bluuebunny/crossref_metadata_2025_split huggingface dataset:
The course of depression in late life: a longitudinal perspective
Authors: de la Torre-Luque Alejandro , Ayuso-Mateos Jose Luis 
Published: July 2020

Abstract
Depression in old age deserves special attention in view of the fact of progressive population ageing, because of the way in which depression and risk factors interact in this period of life and the particularly negative impact of late-life depression on health and quality of life. This editorial aims to provide some insight into longitudinal aspects of depression in old age. Depression may follow varying trajectories (e.g. episode emergence, recurrence) across the lifespan. Late-life depression is not an exception. A symptom-based approach is presented as an appropriate research method to study the predictors and course of affective syndromes in old age. Findings from our studies on depressive symptom trajectories in old age revealed that participants with a course of unremitting elevated symptoms showed the highest levels of loneliness across the trajectory groups and that participants with subclinical symptoms also showed higher levels of loneliness than their counterparts with a minimal-symptom course trajectory. This highlights the need to address loneliness as a way of dealing with depression in old age.
Geomagnetic Field Model Indicates Shrinking Northern Auroral Oval
Authors: Zossi Bruno , Fagre Mariano , Amit Hagay , Elias Ana G. 
Published: July 2020

AbstractPolar cap and auroral oval areas are presented for the period 1900–2015 using a model of the magnetosphere and the International Geomagnetic Reference Field Version 12 (IGRF‐12) model for the geomagnetic field. The effect of the main field long‐term changes is addressed considering steady interplanetary conditions. Until ~1940 both northern and southern polar cap areas increased with time, consistent with the geomagnetic dipole moment decrease during this period. Thereafter, while the southern polar cap area continued to increase steadily, the northern polar cap area has been decreasing rapidly. This hemispherical dichotomy is related to asymmetry in the core field and its secular variation. In the southern polar region the surface field intensity has been decreasing throughout the entire period, whereas in the northern polar region an intensity decrease turned to an increase from 1940 to present day. This recent surface intensity increase stems from intensification of the flux patch below Siberia and cessation of weakening of the flux patch below North America, both on the core‐mantle boundary. The surprising temporal decrease in the area of the northern polar cap has important implications for space weather and communication systems. While the decreasing dipole intensity allows more particles to penetrate the atmosphere, a shrinking northern auroral oval implies an increase in particle precipitation density, resulting in more severe damage to airplanes and ships positioning systems, spacecraft electronic systems and airline passengers when passing above this region. Further study is needed to observationally establish that the northern auroral oval, as defined by optical occurrences of aurora, is indeed shrinking.
First Global Images of Ion Energization in the Terrestrial Foreshock by the Interstellar Boundary Explorer
Authors: Dayeh M. A. , Szalay J. R. , Ogasawara K. , Fuselier S. A. , McComas D. J. , Funsten H. O. , Petrinec S. M. , Schwadron N. A. , Zirnstein E. J. 
Published: July 2020

AbstractThe Interstellar Boundary Explorer (IBEX) mission provides global energetic neutral atom (ENA) observations from the heliosphere and the Earth's magnetosphere, including spatial, temporal, and energy information. IBEX views the magnetosphere from the sides and almost always perpendicular to noon‐midnight plane. We report the first ENA images of the energization process in the Earth's ion foreshock and magnetosheath regions. We show ENA flux and spectral images of the dayside magnetosphere with significant energization of ENA plasma sources (above ~2.7 keV) in the region magnetically connected to the Earth's bow shock (BS) in its quasi‐parallel configuration of the interplanetary magnetic field (IMF). We also show that the ion energization increases gradually with decreasing IMF‐BS angle, suggesting more efficient suprathermal ion acceleration deeper in the quasi‐parallel foreshock.
Precipitation‐Induced Reduction in Surface Ocean pCO2: Observations From the Eastern Tropical Pacific Ocean
Authors: Ho David T. , Schanze Julian J. 
Published: July 2020

AbstractDetermining air‐sea CO2 fluxes using pCO2 disequilibrium requires knowing the gas transfer velocity and air‐sea pCO2 difference. Most pCO2 measurements are made from ships, whose uncontaminated seawater intakes are located at >5‐m depth to prevent ingestion of air. However, there could be bias in determinations of CO2 fluxes if there is disagreement between pCO2 measurements at the surface and 5 m. Seawater measurements made at the near surface and 5 m in the eastern Equatorial Pacific Ocean show that precipitation can dilute surface seawater salinity and lower the pCO2 and dissolved inorganic carbon and raise pH of the same water, and that these changes in ocean chemistry are largely missed by measurements at 5 m. This finding implies that estimates of ocean CO2 uptake might be underestimated, since rain will lower surface ocean pCO2 in both source and sink regions and, hence, increase uptake in sink regions and decrease outgassing in source regions.
Surface Wetness as an Unexpected Control on Forest Exchange of Volatile Organic Acids
Authors: Fulgham S. R. , Millet D. B. , Alwe H. D. , Goldstein A. H. , Schobesberger S. , Farmer D. K. 
Published: July 2020

AbstractWe report bidirectional exchange of volatile acids, including isocyanic and alkanoic acids, over a pine forest across multiple seasons. The exchange velocity of these acids is well correlated with dew point depression, suggesting an equilibrium‐driven continuum of flux. Wetness on forest surfaces impacts the vertical exchange of gases, and we suggest that water films and droplets drive equilibrium partitioning, with acids being solvated in surface wetness and released through evaporation. Despite their volatility, these acids partition into neutral‐to‐alkaline aqueous films, consistent with reported dew pH. This relationship between exchange velocity and dew point depression holds for a wetter mixed forest, but not a very dry orchard. Dew point depression is an excellent indicator of acid fluxes so long as the canopy is occasionally wetted.
Submicrosecond Spectroscopy of Lightning‐Like Discharges: Exploring New Time Regimes
Authors: Kieu N. , Gordillo‐Vázquez F. J. , Passas M. , Sánchez J. , Pérez‐Invernón F. J. , Luque A. , Montanyá J. , Christian H. 
Published: July 2020

AbstractSubmicrosecond (0.476 μs per frame with an exposure time of 160 ns) high‐resolution (0.38 nm) time‐resolved spectra of laboratory‐produced lightning‐like electrical discharges have been recorded for the first time within the visible spectral range (645–665 nm). The spectra were recorded with the GrAnada LIghtning Ultrafast Spectrograph (GALIUS), a high‐speed imaging spectrograph recently developed for lightning research in the IAA‐CSIC. Unprecedented spectral time dynamics are explored for meter long laboratory electrical discharges produced with a 2.0 MV Marx generator. The maximum electron density and gas temperature measured in a timescale of ≤0.50 μs (160 ns) were, respectively, ≃1018 cm−3 and ≃32,000 K. Overpressure in the lightning‐like plasma channel, black‐body dynamics, and self‐absorption in spectral lines were investigated.
Strength Evolution of Ice Plume Deposit Analogs of Enceladus and Europa
Authors: Choukroun M. , Molaro J. L. , Hodyss R. , Marteau E. , Backes P. , Carey E. M. , Dhaouadi W. , Moreland S. , Schulson E. M. 
Published: July 2020

AbstractEnceladus and possibly Europa spew materials from their internal ocean into their exosphere, some of which are deposited back onto the surface of those Ocean Worlds. This setting provides a unique opportunity to seek traces of past or extant life in ice plume deposits on their surfaces. However, the design of lander missions and surface sampling techniques and the choice of sampling locations rely heavily on strength expectations. Here we present an experimental investigation of the evolution in strength of ice plume deposit analogs at several temperatures, as well as a model that predicts first‐order estimates of the strength of evolved ice plume deposits under geologic timescales relevant to Enceladus and Europa. These results suggest that plume deposits remain weak and poorly consolidated on Enceladus, while they may develop substantial strength (comparable to solid ice) within <100 Myr on Europa.
Hydrate is a Nonwetting Phase in Porous Media
Authors: Murphy Zachary W. , DiCarlo David A. , Flemings Peter B. , Daigle Hugh 
Published: July 2020

AbstractIn porous media containing gas hydrate, the hydrate morphology impacts the flow behavior of the fluid phases. We hypothesize that hydrate emplaces itself as a nonwetting phase and use this idea to describe relative permeability of water in a hydrate/water system. We perform steady‐state relative permeability measurements in hydrate‐bearing samples with a range of hydrate saturation. We measure and compare water relative permeability in the presence of gas and in the presence of hydrate and find that the water relative permeability is the same in both cases. This suggests that (1) relative permeability for hydrate systems can be obtained without performing difficult experiments on hydrate bearing sediments, (2) flow properties are porous‐media dependent, and (3) models that assume a fixed pore or tube geometry are inadequate.
The Transition Zone Beneath West Argentina‐Central Chile Using P‐to‐S Converted Waves
Authors: Bonatto Luciana , Piromallo Claudia , Cottaar Sanne 
Published: July 2020

AbstractWe investigate the mantle transition zone beneath the Chile‐Argentina flat subduction region by means of P‐to‐S conversions at mantle discontinuities from teleseismic events recorded at 103 seismic stations. From the analysis of receiver functions, we obtain clear converted phases from the 410 and 660 discontinuities, and we identify a robust precursory signal to P660s, of negative amplitude, that we name P590s. We observe little frequency dependence in the amplitude of the P410s converted phase, while the P660s is less visible toward higher frequencies. The 410 is on average deeper than 410 km by 10 ± 1 km in the higher‐frequency bands, and it is relatively sharp, being consistent with a 10% velocity jump over less than 20 km. The observed 660 depth varies with frequency; it is deeper by up to 18 ± 2 km for lower frequencies and close to reference at higher frequencies, being consistent with a 13% broad velocity gradient over 30–40 km, probably caused by a composite of multiple phase transitions. The transition zone thickness is controlled by the frequency‐dependent depth variability of the 660. Our findings of relative depth, width, and velocity jump of the detected discontinuities, combined with tomographic images of the mantle transition zone, cannot be explained by thermal variations alone. Compositional constraints from mineral physics show that a near pyrolitic mantle is consistent with the ratio of the estimated velocity jumps. However, the negative P590s phase in this region could be signal from the velocity reduction due to basalt accumulation at the base of the transition zone.
Transcriptional activity and strain-specific history of mouse pseudogenes
Authors: Sisu Cristina , Muir Paul , Frankish Adam , Fiddes Ian , Diekhans Mark , Thybert David , Odom Duncan T. , Flicek Paul , Keane Thomas M. , Hubbard Tim , Harrow Jennifer , Gerstein Mark 
Published: July 2020

AbstractPseudogenes are ideal markers of genome remodelling. In turn, the mouse is an ideal platform for studying them, particularly with the recent availability of strain-sequencing and transcriptional data. Here, combining both manual curation and automatic pipelines, we present a genome-wide annotation of the pseudogenes in the mouse reference genome and 18 inbred mouse strains (available via the mouse.pseudogene.org resource). We also annotate 165 unitary pseudogenes in mouse, and 303, in human. The overall pseudogene repertoire in mouse is similar to that in human in terms of size, biotype distribution, and family composition (e.g. with GAPDH and ribosomal proteins being the largest families). Notable differences arise in the pseudogene age distribution, with multiple retro-transpositional bursts in mouse evolutionary history and only one in human. Furthermore, in each strain about a fifth of all pseudogenes are unique, reflecting strain-specific evolution. Finally, we find that ~15% of the mouse pseudogenes are transcribed, and that highly transcribed parent genes tend to give rise to many processed pseudogenes.
Gas hydrate dissociation linked to contemporary ocean warming in the southern hemisphere
Authors: Ketzer Marcelo , Praeg Daniel , Rodrigues Luiz F. , Augustin Adolpho , Pivel Maria A. G. , Rahmati-Abkenar Mahboubeh , Miller Dennis J. , Viana Adriano R. , Cupertino José A. 
Published: July 2020

AbstractOcean warming related to climate change has been proposed to cause the dissociation of gas hydrate deposits and methane leakage on the seafloor. This process occurs in places where the edge of the gas hydrate stability zone in sediments meets the overlying warmer oceans in upper slope settings. Here we present new evidence based on the analysis of a large multi-disciplinary and multi-scale dataset from such a location in the western South Atlantic, which records massive gas release to the ocean. The results provide a unique opportunity to examine ocean-hydrate interactions over millennial and decadal scales, and the first evidence from the southern hemisphere for the effects of contemporary ocean warming on gas hydrate stability. Widespread hydrate dissociation results in a highly focused advective methane flux that is not fully accessible to anaerobic oxidation, challenging the assumption that it is mostly consumed by sulfate reduction before reaching the seafloor.
Detecting sample swaps in diverse NGS data types using linkage disequilibrium
Authors: Javed Nauman , Farjoun Yossi , Fennell Tim J. , Epstein Charles B. , Bernstein Bradley E. , Shoresh Noam 
Published: July 2020

AbstractAs the number of genomics datasets grows rapidly, sample mislabeling has become a high stakes issue. We present CrosscheckFingerprints (Crosscheck), a tool for quantifying sample-relatedness and detecting incorrectly paired sequencing datasets from different donors. Crosscheck outperforms similar methods and is effective even when data are sparse or from different assays. Application of Crosscheck to 8851 ENCODE ChIP-, RNA-, and DNase-seq datasets enabled us to identify and correct dozens of mislabeled samples and ambiguous metadata annotations, representing ~1% of ENCODE datasets.
Microbiota assembly, structure, and dynamics among Tsimane horticulturalists of the Bolivian Amazon
Authors: Sprockett Daniel D. , Martin Melanie , Costello Elizabeth K. , Burns Adam R. , Holmes Susan P. , Gurven Michael D. , Relman David A. 
Published: July 2020

AbstractSelective and neutral forces shape human microbiota assembly in early life. The Tsimane are an indigenous Bolivian population with infant care-associated behaviors predicted to increase mother-infant microbial dispersal. Here, we characterize microbial community assembly in 47 infant-mother pairs from six Tsimane villages, using 16S rRNA gene amplicon sequencing of longitudinal stool and tongue swab samples. We find that infant consumption of dairy products, vegetables, and chicha (a fermented drink inoculated with oral microbes) is associated with stool microbiota composition. In stool and tongue samples, microbes shared between mothers and infants are more abundant than non-shared microbes. Using a neutral model of community assembly, we find that neutral processes alone explain the prevalence of 79% of infant-colonizing microbes, but explain microbial prevalence less well in adults from river villages with more regular access to markets. Our results underscore the importance of neutral forces during microbiota assembly. Changing lifestyle factors may alter traditional modes of microbiota assembly by decreasing the role of neutral processes.
The sponge effect and carbon emission mitigation potentials of the global cement cycle
Authors: Cao Zhi , Myers Rupert J. , Lupton Richard C. , Duan Huabo , Sacchi Romain , Zhou Nan , Reed Miller T. , Cullen Jonathan M. , Ge Quansheng , Liu Gang 
Published: July 2020

AbstractCement plays a dual role in the global carbon cycle like a sponge: its massive production contributes significantly to present-day global anthropogenic CO2 emissions, yet its hydrated products gradually reabsorb substantial amounts of atmospheric CO2 (carbonation) in the future. The role of this sponge effect along the cement cycle (including production, use, and demolition) in carbon emissions mitigation, however, remains hitherto unexplored. Here, we quantify the effects of demand- and supply-side mitigation measures considering this material-energy-emissions-uptake nexus, finding that climate goals would be imperiled if the growth of cement stocks continues. Future reabsorption of CO2 will be significant (~30% of cumulative CO2 emissions from 2015 to 2100), but climate goal compliant net CO2 emissions reduction along the global cement cycle will require both radical technology advancements (e.g., carbon capture and storage) and widespread deployment of material efficiency measures, which go beyond those envisaged in current technology roadmaps.
Optomechanical mass spectrometry
Authors: Sansa Marc , Defoort Martial , Brenac Ariel , Hermouet Maxime , Banniard Louise , Fafin Alexandre , Gely Marc , Masselon Christophe , Favero Ivan , Jourdan Guillaume , Hentz Sébastien 
Published: July 2020

AbstractNanomechanical mass spectrometry has proven to be well suited for the analysis of high mass species such as viruses. Still, the use of one-dimensional devices such as vibrating beams forces a trade-off between analysis time and mass resolution. Complex readout schemes are also required to simultaneously monitor multiple resonance modes, which degrades resolution. These issues restrict nanomechanical MS to specific species. We demonstrate here single-particle mass spectrometry with nano-optomechanical resonators fabricated with a Very Large Scale Integration process. The unique motion sensitivity of optomechanics allows designs that are impervious to particle position, stiffness or shape, opening the way to the analysis of large aspect ratio biological objects of great significance such as viruses with a tail or fibrils. Compared to top-down beam resonators with electrical read-out and state-of-the-art mass resolution, we show a three-fold improvement in capture area with no resolution degradation, despite the use of a single resonance mode.
Alkaline thermal treatment of seaweed for high-purity hydrogen production with carbon capture and storage potential
Authors: Zhang Kang , Kim Woo-Jae , Park Ah-Hyung Alissa 
Published: July 2020

AbstractCurrent thermochemical methods to generate H2 include gasification and steam reforming of coal and natural gas, in which anthropogenic CO2 emission is inevitable. If biomass is used as a source of H2, the process can be considered carbon-neutral. Seaweeds are among the less studied types of biomass with great potential because they do not require freshwater. Unfortunately, reaction pathways to thermochemically convert salty and wet biomass into H2 are limited. In this study, a catalytic alkaline thermal treatment of brown seaweed is investigated to produce high purity H2 with substantially suppressed CO2 formation making the overall biomass conversion not only carbon-neutral but also potentially carbon-negative. High-purity 69.69 mmol-H2/(dry-ash-free)g-brown seaweed is produced with a conversion as high as 71%. The hydroxide is involved in both H2 production and in situ CO2 capture, while the Ni/ZrO2 catalyst enhanced the secondary H2 formation via steam methane reforming and water-gas shift reactions.
Understanding important features of deep learning models for segmentation of high-resolution transmission electron microscopy images
Authors: Horwath James P. , Zakharov Dmitri N. , Mégret Rémi , Stach Eric A. 
Published: July 2020

AbstractCutting edge deep learning techniques allow for image segmentation with great speed and accuracy. However, application to problems in materials science is often difficult since these complex models may have difficultly learning meaningful image features that would enable extension to new datasets. In situ electron microscopy provides a clear platform for utilizing automated image analysis. In this work, we consider the case of studying coarsening dynamics in supported nanoparticles, which is important for understanding, for example, the degradation of industrial catalysts. By systematically studying dataset preparation, neural network architecture, and accuracy evaluation, we describe important considerations in applying deep learning to physical applications, where generalizable and convincing models are required. With a focus on unique challenges that arise in high-resolution images, we propose methods for optimizing performance of image segmentation using convolutional neural networks, critically examining the application of complex deep learning models in favor of motivating intentional process design.
Global reference mapping of human transcription factor footprints
Authors: Vierstra Jeff , Lazar John , Sandstrom Richard , Halow Jessica , Lee Kristen , Bates Daniel , Diegel Morgan , Dunn Douglas , Neri Fidencio , Haugen Eric , Rynes Eric , Reynolds Alex , Nelson Jemma , Johnson Audra , Frerker Mark , Buckley Michael , Kaul Rajinder , Meuleman Wouter , Stamatoyannopoulos John A. 
Published: July 2020

AbstractCombinatorial binding of transcription factors to regulatory DNA underpins gene regulation in all organisms. Genetic variation in regulatory regions has been connected with diseases and diverse phenotypic traits1, but it remains challenging to distinguish variants that affect regulatory function2. Genomic DNase I footprinting enables the quantitative, nucleotide-resolution delineation of sites of transcription factor occupancy within native chromatin3–6. However, only a small fraction of such sites have been precisely resolved on the human genome sequence6. Here, to enable comprehensive mapping of transcription factor footprints, we produced high-density DNase I cleavage maps from 243 human cell and tissue types and states and integrated these data to delineate about 4.5 million compact genomic elements that encode transcription factor occupancy at nucleotide resolution. We map the fine-scale structure within about 1.6 million DNase I-hypersensitive sites and show that the overwhelming majority are populated by well-spaced sites of single transcription factor–DNA interaction. Cell-context-dependent cis-regulation is chiefly executed by wholesale modulation of accessibility at regulatory DNA rather than by differential transcription factor occupancy within accessible elements. We also show that the enrichment of genetic variants associated with diseases or phenotypic traits in regulatory regions1,7 is almost entirely attributable to variants within footprints, and that functional variants that affect transcription factor occupancy are nearly evenly partitioned between loss- and gain-of-function alleles. Unexpectedly, we find increased density of human genetic variation within transcription factor footprints, revealing an unappreciated driver of cis-regulatory evolution. Our results provide a framework for both global and nucleotide-precision analyses of gene regulatory mechanisms and functional genetic variation.