bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Framework for Modeling Linear Surface Waves on Shear Currents in Slowly Varying Waters
Authors: Li Yan , Ellingsen Simen Å. 
Published: February 2019

AbstractWe present a theoretical and numerical framework—which we dub the direct integration method (DIM)—for simple, efficient, and accurate evaluation of surface wave models allowing presence of a current of arbitrary depth dependence and where bathymetry and ambient currents may vary slowly in horizontal directions. On horizontally constant water depth and shear current the DIM numerically evaluates the dispersion relation of linear surface waves to arbitrary accuracy, and we argue that for this purpose it is superior to two existing numerical procedures: the piecewise‐linear approximation and a method due to Dong and Kirby (2012, https://doi.org/10.9753/icce.v33.waves.2). The DIM moreover yields the full linearized flow field at little extra cost. We implement the DIM numerically with iterations of standard numerical methods. The wide applicability of the DIM in an oceanographic setting in four aspects is shown. First, we show how the DIM allows practical implementation of the wave action conservation equation recently derived by Quinn et al. (2017, https://doi.org/10.1016/j.ocemod.2017.03.003). Second, we demonstrate how the DIM handles with ease cases where existing methods struggle, that is, velocity profiles U(z) changing direction with vertical coordinate z and strongly sheared profiles. Third, we use the DIM to calculate and analyze the full linear flow field beneath a 2‐D ring wave upon a near‐surface wind‐driven exponential shear current, revealing striking qualitative differences compared to no shear. Finally we demonstrate that the DIM can be a real competitor to analytical dispersion relation approximations such as that of Kirby and Chen (1989, https://doi.org/10.1029/JC094iC01p01013) even for wave/ocean modeling.
Estimation of Secondary Phytoplankton Pigments From Satellite Observations Using Self‐Organizing Maps (SOMs)
Authors: El Hourany Roy , Abboud‐Abi Saab Marie , Faour Ghaleb , Aumont Olivier , Crépon Michel , Thiria Sylvie 
Published: February 2019

AbstractThis study presents a method for estimating secondary phytoplankton pigments from satellite ocean color observations. We first compiled a large training data set composed of 12,000 samples; each sample is composed of 10 in situ phytoplankton high‐performance liquid chromatography (HPLC)‐measured pigment concentrations, GlobColour products of chlorophyll‐a concentration, and remote sensing reflectance (Rrs(λ)) data at different wavelengths, in addition to advanced very high resolution radiometer sea surface temperature measurements. The resulting data set regroups a large variety of encountered situations between 1997 and 2014. The nonlinear relationship between the in situ and satellite components was identified using a self‐organizing map, which is a neural network classifier. As a major result, the self‐organizing map enabled reliable estimations of the concentration of chlorophyll‐a and of nine different pigments from satellite observations. A cross‐validation procedure showed that the estimations were robust for all pigments (R2 > 0.75 and an average root‐mean‐square error = 0.016 mg/m3). A consistent association of several phytoplankton pigments indicating phytoplankton group specific dynamic was shown at a global scale. We also showed the uncertainties for the estimation of each pigment.
Development of a REgion‐Specific Ecosystem Feedback Fire (RESFire) Model in the Community Earth System Model
Authors: Zou Yufei , Wang Yuhang , Ke Ziming , Tian Hanqin , Yang Jia , Liu Yongqiang 
Published: February 2019

AbstractFires play a critical role in modulating regional and global climate through disturbances on meteorological, biogeochemical, and hydrological processes, while fires are strongly affected by climate, terrestrial ecosystems, and human activities. The complex climate‐fire‐ecosystem interactions with anthropogenic disturbance are not well understood. We developed a REgion‐Specific ecosystem feedback Fire (RESFire) model in the Community Earth System Model (CESM) that provides modeling capability to reproduce the observed burning patterns and trends and to understand fire related climatic processes. Comparing with the default Community Land Model version 4.5 fire model in CESM, the RESFire model includes heterogeneous natural and anthropogenic constraints on fire ignition and spread, improved fire impact parameterization including online fire emissions and fire induced land cover changes, and modeling bias corrections for online fire weather simulation. Evaluation results based on the International Land Model Benchmarking package show significant improvements in fire simulation performance. The overall modeling score of burned area simulation increases from 0.50 with Community Land Model version 4.5 to 0.62 (RESFire driven by the observation‐reanalysis data) and 0.60 (RESFire driven by the bias‐corrected Community Atmosphere Model version 5 simulation). The attribution analysis of decadal burned area trends suggests distinct contributions of natural and anthropogenic forcing in different regions, which are consistent with previous observations. The model also includes a fire impact module for estimating atmospheric responses to fire emissions as well as fire disturbances on ecosystems, land cover, and surface radiation budget. These results demonstrate the latest progress of global fire model development that enables fully interactive climate‐fire‐ecosystem studies using CESM.
A Total Energy Error Analysis of Dynamical Cores and Physics‐Dynamics Coupling in the Community Atmosphere Model (CAM)
Authors: Lauritzen Peter H. , Williamson David L. 
Published: February 2019

AbstractA closed total energy (TE) budget is of utmost importance in coupled climate system modeling; in particular, the dynamical core or physics‐dynamics coupling should ideally not lead to spurious TE sources/sinks. To assess this in a global climate model, a detailed analysis of the spurious sources/sinks of TE in National Center for Atmospheric Research's Community Atmosphere Model (CAM) is given. This includes spurious sources/sinks associated with the parameterization suite, the dynamical core, TE definition discrepancies, and physics‐dynamics coupling. The latter leads to a detailed discussion of the pros and cons of various physics‐dynamics coupling methods commonly used in climate/weather modeling.
The Interplay of Eclogitization and Deformation During Deep Burial of the Lower Continental Crust—A Case Study From the Bergen Arcs (Western Norway)
Authors: Zertani Sascha , Labrousse Loic , John Timm , Andersen Torgeir B. , Tilmann Frederik 
Published: February 2019

AbstractThe island of Holsnøy in the Bergen Arcs, which belong to the Caledonides of western Norway, represents an excellent example of how fluid‐induced eclogitization modifies material deeply buried by subduction and continental collision. We produced a new detailed map of the northwestern part of Holsnøy, differentiating not only the magnitude of eclogitization but also the strain intensity at different spatial scales: from the outcrop to the entire massif. Using structural data from eclogite‐facies shear zones and eclogitized low‐strain domains, we show that fluid‐mediated eclogitization not only progresses via the development of shear zones (dynamic eclogitization) but occurs over large areas of the island without associated deformation, creating a characteristic static eclogite‐facies overprint. Static eclogitization preserves the structural features of the granulitic protolith while the rock body is transformed from a granulite‐ to an eclogite‐facies mineral assemblage. The extent of static eclogitization was underestimated strongly in the past, a finding also relevant for the interpretation of seismological images in currently active orogens, where presumably similar processes are currently occurring. In addition, we find that the general structure of the eclogite‐facies shear zones is scale‐independent over several orders of magnitude. Although crustal‐scale eclogite‐facies complexes are rarely preserved without significant modification during exhumation, this implies that similar geometrical configurations are likely produced at the scale of the whole lower crust during subduction or continental collision and therefore shape the crustal geophysical signature.
Sensory neuron lineage mapping and manipulation in the Drosophila olfactory system
Authors: Chai Phing Chian , Cruchet Steeve , Wigger Leonore , Benton Richard 
Published: February 2019

AbstractNervous systems exhibit myriad cell types, but understanding how this diversity arises is hampered by the difficulty to visualize and genetically-probe specific lineages, especially at early developmental stages prior to expression of unique molecular markers. Here, we use a genetic immortalization method to analyze the development of sensory neuron lineages in theDrosophilaolfactory system, from their origin to terminal differentiation. We apply this approach to define a fate map of nearly all olfactory lineages and refine the model of temporal patterns of lineage divisions. Taking advantage of a selective marker for the lineage that gives rise to Or67d pheromone-sensing neurons and a genome-wide transcription factor RNAi screen, we identify the spatial and temporal requirements for Pointed, an ETS family member, in this developmental pathway. Transcriptomic analysis of wild-type and Pointed-depleted olfactory tissue reveals a universal requirement for this factor as a switch-like determinant of fates in these sensory lineages.
Electrooxidative para-selective C–H/N–H cross-coupling with hydrogen evolution to synthesize triarylamine derivatives
Authors: Liu Kun , Tang Shan , Wu Ting , Wang Shengchun , Zou Minzhu , Cong Hengjiang , Lei Aiwen 
Published: February 2019

AbstractOxidative C–H/N–H cross-coupling is one of the most atom-economical methods for the construction of C–N bonds. However, traditional oxidative C–H/N–H cross-coupling either required the use of strong oxidants or high reaction temperature, which makes it difficult to tolerate redox active functional groups. Herein we describe an external chemical oxidant-free electrooxidative C–H/N–H cross-coupling between electron-rich arenes and diarylamine derivatives. Under undivided electrolytic conditions, a series of triarylamine derivatives are produced from electron-rich arenes and diarylamine derivatives with high functional group tolerance. Both of the coupling partners are redox active in oxidative C–H/N–H cross-coupling, which enables high regioselectivity in C–N bond formation. Exclusive para-selectivity is observed for the coupling with anilines.
PTEN self-regulates through USP11 via the PI3K-FOXO pathway to stabilize tumor suppression
Authors: Park Mi Kyung , Yao Yixin , Xia Weiya , Setijono Stephanie Rebecca , Kim Jae Hwan , Vila Isabelle K. , Chiu Hui-Hsuan , Wu Yun , Billalabeitia Enrique González , Lee Min Gyu , Kalb Robert G. , Hung Mien-Chie , Pandolfi Pier Paolo , Song Su Jung , Song Min Sup 
Published: February 2019

AbstractPTEN is a lipid phosphatase that antagonizes the PI3K/AKT pathway and is recognized as a major dose-dependent tumor suppressor. The cellular mechanisms that control PTEN levels therefore offer potential routes to therapy, but these are as yet poorly defined. Here we demonstrate that PTEN plays an unexpected role in regulating its own stability through the transcriptional upregulation of the deubiquitinase USP11 by the PI3K/FOXO pathway, and further show that this feedforward mechanism is implicated in its tumor-suppressive role, as mice lacking Usp11 display increased susceptibility to PTEN-dependent tumor initiation, growth and metastasis. Notably, USP11 is downregulated in cancer patients, and correlates with PTEN expression and FOXO nuclear localization. Our findings therefore demonstrate that PTEN-PI3K-FOXO-USP11 constitute the regulatory feedforward loop that improves the stability and tumor suppressive activity of PTEN.
High temperature singlet-based magnetism from Hund’s rule correlations
Authors: Miao Lin , Basak Rourav , Ran Sheng , Xu Yishuai , Kotta Erica , He Haowei , Denlinger Jonathan D. , Chuang Yi-De , Zhao Y. , Xu Z. , Lynn J. W. , Jeffries J. R. , Saha S. R. , Giannakis Ioannis , Aynajian Pegor , Kang Chang-Jong , Wang Yilin , Kotliar Gabriel , Butch Nicholas P. , Wray L. Andrew 
Published: February 2019

AbstractUranium compounds can manifest a wide range of fascinating many-body phenomena, and are often thought to be poised at a crossover between localized and itinerant regimes for 5f electrons. The antiferromagnetic dipnictide USb2 has been of recent interest due to the discovery of rich proximate phase diagrams and unusual quantum coherence phenomena. Here, linear-dichroic X-ray absorption and elastic neutron scattering are used to characterize electronic symmetries on uranium in USb2 and isostructural UBi2. Of these two materials, only USb2 is found to enable strong Hund’s rule alignment of local magnetic degrees of freedom, and to undergo distinctive changes in local atomic multiplet symmetry across the magnetic phase transition. Theoretical analysis reveals that these and other anomalous properties of the material may be understood by attributing it as the first known high temperature realization of a singlet ground state magnet, in which magnetism occurs through a process that resembles exciton condensation.
Differential influences of environment and self-motion on place and grid cell firing
Authors: Chen Guifen , Lu Yi , King John A , Cacucci Francesca , Burgess Neil 
Published: February 2019

AbstractPlace and grid cells in the hippocampal formation provide foundational representations of environmental location, and potentially of locations within conceptual spaces. Some accounts predict that environmental sensory information and self-motion are encoded in complementary representations, while other models suggest that both features combine to produce a single coherent representation. Here, we use virtual reality to dissociate visual environmental from physical motion inputs, while recording place and grid cells in mice navigating virtual open arenas. Place cell firing patterns predominantly reflect visual inputs, while grid cell activity reflects a greater influence of physical motion. Thus, even when recorded simultaneously, place and grid cell firing patterns differentially reflect environmental information (or ‘states’) and physical self-motion (or ‘transitions’), and need not be mutually coherent.
Human substance P receptor binding mode of the antagonist drug aprepitant by NMR and crystallography
Authors: Chen Shuanghong , Lu Mengjie , Liu Dongsheng , Yang Lingyun , Yi Cuiying , Ma Limin , Zhang Hui , Liu Qing , Frimurer Thomas M. , Wang Ming-Wei , Schwartz Thue W. , Stevens Raymond C. , Wu Beili , Wüthrich Kurt , Zhao Qiang 
Published: February 2019

AbstractNeurokinin 1 receptor (NK1R) has key regulating functions in the central and peripheral nervous systems, and NK1R antagonists such as aprepitant have been approved for treating chemotherapy-induced nausea and vomiting. However, the lack of data on NK1R structure and biochemistry has limited further drug development targeting this receptor. Here, we combine NMR spectroscopy and X-ray crystallography to provide dynamic and static characterisation of the binding mode of aprepitant in complexes with human NK1R variants. 19F-NMR showed a slow off-rate in the binding site, where aprepitant occupies multiple substates that exchange with frequencies in the millisecond range. The environment of the bound ligand is affected by the amino acid in position 2.50, which plays a key role in ligand binding and receptor signaling in class A GPCRs. Crystal structures now reveal how receptor signaling relates to the conformation of the conserved NP7.50xxY motif in transmembrane helix VII.
The Elongator subunit Elp3 is a non-canonical tRNA acetyltransferase
Authors: Lin Ting-Yu , Abbassi Nour El Hana , Zakrzewski Karol , Chramiec-Głąbik Andrzej , Jemioła-Rzemińska Małgorzata , Różycki Jan , Glatt Sebastian 
Published: February 2019

AbstractThe Elongator complex catalyzes posttranscriptional tRNA modifications by attaching carboxy-methyl (cm5) moieties to uridine bases located in the wobble position. The catalytic subunit Elp3 is highly conserved and harbors two individual subdomains, a radical S-adenosyl methionine (rSAM) and a lysine acetyltransferase (KAT) domain. The details of its modification reaction cycle and particularly the substrate specificity of its KAT domain remain elusive. Here, we present the co-crystal structure of bacterial Elp3 (DmcElp3) bound to an acetyl-CoA analog and compare it to the structure of a monomeric archaeal Elp3 from Methanocaldococcus infernus (MinElp3). Furthermore, we identify crucial active site residues, confirm the importance of the extended N-terminus for substrate recognition and uncover the specific induction of acetyl-CoA hydrolysis by different tRNA species. In summary, our results establish the clinically relevant Elongator subunit as a non-canonical acetyltransferase and genuine tRNA modification enzyme.
Disorder in Mn+1AXn phases at the atomic scale
Authors: Wang Chenxu , Yang Tengfei , Tracy Cameron L. , Lu Chenyang , Zhang Hui , Hu Yong-Jie , Wang Lumin , Qi Liang , Gu Lin , Huang Qing , Zhang Jie , Wang Jingyang , Xue Jianming , Ewing Rodney C. , Wang Yugang 
Published: February 2019

AbstractAtomic disordering in materials alters their physical and chemical properties and can subsequently affect their performance. In complex ceramic materials, it is a challenge to understand the nature of structural disordering, due to the difficulty of direct, atomic-scale experimental observations. Here we report the direct imaging of ion irradiation-induced antisite defects in Mn+1AXn phases using double CS-corrected scanning transmission electron microscopy and provide compelling evidence of order-to-disorder phase transformations, overturning the conventional view that irradiation causes phase decomposition to binary fcc-structured Mn+1Xn. With the formation of uniformly distributed cation antisite defects and the rearrangement of X anions, disordered solid solution γ-(Mn+1A)Xn phases are formed at low ion fluences, followed by gradual transitions to solid solution fcc-structured (Mn+1A)Xn phases. This study provides a comprehensive understanding of the order-to-disorder transformations in Mn+1AXn phases and proposes a method for the synthesis of new solid solution (Mn+1A)Xn phases by tailoring the disorder.
Simultaneous targeting of linked loci in mouse embryos using base editing
Authors: Lee Hye Kyung , Willi Michaela , Smith Harold E. , Miller Shannon M. , Liu David R. , Liu Chengyu , Hennighausen Lothar 
Published: February 2019

AbstractA particular challenge in genome engineering has been the simultaneous introduction of mutations into linked (located on the same chromosome) loci. Although CRISPR/Cas9 has been widely used to mutate individual sites, its application in simultaneously targeting of linked loci is limited as multiple nearby double-stranded DNA breaks created by Cas9 routinely result in the deletion of sequences between the cleavage sites. Base editing is a newer form of genome editing that directly converts C∙G-to-T∙A, or A∙T-to-G∙C, base pairs without introducing double-stranded breaks, thus opening the possibility to generate linked mutations without disrupting the entire locus. Through the co-injection of two base editors and two sgRNAs into mouse zygotes, we introduced C∙G-to-T∙A transitions into two cytokine-sensing transcription factor binding sites separated by 9 kb. We determined that one enhancer activates the two flanking genes in mammary tissue during pregnancy and lactation. The ability to introduce linked mutations simultaneously in one step into the mammalian germline has implications for a wide range of applications, including the functional analysis of linked cis-elements creating disease models and correcting pathogenic mutations.
Dirac potential in a rotational dissipative quantum system
Authors: Ma Yi-Rong , Jia Wei , Lin Shi-Rong , Zhao Qing 
Published: February 2019

AbstractThis study proposes the usage of an effective potential to investigate a dissipative quantum system with rotational velocity. After gauge transformation, a Doebner- Goldin equation (DGE) that describes the dissipative quantum system with a Dirac potential is obtained. The DGE is solved based on constraint of vertical relation between the rotational velocity field and density gradient when a harmonic oscillator model is considered. It is observed that the dissipative quantum system is directly equivalent to a monopole system and that the two gauge potentials that are given by Wu and Yang in the north and south hemispheres can be reproduced. Furthermore, a set of gauge-invariant parameters is obtained to discuss the dissipation characteristics of the system.
Modulation of Human Hsp90α Conformational Dynamics by Allosteric Ligand Interaction at the C-Terminal Domain
Authors: Penkler David L. , Tastan Bishop Özlem 
Published: February 2019

AbstractRecent years have seen heat shock protein 90 kDa (Hsp90) attract significant interest as a viable drug target, particularly for cancer. To date, designed inhibitors that target the ATPase domain demonstrate potent anti-proliferative effects, but have failed clinical trials due to high levels of associated toxicity. To circumvent this, the focus has shifted away from the ATPase domain. One option involves modulation of the protein through allosteric activation/inhibition. Here, we propose a novel approach: we use previously obtained information via residue perturbation scanning coupled with dynamic residue network analysis to identify allosteric drug targeting sites for inhibitor docking. We probe the open conformation of human Hsp90α for druggable sites that overlap with these allosteric control elements, and identify three putative natural compound allosteric modulators: Cephalostatin 17, 20(29)-Lupene-3β-isoferulate and 3′-Bromorubrolide F. We assess the allosteric potential of these ligands by examining their effect on the conformational dynamics of the protein. We find evidence for the selective allosteric activation and inhibition of Hsp90’s conformational transition toward the closed state in response to ligand binding and shed valuable insight to further the understanding of allosteric drug design and Hsp90’s complex allosteric mechanism of action.