bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigating Microtopographic and Soil Controls on a Mountainous Meadow Plant Community Using High‐Resolution Remote Sensing and Surface Geophysical Data
Authors: Falco Nicola , Wainwright Haruko , Dafflon Baptiste , Léger Emmanuel , Peterson John , Steltzer Heidi , Wilmer Chelsea , Rowland Joel C. , Williams Kenneth H. , Hubbard Susan S. 
Published: May 2019

AbstractThis study aims to investigate the microtopographic controls that dictate the heterogeneity of plant communities in a mountainous floodplain‐hillslope system, using remote sensing and surface geophysical techniques. Working within a lower montane floodplain‐hillslope study site (750 m × 750 m) in the Upper Colorado River Basin, we developed a new data fusion framework, based on machine learning and feature engineering, that exploits remote sensing optical and light detection and ranging (LiDAR) data to estimate the distribution of key plant meadow communities at submeter resolution. We collected surface electrical resistivity tomography data to explore the variability in soil properties along a floodplain‐hillslope transect at 0.50‐m resolution and extracted LiDAR‐derived metrics to model the rapid change in microtopography. We then investigated the covariability among the estimated plant community distributions, soil information, and topographic metrics. Results show that our framework estimated the distribution of nine plant communities with higher accuracy (87% versus 80% overall; 85% versus 60% for shrubs) compared to conventional classification approaches. Analysis of the covariabilities reveals a strong correlation between plant community distribution, soil electric conductivity, and slope, indicating that soil moisture is a primary control on heterogeneous spatial distribution. At the same time, microtopography plays an important role in creating particular ecosystem niches for some of the communities. Such relationships could be exploited to provide information about the spatial variability of soil properties. This highly transferable framework can be employed within long‐term monitoring to capture community‐specific physiological responses to perturbations, offering the possibility of bridging local plot‐scale observations with large landscape monitoring.
From Nano to Micro: Evolution of Magnetic Domain Structures in Multidomain Magnetite
Authors: Nagy Lesleis , Williams Wyn , Tauxe Lisa , Muxworthy Adrian R. 
Published: May 2019

AbstractReliability of magnetic recordings of the ancient magnetic field is strongly dependent on the magnetic mineralogy of natural samples. Theoretical estimates of long‐term stability of remanence were restricted to single‐domain (SD) states, but micromagnetic models have recently demonstrated that the so‐called single‐vortex (SV) domain structure can have even higher stability that SD grains. In larger grains (
10 μm in magnetite) the multidomain (MD) state dominates, so that large uniform magnetic domains are separated by narrow domain walls. In this paper we use a parallelized micromagnetic finite element model to provide resolutions of many millions of elements allowing us, for the first time, to examine the evolution of magnetic structure from a uniform state, through the SV state up to the development of the domain walls indicative of MD states. For a cuboctahedral grain of magnetite, we identify clear domain walls in grains as small as ∼3 μm with domain wall widths equal to that expected in large MD grains; we therefore put the SV to MD transition at ∼3 μm for magnetite and expect well‐defined, and stable, SV structures to be present until at least ∼1 μm when reducing the grain size. Reducing the size further shows critical dependence on the history of domain structures, particularly with SV states that transition through a so‐called “unstable zone” leading to the recently observed hard‐aligned SV states that proceed to unwind to SD yet remain hard aligned.
The Equatorial Undercurrent and the Oxygen Minimum Zone in the Pacific
Authors: Busecke Julius J. M. , Resplandy Laure , Dunne John P. 
Published: May 2019

AbstractWarming‐driven expansion of the oxygen minimum zone (OMZ) in the equatorial Pacific would bring very low oxygen waters closer to the ocean surface and possibly impact global carbon/nutrient cycles and local ecosystems. Global coarse Earth System Models (ESMs) show, however, disparate trends that poorly constrain these future changes in the upper OMZ. Using an ESM with a high‐resolution ocean (1/10°), we show that a realistic representation of the Equatorial Undercurrent (EUC) dynamics is crucial to represent the upper OMZ structure and its temporal variability. We demonstrate that coarser ESMs commonly misrepresent the EUC, leading to an unrealistic “tilt” of the OMZ (e.g., shallowing toward the east) and an exaggerated sensitivity to EUC changes overwhelming other important processes like diffusion and biology. This shortcoming compromises the ability to reproduce the OMZ variability and could explain the disparate trends in ESMs projections.
A Spring Barrier for Regional Predictions of Summer Arctic Sea Ice
Authors: Bonan D. B. , Bushuk M. , Winton M. 
Published: May 2019

AbstractSeasonal forecast systems can skillfully predict summer Arctic sea ice up to 4 months in advance. For some regions, however, there is a springtime predictability barrier that causes forecasts initialized prior to May to be less skillful. Since this barrier has only been documented in a few general circulation models (GCMs), we evaluate GCMs participating in phase 5 of the Coupled Model Intercomparison Project. We first show sea ice volume skillfully predicts summer sea ice area (SIA) and has similar skill to a perfect model experiment. Given this result, we assess regional SIA predictability across each GCM and find a universal predictability barrier in late spring. For SIA at each summer target month in the marginal seas of the Arctic basin, a notable drop in prediction skill occurs from June to May in each GCM. This suggests summer sea ice forecasts initialized after 1 June will have substantially better prediction skill than forecasts initialized before.
Algal Export in the Arctic Ocean in Times of Global Warming
Authors: Lalande Catherine , Nöthig Eva‐Maria , Fortier Louis 
Published: May 2019

AbstractSatellite‐derived data suggest an increase in annual primary production following the loss of summer sea ice in the Arctic Ocean. The scarcity of field data to corroborate this enhanced algal production incited a collaborative project combining six annual cycles of sequential sediment trap measurements obtained over a 17‐year period in the Eurasian Arctic Ocean. Here we present microalgal fluxes measured at ~200 m to reflect the bulk of algal carbon production. Ice algae contributed to a large proportion of the microalgal carbon export before complete ice melt and possible detection of their production by satellites. In the northern Laptev Sea, annual microalgal carbon fluxes were lower during the 2007 minimum ice extent than in 2006. In 2012, early snowmelt led to early microalgal carbon flux in the Nansen Basin. Hence, a change in the timing of snowmelt and ice algae release may affect productivity and export over the Arctic basins.
Event Studies of O+Density Variability Within Quiet‐Time Plasma Sheet
Authors: Wang Chih‐Ping , Fuselier Stephen A. , Hairston Marc , Zhang Xiao‐jia , Zou Shasha , Avanov Levon A. , Strangeway Robert J. , Ahmadi Narges , Bortnik Jacob 
Published: May 2019

AbstractTo understand the variations of the O+ ions in the quiet‐time plasma sheet between the regions of cold‐dense plasma sheet (CDPS) and hot plasma sheet (HPS), we conduct three event studies. These studies investigate the O+ densities in the two regions and how they are correlated with the strength of two magnetospheric sources important to ion outflows: the soft electron flux and Poynting flux toward the ionosphere. The CDPS is characterized by two‐component ions (one hot component mixed with one cold component), while the HPS ions consist of only one single hot component. Comparing the O+ density between the CDPS and HPS of the same event, the average CDPS O+ density was higher by a factor of ~2–5. Compared to the HPS, the soft electron flux source within the CDPS was higher, consistent with the fact that the soft electron precipitation and O+ upward number fluxes observed in the ionosphere were also higher within the CDPS. In the plasma sheet, broadband ultralow‐frequency electric and magnetic field waves with the characteristics of kinetic Alfvén waves were often more intense within the CDPS, providing a stronger Poynting flux source. In addition, electron resonant interaction with kinetic Alfvén waves results in acceleration along the magnetic fields and, thus, may drive the observed soft electron precipitation. These correlations suggest that the higher soft electron precipitation and Poynting flux coming from the magnetospheric CDPS likely produce larger ionospheric O+ outflows back to the magnetosphere, thus resulting in the higher O+ density within the CDPS.
Impact of Significant Time‐Integrated Geomagnetic Activity on 2‐MeV Electron Flux
Authors: Mourenas D. , Artemyev A. V. , Zhang X.‐J. 
Published: May 2019

AbstractWe explore the impact on the outer radiation belt of significant time‐integrated ap events of continuously elevated geomagnetic activity, making use of Van Allen Probes measurements in 2013–2017. We show that most high peaks of 1.8‐MeV electron flux occur during the 10 days immediately following such events, with stronger events leading to higher flux. Events larger than 800 nT·hr are always followed by a high peak of flux in the heart of the outer radiation belt. They lead to 10‐day‐averaged 1.8‐MeV electron fluxes of the order of 106 e/cm2/sr/s/MeV in this region and 8×104 e/cm2/sr/s/MeV near geostationary orbit. Accordingly, they can be considered as reliable precursors of high peaks of 2‐MeV electron flux throughout the outer belt. We demonstrate that the flux peaks following such significant events can be parameterized by different geomagnetic indices at different radial locations in 2013–2017. Comparisons between the corresponding modeled flux peaks and observations show a reasonable agreement for both the timing, duration, and level of the peaks with 2015 data from the Van Allen Probes and also with 2002–2012 data from Global Positioning System satellites and 2003–2016 data from Geostationary Operational Environmental Satellites, provided that dropouts are taken into account via an appropriate threshold on solar wind dynamic pressure.
Discovery of processive catalysis by an exo-hydrolase with a pocket-shaped active site
Authors: Streltsov Victor A. , Luang Sukanya , Peisley Alys , Varghese Joseph N. , Ketudat Cairns James R. , Fort Sebastien , Hijnen Marcel , Tvaroška Igor , Ardá Ana , Jiménez-Barbero Jesús , Alfonso-Prieto Mercedes , Rovira Carme , Mendoza Fernanda , Tiessler-Sala Laura , Sánchez-Aparicio José-Emilio , Rodríguez-Guerra Jaime , Lluch José M. , Maréchal Jean-Didier , Masgrau Laura , Hrmova Maria 
Published: May 2019

AbstractSubstrates associate and products dissociate from enzyme catalytic sites rapidly, which hampers investigations of their trajectories. The high-resolution structure of the native Hordeum exo-hydrolase HvExoI isolated from seedlings reveals that non-covalently trapped glucose forms a stable enzyme-product complex. Here, we report that the alkyl β-d-glucoside and methyl 6-thio-β-gentiobioside substrate analogues perfused in crystalline HvExoI bind across the catalytic site after they displace glucose, while methyl 2-thio-β-sophoroside attaches nearby. Structural analyses and multi-scale molecular modelling of nanoscale reactant movements in HvExoI reveal that upon productive binding of incoming substrates, the glucose product modifies its binding patterns and evokes the formation of a transient lateral cavity, which serves as a conduit for glucose departure to allow for the next catalytic round. This path enables substrate-product assisted processive catalysis through multiple hydrolytic events without HvExoI losing contact with oligo- or polymeric substrates. We anticipate that such enzyme plasticity could be prevalent among exo-hydrolases.
Phase evolution of conversion-type electrode for lithium ion batteries
Authors: Li Jing , Hwang Sooyeon , Guo Fangming , Li Shuang , Chen Zhongwei , Kou Ronghui , Sun Ke , Sun Cheng-Jun , Gan Hong , Yu Aiping , Stach Eric A. , Zhou Hua , Su Dong 
Published: May 2019

AbstractBatteries with conversion-type electrodes exhibit higher energy storage density but suffer much severer capacity fading than those with the intercalation-type electrodes. The capacity fading has been considered as the result of contact failure between the active material and the current collector, or the breakdown of solid electrolyte interphase layer. Here, using a combination of synchrotron X-ray absorption spectroscopy and in situ transmission electron microscopy, we investigate the capacity fading issue of conversion-type materials by studying phase evolution of iron oxide composited structure during later-stage cycles, which is found completely different from its initial lithiation. The accumulative internal passivation phase and the surface layer over cycling enforce a rate−limiting diffusion barrier for the electron transport, which is responsible for the capacity degradation and poor rate capability. This work directly links the performance with the microscopic phase evolution in cycled electrode materials and provides insights into designing conversion-type electrode materials for applications.
Colloidal gel elasticity arises from the packing of locally glassy clusters
Authors: Whitaker Kathryn A. , Varga Zsigmond , Hsiao Lilian C. , Solomon Michael J. , Swan James W. , Furst Eric M. 
Published: May 2019

AbstractColloidal gels formed by arrested phase separation are found widely in agriculture, biotechnology, and advanced manufacturing; yet, the emergence of elasticity and the nature of the arrested state in these abundant materials remains unresolved. Here, the quantitative agreement between integrated experimental, computational, and graph theoretic approaches are used to understand the arrested state and the origins of the gel elastic response. The micro-structural source of elasticity is identified by the l-balanced graph partition of the gels into minimally interconnected clusters that act as rigid, load bearing units. The number density of cluster-cluster connections grows with increasing attraction, and explains the emergence of elasticity in the network through the classic Cauchy-Born theory. Clusters are amorphous and iso-static. The internal cluster concentration maps onto the known attractive glass line of sticky colloids at low attraction strengths and extends it to higher strengths and lower particle volume fractions.
Inactivation of nuclear histone deacetylases by EP300 disrupts the MiCEE complex in idiopathic pulmonary fibrosis
Authors: Rubio Karla , Singh Indrabahadur , Dobersch Stephanie , Sarvari Pouya , Günther Stefan , Cordero Julio , Mehta Aditi , Wujak Lukasz , Cabrera-Fuentes Hector , Chao Cho-Ming , Braubach Peter , Bellusci Saverio , Seeger Werner , Günther Andreas , Preissner Klaus T. , Wygrecka Malgorzata , Savai Rajkumar , Papy-Garcia Dulce , Dobreva Gergana , Heikenwalder Mathias , Savai-Pullamsetti Soni , Braun Thomas , Barreto Guillermo 
Published: May 2019

AbstractIdiopathic pulmonary fibrosis (IPF) is a chronic, progressive, and highly lethal lung disease with unknown etiology and poor prognosis. IPF patients die within 2 years after diagnosis mostly due to respiratory failure. Current treatments against IPF aim to ameliorate patient symptoms and to delay disease progression. Unfortunately, therapies targeting the causes of or reverting IPF have not yet been developed. Here we show that reduced levels of miRNA lethal 7d (MIRLET7D) in IPF compromise epigenetic gene silencing mediated by the ribonucleoprotein complex MiCEE. In addition, we find that hyperactive EP300 reduces nuclear HDAC activity and interferes with MiCEE function in IPF. Remarkably, EP300 inhibition reduces fibrotic hallmarks of in vitro (patient-derived primary fibroblast), in vivo (bleomycin mouse model), and ex vivo (precision-cut lung slices, PCLS) IPF models. Our work provides the molecular basis for therapies against IPF using EP300 inhibition.
Imaging gigahertz zero-group-velocity Lamb waves
Authors: Xie Qingnan , Mezil Sylvain , Otsuka Paul H. , Tomoda Motonobu , Laurent Jérôme , Matsuda Osamu , Shen Zhonghua , Wright Oliver B. 
Published: May 2019

AbstractZero-group-velocity (ZGV) waves have the peculiarity of being stationary, and thus locally confining energy. Although they are particularly useful in evaluation applications, they have not yet been tracked in two dimensions. Here we image gigahertz zero-group-velocity Lamb waves in the time domain by means of an ultrafast optical technique, revealing their stationary nature and their acoustic energy localization. The acoustic field is imaged to micron resolution on a nanoscale bilayer consisting of a silicon-nitride plate coated with a titanium film. Temporal and spatiotemporal Fourier transforms combined with a technique involving the intensity modulation of the optical pump and probe beams gives access to arbitrary acoustic frequencies, allowing ZGV modes to be isolated. The dispersion curves of the bilayer system are extracted together with the quality factor Q and lifetime of the first ZGV mode. Applications include the testing of bonded nanostructures.
Local membrane charge regulates β2 adrenergic receptor coupling to Gi3
Authors: Strohman M. J. , Maeda S. , Hilger D. , Masureel M. , Du Y. , Kobilka B. K. 
Published: May 2019

AbstractThe β2 adrenergic receptor (β2AR) signals through both Gs and Gi in cardiac myocytes, and the Gi pathway counteracts the Gs pathway. However, Gi coupling is much less efficient than Gs coupling in most cell-based and biochemical assays, making it difficult to study β2AR−Gi interactions. Here we investigate the role of phospholipid composition on Gs and Gi coupling. While negatively charged phospholipids are known to enhance agonist affinity and stabilize an active state of the β2AR, we find that they impair coupling to Gi3 and facilitate coupling to Gs. Positively charged Ca2+ and Mg2+, known to interact with the negative charge on phospholipids, facilitates Gi3 coupling. Mutational analysis suggests that Ca2+ coordinates an interaction between phospholipid and the negatively charged EDGE motif on the amino terminal helix of Gi3. Taken together, our observations suggest that local membrane charge modulates the interaction between β2AR and competing G protein subtypes.
Genotype–covariate correlation and interaction disentangled by a whole-genome multivariate reaction norm model
Authors: Ni Guiyan , van der Werf Julius , Zhou Xuan , Hyppönen Elina , Wray Naomi R. , Lee S. Hong 
Published: May 2019

AbstractThe genomics era has brought useful tools to dissect the genetic architecture of complex traits. Here we propose a multivariate reaction norm model (MRNM) to tackle genotype–covariate (G–C) correlation and interaction problems. We apply MRNM to the UK Biobank data in analysis of body mass index using smoking quantity as a covariate, finding a highly significant G–C correlation, but only weak evidence for G–C interaction. In contrast, G–C interaction estimates are inflated in existing methods. It is also notable that there is significant heterogeneity in the estimated residual variances (i.e., variances not attributable to factors in the model) across different covariate levels, i.e., residual–covariate (R–C) interaction. We also show that the residual variances estimated by standard additive models can be inflated in the presence of G–C and/or R–C interactions. We conclude that it is essential to correctly account for both interaction and correlation in complex trait analyses.
Aβ34 is a BACE1-derived degradation intermediate associated with amyloid clearance and Alzheimer’s disease progression
Authors: Liebsch Filip , Kulic Luka , Teunissen Charlotte , Shobo Adeola , Ulku Irem , Engelschalt Vivienne , Hancock Mark A. , van der Flier Wiesje M. , Kunach Peter , Rosa-Neto Pedro , Scheltens Philip , Poirier Judes , Saftig Paul , Bateman Randall J. , Breitner John , Hock Christoph , Multhaup Gerhard 
Published: May 2019

AbstractThe beta-site APP cleaving enzyme 1 (BACE1) is known primarily for its initial cleavage of the amyloid precursor protein (APP), which ultimately leads to the generation of Aβ peptides. Here, we provide evidence that altered BACE1 levels and activity impact the degradation of Aβ40 and Aβ42 into a common Aβ34 intermediate. Using human cerebrospinal fluid (CSF) samples from the Amsterdam Dementia Cohort, we show that Aβ34 is elevated in individuals with mild cognitive impairment who later progressed to dementia. Furthermore, Aβ34 levels correlate with the overall Aβ clearance rates in amyloid positive individuals. Using CSF samples from the PREVENT-AD cohort (cognitively normal individuals at risk for Alzheimer’s disease), we further demonstrate that the Aβ34/Aβ42 ratio, representing Aβ degradation and cortical deposition, associates with pre-clinical markers of neurodegeneration. We propose that Aβ34 represents a marker of amyloid clearance and may be helpful for the characterization of Aβ turnover in clinical samples.
Tracking carrier protein motions with Raman spectroscopy
Authors: Epstein Samuel C. , Huff Adam R. , Winesett Emily S. , Londergan Casey H. , Charkoudian Louise K. 
Published: May 2019

AbstractEngineering microbial biosynthetic pathways represents a compelling route to gain access to expanded chemical diversity. Carrier proteins (CPs) play a central role in biosynthesis, but the fast motions of CPs make their conformational dynamics difficult to capture using traditional spectroscopic approaches. Here we present a low-resource method to directly reveal carrier protein-substrate interactions. Chemoenzymatic loading of commercially available, alkyne-containing substrates onto CPs enables rapid visualization of the molecular cargo’s local environment using Raman spectroscopy. This method could clarify the foundations of the chain sequestration mechanism, facilitate the rapid characterization of CPs, and enable visualization of the vectoral processing of natural products both in vitro and in vivo.
Methylation and PTEN activation in dental pulp mesenchymal stem cells promotes osteogenesis and reduces oncogenesis
Authors: Shen Wen-Ching , Lai Yung-Chih , Li Ling-Hui , Liao Kolin , Lai Hung-Chang , Kao Shou-Yen , Wang John , Chuong Cheng-Ming , Hung Shih-Chieh 
Published: May 2019

AbstractLineage commitment and tumorigenesis, traits distinguishing stem cells, have not been well characterized and compared in mesenchymal stem cells derived from human dental pulp (DP-MSCs) and bone marrow (BM-MSCs). Here, we report DP-MSCs exhibit increased osteogenic potential, possess decreased adipogenic potential, form dentin pulp-like complexes, and are resistant to oncogenic transformation when compared to BM-MSCs. Genome-wide RNA-seq and differential expression analysis reveal differences in adipocyte and osteoblast differentiation pathways, bone marrow neoplasm pathway, and PTEN/PI3K/AKT pathway. Higher PTEN expression in DP-MSCs than in BM-MSCs is responsible for the lineage commitment and tumorigenesis differences in both cells. Additionally, the PTEN promoter in BM-MSCs exhibits higher DNA methylation levels and repressive mark H3K9Me2 enrichment when compared to DP-MSCs, which is mediated by increased DNMT3B and G9a expression, respectively. The study demonstrates how several epigenetic factors broadly affect lineage commitment and tumorigenesis, which should be considered when developing therapeutic uses of stem cells.