bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deriving Tidal Flat Topography Using ICESat‐2 Laser Altimetry and Sentinel‐2 Imagery
Authors: Xu Nan , Ma Yue , Yang Jian , Wang Xiao Hua , Wang Yongjun , Xu Rui 
Published: January 2022

AbstractAcquiring accurate and timely datasets on tidal flat topography is fundamental for studies, management, and policy‐making in coastal zones. In this study, we report a fusion method of freely accessed and global‐scale Sentinel‐2 (imagery) and Ice,Cloud, and Land Elevation Satellite‐2 (ICESat‐2) (laser altimetry) datasets for deriving tidal flat topography. The basic idea is to construct a model on characterizing the specific relationship between the elevations of the tidal flat (from ICESat‐2 data) and corresponding inundation frequencies (from Sentinel‐2 time‐series). The proposed method was validated for the largest tidal flat on the Chinese continental shelf with a root mean square error of 0.23 m. We highlight that this method solely relies on satellite data and does not require any in‐situ data because ICESat‐2 provides dense and accurate along‐track points as valuable prior elevation information, which enhance the ability to obtain tidal flat topography in many coastal regions even in the absence of local in‐situ data.
The Alternating Change of Cold and Warm Extremes Over North Asia During Winter 2020/21: Effect of the Annual Cycle Anomaly
Authors: Yu Minjie , Ma Shuangmei , Zhu Congwen 
Published: January 2022

AbstractLarge‐scale cold and warm spells successively attacked North Asia (NA) and resulted in a subseasonal alternation of extreme surface air temperature (SAT) before and after 15 January 2021. Our results show the synergistic effect of annual cycle and intraseasonal oscillation component (AC and ISO) of SAT and circulation anomalies caused temperature extremes. Before 15 January 2021, an eastward‐propagating Rossby wave train strengthened the cold circulation regime with an enhanced Ural blocking high (UBH) and surface Siberian high (SH). Circulation anomalies of the negative ISO were superimposed on the counterpart of AC, which easily resulted in cold extremes via nonlinear interaction of meridional temperature gradient. After mid‐January 2021, however, weakened UBH and SH caused warm advection and spells over NA. This synergistic effect of AC and ISO anomalies in SAT accounted for most historical temperature extremes, implying that AC anomalies have important indications for subseasonal alternation of temperature extremes.
Elastic Wave Velocity Changes Due to the Fracture Aperture and Density, and Direct Correlation With Permeability: An Energetic Approach to Mated Rock Fractures
Authors: Sawayama K. , Ikeda T. , Tsuji T. , Jiang F. , Nishizawa O. , Fujimitsu Y. 
Published: January 2022

AbstractIn an effort to reveal the subsurface hydraulic changes in fractures by seismic monitoring, aperture‐related velocity changes need to be investigated. We developed a numerical approach for calculating changes in elastic wave velocity with fracture aperture opening by determining the internal energy of a digitized fracture model based on natural rough surfaces. The simulated local elastic energy revealed that the interaction energy converged within 1.5 mm of the mean fracture position, and was insignificant unless the fractures intersected. This energetic approach clarified the aperture‐velocity relationship and reproduced the experimental results. Further calculations using digital fractures with various sizes and densities demonstrated that the velocity can be accounted for by the superposition of a linear function of fracture density and quadratic function of aperture, and is insensitive to the fracture size. Although the relationship between fracture permeability and elastic wave velocity (i.e., the k‐V relationship) depends on the fracture density, the offset‐normalized k‐V relationship shows clear linearity with the fracture density. The proposed k‐V relationship as a function of the aperture and fracture density indicates that laboratory‐scale fracture properties of a single fracture can be applied to multiple fractures on a larger scale. Our findings can be used to interpret temporal changes in seismic observations and to monitor fluid flow in fractures.
Seismic Velocity Recovery in the Subsurface: Transient Damage and Groundwater Drainage Following the 2015 Gorkha Earthquake, Nepal
Authors: Illien Luc , Sens‐Schönfelder Christoph , Andermann Christoff , Marc Odin , Cook Kristen L. , Adhikari Lok B. , Hovius Niels 
Published: January 2022

AbstractShallow earthquakes frequently disturb the hydrological and mechanical state of the subsurface, with consequences for hazard and water management. Transient post‐seismic hydrological behavior has been widely reported, suggesting that the recovery of material properties (relaxation) following ground shaking may impact groundwater fluctuations. However, the monitoring of seismic velocity variations associated with earthquake damage and hydrological variations are often done assuming that both effects are independent. In a field site prone to highly variable hydrological conditions, we disentangle the different forcing of the relative seismic velocity variations δv retrieved from a small dense seismic array in Nepal in the aftermath of the 2015 Mw 7.8 Gorkha earthquake. We successfully model transient damage effects by introducing a universal relaxation function that contains a unique maximum relaxation timescale for the main shock and the aftershocks, independent of the ground shaking levels. Next, we remove the modeled velocity from the raw data and test whether the corresponding residuals agree with a background hydrological behavior we inferred from a previously calibrated groundwater model. The fitting of the δv data with this model is improved when we introduce transient hydrological properties in the phase immediately following the main shock. This transient behavior, interpreted as an enhanced permeability in the shallow subsurface, lasts for ∼6 months and is shorter than the damage relaxation (∼1 yr). Thus, we demonstrate the capability of seismic interferometry to deconvolve transient hydrological properties after earthquakes from non‐linear mechanical recovery.
Response of Moist Convection to the Spectral Feature of the Surface Flux Field at Model Resolution Across the Gray Zone
Authors: Ryu Jung‐Hee , Kang Song‐Lak 
Published: January 2022

AbstractThe Weather Research and Forecasting model is run at the effective resolution Δf across the gray zone, or the “terra incognita”, at which Δf ∼ l, where l is the scale of energy‐containing turbulent eddies. We examine the developments of afternoon moist convection over different multiscale features of the surface flux field as a function of the model grid spacing Δ that varies from 100 m to 1 km. Numerical experiments demonstrate that the model performs better under heterogeneous than homogeneous surface conditions in the gray zone in terms of the spatial distribution of moist convection. This improved performance is due to the explicit resolvability of the mesoscale temperature and humidity perturbations, which are critical for the growth of deep moist convection over the heterogeneous surface condition. However, under both heterogeneous and homogeneous surface conditions, the timing and intensity of moist convection vary with the model resolution. Compared with that in the large eddy simulation at Δ = 100 m, the earlier onset of moist convection at coarser resolutions appears to be related to the overestimated total buoyancy fluxes and total kinetic energy near the surface. That is, the more intense vertical mixing near the surface might induce a warmer surface layer, which yields individual cell updrafts strong enough to penetrate the capping inversion. In addition, misrepresentation of the diluting effects of entrainment on the penetrating updrafts in coarser‐resolution simulations could be responsible for the rapid development of deep convection instead of a gradual transition from shallow to deep moist convection.
Disentangling the Influence of Landscape Characteristics, Hydroclimatic Variability and Land Management on Surface Water NO3‐N Dynamics: Spatially Distributed Modeling Over 30 yr in a Lowland Mixed Land Use Catchment
Authors: Wu Songjun , Tetzlaff Doerthe , Yang Xiaoqiang , Soulsby Chris 
Published: January 2022

AbstractNitrate (NO3‐N) mobilization is generally controlled by available sources, hydrological connectivity, and biogeochemical transformations along the dominant flow paths. However, their spatial heterogeneity and complex interactions often impede integrated understanding of NO3‐N dynamics at the catchment scale. To fully integrate spatiotemporal information for NO3‐N simulations, a grid‐based model, mHM‐Nitrate, was applied to a 68 km2 lowland, mixed land use catchment (Demnitzer Millcreek, DMC) near Berlin. The model successfully captured the spatiotemporal distribution of flow and NO3‐N between 2001 and 2019, but was less successful in 1992–2000 due to land management changes. Re‐optimization of relative parameters was subsequently conducted for this period to understand management effects. The simulated results revealed landscape characteristics and hydroclimatic variability as the main controlling factors on respective spatial and temporal patterns. The combined effects of vegetation cover and fertilizer inputs dictated the spatial distribution of water and NO3‐N fluxes, while wetness condition determined the temporal NO3‐N dynamics by regulating hydrological connectivity and NO3‐N mobilization. Denitrification was also closely coupled with hydroclimatic conditions, which accounted for ∼20% of NO3‐N inputs. In contrast, restoration of riparian wetlands had a modest impact on NO3‐N export (∼10% reduction during 2001–2019), suggesting further interventions (e.g., reducing fertilizer application or increased wetland areas) are needed. Our modeling application demonstrated that mHM‐Nitrate could provide robust spatially distributed simulations of hydrological and NO3‐N fluxes over a long‐term period and could successfully differentiate the key controlling factors. This underlines the model's value in contributing to an evidence base to guide future management practices under climate change.
Mid-infrared-perturbed molecular vibrational signatures in plasmonic nanocavities
Authors: Chikkaraddy Rohit , Xomalis Angelos , Jakob Lukas A. , Baumberg Jeremy J. 
Published: January 2022

AbstractRecent developments in surface-enhanced Raman scattering (SERS) enable observation of single-bond vibrations in real time at room temperature. By contrast, mid-infrared (MIR) vibrational spectroscopy is limited to inefficient slow detection. Here we develop a new method for MIR sensing using SERS. This method utilizes nanoparticle-on-foil (NPoF) nanocavities supporting both visible and MIR plasmonic hotspots in the same nanogap formed by a monolayer of molecules. Molecular SERS signals from individual NPoF nanocavities are modulated in the presence of MIR photons. The strength of this modulation depends on the MIR wavelength, and is maximized at the 6–12 μm absorption bands of SiO2 or polystyrene placed under the foil. Using a single-photon lock-in detection scheme we time-resolve the rise and decay of the signal in a few 100 ns. Our observations reveal that the phonon resonances of SiO2 can trap intense MIR surface plasmons within the Reststrahlen band, tuning the visible-wavelength localized plasmons by reversibly perturbing the localized few-nm-thick water shell trapped in the nanostructure crevices. This suggests new ways to couple nanoscale bond vibrations for optomechanics, with potential to push detection limits down to single-photon and single-molecule regimes.
Anti-miR-135/SPOCK1 axis antagonizes the influence of metabolism on drug response in intestinal/colon tumour organoids
Authors: Babaei-Jadidi Roya , Kashfi Hossein , Alelwani Walla , Karimi Bakhtiari Ashkan , Kattan Shahad W. , Mansouri Omniah A. , Mukherjee Abhik , Lobo Dileep N. , Nateri Abdolrahman S. 
Published: January 2022

AbstractLittle is known about the role of microRNAs (miRNAs) in rewiring the metabolism within tumours and adjacent non-tumour bearing normal tissue and their potential in cancer therapy. This study aimed to investigate the relationship between deregulated miRNAs and metabolic components in murine duodenal polyps and non-polyp-derived organoids (mPOs and mNPOs) from a double-mutant ApcMinFbxw7∆G mouse model of intestinal/colorectal cancer (CRC). We analysed the expression of 373 miRNAs and 12 deregulated metabolic genes in mPOs and mNPOs. Our findings revealed miR-135b might target Spock1. Upregulation of SPOCK1 correlated with advanced stages of CRCs. Knockdown of miR-135b decreased the expression level of SPOCK1, glucose consumption and lactic secretion in CRC patient-derived tumours organoids (CRC tPDOs). Increased SPOCK1 induced by miR-135b overexpression promoted the Warburg effect and consequently antitumour effect of 5-fluorouracil. Thus, combination with miR-135b antisense nucleotides may represent a novel strategy to sensitise CRC to the chemo-reagent based treatment.
Long-term outcome following surgical treatment of posttraumatic tethered cord syndrome: a retrospective population-based cohort study
Authors: Stenimahitis Vasilios , Fletcher-Sandersjöö Alexander , Tatter Charles , Elmi-Terander Adrian , Edström Erik 
Published: January 2022

Abstract
Study design
Retrospective population-based cohort study.

Objective
To investigate the long-term outcome following surgery for posttraumatic spinal cord tethering (PSCT).

Setting
Publicly funded tertiary care center.

Methods
Patients surgically treated for PSCT between 2005–2020 were identified and included. No patients were excluded or lost to follow-up. Medical records and imaging data were retrospectively reviewed.

Results
Seventeen patients were included. Median age was 52 (23–69) years and 7 (41%) were female. PSCT was diagnosed at a median of 5.0 (0.6–27) years after the initial trauma. Motor deficit was the most common neurological manifestation (71%), followed by sensory deficit (53%), spasticity (53%), pain (41%) and gait disturbance (24%). Median follow-up time was 5.1 (0.7–13) years. Fifteen patients (88%) showed satisfactory results following untethering, defined as improvement or halted progression of one or more of the presenting symptoms. Treatment goals were met for motor symptoms in 92%, sensory loss in 100%, spasticity in 100%, gait disturbance in 100% and pain in 86%. Statistically, a significant improvement in motor deficit (p = 0.031) and syrinx decrease (p = 0.004) was also seen. A postoperative complication occurred in four patients: three cases of cerebrospinal fluid leakage and one postoperative hematoma. Two patients showed a negative surgical outcome: 1 with increased neck pain and 1 with left arm weakness following the postoperative hematoma.

Conclusion
Surgical treatment of PSCT results in improved neurological function or halted neurological deterioration in the vast majority of patients.
Dexmedetomidine promotes apoptosis and suppresses proliferation of hepatocellular carcinoma cells via microRNA-130a/EGR1 axis
Authors: Zhou Lei , Li Juanni , Liu Xing , Tang Yongzhong , Li Tunliang , Deng Huiyin , Chen Jia , Yin Xinlin , Hu Kuan , Ouyang Wen 
Published: January 2022

AbstractAccumulating evidence has revealed the role of microRNAs (miRs) in hepatocellular carcinoma (HCC). Dexmedetomidine, a highly selective α2-adrenergic agonist, is widely used in perioperative settings for analgesia and sedation. Herein, we aimed to determine whether dexmedetomidine might directly regulate miR-130a/early growth response 1 (EGR1) axis in HCC and explore the related mechanisms. miR-130a and EGR1 expression were determined in HCC tissues and their correlation was evaluated. Human HCC cell line HCCLM3 was selected. Upon the determination of the optimal concentration of dexmedetomidine, HCCLM3 cells were treated with dexmedetomidine, miR-130a- or EGR1-related oligonucleotides or plasmids were transfected into cells to explore their functions in cell biological behaviors. miR-130a and EGR1 levels in cells were tested. The targeting relationship between miR-130a and EGR1 was verified. miR-130a was inhibited while EGR1 was elevated in HCC tissues and they were negatively correlated. EGR1 was targeted by miR-130a. With the increase of dexmedetomidine concentration, HCCLM3 cell viability was correspondingly inhibited, miR-130a expression was elevated and EGR1 expression was decreased. Dexmedetomidine, upregulating miR-130a or downregulating EGR1 inhibited proliferation, invasion and migration, and promoted apoptosis of HCCLM3 cells. MiR-130a upregulation/downregulation enhanced/impaired the effect of dexmedetomidine on cell biological behaviors. Our study provides evidence that raising miR-130a enhances the inhibitory effects of dexmedetomidine on HCC cellular growth via inhibiting EGR1. Thus, miR-130a may be a potential candidate for the treatment of HCC.
Quantification of bone marrow interstitial pH and calcium concentration by intravital ratiometric imaging
Authors: Yeh S-C. A. , Hou J. , Wu J. W. , Yu S. , Zhang Y. , Belfield K. D. , Camargo F. D. , Lin C. P. 
Published: January 2022

AbstractThe fate of hematopoietic stem cells (HSCs) can be directed by microenvironmental factors including extracellular calcium ion concentration ([Ca2+]e), but the local [Ca2+]e around individual HSCs in vivo remains unknown. Here we develop intravital ratiometric analyses to quantify the absolute pH and [Ca2+]e in the mouse calvarial bone marrow, taking into account the pH sensitivity of the calcium probe and the wavelength-dependent optical loss through bone. Unexpectedly, the mean [Ca2+]e in the bone marrow (1.0 ± 0.54 mM) is not significantly different from the blood serum, but the HSCs are found in locations with elevated local [Ca2+]e (1.5 ± 0.57 mM). With aging, a significant increase in [Ca2+]e is found in M-type cavities that exclusively support clonal expansion of activated HSCs. This work thus establishes a tool to investigate [Ca2+]e and pH in the HSC niche with high spatial resolution and can be broadly applied to other tissue types.
The Fe-FeSi phase diagram at Mercury’s core conditions
Authors: Edmund E. , Morard G. , Baron M. A. , Rivoldini A. , Yokoo S. , Boccato S. , Hirose K. , Pakhomova A. , Antonangeli D. 
Published: January 2022

AbstractMercury’s metallic core is expected to have formed under highly reducing conditions, resulting in the presence of significant quantities of silicon alloyed to iron. Here we present the phase diagram of the Fe-FeSi system, reconstructed from in situ X-ray diffraction measurements at pressure and temperature conditions spanning over those expected for Mercury’s core, and ex situ chemical analysis of recovered samples. Under high pressure, we do not observe a miscibility gap between the cubic fcc and B2 structures, but rather the formation of a re-entrant bcc phase at temperatures close to melting. Upon melting, the investigated alloys are observed to evolve towards two distinct Fe-rich and Fe-poor liquid compositions at pressures below 35-38 GPa. The evolution of the phase diagram with pressure and temperature prescribes a range of possible core crystallization regimes, with strong dependence on the Si abundance of the core.
Structure of a type IV secretion system core complex encoded by multi-drug resistance F plasmids
Authors: Liu Xiangan , Khara Pratick , Baker Matthew L. , Christie Peter J. , Hu Bo 
Published: January 2022

AbstractBacterial type IV secretion systems (T4SSs) are largely responsible for the proliferation of multi-drug resistance. We solved the structure of the outer-membrane core complex (OMCCF) of a T4SS encoded by a conjugative F plasmid at <3.0 Å resolution by cryoelectron microscopy. The OMCCF consists of a 13-fold symmetrical outer ring complex (ORC) built from 26 copies of TraK and TraV C-terminal domains, and a 17-fold symmetrical central cone (CC) composed of 17 copies of TraB β-barrels. Domains of TraV and TraB also bind the CC and ORC substructures, establishing that these proteins undergo an intraprotein symmetry alteration to accommodate the C13:C17 symmetry mismatch. We present evidence that other pED208-encoded factors stabilize the C13:C17 architecture and define the importance of TraK, TraV and TraB domains to T4SSF function. This work identifies OMCCF structural motifs of proposed importance for structural transitions associated with F plasmid dissemination and F pilus biogenesis.
The QChip1 knowledgebase and microarray for precision medicine in Qatar
Authors: Rodriguez-Flores Juan L. , Messai-Badji Radja , Robay Amal , Temanni Ramzi , Syed Najeeb , Markovic Monika , Al-khayat Eiman , Qafoud Fatima , Nawaz Zafar , Badii Ramin , Al-Sarraj Yasser , Mbarek Hamdi , Al-Muftah Wadha , Alvi Muhammad , Rostami Mahboubeh R. , Cruzado Juan Carlos Martinez , Mezey Jason G. , Shakaki Alya Al , Malek Joel A. , Greenblatt Matthew B. , Fakhro Khalid A. , Machaca Khaled , Al-Nabet Ajayeb , Afifi Nahla , Brooks Andrew , Ismail Said I. , Althani Asmaa , Crystal Ronald G. 
Published: January 2022

AbstractRisk genes for Mendelian (single-gene) disorders (SGDs) are consistent across populations, but pathogenic risk variants that cause SGDs are typically population-private. The goal was to develop “QChip1,” an inexpensive genotyping microarray to comprehensively screen newborns, couples, and patients for SGD risk variants in Qatar, a small nation on the Arabian Peninsula with a high degree of consanguinity. Over 108variants in 8445 Qatari were identified for inclusion in a genotyping array containing 165,695 probes for 83,542 known and potentially pathogenic variants in 3438 SGDs. QChip1 had a concordance with whole-genome sequencing of 99.1%. Testing of QChip1 with 2707 Qatari genomes identified 32,674 risk variants, an average of 134 pathogenic alleles per Qatari genome. The most common pathogenic variants were those causing homocystinuria (1.12% risk allele frequency), and Stargardt disease (2.07%). The majority (85%) of Qatari SGD pathogenic variants were not present in Western populations such as European American, South Asian American, and African American in New York City and European and Afro-Caribbean in Puerto Rico; and only 50% were observed in a broad collection of data across the Greater Middle East including Kuwait, Iran, and United Arab Emirates. This study demonstrates the feasibility of developing accurate screening tools to identify SGD risk variants in understudied populations, and the need for ancestry-specific SGD screening tools.