bluuebunny/crossref_metadata_2025 huggingface dataset:
BGVD: An Integrated Database for Bovine Sequencing Variations and Selective Signatures
Authors: Chen Ningbo , Fu Weiwei , Zhao Jianbang , Shen Jiafei , Chen Qiuming , Zheng Zhuqing , Chen Hong , Sonstegard Tad S. , Lei Chuzhao , Jiang Yu
Published: June 2020

Next-generation sequencing has yielded a vast amount of cattle genomic data for global characterization of population genetic diversity and identification of genomic regions under natural and artificial selection. However, efficient storage, querying, and visualization of such large datasets remain challenging. Here, we developed a comprehensive database, the Bovine Genome Variation Database (BGVD). It provides six main functionalities: gene search, variation search, genomic signature search, Genome Browser, alignment search tools, and the genome coordinate conversion tool. BGVD contains information on genomic variations comprising ~60.44 M SNPs, ~6.86 M indels, 76,634 CNV regions, and signatures of selective sweeps in 432 samples from modern cattle worldwide. Users can quickly retrieve distribution patterns of these variations for 54 cattle breeds through an interactive source of breed origin map, using a given gene symbol or genomic region for any of the three versions of the bovine reference genomes (ARS-UCD1.2, UMD3.1.1, and Btau 5.0.1). Signals of selection sweep are displayed as Manhattan plots and Genome Browser tracks. To further investigate and visualize the relationships between variants and signatures of selection, the Genome Browser integrates all variations, selection data, and resources, from NCBI, the UCSC Genome Browser, and Animal QTLdb. Collectively, all these features make the BGVD a useful archive for in-depth data mining and analyses of cattle biology and cattle breeding on a global scale. BGVD is publicly available at http://animal.nwsuaf.edu.cn/BosVar.
The Transforming Market for Legal and Law-Related Practitioners in Japan
Authors: FUKUI Kota
Published: June 2020

The legal- and law-related-services market is undergoing significant transformation: it is being expanded and becoming highly competitive, affected by the cultural and economic diversification of the current world society. In Japan, another aspect must be considered in order to clearly understand this transformation. In addition to fully qualified legal professionals, or bengoshi, there are many different certified law-related practitioners such as shihō shoshi (judicial scriveners), gyōsei shoshi (administrative scriveners), zeirishi (certified public tax attorneys), benrishi (patent attorneys), sharōshi (labour and social-security attorneys), and others who are also important actors in the legal- and law-related-services market. These certified law-related practitioners take on important roles not only in services related to civil and administrative law, but also in corporate legal matters in the specialized fields of the business activities of small and medium-sized enterprises (SMEs) in Japan. Traditionally, bengoshi and other certified law-related practitioners have shared the legal-services market symbiotically, without competition. However, the situation has gradually changed since around the 1990s. In this paper, the factors of the transformation of the Japanese legal- and law-related-services market are discussed based on empirical data, and the direction of the transformation in this market is indicated.
Sensitivity of C-reactive protein cut-off values for pyogenic spinal infection in the emergency department
Authors: Davis William T. , April Michael D. , Mehta Sumeru , Long Brit , Boys Gregory , Shroyer Steven
Published: June 2020

Objectives

The aim of this study was to describe the sensitivity of various C-reactive protein (CRP) cut-off values to identify patients requiring magnetic resonance imaging evaluation for pyogenic spinal infection among emergency department (ED) adults presenting with neck or back pain.

Methods

We prospectively enrolled a convenience series of adults presenting to a community ED with neck or back pain in whom ED providers had concern for pyogenic spinal infection in a derivation cohort from 2004 to 2010 and a validation cohort from 2010 to 2018. The validation cohort included only patients with pyogenic spinal infection. We analysed diagnostic test characteristics of various CRP cut-off values.

Results

We enrolled 232 patients and analysed 201 patients. The median age was 55 years, 43.8% were male, 4.0% had history of intravenous drug use, and 20.9% had recent spinal surgery. In the derivation cohort, 38 (23.9%) of 159 patients had pyogenic spinal infection. Derivation sensitivity and specificity of CRP cut-off values were > 3.5 mg/L (100%, 24.8%), > 10 mg/L (100%, 41.3%), > 30 mg/L (100%, 61.2%), and > 50 mg/L (89.5%, 69.4%). Validation sensitivities of CRP cut-off values were > 3.5 mg/L (97.6%), > 10 mg/L (97.6%), > 30 mg/L (90.4%), and > 50 mg/L (85.7%).

Conclusions

CRP cut-offs beyond the upper limit of normal had high sensitivity for pyogenic spinal infection in this adult ED population. Elevated CRP cut-off values of 10 mg/L and 30 mg/L require validation in other settings.
Symbolic dynamics in mean dimension theory
Authors: SHINODA MAO , TSUKAMOTO MASAKI
Published: June 2020

Furstenberg [Disjointness in ergodic theory, minimal sets, and a problem in Diophantine approximation.Math. Syst. Theory1(1967), 1–49] calculated the Hausdorff and Minkowski dimensions of one-sided subshifts in terms of topological entropy. We generalize this to$\mathbb{Z}^{2}$-subshifts. Our generalization involves mean dimension theory. We calculate the metric mean dimension and the mean Hausdorff dimension of$\mathbb{Z}^{2}$-subshifts with respect to a subaction of$\mathbb{Z}$. The resulting formula is quite analogous to Furstenberg’s theorem. We also calculate the rate distortion dimension of$\mathbb{Z}^{2}$-subshifts in terms of Kolmogorov–Sinai entropy.
The Place of Punishment in Twenty-First-Century America: Understanding the Persistence of Mass Incarceration
Authors: Beckett Katherine , Beach Lindsey
Published: June 2020

This study analyzes prison admission and crime data to assess whether the penal system’s response to crime has continued to intensify since mass incarceration’s peak and whether the increasing use of prison in nonurban areas helps explain this trend. The findings show that penal intensity has continued to escalate despite falling crime rates and widespread efforts to reduce prison populations. Further, the justice system’s response to crime is most vigorous in nonurban, and especially rural, counties, where more felony arrests for all types of offenses result in a prison sentence. Although not new, this geographic difference has grown in recent years. While penal intensity thus varies notably within states, case outcomes also vary markedly across states. Comparative case studies of dynamics in a highly punitive state (Kentucky) and a less punitive state (Washington) show how formal law interacts with local dynamics not only by creating “statutory hammers” that are utilized by zealous prosecutors and judges but also by limiting the impact of aggressive prosecutorial practices on prison sentences.
Migrant Rights, Agency, and Vulnerability: Navigating Contradictions in the Eurasian Region
Authors: Schenk Caress
Published: June 2020

Migrants are often presented in simplified terms that focus on the threats they experience or pose to the host society. This produces an image of migrants who have no agency and are victims of their circumstances or who respond to their circumstances by turning to crime and illegality. In this special issue, we reframe migration by highlighting how migrants leverage the various vulnerabilities they encounter, turning them into agency and self-sufficiency. We explore different types of vulnerability and agency for migrants in the Eurasian region, which often originate from the same sources, including structural factors, state and governance practices, social networks, and gender roles. Through interactions with a variety of state and nonstate actors, migrants have the ability to make choices that reduce uncertainty and risk in their migration environment and on returning home. These choices coexist with vulnerability and a lack of formal rights but do not replace them, creating complex and contingent relationships between precarity and agency.
The Curse of Displacement: Local Narratives of Forced Expulsion and the Appropriation of Abandoned Property in Abkhazia
Authors: Peinhopf Andrea
Published: June 2020

Since the end of the Georgian-Abkhaz war, the often-precarious status of the Georgians displaced from Abkhazia has received significant academic attention. In contrast, the consequences of displacement from the reverse perspective—how it has affected the people who stayed behind—remains underanalyzed. Drawing on narratives collected during several months of ethnographic fieldwork, this article argues that although ethnic Abkhazians see themselves as victims of ethnic violence rather than perpetrators, the re-distribution of Georgian property nevertheless caused significant distress. Many condemned the practice of appropriation, suggesting that taking what is not one’s own is not only a violation of the property of the original owner, but also of the Abkhaz moral code and therefore shameful. To them, the trophy houses were a curse, both literally—as spaces haunted by former occupants—and metaphorically, as a source and reminder of a certain “moral corruption” within Abkhazian society. However, while the stories around the trophy houses reflect substantial intra-communal divisions, I suggest that they are also an expression of a shared postwar experience. Like the horror stories of Georgian violence, and the tales of Abkhaz heroism, they have become part of an intimate national repertoire constitutive of Abkhazia’s postwar community.
Precise early Cambrian U–Pb zircon dates bracket the oldest trilobites and archaeocyaths in Moroccan West Gondwana
Authors: Landing Ed , Schmitz Mark D. , Geyer Gerd , Trayler Robin B. , Bowring Samuel A.
Published: June 2020

New U–Pb radioisotopic ages on early Cambrian volcanic zircons condition a high-resolution Bayesian age model that constrains the first occurrences and zonations of West Gondwanan archaeocyaths and trilobites in southern Morocco. The oldest archaeocyaths in the Tiout Member of the Igoudine Formation (519.71 + 0.26/− 0.35 Ma) are c. 6 Ma younger than the oldest Siberian archaeocyaths. The oldest Moroccan trilobite fragments, from the lower member of the Igoudine, are constrained to 519.95 + 0.43/− 0.40 Ma. The succeeding Issendalenian Stage (i.e. Hupetina antique – Eofallotaspis tioutensis – Fallotaspis plana – Choubertella – Daguinaspis trilobite zones) spans c. 1.5 Ma (519.78 + 0.26/− 0.37 Ma to 518.43 + 0.25/− 0.69 Ma). Identifiable Moroccan fallotaspidids and bigotinids, among Earth’s oldest trilobites, occur above a positive δ13C excursion dated with our age model at 520.27 + 0.59/− 0.57 Ma, and correlated with the IV excursion peak within the lower range of Siberian Atdabanian Stage trilobites (Repinaella Zone). This excursion is the best standard for a Cambrian Series 2 base. The oldest West Gondwana trilobite fragments are c. 1 Ma younger than those in Siberia and c. 0.5 Ma older than the oldest Avalonian trilobites (Callavia Zone). This diachrony means a trilobite first appearance datum is an inappropriate chronostratigraphic base for Cambrian Series 2. Taxonomic differences in the oldest trilobites between Cambrian palaeocontinents are in accordance with trace fossil evidence for the group’s appearance possibly as late as c. 530 Ma in the Cambrian Evolutionary Radiation. Coeval 519–517 Ma dates from Avalonia (cool-water siliciclastic shelf) and West Gondwana (tropical carbonate platform) sections with distinct macrofaunas emphasize these successions were latitudinally separate by the late Ediacaran Period.
Strategic sorting: the role of ordeals in health care
Authors: Zeckhauser Richard
Published: June 2020

Ordeals are burdens placed on individuals that yield no benefits to others; hence they represent a dead-weight loss. Ordeals – the most common is waiting time – play a prominent role in rationing health care. The recipients most willing to bear them are those receiving the greatest benefit from scarce health-care resources. Health care is heavily subsidized; hence, moral hazard leads to excess use. Ordeals are intended to discourage expenditures yielding little benefit while simultaneously avoiding the undesired consequences of rationing methods such as quotas or pricing. This analysis diagnoses the economic underpinnings of ordeals. Subsidies for nursing-home care versus home care illustrate.
Eocene (46–44 Ma) Onset of Australia‐Pacific Plate Motion in the Southwest Pacific Inferred From Stratigraphy in New Caledonia and New Zealand
Authors: Dallanave Edoardo , Maurizot Pierre , Agnini Claudia , Sutherland Rupert , Hollis Christopher J. , Collot Julien , Dickens Gerald R. , Bachtadse Valerian , Strogen Dominic , Morgans Hugh E. G.
Published: June 2020

The Pacific plate circuit went through a complex reorganization during the early to middle Eocene, approximately coinciding with the onset of subduction along the western Pacific margin. However, the timing and dynamics of this change in the southwest Pacific and evolution of subduction beneath the Tonga‐Kermadec Arc are not fully resolved. We present magneto‐biostratigraphic data from an early to middle Eocene sedimentary section exposed in the Koumac‐Gomen area, New Caledonia, which is an emerged portion of the Norfolk Ridge. The 260 m‐thick succession contains a transition from pelagic micrite to terrigenous‐rich calciturbidite that is observed regionally in New Caledonia and which is interpreted to represent a shift from sedimentation on a stable submarine plateau to slope formation developed under a convergent tectonic regime. The stratigraphic contact between pelagic micrite and overlying calciturbidite is not exposed, but our magnetic polarity‐based chronology constrains the age of transition to 46–44 Ma, in agreement with the 45.3 Ma age recently obtained from the Noumea area in southern New Caledonia. We integrate records from New Caledonia with recent magnetostratigraphic data from South Island, New Zealand, where marked variations in terrigenous input occurred during the early and middle Eocene. Synchronous sedimentary changes in the southwest Pacific occurred at the same time as onset of rapid seafloor spreading south of Australia and New Zealand. We infer that the underlying cause of stratigraphic change was inception of slip at a new configuration of the Australia‐Pacific plate boundary, which evolved into the Tonga‐Kermadec subduction system.
Silica‐Rich Vein Formation in an Evolving Stress Field, Atlantis Bank Oceanic Core Complex
Authors: Ma Qiang , Dick Henry J. B. , Urann Benjamin , Zhou Huaiyang
Published: June 2020

Drilling 809‐m Hole U1473A in the gabbro batholith at the Atlantis Bank Oceanic Core Complex (OCC) found two felsic vein generations: late magmatic fractionates, rich in deuteric water, hosted by oxide gabbros, and anatectic veins associated with dike intrusion and introduction of seawater‐derived volatiles. Microtextures show a change from compressional to tensional stress during vein formation. Temperatures and oxidation state were obtained from amphibole‐plagioclase and oxide pairs in the adjacent gabbros. Type I veins generally have reverse shear‐sense, with restricted ΔFMQ, high Mt/Ilm ratios, and low‐amphibole Cl/F indicating deuteric fluids. They formed during percolation and fractionation of Fe‐Ti‐rich melts into the primary olivine gabbro. Type II veins are usually hosted by olivine gabbro, occur at dike contacts and the margins of normal‐sense shear zones. They are undeformed or weakly deformed, with highly variable ΔFMQ, low Mt/Ilm ratios, and high‐amphibole Cl/F, indicating seawater‐derived fluids. The detachment fault on which the gabbro massif was emplaced rooted near the base of the dike‐gabbro transition beneath the rift valley. The ingress of seawater volatiles began at >800°C and penetrated at least ~590 m into the lower crust during extensional faulting in the rift valley and adjacent rift mountains. The sequence of the felsic vein formation likely reflects asymmetric diapiric flow, with a reversal of the stress regime, and a transition from juvenile to seawater‐derived volatiles. This, in turn, is consistent with fault capture leading to the large asymmetries in spreading rates during OCC formations and heat flow beneath the rift mountains.
Detection Limits and Near‐Field Ground Motions of Fast and Slow Earthquakes
Authors: Kwiatek Grzegorz , Ben‐Zion Yehuda
Published: June 2020

We investigate theoretical limits to detection of fast and slow seismic events, and spatial variations of ground motion expected from M 6 earthquakes at short epicentral distances. The analyses are based on synthetic velocity seismograms calculated with the discrete wavenumber method assuming seismic velocities and attenuation properties of the crust in Southern California. The examined source properties include different magnitudes (M −1.0 to M 6.0), static stress drops (0.1–10 MPa), and slow and fast ruptures (0.1–0.9 of shear wave velocity). For the M 6 events we also consider variations in rise times producing crack‐ and pulse‐type events and different rupture directivities. Slow events produce ground motion with considerably lower amplitude than corresponding regular fast earthquakes with the same magnitude, and hence are significantly more difficult to detect. The static stress drop and slip rise time also affect the maximum radiated seismic motion, and hence event detectability. Apart from geometrical factors, the saturation and depletion of seismic ground motion at short epicentral distances stem from radiation pattern, earthquake size (magnitude, stress drop), and rupture directivity. The rupture velocity, rise time, and directivity affect significantly the spatial pattern of the ground motions. The results can help optimizing detection of slow and fast small earthquakes and understand the spatial distribution of ground motion generated by large events.
Characteristics of Coastal Low‐Level Jets Over Beibu Gulf, China, During the Early Warm Season
Authors: Kong Hoiio , Zhang Qinghong , Du Yu , Zhang Fan
Published: June 2020

We investigated coastal low‐level jets (CLLJs) over Beibu Gulf, China, during the warm season (May to July) using hourly model simulations from a mesoscale weather research and forecasting model with a 9‐km horizontal resolution. Two high‐incidence CLLJ areas were identified over Beibu Gulf: one located on the leeward side of the Annamite Range that prevailed after sunset and the second off the northwestern coast of Hainan Island that reached its maximum intensity at midnight. The upstream wind of the Annamite Range was too weak to pass over the range during the daytime due to strong turbulent mixing near the land surface of Indochina; however, due to the suppression of the turbulent mixing after sunset, the flow intensified and crossed over the Annamite Range and further formed a hydraulic jump jet downstream. In addition to advection effect from upstream, topographic blocking effect of Hainan Island contributed to the CLLJ off the northwestern coast of Hainan Island, which persisted during the day but became more prevalent at midnight. Further momentum budget analysis and sensitivity experiments indicated that the upstream inertial oscillation due to the diurnal variation in turbulence over land was the primary source of the CLLJ over the ocean. These findings reveal the primary mechanism of CLLJs over Beibu Gulf, providing insight into CLLJ formation in other coastal regions with complex mountain ranges.
A Calibration Framework for High‐Resolution Hydrological Models Using a Multiresolution and Heterogeneous Strategy
Authors: Sun Ruochen , Hernández Felipe , Liang Xu , Yuan Huiling
Published: June 2020

Increasing spatial and temporal resolution of numerical models continues to propel progress in hydrological sciences, but, at the same time, it has strained the ability of modern automatic calibration methods to produce realistic model parameter combinations for these models. This paper presents a new reliable and fast automatic calibration framework to address this issue. In essence, the proposed framework, adopting a divide and conquer strategy, first partitions the parameters into groups of different resolutions based on their sensitivity or importance, in which the most sensitive parameters are prioritized with the highest resolution in the parameter search space, while the least sensitive ones are initially explored with the coarsest resolution. This is followed by an optimization‐based iterative calibration procedure consisting of a series of subtasks or runs. Between consecutive runs, the setup configuration is heterogeneous with parameter search ranges and resolutions varying among groups. At the completion of each subtask, the parameter ranges within each group are systematically refined from their previously estimated ranges, which are initially based on a priori information. Parameters attain stable convergence progressively with each run. A comparison of this new calibration framework with a traditional optimization‐based approach was performed using a quasi‐synthetic double‐model setup experiment to calibrate 134 parameters and two well‐known distributed hydrological models: the Variable Infiltration Capacity (VIC) model and the Distributed Hydrology Soil Vegetation Model (DHSVM). The results demonstrate statistically that the proposed framework can better mitigate equifinality problem, yields more realistic model parameter estimates, and is computationally more efficient.
Bayesian Calibration and Validation of a Large‐Scale and Time‐Demanding Sediment Transport Model
Authors: Beckers Felix , Heredia Andrés , Noack Markus , Nowak Wolfgang , Wieprecht Silke , Oladyshkin Sergey
Published: June 2020

This study suggests a stochastic Bayesian approach for calibrating and validating morphodynamic sediment transport models and for quantifying parametric uncertainties in order to alleviate limitations of conventional (manual, deterministic) calibration procedures. The applicability of our method is shown for a large‐scale (11.0 km) and time‐demanding (9.14 hr for the period 2002–2013) 2‐D morphodynamic sediment transport model of the Lower River Salzach and for three most sensitive input parameters (critical Shields parameter, grain roughness, and grain size distribution). Since Bayesian methods require a significant number of simulation runs, this work proposes to construct a surrogate model, here with the arbitrary polynomial chaos technique. The surrogate model is constructed from a limited set of runs (n=20) of the full complex sediment transport model. Then, Monte Carlo‐based techniques for Bayesian calibration are used with the surrogate model (105 realizations in 4 hr). The results demonstrate that following Bayesian principles and iterative Bayesian updating of the surrogate model (10 iterations) enables to identify the most probable ranges of the three calibration parameters. Model verification based on the maximum a posteriori parameter combination indicates that the surrogate model accurately replicates the morphodynamic behavior of the sediment transport model for both calibration (RMSE = 0.31 m) and validation (RMSE = 0.42 m). Furthermore, it is shown that the surrogate model is highly effective in lowering the total computational time for Bayesian calibration, validation, and uncertainty analysis. As a whole, this provides more realistic calibration and validation of morphodynamic sediment transport models with quantified uncertainty in less time compared to conventional calibration procedures.
Twenty Lessons Drawn From My Subsurface Hydrology Career
Authors: Neuman Shlomo P.
Published: June 2020

This personal perspective complements a Brief Autobiography I (Figure 1) wrote for the journal Ground Water (Neuman, 2008). Whereas there I described my personal life from early childhood to my career stage at the time, here I focus on key science lessons my academic research, teaching, and professional consulting have taught me. Though many of these lessons have been shared with students and colleagues throughout my career, never have I had the opportunity to collect and summarize them for a wider audience as I do here. I thank the Editors for the opportunity to do so, Professor Emeritus Steve Burgess of the University of Washington and Professor Alberto Guadagnini of the Politecnico di Milano, Italy, for helping me to do so better, and hope readers will find some of these lessons intriguing enough to explore and develop the related ideas further.
Visualizing the Deep Carbon Cycle
Authors: Fogerty Christian
Published: June 2020

Geoscientists have created animations to help visualize different components of Earth’s carbon cycle.
Evaluating Spatiotemporal Resolution of Trace Element Concentrations and Pb Isotopic Compositions of Honeybees and Hive Products as Biomonitors for Urban Metal Distribution
Authors: Smith Kate E. , Weis Dominique
Published: June 2020

Assessing metal distributions in cities is an important aspect of urban environmental quality management. Western honeybees (Apis mellifera) and their products are biomonitors that can elucidate small‐scale metal distribution within a city. We compare range and variations in trace element (TE) concentrations and lead (Pb) isotopic compositions of honey, bee tissue, bee pollen, and propolis collected throughout Metro Vancouver (BC, Canada). Honey, bee, and bee pollen results have similar TE and isotopic trends; samples collected in urban and industrialized areas exhibit elevated concentrations of anthropogenically influenced TE (e.g., Pb, Zn, V, and Ti) and a less radiogenic Pb isotopic composition (i.e., lower 206Pb/207Pb and elevated 208Pb/206Pb) relative to their suburban and rural counterparts. For example, 206Pb/207Pb, 208Pb/206Pb in honey range from 1.126, 2.131 and 1.184, 2.063; extremes measured in honey from urban and suburban/rural areas, respectively. Except for propolis, measured and interpolated (kriged) results in all materials reflect the immediate zoning or land use setting near the hive, providing kilometer‐scale geospatial resolution, suitable for monitoring urban systems. Statistical analysis reveals that no systematic variations or intra‐ or inter‐annual trends exist in TE concentrations or Pb isotopic compositions, including among sampling and field methods (i.e., old vs. new hive equipment and honey from the brood nest box vs. honey super). The results of this systematic study using honeybees and hive products in Metro Vancouver provide a robust, current baseline for future comparison of local land use and environmental policy change.
Spatial Distributions of Nitric Oxide in the Antarctic Wintertime Middle Atmosphere During Geomagnetic Storms
Authors: Newnham D. A. , Rodger C. J. , Marsh D. R. , Hervig M. E. , Clilverd M. A.
Published: June 2020

Energetic electron precipitation leads to increased nitric oxide (NO) production in the mesosphere and lower thermosphere. NO distributions in the wintertime, high‐latitude Southern Hemisphere atmosphere during geomagnetic storms are investigated. NO partial columns in the upper mesosphere at altitudes 70–90 km and in the lower thermosphere at 90–110 km have been derived from observations made by the Solar Occultation For Ice Experiment (SOFIE) on board the Aeronomy of Ice in the Mesosphere (AIM) satellite. The SOFIE NO measurements during 17 geomagnetic storms in 2008–2014 have been binned into selected geomagnetic latitude and geographic latitude/longitude ranges. The regions above Antarctica showing the largest instantaneous NO increases coincide with high fluxes of 30–300 keV precipitating electrons from measurements by the second‐generation Space Environment Monitor (SEM‐2) Medium Energy Proton and Electron Detector (MEPED) instrument on the Polar‐orbiting Operational Environmental Satellites (POES). Significant NO increases over the Antarctic Peninsula are likely due to precipitation of >30 keV electrons from the radiation belt slot region. NO transport is estimated using Horizontal Wind Model (HWM14) calculations. In the upper mesosphere strong eastward winds (daily mean zonal wind speed ~20–30 m s−1 at 80 km) during winter transport NO‐enriched air away from source regions 1–3 days following the storms. Mesospheric winds also introduce NO‐poor air into the source regions, quenching initial NO increases. Higher up, in the lower thermosphere, weaker eastward winds (~5–10 m s−1 at 100 km) are less effective at redistributing NO zonally.
A Bayesian Approach for Thermal History Reconstruction in Basin Modeling
Authors: Licciardi A. , Gallagher K. , Clark S. A.
Published: June 2020

We present a novel method for the joint inversion of thermal indicator data (vitrinite reflectance and apatite fission track) and additional data (bottom‐hole temperature and porosity) for thermal history reconstruction in basin modeling. A transdimensional and hierarchical Bayesian formulation is implemented with a reversible jump Markov chain Monte Carlo algorithm, with a 1‐D transient thermal model. The objective of the inverse problem is to infer the heat flow history below a borehole given the data and a set of geological constraints (e.g., burial histories and physical properties of the sediments). The algorithm incorporates an adaptive, data‐driven parametrization of the heat flow history, allows for automatic estimation of the relative importance of each data type and quantification of parameter uncertainties and trade‐offs. Our approach deals with uncertainties on the imposed geological constraints in two ways. First, the amount of erosion and timing of an erosional event are treated as independent parameters. Second, uncertainties on compaction parameters and surface temperature history are directly propagated into the final solution. Synthetic tests show that porosity data can be used to reduce uncertainties on the amount of erosion. This work illustrates a truly probabilistic analysis of the trade‐off between the magnitude of erosion and variations in heat flow histories which is key in basin modeling. The algorithm is then applied to real data from a well in the Barents Sea. Our algorithm can reconcile estimates of erosion from the thermal indicator and porosity data, which is a difficult and subjective task in basin modeling.
The Orinoco Low‐Level Jet: An Investigation of Its Mechanisms of Formation Using the WRF Model
Authors: Jiménez‐Sánchez Giovanni , Markowski Paul M. , Young George S. , Stensrud David J.
Published: June 2020

The Orinoco low‐level jet (OLLJ) is characterized using finer horizontal, vertical, and temporal resolution than possible in previous studies via dynamical downscaling. The investigation relies on a 5‐month‐long simulation (November 2013 to March 2014) performed with the Weather Research and Forecasting (WRF) model, with initial and boundary conditions provided by the Global Forecast System (GFS) analysis. Dynamical downscaling is demonstrated to be an effective method not only to better resolve the horizontal and vertical characteristics of the OLLJ but also to determine the mechanisms leading to its formation. The OLLJ is a single stream tube over Colombia and Venezuela with wind speeds greater than 8 m s−1 and four distinctive cores of higher wind speeds varying in height under the influence of sloping terrain. It is an austral summer phenomenon that exhibits its seasonal maximum wind speed and largest spatial extent (2,100 km × 450 km) in January. The maximum diurnal mean wind speeds (13–17 m s−1) at each core location occur at different times during the night and early morning (2300–0900 LST). The momentum balance analysis in a natural coordinate system reveals that the OLLJ results from four phenomena acting together to accelerate the wind: a sea breeze penetration, katabatic flow, three expansion fans, and diurnal variation of turbulent diffusivity. The latter, in contrast to the heavily studied nocturnal low‐level jet in the U.S. Great Plains region, plays a secondary role in OLLJ acceleration. These results imply that LLJs near the equator may originate from processes other than the inertial oscillation and topographic thermal forcing.
Direct detection of mRNA expression in microbial cells by fluorescence in situ hybridization using RNase H-assisted rolling circle amplification
Authors: Takahashi Hirokazu , Horio Kyohei , Kato Setsu , Kobori Toshiro , Watanabe Kenshi , Aki Tsunehiro , Nakashimada Yutaka , Okamura Yoshiko
Published: June 2020

Meta-analyses using next generation sequencing is a powerful strategy for studying microbiota; however, it cannot clarify the role of individual microbes within microbiota. To know which cell expresses what gene is important for elucidation of the individual cell’s function in microbiota. In this report, we developed novel fluorescence in situ hybridization (FISH) procedure using RNase-H-assisted rolling circle amplification to visualize mRNA of interest in microbial cells without reverse transcription. Our results show that this method is applicable to both Gram-negative and Gram-positive microbes without any noise from DNA, and it is possible to visualize the target mRNA expression directly at the single-cell level. Therefore, our procedure, when combined with data of meta-analyses, can help to understand the role of individual microbes in the microbiota.
A new brilliantly blue-emitting luciferin-luciferase system from Orfelia fultoni and Keroplatinae (Diptera)
Authors: Viviani Vadim R. , Silva Jaqueline R. , Amaral Danilo T. , Bevilaqua Vanessa R. , Abdalla Fabio C. , Branchini Bruce R. , Johnson Carl H.
Published: June 2020

Larvae of O. fultoni (Keroplatidae: Keroplatinae), which occur along river banks in the Appalachian Mountains in Eastern United States, produce the bluest bioluminescence among insects from translucent areas associated to black bodies, which are  located mainly in the anterior and posterior parts of the body. Although closely related to Arachnocampa spp (Keroplatidae: Arachnocampininae), O.fultoni has a morphologically and biochemically distinct bioluminescent system which evolved independently, requiring a luciferase enzyme, a luciferin, a substrate binding fraction (SBF) that releases luciferin in the presence of mild reducing agents, molecular oxygen, and no additional cofactors. Similarly, the closely related Neoceroplatus spp, shares the same kind of luciferin-luciferase system of Orfelia fultoni. However, the molecular properties, identities and functions of luciferases, SBF and luciferin of Orfelia fultoni and other  luminescent members of the Keroplatinae subfamily still remain to be fully elucidated. Using O. fultoni as a source of luciferase, and the recently discovered non-luminescent cave worm Neoditomiya sp as the main source of luciferin and SBF, we isolated and initially characterized these compounds. The luciferase of O. fultoni is a stable enzyme active as an apparent trimer (220 kDa) composed of ~70 kDa monomers, with an optimum pH of 7.8. The SBF, which is found in the black bodies in Orfelia fultoni and in smaller dark granules in Neoditomiya sp, consists of a high molecular weight complex of luciferin and proteins, apparently associated to mitochondria. The luciferin, partially purified from hot extracts by a combination of anion exchange chromatography and TLC, is a very polar and weakly fluorescent compound, whereas its oxidized product displays blue fluorescence with an emission spectrum matching the bioluminescence spectrum (~460 nm), indicating that it is oxyluciferin. The widespread occurrence of luciferin and SBF in both luminescent and non-luminescent Keroplatinae larvae indicate an additional important biological function for the substrate, and therefore the name keroplatin.
Development of a new ‘ultrametric’ method for assessing spawning progression in female teleost serial spawners
Authors: Anderson Kelli C. , Alix Maud , Charitonidou Katerina , Thorsen Anders , Thorsheim Grethe , Ganias Kostas , Schmidt Thassya C. dos Santos , Kjesbu Olav Sigurd
Published: June 2020

The collection and presentation of accurate reproductive data from wild fish has historically been somewhat problematic, especially for serially spawning species. Therefore, the aim of the current study was to develop a novel method of assessing female spawning status that is robust to variation in oocyte dynamics between specimens. Atlantic cod (Barents Sea stock) were used to develop the new ‘ultrametric’ method, that is based on the progressive depletion of the vitellogenic oocyte pool relative to the rather constant previtellogenic oocyte (PVO) pool. Fish were subsequently partitioned into one of four categories that accurately reflected changes in their oocyte size frequency distribution characteristics and gonadosomatic index throughout spawning. The ultrametric method overcomes difficulties associated with presence of bimodal oocyte distributions, oocyte tails, lack of clear hiatus region, and presence of free ova, and can be implemented at a single sampling point. Much of the workflow is fully automated, and the technique may circumvent the need for histological analysis depending on the desired outcome. The ultrametric method differs from the traditional autodiametric method in that PVOs can be separated by ultrasonication and then enumerated, and ovarian homogeneity is not a mandatory requirement per se. The method is designed for determinate spawners but might be extended to include indeterminate spawners.
Periconceptional environment predicts leukocyte telomere length in a cross-sectional study of 7–9 year old rural Gambian children
Authors: Maasen Kim , James Philip T. , Prentice Andrew M. , Moore Sophie E. , Fall Caroline H. , Chandak Giriraj R. , Betts Modupeh , Silver Matt J. , Buxton Jessica L.
Published: June 2020

Early life exposures are important predictors of adult disease risk. Although the underlying mechanisms are largely unknown, telomere maintenance may be involved. This study investigated the relationship between seasonal differences in parental exposures at time of conception and leukocyte telomere length (LTL) in their offspring. LTL was measured in two cohorts of children aged 2 yrs (N = 487) and 7–9 yrs (N = 218). The association between date of conception and LTL was examined using Fourier regression models, adjusted for age, sex, leukocyte cell composition, and other potential confounders. We observed an effect of season in the older children in all models [likelihood ratio test (LRT) χ²2 = 7.1, p = 0.03; fully adjusted model]. LTL was greatest in children conceived in September (in the rainy season), and smallest in those conceived in March (in the dry season), with an effect size (LTL peak–nadir) of 0.60 z-scores. No effect of season was evident in the younger children (LRT χ²2 = 0.87, p = 0.65). The different results obtained for the two cohorts may reflect a delayed effect of season of conception on postnatal telomere maintenance. Alternatively, they may be explained by unmeasured differences in early life exposures, or the increased telomere attrition rate during infancy.
Production of functional eggs and sperm from in vitro-expanded type A spermatogonia in rainbow trout
Authors: Iwasaki-Takahashi Yoshiko , Shikina Shinya , Watanabe Masaya , Banba Akira , Yagisawa Masaru , Takahashi Kasumi , Fujihara Ryo , Okabe Takafumi , Valdez Jr Delgado M. , Yamauchi Akihiro , Yoshizaki Goro
Published: June 2020

Combining cryopreservation of germline stem cells (GSCs) with their subsequent transplantation into recipient fish is a powerful tool for long-term preservation of genetic resources of endangered fishes. However, application of this technique has been limited because endangered species sometimes have small gonads and do not supply enough GSCs to be used for transplantation. This limitation could be overcome by expanding GSCs in vitro, though this has been difficult due to the complexity of reconstructing the gonadal microenvironment that surrounds GSCs. Here, we describe a novel method of in vitro expansion of rainbow trout GSCs using a feeder layer derived from Sertoli cells and a culture medium containing trout plasma. A transplantation assay demonstrated that the in vitro-expanded GSCs exhibited stem cell activity and potency to produce functional eggs, sperm, and eventually healthy offspring. In vitro expansion of GSCs can aid in rescuing fishes that are on the verge of extinction.
Ultra-broadband near-infrared emission CuInS2/ZnS quantum dots with high power efficiency and stability for the theranostic applications of mini light-emitting diodes
Authors: Huang Wen-Tse , Yoon Suk-Young , Wu Bo-Han , Lu Kuang-Mao , Lin Chih-Min , Yang Heesun , Liu Ru-Shi
Published: June 2020

Broadband near-infrared CuInS2/ZnS quantum with up to 94.8% quantum yield was synthesized with fast precursor decomposition. The better power efficiency and stability of CuInS2/ZnS mini-LED were performed with penetration tests and vein imaging.
LMCT transition-based red-light photochemotherapy using a tumour-selective ferrocenyl iron(iii) coumarin conjugate
Authors: Sarkar Tukki , Bhattacharyya Arnab , Banerjee Samya , Hussain Akhtar
Published: June 2020

A mitochondria-targeted ferrocenyl iron(iii) coumarin complex shows red-light toxicity against cancer cells but remains harmless in the dark and to normal cells.
Holding of planar chirality of pillar[5]arene by kinetic trapping using host–guest interactions with achiral guest solvents
Authors: Nagata Yuuya , Suzuki Misaki , Shimada Yasuo , Sengoku Hiroki , Nishida Shungo , Kakuta Takahiro , Yamagishi Tada-aki , Suginome Michinori , Ogoshi Tomoki
Published: June 2020

We report a solvent-dependent switching and holding of planar chirality of pillar[5]arene with stereogenic carbons at both rims by host–guest complexation with achiral guest solvents.
Nd doped CaYAl3O7: exploration and laser performance of a novel disordered laser crystal
Authors: Li Yang , Jia Zhitai , Nie Hongkun , Yin Yanru , Fu Xiuwei , Mu Wenxiang , Zhang Jian , Zhang Baitao , Li Shuchen , Tao Xutang
Published: June 2020

A novel disordered structure crystal has drawn intense interest as a promising ultrafast laser crystal host for its broad absorption and emission bands.
The missing NH stretch fundamental in S1 methyl anthranilate: IR-UV double resonance experiments and local mode theory
Authors: Blodgett Karl N. , Fischer Joshua L. , Zwier Timothy S. , Sibert Edwin L.
Published: June 2020

Hydrogen atom dislocation in S1 methyl anthranilate is characterized with infrared spectroscopy, and a novel explanation for the missing S1 NH stretch fundamental is presented.
Exciton energy transfer reveals spectral signatures of excited states in clusters
Authors: Lu Wenchao , Metz Ricardo B. , Troy Tyler P. , Kostko Oleg , Ahmed Musahid
Published: June 2020

Electronic excitation and concomitant energy transfer leading to Penning ionization in argon–acetylene clusters are investigated with synchrotron-based photoionization mass spectrometry and electronic structure calculations.
Protein packaging in ionic liquid mixtures: an ecofriendly approach towards the improved stability of β-lactoglobulin in cholinium-based mixed ionic liquids
Authors: Sindhu Anamika , Kumar Sumit , Mondal Dibyendu , Bahadur Indra , Venkatesu Pannuru
Published: June 2020

The present work demonstrates a pioneering approach for the packaging of β-LG with improved stability in the presence of aqueous solutions containing cholinium-based ionic liquid mixtures.
Chemical regeneration of granular activated carbon: preliminary evaluation of alternative regenerant solutions
Authors: Larasati Amanda , Fowler Geoffrey D. , Graham Nigel J. D.
Published: June 2020

An adsorption and desorption study has been conducted using five organic compounds of different physico-chemical properties and four regenerant solutions to evaluate the feasibility of a novel on-site chemical regeneration of GAC.
Quantitative NaH catalytic hydroboration of aldimines
Authors: Kim Hanbi , Lee Ji Hye , Hwang Hyonseok , An Duk Keun
Published: June 2020

The catalytic hydroboration of aldimines was demonstrated, with only 3 mol% NaH required for the quantitative production of secondary amines under minimal solvent conditions.
Photo-to-thermal conversion: effective utilization of futile solid-state carbon quantum dots (CQDs) for energy harvesting applications
Authors: Sahadev Nishaina , Anappara Aji A.
Published: June 2020

Dominant non-radiative electronic de-excitation in fluorescence quenched CQDs in the solid state results in excellent photo-to-thermal transduction in the system.
DFT studies on the reaction mechanism for the selective oxidative dehydrogenation of light alkanes by BN catalysts
Authors: Li Anlin , Tian Dongxu , Zhao Zhibing
Published: June 2020

The oxidative dehydrogenation (ODH) reaction mechanism of ethane and propane catalyzed by two kinds of oxygen-species-terminated BN materials, namely BN nanotubes and h-BN, was studied by the B3LYP-D3 functional with the 6-31G(d,p) basis set.
Hot off the Press
Authors: Hill Robert A. , Sutherland Andrew
Published: June 2020

A personal selection of 32 recent papers is presented covering various aspects of current developments in bioorganic chemistry and novel natural products such as sporormielone A from a Sporormiella species.
Light-induced one-pot synthesis of pyrimidine derivatives from vinyl azides
Authors: Nguyen Tuan K. , Titov Gleb D. , Khoroshilova Olesya V. , Kinzhalov Mikhail A. , Rostovskii Nikolai V.
Published: June 2020

A one-pot synthesis of tetrasubstituted dihydropyrimidine and pyrimidine derivatives was developed on the basis of UV-LED photolysis of α-azidocinnamates as a key stage.
Hollow carbon nanospheres: syntheses and applications for post lithium-ion batteries
Authors: Luo Jin-Min , Sun Yong-Gang , Guo Si-Jie , Xu Yan-Song , Chang Bao-Bao , Liu Chun-Tai , Cao An-Min , Wan Li-Jun
Published: June 2020

We summarized the recent progress in the synthesis approaches and representative applications of hollow carbon nanospheres, especially focused on the shape control mechanism and the unique capability as anode materials of post LIBs technologies.
Sustainable production of nano α-Fe2O3/N-doped biochar hybrid nanosheets for supercapacitors
Authors: Li Panyu , Xie Hongyang , Wang Xuqian , Xie Yi , Wang Yabo , Zhang Yongkui
Published: June 2020

Nano α-Fe2O3/N-doped biochar nanosheets were successfully fabricated from biomass waste through a facile, scalable and environmentally friendly molten salt route.
Production of fatty alcohols from non-edible oils by enzymatic cascade reactions
Authors: Ma Yunjian , Zhang Xizhen , Li Yongru , Li Peilin , Hollmann Frank , Wang Yonghua
Published: June 2020

A biocatalytic cascade transforming castor oil into (R,Z)-octadec-9-en-7-ol is presented by combining a lipase catalysed hydrolysis of castor oil into ricinoleic acid followed by a photoenzymatic decarboxylation into (R,Z)-octadec-9-en-7-ol.
Building an artificial solid electrolyte interphase with high-uniformity and fast ion diffusion for ultralong-life sodium metal anodes
Authors: Chen Qianwen , He Heng , Hou Zhen , Zhuang Weiman , Zhang Tianxu , Sun Zongzhao , Huang Limin
Published: June 2020

An artificial SEI consisting of an Na–Sn alloy and NaCl layer possesses high-uniformity and fast ion diffusion, stabilizing Na metal anodes.
pH and singlet oxygen dual-responsive GEM prodrug micelles for efficient combination therapy of chemotherapy and photodynamic therapy
Authors: Chen Liang , Zhuang Weihua , Hu Cheng , Yu Tao , Su Xin , Liang Zhen , Li Gaocan , Wang Yunbing
Published: June 2020

Nanocarriers have been an important strategy for enhancing the combination therapy of chemotherapy and photodynamic therapy (PDT) (Chem-PDT).
A moisturizing chitosan-silk fibroin dressing with silver nanoparticles-adsorbed exosomes for repairing infected wounds
Authors: Qian Zhiyong , Bai Yating , Zhou Jin , Li Linhao , Na Jing , Fan Yubo , Guo Ximin , Liu Haifeng
Published: June 2020

The CTS-SF/SA/Ag-Exo dressing possessed multifunctional properties including broad-spectrum antimicrobial activity, promoting wound healing, retaining moisture and maintaining electrolyte balance.