bluuebunny/crossref_metadata_2025_split huggingface dataset:
Source Region Geochemistry From Unmixing Downstream Sedimentary Elemental Compositions
Authors: Lipp Alex G. , Roberts Gareth G. , Whittaker Alexander C. , Gowing Charles J. B. , Fernandes Victoria M. 
Published: September 2021

AbstractThe geochemistry of river sediments is routinely used to obtain information about geologic and environmental processes occurring upstream. For example, downstream samples are used to constrain chemical weathering and physical erosion rates upstream, as well as the locations of mineral deposits or contaminant sources. Previous work has shown that, by assuming conservative mixing, the geochemistry of downstream samples can be reliably predicted given a known source region geochemistry. In this study, we tackle the inverse problem and “unmix” the composition of downstream river sediments to produce geochemical maps of drainage basins (i.e., source regions). The scheme is tested in a case study of rivers draining the Cairngorms, UK. The elemental geochemistry of the μm fraction of 67 samples gathered from the beds of channels in this region is used to invert for concentrations of major and trace elements upstream. A smoothed inverse problem is solved using the Nelder‐Mead optimization algorithm. Predictions of source region geochemistry are assessed by comparing the spatial distribution of 22 elements of different affinities (e.g., Be, Li, Mg, Ca, Rb, U, V) using independent geochemical survey data. The inverse approach makes reliable predictions of the major and trace element concentration in first order river sediments. We suggest this scheme could be a novel means to generate geochemical baselines across drainage basins and within river channels.
Breaking Down the Computational Barriers to Real‐Time Urban Flood Forecasting
Authors: Ivanov Valeriy Y. , Xu Donghui , Dwelle M. Chase , Sargsyan Khachik , Wright Daniel B. , Katopodes Nikolaos , Kim Jongho , Tran Vinh Ngoc , Warnock April , Fatichi Simone , Burlando Paolo , Caporali Enrica , Restrepo Pedro , Sanders Brett F. , Chaney Molly M. , Nunes Ana M. B. , Nardi Fernando , Vivoni Enrique R. , Istanbulluoglu Erkan , Bisht Gautam , Bras Rafael L. 
Published: September 2021

AbstractFlooding impacts are on the rise globally, and concentrated in urban areas. Currently, there are no operational systems to forecast flooding at spatial resolutions that can facilitate emergency preparedness and response actions mitigating flood impacts. We present a framework for real‐time flood modeling and uncertainty quantification that combines the physics of fluid motion with advances in probabilistic methods. The framework overcomes the prohibitive computational demands of high‐fidelity modeling in real‐time by using a probabilistic learning method relying on surrogate models that are trained prior to a flood event. This shifts the overwhelming burden of computation to the trivial problem of data storage, and enables forecasting of both flood hazard and its uncertainty at scales that are vital for time‐critical decision‐making before and during extreme events. The framework has the potential to improve flood prediction and analysis and can be extended to other hazard assessments requiring intense high‐fidelity computations in real‐time.
Mechanisms of Dune Growth and Decay in Rivers
Authors: Bradley Ryan W. , Venditti Jeremy G. 
Published: September 2021

AbstractThe mechanisms responsible for dune growth and decay remain a major unknown in river dynamics. Two theories have been supported by experiments and numerical models. A hydrodynamic explanation suggests that growth and decay occur due to phase lags between bed topography and sediment flux. Alternatively, kinematic processes have been invoked to explain growth by merger and decay by superimposed bedforms cannibalizing larger dunes. Demonstration of either mechanism in natural rivers has been lacking due to a paucity of high‐resolution topography. Here, we provide the first observations of rapid dune growth by kinematic processes during a rising hydrograph limb, followed by gradual adjustments likely through hydrodynamic processes at high flow. As flow wanes, smaller dunes develop and cannibalize larger features, eventually creating a flattened bed near base flow. Kinematic processes occur at a common threshold shear stress. Superimposed dunes formed during falling limbs of hydrographs are signatures of dune decay.
Global Survey of the MJO and Extreme Precipitation
Authors: Schreck Carl J. 
Published: September 2021

AbstractThis study examines the modulation of land‐based extreme precipitation around the globe by the Madden‐Julian Oscillation (MJO). The upper‐level convergent phase of the MJO inhibits extreme events over most regions but enhancement in other phases falls in three categories. Over Brazil, Southeast Asia, and Australia, 2‐year rainfall events are most common near the core of the upper‐level divergence as expected. For most other regions in the tropics and subtropics, the extreme events occur along the periphery of the MJO's envelope. Previous regional studies suggest these extremes are driven by the MJO's low‐level circulation either advecting moisture or interacting with orography rather than directly increasing the vertical convection. Finally, extratropical extreme events are more likely associated with the MJO's impact on extratropical wave trains or tropical cyclones. Given the increasing skill of numerical models for predicting the MJO, these results could lead to subseasonal forecasts of extreme events.
Broadband Imaging to Study the Spectral Distribution of Meteor Radio Afterglows
Authors: Varghese S. S. , Dowell J. , Obenberger K. S. , Taylor G. B. , Malins J. 
Published: September 2021

AbstractWe present observations of 86 meteor radio afterglows (MRAs) using the new broadband imager at the Long Wavelength Array Sevilleta (LWA‐SV) station. The MRAs were detected using the all‐sky images with a bandwidth up to 20 MHz. We fit the spectra with both a power law and a log‐normal function. When fit with a power law, the spectra varied from flat to steep and the derived spectral index distribution from the fit peaked at −1.73. When fit with a log‐normal function, the spectra exhibits turnovers at frequencies between 30 and 40 MHz, and appear to be a better functional fit to the spectra. We compared the spectral parameters from the two fitting methods with the physical properties of MRAs. We observe a weak correlation between the log‐normal turnover frequency and the altitude of MRAs. The spectral indices from the power law fit do not show any strong correlations with the physical properties of MRAs. However, the full width half maximum (FWHM) duration of MRAs is correlated with the local time, incidence angle, luminosity and optically derived kinetic energy of parent meteoroid. Also, the average luminosity of MRAs seems to be correlated with the kinetic energy of parent meteoroid and the altitude at which they occur.
Modified Parker's Method for Gravitational Forward and Inverse Modeling Using General Polyhedral Models
Authors: Wu Leyuan 
Published: September 2021

AbstractWe propose a new modified Parker's method for efficient gravitational forward modeling and inversion using general polyhedral models. We have made several important modifications to the classical method, including: (a) The new method is now applicable to a general polyhedron represented by triangulated surface or tetrahedral mesh, and with arbitrarily variable 3D density distribution. (b) An optimal Fourier‐domain sampling strategy is used to improve the numerical accuracy of the new algorithm significantly. (c) A simple and effective automatic layering technique is introduced to accelerate the convergence rate of Parker's method. The method is demonstrated using both synthetic and real polyhedral models, including a sphere model approximated by a polyhedron, two asteroids, a digital elevation model in the Himalaya region, and the Yucca Flat basin model in Nevada. The numerical results show that, compared with analytical solutions of polyhedral models in the space domain, the modified Parker's method can improve the computational efficiency by several orders of magnitude while obtaining almost the same simulation results. The difference is well below existing instrumentation error level. By embedding the new forward algorithm into an iterative process, it can be used for fast inversion of density interfaces. Our new method is suitable for the efficient modeling and inversion of gravitational potential, gravitational vector, and gravitational gradient tensor caused by polyhedral models with a large number of faces, representing geological abnormal bodies, asteroids, and single or multilayer density interface models with triangulated surfaces.
A Theory of Inter‐Granular Transient Dislocation Creep: Implications for the Geophysical Studies on Mantle Rheology
Authors: Karato Shun‐ichiro 
Published: September 2021

AbstractTransient creep may play an important role in short‐term (small strain) time‐dependent deformation such as the post‐glacial rebound and the post‐seismic deformation. Among various mechanisms of transient creep, I focus on inter‐granular transient dislocation creep caused by plastic anisotropy in each grain. The essence of this process is the evolution of strain accommodation across grain‐boundaries from elastic to plastic (viscous) accommodation. Extending the previous studies, I show that evolution of strain accommodation leads to two asymptotic behaviors: at small strain, strain accommodation across grain‐boundaries is by elastic deformation and the strength is controlled largely by that of the soft slip system. In contrast, when strain exceeds a threshold value, strain accommodation occurs mostly by plastic deformation and the strength is largely controlled by that of the hard slip system. The model predicts that the threshold strain is on the order of elastic strain (depending also on the degree of plastic anisotropy) and the strength contrast between transient and steady‐state creep depends on the degree of plastic anisotropy of the crystal. Consequently, transient creep plays an important role in these short‐term time‐dependent processes. Since the soft and the hard slip systems have different properties, applications of rheological properties inferred from short‐term time‐dependent deformation to long‐term geodynamic processes needs to be made with a great care.
The Cause of an Extremely Low Salinity Anomaly in the Bay of Bengal During 2012 Spring
Authors: Li Zhiyuan , Lian Tao , Ying Jun , Zhu Xiao‐Hua , Papa Fabrice , Xie Huawei , Long Yu 
Published: September 2021

AbstractAn extremely low salinity anomaly was observed in the Bay of Bengal (BoB) by various in situ and satellite observations during 2012 spring and ranked as the strongest anomaly in the last two decades. By analyzing various observational and reanalysis datasets, we find that the reversing circulation anomalies caused by a rare co‐occurrence of positive Indian Ocean Dipole (pIOD) and La Niña in 2011 were the main cause of this extreme event. In the fall of 2011, the pIOD favored an anticyclonic circulation anomaly flowing from the BoB into the equatorial Indian Ocean, whereas the La Niña event, which matured in the following winter, sharply reversed the circulation anomaly to a cyclonic pattern. As a result, these reversing circulation anomalies inhibited the southward freshwater transport along the two sides of the BoB and trapped substantial freshwater to the northern bay by the end of winter. Thereafter, the strong seasonal anticyclonic circulation transported this freshwater into the central and southern bay from the northeastern BoB coastal area, forming the extremely low salinity anomaly during 2012 spring. The key process in forming the extremely low salinity anomaly was the modulation of the seasonal monsoon by interannual processes, specifically the rare combination of pIOD and La Niña in 2011. Our results highlight the important role of the oceanic circulation in the sea surface salinity (SSS) variability in the BoB. This study provides some new perspectives on the SSS interannual variability in the BoB and the freshwater exchange between the BoB and Arabian Sea.
A Global Thermal Conductivity Model for Lunar Regolith at Low Temperatures
Authors: Martinez A. , Siegler M. A. 
Published: September 2021

AbstractAlthough some of the coldest surface temperatures in the entire Solar System are found near the poles of our own Moon, the thermophysical properties of lunar regolith at these ultracold temperatures (i.e., below ∼150 K) are not well understood. Standard lunar thermal models generally match the surface temperatures observed by global orbital remote sensing data but are inconsistent with infrared data collected from ultracold polar terrain. We build upon previous theoretical work on the low‐temperature physics of lunar regolith to introduce a global thermal conductivity model consistent with the temperature trends observed by the Diviner Lunar Radiometer Experiment (Diviner). This updated thermophysical model primarily affects nighttime surface temperatures, subsurface temperatures at high latitudes, and permanently shadowed regions (PSRs). An additional outcome of this thermophysical model is the ability to accommodate the surface temperature trends observed by Diviner both in warm low latitudes and cold high latitudes. Subsurface temperatures in near‐polar craters are ∼5–10 K warmer than previous thermal models, and cooler nighttime surface temperatures are observed globally. Model results of PSRs reveal larger surface temperature amplitudes (as observed by Diviner) and steeper geothermal gradients. A comprehensive understanding of lunar regolith's low‐temperature thermal behavior is an essential step in modeling the potential location and quantity of cold trapped volatiles in the lunar south pole. Here, we hope to provide theoretical support and motivation for more complete low‐temperature thermal conductivity laboratory measurements.
Neodymium Isotope Records From the Northwestern Pacific: Implication for Deepwater Ventilation at Heinrich Stadial 1
Authors: Horikawa Keiji , Kozaka Yukiko , Okazaki Yusuke , Sagawa Takuya , Onodera Jonaotaro , Asahi Hirofumi , Shin Ki‐Cheol , Asahara Yoshihiro , Takahashi Kozo 
Published: September 2021

AbstractDuring Heinrich Stadial 1 (HS1, 18.0–14.7 kyr ago), the Bering and Okhotsk Seas in the western Subarctic Pacific (SAP) exhibited boundary conditions that enhanced intermediate water convection. However, little is known about the quantitative contribution of the intermediate waters from the Bering and Okhotsk Sea (BSIW and OSIW) to ventilation in the open SAP intermediate–deep layers. In this study, we analyzed the neodymium (Nd) isotopes of fish debris (εNd‐FD) from sediment cores in the Northwestern Pacific, and observed a reduction in εNd (up to −2.6) from the Last Glacial Maximum to HS1 at Sites MD01‐2420 (2,101 m) and KH99‐3 ES (2,388 m). The relevance of reduced HS1 εNd‐FD shifts across the cores cannot be explained by the porewater influence, which generally changes authigenic εNd in opposite ways. Instead, as the εNd‐FD shifts concurred with a reduction in the 14C ventilation age, HS1 εNd‐FD shifts suggest the entrainment of younger and distinct εNd water mass sinking in the Okhotsk and/or Bering Seas. A mixing model applying Nd isotopes, their concentrations, and 14C ventilation ages of BSIW, OSIW, and the Lower Circumpolar Deep Water showed that during HS1, BSIW (36%–41%) was more conducive to the water mass at Site MD01‐2420, compared to OSIW (4%–8%). We argue that the Bering Sea has wider and deeper connections (Kamchatka and Near Straits, ∼4,400–2,200 m) with the western SAP, and the deep conduit would enable BSIW to more effectively flow out into the open Northwestern Pacific deep layer.
Predicting high-grade prostate cancer at initial biopsy: clinical performance of the ExoDx (EPI) Prostate Intelliscore test in three independent prospective studies
Authors: Margolis Erik , Brown Gordon , Partin Alan , Carter Ballentine , McKiernan James , Tutrone Ronald , Torkler Phillipp , Fischer Christian , Tadigotla Vasisht , Noerholm Mikkel , Donovan Michael J. , Skog Johan 
Published: September 2021

Abstract
Background
The ability to discriminate indolent from clinically significant prostate cancer (PC) at the initial biopsy remains a challenge. The ExoDx Prostate (IntelliScore) (EPI) test is a noninvasive liquid biopsy that quantifies three RNA targets in urine exosomes. The EPI test stratifies patients for risk of high-grade prostate cancer (HGPC; ≥ Grade Group 2 [GG] PC) in men ≥ 50 years with equivocal prostate-specific antigen (PSA) (2–10 ng/mL). Here, we present a pooled meta-analysis from three independent prospective-validation studies in men presenting for initial biopsy decision.

Methods
Pooled data from two prospective multi-site validation studies and the control arm of a clinical utility study were analyzed. Performance was evaluated using the area under the receiver-operating characteristic curve (AUC), negative predictive value (NPV), positive predictive value (PPV), sensitivity, and specificity for discriminating ≥ GG2 from GG1 and benign pathology.

Results
The combined cohort (n = 1212) of initial-biopsy subjects had a median age of 63 years and median PSA of 5.2 ng/mL. The EPI AUC (0.70) was superior to PSA (0.56), Prostate Cancer Prevention Trial Risk Calculator (PCPT-RC) (0.62), and The European Randomized Study of Screening for Prostate Cancer (ERSPC) (0.59), (all p-values <0.001) for discriminating GG2 from GG1 and benign histology. The validated cutoff of 15.6 would avoid 23% of all prostate biopsies and 30% of “unnecessary” (benign or Gleason 6/GG1) biopsies, with an NPV of 90%.

Conclusions
EPI is a noninvasive, easy-to-use, urine exosome–RNA assay that has been validated across 3 independent prospective multicenter clinical trials with 1212 subjects. The test can discriminate high-grade (≥GG2) from low-grade (GG1) cancer and benign disease. EPI effectively guides the biopsy-decision process independent of PSA and other standard-of-care factors.
Neuropsychiatric manifestations of COVID-19, potential neurotropic mechanisms, and therapeutic interventions
Authors: Han Ying , Yuan Kai , Wang Zhe , Liu Wei-Jian , Lu Zheng-An , Liu Lin , Shi Le , Yan Wei , Yuan Jun-Liang , Li Jia-Li , Shi Jie , Liu Zhong-Chun , Wang Gao-Hua , Kosten Thomas , Bao Yan-Ping , Lu Lin 
Published: September 2021

AbstractThe coronavirus disease 2019 (COVID-19) pandemic has caused large-scale economic and social losses and worldwide deaths. Although most COVID-19 patients have initially complained of respiratory insufficiency, the presence of neuropsychiatric manifestations is also reported frequently, ranging from headache, hyposmia/anosmia, and neuromuscular dysfunction to stroke, seizure, encephalopathy, altered mental status, and psychiatric disorders, both in the acute phase and in the long term. These neuropsychiatric complications have emerged as a potential indicator of worsened clinical outcomes and poor prognosis, thus contributing to mortality in COVID-19 patients. Their etiology remains largely unclear and probably involves multiple neuroinvasive pathways. Here, we summarize recent animal and human studies for neurotrophic properties of severe acute respiratory syndrome coronavirus (SARS-CoV-2) and elucidate potential neuropathogenic mechanisms involved in the viral invasion of the central nervous system as a cause for brain damage and neurological impairments. We then discuss the potential therapeutic strategy for intervening and preventing neuropsychiatric complications associated with SARS-CoV-2 infection. Time-series monitoring of clinical–neurochemical–radiological progress of neuropsychiatric and neuroimmune complications need implementation in individuals exposed to SARS-CoV-2. The development of a screening, intervention, and therapeutic framework to prevent and reduce neuropsychiatric sequela is urgently needed and crucial for the short- and long-term recovery of COVID-19 patients.
Exposure of a specific pleioform of multifunctional glyceraldehyde 3-phosphate dehydrogenase initiates CD14-dependent clearance of apoptotic cells
Authors: Chaudhary Surbhi , Patidar Anil , Dhiman Asmita , Chaubey Gaurav Kumar , Dilawari Rahul , Talukdar Sharmila , Modanwal Radheshyam , Raje Manoj 
Published: September 2021

AbstractRapid clearance of apoptotic cells by phagocytes is crucial for organogenesis, tissue homeostasis, and resolution of inflammation. This process is initiated by surface exposure of various ‘eat me’ligands. Though phosphatidylserine (PS) is the best recognized general recognition ligand till date, recent studies have shown that PS by itself is not sufficient for clearance of apoptotic cells. In this study, we have identified a specific pleioform of GAPDH (Glyceraldehyde 3-phosphate dehydrogenase) that functions as an ‘eat me’signal on apoptotic cell surface. This specific form of GAPDH which is exposed on surface of apoptotic cells was found to interact with CD14 present on plasma membrane of phagocytes leading to their engulfment. This is the first study demonstrating the novel interaction between multifunctional GAPDH and the phagocytic receptor CD14 resulting in apoptotic cell clearance (efferocytosis).
JCGA: the Japanese version of the Cancer Genome Atlas and its contribution to the interpretation of gene alterations detected in clinical cancer genome sequencing
Authors: Serizawa Masakuni , Mizuguchi Maki , Urakami Kenichi , Nagashima Takeshi , Ohshima Keiichi , Hatakeyama Keiichi , Ohnami Sumiko , Ohnami Shumpei , Maruyama Koji , Ashizawa Tadashi , Iizuka Akira , Horiuchi Yasue , Naruoka Akane , Kenmotsu Hirotsugu , Akiyama Yasuto , Yamaguchi Ken 
Published: September 2021

AbstractWith the emergence of next-generation sequencing (NGS)-based cancer gene panel tests in routine oncological practice in Japan, an easily interpretable cancer genome database of Japanese patients in which mutational profiles are unaffected by racial differences is needed to improve the interpretation of the detected gene alterations. Considering this, we constructed the first Japanese cancer genome database, called the Japanese version of the Cancer Genome Atlas (JCGA), which includes multiple tumor types. The database includes whole-exome sequencing data from 4907 surgically resected primary tumor samples obtained from 4753 Japanese patients with cancer and graphically provides genome information on 460 cancer-associated genes, including the 336 genes that are included in two NGS-based cancer gene panel tests approved by the Pharmaceuticals and Medical Devices Agency. Moreover, most of the contents of this database are written in Japanese; this not only helps physicians explain the results of NGS-based cancer gene panel tests but also enables patients and their families to obtain further information regarding the detected gene alterations.