Resource Partitioning in Real-Time Virtualized Systems: Optimization, Implementation, and Application.

The application of virtualization in safety-critical scenarios with real-time performance requirements is increasingly popular. For Virtual Machine (VM) scheduling in real-time virtualized platforms, a Hierarchical Real-Time Scheduling (HiRTS) framework is proposed. The framework divides the scheduling problem into task-level scheduling, which schedules tasks inside each VM, and resource-level scheduling, which schedules VMs on the physical resources. Accordingly, the Regularity-based Resource Partitioning (RRP) model defines a resource interface specification, which parameterizes the resource partition assigned to each VM, to facilitate communication between the task level and the resource level. To make the RRP model more practical to various scenarios, this dissertation discusses the critical open problems left in the RRP model on three aspects: optimization, implementation, and application. Specifically, as a task-level optimization, we propose more task-level schedulability tests applicable for various scenarios. For resource-level optimization, we introduce fault tolerance to the RRP model by including checkpoints and redundancy areas for re-execution and offer a configurable trade-off between efficiency and resilience. We also propose more efficient resource-level resource partitioning algorithms with proven performance bounds for VM schedule generation with or without the use of reconfiguration. To enable the optimization of the RRP model for industrial usage, we have implemented the RRP model on the hard-real-time hypervisor XtratuM and soft-real-time hypervisor Xen. Numerous experiments and case studies have been conducted to validate the efficacy of the implemented RRP model and to highlight important parameter choices. Last but not least, we discuss the potential application of the implemented RRP model in lowering the cost of deploying irregular High-Performance Computing (HPC) applications and in building the Cyber-Physical Space (CPS) for traffic routing to reduce road congestion

On Maximizing the Throughput of Packet Transmission under Energy Constraints

More and more Internet of Things (IoT) wireless devices have been providing ubiquitous services over the recent years. Since most of these devices are powered by batteries, a fundamental trade-off to be addressed is the depleted energy and the achieved data throughput in wireless data transmission. By exploiting the rate-adaptive capacities of wireless devices, most existing works on energy-efficient data transmission try to design rate-adaptive transmission policies to maximize the amount of transmitted data bits under the energy constraints of devices. Such solutions, however, cannot apply to scenarios where data packets have respective deadlines and only integrally transmitted data packets contribute. Thus, this paper introduces a notion of weighted throughput, which measures how much total value of data packets are successfully and integrally transmitted before their own deadlines. By designing efficient rate-adaptive transmission policies, this paper aims to make the best use of the energy and maximize the weighted throughput. What is more challenging but with practical significance, we consider the fading effect of wireless channels in both offline and online scenarios. In the offline scenario, we develop an optimal algorithm that computes the optimal solution in pseudo-polynomial time, which is the best possible solution as the problem undertaken is NP-hard. In the online scenario, we propose an efficient heuristic algorithm based on optimal properties derived for the optimal offline solution. Simulation results validate the efficiency of the proposed algorithm

Bacteroides salyersiae is a potent chondroitin sulfate-degrading species in the human gut microbiota

Abstract Chondroitin sulfate (CS) has widely been used as a symptomatic slow-acting drug or a dietary supplement for the treatment and prevention of osteoarthritis. However, CS could not be absorbed after oral intake due to its polyanionic nature and large molecular weight. Gut microbiota has recently been proposed to play a pivotal role in the metabolism of drugs and nutrients. Nonetheless, how CS is degraded by the human gut microbiota has not been fully characterized. In the present study, we demonstrated that each human gut microbiota was characterized with a unique capability for CS degradation. Degradation and fermentation of CS by the human gut microbiota produced significant amounts of unsaturated CS oligosaccharides (CSOSs) and short-chain fatty acids. To uncover which microbes were responsible for CS degradation, we isolated a total of 586 bacterial strains with a potential CS-degrading capability from 23 human fecal samples. Bacteroides salyersiae was a potent species for CS degradation in the human gut microbiota and produced the highest amount of CSOSs as compared to other well-recognized CS-degraders, including Bacteroides finegoldii, Bacteroides thetaiotaomicron, Bacteroides xylanisolvens, and Bacteroides ovatus. Genomic analysis suggested that B. salyersiae was armed with multiple carbohydrate-active enzymes that could potentially degrade CS into CSOSs. By using a spent medium assay, we further demonstrated that the unsaturated tetrasaccharide (udp4) produced by the primary degrader B. salyersiae could serve as a “public goods” molecule for the growth of Bacteroides stercoris, a secondary CS-degrader that was proficient at fermenting CSOSs but not CS. Taken together, our study provides insights into the metabolism of CS by the human gut microbiota, which has promising implications for the development of medical and nutritional therapies for osteoarthritis. Video Abstrac

Promotion of Adrenal Pheochromocytoma (PC-12) Cell Proliferation and Outgrowth Using Schwann Cell-Laden Gelatin Methacrylate Substrate

Peripheral nerve injuries cause different degrees of nerve palsy and function loss. Due to the limitations of autografts, nerve tissue engineering (TE) scaffolds incorporated with various neurotrophic factors and cells have been investigated to promote nerve regeneration. However, the molecular mechanism is still poorly understood. In this study, we co-cultured Schwann cells (SCs) and rat adrenal pheochromocytoma (PC-12) cells on 50% degrees of methacryloyl substitution gelatin methacrylate (GelMA) scaffold. The SCs were encapsulated within the GelMA, and PC-12 cells were on the surface. A 5% GelMA was used as the co-culture scaffold since it better supports SCs proliferation, viability, and myelination and promotes higher neurotrophic factors secretion than 10% GelMA. In the co-culture, PC-12 cells demonstrated a higher cell proliferation rate and axonal extension than culturing without SCs, indicating that the secretion of neurotrophic factors from SCs can stimulate PC-12 growth and axonal outgrowth. The mRNA level for neurotrophic factors of SCs in 5% GelMA was further evaluated. We found significant upregulation when compared with a 2D culture, which suggested that this co-culture system could be a potential scaffold to investigate the mechanism of how SCs affect neuronal behaviors

Additional file 1 of Bacteroides salyersiae is a potent chondroitin sulfate-degrading species in the human gut microbiota

Additional file 1: Figure S1. TLC showing the degradation of CS by the human gut microbiota. The degradation was monitored at 12 hours (A), 24 hours (B), 36 hours (C), 48 hours (D), and 72 hours (E). Figure S2. Degradation of CS by the human gut microbiota. Relative CS content in the culture medium at 72 hours (A). UPLC-MS/MS analysis of CSOSs in the culture medium of donor T25 (B). Total ion chromatograms showing the elution profiles of CSOSs in the culture medium of donor T25 at different time points (C). Figure S3. Mass spectrum showing the signals of udp2 (A), udp4 (B), and udp6 (C) according to their m/z ratios. The CSOSs, including udp2, udp4, and udp6 were produced in the culture medium as a result of CS degradation by the human gut microbiota. Figure S4. Changes in the structure of the human gut microbiota before and after fermentation. Venn diagram showing the differences of the operational taxonomic units (OTUs) (A). Observed species (B). Chao1 index (C). Shannon index (D). Heatmap of the abundance of gut bacteria at the genus level (E). Figure S5. Differences in the composition of the human gut microbiota before and after fermentation. Wilcoxon rank-sum test analysis of the gut microbiota at the species level (A). Linear discriminant analysis (LDA) Effect Size (LEfSe) analysis of the gut microbiota at the species level (B). Only bacterial taxa with an LDA score of above 3.0 were listed. Figure S6. Isolation of CS-degrading bacteria from the human gut microbiota. Different species of bacteria were obtained from different human fecal samples (A-W). Figure S7. B. salyersiae CSP6 was identified as a potent bacterium for CS-degradation in the present study. Heatmap of the relative abundance of the consumed CS (A). Phylogenetic tree analysis of the CS-degrading bacteria based on the 16S rRNA gene (B). Figure S8. TLC showing the degradation of CS by different human fecal isolates. The results were presented from B. thetaiotaomicron E1-7 to H. porci E13-26 (A-I). Figure S9. TLC showing the degradation of CS by different human fecal isolates. The results were presented from E. durans E13-16 to S. oneidensis P30-2-30 (A-H). Figure S10. Degradation and fermentation of CS by B. finegoldii B36-12, B. thetaiotaomicron E1-7, B. xylanisolvens B33-17, and B. ovatus B33-4. Concentrations of different SCFAs in the culture medium of B. finegoldii B36-12 (A), B. thetaiotaomicron E1-7 (B), B. xylanisolvens B33-17 (C), and B. ovatus B33-4 (D). * p < 0.05; ** p < 0.01. Figure S11. CS degradation by B. finegoldii B36-12, B. thetaiotaomicron E1-7, B. xylanisolvens B33-17, and B. ovatus B33-4. UPLC-MS/MS analysis of CSOSs produced by B. finegoldii B36-12 (A), B. thetaiotaomicron E1-7 (B), B. xylanisolvens B33-17 (C), and B. ovatus B33-4 (D). Total ion chromatograms showing the elution profiles of CSOSs in the culture medium of B. finegoldii B36-12 (E), B. thetaiotaomicron E1-7 (F), B. xylanisolvens B33-17 (G), and B. ovatus B33-4 (H) at different time points. * p < 0.05. Figure S12. Mass spectrum showing the signals of udp4 (A), udp6 (B), and udp8 (C) according to their m/z ratios. The CSOSs, including udp4, udp6, and udp8 were produced in the culture medium as a result of CS degradation by B. salyersiae CSP6, B. finegoldii B36-12, B. xylanisolvens B33-17, B. thetaiotaomicron E1-7, and B. ovatus B33-4. Figure S13. Degradation of CS by different strains of B. salyersiae. TLC showing the degradation of CS by B. salyersiae CSP6 and B. salyersiae FL17 (A). Relative carbohydrate content in the culture medium at different time points (B). B. salyersiae FL17 was previously isolated from the fecal sample of a healthy individual. This individual has not participated in the present study. Figure S14. Genome analysis of B. salyersiae CSP6. COG function classification (A). KEGG pathway analysis (B). Figure S15. Screening of candidate bacteria that could utilize udp4 using the spent medium assay. TLC showing the utilization of udp4 by different human gut bacteria. (A). List of the tested bacteria (B). Figure S16. Cross-feeding interactions between B. salyersiae and B. stercoris identified using the spent medium assay. Relative carbohydrate content in the culture medium (A). Growth curve (B) and CFU analysis (C). Concentrations of total SCFAs (D), acetate (E), and propionate (F) in the culture medium of B. salyersiae and B. stercoris. * p < 0.05; ** p < 0.01; *** p < 0.001. Figure S17. Mass spectrum showing the signal of udp4 according to the m/z ratio. The udp4 concentration in the spent medium was analyzed using UPLC-MS/MS. Table S1. Summary of CS-degrading bacteria isolated from the human fecal samples. Table S2. Summary of the potential enzymes for CS degradation in B. salyersiae CSP6 based on the genomic analysis. Supplementary Table S3. Genome annotation of B. salyersiae CSP6. Supplementary Table S4. CAZyme annotation of B. salyersiae CSP6

Incidence of Carassius auratus Gibelio Gill Hemorrhagic Disease Caused by CyHV-2 Infection Can Be Reduced by Vaccination with Polyhedra Incorporating Antigens

Encapsulation of antigens within protein microcrystals (polyhedra) is a promising approach for the stable delivery of vaccines. In this study, a vaccine was encapsulated into polyhedra against cyprinid herpesvirus II (CyHV-2). CyHV-2 typically infects gibel carp, Carassius auratus gibelio, causing gill hemorrhagic disease. The vaccine was constructed using a codon-optimized sequence, D4ORF, comprising the ORF72 (region 1–186 nt), ORF66 (region 993–1197 nt), ORF81 (region 603–783 nt), and ORF82 (region 85–186 nt) genes of CyHV-2. The H1-D4ORF and D4ORF-VP3 sequences were, respectively, obtained by fusing the H1-helix sequence (region 1–90 nt) ofBombyx mori cypovirus(BmCPV) polyhedrin to the 5′ terminal end of D4ORF and by fusing a partial sequence (1–279 nt) of the BmCPV VP3 gene to the 3′ terminal end of D4ORF. Furthermore, BmNPV-H1-D4ORF-polh and BmNPV-D4ORF-VP3-polh recombinant B. mori nucleopolyhedroviruses (BmNPVs), belonging to the family Baculoviridae, and co-expressing BmCPV polyhedrin and H1-D4ORF or D4ORF-VP3, were constructed. H1-D4ORF and D4ORF-VP3 fusion proteins were confirmed to be encapsulated into recombinant cytoplasmic polyhedra by Western blotting. Degradation of vaccine proteins was assessed by SDS-PAGE, and the results showed that the encapsulated vaccine proteins in polyhedra could be protected from degradation. Furthermore, when gibel carp were vaccinated with the purified polyhedra from BmNPV-H1-D4ORF-polh and BmNPV-D4ORF-VP3-polh via injection, the antibody titers in the serum of the vaccinated fish reached 1:6400–1:12,800 at 3 weeks post-vaccination. Therelative percentage of survival of immunized gibel carp reached 64.71% and 58.82%, respectively, following challenge with CyHV-2. These results suggest that incorporating vaccine protein into BmCPV polyhedra may be a novel approach for developing aquaculture microencapsulated vaccines

Structure Effects of 2D Materials on α‑Nickel Hydroxide for Oxygen Evolution Reaction

To engineer low-cost, high-efficiency, and stable oxygen evolution reaction (OER) catalysts, structure effects should be primarily understood. Focusing on this, we systematically investigated the relationship between structures of materials and their OER performances by taking four 2D α-Ni­(OH)₂ as model materials, including layer-stacked bud-like Ni­(OH)₂-NB, flower-like Ni­(OH)₂-NF, and petal-like Ni­(OH)₂-NP as well as the ultralarge sheet-like Ni­(OH)₂-NS. For the first three (layer-stacking) catalysts, with the decrease of stacked layers, their accessible surface areas, abilities to adsorb OH^–, diffusion properties, and the intrinsic activities of active sites increase, which accounts for their steadily enhanced activity. As expected, Ni­(OH)₂-NP shows the lowest overpotential (260 mV at 10 mA cm^–2) and Tafel slope (78.6 mV dec^–1) with a robust stability over 10 h among the samples, which also outperforms the benchmark IrO₂ (360 mV and 115.8 mV dec^–1) catalyst. Interestingly, Ni­(OH)₂-NS relative to Ni­(OH)₂-NP exhibits even faster substance diffusion due to the sheet-like structure, but shows inferior OER activity, which is mainly because the Ni­(OH)₂-NP with a smaller size possesses more active boundary sites (higher reactivity of active sites) than Ni­(OH)₂-NS, considering the adsorption properties and accessible surface areas of the two samples are quite similar. By comparing the different structures and their OER behaviors of four α-Ni­(OH)₂ samples, our work may shed some light on the structure effect of 2D materials and accelerate the development of efficient OER catalysts