bluuebunny/crossref_metadata_2025_split huggingface dataset:
The importance of Antarctic krill in biogeochemical cycles
Authors: Cavan E. L. , Belcher A. , Atkinson A. , Hill S. L. , Kawaguchi S. , McCormack S. , Meyer B. , Nicol S. , Ratnarajah L. , Schmidt K. , Steinberg D. K. , Tarling G. A. , Boyd P. W. 
Published: October 2019

AbstractAntarctic krill (Euphausia superba) are swarming, oceanic crustaceans, up to two inches long, and best known as prey for whales and penguins – but they have another important role. With their large size, high biomass and daily vertical migrations they transport and transform essential nutrients, stimulate primary productivity and influence the carbon sink. Antarctic krill are also fished by the Southern Ocean’s largest fishery. Yet how krill fishing impacts nutrient fertilisation and the carbon sink in the Southern Ocean is poorly understood. Our synthesis shows fishery management should consider the influential biogeochemical role of both adult and larval Antarctic krill.
Revealing neural correlates of behavior without behavioral measurements
Authors: Rubin Alon , Sheintuch Liron , Brande-Eilat Noa , Pinchasof Or , Rechavi Yoav , Geva Nitzan , Ziv Yaniv 
Published: October 2019

AbstractMeasuring neuronal tuning curves has been instrumental for many discoveries in neuroscience but requires a priori assumptions regarding the identity of the encoded variables. We applied unsupervised learning to large-scale neuronal recordings in behaving mice from circuits involved in spatial cognition and uncovered a highly-organized internal structure of ensemble activity patterns. This emergent structure allowed defining for each neuron an ‘internal tuning-curve’ that characterizes its activity relative to the network activity, rather than relative to any predefined external variable, revealing place-tuning and head-direction tuning without relying on measurements of place or head-direction. Similar investigation in prefrontal cortex revealed schematic representations of distances and actions, and exposed a previously unknown variable, the ‘trajectory-phase’. The internal structure was conserved across mice, allowing using one animal’s data to decode another animal’s behavior. Thus, the internal structure of neuronal activity itself enables reconstructing internal representations and discovering new behavioral variables hidden within a neural code.
Trisomy 21 activates the kynurenine pathway via increased dosage of interferon receptors
Authors: Powers Rani K. , Culp-Hill Rachel , Ludwig Michael P. , Smith Keith P. , Waugh Katherine A. , Minter Ross , Tuttle Kathryn D. , Lewis Hannah C. , Rachubinski Angela L. , Granrath Ross E. , Carmona-Iragui María , Wilkerson Rebecca B. , Kahn Darcy E. , Joshi Molishree , Lleó Alberto , Blesa Rafael , Fortea Juan , D’Alessandro Angelo , Costello James C. , Sullivan Kelly D. , Espinosa Joaquin M. 
Published: October 2019

AbstractTrisomy 21 (T21) causes Down syndrome (DS), affecting immune and neurological function by ill-defined mechanisms. Here we report a large metabolomics study of plasma and cerebrospinal fluid, showing in independent cohorts that people with DS produce elevated levels of kynurenine and quinolinic acid, two tryptophan catabolites with potent immunosuppressive and neurotoxic properties, respectively. Immune cells of people with DS overexpressIDO1, the rate-limiting enzyme in the kynurenine pathway (KP) and a known interferon (IFN)-stimulated gene. Furthermore, the levels of IFN-inducible cytokines positively correlate with KP dysregulation. Using metabolic tracing assays, we show that overexpression ofIFNreceptors encoded on chromosome 21 contribute to enhanced IFN stimulation, thereby causingIDO1overexpression and kynurenine overproduction in cells with T21. Finally, a mouse model of DS carrying triplication of IFN receptors exhibits KP dysregulation. Together, our results reveal a mechanism by which T21 could drive immunosuppression and neurotoxicity in DS.
Green oxidation of indoles using halide catalysis
Authors: Xu Jun , Liang Lixin , Zheng Haohao , Chi Yonggui Robin , Tong Rongbiao 
Published: October 2019

AbstractOxidation of indoles is a fundamental organic transformation to deliver a variety of synthetically and pharmaceutically valuable nitrogen-containing compounds. Prior methods require the use of either organic oxidants (meta-chloroperoxybenzoic acid, N-bromosuccinimide,t-BuOCl) or stoichiometric toxic transition metals [Pb(OAc)4, OsO4, CrO3], which produced oxidant-derived by-products that are harmful to human health, pollute the environment and entail immediate purification. A general catalysis protocol using safer oxidants (H2O2, oxone, O2) is highly desirable. Herein, we report a unified, efficient halide catalysis for three oxidation reactions of indoles using oxone as the terminal oxidant, namely oxidative rearrangement of tetrahydro-β-carbolines, indole oxidation to 2-oxindoles, and Witkop oxidation. This halide catalysis protocol represents a general, green oxidation method and is expected to be used widely due to several advantageous aspects including waste prevention, less hazardous chemical synthesis, and sustainable halide catalysis.
Multidecade Mortality and a Homolog of Hepatitis C Virus in Bald Eagles (Haliaeetus leucocephalus), the National Bird of the USA
Authors: Goldberg Tony L. , Sibley Samuel D. , Pinkerton Marie E. , Dunn Christopher D. , Long Lindsey J. , White LeAnn C. , Strom Sean M. 
Published: October 2019

AbstractThe bald eagle (Haliaeetus leucocephalus) once experienced near-extinction but has since rebounded. For decades, bald eagles near the Wisconsin River, USA, have experienced a lethal syndrome with characteristic clinical and pathological features but unknown etiology. Here, we describe a novel hepacivirus-like virus (Flaviviridae: Hepacivirus) identified during an investigation of Wisconsin River eagle syndrome (WRES). Bald eagle hepacivirus (BeHV) belongs to a divergent clade of avian viruses that share features with members of the genera Hepacivirus and Pegivirus. BeHV infected 31.9% of eagles spanning 4,254 km of the coterminous USA, with negative strand viral RNA demonstrating active replication in liver tissues. Eagles from Wisconsin were approximately 10-fold more likely to be infected than eagles from elsewhere. Eagle mitochondrial DNA sequences were homogeneous and geographically unstructured, likely reflecting a recent population bottleneck, whereas BeHV envelope gene sequences showed strong population genetic substructure and isolation by distance, suggesting localized transmission. Cophylogenetic analyses showed no congruity between eagles and their viruses, supporting horizontal rather than vertical transmission. These results expand our knowledge of the Flaviviridae, reveal a striking pattern of decoupled host/virus coevolution on a continental scale, and highlight knowledge gaps about health and conservation in even the most iconic of wildlife species.
Testing the competition-colonization trade-off and its correlations with functional trait variations among subtropical tree species
Authors: Bin Yue , Lin Guojun , Russo Sabrina E. , Huang Zhongliang , Shen Yong , Cao Honglin , Lian Juyu , Ye Wanhui 
Published: October 2019

AbstractThe competition-colonization trade-off, by which species can partition spatial niches, is a potentially important mechanism allowing the maintenance of species diversity in plant communities. We examined whether there was evidence for this trade-off among tree species in a subtropical forest and how it correlated with eight functional traits. We developed and estimated a metric for colonization ability that incorporates both fecundity and seed dispersal based on seed trap data and the sizes and distributions of adult trees. Competitive ability was estimated as survival probability under high crowding conditions based on neighborhood models. Although we found no significant relationship between colonization and competitive abilities, there was a significant negative correlation between long distance dispersal ability and competitive ability at the 5 cm size class. Colonizers had traits associated with faster growth, such as large leaves and low leaf lamina density, whereas competitors had traits associated with higher survival, such as dense wood. Our results imply that any trade-off between competition and colonization may be more determined by dispersal ability than by fecundity, suggesting that seed dispersal is an important contributor to diversity maintenance. Future work should test how competitive ability covaries with the components of colonization ability, as we did here.
Relationship between Vision-Related Quality of Life and Central 10° of the Binocular Integrated Visual Field in Advanced Glaucoma
Authors: Yamazaki Yoshio , Sugisaki Kenji , Araie Makoto , Murata Hiroshi , Kanamori Akiyasu , Inoue Toshihiro , Ishikawa Shinichiro , Yoshikawa Keiji , Maeda Hidetaka , Yamada Yuko , Negi Akira , Inatani Masaru , Tanihara Hidenobu , Okinami Satoshi , Mizuki Kenji , Mishima Koichi , Uchida Kenichi , Matsumoto Shun 
Published: October 2019

AbstractTo investigate the relationships between sensitivity loss in various subfields of the central 10° of the binocular integrated visual field (IVF) and vision-related quality of life (VRQoL) in 172 patients with advanced glaucoma. Using the Random Forest algorithm, which controls for inter-correlations among various subfields of the IVF, we analysed the relationships among the Rasch analysis-derived person ability index (RADPAI), age, best-corrected visual acuity (BCVA), mean total deviations (mTDs) of eight quadrant subfields in the IVF measured with the Humphrey Field Analyzer (HFA) 10-2 program (10-2 IVF), and mTDs of the upper/lower hemifields in the IVF measured with the HFA 24-2 program (24-2 IVF). Significant contributors to RADPAIs were as follows: the inner and outer lower-right quadrants of the 10-2 IVF contributed to the dining and total tasks; the lower-left quadrant of the 10-2 IVF contributed to the walking, going out and total tasks; the lower hemifield of the 24-2 IVF contributed to the walking, going out, dining, miscellaneous and total tasks; and BCVA contributed more to the letter, sentence, dressing and miscellaneous tasks than to others. The impact of damage in different 10-2 IVF subfields differed significantly across daily tasks in patients with advanced glaucoma.
Ultraviolet and Infrared luminescent Au-rich nanostructure growth in SiO2 by burrowing and inverse Oswald ripening process
Authors: Datta D. P. , Chettah A. , Maiti Arpan , Satpati B. , Sahoo P. K. 
Published: October 2019

AbstractWe study the evolution of nanoparticle morphology through successive stages when Au-Si bilayer on SiO2 is irradiated with 500 keV Xe-ions and resulting luminescence in the UV, Visible and infrared range. An array of nanoscale island morphology is developed on the silica surface in the initial stage of evolution which undergoes gradual burrowing in the silica matrix accompanied by elongation of large ones in the direction of incident ions under cumulative ion irradiation. Burrowing is found to occur in order to minimize the surface free energy of the nanoparticles. Numerical simulation based on the unified thermal spike model shows formation of molten latent tracks due to ions energy release which drive the dewetting of the metal layer and further give mobility to nanoparticle atoms leading to burrowing in the later stage of evolution and elongation of large nanoparticles. Satellite nanoparticles are observed to grow around Au nanoparticles embedded in silica through nucleation of Au atoms dissolved in the matrix by incident ions. The varying diameters of the Au satellite nanoparticles seem to result in luminescence in the UV and infrared range. The observed structure may find application in surface enhanced Raman scattering, catalysis, and LEDs.
Positive non-linear capacitance: the origin of the steep subthreshold-slope in ferroelectric FETs
Authors: Alam Md Nur K. , Roussel P. , Heyns M. , Van Houdt J. 
Published: October 2019

AbstractWe show that the non-linear positive capacitance (PC) of ferroelectrics (FE) can explain the steep subthreshold-slope (SS) observed in FE based MOSFETs and often attributed to the existence of a negative capacitance in FE capacitors. Physically attainable and unattainable regions of the S-shape curve used in the negative capacitance theory are investigated by self-consistently solving Landau-Khalatnikov and Maxwell equations and by experimental validation. Finally, the conditions for attaining a steep SS in FE based MOSFETs assuming only positive capacitances are discussed.
Laboratory Study Phenomenon of Coal and Gas Outburst Based on a Mid-scale Simulation System
Authors: Nie Baisheng , Ma Yankun , Hu Shoutao , Meng Junqing 
Published: October 2019

AbstractOutburst simulation experiments facilitate understanding coal and gas outburst in underground mining. With the help of the mid-scale simulation system, a model based on similitude principle, coal seam sandwiched by roof and floor, was constructed to conduct an outburst experiment. It had a three-dimensional size of 1500 mm × 600 mm × 1000 mm with 0.5 MPa gas pressure. The experimental procedures include specimen preparation, moulding, sealing, gas charging and adsorption, and completion. The outburst process was investigated by analyzing the gas pressure variation, temperature variation, outburst propagation velocity, particle size of outburst coal and energy transformation. During the experiment, each gas charging was accompanied with gas pressure or temperature fluctuation because of coal behavior of gas adsorption-desorption. The outburst propagation velocity was 17.2 m/s, obtained by a mass-weighted calculation of velocities of outburst coal. The small-size coal particles have a higher desorption rate and tend to participate in outburst process. According to energy conservation law, the energy forms of the outburst included elastic strain energy (Ee), gas expansion energy (Ep), internal energy of coal (ΔU), breakage work (W1), throwing out work (W2) and gas-flow loss energy (ΔE), and each was calculated respectively. Gas potential energy, including gas expansion energy and internal energy of coal, registered a larger percent and was far greater than the strain energy. And it can be the main factor influencing the occurrence of low-threshold outburst. The experimental system provides a feasible way to study the initiation and evolution of coal and gas outbursts.
Quantum speedup, non-Markovianity and formation of bound state
Authors: Ahansaz Bahram , Ektesabi Abbas 
Published: October 2019

AbstractIn this paper, we investigate the relationship between the quantum speedup, non-Markovianity and formation of a system-environment bound state. Previous results show a monotonic relation between these three such that providing bound states with more negative energy can lead to a higher degree of non-Markovianity, and hence to a greater speed of quantum evolution. By studying dynamics of a dissipative two-level system or a V-type three-level system, when similar and additional systems are present, we reveal that the quantum speedup is exclusively related to the formation of the system-environment bound state, while the non-Markovian effect of the system dynamics is neither necessary nor sufficient to speed up the quantum evolution. On the other hand, it is shown that only the formation of the system-environment bound state plays a decisive role in the acceleration of the quantum evolution.
Accuracy of proton magnetic resonance for diagnosing non-alcoholic steatohepatitis: a meta-analysis
Authors: Kim Tae-Hoon , Jeong Chang-Won , Jun Hong Young , Lee ChungSub , Noh SiHyeong , Kim Ji Eon , Kim SeungJin , Yoon Kwon-Ha 
Published: October 2019

AbstractLiver biopsy is the reference standard test to differentiate between non-alcoholic steatohepatitis (NASH) and simple steatosis (SS) in non-alcoholic fatty liver disease (NAFLD), but noninvasive diagnostics are warranted. The diagnostic accuracy in NASH using MR imaging modality have not yet been clearly identified. This study was assessed the accuracy of magnetic resonance imaging (MRI) method for diagnosing NASH. Data were extracted from research articles obtained after a literature search from multiple electronic databases. Random-effects meta-analyses were performed to obtain overall effect size of the area under the receiver operating characteristic(ROC) curve, sensitivity, specificity, likelihood ratios(LR), diagnostic odds ratio(DOR) of MRI method in detecting histopathologically-proven SS(or non-NASH) and NASH. Seven studies were analyzed 485 patients, which included 207 SS and 278 NASH. The pooled sensitivity was 87.4% (95% CI, 76.4–95.3) and specificity was 74.3% (95% CI, 62.4–84.6). Pooled positive LR was 2.59 (95% CI, 1.96–3.42) and negative LR was 0.17 (95% CI, 0.07–0.38). DOR was 21.57 (95% CI, 7.27–63.99). The area under the curve of summary ROC was 0.89. Our meta-analysis shows that the MRI-based diagnostic methods are valuable additions in detecting NASH.
An improved method for the calculation of unsaturated–saturated water flow by coupling the FEM and FDM
Authors: Gao Yulong , Pu Shengyan , Zheng Chunmiao , Yi Shuping 
Published: October 2019

AbstractNumerical modeling of water movement in both unsaturated soils and saturated groundwater aquifers is important for water resource management simulations. The development of efficient numerical algorithms for coupling unsaturated and saturated flow has been a long-lasting challenge in hydrologic modeling, especially for regional-scale modeling. In this study, a new method coupling the Finite Element Method (FEM) and Finite Difference Method (FDM), FE-FDM, is developed to solve Richards equation for simulating unsaturated–saturated water flow. The FEM is adopted to discretize the governing equation in the horizontal direction, while the FDM is used in the vertical direction. This method combines the advantages of FEM in domain discretization, especially for complex computational domain, and the advantages of FDM in modeling simplicity and efficiency. The validity of the new method is demonstrated with three test cases that show that the FE-FDM solutions are accurate and are applicable for regional scale problems. In the test cases, the FE-FDM solutions are compared with experimental data and numerical results calculated with common software packages including FEFLOW and COMSOL. This study verified that the FE-FDM is applicable for simulating water flow in the unsaturated–saturated zone.
X-ray phase contrast imaging of Vitis spp. buds shows freezing pattern and correlation between volume and cold hardiness
Authors: Kovaleski Alisson P. , Londo Jason P. , Finkelstein Kenneth D. 
Published: October 2019

AbstractGrapevine (Vitisspp.) buds must survive winter temperatures in order to resume growth when suitable conditions return in spring. They do so by developing cold hardiness through deep supercooling, but the mechanistic process of supercooling in buds remains largely unknown. Here we use synchrotron X-ray phase contrast imaging to study cold hardiness-related characteristics ofV. amurensis,V. riparia, andV. viniferabuds: time-resolved 2D imaging was used to visualize freezing; and microtomography was used to evaluate morphological changes during deacclimation. Bud cold hardiness was determined (low temperature exotherms; LTEs) using needle thermocouples during 2D imaging as buds were cooled with a N2gas cryostream. Resolution in 2D imaging did not allow for ice crystal identification, but freezing was assessed by movement of tissues coinciding with LTE values. Freezing was observed to propagate from the center of the bud toward the outer bud scales. The freezing events observed lasted several minutes. Additionally, loss of supercooling ability appears to be correlated with increases in bud tissue volume during the process of deacclimation, but major increases in volume occur after most of the supercooling ability is lost, suggesting growth resumption processes are limited by deacclimation state.
Storage media and not extraction method has the biggest impact on recovery of bacteria from the oral microbiome
Authors: Zhou Xiaoyan , Nanayakkara Shanika , Gao Jin-Long , Nguyen Ky-Anh , Adler Christina J. 
Published: October 2019

AbstractNext Generation sequencing has greatly progressed the exploration of the oral microbiome’s role in dental diseases, however, there has been little focus on the effect of sample storage conditions and their interaction with DNA extraction method. Dental plaque samples collected from 20 healthy participants were pooled and stored in either 75% ethanol or Bead solution for up to 6-months at −80 °C, prior to DNA extraction with either QIAamp (non-bead beating) or PowerSoil (bead-beating) kit, followed by Illumina sequencing of 16S rRNA gene. We found that storage media and not extraction method had the biggest influence on the diversity and abundance of the oral microbiota recovered. Samples stored in Bead solution, independent of the extraction kit, retrieved higher diversity (PowerSoil p = 1.64E-07, QIAamp p = 0.0085) and had dissimilar overall ecologies as indicated by lower level of shared diversity (PowerSoil p = 0.0000237, QIAamp p = 0.0088). Comparatively, samples stored in Bead solution and extracted with PowerSoil recovered a higher abundance of Streptococcus species. These data indicate that Bead solution can preserve the oral microbiome in dental plaque reliably, for periods of up to 6-months at −80 °C, and is compatible, with either a bead-beating or non-bead beating DNA extraction method.
Free-space data-carrying bendable light communications
Authors: Zhu Long , Wang Andong , Wang Jian 
Published: October 2019

AbstractBendable light beams have recently seen tremendous applications in optical manipulation, optical imaging, optical routing, micromachining, plasma generation and nonlinear optics. By exploiting curved light beams instead of traditional Gaussian beam for line-of-sight light communications, here we propose and demonstrate the viability of free-space data-carrying bendable light communications along arbitrary trajectories with multiple functionalities. By employing 39.06-Gbit/s 32-ary quadrature amplitude modulation (32-QAM) discrete multi-tone (DMT) signal, we demonstrate free-space bendable light intensity modulated direct detection (IM-DD) communication system under 3 different curved light paths. Moreover, we characterize multiple functionalities of free-space bendable light communications, including bypass obstructions transmission, self-healing transmission, self-broken trajectory transmission, and multi-receiver transmission. The observed results indicate that bendable light beams can make free-space optical communications more flexible, more robust and more multifunctional. The demonstrations may open a door to explore more special light beams enabling advanced free-space light communications with enhanced flexibility, robustness and functionality.