bluuebunny/crossref_metadata_2025_split huggingface dataset:
Warm Arctic, Cold Siberia Pattern: Role of Full Arctic Amplification Versus Sea Ice Loss Alone
Authors: Labe Zachary , Peings Yannick , Magnusdottir Gudrun 
Published: August 2020

AbstractThe effect of future Arctic amplification (AA) on the extratropical atmospheric circulation remains unclear in modeling studies. Using a collection of coordinated atmospheric and coupled global climate model perturbation experiments, we find an emergent relationship between the high‐latitude 1,000–500 hPa thickness response and an enhancement of the Siberian High in winter. This wave number‐1‐like sea level pressure anomaly pattern is linked to an equatorward shift of the eddy‐driven jet and a dynamical cooling response in eastern Asia. Additional simulations, where AA is imposed directly into the model domain by nudging, demonstrate how the sea ice forcing is insufficient by itself to capture the vertical extent of the warming and by extension the amplitude of the response in the Siberian High. This study demonstrates the importance of the vertical extent of the tropospheric warming over the polar cap in revealing the “warm Arctic, cold Siberia” anomaly pattern in future projections.
Understanding Uneven Land Subsidence in Beijing, China, Using a Novel Combination of Geophysical Prospecting and InSAR
Authors: Guo Lin , Gong Huili , Li Jiwei , Zhu Lin , Xue Aimin , Liao Lin , Sun Ying , Li Yongsheng , Zhang Zhenxin , Hu Leyin , Gao Mingliang , Zhou Chaofan , Cheng Rui , Zhou Jiahui 
Published: August 2020

AbstractA novel approach was developed to quantitatively examine land subsidence. It combines a new geophysical (NG) prospecting and the interferometric synthetic aperture radar (InSAR) technology to explore uneven development of land subsidence in Beijing, China. We derived land subsidence spatial information over 4 years (from November 2014 to July 2018) based on Sentinel‐1 satellite imagery and the small‐baseline InSAR (SBAS‐InSAR) method. Also, profile data were acquired using seismic frequency resonance (SFR) approach in a few settlement areas. We developed a geological model based on boreholes and SFR data. Thus, we can quantitively study the driving forces of a typical uneven land subsidence. We found that faults are controlling spatial developments of land subsidence in Beijing. The subsidence rates have different values along the same fault. Also, we revealed the contributions of compressible layers to the formation of uneven land subsidence.
Ionospheric Modulation by Storm Time Pc5 ULF Pulsations and the Structure Detected by PFISR‐THEMIS Conjunction
Authors: Wang Boyi , Nishimura Yukitoshi , Hartinger Michael , Sivadas Nithin , Lyons Larry L. , Varney Roger H. , Angelopoulos Vassilis 
Published: August 2020

AbstractWe investigate a significant duskside ionospheric density modulation in the Pc5 frequency band and related spatial structures during the storm on 28 May 2017. We take advantage of 3‐D ionospheric observations by the PFISR and simultaneous magnetospheric in situ observations. Inversion of the density suggests that the Pc5 pulsations modulated precipitating electrons over a broad range of energies (~5–500 keV). Such strong electron precipitation likely caused a significant density modulation rate of ~8 and ionospheric Pedersen and Hall conductances to vary rapidly and peaked at ~70–100 S. The reflection coefficient was also substantially modulated between 0.5 and 0.9. Moreover, the observations by the multibeam PFISR and THEMIS E both reveal that the Pc5 pulsations propagated westward in the duskside region. It suggests that quasiperiodic activities in the nightside and subsequent duskward drifts were likely the source of the duskside Pc5 pulsations.
Polar Flattening of Jupiter's Magnetosphere
Authors: Ranquist D. A. , Bagenal F. , Wilson R. J. 
Published: August 2020

AbstractJupiter's magnetosphere is filled with plasma that expands from Io into an equatorial plasma disk, which preferentially inflates the magnetosphere against the solar wind equatorially. This results in a polar flattened magnetosphere and changes the dynamics between the solar wind and the magnetopause boundary. The degree of polar flattening at Jupiter, however, is not well known because no spacecraft has traversed the magnetopause at high latitudes. Instead, estimates must be made from much lower latitudes. In this study, we present a new method of estimating the large‐scale shape of magnetospheres by using magnetic field draping within the magnetosheath. Utilizing data of Jupiter's dawn magnetosheath from the Juno spacecraft, we estimate the ratio of the semimajor to semiminor axes of the Jupiter‐Sun‐North Y‐Z elliptical cross section of Jupiter's magnetopause is 1.29 ± 0.29.
Early Tsunami Detection With Near‐Fault Ocean‐Bottom Pressure Gauge Records Based on the Comparison With Seismic Data
Authors: Mizutani Ayumu , Yomogida Kiyoshi , Tanioka Yuichiro 
Published: August 2020

AbstractOffshore real‐time ocean bottom networks of seismometers and ocean bottom pressure (OBP) gauges have been recently established such as DONET and S‐net around the Japanese islands. One of their purposes is to practice rapid and accurate tsunami forecasting. Near‐fault OBP records, however, are always contaminated by nontsunami components such as sea‐bottom acceleration change until an earthquake stops its fault or sea‐floor motions. This study proposes a new method to separate tsunami and ocean bottom displacement components from coseismic OBP records in a real‐time basis. Associated with the Off‐Mie earthquake of 2016 April 1, we first compared OBP data with acceleration, velocity, and displacement seismograms recorded by seismometers at common ocean bottom sites in both time and frequency domains. Based on this comparison, we adopted a band‐pass filter of 0.05–0.15 Hz to remove ocean‐bottom acceleration components from the OBP data. Resulting OBP waveforms agree well with the tsunami components estimated by a 100‐s low‐pass filter with records of several hundred seconds in length. Our method requires only an early portion of a given OBP record after 30 s of an origin time in order to estimate its tsunami component accurately. Our method enhances early tsunami detections with near‐fault OBP data; that is, it will make a tsunami forecasting system faster and more reliable than the previous detection schemes that require data away from source regions or after coseismic motions are over.
In Situ Characterization of Three‐Phase Flow in Mixed‐Wet Porous Media Using Synchrotron Imaging
Authors: Scanziani Alessio , Alhosani Abdulla , Lin Qingyang , Spurin Catherine , Garfi Gaetano , Blunt Martin J. , Bijeljic Branko 
Published: August 2020

AbstractWe use fast synchrotron X‐ray microtomography to understand three‐phase flow in mixed‐wet porous media to design either enhanced permeability or capillary trapping. The dynamics of these phenomena are of key importance in subsurface hydrology, carbon dioxide storage, oil recovery, food and drug manufacturing, and chemical reactors. We study the dynamics of a water‐gas‐water injection sequence in a mixed‐wet carbonate rock. During the initial waterflooding, water displaced oil from pores of all size, indicating a mixed‐wet system with local contact angles both above and below 90°. When gas was injected, gas displaced oil preferentially with negligible displacement of water. This behavior is explained in terms of the gas pressure needed for invasion. Overall, gas behaved as the most nonwetting phase with oil as the most wetting phase; however, pores of all size were occupied by oil, water, and gas, as a signature of mixed‐wet media. Thick oil wetting layers were observed, which increased oil connectivity and facilitated its flow during gas injection. A chase waterflooding resulted in additional oil flow, while gas was trapped by oil and water. Furthermore, we quantified the evolution of the surface areas and both Gaussian and the total curvature, from which capillary pressure could be estimated. These quantities are related to the Minkowski functionals which quantify the degree of connectivity and trapping. The combination of water and gas injection, under mixed‐wet immiscible conditions, leads to both favorable oil flow and significant trapping of gas, which is advantageous for storage applications.
RUNX1 mutations in blast-phase chronic myeloid leukemia associate with distinct phenotypes, transcriptional profiles, and drug responses
Authors: Adnan Awad Shady , Dufva Olli , Ianevski Aleksandr , Ghimire Bishwa , Koski Jan , Maliniemi Pilvi , Thomson Daniel , Schreiber Andreas , Heckman Caroline A. , Koskenvesa Perttu , Korhonen Matti , Porkka Kimmo , Branford Susan , Aittokallio Tero , Kankainen Matti , Mustjoki Satu 
Published: August 2020

AbstractBlast-phase chronic myeloid leukemia (BP-CML) is associated with additional chromosomal aberrations,RUNX1mutations being one of the most common. Tyrosine kinase inhibitor therapy has only limited efficacy in BP-CML, and characterization of more defined molecular subtypes is warranted in order to design better treatment modalities for this poor prognosis patient group. Using whole-exome and RNA sequencing we demonstrate thatPHF6andBCORL1mutations,IKZF1deletions, and AID/RAG-mediated rearrangements are enriched inRUNX1mutBP-CML leading to typical mutational signature. On transcriptional level interferon and TNF signaling were deregulated in primaryRUNX1mutCML cells and stem cell and B-lymphoid factors upregulated giving a rise to distinct phenotype. This was accompanied with the sensitivity ofRUNX1mutblasts to CD19-CAR T cells in ex vivo assays. High-throughput drug sensitivity and resistance testing revealed leukemia cells fromRUNX1mutpatients to be highly responsive for mTOR-, BCL2-, and VEGFR inhibitors and glucocorticoids. These findings were further investigated and confirmed in CRISPR/Cas9-edited homozygousRUNX1−/−and heterozygousRUNX1−/mutBCR-ABL positive cell lines. Overall, our study provides insights into the pathogenic role ofRUNX1mutations and highlights personalized targeted therapy and CAR T-cell immunotherapy as potentially promising strategies for treatingRUNX1mutBP-CML patients.
Fecal microbiota transplantation from patients with autoimmune encephalitis modulates Th17 response and relevant behaviors in mice
Authors: Chen Hao , Chen Zhaoyu , Shen Liping , Wu Xiuhua , Ma Xueying , Lin Dengna , Zhang Man , Ma Xiaomeng , Liu Yingying , Wang Zhanhang , Zhang Yuefeng , Kuang Zuying , Lu Zhiwei , Li Xuefei , Ma Lili , Lin Xiuli , Si Lei , Chen Xiaohong 
Published: August 2020

AbstractThe significance of the microbiota-gut-brain axis has been increasingly recognized as a major modulator of autoimmunity. Here, we aim to characterize the gut microbiota of a large cohort of treatment-naïve anti-N-methyl-d-aspartate receptor (anti-NMDAR) encephalitis patients relative to that of healthy controls (HCs). Relative to HCs, anti-NMDAR encephalitis patients had a decreased microbiome alpha-diversity index, marked disturbances of gut microbial composition and intestinal permeability damage. Disturbed microbiota in anti-NMDAR encephalitis patients might be linked with different clinical characteristics. Imputed KEGG analysis revealed perturbations of functional modules in the gut microbiomes of anti-NMDAR encephalitis. Compared to HCs, microbiota-depleted mice receiving fecal microbiota transplantation (FMT) from anti-NMDAR encephalitis patients had hypersensitivity and cognitive impairment. Furthermore, anti-NMDAR encephalitis FMT mice showed altered T cells in the spleen and small intestine lamina propria with an increased Th17 cells. Overall, this study first suggests that the anti-NMDAR encephalitis microbiome itself can influence neurologic, Th17 response and behavioral function. The gut microbiota is a potential therapeutic target for anti-NMDAR encephalitis.
Synchronization of complex human networks
Authors: Shahal Shir , Wurzberg Ateret , Sibony Inbar , Duadi Hamootal , Shniderman Elad , Weymouth Daniel , Davidson Nir , Fridman Moti 
Published: August 2020

AbstractThe synchronization of human networks is essential for our civilization and understanding its dynamics is important to many aspects of our lives. Human ensembles were investigated, but in noisy environments and with limited control over the network parameters which govern the network dynamics. Specifically, research has focused predominantly on all-to-all coupling, whereas current social networks and human interactions are often based on complex coupling configurations. Here, we study the synchronization between violin players in complex networks with full and accurate control over the network connectivity, coupling strength, and delay. We show that the players can tune their playing period and delete connections by ignoring frustrating signals, to find a stable solution. These additional degrees of freedom enable new strategies and yield better solutions than are possible within current models such as the Kuramoto model. Our results may influence numerous fields, including traffic management, epidemic control, and stock market dynamics.
Blockade of the AHR restricts a Treg-macrophage suppressive axis induced by L-Kynurenine
Authors: Campesato Luis Felipe , Budhu Sadna , Tchaicha Jeremy , Weng Chien-Huan , Gigoux Mathieu , Cohen Ivan Jose , Redmond David , Mangarin Levi , Pourpe Stephane , Liu Cailian , Zappasodi Roberta , Zamarin Dmitriy , Cavanaugh Jill , Castro Alfredo C. , Manfredi Mark G. , McGovern Karen , Merghoub Taha , Wolchok Jedd D. 
Published: August 2020

AbstractTryptophan catabolism by the enzymes indoleamine 2,3-dioxygenase 1 and tryptophan 2,3-dioxygenase 2 (IDO/TDO) promotes immunosuppression across different cancer types. The tryptophan metabolite L-Kynurenine (Kyn) interacts with the ligand-activated transcription factor aryl hydrocarbon receptor (AHR) to drive the generation of Tregs and tolerogenic myeloid cells and PD-1 up-regulation in CD8+ T cells. Here, we show that the AHR pathway is selectively active in IDO/TDO-overexpressing tumors and is associated with resistance to immune checkpoint inhibitors. We demonstrate that IDO-Kyn-AHR-mediated immunosuppression depends on an interplay between Tregs and tumor-associated macrophages, which can be reversed by AHR inhibition. Selective AHR blockade delays progression in IDO/TDO-overexpressing tumors, and its efficacy is improved in combination with PD-1 blockade. Our findings suggest that blocking the AHR pathway in IDO/TDO expressing tumors would overcome the limitation of single IDO or TDO targeting agents and constitutes a personalized approach to immunotherapy, particularly in combination with immune checkpoint inhibitors.
Contributions to the ‘noise floor’ in gene expression in a population of dividing cells
Authors: Jędrak Jakub , Ochab-Marcinek Anna 
Published: August 2020

AbstractExperiments with cells reveal the existence of a lower bound for protein noise, the noise floor, in highly expressed genes. Its origins are still debated. We propose a minimal model of gene expression in a proliferating bacterial cell population. The model predicts the existence of a noise floor and it semi-quantitatively reproduces the curved shape of the experimental noise vs. mean protein concentration plots. When the cell volume increases in a different manner than does the mean protein copy number, the noise floor level is determined by the cell population’s age structure and by the dependence of the mean protein concentration on cell age. Additionally, the noise floor level may depend on a biological limit for the mean number of bursts in the cell cycle. In that case, the noise floor level depends on the burst size distribution width but it is insensitive to the mean burst size. Our model quantifies the contributions of each of these mechanisms to gene expression noise.
On the correlation between second order texture features and human observer detection performance in digital images
Authors: Nisbett William H. , Kavuri Amar , Das Mini 
Published: August 2020

AbstractImage texture, the relative spatial arrangement of intensity values in an image, encodes valuable information about the scene. As it stands, much of this potential information remains untapped. Understanding how to decipher textural details would afford another method of extracting knowledge of the physical world from images. In this work, we attempt to bridge the gap in research between quantitative texture analysis and the visual perception of textures. The impact of changes in image texture on human observer’s ability to perform signal detection and localization tasks in complex digital images is not understood. We examine this critical question by studying task-based human observer performance in detecting and localizing signals in tomographic breast images. We have also investigated how these changes impact the formation of second-order image texture. We used digital breast tomosynthesis (DBT) an FDA approved tomographic X-ray breast imaging method as the modality of choice to show our preliminary results. Our human observer studies involve localization ROC (LROC) studies for low contrast mass detection in DBT. Simulated images are used as they offer the benefit of known ground truth. Our results prove that changes in system geometry or processing leads to changes in image texture magnitudes. We show that the variations in several well-known texture features estimated in digital images correlate with human observer detection–localization performance for signals embedded in them. This insight can allow efficient and practical techniques to identify the best imaging system design and algorithms or filtering tools by examining the changes in these texture features. This concept linking texture feature estimates and task based image quality assessment can be extended to several other imaging modalities and applications as well. It can also offer feedback in system and algorithm designs with a goal to improve perceptual benefits. Broader impact can be in wide array of areas including imaging system design, image processing, data science, machine learning, computer vision, perceptual and vision science. Our results also point to the caution that must be exercised in using these texture features as image-based radiomic features or as predictive markers for risk assessment as they are sensitive to system or image processing changes.
Parallel in time dynamics with quantum annealers
Authors: Jałowiecki Konrad , Więckowski Andrzej , Gawron Piotr , Gardas Bartłomiej 
Published: August 2020

AbstractRecent years have witnessed an unprecedented increase in experiments and hybrid simulations involving quantum computers. In particular, quantum annealers. There exist a plethora of algorithms promising to outperform classical computers in the near-term future. Here, we propose a parallel in time approach to simulate dynamical systems designed to be executed already on present-day quantum annealers. In essence, purely classical methods for solving dynamics systems are serial. Therefore, their parallelization is substantially limited. In the presented approach, however, the time evolution is rephrased as a ground-state search of a classical Ising model. Such a problem is solved intrinsically in parallel by quantum computers. The main idea is exemplified by simulating the Rabi oscillations generated by a two-level quantum system (i.e. qubit) experimentally.
Structural equation modelling of the complex relationship between toothache and its associated factors among Indonesian children
Authors: Bakar Abu , Ningrum Valendriyani , Lee Andy , Hsu Wen-Kuang , Amalia Rosa , Dewanto Iwan , Lee Shih-Chieh 
Published: August 2020

AbstractThe Indonesian family life survey (IFLS) is used for formulating various government policies. Our preliminary study using data from the IFLS showed increase in the prevalence of toothache from 2007 to 2014. Hence, a need to analyse the factors associated with toothache using structural equation modelling (SEM) for identifying the direct and indirect association of factors with toothache was evident. The objective of this study is to analyse the complex relationships between toothache and its associated risk factors. This cross-sectional study was conducted on the data obtained from the IFLS in 2014. The IFLS data pertaining to toothache and its prevalence were analysed using the STATA software, and the multifaceted relationship was analysed using SEM. The prevalence of toothache among Indonesian children was 15.55% (1,959 of 12,595). SEM showed the direct association between toothache and age (p < 0.001) and parent awareness of children's health conditions (p < 0.005) and food consumption frequency (p < 0.001). Parents’ education level and residential area showed an indirect association with toothache, mediated by socio-economic status and parent awareness of children's health conditions (p < 0.001). We identified the multifaceted relationship between toothache and the social covariates. Parents’ awareness of their children’s health conditions mediated several indirect associations, highlighting its importance.
Predicting the chemical space of fungal polyketides by phylogeny-based bioinformatics analysis of polyketide synthase-nonribosomal peptide synthetase and its modification enzymes
Authors: Minami Atsushi , Ugai Takahiro , Ozaki Taro , Oikawa Hideaki 
Published: August 2020

AbstractFungal polyketide synthase (PKS)–nonribosomal peptide synthetase (NRPS) hybrids are key enzymes for synthesizing structurally diverse hybrid natural products (NPs) with characteristic biological activities. Predicting their chemical space is of particular importance in the field of natural product chemistry. However, the unexplored programming rule of the PKS module has prevented prediction of its chemical structure based on amino acid sequences. Here, we conducted a phylogenetic analysis of 884 PKS–NRPS hybrids and a modification enzyme analysis of the corresponding biosynthetic gene cluster, revealing a hidden relationship between its genealogy and core structures. This unexpected result allowed us to predict 18 biosynthetic gene cluster (BGC) groups producing known carbon skeletons (number of BGCs; 489) and 11 uncharacterized BGC groups (171). The limited number of carbon skeletons suggests that fungi tend to select PK skeletons for survival during their evolution. The possible involvement of a horizontal gene transfer event leading to the diverse distribution of PKS–NRPS genes among fungal species is also proposed. This study provides insight into the chemical space of fungal PKs and the distribution of their biosynthetic gene clusters.