Enriching Biomedical Knowledge for Vietnamese Low-resource Language Through Large-Scale Translation

Biomedical data and benchmarks are highly valuable yet very limited in low-resource languages other than English such as Vietnamese. In this paper, we make use of a state-of-the-art translation model in English-Vietnamese to translate and produce both pretrained as well as supervised data in the biomedical domains. Thanks to such large-scale translation, we introduce ViPubmedT5, a pretrained Encoder-Decoder Transformer model trained on 20 million translated abstracts from the high-quality public PubMed corpus. ViPubMedT5 demonstrates state-of-the-art results on two different biomedical benchmarks in summarization and acronym disambiguation. Further, we release ViMedNLI - a new NLP task in Vietnamese translated from MedNLI using the recently public En-vi translation model and carefully refined by human experts, with evaluations of existing methods against ViPubmedT5

Differentiating EDRs from the Background Magnetopause Current Sheet: A Statistical Study

The solar wind is a continuous outflow of charged particles from the Sun's atmosphere into the solar system. At Earth, the solar wind's outward pressure is balanced by the Earth's magnetic field in a boundary layer known as the magnetopause. Plasma density and temperature differences across the boundary layer generate the Chapman-Ferraro current which supports the magnetopause. Along the dayside magnetopause, magnetic reconnection can occur in electron diffusion regions (EDRs) embedded into the larger ion diffusion regions (IDRs). These diffusion regions form when opposing magnetic field lines in the solar wind and Earth's magnetic field merge, releasing magnetic energy into the surrounding plasma. While previous studies have given us a general understanding of the structure of the diffusion regions, we still do not have a good grasp of how they are statistically differentiated from the non-diffusion region magnetopause. By investigating 251 magnetopause crossings from NASA's Magnetospheric Multiscale (MMS) Mission, we demonstrate that EDR magnetopause crossings show current densities an order of magnitude higher than regular magnetopause crossings - crossings that either passed through the reconnection exhausts or through the non-reconnecting magnetopause, providing a baseline for the magnetopause current sheet under a wide range of driving conditions. Significant current signatures parallel to the local magnetic field in EDR crossings are also identified, which is in contrast to the dominantly perpendicular current found in the regular magnetopause. Additionally, we show that the ion velocity along the magnetopause is highly correlated with a crossing's location, indicating the presence of magnetosheath flows inside the magnetopause

Can magnetotail reconnection produce the auroral intensities observed in the conjugate ionosphere?

[1] In a recent case study, Borg et al. (2007) reported that an inverted V structure, caused by a field-aligned potential drop of 30 kV producing very strong X-ray aurora, was found in connection with tail reconnection. However, the in situ particle measurements indicated clearly that the particles responsible for the X-ray aurora were not accelerated by the reconnection process. In this article, we report the predicted auroral intensities of thirteen reconnection events where Cluster passed through the reconnection region. For six of the events, global auroral imaging data were available and the predicted auroral intensities could be compared with the observed intensities. Our main findings are as follows: (1) Acceleration in the reconnection region is generally not sufficient to account for the observed auroral intensities. (2) Additional acceleration between the reconnection region and the ionosphere is needed to explain the auroral intensities. Although we see signatures that point toward potential drops at the flanks of bursty bulk flows (BBFs), we also find signatures of Alfvén wave accelerated electrons at 700 km and we are not able to determine the most likely acceleration mechanism. (3) The reconnection events are observed 2–14 min after substorm onset and indicate that reconnection is an expanding process observed along the poleward boundary of the aurora.publishedVersio

Transport Mechanism of Guest Methane in Water-Filled Nano-Pores

We computed the transport of methane through 1 nm wide slit-shaped pores carved out of selected solid substrates using classical molecular dynamics simulations. The transport mechanism was elucidated via the implementation of the well-tempered metadynamics algorithm, which allowed for the quantification and visualization of the free energy landscape sampled by the guest molecule. Models for silica, magnesium oxide, alumina, muscovite, and calcite were used as solid substrates. Slit-shaped pores of width 1 nm were carved out of these materials and filled with liquid water. Methane was then inserted at low concentration. The results show that the diffusion of methane through the hydrated pores is strongly dependent on the solid substrate. While methane molecules diffuse isotropically along the directions parallel to the pore surfaces in most of the pores considered, anisotropic diffusion was observed in the hydrated calcite pore. The differences observed in the various pores are due to local molecular properties of confined water, including molecular structure and solvation free energy. The transport mechanism and the diffusion coefficients are dependent on the free energy barriers encountered by one methane molecule as it migrates from one preferential adsorption site to a neighboring one. It was found that the heterogeneous water distribution in different hydration layers and the low free energy pathways in the plane parallel to the pore surfaces yield the anisotropic diffusion of methane molecules in the hydrated calcite pore. Our observations contribute to an ongoing debate on the relation between local free energy profiles and diffusion coefficients and could have important practical consequences in various applications, ranging from the design of selective membranes for gas separations to the sustainable deployment of shale gas

Electron Behavior Around the Onset of Magnetic Reconnection

We investigate the onset of magnetic reconnection, utilizing a fully kinetic Particle-In-Cell (PIC) simulation. Characteristic features of the electron phase-space distributions immediately before reconnection onset are identified. These include signatures of pressure non-gyrotropy in the velocity distributions, and lemon shaped distributions in the in-plane velocity directions. Further, we explain how these features form through particle energization by the out-of-plane electric field. Identification of these features in the distributions can aid in analysis of data where clear signatures of ongoing reconnection are not yet present.publishedVersio

Clustering of magnetic reconnection exhausts in the solar wind: An automated detection study

CONTEXT: Magnetic reconnection is a fundamental process in astrophysical plasmas that enables the dissipation of magnetic energy at kinetic scales. Detecting this process in situ is therefore key to furthering our understanding of energy conversion in space plasmas. However, reconnection jets typically scale from seconds to minutes in situ, and as such, finding them in the decades of data provided by solar wind missions since the beginning of the space era is an onerous task. AIMS: In this work, we present a new approach for automatically identifying reconnection exhausts in situ in the solar wind. We apply the algorithm to Solar Orbiter data obtained while the spacecraft was positioned at between 0.6 and 0.8 AU and perform a statistical study on the jets we detect. METHODS: The method for automatic detection is inspired by the visual identification process and strongly relies on the Walén relation. It is enhanced through the use of Bayesian inference and physical considerations to detect reconnection jets with a consistent approach. RESULTS: Applying the detection algorithm to one month of Solar Orbiter data near 0.7 AU, we find an occurrence rate of seven jets per day, which is significantly higher than in previous studies performed at 1 AU. We show that they tend to cluster in the solar wind and are less likely to occur in the tenuous solar wind (< 10 cm−3 near 0.7 AU). We discuss why the source and the degree of Alfvénicity of the solar wind might have an impact on magnetic reconnection occurrence. CONCLUSIONS: By providing a tool to quickly identify potential magnetic reconnection exhausts in situ, we pave the way for broader statistical studies on magnetic reconnection in diverse plasma environments

Electron inflow velocities and reconnection rates at earth's magnetopause and magnetosheath

Electron inflow and outflow velocities during magnetic reconnection at and near the dayside magnetopause are measured using satellites from NASA's Magnetospheric Multiscale (MMS) mission. A case study is examined in detail, and three other events with similar behavior are shown, with one of them being a recently published electron-only reconnection event in the magnetosheath. The measured inflow speeds of 200–400 km/s imply dimensionless reconnection rates of 0.05–0.25 when normalized to the relevant electron Alfvén speed, which are within the range of expectations. The outflow speeds are about 1.5–3 times the inflow speeds, which is consistent with theoretical predictions of the aspect ratio of the inner electron diffusion region. A reconnection rate of 0.04 ± 25% was obtained for the case study event using the reconnection electric field as compared to the 0.12 ± 20% rate determined from the inflow velocity.publishedVersio

Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants. © 2014 Macmillan Publishers Limited. All rights reserved