Multi-Modal Multi-Scale Deep Learning for Large-Scale Image Annotation

Image annotation aims to annotate a given image with a variable number of class labels corresponding to diverse visual concepts. In this paper, we address two main issues in large-scale image annotation: 1) how to learn a rich feature representation suitable for predicting a diverse set of visual concepts ranging from object, scene to abstract concept; 2) how to annotate an image with the optimal number of class labels. To address the first issue, we propose a novel multi-scale deep model for extracting rich and discriminative features capable of representing a wide range of visual concepts. Specifically, a novel two-branch deep neural network architecture is proposed which comprises a very deep main network branch and a companion feature fusion network branch designed for fusing the multi-scale features computed from the main branch. The deep model is also made multi-modal by taking noisy user-provided tags as model input to complement the image input. For tackling the second issue, we introduce a label quantity prediction auxiliary task to the main label prediction task to explicitly estimate the optimal label number for a given image. Extensive experiments are carried out on two large-scale image annotation benchmark datasets and the results show that our method significantly outperforms the state-of-the-art.Comment: Submited to IEEE TI

EFFECTS OF IXERIS CHINENSIS (THUNB.) NAKAI BOILING WATER EXTRACT ON HEPATITIS B VIRAL ACTIVITY AND HEPATOCELLULAR CARCINOMA

Background: Hepatitis B virus (HBV) infection and hepatocellular carcinoma are major diseases that affect the Taiwanese population. Therefore, the development of an alternative herbal medicine that can effectively treat these diseases is a research target. In this study, we tested Ixeris Chinensis (Thunb.) Nakai boiling water extract (ICTN BWE) in vitro and analysed its effects on the HBV and liver cancer. Materials and Methods: We used a human liver cancer cell line (Hep3B, a cell line that continuously secretes HBV particles into a medium) as an experimental model for the screening of various ICTN BWE concentrations and their effects on the HBV in vitro. Results: Our results showed that 75 µg/mL ICTN BWE downregulated the relative expression of the hepatitis B virus surface antigens (HBsAg) to 77.1%. Using the human liver cancer cell lines HuH-7 and HepG2, and 3-(4,5- dimethylthiazol-zyl)-2,5-diphenyl tetrazolium bromide (MTT) and tumour clonogenic assays, we then showed that ICTN BWE inhibits hepatocellular carcinoma growth. Conclusion: Fluorescent microscopy of DAPI(4',6-Diamidino-2-phenylindole)-stained nuclei and DNA fragmentation assays confirmed the inhibitory effects of ICTN BWE on liver tumour cell growth through induction of apoptosis

Lignocellulosic saccharification by a newly isolated bacterium, Ruminiclostridium thermocellum M3 and cellular cellulase activities for high ratio of glucose to cellobiose

Background: Lignocellulosic biomass is one of earth's most abundant resources, and it has great potential for biofuel production because it is renewable and has carbon-neutral characteristics. Lignocellulose is mainly composed of carbohydrate polymers (cellulose and hemicellulose), which contain approximately 75 % fermentable sugars for biofuel fermentation. However, saccharification by cellulases is always the main bottleneck for commercialization. Compared with the enzyme systems of fungi, bacteria have evolved distinct systems to directly degrade lignocellulose. However, most reported bacterial saccharification is not efficient enough without help from additional β-glucosidases. Thus, to enhance the economic feasibility of using lignocellulosic biomass for biofuel production, it will be extremely important to develop a novel bacterial saccharification system that does not require the addition of β-glucosidases. Results: In this study, a new thermophilic bacterium named Ruminiclostridium thermocellum M3, which could directly saccharify lignocellulosic biomass, was isolated from horse manure. The results showed that R. thermocellum M3 can grow at 60 °C on a variety of carbon polymers, including microcrystalline cellulose, filter paper, and xylan. Upon utilization of these substrates, R. thermocellum M3 achieved an oligosaccharide yield of 481.5 ± 16.0 mg/g Avicel, and a cellular β-glucosidase activity of up to 0.38 U/mL, which is accompanied by a high proportion (approximately 97 %) of glucose during the saccharification. R. thermocellum M3 also showed potential in degrading natural lignocellulosic biomass, without additional pretreatment, to oligosaccharides, and the oligosaccharide yields using poplar sawdust, corn cobs, rice straw, and cornstalks were 52.7 ± 2.77, 77.8 ± 5.9, 89.4 ± 9.3, and 107.8 ± 5.88 mg/g, respectively. Conclusions: The newly isolated strain R. thermocellum M3 degraded lignocellulose and accumulated oligosaccharides. R. thermocellum M3 saccharified lignocellulosic feedstock without the need to add β-glucosidases or control the pH, and the high proportion of glucose production distinguishes it from all other known monocultures of cellulolytic bacteria. R. thermocellum M3 is a potential candidate for lignocellulose saccharification, and it is a valuable choice for the refinement of bioproducts

Local Magnetic Field Role in Star Formation

We highlight distinct and systematic observational features of magnetic field morphologies in polarized submm dust continuum. We illustrate this with specific examples and show statistical trends from a sample of 50 star-forming regions.Comment: 4 pages, 3 figures; to appear in the EAS Proceedings of the 6th Zermatt ISM Symposium "Conditions and Impact of Star Formation from Lab to Space", September 201

Magnetic Fields and Massive Star Formation

Massive stars ($M > 8$ \msun) typically form in parsec-scale molecular clumps that collapse and fragment, leading to the birth of a cluster of stellar objects. We investigate the role of magnetic fields in this process through dust polarization at 870 $\mu$m obtained with the Submillimeter Array (SMA). The SMA observations reveal polarization at scales of \lsim 0.1 pc. The polarization pattern in these objects ranges from ordered hour-glass configurations to more chaotic distributions. By comparing the SMA data with the single dish data at parsec scales, we found that magnetic fields at dense core scales are either aligned within $40^\circ$ of or perpendicular to the parsec-scale magnetic fields. This finding indicates that magnetic fields play an important role during the collapse and fragmentation of massive molecular clumps and the formation of dense cores. We further compare magnetic fields in dense cores with the major axis of molecular outflows. Despite a limited number of outflows, we found that the outflow axis appears to be randomly oriented with respect to the magnetic field in the core. This result suggests that at the scale of accretion disks (\lsim 10^3 AU), angular momentum and dynamic interactions possibly due to close binary or multiple systems dominate over magnetic fields. With this unprecedentedly large sample massive clumps, we argue on a statistical basis that magnetic fields play an important role during the formation of dense cores at spatial scale of 0.01 - 0.1 pc in the context of massive star and cluster star formation.Comment: Accepted for publication in Astrophysical Journa

Multi-scale physical properties of NGC 6334 as revealed by local relative orientations between magnetic fields, density gradients, velocity gradients, and gravity

We present ALMA dust polarization and molecular line observations toward 4 clumps (I(N), I, IV, and V) in the massive star-forming region NGC 6334. In conjunction with large-scale dust polarization and molecular line data from JCMT, Planck, and NANTEN2, we make a synergistic analysis of relative orientations between magnetic fields ($\theta_{\mathrm{B}}$), column density gradients ($\theta_{\mathrm{NG}}$), local gravity ($\theta_{\mathrm{LG}}$), and velocity gradients ($\theta_{\mathrm{VG}}$) to investigate the multi-scale (from $\sim$30 pc to 0.003 pc) physical properties in NGC 6334. We find that the relative orientation between $\theta_{\mathrm{B}}$ and $\theta_{\mathrm{NG}}$ changes from statistically more perpendicular to parallel as column density ($N_{\mathrm{H_2}}$) increases, which is a signature of trans-to-sub-Alfv\'{e}nic turbulence at complex/cloud scales as revealed by previous numerical studies. Because $\theta_{\mathrm{NG}}$ and $\theta_{\mathrm{LG}}$ are preferentially aligned within the NGC 6334 cloud, we suggest that the more parallel alignment between $\theta_{\mathrm{B}}$ and $\theta_{\mathrm{NG}}$ at higher $N_{\mathrm{H_2}}$ is because the magnetic field line is dragged by gravity. At even higher $N_{\mathrm{H_2}}$, the angle between $\theta_{\mathrm{B}}$ and $\theta_{\mathrm{NG}}$ or $\theta_{\mathrm{LG}}$ transits back to having no preferred orientation or statistically slightly more perpendicular, suggesting that the magnetic field structure is impacted by star formation activities. A statistically more perpendicular alignment is found between $\theta_{\mathrm{B}}$ and $\theta_{\mathrm{VG}}$ throughout our studied $N_{\mathrm{H_2}}$ range, which indicates a trans-to-sub-Alfv\'{e}nic state at small scales as well. The normalised mass-to-flux ratio derived from the polarization-intensity gradient (KTH) method increases with $N_{\mathrm{H_2}}$.Comment: 35 pages, 18 figures. Accepted by Ap

RNA topoisomerase is prevalent in all domains of life and associates with polyribosomes in animals

DNA Topoisomerases are essential to resolve topological problems during DNA metabolism in all species. However, the prevalence and function of RNA topoisomerases remain uncertain. Here, we show that RNA topoisomerase activity is prevalent in Type IA topoisomerases from bacteria, archaea, and eukarya. Moreover, this activity always requires the conserved Type IA core domains and the same catalytic residue used in DNA topoisomerase reaction; however, it does not absolutely require the non-conserved carboxyl-terminal domain (CTD), which is necessary for relaxation reactions of supercoiled DNA. The RNA topoisomerase activity of human Top3β differs from that of Escherichia coli topoisomerase I in that the former but not the latter requires the CTD, indicating that topoisomerases have developed distinct mechanisms during evolution to catalyze RNA topoisomerase reactions. Notably, Top3β proteins from several animals associate with polyribosomes, which are units of mRNA translation, whereas the Top3 homologs from E. coli and yeast lack the association. The Top3β-polyribosome association requires TDRD3, which directly interacts with Top3β and is present in animals but not bacteria or yeast. We propose that RNA topoisomerases arose in the early RNA world, and that they are retained through all domains of DNA-based life, where they mediate mRNA translation as part of polyribosomes in animals

Upregulation of Pd-L1 by Sars-Cov-2 Promotes Immune Evasion

Patients with severe COVID-19 often suffer from lymphopenia, which is linked to T-cell sequestration, cytokine storm, and mortality. However, it remains largely unknown how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induces lymphopenia. Here, we studied the transcriptomic profile and epigenomic alterations involved in cytokine production by SARS-CoV-2-infected cells. We adopted a reverse time-order gene coexpression network approach to analyze time-series RNA-sequencing data, revealing epigenetic modifications at the late stage of viral egress. Furthermore, we identified SARS-CoV-2-activated nuclear factor-κB (NF-κB) and interferon regulatory factor 1 (IRF1) pathways contributing to viral infection and COVID-19 severity through epigenetic analysis of H3K4me3 chromatin immunoprecipitation sequencing. Cross-referencing our transcriptomic and epigenomic data sets revealed that coupling NF-κB and IRF1 pathways mediate programmed death ligand-1 (PD-L1) immunosuppressive programs. Interestingly, we observed higher PD-L1 expression in Omicron-infected cells than SARS-CoV-2 infected cells. Blocking PD-L1 at an early stage of virally-infected AAV-hACE2 mice significantly recovered lymphocyte counts and lowered inflammatory cytokine levels. Our findings indicate that targeting the SARS-CoV-2-mediated NF-κB and IRF1-PD-L1 axis may represent an alternative strategy to reduce COVID-19 severity