bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid Geodetic Analysis of Subduction Zone Earthquakes Leveraging a 3‐D Elastic Green's Function Library
Authors: Tung S. , Fielding E. J. , Bekaert D. P. S. , Masterlark T. 
Published: February 2019

AbstractThe 2018 M7.2 Pinotepa earthquake ruptured a shallow slab section along the Middle America subduction zone. We demonstrate how a geodetic Green's function (GF) library and efficient modeling algorithm can rapidly resolve earthquake slip and contribute to early warning systems. The source is characterized with InSAR data and a finite‐element model mimicking realistic slab geometry (Slab1.0) and velocity structures (CRUST2.0) that are not considered in the conventional homogeneous (HOM)‐ or layered(1‐D)‐crust solutions. The rupture is imaged 18 min after geodetic data are downloaded to a 16‐CPU‐thread workstation. Nearby Mw8.6‐megathrust scenarios are also studied with synthetic GPS data in the Guerrero/Oaxaca area. Our results show that earthquake slip solutions are sensitive to the materials of elastic‐modeling domains. Attaining smaller misfits or sums of squared errors, models by 3‐D GFs significantly better recover coseismic displacements than those estimated with 1‐D GFs or HOM GFs at 95% confidence.
Object‐Oriented Identification of Coherent Structures in Large Eddy Simulations: Importance of Downdrafts in Stratocumulus
Authors: Brient Florent , Couvreux Fleur , Villefranque Najda , Rio Catherine , Honnert Rachel 
Published: February 2019

AbstractA novel methodology is proposed to characterize coherent structures in large eddy simulations. Based on two passive tracers emitted respectively at the surface and at cloud top, the object‐oriented framework allows individual characterization of coherent tridimensional plumes within the flow. Applying this method in a simulation of the diurnal cycle of a marine stratocumulus‐topped boundary layer shows that coherent updraft and downdraft structures contribute to most of the total transport of heat and moisture, although covering a small part of the domain volume. On average, downdrafts contribute equally compared to updrafts for moisture fluxes and more than updrafts for heat fluxes. The relative contribution of updraft and downdraft objects to heat transport exhibits a large diurnal cycle, which suggests cloud‐turbulence‐radiation interaction. Our results suggest that subgrid downdraft properties within stratocumulus‐topped boundary layers should be represented through nonlocal mass‐flux parameterization in climate models.
Chain‐Style Landslide Hazardous Process: Constraints From Seismic Signals Analysis of the 2017 Xinmo Landslide, SW China
Authors: Li Wei , Chen Yun , Liu Feng , Yang Hongfeng , Liu Jianli , Fu Bihong 
Published: February 2019

AbstractLandslides generally involve rapid acceleration and deceleration of huge mass in just several minutes, and their unpredictability have made real‐time detections of their rapid processes difficult. Seismic signals generated by landslides provide an excellent opportunity to obtain the time‐dependent observations on landslide's processes. We invert the force‐time function by fitting long‐period seismic signals generated by Xinmo landslide on 23 June 2017, SW China, and determine three‐stage dynamic processes within 104‐s duration of this event. Constrained by the field observed runout distance, we deduce the landslide's mass of about 9 × 109 kg with corresponding maximum velocity and acceleration of 58.8 m/s and 4.38 m/s2, respectively. Combining dynamic parameters, apparent friction coefficient, and seismic signal features, we depict a dynamic landslide process initiated by high‐position rockslide, traveled by rapid long runout debris, and deposited over an old landslide's deposition fan. The rapid process of the landslide is affected by multiple preconditions such as the structure, topography, and meteorology of the site, which is characteristic of a typical chain‐style landslide hazard and could be helpful to recognize potential slope instabilities.
Velocity‐Density Systematics of Fe‐5wt%Si: Constraints on Si Content in the Earth's Inner Core
Authors: Edmund E. , Antonangeli D. , Decremps F. , Miozzi F. , Morard G. , Boulard E. , Clark A. N. , Ayrinhac S. , Gauthier M. , Morand M. , Mezouar M. 
Published: February 2019

AbstractThe elasticity of hcp‐Fe‐5wt%Si has been investigated by synchrotron X‐ray diffraction up to 110 GPa and 2,100 K and by picosecond acoustics measurements at ambient temperature up to 115 GPa. The established Pressure‐Volume‐Temperature equation of state shows that the density of the Earth's inner core can be matched by an Fe‐Si alloy with 5wt% Si for all reasonable core temperatures, but that its compressional and shear velocities remain too high with respect to seismological observations. On the other hand, Fe‐Si alloys whose velocities are expected to get close to seismological observations are too dense at relevant temperatures. Thus, based on these combined velocity‐density measurements, silicon is not likely to be the sole light element in the inner core.
Heat and Salt Flow in Subsea Permafrost Modeled with CryoGRID2
Authors: Angelopoulos Michael , Westermann Sebastian , Overduin Paul , Faguet Alexey , Olenchenko Vladimir , Grosse Guido , Grigoriev Mikhail N. 
Published: February 2019

Thawing of subsea permafrost can impact offshore infrastructure, affect coastal erosion, and release permafrost organic matter. Thawing is usually modeled as the result of heat transfer, although salt diffusion may play an important role in marine settings. To better quantify nearshore subsea permafrost thawing, we applied the CryoGRID2 heat diffusion model and coupled it to a salt diffusion model. We simulated coastline retreat and subsea permafrost evolution as it develops through successive stages of a thawing sequence at the Bykovsky Peninsula, Siberia. Sensitivity analyses for seawater salinity were performed to compare the results for the Bykovsky Peninsula with those of typical Arctic seawater. For the Bykovsky Peninsula, the modeled ice‐bearing permafrost table (IBPT) for ice‐rich sand and an erosion rate of 0.25 m/year was 16.7 m below the seabed 350 m offshore. The model outputs were compared to the IBPT depth estimated from coastline retreat and electrical resistivity surveys perpendicular to and crossing the shoreline of the Bykovsky Peninsula. The interpreted geoelectric data suggest that the IBPT dipped to 15–20 m below the seabed at 350 m offshore. Both results suggest that cold saline water forms beneath grounded ice and floating sea ice in shallow water, causing cryotic benthic temperatures. The freezing point depression produced by salt diffusion can delay or prevent ice formation in the sediment and enhance the IBPT degradation rate. Therefore, salt diffusion may facilitate the release of greenhouse gasses to the atmosphere and considerably affect the design of offshore and coastal infrastructure in subsea permafrost areas.
One Step at a Time: How Model Time Step Significantly Affects Convection‐Permitting Simulations
Authors: Barrett Andrew I. , Wellmann Constanze , Seifert Axel , Hoose Corinna , Vogel Bernhard , Kunz Michael 
Published: February 2019

AbstractWe show that there is a strong sensitivity of cloud microphysics to model time step in idealized convection‐permitting simulations using the COnsortium for Small‐scale MOdeling model. Specifically, we found a 53% reduction in precipitation when the time step is increased from 1 to 15 s, changes to the location of precipitation and hail reaching the surface, and changes to the vertical distribution of hydrometeors. The effect of cloud condensation nuclei perturbations on precipitation also changes both magnitude and sign with the changing model time step. The sensitivity arises because of the numerical implementation of processes in the model, specifically the so‐called “splitting” of the dynamics (e.g., advection and diffusion) and the parameterized physics (e.g., microphysics scheme). Calculating one step at a time (sequential‐update splitting) gives a significant time step dependence because large supersaturation with respect to liquid is generated in updraft regions, which strongly affect parameterized microphysical process rates—in particular, ice nucleation. In comparison, calculating both dynamics and microphysics using the same inputs of temperature and water vapor (hybrid parallel splitting) or adding an additional saturation adjustment within the dynamics reduces the time step sensitivity of surface precipitation by limiting the supersaturation seen by the microphysics, although sensitivity to time step remains for some processes.
Comparative cytology, physiology and transcriptomics of Burkholderia insecticola in symbiosis with the bean bug Riptortus pedestris and in culture
Authors: Ohbayashi Tsubasa , Futahashi Ryo , Terashima Mia , Barrière Quentin , Lamouche Florian , Takeshita Kazutaka , Meng Xian-Ying , Mitani Yasuo , Sone Teruo , Shigenobu Shuji , Fukatsu Takema , Mergaert Peter , Kikuchi Yoshitomo 
Published: February 2019

Abstract
In the symbiosis of the bean bug Riptortus pedestris with Burkholderia insecticola, the bacteria occupy an exclusive niche in the insect midgut and favor insect development and reproduction. In order to understand how the symbiotic bacteria stably colonize the midgut crypts and which services they provide to the host, we compared the cytology, physiology, and transcriptomics of free-living and midgut-colonizing B. insecticola. The analyses revealed that midgut-colonizing bacteria were smaller in size and had lower DNA content, they had increased stress sensitivity, lost motility, and an altered cell surface. Transcriptomics revealed what kinds of nutrients are provided by the bean bug to the Burkholderia symbiont. Transporters and metabolic pathways of diverse sugars such as rhamnose and ribose, and sulfur compounds like sulfate and taurine were upregulated in the midgut-colonizing symbionts. Moreover, pathways enabling the assimilation of insect nitrogen wastes, i.e. allantoin and urea, were also upregulated. The data further suggested that the midgut-colonizing symbionts produced all essential amino acids and B vitamins, some of which are scarce in the soybean food of the host insect. Together, these findings suggest that the Burkholderia symbiont is fed with specific nutrients and also recycles host metabolic wastes in the insect gut, and in return, the bacterial symbiont provides the host with essential nutrients limited in the insect food, contributing to the rapid growth and enhanced reproduction of the bean bug host.
Co-culture and biogeography of Prochlorococcus and SAR11
Authors: Becker Jamie W , Hogle Shane L , Rosendo Kali , Chisholm Sallie W 
Published: February 2019

Abstract
Prochlorococcus and SAR11 are among the smallest and most abundant organisms on Earth. With a combined global population of about 2.7 × 1028 cells, they numerically dominate bacterioplankton communities in oligotrophic ocean gyres and yet they have never been grown together in vitro. Here we describe co-cultures of Prochlorococcus and SAR11 isolates representing both high- and low-light adapted clades. We examined: (1) the influence of Prochlorococcus on the growth of SAR11 and vice-versa, (2) whether Prochlorococcus can meet specific nutrient requirements of SAR11, and (3) how co-culture dynamics vary when Prochlorococcus is grown with SAR11 compared with sympatric copiotrophic bacteria. SAR11 grew 15–70% faster in co-culture with Prochlorococcus, while the growth of the latter was unaffected. When Prochlorococcus populations entered stationary phase, this commensal relationship rapidly became amensal, as SAR11 abundances decreased dramatically. In parallel experiments with copiotrophic bacteria; however, the heterotrophic partner increased in abundance as Prochlorococcus densities leveled off. The presence of Prochlorococcus was able to meet SAR11’s central requirement for organic carbon, but not reduced sulfur. Prochlorococcus strain MIT9313, but not MED4, could meet the unique glycine requirement of SAR11, which could be due to the production and release of glycine betaine by MIT9313, as supported by comparative genomic evidence. Our findings also suggest, but do not confirm, that Prochlorococcus MIT9313 may compete with SAR11 for the uptake of 3-dimethylsulfoniopropionate (DMSP). To give our results an ecological context, we assessed the relative contribution of Prochlorococcus and SAR11 genome equivalents to those of identifiable bacteria and archaea in over 800 marine metagenomes. At many locations, more than half of the identifiable genome equivalents in the euphotic zone belonged to Prochlorococcus and SAR11 – highlighting the biogeochemical potential of these two groups.
Polyphosphate recovery by a native Bacillus cereus strain as a direct effect of glyphosate uptake
Authors: Acosta-Cortés Alejandra Guadalupe , Martinez-Ledezma Cesar , López-Chuken Ulrico Javier , Kaushik Garima , Nimesh Surendra , Villarreal-Chiu Juan Francisco 
Published: February 2019

Abstract
Seven bacterial strains isolated from a glyphosate-exposed orange plantation site were exposed to 1 mM N-(phosphonomethyl)glycine supplied as a phosphorus source. While some exhibited good biodegradation profiles, the strain 6 P, identified as Bacillus cereus, was the only strain capable of releasing inorganic phosphate to the culture supernatant, while accumulating polyphosphate intracellularly along the experimentation time. The composition and purity of the intracellular polyphosphate accumulated by the strain 6 P were confirmed by FTIR analysis. To date, the biological conversion of glyphosate into polyphosphate has not been reported. However, given the importance of this biopolymer in the survival of microorganisms, it can be expected that this process could represent an important ecological advantage for the adaptation of this strain to an ecological niche exposed to this herbicide. The polyphosphate production yield was calculated as 4 mg l−1, while the glyphosate biodegradation kinetic constant was calculated on 0.003 h−1 using the modified Hockey–Stick first-order kinetic model, with a half-life of 279 h. Our results suggest that B. cereus 6 P is a potential candidate for the generation of an innovative biotechnological process to produce polyphosphate through the biodegradation of the herbicide glyphosate.
Arctic marine fungi: biomass, functional genes, and putative ecological roles
Authors: Hassett B T , Borrego E J , Vonnahme T R , Rämä T , Kolomiets M V , Gradinger R 
Published: February 2019

Abstract
Recent molecular evidence suggests a global distribution of marine fungi; however, the ecological relevance and corresponding biological contributions of fungi to marine ecosystems remains largely unknown. We assessed fungal biomass from the open Arctic Ocean by applying novel biomass conversion factors from cultured isolates to environmental sterol and CARD-FISH data. We found an average of 16.54 nmol m−3 of ergosterol in sea ice and seawater, which corresponds to 1.74 mg C m−3 (444.56 mg C m−2 in seawater). Using Chytridiomycota-specific probes, we observed free-living and particulate-attached cells that averaged 34.07 µg C m−3 in sea ice and seawater (11.66 mg C m−2 in seawater). Summed CARD-FISH and ergosterol values approximate 1.77 mg C m−3 in sea ice and seawater (456.23 mg C m−2 in seawater), which is similar to biomass estimates of other marine taxa generally considered integral to marine food webs and ecosystem processes. Using the GeoChip microarray, we detected evidence for fungal viruses within the Partitiviridae in sediment, as well as fungal genes involved in the degradation of biomass and the assimilation of nitrate. To bridge our observations of fungi on particulate and the detection of degradative genes, we germinated fungal conidia in zooplankton fecal pellets and germinated fungal conidia after 8 months incubation in sterile seawater. Ultimately, these data suggest that fungi could be as important in oceanic ecosystems as they are in freshwater environments.
Visualizing the dynamics of soil aggregation as affected by arbuscular mycorrhizal fungi
Authors: Morris E K , Morris D J P , Vogt S , Gleber S-C , Bigalke M , Wilcke W , Rillig M C 
Published: February 2019

Abstract
Stable soils provide valuable ecosystem services and mechanical soil stability is enhanced by the presence of arbuscular mycorrhizal fungi (AMF). Soil aggregation, which is the major driver of mechanical soil stability, is often treated as a static phenomenon, even though aggregate turnover is continually ongoing. In fact, some breakdown of macroaggregates is necessary to allow new aggregate formation and inclusion of new organic matter into microaggregates. We determined how aggregate turnover times were affected by AMF by tracking movement of rare earth elements (REE), applied as their immobile oxides, between aggregate size classes, and using X-ray fluorescence microscopy to spatially localize REEs in a sample of aggregates. Here we show that AMF increased large macroaggregate formation and slowed down disintegration of large and small macroaggregates. Microaggregate turnover was increased in the presence of AMF. Internal aggregate organization suggested that although formation of microaggregates by accretion of soil to particulate organic matter is common, it is not the only mechanism in operation.
Genome-wide association scan identifies new variants associated with a cognitive predictor of dyslexia
Authors: Gialluisi Alessandro , Andlauer Till F. M. , Mirza-Schreiber Nazanin , Moll Kristina , Becker Jessica , Hoffmann Per , Ludwig Kerstin U. , Czamara Darina , St Pourcain Beate , Brandler William , Honbolygó Ferenc , Tóth Dénes , Csépe Valéria , Huguet Guillaume , Morris Andrew P. , Hulslander Jacqueline , Willcutt Erik G. , DeFries John C. , Olson Richard K. , Smith Shelley D. , Pennington Bruce F. , Vaessen Anniek , Maurer Urs , Lyytinen Heikki , Peyrard-Janvid Myriam , Leppänen Paavo H. T. , Brandeis Daniel , Bonte Milene , Stein John F. , Talcott Joel B. , Fauchereau Fabien , Wilcke Arndt , Francks Clyde , Bourgeron Thomas , Monaco Anthony P. , Ramus Franck , Landerl Karin , Kere Juha , Scerri Thomas S. , Paracchini Silvia , Fisher Simon E. , Schumacher Johannes , Nöthen Markus M. , Müller-Myhsok Bertram , Schulte-Körne Gerd 
Published: February 2019

AbstractDevelopmental dyslexia (DD) is one of the most prevalent learning disorders, with high impact on school and psychosocial development and high comorbidity with conditions like attention-deficit hyperactivity disorder (ADHD), depression, and anxiety. DD is characterized by deficits in different cognitive skills, including word reading, spelling, rapid naming, and phonology. To investigate the genetic basis of DD, we conducted a genome-wide association study (GWAS) of these skills within one of the largest studies available, including nine cohorts of reading-impaired and typically developing children of European ancestry (N = 2562–3468). We observed a genome-wide significant effect (p < 1 × 10−8) on rapid automatized naming of letters (RANlet) for variants on 18q12.2, within MIR924HG (micro-RNA 924 host gene; rs17663182 p = 4.73 × 10−9), and a suggestive association on 8q12.3 within NKAIN3 (encoding a cation transporter; rs16928927, p = 2.25 × 10−8). rs17663182 (18q12.2) also showed genome-wide significant multivariate associations with RAN measures (p = 1.15 × 10−8) and with all the cognitive traits tested (p = 3.07 × 10−8), suggesting (relational) pleiotropic effects of this variant. A polygenic risk score (PRS) analysis revealed significant genetic overlaps of some of the DD-related traits with educational attainment (EDUyears) and ADHD. Reading and spelling abilities were positively associated with EDUyears (p ~ [10−5–10−7]) and negatively associated with ADHD PRS (p ~ [10−8−10−17]). This corroborates a long-standing hypothesis on the partly shared genetic etiology of DD and ADHD, at the genome-wide level. Our findings suggest new candidate DD susceptibility genes and provide new insights into the genetics of dyslexia and its comorbities.
PET imaging of the mouse brain reveals a dynamic regulation of SERT density in a chronic stress model
Authors: Reisinger Sonali N. , Wanek Thomas , Langer Oliver , Pollak Daniela D. 
Published: February 2019

AbstractThe serotonin transporter (SERT, Slc6a4) plays an important role in the regulation of serotonergic neurotransmission and its aberrant expression has been linked to several psychiatric conditions. While SERT density has been proven to be amenable to in vivo quantitative evaluation by positron emission tomography (PET) in humans, this approach is in its infancy for rodents. Here we set out to evaluate the feasibility of using small-animal PET employing [11C]DASB ([11C]-3-amino-4-(2-dimethylaminomethyl-phenylsulfanyl)-benzonitrile) as a radiotracer to measure SERT density in designated areas of the mouse brain. Using Slc6a4+/+, Slc6a4+/−, and Slc6a4−/− mice as a genetic model of different SERT expression levels, we showed the feasibility of SERT imaging in the mouse brain with [11C]DASB-PET. The PET analysis was complemented by an evaluation of SERT protein expression using western blot, which revealed a highly significant correlation between in vivo and ex vivo measurements. [11C]DASB-PET was then applied to the examination of dynamic changes of SERT levels in different brain areas in the chronic corticosterone mouse model of chronic stress. The observed significant reduction in SERT density in corticosterone-treated mice was independently validated by and correlated with western blot analysis. This is the first demonstration of a quantitative in vivo evaluation of SERT density in subregions of the mouse brain using [11C]DASB-PET. The evidenced decrease in SERT density in response to chronic corticosterone treatment adds a new dimension to the complex involvement of SERT in the pathophysiology of stress-induced mental illnesses.
Identification of lenalidomide resistance pathways in myeloma and targeted resensitization using cereblon replacement, inhibition of STAT3 or targeting of IRF4
Authors: Zhu Yuan Xiao , Shi Chang-Xin , Bruins Laura A. , Wang Xuewei , Riggs Daniel L. , Porter Brooke , Ahmann Jonathan M. , de Campos Cecilia Bonolo , Braggio Esteban , Bergsagel P. Leif , Stewart A. Keith 
Published: February 2019

AbstractTo understand immunomodulatory drug (IMiD) resistance in multiple myeloma (MM), we created isogenic human multiple myeloma cell lines (HMCLs) sensitive and resistant to lenalidomide, respectively. Four HMCLs were demonstrated to be resistant to all IMiDs including lenalidomide, pomalidomide, and CC-220, but not to Bortezomib. In three HMLCs (MM.1.SLenRes, KMS11LenRes and OPM2LenRes), CRBN abnormalities were found, including chromosomal deletion, point mutation, and low CRBN expression. The remaining HMCL, XG1LenRes, showed no changes in CRBN but exhibited CD147 upregulation and impaired IRF4 downregulation after lenalidomide treatment. Depletion of CD147 in XG1LenRes and three additional HMCLs had no significant impact on MM viability and lenalidomide response. Further analysis of XG1LenRes demonstrated increased IL6 expression and constitutive STAT3 activation. Inhibition of STAT3 with a selective compound (PB-1-102) re-sensitized XG1LenRes to lenalidomide. Since XG1LenRes harbors a truncated IRF4 that is not downregulated by lenalidomide, we targeted IRF4/MYC axis with a selective inhibitor of the bromodomain of CBP/EP300 (SGC-CBP30), which restored lenalidomide response in XG1LenRes. This strategy also appeared to be more broadly applicable as SGC-CBP30 could re-sensitize two resistant HMCLs with low but detectable CRBN expression to lenalidomide, suggesting that targeting CBP/E300 is a promising approach to restore IMiD sensitivity in MM with detectable CRBN expression.