bluuebunny/crossref_metadata_2025_split huggingface dataset:
New Insights Into the Rift to Drift Transition Across the Northeastern Nova Scotian Margin From Wide‐Angle Seismic Waveform Inversion and Reflection Imaging
Authors: Jian Hanchao , Nedimović Mladen R. , Canales Juan Pablo , Lau K. W. Helen 
Published: November 2021

AbstractSparse wide‐angle seismic profiling supported by coincident reflection imaging has been instrumental for advancing our knowledge about rifted margins. Nevertheless, features of critical importance for understanding rifting processes have been poorly resolved. We derive a high‐resolution velocity model by applying full waveform inversion to the dense OETR‐2009 wide‐angle seismic profile crossing the northeastern Nova Scotian margin. We then create a coincident reflection image by prestack depth migrating the multichannel seismic data. This allows for the first detailed interpretation of the structures related to the final stages of continental breakup and incipient oceanic accretion at the Eastern North America Margin. Our interpretation includes a hyperextended continental domain overlying partially serpentinized mantle, followed by a 10‐km‐wide domain consisting of a continental block surrounded by layered and bright reflectors indicative of magmatic extrusions. A major fault, representing the continent‐ocean boundary, marks a sharp seaward transition to a 16‐km‐wide domain characterized by smoother basement with chaotic reflectors, where no continental materials are present and a 3‐km‐thick embryonic oceanic crust overlying partially serpentinized mantle is created by the breakup magmatism. Further seaward, thin oceanic crust overlies the serpentinized mantle suggesting magma‐poor oceanic spreading with variable magma supply as determined from variable basement topography, 2–4 km thick volcanic layer, and magnetic anomalies. Our results demonstrate that magmatism played an important role in the lithospheric breakup of the area crossed by the OETR‐2009 profile. Considering that the northeastern Nova Scotian margin has been classified as amagmatic, large margin‐parallel variations in magma supply likely characterize a single rift segment.
Evidence of Recent Active Volcanism in the Balleny Islands (Antarctica) From Ice Core Records
Authors: Tetzner Dieter R. , Thomas Elizabeth R. , Allen Claire S. , Piermattei Alma 
Published: November 2021

AbstractVolcanism can play a key role in modulating climate; however, a lack of historical records has limited our comprehension of Antarctic volcanism and its role on the cryosphere. Remote sensing can provide insight into active volcanism in Antarctica during the satellite era, although the evidence is often inconclusive. Here, we use independent evidence from ice cores to validate one such potential volcanic eruption from the sub‐Antarctic Balleny Islands in 2001 CE. Multiple ice cores from downwind of the eruption site, record elevated input of sulfate, microparticles, and the presence of tephra, coincident with the eruption. In‐phase deposition of volcanic products confirmed a rapid tropospheric transport of volcanic emissions from a small‐to‐moderate, local eruption during 2001. Air mass trajectories demonstrated some air parcels were transported over the West Antarctic ice sheet from the Balleny Islands to ice core sites at the time of the potential eruption, establishing a route for transport and deposition of volcanic products over the ice sheet. The data presented here validate previous remote sensing observations and confirms a volcanic event in the Balleny Islands during 2001 CE. This newly identified eruption provides a case study of recent Antarctic volcanism.
Transit‐Time and Temperature Control the Spatial Patterns of Aerobic Respiration and Denitrification in the Riparian Zone
Authors: Nogueira G. E. H. , Schmidt C. , Brunner P. , Graeber D. , Fleckenstein J. H. 
Published: November 2021

AbstractDuring the flow of stream water from losing reaches through aquifer sediments, aerobic and anaerobic respiration (denitrification) can deplete dissolved oxygen and nitrate (NO3−), impacting water quality in the floodplain and downstream gaining reaches. Such processes, which vary in time with short and long‐term changes in stream flow and temperature, need to be assessed at the stream corridor scale to fully capture their effects on net turnover, but this has rarely been done. To address this gap, we combine a fully‐integrated 3D transient numerical flow model with temperature‐dependent reactive transport along advective subsurface flow paths to assess aerobic and anaerobic respiration dynamics at the stream corridor scale in a predominantly losing stream. Our results suggest that given carbon availability (as an electron donor), complete NO3− removal occurred further away from the stream after complete oxygen depletion and was relatively insensitive to variations in temperature and transit‐times. Conversely, transit‐times and oxygen concentrations constrained nitrate removal along short hyporheic flow paths. Even under limited carbon availability and low‐temperatures, NO3− removal fractions () will be greater at locations further from the stream than along shorter hyporheic flow paths ( = 0.4 and = 0.1, respectively). With increasing temperature, the relative effects of stream flow and solute concentrations on biogeochemical turnover and the redox zonation around the stream decreased. The study highlights the importance of seasonal variations of stream flow and temperature for water quality at the stream‐corridor scale. It also provides an adaptive framework to assess and quantify reach‐scale biogeochemical turnover around dynamic streams.
Identification of a TGF-β/SMAD/lnc-UTGF positive feedback loop and its role in hepatoma metastasis
Authors: Wu Meng-Zhi , Yuan Yi-chuan , Huang Bi-Yu , Chen Jin-Xi , Li Bin-Kui , Fang Jian-Hong , Zhuang Shi-Mei 
Published: November 2021

AbstractAberrant activation of the TGF-β/SMAD signaling pathway is often observed in hepatocellular carcinoma (HCC). Whether lncRNA regulates the TGF-β/SMAD signaling remains largely unknown. Here, we identified an oncogenic lncRNA that was upregulated in HCC and was transcriptionally induced by TGF-β (named lnc-UTGF, lncRNA upregulated by TGF-β). Upon TGF-β stimulation, SMAD2/3 bound to the lnc-UTGF promoter and activated lnc-UTGF expression. In turn, the TGF-β/SMAD signaling was augmented by overexpressing lnc-UTGF, but was inhibited by silencing lnc-UTGF. Mechanism investigations revealed that lnc-UTGF interacted with the mRNAs of SMAD2 and SMAD4 via complementary base-pairing, resulting in enhanced stability of SMAD2/4 mRNAs. These data suggest a novel TGF-β/SMAD/lnc-UTGF positive feedback circuitry. Subsequent gain- and loss-of-function analyses disclosed that lnc-UTGF promoted the migration and invasion of hepatoma cells, and this effect of lnc-UTGF was attenuated by repressing SMAD2/4 expression or by mutating the SMAD2/4-binding sites in lnc-UTGF. Studies using mouse models further confirmed that in vivo metastasis of hepatoma xenografts was inhibited by silencing lnc-UTGF, but was enhanced by ectopic expression of lnc-UTGF. The lnc-UTGF level was positively correlated with the SMAD2/4 levels in xenografts. Consistently, we detected an association of lnc-UTGF upregulation with increase of SMAD2, SMAD4, and their metastasis effector SNAIL1 in human HCC. And high lnc-UTGF level was also significantly associated with enhanced metastasis potential, advanced TNM stages, and worse recurrence-free survival. Conclusion: there exists a lnc-UTGF-mediated positive feedback loop of the TGF-β signaling and its deregulation promotes hepatoma metastasis. These findings may provide a new therapeutic target for HCC metastasis.
Diesel2p mesoscope with dual independent scan engines for flexible capture of dynamics in distributed neural circuitry
Authors: Yu Che-Hang , Stirman Jeffrey N. , Yu Yiyi , Hira Riichiro , Smith Spencer L. 
Published: November 2021

AbstractImaging the activity of neurons that are widely distributed across brain regions deep in scattering tissue at high speed remains challenging. Here, we introduce an open-source system with Dual Independent Enhanced Scan Engines for Large field-of-view Two-Photon imaging (Diesel2p). Combining optical design, adaptive optics, and temporal multiplexing, the system offers subcellular resolution over a large field-of-view of ~25 mm2, encompassing distances up to 7 mm, with independent scan engines. We demonstrate the flexibility and various use cases of this system for calcium imaging of neurons in the living brain.
Unassisted selective solar hydrogen peroxide production by an oxidised buckypaper-integrated perovskite photocathode
Authors: Mehrotra Rashmi , Oh Dongrak , Jang Ji-Wook 
Published: November 2021

AbstractHydrogen peroxide (H2O2) is an eco-friendly oxidant and a promising energy source possessing comparable energy density to that of compressed H2. The current H2O2 production strategies mostly depend on the anthraquinone oxidation process, which requires significant energy and numerous organic chemicals. Photocatalyst-based solar H2O2 production comprises single-step O2 reduction to H2O2, which is a simple and eco-friendly method. However, the solar-to-H2O2 conversion efficiency is limited by the low performance of the inorganic semiconductor-based photoelectrodes and low selectivity and stability of the H2O2 production electrocatalyst. Herein, we demonstrate unassisted solar H2O2 production using an oxidised buckypaper as the H2O2 electrocatalyst combined with a high-performance inorganic-organic hybrid (perovskite) photocathode, without the need for additional bias or sacrificial agents. This integrated photoelectrode system shows 100% selectivity toward H2O2 and a solar-to-chemical conversion efficiency of ~1.463%.
Structures of prokaryotic ubiquitin-like protein Pup in complex with depupylase Dop reveal the mechanism of catalytic phosphate formation
Authors: Cui Hengjun , Müller Andreas U. , Leibundgut Marc , Tian Jiawen , Ban Nenad , Weber-Ban Eilika 
Published: November 2021

AbstractPupylation is the post-translational modification of lysine side chains with prokaryotic ubiquitin-like protein (Pup) that targets proteins for proteasomal degradation in mycobacteria and other members of Actinobacteria. Pup ligase PafA and depupylase Dop are the two enzymes acting in this pathway. Although they share close structural and sequence homology indicative of a common evolutionary origin, they catalyze opposing reactions. Here, we report a series of high-resolution crystal structures of Dop in different functional states along the reaction pathway, including Pup-bound states in distinct conformations. In combination with biochemical analysis, the structures explain the role of the C-terminal residue of Pup in ATP hydrolysis, the process that generates the catalytic phosphate in the active site, and suggest a role for the Dop-loop as an allosteric sensor for Pup-binding and ATP cleavage.
Mechanical forces drive a reorientation cascade leading to biofilm self-patterning
Authors: Nijjer Japinder , Li Changhao , Zhang Qiuting , Lu Haoran , Zhang Sulin , Yan Jing 
Published: November 2021

AbstractIn growing active matter systems, a large collection of engineered or living autonomous units metabolize free energy and create order at different length scales as they proliferate and migrate collectively. One such example is bacterial biofilms, surface-attached aggregates of bacterial cells embedded in an extracellular matrix that can exhibit community-scale orientational order. However, how bacterial growth coordinates with cell-surface interactions to create distinctive, long-range order during biofilm development remains elusive. Here we report a collective cell reorientation cascade in growingVibrio choleraebiofilms that leads to a differentially ordered, spatiotemporally coupled core-rim structure reminiscent of a blooming aster. Cell verticalization in the core leads to a pattern of differential growth that drives radial alignment of the cells in the rim, while the growing rim generates compressive stresses that expand the verticalized core. Such self-patterning disappears in nonadherent mutants but can be restored through opto-manipulation of growth. Agent-based simulations and two-phase active nematic modeling jointly reveal the strong interdependence of the driving forces underlying the differential ordering. Our findings offer insight into the developmental processes that shape bacterial communities and provide ways to engineer phenotypes and functions in living active matter.
Optical emissions associated with narrow bipolar events from thunderstorm clouds penetrating into the stratosphere
Authors: Liu Feifan , Lu Gaopeng , Neubert Torsten , Lei Jiuhou , Chanrion Oliver , Østgaard Nikolai , Li Dongshuai , Luque Alejandro , Gordillo-Vázquez Francisco J. , Reglero Victor , Lyu Weitao , Zhu Baoyou 
Published: November 2021

AbstractNarrow bipolar events (NBEs) are signatures in radio signals from thunderstorms observed by ground-based receivers. NBEs may occur at the onset of lightning, but the discharge process is not well understood. Here, we present spectral measurements by the Atmosphere‐Space Interactions Monitor (ASIM) on the International Space Station that are associated with nine negative and three positive NBEs observed by a ground‐based array of receivers. We found that both polarities NBEs are associated with emissions at 337 nm with weak or no detectable emissions at 777.4 nm, suggesting that NBEs are associated with streamer breakdown. The rise times of the emissions for negative NBEs are about 10 μs, consistent with source locations at cloud tops where photons undergo little scattering by cloud particles, and for positive NBEs are ~1 ms, consistent with locations deeper in the clouds. For negative NBEs, the emission strength is almost linearly correlated with the peak current of the associated NBEs. Our findings suggest that ground-based observations of radio signals provide a new means to measure the occurrences and strength of cloud-top discharges near the tropopause.
Sequence logic at enhancers governs a dual mechanism of endodermal organ fate induction by FOXA pioneer factors
Authors: Geusz Ryan J. , Wang Allen , Lam Dieter K. , Vinckier Nicholas K. , Alysandratos Konstantinos-Dionysios , Roberts David A. , Wang Jinzhao , Kefalopoulou Samy , Ramirez Araceli , Qiu Yunjiang , Chiou Joshua , Gaulton Kyle J. , Ren Bing , Kotton Darrell N. , Sander Maike 
Published: November 2021

AbstractFOXA pioneer transcription factors (TFs) associate with primed enhancers in endodermal organ precursors. Using a human stem cell model of pancreas differentiation, we here discover that only a subset of pancreatic enhancers is FOXA-primed, whereas the majority is unprimed and engages FOXA upon lineage induction. Primed enhancers are enriched for signal-dependent TF motifs and harbor abundant and strong FOXA motifs. Unprimed enhancers harbor fewer, more degenerate FOXA motifs, and FOXA recruitment to unprimed but not primed enhancers requires pancreatic TFs. Strengthening FOXA motifs at an unprimed enhancer near NKX6.1 renders FOXA recruitment pancreatic TF-independent, induces priming, and broadens the NKX6.1 expression domain. We make analogous observations about FOXA binding during hepatic and lung development. Our findings suggest a dual role for FOXA in endodermal organ development: first, FOXA facilitates signal-dependent lineage initiation via enhancer priming, and second, FOXA enforces organ cell type-specific gene expression via indirect recruitment by lineage-specific TFs.
Rapid and flexible segmentation of electron microscopy data using few-shot machine learning
Authors: Akers Sarah , Kautz Elizabeth , Trevino-Gavito Andrea , Olszta Matthew , Matthews Bethany E. , Wang Le , Du Yingge , Spurgeon Steven R. 
Published: November 2021

AbstractAutomatic segmentation of key microstructural features in atomic-scale electron microscope images is critical to improved understanding of structure–property relationships in many important materials and chemical systems. However, the present paradigm involves time-intensive manual analysis that is inherently biased, error-prone, and unable to accommodate the large volumes of data produced by modern instrumentation. While more automated approaches have been proposed, many are not robust to a high variety of data, and do not generalize well to diverse microstructural features and material systems. Here, we present a flexible, semi-supervised few-shot machine learning approach for segmentation of scanning transmission electron microscopy images of three oxide material systems: (1) epitaxial heterostructures of SrTiO3/Ge, (2) La0.8Sr0.2FeO3 thin films, and (3) MoO3 nanoparticles. We demonstrate that the few-shot learning method is more robust against noise, more reconfigurable, and requires less data than conventional image analysis methods. This approach can enable rapid image classification and microstructural feature mapping needed for emerging high-throughput characterization and autonomous microscope platforms.
EVN observations of 6.7 GHz methanol maser polarization in massive star-forming regions
Authors: Surcis G. , Vlemmings W. H. T. , van Langevelde H. J. , Hutawarakorn Kramer B. , Bartkiewicz A. 
Published: November 2021

Context. Although the role of magnetic fields in launching molecular outflows in massive young stellar objects has been convincingly demonstrated by theoretical arguments, observationally, the alignment of the magnetic field lines with the molecular outflows is still under debate.
Aims. We aim to complete the measurements of the direction of the magnetic fields at milliarcsecond resolution around a sample of massive star-forming regions to determine whether the magnetic field and outflows are aligned.
Methods. In 2012, we started a large very long baseline interferometry campaign with the European VLBI Network to measure the magnetic field orientation and strength toward a sample of 31 massive star-forming regions (called the flux-limited sample) by analyzing the polarized emission of 6.7 GHz CH3OH masers. In the previous papers of the series, we have presented 80% of the sample. Here, we report the linearly and circularly polarized emission of 6.7 GHz CH3OH masers toward the last five massive star-forming regions of the flux-limited sample. The sources are G30.70-0.07, G30.76-0.05, G31.28+0.06, G32.03+0.06, and G69.52-0.97.
Results. We detected a total of 209 CH3OH maser cloudlets, 15% of which show linearly polarized emission (0.07–16.7%), and 2% of which show circularly polarized emission (0.2–4.2%). As reported in previous papers, in the last five sources of the flux-limited sample, we also measured well-ordered linear polarization vectors. Zeeman splitting was measured toward G30.70-0.07, G32.03+0.06, and G69.52-0.97.
Conclusions. The statistical analysis of the entire flux-limited sample shows that the observations are consistent with a bimodal distribution in the difference between the 3D magnetic field direction and the outflow axis, with half the magnetic field directions being perpendicular and the other half being parallel to the outflow. In addition, we determined that typical values of the linear and circular polarization fractions for 6.7 GHz CH3OH masers are Pl = 1.0–2.5% and PV = 0.5–0.75%, respectively. From the circularly polarized spectra of the CH3OH maser features, we found that a typical Zeeman splitting is in the range between 0.5 m s−1 and 2.0 m s−1. This would correspond to 9 mG < |B||| < 40 mG if F = 3 → 4 is the most favored of the eight hyperfine transitions that might contribute to the maser emission.
Ammonia-methane ratios from H-band near-infrared spectra of late-T and Y dwarfs
Authors: Martín E. L. , Zhang J.-Y. , Esparza P. , Gracia F. , Rasilla J. L. , Masseron T. , Burgasser A. J. 
Published: November 2021

Aims. Our goals are to investigate the relative absorption strengths of ammonia and methane using low-resolution H-band (1.5−1.7 microns) spectra obtained in the laboratory and compared with observational spectra of late-T and Y dwarfs, and to estimate what can be expected from the wide-angle low-resolution near-infrared spectroscopic survey that will be provided by the upcoming Euclid space mission.
Methods. Gas cells containing ammonia and methane at atmospheric pressure were custom-made in our chemical laboratory. Low-resolution near-infrared spectroscopy of these gas cells was collected in our optical laboratory. It is compared with simulated spectra using the high-resolution transmission molecular absorption database (HITRAN) for temperatures of 300 K and 500 K, and with near-infrared spectra of late-T dwarfs, Y dwarfs, Jupiter, and Saturn. We selected for this investigation the spectral region between 1.5 and 1.7 microns (H band) because it is covered by the Euclid red grism, it is particularly sensitive to the relative proportions of ammonia and methane opacity, and it is free from strong contributions of other abundant molecules, such as water vapor.
Results. The laboratory spectra showed that the ammonia and methane features present in the simulations that used the HITRAN database are incomplete. Using our laboratory spectra, we propose a modified version of the NH3-H spectral ratio with expanded integration limits that increases the amplitude of variation in the index with respect to spectral type. Combinations of our laboratory spectra were used to find the best fits to the observed spectra with the relative absorption ratio of ammonia to methane as a free parameter. A relationship was found between the Teff and the ratio of ammonia to methane from spectral classes T5 to Y2 (1100 K–350 K), in fairly good qualitative agreement with theoretical predictions for high-gravity objects and temperatures from 1100 K to 500 K. The ammonia-to-methane ratios in late-T and Y dwarfs are similar to that of Jupiter, suggesting a similar chemical composition. Simulations of the spectroscopic performance of Euclid suggest that it will yield Teff values and ratios of ammonia to methane for over 103 late-T dwarfs in the entire wide survey.