Detecting contradictions from IoT protocol specification documents based on neural generated knowledge graph

Due to the boom of Internet of Things (IoT) in recent years, various IoT devices are connected to the Internet and communicate with each other through network protocols such as the Constrained Application Protocol (CoAP). These protocols are typically defined and described in specification documents, such as Request for Comments (RFC), which are written in natural or semi-formal languages. Since developers largely follow the specification documents when implementing web protocols, they have become the de facto protocol specifications. Therefore, it must be ensured that the descriptions in them are consistent to avoid technological issues, incompatibility, security risks, or even legal concerns. In this work, we propose Neural RFC Knowledge Graph (NRFCKG), a neural network-generated knowledge graph based contradictions detection tool for IoT protocol specification documents. Our approach can automatically parse the specification documents and construct knowledge graphs from them through entity extraction, relation extraction, and rule extraction with large language models. It then conducts an intra-entity and inter-entity contradiction detection over the generated knowledge graph. We implement NRFCKG and apply it to the most extensively used messaging protocols in IoT, including the main RFC (RFC7252) of CoAP, the specification document of MQTT, and the specification document of AMQP. Our evaluation shows that NRFCKG generalizes well to other specification documents and it manages to detect contradictions from these IoT protocol specification documents.

Real-time collision-free motion planning of a mobile robot using a Neural Dynamics-based approach

A neural dynamics based approach is proposed for real-time motion planning with obstacle avoidance of a mobile robot in a nonstationary environment. The dynamics of each neuron in the topologically organized neural network is characterized by a shunting equation or an additive equation. The real-time collision-free robot motion is planned through the dynamic neural activity landscape of the neural network without any learning procedures and without any local collision-checking procedures at each step of the robot movement. Therefore the model algorithm is computationally simple. There are only local connections among neurons. The computational complexity linearly depends on the neural network size. The stability of the proposed neural network system is proved by qualitative analysis and a Lyapunov stability theory. The effectiveness and efficiency of the proposed approach are demonstrated through simulation studies.

Catalytic mechanism of xylose (glucose) isomerase from Clostridium thermosulfurogenes. Characterization of the structural gene and function of active site histidine

The gene coding for thermophilic xylose (glucose) isomerase of Clostridium thermosulfurogenes was isolated and its complete nucleotide sequence was determined. The structural gene (xylA) for xylose isomerase encodes a polypeptide of 439 amino acids with an estimated molecular weight of 50,474. The deduced amino acid sequence of thermophilic C. thermosulfurogenes xylose isomerase displayed higher homology with those of thermolabile xylose isomerases from Bacillus subtilis (70%) and Escherichia coli (50%) than with those of thermostable xylose isomerases from Ampullariella (22%), Arthrobacter (23%), and Streptomyces violaceoniger (24%). Several discrete regions were highly conserved throughout the amino acid sequences of all these enzymes. To identify the histidine residue of the active site and to elucidate its function during enzymatic xylose or glucose isomerization, histidine residues at four different positions in the C. thermosulfurogenes enzyme were individually modified by site-directed mutagenesis. Substitution of His101 by phenylalanine completely abolished enzyme activity whereas substitution of other histidine residues by phenylalanine had no effect on enzyme activity. When His101 was changed to glutamine, glutamic acid, asparagine, or aspartic acid, approximately 10-16% of wild-type enzyme activity was retained by the mutant enzymes. The Gln101 mutant enzyme was resistant to diethylpyrocarbonate inhibition which completely inactivated the wild-type enzyme, indicating that His101 is the only essential histidine residue involved directly in enzyme catalysis. The constant Vmax values of the Gln101, Glu101, Asn101, and Asp101 mutant enzymes over the pH range of 5.0-8.5 indicate that protonation of His101 is responsible for the reduced Vmax values of the wild-type enzyme at pH below 6.5. Deuterium isotope effects by D-[2-2H]glucose on the rate of glucose isomerization indicated that hydrogen transfer and not substrate ring opening is the rate-determining step for both the wild-type and Gln101 mutant enzymes. These results suggest that the enzymatic sugar isomerization does not involve a histidine-catalyzed proton transfer mechanism. Rather, essential histidine functions to stabilize the transition state by hydrogen bonding to the C5 hydroxyl group of the substrate and this enables a metal-catalyzed hydride shift from C2 to C1.

[Large-scale production of monoclonal antibodies using hollow fiber bioreactor]

Development of large-scale monoclonal antibody production using industrial scale hollow fiber bioreactor is described. Hybridoma cell lines H505AC and A306AA were cultivated in the hollow fiber perfusion bioreactor with a total fiber surface area of 7.2 m2 (6 x 1.2 m2) to produce anti-hepatitis B surface antigen (anti-HBsAg) monoclonal antibody IgM and anti-alpha-fetal protein (anti-AFP) monoclonal antibody IgG. The highest anti-HBsAg IgM productivity obtained during 49 days cultivation of H505AC was 0.135 g/day and the total accumulated IgM was 1.90 g. Results from the cultivation of A306AA in the hollow fiber module for 23 days showed the highest anti-AFP IgG productivity and the total accumulated IgG were 0.672 g/day and 7.21 g, respectively.

[Continuous production of anti-hepatitis B surface antigen monoclonal antibody in hollow fiber perfusion bioreactor]

Hybridoma cell line H440Ac was cultivated continuously in hollow fiber perfusion bioreactor for fifty days to produce anti-hepatitis B surface antigen (anti-HBsAg) monoclonal antibody. A total of 90 mg anti-HBsAg antibody was produced in the hollow fiber bioreactor with 1000 cm2 membrane surface area. The collected production medium has an average antibody concentration of 0.45 mg/ml with a high concentration of 2.3 mg/ml. This compares with 0.016 and 1.1 mg/ml antibody concentration as collected from spinner flask and mouse ascites. The purity of the produced antibody is 0.085, 0.0028 and 0.026 mg antibody per mg of total harvested protein in the culture media produced from the hollow fiber bioreactor, spinner flasks and mouse ascites, respectively.