Synthetic Biology: A Bridge between Artificial and Natural Cells.

Artificial cells are simple cell-like entities that possess certain properties of natural cells. In general, artificial cells are constructed using three parts: (1) biological membranes that serve as protective barriers, while allowing communication between the cells and the environment; (2) transcription and translation machinery that synthesize proteins based on genetic sequences; and (3) genetic modules that control the dynamics of the whole cell. Artificial cells are minimal and well-defined systems that can be more easily engineered and controlled when compared to natural cells. Artificial cells can be used as biomimetic systems to study and understand natural dynamics of cells with minimal interference from cellular complexity. However, there remain significant gaps between artificial and natural cells. How much information can we encode into artificial cells? What is the minimal number of factors that are necessary to achieve robust functioning of artificial cells? Can artificial cells communicate with their environments efficiently? Can artificial cells replicate, divide or even evolve? Here, we review synthetic biological methods that could shrink the gaps between artificial and natural cells. The closure of these gaps will lead to advancement in synthetic biology, cellular biology and biomedical applications

Engineering Performance of Polyurethane Bonded Aggregates

In this paper the engineering performance of polyurethane (PUR) bonded aggregate were studied. The engineering performance, including compressive and flexural mechanical properties, void ratio, and coefficient of permeability were determined through laboratory tests. Moreover, the effects of two different curing conditions on the compressive strength properties of a PUR bonded aggregate were also evaluated. The compressive strengths of PUR bonded aggregates were found to be lower than that of conventional porous concrete, which is a commonly used cushion material. However, experimental results indicated a higher void ratio and coefficient of permeability, lower elasticity modulus, better toughness, and stronger adaptability to flexural deformation compared to porous concrete. Consequently, PUR bonded aggregate is a better solution than porous concrete when used as the cushion material of a geomembrane surface barrier for a high rock-fill dam

Wilson-loop One-point Functions in ABJM Theory

In this paper we initiate the study of correlation functions of a single trace operator and a circular supersymmetric Wilson loop in ABJM theory. The single trace operator is in the scalar sector and is an eigenstate of the planar two-loop dilatation operator. The Wilson loop is in the fundamental representation of the gauge group or a suitable (super-)group. Such correlation functions at tree level can be written as an overlap of the Bethe state corresponding to the single trace operator and a boundary state which corresponds to the Wilson loop. There are various type of supersymmetric Wilson loops in ABJM theory. We show that some of them correspond to integrable boundary states while some are not. For the integrable ones, we prove their integrability and obtain analytic formula for the overlaps. For the non-integrable ones, we give examples of non-vanishing overlaps for Bethe states which violate selection rules.Comment: 32 pages, 3 figure

Route Choice Model Based on Game Theory for Commuters

The traffic behaviours of commuters may cause traffic congestion during peak hours. Advanced Traffic Information System can provide dynamic information to travellers. Due to the lack of timeliness and comprehensiveness, the provided information cannot satisfy the travellers’ needs. Since the assumptions of traditional route choice model based on Expected Utility Theory conflict with the actual situation, a route choice model based on Game Theory is proposed to provide reliable route choice to commuters in actual situation in this paper. The proposed model treats the alternative routes as game players and utilizes the precision of predicted information and familiarity of traffic condition to build a game. The optimal route can be generated considering Nash Equilibrium by solving the route choice game. Simulations and experimental analysis show that the proposed model can describe the commuters’ routine route choice decisionexactly and the provided route is reliable.</p

Assessment of data processing to improve reliability of microarray experiments using genomic DNA reference

<p>Abstract</p> <p>Background</p> <p>Using genomic DNA as common reference in microarray experiments has recently been tested by different laboratories. Conflicting results have been reported with regard to the reliability of microarray results using this method. To explain it, we hypothesize that data processing is a critical element that impacts the data quality.</p> <p>Results</p> <p>Microarray experiments were performed in a γ-proteobacterium <it>Shewanella oneidensis</it>. Pair-wise comparison of three experimental conditions was obtained either with two labeled cDNA samples co-hybridized to the same array, or by employing <it>Shewanella </it>genomic DNA as a standard reference. Various data processing techniques were exploited to reduce the amount of inconsistency between both methods and the results were assessed. We discovered that data quality was significantly improved by imposing the constraint of minimal number of replicates, logarithmic transformation and random error analyses.</p> <p>Conclusion</p> <p>These findings demonstrate that data processing significantly influences data quality, which provides an explanation for the conflicting evaluation in the literature. This work could serve as a guideline for microarray data analysis using genomic DNA as a standard reference.</p

シンコウキメイ ノ デザイン セイ ニ カンスル ケンキュウ

例会発表要旨第247回 意匠学会例会 2022年2月12日　オンライン発

Biostatistical Considerations of the Use of Genomic DNA Reference in Microarrays

Using genomic DNA as common reference in microarray experiments has recently been tested by different laboratories (2, 3, 5, 7, 9, 20, 24-26). While some reported that experimental results of microarrays using genomic DNA reference conformed nicely to those obtained by cDNA: cDNA co-hybridization method, others acquired poor results. We hypothesized that these conflicting reports could be resolved by biostatistical analyses. To test it, microarray experiments were performed in a 4 proteobacterium Shewanella oneidensis. Pair-wise comparison of three experimental conditions was obtained either by direct cDNA: cDNA co-hybridization, or by indirect calculation through a Shewanella genomic DNA reference. Several major biostatistical techniques were exploited to reduce the amount of inconsistency between both methods and the results were assessed. We discovered that imposing the constraint of minimal number of replicates, logarithmic transformation and random error analyses significantly improved the data quality. These findings could potentially serve as guidelines for microarray data analysis using genomic DNA as reference

Structure and Properties of Dense Silica Glass

The O K-edge x-ray Raman scattering (XRS), Brillouin scattering and diffraction studies on silica glass at high pressure have been elucidated in a unified manner using model structures obtained from First-Principles molecular dynamics calculations. This study provides a comprehensive understanding on how the structure is related to the physical and electronic properties. The origin of the "two peak" pattern in the XRS is found to be the result of increased packing of oxygen near the Si and is not a specific sign for sixfold coordination. The compression mechanism involving the presence of 5- and 6-fold coordinated silicon is confirmed. A slight increase in the silicon-oxygen coordination higher than six was found to accompany the increase in the acoustic wave velocity near 140 GPa