bluuebunny/crossref_metadata_2025_split huggingface dataset:
S Wave Anelastic Attenuation of Shallow Sediments in Mainland China
Authors: Tian Wen , Li Zhiwei 
Published: October 2020

AbstractFrequency‐dependent anelastic attenuation is a fact that must be considered when inverting seismic data. The shallow attenuation characteristics of large sedimentary basins with frequent earthquakes in mainland China are still unclear, which hinders the study of strong ground motion. Borehole seismometers distributed in these areas provide information on shallow structures. In this study, the direct and surface‐reflected phases in local earthquake borehole seismograms were extracted to calculate the average S wave anelastic attenuation of shallow sediments in mainland China. Relying on the seismograms recorded by 103 borehole stations, the attenuation values and lithologies of the shallow sediments above the borehole seismometers were estimated by applying a multi‐time window analysis method. We suggested that the
values generally decrease from 0.04–0.50 at 1 Hz to 0.01–0.05 at 10 Hz. We obtained the empirical relationships among attenuation, velocity, and depth and found that the dominant mechanisms for attenuation above and below a depth of 400 m could be different due to sediment compositions and scales. Certain borehole depths and corresponding Vs values were corrected by analyzing the time difference variation and the
distinction.
Numerically Bounded Linguistic Probability Schemes Are Unlikely to Communicate Uncertainty Effectively
Authors: Mandel D. R. , Wallsten T. S. , Budescu D. V. 
Published: October 2020

AbstractIn a recent issue of Earth's Future (vol. 7, pp. 1020–1026), S. C. Lewis et al. (2019, https://doi.org/10.1029/2019EF001273) recommended a numerically bounded linguistic probability (NBLP) scheme for communicating probabilistic information in extreme event attribution studies. We provide a critique of NBLP schemes in general and of Lewis et al.'s in particular, noting two key points. First, evidence from voluminous behavioral science research on the interpretation of linguistic probabilities indicates that NBLP schemes are an ineffective means of communicating uncertainty to others. Second, where the motivation to implement such schemes nevertheless persists, the schemes should be developed through an evidence‐based approach that seeks to optimize interpretational agreement between the scheme and users.
Global Radiative Impacts of Black Carbon Acting as Ice Nucleating Particles
Authors: McGraw Zachary , Storelvmo Trude , Samset Bjørn Hallvard , Stjern Camilla Weum 
Published: October 2020

AbstractBlack carbon (BC) aerosols from incomplete combustion generally warm the climate, but the magnitudes of their various interactions with climate are still uncertain. A key knowledge gap is their role as ice nucleating particles (INPs), enabling ice formation in clouds. Here we assess the global radiative impacts of BC acting as INPs, using simulations with the Community Earth System Model 2 climate model updated to include new laboratory‐based ice nucleation parameterizations. Overall, we find a moderate cooling through changes to stratiform cirrus clouds, counteracting the well‐known net warming from BC's direct scattering and absorption of radiation. Our best estimates indicate that BC INPs generally thin cirrus by indirectly inhibiting the freezing of solution aerosol, with a global net radiative impact of −0.13 ± 0.07 W/m2. Sensitivity tests of BC amounts and ice nucleating efficiencies, and uncertainties in the environment where ice crystals form, show a potential range of impacts from −0.30 to +0.02 W/m2.
Thermodynamical Modeling of Liquid Fe‐Si‐Mg‐O:Molten Magnesium Silicate Release From the Core
Authors: Helffrich George , Hirose Kei , Nomura Ryuichi 
Published: October 2020

AbstractWe developed a thermodynamic model to explore the joint solubility of Mg, Si, and O in liquid Fe on the basis of high‐pressure metal‐silicate partitioning data in the literature, with more Mg kept in the metal when Si and O are present. With <1.7 ± 0.5 wt% Mg, the metal in the young Earth's core retains Mg as the core evolves and crystallizes SiO2. Higher Mg concentrations require either the late addition of metal that equilibrated with silicate in a super‐liquidus magma ocean or the assimilation of silicate into the core at the time of a giant impact. Above 1.7 wt% Mg, (Mg,Fe)‐silicate melts also exsolve from the core and transfer core‐hosted elements to the mantle. Fractional crystallization of the core‐derived silicate melts in the core or at the core‐mantle boundary could, additionally, yield a persistent molten silicate layer that could also contribute to ultralow velocity zone formation in the lowermost mantle.
Overexpression of Cyclin E1 or Cdc25A leads to replication stress, mitotic aberrancies, and increased sensitivity to replication checkpoint inhibitors
Authors: Kok Yannick P. , Guerrero Llobet Sergi , Schoonen Pepijn M. , Everts Marieke , Bhattacharya Arkajyoti , Fehrmann Rudolf S. N. , van den Tempel Nathalie , van Vugt Marcel A. T. M. 
Published: October 2020

AbstractOncogene-induced replication stress, for instance as a result of Cyclin E1 overexpression, causes genomic instability and has been linked to tumorigenesis. To survive high levels of replication stress, tumors depend on pathways to deal with these DNA lesions, which represent a therapeutically actionable vulnerability. We aimed to uncover the consequences of Cyclin E1 or Cdc25A overexpression on replication kinetics, mitotic progression, and the sensitivity to inhibitors of the WEE1 and ATR replication checkpoint kinases. We modeled oncogene-induced replication stress using inducible expression of Cyclin E1 or Cdc25A in non-transformed RPE-1 cells, either in a TP53 wild-type or TP53-mutant background. DNA fiber analysis showed Cyclin E1 or Cdc25A overexpression to slow replication speed. The resulting replication-derived DNA lesions were transmitted into mitosis causing chromosome segregation defects. Single cell sequencing revealed that replication stress and mitotic defects upon Cyclin E1 or Cdc25A overexpression resulted in genomic instability. ATR or WEE1 inhibition exacerbated the mitotic aberrancies induced by Cyclin E1 or Cdc25A overexpression, and caused cytotoxicity. Both these phenotypes were exacerbated upon p53 inactivation. Conversely, downregulation of Cyclin E1 rescued both replication kinetics, as well as sensitivity to ATR and WEE1 inhibitors. Taken together, Cyclin E1 or Cdc25A-induced replication stress leads to mitotic segregation defects and genomic instability. These mitotic defects are exacerbated by inhibition of ATR or WEE1 and therefore point to mitotic catastrophe as an underlying mechanism. Importantly, our data suggest that Cyclin E1 overexpression can be used to select patients for treatment with replication checkpoint inhibitors.
Framework for quality assessment of whole genome cancer sequences
Authors: Whalley Justin P. , Buchhalter Ivo , Rheinbay Esther , Raine Keiran M. , Stobbe Miranda D. , Kleinheinz Kortine , Werner Johannes , Beltran Sergi , Gut Marta , Hübschmann Daniel , Hutter Barbara , Livitz Dimitri , Perry Marc D. , Rosenberg Mara , Saksena Gordon , Trotta Jean-Rémi , Eils Roland , Gerhard Daniela S. , Campbell Peter J. , Schlesner Matthias , Gut Ivo G. 
Published: October 2020

AbstractBringing together cancer genomes from different projects increases power and allows the investigation of pan-cancer, molecular mechanisms. However, working with whole genomes sequenced over several years in different sequencing centres requires a framework to compare the quality of these sequences. We used the Pan-Cancer Analysis of Whole Genomes cohort as a test case to construct such a framework. This cohort contains whole cancer genomes of 2832 donors from 18 sequencing centres. We developed a non-redundant set of five quality control (QC) measurements to establish a star rating system. These QC measures reflect known differences in sequencing protocol and provide a guide to downstream analyses and allow for exclusion of samples of poor quality. We have found that this is an effective framework of quality measures. The implementation of the framework is available at: https://dockstore.org/containers/quay.io/jwerner_dkfz/pancanqc:1.2.2.
Dissolved black carbon is not likely a significant refractory organic carbon pool in rivers and oceans
Authors: Qi Yuanzhi , Fu Wenjing , Tian Jiwei , Luo Chunle , Shan Sen , Sun Shuwen , Ren Peng , Zhang Hongmei , Liu Jiwen , Zhang Xiaohua , Wang Xuchen 
Published: October 2020

AbstractRivers are the major carriers of dissolved black carbon (DBC) from land to ocean; the sources of DBC during its continuous transformation and cycling in the ocean, however, are not well characterized. Here, we present new carbon isotope data for DBC in four large and two small mountainous rivers, the Yangtze and Yellow river estuaries, the East China Sea and the North Pacific Ocean. We found that the carbon isotope signatures of DBC are relatively homogeneous, and the DBC 14C ages in rivers are predominantly young and increase during continuous transport and cycling in the ocean. The results of charcoal leaching experiments indicate that DBC is released from charcoal and degraded by bacteria. Our study suggests that riverine DBC is labile and respired during transport and mixing into the ocean and that residual DBC is cycled and aged on the same time scales as bulk DOC in the ocean.
Attosecond electron–spin dynamics in Xe 4d photoionization
Authors: Zhong Shiyang , Vinbladh Jimmy , Busto David , Squibb Richard J. , Isinger Marcus , Neoričić Lana , Laurell Hugo , Weissenbilder Robin , Arnold Cord L. , Feifel Raimund , Dahlström Jan Marcus , Wendin Göran , Gisselbrecht Mathieu , Lindroth Eva , L’Huillier Anne 
Published: October 2020

AbstractThe photoionization of xenon atoms in the 70–100 eV range reveals several fascinating physical phenomena such as a giant resonance induced by the dynamic rearrangement of the electron cloud after photon absorption, an anomalous branching ratio between intermediate Xe+ states separated by the spin-orbit interaction and multiple Auger decay processes. These phenomena have been studied in the past, using in particular synchrotron radiation, but without access to real-time dynamics. Here, we study the dynamics of Xe 4d photoionization on its natural time scale combining attosecond interferometry and coincidence spectroscopy. A time-frequency analysis of the involved transitions allows us to identify two interfering ionization mechanisms: the broad giant dipole resonance with a fast decay time less than 50 as, and a narrow resonance at threshold induced by spin-flip transitions, with much longer decay times of several hundred as. Our results provide insight into the complex electron-spin dynamics of photo-induced phenomena.
Policy, toxicology and physicochemical considerations on the inhalation of high concentrations of food flavour
Authors: Dinu Vlad , Kilic Azad , Wang Qingqi , Ayed Charfedinne , Fadel Abdulmannan , Harding Stephen E. , Yakubov Gleb E. , Fisk Ian D. 
Published: October 2020

AbstractFood flavour ingredients are required by law to obtain prior approval from regulatory bodies, such as the U.S. Food and Drug Administration (FDA) or the European Food Safety Authority (EFSA) in terms of toxicological data and intended use levels. However, there are no regulations for labelling the type and concentration of flavour additives on the product, primarily due to their low concentration in food and generally recognised as safe (GRAS) status determined by the flavour and extract manufacturers’ association (FEMA). Their status for use in e-cigarettes and other vaping products challenges these fundamental assumptions, because their concentration can be over ten-thousand times higher than in food, and the method of administration is through inhalation, which is currently not evaluated by the FEMA expert panel. This work provides a review of some common flavour ingredients used in food and vaping products, their product concentrations, inhalation toxicity and aroma interactions reported with different biological substrates. We have identified several studies, which suggest that the high concentrations of flavour through inhalation may pose a serious health threat, especially in terms of their cytotoxicity. As a result of the wide range of possible protein-aroma interactions reported in our diet and metabolism, including links to several non-communicable diseases, we suggest that it is instrumental to update current flavour- labelling regulations, and support new strategies of understanding the effects of flavour uptake on the digestive and respiratory systems, in order to prevent the onset of future non-communicable diseases.
Permafrost dynamics and the risk of anthrax transmission: a modelling study
Authors: Stella Elisa , Mari Lorenzo , Gabrieli Jacopo , Barbante Carlo , Bertuzzo Enrico 
Published: October 2020

AbstractA recent outbreak of anthrax disease, severely affecting reindeer herds in Siberia, has been reportedly associated to the presence of infected carcasses or spores released from the active layer over permafrost, which is thawing and thickening at increasing rates, thus underlying the re-emerging nature of this pathogen in the Arctic region because of warming temperatures. Anthrax is a global zoonotic and epizootic disease, with a high case-fatality ratio in infected animals. Its transmission is mediated by environmental contamination through highly resistant spores which can persist in the soil for several decades. Here we develop and analyze a new epidemiological model for anthrax transmission that is specifically tailored to the Arctic environmental conditions. The model describes transmission dynamics including also herding practices (e.g. seasonal grazing) and the role of the active layer over permafrost acting as a long-term storage of spores that could be viable for disease transmission during thawing periods. Model dynamics are investigated through linear stability analysis, Floquet theory for periodically forced systems, and a series of simulations with realistic forcings. Results show how the temporal variability of grazing and active layer thawing may influence the dynamics of anthrax disease and, specifically, favor sustained pathogen transmission. Particularly warm years, favoring deep active layers, are shown to be associated with an increase risk of anthrax outbreaks, and may also foster infections in the following years. Our results enable preliminary insights into measures (e.g. changes in herding practice) that may be adopted to decrease the risk of infection and lay the basis to possibly establish optimal procedures for preventing transmission; furthermore, they elicit the need of further investigations and observation campaigns focused on anthrax dynamics in the Arctic environment.
Multi-level modeling with nonlinear movement metrics to classify self-injurious behaviors in autism spectrum disorder
Authors: Cantin-Garside Kristine D. , Srinivasan Divya , Ranganathan Shyam , White Susan W. , Nussbaum Maury A. 
Published: October 2020

AbstractSelf-injurious behavior (SIB) is among the most dangerous concerns in autism spectrum disorder (ASD), often requiring detailed and tedious management methods. Sensor-based behavioral monitoring could address the limitations of these methods, though the complex problem of classifying variable behavior should be addressed first. We aimed to address this need by developing a group-level model accounting for individual variability and potential nonlinear trends in SIB, as a secondary analysis of existing data. Ten participants with ASD and SIB engaged in free play while wearing accelerometers. Movement data were collected from > 200 episodes and 18 different types of SIB. Frequency domain and linear movement variability measures of acceleration signals were extracted to capture differences in behaviors, and metrics of nonlinear movement variability were used to quantify the complexity of SIB. The multi-level logistic regression model, comprising of 12 principal components, explained > 65% of the variance, and classified SIB with > 75% accuracy. Our findings imply that frequency-domain and movement variability metrics can effectively predict SIB. Our modeling approach yielded superior accuracy than commonly used classifiers (~ 75 vs. ~ 64% accuracy) and had superior performance compared to prior reports (~ 75 vs. ~ 69% accuracy) This work provides an approach to generating an accurate and interpretable group-level model for SIB identification, and further supports the feasibility of developing a real-time SIB monitoring system.
Synthesis and structure of a new thiazoline-based palladium(II) complex that promotes cytotoxicity and apoptosis of human promyelocytic leukemia HL-60 cells
Authors: Espino Javier , Fernández-Delgado Elena , Estirado Samuel , de la Cruz-Martinez Felipe , Villa-Carballar Sergio , Viñuelas-Zahínos Emilio , Luna-Giles Francisco , Pariente José A. 
Published: October 2020

AbstractCisplatin is one of the most widely used chemotherapeutic agents in the treatment of different tumors but has high toxicity and side effects. Therefore, the synthesis of new chemotherapeutic agents is necessary, so that they are effective in the treatment of cancer while avoiding such toxicity. In this study, we have synthesized and characterized a palladium(II) complex, [PdCl2(µ-PyTT)2]Cl2·4H2O (PdPyTT), with 2-(2-pyridyl)imine-N-(2-thiazolin-2-yl)thiazolidine (PyTT) as a ligand; besides, its cytotoxicity and pro-apoptotic capacity was tested in human promyelocytic leukemia HL-60 cell line. Similar to cisplatin, PdPyTT produced a time- and dose-dependent decrease in cell viability. Additionally, the palladium complex increased both the proportion of cells with apoptotic morphology and the activation of caspase-3 and -9. PdPyTT, like cisplatin, also increased intracellular ROS production and DNA oxidative damage. Therefore, our findings demonstrated the promising application of palladium(II) complexes as novel anti-leukemic agents.
Analysis of Plasmodium vivax schizont transcriptomes from field isolates reveals heterogeneity of expression of genes involved in host-parasite interactions
Authors: Siegel Sasha V. , Chappell Lia , Hostetler Jessica B. , Amaratunga Chanaki , Suon Seila , Böhme Ulrike , Berriman Matthew , Fairhurst Rick M. , Rayner Julian C. 
Published: October 2020

AbstractPlasmodium vivaxgene regulation remains difficult to study due to the lack of a robust in vitro culture method, low parasite densities in peripheral circulation and asynchronous parasite development. We adapted an RNA-seq protocol “DAFT-seq” to sequence the transcriptome of fourP. vivaxfield isolates that were cultured for a short period ex vivo before using a density gradient for schizont enrichment. Transcription was detected from 78% of the PvP01 reference genome, despite being schizont-enriched samples. This extensive data was used to define thousands of 5′ and 3′ untranslated regions, some of which overlapped with neighbouring transcripts, and to improve the gene models of 352 genes, including identifying 20 novel gene transcripts. This dataset has also significantly increased the known amount of heterogeneity betweenP. vivaxschizont transcriptomes from individual patients. The majority of genes found to be differentially expressed between the isolates lackPlasmodium falciparumhomologs and are predicted to be involved in host-parasite interactions, with an enrichment in reticulocyte binding proteins, merozoite surface proteins and exported proteins with unknown function. An improved understanding of the diversity withinP. vivaxtranscriptomes will be essential for the prioritisation of novel vaccine targets.
Dynamics of a neuronal pacemaker in the weakly electric fish Apteronotus
Authors: Shifman Aaron R. , Sun Yiren , Benoit Chloé M. , Lewis John E. 
Published: October 2020

AbstractThe precise timing of neuronal activity is critical for normal brain function. In weakly electric fish, the medullary pacemaker network (PN) sets the timing for an oscillating electric organ discharge (EOD) used for electric sensing. This network is the most precise biological oscillator known, with sub-microsecond variation in oscillator period. The PN consists of two principle sets of neurons, pacemaker and relay cells, that are connected by gap junctions and normally fire in synchrony, one-to-one with each EOD cycle. However, the degree of gap junctional connectivity between these cells appears insufficient to provide the population averaging required for the observed temporal precision of the EOD. This has led to the hypothesis that individual cells themselves fire with high precision, but little is known about the oscillatory dynamics of these pacemaker cells. As a first step towards testing this hypothesis, we have developed a biophysical model of a pacemaker neuron action potential based on experimental recordings. We validated the model by comparing the changes in oscillatory dynamics produced by different experimental manipulations. Our results suggest that this relatively simple model can capture a large range of channel dynamics exhibited by pacemaker cells, and will thus provide a basis for future work on network synchrony and precision.
Quantum transport in a chain of quantum dots with inhomogeneous size distribution and manifestation of 1D Anderson localization
Authors: Cha Moon-Hyun , Hwang Jeongwoon 
Published: October 2020

AbstractThe effect of inhomogeneous quantum dot (QD) size distribution on the electronic transport of one-dimensional (1D) QD chains (QDCs) is theoretically investigated. The non-equilibrium Green function method is employed to compute the electron transmission probabilities of QDCs. The ensemble averaged transmission probability shows a close agreement with the conductivity equation predicted by Anderson et al. for a disordered electronic system. The fidelity of quantum transport is defined as the transmission performance of an ensemble of QDCs of length N (N-QDCs) to assess the robustness of QDCs as a practical electronic device. We found that the fidelity of inhomogeneous N-QDCs with the standard deviation of energy level distribution σε is a Lorentzian function of variable Nσε2. With these analytical expressions, we can predict the conductance and fidelity of any QDC characterized by (N, σε). Our results can provide a guideline for combining the chain length and QD size distributions for high-mobility electron transport in 1D QDCs.
Comparing fish prey diversity for a critically endangered aquatic mammal in a reserve and the wild using eDNA metabarcoding
Authors: Qu Chanjuan , Stewart Kathryn A. , Clemente-Carvalho Rute , Zheng Jinsong , Wang Yuxiang , Gong Cheng , Ma Limin , Zhao Jianfu , Lougheed Stephen C. 
Published: October 2020

AbstractUsing environmental DNA (eDNA) metabarcoding, we compared fish diversity in two distinct water bodies within the Yangtze River Basin with known populations of the critically endangered Yangtze finless porpoise (Neophocaena asiaeorientalis; YFP): the Tian-e-Zhou Reserve and Poyang Lake. We aimed to create a fish surveying tool for use in the Yangtze River Basin, while also gaining a better understanding of the prey distribution and diversity within two of the remaining strongholds of YFP. 16S rRNA universal primers were developed to amplify fish eDNA. After high-throughput sequencing and stringent data filtering, we identified a total of 75 fish species (6 orders, 9 families, 57 genera) across seasons and regions. Nine of the 75 fish species were among the 28 known YFP prey species, three of which were detected in all water samples. Our eDNA metabarcoding identified many species that had been previously captured using traditional netting practices, but also numerous species not previously collected in these water bodies. Fish diversity was higher in Poyang Lake than in Tian-e-Zhou Reserve, as well as higher in the spring than in summer. These methods provide a broadly applicable tool to quantify fish diversity and distributions throughout the Yangtze River Basin, and to inform conservation strategies of YFP.