bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Novel Method for the Extraction, Purification, and Characterization of Noble Gases in Produced Fluids
Authors: Tyne R. L. , Barry P. H. , Hillegonds D. J. , Hunt A. G . , Kulongoski J. T. , Stephens M. J. , Byrne D. J. , Ballentine C. J. 
Published: October 2019

AbstractHydrocarbon systems with declining or viscous oil production are often stimulated using enhanced oil recovery (EOR) techniques, such as the injection of water, steam, and CO2, in order to increase oil and gas production. As EOR and other methods of enhancing production such as hydraulic fracturing have become more prevalent, environmental concerns about the impact of both new and historical hydrocarbon production on overlying shallow aquifers have increased. Noble gas isotopes are powerful tracers of subsurface fluid provenance and can be used to understand the impact of EOR on hydrocarbon systems and potentially overlying aquifers. In oil systems, produced fluids can consist of a mixture of oil, water and gas. Noble gases are typically measured in the gas phase; however, it is not always possible to collect gases and therefore produced fluids (which are water, oil, and gas mixtures) must be analyzed. We outline a new technique to separate and analyze noble gases in multiphase hydrocarbon‐associated fluid samples. An offline double capillary method has been developed to quantitatively isolate noble gases into a transfer vessel, while effectively removing all water, oil, and less volatile hydrocarbons. The gases are then cleaned and analyzed using standard techniques. Air‐saturated water reference materials (n = 24) were analyzed and results show a method reproducibility of 2.9% for 4He, 3.8% for 20Ne, 4.5% for 36Ar, 5 .3% for 84Kr, and 5.7% for 132Xe. This new technique was used to measure the noble gas isotopic compositions in six produced fluid samples from the Fruitvale Oil Field, Bakersfield, California.
Stormquakes
Authors: Fan Wenyuan , McGuire Jeffrey J. , de Groot‐Hedlin Catherine D. , Hedlin Michael A. H. , Coats Sloan , Fiedler Julia W. 
Published: October 2019

AbstractSeismic signals from ocean‐solid Earth interactions are ubiquitously recorded on our planet. However, these wavefields are typically incoherent in the time domain limiting their utilization for understanding ocean dynamics or solid Earth properties. In contrast, we find that during large storms such as hurricanes and Nor'easters the interaction of long‐period ocean waves with shallow seafloor features located near the edge of continental shelves, known as ocean banks, excites coherent transcontinental Rayleigh wave packets in the 20‐ to 50‐s period band. These “stormquakes” migrate coincident with the storms but are effectively spatiotemporally focused seismic point sources with equivalent earthquake magnitudes that can be greater than 3.5. Stormquakes thus provide new coherent sources to investigate Earth structure in locations that typically lack both seismic instrumentation and earthquakes. Moreover, they provide a new geophysical observable with high spatial and temporal resolution with which to investigate ocean wave dynamics during large storms.
Plasmapause, Convection, and Reconnection
Authors: Nishida A. 
Published: October 2019

AbstractBeing one of the first generation of space scientists who entered this field right after the space became accessible to in situ observations, I had good luck of addressing some of the basic questions in this field from the early years of my carrier. These are development of global convection in the magnetosphere when the interplanetary magnetic field has the southward polarity, changes in the structure of the magnetotail leading to the onset of substorm expansion phase, and physics of the plasmapause formation. My career culminated with promotion and implementation of the Geotail spacecraft mission. In this article I shall present my personal recollections on these efforts including interactions with colleagues worldwide who shared the common interest.
Improving Absolute Earthquake Location in West Texas Using Probabilistic, Proxy Ground‐Truth Station Corrections
Authors: Lomax Anthony , Savvaidis Alexandros 
Published: October 2019

AbstractAn increase in induced seismicity in the central United States since 2009 led to establishment of TexNet seismic‐monitoring in Texas. Accurate, absolute seismic‐event location is critical to TexNet, allowing quantitative evaluation of possible association of seismicity with human activity. For the Delaware Basin, western Texas, relocation using different velocity models and TexNet station subsets shows absolute location error up to 4–5 km. The preferred method to reduce absolute error, ground‐truth calibration, is not available in this area. Alternatively, we used industrial well activity as proxy, ground‐truth for developing probabilistic, proxy ground‐truth (PPGT) station corrections for relocation. Assuming well activity causes seismicity, we defined a distance–time probability associating events and well activity. We used these associations and other evidence to show some seismicity in the Delaware Basin is more likely due to hydraulic‐fracturing than saltwater disposal. We then probabilistically accumulated PPGT station corrections using event hypocenters constrained to associated fracturing‐well locations. We applied this procedure within 12 km of TexNet station PB02, optimizing the procedure through comparison of rates of causal and acausal associations. Relative to the initial locations, final PPGT relocations show smaller residuals and shifts in epicenter as much as 3 km, predominantly toward the north and northwest. PPGT residuals are similar to those from relocation with standard station corrections. The initial hypocenters showed an unreasonable deepening with distance from station PB02, whereas PPGT relocations produced an overall flattening of event depths. These results are consistent with PPGT corrections giving real improvement in absolute location accuracy.
Water Availability and Deformation Processes in Smectite‐Rich Gouges During Seismic Slip
Authors: Aretusini S. , Spagnuolo E. , Dalconi M. C. , Di Toro G. , Rutter E. H. 
Published: October 2019

AbstractSmectite clays occur in subduction zone fault cores at shallow depth (approximately 1 km; e.g., Japan Trench) and landslide décollements (e.g., Vajont, Italy, 1963). The availability of pore fluids affects the likelihood that seismic slip propagates from deeper to shallow fault depths or that a landslide accelerates to its final collapse. To investigate the deformation processes active during seismic faulting we performed friction experiments with a rotary machine on 2‐mm‐thick smectite‐rich gouge layers (70/30 wt % Ca‐montmorillonite/opal) sheared at 5‐MPa normal stress, at slip rates of 0.001, 0.01, 0.1, and 1.3 m/s, and total displacement of 3 m. Experiments were performed on predried gouges under vacuum, under room humidity and under partly saturated conditions. The fault shear strength measured in the experiments was included in a one‐dimensional numerical model incorporating frictional heating, thermal, and thermochemical pressurization. Quantitative X‐ray powder diffraction and scanning electron microscopy investigations were performed on pristine and deformed smectite‐rich gouges. Under dry conditions, cataclasis and amorphization dominated at slip rates of 0.001–0.1 m/s, whereas grain size sensitive flow and, under vacuum, frictional melting occurred at fast slip rates (1.3 m/s). Under partly saturated conditions, frictional slip in a smectite foliation occurred in combination with pressurization of water by shear‐enhanced compaction and, for V = 0.01–1.3 m/s, with thermal pressurization. Pseudotachylytes, the only reliable microstructural markers for seismic slip, formed only with large frictional power (>2 MW/m2), which could be achieved at shallow depth with high slip rates, or, at depth, with high shear stress in dehydrated smectites.
Network Topology and Rainfall Controls on the Variability of Combined Sewer Overflows and Loads
Authors: McGrath Gavan , Kaeseberg Thomas , Reyes Silva Julian David , Jawitz James W. , Blumensaat Frank , Borchardt Dietrich , Mellander Per‐Erik , Paik Kyungrock , Krebs Peter , Rao P. Suresh C. 
Published: October 2019

AbstractWater and pollutant fluxes from combined sewer overflows (CSO) have a significant impact on receiving waters. The random nature of rainfall forcing dominates the variability of sewer discharges, pollutant loads, and concentrations. An analytical model developed here shows how sewer network topology and rainfall properties variously impact the stochasticity of CSO functioning. Probability distributions of sewer discharge and concentration compare well with the results from a calibrated Storm Water Management Model in an application to a sewershed located in Dresden, Germany. The model is determined by only four parameters, three of which can be predicted a priori, two from the rainfall record and one from the network topology using geomorphological flow recession theory, while the fourth can be estimated from a short discharge time series. The sensitivity of CSO and wastewater treatment loads to network structure suggests simple topologies may be more vulnerable to poor performance. The analytical model is useful for evaluating various CSO management strategies to reduce adverse impacts on receiving waters in a probabilistic setting.
Integrated nuclear proteomics and transcriptomics identifies S100A4 as a therapeutic target in acute myeloid leukemia
Authors: Alanazi Bader , Munje Chinmay R. , Rastogi Namrata , Williamson Andrew J. K. , Taylor Samuel , Hole Paul S. , Hodges Marie , Doyle Michelle , Baker Sarah , Gilkes Amanda F. , Knapper Steven , Pierce Andrew , Whetton Anthony D. , Darley Richard L. , Tonks Alex 
Published: October 2019

AbstractInappropriate localization of proteins can interfere with normal cellular function and drive tumor development. To understand how this contributes to the development of acute myeloid leukemia (AML), we compared the nuclear proteome and transcriptome of AML blasts with normal human CD34+cells. Analysis of the proteome identified networks and processes that significantly affected transcription regulation including misexpression of 11 transcription factors with seven proteins not previously implicated in AML. Transcriptome analysis identified changes in 40 transcription factors but none of these were predictive of changes at the protein level. The highest differentially expressed protein in AML nuclei compared with normal CD34+nuclei (not previously implicated in AML) was S100A4. In an extended cohort, we found that over-expression of nuclear S100A4 was highly prevalent in AML (83%; 20/24 AML patients). Knock down of S100A4 in AML cell lines strongly impacted their survival whilst normal hemopoietic stem progenitor cells were unaffected. These data are the first analysis of the nuclear proteome in AML and have identified changes in transcription factor expression or regulation of transcription that would not have been seen at the mRNA level. These data also suggest that S100A4 is essential for AML survival and could be a therapeutic target in AML.
Global ecotypes in the ubiquitous marine clade SAR86
Authors: Hoarfrost Adrienne , Nayfach Stephen , Ladau Joshua , Yooseph Shibu , Arnosti Carol , Dupont Chris L , Pollard Katherine S 
Published: October 2019

Abstract
SAR86 is an abundant and ubiquitous heterotroph in the surface ocean that plays a central role in the function of marine ecosystems. We hypothesized that despite its ubiquity, different SAR86 subgroups may be endemic to specific ocean regions and functionally specialized for unique marine environments. However, the global biogeographical distributions of SAR86 genes, and the manner in which these distributions correlate with marine environments, have not been investigated. We quantified SAR86 gene content across globally distributed metagenomic samples and modeled these gene distributions as a function of 51 environmental variables. We identified five distinct clusters of genes within the SAR86 pangenome, each with a unique geographic distribution associated with specific environmental characteristics. Gene clusters are characterized by the strong taxonomic enrichment of distinct SAR86 genomes and partial assemblies, as well as differential enrichment of certain functional groups, suggesting differing functional and ecological roles of SAR86 ecotypes. We then leveraged our models and high-resolution, remote sensing-derived environmental data to predict the distributions of SAR86 gene clusters across the world’s oceans, creating global maps of SAR86 ecotype distributions. Our results reveal that SAR86 exhibits previously unknown, complex biogeography, and provide a framework for exploring geographic distributions of genetic diversity from other microbial clades.
Density-dependent oxylipin production in natural diatom communities: possible implications for plankton dynamics
Authors: Russo Ennio , d’Ippolito Giuliana , Fontana Angelo , Sarno Diana , D’Alelio Domenico , Busseni Greta , Ianora Adrianna , von Elert Eric , Carotenuto Ylenia 
Published: October 2019

Abstract
Oxylipins are important signal transduction lipoxygenase-derived products of fatty acids that regulate a variety of physiological and pathological processes in plants and animals. In marine diatoms, these molecules can be highly bioactive, impacting zooplankton grazers, bacteria and other phytoplankton. However, the ultimate cause for oxylipin production in diatoms is still poorly understood, from an evolutionary perspective. Here we analysed production of particulate linear oxygenated fatty acids (LOFAs, previously named non-volatile oxylipins) from natural phytoplankton collected weekly for 1 year. We demonstrate for the first time that diatoms are the main LOFA producers in natural phytoplankton assemblages. Interestingly, LOFA-per-cell production decreased with increasing diatom density and was not due to major changes in diatom community composition. An inverse relation was confirmed at a global scale by analysing diatom lipoxygenase unigenes and metagenomes from Tara Oceans datasets. A network analysis suggested that different LOFAs could contribute to modulate co-variations of different diatom taxa. Overall, we offer new insights in diatom chemical ecology, possibly explaining the evolution of oxylipin synthesis in diatoms.
Balance between community assembly processes mediates species coexistence in agricultural soil microbiomes across eastern China
Authors: Jiao Shuo , Yang Yunfeng , Xu Yiqin , Zhang Jie , Lu Yahai 
Published: October 2019

Abstract
Revealing the linkages between community assembly and species coexistence, which is crucial for the understanding of ecosystem diversity and functioning, is a fundamental but rarely investigated subject in microbial ecology. Here we examined archaeal, bacterial, and fungal community assembly in adjacent pairs of maize (water-unsaturated) and rice (water-saturated) fields across different habitats and regions throughout Eastern China. The high-throughput sequencing dataset was analyzed by variation partitioning, null model, and neutral community model analyses. We demonstrated that microbial community assembly was governed more by species sorting than by dispersal limitation in maize fields, and to a lesser extent in rice fields. The relative importance of species sorting in maize soils was greater at low latitudes than at high latitudes, while rice soils exhibited an opposite trend. Microbial co-occurrence associations tended to be higher when communities were primarily driven by dispersal limitation relative to species sorting. There were greater community dissimilarities between maize and rice soils in low-latitude regions, which was consistent with the higher proportion of negative edges in the correlation networks. The results indicate that a balance between species sorting and dispersal limitation mediates species coexistence in soil microbiomes. This study enhances our understanding of contemporary coexistence theory in microbial ecosystems.
Cannabidiol directly targets mitochondria and disturbs calcium homeostasis in acute lymphoblastic leukemia
Authors: Olivas-Aguirre Miguel , Torres-López Liliana , Valle-Reyes Juan Salvador , Hernández-Cruz Arturo , Pottosin Igor , Dobrovinskaya Oxana 
Published: October 2019

AbstractAnticancer properties of non-psychoactive cannabinoid cannabidiol (CBD) have been demonstrated on tumors of different histogenesis. Different molecular targets for CBD were proposed, including cannabinoid receptors and some plasma membrane ion channels. Here we have shown that cell lines derived from acute lymphoblastic leukemia of T lineage (T-ALL), but not resting healthy T cells, are highly sensitive to CBD treatment. CBD effect does not depend on cannabinoid receptors or plasma membrane Ca2+-permeable channels. Instead, CBD directly targets mitochondria and alters their capacity to handle Ca2+. At lethal concentrations, CBD causes mitochondrial Ca2+ overload, stable mitochondrial transition pore formation and cell death. Our results suggest that CBD is an attractive candidate to be included into chemotherapeutic protocols for T-ALL treatment.
Application of spherical substrate to observe bacterial motility machineries by Quick-Freeze-Replica Electron Microscopy
Authors: Katayama Eisaku , Tahara Yuhei O. , Bertin Clothilde , Shibata Satoshi 
Published: October 2019

Abstract3-D Structural information is essential to elucidate the molecular mechanisms of various biological machineries. Quick-Freeze Deep-Etch-Replica Electron Microscopy is a unique technique to give very high-contrast surface profiles of extra- and intra-cellular apparatuses that bear numerous cellular functions. Though the global architecture of those machineries is primarily required to understand their functional features, it is difficult or even impossible to depict side- or highly-oblique views of the same targets by usual goniometry, inasmuch as the objects (e.g. motile microorganisms) are placed on conventional flat substrates. We introduced silica-beads as an alternative substrate to solve such crucial issue. Elongated Flavobacterium and globular Mycoplasmas cells glided regularly along the bead’s surface, similarly to those on a flat substrate. Quick-freeze replicas of those cells attached to the beads showed various views; side-, oblique- and frontal-views, enabling us to study not only global but potentially more detailed morphology of complicated architecture. Adhesion of the targets to the convex surface could give surplus merits to visualizing intriguing molecular assemblies within the cells, which is relevant to a variety of motility machinery of microorganisms.
TNFα-signal and cAMP-mediated signals oppositely regulate melanoma- associated ganglioside GD3 synthase gene in human melanocytes
Authors: Takeuchi Rika , Kambe Mariko , Miyata Maiko , Jeyadevan Upul , Tajima Orie , Furukawa Koichi , Furukawa Keiko 
Published: October 2019

AbstractAnalyses of expression and regulation of ganglioside synthases in melanocytes are important to understand roles of gangliosides in melanomagenesis. In this study, we analyzed the expression and regulatory mechanisms of glycosyltransferase genes responsible for ganglioside synthesis in normal melanocytes. We reported previously that culture supernatants of UVB-irradiated keratinocytes induced upregulation of ganglioside GD3 synthase gene in melanocytes, and mainly TNFα was responsible for it. Then, we found that elimination of dibutyryl cyclic AMP and IBMX from the medium also resulted in upregulation of the GD3 synthase gene. The addition of α-melanocyte-stimulating hormone which increases cAMP, to the medium led to a significant reduction in the GD3 synthase gene expression level, and a PKA inhibitor enhanced the GD3 synthase gene level. These results suggest that signals mediated via TNFα and cAMP oppositely regulate GD3 synthase gene expression in melanocytes. The results of an IKK inhibitor indicate the possibility that TNFα induces GD3 synthase gene expression via NF-κB signaling in melanocytes. When melanoma cells were treated by these factors, no fluctuation in the GD3 synthase gene expression level was observed, although an IKK inhibitor significantly suppressed it, suggesting that ganglioside synthase genes are regulated in distinct manners between melanocytes and melanomas.
Progress in loop-mediated isothermal amplification assay for detection of Schistosoma mansoni DNA: towards a ready-to-use test
Authors: García-Bernalt Diego J. , Fernández-Soto P. , Crego-Vicente B. , Alonso-Castrillejo S. , Febrer-Sendra B. , Gómez-Sánchez A. , Vicente B. , López-Abán J. , Muro A. 
Published: October 2019

AbstractSchistosomiasis is one of the most prevalent Neglected Tropical Disease, affecting approximately 250 million people worldwide. Schistosoma mansoni is the most important species causing human intestinal schistosomiasis. Despite significant efforts in recent decades, the global disease burden of schistosomiasis remains extremely high. This could partly be attributed to the absence of accurate diagnostic tools, primarily in endemic areas. Loop-mediated isothermal amplification (LAMP) is increasingly used in molecular diagnostics as a field-friendly alternative to many other complex molecular methods and it has been proposed as an ideal candidate for revolutionizing point-of-care molecular diagnostics. In a previous work, a LAMP-based method to detect S. mansoni DNA (SmMIT-LAMP) was developed by our research group for early diagnosis of active schistosomiasis in an experimental infection murine model. The SmMIT-LAMP has been further successfully evaluated in both human stool and snail samples and, recently, in human urine samples. In this study, we developed an important improvement for SmMIT-LAMP molecular assay, transforming it into a cold maintenance dry format suitable for potentially manufacturing as kit for ready-to-use for schistosomiasis diagnosis. This procedure could be applied to create dry LAMP kits for a laboratory setting and for diagnostic applications for other neglected tropical diseases.
Preterm and full term infant vocalization and the origin of language
Authors: Oller D. Kimbrough , Caskey Melinda , Yoo Hyunjoo , Bene Edina R. , Jhang Yuna , Lee Chia-Cheng , Bowman Dale D. , Long Helen L. , Buder Eugene H. , Vohr Betty 
Published: October 2019

AbstractHow did vocal language originate? Before trying to determine how referential vocabulary or syntax may have arisen, it is critical to explain how ancient hominins began to produce vocalization flexibly, without binding to emotions or functions. A crucial factor in the vocal communicative split of hominins from the ape background may thus have been copious, functionally flexible vocalization, starting in infancy and continuing throughout life, long before there were more advanced linguistic features such as referential vocabulary. 2–3 month-old modern human infants produce “protophones”, including at least three types of functionally flexible non-cry precursors to speech rarely reported in other ape infants. But how early in life do protophones actually appear? We report that the most common protophone types emerge abundantly as early as vocalization can be observed in infancy, in preterm infants still in neonatal intensive care. Contrary to the expectation that cries are the predominant vocalizations of infancy, our all-day recordings showed that protophones occurred far more frequently than cries in both preterm and full-term infants. Protophones were not limited to interactive circumstances, but also occurred at high rates when infants were alone, indicating an endogenous inclination to vocalize exploratorily, perhaps the most fundamental capacity underlying vocal language.