Gene knockout inference with variational graph autoencoder learning single-cell gene regulatory networks.

In this paper, we introduce Gene Knockout Inference (GenKI), a virtual knockout (KO) tool for gene function prediction using single-cell RNA sequencing (scRNA-seq) data in the absence of KO samples when only wild-type (WT) samples are available. Without using any information from real KO samples, GenKI is designed to capture shifting patterns in gene regulation caused by the KO perturbation in an unsupervised manner and provide a robust and scalable framework for gene function studies. To achieve this goal, GenKI adapts a variational graph autoencoder (VGAE) model to learn latent representations of genes and interactions between genes from the input WT scRNA-seq data and a derived single-cell gene regulatory network (scGRN). The virtual KO data is then generated by computationally removing all edges of the KO gene-the gene to be knocked out for functional study-from the scGRN. The differences between WT and virtual KO data are discerned by using their corresponding latent parameters derived from the trained VGAE model. Our simulations show that GenKI accurately approximates the perturbation profiles upon gene KO and outperforms the state-of-the-art under a series of evaluation conditions. Using publicly available scRNA-seq data sets, we demonstrate that GenKI recapitulates discoveries of real-animal KO experiments and accurately predicts cell type-specific functions of KO genes. Thus, GenKI provides an in-silico alternative to KO experiments that may partially replace the need for genetically modified animals or other genetically perturbed systems.

Realization of tunable-performance in atomic layer deposited Hf-doped In2O3 thin film transistor via oxygen vacancy modulation.

Due to the limitation of inherent ultra-high electron concentration, the electrical properties of In2O3 resemble those of conductors rather than semiconductors prior to special treatment. In this study, the effect of various annealing treatments on the microstructure, optical properties, and oxygen vacancies of the films and transistors is systematically investigated. Our finding reveals a progressive crystallization trend in the films with increasing annealing temperature. In addition, a higher annealing temperature is also associated with the reduction in the concentration of oxygen vacancies, as well as an elevation in both optical transmittance and optical bandgap. Furthermore, with the implementation of annealing process, the devices gradually transform from no pronounced gate control to exhibit with excellent gate control and electrical performances. The atomic layer deposited Hf-doped In2O3 thin film transistor annealed at 250 °C exhibits optimal electrical properties, with a field-effect mobility of 18.65 cm2 V-1 s-1, a subthreshold swing of 0.18 V/dec, and an Ion/Ioff ratio of 2.76 × 106. The results indicate that the impact of varying annealing temperatures can be attributed to the modulation of oxygen vacancies within the films. This work serves as a complementary study for the existing post-treatment of oxide films and provides a reliable reference for utilization of the annealing process in practical applications.

Integrating Citizen Scientist Data into the Surveillance System for Avian Influenza Virus, Taiwan.

The continuing circulation and reassortment with low-pathogenicity avian influenza Gs/Gd (goose/Guangdong/1996)-like avian influenza viruses (AIVs) has caused huge economic losses and raised public health concerns over the zoonotic potential. Virologic surveillance of wild birds has been suggested as part of a global AIV surveillance system. However, underreporting and biased selection of sampling sites has rendered gaining information about the transmission and evolution of highly pathogenic AIV problematic. We explored the use of the Citizen Scientist eBird database to elucidate the dynamic distribution of wild birds in Taiwan and their potential for AIV exchange with domestic poultry. Through the 2-stage analytical framework, we associated nonignorable risk with 10 species of wild birds with >100 significant positive results. We generated a risk map, which served as the guide for highly pathogenic AIV surveillance. Our methodologic blueprint has the potential to be incorporated into the global AIV surveillance system of wild birds.

Unveiling the biology of defective viral genomes in vitro and in vivo: implications for gene expression and pathogenesis of coronavirus.

BACKGROUND: Defective viral genome (DVG) is a truncated version of the full-length virus genome identified in most RNA viruses during infection. The synthesis of DVGs in coronavirus has been suggested; however, the fundamental characteristics of coronavirus DVGs in gene expression and pathogenesis have not been systematically analyzed. METHODS: Nanopore direct RNA sequencing was used to investigate the characteristics of coronavirus DVGs in gene expression including reproducibility, abundance, species and genome structures for bovine coronavirus in cells, and for mouse hepatitis virus (MHV)-A59 (a mouse coronavirus) in cells and in mice. The MHV-A59 full-length genomic cDNAs (~ 31 kilobases) were in vitro constructed to experimentally validate the origin of coronavirus DVG. The synthesis of DVGs was also experimentally identified by RT-PCR followed by sequencing. In addition, the alterations of DVGs in amounts and species under different infection environments and selection pressures including the treatment of antiviral remdesivir and interferon were evaluated based on the banding patterns by RT-PCR. RESULTS: The results are as follows: (i) the structures of DVGs are with diversity, (ii) DVGs are overall synthesized with moderate (MHV-A59 in cells) to high (BCoV in cells and MHV-A59 in mice) reproducibility under regular infection with the same virus inoculum, (iii) DVGs can be synthesized from the full-length coronavirus genome, (iv) the sequences flanking the recombination point of DVGs are AU-rich and thus may contribute to the recombination events during gene expression, (v) the species and amounts of DVG are altered under different infection environments, and (vi) the biological nature of DVGs between in vitro and in vivo is similar. CONCLUSIONS: The identified biological characteristics of coronavirus DVGs in terms of abundance, reproducibility, and variety extend the current model for coronavirus gene expression. In addition, the biological features of alterations in amounts and species of coronavirus DVGs under different infection environments may assist the coronavirus to adapt to the altered environments for virus fitness and may contribute to the coronavirus pathogenesis. Consequently, the unveiled biological features may assist the community to study the gene expression mechanisms of DVGs and their roles in pathogenesis, contributing to the development of antiviral strategy and public health.

Biological characterization of coronavirus noncanonical transcripts in vitro and in vivo.

BACKGROUND: In addition to the well-known coronavirus genomes and subgenomic mRNAs, the existence of other coronavirus RNA species, which are collectively referred to as noncanonical transcripts, has been suggested; however, their biological characteristics have not yet been experimentally validated in vitro and in vivo. METHODS: To comprehensively determine the amounts, species and structures of noncanonical transcripts for bovine coronavirus in HRT-18 cells and mouse hepatitis virus A59, a mouse coronavirus, in mouse L cells and mice, nanopore direct RNA sequencing was employed. To experimentally validate the synthesis of noncanonical transcripts under regular infection, Northern blotting was performed. Both Northern blotting and nanopore direct RNA sequencing were also applied to examine the reproducibility of noncanonical transcripts. In addition, Northern blotting was also employed to determine the regulatory features of noncanonical transcripts under different infection conditions, including different cells, multiplicities of infection (MOIs) and coronavirus strains. RESULTS: In the current study, we (i) experimentally determined that coronavirus noncanonical transcripts were abundantly synthesized, (ii) classified the noncanonical transcripts into seven populations based on their structures and potential synthesis mechanisms, (iii) showed that the species and amounts of the noncanonical transcripts were reproducible during regular infection but regulated in altered infection environments, (iv) revealed that coronaviruses may employ various mechanisms to synthesize noncanonical transcripts, and (v) found that the biological characteristics of coronavirus noncanonical transcripts were similar between in vitro and in vivo conditions. CONCLUSIONS: The biological characteristics of noncanonical coronavirus transcripts were experimentally validated for the first time. The identified features of noncanonical transcripts in terms of abundance, reproducibility and variety extend the current model for coronavirus gene expression. The capability of coronaviruses to regulate the species and amounts of noncanonical transcripts may contribute to the pathogenesis of coronaviruses during infection, posing potential challenges in disease control. Thus, the biology of noncanonical transcripts both in vitro and in vivo revealed here can provide a database for biological research, contributing to the development of antiviral strategies.

Tunable-performance all-oxide structure field-effect transistor based atomic layer deposited Hf-doped In2O3 thin films.

The relocation of peripheral transistors from the front-end-of-line (FEOL) to the back-end-of-line (BEOL) in fabrication processes is of significant interest, as it allows for the introduction of novel functionality in the BEOL while providing additional die area in the FEOL. Oxide semiconductor-based transistors serve as attractive candidates for BEOL. Within these categories, In2O3 material is particularly notable; nonetheless, the excessive intrinsic carrier concentration poses a limitation on its broader applicability. Herein, the deposition of Hf-doped In2O3 (IHO) films via atomic layer deposition for the first time demonstrates an effective method for tuning the intrinsic carrier concentration, where the doping concentration plays a critical role in determine the properties of IHO films and all-oxide structure transistors with Au-free process. The all-oxide transistors with In2O3: HfO2 ratio of 10:1 exhibited optimal electrical properties, including high on-current with 249 µA, field-effect mobility of 13.4 cm2 V-1 s-1, and on/off ratio exceeding 106, and also achieved excellent stability under long time positive bias stress and negative bias stress. These findings suggest that this study not only introduces a straightforward and efficient approach to improve the properties of In2O3 material and transistors, but as well paves the way for development of all-oxide transistors and their integration into BEOL technology.

Experimental and analytical pipeline for sub-genomic RNA landscape of coronavirus by Nanopore sequencer.

Coronaviruses (CoVs), including severe acute respiratory syndrome coronavirus 2, can infect a variety of mammalian and avian hosts with significant medical and economic consequences. During the life cycle of CoV, a coordinated series of subgenomic RNAs, including canonical subgenomic messenger RNA and non-canonical defective viral genomes (DVGs), are generated with different biological implications. Studies that adopted the Nanopore sequencer (ONT) to investigate the landscape and dynamics of viral RNA subgenomic transcriptomes applied arbitrary bioinformatics parameters without justification or experimental validation. The current study used bovine coronavirus (BCoV), which can be performed under biosafety level 2 for library construction and experimental validation using traditional colony polymerase chain reaction and Sanger sequencing. Four different ONT protocols, including RNA direct and cDNA direct sequencing with or without exonuclease treatment, were used to generate RNA transcriptomic libraries from BCoV-infected cell lysates. Through rigorously examining the k-mer, gap size, segment size, and bin size, the optimal cutoffs for the bioinformatic pipeline were determined to remove the sequence noise while keeping the informative DVG reads. The sensitivity and specificity of identifying DVG reads using the proposed pipeline can reach 82.6% and 99.6% under the k-mer size cutoff of 15. Exonuclease treatment reduced the abundance of RNA transcripts; however, it was not necessary for future library preparation. Additional recovery of clipped BCoV nucleotide sequences with experimental validation expands the landscape of the CoV discontinuous RNA transcriptome, whose biological function requires future investigation. The results of this study provide the benchmarks for library construction and bioinformatic parameters for studying the discontinuous CoV RNA transcriptome.IMPORTANCEFunctional defective viral genomic RNA, containing all the cis-acting elements required for translation or replication, may play different roles in triggering cell innate immune signaling, interfering with the canonical subgenomic messenger RNA transcription/translation or assisting in establishing persistence infection. This study does not only provide benchmarks for library construction and bioinformatic parameters for studying the discontinuous coronavirus RNA transcriptome but also reveals the complexity of the bovine coronavirus transcriptome, whose functional assays will be critical in future studies.

Post-annealing optimization of the heteroepitaxial La-doped SrSnO3 integrated on silicon via ALD.

Wide band gap (WBG) alkaline-earth stannate transparent oxide semiconductors (TOSs) have attracted increasing attention in recent years for their high carrier mobility and outstanding optoelectronic properties, and have been applied widely in various devices, such as flat-panel displays. Most alkaline-earth stannates are grown by molecular beam epitaxy (MBE); there are some intractable issues with the tin source including the volatility with SnO and Sn sources and the decomposition of the SnO2 source. In contrast, atomic layer deposition (ALD) serves as an ideal technique for the growth of complex stannate perovskites with precise stoichiometry control and tunable thickness at the atomic scale. Herein, we report the La-SrSnO3/BaTiO3 perovskite heterostructure heterogeneously integrated on Si (001), which uses ALD-grown La-doped SrSnO3 (LSSO) as a channel material and MBE-grown BaTiO3 (BTO) as a dielectric material. The reflective high-energy electron diffraction and X-ray diffraction results indicate the crystallinity of each epitaxial layer with a full width at half maximum (FWHM) of 0.62°. In situ X-ray photoelectron spectroscopy results confirm that there was no Sn0 state in ALD-deposited LSSO. Besides, we report a strategy for the post-treatment of LSSO/BTO perovskite heterostructures by controlling the oxygen annealing temperature and time, with a maximum oxide capacitance Cox of 0.31 µF cm-2 and a minimum low-frequency dispersion for the devices with 7 h oxygen annealing at 400 °C. The enhancement of capacitance properties is primarily attributed to a decrease of oxygen vacancies in the films and interface defects in the heterostructure interfaces during an additional ex situ excess oxygen annealing. This work expands current optimization methods for reducing defects in epitaxial LSSO/BTO perovskite heterostructures and shows that excess oxygen annealing is a powerful tool for enhancing the capacitance properties of LSSO/BTO heterostructures.