Dynamical complexity in the perception-based network formation model

Many link formation mechanisms for the evolution of social networks have been successful to reproduce various empirical findings in social networks. However, they have largely ignored the fact that individuals make decisions on whether to create links to other individuals based on cost and benefit of linking, and the fact that individuals may use perception of the network in their decision making. In this paper, we study the evolution of social networks in terms of perception-based strategic link formation. Here each individual has her own perception of the actual network, and uses it to decide whether to create a link to another individual. An individual with the least perception accuracy can benefit from updating her perception using that of the most accurate individual via a new link. This benefit is compared to the cost of linking in decision making. Once a new link is created, it affects the accuracies of other individuals' perceptions, leading to a further evolution of the actual network. As for initial actual networks, we consider homogeneous and heterogeneous cases. The homogeneous initial actual network is modeled by Erd\H{o}s-R\'enyi (ER) random networks, while we take a star network for the heterogeneous case. In any cases, individual perceptions of the actual network are modeled by ER random networks with controllable linking probability. Then the stable link density of the actual network is found to show discontinuous transitions or jumps according to the cost of linking. As the number of jumps is the consequence of the dynamical complexity, we discuss the effect of initial conditions on the number of jumps to find that the dynamical complexity strongly depends on how much individuals initially overestimate or underestimate the link density of the actual network. For the heterogeneous case, the role of the highly connected individual as an information spreader is discussed.Comment: 8 pages, 7 figure

Coevolution of a network and perception

How does an individual's cognition change a system which is a collective behavior of individuals? Or, how does a system affect an individual's cognition? To examine the interplay between a system and individuals, we study a cognition-based network formation. When a network is not fully observable, individuals' perception of a network plays an important role in decision making. Assuming that a communication link is costly, and more accurate perception yields higher network utility, an agent decides whether to form a link in order to get better information or not. Changes in a network with newly added links affect individuals' perception accuracy, which may cause further changes in a network. We characterize the early stage of network dynamics and information dispersion. Network structures in a steady state are also examined. Additionally, we discuss local interactions and a link concentration in a frequently changing network.Comment: 32 pages, 8 figure

A newly identified glutaminase-free ʟ-asparaginase (ʟ-ASPG86) from the marine bacterium Mesoflavibacter zeaxanthinifaciens

ʟ-Asparaginase (EC 3.5.1.1) is an enzyme involved in asparagine hydrolysis and has the potential to effect leukemic cells and various other cancer cells. We identified the ʟ-asparaginase gene (ʟ-ASPG86) in the genus Mesoflavibacter, which consists of a 1035-bp open reading frame (ORF) encoding 344 amino acids (aa). Following phylogenetic analysis, the deduced amino acid sequence of ʟ-ASPG86 (ʟ-ASPG86) grouped as a type I asparaginase with respective homologs in Escherichia coli and Yersinia pseudotuberculosis. The ʟ-ASPG86 gene was cloned into the pET-16b vector to express the respective protein in E. coli BL21 (DE3) cells. Recombinant ʟ-asparaginase (r-ʟ-ASPG86) showed optimum conditions at 37-40oC, pH 9. Moreover, r-ʟ-ASPG86 did not exhibit glutaminase activity. In the metal ions test, its enzymatic activity was highly improved upon addition of 5 mM manganese (3.97-fold) and magnesium (3.35-fold) compared with the untreated control. The specific activity of r-ʟ-ASPG86 was 687.1 units/mg under optimum conditions (37oC, pH 9 and 5 mM MnSO4). Please click Additional Files below to see the full abstract

Molecular cloning and Biochemical properties of GH-16 β-agarase from Gilvimarinus agarolyticus JEA5

Agar is complex polysaccharide founds in the cell walls of some red algae and up to 70 % of the algal cell wall can be agar polymers. Agar was formed by a mixture of two polysaccharides named agarose and agaropectin. Agarose can be hydrolyzed by α-agarase (E.C. 3.2.1.158) and by β-agarase (E.C. 3.2.1.81); the former cleaves the α-1, 3 linkage of agarose to generate agaro-oligosaccharides, and the latter cleaves the β-1,4 linkage to generate neoagaro-oligosaccharides. Agarases have been isolated from many sources, including seawater, marine sediments, marine algae, marine mollusks, fresh water and soil. Recently, Givimarinus chinensis, G. polysacchalyticus, G. agarilyticus were identified and their agarolytic activity also reported. However, there are no report published that molecular and functional characterization of agarase from Givimarinus genus. In this study, we first report molecular characterization and biochemical properties of agarase from Gilvimarinus genus. Please click Additional Files below to see the full abstract

Biochemical properties of a novel neoagarotriose-producing β-agarase from Gilvimarinus agarolyticus JEA5

An agar degrading bacterium was isolated from seawater, collected from the east coast of Jeju Island, republic of Korea and identified as Gilvimarinus agarolyticus JEA5. The β-agarase gene from Gilvimarinus agarolyticus JEA5 (rGaa16B) was identified from draft genome sequence by BLAST. Gaa16B has 1800 bp of open reading frame encoding 636 amino acids (aa), and include glycosyl hydrolase family 16 (GH16) β-agarase module and two carbohydrate binding module 6 (CBM6). The Gaa16b was cloned and overexpressed as a MBP-fusion recombinant β-agarase (without signal peptide and two CBM6) in E. coil. rGaa16B showed highest activity at 60°C and pH 7. After incubation at 45OC for 90 min, rGaa16B showed over than 95% of its initial activity. rGaa16B were enhanced in the presence of MnCl2, KCl2, MgCl2, FeSO4. rGaa16B showed 2112.1 unit/mg in the presence of 2.5 mM of MnCl2. rGaa16B produce mainly neoagartetraose (NA4) and neoagarobiose (NA2). Interestingly, we observed neoagartriose (NA3) from hydrolytic products of rGaa16B. LC/Mass analysis was performed to confirm the hydrolytic products containing neoagarotriose. We found three different hydrolytic products which showed 324.28, 468.41, 630.55 Da of molecular weight, respectively. Please click Additional Files below to see the full abstract

Synergistic effect of acetyl xylan esterase on xylanase reaction originated from Ochrovirga pacifica

Acetyl xylan esterase plays an important role in complete enzymatic hydrolysis of lignocellulosic materials into fermentable sugars. It hydrolyzes ester linkages of acetic acid in xylan polysaccharide and supports to enhance the activity of xylanase. This study was conducted to recognize and overexpress the acetyl xylan esterase gene found from Ochrovirga pacifica strain S85 which was isolated from Chuuk state, Micronesia. The genome sequence was analyzed with genome sequencer-FLX and acetyl xylan esterase gene (Axe) was detected. The gene had an open reading frame of 864 bp encoding a polypeptide of 287 amino acids. Theoretical molecular mass and isoelectric point (pI) were 32 kDa and 5.9, respectively. The deduced amino acid sequence of the Axe showed 35.1% similarity with both endo-1,4-β-xylanase B from Robiginitalea biformata HTCC2501. The mature protein displayed the catalytic residues classically found in enzymes belonged to GH16 family. Axe was cloned into pET11a vector and recombinant protein was expressed in E. coli BL21 (DE3), purified by nickel affinity chromatography and its purity was visualized on SDS-PAGE. Commercial xylanase activity was tested after treatment of recombinant acetyl xylan esterase (rAXE) to birchwood xylan substrate. The xylanase activity of rAXE treated sample was about 2 times higher than xylanase only treated sample. Please click Additional Files below to see the full abstract

Recombinant protein production in Escherichia coli by combining of signal peptide originated from Bacillus subtilis

We isolated chitosanase secreting B. subtilis CH2 and identified the chitosanase nucleotide sequence. Analyzed the sequence showed that it consisted of 813 bp, including 87 bp signal sequence. The signal sequence leads the target protein to the cell-membrane of the B. subtilis CH2 and then secret the chitosanase out of the cell. The signal peptide showed 6 amino acids deletion compared to other B. subtilis chitosanase signal peptides. The chitosanase sequence including signal peptide was cloned into pET11a vector without fusion and expressed in E. coli BL21(DE3). The expressed chitosanase in E. coli showed two distinct bands which represent the pro-chitosanase in cytoplasm and mature chitosanase in periplasm. Time frame induction and results showed that muture chitosanase was increased. Subsequently, we linked this chitosanase signal sequence in front of B. subtilis CH2 xylanase and human superoxide distimutase 1 (hSOD1) sequences, and expressed it in E. coli BL21(DE3). The recombinant xylanase and hSOD1 moved to periplasmic space with high efficiency. This signal sequence is useful for bio-medical protein production in E. coli. Please click Additional Files below to see the full abstract

Clinical application of the Panbio™ COVID-19 Ag rapid test device and SSf-COVID19 kit for the detection of SARS-CoV-2 infection

Objective We evaluated the sensitivity and specificity of the Panbio™ COVID-19 Ag rapid test device using nasal swabs and those of the SSf-COVID19 kit, one of RT-PCR tests, using saliva specimens. These tests were compared with RT-PCR tests using nasopharyngeal swabs for the diagnosis of SARS-CoV-2 infection. The three diagnostic tests were simultaneously conducted for patients aged ≥ 18 years, who were about to be hospitalized or had been admitted for COVID-19 confirmed by RT-PCR in two research hospitals from August 20 to October 29, 2021. Nasal swabs were tested using the Panbio™ COVID-19 Ag rapid test device. More than 1 mL of saliva was self-collected and tested using the SSf-COVID19 kit. Results In total, 157 patients were investigated; 124 patients who were about to be hospitalized and 33 patients already admitted for COVID-19. The overall sensitivity and specificity of the Panbio™ COVID-19 Ag rapid test device with nasal swabs were 64.7% (95% confidence interval [CI] 47.9–78.5%) and 100.0% (95% CI 97.0–100.0%), respectively. The median time to confirm a positive result was 180 s (interquartile range 60–255 s). The overall sensitivity and specificity of the SSf-COVID19 kit with saliva specimens were 94.1% (95% CI 80.9–98.4%) and 100.0% (95% CI 97.0–100.0%), respectively.This work was supported by a grant from research fund of Seoul National University Hospital (Grant No. 2021–3148