Deep dielectric charging of regolith within the Moon\u27s permanently shadowed regions

Abstract Energetic charged particles, such as galactic cosmic rays (GCRs) and solar energetic particles (SEPs), can penetrate deep within the lunar surface, resulting in deep dielectric charging. This charging process depends on the GCR and SEP currents, as well as on the regolith\u27s electrical conductivity and permittivity. In permanently shadowed regions (PSRs) near the lunar poles, the discharging timescales are on the order of a lunation (∼20 days). We present the first predictions for deep dielectric charging of lunar regolith. To estimate the resulting subsurface electric fields, we develop a data-driven, one-dimensional, time-dependent model. For model inputs, we use GCR data from the Cosmic Ray Telescope for the Effects of Radiation on board the Lunar Reconnaissance Orbiter and SEP data from the Electron, Proton, and Alpha Monitor on the Advanced Composition Explorer. We find that during the recent solar minimum, GCRs create persistent electric fields up to ∼700 V/m. We also find that large SEP events create transient but strong electric fields (≥106 V/m) that may induce dielectric breakdown. Such breakdown would likely result in significant modifications to the physical and chemical properties of the lunar regolith within PSRs. Key Points Energetic charged particles deep dielectrically charge the lunar regolithWe model the resulting subsurface electric fieldsThe electric fields may be great enough to induce dielectric breakdown

WeFaceNano:a user-friendly pipeline for complete ONT sequence assembly and detection of antibiotic resistance in multi-plasmid bacterial isolates

Background: Bacterial plasmids often carry antibiotic resistance genes and are a significant factor in the spread of antibiotic resistance. The ability to completely assemble plasmid sequences would facilitate the localization of antibiotic resistance genes, the identification of genes that promote plasmid transmission and the accurate tracking of plasmid mobility. However, the complete assembly of plasmid sequences using the currently most widely used sequencing platform (Illumina-based sequencing) is restricted due to the generation of short sequence lengths. The long-read Oxford Nanopore Technologies (ONT) sequencing platform overcomes this limitation. Still, the assembly of plasmid sequence data remains challenging due to software incompatibility with long-reads and the error rate generated using ONT sequencing. Bioinformatics pipelines have been developed for ONT-generated sequencing but require computational skills that frequently are beyond the abilities of scientific researchers. To overcome this challenge, the authors developed ‘WeFaceNano’, a user-friendly Web interFace for rapid assembly and analysis of plasmid DNA sequences generated using the ONT platform. WeFaceNano includes: a read statistics report; two assemblers (Miniasm and Flye); BLAST searching; the detection of antibiotic resistance- and replicon genes and several plasmid visualizations. A user-friendly interface displays the main features of WeFaceNano and gives access to the analysis tools. Results: Publicly available ONT sequence data of 21 plasmids were used to validate WeFaceNano, with plasmid assemblages and anti-microbial resistance gene detection being concordant with the published results. Interestingly, the “Flye” assembler with “meta” settings generated the most complete plasmids. Conclusions: WeFaceNano is a user-friendly open-source software pipeline suitable for accurate plasmid assembly and the detection of anti-microbial resistance genes in (clinical) samples where multiple plasmids can be present.</p

Dielectric breakdown weathering of the Moon\u27s polar regolith

Abstract Galactic cosmic rays and solar energetic particles (SEPs) can charge the Moon\u27s subsurface, a process expected to be particularly important in the polar regions. Experiments have shown that sufficient fluences (i.e., time-integrated fluxes) of energetic charged particles can cause dielectric breakdown, in which the electric field rapidly vaporizes small, filamentary channels within a dielectric. Lunar regolith has both the characteristics and, in some polar locations, the environment needed to make breakdown likely. We combine the Jet Propulsion Laboratory proton fluence model with temperature measurements from the Lunar Reconnaissance Orbiter\u27s (LRO\u27s) Diviner instrument and related temperature modeling to estimate how often breakdown occurs in the polar regions. We find that all gardened regolith within permanently shadowed regions (PSRs) has likely experienced up to 2×106 SEP events capable of causing breakdown, while the warmest polar regions have experienced about 2 orders of magnitude fewer events. We also use measurements from the Cosmic Ray Telescope for the Effects of Radiation on LRO to show that at least two breakdown-inducing events may have occurred since LRO arrived at the Moon in 2009. Finally, we discuss how such “breakdown weathering” may increase the percentage of fine and monomineralic grains within PSRs; explain the presence of so-called “fairy castle” regolith structures; and contribute to other low-albedo features detected by LRO\u27s Lyman Alpha Mapping Project, possibly establishing a correlation between these features and the average temperatures within craters that are only partly in permanent shadow

Deciphering Tumour Microenvironment of Liver Cancer through Deconvolution of Bulk RNA-Seq Data with Single-Cell Atlas

Liver cancers give rise to a heavy burden on healthcare worldwide. Understanding the tumour microenvironment (TME) underpins the development of precision therapy. Single-cell RNA sequencing (scRNA-seq) technology has generated high-quality cell atlases of the TME, but its wider application faces enormous costs for various clinical circumstances. Fortunately, a variety of deconvolution algorithms can instead repurpose bulk RNA-seq data, alleviating the need for generating scRNA-seq datasets. In this study, we reviewed major public omics databases for relevance in this study and utilised eight RNA-seqs and one microarray dataset from clinical studies. To decipher the TME of liver cancer, we estimated the fractions of liver cell components by deconvoluting the samples with Cibersortx using three reference scRNA-seq atlases. We also confirmed that Cibersortx can accurately deconvolute cell types/subtypes of interest. Compared with non-tumorous liver, liver cancers showed multiple decreased cell types forming normal liver microarchitecture, as well as elevated cell types involved in fibrogenesis, abnormal angiogenesis, and disturbed immune responses. Survival analysis shows that the fractions of five cell types/subtypes significantly correlated with patient outcomes, indicating potential therapeutic targets. Therefore, deconvolution of bulk RNA-seq data with scRNA-seq atlas references can be a useful tool to help understand the TME

Evaluation of the antigen-experienced B-cell receptor repertoire in healthy children and adults

Upon antigen recognition via their B cell receptor (BR), B cells migrate to the germinal center where they undergo somatic hypermutation (SHM) to increase their affinity for the antigen, and class switch recombination (CSR) to change the effector function of the secreted antibodies. These steps are essential to create an antigen-experienced BR repertoire that efficiently protects the body against pathogens. At the same time, the BR repertoire should be selected to protect against responses to self-antigen or harmless antigens. Insights into the processes of SHM, selection, and CSR can be obtained by studying the antigen-experienced BR repertoire. Currently, a large reference data set of healthy children and adults, which ranges from neonates to the elderly, is not available. In this study, we analyzed the antigen-experienced repertoire of 38 healthy donors (HD), ranging from cord blood to 74 years old, by sequencing IGA and IGG transcripts using next generation sequencing. This resulted in a large, freely available reference data set containing 412,890 IGA and IGG transcripts. We used this data set to study mutation levels, SHM patterns, antigenic selection, and CSR from birth to elderly HD. Only small differences were observed in SHM patterns, while the mutation levels increase in early childhood and stabilize at 6 years of age at around 7%. Furthermore, comparison of the antigen-experienced repertoire with sequences from the naive immune repertoire showed that features associated with autoimmunity such as long CDR3 length and IGHV4-34 usage are reduced in the antigen-experienced repertoire. Moreover, IGA2 and IGG2 usage was increased in HD in higher age categories, while IGG1 usage was decreased. In addition, we studied clonal relationship in the different samples. Clonally related sequences were found with different subclasses. Interestingly, we found transcripts with the same CDR1-CDR3 sequence, but different subclasses. Together, these data suggest that a single antigen can provoke a B-cell response with BR of different subclasses and that, during the course of an immune response, some B cells change their isotype without acquiring additional SHM or can directly switch to different isotypes

Spectroscopy of High-Redshift Supernovae from the ESSENCE Project: The First Two Years

We present the results of spectroscopic observations of targets discovered during the first two years of the ESSENCE project. The goal of ESSENCE is to use a sample of ~200 Type Ia supernovae (SNe Ia) at moderate redshifts (0.2 < z < 0.8) to place constraints on the equation of state of the Universe. Spectroscopy not only provides the redshifts of the objects, but also confirms that some of the discoveries are indeed SNe Ia. This confirmation is critical to the project, as techniques developed to determine luminosity distances to SNe Ia depend upon the knowledge that the objects at high redshift are the same as the ones at low redshift. We describe the methods of target selection and prioritization, the telescopes and detectors, and the software used to identify objects. The redshifts deduced from spectral matching of high-redshift SNe Ia with low-redshift SNe Ia are consistent with those determined from host-galaxy spectra. We show that the high-redshift SNe Ia match well with low-redshift templates. We include all spectra obtained by the ESSENCE project, including 52 SNe Ia, 5 core-collapse SNe, 12 active galactic nuclei, 19 galaxies, 4 possibly variable stars, and 16 objects with uncertain identifications.Comment: 38 pages, 9 figures (many with multiple parts), submitted to A

Using Line Profiles to Test the Fraternity of Type Ia Supernovae at High and Low Redshifts

Using archival data of low-redshift (z < 0.01) Type Ia supernovae (SN Ia) and recent observations of high-redshift (0.16 < z <0.64; Matheson et al. 2005) SN Ia, we study the "uniformity'' of the spectroscopic properties of nearby and distant SN Ia. We find no difference in the measures we describe here. In this paper, we base our analysis solely on line-profile morphology, focusing on measurements of the velocity location of maximum absorption (vabs) and peak emission (vpeak). We find that the evolution of vabs and vpeak for our sample lines (Ca II 3945, Si II 6355, and S II 5454, 5640) is similar for both the low- and high-redshift samples. We find that vabs for the weak S II 5454, 5640 lines, and vpeak for S II 5454, can be used to identify fast-declining [dm15 > 1.7] SN Ia, which are also subluminous. In addition, we give the first direct evidence in two high-z SN Ia spectra of a double-absorption feature in Ca II 3945, an event also observed, though infrequently, in low-redshift SN Ia spectra (6/22 SN Ia in our local sample). We report for the first time the unambiguous and systematic intrinsic blueshift of peak emission of optical P-Cygni line profiles in Type Ia spectra, by as much as 8000 km/s. All the high-z SN Ia analyzed in this paper were discovered and followed up by the ESSENCE collaboration, and are now publicly available.Comment: 28 pages (emulateapj), 15 figures; accepted for publication in A