bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lagrangian Views of the Pathways of the Atlantic Meridional Overturning Circulation
Authors: Bower A. , Lozier S. , Biastoch A. , Drouin K. , Foukal N. , Furey H. , Lankhorst M. , Rühs S. , Zou S. 
Published: July 2019

AbstractThe Lagrangian method—where current location and intensity are determined by tracking the movement of flow along its path—is the oldest technique for measuring the ocean circulation. For centuries, mariners used compilations of ship drift data to map out the location and intensity of surface currents along major shipping routes of the global ocean. In the mid‐20th century, technological advances in electronic navigation allowed oceanographers to continuously track freely drifting surface buoys throughout the ice‐free oceans and begin to construct basin‐scale, and eventually global‐scale, maps of the surface circulation. At about the same time, development of acoustic methods to track neutrally buoyant floats below the surface led to important new discoveries regarding the deep circulation. Since then, Lagrangian observing and modeling techniques have been used to explore the structure of the general circulation and its variability throughout the global ocean, but especially in the Atlantic Ocean. In this review, Lagrangian studies that focus on pathways of the upper and lower limbs of the Atlantic Meridional Overturning Circulation (AMOC), both observational and numerical, have been gathered together to illustrate aspects of the AMOC that are uniquely captured by this technique. These include the importance of horizontal recirculation gyres and interior (as opposed to boundary) pathways, the connectivity (or lack thereof) of the AMOC across latitudes, and the role of mesoscale eddies in some regions as the primary AMOC transport mechanism. There remain vast areas of the deep ocean where there are no direct observations of the pathways of the AMOC.
Quantifying the Relative Importance of Riverine and Open‐Ocean Nitrogen Sources for Hypoxia Formation in the Northern Gulf of Mexico
Authors: Große Fabian , Fennel Katja , Laurent Arnaud 
Published: July 2019

AbstractThe Mississippi and Atchafalaya River System discharges large amounts of freshwater and nutrients into the northern Gulf of Mexico (NGoM). These lead to increased stratification and elevate primary production in the outflow region. Consequently, hypoxia (oxygen <62.5 mmol/m3), extending over an area of roughly 15,000 km2, forms every summer in bottom waters. High‐resolution models have significantly improved our understanding of the processes controlling hypoxia formation in the NGoM and have strongly implicated riverine nutrients as the dominant nutrient source. However, the relative importance of different nutrient sources (i.e., the Mississippi and Atchafalaya Rivers and offshore) has not been assessed before now. Here, we combine a high‐resolution model with an element tracing method to directly quantify the relative contributions of nitrogen from the two rivers and the open ocean to primary production and sediment oxygen consumption, which is the main oxygen sink contributing to hypoxia in the NGoM. Our results indicate that, averaged over 2001–2011, Mississippi and Atchafalaya nitrogen support 51 ± 9% and 33 ± 9% of summer sediment oxygen consumption, respectively, while open‐ocean nitrogen supports 16 ± 2%. The higher relative impact of Mississippi inputs results from longer transit times compared to those of Atchafalaya inputs. We also analyze the effect of riverine nitrogen load reductions and a larger diversion of discharge to the Atchafalaya River. These scenario simulations show that nutrient load reductions are most effective in mitigating hypoxia.
Deformation of a Warm Eddy in the Northern South China Sea
Authors: Qiu Chunhua , Mao Huabin , Liu Hailong , Xie Qiang , Yu Jiancheng , Su Danyi , Ouyang Juan , Lian Shumin 
Published: July 2019

AbstractMesoscale eddies are important for regulating oceanic energy. Variation in eddy shapes leads to uncertainty in calculations of heat or energy content. In this study, we investigated the deformation of a warm eddy in the northern South China Sea from April to June 2018 and elucidated the mechanism governing the deformation. Satellite altimetry images showed that the warm eddy originated from Luzon Strait (LS eddy), migrated westward, and then moved along 500‐m isobaths until it approached the east of Hainan Island. Thereafter, the LS eddy deformed, moved southward, merged with other eddies, and finally dissipated. Using ship and virtual‐mooring Chinese underwater glider observations, we examined the three‐dimensional structure of the LS eddy. The warm eddy had a low‐density core that reached a depth of 250 m. The LS eddy gave rise to a front along its eastern edge, and two associate submesoscale eddies with horizontal radii of approximately 10 km were found at the front. The warm eddy was circular before deformation but morphed into an egg shape after deformation. This shape change allowed the eddy to entrain additional water mass (approximately 1014 kg). The deformation event was able to be forecasted by the vorticity and deformation index, as the eddy deformed by leaking into the zone with a high vorticity and deformation index. We used modeling and energy transformation calculations to analyze the mechanism of the warm eddy deformation. Our results revealed that baroclinic instability played a primary role in the deformation event.
Cassini UVIS Detection of Saturn's North Polar Hexagon in the Grand Finale Orbits
Authors: Pryor W. R. , Esposito L. W. , Jouchoux A. , West R. A. , Grodent D. , Gérard J.‐C. , Radioti A. , Lamy L. , Koskinen T. 
Published: July 2019

AbstractCassini's final orbits in 2016 and 2017 provided unprecedented spatial resolution of Saturn's polar regions from near‐polar spacecraft viewing geometries. Long‐wavelength channels of Cassini's Ultraviolet Imaging Spectrograph instrument detected Saturn's UV‐dark north polar hexagon near 180 nm at planetocentric latitudes near 75°N. The dark polar hexagon is surrounded by a larger, less UV‐dark collar poleward of planetocentric latitude 65°N associated with the dark north polar region seen in ground‐based images. The hexagon is closely surrounded by the main arc of Saturn's UV aurora. The UV‐dark material was locally darkest on one occasion (23 January 2017) at the boundary of the hexagon; in most Ultraviolet Imaging Spectrograph images the dark material more uniformly fills the hexagon. The observed UV‐dark stratospheric material may be a hydrocarbon haze produced by auroral ion‐neutral chemistry at submicrobar pressure levels. Ultraviolet Imaging Spectrograph polar observations are sensitive to UV‐absorbing haze particles at pressures lower than about 10–20 mbar.
Sensitivity of Limited Area Atmospheric Simulations to Lateral Boundary Conditions in Idealized Experiments
Authors: Leps Nora , Brauch Jennifer , Ahrens Bodo 
Published: July 2019

AbstractThe goal of limited area models (LAMs) is to downscale coarse‐gridded general circulation model output to represent small‐scale features of weather and climate. The LAM needs information from the driving coarse‐gridded model passing through its lateral boundaries. The treatment of this information transfer causes inconsistencies between driving and nested models and, subsequently, issues in regional weather and climate simulations. This work examines errors arising from choices taken by the modeler (temporal update frequency of boundary data, spatial resolution jump, and numerical lateral boundary formulation) systematically in an idealized simulation environment. So‐called Big‐Brother Experiments were performed with the LAM COSMO‐CLM (0.11° grid spacing). A baroclinic wave in a zonal channel was simulated over flat terrain with and without a Gaussian hill. The results reveal that the quality of the driving data, here represented by simulations only differing from the LAM simulations by reduced spatial resolution, dominates the performance of the nested model. Consequently, at the simulated mesoscale, the performance of the nested small‐scale model simulations is weakly sensitive to the numerical lateral boundary formulation (Davies relaxation or the newly implemented, computationally less demanding Mesinger Eta‐model formulation). The performance sensitivity to boundary update frequency and resolution jump is small when at least 6‐hourly updates and a resolution jump factor of maximally six is used. Gaussian hill LAM simulations illustrated the strength of downscaling; they can represent small‐scale features missing in the coarse‐scale driving simulations. In the idealized simulation experiments, spectral nudging is not advisable as it imprints the driving models deficits on the nested simulation.
Acetate attenuates inflammasome activation through GPR43-mediated Ca2+-dependent NLRP3 ubiquitination
Authors: Xu Mengda , Jiang Zhengyu , Wang Changli , Li Na , Bo Lulong , Zha Yanping , Bian Jinjun , Zhang Yan , Deng Xiaoming 
Published: July 2019

AbstractAcetate has been indicated to be elevated and to regulate inflammation in inflammatory and metabolic diseases. The inflammasome serves as a key component of immune homeostasis, and its dysregulation can lead to various inflammatory disorders. However, little is known about the effects of acetate on inflammasome activation and the underlying mechanism. Here, we demonstrate that acetate attenuates inflammasome activation via GPR43 in a Ca2+-dependent manner. Through binding to GPR43, acetate activates the Gq/11 subunit and subsequent phospholipase C-IP3 signaling to decrease Ca2+ mobilization. In addition, acetate activates soluble adenylyl cyclase (sAC), promotes NLRP3 inflammasome ubiquitination by PKA, and ultimately induces NLRP3 degradation through autophagy. In vivo, acetate protects mice from NLRP3 inflammasome-dependent peritonitis and LPS-induced endotoxemia. Collectively, our research demonstrates that acetate regulates the NLRP3 inflammasome via GPR43 and Ca2+-dependent mechanisms, which reveals the mechanism of metabolite-mediated NLRP3 inflammasome attenuation and highlights acetate as a possible therapeutic strategy for NLRP3 inflammasome-related diseases.
DMSO cryopreservation is the method of choice to preserve cells for droplet-based single-cell RNA sequencing
Authors: Wohnhaas Christian T. , Leparc Germán G. , Fernandez-Albert Francesc , Kind David , Gantner Florian , Viollet Coralie , Hildebrandt Tobias , Baum Patrick 
Published: July 2019

AbstractCombining single-cell RNA sequencing (scRNA-seq) with upstream cell preservation procedures such as cryopreservation or methanol fixation has recently become more common. By separating cell handling and preparation, from downstream library generation, scRNA-seq workflows are more flexible and manageable. However, the inherent transcriptomic changes associated with cell preservation and how they may bias further downstream analysis remain unknown. Here, we present a side-by-side droplet-based scRNA-seq analysis, comparing the gold standard – fresh cells – to three different cell preservation workflows: dimethyl sulfoxide based cryopreservation, methanol fixation and CellCover reagent. Cryopreservation proved to be the most robust protocol, maximizing both cell integrity and low background ambient RNA. Importantly, gene expression profiles from fresh cells correlated most with those of cryopreserved cells. Such similarities were consistently observed across the tested cell lines (R ≥ 0.97), monocyte-derived macrophages (R = 0.97) and immune cells (R = 0.99). In contrast, both methanol fixation and CellCover preservation showed an increased ambient RNA background and an overall lower gene expression correlation to fresh cells. Thus, our results demonstrate the superiority of cryopreservation over other cell preservation methods. We expect our comparative study to provide single-cell omics researchers invaluable support when integrating cell preservation into their scRNA-seq studies.
Inelastic collapse of perfectly inelastic particles
Authors: Topic Nikola , Pöschel Thorsten 
Published: July 2019

AbstractOne of the most intensively discussed subjects in the dynamics of dissipative hard sphere systems is the effect of inelastic collapse, where the entire kinetic energy of the relative motion of a set of particles is dissipated in finite time due to an infinite sequence of collisions. The known collapse scenarios imply two preconditions: inertia of the particles and at least some degree of elasticity. For completely inelastic particles, collapse scenarios degenerate to a single sticky contact. By considering the overdamped motion of a frictional particle along the steepest descent in a rigid landscape, here we show that there exist collapse scenarios of novel type even if neither of these preconditions hold true. By means of numerical simulations we show that such collapses are no rare events due to particular particle shape and/or initial conditions and, thus, may be considered as an alternative scenario of granular cluster formation.
Fast and robust map‐matching algorithm based on a global measure and dynamic programming for sparse probe data
Authors: Yokota Takayoshi , Okude Mariko , Sakamoto Toshiyuki , Kitahara Reiji 
Published: July 2019

The location data from positioning devices such as those utilising global navigation satellite system (GNSS) provides vital information for the probe‐car systems aiming at solving road‐traffic problems. In the case of the Japanese Electronic Toll Collection System 2.0, a huge amount of probe data can be gathered at intervals of 200 m throughout the country. However, it is not easy for conventional map‐matching algorithms to perform appropriately when they target this sparse probe data. Since for the sparser probe data of this range, it is required to check the reachability of the probe car between adjacent position fixes by using the Dijkstra's algorithm or A* algorithms. These algorithms, however, consume much computation power and can be a serious obstacle for map‐matching processing, especially in real‐time applications. The authors propose a new dynamic‐programming‐based map‐matching algorithm, which can also reduce the calculation time for the reachability test by introducing a hash algorithm. The results of the evaluation confirm the robustness and the effectiveness of the proposed algorithm in terms of both accuracy and computational performance.
Fragmentation, rotation, and outflows in the high-mass star-forming region IRAS 23033+5951
Authors: Bosco F. , Beuther H. , Ahmadi A. , Mottram J. C. , Kuiper R. , Linz H. , Maud L. , Winters J. M. , Henning T. , Feng S. , Peters T. , Semenov D. , Klaassen P. D. , Schilke P. , Urquhart J. S. , Beltrán M. T. , Lumsden S. L. , Leurini S. , Moscadelli L. , Cesaroni R. , Sánchez-Monge Á. , Palau A. , Pudritz R. , Wyrowski F. , Longmore S. 
Published: July 2019

Context. The formation process of high-mass stars (>8 M⊙) is poorly constrained, particularly the effects of clump fragmentation creating multiple systems and the mechanism of mass accretion onto the cores.
Aims. We study the fragmentation of dense gas clumps, and trace the circumstellar rotation and outflows by analyzing observations of the high-mass (~500 M⊙) star-forming region IRAS 23033+5951.
Methods. Using the Northern Extended Millimeter Array (NOEMA) in three configurations and the IRAM 30 m single-dish telescope at 220 GHz, we probe the gas and dust emission at an angular resolution of ~0.45′′, corresponding to 1900 au.
Results. In the millimeter (mm) continuum emission, we identify a protostellar cluster with at least four mm-sources, where three of them show a significantly higher peak intensity well above a signal-to-noise ratio of 100. Hierarchical fragmentation from large to small spatial scales is discussed. Two fragments are embedded in rotating structures and drive molecular outflows, traced by 13CO (2–1) emission. The velocity profiles across two of the cores are similar to Keplerian but are missing the highest-velocity components close to the center of rotation, which is a common phenomena from observations like these, and other rotation scenarios are not excluded entirely. Position–velocity diagrams suggest protostellar masses of ~6 and 19 M⊙. Rotational temperatures from fitting CH3CN (12K− 11K) spectra are used for estimating the gas temperature and thereby also the disk stability against gravitational fragmentation, utilizing Toomre’s Q parameter. Assuming that the candidate disk is in Keplerian rotation about the central stellar object and considering different disk inclination angles, we identify only one candidate disk as being unstable against gravitational instability caused by axisymmetric perturbations.
Conclusions. The dominant sources cover different evolutionary stages within the same maternal gas clump. The appearance of rotation and outflows of the cores are similar to those found in low-mass star-forming regions.
Anharmonicity in the mid-infrared spectra of polycyclic aromatic hydrocarbons: molecular beam spectroscopy and calculations
Authors: Lemmens A. K. , Rap D. B. , Thunnissen J. M. M. , Mackie C. J. , Candian A. , Tielens A. G. G. M. , Rijs A. M. , Buma W. J. 
Published: July 2019

Aims. In this work we determine the effects of anharmonicity on the mid-infrared spectra of the linear polycyclic aromatic hydrocarbons (PAHs) naphthalene, anthracene, tetracene and pentacene recorded using the free electron laser FELIX.
Methods. Comparison of experimental spectra obtained under supersonic jet conditions with theoretically predicted spectra was used to show if anharmonicity explicitly needs to be taken into account.
Results. Anharmonic spectra obtained using second-order vibrational perturbation theory agree on average within 0.5% of the experimental frequencies. Importantly, they confirm the presence of combination bands with appreciable intensity in the 5–6 μm region. These combination bands contain a significant fraction of the IR absorption, which scales linearly with the size of the PAH. Detection and assignment of the combination bands are a preliminary indication of the accuracy of far-IR modes in our anharmonic theoretical spectra. Detailed analysis of the periphery-sensitive CH out-of-plane band of naphthalene reveals that there is still room for improvement of the VPT2 approach. In addition, the implications of our findings for the analysis of the aromatic infrared bands are discussed.
The allosteric mechanism of substrate-specific transport in SLC6 is mediated by a volumetric sensor
Authors: LeVine Michael V. , Terry Daniel S. , Khelashvili George , Siegel Zarek S. , Quick Matthias , Javitch Jonathan A. , Blanchard Scott C. , Weinstein Harel 
Published: July 2019

Significance
The combination of molecular dynamics simulation, single-molecule imaging, and functional assays described here reveals a mechanism of substrate selectivity in the SLC6 family of neurotransmitter transporters. We show that the rotameric state of a volumetric sensor in the substrate binding site is allosterically coupled to conformational changes necessary for transport, and as a consequence, upon binding large substrates, the transporter becomes stabilized in an inactive, nontransporting state upon binding larger substrates. This mechanistic insight suggests the possibility that medically relevant SLC6 transporters may be targeted by inhibitors that specifically modulate this sensor.
Consistent female preference for rare and unfamiliar male color patterns in wild guppy populations
Authors: Valvo Jennifer J , Rodd F Helen , Hughes Kimberly A 
Published: July 2019

AbstractHow genetic variation is maintained in ecologically important traits is a central question in evolutionary biology. Male Trinidadian guppies, Poecilia reticulata, exhibit high genetic diversity in color patterns within populations, and field and laboratory studies implicate negative frequency-dependent selection in maintaining this variation. However, behavioral and ecological processes that mediate this selection in natural populations are poorly understood. We evaluated female mate preference in 11 natural guppy populations, including paired populations from high- and low-predation habitats, to determine if this behavior is responsible for negative frequency-dependent selection and to evaluate its prevalence in nature. Females directed significantly more attention to males with rare and unfamiliar color patterns than to males with common patterns. Female attention also increased with the area of male orange coloration, but this preference was independent of the preference for rare and unfamiliar patterns. We also found an overall effect of predation regime; females from high-predation populations directed more attention toward males than those from low-predation populations. Again, however, the habitat-linked preference was statistically independent from the preference for rare and unfamiliar patterns. Because previous research indicates that female attention to males predicts male mating success, we conclude that the prevalence of female preference for males with rare and unfamiliar color patterns across many natural populations supports the hypothesis that female preference is an important process underlying the maintenance of high genetic variation in guppy color patterns.
Threatened habitat at Great Salt Lake: Importance of shallow-water and brackish habitats to Wilson’s and Red-necked phalaropes
Authors: Frank Maureen G , Conover Michael R 
Published: July 2019

Abstract
Great Salt Lake (GSL) is the largest hypersaline lake in North America and is the fall staging area for a high proportion of North America’s Wilson’s Phalaropes (Phalaropus tricolor) and Red-necked Phalaropes (Phalaropus lobatus). Unfortunately, diversion of freshwater for agriculture and development has decreased the size of GSL by 48%. To assess the potential impact of a smaller GSL on phalaropes, we collected data from 2013 to 2015 from sites where large, dense flocks of phalaropes congregated and sites where there were no phalaropes. At each site, we measured the densities of invertebrates that were preyed upon by phalaropes, including larval and adult brine flies (Ephydridae), adult brine shrimp (Artemia franciscana), chironomid larvae (Chironomidae), and corixid adults (Corixidae). Abiotic characteristics measured included water depth, water salinity, water temperature, wind speed, and benthic substrate. We analyzed high-salinity sites separately from low-salinity sites because they contained different invertebrates. High-salinity sites were in Carrington and Gilbert bays and were relatively deep (mostly &lt;2 m). At the high-salinity sites, phalaropes exhibited a preference for sites with an abundance of adult brine flies and for microbialite substrates. The low-salinity sites were in Ogden and Farmington bays and were shallow (&lt;1 m). At low-salinity sites, large phalarope flocks were more likely to occur at sites that were shallower, less saline, and had a high biomass of benthic macroinvertebrates. Our results indicate that physical features and prey availability are both important in determining phalarope habitat use at GSL. Phalaropes prefer to use shallower parts of GSL and brackish waters. These areas will be especially impacted by decreased freshwater inflow into GSL.