bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exaggerated Effect of Urbanization in the Diurnal Temperature Range Via “Observation minus Reanalysis” and the Physical Causes
Authors: Wang Jun , Yan Zhongwei , Feng Jinming 
Published: June 2018

AbstractThe observation minus reanalysis (OMR) method is widely used to investigate the impact of urbanization and land use changes on regional climate. Based on homogenized temperature observations and the National Centers for Environmental Prediction/Department of Energy Atmospheric Model Intercomparison Project II reanalysis surface temperatures, we estimate the trend in diurnal temperature range (DTR) using the OMR method to be −0.324 ± 0.063 °C per decade for the period of 1980–2009 in eastern China. However, we find that reanalysis data produce a positive trend in downward surface solar radiation, while the observations do not, because the reanalysis data significantly overestimate the negative trend in total cloud coverage in the region. Moreover, the reanalysis considerably overestimates the negative trend in the local precipitation. These systematic biases cause an overestimation of the warming rate in daily maximum temperature in the reanalysis and therefore lead to the exaggerated effect of urbanization on the DTR via the OMR analysis. After adjusting the systematic bias in the trend of daily maximum temperature in the reanalysis data, the regional mean OMR trend in the DTR is estimated to be −0.065 °C per decade, which becomes much smaller than previous OMR calculations, and is more consistent with the previous estimates based on the comparison of urban and rural stations. These results not only indicate the methodological problem of the OMR method in many studies of urbanization effects but also hint at important aspects for improving the current reanalysis system.
Making Sense of Massive Carbon Isotope Excursions With an Inverse Carbon Cycle Model
Authors: Miyazaki Yoshinori , Planavsky Noah J. , Bolton Edward W. , Reinhard Christopher T. 
Published: June 2018

AbstractThe beginning and end of the Proterozoic Eon are marked by extreme variations in carbonate carbon isotope values that have been interpreted to record massive perturbations to the global carbon cycle. The lower Proterozoic contains an extended interval of strata characterized by positive carbonate δ13C values. Conversely, uppermost Proterozoic carbonate strata contain thick intervals with extremely negative δ13C values and multiple large swings in carbonate δ13C. Previous attempts to model these pronounced carbon isotope excursions as shifts in the global marine dissolved inorganic carbon (DIC) reservoir have proved to be problematic, as the direction and magnitude of these positive and negative carbon isotope excursions require unrealistic amounts of either organic carbon burial or organic carbon oxidation, respectively. Here we present a modified global carbon cycle model—coupled with oxygen and sulfur cycle mass balances—that includes a parameterization of the recycling of sedimentary isotope anomalies and allows the extent of organic carbon oxidation to vary as a function of atmospheric oxygen levels. Our model is designed to match carbon isotope records while maintaining redox and mass balance with a given set of initial conditions and carbon cycle parameterizations. Using this approach, we demonstrate that there is a range of plausible biogeochemical perturbations that could induce substantial δ13C excursions in the global marine DIC reservoir. However, we also find that there are multiple, nonunique Earth system states for any observed marine δ13C value.
Tree Mortality From Insect Infestation Enhances Carbon Stabilization in Southern Appalachian Forest Soils
Authors: Fraterrigo Jennifer M. , Ream Kelsey , Knoepp Jennifer D. 
Published: June 2018

AbstractForest insect and pathogen outbreaks may exacerbate anthropogenic climate change if they accelerate soil carbon loss to the atmosphere. We quantified soil respiration and carbon content for nearly a decade after girdling or natural infestation of hemlock (Tsuga canadensis L. Carr., a codominant species in southern Appalachian forests) by hemlock woolly adelgid (Adelges tsugae) to improve understanding of soil carbon response to disturbance from forest insect and pathogens. From 2005 to 2013, net soil respiration was similar among hemlock mortality (~50% basal area reduction) and reference hardwood plots, but both girdled and hemlock woolly adelgid‐infested plots showed greater activities of β‐glucosidase (a cellulose‐hydrolyzing extracellular enzyme), decreased O‐horizon, and decreased fine root biomass. During this period, mineral soil carbon accumulated at a higher rate in hemlock mortality plots than in reference plots in both surface (0–10 cm) and subsurface (10–30 cm) soils, driven by increases in the mineral‐associated fraction of the soil organic matter. In contrast, particulate organic matter (POM) carbon accrued slowly in surface soils and declined in the subsurface of girdled plots. δ13C values of the POM fraction demonstrate increased microbial processing of surface soil organic matter over time, suggesting enhanced decomposition of organic matter in this pool. These findings indicate that hemlock mortality in this system has led to enhanced soil carbon stabilization through the transformation and translocation of carbon from detrital and POM pools to the mineral‐associated organic matter pool. Accelerated responses in the girdled versus naturally infested treatments highlight limitations associated with using girdling to simulate natural mortality.
Benthic Biotic Response to Climate Changes Over the Last 700,000 Years in a Deep Marginal Sea: Impacts of Deoxygenation and the Mid‐Brunhes Event
Authors: Huang Huai‐Hsuan M. , Yasuhara Moriaki , Iwatani Hokuto , Alvarez Zarikian Carlos A. , Bassetti Maria‐Angela , Sagawa Takuya 
Published: June 2018

AbstractThe Sea of Japan is a marginal sea, connecting to adjacent seas by four shallow straits (water depths <130 m). Marginal seas are ideal for studying biotic responses to large‐scale environmental changes as they often are sensitive to glacial‐interglacial and stadial‐interstadial climatic cycles. However, only a limited number of studies cover time periods beyond the last two glacial‐interglacial cycles. Here we present a 700,000‐year record of benthic biotic response to paleoceanographic changes in the southern Sea of Japan, covering the past seven glacial‐interglacial cycles, based on ostracode assemblages at the Integrated Ocean Drilling Program (IODP) Site U1427. The results indicate that long‐term oxygen variability in the bottom water has been the major control impacting the marginal‐sea biota. Five local extirpation events were recognized as barren zones during glacial maxima immediately before terminations I, II, IV, V, and VII, which are probably caused by bottom‐water deoxygenation. Results of multivariate analyses indicated clear faunal cyclicity influenced by glacial‐interglacial oxygen variability with a succession from opportunistic species dominance through tolerant infauna dominance to barren zone during the deoxygenation processes and the opposite succession during the recovery processes. The Sea of Japan ostracode faunal composition showed distinct difference between the post‐MBE and pre‐MBE (Mid‐Brunhes Event) periods, indicating the MBE as a major disturbance event in marginal‐sea ecosystems. The MBE shortened the duration of the extirpation events, fostered dominance of warmer‐water species, and amplified the glacial‐interglacial faunal cyclicity. Our long‐term biotic response study clearly indicates that deep marginal sea ecosystems are dynamic and vulnerable to climate changes.
Orbitally Forced Hydrological Balance During the Messinian Salinity Crisis: Insights From Strontium Isotopes (87Sr/86Sr) in the Vena del Gesso Basin (Northern Apennines, Italy)
Authors: Reghizzi Matteo , Lugli Stefano , Manzi Vinicio , Rossi Francesco Paolo , Roveri Marco 
Published: June 2018

AbstractThe87Sr/86Sr ratio is a proxy of the hydrologic structure of marginal basins characterized by the mixing between marine and continental waters. This reliable paleoceanographic and paleoclimatic tool is considered a key to the reconstruction of high‐amplitude hydrologic changes that governed the evolution of the Mediterranean region during the Messinian salinity crisis (MSC), when reduced connections with the global ocean resulted in the deposition of the most studied Earth's salt giant. Paleohydrological dynamics leading to the deposition of the Primary Lower Gypsum during the first stage of the MSC were revealed by the study of the87Sr/86Sr composition of 114 samples from the Vena del Gesso basin (Northern Apennines, Italy). The analysis of seven high‐resolution87Sr/86Sr profiles from individual gypsum beds suggests a climatic influence of precessional‐scale orbital parameters during evaporite deposition. The variations of Sr isotope ratios over time indicate that gypsum precipitation started from a seawater body dominated by continental contributions, followed by a relative increase of marine input. The overall results show a gradual upward detachment from the global ocean87Sr/86Sr curve, with crucial steps corresponding to the most extreme eccentricity minima, suggesting an orbital influence on the hydrological balance of the basin. Given the sedimentological and geochemical analogies shared by the Mediterranean marginal basins that hosted the Primary Lower Gypsum deposition, the87Sr/86Sr evolution of the Vena del Gesso basin may be considered as indicative of Mediterranean‐scale hydrologic dynamics, driven by gradual reduction of exchanges with the Atlantic and variable freshwater input.
Complete characterization of ultrashort optical pulses with a phase-shifting wedged reversal shearing interferometer
Authors: Lam Billy , Guo Chunlei 
Published: June 2018

AbstractThe ability of an interferometer to characterize the spatial information of a light beam is often limited by the temporal profile of the beam, with femtosecond pulse characterization being particularly challenging. In this study, we developed a simple, stable, controllable shearing and vectorial phase-shifting wedged reversal shearing interferometer that is able to characterize all types of coherent and partially coherent light beams. The proposed interferometer consists of only a single beam splitter cube with one wedged entrance face and is insensitive to environmental vibration due to its common path configuration. A near zero-path length difference of the proposed interferometer ensures its operation for ultrashort pulses, providing, for the first time, a simple and stable interferometric tool to fully characterize sub-100  fs laser pulses. All common beam characterization can be carried out with the interferometer, such as the amplitude, phase, polarization, wavelength, and pulse duration. Furthermore, this technique is sensitive to the wavefront tilt and can be used for precise beam alignment. Therefore, this interferometer can be an essential tool for beam characterization, optical imaging, and the testing required for a wide range of applications, including astronomy, biomedicine, ophthalmology, optical testing and imaging systems, and adaptive optics.
Subnanometer localization accuracy in widefield optical microscopy
Authors: Copeland Craig R. , Geist Jon , McGray Craig D. , Aksyuk Vladimir A. , Liddle J. Alexander , Ilic B. Robert , Stavis Samuel M. 
Published: June 2018

AbstractThe common assumption that precision is the limit of accuracy in localization microscopy and the typical absence of comprehensive calibration of optical microscopes lead to a widespread issue—overconfidence in measurement results with nanoscale statistical uncertainties that can be invalid due to microscale systematic errors. In this article, we report a comprehensive solution to this underappreciated problem. We develop arrays of subresolution apertures into the first reference materials that enable localization errors approaching the atomic scale across a submillimeter field. We present novel methods for calibrating our microscope system using aperture arrays and develop aberration corrections that reach the precision limit of our reference materials. We correct and register localization data from multiple colors and test different sources of light emission with equal accuracy, indicating the general applicability of our reference materials and calibration methods. In a first application of our new measurement capability, we introduce the concept of critical-dimension localization microscopy, facilitating tests of nanofabrication processes and quality control of aperture arrays. In a second application, we apply these stable reference materials to answer open questions about the apparent instability of fluorescent nanoparticles that commonly serve as fiducial markers. Our study establishes a foundation for subnanometer localization accuracy in widefield optical microscopy.
TGF-β signaling alters H4K20me3 status via miR-29 and contributes to cellular senescence and cardiac aging
Authors: Lyu Guoliang , Guan Yiting , Zhang Chao , Zong Le , Sun Lei , Huang Xiaoke , Huang Li , Zhang Lijun , Tian Xiao-Li , Zhou Zhongjun , Tao Wei 
Published: June 2018

AbstractCellular senescence is a well-orchestrated programmed process involved in age-related pathologies, tumor suppression and embryonic development. TGF-β/Smad is one of the predominant pathways that regulate damage-induced and developmentally programmed senescence. Here we show that canonical TGF-β signaling promotes senescence via miR-29-induced loss of H4K20me3. Mechanistically, oxidative stress triggers TGF-β signaling. Activated TGF-β signaling gives rise to acute accumulation of miR-29a and miR-29c, both of which directly suppress their novel target, Suv4-20h, thus reducing H4K20me3 abundance in a Smad-dependent manner, which compromises DNA damage repair and genome maintenance. Loss of H4K20me3 mediated by the senescent TGF-β/miR-29 pathway contributes to cardiac aging in vivo. Disruption of TGF-β signaling restores H4K20me3 and improves cardiac function in aged mice. Our study highlights the sequential mechanisms underlying the regulation of senescence, from senescence-inducing triggers to activation of responsive signaling followed by specific epigenetic alterations, shedding light on potential therapeutic interventions in cardiac aging.
Dedicated surveillance mechanism controls G-quadruplex forming non-coding RNAs in human mitochondria
Authors: Pietras Zbigniew , Wojcik Magdalena A. , Borowski Lukasz S. , Szewczyk Maciej , Kulinski Tomasz M. , Cysewski Dominik , Stepien Piotr P. , Dziembowski Andrzej , Szczesny Roman J. 
Published: June 2018

AbstractThe GC skew in vertebrate mitochondrial genomes results in synthesis of RNAs that are prone to form G-quadruplexes (G4s). Such RNAs, although mostly non-coding, are transcribed at high rates and are degraded by an unknown mechanism. Here we describe a dedicated mechanism of degradation of G4-containing RNAs, which is based on cooperation between mitochondrial degradosome and quasi-RNA recognition motif (qRRM) protein GRSF1. This cooperation prevents accumulation of G4-containing transcripts in human mitochondria. In vitro reconstitution experiments show that GRSF1 promotes G4 melting that facilitates degradosome-mediated decay. Among degradosome and GRSF1 regulated transcripts we identified one that undergoes post-transcriptional modification. We show that GRSF1 proteins form a distinct qRRM group found only in vertebrates. The appearance of GRSF1 coincided with changes in the mitochondrial genome, which allows the emergence of G4-containing RNAs. We propose that GRSF1 appearance is an evolutionary adaptation enabling control of G4 RNA.
Nuclear microtubule filaments mediate non-linear directional motion of chromatin and promote DNA repair
Authors: Oshidari Roxanne , Strecker Jonathan , Chung Daniel K. C. , Abraham Karan J. , Chan Janet N. Y. , Damaren Christopher J. , Mekhail Karim 
Published: June 2018

AbstractDamaged DNA shows increased mobility, which can promote interactions with repair-conducive nuclear pore complexes (NPCs). This apparently random mobility is paradoxically abrogated upon disruption of microtubules or kinesins, factors that typically cooperate to mediate the directional movement of macromolecules. Here, we resolve this paradox by uncovering DNA damage-inducible intranuclear microtubule filaments (DIMs) that mobilize damaged DNA and promote repair. Upon DNA damage, relief of centromeric constraint induces DIMs that cooperate with the Rad9 DNA damage response mediator and Kar3 kinesin motor to capture DNA lesions, which then linearly move along dynamic DIMs. Decreasing and hyper-inducing DIMs respectively abrogates and hyper-activates repair. Accounting for DIM dynamics across cell populations by measuring directional changes of damaged DNA reveals that it exhibits increased non-linear directional behavior in nuclear space. Abrogation of DIM-dependent processes or repair-promoting factors decreases directional behavior. Thus, inducible and dynamic nuclear microtubule filaments directionally mobilize damaged DNA and promote repair.
Migrating the SNP array-based homologous recombination deficiency measures to next generation sequencing data of breast cancer
Authors: Sztupinszki Zsofia , Diossy Miklos , Krzystanek Marcin , Reiniger Lilla , Csabai István , Favero Francesco , Birkbak Nicolai J. , Eklund Aron C. , Syed Ali , Szallasi Zoltan 
Published: June 2018

AbstractThe first genomic scar-based homologous recombination deficiency (HRD) measures were produced using SNP arrays. As array-based technology has been largely replaced by next generation sequencing approaches, it has become important to develop algorithms that derive the same type of genomic scar scores from next generation sequencing (whole exome “WXS”, whole genome “WGS”) data. In order to perform this analysis, we introduce here the scarHRD R package and show that using this method the SNP array-based and next generation sequencing-based derivation of HRD scores show good correlation (Pearson correlation between 0.73 and 0.87 depending on the actual HRD measure) and that the NGS-based HRD scores distinguish similarly well between BRCA mutant and BRCA wild-type cases in a cohort of triple-negative breast cancer patients of the TCGA data set.
Competing Coulomb and electron–phonon interactions in NbS2
Authors: van Loon Erik G. C. P. , Rösner Malte , Schönhoff Gunnar , Katsnelson Mikhail I. , Wehling Tim O. 
Published: June 2018

AbstractThe interplay of Coulomb and electron–phonon interactions with thermal and quantum fluctuations facilitates rich phase diagrams in two-dimensional electron systems. Layered transition metal dichalcogenides hosting charge, excitonic, spin and superconducting order form an epitomic material class in this respect. Theoretical studies of materials like NbS2 have focused on the electron–phonon coupling, whereas the Coulomb interaction, particularly strong in the monolayer limit, remained essentially untouched. Here, we analyze the interplay of short- and long-range Coulomb as well as electron–phonon interactions in NbS2 monolayers. The combination of these interactions causes electronic correlations that are fundamentally different to what would be expected from the interaction terms separately. The fully interacting electronic spectral function resembles the non-interacting band structure but with appreciable broadening. An unexpected coexistence of strong charge and spin fluctuations puts NbS2 close to spin and charge order, suggesting monolayer NbS2 as a platform for atomic scale engineering of electronic quantum phases.
Production, quality control, stability, and potency of cGMP-produced Plasmodium falciparum RH5.1 protein vaccine expressed in Drosophila S2 cells
Authors: Jin Jing , Tarrant Richard D. , Bolam Emma J. , Angell-Manning Philip , Soegaard Max , Pattinson David J. , Dulal Pawan , Silk Sarah E. , Marshall Jennifer M. , Dabbs Rebecca A. , Nugent Fay L. , Barrett Jordan R. , Hjerrild Kathryn A. , Poulsen Lars , Jørgensen Thomas , Brenner Tanja , Baleanu Ioana N. , Parracho Helena M. , Tahiri-Alaoui Abdessamad , Whale Gary , Moyle Sarah , Payne Ruth O. , Minassian Angela M. , Higgins Matthew K. , Detmers Frank J. , Lawrie Alison M. , Douglas Alexander D. , Smith Robert , de Jongh Willem A. , Berrie Eleanor , Ashfield Rebecca , Draper Simon J. 
Published: June 2018

AbstractPlasmodium falciparum reticulocyte-binding protein homolog 5 (PfRH5) is a leading asexual blood-stage vaccine candidate for malaria. In preparation for clinical trials, a full-length PfRH5 protein vaccine called “RH5.1” was produced as a soluble product under cGMP using the ExpreS2 platform (based on a Drosophila melanogaster S2 stable cell line system). Following development of a high-producing monoclonal S2 cell line, a master cell bank was produced prior to the cGMP campaign. Culture supernatants were processed using C-tag affinity chromatography followed by size exclusion chromatography and virus-reduction filtration. The overall process yielded >400 mg highly pure RH5.1 protein. QC testing showed the MCB and the RH5.1 product met all specified acceptance criteria including those for sterility, purity, and identity. The RH5.1 vaccine product was stored at −80 °C and is stable for over 18 months. Characterization of the protein following formulation in the adjuvant system AS01B showed that RH5.1 is stable in the timeframe needed for clinical vaccine administration, and that there was no discernible impact on the liposomal formulation of AS01B following addition of RH5.1. Subsequent immunization of mice confirmed the RH5.1/AS01B vaccine was immunogenic and could induce functional growth inhibitory antibodies against blood-stage P. falciparum in vitro. The RH5.1/AS01B was judged suitable for use in humans and has since progressed to phase I/IIa clinical trial. Our data support the future use of the Drosophila S2 cell and C-tag platform technologies to enable cGMP-compliant biomanufacture of other novel and “difficult-to-express” recombinant protein-based vaccines.
Potential formula of an m × n globe network and its application
Authors: Tan Zhen , Tan Zhi-Zhong 
Published: June 2018

AbstractSearching for the explicit solutions of the potential function in an arbitrary resistor network is important but difficult in physics. We investigate the problem of potential formula in an arbitrary m × n globe network of resistors, which has not been resolved before (the previous study only calculated the resistance). In this paper, an exact potential formula of an arbitrary m × n globe network is discovered by means of the Recursion-Transform method with current parameters (RT-I). The key process of RT method is to set up matrix equation and to transform two-dimensional matrix equation into one-dimensional matrix equation. In order to facilitate practical application, we deduced a series of interesting results of potential by means of the general formula, and the effective resistance between two nodes in the m × n globe network is derived naturally by making use of potential formula.