bluuebunny/crossref_metadata_2025_split huggingface dataset:
Early Indian Summer Monsoon Onset Driven by Low Soil Moisture in the Iranian Desert
Authors: Moon Suyeon , Ha Kyung‐Ja 
Published: August 2019

AbstractAdvancing the leading time for onset prediction of the Indian summer monsoon (ISM) onset is an imperative task; however, it has remained a challenging subject. In particular, the land‐atmosphere coupling associated with monsoon onset prediction is poorly understood. Here we attempt to investigate the land factor as the ISM onset precursor through studying the internal mechanism of atmospheric heating, which is distinguished by monsoon onset. The low (high) soil moisture in the Iranian desert during March and April advances (delays) ISM onset by enhancing (disturbing) the vertical easterly wind shear. In addition, midtropospheric heating is affected by soil moisture in the Iranian desert. By investigating the internal atmospheric heating process and suggesting the relationship between low soil moisture and ISM onset, these findings clarify the monsoon onset mechanism in terms of the vertical atmospheric profile and land‐atmosphere interaction, which eventually extend the lead time for the onset prediction.
Singular Spectral Analysis of the aa and Dst Geomagnetic Indices
Authors: Le Mouël J. L. , Lopes F. , Courtillot V. 
Published: August 2019

AbstractWe apply singular spectrum analysis in order to identify trends and quasi‐periodic oscillations in the aa and Dst series of geomagnetic activity. We also analyze the sunspot number International SunSpot Number (ISSN) and the number of polar faculae Polar Faculae (PF). Singular spectrum analysis provides the eigenvalues and therefore trends and oscillatory components of the four series. ISSN is dominated by a trend (the Gleissberg cycle), followed by 10.6, 35.5 years, two ~8‐year components, 21.4 and 5.3 year. aa shows the same trend, a ~47‐year component, then 10.8, 32.3, 21.8, and a series of three close components at 10.6, 12.2, and 9.2 years, followed by a 6 month seasonal component. PF is dominated by the 20.7‐year period, followed by 10.2, 8.3, 41, and 31 years, then a 5.2 year component. Dst is dominated by a trend, then a strong 6‐month component; next are found a 47‐year component, the 10.6 years and a second seasonal line at 1 year. The ~22‐, ~11‐, and ~5.5‐year components are common to the four indices. These “pseudo harmonic” components are evidence of solar activity. Singular spectrum analysis identifies components that vary in frequency and amplitude. The phase relationships of any two components over time can be studied in detail. An illustration is given by the remarkable phase coherency of the 5.3‐year component. But the components are neither truly periodical nor exact multiples of each other. These differences reflect the complex mechanisms that govern solar‐terrestrial relationships.
Equation of State for Shocked Fe‐8.6 wt% Si up to 240 GPa and 4,670 K
Authors: Huang Haijun , Leng Chunwei , Wang Qingsong , Young Gang , Liu Xun , Wu Ye , Xu Feng , Fei Yingwei 
Published: August 2019

AbstractUsing dynamic compression technique, the equation of state for Fe‐8.6 wt% Si was measured up to 240 GPa and 4,670 K. A least squares fit to the experimental data yields the Hugoniot parameters C0 = 4.603±0.101 km/s and λ = 1.505±0.037 with initial density ρ0=7.386±0.021 g/cm3. Based on the Hugoniot data, the calculated isothermal equation of state is consistent with static compression data when the lattice Grüneisen parameter γl =1.65(7.578/ρ) and electronic Grüneisen parameter γe=1.83. The calculated pressure‐density data at 300 K were fitted to a third‐order Birch‐Murnaghan equation of state with zero pressure the parameters K0=192.1±6.3 GPa,
=4.71±0.27 with fixed ρ0ε =7.578±0.050 g/cm3. Under the conditions of Earth's core, the densities of Fe‐8.6±2.0 wt% Si and Fe‐3.8±2.9 wt% Si agree with preliminary reference Earth mode (PREM) data of the outer and the inner core, respectively. These are the upper limits for Si in the core assuming Si is the only light element. Simultaneously considering the geophysical and geochemical constraints for a Si‐S‐bearing core, the outer core may contain 3.8±2.9 wt% Si and 5.6±3.0 wt% S.
Plio‐Quaternary Outer Forearc Deformation and Mass Balance of the Southern Costa Rica Convergent Margin
Authors: Morell Kristin D. , Fisher Donald M. , Bangs Nathan 
Published: August 2019

AbstractIdentifying the processes that control the rates, magnitudes, and longevity of outer forearc deformation is fundamental to our understanding of how mass is distributed within subduction zone systems. The margin of southern Costa Rica has been the target of numerous onland field studies, geophysical surveys, and the Costa Rica Seismogenesis Project (CRISP) drilling expedition. Despite these extensive data sets, the relative roles that subduction erosion, shortening, and seamount subduction play in shaping the behavior and evolution of the outer forearc remain debated. Here we analyze new and existing geomorphic, geologic, stratigraphic, and geochronologic data sets across the entire forearc‐arc‐backarc system near the Costa Rica Seismogenesis Project transect to test several conceptual models for outer forearc deformation in southern Costa Rica. The results from the compilation agree with a model where recent arcward retreat of the trench (movement of the trench in the direction of the arc) occurs due to underthrusting of the outer forearc beneath the inner forearc, and outer forearc deformation occurs primarily by transient rapid vertical tectonism due to the subduction of bathymetric relief. These results lead to a new conceptual model for Plio‐Quaternary outer forearc deformation in southern Costa Rica that does not require large amounts of net mass loss within the upper plate.
Leaf Wax δD and δ13C in Soils Record Hydrological and Environmental Information Across a Climatic Gradient in Israel
Authors: Goldsmith Yonaton , Polissar Pratigya J. , deMenocal Peter B. , Broecker Wallace S. 
Published: August 2019

AbstractThe hydrogen (δDwax) and carbon (δ13Cwax) isotope compositions of long‐chain alkanes derived from plant waxes record hydrological and environmental conditions. However, the integration of plant n‐alkanes into the sedimentary cycle, the variability of δDwax and δ13Cwax in soils, and the paleoclimate applicability in paleosols and archaeological sediments are poorly constrained. We sampled plants and soils across a steep climate transect in Israel to understand how plant type and environmental parameters shape δ13Cwax and δDwax. This transect has three advantages: existence of long‐term precipitation isotopic composition (δDr) records, a single wet season potentially reduces variability due to seasonality, and abandoned Byzantine period (~300–600 AD) agricultural terraces that reduce modern and ancient soil mixing and provide age constraints. We find that soil δ13Cwax is constant (0.4‰, 1σ) across a 500‐ to 1,300‐mm/year rainfall gradient and appears insensitive to rainfall amount, unlike bulk plant δ13C. The absence of a rainfall effect suggests that δ13Cwax may be better suited to reconstructing C3/C4 plant ratios than bulk δ13C. Homologue average soil δDwax significantly correlate with δDr, and the offset between δDr and soil δDwax (εapp) correlates with growing season relative humidity. The seasonality of leaf production accounted for at most ~10% of total plant δDwax variability. Lastly, soil δDwax and δ13Cwax variability is reduced by ~80% relative to plant δDwax and δ13Cwax variability. Our results show that soil δDwax and δ13Cwax faithfully record δDr and landscape C3‐C4 plant contributions and thus support the utility of these proxy data in paleosols and archaeological sites.
DeepCC: a novel deep learning-based framework for cancer molecular subtype classification
Authors: Gao Feng , Wang Wei , Tan Miaomiao , Zhu Lina , Zhang Yuchen , Fessler Evelyn , Vermeulen Louis , Wang Xin 
Published: August 2019

AbstractMolecular subtyping of cancer is a critical step towards more individualized therapy and provides important biological insights into cancer heterogeneity. Although gene expression signature-based classification has been widely demonstrated to be an effective approach in the last decade, the widespread implementation has long been limited by platform differences, batch effects, and the difficulty to classify individual patient samples. Here, we describe a novel supervised cancer classification framework, deep cancer subtype classification (DeepCC), based on deep learning of functional spectra quantifying activities of biological pathways. In two case studies about colorectal and breast cancer classification, DeepCC classifiers and DeepCC single sample predictors both achieved overall higher sensitivity, specificity, and accuracy compared with other widely used classification methods such as random forests (RF), support vector machine (SVM), gradient boosting machine (GBM), and multinomial logistic regression algorithms. Simulation analysis based on random subsampling of genes demonstrated the robustness of DeepCC to missing data. Moreover, deep features learned by DeepCC captured biological characteristics associated with distinct molecular subtypes, enabling more compact within-subtype distribution and between-subtype separation of patient samples, and therefore greatly reduce the number of unclassifiable samples previously. In summary, DeepCC provides a novel cancer classification framework that is platform independent, robust to missing data, and can be used for single sample prediction facilitating clinical implementation of cancer molecular subtyping.
Expression of CD20 after viral reactivation renders HIV-reservoir cells susceptible to Rituximab
Authors: Serra-Peinado Carla , Grau-Expósito Judith , Luque-Ballesteros Laura , Astorga-Gamaza Antonio , Navarro Jordi , Gallego-Rodriguez Jenny , Martin Mario , Curran Adrià , Burgos Joaquin , Ribera Esteban , Raventós Berta , Willekens Rein , Torrella Ariadna , Planas Bibiana , Badía Rosa , Garcia Felipe , Castellví Josep , Genescà Meritxell , Falcó Vicenç , Buzon Maria J. 
Published: August 2019

AbstractThe identification of exclusive markers to target HIV-reservoir cells will represent a significant advance in the search for therapies to cure HIV. Here, we identify the B lymphocyte antigen CD20 as a marker for HIV-infected cells in vitro and in vivo. The CD20 molecule is dimly expressed in a subpopulation of CD4-positive (CD4+) T lymphocytes from blood, with high levels of cell activation and heterogeneous memory phenotypes. In lymph node samples from infected patients, CD20 is present in productively HIV-infected cells, and ex vivo viral infection selectively upregulates the expression of CD20 during early infection. In samples from patients on antiretroviral therapy (ART) this subpopulation is significantly enriched in HIV transcripts, and the anti-CD20 monoclonal antibody Rituximab induces cell killing, which reduces the pool of HIV-expressing cells when combined with latency reversal agents. We provide a tool for targeting this active HIV-reservoir after viral reactivation in patients while on ART.
N-glycosylation-defective splice variants of neuropilin-1 promote metastasis by activating endosomal signals
Authors: Huang Xiuping , Ye Qing , Chen Min , Li Aimin , Mi Wenting , Fang Yuxin , Zaytseva Yekaterina Y. , O’Connor Kathleen L. , Vander Kooi Craig W. , Liu Side , She Qing-Bai 
Published: August 2019

AbstractNeuropilin-1 (NRP1) is an essential transmembrane receptor with a variety of cellular functions. Here, we identify two human NRP1 splice variants resulting from the skipping of exon 4 and 5, respectively, in colorectal cancer (CRC). Both NRP1 variants exhibit increased endocytosis/recycling activity and decreased levels of degradation, leading to accumulation on endosomes. This increased endocytic trafficking of the two NRP1 variants, upon HGF stimulation, is due to loss of N-glycosylation at the Asn150 or Asn261 site, respectively. Moreover, these NRP1 variants enhance interactions with the Met and β1-integrin receptors, resulting in Met/β1-integrin co-internalization and co-accumulation on endosomes. This provides persistent signals to activate the FAK/p130Cas pathway, thereby promoting CRC cell migration, invasion and metastasis. Blocking endocytosis or endosomal Met/β1-integrin/FAK signaling profoundly inhibits the oncogenic effects of both NRP1 variants. These findings reveal an important role for these NRP1 splice variants in the regulation of endocytic trafficking for cancer cell dissemination.
3D sub-diffraction imaging in a conventional confocal configuration by exploiting super-linear emitters
Authors: Denkova Denitza , Ploschner Martin , Das Minakshi , Parker Lindsay M. , Zheng Xianlin , Lu Yiqing , Orth Antony , Packer Nicolle H. , Piper James A. 
Published: August 2019

AbstractSub-diffraction microscopy enables bio-imaging with unprecedented clarity. However, most super-resolution methods require complex, costly purpose-built systems, involve image post-processing and struggle with sub-diffraction imaging in 3D. Here, we realize a conceptually different super-resolution approach which circumvents these limitations and enables 3D sub-diffraction imaging on conventional confocal microscopes. We refer to it as super-linear excitation-emission (SEE) microscopy, as it relies on markers with super-linear dependence of the emission on the excitation power. Super-linear markers proposed here are upconversion nanoparticles of NaYF4, doped with 20% Yb and unconventionally high 8% Tm, which are conveniently excited in the near-infrared biological window. We develop a computational framework calculating the 3D resolution for any viable scanning beam shape and excitation-emission probe profile. Imaging of colominic acid-coated upconversion nanoparticles endocytosed by neuronal cells, at resolutions twice better than the diffraction limit both in lateral and axial directions, illustrates the applicability of SEE microscopy for sub-cellular biology.
A [13]rotaxane assembled via a palladium molecular capsule
Authors: Ferrando-Soria Jesus , Fernandez Antonio , Asthana Deepak , Nawaz Selina , Vitorica-Yrezabal Iñigo J. , Whitehead George F. S. , Muryn Christopher A. , Tuna Floriana , Timco Grigore A. , Burton Neil D. , Winpenny Richard E. P. 
Published: August 2019

AbstractMolecules that are the size of small proteins are difficult to make. The most frequently examined route is via self-assembly, and one particular approach involves molecular nanocapsules, where ligands are designed that will enforce the formation of specific polyhedra of metals within the core of the structure. Here we show that this approach can be combined with mechanically interlocking molecules to produce nanocapsules that are decorated on their exterior. This could be a general route to very large molecules, and is exemplified here by the synthesis and structural characterization of a [13]rotaxane, containing 150 metal centres. Small angle X-ray scattering combined with atomistic molecular dynamics simulations demonstrate the compound is intact in solution.
Chemical compass behaviour at microtesla magnetic fields strengthens the radical pair hypothesis of avian magnetoreception
Authors: Kerpal Christian , Richert Sabine , Storey Jonathan G. , Pillai Smitha , Liddell Paul A. , Gust Devens , Mackenzie Stuart R. , Hore P. J. , Timmel Christiane R. 
Published: August 2019

AbstractThe fact that many animals, including migratory birds, use the Earth’s magnetic field for orientation and compass-navigation is fascinating and puzzling in equal measure. The physical origin of these phenomena has not yet been fully understood, but arguably the most likely hypothesis is based on the radical pair mechanism (RPM). Whilst the theoretical framework of the RPM is well-established, most experimental investigations have been conducted at fields several orders of magnitude stronger than the Earth’s. Here we use transient absorption spectroscopy to demonstrate a pronounced orientation-dependence of the magnetic field response of a molecular triad system in the field region relevant to avian magnetoreception. The chemical compass response exhibits the properties of an inclination compass as found in migratory birds. The results underline the feasibility of a radical pair based avian compass and also provide further guidelines for the design and operation of exploitable chemical compass systems.
RETRACTED ARTICLE: Mechanically interlocked architecture aids an ultra-stiff and ultra-hard elastically bendable cocrystal
Authors: Dey Somnath , Das Susobhan , Bhunia Surojit , Chowdhury Rituparno , Mondal Amit , Bhattacharya Biswajit , Devarapalli Ramesh , Yasuda Nobuhiro , Moriwaki Taro , Mandal Kapil , Mukherjee Goutam Dev , Reddy C. Malla 
Published: August 2019

AbstractMolecular crystals are not known to be as stiff as metals, composites and ceramics. Here we report an exceptional mechanical stiffness and high hardness in a known elastically bendable organic cocrystal [caffeine (CAF), 4-chloro-3-nitrobenzoic acid (CNB) and methanol (1:1:1)] which is comparable to certain low-density metals. Spatially resolved atomic level studies reveal that the mechanically interlocked weak hydrogen bond networks which are separated by dispersive interactions give rise to these mechanical properties. Upon bending, the crystals significantly conserve the overall energy by efficient redistribution of stress while perturbations in hydrogen bonds are compensated by strengthened π-stacking. Furthermore we report a remarkable stiffening and hardening in the elastically bent crystal. Hence, mechanically interlocked architectures provide an unexplored route to reach new mechanical limits and adaptability in organic crystals. This proof of concept inspires the design of light-weight, stiff crystalline organics with potential to rival certain inorganics, which currently seem inconceivable.
On demand delivery and analysis of single molecules on a programmable nanopore-optofluidic device
Authors: Rahman M. , Stott M. A. , Harrington M. , Li Y. , Sampad M. J. N. , Lancaster L. , Yuzvinsky T. D. , Noller H. F. , Hawkins A. R. , Schmidt H. 
Published: August 2019

AbstractNanopore-based single nanoparticle detection has recently emerged as a vibrant research field with numerous high-impact applications. Here, we introduce a programmable optofluidic chip for nanopore-based particle analysis: feedback-controlled selective delivery of a desired number of biomolecules and integration of optical detection techniques on nanopore-selected particles. We demonstrate the feedback-controlled introduction of individual biomolecules, including 70S ribosomes, DNAs and proteins into a fluidic channel where the voltage across the nanopore is turned off after a user-defined number of single molecular insertions. Delivery rates of hundreds/min with programmable off-times of the pore are demonstrated using individual 70S ribosomes. We then use real-time analysis of the translocation signal for selective voltage gating of specific particles from a mixture, enabling selection of DNAs from a DNA-ribosome mixture. Furthermore, we report optical detection of nanopore-selected DNA molecules. These capabilities point the way towards a powerful research tool for high-throughput single-molecule analysis on a chip.
Integrated 9Be+ multi-qubit gate device for the ion-trap quantum computer
Authors: Hahn H. , Zarantonello G. , Schulte M. , Bautista-Salvador A. , Hammerer K. , Ospelkaus C. 
Published: August 2019

AbstractWe demonstrate the experimental realization of a two-qubit Mølmer–Sørensen gate on a magnetic field-insensitive hyperfine transition in 9Be+ ions using microwave near-fields emitted by a single microwave conductor embedded in a surface-electrode ion trap. The design of the conductor was optimized to produce a high oscillating magnetic field gradient at the ion position. The measured gate fidelity is determined to be 98.2 ± 1.2% and is limited by technical imperfections, as is confirmed by a comprehensive numerical error analysis. The conductor design can potentially simplify the implementation of multi-qubit gates and represents a self-contained, scalable module for entangling gates within the quantum CCD architecture for an ion-trap quantum computer.
Creating a surrogate commuter network from Australian Bureau of Statistics census data
Authors: Fair Kristopher M. , Zachreson Cameron , Prokopenko Mikhail 
Published: August 2019

AbstractBetween the 2011 and 2016 national censuses, the Australian Bureau of Statistics changed its anonymity policy compliance system for the distribution of census data. The new method has resulted in dramatic inconsistencies when comparing low-resolution data to aggregated high-resolution data. Hence, aggregated totals do not match true totals, and the mismatch gets worse as the data resolution gets finer. Here, we address several aspects of this inconsistency with respect to the 2016 usual-residence to place-of-work travel data. We introduce a re-sampling system that rectifies many of the artifacts introduced by the new ABS protocol, ensuring a higher level of consistency across partition sizes. We offer a surrogate high-resolution 2016 commuter dataset that reduces the difference between the aggregated and true commuter totals from ~34% to only ~7%, which is on the order of the discrepancy across partition resolutions in data from earlier years.
HBcAb seropositivity is correlated with poor HIV viremia control in an Italian cohort of HIV/HBV-coinfected patients on first-line therapy
Authors: Malagnino Vincenzo , Cerva Carlotta , Maffongelli Gaetano , Teti Elisabetta , Foroghi Biland Luca , Cesta Novella , De Masi Margherita , Stingone Christof , Armenia Daniele , Svicher Valentina , Salpini Romina , Andreoni Massimo , Sarmati Loredana 
Published: August 2019

AbstractThe morbidity and mortality rates of human immunodeficiency virus (HIV)-hepatitis B virus (HBV) coinfection are higher than that of either infection alone. Outcomes and the virological response to antiretrovirals (combination antiretroviral therapy, cART) were explored in HIV/HBV subjects in a cohort of Italian patients treated with cART. A single-center retrospective analysis of patients enrolled from January 2007 to June 2018 was conducted by grouping patients by HBV status and recording baseline viro-immunological features, the history of virological failure, the efficacy of cART in achieving HIV viral undetectability, viral blip detection and viral rebound on follow up. Among 231 enrolled patients, 10 (4.3%) were HBV surface (s) antigen (HBsAg)-positive, 85 (36.8%) were positive for antibodies to HBV c antigen (HBcAb) and with or without antibodies to HBV s antigen (HBsAb), and 136 were (58.9%) HBV-negative. At baseline, HBcAb/HBsAb+/−-positive patients had lower CD4+ cell counts and CD4+ nadirs (188 cell/mmc, IQR 78–334, p = 0.02 and 176 cell/mmc, IQR 52–284, p = 0,001, respectively). There were significantly higher numbers of AIDS and non-AIDS events in the HBcAb+/HBsAb+/−-positive subjects than in the HBV-negative patients (41.1% vs 19.1%, p = 0.002 and 56.5% vs 28.7%, respectively, p ≤ 0.0001); additionally, HIV viremia undetectability was achieved a significantly longer time after cART was begun in the former than in the latter population (6 vs 4 months, p = 0.0001). Cox multivariable analysis confirmed that after starting cART, an HBcAb+/HBsAb+/−-positive status is a risk factor for a lower odds of achieving virological success and a higher risk of experiencing virological rebound (AHR 0.63, CI 95% 0.46–0.87, p = 0.004 and AHR 2.52, CI 95% 1.09–5.80, p = 0.030). HBcAb-positive status resulted in a delay in achieving HIV < 50 copies/mL and the appearance of viral rebound in course of cART, hence it is related to a poor control of HIV infection in a population of coinfected patients.