bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of fine atmospheric scales on ocean eddies and deep convection in the Subpolar Northern Atlantic
Authors: Verezemskaya P S , Barnier B , Gavrikov A V , Gulev S K , Molines-Marc J-M 
Published: November 2020

Abstract
In this study we examine the sensitivity of the high-resolution regional ocean model solution to the atmospheric forcing of low (70 km - LoRes) and high (14 km - HiRes) spatial resolutions over the North Atlantic. To force the regional set up of NEMO ocean general circulation model (OGCM) we use the North Atlantic Atmospheric Downscaling (NAAD) product, which is the result of the Weather Research and Forecasting (WRF) atmospheric GCM with ERA-Interim as a boundary condition. Increase of the of the resolution of the atmospheric forcing and thus, representation of the surface turbulent heat and radiative fluxes in HiRes and LoRes atmospheric forcing, cause the 1.5° negative difference between sea surface temperature and -0.15 PSU in sea water salinity over the whole domain. The output of the OGCM forced by the high-resolution atmosphere is almost equal to the observational datasets. More intensive turbulent heat loss from the ocean surface and ventilation processes result in lower ocean heat content in the upper ocean (0-700 m) and at intermediate depth (700-1500 m) when the model is forced by HiRes. HiRes-driven experiment shows more intense coastal currents and less intensive large-scale currents. Ventilation processes are sensitive to the mesoscale atmospheric events representation: HiRes experiment provides deeper by 100 m mixed layer depths and its later in time deepening and restratification.
Controllable singular skeleton formation by means of the Kummer optical-vortex diffraction at a rectilinear phase step
Authors: Bekshaev Aleksandr , Chernykh Aleksey , Khoroshun Anna , Masajada Jan , Popiołek-Masajada Agnieszka , Riazantsev Andrii 
Published: November 2020

Abstract
We study positions and morphology of optical vortices (OVs) within the field obtained after transmitting a circular single-charged OV-beam through the transparent screen with a rectilinear π-phase step. Experimental results are obtained with the help of a programmable spatial light modulator which is used for the Kummer beam formation and for introduction of the π-step phase difference at a desirable position within the incident beam cross section. The theory based on the Kirchhoff–Fresnel approximation shows a good agreement with the experimental data; peculiar features of the Kummer beam diffraction are elucidated in the course of confrontation against the results involving the Laguerre–Gaussian beam model with the same transverse size and spherical wavefront component. The diffracted field contains a system of interacting OVs (singular skeleton) which demonstrate a regular evolution (migration) within the diffracted beam cross section while the π-phase step translates across the incident beam; depending on the step position, new OV pairs may emerge and/or annihilate in the topological reactions. The morphology parameters of the separate diffracted-field OVs (orientations and form-factors of the near-core equal-intensity ellipses) also depend on the stage of the OV evolution and indicate conditions favorable for the efficient trapping and guiding of microparticles. The results may be useful for the diagnostics of OVs, experimental measurements of phase objects and in micromanipulation techniques.
Geometric treatment of the radiation captured by the Large Millimeter Telescope (LMT/GTM) and ronchigrams at the caustic region for a static source
Authors: González-Juárez Adriana , Silva-Ortigoza Gilberto , Espíndola-Ramos Ernesto 
Published: November 2020

Abstract
The aim of the present work is to determine the reflected light rays, wavefronts, caustic and the ronchigram associated with the reflection phenomenon of a plane wave on a parabolic mirror, in particular on the parabolic antenna of the Large Millimeter Telescope (LMT/GTM). The results presented here are general in the sense that the incident plane wavefront has an arbitrary direction

I
ˆ

(
α
,
β
)

, determined by the angles α and β. We present numerical results for two different cases: (

α
=
π

/

200
,
β
=
0

) and (

α
=
π

/

10
,
β
=
0

). From these results we find that in general the caustic is a surface with a stable singularity of a hyperbolic umbilic type. For these cases we compute the distribution of the reflected light rays at some representative planes, determined by the form and dimensions of the caustic, then assuming that the ronchigrating is placed at those representative planes we compute the associated ronchigram. These results are important because they could describe the behavior of the light emitted by a static pointlike source located far away in the Universe.
Plasmonic properties of folded graphene nanodisks
Authors: Zhang Rui , Wang Shengchuan , You Bin , Han Kui , Shen Xiaopeng , Wang Weihua 
Published: November 2020

Abstract
Graphene and its relatives, such as bilayer and trilayer graphene, are promising plasmonic materials. Very recently, graphene has been demonstrated to be precisely folded (Chen et al 2019 Science
365 1036–40), thus folded graphene provides another appealing platform for plasmonics. In folded graphene nanodisks, we find fundamental dipole modes (DMs) will exhibit mode splitting, with one parallel and another perpendicular to the folding axis. The two DMs show differences in field patterns and folding angle dependence, but they both can be tuned by the size of structures and the Fermi level of graphene. Some interesting high order modes are introduced as well, which can be further engineered by folding. Our studies enrich the current research of graphene plasmonics, and pave the way for particular plasmonic device applications.
Polarized plasmon resonance spectra of electrochemically modified titanium surfaces with gold nanoparticles
Authors: Tcibulnikova Anna V , Khankaev Artemii A , Samusev Ilia G , Slezhkin Vasily A , Bryukhanov Valery V , Demin Maxim V , Myslitskaya Natalia A , Lyatun Ivan I , Medvedskaya Polina N 
Published: November 2020

Abstract
In this paper, the plasmon resonance on electrochemically modified titanium surfaces synthesized by anodic dissolution method has been studied in the presence with gold ablative nanoparticles. The permittivity functions and reflection coefficients of p- and s-polarized light spectra on the titanium oxide surface of various modification (roughness) have been analyzed. Spectral features of the negative refractive index in the area of surface plasmon generation on the rough titanium-oxide film interface have been also presented in this paper.
Experimental comparison of four nonlinear magnetic detection methods and considerations on clinical usability
Authors: van de Loosdrecht M M , Abelmann L , ten Haken B 
Published: November 2020

Abstract
Superparamagnetic iron oxide nanoparticles (SPIONs) are promising for clinical applications, because they have a characteristic nonlinear magnetic response when an external magnetic field is applied. This nonlinearity enables the distinct detection of SPIONs and makes measurements less sensitive to the human body and surgical steel instruments. In clinical applications, only a limited field strength for the magnetic detection is allowed. The signal to noise ratios (SNRs) of four nonlinear magnetic detection methods are compared. These methods include differential magnetometry and three variations of magnetic particle spectroscopy: frequency mixing, second harmonic detection and third harmonic detection. All methods were implemented on the same hardware and experimentally compared for various field strengths. To make the comparison fair, the same power was supplied to the excitation coil each time. In general, the SNR increases with increasing field strength. The SNR per drive field of all methods stabilizes or even decreases for field strengths above 6 mT. The second harmonic detection has the best SNR and the most room for improvement.
Erosion research of CX-2002U carbon composites under low-temperature high-flux hydrogen plasma
Authors: GUO Hengxin , YE Zongbiao , SHEN Bizhou , WEI Jianjun , WANG Bo , LUO Yuchuan , ZHANG Kun , GOU Fujun , CHEN Jianjun , CHEN Bo 
Published: November 2020

Abstract
The net erosion yield of CX-2002U carbon fiber composites under high-flux low-temperature hydrogen plasma is investigated using a linear plasma device. It is found that the net erosion yield decreases rapidly first, and then tends to saturate with the increase of hydrogen–plasma flux. When the temperature of the sample eroded by hydrogen plasma is above 300 °C, the hybridization of electrons outside the carbon atom would change. Then the carbon atoms combine with hydrogen atoms to form massive spherical nanoparticles of hydrocarbon compounds and deposit on the surface at the flux condition of 1.77 × 1022 m−2·s−1. Under the irradiation of hydrogen plasma loaded with negative bias, the surface morphology of the matrix carbon is changed dramatically. Moreover, the energy dependence of mass loss does not increase in proportion to the increase of hydrogen–plasma energy, but reaches a peak around 20 V negative bias voltage. Based on the analysis of different samples, it can be concluded that the enhancement of energy could make a contribution to chemical erosion and enlarge the size of pores existing on the surface.
Adhesional rolling behavior of micro-cylinder: Experimental observation of adhesional contacts and measurement of critical rolling resistance
Authors: Taoka Yuki , Watanabe Taihei , Iguchi Yoji , Hemthavy Pasomphone , Takahashi Kunio , Saito Shigeki 
Published: November 2020

Abstract
There has been much research offering theoretical explanations of rolling behavior considering the effect of adhesion, which is essential when the object is small. However, there has been a shortage of experimental verifications because objects are too small to manipulate and observe directly. This study measured the moment and observed the contact area before, during, and after rolling with an experimental setup on a relatively large scale. The experiment setup consisted of two glass cylinders which were placed in between two PDMS blocks. This paper reports three main findings: the results suggest that viscosity influences the transition of states of the contact. The critical rolling resistance is dependent on the radius of the cylinders and the applied weight to the cylinders. The results support the theoretical expectation of the value of a critical rolling resistance, which is the product of the radius of the cylinders and the work of adhesion. This study offers experimental foundations to develop theories of rolling of micro-cylinders.
Plastome phylogenomics ofCephalotaxus(Cephalotaxaceae) and allied genera
Authors: Ji Yunheng , Liu Changkun , Landis Jacob B , Deng Min , Chen Jiahui 
Published: November 2020

AbstractBackground and AimsCephalotaxus is a paleo-endemic genus in East Asia that consists of about 7–9 conifer species. Despite its great economic and ecological importance, the relationships between Cephalotaxus and related genera, as well as the interspecific relationships within Cephalotaxus, have long been controversial, resulting in contrasting taxonomic proposals in delimitation of Cephalotaxaceae and Taxaceae. Based on plastome data, this study aims to reconstruct a robust phylogeny to infer the systematic placement and the evolutionary history of Cephalotaxus.MethodsA total of 11 plastomes, representing all species currently recognized in Cephalotaxus and two Torreya species, were sequenced and assembled. Combining these with previously published plastomes, we reconstructed a phylogeny of Cephalotaxaceae and Taxaceae with nearly full taxonomic sampling. Under a phylogenetic framework and molecular dating, the diversification history of Cephalotaxus and allied genera was explored.Key ResultsPhylogenetic analyses of 81 plastid protein-coding genes recovered robust relationships between Cephalotaxus and related genera, as well as providing a well-supported resolution of interspecific relationships within Cephalotaxus, Taxus, Torreya and Amentotaxus. Divergence time estimation indicated that most extant species of these genera are relatively young, although fossil and other molecular evidence consistently show that these genera are ancient plant lineages.ConclusionsOur results justify the taxonomic proposal that recognizes Cephalotaxaceae as a monotypic family, and contribute to a clear-cut delineation between Cephalotaxaceae and Taxaceae. Given that extant species of Cephalotaxus are derived from recent divergence events associated with the establishment of monsoonal climates in East Asia and Pleistocene climatic fluctuations, they are not evolutionary relics.
Deciphering RNA modifications at base resolution: from chemistry to biology
Authors: Debnath Turja K , Xhemalçe Blerta 
Published: November 2020

Abstract
Nearly 200 distinct chemical modifications of RNAs have been discovered to date. Their analysis via direct methods has been possible in abundant RNA species, such as ribosomal, transfer or viral RNA, since several decades. However, their analysis in less abundant RNAs species, especially cellular messenger RNAs, was rendered possible only recently with the advent of high throughput sequencing techniques. Given the growing biomedical interest of the proteins that write, erase and read RNA modifications, ingenious new methods to enrich and identify RNA modifications at base resolution have been implemented, and more efforts are underway to render them more quantitative. Here, we review several crucial modification-specific (bio)chemical approaches and discuss their advantages and shortcomings for exploring the epitranscriptome.
Rapid screening and detection of inter-type viral recombinants using phylo-k-mers
Authors: Scholz Guillaume E , Linard Benjamin , Romashchenko Nikolai , Rivals Eric , Pardi Fabio 
Published: November 2020

Abstract

Motivation
Novel recombinant viruses may have important medical and evolutionary significance, as they sometimes display new traits not present in the parental strains. This is particularly concerning when the new viruses combine fragments coming from phylogenetically distinct viral types. Here, we consider the task of screening large collections of sequences for such novel recombinants. A number of methods already exist for this task. However, these methods rely on complex models and heavy computations that are not always practical for a quick scan of a large number of sequences.

Results
We have developed SHERPAS, a new program to detect novel recombinants and provide a first estimate of their parental composition. Our approach is based on the precomputation of a large database of ‘phylogenetically-informed k-mers’, an idea recently introduced in the context of phylogenetic placement in metagenomics. Our experiments show that SHERPAS is hundreds to thousands of times faster than existing software, and enables the analysis of thousands of whole genomes, or long-sequencing reads, within minutes or seconds, and with limited loss of accuracy.

Availability and implementation
The source code is freely available for download at https://github.com/phylo42/sherpas.

Supplementary information
Supplementary data are available at Bioinformatics online.
Recent diversification in the high Andes: unveiling the evolutionary history of the Ecuadorian hillstar,Oreotrochilus chimborazo(Apodiformes: Trochilidae)
Authors: Bonaccorso Elisa , Rodríguez-Saltos Carlos A , Freile Juan F , Peñafiel Nicolás , Rosado-Llerena Laura , Oleas Nora H 
Published: November 2020

AbstractStudying the genetic signatures of evolutionary diversification in young lineages is among the most promising approaches for unveiling the processes behind speciation. Here, we focus on Oreotrochilus chimborazo, a high Andean species of hummingbird that might have experienced rapid diversification in the recent past. To understand the evolution of this species, we generated a dataset of ten microsatellite markers and complementary data on morphometrics, plumage variation and ecological niches. We applied a series of population and coalescent-based analyses to understand the population structure and differentiation within the species, in addition to the signatures of current and historical gene flow, the location of potential contact zones and the relationships among lineages. We found that O. chimborazo comprises three genetic groups: one corresponding to subspecies O. c. chimborazo, from Chimborazo volcano and surroundings, and two corresponding to the northern and southern ranges of subspecies O. c. jamesonii, found from the extreme south of Colombia to southern Ecuador. We inferred modest levels of both contemporary and historical gene flow and proposed the location of a contact zone between lineages. Also, our coalescent-based analyses supported a rapid split among these three lineages during the mid-to-late Holocene. We discuss our results in the light of past and present potential distributions of the species, in addition to evolutionary trends seen in other Andean hummingbirds.
Pollination in thecampo rupestre: a test of hypothesis for an ancient tropical mountain vegetation
Authors: Monteiro Beatriz Lopes , Camargo Maria Gabriela Gutierrez , Loiola Priscilla De Paula , Carstensen Daniel Wisbech , Gustafsson Simone , Morellato Leonor Patricia Cerdeira 
Published: November 2020

AbstractThe campo rupestre is a Neotropical OCBIL (old, climatically buffered infertile landscape), a grassy-shrub vegetation with high species richness and endemism, characterized by rocky outcrops surrounded by grasslands distributed in South American ancient mountaintops. We tested one OCBIL prediction: the prevalence of long-distance pollinators ensuring cross-pollination across the archipelago-like landscapes of the campo rupestre. We described the pollination systems and tested whether their frequency differed across vegetation types and elevation, focusing on long-distance systems. We performed non-systematic and systematic surveys of plants and plant-pollinator interactions across the elevation gradient and vegetation types. We also reviewed the literature on campo rupestre pollination and applied an accuracy criterion to infer 11 pollination systems. The bee system was split into large bee (long-distance) and small bee (shorter distances) to test the prevalence of long-distance pollination systems. We surveyed 413 pollinator species, mostly bees (220) and flies (69). Among the 636 plant species studied, the bee pollination system was dominant (56%), followed by wind and hummingbird. Wind, small-bee and fly pollination systems increased with elevation, and small-bee and wind pollination systems prevailed in grasslands. Large-bee and hummingbird long-distance pollination systems remained unchanged with elevation and were more frequent in the highly isolated rocky outcrops corroborating the OCBIL theory.
Ecomorphological divergence and trophic resource partitioning in 15 syntopic Indo-Pacific parrotfishes (Labridae: Scarini)
Authors: Nicholson Georgina M , Clements Kendall D 
Published: November 2020

AbstractAdaptive diversification is a product of both phylogenetic constraint and ecological opportunity. The species-rich parrotfish genera Scarus and Chlorurus display considerable variation in trophic cranial morphology, but these parrotfishes are often described as generalist herbivores. Recent work has suggested that parrotfish partition trophic resources at very fine spatial scales, raising the question of whether interspecific differences in cranial morphology reflect trophic partitioning. We tested this hypothesis by comparing targeted feeding substrata with a previously published dataset of nine cranial morphological traits. We sampled feeding substrata of 15 parrotfish species at Lizard Island, Great Barrier Reef, Australia, by following individuals until focused biting was observed, then extracting a bite core 22 mm in diameter. Three indices were parameterized for each bite core: substratum taphonomy, maximum turf height and cover of crustose coralline algae. Parrotfish species were spread along a single axis of variation in feeding substrata: successional status of the substratum taphonomy and epilithic and endolithic biota. This axis of trophic variation was significantly correlated with cranial morphology, indicating that morphological disparity within this clade is associated with interspecific partitioning of feeding substrata. Phylogenetic signal and phylomorphospace analyses revealed that the evolution of this clade involved a hitherto-unrecognized level of trophic diversification.
Transcranial magnetic stimulation reveals diminished homoeostatic metaplasticity in cognitively impaired adults
Authors: Sundman Mark H , Lim Koeun , Ton That Viet , Mizell Jack-Morgan , Ugonna Chidi , Rodriguez Rudolph , Chen Nan-Kuei , Fuglevand Andrew J , Liu Yilin , Wilson Robert C , Fellous Jean-Marc , Rapcsak Steven , Chou Ying-Hui 
Published: November 2020

AbstractHomoeostatic metaplasticity is a neuroprotective physiological feature that counterbalances Hebbian forms of plasticity to prevent network destabilization and hyperexcitability. Recent animal models highlight dysfunctional homoeostatic metaplasticity in the pathogenesis of Alzheimer’s disease. However, the association between homoeostatic metaplasticity and cognitive status has not been systematically characterized in either demented or non-demented human populations, and the potential value of homoeostatic metaplasticity as an early biomarker of cognitive impairment has not been explored in humans. Here, we report that, through pre-conditioning the synaptic activity prior to non-invasive brain stimulation, the association between homoeostatic metaplasticity and cognitive status could be established in a population of non-demented human subjects (older adults across cognitive spectrums; all within the non-demented range). All participants (n = 40; age range, 65–74, 47.5% female) underwent a standardized neuropsychological battery, magnetic resonance imaging and a transcranial magnetic stimulation protocol. Specifically, we sampled motor-evoked potentials with an input/output curve immediately before and after repetitive transcranial magnetic stimulation to assess neural plasticity with two experimental paradigms: one with voluntary muscle contraction (i.e. modulated synaptic activity history) to deliberately introduce homoeostatic interference, and one without to serve as a control condition. From comparing neuroplastic responses across these experimental paradigms and across cohorts grouped by cognitive status, we found that (i) homoeostatic metaplasticity is diminished in our cohort of cognitively impaired older adults and (ii) this neuroprotective feature remains intact in cognitively normal participants. This novel finding suggests that (i) future studies should expand their scope beyond just Hebbian forms of plasticity that are traditionally assessed when using non-invasive brain stimulation to investigate cognitive ageing and (ii) the potential value of homoeostatic metaplasticity in serving as a biomarker for cognitive impairment should be further explored.