NOE3D has better capability in predicting the NO emission than the Thermosphere‐Ionosphere Electrodynamics General Circulation Model. More importantly, NOE3D is capable of providing the variations of NO emission during extremely disturbed times.
Unsteady‐State Contact Angle Hysteresis During Droplet Oscillation in Capillary Pores: Theoretical Model and VOF Simulation
Authors: Zeng Chao , Deng Wen , Wang Lichun 
Published: March 2021

AbstractContact angle hysteresis (CAH) is a critical phenomenon that could significantly affect the fate of immiscible bubbles/droplets in vadose zones, nonaqueous phase liquid contaminated aquifers, and saline aquifers for CO2 sequestration in terms of infiltration patterns and residual trapping mechanisms. When external physical impacts such as oscillatory excitation or pulse forcing are applied, it could result in pinned oscillation of droplets due to this CAH or mobilization of pinned droplets. Conventional steady‐state analysis of contact angle could underestimate CAH. As the first time to take unsteady‐state effect into consideration, a hydrodynamic analysis is developed in this study to address the unsteady‐state CAH theoretically, and this hydrodynamic model is also validated against volume‐of‐fluid‐based computational fluid dynamics simulations. It is found that the unsteady‐state CAH of drop can significantly lower the critical acceleration amplitude of excitation to achieve the depinning of contact lines of drops.
GASC1 promotes hepatocellular carcinoma progression by inhibiting the degradation of ROCK2
Authors: Shao Na , Cheng Jiamin , Huang Hong , Gong Xiaoshan , Lu Yongling , Idris Muhammad , Peng Xu , Ong Belinda X. , Zhang Qiongyi , Xu Feng , Liu Chungang 
Published: March 2021

AbstractHepatocellular carcinoma (HCC) is a devastating malignancy without targeted therapeutic options. Our results indicated that the histone demethylase GASC1 signature is associated with later tumor stage and poorer survival in HCC patients. GASC1 depletion led to diminished HCC proliferation and tumor growth. A distinct heterogeneity in GASC1 levels was observed among HCC cell populations, predicting their inherent high or low tumor-initiating capacity. Mechanistically, GASC1 is involved in the regulation of several components of the Rho-GTPase signaling pathway including its downstream target ROCK2. GASC1 demethylase activity ensured the transcriptional repression of FBXO42, a ROCK2 protein-ubiquitin ligase, thereby inhibiting ROCK2 degradation via K63-linked poly-ubiquitination. Treatment with the GASC1 inhibitor SD70 impaired the growth of both HCC cell lines and xenografts in mice, sensitizing them to standard-of-care chemotherapy. This work identifies GASC1 as a malignant-cell-selective target in HCC, and GASC1-specific therapeutics represent promising candidates for new treatment options to control this malignancy.
Twist-angle engineering of excitonic quantum interference and optical nonlinearities in stacked 2D semiconductors
Authors: Lin Kai-Qiang , Faria Junior Paulo E. , Bauer Jonas M. , Peng Bo , Monserrat Bartomeu , Gmitra Martin , Fabian Jaroslav , Bange Sebastian , Lupton John M. 
Published: March 2021

AbstractTwist-engineering of the electronic structure in van-der-Waals layered materials relies predominantly on band hybridization between layers. Band-edge states in transition-metal-dichalcogenide semiconductors are localized around the metal atoms at the center of the three-atom layer and are therefore not particularly susceptible to twisting. Here, we report that high-lying excitons in bilayer WSe2 can be tuned over 235 meV by twisting, with a twist-angle susceptibility of 8.1 meV/°, an order of magnitude larger than that of the band-edge A-exciton. This tunability arises because the electronic states associated with upper conduction bands delocalize into the chalcogenide atoms. The effect gives control over excitonic quantum interference, revealed in selective activation and deactivation of electromagnetically induced transparency (EIT) in second-harmonic generation. Such a degree of freedom does not exist in conventional dilute atomic-gas systems, where EIT was originally established, and allows us to shape the frequency dependence, i.e., the dispersion, of the optical nonlinearity.
Properties of repression condensates in living Ciona embryos
Authors: Treen Nicholas , Shimobayashi Shunsuke F. , Eeftens Jorine , Brangwynne Clifford P. , Levine Michael 
Published: March 2021

AbstractRecent studies suggest that transcriptional activators and components of the pre-initiation complex (PIC) form higher order associations—clusters or condensates—at active loci. Considerably less is known about the distribution of repressor proteins responsible for gene silencing. Here, we develop an expression assay in living Ciona embryos that captures the liquid behavior of individual nucleoli undergoing dynamic fusion events. The assay is used to visualize puncta of Hes repressors, along with the Groucho/TLE corepressor. We observe that Hes.a/Gro puncta have the properties of viscous liquid droplets that undergo limited fusion events due to association with DNA. Hes.a mutants that are unable to bind DNA display hallmarks of liquid–liquid phase separation, including dynamic fusions of individual condensates to produce large droplets. We propose that the DNA template serves as a scaffold for the formation of Hes condensates, but limits the spread of transcriptional repressors to unwanted regions of the genome.
easyCLIP analysis of RNA-protein interactions incorporating absolute quantification
Authors: Porter Douglas F. , Miao Weili , Yang Xue , Goda Grant A. , Ji Andrew L. , Donohue Laura K. H. , Aleman Maria M. , Dominguez Daniel , Khavari Paul A. 
Published: March 2021

AbstractQuantitative criteria to identify proteins as RNA-binding proteins (RBPs) are presently lacking, as are criteria to define RBP target RNAs. Here, we develop an ultraviolet (UV) cross-linking immunoprecipitation (CLIP)-sequencing method, easyCLIP. easyCLIP provides absolute cross-link rates, as well as increased simplicity, efficiency, and capacity to visualize RNA libraries during sequencing library preparation. Measurement of >200 independent cross-link experiments across >35 proteins identifies an RNA cross-link rate threshold that distinguishes RBPs from non-RBPs and defines target RNAs as those with a complex frequency unlikely for a random protein. We apply easyCLIP to the 33 most recurrent cancer mutations across 28 RBPs, finding increased RNA binding per RBP molecule for KHDRBS2 R168C, A1CF E34K and PCBP1 L100P/Q cancer mutations. Quantitating RBP-RNA interactions can thus nominate proteins as RBPs and define the impact of specific disease-associated RBP mutations on RNA association.
Structural basis for VPS34 kinase activation by Rab1 and Rab5 on membranes
Authors: Tremel Shirley , Ohashi Yohei , Morado Dustin R. , Bertram Jessie , Perisic Olga , Brandt Laura T. L. , von Wrisberg Marie-Kristin , Chen Zhuo A. , Maslen Sarah L. , Kovtun Oleksiy , Skehel Mark , Rappsilber Juri , Lang Kathrin , Munro Sean , Briggs John A. G. , Williams Roger L. 
Published: March 2021

AbstractThe lipid phosphatidylinositol-3-phosphate (PI3P) is a regulator of two fundamental but distinct cellular processes, endocytosis and autophagy, so its generation needs to be under precise temporal and spatial control. PI3P is generated by two complexes that both contain the lipid kinase VPS34: complex II on endosomes (VPS34/VPS15/Beclin 1/UVRAG), and complex I on autophagosomes (VPS34/VPS15/Beclin 1/ATG14L). The endosomal GTPase Rab5 binds complex II, but the mechanism of VPS34 activation by Rab5 has remained elusive, and no GTPase is known to bind complex I. Here we show that Rab5a–GTP recruits endocytic complex II to membranes and activates it by binding between the VPS34 C2 and VPS15 WD40 domains. Electron cryotomography of complex II on Rab5a-decorated vesicles shows that the VPS34 kinase domain is released from inhibition by VPS15 and hovers over the lipid bilayer, poised for catalysis. We also show that the GTPase Rab1a, which is known to be involved in autophagy, recruits and activates the autophagy-specific complex I, but not complex II. Both Rabs bind to the same VPS34 interface but in a manner unique for each. These findings reveal how VPS34 complexes are activated on membranes by specific Rab GTPases and how they are recruited to unique cellular locations.
How antisolvent miscibility affects perovskite film wrinkling and photovoltaic properties
Authors: Kim Seul-Gi , Kim Jeong-Hyeon , Ramming Philipp , Zhong Yu , Schötz Konstantin , Kwon Seok Joon , Huettner Sven , Panzer Fabian , Park Nam-Gyu 
Published: March 2021

AbstractCharge carriers’ density, their lifetime, mobility, and the existence of trap states are strongly affected by the microscopic morphologies of perovskite films, and have a direct influence on the photovoltaic performance. Here, we report on micro-wrinkled perovskite layers to enhance photocarrier transport performances. By utilizing temperature-dependent miscibility of dimethyl sulfoxide with diethyl ether, the geometry of the microscopic wrinkles of the perovskite films are controlled. Wrinkling is pronounced as temperature of diethyl ether (TDE) decreases due to the compressive stress relaxation of the thin rigid film-capped viscoelastic layer. Time-correlated single-photon counting reveals longer carrier lifetime at the hill sites than at the valley sites. The wrinkled morphology formed at TDE = 5 °C shows higher power conversion efficiency (PCE) and better stability than the flat one formed at TDE = 30 °C. Interfacial and additive engineering improve further PCE to 23.02%. This study provides important insight into correlation between lattice strain and carrier properties in perovskite photovoltaics.
Fragility of surface states in topological superfluid 3He
Authors: Heikkinen P. J. , Casey A. , Levitin L. V. , Rojas X. , Vorontsov A. , Sharma P. , Zhelev N. , Parpia J. M. , Saunders J. 
Published: March 2021

AbstractSuperfluid 3He, with unconventional spin-triplet p-wave pairing, provides a model system for topological superconductors, which have attracted significant interest through potential applications in topologically protected quantum computing. In topological insulators and quantum Hall systems, the surface/edge states, arising from bulk-surface correspondence and the momentum space topology of the band structure, are robust. Here we demonstrate that in topological superfluids and superconductors the surface Andreev bound states, which depend on the momentum space topology of the emergent order parameter, are fragile with respect to the details of surface scattering. We confine superfluid 3He within a cavity of height D comparable to the Cooper pair diameter ξ0. We precisely determine the superfluid transition temperature Tc and the suppression of the superfluid energy gap, for different scattering conditions tuned in situ, and compare to the predictions of quasiclassical theory. We discover that surface magnetic scattering leads to unexpectedly large suppression of Tc, corresponding to an increased density of low energy bound states.
Unusual hydrogen implanted gold with lattice contraction at increased hydrogen content
Authors: Nguyen Khac Thuan , Hiep Vuong Van , Nguyen The Nghia , Nguyen Trong Tinh , Yamamoto Tomoyuki , Hoang Nam Nhat 
Published: March 2021

AbstractThe experimental evidence for the contraction of volume of gold implanted with hydrogen at low doses is presented. The contraction of lattice upon the addition of other elements is very rare and extraordinary in the solid-state, not only for gold but also for many other solids. To explain the underlying physics, the pure kinetic theory of absorption is not adequate and the detailed interaction of hydrogen in the lattice needs to be clarified. Our analysis points to the importance of the formation of hydride bonds in a dynamic manner and explains why these bonds become weak at higher doses, leading to the inverse process of volume expansion frequently seen in metallic hydrogen containers.
Stereoselectivity in spontaneous assembly of rolled incommensurate carbon bilayers
Authors: Matsuno Taisuke , Ohtomo Yutaro , Someya Maki , Isobe Hiroyuki 
Published: March 2021

AbstractThe periodicity of two-dimensional entities can be manipulated by their stacking assembly, and incommensurate stacks of bilayers are attracting considerable interest in materials science. Stereoisomerism in incommensurate bilayers was first noted with incommensurate double-wall carbon nanotubes composed of helical carbon networks, but the lack of structural information hampered the chemical understanding such as the stereoselectivity during bilayer formation. In this study, we construct a finite molecular version of incommensurate carbon bilayers by assembling two helical cylindrical molecules in solution. An outer cylindrical molecule is designed to encapsulate a small-bore helical cylindrical molecule, and the spontaneous assembly of coaxial complexes proceeds in a stereoselective manner in solution with a preference for heterohelical combinations over diastereomeric, homohelical combinations. The rational design of incommensurate bilayers for material applications may be facilitated by the design and development of molecular versions with discrete structures with atomic precision.
Meta-analysis of the Parkinson’s disease gut microbiome suggests alterations linked to intestinal inflammation
Authors: Romano Stefano , Savva George M. , Bedarf Janis R. , Charles Ian G. , Hildebrand Falk , Narbad Arjan 
Published: March 2021

AbstractThe gut microbiota is emerging as an important modulator of neurodegenerative diseases, and accumulating evidence has linked gut microbes to Parkinson’s disease (PD) symptomatology and pathophysiology. PD is often preceded by gastrointestinal symptoms and alterations of the enteric nervous system accompany the disease. Several studies have analyzed the gut microbiome in PD, but a consensus on the features of the PD-specific microbiota is missing. Here, we conduct a meta-analysis re-analyzing the ten currently available 16S microbiome datasets to investigate whether common alterations in the gut microbiota of PD patients exist across cohorts. We found significant alterations in the PD-associated microbiome, which are robust to study-specific technical heterogeneities, although differences in microbiome structure between PD and controls are small. Enrichment of the generaLactobacillus,Akkermansia, andBifidobacteriumand depletion of bacteria belonging to the Lachnospiraceae family and theFaecalibacteriumgenus, both important short-chain fatty acids producers, emerged as the most consistent PD gut microbiome alterations. This dysbiosis might result in a pro-inflammatory status which could be linked to the recurrent gastrointestinal symptoms affecting PD patients.
Quality by design approach identifies critical parameters driving oxygen delivery performance in vitro for perfluorocarbon based artificial oxygen carriers
Authors: Lambert Eric , Janjic Jelena M. 
Published: March 2021

AbstractPerfluorocarbons (PFCs) exhibiting high solubility for oxygen are attractive materials as artificial oxygen carriers (AOC), an alternative to whole blood or Haemoglobin-based oxygen carriers (HBOCs). PFC-based AOCs, however, met clinical translation roadblocks due to product quality control challenges. To overcome these issues, we present an adaptation of Quality by Design (QbD) practices to optimization of PFC nanoemulsions (PFC-NEs) as AOCs. QbD elements including quality risk management, design of experiments (DoE), and multivariate data analysis facilitated the identification of composition and process parameters that strongly impacted PFC colloidal stability and oxygen transport function. Resulting quantitative relationships indicated a composition-driven tradeoff between stability and oxygen transport. It was found that PFC content was most predictive of in vitro oxygen release, but the PFC type (perfluoro-15-crown-5-ether, PCE or perfluorooctyl bromide, PFOB) had no effect on oxygen release. Furthermore, we found, under constant processing conditions, all PFC-NEs, comprised of varied PFC and hydrocarbon content, exhibited narrow droplet size range (100–150 nm) and narrow size distribution. Representative PFOB-NE maintained colloidal attributes upon manufacturing on larger scale (100 mL). QbD approach offers unique insights into PFC AOC performance, which will overcome current product development challenges and accelerate clinical translation.
Atomic-level breakdown of Green–Kubo relations provides new insight into the mechanisms of thermal conduction
Authors: Manjunatha Likhith , Takamatsu Hiroshi , Cannon James J. 
Published: March 2021

AbstractPrecise control of thermophysical properties of liquids through tailor-made design of the liquid molecular structure is a goal that, if achieved, could have significant positive impacts on machine design, performance and durability. In this work we show how the breakdown of the Green–Kubo relations down to the atomic level in molecular dynamics simulation can give useful insight into the mechanisms of thermal conduction. Using a group of five small alcohols as a case study, we demonstrate how combining this level of insight with differential-structure analysis reveals the competition for conduction between carbon and hydroxyl group atoms, and show how this competition contributes to the change in thermal conductivity observed in experiment. We hope that this method will become a useful tool in the quest for molecular-structure based thermal design.
An immersive first-person navigation task for abstract knowledge acquisition
Authors: Kuhrt Doerte , St. John Natalie R. , Bellmund Jacob L. S. , Kaplan Raphael , Doeller Christian F. 
Published: March 2021

AbstractAdvances in virtual reality (VR) technology have greatly benefited spatial navigation research. By presenting space in a controlled manner, changing aspects of the environment one at a time or manipulating the gain from different sensory inputs, the mechanisms underlying spatial behaviour can be investigated. In parallel, a growing body of evidence suggests that the processes involved in spatial navigation extend to non-spatial domains. Here, we leverage VR technology advances to test whether participants can navigate abstract knowledge. We designed a two-dimensional quantity space—presented using a head-mounted display—to test if participants can navigate abstract knowledge using a first-person perspective navigation paradigm. To investigate the effect of physical movement, we divided participants into two groups: one walking and rotating on a motion platform, the other group using a gamepad to move through the abstract space. We found that both groups learned to navigate using a first-person perspective and formed accurate representations of the abstract space. Interestingly, navigation in the quantity space resembled behavioural patterns observed in navigation studies using environments with natural visuospatial cues. Notably, both groups demonstrated similar patterns of learning. Taken together, these results imply that both self-movement and remote exploration can be used to learn the relational mapping between abstract stimuli.
Validation of a multicellular tumor microenvironment system for modeling patient tumor biology and drug response
Authors: Roller Devin G. , Hoang Stephen A. , Rawls Kristopher D. , Owen Katherine A. , Simmers Michael B. , Figler Robert A. , Wulfkuhle Julia D. , Petricoin Emanuel F. , Wamhoff Brian R. , Gioeli Daniel 
Published: March 2021

AbstractLung cancer rates are rising globally and non-small cell lung cancer (NSCLC) has a five year survival rate of only 24%. Unfortunately, the development of drugs to treat cancer is severely hampered by the inefficiency of translating pre-clinical studies into clinical benefit. Thus, we sought to apply a tumor microenvironment system (TMES) to NSCLC. Using microvascular endothelial cells, lung cancer derived fibroblasts, and NSCLC tumor cells in the presence of in vivo tumor-derived hemodynamic flow and transport, we demonstrate that the TMES generates an in-vivo like biological state and predicts drug response to EGFR inhibitors. Transcriptomic and proteomic profiling indicate that the TMES recapitulates the in vivo and patient molecular biological state providing a mechanistic rationale for the predictive nature of the TMES. This work further validates the TMES for modeling patient tumor biology and drug response indicating utility of the TMES as a predictive tool for drug discovery and development and potential for use as a system for patient avatars.
The duration-energy-size enigma for acoustic emission
Authors: Casals Blai , Dahmen Karin A. , Gou Boyuan , Rooke Spencer , Salje Ekhard K. H. 
Published: March 2021

AbstractAcoustic emission (AE) measurements of avalanches in different systems, such as domain movements in ferroics or the collapse of voids in porous materials, cannot be compared with model predictions without a detailed analysis of the AE process. In particular, most AE experiments scale the avalanche energy E, maximum amplitude Amax and duration D as E ~ Amaxx and Amax ~ Dχ with x = 2 and a poorly defined power law distribution for the duration. In contrast, simple mean field theory (MFT) predicts that x = 3 and χ = 2. The disagreement is due to details of the AE measurements: the initial acoustic strain signal of an avalanche is modified by the propagation of the acoustic wave, which is then measured by the detector. We demonstrate, by simple model simulations, that typical avalanches follow the observed AE results with x = 2 and ‘half-moon’ shapes for the cross-correlation. Furthermore, the size S of an avalanche does not always scale as the square of the maximum AE avalanche amplitude Amax as predicted by MFT but scales linearly S ~ Amax. We propose that the AE rise time reflects the atomistic avalanche time profile better than the duration of the AE signal.