bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ancient Refertilization Process Preserved in the Plagioclase Peridotites: An Example From the Shuanggou Ophiolite, Southwest China
Authors: Hu Wen‐Jun , Zhong Hong , Chu Zhu‐Yin , Zhu Wei‐Guang , Bai Zhong‐Jie , Zhang Chang 
Published: November 2019

AbstractPetrology, geochemistry, platinum group elements (PGEs: Os, Ir, Ru, Rh, Pt, and Pd), and Re‐Os isotope data of harzburgites and plagioclase lherzolites from the Shuanggou ophiolite (southwest China) are presented in this study, in order to determine whether ancient refertilization process can be preserved in ophiolitic plagioclase peridotites. The harzburgites in the Shuanggou ophiolite are divided into two groups: (1) the Group‐1 harzburgites have 187Os/188Os ratios (0.12297–0.12727) and PGE abundances similar to those of oceanic peridotites, thereby representing the convecting upper mantle; (2) the Group‐2 harzburgites have extremely low 187Os/188Os ratios (0.11307–0.11651) with considerable fractionation in iridium group PGEs (Os, Ir, and Ru), indicative of an ancient refractory mantle in the oceanic lithosphere. The plagioclase lherzolites were formed by melt impregnation of the Group‐2 harzburgites, according to the PGE compositions and the petrographic features. However, the large Os isotope difference between the lherzolites (187Os/188Os: 0.12470–0.12666) and the Group‐2 harzburgites indicates that the refertilization process took place much earlier than the exhumation of the mantle at 0.4 Ga. In addition, clinopyroxene composition suggests that the percolating melt is different from the Shuanggou diabases and typical mid‐ocean ridge basalts. This study therefore demonstrates that some plagioclase lherzolites possibly were not related to mantle exhumation beneath the spreading center but formed by much older melt impregnation processes in the mantle instead.
High Pressure‐Temperature Study on the Thermal Equations of State of Seifertite andCaCl2‐Type SiO2
Authors: Sun Ningyu , Shi Weigang , Mao Zhu , Zhou Cijin , Prakapenka Vitali B. 
Published: November 2019

AbstractIn this study, we have determined the thermal equations of state (EoS) of CaCl2‐type SiO2 and seifertite (α‐PbO2‐type SiO2) from 55 to 147 GPa up to 3500 K using X‐ray diffraction in laser‐heated diamond anvil cells. The phase transition from stishovite to CaCl2‐type SiO2 is in good agreement with previous experimental results, whereas the transition from CaCl2‐type SiO2 to seifertite was observed to strongly rely on the starting material. For CaCl2‐type SiO2, we obtained a bulk modulus, KT0 = 245(7) GPa with a fixed KT′ = 4, V0 = 48.1(2) Å3, γ0 = 1.3(3), q = 1(fixed), and θD0 = 1100(400) K. Seifertite has a greater KT0 = 290(10) GPa (KT′ = 4 fixed) than CaCl2‐type SiO2. Other thermoelastic parameters of seifertite are V0 = 92.3(5) Å3, γ0 = 1.6(2), q = 1 (fixed), and θD0 = 1600(200) K. Using the obtained results and phase boundary in previous studies, we have found that the phase transition from stishovite to CaCl2‐type SiO2 cannot cause a noticeable change in density but can lower the bulk sound velocity (VФ) by ~10%. This phase transition in the subducted oceanic crust with 20 vol.% SiO2 was estimated to generate a ~2% discontinuity in VФ, which could be related to the observed seismic velocity anomalies at depths of 1,400–1,800 km. At the bottom of the lower mantle, CaCl2‐type SiO2 to seifertite phase transition can lead to a 0.3% jump in ρ and a 0.8% jump in VΦ considering 20 vol.% SiO2 in the subducted mid‐ocean ridge basalt, which may contribute to the formation of the D″ discontinuity above the core‐mantle boundary.
Insights From Micromechanical Modeling of Intact Rock Failure: Event Characteristics, Stress Drops, and Force Networks
Authors: van der Baan Mirko , Chorney Drew 
Published: November 2019

AbstractWe use a bonded‐particle method to investigate event characteristics, b values, internal force distributions, and stress drops in triaxial deformation tests. We simulate brittle through ductile deformation regimes. We find the following: (1) Event rates are proportional to anelastic axial strain: (i) significant and accelerating events rates only occur near peak stress (brittle deformation); (ii) event rates gradually increase until the anelastic strain plateaus (ductile deformation). (2) b value patterns show a systematic decrease when approaching peak stress, after which (i) they increase again (brittle case) or (ii) reach a constant minimum (ductile case). A decrease in b values is indicative of progressive internal damage, with an increasing event rate. (3) Weak‐ and strong‐force networks exist within the sample. Macrofailure of the sample occurs due to collapse of the strong‐force network. Acoustic emissions predominantly occur (i) within the weak‐force network allowing for tensile crack opening and closing despite the large compressive external stresses, and (ii) in areas with the largest spatial force gradients, close to the strong‐force networks. All internal compressive and extensional normal forces display exponential distributions despite uniform boundary stresses. (4) Stress drops of the largest events are inversely proportional to peak stress; the largest stress drops occur for brittle failure, progressively approaching a zero magnitude for ductile deformation. The systemic correlations between b values, the number of acoustic emissions, and stress drops with the maximum principal stress may offer opportunities to invert for changes in the stress state from these remote observables during earthquake cycles.
Radiolysis of Macromolecular Organic Material in Mars‐Relevant Mineral Matrices
Authors: Fox A. C. , Eigenbrode J. L. , Freeman K. H. 
Published: November 2019

AbstractThe fate of organic material on Mars after deposition is crucial to interpreting the source of these molecules. Previous work has addressed how various organic compounds at millimeter depths in sediments respond to ultraviolet radiation. In contrast, this study addressed how high‐energy particle radiation (200‐MeV protons, simulating the effect of galactic cosmic rays and solar wind at depths of <4–5 cm) influences organic macromolecules in sediments. Specifically, we report the generation of organic‐acid radiolysis products after exposure to radiation doses equivalent to geological time scales (1–7 Myr). We found that formate and oxalate were produced from a variety of organic starting materials and mineral matrices. Unlike ultraviolet‐driven reactions that can invoke Fenton chemistry to produce organic acids, our work suggests that irradiation of semiconductor surfaces, such as TiO2 or possible clay minerals found on Mars, forms oxygen and hydroxyl radical species, which can break down macromolecules into organic acids. We also investigated the metastability of benzoate in multiple mineral matrices. Benzoate was added to samples prior to irradiation and persisted up to 500 kGys of exposure. Our findings suggest that organic acids are likely a major component of organic material buried at depth on Mars.
In-cell identification and measurement of RNA-protein interactions
Authors: Graindorge Antoine , Pinheiro Inês , Nawrocka Anna , Mallory Allison C. , Tsvetkov Peter , Gil Noa , Carolis Carlo , Buchholz Frank , Ulitsky Igor , Heard Edith , Taipale Mikko , Shkumatava Alena 
Published: November 2019

AbstractRegulatory RNAs exert their cellular functions through RNA-binding proteins (RBPs). Identifying RNA-protein interactions is therefore key for a molecular understanding of regulatory RNAs. To date, RNA-bound proteins have been identified primarily through RNA purification followed by mass spectrometry. Here, we develop incPRINT (in cell protein-RNA interaction), a high-throughput method to identify in-cell RNA-protein interactions revealed by quantifiable luminescence. Applying incPRINT to long noncoding RNAs (lncRNAs), we identify RBPs specifically interacting with the lncRNA Firre and three functionally distinct regions of the lncRNA Xist. incPRINT confirms previously known lncRNA-protein interactions and identifies additional interactions that had evaded detection with other approaches. Importantly, the majority of the incPRINT-defined interactions are specific to individual functional regions of the large Xist transcript. Thus, we present an RNA-centric method that enables reliable identification of RNA-region-specific RBPs and is applicable to any RNA of interest.
SERS discrimination of single DNA bases in single oligonucleotides by electro-plasmonic trapping
Authors: Huang Jian-An , Mousavi Mansoureh Z. , Zhao Yingqi , Hubarevich Aliaksandr , Omeis Fatima , Giovannini Giorgia , Schütte Moritz , Garoli Denis , De Angelis Francesco 
Published: November 2019

AbstractSurface-enhanced Raman spectroscopy (SERS) sensing of DNA bases by plasmonic nanopores could pave a way to novel methods for DNA analyses and new generation single-molecule sequencing platforms. The SERS discrimination of single DNA bases depends critically on the time that a DNA strand resides within the plasmonic hot spot. In fact, DNA molecules flow through the nanopores so rapidly that the SERS signals collected are not sufficient for single-molecule analysis. Here, we report an approach to control the residence time of molecules in the hot spot by an electro-plasmonic trapping effect. By directly adsorbing molecules onto a gold nanoparticle and then trapping the single nanoparticle in a plasmonic nanohole up to several minutes, we demonstrate single-molecule SERS detection of all four DNA bases as well as discrimination of single nucleobases in a single oligonucleotide. Our method can be extended easily to label-free sensing of single-molecule amino acids and proteins.
Anomalous magnetoresistance due to longitudinal spin fluctuations in a Jeff = 1/2 Mott semiconductor
Authors: Hao Lin , Wang Zhentao , Yang Junyi , Meyers D. , Sanchez Joshua , Fabbris Gilberto , Choi Yongseong , Kim Jong-Woo , Haskel Daniel , Ryan Philip J. , Barros Kipton , Chu Jiun-Haw , Dean M. P. M. , Batista Cristian D. , Liu Jian 
Published: November 2019

AbstractAs a hallmark of electronic correlation, spin-charge interplay underlies many emergent phenomena in doped Mott insulators, such as high-temperature superconductivity, whereas the half-filled parent state is usually electronically frozen with an antiferromagnetic order that resists external control. We report on the observation of a positive magnetoresistance that probes the staggered susceptibility of a pseudospin-half square-lattice Mott insulator built as an artificial SrIrO3/SrTiO3 superlattice. Its size is particularly large in the high-temperature insulating paramagnetic phase near the Néel transition. This magnetoresistance originates from a collective charge response to the large longitudinal spin fluctuations under a linear coupling between the external magnetic field and the staggered magnetization enabled by strong spin-orbit interaction. Our results demonstrate a magnetic control of the binding energy of the fluctuating particle-hole pairs in the Slater-Mott crossover regime analogous to the Bardeen-Cooper-Schrieffer-to-Bose-Einstein condensation crossover of ultracold-superfluids.
Disentangling the role of Africa in the global spread of H5 highly pathogenic avian influenza
Authors: Fusaro Alice , Zecchin Bianca , Vrancken Bram , Abolnik Celia , Ademun Rose , Alassane Abdou , Arafa Abdelsatar , Awuni Joseph Adongo , Couacy-Hymann Emmanuel , Coulibaly M.’ Bétiégué , Gaidet Nicolas , Go-Maro Emilie , Joannis Tony , Jumbo Simon Dickmu , Minoungou Germaine , Meseko Clement , Souley Maman Moutari , Ndumu Deo Birungi , Shittu Ismaila , Twabela Augustin , Wade Abel , Wiersma Lidewij , Akpeli Yao P. , Zamperin Gianpiero , Milani Adelaide , Lemey Philippe , Monne Isabella 
Published: November 2019

AbstractThe role of Africa in the dynamics of the global spread of a zoonotic and economically-important virus, such as the highly pathogenic avian influenza (HPAI) H5Nx of the Gs/GD lineage, remains unexplored. Here we characterise the spatiotemporal patterns of virus diffusion during three HPAI H5Nx intercontinental epidemic waves and demonstrate that Africa mainly acted as an ecological sink of the HPAI H5Nx viruses. A joint analysis of host dynamics and continuous spatial diffusion indicates that poultry trade as well as wild bird migrations have contributed to the virus spreading into Africa, with West Africa acting as a crucial hotspot for virus introduction and dissemination into the continent. We demonstrate varying paths of avian influenza incursions into Africa as well as virus spread within Africa over time, which reveal that virus expansion is a complex phenomenon, shaped by an intricate interplay between avian host ecology, virus characteristics and environmental variables.
Enhancing materials property prediction by leveraging computational and experimental data using deep transfer learning
Authors: Jha Dipendra , Choudhary Kamal , Tavazza Francesca , Liao Wei-keng , Choudhary Alok , Campbell Carelyn , Agrawal Ankit 
Published: November 2019

AbstractThe current predictive modeling techniques applied to Density Functional Theory (DFT) computations have helped accelerate the process of materials discovery by providing significantly faster methods to scan materials candidates, thereby reducing the search space for future DFT computations and experiments. However, in addition to prediction error against DFT-computed properties, such predictive models also inherit the DFT-computation discrepancies against experimentally measured properties. To address this challenge, we demonstrate that using deep transfer learning, existing large DFT-computational data sets (such as the Open Quantum Materials Database (OQMD)) can be leveraged together with other smaller DFT-computed data sets as well as available experimental observations to build robust prediction models. We build a highly accurate model for predicting formation energy of materials from their compositions; using an experimental data set of$$1,643$$1,643observations, the proposed approach yields a mean absolute error (MAE) of$$0.07$$0.07eV/atom, which is significantly better than existing machine learning (ML) prediction modeling based on DFT computations and is comparable to the MAE of DFT-computation itself.
Dynamic constriction and fission of endoplasmic reticulum membranes by reticulon
Authors: Espadas Javier , Pendin Diana , Bocanegra Rebeca , Escalada Artur , Misticoni Giulia , Trevisan Tatiana , Velasco del Olmo Ariana , Montagna Aldo , Bova Sergio , Ibarra Borja , Kuzmin Peter I. , Bashkirov Pavel V. , Shnyrova Anna V. , Frolov Vadim A. , Daga Andrea 
Published: November 2019

AbstractThe endoplasmic reticulum (ER) is a continuous cell-wide membrane network. Network formation has been associated with proteins producing membrane curvature and fusion, such as reticulons and atlastin. Regulated network fragmentation, occurring in different physiological contexts, is less understood. Here we find that the ER has an embedded fragmentation mechanism based upon the ability of reticulon to produce fission of elongating network branches. In Drosophila, Rtnl1-facilitated fission is counterbalanced by atlastin-driven fusion, with the prevalence of Rtnl1 leading to ER fragmentation. Ectopic expression of Drosophila reticulon in COS-7 cells reveals individual fission events in dynamic ER tubules. Consistently, in vitro analyses show that reticulon produces velocity-dependent constriction of lipid nanotubes leading to stochastic fission via a hemifission mechanism. Fission occurs at elongation rates and pulling force ranges intrinsic to the ER, thus suggesting a principle whereby the dynamic balance between fusion and fission controlling organelle morphology depends on membrane motility.
Phase-field lattice Boltzmann model for dendrites growing and moving in melt flow
Authors: Rátkai László , Pusztai Tamás , Gránásy László 
Published: November 2019

AbstractThe phase-field and lattice Boltzmann methods have been combined to simulate the growth of solid particles moving in melt flow. To handle mobile particles, an overlapping multigrid scheme was developed, in which each individual particle has its own moving grid, with local fields attached to it. Using this approach we were able to simulate simultaneous binary solidification, solute diffusion, melt flow, solid motion, the effect of gravity, and collision of the particles. The method has been applied for describing two possible modes of columnar to equiaxed transition in the Al–Ti system.
Prediction of room-temperature half-metallicity in layered halide double perovskites
Authors: Xu Jian , Xu Changsong , Liu Jian-Bo , Bellaiche Laurent , Xiang Hongjun , Liu Bai-Xin , Huang Bing 
Published: November 2019

AbstractHalf-metallic ferromagnets (HMFs) that possess intriguing physical properties with completely spin-polarized current are key candidates for high-efficiency spintronic devices. However, HMFs that could simultaneously have high Curie temperature (Tc), wide half-metallic gap (ΔHM), and large bulk magnetocrystalline anisotropy energy (MAE) are very rare, which significantly restrict their room-temperature (RT) applications. In this article, through materials screening in layered halide double perovskites (LHDPs), we have theoretically identified that Cs4FePb2Cl12, which has good crystallographic, dynamic and thermal stabilities, possesses an intrinsic half-metallic ground-state with a high Tc ~ 450 K. Interestingly, the long-range ferromagnetic ordering in bulk Cs4FePb2Cl12 is contributed by the strong super-superexchange interactions between the neighboring Fe d orbitals mediated by different anionic Cl p orbitals. The high Tc of layered Cs4FePb2Cl12 can be well maintained even in the monolayer limitation, i.e., Tc ~ 370 K for Cs4FePb2Cl12 monolayer, which is critical for nanoscale device applications. Moreover, both bulk and monolayer Cs4FePb2Cl12 can exhibit wide ΔHM ~ 0.55 eV and large MAE >320 μeV/Fe, comparable to that of the best HMFs reported in the literature. Our findings can significantly extend the potentials of LHDPs for high-temperature spintronic applications.
A simple method for sequencing the whole human mitochondrial genome directly from samples and its application to genetic testing
Authors: Yao Yue , Nishimura Motoi , Murayama Kei , Kuranobu Naomi , Tojo Satomi , Beppu Minako , Ishige Takayuki , Itoga Sakae , Tsuchida Sachio , Mori Masato , Takayanagi Masaki , Yokoyama Masataka , Yamagata Kazuyuki , Kishita Yoshihito , Okazaki Yasushi , Nomura Fumio , Matsushita Kazuyuki , Tanaka Tomoaki 
Published: November 2019

AbstractNext-generation sequencing (NGS) is a revolutionary sequencing technology for analyzing genomes. However, preprocessing methods for mitochondrial DNA (mtDNA) sequencing remain complex, and it is required to develop an authenticated preprocessing method. Here, we developed a simple and easy preprocessing method based on isothermal rolling circle mtDNA amplification using commercially available reagents. Isothermal amplification of mtDNA was successfully performed using both nanoliter quantities of plasma directly and 25 ng of total DNA extracted from blood or tissue samples. Prior to mtDNA amplification, it was necessary to treat the extracted total DNA with Exonuclease V, but it was not required to treat plasma. The NGS libraries generated from the amplified mtDNA provided sequencing coverage of the entire human mitochondrial genome. Furthermore, the sequencing results successfully detected heteroplasmy in patient samples, with called mutations and variants matching those from previous, independent, Sanger sequencing analysis. Additionally, a novel single nucleotide variant was detected in a healthy volunteer. The successful analysis of mtDNA using very small samples from patients is likely to be valuable in clinical medicine, as it could reduce patient discomfort by reducing sampling-associated damage to tissues. Overall, the simple and convenient preprocessing method described herein may facilitate the future development of NGS-based clinical and forensic mtDNA tests.
Global Phylogeographic and Admixture Patterns in Grey Wolves and Genetic Legacy of An Ancient Siberian Lineage
Authors: Pilot Małgorzata , Moura Andre E. , Okhlopkov Innokentiy M. , Mamaev Nikolay V. , Alagaili Abdulaziz N. , Mohammed Osama B. , Yavruyan Eduard G. , Manaseryan Ninna H. , Hayrapetyan Vahram , Kopaliani Natia , Tsingarska Elena , Krofel Miha , Skoglund Pontus , Bogdanowicz Wiesław 
Published: November 2019

AbstractThe evolutionary relationships between extinct and extant lineages provide important insight into species’ response to environmental change. The grey wolf is among the few Holarctic large carnivores that survived the Late Pleistocene megafaunal extinctions, responding to that period’s profound environmental changes with loss of distinct lineages and phylogeographic shifts, and undergoing domestication. We reconstructed global genome-wide phylogeographic patterns in modern wolves, including previously underrepresented Siberian wolves, and assessed their evolutionary relationships with a previously genotyped wolf from Taimyr, Siberia, dated at 35 Kya. The inferred phylogeographic structure was affected by admixture with dogs, coyotes and golden jackals, stressing the importance of accounting for this process in phylogeographic studies. The Taimyr lineage was distinct from modern Siberian wolves and constituted a sister lineage of modern Eurasian wolves and domestic dogs, with an ambiguous position relative to North American wolves. We detected gene flow from the Taimyr lineage to Arctic dog breeds, but population clustering methods indicated closer similarity of the Taimyr wolf to modern wolves than dogs, implying complex post-divergence relationships among these lineages. Our study shows that introgression from ecologically diverse con-specific and con-generic populations was common in wolves’ evolutionary history, and could have facilitated their adaptation to environmental change.
Overestimated climate warming and climate variability due to spatially homogeneous CO2 in climate modeling over the Northern Hemisphere since the mid-19th century
Authors: Zhang Xuezhen , Li Xiaxiang , Chen Deliang , Cui Huijuan , Ge Quansheng 
Published: November 2019

AbstractSince the mid-19th century, the global atmospheric CO2 concentration (ACC) has increased dramatically due to the burning of fossil fuels. Because of unequal population growth and economic development among regions, the ACC increases possess strong spatial variability. Particularly, the increase in ACC has been larger in the mid-latitudes of the Northern Hemisphere (NH) than that at high- and low-latitudes. It is widely accepted that the ACC increase is the main reason for climate change, but the potential impacts of its spatial distribution on the climate system remain unclear. Therefore, we carried out two groups of 150-year experiments with the Community Earth System Model (CESM), using both spatially inhomogeneous (hereafter the SIC experiment) and homogenous (hereafter the SHC experiment) ACC increases in their settings. We found that the models’ divergences occurred over the NH mid-latitudes, the Arctic and the western part of the tropical Pacific. SHC overestimated (underestimated) climate warming over the Artic (mid-latitudes), which may be induced by the intensified westerly and weakened meridional heat exchange between mid- and high latitudes in the NH. Over the tropical Pacific, the overestimation of climate warming may be induced by intensified Walker circulation coupled with the La Niña climate mode. For the entire NH, relative to SIC, SHC overestimated the climate warming from 1850 to 1999 by ~10%. Meanwhile, the SHC experiment also overestimated the interannual variabilities in temperature and precipitation, resulting in more serious extreme events. These findings suggest that human contributions to climate warming and increased extreme events since the industrial revolution may be overestimated when using a spatially homogenous ACC.