Application of Butterfly Clos-Network in Network-on-Chip

This paper studied the topology of NoC (Network-on-Chip). By combining the characteristics of the Clos network and butterfly network, a new topology named BFC (Butterfly Clos-network) network was proposed. This topology integrates several modules, which belongs to the same layer but different dimensions, into a new module. In the BFC network, a bidirectional link is used to complete information exchange, instead of information exchange between different layers in the original network. During the routing period, other nondestination nodes can be used as middle stages to transfer data packets to complete the routing mission. Therefore, this topology has the characteristic of multistage. Simulation analyses show that BFC inherits the rich path diversity of Clos network, and it has a better performance than butterfly network in throughput and delay in a quite congested traffic pattern

Cheetah: Lean and Fast Secure Two-Party Deep Neural Network Inference

Secure two-party neural network inference (2PC-NN) can offer privacy protection for both the client and the server and is a promising technique in the machine-learning-as-a-service setting. However, the large overhead of the current 2PC-NN in- ference systems is still being a headache, especially when applied to deep neural networks such as ResNet50. In this work, we present Cheetah, a new 2PC-NN inference system that is faster and more communication-efficient than state-of-the-arts. The main contributions of Cheetah are two-fold: the first part includes carefully designed homomorphic encryption-based protocols that can evaluate the linear layers (namely convolution, batch normalization, and fully-connection) without any expensive rotation operation. The second part includes several lean and communication-efficient primitives for the non-linear functions (e.g., ReLU and truncation). Using Cheetah, we present intensive benchmarks over several large-scale deep neural networks. Take ResNet50 for an example, an end- to-end execution of Cheetah under a WAN setting costs less than 2.5 minutes and 2.3 gigabytes of communication, which outperforms CrypTFlow2 (ACM CCS 2020) by about 5.6× and 12.9×, respectively

Divergent dynamics between grassland greenness and gross primary productivity across China

peer reviewedGrassland, the most widespread vegetation type in China, has been greening recently.However, the extent to which the greenness has been translated into productivity and the underlying mechanism of the decoupled grassland greenness and productivity remains unclear. In this study, we detected the trend of normalized difference vegetation index (NDVI) and gross primary productivity (GPP) of grassland in China from 2000 to 2019 and analyzed the driving mechanism of the inconsistency between them. It was found that the relative increase rate of productivity (27.27%, p < 0.05) was much greater than that of greenness (14.54%, p < 0.05) across grasslands in China from 2000 to 2019, especially in temperate regions. The temperature and precipitation were the main factors influencing the grassland growth change, and the impact of temperature and shortwave radiation on productivity was greater than on greenness. However, the increase of grassland greenness was not fully translated into productivity in subtropical and tropical grass as well as shrub. This study revealed the dominance of climatic factors in the translation process from ecosystem structure to function, which highlighted the challenge in enhancing carbon uptake capacity of terrestrial ecosystem facing accelerated climate change

Attenuation of Relapsing Fever Neuroborreliosis in Mice by IL-17A Blockade

Relapsing fever due to Borrelia hermsiiis characterized by recurrent bacteremia episodes. However, infection of B. hermsii, if not treated early, can spread to various organs including the central nervous system (CNS). CNS disease manifestations are commonly referred to as relapsing fever neuroborreliosis (RFNB). In the mouse model of B. hermsiiinfection, we have previously shown that the development of RFNB requires innate immune cells as well as T cells. Here, we found that prior to the onset of RFNB, an increase in the systemic proinflammatory cytokine response followed by sustained levels of IP-10 concurrent with the CNS disease phase. RNA sequencing analysis of the spinal cord tissue during the disease phase revealed an association of the interleukin (IL)-17 signaling pathway in RFNB. To test a possible role for IL-17 inRFNB, we compared B. hermsii infection in wild-type and IL-17A2/2mice. Although the onset of bacteremia and protective anti-B. hermsii antibody responses occurred similarly, the blood-brain barrier permeability, proinflammatory cytokine levels, immune cell infiltration in the spinal cord, and RFNB manifestations were significantly diminished in IL-17A2/2mice compared to wild-type mice. Treatment of B. hermsii-infected wild-type mice with anti-IL-17A antibody ameliorated the severity of spinal cord inflammation, microglial cell activation, and RFNB. These data suggest that the IL-17signaling pathway plays a major role in the pathogenesis of RFNB, and IL-17A blockade may be a therapeutic modality for controlling neuroborreliosis

Mir-382 Promotes Differentiation of Rat Liver Progenitor Cell WB-F344 by Targeting Ezh2

Background/Aims: Liver progenitor cells (LPCs) were considered as a promising hepatocyte source of cell therapy for liver disease due to their self-renewal and differentiation capacities, while little is known about the mechanism of LPC differentiate into hepatocytes. This study aims to explore the effect of miR-382, a member of Dlk1-Dio3 microRNA cluster, during hepatic differentiation from LPCs. Methods: In this study, we used rat liver progenitor cell WB-F344 as LPC cell model and HGF as inducer to simulate the process of LPCs hepatic differentiation, then microRNAs were quantified by qPCR. Next, WB-F344 cell was transfected with miR-382 mimics, then hepatocyte cell trait was characterized by multiple experiments, including that periodic acid schiff staining and cellular uptake and excretion of indocyanine green to evaluate the hepatocellular function, qPCR and Western Blotting analysis to detect the hepatocyte-specific markers (ALB, Ttr, Apo E and AFP) and transmission electron microscopy to observe the hepatocellular morphology. Moreover, Luciferase reporter assay was used to determine whether Ezh2 is the direct target of miR-382. Results: We found that miR-382 increased gradually and was inversely correlated with the potential target, Ezh2, during WB-F344 hepatic differentiation. In addition, functional studies indicated that miR-382 increased the level of hepatocyte-specific genes. Conclusions: This study demonstrates that miR-382 may be a novel regulator of LPCs differentiation by targeting Ezh2

Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature

Motivation: In this work, we aim to develop a computational approach for predicting DNA-binding sites in proteins from amino acid sequences. To avoid overfitting with this method, all available DNA-binding proteins from the Protein Data Bank (PDB) are used to construct the models. The random forest (RF) algorithm is used because it is fast and has robust performance for different parameter values. A novel hybrid feature is presented which incorporates evolutionary information of the amino acid sequence, secondary structure (SS) information and orthogonal binary vector (OBV) information which reflects the characteristics of 20 kinds of amino acids for two physical–chemical properties (dipoles and volumes of the side chains). The numbers of binding and non-binding residues in proteins are highly unbalanced, so a novel scheme is proposed to deal with the problem of imbalanced datasets by downsizing the majority class

Head-to-Head Comparison of Poxvirus NYVAC and ALVAC Vectors Expressing Identical HIV-1 Clade C Immunogens in Prime-Boost Combination with Env Protein in Nonhuman Primates.

UNLABELLED: We compared the HIV-1-specific cellular and humoral immune responses elicited in rhesus macaques immunized with two poxvirus vectors (NYVAC and ALVAC) expressing the same HIV-1 antigens from clade C, Env gp140 as a trimeric cell-released protein and a Gag-Pol-Nef polyprotein as Gag-induced virus-like particles (VLPs) (referred to as NYVAC-C and ALVAC-C). The immunization protocol consisted of two doses of the corresponding poxvirus vector plus two doses of a combination of the poxvirus vector and a purified HIV-1 gp120 protein from clade C. This immunogenicity profile was also compared to that elicited by vaccine regimens consisting of two doses of the ALVAC vector expressing HIV-1 antigens from clades B/E (ALVAC-vCP1521) plus two doses of a combination of ALVAC-vCP1521 and HIV-1 gp120 protein from clades B/E (similar to the RV144 trial regimen) or clade C. The results showed that immunization of macaques with NYVAC-C stimulated at different times more potent HIV-1-specific CD4(+) T-cell responses and induced a trend toward higher-magnitude HIV-1-specific CD8(+) T-cell immune responses than did ALVAC-C. Furthermore, NYVAC-C induced a trend toward higher levels of binding IgG antibodies against clade C HIV-1 gp140, gp120, or murine leukemia virus (MuLV) gp70-scaffolded V1/V2 and toward best cross-clade-binding IgG responses against HIV-1 gp140 from clades A, B, and group M consensus, than did ALVAC-C. Of the linear binding IgG responses, most were directed against the V3 loop in all immunization groups. Additionally, NYVAC-C and ALVAC-C also induced similar levels of HIV-1-neutralizing antibodies and antibody-dependent cellular cytotoxicity (ADCC) responses. Interestingly, binding IgA antibody levels against HIV-1 gp120 or MuLV gp70-scaffolded V1/V2 were absent or very low in all immunization groups. Overall, these results provide a comprehensive survey of the immunogenicity of NYVAC versus ALVAC expressing HIV-1 antigens in nonhuman primates and indicate that NYVAC may represent an alternative candidate to ALVAC in the development of a future HIV-1 vaccine. IMPORTANCE: The finding of a safe and effective HIV/AIDS vaccine immunogen is one of the main research priorities. Here, we generated two poxvirus-based HIV vaccine candidates (NYVAC and ALVAC vectors) expressing the same clade C HIV-1 antigens in separate vectors, and we analyzed in nonhuman primates their immunogenicity profiles. The results showed that immunization with NYVAC-C induced a trend toward higher HIV-1-specific cellular and humoral immune responses than did ALVAC-C, indicating that this new NYVAC vector could be a novel optimized HIV/AIDS vaccine candidate for human clinical trials.This investigation was supported by the PTVDC/CAVD program with support from the Bill and Melinda Gates Foundation (BMGF). Humoral immune monitoring data was supported by the BMGF CAVIMC 1032144 grant and the NIH/NIAID Duke Center for AIDS Research (CFAR) 5P30 AI064518. Novartis Vaccines received support for this work under contract number HHSN266200500007C from DAIDS-NIAID-NIH.This is the accepted manuscript. The final version is available at http://jvi.asm.org/content/early/2015/05/29/JVI.01265-15.abstract

Derivatization of DNAs with selenium at 6-position of guanine for function and crystal structure studies

To investigate nucleic acid base pairing and stacking via atom-specific mutagenesis and crystallography, we have synthesized for the first time the 6-Se-deoxyguanosine phosphoramidite and incorporated it into DNAs via solid-phase synthesis with a coupling yield over 97%. We found that the UV absorption of the Se-DNAs red-shifts over 100 nm to 360 nm (ε = 2.3 × 104 M−1 cm−1), the Se-DNAs are yellow colored, and this Se modification is relatively stable in water and at elevated temperature. Moreover, we successfully crystallized a ternary complex of the Se-G-DNA, RNA and RNase H. The crystal structure determination and analysis reveal that the overall structures of the native and Se-modified nucleic acid duplexes are very similar, the selenium atom participates in a Se-mediated hydrogen bond (Se … H–N), and the SeG and C form a base pair similar to the natural G–C pair though the Se-modification causes the base-pair to shift (approximately 0.3 Å). Our biophysical and structural studies provide new insights into the nucleic acid flexibility, duplex recognition and stability. Furthermore, this novel selenium modification of nucleic acids can be used to investigate chemogenetics and structure of nucleic acids and their protein complexes