bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impacts of Tiled Land Cover Characterization on Global Meteorological Predictions Using the MPAS‐A
Authors: Campbell Patrick C. , Bash Jesse O. , Herwehe Jerold A. , Gilliam Robert C. , Li Dan 
Published: June 2020

AbstractParameterization of subgrid‐scale variability of land cover characterization (LCC) is an active area of research and can improve model performance compared to the dominant (i.e., most abundant tile) approach. The “Noah” land surface model implementation in the global Model for Prediction Across Scales‐Atmosphere (MPAS‐A), however, only uses the dominant LCC approach that leads to oversimplification in regions of highly heterogeneous LCC (e.g., urban/suburban settings). Thus, in this work we implement a subgrid tiled approach as an option in MPAS‐A, version 6.0, and assess the impacts of tiled LCC on meteorological predictions for two gradually refining meshes (92–25 and 46–12 km) focused on the conterminous United States for January and July 2016. Compared to the dominant approach, results show that using the tiled LCC leads to pronounced global changes in 2‐m temperature (July global average change approximately −0.4 K), 2‐m moisture, and 10‐m wind speed for the 92–25 km mesh. The tiled LCC reduces mean biases in 2‐m temperature (July U.S. average bias reduction approximately factor of 4) and specific humidity in the central and western United States for the 92–25 km mesh and improves the agreement of vertical profiles (e.g., temperature, humidity, and wind speed) with observed radiosondes; however, there is increased bias and error for incoming solar radiation at the surface. The inclusion of subgrid LCC has implications for reducing systematic temperature biases found in numerical weather prediction models, particularly those that employ a dominant LCC approach.
Seismic Evidence for a Hot Mantle Transition Zone Beneath the Indian Ocean Geoid Low
Authors: Rao B. Padma , Kumar M. Ravi , Saikia Dipankar 
Published: June 2020

AbstractThe Indian Ocean Geoid Low (IOGL) is the most prominent geoid anomaly (−106 m) on the globe, whose origin remains elusive. In the present study, we investigate the mantle transition zone (MTZ) structure beneath the region using P receiver functions (PRFs), to examine its role in the genesis of this feature. Results from 3‐D time to depth migration of PRFs reveal a thin MTZ primarily due to an elevation of the 660 km discontinuity. This is suggestive of anomalously hot temperatures in the mid mantle beneath the IOGL region, possibly sourced from the African Large Low Shear Velocity Province (LLSVP). The combined effect of the hot (low‐density) material in the MTZ proposed in this study and the (high‐density) cold slab graves atop the core‐mantle boundary inferred from previous studies can possibly explain this geoid low.
Modeling Earthquake‐Induced Spring Discharge and Temperature Changes in a Fault Zone Hydrothermal System
Authors: Yan Xin , Shi Zheming , Zhou Pengpeng , Zhang Hui , Wang Guangcai 
Published: June 2020

AbstractAlthough different methods have been employed to study the earthquake‐induced changes in aquifer permeability (e.g., tidal/barometric pressure response and analytical models), identification of the mechanism is usually hindered by the limitation of application conditions or multiplicity of solutions. A numerical simulation that couples flow and heat transport is developed in the present study to explain the coseismic responses that followed two large earthquakes (Mw 7.0 Lijiang earthquake on 3 February 1996 and Mw 9.1 Sumatra earthquake on 26 December 2004) at Banglazhang #1 hot spring, China. The results show that decreased spring discharge and temperature are attributable to earthquake‐induced permeability decrease, which can be related to the blocking of narrow fracture apertures. Analysis of the model revealed that seismic waves may have caused heterogeneous changes in permeability within the fault zone hydrothermal system, which led to nonsynchronous changes in spring flow and temperature. Our study contributes to an enhanced understanding of the impact of the evolution of earthquake‐induced permeability in hydrothermal systems.
Present‐Day and Long‐Term Uplift Across the Western Transverse Ranges of Southern California
Authors: Johnson K. M. , Hammond W. C. , Burgette R. J. , Marshall S. T. , Sorlien C. C. 
Published: June 2020

AbstractIt has been known for decades that the present‐day shortening rates across the Western Transverse Ranges (WTR) in Southern California are rapid, reaching 10–15 mm/year near the heavily populated Los Angeles area. However, only recently have geodetic measurements of vertical motion in the WTR been sufficiently dense to resolve a tectonic vertical signal. In this study, we show that much of the geodetically derived vertical velocity field in the WTR can be attributed to the interseismic signal of strain accumulation on reverse faults. We invert geodetic and geologic data for slip rate and interseismic coupling on faults using a kinematic model consisting of faults embedded in an elastic crust over an inviscid mantle. This method allows us to infer the permanent, long‐term component of vertical motions from recoverable, short‐term motions. We infer that much of the geodetically observed 3–4 mm/year of differential vertical motion across the WTR, involving subsidence along the Santa Barbara coastline and uplift of the Santa Ynez Range, can be attributed to recoverable elastic deformation associated with interseismic locking on faults dipping under the WTR. The sum of dip‐slip rates across the WTR decreases from 10.5–14.6 mm/year on the east side near Ventura, California to 5–6.2 mm/year across the western side of the Santa Barbara Channel. The total moment accumulation rate in both the Santa Barbara Channel and the combined San Fernando Valley‐LA Basin regions is equivalent to about two Mw = 7 earthquakes every 100 years.
Optimization of the Match‐Filtering Method for Robust Repeating Earthquake Detection: The Multisegment Cross‐Correlation Approach
Authors: Gao Dawei , Kao Honn 
Published: June 2020

AbstractWaveform match‐filtering (MF), based on cross‐correlation between an earthquake pair, is a powerful and widely used tool in seismology. However, its performance can be severely affected by several factors, including the length of the cross‐correlation window, the frequency band of the applied digital filter, and the presence of a large‐amplitude phase(s). To optimize the performance of MF, we first systematically examine the effects of different operational parameters and determine the generic rules for selecting the window length and the optimal frequency passband. To minimize the influence of a large‐amplitude phase(s), we then propose a new approach, namely, MF with multisegment cross‐correlation (MFMC). By equally incorporating the contributions from various segments of the waveforms, this new approach is much more sensitive to small separation between two sources compared to the conventional MF method using the entire waveform template. To compare the reliability and effectiveness of both methods in capturing interevent source separation and identifying repeating earthquakes, we systematically conduct experiments with both synthetic data and real observations. The results demonstrate that the conventional MF method can detect the existence of an event but sometimes lacks the resolution to tell whether the template and detected events are co‐located or not, whereas MFMC works in all cases. The far‐reaching implication from this study is that inferring source separation between an earthquake pair based on the conventional MF method, particularly with data from a single channel/station, may not be reliable.
Mixing State of Black Carbon Particles in Asian Outflow Observed at a Remote Site in Taiwan in the Spring of 2017
Authors: Sun Cuizhi , Adachi Kouji , Misawa Kentaro , Cheung Hing Cho , Chou Charles C.‐K. , Takegawa Nobuyuki 
Published: June 2020

AbstractAnthropogenic emissions of aerosols and trace gases from East Asia have significant impacts on air quality and climate on regional and global scales. We conducted intensive measurements of aerosols at a remote site (Cape Fuguei; 25.30°N, 121.54°E) in Taiwan in the spring of 2017, focusing on the chemical composition and mixing state of aerosols in Asian outflow. A laser‐induced incandescence–mass spectrometric analyzer (LII‐MS) was used to measure the chemical composition of aerosols internally or externally mixed with black carbon (BC). Offline analysis by transmission electron microscopy (TEM) was used to characterize the mixing state of aerosols. The observation period was classified into long‐range transport (LRT) periods and local pollution periods on the basis of cluster analysis of 3‐day backward trajectories. LII‐MS data showed that the average mass fractions of sulfate and nitrate internally mixed with BC were 7% ± 13% and 11% ± 15%, respectively, for high‐pollution episodes during LRT periods. By TEM analysis of selected samples from LRT periods, the number fraction of aerosol particles internally mixed with BC was estimated to be 5%–36% for core–shell types and 5%–23% for attached types. Factors affecting the differences between LII‐MS and TEM measurements are discussed. TEM data indicated the presence of a variety of aerosol mixing states in widespread regional pollution transported 500–1,000 km downwind of emission sources. Our results provide new constraints for three‐dimensional models that might resolve the mixing state of aerosol particles, which are critical for accurately estimating the radiative impact of BC.
SUMOylation stabilizes hSSB1 and enhances the recruitment of NBS1 to DNA damage sites
Authors: Zhou Liwen , Zheng Lisi , Hu Kaishun , Wang Xin , Zhang Ruhua , Zou Yezi , Zhong Li , Wang Shang , Wu Yuanzhong , Kang Tiebang 
Published: June 2020

AbstractHuman single-stranded DNA-binding protein 1 (hSSB1) is required for the efficient recruitment of the MRN complex to DNA double-strand breaks and is essential for the maintenance of genome integrity. However, the mechanism by which hSSB1 recruits NBS1 remains elusive. Here, we determined that hSSB1 undergoes SUMOylation at both K79 and K94 under normal conditions and that this modification is dramatically enhanced in response to DNA damage. SUMOylation of hSSB1, which is specifically fine-tuned by PIAS2α, and SENP2, not only stabilizes the protein but also enhances the recruitment of NBS1 to DNA damage sites. Cells with defective hSSB1 SUMOylation are sensitive to ionizing radiation, and global inhibition of SUMOylation by either knocking out UBC9 or adding SUMOylation inhibitors significantly enhances the sensitivity of cancer cells to etoposide. Our findings reveal that SUMOylation, as a novel posttranslational modification of hSSB1, is critical for the functions of this protein, indicating that the use of SUMOylation inhibitors (e.g., 2-D08 and ML-792) may be a new strategy that would benefit cancer patients being treated with chemo- or radiotherapy.
Symmetries and cluster synchronization in multilayer networks
Authors: Della Rossa Fabio , Pecora Louis , Blaha Karen , Shirin Afroza , Klickstein Isaac , Sorrentino Francesco 
Published: June 2020

AbstractReal-world systems in epidemiology, social sciences, power transportation, economics and engineering are often described as multilayer networks. Here we first define and compute the symmetries of multilayer networks, and then study the emergence of cluster synchronization in these networks. We distinguish between independent layer symmetries, which occur in one layer and are independent of the other layers, and dependent layer symmetries, which involve nodes in different layers. We study stability of the cluster synchronous solution by decoupling the problem into a number of independent blocks and assessing stability of each block through a Master Stability Function. We see that blocks associated with dependent layer symmetries have a different structure to the other blocks, which affects the stability of clusters associated with these symmetries. Finally, we validate the theory in a fully analog experiment in which seven electronic oscillators of three kinds are connected with two kinds of coupling.
Climate change will affect global water availability through compounding changes in seasonal precipitation and evaporation
Authors: Konapala Goutam , Mishra Ashok K. , Wada Yoshihide , Mann Michael E. 
Published: June 2020

AbstractBoth seasonal and annual mean precipitation and evaporation influence patterns of water availability impacting society and ecosystems. Existing global climate studies rarely consider such patterns from non-parametric statistical standpoint. Here, we employ a non-parametric analysis framework to analyze seasonal hydroclimatic regimes by classifying global land regions into nine regimes using late 20th century precipitation means and seasonality. These regimes are used to assess implications for water availability due to concomitant changes in mean and seasonal precipitation and evaporation changes using CMIP5 model future climate projections. Out of 9 regimes, 4 show increased precipitation variation, while 5 show decreased evaporation variation coupled with increasing mean precipitation and evaporation. Increases in projected seasonal precipitation variation in already highly variable precipitation regimes gives rise to a pattern of “seasonally variable regimes becoming more variable”. Regimes with low seasonality in precipitation, instead, experience increased wet season precipitation.
Using arterial–venous analysis to characterize cancer metabolic consumption in patients
Authors: Xiong Nanxiang , Gao Xiaofei , Zhao Hongyang , Cai Feng , Zhang Fang-cheng , Yuan Ye , Liu Weichao , He Fangping , Zacharias Lauren G. , Lin Hong , Vu Hieu S. , Xing Chao , Yao Dong-Xiao , Chen Fei , Luo Benyan , Sun Wenzhi , DeBerardinis Ralph J. , Xu Hao , Ge Woo-ping 
Published: June 2020

AbstractUnderstanding tumor metabolism holds the promise of new insights into cancer biology, diagnosis and treatment. To assess human cancer metabolism, here we report a method to collect intra-operative samples of blood from an artery directly upstream and a vein directly downstream of a brain tumor, as well as samples from dorsal pedal veins of the same patients. After performing targeted metabolomic analysis, we characterize the metabolites consumed and produced by gliomas in vivo by comparing the arterial supply and venous drainage. N-acetylornithine, D-glucose, putrescine, and L-acetylcarnitine are consumed in relatively large amounts by gliomas. Conversely, L-glutamine, agmatine, and uridine 5-monophosphate are produced in relatively large amounts by gliomas. Further we verify that D-2-hydroxyglutarate (D-2HG) is high in venous plasma from patients with isocitrate dehydrogenases1 (IDH1) mutations. Through these paired comparisons, we can exclude the interpatient variation that is present in plasma samples usually taken from the cubital vein.
TLR2 on blood monocytes senses dengue virus infection and its expression correlates with disease pathogenesis
Authors: Aguilar-Briseño José A. , Upasani Vinit , Ellen Bram M. ter , Moser Jill , Pauzuolis Mindaugas , Ruiz-Silva Mariana , Heng Sothy , Laurent Denis , Choeung Rithy , Dussart Philippe , Cantaert Tineke , Smit Jolanda M. , Rodenhuis-Zybert Izabela A. 
Published: June 2020

AbstractVascular permeability and plasma leakage are immune-pathologies of severe dengue virus (DENV) infection, but the mechanisms underlying the exacerbated inflammation during DENV pathogenesis are unclear. Here, we demonstrate that TLR2, together with its co-receptors CD14 and TLR6, is an innate sensor of DENV particles inducing inflammatory cytokine expression and impairing vascular integrity in vitro. Blocking TLR2 prior to DENV infection in vitro abrogates NF-κB activation while CD14 and TLR6 block has a moderate effect. Moreover, TLR2 block prior to DENV infection of peripheral blood mononuclear cells prevents activation of human vascular endothelium, suggesting a potential role of the TLR2-responses in vascular integrity. TLR2 expression on CD14 + + classical monocytes isolated in an acute phase from DENV-infected pediatric patients correlates with severe disease development. Altogether, these data identify a role for TLR2 in DENV infection and provide insights into the complex interaction between the virus and innate receptors that may underlie disease pathogenesis.
Ultra-large chemical libraries for the discovery of high-affinity peptide binders
Authors: Quartararo Anthony J. , Gates Zachary P. , Somsen Bente A. , Hartrampf Nina , Ye Xiyun , Shimada Arisa , Kajihara Yasuhiro , Ottmann Christian , Pentelute Bradley L. 
Published: June 2020

AbstractHigh-diversity genetically-encoded combinatorial libraries (108−1013 members) are a rich source of peptide-based binding molecules, identified by affinity selection. Synthetic libraries can access broader chemical space, but typically examine only ~ 106 compounds by screening. Here we show that in-solution affinity selection can be interfaced with nano-liquid chromatography-tandem mass spectrometry peptide sequencing to identify binders from fully randomized synthetic libraries of 108 members—a 100-fold gain in diversity over standard practice. To validate this approach, we show that binders to a monoclonal antibody are identified in proportion to library diversity, as diversity is increased from 106–108. These results are then applied to the discovery of p53-like binders to MDM2, and to a family of 3–19 nM-affinity, α/β-peptide-based binders to 14-3-3. An X-ray structure of one of these binders in complex with 14-3-3σ is determined, illustrating the role of β-amino acids in facilitating a key binding contact.
The mutREAD method detects mutational signatures from low quantities of cancer DNA
Authors: Perner Juliane , Abbas Sujath , Nowicki-Osuch Karol , Devonshire Ginny , Eldridge Matthew D. , Tavaré Simon , Fitzgerald Rebecca C. 
Published: June 2020

AbstractMutational processes acting on cancer genomes can be traced by investigating mutational signatures. Because high sequencing costs limit current studies to small numbers of good-quality samples, we propose a robust, cost- and time-effective method, called mutREAD, to detect mutational signatures from small quantities of DNA, including degraded samples. We show that mutREAD recapitulates mutational signatures identified by whole genome sequencing, and will ultimately allow the study of mutational signatures in larger cohorts and, by compatibility with formalin-fixed paraffin-embedded samples, in clinical settings.
Crystal structures of SAMHD1 inhibitor complexes reveal the mechanism of water-mediated dNTP hydrolysis
Authors: Morris Elizabeth R. , Caswell Sarah J. , Kunzelmann Simone , Arnold Laurence H. , Purkiss Andrew G. , Kelly Geoff , Taylor Ian A. 
Published: June 2020

AbstractSAMHD1 regulates cellular 2′-deoxynucleoside-5′-triphosphate (dNTP) homeostasis by catalysing the hydrolysis of dNTPs into 2′-deoxynucleosides and triphosphate. In CD4+ myeloid lineage and resting T-cells, SAMHD1 blocks HIV-1 and other viral infections by depletion of the dNTP pool to a level that cannot support replication. SAMHD1 mutations are associated with the autoimmune disease Aicardi–Goutières syndrome and hypermutated cancers. Furthermore, SAMHD1 sensitises cancer cells to nucleoside-analogue anti-cancer therapies and is linked with DNA repair and suppression of the interferon response to cytosolic nucleic acids. Nevertheless, despite its requirement in these processes, the fundamental mechanism of SAMHD1-catalysed dNTP hydrolysis remained unknown. Here, we present structural and enzymological data showing that SAMHD1 utilises an active site, bi-metallic iron-magnesium centre that positions a hydroxide nucleophile in-line with the Pα-O5′ bond to catalyse phosphoester bond hydrolysis. This precise molecular mechanism for SAMHD1 catalysis, reveals how SAMHD1 down-regulates cellular dNTP and modulates the efficacy of nucleoside-based anti-cancer and anti-viral therapies.
Klenkia terrae resistant to DNA extraction in germ-free mice stools illustrates the extraction pitfall faced by metagenomics
Authors: Andreani Julien , Million Matthieu , Baudoin Jean-Pierre , Ominami Yusuke , Khalil Jacques Yaacoub Bou , Frémond Cécile , Khelaifia Saber , Levasseur Anthony , Raoult Didier , La Scola Bernard 
Published: June 2020

AbstractOver the past decade, metagenomics has become the preferred method for exploring complex microbiota such as human gut microbiota. However, several bias affecting the results of microbiota composition, such as those due to DNA extraction, have been reported. These bias have been confirmed with the development of culturomics technique. In the present study, we report the contamination of a gnotobiotic mice unit with a bacterium first detected by gram staining. Scanning electron microscopy and transmission electron microscopy permitted to detect a bacterium with a thick cell wall. However, in parallel, the first attempt to identify and culture this bacterium by gene amplification and metagenomics of universal 16S rRNA failed. Finally, the isolation in culture of a fastidious bacterium not detected by using universal PCR was successfully achieved by using a BCYE agar plate with CO2 atmosphere at 30 °C. We performed genome sequencing of this bacterium using a strong extraction procedure. The genomic comparison allowed us to classify this bacterium as Klenkia terrae. And finally, it was also detected in the stool and kibble that caused the contamination by using specific qPCR against this bacterium. The elucidation of this contamination provides additional evidence that DNA extraction could be a bias for the study of the microbiota. Currently, most studies that strive to analyze and compare the gut microbiota are based on metagenomics. In a gnotobiotic mice unit contaminated with the fastidious Actinobacteria Klenkia terrae, standard culture, 16S rRNA gene amplification and metagenomics failed to identify the micro-organism observed in stools by gram-staining. Only a procedure based on culturomics allowed us to identify this bacterium and to elucidate the mode of contamination of the gnotobiotic mice unit through diet.
Environmental Remediation of the difficult-to-return zone in Tomioka Town, Fukushima Prefecture
Authors: Cui Limeng , Taira Yasuyuki , Matsuo Masahiko , Orita Makiko , Yamada Yumiko , Takamura Noboru 
Published: June 2020

AbstractTemporal variations in ambient dose rates in a restricted area designated as “difficult-to-return” for residents of Tomioka Town, Fukushima Prefecture were evaluated in a car-borne survey during 2018–2019. The median dose rates in the “Decontaminated area” in the difficult-to-return zone decreased rapidly from 1.0 μSv/h to 0.32 μSv/h; however, the median dose rates in the “Non-decontaminated area” and “Radioactive waste storage area” fluctuated between 1.1–1.4 μSv/h and 0.46–0.61 μSv/h, respectively. The detected rate of the cesium-137 (137Cs) (137Cs-detected points per all measuring points) in the “Decontaminated area” also decreased rapidly from 64% to 6.7%, accompany with decreasing in ambient dose rates. On the other hand, the detection of 137Cs in the “Radioactive waste storage area” and “Non-decontaminated area” decreased from 53% to 17% and 93% to 88%, respectively. We confirmed that the dose rates in the Decontaminated area dramatically decreased due to decontamination work aiming to help residents return home. Moreover, the estimated external exposure dose of workers during the present survey was 0.66 mSv/y in the Decontaminated area and 0.55 mSv/y in the Radioactive waste storage area, respectively. This case of Tomioka Town within the “difficult-to-return zone” may be the first reconstruction model for evaluating environmental contamination and radiation exposure dose rates due to artificial radionuclides derived from the nuclear disaster.