123 research outputs found
Real-Time Parallel Trajectory Optimization with Spatiotemporal Safety Constraints for Autonomous Driving in Congested Traffic
Multi-modal behaviors exhibited by surrounding vehicles (SVs) can typically
lead to traffic congestion and reduce the travel efficiency of autonomous
vehicles (AVs) in dense traffic. This paper proposes a real-time parallel
trajectory optimization method for the AV to achieve high travel efficiency in
dynamic and congested environments. A spatiotemporal safety module is developed
to facilitate the safe interaction between the AV and SVs in the presence of
trajectory prediction errors resulting from the multi-modal behaviors of the
SVs. By leveraging multiple shooting and constraint transcription, we transform
the trajectory optimization problem into a nonlinear programming problem, which
allows for the use of optimization solvers and parallel computing techniques to
generate multiple feasible trajectories in parallel. Subsequently, these
spatiotemporal trajectories are fed into a multi-objective evaluation module
considering both safety and efficiency objectives, such that the optimal
feasible trajectory corresponding to the optimal target lane can be selected.
The proposed framework is validated through simulations in a dense and
congested driving scenario with multiple uncertain SVs. The results demonstrate
that our method enables the AV to safely navigate through a dense and congested
traffic scenario while achieving high travel efficiency and task accuracy in
real time.Comment: 8 pages, 7 figures, accepted for publication in the 26th IEEE
International Conference on Intelligent Transportation Systems (ITSC 2023
Emergency vaccination alleviates highly pathogenic porcine reproductive and respiratory syndrome virus infection after contact exposure
Cyclooxygenase-2 Facilitates Newcastle Disease Virus Proliferation and Is as a Target for Canthin-6-One Antiviral Activity
Construction of a camelid VHH yeast two-hybrid library and the selection of VHH against haemagglutinin-neuraminidase protein of the Newcastle disease virus
Humoral immune response after immunization. Sera from IIama was collected, two-fold diluted and tested by HI using LaSota as antigen. Figure S1 Amplification of VHH through a nested PCR. (A) First round PCR to separate VH from VHH. The upper 900 bp bands represent the VH-CH1-Hinge-CH2 of conventional Abs (lane 1–8). The lower 600 bp bands represent the VHH-Hinge-CH2 of HCAbs (lane 1–8). (B) VHH amplified through nested PCR using 600 bp fragment recovered from first round PCR as template (lane 1–4). M in A and B was the DL2000 DNA marker. C in A and B represent the negative control. Figure S2 PCR identification of inserted VHH. 47 clones were randomly picked to determine the library functional diversity by PCR using universal primers T7 and 3’AD (Table 1). Meanwhile, Sterile water was used as negative controls. 45 clones have amplified the 500 bp VHH fragments (lane 1–47), while negative templates control haven’t amplified any bands (lane C). M indicated the DL2000 DNA marker. Figure S3 Detection of library capacity and library titer. (A) 10-3 dilution plating of the transformed cells calculated a library capacity of 1.25 × 107 independent clones. (B) 10-5 dilution plating of the cultured library indicated a library titer of 3.45 × 108 cfu/mL. Figure S4 Deduced amino acid aligment of 10 random picked VHH. Deduced amino acid sequences were analyzed according to the Kabat numbering. Differences in the sequences are pinked, and the dash represent the missing sequences. Two hallmark Cys residues are labeled by the thick-line boxes. The four conservative hallmark residues of VHH in FR2 are labeled by the dotted line boxes. Figure S5 pGBKT7-HN bait plasmid construction. (A) PCR was carried out to amplify a truncate HN gene (without transmembrane region) from La Sota strain. M, 5000 DNA marker. 1, Truncate HN. C, Negative control. (B) A truncate HN was cloned into pGBKT7 through BamH I and Sal I. M, 5000 DNA marker. 1, Double restriction enzyme digestion of pGBKT7-HN. Figure S6 pHSIE-VHH plasmid construction. (A) 7 positive VHH fragment were amplified from recovered positive clones containing pGADT7-VHH by PCR. M, 5000 DNA marker. 1–7, VHH 1–7. C, Negative control. (B) Double restriction enzyme digestion of pHSIE-VHHs. M, 5000 DNA marker. 1–7, pHSIE-VHH 1–7. Figure S7 Western blot analysis of bait protein expression. 2 mL of Y2HGold(pGBKT7-HN) culture liquid was extracted using yeast protein extraction reagent (Takara). c-Myc tag monoclonal antibody (1:4000 dilution) was used as first antibody and HRP-labeled goat anti-mouse antibody (1:5000) was used as second antibody. The immunoreactive was visualized with cECL Plus Western blotting detection reagent (CWBIO). (DOC 1129 kb
IncHI1 plasmids mediated the tet(X4) gene spread in Enterobacteriaceae in porcine
The tigecycline resistance gene tet(X4) was widespread in various bacteria. However, limited information about the plasmid harboring the tet(X4) gene spread among the different species is available. Here, we investigated the transmission mechanisms of the tet(X4) gene spread among bacteria in a pig farm. The tet(X4) positive Escherichia coli, Klebsiella pneumoniae, Enterobacter cloacae and Enterobacter hormaeche were identified in the same farm. The whole genome sequencing (WGS) analysis showed that the K. pneumoniae belonged to ST727 (n = 11) and ST3830 (n = 1), E. cloacae and E. hormaeche belonged to ST524 (n = 1) and ST1862 (n = 1). All tet(X4) genes were located on the IncHI1 plasmids that could be conjugatively transferred into the recipient E. coli C600 at 30°C. Moreover, a fusion plasmid was identified that the IncHI1 plasmid recombined with the IncN plasmid mediated by ISCR2 during the conjugation from strains B12L to C600 (pB12L-EC-1). The fusion plasmid also has been discovered in a K. pneumoniae (K1L) that could provide more opportunities to spread antimicrobial resistance genes. The tet(X4) plasmids in these bacteria are derived from the same plasmid with a similar structure. Moreover, all the IncHI1 plasmids harboring the tet(X4) gene in GenBank belonged to the pST17, the newly defined pMLST. The antimicrobial susceptibility testing was performed by broth microdilution method showing the transconjugants acquired the most antimicrobial resistance from the donor strains. Taken together, this report provides evidence that IncHI1/pST17 is an important carrier for the tet(X4) spread in Enterobacteriaceae species, and these transmission mechanisms may perform in the environment
Nanopore-Based Direct RNA-Sequencing Reveals a High-Resolution Transcriptional Landscape of Porcine Reproductive and Respiratory Syndrome Virus
The TRS-mediated discontinuous transcription process is a hallmark of Arteriviruses. Precise assessment of the intricate sub genomic RNA (sg mRNA) populations is required to understand the kinetics of viral transcription. It is difficult to reconstruct and comprehensively quantify splicing events using short-read sequencing, making the identification of transcription-regulatory sequences (TRS) particularly problematic. Here, we applied long-read direct RNA sequencing to characterize the recombined RNA molecules produced in porcine alveolar macrophages during early passage infection of porcine reproductive and respiratory syndrome virus (PRRSV). Based on sequencing two PRRSV isolates, namely XM-2020 and GD, we revealed a high-resolution and diverse transcriptional landscape in PRRSV. The data revealed intriguing differences in sub genomic recombination types between the two PRRSVs while also demonstrating TRS-independent heterogeneous subpopulation not previously observed in Arteriviruses. We find that TRS usage is a regulated process and share the common preferred TRS in both strains. This study also identified a substantial number of TRSmediated transcript variants, including alternative-sg mRNAs encoding the same annotated ORF, as well as putative sg mRNAs encoded nested internal ORFs, implying that the genetic information encoded in PRRSV may be more intensively expressed. Epigenetic modifications have emerged as an essential regulatory layer in gene expression. Here, we gained a deeper understanding of m5C modification in poly(A) RNA, elucidating a potential link between methylation and transcriptional regulation. Collectively, our findings provided meaningful insights for redefining the transcriptome complexity of PRRSV. This will assist in filling the research gaps and developing strategies for better control of the PRRS
A NADC30-like PRRSV causes serious intestinal infections and tropism in piglets
Porcine reproductive and respiratory syndrome virus (PRRSV) causes huge economic loss to China's swine industry. Currently, a novel type 2 PRRSV, called the NADC30-like strain, is epidemic in numerous provinces of China. In this study, a NADC30-Like PRRSV strain was isolated in primary alveolar macrophage (PAM) cells from fecal samples collected from a local pig farm, which suffered severe diarrhea. A pathogenicity comparison study was conducted in 6–week‐old piglets by inoculating highly pathogenic HP-PRRSV and NADC30-Like PRRSV isolates. RT-qPCR revealed detection of NADC30-Like PRRSV but not the HP-PRRSV in the intestine. PRRSV infection-related lesions were observed in the intestine were further confirmed by histopathological and immunohistochemically examination (IHC). In addition, severe virus infections were also detected by RT-qPCR. Based on clinical observation and pathogenicity experiments, we confirmed that NADC30-Like PRRSV gained more tissue tropism, especially in the small intestine. This may be the one reason explaining why NADC-Like 30 PRRSV become a major epidemic strain in China since the first outbreak in 2013
Simultaneous Expression of Chicken Granulocyte Monocyte Colony-Stimulating Factor and the Hemagglutinin-Neuraminidase Epitope of the Virulent Newcastle Disease Virus Genotype VII C22 Strain in a Functional Synthetic Recombinant Adenovirus as a Genotype-Matched Vaccine with Potential Antiviral Activity
The transcriptional characteristics of NADC34-like PRRSV in porcine alveolar macrophages
The widespread and endemic circulation of porcine reproductive and respiratory syndrome virus (PRRSV) cause persistent financial losses to the swine industry worldwide. In 2017, NADC34-like PRRSV-2 emerged in northeastern China and spread rapidly. The dynamics analysis of immune perturbations associated with novel PRRSV lineage is still incomplete. This study performed a time-course transcriptome sequencing of NADC34-like PRRSV strain YC-2020-infected porcine alveolar macrophages (PAMs) and compared them with JXA1-infected PAMs. The results illustrated dramatic changes in the host’s differentially expressed genes (DEGs) presented at different timepoints after PRRSV infection, and the expression profile of YC-2020 group is distinct from that of JXA1 group. Functional enrichment analysis showed that the expression of many inflammatory cytokines was up-regulated following YC-2020 infection but at a significantly lower magnitude than JXA1 group, in line with the trends for most interferon-stimulated genes (ISGs) and their regulators. Meanwhile, numerous components of histocompatibility complex (MHC) class II and phagosome presented a stronger transcription suppression after the YC-2020 infection. All results imply that YC-2020 may induce milder inflammatory responses, weaker antiviral processes, and more severe disturbance of antigen processing and presentation compared with HP-PRRSV. Additionally, LAPTM4A, GLMP, and LITAF, which were selected from weighted gene co-expression network analysis (WGCNA), could significantly inhibit PRRSV proliferation. This study provides fundamental data for understanding the biological characteristics of NADC34-like PRRSV and new insights into PRRSV evolution and prevention
A novel Pseudorabies virus vaccine developed using HDR-CRISPR/Cas9 induces strong humoral and cellular immune response in mice
Outbreaks of Pseudorabies (PR) by numerous highly virulent and antigenic variant Pseudorabies virus (PRV) strains have been causing severe economic losses to the pig industry in China since 2011. However, current commercial vaccines are often unable to induce thorough protective immunity. In this study, a TK/gI/gE deleted recombinant PRV expressing GM-CSF was developed by using the HDR-CRISPR/Cas9 system. Here, a four-sgRNA along with the Cas9D10A targeting system was utilized for TK/gI/gE gene deletion and GM-CSF insertion. Our study showed that the four-sgRNA targeting system appeared to have higher knock-in efficiency for PRVs editing. The replication of the recombinant PRVs were slightly lower than that of the parental strain, but they appeared to have similar properties in terms of growth curves and plaque morphology. The mice vaccinated with the recombinant PRV expressing GM-CSF via intramuscular injection showed no obvious clinical symptoms, milder pathological lesions, and were completely protected against wild-type PRV challenge. When compared to the triple gene-deleted PRV, the gB antibodies and neutralizing antibody titers were improved and the immunized mice appeared to have lower viral load and higher mRNA levels of IL-2, IL-4, IL-6, and IFN-γ in spleens. Our study offers a novel approach for recombinant PRV construction, and the triple gene-deleted PRV expressing GM-CSF could serve as a promising vaccine candidate for PR control
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